title: L041T

description:
HCC.RNA-seq.35.samples.fpkm.txt
362T


title: L045T

status: Public on Mar 03 2019

type: SRA

city: Beijing

first: Ying

last: Jiang

address: Life Science Park Road

country: China

institute: National Center for Protein Sciences (Beijing)

description:
HCC.RNA-seq.35.samples.fpkm.txt
417T

library_source: transcriptomic

data_processing:
RNA-seq reads per sample were mapped to the reference using Tophat11 v2.0.12. The reference consists of the human reference genome and the Ensembl annotated human transcriptome (GRCh37/hg19 assembly). The mapped reads were processed using cufflinks12 v2.2.1 with the ‘classic-fpkm’ library normalization method and ‘fr-unstranded’ library type to quantitate gene expression against Ensembl transcript annotation.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data file L*.fpkm.txt has two columns. The first represets the Ensembl gene ID, and the second represents the FPKM of the corresponding gene.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
The TRIzol method was used for RNA extraction of liver tissues. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the Nano Photometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using the Qubit® RNA Assay Kit in Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library PrepKit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

tag: tissue

value: HCC

tag: tumor stage

value: early stage


title: T0_0h_81.62oxygen_C

status: Public on Mar 04 2019

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

country: USA

institute: Institute for Systems Biology

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were aligned using Bowtie2 and processed using the R package DuffyNGS.
Genome_build: Mycobacterium tuberculosis H37Rv ASM19595v2
Supplementary_files_format_and_content: tab-delimited text file includes RPKM for each sample, meta-data (time and dissolved oxygen for each sample)

organism: Mycobacterium tuberculosis

source_name: bacterial culture

extract_protocol:
Biological triplicate cultures (A-C) of M. tuberculosis H37Rv wildtype in 7H9 media, were grown as 750 mL cultures in 2L spinner flasks, at 37ºC, 5%CO2. Mass flow controllers were used to adjust the amount of nitrogen and air flowing into the headspace. Sample were collected via syringe through sampling port. After harvesting, cells were spun down, flash frozen as cell pellets and kept frozen at -80 until RNA isolation. Cell pellets were resuspended in lysing buffer and transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using chloroform/isopropanol extraction with DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: wildtype

tag: age

value: 0 h

tag: dissolved oxygen


title: L037T

description:
HCC.RNA-seq.35.samples.fpkm.txt
350T


title: L035T

description:
HCC.RNA-seq.35.samples.fpkm.txt
342T


title: L039T

description:
HCC.RNA-seq.35.samples.fpkm.txt
356T


title: WT3

type: RNA

city: Rockville

first: Tongwu

last: Zhang

state: MD

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

description: RNA was purified using Rneasy Fibrous Tissue Kit

hyb_protocol: The reaction mixes were loaded onto the Nanostring nCounter Prep Station for binding and wahing.

scan_protocol: The resulting cartridge was transferred to the Nanostring nCounter digital analyzer for scanning

data_processing:
The data collection was done by Nanostring nCounter digital analyzer. Quantified expression data were analyzed using Nanostring nSolver Analysis software v2.0.
Data were log2-transformed and used for further analysis. Student's t-test was applied to compare normalized expression values between groups.

label: Biotin & color-coded tag

organism: Mus musculus

source_name: Yumm1.5 melanoma

label_protocol: For each Nanostring assay, an aliquot of 100ng RNA was mixed with a Nanostring code set mix and incubated at 65 C for overnight.

growth_protocol: Yumm1.5 cells wer cultured in DMEM media.

extract_protocol: RNA from tumors was purified using Rneasy Fibrous Tissue Kit.Purity and concentration of extracted RNA were checked and quantified by reading at 260 and 280 nm in a NanoDrop spectrophotometer (Thermo Fisher)

treatment_protocol: Yumm1.5 tumor cells were injected into WT or Rnf5-/- mice.The tumor were collected at day 10 after injection.

value: melanoma

tag: cell line

tag: mouse genotype

value: WT


title: L033T

description:
HCC.RNA-seq.35.samples.fpkm.txt
338T


title: L042T

description:
HCC.RNA-seq.35.samples.fpkm.txt
366T


title: WT2


title: L032T

description:
HCC.RNA-seq.35.samples.fpkm.txt
337T


title: L030T

description:
HCC.RNA-seq.35.samples.fpkm.txt
334T


title: L025T

description:
HCC.RNA-seq.35.samples.fpkm.txt
314T


title: L028T

description:
HCC.RNA-seq.35.samples.fpkm.txt
324T


title: L024T

description:
HCC.RNA-seq.35.samples.fpkm.txt
311T


title: L052T

description:
HCC.RNA-seq.35.samples.fpkm.txt
424T


title: L023T

description:
HCC.RNA-seq.35.samples.fpkm.txt
308T


title: L021T

description:
HCC.RNA-seq.35.samples.fpkm.txt
304T


title: L019T

description:
HCC.RNA-seq.35.samples.fpkm.txt
298T


title: L048T

description:
HCC.RNA-seq.35.samples.fpkm.txt
420T


title: L040T

description:
HCC.RNA-seq.35.samples.fpkm.txt
360T


title: L038T

description:
HCC.RNA-seq.35.samples.fpkm.txt
355T


title: L010T

description:
HCC.RNA-seq.35.samples.fpkm.txt
280T


title: L014T

description:
HCC.RNA-seq.35.samples.fpkm.txt
288T


title: L005T

description:
HCC.RNA-seq.35.samples.fpkm.txt
268T


title: L012T

description:
HCC.RNA-seq.35.samples.fpkm.txt
283T


title: L017T

description:
HCC.RNA-seq.35.samples.fpkm.txt
295T


title: L026T

description:
HCC.RNA-seq.35.samples.fpkm.txt
322T


title: L004T

description:
HCC.RNA-seq.35.samples.fpkm.txt
266T


title: L056P

description:
HCC.RNA-seq.35.samples.fpkm.txt
429P

value: non-tumor


title: L052P

description:
HCC.RNA-seq.35.samples.fpkm.txt
424P


title: L047P

description:
HCC.RNA-seq.35.samples.fpkm.txt
419P


title: L048P

description:
HCC.RNA-seq.35.samples.fpkm.txt
420P


title: L046P

description:
HCC.RNA-seq.35.samples.fpkm.txt
418P


title: L042P

description:
HCC.RNA-seq.35.samples.fpkm.txt
366P


title: L044P

description:
HCC.RNA-seq.35.samples.fpkm.txt
416P


title: L041P

description:
HCC.RNA-seq.35.samples.fpkm.txt
362P


title: L016T

description:
HCC.RNA-seq.35.samples.fpkm.txt
293T


title: L035P

description:
HCC.RNA-seq.35.samples.fpkm.txt
342P


title: L040P

description:
HCC.RNA-seq.35.samples.fpkm.txt
360P


title: L037P

description:
HCC.RNA-seq.35.samples.fpkm.txt
350P


title: L039P

description:
HCC.RNA-seq.35.samples.fpkm.txt
356P


title: L038P

description:
HCC.RNA-seq.35.samples.fpkm.txt
355P


title: L008T

description:
HCC.RNA-seq.35.samples.fpkm.txt
277T


title: L033P

description:
HCC.RNA-seq.35.samples.fpkm.txt
338P


title: L032P

description:
HCC.RNA-seq.35.samples.fpkm.txt
337P


title: L030P

description:
HCC.RNA-seq.35.samples.fpkm.txt
334P


title: L003T

description:
HCC.RNA-seq.35.samples.fpkm.txt
265T


title: L028P

description:
HCC.RNA-seq.35.samples.fpkm.txt
324P


title: L024P

description:
HCC.RNA-seq.35.samples.fpkm.txt
311P


title: L025P

description:
HCC.RNA-seq.35.samples.fpkm.txt
314P


title: L023P

description:
HCC.RNA-seq.35.samples.fpkm.txt
308P


title: L017P

description:
HCC.RNA-seq.35.samples.fpkm.txt
295P


title: L045P

description:
HCC.RNA-seq.35.samples.fpkm.txt
417P


title: L026P

description:
HCC.RNA-seq.35.samples.fpkm.txt
322P


title: L019P

description:
HCC.RNA-seq.35.samples.fpkm.txt
298P


title: L076P

description:
HCC.RNA-seq.35.samples.fpkm.txt
4P


title: L016P

description:
HCC.RNA-seq.35.samples.fpkm.txt
293P


title: L014P

description:
HCC.RNA-seq.35.samples.fpkm.txt
288P


title: L001T

description:
HCC.RNA-seq.35.samples.fpkm.txt
262T


title: L010P

description:
HCC.RNA-seq.35.samples.fpkm.txt
280P


title: L012P

description:
HCC.RNA-seq.35.samples.fpkm.txt
283P


title: L004P

description:
HCC.RNA-seq.35.samples.fpkm.txt
266P


title: L003P

description:
HCC.RNA-seq.35.samples.fpkm.txt
265P


title: L001P

description:
HCC.RNA-seq.35.samples.fpkm.txt
262P


title: Ets1-CD4-cKO_2_TFH

city: Pohang

first: Chan Johng

last: Kim

state: Gyeongbuk

address: Nam-Gu, Cheongam-Ro 77, POSTECH Biotech Center

country: South Korea

institute: Institute for Basic Science / Pohang University of Science and Technology

