title: 020416-59_56458_TRCN0000233396

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000233396 targeting entrez GeneID 56458


title: 020416-52_60611_TRCN0000084290

status: Public on Feb 03 2025

type: SRA

city: New York

first: Mariano

middle: Javier

last: Alvarez

state: NY

address: 1130 St. Nicholas ave.

department: Systems Biology

country: USA

institute: Columbia University

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000084290 targeting entrez GeneID 60611

library_source: transcriptomic

data_processing:
Sequencing data was demultiplexed, debarcoded, and mapped to the mouse genome GRCm38 (mm10) with the STAR aligner (PMID: 23104886) and counted using ENSEMBL gene annotation.
Gene identifiers were transformed to Entrez GeneIDs.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Raw-counts per known gene using EntrezID gene identifiers

molecule: total RNA

organism: Mus musculus

source_name: Epiblast Stem Cell

growth_protocol: Cells are cultured in Matrigel coated plates with filtered MEF conditioned media (EpiSC basal media harvested after culturing with inactivated MEFs for 24h) supplemented with 12.5ng/ml bFGF and 10ng/ml Activin (CMAF).

extract_protocol:
72h after transduction the cells were lysed with Trizol (ThermoFisher, 15596018).
Sample processing and library preparation were performed as described for PLATE-Seq (PMID 28740083).

treatment_protocol: shRNA hairpins targeting to candidate pluripotency regulators were selected and ordered from MISSION shRNA Lentiviral library. All the shRNA lentivirus used for initial screen are produced by Sigma, and tested for high titer. EpiSCs were passaged onto matrigel-coated 96-well plates (Greiner 655090) at a density of 3,000 cells per well, with 100ul CMAF medium supplemented with 10uM Y27632 added in each well. 12 hours after passaging, when cells re-attached to the plate, 50ul of the culturing medium is replaced with 50ul lentivirus supplemented with 8ug/ml Polybrene. 24 hrs after lentivirus transduction, culturing medium is replaced with 100ul CMAF + 2ug/ml Puromycin (Sigma, P7255) for selecting stably integrated cells. Concentration of Puromycin is increased to 4ug/ml by replacing the medium again at 48 h after transduction.

tag: cell type

value: EpiSC

tag: strain

tag: shRNA clone

tag: shRNA geneid


title: 020416-60_74164_TRCN0000304625

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000304625 targeting entrez GeneID 74164


title: 020416-55_83395_TRCN0000082179

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000082179 targeting entrez GeneID 83395


title: 020416-54_243983_TRCN0000416358

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000416358 targeting entrez GeneID 243983


title: 020416-53_66863_TRCN0000287309

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000287309 targeting entrez GeneID 66863


title: 020416-50_22433_TRCN0000232021

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000232021 targeting entrez GeneID 22433


title: 020416-48_18424_TRCN0000438502

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000438502 targeting entrez GeneID 18424


title: 020416-46_243983_TRCN0000081753

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000081753 targeting entrez GeneID 243983


title: 020416-43_56458_TRCN0000054878

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000054878 targeting entrez GeneID 56458


title: 020416-51_56458_TRCN0000233397

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000233397 targeting entrez GeneID 56458


title: 020416-38_68310_TRCN0000306161

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000306161 targeting entrez GeneID 68310


title: 020416-44_60611_TRCN0000084289

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000084289 targeting entrez GeneID 60611


title: 020416-40_102162_TRCN0000287472

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000287472 targeting entrez GeneID 102162


title: 020416-34_12913_TRCN0000085574

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000085574 targeting entrez GeneID 12913


title: 020416-47_77286_TRCN0000123965

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000123965 targeting entrez GeneID 77286


title: 020416-32_102162_TRCN0000287552

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000287552 targeting entrez GeneID 102162


title: 020416-35_55927_TRCN0000304636

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000304636 targeting entrez GeneID 55927


title: 020416-42_12913_TRCN0000085575

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000085575 targeting entrez GeneID 12913


title: 020416-31_77110_TRCN0000246902

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000246902 targeting entrez GeneID 77110


title: 020416-27_55927_TRCN0000311064

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000311064 targeting entrez GeneID 55927


title: 020416-25_22680_TRCN0000225904

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000225904 targeting entrez GeneID 22680


title: 020416-24_102162_TRCN0000294963

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000294963 targeting entrez GeneID 102162


title: 020416-26_12913_TRCN0000085573

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000085573 targeting entrez GeneID 12913


title: 020416-23_77110_TRCN0000246903

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000246903 targeting entrez GeneID 77110


title: 020416-22_68310_TRCN0000113550

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000113550 targeting entrez GeneID 68310


title: 020416-20_58208_TRCN0000238422

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000238422 targeting entrez GeneID 58208


title: 020416-17_22680_TRCN0000225903

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000225903 targeting entrez GeneID 22680


title: 020416-16_142682_TRCN0000313590

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000313590 targeting entrez GeneID 142682


title: 020416-14_52231_TRCN0000190165

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000190165 targeting entrez GeneID 52231


title: 020416-19_55927_TRCN0000085783

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000085783 targeting entrez GeneID 55927


title: 020416-12_58208_TRCN0000096234

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000096234 targeting entrez GeneID 58208


title: 020416-9_22680_TRCN0000082273

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000082273 targeting entrez GeneID 22680


title: 020416-6_13813_TRCN0000082255

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000082255 targeting entrez GeneID 13813


title: 032916-95_NT_NT

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of NT targeting entrez GeneID NT

value: NT


title: 020416-36_60611_TRCN0000084288

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000084288 targeting entrez GeneID 60611


title: 020416-4_54139_TRCN0000321594

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000321594 targeting entrez GeneID 54139


title: 032916-93_NT_Shc002

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of Shc002 targeting entrez GeneID NT


title: 032916-90_NT_NT


title: 020416-11_50524_TRCN0000218200

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000218200 targeting entrez GeneID 50524


title: 020416-15_77110_TRCN0000191795

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000191795 targeting entrez GeneID 77110


title: 032916-92_NT_NT


title: 032916-89_NT_NT


title: 032916-86_18021_TRCN0000308439

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000308439 targeting entrez GeneID 18021


title: 032916-91_NT_NT


title: 032916-94_NT_Shc202

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of Shc202 targeting entrez GeneID NT


title: 032916-88_NT_NT


title: 032916-85_16842_TRCN0000360344

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000360344 targeting entrez GeneID 16842


title: 032916-83_20183_TRCN0000445690

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000445690 targeting entrez GeneID 20183


title: 032916-80_NT_NT


title: 032916-78_18021_TRCN0000305026

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000305026 targeting entrez GeneID 18021


title: 032916-77_16842_TRCN0000218932

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000218932 targeting entrez GeneID 16842


title: 032916-74_17129_TRCN0000436791

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000436791 targeting entrez GeneID 17129


title: 032916-67_20183_TRCN0000027052

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000027052 targeting entrez GeneID 20183


title: 032916-69_16842_TRCN0000225790

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000225790 targeting entrez GeneID 16842


title: 032916-65_12014_TRCN0000432631

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000432631 targeting entrez GeneID 12014


title: 032916-63_20893_TRCN0000226075

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000226075 targeting entrez GeneID 20893


title: 032916-81_12705_TRCN0000095234

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000095234 targeting entrez GeneID 12705


title: 032916-60_13017_TRCN0000295115

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000295115 targeting entrez GeneID 13017


title: 032916-57_12014_TRCN0000084329

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000084329 targeting entrez GeneID 12014


title: 032916-55_20893_TRCN0000226076

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000226076 targeting entrez GeneID 20893


title: 032916-44_11568_TRCN0000287914

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000287914 targeting entrez GeneID 11568


title: 032916-48_22608_TRCN0000333886

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000333886 targeting entrez GeneID 22608


title: 032916-49_239102_TRCN0000234213

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000234213 targeting entrez GeneID 239102


title: 032916-56_22608_TRCN0000334022

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000334022 targeting entrez GeneID 22608


title: 032916-46_17684_TRCN0000257264

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000257264 targeting entrez GeneID 17684


title: 032916-39_18813_TRCN0000236755

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000236755 targeting entrez GeneID 18813


title: 032916-52_13017_TRCN0000109335

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000109335 targeting entrez GeneID 13017


title: 032916-41_239102_TRCN0000234214

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000234214 targeting entrez GeneID 239102


title: 032916-38_17684_TRCN0000234123

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000234123 targeting entrez GeneID 17684


title: 032916-68_13017_TRCN0000295114

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000295114 targeting entrez GeneID 13017


title: 032916-40_22608_TRCN0000333885

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000333885 targeting entrez GeneID 22608


title: 032916-82_17129_TRCN0000443789

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000443789 targeting entrez GeneID 17129


title: 032916-36_11568_TRCN0000307526

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000307526 targeting entrez GeneID 11568


title: 032916-75_20183_TRCN0000438766

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000438766 targeting entrez GeneID 20183


title: 032916-32_21849_TRCN0000071366

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000071366 targeting entrez GeneID 21849


title: 032916-31_18813_TRCN0000236756

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000236756 targeting entrez GeneID 18813


title: 032916-30_17684_TRCN0000055104

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000055104 targeting entrez GeneID 17684


title: 032916-73_12014_TRCN0000436191

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000436191 targeting entrez GeneID 12014


title: 032916-33_68750_TRCN0000376250

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000376250 targeting entrez GeneID 68750


title: 032916-23_18813_TRCN0000236753

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000236753 targeting entrez GeneID 18813


title: 032916-22_17354_TRCN0000072137

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000072137 targeting entrez GeneID 17354


title: 032916-47_20893_TRCN0000226078

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000226078 targeting entrez GeneID 20893


title: 032916-19_18612_TRCN0000055129

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000055129 targeting entrez GeneID 18612


title: 032916-14_17354_TRCN0000072136

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000072136 targeting entrez GeneID 17354


title: 032916-15_18021_TRCN0000308369

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000308369 targeting entrez GeneID 18021


title: 032916-12_22772_TRCN0000095250

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000095250 targeting entrez GeneID 22772


title: 032916-35_18612_TRCN0000055130

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000055130 targeting entrez GeneID 18612


title: EpiSC-5_BMP4_72H-6

description: Mouse EpiSC-5 cells, perturbed for 72H with BMP4

data_processing:
Sequencing data was mapped to the mouse genome MGSCv37 with TopHat v1.3.3 (PMID: 19289445). Reads mapping to known genes, based on Entrez gene identifiers, were then counted using the GenomicFeatures R-system package available from Bioconductor (PMID: 15461798).
We computed a size factor for each sample using the median log-ratio method. Expression data were then normalized by equivariance transformation, based on the negative binomial distribution with the DESeq R-system package (PMID: 20979621).
Assembly: mm9 (MGSCv37)
Supplementary files format and content: Raw-counts per known gene using EntrezID gene identifiers

extract_protocol:
Cells grown on 6-well plates are lysed with Trizol (ThermoFisher, 15596018), and transferred into Eppendorf tubes for short-term storage at -80 degree. 600ul of cell lysate is used for total RNA extraction using column-based kit (Clontech, 740955).
mRNA is enriched by poly-A pull down, and library is synthesized using Illumina TruSeq RNA prep kit (Illumina, RS-122-2001). Libraries are pooled and sequenced using Illumina HiSeq2500 or 4000 platform, yielding approximately 30 million single-ended reads per sample.

