title: BY_rep1

city: Edinburgh

first: Nic

last: Robertson

address: Swann Building, Max Born Crescent

department: Tollervey Lab

country: United Kingdom

institute: University of Edinburgh

description:
negative control
NNNTAAGC_NR43BYAa

data_processing:
Demultiplexing: ran pyBarcodeFilter from pyCRAC library 3.0. Barcodes are the nucleotides at the start of the sample names.
Removal of adaptors and low-quality sequences: ran Flexbar with following options:  --qtrim-format solexa -as TGGAATTCTCGGGTGCCAAGGC -u 3 -n 1 -m 17
Collapsing duplicate reads: ran pyFastqDuplicateRemover from pyCRAC library (3.0)
Aligned: aligned to reference genome with Novolign (2.07.00MT) with parameters: -c 55 -5 random -s 1
Genome_build: Saccharomyces_cerevisiae.EF4.74
Supplementary_files_format_and_content: Genomic coordinates of mapped reads in BigWig format

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking

tag: strain

tag: tag


title: POP1_rep1

status: Public on Mar 29 2021

type: SRA

description:
RNA covalently attached to Pop1
NNNATTAGC_NR43POP1Ab

library_source: transcriptomic

molecule: total RNA


title: POP1_rep2

description:
RNA covalently attached to Pop1
NNNTCTCTAGC_NR45POP1Bd


title: TF ChIP-seq from transverse colon (ENCLB674MYY)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR449SEF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR449SEF
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB674MYY
fragmentation methods: sonication (generic)
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens female adult (51 years) transverse colon tissue

tag: antibody

value: CTCF

value: transverse colon

value: tissue

tag: description

value: EnTEX:Colon - Transverse

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

tag: age

value: 51 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS515RIZ at ENCODE; https://www.encodeproject.org/ENCBS515RIZ/

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


title: TF ChIP-seq from transverse colon (ENCLB710CAW)

description:
https://www.encodeproject.org/experiments/ENCSR449SEF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR449SEF
assay title: TF ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB710CAW
fragmentation methods: sonication (generic)
size range: 200-600


title: AR WT RNA rep1

city: Hanzhou

first: Lei

last: Gu

address: 79 Qingchun Rd

country: China

institute: First Affiliated Hospital, Zhejiang University School of Medicine

description:
processed data file: TET2_WT_AR_DESeq.csv (column V1)
WT_AR1

data_processing:
RNA-seq reads were aligned using STAR v2.7 (--sjdbInsertSave All --chimSegmentMin  10 --chimJunctionOverhangMin 10 ) reference genome GRCm38. and differential expression values were extracted using DESeq2 v1.26.0 . Genes with absolute fold change > 1.8 (WT group absolute fold change >1.4) and p-value < 0.05 were defined as differentially expressed genes.
5hmC captured sequencing: All sequencing libraries were run on Illumina Hi-seq 2000 machines. FASTQ sequence files from biological replicates were concatenated and aligned to the M. musculus reference genome (GRCm38/mm10) using Bowtie2 v2.3.5.1 (--no-mixed --no-discordant),  keeping unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp.
MACS2 v2.2.6 was used to find candidate peak location (tag size = 38, bandwidth = 300, P value cutoff = 1.00 * 105). All the candidate peak loci were summarized and binned the whole genome. We then used R to count sample’s read number in each candidate loci, then used DESeq2 v1.26.0 to find DhMR (any peak loci which was p-value <0.05 and absolute fold change > 1.8).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-seq: DESeq2 normalized seq counts output for each genome type
Supplementary_files_format_and_content: ChIP-seq: MACS2 peak calling output for each sample

organism: Mus musculus

source_name: AR WT RNA_nasal musosa

extract_protocol:
RNA-seq: Nasal mucosa samples were homogenized in TRIzol (Invitrogen, cat# 15596026) and processed according to the manufacturer’s instructions.
RNA-seq: RNA was then reverse transcribed using a SuperScript III First-Strand Synthesis System (Thermo Fisher, cat# 18080051). cDNA was quantified by qPCR using TaqMan Universal PCR Master Mix (Thermo Fisher, cat# 4304437) and SYBR Green PCR Master Mix (Thermo Fisher, cat# 4309155). Each reaction was run in triplicate and analyzed following the ΔΔCT method using glyceralde-hyde-3-phosphate dehydrogenase (Gapdh) as normalization control.
ChIP-seq: Genomic DNA was isolated from nasal tissues in 550μl of digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), then treated with Proteinase K (Thermo) at 55 °C overnight. The second day, 550μl of phenol: chloroform: isoamyl alcohol (25:24:1 saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer was transferred into a new Eppendorf tube and precipitated with 600μl of isopropanol. The pellet was washed with 75% ethanol, air-dried, and resuspended with Nuclease-Free Water (Ambion). DNA samples were treated extensively with an RNase cocktail (Ambion) to remove contaminating RNA.
ChIP-seq: DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25–50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. All sequencing libraries were run on Illumina Hi-seq 2000 machines. FASTQ sequence files from biological replicates were concatenated and aligned to the M. musculus reference genome (GRCm38/mm10) using Bowtie2 v2.3.5.139, keeping unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp.

treatment_protocol:
RNA-seq: Mice were sensitized by administration of an intraperitoneal injection of ovalbumin (OVA, 75ug) in 200ul of phosphate-buffered solution (PBS) containing 2mg of aluminum hydroxide (sigma Aldrich, St. Louis, MO, USA) in a total volume of 200ul on days 0, 7, 14. After initial sensitization, mice were challenged with nasal instillation of OVA 500ug in 20ul of PBS into bilateral nasal cavities on day16-25. The control group was challenged with PBS instead of OVA.
ChIP-seq: Mice were sensitized by administration of an intraperitoneal injection of ovalbumin (OVA, 75ug) in 200ul of phosphate-buffered solution (PBS) containing 2mg of aluminum hydroxide (sigma Aldrich, St. Louis, MO, USA) in a total volume of 200ul on days 0, 7, 14. After initial sensitization, mice were challenged with nasal instillation of OVA 500ug in 20ul of PBS into bilateral nasal cavities on day16-25. The control group was challenged with PBS instead of OVA.

tag: strain background

tag: genotype

value: WT

tag: treatment

value: OVA-treatment

tag: tissue

value: nasal mucosa


title: Control ChIP-seq from K562 (ENCLB783NAC)

description:
https://www.encodeproject.org/experiments/ENCSR012KTG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR012KTG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB783NAC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

tag: passage number

value: ENCBS532SKO at ENCODE; https://www.encodeproject.org/ENCBS532SKO/

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


title: BY_rep2

description:
negative control
NNNAGAGC_NR45BYBa

tag: strain

tag: tag


title: ATAC-seq from mucosa of descending colon (ENCLB908DZP)

description:
https://www.encodeproject.org/experiments/ENCSR491VXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR491VXJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB908DZP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (26 years) mucosa of descending colon tissue, preserved by cryopreservation

value: mucosa of descending colon

value: tissue

value: male

value: DM:no; HTN:no; CAD:no

value: 26 year

value: Yiing Lin, MD, PhD

value: ENCBS013VNY at ENCODE; https://www.encodeproject.org/ENCBS013VNY/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: TF ChIP-seq from heart left ventricle (ENCLB113UJK)

description:
https://www.encodeproject.org/experiments/ENCSR778ZPK/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on heart left ventricle female adult (59 years)
experiment encode accession: ENCSR778ZPK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR120ITZ
encode release date: 2020-09-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB113UJK
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (59 years) heart left ventricle tissue, preserved by flash-freezing

tag: antibody

value: CTCF

value: heart left ventricle

value: female

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 59 year

value: ENCBS830TZX at ENCODE; https://www.encodeproject.org/ENCBS830TZX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: Control ChIP-seq from endothelial cell of umbilical vein (ENCLB138KTY)

description:
https://www.encodeproject.org/experiments/ENCSR049NDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049NDZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB138KTY

source_name: Homo sapiens male newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: primary cell

tag: biosample encode accession

value: unknown

value: newborn

value: Yijun Ruan, JAX

value: Lonza

value: ENCBS239PAD at ENCODE; https://www.encodeproject.org/ENCBS239PAD/

value: Derived from ENCODE donor ENCDO341AAA; https://www.encodeproject.org/ENCDO341AAA/


