title: Mint-ChIP-seq from T-helper 17 cell (ENCLB888TDF)

description:
https://www.encodeproject.org/experiments/ENCSR103GBF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR103GBF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR104DYP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB888TDF

source_name: Homo sapiens male adult (50 years) T-helper 17 primary cell

tag: antibody

value: T-helper 17 cell

value: ENCBS720LKW at ENCODE; https://www.encodeproject.org/ENCBS720LKW/


title: larvae, nphp8 mutant 1

status: Public on Jul 22 2022

type: SRA

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

library_source: transcriptomic

data_processing:
Using STAR 2.7.3a (58) with default parameters, the fastq files were aligned to zebrafish reference genome assembly GRCz11, with genome sequence and gene annotation files downloaded from Ensembl release 104.
Quantification of gene expression was performed using RSEM v1.3.1 (59), and TPM (Transcripts Per Kilobase Million) values were generated per gene and sample.
Assembly: GRCz11
Supplementary files format and content: TPM (Transcripts Per Kilobase Million) matrix

molecule: total RNA

organism: Danio rerio

source_name: whole larvae

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Eurofins Genomics (Konstanz, Germany) proprietary library preparation protocol

tag: tissue

value: whole larvae

tag: genotype

tag: treatment


title: larvae, control 4

value: WT


title: Control ChIP-seq from middle frontal area 46 (ENCLB976GNT)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR103IXF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR103IXF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB976GNT
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

value: middle frontal area 46

value: tissue

tag: biosample encode accession

tag: age

value: 90 or above year

tag: Sex

value: female

tag: dev stage

value: adult

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Rush University

tag: link

value: ENCBS112RAT at ENCODE; https://www.encodeproject.org/ENCBS112RAT/

value: Derived from ENCODE donor ENCDO597SRH; https://www.encodeproject.org/ENCDO597SRH/


title: Whole worm, ppw-1, rep1

city: Toronto

first: Uri

last: Seroussi

address: 661 University Ave.

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Adapter sequences were then removed using cutadapt (version 1.15, (Martin, 2011)) using the following command: -a ADAPTER -f fastq -m 16 -M 30 --discard-untrimmed.
The trimmed reads were then aligned to the C. elegans PRJNA13758 ce11 genome assembly (WormBase version WS276) with STAR (version 2.6.0c, (Dobin et al., 2013)) using the following commands: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1.
The reads were then counted using a custom R (version 3.6.3) script against publicly available genome annotations. The WormBase version WS276 PRJNA13758 ce11 canonical geneset annotations were used (excluding miRNAs, repeats and transposons). C. elegans miRNA annotations were obtained from miRBase (release 22.1). For repeats and transposons RepeatMasker + Dfam (ce10 - Oct 2010 - RepeatMasker open-4.0.6 - Dfam 2.0) annotations were used. The UCSC Lift Genome Annotations tool was used to convert ce10 coordinates to ce11 coordinates. Briefly, the counting script used the findOverlaps function from the GenomicAlignments package (version 1.22.1) to assign reads to features. Multiple aligning reads or reads that align to more than one feature were dealt with by counting reads in a sequential manner to the different gene biotypes in the following order (AS stands for antisense): miRNA, piRNA, rRNA, snoRNA, snRNA, tRNA, ncRNA, lincRNA, repeats AS, protein coding AS, pseudogene AS, lincRNA AS, antisense RNA, rRNA AS, snoRNA AS, snRNA AS, tRNA AS, ncRNA AS, miRNA AS, piRNA AS, protein coding, pseudogene, antisense RNA AS, repeats. For reads that align to more than one feature in the same biotype group, the read count was split between the features based on the fraction of uniquely aligned reads to each of those features (unique weighing). See https://github.com/ClaycombLab/Seroussi_2022.
To determine differential expression of small RNAs in mutant argonaute strains, we used the R package DESeq2 (version 3.14 (Love, Huber and Anders, 2014))
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:
Synchronized populations of worms were grown on 3.5cm OP-50 seeded NGM plates for 58h at 20°C. Worms were collected and washed three times with M9 buffer (22mM KH2PO4, 42mM Na2HPO4, 86mM NaCl) and 100μl (~5,000 worms) of worms were used as starting material. 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


title: Mint-ChIP-seq from T-helper 17 cell (ENCLB158XUW)

description:
https://www.encodeproject.org/experiments/ENCSR103GBF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR103GBF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR104DYP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB158XUW

value: T-helper 17 cell

value: primary cell

value: 50 year

value: male

value: John Stamatoyannopoulos

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

description:
∆sigH (10 min heatshock, 50°C) vs. ∆sigH-rep3
Biological replicate 3 of 3
GAL file:
CG_GAL_PCR_Layout_15.gal

hyb_protocol: Gene expression changes were compared using self-made PCR-product based DNA microarrays (Lange et al. 2003), custom-made DNA microarrays with 70-mer oligonucleotides obtained from Operon Biotechnologies (Cologne, Germany) or custom-made 4x44K 60mer DNA microarrays from Agilent Technologies (Waldbronn, Germany). Hybridization of mixtures of Cy3- and Cy5-labelled cDNA on the arrays and washing of the arrays were performed as described by Frunzke et al. 2008, Polen & Wendisch 2003, and Vogt et al. 2014.

scan_protocol: The fluorescence of DNA microarrays was determined at 532 nm (Cy2-dUTP) and 635 nm (Cy5-dUTP) at 5 or 10 µm resolution with a GenePix 4000B laser scanner and GenePix Pro Software (Molecular Devices, Sunnyvale, USA).

data_processing:
The raw results were saved as GPR-files and processed and normalized using the BioConductor R packages limma and marray (http://www.bioconductor.org). For further analysis, loess-normalized data were saved in the in-house DNA microarray database (Polen et al. 2004) including detailed information about each experiment following MIAME standards (Brazma et al. 2009). Normalized ratios of medians reflecting the relative mRNA level were filtered for a signal-to-noise ratio ((F635Median/B635Median) or (F532Median/B532Median)) higher than 3. Statistical analysis for calculation of p-values was performed with a paired Student´s t-test comparing relative RNA levels for a gene to the relative RNA levels of all other genes in the replicates.
All listed GAL files are included in a tar archive on the SERIES record. The 'ID' field of the GAL files includes the Biomax IDs. A supplementary file provides the CG IDs for the Biomax IDs.

