title: Mint-ChIP-seq from HCT116 (ENCLB503ASF)

description:
https://www.encodeproject.org/experiments/ENCSR323XBZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR323XBZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR642FUX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503ASF

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS891BUF at ENCODE; https://www.encodeproject.org/ENCBS891BUF/

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


title: Mint-ChIP-seq from H9 (ENCLB437YXB)

status: Public on Jul 22 2022

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR016RFN/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR016RFN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB437YXB
fragmentation methods: none

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens H9 cell line

tag: antibody

tag: line

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: embryonic

tag: age

value: 5 day

tag: lab

tag: source

value: Joseph Bonventre

tag: health state

value: healthy

tag: passage number

tag: link

value: ENCBS877WZR at ENCODE; https://www.encodeproject.org/ENCBS877WZR/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: dis3l2_cKO_2_3_rM

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: GV oocytes

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

tag: tissue

value: GV oocytes

tag: genotype

value: cKO


title: Histone ChIP-seq from ovary (ENCLB622CSW)

description:
https://www.encodeproject.org/experiments/ENCSR509SNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR509SNH
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR583MIW
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622CSW
size range: 200-600

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

value: ovary

value: tissue

value: 41 year

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

value: Shin Lin

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

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


type: RNA

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

country: Germany

institute: Forschungszentrum Jülich GmbH

description:
∆rosR (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

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: ∆rosR (CGXII, 4% glucose)

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

source_name: WT (CGXII, 4% glucose)

value: wild type

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


title: Mint-ChIP-seq from HCT116 (ENCLB312YBW)

description:
https://www.encodeproject.org/experiments/ENCSR323XBZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR323XBZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR642FUX
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB312YBW

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

value: Erez Aiden

value: ENCBS891BUF at ENCODE; https://www.encodeproject.org/ENCBS891BUF/

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


title: dis3l2_cKO_1_4_rM

value: GV oocytes

value: cKO


description:
∆rosR (CGXII, 4% glucose) vs. WT (CGXII, 4% glucose)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from H9 (ENCLB494XJL)

description:
https://www.encodeproject.org/experiments/ENCSR016RFN/
***************
biological replicate number: 1
technical replicate number: 4
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR016RFN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB494XJL
fragmentation methods: none

value: female

value: healthy

value: embryonic

value: 5 day

value: Joseph Bonventre

value: ENCBS965ZIX at ENCODE; https://www.encodeproject.org/ENCBS965ZIX/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Control Mint-ChIP-seq from T-helper 17 cell (ENCLB757OKZ)

description:
https://www.encodeproject.org/experiments/ENCSR104DYP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR104DYP
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-04-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB757OKZ

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

value: T-helper 17 cell

value: primary cell

value: 50 year

value: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB738NVQ)

description:
https://www.encodeproject.org/experiments/ENCSR919UYS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR919UYS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB738NVQ

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

value: 36 year

value: male

value: adult

value: Bradley Bernstein, Broad

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

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


title: Mint-ChIP-seq from H9 (ENCLB269DFN)

description:
https://www.encodeproject.org/experiments/ENCSR016RFN/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 Mint-ChIP-seq on human H9
experiment encode accession: ENCSR016RFN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR854TWQ
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269DFN
fragmentation methods: none

value: cell line

value: female

value: healthy

value: embryonic


title: dis3l2_cKO_1_3_rM

value: GV oocytes

value: cKO


title: dis3l2_cKO_1_1_rM


title: Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB688RBK)

description:
https://www.encodeproject.org/experiments/ENCSR919UYS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR919UYS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR308NMT
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB688RBK

value: primary cell


title: Mint-ChIP-seq from brain (ENCLB883EVD)

description:
https://www.encodeproject.org/experiments/ENCSR000FYV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR000FYV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883EVD
fragmentation methods: none

source_name: Homo sapiens female embryo (5 days) brain organoid, 30 days post differentiation

value: brain

value: organoid

value: 5 day

value: Paola Arlotta

value: ENCBS219JHY at ENCODE; https://www.encodeproject.org/ENCBS219JHY/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Mint-ChIP-seq from brain (ENCLB514TMA)

description:
https://www.encodeproject.org/experiments/ENCSR000FYV/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR000FYV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB514TMA
fragmentation methods: none


title: ∆cydAB ∆qcrBAC (BHI) vs. WT (BHI)-rep3

description:
∆cydAB ∆qcrBAC (BHI) vs. WT (BHI)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cydAB ∆qcrBAC (BHI)

value: deletion mutant

value: delta_cydAB delta_qcrBAC harvested during exponential growth phase, BHI, date of experiment:2011-04/2011-07

source_name: WT (BHI)

value: wild type

value: WT harvested during exponential growth phase, BHI, date of experiment:2011-04/2011-07


title: dis3l2_cKO_1_2_rM


title: Control Mint-ChIP-seq from HCT116 (ENCLB610ZRR)

description:
https://www.encodeproject.org/experiments/ENCSR508TCS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR508TCS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB610ZRR

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

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: ENCBS271TPC at ENCODE; https://www.encodeproject.org/ENCBS271TPC/

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


title: Control Mint-ChIP-seq from HCT116 (ENCLB557HOV)

description:
https://www.encodeproject.org/experiments/ENCSR508TCS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR508TCS
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB557HOV


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB105USR)

description:
https://www.encodeproject.org/experiments/ENCSR507SXH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR507SXH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR212ZBB
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB105USR

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: John Stamatoyannopoulos

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

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


title: Mint-ChIP-seq from brain (ENCLB864TWI)

description:
https://www.encodeproject.org/experiments/ENCSR000FYV/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR000FYV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB864TWI
fragmentation methods: none

value: brain

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Paola Arlotta

value: ENCBS001KQF at ENCODE; https://www.encodeproject.org/ENCBS001KQF/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: dis3l2MII_ctr_f6_32_pA

molecule: polyA RNA

source_name: MII oocytes

value: MII oocytes

value: ctr


title: ∆cydAB ∆qcrBAC (BHI) vs. WT (BHI)-rep2

description:
∆cydAB ∆qcrBAC (BHI) vs. WT (BHI)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cydAB delta_qcrBAC harvested during exponential growth phase, BHI, date of experiment:2011-04/2011-07

value: wild type

value: WT harvested during exponential growth phase, BHI, date of experiment:2011-04/2011-07


title: dis3l2MII_ctr_f6_31_pA


description:
∆cydAB ∆qcrBAC (CGXII, 2 g/L peptone) vs. WT CGXII (2 g/l peptone)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cydAB ∆qcrBAC (CGXII, 2 g/L peptone)

value: delta_cydAB delta_qcrBAC harvested during exponential growth phase, CGXII glucose 2 g/L peptone, date of experiment:2011-04/2011-07

source_name: WT CGXII (2 g/l peptone)

