title: TF ChIP-seq from K562 (ENCLB700ADA)

description:
https://www.encodeproject.org/experiments/ENCSR567QAD/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB34 ChIP-seq on human K562
experiment encode accession: ENCSR567QAD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR065HVA
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB700ADA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB34

value: ATCC

value: ENCBS708NSH at ENCODE; https://www.encodeproject.org/ENCBS708NSH/

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


title: TF ChIP-seq from K562 (ENCLB571XKL)

status: Public on Jul 22 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR861UWB/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HOXB6 ChIP-seq on human K562
experiment encode accession: ENCSR861UWB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR833ZKY, ENCSR532WSQ
encode release date: 2022-05-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB571XKL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HOXB6

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: age

value: 53 year

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

tag: link

value: ENCBS927SDR at ENCODE; https://www.encodeproject.org/ENCBS927SDR/


title: U2OS_TIP60_KO_sgRNA2_2

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the combined human and drosophila genomes by Rsubread version 2.2.6
Fragment (read-pair) counts were summarized by human Ensembl Gene ID and drosophila chromosome using the Rsubread featureCounts function
Human genes were identified using Gencode annotation version 35
Assembly: Human - hg38, drosophila melanogaser - R6.35
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent human Ensembl Gene ID/drosophila chromosome ID, total region length (for genes, total base count of all exons) and the number of fragments mapping to that region

molecule: total RNA

source_name: Human U2OS cells and drosophila S2 cells

growth_protocol: U2OS cells were cultured in DMEM, 10% FBS, and 2mM GlutaMAXTM medium at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated using RNeasy Kit (Qiagen, 74106). Drosophila S2 cell total RNA was spiked-in with U2OS total RNA before library preparation.
The Stranded TruSeq mRNA Library Kit (Illumina, 20020594) was used to generate barcoded cDNA libraries. The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions, generating 80 bp paired-end reads.

treatment_protocol: The expression of the single guide RNAs was induced with 1 μg/ml doxycycline treatment for 4 days.

tag: cell type

tag: genotype

tag: sgrna

tag: replicate


title: Control ChIP-seq from K562 (ENCLB931CZX)

description:
https://www.encodeproject.org/experiments/ENCSR292SJS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR292SJS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB931CZX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB12

value: Kevin White

value: ENCBS552YAG at ENCODE; https://www.encodeproject.org/ENCBS552YAG/


title: STEC_EA

city: Santiago

first: Mauricio

middle: J.

last: Farfan

address: Antonio Varas 360, Providencia

department: Departamento de Pediatria y Cirugia Infantil

country: Chile

institute: Universidad de Chile

data_processing:
Quality control of the sequenced raw reads were analyzed with FastQC v0.11.5
Low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates were removed, using Trimmomatic v0.32
Trimmed reads were mapped to Escherichia coli 042 or Escherichia coli strain NADC 5570/86-24/6564 reference genome with Bowtie v1.1.2
HTseq v0.6.1p1 was used for expression profiling. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand. Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value
DEG (Differentially Expressed Genes) analysis was performed on a 2 comparisons pairs using RPKM.
Genome_build: ASM180628v1 (Escherichia coli strain NADC 5570/86-24/6564)
Genome_build: ASM2712v1 (Escherichia coli 042)
Supplementary_files_format_and_content: tab-delimited text files include counts values for each gene in sample
Supplementary_files_format_and_content: GFF (General Feature Format) files including gene annotation for STEC or EAEC

organism: Escherichia coli

source_name: bacterial cells

growth_protocol: STEC and EAEC overnight culture were diluted 1/50 in DMEM media and left to grow for ~3 h at 37 ºC and 180 rpm, until bacteria reached an OD600 equal to 0.3.

extract_protocol:
Total RNA was harvested using Trizol reagent
RNA libraries were prepared using Ribo-Zero rRNA Removal Kit (Bacteria) and TruSeq Stranded Total RNA Sample Prep Kit

treatment_protocol: STEC and EAEC were centrifuged at 5000 rpm for 10 min. The supernatant was removed and the pellet was resuspended with M9 media (control), supernatant from Citrobacter werkmanii (CW) or supernatant from Escherichia albertii (EA) and incubated for 3 h at 37 ºC and 150 rpm

tag: sample type

value: Shiga toxin-producing Escherichia coli

tag: strain

tag: treatment

value: Incubation with supernatant from Escherichia albertii culture


title: TF ChIP-seq from K562 (ENCLB397PKB)

description:
https://www.encodeproject.org/experiments/ENCSR567QAD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB34 ChIP-seq on human K562
experiment encode accession: ENCSR567QAD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR065HVA
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB397PKB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: ENCBS301NPG at ENCODE; https://www.encodeproject.org/ENCBS301NPG/


title: U2OS_TIP60_KO_sgRNA2_3

value: Human U2OS cells and drosophila S2 cells


title: U2OS_Control_sgRNA2_3

value: Control


title: STEC

value: Incubation with M9 media (control)


title: TF ChIP-seq from K562 (ENCLB120PAQ)

description:
https://www.encodeproject.org/experiments/ENCSR468DVP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB11 ChIP-seq on human K562
experiment encode accession: ENCSR468DVP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR099ETQ, ENCSR328FYU
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB120PAQ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB11

tag: line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB11.

value: ENCBS577CWA at ENCODE; https://www.encodeproject.org/ENCBS577CWA/


title: TF ChIP-seq from K562 (ENCLB808FTV)

description:
https://www.encodeproject.org/experiments/ENCSR468DVP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB11 ChIP-seq on human K562
experiment encode accession: ENCSR468DVP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR099ETQ, ENCSR328FYU
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB808FTV
size range: 450-650

value: cell line

tag: biosample encode accession

tag: age

value: ENCBS925WYS at ENCODE; https://www.encodeproject.org/ENCBS925WYS/

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


title: TF ChIP-seq from HepG2 (ENCLB388RDY)

description:
https://www.encodeproject.org/experiments/ENCSR154YWK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR154YWK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB388RDY
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF558

value: 15 year

tag: Sex

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS680WYU at ENCODE; https://www.encodeproject.org/ENCBS680WYU/

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


title: B3: Foxofl/flxCD4Cre+

city: Faridabad

first: Srikanth

last: Sadhu

state: Haryana

address: Faridabad Gurugram Expressway

country: India

institute: Transational health science and Technology institute

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (parameter- Quality phred threshold: 30)
Trimmed sequence reads were mapped to GrCM39/mm39 using hisat (v2.2.0) (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Transcripts were assembled and quantified using Stringtie
Read counts were extracted using prepDE for downstream analysis
Assembly: GrCM39/mm39
Supplementary files format and content: TAB separated file of Raw read counts

organism: Mus musculus

source_name: Lung

extract_protocol:
RNA was extracted by Trizol(Invitrogen) method and quality checking bdone by Nanodrop.
NEB Next Ultra II Directional RNA Library Prep Kit using manufacturer’s protocols

tag: tissue

value: Lung


title: TF ChIP-seq from WTC11 (ENCLB718LFC)

description:
https://www.encodeproject.org/experiments/ENCSR762LIP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-AR ChIP-seq on human WTC11
experiment encode accession: ENCSR762LIP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR267JAO
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB718LFC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens AR

value: AR

value: 30 year

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

value: ENCBS921ATP at ENCODE; https://www.encodeproject.org/ENCBS921ATP/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: U2OS_Control_sgRNA2_2

tag: cell type

value: Human U2OS cells and drosophila S2 cells

tag: genotype

value: Control


title: Control ChIP-seq from SK-N-SH (ENCLB209EOT)

description:
https://www.encodeproject.org/experiments/ENCSR459TUR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR459TUR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB209EOT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF608 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

value: 4 year

value: female

value: Metastatic neuroblastoma from bone marrow

value: ATCC

tag: treatments

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

tag: link

value: ENCBS199MDS at ENCODE; https://www.encodeproject.org/ENCBS199MDS/

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


title: B2: Foxofl/flxCD4Cre+

value: Lung


title: B1: Foxofl/flxCD4Cre+


title: TF ChIP-seq from K562 (ENCLB053JRG)

description:
https://www.encodeproject.org/experiments/ENCSR567NTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TCF15 ChIP-seq on human K562
experiment encode accession: ENCSR567NTZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB053JRG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TCF15