organism: Corynebacterium glutamicum

source_name: ∆sigH (10 min heatshock, 50°C)

label_protocol: Equal amounts of RNA (15-30 µg) were used for random hexamer primed synthesis of fluorescently labelled cDNA using the nucleotide analogous Cy3-dUTP or Cy5-dUTP (GE Healthcare, Eindhoven, Netherlands).

extract_protocol: Total RNA was isolated using the RNeasy Kit (Qiagen, Hilden, Germany) or as described by Wendisch et al. 2001.

value: deletion mutant

tag: condition

value: delta_sigH harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2003-09/2003-10

source_name: ∆sigH

value: delta_sigH harvested during exponential growth phase, CGXII glucose, date of experiment:2003-09/2003-10


title: WT pEKEx2-cgtR2 vs. WT pEKEx2-rep4

description:
WT pEKEx2-cgtR2 vs. WT pEKEx2-rep4
Biological replicate 4 of 5
original platform:
GPL15451

source_name: WT pEKEx2-cgtR2

value: WT + overexpression

value: WT pEKEx2-cgtR2 harvested during exponential growth phase 60 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-11/2011-12

source_name: WT pEKEx2

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase 60 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-11/2011-12


title: Whole worm, N2, rep1

value: Whole worm

value: wild-type


title: Whole worm, rde-1, rep1

value: young adult

value: hermaphrodite


title: WT pEKEx2-cgtR2 vs. WT pEKEx2-rep1

description:
WT pEKEx2-cgtR2 vs. WT pEKEx2-rep1
Biological replicate 1 of 5
original platform:
GPL15451


title: larvae, control 2

value: whole larvae

value: WT


title: larvae, control 3


title: Whole worm, nrde-3, rep1

value: 20 degrees C


title: Whole worm, hrde-1, rep1


title: Control ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB297EVL)

description:
https://www.encodeproject.org/experiments/ENCSR701JGD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR701JGD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB297EVL
size range: 200-600

source_name: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 21 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS529SCX at ENCODE; https://www.encodeproject.org/ENCBS529SCX/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


title: Mint-ChIP-seq from natural killer cell (ENCLB762IQK)

description:
https://www.encodeproject.org/experiments/ENCSR701GXD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR701GXD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR294RLP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB762IQK

source_name: Homo sapiens female adult (41 years) natural killer primary cell

value: natural killer cell

value: 41 year

value: female

value: John Stamatoyannopoulos

value: ENCBS543UGM at ENCODE; https://www.encodeproject.org/ENCBS543UGM/

value: Derived from ENCODE donor ENCDO911LCI; https://www.encodeproject.org/ENCDO911LCI/


title: Whole worm, ppw-2, rep1

value: Whole worm

value: young adult

value: hermaphrodite


title: Whole worm, ergo-1, rep1

value: 20 degrees C


title: Mint-ChIP-seq from natural killer cell (ENCLB637ESZ)

description:
https://www.encodeproject.org/experiments/ENCSR701GXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR701GXD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR294RLP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB637ESZ

value: primary cell


title: larvae, control 1

value: whole larvae

value: WT


title: ∆mtrB vs. WT-rep4

description:
∆mtrB vs. WT-rep4
Biological replicate 4 of 4
GAL file:
CG_GAL_PCR_Layout_05.gal

source_name: ∆mtrB

value: deletion mutant

value: delta_mtrB harvested during exponential growth phase, CGXII glucose, date of experiment:2005-08/2005-10

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2005-08/2005-10


title: Whole worm, DA1316, rep1


title: ∆mtrB vs. WT-rep2

description:
∆mtrB vs. WT-rep2
Biological replicate 2 of 4
GAL file:
CG_GAL_PCR_Layout_12.gal


description:
∆sigH (10 min heatshock, 50°C) vs. ∆sigH-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_14.gal

value: delta_sigH harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2003-09/2003-10

value: delta_sigH harvested during exponential growth phase, CGXII glucose, date of experiment:2003-09/2003-10


title: Whole worm, c04f12.1, rep1


title: Histone ChIP-seq from heart right ventricle (ENCLB503IBP)

description:
https://www.encodeproject.org/experiments/ENCSR501GLO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on heart right ventricle tissue male adult (66 years).
experiment encode accession: ENCSR501GLO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR898WPF
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503IBP
size range: 200-600

source_name: Homo sapiens male adult (66 years) heart right ventricle tissue

value: heart right ventricle

value: tissue

value: male

tag: health state

value: ischemic (EF 29% LVEDD 5.4; RV normal size, mild dysfunction)

value: adult

value: 66 year

value: Bradley Bernstein, Broad

value: Shin Lin

value: ENCBS948AHG at ENCODE; https://www.encodeproject.org/ENCBS948AHG/

value: Derived from ENCODE donor ENCDO926KEV; https://www.encodeproject.org/ENCDO926KEV/


title: Histone ChIP-seq from heart right ventricle (ENCLB215RCM)

description:
https://www.encodeproject.org/experiments/ENCSR501GLO/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 ChIP-seq on heart right ventricle tissue male adult (66 years).
experiment encode accession: ENCSR501GLO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR898WPF
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB215RCM
size range: 200-600


title: Preweaning 2 developmental time replication 3

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

description: Preweaning 2 developmental time, postnatal d 65, replication 3

data_processing:
Novogene's custom perl and python scripts were used to clean and filter the raw data
Bowtie 0.12.9 without mismatch for alignment
miRBase 20.0
mirdeep2 0.0.5
srna-tools-cli
RepeatMasker 4.0.3
miREvo v1.1
miRanda v3.3
DeSeq 1.12.0
GOSeq 2.12
KOBAS v 2.0
Assembly: Ovis aries (TEXEL) ensembl release 96
Supplementary files format and content: Text file of raw read counts for all miRNA features for all samples.

organism: Ovis aries

source_name: Longissimus

extract_protocol:
Total RNA was extracted with Trizol according to manufactures specifications. Qantificatioon and qualification were checked by 1% agarose gel, NanoPhotometer spectrophotometer, and Agilent Bioanalyzer 2100 system.
The NEBNext Multiplex Small RNA Library Prep Set for Illumina following manufacturer's recommendation and index codes were used to prepare the sequencing library.