value: WT harvested during exponential growth phase, CGXII glucose 2 g/L peptone, date of experiment:2011-04/2011-07


title: Mint-ChIP-seq from brain (ENCLB176NPW)

description:
https://www.encodeproject.org/experiments/ENCSR000FYV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR000FYV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB176NPW
fragmentation methods: none

value: brain

value: Bradley Bernstein, Broad

value: ENCBS337FMJ at ENCODE; https://www.encodeproject.org/ENCBS337FMJ/


title: ∆cydAB ∆qcrBAC (BHI) vs. WT (BHI)-rep1

description:
∆cydAB ∆qcrBAC (BHI) vs. WT (BHI)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


description:
∆cydAB ∆qcrBAC (CGXII, 2 g/L peptone) vs. WT CGXII (2 g/l peptone)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB268PHY)

description:
https://www.encodeproject.org/experiments/ENCSR507SXH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR507SXH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR212ZBB
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB268PHY

value: primary cell

value: 50 year

value: male

value: adult

value: John Stamatoyannopoulos

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

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


title: dis3l2MII_ctr_f6_30_pA

value: MII oocytes

value: ctr


description:
∆cydAB ∆qcrBAC (CGXII, 2 g/L peptone) vs. WT CGXII (2 g/l peptone)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant


title: Mint-ChIP-seq from brain (ENCLB452OVX)

description:
https://www.encodeproject.org/experiments/ENCSR000FYV/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR000FYV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB452OVX
fragmentation methods: none

value: organoid

value: female

value: healthy

value: embryonic

value: 5 day

value: Paola Arlotta

value: ENCBS001KQF at ENCODE; https://www.encodeproject.org/ENCBS001KQF/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


description:
∆cydAB (stationary phase) vs. WT (stationary phase)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cydAB (stationary phase)

value: delta_cydAB harvested during stationary growth phase, CGXII glucose, date of experiment:2009-06

source_name: WT (stationary phase)

value: wild type

value: Wt harvested during stationary growth phase, CGXII glucose, date of experiment:2009-06


title: Histone ChIP-seq from middle frontal area 46 (ENCLB388PIJ)

description:
https://www.encodeproject.org/experiments/ENCSR706PAK/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR706PAK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB388PIJ
size range: 200-600

source_name: Homo sapiens female adult (79 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 79 year

value: adult

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS836MZE at ENCODE; https://www.encodeproject.org/ENCBS836MZE/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: dis3l2MII_ctr_f5_28_pA

value: MII oocytes

value: ctr


description:
∆cydAB (stationary phase) vs. WT (stationary phase)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant


description:
∆cydAB (stationary phase) vs. WT (stationary phase)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: dis3l2MII_ctr_f5_27_pA


title: Histone ChIP-seq from middle frontal area 46 (ENCLB361ORL)

description:
https://www.encodeproject.org/experiments/ENCSR706PAK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR706PAK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361ORL
size range: 200-600

value: female

value: ENCBS246FGU at ENCODE; https://www.encodeproject.org/ENCBS246FGU/


title: Mint-ChIP-seq from brain (ENCLB469XLP)

description:
https://www.encodeproject.org/experiments/ENCSR000FYV/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human H9 derived brain organoid
experiment encode accession: ENCSR000FYV
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR824UQL
encode release date: 2021-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB469XLP
fragmentation methods: none

value: brain

value: organoid

value: healthy

value: embryonic

value: 5 day

value: Paola Arlotta

value: ENCBS337FMJ at ENCODE; https://www.encodeproject.org/ENCBS337FMJ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Histone ChIP-seq from middle frontal area 46 (ENCLB611PGM)

description:
https://www.encodeproject.org/experiments/ENCSR706PAK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR706PAK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB611PGM
size range: 200-600

value: middle frontal area 46

value: tissue

value: 79 year

value: adult

value: Bradley Bernstein, Broad


title: dis3l2MII_ctr_f5_26_pA

value: MII oocytes

value: ctr


title: dis3l2MII_ctr_f5_25_pA


title: Whole worm, wago-1, rep3

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: Whole worm, wago-10, rep3


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB728FMV)

description:
https://www.encodeproject.org/experiments/ENCSR322MTA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR322MTA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB728FMV

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

tag: antibody

value: primary cell

tag: description

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

value: not collected

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, sago-1, rep3


title: Whole worm, sago-2, rep3

value: sago-2 (tor135)


title: ∆cydAB vs. WT-rep6

description:
∆cydAB vs. WT-rep6
Biological replicate 6 of 6
original platform:
GPL15451

source_name: ∆cydAB

value: deletion mutant

value: delta_cydAB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06


title: Histone ChIP-seq from middle frontal area 46 (ENCLB982DUZ)

description:
https://www.encodeproject.org/experiments/ENCSR706PAK/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K27me3 ChIP-seq on middle frontal area 46 tissue female adult (79 years)
experiment encode accession: ENCSR706PAK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR968XKG
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB982DUZ
size range: 200-600

value: middle frontal area 46

value: tissue

tag: biosample encode accession

value: female

value: adult

value: 79 year

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS246FGU at ENCODE; https://www.encodeproject.org/ENCBS246FGU/

value: Derived from ENCODE donor ENCDO609ZOG; https://www.encodeproject.org/ENCDO609ZOG/


title: dis3l2MII_ctr_f6_29_pA

value: MII oocytes

value: ctr


title: Whole worm, wago-4, rep3

value: Whole worm

value: young adult

tag: Sex

value: hermaphrodite

value: 20 degrees C


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB324SSF)

description:
https://www.encodeproject.org/experiments/ENCSR322MTA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR322MTA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR963EAC
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB324SSF

value: primary cell

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

value: not collected

value: multiple sclerosis

tag: dev stage

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: ∆cydAB vs. WT-rep5

description:
∆cydAB vs. WT-rep5
Biological replicate 5 of 6
original platform:
GPL15451

value: deletion mutant

value: delta_cydAB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06


title: Whole worm, rde-1, rep3


title: ∆cydAB vs. WT-rep4

description:
∆cydAB vs. WT-rep4
Biological replicate 4 of 6
original platform:
GPL15451


title: dis3l2MII_cKO_f9_46_pA

value: MII oocytes

value: cKO


title: ∆cydAB vs. WT-rep3

description:
∆cydAB vs. WT-rep3
Biological replicate 3 of 6
original platform:
GPL15451


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB113YRP)

description:
https://www.encodeproject.org/experiments/ENCSR317QET/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR317QET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR404OWA
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB113YRP

source_name: Homo sapiens male adult (38 years) naive thymus-derived CD4-positive, alpha-beta T primary cell

tag: age

value: 38 year

value: male

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS995TBT at ENCODE; https://www.encodeproject.org/ENCBS995TBT/

