title: Photoreceptor_H3K4me3_Rep3[CUT&Tag]

city: West Lafayette

first: Vikki

middle: M

last: Weake

state: Indiana

address: 175 S University St

department: Biochemistry

institute: Purdue University

data_processing:
Library strategy: CUT&Tag
Sanger/Illumina 1.9 used for base calling
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:75. Additionally, Omni-ATAC and CUT&Tag reads included  HEADCROP:10, and CROP:50 only for Omni-ATAC
For RNA-seq, cleaned reads were mapped to Drosophila melanogaster genome version dm6 using STAR with settings: --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
For Omni-ATAC, ChIP-seq and CUT&Tag, cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 with settings: --sensitive
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Bigwig files were generated using deepTools subpackage bamCoverage, and bigwig files were analyzed using multiBigwigSummary, computeMatrix, plotCorrelation, plotProfile and plotHeatmap.  Dm6 refGene GTF file was used for all analysis, available at UCSC
Differential expression analysis was performed using DESeq2. Peak calling was performed with MACS2 and peak annotation was performed using HOMER.
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6

organism: Drosophila melanogaster

source_name: Retina

growth_protocol: Flies (genotype: w;;P{w[+mC]=[UAS-GFP-Msp300KASH}attP2, P{ry[+t7.2]=rh1-GAL4}3, ry[506]) were raised at 12:12 light:dark cycle at 25 degrees C on standard fly food. Following eclosion (day 1), they were aged for 10 with transfer to new food every other day.

extract_protocol:
Male flies were harvested at indicated time point and heads were removed by freezing the flies in liquid nitrogen followed by five rounds of vortexing and freezing. RNA was extracted from isolated GFP-tagged photoreceptor nuclei using the method described in this manuscript
ChIP-seq libraries were made with Nugen Ovation Ultralow V2 using 2 ng of DNA as starting material. CUT&Tag librares were made following Epicypher protocol, including the IDT adapters, RNA-seq libraries were made with Nugen SoLo RNAseq system using 10 ng RNA as starting material. ATAC-seq libraries were made using IDT for Illumina primers Set A

tag: cell-type

value: Photoreceptor neuron

value: day 10 post eclosion

value: male

tag: genotype

tag: antibody


title: Photoreceptor_H3K4me3_Rep4[CUT&Tag]

status: Public on May 23 2021

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: age

tag: Sex


title: Photoreceptor_H3K4me3_Rep1[CUT&Tag]


title: Photoreceptor_H3K4me3_Rep2[CUT&Tag]


title: Histone ChIP-seq from middle frontal area 46 (ENCLB132ZZJ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR965CIV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR965CIV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR347KLR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB132ZZJ
size range: 200-600

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

organism: Homo sapiens

source_name: Homo sapiens male adult (86 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

tag: biosample encode accession

tag: dev stage

value: adult

value: 86 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Rush University

tag: link

value: ENCBS940YCN at ENCODE; https://www.encodeproject.org/ENCBS940YCN/

value: Derived from ENCODE donor ENCDO666UNK; https://www.encodeproject.org/ENCDO666UNK/


title: H3K27ac-DEX2-ChIP-seq

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

country: China

institute: Nanjing University

data_processing:
ChIP-seq clean reads were aligned to hg19 or hg38 genome and call peaks use Macs2.
Genome_build: hg19,hg38
Supplementary_files_format_and_content: bed, bedgraph, hic

source_name: Podocyte

growth_protocol: The cells grew at 33°and differentiated at 37°

extract_protocol: libraries were constructed according to  the Illumina instruction

treatment_protocol: treat with 1uM DEX for 5 days or 1h

tag: chip antibody

value: Abcam, ab4729

tag: treatment

value: DEX 5 days

tag: tissue

value: Podocyte


title: Histone ChIP-seq from middle frontal area 46 (ENCLB665OYJ)

description:
https://www.encodeproject.org/experiments/ENCSR965CIV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR965CIV
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR347KLR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB665OYJ
size range: 200-600


title: TF ChIP-seq from nephron (ENCLB750TGR)

description:
https://www.encodeproject.org/experiments/ENCSR966OUM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on nephron female embryo (5 days) originated from H9
experiment encode accession: ENCSR966OUM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR008HBN
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB750TGR
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: nephron

value: organoid

tag: description

value: H9 derived nephron organoid 21 days

value: female

tag: health state

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: Histone ChIP-seq from middle frontal area 46 (ENCLB784EKD)

description:
https://www.encodeproject.org/experiments/ENCSR957YLX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR957YLX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB784EKD
size range: 200-600

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue with Alzheimer's disease, Cognitive impairment

value: middle frontal area 46

value: tissue

value: adult

value: 87 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS592YXK at ENCODE; https://www.encodeproject.org/ENCBS592YXK/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: H3K27ac-CTL2-ChIP-seq

value: Abcam, ab4729

value: NO DEX

value: Podocyte


title: Histone ChIP-seq from middle frontal area 46 (ENCLB785FDI)

description:
https://www.encodeproject.org/experiments/ENCSR957YLX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR957YLX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785FDI
size range: 200-600

value: female


title: TF ChIP-seq from nephron (ENCLB604QJK)

description:
https://www.encodeproject.org/experiments/ENCSR966OUM/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on nephron female embryo (5 days) originated from H9
experiment encode accession: ENCSR966OUM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR008HBN
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB604QJK
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: nephron

value: organoid

value: H9 derived nephron organoid 21 days

value: healthy

value: embryonic


title: Histone ChIP-seq from middle frontal area 46 (ENCLB374XVT)

description:
https://www.encodeproject.org/experiments/ENCSR943TBH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR943TBH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR613JAK
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB374XVT
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with mild cognitive impairment

value: middle frontal area 46

value: tissue

value: 90 or above year

value: ENCBS345MLG at ENCODE; https://www.encodeproject.org/ENCBS345MLG/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: GR-ChIP-seq-rep2

value: Santa Cruz Biotechnology, sc1003x

value: DEX 5 days


title: Photoreceptor_100ng_ATAC-seq

data_processing:
Sanger/Illumina 1.9 used for base calling
Raw reads were trimmed to discard adapter reads and low quality reads (Q<30) using Trimmomatic settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:75. Additionally, Omni-ATAC and CUT&Tag reads included  HEADCROP:10, and CROP:50 only for Omni-ATAC
For RNA-seq, cleaned reads were mapped to Drosophila melanogaster genome version dm6 using STAR with settings: --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
For Omni-ATAC, ChIP-seq and CUT&Tag, cleaned reads were mapped to Drosophila melanogaster genome version dm6 using Bowtie2 with settings: --sensitive
Samtools was used to convert SAM to BAM, sort and index corresponding BAM files.
Bigwig files were generated using deepTools subpackage bamCoverage, and bigwig files were analyzed using multiBigwigSummary, computeMatrix, plotCorrelation, plotProfile and plotHeatmap.  Dm6 refGene GTF file was used for all analysis, available at UCSC
Differential expression analysis was performed using DESeq2. Peak calling was performed with MACS2 and peak annotation was performed using HOMER.
Genome_build: UCSC Aug. 2014 - BDGP Release 6 + ISO1 MT/dm6

value: Photoreceptor neuron

value: mixed age

value: male


title: TF ChIP-seq from brain (ENCLB282JDI)

description:
https://www.encodeproject.org/experiments/ENCSR930SOT/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR930SOT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR553CWR
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282JDI
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female embryo (5 days) brain organoid

value: brain

value: female

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS534HJQ at ENCODE; https://www.encodeproject.org/ENCBS534HJQ/

