title: PBMC_8780_CD_1

description:
Library name: PBMC_8780_CD_1
RNA-Seq of CHIM PBMC

data_processing:
Paired-end reads that passed Illumina quality filters were further screened to remove sequences aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The remaining reads were aligned to the GRCh38 human reference genome with Gencode v27 annotations using STAR (v2.6.1) [PMID: 23104886]. Read complexity was assessed with PRINSEQ Lite (v0.20.3) [PMID: 21278185], and low-complexity reads (DUST score > 4) were excluded from the BAM files. The alignment results were parsed via the SAMtools [PMID: 19505943] to generate SAM files. Gene-level counts were then obtained using featureCounts (v1.6.5) [PMID: 24227677] using the default option along with a minimum quality cut-off (Phred > 10), and transcripts per million (TPM) reads values were calculated. T cell receptor (TCR) transcripts were aggregated into four groups: TCR-α, TCR-β, TCR-γ, and TCR-δ. B cell receptor (BCR) transcripts were aggregated into light chains (IGK and IGL) and heavy chains (IGH-), with isotype transcripts (IGHG1-4, IGHM, IGHD, IGHE, IGHA1-2) analyzed separately. Transcripts were filtered using EdgeR’s filterByExpr function (v4.2.2) [PMID: 39844453] with “participants + timepoint” as the design. For each participant, baseline TPMs were averaged and raw counts were summed. Differential expression was assessed using the DESeq2 package (v1.44.0) [PMID: 25516281] for NPS and EdgeR for PBMCs in an R (v4.4.0) environment, with gene expression called differential with an FDR<0.05. Gene set enrichment analysis (GSEA) was performed using Metascape [PMID: 30944313] and GSEA (v4.4.0) [PMID: 16199517], both with the Gene Ontology (GO) gene sets [PMID: 36866529].
Assembly: GRCh38
Supplementary files format and content: "PBMC_counts.tsv" contains raw count values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm.tsv" contains TPM values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm_baseline_means_BCR_TCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were averaged.
Supplementary files format and content: "PBMC_counts_baseline_sums_BCR_TCR_aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were summed.
Supplementary files format and content: "NPS_counts.csv" contains raw count values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm.csv" contains TPM values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm_baseline_means_TCR_BCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were averaged.
Supplementary files format and content: NPS_counts_baseline_sums_BCR.TCR.aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were summed.
Supplementary files format and content: "participant_metadata_filtered.csv" contains metadata per participant.

extract_protocol:
NPS: RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA was quantified by qPCR using the housekeeping gene B2M.
PBMC: 500K cells were stored in 750 μL TRIzol at -80°C. RNA until further processing. RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NPS: For cDNA synthesis, 10 ng of RNA was reverse-transcribed and pre-amplified (14 cycles) according to the Smart-Seq2 protocol. cDNA was purified with AMPure XP beads (Beckman Coulter), and 0.5 ng was used for Nextera XT sequencing library preparation with 8-bp Unique Dual Index (UDI) barcodes (IDT, Illumina) and the Nextera XT DNA Library Preparation Kit (Illumina). To minimize inter-assay variability, all purification steps were performed using an EpMotion 5075 (Eppendorf), and sequencing libraries were prepared in a 96-well format using a Mantis microfluidics liquid dispenser (Formulamatrix). Quality control included assessment of total RNA quality and quantity, optimization of pre-amplification cycle numbers, and fragment size analysis by capillary electrophoresis (5300 Fragment Analyzer, Agilent). cDNA and final libraries were quantified with the Quant-iT PicoGreen assay (Thermo Fisher Scientific). All samples passed quality thresholds, with >70% of fragments ranging from 300–700 bp and <5% primer dimers. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche), normalized to equimolar concentrations, and loaded onto a NovaSeq X Plus sequencing platform (Illumina) with a 25B flow cell. Paired-end sequencing (150 bp) yielded 4.2 billion total reads, corresponding to an average depth of ~15 million reads per sample.
PBMC: Quantabio Sparq mRNA-Seq kit was used to prepare stranded libraries using 8 ng of high-quality total RNA as input, except in 10 samples where the yield was below 8 ng. Libraries underwent 16-18 PCR amplification cycles and libraries were indexed with xGen 10 nt Unique Dual Indexes (UDIs). Paired-end (50x50) sequencing was performed on a NovaSeq 6000 targeting 40 million reads per library.

value: Blood

tag: age

value: PBMC

value: female


title: AB13522

status: Public on Jul 21 2026

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample1412
MARS_v2

library_source: transcriptomic

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

molecule: polyA RNA

organism: Homo sapiens

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

tag: tissue

value: BM

tag: gate

tag: batch


title: AB13519

description:
Library name: Sample1409
MARS_v2


title: AB13520

description:
Library name: Sample1410
MARS_v2

value: PC


title: AB13518

description:
Library name: Sample1408
MARS_v2


title: AB13517

description:
Library name: Sample1407
MARS_v2


title: AB13516

description:
Library name: Sample1406
MARS_v2


title: AB13515

description:
Library name: Sample1405
MARS_v2


title: AB13514

description:
Library name: Sample1404
MARS_v2


title: AB13509

description:
Library name: Sample1399
MARS_v2


title: AB13510

description:
Library name: Sample1400
MARS_v2


title: AB13512

description:
Library name: Sample1402
MARS_v2


title: AB13513

description:
Library name: Sample1403
MARS_v2


title: AB13506

description:
Library name: Sample1396
MARS_v2


title: AB13507

description:
Library name: Sample1397
MARS_v2


title: AB13505

description:
Library name: Sample1395
MARS_v2


title: AB13504

description:
Library name: Sample1394
MARS_v2


title: AB13502

description:
Library name: Sample1392
MARS_v2


title: AB13501

description:
Library name: Sample1391
MARS_v2


title: AB13503

description:
Library name: Sample1393
MARS_v2


title: AB13500

description:
Library name: Sample1390
MARS_v2


title: AB13498

description:
Library name: Sample1388
MARS_v2


title: AB13496

description:
Library name: Sample1386
MARS_v2


title: AB13494

description:
Library name: Sample1384
MARS_v2


title: AB13495

description:
Library name: Sample1385
MARS_v2


title: AB13493

description:
Library name: Sample1383
MARS_v2


title: AB13491

description:
Library name: Sample1381
MARS_v2


title: AB13492

description:
Library name: Sample1382
MARS_v2


title: AB13489

description:
Library name: Sample1379
MARS_v2


title: AB13490

description:
Library name: Sample1380
MARS_v2


title: AB13256

description:
Library name: Sample1378
MARS_v2


title: AB13253

description:
Library name: Sample1375
MARS_v2


title: AB13252

description:
Library name: Sample1374
MARS_v2


title: AB13251

description:
Library name: Sample1373
MARS_v2


title: AB13250

description:
Library name: Sample1372
MARS_v2


title: AB13246

description:
Library name: Sample1368
MARS_v2


title: AB13248

description:
Library name: Sample1370
MARS_v2


title: AB13242

description:
Library name: Sample1367
MARS_v2


title: AB13239

description:
Library name: Sample1364
MARS_v2


title: AB13238

description:
Library name: Sample1363
MARS_v2


title: AB13237

description:
Library name: Sample1362
MARS_v2


title: AB11144

description:
Library name: Sample70
MARS


title: AB13236

description:
Library name: Sample1361
MARS_v2


title: AB13233

description:
Library name: Sample1359
MARS_v2


title: AB13232

description:
Library name: Sample1358
MARS_v2


title: AB13231

description:
Library name: Sample1357
MARS_v2


title: AB13227

description:
Library name: Sample1354
MARS_v2


title: AB13228

description:
Library name: Sample1355
MARS_v2


title: AB13224

description:
Library name: Sample1352
MARS_v2


title: AB13225

description:
Library name: Sample1353
MARS_v2


title: AB13222

description:
Library name: Sample1350
MARS_v2


title: AB13218

description:
Library name: Sample1348
MARS_v2


title: AB13220

description:
Library name: Sample1349
MARS_v2


title: AB13508

description:
Library name: Sample1398
MARS_v2


title: AB13216

description:
Library name: Sample1347
MARS_v2


title: AB13214

description:
Library name: Sample1345
MARS_v2


title: AB13211

description:
Library name: Sample1344
MARS_v2


title: AB13209

description:
Library name: Sample1343
MARS_v2


title: AB13208

description:
Library name: Sample1342
MARS_v2


title: AB13204

description:
Library name: Sample1339
MARS_v2


title: AB13207

description:
Library name: Sample1341
MARS_v2


title: AB13206

description:
Library name: Sample1340
MARS_v2


title: AB13203

description:
Library name: Sample1338
MARS_v2


title: AB13202

description:
Library name: Sample1337
MARS_v2


title: AB13201

description:
Library name: Sample1336
MARS_v2


title: AB13200

description:
Library name: Sample1335
MARS_v2


title: siBACH1_H3k27

status: Public on Jul 22 2026

city: Beijing

first: Zishanbai

last: Zhang

address: No.1 Dongjiaominxiang, Dongcheng District

country: China

institute: Beijing Tongren Hospital

description:
Library name: siBACH1_H3k27
The raw data are being made available by Bowtie2 and MACS2 callpeak

library_source: genomic

data_processing:
Upload fq.gz data to Galaxy version 23.2 rc1, Using FastQC to evaluate the quality of data, using cutadapt to de concatenate raw data
Reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.0.
To create coverage plots, the locations of the mapped reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called using MACS2 callpeak v3.5.4 with the significance cut-off p-value <=0.00001
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: FaDu

growth_protocol: FaDu were cultured in MEM medium supplemented with 10 % fetal bovine serum, 100 U mL-1 penicillin, and 100 U mL-1 streptomycin (Gibco)

extract_protocol:
1 × 105 FaDu cells were collected,for the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme)
For the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme). Briefly, 1 × 105 FaDu cells were collected, resuspended in 100 μL wash buffer, transferred to an 8-tube strip containing activated ConA beads, and incubated for 10 min. Subsequently, 50 μL prechilled antibody buffer containing BACH1 or BRG1 antibodies was added to cells and incubated at 4 °C overnight, followed by the addition of diluted secondary antibodies and incubation for 60 min. After washing thrice with DIG wash buffer, samples were incubated with diluted pA/G-Tnp transposase for 1 h. Next, 50 μL diluted TTBL was added, and samples were incubated at 37 °C in a PCR instrument for 60 min for fragmentation. Subsequently, DNA extraction was performed by adding 5 μL proteinase K, 100 μL buffer L/B, and 20 μL DNA extract beads on the fragmented samples and incubating at 55 °C for 10 min. Following washes with WA and WB buffers, samples were eluted using sterile ultrapure water. The extracted DNA underwent library amplification using the TruePrep Index Kit V2 for Illumina (TD202, Vazyme). PCR products were treated with VAHTS DNA clean beads (N411, Vazyme) for 5 min, the supernatant then was discarded, samples were washed with 80% ethanol, eluted using sterile ultrapure water, and the library was sequenced on the Illumina NovaSeq platform.