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


title: Whole worm, prg-1, rep3

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB370QWQ)

description:
https://www.encodeproject.org/experiments/ENCSR317QET/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR317QET
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR404OWA
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB370QWQ

value: primary cell

tag: lab


title: dis3l2MII_cKO_f9_47_pA


title: TF ChIP-seq from middle frontal area 46 (ENCLB622UEX)

description:
https://www.encodeproject.org/experiments/ENCSR705DNM/
***************
biological replicate number: 1
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)
experiment encode accession: ENCSR705DNM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR576VXL
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622UEX
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

tag: source

value: Rush University

value: ENCBS227KZL at ENCODE; https://www.encodeproject.org/ENCBS227KZL/

value: Derived from ENCODE donor ENCDO218FFZ; https://www.encodeproject.org/ENCDO218FFZ/


title: ∆cydAB vs. WT-rep2

description:
∆cydAB vs. WT-rep2
Biological replicate 2 of 6
original platform:
GPL15451

value: deletion mutant

value: delta_cydAB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06


title: dis3l2MII_cKO_f9_45_pA

value: MII oocytes

value: cKO


title: dis3l2MII_cKO_f9_44_pA


title: TF ChIP-seq from middle frontal area 46 (ENCLB400ZUJ)

description:
https://www.encodeproject.org/experiments/ENCSR705DNM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)
experiment encode accession: ENCSR705DNM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR576VXL
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB400ZUJ
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: Whole worm, ppw-1, rep3

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


description:
∆sigE pEKEx2-AmyE (1 mM IPTG) vs. ∆sigE pEKEx2-AmyE (w/o IPTG)-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆sigE pEKEx2-AmyE (1 mM IPTG)

value: deletion mutant + overexpression

value: delta_sigE pEKEx2-AmyE (Bacillus subtili) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, BHI, date of experiment:2011-07

source_name: ∆sigE pEKEx2-AmyE (w/o IPTG)

value: deletion mutant + control

value: delta_sigE pEKEx2-AmyE (Bacillus subtili) harvested during exponential growth phase, BHI, w/o IPTG, date of experiment:2011-07


title: dis3l2MII_cKO_f8_40_pA


title: TF ChIP-seq from middle frontal area 46 (ENCLB504HVA)

description:
https://www.encodeproject.org/experiments/ENCSR705DNM/
***************
biological replicate number: 2
technical replicate number: 2
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)
experiment encode accession: ENCSR705DNM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR576VXL
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504HVA
size range: 200-600

value: CTCF

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS630ZNN at ENCODE; https://www.encodeproject.org/ENCBS630ZNN/

value: Derived from ENCODE donor ENCDO218FFZ; https://www.encodeproject.org/ENCDO218FFZ/


title: Whole worm, ppw-2, rep3


title: ∆cydAB vs. WT-rep1

description:
∆cydAB vs. WT-rep1
Biological replicate 1 of 6
original platform:
GPL15451

value: deletion mutant

value: delta_cydAB harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2009-06


title: Whole worm, N2, rep3

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: wild-type


title: Whole worm, nrde-3, rep3


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

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

value: delta_sigE harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2004-02

source_name: ∆sigE

value: delta_sigE harvested during exponential growth phase, CGXII glucose, date of experiment:2004-02


description:
∆sigE pEKEx2-AmyE (1 mM IPTG) vs. ∆sigE pEKEx2-AmyE (w/o IPTG)-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_sigE pEKEx2-AmyE (Bacillus subtili) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, BHI, date of experiment:2011-07

value: deletion mutant + control

value: delta_sigE pEKEx2-AmyE (Bacillus subtili) harvested during exponential growth phase, BHI, w/o IPTG, date of experiment:2011-07


title: dis3l2MII_cKO_f7_37_pA

value: MII oocytes

value: cKO


description:
∆sigE (10 min heatshock, 50°C) vs. ∆sigE-rep2
Biological replicate 2 of 3
GAL file:
CG_GAL_PCR_Layout_15.gal

value: deletion mutant


title: Control ChIP-seq from placenta (ENCLB977QEM)

description:
https://www.encodeproject.org/experiments/ENCSR918ESG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR918ESG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB977QEM
size range: 200-600

source_name: Homo sapiens male embryo placenta tissue

value: placenta

value: tissue

value: unknown

value: male

value: embryonic

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

value: ENCBS834VHU at ENCODE; https://www.encodeproject.org/ENCBS834VHU/

value: Derived from ENCODE donor ENCDO225QCT; https://www.encodeproject.org/ENCDO225QCT/


title: TF ChIP-seq from middle frontal area 46 (ENCLB522OOE)

description:
https://www.encodeproject.org/experiments/ENCSR705DNM/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)
experiment encode accession: ENCSR705DNM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR576VXL
encode release date: 2022-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB522OOE
size range: 200-600

value: CTCF

value: middle frontal area 46

value: 90 or above year

value: female

value: adult

value: Rush University

value: ENCBS630ZNN at ENCODE; https://www.encodeproject.org/ENCBS630ZNN/

value: Derived from ENCODE donor ENCDO218FFZ; https://www.encodeproject.org/ENCDO218FFZ/


title: Control ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB049AKQ)

description:
https://www.encodeproject.org/experiments/ENCSR314QKF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314QKF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB049AKQ
size range: 200-600

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

value: primary cell

value: 21 year

value: Charles Lee

value: ENCBS374RGV at ENCODE; https://www.encodeproject.org/ENCBS374RGV/

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


title: Whole worm, DA1316, rep3

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: dis3l2MII_cKO_f8_38_pA

source_name: MII oocytes

value: MII oocytes

value: cKO


description:
∆sigE (10 min heatshock, 50°C) vs. ∆sigE-rep1
Biological replicate 1 of 3
GAL file:
CG_GAL_PCR_Layout_15.gal

value: deletion mutant

value: delta_sigE harvested during exponential growth phase 10 min after heatshock at 50°C, CGXII glucose, date of experiment:2004-02

value: delta_sigE harvested during exponential growth phase, CGXII glucose, date of experiment:2004-02


title: dis3l2MII_cKO_f7_34_pA


title: Whole worm, ergo-1, rep3


description:
∆ripA (100 µM FeSO4) vs. WT (100 µM FeSO4)-rep2
Biological replicate 2 of 2
GAL file:
CG_GAL_PCR_Layout_12.gal

source_name: ∆ripA (100 µM FeSO4)

value: delta_ripA harvested during exponential growth phase, CGXII glucose 100 µM FeSO4, date of experiment:2005-06

source_name: WT (100 µM FeSO4)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose 100 µM FeSO4, date of experiment:2005-06


title: dis3l2MII_cKO_f7_33_pA


title: dis3l2MII_cKO_f8_39_pA


title: Control ChIP-seq from activated CD8-positive, alpha-beta T cell (ENCLB515ECR)