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS590FUV at ENCODE; https://www.encodeproject.org/ENCBS590FUV/

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


title: Control ChIP-seq from SK-N-SH (ENCLB579GKV)

description:
https://www.encodeproject.org/experiments/ENCSR850KFE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR850KFE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB579GKV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens CSDC2 treated with 6uM all-trans-retinoic acid for 48 hours

value: child

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS769VOW at ENCODE; https://www.encodeproject.org/ENCBS769VOW/


title: U2OS_Control_sgRNA2_1

value: Human U2OS cells and drosophila S2 cells

value: Control

tag: sgrna

tag: replicate


title: TF ChIP-seq from HepG2 (ENCLB590CKZ)

description:
https://www.encodeproject.org/experiments/ENCSR154YWK/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR154YWK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB590CKZ
fragmentation methods: sonication (generic)

tag: antibody

value: cell line

value: 15 year

value: male

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS735RDM at ENCODE; https://www.encodeproject.org/ENCBS735RDM/

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


title: U2OS_TIP60_KO_sgRNA2_1


title: Control ChIP-seq from HepG2 (ENCLB795NQF)

description:
https://www.encodeproject.org/experiments/ENCSR454HXD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human HepG2
experiment encode accession: ENCSR454HXD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-04-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB795NQF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line

tag: line

value: ATCC

value: ENCBS236TVX at ENCODE; https://www.encodeproject.org/ENCBS236TVX/


title: TF ChIP-seq from WTC11 (ENCLB133NVT)

description:
https://www.encodeproject.org/experiments/ENCSR762LIP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-AR ChIP-seq on human WTC11
experiment encode accession: ENCSR762LIP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR267JAO
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB133NVT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: AR

value: 30 year

value: adult

value: ENCBS126ZXI at ENCODE; https://www.encodeproject.org/ENCBS126ZXI/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: U2OS_TIP60_KO_sgRNA1_3

value: Human U2OS cells and drosophila S2 cells


title: U2OS_TIP60_KO_sgRNA1_2


title: Control ChIP-seq from GM12878 (ENCLB851HWL)

description:
https://www.encodeproject.org/experiments/ENCSR446IEV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human GM12878
experiment encode accession: ENCSR446IEV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-03-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB851HWL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens GM12878 cell line

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS650AGA at ENCODE; https://www.encodeproject.org/ENCBS650AGA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: D2: Foxofl/flxCD4Cre-

value: Lung


title: Control ChIP-seq from A549 (ENCLB037GFS)

description:
https://www.encodeproject.org/experiments/ENCSR636AAQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR636AAQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB037GFS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TP53

value: cell line

value: 58 year

value: male

value: ENCBS263CJR at ENCODE; https://www.encodeproject.org/ENCBS263CJR/

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


title: U2OS_TIP60_KO_sgRNA1_1


title: Control ChIP-seq from K562 (ENCLB305WMV)

description:
https://www.encodeproject.org/experiments/ENCSR444SQF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR444SQF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB305WMV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens PPARD

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS221GHQ at ENCODE; https://www.encodeproject.org/ENCBS221GHQ/

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


title: TF ChIP-seq from K562 (ENCLB696CWI)

description:
https://www.encodeproject.org/experiments/ENCSR567NTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TCF15 ChIP-seq on human K562
experiment encode accession: ENCSR567NTZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB696CWI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: adult

value: ENCBS450HVA at ENCODE; https://www.encodeproject.org/ENCBS450HVA/


title: U2OS_Control_sgRNA1_3

value: Human U2OS cells and drosophila S2 cells

value: Control


title: TF ChIP-seq from HepG2 (ENCLB011ZZH)

description:
https://www.encodeproject.org/experiments/ENCSR151WAM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-MBNL3 ChIP-seq on human HepG2
experiment encode accession: ENCSR151WAM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR454HXD
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB011ZZH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MBNL3

value: 15 year

value: hepatocellular carcinoma

value: child

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS531QLZ at ENCODE; https://www.encodeproject.org/ENCBS531QLZ/

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


title: D1: Foxofl/flxCD4Cre-

value: Lung


title: Control ChIP-seq from A549 (ENCLB590PVX)

description:
https://www.encodeproject.org/experiments/ENCSR841MVT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR841MVT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB590PVX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HOXB13

value: cell line

value: 58 year

value: male

value: Michael Snyder

value: ENCBS115VII at ENCODE; https://www.encodeproject.org/ENCBS115VII/

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


title: Mint-ChIP-seq from immature natural killer cell (ENCLB236AOZ)

description:
https://www.encodeproject.org/experiments/ENCSR565WDW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR565WDW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR169WAD
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB236AOZ
fragmentation methods: none

source_name: Homo sapiens immature natural killer primary cell with multiple sclerosis

value: immature natural killer cell

value: primary cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS911UEN at ENCODE; https://www.encodeproject.org/ENCBS911UEN/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: HEK293_Control_sgRNA2_2

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the human genome by Rsubread version 1.30.5
Fragment (read-pair) counts were summarized by RefSeq Gene ID using the Rsubread featureCounts function
Genes were identified using Rsubreads inbuilt hg38 annotation
Assembly: hg38
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent RefSeq Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

source_name: human embryonic kidney cells 293 (HEK293)

growth_protocol: HEK293 cells were cultured in DMEM, 10% FBS, and 2mM GlutaMAXTM medium at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated using RNeasy Kit (Qiagen, 74106).
The Stranded TruSeq mRNA Library Kit (Illumina, 20020594) was used to generate barcoded cDNA libraries. The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions, generating 80 bp paired-end reads.

treatment_protocol: The expression of the single guide RNAs was induced with 1 μg/ml doxycycline treatment for 3 days.

