title: PHH - S1295T_MEDIUM_0_TP-8_REP-3 [3d01_8hrDonor1TNF0]

description:
3d01_8hrDonor1TNF0
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_333_TP-8_REP-2 [2a05_8hrDonor1DEM333]

status: Public on Feb 18 2021

type: SRA

city: Leiden

first: Bob

last: van de Water

address: Einsteinweg 55

department: Division of Drug Discovery and Safety

country: Netherlands

institute: Leiden Academic Centre for Drug Research (LACDR), Leiden University

description:
2a05_8hrDonor1DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt

library_source: transcriptomic

data_processing:
Library strategy: TempO-seq
Alignment of reads was done using the TempO-seqR package done by BioSpyder Technologies.
Samples were excluded for further analysis if library size was lower than 100.000 counts.
Raw counts were normalized using the DESeq2 R package (Love et al. 2014).
Normalized counts were log2 transformed.
Genome_build: BioSpyder manifest "Human Tox Panel TempO-Seq Probe Manifest 041416".
Supplementary_files_format_and_content: count.txt: Matrix table with raw counts for every probe and every sample.
Supplementary_files_format_and_content: count_log2LibSizenorm.txt: Matrix table with log2 normalized counts for every probe and every sample.

molecule: total RNA

organism: Homo sapiens

source_name: PHH - S1295T

extract_protocol:
Cells were washed with PBS and lysed with 1x BNN lysis buffer (provided by BioSpyder) followed by incubation of 15 min at RT. Thereafter plate with cell lysates was sealed and stored at -80 degrees until shipment. Cell lysates were send to BioSpyder for TempO-seq targeted transcriptome analysis.
mRNA in the lysates was hybridized with detector oligo mix, and amplified using barcoded primer pairs to add a unique tag for each of the samples. The detector oligo mix targets a set of genes which were selected based on the S1500+ gene list of NIEHS (Mav et al. 2018). This list contains 2736 genes that provide maximal toxicogenomic information on chemical perturbations that reflect general cellular responses. We supplemented this list with another 245 genes that are involved in hiPSC to hepatocyte differentiation, cellular stress pathways activated in PHH and were missing in the S1500 list. Sample amplicons were pooled and purified. The libraries were sequenced using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

tag: cell type

value: Primary human hepatocytes

tag: compound

value: Diethyl-maleate (DEM)

tag: concentration

tag: time point

value: 8 hr

tag: replicate


title: PHH - S1295T_DEM_100_TP-8_REP-2 [2a04_8hrDonor1DEM100]

description:
2a04_8hrDonor1DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_333_TP-8_REP-1 [1a05_8hrDonor1DEM333]

description:
1a05_8hrDonor1DEM333
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_100_TP-8_REP-3 [3a04_8hrDonor1DEM100]

description:
3a04_8hrDonor1DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_100_TP-8_REP-1 [1a04_8hrDonor1DEM100]

description:
1a04_8hrDonor1DEM100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_10_TP-8_REP-3 [3a03_8hrDonor1DEM10]

description:
3a03_8hrDonor1DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: PHH - S1295T_DEM_10_TP-8_REP-2 [2a03_8hrDonor1DEM10]

description:
2a03_8hrDonor1DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_10_TP-8_REP-1 [1a03_8hrDonor1DEM10]

description:
1a03_8hrDonor1DEM10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_1_TP-8_REP-2 [2a02_8hrDonor1DEM1]

description:
2a02_8hrDonor1DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: PHH - S1295T_DEM_1_TP-8_REP-3 [3a02_8hrDonor1DEM1]

description:
3a02_8hrDonor1DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_100_TP-8_REP-3 [3c07_8hrDonor1CPT100]

description:
3c07_8hrDonor1CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: PHH - S1295T_DEM_1_TP-8_REP-1 [1a02_8hrDonor1DEM1]

description:
1a02_8hrDonor1DEM1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_100_TP-8_REP-2 [2c07_8hrDonor1CPT100]

description:
2c07_8hrDonor1CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_100_TP-8_REP-1 [1c07_8hrDonor1CPT100]

description:
1c07_8hrDonor1CPT100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_33_TP-8_REP-3 [3c06_8hrDonor1CPT33]

description:
3c06_8hrDonor1CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: PHH - S1295T_CPT_33_TP-8_REP-2 [2c06_8hrDonor1CPT33]

description:
2c06_8hrDonor1CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_DEM_1000_TP-8_REP-1 [1a06_8hrDonor1DEM1000]

description:
1a06_8hrDonor1DEM1000
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_33_TP-8_REP-1 [1c06_8hrDonor1CPT33]

description:
1c06_8hrDonor1CPT33
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_3.3_TP-8_REP-3 [3c04_8hrDonor1CPT3.3]

description:
3c04_8hrDonor1CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_10_TP-8_REP-3 [3c05_8hrDonor1CPT10]

description:
3c05_8hrDonor1CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_10_TP-8_REP-1 [1c05_8hrDonor1CPT10]

description:
1c05_8hrDonor1CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_3.3_TP-8_REP-2 [2c04_8hrDonor1CPT3.3]

description:
2c04_8hrDonor1CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_10_TP-8_REP-2 [2c05_8hrDonor1CPT10]

description:
2c05_8hrDonor1CPT10
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_1_TP-8_REP-2 [2c03_8hrDonor1CPT1]

description:
2c03_8hrDonor1CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_0.01_TP-8_REP-3 [3c02_8hrDonor1CPT0.01]

description:
3c02_8hrDonor1CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_1_TP-8_REP-1 [1c03_8hrDonor1CPT1]

description:
1c03_8hrDonor1CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_0.01_TP-8_REP-2 [2c02_8hrDonor1CPT0.01]

description:
2c02_8hrDonor1CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_1_TP-8_REP-3 [3c03_8hrDonor1CPT1]

description:
3c03_8hrDonor1CPT1
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_0.01_TP-8_REP-1 [1c02_8hrDonor1CPT0.01]

description:
1c02_8hrDonor1CPT0.01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_10_TP-8_REP-B [Bas317]

description:
Bas317
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: Immature hepatocyte - Day 12

value: Immature hepatocytes

value: Tunicamycin (TUN)


title: Immature hepatocyte - Day 12_TUN_100_TP-8_REP-A [Bas324]

description:
Bas324
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_10_TP-8_REP-A [Bas316]

description:
Bas316
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_10_TP-8_REP-C [Bas318]

description:
Bas318
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_1_TP-8_REP-C [Bas310]

description:
Bas310
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_1_TP-8_REP-B [Bas309]

description:
Bas309
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.01_TP-8_REP-C [Bas294]

description:
Bas294
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.1_TP-8_REP-C [Bas302]

description:
Bas302
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.1_TP-8_REP-B [Bas301]

description:
Bas301
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_100_TP-8_REP-B [Bas325]

description:
Bas325
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.1_TP-8_REP-A [Bas300]

description:
Bas300
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_1_TP-8_REP-A [Bas308]

description:
Bas308
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.01_TP-8_REP-A [Bas292]

description:
Bas292
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.01_TP-8_REP-B [Bas293]

description:
Bas293
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: PHH - S1295T_CPT_3.3_TP-8_REP-1 [1c04_8hrDonor1CPT3.3]

description:
1c04_8hrDonor1CPT3.3
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_50_TP-8_REP-C [Bas372]

description:
Bas372
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: Immature hepatocyte - Day 12_TNF_50_TP-8_REP-A [Bas370]

description:
Bas370
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_10_TP-8_REP-B [Bas364]

description:
Bas364
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL


title: Immature hepatocyte - Day 12_TNF_10_TP-8_REP-C [Bas365]

description:
Bas365
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_10_TP-8_REP-A [Bas363]

description:
Bas363
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.001_TP-8_REP-B [Bas285]

description:
Bas285
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_7.5_TP-8_REP-C [Bas358]

description:
Bas358
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: Immature hepatocyte - Day 12_TUN_100_TP-8_REP-C [Bas326]

description:
Bas326
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_7.5_TP-8_REP-B [Bas357]

description:
Bas357
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_5_TP-8_REP-B [Bas349]

description:
Bas349
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: Immature hepatocyte - Day 12_TNF_5_TP-8_REP-C [Bas350]

description:
Bas350
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_5_TP-8_REP-A [Bas348]

description:
Bas348
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_2.5_TP-8_REP-B [Bas341]

description:
Bas341
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL


title: Immature hepatocyte - Day 12_TNF_2.5_TP-8_REP-C [Bas342]

description:
Bas342
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_2.5_TP-8_REP-A [Bas340]

description:
Bas340
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_1_TP-8_REP-B [Bas333]

description:
Bas333
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: Immature hepatocyte - Day 12_TNF_1_TP-8_REP-C [Bas334]

description:
Bas334
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_MEDIUM_0_TP-8_REP-C [Bas323]

description:
Bas323
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: Immature hepatocyte - Day 12_TNF_1_TP-8_REP-A [Bas332]

description:
Bas332
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_MEDIUM_0_TP-8_REP-C [Bas369]

description:
Bas369
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_MEDIUM_0_TP-8_REP-B [Bas362]

description:
Bas362
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.001_TP-8_REP-C [Bas286]

description:
Bas286
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_MEDIUM_0_TP-8_REP-B [Bas315]

description:
Bas315
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TUN_0.001_TP-8_REP-A [Bas284]

description:
Bas284
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DMSO_0_TP-8_REP-C [Bas347]

description:
Bas347
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: Immature hepatocyte - Day 12_MEDIUM_0_TP-8_REP-A [Bas355]

description:
Bas355
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DMSO_0_TP-8_REP-C [Bas299]

description:
Bas299
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_50_TP-8_REP-B [Bas371]

description:
Bas371
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_MEDIUM_0_TP-8_REP-A [Bas307]

description:
Bas307
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DMSO_0_TP-8_REP-B [Bas339]

description:
Bas339
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DMSO_0_TP-8_REP-B [Bas291]

description:
Bas291
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_TNF_7.5_TP-8_REP-A [Bas356]

description:
Bas356
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_3300_TP-8_REP-B [Bas321]

description:
Bas321
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: Immature hepatocyte - Day 12_DEM_3300_TP-8_REP-C [Bas322]

description:
Bas322
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: Immature hepatocyte - Day 12_DMSO_0_TP-8_REP-A [Bas331]

description:
Bas331
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DMSO_0_TP-8_REP-A [Bas283]

description:
Bas283
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_1000_TP-8_REP-C [Bas314]

description:
Bas314
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_1000_TP-8_REP-B [Bas313]

description:
Bas313
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_3300_TP-8_REP-A [Bas320]

description:
Bas320
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_333_TP-8_REP-C [Bas306]

description:
Bas306
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_1000_TP-8_REP-A [Bas312]

description:
Bas312
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_100_TP-8_REP-B [Bas297]

description:
Bas297
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_333_TP-8_REP-A [Bas304]

description:
Bas304
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_333_TP-8_REP-B [Bas305]

description:
Bas305
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_100_TP-8_REP-A [Bas296]

description:
Bas296
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_10_TP-8_REP-C [Bas290]

description:
Bas290
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: Immature hepatocyte - Day 12_DEM_10_TP-8_REP-A [Bas288]

description:
Bas288
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_1_TP-8_REP-B [Bas281]

description:
Bas281
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: Immature hepatocyte - Day 12_DEM_10_TP-8_REP-B [Bas289]