description:
https://www.encodeproject.org/experiments/ENCSR314QKF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR314QKF
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB515ECR
size range: 200-600

value: primary cell

value: male

value: adult

value: Bradley Bernstein, Broad


description:
∆ripA (100 µM FeSO4) vs. WT (100 µM FeSO4)-rep1
Biological replicate 1 of 2
GAL file:
CG_GAL_PCR_Layout_12.gal


title: dis3l2GV_ctr_f2_8_pA

source_name: GV oocytes

value: GV oocytes

value: ctr


title: Whole worm, c04f12.1, rep3

value: Whole worm

value: young adult


title: Whole worm, alg-5, rep3

value: hermaphrodite

value: 20 degrees C


title: dis3l2GV_ctr_f2_6_pA


title: Whole worm, csr-1, rep3


title: Control ChIP-seq from placenta (ENCLB984UBT)

description:
https://www.encodeproject.org/experiments/ENCSR918ESG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR918ESG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB984UBT
size range: 200-600

value: placenta

value: tissue

value: unknown

value: embryonic

value: John Stamatoyannopoulos

value: ENCBS834VHU at ENCODE; https://www.encodeproject.org/ENCBS834VHU/

value: Derived from ENCODE donor ENCDO225QCT; https://www.encodeproject.org/ENCDO225QCT/


description:
∆ripA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep5
Biological replicate 5 of 5
GAL file:
CG_GAL_PCR_Layout_12.gal

source_name: ∆ripA (1 µM FeSO4)

value: deletion mutant

value: delta_ripA harvested during exponential growth phase, CGXII glucose 1 µM FeSO4, date of experiment:2005-04

source_name: WT (1 µM FeSO4)

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose 1 µM FeSO4, date of experiment:2005-04


title: Whole worm, alg-4, rep3

source_name: Whole worm


title: Mint-ChIP-seq from HCT116 (ENCLB074XBH)

description:
https://www.encodeproject.org/experiments/ENCSR314MXA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR314MXA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR846UXS
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB074XBH

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens RAD21 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

tag: line

value: cell line

value: 48 year

value: male

tag: health state

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: ENCBS720OOT at ENCODE; https://www.encodeproject.org/ENCBS720OOT/

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


description:
∆ripA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep4
Biological replicate 4 of 5
GAL file:
CG_GAL_PCR_Layout_12.gal


description:
∆ripA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep3
Biological replicate 3 of 5
GAL file:
CG_GAL_PCR_Layout_12.gal


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB865FAF)

description:
https://www.encodeproject.org/experiments/ENCSR915ISE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR915ISE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR737MLQ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB865FAF

source_name: Homo sapiens IgD-negative memory B primary cell, preserved by cryopreservation

value: IgD-negative memory B cell

value: primary cell

value: B memory CD3- CD14- CD19+ CD27+ IgD-

value: not collected

value: healthy

value: unknown

value: David Hafler

tag: link

value: ENCBS793OUV at ENCODE; https://www.encodeproject.org/ENCBS793OUV/

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


title: dis3l2GV_ctr_f1_4_pA

tag: tissue

value: GV oocytes

value: ctr


title: Whole worm, alg-3, rep3

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

tag: genotype


title: dis3l2GV_ctr_f1_3_pA


title: Mint-ChIP-seq from IgD-negative memory B cell (ENCLB448ARC)

description:
https://www.encodeproject.org/experiments/ENCSR915ISE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR915ISE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR737MLQ
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB448ARC

value: Bradley Bernstein, Broad


title: Whole worm, alg-2, rep3


title: dis3l2GV_ctr_f1_2_pA


description:
∆ripA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep1
Biological replicate 1 of 5
GAL file:
CG_GAL_PCR_Layout_12.gal

value: deletion mutant

tag: condition

value: delta_ripA harvested during exponential growth phase, CGXII glucose 1 µM FeSO4, date of experiment:2005-04

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose 1 µM FeSO4, date of experiment:2005-04


title: Control Mint-ChIP-seq from HCT116 (ENCLB320QNB)

description:
https://www.encodeproject.org/experiments/ENCSR704TRV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR704TRV
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB320QNB

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult

value: Erez Aiden

value: ENCBS982XND at ENCODE; https://www.encodeproject.org/ENCBS982XND/

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


title: Whole worm, alg-1, rep3

value: Whole worm


description:
∆ripA (1 µM FeSO4) vs. WT (1 µM FeSO4)-rep2
Biological replicate 2 of 5
GAL file:
CG_GAL_PCR_Layout_12.gal


title: dis3l2GV_ctr_f2_7_pA

value: GV oocytes

value: ctr


title: Control Mint-ChIP-seq from HCT116 (ENCLB892QQS)

description:
https://www.encodeproject.org/experiments/ENCSR704TRV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR704TRV
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB892QQS


title: Histone ChIP-seq from middle frontal area 46 (ENCLB454JAH)

description:
https://www.encodeproject.org/experiments/ENCSR703AIO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR703AIO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB454JAH
size range: 200-600

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

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS454HCI at ENCODE; https://www.encodeproject.org/ENCBS454HCI/

value: Derived from ENCODE donor ENCDO470GFA; https://www.encodeproject.org/ENCDO470GFA/


title: Mint-ChIP-seq from HCT116 (ENCLB572CGC)

description:
https://www.encodeproject.org/experiments/ENCSR314MXA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR314MXA
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR846UXS
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572CGC

value: cell line

value: 48 year

value: Bradley Bernstein, Broad

tag: treatments

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

value: ENCBS720OOT at ENCODE; https://www.encodeproject.org/ENCBS720OOT/


title: dis3l2GV_ctr_f1_1_pA


title: Histone ChIP-seq from middle frontal area 46 (ENCLB062NUQ)

description:
https://www.encodeproject.org/experiments/ENCSR703AIO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR703AIO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062NUQ
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: adult

value: ENCBS965OCN at ENCODE; https://www.encodeproject.org/ENCBS965OCN/


title: Whole worm, wago-4, rep2

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

value: 20 degrees C


title: ∆cgtSR10 vs. WT-rep2

description:
∆cgtSR10 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cgtSR10 harvested during exponential growth phase, CGXII glucose, date of experiment:2011-04