tag: cell line


title: CD4+ T cells, SAG-PD1-high (Donor 4)

city: New Haven

first: Shaoxun

last: Wang

state: CT

address: 11 Dixwell Ave, Apt 212

institute: Yale University

description:
2-SAG-PD1-High
SAG_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210702_RNAseq_hg38_n8.gene_count_matrix

data_processing:
Low quality reads were trimmed and adaptor contamination were removed using Trim Galore (v0.5.0)
Trimmed reads were mapped to the human reference genome (hg38) using HISAT2 (v2.1.0)
Gene expression levels were quantified using StringTie (v1.3.3b)
with gene models (v27) from the GENCODE project. Differentially expressed genes were identified using DESeq2 (v 1.22.1)
Assembly: human reference genome (hg38) using HISAT2 (v2.1.0)
Supplementary files format and content: DESeq2 (v 1.22.1)
Supplementary files format and content: gene counts, DESeq2_fulltables

source_name: PBMC

growth_protocol: T cells were cutured in RPMI supplemented with 10% fetal bovine serum

extract_protocol:
RNA was isalated using Rneasy Mini Ki (250) from QIAGEN
NEBNext Single Cell Low-input RNA library prep kit

treatment_protocol: To do this, Tmem from 4 donors were stimulated with anti-CD3 in the presence of either anti-CD28 or SAG

tag: individual

value: Donor 4

value: PBMC

value: T cells

value: WT

tag: treatment

value: Anti-CD3 and anti-SAG

tag: pd-1 expression


title: TF ChIP-seq from K562 (ENCLB943QQS)

description:
https://www.encodeproject.org/experiments/ENCSR358PJI/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF277 ChIP-seq on human K562
experiment encode accession: ENCSR358PJI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB943QQS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF277

value: cell line

tag: biosample encode accession

tag: age

value: 53 year

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS951SBL at ENCODE; https://www.encodeproject.org/ENCBS951SBL/

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


title: CD4+ T cells, SAG-PD1-high (Donor 2)

description:
4-SAG-PD-1-High
SAG_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210513_RNAseq_hg38_n8.gene_count_matrix

value: Donor 2

tag: tissue

tag: cell type


title: CD4+ T cells, SAG-PD1-high (Donor 3)

description:
1-SAG-PD1-High
SAG_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210702_RNAseq_hg38_n8.gene_count_matrix

value: Donor 3

tag: genotype


title: D3: Foxofl/flxCD4Cre-

value: Lung


title: TF ChIP-seq from SK-N-SH (ENCLB980TWM)

description:
https://www.encodeproject.org/experiments/ENCSR630GGD/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-TFAP2B ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR630GGD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR245JGC
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB980TWM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens TFAP2B treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

tag: dev stage

value: child

tag: lab

tag: source

value: Michael Snyder

tag: treatments

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

tag: link

value: ENCBS539OMW at ENCODE; https://www.encodeproject.org/ENCBS539OMW/

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


title: Control ChIP-seq from K562 (ENCLB840VZP)

description:
https://www.encodeproject.org/experiments/ENCSR440KRG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR440KRG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB840VZP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF449

tag: line

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS299VOZ at ENCODE; https://www.encodeproject.org/ENCBS299VOZ/


title: TF ChIP-seq from K562 (ENCLB446PBZ)

description:
https://www.encodeproject.org/experiments/ENCSR358PJI/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF277 ChIP-seq on human K562
experiment encode accession: ENCSR358PJI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB446PBZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS750KUV at ENCODE; https://www.encodeproject.org/ENCBS750KUV/

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


title: HEK293_Control_sgRNA1_2

tag: cell line

value: human embryonic kidney cells 293 (HEK293)

tag: sgrna

tag: replicate


title: TF ChIP-seq from SK-N-SH (ENCLB976XNX)

description:
https://www.encodeproject.org/experiments/ENCSR630GGD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TFAP2B ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR630GGD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR245JGC
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB976XNX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: SK-N-SH

tag: biosample encode accession

value: 4 year

value: Metastatic neuroblastoma from bone marrow


title: CD4+ T cells, CD28-PD1-high (Donor 4)

description:
2-CD28-PD1-High
CD28_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210702_RNAseq_hg38_n8.gene_count_matrix

tag: individual

value: Donor 4

value: PBMC

value: T cells

value: WT

tag: treatment

value: Anti-CD3 and anti-CD28

tag: pd-1 expression


title: HEK293_Control_sgRNA2_1


title: HEK293_Control_sgRNA1_1


title: CD4+ T cells, SAG-PD1-high (Donor 1)

description:
1_SAG_high
SAG_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210513_RNAseq_hg38_n8.gene_count_matrix

value: Donor 1

tag: tissue

value: Anti-CD3 and anti-SAG


title: Control ChIP-seq from motor neuron (ENCLB425MHC)

description:
https://www.encodeproject.org/experiments/ENCSR744SMV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human motor neuron
experiment encode accession: ENCSR744SMV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-12-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB425MHC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens female adult motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

tag: age

value: unknown

tag: Sex

value: female

tag: health state

value: Healthy donor

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS910WSK at ENCODE; https://www.encodeproject.org/ENCBS910WSK/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: U2OS_Control_sgRNA1_1

source_name: Human U2OS cells and drosophila S2 cells

tag: cell type

tag: genotype

value: Control


title: CD4+ T cells, CD28-PD1-high (Donor 3)

description:
1-CD28-PD1-High
CD28_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210702_RNAseq_hg38_n8.gene_count_matrix

value: Donor 3


title: TF ChIP-seq from K562 (ENCLB619GWJ)

description:
https://www.encodeproject.org/experiments/ENCSR948JND/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF398 ChIP-seq on human K562
experiment encode accession: ENCSR948JND
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR236QAK, ENCSR328FYU
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB619GWJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF398

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Kevin White

tag: link

value: ENCBS367DUZ at ENCODE; https://www.encodeproject.org/ENCBS367DUZ/

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


title: HEK293_TIP60_KO_sgRNA2_2

tag: cell line

value: human embryonic kidney cells 293 (HEK293)

tag: sgrna


title: Control ChIP-seq from K562 (ENCLB834OGN)

description:
https://www.encodeproject.org/experiments/ENCSR357LCN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR357LCN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB834OGN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

tag: line

tag: biosample encode accession

value: ATCC

value: ENCBS886XVQ at ENCODE; https://www.encodeproject.org/ENCBS886XVQ/


title: HEK293_TIP60_KO_sgRNA2_1

tag: replicate


title: Control ChIP-seq from SK-N-SH (ENCLB707VBF)

description:
https://www.encodeproject.org/experiments/ENCSR835DTI/
***************
biological replicate number: 1
technical replicate number: 1
description: SK-N-SH immortalized cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing C-terminal eGFP-ZNF70 fusion protein.
experiment encode accession: ENCSR835DTI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB707VBF
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF70 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF70.

value: 4 year

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder

tag: treatments

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

value: ENCBS181GBE at ENCODE; https://www.encodeproject.org/ENCBS181GBE/

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


title: Control ChIP-seq from excitatory neuron (ENCLB416EIG)

description:
https://www.encodeproject.org/experiments/ENCSR548RFU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR548RFU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-04-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB416EIG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (30 years) excitatory neuron in vitro differentiated cells genetically modified (insertion) using TALEN inserting M. musculus Neurog2 originated from WTC11

value: excitatory neuron

value: in vitro differentiated cells

value: 30 year

value: male

value: adult

value: Michael Snyder, Stanford

value: ENCBS388KPW at ENCODE; https://www.encodeproject.org/ENCBS388KPW/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: CD4+ T cells, CD28-PD1-high (Donor 2)

description:
3-CD28-PD-1-High
CD28_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210513_RNAseq_hg38_n8.gene_count_matrix

tag: individual

value: Donor 2

tag: tissue

value: PBMC

value: T cells

value: WT

tag: treatment

value: Anti-CD3 and anti-CD28

tag: pd-1 expression


title: Control ChIP-seq from SK-N-SH (ENCLB849HFI)

description:
https://www.encodeproject.org/experiments/ENCSR247NVH/
***************
biological replicate number: 1
technical replicate number: 1
description: SK-N-SH immortalized cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing C-terminal eGFP-ZNF565 fusion protein.
experiment encode accession: ENCSR247NVH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB849HFI
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF565 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: cell line

tag: description

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF565.

tag: age

value: 4 year

tag: Sex

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder

value: ENCBS684BHI at ENCODE; https://www.encodeproject.org/ENCBS684BHI/


title: Control ChIP-seq from K562 (ENCLB099NXC)

description:
https://www.encodeproject.org/experiments/ENCSR822AWY/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF347 fusion protein.
experiment encode accession: ENCSR822AWY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB099NXC
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF347

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF347.