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


title: TF ChIP-seq from brain (ENCLB651VSF)

description:
https://www.encodeproject.org/experiments/ENCSR930SOT/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR930SOT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR553CWR
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB651VSF
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: organoid

value: healthy

value: embryonic


title: Histone ChIP-seq from middle frontal area 46 (ENCLB200CFK)

description:
https://www.encodeproject.org/experiments/ENCSR935EPK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR935EPK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR394ZWY
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200CFK
size range: 200-600

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue with mild cognitive impairment

value: middle frontal area 46

value: tissue

value: adult

value: 87 year

value: Rush University

value: ENCBS401VAK at ENCODE; https://www.encodeproject.org/ENCBS401VAK/

value: Derived from ENCODE donor ENCDO354SJE; https://www.encodeproject.org/ENCDO354SJE/


title: TF ChIP-seq from brain (ENCLB927FNL)

description:
https://www.encodeproject.org/experiments/ENCSR930SOT/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR930SOT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR553CWR
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927FNL
fragmentation methods: sonication (generic)
size range: 200-600

value: brain

value: female

value: ENCBS022EUB at ENCODE; https://www.encodeproject.org/ENCBS022EUB/


title: sgRNA counts (day zero) rep1

city: Oxford

first: Thomas

last: Milne

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
Sequencing of THP1 sgRNA representation  at day 0
T0_control_rep1

data_processing:
Library strategy: amplicon DNA sequencing
Combine and merge Read 1 and 2 using BBMerge (quality score threshold = 30)
Count sgRNA sequences using CRISPRessoCount ("-t GTTTTAGAGCTAGAAATAGC")
MAGeCK-RRA v0.5.7 with CNV normalisation (based on THP-1 gene copy numbers derived from Affymetrix SNP6.0 arrays, downloaded from Cancer Cell Line Encyclopedia) and 10,000 permutations
MAGeCK-Flute v1.3.1 for volcano plots
Genome_build: TKOv3 sgRNA library
Supplementary_files_format_and_content: Normalized sgRNA read counts

source_name: Leukemia cell line (THP1)

growth_protocol: lentiviral pooled CRISPR screening with lentiCRISPRv2-TKOv3; cells grown in RPMI 1640 + 10% FBS and passaged every 72h

extract_protocol:
QIAamp DNA Blood Maxi Kit (Qiagen)
Sequencing libraries were prepared in two PCR steps, the first to enrich sgRNA regions from the genome, and the second to amplify sgRNA and attach sequencing adapters and indices (based on Aregger, M., Chandrashekhar, M., Tong, A. H. Y., Chan, K. & Moffat, J. in Methods Mol. Biol. 169–188 (2019). doi:10.1007/978-1-4939-8805-1_15)

treatment_protocol: half the transduced cells were continuously treated with venetoclax for 18 days (6 passages)

tag: cell line

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation

tag: crispr sgrna library


title: Photoreceptor_RNA-seq_Rep3

library_source: transcriptomic

molecule: nuclear RNA

tag: cell-type

value: Photoreceptor neuron

value: day 10 post eclosion

value: male


title: Photoreceptor_RNA-seq_Rep1

tag: genotype


title: Photoreceptor_RNA-seq_Rep2


title: TF ChIP-seq from brain (ENCLB588QYZ)

description:
https://www.encodeproject.org/experiments/ENCSR930SOT/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR930SOT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR553CWR
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB588QYZ
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

value: CTCF

value: organoid

value: 5 day

value: Bradley Bernstein, Broad

value: Paola Arlotta

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


title: Photoreceptor_ATAC-seq_Rep4

tag: age


title: Histone ChIP-seq from middle frontal area 46 (ENCLB734YNM)

description:
https://www.encodeproject.org/experiments/ENCSR927IOS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR927IOS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR917XOL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB734YNM
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with Alzheimer's disease

value: middle frontal area 46

value: tissue

tag: Sex

value: adult

value: 90 or above year

value: ENCBS837PKE at ENCODE; https://www.encodeproject.org/ENCBS837PKE/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB803KEW)

description:
https://www.encodeproject.org/experiments/ENCSR943TBH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR943TBH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR613JAK
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB803KEW
size range: 200-600

tag: biosample encode accession

value: female

value: Rush University

value: ENCBS345MLG at ENCODE; https://www.encodeproject.org/ENCBS345MLG/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: Photoreceptor_ATAC-seq_Rep3

value: Photoreceptor neuron

value: day 10 post eclosion

value: male


title: Control ChIP-seq from middle frontal area 46 (ENCLB410QXN)

description:
https://www.encodeproject.org/experiments/ENCSR917XOL/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR917XOL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB410QXN
size range: 200-600

tag: dev stage


title: Photoreceptor_ATAC-seq_Rep2


title: Photoreceptor_ATAC-seq_Rep1


title: Histone ChIP-seq from middle frontal area 46 (ENCLB838TFL)

description:
https://www.encodeproject.org/experiments/ENCSR914RMX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR914RMX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR638CSE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB838TFL
size range: 200-600

tag: lab

value: ENCBS033DPJ at ENCODE; https://www.encodeproject.org/ENCBS033DPJ/

value: Derived from ENCODE donor ENCDO153NUY; https://www.encodeproject.org/ENCDO153NUY/


title: Histone ChIP-seq from left lung (ENCLB365GPB)

description:
https://www.encodeproject.org/experiments/ENCSR510RPC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on left lung tissue female child (16 years)
experiment encode accession: ENCSR510RPC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR650AIN
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB365GPB
size range: 200-600

source_name: Homo sapiens female child (16 years) left lung tissue

value: left lung

value: child

value: 16 year

value: Bradley Bernstein, Broad

tag: source

value: Shin Lin

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

value: ENCBS892NYC at ENCODE; https://www.encodeproject.org/ENCBS892NYC/

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


title: Histone ChIP-seq from left lung (ENCLB813QQQ)

description:
https://www.encodeproject.org/experiments/ENCSR510RPC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on left lung tissue female child (16 years)
experiment encode accession: ENCSR510RPC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR650AIN
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813QQQ
size range: 200-600

value: tissue

value: female

tag: link


title: Histone ChIP-seq from left lung (ENCLB085HNL)

description:
https://www.encodeproject.org/experiments/ENCSR904KDP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on left lung tissue female child (16 years)
experiment encode accession: ENCSR904KDP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR650AIN
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB085HNL
size range: 200-600


title: Photoreceptor_H3K36me3_Rep3


title: Photoreceptor_H3K36me3_Rep2


title: Histone ChIP-seq from middle frontal area 46 (ENCLB008FVZ)

description:
https://www.encodeproject.org/experiments/ENCSR935EPK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR935EPK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR394ZWY
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB008FVZ
size range: 200-600

value: middle frontal area 46

value: adult

value: 87 year

value: Rush University

value: ENCBS401VAK at ENCODE; https://www.encodeproject.org/ENCBS401VAK/

value: Derived from ENCODE donor ENCDO354SJE; https://www.encodeproject.org/ENCDO354SJE/


title: Histone ChIP-seq from left lung (ENCLB595MDM)

