title: Whole worm, GFP-3xFLAG-ALG-1, IP, rep1

value: tor137[GFP::3xFLAG::alg-1b] X

value: IP (Argonaute)


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB877LJL)

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/ENCSR033WMA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR033WMA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR414ZUR
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB877LJL

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male adult (36 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

tag: antibody

value: primary cell

tag: biosample encode accession

tag: age

value: 36 year

tag: Sex

value: male

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: John Stamatoyannopoulos

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

tag: link

value: ENCBS253TXN at ENCODE; https://www.encodeproject.org/ENCBS253TXN/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: Fig5c_RTprimer3

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

country: China

institute: ShanghaiTech University

library_source: transcriptomic

data_processing:
quality trimming step using cutadapt (v2.10) command with a quality threshold of 20
the pooled sample was demultiplexed according to the anchored barcode of the first seven nucleotides at the 5’-end from the first read
internal adaptor sequence embedding in some second reads with too short insert was also trimmed
a minimum length threshold of 20 bp for both the first and second reads was used to filter out those pair-end reads with too short insert
bowtie2 (v2.4.1) to align the second read to a reference genome (NC000913.3) (default setting)
Feature counting was carried out using R method summarizeOverlaps from GenomicAlignments package (v1.26.0) in a strand-specific manner, giving rise to a read count table for each gene.
Genome_build: NC000913.3
Supplementary_files_format_and_content: gene raw count data, comma-delimited matrix table

molecule: total RNA

organism: Escherichia coli BW25113

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 3

growth_protocol: Single colony was picked up from a stock LB agar plate and was grown aerobically with shaking at 220 rpm in LB medium overnight (typically 12 hours) as the seed culture. A subculture was established by firstly washing the bacteria once using M63B1 medium (centrifuge by 7000 g, 3 minutes) and resuspension; and then cultivating the seed culture into fresh M63B1 medium (4% volume) and grown for 10 hours with shaking at 220 rpm to reach exponential stage (OD600 ~ 0.6).

extract_protocol:
Bacterial RNA was obtained utilizing the RNAClean XP beads (Beckman, A63987). Lysate was prepared using lysozyme and proteinase K
miniBac-seq, a customized bacterial RNA-seq library construction method, see description of our paper for details

tag: strain


title: TF ChIP-seq from K562 (ENCLB402IEV)

description:
https://www.encodeproject.org/experiments/ENCSR579XWM/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HSF4 ChIP-seq on human K562
experiment encode accession: ENCSR579XWM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR065HVA
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB402IEV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens HSF4

tag: line

value: cell line

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS047IRC at ENCODE; https://www.encodeproject.org/ENCBS047IRC/

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


title: Whole worm, 3xFLAG-WAGO-1, IP, rep1

city: Toronto

first: Uri

last: Seroussi

address: 661 University Ave.

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Adapter sequences were then removed using cutadapt (version 1.15, (Martin, 2011)) using the following command: -a ADAPTER -f fastq -m 16 -M 30 --discard-untrimmed.
The trimmed reads were then aligned to the C. elegans PRJNA13758 ce11 genome assembly (WormBase version WS276) with STAR (version 2.6.0c, (Dobin et al., 2013)) using the following commands: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1.
The reads were then counted using a custom R (version 3.6.3) script against publicly available genome annotations. The WormBase version WS276 PRJNA13758 ce11 canonical geneset annotations were used (excluding miRNAs, repeats and transposons). C. elegans miRNA annotations were obtained from miRBase (release 22.1). For repeats and transposons RepeatMasker + Dfam (ce10 - Oct 2010 - RepeatMasker open-4.0.6 - Dfam 2.0) annotations were used. The UCSC Lift Genome Annotations tool was used to convert ce10 coordinates to ce11 coordinates. Briefly, the counting script used the findOverlaps function from the GenomicAlignments package (version 1.22.1) to assign reads to features. Multiple aligning reads or reads that align to more than one feature were dealt with by counting reads in a sequential manner to the different gene biotypes in the following order (AS stands for antisense): miRNA, piRNA, rRNA, snoRNA, snRNA, tRNA, ncRNA, lincRNA, repeats AS, protein coding AS, pseudogene AS, lincRNA AS, antisense RNA, rRNA AS, snoRNA AS, snRNA AS, tRNA AS, ncRNA AS, miRNA AS, piRNA AS, protein coding, pseudogene, antisense RNA AS, repeats. For reads that align to more than one feature in the same biotype group, the read count was split between the features based on the fraction of uniquely aligned reads to each of those features (unique weighing). See https://github.com/ClaycombLab/Seroussi_2022.
Reads were normalized to library size minus sense reads of: rRNA, snoRNA, snRNA, tRNA, ncRNA, lincRNA, protein coding, and pseudogene. These likely represent RNA degradation products so removing them may eliminate noise. To determine whether small RNAs against a particular target were enriched in an Argonaute IP, the following calculation was made: Enrichment = IP RPM + 0.01 / Input RPM + 0.01. The 0.01 represents a pseudocount to eliminate the possibility of dividing by zero. A target was considered enriched if in every replicate it was at least 2-fold enriched and had at least 5 RPM in the IP replicates. To further refine the analysis, where indicated in the text, only 22G or 26G-RNAs were used to calculate enrichment. These were defined as reads of 20-24nt and 25-27nt respectively with no 5' nucleotide constraints.
Assembly: WS276 PRJNA13758 ce11
Supplementary files format and content: xlsx file containing the results of the enrichment analysis is available on the SuperSeries record.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