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS897RCY at ENCODE; https://www.encodeproject.org/ENCBS897RCY/

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


title: TF ChIP-seq from K562 (ENCLB471NRR)

description:
https://www.encodeproject.org/experiments/ENCSR948JND/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF398 ChIP-seq on human K562
experiment encode accession: ENCSR948JND
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR236QAK, ENCSR328FYU
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB471NRR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

tag: source

tag: link

value: ENCBS125MTF at ENCODE; https://www.encodeproject.org/ENCBS125MTF/


title: HEK293_TIP60_KO_sgRNA1_2

tag: cell line

value: human embryonic kidney cells 293 (HEK293)

tag: genotype

tag: sgrna


title: Control ChIP-seq from K562 (ENCLB739FEI)

description:
https://www.encodeproject.org/experiments/ENCSR231MJJ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZBTB9 fusion protein.
experiment encode accession: ENCSR231MJJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB739FEI
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB9

tag: line

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB9.

tag: biosample encode accession

value: ENCBS259CVT at ENCODE; https://www.encodeproject.org/ENCBS259CVT/


title: HEK293_TIP60_KO_sgRNA1_1

tag: replicate


title: CD4+ T cells, CD3-PD1-high (Donor 4)

description:
2-CD3-PD1-High
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210702_RNAseq_hg38_n8.gene_count_matrix

tag: individual

value: Donor 4

tag: tissue

value: PBMC

tag: cell type

value: T cells

value: WT

tag: treatment


title: TF ChIP-seq from HepG2 (ENCLB422FYD)

description:
https://www.encodeproject.org/experiments/ENCSR151WAM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-MBNL3 ChIP-seq on human HepG2
experiment encode accession: ENCSR151WAM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR454HXD
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB422FYD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MBNL3

tag: age

value: 15 year

tag: Sex

value: male

value: hepatocellular carcinoma

value: child

value: ATCC

value: ENCBS464DPO at ENCODE; https://www.encodeproject.org/ENCBS464DPO/

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


title: Control ChIP-seq from GM12878 (ENCLB680ZNZ)

description:
https://www.encodeproject.org/experiments/ENCSR413QNG/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-PRDM15 fusion protein.
experiment encode accession: ENCSR413QNG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB680ZNZ
size range: 450-650

source_name: Homo sapiens GM12878 cell line genetically modified (insertion) using CRISPR targeting H. sapiens PRDM15

tag: description

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to PRDM15.

value: unknown

value: female

tag: health state

tag: dev stage

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS768UNQ at ENCODE; https://www.encodeproject.org/ENCBS768UNQ/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: TF ChIP-seq from A549 (ENCLB062ZOO)

description:
https://www.encodeproject.org/experiments/ENCSR548FLW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN20 ChIP-seq on human A549
experiment encode accession: ENCSR548FLW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR331KRW
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB062ZOO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZSCAN20

tag: antibody

value: cell line

value: 58 year

tag: lab

tag: source

value: ENCBS687TPH at ENCODE; https://www.encodeproject.org/ENCBS687TPH/

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


title: CD4+ T cells, CD3-PD1-high (Donor 3)

description:
1-CD3-PD1-High
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210702_RNAseq_hg38_n8.gene_count_matrix

value: Donor 3

value: PBMC

value: T cells

tag: genotype

value: WT

tag: pd-1 expression


title: TF ChIP-seq from A549 (ENCLB720CYK)

description:
https://www.encodeproject.org/experiments/ENCSR548FLW/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN20 ChIP-seq on human A549
experiment encode accession: ENCSR548FLW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR331KRW
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB720CYK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: male

value: ATCC

tag: link

value: ENCBS780RNG at ENCODE; https://www.encodeproject.org/ENCBS780RNG/


title: Control ChIP-seq from K562 (ENCLB052UJM)

description:
https://www.encodeproject.org/experiments/ENCSR213ZCM/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-DDIT3 fusion protein.
experiment encode accession: ENCSR213ZCM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB052UJM
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens DDIT3

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to DDIT3.

tag: biosample encode accession

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS839RLM at ENCODE; https://www.encodeproject.org/ENCBS839RLM/

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


title: U2OS_IgG_CTL_sgRNA1

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the combined human, drosophila and E. coli genomes by Rsubread version 2.0.1
Fragment (read-pair) counts were summarized by human Ensembl Gene transcriptional start site (TSS) +/- 1kbp and drosophila chromosome using the Rsubread featureCounts function
Human genes TSS were identified using Gencode annotation version 35
Assembly: Human - hg38, drosophila melanogaser - R6.35, Escherichia coli - strain K12 substrain MG1655
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent human Ensembl Gene ID/drosophila chromosome, total region length (for genes, total base count of all exons) and the number of fragments mapping to that region
Library strategy: CUT&Tag