description:
https://www.encodeproject.org/experiments/ENCSR904KDP/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on left lung tissue female child (16 years)
experiment encode accession: ENCSR904KDP
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR650AIN
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB595MDM
size range: 200-600


title: Photoreceptor_50ng_ATAC-seq

value: Photoreceptor neuron

value: mixed age

value: male


title: Photoreceptor_H3K36me3_Rep4

value: day 10 post eclosion


title: Photoreceptor_H3K4me3_Rep4


title: Histone ChIP-seq from middle frontal area 46 (ENCLB667XNN)

description:
https://www.encodeproject.org/experiments/ENCSR901ZXU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR901ZXU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR291VCJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB667XNN
size range: 200-600

source_name: Homo sapiens female adult (88 years) middle frontal area 46 tissue

value: 88 year

value: Bradley Bernstein, Broad

value: ENCBS844HXF at ENCODE; https://www.encodeproject.org/ENCBS844HXF/

value: Derived from ENCODE donor ENCDO669IVL; https://www.encodeproject.org/ENCDO669IVL/


title: Photoreceptor_H3K36me3_Rep1


title: Histone ChIP-seq from middle frontal area 46 (ENCLB423PTK)

description:
https://www.encodeproject.org/experiments/ENCSR901ZXU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR901ZXU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR291VCJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB423PTK
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB534IWU)

description:
https://www.encodeproject.org/experiments/ENCSR927IOS/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR927IOS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR917XOL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB534IWU
size range: 200-600

value: 90 or above year

value: ENCBS837PKE at ENCODE; https://www.encodeproject.org/ENCBS837PKE/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: Photoreceptor_H3K4me3_Rep2


title: TF ChIP-seq from heart right ventricle (ENCLB800CUN)

description:
https://www.encodeproject.org/experiments/ENCSR505RTK/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on heart right ventricle female adult (46 years)
experiment encode accession: ENCSR505RTK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR519UXW
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800CUN
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (46 years) heart right ventricle tissue, preserved by flash-freezing

value: CTCF

value: heart right ventricle

value: tissue

value: female

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

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS824CUX at ENCODE; https://www.encodeproject.org/ENCBS824CUX/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: TF ChIP-seq from progenitor cell of endocrine pancreas (ENCLB449AKL)

description:
https://www.encodeproject.org/experiments/ENCSR901NIN/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR901NIN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR077RBB
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB449AKL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female embryo (5 days) progenitor of endocrine pancreas in vitro differentiated cells originated from progenitor cell of endocrine pancreas

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/

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


title: Photoreceptor_H3K4me3_Rep3

value: Photoreceptor neuron

value: day 10 post eclosion

value: male


title: Control ChIP-seq from middle frontal area 46 (ENCLB323QKS)

description:
https://www.encodeproject.org/experiments/ENCSR917XOL/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR917XOL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB323QKS
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS837PKE at ENCODE; https://www.encodeproject.org/ENCBS837PKE/

value: Derived from ENCODE donor ENCDO201EUI; https://www.encodeproject.org/ENCDO201EUI/


title: Photoreceptor_H3K4me3_Rep1


title: Photoreceptor-H3_Rep4


title: TF ChIP-seq from heart right ventricle (ENCLB714SJK)

description:
https://www.encodeproject.org/experiments/ENCSR505RTK/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on heart right ventricle female adult (46 years)
experiment encode accession: ENCSR505RTK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR519UXW
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB714SJK
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: heart right ventricle

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

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS824CUX at ENCODE; https://www.encodeproject.org/ENCBS824CUX/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: TF ChIP-seq from progenitor cell of endocrine pancreas (ENCLB601KYC)

description:
https://www.encodeproject.org/experiments/ENCSR901NIN/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas
experiment encode accession: ENCSR901NIN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR077RBB
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB601KYC
fragmentation methods: sonication (generic)
size range: 200-600

value: progenitor cell of endocrine pancreas

value: in vitro differentiated cells

value: WA09 derived pancreatic progenitor cells

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS825BIV at ENCODE; https://www.encodeproject.org/ENCBS825BIV/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB528YXH)

description:
https://www.encodeproject.org/experiments/ENCSR914RMX/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR914RMX
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR638CSE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB528YXH
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS033DPJ at ENCODE; https://www.encodeproject.org/ENCBS033DPJ/

value: Derived from ENCODE donor ENCDO153NUY; https://www.encodeproject.org/ENCDO153NUY/


title: Photoreceptor-H3_Rep2

value: Photoreceptor neuron

value: day 10 post eclosion

value: male


title: Histone ChIP-seq from middle frontal area 46 (ENCLB684RHO)

description:
https://www.encodeproject.org/experiments/ENCSR901EDL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR901EDL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR557HEX
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB684RHO
size range: 200-600

source_name: Homo sapiens male adult (89 years) middle frontal area 46 tissue with mild cognitive impairment

value: 89 year

value: ENCBS273TDM at ENCODE; https://www.encodeproject.org/ENCBS273TDM/

value: Derived from ENCODE donor ENCDO697SWU; https://www.encodeproject.org/ENCDO697SWU/


title: Photoreceptor-H3_Rep1


title: Histone ChIP-seq from middle frontal area 46 (ENCLB366ZCE)

description:
https://www.encodeproject.org/experiments/ENCSR901EDL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR901EDL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR557HEX
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB366ZCE
size range: 200-600


title: Photoreceptor_InputDNA_Rep4


title: Histone ChIP-seq from pancreas (ENCLB523CWO)

description:
https://www.encodeproject.org/experiments/ENCSR499GKR/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27me3 ChIP-seq on pancreas tissue female adult (41 years)
experiment encode accession: ENCSR499GKR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR462ZQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB523CWO
size range: 200-600

source_name: Homo sapiens female adult (41 years) pancreas tissue, preserved by flash-freezing

value: pancreas

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

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS212NYF at ENCODE; https://www.encodeproject.org/ENCBS212NYF/

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


title: Photoreceptor_InputDNA_Rep2


title: Histone ChIP-seq from pancreas (ENCLB083YEX)

description:
https://www.encodeproject.org/experiments/ENCSR499GKR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on pancreas tissue female adult (41 years)
experiment encode accession: ENCSR499GKR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR462ZQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB083YEX
size range: 200-600

value: tissue

value: female

value: adult


title: Histone ChIP-seq from middle frontal area 46 (ENCLB702XXJ)

description:
https://www.encodeproject.org/experiments/ENCSR497URO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR497URO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR638CSE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB702XXJ
size range: 200-600

value: middle frontal area 46

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS033DPJ at ENCODE; https://www.encodeproject.org/ENCBS033DPJ/

value: Derived from ENCODE donor ENCDO153NUY; https://www.encodeproject.org/ENCDO153NUY/


title: Photoreceptor_InputDNA_Rep1

value: Photoreceptor neuron

value: day 10 post eclosion

value: male


title: Histone ChIP-seq from middle frontal area 46 (ENCLB584CSZ)

description:
https://www.encodeproject.org/experiments/ENCSR495HIT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR495HIT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR714GKF
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584CSZ
size range: 200-600

source_name: Homo sapiens male adult (71 years) middle frontal area 46 tissue

value: 71 year

value: ENCBS552CLR at ENCODE; https://www.encodeproject.org/ENCBS552CLR/

value: Derived from ENCODE donor ENCDO570AKP; https://www.encodeproject.org/ENCDO570AKP/


title: 24_Ash1LKO_NPC_differentiation_T24_rep4

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description: nerual progenitor cell differentiation medium 24 hrs

data_processing:
For the RNA-Seq data analysis, all sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using Tophat2.
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 1.5-fold RPKM change between samples.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: Neural progenetor cell isolated from mouse brain

growth_protocol: Neurospheres are cultured in the Neurobasal medium (Life Technologies) that was supplemented with 1x B27 supplement (Gibco), 1x GlutaMAX (Life Technologies), 20 ng/ml murine epithelial growth factor (Peprotech), 20 ng/ml basic fibroblast growth factor (Peprotech), and 100U/ml penicillin/streptomycin (Life Technologies). Monolayer neural progenitor cells are cultured on the Poly-L-Ornithine (R&D systems) and Laminin (Corning)-coated plates in the same NPC culture medium.