tag: cell line

value: FaDu

tag: cell type

value: Human medulloblastoma cell

value: H3K27 (ABclonal, A22006)


title: AB13020

description:
Library name: Sample1331
MARS_v2


title: AB13022

description:
Library name: Sample1333
MARS_v2


title: AB13021

description:
Library name: Sample1332
MARS_v2


title: AB13497

description:
Library name: Sample1387
MARS_v2


title: AB13018

description:
Library name: Sample1330
MARS_v2


title: AB13015

description:
Library name: Sample1329
MARS_v2


title: AB13254

description:
Library name: Sample1376
MARS_v2


title: AB13011

description:
Library name: Sample1327
MARS_v2


title: PBMC_8779_CD_1_reprep

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description:
Library name: PBMC_8779_CD_1_reprep
RNA-Seq of CHIM PBMC

source_name: Blood

tag: days post_challenge

tag: reprep

value: Yes

tag: Sex


title: AB13007

description:
Library name: Sample1326
MARS_v2


title: AB13006

description:
Library name: Sample1325
MARS_v2


title: AB13001

description:
Library name: Sample1321
MARS_v2


title: AB12997

description:
Library name: Sample1319
MARS_v2


title: AB13234

description:
Library name: Sample1360
MARS_v2


title: AB12995

description:
Library name: Sample1317
MARS_v2


title: AB12996

description:
Library name: Sample1318
MARS_v2


title: AB12994

description:
Library name: Sample1316
MARS_v2


title: AB12992

description:
Library name: Sample1314
MARS_v2


title: AB13223

description:
Library name: Sample1351
MARS_v2


title: AB12991

description:
Library name: Sample1313
MARS_v2


title: AB12990

description:
Library name: Sample1312
MARS_v2


title: AB12980

description:
Library name: Sample1310
MARS_v2


title: AB12979

description:
Library name: Sample1309
MARS_v2


title: AB12989

description:
Library name: Sample1311
MARS_v2


title: AB12977

description:
Library name: Sample1308
MARS_v2


title: AB12976

description:
Library name: Sample1307
MARS_v2


title: AB12974

description:
Library name: Sample1305
MARS_v2


title: AB12975

description:
Library name: Sample1306
MARS_v2


title: AB12971

description:
Library name: Sample1302
MARS_v2


title: AB12973

description:
Library name: Sample1304
MARS_v2


title: AB12972

description:
Library name: Sample1303
MARS_v2


title: AB12969

description:
Library name: Sample1300
MARS_v2


title: AB12968

description:
Library name: Sample1299
MARS_v2


title: AB12966

description:
Library name: Sample1297
MARS_v2


title: AB12965

description:
Library name: Sample1296
MARS_v2


title: AB12964

description:
Library name: Sample1295
MARS_v2


title: AB12963

description:
Library name: Sample1294
MARS_v2


title: AB12962

description:
Library name: Sample1293
MARS_v2


title: AB12545

description:
Library name: Sample1290
MARS_v2


title: AB12548

description:
Library name: Sample1292
MARS_v2


title: AB12544

description:
Library name: Sample1289
MARS_v2


title: AB12539

description:
Library name: Sample1287
MARS_v2


title: AB12531

description:
Library name: Sample1286
MARS_v2


title: AB12525

description:
Library name: Sample1284
MARS_v2


title: AB12511

description:
Library name: Sample1283
MARS_v2


title: AB12510

description:
Library name: Sample1282
MARS_v2


title: AB12506

description:
Library name: Sample1281
MARS_v2


title: AB12504

description:
Library name: Sample1280
MARS_v2


title: AB12503

description:
Library name: Sample1279
MARS_v2


title: AB12499

description:
Library name: Sample1278
MARS_v2


title: AB12498

description:
Library name: Sample1277
MARS_v2


title: AB12497

description:
Library name: Sample1276
MARS_v2


title: AB12496

description:
Library name: Sample1275
MARS_v2


title: AB12494

description:
Library name: Sample1273
MARS_v2


title: AB12493

description:
Library name: Sample1272
MARS_v2


title: AB12492

description:
Library name: Sample1271
MARS_v2


title: AB12495

description:
Library name: Sample1274
MARS_v2


title: AB12970

description:
Library name: Sample1301
MARS_v2


title: AB12490

description:
Library name: Sample1269
MARS_v2


title: AB12967

description:
Library name: Sample1298
MARS_v2


title: AB12489

description:
Library name: Sample1268
MARS_v2


title: AB12488

description:
Library name: Sample1267
MARS_v2


title: AB12487

description:
Library name: Sample1266
MARS_v2


title: AB12546

description:
Library name: Sample1291
MARS_v2


title: AB12486

description:
Library name: Sample1265
MARS_v2


title: AB12484

description:
Library name: Sample1264
MARS_v2


title: AB12483

description:
Library name: Sample1263
MARS_v2


title: AB12491

description:
Library name: Sample1270
MARS_v2


title: AB12541

description:
Library name: Sample1288
MARS_v2


title: AB12360

description:
Library name: Sample1262
MARS_v2


title: AB12352

description:
Library name: Sample1260
MARS_v2


title: AB12354

description:
Library name: Sample1261
MARS_v2


title: AB12351

description:
Library name: Sample1259
MARS_v2


title: AB12348

description:
Library name: Sample1257
MARS_v2


title: AB12349

description:
Library name: Sample1258
MARS_v2


title: AB12347

description:
Library name: Sample1256
MARS_v2


title: AB12528

description:
Library name: Sample1285
MARS_v2


title: AB12345

description:
Library name: Sample1255
MARS_v2


title: AB12330

description:
Library name: Sample1254
MARS_v2


title: AB12326

description:
Library name: Sample1253
MARS_v2


title: AB12325

description:
Library name: Sample1252
MARS_v2


title: AB12317

description:
Library name: Sample1250
MARS_v2


title: AB12324

description:
Library name: Sample1251
MARS_v2


title: AB12315

description:
Library name: Sample1248
MARS_v2


title: AB12316

description:
Library name: Sample1249
MARS_v2


title: AB12314

description:
Library name: Sample1247
MARS_v2


title: AB12313

description:
Library name: Sample1246
MARS_v2


title: AB12312

description:
Library name: Sample1245
MARS_v2


title: AB12311

description:
Library name: Sample1244
MARS_v2


title: AB12310

description:
Library name: Sample1243
MARS_v2


title: AB12307

description:
Library name: Sample1240
MARS_v2


title: AB12308

description:
Library name: Sample1241
MARS_v2


title: AB12309

description:
Library name: Sample1242
MARS_v2


title: AB12302

description:
Library name: Sample1239
MARS_v2


title: AB12300

description:
Library name: Sample1238
MARS_v2


title: AB12299

description:
Library name: Sample1237
MARS_v2


title: AB12298

description:
Library name: Sample1236
MARS_v2


title: AB12296

description:
Library name: Sample1235
MARS_v2


title: AB12295

description:
Library name: Sample1234
MARS_v2


title: AB12288

description:
Library name: Sample1233
MARS_v2


title: AB12284

description:
Library name: Sample1232
MARS_v2


title: AB12283

description:
Library name: Sample1231
MARS_v2


title: AB12282

description:
Library name: Sample1230
MARS_v2


title: AB12280

description:
Library name: Sample1229
MARS_v2


title: AB12279

description:
Library name: Sample1228
MARS_v2


title: AB12277

description:
Library name: Sample1226
MARS_v2


title: AB12278

description:
Library name: Sample1227
MARS_v2


title: AB13521

description:
Library name: Sample1411
MARS_v2


title: AB12276

description:
Library name: Sample1225
MARS_v2


title: AB12274

description:
Library name: Sample1224
MARS_v2


title: AB12272

description:
Library name: Sample1223
MARS_v2


title: AB12271

description:
Library name: Sample1222
MARS_v2


title: AB12270

description:
Library name: Sample1221
MARS_v2


title: AB12269

description:
Library name: Sample1220
MARS_v2


title: AB12263

description:
Library name: Sample1219
MARS_v2


title: AB12262

description:
Library name: Sample1218
MARS_v2


title: AB12261

description:
Library name: Sample1217
MARS_v2


title: AB12260

description:
Library name: Sample1216
MARS_v2


title: AB12255

description:
Library name: Sample1215
MARS_v2


title: AB12249

description:
Library name: Sample1213
MARS_v2


title: AB12254

description:
Library name: Sample1214
MARS_v2


title: AB12248

description:
Library name: Sample1212
MARS_v2


title: AB12247

description:
Library name: Sample1211
MARS_v2


title: AB12244

description:
Library name: Sample1210
MARS_v2


title: AB11788

description:
Library name: Sample1204
MARS_v2


title: AB12243

description:
Library name: Sample1209
MARS_v2


title: AB11791

description:
Library name: Sample1205
MARS_v2


title: AB11795

description:
Library name: Sample1206
MARS_v2


title: AB12241

description:
Library name: Sample1207
MARS_v2


title: AB12242

description:
Library name: Sample1208
MARS_v2


title: AB11787

description:
Library name: Sample1203
MARS_v2


title: AB11785

description:
Library name: Sample1202
MARS_v2


title: AB11783

description:
Library name: Sample1201
MARS_v2


title: AB11782

description:
Library name: Sample1200
MARS_v2


title: AB11780

description:
Library name: Sample1198
MARS_v2


title: AB11781

description:
Library name: Sample1199
MARS_v2


title: AB11778

description:
Library name: Sample1196
MARS_v2


title: AB11779

description:
Library name: Sample1197
MARS_v2


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description:
Library name: Sample1195
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description:
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description:
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description:
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title: AB11770

