title: PPs3 (RNA-Seq)

status: Public on Jun 25 2021

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. We used Tophat v2.0.9 to map the cleaned reads to the rat Rnor_6.0.95 reference genome with two mismatches.
After genome mapping, Cufflinks v2.1.1 wasrun with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using Cuffdiff
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) [3,4]. The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: Rnor_6.0.95
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and raw gene counts for each Sample

organism: Rattus norvegicus

source_name: Colonic epithelia

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).Paired-end libraries were synthesized by using the TruSeq®RNA Sample Preparation Kit (Illumina, USA) following TruSeq®RNA Sample Preparation Guide.
Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq X10(Illumina, USA).

value: SD

tag: gender

value: male

value: PPs-treated rats

value: Colonic epithelia


title: FFPE_ATAC_colon1_rep1

status: Public on Jun 30 2021

type: SRA

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

library_source: genomic

data_processing:
Reads were aligned to the mm9 genome/hg19 genome using bowtie2
duplicate reads were removed with Picard
MACS2  was used call narrow peak
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Homo sapiens

source_name: colon

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA with T7-Tn5. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

tag: treatment

value: FFPE

tag: tissue

value: colon


title: CNP1 (RNA-Seq)

country: China

library_source: transcriptomic

molecule: total RNA

tag: strain

value: CNP rats

tag: cell type


title: FFPE_ATAC_colon3_rep2


title: CNP2 (RNA-Seq)


title: Standard_ATAC_on_frozen_liver_rep2

status: Public on Jul 02 2021

organism: Mus musculus

source_name: Liver

value: FVBN

value: frozon


title: CNP3 (RNA-Seq)


title: Omni_ATAC_liver_rep1

source_name: liver

value: liver


title: FFPE_ATAC_kidney_rep1

source_name: kidney

value: kidney


title: CTL1 (RNA-Seq)

value: control rats


title: Omni_ATAC_kidney_rep2


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose, alpha-factor arrested, and induced with galactose, input

city: Seattle

first: Monica

middle: S

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

country: USA

institute: University of Washington

description: Strains were grown in YEP+2% raffinose to OD 0.3, alpha-factor was added to 1 μg/mL for 2 hr, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and then fixed by the addition 1% formaldehyde (final concentrations). ChIP was then performed as described.

data_processing:
Reads were aligned to Saccharomyces cerevisiae (S288C Scer3) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
Genome_build: Scer3
Supplementary_files_format_and_content: Tab delimited files, columns containing index positions, chromosome, chromosome positions, number of reads, and normalized number of reads.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Strains were grown as described, and 2% galactose was added for 6 hr to induce GapR. Cells then fixed by the addition 1% formaldehyde (final concentrations).

extract_protocol:
ChIP was performed as previously reported (Guo et al, 2018).
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 200-500 bp.

treatment_protocol: If indicated cells were treated with alpha-factor. Cells were subsequently induced with 2% galactose for 6 hr.

tag: growth stage

value: exponential phase

tag: media

value: YEP + 2% raffinose + alpha-factor


title: FFPE_ATAC_colon4_rep2


title: Omni_ATAC_kidney_rep1


title: PPs1 (RNA-Seq)


title: FFPE_ATAC_kidney_rep2


title: FFPE_ATAC_rectum2_rep2

source_name: rectum

value: rectum


title: FFPE_ATAC_rectum2_rep1


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose and induced with galactose, replicate 2

description: Strains were grown in YEP+2% raffinose to OD 0.05, and 2% galactose was added. Cells were grown for 6 hr (OD ~1.0) and then fixed by the addition 1% formaldehyde (final concentrations). ChIP was then performed as described.

value: YEP + 2% raffinose


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in glycerol and induced with galactose, replicate 1

data_processing:
Reads were aligned to Saccharomyces cerevisiae (S288C Scer3) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
Genome_build: Scer3
Supplementary_files_format_and_content: txt files (5 columns:  1) Index position, 2) chromosome, 3) chromosome position, 4) ChIP coverage, 5) Gaussian-normalized ChIP)

growth_protocol: Strains were grown in YEP+2% glycerol to OD 0.5, and 2% galactose was added. Cells were grown for 6 hr (OD ~1.0) and then fixed by the addition 1% formaldehyde (final concentrations).

extract_protocol:
ChIP was performed as previously reported (Guo et al, 2018). ChIP antibody is Mouse monoclonal anti-FLAG from Sigma (Cat #: F1804).
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 200-500 bp.

treatment_protocol: Cells were induced with 2% galactose for 6 hr.

value: YEP + 2% galactose


title: FFPE_ATAC_cere_rep1

source_name: cerebellum

value: cerebellum


title: Circulating blood monocytes rep 3

status: Public on Jun 01 2021

city: Debrecen

first: Nikolaos

last: Giannakis

address: Egyetem ter 1

department: Department of Biochemistry and Molecular  Biology

country: Hungary

institute: University of Debrecen

description: adult female 2-4 months old

data_processing:
Alignment was performed  with TopHat v2.0.7 using default parameters.
Data analysis was performed using Strand NGS software, Version 3.4, Build 230243. © Strand Life Sciences, Bangalore, India
Read counts were calculated based on manufacturer's default parameters.
Normalisation of the read counts was performed with the Deseq method. The normalized counts are log transformed  and baselined.This method is based on the paper ‘Differential expression analysis for sequence count data’ by  Simon Anders and Wolfgang Huber.
Changes in genes in the pairwise comparisons with FC>=1.5 and p-value<0.05 were considered to be statistically significant. Filtering was performed for genes with normalized expression >=3 in at least one condition.
Genome_build: mm10
Supplementary_files_format_and_content: Pairwise comparisons with Fold Changes and Averaged raw and normalised counts based on DESeq (abundance) measurements.