description:
Bas289
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_1_TP-8_REP-A [Bas280]

description:
Bas280
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_100_TP-8_REP-C [Bas368]

description:
Bas368
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: Immature hepatocyte - Day 12_DEM_1_TP-8_REP-C [Bas282]

description:
Bas282
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_100_TP-8_REP-B [Bas367]

description:
Bas367
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_100_TP-8_REP-A [Bas366]

description:
Bas366
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_33_TP-8_REP-B [Bas360]

description:
Bas360
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: Immature hepatocyte - Day 12_CPT_33_TP-8_REP-A [Bas359]

description:
Bas359
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Immature hepatocytes


title: Immature hepatocyte - Day 12_CPT_33_TP-8_REP-C [Bas361]

description:
Bas361
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_10_TP-8_REP-A [Bas352]

description:
Bas352
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_3.3_TP-8_REP-B [Bas345]

description:
Bas345
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_3.3_TP-8_REP-A [Bas344]

description:
Bas344
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_1_TP-8_REP-C [Bas338]

description:
Bas338
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_1_TP-8_REP-A [Bas336]

description:
Bas336
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_DEM_100_TP-8_REP-C [Bas298]

description:
Bas298
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_3.3_TP-8_REP-C [Bas346]

description:
Bas346
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_1_TP-8_REP-B [Bas337]

description:
Bas337
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_10_TP-8_REP-B [Bas353]

description:
Bas353
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_0.01_TP-8_REP-B [Bas329]

description:
Bas329
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_0.01_TP-8_REP-A [Bas328]

description:
Bas328
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_100_TP-8_REP-B [Bas046]

description:
Bas046
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: hiPSC - Day 0

value: hiPSC

value: Tunicamycin (TUN)


title: FAGs_A2

city: Larisa

first: Maria Eleni

last: Gregoriou

address: Viopolis

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

description:
R_2015_01_20_12_13_52_user_ION-124-KMathiopoulos_RNAseq_150120_KMR25-26-29-30.KMR26.IonXpressRNA_003
processed data file:
Fags BvsA.xlsx
FAGs.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv

data_processing:
Base calling and adapter trimming was performed using software onboard the Ion Proton sequencer.
The representative de novo assembly and transcript abundance estimation were obtained with the Trinity pipeline (version 2.4.0) according to the Trinity protocol. Abundances were estimated using RSEM (version 1.3.1). Differential expression was assesed with the edgeR (version 3.8.0) algorithm. Functional annotation was performed using BLAST2GO (v.2) tool.
The reference used for alignement is the de novo assembly file specified in the processed data file named Trinity-olfly-transcriptome-reference.fa
Genome_build: Trinity-olfly-transcriptome-reference.fa
Supplementary_files_format_and_content: The file Trinity-olfly-transcriptome-reference.fa is in fasta format and contains the representative de novo transcriptome assembly. The file isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv is in csv format and contains the edgeR differential expression analysis for each isoform together with the blast2go annotation in the last column in the format blast_hit|Evalue|bitscore.

organism: Bactrocera oleae

source_name: insect tissue

growth_protocol: The flies are reared at 25°C with a 12h light/12h dark photoperiod and humidity 65% in laboratory cages with diameter 303030cm3 with wax cones inside for oviposition

extract_protocol:
The RNA isolation from the tissues was performed based on the TRIzol Reagent following the manufacturer’s instructions with slight modifications.
The isolated mRNA was digested with RNaseIII, hybridized and ligated to Ion Adaptors, reverse transcribed, barcoded and amplified, using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA, USA).

treatment_protocol: two biological replicates of the following samples: female lower reproductive tract and male accessory glands. Two different conditions: virgin, 7 day old flies and once mated.

tag: strain

value: Demokritos

tag: condition

value: mated once, 7 day old, female insects

tag: tissue

value: lower reproductive tract


title: MAGS_A2

description:
R_2015_01_20_12_13_52_user_ION-124-KMathiopoulos_RNAseq_150120_KMR25-26-29-30.KMR30.IonXpressRNA_009
processed data file:
Mags AvsB.xlsx
mags.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv

value: mated once, 7 day old, male insects

value: male accessory glands


title: MAGS_B2

description:
R_2015_01_21_12_34_28_user_ION-125-KMathiopoulos_RNAseq_150121_KMR27-28-31-32-33.KMR32.IonXpressRNA_016
processed data file:
Mags AvsB.xlsx
mags.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv

value: virgin, 7 day old, female insects


title: hiPSC - Day 0_TUN_10_TP-8_REP-C [Bas039]

description:
Bas039
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MAGS_B1

description:
R_2015_01_21_12_34_28_user_ION-125-KMathiopoulos_RNAseq_150121_KMR27-28-31-32-33.KMR31.IonXpressRNA_013
processed data file:
Mags AvsB.xlsx
mags.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv


title: Immature hepatocyte - Day 12_CPT_10_TP-8_REP-C [Bas354]

description:
Bas354
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_10_TP-8_REP-B [Bas038]

description:
Bas038
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_10_TP-8_REP-A [Bas037]

description:
Bas037
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: FAGs_B2

description:
R_2015_01_21_12_34_28_user_ION-125-KMathiopoulos_RNAseq_150121_KMR27-28-31-32-33.KMR28.IonXpressRNA_012
processed data file:
Fags BvsA.xlsx
FAGs.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv


title: FAGs_B1

description:
R_2015_01_21_12_34_28_user_ION-125-KMathiopoulos_RNAseq_150121_KMR27-28-31-32-33.KMR27.IonXpressRNA_011
processed data file:
Fags BvsA.xlsx
FAGs.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv


title: hiPSC - Day 0_TUN_1_TP-8_REP-C [Bas031]

description:
Bas031
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_1_TP-8_REP-A [Bas029]

description:
Bas029
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Immature hepatocyte - Day 12_CPT_0.01_TP-8_REP-C [Bas330]

description:
Bas330
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_0.1_TP-8_REP-C [Bas023]

description:
Bas023
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 0442_Cu_B

city: Exeter

first: Jack

last: Plume

address: Geoffrey Pope, University of Exeter, Stocker Road

department: Biological Sciences

country: United Kingdom

institute: University of Exeter

data_processing:
Sequencing was performed on an Illumina HiSeq2500 platform yielding 72 million 125 bp paired end reads
Reads were checked for quality using FastQC and for contamination using Fastq_screen. Sequencing adapters and low quality bases (< Q22) were removed using cutadapt and reads shorter than 75 bp were discarded
Salmon was used to quantify transcript expression against the B. cenocepacia J2315 genome and annotation
An adjusted p value of p < 0.05 and a fold change of > 2 was used to define significantly differentially expressed genes.
Genome_build: GCF_000009485.1 - Burkholderia cenocepacia J2315
Supplementary_files_format_and_content: .csv file containing abundance and counts data for each gene as generatted by salmon

organism: Burkholderia cenocepacia

source_name: Δbcam0442/3 B. cenocepacia K56-2

growth_protocol: Overnight LB cultures grown at 37 °C at 200 rpm were standardised to OD600 1 ± 0.05, with 50 μl being added to a 50 ml falcon tube containing either 10 ml of LB or LB supplemented with 1 mM CuCl2. Each strain was added to each condition in triplicate, resulting in 12 total RNA extractions.

extract_protocol:
Extraction of total RNA was performed using the RiboPure RNA Purification Kit (Thermo Fisher Scientific) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After 8 hours of growth, 2 ml of each culture was pelleted and resuspended in 10 ml of RNAlater stabilisation solution (Thermo Fisher Scientific) and stored at 4 °C overnight, followed by longer-term storage at -20 °C.


title: 0442_Cu_A


title: 0442_Cu_C


title: 0442_LB_B


title: MAGS_A1

description:
R_2015_01_20_12_13_52_user_ION-124-KMathiopoulos_RNAseq_150120_KMR25-26-29-30.KMR29.IonXpressRNA_004
processed data file:
Mags AvsB.xlsx
mags.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv


title: hiPSC - Day 0_TUN_100_TP-8_REP-C [Bas047]

description:
Bas047
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 0442_LB_A


title: hiPSC - Day 0_TUN_0.01_TP-8_REP-C [Bas015]

description:
Bas015
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_0.1_TP-8_REP-B [Bas022]

description:
Bas022
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 0442_LB_C


title: hiPSC - Day 0_TUN_100_TP-8_REP-A [Bas045]

description:
Bas045
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: FAGs_A1

description:
R_2015_01_20_12_13_52_user_ION-124-KMathiopoulos_RNAseq_150120_KMR25-26-29-30.KMR25.IonXpressRNA_001
processed data file:
Fags BvsA.xlsx
FAGs.xlsx
isoforms_tr3.counts.matrix.FAGs_vs_MAGs.edgeR.DE_results.csv


title: hiPSC - Day 0_TUN_0.1_TP-8_REP-A [Bas021]

description:
Bas021
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT_Cu_C

source_name: WT B. cenocepacia K56-2


title: hiPSC - Day 0_TUN_0.01_TP-8_REP-B [Bas014]

description:
Bas014
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT_Cu_B


title: WT_Cu_A


title: hiPSC - Day 0_TUN_0.001_TP-8_REP-B [Bas006]

description:
Bas006
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_0.01_TP-8_REP-A [Bas013]

description:
Bas013
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT_LB_C


title: WT_LB_B


title: hiPSC - Day 0_TUN_0.001_TP-8_REP-C [Bas007]

description:
Bas007
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TUN_1_TP-8_REP-B [Bas030]

description:
Bas030
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT_LB_A


title: hiPSC - Day 0_TUN_0.001_TP-8_REP-A [Bas005]

description:
Bas005
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TNF_50_TP-8_REP-C [Bas093]

description:
Bas093
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: hiPSC - Day 0_TNF_50_TP-8_REP-B [Bas092]

description:
Bas092
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: sCK-EVs_rep3

city: Torino

first: Giovanni

last: Birolo

state: TO

address: Via Santena 19

department: Medical Sciences

country: Italy

institute: University of Turin

description:
EVs_CK_cells_S33
processed data file: human_evs_raw_expression.xlsx

data_processing:
Cutadapt
BWA
Genome_build: NOT PROVIDED; REQUESTED
Supplementary_files_format_and_content: raw expression

source_name: in vitro differentiated subcutaneous lean adipocytes_sCK-EVs

growth_protocol:
Human primary preadipocytes were cultured in DMEM/F12 (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% Fetal Bovine Serum (FBS) ( Sigma-Aldrich, St. Louis, MO, USA) and maintained at 37°C in a humidified atmosphere of 5% CO2
Differentiation Protocol: Cells were maintained in DMEM with 10% FBS, HEPES, biotin, pantothenate,  transferrin,  insulin, dexamethasone, and IBMX (Sigma-Aldrich, St. Louis, MO, USA) for 3 days to initiate differentiation. At day 4 dexamethasone and IBMX were removed from the medium and the cells were cultured for further 21 days .