description:
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description:
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title: AB11762

description:
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title: AB11763

description:
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title: AB11761

description:
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description:
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description:
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description:
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description:
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title: AB13000

description:
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description:
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description:
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title: AB11527

description:
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MARS_v2


title: AB11526

description:
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title: AB11522

description:
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MARS_v2


title: AB11521

description:
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MARS_v2


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description:
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description:
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title: AB11519

description:
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title: AB11516

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description:
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description:
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description:
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description:
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description:
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description:
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description:
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MARS_v2


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description:
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description:
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description:
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description:
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MARS_v2


title: AB11281

description:
Library name: Sample1071
MARS_v2


title: AB11279

description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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MARS_v2


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description:
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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


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description:
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MARS_v2


title: AB10810

description:
Library name: Sample1028
MARS_v2

source_name: EMD

value: EMD


title: AB10809

description:
Library name: Sample1027
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title: AB10808

description:
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description:
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description:
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description:
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description:
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description:
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description:
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MARS_v2


title: AB10481

description:
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title: AB10303

description:
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MARS_v2


title: AB10302

description:
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MARS_v2


title: AB10479

description:
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MARS_v2


title: AB10301

description:
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MARS_v2


title: AB10300

description:
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MARS_v2


title: AB10299

description:
Library name: Sample1013
MARS_v2


title: U937 cells, control, rep3

city: Hefei

first: Mengqing

last: Gao

state: Anhui

department: Department of Hematology

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

data_processing:
Raw fastq reads were processed using fastp to remove low-quality reads, resulting in clean reads for subsequent data analysis.
HISAT2 was used for alignment to the reference genome hg38.
Gene expression levels were calculated in FPKM and the read counts for each gene were obtained using HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

growth_protocol: U937 cells were maintained in RPMI-1640 supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Total RNA from U937 cells was extracted with TRIzol reagent (Invitrogen, 15596026CN). RNAs from primary samples were extracted using AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, Cat# 80004) according to the manufacturer’s instructions.
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep Kit (Vazyme) for AML primary samples and Fast RNA-seq Lib Prep Kit V2 (ABclonal) for cell lines according to the manufacturer's instructions

treatment_protocol: U937 NT, KO1, KO2 were deprived of glutamine for 6 hours. U937 cells were treated with 0.5 μM JQ1 for 24 hours.

value: acute myeloid leukemia cell lines

tag: treatment

value: DMSO


title: AB10298

description:
Library name: Sample1012
MARS_v2


title: AB10297

description:
Library name: Sample1011
MARS_v2


title: U937 cells, JQ1, rep2


title: AB10271

description:
Library name: Sample1009
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title: AB10296

description:
Library name: Sample1010
MARS_v2


title: AB10270

description:
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description:
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description:
Library name: Sample1006
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description:
Library name: Sample1005
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description:
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MARS_v2


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description:
Library name: Sample1003
MARS_v2


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description:
Library name: Sample1000
MARS_v2


title: AB10264

description:
Library name: Sample1002
MARS_v2


title: AB10263

description:
Library name: Sample1001
MARS_v2


title: AB10260

description:
Library name: Sample998
MARS_v2


title: AB10261

description:
Library name: Sample999
MARS_v2


title: AB10259

description:
Library name: Sample997
MARS_v2


title: AB10258

description:
Library name: Sample996
MARS_v2


title: AB10151

description:
Library name: Sample994
MARS_v2


title: AB10152

description:
Library name: Sample995
MARS_v2


title: AB10150

description:
Library name: Sample993
MARS_v2


title: AB10143

description:
Library name: Sample991
MARS_v2


title: AB10149

description:
Library name: Sample992
MARS_v2


title: AB10137

description:
Library name: Sample990
MARS_v2


title: AB10135

description:
Library name: Sample988
MARS_v2


title: AB10136

description:
Library name: Sample989
MARS_v2


title: AB10133

description:
Library name: Sample987
MARS_v2


title: AB10132

description:
Library name: Sample986
MARS_v2


title: AB10131

description:
Library name: Sample985
MARS_v2


title: acRIP-seq NAT10 knock out IP of ac4C mRNA in K562 cell line [KO_IP_1]

first: Yanran

last: Wang

address: No.5, Dongdan Sanjiao, Dongcheng District, Beijing

department: State Key Laboratory of Medical Molecular Biology

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were aligned to the Homo sapiens transcripts using bowtie2. ac4C peaks were detected by MACS2, and filtered by log10P < -3. Input samples were used as controls for peak calling. Screening of differential peaks using BEDTools map. ac4C sites that resided in protein coding genes were analyzed for downstream analysis. ChIPseeker was used for annotating the peaks.
Assembly: GENCODE Release 36, GRCh38.p13, transcripts
Supplementary files format and content: bigWig, narrowPeak

source_name: K562 cell line

growth_protocol: NAT10 knock-out k562 cells were grown in RPMI-1640 media supplemented with 10% FBS at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNA was rRNA depleted with the NEBNext® rRNA Depletion Kit v2 (Promega) and then subjected to immunoprecipitation. Briefly, RNA was randomly fragmented to ~100 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody or Normal Rabbit IgG antibody by rotating at room temperature for 2 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
RNA extracted from IP, IgG and input samples obtained from NAT10 knock-out k562 cells was then constructed using the NEBNext® Ultra™ RNA Library Prep Kit,, following the manufacturer's instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a Novaseq 6000 platform (Illumina).

value: K562 cell line

tag: genotype

value: NAT10 knock out


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description:
Library name: Sample984
MARS_v2


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description:
Library name: Sample982
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description:
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MARS_v2


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description:
Library name: Sample981
MARS_v2


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description:
Library name: Sample980
MARS_v2


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description:
Library name: Sample979
MARS_v2


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description:
Library name: Sample978
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description:
Library name: Sample975
MARS_v2


title: AB10122

description:
Library name: Sample976
MARS_v2


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description:
Library name: Sample974
MARS_v2


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description:
Library name: Sample973
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description:
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description:
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MARS_v2


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description:
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MARS_v2


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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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title: AB9030

description:
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description:
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description:
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description:
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description:
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description:
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description:
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MARS


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description:
Library name: Sample954
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description:
Library name: Sample953
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description:
Library name: Sample951
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description:
Library name: Sample952
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description:
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description:
Library name: Sample948
MARS


title: AB8735

description:
Library name: Sample947
MARS


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description:
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description:
Library name: Sample946
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description:
Library name: Sample945
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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title: AB7935

description:
Library name: Sample928
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description:
Library name: Sample927
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title: AB7933

description:
Library name: Sample926
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description:
Library name: Sample924
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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title: AB7731

description:
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title: AB7730

description:
Library name: Sample915
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description:
Library name: Sample914
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description:
Library name: Sample912
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description:
Library name: Sample913
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description:
Library name: Sample911
MARS