extract_protocol:
Synchronous populations of ~100,000 L1 worms were plated on 15 cm NGM plates with ~2ml of 5x concentrated OP50 E. coli as a food source. Five of these plates were used as starting material for protein isolation. Worms were grown for 48h for L4 staged worms or 58h for young adults (worms that had transitioned to producing oocytes but not yet with embryos). Worms were washed three times with M9 buffer (22mM KH2PO4, 42mM Na2HPO4, 86mM NaCl) and one time with EDTA buffer (10% glycerol, 10mM EDTA, 30mM HEPES, 100mM Potassium Acetate). The pellet was flash frozen in a dry ice/ethanol bath. The frozen pellets were stored at -80°C. The frozen pellet was resuspended 1.5:1 (v/v) in ice-cold IP buffer (10% glycerol, 10mM EDTA, 30mM HEPES, 100mM Potassium Acetate, 2mM DTT, 0.1% NP-40) supplemented with protease and phosphatase inhibitors (1 tablet per 5ml buffer of cOmplete™, mini, EDTA-free protease inhibitor cocktail [Roche], 1:100 phosphatase inhibitor cocktail 2 [Sigma], 1:100 phosphatase inhibitor cocktail 3 [Sigma]). If the pellet was to be used for RNA purification, 1% (v/v) SuperaseIN RNAse inhibitor (ThermoFisher) was added. The pellet was homogenized using a stainless steel dounce homogenizer (Wheaton Incorporated) until intact worms were no longer visible. Extracts were centrifuged at 13,000g for 10 min at 4°C, and the supernatant transferred to a fresh tube. A Lowry assay (Lowry et al., 1951) was performed to determine total protein concentration using a Nanodrop 1800C spectrophotometer (ThermoFisher). All IPs were conducted on 5mg of total protein per reaction. Input control samples were made by taking 10% of the lysate before the addition of antibodies. For the IP of GFP tagged Argonautes, GFP-Trap_MA beads (ChromoTek) were equilibrated by washing them three times in 1ml of IP buffer. 20μl of beads were added to 5mg total protein in a reaction volume of 500μl and rotated at 4°C for an hour. The beads were then washed four times with 1ml of IP buffer, separated from the supernatant on a magnetic stand, and rotated for 10 min at 4°C between each wash. For the IP of 3xFLAG tagged Argonautes, Monoclonal Anti-FLAG M2 (Sigma-Aldrich) were bound to Dynabeads™ Protein G (ThermoFisher) or GB-Magic Protein A/G Immunoprecipitation Magnetic Beads according to manufacturer's instructions. 5μg of Anti-FLAG M2 in 200μl of PBS-T were added to 50μl of Dynabeads and rotated at room temperature for 10 min. Then IPs were conducted as described above except the whole 50μl of ANTI-FLAG M2 bound beads were used in the IP. For small RNA sequencing, three to six IP reactions were combined in 200μl of IP buffer. 800μl of Tri Reagent (Molecular Research Centre) was added and the samples were frozen at -80°C. RNA was isolated using Tri Reagent (Molecular Research Centre). Samples were mixed with Tri Reagent in a 1:4 ratio and frozen at -80°C. Samples were vortexed at room temperature for 15min and frozen again at -80°C for 15min. This was repeated for a total of three times. 100μl of chloroform was then added to the samples and centrifuged at 12,000g for 15min at 4°C. The top aqueous phase was transferred to a fresh tube. Phenol:chloroform:isoamyl alcohol (Sigma-Aldrich) was added in a 1:1 ratio and centrifuged at 12,000g for 15min at 4°C. The top aqueous phase was transferred to a fresh tube. 20μg of glycogen (Ambion) and a 1:1 ratio of isopropanol was added to the samples and incubated at -20°C for 30min. Samples were then centrifuged at 16,000g for 30min at 4°C and the supernatant was removed. The pellet was washed with 900μl of 70% ice-cold ethanol for 10min and centrifuged at 16,000g for 10min at 4°C. This was repeated twice. The pellet was then left to air dry for 10min at room temperature and then resuspended in 6-25μl of RNase free water preheated to 70°C.
Small RNA libraries were prepared with the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) following the protocol provided by the manufacturer. 1μg of total RNA or immunoprecipitated RNA was used as starting material. The resulting DNA library was visualized using 8% PAGE and bands corresponding to small RNAs of size range 16-30bp (∼135-150bp on gel) were excised. The DNA was eluted from the excised bands by rotating overnight in 500μl of DNA Gel Elution buffer at room temperature. The DNA was precipitated with 20μg glycogen (Ambion), 50μl of 3M Sodium Acetate pH 5.2 and 1 volume of isopropanol (Sigma-Aldrich) as described above and ultimately resuspended in 12μl of Ultra-Pure water. The library DNA was quantified using a Qubit HS DNA kit (ThermoFisher). Between 12-19 Libraries were pooled in equal amounts and sequenced on a HiSeq 2500 Sequencing System (Illumina).

tag: tissue

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

tag: genotype

tag: treatment

value: IP (Argonaute)


title: Fig5c_RTprimer1

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 1


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB646JBZ)

description:
https://www.encodeproject.org/experiments/ENCSR030KTV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR030KTV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB646JBZ

source_name: Homo sapiens male adult (33 years) stimulated activated naive CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

tag: antibody

value: primary cell

value: 33 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS261THR at ENCODE; https://www.encodeproject.org/ENCBS261THR/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: Fig5c_RTprimer2

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 2


title: Whole worm, 3xFLAG-WAGO-1, input, rep1

value: input (total RNA)


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB673DSL)

description:
https://www.encodeproject.org/experiments/ENCSR030KTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR030KTV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457KLD
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB673DSL

tag: biosample encode accession

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;


title: Mint-ChIP-seq from natural killer cell (ENCLB348CYW)

description:
https://www.encodeproject.org/experiments/ENCSR025UNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR025UNZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB348CYW

source_name: Homo sapiens male adult (33 years) natural killer primary cell

value: natural killer cell

tag: age

value: Charles Lee

value: ENCBS358EEP at ENCODE; https://www.encodeproject.org/ENCBS358EEP/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: Whole worm, 3xFLAG-NRDE-3, input, rep1

value: Whole worm

value: young adult

tag: Sex

value: hermaphrodite

value: tor134[3xFLAG::nrde-3] X


title: TF ChIP-seq from K562 (ENCLB048NSC)

description:
https://www.encodeproject.org/experiments/ENCSR788DXU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR788DXU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB048NSC
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXA3

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS392EUI at ENCODE; https://www.encodeproject.org/ENCBS392EUI/