source_name: Human U2OS cells, drosophila S2 cells and E. coli

extract_protocol:
An input of 100,000 cells per sample was used as described by the Henikoff laboratory with slight modifications. pAG-Tn5 with adapters were generously gifted by the Henikoff laboratory and later ordered commercially (EpiCypher, 15-1017). All buffers were made up fresh. Digitonin stock solution was made up fresh as 5% (w/v) in DMSO (CST, 12611P). 10 μl concanavalin-A beads (Bangs Laboratories, BP531) per sample were washed twice in 10 volumes of binding buffer (20 mM HEPES pH 7.5 (Sigma, 83264), 10 mM KCl (Sigma, 60142), 1 mM CaCl2 (Sigma, 21115), and 1 mM MnCl2 (Sigma, M1787)) and resuspended in 10 μl binding buffer per sample. Cells were washed twice with PBS, scraped in PBS, counted and mixed with spike-in S2 D. melanogaster cells in a ratio of 43:57 (Mammalian cells: S2 cells) for a combined cell number of 100,000 cells per sample. Cells were washed twice in 1 ml wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl (Sigma, 71386), 0.5 mM spermidine (Sigma, S0266), and 1 protease inhibitor tablet per 50 ml buffer (Roche, 05056489001)), resuspended in 90 μl wash buffer per sample, and concanavalin-A beads were added dropwise while vortexing on low setting, incubated for 10 min at RT on a roller. The supernatant was removed with a magnetic rack, and cells resuspended in 100 μl ice-cold antibody buffer (wash buffer supplemented with 0.05 % (w/v) digitonin (Merck, 300410), 2 mM EDTA (Invitrogen, 15575020), and 0.1 % (w/v) BSA (Sigma, A8577)) per sample and split into 50 μl aliquots. Primary antibody was added to respective tubes as indicated in Methods Table 3 and incubated for 2 h, at RT on a roller. The supernatant was removed, 100 μl ice cold dig-wash buffer (wash buffer supplemented with 0.05% (w/v) digitonin) containing secondary antibody as indicated in Methods Table 3 was added to the cells, incubated for 60 min at RT on a roller, washed trice in 1 ml dig-wash buffer, resuspend in 100 μl ice-cold dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01 % (w/v) digitonin, and 1 protease inhibitor tablet per 50 ml buffer) supplemented with 1:250 pA-Tn5 adapter complex and incubated for 60 min at RT on a roller. Cells were washed trice in 1 ml dig-300 buffer, resuspended in 100 μl tagmentation buffer (dig-300 buffer supplemented with 0.01 mM MgCl2 (Sigma, 63069)) while gently vortexing and incubated at 37˚C for 60 min. Tagmentation was stopped by adding 3.34 μl 0.5 M EDTA, 1 μl 10% (w/v) SDS (Sigma, 71736), and 0.83 μl 20 mg/ml thermolabile proteinase K (NEB, P8111S) to each sample, mixed by vortexing on full speed and incubated at 37ÅãC for 60 min and 800 rpm shaking followed by heat inactivation at 55˚C for 10 min. DNA was extracted via Ampure XP beads (Beckman, A63880). Briefly, 122 μl Ampure XP beads were added to each sample and incubated for 5 min at RT, washed twice in 1 ml 80% ethanol without removing from the magnetic rack. All residual ethanol was removed beads were air-dried for 5 min at RT. DNA fragments were eluted in 25 μl TE buffer (10 mM Tris-HCl pH 8.0 (Invitrogen, 15568025), 1 mM EDTA, and 25 μg/ml RNAse A (ThermoFisher, EN0531)) by vortexing and incubation at 37˚C for 10 min, and transferred to a new tube.
10 μl sample DNA fragments were used in library PCR mixtures with 100 nM sample specific nextera i5 and i7 primer combinations and 12.5 μl 2X NEBNext Ultra II Q5 Master Mix (NEB, M0541L) in a total of 25 μl and amplified with the following PCR settings: 72˚C for 5 min followed by 13 cycles of 98˚C for 30 sec, 98˚C for 10 sec and 63˚C for 10 sec, and 72˚C for 1 min. PCR products were cleaned up using 30 μl Ampure XP beads as described above, eluted in 25 μl 10 mM Tris-HCl pH 8.0, and stored at -20˚C. The clean libraries were analyzed by High Sensitivity D1000 gels (Agilent, 5067- 5584) on an Agilent 4200 tapestation using 2 μl sample and an electronic ladder. Library concentrations were measured between 125 bp and 1200 bp. Libraries were pooled into a 10 nM library of 20 μl. The pooled indexed libraries were diluted to 1.5 pM for paired end sequencing (2x 36 cycles) on a NextSeq 500 instrument using the v2 150 cycle Mid Output kit (Illumina) as per manufacturer’s instructions, generating 36 bp paired-end reads. The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6, while the FASTQ file generation and de-multiplexing utilized bcl2fastq conversion software v2.15.0.4.

value: Control

tag: sgrna

value: IgG


title: Control ChIP-seq from K562 (ENCLB031LDL)

description:
https://www.encodeproject.org/experiments/ENCSR209QEB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR209QEB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB031LDL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens DMBX1

value: cell line

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS774HZB at ENCODE; https://www.encodeproject.org/ENCBS774HZB/


title: CD4+ T cells, CD3-PD1-high (Donor 2)

description:
2-CD3-PD-1-High
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210513_RNAseq_hg38_n8.gene_count_matrix

source_name: PBMC

tag: individual

value: Donor 2

tag: tissue

value: PBMC

value: T cells

value: WT


title: CD4+ T cells, CD3-PD1-high (Donor 1)

description:
1_CD3_high
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210513_RNAseq_hg38_n8.gene_count_matrix

value: Donor 1

tag: cell type

tag: treatment


title: TF ChIP-seq from K562 (ENCLB747QVJ)

description:
https://www.encodeproject.org/experiments/ENCSR946WBN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR946WBN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB747QVJ
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens JUN

value: JUN

tag: age

value: 53 year

tag: Sex

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS619TUZ at ENCODE; https://www.encodeproject.org/ENCBS619TUZ/


title: U2OS_H3K27me3_CTL_sgRNA1

value: Human U2OS cells, drosophila S2 cells and E. coli

value: Control


title: U2OS_H4K16ac_TIP60_KO_sgRNA2


title: Control ChIP-seq from K562 (ENCLB103XOQ)

description:
https://www.encodeproject.org/experiments/ENCSR610PBT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR610PBT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-06-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB103XOQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CAMTA2

value: cell line

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS358LHX at ENCODE; https://www.encodeproject.org/ENCBS358LHX/

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


title: U2OS_H4K16ac_TIP60_KO_sgRNA1


title: Control ChIP-seq from K562 (ENCLB515KYA)

description:
https://www.encodeproject.org/experiments/ENCSR405WWL/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZBTB17 fusion protein.
experiment encode accession: ENCSR405WWL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB515KYA
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB17

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB17.

tag: dev stage

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS676IFC at ENCODE; https://www.encodeproject.org/ENCBS676IFC/


title: CD4+ T cells, CD28-PD1-high (Donor 1)

description:
1_CD28_high
CD28_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
SAG_PD1High_vs_CD28_PD1High_DESeq2_fulltable.xlsx
20210513_RNAseq_hg38_n8.gene_count_matrix

value: Donor 1

value: PBMC

value: T cells

value: WT

value: Anti-CD3 and anti-CD28


title: CD4+ T cells, CD3-PD1-Low (Donor 4)

description:
2-CD3-PD1-Low
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210702_RNAseq_hg38_n8.gene_count_matrix

value: Donor 4


title: CD4+ T cells, CD3-PD1-Low (Donor 3)

description:
1-CD3-PD1-Low
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210702_RNAseq_hg38_n8.gene_count_matrix

value: Donor 3


title: U2OS_H4K16ac_CTL_sgRNA2

value: Human U2OS cells, drosophila S2 cells and E. coli

value: Control

tag: antibody


title: TF ChIP-seq from K562 (ENCLB431LME)

description:
https://www.encodeproject.org/experiments/ENCSR939CDD/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR939CDD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB431LME
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ARID4B

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

value: ENCBS325WNA at ENCODE; https://www.encodeproject.org/ENCBS325WNA/


title: Control ChIP-seq from GM12878 (ENCLB678UBN)

description:
https://www.encodeproject.org/experiments/ENCSR583RUC/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-MAZ fusion protein.
experiment encode accession: ENCSR583RUC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB678UBN
size range: 450-650

source_name: Homo sapiens GM12878 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MAZ

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to MAZ.

value: unknown

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS802MWC at ENCODE; https://www.encodeproject.org/ENCBS802MWC/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: TF ChIP-seq from K562 (ENCLB124TAM)

description:
https://www.encodeproject.org/experiments/ENCSR939CDD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR939CDD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB124TAM
fragmentation methods: sonication (generic)

value: ENCBS377IWJ at ENCODE; https://www.encodeproject.org/ENCBS377IWJ/

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


title: TF ChIP-seq from HepG2 (ENCLB785DXS)

description:
https://www.encodeproject.org/experiments/ENCSR347HAM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR347HAM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB785DXS
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF221

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS570WRY at ENCODE; https://www.encodeproject.org/ENCBS570WRY/