extract_protocol: Total RNA from EVs was extracted with mirVana kit (Ambion, LifeTechnologies, Carlsbad, USA) according to the manufacturer’s instructions

treatment_protocol: After differentiation, 3T3-L1 and human adipocytes were washed with PBS and cultured in RPMI-1640 (Sigma-Aldrich, St. Louis, MO, USA) without serum for 24 h, in the presence or absence of CKs [tumor necrosis factor-alpha (TNF-α)/interferon-gamma (INF-γ)/ interleukin-1 beta (IL-1β) (50, 25 and 2.5 ng/ml, respectively)] (PeproTech EC Ltd.). EVs were collected from supernatants by ultracentrifugation for 2 h at 4 °C.

tag: tissue source

value: human subcutaneus adipose tissue

value: Human primary preadipocytes

tag: treatment

value: inflammatory  cytokines (CK)


title: sCK-EVs_rep2

description:
CellCK2_S23
processed data file: human_evs_raw_expression.xlsx


title: sAd-EVs_rep3

description:
EVs_Ctrl_cells_S32
processed data file: human_evs_raw_expression.xlsx

source_name: in vitro differentiated subcutaneous lean adipocytes_sAd-Evs

value: untreated


title: sCK-EVs_rep1

description:
CellCK1_S22
processed data file: human_evs_raw_expression.xlsx


title: hiPSC - Day 0_TNF_10_TP-8_REP-B [Bas085]

description:
Bas085
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL

value: 8 hr


title: sAd-EVs_rep1

description:
CellCtr1_S19
processed data file: human_evs_raw_expression.xlsx


title: sAd-EVs_rep2

description:
CellCtr2_S20
processed data file: human_evs_raw_expression.xlsx


title: hiPSC - Day 0_TNF_10_TP-8_REP-A [Bas084]

description:
Bas084
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TNF_7.5_TP-8_REP-A [Bas077]

description:
Bas077
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: hiPSC - Day 0_TNF_7.5_TP-8_REP-B [Bas078]

description:
Bas078
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: hiPSC


title: hiPSC - Day 0_TNF_5_TP-8_REP-C [Bas071]

description:
Bas071
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: MDAMB-RNA2: STAT3i_MDAMB231_1

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharamcology

country: USA

institute: Harvard Medical School

data_processing:
base-calling performed by Illumina Hiseq 2000
Trim adapter
Align reads using STAR
Estimate genecounts using RSEM
Genome_build: hg38

source_name: Breast cancer cell line

growth_protocol: MCF-10A-ER-Src cells (Iliopoulos et al., 2009; Iliopoulos et al., 2010) were grown in DMEM/F12 without phenol red (Thermo Fisher Scientific, 11039-047) + 5% charcoal stripped FBS (Sigma, F6765) + 1% pen/strep (Thermo Fisher Scientific, 15140122)+20 ng/ml EGF (Peprotech, AF-100-15) + 0.5 μg/ml Hydrocortisone (Sigma, H-0888) + 0.1 μg/ml cholera toxin (Sigma, C-8052) + 10 μg/ml insulin (Sigma, 10516).

extract_protocol:
RNA was prepared used mRNeasy Mini Kit (Qiagen, No. 217004).
RNA-seq libraries were generated using TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).

treatment_protocol: 1-0.4 μM Tamoxifen (Sigma, H7904) + 2-4 μM AZD0530 (Selleck Chemicals, S1006) were used to induce the transformation.

tag: cell line

value: MDA-MB-231 cells

tag: transformation status


title: MDAMB-RNA2: JUNBi_MDAMB231_2


title: MDAMB-RNA2: STAT3i_MDAMB231_2


title: hiPSC - Day 0_TNF_5_TP-8_REP-B [Bas070]

description:
Bas070
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA2: Ctrli_MDAMB231_4


title: MDAMB-RNA1: TEADi_MDAMB231_2


title: hiPSC - Day 0_TNF_2.5_TP-8_REP-C [Bas063]

description:
Bas063
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL


title: MDAMB-RNA2: Ctrli_MDAMB231_3


title: hiPSC - Day 0_TNF_2.5_TP-8_REP-B [Bas062]

description:
Bas062
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA2: JUNBi_MDAMB231_1


title: hiPSC - Day 0_TNF_5_TP-8_REP-A [Bas069]

description:
Bas069
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TNF_2.5_TP-8_REP-A [Bas061]

description:
Bas061
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA1: TEADi_MDAMB231_1


title: MDAMB-RNA1: YAPi_TAZi_MDAMB231_2


title: hiPSC - Day 0_TNF_50_TP-8_REP-A [Bas091]

description:
Bas091
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TNF_10_TP-8_REP-C [Bas086]

description:
Bas086
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TNF_1_TP-8_REP-C [Bas055]

description:
Bas055
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: MDAMB-RNA1: YAPi_TAZi_MDAMB231_1


title: hiPSC - Day 0_TNF_1_TP-8_REP-B [Bas054]

description:
Bas054
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_TNF_1_TP-8_REP-A [Bas053]

description:
Bas053
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA1: TAZi_MDAMB231_1


title: MDAMB-RNA1: TAZi_MDAMB231_2


title: hiPSC - Day 0_TNF_7.5_TP-8_REP-C [Bas079]

description:
Bas079
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_MEDIUM_0_TP-8_REP-C [Bas090]

description:
Bas090
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: hiPSC - Day 0_MEDIUM_0_TP-8_REP-C [Bas044]

description:
Bas044
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_MEDIUM_0_TP-8_REP-B [Bas083]

description:
Bas083
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA1: YAPi_MDAMB231_1


title: hiPSC - Day 0_MEDIUM_0_TP-8_REP-B [Bas036]

description:
Bas036
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA1: Ctrli_MDAMB231_2


title: hiPSC - Day 0_MEDIUM_0_TP-8_REP-A [Bas076]

description:
Bas076
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: JUNBi_TAM_2

source_name: Breast cell line

value: MCF10A ER-Src cells

value: transformed


title: MDAMB-RNA1: Ctrli_MDAMB231_1


title: hiPSC - Day 0_DMSO_0_TP-8_REP-C [Bas068]

description:
Bas068
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: ERSRC-RNA1: JUNBi_TAM_1


title: ERSRC-RNA1: JUNBi_ETH_1

value: non-transformed


title: ERSRC-RNA1: STAT3i_TAM_2


title: hiPSC - Day 0_DMSO_0_TP-8_REP-B [Bas012]

description:
Bas012
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_DMSO_0_TP-8_REP-B [Bas060]

description:
Bas060
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_DMSO_0_TP-8_REP-C [Bas020]

description:
Bas020
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: STAT3i_ETH_2


title: hiPSC - Day 0_DMSO_0_TP-8_REP-A [Bas052]

description:
Bas052
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: STAT3i_TAM_1


title: hiPSC - Day 0_DEM_3300_TP-8_REP-C [Bas043]

description:
Bas043
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: hiPSC - Day 0_DMSO_0_TP-8_REP-A [Bas004]

description:
Bas004
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: TAZi_TAM_2


title: ERSRC-RNA1: STAT3i_ETH_1


title: hiPSC - Day 0_DEM_3300_TP-8_REP-B [Bas042]

description:
Bas042
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB-RNA1: YAPi_MDAMB231_2


title: hiPSC - Day 0_DEM_3300_TP-8_REP-A [Bas041]

description:
Bas041
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: TAZi_TAM_1


title: hiPSC - Day 0_DEM_1000_TP-8_REP-C [Bas035]

description:
Bas035
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_MEDIUM_0_TP-8_REP-A [Bas028]

description:
Bas028
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_DEM_1000_TP-8_REP-B [Bas034]

description:
Bas034
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: JUNBi_ETH_2


title: ERSRC-RNA1: YAPi_TAM_2


title: ERSRC-RNA1: TAZi_ETH_1


title: ERSRC-RNA1: YAPi_ETH_2


title: ERSRC-RNA1: YAPi_TAM_1


title: hiPSC - Day 0_DEM_333_TP-8_REP-C [Bas027]

description:
Bas027
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_DEM_1000_TP-8_REP-A [Bas033]

description:
Bas033
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_DEM_333_TP-8_REP-B [Bas026]

description:
Bas026
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: YAPi_ETH_1


title: hiPSC - Day 0_DEM_333_TP-8_REP-A [Bas025]

description:
Bas025
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_DEM_100_TP-8_REP-C [Bas019]

description:
Bas019
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: Ctrli_ETH_2


title: ERSRC-RNA1: Ctrli_TAM_2


title: ERSRC-RNA1: Ctrli_ETH_1


title: hiPSC - Day 0_DEM_100_TP-8_REP-B [Bas018]

description:
Bas018
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC-RNA1: TAZi_ETH_2


title: hiPSC - Day 0_DEM_10_TP-8_REP-C [Bas011]

description:
Bas011
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: hiPSC - Day 0_DEM_10_TP-8_REP-B [Bas010]

description:
Bas010
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB3: STAT3_MDAMB231_2

library_source: genomic

data_processing:
base-calling performed by Illumina Hiseq 2000
process the fastq file follwing ENCODE ChIP-seq pipeline to obtain IDR peaks
remove IDR peaks that overlap manually picked blacklisted regions and centromere regions
Genome_build: hg38

molecule: genomic DNA

growth_protocol:
MCF-10A-ER-Src cells (Iliopoulos et al., 2009; Iliopoulos et al., 2010) were grown in DMEM/F12 without phenol red (Thermo Fisher Scientific, 11039-047) + 5% charcoal stripped FBS (Sigma, F6765) + 1% pen/strep (Thermo Fisher Scientific, 15140122)+20 ng/ml EGF (Peprotech, AF-100-15) + 0.5 μg/ml Hydrocortisone (Sigma, H-0888) + 0.1 μg/ml cholera toxin (Sigma, C-8052) + 10 μg/ml insulin (Sigma, 10516).
MDA-MB-231 cells were grown in DMEM (Thermo Fisher Scientific, 11995-073) + 10% FBS (Sigma, TMS-013-B) + 1% pen/strep.