treatment_protocol: EpiSC were perturbed with different differentiation morphogens or control culture conditions and expression profiles were obtained at the indicated time points. Conditions for five treatments are as follows: For Retinoic acid treatment, MEF conditioned media without supplementation of bFGF or Activin A (CM) + 5uM RA are used to culture EpiSC for 72h; For BMP4 treatment, CM + 100ng/ml BMP4 are used to culture EpiSC for 72h; For SB431542 treatment, 10nM SB431542 is added to the culture media containing DMEM/F12 + 1 X Glutamax + 1 X Insulin-Transferrin-Selenium + 1 X NEAA + 2% B27 (Gibco 17504-044) + 90uM 2-Merceptoethanol and EpiSCs are cultured for 72h. For Endoderm differentiation, EpiSCs are firstly cultured in RPMI (Gibco 21870-076) + Glutamax + Activin A (100ng/ml) + Wnt3a (25ng/ml) + 0.075 mM EGTA for 24h, and then switched to RPMI + Glutamax + Activin A (100ng/ml) + 0.2% FBS to culture for another 48h. For mesoderm differentiation, protocol is adapted from PMID: 20967028. In brief, EpiSCs are cultured in basal media + 25 ng/ml Wnt3a + 50 ng/ml of Activin A on Day 1, basal media + 25 ng/ml Wnt3a + 25ng/ml Activin A + 20 ng/ml FGF2 on Day 2, and basal media + 25 ng/ml Wnt3a + 10ng/ml Activin A + 20 ng/ml FGF2 + 40ng/ml BMP4 on Day 3.

tag: treatment

tag: time


title: 032916-10_12705_TRCN0000095235

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000095235 targeting entrez GeneID 12705


title: EpiSC-5_BMP4_72H-5


title: 032916-17_68750_TRCN0000367160

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000367160 targeting entrez GeneID 68750


title: EpiSC-5_BMP4_72H-4


title: 032916-11_17129_TRCN0000068271

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000068271 targeting entrez GeneID 17129


title: EpiSC-5_BMP4_72H-1


title: EpiSC-5_BMP4_72H-3


title: EpiSC-5_BMP4_6H-5

description: Mouse EpiSC-5 cells, perturbed for 6H with BMP4


title: EpiSC-5_BMP4_6H-6


title: EpiSC-5_BMP4_6H-2


title: 032916-28_11568_TRCN0000031351

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000031351 targeting entrez GeneID 11568


title: EpiSC-5_BMP4_6H-4


title: 032916-27_18612_TRCN0000295466

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000295466 targeting entrez GeneID 18612


title: EpiSC-5_BMP4_48H-2

description: Mouse EpiSC-5 cells, perturbed for 48H with BMP4


title: 032916-20_22772_TRCN0000095249

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000095249 targeting entrez GeneID 22772


title: 032916-25_68750_TRCN0000376248

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000376248 targeting entrez GeneID 68750


title: EpiSC-5_BMP4_48H-1


title: 032916-18_12705_TRCN0000095237

description: Mouse EpiSC-5 cells, 72h after lentivirus-mediated transduccion of TRCN0000095237 targeting entrez GeneID 12705