source_name: Blood

extract_protocol:
Total RNA was isolated with TRIZOL reagent according to the manufacturer’s recommendation. 20ug glycogen (Ambion) was added as carrier for RNA ethanol precipitation
cDNA library for RNA-Seq was generated from 100ng-400ng total RNA using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol. Briefly poly-A tailed RNA molecules were pulled down with poly-T oligo attached magnetic beads. Following purification, mRNA was fragmented with divalent cations at 85C, and then cDNA was generated by random primers and SuperScript II enzyme (Life Technologies). Second strand synthesis was performed followed by end repair, single `A` base addition and ligation of barcode indexed adaptors to the DNA fragments. Adapter specific PCRs were performed to generate sequencing libraries. Libraries were size selected with E-Gel EX 2% agarose gels (Life Technologies) and purified by QIAquick Gel Extraction Kit (Qiagen). Libraries were sequenced on HiSeq 2500 instrument.

value: Blood

value: Ly6Chigh blood circulating monocytes


title: CTL2 (RNA-Seq)

value: SD

value: male

value: Colonic epithelia


title: Circulating blood monocytes rep 2

description: adult female 2-4 months old


title: PPs2 (RNA-Seq)

value: colon

value: PPs-treated rats


title: Circulating blood monocytes rep 1

description: adult female 2-4 months old


title: TA muscle Ly6Chigh macrophage day 1 after CTX rep 2

description: adult male 2-4 months old

source_name: TA muscle

value: muscle

value: Ly6Chigh macrophages day 1 after CTX


title: PIlot_sample 10_preBötC inspiratory neuron

status: Public on May 28 2021

city: Williamsburg

first: Prajkta

last: Kallurkar

state: VA

address: 540 Landrum Dr, Integrated Science Center 3

institute: William & Mary

description: Sample 10

data_processing:
The quality of reads was verified using FastQC v0.11.8 (Andrews 2015).
Adapter reads (Read 1: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, Read 2: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG) were trimmed using bbduk v38.00 (https://sourceforge.net/projects/bbmap/) using the following command: sh bbduk.sh in1=inputFASTQFile1.fastq. in2=inputFASTQFile2.fastq out1=outputFASTQFile1.fastq out2=outputFASTQFile2.fastq ktrim=r -Xmx27g mm=f k=33 hdist=1 literal=TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG,GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG tbo tpe
The mouse reference genome, mm10 from Ensembl, was used to create genome directory for aligning the reads in STAR (Dobin et al. 2013) using the following commands: STAR --runMode genomeGenerate --genomeDir mm10ReferenceGenome --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.102.gtf --sjdbOverhang 149 --genomeSAsparseD 2
The sequences were then aligned to mm10 reference genome using STAR v2.7.7a (Dobin et al. 2013) using the following command: STAR --genomeDir mm10ReferenceGenome --readFilesIn inputFASTQFile1.fastq inputFASTQFile2.fastq --outFileNamePrefix outputBAMFile --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing fragment counts for all the samples.
Supplementary_files_format_and_content: tab-delimited text file with gene length
Supplementary_files_format_and_content: tab-delimited text file containing FPKM for all the samples.

source_name: preBötC in the brainstem

growth_protocol: All experiments employed CD-1 mice or mice with Cre-dependent expression of fluorescent Ca2+ indicator GCaMP6f, dubbed Ai148, by the Allen Institute (RRID: IMSR_JAX:030328, Daigle et al. 2018). To identify Dbx1-derived preBötC neurons, we crossed Dbx1cre mice with Ai148 mice. We used their offspring, referred to as Dbx1; Ai148 mice (P0-3). All Dbx1; Ai148 mice were C57Bl/6J or mixed C57Bl/6J; CD1 genetic background. Dbx1; Ai148 pups have fluorescent labeling in Dbx1-derived preBötC neurons.

extract_protocol:
Once the electrical phenotype of preBötC inspiratory neurons was determined, the cellular contents of the neuron were extracted by applying gentle negative pressure (0.7-1.5 psi). The patch pipette was quickly retracted, and the extracted cellular contents were ejected by breaking the tip of the pipette at the bottom of the RNase-free PCR tube containing 4 µL nuclease-free water with 2% RRI. The sample was briefly spun, snap-frozen in liquid nitrogen and stored at -80˚C. The extracted RNA from patch-clamped neurons was converted to cDNA according to SMART-Seq v4 ultra low input RNA kit for Sequencing protocol.  First strand cDNA was synthesized by performing reverse transcription in a thermal cycler (42 °C for 90 min, 70 °C for 10 min). The cDNA was then amplified by at 95 °C for 1 min, 17 cycles of 98 °C for 10 s, 65 °C for 30 s, 68 °C for 3 min; 72 °C for 10 min. PCR-amplified cDNA was purified by immobilization on AMPure beads, which were then washed with 80% ethanol and eluted.
Amplified cDNA was validated using the Agilent 2100 Bioanalyzer and Agilent’s High Sensitivity Kit (5067-4626, Agilent Technologies, CA), and its concentration was determined using Qubit dsDNA High-sensitivity Assay Kit (Molecular Probes). The full-length cDNA output was processed with the Nextera Library Preparation Kits (FC-131-1024, Illumina, San Diego, CA) to obtain cDNA libraries for RNA-Seq experiments. The cDNA libraries were sequenced using an Illumina HiSeq 4000 Sequencing system with paired end (150 bp) reads. Investigators were blinded to cell type during library construction and sequencing.