extract_protocol:
Cells were dual cross-linking with a mixture of 2 mM each of ethylene glycol bis (succinimidyl succinate) (EGS) and disuccinimidyl glutarate (DSG) and 1% formaldehyde. Chromatin was digested with 60 units MNase (New England Biolabs, M0247S) at 37 0C for 10 minutes and then sonicated using Branson Microtip Sonifier 450 (4X15 second at output 4.5 and duty cycle 60%) to the sizes mostly between 150-500 bp.
50 μg chromatin, antibodies for transcription factors (listed in Table S6), and 15 μl Dynabead protein G (Thermo Fisher Scientific, 10004D) was used for the chromatin immunoprecipitation (ChIP)

tag: chip antibody

value: JUNB (Cell Signaling Technology, 3753s)


title: hiPSC - Day 0_DEM_100_TP-8_REP-A [Bas017]

description:
Bas017
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB3: STAT3_MDAMB231_1


title: hiPSC - Day 0_DEM_1_TP-8_REP-C [Bas003]

description:
Bas003
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: MDAMB2: JUNB_MBMDA231_1

value: STAT3 (Cell Signaling Technology, 9139s)


title: hiPSC - Day 0_DEM_1_TP-8_REP-B [Bas002]

description:
Bas002
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MDAMB1: TEAD_MDAMB231_2

value: TEAD(Cell Signaling Technology, 13295 )


title: MDAMB2: JUNB_MBMDA231_2


title: hiPSC - Day 0_DEM_1_TP-8_REP-A [Bas001]

description:
Bas001
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: hiPSC


title: MDAMB1: TAZ_MDAMB231_2

value: TAZ (Cell Signaling Technology, 4883s)


title: MDAMB1: TEAD_MDAMB231_1

value: MDA-MB-231 cells


title: hiPSC - Day 0_CPT_100_TP-8_REP-C [Bas089]

description:
Bas089
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: hiPSC - Day 0_CPT_100_TP-8_REP-B [Bas088]

description:
Bas088
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB1: TAZ_MDAMB231_1


title: hiPSC - Day 0_CPT_100_TP-8_REP-A [Bas087]

description:
Bas087
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MDAMB1: YAP_MDAMB231_1

value: YAP (Bethyl Laboratories, A302-309A)


title: ERSRC-RNA1: Ctrli_TAM_1


title: hiPSC - Day 0_CPT_33_TP-8_REP-B [Bas081]

description:
Bas081
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: hiPSC - Day 0_CPT_33_TP-8_REP-C [Bas082]

description:
Bas082
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC5: JUNB_TAM_2

value: MCF10A ER-Src cells


title: hiPSC - Day 0_CPT_10_TP-8_REP-C [Bas075]

description:
Bas075
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC5: JUNB_TAM_1

value: transformed


title: hiPSC - Day 0_DEM_10_TP-8_REP-A [Bas009]

description:
Bas009
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC5: JUNB_ETH_1


title: hiPSC - Day 0_CPT_3.3_TP-8_REP-C [Bas067]

description:
Bas067
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_CPT_3.3_TP-8_REP-A [Bas065]

description:
Bas065
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_CPT_1_TP-8_REP-C [Bas059]

description:
Bas059
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC5: STAT3_TAM_2


title: ERSRC5: STAT3_ETH_2


title: hiPSC - Day 0_CPT_0.01_TP-8_REP-C [Bas051]

description:
Bas051
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC4: TAZ in YAP-ko cells_ETH


title: ERSRC5: STAT3_TAM_1


title: ERSRC4: TAZ in YAP-ko cells_TAM


title: hiPSC - Day 0_CPT_0.01_TP-8_REP-B [Bas050]

description:
Bas050
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC4: YAP in TAZ-ko cells_TAM


title: hiPSC - Day 0_CPT_1_TP-8_REP-A [Bas057]

description:
Bas057
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC4: YAP in TAZ-ko cells_ETH


title: hiPSC - Day 0_CPT_0.01_TP-8_REP-A [Bas049]

description:
Bas049
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ERSRC5: STAT3_ETH_1


title: ERSRC2: TEADs_TAM_2


title: hiPSC - Day 0_CPT_3.3_TP-8_REP-B [Bas066]

description:
Bas066
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hiPSC - Day 0_CPT_1_TP-8_REP-B [Bas058]

description:
Bas058
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_MEDIUM_0_TP-8_REP-3 [HepG2_P120-G02]

description:
HepG2_P120-G02
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: HepG2 WT

value: MEDIUM


title: HepG2 WT_TNF_33_TP-8_REP-3 [HepG2_P120-F04]

description:
HepG2_P120-F04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 33 ng/mL


title: MDAMB1: YAP_MDAMB231_2


title: ERSRC1: TEADs_TAM_1


title: ERSRC2: TAZ_TAM_2


title: HepG2 WT_DMSO_0.2_TP-8_REP-3 [HepG2_P120-G01]

description:
HepG2_P120-G01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: hiPSC - Day 0_CPT_10_TP-8_REP-B [Bas074]

description:
Bas074
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: HepG2 WT_TUN_10_TP-8_REP-3 [HepG2_P120-F03]

description:
HepG2_P120-F03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Tunicamycin (TUN)


title: ERSRC5: JUNB_ETH_2

value: non-transformed

value: JUNB (Cell Signaling Technology, 3753s)


title: ERSRC1: TEADs_ETH_1

value: TEAD(Cell Signaling Technology, 13295 )


title: hiPSC - Day 0_CPT_10_TP-8_REP-A [Bas073]

description:
Bas073
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: hiPSC

value: 8 hr


title: ERSRC2: TEADs_ETH_2


title: ERSRC3: TAZ_TAM_3

value: TAZ (Cell Signaling Technology, 4883s)


title: ERSRC2: YAP_TAM_2


title: ERSRC2: TAZ_ETH_2


title: ERSRC3: TAZ_ETH_3


title: ERSRC1: YAP_ETH_1


title: ERSRC1: YAP_TAM_1


title: HepG2 WT_DEM_3300_TP-8_REP-3 [HepG2_P120-F01]

description:
HepG2_P120-F01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: HepG2 WT_TUN_1_TP-8_REP-3 [HepG2_P120-E03]

description:
HepG2_P120-E03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: HepG2 WT_CPT_33_TP-8_REP-3 [HepG2_P120-E02]

description:
HepG2_P120-E02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)

value: 33 uM


title: ERSRC2: YAP_ETH_2

value: MCF10A ER-Src cells

value: YAP (Bethyl Laboratories, A302-309A)


title: HepG2 WT_DEM_330_TP-8_REP-3 [HepG2_P120-D01]

description:
HepG2_P120-D01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_CPT_100_TP-8_REP-3 [HepG2_P120-F02]

description:
HepG2_P120-F02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_DEM_1000_TP-8_REP-3 [HepG2_P120-E01]

description:
HepG2_P120-E01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_10_TP-8_REP-3 [HepG2_P120-E04]

description:
HepG2_P120-E04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 10 ng/mL


title: HepG2 WT_TUN_0.1_TP-8_REP-3 [HepG2_P120-D03]

description:
HepG2_P120-D03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_1_TP-8_REP-3 [HepG2_P120-C04]

description:
HepG2_P120-C04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: HepG2 WT_CPT_10_TP-8_REP-3 [HepG2_P120-D02]

description:
HepG2_P120-D02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: HepG2 WT_TNF_3.3_TP-8_REP-3 [HepG2_P120-D04]

description:
HepG2_P120-D04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 3.3 ng/mL


title: HepG2 WT_TUN_0.01_TP-8_REP-3 [HepG2_P120-C03]

description:
HepG2_P120-C03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Tunicamycin (TUN)


title: HepG2 WT_DEM_100_TP-8_REP-3 [HepG2_P120-C01]

description:
HepG2_P120-C01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_0.3_TP-8_REP-3 [HepG2_P120-B04]

description:
HepG2_P120-B04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 0.3 ng/mL


title: HepG2 WT_CPT_3.3_TP-8_REP-3 [HepG2_P120-C02]

description:
HepG2_P120-C02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Low risk post-op patient 10

type: RNA

city: Auckland

first: Jiwon

last: Hong

state: Auckland

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

hyb_protocol: Affy protocol

scan_protocol: Affy protocol

data_processing: Affy TAC and GEC

label: Biotin

source_name: plasma

label_protocol: FlashTag HSR

growth_protocol: Patients after heart surgery

extract_protocol: RNA from human plasma with Macherey Nagel miRNA plasma kit

treatment_protocol: Non-occlusive mesenteric ischemia

tag: nomi risk status

value: Low


title: Low risk post-op patient 9


title: Low risk post-op patient 11


title: HepG2 WT_CPT_1_TP-8_REP-3 [HepG2_P120-B02]

description:
HepG2_P120-B02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TUN_0.001_TP-8_REP-3 [HepG2_P120-B03]

description:
HepG2_P120-B03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Low risk post-op patient 6


title: HepG2 WT_DEM_10_TP-8_REP-3 [HepG2_P120-B01]

description:
HepG2_P120-B01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_0.1_TP-8_REP-3 [HepG2_P120-A04]

description:
HepG2_P120-A04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 0.1 ng/mL


title: HepG2 WT_TUN_0.0001_TP-8_REP-3 [HepG2_P120-A03]

description:
HepG2_P120-A03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: HepG2 WT_CPT_0.1_TP-8_REP-3 [HepG2_P120-A02]

description:
HepG2_P120-A02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_MEDIUM_0_TP-8_REP-2 [HepG2_P119-G02]

description:
HepG2_P119-G02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: HepG2 WT_DEM_1_TP-8_REP-3 [HepG2_P120-A01]

description:
HepG2_P120-A01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: HepG2 WT_TNF_33_TP-8_REP-2 [HepG2_P119-F04]

description:
HepG2_P119-F04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 ng/mL


title: HepG2 WT_TUN_10_TP-8_REP-2 [HepG2_P119-F03]

description:
HepG2_P119-F03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Low risk post-op patient 8


title: Low risk post-op patient 5


title: Low risk post-op patient 1


title: Low risk post-op patient 3


title: High risk post-op patient 8

value: High


title: High risk post-op patient 9


title: Low risk post-op patient 7


title: High risk post-op patient 5


title: HepG2 WT_CPT_100_TP-8_REP-2 [HepG2_P119-F02]

description:
HepG2_P119-F02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: High risk post-op patient 6


title: High risk post-op patient 4


title: Low risk post-op patient 4


title: High risk post-op patient 2


title: High risk post-op patient 3


title: High risk post-op patient 7


title: HepG2 WT_DMSO_0.2_TP-8_REP-2 [HepG2_P119-G01]

description:
HepG2_P119-G01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: HepG2 WT_DEM_3300_TP-8_REP-2 [HepG2_P119-F01]

description:
HepG2_P119-F01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_10_TP-8_REP-2 [HepG2_P119-E04]

description:
HepG2_P119-E04
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_CPT_33_TP-8_REP-2 [HepG2_P119-E02]

description:
HepG2_P119-E02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: High risk post-op patient 1


title: HepG2 WT_TUN_1_TP-8_REP-2 [HepG2_P119-E03]

description:
HepG2_P119-E03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: HepG2 WT_DEM_1000_TP-8_REP-2 [HepG2_P119-E01]

description:
HepG2_P119-E01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_3.3_TP-8_REP-2 [HepG2_P119-D04]

description:
HepG2_P119-D04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha


title: Low-risk pre-op patient 8


title: HepG2 WT_TUN_0.1_TP-8_REP-2 [HepG2_P119-D03]

description:
HepG2_P119-D03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_CPT_10_TP-8_REP-2 [HepG2_P119-D02]

description:
HepG2_P119-D02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Low-risk pre-op patient 11


title: HepG2 WT_TUN_0.01_TP-8_REP-2 [HepG2_P119-C03]

description:
HepG2_P119-C03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_DEM_330_TP-8_REP-2 [HepG2_P119-D01]

description:
HepG2_P119-D01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_1_TP-8_REP-2 [HepG2_P119-C04]

description:
HepG2_P119-C04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: HepG2 WT_CPT_3.3_TP-8_REP-2 [HepG2_P119-C02]

description:
HepG2_P119-C02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: CK-EVs_rep3

description:
CK3_S6
processed data file: mouse_evs_raw_expression.xlsx

organism: Mus musculus

growth_protocol:
3T3-L1 murine preadipocytes (ATCC, Manassas, USA) were maintained in Dulbecco Modified Eagle’s Medium (DMEM) (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal calf serum (FCS) (Life Technologies, Carlsbad, CA, USA)  and maintained at 37°C in a humidified atmosphere of 5% CO2.
Differentiation Protocol: Cells were mantained in DMEM at 10% of FBS supplemented with insulin, dexamethasone and IBMX (Sigma-Aldrich, St. Louis, MO, USA). At day 2, cells were switched to DMEM with 10% FBS and insulin until day 8

