title: YY1 Day4 2 CnR 531

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford

description: control: IgG_Day4_1_CnR_501, batch: 231204_cnr14, high stringency buffer?: No

data_processing:
CUT&RUN analysis was performed with custom Snakemake pipelines. Adapters were removed using cutadapt20 v.4.5, aligned to hg38 with bowtie221 v.2.4.2 (--end-to-end --very-sensitive --no-mixed --no-discordant -I 10 -X 700), and duplicates removed  (samtools fixmate -m {input} - |  samtools sort -T {params.tmp} - | samtools markdup - - | samtools view -b -f 0x3 -F 0x400 –). Replicates were combined with samtools merge. Peaks were called with MACS222 (v.2.2.9.1) vs IgG controls (macs2 callpeak -t {input.expt} -c {input.ctrl} -g hs -f BAMPE -q 0.1). Peaks were filtered using the ENCODE exclusion list (ENCFF356LFX).
Assembly: hg38
Supplementary files format and content: Bigwig files scaled to reads per million, and for non-IgG samples, MACS2 peaks called with the default settings vs the IgG controls.
Library strategy: CUT&RUN

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500).

extract_protocol:
CUT&RUN was performed without fixation according mostly to the Epicypher protocol. CUT&RUN was performed on 0.4-1 million primary keratinocytes/experiment using reagents from the EpiCypher kit (EpiCypher, 14-1048), either using antibody to the endogenous TF (the majority) or infected with virus expressing HA-tagged TF (NRF1 and ZNF217). Keratinocytes were washed with PBS, harvested with trypsin, quenched with DMEM, and resuspended in cold PBS + 0.1% BSA to be maintained afterwards at 4°C. Cells were washed twice with PBS + 0.1% BSA, and quantified with a Countess. Nuclei were extracted by resuspending in 100 μL nuclei extraction buffer per 1-2.5 M cells (20 mM HEPES pH 7.5, 10 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 0.1% NP-40, and 1 tablet Roche mini protease inhibitor per 10-15 mL) and incubating for 10 minutes on ice. 5-10 volumes of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% BSA, 0.05%Triton X-100, and Roche protease inhibitor) were added, cells centrifuged at 600 RCF, and supernatant removed. After an additional wash, cells were quantified using a Countess. 400K-1M nuclei were bound to 10 μL activated Concanavalin A beads (EpiCypher, 21-1401) per sample for 10 min incubation at 4°C. After removing supernatant, beads were incubated with rocking at 4°C for 2 hrs with antibody diluted in 50 μL Antibody Buffer (wash buffer with 2 mM EDTA). After staining, cells were washed twice with wash buffer, and incubated with 1.5-2.5 μL pAG-MNase (EpiCypher, 15-1016) per sample for 1 hour at 4°C with rocking, then washed with once with 150 μL wash buffer, then 150 μL low salt buffer (3.5 mM HEPES pH 7.5, 0.5 mM spermidine, 0.1% BSA, 0.05%Triton X-100, and Roche protease inhibitor) and resuspend in 50 µL low salt buffer. After 5 minutes on ice, 2 μL of 250 mM CaCl2 was added to the beads and beads were subsequentially incubated on ice for 18-25 minutes. The reactions were quenched with an equal volume 2X STOP buffer (300 mM NaCl, 20 mM EDTA, 40 mM EGTA, 0.025% SDS, 0.5% Triton X100, 0.05 mg/mL RNAse A, 0.05 mg/mL glycogen) for 30 minutes at 37°C according to the manufacturer’s protocol. Beads were placed on a magnet, and supernatant containing released fragments was removed.
DNA was extracted by a Zymo DNA Clean and Concentrator (Zymo Research, D4014), eluting in 27 μL water. Library was prepared using the NEB Ultra II DNA library prep kit (NEB, E7103S) following dx.doi.org/10.17504/protocols.io.bagaibse6, with the following modifications: the adapter was diluted 20-25 fold, PCR was performed with SYBR dye to visualize amplification, and after PCR, 20 μL of water, then 30 μL of beads (0.6X instead of 0.8X) beads were added for the initial selection to remove large small fragments, followed by the second size selection using the addition of 20 μL beads (1X instead of 1.2X) for library capture. Sequencing was performed on a NovaSeq X Plus, paired-end, 150 bp length, with 15-20 M reads for each sample.

treatment_protocol: If differentiated ("Day 4"), cells were induced to differentiate by the addition of 1.2 mM calcium for 4 days at full confluence.

tag: antibody

value: Primary keratinocytes

tag: genotype

value: Differentiated


title: YY1 Day4 4 CnR 532

status: Public on Jul 21 2025

type: SRA

country: USA

description: control: IgG_Day4_2_CnR_502, batch: 231204_cnr14, high stringency buffer?: No

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: treatment


title: A3_Molm13_colony_rep1, RNA

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

library_source: transcriptomic

data_processing:
bisulfite libraries were processed using Bismark (v0.22.3) and as previously described [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
After initial demultiplexing of primary Illumina indexes, Cutadapt (v2.10) [18] was used to demultiplex pools based on custom secondary indexes
Commands –g and -G were used to pass named forward and reverse index lists as a .fasta file to Cutadapt for demultiplexing
Bisulfite reads were trimmed using Trim Galore (v0.6.5). 10bp was trimmed from both the 5’ and 3’ ends to remove oligo sequences from reads.
Reads were mapped to Bowtie2 (v 2.4.1) indexed human genome (GRCh38) non-directionally and as paired end using Bismark (v0.22.3)
The methylation extraction module from Bismark was then used to produce coverage files (.cov) for methylation analysis.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Following demultiplexing, squencing runs with multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element countreateds from unique and ambiguously aligned reads (bam files) using TEcountreated with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single countreated table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Countreateds for individual samples are contained in column 14 onwards.

molecule: polyA RNA

source_name: Peripheral blood

growth_protocol:
Cell lines were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium.  HL-60 cells were maintained in Iscove's Modified Dulbecco's media supplemented with 4mM GlutaMAX and 10% Fetal Bovine Serum (FBS). MOLM-13 and MV-4-11 cells were maintained in Roswell Park Memorial Institute 1640 media supplemented with 2mM GlutaMAX and 10% FBS.
Treated cells were seeded in MethoCult Optimum (H4034; STEMCELL Technologies Inc.) at 500 cells/well in 6-well plates. Cells were then cultured at 37°C, 5% CO2 for 14 days to allow colony formation. Wells containing colonies were imaged using Cytation3 (Biotek). Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C.

extract_protocol:
Individual colonies were manually plucked using a 20µL pipette tip into 100µL of media, centrifuged at 200xg for 5 mins, and then resuspended in 20µL of RLT PLUS buffer before storage at −80°C. Lysates from single colonies (HL-60: 7.5µL; MOLM-13 and MV-4-11: 2.5µL) were used to separate genomic DNA and mRNA by G&T separation and as previously described following 'scTEM-seq for low-input samples' [Hunt, K. V. et al. sTEM-seq: Single-cell analysis of transposable element methylation to link global epigenetic heterogeneity with transcriptional programs. Scientific Reports (2022)] [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)].
Single colony TEM-seq and parallel RNA-seq analysis was performed as described, with minor modifications. During single colony TEM-seq library preparation, the number of SINE Alu amplification cycles was reduced to 29. For RNA-seq analysis, 15 cycles of cDNA amplification were used. [Hunt, K. V. et al.  Protocol for targeted analysis of transposable element methylation levels and transcriptome in single cells using scTEM-seq. Protocol Exchange  (2022)]

treatment_protocol: Cell lines were treated with HMAs at various doses in suspension culture, every 24h for 72h total. All cell lines were treated with 100nM decitabine (DAC; Selleckchem #S1200), HL-60 cells were treated with 2000nM azacytidine (AZA; Selleckchem # S1782), and MOLM-13 and MV-4-11 cells were treated with 500nM AZA. Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a control.

value: Peripheral blood

tag: cell line

tag: cell type

value: acute myeloid leukemia

tag: disease/cancer type

value: Acute myeloid leukemia (M5a)

tag: Sex

value: Male

tag: age

tag: batch

tag: paired sample_id

tag: processing protocol

value: RNA-Seq

value: untreated


title: YY1 Day4 2 CnR 364

description: control: IgG_Day4_2_CnR_358, batch: 230814_cnr9, high stringency buffer?: No


title: A1_Molm13_colony_rep1, RNA


title: YY1 Day4 1 CnR 153

description: control: IgG_Day4_2_CnR_150, batch: 230407_cnr4, high stringency buffer?: Yes


title: YY1 Day4 1 CnR 197

description: control: IgG_Day4_1_CnR_193, batch: 230517_cnr6, high stringency buffer?: Yes


title: YY1 Day4 1 CnR 363

description: control: IgG_Day4_1_CnR_357, batch: 230814_cnr9, high stringency buffer?: No


title: YY1 Prog 1 CnR 552

description: control: IgG_Prog_1_CnR_533, batch: 231204_cnr14, high stringency buffer?: nan

tag: treatment:


title: YY1 Prog 1 CnR 331

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: YY1 Prog 2 CnR 332

description: control: IgG_Prog_2_CnR_326, batch: 230814_cnr9, high stringency buffer?: No


title: YY1 Prog 321

description: control: IgG_Prog_304, batch: 230803_cnr8, high stringency buffer?: Yes


title: YY1 Prog 1 CnR 181

description: control: IgG_Prog_1_CnR_177, batch: 230517_cnr6, high stringency buffer?: Yes


title: TFAP2C Day4 2 CnR 514


title: TFAP2C Day4 1 CnR 513


title: TFAP2C Prog 2 CnR 546

description: control: IgG_Prog_2_CnR_534, batch: 231204_cnr14, high stringency buffer?: No


title: TFAP2C Prog 1 CnR 545

description: control: IgG_Prog_1_CnR_533, batch: 231204_cnr14, high stringency buffer?: No


title: TFAP2A Day4 2 CnR 408

description: control: IgG_Day4_2_CnR_390, batch: 230818_cnr10, high stringency buffer?: No


title: TFAP2A Day4 1 CnR 407

description: control: IgG_Day4_1_CnR_389, batch: 230818_cnr10, high stringency buffer?: No


title: TFAP2A Day4 3 CnR 388


title: TFAP2A Day4 1 CnR 361


title: TFAP2A Day4 1 CnR 194


title: TFAP2A Day4 1 CnR 160

description: control: IgG_Day4_1_CnR_159, batch: 230418_cnr5, high stringency buffer?: Yes


title: TFAP2A Prog 2 CnR 432

description: control: IgG_Prog_2_CnR_422, batch: 230818_cnr10, high stringency buffer?: No


title: TFAP2A Prog 2 CnR 441

description: control: IgG_Prog_2_CnR_438, batch: 230911_cnr11, high stringency buffer?: No


title: TFAP2A Prog 1 CnR 440

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No


title: TFAP2A Prog 1 CnR 431

description: control: IgG_Prog_1_CnR_421, batch: 230818_cnr10, high stringency buffer?: No


title: TEAD3 Day4 2 CnR 527

description: control: IgG_Day4_1_CnR_501, batch: 231204_cnr14, high stringency buffer?: No


title: TFAP2A Prog 2 CnR 330


title: TFAP2A Prog 1 CnR 329


title: TFAP2A Prog 1 CnR 168

description: control: IgG_Prog_1_CnR_167, batch: 230418_cnr5, high stringency buffer?: Yes


title: TEAD3 Prog 1 CnR 255

description: control: IgG_Prog_1_CnR_239, batch: 230608_cnr7, high stringency buffer?: Yes


title: TEAD1 Day4 3 CnR 525


title: TEAD1 Day4 2 CnR 374

description: control: IgG_Day4_2_CnR_358, batch: 230814_cnr9, high stringency buffer?: No


title: TEAD1 Day4 1 CnR 202

description: control: IgG_Day4_1_CnR_193, batch: 230517_cnr6, high stringency buffer?: Yes


title: TEAD1 Day4 1 CnR 373

description: control: IgG_Day4_1_CnR_357, batch: 230814_cnr9, high stringency buffer?: No


title: TFAP2A Day4 2 CnR 473

description: control: IgG_Day4_2_CnR_470, batch: 230911_cnr11, high stringency buffer?: No


title: TEAD1 Prog 2 CnR 548


title: TEAD1 Prog 1 CnR 547


title: TEAD1 Prog 1 CnR 341

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: TEAD1 Prog 1 CnR 186

description: control: IgG_Prog_1_CnR_177, batch: 230517_cnr6, high stringency buffer?: Yes


title: TADA2B Day4 297

description: control: IgG_Day4_284, batch: 230803_cnr8, high stringency buffer?: Yes