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


title: Control ChIP-seq from A549 (ENCLB554MTT)

description:
https://www.encodeproject.org/experiments/ENCSR580TXR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR580TXR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB554MTT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HMGXB4

value: cell line

value: 58 year

value: Michael Snyder

value: ENCBS679IVP at ENCODE; https://www.encodeproject.org/ENCBS679IVP/

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


title: CD4+ T cells, CD3-PD1-Low (Donor 1)

description:
1-CD3-PD-1-Low
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210513_RNAseq_hg38_n8.gene_count_matrix

value: Donor 1

value: PBMC

value: T cells

tag: genotype

value: WT

tag: pd-1 expression


title: Control ChIP-seq from K562 (ENCLB745VPP)

description:
https://www.encodeproject.org/experiments/ENCSR580RLH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR580RLH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB745VPP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF23

tag: line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: Kevin White

tag: link

value: ENCBS872RBP at ENCODE; https://www.encodeproject.org/ENCBS872RBP/


title: U2OS_H4K16ac_CTL_sgRNA1

value: Human U2OS cells, drosophila S2 cells and E. coli

value: Control

tag: sgrna


title: TF ChIP-seq from HepG2 (ENCLB239VVR)

description:
https://www.encodeproject.org/experiments/ENCSR347HAM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR347HAM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB239VVR
fragmentation methods: sonication (generic)

value: cell line

tag: biosample encode accession

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS837HOV at ENCODE; https://www.encodeproject.org/ENCBS837HOV/

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


title: CD4+ T cells, CD3-PD1-Low (Donor 2)

description:
CD3_low
CD3_PD1High_vs_CD3_PD1Low_DESeq2_fulltable
20210513_RNAseq_hg38_n8.gene_count_matrix

tag: individual

value: Donor 2

tag: tissue

value: PBMC

value: T cells

value: WT


title: TF ChIP-seq from K562 (ENCLB476FEU)

description:
https://www.encodeproject.org/experiments/ENCSR946WBN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR946WBN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB476FEU
fragmentation methods: sonication (generic)

value: JUN

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS108KEO at ENCODE; https://www.encodeproject.org/ENCBS108KEO/

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


title: TF ChIP-seq from K562 (ENCLB757VIX)

description:
https://www.encodeproject.org/experiments/ENCSR935UQL/
***************
biological replicate number: 4
technical replicate number: 1
description: MECOM ChIP-seq on human K562
experiment encode accession: ENCSR935UQL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR232JJY, ENCSR012KTG
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB757VIX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MECOM

value: MECOM

value: cell line

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS179UVD at ENCODE; https://www.encodeproject.org/ENCBS179UVD/


title: Control ChIP-seq from K562 (ENCLB532BUO)

description:
https://www.encodeproject.org/experiments/ENCSR796QVL/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF84 fusion protein.
experiment encode accession: ENCSR796QVL
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB532BUO
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF84

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF84.

value: Kevin White

value: ENCBS689HQL at ENCODE; https://www.encodeproject.org/ENCBS689HQL/


title: U2OS_H4K8ac_TIP60_KO_sgRNA1

tag: cell type

value: Human U2OS cells, drosophila S2 cells and E. coli


title: Control ChIP-seq from K562 (ENCLB449XAY)

description:
https://www.encodeproject.org/experiments/ENCSR193NPW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR193NPW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB449XAY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF583

tag: age

value: ENCBS941GFE at ENCODE; https://www.encodeproject.org/ENCBS941GFE/


title: Control ChIP-seq from K562 (ENCLB465PNX)

description:
https://www.encodeproject.org/experiments/ENCSR186SKI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR186SKI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB465PNX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF785

tag: Sex

value: ENCBS141NYD at ENCODE; https://www.encodeproject.org/ENCBS141NYD/


title: TF ChIP-seq from WTC11 (ENCLB808CMH)

description:
https://www.encodeproject.org/experiments/ENCSR717QWW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF425 ChIP-seq on human WTC11
experiment encode accession: ENCSR717QWW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR181GRP
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB808CMH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF425

value: 30 year

value: male

value: Richard Myers

value: ENCBS382RTD at ENCODE; https://www.encodeproject.org/ENCBS382RTD/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: U2OS_H4K8ac_TIP60_KO_sgRNA2


title: Control ChIP-seq from K562 (ENCLB155AUZ)

description:
https://www.encodeproject.org/experiments/ENCSR578HPA/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-REST fusion protein.
experiment encode accession: ENCSR578HPA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB155AUZ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens REST

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to REST.

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS295CHT at ENCODE; https://www.encodeproject.org/ENCBS295CHT/

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


title: TF ChIP-seq from WTC11 (ENCLB592DKP)

description:
https://www.encodeproject.org/experiments/ENCSR717QWW/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF425 ChIP-seq on human WTC11
experiment encode accession: ENCSR717QWW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR181GRP
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB592DKP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: Michael Snyder, Stanford

value: ENCBS811SPH at ENCODE; https://www.encodeproject.org/ENCBS811SPH/


title: Control ChIP-seq from SK-N-SH (ENCLB797WME)

description:
https://www.encodeproject.org/experiments/ENCSR995TTS/
***************
biological replicate number: 1
technical replicate number: 1
description: SK-N-SH immortalized cell line (treated with 6 uM all-trans-retinoic acid for 48 hours) stably expressing C-terminal eGFP-ZNF8 fusion protein.
experiment encode accession: ENCSR995TTS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB797WME
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF8 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

tag: description

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF8.

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder

tag: treatments

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

value: ENCBS098BDO at ENCODE; https://www.encodeproject.org/ENCBS098BDO/

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


title: U2OS_H2AZ_TIP60_KO_sgRNA1

source_name: Human U2OS cells, drosophila S2 cells and E. coli

tag: antibody


title: e3.TMAO.4

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: experiment 3, invivo, TMAO treatment, replicate 4

data_processing:
RNA-Seq data analysis was done with RSEM (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for downstream analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file include counts for each sample

molecule: polyA RNA

source_name: TAM

extract_protocol:
Total RNA was extracted from BMDM or sorted F4/80+CD11b+ TAMs using RNeasy Plus Micro Kit (Qiagen, 74034). RNA quality was validated using the TapeStation High Sensitivity RNA ScreenTape (Agilent)
Libraries were prepared using Illumina Stranded mRNA Prep kit (500 ng DNase1 treated total RNA was used)

value: TAM

tag: group

value: invivo

tag: treatment

value: TMAO

tag: replicate


title: e3.TMAO.2

description: experiment 3, invivo, TMAO treatment, replicate 2

tag: source


title: e3.ctrl.4

description: experiment 3, invivo, control treatment, replicate 4

value: control


title: e3.TMAO.1

description: experiment 3, invivo, TMAO treatment, replicate 1


title: U2OS_H2AZ_TIP60_KO_sgRNA2

value: Human U2OS cells, drosophila S2 cells and E. coli

tag: genotype


title: Control ChIP-seq from K562 (ENCLB306IPB)

description:
https://www.encodeproject.org/experiments/ENCSR178RBD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR178RBD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB306IPB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF445

tag: line

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: lab

value: Kevin White

tag: link

value: ENCBS649GGR at ENCODE; https://www.encodeproject.org/ENCBS649GGR/

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


title: TF ChIP-seq from K562 (ENCLB799SYL)

description:
https://www.encodeproject.org/experiments/ENCSR530WIV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR530WIV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB799SYL
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXP1