value: embryo

value: 3T3-L1 murine preadipocytes

value: inflammatory  cytokines (CK)


title: Low-risk pre-op patient 7


title: 2805.adult_pGM_wt.1

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

institute: Washington University School of Medicine

description:
wild type pGMs
2805.adult_pGM_wt.1

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

extract_protocol:
Qiagen RNAeasy micro plus
Clontech SMRTr

tag: age

value: 8 week old

tag: genotype

value: wild type

value: pGMs


title: 2805.adult_pGM_wt.3

description:
wild type pGMs
2805.adult_pGM_wt.3


title: 2805.adult_pGM_wt.4

description:
wild type pGMs
2805.adult_pGM_wt.4


title: CK-EVs_rep2

description:
CK2_S5
processed data file: mouse_evs_raw_expression.xlsx


title: 2805.adult_pGM_ko.4

description:
Kmt2c -/- pGMs
2805.adult_pGM_ko.4

value: Kmt2c f/f; Vav-Cre


title: Low-risk pre-op patient 5

value: Low


title: Low-risk pre-op patient 6


title: Low-risk pre-op patient 9


title: Low-risk pre-op patient 4


title: 2805.adult_pGM_ko.3

description:
Kmt2c -/- pGMs
2805.adult_pGM_ko.3


title: Low-risk pre-op patient 10


title: Low-risk pre-op patient 2


title: 2805.adult_pGM_ko.2

description:
Kmt2c -/- pGMs
2805.adult_pGM_ko.2


title: HepG2 WT_TNF_0.3_TP-8_REP-2 [HepG2_P119-B04]

description:
HepG2_P119-B04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 0.3 ng/mL

value: 8 hr


title: HepG2 WT_DEM_100_TP-8_REP-2 [HepG2_P119-C01]

description:
HepG2_P119-C01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: Low-risk pre-op patient 1


title: Low-risk pre-op patient 3


title: 2805.adult_pGM_ko.1

description:
Kmt2c -/- pGMs
2805.adult_pGM_ko.1


title: Ad-EVs_rep3

description:
Ctr3_S3
processed data file: mouse_evs_raw_expression.xlsx

value: untreated


title: 2805.adult_pGM_wt.2

description:
wild type pGMs
2805.adult_pGM_wt.2


title: 2805.adult_pGM_het.4

description:
Kmt2c +/- pGMs
2805.adult_pGM_het.4

value: Kmt2c f/+; Vav-Cre


title: 2805.adult_pGM_het.1

description:
Kmt2c +/- pGMs
2805.adult_pGM_het.1


title: HepG2 WT_DEM_10_TP-8_REP-2 [HepG2_P119-B01]

description:
HepG2_P119-B01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: 2805.adult_pGM_het.2

description:
Kmt2c +/- pGMs
2805.adult_pGM_het.2


title: Ad-EVs_rep2

description:
Ctr2_S2
processed data file: mouse_evs_raw_expression.xlsx


title: CK-EVs_rep1

description:
CK1_S4
processed data file: mouse_evs_raw_expression.xlsx


title: Ad-EVs_rep1

description:
Ctr1_S1
processed data file: mouse_evs_raw_expression.xlsx


title: HepG2 WT_CPT_1_TP-8_REP-2 [HepG2_P119-B02]

description:
HepG2_P119-B02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)

value: 1 uM


title: 2805.adult_HSC_wt.1

description:
wild type HSCs
2805.adult_HSC_wt.1

value: HSCs


title: 2805.adult_HSC_wt.2

description:
wild type HSCs
2805.adult_HSC_wt.2


title: 2805.adult_HSC_wt.4

description:
wild type HSCs
2805.adult_HSC_wt.4


title: 2805.adult_HSC_wt.3

description:
wild type HSCs
2805.adult_HSC_wt.3


title: HepG2 WT_CPT_0.1_TP-8_REP-2 [HepG2_P119-A02]

description:
HepG2_P119-A02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 2805.adult_HSC_mll3ko.2

description:
Kmt2c -/- HSCs
2805.adult_HSC_mll3ko.2


title: 2805.adult_HSC_mll3ko.1

description:
Kmt2c -/- HSCs
2805.adult_HSC_mll3ko.1


title: HepG2 WT_DEM_1_TP-8_REP-2 [HepG2_P119-A01]

description:
HepG2_P119-A01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_TNF_0.1_TP-8_REP-2 [HepG2_P119-A04]

description:
HepG2_P119-A04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 0.1 ng/mL


title: 2805.adult_HSC_mll3ko.3

description:
Kmt2c -/- HSCs
2805.adult_HSC_mll3ko.3


title: HepG2 WT_TUN_0.0001_TP-8_REP-2 [HepG2_P119-A03]

description:
HepG2_P119-A03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Tunicamycin (TUN)


title: HepG2 WT_TUN_0.001_TP-8_REP-2 [HepG2_P119-B03]

description:
HepG2_P119-B03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 2805.adult_HSC_mll3het.4

description:
Kmt2c +/- HSCs
2805.adult_HSC_mll3het.4

value: 8 week old


title: 2805.adult_pGM_het.3

description:
Kmt2c +/- pGMs
2805.adult_pGM_het.3


title: HepG2 WT_MEDIUM_0_TP-8_REP-1 [HepG2_P118-G02]

description:
HepG2_P118-G02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: CAF-D3

city: Daegu

first: SU YOUNG

last: OH

address: Dalgubeol-daero, 2177

country: South Korea

institute: Kyungpook national university

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit(900720, Thermo Fisher Scientific) using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Human Gene 2.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

label: biotin

source_name: CAF-defense cells

label_protocol: The GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using GeneChip™ WT PLUS Reagent Kit(902280, Thermo Fisher Scientific).

extract_protocol: RNA was prepared using theTrizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: cancer-associated fibroblasts of HNSCC


title: CAF-P2

source_name: CAF-promote cells


title: CAF-P3


title: CAF-P1


title: 2805.adult_HSC_mll3het.2

description:
Kmt2c +/- HSCs
2805.adult_HSC_mll3het.2


title: 2805.adult_HSC_mll3het.1

description:
Kmt2c +/- HSCs
2805.adult_HSC_mll3het.1


title: HepG2 WT_DMSO_0.2_TP-8_REP-1 [HepG2_P118-G01]

description:
HepG2_P118-G01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: 2805.adult_HPC_wt.4

description:
wild type HPCs
2805.adult_HPC_wt.4

value: wild type

value: HPCs


title: 2805.adult_HSC_mll3ko.4

description:
Kmt2c -/- HSCs
2805.adult_HSC_mll3ko.4

value: Kmt2c f/f; Vav-Cre


title: 3050.input.1

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by novoalign (versoin 3.04.06)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab AQUAS TF and histone ChIP-seq pipeline (https://github.com/kundajelab/chipseq_pipeline version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.
ChIPmentation, Illumina

value: 8-10 weeks old


title: 2805.adult_HPC_wt.3

description:
wild type HPCs
2805.adult_HPC_wt.3


title: HepG2 WT_TNF_33_TP-8_REP-1 [HepG2_P118-F04]

description:
HepG2_P118-F04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 ng/mL

value: 8 hr


title: 2805.adult_HPC_wt.2

description:
wild type HPCs
2805.adult_HPC_wt.2


title: 2805.adult_HPC_wt.1

description:
wild type HPCs
2805.adult_HPC_wt.1


title: 3050_HPC_wt_PBS_H3K27ac.4

description:
vehicle (PBS)  x3 days
wild type PBS treated HPCs
HPC_wt_PBS.fc.signal.bigwig
HPC_wt_PBS.filt.narrowPeak.gz

value: wild type PBS treated HPCs


title: HepG2 WT_TUN_10_TP-8_REP-1 [HepG2_P118-F03]

description:
HepG2_P118-F03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: 2805.adult_HPC_mll3ko.2

description:
Kmt2c -/- HPCs
2805.adult_HPC_mll3ko.2


title: HepG2 WT_CPT_100_TP-8_REP-1 [HepG2_P118-F02]

description:
HepG2_P118-F02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: CAF-D1


title: 2805.adult_HPC_mll3ko.3

description:
Kmt2c -/- HPCs
2805.adult_HPC_mll3ko.3


title: 2805.adult_HPC_mll3ko.4

description:
Kmt2c -/- HPCs
2805.adult_HPC_mll3ko.4


title: 3050_HPC_wt_PBS_H3K27ac.3


title: 3050_HPC_wt_PBS_H3K27ac.2


title: 2805.adult_HPC_mll3ko.1

description:
Kmt2c -/- HPCs
2805.adult_HPC_mll3ko.1


title: HepG2 WT_DEM_3300_TP-8_REP-1 [HepG2_P118-F01]

description:
HepG2_P118-F01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: 2805.adult_HPC_mll3het.4

description:
Kmt2c +/- HPCs
2805.adult_HPC_mll3het.4

value: Kmt2c f/+; Vav-Cre


title: CAF-D2


title: 3050_HPC_wt_PBS_H3K27ac.1


title: HepG2 WT_TNF_10_TP-8_REP-1 [HepG2_P118-E04]

description:
HepG2_P118-E04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 10 ng/mL


title: 3050_HPC_wt_IL1_H3K27ac.4

description:
0.5 microgram IL-1 per day  x3 days
wild type IL-1 treated HPCs
HPC_wt_IL1.fc.signal.bigwig
HPC_wt_IL1.filt.narrowPeak.gz

value: wild type IL-1 treated HPCs


title: 2805.adult_HPC_mll3het.2

description:
Kmt2c +/- HPCs
2805.adult_HPC_mll3het.2

value: 8 week old


title: 2805.adult_HPC_mll3het.3

description:
Kmt2c +/- HPCs
2805.adult_HPC_mll3het.3


title: 2805.adult_GMP_wt.4

description:
wild type GMPs
2805.adult_GMP_wt.4

value: GMPs


title: 3050_HPC_wt_IL1_H3K27ac.3


title: HepG2 WT_CPT_33_TP-8_REP-1 [HepG2_P118-E02]

description:
HepG2_P118-E02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: 3050_HPC_wt_IL1_H3K27ac.2


title: 2805.adult_GMP_wt.2

description:
wild type GMPs
2805.adult_GMP_wt.2

value: wild type


title: HepG2 WT_DEM_1000_TP-8_REP-1 [HepG2_P118-E01]

description:
HepG2_P118-E01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 3050_HPC_wt_IL1_H3K27ac.1


title: 3050_HPC_ko_PBS_H3K27ac.4

description:
vehicle (PBS)  x3 days
Kmt2c f/f; Vav-Cre; PBS treated HPCs
HPC_ko_PBS.fc.signal.bigwig
HPC_ko_PBS.filt.narrowPeak.gz

value: Kmt2c f/f; Vav-Cre; PBS treated HPCs


title: 2805.adult_GMP_ko.2

description:
Kmt2c -/- GMPs
2805.adult_GMP_ko.2

value: Kmt2c f/f; Vav-Cre


title: HepG2 WT_TUN_1_TP-8_REP-1 [HepG2_P118-E03]

description:
HepG2_P118-E03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Tunicamycin (TUN)

value: 1 uM


title: 2805.adult_GMP_ko.3

description:
Kmt2c -/- GMPs
2805.adult_GMP_ko.3


title: 2805.adult_HPC_mll3het.1

description:
Kmt2c +/- HPCs
2805.adult_HPC_mll3het.1

value: HPCs


title: HepG2 WT_TUN_0.1_TP-8_REP-1 [HepG2_P118-D03]

