title: Fm_Let7e5_eWAT

growth_protocol: C57BL/6 male Fm mice were fed with chow diet from weaning to 6-week-old and then kept with LFD until 15-week-old.

treatment_protocol: Male mice of Fm generation were sired from Zygote microinjected with miR-let-7d/e or negative control.

tag: genotype

tag: generation

value: Fm

tag: age weeks

value: LFD

tag: treatment


title: 3c4_Participant_001_week_7

status: Public on Jan 14 2025

type: SRA

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

library_source: transcriptomic

data_processing:
Quality control with Trimmomatic version 0.38
Gene count matrix was generated with FeatureCounts version 1.5.0-p2 and Ensembl 101
Aligned to genome using HISAT2 version 2.1.0
Assembly: GRCh38
Supplementary files format and content: FeatureCounts per gene counts

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
RNA extraction and genomic DNA elimination was carried out using the PAXgene® Blood RNA kit (762164, Qiagen, Feldbachstrasse, Germany) as per the manufacturer’s instructions
Total RNA was converted to strand-specific Illumina compatible sequencing libraries using the Nugen Universal Plus Total RNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturer’s instructions (MO1523 v2) using 12 cycles of PCR amplification for the final libraries. An Anydeplete probe mix targeting both human ribosomal and adult globin transcripts (HBA1, HBA2, HBB, HBD) was used to deplete these transcripts.

tag: age

tag: Sex

value: M

tag: timepoint

tag: sample number

tag: tissue

value: Peripheral blood


title: scRNA-seq from forelimb (ENCLB261TVA)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR337QTQ/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 15.0 day embryonic mouse forelimb
experiment encode accession: ENCSR337QTQ
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB261TVA
size range: 300-600

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

organism: Mus musculus

source_name: Mus musculus strain B6NCrl embryo (15 days) forelimb tissue

value: forelimb

value: tissue

tag: biosample encode accession

tag: note

value: not collected

tag: dev stage

value: embryonic

value: 15 day

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS301BBL at ENCODE; https://www.encodeproject.org/ENCBS301BBL/


title: MouseLiver_HFHS_0W

type: RNA

city: Tokyo

first: Nobuhito

last: Goda

address: TWIns 02C218, 2-2 Wakamatsu-cho, Shinjuku-ku

country: Japan

institute: Waseda University, Faculty of Science and Engineering

description: gene expression after 0 wks in HFHS-treated mouse liver

hyb_protocol: 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

source_name: Liver, 0wks

label_protocol: RNA samples (100ng) were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies)

extract_protocol: RNA was prepared from frozen liver of mice fed a high-fat, high-sucrose diet for the indicated time using RNAiso Plus (Takara Bio) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: C57BL/6 mice (male, 5 weeks-old) were fed a high-fat, high-sucrose diet for either 0, 5, 10 or 15 weeks

value: liver

tag: gender

value: male


title: scRNA-seq from forelimb (ENCLB836HUJ)

description:
https://www.encodeproject.org/experiments/ENCSR306UHC/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 15.0 day embryonic mouse forelimb
experiment encode accession: ENCSR306UHC
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB836HUJ
size range: 300-600

value: ENCBS632QGY at ENCODE; https://www.encodeproject.org/ENCBS632QGY/


title: scRNA-seq from forelimb (ENCLB935EGG)

description:
https://www.encodeproject.org/experiments/ENCSR476JWN/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 13.0 day embryonic mouse forelimb
experiment encode accession: ENCSR476JWN
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB935EGG
size range: 300-600

source_name: Mus musculus strain B6NCrl embryo (13 days) forelimb tissue

value: 13 day

value: ENCBS542JZK at ENCODE; https://www.encodeproject.org/ENCBS542JZK/


title: HeLa cells, +rReprimo_0.5 ug/ml, 32 hr

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: Library name: Sample 4

data_processing:
Basecalls were performed using bcl2fastq.
Sequenced reads from RNA-seq experiments were aligned by using HISAT2 v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1.
Assembly: Assembly: hg19
Supplementary files format and content: xlsx file include FPKM values for each sample

source_name: HeLa

growth_protocol: HeLa or H1299 cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Total RNA Extraction Kit Mini (RBC Bioscience)
Libraries were prepared TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: HeLa or H1299 cells were inoculated at 3.8x10^4 cells/cm2 at day0. Low cell density samples or high cell density samples were harvested at day1 (approximately -80% confluent) or day2, respectively. Recombinant Reprimo proteins were introduced to DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

tag: cell line

value: HeLa

value: recombinant Reprimo protein


title: HeLa cells, +rReprimo_0.5 ug/ml, 8 hr

description: Library name: Sample 3


title: Fm_Let7e4_eWAT

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequencing reads were aligned to the mouse reference genome from Gencode (vM25) using STAR aligner and gene features were counted by using featureCountsv (2.0.3).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw reads for each sample.
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample.