title: AB7480

description:
Library name: Sample910
MARS


title: AB7479

description:
Library name: Sample909
MARS


title: AB7299

description:
Library name: Sample908
MARS


title: AB7297

description:
Library name: Sample906
MARS


title: AB7298

description:
Library name: Sample907
MARS


title: AB7296

description:
Library name: Sample905
MARS


title: AB7295

description:
Library name: Sample904
MARS


title: AB7294

description:
Library name: Sample903
MARS


title: AB7293

description:
Library name: Sample902
MARS


title: AB7290

description:
Library name: Sample899
MARS


title: AB7292

description:
Library name: Sample901
MARS


title: AB7291

description:
Library name: Sample900
MARS


title: AB7289

description:
Library name: Sample898
MARS


title: AB7286

description:
Library name: Sample895
MARS


title: AB7288

description:
Library name: Sample897
MARS


title: AB7287

description:
Library name: Sample896
MARS


title: AB7285

description:
Library name: Sample894
MARS


title: AB7284

description:
Library name: Sample893
MARS


title: AB7108

description:
Library name: Sample892
MARS


title: AB7107

description:
Library name: Sample891
MARS


title: AB7106

description:
Library name: Sample890
MARS


title: AB7105

description:
Library name: Sample889
MARS


title: AB7104

description:
Library name: Sample888
MARS


title: AB7102

description:
Library name: Sample886
MARS


title: AB7103

description:
Library name: Sample887
MARS


title: AB7101

description:
Library name: Sample885
MARS


title: AB7059

description:
Library name: Sample884
MARS


title: AB7057

description:
Library name: Sample882
MARS


title: AB7058

description:
Library name: Sample883
MARS


title: AB7056

description:
Library name: Sample881
MARS


title: AB7055

description:
Library name: Sample880
MARS


title: AB7054

description:
Library name: Sample879
MARS


title: AB6888

description:
Library name: Sample877
MARS


title: AB6889

description:
Library name: Sample878
MARS


title: AB6887

description:
Library name: Sample876
MARS


title: AB6886

description:
Library name: Sample875
MARS


title: AB6885

description:
Library name: Sample874
MARS


title: AB6884

description:
Library name: Sample873
MARS


title: AB6883

description:
Library name: Sample872
MARS


title: AB6882

description:
Library name: Sample871
MARS


title: AB6686

description:
Library name: Sample869
MARS


title: AB6881

description:
Library name: Sample870
MARS


title: AB6683

description:
Library name: Sample866
MARS


title: AB6684

description:
Library name: Sample867
MARS


title: AB6682

description:
Library name: Sample865
MARS


title: AB6681

description:
Library name: Sample864
MARS


title: AB6685

description:
Library name: Sample868
MARS


title: AB6679

description:
Library name: Sample862
MARS


title: AB6680

description:
Library name: Sample863
MARS


title: AB6677

description:
Library name: Sample860
MARS


title: AB6676

description:
Library name: Sample859
MARS


title: AB6678

description:
Library name: Sample861
MARS


title: AB6673

description:
Library name: Sample856
MARS


title: AB6674

description:
Library name: Sample857
MARS


title: AB6675

description:
Library name: Sample858
MARS


title: AB6672

description:
Library name: Sample855
MARS


title: AB6671

description:
Library name: Sample854
MARS


title: AB6501

description:
Library name: Sample853
MARS


title: AB6499

description:
Library name: Sample851
MARS


title: AB6500

description:
Library name: Sample852
MARS


title: AB6498

description:
Library name: Sample850
MARS


title: AB6497

description:
Library name: Sample849
MARS


title: AB6496

description:
Library name: Sample848
MARS


title: AB6494

description:
Library name: Sample846
MARS


title: AB6495

description:
Library name: Sample847
MARS


title: AB6492

description:
Library name: Sample844
MARS


title: AB6491

description:
Library name: Sample843
MARS


title: AB6493

description:
Library name: Sample845
MARS


title: AB6490

description:
Library name: Sample842
MARS


title: ARPE-19 cells, PM2.5 plus fucoidan, biological replicate 1

city: Taipei

first: ZHI-HU

last: LIN

address: No. 145, Zhengzhou Rd

department: Department of Ophthalmology

country: Taiwan

institute: Taipei City Hospital

description:
Library name: PF_1
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_PF_1(FP) and TPM_PF_1(FP).

data_processing:
Raw BCL/CBCL files were converted to FASTQ format using bcl2fastq.
Adapter sequences, low-quality bases, and reads containing excessive ambiguous nucleotides were removed using fastp v0.20.0. Raw and cleaned reads were assessed using FastQC v0.11.9.
SortMeRNA filtering was not performed. Clean reads were aligned to the Homo sapiens reference genome Homo_sapiens.GRCh38.98 using HISAT2 v2.1.0.
Gene-level raw read counts were generated using featureCounts from Subread v2.0.1.
TPM values were calculated for gene-expression normalization. All genes were retained without TPM filtering.
Assembly: GRCh38; Ensembl release 98 (Homo_sapiens.GRCh38.98)
Supplementary files format and content: Fulltable.xlsx is an Excel workbook containing gene-level raw counts and TPM values for all eight samples, together with Ensembl gene identifiers, gene symbols, gene descriptions, and Entrez Gene identifiers.

source_name: retina

growth_protocol: ARPE-19 human retinal pigment epithelial cells were obtained from the Bioresource Collection and Research Center (BCRC 60383, Taiwan). Cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum without antibiotics. Treatments were initiated when cells reached approximately 80% confluence.

extract_protocol:
Total RNA was extracted, purified, and quality assessed by Genomics BioSci & Tech Co., Ltd. One microgram of purified total RNA from each sample was used for library preparation. The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations.
Strand-specific mRNA sequencing libraries were prepared from 1 μg of purified total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, polyadenylated mRNA was enriched from total RNA using oligo(dT)-coupled magnetic beads and fragmented at an elevated temperature. First-strand cDNA was synthesized using random primers and reverse transcriptase, followed by second-strand cDNA synthesis. The resulting double-stranded cDNA was purified, end-repaired, 3′-adenylated, and ligated to sequencing adapters. Adapter-ligated fragments were enriched by PCR and purified using the AMPure XP system (Beckman Coulter, Beverly, MA, USA). Library fragment size and quality were assessed using the Qsep400 System (BiOptic Inc., Taiwan), and library concentration was measured using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform using 150-bp paired-end sequencing by Genomics, BioSci & Tech Co. (New Taipei City, Taiwan).

treatment_protocol: Cells were treated for 24 hours with vehicle control (an equivalent volume of PBS), fucoidan from Fucus vesiculosus (Sigma-Aldrich, Cat. No. F5631, crude grade) at 400 micrograms/mL, diesel particulate matter (Standard Reference Material 1650b; NIST SRM 1650b, National Institute of Standards and Technology, Gaithersburg, MD, USA) at 200 micrograms/mL, or the combination of fucoidan and PM2.5 added simultaneously. Fucoidan was dissolved in PBS. PM2.5 was initially suspended in DMSO and subsequently diluted with PBS; the final DMSO concentration was below 0.1%. Stock preparations were stored at -80 degrees C.

value: retina

value: retinal pigment epithelial cells

value: Fucoidan 400 micrograms/mL and diesel particulate matter (NIST SRM 1650b) 200 micrograms/mL, added simultaneously for 24 hours


title: ARPE-19 cells, PM2.5 200 micrograms/mL, biological replicate 2

description:
Library name: P200_2
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_P200_2(P200) and TPM_P200_2(P200).

value: Diesel particulate matter (NIST SRM 1650b), 200 micrograms/mL, for 24 hours


title: ARPE-19 cells, PM2.5 plus fucoidan, biological replicate 2

description:
Library name: PF_2
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_PF_2(FP) and TPM_PF_2(FP).


title: ARPE-19 cells, PM2.5 200 micrograms/mL, biological replicate 1

description:
Library name: P200_1
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_P200_1(P200) and TPM_P200_1(P200).


title: ARPE-19 cells, fucoidan 400 micrograms/mL, biological replicate 2

description:
Library name: F400_2
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_F400_2(F400) and TPM_F400_2(F400).

value: Fucoidan from Fucus vesiculosus (Sigma-Aldrich, F5631), 400 micrograms/mL, for 24 hours


title: ARPE-19 cells, fucoidan 400 micrograms/mL, biological replicate 1

description:
Library name: F400_1
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_F400_1(F400) and TPM_F400_1(F400).


title: ARPE-19 cells, vehicle control, biological replicate 2

description:
Library name: CTL_2
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_CTL_2(CTL) and TPM_CTL_2(CTL).

value: Equivalent volume of PBS for 24 hours


title: ARPE-19 cells, vehicle control, biological replicate 1

description:
Library name: CTL_1
Biological replicate; corresponding columns in Fulltable.xlsx: Counts_CTL_1(CTL) and TPM_CTL_1(CTL).


title: MSH3-11-3

city: Philadelphia

first: Paul

middle: T

last: Ranum

state: PA

address: Latus Bio, 2929 Arch Street CIRA Center, 8th Floor - Suite 2

department: Research

country: USA

institute: Latus Bio

description: Library name: HEK293_12

data_processing:
Alignment with STAR (v.2.7.9a)
UMI deduplication with UMITools
counts per gene were calculated using cbquant (v.0.3.11)
differential expression was performed with DESeq2 (v.1.38.3)
data visualization was performed in R using Rstudio
Assembly: GRCh38
Supplementary files format and content: iPSC Processed Data file is a single counts/gene expression matrix for all samples where each sample appears as a separate column.
Supplementary files format and content: HEK293 Processed Data files are provided as individual counts/gene files one for each sample.

source_name: Cultured Cells

extract_protocol:
Total RNA was isolated by lysing cells in 350 µL RLT Buffer (containing 1% 2-mercaptoethanol) and homogenized with the QiaShredder (Qiagen 79656), followed by extraction with the RNeasy Micro Kit (Qiagen 74004) according to manufacturer’s instructions including the optional on-column DNase digestion (Qiagen 79254). RNA was eluted in RNAse-free water and RIN and concentration were measured using the Fragment analyzer 5300 (Agilent). Samples with RIN > 7 were further analyzed.
Libraries were prepared with 300 ng of RNA input by the Biomek i7 Hybrid automation (Beckman Coulter) with the Universal Plus mRNA-Seq with NuQuant kit with Custom AnyDeplete (NuGen 0522-A01). Library preparation with polyA transcript selection followed the supplier protocol and libraries were amplified with 13 cycles.

treatment_protocol: iPSC samples were treated with the indicated AAV construct or control at the indicated dose.  HEK-293 cells were transfected with the indicated miRNA expression plasmid using lypofectamine 2000.