description:
HepG2_P118-D03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: 3050_HPC_ko_PBS_H3K27ac.3

value: 8-10 weeks old


title: 2805.adult_GMP_het.4

description:
Kmt2c +/- GMPs
2805.adult_GMP_het.4


title: 2805.adult_GMP_het.1

description:
Kmt2c +/- GMPs
2805.adult_GMP_het.1


title: 2805.adult_GMP_het.3

description:
Kmt2c +/- GMPs
2805.adult_GMP_het.3


title: HepG2 WT_DEM_330_TP-8_REP-1 [HepG2_P118-D01]

description:
HepG2_P118-D01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HepG2 WT_CPT_10_TP-8_REP-1 [HepG2_P118-D02]

description:
HepG2_P118-D02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)

value: 10 uM


title: 2805.adult_GMP_het.2

description:
Kmt2c +/- GMPs
2805.adult_GMP_het.2

value: Kmt2c f/+; Vav-Cre


title: 3050_HPC_ko_PBS_H3K27ac.2


title: HepG2 WT_TNF_1_TP-8_REP-1 [HepG2_P118-C04]

description:
HepG2_P118-C04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 1 ng/mL


title: MDA-mb231 Ki-67-KO rep3

city: Montpellier

first: Daniel

last: Fisher

address: 1919 Route de Mende

department: IGMM

country: France

institute: CNRS

data_processing:
Base calling was performed with ZebraCallV2 software  FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p13 genome using STAR_2.6.0c with default parameters.
Counts of the reads per genes were calculated in the mapping step with the STAR software using the gencode vM35 gene annotations.
Differential expression analysis were performed using an Ad hoc script using the R programming software based on the Deseq2 library
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Raw counts of reads per gene

source_name: MDA-mb231 cell line

growth_protocol: Cells were grown in Dulbecco modified Eagle medium (DMEM - high glucose, pyruvate, GlutaMAX – Gibco® Life LifeTechnologies) supplemented with 10% foetal bovine serum (SIGMA or DUTSCHER). Cells were grown under standard conditions at 37°C in humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted from about 5M cells from MDA-MB-231 WT and Ki-67 KO independent clones, that were trypsinized and centrifuged, cell pellet was treated with 1ml Trizol (Life Technologies). Then following the manufacturer’s instructions, samples were incubated 5 min at RT, added 0,2 ml Chloroform and shaked the tubes. Tubes were incubated 3 min at RT, centrifuged 12000g 15 min at 4ºC, and aqueous phase was transferred to new (RNAse free) eppendorf tubes. Followed the procedure with the RNAeasy kit from Qiagen, adding the aqueous phase to the gDNA eliminator column step from the RNAeasy kit and continued the protocol following the manufacturer’s instructions. RNA integrity was analysed on Agilent 2100 bioanalyzer.
mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperture. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. PCR was used to amplify the cDNA fragments with adapters from previous step and the products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution.


title: 2805.adult_GMP_wt.3

description:
wild type GMPs
2805.adult_GMP_wt.3


title: 2805.adult_GMP_wt.1

description:
wild type GMPs
2805.adult_GMP_wt.1


title: MDA-mb231 Ki-67-KO rep2


title: 3050_HPC_ko_PBS_H3K27ac.1


title: HepG2 WT_TNF_3.3_TP-8_REP-1 [HepG2_P118-D04]

description:
HepG2_P118-D04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 3.3 ng/mL


title: 2805.adult_GMP_ko.1

description:
Kmt2c -/- GMPs
2805.adult_GMP_ko.1

value: 8 week old


title: MDA-mb231 WT rep3


title: MDA-mb231 Ki-67-KO rep1


title: HepG2 WT_TUN_0.01_TP-8_REP-1 [HepG2_P118-C03]

description:
HepG2_P118-C03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 3050_HPC_ko_IL1_H3K27ac.4

description:
0.5 microgram IL-1 per day  x3 days
Kmt2c f/f; Vav-Cre; IL-1 treated HPCs
HPC_ko_IL1.fc.signal.bigwig
HPC_ko_IL1.filt.narrowPeak.gz

value: Kmt2c f/f; Vav-Cre; IL-1 treated HPCs


title: MDA-mb231 WT rep2


title: 2805.adult_GMP_ko.4

description:
Kmt2c -/- GMPs
2805.adult_GMP_ko.4

value: GMPs


title: MDA-mb231 WT rep1

value: wild type


title: LAMA3_KO 3

city: Cologne

first: Monique

middle: Marie

last: Aumailley

address: Joseph-Stelzmann-str. 52

country: Germany

institute: University of Cologne

description:
SN7640321_38583_458
KO3_(458)__accepted_hits.bam_gene.featureCounts.txt

data_processing:
TopHat v 1.3.3. was used to map reads
featureCounts v. 1.4.6 was used to estimate gene counts
CuffDiff v. 1.3.0 was used to calculate pairwise differential gene expression
Genome_build: GRCm38.80
Supplementary_files_format_and_content: counts_all.txt containing read counts

source_name: mouse epidermis_LAMA3_KO

extract_protocol:
RNA was prepared from keratinocytes isolated from laminin 332-depleted skin and control animals (three mice each).
Library preparation and sequencing was performed at the facilities of the Cologne Center for Genomics (University of Cologne).

tag: strain background

tag: genotype/variation

value: skin; epidermis


title: 3050_HPC_ko_IL1_H3K27ac.2


title: HepG2 WT_DEM_100_TP-8_REP-1 [HepG2_P118-C01]

description:
HepG2_P118-C01
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: cell type

tag: compound

value: Diethyl-maleate (DEM)


title: LAMA3_KO 2

description:
SN7640321_38580_455
KO2_(455)__accepted_hits.bam_gene.featureCounts.txt


title: LAMA3_KO 1

description:
SN7640321_38579_452
KO1_(452)__accepted_hits.bam_gene.featureCounts.txt


title: Control 3

description:
SN7640321_38584_459
control3_(459)__accepted_hits.bam_gene.featureCounts.txt

source_name: mouse epidermis_control


title: Control 2

description:
SN7640321_38582_457
control2_(457)__accepted_hits.bam_gene.featureCounts.txt


title: HepG2 WT_TNF_0.3_TP-8_REP-1 [HepG2_P118-B04]

description:
HepG2_P118-B04
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: concentration

value: 0.3 ng/mL

tag: time point


title: Control 1

description:
SN7640321_38581_456
control1_(456)__accepted_hits.bam_gene.featureCounts.txt


title: HepG2 WT_TUN_0.001_TP-8_REP-1 [HepG2_P118-B03]

description:
HepG2_P118-B03
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Tunicamycin (TUN)

tag: replicate


title: R2-KO-H3K27ac, 2

description:
carcinoma
KO_H3K27ac_spikeInNormalized_IgGsubstracted.bw

data_processing:
For the ChIP-seq analysis, the reads that passed the quality control were aligned with Bowtie2 (v2.3.5.1) (cite) to the GRCm38.p6 version of the mouse genome.
The total count of reads mapped to the fly genome (BDGP6.28) was used for the spike-in normalization.
Reads pairs were only considered if both were mapped correctly to the genome (SAM flag=2). Mapped reads were subject to spike-normalization, input (IgG) subtraction and binning using the deepTools API (cite). The same tool was used for generating the heatmaps.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: binned coverage in BigWig format

source_name: 4T1 cells

extract_protocol:
Cells were cross-linked in 1% formaldehyde (28908, Thermo Fisher Scientific) for 10 min at RT with intermittent agitation every 2 min. After fixation, cells were washed 3 times with ice-cold PBS and scraped in PBS with 1× protease inhibitor cocktail mix (05056489001, Sigma-Aldrich). Cells were collected by centrifugation (8 min, 1500 rpm, 4°C) and resuspended (108 cells) in 50 ml of lysis buffer (50 mM HEPES [pH 7.5], 140 mM NaCl, 0.1% Na-deoxycholate, 1 mM EDTA, 0.1% SDS, 1% NP-40 [IPEGAL], 1X protease inhibitor cocktail mix) for 30 min on ice. Nuclei were collected by brief centrifugation (2,500 rpm, 10 min, 4°C) and resuspended (nuclei/10M cells) in 300 µl of sonication buffer (10 mM Tris-HCl [pH 8.0], 100 mM NaCl, 1 mM EDTA, 1% SDS, and 1X protease inhibitor cocktail mix) and sonicated using a Diagenode bioruptor to generate 200- to 1,000-bp fragments, as determined by agarose gel electrophoresis. 30 µl magnetic beads (Protein A, 10002D, Life technologies) slurry was pre-washed three times with 1ml of PBS (1% BSA) before antibody incubation. Beads were collected and resuspended in 300ul of PBS (1% BSA). 5μl of H3K27me3 antibody (17-622; Merck-Millipore), 2 µl of H3K4me3 antibody (ab8580; Abcam) and 5 µl of H3K27ac antibody (ab4729; Abcam) were added for each ChIP and incubated for 4 hours at 4°C. Antibody coupled magnetic beads were washed three times with PBS (1% BSA), and 300 µl of sonicated cell lysates were diluted 6 fold in binding buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl [pH 8.0]). The diluted chromatin was incubated over night with antibody coupled magnetic beads at 4°C. The immunoprecipitates were washed 5 times with RIPA buffer (50 mM HEPES [pH 7.6], 1 mM EDTA, 0.7% Na-deoxycholate, 1% NP-40, 0.5M LiCl) and twice with TE buffer (10 mM Tris-HCl [pH 8.0], 0.1 mM EDTA). The DNA was recovered by reversing the cross-links in 1% SDS, 0.1 M NaHCO3 for 6 h at 65°C, purified using ChIP DNA clean and concentrator kit (Ozyme/Cell Signaling Technology) and eluted in 30 µl of elution buffer provided with the kit. Eluted DNA was quantified by using Qubit ds DNA high sensitivity kit (Life Technologies) and treated with RNase A at 37°C for 1hour. Two columns were combined to get the desired amount of DNA for library preparation (30 ng) for respective histone marks and experiments were done in duplicates for each histone mark. For the spike-in, 2 µl of spike-in-antibody (61686, Active motif) was added with the respective anti-histone antibodies during antibody incubation with the beads and 7 µl of spike-in chromatin (53083, Active motif) was added with the sonicated chromatin (300µl) for each CHIP experiment.
The libraries were prepared by MGX Sequencing platform (Montpellier, France) using TruSeq CHIP library preparation kit (Illumina) following guidelines and sequenced using HiSeq-2500 apparatus.