source_name: eWAT

extract_protocol:
RNA was harvested using TRI reagent (Sigma) followed by clean-up with RPE buffer (Qiagen, Germany). 1 ug of total RNA was used for the consturction of sequncing libraries.
RNA libraries for RNA-seq were prepared using NovaSeq 6000 SP Reagent Kit.

value: eWAT

tag: strain

tag: genotype

value: WT

tag: generation

value: Fm

tag: age weeks

tag: diet

value: LFD


title: 3c2_Participant_021_week_7

tag: age

tag: Sex

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: Fm_Let7e6_eWAT

tag: tissue

tag: treatment


title: Fm_Let7e3_eWAT


title: Mast cells, FosbNG-2F R1 001

city: East Lansing

first: Dimitri

last: Joseph

state: MI

address: 8254 Life Science Bldg

department: Pharmacology and Toxicology

institute: Michigan State University

description: Library name: FosbNG-2F_R1.fastq.gz

library_source: genomic

data_processing:
Bone marrow-derived mast cell (BMMC) samples were sensitized with IgE and incubated with vehicle or DNP for 60 minutes. After centrifugation, cell pellets (~1 × 10⁶ cells per sample) were frozen on dry ice. DNA fragments were processed using CUT&RUN, followed by library preparation and sequencing.  Sequencing reads were aligned to the mouse mm10 genome using Bowtie2 (v.2.4.2). Peaks were called using MACS2 (v.2.2.6) and filtered with the Irreproducible Discovery Rate (IDR) framework (v.2.0.4.2) to obtain high-confidence peaks. Peaks were annotated using ChIPseeker (v.1.22.1) in R and further analyzed with Bedtools (v.2.29.2). Motif enrichment and Venn diagram analyses were performed using HOMER (v.4.9).  BigWig (.bw) files representing genome-wide coverage tracks were generated for visualization and downstream analysis.
Assembly: mm10
Supplementary files format and content: The processed data files are provided in BigWig (.bw) format. These files represent genome-wide signal coverage tracks derived from the CUT&RUN sequencing data, where signal intensity corresponds to the normalized read depth across genomic regions.
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: Bone marrow progenitor cells were harvested from the femurs of 6-8-week-old male WT and MCFosB- mice. Following established protocols18,55, the isolated cells were cultured in a controlled environment at 37°C with 5% CO2. The cultures were maintained in 175 cm² flasks filled with 70 mL of complete medium, which consisted of RPMI 1640 (containing L-glutamine), supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1x MEM non-essential amino acids, 10 mmol/L HEPES buffer, 1 mmol/L sodium pyruvate, 100 U/mL penicillin, and 100 μg/mL streptomycin. Additionally, the medium was enriched with recombinant murine interleukin-3 (IL-3; 5 ng/mL) and stem cell factor (SCF; 5 ng/mL) from R&D Systems, Minneapolis, MN. Non-adherent cells were gently transferred to fresh complete medium every 4-5 days. 6 weeks later, purity of mast cell population (>98%) was confirmed using 0.5% toluidine blue staining at pH 0.5 and flow cytometry analysis (BD LSR II) using fluorescently labeled c-kit (BioLegend, San Diego, Calif) and high-affinity IgE receptor (FcεRI) antibodies (eBioscience, San Diego, Calif).

extract_protocol:
Bone marrow progenitor cells were harvested from the femurs of 6-8-week-old male WT and MCFosB- mice. Following established protocols, the isolated cells were cultured in a controlled environment at 37°C with 5% CO2.Nuclei were isolated from frozen BMMC pellets. Pellets were homogenized with Dounce homogenizers.
Chromatin profiling was performed using the CUT&RUN (Cleavage Under Targets and Release Using Nuclease) technique. Nuclei were isolated from cells and incubated with antibodies targeting specific proteins (e.g., FosB or IgG). Protein A-MNase (micrococcal nuclease) was then added to bind to the antibody-protein-DNA complexes, cleaving DNA fragments at binding sites upon activation with calcium. The released DNA fragments were purified, size-selected, and used for library construction.  Library preparation Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) based on manufacture instructions. Libraries were submitted for sequencing by GENEWIZ on Illumina HiSeq 4000 or NovaSeq machine with a 2 × 150-bp paired-end read configuration to a minimum depth of 25 million reads   The libraries were size-selected to enrich for fragments appropriate for paired-end sequencing and quality-checked before sequencing

value: Bone marrow

tag: cell type

value: Mast Cells

tag: antibody

value: FosB


title: 3c1_Participant_021_week_6


title: HeLa cells, Low cell density, 0 hr

description: Library name: Sample 1


title: scRNA-seq from forelimb (ENCLB497BTJ)

description:
https://www.encodeproject.org/experiments/ENCSR156HHE/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 13.0 day embryonic mouse forelimb
experiment encode accession: ENCSR156HHE
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB497BTJ
size range: 300-600