treatment_protocol: In Dbx1; Ai148 mice, inspiratory preBötC inspiratory neurons were selected visually based on rhythmic fluorescence changes in Dbx1-derived preBötC neurons. In CD-1 mice, we only used cells from preBötC inspiratory neurons that were active in sync with hypoglosaal (XII) motor output. Patch pipettes, of resistance 3-5 MΩ, were fabricated from autoclaved borosilicate glass electrodes (OD: 1.5 mm, ID: 0.86 mm). The patch pipette was filled with an internal solution containing (in mM): 123 K-gluconate, 12 KCl, 10 HEPES, 0.2 EGTA, 4 Mg-ATP, 0.3 Na-GTP, 10 Na2-phosphocreatine, and 13 Glycogen. 0.8% Recombinant Ribonuclease Inhibitor (RRI) was added to the internal solution right before the experiment, to preserve the RNA of the cell. Whole-cell patch-clamp recordings were made using an EPC-10 patch-clamp amplifier (HEKA Instruments, Germany).

value: brainstem

tag: age

tag: electrophysiological phenotype

value: Unknown

value: WT


title: PIlot_sample 8_preBötC inspiratory neuron

description: Sample 8


title: FFPE_ATAC_cere_rep2

value: FVBN

value: FFPE


title: PIlot_sample 9_preBötC inspiratory neuron

description: Sample 9


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose, alpha-factor arrested, and induced with galactose, replicate 2

value: exponential phase

value: YEP + 2% raffinose + alpha-factor


title: CTL3 (RNA-Seq)

value: control rats


title: PIlot_sample 7_Dbx1-derived preBötC neuron

description: Sample 7


title: PIlot_sample 6_Dbx1-derived preBötC neuron

description: Sample 6


title: PIlot_sample 5_Dbx1-derived preBötC neuron

description: Sample 5


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose, alpha-factor arrested, and induced with galactose, replicate 1

description: Strains were grown in YEP+2% raffinose to OD 0.3, alpha-factor was added to 1 μg/mL for 2 hr, and 2% galactose was added. Cells were grown for 6 hr (maintaining OD <1.0) and  then fixed by the addition 1% formaldehyde (final concentrations). ChIP was then performed as described.


title: PIlot_sample 1_Dbx1-derived preBötC neuron

description: Sample 1


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in glycerol and induced with galactose, replicate 2

value: YEP + 2% galactose


title: ML3288 (OAY470 LEU2::-gal1/10-GapR) in glycerol and induced with galactose, replicate 2


title: TA muscle Ly6Chigh macrophage day 1 after CTX rep 1

description: adult male 2-4 months old


title: ML3288 (OAY470 LEU2::-gal1/10-GapR) in raffinose and induced with galactose

value: YEP + 2% raffinose


title: Ethanol_16_S2 (Liver-Chip)

status: Public on May 25 2021

city: Los Angeles

first: Janna

last: Nawroth

state: CA

address: 2011 Zonal Avenue

institute: USC

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: Primary Human Hepatocytes

growth_protocol: Liver-Chips were seeded with primary human hepatocytes  (introduced in the top channel of an Organ-on-Chip) and human liver sinusoidal endothelial cells (LSECs) and Kupffer cells (introduced into the bottom channel). The chips were maintained under constant perfusion of fresh media at 30 µl/hr through the top channel with in William’s E Medium (WEM) medium and bottom channel with endothelial medium.

extract_protocol:
RNA was extracted using PureLink RNA Mini Kit lyse buffer (Thermo Fischer #12183018)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 48h ethanol dosing of the medium (0.08% to 0.16% ethanol, i.e., 80 mg/ml to 160 mg/ml) was performed starting on day 7 of cluture

value: 48h ethanol dosing of the medium (0.16% ethanol, i.e., 160 mg/ml) was performed starting on day 7 of cluture

value: Primary Human Hepatocytes


title: ML3288 (OAY470 LEU2::-gal1/10-GapR) in glycerol and induced with galactose, replicate 1


title: TA muscle Ly6Chigh macrophage day 1 after CTX rep 3

description: adult male 2-4 months old


title: ML3288 (OAY470 LEU2::-gal1/10-GapR) in raffinose, alpha-factor arrested, and induced with galactose