title: ATAC-seq from esophagus mucosa (ENCLB088AEN)

description:
https://www.encodeproject.org/experiments/ENCSR303PWB/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human esophagus mucosa
experiment encode accession: ENCSR303PWB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB088AEN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (47 years) esophagus mucosa tissue, preserved by flash-freezing

value: esophagus mucosa

value: tissue

tag: Sex

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS928KHZ at ENCODE; https://www.encodeproject.org/ENCBS928KHZ/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: ATAC-seq from mucosa of descending colon (ENCLB166WNT)

description:
https://www.encodeproject.org/experiments/ENCSR491VXJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human mucosa of descending colon
experiment encode accession: ENCSR491VXJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB166WNT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: mucosa of descending colon

value: male

value: DM:no; HTN:no; CAD:no

tag: dev stage

value: adult

value: 26 year

value: ENCBS013VNY at ENCODE; https://www.encodeproject.org/ENCBS013VNY/

value: Derived from ENCODE donor ENCDO221IPH; https://www.encodeproject.org/ENCDO221IPH/


title: HU3_2h [RNAseqHU12]

city: Ann Arbor

first: Lyle

middle: A.

last: Simmons

state: MI

address: 1105 N. University Ave.

department: Molecular, Cellular, & Developmental Biology

institute: University of Michigan

description:
84976_ACTGAT_S12_L004
RNAseqHU12_sort.bam

data_processing:
align files to reference genome using BWA
samtools to generate a fast QC report for quality assessment
checking mapped vs. unmapped reads using samtools
calculate RPKMs in R, then used limma implementation to detect differential expression
generated top tables with a p-value cut off at 0.05
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000497485.1/
Supplementary_files_format_and_content: .csv files generated detailing differential expression

organism: Bacillus subtilis

source_name: whole cells

growth_protocol: PY79 was grown to an OD600 of 0.2 in LB medium at 30oC and supplemented with 25 mM HU for 1 and 2 hours before collecting cell pellets for nucleic acid extraction.

extract_protocol: RNA-SNAP from Stead et al. 2012

treatment_protocol: 25 mM HU or water (vehicle control) was incubated with cells for 1 and 2 hours post-treatment

value: hydroxyurea

tag: timepoint

value: 2 hours


title: control2_2h [RNAseqHU5]

description:
84969_ACAGTG_S5_L004
RNAseqHU5_sort.bam

value: vehicle control


title: HU2_1h [RNAseqHU8]

description:
84972_CTTGTA_S8_L004
RNAseqHU8_sort.bam

value: 1 hour


title: control3_1h [RNAseqHU3]

description:
84967_AGTCAA_S3_L004
RNAseqHU3_sort.bam


title: HU2_2h [RNAseqHU11]

description:
84975_GATCAG_S11_L004
RNAseqHU11_sort.bam


title: control1_2h [RNAseqHU4]

description:
84968_GTCCGC_S4_L004
RNAseqHU4_sort.bam


title: HU1_2h [RNAseqHU10]

description:
84974_TTAGGC_S10_L004
RNAseqHU10_sort.bam


title: control2_1h [RNAseqHU2]

description:
84966_GTGGCC_S2_L004
RNAseqHU2_sort.bam


title: HU1_1h [RNAseqHU7]

description:
84971_ATGTCA_S7_L004
RNAseqHU7_sort.bam


title: HU3_1h [RNAseqHU9]

description:
84973_CCGTCC_S9_L004
RNAseqHU9_sort.bam


title: control1_1h [RNAseqHU1]

description:
84965_TAGCTT_S1_L004
RNAseqHU1_sort.bam


title: control3_2h [RNAseqHU6]

description:
84970_GCCAAT_S6_L004
RNAseqHU6_sort.bam


title: ATAC-seq from right lobe of liver (ENCLB334UWD)

description:
https://www.encodeproject.org/experiments/ENCSR836FIL/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right lobe of liver
experiment encode accession: ENCSR836FIL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB334UWD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (40 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

value: DM:no; HTN:yes; CAD:no

tag: age

value: 40 year

tag: lab

value: ENCBS009YPS at ENCODE; https://www.encodeproject.org/ENCBS009YPS/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/


title: ATAC-seq from right lobe of liver (ENCLB277LSS)

description:
https://www.encodeproject.org/experiments/ENCSR836FIL/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human right lobe of liver
experiment encode accession: ENCSR836FIL
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB277LSS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link


title: ATAC-seq from esophagus mucosa (ENCLB997EAN)

description:
https://www.encodeproject.org/experiments/ENCSR303PWB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human esophagus mucosa
experiment encode accession: ENCSR303PWB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB997EAN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: esophagus mucosa

value: female

value: DM:yes; HTN:yes; CAD:no

value: 47 year

value: ENCBS928KHZ at ENCODE; https://www.encodeproject.org/ENCBS928KHZ/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: TF ChIP-seq from heart left ventricle (ENCLB200LVJ)

description:
https://www.encodeproject.org/experiments/ENCSR778ZPK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on heart left ventricle female adult (59 years)
experiment encode accession: ENCSR778ZPK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR120ITZ
encode release date: 2020-09-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200LVJ
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: heart left ventricle

value: adult

value: 59 year

value: ENCBS830TZX at ENCODE; https://www.encodeproject.org/ENCBS830TZX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: Control ChIP-seq from MCF 10A (ENCLB123YSQ)

description:
https://www.encodeproject.org/experiments/ENCSR775RVY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR775RVY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB123YSQ

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: fibrocystic disease

value: 36 year

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS923MAJ at ENCODE; https://www.encodeproject.org/ENCBS923MAJ/

value: Derived from ENCODE donor ENCDO000AAP; https://www.encodeproject.org/ENCDO000AAP/


title: ATAC-seq from heart left ventricle (ENCLB098UII)

description:
https://www.encodeproject.org/experiments/ENCSR286STX/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR286STX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB098UII
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (66 years) heart left ventricle tissue

value: tissue

value: male

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS313KIW at ENCODE; https://www.encodeproject.org/ENCBS313KIW/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: ATAC-seq from pancreas (ENCLB017VKK)

description:
https://www.encodeproject.org/experiments/ENCSR808ZMK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human pancreas
experiment encode accession: ENCSR808ZMK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB017VKK
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (41 years) pancreas tissue, preserved by cryopreservation

value: pancreas

value: female

value: DM:no; HTN:no; CAD:no

value: adult

value: 41 year

value: Yiing Lin, MD, PhD

value: ENCBS094RCD at ENCODE; https://www.encodeproject.org/ENCBS094RCD/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: ATAC-seq from pancreas (ENCLB520BRU)

description:
https://www.encodeproject.org/experiments/ENCSR808ZMK/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human pancreas
experiment encode accession: ENCSR808ZMK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB520BRU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000


title: Control ChIP-seq from HepG2 (ENCLB147YDR)

description:
https://www.encodeproject.org/experiments/ENCSR479INP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR479INP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB147YDR
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS370BPO at ENCODE; https://www.encodeproject.org/ENCBS370BPO/

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


title: ATAC-seq from heart left ventricle (ENCLB423LCX)

description:
https://www.encodeproject.org/experiments/ENCSR286STX/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart left ventricle
experiment encode accession: ENCSR286STX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB423LCX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart left ventricle

value: tissue

value: male

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: Michael Snyder, Stanford

value: Shin Lin

value: ENCBS313KIW at ENCODE; https://www.encodeproject.org/ENCBS313KIW/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: Control ChIP-seq from SK-N-SH (ENCLB521XWD)

description:
https://www.encodeproject.org/experiments/ENCSR086KKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on SK-N-SH
experiment encode accession: ENCSR086KKZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB521XWD
fragmentation methods: sonication (generic)

source_name: Homo sapiens SK-N-SH cell line

value: SK-N-SH

value: cell line

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 year

value: ENCBS372QOL at ENCODE; https://www.encodeproject.org/ENCBS372QOL/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/


title: Control ChIP-seq from A549 (ENCLB780VPU)

description:
https://www.encodeproject.org/experiments/ENCSR002ABL/
***************
biological replicate number: 1
technical replicate number: 1
description: A549 immortalized cell line stably expressing C-terminal eGFP-FOSL2 fusion protein.
experiment encode accession: ENCSR002ABL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB780VPU
size range: 450-650