value: forelimb

value: tissue

tag: biosample encode accession

tag: note

value: not collected

tag: dev stage

value: embryonic

tag: lab

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS096TLI at ENCODE; https://www.encodeproject.org/ENCBS096TLI/


title: Fm_Let7d6_eWAT

value: eWAT

tag: strain

tag: genotype

tag: generation

tag: age weeks

value: male


title: 3b6_Participant_101_week_7

tag: age

tag: Sex

value: F

tag: timepoint


title: Mast cells, FosbNG-1F R1 001

description: Library name: FosbNG-1F_R1.fastq.gz

tag: tissue

tag: treatment


title: snATAC-seq from transverse colon (ENCLB048OCP)

description:
https://www.encodeproject.org/experiments/ENCSR997YNO/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human colon transverse
experiment encode accession: ENCSR997YNO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB048OCP
size range: 200-750

source_name: Homo sapiens female adult (53 years) transverse colon tissue

value: transverse colon

value: female

value: adult

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

tag: link

value: ENCBS863DXG at ENCODE; https://www.encodeproject.org/ENCBS863DXG/


title: Mast cells, FosbNG-2C R1 001

description: Library name: FosbNG-2C_R1.fastq.gz

value: Bone marrow

tag: cell type

value: Mast Cells

tag: antibody

value: IgG


title: Fm_Let7d5_eWAT

value: WT

value: Fm

tag: diet

value: LFD


title: snATAC-seq from body of pancreas (ENCLB533NMW)

description:
https://www.encodeproject.org/experiments/ENCSR979ZOG/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human body of pancreas
experiment encode accession: ENCSR979ZOG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB533NMW
size range: 200-750

source_name: Homo sapiens female adult (53 years) body of pancreas tissue

value: body of pancreas

value: tissue

tag: biosample encode accession

tag: dev stage

tag: lab

value: not applicable

value: ENCBS005QTX at ENCODE; https://www.encodeproject.org/ENCBS005QTX/


title: 3b5_Participant_101_week_6

value: F

tag: sample number

value: Peripheral blood


title: Fm_Let7d4_eWAT

value: eWAT

tag: strain

value: male


title: snATAC-seq from upper lobe of left lung (ENCLB167ZGU)

description:
https://www.encodeproject.org/experiments/ENCSR952HMV/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human upper lobe of left lung
experiment encode accession: ENCSR952HMV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB167ZGU
size range: 200-750

source_name: Homo sapiens male adult (37 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: adult

value: 37 year

value: ENCODE Consortium

tag: source

value: LEIDOS

tag: collection date

tag: geographic location

value: ENCBS360NWY at ENCODE; https://www.encodeproject.org/ENCBS360NWY/


title: Mast cells, FosbNG-1C R1 001

description: Library name: FosbNG-1C_R1.fastq.gz

value: Bone marrow

value: Mast Cells

value: IgG

tag: genotype


title: 3b4_Participant_025_week_7

tag: age

tag: Sex

value: M


title: HeLa cells, High cell density, 0 hr

description: Library name: Sample 2

tag: cell line

value: HeLa


title: Fm_Let7d3_eWAT

tag: tissue

value: WT

tag: generation

value: Fm

tag: age weeks

value: LFD

tag: treatment


title: 3b3_Participant_025_week_6

tag: timepoint

value: Peripheral blood


title: Fm_NegativeControl6_eWAT

value: eWAT

tag: diet


title: Mast cells, FosbDNP-2F R1 001

description: Library name: FosbDNP-2F_R1.fastq.gz

tag: cell type

tag: antibody

value: FosB

value: DNP


title: Mast cells, FosbDNP-2C R1 001

description: Library name: FosbDNP-2C_R1.fastq.gz


title: snATAC-seq from stomach (ENCLB165XIX)

description:
https://www.encodeproject.org/experiments/ENCSR940QRM/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human stomach
experiment encode accession: ENCSR940QRM
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB165XIX
size range: 200-750

source_name: Homo sapiens female adult (53 years) stomach tissue

value: stomach

value: tissue

tag: biosample encode accession

value: female

tag: dev stage

value: adult

value: 53 year

tag: lab

value: Bing Ren, UCSD

value: Kristin Ardlie

value: not applicable

tag: link

value: ENCBS175BWJ at ENCODE; https://www.encodeproject.org/ENCBS175BWJ/


title: Fm_NegativeControl5_eWAT

tag: strain

value: male


title: 3b2_Participant_049_week_7

value: M

tag: sample number


title: Mast cells, FosbDNP-1F R1 001

description: Library name: FosbDNP-1F_R1.fastq.gz

value: Bone marrow

value: Mast Cells

tag: genotype


title: snATAC-seq from body of pancreas (ENCLB756FMH)

description:
https://www.encodeproject.org/experiments/ENCSR893WOE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human body of pancreas
experiment encode accession: ENCSR893WOE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB756FMH
size range: 200-750