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose and induced with galactose, input


title: ML3289 (OAY470 LEU2::-gal1/10-GapR-3xFLAG) in raffinose and induced with galactose, replicate 1


title: Ethanol_16_S1 (Liver-Chip)


title: PIlot_sample 3_preBötC inspiratory neuron

description: Sample 3


title: Ethanol_08_S1 (Liver-Chip)

value: 48h ethanol dosing of the medium (0.08% ethanol, i.e., 80 mg/ml) was performed starting on day 7 of cluture


title: PIlot_sample 4_preBötC inspiratory neuron

description: Sample 4


title: Vehicle_S2 (Liver-Chip)


title: Ethanol_08_S2 (Liver-Chip)


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB083WVA)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR392EMS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR392EMS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR488AHQ
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB083WVA

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 2.5 days

tag: antibody

value: foreskin keratinocyte

value: primary cell

tag: description

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: newborn

value: 2-4 day

tag: lab

value: Paul Khavari, Stanford

tag: source

value: Paul Khavari

tag: treatments

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

tag: health state

value: Healthy

tag: passage number

tag: link

value: ENCBS299ONK at ENCODE; https://www.encodeproject.org/ENCBS299ONK/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: PIlot_sample 2_preBötC inspiratory neuron

description: Sample 2

tag: tissue

value: brainstem

value: Unknown

value: WT


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB948REB)

description:
https://www.encodeproject.org/experiments/ENCSR392EMS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR392EMS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR488AHQ
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB948REB

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: Ethanol_08_S3 (Liver-Chip)

tag: treatment

value: 48h ethanol dosing of the medium (0.08% ethanol, i.e., 80 mg/ml) was performed starting on day 7 of cluture

tag: cell type

value: Primary Human Hepatocytes


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB560DPP)

description:
https://www.encodeproject.org/experiments/ENCSR812GLE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR812GLE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR528SMB
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB560DPP

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5.5 days

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB046OJA)

description:
https://www.encodeproject.org/experiments/ENCSR793NQA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR793NQA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113CMI
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB046OJA

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB066IYV)

description:
https://www.encodeproject.org/experiments/ENCSR487KVV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR487KVV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR631ESZ
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB066IYV

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

value: Healthy

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB887EFK)

description:
https://www.encodeproject.org/experiments/ENCSR243ZGI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR243ZGI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR335GGM
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB887EFK

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB706KOU)

description:
https://www.encodeproject.org/experiments/ENCSR487KVV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR487KVV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR631ESZ
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB706KOU

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB758VJC)

description:
https://www.encodeproject.org/experiments/ENCSR709ABP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR709ABP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113CMI
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB758VJC

value: foreskin keratinocyte

value: primary cell

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB295OCL)

description:
https://www.encodeproject.org/experiments/ENCSR709ABP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR709ABP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113CMI
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB295OCL

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: male

value: ENCBS299ONK at ENCODE; https://www.encodeproject.org/ENCBS299ONK/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB338DMO)

description:
https://www.encodeproject.org/experiments/ENCSR637ISS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR637ISS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR528SMB
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB338DMO

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/


title: ActD_RnaseH1MNase_3

status: Public on May 04 2021

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

description: imb_beli_2020_02_18_ActD_RnaseH1MNase_3_S18

data_processing:
Base calling was performed with RTA v.2.4.11  and demultiplexing was done using bcl2fastq v.2.19.1
Mapping was done against hg38.
Sequencing depth normalized coverage tracks were created using Deeptools (v3.4.1)
Genome_build: hg38
Supplementary_files_format_and_content: spike and and sequencing depth normalized bigwig tracks

growth_protocol: U2OS cells were cultured in DMEM containing 10% FBS, Pen-Strep,1% Glutamine

extract_protocol:
Mnase activity was induced by addition of 2mM CaCl2 for 30 min on ice. Chromatin fragments were released by incubating the samples for 20 minutes at 37°C and centrifugation at 16.000×g for 10 minutes at 4°C. Supernatants were incubated at 70°C in the presence of 0.1% SDS and 5 µg proteinase K. DNA was cleaned-up using phenol/chloroform extraction
NGS library preparation was performed using NuGEN´s Ovation Ultralow System V2 (M01379 v5). Libraries were prepared with a starting amount of 1 ng of DNA and were amplified in 12 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies).

treatment_protocol: Cells were treated 6 hours with 4 µM ActinomycinD. Knockdowns were induced for 48 hourse using pool siRNAs.

tag: cell line

value: ActD treatment

tag: treatment 2

value: RnaseH1MNase1 digestion

tag: replicate


title: ActD_RnaseH1MNase_2

description: imb_beli_2020_02_17_ActD_RnaseH1MNase_2_S17


title: ActD_RnaseH1MNase_1

description: imb_beli_2020_02_16_ActD_RnaseH1MNase_1_S16


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB472VBJ)

description:
https://www.encodeproject.org/experiments/ENCSR621FNM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR621FNM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR982AYN
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB472VBJ

tag: antibody

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

tag: age

value: Paul Khavari

value: Healthy

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/


title: siCtrl_RnaseH1MNase_1

description: imb_beli_2020_02_10_siCtrl_RnaseH1MNase_1_S10

value: si control knockdown


title: siCtrl_RnaseH1MNase_3

description: imb_beli_2020_02_12_siCtrl_RnaseH1MNase_3_S12


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB513AJQ)

description:
https://www.encodeproject.org/experiments/ENCSR812GLE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR812GLE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR528SMB
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB513AJQ

value: foreskin keratinocyte

value: primary cell

tag: description

tag: biosample encode accession

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ActD_pAMNase_3

value: pAMNase digestion


title: Vehicle_S1 (Liver-Chip)

value: Primary Human Hepatocytes


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB231UYO)

description:
https://www.encodeproject.org/experiments/ENCSR793NQA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on primary keratinocytes in day 3 of differentiation
experiment encode accession: ENCSR793NQA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113CMI
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB231UYO