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2011-04


title: ∆cgtSR10 vs. WT-rep3

description:
∆cgtSR10 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451


title: Whole worm, wago-1, rep2

tag: growth temperature


title: Whole worm, wago-10, rep2


title: dis3l2GV_cKO_f4_23_pA

value: GV oocytes

value: cKO


title: Histone ChIP-seq from middle frontal area 46 (ENCLB907NHR)

description:
https://www.encodeproject.org/experiments/ENCSR703AIO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR703AIO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB907NHR
size range: 200-600

tag: antibody

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS454HCI at ENCODE; https://www.encodeproject.org/ENCBS454HCI/

value: Derived from ENCODE donor ENCDO470GFA; https://www.encodeproject.org/ENCDO470GFA/


title: ∆cgtSR10 vs. WT-rep1

description:
∆cgtSR10 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: dis3l2GV_cKO_f4_20_pA


title: dis3l2GV_cKO_f4_19_pA


description:
∆htrA pEKEx2-AmyE (1 mM IPTG) vs. ∆htrA pEKEx2-AmyE (w/o IPTG)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆htrA pEKEx2-AmyE (1 mM IPTG)

value: deletion mutant + overexpression

value: delta_htrA pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2010-07/2010-08

source_name: ∆htrA pEKEx2-AmyE (w/o IPTG)

value: deletion mutant + control

value: delta_htrA pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, w/o IPTG, date of experiment:2010-07/2010-08


title: dis3l2GV_cKO_f4_18_pA


description:
∆htrA pEKEx2-AmyE (1 mM IPTG) vs. ∆htrA pEKEx2-AmyE (w/o IPTG)-rep2
Biological replicate 2 of 3
original platform:
GPL15451


title: Whole worm, sago-2, rep2

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C

value: sago-2 (tor135)


title: Histone ChIP-seq from middle frontal area 46 (ENCLB903CPS)

description:
https://www.encodeproject.org/experiments/ENCSR703AIO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR703AIO
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR572GRM
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB903CPS
size range: 200-600

value: adult

value: Bradley Bernstein, Broad

value: ENCBS965OCN at ENCODE; https://www.encodeproject.org/ENCBS965OCN/


title: dis3l2GV_cKO_f4_17_pA

value: GV oocytes

value: cKO


title: Histone ChIP-seq from middle frontal area 46 (ENCLB730LXQ)

description:
https://www.encodeproject.org/experiments/ENCSR914ETY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR914ETY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR243LHN
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB730LXQ
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Rush University

value: ENCBS708DHS at ENCODE; https://www.encodeproject.org/ENCBS708DHS/

value: Derived from ENCODE donor ENCDO223NTQ; https://www.encodeproject.org/ENCDO223NTQ/


title: Whole worm, sago-1, rep2

value: Whole worm


title: Whole worm, rde-1, rep2

value: young adult


title: dis3l2GV_cKO_f3_9_pA


description:
∆htrA pEKEx2-AmyE (1 mM IPTG) vs. ∆htrA pEKEx2-AmyE (w/o IPTG)-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_htrA pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2010-07/2010-08

value: deletion mutant + control

value: delta_htrA pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, w/o IPTG, date of experiment:2010-07/2010-08


title: Histone ChIP-seq from middle frontal area 46 (ENCLB041PTJ)

description:
https://www.encodeproject.org/experiments/ENCSR914ETY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR914ETY
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR243LHN
encode release date: 2022-06-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB041PTJ
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: Whole worm, prg-1, rep2

value: hermaphrodite

value: 20 degrees C


description:
∆htrA pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep4
Biological replicate 4 of 4
original platform:
GPL15451

source_name: ∆htrA pEKEx2-AmyE

source_name: WT pEKEx2-AmyE

value: wild type + overexpression

value: WT pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2010-07/2010-08


title: dis3l2GV_cKO_f3_14_pA

value: GV oocytes

value: cKO


description:
∆htrA pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep3
Biological replicate 3 of 4
original platform:
GPL15451


title: Whole worm, ppw-2, rep2


title: Whole worm, ppw-1, rep2


title: dis3l2GV_cKO_f3_13_pA


title: dis3l2GV_cKO_f3_12_pA


title: Mint-ChIP-seq from T-cell (ENCLB538TSS)

description:
https://www.encodeproject.org/experiments/ENCSR912FCF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR912FCF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB538TSS

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

value: T-cell

value: primary cell

value: 21 year

value: female

value: John Stamatoyannopoulos

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

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


description:
∆htrA pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep2
Biological replicate 2 of 4
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_htrA pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2010-07/2010-08


title: Control ChIP-seq from right lobe of liver (ENCLB243ZLB)

description:
https://www.encodeproject.org/experiments/ENCSR309LQG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR309LQG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB243ZLB
size range: 200-600

source_name: Homo sapiens female adult (41 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

value: 41 year

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

value: adult

value: Shin Lin

value: ENCBS971GGI at ENCODE; https://www.encodeproject.org/ENCBS971GGI/

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


description:
∆htrA pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep1
Biological replicate 1 of 4
original platform:
GPL15451

value: wild type + overexpression

value: WT pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, 1 mM IPTG, date of experiment:2010-07/2010-08


title: Control ChIP-seq from right lobe of liver (ENCLB224KRT)

description:
https://www.encodeproject.org/experiments/ENCSR309LQG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR309LQG
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-06-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB224KRT
size range: 200-600

value: Bradley Bernstein, Broad


title: Whole worm, nrde-3, rep2

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: dis3l2GV_cKO_f3_10_pA

value: GV oocytes

value: cKO


description:
∆cgtSR2 pCLTON2-cgtR2 pEKEx2-cgtR2 vs. WT pCLTON2 pEKEx2-rep3
Biological replicate 3 of 3
original platform:
GPL15451

source_name: ∆cgtSR2 pCLTON2-cgtR2 pEKEx2-cgtR2

value: deletion mutant + overexpression

value: delta_cgtSR2 pCLTON2-cgtR2 pEKEx2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline and 1 mM IPTG, CGXII glucose, date of experiment:2011-11

source_name: WT pCLTON2 pEKEx2

value: wild type + control

value: WT pCLTON2-cgtR2 pEKEx2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline and 1 mM IPTG, CGXII glucose, date of experiment:2011-11


title: Whole worm, N2, rep2

value: wild-type


title: dis3l2GV_cKO_f3_11_pA

source_name: GV oocytes


title: Mint-ChIP-seq from T-cell (ENCLB340WQE)

description:
https://www.encodeproject.org/experiments/ENCSR912FCF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR912FCF
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR367LFV
encode release date: 2022-04-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340WQE

value: T-cell

value: primary cell

value: 21 year

value: female

value: adult

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, hrde-1, rep2

value: Whole worm

value: young adult

value: hermaphrodite


title: Control Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB796LQK)

description:
https://www.encodeproject.org/experiments/ENCSR308NMT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR308NMT
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB796LQK