tag: strain

value: BALB/c

value: mammary epithelium

tag: antibody


title: HepG2 WT_CPT_1_TP-8_REP-1 [HepG2_P118-B02]

description:
HepG2_P118-B02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM

value: 8 hr


title: HepG2 WT_DEM_10_TP-8_REP-1 [HepG2_P118-B01]

description:
HepG2_P118-B01
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: R2-KO-H3K4me3, 2

description:
carcinoma
KO_H3K4me3_spikeInNormalized_IgGsubstracted.bw

tag: tissue


title: 3050_HPC_ko_IL1_H3K27ac.3

value: 8-10 weeks old


title: R1-KO-H3K4me3, 1


title: R1-KO-H3K27ac, 1


title: HepG2 WT_TNF_0.1_TP-8_REP-1 [HepG2_P118-A04]

description:
HepG2_P118-A04
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 0.1 ng/mL


title: HepG2 WT_CPT_3.3_TP-8_REP-1 [HepG2_P118-C02]

description:
HepG2_P118-C02
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: R2-KO-H3K27me3, 2

description:
carcinoma
KO_H3K27me3_spikeInNormalized_IgGsubstracted.bw


title: 3050_HPC_ko_IL1_H3K27ac.1

description:
0.5 microgram IL-1 per day  x3 days
Kmt2c f/f; Vav-Cre; IL-1 treated HPCs
HPC_ko_IL1.fc.signal.bigwig
HPC_ko_IL1.filt.narrowPeak.gz


title: HepG2 WT_TUN_0.0001_TP-8_REP-1 [HepG2_P118-A03]

description:
HepG2_P118-A03
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: R1-KO-H3K27me3, 1


title: HepG2 WT_CPT_0.1_TP-8_REP-1 [HepG2_P118-A02]

description:
HepG2_P118-A02
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: R2-KO-IgG, 2

description: carcinoma

value: IgG


title: HepG2 WT_DEM_1_TP-8_REP-1 [HepG2_P118-A01]

description:
HepG2_P118-A01
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: R1-KO-IgG, 1

description: carcinoma


title: HEK293T-SF3B1-K666T

city: Paris

first: Alexandre

last: Houy

address: 26 rue d'Ulm

institute: Institut Curie

description:
D411T39
RNA-seq data

data_processing:
Fastq files were mapped on Human genome (hg19) using STAR (v2.5.3a) with default parameters and with –quandMode GeneCounts.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab: Tab-delimited text files containing the number of reads per gene. _ReadsPerGene.out.tab format: column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse).
Supplementary_files_format_and_content: *_SJ.out.tab: Tab-delimited text files containing the number of reads per splice junction. _SJ.out.tab format: column 1: chromosome; column 2: first base of the intron (1-based); column 3: last base of the intron (1-based); column 4: strand (0: undefined, 1: +, 2: -); column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT; column 6: 0: unannotated, 1: annotated (only if splice junctions database is used); column 7: number of uniquely mapping reads crossing the junction; column 8: number of multi-mapping reads crossing the junction; column 9: maximum spliced alignment overhang.

source_name: HEK293T cells transfected with SF3B1-K666T expression vector

growth_protocol: HEK293T cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted with NucleoSpin RNA kit (Macherey-Nagel). The quantity and quality of RNA were determined by spectrophotometry (NanoDrop Technologies). Five hundred nanograms of RNA was used as a template for cDNA synthesis with the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and sequenced on an Illumina NovaSeq 6000 platform using a 100-bp paired-end sequencing strategy.

treatment_protocol: Plasmid transfections were carried out in cell lines using 1000 ng (for R625H and K666T mutants) or 2000 ng (for K700E mutant) of plasmid constructs and Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s instructions.

tag: expression vector


title: HEK293T-SF3B1-K700E

description:
D411T40
RNA-seq data

source_name: HEK293T cells transfected with SF3B1-K700E expression vector

tag: cell line


title: hepatocyte-like cell - Day 25_MEDIUM_0_TP-8_REP-C [Bas555]

description:
Bas555
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: hepatocyte-like cell - Day 25

value: Hepatocyte-like cells

value: MEDIUM


title: HEK293T-SF3B1-R625H

description:
D411T38
RNA-seq data

source_name: HEK293T cells transfected with SF3B1-R625H expression vector


title: R1-CT-H3K27ac, 2

description:
carcinoma
CT_H3K27ac_spikeInNormalized_IgGsubstracted.bw

value: wild type


title: hepatocyte-like cell - Day 25_MEDIUM_0_TP-8_REP-B [Bas548]

description:
Bas548
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HEK293T-SF3B1-WT

description:
D411T37
RNA-seq data

source_name: HEK293T cells transfected with Wildtype SF3B1 expression vector

value: Wildtype SF3B1


title: HeLa Ki-67 shRNA_rep2

description: Gene expression in Ki-67 knockdown HeLa cells, replicate 2

hyb_protocol: Cy3-labelled RNA was fragmented by denaturation at 60°C for 30 minutes, and 600 ng was hybridised at 65°C for 17h to SurePrint G3 Human GE v2 8x60K Microarrays

scan_protocol: Slides were scanned using the G2505C Scanner (Agilent) with the following parameters: dye channel G, Region Agilent HD (61 x 21.6mm), resolution 3µM, PMI gain 100%

data_processing: Scanned images were analysed with Feature Extraction 11.5.1.1, with included features uniform non-outlier, non-saturated and above background

source_name: cultured HeLa cervical cancer cells

label_protocol: Labelling was performed by linear amplification on 100 ng of total RNA, using the Low Input Quick amp one-color kit (Agilent) followed by purification using the Rneasy mini kit (Qiagen). Yield of >600ng and specific activity >15pmol Cy3/µg RNA were verified using the Nanodrop ND-1000.  Analysis of size distribution uniformity was performed using the Bioanalyser 2100.

growth_protocol: Cells were grown in 10% FBS in DMEM at 37°C in a CO2 controlled incubator

extract_protocol: RNA was extracted using the Rneasy kit (Qiagen) according to manufacturer's instructions, quantified using a Nanodrop ND-1000 and the integrity verified using a Bioanalyser 2100. The RNA integrity number was between 9.80 and 9.90 for all samples.

treatment_protocol: Cells were stably transduced with control shRNA (non-targeting from Thermo Fisher) or Ki-67 shRNA (Thermo Fisher) by lentiviral infection with shRNA-armed pGIPZ plasmids

value: HeLa

tag: lentivirus

value: shRNA Ki-67


title: HeLa Ki-67 shRNA_rep3

description: Gene expression in Ki-67 knockdown HeLa cells, replicate 3


title: R1-CT-H3K27ac, 1


title: HeLa Ki-67 shRNA_rep1

description: Gene expression in Ki-67 knockdown HeLa cells, replicate 1


title: HeLa shRNA control tumour_mouse_3

description: Gene expression in tumours derived from control knockdown HeLa cells, mouse 3, left flank

source_name: Tumour derived from HeLa cervical cancer cells grafted into athymic nude mice

value: shRNA control


title: HeLa control shRNA_rep3

description: Gene expression in control knockdown HeLa cells, replicate 3


title: hepatocyte-like cell - Day 25_MEDIUM_0_TP-8_REP-A [Bas541]

description:
Bas541
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: HeLa control shRNA_rep2

description: Gene expression in control knockdown HeLa cells, replicate 2


title: HeLa shRNA Ki-67 tumour_mouse_3

description: Gene expression in tumours derived from Ki-67 knockdown HeLa cells, mouse 3, right flank


title: HeLa shRNA control tumour_mouse_1

description: Gene expression in tumours derived from control knockdown HeLa cells, mouse 1, left flank


title: HeLa shRNA control tumour_mouse_2

description: Gene expression in tumours derived from control knockdown HeLa cells, mouse 2, left flank


title: HeLa shRNA Ki-67 tumour_mouse_1

description: Gene expression in tumours derived from Ki-67 knockdown HeLa cells, mouse 1, right flank


title: HeLa control shRNA_rep1

description: Gene expression in control knockdown HeLa cells, replicate 1


title: MLC39830

city: Hangzhou

first: Yang

last: Xia

state: Zhejiang

address: 88 Jiefang Road

department: Department of Respiratory and Critical Care Medicine

country: China

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

organism: Bronchus

source_name: Bronchial epithelial cell

extract_protocol:
Bronchial epithelial cells were obtained via bronchial brushings. RNA was extracted using a protocol of the RNeasy Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared according to the manufacturer’s instructions for the NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

tag: diagnosis

value: Non-cancer

tag: smoking status

value: Non-smoker

tag: Sex

value: Female

value: Bronchial epithelial cell


title: MLC39630

institute: Second Affiliated Hospital of Zhejiang University School

value: Cancer

value: Current smoker

value: Male


title: MLC39730

value: Former smoker


title: hepatocyte-like cell - Day 25_DMSO_0_TP-8_REP-C [Bas533]

description:
Bas533
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO

value: 8 hr


title: MLC39530


title: 2805.adult_HSC_mll3het.3

description:
Kmt2c +/- HSCs
2805.adult_HSC_mll3het.3

tag: age

value: 8 week old

tag: genotype

value: Kmt2c f/+; Vav-Cre

value: HSCs

tag: treatment


title: MLC39230


title: hepatocyte-like cell - Day 25_DMSO_0_TP-8_REP-B [Bas525]

description:
Bas525
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: cell type

value: Hepatocyte-like cells


title: R1-CT-H3K4me3, 1

description:
carcinoma
CT_H3K4me3_spikeInNormalized_IgGsubstracted.bw

value: BALB/c

value: mammary epithelium

value: wild type


title: MLC39330

value: Non-cancer


title: R2-CT-H3K27me3, 2

description:
carcinoma
CT_H3K27me3_spikeInNormalized_IgGsubstracted.bw


title: HeLa shRNA Ki-67 tumour_mouse_2

description: Gene expression in tumours derived from Ki-67 knockdown HeLa cells, mouse 2, right flank

value: HeLa

value: shRNA Ki-67


title: MLC39030

value: Bronchial epithelial cell


title: MLC38777

value: Non-smoker

value: Female


title: MLC38775

value: Male


title: hepatocyte-like cell - Day 25_DMSO_0_TP-8_REP-A [Bas517]

description:
Bas517
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: compound


title: R1-CT-H3K27me3, 1


title: hepatocyte-like cell - Day 20_TUN_100_TP-8_REP-C [Bas419]

description:
Bas419
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: hepatocyte-like cell - Day 20

value: Tunicamycin (TUN)

tag: concentration


title: R2-CT-IgG, 2

description: carcinoma

value: IgG


title: MLC38709


title: R2-CT-H3K4me3, 2


title: MLC39430

value: Cancer

value: Current smoker


title: MLC38677

value: Former smoker


title: MLC38609


title: hepatocyte-like cell - Day 20_TUN_100_TP-8_REP-B [Bas418]

description:
Bas418
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: time point

value: 8 hr


title: hepatocyte-like cell - Day 20_TUN_100_TP-8_REP-A [Bas417]

description:
Bas417
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells

tag: replicate


title: 4T1 Ki-67-KO rep3

data_processing:
Base calling was performed with Illumina RTA software. FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.93 genome using STAR_2.6.0c with default parameters.
Counts of the reads per genes were calculated in the mapping step with the STAR software using the gencode vM18 gene annotations.
Differential expression analysis were performed using an Ad hoc script using the R programming software based on the Deseq2 library
Genome_build: GRCm38.93
Supplementary_files_format_and_content: Raw counts of reads per gene

source_name: 4T1 Tumors in mice

growth_protocol: Cells were grown in Dulbecco modified Eagle medium (DMEM - high glucose, pyruvate, GlutaMAX – Gibco® Life LifeTechnologies) supplemented with 10% foetal bovine serum (SIGMA or DUTSCHER). Cells were grown under standard conditions at 37°C in humidified incubator containing 5% CO2. Nude mice were inoculated orthotopically in the mammary fat pad with 1×106  4T1 cells either wt or KO for Ki67. Three weeks later, tumors were collected and weighed. The tissue was cut into smaller pieces and stored in Trizol.