tag: breed

value: SuffolkxTexel

value: Postnatal d 65

tag: replicate

value: replicate 3


title: Whole worm, csr-1, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: Preweaning 1 developmental time replication 3

description: Preweaning 1 developmental time, postnatal d 42, replication 3

value: Postnatal d 42


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB630KEQ)

description:
https://www.encodeproject.org/experiments/ENCSR101QKW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR101QKW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB630KEQ

source_name: Homo sapiens male adult (48 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

tag: antibody

value: primary cell

value: 48 year

value: John Stamatoyannopoulos

value: ENCBS684ANF at ENCODE; https://www.encodeproject.org/ENCBS684ANF/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: Preweaning 2 developmental time replication 2

description: Preweaning 2 developmental time, postnatal d 65, replication 2

value: replicate 2


title: Whole worm, alg-5, rep1

tag: tissue


title: Preweaning 1 developmental time replication 2

description: Preweaning 1 developmental time, postnatal d 42, replication 2


title: Control ChIP-seq from CD8-positive, alpha-beta T cell (ENCLB402XLB)

description:
https://www.encodeproject.org/experiments/ENCSR701JGD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR701JGD
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB402XLB
size range: 200-600

value: CD8-positive, alpha-beta T cell

value: 21 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS529SCX at ENCODE; https://www.encodeproject.org/ENCBS529SCX/

value: Derived from ENCODE donor ENCDO781BMZ; https://www.encodeproject.org/ENCDO781BMZ/


description:
∆sigH (10 min heatshock, 50°C) vs. ∆sigH-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_14.gal

tag: genotype

value: deletion mutant

value: delta_sigH harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2003-09/2003-10

value: delta_sigH harvested during exponential growth phase, CGXII glucose, date of experiment:2003-09/2003-10


title: Histone ChIP-seq from heart left ventricle (ENCLB228NIF)

description:
https://www.encodeproject.org/experiments/ENCSR300WWL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR300WWL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB228NIF
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: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB369EQD)

description:
https://www.encodeproject.org/experiments/ENCSR101QKW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101QKW
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR358BNI
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB369EQD

value: primary cell

value: 48 year

value: John Stamatoyannopoulos

value: ENCBS684ANF at ENCODE; https://www.encodeproject.org/ENCBS684ANF/

value: Derived from ENCODE donor ENCDO662KZD; https://www.encodeproject.org/ENCDO662KZD/


title: Prenatal 3 developmental time replicate 3

description: Prenatal 3 developmental time, d 133 of gestation replicate 3

value: SuffolkxTexel

value: d 133 of gestation

value: replicate 3


title: ∆mtrB vs. ∆mtrA-rep1

description:
∆mtrB vs. ∆mtrA-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_01.gal

value: deletion mutant

value: delta_mtrB harvested during exponential growth phase, CGXII glucose, date of experiment:2005-09/2005-10

source_name: ∆mtrA

value: delta_mtrA harvested during exponential growth phase, CGXII glucose, date of experiment:2005-09/2005-10


title: ∆mtrB vs. ∆mtrA-rep2

description:
∆mtrB vs. ∆mtrA-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_05.gal


title: Histone ChIP-seq from heart left ventricle (ENCLB837PXT)

description:
https://www.encodeproject.org/experiments/ENCSR300WWL/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 ChIP-seq on heart left ventricle tissue male adult (54 years).
experiment encode accession: ENCSR300WWL
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR040TRJ
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB837PXT
size range: 200-600

value: heart left ventricle

value: tissue

value: male

value: adult

value: Bradley Bernstein, Broad


title: Whole worm, alg-2, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


description:
∆mtrAB 500 µg/mL ethambutol vs. ∆mtrAB-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆mtrAB 500 µg/mL ethambutol

value: delta_mtrAB harvested during exponential growth phase, CGXII glucose, 500 µg/mL ethambutol, date of experiment:2009-02/2009-03

source_name: ∆mtrAB

value: delta_mtrAB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-02/2009-03


title: ∆mtrB vs. ∆mtrA-rep3

description:
∆mtrB vs. ∆mtrA-rep3
Biological replicate 3 of 3
GAL file:
CG_GAL_PCR_Layout_10.gal


title: Preweaning 1 developmental time replication 1

description: Preweaning 1 developmental time, postnatal d 42, replication 1

value: SuffolkxTexel

value: Postnatal d 42

value: replicate 1


description:
∆mtrAB 500 µg/mL ethambutol vs. ∆mtrAB-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant


title: ∆mtrB vs. WT-rep3

description:
∆mtrB vs. WT-rep3
Biological replicate 3 of 4
GAL file:
CG_GAL_PCR_Layout_13.gal

value: delta_mtrB harvested during exponential growth phase, CGXII glucose, date of experiment:2005-08/2005-10

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2005-08/2005-10


title: Control Mint-ChIP-seq from HCT116 (ENCLB982YUS)

description:
https://www.encodeproject.org/experiments/ENCSR500IKB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR500IKB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB982YUS

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CTCF

tag: line

value: cell line

value: 48 year

value: colorectal carcinoma

value: Erez Aiden

value: ENCBS844UBK at ENCODE; https://www.encodeproject.org/ENCBS844UBK/

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


title: Prenatal 3 developmental time replicate 2

description: Prenatal 3 developmental time, d 133 of gestation replicate 2

value: d 133 of gestation

value: replicate 2


title: Whole worm, alg-4, rep1

source_name: Whole worm

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: ∆mtrB vs. WT-rep1

description:
∆mtrB vs. WT-rep1
Biological replicate 1 of 4
GAL file:
CG_GAL_PCR_Layout_11.gal


title: Control Mint-ChIP-seq from HCT116 (ENCLB920KQX)

description:
https://www.encodeproject.org/experiments/ENCSR500IKB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR500IKB
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB920KQX

tag: biosample encode accession

value: male

value: adult

value: Bradley Bernstein, Broad


title: Preweaning 2 developmental time replication 1

description: Preweaning 2 developmental time, postnatal d 65, replication 1

value: SuffolkxTexel

tag: age

value: Postnatal d 65

value: replicate 1


description:
∆mtrAB 500 µg/mL ethambutol vs. ∆mtrAB-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_mtrAB harvested during exponential growth phase, CGXII glucose, 500 µg/mL ethambutol, date of experiment:2009-02/2009-03

value: delta_mtrAB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-02/2009-03


title: Prenatal 3 developmental time replicate 1

description: Prenatal 3 developmental time, d 133 of gestation replicate 1


title: Whole worm, alg-1, rep1

tag: Sex


title: Whole worm, alg-3, rep1


title: Prenatal 2 developmental time replicate 3

description: Prenatal 2 developmental time, d 110 of gestation, replicate 3

value: d 110 of gestation

value: replicate 3


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

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

molecule: polyA RNA

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

tag: treatment

value: IP + RNase (Argonaute)