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


title: Fig4ab_100fg_replicate2

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 100 fg total RNA, replicate 2


title: Whole worm, 3xFLAG-NRDE-3, IP, rep1

value: 20 degrees C

value: IP (Argonaute)


title: TF ChIP-seq from K562 (ENCLB463ZLR)

description:
https://www.encodeproject.org/experiments/ENCSR996SKD/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-CXXC5 ChIP-seq on human K562
experiment encode accession: ENCSR996SKD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR298RRI, ENCSR328FYU
encode release date: 2022-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB463ZLR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CXXC5

value: adult

tag: lab

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS130ZCA at ENCODE; https://www.encodeproject.org/ENCBS130ZCA/


title: Fig4ab_100fg_replicate1

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 100 fg total RNA, replicate 1


title: Control ChIP-seq from WTC11 (ENCLB380FKS)

description:
https://www.encodeproject.org/experiments/ENCSR181GRP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR181GRP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB380FKS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line

value: 30 year

value: male

tag: source

value: ENCBS052ANW at ENCODE; https://www.encodeproject.org/ENCBS052ANW/

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


title: TF ChIP-seq from K562 (ENCLB457JCG)

description:
https://www.encodeproject.org/experiments/ENCSR996SKD/
***************
biological replicate number: 4
technical replicate number: 1
description: eGFP-CXXC5 ChIP-seq on human K562
experiment encode accession: ENCSR996SKD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR298RRI, ENCSR328FYU
encode release date: 2022-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB457JCG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 53 year

value: ENCBS774DNU at ENCODE; https://www.encodeproject.org/ENCBS774DNU/


title: Mint-ChIP-seq from natural killer cell (ENCLB187UXR)

description:
https://www.encodeproject.org/experiments/ENCSR025UNZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR025UNZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB187UXR

value: natural killer cell

value: primary cell

value: 33 year

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS358EEP at ENCODE; https://www.encodeproject.org/ENCBS358EEP/

value: Derived from ENCODE donor ENCDO195VEA; https://www.encodeproject.org/ENCDO195VEA/


title: Whole worm, 3xFLAG-C04F12.1, IP, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: IP (Argonaute)


title: Mint-ChIP-seq from naive B cell (ENCLB744MBE)

description:
https://www.encodeproject.org/experiments/ENCSR024NBY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR024NBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR575ZCX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744MBE

source_name: Homo sapiens female adult (39 years) naive B primary cell

value: naive B cell

value: 39 year

value: female

value: adult

value: John Stamatoyannopoulos

value: ENCBS531INH at ENCODE; https://www.encodeproject.org/ENCBS531INH/

value: Derived from ENCODE donor ENCDO352FHC; https://www.encodeproject.org/ENCDO352FHC/


title: Whole worm, 3xFLAG-C04F12.1, input, rep1

value: input (total RNA)


title: TF ChIP-seq from K562 (ENCLB600ZWN)

description:
https://www.encodeproject.org/experiments/ENCSR787CHF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR787CHF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB600ZWN
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens USF1

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS577OTZ at ENCODE; https://www.encodeproject.org/ENCBS577OTZ/

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


title: Fig4ab_1pg_replicate2

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 1 pg total RNA, replicate 2


title: Control ChIP-seq from K562 (ENCLB446ZMZ)

description:
https://www.encodeproject.org/experiments/ENCSR695PSG/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF436 fusion protein.
experiment encode accession: ENCSR695PSG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB446ZMZ
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF436

tag: description

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF436.

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS391DOM at ENCODE; https://www.encodeproject.org/ENCBS391DOM/


title: Mint-ChIP-seq from naive B cell (ENCLB567OGP)

description:
https://www.encodeproject.org/experiments/ENCSR024NBY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR024NBY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR575ZCX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB567OGP

value: naive B cell

value: primary cell

value: 39 year

value: female

value: Bradley Bernstein, Broad

tag: link


title: TF ChIP-seq from K562 (ENCLB482JMW)

description:
https://www.encodeproject.org/experiments/ENCSR787CHF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR787CHF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB482JMW
fragmentation methods: sonication (generic)

value: adult

value: ENCBS530WMR at ENCODE; https://www.encodeproject.org/ENCBS530WMR/


title: Fig4ab_10pg_replicate2

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 10 pg total RNA, replicate 2

tag: strain


title: TF ChIP-seq from K562 (ENCLB005MLD)

description:
https://www.encodeproject.org/experiments/ENCSR788DXU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR788DXU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB005MLD
fragmentation methods: sonication (generic)

tag: line

value: cell line

value: 53 year

value: ENCBS192LBY at ENCODE; https://www.encodeproject.org/ENCBS192LBY/


title: Fig4ab_1pg_replicate1

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 1 pg total RNA, replicate 1


title: HDMI-oligo

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Contains 32-mer random sequence as HDMI

data_processing:
Library strategy: Seq-scope
1st-Seq and 2nd-Seq data were processed as previously described (PMID: 34115981).
Sequencing by Illumina HiSeq2500 (1st-Seq) and HiSeq-X (2nd-Seq) platforms.
Alignment: From 1st-Seq data, HDMI sequences of clusters located on the bottom tile were extracted and used as a “whitelist” for the cell (HDMI) barcode. First 9 basepairs of 2nd-Seq data Read 2 were copied to Read 1 and used as the unique molecular identifier (UMI). Read 2 was trimmed at the 3’end to remove polyA tails of length 10 or greater, then aligned to human genome (GRCh38) using GeneFull option with no length threshold and no cell filtering using Star/StarSolo 2.7.5c.
Data Binning and Collapsing: The digital expression matrix generated by STARsolo with GeneFull option were combined with spatial information, and further the imaging space were divided into into 100 μm2 (10 μm-sided) square grids and collapsing all HDMI-UMI information into one barcode per grid. We then further refined the spatial resolution of the dataset by transferring the annotations obtained under 10 um grids to the sliding-grid datasets with 5 um, 2 um and 1 um intervals between grids. These processed data are not accepted by GEO, so will be made available in a separate deposit.
Genome_build: human genome (GRCh38)

organism: synthetic construct

source_name: HDMI32 oligonucleotide

extract_protocol:
A 6 mm punch skin biopsy was frozen in OCT medium and stored at -80°C until sectioning.
Seq-scope: 1st-Seq was performed using synthetic HDMI-oligo library. 2nd-Seq was constructed from the tissue as previously described (PMID: 34115981)

value: Synthetic ssDNA library


title: Mint-ChIP-seq from activated T-cell (ENCLB697NBX)

description:
https://www.encodeproject.org/experiments/ENCSR022SNQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR022SNQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR619MIA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB697NBX

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: 43 year

value: male

value: John Stamatoyannopoulos

tag: treatments

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS496KUK at ENCODE; https://www.encodeproject.org/ENCBS496KUK/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: Mint-ChIP-seq from activated T-cell (ENCLB369TOP)

description:
https://www.encodeproject.org/experiments/ENCSR022SNQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR022SNQ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR619MIA
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB369TOP

value: primary cell


title: Fig4ab_10pg_replicate1

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 10 pg total RNA, replicate 1


title: Control ChIP-seq from WTC11 (ENCLB262ZGP)

description:
https://www.encodeproject.org/experiments/ENCSR395ZBR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR395ZBR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB262ZGP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 30 year

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS963XPM at ENCODE; https://www.encodeproject.org/ENCBS963XPM/

