1. What CLASH data is currently available in CLASHub?
CLASHub hosts data from four species: Human, Mouse, Drosophila melanogaster, and Caenorhabditis elegans. Below is the summary of available datasets:
Human
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | ZSWIM8 Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| A549 | — | 6 | 6 | PRJNA1166120 | SRR34738798, SRR34738799, SRR34738800, SRR34738801, SRR34738802, SRR34738803, SRR34738804, SRR34738805, SRR34738790, SRR34738791, SRR34738792, SRR34738793 |
| Colorectal | 2 | — | — | PRJNA1166120 | SRR37216684, SRR37216685 |
| D425 | 3 | — | — | PRJNA1166120 | SRR34757946, SRR34757949, SRR34757950 |
| ES2 | — | 3 | 3 | PRJNA1166120 | SRR34757940, SRR34757941, SRR34757942, SRR34757943, SRR34757944, SRR34757945 |
| HCT116 | 5 | — | 3 | GSE164634, PRJNA1166120 | SRR13415087, SRR13415088, SRR13415089, SRR13415090, SRR13415091, SRR34757939, SRR34757947, SRR34757948 |
| HEK293T | 8 | — | — | GSE198250, PRJNA1166120 | SRR18281055, SRR18281057, SRR18281067, SRR18281068, SRR34761041, SRR34761042, SRR34761043, SRR34761044 |
| HepG2 | 3 | — | — | PRJNA1166120 | SRR34783077, SRR34783079, SRR34783080 |
| H1299 | — | 3 | 3 | PRJNA1166120 | SRR34768260, SRR34768261, SRR34768262, SRR34768263, SRR34768274, SRR34768275 |
| MB002 | — | 4 | 4 | PRJNA1166120 | SRR34783070, SRR34783071, SRR34783072, SRR34783073, SRR34783074, SRR34783075, SRR34783076, SRR34783078 |
| MDA-MB-231 | — | 6 | 6 | PRJNA1166120 | SRR30817646, SRR30817647, SRR30817648, SRR30817649, SRR30817650, SRR30817651, SRR34738794, SRR34738795, SRR34738796, SRR34738797, SRR34738806, SRR34738807 |
| OVCAR8 | — | 3 | 3 | PRJNA1166120 | SRR34768264, SRR34768265, SRR34768266, SRR34768267, SRR34768276, SRR34768277 |
| TIVE-EX-LTC | 3 | — | — | GSE101978 | SRR5876947, SRR5876948, SRR5876949 |
| T98G | — | 3 | 3 | PRJNA1166120 | SRR34743309, SRR34743310, SRR34743311, SRR34743312, SRR34743317, SRR34743318 |
| U87MG | — | 3 | 3 | PRJNA1166120 | SRR34743313, SRR34743314, SRR34743315, SRR34743316, SRR34743319, SRR34743320 |
| 501Mel | — | 3 | 3 | PRJNA1166120 | SRR34768268, SRR34768269, SRR34768270, SRR34768271, SRR34768272, SRR34768273 |
Mouse
All mouse sources searches the reviewed CLASH V2 datasets below at request time. Evidence remains source-labelled, and Direct chimeras remain separate from AGO peak-supported candidates. The two kidney studies are independent experiments and are not pooled.