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA (1 µg) was used to generate RNA-seq library using NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England BioLabs, Inc) according to the manufacturer’s instructions. Adapter-ligated cDNA was amplified by PCR and followed by size selection using agarose gel electrophoresis. The DNA was purified using Qiaquick gel extraction kit (Qiagen) and quantified both with an Agilent Bioanalyzer and Invitrogen Qubit. The libraries were diluted to a working concentration of 10nM prior to sequencing. Sequencing on an Illumina HiSeq4000 instrument was carried out by the Genomics Core Facility at Michigan State University.

treatment_protocol: To induce NPCs differentiation, the NPC monolayer cells were gently washed with PBS for 3 times and cultured under the Neurobasal medium supplemented with 1x N2 supplement (Giboco), 1x GlutaMAX (Life Technologies).

tag: cell type

value: Neural progenetor

value: Ash1L knockout

tag: strain

value: B6 strain

value: differentiation medium 24 hrs


title: 23_Ash1LKO_NPC_differentiation_T24_rep3

tag: treatment


title: 22_Ash1LKO_NPC_differentiation_T24_rep2


title: Photoreceptor-H3_Rep3

source_name: Retina


title: Histone ChIP-seq from middle frontal area 46 (ENCLB552TKH)

description:
https://www.encodeproject.org/experiments/ENCSR495HIT/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR495HIT
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR714GKF
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB552TKH
size range: 200-600

value: tissue

value: adult


title: TF ChIP-seq from excitatory neuron (ENCLB971YPE)

description:
https://www.encodeproject.org/experiments/ENCSR489QDF/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on excitatory neuron
experiment encode accession: ENCSR489QDF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR408LXD
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971YPE
fragmentation methods: sonication (generic)
size range: 200-600

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

extract_protocol: not provided

value: CTCF

value: excitatory neuron

value: in vitro differentiated cells

tag: description

value: PGP1 derived excitatory cortical neurons

value: 53 year

value: George Church

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

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


title: 21_Ash1LKO_NPC_differentiation_T24_rep1


title: 20_Ash1LKO_NPC_differentiation_T12_rep4

description: nerual progenitor cell differentiation medium 12 hrs

value: differentiation medium 12 hrs


title: 17_Ash1LKO_NPC_differentiation_T12_rep1


title: 19_Ash1LKO_NPC_differentiation_T12_rep3


title: 18_Ash1LKO_NPC_differentiation_T12_rep2


title: TF ChIP-seq from excitatory neuron (ENCLB200LAA)

description:
https://www.encodeproject.org/experiments/ENCSR489QDF/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on excitatory neuron
experiment encode accession: ENCSR489QDF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR408LXD
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB200LAA
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: Bradley Bernstein, Broad


title: TF ChIP-seq from excitatory neuron (ENCLB039IFQ)

description:
https://www.encodeproject.org/experiments/ENCSR489QDF/
***************
biological replicate number: 1
technical replicate number: 4
description: CTCF ChIP-seq on excitatory neuron
experiment encode accession: ENCSR489QDF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR408LXD
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039IFQ
fragmentation methods: sonication (generic)
size range: 200-600


title: 16_Ash1LKO_NPC_differentiation_T0_rep4

description: nerual progenitor cell differentiation medium 0 hrs

value: Neural progenetor

value: differentiation medium 0 hrs


title: Histone ChIP-seq from middle frontal area 46 (ENCLB950RMA)

description:
https://www.encodeproject.org/experiments/ENCSR889TEU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR889TEU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB950RMA
size range: 200-600

value: middle frontal area 46

value: female

value: 87 year

value: Rush University

value: ENCBS592YXK at ENCODE; https://www.encodeproject.org/ENCBS592YXK/

value: Derived from ENCODE donor ENCDO940VNT; https://www.encodeproject.org/ENCDO940VNT/


title: Histone ChIP-seq from pancreas (ENCLB527QGM)

description:
https://www.encodeproject.org/experiments/ENCSR499GKR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on pancreas tissue female adult (41 years)
experiment encode accession: ENCSR499GKR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR462ZQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB527QGM
size range: 200-600

value: pancreas

value: tissue

tag: health state

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

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS212NYF at ENCODE; https://www.encodeproject.org/ENCBS212NYF/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB070QPC)

description:
https://www.encodeproject.org/experiments/ENCSR889TEU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR889TEU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR376YUP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB070QPC
size range: 200-600

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from middle frontal area 46 (ENCLB671TUH)

description:
https://www.encodeproject.org/experiments/ENCSR888NRO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR888NRO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR698YQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB671TUH
size range: 200-600

source_name: Homo sapiens female adult (74 years) middle frontal area 46 tissue with Alzheimer's disease

value: 74 year

value: ENCBS242LMI at ENCODE; https://www.encodeproject.org/ENCBS242LMI/

value: Derived from ENCODE donor ENCDO907CMO; https://www.encodeproject.org/ENCDO907CMO/


title: Photoreceptor_InputDNA_Rep3

value: Photoreceptor neuron

value: day 10 post eclosion

value: male


title: 14_Ash1LKO_NPC_differentiation_T0_rep2

value: Neural progenetor

value: Ash1L knockout

value: B6 strain

value: differentiation medium 0 hrs


title: 15_Ash1LKO_NPC_differentiation_T0_rep3


title: Histone ChIP-seq from middle frontal area 46 (ENCLB772IEE)

description:
https://www.encodeproject.org/experiments/ENCSR497URO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR497URO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR638CSE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB772IEE
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 90 or above year

value: Rush University

value: ENCBS033DPJ at ENCODE; https://www.encodeproject.org/ENCBS033DPJ/

value: Derived from ENCODE donor ENCDO153NUY; https://www.encodeproject.org/ENCDO153NUY/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB385SFZ)

description:
https://www.encodeproject.org/experiments/ENCSR888NRO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR888NRO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR698YQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385SFZ
size range: 200-600

value: 74 year

value: Bradley Bernstein, Broad

value: ENCBS242LMI at ENCODE; https://www.encodeproject.org/ENCBS242LMI/


title: 13_Ash1LKO_NPC_differentiation_T0_rep1


title: 12_wtNPC_differentiation_T24_rep4

value: wild-type

value: differentiation medium 24 hrs


title: Histone ChIP-seq from adrenal gland (ENCLB488KNU)

description:
https://www.encodeproject.org/experiments/ENCSR886FKD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR886FKD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB488KNU
size range: 200-600

source_name: Homo sapiens female adult (41 years) adrenal gland tissue, preserved by flash-freezing

value: adrenal gland

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

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

value: ENCBS491ORA at ENCODE; https://www.encodeproject.org/ENCBS491ORA/

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


title: Histone ChIP-seq from adrenal gland (ENCLB554YMU)

description:
https://www.encodeproject.org/experiments/ENCSR886FKD/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K9me3 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR886FKD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB554YMU
size range: 200-600

source_name: Homo sapiens female adult (41 years) adrenal gland tissue

value: tissue

value: female

value: adult

value: Shin Lin

value: ENCBS648AMG at ENCODE; https://www.encodeproject.org/ENCBS648AMG/


title: 10_wtNPC_differentiation_T24_rep2

value: Neural progenetor

value: B6 strain


title: 9_wtNPC_differentiation_T24_rep1


title: 11_wtNPC_differentiation_T24_rep3


title: Histone ChIP-seq from adrenal gland (ENCLB893XBX)

description:
https://www.encodeproject.org/experiments/ENCSR886FKD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR886FKD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB893XBX
size range: 200-600