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting FOSL2

tag: description

value: A549 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOSL2.

value: adult

value: 58 year

value: Michael Snyder

value: ENCBS089RZU at ENCODE; https://www.encodeproject.org/ENCBS089RZU/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ATAC-seq from sciatic nerve (ENCLB641SGD)

description:
https://www.encodeproject.org/experiments/ENCSR072UYN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR072UYN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB641SGD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female child (16 years) sciatic nerve tissue, preserved by flash-freezing

value: sciatic nerve

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS043LJN at ENCODE; https://www.encodeproject.org/ENCBS043LJN/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: Static_S6_1

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of mm10 was performed with Tophat2 (2.1.1) using default settings.
Counting: Gene expression was counted with Htseq-count (0.6.1) using the union mode and counts per million were calculated for each gene.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file containing raw Htseq counts and normalized counts (counts per million) for each gene in each sample.

molecule: polyA RNA

source_name: HUVEC

growth_protocol: HUVEC (Lonza, #C2519A, passages 2-4) were cultured in EBM-2 Endothelial Cell Growth Basal Medium-2 (Lonza, #CC-3156) supplemented with EGM-2 SingleQuots Supplements (Lonza, #CC-4176) at 37°C and 5% CO2.

extract_protocol:
After three days of flow, cells were collected and lysed in TRIzol.
Illumina libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: HUVEC were transfected with non-targeting siRNA (NT, Life Technologies, #4390847) or experimental siRNAs (Life Technologies Silencer Select) using the standard Lipofectamine 2000 (Invitrogen, 11668027) manufacturer's protocol. At 24 hr post transfection, cells were were plated at 100% confluency in each lane of a µ-Slide VI0.4 (Ibidi, #80601) coated with fibronectin (Millipore Sigma, F2006, 5ug/mL) and culured for 2 hr in their normal growth media. Then the slides were washed 3 times in flow medium (EBM-2 with 10% FBS (Gibco, #26140-079) and 1X Antibiotic-Antimycotic (Gibco, #15240-062)), and incubated in flow medium for 2 hr prior to flow onset. Uniform laminar shear stress was generated by attaching slide chambers to a pump system (Ibidi, #10902) with both the slide and the pump apparatus kept at 37C and 5% CO2. To reduce cell shearing off the slide, flow was applied for 30 min at 5 d/cm2, then 30 min at 10 dynes/cm2, followed by 72 hr at 15 d/cm2.

tag: cell type

value: HUVEC

tag: sirna transfection

tag: culture condition

value: Static


title: ATAC-seq from sciatic nerve (ENCLB492MPX)

description:
https://www.encodeproject.org/experiments/ENCSR072UYN/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human sciatic nerve
experiment encode accession: ENCSR072UYN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB492MPX
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: female

tag: health state


title: ATAC-seq from heart right ventricle (ENCLB379PQL)

description:
https://www.encodeproject.org/experiments/ENCSR053SGP/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR053SGP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB379PQL
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (54 years) heart right ventricle tissue

value: heart right ventricle

value: male

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: adult

value: 54 year

value: Shin Lin

value: ENCBS735IQJ at ENCODE; https://www.encodeproject.org/ENCBS735IQJ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Flow_NT_2

value: siNT

value: Flow


title: Flow_S6_2


title: Control ChIP-seq from K562 (ENCLB463WIF)

description:
https://www.encodeproject.org/experiments/ENCSR200QDR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR200QDR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB463WIF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF133

tag: line

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS498UJD at ENCODE; https://www.encodeproject.org/ENCBS498UJD/

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


title: Flow_S6_1

value: HUVEC


title: Static_NT_1

value: Static


title: Control ChIP-seq from astrocyte (ENCLB976DVU)

description:
https://www.encodeproject.org/experiments/ENCSR730VRY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on astrocyte originated from astrocyte
experiment encode accession: ENCSR730VRY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB976DVU
size range: 200-600

source_name: Homo sapiens male adult (53 years) astrocyte in vitro differentiated cells originated from astrocyte, preserved by cryopreservation

value: astrocyte

value: in vitro differentiated cells

value: PGP1 derived astrocytes

value: male

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS534DJA at ENCODE; https://www.encodeproject.org/ENCBS534DJA/

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


title: Flow_NT_1

value: siNT

value: Flow


title: ATAC-seq from heart right ventricle (ENCLB460DEA)

description:
https://www.encodeproject.org/experiments/ENCSR053SGP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR053SGP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB460DEA
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart right ventricle

value: tissue

value: ischemic (EF 13 %, LVEDD 7.1; RV severe dilation, severe dysfunction)

value: adult

value: 54 year

value: Shin Lin

value: ENCBS735IQJ at ENCODE; https://www.encodeproject.org/ENCBS735IQJ/

value: Derived from ENCODE donor ENCDO039RUH; https://www.encodeproject.org/ENCDO039RUH/


title: Control ChIP-seq from HepG2 (ENCLB730UCF)

description:
https://www.encodeproject.org/experiments/ENCSR020QUJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR020QUJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB730UCF
fragmentation methods: sonication (generic)

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS985KHJ at ENCODE; https://www.encodeproject.org/ENCBS985KHJ/

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


title: ATAC-seq from uterus (ENCLB065SZZ)

description:
https://www.encodeproject.org/experiments/ENCSR775SYU/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human uterus
experiment encode accession: ENCSR775SYU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB065SZZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) uterus tissue, preserved by flash-freezing

value: uterus

value: female

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS876AUX at ENCODE; https://www.encodeproject.org/ENCBS876AUX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: Static_NT_2

value: HUVEC

value: siNT

value: Static


title: Control ChIP-seq from K562 (ENCLB912ZKC)

description:
https://www.encodeproject.org/experiments/ENCSR006OWT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR006OWT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB912ZKC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF41

value: cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Kevin White

value: ENCBS457SBZ at ENCODE; https://www.encodeproject.org/ENCBS457SBZ/

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


title: Control ChIP-seq from A549 (ENCLB254QZI)

description:
https://www.encodeproject.org/experiments/ENCSR414IDX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR414IDX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-09-28
lab: Yijun Ruan, JAX
library encode accession: ENCLB254QZI

source_name: Homo sapiens A549 cell line

value: male

value: 58 year

value: Yijun Ruan, JAX

value: ATCC

value: ENCBS972LHT at ENCODE; https://www.encodeproject.org/ENCBS972LHT/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: Control ChIP-seq from HepG2 (ENCLB645CSO)

description:
https://www.encodeproject.org/experiments/ENCSR776XHE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR776XHE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-14
lab: Richard Myers, HAIB
library encode accession: ENCLB645CSO
fragmentation methods: sonication (generic)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS812MOA at ENCODE; https://www.encodeproject.org/ENCBS812MOA/

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


title: Control ChIP-seq from endothelial cell (ENCLB619CLY)

description:
https://www.encodeproject.org/experiments/ENCSR233WMP/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on endothelial cell
experiment encode accession: ENCSR233WMP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB619CLY
size range: 200-600

source_name: Homo sapiens male adult (53 years) endothelial in vitro differentiated cells, preserved by cryopreservation

value: endothelial cell

value: in vitro differentiated cells

value: PGP1 derived endothelial cells

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/

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


title: ATAC-seq from psoas muscle (ENCLB426YUP)

description:
https://www.encodeproject.org/experiments/ENCSR774NXA/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human psoas muscle
experiment encode accession: ENCSR774NXA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB426YUP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: tissue