title: TFAP2A Day4 2 CnR 362


title: TADA2B Day4 1 CnR 259

description: control: IgG_Day4_1_CnR_263, batch: 230608_cnr7, high stringency buffer?: Yes


title: TADA2B Day4  CnR 215

description: control: IgG_Day4_1_CnR_220, batch: 230608_cnr7, high stringency buffer?: Yes


title: TADA2B Prog 1 CnR 235


title: SP3 Day4 1 CnR 507


title: TADA2B Prog 315

description: control: IgG_Prog_304, batch: 230803_cnr8, high stringency buffer?: Yes


title: TFAP2A Prog 1 CnR 178


title: SP3 Day4 1 CnR 489

description: control: IgG_Day4_1_CnR_469, batch: 230911_cnr11, high stringency buffer?: No


title: SP3 Day4 1 CnR 121

description: control: IgG_Day4_1_CnR_127, batch: 230403_cnr3, high stringency buffer?: Yes


title: TEAD3 Day4 1 CnR 279


title: SP3 Prog 2 CnR 540

description: control: IgG_Prog_2_CnR_534, batch: 231204_cnr14, high stringency buffer?: No


title: SP3 Prog 1 CnR 539

description: control: IgG_Prog_1_CnR_533, batch: 231204_cnr14, high stringency buffer?: No


title: SP3 Prog 1 CnR 457

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No


title: SP3 Prog 2 CnR 104

description: control: IgG_Prog_2_CnR_106, batch: 230403_cnr3, high stringency buffer?: Yes


title: TEAD3 Prog 1 CnR 549


title: TEAD1 Day4 1 CnR 526

description: control: IgG_Day4_2_CnR_502, batch: 231204_cnr14, high stringency buffer?: No


title: SP1 Day4 2 CnR 368

description: control: IgG_Day4_2_CnR_358, batch: 230814_cnr9, high stringency buffer?: No


title: SP1 Day4 1 CnR 505

description: control: IgG_Day4_1_CnR_501, batch: 231204_cnr14, high stringency buffer?: No


title: SP1 Day4 2 CnR 506


title: SP1 Day4 2 CnR 116

description: control: IgG_Day4_2_CnR_128, batch: 230403_cnr3, high stringency buffer?: Yes


title: SP3 Prog 1 CnR 103

description: control: IgG_Prog_3_CnR_107, batch: 230403_cnr3, high stringency buffer?: Yes


title: TEAD1 Prog 2 CnR 342

description: control: IgG_Prog_2_CnR_326, batch: 230814_cnr9, high stringency buffer?: No


title: SP1 Prog 2 CnR 538


title: SP1 Day4 1 CnR 115


title: SP1 Prog 1 CnR 537


title: SP1 Prog 2 CnR 336


title: SP1 Prog 1 CnR 335

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: SP1 Prog 1 CnR 96


title: SP1 Prog 2 CnR 97


title: SOX9 Day4 1 CnR 484


title: SP3 Day4 2 CnR 122


title: SOX9 Day4 1 CnR 217


title: SOX9 Prog 1 CnR 452


title: SNAI2 Day4 2 CnR 402

description: control: IgG_Day4_2_CnR_390, batch: 230818_cnr10, high stringency buffer?: No


title: SOX9 Prog 1 CnR 236

description: control: IgG_Prog_1_CnR_239, batch: 230608_cnr7, high stringency buffer?: Yes


title: SNAI2 Day4 1 CnR 401

description: control: IgG_Day4_1_CnR_389, batch: 230818_cnr10, high stringency buffer?: No


title: SNAI2 Day4 3 CnR 387

description: control: IgG_Day4_1_CnR_357, batch: 230814_cnr9, high stringency buffer?: No


title: SNAI2 Day4 2 CnR 380


title: SNAI2 Day4 1 CnR 379


title: SNAI2 Day4 2 CnR 208

description: control: IgG_Day4_2_CnR_201, batch: 230517_cnr6, high stringency buffer?: Yes


title: SNAI2 Day4 1 CnR 195

description: control: IgG_Day4_1_CnR_193, batch: 230517_cnr6, high stringency buffer?: Yes


title: SNAI2 Day4 1 CnR 157

description: control: IgG_Day4_1_CnR_159, batch: 230418_cnr5, high stringency buffer?: Yes


title: SP1 Day4 1 CnR 367


title: SNAI2 Prog 2 CnR 418

description: control: IgG_Prog_2_CnR_422, batch: 230818_cnr10, high stringency buffer?: No


title: SNAI2 Prog 1 CnR 347


title: SNAI2 Prog 2 CnR 348


title: SNAI2 Prog 1 CnR 417

description: control: IgG_Prog_1_CnR_421, batch: 230818_cnr10, high stringency buffer?: No


title: SNAI2 Prog 1 CnR 179

description: control: IgG_Prog_1_CnR_177, batch: 230517_cnr6, high stringency buffer?: Yes


title: RUNX1 Day4 2 CnR 396


title: RUNX1 Day4 1 CnR 395


title: SNAI2 Prog 1 CnR 165


title: RUNX1 Prog 2 CnR 446

description: control: IgG_Prog_2_CnR_438, batch: 230911_cnr11, high stringency buffer?: No


title: RUNX1 Prog 1 CnR 445

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No


title: RUNX1 Day4 1 CnR 262

description: control: IgG_Day4_1_CnR_263, batch: 230608_cnr7, high stringency buffer?: Yes


title: RUNX1 Prog 2 CnR 428


title: SOX9 Day4 1 CnR 260


title: RUNX1 Prog 1 CnR 427


title: RUNX1 Prog 320

description: control: IgG_Prog_304, batch: 230803_cnr8, high stringency buffer?: Yes


title: P63 Day4 2 CnR 478

description: control: IgG_Day4_2_CnR_470, batch: 230911_cnr11, high stringency buffer?: No


title: RUNX1 Prog 1 CnR 238


title: P63 Day4 1 CnR 477

description: control: IgG_Day4_1_CnR_469, batch: 230911_cnr11, high stringency buffer?: No


title: P63 Day4 1 CnR 403


title: P63 Day4 2 CnR 404


title: P63 Day4 3 CnR 386


title: P63 Day4 2 CnR 360

description: control: IgG_Day4_2_CnR_358, batch: 230814_cnr9, high stringency buffer?: No


title: P63 Prog 2 CnR 420


title: P63 Day4 1 CnR 222

description: control: IgG_Day4_1_CnR_220, batch: 230608_cnr7, high stringency buffer?: Yes


title: P63 Day4 1 CnR 265


title: P63 Day4 1 CnR 359


title: P63 Prog 1 CnR 419


title: P63 Prog 1 CnR 327

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: P63 Prog 2 CnR 328

description: control: IgG_Prog_2_CnR_326, batch: 230814_cnr9, high stringency buffer?: No


title: P63 Prog 319


title: OVOL1 Day4 2 CnR 516

description: control: IgG_Day4_2_CnR_502, batch: 231204_cnr14, high stringency buffer?: No


title: OVOL1 Day4 1 CnR 515

description: control: IgG_Day4_1_CnR_501, batch: 231204_cnr14, high stringency buffer?: No


title: P63 Prog 1 CnR 241

description: control: IgG_Prog_1_CnR_239, batch: 230608_cnr7, high stringency buffer?: Yes


title: OVOL1 Day4 2 CnR 406

description: control: IgG_Day4_2_CnR_390, batch: 230818_cnr10, high stringency buffer?: No


title: OVOL1 Day4 1 CnR 371

description: control: IgG_Day4_1_CnR_357, batch: 230814_cnr9, high stringency buffer?: No


title: OVOL1 Day4 1 CnR 405

description: control: IgG_Day4_1_CnR_389, batch: 230818_cnr10, high stringency buffer?: No


title: OVOL1 Day4 2 CnR 372


title: OVOL1 Day4 2 CnR 232


title: OVOL1 Day4 1 CnR 213


title: OVOL1 Day4 1 CnR 257


title: OVOL1 Prog 2 CnR 430

description: control: IgG_Prog_2_CnR_422, batch: 230818_cnr10, high stringency buffer?: No


title: OVOL1 Prog 1 CnR 429

description: control: IgG_Prog_1_CnR_421, batch: 230818_cnr10, high stringency buffer?: No


title: OVOL1 Prog 1 CnR 233


title: OVOL1 Prog 2 CnR 340


title: OVOL1 Prog 1 CnR 339


title: OVOL1 Prog 2 CnR 212

description: control: IgG_Prog_1_CnR_242, batch: 230608_cnr7, high stringency buffer?: Yes


title: KLF5 Day4 2 CnR 510


title: KLF5 Day4 1 CnR 509


title: KLF5 Day4 2 CnR 392


title: KLF5 Day4 1 CnR 391


title: KLF5 Day4 1 CnR 214


title: KLF5 Prog 2 CnR 424


title: KLF5 Day4 1 CnR 258

description: control: IgG_Day4_1_CnR_263, batch: 230608_cnr7, high stringency buffer?: Yes


title: KLF5 Prog 1 CnR 541

description: control: IgG_Prog_1_CnR_533, batch: 231204_cnr14, high stringency buffer?: No


title: KLF5 Prog 2 CnR 542

description: control: IgG_Prog_2_CnR_534, batch: 231204_cnr14, high stringency buffer?: No


title: KLF5 Prog 1 CnR 423


title: KLF4 Day4 2 CnR 504


title: KLF4 Day4 1 CnR 503


title: KLF4 Day4 1 CnR 369


title: KLF4 Day4 1 CnR 145

description: control: IgG_Day4_1_CnR_141, batch: 230407_cnr4, high stringency buffer?: Yes


title: KLF4 Day4 1 CnR 142


title: KLF4 Prog 1 CnR 535


title: KLF4 Prog 2 CnR 536


title: KLF4 Prog 1 CnR 137

description: control: IgG_Prog_1_CnR_133, batch: 230407_cnr4, high stringency buffer?: Yes


title: KHDRBS1 Day4 1 CnR 476

description: control: IgG_Day4_1_CnR_469, batch: 230911_cnr11, high stringency buffer?: No


title: KLF4 Prog 1 CnR 337

description: control: IgG_Prog_1_CnR_325, batch: 230814_cnr9, high stringency buffer?: No


title: KHDRBS1 Day4 1 CnR 385


title: KHDRBS1 Prog 1 CnR 444

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No


title: JUNB Day4 2 CnR 499

description: control: IgG_Day4_2_CnR_470, batch: 230911_cnr11, high stringency buffer?: No

value: JUNB


title: JUNB Day4 2 CnR 394


title: JUNB Day4 1 CnR 393


title: JUNB Day4 283

description: control: IgG_Day4_284, batch: 230803_cnr8, high stringency buffer?: Yes


title: JUNB Prog 2 CnR 426


title: JUNB Prog 1 CnR 425


title: JUNB Day4 1 CnR 203

description: control: IgG_Day4_1_CnR_193, batch: 230517_cnr6, high stringency buffer?: Yes


title: JUNB Prog 303

description: control: IgG_Prog_304, batch: 230803_cnr8, high stringency buffer?: Yes


title: IgG Day4 2 CnR 524

description: control: nan, batch: 231204_cnr14, high stringency buffer?: No

value: IgG


title: KLF5 Prog 1 CnR 234

description: control: IgG_Prog_1_CnR_239, batch: 230608_cnr7, high stringency buffer?: Yes


title: JUNB Prog 1 CnR 187

description: control: IgG_Prog_1_CnR_177, batch: 230517_cnr6, high stringency buffer?: Yes


title: IgG Day4 1 CnR 501


title: KLF5 Prog 318


title: IgG Day4 2 CnR 502


title: KLF4 Day4 2 CnR 370

description: control: IgG_Day4_2_CnR_358, batch: 230814_cnr9, high stringency buffer?: No


title: IgG Day4 1 CnR 469

description: control: nan, batch: 230911_cnr11, high stringency buffer?: No


title: IgG Day4 2 CnR 470


title: KLF4 Prog 1 CnR 134


title: KLF4 Prog 2 CnR 338

description: control: IgG_Prog_2_CnR_326, batch: 230814_cnr9, high stringency buffer?: No


title: IgG Day4 2 CnR 390

description: control: nan, batch: 230818_cnr10, high stringency buffer?: No


title: IgG Day4 2 CnR 358

description: control: nan, batch: 230814_cnr9, high stringency buffer?: No


title: IgG Day4 1 CnR 389


title: IgG Day4 1 CnR 357


title: IgG Day4 284

description: control: nan, batch: 230803_cnr8, high stringency buffer?: Yes


title: IgG Day4 2 CnR 223

description: control: nan, batch: 230608_cnr7, high stringency buffer?: Yes


title: JUNB Day4 1 CnR 498

description: control: IgG_Day4_1_CnR_469, batch: 230911_cnr11, high stringency buffer?: No


