title: TF ChIP-seq from K562 (ENCLB294GHF)

description:
https://www.encodeproject.org/experiments/ENCSR307YJU/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-MYNN ChIP-seq on human K562
experiment encode accession: ENCSR307YJU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR357LCN
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB294GHF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: MYNN

value: ATCC

value: ENCBS647SJT at ENCODE; https://www.encodeproject.org/ENCBS647SJT/


title: Control ChIP-seq from K562 (ENCLB795CCP)

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/ENCSR765BVG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR765BVG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB795CCP
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 HEY1

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

value: Kevin White

tag: link

value: ENCBS652IGV at ENCODE; https://www.encodeproject.org/ENCBS652IGV/

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


title: Control ChIP-seq from K562 (ENCLB795AAQ)

description:
https://www.encodeproject.org/experiments/ENCSR963WAA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR963WAA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB795AAQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF215

value: ENCBS784ZIC at ENCODE; https://www.encodeproject.org/ENCBS784ZIC/


title: e1.ctrl.1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

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

library_source: transcriptomic

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

organism: Mus musculus

source_name: BMDM

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)

tag: cell type

value: BMDM

tag: group

tag: treatment

value: control

tag: replicate


title: TPC-1-2

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

molecule: total RNA

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

tag: cancer type

value: Papillary Thyroid Cancer


title: TF ChIP-seq from SK-N-SH (ENCLB882AJP)

description:
https://www.encodeproject.org/experiments/ENCSR701SED/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-OSR1 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR701SED
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR301FVM
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB882AJP
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 OSR1 treated with 6uM all-trans-retinoic acid for 48 hours

tag: antibody

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

tag: treatments

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

value: ENCBS242NBY at ENCODE; https://www.encodeproject.org/ENCBS242NBY/

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


title: TF ChIP-seq from SK-N-SH (ENCLB234RAO)

description:
https://www.encodeproject.org/experiments/ENCSR701SED/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-OSR1 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR701SED
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR301FVM
encode release date: 2022-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB234RAO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: cell line

value: female

value: Michael Snyder

value: ENCBS678TES at ENCODE; https://www.encodeproject.org/ENCBS678TES/


title: C643-3

value: Anaplastic Thyroid Cancer


title: TF ChIP-seq from K562 (ENCLB701QIC)

description:
https://www.encodeproject.org/experiments/ENCSR775NLJ/
***************
biological replicate number: 2
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: ENCLB701QIC
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

tag: biosample encode accession

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS740MFH at ENCODE; https://www.encodeproject.org/ENCBS740MFH/

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


title: Sample_9_PDAC_KPC_ChemoImmue

city: St. Louis

first: Chong

last: Zuo

address: 4559 Scott Ave

institute: Washington University in Saint Louis

description:
PDAC Immune Cells
10x Genomics

library_source: transcriptomic single cell

data_processing:
The generated libraries were sequenced by a NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) to an average of 50,000 mean reads per cell. Cellranger mkfastq pipeline (10X Genomics) was used to demultiplex illumine base call files to FASTQ files. Afterward, fastq files from each sample were processed with Cellranger counts and aligned to the mouse mm10 reference genome (Cellranger v.4.0.0, 10X Genomics, mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) to generate feature barcode matrix.
Assembly: mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
Supplementary files format and content: Cell barcodes: TSV, features: TSV, expression matrix: MTX

source_name: Pancreatic Tumor

extract_protocol:
Mice were sacrificed by cardiac perfusion with ~10-15mL PBS-heparin under isofluorane anesthesia. Pancreas or tumor tissue was then isolated, minced with scissors, and digested in ~15-25mL Dulbecco’s Modified Eagle Medium (DMEM) with 2mg/mL Collagenase A and 1x DNase I for either 15 minutes (steady-state pancreas and cerulein treated pancreas) or 25 minutes (tumor tissue) at 37°C with constant stirring. Digestion buffer was quenched with 3mL fetal bovine serum (FBS) and filtered through 100uM Nylon mesh, pelleted by centrifugation (2000rmp for 5 min) and resuspended in FACS buffer (1% BSA in PBS). Cells were then resuspended in FACS Buffer containing CD16/CD32 antibodies to block for 10 minutes on ice, pelleted by centrifugation, then resuspended in fluorophore-conjugated antibodies, stained for 25 minutes on ice, then washed with FACS Buffer. Cells were then immediately sorted on Aria-II (BD Biosciences).  For homeostatic pancreas, live macrophages (CD45+CD11b+CD3-CD19-B220-SiglecF-Ly6G-Ly6C-7AAD-F4/80+MHCIIHI/Lo) were sorted. For PDAC samples, live macrophages and DC enriched immune cells(CD45+CD3-CD19-SiglecF-Ly6G-7AAD-) were sorted. After cells were sorted into FACS Buffer, they were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained.
For homeostatic pancreas, live macrophages (CD45+CD11b+CD3-CD19-B220-SiglecF-Ly6G-Ly6C-7AAD-F4/80+MHCIIHI/Lo) were sorted. For PDAC samples, live macrophages and DC enriched immunecells(CD45+CD3-CD19-SiglecF-Ly6G-7AAD-) were sorted. After cells were sorted into FACS Buffer, they were pelleted by centrifugation, resuspended in 0.04% BSA in PBS, and cell counts were obtained. For GEM/PTX and DMSO treated mice, live immune cells (CD45+EPCAM-CD31-) were sorted

treatment_protocol:
For steady-state samples, no treatment was done. For orthotopic PDAC samples, mice were injected with 50K KP2 cell line derived from KPC mice  in 5uL serum-free DME/F-12 and 45uL Cultrex (Trevigen) directly into the pancreas.
For chemotherapy treatment mice recevied Gemcitabine (50mg/kg) & Palitaxol (5mg/kg) every five days since diagnosis  i.v.

value: ImmuneCells

tag: tissue

value: Pancreatic Tumor

tag: strain

tag: age


title: TPC-1-1

value: Papillary Thyroid Cancer


title: TF ChIP-seq from K562 (ENCLB451JPM)

description:
https://www.encodeproject.org/experiments/ENCSR506SSQ/
***************
biological replicate number: 2
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: ENCLB451JPM
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

tag: Sex

tag: health state

tag: dev stage

value: Kevin White

value: ENCBS968WKY at ENCODE; https://www.encodeproject.org/ENCBS968WKY/


title: Control ChIP-seq from HepG2 (ENCLB697YXY)

description:
https://www.encodeproject.org/experiments/ENCSR149IMO/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 immortalized cell line stably expressing C-terminal eGFP-ATF4 fusion protein.
experiment encode accession: ENCSR149IMO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB697YXY
size range: 450-650

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ATF4

value: cell line

tag: description

value: HepG2 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ATF4.