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

value: Whole worm


title: ∆mtrAB vs. WT Operon-Oligo-rep2

description:
∆mtrAB vs. WT Operon-Oligo-rep2
Biological replicate 2 of 2
original platform:
GPL15451

value: delta_mtrAB harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04

source_name: WT Operon-Oligo

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04


title: Prenatal 2 developmental time replicate 2

description: Prenatal 2 developmental time, d 110 of gestation, replicate 2

value: replicate 2


title: Control Mint-ChIP-seq from HCT116 (ENCLB444TVM)

description:
https://www.encodeproject.org/experiments/ENCSR099TYF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR099TYF
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB444TVM

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

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

tag: dev stage

value: adult

tag: lab

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: ENCBS033MSP at ENCODE; https://www.encodeproject.org/ENCBS033MSP/

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


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

tag: developmental stage

value: young adult

value: hermaphrodite

value: 20 degrees C

value: Mock IP


title: Prenatal 2 developmental time replicate 1

description: Prenatal 2 developmental time, d 110 of gestation, replicate 1

value: SuffolkxTexel

value: d 110 of gestation

value: replicate 1


title: ∆mtrAB vs. WT Operon-Oligo-rep1

description:
∆mtrAB vs. WT Operon-Oligo-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant

value: delta_mtrAB harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2007-04


title: Prenatal 1 developmental time replicate 3

description: Prenatal 1 developmental time, d 85 of gestation, replicate 3

value: d 85 of gestation

value: replicate 3


title: Prenatal 1 developmental time replicate 2

description: Prenatal 1 developmental time, d 85 of gestation, replicate 2

value: replicate 2


title: Control Mint-ChIP-seq from HCT116 (ENCLB753KJB)

description:
https://www.encodeproject.org/experiments/ENCSR099TYF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR099TYF
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753KJB

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

tag: source

value: Erez Aiden

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

tag: link


description:
∆mtrA pEKEx2-mtrA(Asp53Asn) vs. ∆mtrA pEKEx2-mtrA-rep4
Biological replicate 4 of 4
original platform:
GPL15451

source_name: ∆mtrA pEKEx2-mtrA(Asp53Asn)

value: deletion mutant + overexpression

tag: condition

value: delta_mtrA pEKEx2-mtrA (Asp53Asn) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-05/2007-08

source_name: ∆mtrA pEKEx2-mtrA

value: deletion mutant + control

value: delta_mtrA pEKEx2 harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-05/2007-08


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

value: Whole worm

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

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

value: IP (Argonaute)


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


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB805BJX)

description:
https://www.encodeproject.org/experiments/ENCSR093VUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR093VUP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB805BJX

source_name: Homo sapiens with multiple sclerosis; CD4-positive, CD25-positive, alpha-beta regulatory T primary cell, preserved by cryopreservation

value: primary cell

tag: description

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

value: not collected

tag: health state

value: multiple sclerosis

value: unknown

value: David Hafler

value: ENCBS781DHR at ENCODE; https://www.encodeproject.org/ENCBS781DHR/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


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

tag: tissue

value: Mock IP


description:
∆mtrA pEKEx2-mtrA(Asp53Asn) vs. ∆mtrA pEKEx2-mtrA-rep2
Biological replicate 2 of 4
original platform:
GPL15451

tag: genotype

value: deletion mutant + overexpression

value: delta_mtrA pEKEx2-mtrA (Asp53Asn) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-05/2007-08

value: deletion mutant + control


description:
∆mtrA pEKEx2-mtrA(Asp53Asn) vs. ∆mtrA pEKEx2-mtrA-rep3
Biological replicate 3 of 4
original platform:
GPL15451

value: delta_mtrA pEKEx2 harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-05/2007-08


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

value: Whole worm

value: young adult

value: hermaphrodite

value: input (total RNA)


title: Mint-ChIP-seq from HCT116 (ENCLB515PIM)

description:
https://www.encodeproject.org/experiments/ENCSR098CPV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR098CPV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR099TYF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515PIM

tag: antibody

tag: line

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

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: ENCBS033MSP at ENCODE; https://www.encodeproject.org/ENCBS033MSP/

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


title: Mature developmental time replicate 2

description: Mature developmental time, postnatal d 243, replicate 2

tag: breed

value: SuffolkxTexel

tag: age

value: Postnatal d 243

tag: replicate

value: replicate 2


title: Prenatal 1 developmental time replicate 1

description: Prenatal 1 developmental time, d 85 of gestation, replicate 1

value: d 85 of gestation

value: replicate 1


title: ∆mtrA vs. WT PCR-Product-rep2

description:
∆mtrA vs. WT PCR-Product-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_04.gal

value: deletion mutant

value: delta_mtrA harvested during exponential growth phase, CGXII glucose, date of experiment:2004-09

source_name: WT PCR-Product

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2004-09


title: ∆mtrA vs. WT PCR-Product-rep3

description:
∆mtrA vs. WT PCR-Product-rep3
Biological replicate 3 of 3
GAL file:
CG_GAL_PCR_Layout_00.gal


description:
∆mtrA pEKEx2-mtrA(Asp53Asn) vs. ∆mtrA pEKEx2-mtrA-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_mtrA pEKEx2-mtrA (Asp53Asn) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-05/2007-08

value: deletion mutant + control

value: delta_mtrA pEKEx2 harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2007-05/2007-08


title: Whole worm, GFP-3xFLAG-ERGO-1, input for FLAG IP

value: Whole worm

value: young adult

tag: Sex

value: hermaphrodite

value: 20 degrees C

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

tag: treatment

value: input (total RNA)