title: IgG Day4 1 CnR 159

description: control: nan, batch: 230418_cnr5, high stringency buffer?: Yes


title: IgG Day4 1 CnR 141

description: control: nan, batch: 230407_cnr4, high stringency buffer?: Yes


title: IgG Day4 1 CnR 193

description: control: nan, batch: 230517_cnr6, high stringency buffer?: Yes


title: IgG Day4 2 CnR 201


title: IgG Day4 4 CnR 130

description: control: nan, batch: 230403_cnr3, high stringency buffer?: Yes


title: IgG Day4 2 CnR 128


title: IgG Day4 1 CnR 127


title: IgG Day4 5 CnR 70

description: control: nan, batch: 230302_merged, high stringency buffer?: Yes


title: IgG Day4 3 CnR 129


title: IgG Day4 4 CnR 69


title: IgG Day4 6 CnR 71


title: IgG Day4 2 CnR 64


title: IgG Day4 1 CnR 63


title: IgG Day4 3 CnR 65


title: IgG Day4 1 CnR 29


title: IgG Prog 1 CnR 533


title: IgG Day4 2 CnR 30


title: IgG Prog 1 CnR 437


title: IgG Day4 1 CnR 266


title: IgG Day4 1 CnR 263


title: IgG Prog 3 CnR 468


title: IgG Prog 2 CnR 326


title: IgG Prog 2 CnR 422


title: IgG Prog 1 CnR 325


title: IgG Prog 1 CnR 421


title: IgG Day4 1 CnR 220


title: IgG Prog 322


title: IgG Day4 2 CnR 150


title: IgG Prog 2 CnR 185


title: IgG Prog 1 CnR 239


title: IgG Prog 1 CnR 177


title: IgG Prog 1 CnR 242


title: IgG Prog 1 CnR 133


title: IgG Prog 2 CnR 176


title: IgG Prog 1 CnR 167


title: IgG Prog 1 CnR 105


title: IgG Prog 4 CnR 66


title: IgG Prog 2 CnR 106


title: IgG Prog 3 CnR 62


title: IgG Prog 2 CnR 438


title: IgG Prog 2 CnR 534


title: IgG Prog 5 CnR 67


title: IgG Prog 6 CnR 68


title: IgG Prog 2 CnR 61


title: IgG Prog 1 CnR 60


title: HOPX Day4 1 CnR 483

value: HOPX


title: HA-ZNF217 Day4 3 CnR 77

description: control: IgG_Day4_3_CnR_65, batch: 230302_merged, high stringency buffer?: Yes


title: HA-ZNF217 Day4 2 CnR 76

description: control: IgG_Day4_2_CnR_64, batch: 230302_merged, high stringency buffer?: Yes


title: IgG Prog 1 CnR 27


title: HOPX Prog 1 CnR 451

description: control: IgG_Prog_1_CnR_437, batch: 230911_cnr11, high stringency buffer?: No


title: HA-ZNF217 Day4 1 CnR 75

description: control: IgG_Day4_1_CnR_63, batch: 230302_merged, high stringency buffer?: Yes


title: IgG Prog 2 CnR 28


title: HA-ZNF217 Day4 1 CnR 33

description: control: IgG_Day4_1_CnR_29, batch: 230302_merged, high stringency buffer?: Yes


title: HA-ZNF217 Prog 2 CnR 32

description: control: IgG_Prog_2_CnR_28, batch: 230302_merged, high stringency buffer?: Yes


title: IgG Prog 304


title: HA-ZNF217 Prog 1 CnR 31

description: control: IgG_Prog_1_CnR_27, batch: 230302_merged, high stringency buffer?: Yes


title: HA-NRF1 Day4 5 CnR 82

description: control: IgG_Day4_5_CnR_70, batch: 230302_merged, high stringency buffer?: Yes


title: HA-NRF1 Day4 6 CnR 83

description: control: IgG_Day4_6_CnR_71, batch: 230302_merged, high stringency buffer?: Yes


title: IgG Prog 3 CnR 107


title: HA-NRF1 Prog 6 CnR 80

description: control: IgG_Prog_6_CnR_68, batch: 230302_merged, high stringency buffer?: Yes


title: HA-NRF1 Prog 5 CnR 79

description: control: IgG_Prog_5_CnR_67, batch: 230302_merged, high stringency buffer?: Yes


title: HA-NRF1 Prog 4 CnR 78

description: control: IgG_Prog_4_CnR_66, batch: 230302_merged, high stringency buffer?: Yes


title: H3K27me3 Day4 1 CnR 85


title: H3K27me3 Day4 1 CnR 86

description: control: IgG_Day4_4_CnR_69, batch: 230302_merged, high stringency buffer?: Yes


title: H3K27me3 Prog 1 CnR 465


title: H3K27me3 Prog 1 CnR 84

description: control: IgG_Prog_1_CnR_60, batch: 230302_merged, high stringency buffer?: Yes


title: ETV3 Day4 2 CnR 480

description: control: IgG_Day4_2_CnR_470, batch: 230911_cnr11, high stringency buffer?: No


title: GRHL1 Day4 1 CnR 261

description: control: IgG_Day4_1_CnR_263, batch: 230608_cnr7, high stringency buffer?: Yes


title: ETV3 Day4 1 CnR 479

description: control: IgG_Day4_1_CnR_469, batch: 230911_cnr11, high stringency buffer?: No


title: GRHL1 Prog 1 CnR 237

description: control: IgG_Prog_1_CnR_239, batch: 230608_cnr7, high stringency buffer?: Yes


title: GRHL1 Day4 1 CnR 218

description: control: IgG_Day4_1_CnR_220, batch: 230608_cnr7, high stringency buffer?: Yes


title: ETV3 Prog 2 CnR 448

description: control: IgG_Prog_2_CnR_438, batch: 230911_cnr11, high stringency buffer?: No


title: HA-ZNF217 Day4 2 CnR 34

description: control: IgG_Day4_2_CnR_30, batch: 230302_merged, high stringency buffer?: Yes


title: OE_CBX7_2

city: Tianjin

first: Bei

last: Lan

state: 天津Tianjin

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

country: China

institute: Tianjin Medical University

description: Library name: Sample 4

data_processing:
Reads were aligned to the human genome (UCSC hg38) using HISAT2 (v2.2.1) with the following parameters: --no-mixed --no-discordant.
Gene expression levels were quantified by StringTie (v2.2.1).
DESeq2  was used to perform differential expression analysis.
Assembly: hg38
Supplementary files format and content: gene_count.csv: comma-separated table file includes raw count for each example.

molecule: total RNA

source_name: Lung

growth_protocol: A549 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CBX7 expression and control constructs were introduced into A549 cells via lentiviral infection to establish stable CBX7 overexpressing cell line and control cell line.

value: Lung

value: human lung adenocarcinoma cell

value: CBX7 overexpression


title: OE_CBX7_1

description: Library name: Sample 3


title: VM16

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description: Library name: S1429939.4_S76

data_processing:
Raw reads quality and adapter sequences were checked using FastQC (v. 0.11.8, RRID:SCR_014583). Sequencing reads were mapped using STAR (RRID:SCR_004463) against the human genome build (UCSC hg38), and gene level quantification was performed with featureCounts (RRID:SCR_012919).
Assembly: hg38
Supplementary files format and content: CSV file with raw counts for each sample

source_name: CRC

extract_protocol:
RNA was isolated using the Roche KAPA Stranded RNA-Seq kit with RiboErase according to the manufacturer protocol
Roche KAPA Stranded RNA-Seq kit with RiboErase

value: CRC

tag: subject

tag: time for_draw

value: Baseline

tag: response

value: PR


title: Control_2

description: Library name: Sample 2

value: WT


title: VM23

description: Library name: S1486200.6_S78


title: VM19

description: Library name: S1438442.6_S77

value: nonPR


title: VM8

description: Library name: S1319204.5_S78


title: HA-NRF1 Day4 4 CnR 81

value: Primary keratinocytes

value: Differentiated


title: Control_1

description: Library name: Sample 1


title: VM13

description: Library name: S1385330.2_S74


title: VM7

description: Library name: S1313797.6_S77


title: H3K27me3 Day4 1 CnR 496


title: VM5

description: Library name: S1292511.6_S75


title: VM6

description: Library name: S1298900.2_S76


title: VM4

description: Library name: S1291849.6_S74


title: VM1

description: Library name: S1276116.6_S73


title: VM14

description: Library name: S1385735.2_S75


title: VM25.1_S18

description: Library name: VM25.1

source_name: evRNA from blood

extract_protocol:
RNA was isolated using Invitrogen total exosome RNA & Protein Isolation kit according to the manufacturer protocol
SMART-Seq® v4 Ultra® low input RNA kit followed by Illumina Nextera XT DNA Library Preparation

value: evRNA from blood


title: VM12

description: Library name: S1357253.6_S73


title: VM23.2_S6

description: Library name: VM23.2

value: encorafenib, cetuximab, and nivolumab


title: VM24.1_S45

description: Library name: VM24.1


title: VM24.2_S16

description: Library name: VM24.2


title: VM22.1_S41

description: Library name: VM22.1


title: VM22.2_S43

description: Library name: VM22.2


title: VM20.2_S51

description: Library name: VM20.2


title: VM21.1_S52

description: Library name: VM21.1


title: VM20.1_S50

description: Library name: VM20.1


title: VM23.1_S47

description: Library name: VM23.1


title: VM21.2_S46

description: Library name: VM21.2


title: VM19.1_S54

description: Library name: VM19.1


title: VM19.2_S42

description: Library name: VM19.2


title: VM18.2_S49

description: Library name: VM18.2


title: VM18.1_S56

description: Library name: VM18.1


title: VM17.1_S55

description: Library name: VM17.1


title: VM17.2_S48

description: Library name: VM17.2


title: VM15.2_S1

description: Library name: VM15.2


title: VM16.1_S62

description: Library name: VM16.1


title: VM15.1_S17

description: Library name: VM15.1


title: VM16.2_S44

description: Library name: VM16.2


title: VM14.2_S11

description: Library name: VM14.2


title: VM25.2_S24

description: Library name: VM25.2


title: VM14.1_S19

description: Library name: VM14.1


title: VM13.2_S10

description: Library name: VM13.2


title: VM13.1_S21

description: Library name: VM13.1


title: VM12.1_S59

description: Library name: VM12.1


title: VM12.2_S15

description: Library name: VM12.2


title: VM11.2_S66

description: Library name: VM11.2


title: VM9.2_S65

description: Library name: VM9.2


title: VM10.2_S64

description: Library name: VM10.2


title: VM10.1_S22

description: Library name: VM10.1


title: VM8.2_S63

description: Library name: VM8.2


title: VM8.1_S14

description: Library name: VM8.1


title: VM7.2_S13

description: Library name: VM7.2


title: VM9.1_S9

description: Library name: VM9.1


title: VM7.1_S20

description: Library name: VM7.1


title: VM5.1_S53

description: Library name: VM5.1


title: VM6.1_S58

description: Library name: VM6.1


title: VM6.2_S7

description: Library name: VM6.2


title: VM3.2_S61

description: Library name: VM3.2


title: VM4.1_S2

description: Library name: VM4.1


title: VM4.2_S57

description: Library name: VM4.2


title: VM2.1_S4

description: Library name: VM2.1


title: VM3.1_S3

description: Library name: VM3.1


title: VM1.2_S8

description: Library name: VM1.2


title: VM2.2_S23

description: Library name: VM2.2


title: VM1.1_S12

description: Library name: VM1.1


title: VM11.1_S60

description: Library name: VM11.1


title: biorep2 KRT10sorted high batch2

description: Library name: biorep2_KRT10sorted_high_batch2

library_source: other

data_processing:
Raw fastq files were processed with "umi_tools extract --bc-pattern=NNNNNNNNN " followed by  "fastx_trimmer -f 22 -l 41 -Q33" to move the UMI to the read name and then subset to the guide region. The product of these two steps is the uploaded files. Reads not mapping to the guide library were removed before upload.
Reads were then mapped to a genome of the guide library with "bowtie2 -p 8 -k 1 --norc ", followed by counting UMIs using "umi_tools dedup" and "umi_tools count_tab".
The number of UMIs per guide were input to MageCK RRA analysis, pairing biological samples together (“paired” option) and using the safe targeting guides as controls.
Assembly: Custom, based on supplementary guide fasta file.
Supplementary files format and content: UMI counts per guide, raw.
Library strategy: CRISPR Screen