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


title: TF ChIP-seq from GM12878 (ENCLB806SSD)

description:
https://www.encodeproject.org/experiments/ENCSR691IQB/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB4 fusion protein.
experiment encode accession: ENCSR691IQB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR919BBP
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB806SSD
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

tag: health state

value: adult

value: Kevin White

value: ENCBS657BYW at ENCODE; https://www.encodeproject.org/ENCBS657BYW/

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


title: Control ChIP-seq from middle frontal area 46 (ENCLB982VSV)

description:
https://www.encodeproject.org/experiments/ENCSR018KWK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018KWK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB982VSV
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: male

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS641FUL at ENCODE; https://www.encodeproject.org/ENCBS641FUL/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: Fig4ab_100pg_replicate2

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 100 pg total RNA, replicate 2


title: Control ChIP-seq from A549 (ENCLB329VOT)

description:
https://www.encodeproject.org/experiments/ENCSR689IML/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human A549
experiment encode accession: ENCSR689IML
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB329VOT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NR2E3

value: 58 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS581NNA at ENCODE; https://www.encodeproject.org/ENCBS581NNA/

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


title: Fig4ab_100pg_replicate1

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 100 pg total RNA, replicate 1


title: TF ChIP-seq from HepG2 (ENCLB307HXZ)

description:
https://www.encodeproject.org/experiments/ENCSR577YCO/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR577YCO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR239QGH
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB307HXZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ARHGAP35

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS583WOV at ENCODE; https://www.encodeproject.org/ENCBS583WOV/

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


title: Histone ChIP-seq from heart left ventricle (ENCLB047RRZ)

description:
https://www.encodeproject.org/experiments/ENCSR017LLJ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 ChIP-seq on heart left ventricle tissue female adult (56 years).
experiment encode accession: ENCSR017LLJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR261PLD
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047RRZ
size range: 200-600

source_name: Homo sapiens female adult (56 years) heart left ventricle tissue

value: heart left ventricle

value: tissue

value: female

value: PGD

value: adult

value: 56 year

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS906ICM at ENCODE; https://www.encodeproject.org/ENCBS906ICM/

value: Derived from ENCODE donor ENCDO907YUG; https://www.encodeproject.org/ENCDO907YUG/


title: TF ChIP-seq from GM12878 (ENCLB646CSO)

description:
https://www.encodeproject.org/experiments/ENCSR691IQB/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878 immortalized cell line stably expressing C-terminal eGFP-ZBTB4 fusion protein.
experiment encode accession: ENCSR691IQB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR919BBP
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB646CSO
size range: 450-650

value: cell line

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

value: unknown

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS824EQX at ENCODE; https://www.encodeproject.org/ENCBS824EQX/

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


title: Fig4ab_1ng_replicate2

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 1 ng total RNA, replicate 2


title: TF ChIP-seq from A549 (ENCLB931BPN)

description:
https://www.encodeproject.org/experiments/ENCSR995CFS/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HEYL ChIP-seq on human A549
experiment encode accession: ENCSR995CFS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR331KRW
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB931BPN
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: HEYL

value: 58 year

value: male

value: ATCC

value: ENCBS255MXO at ENCODE; https://www.encodeproject.org/ENCBS255MXO/

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


title: Histone ChIP-seq from heart left ventricle (ENCLB436MES)

description:
https://www.encodeproject.org/experiments/ENCSR017LLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on heart left ventricle tissue female adult (56 years).
experiment encode accession: ENCSR017LLJ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR261PLD
encode release date: 2022-02-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB436MES
size range: 200-600

value: heart left ventricle

value: tissue

value: female

value: PGD

value: adult

value: 56 year

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB944FTY)

description:
https://www.encodeproject.org/experiments/ENCSR016WNP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR016WNP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB944FTY

source_name: Homo sapiens male adult (36 years) central memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: 36 year

value: John Stamatoyannopoulos

value: ENCBS900WYP at ENCODE; https://www.encodeproject.org/ENCBS900WYP/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: Control ChIP-seq from K562 (ENCLB907YDC)

description:
https://www.encodeproject.org/experiments/ENCSR497AAP/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ELK3 fusion protein.
experiment encode accession: ENCSR497AAP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB907YDC
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ELK3

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELK3.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS621NZQ at ENCODE; https://www.encodeproject.org/ENCBS621NZQ/

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


title: Fig3bc_TruSeq

source_name: RNA-seq data in Fig. 3bc, using TruSeq kit to generate RNA-seq data


title: Control ChIP-seq from K562 (ENCLB234WJB)

description:
https://www.encodeproject.org/experiments/ENCSR871LVN/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-FOXA3 fusion protein.
experiment encode accession: ENCSR871LVN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB234WJB
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXA3

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOXA3.

value: female

value: ENCBS869ABD at ENCODE; https://www.encodeproject.org/ENCBS869ABD/


title: TF ChIP-seq from A549 (ENCLB044TEK)

description:
https://www.encodeproject.org/experiments/ENCSR995CFS/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-HEYL ChIP-seq on human A549
experiment encode accession: ENCSR995CFS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR331KRW
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB044TEK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: HEYL

value: 58 year

value: male

value: adult

value: ATCC

value: ENCBS728SHN at ENCODE; https://www.encodeproject.org/ENCBS728SHN/

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


title: TF ChIP-seq from HepG2 (ENCLB520HOM)

description:
https://www.encodeproject.org/experiments/ENCSR577YCO/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR577YCO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR239QGH
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB520HOM
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS137IAU at ENCODE; https://www.encodeproject.org/ENCBS137IAU/

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


title: Fig3bcde_ourmethod

source_name: RNA-seq data in Fig. 3bcde, using miniBac-seq method to generate RNA-seq data


title: Control ChIP-seq from motor neuron (ENCLB104ZBF)

description:
https://www.encodeproject.org/experiments/ENCSR175HRD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human motor neuron
experiment encode accession: ENCSR175HRD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-12-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB104ZBF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male child (6 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: 6 year

value: Healthy donor

value: Michael Snyder, Stanford

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

value: ENCBS479HWG at ENCODE; https://www.encodeproject.org/ENCBS479HWG/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB535DHW)

description:
https://www.encodeproject.org/experiments/ENCSR016WNP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR016WNP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB535DHW

value: primary cell

value: 36 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS900WYP at ENCODE; https://www.encodeproject.org/ENCBS900WYP/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: Control ChIP-seq from K562 (ENCLB323UBL)

description:
https://www.encodeproject.org/experiments/ENCSR293CYB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR293CYB
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB323UBL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF444