source_name: Homo sapiens male adult (37 years) body of pancreas tissue

value: body of pancreas

tag: Sex

tag: age

value: 37 year

value: ENCODE Consortium

tag: source

value: LEIDOS

tag: collection date

tag: geographic location

value: ENCBS335JSV at ENCODE; https://www.encodeproject.org/ENCBS335JSV/


title: Fm_NegativeControl4_eWAT

tag: tissue

value: eWAT

value: WT

tag: generation

value: Fm

tag: age weeks

value: LFD

tag: treatment


title: 3b1_Participant_049_week_6

tag: timepoint

value: Peripheral blood


title: Mast cells, FosbDNP-1C R1 001

description: Library name: FosbDNP-1C_R1.fastq.gz

tag: cell type

tag: antibody

value: IgG

value: DNP


title: Fm_NegativeControl3_eWAT

tag: diet


title: 3a6_Participant_029_week_7

value: F


title: snATAC-seq from esophagus muscularis mucosa (ENCLB305DOT)

description:
https://www.encodeproject.org/experiments/ENCSR871CTA/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus muscularis mucosa
experiment encode accession: ENCSR871CTA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB305DOT
size range: 200-750

source_name: Homo sapiens male adult (37 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: tissue

tag: biosample encode accession

value: male

tag: dev stage

value: adult

tag: lab

value: not applicable

tag: link

value: ENCBS134YYY at ENCODE; https://www.encodeproject.org/ENCBS134YYY/


title: 3a5_Participant_029_week_6

tag: Sex

tag: sample number


title: Mast cells, F362C R1 001

description: Library name: F362C_R1.fastq.gz

value: Bone marrow

value: Mast Cells

tag: genotype


title: Mast cells, F362F R1 001

description: Library name: F362F_R1.fastq.gz

value: FosB


title: Fm_NegativeControl1_eWAT

value: eWAT

tag: strain


title: snATAC-seq from gastroesophageal sphincter (ENCLB230BSJ)

description:
https://www.encodeproject.org/experiments/ENCSR868ZEI/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastroesophageal sphincter
experiment encode accession: ENCSR868ZEI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB230BSJ
size range: 200-750

source_name: Homo sapiens male adult (54 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

tag: age

value: 54 year

value: ENCODE Consortium

tag: source

value: LEIDOS

tag: collection date

tag: geographic location

value: ENCBS440MMR at ENCODE; https://www.encodeproject.org/ENCBS440MMR/


title: Mast cells, F30F R1 001

description: Library name: F30F_R1.fastq.gz

tag: tissue

value: WT

tag: treatment


title: snATAC-seq from stomach (ENCLB670TOJ)

description:
https://www.encodeproject.org/experiments/ENCSR848EID/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human stomach
experiment encode accession: ENCSR848EID
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB670TOJ
size range: 200-750

source_name: Homo sapiens female adult (51 years) stomach tissue

value: stomach

value: female

value: 51 year

value: ENCBS192TUB at ENCODE; https://www.encodeproject.org/ENCBS192TUB/


title: 3a4_Participant_136_week_7

value: M

tag: timepoint

value: Peripheral blood


title: snATAC-seq from breast epithelium (ENCLB315KTI)

description:
https://www.encodeproject.org/experiments/ENCSR845QFX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human breast epithelium
experiment encode accession: ENCSR845QFX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB315KTI
size range: 200-750

source_name: Homo sapiens female adult (51 years) breast epithelium tissue

value: breast epithelium

value: tissue

value: adult

value: not applicable

value: ENCBS862HIX at ENCODE; https://www.encodeproject.org/ENCBS862HIX/


title: Fm_Let7e2_eWAT

value: eWAT

tag: generation

value: Fm

tag: age weeks

value: LFD

value: male


title: snATAC-seq from thyroid gland (ENCLB371ZZB)

description:
https://www.encodeproject.org/experiments/ENCSR909OXO/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human thyroid
experiment encode accession: ENCSR909OXO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB371ZZB
size range: 200-750

source_name: Homo sapiens male adult (54 years) thyroid gland tissue

value: thyroid gland

tag: biosample encode accession

value: 54 year

value: ENCODE Consortium

value: LEIDOS

value: ENCBS855YAD at ENCODE; https://www.encodeproject.org/ENCBS855YAD/


title: snATAC-seq from thoracic aorta (ENCLB671BGH)

description:
https://www.encodeproject.org/experiments/ENCSR822GXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human thoracic aorta
experiment encode accession: ENCSR822GXQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB671BGH
size range: 200-750