Reviewed CLASH V2 source datasets
| Dataset | AGO antibody / experimental method | Groups represented in the database | Public accession | Positive-library SRRs |
|---|---|---|---|---|
| Cortex | pan-AGO 2A8 CLEAR-CLIP | 20 reviewed analysis units | GSE73058 | SRR2413277–SRR2413302, excluding SRR2413280, SRR2413281, SRR2413283, and SRR2413286 |
| Skeletal muscle | AGO2 chimeric eCLIP | AGO2-IP skeletal-muscle libraries | GSE173821 | SRR14416844, SRR14416845, SRR14416850, SRR14416851 |
| Liver — Total and probe-enriched | AGO2 NoGel chimeric eCLIP | Total liver, let-7-enriched, and miR-122-enriched | GSE198250 | SRR18280918–SRR18280926 |
| Thymocytes — Wild type vs miR-181 knockout | AGO2 miR-eCLIP | AGO2-IP and miR-181-enriched, each WT vs miR-181 knockout | GSE241905 | SRR25792439–SRR25792444 and SRR25792451–SRR25792456 |
| CD4+ T cells — Wild type vs miR-155 knockout | AGO2 HITS-CLIP | Wild type and miR-155 knockout, 12 biological replicates per genotype | GSE41285 | SRR578782–SRR578805 |
| Embryonic stem cells — Wild type | AGO2 HITS-CLIP | Two biological replicates; WT1A and WT1B are merged technical replicates, and WT2 is the second biological replicate | GSE25310 | SRR072951, SRR072952, SRR072953 |
| Bone marrow-derived macrophages — Wild type vs APOBEC1 knockout | AGO HITS-CLIP | Wild type and APOBEC1 knockout, three biological replicates per genotype | GSE58798 | SRR1460498–SRR1460503 |
| Primary keratinocytes — Wild type | AGO2 HITS-CLIP | Four biological replicates | GSE66054 | SRR1810469–SRR1810472 |
| Embryonic stem cells — FLAG-HA-tagged AGO2 | AGO2 iCLIP | One tagged AGO2 positive library | GSE61347 | SRR1573590 |
| Bone marrow-derived macrophages — Wild type vs ELAVL1 knockout | AGO2 PAR-CLIP | One pooled wild-type library and one pooled ELAVL1-knockout library, summarized separately | GSE63199 | SRR1648881, SRR1648882 |
| P19 cells | AGO2 HITS-CLIP | Three biological replicates | GSE85219 | SRR4000655–SRR4000657 |
| Liver — Wild type vs miR-122 knockout | AGO HITS-CLIP | Five wild-type/floxed controls and four miR-122-knockout biological replicates, summarized separately | GSE97058 | SRR5379106–SRR5379114 |
| Embryonic stem cells / C2C12 differentiated myocytes — Cytoplasm and nucleus | AGO PAR-CLIP | Four cell/fraction groups, one library each. ESC: inducible tagged AGO2; C2C12: pan-AGO affinity purification. Sarshad et al., Molecular Cell (2018) | GSE108795 | SRR6442803–SRR6442806 |
| B cells / dendritic cells / macrophages / CD4+ T cells — Wild type vs miR-155 knockout | AGO2 iCLIP | Eight cell-type/genotype groups, four biological replicates per group, summarized separately. Hsin et al., Nature Immunology (2018) | GSE116466 | SRR7457034–SRR7457065 |
| Abelson-transformed B-cell progenitors — WT vs Bim 3′UTR mutant | AGO2 PAR-CLIP | Two biological replicates per genotype, summarized separately. Standard-reference reanalysis; engineered-site differences require mutation-aware interpretation. Labi et al., Genes & Development (2019) | GSE124605 | SRR8388921–SRR8388924 |