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

tag: Sex

value: male

tag: dev stage

value: newborn

value: 2-4 day

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ActD_pAMNase_1

value: ActD treatment


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB085YGB)

description:
https://www.encodeproject.org/experiments/ENCSR736ZEG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR736ZEG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR982AYN
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB085YGB

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

tag: lab

value: Paul Khavari, Stanford

tag: source

value: Paul Khavari

value: Healthy

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/


title: siDDX41_RnaseH1MNase_2

description: imb_beli_2020_02_14_siDDX41_RnaseH1MNase_2_S14

value: siDDX41 knockdown

value: RnaseH1MNase1 digestion


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB944DGO)

description:
https://www.encodeproject.org/experiments/ENCSR736ZEG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR736ZEG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR982AYN
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB944DGO

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

tag: health state

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/


title: siDDX41_RnaseH1MNase_1

description: imb_beli_2020_02_13_siDDX41_RnaseH1MNase_1_S13


title: siDDX41_RnaseH1MNase_3

description: imb_beli_2020_02_15_siDDX41_RnaseH1MNase_3_S15


title: siCtrl_pAMNase_3

value: si control knockdown

value: pAMNase digestion


title: siCtrl_pAMNase_2


title: ActD_pAMNase_2


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB017KVF)

description:
https://www.encodeproject.org/experiments/ENCSR621FNM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR621FNM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR982AYN
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB017KVF

value: male

value: newborn

value: 2-4 day

tag: passage number

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: siDDX41_pAMNase_3

description: imb_beli_2020_02_06_siDDX41_pAMNase_3_S6


title: ATAC-seq from foreskin keratinocyte (ENCLB027OPY)

status: Public on Apr 22 2021

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB027OPY

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 1 day

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 1.5

tag: treatments

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1; duration_units:day;

tag: link

value: ENCBS839SEF at ENCODE; https://www.encodeproject.org/ENCBS839SEF/


title: ATAC-seq from foreskin keratinocyte (ENCLB849HRI)

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB849HRI

value: Paul Khavari, Stanford

value: Paul Khavari

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB344ZFY)

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB344ZFY

value: ENCBS819VZU at ENCODE; https://www.encodeproject.org/ENCBS819VZU/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB077FPU)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB077FPU

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: ENCBS299ONK at ENCODE; https://www.encodeproject.org/ENCBS299ONK/


title: ATAC-seq from foreskin keratinocyte (ENCLB628KNN)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB628KNN

value: male

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB489QAP)

description:
https://www.encodeproject.org/experiments/ENCSR637ISS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR637ISS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR528SMB
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB489QAP

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: newborn

value: 2-4 day

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/


title: Histone ChIP-seq from foreskin keratinocyte (ENCLB470USE)

description:
https://www.encodeproject.org/experiments/ENCSR243ZGI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR243ZGI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR335GGM
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB470USE

value: Paul Khavari, Stanford

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/


title: ATAC-seq from foreskin keratinocyte (ENCLB131MEC)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB131MEC

value: Paul Khavari

value: Healthy


title: siDDX41_pAMNase_1

description: imb_beli_2020_02_04_siDDX41_pAMNase_1_S4

tag: treatment

value: siDDX41 knockdown

value: pAMNase digestion


title: ATAC-seq from foreskin keratinocyte (ENCLB641DTG)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB641DTG

value: foreskin keratinocyte

value: primary cell

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB040XMV)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB040XMV

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: ENCBS299ONK at ENCODE; https://www.encodeproject.org/ENCBS299ONK/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB521NFC)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB521NFC

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 3 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.5

value: male

value: newborn

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:3; duration_units:day;

value: ENCBS257OKQ at ENCODE; https://www.encodeproject.org/ENCBS257OKQ/


title: ATAC-seq from foreskin keratinocyte (ENCLB019BEC)

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB019BEC

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 1.5

value: 2-4 day

value: Paul Khavari, Stanford

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1; duration_units:day;

value: ENCBS819VZU at ENCODE; https://www.encodeproject.org/ENCBS819VZU/


title: siCtrl_pAMNase_1

value: si control knockdown

value: pAMNase digestion


title: ATAC-seq from foreskin keratinocyte (ENCLB921NUM)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB921NUM

value: foreskin keratinocyte

value: primary cell

value: Paul Khavari

value: Healthy

value: ENCBS408RGJ at ENCODE; https://www.encodeproject.org/ENCBS408RGJ/


title: siDDX41_pAMNase_2

description: imb_beli_2020_02_05_siDDX41_pAMNase_2_S5

value: siDDX41 knockdown


title: ATAC-seq from foreskin keratinocyte (ENCLB660GSC)