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from adrenal gland (ENCLB597KGR)

description:
https://www.encodeproject.org/experiments/ENCSR886FKD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on adrenal gland tissue female adult (41 years)
experiment encode accession: ENCSR886FKD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB597KGR
size range: 200-600


title: TF ChIP-seq from excitatory neuron (ENCLB445STV)

description:
https://www.encodeproject.org/experiments/ENCSR489QDF/
***************
biological replicate number: 1
technical replicate number: 3
description: CTCF ChIP-seq on excitatory neuron
experiment encode accession: ENCSR489QDF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR408LXD
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB445STV
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: excitatory neuron

value: in vitro differentiated cells

value: PGP1 derived excitatory cortical neurons

value: male

value: 53 year

value: George Church

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

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB562UEL)

description:
https://www.encodeproject.org/experiments/ENCSR882ZTE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR882ZTE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR714GKF
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562UEL
size range: 200-600

value: middle frontal area 46

value: tissue

value: 71 year

value: Rush University

value: ENCBS552CLR at ENCODE; https://www.encodeproject.org/ENCBS552CLR/

value: Derived from ENCODE donor ENCDO570AKP; https://www.encodeproject.org/ENCDO570AKP/


title: 7_wtNPC_differentiation_T12_rep3

value: Neural progenetor

value: wild-type

value: B6 strain

value: differentiation medium 12 hrs


title: 8_wtNPC_differentiation_T12_rep4


title: 5_wtNPC_differentiation_T12_rep1


title: 4_wtNPC_differentiation_T0_rep4

value: differentiation medium 0 hrs


title: 6_wtNPC_differentiation_T12_rep2


title: TF ChIP-seq from heart right ventricle (ENCLB232SNY)

description:
https://www.encodeproject.org/experiments/ENCSR473DVS/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on heart right ventricle male adult (40 years)
experiment encode accession: ENCSR473DVS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR839VEU
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB232SNY
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (40 years) heart right ventricle tissue, preserved by flash-freezing

value: CTCF

value: heart right ventricle

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

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS480XPH at ENCODE; https://www.encodeproject.org/ENCBS480XPH/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB033AKS)

description:
https://www.encodeproject.org/experiments/ENCSR882ZTE/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR882ZTE
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR714GKF
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB033AKS
size range: 200-600

value: middle frontal area 46

value: tissue

value: male

value: 71 year

value: Bradley Bernstein, Broad

value: Rush University


title: TF ChIP-seq from heart right ventricle (ENCLB293JMQ)

description:
https://www.encodeproject.org/experiments/ENCSR473DVS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on heart right ventricle male adult (40 years)
experiment encode accession: ENCSR473DVS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR839VEU
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB293JMQ
fragmentation methods: sonication (generic)
size range: 200-600


title: TF ChIP-seq from H9 (ENCLB862VLL)

description:
https://www.encodeproject.org/experiments/ENCSR871MKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR871MKQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR686HII
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB862VLL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens H9 cell line originated from H9

tag: line

value: cell line

value: WA09 ES cells

value: female

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS713BMM at ENCODE; https://www.encodeproject.org/ENCBS713BMM/

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


title: 3_wtNPC_differentiation_T0_rep3

description: nerual progenitor cell differentiation medium 0 hrs

value: Neural progenetor

value: wild-type

value: B6 strain

value: differentiation medium 0 hrs


title: TF ChIP-seq from H9 (ENCLB569CWY)

description:
https://www.encodeproject.org/experiments/ENCSR871MKQ/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR871MKQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR686HII
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB569CWY
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/


title: 1_wtNPC_differentiation_T0_rep1


title: 2_wtNPC_differentiation_T0_rep2


title: Y4_PreTx

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

data_processing:
Sequencing quality control was performed using FastQC and MultiQC, which revealed Nextera sequencing adapter contamination that was removed using the Trim Galore Cutadapt wrapper in paired end mode, followed by confirmation of adapter removal with FastQC.  For pathway enrichment analysis, we annotated promoter proximal peaks within ± 1000bp of the transcription start site (TSS) using TxDb.Mmusculus.UCSC.mm10.knownGene.
Rsubread was used to align samples to the mm10 genome. Rsamtools was used to sort and index output BAM files. BAM files were quality controlled by looking at the distribution of reads aligning to chromosomes and the distribution of insert sizes.
We next utilized Genrich (Harvard FAS Informatics) to call peaks in ATAC seq mode using a maximum q value threshold of 0.05 for peak calling, removing PCR duplicates and excluding reads that mapped to the mitochondrial genome and the Y chromosome. NarrowPeak files generated by Genrich were quality controlled for distribution of reads mapping to mm10 genomic regions using the R CHIPseeker package and Tx.Db.mmusculus.UCSC.mm10.knowngene annotation.
For differential ATAC-seq, a GRanges consensus peak object was generated using ChIPQC48 containing non-redundant open regions present in any sample, excluding known mm10 ATAC-seq blacklisted regions obtained from Encode (ENCFF547MET). Nucleosome free regions (<100bp fragment length) from sample BAM files were counted using FeatureCounts against the consensus peak annotation.
Sample counts were imported into a dds object using DESeq2, and exploratory data analysis was performed using rlog normalized count data and PCA. For differential peak accessibility calling between groups, we used DESeq2 using the results function and the DESeq2 estimator.
Genome_build: We used ReactomePA to test for Reactome pathway enrichment in peaks with increased relative peak accessibility in a given comparison using a log2 fold change threshold of >= 0.05 and a pvalue cutoff of 0.05.

source_name: Hematopoietic stem cells

extract_protocol:
Hematopoietic stem cells were isolated from the bone marrow of mice through a standardized process of bone marrow extraction, creation of a single cell suspension, and flow cytometry based cell sorting. Cells were lysed and transposed following the Corces et al. Nature Methods 2017 Omni-ATAC seq protocol. Transposed DNA was purifed using a Zymo 5 Clean and Concentrator kit and stored at -20 C until library preparation. Libraries were quality controlled using Qubit and Agilent Bioanalyzer.
ATAC-seq libraries were made with Nextera sequencing adapters and NEBnext Master Mix as in Corces et al. Nature Methods 2017. Libraries were purified with double-sided AMPure XP beads.