title: EpiSC-5_BMP4_36H-1

description: Mouse EpiSC-5 cells, perturbed for 36H with BMP4


title: EpiSC-5_BMP4_24H-2

description: Mouse EpiSC-5 cells, perturbed for 24H with BMP4


title: EpiSC-5_BMP4_24H-3


title: EpiSC-5_BMP4_24H-1


title: EpiSC-5_BMP4_18H-1

description: Mouse EpiSC-5 cells, perturbed for 18H with BMP4


title: EpiSC-5_BMP4_12H-2

description: Mouse EpiSC-5 cells, perturbed for 12H with BMP4


title: EpiSC-5_BMP4_12H-1


title: EpiSC-5_BMP4_18H-2


title: EpiSC-5_BMP4_6H-3


title: EpiSC-5_CMAF_0H-4

description: Mouse EpiSC-5 cells, perturbed for 0H with CMAF

value: CMAF


title: EpiSC-5_BMP4_24H-5


title: EpiSC-5_CMAF_0H-5


title: EpiSC-5_CMAF_0H-6


title: EpiSC-5_Retinoic acid_72H-6

description: Mouse EpiSC-5 cells, perturbed for 72H with Retinoic acid

value: Retinoic acid


title: EpiSC-5_CMAF_0H-1


title: EpiSC-5_BMP4_3H-2

description: Mouse EpiSC-5 cells, perturbed for 3H with BMP4


title: EpiSC-5_BMP4_72H-2

description: Mouse EpiSC-5 cells, perturbed for 72H with BMP4


title: EpiSC-5_Retinoic acid_72H-3


title: EpiSC-5_Retinoic acid_6H-6

description: Mouse EpiSC-5 cells, perturbed for 6H with Retinoic acid


title: EpiSC-5_BMP4_3H-1


title: EpiSC-5_Retinoic acid_72H-5


title: EpiSC-5_Retinoic acid_72H-1


title: EpiSC-5_Retinoic acid_6H-5


title: EpiSC-5_Retinoic acid_72H-2


title: EpiSC-5_CMAF_0H-2


title: EpiSC-5_Retinoic acid_72H-4


title: EpiSC-5_Retinoic acid_6H-4


title: EpiSC-5_BMP4_24H-6


title: EpiSC-5_Retinoic acid_6H-1


title: EpiSC-5_Retinoic acid_48H-2

description: Mouse EpiSC-5 cells, perturbed for 48H with Retinoic acid


title: EpiSC-5_Retinoic acid_6H-2


title: EpiSC-5_BMP4_6H-1

description: Mouse EpiSC-5 cells, perturbed for 6H with BMP4


title: EpiSC-5_Retinoic acid_6H-3


title: EpiSC-5_CMAF_0H-3


title: EpiSC-5_Retinoic acid_3H-1

description: Mouse EpiSC-5 cells, perturbed for 3H with Retinoic acid


title: EpiSC-5_Retinoic acid_48H-1


title: EpiSC-5_BMP4_24H-4


title: EpiSC-5_Retinoic acid_24H-6

description: Mouse EpiSC-5 cells, perturbed for 24H with Retinoic acid


title: EpiSC-5_Retinoic acid_24H-5


title: EpiSC-5_Retinoic acid_24H-4


title: EpiSC-5_Retinoic acid_18H-2

description: Mouse EpiSC-5 cells, perturbed for 18H with Retinoic acid


title: EpiSC-5_Retinoic acid_24H-3


title: EpiSC-5_SB431542_72H-4

description: Mouse EpiSC-5 cells, perturbed for 72H with SB431542


title: EpiSC-5_Retinoic acid_18H-1


title: EpiSC-5_SB431542_72H-2


title: EpiSC-5_Retinoic acid_12H-2

description: Mouse EpiSC-5 cells, perturbed for 12H with Retinoic acid


title: EpiSC-5_SB431542_72H-3


title: EpiSC-5_SB431542_72H-6


title: EpiSC-5_SB431542_72H-1


title: EpiSC-5_Retinoic acid_24H-2


title: EpiSC-5_Retinoic acid_36H-1

description: Mouse EpiSC-5 cells, perturbed for 36H with Retinoic acid


title: EpiSC-5_Retinoic acid_24H-1


title: EpiSC-5_SB431542_72H-5


title: EpiSC-5_Retinoic acid_12H-1


title: EpiSC-5_SB431542_6H-4

description: Mouse EpiSC-5 cells, perturbed for 6H with SB431542


title: EpiSC-5_SB431542_6H-6


title: EpiSC-5_SB431542_6H-1


title: EpiSC-5_SB431542_48H-2

description: Mouse EpiSC-5 cells, perturbed for 48H with SB431542


title: EpiSC-5_SB431542_6H-5


title: EpiSC-5_Retinoic acid_36H-2


title: EpiSC-5_SB431542_6H-3


title: EpiSC-5_SB431542_3H-2

description: Mouse EpiSC-5 cells, perturbed for 3H with SB431542


title: EpiSC-5_SB431542_3H-1


title: EpiSC-5_SB431542_48H-1


title: EpiSC-5_SB431542_36H-1

description: Mouse EpiSC-5 cells, perturbed for 36H with SB431542


title: EpiSC-5_SB431542_6H-2


title: EpiSC-5_SB431542_36H-2


title: EpiSC-5_SB431542_24H-6

description: Mouse EpiSC-5 cells, perturbed for 24H with SB431542


title: EpiSC-5_SB431542_24H-5


title: EpiSC-5_WAFB_72H-6

description: Mouse EpiSC-5 cells, perturbed for 72H with WAFB

value: WAFB


title: EpiSC-5_SB431542_18H-2

description: Mouse EpiSC-5 cells, perturbed for 18H with SB431542


title: EpiSC-5_WAFB_6H-6

description: Mouse EpiSC-5 cells, perturbed for 6H with WAFB


title: EpiSC-5_SB431542_24H-3


title: EpiSC-5_SB431542_24H-4


title: EpiSC-5_BMP4_36H-2

description: Mouse EpiSC-5 cells, perturbed for 36H with BMP4


title: EpiSC-5_WAFB_72H-4


title: EpiSC-5_SB431542_24H-1


title: EpiSC-5_SB431542_12H-2

description: Mouse EpiSC-5 cells, perturbed for 12H with SB431542


title: EpiSC-5_WAFB_6H-3


title: EpiSC-5_SB431542_18H-1


title: EpiSC-5_SB431542_24H-2


title: EpiSC-5_WAFB_48H-1

description: Mouse EpiSC-5 cells, perturbed for 48H with WAFB


title: EpiSC-5_SB431542_12H-1


title: EpiSC-5_WAFB_72H-5


title: EpiSC-5_WAFB_3H-2

description: Mouse EpiSC-5 cells, perturbed for 3H with WAFB


title: EpiSC-5_WAFB_24H-6

description: Mouse EpiSC-5 cells, perturbed for 24H with WAFB


title: EpiSC-5_WAFB_36H-2

description: Mouse EpiSC-5 cells, perturbed for 36H with WAFB


title: EpiSC-5_WAFB_3H-1


title: EpiSC-5_WAFB_72H-1


title: EpiSC-5_WAFB_6H-5


title: EpiSC-5_WAFB_6H-4


title: EpiSC-5_WAFB_6H-1


title: EpiSC-5_WAFB_6H-2


title: EpiSC-5_WAFB_24H-4


title: EpiSC-5_WAFB_24H-1


title: EpiSC-5_WAFB_48H-2


title: EpiSC-5_WAFB_72H-3


title: EpiSC-5_WAFB_12H-2

description: Mouse EpiSC-5 cells, perturbed for 12H with WAFB


title: EpiSC-5_WAFB_18H-1

description: Mouse EpiSC-5 cells, perturbed for 18H with WAFB


title: EpiSC-5_WAFB_24H-3


title: EpiSC-5_WAFB_18H-2


title: EpiSC-5_WAFB_24H-2


title: EpiSC-5_WAFB_12H-1


title: EpiSC-5_WAFB_72H-2


title: EpiSC-5_WA_72H-2

description: Mouse EpiSC-5 cells, perturbed for 72H with WA

value: WA


title: EpiSC-5_WA_72H-1


title: EpiSC-5_WA_72H-3


title: EpiSC-5_WAFB_36H-1


title: EpiSC-5_WA_6H-5

description: Mouse EpiSC-5 cells, perturbed for 6H with WA


title: EpiSC-5_WA_72H-5


title: EpiSC-5_WA_6H-4


title: EpiSC-5_WA_72H-4


title: EpiSC-5_WAFB_24H-5


title: EpiSC-5_WA_6H-3


title: EpiSC-5_WA_72H-6


title: EpiSC-5_WA_6H-6


title: EpiSC-5_WA_6H-2


title: EpiSC-5_WA_48H-1

description: Mouse EpiSC-5 cells, perturbed for 48H with WA


title: EpiSC-5_WA_3H-2

description: Mouse EpiSC-5 cells, perturbed for 3H with WA


title: EpiSC-5_WA_6H-1


title: EpiSC-5_WA_36H-2

description: Mouse EpiSC-5 cells, perturbed for 36H with WA


title: EpiSC-5_WA_3H-1


title: EpiSC-5_WA_36H-1


title: EpiSC-5_WA_24H-3

description: Mouse EpiSC-5 cells, perturbed for 24H with WA


title: EpiSC-5_WA_24H-6


title: EpiSC-5_WA_24H-4


title: EpiSC-5_WA_18H-2

description: Mouse EpiSC-5 cells, perturbed for 18H with WA


title: EpiSC-5_WA_24H-1


title: EpiSC-5_WA_24H-2


title: EpiSC-5_WA_18H-1


title: EpiSC-5_WA_12H-1

description: Mouse EpiSC-5 cells, perturbed for 12H with WA


title: EpiSC-5_WA_24H-5


title: aD_4OHT

city: Shenzhen

first: Jun

last: Zhang

state: Guangdong Province

address: Xueyuan Avenue

department: School of Medicine

country: China

institute: Shenzhen University

description: Library name: aD_4OHT

library_source: genomic

data_processing:
The raw reads are processed using Fastp (v 0.23.4) to eliminate adaptor and sequences of low quality.
Thereafter, bowtie2 (v 2.5.4) is applied for alignment to the hg38 human genome reference, employing the parameters "--very-sensitive --no-mixed --no-discordant."
Samtools facilitates the conversion of sam files to bam format, enforcing a filter criterion of a minimum mapping quality (MAPQ) score of 10.
Duplicate reads are subsequently removed using the Picard tool.
Assembly: hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were routinely maintained in high glucose DMEM medium supplied with 10%FBS and 1% P/S in 37 degree incubator, and after 90% confluence, the cells were treated and harvested for ChIP assay.

extract_protocol:
Lysates were clarified from sonicated nuclei and pan-Kac-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD501-01). After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 500 nM 4-OHT treatment for 4 hours

tag: cell line

value: human osteosarcoma cell


title: R_Pi

description: Library name: R_Pi

data_processing:
The raw reads are processed using Fastp (v 0.23.4) to eliminate adaptor and sequences of low quality.
Thereafter, bowtie2 (v 2.5.4) is applied for alignment to the hg38 human genome reference, employing the parameters "--very-sensitive --no-mixed --no-discordant."
Samtools facilitates the conversion of sam files to bam format, enforcing a filter criterion of a minimum mapping quality (MAPQ) score of 10.
Duplicate reads are subsequently removed using the Picard tool.
Assembly: hg38
Supplementary files format and content: bw

value: No Treatment


title: NC_4OHT

description: Library name: NC_4OHT


title: SI_4OHT

description: Library name: SI_4OHT


title: CT_4OHT

description: Library name: CT_4OHT


title: aD

description: Library name: aD


title: ac_4OHT

description: Library name: ac_4OHT


title: CT

description: Library name: CT


title: A

description: Library name: A


title: ac

description: Library name: ac


title: R_Pi_4OHT

description: Library name: R_Pi_4OHT


title: A_4OHT

description: Library name: A_4OHT


title: ND_4OHT

description: Library name: ND_4OHT


title: ND

description: Library name: ND


title: S1, scRNAseq

city: Genoa

first: Davide

last: Cangelosi

address: Via 5 maggio,5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: Chromium Controller (10x Genomics)

library_source: transcriptomic single cell

data_processing:
Raw sequencing data (FASTQ files) were processed by Cell Ranger 88 version 7.2.0 to obtain feature-barcode matrices. GRCh38-2020-A was used as reference transcriptome for aligning sequencing reads in FASTQ files. Estimated Number of Cells, Mean Reads per Cell, and Median Genes per Cell from Cell Ranger count pipeline report were used as metrics to evaluate data quality control. scRNAseq data files were imported, normalized, scaled and clustered using Seurat R package 89 version 5.1.0. Cell heterogeneity was visualized using uniform manifold approximation and projection (UMAP).
The function ‘FindAllMarkers’ with parameters “only.pos = TRUE, min.pct = 0.25” in the R package Seuratwas used to identify marker genes. Top 10 marker genes of each cell cluster were selected and visualized by the function ‘DoHeatmap’.
Cell identity annotation was performed using ScType method. ‘Brain’ cell markers were used for cell annotation. ScType score lower than a quarter of the number of cells in a cluster or a negative ScType score were considered low-confidence cell type annotations and were assigned to “unknown” cell types.
To gain insight into the mechanisms driving cellular heterogeneity, the activity of the gene regulatory networks in each cell was evaluated using single-cell regulatory network inference and clustering (SCENIC). Nextflow pipeline using Docker profile with parameters “TFs: hs_hgnc_curated_tfs.txt, motifs: motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl, db: *feather, hr_min_genes: 1”. genome-ranking.feather and hg38\_refseq-r80_10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather were used as precomputed databases for co-expression modules and motif enrichments. The function ‘calcRSS’ was used to calculate the regulon specificity score. The function ‘binarizeAUC’ was used to binarize regulon activity. ComplexHeatmap R package was used to visualize binarized regulon activities.
Assembly: hg38
Supplementary files format and content: Compressed tab-separated values file and matrix in gzip format

source_name: iPSC lines

extract_protocol:
iPSC-derived NPCs or neurons were washed in PBS and detached as single cells by 5 minutes incubation with accutase. Single cells were suspended in PBS w/o Ca2+/Mg2+ containing 0.04% BSA, filtered using a 70 mm cell strainer Flowmi™ (734-2709, VWR), and counted with LUNA-II Automated Cell Counter (Logos Biosystems).
Cell suspensions were loaded onto the Chromium Next GEM Chip G (10x Genomics) and run on the Chromium Controller (10x Genomics) to generate single-cell gel bead emulsion, according to the manufacturer’s protocol (User Guide - Rev E). The Chromium Next GEM Single Cell 3’ Kit v3.1 and the Chromium™ Next GEM Chip G Single Cell Kit (10x Genomics) were used to generate cDNA and the final libraries. The cDNA quality was assessed using high-sensitivity D5000 screen tape on TapeStation system 4150 (Agilent Technologies). Quality of libraries was assessed by using high sensitivity D1000 screen tape (Agilent Technologies). Finally, the libraries were sequenced on Novaseq6000 sequencer (Illumina) according to manufacturer specifications.

value: iPSC lines

value: Isogenic mutated iPSC-derived neuronal cell lines

tag: age

value: neonatal

tag: Sex

value: male

tag: ethnicity

value: African American

tag: clinical information

value: normal/healthy

tag: genetic modification


title: NC

description: Library name: NC


title: S2, scRNAseq

description: Chromium Controller (10x Genomics)

value: Isogenic control iPSC-derived neuronal cell lines

value: Control


title: S3, scRNAseq

description: Chromium Controller (10x Genomics)

value: Isogenic control iPSC-derived neuroprogenitor cell lines


title: Twin_set_6, subject 4012, T3 group, Day7

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

data_processing:
FASTQ files were pre-filtered to remove low-quality bases, TruSeq dual-index adapter sequences, and unpaired reads using Trimmomatic
Transcript-level mapping and gene-level quantification were conducted in STAR aligner (version 2.7.0a) using human genome and transcriptome reference sequences from Gencode.
Gene-level quantification and annotation were done using Tximeta Bioconductor utility
Gene count matrices were normalized, and differential expression analyses were done in DESeq2  Bioconductor utility.
Assembly: Human Genome Build GRCh38.p13 (Gencode 43)
Supplementary files format and content: tab-delimited text file for each sample generated using STAR aligner (column 1: gene Ensembl ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA; column 4: counts for the 2nd read strand aligned with RNA)

source_name: blood

extract_protocol:
Blood samples were obtained by venous puncture and collected in BD PAXgene™ tubes (BD, Franklin Lakes, NJ) for isolation of RNA. Qiagen RNA purification kit for PAXgene was used for total RNA extraction. RNA quality was controlled using Agilent Tapestation. 500 ng of total RNA was used for library construction.
Libraries were prepared with Illumina Stranded Total RNA Prep. Ribo-Zero Plus was applied to deplete abundant transcripts, including human cytoplasmic and mitochondria rRNA, and human beta-globin mRNAs.

tag: tissue

value: blood

value: intense meditation


title: Twin_set_3, subject 4010, T3 group, Day7


title: Twin_set_5, subject 4008, T3 group, Day7


title: Twin_set_5, subject 4007, T3 group, Day7


title: SI

description: Library name: SI


title: EpiSC-5_WA_12H-2

value: EpiSC


title: Twin_set_6, subject 4004, T3 group, Day7


title: Twin_set_2, subject 4011, T3 group, Day7


title: Twin_set_4, subject 4003, T3 group, Day7


title: Twin_set_2, subject 4005, T3 group, Day7


title: Twin_set_3, subject 4010, T2 group, Day5


title: Twin_set_3, subject 4009, T3 group, Day7


title: Twin_set_2, subject 4011, T2 group, Day5


title: Twin_set_1, subject 4001, T3 group, Day7


title: Twin_set_4, subject 4002, T2 group, Day5


title: Twin_set_6, subject 4004, T2 group, Day5


title: Twin_set_6, subject 4012, T2 group, Day5


title: Twin_set_3, subject 4009, T2 group, Day5


title: Twin_set_5, subject 4007, T2 group, Day5


title: S4, scRNAseq

description: Chromium Controller (10x Genomics)

value: Isogenic mutated iPSC-derived neuroprogenitor cell lines


title: Twin_set_2, subject 4011, T1 group, Day3


title: Twin_set_3, subject 4010, T1 group, Day3


title: Twin_set_1, subject 4000, T3 group, Day7


title: Twin_set_4, subject 4003, T2 group, Day5


title: Twin_set_1, subject 4000, T2 group, Day5


title: Twin_set_3, subject 4009, T1 group, Day3


title: Twin_set_6, subject 4012, T1 group, Day3


title: SC18M

type: RNA

city: Worcester

first: Violeta

last: Duran Laforet

address: 365 Plantation St

department: Neurobiology

institute: University of Massachusetts Chan Medical School

hyb_protocol: Tissue was washed and hybridized for 15 minutes with DAPI and polyT solution and washed with formamide wash buffer for 10 minutes.

scan_protocol: MERFISH imaging was performed according to Vizgen MERSCOPE instructions

data_processing:
Raw data were decoded using Vizgen's MERLIN pipeline incorporated in the MERSCOPE. Vizgen's postprocessing tool was applied to obtain the cell segmentation based on the DAPI staining by using the CellPose algorithim.
counts_and_metadata.csv files contain matrices of cell IDs as rows, genes and metadata as columns. Matrix contains raw counts of detected transcripts. Volume metadata is provided in cubic microns. X and Y metadata are provided in microns.