molecule: other

growth_protocol: Two biological replicates of primary human keratinocytes from separate donors were infected with lentivirus containing the transcription factor knock-out library. Specifically, 16 million cells in 8 15 cm plates, in 20 mL 50:50 media, were infected with 100 µL polybrene, Cas9 and guide library virus. The next day, cells were lifted and replated at 2 million cells per 15 cm plate with Blasticidin and Puromycin, while also plating 100,000 cells per well in a 6-well plate to determine survival by the Cell-Titer Blue assay in the presence or absence of drug. Cell-Titer Blue measured survival at ~18-20%, giving ~400 cells per guide. Nine days after infection, 40 million cells were harvested and seeded for differentiation across 18 wells at 1.6 million cells per well in 6-well plates. At the same time, five 10 cm plates were seeded at 100,000 cells per plate for the “progenitor” population. The next day, Ca2+ was added to 1.2 mM in the media of the differentiating cells and half of the media was replaced each day until harvesting after four days.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136).
To extract DNA, cells were resuspened in 200-400 µl of lysis buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 1% SDS), and heated at 65 °C for 10 min with shaking to reverse formaldehyde cross-linking. Samples were cooled and 4 µL 100 mg/mL RNAse A (Qiagen, #19101) was added. Samples were mixed and incubated at 37° for 30 minutes with shaking. After RNAse digestion, 20 µL proteinase K (20 mg/mL, ThermoFisher AM2546) was added and samples were incubated for 2 hours at 37°, then 95° for 20 minutes (no shaking). DNA was purified using Ampure/SPRI beads. Specifically, 1.8X sample volume of beads was added, mixed by pipetting and incubated for 4 minutes before loading on a magnet, incubating for 5 minutes and discarding the supernatant, then washing twice with 80% ethanol, air-drying the beads for 5 minutes and eluting in 100 µL 10 mM Tris pH 7.5. A typical yield was ~4-5 µg DNA per million cells. PrimeStar (Takara, #R045B) PCR reactions in 100 µL reaction volumes were performed with 500 ng genomic DNA and 20 pmol each primer (GGW130/GGW209) per reaction. The PCR program was 98° for 1 minute, then 5 cycles of 98° 10 s, 56° 10 s, 72° 15 s, and a final 72° for one minute at the end. A Zymo PCR cleanup kit (#D4013 or #D4029 for large volumes) was used to combine the PCR reactions, eluting in 100 µL of the kit’s elution buffer. A SPRI clean-up was then performed to remove primers. Specifically, 1.1X bead volume SPRIselect beads were added to the reactions, pipet mixed 15 times, incubated at room temperature for 5 minutes, placed on a magnet, supernatant removed, washed twice with 200 µL 80% ethanol, air dried for 2 minutes, removed from the magnet, pipet mixed 15 times with 46 µL 10 mM Tris pH 7.5, incubated for 2 minutes at room temperature, placed again on the magnet, and 45 µL transferred to a new tube. This purified product was then input to a second PrimeStar PCR reaction in 100 µL volumes to attach the full sequencing primers and barcodes. 20 pmol of each primer (TruSeq adapters with dual i5/i7 indexing) were combined with 50 µL PrimeSTAR, 43 µL water and 3 µL 33X SYBR dye. The PCR program was the same as the first, except without the final 72° elongation for one minute, and samples were stopped after 20 cycles based on the amplification trace. PCR product was then run on a 2% agarose gel and gel purified before sequencing.

treatment_protocol: Cells were resuspended in Cell Staining Buffer (Biolegend, #420201) at 100 µL per million cells, combined with 1.5 volumes Fix/Perm buffer (Biolegend, #426803), incubated for 20 minutes at room temperature, washed once with Perm/Wash buffer (10 mL per sample, Biolegend #426803), then with Cell Staining Buffer and stored at 4° until stained. For staining, cells were washed with Perm/Wash buffer, then stained with 1 µL anti-KRT10, AF647-conjugated antibody (Novus Bio, NBP2-47825AF647) per 1 million cells for 20 minutes in the dark at room temperature. Cells were then washed with Perm/Wash buffer, then Cell Staining Buffer. After washing, cells were resuspended in 5 mL Cell Staining Buffer and passed through the filter lid of a FACS tube. 400 µL of the filtered, differentiated cells was aliquoted as the “unsorted” population. Cells were sorted on a FACSymphony S6 Sorter into high, medium and low KRT10 populations. Sorted cells were washed with PBS with 0.1% BSA once, transferred to 1.6 mL Eppendorf tubes and frozen.


title: biorep2 KRT10sorted med batch2

description: Library name: biorep2_KRT10sorted_med_batch2


title: biorep2 D4 unsorted batch2

description: Library name: biorep2_D4_unsorted_batch2


title: biorep2 KRT10sorted low batch2

description: Library name: biorep2_KRT10sorted_low_batch2


title: biorep1 KRT10sorted med batch2

description: Library name: biorep1_KRT10sorted_med_batch2


title: pdna batch0

description: Library name: pdna_batch0

source_name: Synthetic library

value: Synthetic library


title: biorep2 prog unsorted batch2

description: Library name: biorep2_prog_unsorted_batch2

value: Progenitor


title: biorep1 KRT10sorted low batch2

description: Library name: biorep1_KRT10sorted_low_batch2


title: biorep1 prog unsorted batch2

description: Library name: biorep1_prog_unsorted_batch2


title: biorep1 D4 unsorted batch2

description: Library name: biorep1_D4_unsorted_batch2


title: VM5.2_S5

description: Library name: VM5.2


title: biorep2 KRT10sorted high batch1

description: Library name: biorep2_KRT10sorted_high_batch1


title: biorep2 KRT10sorted med batch1

description: Library name: biorep2_KRT10sorted_med_batch1


title: biorep2 D4 unsorted batch1

description: Library name: biorep2_D4_unsorted_batch1


title: biorep2 KRT10sorted low batch1

description: Library name: biorep2_KRT10sorted_low_batch1


title: biorep1 KRT10sorted low batch1

description: Library name: biorep1_KRT10sorted_low_batch1


title: biorep1 KRT10sorted med batch1

description: Library name: biorep1_KRT10sorted_med_batch1


title: biorep2 prog unsorted batch1

description: Library name: biorep2_prog_unsorted_batch1


title: biorep1 KRT10sorted high batch1

description: Library name: biorep1_KRT10sorted_high_batch1


title: biorep1 D4 unsorted batch1

description: Library name: biorep1_D4_unsorted_batch1


title: biorep1 prog unsorted batch1

description: Library name: biorep1_prog_unsorted_batch1


title: MPRA D6 NRF1 rep2

description:
Library name: MPRA_D6_NRF1_rep2
MPRA of skin-disease associated variants across epidermal differentiation

data_processing:
The initial command (using D3_rep2 as an example), which generated the uploaded files: umi_tools extract --extract-method regex --bc-pattern .{16}(?P<discard_1>.*) --bc-pattern2 (?P<discard_1>.*)(?P<umi_1>.{12}) --stdin D3_rep2_R1.fastq.gz --read2-in D3_rep2_I2.fastq.gz --stdout D3_rep2.fastq.gz
Barcodes were mapped to a bowtie genome of the barcodes with bowtie --sam -v 1 -y --best --nofw -t
Barcodes were called with umi_tools count --per-contig --method=directional
Supplementary files format and content: Number of UMIs per MPRA barcode

growth_protocol: Primary human neonatal foreskin keratinocytes were isolated and cultured in 50% Keratinocyte-SFM (Life Technologies 17005-142) and 50% Medium 154 (Life Technologies M-154-500) with the addition of Pen/Strep (Life Technologies 15140-122), the composition termed 50:50 media. Progenitor keratinocytes were maintained at subconfluence.

extract_protocol:
total RNA was isolated using Qiagen’s RNeasy Plus kit (Qiagen, #74136) and mRNA subsequently purified using Dynabeads mRNA DIRECT purification kit (ThermoFisher, 61011).
Libraries were prepared according to PMID: 34650237. Reverse transcription was performed with 500 ng mRNA, 100 nM primer and SuperScript IV (ThermoFisher, 18090050) according to the manufacturer’s protocol. Reactions were incubated with 1 µL Themolabile Exonuclease I (NEB, M0568L) at 10 min at 37°, followed by inactivation at 85° for 5 min and cDNA purification with AMPure XP beads (Beckman Coulter, A63880) at a 1:1.1 sample-to-bead ratio. PCR amplification was performed in 50 µL reactions containing 5 µL cDNA, SYBR green (ThermoFisher, S7563), and PrimeStar Max DNA Polymerase (Takara, R045B). Reactions stopped in the early exponential phase, pooled, concentrated, gel purified and sequenced.

treatment_protocol: For each MPRA biological replicate, 10 million keratinocytes were transduced in 15 cm plates in 50:50 with the addition of 5 µg/mL polybrene. If a knock-down was performed, lentivirus expressing a lenticrispr v.2 construct with Cas9 and a guide against the knock-down factor was infected at the same time as the guide library: IRF6 (CAT AAG TAG ATC TCA AAC GG), SNAI2 (CCT TGT GTT TGC AAG ATC TG) or NRF1 (AAT TGG GCC ACG TTA CAG GG). Cells were selected in 0.8 µg/mL puromycin for 24-48 hours after transduction. Once selected, cells were seeded for progenitor and differentiation conditions using 1.2 mM Ca2+. Half of the media was replaced each day until the indicated time point of harvest.

value: Differentiated for 6 Days. CRISPR KO of NRF1.


title: MPRA D6 NRF1 rep3

description:
Library name: MPRA_D6_NRF1_rep3
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D6 SNAI2 rep3

description:
Library name: MPRA_D6_SNAI2_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 6 Days. CRISPR KO of SNAI2.


title: MPRA D6 IRF6 rep3

description:
Library name: MPRA_D6_IRF6_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 6 Days. CRISPR KO of IRF6.


title: MPRA D6 SNAI2 rep2

description:
Library name: MPRA_D6_SNAI2_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D6 IRF6 rep2

description:
Library name: MPRA_D6_IRF6_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D6 ST26 rep2

description:
Library name: MPRA_D6_ST26_rep2
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 6 Days. Safe target (ST26) CRISPR KO control.


title: MPRA D3 NRF1 rep3

description:
Library name: MPRA_D3_NRF1_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 3 Days. CRISPR KO of NRF1.


title: MPRA D3 ST26 rep3

description:
Library name: MPRA_D3_ST26_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 3 Days. Safe target (ST26) CRISPR KO control.


title: MPRA D6 NRF1 rep1

description:
Library name: MPRA_D6_NRF1_rep1
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D3 SNAI2 rep3

description:
Library name: MPRA_D3_SNAI2_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 3 Days. CRISPR KO of SNAI2.


title: MPRA D3 IRF6 rep3

description:
Library name: MPRA_D3_IRF6_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 3 Days. CRISPR KO of IRF6.


title: MPRA D3 IRF6 rep2

description:
Library name: MPRA_D3_IRF6_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D3 NRF1 rep2

description:
Library name: MPRA_D3_NRF1_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D3 ST26 rep2

description:
Library name: MPRA_D3_ST26_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D0 SNAI2 rep3

description:
Library name: MPRA_D0_SNAI2_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 0 Days. CRISPR KO of SNAI2.


title: biorep1 KRT10sorted high batch2

description: Library name: biorep1_KRT10sorted_high_batch2


title: MPRA D0 NRF1 rep3

description:
Library name: MPRA_D0_NRF1_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: WT

value: Differentiated for 0 Days. CRISPR KO of NRF1.


title: MPRA D0 ST26 rep3

description:
Library name: MPRA_D0_ST26_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Primary keratinocytes

value: Differentiated for 0 Days. Safe target (ST26) CRISPR KO control.


title: MPRA D0 IRF6 rep3

description:
Library name: MPRA_D0_IRF6_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 0 Days. CRISPR KO of IRF6.


title: MPRA D0 NRF1 rep2

description:
Library name: MPRA_D0_NRF1_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D0 SNAI2 rep2

description:
Library name: MPRA_D0_SNAI2_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D6 ST26 rep3

description:
Library name: MPRA_D6_ST26_rep3
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D0 NRF1 rep1

description:
Library name: MPRA_D0_NRF1_rep1
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA pDNA rep2

description:
Library name: MPRA_pDNA_rep2
MPRA of skin-disease associated variants across epidermal differentiation. Plasmid DNA.

value: Plasmid DNA


title: MPRA wt D6 rep1

description:
Library name: MPRA_wt_D6_rep1
MPRA of skin-disease associated variants across epidermal differentiation

treatment_protocol: For each MPRA biological replicate, 10 million keratinocytes were transduced in 15 cm plates in 50:50 with the addition of 5 µg/mL polybrene. Cells were selected in 0.8 µg/mL puromycin for 24-48 hours after transduction. Once selected, cells were seeded for progenitor and differentiation conditions using 1.2 mM Ca2+. Half of the media was replaced each day until the indicated time point of harvest.