value: Cultured Cells

value: Human Embryonic Kidney

value: WT

value: plasmid transfection CMV-miMSH3-11


title: MSH3-11-2

description: Library name: HEK293_11


title: MSH3-6-3

description: Library name: HEK293_9

value: plasmid transfection CMV-miMSH3-6


title: MSH3-11-1

description: Library name: HEK293_10


title: AB13523

description:
Library name: Sample1413
MARS_v2

value: BM

value: PC


title: HDS1-2

description: Library name: HEK293_5

value: plasmid transfection CMV-miHDS1


title: MSH3-6-2

description: Library name: HEK293_8


title: MSH3-6-1

description: Library name: HEK293_7


title: HDS1-1

description: Library name: HEK293_4


title: HDS1-3

description: Library name: HEK293_6


title: CMV-3

description: Library name: HEK293_3

value: plasmid transfection CMV promoter only


title: CMV-2

description: Library name: HEK293_2


title: CMV-1

description: Library name: HEK293_1


title: 96_UHRR

description:
Library name: EVTHH017717
96_UHRR

source_name: HD iPSC Neurons

value: HD iPSC Neurons

value: HD Patient Derived iPSC 49 CAG

value: iPSC Neurons

value: Het

value: UHRR


title: 94_NTC_H2O

description:
Library name: EVTHH017709
94_NTC_H2O


title: 93_NTC_H2O

description:
Library name: EVTHH017701
93_NTC_H2O


title: 92_NTC_H2O

description:
Library name: EVTHH017693
92_NTC_H2O


title: 91_NTC_H2O

description:
Library name: EVTHH017685
91_NTC_H2O


title: 95_UHRR

description:
Library name: EVTHH017629
95_UHRR


title: 88_NTC_H2O

description:
Library name: EVTHH017661
88_NTC_H2O


title: 86_NTC_H2O

description:
Library name: EVTHH017645
86_NTC_H2O


title: 84_N_A_Vehicle_control_rep4_7_days

description:
Library name: EVTHH017716
84_N_A_Vehicle_control_rep4_7_days

value: Vehicle control-NA


title: 83_N_A_Vehicle_control_rep3_7_days

description:
Library name: EVTHH017708
83_N_A_Vehicle_control_rep3_7_days


title: 82_N_A_Vehicle_control_rep2_7_days

description:
Library name: EVTHH017700
82_N_A_Vehicle_control_rep2_7_days


title: 81_N_A_Vehicle_control_rep1_7_days

description:
Library name: EVTHH017692
81_N_A_Vehicle_control_rep1_7_days


title: 80_1E4_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017684
80_1E4_AAV-TFP1_rep4_7_days


title: 79_1E4_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017676
79_1E4_AAV-TFP1_rep3_7_days


title: 78_1E4_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017668
78_1E4_AAV-TFP1_rep2_7_days


title: 76_1E5_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017652
76_1E5_AAV-TFP1_rep4_7_days


title: 75_1E5_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017644
75_1E5_AAV-TFP1_rep3_7_days


title: 73_1E5_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017628
73_1E5_AAV-TFP1_rep1_7_days


title: 77_1E4_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017660
77_1E4_AAV-TFP1_rep1_7_days


title: 74_1E5_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017636
74_1E5_AAV-TFP1_rep2_7_days


title: 72_1E6_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017715
72_1E6_AAV-TFP1_rep4_7_days


title: 70_1E6_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017699
70_1E6_AAV-TFP1_rep2_7_days


title: 71_1E6_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017707
71_1E6_AAV-TFP1_rep3_7_days


title: 69_1E6_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017691
69_1E6_AAV-TFP1_rep1_7_days


title: 68_1E4_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017683
68_1E4_AAV-miMSH3_rep4_7_days


title: AB13249

description:
Library name: Sample1371
MARS_v2


title: AB13499

description:
Library name: Sample1389
MARS_v2


title: AB13511

description:
Library name: Sample1401
MARS_v2


title: AB13247

description:
Library name: Sample1369
MARS_v2


title: AB13241

description:
Library name: Sample1366
MARS_v2


title: AB13255

description:
Library name: Sample1377
MARS_v2


title: AB13240

description:
Library name: Sample1365
MARS_v2


title: 67_1E4_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017675
67_1E4_AAV-miMSH3_rep3_7_days


title: 66_1E4_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017667
66_1E4_AAV-miMSH3_rep2_7_days


title: 65_1E4_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017659
65_1E4_AAV-miMSH3_rep1_7_days


title: 64_1E5_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017651
64_1E5_AAV-miMSH3_rep4_7_days


title: 62_1E5_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017635
62_1E5_AAV-miMSH3_rep2_7_days


title: 63_1E5_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017643
63_1E5_AAV-miMSH3_rep3_7_days


title: 61_1E5_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017627
61_1E5_AAV-miMSH3_rep1_7_days


title: 60_1E6_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017714
60_1E6_AAV-miMSH3_rep4_7_days


title: 59_1E6_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017706
59_1E6_AAV-miMSH3_rep3_7_days


title: 57_1E6_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017690
57_1E6_AAV-miMSH3_rep1_7_days


title: 56_N_A_Vehicle_control_rep4_7_days

description:
Library name: EVTHH017682
56_N_A_Vehicle_control_rep4_7_days

value: Vehicle control-N/A


title: 55_N_A_Vehicle_control_rep3_7_days

description:
Library name: EVTHH017674
55_N_A_Vehicle_control_rep3_7_days


title: 58_1E6_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017698
58_1E6_AAV-miMSH3_rep2_7_days


title: 54_N_A_Vehicle_control_rep2_7_days

description:
Library name: EVTHH017666
54_N_A_Vehicle_control_rep2_7_days


title: 51_1E4_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017642
51_1E4_AAV-TFP1_rep3_7_days


title: 53_N_A_Vehicle_control_rep1_7_days

description:
Library name: EVTHH017658
53_N_A_Vehicle_control_rep1_7_days


title: 49_1E4_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017626
49_1E4_AAV-TFP1_rep1_7_days


title: 50_1E4_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017634
50_1E4_AAV-TFP1_rep2_7_days


title: 46_1E5_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017697
46_1E5_AAV-TFP1_rep2_7_days


title: 45_1E5_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017689
45_1E5_AAV-TFP1_rep1_7_days


title: 48_1E5_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017713
48_1E5_AAV-TFP1_rep4_7_days


title: 47_1E5_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017705
47_1E5_AAV-TFP1_rep3_7_days


title: 43_1E6_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017673
43_1E6_AAV-TFP1_rep3_7_days


title: 44_1E6_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017681
44_1E6_AAV-TFP1_rep4_7_days


title: 39_1E4_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017641
39_1E4_AAV-miMSH3_rep3_7_days


title: 42_1E6_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017665
42_1E6_AAV-TFP1_rep2_7_days


title: 41_1E6_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017657
41_1E6_AAV-TFP1_rep1_7_days


title: 40_1E4_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017649
40_1E4_AAV-miMSH3_rep4_7_days


title: 38_1E4_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017633
38_1E4_AAV-miMSH3_rep2_7_days


title: 37_1E4_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017625
37_1E4_AAV-miMSH3_rep1_7_days


title: 36_1E5_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017712
36_1E5_AAV-miMSH3_rep4_7_days


title: 35_1E5_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017704
35_1E5_AAV-miMSH3_rep3_7_days


title: 34_1E5_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017696
34_1E5_AAV-miMSH3_rep2_7_days


title: 32_1E6_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017680
32_1E6_AAV-miMSH3_rep4_7_days


title: 33_1E5_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017688
33_1E5_AAV-miMSH3_rep1_7_days


title: 30_1E6_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017664
30_1E6_AAV-miMSH3_rep2_7_days


title: 31_1E6_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017672
31_1E6_AAV-miMSH3_rep3_7_days


title: 27_N_A_Vehicle_control_rep3_7_days

description:
Library name: EVTHH017640
27_N_A_Vehicle_control_rep3_7_days


title: 28_N_A_Vehicle_control_rep4_7_days

description:
Library name: EVTHH017648
28_N_A_Vehicle_control_rep4_7_days


title: 26_N_A_Vehicle_control_rep2_7_days

description:
Library name: EVTHH017632
26_N_A_Vehicle_control_rep2_7_days


title: 25_N_A_Vehicle_control_rep1_7_days

description:
Library name: EVTHH017624
25_N_A_Vehicle_control_rep1_7_days


title: 24_1E4_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017711
24_1E4_AAV-TFP1_rep4_7_days


title: 23_1E4_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017703
23_1E4_AAV-TFP1_rep3_7_days


title: 22_1E4_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017695
22_1E4_AAV-TFP1_rep2_7_days


title: 19_1E5_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017671
19_1E5_AAV-TFP1_rep3_7_days


title: 20_1E5_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017679
20_1E5_AAV-TFP1_rep4_7_days


title: 21_1E4_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017687
21_1E4_AAV-TFP1_rep1_7_days


title: 18_1E5_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017663
18_1E5_AAV-TFP1_rep2_7_days


title: 17_1E5_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017655
17_1E5_AAV-TFP1_rep1_7_days


title: 14_1E6_AAV-TFP1_rep2_7_days

description:
Library name: EVTHH017631
14_1E6_AAV-TFP1_rep2_7_days


title: 16_1E6_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017647
16_1E6_AAV-TFP1_rep4_7_days


title: 15_1E6_AAV-TFP1_rep3_7_days

description:
Library name: EVTHH017639
15_1E6_AAV-TFP1_rep3_7_days


title: 13_1E6_AAV-TFP1_rep1_7_days

description:
Library name: EVTHH017623
13_1E6_AAV-TFP1_rep1_7_days


title: 12_1E4_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017710
12_1E4_AAV-miMSH3_rep4_7_days


title: 11_1E4_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017702
11_1E4_AAV-miMSH3_rep3_7_days


title: 10_1E4_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017694
10_1E4_AAV-miMSH3_rep2_7_days


title: 07_1E5_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017670
07_1E5_AAV-miMSH3_rep3_7_days


title: 06_1E5_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017662
06_1E5_AAV-miMSH3_rep2_7_days


title: 04_1E6_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017646
04_1E6_AAV-miMSH3_rep4_7_days


title: 03_1E6_AAV-miMSH3_rep3_7_days

description:
Library name: EVTHH017638
03_1E6_AAV-miMSH3_rep3_7_days


title: 02_1E6_AAV-miMSH3_rep2_7_days

description:
Library name: EVTHH017630
02_1E6_AAV-miMSH3_rep2_7_days


title: 05_1E5_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017654
05_1E5_AAV-miMSH3_rep1_7_days


title: RBMS1-Input-1

city: Harbin

first: Jing

last: Tang

state: Heilongjiang

address: No. 157 Baojian Road, Nangang District

institute: Harbin medical university

description:
Library name: RBMS1, INPUT
2_INPUT

data_processing:
Peak calling and target gene identification were performed using MACS2 software.
RBMS1‑binding mRNAs were defined as peaks with signal value ≥ 4 and −log10 (q-value) ≥ 2. Two biological replicates were included for both RIP and Input groups. Overlapping peaks from the two replicates yielded a total of 3889 candidate genes. Differential expression analysis between RIP and Input samples was performed using the DESeq2 R package. Genes with |log2(fold change)| > 1 and adjusted p-value < 0.05 were defined as significantly enriched.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RIP‑seq was performed using anti‑RBMS1 antibody, with IgG serving as the negative control. After immunoprecipitation, bound RNA was extracted, purified, fragmented, and reverse‑ transcribed to construct cDNA libraries.
RIP-seq was performed by Annoroad Gene Technology Co., Ltd. (Beijing, China) on an Illumina platform.