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences: Raw read quality evaluation by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with default options.
QC/adapter sequence trimming for raw FASTQ sequences: Adapter sequence trimming by CutAdapt (https://pypi.python.org/pypi/cutadapt)
Mapping on mouse reference genome: TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
Expression analysis by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options[4]
Expression and DEG analysis: DEG analysis by CuffDiff (http://cufflinks.cbcb.umd.edu) with significance thresholds as FDR<0.05, p<0.001, and p<0.01. Scatter plot and volcano plot by in-house R scripts. Unsupervised clustering by in-house R scripts
Genome_build: mm10

source_name: KO SP-TFH

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)

value: CD4-cre Ets1 flox/flox

value: spleen


title: WT_3_TFH

source_name: WT SP-TFH

value: Ets1 flox/flox


title: WT_1_TFH


title: WT_2_TFH


title: Ets1-CD4-cKO_2_Non-TFH

source_name: KO SP-NonTFH


title: L021P

description:
HCC.RNA-seq.35.samples.fpkm.txt
304P


title: Ets1-CD4-cKO_1_TFH


title: Ets1-CD4-cKO_3_TFH


title: WT_3_Non-TFH

source_name: WT SP-NonTFH


title: WT_1_Non-TFH


title: Mo_Veh_4C_IRAK3

city: Nijmegen

first: Cheng

last: Wang

address: Geert Grooteplein 28

department: Molecular biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Monocytes were cultured with DMSO (Veh control) for 4 hours.

library_source: genomic

data_processing:
Library strategy: 4C-seq
Illumina Casava software 1.8.2 used for basecalling.
Library strategy: Kapa hyperprep
Fastq data was processed with 4Cseqpipe.
DpnII read primer was removed, the fastq was mapped to hg19 using bwa, DpnII fragments around the viewpoint were qualitied using peakstats.
The viewpoint +/- 5 kb counts were ignored, CPM (counts per million) counts for bedGraph for UCSC genome browser visualization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraph files

molecule: genomic DNA

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were obtained by depletion of CD3, CD19 and CD56 positive cells from PBMCs obtained upon Ficoll isolation of a buffycoat. Macrophages were differentiated from monocytes with 6 days culture in RPMI plus 10% charcoal stripped human serum.

extract_protocol:
Monocytes were fixed with formaldehyde and then lysed. Isolated nuclei were then fully digested by DpnII followed by overnight ligation. Ligated cycle DNA were purified after de-crosslinking incubation with proteinase K at 65 degree for 4 hours, followed by further digestion by NlaIII. The digested DNA were ligated again and purified.
The 4C library was amplified with the viewpoint specific primers with inverse PCR. For each viewpoint, 8 PCR reaction products were pooled to enhance the library complexity.
Kapa hyperprep kit.

treatment_protocol: Monocytes were treated with 1 uM triamcinolone acetonide (TA) for 4 hours.

tag: disease status

value: Healthy

tag: cell type

value: Monocytes

tag: treatment

value: DMSO (Veh control) for 4 hours

tag: viewpoint


title: Mo_TA_4C_PER1

description: Monocytes were treated with 1 uM triamcinolone acetonide (TA) for 4 hours.

value: 1 uM TA for 4 hours


title: Mo_TA_4C_IRAK3


title: Mo_Veh_4C_PER1


title: Ets1-CD4-cKO_1_Non-TFH


title: L008P

description:
HCC.RNA-seq.35.samples.fpkm.txt
277P


title: L005P

description:
HCC.RNA-seq.35.samples.fpkm.txt
268P


title: siNC5

city: Daejon

first: Hyunsoo

last: Cho

address: Daehak-ro

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include quantile-normalized read count values for each Sample

source_name: HDLEC

growth_protocol: HDLECs were cultured in 60 mm dish until cells reach confluent state.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: HDLECSs were incubated with 20 nM of siYAP/TAZ or siControl for 48 hours and harvested, or were incubated with YAP-5SA retrovirus or MOCK for 12 hours and harvested 36 hours later.

tag: passage number

value: Passage 7

value: human dermal lymphatic endothelial cells (HDLEC)

tag: genotype/variation

value: siControl


title: siYT2

value: siYAP/TAZ


title: siYT6


title: siNC4


title: siYT3


title: siYT4


title: 5SA3


title: 5SA4


title: siNC2


title: Ets1-CD4-cKO_3_Non-TFH


title: WT4


title: 5SA2


title: 5SA1


title: WT2


title: WT3


title: HeLa_TA_rep4

description: HeLa cells were treated with 100 nM TA for 4 hours.

data_processing:
Illumina Casava software 1.8.2 used for basecalling.
STAR was used to infer gene expression levels.
Reads were mapped to human gene annotation using STAR (Ensembl release 72).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_ReadsPerGene.out.tab: RNA files are in a ReadsPerGene.out.tab, containing counts per gene. They are STAR standard output, column 4 will be selected for down-stream analysis.
column 1: gene ID
column 2: counts for unstranded RNA-seq
column 3: counts for the 1st read strand aligned with RNA
column 4: counts for the 2nd read strand aligned with RNA

source_name: HeLa cells

growth_protocol: HeLa cells were cultured with DMEM plus 10% charcoal-stripped FBS for 72 hours before treatment.

extract_protocol:
RNA was extracted using the RNeasy mini kit.
rRNA was depleted with RiboZero Kit. Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: HeLa cells were treated with 100 nM triamcinolone acetonide (TA) for 4 hours.

value: HeLa cells

value: 100 nM TA for 4 hrs


title: HeLa_TA_rep6


title: WT1


title: HeLa_TA_rep5


title: HeLa_TA_rep3


title: HeLa_TA_rep2


title: HeLa_TA_rep1


title: HeLa_Veh_rep3

description: HeLa cells were treated with DMSO (Veh control) for 4 hours.

value: DMSO (Veh control) for 4 hrs


title: HeLa_Veh_rep5


title: HeLa_Veh_rep6


title: HeLa_Veh_rep1


title: HeLa_Veh_rep2


title: HeLa_Veh_rep4


title: siNC3


title: Monocyte_100nM_Dex_rep2

description: Monocytes were cultured with 100 nM Dexamethasone (Dex) for 4 hours.

data_processing:
Illumina Casava software 1.8.2 used for basecalling of NextSeq 500 data.
MMSEQ package was used to infer gene expression levels.
Reads were mapped to human gene annotation using Bowtie1 (Ensembl release 72).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.gene.mmseq.txt: Tab-delimited text; RNA files containing counts per gene.
Supplementary_files_format_and_content: *.bw: bigWig files.

treatment_protocol: Monocytes were treated with 100 nM different ligand glucocorticoid for 4 hours.

value: Dexamethasone (Dex)

tag: donor

value: buffycoat 53


title: Monocyte_100nM_Pred_rep1

description: Monocytes were cultured with 100 nM Prednisolone (Pred) for 4 hours.

value: Prednisolone (Pred)

value: buffycoat 52


title: Monocyte_100nM_Pred_rep2


title: Monocyte_100nM_Dex_rep1


title: Monocyte_Veh_rep2

value: DMSO vehicle


title: Monocyte_100nM_TA_rep2

description: Monocytes were cultured with 100 nM triamcinolone acetonide (TA) for 4 hours.

value: Triamcinolone acetonide (TA)


title: Monocyte_Veh_rep1

value: Healthy


title: Donor4_RNA_Macrophage_TA

description: Macrophages were treated with TA for 4 hours

data_processing:
Illumina Casava software 1.8.2  was used for basecalling.
Library strategy: strand-specific RNA-seq.
MMSEQ package was used to infer gene expression levels.
Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 72).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq.txt format, containing counts per gene.

growth_protocol: Monocytes were obtained by depletion of CD3, CD19 and CD56 positive cells from PBMCs obtained upon Ficoll isolation of a buffycoat. Macrophages were differetated from monocytes with 6 days culture in RPMI and 10% charcoal stripped human serum.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
rRNA was depleted using the RiboZero Kit. Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Monocytes and macrophages were treated with 1 micromolar (1 µM) TA for 4 hours.