value: Differentiated for 6 Days


title: MPRA wt D3 rep2

description:
Library name: MPRA_wt_D3_rep2
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 3 Days


title: MPRA wt D6 rep3

description:
Library name: MPRA_wt_D6_rep3
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA wt D3 rep3

description:
Library name: MPRA_wt_D3_rep3
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA wt D0 rep3

description:
Library name: MPRA_wt_D0_rep3
MPRA of skin-disease associated variants across epidermal differentiation

value: Differentiated for 0 Days


title: MPRA D3 SNAI2 rep2

description:
Library name: MPRA_D3_SNAI2_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA wt D0 rep2

description:
Library name: MPRA_wt_D0_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA wt D0 rep1

description:
Library name: MPRA_wt_D0_rep1
MPRA of skin-disease associated variants across epidermal differentiation


title: MPRA D3 NRF1 rep1

description:
Library name: MPRA_D3_NRF1_rep1
MPRA of skin-disease associated variants across epidermal differentiation


title: COVID-19,Convalescent,individual099,Visit1

city: Ulsan

first: Jong

last: Bhak

state: Ulju-gun/Eonyang-eup

address: 50 UNIST-gil,

department: Biomedical Engineering (BME)

country: South Korea

institute: Korean Genomics Center (KOGIC)

description: Library name: C19-R099-V1

data_processing:
Raw sequencing reads were processed using Fastp (v0.23.1) to remove adapters and low-quality bases, with the following parameters: --cut_front 1 --cut_right 0 --cut_tail 1 --detect_adapter_for_pe --trim_front1 15 --trim_front2 15 --trim_tail1 0 --trim_tail2 0 --cut_mean_quality 20 --n_base_limit 1 --average_qual 20 34. Read quality was assessed before and after filtering reads using FastQC (v0.11.9)
Filtered reads were aligned to the human reference genome (GRCh38.p13) using Bismark (v0.23.1), a bisulfite-aware aligner.
Methylation calling and quantification were conducted using the methylKit R package (v1.20.0).
Assembly: GRCh38.p13 (GENCODE v42)
Supplementary files format and content: tab-delimited text file includes methylation beta values for each Sample

source_name: Whole blood

extract_protocol:
Frozen whole blood samples collected in EDTA tubes (Becton Dickinson, #367856) were used for genomic DNA (gDNA) extraction, performed using the DNeasy Blood & Tissue Kit (Qiagen, #69506) according to the manufacturer’s instructions.
Bisulfite-converted DNA libraries were prepared using the SureSelectXT Methyl-Seq Target Enrichment System Kit (Agilent, #G9651), following the manufacturer's protocol. Sequencing was performed on the NovaSeq 6000 platform (Illumina), generating 150 bp paired-end reads.

value: Whole blood

value: F

tag: severity scale

tag: severity class

tag: visit number


title: COVID-19,Convalescent,individual097,Visit1

description: Library name: C19-R097-V1

tag: tissue


title: MPRA D0 IRF6 rep2

description:
Library name: MPRA_D0_IRF6_rep2
MPRA of skin-disease associated variants across epidermal differentiation

tag: genotype

tag: treatment


title: COVID-19,Convalescent,individual098,Visit1

description: Library name: C19-R098-V1


title: COVID-19,Convalescent,individual094,Visit1

description: Library name: C19-R094-V1


title: MPRA D0 ST26 rep2

description:
Library name: MPRA_D0_ST26_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: COVID-19,Convalescent,individual093,Visit1

description: Library name: C19-R093-V1


title: COVID-19,Convalescent,individual090,Visit1

description: Library name: C19-R090-V1

value: M


title: COVID-19,Convalescent,individual100,Visit1

description: Library name: C19-R100-V1


title: COVID-19,Convalescent,individual092,Visit1

description: Library name: C19-R092-V1


title: COVID-19,Convalescent,individual089,Visit1

description: Library name: C19-R089-V1


title: COVID-19,Convalescent,individual088,Visit1

description: Library name: C19-R088-V1


title: MPRA pDNA rep1

description:
Library name: MPRA_pDNA_rep1
MPRA of skin-disease associated variants across epidermal differentiation. Plasmid DNA.


title: MPRA wt pDNA rep1

description:
Library name: MPRA_wt_pDNA_rep1
MPRA of skin-disease associated variants across epidermal differentiation.


title: COVID-19,Convalescent,individual096,Visit1

description: Library name: C19-R096-V1


title: COVID-19,Convalescent,individual091,Visit1

description: Library name: C19-R091-V1


title: MPRA wt D6 rep2

description:
Library name: MPRA_wt_D6_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: COVID-19,Convalescent,individual087,Visit1

description: Library name: C19-R087-V1


title: COVID-19,Convalescent,individual086,Visit1

description: Library name: C19-R086-V1


title: COVID-19,Convalescent,individual085,Visit1

description: Library name: C19-R085-V1


title: COVID-19,Convalescent,individual083,Visit1

description: Library name: C19-R083-V1


title: COVID-19,Convalescent,individual082,Visit1

description: Library name: C19-R082-V1


title: MPRA wt pDNA rep2

description:
Library name: MPRA_wt_pDNA_rep2
MPRA of skin-disease associated variants across epidermal differentiation