| P0 whole brain — WT vs FMR1 knockout | AGO2 eCLIP | One AGO2-IP library per genotype; Input controls are QC-only. Standard-reference reanalysis does not reproduce the original IP-versus-Input enrichment test. | GSE129885 | IP: SRR8908950–SRR8908951; Input: SRR8908952–SRR8908953 |
| Kidney — Control vs cisplatin | AGO2 chimeric eCLIP | Control and cisplatin-treated kidney | GSE242806 | SRR25994653–SRR25994664 |
| Kidney — Wild type | pan-AGO 4F9 chimeric eCLIP | Two WT kidney biological replicates | PRJNA1166120 | SRR34793105, SRR34793106 |
| Pineal tumor — IPRb1 cells | AGO2 miR-eCLIP | Two AGO2-IP biological replicates | GSE255909 | SRR27985089, SRR27985088 |
| Lung — Six-day bleomycin treatment | AGO2-eCLIP | Two AGO2-IP biological replicates | GSE287950 | SRR32112150, SRR32112147 |
Additional mouse datasets
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | Zswim8 Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| HE2.1B | 6 | — | — | GSE124687 | SRR8395242, SRR8395243, SRR8395244, SRR8395245, SRR8395246, SRR8395247 |
| MEF | — | 2 | 2 | PRJNA1166120 | SRR34793109, SRR34793110, SRR34793111, SRR34793112 |
| Striatal cell | — | 4 | 4 | PRJNA1093144 | SRR28497185, SRR28497186, SRR28497189, SRR28497190, SRR2849718, 6SRR28497197, SRR28497198, SRR28497199, SRR28497200 |
| 3T12 | 3 | — | — | GSE124687 | SRR8395248, SRR8395249, SRR8395250 |
| Cortex (pan-AGO 2A8 CLEAR-CLIP) | 20 reviewed analysis units | — | — | GSE73058 | SRR2413277–SRR2413302, excluding SRR2413280, SRR2413281, SRR2413283, and SRR2413286 |
| Heart (pan-AGO 4F9 chimeric eCLIP) | 2 | — | — | PRJNA1166120 | SRR34793107, SRR34793108 |
| Kidney — Wild type (pan-AGO 4F9 chimeric eCLIP) | 2 | — | — | PRJNA1166120 | SRR34793105, SRR34793106 |
Drosophila melanogaster
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | Dora Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| S2 cells | — | 3 | 3 | PRJNA896239 | SRR22129325, SRR22129327, SRR22129328, SRR22129284, SRR22129287, SRR22129298 |
Caenorhabditis elegans
The All C. elegans sources option searches the three current datasets below at request time. It counts source-level Direct and AGO support without averaging CPM or replicate support across studies.
| Dataset | Included biological groups | Excluded study/QC data | Public accession | Included sequencing data |
|---|---|---|---|---|
| Mixed embryos (ALG-2 chimeric eCLIP) | Tagged wild type (n = 4); ebax-1(null) (n = 4) | Untagged wild-type negative controls (n = 2) | GSE303817 / PRJNA1297724 | Eight tagged biological samples; two A/B sequencing runs merged within each replicate |
| L3 whole worms (ALG-1 iPAR-CLIP) | Standard iPAR-CLIP (n = 2); ligation-enhanced iPAR-CLIP (n = 2) | SRR1207391 archived duplicate; no-ligase controls SRR1207392 and SRR1207395 | GSE56180 / PRJNA242650 / SRP040587 | SRR1207389, SRR1207393, SRR1207390, SRR1207394 |
| Mid-L4 N2 whole worms (ALG-1 iCLIP) | N2 biological replicates (n = 5) | None from the reviewed biological-replicate set | PRJNA328816 / SRP078361 | SRR3882724, SRR3882728, SRR3882949, SRR3882950, SRR3882951 |