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

tag: lab

tag: source

tag: link

value: ENCBS674FJH at ENCODE; https://www.encodeproject.org/ENCBS674FJH/

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


title: C643-2

value: Anaplastic Thyroid Cancer


title: TF ChIP-seq from K562 (ENCLB962CXE)

description:
https://www.encodeproject.org/experiments/ENCSR307YJU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-MYNN ChIP-seq on human K562
experiment encode accession: ENCSR307YJU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR357LCN
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB962CXE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: MYNN

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS369YOJ at ENCODE; https://www.encodeproject.org/ENCBS369YOJ/


title: Sample_8_PDAC_KPC_VehImmue

description:
PDAC Immune Cells
10x Genomics

tag: cell type

value: ImmuneCells

value: Pancreatic Tumor


title: C643-1

tag: cell line


title: Sample_6_PDAC_p21CE_Immune_2

description:
PDAC Immune Cells (Macrophages and DC-enriched)
10x Genomics


title: Control ChIP-seq from K562 (ENCLB573NUK)

description:
https://www.encodeproject.org/experiments/ENCSR956GFH/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF778 fusion protein.
experiment encode accession: ENCSR956GFH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB573NUK
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF778

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF778.

value: Kevin White

value: ENCBS371XJU at ENCODE; https://www.encodeproject.org/ENCBS371XJU/

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


title: TF ChIP-seq from K562 (ENCLB048FVM)

description:
https://www.encodeproject.org/experiments/ENCSR303SHG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF699 ChIP-seq on human K562
experiment encode accession: ENCSR303SHG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR790UBY
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB048FVM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF699

value: ENCBS282RKG at ENCODE; https://www.encodeproject.org/ENCBS282RKG/


title: Sample_7_PDAC_KPC_Immune


title: SW1736-3

tag: cancer type

value: Anaplastic Thyroid Cancer


title: Sample_5_PDAC_p21CE_Immune


title: Control ChIP-seq from K562 (ENCLB273QVY)

description:
https://www.encodeproject.org/experiments/ENCSR146HFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR146HFQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB273QVY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF311

value: ENCBS763JWT at ENCODE; https://www.encodeproject.org/ENCBS763JWT/


title: Control ChIP-seq from K562 (ENCLB367FDA)

description:
https://www.encodeproject.org/experiments/ENCSR754EHE/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF586 fusion protein.
experiment encode accession: ENCSR754EHE
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB367FDA
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF586

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF586.

value: 53 year

value: ENCBS187TUK at ENCODE; https://www.encodeproject.org/ENCBS187TUK/


title: TF ChIP-seq from K562 (ENCLB937YBJ)

description:
https://www.encodeproject.org/experiments/ENCSR303SHG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF699 ChIP-seq on human K562
experiment encode accession: ENCSR303SHG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR790UBY
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB937YBJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS659QTS at ENCODE; https://www.encodeproject.org/ENCBS659QTS/


title: TF ChIP-seq from HepG2 (ENCLB817ZMD)

description:
https://www.encodeproject.org/experiments/ENCSR905BNO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR905BNO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR356LLA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB817ZMD
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF816

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS939CAV at ENCODE; https://www.encodeproject.org/ENCBS939CAV/

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


title: Control ChIP-seq from K562 (ENCLB411SHK)

description:
https://www.encodeproject.org/experiments/ENCSR373JEF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR373JEF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB411SHK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB1

value: cell line

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS807ENP at ENCODE; https://www.encodeproject.org/ENCBS807ENP/

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


title: SW1736-2

value: Anaplastic Thyroid Cancer


title: Mint-ChIP-seq from immature natural killer cell (ENCLB576TJJ)

description:
https://www.encodeproject.org/experiments/ENCSR102BZX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human immature natural killer cell.
experiment encode accession: ENCSR102BZX
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR050UUC
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576TJJ
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: Control ChIP-seq from K562 (ENCLB400KNU)

description:
https://www.encodeproject.org/experiments/ENCSR737ZKM/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZSCAN32 fusion protein.
experiment encode accession: ENCSR737ZKM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB400KNU
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZSCAN32

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZSCAN32.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS568XAR at ENCODE; https://www.encodeproject.org/ENCBS568XAR/


title: TF ChIP-seq from HepG2 (ENCLB180UMV)

description:
https://www.encodeproject.org/experiments/ENCSR905BNO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR905BNO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR356LLA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB180UMV
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS149QYV at ENCODE; https://www.encodeproject.org/ENCBS149QYV/

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


title: Sample_4_PDAC_p21WT_Immune_2

value: ImmuneCells

value: Pancreatic Tumor


title: Control ChIP-seq from SK-N-SH (ENCLB303LUD)

description:
https://www.encodeproject.org/experiments/ENCSR349JRD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR349JRD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB303LUD
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 ZFP3 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: Michael Snyder, Stanford

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: ENCBS337BOW at ENCODE; https://www.encodeproject.org/ENCBS337BOW/

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


title: TF ChIP-seq from HepG2 (ENCLB686EBZ)

description:
https://www.encodeproject.org/experiments/ENCSR903JFF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR903JFF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB686EBZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF605

tag: line

value: cell line

value: 15 year

value: male

value: ENCBS212UVU at ENCODE; https://www.encodeproject.org/ENCBS212UVU/


title: SW1736-1

value: Anaplastic Thyroid Cancer


title: Sample_2_Normal_pancreas_Flt3_YFPpositive_Macrophages

description:
Steady-state pancreas macrophages
10x Genomics

source_name: Pancreas

value: macrophages

value: Pancreas

value: Flt3-Cre;LSL-YFP (C57BL/6)


title: P47S p53, 24hours, replicate 2

description:
P47S p53, 24hours, replicate 2
S47.24h.2

data_processing:
RNA-Seq data was aligned using bowtie2 against hg38 version of genome and rsem (ver. 1.2.12) with Ensemble transcriptome information used for gene count
DESeq2 was used for differentail expression analysis
Assembly: hg38
Supplementary files format and content: Prosessed files contains the raw counts for each gene

source_name: lymphoblastoid cell lines

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with Lexogen  QuantSeq 3’mRNA-Seq library prep kit at the Wistar Institute Genomics Facility and subjected to a 75 bp single-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.

tag: treatment

tag: replicate


title: Sample_1_Normal_pancreas_Flt3_YFPnegative_Macrophages

tag: tissue

tag: strain


title: P47S p53, 24hours, replicate 3

description:
P47S p53, 24hours, replicate 3
S47.24h.3


title: Sample_3_PDAC_p21WT_Immune

value: ImmuneCells

value: Pancreatic Tumor

tag: age


title: TF ChIP-seq from HepG2 (ENCLB032KJA)

description:
https://www.encodeproject.org/experiments/ENCSR903JFF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR903JFF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB032KJA
fragmentation methods: sonication (generic)

tag: biosample encode accession

tag: Sex

tag: health state

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS234KHX at ENCODE; https://www.encodeproject.org/ENCBS234KHX/

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


title: Control ChIP-seq from A549 (ENCLB761ILB)

description:
https://www.encodeproject.org/experiments/ENCSR344EOM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR344EOM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB761ILB
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TFCP2L1

value: 58 year

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS248MOI at ENCODE; https://www.encodeproject.org/ENCBS248MOI/