source_name: Homo sapiens male adult (54 years) thoracic aorta tissue

value: thoracic aorta

tag: dev stage

value: ENCBS380CLT at ENCODE; https://www.encodeproject.org/ENCBS380CLT/


title: 3a2_Participant_028_week_7

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

source_name: Peripheral blood

value: M

value: Peripheral blood


title: Fm_Let7e1_eWAT

value: WT

tag: diet


title: Mast cells, F30C R1 001

description: Library name: F30C_R1.fastq.gz

value: Bone marrow

tag: cell type

value: Mast Cells

tag: antibody

value: IgG


title: 3a1_Participant_028_week_6

tag: Sex

tag: sample number


title: Mast cells, F262F R1 001

description: Library name: F262F_R1.fastq.gz

value: FosB

tag: genotype

value: DNP


title: snATAC-seq from thyroid gland (ENCLB297JFC)

description:
https://www.encodeproject.org/experiments/ENCSR817VFO/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human thyroid
experiment encode accession: ENCSR817VFO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB297JFC
size range: 200-750

source_name: Homo sapiens female adult (53 years) thyroid gland tissue

value: tissue

value: female

value: adult

tag: age

value: 53 year

tag: lab

value: Bing Ren, UCSD

value: Kristin Ardlie

value: not applicable

tag: link

value: ENCBS754LSE at ENCODE; https://www.encodeproject.org/ENCBS754LSE/


title: Mast cells, F20F R1 001

description: Library name: F20F_R1.fastq.gz


title: Fm_Let7d2_eWAT

value: eWAT

tag: strain

value: Fm

value: LFD

value: male


title: snATAC-seq from gastrocnemius medialis (ENCLB414HPK)

description:
https://www.encodeproject.org/experiments/ENCSR819EGE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastrocnemius medialis
experiment encode accession: ENCSR819EGE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB414HPK
size range: 200-750

source_name: Homo sapiens female adult (53 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

tag: source

tag: collection date

tag: geographic location

value: ENCBS925LDO at ENCODE; https://www.encodeproject.org/ENCBS925LDO/


title: Fm_NegativeControl2_eWAT

tag: tissue

value: WT

tag: generation

tag: treatment


title: Mast cells, F262C R1 001

description: Library name: F262C_R1.fastq.gz

value: Bone marrow

value: Mast Cells

value: IgG


title: 2h3_Participant_030_week_6

value: M

tag: timepoint

value: Peripheral blood


title: Mast cells, F20C R1 001

description: Library name: F20C_R1.fastq.gz


title: Fm_Let7d1_eWAT

tag: age weeks

tag: diet


title: 3a3_Participant_136_week_6


title: snATAC-seq from thyroid gland (ENCLB387CYI)

description:
https://www.encodeproject.org/experiments/ENCSR796RXX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human thyroid
experiment encode accession: ENCSR796RXX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB387CYI
size range: 200-750

source_name: Homo sapiens female adult (51 years) thyroid gland tissue

value: thyroid gland

value: tissue

tag: biosample encode accession

value: female

tag: dev stage

value: adult

value: 51 year

value: ENCODE Consortium

value: LEIDOS

value: ENCBS246ZPO at ENCODE; https://www.encodeproject.org/ENCBS246ZPO/


title: F1_HFLF5_eWAT_s

data_processing:
Raw miRNA sequence reads underwent a quality check, and the 3´ and 5´ adapter sequences were removed through the utilization of cutadapt, with the exclusion of reads shorter than 20 nucleotides.
The obtained sequence reads were mapped using miRDeep2, employing the Bowtie algorithm for alignment. Digital expression levels were normalized, taking into account the length of miRNAs and the total number of miRNA reads generated in each library, using Trimmed Mean of M-values (TMM) normalization.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files includes raw reads for each sample.

source_name: eWAT

growth_protocol: C57BL/6 male F1 mice were fed with chow diet from weaning to 6-week-old and then kept with specific diet until 24-week-old.

extract_protocol:
RNA was harvested using TRI reagent (Sigma) followed by clean-up with RPE buffer (Qiagen, Germany). 1 ug of total RNA was used for the consturction of sequncing libraries.
RNA libraries for small RNA-seq were prepared using NEXTFLEX Small RNA-seq Kit v3 with UDIs.

treatment_protocol: 6-week-old mice were fed with LFD (18 weeks).

value: eWAT

value: HFLFD

tag: Sex

value: male


title: F1_HFLF6_eWAT_s

tag: genotype

value: WT


title: Mast cells, F162F R1 001

description: Library name: F162F_R1.fastq.gz

source_name: Bone marrow

value: Bone marrow

tag: cell type

tag: antibody

value: FosB

value: DNP


title: 2g5_Participant_080_week_6

tag: age

value: M

tag: sample number


title: 2h1_Participant_024_week_6

value: Peripheral blood


title: 2g6_Participant_080_week_7


title: snATAC-seq from esophagus squamous epithelium (ENCLB706DKU)

description:
https://www.encodeproject.org/experiments/ENCSR757EGB/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus squamous epithelium
experiment encode accession: ENCSR757EGB
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB706DKU
size range: 200-750

source_name: Homo sapiens male adult (54 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: 54 year

tag: lab

tag: source

value: not applicable

tag: link

value: ENCBS348ASN at ENCODE; https://www.encodeproject.org/ENCBS348ASN/


title: snATAC-seq from right atrium auricular region (ENCLB936CVN)