value: Adult Human Peripheral Blood

value: Macrophages

value: Buffycoat 28


title: WT_2_Non-TFH

value: Ets1 flox/flox

value: spleen


title: Donor4_RNA_Macrophage_Veh

description: Macrophages were treated with DMSO(Veh control) for 4 hours


title: Donor3_RNA_Macrophage_TA

value: Buffycoat 27


title: Donor4_RNA_Monocyte_Veh

description: Monocytes were cultured with DMSO(Veh control) for 4 hours

value: Monocytes


title: Donor2_RNA_Monocyte_Veh

value: Buffycoat 12


title: Donor3_RNA_Macrophage_Veh


title: Donor3_RNA_Monocyte_Veh


title: Donor3_RNA_Monocyte_TA

description: Monocytes were cultured with TA for 4 hours


title: Donor2_RNA_Macrophage_TA


title: Donor2_RNA_Macrophage_Veh


title: Donor1_RNA_Macrophage_TA

value: Buffycoat 9


title: Donor1_RNA_Monocyte_Veh


title: Donor1_RNA_Macrophage_Veh


title: Macrophage_TA_GR_rep1

description: Macrophages were treated withTA for 4 hours.

data_processing:
Illumina Casava software 1.8.2  used for basecalling.
fastq was mapped to hg19 by bwa.
MACS2 was used to detect the binding sites for the three studied histone marks and GR  at p-value of 10-8. H3K27ac, H3K4me3 and GR were called using the default (narrow) setting of MACS2. H3K4me1 peaks were called using the broad setting.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
The ChIPseq experiments were followed the Blueprint protocol, http://www.blueprint-epigenome.eu/.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Monocytes and macrophages were treated with 1 micromolar (1µM) TA for 4 hours.

tag: chip-antibody

value: Glucocorticoid receptor

value: Buffycoat 11


title: Donor1_RNA_Monocyte_TA


title: Macrophage_Veh_GR_rep1

description: Macrophages were treated with DMSO (Veh control) for4 hours.


title: Monocyte_TA_GR_rep2

description: Monocytes were treated with TA for 4 hours.

value: Buffycoat 33


title: Macrophage_Veh_GR_rep2

value: Buffycoat 45


title: Macrophage_TA_GR_rep2

description: Macrophages were treated with TA for 4 hours.


title: Monocyte_TA_GR_rep1


title: Monocyte_Veh_GR_rep2

description: Monocytes were treated with DMSO (Veh control) for 4 hours.


title: Donor4_RNA_Monocyte_TA


title: Macrophage_TA_H3K4me1_rep1

description: Macrophagess were treated with TA for 4 hours.


title: Macrophage_TA_H3K4me1_rep2

value: Buffycoat 19


title: Macrophage_Veh_H3K4me1_rep2

description: Macrophagess were treated with DMSO (Veh control) for 4 hours.


title: Monocyte_Veh_H3K4me1_rep2


title: Donor2_RNA_Monocyte_TA


title: Monocyte_TA_H3K4me1_rep1


title: Macrophage_TA_H3K4me3_rep2


title: Monocyte_TA_H3K4me1_rep2


title: Monocyte_100nM_TA_rep1

value: buffycoat 52


title: Monocyte_Veh_H3K4me1_rep1


title: Macrophage_TA_H3K4me3_rep1

value: Buffycoat 10


title: Macrophage_Veh_H3K4me3_rep1


title: Macrophage_Veh_H3K4me3_rep2


title: Monocyte_TA_H3K4me3_rep2


title: Monocyte_TA_H3K4me3_rep1


title: Macrophage_TA_H3K27ac_rep2

value: Buffycoat 16


title: Macrophage_TA_H3K27ac_rep1

value: Adult Human Peripheral Blood


title: Macrophage_Veh_H3K27ac_rep2

value: Macrophages


title: Monocyte_Veh_H3K4me3_rep1


title: Monocyte_TA_H3K27ac_rep2


title: Monocyte_Veh_H3K27ac_rep2


title: Macrophage_Veh_H3K4me1_rep1


title: Monocyte_Veh_GR_rep1


title: Macrophage_Veh_H3K27ac_rep1


title: Monocyte_TA_H3K27ac_rep1


title: Monocyte_Veh_H3K27ac_rep1


title: s_5_16_NDLl3_Fr

city: Davis

first: Alexander

middle: D

last: Borowsky

state: California

address: 1 Shields Ave

institute: University of California at Davis

data_processing:
Image processing, base calling, and quality scoring (Phred) were executed by SCS 2.6/RTA 1.6 software (Illumina, Inc.).
FASTQ-formatted sequence data was processed using a standard TopHat-Cufflinks workflow for the analysis of gene and transcript isoform expression. For this, read alignment to the reference mouse genomic sequence (July 2007 NCBI37/mm9) and splice junction mapping were performed with TopHat and allowing for a maximum of two mismatches. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values were utilized for downstream analysis steps.
Processed data are Cufflinks output files and contain tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM values (FPKM, FPKM_conf_lo, FPKM_conf_hi), and FPKM_status.
Genome_build: July, 2007. NCBI37/mm9
Supplementary_files_format_and_content: Tab-delimited text files include tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM values (FPKM, FPKM_conf_lo, FPKM_conf_hi), and FPKM_status for each transcript and are the Cufflinks gene-level output files.

source_name: NDL(UCD) transplantable mouse mammary tumor line, snap-frozen tumor sample

growth_protocol: The NDL(UCD) transplantable mouse mammary tumor cell line was propagated in vitro and then injected as a bolus (0.1 – 2.0 x 10^6 cells) bilaterally into the uncleared #2, #3, and #4 mammary fat pads of 6- to 8-week-old female FVB/NJ mice.  Tumors were harvested when they reached a maximum width of 5-10 mm, cut into 1-2mm sections, and then immediately snap-frozen.

extract_protocol:
RNA was isolated from frozen samples using the miRNeasy FFPE Kit (Qiagen) according to the manufacturer’s protocols.  Total RNA was eluted from the columns in nuclease-free water and stored at -80°C.
Total RNA-Seq sequencing libraries were prepared from both intact RNA derived from flash-frozen samples and severely fragmented RNA isolated from FFPE samples.  Briefly, rRNA-depleted RNA was prepared from total RNA input (1-5 ug) using the Ribo-Zero rRNA Removal Kit (Epicentre), which selectively depletes rRNA by hybridization to biotinylated capture probes followed by microsphere bead capture. Subsequently, directional Total RNA-Seq libraries were prepared from rRNA-depleted RNA (50 ng) using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer’s protocol. Briefly, 5’,3’-di-tagged cDNA was synthesized using tagged random hexamer-primed cDNA synthesis primers followed by annealing of 3’-terminal-tagging oligo (TTO) and extension with DNA Polymerase. The cDNA was then purified with Agencourt AMPure XP beads (Beckman Coulter, Inc.) or with the MinElute PCR Purification Kit (Qiagen), depending upon the source of RNA from flash-frozen or FFPE samples respectively. Illumina adaptor sequences and indexes were then incorporated during library amplification with the appropriate PCR primers and high-fidelity FailSafe PCR Enzyme Mix. Subsequently, the libraries were purified in a similar manner to that described above for the cDNA preparations. The ScriptSeq v2 libraries were then quantitated with the Qubit fluorometer (Invitrogen Life Sciences) and insert sizes determined with the Agilent 2100 Bioanalyzer. The molar concentration of PCR-competent sequencing templates in the libraries was then determined using by quantitative PCR with the KAPA Library Quantification Kit (Kapa Biosystems, Inc.).

value: mammary tumor

value: FVB/N

tag: gender

value: female


title: s_3_15_NDLl4_Fr

tag: tissue


title: s_1_6_NDL_Fr


title: WT-TFH

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences: Raw read quality evaluation by FastQC (FastQC v0.11.7).
QC/adapter sequence trimming for raw FASTQ sequences: Adapter sequence trimming by CutAdapt (Cutadapt v1.9.1)
ATAC-seq data was analyzed using customized version of ATAC-seq/DNase-Seq pipeline developed by Kundaje Lab. SAMtools v1.2, sambamba v0.6.5, Bowtie2 v2.2.6, MarkDuplicates v1.126, bedtools 2.26 and MACSv2 were used as components of the pipeline.
Mapping on mouse reference genome: TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
The data analysis operation was performed in Conda3 environment with BigDataScript version v0.99999e and JDK/JRE version >=1.8. Generated *.bigwig files from each of the ATAC-Seq experiments were compared using BigwigCompare v2.5.4 & plots were made using IGV browser (https://github.com/kundajelab/atac_dnase_pipelines).
Genome_build: mm10

source_name: WT TFH

extract_protocol:
Cells were sorted using Aria II and DNA was extracted directly.
Nextera DNA Library Prep Kit (Illumina)

value: Ets1 flox/flox

value: spleen


title: KO-TFH

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences:  Raw read quality evaluation by FastQC (FastQC v0.11.7).  Adapter sequence trimming by CutAdapt (Cutadapt v1.9.1)
ATAC-seq data was analyzed using customized version of ATAC-seq/DNase-Seq pipeline developed by Kundaje Lab. SAMtools v1.2, sambamba v0.6.5, Bowtie2 v2.2.6, MarkDuplicates v1.126, bedtools 2.26 and MACSv2 were used as components of the pipeline.
Mapping on mouse reference genome:  TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
The data analysis operation was performed in Conda3 environment with BigDataScript version v0.99999e and JDK/JRE version >=1.8. Generated *.bigwig files from each of the ATAC-Seq experiments were compared using BigwigCompare v2.5.4 & plots were made using IGV browser (https://github.com/kundajelab/atac_dnase_pipelines).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: KO-TFH

value: CD4-cre Ets1 flox/flox


title: WT-TN

source_name: WT T naïve


title: Monocyte_Veh_H3K4me3_rep2

value: Monocytes


title: KO-TN

source_name: KO T naïve


title: D046_2018-02-13

city: Heidelberg

first: Johannes

last: Betge

address: Im Neuenheimer Feld 580

department: Signaling and Functional Genomics

country: Germany

institute: German Cancer Research Center (DKFZ)

description: replicate 2

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731)

data_processing:
Data were normalized using the 'affy' R/Bioconductor package. Normalization steps include background correction using the 'rma' method and quantile normalization.
Expression values are as provided by the 'affy' R/Bioconductor software.