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


title: TF ChIP-seq from WTC11 (ENCLB893KET)

description:
https://www.encodeproject.org/experiments/ENCSR096OUP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NFATC4 ChIP-seq on human WTC11
experiment encode accession: ENCSR096OUP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR267JAO
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB893KET
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NFATC4

value: cell line

value: 30 year

value: male

tag: source

tag: link

value: ENCBS777SQN at ENCODE; https://www.encodeproject.org/ENCBS777SQN/

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


title: P47S p53, 24hours, replicate 1

description:
P47S p53, 24hours, replicate 1
S47.24h.1


title: Control ChIP-seq from K562 (ENCLB438ABX)

description:
https://www.encodeproject.org/experiments/ENCSR724LHB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR724LHB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB438ABX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF700

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS618LAH at ENCODE; https://www.encodeproject.org/ENCBS618LAH/

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


title: P47S p53, 8hours, replicate 3

description:
P47S p53, 8hours, replicate 3
S47.08h.3


title: Control ChIP-seq from SK-N-SH (ENCLB120ZOG)

description:
https://www.encodeproject.org/experiments/ENCSR094JSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR094JSJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB120ZOG
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: ATCC

value: ENCBS294PHT at ENCODE; https://www.encodeproject.org/ENCBS294PHT/

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


title: M16

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

description:
164_HSD (Muscle)
P13605_164_S64

data_processing:
Kallisto
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited Raw counts for every gene and samples
Supplementary_files_format_and_content: Tab-delimited TPM counts for every gene and samples

source_name: Muscle

extract_protocol: At the age of 16 weeks, all mice are sacrificed and necropsies from liver, muscle, WAT and heart tissue were taken for RNA sequencing and lipid quantification.

treatment_protocol: Eight male C57BL/6J mice wild-type mice and eight Pklr-/- mutant mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, both the wild-type and mutant mice were then divided into two groups of 4 mice fed with chow diet, high-sucrose diet for another 8 weeks, respectively.

tag: genotype

value: CTRL

value: Muscle

tag: diet

value: HSD


title: M15

description:
163_HSD (Muscle)
P13605_163_S63

value: male


title: Control ChIP-seq from K562 (ENCLB496HPD)

description:
https://www.encodeproject.org/experiments/ENCSR343BAV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR343BAV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB496HPD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF764

value: cell line

value: 53 year

value: adult

value: Michael Snyder, Stanford

value: ENCBS604SPD at ENCODE; https://www.encodeproject.org/ENCBS604SPD/


title: P47S p53, 8hours, replicate 2

description:
P47S p53, 8hours, replicate 2
S47.08h.2


title: TF ChIP-seq from K562 (ENCLB758WPD)

description:
https://www.encodeproject.org/experiments/ENCSR336GFK/
***************
biological replicate number: 1
technical replicate number: 1
description: CAMTA2 ChIP-seq on human K562
experiment encode accession: ENCSR336GFK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR610PBT, ENCSR275WKO
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB758WPD
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

tag: antibody

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS318YVC at ENCODE; https://www.encodeproject.org/ENCBS318YVC/

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


title: TF ChIP-seq from WTC11 (ENCLB143ZRC)

description:
https://www.encodeproject.org/experiments/ENCSR096OUP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NFATC4 ChIP-seq on human WTC11
experiment encode accession: ENCSR096OUP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR267JAO
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB143ZRC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 30 year

value: Richard Myers

value: ENCBS216HTR at ENCODE; https://www.encodeproject.org/ENCBS216HTR/

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


title: M14

description:
162_HSD (Muscle)
P13605_162_S62

value: CTRL


title: P47S p53, 8hours, replicate 1

description:
P47S p53, 8hours, replicate 1
S47.08h.1


title: M13

description:
161_HSD (Muscle)
P13605_161_S61

value: Muscle


title: TF ChIP-seq from K562 (ENCLB942PDT)

description:
https://www.encodeproject.org/experiments/ENCSR336GFK/
***************
biological replicate number: 2
technical replicate number: 1
description: CAMTA2 ChIP-seq on human K562
experiment encode accession: ENCSR336GFK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR610PBT, ENCSR275WKO
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB942PDT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ATCC

value: ENCBS337TXB at ENCODE; https://www.encodeproject.org/ENCBS337TXB/


title: TF ChIP-seq from K562 (ENCLB165VOZ)

description:
https://www.encodeproject.org/experiments/ENCSR077TKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF707 ChIP-seq on human K562
experiment encode accession: ENCSR077TKJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB165VOZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF707

value: cell line

value: Kevin White

value: ENCBS405OBS at ENCODE; https://www.encodeproject.org/ENCBS405OBS/


title: P47S p53, untreated, replicate 3

description:
P47S p53, untreated, replicate 3
S47.unt.3

value: untreated


title: P47S p53, untreated, replicate 2

description:
P47S p53, untreated, replicate 2
S47.unt.2


title: Control ChIP-seq from SK-N-SH (ENCLB590JBH)

description:
https://www.encodeproject.org/experiments/ENCSR715EHB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR715EHB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB590JBH
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 RARB treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder, Stanford

tag: treatments

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

value: ENCBS840RKQ at ENCODE; https://www.encodeproject.org/ENCBS840RKQ/

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


title: TF ChIP-seq from K562 (ENCLB946CWQ)

description:
https://www.encodeproject.org/experiments/ENCSR077TKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF707 ChIP-seq on human K562
experiment encode accession: ENCSR077TKJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB946CWQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS990JOX at ENCODE; https://www.encodeproject.org/ENCBS990JOX/

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


title: P47S p53, untreated, replicate 1

description:
P47S p53, untreated, replicate 1
S47.unt.1

tag: treatment


title: TF ChIP-seq from HepG2 (ENCLB156QRR)

description:
https://www.encodeproject.org/experiments/ENCSR066EWR/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR066EWR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB156QRR
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZMYM2

value: cell line

value: 15 year

value: male

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS220SKX at ENCODE; https://www.encodeproject.org/ENCBS220SKX/

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


title: M11

description:
159_Chow (Muscle)
P13605_159_S59

value: CTRL

value: Muscle

value: Chow


title: M12

description:
160_Chow (Muscle)
P13605_160_S60


title: Control ChIP-seq from K562 (ENCLB828VZE)

description:
https://www.encodeproject.org/experiments/ENCSR335HNV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR335HNV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB828VZE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF397

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS047LLP at ENCODE; https://www.encodeproject.org/ENCBS047LLP/


title: M10

description:
158_Chow (Muscle)
P13605_158_S58


title: Control ChIP-seq from K562 (ENCLB628QNP)

description:
https://www.encodeproject.org/experiments/ENCSR065HVA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR065HVA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB628QNP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ATCC

value: ENCBS255HXU at ENCODE; https://www.encodeproject.org/ENCBS255HXU/


title: TF ChIP-seq from HepG2 (ENCLB396VKD)

description:
https://www.encodeproject.org/experiments/ENCSR066EWR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR066EWR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB396VKD
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: ENCBS810IXB at ENCODE; https://www.encodeproject.org/ENCBS810IXB/


title: Control ChIP-seq from K562 (ENCLB637WZW)

description:
https://www.encodeproject.org/experiments/ENCSR333CHZ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-NR2F6 fusion protein.
experiment encode accession: ENCSR333CHZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB637WZW
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NR2F6

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2F6.

value: ENCBS517KZB at ENCODE; https://www.encodeproject.org/ENCBS517KZB/

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


title: WT p53, 24hours, replicate 3

description:
WT p53, 24hours, replicate 3
WT.24h.3

value: WT

tag: replicate


title: Control ChIP-seq from K562 (ENCLB960EVZ)

description:
https://www.encodeproject.org/experiments/ENCSR710DAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-TFE3 fusion protein.
experiment encode accession: ENCSR710DAJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB960EVZ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TFE3

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TFE3.