source_name: Spinal Cord

label_protocol: Tissue on coverslips was fixed for 15 minutes at room temperature in 4% paraformaldehyde in PBS, followed by three washes with PBS. Tissue was then permeabilized in 70% ethanol for 24 hours. After a wash with Formamide Wash Buffer  (30% formamide in 2X saline sodium citrate (SSC)), the MERFISH library mix was added and allowed to hybridize to occur for 48 hours. Sample was then washed and incubated at 47°C with Formamide Wash Buffer twice  and then the tissue was embedded in a polyacrylamide gel followed by incubation with tissue clearing solution (2X SSC, 2% SDS, 0.5% v/v Triton X-100, and proteinase K 1:100) overnight at 37°C.

extract_protocol: To identify the lesion, 500 ul of 1% neutral red dye in PBS was injected intraperitoneally 2h prior to cardiac perfusion with ice-cold RNA-ase free 1X PBS. Spinal cords were flash frozen in isopentane and embedded in OCT on dry ice.

treatment_protocol: Lesions were induced by injection of 1% LPC between the T11-12 vertebrae into the ventral white watter columns of the spinal cord.

tag: genotype

value: 18 months

value: Spinal Cord

value: LPC focal demyelination

tag: timepoint

value: 5 days post lesion


title: Twin_set_5, subject 4007, T1 group, Day3


title: SC3M

value: 3 months


title: Twin_set_4, subject 4002, T3 group, Day7


title: Twin_set_6, subject 4004, T1 group, Day3


title: Twin_set_5, subject 4008, T1 group, Day3


title: Twin_set_4, subject 4003, T1 group, Day3


title: Twin_set_2, subject 4006, T2 group, Day5


title: catd_rep1

type: genomic

city: Houston

first: Isaac

middle: B.

last: Hilton

state: TX

address: 6500 Main Street

institute: Rice University

hyb_protocol: Infinium Human Methylation EPIC BeadChip

scan_protocol: Illumina iScan SQ

data_processing: minfi package in R

label: Cy3 and Cy5

source_name: primary human T cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from sorted cells using the Qiagen DNeasy Blood & Tissue Kit according to manufacturer's instructions.

value: primary human T cells


title: Twin_set_1, subject 4001, T2 group, Day5


title: Twin_set_4, subject 4002, T1 group, Day3


title: V3_rep1


title: V3_rep2


title: Twin_set_1, subject 4000, T1 group, Day3


title: Twin_set_1, subject 4001, T1 group, Day3


title: V2_rep1


title: V2_rep2


title: Twin_set_6, subject 4012, baseline group, Day0

value: pre-meditation


title: Twin_set_2, subject 4011, baseline group, Day0


title: Twin_set_5, subject 4008, baseline group, Day0


title: Twin_set_5, subject 4007, baseline group, Day0


title: WT_rep2


title: WT_rep1


title: V1_rep2


title: V1_rep1


title: Twin_set_2, subject 4006, T1 group, Day3


title: Twin_set_2, subject 4006, baseline group, Day0


title: Twin_set_3, subject 4009, baseline group, Day0


title: NTC_rep2


title: Twin_set_6, subject 4004, baseline group, Day0


title: Twin_set_4, subject 4003, baseline group, Day0


title: NTC_rep1


title: catd_rep2


title: Twin_set_4, subject 4002, baseline group, Day0


title: Wab1-R-stg2-rep4

city: St. Louis

first: Andrea

last: Eveland

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints

data_processing:
Paired-end reads were first trimmed for adapter sequences using Cutadapt v2.3 and the wrapper tool TrimGalore v0.6.2 with default parameters except for --length 70 --trim-n --illumina.
Clean reads were used to quantify the maize B73 AGPv4 gene models with Salmon v1.4.0 using the selective alignment method with a decoy-aware transcriptome.
Supplementary_files_format_and_content: salmon_output.tgz:This file contains all the expression data generated with Salmon, the metadata file of the sample dataset and the script to import the data in R

molecule: polyA RNA

organism: Zea mays

growth_protocol: Plant materials were sown into cone trays (5 cm diameter, 11.5 cm depth, 142 ml total volume) in Metromix 360 - Turface blend and grown in controlled growth chambers at the Danforth Center’s growth facility with 14 hr days, 28° C / 24° C, 50% humidity and 450 µMol light. At 14 DAS, seedlings were transplanted to 3 gallon pots (9.5” by 11” diameter) with Berger 35% with 2 tsp corn top dressing, 3 seedlings per pot.

extract_protocol:
Poly-A+ RNA-seq libraries were generated from pools of hand-dissected inflorescence primordia and shoots (apex1 and apex2) from wild-type (B73) and maize mutants. RNA isolation from tassel material was performed using the PicoPure RNA isolation kit (ThermoFisher Scientific) according to manufacturer's instructions with the following adjustments: 40 µl and 60 µl of RNA extraction buffer were added respectively to stage 1 and stage 2 ground tassels. After 30 min incubation at 42°C, samples were centrifuged at 800g for 2 min. Equal volume of 70% EtOH was added to samples and processed according to kit directions. RNA isolation from shoot apex samples was performed using the Zymo quick-RNA plant kit according to manufacturer instructions with following adjustments: Lysis buffer was added directly to the ground tissue and centrifuged, supernatant was added directly to the filtration column.
Library preparation was outsourced to Novogene (USA).
RNA-seq libraries were processed using an Illumina HiSeq 4000 platform at Novogene with a 150 bp paired-end sequencing design.

tag: developmental stage


title: Twin_set_1, subject 4001, baseline group, Day0


title: Wab1-R-stg2-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: Wab1-R-stg2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: Twin_set_1, subject 4000, baseline group, Day0


title: Twin_set_3, subject 4010, baseline group, Day0


title: Wab1-R-stg1-rep3


title: Wab1-R-stg1-rep4


title: Wab1-R-stg2-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: Wab1-R-stg1-rep2


title: Wab1-R-apex1-rep4


title: Wab1-R-apex1-rep3


title: Wab1-R-stg1-rep1


title: Wab1-R-apex1-rep1


title: Wab1-R-apex1-rep2


title: Wab1-R-apex2-rep3


title: Wab1-R-apex2-rep2


title: Wab1-R-apex2-rep4


title: Wab1-R-apex2-rep1


title: ADLI40062111_CHD1_Auxin_24h_rep1, treated

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description: Library name: 23247FL-01-03-11

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: featureCounts.csv genesCounts.csv genesRawCounts.csv genesTPM.csv stats.csv txCounts.csv txRawCounts.csv txTPM.csv

source_name: CHD1 knock-in of the AID at C-terminus, treated with IAA to induce rapid degradation of the tagged protein, 24h

extract_protocol:
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
Paired-end libraries
Bulk RNA-sequencing

value: iPSC

tag: editing strategy

value: Knock-in of inducible C-terminal degron

tag: altered gene_symbol

value: 24 hours

tag: model system

tag: condition

value: Auxin

tag: parental cell_line

value: KOLF2.2J OCP74G


title: wab-rev-stg2-rep3

value: wab-rev


title: ADLI40062111_CHD1_Auxin_24h_rep2, treated

description: Library name: 23247FL-01-03-12

tag: cell type


title: wab-rev-stg2-rep4


title: ADLI40062111_CHD1_Auxin_6h_rep2, treated

description: Library name: 23247FL-01-03-10

source_name: CHD1 knock-in of the AID at C-terminus, treated with IAA to induce rapid degradation of the tagged protein, 6h

tag: time

value: 6 hours


title: wab-rev-stg2-rep2


title: ADLI40062111_CHD1_Auxin_6h_rep1, treated

description: Library name: 23247FL-01-03-09

tag: cell line


title: wab-rev-stg1-rep4


title: ADLI40062111_CHD1_Auxin_0h_rep1, control

description: Library name: 23247FL-01-03-07

source_name: CHD1 knock-in of the AID at C-terminus, DMSO treated, control for IAA

value: DMSO


title: wab-rev-stg1-rep3


title: ADLI40062111_CHD1_Auxin_0h_rep2, control

description: Library name: 23247FL-01-03-08


title: wab-rev-stg2-rep1


title: wab-rev-stg1-rep2


title: ADLI00042105_RBBP4_Auxin_24h_rep2, treated

description: Library name: 23247FL-01-03-06

source_name: RBBP4 knock-in of the AID at C-terminus, treated with IAA to induce rapid degradation of the tagged protein, 24h

value: KOLF2.2J OCM_108


title: ADLI00042105_RBBP4_Auxin_24h_rep1, treated

description: Library name: 23247FL-01-03-05


title: wab-rev-stg1-rep1


title: ADLI00042105_RBBP4_Auxin_6h_rep2, treated

description: Library name: 23247FL-01-03-04

source_name: RBBP4 knock-in of the AID at C-terminus, treated with IAA to induce rapid degradation of the tagged protein, 6h


title: ra2-stg2-rep4


title: ADLI00042105_RBBP4_Auxin_0h_rep2, control

description: Library name: 23247FL-01-03-02

source_name: RBBP4 knock-in of the AID at C-terminus, DMSO treated, control for IAA


title: ADLI00042105_RBBP4_Auxin_0h_rep1, control

description: Library name: 23247FL-01-03-01


title: ra2-stg2-rep2


title: ADLI00042105_RBBP4_Auxin_6h_rep1, treated

description: Library name: 23247FL-01-03-03


title: ra2-stg2-rep1


title: PrS-MOK20045-WT1, WT

description:
Library name: BMLHE40_WT_1_GT24-00872_GTGTCGGA-GCGCAAGC_S193
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study2_featureCounts.csv study2_genesCounts.csv study2_genesRawCounts.csv study2_genesTPM.csv study2_stats.csv study2_txCounts.csv study2_txRawCounts.csv study2_txTPM.csv

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: Not Applicable

tag: altered locus

value: day 6

value: primitive syncytium


title: ra2-stg1-rep2


title: PrS-MOK20045P-C11, KO

description:
Library name: BMLHE40_PTC_C11_GT24-00870_CCATTCGA-CGGACAAC_S197
KOLF2.2J derived knockout cell line, BHLHE40 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: PrS-MOK20045P-B12, KO

description:
Library name: BMLHE40_PTC_B12_GT24-00869_TTGCCTAG-TAAGTGGT_S196
KOLF2.2J derived knockout cell line, BHLHE40 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20045-WT3, WT

description:
Library name: BMLHE40_WT_3_GT24-00874_CCTTCACC-GGAGCGTC_S188
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20045C-H05, KO

description:
Library name: BMLHE40_CE_H05_GT24-00868_TAAGGTCA-CTACGACA_S192
KOLF2.2J derived knockout cell line, BHLHE40 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Critical exon


title: ra1-stg2-rep3


title: PrS-MOK20045P-D09, KO

description:
Library name: BMLHE40_PTC_D09_GT24-00871_ACACTAAG-ATATGGAT_S195
KOLF2.2J derived knockout cell line, BHLHE40 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20045C-B06, KO

description:
Library name: BMLHE40_CE_B06_GT24-00867_CGGAACTG-TCGTAGTG_S194
KOLF2.2J derived knockout cell line, BHLHE40 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ra1-stg2-rep4


title: ra2-stg1-rep1


title: ra2-stg1-rep3


title: ra2-stg1-rep4


title: PrS-MOK20045-WT2, WT

description:
Library name: BMLHE40_WT_2_GT24-00873_TTCCTGTT-AAGATACT_S191
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ra1-stg2-rep2


title: ra2-stg2-rep3


title: ra1-stg2-rep1


title: PrS-MOK20045C-A06, KO

description:
Library name: BMLHE40_CE_A06_GT24-00866_AGCTCGCT-GATTCTGC_S190
KOLF2.2J derived knockout cell line, BHLHE40 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20045W-D01, KO

description:
Library name: BMLHE40_KO_D01_GT24-00865_GATCTATC-AGCCTCAT_S189
KOLF2.2J derived knockout cell line, BHLHE40 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Full coding length


title: lg2-stg2-rep3


title: ra1-stg1-rep3


title: ra1-stg1-rep2


title: PrS-MOK20044P-A11, KO

description:
Library name: NC0A3_PTC_A11_GT24-01173_GCACGGAC-TGCGAGAC_S149
KOLF2.2J derived knockout cell line, NCOA3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: sh_AL2_1