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB107IDI)

description:
https://www.encodeproject.org/experiments/ENCSR093VUP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR093VUP
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB107IDI

value: primary cell

value: Treg CD3+ CD4+ CD8- CD25+ CD127-

tag: biosample encode accession

value: not collected

value: multiple sclerosis

tag: dev stage

value: unknown

tag: lab

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS781DHR at ENCODE; https://www.encodeproject.org/ENCBS781DHR/

value: Derived from ENCODE donor ENCDO157PKH; https://www.encodeproject.org/ENCDO157PKH/


title: Mature developmental time replicate 3

description: Mature developmental time, postnatal d 243, replicate 3

value: SuffolkxTexel

value: Postnatal d 243

value: replicate 3


title: Whole worm, GFP-3xFLAG-WAGO-4, IP, rep2

value: Whole worm

tag: developmental stage

value: young adult

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

value: IP (Argonaute)


title: Mature developmental time replicate 1

description: Mature developmental time, postnatal d 243, replicate 1

value: replicate 1


title: Mint-ChIP-seq from HCT116 (ENCLB823WQJ)

description:
https://www.encodeproject.org/experiments/ENCSR088ZGM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR088ZGM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB823WQJ

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

tag: source

value: Erez Aiden

tag: link

value: ENCBS456GWO at ENCODE; https://www.encodeproject.org/ENCBS456GWO/

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


title: paiso_GV_ctr_F4_6_SMRTCell1541

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

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

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

value: GV oocytes

value: ctr


title: Mint-ChIP-seq from HCT116 (ENCLB828AKP)

description:
https://www.encodeproject.org/experiments/ENCSR088ZGM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR088ZGM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR608WUK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB828AKP

value: Bradley Bernstein, Broad


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

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

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


title: paiso_GV_ctr_F4_7_SMRTCell1541


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

value: Whole worm

value: young adult

value: input (total RNA)


title: Mint-ChIP-seq from HCT116 (ENCLB772KTC)

description:
https://www.encodeproject.org/experiments/ENCSR098CPV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR098CPV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR099TYF
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB772KTC

value: cell line

tag: health state

tag: treatments

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

value: ENCBS033MSP at ENCODE; https://www.encodeproject.org/ENCBS033MSP/


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB958VJU)

description:
https://www.encodeproject.org/experiments/ENCSR082DLA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR082DLA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR212ZBB
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB958VJU

source_name: Homo sapiens male adult (50 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

value: primary cell

value: 50 year

value: male

value: John Stamatoyannopoulos

value: ENCBS552ZBM at ENCODE; https://www.encodeproject.org/ENCBS552ZBM/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: paiso_GV_cKO_F1_7_SMRTCell1541

tag: tissue

value: GV oocytes

tag: genotype

value: cKO


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB469MRJ)

description:
https://www.encodeproject.org/experiments/ENCSR082DLA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR082DLA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR212ZBB
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469MRJ

tag: antibody

value: adult

value: Bradley Bernstein, Broad


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB506FQE)

description:
https://www.encodeproject.org/experiments/ENCSR081XLT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR081XLT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR761HQT
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB506FQE

source_name: Homo sapiens male adult (30 years) CD8-positive naive resting alpha-beta T primary cell

value: 30 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS845PJM at ENCODE; https://www.encodeproject.org/ENCBS845PJM/

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


title: paiso_GV_ctr_F4_5_SMRTCell1541

value: ctr


title: TF ChIP-seq from WTC11 (ENCLB567ARD)

description:
https://www.encodeproject.org/experiments/ENCSR127NBZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ERG ChIP-seq on human WTC11
experiment encode accession: ENCSR127NBZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR395ZBR
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB567ARD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: ERG

tag: line

value: cell line

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS631AHS at ENCODE; https://www.encodeproject.org/ENCBS631AHS/

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


title: TF ChIP-seq from HepG2 (ENCLB308WMN)

description:
https://www.encodeproject.org/experiments/ENCSR678KUJ/
***************
biological replicate number: 1
technical replicate number: 2
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR678KUJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR770PLF
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB308WMN
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZFP91

tag: age

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: ENCBS100LHF at ENCODE; https://www.encodeproject.org/ENCBS100LHF/

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


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB454EQB)

description:
https://www.encodeproject.org/experiments/ENCSR081XLT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR081XLT
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR761HQT
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB454EQB

value: primary cell

value: adult

value: 30 year

value: Yijun Ruan, JAX

value: AllCells


title: Mint-ChIP-seq from T-helper 17 cell (ENCLB684HVQ)

description:
https://www.encodeproject.org/experiments/ENCSR079EXG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR079EXG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR104DYP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB684HVQ

source_name: Homo sapiens male adult (50 years) T-helper 17 primary cell

value: T-helper 17 cell

value: 50 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS720LKW at ENCODE; https://www.encodeproject.org/ENCBS720LKW/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: paiso_GV_ctr_F3_8_SMRTCell1541

value: GV oocytes

value: ctr


title: Whole worm, GFP-3xFLAG-WAGO-4, input, rep2

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

value: input (total RNA)


title: TF ChIP-seq from HepG2 (ENCLB469OKH)

description:
https://www.encodeproject.org/experiments/ENCSR678KUJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR678KUJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR770PLF
encode release date: 2022-03-28
lab: Richard Myers, HAIB
library encode accession: ENCLB469OKH
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS349EKM at ENCODE; https://www.encodeproject.org/ENCBS349EKM/

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


title: TF ChIP-seq from WTC11 (ENCLB362COO)

description:
https://www.encodeproject.org/experiments/ENCSR127NBZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ERG ChIP-seq on human WTC11
experiment encode accession: ENCSR127NBZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR395ZBR
encode release date: 2021-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB362COO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ERG

value: 30 year

value: adult

value: Michael Snyder, Stanford

value: ENCBS868NKT at ENCODE; https://www.encodeproject.org/ENCBS868NKT/

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


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

value: IP (Argonaute)


title: Mint-ChIP-seq from naive B cell (ENCLB057EHX)

description:
https://www.encodeproject.org/experiments/ENCSR077XOM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR077XOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR056PPJ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB057EHX