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS357QVK at ENCODE; https://www.encodeproject.org/ENCBS357QVK/


title: M8

description:
156_HSD (Muscle)
P13605_156_S56

tag: strain

value: KO

tag: tissue

value: Muscle

value: HSD


title: TF ChIP-seq from K562 (ENCLB546PES)

description:
https://www.encodeproject.org/experiments/ENCSR026RAK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-MXD1 ChIP-seq on human K562
experiment encode accession: ENCSR026RAK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR357LCN
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB546PES
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MXD1

value: cell line

tag: biosample encode accession

tag: age

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ATCC

value: ENCBS768TBC at ENCODE; https://www.encodeproject.org/ENCBS768TBC/


title: Control ChIP-seq from K562 (ENCLB200YJI)

description:
https://www.encodeproject.org/experiments/ENCSR125OAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-TFCP2 fusion protein.
experiment encode accession: ENCSR125OAJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB200YJI
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TFCP2

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TFCP2.

tag: Sex

tag: health state

value: ENCBS467QNJ at ENCODE; https://www.encodeproject.org/ENCBS467QNJ/


title: TF ChIP-seq from K562 (ENCLB574NTW)

description:
https://www.encodeproject.org/experiments/ENCSR115HLM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB26 ChIP-seq on human K562
experiment encode accession: ENCSR115HLM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR093AOE, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB574NTW
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB26

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB26.

tag: dev stage

tag: lab

value: ENCBS172PVH at ENCODE; https://www.encodeproject.org/ENCBS172PVH/

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


title: WT p53, 24hours, replicate 1

description:
WT p53, 24hours, replicate 1
WT.24h.1

source_name: lymphoblastoid cell lines

value: WT


title: M9

description:
157_Chow (Muscle)
P13605_157_S57

value: male

value: CTRL

value: Chow


title: M7

description:
155_HSD (Muscle)
P13605_155_S55

value: KO

value: Muscle


title: TF ChIP-seq from K562 (ENCLB678RNW)

description:
https://www.encodeproject.org/experiments/ENCSR026RAK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-MXD1 ChIP-seq on human K562
experiment encode accession: ENCSR026RAK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR357LCN
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB678RNW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 53 year

value: Michael Snyder, Stanford

tag: source

tag: link

value: ENCBS805GNZ at ENCODE; https://www.encodeproject.org/ENCBS805GNZ/


title: WT p53, 8hours, replicate 3

description:
WT p53, 8hours, replicate 3
WT.08h.3


title: M6

description:
154_HSD (Muscle)
P13605_154_S54

tag: genotype

tag: diet

value: HSD


title: TF ChIP-seq from WTC11 (ENCLB997QWD)

description:
https://www.encodeproject.org/experiments/ENCSR023IPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PRRX2 ChIP-seq on human WTC11
experiment encode accession: ENCSR023IPQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR395ZBR
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB997QWD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens PRRX2

tag: antibody

value: 30 year

value: adult

value: Richard Myers

value: ENCBS806BOS at ENCODE; https://www.encodeproject.org/ENCBS806BOS/

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


title: Control ChIP-seq from MCF-7 (ENCLB773GJI)

description:
https://www.encodeproject.org/experiments/ENCSR517FPJ/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF7 immortalized cell line stably expressing C-terminal eGFP-ESR1 fusion protein.
experiment encode accession: ENCSR517FPJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB773GJI
size range: 450-650

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ESR1

tag: line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ESR1.

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: Michael Snyder

value: ENCBS856YSY at ENCODE; https://www.encodeproject.org/ENCBS856YSY/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: TF ChIP-seq from WTC11 (ENCLB904XFC)

description:
https://www.encodeproject.org/experiments/ENCSR023IPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-PRRX2 ChIP-seq on human WTC11
experiment encode accession: ENCSR023IPQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR395ZBR
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB904XFC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

value: ENCBS497WYL at ENCODE; https://www.encodeproject.org/ENCBS497WYL/


title: Control ChIP-seq from SK-N-SH (ENCLB116UKH)

description:
https://www.encodeproject.org/experiments/ENCSR921JGF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR921JGF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB116UKH
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 CSRNP3 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder, Stanford

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;

value: ENCBS521JKM at ENCODE; https://www.encodeproject.org/ENCBS521JKM/

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


title: WT p53, 8hours, replicate 1

description:
WT p53, 8hours, replicate 1
WT.08h.1

value: WT

tag: treatment


title: TF ChIP-seq from K562 (ENCLB541YPP)

description:
https://www.encodeproject.org/experiments/ENCSR115HLM/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB26 ChIP-seq on human K562
experiment encode accession: ENCSR115HLM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR093AOE, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB541YPP
size range: 450-650

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB26.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Kevin White

value: ENCBS129ZAS at ENCODE; https://www.encodeproject.org/ENCBS129ZAS/

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


title: TF ChIP-seq from HepG2 (ENCLB323BEV)

description:
https://www.encodeproject.org/experiments/ENCSR015LYB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR015LYB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR388OQM
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB323BEV
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HIC2

value: cell line

value: 15 year

value: male

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS007NRR at ENCODE; https://www.encodeproject.org/ENCBS007NRR/

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


title: Control ChIP-seq from WTC11 (ENCLB413QHG)

description:
https://www.encodeproject.org/experiments/ENCSR325SCU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR325SCU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB413QHG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GTF2I

value: 30 year

value: Michael Snyder, Stanford

value: ENCBS237NXT at ENCODE; https://www.encodeproject.org/ENCBS237NXT/

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


title: WT p53, 8hours, replicate 2

description:
WT p53, 8hours, replicate 2
WT.08h.2

value: WT

tag: replicate


title: M3

description:
151_Chow (Muscle)
P13605_151_S51

source_name: Muscle

tag: strain

value: KO

tag: tissue

value: Muscle

value: Chow


title: M4

description:
152_Chow (Muscle)
P13605_152_S52


title: M5

description:
153_HSD (Muscle)
P13605_153_S53

value: HSD


title: WT p53, untreated, replicate 3

description:
WT p53, untreated, replicate 3
WT.unt.3

value: untreated


title: WT p53, 24hours, replicate 2

description:
WT p53, 24hours, replicate 2
WT.24h.2


title: TF ChIP-seq from HepG2 (ENCLB889MFV)

description:
https://www.encodeproject.org/experiments/ENCSR015LYB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR015LYB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR388OQM
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB889MFV
fragmentation methods: sonication (generic)

value: cell line

tag: biosample encode accession

tag: age

value: 15 year

value: child

value: ENCBS766YMB at ENCODE; https://www.encodeproject.org/ENCBS766YMB/


title: TF ChIP-seq from K562 (ENCLB333HRZ)

description:
https://www.encodeproject.org/experiments/ENCSR103TYK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HBP1 ChIP-seq on human K562
experiment encode accession: ENCSR103TYK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR028MGN, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB333HRZ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HBP1