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS109TNY at ENCODE; https://www.encodeproject.org/ENCBS109TNY/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Control ChIP-seq from endothelial cell (ENCLB717JXP)

description:
https://www.encodeproject.org/experiments/ENCSR233WMP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on endothelial cell
experiment encode accession: ENCSR233WMP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB717JXP
size range: 200-600

value: endothelial cell

value: in vitro differentiated cells

value: male


title: ATAC-seq from psoas muscle (ENCLB329UYI)

description:
https://www.encodeproject.org/experiments/ENCSR774NXA/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human psoas muscle
experiment encode accession: ENCSR774NXA
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB329UYI
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult


title: Static_S6_2

value: HUVEC

value: Static


title: Control ChIP-seq from HepG2 (ENCLB006JVG)

description:
https://www.encodeproject.org/experiments/ENCSR770PLF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR770PLF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB006JVG
fragmentation methods: sonication (generic)

value: cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS867PTM at ENCODE; https://www.encodeproject.org/ENCBS867PTM/

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


title: Control ChIP-seq from astrocyte (ENCLB726AVL)

description:
https://www.encodeproject.org/experiments/ENCSR730VRY/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on astrocyte originated from astrocyte
experiment encode accession: ENCSR730VRY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726AVL
size range: 200-600

value: astrocyte

value: PGP1 derived astrocytes

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS534DJA at ENCODE; https://www.encodeproject.org/ENCBS534DJA/

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


title: Control ChIP-seq from HepG2 (ENCLB423PNM)

description:
https://www.encodeproject.org/experiments/ENCSR042HRU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR042HRU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB423PNM
fragmentation methods: sonication (generic)

value: male

value: ENCBS180NKP at ENCODE; https://www.encodeproject.org/ENCBS180NKP/


title: ATAC-seq from pancreas (ENCLB032UJR)

description:
https://www.encodeproject.org/experiments/ENCSR251POP/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human pancreas
experiment encode accession: ENCSR251POP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB032UJR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (61 years) pancreas tissue, preserved by cryopreservation

value: pancreas

value: tissue

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS035WEB at ENCODE; https://www.encodeproject.org/ENCBS035WEB/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: ATAC-seq from heart right ventricle (ENCLB544NXT)

description:
https://www.encodeproject.org/experiments/ENCSR439TZT/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR439TZT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB544NXT
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (66 years) heart right ventricle tissue

value: heart right ventricle

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: 66 year

value: Shin Lin

value: ENCBS406VSG at ENCODE; https://www.encodeproject.org/ENCBS406VSG/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: Control ChIP-seq from excitatory neuron (ENCLB523OFL)

description:
https://www.encodeproject.org/experiments/ENCSR408LXD/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on excitatory neuron
experiment encode accession: ENCSR408LXD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB523OFL
size range: 200-600

source_name: Homo sapiens male adult (53 years) excitatory neuron in vitro differentiated cells, preserved by cryopreservation

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: male

value: 53 year

value: Bradley Bernstein, Broad

value: George Church

value: ENCBS932EVS at ENCODE; https://www.encodeproject.org/ENCBS932EVS/

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


title: Control ChIP-seq from excitatory neuron (ENCLB413LQF)

description:
https://www.encodeproject.org/experiments/ENCSR408LXD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on excitatory neuron
experiment encode accession: ENCSR408LXD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB413LQF
size range: 200-600

value: adult


title: Control ChIP-seq from nephron (ENCLB838INU)

description:
https://www.encodeproject.org/experiments/ENCSR008HBN/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on nephron female embryo (5 days) originated from H9
experiment encode accession: ENCSR008HBN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB838INU
size range: 200-600

source_name: Homo sapiens female embryo (5 days) nephron organoid originated from H9, preserved by cryopreservation

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS202RGJ at ENCODE; https://www.encodeproject.org/ENCBS202RGJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ATAC-seq from uterus (ENCLB557IHG)

description:
https://www.encodeproject.org/experiments/ENCSR775SYU/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human uterus
experiment encode accession: ENCSR775SYU
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB557IHG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: uterus

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS876AUX at ENCODE; https://www.encodeproject.org/ENCBS876AUX/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: ATAC-seq from heart right ventricle (ENCLB073SXC)

description:
https://www.encodeproject.org/experiments/ENCSR439TZT/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR439TZT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB073SXC
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: heart right ventricle

value: male

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: adult

value: 66 year

value: Shin Lin

value: ENCBS406VSG at ENCODE; https://www.encodeproject.org/ENCBS406VSG/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: Control ChIP-seq from nephron (ENCLB033KJN)

description:
https://www.encodeproject.org/experiments/ENCSR008HBN/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on nephron female embryo (5 days) originated from H9
experiment encode accession: ENCSR008HBN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB033KJN
size range: 200-600

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: Joseph Bonventre

value: ENCBS202RGJ at ENCODE; https://www.encodeproject.org/ENCBS202RGJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ATAC-seq from psoas muscle (ENCLB799QBP)

description:
https://www.encodeproject.org/experiments/ENCSR040DJK/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human psoas muscle
experiment encode accession: ENCSR040DJK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB799QBP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) psoas muscle tissue, preserved by flash-freezing

value: psoas muscle

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS763TNR at ENCODE; https://www.encodeproject.org/ENCBS763TNR/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: ATAC-seq from psoas muscle (ENCLB294GNU)

description:
https://www.encodeproject.org/experiments/ENCSR040DJK/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human psoas muscle
experiment encode accession: ENCSR040DJK
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB294GNU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult


title: Control ChIP-seq from HepG2 (ENCLB643DUF)

description:
https://www.encodeproject.org/experiments/ENCSR257XAX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR257XAX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-02-25
lab: Richard Myers, HAIB
library encode accession: ENCLB643DUF
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS258BMB at ENCODE; https://www.encodeproject.org/ENCBS258BMB/

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


title: Control ChIP-seq from chondrocyte (ENCLB267GEV)

description:
https://www.encodeproject.org/experiments/ENCSR004UBJ/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on chondrocyte originated from chondrocyte
experiment encode accession: ENCSR004UBJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB267GEV
size range: 200-600

source_name: Homo sapiens female embryo (5 days) chondrocyte in vitro differentiated cells originated from chondrocyte

value: chondrocyte

value: in vitro differentiated cells

value: WA09 derived chondrocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS434TAN at ENCODE; https://www.encodeproject.org/ENCBS434TAN/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control ChIP-seq from chondrocyte (ENCLB382CEH)

description:
https://www.encodeproject.org/experiments/ENCSR004UBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on chondrocyte originated from chondrocyte
experiment encode accession: ENCSR004UBJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB382CEH
size range: 200-600

value: ENCBS497BNU at ENCODE; https://www.encodeproject.org/ENCBS497BNU/


title: Control ChIP-seq from chondrocyte (ENCLB617SHL)

description:
https://www.encodeproject.org/experiments/ENCSR004UBJ/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on chondrocyte originated from chondrocyte
experiment encode accession: ENCSR004UBJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB617SHL
size range: 200-600


title: Control ChIP-seq from chondrocyte (ENCLB093JNN)

description:
https://www.encodeproject.org/experiments/ENCSR004UBJ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on chondrocyte originated from chondrocyte
experiment encode accession: ENCSR004UBJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB093JNN
size range: 200-600


title: ALDH-high cells of locally advanced stage NSCLC

type: RNA

city: Modena

first: Beatrice

last: Aramini

state: italy

address: via del pozzo 71, via del pozzo 71

country: Italy

institute: University Hospital of Modena

data_processing:
The analysis was carried out separately for patients with early-stage (I-II) NSCLC and locally advanced stage (IIIA) NSCLC.
Normalization of mRNA expression was performed by considering the expressions of three housekeeping genes (RPL13A, RPL4, and RPS29).
Undetermined Ct values obtained from RT-PCR experiments were imputed. When one of the two duplicates had undetermined Ct value, it was set equal to the Ct of the other replicate. Then the remaining Ct values were imputed as the maximum observed value for the specific target gene. This was done only for patients that had at least one valid Ct value for that gene in ALDH-high or ALDH-low cells.
The relative mRNA expression of each of the 31 target genes was assessed, comparing ALDH-high to ALDH-low cell populations, by using linear mixed models (LMM). The dependent variable in LMM was the Ct value, and the independent variables were ALDH (high vs. low), gene (target gene compared to the average of housekeeping genes), ALDH - gene interaction, histotype (adenocarcinoma or squamous cell carcinoma). The models also included a random intercept and a random ALDH - gene interaction term that was specific for each patient, to account for correlations in individual Ct values. LMMs were estimated for each gene on those patients that had at least one available Ct value for that target gene in ALDH-high or ALDH-low cells.
The non-normalized.txt  reports average raw Ct values calculated on the set of patients that had at least one available Ct value for that target gene in ALDH-high or ALDH-low cells.
Thefold_change.txt reports test/control (i.e., ALDH-high / ALDH-low) ratios separately for patients with early-stage (I-II) NSCLC and locally advanced stage (IIIA) NSCLC (i.e., FC = 2^[-DeltaDeltaCt]).