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

value: naive B cell

value: primary cell

value: 40 year

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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-RDE-1, IP, rep2

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


title: paiso_GV_cKO_F1_6_SMRTCell1541

value: GV oocytes

value: cKO


title: Mint-ChIP-seq from T-helper 17 cell (ENCLB205PXZ)

description:
https://www.encodeproject.org/experiments/ENCSR079EXG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR079EXG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR104DYP
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB205PXZ

value: T-helper 17 cell

value: 50 year

value: adult

value: ENCBS720LKW at ENCODE; https://www.encodeproject.org/ENCBS720LKW/

value: Derived from ENCODE donor ENCDO641WTL; https://www.encodeproject.org/ENCDO641WTL/


title: paiso_GV_cKO_F1_5_SMRTCell1541


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

value: input (total RNA)


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB153KOF)

description:
https://www.encodeproject.org/experiments/ENCSR889VGA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR889VGA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR509FRR
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB153KOF
fragmentation methods: none

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

value: CD14-positive monocyte

value: primary cell

tag: description

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

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

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


title: paiso_GV_ctr_F4_7_SMRTCell1537

value: GV oocytes

value: ctr


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB352EOZ)

description:
https://www.encodeproject.org/experiments/ENCSR889VGA/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR889VGA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR509FRR
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB352EOZ
fragmentation methods: none

tag: Sex


title: Mint-ChIP-seq from naive B cell (ENCLB169IVA)

description:
https://www.encodeproject.org/experiments/ENCSR077XOM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR077XOM
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR056PPJ
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB169IVA

value: naive B cell

value: 40 year

value: male

value: adult

value: John Stamatoyannopoulos

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, IP, rep2

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

tag: treatment

value: IP (Argonaute)


title: WT pEKEx2-cgtR2 vs. WT pEKEx2-rep5

description:
WT pEKEx2-cgtR2 vs. WT pEKEx2-rep5
Biological replicate 5 of 5
original platform:
GPL15451

source_name: WT pEKEx2-cgtR2

value: WT + overexpression

tag: condition

value: WT pEKEx2-cgtR2 harvested during exponential growth phase 60 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-11/2011-12

source_name: WT pEKEx2

value: wild type + control

value: WT pEKEx2 harvested during exponential growth phase 60 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-11/2011-12


title: TF ChIP-seq from B cell (ENCLB112DVP)

description:
https://www.encodeproject.org/experiments/ENCSR075NRV/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR075NRV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR437VOU
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB112DVP
size range: 200-600

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

value: CTCF

value: B cell

value: primary cell

tag: biosample encode accession

value: 22 year

tag: dev stage

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS822FPE at ENCODE; https://www.encodeproject.org/ENCBS822FPE/

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


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

source_name: Whole worm

value: Whole worm

tag: developmental stage

value: young adult

value: input (total RNA)


title: TF ChIP-seq from K562 (ENCLB102CHI)

description:
https://www.encodeproject.org/experiments/ENCSR682AAS/
***************
biological replicate number: 4
technical replicate number: 1
description: ZNF668 ChIP-seq on human K562
experiment encode accession: ENCSR682AAS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR926XXG
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB102CHI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF668

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

tag: lab

value: Michael Snyder, Stanford

tag: source

value: ATCC

value: ENCBS784NWR at ENCODE; https://www.encodeproject.org/ENCBS784NWR/

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


title: paiso_GV_ctr_F3_8_SMRTCell1537

value: GV oocytes

value: ctr


title: TF ChIP-seq from WTC11 (ENCLB668ZTS)

description:
https://www.encodeproject.org/experiments/ENCSR499FDW/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN18 ChIP-seq on human WTC11
experiment encode accession: ENCSR499FDW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR294TOY
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB668ZTS
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZSCAN18

value: 30 year

value: male

value: Richard Myers

tag: link

value: ENCBS187HTQ at ENCODE; https://www.encodeproject.org/ENCBS187HTQ/

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


title: TF ChIP-seq from B cell (ENCLB327EUJ)

description:
https://www.encodeproject.org/experiments/ENCSR075NRV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR075NRV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR437VOU
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327EUJ
size range: 200-600

value: CTCF

value: B cell

value: primary cell

value: 22 year

value: Bradley Bernstein, Broad

value: Charles Lee

value: ENCBS822FPE at ENCODE; https://www.encodeproject.org/ENCBS822FPE/

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


title: TF ChIP-seq from B cell (ENCLB634YBK)

description:
https://www.encodeproject.org/experiments/ENCSR075NRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075NRV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR437VOU
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB634YBK
size range: 200-600

value: adult


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

value: Whole worm

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

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

value: IP (Argonaute)


title: paiso_GV_cKO_F1_7_SMRTCell1537

value: GV oocytes

value: cKO


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

value: input (total RNA)


title: TF ChIP-seq from K562 (ENCLB286GXR)

description:
https://www.encodeproject.org/experiments/ENCSR682AAS/
***************
biological replicate number: 3
technical replicate number: 1
description: ZNF668 ChIP-seq on human K562
experiment encode accession: ENCSR682AAS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR926XXG
encode release date: 2022-06-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB286GXR
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS223UXN at ENCODE; https://www.encodeproject.org/ENCBS223UXN/

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


title: Mint-ChIP-seq from T-cell (ENCLB142CME)

description:
https://www.encodeproject.org/experiments/ENCSR073ORI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR073ORI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB142CME

source_name: Homo sapiens female adult (21 years) T-cell primary cell

value: T-cell

value: primary cell

value: 21 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: paiso_GV_cKO_F1_6_SMRTCell1537

tag: tissue

value: GV oocytes

value: cKO


title: Control ChIP-seq from WTC11 (ENCLB940RKG)

description:
https://www.encodeproject.org/experiments/ENCSR294TOY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR294TOY
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB940RKG
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: Richard Myers

value: ENCBS235FKM at ENCODE; https://www.encodeproject.org/ENCBS235FKM/

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


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

tag: genotype

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

value: input (total RNA)


title: paiso_GV_ctr_F4_6_SMRTCell1537

value: ctr


title: Control ChIP-seq from K562 (ENCLB271UTF)

description:
https://www.encodeproject.org/experiments/ENCSR490VNA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR490VNA
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-04
lab: Richard Myers, HAIB
library encode accession: ENCLB271UTF
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Richard Myers, HAIB

value: ENCBS501ZZR at ENCODE; https://www.encodeproject.org/ENCBS501ZZR/

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


title: Mint-ChIP-seq from T-cell (ENCLB280OJC)

description:
https://www.encodeproject.org/experiments/ENCSR073ORI/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR073ORI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB280OJC

tag: antibody

value: T-cell

value: primary cell

value: 21 year

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

value: IP (Argonaute)


title: TF ChIP-seq from WTC11 (ENCLB076FCC)

description:
https://www.encodeproject.org/experiments/ENCSR499FDW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN18 ChIP-seq on human WTC11
experiment encode accession: ENCSR499FDW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR294TOY
encode release date: 2022-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB076FCC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: cell line

value: 30 year

value: male

value: adult

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS625XGB at ENCODE; https://www.encodeproject.org/ENCBS625XGB/