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS790OKN at ENCODE; https://www.encodeproject.org/ENCBS790OKN/

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


title: Control ChIP-seq from WTC11 (ENCLB069VET)

description:
https://www.encodeproject.org/experiments/ENCSR178OJR/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR178OJR
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-04-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB069VET
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using TALEN inserting M. musculus Neurog2

value: 30 year

value: Michael Snyder, Stanford

value: ENCBS561HIP at ENCODE; https://www.encodeproject.org/ENCBS561HIP/

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


title: TF ChIP-seq from HepG2 (ENCLB942PAN)

description:
https://www.encodeproject.org/experiments/ENCSR170AMG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR170AMG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR479INP
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB942PAN
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXC1

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS073YLW at ENCODE; https://www.encodeproject.org/ENCBS073YLW/

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


title: Control ChIP-seq from middle frontal area 46 (ENCLB223YES)

description:
https://www.encodeproject.org/experiments/ENCSR018KWK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR018KWK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB223YES
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: adult

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS641FUL at ENCODE; https://www.encodeproject.org/ENCBS641FUL/

value: Derived from ENCODE donor ENCDO197QVG; https://www.encodeproject.org/ENCDO197QVG/


title: TF ChIP-seq from HepG2 (ENCLB530HUV)

description:
https://www.encodeproject.org/experiments/ENCSR170AMG/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR170AMG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR479INP
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB530HUV
fragmentation methods: sonication (generic)

value: cell line

value: ENCBS939VVY at ENCODE; https://www.encodeproject.org/ENCBS939VVY/


title: Control ChIP-seq from MCF-7 (ENCLB958NKR)

description:
https://www.encodeproject.org/experiments/ENCSR298PFG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR298PFG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB958NKR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting H. sapiens BRCA2

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS099MVH at ENCODE; https://www.encodeproject.org/ENCBS099MVH/

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


title: Mint-ChIP-seq from dendritic cell (ENCLB897WSK)

description:
https://www.encodeproject.org/experiments/ENCSR015IZP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR015IZP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB897WSK

source_name: Homo sapiens male adult (51 years) dendritic primary cell

value: dendritic cell

value: primary cell

value: 51 year

value: male

value: Charles Lee

value: ENCBS682CBV at ENCODE; https://www.encodeproject.org/ENCBS682CBV/

value: Derived from ENCODE donor ENCDO346BRO; https://www.encodeproject.org/ENCDO346BRO/


title: Fig3a_replicate2_4ab_5ng

source_name: RNA-seq data in Fig. 3a, using miniBac-seq method to generate RNA-seq data from 5 ng total RNA, replicate 2


title: Mint-ChIP-seq from dendritic cell (ENCLB872NBJ)

description:
https://www.encodeproject.org/experiments/ENCSR015IZP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR015IZP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872NBJ

value: adult

value: Bradley Bernstein, Broad


title: TF ChIP-seq from K562 (ENCLB751KME)

description:
https://www.encodeproject.org/experiments/ENCSR494ZGC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ELF4 ChIP-seq on human K562
experiment encode accession: ENCSR494ZGC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR099EPT, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB751KME
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ELF4

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELF4.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS774SNZ at ENCODE; https://www.encodeproject.org/ENCBS774SNZ/

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


title: Control ChIP-seq from MCF 10A (ENCLB234ZVT)

description:
https://www.encodeproject.org/experiments/ENCSR011HCN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR011HCN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB234ZVT
size range: 200-600

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: 36 year

value: female

value: fibrocystic disease

value: Mats Ljungman

value: ENCBS491FRZ at ENCODE; https://www.encodeproject.org/ENCBS491FRZ/

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


title: Control ChIP-seq from K562 (ENCLB772WJI)

description:
https://www.encodeproject.org/experiments/ENCSR577XMD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR577XMD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-03-22
lab: Michael Snyder, Stanford
library encode accession: ENCLB772WJI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF800

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS881OLI at ENCODE; https://www.encodeproject.org/ENCBS881OLI/


title: Control ChIP-seq from MCF 10A (ENCLB301FEZ)

description:
https://www.encodeproject.org/experiments/ENCSR011HCN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR011HCN
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB301FEZ
size range: 200-600

value: cell line

value: adult

value: Bradley Bernstein, Broad


title: TF ChIP-seq from K562 (ENCLB360XPV)

description:
https://www.encodeproject.org/experiments/ENCSR576AMK/
***************
biological replicate number: 2
technical replicate number: 1
description: PPARD ChIP-seq on human K562
experiment encode accession: ENCSR576AMK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR444SQF, ENCSR328FYU
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB360XPV
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: PPARD

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS381ZUY at ENCODE; https://www.encodeproject.org/ENCBS381ZUY/


title: Fig2bc_Customized rRNA depletion

source_name: RNA-seq data in Fig. 2b, c, using our customized rRNA depletion method


title: Fig2bc_Commercial rRNA depletion

source_name: RNA-seq data in Fig. 2b, c, using commercial rRNA depletion method


title: TF ChIP-seq from K562 (ENCLB548YQC)

description:
https://www.encodeproject.org/experiments/ENCSR576AMK/
***************
biological replicate number: 1
technical replicate number: 1
description: PPARD ChIP-seq on human K562
experiment encode accession: ENCSR576AMK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR444SQF, ENCSR328FYU
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB548YQC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: Kevin White

value: ENCBS039AWE at ENCODE; https://www.encodeproject.org/ENCBS039AWE/

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


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB823RWC)

description:
https://www.encodeproject.org/experiments/ENCSR386JFM/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR386JFM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR917PCR
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB823RWC
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS802GRA at ENCODE; https://www.encodeproject.org/ENCBS802GRA/

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


title: Control ChIP-seq from K562 (ENCLB664XAP)

description:
https://www.encodeproject.org/experiments/ENCSR493HMV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR493HMV
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB664XAP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: cell line

value: female

value: adult

value: Michael Snyder, Stanford

value: ENCBS105BIG at ENCODE; https://www.encodeproject.org/ENCBS105BIG/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB877UCD)

description:
https://www.encodeproject.org/experiments/ENCSR010HNY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR010HNY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB877UCD
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS270KUL at ENCODE; https://www.encodeproject.org/ENCBS270KUL/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: Fig3a_replicate1_4ab_5ng

source_name: RNA-seq data in Fig. 3a, using miniBac-seq method to generate RNA-seq data from 5 ng total RNA, replicate 1