label: FAM

source_name: Test for locally advanced stage NSCLC

label_protocol: Revert Aid first strand cDNA synthesis Kit- Thermo Scientific

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Samples were digested for 60 min at 37 °C in a gentle MACS Octo dissociator according to the manufacturer’s instructions, with Milteny tumor dissociation in a MACS™ C-Tube (Miltenyi Biotec, Italy).

value: Lung cancer stem cells

tag: tumor stage

value: locally advanced


title: ALDH-low cells of locally advanced stage NSCLC

source_name: Control for locally advanced stage NSCLC

value: Lung epithelial cancer cells


title: ALDH-low cells of early stage NSCLC

source_name: Control for early stage NSCLC

value: early


title: ATAC-seq from pancreas (ENCLB751TGN)

description:
https://www.encodeproject.org/experiments/ENCSR251POP/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human pancreas
experiment encode accession: ENCSR251POP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB751TGN
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS035WEB at ENCODE; https://www.encodeproject.org/ENCBS035WEB/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: Control ChIP-seq from osteocyte (ENCLB913WFA)

description:
https://www.encodeproject.org/experiments/ENCSR702WFF/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on osteocyte originated from osteocyte
experiment encode accession: ENCSR702WFF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB913WFA
size range: 200-600

source_name: Homo sapiens female embryo (5 days) osteocyte in vitro differentiated cells originated from osteocyte

value: osteocyte

value: in vitro differentiated cells

value: WA09 derived osteocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS034WOR at ENCODE; https://www.encodeproject.org/ENCBS034WOR/


title: Control ChIP-seq from osteocyte (ENCLB839NAY)

description:
https://www.encodeproject.org/experiments/ENCSR702WFF/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq on osteocyte originated from osteocyte
experiment encode accession: ENCSR702WFF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB839NAY
size range: 200-600

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control ChIP-seq from osteocyte (ENCLB416XES)

description:
https://www.encodeproject.org/experiments/ENCSR702WFF/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on osteocyte originated from osteocyte
experiment encode accession: ENCSR702WFF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB416XES
size range: 200-600

value: ENCBS572IFJ at ENCODE; https://www.encodeproject.org/ENCBS572IFJ/


title: ALDH-high cells of early stage NSCLC

source_name: Test for early stage NSCLC

value: Lung cancer stem cells

value: early


title: ATAC-seq from adrenal gland (ENCLB064BPS)

description:
https://www.encodeproject.org/experiments/ENCSR241OBO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human adrenal gland
experiment encode accession: ENCSR241OBO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB064BPS
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) adrenal gland tissue, preserved by cryopreservation

value: adrenal gland

value: tissue

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 59 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS767STY at ENCODE; https://www.encodeproject.org/ENCBS767STY/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: ATAC-seq from heart right ventricle (ENCLB425BUW)

description:
https://www.encodeproject.org/experiments/ENCSR437OOJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR437OOJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB425BUW
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) heart right ventricle tissue, preserved by cryopreservation

value: heart right ventricle

value: female

value: ENCBS608WCQ at ENCODE; https://www.encodeproject.org/ENCBS608WCQ/


title: LG101

city: Melbourne

first: Paul

last: Beavis

state: Victoria

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Genome_build: hg19
Supplementary_files_format_and_content: count file generated by featureCounts

source_name: CAR T cells from PBMC

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from normal buffy coats using Ficoll centrifugation and (PBMCs) were cultured in RPMI supplemented with 10% FCS, sodium pyruvate, glutamax, NEAA, HEPES and penicillin/streptomycin. PBMCs were activated with antihuman CD3 (30ng/ ml) and IL-2 (100 IU/ml) for 48 hours before transduction with a retrovirus encoding a second generation scFv–anti–Lewis-Y CAR (CD28 and CD3ζ). Retroviral supernantant was obtained from a modified PG13 packaging line and 5ml added to retronectin-coated (15 μg/ml) 6-well plates which were centrifuged at 1200g for 1hr. Activated PBMCs were resuspended at a concentration of 0.5x106 per ml in fresh 5ml of retrovirus containing IL-2 and added to the retronectin coated plates following the removal of the viral supernatant used during the coating phase. Cells were centrifuged for 1hr (1200g) followed by overnight incubation and a second round of transduction the next day. Cells were cultured at a density of 1.5x106/ml following the transduction process.

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

treatment_protocol: Stimulated with plate bound anti-idiotype-LeY (anti-CAR) antibody in the presence or absence of NECA (10 µM) for 8 hours.

value: T cell

tag: donor

value: Healthy donor

tag: car

value: α-Lewis-Y

tag: genotype

value: MOCK

tag: stimulation

tag: treatment

tag: coculture time

value: 8 hours


title: ATAC-seq from adrenal gland (ENCLB873DIU)

description:
https://www.encodeproject.org/experiments/ENCSR241OBO/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human adrenal gland
experiment encode accession: ENCSR241OBO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB873DIU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adrenal gland

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: age


title: ATAC-seq from heart right ventricle (ENCLB653ZDR)

description:
https://www.encodeproject.org/experiments/ENCSR437OOJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR437OOJ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB653ZDR
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

tag: lab

tag: source

tag: link


title: LG102

tag: cell type


title: LG103

value: plate bound anti-idiotype LeY


title: LG107

value: A2AR KO


title: LG105

value: NECA (10μM)


title: LG108


title: LG106


title: LG104


title: LG109


title: Control ChIP-seq from HepG2 (ENCLB817NND)

description:
https://www.encodeproject.org/experiments/ENCSR743HNM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR743HNM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-14
lab: Richard Myers, HAIB
library encode accession: ENCLB817NND
fragmentation methods: sonication (generic)

value: cell line

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS612YFV at ENCODE; https://www.encodeproject.org/ENCBS612YFV/

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


title: LG110

value: T cell

value: Healthy donor

value: α-Lewis-Y


title: LG111

value: 8 hours


title: GM12878_singlecell_4-O

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: XRBS library

data_processing:
library strategy: Bisulfite-Seq (extended representation); XRBS
Raw sequencing reads were demultiplexed by the first 8bp of read 2 (representing the adapter barcode sequence). Up to one mismatch to expected barcode sequences was allowed. Barcode sequences were cut from sequencing reads and appended to read identifiers.
Similarly, the first 6bp of read 1 (representing the hexamer sequence) were also cut and appended to read identifiers. Files for read 1 and read 2 were switched to allow compatibility with downstream alignment tools. Resulting fastq files are shared on GEO/SRA.
Genomic alignment of bisulfite-converted reads was perfomed using methylCtools version 1.0.0 (Hovestadt et al., 2014, https://github.com/hovestadt/methylCtools) and bwa mem version 0.7.17.
Alignments were futher filtered to only include reads that are uniquely aligned, map to an MspI cut site, and do not represent PCR duplicates (taking into account the hexamer sequence as a unique molecular identifier).
Methylation calls were generated using methylCtools. Resulting text files are shared on GEO.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Tab-delimited text file containing methylation calls of covered CpGs. Columns: Chromosome, Position, Strand, Context, Methylated, Unmethylated.

source_name: GM12878 cells

growth_protocol: Cells were maintained in exponential phase growth by passaging every 3 to 4 days. Cells were grown in RPMI supplemented with 10% heat inactivated fetal bovine serum and 1% penicillin/streptomycin. All cell lines were routinely tested for mycoplasma contamination and maintained in a 37C humidity-controlled incubator with 5.0% CO2.