label: biotin

source_name: patient derived cancer organoids

label_protocol: The Affymetrix Gene Chip 3´IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA, Label: Biotin

growth_protocol: Organoids were cultured in ENA media

extract_protocol: Qiagen RNeasy Extraction Kit

treatment_protocol: Organoids were not treated with any additional compounds.

tag: disease state

value: colorectal cancer

tag: sample type

value: patient derived cancer organoids

tag: sample id

tag: patient age

tag: tumor stage

tag: tumor location

value: rectum


title: D046_2018-01-30

description: replicate 1


title: D027_2017-05-19

description: replicate 1


title: D030_2017-09-05

description: replicate 2

value: ascending


title: D022_2017-05-19

description: replicate 1


title: D030_2017-05-19

description: replicate 1


title: D022_2017-09-05

description: replicate 2


title: D027_2017-09-05

description: replicate 2


title: D020_2018-02-13

description: replicate 2


title: D019_2017-05-19

description: replicate 1

value: sigmoid


title: D013_2017-09-05

description: replicate 2


title: D018_2017-05-19

description: replicate 1


title: D020_2018-01-30

description: replicate 1


title: D019_2017-09-05

description: replicate 2


title: oropharyngeal squamous cell carcinoma 33

type: genomic

city: Sao Paulo

first: mateus

middle: camargo

last: barros filho

state: SP

address: Tagua Street 440

country: Brazil

institute: AC Camargo Cancer Center

description:
OSCC33
target sample Cy3-labeled mixed with reference sample Cy5-labeled

hyb_protocol: Samples were hybridized using the SurePrint G3 Human CGH Microarray 4x180K (Agilent Technologies), following the manufacturer instructions

scan_protocol: The microarray image analysis was performed using the Agilent Feature Extraction Software v.10.1.1.1 software (Agilent Technologies)

data_processing: Data was processed and quality control filtered using the Feature Extraction v.10.1.1.1 software (Agilent Technologies) and an in-house pipeline

source_name: oropharynx tumor labeled with Cyanine-3 (green)

label_protocol: The tumors and reference genomic DNA were differentially labeled using a Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: OPSCC samples were macrodissected to guarantee at least 80% of tumor cells for nucleic acids extraction. Total DNA were extracted using Qiagen DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA), following the manufacturer’s recommendations.

value: oropharynx tumor

tag: topology

value: tonsil

value: male

tag: age

tag: hpv status

value: negative

tag: tnm staging

tag: risk stratification (ang's 2012)

value: intermediate

tag: death

value: No

tag: overall survival (months)

source_name: Reference genomic DNA (Promega)

value: Reference genomic DNA (Promega)


title: D021_2017-09-05

description: replicate 1


title: D015_2018-01-30

description: replicate 1

value: descending


title: oropharyngeal squamous cell carcinoma 31

description:
OSCC31
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: high

value: Yes


title: oropharyngeal squamous cell carcinoma 24

description:
OSCC24
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: base of the tongue


title: oropharyngeal squamous cell carcinoma 30

description:
OSCC30
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: soft palate


title: D018_2017-09-05

description: replicate 2

value: colorectal cancer


title: oropharyngeal squamous cell carcinoma 25

description:
OSCC25
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: oropharyngeal squamous cell carcinoma 23

description:
OSCC23
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: HPV 16


title: oropharyngeal squamous cell carcinoma 22

description:
OSCC22
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: low


title: oropharyngeal squamous cell carcinoma 27

description:
OSCC27
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: D010_2018-02-13

description: replicate 2

value: patient derived cancer organoids


title: D013_2017-05-19

description: replicate 1

value: rectum


title: oropharyngeal squamous cell carcinoma 28

description:
OSCC28
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: oropharynx tumor


title: D015_2018-02-13

description: replicate 2


title: oropharyngeal squamous cell carcinoma 29

description:
OSCC29
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: tonsil


title: oropharyngeal squamous cell carcinoma 26

description:
OSCC26
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: male


title: oropharyngeal squamous cell carcinoma 32

description:
OSCC32
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: negative


title: 88_14-cl65-mut

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Raw reads were trimmed with cutadapt (1.12) using the Trim Galore! (0.4.4) wrapper and subsequently aligned to the complete human ribosomal RNA sequence with bowtie (1.2).
Reads that did not align to rRNA were then mapped to the human reference genome (GRCh37/hg19) and read counts per gene were generated with with STAR (2.5.2b) --quantMode GeneCounts.
The GTF file was obtained from genocdegenes.org (comprehensive gene annotation Release 19/GRCh37.p13)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: counts

growth_protocol: ipNF05.5 cells were cultured in DMEM media supplemented with 10% FBS and 1% L-Glutamine and 1% non essential amino acids. 88.14 cells were cultured in RPMI advanced medium supplemented with 20% FBS and 0.32% bovine pituitary extract.

extract_protocol:
Total RNA was extracted using Trizol reageant following manufacturer's instructions
Libraries were prepaired using Illumina TruSeq Stranded mRNA Library Prep.

tag: cell line

value: 88-14 MPNST cell line

tag: genotype

value: EZH1 EZH2 KO


title: 88_14-cl48-mut


title: D010_2018-01-30

description: replicate 1

value: sigmoid


title: 88_14-cl33-mut


title: D007_2017-09-05

description: replicate 1


title: D007_2017-10-10

description: replicate 2


title: D004_2017-09-05

description: replicate 2


title: oropharyngeal squamous cell carcinoma 21

description:
OSCC21
target sample Cy3-labeled mixed with reference sample Cy5-labeled

tag: gender

value: intermediate

value: No

value: Reference genomic DNA (Promega)


title: D004_2017-05-19

description: replicate 1


hyb_protocol: Labeled and hybridized using the Two-Color Human GE 4x44K microarray platform (Agilent Technologies), following the manufacturer instructions

data_processing: Data was processed, quality control filtered and normalized (median-centering genes for each array using log2 ratio) using the Feature Extraction v.10.1.1.1 software (Agilent Technologies) and an in-house pipeline

extract_protocol: OPSCC samples were macrodissected to guarantee at least 80% of tumor cells for nucleic acids extraction. Total RNA were extracted using RNeasy MiniKit (Qiagen, Valencia, CA), following the manufacturer’s recommendations.

tag: tissue

source_name: custom reference sample (pooled of 15 different human cell lines) labeled with Cyanine-5 (red)


label_protocol: Labeled and hybridized using the Two-Color Human GE 4x44K microarray platform (Agilent Technologies), following the manufacturer instructions

value: high

value: Yes

value: custom reference sample (pooled of 15 different human cell lines)


title: oropharyngeal squamous cell carcinoma 19

description:
OSCC19
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: base of the tongue

value: HPV 16


title: oropharyngeal squamous cell carcinoma 17

description:
OSCC17
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: low


title: 88_14-cl16-WT

value: WT


title: oropharyngeal squamous cell carcinoma 18

description:
OSCC18
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: oropharynx tumor


title: oropharyngeal squamous cell carcinoma 16

description:
OSCC16
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: female


title: 88_14-cl18-WT


title: oropharyngeal squamous cell carcinoma 15

description:
OSCC15
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: male


value: tonsil


title: oropharyngeal squamous cell carcinoma 14

description:
OSCC14
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: negative


title: 88_14-cl14-WT

value: 88-14 MPNST cell line


title: oropharyngeal squamous cell carcinoma 13

description:
OSCC13
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: oropharyngeal squamous cell carcinoma 20

description:
OSCC20
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: tSUZ12_C44

value: ipNF05.5 neurofibroma cell line

value: SUZ12 KO


value: No


value: intermediate


title: tSUZ12_C11


title: tEZH1and2_C66

value: EZH1 EZH2 KO


title: oropharyngeal squamous cell carcinoma 12

description:
OSCC12
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: Reference genomic DNA (Promega)


value: custom reference sample (pooled of 15 different human cell lines)


title: tEZH1and2_C5


value: base of the tongue

value: Yes


value: high


value: HPV 16

value: low


value: oropharynx tumor


title: tEZH2_C42

value: EZH2 KO


title: oropharyngeal squamous cell carcinoma 11

description:
OSCC11
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: tonsil