tag: age at procedure

value: 8-12 weeks

tag: transposition day

value: Male


title: TF ChIP-seq from brain (ENCLB936ASB)

description:
https://www.encodeproject.org/experiments/ENCSR467EQP/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR467EQP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR688WUZ
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB936ASB
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female embryo (5 days) brain organoid

value: brain

value: organoid

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS678HIV at ENCODE; https://www.encodeproject.org/ENCBS678HIV/


title: TF ChIP-seq from astrocyte (ENCLB266LTA)

description:
https://www.encodeproject.org/experiments/ENCSR461VHZ/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on astrocyte originated from astrocyte
experiment encode accession: ENCSR461VHZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR730VRY
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB266LTA
fragmentation methods: sonication (generic)
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: adult

value: 53 year

value: George Church

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

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


title: TF ChIP-seq from astrocyte (ENCLB752BEM)

description:
https://www.encodeproject.org/experiments/ENCSR461VHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on astrocyte originated from astrocyte
experiment encode accession: ENCSR461VHZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR730VRY
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB752BEM
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF


title: Y3_PostTx

value: 8-12 weeks


title: Y4_PostTx

value: Male


title: Y2_PostTx


title: Histone ChIP-seq from middle frontal area 46 (ENCLB813JNC)

description:
https://www.encodeproject.org/experiments/ENCSR461GYN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR461GYN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR518COE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB813JNC
size range: 200-600

source_name: Homo sapiens female adult (78 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: 78 year

value: Rush University

value: ENCBS882DOK at ENCODE; https://www.encodeproject.org/ENCBS882DOK/

value: Derived from ENCODE donor ENCDO236YSH; https://www.encodeproject.org/ENCDO236YSH/


title: Y2_PreTx


title: Y1_PreTx


title: TF ChIP-seq from H9 (ENCLB978FBZ)

description:
https://www.encodeproject.org/experiments/ENCSR871MKQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on H9 originated from H9
experiment encode accession: ENCSR871MKQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR686HII
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB978FBZ
fragmentation methods: sonication (generic)
size range: 200-600

value: cell line

value: WA09 ES cells

value: healthy

value: embryonic

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

value: ENCBS654ADT at ENCODE; https://www.encodeproject.org/ENCBS654ADT/

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


title: Y1_PostTx

value: 8-12 weeks

value: Male


title: Histone ChIP-seq from middle frontal area 46 (ENCLB515AWE)

description:
https://www.encodeproject.org/experiments/ENCSR461GYN/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR461GYN
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR518COE
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515AWE
size range: 200-600

value: middle frontal area 46

value: tissue

value: adult


title: Control ChIP-seq from mucosa of descending colon (ENCLB544IQH)

description:
https://www.encodeproject.org/experiments/ENCSR856YCA/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on mucosa of descending colon tissue male adult (40 years)
experiment encode accession: ENCSR856YCA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB544IQH
size range: 200-600

source_name: Homo sapiens male adult (40 years) mucosa of descending colon tissue

value: mucosa of descending colon

value: male

value: 40 year

value: Shin Lin

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

value: ENCBS724VYT at ENCODE; https://www.encodeproject.org/ENCBS724VYT/

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


title: O4_PreTx

value: 24 months old


title: O4_PostTx


title: Control ChIP-seq from mucosa of descending colon (ENCLB501QWB)

description:
https://www.encodeproject.org/experiments/ENCSR856YCA/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on mucosa of descending colon tissue male adult (40 years)
experiment encode accession: ENCSR856YCA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB501QWB
size range: 200-600

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from middle frontal area 46 (ENCLB661EHT)

description:
https://www.encodeproject.org/experiments/ENCSR852VZG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR852VZG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR613JAK
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB661EHT
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue with mild cognitive impairment

value: female

value: 90 or above year

value: Rush University

value: ENCBS345MLG at ENCODE; https://www.encodeproject.org/ENCBS345MLG/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB835AYF)

description:
https://www.encodeproject.org/experiments/ENCSR855NCG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR855NCG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR799VTP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB835AYF
size range: 200-600

source_name: Homo sapiens female adult (83 years) middle frontal area 46 tissue with mild cognitive impairment

value: middle frontal area 46

value: 83 year

value: ENCBS104CPK at ENCODE; https://www.encodeproject.org/ENCBS104CPK/

value: Derived from ENCODE donor ENCDO832DBZ; https://www.encodeproject.org/ENCDO832DBZ/


title: TF ChIP-seq from type B pancreatic cell (ENCLB180ZJW)

description:
https://www.encodeproject.org/experiments/ENCSR458PYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR458PYQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR394CIG
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB180ZJW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female embryo (5 days) type B pancreatic in vitro differentiated cells originated from type B pancreatic cell

value: CTCF

value: type B pancreatic cell

value: in vitro differentiated cells

value: WA09 derived insulin producing beta-like cells

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS251SEQ at ENCODE; https://www.encodeproject.org/ENCBS251SEQ/

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


title: TF ChIP-seq from brain (ENCLB507QDF)

description:
https://www.encodeproject.org/experiments/ENCSR467EQP/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on brain female embryo (5 days)
experiment encode accession: ENCSR467EQP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR688WUZ
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB507QDF
fragmentation methods: sonication (generic)
size range: 200-600

value: brain

value: organoid

value: female

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS678HIV at ENCODE; https://www.encodeproject.org/ENCBS678HIV/


title: Y3_PreTx

value: 8-12 weeks

value: Male


title: O3_PostTx

value: 24 months old


title: O1_PreTx


title: O2_PostTx


title: O2_PreTx


title: TF ChIP-seq from type B pancreatic cell (ENCLB608EJI)

description:
https://www.encodeproject.org/experiments/ENCSR458PYQ/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR458PYQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR394CIG
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB608EJI
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: type B pancreatic cell

value: in vitro differentiated cells


title: TF ChIP-seq from type B pancreatic cell (ENCLB275MCA)

description:
https://www.encodeproject.org/experiments/ENCSR458PYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR458PYQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR394CIG
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB275MCA
fragmentation methods: sonication (generic)
size range: 200-600

value: WA09 derived insulin producing beta-like cells

value: healthy

value: embryonic

value: ENCBS779FCS at ENCODE; https://www.encodeproject.org/ENCBS779FCS/


title: Control ChIP-seq from middle frontal area 46 (ENCLB979EKB)

description:
https://www.encodeproject.org/experiments/ENCSR437DCH/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR437DCH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB979EKB
size range: 200-600

value: middle frontal area 46

value: tissue

value: adult

value: 90 or above year

value: Rush University

value: ENCBS152TRC at ENCODE; https://www.encodeproject.org/ENCBS152TRC/

value: Derived from ENCODE donor ENCDO634UMA; https://www.encodeproject.org/ENCDO634UMA/


title: O1_PostTx


title: TF ChIP-seq from type B pancreatic cell (ENCLB071CDF)

description:
https://www.encodeproject.org/experiments/ENCSR458PYQ/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on type B pancreatic cell originated from type B pancreatic cell
experiment encode accession: ENCSR458PYQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR394CIG
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB071CDF
fragmentation methods: sonication (generic)
size range: 200-600

value: female

value: 5 day

value: Bradley Bernstein, Broad

value: SESCC

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


title: 3_wrky25/33_24h_rep3

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

data_processing:
1-5: STAR for genome mapping; 6: Botwie 2 for genome mapping
Genome_build: Arabidopisis: TAIR10; Marantica v3.1; Ricd: MSU7
Supplementary_files_format_and_content: 1-5: raw counts; 6: bigwig