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to HBP1.

value: 53 year

tag: Sex

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: Kevin White

value: ENCBS204NUR at ENCODE; https://www.encodeproject.org/ENCBS204NUR/

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


title: TF ChIP-seq from SK-N-SH (ENCLB389LKN)

description:
https://www.encodeproject.org/experiments/ENCSR008LHT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ISL1 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR008LHT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR094JSJ
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB389LKN
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 ISL1 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

tag: lab

value: Michael Snyder, Stanford

value: ATCC

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

value: ENCBS398DCU at ENCODE; https://www.encodeproject.org/ENCBS398DCU/

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


title: M2

description:
150_Chow (Muscle)
P13605_150_S50

value: male

value: KO

value: Muscle

value: Chow


title: WT p53, untreated, replicate 1

description:
WT p53, untreated, replicate 1
WT.unt.1

value: WT

value: untreated


title: TF ChIP-seq from K562 (ENCLB637EKB)

description:
https://www.encodeproject.org/experiments/ENCSR103TYK/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HBP1 ChIP-seq on human K562
experiment encode accession: ENCSR103TYK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR028MGN, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB637EKB
size range: 450-650

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to HBP1.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

tag: source

value: Kevin White

tag: link

value: ENCBS048EYN at ENCODE; https://www.encodeproject.org/ENCBS048EYN/


title: H16

description:
148_HSD (Heart)
P13605_148_S48

source_name: Heart

tag: genotype

value: CTRL

value: Heart

tag: diet

value: HSD


title: TF ChIP-seq from SK-N-SH (ENCLB361KMV)

description:
https://www.encodeproject.org/experiments/ENCSR008LHT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ISL1 ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR008LHT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR094JSJ
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB361KMV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

tag: line

value: SK-N-SH

value: 4 year

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder, Stanford

value: ATCC

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

value: ENCBS536OWV at ENCODE; https://www.encodeproject.org/ENCBS536OWV/

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


title: Control ChIP-seq from GM12878 (ENCLB865XJQ)

description:
https://www.encodeproject.org/experiments/ENCSR919BBP/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB4 fusion protein.
experiment encode accession: ENCSR919BBP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB865XJQ
size range: 450-650

source_name: Homo sapiens GM12878 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB4

value: cell line

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB4.

value: unknown

value: female

value: ENCBS890AIO at ENCODE; https://www.encodeproject.org/ENCBS890AIO/

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


title: 361+d IRF5+_6

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina Bcl2fastq2 (2.18)  software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded
Reads were then aligned against Homo sapiens genome from Ensembl version 91 using STAR (version 2.5.2b)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, Homo sapiens GTF genome annotation version 91 from Ensembl was used
All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq2 1.8.1
Statistical treatments and differential analyses were also performed using DESeq2 1.8.1
Genome_build: Homo sapiens Ensembl version 91
Supplementary_files_format_and_content: tsv files containing raw counts

source_name: venous blood

extract_protocol:
Cells were FACS sorted into RNA extraction buffer and flash frozen until extraction with the Qiagen RNEasy kit
20 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech).
Afterwards an average of 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina).
Libraries were multiplexed by 12 on a high-output flowcells.

tag: disease state

value: Type-2 diabetes

value: Blood

value: Adult

tag: sorted cells


title: M1

description:
149_Chow (Muscle)
P13605_149_S49

value: male

value: KO

value: Muscle

value: Chow


title: WT p53, untreated, replicate 2

description:
WT p53, untreated, replicate 2
WT.unt.2

value: WT

tag: treatment

value: untreated

tag: replicate


title: Control ChIP-seq from K562 (ENCLB742YMB)

description:
https://www.encodeproject.org/experiments/ENCSR316UUM/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-TBPL1 fusion protein.
experiment encode accession: ENCSR316UUM
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB742YMB
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TBPL1

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TBPL1.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS977QSE at ENCODE; https://www.encodeproject.org/ENCBS977QSE/

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


title: 361+c IRF5+_6

value: Type-2 diabetes

tag: tissue


title: H15

description:
147_HSD (Heart)
P13605_147_S47

tag: strain

value: CTRL

value: Heart

value: HSD


title: H14

description:
146_HSD (Heart)
P13605_146_S46

tag: Sex

value: male


title: COV_NPC_46

city: New York

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

institute: Columbia University Irving Medical Center

data_processing:
Paired-end sequencing reads were processed using STAR (v. 2.7.3a). We aligned sequencing reads to reference genome in chimeric mode.
Genome_build: GRCh38.Gencode.v30

source_name: Neural progenitor cells

growth_protocol: hNPCs were cultured in DMEM/F12 supplemented with 1x N-2, 1x B-27-RA and 20ng/mL FGF2 on matrigel until transduction. O the 4th day after transduction and selection, media was changed to Brainphys neuron medium plus 1ug/mL dox.

extract_protocol:
Cells were collected in QIAzol (cat. No. 79306) and RNA was isolated using standard methods recommended by the manufacturer. Isolated RNA was cleaned up using the Qiagen Rneasy Mini Kit (cat. No. 74106).
Libraries were prepared from RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR).  Libraries were prepared for SARS-CoV-2 detection using the AmpliSeq for SARS-CoV-2 by Illumina.

treatment_protocol: NPCs stably expressing dCas9-VPR were infected with the gRNA viruses and NGN2 virus and then activated with doxycycline, selected with antibiotics and differentiated for 7 days until SARS-CoV-2 infection. NPC-derived neurons were infected with SARS-CoV-2 (MOI of 0.1) for 24hrs before collection in lysis buffer.

tag: cell type

value: Neural progenitor cells

tag: infection state

value: CoV-

tag: treatment category

value: CRISPRa

value: IL10RB-4 gRNA


title: Control ChIP-seq from K562 (ENCLB459VPW)

description:
https://www.encodeproject.org/experiments/ENCSR506DBU/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-MLX fusion protein.
experiment encode accession: ENCSR506DBU
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB459VPW
size range: 450-650