value: male


title: oropharyngeal squamous cell carcinoma 10

description:
OSCC10
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: tEZH1_C20

value: EZH1 KO


title: oropharyngeal squamous cell carcinoma 8

description:
OSCC8
target sample Cy3-labeled mixed with reference sample Cy5-labeled


value: negative


title: oropharyngeal squamous cell carcinoma 9

description:
OSCC9
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: female


value: No


title: tEZH2_C48

value: ipNF05.5 neurofibroma cell line


title: oropharyngeal squamous cell carcinoma 4

description:
OSCC4
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: oropharyngeal squamous cell carcinoma 5

description:
OSCC5
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: oropharyngeal squamous cell carcinoma 6

description:
OSCC6
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: tEZH1_C40


title: oropharyngeal squamous cell carcinoma 9


title: oropharyngeal squamous cell carcinoma 7

description:
OSCC7
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: intermediate


title: oropharyngeal squamous cell carcinoma 7


title: oropharyngeal squamous cell carcinoma 3

description:
OSCC3
target sample Cy3-labeled mixed with reference sample Cy5-labeled


title: oropharyngeal squamous cell carcinoma 4

value: Reference genomic DNA (Promega)


title: P13

value: WT


title: oropharyngeal squamous cell carcinoma 5


title: oropharyngeal squamous cell carcinoma 6


title: oropharyngeal squamous cell carcinoma 3

value: base of the tongue


title: K27_SUZ12_KO

data_processing:
Reads were mapped to the human reference genome (GRCh37/hg19) with Bowtie2 (2.2.9) using the following parameters: --very-sensitive --end-to-end --reorder.
PCR duplicates were removed with Picard Tools MarkDuplicates (1.97)
BAM files were filtered to include reads with MAPQ>10 and blacklist regions were excluded. The merged consensus blacklist was obtained from the Kundaje lab at Stanford University (Stanford, CA, USA).
Reads were extended to mean fragment length and RPKM normalized counting only reads from the first mate in bins of length 50 and converted to bigWig format using DeepTools (2.4.1).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: ipNF05.5 cells were cultured in DMEM media supplemented with 10% FBS and 1% L-Glutamine and 1% non essential amino acids.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an antibody specific for H3K27me3 (Cell Signaling Technology, C36B11).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

value: SUZ12 KO

tag: chip antibody


title: P12


title: K27_WT

value: H3K27me3 (Cell Signaling Technology, C36B11)


title: ChIP-seq from gastrocnemius medialis (ENCLB766QBO)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR903SJC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human gastrocnemius medialis
experiment encode accession: ENCSR903SJC
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB766QBO
size range: 450-650

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

source_name: Homo sapiens male adult (37 years) gastrocnemius medialis tissue

tag: antibody

value: Control

value: gastrocnemius medialis

value: tissue

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

value: 37 year

tag: lab

value: Michael Snyder, Stanford

tag: link

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS168UHK at ENCODE; https://www.encodeproject.org/ENCBS168UHK/


title: 160217_Prmt5_ko: Prmt5-KO_Replicate 2

city: Singapore

last: Li

state: --- Select a state ---

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Reads of RNA-seq data were mapped to mouse mm10 genome by STAR aligner using default parameters
Mapped reads number of each gene were used to identify gene expression by featureCounts using default parameters for paired-end data
Gene expression counts were further normalized among samples based on the Cross-Correlation method
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file for gene exprssion of RNA-seq

source_name: Hematopoietic stem cells

extract_protocol:
Trizol reagent (Invitrogen) was used with the following modifications: phase separation was repeated to minimize gDNA carryover, ethachinmate (Wako) was used to facilitate RNA precipitation, and RNA wash was repeated to minimize carryover of salts/organic contaminants.
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) was used for cDNA synthesis and amplification of mRNA. Library preparation was performed using Nextera® XT DNA Library Preparation Kit (Illumina).

tag: strain

value: Hematopoietic stem cells (HSCs)


title: 160224_Prmt5_ko: Prmt5-KO_Replicate 3


title: oropharyngeal squamous cell carcinoma 2

description:
OSCC2
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: oropharynx tumor

tag: topology

value: tonsil

value: male

tag: age

tag: hpv status

value: low

value: No

value: custom reference sample (pooled of 15 different human cell lines)


title: 309-5 16E6E7Nor3

first: Martina

last: Niebler

address: Im Neuenheimer Feld 242

institute: German Cancer Research Center

data_processing:
Illumina bcl2fastq 2.19.0.316 was used for base calling
bowtie2 (v2.2.4) and HISAT2 (v2-2.1.0) were used for alignment, Salmon (v0.8.2) was used for pseudo-alignment
StringTie (v1.3.3b) was used for transcrip assembly
DESeq2 (v1.16.1) and sleuth (v0.29.0) were used for differential expression analysis
Supplementary_files_format_and_content: Processed data files were Excel files including log2fc and q-value of genes
Supplementary_files_format_and_content: BtDe full.xlsx: generated by bowtie2+DESeq2
Supplementary_files_format_and_content: HsStDe_gene_1.xlsx: generated by HISAT2+StringTie+DESeq2
Supplementary_files_format_and_content: SmDe_1.xlsx: generated by Salmon+DESeq2
Supplementary_files_format_and_content: SmSu_wt_1.xlsx: generated by Salmon+sleuth
Supplementary_files_format_and_content: *counting.txt: BtDe counts file
Supplementary_files_format_and_content: *data_stringtie_count.ctab.txt: HsStDe counts file
Supplementary_files_format_and_content: *quant_salmon.sf.txt: SmDe & SmSu counts file

source_name: Mucosa

growth_protocol: NOKs pWPI cells and NOKs HPV16E6E7 were kept in Keratinocyte-SFM medium (Life Technologies) containing rhEGF and bovine pituitary gland extract (Life Technologies) for daily cultivating and passaging. Cells were switched into FAD medium containing 75% Ham´s F-12, 25% Dulbecco modified Eagle’s medium (DMEM), 5% fetal bovine serum (FBS), insulin (5 μg/ml), epidermal growth factor (10 ng/ml), cholera toxin (8.4 ng/ml), adenine (24 μg/ml) and hydrocortisone (0.4 μg/ml) for one passage before using for experiments.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNase-Free DNase Set (Qiagen) was used to remove residual DNA for downstream applications. RNA concentrations were determined by NanoDrop™ and 1 µg of RNA was reverse transcribed by RevertAid RT Reverse Transcription Kit (Thermo Fisher Scientific) and oligo dT22 primers (Thermo Fisher Scientific) according to the manufacturer's instructions.
Illumina TruSeq Stranded RNA was used according to Illuminas protocols and sequenced on Hiseq 2000 v4

treatment_protocol: 293T cells were co-transfected by the respective pWPI lentiviral expression plasmids, packaging plasmid psPAX2 (Addgene #12260) and enveloping plasmid pMD2.G (Addgene #12259; gift from Didier Trono) using 25kD linear polyethylenimine (Polysciences). 48h after transfection, supernatant was collected, filtered and applied to NOK cells in the presence of 10 µg/ml polybrene (Santa Cruz). Medium was refreshed after 24h and cells were kept in medium supplemented with 1µg/ml puromycin (Sigma-Aldrich) for selection until all untransduced control cells were dead. Only cells within 10 passages after selection were used for experiments.

value: Normal oral keratinocytes

value: HPV16 E6E7


title: 308-5 16E6E7Nor2


title: 160212_Prmt5_ko: Prmt5-KO_Replicate 1


title: ChIP-seq from HEK293 (ENCLB749WBM)

description:
https://www.encodeproject.org/experiments/ENCSR776MDR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF577 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR776MDR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2018-01-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB749WBM
size range: 450-650

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-ZNF577 originated from HEK293

tag: line

value: cell line

value: female

tag: health state

value: unknown

value: embryonic

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS904ONI at ENCODE; https://www.encodeproject.org/ENCBS904ONI/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: NDL frozen tissue 3

description: Gene expression data of NDL flash frozen tumor sample.

hyb_protocol: Following fragmentation and labeling, 2.3 ug of fragmented and labeled ss-DNA were hybridized for 16 hr at 45C on the Affymetrix GeneChip Mouse Gene 1.0 Sense Target (ST) Arrays using Affymetrix hybridization kit materials. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007

scan_protocol: Affymetrix Genechip Scanner 3000 7G

data_processing: The microarray processing and statistical analysis were made in the R language and statistical environment (www.r-project.org) using the Robust Multi-array Average (RMA) method with the “oligo” Bioconductor package (version 1.40.2)

source_name: NDL snap frozen tumor sample

label_protocol: Biotinylated sense strand DNA targets were prepared from total RNA (100 ng) using the Ambion WT Expression Kit and Affymetrix GeneChip WT Terminal Labeling Kit according to the standard manufacturers’ protocols. Briefly, double-stranded cDNA was prepared followed by in vitro transcription to generate antisence cRNA (aRNA), which was used as template for a second cyle cDNA synthesis in a dUTP-containing reaction mixture. The dUTP-containing cDNA was fragmented by treatment with uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1). DNA was then end-labeled with biotin using the DNA Labeling Reagent and deoxynucleotidyl transferase (TdT). All microarray processing procedures, including target hybridization, washing, staining, and array scanning were performed according to the Affymetrix’s standard protocols.