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB660GSC

value: male

value: ENCBS839SEF at ENCODE; https://www.encodeproject.org/ENCBS839SEF/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: siCtrl_RnaseH1MNase_2

description: imb_beli_2020_02_11_siCtrl_RnaseH1MNase_2_S11

value: RnaseH1MNase1 digestion


title: ATAC-seq from foreskin keratinocyte (ENCLB139QTU)

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB139QTU

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 1.5

value: newborn

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB270EEK)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 1
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB270EEK

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: 2-4 day

value: Paul Khavari, Stanford

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/


title: ATAC-seq from foreskin keratinocyte (ENCLB374IXL)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB374IXL

value: foreskin keratinocyte

value: primary cell

value: ENCBS299ONK at ENCODE; https://www.encodeproject.org/ENCBS299ONK/


title: ATAC-seq from foreskin keratinocyte (ENCLB832JSY)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB832JSY

value: Paul Khavari

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB329GHI)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 1
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB329GHI

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.5

value: male

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:3; duration_units:day;

value: ENCBS257OKQ at ENCODE; https://www.encodeproject.org/ENCBS257OKQ/


title: ATAC-seq from foreskin keratinocyte (ENCLB811FRL)

description:
https://www.encodeproject.org/experiments/ENCSR247PVM/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 1.5 of differentiation
experiment encode accession: ENCSR247PVM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB811FRL

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 1.5

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1; duration_units:day;

value: ENCBS839SEF at ENCODE; https://www.encodeproject.org/ENCBS839SEF/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB724FGU)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB724FGU

value: newborn

value: 2-4 day

value: ENCBS408RGJ at ENCODE; https://www.encodeproject.org/ENCBS408RGJ/


title: ATAC-seq from foreskin keratinocyte (ENCLB365GKG)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB365GKG

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.0

value: Paul Khavari, Stanford

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2.5; duration_units:day;


title: ATAC-seq from foreskin keratinocyte (ENCLB824NWT)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 1
technical replicate number: 6
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB824NWT

value: foreskin keratinocyte

value: primary cell

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB989KEL)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB989KEL

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.5

value: Paul Khavari

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB674LTT)

description:
https://www.encodeproject.org/experiments/ENCSR245LNF/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 3.0 of differentiation
experiment encode accession: ENCSR245LNF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB674LTT

value: male

value: ENCBS079LRU at ENCODE; https://www.encodeproject.org/ENCBS079LRU/


title: ATAC-seq from foreskin keratinocyte (ENCLB225XVU)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB225XVU

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:3; duration_units:day;

value: ENCBS257OKQ at ENCODE; https://www.encodeproject.org/ENCBS257OKQ/


title: ATAC-seq from foreskin keratinocyte (ENCLB655ODB)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB655ODB

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB895OCD)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB895OCD

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.5

value: newborn

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration_units:day;

value: ENCBS978XWC at ENCODE; https://www.encodeproject.org/ENCBS978XWC/


title: ATAC-seq from foreskin keratinocyte (ENCLB577OSB)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB577OSB

value: 2-4 day

value: Paul Khavari, Stanford

value: ENCBS408RGJ at ENCODE; https://www.encodeproject.org/ENCBS408RGJ/


title: ATAC-seq from foreskin keratinocyte (ENCLB971GPW)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB971GPW

value: foreskin keratinocyte

value: primary cell


title: ATAC-seq from foreskin keratinocyte (ENCLB153AQG)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB153AQG


title: ATAC-seq from foreskin keratinocyte (ENCLB676EPF)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB676EPF

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.5


title: ATAC-seq from foreskin keratinocyte (ENCLB436WON)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB436WON

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 4.5 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.0

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4.5; duration_units:day;

value: ENCBS379WNC at ENCODE; https://www.encodeproject.org/ENCBS379WNC/


title: ATAC-seq from foreskin keratinocyte (ENCLB452CAH)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB452CAH

value: male

value: Healthy

value: ENCBS927PYN at ENCODE; https://www.encodeproject.org/ENCBS927PYN/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB996QFW)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB996QFW

value: newborn

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB939WGI)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB939WGI


title: ATAC-seq from foreskin keratinocyte (ENCLB920SPF)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 2
technical replicate number: 6
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB920SPF


title: ATAC-seq from foreskin keratinocyte (ENCLB524BPZ)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB524BPZ

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.5

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration_units:day;

value: ENCBS978XWC at ENCODE; https://www.encodeproject.org/ENCBS978XWC/


title: ATAC-seq from foreskin keratinocyte (ENCLB129MVO)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB129MVO

value: 2-4 day

value: Paul Khavari, Stanford


title: ATAC-seq from foreskin keratinocyte (ENCLB684RWM)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB684RWM

value: foreskin keratinocyte

value: primary cell


title: ATAC-seq from foreskin keratinocyte (ENCLB631VIN)

description:
https://www.encodeproject.org/experiments/ENCSR677MJF/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 0.5 of differentiation
experiment encode accession: ENCSR677MJF
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB631VIN


title: ATAC-seq from foreskin keratinocyte (ENCLB236UMT)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB236UMT