value: ovarian cancer


title: RBMS1-RIP-1

description:
Library name: RBMS1, RIP
1_RIP

library_source: other

molecule: other


title: Non_EP_4

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample 21
Non-eosinophilic CRSwNP nasal polyp tissue sample

data_processing:
Raw sequencing reads were subjected to quality control using fastp to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the human reference genome GRCh38 using HISAT2.
Gene expression quantification was performed using featureCounts to generate raw read count matrices.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) file containing gene-level expression data, including raw read counts generated by featureCounts and FPKM-normalized expression values for each sample.

source_name: nasal polyp tissue

extract_protocol:
Total RNA was extracted from frozen nasal tissue samples. Nasal polyp tissues from patients with eosinophilic CRSwNP (eCRSwNP) and non-eosinophilic CRSwNP (neCRSwNP), and inferior turbinate mucosa tissues from healthy controls were immediately rinsed with sterile saline, stored in RNase-free tubes, rapidly frozen in liquid nitrogen, and stored at −80°C until RNA extraction. The concentration and purity of total RNA were assessed using a NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific, USA). RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and qualified RNA samples were used for subsequent library construction.
RNA sequencing libraries were constructed using total RNA. Polyadenylated mRNA was enriched from total RNA using Oligo(dT) magnetic beads. The enriched mRNA was fragmented into approximately 300 bp fragments using ion fragmentation. First-strand and second-strand cDNA were synthesized, followed by cDNA amplification and fragment size selection. Sequencing libraries with approximately 450 bp insert sizes were obtained after library preparation and quality assessment. Indexed libraries were pooled and sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp sequencing.

value: nasal polyp tissue

value: neCRSwNP


title: Non_EP_3

description:
Library name: Sample 20
Non-eosinophilic CRSwNP nasal polyp tissue sample


title: Non_EP_5

description:
Library name: Sample 22
Non-eosinophilic CRSwNP nasal polyp tissue sample


title: Non_EP_2

description:
Library name: Sample 19
Non-eosinophilic CRSwNP nasal polyp tissue sample


title: Non_EP_1

description:
Library name: Sample 18
Non-eosinophilic CRSwNP nasal polyp tissue sample


title: EosNP_9

description:
Library name: Sample 17
Eosinophilic CRSwNP nasal polyp tissue sample

value: eCRSwNP


title: 01_1E6_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017622
01_1E6_AAV-miMSH3_rep1_7_days


title: EosNP_8

description:
Library name: Sample 16
Eosinophilic CRSwNP nasal polyp tissue sample


title: EosNP_7

description:
Library name: Sample 15
Eosinophilic CRSwNP nasal polyp tissue sample


title: EosNP_6

description:
Library name: Sample 14
Eosinophilic CRSwNP nasal polyp tissue sample


title: EosNP_4

description:
Library name: Sample 12
Eosinophilic CRSwNP nasal polyp tissue sample


title: EosNP_3

description:
Library name: Sample 11
Eosinophilic CRSwNP nasal polyp tissue sample


title: EosNP_2

description:
Library name: Sample 10
Eosinophilic CRSwNP nasal polyp tissue sample


title: Control7

description:
Library name: Sample 7
Healthy control nasal mucosa sample

source_name: inferior turbinate mucosa tissue

value: inferior turbinate mucosa tissue

value: Control


title: Control8

description:
Library name: Sample 8
Healthy control nasal mucosa sample


title: Control3

description:
Library name: Sample 3
Healthy control nasal mucosa sample


title: Control6

description:
Library name: Sample 6
Healthy control nasal mucosa sample


title: Control4

description:
Library name: Sample 4
Healthy control nasal mucosa sample


title: Control1

description:
Library name: Sample 1
Healthy control nasal mucosa sample


title: Feature Barcode library of CD34 positive rxn 4 replicate 1

city: La Jolla

first: Bryan

last: Briney

state: CA

address: 10550 N Torrey Pines Rd

department: Immunology and Microbiology

institute: Scripps Research

description:
Library name: CD34_1_220524_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)

data_processing:
FASTQ files were generated from raw base call files using CellRanger, and downstream analyses were performed with scab (Hurtado et al. 2022). Matrices of VDJ contigs and counts were assembled by alignment to VDJ and transcriptome reference genomes, outputting full-length per cell VDJ sequences as FASTA files and expression profiles (cells x genes) as an .h5 file, differentiating individual cells by barcode. Antibody sequences were annotated using abstar (Briney and Burton 2018) and integrated with gene expression and cellhash data using scab. Donors were demultiplexed by cellhash using scab. Because samples had different read depths, cell hash thresholds were incorrectly high for some of the samples with fewer reads per cell. Reads were thus normalized to ensure equal representation from each donor. To further refine the expression matrix, cells with fewer than 200 and greater than 6000 genes were removed. Genes which appeared in fewer than 50 cells were also removed. Normalization, log plus one transformation, and scaling were performed using scab and scanpy. Scab’s dimensionality reduction tool performed principle component analysis, neighborhood graphing, and cell clustering according to the Leiden algorithm and utilized UMAP for embedding (Traag, Waltman, and van Eck 2019; Becht et al. 2018; McInnes, Healy, and Melville 2018). Doublets were identified using Scrublet (Wolock, Lopez, and Klein 2019) and all doublets, including entire clusters containing primarily doublets, were removed. Cells were then re-clustered without doublets and identified as lymphoid, myeloid, erythroid, plasma cells, T cells, or B cells according to gene expression profiles. B cells were then separated out, clustered again for granularity, and subset into developmental phases also according to gene expression profiles.
Assembly: gene expression assembly - refdata-gex-GRCh38-2020-A, for V(D)J assembly - refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, all_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: Bone marrow

extract_protocol:
Bone marrow samples from four healthy adult donors were obtained through our commercial clinical partner (ALLCELLS). Lymphocytes were isolated by density gradient centrifugation using Lymphoprep (StemCell Technologies). To ensure representation of early progenitors and developing B cell populations, donor samples were individually enriched for B cells and hematopoietic stem cells by EasySep Human B Cell Enrichment and Human CD34+ Selection Kits (StemCell Technologies).
Single-cell RNA sequencing (scRNAseq) was performed on over 3.8x105 cells from bone marrow and enriched samples with the 10x Genomics 5’ Single Cell Immune Profiling Kit (v2). Briefly, donor samples were individually labelled with Totalseq Anti-Human Hashtags (Biolegend) and pooled prior to overloading the 10x Genomic reaction, targeting 4-6x104 cells per run (Stoeckius et al. 2018). Single-cell emulsion generation, barcoding, V(D)J enrichment, and sequencing library construction were carried out according to theChromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) protocol (CG000330 Rev A). Final libraries were sequenced on a NovaSeq 6000 using a 26-10-10-90 read configuration, with minimum target sequencing depths of 5,000 reads per cell for Cell Surface Protein libraries, 10,000 reads per cell for V(D)J libraries, and 30,000 reads per cell for Gene expression libraries.

value: Bone marrow

value: Lymphocyte

tag: library type

value: HTO


title: Feature Barcode library of CD34 positive rxn 2 replicate 2

description:
Library name: CD34_2.2_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of CD34 positive rxn 3 replicate 2

description:
Library name: CD34_2.3_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of CD34 positive rxn 1 replicate 2

description:
Library name: CD34_2.1_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of CD34 positive  rxn 2 replicate 1

description:
Library name: CD34_1.2_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of B cell  rxn 4 replicate 2

description:
Library name: Bcell2_220524_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)

value: B-cell


title: Feature Barcode library of B cell  rxn 4 replicate 1

description:
Library name: Bcell1_220524_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of B cell  rxn 3 replicate 2

description:
Library name: Bcell2.3_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of B cell  rxn 1 replicate 2

description:
Library name: Bcell2.1_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of B cell  rxn 3 replicate 1

description:
Library name: Bcell1.3_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of Whole Bone Marrow  rxn 3 replicate 2

description:
Library name: BM2_220524_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode of Whole Bone Marrow  rxn 2 replicate 2

description:
Library name: BM2.2_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of Whole Bone Marrow  rxn 3 replicate 1

description:
Library name: BM1_220524_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of Whole Bone Marrow  rxn 2 replicate 1

description:
Library name: BM2.1_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Feature Barcode library of Whole Bone Marrow  rxn 1 replicate 2

description:
Library name: BM1.2_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: V(D)J library of CD34 positive rxn 4 replicate 2

description:
Library name: CD34_2_220524_BCR
10x Genomic HT, V(D)J

value: mRNA


title: 2497441_D4

city: Memphis

first: Mitchell

last: Weiss

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

data_processing:
STAR software was utilized for read alignment to thereference genome. Gene level quantification is determined by RSEM.
Read counts per gene are analyzed using R software using the following methods: Only confidently annotated (level 1 (verified) and 2 (manually annotated) gene annotation), protein-coding genes are considered in the standard differential expression analysis. Low count genes were removed from analysis using a raw count cutoff of 10 reads (before Oct., 2022) or a library.size adjusted cutoff ( after Oct., 2022) . Normalization factors were generated using the TMM method. Counts were normalized using voom. Voom normalized counts were analyzed using the lmFit and eBayes functions of the limma software package.
Assembly: mm10
Supplementary files format and content: gene expression and differential gene tables

organism: Mus musculus

source_name: Thymus

growth_protocol: All mouse studies were approved by the Institutional Animal Care and Use Committee (IACUC, approval number 612) at St. Jude Children’s Research Hospital and maintained under specific pathogen-free conditions.