growth_protocol: The NDL(UCD) SSM2(UCD) and Met1(UCD) transplantable mouse mammary tumor cell line was propagated in vitro and then injected as a bolus (0.1 – 2.0 x 10^6 cells) bilaterally into the uncleared #2, #3, and #4 mammary fat pads of 6- to 8-week-old female FVB/NJ mice.  Tumors were harvested when they reached a maximum width of 5-10 mm, cut into 1-2mm sections, and then immediately snap-frozen.

extract_protocol: RNA was isolated from frozen  samples using the miRNeasy FFPE Kit (Qiagen) according to the manufacturer’s protocols specific for each type of specimen.

value: FVB/N

value: mammary tumor

tag: cell line

value: NDL


title: Met1 frozen tissue 2

description: Gene expression data of Met1 flash frozen tumor sample.

source_name: Met1 snap frozen tumor sample


title: oropharyngeal squamous cell carcinoma 1

description:
OSCC1
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: oropharynx tumor

value: tonsil

value: HPV 18

tag: tnm staging

tag: risk stratification (ang's 2012)

tag: death

value: Yes

tag: overall survival (months)


title: NDL frozen tissue 2

tag: gender

tag: tissue


title: 309-1 emptyNor3

tag: genotype

value: empty vector pWPI


title: Met1 frozen tissue 3


title: 160212_Prmt5_ff: Prmt5-fl/fl_Replicate 1

value: Hematopoietic stem cells (HSCs)


title: 307-1 emptyNor1

value: Normal oral keratinocytes


title: NDL frozen tissue 1


title: SSM2 frozen tissue 1

description: Gene expression data of SSM2 flash frozen tumor sample.

source_name: SSM2 snap frozen tumor sample


title: SSM2 frozen tissue 3


title: Met1 frozen tissue 1


title: 308-1 emptyNor2


title: oropharyngeal squamous cell carcinoma 1

value: male

value: low

value: Reference genomic DNA (Promega)


title: SSM2 frozen tissue 2

value: female


title: 307-5 16E6E7Nor1

value: HPV16 E6E7


title: 160224_Prmt5_ff: Prmt5-fl/fl_Replicate 3


title: ChIP-seq from HEK293 (ENCLB881EUJ)

status: Public on Mar 02 2019

description:
https://www.encodeproject.org/experiments/ENCSR776MDR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF577 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR776MDR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2018-01-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB881EUJ
size range: 450-650

tag: antibody

value: cell line

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF577 under the control of a CMV promoter.

tag: biosample encode accession

tag: Sex

value: unknown

tag: dev stage

value: embryonic

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS990KNH at ENCODE; https://www.encodeproject.org/ENCBS990KNH/


title: ChIP-seq from K562 (ENCLB359XFK)

description:
https://www.encodeproject.org/experiments/ENCSR621ATC/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF184 ChIP-seq on human K562
experiment encode accession: ENCSR621ATC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB359XFK
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: adult

tag: age

value: 53 year

tag: lab

value: chronic myelogenous leukemia (CML)

tag: link

value: ENCBS398HUM at ENCODE; https://www.encodeproject.org/ENCBS398HUM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from K562 (ENCLB610WMP)

description:
https://www.encodeproject.org/experiments/ENCSR497VFH/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF639 ChIP-seq on human K562
experiment encode accession: ENCSR497VFH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB610WMP
size range: 450-650

tag: line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

tag: health state

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: oropharyngeal squamous cell carcinoma 2

value: oropharynx tumor

tag: topology

value: tonsil

value: male

tag: hpv status

tag: tnm staging

value: low

value: No

value: Reference genomic DNA (Promega)


title: ChIP-seq from HepG2 (ENCLB799ZNS)

description:
https://www.encodeproject.org/experiments/ENCSR210HBN/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR210HBN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2018-02-12
lab: Richard Myers, HAIB
library encode accession: ENCLB799ZNS

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting 3xFLAG-IKZF5

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCBS012JNE at ENCODE; https://www.encodeproject.org/ENCBS012JNE/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from vagina (ENCLB162JLP)

description:
https://www.encodeproject.org/experiments/ENCSR475KZM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Sun Oct 30 2016 23:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR475KZM
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB162JLP

source_name: Homo sapiens vagina tissue female adult (53 years)

value: Control

value: vagina

value: tissue

value: female

value: 53 year

value: adult

value: ENCBS698MLA at ENCODE; https://www.encodeproject.org/ENCBS698MLA/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/4f67ef38-4ded-41cb-b456-56c2bc46dc9d/@@download/attachment/83378.svs


title: ChIP-seq from HepG2 (ENCLB259TIL)

description:
https://www.encodeproject.org/experiments/ENCSR210HBN/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR210HBN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2018-02-12
lab: Richard Myers, HAIB
library encode accession: ENCLB259TIL

value: cell line

value: male

value: ENCBS848VTV at ENCODE; https://www.encodeproject.org/ENCBS848VTV/


title: ChIP-seq from sigmoid colon (ENCLB282IIO)

description:
https://www.encodeproject.org/experiments/ENCSR481ZPB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 19 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR481ZPB
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB282IIO

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

value: sigmoid colon

value: ENCBS440VLN at ENCODE; https://www.encodeproject.org/ENCBS440VLN/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/6e608c6e-94f9-4c52-b54d-8a54a2f1adee/@@download/attachment/83394.svs


title: ChIP-seq from K562 (ENCLB685IPG)

description:
https://www.encodeproject.org/experiments/ENCSR497VFH/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF639 ChIP-seq on human K562
experiment encode accession: ENCSR497VFH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB685IPG
size range: 450-650

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB008DQB)

description:
https://www.encodeproject.org/experiments/ENCSR494UQJ/
***************
biological replicate number: 2
technical replicate number: 1
description: NR3C1 ChIP-seq on human K562
experiment encode accession: ENCSR494UQJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB008DQB
size range: 450-650

value: 53 year

value: female

value: ENCBS837GDT at ENCODE; https://www.encodeproject.org/ENCBS837GDT/


title: oropharyngeal squamous cell carcinoma 8

description:
OSCC8
target sample Cy3-labeled mixed with reference sample Cy5-labeled

value: oropharynx tumor

value: base of the tongue

value: HPV 16

tag: risk stratification (ang's 2012)

value: low

tag: death

value: Yes

tag: overall survival (months)

value: custom reference sample (pooled of 15 different human cell lines)


title: ChIP-seq from K562 (ENCLB278NYK)

description:
https://www.encodeproject.org/experiments/ENCSR996ESX/
***************
biological replicate number: 2
technical replicate number: 1
description: NFRKB ChIP-seq on human K562
experiment encode accession: ENCSR996ESX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB278NYK
size range: 450-650

value: NFRKB

value: cell line

value: adult

value: ENCBS344LIE at ENCODE; https://www.encodeproject.org/ENCBS344LIE/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from prostate gland (ENCLB085KYL)

description:
https://www.encodeproject.org/experiments/ENCSR467YGK/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Sun Oct 30 2016 23:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR467YGK
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB085KYL

source_name: Homo sapiens male adult (54 years) prostate gland tissue

value: Control

value: prostate gland

value: tissue

value: male

value: 54 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS369BBR at ENCODE; https://www.encodeproject.org/ENCBS369BBR/


title: ChIP-seq from K562 (ENCLB663GQH)

description:
https://www.encodeproject.org/experiments/ENCSR621ATC/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF184 ChIP-seq on human K562
experiment encode accession: ENCSR621ATC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB663GQH
size range: 450-650

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from K562 (ENCLB441OFW)

description:
https://www.encodeproject.org/experiments/ENCSR996ESX/
***************
biological replicate number: 1
technical replicate number: 1
description: NFRKB ChIP-seq on human K562
experiment encode accession: ENCSR996ESX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB441OFW
size range: 450-650

value: NFRKB

value: cell line

value: adult

value: ENCBS831ATS at ENCODE; https://www.encodeproject.org/ENCBS831ATS/


title: ChIP-seq from K562 (ENCLB223KKX)

description:
https://www.encodeproject.org/experiments/ENCSR474CVP/
***************
biological replicate number: 3
technical replicate number: 1
description: TRIM28 ChIP-seq on human K562
experiment encode accession: ENCSR474CVP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB223KKX

value: ENCBS596DHR at ENCODE; https://www.encodeproject.org/ENCBS596DHR/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from K562 (ENCLB092AME)

description:
https://www.encodeproject.org/experiments/ENCSR474CVP/
***************
biological replicate number: 1
technical replicate number: 1
description: TRIM28 ChIP-seq on human K562
experiment encode accession: ENCSR474CVP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-11-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB092AME
size range: 450-650

value: ENCBS320BUL at ENCODE; https://www.encodeproject.org/ENCBS320BUL/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from HepG2 (ENCLB182XTB)

description:
https://www.encodeproject.org/experiments/ENCSR485OYR/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR485OYR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2018-02-12
lab: Richard Myers, HAIB
library encode accession: ENCLB182XTB