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.0

value: ENCBS616IKM at ENCODE; https://www.encodeproject.org/ENCBS616IKM/


title: ATAC-seq from foreskin keratinocyte (ENCLB497UOW)

description:
https://www.encodeproject.org/experiments/ENCSR460DKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 3.5 of differentiation
experiment encode accession: ENCSR460DKJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB497UOW

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 3.5

value: Paul Khavari

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:3; duration_units:day;

value: ENCBS257OKQ at ENCODE; https://www.encodeproject.org/ENCBS257OKQ/


title: ATAC-seq from foreskin keratinocyte (ENCLB123VPU)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 7
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB123VPU

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 4 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 4.5

value: male

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4; duration_units:day;

value: Healthy

value: ENCBS623QHX at ENCODE; https://www.encodeproject.org/ENCBS623QHX/


title: ATAC-seq from foreskin keratinocyte (ENCLB252RPL)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB252RPL

value: newborn

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4.5; duration_units:day;

value: ENCBS379WNC at ENCODE; https://www.encodeproject.org/ENCBS379WNC/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB771QQE)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB771QQE

value: foreskin keratinocyte

value: 2-4 day

value: Paul Khavari, Stanford

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB889CVO)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB889CVO

value: primary cell

value: ENCBS473PMP at ENCODE; https://www.encodeproject.org/ENCBS473PMP/


title: ATAC-seq from foreskin keratinocyte (ENCLB034CND)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB034CND

value: Paul Khavari


title: ATAC-seq from foreskin keratinocyte (ENCLB892XGI)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB892XGI


title: ATAC-seq from foreskin keratinocyte (ENCLB097FAS)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB097FAS


title: ATAC-seq from foreskin keratinocyte (ENCLB458BOO)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB458BOO

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.0


title: ATAC-seq from foreskin keratinocyte (ENCLB431NYD)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB431NYD

value: ENCBS616IKM at ENCODE; https://www.encodeproject.org/ENCBS616IKM/


title: ATAC-seq from foreskin keratinocyte (ENCLB526RLC)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB526RLC

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 4.5

value: male


title: ATAC-seq from foreskin keratinocyte (ENCLB987CDQ)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB987CDQ

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4; duration_units:day;

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB713KDG)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB713KDG

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 2 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.5

value: newborn

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2; duration_units:day;

value: ENCBS024RNH at ENCODE; https://www.encodeproject.org/ENCBS024RNH/


title: ATAC-seq from foreskin keratinocyte (ENCLB990XWX)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB990XWX

value: foreskin keratinocyte

value: ENCBS623QHX at ENCODE; https://www.encodeproject.org/ENCBS623QHX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB934SDL)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB934SDL

value: 2-4 day

value: Paul Khavari, Stanford

value: ENCBS924PBK at ENCODE; https://www.encodeproject.org/ENCBS924PBK/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB129DAM)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB129DAM

value: primary cell

value: Paul Khavari


title: ATAC-seq from foreskin keratinocyte (ENCLB627NLP)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB627NLP

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5 days

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.5

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5; duration_units:day;

value: ENCBS797AGG at ENCODE; https://www.encodeproject.org/ENCBS797AGG/


title: ATAC-seq from foreskin keratinocyte (ENCLB215IKE)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB215IKE

value: male

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB472LYY)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 1
technical replicate number: 6
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB472LYY

value: newborn


title: ATAC-seq from foreskin keratinocyte (ENCLB633BPS)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB633BPS

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 4.5

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4; duration_units:day;

value: ENCBS473PMP at ENCODE; https://www.encodeproject.org/ENCBS473PMP/


title: ATAC-seq from foreskin keratinocyte (ENCLB012MNW)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB012MNW

value: foreskin keratinocyte

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.5

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2; duration_units:day;

value: ENCBS024RNH at ENCODE; https://www.encodeproject.org/ENCBS024RNH/


title: ATAC-seq from foreskin keratinocyte (ENCLB830PDW)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB830PDW

value: 2-4 day

value: Paul Khavari, Stanford

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB237QTU)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB237QTU

value: primary cell

value: Paul Khavari

value: ENCBS924PBK at ENCODE; https://www.encodeproject.org/ENCBS924PBK/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB602YIV)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB602YIV

value: male


title: ATAC-seq from foreskin keratinocyte (ENCLB628QOF)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 6
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB628QOF

value: Healthy

value: ENCBS623QHX at ENCODE; https://www.encodeproject.org/ENCBS623QHX/


title: ATAC-seq from foreskin keratinocyte (ENCLB561JGB)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB561JGB

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.5

value: newborn

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5; duration_units:day;

value: ENCBS194HUS at ENCODE; https://www.encodeproject.org/ENCBS194HUS/


title: ATAC-seq from foreskin keratinocyte (ENCLB131WIP)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 1
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB131WIP

value: foreskin keratinocyte

value: ENCBS797AGG at ENCODE; https://www.encodeproject.org/ENCBS797AGG/


title: ATAC-seq from foreskin keratinocyte (ENCLB936EWE)

description:
https://www.encodeproject.org/experiments/ENCSR923WGJ/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 4.5 of differentiation
experiment encode accession: ENCSR923WGJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB936EWE

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 4.5

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4; duration_units:day;


title: ATAC-seq from foreskin keratinocyte (ENCLB554GEK)

description:
https://www.encodeproject.org/experiments/ENCSR939WVU/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 5.0 of differentiation
experiment encode accession: ENCSR939WVU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB554GEK