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


title: Mint-ChIP-seq from T-cell (ENCLB294SSW)

description:
https://www.encodeproject.org/experiments/ENCSR073ORI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR073ORI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB294SSW

value: T-cell

value: primary cell

tag: age

value: 21 year

value: female

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos


title: TF ChIP-seq from K562 (ENCLB817OVT)

description:
https://www.encodeproject.org/experiments/ENCSR279OXE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZFP30 ChIP-seq on human K562
experiment encode accession: ENCSR279OXE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-04-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB817OVT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Kevin White

value: ENCBS859MVC at ENCODE; https://www.encodeproject.org/ENCBS859MVC/

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


title: paiso_GV_ctr_F3_7_SMRTCell1540

source_name: GV oocytes

value: GV oocytes

value: ctr


title: paiso_GV_cKO_F1_5_SMRTCell1537

value: cKO


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

value: input (total RNA)


title: paiso_GV_ctr_F4_5_SMRTCell1537


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

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


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB576EZC)

description:
https://www.encodeproject.org/experiments/ENCSR665QZU/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR665QZU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365IQY
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576EZC
fragmentation methods: none

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

value: CD14-positive monocyte

value: primary cell

tag: description

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS747UFJ at ENCODE; https://www.encodeproject.org/ENCBS747UFJ/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


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

value: Whole worm

tag: Sex

value: IP (Argonaute)


title: Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB102AWJ)

description:
https://www.encodeproject.org/experiments/ENCSR072ORU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR072ORU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR368JDN
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB102AWJ

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

value: 33 year

value: male

value: adult

value: John Stamatoyannopoulos

tag: treatments

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

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

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


title: Mint-ChIP-seq from T-cell (ENCLB538RLV)

description:
https://www.encodeproject.org/experiments/ENCSR073ORI/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR073ORI
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB538RLV

value: T-cell

value: primary cell

value: 21 year

value: female

value: ENCBS891XZS at ENCODE; https://www.encodeproject.org/ENCBS891XZS/

value: Derived from ENCODE donor ENCDO282XZV; https://www.encodeproject.org/ENCDO282XZV/


title: Mint-ChIP-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCLB586MEM)

description:
https://www.encodeproject.org/experiments/ENCSR072ORU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR072ORU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR368JDN
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB586MEM

value: Bradley Bernstein, Broad


title: paiso_GV_ctr_F3_6_SMRTCell1540

value: GV oocytes

value: ctr


title: Control ChIP-seq from motor neuron (ENCLB716QSL)

description:
https://www.encodeproject.org/experiments/ENCSR663GIS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human motor neuron
experiment encode accession: ENCSR663GIS
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-12-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB716QSL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (49 years) motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: 49 year

value: Donor with Amyotrophic Lateral Sclerosis

value: Michael Snyder, Stanford

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

value: ENCBS463FLE at ENCODE; https://www.encodeproject.org/ENCBS463FLE/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: paiso_GV_cKO_F2_7_SMRTCell1540

value: cKO


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB884GKP)

description:
https://www.encodeproject.org/experiments/ENCSR665QZU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR665QZU
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR365IQY
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB884GKP
fragmentation methods: none

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

value: not collected

value: healthy

value: unknown

value: David Hafler

value: ENCBS747UFJ at ENCODE; https://www.encodeproject.org/ENCBS747UFJ/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: paiso_GV_ctr_F3_5_SMRTCell1540

value: GV oocytes

value: ctr


title: paiso_GV_cKO_F2_5_SMRTCell1540


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

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

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

tag: treatment

value: IP (Argonaute)


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

value: input (total RNA)


title: TF ChIP-seq from K562 (ENCLB128CAZ)

description:
https://www.encodeproject.org/experiments/ENCSR659CCI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR659CCI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR859ZNT
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB128CAZ
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens FOXK1

value: cell line

tag: biosample encode accession

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS167MIB at ENCODE; https://www.encodeproject.org/ENCBS167MIB/

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


title: Control Mint-ChIP-seq from HCT116 (ENCLB425MNM)

description:
https://www.encodeproject.org/experiments/ENCSR071RJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR071RJS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB425MNM

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

value: 48 year

value: male

value: colorectal carcinoma

tag: dev stage

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS816ZRZ at ENCODE; https://www.encodeproject.org/ENCBS816ZRZ/

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


title: paiso_GV_cKO_F1_8_SMRTCell1540

value: GV oocytes

value: cKO


title: TF ChIP-seq from K562 (ENCLB604GBL)

description:
https://www.encodeproject.org/experiments/ENCSR659YWQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF449 ChIP-seq on human K562
experiment encode accession: ENCSR659YWQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-04-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB604GBL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: cell line

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS019ZMO at ENCODE; https://www.encodeproject.org/ENCBS019ZMO/


title: paiso_GV_cKO_F2_6_SMRTCell1540


title: Mint-ChIP-seq from HCT116 (ENCLB170OBC)

description:
https://www.encodeproject.org/experiments/ENCSR070KNB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR070KNB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR861TAI
encode release date: 2022-07-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB170OBC

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens SUPT16H treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: adult