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

value: 36 year

value: male

value: Bradley Bernstein, Broad

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

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


title: Control ChIP-seq from keratinocyte (ENCLB161XZM)

description:
https://www.encodeproject.org/experiments/ENCSR678FZH/
***************
biological replicate number: 1
technical replicate number: 1
description: NHEK
experiment encode accession: ENCSR678FZH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-06-28
lab: Vishwanath Iyer, UTA
library encode accession: ENCLB161XZM

source_name: Homo sapiens female keratinocyte primary cell

value: keratinocyte

tag: description

value: epidermal keratinocytes

value: unknown

value: Vishwanath Iyer, UTA

value: Lonza

tag: ethnicity

value: ENCBS611ENC at ENCODE; https://www.encodeproject.org/ENCBS611ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/


title: Whole worm, ergo-1, rep2

source_name: Whole worm

tag: Sex

value: 20 degrees C


description:
∆cgtSR2 pCLTON2-cgtR2 pEKEx2-cgtR2 vs. WT pCLTON2 pEKEx2-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_cgtSR2 pCLTON2-cgtR2 pEKEx2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline and 1 mM IPTG, CGXII glucose, date of experiment:2011-11

value: wild type + control

value: WT pCLTON2-cgtR2 pEKEx2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline and 1 mM IPTG, CGXII glucose, date of experiment:2011-11


title: Control Mint-ChIP-seq from central memory CD8-positive, alpha-beta T cell (ENCLB199UPZ)

description:
https://www.encodeproject.org/experiments/ENCSR308NMT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR308NMT
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB199UPZ

value: primary cell

tag: biosample encode accession

value: 36 year

tag: dev stage

value: adult

value: John Stamatoyannopoulos


description:
∆cgtSR2 pCLTON2-cgtR2 pEKEx2-cgtR2 vs. WT pCLTON2 pEKEx2-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB964GIE)

description:
https://www.encodeproject.org/experiments/ENCSR910OOE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR910OOE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB964GIE

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens CDK7 treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

tag: age

value: 48 year

value: male

value: colorectal carcinoma

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: ENCBS271TPC at ENCODE; https://www.encodeproject.org/ENCBS271TPC/

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


title: Control ChIP-seq from keratinocyte (ENCLB086PUJ)

description:
https://www.encodeproject.org/experiments/ENCSR678FZH/
***************
biological replicate number: 2
technical replicate number: 1
description: NHEK
experiment encode accession: ENCSR678FZH
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-06-28
lab: Vishwanath Iyer, UTA
library encode accession: ENCLB086PUJ

value: keratinocyte

value: NHEK

value: unknown

value: female

value: Vishwanath Iyer, UTA

tag: source

value: Unknown Source

value: ENCBS026FRM at ENCODE; https://www.encodeproject.org/ENCBS026FRM/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/


title: Mint-ChIP-seq from HCT116 (ENCLB710WTS)

description:
https://www.encodeproject.org/experiments/ENCSR910OOE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR910OOE
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR508TCS
encode release date: 2022-03-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB710WTS

tag: line

value: cell line

tag: health state

value: adult


title: Control ChIP-seq from GM12878 (ENCLB638QML)

description:
https://www.encodeproject.org/experiments/ENCSR356PFJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR356PFJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2016-06-28
lab: Vishwanath Iyer, UTA
library encode accession: ENCLB638QML

source_name: Homo sapiens GM12878 cell line

tag: link

value: ENCBS882WSF at ENCODE; https://www.encodeproject.org/ENCBS882WSF/

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


description:
∆cgtSR2 pCLTON2-cgtSR2 vs. WT pCLTON2-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆cgtSR2 pCLTON2-cgtSR2

tag: genotype

value: deletion mutant + overexpression

value: delta_cgtSR2 pCLTON2-cgtSR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09/2011-11

source_name: WT pCLTON2

value: wild type + overexpression

value: WT pCLTON2-cgtSR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09/2011-11


title: Whole worm, DA1316, rep2

tag: tissue

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB630OJW)

description:
https://www.encodeproject.org/experiments/ENCSR505DQN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR505DQN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB630OJW

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

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX

value: AllCells

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

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


title: Whole worm, hrde-1, rep3


title: Control ChIP-seq from GM12878 (ENCLB242AEE)

description:
https://www.encodeproject.org/experiments/ENCSR356PFJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR356PFJ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2016-06-28
lab: Vishwanath Iyer, UTA
library encode accession: ENCLB242AEE

value: cell line

value: unknown

value: female

value: adult

value: Vishwanath Iyer, UTA

value: Unknown Source

value: ENCBS882WSF at ENCODE; https://www.encodeproject.org/ENCBS882WSF/


description:
∆cgtSR2 pCLTON2-cgtSR2 vs. WT pCLTON2-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant + overexpression

tag: condition

value: delta_cgtSR2 pCLTON2-cgtSR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09/2011-11

value: wild type + overexpression

value: WT pCLTON2-cgtSR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09/2011-11


description:
∆cgtSR2 pCLTON2-cgtR2 vs. WT pCLTON2-rep2
Biological replicate 2 of 2
original platform:
GPL15451

source_name: ∆cgtSR2 pCLTON2-cgtR2

value: delta_cgtSR2 pCLTON2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09

value: WT pCLTON2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09


title: Mint-ChIP-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCLB555ONQ)

description:
https://www.encodeproject.org/experiments/ENCSR505DQN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR505DQN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR069ZFG
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB555ONQ

value: primary cell

value: male

value: 35 year

value: Yijun Ruan, JAX


title: Whole worm, c04f12.1, rep2

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

value: 20 degrees C


title: Mint-ChIP-seq from HCT116 (ENCLB058WJO)

description:
https://www.encodeproject.org/experiments/ENCSR702AWL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR702AWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR898CSY
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB058WJO

source_name: Homo sapiens HCT116 cell line genetically modified (insertion) using CRISPR inserting O. sativa LOC4335696, genetically modified (insertion) using CRISPR targeting H. sapiens POLR2A treated with 1uM 5-Phenyl-1H-indole-3-acetic acid for 6 hours

value: cell line

value: 48 year

value: colorectal carcinoma

value: adult

value: Bradley Bernstein, Broad

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: ENCBS929EFP at ENCODE; https://www.encodeproject.org/ENCBS929EFP/