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.0

value: 2-4 day

value: Paul Khavari, Stanford

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:4.5; duration_units:day;

value: ENCBS616IKM at ENCODE; https://www.encodeproject.org/ENCBS616IKM/


title: ATAC-seq from foreskin keratinocyte (ENCLB707DOJ)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB707DOJ

value: primary cell

value: Paul Khavari

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB413SEK)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB413SEK

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

value: male

value: Healthy

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB435ETQ)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB435ETQ

value: foreskin keratinocyte

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.5

value: newborn

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5; duration_units:day;


title: ATAC-seq from foreskin keratinocyte (ENCLB126RNA)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB126RNA

value: ENCBS194HUS at ENCODE; https://www.encodeproject.org/ENCBS194HUS/


title: ATAC-seq from foreskin keratinocyte (ENCLB623MJD)

description:
https://www.encodeproject.org/experiments/ENCSR158XTU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 2.5 of differentiation
experiment encode accession: ENCSR158XTU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB623MJD

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.5

value: 2-4 day

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:2; duration_units:day;

value: ENCBS924PBK at ENCODE; https://www.encodeproject.org/ENCBS924PBK/


title: ATAC-seq from foreskin keratinocyte (ENCLB167MTB)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB167MTB

value: primary cell

value: Paul Khavari, Stanford


title: ATAC-seq from foreskin keratinocyte (ENCLB228YJR)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB228YJR

value: Paul Khavari

value: ENCBS797AGG at ENCODE; https://www.encodeproject.org/ENCBS797AGG/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB417OAH)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 2
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB417OAH

value: male

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB904SZX)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB904SZX

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/


title: ATAC-seq from foreskin keratinocyte (ENCLB694JTW)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB694JTW

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 1.5 days

value: foreskin keratinocyte

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1.5; duration_units:day;

value: ENCBS903GAF at ENCODE; https://www.encodeproject.org/ENCBS903GAF/


title: ATAC-seq from foreskin keratinocyte (ENCLB080YOM)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 2
technical replicate number: 6
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB080YOM

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

value: newborn

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB597PAR)

description:
https://www.encodeproject.org/experiments/ENCSR649RCV/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 5.5 of differentiation
experiment encode accession: ENCSR649RCV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB597PAR

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 5.5

value: 2-4 day

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5; duration_units:day;

value: ENCBS194HUS at ENCODE; https://www.encodeproject.org/ENCBS194HUS/


title: ATAC-seq from foreskin keratinocyte (ENCLB551ZIG)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB551ZIG

value: male

value: Paul Khavari, Stanford

value: Paul Khavari


title: ATAC-seq from foreskin keratinocyte (ENCLB762MLF)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB762MLF

value: Healthy


title: ATAC-seq from foreskin keratinocyte (ENCLB585OEK)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB585OEK

value: foreskin keratinocyte


title: ATAC-seq from foreskin keratinocyte (ENCLB250SBS)

description:
https://www.encodeproject.org/experiments/ENCSR356KRQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 0.0 of differentiation
experiment encode accession: ENCSR356KRQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB250SBS

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB850SWS)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 2
technical replicate number: 5
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB850SWS

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1.5; duration_units:day;

value: ENCBS242GKJ at ENCODE; https://www.encodeproject.org/ENCBS242GKJ/


title: ATAC-seq from foreskin keratinocyte (ENCLB261UYB)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB261UYB

value: newborn

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: ATAC-seq from foreskin keratinocyte (ENCLB072QRI)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 2
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB072QRI

value: primary cell


title: ATAC-seq from foreskin keratinocyte (ENCLB760VXI)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB760VXI

value: 2-4 day

value: ENCBS903GAF at ENCODE; https://www.encodeproject.org/ENCBS903GAF/


title: ATAC-seq from foreskin keratinocyte (ENCLB233PHZ)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB233PHZ


title: ATAC-seq from foreskin keratinocyte (ENCLB418FDD)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB418FDD

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/


title: ATAC-seq from foreskin keratinocyte (ENCLB517XIL)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 1
technical replicate number: 4
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB517XIL

value: male

value: Paul Khavari, Stanford

value: Paul Khavari


title: ATAC-seq from foreskin keratinocyte (ENCLB891CCF)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB891CCF

value: foreskin keratinocyte

value: Healthy

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/


title: ATAC-seq from foreskin keratinocyte (ENCLB190HQK)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 2
technical replicate number: 2
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB190HQK


title: ATAC-seq from foreskin keratinocyte (ENCLB751PIE)

description:
https://www.encodeproject.org/experiments/ENCSR798IJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on primary keratinocytes in day 6.0 of differentiation
experiment encode accession: ENCSR798IJQ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB751PIE

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: ATAC-seq from foreskin keratinocyte (ENCLB551WGV)

description:
https://www.encodeproject.org/experiments/ENCSR572UDP/
***************
biological replicate number: 2
technical replicate number: 3
description: ATAC-seq on primary keratinocytes in day 2.0 of differentiation
experiment encode accession: ENCSR572UDP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Will Greenleaf, Stanford
library encode accession: ENCLB551WGV

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 2.0

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:1.5; duration_units:day;