extract_protocol:
Cells were collected and washed in cold PBS twice and then the pellet was snap frozen in liquid nitrogen. DNA was harvested by thawing the cell pellets at room temperature and resuspending in PBS, as directed by the Qiagen DNA Mini Blood Kit (51104). For experiment performed on sorted cells, cells were counterstained with 1:1000 µL of PI in PB and sorted in Sony SH800 sorter. Viable single cells were gated and used for sorting into 96 well plates preloaded with 3 uL of lysis buffer (40 mM Tris-Ac, 1mM EDTA, and 1 mM DTT). Incubation at 75°C for 30 minutes is followed by adding 0.5 µL of Qiagen Protease and a 4 hour incubation at 55°C and a 30 minute incubation at 75°C to inactivate the proteinase (Chen et al. 2017).
Here we present a novel extended representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design draws a balance between expanding coverage of regulatory elements and enriching for informative CpG dinucleotides. Barcoded DNA fragments are pooled prior to bisulfite conversion, allowing multiplex processing, improving consistency, and reducing cost and labor. Linear amplification of single stranded bisulfite-treated DNA enables library generation from fragmented and low input DNA samples.

treatment_protocol: HL-60 and OCI-AML3 cells were treated with 300 nM decitabine in 6 well plates. Cells were harvested after 5 days.

tag: cell line

value: GM12878 cells

tag: input

value: 1 cell


title: Control ChIP-seq from osteocyte (ENCLB354BUQ)

description:
https://www.encodeproject.org/experiments/ENCSR702WFF/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on osteocyte originated from osteocyte
experiment encode accession: ENCSR702WFF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-07-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB354BUQ
size range: 200-600

value: osteocyte

value: in vitro differentiated cells

tag: description

value: WA09 derived osteocytes

value: female

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS572IFJ at ENCODE; https://www.encodeproject.org/ENCBS572IFJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: LG112

value: T cell

tag: donor

tag: car

value: A2AR KO

value: plate bound anti-idiotype LeY

value: NECA (10μM)


title: GM12878_singlecell_4-N

description: XRBS library

value: GM12878 cells


title: AR Tet2-/- 5hmC rep2

description:
T2-17
19149FL-16-01-02_S62_L007

source_name: AR Tet2-/- 5hmC_nasal musosa

tag: strain background

tag: genotype

value: OVA-treatment

tag: tissue

value: nasal mucosa

tag: molecule subtype

value: 5hmC captured DNA


title: GM12878_singlecell_4-K

description: XRBS library

value: 1 cell

tag: treatment


title: GM12878_singlecell_4-L

description: XRBS library


title: GM12878_singlecell_3-N

description: XRBS library


title: GM12878_singlecell_4-M

description: XRBS library


title: GM12878_singlecell_3-M

description: XRBS library


title: GM12878_singlecell_3-P

description: XRBS library


title: GM12878_singlecell_3-O

description: XRBS library


title: GM12878_singlecell_4-J

description: XRBS library


title: GM12878_singlecell_4-I

description: XRBS library


title: GM12878_singlecell_3-L

description: XRBS library


title: Control ChIP-seq from HepG2 (ENCLB984OEM)

description:
https://www.encodeproject.org/experiments/ENCSR730QNM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR730QNM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-26
lab: Richard Myers, HAIB
library encode accession: ENCLB984OEM
fragmentation methods: sonication (generic)

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS011RUM at ENCODE; https://www.encodeproject.org/ENCBS011RUM/

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


title: GM12878_singlecell_3-K

description: XRBS library


title: GM12878_singlecell_2-H

description: XRBS library


title: GM12878_singlecell_2-G

description: XRBS library


title: GM12878_singlecell_3-J

description: XRBS library


title: GM12878_singlecell_2-F

description: XRBS library


title: GM12878_singlecell_2-D

description: XRBS library


title: AR Tet2+/- 5hmC rep3

description:
T2-25
19149FL-16-01-06_S66_L007

source_name: AR Tet2+/- 5hmC_nasal musosa

tag: age


title: GM12878_singlecell_2-E

description: XRBS library


title: GM12878_singlecell_2-C

description: XRBS library


title: GM12878_singlecell_2-B

description: XRBS library


title: GM12878_singlecell_4-P

description: XRBS library


title: GM12878_singlecell_2-A

description: XRBS library


title: GM12878_singlecell_1-X

description: XRBS library


title: ATAC-seq from ovary (ENCLB392GEG)

description:
https://www.encodeproject.org/experiments/ENCSR227FVE/
***************
biological replicate number: 1
technical replicate number: 3
description: ATAC-seq on human ovary
experiment encode accession: ENCSR227FVE
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB392GEG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) ovary tissue, preserved by cryopreservation

value: ovary

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 59 year

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS015NSJ at ENCODE; https://www.encodeproject.org/ENCBS015NSJ/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: GM12878_singlecell_1-W

description: XRBS library

tag: cell line

value: GM12878 cells

tag: input

value: 1 cell


title: GM12878_singlecell_1-V

description: XRBS library


title: GM12878_singlecell_1-U

description: XRBS library


title: ATAC-seq from ovary (ENCLB048OAY)

description:
https://www.encodeproject.org/experiments/ENCSR227FVE/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human ovary
experiment encode accession: ENCSR227FVE
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB048OAY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

tag: health state


title: GM12878_singlecell_1-T

description: XRBS library


title: K562_singlecell_4-E

description: XRBS library

source_name: K562 cells

value: K562 cells


title: GM12878_singlecell_1-R

description: XRBS library


title: GM12878_singlecell_1-S

description: XRBS library


title: K562_singlecell_4-F

description: XRBS library


title: GM12878_singlecell_1-Q

description: XRBS library


title: K562_singlecell_4-D

description: XRBS library


title: K562_singlecell_4-H

description: XRBS library


title: K562_singlecell_4-C

description: XRBS library


title: GM12878_singlecell_3-I

description: XRBS library


title: Control ChIP-seq from HepG2 (ENCLB010RKE)

description:
https://www.encodeproject.org/experiments/ENCSR019ZGX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR019ZGX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-14
lab: Richard Myers, HAIB
library encode accession: ENCLB010RKE
fragmentation methods: sonication (generic)

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: ENCBS065WJQ at ENCODE; https://www.encodeproject.org/ENCBS065WJQ/


title: K562_singlecell_4-A

description: XRBS library


title: K562_singlecell_4-B

description: XRBS library


title: K562_singlecell_3-T

description: XRBS library


title: K562_singlecell_3-S

description: XRBS library


title: K562_singlecell_3-V

description: XRBS library


title: K562_singlecell_3-Q

description: XRBS library


title: K562_singlecell_2-P

description: XRBS library


title: K562_singlecell_3-R

description: XRBS library


title: K562_singlecell_2-O

description: XRBS library


title: K562_singlecell_2-N

description: XRBS library


title: ATAC-seq from heart right ventricle (ENCLB000XTG)

description:
https://www.encodeproject.org/experiments/ENCSR710SMN/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR710SMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB000XTG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (58 years) heart right ventricle tissue, preserved by cryopreservation

value: heart right ventricle

value: tissue

value: female

value: Ischemic cardiomyopathy

value: 58 year

value: Shin Lin

value: ENCBS893AZK at ENCODE; https://www.encodeproject.org/ENCBS893AZK/

value: Derived from ENCODE donor ENCDO719HSJ; https://www.encodeproject.org/ENCDO719HSJ/


title: K562_singlecell_2-M

description: XRBS library

value: 1 cell


title: K562_singlecell_2-L

description: XRBS library

value: K562 cells


title: ATAC-seq from heart right ventricle (ENCLB030ARZ)

description:
https://www.encodeproject.org/experiments/ENCSR710SMN/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR710SMN
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB030ARZ
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: adult

value: Michael Snyder, Stanford


title: K562_singlecell_4-G

description: XRBS library


title: K562_singlecell_2-K

description: XRBS library


title: K562_singlecell_2-J

description: XRBS library


title: K562_singlecell_2-I

description: XRBS library


title: K562_singlecell_3-X

description: XRBS library


title: K562_singlecell_3-W

description: XRBS library


title: K562_singlecell_3-U

description: XRBS library


title: K562_singlecell_1-E

description: XRBS library


title: K562_singlecell_1-G

description: XRBS library


title: K562_singlecell_1-D

description: XRBS library


title: K562_singlecell_1-C

description: XRBS library


title: K562_singlecell_1-F

description: XRBS library


title: K562_singlecell_1-H

description: XRBS library


title: shamS_input

city: Hangzhou

first: Longfei

last: Ma

address: 88 Jiefang Road

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference Mus musculus (Version: GRCm38).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).  HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo  motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Genome_build: GRCm38
Supplementary_files_format_and_content: text files include m6A peak information for each group

growth_protocol: 6-8 weeks old C57BL/6J mice

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average  size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: The sciatic nerve was loosely ligated with 6-0 silk thread at four sites for chronic constriction injury mice. Identical procedures without the ligature of the sciatic nerve was undertaken for the sham mice.