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 1: 7-day-old Col-0  seedlings liquid grown in 1/2 MS, continuous light; 2: 7-day-old Tak1 gemma liquid grown in 1/2 B5, continuous light; 3: 7-day-old Col-0 and wrky25/33 ko mutant  seedlings liquid grown in 1/2 MS, continuous light; 4: 7-day-old NB seedlings grwon on 1/2 MS plates, 16/8 Light/Dark cycle; 5: 7-day-old Tak1 gemma liquid grown in 1/2 B5, continuous light; 6: 14-day-old Tak1 and respecitive WRKY 0E lines gemma liquid grown in 1/2 B5, continuous light

extract_protocol:
1-5: Plant samples were frozen in liquid nitrogen, and followed by RNA extraction using Rneasy Plant Mini Kit (Qiagen); 6: Nuclei was carried out by standard ChIP protocol, pull-down by tagRFP TRAP (Chromotek)
1-5: RNA libraries were prepared for sequencing using standard Illumina protocols; 6: Libraries were prepared according to Illumina's instructions

treatment_protocol: 1/2 Ms + 100 mM NaCl treatment for 0, 1, 3, 6, 12, 24, 48 and 72 hr

tag: tissue

value: seedlings

tag: day

tag: genotype

value: wrky25/33 ko mutant

tag: time point


title: Control ChIP-seq from middle frontal area 46 (ENCLB464PAB)

description:
https://www.encodeproject.org/experiments/ENCSR437DCH/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR437DCH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB464PAB
size range: 200-600

tag: biosample encode accession

tag: Sex

tag: age


title: 3_wrky25/33_2h_rep2


title: Histone ChIP-seq from middle frontal area 46 (ENCLB491XLX)

description:
https://www.encodeproject.org/experiments/ENCSR852VZG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR852VZG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR613JAK
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB491XLX
size range: 200-600

tag: antibody

tag: dev stage

tag: lab

tag: source

value: ENCBS345MLG at ENCODE; https://www.encodeproject.org/ENCBS345MLG/

value: Derived from ENCODE donor ENCDO660TGP; https://www.encodeproject.org/ENCDO660TGP/


title: 3_wrky25/33_24h_rep1


title: Histone ChIP-seq from pancreas (ENCLB242TSO)

description:
https://www.encodeproject.org/experiments/ENCSR423OOD/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on pancreas tissue female adult (61 years)
experiment encode accession: ENCSR423OOD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR130HAG
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB242TSO
size range: 200-600

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

value: pancreas

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

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

tag: link

value: ENCBS297KRV at ENCODE; https://www.encodeproject.org/ENCBS297KRV/

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


title: O3_PreTx

value: 24 months old

value: Male


title: 3_wrky25/33_2h_rep1


title: Histone ChIP-seq from pancreas (ENCLB273NUF)

description:
https://www.encodeproject.org/experiments/ENCSR423OOD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on pancreas tissue female adult (61 years)
experiment encode accession: ENCSR423OOD
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR130HAG
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB273NUF
size range: 200-600

value: tissue

value: female

value: adult


title: 3_wrky25/33_2h_rep3


title: Histone ChIP-seq from middle frontal area 46 (ENCLB559LRY)

description:
https://www.encodeproject.org/experiments/ENCSR855NCG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR855NCG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR799VTP
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB559LRY
size range: 200-600

value: middle frontal area 46

value: 83 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS104CPK at ENCODE; https://www.encodeproject.org/ENCBS104CPK/

value: Derived from ENCODE donor ENCDO832DBZ; https://www.encodeproject.org/ENCDO832DBZ/


title: 3_wrky25/33_24h_rep2

value: seedlings

value: wrky25/33 ko mutant


title: 3_wrky25/33_0h_rep3


title: Histone ChIP-seq from adrenal gland (ENCLB060VHC)

description:
https://www.encodeproject.org/experiments/ENCSR837CSL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on adrenal gland female adult (41 years)
experiment encode accession: ENCSR837CSL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060VHC
fragmentation methods: sonication (generic)
size range: 200-600

value: adrenal gland

value: 41 year

value: Michael Snyder, Stanford

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

value: ENCBS491ORA at ENCODE; https://www.encodeproject.org/ENCBS491ORA/

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


title: Histone ChIP-seq from adrenal gland (ENCLB646UOD)

description:
https://www.encodeproject.org/experiments/ENCSR837CSL/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27ac ChIP-seq on adrenal gland female adult (41 years)
experiment encode accession: ENCSR837CSL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB646UOD
size range: 200-600

value: tissue

value: Shin Lin

value: ENCBS648AMG at ENCODE; https://www.encodeproject.org/ENCBS648AMG/


title: Histone ChIP-seq from adrenal gland (ENCLB919DIN)

description:
https://www.encodeproject.org/experiments/ENCSR837CSL/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27ac ChIP-seq on adrenal gland female adult (41 years)
experiment encode accession: ENCSR837CSL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919DIN
size range: 200-600

value: female

value: adult

value: Yiing Lin, MD, PhD


title: 3_wrky25/33_0h_rep1


title: Histone ChIP-seq from adrenal gland (ENCLB095THJ)

description:
https://www.encodeproject.org/experiments/ENCSR837CSL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on adrenal gland female adult (41 years)
experiment encode accession: ENCSR837CSL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB095THJ
size range: 200-600

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from adrenal gland (ENCLB278KZX)

description:
https://www.encodeproject.org/experiments/ENCSR837CSL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on adrenal gland female adult (41 years)
experiment encode accession: ENCSR837CSL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR071ILJ
encode release date: 2020-09-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB278KZX
fragmentation methods: sonication (generic)
size range: 200-600


title: 3_col-0_24h_rep3


title: 3_col-0_24h_rep2


title: Histone ChIP-seq from middle frontal area 46 (ENCLB249QVM)

description:
https://www.encodeproject.org/experiments/ENCSR830EXC/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR830EXC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR698YQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB249QVM
size range: 200-600

value: middle frontal area 46

value: 74 year

value: Rush University

value: ENCBS242LMI at ENCODE; https://www.encodeproject.org/ENCBS242LMI/

value: Derived from ENCODE donor ENCDO907CMO; https://www.encodeproject.org/ENCDO907CMO/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB015FXT)

description:
https://www.encodeproject.org/experiments/ENCSR830EXC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR830EXC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR698YQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB015FXT
size range: 200-600


title: 3_col-0_24h_rep1

value: seedlings


title: Histone ChIP-seq from pancreas (ENCLB118KTS)

description:
https://www.encodeproject.org/experiments/ENCSR829EYM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on pancreas tissue female adult (41 years)
experiment encode accession: ENCSR829EYM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR462ZQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB118KTS
size range: 200-600

source_name: Homo sapiens female adult (41 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: 41 year

value: Michael Snyder, Stanford

value: ENCBS212NYF at ENCODE; https://www.encodeproject.org/ENCBS212NYF/


title: 3_col-0_2h_rep3


title: 3_col-0_2h_rep2


title: 3_col-0_2h_rep1


title: TF ChIP-seq from endodermal cell (ENCLB455RTU)

description:
https://www.encodeproject.org/experiments/ENCSR398RET/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR398RET
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR273FER
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB455RTU
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: endodermal cell