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

value: cell line

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

tag: biosample encode accession

tag: age

value: female

tag: health state

tag: dev stage

tag: lab

tag: source

value: ENCBS807DUH at ENCODE; https://www.encodeproject.org/ENCBS807DUH/


title: Control ChIP-seq from K562 (ENCLB517IVG)

description:
https://www.encodeproject.org/experiments/ENCSR504LIP/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF57 fusion protein.
experiment encode accession: ENCSR504LIP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB517IVG
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF57

tag: line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF57.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

tag: link

value: ENCBS764KEC at ENCODE; https://www.encodeproject.org/ENCBS764KEC/


title: 361+b IRF5+_6

tag: disease state

value: Type-2 diabetes

value: Blood

value: Adult

tag: sorted cells


title: COV_NPC_45

value: Neural progenitor cells

value: CoV+

tag: treatment


title: 361+a IRF5+_6

tag: tissue


title: H13

description:
145_HSD (Heart)
P13605_145_S45

tag: strain

value: male

tag: genotype

value: CTRL

value: Heart

tag: diet

value: HSD


title: COV_NPC_44

tag: cell type

tag: infection state

value: CRISPRa

value: IL10RB-4 gRNA


title: H12

description:
144_Chow (Heart)
P13605_144_S44

tag: Sex

value: Chow


title: 359+d IRF5+_5

tag: age


title: COV_NPC_48

value: CoV-

tag: treatment category


title: 359+c IRF5+_5


title: TF ChIP-seq from K562 (ENCLB425PXA)

description:
https://www.encodeproject.org/experiments/ENCSR504HOI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-SRF ChIP-seq on human K562
experiment encode accession: ENCSR504HOI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB425PXA
size range: 450-650

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

tag: antibody

value: SRF

value: cell line

tag: description

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

tag: biosample encode accession

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: Kevin White

value: ENCBS976URJ at ENCODE; https://www.encodeproject.org/ENCBS976URJ/

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


title: TF ChIP-seq from K562 (ENCLB564IPK)

description:
https://www.encodeproject.org/experiments/ENCSR504HOI/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-SRF ChIP-seq on human K562
experiment encode accession: ENCSR504HOI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB564IPK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

tag: link

value: ENCBS939PQT at ENCODE; https://www.encodeproject.org/ENCBS939PQT/


title: COV_NPC_43

value: Neural progenitor cells

value: CoV+

tag: treatment


title: Control ChIP-seq from K562 (ENCLB645LVM)

description:
https://www.encodeproject.org/experiments/ENCSR099ETQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR099ETQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB645LVM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: ATCC

value: ENCBS526AHJ at ENCODE; https://www.encodeproject.org/ENCBS526AHJ/


title: COV_NPC_47

value: CoV-

value: CRISPRa

value: IL10RB-4 gRNA


title: H10

description:
142_Chow (Heart)
P13605_142_S42

tag: strain

value: male

tag: genotype

value: CTRL

tag: tissue

value: Heart

value: Chow


title: H11

description:
143_Chow (Heart)
P13605_143_S43

tag: diet


title: 359+b IRF5+_5

tag: disease state

value: Type-2 diabetes

value: Blood

value: Adult

tag: sorted cells


title: 359+a IRF5+_5

tag: age


title: COV_NPC_42

tag: cell type

tag: infection state

tag: treatment category

value: IL10RB-3 gRNA


title: TF ChIP-seq from GM12878 (ENCLB138WUA)

description:
https://www.encodeproject.org/experiments/ENCSR057DTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB11 fusion protein.
experiment encode accession: ENCSR057DTZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR161EAA, ENCSR446IEV
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB138WUA
size range: 450-650

source_name: Homo sapiens GM12878 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB11

tag: antibody

value: cell line

tag: description

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB11.

tag: biosample encode accession

value: unknown

tag: Sex

value: female

tag: health state

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS272XAV at ENCODE; https://www.encodeproject.org/ENCBS272XAV/

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


title: COV_NPC_40

value: Neural progenitor cells

value: CoV-

value: CRISPRa


title: 333+d IRF5+_4


title: H8

description:
140_HSD (Heart)
P13605_140_S40

value: male

value: KO

value: Heart

value: HSD


title: COV_NPC_39

value: CoV+

value: IL10RB-3 gRNA


title: TF ChIP-seq from GM12878 (ENCLB718IYR)

description:
https://www.encodeproject.org/experiments/ENCSR057DTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB11 fusion protein.
experiment encode accession: ENCSR057DTZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR161EAA, ENCSR446IEV
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB718IYR
size range: 450-650

tag: line

value: cell line

value: GM12878 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZBTB11.

tag: dev stage

tag: lab

tag: source

tag: link

value: ENCBS320NPK at ENCODE; https://www.encodeproject.org/ENCBS320NPK/


title: Control ChIP-seq from MCF-7 (ENCLB975HBP)

description:
https://www.encodeproject.org/experiments/ENCSR044HDZ/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF7 immortalized cell line stably expressing C-terminal eGFP-SRF fusion protein.
experiment encode accession: ENCSR044HDZ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2020-08-03
lab: Michael Snyder, Stanford
library encode accession: ENCLB975HBP
size range: 450-650

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SRF

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to SRF.

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: adult

value: ENCBS638SNW at ENCODE; https://www.encodeproject.org/ENCBS638SNW/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/


title: 333+c IRF5+_4

value: Type-2 diabetes

tag: tissue

value: Blood

value: Adult


title: 333+b IRF5+_4

tag: disease state


title: H9

description:
141_Chow (Heart)
P13605_141_S41

tag: strain

value: male

tag: genotype

value: CTRL

value: Heart

tag: diet

value: Chow


title: TF ChIP-seq from K562 (ENCLB809BDQ)

description:
https://www.encodeproject.org/experiments/ENCSR041QAZ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNF219 ChIP-seq on human K562
experiment encode accession: ENCSR041QAZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR926XXG
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB809BDQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens RNF219

value: cell line

tag: age

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS010KHM at ENCODE; https://www.encodeproject.org/ENCBS010KHM/

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


title: H6

description:
138_HSD (Heart)
P13605_138_S38

value: KO

value: HSD


title: COV_NPC_37

tag: cell type

value: Neural progenitor cells

tag: infection state

value: CoV+

tag: treatment category

value: CRISPRa

tag: treatment

value: IL10RB-3 gRNA


title: 332+d IRF5+_3

value: Type-2 diabetes

value: Blood

value: Adult

tag: sorted cells


title: U2OS_H2AZK4_7ac_CTL_sgRNA1

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

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

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

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.

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

value: Control

tag: sgrna

tag: antibody


title: COV_NPC_41

value: CoV-


title: H5

description:
137_HSD (Heart)
P13605_137_S37

tag: Sex

value: male

value: Heart


title: Control ChIP-seq from K562 (ENCLB923SKS)

description:
https://www.encodeproject.org/experiments/ENCSR093QJW/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-RAD21 fusion protein.
experiment encode accession: ENCSR093QJW
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB923SKS
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

tag: line

value: cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to RAD21.