title: COVID-19,Convalescent,individual084,Visit1

description: Library name: C19-R084-V1


title: COVID-19,Convalescent,individual081,Visit1

description: Library name: C19-R081-V1


title: COVID-19,Convalescent,individual080,Visit1

description: Library name: C19-R080-V1


title: COVID-19,Convalescent,individual078,Visit1

description: Library name: C19-R078-V1


title: COVID-19,Convalescent,individual079,Visit1

description: Library name: C19-R079-V1


title: COVID-19,Convalescent,individual095,Visit1

description: Library name: C19-R095-V1


title: COVID-19,Convalescent,individual077,Visit1

description: Library name: C19-R077-V1


title: COVID-19,Convalescent,individual075,Visit1

description: Library name: C19-R075-V1


title: COVID-19,Convalescent,individual076,Visit1

description: Library name: C19-R076-V1


title: COVID-19,Convalescent,individual074,Visit1

description: Library name: C19-R074-V1


title: COVID-19,Convalescent,individual073,Visit1

description: Library name: C19-R073-V1


title: COVID-19,Convalescent,individual072,Visit1

description: Library name: C19-R072-V1


title: COVID-19,Convalescent,individual069,Visit1

description: Library name: C19-R069-V1


title: COVID-19,Convalescent,individual071,Visit1

description: Library name: C19-R071-V1


title: COVID-19,Convalescent,individual070,Visit1

description: Library name: C19-R070-V1


title: COVID-19,Convalescent,individual067,Visit1

description: Library name: C19-R067-V1


title: COVID-19,Convalescent,individual068,Visit1

description: Library name: C19-R068-V1


title: COVID-19,Convalescent,individual066,Visit1

description: Library name: C19-R066-V1


title: COVID-19,Convalescent,individual061,Visit1

description: Library name: C19-R061-V1


title: COVID-19,Convalescent,individual065,Visit1

description: Library name: C19-R065-V1


title: COVID-19,Convalescent,individual062,Visit1

description: Library name: C19-R062-V1


title: COVID-19,Convalescent,individual064,Visit1

description: Library name: C19-R064-V1


title: COVID-19,Convalescent,individual060,Visit1

description: Library name: C19-R060-V1


title: COVID-19,Convalescent,individual058,Visit1

description: Library name: C19-R058-V1


title: COVID-19,Convalescent,individual054,Visit1

description: Library name: C19-R054-V1


title: COVID-19,Convalescent,individual053,Visit1

description: Library name: C19-R053-V1


title: COVID-19,Convalescent,individual052,Visit1

description: Library name: C19-R052-V1


title: COVID-19,Convalescent,individual059,Visit1

description: Library name: C19-R059-V1


title: COVID-19,Convalescent,individual057,Visit1

description: Library name: C19-R057-V1


title: COVID-19,Convalescent,individual056,Visit1

description: Library name: C19-R056-V1


title: COVID-19,Convalescent,individual051,Visit1

description: Library name: C19-R051-V1


title: COVID-19,Convalescent,individual055,Visit1

description: Library name: C19-R055-V1


title: COVID-19,Convalescent,individual050,Visit1

description: Library name: C19-R050-V1


title: COVID-19,Convalescent,individual049,Visit1

description: Library name: C19-R049-V1


title: COVID-19,Convalescent,individual048,Visit1

description: Library name: C19-R048-V1


title: COVID-19,Convalescent,individual046,Visit1

description: Library name: C19-R046-V1


title: COVID-19,Convalescent,individual063,Visit1

description: Library name: C19-R063-V1


title: COVID-19,Convalescent,individual045,Visit1

description: Library name: C19-R045-V1


title: COVID-19,Convalescent,individual044,Visit1

description: Library name: C19-R044-V1


title: COVID-19,Convalescent,individual043,Visit1

description: Library name: C19-R043-V1


title: COVID-19,Convalescent,individual047,Visit1

description: Library name: C19-R047-V1


title: COVID-19,Convalescent,individual039,Visit1

description: Library name: C19-R039-V1


title: COVID-19,Convalescent,individual038,Visit1

description: Library name: C19-R038-V1


title: COVID-19,Convalescent,individual040,Visit1

description: Library name: C19-R040-V1


title: COVID-19,Convalescent,individual041,Visit1

description: Library name: C19-R041-V1


title: COVID-19,Convalescent,individual042,Visit1

description: Library name: C19-R042-V1


title: COVID-19,Convalescent,individual037,Visit1

description: Library name: C19-R037-V1


title: COVID-19,Convalescent,individual035,Visit1

description: Library name: C19-R035-V1


title: COVID-19,Convalescent,individual036,Visit1

description: Library name: C19-R036-V1


title: COVID-19,Convalescent,individual034,Visit1

description: Library name: C19-R034-V1


title: COVID-19,Convalescent,individual033,Visit1

description: Library name: C19-R033-V1


title: COVID-19,Convalescent,individual032,Visit1

description: Library name: C19-R032-V1


title: COVID-19,Convalescent,individual030,Visit1

description: Library name: C19-R030-V1


title: COVID-19,Convalescent,individual029,Visit1

description: Library name: C19-R029-V1


title: COVID-19,Convalescent,individual031,Visit1

description: Library name: C19-R031-V1


title: COVID-19,Convalescent,individual028,Visit1

description: Library name: C19-R028-V1


title: COVID-19,Convalescent,individual027,Visit1

description: Library name: C19-R027-V1


title: COVID-19,Convalescent,individual026,Visit1

description: Library name: C19-R026-V1


title: COVID-19,Convalescent,individual024,Visit1

description: Library name: C19-R024-V1


title: COVID-19,Convalescent,individual025,Visit1

description: Library name: C19-R025-V1


title: COVID-19,Convalescent,individual022,Visit1

description: Library name: C19-R022-V1


title: COVID-19,Convalescent,individual020,Visit1

description: Library name: C19-R020-V1


title: COVID-19,Convalescent,individual023,Visit1

description: Library name: C19-R023-V1


title: COVID-19,Convalescent,individual019,Visit1

description: Library name: C19-R019-V1


title: COVID-19,Convalescent,individual021,Visit1

description: Library name: C19-R021-V1


title: COVID-19,Convalescent,individual018,Visit1

description: Library name: C19-R018-V1


title: COVID-19,Convalescent,individual014,Visit1

description: Library name: C19-R014-V1


title: COVID-19,Convalescent,individual016,Visit1

description: Library name: C19-R016-V1


title: COVID-19,Convalescent,individual017,Visit1

description: Library name: C19-R017-V1


title: COVID-19,Convalescent,individual015,Visit1

description: Library name: C19-R015-V1


title: COVID-19,Convalescent,individual010,Visit1

description: Library name: C19-R010-V1


title: COVID-19,Convalescent,individual012,Visit1

description: Library name: C19-R012-V1


title: COVID-19,Convalescent,individual009,Visit1

description: Library name: C19-R009-V1


title: COVID-19,Convalescent,individual007,Visit1

description: Library name: C19-R007-V1


title: COVID-19,Convalescent,individual004,Visit1

description: Library name: C19-R004-V1


title: COVID-19,Convalescent,individual008,Visit1

description: Library name: C19-R008-V1


title: COVID-19,Convalescent,individual001,Visit1

description: Library name: C19-R001-V1


title: COVID-19,Convalescent,individual003,Visit1

description: Library name: C19-R003-V1


title: COVID-19,Convalescent,individual002,Visit1

description: Library name: C19-R002-V1


title: COVID-19,Hospitalized,patient059,Visit1

description: Library name: C19-C059-V1

value: Mild-Moderate


title: COVID-19,Hospitalized,patient059,Visit3

description: Library name: C19-C059-V3


title: COVID-19,Hospitalized,patient057,Visit3

description: Library name: C19-C057-V3


title: COVID-19,Hospitalized,patient057,Visit1

description: Library name: C19-C057-V1


title: COVID-19,Hospitalized,patient054,Visit3

description: Library name: C19-C054-V3

value: Severe-Critical


title: COVID-19,Hospitalized,patient049,Visit3

description: Library name: C19-C049-V3


title: COVID-19,Hospitalized,patient049,Visit1

description: Library name: C19-C049-V1


title: COVID-19,Hospitalized,patient054,Visit1

description: Library name: C19-C054-V1


title: COVID-19,Hospitalized,patient048,Visit3

description: Library name: C19-C048-V3


title: COVID-19,Convalescent,individual011,Visit1

description: Library name: C19-R011-V1


title: COVID-19,Hospitalized,patient046,Visit3

description: Library name: C19-C046-V3


title: COVID-19,Hospitalized,patient048,Visit1

description: Library name: C19-C048-V1


title: COVID-19,Hospitalized,patient046,Visit1

description: Library name: C19-C046-V1


title: COVID-19,Hospitalized,patient044,Visit3

description: Library name: C19-C044-V3


title: COVID-19,Convalescent,individual006,Visit1

description: Library name: C19-R006-V1


title: COVID-19,Convalescent,individual005,Visit1

description: Library name: C19-R005-V1


title: COVID-19,Hospitalized,patient042,Visit3

description: Library name: C19-C042-V3


title: COVID-19,Hospitalized,patient043,Visit1

description: Library name: C19-C043-V1


title: COVID-19,Hospitalized,patient044,Visit1

description: Library name: C19-C044-V1


title: COVID-19,Convalescent,individual013,Visit1

description: Library name: C19-R013-V1


title: COVID-19,Hospitalized,patient043,Visit3

description: Library name: C19-C043-V3


title: COVID-19,Hospitalized,patient041,Visit1

description: Library name: C19-C041-V1


title: COVID-19,Hospitalized,patient041,Visit3

description: Library name: C19-C041-V3


title: COVID-19,Hospitalized,patient058,Visit3

description: Library name: C19-C058-V3


title: COVID-19,Hospitalized,patient040,Visit1

description: Library name: C19-C040-V1


title: COVID-19,Hospitalized,patient039,Visit3

description: Library name: C19-C039-V3


title: COVID-19,Hospitalized,patient042,Visit1

description: Library name: C19-C042-V1


title: COVID-19,Hospitalized,patient058,Visit1

description: Library name: C19-C058-V1


title: COVID-19,Hospitalized,patient038,Visit3

description: Library name: C19-C038-V3


title: COVID-19,Hospitalized,patient039,Visit1

description: Library name: C19-C039-V1


title: COVID-19,Hospitalized,patient037,Visit3

description: Library name: C19-C037-V3


title: COVID-19,Hospitalized,patient038,Visit1

description: Library name: C19-C038-V1


title: COVID-19,Hospitalized,patient037,Visit1

description: Library name: C19-C037-V1


title: COVID-19,Hospitalized,patient036,Visit1

description: Library name: C19-C036-V1


title: COVID-19,Hospitalized,patient034,Visit3

description: Library name: C19-C034-V3


title: COVID-19,Hospitalized,patient035,Visit3

description: Library name: C19-C035-V3


title: COVID-19,Hospitalized,patient034,Visit1

description: Library name: C19-C034-V1


title: COVID-19,Hospitalized,patient033,Visit1

description: Library name: C19-C033-V1


title: COVID-19,Hospitalized,patient032,Visit1

description: Library name: C19-C032-V1


title: COVID-19,Hospitalized,patient031,Visit3

description: Library name: C19-C031-V3


title: COVID-19,Hospitalized,patient029,Visit3

description: Library name: C19-C029-V3


title: COVID-19,Hospitalized,patient040,Visit3

description: Library name: C19-C040-V3


title: COVID-19,Hospitalized,patient030,Visit3

description: Library name: C19-C030-V3


title: COVID-19,Hospitalized,patient029,Visit1

description: Library name: C19-C029-V1


title: COVID-19,Hospitalized,patient030,Visit1

description: Library name: C19-C030-V1


title: COVID-19,Hospitalized,patient031,Visit1

description: Library name: C19-C031-V1


title: COVID-19,Hospitalized,patient028,Visit1

description: Library name: C19-C028-V1


title: COVID-19,Hospitalized,patient026,Visit1

description: Library name: C19-C026-V1


title: COVID-19,Hospitalized,patient027,Visit3

description: Library name: C19-C027-V3


title: COVID-19,Hospitalized,patient028,Visit3

description: Library name: C19-C028-V3


title: COVID-19,Hospitalized,patient027,Visit1

description: Library name: C19-C027-V1


title: COVID-19,Hospitalized,patient024,Visit3

description: Library name: C19-C024-V3


title: COVID-19,Hospitalized,patient035,Visit1

description: Library name: C19-C035-V1


title: COVID-19,Hospitalized,patient026,Visit3

description: Library name: C19-C026-V3


title: COVID-19,Hospitalized,patient024,Visit1

description: Library name: C19-C024-V1


title: COVID-19,Hospitalized,patient025,Visit1

description: Library name: C19-C025-V1


title: COVID-19,Hospitalized,patient036,Visit3

description: Library name: C19-C036-V3


title: COVID-19,Hospitalized,patient020,Visit4

description: Library name: C19-C020-V4


title: COVID-19,Hospitalized,patient023,Visit1

description: Library name: C19-C023-V1


title: COVID-19,Hospitalized,patient019,Visit4

description: Library name: C19-C019-V4


title: COVID-19,Hospitalized,patient020,Visit1

description: Library name: C19-C020-V1


title: COVID-19,Hospitalized,patient019,Visit1

description: Library name: C19-C019-V1


title: COVID-19,Hospitalized,patient025,Visit3

description: Library name: C19-C025-V3


title: COVID-19,Hospitalized,patient017,Visit1

description: Library name: C19-C017-V1


title: COVID-19,Hospitalized,patient033,Visit3

description: Library name: C19-C033-V3


title: COVID-19,Hospitalized,patient014,Visit1

description: Library name: C19-C014-V1


title: COVID-19,Hospitalized,patient017,Visit4

description: Library name: C19-C017-V4


title: COVID-19,Hospitalized,patient032,Visit3

description: Library name: C19-C032-V3


title: COVID-19,Hospitalized,patient018,Visit1

description: Library name: C19-C018-V1


title: COVID-19,Hospitalized,patient018,Visit4

description: Library name: C19-C018-V4


title: COVID-19,Hospitalized,patient023,Visit4

description: Library name: C19-C023-V4


title: COVID-19,Hospitalized,patient015,Visit1

description: Library name: C19-C015-V1


title: COVID-19,Hospitalized,patient006,Visit4

description: Library name: C19-C006-V4


title: COVID-19,Hospitalized,patient015,Visit4

description: Library name: C19-C015-V4


title: COVID-19,Hospitalized,patient014,Visit4

description: Library name: C19-C014-V4


title: COVID-19,Hospitalized,patient013,Visit4

description: Library name: C19-C013-V4


title: COVID-19,Hospitalized,patient013,Visit1

description: Library name: C19-C013-V1


title: COVID-19,Hospitalized,patient005,Visit4

description: Library name: C19-C005-V4


title: COVID-19,Hospitalized,patient006,Visit1

description: Library name: C19-C006-V1


title: COVID-19,Hospitalized,patient008,Visit4

description: Library name: C19-C008-V4


title: COVID-19,Hospitalized,patient010,Visit1

description: Library name: C19-C010-V1


title: COVID-19,Hospitalized,patient012,Visit4

description: Library name: C19-C012-V4


title: COVID-19,Hospitalized,patient003,Visit1

description: Library name: C19-C003-V1


title: COVID-19,Hospitalized,patient008,Visit1

description: Library name: C19-C008-V1


title: COVID-19,Hospitalized,patient003,Visit4

description: Library name: C19-C003-V4


title: COVID-19,Hospitalized,patient001,Visit4

description: Library name: C19-C001-V4


title: COVID-19,Hospitalized,patient012,Visit1

description: Library name: C19-C012-V1


title: COVID-19,Hospitalized,patient007,Visit4

description: Library name: C19-C007-V4


title: MGC803 STAT1-K193R cells (ChIP)

city: Jinan

first: Duanrui

last: Liu

address: Address:No. 324, Jingwu Weiqi Road

institute: Shandong Provincial Hospital

description: Library name: MGC803 STAT1-K193R ChIP

data_processing:
Raw reads were obtained after ChIP-seq sequencing, filtered to remove splices and contamination, aligned to the reference genome, and then analyzed using high-quality mapped reads (MAPQ greater than or equal to 30).
Assembly: hg19
Supplementary files format and content: BigWig

source_name: MGC803 STAT3-K193R

growth_protocol: DMEM,15% fetalbovine serum,2mM glutamine,1xpenicillin/streptomycin.Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells werefixed with1%formaldehydefor10minutes.After quenching and cell lysis, chromatin was sonicated using a E220focused-ultrasonicator(Covaris).
ChlP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXT flex DNABar codes from Bio Scientific.10 ng of DNA was used as starting material for input and ip samples.Libraries were amplified using 13 cycles on the thermocycler.Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

tag: cell type

value: Human gastric cancer cells

value: ChIP antibody:anti-STAT1-K193la antibody (PTM BIO)


title: MGC803 STAT1-WT cells (ChIP)

description: Library name: MGC803 STAT1-WT ChIP

source_name: MGC803 STAT1-WT


title: MGC803 STAT1-WT cells (Input)

description: Library name: MGC803 STAT1-WT Input

source_name: MGC803 STAT2-WT


title: COVID-19,Hospitalized,patient007,Visit1

description: Library name: C19-C007-V1

tag: Sex


title: KYSE-450 cells, dTAG-SOX2 3h, H4ac ChIP

city: Shanghai

first: ruofei

last: dai

address: dong'an road 130

institute: Fudan University

description: Library name: DA4

data_processing:
The ChIP-seq reads were aligned to the human genome build hg19 and mouse genome build mm10 using the bowtie2 (v2.3.4.1) with the default parameters and duplicate reads were removed by picard MarkDuplicates. The human ChIP-seq reads were multiplied by a scale factor which, when multiplied, equalized Mus musculus mapped reads and visualized in UCSC genome browser. The ChIP-seq peaks of SOX2 in control and SOX2 knockdown cells were called by MACS2 (v2.1.2) with the parameters --fix-bimodal -p 0.05 because SOX2 signals were weak, and the ChIP-seq peaks of H4ac were called with the parameters -B -q 0.01 --nomodel -extsize 150. The differential ChIP-seq peaks were called with -p 1e-7, and further filtered to acquire at least 1.5-fold changed peaks. The genome distribution of SOX2 ChIP-seq peaks was calculated by R package ChIPseeker and plotted by EXCEL. The motifs of SOX2 binding sites were identified by Homer. The heatmaps and the emission profiles were plotted by Deeptools.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: The ESCC cells were cultured in RPMI1640 medium (Invitrogen) and supplemented with 10% fetal bovine serum (Sigma, F8318) and 1% penicillin/streptomycin at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol:
The cells were crosslinked with 1% formaldehyde for 10 min and then quenched by adding 125 mM glycine. Chromatin samples were sonicated in lysis buffer (high salt buffer with 0.1% SDS and protease inhibitors).
The DNA samples were directly used for library generation using a Vazyme kit (Vazyme, ND607), libraries were pooled and sequenced on the Illumina NovaSeq 6000 sequencer with paired-end sequencing.

treatment_protocol: We construct a donor vector (pUC57-SOX2-dTAG donor) containing the knockin sequence, the pX459-sgSOX2 plasmid with a gene-specific sgRNA targeting the SOX2 N-terminal genomic locus, and the pX459-sgPITCh plasmid with the PITCh-specific sgRNA targeting the pPUC57-SOX2-dTAG donor construct. We set up transfection system: pX459-sgPITCh: pX459-sgSOX2: pUC57-SOX2-dTAG donor = 1: 2: 2 by using LipoFilter (HB-TRLF-1000) in K450. At 48 h after transfection, the cells were cultured with the medium containing 1μg/mL puromycin (MCE, Cat. #HY-B1743) for another 48 h to select puromycin-positive single cells into the 96-well plates and then allowed them to expand for 2 weeks with basic culture medium. The correct SOX2-dTAG knock-in cell line was verified by both Sanger sequencing of genomic DNA and western blot by DMSO or 1 μM dTAG-V1 (Tocris, Cat. #6914/5) treatment.