description:
https://www.encodeproject.org/experiments/ENCSR776EOI/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human right atrium auricular region
experiment encode accession: ENCSR776EOI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB936CVN
size range: 200-750

source_name: Homo sapiens female adult (51 years) right atrium auricular region tissue

value: right atrium auricular region

value: tissue

value: female

value: adult

value: 51 year

tag: collection date

tag: geographic location

value: ENCBS280LSO at ENCODE; https://www.encodeproject.org/ENCBS280LSO/


title: F1_HFLF3_eWAT_s

tag: tissue

value: eWAT

tag: strain

tag: generation

value: HFLFD

value: male


title: Mast cells, F162C R1 001

description: Library name: F162C_R1.fastq.gz

value: Bone marrow

value: Mast Cells

value: IgG

value: WT

tag: treatment


title: 2g4_Participant_077_week_7

value: M

tag: timepoint

value: Peripheral blood


title: snATAC-seq from lower leg skin (ENCLB924VQH)

description:
https://www.encodeproject.org/experiments/ENCSR733SZL/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human lower leg skin
experiment encode accession: ENCSR733SZL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB924VQH
size range: 200-750

source_name: Homo sapiens male adult (54 years) lower leg skin tissue

value: lower leg skin

tag: biosample encode accession

tag: dev stage

value: 54 year

value: ENCODE Consortium

value: LEIDOS

value: not applicable

value: ENCBS005MNT at ENCODE; https://www.encodeproject.org/ENCBS005MNT/


title: F1_HFLF2_eWAT_s

tag: genotype

tag: age weeks

tag: diet

tag: Sex


title: 2h2_Participant_024_week_7

tag: age

tag: sample number


title: Mast cells, F10C R1 001

description: Library name: F10C_R1.fastq.gz

tag: cell type

tag: antibody


title: snATAC-seq from ascending aorta (ENCLB580CIM)

description:
https://www.encodeproject.org/experiments/ENCSR808WCV/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human ascending aorta
experiment encode accession: ENCSR808WCV
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB580CIM
size range: 200-750

source_name: Homo sapiens female adult (53 years) ascending aorta tissue

value: ascending aorta

value: tissue

value: female

value: adult

value: 53 year

tag: lab

value: Bing Ren, UCSD

tag: source

value: Kristin Ardlie

tag: collection date

tag: link

value: ENCBS740ACE at ENCODE; https://www.encodeproject.org/ENCBS740ACE/


title: 2g3_Participant_077_week_6

tag: tissue


title: F1_HF6_eWAT_s

value: eWAT

tag: strain

value: WT

tag: generation

value: HFD

value: male


title: F1_HFLF4_eWAT_s

value: HFLFD


title: F1_HFLF1_eWAT_s


title: Day 30_5

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

data_processing:
Samples were sequenced using a 2x150bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts  were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
Assembly: mm10
Supplementary files format and content: raw count

source_name: lung

growth_protocol: C57BL/6 mice were either untreated or transplanted with Balb/c lungs with costimulatory blockade. Infiltrating lung eosinophils are recipient origin in this lung transplant model. Eosinophils were isolated by flow cytometry sorting on resting, day 7 or day 30 post-transplant lungs.

extract_protocol:
Trizol Extraction
NEBNext Ultra II RNA Library Prep Kit

value: lung

value: Eosinophil

tag: treatment

value: transplant with CSB Day 30


title: Day 30_4


title: snATAC-seq from upper lobe of left lung (ENCLB299XWA)

description:
https://www.encodeproject.org/experiments/ENCSR718WGE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human upper lobe of left lung
experiment encode accession: ENCSR718WGE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB299XWA
size range: 200-750

source_name: Homo sapiens female adult (51 years) upper lobe of left lung tissue

value: upper lobe of left lung

tag: biosample encode accession

tag: dev stage

value: 51 year

value: ENCODE Consortium

value: LEIDOS

value: not applicable

tag: geographic location

value: ENCBS397VQB at ENCODE; https://www.encodeproject.org/ENCBS397VQB/


title: 2g1_Participant_068_week_6

value: M

tag: timepoint

value: Peripheral blood


title: snATAC-seq from right atrium auricular region (ENCLB479CUF)

description:
https://www.encodeproject.org/experiments/ENCSR717FVA/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human right atrium auricular region
experiment encode accession: ENCSR717FVA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB479CUF
size range: 200-750

source_name: Homo sapiens female adult (53 years) right atrium auricular region tissue

value: right atrium auricular region

value: tissue

tag: Sex

value: female

value: adult

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

value: ENCBS832NLG at ENCODE; https://www.encodeproject.org/ENCBS832NLG/


title: Mast cells, F10F R1 001

description: Library name: F10F_R1.fastq.gz

value: Bone marrow

value: Mast Cells

value: FosB

tag: genotype

value: WT


title: Day 30_3

value: lung

value: Eosinophil

value: transplant with CSB Day 30


title: snATAC-seq from heart left ventricle (ENCLB077OMB)