tag: strain

value: control

tag: rip antibody

value: spinal cord


title: K562_singlecell_1-A

description: XRBS library


title: HL60_1000cells_highcov

description: XRBS library

source_name: HL-60 cells

value: HL-60 cells

value: 1000 cells


title: CCIS_input

value: chronic constriction injury


title: Non-hematopoietic cells from Flk2-cre+ Cxcr4fl/+ mouse [CTL-CXCR4]

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

data_processing:
Cellranger (v4.0) count function with the default parameters was run to generate single cell feature counts from FASTQ files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated file, feature counts amd indexes

source_name: Bone marrow

extract_protocol:
Bone marrow stromal cells and bone surface cells were isolated. CD45- Ter119- Lineage (B220, CD19, CD11b, Gr1, CD3e)- CD31- CD144- CD71- cells were sorted by the BD FACS Aria II machine into DMEM with 20% FBS.
scRNA-Seq library was generated using Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) following the manufacturer’s protocol.

tag: genotype

value: Flk2-cre+ Cxcr4fl/+

value: 6.5 weeks

value: Bone marrow

tag: cell type

value: Non-hematopoietic cells


title: Non-hematopoietic cells from Flk2-cre+ Cxcr4fl/fl mouse [KO-CXCR4]

value: Flk2-cre+ Cxcr4fl/fl

tag: tissue


title: HL60_10ng_decitabine

description: XRBS library

value: 10ng purified DNA

tag: treatment

value: Decitabine


title: shamS_IP

value: m6A-specific antibody (No. 202003, Synaptic Systems, Germany)


title: HL60_1000cells_lowcov

description: XRBS library


title: ATAC-seq from pancreas (ENCLB947OUY)

description:
https://www.encodeproject.org/experiments/ENCSR705KEB/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human pancreas
experiment encode accession: ENCSR705KEB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB947OUY
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) pancreas tissue, preserved by cryopreservation

value: pancreas

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: 59 year

value: Yiing Lin, MD, PhD

value: ENCBS103EAQ at ENCODE; https://www.encodeproject.org/ENCBS103EAQ/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: HL60_100cells_lowcov

description: XRBS library

value: HL-60 cells

value: 100 cells


title: HL60_10ng_lowcov

description: XRBS library


title: Multiplexed06_Tumor_GEMy_HTO

city: Bethesda

first: Michael

middle: C

last: Kelly

state: MD

address: 41 Center Drive

department: Center for Cancer Research

institute: NCI

description: Multiplexed06_Tumor_GEMy_filtered_feature_bc_matrix.h5

data_processing:
Fastq demultiplexing with cellranger v3.0.2
Read alignment and single cell data parsing with cellranger v3.0.2
Sample multiplexing feature barcode reads aligned to custome reference containing TotalSeq A hashtag barcode sequences
Genome_build: mm10 (refdata-cellranger-mm10-3.0.0)
Supplementary_files_format_and_content: 10x Genomics filtered h5 files contain the gene expression and cell hashing feature barcode data for each of the multiplexed samples.

source_name: Tumor + IL12-GEMy 1+2

extract_protocol: Lungs were perfused with PBS and inflated with digestion medium (HBSS supplemented with 1 mg/mL collagenase I, 20 μg/mL DNAse I and Dispase II). Single-cell suspensions were prepared by finely mincing tissues with a scalpel and incubating the tissue on a shaker at 37°C for 20 minutes in 1 mL of digestion media. Tissue was passed through a 70 μM mesh strainer and washed with collection media twice. Cell suspensions were labeled with TotalSeqA hashtag oligo antibodies (BioLegend) before being combined for multiplexed loading on the 10x Genomics Chromium instrument using 3’ v3 chemistry. Libraries were constructed according to 10x Genomics User Guide (Chromium 3' v3) with a modification to include antibody cell labeling barcode libraries according to Stoeckius et al, 2018.

value: Lung

tag: disease state

value: M3-9-M Tumor-Bearing


title: Multiplexed06_Tumor_GEMy_GEX


title: Multiplexed07_Tumor_GEMy_HTO

description: Multiplexed07_Tumor_GEMy_filtered_feature_bc_matrix.h5

source_name: Tumor + IL12-GEMy 3+4


title: Multiplexed07_Tumor_GEMy_GEX


title: ATAC-seq from pancreas (ENCLB670MPP)

description:
https://www.encodeproject.org/experiments/ENCSR705KEB/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human pancreas
experiment encode accession: ENCSR705KEB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB670MPP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

tag: biosample encode accession

value: adult

value: Michael Snyder, Stanford


title: Multiplexed05_Tumor_NoGEMy_HTO

description: Multiplexed05_Tumor_NoGEMy_filtered_feature_bc_matrix.h5

source_name: Tumor No Treatment 3+4

value: No Treatment


title: K562_singlecell_1-B

description: XRBS library

value: K562 cells

value: 1 cell


title: Multiplexed05_Tumor_NoGEMy_GEX


title: OCIAML3_1000cells_highcov

description: XRBS library

source_name: OCI-AML3 cells

value: OCI-AML3 cells

value: 1000 cells


title: Multiplexed04_Tumor_NoGEMy_HTO

description: Multiplexed04_Tumor_NoGEMy_filtered_feature_bc_matrix.h5

source_name: Tumor No Treatment 1+2


title: ATAC-seq from right cardiac atrium (ENCLB741WSM)

description:
https://www.encodeproject.org/experiments/ENCSR213YPO/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human right cardiac atrium
experiment encode accession: ENCSR213YPO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB741WSM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (60 years) right cardiac atrium tissue, preserved by cryopreservation

value: right cardiac atrium

value: tissue

tag: Sex

value: male

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: 60 year

value: ENCBS401BIU at ENCODE; https://www.encodeproject.org/ENCBS401BIU/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: ATAC-seq from right cardiac atrium (ENCLB893GWV)

description:
https://www.encodeproject.org/experiments/ENCSR213YPO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human right cardiac atrium
experiment encode accession: ENCSR213YPO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-10-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB893GWV
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

tag: dev stage

value: Yiing Lin, MD, PhD


title: OCIAML3_100cells_lowcov

description: XRBS library

value: 100 cells


title: OCIAML3_10ng_dmso

description: XRBS library

value: 10ng purified DNA

value: DMSO


title: Multiplexed03_NoTumor_GEMy_HTO

description: Multiplexed03_NoTumor_GEMy_filtered_feature_bc_matrix.h5

source_name: No Tumor + IL12-GEMy 1+2

value: Lung

value: Naïve


title: Multiplexed04_Tumor_NoGEMy_GEX

value: M3-9-M Tumor-Bearing

value: No Treatment


title: Multiplexed03_NoTumor_GEMy_GEX


title: Multiplexed02_NoTumor_NoGEMy_HTO

description: Multiplexed02_NoTumor_NoGEMy_filtered_feature_bc_matrix.h5

source_name: No Tumor No Treatment 3+4


title: ATAC-seq from fallopian tube (ENCLB022QIU)

description:
https://www.encodeproject.org/experiments/ENCSR212LAZ/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human fallopian tube
experiment encode accession: ENCSR212LAZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB022QIU
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult (59 years) fallopian tube tissue, preserved by flash-freezing

value: fallopian tube

value: female

value: DM:yes; HTN:yes; CAD:no

value: adult

tag: age

value: 59 year

value: Michael Snyder, Stanford

value: ENCBS960SON at ENCODE; https://www.encodeproject.org/ENCBS960SON/

value: Derived from ENCODE donor ENCDO856ZOJ; https://www.encodeproject.org/ENCDO856ZOJ/