value: Human ESCC cell line

value: dTAG-SOX2, 3h


title: KYSE-450 cells, dTAG-SOX2 24h, input

description: Library name: V24I3

value: dTAG-SOX2, 24h


title: KYSE-450 cells, dTAG-SOX2 24h, H4ac ChIP

description: Library name: V3A5


title: COVID-19,Hospitalized,patient002,Visit4

description: Library name: C19-C002-V4

tag: age


title: COVID-19,Hospitalized,patient004,Visit4

description: Library name: C19-C004-V4


title: COVID-19,Hospitalized,patient004,Visit1

description: Library name: C19-C004-V1


title: COVID-19,Hospitalized,patient002,Visit1

description: Library name: C19-C002-V1


title: Input UL3 Rep2

city: Research Triangle Park

first: Nolan

middle: Garrity

last: Gokey

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

description:
Library name: Sample 14
ChIP-seq

data_processing:
The BBMap suite was used to trim adapter sequences, remove low quality reads and map ChIP-seq reads
to the human reference genome (T2Tv2) using default paramters.
Assembly: T2Tv2
Supplementary files format and content: bigwig files

source_name: human osteosarcoma cell line

growth_protocol: All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum (Atlanta Biologicals, Atlanta, GA, USA), and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
ChIP-seq was performed as described in Hoffman 2018).
Libraries were generated using either the Nextera Tn5 kit (Illumina) or the Swift Biosciences DNA kit according to manufacturer's instructions.

value: human osteosarcoma cell line

value: UL3 cells

value: osteosarcoma

value: wild-type

value: vehicle

tag: batch


title: Input UL3 Rep1

description:
Library name: Sample 13
ChIP-seq


title: MGC803 STAT1-K193R cells (Input)

description: Library name: MGC803 STAT1-K193R Input

source_name: MGC803 STAT4-K193R


title: H3K27ac UL3 dH1 cloneB Rep2

description:
Library name: Sample 6
ChIP-seq


title: KYSE-450 cells, DMSO, H4ac ChIP

description: Library name: V24A6

value: DMSO


title: H3K27ac UL3 dH1 cloneB Rep1

description:
Library name: Sample 5
ChIP-seq


title: H3K27ac UL3 Rep1

description:
Library name: Sample 1
ChIP-seq


title: KYSE-450 cells, dTAG-SOX2 3h, input

description: Library name: V3I2


title: COVID-19,Hospitalized,patient001,Visit1

description: Library name: C19-C001-V1


title: ATACseq UL3 dH1 cloneB Rep3

description:
Library name: Sample 12
ATAC-seq

data_processing:
The BBMap suite was used to trim adapter sequences, remove low quality reads and map ATAC-seq reads
to the human reference genome (T2Tv2) using default paramters.
Peaks were called using MACS2 (Zhang 2008), merged and analyzed as described.
Assembly: T2Tv2
Supplementary files format and content: bigwig files
Supplementary files format and content: text files

extract_protocol:
Nuclei were purified as in (Williams et al., 2015) and ATAC seq performed as in (Buenrostro et al., 2015).
Libraries were generated using the Nextera kit according to manufacturer's instructions (Illumina).


title: KYSE-450 cells, DMSO, input

description: Library name: DI1


title: COVID-19,Hospitalized,patient005,Visit1

description: Library name: C19-C005-V1


title: Input UL3 dH1 cloneB Rep2

description:
Library name: Sample 18
ChIP-seq


title: ATACseq UL3 dH1 cloneB Rep1

description:
Library name: Sample 10
ATAC-seq


title: H3K4me1 UL3 dH1 cloneB Rep2

description:
Library name: Sample 12
ChIP-seq


title: MART_IST, rep 4, EM Seq

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

description:
Library name: 3197445
EM Seq

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the mm10 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: mm10
Supplementary files format and content: txt files with columns of chr, loc, cov, meth
Library strategy: Enzymatic Methyl-seq

source_name: PBMC

extract_protocol:
Genomic DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen, 69504) from unsorted untreated cells (UN) or MART-1-specific CD8+ T cells (DC and IST) stained with tetramer for 25 minutes in the dark at a 1:350 dilution prior to isolation by flow cytometric sorting on BD FACSAria™ III Cell Sorter.
Genomic DNA extraction and enzymatic conversion were performed using NEBNext Enzymatic Methyl-seq Kit. Converted genomic DNA were submitted to the Hartwell Center at SJCRH for library construction and sequencing on the Illumina NovaSeq platform with 150bp paired-end and target reads of 500 million per sample.

value: PBMC

value: CD8 T cells

tag: patient

value: MART1 IST


title: H3K4me1 UL3 dH1 cloneB Rep1

description:
Library name: Sample 11
ChIP-seq


title: ATACseq UL3 dH1 cloneA Rep1

description:
Library name: Sample 5
ATAC-seq


title: MART_IST, rep 3, EM Seq

description:
Library name: 3197444
EM Seq


title: H3K4me1 UL3 Rep1

description:
Library name: Sample 7
ChIP-seq


title: H3K4me1 UL3 Rep2

description:
Library name: Sample 8
ChIP-seq


title: H3K27ac UL3 Rep2

description:
Library name: Sample 2
ChIP-seq


title: Input UL3 dH1 cloneB Rep1

description:
Library name: Sample 17
ChIP-seq


title: SL9_IST, rep 2, EM Seq

description:
Library name: 3197437
EM Seq

value: SL9 IST


title: ATACseq UL3 dH1 cloneA Rep3

description:
Library name: Sample 7
ATAC-seq


title: ATACseq UL3 dH1 cloneB Rep4

description:
Library name: Sample 13
ATAC-seq


title: ATACseq UL3 dH1 cloneA Rep2

description:
Library name: Sample 6
ATAC-seq


title: ATACseq UL3 Rep2

description:
Library name: Sample 2
ATAC-seq


title: ATACseq UL3 Rep1

description:
Library name: Sample 1
ATAC-seq


title: MART_IST, rep 2, EM Seq

description:
Library name: 3155244
EM Seq


title: MART_DC, rep 4, EM Seq

description:
Library name: 3197443
EM Seq

value: MART1 DC


title: MART_DC, rep 3, EM Seq

description:
Library name: 3197442
EM Seq


title: UNSTIM, rep 6, EM Seq

description:
Library name: 3197441
EM Seq


title: SL9_IST, rep 4, EM Seq

description:
Library name: 3197439
EM Seq


title: SL9_IST, rep 3, EM Seq

description:
Library name: 3197438
EM Seq


title: ATACseq UL3 dH1 cloneB Rep2

description:
Library name: Sample 11
ATAC-seq


title: HSC-GFP-Galunisertib-Sample 2

city: Salamanca

first: Javier

last: Vaquero

address: Campus Miguel de Unamuno, SN

department: CIC-IBMCC

country: Spain

institute: CSIC

data_processing:
Reads mapped with STAR v2.7.8a
Genes quantified with RSEM v1.3.0
Assembly: GRCh38
Supplementary files format and content: Tab-delimeted text file with raw counts for each sample.

source_name: HSC-GFP

growth_protocol: HuCCT1 and RBE cells were maintained in DMEM low glucose (1g/l) supplemented with 10% fetal bovine serum (FBS) and antibiotics/antimicotics in a humidified atmopshere with 5% CO2 at 37ºC. LX2-HSC and hTERT-HSC cells were maintained in DMEM high glucose (4,5g/l) supplemented with 10% fetal bovine serum (FBS) and antibiotics/antimicotics in a humidified atmopshere with 5% CO2 at 37ºC. HSC-GFP cells were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum (FBS) and antibiotics/antimicotics in a humidified atmopshere with 5% CO2 at 37ºC.

extract_protocol:
RNA was harvested using the E.Z.N.A. Total RNA kit II.
RNA libraries were prepared KAPA Stranded mRNA-Seq Kit following manufacturer's recommendations.

treatment_protocol:
Cells were plated, the following day they were starved overnight and the following day they were exposed to the different drugs/compounds for the appropiate times (CCA cells for 16 h and HSC cells for 48 h).
Concentrations used were: TGF-beta 1 (2 ng/ml), galunisertib (10 µM) and setanaxib (40 µM).

value: HSC-GFP

value: Primary Hepatic Stellate Cells

value: WT

value: Galunisertib


title: UNSTIM, rep 4, EM Seq

description:
Library name: 3197435
EM Seq


title: SL9_IST, rep 1, EM Seq

description:
Library name: 3197436
EM Seq


title: HSC-GFP-Galunisertib-Sample 1


title: UNSTIM, rep 3, EM Seq

description:
Library name: 3197434
EM Seq


title: HSC-GFP-Setanaxib-Sample 3

value: Setanaxib


title: MART_IST, rep 1, EM Seq

description:
Library name: 3155243
EM Seq


title: UNSTIM, rep 2, EM Seq

description:
Library name: 3155242
EM Seq


title: UNSTIM, rep 1, EM Seq

description:
Library name: 3155241
EM Seq


title: MART_DC, rep 2, EM Seq

description:
Library name: 3155240
EM Seq


title: hTERT-HSC-Galunisertib-Sample 3

source_name: hTERT-HSC

value: hTERT-HSC

value: Hepatic Stellate Cell line


title: HSC-GFP-Galunisertib-Sample 3


title: MART_DC, rep 1, EM Seq

description:
Library name: 3155239
EM Seq


title: HSC-GFP-Vehicle-Sample 1

value: Vehicle


title: HSC-GFP-Setanaxib-Sample 2


title: COVID-19,Hospitalized,patient010,Visit4

description: Library name: C19-C010-V4

value: Whole blood

value: M

value: Mild-Moderate


title: UNSTIM, rep 5, EM Seq

description:
Library name: 3197440
EM Seq


title: hTERT-HSC-Galunisertib-Sample 1


title: HSC-GFP-Setanaxib-Sample 1


title: hTERT-HSC-Setanaxib-Sample 2


title: hTERT-HSC-Galunisertib-Sample 2


title: HSC-GFP-Vehicle-Sample 2


title: hTERT-HSC-Setanaxib-Sample 1


title: HSC-GFP-Vehicle-Sample 3


title: hTERT-HSC-Setanaxib-Sample 3


title: hTERT-HSC-Vehicle-Sample 3


title: hTERT-HSC-Vehicle-Sample 2


title: LX2-HSC-Galunisertib-Sample 3


title: hTERT-HSC-Vehicle-Sample 1


title: LX2-HSC-Setanaxib-Sample 3


title: LX2-HSC-Galunisertib-Sample 2


title: LX2-HSC-Galunisertib-Sample 1


title: LX2-HSC-Setanaxib-Sample 1


title: LX2-HSC-Vehicle-Sample 2


title: Endometrial tissue, treated

city: Chengdu

first: Ming

last: Zhang

state: Sichuan

address: Sichuan Agricultural University, Huimin Road, Wenjiang District

department: Animal Reproduction

institute: Sichuan Agricultural University, China

description:
Library name: Sample 2
SeekGene

library_source: transcriptomic single cell

data_processing:
Seeksoultools software was used for the generation of gene expression matrices and aggregation of sample data. Seurat in R software (version 4.1.1) was applied for further processing of the raw data
Quality control-find clusters-cluster markers-cluster annotation
Cell fate trajectory analysis
Cell communication analysis
Assembly: Mouse mm10
Assembly: Lipopolysaccharides
Supplementary files format and content: The file format is tsv.gz, mtx.gz and fastq.gz. The content of the files related to it’s the file name.

organism:
Mus musculus
Escherichia coli O111:B4

source_name: Endometrium along embryo

extract_protocol:
The mice were killed by cervical dislocation and uterine samples along with embryos were collected. At the time of sample collections, half of the one uterine horn flushed with saline to collect the blastocyst for confirmation of pregnancy and early embryonic growth. Samples from each group were pooled, washed , and dissociated with the help of SeekMate reagent kit A Pro (SeekGene, K01801301). Then samples were filtered using different reagents and cell viability checked using Cell analyzer (Counterstar®)
Library was prepared using SeekOne® Digital Droplet Single Cell 3’ library preparation kit (SeekGene, Catalog No. K00202). Briefly, appropriate samples, Barcoded hydrogen beads and oil were added to the SeekOne® chip S3. cDNA amplification was done using PCR reaction following the purification and processed it to ligated with the adaptor for sequencing. The index sequenced libraries were filtered using Qubit (Thermo Fisher Scientific Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400)  and finally generated libraries were sequenced using the Illumina NovaSeq 6000 (PE150 read length).