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

value: ENCBS456IZA at ENCODE; https://www.encodeproject.org/ENCBS456IZA/


title: Control Mint-ChIP-seq from HCT116 (ENCLB732BXB)

description:
https://www.encodeproject.org/experiments/ENCSR071RJS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR071RJS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB732BXB

value: 48 year


title: TF ChIP-seq from K562 (ENCLB034QNT)

description:
https://www.encodeproject.org/experiments/ENCSR659YWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF449 ChIP-seq on human K562
experiment encode accession: ENCSR659YWQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2022-04-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB034QNT
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS846FUW at ENCODE; https://www.encodeproject.org/ENCBS846FUW/

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


title: TF ChIP-seq from HepG2 (ENCLB685GJW)

description:
https://www.encodeproject.org/experiments/ENCSR268XPQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR268XPQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR693GOR
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB685GJW
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TCF12

value: 15 year

value: male

value: hepatocellular carcinoma

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS297BTA at ENCODE; https://www.encodeproject.org/ENCBS297BTA/

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


title: Whole worm, GFP-3xFLAG-ALG-5, IP, rep2

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

value: 20 degrees C

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

value: IP (Argonaute)


title: Mint-ChIP-seq from HCT116 (ENCLB253QLR)

description:
https://www.encodeproject.org/experiments/ENCSR070KNB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR070KNB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR861TAI
encode release date: 2022-07-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB253QLR

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

tag: lab

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: ENCBS456IZA at ENCODE; https://www.encodeproject.org/ENCBS456IZA/

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


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

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


title: paiso_GV_ctr_F3_5_SMRTCell1536

value: GV oocytes

value: ctr


title: paiso_GV_ctr_F3_7_SMRTCell1536


title: Whole worm, GFP-3xFLAG-ALG-5, input, rep2

value: Whole worm

value: young adult

value: input (total RNA)


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB790LLE)

description:
https://www.encodeproject.org/experiments/ENCSR070AET/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR070AET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR239ZVK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790LLE

source_name: Homo sapiens male adult (33 years) naive thymus-derived CD8-positive, alpha-beta T primary cell

value: primary cell

value: 33 year

value: male

tag: source

value: John Stamatoyannopoulos

value: ENCBS538USD at ENCODE; https://www.encodeproject.org/ENCBS538USD/

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


title: paiso_GV_ctr_F3_6_SMRTCell1536


title: TF ChIP-seq from K562 (ENCLB131ZHO)

description:
https://www.encodeproject.org/experiments/ENCSR659CCI/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR659CCI
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR859ZNT
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB131ZHO
fragmentation methods: sonication (generic)

value: cell line

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: Richard Myers, HAIB

value: Richard Myers

tag: link

value: ENCBS726VDS at ENCODE; https://www.encodeproject.org/ENCBS726VDS/

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


title: Mint-ChIP-seq from activated T-helper 1 cell (ENCLB551SRM)

description:
https://www.encodeproject.org/experiments/ENCSR068YVZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ug/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR068YVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR188HBL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB551SRM

source_name: Homo sapiens male adult (35 years) activated T-helper 1 primary cell treated with 1ug/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads

value: activated T-helper 1 cell

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:Interleukin-4 antibody; treatment_type:antibody; treatment_term_id:UniProtKB:P29459; treatment_term_name:Interleukin-12 subunit alpha; treatment_type:protein; treatment_term_id:UniProtKB:P29460; treatment_term_name:Interleukin-12 subunit beta; treatment_type:protein; treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS279ECG at ENCODE; https://www.encodeproject.org/ENCBS279ECG/

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


title: Mint-ChIP-seq from activated T-helper 1 cell (ENCLB803CEE)

description:
https://www.encodeproject.org/experiments/ENCSR068YVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 Mint-ChIP-seq on activated T-helper 1 cell male adult (35 years) treated with 1 ug/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads
experiment encode accession: ENCSR068YVZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR188HBL
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB803CEE

source_name: Homo sapiens male adult (35 years) activated T-helper 1 primary cell treated with 1 u/mL Interleukin-4 antibody , 30 ng/mL Interleukin-12 subunit alpha , 30 ng/mL Interleukin-12 subunit beta , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male


title: TF ChIP-seq from HepG2 (ENCLB032YFS)

description:
https://www.encodeproject.org/experiments/ENCSR268XPQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR268XPQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR693GOR
encode release date: 2022-01-13
lab: Richard Myers, HAIB
library encode accession: ENCLB032YFS
fragmentation methods: sonication (generic)

value: cell line

value: 15 year

value: hepatocellular carcinoma

value: child

value: ENCBS727RQT at ENCODE; https://www.encodeproject.org/ENCBS727RQT/

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


title: Whole worm, GFP-3xFLAG-ALG-4, IP, rep2

source_name: Whole worm

value: Whole worm

value: hermaphrodite

tag: growth temperature

value: 20 degrees C

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

value: IP (Argonaute)


title: Mint-ChIP-seq from naive thymus-derived CD8-positive, alpha-beta T cell (ENCLB974FDB)

description:
https://www.encodeproject.org/experiments/ENCSR070AET/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR070AET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR239ZVK
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB974FDB

value: 33 year

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS538USD at ENCODE; https://www.encodeproject.org/ENCBS538USD/

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


title: Whole worm, GFP-3xFLAG-ALG-4, input, rep2

value: input (total RNA)


title: Control ChIP-seq from WTC11 (ENCLB889CQL)

description:
https://www.encodeproject.org/experiments/ENCSR267JAO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human WTC11
experiment encode accession: ENCSR267JAO
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2021-09-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB889CQL
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: 30 year

value: male

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS479DYT at ENCODE; https://www.encodeproject.org/ENCBS479DYT/

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


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

value: Whole worm

value: hermaphrodite

value: 20 degrees C

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


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

value: IP (Argonaute)


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

value: young adult

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


title: paiso_GV_cKO_F2_7_SMRTCell1536

value: GV oocytes

value: cKO


title: Control ChIP-seq from K562 (ENCLB783RWA)

description:
https://www.encodeproject.org/experiments/ENCSR859ZNT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR859ZNT
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-04
lab: Richard Myers, HAIB
library encode accession: ENCLB783RWA
fragmentation methods: sonication (generic)

value: 53 year

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: Richard Myers, HAIB

value: ENCBS435AEJ at ENCODE; https://www.encodeproject.org/ENCBS435AEJ/

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


title: paiso_GV_cKO_F2_5_SMRTCell1536

tag: tissue