tag: biosample encode accession

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS242GFD at ENCODE; https://www.encodeproject.org/ENCBS242GFD/


title: U2OS_H2AZ_CTL_sgRNA2

tag: cell type

value: Control

tag: sgrna


title: e3.ctrl.3

description: experiment 3, invivo, control treatment, replicate 3

value: TAM


title: TF ChIP-seq from K562 (ENCLB769YYD)

description:
https://www.encodeproject.org/experiments/ENCSR935UQL/
***************
biological replicate number: 3
technical replicate number: 1
description: MECOM ChIP-seq on human K562
experiment encode accession: ENCSR935UQL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR232JJY, ENCSR012KTG
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB769YYD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: MECOM

tag: age

tag: Sex

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS124IQN at ENCODE; https://www.encodeproject.org/ENCBS124IQN/


title: Control ChIP-seq from motor neuron (ENCLB661QYG)

description:
https://www.encodeproject.org/experiments/ENCSR124KQG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human motor neuron
experiment encode accession: ENCSR124KQG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-12-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB661QYG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (47 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

value: 47 year

value: male

tag: health state

value: Donor with Amyotrophic Lateral Sclerosis

value: Cooper-Knock lab, University of Sheffield, UK

value: ENCBS185WTO at ENCODE; https://www.encodeproject.org/ENCBS185WTO/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: Control ChIP-seq from A549 (ENCLB621XJZ)

description:
https://www.encodeproject.org/experiments/ENCSR331KRW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR331KRW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB621XJZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line

value: cell line

value: 58 year

value: adult

value: ENCBS447IFV at ENCODE; https://www.encodeproject.org/ENCBS447IFV/

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


title: Control ChIP-seq from GM23338 (ENCLB044LDL)

description:
https://www.encodeproject.org/experiments/ENCSR178GOM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human GM23338
experiment encode accession: ENCSR178GOM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB044LDL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens GM23338 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF331

value: 53 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS766JVT at ENCODE; https://www.encodeproject.org/ENCBS766JVT/

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


title: U2OS_H4K8ac_CTL_sgRNA2

value: Human U2OS cells, drosophila S2 cells and E. coli

value: Control

tag: antibody


title: U2OS_H2AZ_CTL_sgRNA1


title: e3.TMAO.3

description: experiment 3, invivo, TMAO treatment, replicate 3

value: TAM

tag: group

value: invivo

value: TMAO


title: e3.ctrl.2

description: experiment 3, invivo, control treatment, replicate 2

tag: treatment

value: control


title: U2OS_H4K8ac_CTL_sgRNA1


title: Control ChIP-seq from K562 (ENCLB973YBY)

description:
https://www.encodeproject.org/experiments/ENCSR781PVO/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ERF fusion protein.
experiment encode accession: ENCSR781PVO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB973YBY
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ERF

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ERF.

value: female

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS605YSU at ENCODE; https://www.encodeproject.org/ENCBS605YSU/

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


title: U2OS_H2AZK4_7ac_TIP60_KO_sgRNA1


title: e2.TCM.TMAO.3

description: experiment 2, BMDM cell lines, TCM+TMAO treatment, replicate 3

source_name: BMDM

value: BMDM

value: TCM+TMAO

tag: replicate


title: TF ChIP-seq from K562 (ENCLB537NFY)

description:
https://www.encodeproject.org/experiments/ENCSR530WIV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR530WIV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB537NFY
fragmentation methods: sonication (generic)

value: cell line

value: 53 year

value: adult

value: Richard Myers, HAIB

tag: source

value: Richard Myers

value: ENCBS276WKZ at ENCODE; https://www.encodeproject.org/ENCBS276WKZ/


title: Control ChIP-seq from SK-N-SH (ENCLB465IBU)

description:
https://www.encodeproject.org/experiments/ENCSR927UOT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR927UOT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB465IBU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens SK-N-SH cell line

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS956XSH at ENCODE; https://www.encodeproject.org/ENCBS956XSH/

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


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB062GRY)

description:
https://www.encodeproject.org/experiments/ENCSR521SFR/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR521SFR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR019FIH
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062GRY
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell with multiple sclerosis, preserved by cryopreservation

value: CD8-positive, alpha-beta memory T cell

value: primary cell

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS229YZM at ENCODE; https://www.encodeproject.org/ENCBS229YZM/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: U2OS_H2AZK4_7ac_CTL_sgRNA2

value: Human U2OS cells, drosophila S2 cells and E. coli

tag: genotype

value: Control


title: Control ChIP-seq from HepG2 (ENCLB565SUY)

description:
https://www.encodeproject.org/experiments/ENCSR387ACQ/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 immortalized cell line stably expressing C-terminal eGFP-NR2F1 fusion protein.
experiment encode accession: ENCSR387ACQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB565SUY
size range: 450-650

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NR2F1

tag: line

value: cell line

value: HepG2 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2F1.

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Michael Snyder

value: ENCBS854ZPI at ENCODE; https://www.encodeproject.org/ENCBS854ZPI/

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


title: e3.ctrl.1

description: experiment 3, invivo, control treatment, replicate 1

value: TAM

value: invivo

value: control


title: TF ChIP-seq from HepG2 (ENCLB251YLH)

description:
https://www.encodeproject.org/experiments/ENCSR516SMM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR516SMM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR690IYP, ENCSR555EMB
encode release date: 2022-02-08
lab: Richard Myers, HAIB
library encode accession: ENCLB251YLH
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SRF

value: SRF

tag: dev stage

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS828SDX at ENCODE; https://www.encodeproject.org/ENCBS828SDX/


title: e2.TCM.TMAO.2

description: experiment 2, BMDM cell lines, TCM+TMAO treatment, replicate 2

value: BMDM

value: TCM+TMAO


title: TF ChIP-seq from K562 (ENCLB463CLW)

description:
https://www.encodeproject.org/experiments/ENCSR775NLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CHCHD3 ChIP-seq on human K562
experiment encode accession: ENCSR775NLJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR334KTB
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB463CLW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CHCHD3

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

tag: lab

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS280DAR at ENCODE; https://www.encodeproject.org/ENCBS280DAR/

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


title: U2OS_H2AZK4_7ac_TIP60_KO_sgRNA2

value: Human U2OS cells, drosophila S2 cells and E. coli


title: TF ChIP-seq from K562 (ENCLB164EBE)

description:
https://www.encodeproject.org/experiments/ENCSR922YDT/
***************
biological replicate number: 1
technical replicate number: 1
description: SLC30A9 ChIP-seq on human K562
experiment encode accession: ENCSR922YDT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR065HVA
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB164EBE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SLC30A9

tag: link

value: ENCBS089IFR at ENCODE; https://www.encodeproject.org/ENCBS089IFR/


title: TF ChIP-seq from HepG2 (ENCLB684FKX)

description:
https://www.encodeproject.org/experiments/ENCSR516SMM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR516SMM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR690IYP, ENCSR555EMB
encode release date: 2022-02-08
lab: Richard Myers, HAIB
library encode accession: ENCLB684FKX
fragmentation methods: sonication (generic)

value: SRF

tag: biosample encode accession

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS650YEX at ENCODE; https://www.encodeproject.org/ENCBS650YEX/

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


title: TF ChIP-seq from K562 (ENCLB091KRG)

description:
https://www.encodeproject.org/experiments/ENCSR922YDT/
***************
biological replicate number: 2
technical replicate number: 1
description: SLC30A9 ChIP-seq on human K562
experiment encode accession: ENCSR922YDT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR065HVA
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB091KRG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 53 year

value: ENCBS305SGJ at ENCODE; https://www.encodeproject.org/ENCBS305SGJ/


title: U2OS_H2AZK4_7_11ac_TIP60_KO_sgRNA2

tag: cell type


title: Control ChIP-seq from K562 (ENCLB798GZS)

description:
https://www.encodeproject.org/experiments/ENCSR572XHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF212 fusion protein.
experiment encode accession: ENCSR572XHZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB798GZS
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF212

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF212.