2. What Gene Expression Profile data is available in CLASHub?
Gene Expression Profile from four species: Human, Mouse, Drosophila melanogaster, and Caenorhabditis elegans. Below is the summary of available datasets:
Human
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | ZSWIM8 Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| A549 | 7 | — | — | GSE263036, GSE212057, GSE199309 | SRR28535493, SRR28535494, SRR28535495, SRR21237863, SRR21237869, SRR21237879, SRR18462418 |
| D425 | 5 | — | — | GSE151810, GSE185024, GSE123760 | SRR11924485, SRR11924486, SRR16119415, SRR16119416, SRR8315029 |
| ES2 | 6 | — | — | GSE218794, GSE245778 | SRR22410790, SRR22410791, SRR22410792, SRR26439462, SRR26439463, SRR26439464 |
| HEK293T | 7 | — | — | GSE231583, GSE196043 | SRR24421974, SRR24421975, SRR24421976, SRR18074813, SRR18074814, SRR18074815, SRR18074816 |
| Hela | 7 | — | — | GSE273634, GSE218727, GSE199309 | SRR30058518, SRR30058519, SRR30058520, SRR22407570, SRR22407571, SRR22407572, SRR18462415 |
| HepG2 | 5 | — | — | GSE224980, GSE264010 | SRR28685775, SRR28685776, SRR28685777, SRR23387178, SRR23387179 |
| H1299 | 4 | — | — | GSE212057, GSE199309 | SRR21237865, SRR21237873, SRR21237881, SRR18462412 |
| K562 | 6 | — | — | GSE199309, GSE167869 | SRR18462409, SRR13800753, SRR13800754, SRR13800737, SRR13800738, SRR13800739 |
| MB002 | 5 | — | — | GSE229150 GSE261568 | SRR28341540, SRR28341541, SRR28341542,SRR28341543 |
| MCF7 | 7 | — | — | GSE195761, GSE178905, GSE163791 | SRR17944548, SRR17944549, SRR14915857, SRR14915858, SRR13296901, SRR13296902, SRR13296903 |
| MDA-MB-231 | 6 | — | — | GSE178532 | SRR11544576, SRR11544577, SRR11544578, SRR14870088, SRR14870089, SRR14870090 |
| OVCAR8 | 4 | — | — | GSE246325 | SRR26536798, SRR26536799, SRR26536802, SRR26536803 |
| T98G | 5 | — | — | GSE112241, PRJNA580150 | SRR10358029, SRR10358030, SRR10358031, SRR6881782, SRR6881783 |
| U87MG | 6 | — | — | GSE147626, GSE235568 | SRR11433766, SRR11433767, SRR11433768, SRR24991947, SRR24991948, SRR24991949 |
| 501Mel | 7 | — | — | PRJNA515302, GSE104869 | SRR8473015, SRR8473019, SRR8473020, SRR6163777, SRR6163778, SRR6163779, SRR6163780 |
Mouse
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | Zswim8 Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| Eye | — | 3 | 3 | GSE231447 | SRR24391488, SRR24391489, SRR24391526, SRR24391480, SRR24391481, SRR24391536 |
| Forebrain | — | 3 | 3 | GSE231447 | SRR24391522, SRR24391523, SRR24391534, SRR24391514, SRR24391515, SRR24391547 |
| Heart | — | 3 | 3 | GSE231447 | SRR24391502, SRR24391503, SRR24391533, SRR24391510, SRR24391511, SRR24391543 |
| Hindbrain | — | 3 | 3 | GSE231447 | SRR24391520, SRR24391521, SRR24391538, SRR24391512, SRR24391513, SRR24391546 |