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

description: genomic DNA extracted from ALKBH5-sh2 HCT116 cell

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi.

label: Cy5 and Cy3

source_name: Human colon cancer cell line HCT116_ALKBH5 knock-down

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: transfection

value: colon cancer


title: PrS-MOK20044-WT3, WT

description:
Library name: NC0A3_WT_3_GT24-01177_ATGAGGCC-CAATTAAC_S131
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20044P-F10, KO

description:
Library name: NC0A3_PTC_F10_GT24-01174_GGTACCTT-GACGTCTT_S151
KOLF2.2J derived knockout cell line, NCOA3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20045W-A01, KO

description:
Library name: BMLHE40_KO_A01_GT24-00863_TGCGGCGT-TACCGAGG_S198
KOLF2.2J derived knockout cell line, BHLHE40 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg2-stg2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: lg2-stg2-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: lg2-stg2-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: sh_AL1_1

description: genomic DNA extracted from ALKBH5-sh1 HCT116 cell


title: PrS-MOK20045W-A03, KO

description:
Library name: BMLHE40_KO_A03_GT24-00864_CATAATAC-CGTTAGAA_S187
KOLF2.2J derived knockout cell line, BHLHE40 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ra1-stg1-rep1


title: lg2-stg1-rep4


title: PrS-MOK20044P-A10, KO

description:
Library name: NC0A3_PTC_A10_GT24-01172_ATGTAAGT-CATAGAGT_S132
KOLF2.2J derived knockout cell line, NCOA3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20044C-H06, KO

description:
Library name: NC0A3_CE_H06_GT24-01171_CGGCGTGA-ACAGGCGC_S141
KOLF2.2J derived knockout cell line, NCOA3 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg2-stg1-rep1


title: ra1-stg1-rep4


title: sh_AL2_2


title: DLD1EV1

description: genomic DNA extracted from DLD1 cell transfected with empty vector

source_name: Human colon cancer cell line DLD1_transfected with empty vector

value: empty vector


title: DLD1A3A1

description: genomic DNA extracted from DLD1 cell_APOBEC3A overexpression

source_name: Human colon cancer cell line DLD1_APOBEC3A overexpression

value: APOBEC3A overexpression


title: lg2-stg1-rep2


title: PrS-MOK20044C-G05, KO

description:
Library name: NC0A3_CE_G05_GT24-01170_TAATACAG-GTGAATAT_S130
KOLF2.2J derived knockout cell line, NCOA3 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: lg2-apex1-rep1


title: lg2-apex1-rep4


title: lg2-apex1-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20044W-A02, KO

description:
Library name: NC0A3_KO_A02_GT24-01166_CCAAGTCT-TCATCCTT_S138
KOLF2.2J derived knockout cell line, NCOA3 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ExM-MOK20024-WT3, WT

description:
Library name: MEF2C_WT3_GT23-13709_GGACTTGG-CGTCTGCG_S166
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: fibroblast of villous mesenchyme (CL:0002558)


title: DLD1EV3


title: ExM-MOK20024-WT2, WT

description:
Library name: MEF2C_WT2_GT23-13708_TTATAACC-TCGATATC_S162
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: lg2-apex2-rep3


title: lg2-stg1-rep3


title: sh_NC_1

description: genomic DNA extracted from NT HCT116 cell

source_name: Human colon cancer cell line HCT116_non target


title: DLD1A3A2


title: DLD1EV2


title: PrS-MOK20044W-A12, KO

description:
Library name: NC0A3_KO_A12_GT24-01167_TTGGACTC-CTGCTTCC_S147
KOLF2.2J derived knockout cell line, NCOA3 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20044-WT2, WT

description:
Library name: NC0A3_WT_2_GT24-01176_GCAGAATT-TGGCCGGT_S146
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20044W-D11, KO

description:
Library name: NC0A3_KO_D11_GT24-01168_CAGTAGGC-ATTCGTCA_S133
KOLF2.2J derived knockout cell line, NCOA3 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: sh_NC_2


title: lg2-apex2-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: lg2-apex1-rep2


title: lg2-apex2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: ExM-MOK20024-WT1, WT

description:
Library name: MEF2C_WT1_GT23-13707_CCGCGGTT-CTAGCGCT_S165
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: lg1-stg2-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: ExM-MOK20024P-B03, KO

description:
Library name: MEF2C_PTC_B03_GT23-13717_TCTCTACT-GAACCGCG_S177
KOLF2.2J derived knockout cell line, MEF2C PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: sh_AL1_2

description: genomic DNA extracted from ALKBH5-sh1 HCT116 cell


title: ExM-MOK20024P-D07, KO

description:
Library name: MEF2C_PTC_D07_GT23-13718_CTCTCGTC-AGGTTATA_S156
KOLF2.2J derived knockout cell line, MEF2C PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: PrS-MOK20044C-F08, KO

description:
Library name: NC0A3_CE_F08_GT24-01169_TGACGAAT-GCCTACTG_S137
KOLF2.2J derived knockout cell line, NCOA3 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg1-stg2-rep3


title: ExM-MOK20024P-A01, KO

description:
Library name: MEF2C_PTC_A01_GT23-13716_GACCTGAA-CTCACCAA_S160
KOLF2.2J derived knockout cell line, MEF2C PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20024C-A05, KO

description:
Library name: MEF2C_CE_A05_GT23-13713_CAAGCTAG-CGCTATGT_S168
KOLF2.2J derived knockout cell line, MEF2C CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20024C-C07, KO

description:
Library name: MEF2C_CE_C07_GT23-13714_TGGATCGA-TATCGCAC_S158
KOLF2.2J derived knockout cell line, MEF2C CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: lg1-stg2-rep1


title: lg1-stg1-rep1


title: ExM-MOK20024W-D03, KO

description:
Library name: MEF2C_KO_D03_GT23-13711_ATCCACTG-ACGCACCT_S169
KOLF2.2J derived knockout cell line, MEF2C KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: lg1-stg1-rep4


title: PrS-MOK20011-WT3, WT

description:
Library name: RUNX1_WT3_GT23-13721_GGCTTAAG-GGTCACGA_S174
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg1-apex1-rep4


title: lg2-apex2-rep4


title: lg1-stg1-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: ExM-MOK20024W-G01, KO

description:
Library name: MEF2C_KO_G01_GT23-13712_GCTTGTCA-GTATGTTC_S179
KOLF2.2J derived knockout cell line, MEF2C KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: lg1-stg1-rep2


title: lg1-apex1-rep3


title: lg1-apex1-rep2


title: PrS-MOK20011-WT2, WT

description:
Library name: RUNX1_WT2_GT23-13720_TTGGACTC-CTGCTTCC_S157
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20011P-F09, KO

description:
Library name: RUNX1_PTC_F09_GT23-13730_ATGAGGCC-CAATTAAC_S171
KOLF2.2J derived knockout cell line, RUNX1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20011-WT1, WT

description:
Library name: RUNX1_WT1_GT23-13719_CCAAGTCT-TCATCCTT_S170
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg1-apex1-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20011C-D02, KO

description:
Library name: RUNX1_CE_D02_GT23-13727_GGTACCTT-GACGTCTT_S172
KOLF2.2J derived knockout cell line, RUNX1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg1-apex2-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20011C-A11, KO

description:
Library name: RUNX1_CE_A11_GT23-13725_ATGTAAGT-CATAGAGT_S161
KOLF2.2J derived knockout cell line, RUNX1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20011P-C12, KO

description:
Library name: RUNX1_PTC_C12_GT23-13728_AACGTTCC-AGTACTCC_S176
KOLF2.2J derived knockout cell line, RUNX1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ExM-MOK20024C-D08, KO

description:
Library name: MEF2C_CE_D08_GT23-13715_AGTTCAGG-TCTGTTGG_S159
KOLF2.2J derived knockout cell line, MEF2C CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: PrS-MOK20011P-D09, KO

description:
Library name: RUNX1_PTC_D09_GT23-13729_GCAGAATT-TGGCCGGT_S167
KOLF2.2J derived knockout cell line, RUNX1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20011C-B02, KO

description:
Library name: RUNX1_CE_B02_GT23-13726_GCACGGAC-TGCGAGAC_S178
KOLF2.2J derived knockout cell line, RUNX1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg1-apex2-rep3


title: fun-apex1-rep3

value: fun


title: lg1-apex2-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: fun-apex1-rep4


title: PrS-MOK20011W-G07, KO

description:
Library name: RUNX1_KO_G07_GT23-13724_CGGCGTGA-ACAGGCGC_S175
KOLF2.2J derived knockout cell line, RUNX1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: fun-apex1-rep2


title: PrS-MOK20011W-F08, KO

description:
Library name: RUNX1_KO_F08_GT23-13723_TAATACAG-GTGAATAT_S173
KOLF2.2J derived knockout cell line, RUNX1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: lg1-apex2-rep1


title: PrS-MOK20011W-B07, KO

description:
Library name: RUNX1_KO_B07_GT23-13722_TGACGAAT-GCCTACTG_S163
KOLF2.2J derived knockout cell line, RUNX1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ExM-MOK20025-WT1, WT

description:
Library name: MEIS2_WT_1_GT23-12168_CAATTAAC-ATATCTCG_S18
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: fun-apex2-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: fun-apex2-rep4


title: ExM-MOK20025-WT2, WT

description:
Library name: MEIS2_WT_2_GT23-12169_TGGCCGGT-GCGCTCTA_S6
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: fun-apex2-rep1


title: fun-apex2-rep2


title: DLD1A3A3

description: genomic DNA extracted from DLD1 cell_APOBEC3A overexpression


title: ExM-MOK20025P-E11, KO

description:
Library name: MEIS2_PTC_E11_GT23-12178_AACTGTAG-TGCGGCGT_S16
KOLF2.2J derived knockout cell line, MEIS2 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: PrS-MOK20044-WT1, WT

description:
Library name: NC0A3_WT_1_GT24-01175_AACGTTCC-AGTACTCC_S144
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: bri1-RNAi-stg2-rep2


title: bri1-RNAi-stg2-rep3


title: ExM-MOK20025C-A06, KO

description:
Library name: MEIS2_CE_A06_GT23-12174_TGCGAGAC-CAACAATG_S1
KOLF2.2J derived knockout cell line, MEIS2 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20025P-B09, KO

description:
Library name: MEIS2_PTC_B09_GT23-12177_GTGAATAT-GAATGAGA_S19
KOLF2.2J derived knockout cell line, MEIS2 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bri1-RNAi-stg1-rep4