value: in vitro differentiated cells

tag: description

value: WA09 derived endoderm cells

value: healthy

value: embryonic

value: 5 day

value: SESCC

value: ENCBS958FWY at ENCODE; https://www.encodeproject.org/ENCBS958FWY/

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


title: 3_wrky25/33_0h_rep2

value: wrky25/33 ko mutant


title: TF ChIP-seq from endodermal cell (ENCLB124SMZ)

description:
https://www.encodeproject.org/experiments/ENCSR398RET/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR398RET
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR273FER
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB124SMZ
fragmentation methods: sonication (generic)
size range: 200-600

value: female

tag: health state

value: Bradley Bernstein, Broad

value: ENCBS601OTT at ENCODE; https://www.encodeproject.org/ENCBS601OTT/


title: TF ChIP-seq from endodermal cell (ENCLB284MEB)

description:
https://www.encodeproject.org/experiments/ENCSR398RET/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on endodermal cell originated from endodermal cell
experiment encode accession: ENCSR398RET
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR273FER
encode release date: 2021-04-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB284MEB
fragmentation methods: sonication (generic)
size range: 200-600


title: 3_col-0_0h_rep2

value: seedlings


title: 3_col-0_0h_rep1


title: 3_col-0_0h_rep3


title: Control ChIP-seq from middle frontal area 46 (ENCLB198FBN)

description:
https://www.encodeproject.org/experiments/ENCSR394ZWY/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR394ZWY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB198FBN
size range: 200-600

source_name: Homo sapiens female adult (87 years) middle frontal area 46 tissue with mild cognitive impairment

value: middle frontal area 46

value: tissue

value: adult

value: 87 year

value: Rush University

value: ENCBS401VAK at ENCODE; https://www.encodeproject.org/ENCBS401VAK/

value: Derived from ENCODE donor ENCDO354SJE; https://www.encodeproject.org/ENCDO354SJE/


title: Control ChIP-seq from middle frontal area 46 (ENCLB345CJI)

description:
https://www.encodeproject.org/experiments/ENCSR822YWX/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (86 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR822YWX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB345CJI
size range: 200-600

source_name: Homo sapiens female adult (86 years) middle frontal area 46 tissue with Cognitive impairment

value: 86 year

value: ENCBS821RYQ at ENCODE; https://www.encodeproject.org/ENCBS821RYQ/

value: Derived from ENCODE donor ENCDO845GYA; https://www.encodeproject.org/ENCDO845GYA/


title: Control ChIP-seq from middle frontal area 46 (ENCLB721DYT)

description:
https://www.encodeproject.org/experiments/ENCSR822YWX/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (86 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR822YWX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB721DYT
size range: 200-600


title: Control ChIP-seq from foreskin keratinocyte (ENCLB657HCI)

description:
https://www.encodeproject.org/experiments/ENCSR982AYN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq control (input DNA) on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR982AYN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB657HCI

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

value: foreskin keratinocyte

value: primary cell

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

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: Healthy

tag: passage number

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

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


title: Control ChIP-seq from middle frontal area 46 (ENCLB996LNJ)

description:
https://www.encodeproject.org/experiments/ENCSR394ZWY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR394ZWY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-04-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB996LNJ
size range: 200-600

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 87 year

value: Bradley Bernstein, Broad

value: Rush University


title: Control ChIP-seq from foreskin keratinocyte (ENCLB152VVS)

description:
https://www.encodeproject.org/experiments/ENCSR982AYN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq control (input DNA) on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR982AYN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB152VVS

value: foreskin keratinocyte

value: primary cell

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

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

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


title: Control ChIP-seq from SK-N-SH (ENCLB714BHN)

description:
https://www.encodeproject.org/experiments/ENCSR759IVF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR759IVF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB714BHN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line treated with 6 uM all-trans-retinoic acid for 48 hours

tag: line

value: SK-N-SH

value: cell line

value: 4 year

value: child

value: Metastatic neuroblastoma from bone marrow

value: Michael Snyder, Stanford

tag: treatments

value: treatment_term_id:CHEBI:15367; treatment_term_name:all-trans-retinoic acid; treatment_type:chemical; duration:48; duration_units:hour;

value: ENCBS989ENM at ENCODE; https://www.encodeproject.org/ENCBS989ENM/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB960AGY)

description:
https://www.encodeproject.org/experiments/ENCSR391SNO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR391SNO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR739QEI
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB960AGY
size range: 200-600

source_name: Homo sapiens male adult (87 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: male

value: adult

value: 87 year

value: ENCBS552HSQ at ENCODE; https://www.encodeproject.org/ENCBS552HSQ/

value: Derived from ENCODE donor ENCDO203ASI; https://www.encodeproject.org/ENCDO203ASI/


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCLB745JJZ)

description:
https://www.encodeproject.org/experiments/ENCSR384AGH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR384AGH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB745JJZ
size range: 200-600

source_name: Homo sapiens male adult (60 years) left ventricle myocardium inferior tissue

value: left ventricle myocardium inferior

value: 60 year

value: Bradley Bernstein, Broad

value: Shin Lin

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

value: ENCBS267RXN at ENCODE; https://www.encodeproject.org/ENCBS267RXN/

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


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCLB874SPO)

description:
https://www.encodeproject.org/experiments/ENCSR384AGH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR384AGH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB874SPO
size range: 200-600


title: Histone ChIP-seq from left ventricle myocardium inferior (ENCLB938EYZ)

description:
https://www.encodeproject.org/experiments/ENCSR384AGH/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 ChIP-seq on left ventricle myocardium inferior tissue male adult (60 years)
experiment encode accession: ENCSR384AGH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR608IVH
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB938EYZ
size range: 200-600

value: ENCBS672IKS at ENCODE; https://www.encodeproject.org/ENCBS672IKS/


title: Histone ChIP-seq from pancreas (ENCLB526ACW)

description:
https://www.encodeproject.org/experiments/ENCSR829EYM/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K4me1 ChIP-seq on pancreas tissue female adult (41 years)
experiment encode accession: ENCSR829EYM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR462ZQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB526ACW
size range: 200-600

value: pancreas

value: female

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

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS212NYF at ENCODE; https://www.encodeproject.org/ENCBS212NYF/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB412DAI)

description:
https://www.encodeproject.org/experiments/ENCSR372YQR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR372YQR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR347KLR
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB412DAI
size range: 200-600

source_name: Homo sapiens male adult (86 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: male

value: adult

value: 86 year

value: Rush University

value: ENCBS940YCN at ENCODE; https://www.encodeproject.org/ENCBS940YCN/

value: Derived from ENCODE donor ENCDO666UNK; https://www.encodeproject.org/ENCDO666UNK/


title: Histone ChIP-seq from pancreas (ENCLB348SES)

description:
https://www.encodeproject.org/experiments/ENCSR829EYM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on pancreas tissue female adult (41 years)
experiment encode accession: ENCSR829EYM
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR462ZQL
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB348SES
size range: 200-600


title: Histone ChIP-seq from middle frontal area 46 (ENCLB279FRT)

description:
https://www.encodeproject.org/experiments/ENCSR391SNO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (87 years) originated from dorsolateral prefrontal cortex
experiment encode accession: ENCSR391SNO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR739QEI
encode release date: 2021-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB279FRT
size range: 200-600

value: 87 year

value: Bradley Bernstein, Broad

value: ENCBS552HSQ at ENCODE; https://www.encodeproject.org/ENCBS552HSQ/

value: Derived from ENCODE donor ENCDO203ASI; https://www.encodeproject.org/ENCDO203ASI/