title: OCIAML3_10ng_lowcov

description: XRBS library

value: OCI-AML3 cells


title: ATAC-seq from fallopian tube (ENCLB400DMG)

description:
https://www.encodeproject.org/experiments/ENCSR212LAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human fallopian tube
experiment encode accession: ENCSR212LAZ
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB400DMG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

tag: lab

value: Yiing Lin, MD, PhD


title: HL60_10ng_dmso

description: XRBS library

value: HL-60 cells

value: 10ng purified DNA


title: Multiplexed01_NoTumor_NoGEMy_HTO

description: Multiplexed01_NoTumor_NoGEMy_filtered_feature_bc_matrix.h5

source_name: No Tumor No Treatment 1+2

value: Lung


title: Kasumi1_1000cells_highcov

description: XRBS library

source_name: Kasumi-1 cells

value: Kasumi-1 cells

value: 1000 cells


title: Kasumi1_1000cells_lowcov

description: XRBS library


title: Kasumi1_10ng_lowcov

description: XRBS library


title: Multiplexed02_NoTumor_NoGEMy_GEX

value: Naïve

value: No Treatment


title: Multiplexed01_NoTumor_NoGEMy_GEX

extract_protocol: Lungs were perfused with PBS and inflated with digestion medium (HBSS supplemented with 1 mg/mL collagenase I, 20 μg/mL DNAse I and Dispase II). Single-cell suspensions were prepared by finely mincing tissues with a scalpel and incubating the tissue on a shaker at 37°C for 20 minutes in 1 mL of digestion media. Tissue was passed through a 70 μM mesh strainer and washed with collection media twice. Cell suspensions were labeled with TotalSeqA hashtag oligo antibodies (BioLegend) before being combined for multiplexed loading on the 10x Genomics Chromium instrument using 3’ v3 chemistry. Libraries were constructed according to 10x Genomics User Guide (Chromium 3' v3) with a modification to include antibody cell labeling barcode libraries according to Stoeckius et al, 2018.Libraries were constructed according to 10x Genomics User Guide (Chromium 3' v3) with a modification to include antibody cell labeling barcode libraries according to Stoeckius et al, 2018.


title: K562_1000cells_highcov

description: XRBS library

value: K562 cells


title: K562_1000cells_lowcov

description: XRBS library


title: ATAC-seq from heart right ventricle (ENCLB955QQG)

description:
https://www.encodeproject.org/experiments/ENCSR204SMO/
***************
biological replicate number: 1
technical replicate number: 1
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR204SMO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB955QQG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (46 years) heart right ventricle tissue, preserved by cryopreservation

value: heart right ventricle

value: male

value: Arrhythmogenic right ventricular cardiomyopathy

value: 46 year

tag: source

value: Shin Lin

value: ENCBS763SVQ at ENCODE; https://www.encodeproject.org/ENCBS763SVQ/

value: Derived from ENCODE donor ENCDO014LAW; https://www.encodeproject.org/ENCDO014LAW/


title: ATAC-seq from heart right ventricle (ENCLB508UGM)

description:
https://www.encodeproject.org/experiments/ENCSR204SMO/
***************
biological replicate number: 1
technical replicate number: 2
description: ATAC-seq on human heart right ventricle
experiment encode accession: ENCSR204SMO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2020-08-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB508UGM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: tissue

value: adult

value: Michael Snyder, Stanford

tag: link


title: gso30.IFNAR.N.HK.24h.4

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Title code = experiment.genotype.treatment.infection.infectionTime.mouse

data_processing:
Perform initial quality assessment using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) version 0.11.9
Read ends consisting of 50 or more of the same nucleotide were removed.
Reads were aligned to the mouse genome using GSNAP version 2018-07-04 (http://research-pub.gene.com/gmap/) called with args: gsnap.avx2 -N 1 -t 23 -D /gmapdb -d mm10ex_MTb -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 --format=sam
Feature counts were extracted from gsnap outputs using the featureCounts software (http://bioinf.wehi.edu.au/featureCounts/) part of Subread package v1.5.2
Differential expression of genes was calculated using edgeR (http://bioconductor.org/packages/edgeR/) version 3.26.8
Genome_build: mm10 + H37Rv Mtb
Supplementary_files_format_and_content: a .tsv with rows of raw counts of all genes (identified by MGI name in "gene" column and Ensembl stable ID in "Geneid" column) detected in at least 2 samples for each sample as columns (sample titles are column headers)

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow was harvested from femurs and bone marrow derived macrophages differentiated in RPMI + 50 ng/mL rM-CSF for 6 days before plating.

extract_protocol:
Cells were lysed in TRIzol reagent and frozen at -80. TRIzol was thawed and total RNA extracted using Zymo Research Direct-zol extraction kits according to manufacturer's instruction, including an on-column DNase treatment.
For samples with sequencing characteristic "BGI": RNA samples were sent to BGI (bgi.com) for library preparation and sequencing. The BGI BV01 library prep was used and then the libraries were sequenced on their DNBSEQ-G400 platform. For samples with sequencing characteristic "Psomagen": RNA samples were sent to Psomagen (psomagen.com) for library preparation and sequencing. The Illumina TruSeq stranded kit was used for library prep and then the libraries were sequenced on an Illumina NovaSeq6000 S4.

treatment_protocol: Conditions had 2 possible interventions, treatment with either recombinant IFNbeta (500 U/mL) or media for four hours, and then infection with either live or heat-killed H37Rv (Mycobacterium tuberculosis strain) (at an MOI 10) or mock-infected for 4 or 24 hours before RNA collection.

value: M-CSF differentiated bone marrow derived macrophages

tag: experiment

value: IFNAR KO

value: Untreated

tag: infection

value: Heat killed H37Rv

tag: hour post infection

tag: mouse identifier

tag: sequencing

value: Psomagen


title: OCIAML3_10ng_decitabine

description: XRBS library

tag: cell line

value: OCI-AML3 cells

tag: input

value: 10ng purified DNA

value: Decitabine


title: gso30.IFNAR.N.Rv.24h.4

tag: cell type

tag: genotype

value: Live H37Rv


title: gso30.IFNAR.N.HK.4h.4

tag: treatment


title: mesenchymal stem/progenitor cells of cKO mouse rep4 [26]

description: biological replicate 4

data_processing:
Sequencing reads were trimmed for bases with base quality score less than 20
Trimmed sequencing reads were aligned to mouse transcriptome mm10 using HISAT2
Transcript abundances were estimated by HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated file

extract_protocol:
Bone marrow cells were digested and harvested. Stromal cells were enriched by depleting hematopoietic cells with biotin-conjugated CD45 and Ter119 antibodies, and Dynabeads® Biotin Binder (Invitrogen #11047). CD45- Ter119- CD31- CD144- PDGFRα+ SCF-GFP+ cells were sorted into 350 μL RLT plus buffer with 3.5 μL β-mercaptoethanol. RNA was extracted using the RNeasy® Plus Micro Kit (Qiagen #74034).
Libraries were prepared after Poly A selection

tag: strain background

value: Flk2-cre+ Cxcr4fl/fl

value: 6 weeks

tag: tissue

value: Bone marrow

value: mesenchymal stem/progenitor cells


title: K562_10ng_rep1

description: XRBS library

source_name: K562 cells

value: K562 cells


title: K562_100cells_lowcov

description: XRBS library

value: 100 cells


title: OCIAML3_1000cells_lowcov

description: XRBS library

value: 1000 cells


title: mesenchymal stem/progenitor cells of cKO mouse rep3 [67]

description: biological replicate 3


title: K562_10ng_lowcov

description: XRBS library


title: gso30.IFNAR.N.Rv.4h.4


title: K562_10ng_nobiotin

description: XRBS library


title: K562_10ng_rep2

description: XRBS library


title: gso30.IFNAR.N.N.24h.4

value: Mock infected


title: gso30.IFNAR.N.N.4h.4

value: M-CSF differentiated bone marrow derived macrophages


title: gso30.IFNAR.N.Rv.4h.3

value: IFNAR KO


title: gso30.IFNAR.N.HK.24h.3

value: Untreated


title: gso30.IFNAR.N.Rv.24h.3