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB216DMO)

description:
https://www.encodeproject.org/experiments/ENCSR386JFM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell.
experiment encode accession: ENCSR386JFM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR917PCR
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216DMO
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500,Illumina NextSeq 500

value: CD4-positive, alpha-beta memory T cell

value: primary cell

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

value: not collected

value: healthy


title: Control ChIP-seq from K562 (ENCLB013CBB)

description:
https://www.encodeproject.org/experiments/ENCSR675PWC/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZFP1 fusion protein.
experiment encode accession: ENCSR675PWC
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB013CBB
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZFP1

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZFP1.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS004ICW at ENCODE; https://www.encodeproject.org/ENCBS004ICW/

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


title: Control Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB836LRE)

description:
https://www.encodeproject.org/experiments/ENCSR007JEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007JEX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB836LRE

source_name: Homo sapiens male adult (38 years) activated naive CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours

value: 38 year

value: male

value: adult

value: John Stamatoyannopoulos

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS567USS at ENCODE; https://www.encodeproject.org/ENCBS567USS/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: Astro_3_L2

city: Eugene

first: Austin

last: Seroka

state: Oregon

address: 1440 Franklin Blvd

department: Institute of Neuroscience

institute: University of Oregon

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Drosophila BDGP6.22
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: embryos were reared at 25 degree Celsius until indicated stage

extract_protocol:
We dissociated a 50-100 µl pool of surface-sterilized Drosophila embryos (stage 17, 17-18.5 hours after egg laying) in C+G medium using a dounce homogenizer. Cells were then washed and filtered with 40 µm cell strainer. The concentration of viable cells was quantified with Trypan blue using a TC20 automated cell counter. Samples with a minimum viability of 80% were then diluted to 1000 cells/ µl in 1X PBS supplemented with .04% BSA and sequenced using the 10X NextGem v3.1 single cell platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction.

tag: cell type

value: whole embryo

tag: tissue

value: alrm-gal4, UAS myr::GFP; 25H07-gal4, UAS-redstinger::NLS


title: Astro_1_L2

description: 10x Genomics


title: Astro_4_L2

description: 10x Genomics


title: TF ChIP-seq from K562 (ENCLB517LMY)

description:
https://www.encodeproject.org/experiments/ENCSR867MET/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-THRB ChIP-seq on human K562
experiment encode accession: ENCSR867MET
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR226CLB, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB517LMY
size range: 450-650

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

value: THRB

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

value: female

value: Michael Snyder, Stanford

value: ENCBS219SPR at ENCODE; https://www.encodeproject.org/ENCBS219SPR/


title: Astro_2_L2

description: 10x Genomics


title: TF ChIP-seq from HepG2 (ENCLB833AES)

description:
https://www.encodeproject.org/experiments/ENCSR159RBE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR159RBE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB833AES
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens GLYR1

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS385DIB at ENCODE; https://www.encodeproject.org/ENCBS385DIB/

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


title: TF ChIP-seq from HepG2 (ENCLB488CRD)

description:
https://www.encodeproject.org/experiments/ENCSR159RBE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR159RBE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB488CRD
fragmentation methods: sonication (generic)

value: male

value: ENCBS309WID at ENCODE; https://www.encodeproject.org/ENCBS309WID/


title: Control ChIP-seq from K562 (ENCLB567MET)

description:
https://www.encodeproject.org/experiments/ENCSR485MYT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR485MYT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-05-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB567MET
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

value: Kevin White

value: ENCBS757VYY at ENCODE; https://www.encodeproject.org/ENCBS757VYY/

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


title: Astro_4_L1

description: 10x Genomics

value: whole embryo

value: alrm-gal4, UAS myr::GFP; 25H07-gal4, UAS-redstinger::NLS


title: Mint-ChIP-seq from activated T-cell (ENCLB127SIA)

description:
https://www.encodeproject.org/experiments/ENCSR006QLV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR006QLV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR619MIA
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB127SIA

source_name: Homo sapiens male adult (43 years) activated T-cell primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated T-cell

value: primary cell

value: 43 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS496KUK at ENCODE; https://www.encodeproject.org/ENCBS496KUK/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB979BWO)

description:
https://www.encodeproject.org/experiments/ENCSR010HNY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR010HNY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR373OML
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB979BWO
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS270KUL at ENCODE; https://www.encodeproject.org/ENCBS270KUL/

value: Derived from ENCODE donor ENCDO258GJF; https://www.encodeproject.org/ENCDO258GJF/


title: TF ChIP-seq from K562 (ENCLB118VVL)

description:
https://www.encodeproject.org/experiments/ENCSR279OXE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZFP30 ChIP-seq on human K562
experiment encode accession: ENCSR279OXE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-04-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB118VVL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZFP30

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS732WSM at ENCODE; https://www.encodeproject.org/ENCBS732WSM/

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


title: TF ChIP-seq from A549 (ENCLB487YLP)

description:
https://www.encodeproject.org/experiments/ENCSR769FXE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NPAS2 ChIP-seq on human A549
experiment encode accession: ENCSR769FXE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR331KRW
encode release date: 2022-05-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB487YLP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NPAS2

value: 58 year

value: male

value: ATCC

value: ENCBS089JVD at ENCODE; https://www.encodeproject.org/ENCBS089JVD/

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


title: Astro_3_L1

description: 10x Genomics

value: whole embryo

value: alrm-gal4, UAS myr::GFP; 25H07-gal4, UAS-redstinger::NLS


title: Control ChIP-seq from K562 (ENCLB300HVY)

description:
https://www.encodeproject.org/experiments/ENCSR479AEG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR479AEG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB300HVY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF696

value: female

value: ENCBS890GOD at ENCODE; https://www.encodeproject.org/ENCBS890GOD/


title: Mint-ChIP-seq from activated T-cell (ENCLB969KIM)

description:
https://www.encodeproject.org/experiments/ENCSR006QLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR006QLV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR619MIA
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB969KIM

value: activated T-cell

value: primary cell

value: 43 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour;

value: ENCBS496KUK at ENCODE; https://www.encodeproject.org/ENCBS496KUK/

value: Derived from ENCODE donor ENCDO106CDP; https://www.encodeproject.org/ENCDO106CDP/


title: TF ChIP-seq from A549 (ENCLB375GEE)

description:
https://www.encodeproject.org/experiments/ENCSR769FXE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NPAS2 ChIP-seq on human A549
experiment encode accession: ENCSR769FXE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR331KRW
encode release date: 2022-05-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB375GEE
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 58 year

value: adult

value: Michael Snyder, Stanford

value: ENCBS766SOH at ENCODE; https://www.encodeproject.org/ENCBS766SOH/


title: Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB491VTV)

description:
https://www.encodeproject.org/experiments/ENCSR004YPL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR004YPL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR368JDN
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB491VTV

source_name: Homo sapiens male adult (33 years) stimulated activated effector memory CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, 100 ng/mL Interleukin-1...

value: 33 year

value: male

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS523QRO at ENCODE; https://www.encodeproject.org/ENCBS523QRO/

value: Derived from ENCODE donor ENCDO830ROH; https://www.encodeproject.org/ENCDO830ROH/


title: Control ChIP-seq from SK-N-SH (ENCLB092QGD)

description:
https://www.encodeproject.org/experiments/ENCSR477JXX/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR477JXX
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB092QGD
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 ELK3 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: 4 year

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder

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

value: ENCBS302FUH at ENCODE; https://www.encodeproject.org/ENCBS302FUH/

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


title: Astro_2_L1

description: 10x Genomics

value: whole embryo

value: alrm-gal4, UAS myr::GFP; 25H07-gal4, UAS-redstinger::NLS


title: Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB337UFE)

description:
https://www.encodeproject.org/experiments/ENCSR004YPL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR004YPL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR368JDN
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB337UFE

value: primary cell

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos


title: Control Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB529QOS)

description:
https://www.encodeproject.org/experiments/ENCSR007JEX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR007JEX
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB529QOS

value: 38 year

value: male

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS567USS at ENCODE; https://www.encodeproject.org/ENCBS567USS/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: TF ChIP-seq from K562 (ENCLB663AOB)

description:
https://www.encodeproject.org/experiments/ENCSR158LJN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR158LJN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB663AOB
fragmentation methods: sonication (generic)

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

value: MAX

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS079SLQ at ENCODE; https://www.encodeproject.org/ENCBS079SLQ/

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


title: TF ChIP-seq from K562 (ENCLB808KVI)

description:
https://www.encodeproject.org/experiments/ENCSR867MET/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-THRB ChIP-seq on human K562
experiment encode accession: ENCSR867MET
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR226CLB, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB808KVI
size range: 450-650

value: THRB

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

value: adult

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS488RWT at ENCODE; https://www.encodeproject.org/ENCBS488RWT/


title: Astro_1_L1

description: 10x Genomics

value: whole embryo

value: alrm-gal4, UAS myr::GFP; 25H07-gal4, UAS-redstinger::NLS


title: TF ChIP-seq from K562 (ENCLB895TEI)

description:
https://www.encodeproject.org/experiments/ENCSR158LJN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR158LJN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB895TEI
fragmentation methods: sonication (generic)

value: MAX

value: ENCBS149HDM at ENCODE; https://www.encodeproject.org/ENCBS149HDM/


title: Control ChIP-seq from activated B cell (ENCLB537IWY)

description:
https://www.encodeproject.org/experiments/ENCSR003FJP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR003FJP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB537IWY
size range: 200-600

source_name: Homo sapiens male adult (22 years) activated B primary cell

value: activated B cell

value: primary cell

value: 22 year

value: male

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS458DQO at ENCODE; https://www.encodeproject.org/ENCBS458DQO/

value: Derived from ENCODE donor ENCDO383AQS; https://www.encodeproject.org/ENCDO383AQS/


title: TF ChIP-seq from K562 (ENCLB163UVX)

description:
https://www.encodeproject.org/experiments/ENCSR475ZYA/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-OTX1 ChIP-seq on human K562
experiment encode accession: ENCSR475ZYA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-02-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB163UVX
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens OTX1

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to OTX1.

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS140JOU at ENCODE; https://www.encodeproject.org/ENCBS140JOU/

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


title: HepG2 siLINC01186 rep2

city: Guangzhou

first: Xingyuan

last: Liu

state: Guangdong

address: Guangzhou, Guangdong, China

department: Public Health

institute: Southern Medical University

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM values for each Sample.

growth_protocol: HepG2 were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with siNC or siLINC01186 with transfection reagent when the cells were about 70% confluency and then cells were incubate in non-serum DMEM at 37°C with 5% CO2 for 6 hour. After 6h change the medium with 10% serum DMEM and continuously incubate  24h.

tag: cell line


title: HepG2 siNC rep2

tag: treatment

value: siNC


title: Control ChIP-seq from activated B cell (ENCLB018BVA)

description:
https://www.encodeproject.org/experiments/ENCSR003FJP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR003FJP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB018BVA
size range: 200-600

value: adult


title: Fig4ab_1ng_replicate1

source_name: RNA-seq data in Fig. 4a, b, using miniBac-seq method to generate RNA-seq data from 1 ng total RNA, replicate 1


title: TF ChIP-seq from K562 (ENCLB723MTO)

description:
https://www.encodeproject.org/experiments/ENCSR475ZYA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-OTX1 ChIP-seq on human K562
experiment encode accession: ENCSR475ZYA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-02-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB723MTO
size range: 450-650

tag: antibody

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS455GBQ at ENCODE; https://www.encodeproject.org/ENCBS455GBQ/


title: Control ChIP-seq from K562 (ENCLB326KDA)

description:
https://www.encodeproject.org/experiments/ENCSR865FVS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR865FVS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-07-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB326KDA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF324

tag: biosample encode accession

value: ENCBS921ANB at ENCODE; https://www.encodeproject.org/ENCBS921ANB/


title: Control ChIP-seq from K562 (ENCLB134PWD)

description:
https://www.encodeproject.org/experiments/ENCSR270QJI/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 immortalized cell line stably expressing C-terminal eGFP-ZNF561 fusion protein.
experiment encode accession: ENCSR270QJI
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB134PWD
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF561

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF561.

tag: age

value: ENCBS504NTW at ENCODE; https://www.encodeproject.org/ENCBS504NTW/


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB361LRN)

description:
https://www.encodeproject.org/experiments/ENCSR002YXM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR002YXM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR569JUB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361LRN

source_name: Homo sapiens male adult (36 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

value: 36 year

tag: Sex

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS793QJH at ENCODE; https://www.encodeproject.org/ENCBS793QJH/

value: Derived from ENCODE donor ENCDO424UPQ; https://www.encodeproject.org/ENCDO424UPQ/


title: HepG2 siLINC01186 rep1


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB746DUJ)

description:
https://www.encodeproject.org/experiments/ENCSR002YXM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR002YXM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR569JUB
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB746DUJ

tag: dev stage


title: HepG2 siNC rep1


title: TF ChIP-seq from K562 (ENCLB161OLH)

description:
https://www.encodeproject.org/experiments/ENCSR377HQG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF140 ChIP-seq on human K562
experiment encode accession: ENCSR377HQG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB161OLH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF140

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

tag: lab

value: ENCBS726FLJ at ENCODE; https://www.encodeproject.org/ENCBS726FLJ/


title: TF ChIP-seq from right lobe of liver (ENCLB377ZMO)

description:
https://www.encodeproject.org/experiments/ENCSR000VGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000VGD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR886ATT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB377ZMO
size range: 200-600

source_name: Homo sapiens female adult (47 years) right lobe of liver tissue

value: CTCF

value: right lobe of liver

value: tissue

value: 47 year

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

value: adult

tag: source

value: Shin Lin

value: ENCBS025MJZ at ENCODE; https://www.encodeproject.org/ENCBS025MJZ/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: TF ChIP-seq from K562 (ENCLB642YXU)

description:
https://www.encodeproject.org/experiments/ENCSR158BGH/
***************
biological replicate number: 4
technical replicate number: 1
description: MBD1 ChIP-seq on human K562
experiment encode accession: ENCSR158BGH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR207GLV, ENCSR012KTG
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB642YXU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MBD1

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS248MKT at ENCODE; https://www.encodeproject.org/ENCBS248MKT/

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


title: TF ChIP-seq from K562 (ENCLB258NRA)

description:
https://www.encodeproject.org/experiments/ENCSR377HQG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF140 ChIP-seq on human K562
experiment encode accession: ENCSR377HQG
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB258NRA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 53 year

value: Kevin White

value: ENCBS903KYK at ENCODE; https://www.encodeproject.org/ENCBS903KYK/


title: Control ChIP-seq from SK-N-SH (ENCLB311HEF)

description:
https://www.encodeproject.org/experiments/ENCSR983OYA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human SK-N-SH
experiment encode accession: ENCSR983OYA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-04-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB311HEF
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 NR1D1 treated with 6uM all-trans-retinoic acid for 48 hours

value: SK-N-SH

value: 4 year

value: female

value: Metastatic neuroblastoma from bone marrow

value: child

value: Michael Snyder

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

value: ENCBS507IGE at ENCODE; https://www.encodeproject.org/ENCBS507IGE/

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


title: TF ChIP-seq from MCF-7 (ENCLB319WSU)

description:
https://www.encodeproject.org/experiments/ENCSR658GYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TSC22D2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR658GYQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR439GBR, ENCSR734XLI
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB319WSU
size range: 450-650

source_name: Homo sapiens MCF-7 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TSC22D2

tag: description

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TSC22D2.

value: 69 year

value: breast cancer (adenocarcinoma)

value: adult

value: Michael Snyder, Stanford

value: ENCBS308UUT at ENCODE; https://www.encodeproject.org/ENCBS308UUT/

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


title: EAEC_CW

city: Santiago

first: Mauricio

middle: J.

last: Farfan

address: Antonio Varas 360, Providencia

department: Departamento de Pediatria y Cirugia Infantil

country: Chile

institute: Universidad de Chile

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

organism: Escherichia coli

source_name: bacterial cells

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

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

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

tag: sample type

value: Enteroaggregative Escherichia coli

value: Incubation with supernatant from Citrobacter werkmanii culture


title: TF ChIP-seq from K562 (ENCLB040QPF)

description:
https://www.encodeproject.org/experiments/ENCSR494ZGC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ELF4 ChIP-seq on human K562
experiment encode accession: ENCSR494ZGC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR099EPT, ENCSR328FYU
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB040QPF
size range: 450-650

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ELF4

value: cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELF4.

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White

tag: link

value: ENCBS775VXL at ENCODE; https://www.encodeproject.org/ENCBS775VXL/

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


title: EAEC_EA

tag: strain

value: Incubation with supernatant from Escherichia albertii culture


title: TF ChIP-seq from right lobe of liver (ENCLB570ZKM)

description:
https://www.encodeproject.org/experiments/ENCSR000VGD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR000VGD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR886ATT
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB570ZKM
size range: 200-600

value: CTCF

value: right lobe of liver

value: tissue

value: 47 year

value: female

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

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS025MJZ at ENCODE; https://www.encodeproject.org/ENCBS025MJZ/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: TF ChIP-seq from MCF-7 (ENCLB572YST)

description:
https://www.encodeproject.org/experiments/ENCSR658GYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TSC22D2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR658GYQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR439GBR, ENCSR734XLI
encode release date: 2022-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB572YST
size range: 450-650

tag: line

value: cell line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TSC22D2.

value: 69 year

value: breast cancer (adenocarcinoma)

value: adult

value: Michael Snyder, Stanford

value: ENCBS436DTI at ENCODE; https://www.encodeproject.org/ENCBS436DTI/

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


title: TF ChIP-seq from K562 (ENCLB401MXI)

description:
https://www.encodeproject.org/experiments/ENCSR158BGH/
***************
biological replicate number: 3
technical replicate number: 1
description: MBD1 ChIP-seq on human K562
experiment encode accession: ENCSR158BGH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR207GLV, ENCSR012KTG
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB401MXI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

value: ATCC

value: ENCBS941UBC at ENCODE; https://www.encodeproject.org/ENCBS941UBC/

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


title: EAEC

value: Enteroaggregative Escherichia coli

value: Incubation with M9 media (control)


title: STEC_CW

value: Shiga toxin-producing Escherichia coli

value: Incubation with supernatant from Citrobacter werkmanii culture


title: Control ChIP-seq from HepG2 (ENCLB242VDC)

description:
https://www.encodeproject.org/experiments/ENCSR268KJF/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 immortalized cell line stably expressing C-terminal eGFP-SOX13 fusion protein.
experiment encode accession: ENCSR268KJF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB242VDC
size range: 450-650

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SOX13

value: cell line

value: HepG2 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to SOX13.

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Michael Snyder

value: ENCBS562PTI at ENCODE; https://www.encodeproject.org/ENCBS562PTI/

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


title: TF ChIP-seq from K562 (ENCLB403CUM)

description:
https://www.encodeproject.org/experiments/ENCSR861UWB/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-HOXB6 ChIP-seq on human K562
experiment encode accession: ENCSR861UWB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR833ZKY, ENCSR532WSQ
encode release date: 2022-05-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB403CUM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: ENCBS925ZHI at ENCODE; https://www.encodeproject.org/ENCBS925ZHI/