| Intestine | — | 3 | 3 | GSE231447 | SRR24391494, SRR24391495, SRR24391530, SRR24391486, SRR24391487, SRR24391545 |
| Kidney | — | 3 | 3 | GSE231447 | SRR24391490, SRR24391491, SRR24391531, SRR24391482, SRR24391483, SRR24391539 |
| Liver | — | 3 | 3 | GSE231447 | SRR24391492, SRR24391493, SRR24391527, SRR24391484, SRR24391485, SRR24391540 |
| Lung | — | 3 | 3 | GSE231447 | SRR24391500, SRR24391501, SRR24391532, SRR24391508, SRR24391509, SRR24391542 |
| Muscle | — | 3 | 3 | GSE231447 | SRR24391518, SRR24391519, SRR24391525, SRR24391478, SRR24391479, SRR24391535 |
| Placenta | — | 3 | 3 | GSE231447 | SRR24391516, SRR24391517, SRR24391524, SRR24391476, SRR24391477, SRR24391537 |
| Skin | — | 3 | 3 | GSE231447 | SRR24391496, SRR24391497, SRR24391528, SRR24391504, SRR24391505, SRR24391541 |
| Stomach | — | 3 | 3 | GSE231447 | SRR24391498, SRR24391499, SRR24391529, SRR24391506, SRR24391507, SRR24391544 |
| Embryonic Stem Cell | 2 | — | — | PRJEB27315 | ERR2640636, ERR2640637 |
| iNeuron | 3 | — | — | PRJEB27315 | ERR2640652, ERR2640653, ERR2640654 |
| MEF | 3 | — | — | GSE239373 | SRR25443485, SRR25443484, SRR25443483 |
| Neural Precursor | 2 | — | — | PRJEB27315 | ERR2640640, ERR2640641 |
| Striatal cell | — | 4 | 4 | PRJNA1093144 | SRR34804890, SRR34804891, SRR34804892, SRR34804893, SRR34804894, SRR34804895, SRR34804896, SRR34804897 |
Drosophila melanogaster
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | Dora Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| S2 cells | 5 | — | 3 | GSE196837, | SRR18048483, SRR18048484, SRR18048425, SRR18048423, SRR18048424, SRR18048427, SRR18048468, SRR18048426 |
| 0–4 h Embryos | 4 | — | — | GSE196837 | SRR18048437, SRR18048436, SRR18048435, SRR18048446 |
| 8–12 h Embryos | 6 | — | 4 | GSE196837 | SRR18048461, SRR18048433, SRR18048512, SRR18048481, SRR18048482, SRR18048434, SRR18048499, SRR18048531, SRR18048442, SRR18048532 |
| 12–16 h Embryos | 6 | — | 4 | GSE196837 | SRR18048539, SRR18048525, SRR18048508, SRR18048459, SRR18048432, SRR18048465, SRR18048448, SRR18048497, SRR18048529, SRR18048516 |
| 16–20 h Embryos wild type | 5 | — | 4 | GSE196837 | SRR18048421, SRR18048538, SRR18048479, SRR18048463, SRR18048527, SRR18048542, SRR18048443, SRR18048495, SRR18048501 |
| Fly Non-targeting Control | — | 3 | — | PRJNA896239 | SRR22129292, SRR22129294, SRR22129296 |
Caenorhabditis elegans
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | Ebax Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| Embryos | 4 | — | — | PRJNA922944 | SRR23049957, SRR23049959, SRR23049928, SRR23049954 |
| L1 | 5 | — | 2 | GSE68588, GSE262626, GSE267368 | SRR2010468, SRR2010469, SRR28479534, SRR29013568, SRR29013569, SRR29013570, SRR29013571 |