title: bri1-RNAi-stg2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: ExM-MOK20025-WT3, WT

description:
Library name: MEIS2_WT_3_GT23-12170_AGTACTCC-AACAGGTT_S13
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bri1-RNAi-stg1-rep3


title: ExM-MOK20025W-C02, KO

description:
Library name: MEIS2_KO_C02_GT23-12173_GACGTCTT-GGTGAACC_S28
KOLF2.2J derived knockout cell line, MEIS2 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20025C-C08, KO

description:
Library name: MEIS2_CE_C08_GT23-12176_ACAGGCGC-AGGCAGAG_S7
KOLF2.2J derived knockout cell line, MEIS2 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bri1-RNAi-stg1-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20016-WT3, WT

description:
Library name: MDX1_KOLF2_3_GT23-10878_TACCGAGG-AGTTCAGG_S13
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20016-WT2, WT

description:
Library name: MDX1_KOLF2_2_GT23-10877_AATGCCTC-TGGATCGA_S3
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: bri1-RNAi-stg1-rep1


title: bri1-RNAi-apex1-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20016-WT1, WT

description:
Library name: MDX1_KOLF2_1_GT23-10876_GGCATTCT-CAAGCTAG_S8
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ExM-MOK20025P-G09, KO

description:
Library name: MEIS2_PTC_G09_GT23-12179_GGTCACGA-CATAATAC_S14
KOLF2.2J derived knockout cell line, MEIS2 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: PrS-MOK20016P-G10, KO

description:
Library name: MDX1_PTC_G10_GT23-10884_TAAGTGGT-GGCTTAAG_S34
KOLF2.2J derived knockout cell line, MXD1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20016P-C11, KO

description:
Library name: MDX1_PTC_C11_GT23-10883_CTACGACA-TTGGACTC_S18
KOLF2.2J derived knockout cell line, MXD1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: bri1-RNAi-stg2-rep4


title: bri1-RNAi-apex1-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: bri1-RNAi-apex1-rep1


title: bri1-RNAi-apex1-rep2


title: PrS-MOK20016C-H08, KO

description:
Library name: MDX1_CE_H08_GT23-10887_GCGCAAGC-CGGCGTGA_S25
KOLF2.2J derived knockout cell line, MXD1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20016P-B10, KO

description:
Library name: MDX1_PTC_B10_GT23-10882_TCGTAGTG-CCAAGTCT_S4
KOLF2.2J derived knockout cell line, MXD1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ExM-MOK20025C-C06, KO

description:
Library name: MEIS2_CE_C06_GT23-12175_CATAGAGT-TGGTGGCA_S10
KOLF2.2J derived knockout cell line, MEIS2 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: PrS-MOK20016C-H05, KO

description:
Library name: MDX1_CE_H05_GT23-10886_ATATGGAT-TAATACAG_S10
KOLF2.2J derived knockout cell line, MXD1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: bri1-RNAi-apex2-rep3


title: bri1-RNAi-apex2-rep4


title: bin2-RNAi-stg2-rep4


title: bri1-RNAi-apex2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20016W-C03, KO

description:
Library name: MDX1_KO_C03_GT23-10879_CGTTAGAA-GACCTGAA_S5
KOLF2.2J derived knockout cell line, MXD1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: ExM-MOK20014-WT3, WT

description:
Library name: MEIS1_WT_3_GT23-12158_TTGCCTAG-TAAGTGGT_S22
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bin2-RNAi-stg2-rep2


title: PrS-MOK20016C-F07, KO

description:
Library name: MDX1_CE_F07_GT23-10885_CGGACAAC-AATCCGGA_S40
KOLF2.2J derived knockout cell line, MXD1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20016W-D01, KO

description:
Library name: MDX1_KO_D01_GT23-10881_GATTCTGC-CTCTCGTC_S9
KOLF2.2J derived knockout cell line, MXD1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: bin2-RNAi-stg2-rep3


title: ExM-MOK20014P-G09, KO

description:
Library name: MEIS1_PTC_G9_GT23-12166_ACTCGTGT-GTTCCAAT_S4
KOLF2.2J derived knockout cell line, MEIS1 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20014P-G11, KO

description:
Library name: MEIS1_PTC_G11_GT23-12167_GTCTACAC-ACCTTGGC_S31
KOLF2.2J derived knockout cell line, MEIS1 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: PrS-MOK20016W-C04, KO

description:
Library name: MDX1_KO_C04_GT23-10880_AGCCTCAT-TCTCTACT_S11
KOLF2.2J derived knockout cell line, MXD1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: bin2-RNAi-stg1-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: bin2-RNAi-stg2-rep1


title: ExM-MOK20014-WT1, WT

description:
Library name: MEIS1_WT_1__GT23-12156_CGGAACTG-TCGTAGTG_S62
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20014P-F12, KO

description:
Library name: MEIS1_PTC_F12_GT23-12165_ATTGTGAA-GCAATGCA_S8
KOLF2.2J derived knockout cell line, MEIS1 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20014C-C07, KO

description:
Library name: MEIS1_CE_C07_GT23-12163_CCTTCACC-GGAGCGTC_S30
KOLF2.2J derived knockout cell line, MEIS1 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bin2-RNAi-stg1-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: ExM-MOK20014C-H08, KO

description:
Library name: MEIS1_CE_H08_GT23-12162_TTCCTGTT-AAGATACT_S12
KOLF2.2J derived knockout cell line, MEIS1 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20014-WT2, WT

description:
Library name: MEIS1_WT_2_GT23-12157_TAAGGTCA-CTACGACA_S9
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bin2-RNAi-apex1-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: bin2-RNAi-apex1-rep1


title: bin2-RNAi-apex1-rep4


title: bin2-RNAi-stg1-rep1


title: ExM-MOK20014C-E06, KO

description:
Library name: MEIS1_CE_E06_GT23-12164_GCCACAGG-ATGGCATG_S2
KOLF2.2J derived knockout cell line, MEIS1 CE, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: ExM-MOK20014W-H03, KO

description:
Library name: MEIS1_KO_H03_GT23-12161_GTGTCGGA-GCGCAAGC_S25
KOLF2.2J derived knockout cell line, MEIS1 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bin2-RNAi-apex2-rep4


title: CBO-MOK2008R-WT3, WT

description:
Library name: PAX6_WT_3_GT24-04406_CTAGCGCT-GTCTACAC_S202
KOLF2.2J differentiated to cortical brain organoid

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: Not applicable

value: day 9

value: Cortical brain (dorsal forebrain patterning)


title: bin2-RNAi-apex2-rep3


title: bin2-RNAi-stg1-rep3


title: bri1-RNAi-apex2-rep2


title: CBO-MOK2008R-WT2, WT

description:
Library name: PAX6_WT_2_GT24-04405_TCGATATC-ACTCGTGT_S199
KOLF2.2J differentiated to cortical brain organoid


title: bin2-RNAi-apex2-rep2


title: ExM-MOK20014W-E03, KO

description:
Library name: MEIS1_KO_E03_GT23-12159_CCATTCGA-CGGACAAC_S26
KOLF2.2J derived knockout cell line, MEIS1 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: bin2-RNAi-apex2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: CBO-MOK20008R-E03, REV

description:
Library name: PAX6_R_PTC_E03_GT24-04400_CGCTATGT-GTGTCGGA_S196
KOLF2.2J derived knockout cell line, PAX6 PTC, subsequently reverted back to wild type and then differentiated to cortical brain organoid.

value: reversion of termination codon to wildtype


title: CBO-MOK2008R-WT1, WT

description:
Library name: PAX6_WT_1_GT24-04404_CGTCTGCG-ATTGTGAA_S197
KOLF2.2J differentiated to cortical brain organoid


title: CBO-MOK20008R-C03, REV

description:
Library name: PAX6_R_PTC_C03_GT24-04399_TATCGCAC-ACACTAAG_S201
KOLF2.2J derived knockout cell line, PAX6 PTC, subsequently reverted back to wild type and then differentiated to cortical brain organoid.


title: B73-stg5-rep4


title: B73-stg5-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: CBO-MOK20008P-D09, KO

description:
Library name: PAX6_PTC_D09_GT24-04403_TACTCATA-GCCACAGG_S204
KOLF2.2J derived knockout cell line, PAX6 PTC, differentiated to cortical brain organoid


title: CBO-MOK20008P-A11, KO

description:
Library name: PAX6_PTC_A11_GT24-04402_ACGCACCT-CCTTCACC_S198
KOLF2.2J derived knockout cell line, PAX6 PTC, differentiated to cortical brain organoid


title: CBO-MOK20008R-A04, REV

description:
Library name: PAX6_R_PTC_A04_GT24-04398_TCTGTTGG-CCATTCGA_S200
KOLF2.2J derived knockout cell line, PAX6 PTC, subsequently reverted back to wild type and then differentiated to cortical brain organoid.


title: B73-stg5-rep3


title: ExM-MOK20014W-F04, KO

description:
Library name: MEIS1_KO_F04_GT23-12160_ACACTAAG-ATATGGAT_S11
KOLF2.2J derived knockout cell line, MEIS1 KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation


title: B73-stg4-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: B73-stg4-rep3


title: B73-stg4-rep1


title: CBO-MOK20008P-A09, KO

description:
Library name: PAX6_PTC_A09_GT24-04401_GTATGTTC-TTCCTGTT_S203
KOLF2.2J derived knockout cell line, PAX6 PTC, differentiated to cortical brain organoid


title: PrS-MOK20022R-D09, REV

description:
Library name: GRHL1_R_PTC_D09_GT24-02286_TGGTGGCA-TTACAGGA_S187
KOLF2.2J derived knockout cell line, GRHL1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20013R_22R-WT1, WT

description:
Library name: GCM1_GRHL1_WT_1_GT24-02287_GTTCGCCG-CAATGAGC_S186
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B73-stg4-rep2


title: B73-stg3-rep1


title: B73-stg3-rep4

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20022R-D07, REV

description:
Library name: GRHL1_R_PTC_D07_GT24-02285_CAACAATG-CCGTGAAG_S206
KOLF2.2J derived knockout cell line, GRHL1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20013R-C04, REV

description:
Library name: GCM1_R_PTC_C04_GT24-02283_AACAGGTT-CTTGGTAT_S200
KOLF2.2J reverted GCM1 deletion by removal of PTC derived primitive syncytium


title: B73-stg5-rep1


title: B73-stg2-rep3


title: PrS-MOK20013R_22R-WT3, WT

description:
Library name: GCM1_GRHL1_WT_3_GT24-02289_TGCGGCGT-TACCGAGG_S199
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20022R-C09, REV

description:
Library name: GRHL1_R_PTC_C09_GT24-02284_GGTGAACC-TCCAACGC_S198
KOLF2.2J derived knockout cell line, GRHL1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B73-stg2-rep4


title: B73-stg2-rep2


title: PrS-MOK20013R-B06, REV

description:
Library name: GCM1_R_PTC_B06_GT24-02282_GCGCTCTA-GTCGGAGC_S195
KOLF2.2J reverted GCM1 deletion by removal of PTC derived primitive syncytium


title: PrS-MOK20013R-B01, REV

description:
Library name: GCM1_R_PTC_B01_GT24-02281_ATATCTCG-ACTAAGAT_S196
KOLF2.2J reverted GCM1 deletion by removal of PTC derived primitive syncytium