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Kevin White

value: ENCBS763BAJ at ENCODE; https://www.encodeproject.org/ENCBS763BAJ/


title: U2OS_H2AZK4_7_11ac_CTL_sgRNA1

value: Human U2OS cells, drosophila S2 cells and E. coli

value: Control

tag: sgrna


title: e2.TCM.2

description: experiment 2, BMDM cell lines, TCM treatment, replicate 2

value: BMDM

value: TCM


title: U2OS_H2AZK4_7_11ac_CTL_sgRNA2


title: e2.TCM.3

description: experiment 2, BMDM cell lines, TCM treatment, replicate 3


title: Control ChIP-seq from K562 (ENCLB207MQH)

description:
https://www.encodeproject.org/experiments/ENCSR385JMD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR385JMD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB207MQH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GMEB1

tag: age

value: Michael Snyder, Stanford

value: ENCBS487FIM at ENCODE; https://www.encodeproject.org/ENCBS487FIM/

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


title: U2OS_H2AZK4_7_11ac_TIP60_KO_sgRNA1

source_name: Human U2OS cells, drosophila S2 cells and E. coli


title: e2.TCM.1

description: experiment 2, BMDM cell lines, TCM treatment, replicate 1


title: Control ChIP-seq from K562 (ENCLB098VMX)

description:
https://www.encodeproject.org/experiments/ENCSR984XPC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR984XPC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-02-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB098VMX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF319

tag: Sex

value: ATCC

value: ENCBS331ARR at ENCODE; https://www.encodeproject.org/ENCBS331ARR/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB282HVO)

description:
https://www.encodeproject.org/experiments/ENCSR707HMU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD14-positive monocyte.
experiment encode accession: ENCSR707HMU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR509FRR
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282HVO
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: primary cell

tag: description

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS080GJD at ENCODE; https://www.encodeproject.org/ENCBS080GJD/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: BCPAP-3

city: Baltimore

first: Bonita

middle: H

last: Powell

state: MD

address: 733 N Broadway, MRB 8 829

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University School of Medicine

data_processing:
Quality-checking and trimming:Reads were checked and run to remove the low quality and the primer sequences.Trimming bases 26-51 (i.e., retaining bases 1-25) from all reads led to the highest mapping rates. 88.4% when mapping reads with bowtie and 81.6% when mapping with Tophat.
Read mapping: After trimming the reads, the mapping rates for all samples to hg38 with Bowtie varied between 82-88%, and with Tophat between 76-84%. Bowtie produced more duplicate matches for the reads, about 45-55%, compared to 30-40% for Tophat.
Differential expression:Cuffdiff was run on the 6 ATC samples vs the 6 PTC samples, separately with the Tophat alignments and with the Bowtie alignments. The Tophat alignments led to 38 differentially expressed (DE) precursor miRNAs and no DE mature sequence, and the Bowtie alignments led to 45 DE precursors and 1 DE mature miRNA (mir0373-p). The two sets of precursors had 30 sequences in common.
Assembly: Hg38

source_name: Thyroid

extract_protocol:
Total RNA was extracted from cell lyates by mirVana RNA isolatation kit according to manufacturer's instructions.
Small RNA libraries were constructed using the NEBnext small RNA library preparation method .

tag: cell line

value: BCPAP

tag: cancer type

value: Papillary Thyroid Cancer


title: BCPAP-2


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB931SKC)

description:
https://www.encodeproject.org/experiments/ENCSR707HMU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD14-positive monocyte.
experiment encode accession: ENCSR707HMU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR509FRR
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB931SKC
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: antibody

tag: health state


title: TF ChIP-seq from K562 (ENCLB881XBE)

description:
https://www.encodeproject.org/experiments/ENCSR506SSQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF354C ChIP-seq on human K562
experiment encode accession: ENCSR506SSQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-04-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB881XBE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF354C

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS329AFH at ENCODE; https://www.encodeproject.org/ENCBS329AFH/


title: e1.ctrl.3

description: experiment 1, BMDM cell lines, control, replicate 3

value: BMDM

tag: group

tag: treatment

value: control

tag: replicate


title: e2.TCM.TMAO.1

description: experiment 2, BMDM cell lines, TCM+TMAO treatment, replicate 1

tag: source

value: TCM+TMAO


title: e1.TCM.2

description: experiment 1, BMDM cell lines, TCM treatment, replicate 2

value: TCM


title: e1.TCM.1

description: experiment 1, BMDM cell lines, TCM treatment, replicate 1


title: Control ChIP-seq from K562 (ENCLB272MXY)

description:
https://www.encodeproject.org/experiments/ENCSR775DEO/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-DEAF1 fusion protein.
experiment encode accession: ENCSR775DEO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB272MXY
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens DEAF1

tag: line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to DEAF1.

tag: dev stage

value: ENCBS592TSF at ENCODE; https://www.encodeproject.org/ENCBS592TSF/

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


title: TF ChIP-seq from SK-N-SH (ENCLB221TBD)

description:
https://www.encodeproject.org/experiments/ENCSR376QPI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP30 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR376QPI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR618JZG
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB221TBD
size range: 450-650

source_name: Homo sapiens SK-N-SH cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZFP30 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: SK-N-SH cell line (treated with 6uM all-trans-retinoic acid for 48 hours) stably expressing a C-terminal LAP-tag containing eGFP, fused to ZFP30.

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

tag: lab

value: Michael Snyder

tag: treatments

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

tag: link

value: ENCBS329CJL at ENCODE; https://www.encodeproject.org/ENCBS329CJL/

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


title: e1.TCM.3

description: experiment 1, BMDM cell lines, TCM treatment, replicate 3

tag: cell type


title: TPC-1-3

value: Papillary Thyroid Cancer


title: e1.ctrl.2

description: experiment 1, BMDM cell lines, control, replicate 2

value: BMDM


title: TF ChIP-seq from SK-N-SH (ENCLB619EQB)

description:
https://www.encodeproject.org/experiments/ENCSR376QPI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP30 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR376QPI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR618JZG
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB619EQB
size range: 450-650

value: cell line

tag: biosample encode accession

tag: age

value: female

value: Michael Snyder, Stanford

value: ENCBS219QQR at ENCODE; https://www.encodeproject.org/ENCBS219QQR/


title: BCPAP-1

value: BCPAP


title: Control ChIP-seq from K562 (ENCLB246NSA)

description:
https://www.encodeproject.org/experiments/ENCSR972WGP/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-FOXO4 fusion protein.
experiment encode accession: ENCSR972WGP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB246NSA
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXO4

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOXO4.

value: 53 year

tag: Sex

value: chronic myelogenous leukemia (CML)

value: adult

value: Kevin White

value: ENCBS181OFD at ENCODE; https://www.encodeproject.org/ENCBS181OFD/

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