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher, 15596-026)
library construction using the KAPA RNA HyperPrep kit (Roche, KK8540) according to the manufacturer’s manual.

treatment_protocol: 10 μg/g body weight of Tamoxifen dissolved in olive oil was administered by intraperitoneal injection. Mice were harvested for sorting at 7 days after tamoxifen.

value: Thymus

value: tdt--Treg


title: V(D)J library of CD34 positive rxn 3 replicate 2

description:
Library name: CD34_2.3_BCR
10x Genomic HT, V(D)J


title: V(D)J library of CD34 positive rxn 2 replicate 2

description:
Library name: CD34_2.2_BCR
10x Genomic HT, V(D)J


title: V(D)J library of CD34 positive rxn 1 replicate 2

description:
Library name: CD34_2.1_BCR
10x Genomic HT, V(D)J


title: 2497440_D3

value: tdt+Tconv


title: Control5

description:
Library name: Sample 5
Healthy control nasal mucosa sample


title: Feature Barcode library of CD34 positive rxn 4 replicate 2

description:
Library name: CD34_2_220524_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: 2497439_D2


title: 2497438_D1


title: V(D)J library of CD34 positive rxn 3 replicate 1

description:
Library name: CD34_1.3_BCR
10x Genomic HT, V(D)J


title: V(D)J library of CD34 positive  rxn 2 replicate 1

description:
Library name: CD34_1.2_BCR
10x Genomic HT, V(D)J


title: V(D)J library of CD34 positive  rxn 1 replicate 1

description:
Library name: CD34_1.1_BCR
10x Genomic HT, V(D)J


title: 2497437_B4


title: 2497436_B3


title: V(D)J library of B cell  rxn 4 replicate 2

description:
Library name: Bcell2_220524_BCR
10x Genomic HT, V(D)J


title: 2497435_B2


title: V(D)J library of B cell  rxn 4 replicate 1

description:
Library name: Bcell1_220524_BCR
10x Genomic HT, V(D)J


title: V(D)J library of B cell  rxn 3 replicate 2

description:
Library name: Bcell2.3_BCR
10x Genomic HT, V(D)J


title: V(D)J library of B cell  rxn 2 replicate 2

description:
Library name: Bcell2.2_BCR
10x Genomic HT, V(D)J


title: V(D)J library of B cell  rxn 1 replicate 2

description:
Library name: Bcell2.1_BCR
10x Genomic HT, V(D)J


title: 2497431_A2


title: 2497430_A1


title: V(D)J library of B cell  rxn 3 replicate 1

description:
Library name: Bcell1.3_BCR
10x Genomic HT, V(D)J


title: 52_1E4_AAV-TFP1_rep4_7_days

description:
Library name: EVTHH017650
52_1E4_AAV-TFP1_rep4_7_days

value: HD iPSC Neurons

value: HD Patient Derived iPSC 49 CAG

value: iPSC Neurons

value: Het


title: V(D)J library of B cell  rxn 2 replicate 1

description:
Library name: Bcell1.2_BCR
10x Genomic HT, V(D)J


title: AB4934

description:
Library name: Sample733
MARS

value: BM

value: PC


title: 29_1E6_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017656
29_1E6_AAV-miMSH3_rep1_7_days


title: V(D)J library of B cell  rxn 1 replicate 1

description:
Library name: Bcell1.1_BCR
10x Genomic HT, V(D)J


title: AB4933

description:
Library name: Sample732
MARS


title: 08_1E5_AAV-miMSH3_rep4_7_days

description:
Library name: EVTHH017678
08_1E5_AAV-miMSH3_rep4_7_days


title: 09_1E4_AAV-miMSH3_rep1_7_days

description:
Library name: EVTHH017686
09_1E4_AAV-miMSH3_rep1_7_days


title: AB4932

description:
Library name: Sample731
MARS


title: V(D)J library of Whole Bone Marrow  rxn 3 replicate 1

description:
Library name: BM1_220524_BCR
10x Genomic HT, V(D)J


title: V(D)J library of Whole Bone Marrow  rxn 3 replicate 2

description:
Library name: BM2_220524_BCR
10x Genomic HT, V(D)J


title: 2497433_A4


title: 2497434_B1


title: RBMS1-Input-2

description:
Library name: RBMS1-2,INPUT
4_INPUT

value: ovarian cancer


title: 2497432_A3


title: RBMS1-RIP-2

description:
Library name: RBMS1-2,RIP
3_RIP


title: AB4931

description:
Library name: Sample730
MARS


title: AB4930

description:
Library name: Sample729
MARS


title: V(D)J library of Whole Bone Marrow  rxn 2 replicate 1

description:
Library name: BM2.1_BCR
10x Genomic HT, V(D)J


title: V(D)J library of Whole Bone Marrow  rxn 2 replicate 2

description:
Library name: BM2.2_BCR
10x Genomic HT, V(D)J


title: V(D)J library of Whole Bone Marrow  rxn 1 replicate 1

description:
Library name: BM1.1_BCR
10x Genomic HT, V(D)J


title: EosNP_5

description:
Library name: Sample 13
Eosinophilic CRSwNP nasal polyp tissue sample

value: nasal polyp tissue

value: eCRSwNP


title: AB4746

description:
Library name: Sample725
MARS


title: Gene expression library of CD34 positive rxn 4 replicate 2

description:
Library name: CD34_2_220524_GEX
10x Genomic HT, Gene Expression

value: Bone marrow


title: Gene expression library of CD34 positive rxn 4 replicate 1

description:
Library name: CD34_1_220524_GEX
10x Genomic HT, Gene Expression

value: Lymphocyte


title: EosNP_1

description:
Library name: Sample 9
Eosinophilic CRSwNP nasal polyp tissue sample


title: Control2

description:
Library name: Sample 2
Healthy control nasal mucosa sample

value: inferior turbinate mucosa tissue

value: Control


title: AB4745

description:
Library name: Sample724
MARS


title: Gene expression library of CD34 positive rxn 3 replicate 2

description:
Library name: CD34_2.3_GEX
10x Genomic HT, Gene Expression

value: mRNA


title: AB4748

description:
Library name: Sample727
MARS


title: AB4929

description:
Library name: Sample728
MARS


title: V(D)J library of Whole Bone Marrow  rxn 1 replicate 2

description:
Library name: BM1.2_BCR
10x Genomic HT, V(D)J


title: Gene expression library of CD34 positive rxn 2 replicate 2

description:
Library name: CD34_2.2_GEX
10x Genomic HT, Gene Expression


title: AB4741

description:
Library name: Sample721
MARS


title: Gene expression library of CD34 positive rxn 1 replicate 2

description:
Library name: CD34_2.1_GEX
10x Genomic HT, Gene Expression


title: AB4740

description:
Library name: Sample720
MARS


title: Feature Barcode library of CD34 positive rxn 3 replicate 1

description:
Library name: CD34_1.3_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)

value: HTO


title: Gene expression library of CD34 positive  rxn 2 replicate 1

description:
Library name: CD34_1.2_GEX
10x Genomic HT, Gene Expression


title: Gene expression library of CD34 positive  rxn 1 replicate 1

description:
Library name: CD34_1.1_GEX
10x Genomic HT, Gene Expression


title: AB4737

description:
Library name: Sample717
MARS


title: AB4735

description:
Library name: Sample715
MARS


title: Gene expression library of B cell  rxn 2 replicate 2

description:
Library name: Bcell2.2_GEX
10x Genomic HT, Gene Expression

value: B-cell


title: Gene expression library of CD34 positive rxn 3 replicate 1

description:
Library name: CD34_1.3_GEX
10x Genomic HT, Gene Expression


title: AB4744

description:
Library name: Sample723
MARS


title: AB4747

description:
Library name: Sample726
MARS


title: AB4743

description:
Library name: Sample722
MARS


title: AB4738

description:
Library name: Sample718
MARS


title: AB4733

description:
Library name: Sample714
MARS


title: AB4739

description:
Library name: Sample719
MARS


title: Gene expression library of B cell  rxn 4 replicate 2

description:
Library name: Bcell2_220524_GEX
10x Genomic HT, Gene Expression


title: Gene expression library of B cell  rxn 4 replicate 1

description:
Library name: Bcell1_220524_GEX
10x Genomic HT, Gene Expression


title: Feature Barcode library of CD34 positive  rxn 1 replicate 1

description:
Library name: CD34_1.1_FBC
10x Genomic HT, Hashtag-derived oligonucleotide(HTO)


title: Gene expression library of B cell  rxn 3 replicate 1

description:
Library name: Bcell1.3_GEX
10x Genomic HT, Gene Expression


title: AB4732

description:
Library name: Sample713
MARS


title: AB4731

description:
Library name: Sample712
MARS


title: Gene expression library of B cell  rxn 2 replicate 1

description:
Library name: Bcell1.2_GEX
10x Genomic HT, Gene Expression


title: AB4730

description:
Library name: Sample711
MARS


title: Gene expression library of B cell  rxn 1 replicate 1

description:
Library name: Bcell1.1_GEX
10x Genomic HT, Gene Expression


title: Gene expression library of Whole Bone Marrow  rxn 3 replicate 2

description:
Library name: BM2_220524_GEX
10x Genomic HT, Gene Expression


title: AB4727

description:
Library name: Sample708
MARS


title: Gene expression library of Whole Bone Marrow  rxn 2 replicate 2

description:
Library name: BM2.2_GEX
10x Genomic HT, Gene Expression


title: AB4724

description:
Library name: Sample707
MARS


title: AB4657

description:
Library name: Sample706
MARS


title: Gene expression library of Whole Bone Marrow  rxn 1 replicate 2

description:
Library name: BM1.2_GEX
10x Genomic HT, Gene Expression


title: AB4655

description:
Library name: Sample704
MARS


title: Gene expression library of Whole Bone Marrow  rxn 1 replicate 1

description:
Library name: BM1.1_GEX
10x Genomic HT, Gene Expression


title: SAF-YML0127_P

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description:
Library name: sample47
processed Cell Ranger single-cell gene expression output archive