extract_protocol:
Tumors were removed from Trizol, grinded in liquid nitrogen using a mortar and pestle then put back in Trizol to complete cell lysis. Chloroform was added and after centrifugation, the upper aqueous layer was isolated, and ethanol was added to it. RNA was then bound to an RNeasy column. Contaminating genomic DNA was degraded after an on-column DNaseI treatment. After thorough washing steps, RNA was eluted, and its integrity was analyzed on Agilent 2100 bio analyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4T1 Tumors


title: MLC38477


title: MLC38577


title: MLC38575


title: hepatocyte-like cell - Day 20_TUN_10_TP-8_REP-C [Bas411]

description:
Bas411
Cell lysate
count.txt
count_log2LibSizenorm.txt

data_processing:
Library strategy: TempO-seq
Alignment of reads was done using the TempO-seqR package done by BioSpyder Technologies.
Samples were excluded for further analysis if library size was lower than 100.000 counts.
Raw counts were normalized using the DESeq2 R package (Love et al. 2014).
Normalized counts were log2 transformed.
Genome_build: BioSpyder manifest "Human Tox Panel TempO-Seq Probe Manifest 041416".
Supplementary_files_format_and_content: count.txt: Matrix table with raw counts for every probe and every sample.
Supplementary_files_format_and_content: count_log2LibSizenorm.txt: Matrix table with log2 normalized counts for every probe and every sample.

extract_protocol:
Cells were washed with PBS and lysed with 1x BNN lysis buffer (provided by BioSpyder) followed by incubation of 15 min at RT. Thereafter plate with cell lysates was sealed and stored at -80 degrees until shipment. Cell lysates were send to BioSpyder for TempO-seq targeted transcriptome analysis.
mRNA in the lysates was hybridized with detector oligo mix, and amplified using barcoded primer pairs to add a unique tag for each of the samples. The detector oligo mix targets a set of genes which were selected based on the S1500+ gene list of NIEHS (Mav et al. 2018). This list contains 2736 genes that provide maximal toxicogenomic information on chemical perturbations that reflect general cellular responses. We supplemented this list with another 245 genes that are involved in hiPSC to hepatocyte differentiation, cellular stress pathways activated in PHH and were missing in the S1500 list. Sample amplicons were pooled and purified. The libraries were sequenced using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

value: 10 uM


title: MLC38409


title: hepatocyte-like cell - Day 20_TUN_10_TP-8_REP-B [Bas410]

description:
Bas410
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 4T1 Ki-67-KO rep2


title: MLC38475


title: MLC38375


title: MLC38277


title: 4T1 Ki-67-KO rep1


title: MLC38309


title: hepatocyte-like cell - Day 20_TUN_10_TP-8_REP-A [Bas409]

description:
Bas409
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 4T1 Wild Type rep3

value: wild type


title: hepatocyte-like cell - Day 20_TUN_1_TP-8_REP-C [Bas403]

description:
Bas403
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: 4T1 Wild Type rep2


title: MLC38275

value: Non-cancer


title: MLC38175


title: R1-CT-IgG, 1

description: carcinoma

tag: strain

value: BALB/c

value: mammary epithelium


title: hepatocyte-like cell - Day 20_TUN_1_TP-8_REP-B [Bas402]

description:
Bas402
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC38109

value: Non-smoker

value: Bronchial epithelial cell


title: 4T1 Wild Type rep1


title: MLC38077

value: Male


title: hepatocyte-like cell - Day 20_TUN_1_TP-8_REP-A [Bas401]

description:
Bas401
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Tunicamycin (TUN)


title: 4T1 Ki-67-KO clone 2 rep2

data_processing:
Base calling was performed with Illumina RTA software. FastQC was used to perform quality control of the sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.93 genome using STAR_2.6.0c with default parameters.
Counts of the reads per genes were calculated in the mapping step with the STAR software using the gencode vM18 gene annotations.
Differential expression analysis were performed using an Ad hoc
Supplementary_files_format_and_content: Raw counts of reads per gene

extract_protocol:
Total RNA was extracted from about 5M cells using Trizol (Life Technologies) following manufacturer's instructions from wild type and two clones of 4T1 Ki-67 knockout cell lines. RNA integrity was analysed on Agilent 2100 bioanalyzer. For library preparation, cDNA synthesis was performed on rRNA-depleted samples using the TruSeq Stranded Total RNA Library Preparation (RS-122-2301).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: carcinoma


title: MLC38009

value: Cancer


title: MLC38075

value: Female


title: hepatocyte-like cell - Day 20_TUN_0.1_TP-8_REP-C [Bas395]

description:
Bas395
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 4T1 Ki-67-KO clone 2 rep1


title: MLC37851

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Former smoker


title: hepatocyte-like cell - Day 20_TUN_0.1_TP-8_REP-B [Bas394]

description:
Bas394
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC37651


title: MLC37751


title: MLC37551


title: MLC37451

value: Current smoker


title: 4T1 Ki-67-KO clone 1 rep2


title: MLC38177


title: 4T1 Ki-67-KO clone 1 rep1


title: MLC37151


title: hepatocyte-like cell - Day 20_TUN_0.01_TP-8_REP-C [Bas387]

description:
Bas387
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: 4T1 WT rep2


title: hepatocyte-like cell - Day 20_TUN_0.01_TP-8_REP-B [Bas386]

description:
Bas386
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC37051


title: is_133_029

city: Uppsala

first: Peter

last: Seiron

address: Rudbecklaboratoriet

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
normalized_counts
Raw counts at GEO: GSE162689

data_processing:
The raw counts were generated at a separate facility using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.  The produced reads were aligned to hg19 AmpliSeq Transcriptome ERCC v1. All further analysis was done using the raw counts estimated after mapping. Raw sequence data is not available.
Normalization of the raw count data was performed using the edgeR workflow(calcNormFactors and cpm(, method="TMM", log=FALSE) after filtering out lowly expressed genes with the filterByExpr command using default settings.
Raw counts from 5 samples (#31-35) were used from a previously uploaded project collected in a similar fashion. All samples were normalized together and corrected for batch effect.
ip_293_25 was excluded due to not passing QC analysis after sequencing. Ip_293_24 was excluded as an outlier after visual inspection of a principal component analysis.
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1
Supplementary_files_format_and_content: Raw_counts.xlsx, normalized_counts.xlsx

source_name: human pancreatic islet tissue

extract_protocol:
Pancreases from heart-beating organ donors were used. Biopsies were immediately snap-frozen in liquid nitrogen and subsequently stored at -80 °C. The frozen biopsies  were sectione, thawed and dehydrated. Laser Capture Microdissection (LCM) was used to extract islets, >20 islet sections per sample. Samples were subsequently incubated in 20 µl of RLT Plus buffer with 1% beta-Mercaptoethanol in a heating block, lysing the tissue. total RNA was extracted with the RNeasy Plus Micro kit.
Libraries were constructed using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit. total RNA seq was then done using the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.

value: Islet tissue

tag: gender

value: M


title: 4T1 WT rep1

tag: tissue

value: wild type


title: MLC35822

value: Non-cancer


title: hepatocyte-like cell - Day 20_TUN_0.01_TP-8_REP-A [Bas385]

description:
Bas385
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: is_133_026


title: hepatocyte-like cell - Day 20_TUN_0.001_TP-8_REP-C [Bas379]

description:
Bas379
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC35722


title: is_133_013

value: F


title: hepatocyte-like cell - Day 20_TUN_0.1_TP-8_REP-A [Bas393]

description:
Bas393
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hepatocyte-like cell - Day 20_TUN_0.001_TP-8_REP-B [Bas378]

description:
Bas378
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: is_133_009


title: hepatocyte-like cell - Day 20_TUN_0.001_TP-8_REP-A [Bas377]

description:
Bas377
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: is_133_005


title: hepatocyte-like cell - Day 20_TNF_50_TP-8_REP-C [Bas465]

description:
Bas465
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: ip_293_30

description:
normalized_counts
raw_counts


title: MLC35022

value: Bronchial epithelial cell


title: MLC35522

value: Non-smoker


title: MLC37351

value: Male


title: NIH/3T3 Ki-67-KO clone 1 rep2

source_name: NIH/3T3 cells

growth_protocol: cells were grown in Dulbecco modified Eagle medium (DMEM - high glucose, pyruvate, GlutaMAX – Gibco® Life LifeTechnologies) supplemented with 10% foetal bovine serum (SIGMA or DUTSCHER). Cells were grown under standard conditions at 37°C in humidified incubator containing 5% CO2.

value: Swiss albino mouse

value: fibroblasts

value: embryo


title: MLC35222

value: Cancer

value: Former smoker


title: NIH/3T3 WT rep2


title: hepatocyte-like cell - Day 20_TNF_50_TP-8_REP-B [Bas464]

description:
Bas464
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: NIH/3T3 WT rep1


title: hepatocyte-like cell - Day 20_TNF_50_TP-8_REP-A [Bas463]

description:
Bas463
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: MLC33798


title: NIH/3T3 Ki-67-KO clone 2 rep2


title: MLC33698

value: Female


title: ip_293_29

description:
normalized_counts
raw_counts

value: Islet tissue

value: M


title: 2921.input.2

description: input chromatin

source_name: input chromatin

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

tag: chip target

value: none (input)

value: 8 weeks old


title: NIH/3T3 Ki-67-KO clone 2 rep1


title: hepatocyte-like cell - Day 20_TNF_10_TP-8_REP-C [Bas458]

description:
Bas458
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 10 ng/mL


title: ip_293_27

description:
normalized_counts
raw_counts

value: F


title: MLC33673

value: Current smoker

value: Bronchial epithelial cell


title: hepatocyte-like cell - Day 20_TNF_10_TP-8_REP-B [Bas457]

description:
Bas457
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 2921.input.1

description: input chromatin


title: NIH/3T3 Ki-67-KO clone 1 rep1

value: Swiss albino mouse


title: ip_293_26

description:
normalized_counts
raw_counts


title: adult_HSC_wt_h3k4me1.3

description:
wild type HSCs
adult_HSC_wt_h3k4me1.fc.signal.bigwig
adult_HSC_wt_h3k4me1.filt.narrowPeak.gz

source_name: wild type HSCs

value: HSCs

tag: chip antibody

value: wild type HSCs


title: MLC33598

value: Non-cancer

value: Non-smoker

value: Male


title: ip_293_25

description:
Excluded (Did not pass QC)
normalized_counts
raw_counts


title: adult_HSC_wt_h3k4me1.2


title: hepatocyte-like cell - Day 20_TNF_10_TP-8_REP-A [Bas456]

description:
Bas456
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells

value: 8 hr


title: hepatocyte-like cell - Day 20_TNF_7.5_TP-8_REP-B [Bas450]

description:
Bas450
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: ip_293_28

description:
normalized_counts
raw_counts

value: Islet tissue

value: M


title: adult_HSC_wt_h3k4me1.1

value: 8 weeks old


title: ip_293_24

description:
Excluded (Outlier in PCA)
normalized_counts
raw_counts


title: MLC33573

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Former smoker


title: MLC33498

value: Cancer


title: MLC33773


title: ip_293_23

description:
normalized_counts
raw_counts