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting 3xFLAG-ZBTB25

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCBS176URZ at ENCODE; https://www.encodeproject.org/ENCBS176URZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from suprapubic skin (ENCLB155ECF)

description:
https://www.encodeproject.org/experiments/ENCSR491PTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on suprapubic skin
experiment encode accession: ENCSR491PTJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR972HZL
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB155ECF

source_name: Homo sapiens suprapubic skin tissue female adult (51 year)

value: suprapubic skin

value: tissue

value: female

value: 51 year

value: ENCBS588FXB at ENCODE; https://www.encodeproject.org/ENCBS588FXB/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/c8b1c1d7-21b2-42ca-b898-8abf625ea8af/@@download/attachment/84266.svs


title: ChIP-seq from HEK293 (ENCLB263DRQ)

description:
https://www.encodeproject.org/experiments/ENCSR993DED/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF214 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR993DED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-11-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB263DRQ
size range: 450-650

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-ZNF214 originated from HEK293

value: cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF214 under the control of a CMV promoter.

value: unknown

value: embryonic

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS808LHN at ENCODE; https://www.encodeproject.org/ENCBS808LHN/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: ChIP-seq from suprapubic skin (ENCLB816RXF)

description:
https://www.encodeproject.org/experiments/ENCSR464CSO/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on suprapubic skin
experiment encode accession: ENCSR464CSO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011LTA
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB816RXF

source_name: Homo sapiens suprapubic skin tissue male adult (37 years)

value: male

value: Richard Myers, HAIB

value: 37 year

value: adult

value: ENCBS090NNK at ENCODE; https://www.encodeproject.org/ENCBS090NNK/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ChIP-seq from esophagus muscularis mucosa (ENCLB418ITX)

description:
https://www.encodeproject.org/experiments/ENCSR442ZTI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on muscle layer of esophagus
experiment encode accession: ENCSR442ZTI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR089MPD
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB418ITX

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (51 year)

value: esophagus muscularis mucosa

value: tissue

value: female

value: 51 year

value: ENCBS256BDN at ENCODE; https://www.encodeproject.org/ENCBS256BDN/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/ff8c38b8-9743-4b9d-92df-11776af354c5/@@download/attachment/84275.svs


title: ChIP-seq from HEK293 (ENCLB194OXD)

description:
https://www.encodeproject.org/experiments/ENCSR993DED/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF214 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR993DED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-11-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB194OXD
size range: 450-650

value: cell line

value: unknown

value: embryonic

value: ENCBS289YRD at ENCODE; https://www.encodeproject.org/ENCBS289YRD/


title: ChIP-seq from K562 (ENCLB515YKR)

description:
https://www.encodeproject.org/experiments/ENCSR494UQJ/
***************
biological replicate number: 1
technical replicate number: 1
description: NR3C1 ChIP-seq on human K562
experiment encode accession: ENCSR494UQJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB515YKR
size range: 450-650

value: 53 year

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS734NZL at ENCODE; https://www.encodeproject.org/ENCBS734NZL/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from RWPE2 (ENCLB446XXQ)

description:
https://www.encodeproject.org/experiments/ENCSR987PNT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human RWPE2
experiment encode accession: ENCSR987PNT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR394DWD
encode release date: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB446XXQ
size range: 450-650

source_name: Homo sapiens RWPE2 cell line

value: RWPE-2 cells were derived from RWPE-1 cells (ATCC CRL-11609) by transformation with Ki-ras using the Kirsten murine sarcoma virus (Ki-MuSV). Epithelial cells from the peripheral zone of a histologically normal adult human prostate were transfected with a plasmid carrying one copy of the human papilloma virus 18 (HPV-18) genome to establish the RWPE-1 cell line (ATCC CRL-11609).

value: male

value: normal

value: adult

value: 54 year

value: Derived from ENCODE donor ENCDO000ADM; https://www.encodeproject.org/ENCDO000ADM/

value: ENCBS796LYI at ENCODE; https://www.encodeproject.org/ENCBS796LYI/

value: ENCODE dbxrefs Cellosaurus CVCL_3792; https://web.expasy.org/cellosaurus/CVCL_3792


title: ChIP-seq from prostate gland (ENCLB007NCR)

description:
https://www.encodeproject.org/experiments/ENCSR442CIF/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on prostate
experiment encode accession: ENCSR442CIF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR467YGK
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB007NCR

value: prostate gland

value: tissue

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: ENCBS369BBR at ENCODE; https://www.encodeproject.org/ENCBS369BBR/


title: ChIP-seq from RWPE2 (ENCLB566UMR)

description:
https://www.encodeproject.org/experiments/ENCSR987PNT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human RWPE2
experiment encode accession: ENCSR987PNT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR394DWD
encode release date: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB566UMR
size range: 450-650

value: cell line

value: Michael Snyder, Stanford

value: ENCBS942OEI at ENCODE; https://www.encodeproject.org/ENCBS942OEI/


title: ChIP-seq from K562 (ENCLB968LBD)

description:
https://www.encodeproject.org/experiments/ENCSR439OCL/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF407 ChIP-seq on human K562
experiment encode accession: ENCSR439OCL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB968LBD
size range: 450-650

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB523DLK)

description:
https://www.encodeproject.org/experiments/ENCSR439OCL/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF407 ChIP-seq on human K562
experiment encode accession: ENCSR439OCL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB523DLK
size range: 450-650

value: adult

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from suprapubic skin (ENCLB422OQD)

description:
https://www.encodeproject.org/experiments/ENCSR467CRM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR467CRM
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB422OQD

source_name: Homo sapiens suprapubic skin tissue male adult (54 years)

value: Control

value: suprapubic skin

value: tissue

value: male

value: 54 year

value: ENCBS471QWL at ENCODE; https://www.encodeproject.org/ENCBS471QWL/

value: derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/f5435929-2851-47b5-adeb-b58261a3b1e7/@@download/attachment/82377.svs


title: ChIP-seq from sigmoid colon (ENCLB082KDK)

description:
https://www.encodeproject.org/experiments/ENCSR978LQC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on sigmoid colon
experiment encode accession: ENCSR978LQC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR883DDV
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB082KDK

source_name: Homo sapiens sigmoid colon tissue male adult (54 years)

value: sigmoid colon

value: Richard Myers, HAIB

value: ENCBS089VLX at ENCODE; https://www.encodeproject.org/ENCBS089VLX/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/f08e09e8-d571-4a80-b574-da7e167668d5/@@download/attachment/82367.svs


title: ChIP-seq from K562 (ENCLB210KUL)

description:
https://www.encodeproject.org/experiments/ENCSR431XGJ/
***************
biological replicate number: 3
technical replicate number: 1
description: PYGO2 ChIP-seq on human K562
experiment encode accession: ENCSR431XGJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB210KUL
size range: 450-650

value: cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from breast epithelium (ENCLB236YEJ)

description:
https://www.encodeproject.org/experiments/ENCSR951JUP/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR951JUP
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB236YEJ

source_name: Homo sapiens breast epithelium tissue male adult (54 years)

value: Control

value: breast epithelium

value: tissue

value: male

value: adult

value: ENCBS173VHR at ENCODE; https://www.encodeproject.org/ENCBS173VHR/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/3a8c7636-3c0d-4a8c-b793-17502ed1acc2/@@download/attachment/82375.svs


title: ChIP-seq from upper lobe of left lung (ENCLB176KTC)

description:
https://www.encodeproject.org/experiments/ENCSR986QAR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on upper lobe of left lung
experiment encode accession: ENCSR986QAR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR762NXP
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB176KTC