description:
https://www.encodeproject.org/experiments/ENCSR704SKG/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human heart left ventricle
experiment encode accession: ENCSR704SKG
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB077OMB
size range: 200-750

source_name: Homo sapiens female adult (53 years) heart left ventricle tissue

value: heart left ventricle

tag: age

value: not applicable

value: ENCBS688DOY at ENCODE; https://www.encodeproject.org/ENCBS688DOY/


title: F1_HF5_eWAT_s

value: eWAT

tag: age weeks

tag: diet

value: HFD

value: male


title: 2f6_Participant_109_week_7

value: M

tag: sample number

value: Peripheral blood


title: snATAC-seq from gastrocnemius medialis (ENCLB604ZJP)

description:
https://www.encodeproject.org/experiments/ENCSR696YOC/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastrocnemius medialis
experiment encode accession: ENCSR696YOC
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB604ZJP
size range: 200-750

source_name: Homo sapiens male adult (37 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

value: tissue

value: adult

value: 37 year

tag: lab

value: ENCODE Consortium

tag: source

value: LEIDOS

value: ENCBS564MPZ at ENCODE; https://www.encodeproject.org/ENCBS564MPZ/


title: 2f5_Participant_109_week_6


title: Day 30_2

value: lung

tag: cell type

value: Eosinophil


title: F1_HF3_eWAT_s

tag: tissue

value: WT


title: Day 30_1

tag: strain

value: transplant with CSB Day 30


title: F1_HF2_eWAT_s

tag: generation


title: snATAC-seq from esophagus muscularis mucosa (ENCLB796REL)

description:
https://www.encodeproject.org/experiments/ENCSR660NEE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus muscularis mucosa
experiment encode accession: ENCSR660NEE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB796REL
size range: 200-750

source_name: Homo sapiens female adult (51 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: female

value: 51 year

tag: collection date

value: not applicable

tag: link

value: ENCBS358ZHI at ENCODE; https://www.encodeproject.org/ENCBS358ZHI/


title: Day 7_5

tag: treatment

value: transplant with CSB Day 7


title: 2f4_Participant_075_week_7

value: F

value: Peripheral blood


title: 2g2_Participant_068_week_7

value: M


title: snATAC-seq from tibial nerve (ENCLB498VFS)

description:
https://www.encodeproject.org/experiments/ENCSR726QTF/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human tibial nerve
experiment encode accession: ENCSR726QTF
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB498VFS
size range: 200-750

source_name: Homo sapiens female adult (53 years) tibial nerve tissue

value: tibial nerve

value: tissue

tag: biosample encode accession

tag: dev stage

value: adult

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

tag: geographic location

value: ENCBS227WJZ at ENCODE; https://www.encodeproject.org/ENCBS227WJZ/


title: 2f3_Participant_075_week_6

source_name: Peripheral blood

tag: Sex

tag: timepoint


title: snATAC-seq from Peyer's patch (ENCLB441KQZ)

description:
https://www.encodeproject.org/experiments/ENCSR652WJE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human Peyer's patch
experiment encode accession: ENCSR652WJE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB441KQZ
size range: 200-750

source_name: Homo sapiens male adult (54 years) Peyer's patch tissue

value: Peyer's patch

value: male

tag: age

value: 54 year

value: ENCODE Consortium

value: LEIDOS

value: ENCBS359ZEG at ENCODE; https://www.encodeproject.org/ENCBS359ZEG/


title: Day 7_4

value: lung

value: Eosinophil

value: transplant with CSB Day 7


title: F1_HF1_eWAT_s

value: eWAT

tag: genotype

value: WT

tag: age weeks

tag: diet

value: HFD


title: 2f2_Participant_060_week_7

value: F

tag: sample number

value: Peripheral blood


title: snATAC-seq from ovary (ENCLB946RZG)

description:
https://www.encodeproject.org/experiments/ENCSR582VOF/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human ovary
experiment encode accession: ENCSR582VOF
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB946RZG
size range: 200-750

source_name: Homo sapiens female adult (53 years) ovary tissue

value: ovary

value: tissue

value: female

value: adult

value: 53 year

tag: lab

value: Bing Ren, UCSD

tag: source

value: not applicable

value: ENCBS048FUR at ENCODE; https://www.encodeproject.org/ENCBS048FUR/


title: F1_LF6_eWAT_s

tag: tissue

tag: strain

value: LFD

value: male


title: Day 7_3

value: lung

tag: cell type

value: Eosinophil


title: F1_LF5_eWAT_s

value: eWAT

tag: generation


title: Day 7_2

tag: treatment

value: transplant with CSB Day 7


title: F1_HF4_eWAT_s

value: WT

value: HFD


title: F1_LF4_eWAT_s


title: 2e6_Participant_063_week_7

value: M

value: Peripheral blood


title: 2f1_Participant_060_week_6

value: F


title: 2e5_Participant_063_week_6


title: Resting_Lung 5


title: snATAC-seq from right lobe of liver (ENCLB283SGO)