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files generated from the 10x Genomics platform were aligned to the human GRCh38 reference genome (reference version 6.1.2), and gene expression matrices were quantified with Cell Ranger v4.3.0 using default parameters.
For each sample, Cell Ranger output files containing filtered gene expression matrices and associated barcode and feature annotations were compressed as sample-specific .tar.gz archives. The per-sample processed outputs were also collected into a combined .tar.gz archive for convenient GEO submission.
Cell Ranger count matrices were imported into Seurat v4.0 for downstream quality control and analysis. Potential doublets were detected with Scrublet v0.2.3; low-quality cells and genes were filtered before normalization and integration.
For downstream analysis, counts were normalized and log-transformed, highly variable genes were selected, and batch effects across transplant samples were corrected using a mutual-nearest-neighbor/FastMNN-based workflow. Clustering was performed with graph-based methods and visualized by UMAP.
Major immune and blood cell populations and finer cell states were annotated by comparing cluster-specific differentially expressed genes with canonical markers and the relevant literature.
Assembly: Homo sapiens GRCh38 (10x Genomics/Cell Ranger human reference, version 6.1.2)
Supplementary files format and content: Sample-specific processed data files are .tar.gz archives of Cell Ranger outputs. Each archive contains analysis-ready 10x Genomics single-cell gene expression matrix files, including filtered matrix, barcode and feature/gene annotation files, and associated Cell Ranger summary or metadata files where available.
Supplementary files format and content: A combined .tar.gz archive contains all per-sample Cell Ranger processed outputs for kidney graft tissue and peripheral blood single-cell RNA-seq samples.

source_name: peripheral blood

extract_protocol:
Fresh peripheral blood and kidney graft tissue samples were processed immediately after collection to generate single-cell suspensions for single-cell RNA sequencing. Peripheral blood mononuclear cells were isolated by density-gradient centrifugation, followed by red blood cell lysis with ammonium chloride-based lysis buffer on ice for 5-7 min. Cells were washed twice with pre-chilled PBS and resuspended in PBS containing 0.04% BSA. Kidney tissue was minced on ice, enzymatically dissociated according to the 10x Genomics tissue dissociation workflow, mechanically triturated, sequentially filtered through 70-um and 40-um strainers, centrifuged and resuspended in PBS containing 0.04% BSA. Cell viability was assessed by trypan blue exclusion, and debris removal was performed when necessary before single-cell capture.
Single-cell suspensions were loaded onto 10x Genomics Chromium microfluidic chips using 3' v3 chemistry and processed with the Chromium Controller to generate barcoded gel-bead emulsions. cDNA synthesis and gene expression library construction were performed with the Chromium Single Cell 3' v3 reagent kit according to the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

value: peripheral blood

tag: subject status

value: SAF

tag: cohort

value: Validation

value: M

tag: age（years）

tag: donor type

value: Deceased donor

tag: post-transplant time_(years)

tag: maintenance immunosuppressive_regimen

value: Tacrolimus + mycophenolate mofetil + corticosteroids

tag: clinical sample_id


title: SAF-ZP0127_P

description:
Library name: sample48
processed Cell Ranger single-cell gene expression output archive

tag: tissue


title: AB4651

description:
Library name: Sample702
MARS

value: BM

tag: gate

value: PC

tag: batch


title: SAF-XQ_P

description:
Library name: sample46
processed Cell Ranger single-cell gene expression output archive

value: F


title: AB4650

description:
Library name: Sample701
MARS


title: SAF-WLH_P

description:
Library name: sample45
processed Cell Ranger single-cell gene expression output archive

value: Living donor


title: SAF07_P

description:
Library name: sample44
processed Cell Ranger single-cell gene expression output archive

value: Discovery


title: AB4624

description:
Library name: Sample699
MARS


title: SAF06_P

description:
Library name: sample43
processed Cell Ranger single-cell gene expression output archive


title: AB4623

description:
Library name: Sample698
MARS


title: AB4621

description:
Library name: Sample697
MARS


title: AB4620

description:
Library name: Sample696
MARS


title: SAF04_P

description:
Library name: sample41
processed Cell Ranger single-cell gene expression output archive


title: SAF05_P

description:
Library name: sample42
processed Cell Ranger single-cell gene expression output archive


title: SAF03_P

description:
Library name: sample40
processed Cell Ranger single-cell gene expression output archive


title: SAF01_P

description:
Library name: sample39
processed Cell Ranger single-cell gene expression output archive


title: AB4619

description:
Library name: Sample695
MARS


title: HC-N4TQL_P

description:
Library name: sample38
processed Cell Ranger single-cell gene expression output archive

value: HC

value: healthy control


title: AB4618

description:
Library name: Sample694
MARS


title: AB4617

description:
Library name: Sample693
MARS


title: HC-N3FY_P

description:
Library name: sample37
processed Cell Ranger single-cell gene expression output archive


title: HC-N2DXH_P

description:
Library name: sample36
processed Cell Ranger single-cell gene expression output archive


title: AB4728

description:
Library name: Sample709
MARS


title: Gene expression library of Whole Bone Marrow  rxn 3 replicate 1

description:
Library name: BM1_220524_GEX
10x Genomic HT, Gene Expression

value: Bone marrow

tag: cell type

value: Lymphocyte


title: AB4614

description:
Library name: Sample691
MARS


title: AB4613

description:
Library name: Sample690
MARS


title: HC-N1LLM_P

description:
Library name: sample35
processed Cell Ranger single-cell gene expression output archive


title: Gene expression library of Whole Bone Marrow  rxn 2 replicate 1

description:
Library name: BM2.1_GEX
10x Genomic HT, Gene Expression

value: mRNA


title: HC05_P

description:
Library name: sample34
processed Cell Ranger single-cell gene expression output archive


title: AB4656

description:
Library name: Sample705
MARS


title: AB4612

description:
Library name: Sample689
MARS


title: AB4611

description:
Library name: Sample688
MARS


title: HC04_P

description:
Library name: sample33
processed Cell Ranger single-cell gene expression output archive


title: HC03_P

description:
Library name: sample32
processed Cell Ranger single-cell gene expression output archive


title: AB4653

description:
Library name: Sample703
MARS


title: HC02_P

description:
Library name: sample31
processed Cell Ranger single-cell gene expression output archive


title: HC01_P

description:
Library name: sample30
processed Cell Ranger single-cell gene expression output archive


title: AB4540

description:
Library name: Sample687
MARS


title: AB4538

description:
Library name: Sample686
MARS


title: AB4625

description:
Library name: Sample700
MARS


title: AB4537

description:
Library name: Sample685
MARS


title: CAR38_P

description:
Library name: sample29
processed Cell Ranger single-cell gene expression output archive

value: CAMR


title: AB4536

description:
Library name: Sample684
MARS


title: CAR37_P

description:
Library name: sample28
processed Cell Ranger single-cell gene expression output archive

value: peripheral blood


title: AB4535

description:
Library name: Sample683
MARS


title: CAR35_P

description:
Library name: sample26
processed Cell Ranger single-cell gene expression output archive


title: AB4534

description:
Library name: Sample682
MARS


title: AB4533

description:
Library name: Sample681
MARS


title: CAR36_P

description:
Library name: sample27
processed Cell Ranger single-cell gene expression output archive


title: CAR34_P

description:
Library name: sample25
processed Cell Ranger single-cell gene expression output archive


title: AB4532

description:
Library name: Sample680
MARS


title: CAR33_P

description:
Library name: sample24
processed Cell Ranger single-cell gene expression output archive


title: AB4531

description:
Library name: Sample679
MARS


title: CAR30_P

description:
Library name: sample23
processed Cell Ranger single-cell gene expression output archive


title: AB4530

description:
Library name: Sample678
MARS


title: CAR26_P

description:
Library name: sample22
processed Cell Ranger single-cell gene expression output archive


title: AB4480

description:
Library name: Sample677
MARS


title: CAR21_P

description:
Library name: sample21
processed Cell Ranger single-cell gene expression output archive

value: Tacrolimus + mizoribine + corticosteroids


title: AB4478

description:
Library name: Sample676
MARS


title: CAR19_P

description:
Library name: sample20
processed Cell Ranger single-cell gene expression output archive


title: AB4477

description:
Library name: Sample675
MARS


title: AB4476

description:
Library name: Sample674
MARS


title: CAR18_P

description:
Library name: sample19
processed Cell Ranger single-cell gene expression output archive


title: CAR16_P

description:
Library name: sample18
processed Cell Ranger single-cell gene expression output archive