title: PrS-MOK20012R-WT3-hyp, WT

description:
Library name: EPAS1_R_WT3_H_GT24-02295_TTGCCTAG-TAAGTGGT_S185
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: hypoxia


title: B73-stg2-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20012R-WT2-hyp, WT

description:
Library name: EPAS1_R_WT2_H_GT24-02293_CGGAACTG-TCGTAGTG_S189
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: PrS-MOK20013R_22R-WT2, WT

description:
Library name: GCM1_GRHL1_WT_2_GT24-02288_CACGAGCG-TGGCAGAT_S204
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B73-stg1-rep4


title: PrS-MOK20012R-WT1-hyp, WT

description:
Library name: EPAS1_R_WT1_H_GT24-02291_GATCTATC-AGCCTCAT_S197
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: B73-stg1-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: PrS-MOK20012R-A06-hyp, REV

description:
Library name: EPAS1_R_PTC_A06_H_GT24-02301_GCCACAGG-ATGGCATG_S205
KOLF2.2J derived knockout cell line, EPAS1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: B73-stg3-rep2


title: B73-apex1-rep4

description:
rep4
salmon_output.gz this folder contains all the 140 expression datapoints


title: B73-apex1-rep3


title: PrS-MOK20012R-A05-hyp, REV

description:
Library name: EPAS1_R_PTC_A05_H_GT24-02299_TTCCTGTT-AAGATACT_S202
KOLF2.2J derived knockout cell line, EPAS1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: PrS-MOK20012R-A03-hyp, REV

description:
Library name: EPAS1_R_PTC_A03_H_GT24-02297_ACACTAAG-ATATGGAT_S192
KOLF2.2J derived knockout cell line, EPAS1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: PrS-MOK20012R-WT3-nor, WT

description:
Library name: EPAS1_R_WT3_N_GT24-02294_TAAGGTCA-CTACGACA_S191
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: normoxia


title: B73-stg1-rep1


title: B73-apex1-rep2


title: PrS-MOK20012R-WT2-nor, WT

description:
Library name: EPAS1_R_WT2_N_GT24-02292_AGCTCGCT-GATTCTGC_S184
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: day 6


title: B73-apex1-rep1


title: PrS-MOK20012R-WT1-nor, WT

description:
Library name: EPAS1_R_WT1_N_GT24-02290_CATAATAC-CGTTAGAA_S190
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: primitive syncytium


title: B73-apex2-rep4


title: Pull down by luciferase 2 (negative control)

city: Wageningen

first: Filippo

last: Guerra

address: Droevendaalsesteeg 1, 107/W0.Aa.081

country: Netherlands

institute: Wageningen University

description: Library name: LucNv2

data_processing:
1. Reads were demultiplexed by the company providing the sequencing services (Novogene).
2. Adaptors were removed by using cutadapt (v0.1).
3. Reads were aligned on the genome using BOWTIE2 (v2.3.5.1).
4. Enriched peaks were identified using MACS2 (v2.2.5); in the comparison, the 4 libraries enriched with DSX were used as positives, and the 3 libraries enriched using luciferase were used as negative control.
5. The nucleotide sequences under the enrichment peaks identified by MACS2 were retrived with bedtools (v2.28.0).
6. The retrieved sequences were scanned by MEME-chip (v5.1.0) to identify conserved motives (DSX binding sites) and their genomic location.
Assembly: GCA_009193385.2 Nvit_psr_1.1
Supplementary files format and content: peaks_MACS2.bed -This file contains the positions of the 2307 peaks identified by MACS2 as described in step 5 of "data processing step". The format is standard BED, with the quality score reported as -LOG10(qvalue).
Supplementary files format and content: DSX_bindingsites.tsv -This file contains the DSX binding sites identified by MEME-chip as described in step 6 of "data processing step". The format is a TSV, and has information about position, scores, and sequence of the 1485 DSX binding sites identified.

organism: Nasonia vitripennis

source_name: Whole body

extract_protocol:
DNA was extracted with a high salt protocol, RNAse digested and phenol-chloroform purified.
DNA was fragmented with Covaris ultrasonicator with a target size of 150bp. Fragments were repaired and Y shaped adaptors were ligated at the extremities. The library was then subjected to enrichment with either DSX or Luciferase. The retrieved DNA was aplified via PCR; unique indexes were added to each sample during this step. The samples were then sequencend by Illumina, 150PE.

value: Whole body

value: AsymCX

tag: treatment

value: Enriched using Luciferase


title: Pull down by luciferase 1 (negative control)

description: Library name: LucNv1


title: PrS-MOK20012R-A06-nor, REV

description:
Library name: EPAS1_R_PTC_A06_N_GT24-02300_CCTTCACC-GGAGCGTC_S208
KOLF2.2J derived knockout cell line, EPAS1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: B73-stg1-rep3

description:
rep3
salmon_output.gz this folder contains all the 140 expression datapoints


title: Pull down by NvDSX 4

description: Library name: DsxNvM2

value: Enriched using DSX


title: PrS-MOK20012R-A05-nor, REV

description:
Library name: EPAS1_R_PTC_A05_N_GT24-02298_GTGTCGGA-GCGCAAGC_S203
KOLF2.2J derived knockout cell line, EPAS1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: Pull down by NvDSX 3

description: Library name: DsxNvM1


title: B73-apex2-rep3


title: PrS-MOK20012R-A03-nor, REV

description:
Library name: EPAS1_R_PTC_A03_N_GT24-02296_CCATTCGA-CGGACAAC_S183
KOLF2.2J derived knockout cell line, EPAS1 PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: Pull down by NvDSX 1

description: Library name: DsxNvF1


title: B73-apex2-rep1


title: B73-apex2-rep2


title: Pull down by NvDSX 2

description: Library name: DsxNvF2


title: PrS-MOK20026R-WT3, WT

description:
Library name: PPARG_R_WT_3_GT24-02468_ATGAGGCC-CAATTAAC_S21
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: EB_Day_10_Rep3

description: Library name: EB_Day_10_Rep3

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: csv files including raw and normalised counts

source_name: Embryoid Body Day 10 generated from KOLF2.2J AAVS1 inducible CRISPRi

extract_protocol:
Lexogen's CORALL RNA-Seq V2 Kit
paired-end library
Bulk RNA-sequencing

value: 10 days

value: Pluripotent


title: PrS-MOK20026R-WT2, WT

description:
Library name: PPARG_R_WT_2_GT24-02467_GCAGAATT-TGGCCGGT_S15
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC


title: WE U18, Biol rep 3

city: Santiago

first: Benjamín

last: Szenfeld

state: Las Condes

address: Av Plaza 680

department: Genetics and Genomics

country: Chile

institute: Institute of Science and Innovation in Medicine

description: Library name: Sample 24

data_processing:
Galaxy Europe was used to upload the RNA-seq FASTQ files and generate paired datasets for each sample (forward and reverse reads). Then, the Salmon tool was employed to map the sequences to the reference transcriptome and obtain expression quantifications per sample in the form of TPMs and counts.
Assembly: sacCer3
Supplementary files format and content: Tabular files include, for each gene, the raw counts, TPM, Length, and EffectiveLength.

organism: Saccharomyces cerevisiae

source_name: DBVPG6765 (Wine/European, "WE")

growth_protocol: Yeast taken from patches on YPD plates were grown in triplicates at 28 °C.

extract_protocol:
Cells were centrifuged and treated with 2U zymolyase for 30 minutes at 37°C. RNA was extracted using the E.Z.N.A. Total RNA Kit I (OMEGA), according to the manufacturer's instructions. Subsequently, the samples were treated with DNase I (Promega) to eliminate genomic DNA contamination. RNA integrity was confirmed using a Fragment Analyzer (Agilent).
The samples were then sent to BGI, where the preparation of the libraries and sequencing were carried out employing DNBseqTM technology.

treatment_protocol: Control (5 mL of YNB medium) and treated with U18 (5 mL of YNB medium containing 200 mg/mL U18666A)

value: DBVPG6765 (Wine/European, "WE")

value: WT (ho::NatMX, ura3::KanMX)


title: EB_Day_4_Rep3

description: Library name: EB_Day_4_Rep3

source_name: Embryoid Body Day 4 generated from KOLF2.2J AAVS1 inducible CRISPRi

value: 4 days


title: EB_Day_6_Rep3

description: Library name: EB_Day_6_Rep3

source_name: Embryoid Body Day 6 generated from KOLF2.2J AAVS1 inducible CRISPRi

value: 6 days


title: Pull down by luciferase 3 (negative control)

description: Library name: LucNv3


title: EB_Day_2_Rep3

description: Library name: EB_Day_2_Rep3

source_name: Embryoid Body Day 2 generated from KOLF2.2J AAVS1 inducible CRISPRi

value: 2 days


title: EB_Day_0_Rep3

description: Library name: EB_Day_0_Rep3

source_name: Embryoid Body Day 0 generated from KOLF2.2J AAVS1 inducible CRISPRi

value: 0 days


title: fun-apex1-rep1

description:
rep1
salmon_output.gz this folder contains all the 140 expression datapoints

value: fun


title: iPSC_Rep3, control

description: Library name: iPSC_Rep3

source_name: Doxycycline inducible CRISPRi iPSC line


title: WE U18, Biol rep 1

description: Library name: Sample 22


title: ExM-MOK20024W-B01, KO

description:
Library name: MEF2C_KO_B01_GT23-13710_AAGTCCAA-TACTCATA_S164
KOLF2.2J derived knockout cell line, MEF2C KO, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: Full coding length

value: fibroblast of villous mesenchyme (CL:0002558)


title: PrS-MOK20026R-WT1, WT

description:
Library name: PPARG_R_WT_1_GT24-02466_AACGTTCC-AGTACTCC_S4
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not applicable

value: day 6

value: primitive syncytium


title: PrS-MOK20026R-A09, REV

description:
Library name: PPARG_R_PTC_A09_GT24-02465_GGTACCTT-GACGTCTT_S31
KOLF2.2J derived knockout cell line, PPARG PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: reversion of termination codon to wildtype

value: PPARG


title: EB_Day_10_Rep2

description: Library name: EB_Day_10_Rep2

value: 10 days


title: PrS-MOK20026R-A08, REV

description:
Library name: PPARG_R_PTC_A08_GT24-02464_GCACGGAC-TGCGAGAC_S19
KOLF2.2J derived knockout cell line, PPARG PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: EB_Day_6_Rep2

description: Library name: EB_Day_6_Rep2

value: Pluripotent


title: NA U18, Biol rep 3

description: Library name: Sample 21

source_name: YPS128 (North American, "NA")

value: YPS128 (North American, "NA")


title: lg1-stg2-rep2

description:
rep2
salmon_output.gz this folder contains all the 140 expression datapoints


title: B73-stg3-rep3


title: EB_Day_8_Rep3

description: Library name: EB_Day_8_Rep3

source_name: Embryoid Body Day 8 generated from KOLF2.2J AAVS1 inducible CRISPRi

value: iPSC

value: 8 days


title: EB_Day_2_Rep2

description: Library name: EB_Day_2_Rep2


title: NA U18, Biol rep 2

description: Library name: Sample 20

value: WT (ho::NatMX, ura3::KanMX)


title: CBO-MOW20008-WT4, WT

description:
Library name: PAX6_W_Day9_WT_4_GT24-02474_TTACAGGA-GCTTGTCA_S9
WIBJ2.2J differentiated to cortical brain organoid