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


title: Control ChIP-seq from H1 (ENCLB920FDD)

description:
https://www.encodeproject.org/experiments/ENCSR704AQC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR704AQC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-06-28
lab: Vishwanath Iyer, UTA
library encode accession: ENCLB920FDD

source_name: Homo sapiens H1 cell line

value: unknown

value: healthy

value: embryonic

value: Vishwanath Iyer, UTA

value: Unknown Source

value: ENCBS704NOS at ENCODE; https://www.encodeproject.org/ENCBS704NOS/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: Whole worm, alg-5, rep2

value: Whole worm

value: young adult

value: hermaphrodite

tag: growth temperature

value: 20 degrees C


title: Whole worm, alg-4, rep2


title: Mint-ChIP-seq from HCT116 (ENCLB460PHY)

description:
https://www.encodeproject.org/experiments/ENCSR702AWL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR702AWL
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR898CSY
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460PHY

tag: antibody

value: cell line

value: 48 year

value: male

value: colorectal carcinoma

value: adult


description:
∆cgtSR2 pEKEx2-AmyE (1 mM IPTG) vs. ∆cgtSR2 pEKEx2-AmyE (w/o IPTG)-rep2
Biological replicate 2 of 3
original platform:
GPL15451

source_name: ∆cgtSR2 pEKEx2-AmyE (1 mM IPTG)

value: deletion mutant + overexpression

value: delta_cgtSR2 pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-07/2011-10

source_name: ∆cgtSR2 pEKEx2-AmyE (w/o IPTG)

value: deletion mutant + control

value: delta_cgtSR2 pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, w/o IPTG, date of experiment:2011-07/2011-10


title: Whole worm, alg-3, rep2


title: Whole worm, csr-1, rep2


title: Mint-ChIP-seq from HCT116 (ENCLB417KBI)

description:
https://www.encodeproject.org/experiments/ENCSR906ZFR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR906ZFR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR898CSY
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB417KBI

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: ENCBS929EFP at ENCODE; https://www.encodeproject.org/ENCBS929EFP/

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


description:
∆cgtSR2 pEKEx2-AmyE (1 mM IPTG) vs. ∆cgtSR2 pEKEx2-AmyE (w/o IPTG)-rep1
Biological replicate 1 of 3
original platform:
GPL15451


title: Mint-ChIP-seq from HCT116 (ENCLB202ZTT)

description:
https://www.encodeproject.org/experiments/ENCSR906ZFR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906ZFR
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR898CSY
encode release date: 2022-06-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB202ZTT


title: Histone ChIP-seq from E14TG2a.4 (ENCLB888OMB)

description:
https://www.encodeproject.org/experiments/ENCSR253QPK/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K36me3 ChIP-seq
experiment encode accession: ENCSR253QPK
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-11
lab: Ross Hardison, PennState
library encode accession: ENCLB888OMB
fragmentation methods: see document

source_name: Mus musculus strain 129/Ola E14TG2a.4 cell line

tag: description

value: mouse embryonic stem cell line E14

value: embryonic

value: 3.5 day

value: Ross Hardison, PennState

value: unknown

value: ENCBS171HGC at ENCODE; https://www.encodeproject.org/ENCBS171HGC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: Whole worm, alg-1, rep2

value: Whole worm

value: young adult

tag: Sex

value: hermaphrodite

value: 20 degrees C


title: Control ChIP-seq from H1 (ENCLB447OZO)

description:
https://www.encodeproject.org/experiments/ENCSR704AQC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR704AQC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-06-28
lab: Vishwanath Iyer, UTA
library encode accession: ENCLB447OZO

value: cell line

tag: biosample encode accession

value: male

value: healthy

value: Vishwanath Iyer, UTA

value: Unknown Source

value: ENCBS649THQ at ENCODE; https://www.encodeproject.org/ENCBS649THQ/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB228YTT)

description:
https://www.encodeproject.org/experiments/ENCSR103OSN/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR103OSN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR885JZJ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB228YTT

source_name: Homo sapiens male adult (50 years) activated naive CD4-positive, alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: primary cell

value: 50 year

tag: dev stage

value: adult

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

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

value: ENCBS572PDL at ENCODE; https://www.encodeproject.org/ENCBS572PDL/

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


description:
∆cgtSR2 pCLTON2-cgtR2 vs. WT pCLTON2-rep1
Biological replicate 1 of 2
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_cgtSR2 pCLTON2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09

value: wild type + overexpression

value: WT pCLTON2-cgtR2 harvested during exponential growth phase 60 min after addition of 250 ng/mL anhydrotetracycline, BHI, date of experiment:2011-09


title: TF ChIP-seq from liver (ENCLB915RKY)

description:
https://www.encodeproject.org/experiments/ENCSR194GNY/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse Liver GATA4 ChIP-seq
experiment encode accession: ENCSR194GNY
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR734EYQ
encode release date: 2014-03-14
lab: Ross Hardison, PennState
library encode accession: ENCLB915RKY
fragmentation methods: see document

source_name: Mus musculus adult liver tissue

value: liver

value: tissue

value: Whole liver

tag: age

value: unknown

value: not collected

value: healthy

value: Ross Hardison, PennState

value: Gerd Blobel

value: ENCBS044FEB at ENCODE; https://www.encodeproject.org/ENCBS044FEB/

value: Derived from ENCODE donor ENCDO221RVN; https://www.encodeproject.org/ENCDO221RVN/


title: TF ChIP-seq from liver (ENCLB221RRS)

description:
https://www.encodeproject.org/experiments/ENCSR194GNY/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse Liver GATA4 ChIP-seq
experiment encode accession: ENCSR194GNY
assay title: TF ChIP-seq
assembly: mm10
possible controls: ENCSR734EYQ
encode release date: 2014-03-14
lab: Ross Hardison, PennState
library encode accession: ENCLB221RRS
fragmentation methods: see document

value: adult

tag: lab


title: Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB111PBO)

description:
https://www.encodeproject.org/experiments/ENCSR103OSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR103OSN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR885JZJ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB111PBO

value: primary cell

value: 50 year

value: male

value: Bradley Bernstein, Broad

tag: source

value: John Stamatoyannopoulos

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

value: ENCBS572PDL at ENCODE; https://www.encodeproject.org/ENCBS572PDL/


title: Whole worm, wago-10, rep1

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: Whole worm, wago-4, rep1


title: Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB037JNR)

description:
https://www.encodeproject.org/experiments/ENCSR103OSN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR103OSN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR885JZJ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB037JNR

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


title: Control ChIP-seq from liver (ENCLB331SIP)

description:
https://www.encodeproject.org/experiments/ENCSR734EYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse Liver Control ChIP-seq
experiment encode accession: ENCSR734EYQ
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2014-03-11
lab: Ross Hardison, PennState
library encode accession: ENCLB331SIP
fragmentation methods: see document

value: liver

value: tissue

value: Whole liver

value: unknown

value: not collected

value: healthy

value: Ross Hardison, PennState


title: Whole worm, wago-1, rep1


description:
∆cgtSR2 pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep1
Biological replicate 1 of 2
original platform:
GPL15451

source_name: ∆cgtSR2 pEKEx2-AmyE

value: deletion mutant + overexpression

value: delta_cgtSR2 pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, BHI, 10 µM IPTG, date of experiment:2010-10/2011-07

source_name: WT pEKEx2-AmyE

value: wild type + overexpression

value: WT pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, BHI, 10 µM IPTG, date of experiment:2010-10/2011-07


title: ∆cgtSR2 vs. WT-rep2

description:
∆cgtSR2 vs. WT-rep2
Biological replicate 2 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cgtSR2 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02

source_name: WT

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02


description:
∆cgtSR2 pEKEx2-AmyE vs. WT pEKEx2-AmyE-rep2
Biological replicate 2 of 2
original platform:
GPL15451