tag: biosample encode accession

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS139XSH at ENCODE; https://www.encodeproject.org/ENCBS139XSH/


title: COV_NPC_36

value: Neural progenitor cells

value: CRISPRa

value: IL10RB-2 gRNA


title: H7

description:
139_HSD (Heart)
P13605_139_S39

tag: strain

tag: genotype

value: KO

tag: tissue

value: HSD


title: COV_NPC_35

tag: cell type

value: CoV-


title: H4

description:
136_Chow (Heart)
P13605_136_S36

value: male

tag: diet

value: Chow


title: COV_NPC_38

tag: infection state

value: CoV+

tag: treatment category

value: IL10RB-3 gRNA


title: 332+c IRF5+_3

tag: disease state

value: Type-2 diabetes

value: Blood

tag: age

value: Adult

tag: sorted cells


title: H3

description:
135_Chow (Heart)
P13605_135_S35

tag: Sex

value: Heart


title: COV_NPC_34

tag: treatment


title: 332+b IRF5+_3


title: Control ChIP-seq from K562 (ENCLB122MQH)

description:
https://www.encodeproject.org/experiments/ENCSR015BRP/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF695 fusion protein.
experiment encode accession: ENCSR015BRP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB122MQH
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF695

tag: line

value: cell line

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF695.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

tag: source

tag: link

value: ENCBS534XLV at ENCODE; https://www.encodeproject.org/ENCBS534XLV/

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


title: Control ChIP-seq from K562 (ENCLB826PBT)

description:
https://www.encodeproject.org/experiments/ENCSR029KZF/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-MAZ fusion protein.
experiment encode accession: ENCSR029KZF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB826PBT
size range: 450-650

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

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

tag: biosample encode accession

tag: health state

tag: dev stage

tag: lab

value: Kevin White

value: ENCBS443HQV at ENCODE; https://www.encodeproject.org/ENCBS443HQV/


title: COV_NPC_33

tag: cell type

value: Neural progenitor cells

value: CoV+

value: CRISPRa

value: IL10RB-2 gRNA


title: H2

description:
134_Chow (Heart)
P13605_134_S34

tag: strain

value: male

tag: genotype

value: KO

tag: tissue

value: Heart

tag: diet

value: Chow


title: 332+a IRF5+_3

tag: disease state

value: Type-2 diabetes

value: Blood

tag: age

value: Adult


title: H1

description:
133_Chow (Heart)
P13605_133_S33

tag: Sex


title: Control ChIP-seq from SK-N-SH (ENCLB198GCC)

description:
https://www.encodeproject.org/experiments/ENCSR000SND/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR000SND
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB198GCC
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 GLIS3 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: child

value: Michael Snyder, Stanford

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: ENCBS897JRP at ENCODE; https://www.encodeproject.org/ENCBS897JRP/

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


title: COV_NPC_32

value: Neural progenitor cells

tag: infection state

value: CoV+

tag: treatment category

value: CRISPRa

tag: treatment

value: IL10RB-2 gRNA


title: W16

description:
132_HSD (WAT)
P13605_132_S32

source_name: WAT

value: male

value: CTRL

value: WAT

value: HSD


title: TF ChIP-seq from K562 (ENCLB111OVT)

description:
https://www.encodeproject.org/experiments/ENCSR041QAZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNF219 ChIP-seq on human K562
experiment encode accession: ENCSR041QAZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR926XXG
encode release date: 2022-01-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB111OVT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

tag: line

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

tag: source

value: ATCC

tag: link

value: ENCBS602TMG at ENCODE; https://www.encodeproject.org/ENCBS602TMG/

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


title: COV_NPC_31


title: 331+d IRF5+_2

value: Type-2 diabetes

value: Blood

value: Adult

tag: sorted cells


title: W15

description:
131_HSD (WAT)
P13605_131_S31


title: 331+c IRF5+_2


title: WT_restingBcells_rep3 [miRNA-seq]

city: Bethesda

first: Joana

middle: A

last: Vidigal

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

data_processing:
Raw reads were processed using cutadapt v4.0 (Martin, 2011) and umitools v1.1.2 (Smith et al., 2017). Briefly, Illumina Universal Adaptor sequences were removed from the 3’ end of the read with ‘cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 20 -q 10 -j 12 --discard-untrimmed -o sample_step1.fastq.gz  --quiet sample.fastq.gz’. A unique molecular identifier (UMI) of 12 random base pairs was removed from the 3’ end of the read and added to the read header using ‘umi_tools extract --3prime --stdin= sample_step1.fastq.gz   --bc-pattern=NNNNNNNNNNNN --stdout= sample_step2.fastq.gz ’. Adaptor sequences were removed from the 5’ end of reads using ‘cutadapt -g GTTCAGAGTTCTACAGTCCGACGATC -m 20 -j 12 -o sample_step3.fastq.gz --quiet sample_step2.fastq.gz’. The remainder 3’adaptor sequence was removed with ‘cutadapt -a AACTGTAGGCACCATCAAT -m 10 -q 10 -j 12 --discard-untrimmed -o Processed_sample.fastq.gz --quiet sample_step3.fastq.gz’. Processed reads were mapped to the mm10 genome with STAR v2.7.9a with the parameters ‘STAR --readFilesIn Processed_sample.fastq.gz --genomeDir mm10 --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999’ as previously described for transposons (Teissandier et al., 2019). Duplicates of mapped reads were removed based on the UMI sequence using umitools, and fastq files generated from deduplicated mapped reads using samtools v1.15 (Danecek et al., 2021). Fastq files from deduplicated reads were re-mapped to the consensus sequence of mouse retrotransposon elements as above. These consensus sequences were downloaded from the SalmonTE github repository (https://github.com/hyunhwan-jeong/SalmonTE/blob/master/reference/mm/mm.fa) which is derived from RepBase v22.06.
Assembly: mm10
Supplementary files format and content: wig

organism: Mus

source_name: Spleen

extract_protocol:
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Cells were used immediately after isolation.
QIAseq miRNA Library kit (Qiagen)

value: Spleen

tag: cell type

value: B cell

tag: molecule type

value: small RNA


title: W14

description:
130_HSD (WAT)
P13605_130_S30

tag: strain

value: male

tag: genotype


title: WT_restingBcells_rep2 [miRNA-seq]

tag: tissue


title: COV_NPC_30

value: Neural progenitor cells

value: CoV-

value: CRISPRa

value: Scramble gRNA


title: 331+b IRF5+_2

source_name: venous blood

tag: disease state


title: 331+a IRF5+_2

tag: age


title: WT_restingBcells_rep1 [miRNA-seq]


title: COV_NPC_28


title: 330+d IRF5+_1


title: COV_NPC_27

value: CoV+


title: WT_restingBcells_rep1

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm10) using bowtie2 (Langmead and Salzberg, 2012) with the options ‘-p 40 --very-sensitive --end-to-end --no-discordant --no-unal --phred33’.  High quality-mapped reads, that we considered as mapping uniquely, were identified with samtools v1.15 (Danecek et al., 2021) using ‘samtools view -q 30’. SAM files containing either all reads or only unique reads were filtered using bedtools v2.30.0 (Quinlan and Hall, 2010) to exclude reads overlapping with the mm10 blacklist (Amemiya et al., 2019; Consortium, 2012). Duplicates were removed with the “Picard Toolkit.” from the Broad Institute (GitHub Repository: https://broadinstitute.github.io/picard/) using ‘java -jar picard.jar MarkDuplicates’. BigWig files were generated using deeptools v3.5.1 (Ramirez et al., 2016) using the RPKM normalization method and visualized on the IGV browser (Robinson et al., 2011).
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Resting primary B cells were isolated from mouse spleens by negative selection using Mouse CD43 (Untouched™ B Cells; Invitrogen). Cells were used immediately after isolation.
libraries were generated using Thruplex DNA-seq Kit from Takara according to manufactures’ instructions.