value: day 9

value: Cortical brain (dorsal forebrain patterning)


title: WE U18, Biol rep 2

description: Library name: Sample 23

value: DBVPG6765 (Wine/European, "WE")


title: iPSC_Rep2, control

description: Library name: iPSC_Rep2

value: 0 days


title: PrS-MOK20026R-A07, REV

description:
Library name: PPARG_R_PTC_A07_GT24-02463_ATGTAAGT-CATAGAGT_S13
KOLF2.2J derived knockout cell line, PPARG PTC, subsequently reverted back to wild type and then differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: SA U18, Biol rep 3

description: Library name: Sample 18

source_name: Y12 (Sake, "SA")

value: Y12 (Sake, "SA")


title: CBO-MOW20008-WT2, WT

description:
Library name: PAX6_W_Day9_WT_2_GT24-02473_CCGTGAAG-ATCCACTG_S7
WIBJ2.2J differentiated to cortical brain organoid


title: EB_Day_0_Rep2

description: Library name: EB_Day_0_Rep2


title: EB_Day_10_Rep1

description: Library name: EB_Day_10_Rep1


title: EB_Day_8_Rep1

description: Library name: EB_Day_8_Rep1


title: EB_Day_8_Rep2

description: Library name: EB_Day_8_Rep2


title: CBO-MOW20008-WT1, WT

description:
Library name: PAX6_W_Day9_WT_1_GT24-02472_TCCAACGC-AAGTCCAA_S20
WIBJ2.2J differentiated to cortical brain organoid


title: SA U18, Biol rep 2

description: Library name: Sample 17


title: EB_Day_4_Rep1

description: Library name: EB_Day_4_Rep1

value: 4 days


title: EB_Day_6_Rep1

description: Library name: EB_Day_6_Rep1

value: 6 days


title: CBO-MOW20008-B04, WT

description:
Library name: PAX6_W_Day9_PTC_B04_GT24-02471_CTTGGTAT-GGACTTGG_S5
WIBJ2.2J derived knockout cell line, PAX6 PTC, differentiated to cortical brain organoid

value: Termination codon


title: SA U18, Biol rep 1

description: Library name: Sample 16


title: EB_Day_0_Rep1

description: Library name: EB_Day_0_Rep1


title: EB_Day_4_Rep2

description: Library name: EB_Day_4_Rep2


title: WA U18, Biol rep 3

description: Library name: Sample 15

source_name: DBVPG6044 (West African, "WA")

value: DBVPG6044 (West African, "WA")


title: EB_Day_2_Rep1

description: Library name: EB_Day_2_Rep1

value: 2 days


title: iPSC_Rep1, control

description: Library name: iPSC_Rep1


title: CBO-MOW20008-A03, WT

description:
Library name: PAX6_W_Day9_PTC_A03_GT24-02469_ACTAAGAT-CCGCGGTT_S22
WIBJ2.2J derived knockout cell line, PAX6 PTC, differentiated to cortical brain organoid


title: WA U18, Biol rep 2

description: Library name: Sample 14


title: CAR-T Cells, GSK343_ID04

city: São Paulo

first: Alexandre

last: Defelicibus

address: Rua Tagua

country: Brazil

data_processing:
In-house RNASeq pipeline analysis
Raw sequence reads were aligned to ribosomal genome using BWA MEM algorithm and aligned reads were removed.
Filtered reads were aligned to GRCh38/hg38 using STAR with default parameters.
Read count extraction was performed using htseq-count and normalization was using in-house script.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: PBMC (Healthy Donor)

extract_protocol:
Total RNA from CAR-T cells was extracted using ReliaPrep RNA Tissue Miniprep System (Promega) according to the manufacturer’s instructions
cDNA libraries were constructed from 400 ng of RNA using the Stranded mRNA Prep Ligation kit (Illumina)

value: Blood

value: CD3 Cells

value: CAR-T Cells

value: 7 Days


title: WA U18, Biol rep 1

description: Library name: Sample 13


title: CAR-T Cells, GSK343_ID03


title: CAR-T Cells, DMSO_ID04


title: NA U18, Biol rep 1

description: Library name: Sample 19

value: YPS128 (North American, "NA")


title: CAR-T Cells, DMSO_ID03


title: PrS-MOW20022_13-WT3, WT

description:
Library name: GRHL1_W2_WT_3_GT24-02450_GCTTGTCA-GTATGTTC_S16
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Not applicable

value: day 6

value: primitive syncytium


title: WE Control, Biol rep 3

description: Library name: Sample 12

value: DBVPG6765 (Wine/European, "WE")

value: WT (ho::NatMX, ura3::KanMX)

value: Control


title: CAR-T Cells, GSK343_ID02


title: PrS-MOW20022_13-WT2, WT

description:
Library name: GRHL1_W2_WT_2_GT24-02449_ATCCACTG-ACGCACCT_S6
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: CAR-T Cells, A395_ID03


title: WE Control, Biol rep 2

description: Library name: Sample 11


title: PrS-MOW20022_13-WT1, WT

description:
Library name: GRHL1_W2_WT_1_GT24-02448_AAGTCCAA-TACTCATA_S30
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOW20013-D06, WT

description:
Library name: GCM1_W2_PTC_D06_GT24-01222_TCTCTACT-GAACCGCG_S13
WIBJ2.2J derived knockout cell line, GCM1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: CAR-T Cells, GSK343_ID01


title: CAR-T Cells, DMSO_ID01


title: CAR-T Cells, DMSO_ID02


title: CBO-MOW20008-B02, WT

description:
Library name: PAX6_W_Day9_PTC_B02_GT24-02470_GTCGGAGC-TTATAACC_S17
WIBJ2.2J derived knockout cell line, PAX6 PTC, differentiated to cortical brain organoid

value: day 9

value: Cortical brain (dorsal forebrain patterning)


title: CAR-T Cells, A395_ID02


title: CAR-T Cells, A395_ID01


title: PrS-MOW20013-A04, WT

description:
Library name: GCM1_W2_PTC_A04_GT24-01220_AGTTCAGG-TCTGTTGG_S27
WIBJ2.2J derived knockout cell line, GCM1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon


title: NA Control, Biol rep 2

description: Library name: Sample 8


title: doubles_GEN1 rep1

city: Zürich

first: Markus

middle: S

last: Schröder

state: Zürich

address: Otto-Stern-Weg 7

department: Biology, Molecular Health Sciences

country: Switzerland

institute: ETH Zürich

data_processing:
Raw paired-end FASTQ files were aligned to the GRCh38 reference genome using bowtie2 version 2.4.4
BAM files were sorted and indexed with samtools version 1.6
Total read counts were calculated for each sample and used to generate comparable bigwig files for visualization using bamCoverage version 3.3.0 and the scaleFactor option
Assembly: GRCh38
Supplementary files format and content: Scaled bigwig coverage files for all samples

source_name: RPE-1 TP53 KO FANCM KO SMARCAL1 KO GEN1 KO

growth_protocol: Ten million cells for each condition were fixed in 1% formaldehyde at room temperature for 15 minutes. The fixation reaction was quenched with glycine to a final concentration of 125 mM. Cells were harvested and washed twice with chilled PBS, and pellets were snap frozen in a dry ice-ethanol bath before storing at -80°C.

extract_protocol:
When ready to process, cell pellets were thawed on ice and incubated with lysis buffer 1 on ice for 10 minutes. Cells were pelleted by centrifugation and incubated with LB2 for 5 minutes on ice. The extracted nuclei were pelleted by centrifugation and resuspended in LB3. Nuclei were sonicated using a Covaris S2 sonicator. Debris were pelleted by centrifugation at 4°C and the supernatant was transferred to a 5 mL tube. 100 µL of Dynabeads protein A that had been prebound with MRE11 antibody (Novus, Cat# NB100-142) were added to the cell lysate and samples were incubated at 4°C overnight with rotation. Beads were collected on a magnetic stand and washed with ice-cold RIPA buffer 6 times, followed by a final wash with TBS before resuspending beads in 200 µL of elution buffer (50 mM Tris–HCl, pH 8; 10 mM EDTA; 1% SDS). The bead slurries were incubated overnight at 65°C to reverse crosslinks. Samples were treated with 1 mg/mL RNaseA (Ambion, Cat# 2271) for 30 minutes at 37°C, followed by proteinase K treatment 20 mg/mL (Invitrogen, Cat# 25530-049) for 1 hour at 55°C.
DNA was then purified using a MinElute PCR Purification Kit (Qiagen, Cat# 28004) and sequencing libraries were prepared using a NEBNext Ultra II kit.


title: PrS-MOW20013-B08, WT

description:
Library name: GCM1_W2_PTC_B08_GT24-01221_GACCTGAA-CTCACCAA_S14
WIBJ2.2J derived knockout cell line, GCM1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: doubles_ERCC4 rep1

source_name: RPE-1 TP53 KO FANCM KO SMARCAL1 KO ERCC4 KO


title: doubles_MUS81 rep1

source_name: RPE-1 TP53 KO FANCM KO SMARCAL1 KO MUS81 KO


title: NA Control, Biol rep 1

description: Library name: Sample 7


title: PrS-MOW20022-B12, WT

description:
Library name: GRHL1_W2_PTC_B12_GT24-02447_GGACTTGG-CGTCTGCG_S24
WIBJ2.2J derived knockout cell line, GRHL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOW20022-B10, WT

description:
Library name: GRHL1_W2_PTC_B10_GT24-02446_TTATAACC-TCGATATC_S23
WIBJ2.2J derived knockout cell line, GRHL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: SMARCAL1KOsgFANCM_X rep1

source_name: RPE-1 TP53 KO FANCM KO SMARCAL1 KO

value: RPE-1 TP53 KO FANCM KO SMARCAL1 KO


title: CAR-T Cells, A395_ID04


title: sgFANCM_X rep1

source_name: RPE-1 TP53 KO FANCM KO

value: RPE-1 TP53 KO FANCM KO


title: SA Control, Biol rep 2

description: Library name: Sample 5

value: Y12 (Sake, "SA")


title: WE Control, Biol rep 1

description: Library name: Sample 10


title: SA Control, Biol rep 1

description: Library name: Sample 4


title: WT_X rep1

source_name: RPE-1 TP53 KO

value: RPE-1 TP53 KO


title: SMARCAL1_FANCMKO rep1

source_name: RPE-1 TP53 KO SMARCAL1 KO FANCM KO

value: RPE-1 TP53 KO SMARCAL1 KO FANCM KO


title: PrS-MOW20012-WT3-hyp, WT

description:
Library name: EPAS1_W_WT_3_3__GT24-02456_CTCTCGTC-AGGTTATA_S12
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: NA Control, Biol rep 3

description: Library name: Sample 9


title: FANCM_SMARCAL1KO rep1


title: PrS-MOW20012-WT2-hyp, WT

description:
Library name: EPAS1_W_WT_2_3__GT24-02455_TCTCTACT-GAACCGCG_S18
WIBJ2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: doubles_ERCC1 rep1

source_name: RPE-1 TP53 KO FANCM KO SMARCAL1 KO ERCC1 KO


title: FANCM_WT rep1


title: SMARCAL1_WT rep1

source_name: RPE-1 TP53 KO SMARCAL1 KO

value: RPE-1 TP53 KO SMARCAL1 KO