title: Histone ChIP-seq from E14TG2a.4 (ENCLB297KPD)

description:
https://www.encodeproject.org/experiments/ENCSR253QPK/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K36me3 ChIP-seq
experiment encode accession: ENCSR253QPK
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-11
lab: Ross Hardison, PennState
library encode accession: ENCLB297KPD
fragmentation methods: see document

tag: line

value: cell line

value: mouse embryonic stem cell line E14

value: male

value: embryonic

value: 3.5 day

value: ENCBS705LKU at ENCODE; https://www.encodeproject.org/ENCBS705LKU/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: Whole worm, alg-2, rep2

source_name: Whole worm

value: Whole worm

value: young adult

value: hermaphrodite

value: 20 degrees C


title: Histone ChIP-seq from E14TG2a.4 (ENCLB228HGL)

description:
https://www.encodeproject.org/experiments/ENCSR059MBO/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K27me3 ChIP-seq
experiment encode accession: ENCSR059MBO
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-12
lab: Ross Hardison, PennState
library encode accession: ENCLB228HGL
fragmentation methods: see document

value: Ross Hardison, PennState

tag: health state

value: unknown


description:
∆cgtSR2 pEKEx2-AmyE (1 mM IPTG) vs. ∆cgtSR2 pEKEx2-AmyE (w/o IPTG)-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant + overexpression

value: delta_cgtSR2 pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase 30 min after addition of 1 mM IPTG, CGXII glucose, date of experiment:2011-07/2011-10

value: deletion mutant + control

value: delta_cgtSR2 pEKEx2-amyE (Bacillus subtilis) harvested during exponential growth phase, CGXII glucose, w/o IPTG, date of experiment:2011-07/2011-10


title: Control ChIP-seq from liver (ENCLB551HKK)

description:
https://www.encodeproject.org/experiments/ENCSR734EYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: PSU mouse Liver Control ChIP-seq
experiment encode accession: ENCSR734EYQ
assay title: Control ChIP-seq
assembly: mm10
encode release date: 2014-03-11
lab: Ross Hardison, PennState
library encode accession: ENCLB551HKK
fragmentation methods: see document

value: liver

value: tissue

value: Whole liver

value: not collected

value: healthy

value: adult

value: Gerd Blobel

tag: link

value: ENCBS044FEB at ENCODE; https://www.encodeproject.org/ENCBS044FEB/

value: Derived from ENCODE donor ENCDO221RVN; https://www.encodeproject.org/ENCDO221RVN/


title: Whole worm, sago-2, rep1

value: Whole worm

value: young adult

value: hermaphrodite

tag: genotype

value: sago-2 (tor135)


title: ∆cgtSR2 vs. WT-rep3

description:
∆cgtSR2 vs. WT-rep3
Biological replicate 3 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cgtSR2 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02


title: Whole worm, sago-1, rep1

tag: tissue

value: 20 degrees C


title: larvae, nphp8 mutant 4

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

institute: University Freiburg Medical Center

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

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

value: whole larvae

tag: treatment


title: Control ChIP-seq from middle frontal area 46 (ENCLB805ETL)

description:
https://www.encodeproject.org/experiments/ENCSR103IXF/
***************
biological replicate number: 2
technical replicate number: 1
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: ENCLB805ETL
size range: 200-600

source_name: Homo sapiens female adult (90 or above years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: Bradley Bernstein, Broad

value: Rush University

value: ENCBS825MDV at ENCODE; https://www.encodeproject.org/ENCBS825MDV/

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


title: Histone ChIP-seq from E14TG2a.4 (ENCLB738HLN)

description:
https://www.encodeproject.org/experiments/ENCSR059MBO/
***************
biological replicate number: 2
technical replicate number: 1
description: PSU mouse E14Tg2a.4 H3K27me3 ChIP-seq
experiment encode accession: ENCSR059MBO
assay title: Histone ChIP-seq
assembly: mm10
possible controls: ENCSR326ULS
encode release date: 2014-02-12
lab: Ross Hardison, PennState
library encode accession: ENCLB738HLN
fragmentation methods: see document

value: cell line

value: mouse embryonic stem cell line E14

value: male

value: embryonic

value: 3.5 day

value: Ross Hardison, PennState

value: unknown

value: ENCBS171HGC at ENCODE; https://www.encodeproject.org/ENCBS171HGC/

value: Derived from ENCODE donor ENCDO015AAA; https://www.encodeproject.org/ENCDO015AAA/


title: Control ChIP-seq from middle frontal area 46 (ENCLB724MCU)

description:
https://www.encodeproject.org/experiments/ENCSR103IXF/
***************
biological replicate number: 1
technical replicate number: 1
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: ENCLB724MCU
size range: 200-600

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

value: middle frontal area 46

value: adult

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


title: WT pEKEx2-cgtR2 vs. WT pEKEx2-rep3

description:
WT pEKEx2-cgtR2 vs. WT pEKEx2-rep3
Biological replicate 3 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: larvae, nphp8 mutant 3

value: whole larvae


title: Whole worm, prg-1, rep1

value: Whole worm

tag: developmental stage

value: young adult

value: hermaphrodite

value: 20 degrees C


title: ∆cgtSR2 vs. WT-rep1

description:
∆cgtSR2 vs. WT-rep1
Biological replicate 1 of 3
original platform:
GPL15451

value: deletion mutant

value: delta_cgtSR2 harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02

value: wild type

value: WT harvested during exponential growth phase, CGXII glucose, date of experiment:2012-02


title: larvae, nphp8 mutant 2


title: WT pEKEx2-cgtR2 vs. WT pEKEx2-rep2

description:
WT pEKEx2-cgtR2 vs. WT pEKEx2-rep2
Biological replicate 2 of 5
original platform:
GPL15451


title: Mint-ChIP-seq from activated naive CD4-positive, alpha-beta T cell (ENCLB274DOW)

description:
https://www.encodeproject.org/experiments/ENCSR103OSN/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR103OSN
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR885JZJ
encode release date: 2022-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB274DOW

value: primary cell

value: 50 year

value: male

value: Bradley Bernstein, Broad

value: John Stamatoyannopoulos

tag: treatments

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

value: ENCBS572PDL at ENCODE; https://www.encodeproject.org/ENCBS572PDL/

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


title: Control ChIP-seq from middle frontal area 46 (ENCLB317XLQ)

description:
https://www.encodeproject.org/experiments/ENCSR103IXF/
***************
biological replicate number: 2
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: ENCLB317XLQ
size range: 200-600

value: middle frontal area 46

value: tissue

value: 90 or above year

value: female

value: adult

value: Rush University

value: ENCBS825MDV at ENCODE; https://www.encodeproject.org/ENCBS825MDV/

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