| L2 | 3 | — | — | GSE266398 | SRR28868053, SRR28868054, SRR28868055 |
| L3 | 3 | — | — | PRJNA684142 | SRR13238604, SRR13238605, SRR13238606 |
| L4 | 3 | — | — | PRJNA922944 | SRR23049963, SRR23049955, SRR23049961 |
| Adult | 4 | — | — | PRJNA922944, GSE267368 | SRR23049965, SRR23049966, SRR23049906, SRR23049937 |
3. What miRNA Expression Profile data is available in CLASHub?
microRNA Expression Profile data from four species: Human, Mouse, Drosophila melanogaster, and Caenorhabditis elegans. Below is the summary of available datasets:
Human
| Sample Name | Wild Type (#) | Non-targeting sgRNA Control (#) | ZSWIM8 Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| A549 | — | 3 | 3 | GSE163387 | SRR13264637, SRR13264638, SRR13264639, SRR13264640, SRR13264641, SRR13264642 |
| HEK293T | — | 3 | 3 | GSE123627, GSE158025 | SRR12650650, SRR12650651, SRR12650652, SRR12650653, SRR12650654, SRR12650655 |
| HeLa | — | 3 | 3 | GSE123627, GSE163387 | SRR13264643, SRR13264644, SRR13264645, SRR13264646, SRR13264647, SRR13264648 |
| K562 | 6 | — | 6 | GSE158025, GSE163388 | SRR12650656, SRR12650657, SRR12650658, SRR13264707, SRR13264708, SRR13264709, SRR12650659, SRR12650660, SRR12650661, SRR13264710, SRR13264711, SRR13264712 |
| MCF7 | — | 2 | 3 | GSE163388 | SRR13264649, SRR13264650, SRR13264651, SRR13264652, SRR13264653 |
Mouse
| Sample Name | wild type (#) | Non-targeting sgRNA Control (#) | Zswim8 Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| Brain | 3 | — | 3 | GSE235065 | SRR24941005, SRR24941026, SRR24940996, SRR24941021, SRR24941036, SRR24941000 |
| Heart | 3 | — | 3 | GSE235065 | SRR24941003, SRR24941027, SRR24940995, SRR24941022, SRR24941035, SRR24940999 |
| Kidney | 3 | — | 3 | GSE235065 | SRR24941001, SRR24940993, SRR24941029, SRR24941011, SRR24941033, SRR24941017 |
| Liver | 3 | — | 3 | GSE235065 | SRR24941004, SRR24940989, SRR24941030, SRR24941010, SRR24941032, SRR24941016 |
| Lung | 3 | — | 3 | GSE235065 | SRR24940992, SRR24940998, SRR24941018, SRR24941008, SRR24941031, SRR24941015 |
| Intestine | 3 | — | 3 | GSE235065 | SRR24941002, SRR24940994, SRR24941028, SRR24941023, SRR24941012, SRR24941034 |
| Neuron | — | 3 | 2 | GSE163387 | SRR13264632, SRR13264633, SRR13264634, SRR13264635, SRR13264636 |
| MEF | — | 6 | 6 | GSE163387, GSE158025 | SRR13264626, SRR13264627, SRR13264628, SRR12650662, SRR12650663, SRR12650664, SRR13264629, SRR13264630, SRR13264631, SRR12650665, SRR12650666, SRR12650667 |
| Stomach | 3 | — | 3 | GSE235065 | SRR24941020, SRR24941009, SRR24940990, SRR24941006, SRR24941025, SRR24941013 |
| Skin | 3 | — | 3 | GSE235065 | SRR24941019, SRR24940991, SRR24940997, SRR24941024, SRR24941007, SRR24941014 |
| Striatal cell | — | 4 | 4 | PRJNA1093144 | SRR28497187, SRR28497188, SRR28497191, SRR28497192, SRR28497193, SRR28497194, SRR28497195, SRR28497196 |
Drosophila melanogaster
| Sample Name | Wild Type (#) | Non-targeting sgRNA Control (#) | Dora Knockout (#) | BioProject Number | SRR Number |
|---|---|---|---|---|---|
| S2 cells | 3 | — | 3 | GSE163388 | SRR13264713, SRR13264714, SRR13264715, SRR13264716, SRR13264717, SRR13264718 |
Caenorhabditis elegans
| Sample Name | Wild Type (#) | Non-targeting sgRNA Control (#) | Ebax Knockout (#) | BioProject Number | Data Source |
|---|---|---|---|---|---|
| Early Embryo | 2 | — | 2 | GSE267367 | SRR29013903, SRR29013904, SRR29013905, SRR29013906 |
| Late Embryo | 2 | — | 2 | GSE267367 | SRR29013899, SRR29013900, SRR29013901, SRR29013902 |
| L1 | 4 | — | 4 | GSE267367 | SRR29013871, SRR29013872, SRR29013873, SRR29013874, SRR29013895, SRR29013896, SRR29013897, SRR29013898 |
| L2 | 2 | — | 2 | GSE267367 | SRR29013891, SRR29013892, SRR29013893, SRR29013894 |
| L3 | 2 | — | 2 | GSE267367 | SRR29013887, SRR29013888, SRR29013889, SRR29013890 |
| L4 | 5 | — | 4 | GSE267367 | SRR29013866, SRR29013867, SRR29013868, SRR29013869, SRR29013870, SRR29013883, SRR29013884, SRR29013885, SRR29013886 |
| Gravid adult | 2 | — | 2 | GSE267367 | SRR29013879, SRR29013880, SRR29013881, SRR29013882 |
| Glp-4 | 2 | — | 2 | GSE267367 | SRR29013875, SRR29013876, SRR29013877, SRR29013878 |
4. How is CLASH V2 data analyzed in CLASHub?
Choose the data source. Public data is recommended: enter one GSE, PRJNA, or SRP study, or up to 20 SRR runs. CLASHub checks the archive records and lets you select the runs before confirmation. Paired-end or single-end FASTQ.gz and cleaned FASTA.gz uploads remain supported.