value: resting B cells

tag: chip antibody


title: W11

description:
127_Chow (WAT)
P13605_127_S27

tag: Sex

value: CTRL

value: WAT

tag: diet

value: Chow


title: SL2 mycelia replicate 3

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

country: China

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) were processed using Trimmomatic (Bolger, Lohse et al. 2014). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Downstream analysis of the cleaned reads was performed using the following software tool in UseGalaxy.eu (Afgan, Baker et al. 2018)
The cleaned reads were mapped using HISAT2 Galaxy version 2.1.0 (Kim, Langmead et al. 2015) to the SWQ7 genome assembly described earlier.
All reads ≥ an alignment quality of 10 were counted using HTSeq-count Galaxy version 0.9.1 where the union mode was used to handle reads overlapping more than one feature and uniquely mapping reads were counted (Anders, Pyl et al. 2015).
The FPKM values were calculated by expressing the counts for a gene per the Kb gene length and per the million mapped counts to all genes.
Genome_build: JAAS_PmSWQ7_1_0_assembly.fsa (PRJNA692555)
Supplementary_files_format_and_content: tab-delimited text files include read counts and FPKM values for each sample; GFF file

organism: Pythium myriotylum

source_name: mycelia

growth_protocol: Fresh cultures of the SWQ7 and SL2 isolates on 10% V8 agar were used to inoculate 10% V8 liquid media. The outer two-thirds of the colony on a single plate was sectioned into ~0.5 cm x ~0.5 cm agar squares and all of the agar squares were transferred to a 9 cm Petri dish containing 10% V8 liquid media. The Petri dishes containing the agar squares inoculum were incubated in the dark at 25°C for 36 h without shaking. The mycelium was harvested (whereby the agar squared were separated from the mycelial mat), washed twice in water, and either collected and flash frozen in liquid nitrogen to use as the control non-infected condition or placed between two ginger leaves. Healthy ginger leaves ~10 cm in length were taken from young plants grown in a greenhouse. Each infection replicate consisted of six ginger leaves forming three side-by-side sandwiches between the mycelia (washed mycelia harvested from one plate was used for each infection replicate). The leaf and mycelia sandwiches were kept moist by placing in a plastic film-covered tray on wetted filter paper where the base of the leaf that was wrapped in wetted tissue was in contact with the wetted filter paper layer. The leaf and mycelia sandwiches were incubated at 25°C in the dark for 24 h. For harvesting from the sandwiches, the parts of the leaves not contacting the mycelia were cut-off and then the free-mycelia between the leaves was gently peeled away (note that this mycelium was not used for RNA extraction). The leaf containing the closely attached mycelia was gently blotted to remove excess liquid and flash frozen in liquid nitrogen and stored at -80°C before extracting the RNA.

extract_protocol:
The infected-leaf samples and mycelia control samples were ground in liquid nitrogen and RNA was extracted using the Trizol reagent. Residual DNA was removed from the RNA samples using a DNase treatment. The RNA integrity was verified using a Bioanalyzer and the RNA purity was measured using a spectrophotometer.
A paired non-stranded library 2x150 bp was prepared using the TruSeq Stranded mRNA LTSample Prep Kit (Illumina).

tag: isolate


title: W10

description:
126_Chow (WAT)
P13605_126_S26


title: 330+b IRF5+_1


title: SL2 mycelia replicate 2


title: COV_NPC_25

source_name: Neural progenitor cells

tag: infection state

tag: treatment category

tag: treatment


title: COV_NPC_29


title: 361-d IRF5-_6


title: W9

description:
125_Chow (WAT)
P13605_125_S25


title: HA_restingBcells_rep1


title: COV_NPC_24

value: shRNA

value: IFNAR2 shRNA


title: 330+a IRF5+_1

value: Type-2 diabetes

value: Blood


title: W12

description:
128_Chow (WAT)
P13605_128_S28


title: SWQ7 mycelia replicate 3


title: COV_NPC_23


title: COV_NPC_22


title: 361-c IRF5-_6

value: Adult


title: SWQ7 mycelia replicate 2


title: 330+c IRF5+_1


title: W8

description:
124_HSD (WAT)
P13605_124_S24

value: KO

value: HSD


title: W7

description:
123_HSD (WAT)
P13605_123_S23

value: male


title: SWQ7 mycelia replicate 1


title: W6

description:
122_HSD (WAT)
P13605_122_S22


title: W5

description:
121_HSD (WAT)
P13605_121_S21


title: 361-a IRF5-_6


title: COV_NPC_21

value: Neural progenitor cells


title: SL2 mycelia replicate 1


title: 361-b IRF5-_6


title: COV_NPC_20


title: W13

description:
129_HSD (WAT)
P13605_129_S29


title: SL2 infection replicate 2


title: SL2 infection replicate 3


title: W3

description:
119_Chow (WAT)
P13605_119_S19


title: W4

description:
120_Chow (WAT)
P13605_120_S20


title: COV_NPC_18

value: CoV-

value: IL10RB shRNA


title: W2

description:
118_Chow (WAT)
P13605_118_S18


title: 359-b IRF5-_5


title: COV_NPC_19


title: W1

description:
117_Chow (WAT)
P13605_117_S17


title: SWQ7 infection replicate 2


title: SL2 infection replicate 1


title: SWQ7 infection replicate 3


title: 359-c IRF5-_5


title: 359-a IRF5-_5


title: COV_NPC_16


title: COV_NPC_17


title: 359-d IRF5-_5


title: 333-d IRF5-_4


title: 333-c IRF5-_4


title: COV_NPC_14


title: L14

description:
114_HSD (Liver)
P13605_114_S14

source_name: Liver

value: Liver


title: CNTNAP4-KO mice 3

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain; basolateral amygdala

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain; basolateral amygdala

tag: gender


title: CNTNAP4-KO mice 2


title: CNTNAP4-KO mice 1


title: L13

description:
113_HSD (Liver)
P13605_113_S13


title: L12

description:
112_Chow (Liver)
P13605_112_S12


title: 332-d IRF5-_3


title: COV_NPC_12

value: Scramble shRNA


title: Wild type mice 3

value: Wild type


title: COV_NPC_15

value: CoV+


title: L15

description:
115_HSD (Liver)
P13605_115_S15

value: CTRL


title: COV_NPC_10

value: shRNA


title: 332-c IRF5-_3


title: 333-b IRF5-_4


title: Wild type mice 1


title: L11

description:
111_Chow (Liver)
P13605_111_S11

value: Chow


title: COV_NPC_9


title: COV_NPC_13


title: SWQ7 infection replicate 1


title: L9

description:
109_Chow (Liver)
P13605_109_S9


title: 332-b IRF5-_3

value: Type-2 diabetes


title: L16

description:
116_HSD (Liver)
P13605_116_S16


title: 333-a IRF5-_4

value: Blood


title: 331-d IRF5-_2

value: Adult


title: COV_NPC_8