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

value: upper lobe of left lung

value: Richard Myers, HAIB

value: ENCBS226JGR at ENCODE; https://www.encodeproject.org/ENCBS226JGR/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/44e530bc-7fde-47cd-bf10-ba0046f1664e/@@download/attachment/83373.svs


title: ChIP-seq from K562 (ENCLB525DKZ)

description:
https://www.encodeproject.org/experiments/ENCSR953DVM/
***************
biological replicate number: 2
technical replicate number: 1
description: E2F8 ChIP-seq on human K562
experiment encode accession: ENCSR953DVM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB525DKZ
size range: 450-650

value: cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: female

value: 53 year

value: ENCBS048GNZ at ENCODE; https://www.encodeproject.org/ENCBS048GNZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from spleen (ENCLB591PUT)

description:
https://www.encodeproject.org/experiments/ENCSR959UQA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on spleen
experiment encode accession: ENCSR959UQA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR936XMR
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB591PUT

source_name: Homo sapiens female adult (53 years) spleen tissue

value: spleen

value: tissue

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS992BBW at ENCODE; https://www.encodeproject.org/ENCBS992BBW/


title: ChIP-seq from K562 (ENCLB130SGR)

description:
https://www.encodeproject.org/experiments/ENCSR426URK/
***************
biological replicate number: 1
technical replicate number: 1
description: AFF1 ChIP-seq on human K562
experiment encode accession: ENCSR426URK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB130SGR
size range: 450-650

value: adult

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS207UAM at ENCODE; https://www.encodeproject.org/ENCBS207UAM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from K562 (ENCLB363HFK)

description:
https://www.encodeproject.org/experiments/ENCSR949NVY/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF639 ChIP-seq on human K562
experiment encode accession: ENCSR949NVY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB363HFK
size range: 450-650

value: ENCBS839CNN at ENCODE; https://www.encodeproject.org/ENCBS839CNN/


title: ChIP-seq from K562 (ENCLB085JZD)

description:
https://www.encodeproject.org/experiments/ENCSR426URK/
***************
biological replicate number: 2
technical replicate number: 1
description: AFF1 ChIP-seq on human K562
experiment encode accession: ENCSR426URK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB085JZD
size range: 450-650

value: cell line

value: ENCBS603CUX at ENCODE; https://www.encodeproject.org/ENCBS603CUX/


title: ChIP-seq from K562 (ENCLB757NKI)

description:
https://www.encodeproject.org/experiments/ENCSR949NVY/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF639 ChIP-seq on human K562
experiment encode accession: ENCSR949NVY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB757NKI
size range: 450-650

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: female

value: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/


title: ChIP-seq from spleen (ENCLB649VDV)

description:
https://www.encodeproject.org/experiments/ENCSR950CUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on spleen
experiment encode accession: ENCSR950CUQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384HXX
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB649VDV

source_name: Homo sapiens male adult (37 years) spleen tissue

value: male

value: 37 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/

value: ENCBS017NWO at ENCODE; https://www.encodeproject.org/ENCBS017NWO/


title: ChIP-seq from spleen (ENCLB987SHU)

description:
https://www.encodeproject.org/experiments/ENCSR936XMR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Thu Nov 10 2016 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR936XMR
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB987SHU

value: Control

value: spleen

value: tissue

value: 53 year

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: ENCBS992BBW at ENCODE; https://www.encodeproject.org/ENCBS992BBW/


title: ChIP-seq from HEK293 (ENCLB157EQB)

description:
https://www.encodeproject.org/experiments/ENCSR946ZLI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-KLF13 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR946ZLI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB157EQB
size range: 450-650

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-KLF13 originated from HEK293

value: unknown

value: embryonic

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS842XAE at ENCODE; https://www.encodeproject.org/ENCBS842XAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: ChIP-seq from bipolar neuron (ENCLB551ZEL)

description:
https://www.encodeproject.org/experiments/ENCSR418KUS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on biopolar spindle neuron
experiment encode accession: ENCSR418KUS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138PGW
encode release date: 2018-03-16
lab: Richard Myers, HAIB
library encode accession: ENCLB551ZEL

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: bipolar neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: ChIP-seq from HepG2 (ENCLB259EQS)

description:
https://www.encodeproject.org/experiments/ENCSR412ZDC/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR412ZDC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2018-02-10
lab: Richard Myers, HAIB
library encode accession: ENCLB259EQS

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting 3xFLAG-AHR

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCBS340PRE at ENCODE; https://www.encodeproject.org/ENCBS340PRE/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; https://web.expasy.org/cellosaurus/CVCL_0027


title: ChIP-seq from HEK293 (ENCLB373FPZ)

description:
https://www.encodeproject.org/experiments/ENCSR946ZLI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-KLF13 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR946ZLI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB373FPZ
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-KLF13 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: Michael Snyder, Stanford

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS919NDB at ENCODE; https://www.encodeproject.org/ENCBS919NDB/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: ChIP-seq from HepG2 (ENCLB962ATD)

description:
https://www.encodeproject.org/experiments/ENCSR404JRP/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse crosslink control Chip-Seq on HepG2 human (fragmentation date 8-22-2013)
experiment encode accession: ENCSR404JRP
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB962ATD

source_name: Homo sapiens HepG2 immortalized cell line

value: Control

value: HepG2, hepatocellular carcinoma

value: male

value: ENCBS485OKN at ENCODE; https://www.encodeproject.org/ENCBS485OKN/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: ChIP-seq from breast epithelium (ENCLB487JBZ)

description:
https://www.encodeproject.org/experiments/ENCSR939FGB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on mammary gland
experiment encode accession: ENCSR939FGB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR621IYT
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB487JBZ

source_name: Homo sapiens breast epithelium tissue female adult (53 years)

value: breast epithelium

value: tissue

value: Richard Myers, HAIB

value: 53 year

value: adult

value: ENCBS377TON at ENCODE; https://www.encodeproject.org/ENCBS377TON/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/0d43876e-94ba-4c85-a056-01dbc5065e3d/@@download/attachment/83392.svs


title: ChIP-seq from esophagus muscularis mucosa (ENCLB189ERU)

description:
https://www.encodeproject.org/experiments/ENCSR936JHB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on muscle layer of esophagus
experiment encode accession: ENCSR936JHB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR240SYZ
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB189ERU

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

value: esophagus muscularis mucosa

value: female

value: ENCBS078KRE at ENCODE; https://www.encodeproject.org/ENCBS078KRE/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/cfd92841-5b08-4c14-8e0b-4d4f6420f799/@@download/attachment/83388.svs


title: ChIP-seq from neural cell (ENCLB650LAA)

description:
https://www.encodeproject.org/experiments/ENCSR934NHU/
***************
biological replicate number: 1
technical replicate number: 2
description: MXI1 ChIP-seq on human neural cell
experiment encode accession: ENCSR934NHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB650LAA

source_name: Homo sapiens neural in vitro differentiated cells male embryo originated from H1-hESC

value: neural cell

value: in vitro differentiated cells

value: Neurons derived from H1 embryonic stem cells

value: Michael Snyder, Stanford

value: healthy

value: unknown

value: embryonic

value: ENCBS980OYK at ENCODE; https://www.encodeproject.org/ENCBS980OYK/

value: derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons


title: ChIP-seq from neural cell (ENCLB654YJJ)

description:
https://www.encodeproject.org/experiments/ENCSR934NHU/
***************
biological replicate number: 1
technical replicate number: 1
description: MXI1 ChIP-seq on human neural cell
experiment encode accession: ENCSR934NHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB654YJJ
size range: 450-650

value: male


title: ChIP-seq from prostate gland (ENCLB639MMR)

description:
https://www.encodeproject.org/experiments/ENCSR404VWY/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on prostate
experiment encode accession: ENCSR404VWY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GGB
encode release date: 2017-10-31
lab: Richard Myers, HAIB
library encode accession: ENCLB639MMR

source_name: Homo sapiens prostate gland tissue male adult (37 years)

value: prostate gland

value: tissue

value: Richard Myers, HAIB

value: 37 year

value: adult

value: ENCBS720KJI at ENCODE; https://www.encodeproject.org/ENCBS720KJI/

value: derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ChIP-seq from neural cell (ENCLB724JFH)

description:
https://www.encodeproject.org/experiments/ENCSR934NHU/
***************
biological replicate number: 2
technical replicate number: 1
description: MXI1 ChIP-seq on human neural cell
experiment encode accession: ENCSR934NHU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB724JFH
size range: 450-650

value: neural cell

value: in vitro differentiated cells

value: ENCBS163EMU at ENCODE; https://www.encodeproject.org/ENCBS163EMU/


title: ChIP-seq from suprapubic skin (ENCLB559OUW)

description:
https://www.encodeproject.org/experiments/ENCSR972HZL/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR972HZL
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB559OUW

source_name: Homo sapiens suprapubic skin tissue female adult (51 year)

value: Control

value: suprapubic skin

value: female

value: 51 year

value: ENCBS588FXB at ENCODE; https://www.encodeproject.org/ENCBS588FXB/

value: derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/c8b1c1d7-21b2-42ca-b898-8abf625ea8af/@@download/attachment/84266.svs


title: ChIP-seq from K562 (ENCLB545MFG)

description:
https://www.encodeproject.org/experiments/ENCSR431XGJ/
***************
biological replicate number: 2
technical replicate number: 1
description: PYGO2 ChIP-seq on human K562
experiment encode accession: ENCSR431XGJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB545MFG
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ENCBS125ACM at ENCODE; https://www.encodeproject.org/ENCBS125ACM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004


title: ChIP-seq from neural cell (ENCLB221JHM)

description:
https://www.encodeproject.org/experiments/ENCSR404BPV/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on human neural cell
experiment encode accession: ENCSR404BPV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB221JHM
size range: 450-650

value: neural cell

value: Neurons derived from H1 embryonic stem cells

value: male

value: healthy

value: unknown

value: embryonic

value: ENCBS980OYK at ENCODE; https://www.encodeproject.org/ENCBS980OYK/

value: derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons