title: TF ChIP-seq from middle frontal area 46 (ENCLB971DVA)

description:
https://www.encodeproject.org/experiments/ENCSR068DJS/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue male adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR068DJS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR105CRB
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971DVA
size range: 200-600

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

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: male

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS049LCH at ENCODE; https://www.encodeproject.org/ENCBS049LCH/

value: Derived from ENCODE donor ENCDO877NVF; https://www.encodeproject.org/ENCDO877NVF/


title: paiso_GV_cKO_F2_6_SMRTCell1536

status: Public on Jul 22 2022

type: SRA

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

country: USA

institute: HHMI Janelia

library_source: transcriptomic

data_processing:
For PAIso-seq: Subreads were converted into circular consensus sequences (CCS) by number of passes ≥10. CCS-LIMA barcode detection process was run to mark the reads for the presence of barcodes. The IsoSeq Refine step was run to find full-length non-chimeric (FLNC) reads classified by (a) the presence of 5’ and 3’ primer sequences on ends, (b) the correct orientation of the 5’ and 3’ barcode sequences, (c) the presence of poly(A), (d) the chimeric sequences with barcode in the middle were removed. Fastq read and poly(A) length were processed (Liu et al. 2019). For mapping analysis, the sam files were processed using id_features_pandas.py file using Mus_musculus.GRCm38.102.gtf as the reference (details in mapping.ipynb). The 3’ unmapped region was extracted using get_sam_tails.py using all the sam files as the input. The length of the unmapped region of each transcript was recorded as cigar_S_len (details in get_sam_unmapped_tails.ipynb). The summarized information for all transcripts of all libraries is in the PAIsoSeq_Wu_2022.csv file. For all PAIso-seq analysis and figure preparation, codes are available at https://github.com/Di-aswater/public-dis3l2-analysis.
For RNA-seq: When processing sequencing data, original FASTQ files were mapped to mm10 using STAR (2.7.8a) (Dobin et al. 2013). BAM files were counted using HTSeq (0.11.4) (Anders et al. 2015). Differential analysis was performed using DESeq2 (Love et al. 2014). All the RNA-seq analysis codes are available at https://github.com/Di-aswater/public-dis3l2-analysis.
Assembly: mm10
Supplementary files format and content: All count.txt files contain the raw reads of each gene.
Supplementary files format and content: All report.csv files contain the information of each CCS read, including length, polyA, etc.
Supplementary files format and content: The PAIsoSeq_Wu_2022.csv matrix contains summarized information of all PAIso-seq results. Columns include CCS_ID, genotype, mouse ID, oocyte ID, gene ID, gene name, fastq sequence, polyA sequence, polyA length, tail sequence, tail length, uracil number and percent and transcript type

molecule: polyA RNA

organism: Mus musculus

source_name: GV oocytes

extract_protocol:
For PAIso-seq, single oocytes were lysed in 11 microliters of newly prepared lysis buffer. The lysis buffer contained 0.5 microliter of SUPERase• In™ RNase Inhibitor (20 U/microliter) (ThermoFisher AM2696) and 10 microliters of 0.2% Triton X-100 in PBS. For regular single oocyte RNA-seq, in poly(A)-based RNA, the single oocyte was lysed in 2.5 microliters of RLT+; in ribominus RNA-seq, the single oocyte was lysed in the lysis buffer from the Ovation Solo kit.
For PAIso-seq: Oocyte lysate was heated at 80 °C for 5 min. 1 microliter of 1:10^5 diluted ERCC was added to each oocyte lysate. Each oocyte was barcoded at the end extension step with differently indexed dU-containing DNA templates. In each 12 microliter oocyte lysate, 1 microliter end extension oligo (50 micromolar) was added and reaction was incubated at 80 °C for 5 min, 37 °C for 10 min to anneal the end extension oligo to the poly(A) of RNA. After annealing, 1 microliter DTT (100 micromolar, SuperScript™ II Reverse Transcriptase kit, Thermo Fisher 18064014), 4 microliter of Superscript II first-strand buffer (5X), 1 microliter dNTP mix (Thermo Fisher 18427013), 0.5 microliter SUPERase• In™ RNase Inhibitor (20 U/microliter) (ThermoFisher AM2696), 1 microliter Klenow Fragment (3'→5' exo-) (NEB M0212S), 0.5 microliter nuclease-free water was added to each reaction. Oocyte lysates were incubated at 37 °C for 1 h and 80 °C for 10 min. 1 microliter USER enzyme (NEB M5505S) was added to each reaction and incubated at 37 °C for 30 min to digest the end-extension oligos. RNA from each reaction was purified using NucleoSpin RNA XS Micro kit (Takara 740902.50). Each sample was eluted using 15 microliter nuclease-free water.   7 microliter of the above purified end-extended RNA was used for reverse transcription and template switching. In each reaction, there was 7 microliter RNA, 0.4 microliter RT primer and 1 microliter dNTP. Reaction was incubated at 72 °C for 3 min and put on ice immediately. 1 microliter SuperScript II reverse transcriptase (200 U/microliter) (Thermo Fisher 18064014), 0.5 microliter RNase Inhibitor (ThermoFisher AM2696), 4 microliter Superscript II first-strand buffer (5X), 1 microliter DTT, 4 microliter Betaine (5M) (Sigma Aldrich B0300-1VL), 0.12 microliter MgCl2 (1M), 0.2 microliter template switch oligo, 0.78 microliter nuclease free water was added to each reaction. Reactions were incubated at 42 °C for 90 min, 10 cycles of 50 °C for 2 min followed by 42 °C for 2 min and 70 °C for 15 min. Reactions were then amplified by PCR for 26 cycles. In each PCR reaction, there were 20 microliter reverse transcription product, 25 microliter KAPA HiFi HotStart ReadyMix (2X) (KAPA Biosystems KK2601), 5 microliter PCR primer. PCR reaction was purified using AMPure XP beads (Beckman Coulter A63881). cDNA samples were then processed at National Information Solutions Cooperative (NISC) for PacBio sequencing library preparation and PacBio sequencing. Samples were run on 2 SMRTCells and sequenced on the Sequel II (25 h collection time).
For poly(A) based RNA seq: Poly(A) RNA was enriched by oligo-dT beads and reverse transcribed. cDNA was amplified and purified for library construction using the Nextera XT kit. For ribominus RNA-seq, the library was constructed following the Ovation Solo Kit protocol

tag: tissue

value: GV oocytes

tag: genotype

value: cKO


title: TF ChIP-seq from WTC11 (ENCLB970KMJ)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR260GQA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF671 ChIP-seq on human WTC11
experiment encode accession: ENCSR260GQA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR267JAO
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB970KMJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF671

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: age

value: 30 year

tag: Sex

tag: dev stage

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Richard Myers

tag: link

value: ENCBS262DYC at ENCODE; https://www.encodeproject.org/ENCBS262DYC/

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


title: TF ChIP-seq from middle frontal area 46 (ENCLB892HAV)

description:
https://www.encodeproject.org/experiments/ENCSR068DJS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue male adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR068DJS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR105CRB
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB892HAV
size range: 200-600

value: CTCF

value: middle frontal area 46


title: TF ChIP-seq from WTC11 (ENCLB542ZJZ)

description:
https://www.encodeproject.org/experiments/ENCSR260GQA/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF671 ChIP-seq on human WTC11
experiment encode accession: ENCSR260GQA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR267JAO
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB542ZJZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS749ATC at ENCODE; https://www.encodeproject.org/ENCBS749ATC/


title: TF ChIP-seq from HepG2 (ENCLB387ETV)

description:
https://www.encodeproject.org/experiments/ENCSR448RAP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR448RAP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR856RWG
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB387ETV
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF552

value: 15 year

value: male

tag: health state

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: ENCBS413FOG at ENCODE; https://www.encodeproject.org/ENCBS413FOG/

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


title: Whole worm, GFP-3xFLAG-ALG-2, IP, rep2

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.

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).

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

value: tor139[GFP::3xFLAG::alg-2b] II

tag: treatment

value: IP (Argonaute)


title: Whole worm, GFP-3xFLAG-ALG-1, IP, rep2

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


title: paiso_GV_ctr_F4_6_SMRTCell1527

value: GV oocytes

value: ctr


title: Mint-ChIP-seq from activated T-cell (ENCLB609ESS)

description:
https://www.encodeproject.org/experiments/ENCSR068BIF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR068BIF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR975DSD
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB609ESS

source_name: Homo sapiens male adult (42 years) activated T-cell primary cell

value: activated T-cell

value: primary cell

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS351GLT at ENCODE; https://www.encodeproject.org/ENCBS351GLT/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: paiso_GV_cKO_F1_8_SMRTCell1536

value: cKO


title: Control ChIP-seq from WTC11 (ENCLB898NZS)

description:
https://www.encodeproject.org/experiments/ENCSR851USP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR851USP
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB898NZS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line

value: cell line

value: 30 year

value: male

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS684REI at ENCODE; https://www.encodeproject.org/ENCBS684REI/

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


title: Mint-ChIP-seq from activated T-cell (ENCLB744GYH)

description:
https://www.encodeproject.org/experiments/ENCSR068BIF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR068BIF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR975DSD
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744GYH


title: Whole worm, GFP-3xFLAG-ALG-2, input, rep2

molecule: total RNA

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: tor139[GFP::3xFLAG::alg-2b] II

value: input (total RNA)


title: paiso_GV_ctr_F4_5_SMRTCell1527

value: GV oocytes

value: ctr


title: Control ChIP-seq from motor neuron (ENCLB343PYI)

description:
https://www.encodeproject.org/experiments/ENCSR255MIG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human motor neuron
experiment encode accession: ENCSR255MIG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-12-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB343PYI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (55 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

value: 55 year

value: Healthy donor

value: adult

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

value: ENCBS155RDX at ENCODE; https://www.encodeproject.org/ENCBS155RDX/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: Whole worm, 3xFLAG-WAGO-10, IP, rep2

value: Whole worm

value: IP (Argonaute)


title: Whole worm, GFP-3xFLAG-ALG-1, input, rep2

value: young adult

value: hermaphrodite

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


title: Whole worm, 3xFLAG-WAGO-10, input, rep2

value: 20 degrees C

value: input (total RNA)


title: TF ChIP-seq from WTC11 (ENCLB908MUY)

description:
https://www.encodeproject.org/experiments/ENCSR444BFV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF532 ChIP-seq on human WTC11
experiment encode accession: ENCSR444BFV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR851USP
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB908MUY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF532

value: cell line

value: 30 year

value: male

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS480ZVW at ENCODE; https://www.encodeproject.org/ENCBS480ZVW/

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


title: paiso_GV_ctr_F4_7_SMRTCell1527

value: GV oocytes

value: ctr


title: Mint-ChIP-seq from natural killer cell (ENCLB433WDY)

description:
https://www.encodeproject.org/experiments/ENCSR067KOO/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR067KOO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB433WDY

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

value: natural killer cell

value: primary cell

value: 33 year

value: adult

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: TF ChIP-seq from HepG2 (ENCLB991IZS)

description:
https://www.encodeproject.org/experiments/ENCSR448RAP/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR448RAP
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR856RWG
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB991IZS
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: ENCBS815YYM at ENCODE; https://www.encodeproject.org/ENCBS815YYM/

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


title: TF ChIP-seq from WTC11 (ENCLB592TMX)

description:
https://www.encodeproject.org/experiments/ENCSR444BFV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF532 ChIP-seq on human WTC11
experiment encode accession: ENCSR444BFV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR851USP
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB592TMX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 30 year

value: male

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS526KKV at ENCODE; https://www.encodeproject.org/ENCBS526KKV/

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


title: Mint-ChIP-seq from natural killer cell (ENCLB879SPL)

description:
https://www.encodeproject.org/experiments/ENCSR067KOO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR067KOO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB879SPL

value: natural killer cell

value: primary cell

value: 33 year

value: adult

value: Bradley Bernstein, Broad


title: Whole worm, 3xFLAG-WAGO-1, IP, rep2

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: IP (Argonaute)


title: Histone ChIP-seq from heart left ventricle (ENCLB515WLI)

description:
https://www.encodeproject.org/experiments/ENCSR066SQU/
***************
biological replicate number: 1
technical replicate number: 3
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR066SQU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515WLI
size range: 200-600

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

value: heart left ventricle

value: tissue

value: 54 year

value: Shin Lin

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

value: ENCBS115UFJ at ENCODE; https://www.encodeproject.org/ENCBS115UFJ/

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


title: paiso_GV_cKO_F1_5_SMRTCell1527

value: GV oocytes

value: cKO


title: Mint-ChIP-seq from natural killer cell (ENCLB791YXH)

description:
https://www.encodeproject.org/experiments/ENCSR067KOO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR067KOO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB791YXH

value: natural killer cell

value: primary cell

value: 33 year

value: male

value: Charles Lee

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

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


title: Mint-ChIP-seq from natural killer cell (ENCLB524NYD)

description:
https://www.encodeproject.org/experiments/ENCSR067KOO/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR067KOO
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR457FTM
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB524NYD

value: adult

value: Bradley Bernstein, Broad


title: paiso_GV_cKO_F1_6_SMRTCell1527


title: Histone ChIP-seq from heart left ventricle (ENCLB313HYP)

description:
https://www.encodeproject.org/experiments/ENCSR066SQU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR066SQU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB313HYP
size range: 200-600

value: heart left ventricle

value: tissue


title: paiso_GV_cKO_F1_7_SMRTCell1527


title: Whole worm, 3xFLAG-WAGO-1, input, rep2

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: input (total RNA)


title: Whole worm, 3xFLAG-NRDE-3, input, rep2

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


title: Whole worm, 3xFLAG-NRDE-3, IP, rep2

value: IP (Argonaute)


title: TF ChIP-seq from WTC11 (ENCLB096HKZ)

description:
https://www.encodeproject.org/experiments/ENCSR440UPD/
***************
biological replicate number: 1
technical replicate number: 1
description: EMX1 ChIP-seq on human WTC11
experiment encode accession: ENCSR440UPD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR395ZBR
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB096HKZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens EMX1

value: cell line

value: 30 year

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS886NNV at ENCODE; https://www.encodeproject.org/ENCBS886NNV/

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


title: TF ChIP-seq from WTC11 (ENCLB922DQD)

description:
https://www.encodeproject.org/experiments/ENCSR440UPD/
***************
biological replicate number: 2
technical replicate number: 1
description: EMX1 ChIP-seq on human WTC11
experiment encode accession: ENCSR440UPD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR395ZBR
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB922DQD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: adult

value: ENCBS208WTG at ENCODE; https://www.encodeproject.org/ENCBS208WTG/


title: Histone ChIP-seq from heart left ventricle (ENCLB808EOT)

description:
https://www.encodeproject.org/experiments/ENCSR066SQU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR066SQU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB808EOT
size range: 200-600

value: heart left ventricle

value: tissue

value: 54 year

value: Bradley Bernstein, Broad

value: Shin Lin

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

value: ENCBS115UFJ at ENCODE; https://www.encodeproject.org/ENCBS115UFJ/

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


title: TF ChIP-seq from HepG2 (ENCLB566FVH)

description:
https://www.encodeproject.org/experiments/ENCSR631JFU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR631JFU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB566FVH
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens IRF9

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: ENCBS545POZ at ENCODE; https://www.encodeproject.org/ENCBS545POZ/

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


title: paiso_GV_ctr_F3_8_SMRTCell1527

value: GV oocytes

value: ctr


title: Mint-ChIP-seq from HCT116 (ENCLB642YBW)

description:
https://www.encodeproject.org/experiments/ENCSR065OMZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR065OMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642YBW

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens BRD4 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

tag: treatments

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS087RNX at ENCODE; https://www.encodeproject.org/ENCBS087RNX/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: Whole worm, 3xFLAG-C04F12.1, IP, rep2

tag: tissue

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: IP (Argonaute)


title: patient 10 MM LDS

type: RNA

city: xi'an

first: aili

last: He

address: NO.157 Xiwu Road, Lianhu District

department: Department of Hematology

country: China

institute: the Second Affiliated Hospital of Xi'an Jiaotong University

description: circular RNA expression  in  human bone marrow mononuclear cells(BMNCs)

hyb_protocol: Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing. Equilibrate water bath to 60°C. For each microarray, add 1.5ug cyanine 3-labeled, linearly amplified cRNA, etc to a 1.5 mL nuclease-free microfuge tube: Mix well but gently on a vortex mixer. Incubate at 60°C for exactly 30 minutes to fragment RNA. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction. Place sample on ice and load onto the array as soon as possible. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Hand-tighten the clamp onto the chamber. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm. Hybridize at 65°C for 17 hours.

scan_protocol: Assemble the slides into an slide holder. Place assembled slide holders into scanner carousel. Verify scan settings for one-color scans. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Open the Agilent Feature Extraction (FE) software. Add the images (.tif) to be extracted to the FE Project. Set FE Project Properties. Check the Extraction Set Configuration. Save the FE Project (.fep) by selecting File > Save As and browse for desired location. Select Project > Start Extracting and export data to txt.

source_name: bone marrow

label_protocol: Add 1ug of total RNA to a 1.5-mL microcentrifuge tube. Add 1.2 μL of T7 Promoter Primer. Use nuclease-free water to bring the total reaction volume to 11.5 μL. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes. Place the reactions on ice and incubate for 5 minutes.Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down. Incubate samples at 40°C in a circulating water bath for 2 hours. Move samples to a 65°C circulating water bath and incubate for 15 minutes. Move samples to ice. Incubate for 5 minutes. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting. Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: Bone marrow mononuclear cells (BMNCs) were isolated using lymphocyte separation liquid within eight hours after bone marrow samples were harvested and subjected for isolation of total cellular RNA, then stored at -80°C,Add 1ml Trizol per 5x10^6 cells.

tag: disease state

value: MM

value: bone marrow mononuclear cells

tag: gender

value: female


title: patient 9 MM ZRS


title: TF ChIP-seq from HepG2 (ENCLB213ADW)

description:
https://www.encodeproject.org/experiments/ENCSR631JFU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR631JFU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB213ADW
fragmentation methods: sonication (generic)

tag: antibody

tag: line

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS414TJR at ENCODE; https://www.encodeproject.org/ENCBS414TJR/

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


title: Whole worm, GFP-3xFLAG-WAGO-4, IP, rep1

tag: genotype

value: tor117[GFP::3xFLAG::wago-4] II


title: Whole worm, GFP-3xFLAG-WAGO-4, input, rep1

value: Whole worm

tag: Sex

value: input (total RNA)


title: Mint-ChIP-seq from HCT116 (ENCLB054NFN)

description:
https://www.encodeproject.org/experiments/ENCSR065OMZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR065OMZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR614CRT
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB054NFN

tag: biosample encode accession

tag: age

value: 48 year

value: male

value: colorectal carcinoma

tag: dev stage

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: treatment_term_name:5-Phenyl-1H-indole-3-acetic acid; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS087RNX at ENCODE; https://www.encodeproject.org/ENCBS087RNX/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/


title: TF ChIP-seq from K562 (ENCLB733ZBT)

description:
https://www.encodeproject.org/experiments/ENCSR438RRM/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-Seq on K562
experiment encode accession: ENCSR438RRM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR953NJZ
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB733ZBT
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXM1

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

tag: lab

tag: source

tag: link

value: ENCBS026ZEH at ENCODE; https://www.encodeproject.org/ENCBS026ZEH/

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


title: Whole worm, 3xFLAG-C04F12.1, input, rep2

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C


title: Whole worm, GFP-3xFLAG-SAGO-2, input, rep1

value: tor121[GFP::3xFLAG::sago-2c] I

tag: treatment

value: input (total RNA)


title: patient 7 MM SFM

value: MM

value: bone marrow mononuclear cells


title: patient 8 MM FAQ


title: patient 5 IDA JLL

value: IDA


title: Histone ChIP-seq from ovary (ENCLB766VCE)

description:
https://www.encodeproject.org/experiments/ENCSR061IAQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR061IAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB766VCE
size range: 200-600

source_name: Homo sapiens female adult (41 years) ovary tissue

value: ovary

value: tissue

value: 41 year

tag: health state

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

value: adult

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS327NVM at ENCODE; https://www.encodeproject.org/ENCBS327NVM/

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


title: Histone ChIP-seq from ovary (ENCLB802EIP)

description:
https://www.encodeproject.org/experiments/ENCSR061IAQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR061IAQ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB802EIP
size range: 200-600

value: female


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

tag: tissue

value: Whole worm

value: young adult

value: hermaphrodite

value: tor123[GFP::3xFLAG::sago-1] V

value: IP (Argonaute)


title: patient 4 IDA WXY

tag: disease state

value: bone marrow mononuclear cells


title: TF ChIP-seq from K562 (ENCLB990SXT)

description:
https://www.encodeproject.org/experiments/ENCSR438RRM/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-Seq on K562
experiment encode accession: ENCSR438RRM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR953NJZ
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB990SXT
fragmentation methods: sonication (generic)

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS086UCT at ENCODE; https://www.encodeproject.org/ENCBS086UCT/

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


title: TF ChIP-seq from WTC11 (ENCLB931FIN)

description:
https://www.encodeproject.org/experiments/ENCSR623TZE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR623TZE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR421QOH
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB931FIN
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SMAD4

value: 30 year

value: male

value: adult

value: ENCBS853PVZ at ENCODE; https://www.encodeproject.org/ENCBS853PVZ/

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


title: Control ChIP-seq from WTC11 (ENCLB265DYD)

description:
https://www.encodeproject.org/experiments/ENCSR826WZK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR826WZK
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB265DYD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: Michael Snyder, Stanford

value: ENCBS629HOS at ENCODE; https://www.encodeproject.org/ENCBS629HOS/


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB725ZBM)

description:
https://www.encodeproject.org/experiments/ENCSR061PIA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR061PIA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB725ZBM

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

value: primary cell

value: 36 year

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: patient 6 MM MZT

value: MM

value: bone marrow mononuclear cells

tag: gender

value: female


title: Whole worm, GFP-3xFLAG-SAGO-2, IP, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: tor121[GFP::3xFLAG::sago-2c] I

value: IP (Argonaute)


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB868COX)

description:
https://www.encodeproject.org/experiments/ENCSR061PIA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR061PIA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB868COX

tag: antibody

value: male

value: adult


title: TF ChIP-seq from K562 (ENCLB658FFM)

description:
https://www.encodeproject.org/experiments/ENCSR427WZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR427WZJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB658FFM
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF143

tag: line

value: cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS323QWI at ENCODE; https://www.encodeproject.org/ENCBS323QWI/

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


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB522LRO)

description:
https://www.encodeproject.org/experiments/ENCSR055TVU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR055TVU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR809CJF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB522LRO

source_name: Homo sapiens male adult (33 years) effector memory CD8-positive, alpha-beta T primary cell

value: primary cell

value: 33 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS509OFL at ENCODE; https://www.encodeproject.org/ENCBS509OFL/

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


title: TF ChIP-seq from K562 (ENCLB997MOU)

description:
https://www.encodeproject.org/experiments/ENCSR620MHD/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-KDM2B ChIP-seq on human K562
experiment encode accession: ENCSR620MHD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR357LCN
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB997MOU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens KDM2B

value: female

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS593WGG at ENCODE; https://www.encodeproject.org/ENCBS593WGG/


title: TF ChIP-seq from K562 (ENCLB046RFO)

description:
https://www.encodeproject.org/experiments/ENCSR427WZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR427WZJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB046RFO
fragmentation methods: sonication (generic)

value: cell line

value: adult

value: ENCBS295OYE at ENCODE; https://www.encodeproject.org/ENCBS295OYE/


title: Control Mint-ChIP-seq from naive B cell (ENCLB300YOE)

description:
https://www.encodeproject.org/experiments/ENCSR056PPJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR056PPJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB300YOE

source_name: Homo sapiens male adult (40 years) naive B primary cell

value: naive B cell

value: 40 year

value: male

value: ENCBS857XIR at ENCODE; https://www.encodeproject.org/ENCBS857XIR/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: TF ChIP-seq from K562 (ENCLB380EOG)

description:
https://www.encodeproject.org/experiments/ENCSR620MHD/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-KDM2B ChIP-seq on human K562
experiment encode accession: ENCSR620MHD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR357LCN
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB380EOG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS134AFA at ENCODE; https://www.encodeproject.org/ENCBS134AFA/

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


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB699GQO)

description:
https://www.encodeproject.org/experiments/ENCSR055TVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR055TVU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR809CJF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB699GQO

value: primary cell

value: 33 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS509OFL at ENCODE; https://www.encodeproject.org/ENCBS509OFL/

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


title: Fig6_pos_replicate2

city: Shanghai

first: Tianmin

last: Wang

address: Huaxia Middle Road, 393

department: School of Life Science and Technology

institute: ShanghaiTech University

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

organism: Escherichia coli BW25113

source_name: RNA-seq data in Fig. 6, using miniBac-seq method to generate RNA-seq data with RT primer 24

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: Whole worm, GFP-3xFLAG-SAGO-1, input, rep1

source_name: Whole worm

value: Whole worm

value: young adult

tag: Sex

value: hermaphrodite

value: 20 degrees C

tag: genotype

value: tor123[GFP::3xFLAG::sago-1] V

value: input (total RNA)


title: patient 3 IDA CHQ

description: circular RNA expression  in  human bone marrow mononuclear cells(BMNCs)

value: IDA

value: bone marrow mononuclear cells

value: female

tag: age


title: Mint-ChIP-seq from stimulated activated memory B cell (ENCLB113IEZ)

description:
https://www.encodeproject.org/experiments/ENCSR053RFF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR053RFF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR655TYY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB113IEZ

source_name: Homo sapiens male adult (40 years) stimulated activated memory B primary cell treated with 1ug/mL anti-CD40 for 72 hours, 100 ng/mL Interleukin-4 for 72 hours, 10ug/mL anti-IgM for 72 hours

value: stimulated activated memory B cell

tag: biosample encode accession

value: 40 year

value: male

tag: dev stage

value: adult

tag: treatments

value: treatment_term_name:anti-CD40; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-IgM; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS619HZC at ENCODE; https://www.encodeproject.org/ENCBS619HZC/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: Fig6_neg_replicate2


title: TF ChIP-seq from WTC11 (ENCLB225BKA)

description:
https://www.encodeproject.org/experiments/ENCSR623TZE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR623TZE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR421QOH
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB225BKA
fragmentation methods: sonication (generic)

value: cell line

value: 30 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: link

value: ENCBS448XBQ at ENCODE; https://www.encodeproject.org/ENCBS448XBQ/

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


title: patient 1 IDA XLX


title: Fig6_neg_replicate1


title: TF ChIP-seq from WTC11 (ENCLB180BHL)

description:
https://www.encodeproject.org/experiments/ENCSR422ODX/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF396 ChIP-seq on human WTC11
experiment encode accession: ENCSR422ODX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR826WZK
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB180BHL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF396

value: Michael Snyder, Stanford

value: ENCBS981BOA at ENCODE; https://www.encodeproject.org/ENCBS981BOA/


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

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

value: tor153[GFP::3xFLAG::rde-1] V

tag: treatment

value: IP (Argonaute)


title: Fig6_pos_replicate1


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB370NCG)

description:
https://www.encodeproject.org/experiments/ENCSR049YHC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049YHC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR995LKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB370NCG

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

value: primary cell

value: 36 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS527GUI at ENCODE; https://www.encodeproject.org/ENCBS527GUI/

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


title: Fig5c_RTprimer24

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 24


title: Whole worm, GFP-3xFLAG-RDE-1, input, rep1

tag: tissue

value: input (total RNA)


title: Control Mint-ChIP-seq from naive B cell (ENCLB326ZEA)

description:
https://www.encodeproject.org/experiments/ENCSR056PPJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR056PPJ
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB326ZEA

value: naive B cell

value: 40 year

value: ENCBS857XIR at ENCODE; https://www.encodeproject.org/ENCBS857XIR/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: Whole worm, GFP-3xFLAG-PRG-1, input, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: tor149[GFP::3xFLAG::prg-1] I


title: Whole worm, GFP-3xFLAG-PPW-2, input, rep1

value: 20 degrees C

value: tor115[GFP::3xFLAG::ppw-2] I


title: Mint-ChIP-seq from stimulated activated memory B cell (ENCLB419ABY)

description:
https://www.encodeproject.org/experiments/ENCSR053RFF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR053RFF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR655TYY
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB419ABY

value: stimulated activated memory B cell

value: primary cell

value: male

value: treatment_term_name:anti-CD40; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius; treatment_term_id:UniProtKB:P05112; treatment_term_name:Interleukin-4; treatment_type:protein; duration:72; duration_units:hour; treatment_term_name:anti-IgM; treatment_type:antibody; duration:72; duration_units:hour; temperature:37; temperature_units:Celsius;

value: ENCBS619HZC at ENCODE; https://www.encodeproject.org/ENCBS619HZC/


title: Whole worm, GFP-3xFLAG-PPW-2, IP, rep1

value: IP (Argonaute)


title: Mint-ChIP-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB958JEJ)

description:
https://www.encodeproject.org/experiments/ENCSR049YHC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR049YHC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR995LKY
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB958JEJ

value: 36 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS527GUI at ENCODE; https://www.encodeproject.org/ENCBS527GUI/

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


title: TF ChIP-seq from K562 (ENCLB395YLP)

description:
https://www.encodeproject.org/experiments/ENCSR817FMN/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR817FMN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB395YLP
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TEAD4

value: cell line

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS432HVB at ENCODE; https://www.encodeproject.org/ENCBS432HVB/

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


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: tor119[GFP::3xFLAG::ppw-1c] I


title: patient 1 IDA SHN

tag: disease state

value: IDA

value: bone marrow mononuclear cells

tag: gender


title: TF ChIP-seq from K562 (ENCLB376JET)

description:
https://www.encodeproject.org/experiments/ENCSR228ELU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR228ELU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB376JET
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TEAD1

tag: antibody

tag: line

value: adult

value: ENCBS408JDP at ENCODE; https://www.encodeproject.org/ENCBS408JDP/


title: Mint-ChIP-seq from MCF 10A (ENCLB679VJF)

description:
https://www.encodeproject.org/experiments/ENCSR049WGG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR049WGG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB679VJF

source_name: Homo sapiens MCF 10A cell line

value: MCF 10A

value: cell line

value: 36 year

tag: Sex

value: fibrocystic disease

value: Bradley Bernstein, Broad

value: Mats Ljungman

value: ENCBS654ZDZ at ENCODE; https://www.encodeproject.org/ENCBS654ZDZ/

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


title: TF ChIP-seq from K562 (ENCLB072AUL)

description:
https://www.encodeproject.org/experiments/ENCSR228ELU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR228ELU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB072AUL
fragmentation methods: sonication (generic)

tag: age

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS350TEC at ENCODE; https://www.encodeproject.org/ENCBS350TEC/

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


title: TF ChIP-seq from K562 (ENCLB885XPD)

description:
https://www.encodeproject.org/experiments/ENCSR817FMN/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR817FMN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR490VNA
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB885XPD
fragmentation methods: sonication (generic)

tag: biosample encode accession

value: adult

value: ENCBS081KMP at ENCODE; https://www.encodeproject.org/ENCBS081KMP/


title: Mint-ChIP-seq from dendritic cell (ENCLB388ZWL)

description:
https://www.encodeproject.org/experiments/ENCSR047WCC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR047WCC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB388ZWL

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

value: dendritic cell

value: primary cell

value: 51 year

value: male

tag: dev stage

value: Charles Lee

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

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


title: Control ChIP-seq from WTC11 (ENCLB216WMR)

description:
https://www.encodeproject.org/experiments/ENCSR421QOH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR421QOH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-04
lab: Richard Myers, HAIB
library encode accession: ENCLB216WMR
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line

value: cell line

value: 30 year

value: ENCBS682INJ at ENCODE; https://www.encodeproject.org/ENCBS682INJ/

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


title: Fig5c_RTprimer21

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 21

tag: strain


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

tag: genotype

value: tor125[GFP::3xFLAG::hrde-1] III

value: IP (Argonaute)


title: Fig5c_RTprimer23

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 23


title: Mint-ChIP-seq from dendritic cell (ENCLB469GTU)

description:
https://www.encodeproject.org/experiments/ENCSR047WCC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR047WCC
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR992JBX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469GTU

value: dendritic cell

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source


title: Fig5c_RTprimer20

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 20


title: Whole worm, GFP-3xFLAG-HRDE-1, input, rep1

tag: developmental stage

value: input (total RNA)


title: Fig5c_RTprimer22

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 22


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

tag: growth temperature

value: tor147[GFP::3xFLAG::ergo-1a] V


title: TF ChIP-seq from WTC11 (ENCLB345SQI)

description:
https://www.encodeproject.org/experiments/ENCSR413CVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF423 ChIP-seq on human WTC11
experiment encode accession: ENCSR413CVQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR294TOY
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB345SQI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF423

value: male

value: Michael Snyder, Stanford

value: Richard Myers

tag: link

value: ENCBS509EYZ at ENCODE; https://www.encodeproject.org/ENCBS509EYZ/


title: TF ChIP-seq from WTC11 (ENCLB369ZTC)

description:
https://www.encodeproject.org/experiments/ENCSR413CVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF423 ChIP-seq on human WTC11
experiment encode accession: ENCSR413CVQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR294TOY
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB369ZTC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 30 year

value: ENCBS193YIA at ENCODE; https://www.encodeproject.org/ENCBS193YIA/


title: Whole worm, GFP-3xFLAG-PPW-1, input, rep1

tag: tissue

value: Whole worm

value: young adult

value: tor119[GFP::3xFLAG::ppw-1c] I

tag: treatment


title: TF ChIP-seq from K562 (ENCLB306UEI)

description:
https://www.encodeproject.org/experiments/ENCSR208VNN/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-IFI16 ChIP-seq on human K562
experiment encode accession: ENCSR208VNN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB306UEI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens IFI16

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS605SEG at ENCODE; https://www.encodeproject.org/ENCBS605SEG/

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


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

value: hermaphrodite

value: 20 degrees C

value: csr-1(tor104[csr-1 exon1::GFP::Flag IV:7957568]) IV

value: IP (Argonaute)


title: Whole worm, GFP-3xFLAG-ERGO-1, input, rep1

value: tor147[GFP::3xFLAG::ergo-1a] V

value: input (total RNA)


title: Mint-ChIP-seq from naive B cell (ENCLB441FKT)

description:
https://www.encodeproject.org/experiments/ENCSR040ZML/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR040ZML
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR575ZCX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB441FKT

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

value: naive B cell

value: primary cell

value: 39 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from MCF 10A (ENCLB975LMQ)

description:
https://www.encodeproject.org/experiments/ENCSR049WGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR049WGG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR550WPO
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB975LMQ

value: MCF 10A

value: cell line

value: 36 year

value: female

value: fibrocystic disease

value: Mats Ljungman

value: ENCBS654ZDZ at ENCODE; https://www.encodeproject.org/ENCBS654ZDZ/

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


title: Mint-ChIP-seq from naive B cell (ENCLB704CJO)

description:
https://www.encodeproject.org/experiments/ENCSR040ZML/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR040ZML
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR575ZCX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB704CJO


title: Fig5c_RTprimer14

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 14


title: Fig5c_RTprimer17

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 17


title: TF ChIP-seq from WTC11 (ENCLB439OTH)

description:
https://www.encodeproject.org/experiments/ENCSR422ODX/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF396 ChIP-seq on human WTC11
experiment encode accession: ENCSR422ODX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR826WZK
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB439OTH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF396

value: 30 year

value: male

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS638NFH at ENCODE; https://www.encodeproject.org/ENCBS638NFH/

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


title: TF ChIP-seq from mucosa of descending colon (ENCLB703OBD)

description:
https://www.encodeproject.org/experiments/ENCSR038VWU/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on mucosa of descending colon tissue male adult (40 years)
experiment encode accession: ENCSR038VWU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR856YCA
encode release date: 2022-02-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB703OBD
size range: 200-600

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

value: CTCF

value: mucosa of descending colon

value: tissue

value: adult

value: 40 year

value: Bradley Bernstein, Broad

value: Shin Lin

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

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

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


title: Fig5c_RTprimer13

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 13


title: Whole worm, GFP-3xFLAG-ALG-4, IP, rep1

source_name: Whole worm

value: Whole worm

value: hermaphrodite

value: 20 degrees C

value: tor143[GFP::3xFLAG::alg-4] III

value: IP (Argonaute)


title: Fig5c_RTprimer19

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 19


title: Whole worm, GFP-3xFLAG-ALG-5, IP, rep1

value: young adult

value: tor145[GFP::3xFLAG::alg-5] I


title: Fig5c_RTprimer15

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 15


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB061VMU)

description:
https://www.encodeproject.org/experiments/ENCSR038NSJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR038NSJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB061VMU

source_name: Homo sapiens male adult (35 years) CD4-positive naive resting alpha-beta T primary cell

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS417NZZ at ENCODE; https://www.encodeproject.org/ENCBS417NZZ/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: TF ChIP-seq from mucosa of descending colon (ENCLB125XSZ)

description:
https://www.encodeproject.org/experiments/ENCSR038VWU/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on mucosa of descending colon tissue male adult (40 years)
experiment encode accession: ENCSR038VWU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR856YCA
encode release date: 2022-02-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB125XSZ
size range: 200-600

value: CTCF

value: mucosa of descending colon

value: tissue

value: adult

value: 40 year

value: Bradley Bernstein, Broad

value: Shin Lin

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


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB567MYL)

description:
https://www.encodeproject.org/experiments/ENCSR040TXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR040TXN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB567MYL

source_name: Homo sapiens male adult (36 years) central memory CD8-positive, alpha-beta T 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: TF ChIP-seq from WTC11 (ENCLB491RPG)

description:
https://www.encodeproject.org/experiments/ENCSR803FIV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-MXD4 ChIP-seq on human WTC11
experiment encode accession: ENCSR803FIV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR826WZK
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB491RPG
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MXD4

value: cell line

value: 30 year

value: male

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS199QLV at ENCODE; https://www.encodeproject.org/ENCBS199QLV/

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


title: TF ChIP-seq from HepG2 (ENCLB490AAZ)

description:
https://www.encodeproject.org/experiments/ENCSR204ALX/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR204ALX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB490AAZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF431

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: ENCBS644DSP at ENCODE; https://www.encodeproject.org/ENCBS644DSP/

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


title: TF ChIP-seq from HepG2 (ENCLB662AES)

description:
https://www.encodeproject.org/experiments/ENCSR204ALX/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR204ALX
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB662AES
fragmentation methods: sonication (generic)

value: ENCBS949HPX at ENCODE; https://www.encodeproject.org/ENCBS949HPX/


title: Fig5c_RTprimer18

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 18


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

value: Whole worm

value: hermaphrodite

value: 20 degrees C

value: tor141[GFP::3xFLAG::alg-3] IV

value: IP (Argonaute)


title: Fig5c_RTprimer11

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 11


title: Whole worm, GFP-3xFLAG-ALG-5, input, rep1

value: young adult

value: tor145[GFP::3xFLAG::alg-5] I

value: input (total RNA)


title: Fig5c_RTprimer12

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 12


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB006LFA)

description:
https://www.encodeproject.org/experiments/ENCSR040TXN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR040TXN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB006LFA

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: TF ChIP-seq from K562 (ENCLB225BVM)

description:
https://www.encodeproject.org/experiments/ENCSR208VNN/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-IFI16 ChIP-seq on human K562
experiment encode accession: ENCSR208VNN
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB225BVM
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens IFI16

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS310HCY at ENCODE; https://www.encodeproject.org/ENCBS310HCY/

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


title: TF ChIP-seq from K562 (ENCLB895ZHE)

description:
https://www.encodeproject.org/experiments/ENCSR579YNY/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-Seq on K562
experiment encode accession: ENCSR579YNY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR080NUS
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB895ZHE
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZBTB40

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS355ATX at ENCODE; https://www.encodeproject.org/ENCBS355ATX/


title: Whole worm, GFP-3xFLAG-ALG-3, input, rep1

value: Whole worm

value: hermaphrodite

value: 20 degrees C

value: tor141[GFP::3xFLAG::alg-3] IV

value: input (total RNA)


title: Fig5c_RTprimer16

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 16


title: Whole worm, GFP-3xFLAG-CSR-1, input, rep1

value: young adult

value: csr-1(tor104[csr-1 exon1::GFP::Flag IV:7957568]) IV


title: TF ChIP-seq from K562 (ENCLB225USR)

description:
https://www.encodeproject.org/experiments/ENCSR579YNY/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-Seq on K562
experiment encode accession: ENCSR579YNY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR080NUS
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB225USR
fragmentation methods: sonication (generic)

value: cell line

value: 53 year

value: adult

value: ENCBS905PUR at ENCODE; https://www.encodeproject.org/ENCBS905PUR/


title: TF ChIP-seq from WTC11 (ENCLB684YNR)

description:
https://www.encodeproject.org/experiments/ENCSR803FIV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-MXD4 ChIP-seq on human WTC11
experiment encode accession: ENCSR803FIV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR826WZK
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB684YNR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 30 year

value: male

value: Michael Snyder, Stanford

value: ENCBS801MHK at ENCODE; https://www.encodeproject.org/ENCBS801MHK/

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


title: Control ChIP-seq from motor neuron (ENCLB589CLO)

description:
https://www.encodeproject.org/experiments/ENCSR201VAH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human motor neuron
experiment encode accession: ENCSR201VAH
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-12-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB589CLO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

value: 47 year

value: Donor with Amyotrophic Lateral Sclerosis

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

value: ENCBS608VMY at ENCODE; https://www.encodeproject.org/ENCBS608VMY/

value: Derived from ENCODE donor ENCDO908CUN; https://www.encodeproject.org/ENCDO908CUN/


title: Fig5c_RTprimer9

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 9


title: Whole worm, GFP-3xFLAG-ALG-2, IP, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: tor139[GFP::3xFLAG::alg-2b] II

value: IP (Argonaute)


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB866GBN)

description:
https://www.encodeproject.org/experiments/ENCSR038NSJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR038NSJ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB866GBN

tag: antibody

value: primary cell

value: male

value: adult

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS417NZZ at ENCODE; https://www.encodeproject.org/ENCBS417NZZ/

value: Derived from ENCODE donor ENCDO374BBL; https://www.encodeproject.org/ENCDO374BBL/


title: Control ChIP-seq from K562 (ENCLB281ZYG)

description:
https://www.encodeproject.org/experiments/ENCSR792WBF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR792WBF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-04-01
lab: Richard Myers, HAIB
library encode accession: ENCLB281ZYG
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS108WVQ at ENCODE; https://www.encodeproject.org/ENCBS108WVQ/

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


title: Histone ChIP-seq from middle frontal area 46 (ENCLB799FXQ)

description:
https://www.encodeproject.org/experiments/ENCSR036OBW/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR036OBW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR105CRB
encode release date: 2022-02-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB799FXQ
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

tag: Sex

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS049LCH at ENCODE; https://www.encodeproject.org/ENCBS049LCH/

value: Derived from ENCODE donor ENCDO877NVF; https://www.encodeproject.org/ENCDO877NVF/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB670TRZ)

description:
https://www.encodeproject.org/experiments/ENCSR036OBW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue male adult (90 or above years) with mild cognitive impairment
experiment encode accession: ENCSR036OBW
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR105CRB
encode release date: 2022-02-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670TRZ
size range: 200-600

tag: age

value: male

value: adult


title: Mint-ChIP-seq from activated naive CD8-positive, alpha-beta T cell (ENCLB151JLF)

description:
https://www.encodeproject.org/experiments/ENCSR036DBU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR036DBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR803FCO
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB151JLF

source_name: Homo sapiens male adult (30 years) activated CD8-positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

tag: biosample encode accession

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS777LNY at ENCODE; https://www.encodeproject.org/ENCBS777LNY/

value: Derived from ENCODE donor ENCDO166AGR; https://www.encodeproject.org/ENCDO166AGR/


title: Fig5c_RTprimer7

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 7

tag: strain


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

source_name: Whole worm

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

tag: genotype

value: tor149[GFP::3xFLAG::prg-1] I

value: IP (Argonaute)


title: Fig5c_RTprimer6

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 6


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

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

value: input (total RNA)


title: Mint-ChIP-seq from activated naive CD8-positive, alpha-beta T cell (ENCLB878KGI)

description:
https://www.encodeproject.org/experiments/ENCSR036DBU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR036DBU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR803FCO
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB878KGI

value: male

tag: dev stage

tag: lab


title: Fig5c_RTprimer10

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 10


title: Mint-ChIP-seq from natural killer cell (ENCLB116XRX)

description:
https://www.encodeproject.org/experiments/ENCSR035FAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR035FAV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR387IEL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB116XRX

source_name: Homo sapiens male adult (47 years) natural killer primary cell treated with 100 ng/mL Interleukin-18 for 72 hours, 100 ng/mL Interleukin-12 subunit beta for 72 hours, 100 ng/mL Interleukin-12 subunit alpha for 72 hours, 100 ng/mL Interleukin-15 for 7...

value: natural killer cell

value: 47 year

value: adult

value: Bradley Bernstein, Broad

tag: source

value: John Stamatoyannopoulos

value: treatment_term_id:UniProtKB:Q14116; treatment_term_name:Interleukin-18; treatment_type:protein; 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; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

value: ENCBS177IBD at ENCODE; https://www.encodeproject.org/ENCBS177IBD/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: TF ChIP-seq from HepG2 (ENCLB353DSO)

description:
https://www.encodeproject.org/experiments/ENCSR401VBM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR401VBM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR020QUJ
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB353DSO
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZHX2

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS930BLB at ENCODE; https://www.encodeproject.org/ENCBS930BLB/

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


title: Mint-ChIP-seq from natural killer cell (ENCLB658HIO)

description:
https://www.encodeproject.org/experiments/ENCSR035FAV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR035FAV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR387IEL
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB658HIO

value: primary cell

value: male


title: Fig5c_RTprimer8

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 8


title: Whole worm, GFP-3xFLAG-ALG-4, input, rep1

value: Whole worm

tag: developmental stage

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

value: tor143[GFP::3xFLAG::alg-4] III

value: input (total RNA)


title: Control ChIP-seq from K562 (ENCLB147CSU)

description:
https://www.encodeproject.org/experiments/ENCSR790UBY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR790UBY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-11-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB147CSU
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Michael Snyder, Stanford

value: ATCC

tag: link

value: ENCBS466CEE at ENCODE; https://www.encodeproject.org/ENCBS466CEE/

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


title: Whole worm, 3xFLAG-WAGO-10, IP, rep1

tag: tissue

tag: treatment

value: IP (Argonaute)


title: Fig5c_RTprimer5

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


title: TF ChIP-seq from HepG2 (ENCLB208RMM)

description:
https://www.encodeproject.org/experiments/ENCSR401VBM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR401VBM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR020QUJ
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB208RMM
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

tag: health state

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS718YYO at ENCODE; https://www.encodeproject.org/ENCBS718YYO/

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


title: Fig5c_RTprimer4

source_name: RNA-seq data in Fig. 5c, using miniBac-seq method to generate RNA-seq data with RT primer 4


title: TF ChIP-seq from K562 (ENCLB103EEO)

description:
https://www.encodeproject.org/experiments/ENCSR579XWM/
***************
biological replicate number: 1
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: ENCLB103EEO
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: antibody

value: 53 year

value: ENCBS113KDV at ENCODE; https://www.encodeproject.org/ENCBS113KDV/


title: Whole worm, GFP-3xFLAG-ALG-2, input, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: tor139[GFP::3xFLAG::alg-2b] II

value: input (total RNA)


title: Whole worm, 3xFLAG-WAGO-10, input, rep1


title: Mint-ChIP-seq from stimulated activated naive CD8-positive, alpha-beta T cell (ENCLB670NDH)

description:
https://www.encodeproject.org/experiments/ENCSR033WMA/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB670NDH

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

value: primary cell

value: 36 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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;

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

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