treatment_protocol: The mice were purchased and kept under controlled enviroment, then synchronized using PMSG and hCG followed by natural mating (1:1 male:female). The vaginal plug was observed on second day to confirm the successful mating. The mice were divided into two groups, control and LPS gorup. The Lipopolysaccharides (LPS) are administered to the LPS group on third day of pregnancy while normal saline to the control group on same time.

value: Endometrium along embryo

value: 8-16 weeks

tag: bacterial strain

value: Escherichia coli O111:B4


title: OTX2-dTAG_PS_K27ac_dTAG_Rep3

first: Ly-sha

last: Ee

address: 413 E 69th Street

institute: Weill Cornell Medicine

description: Library name: PS_K27ac_13_7H2

data_processing:
Reads were trimmed using bbmap (v38.95) with parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hist= 1 mink=11.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2 (v2.3.5.1) with parameters --local --very-sensitive-local --no-mixed--no-discordant --phred33 -I 5 -X 999 (Langmead and Salzberg, 2012)
Reads with a MAPQ score less than 5 were removed with samtools (v1.14) (Li, et al., 2009).
PCR duplicates were removed with Picard (v2.26.10) using parameter
VALIDATION_STRINGENCY=LENIENT. Bigwigs were generated from bam files using bedtools (v2.30) normalizing to sequencing depth using the formula: (effective_genome_size / read_count * read_length) with 1870000000 as the effective genome size (Quinlan and Hall, 2010)
Assembly: Bam files were converted to bed files with bedtools (v2.30) with parameter - bedpe. MACS (v2.2.6) was used to call peaks on individual and merged replicates using parameters -g 1870000000 --nomodel --seed 123 -keep-dup all (Zhang, et al., 2008)
Supplementary files format and content: BigWig, narrowPeak
Supplementary files format and content: Bed
Library strategy: CUT&Tag

organism: Mus musculus

source_name: 7H2 OTX2-dTAG-EGFP

growth_protocol: All cells cultured at 37C, 5% CO2. EpiSCs are grown in N2B27, 20ng/ml Activin A, 12.5ng/ml FGF2, 175nM NVP. PS and DE are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs followed by 100ng/ml Activin A, 100nM LDN for 24hrs

extract_protocol:
CUT&TAG on H3K27ac and H3K4me1 was performed on 100,000-400,000 EpiSCs, PS or DE cells per sample using BioMag Plus Concanavalin A beads (ConA beads, PolySciences NC1358578), 1:100 anti-H3K27ac (EpiCypher) or anti-H3K4me1 (Abcam8895), and ProteinA/G Tn5 (EpiCypher).
Tagmented DNA was amplified using Non-Hot Start 2X PCR Master Mix (EpiCypher). Cycles for PCR amplification were determined individually for each sample by qPCR. Libraries were size selected using SPRI beads (Beckman Coulter)

treatment_protocol: Live DE cells were sorted for CUT&TAG with magnetic-assisted sorting.

value: 7H2 OTX2-dTAG-EGFP

value: Primitive Streak

value: BL6/129 hybrid


title: LX2-HSC-Vehicle-Sample 1


title: OTX2-dTAG_PS_K27ac_DMSO_Rep3

description: Library name: PS_K27ac_DM_7H2

value: DMSO


title: OTX2-dTAG_PS_K27ac_dTAG_Rep2

description: Library name: PS_K27ac_13_7H1

source_name: 7H1 OTX2-dTAG-EGFP

value: 7H1 OTX2-dTAG-EGFP


title: LX2-HSC-Vehicle-Sample 3

value: WT


title: RBE-Galunisertib-Sample 1

source_name: RBE

value: RBE

value: cholangiocarcinoma tumour cell

value: Galunisertib


title: RBE-Galunisertib-Sample 2


title: OTX2-dTAG_PS_K27ac_DMSO_Rep2

description: Library name: PS_K27ac_DM_7H1


title: OTX2-dTAG_PS_K27ac_dTAG_Rep1

description: Library name: PS_K27ac_13_7H

source_name: 7H OTX2-dTAG-EGFP

value: 7H OTX2-dTAG-EGFP


title: RBE-TGF-β1-Sample 2

value: TGF-β


title: OTX2-dTAG_PS_K27ac_DMSO_Rep1

description: Library name: PS_K27ac_DM_7H


title: RBE-TGF-β1-Sample 3


title: RBE-Galunisertib-Sample 3


title: RBE-Vehicle-Sample 3

value: Vehicle


title: OTX2-dTAG_EPI_K27ac_dTAG_Rep3

description: Library name: EPI_K27ac_13_7H2

value: Epiblast stem cells


title: OTX2-dTAG_EPI_K27ac_DMSO_Rep3

description: Library name: EPI_K27ac_DM_7H2


title: RBE-Vehicle-Sample 2


title: RBE-Vehicle-Sample 1


title: RBE-TGF-β1-Sample 1


title: OTX2-dTAG_EPI_K27ac_dTAG_Rep2

description: Library name: EPI_K27ac_13_7H1


title: LX2-HSC-Setanaxib-Sample 2

value: Hepatic Stellate Cell line

value: Setanaxib


title: OTX2-dTAG_EPI_K27ac_DMSO_Rep2

description: Library name: EPI_K27ac_DM_7H1


title: OTX2-dTAG_EPI_K27ac_dTAG_Rep1

description: Library name: EPI_K27ac_13_7H


title: HuCCT1-Galunisertib-Sample 2


title: HuCCT1-Galunisertib-Sample 3


title: OTX2-dTAG_EPI_K27ac_DMSO_Rep1

description: Library name: EPI_K27ac_DM_7H


title: HuCCT1-Galunisertib-Sample 1


title: HuCCT1-TGF-β1-Sample 3


title: OTX2-dTAG_DE1_K27ac_dTAG_Rep2

description: Library name: DE1_K27ac_13_7H2

value: Definitive Endoderm


title: HuCCT1-TGF-β1-Sample 2


title: OTX2-dTAG_DE1_K27ac_DMSO_Rep2

description: Library name: DE1_K27ac_DM_7H2


title: OTX2-dTAG_DE1_K27ac_dTAG_Rep1

description: Library name: DE1_K27ac_13_7H1


title: HuCCT1-TGF-β1-Sample 1


title: HuCCT1-Vehicle-Sample 3


title: OTX2-dTAG_DE1_K27ac_DMSO_Rep1

description: Library name: DE1_K27ac_DM_7H1


title: HuCCT1-Vehicle-Sample 1


title: OTX2-dTAG_PS_K4me1_dTAG_Rep2

description: Library name: PS_K4me1_13_7H1


title: OTX2-dTAG_PS_K4me1_DMSO_Rep2

description: Library name: PS_K4me1_DM_7H1


title: Zrfus DBD3aa 2

first: Stephen

middle: C

last: Mack

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

data_processing:
Sequencing reads were adapter trimmed using Trimgalore and aligned to hg38 using STAR. The read counts for Refseq genes were quantified using htseq-count. Differential expression analysis was performed using DEseq2.
Assembly: hg38
Supplementary files format and content: tab delimited file includes raw counts

extract_protocol:
RNA was extracted using miRNeasy Cell/Tissue advanced kit following manufacturer's recommendation. All the steps were performed in a benchtop PCR hood and all the equipments were treated with RNase away.
KAPA Hyper Prep Kit (catalog no. KK8504, KAPA Biosystems) and KAPA Dual-indexed Adapter Kit (catalog no. KK8722 KAPA Biosystems) were used to construct the CUT&RUN DNA library for sequencing on an Illumina platform following the manufacturer's instructions. After adaptor ligation, 2× volume of AMPure XP beads was used to recover the small fragments. After 12–14 cycles of PCR amplification, the product was cleaned up with AMPure XP beads. 3% gel purification was performed if the PCR dimers were too much.

value: Zrfus DBD3aa


title: Zrfus DBD3aa 3


title: OTX2-dTAG_PS_K4me1_dTAG_Rep1

description: Library name: PS_K4me1_13_7H


title: OTX2-dTAG_PS_K4me1_DMSO_Rep1

description: Library name: PS_K4me1_DM_7H


title: Zrfus DBD3aa 1


title: Zrfus ZF2a 3

value: Zrfus ZF2a


title: OTX2-dTAG_EPI_K4me1_dTAG_Rep3

description: Library name: EPI_K4me1_13_7H2

value: 7H2 OTX2-dTAG-EGFP


title: Zrfus ZF2a 1


title: OTX2-dTAG_EPI_K4me1_DMSO_Rep2

description: Library name: EPI_K4me1_DM_7H1

value: BL6/129 hybrid


title: Zrfus WT 3

value: Zrfus WT


title: OTX2-dTAG_EPI_K4me1_dTAG_Rep1

description: Library name: EPI_K4me1_13_7H


title: OTX2-dTAG_EPI_K4me1_DMSO_Rep3

description: Library name: EPI_K4me1_DM_7H2

value: DMSO


title: Zrfus WT 1


title: Zrfus IDR3 deletion 3

value: Zrfus IDR3 deletion


title: OTX2-dTAG_EPI_K4me1_dTAG_Rep2

description: Library name: EPI_K4me1_13_7H1

value: 7H1 OTX2-dTAG-EGFP


title: OTX2-dTAG_DE1_K4me1_dTAG_Rep3

description: Library name: DE1_K4me1_13_7H2


title: OTX2-dTAG_PS_K4me1_DMSO_Rep3

description: Library name: PS_K4me1_DM_7H2

value: Primitive Streak


title: OTX2-dTAG_PS_K4me1_dTAG_Rep3

description: Library name: PS_K4me1_13_7H2


title: Zrfus WT 2


title: Zrfus IDR3 deletion 1


title: OTX2-dTAG_DE1_K4me1_dTAG_Rep2

description: Library name: DE1_K4me1_13_7H1


title: OTX2-dTAG_DE1_K4me1_DMSO_Rep3

description: Library name: DE1_K4me1_DM_7H2


title: HuCCT1-Vehicle-Sample 2

value: cholangiocarcinoma tumour cell

value: WT


title: Zrfus ZF2a 2


title: OTX2-dTAG_DE1_K4me1_DMSO_Rep2

description: Library name: DE1_K4me1_DM_7H1


title: GFP control 2

value: GFP control


title: Zrfus IDR3 deletion 2


title: OTX2-dTAG_PS_HA_Rep3

description: Library name: u57_HA_7H2

data_processing:
Reads were trimmed using bbmap (v38.95) with parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2 (v2.3.5.1) with parameters --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 5 -X 999 (Langmead and Salzberg, 2012)
Reads with a MAPQ score less than 5 were removed with samtools (v1.14) (Li, et al., 2009).
PCR duplicates were removed with Picard (v2.26.10) using parameter VALIDATION_STRINGENCY=LENIENT. Fragments between 20 and 120bp were isolated using a custom awk script
Bigwigs were generated from bam files using bedtools (v2.30) normalizing to sequencing depth using the formula: (effective_genome_size / read_count * read_length) with 1870000000 as the effective genome size (Quinlan and Hall, 2010)
Bam files were converted to bed files with bedtools (v2.30) with parameter -bedpe. MACS (v2.2.6) was used to call peaks on individual and merged replicates using parameters -g 1870000000 --nomodel --seed 123 –keep-dup all (Zhang, et al., 2008)
Assembly: mm10
Supplementary files format and content: BigWig, narrowPeak, bed
Supplementary files format and content: txt
Library strategy: CUT&Run

growth_protocol: All cells cultured at 37C, 5% CO2. EpiSCs are grown in N2B27, 20ng/ml Activin A, 12.5ng/ml FGF2, 175nM NVP. DE are differentiated in CDM, 40ng/ml Activin A, 3uM CHIR for 16hrs (PS) followed by 100ng/ml Activin A, 100nM LDN for 24hrs (DE)

extract_protocol:
CUT&RUN on OTX2-HA was performed on 500,000 EpiSCs, PS or DE cells per sample using BioMag Plus Concanavalin A beads (ConA beads, PolySciences NC1358578), 1:100 anti-HA (CST C29F4 #3724) or anti-IgG (EpiCypher 130042), and ProteinA/G MNase (EpiCypher). Fragmented DNA was isolated by phenolchloroform extraction and EtOH precipitation
CUT&RUN libraries were constructed using the Takara Thruplex Library Prep and Unique Dual Index kits. Cycles for PCR amplification were determined individually for each sample by qPCR. Libraries were size selected using SPRI beads (Beckman Coulter)

treatment_protocol: Live DE cells were sorted for CUT&RUN with DAPI on BD-Influx


title: OTX2-dTAG_DE1_K4me1_DMSO_Rep1

description: Library name: DE1_K4me1_DM_7H

value: 7H OTX2-dTAG-EGFP


title: OTX2-dTAG_DE1_K4me1_dTAG_Rep1

description: Library name: DE1_K4me1_13_7H