Review preprocessing. Automatic adapter and read-structure detection is the default for FASTQ data. AI-assisted review can interpret public protocol information, but deterministic read evidence and remapping safety checks decide the adapter and UMI plan that is executed.
Run CLASH V2. The pipeline analyzes direct chimeric reads and AGO peak-supported candidate sites while keeping direct, ago_peak, and direct+ago_peak evidence separate.
Open the results. Completed jobs provide an HTML report, a miRNA-target result table, and an AGO coverage track when available. Results remain private job files and are not automatically imported into the public database.
5. How is miRNA-seq V2 data analyzed in CLASHub?
Choose the data source. Enter one GSE, PRJNA, or SRP study, or up to 12 SRR runs. After checking the accession, select the samples, verify the detected species, and confirm by email. Paired-end or single-end FASTQ.gz and cleaned FASTA.gz uploads remain supported.
Review preprocessing. Public FASTQ data uses automatic adapter and read-structure detection. AI-assisted protocol review can propose adapter or UMI candidates, but the executed plan must pass deterministic sample evidence and remapping checks.
Quantify miRNA. Selected runs remain separate samples. The V2 workflow uses the shared species-specific miRNA reference and preserves its documented identity and isomiR rules.
Open the results. Outputs include raw counts, CPM, isomiR information, preprocessing records, and an HTML report. Results are not automatically imported into the public database.
6. How is RNA-seq V2 data analyzed in CLASHub?
Choose the data source. Enter one GSE, PRJNA, or SRP study, one supported Dryad dataset, or up to 20 SRR runs. Public files are checked before transfer. Single-end and paired-end FASTQ.gz uploads remain available.
Review the samples. Select the runs, verify the species and read layout, choose the library type, and confirm the request by email. Each selected run remains a separate sample unless a reviewed design says otherwise.
Run preprocessing and quantification. Automatic adapter and terminal-structure handling is checked against the reads and genome-remapping evidence. RNA-seq V2 then aligns and quantifies each sample.
Open the results. The current V2 form produces gene Counts and TPM matrices without requiring control/treatment groups or replicates. Optional exon and intron count matrices are available. Differential expression is not part of this quantification request.
7. How is cumulative fraction curve analysis performed in CLASHub?
Step 1: Data Upload and Input
Users upload a differential gene expression CSV file containing GeneName, BaseMean, and log2FoldChange. A BaseMean threshold (default: 100) filters out low-expression transcripts to ensure robust results.
Step 2: Target Identification
Target genes are classified into two groups:
2.1 CLASH-Derived Targets: Identified via experimental CLASH data (Conserved and All targets).
2.2 TargetScan-Derived Targets: Predicted interactions extracted from TargetScan databases.
Step 3: Curve Generation and Analysis Modes
The tool compares fold change distributions between miRNA targets and non-target genes using two available modes:
3.1 Standard Analysis: Groups targets by broad conservation status.
3.2 Stringent Filtering: Narrows the analysis specifically to the top 25% of high-efficacy targets based on TargetScan Context++ scores, revealing more pronounced repression patterns.
Statistical differences between target groups and background non-targets are quantified via Mann–Whitney U tests.
Step 4: Output Results
Outputs include SVG files of the Cumulative Fraction Curves visually plotting the repression shifts, alongside a comprehensive merged CSV dataset that annotates each gene with its specific target classification (e.g., top 25% Context++, high-confidence CLASH overlaps, or non-targets).