description:
https://www.encodeproject.org/experiments/ENCSR559MJT/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human right lobe of liver
experiment encode accession: ENCSR559MJT
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB283SGO
size range: 200-750

source_name: Homo sapiens female adult (53 years) right lobe of liver tissue

value: right lobe of liver

value: tissue

tag: biosample encode accession

value: female

value: Kristin Ardlie

tag: collection date

tag: link

value: ENCBS504CPU at ENCODE; https://www.encodeproject.org/ENCBS504CPU/


title: F1_LF3_eWAT_s

source_name: eWAT

tag: Sex


title: 2e4_Participant_105_week_7

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

tag: timepoint


title: snATAC-seq from esophagus muscularis mucosa (ENCLB782HQD)

description:
https://www.encodeproject.org/experiments/ENCSR577BWJ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus muscularis mucosa
experiment encode accession: ENCSR577BWJ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB782HQD
size range: 200-750

source_name: Homo sapiens male adult (54 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

tag: dev stage

value: adult

tag: age

value: 54 year

value: ENCODE Consortium

value: LEIDOS

value: not applicable

tag: geographic location

value: ENCBS575GLZ at ENCODE; https://www.encodeproject.org/ENCBS575GLZ/


title: Day 7_1

value: lung

value: Eosinophil

value: transplant with CSB Day 7


title: Resting_Lung 4


title: snATAC-seq from heart left ventricle (ENCLB355WXY)

description:
https://www.encodeproject.org/experiments/ENCSR538FPK/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human heart left ventricle
experiment encode accession: ENCSR538FPK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB355WXY
size range: 200-750

source_name: Homo sapiens female adult (51 years) heart left ventricle tissue

value: heart left ventricle

value: 51 year

value: ENCBS315ZGI at ENCODE; https://www.encodeproject.org/ENCBS315ZGI/


title: snATAC-seq from stomach (ENCLB860ACZ)

description:
https://www.encodeproject.org/experiments/ENCSR549JEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human stomach
experiment encode accession: ENCSR549JEQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB860ACZ
size range: 200-750

source_name: Homo sapiens male adult (54 years) stomach tissue

value: stomach

value: tissue

value: male

value: ENCBS085XRH at ENCODE; https://www.encodeproject.org/ENCBS085XRH/


title: 2e1_Participant_098_week_6

value: F

value: Peripheral blood


title: Resting_Lung 3


title: F1_HFLF6_LIV_s

source_name: liver

value: liver

tag: genotype

value: WT

tag: age weeks

tag: diet

value: HFLFD


title: F1_LF1_eWAT_s

value: eWAT

value: LFD


title: Resting_Lung 2

value: lung


title: snATAC-seq from omental fat pad (ENCLB884ITS)

description:
https://www.encodeproject.org/experiments/ENCSR644SCP/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human omental fat pad
experiment encode accession: ENCSR644SCP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB884ITS
size range: 200-750

source_name: Homo sapiens male adult (37 years) omental fat pad tissue

value: omental fat pad

value: adult

value: 37 year

tag: lab

value: ENCODE Consortium

tag: source

value: LEIDOS

value: not applicable

value: ENCBS307LZC at ENCODE; https://www.encodeproject.org/ENCBS307LZC/


title: 2d6_Participant_130_week_7

value: M

tag: sample number

tag: tissue


title: snATAC-seq from lower leg skin (ENCLB994QFR)

description:
https://www.encodeproject.org/experiments/ENCSR513HZN/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human lower leg skin
experiment encode accession: ENCSR513HZN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB994QFR
size range: 200-750

source_name: Homo sapiens female adult (53 years) lower leg skin tissue

value: lower leg skin

value: tissue

value: female

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

value: ENCBS488BSF at ENCODE; https://www.encodeproject.org/ENCBS488BSF/


title: F1_HFLF5_LIV_s

value: liver

tag: strain

value: WT

tag: generation

value: HFLFD

value: male


title: snATAC-seq from transverse colon (ENCLB296NNI)

description:
https://www.encodeproject.org/experiments/ENCSR506YMX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human transverse colon
experiment encode accession: ENCSR506YMX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB296NNI
size range: 200-750

source_name: Homo sapiens female adult (51 years) transverse colon tissue

value: transverse colon

tag: biosample encode accession

value: adult

value: 51 year

value: ENCBS232KDF at ENCODE; https://www.encodeproject.org/ENCBS232KDF/


title: Resting_Lung 1

source_name: lung

value: lung

tag: cell type

value: Eosinophil

tag: treatment


title: snATAC-seq from omental fat pad (ENCLB221DDF)

description:
https://www.encodeproject.org/experiments/ENCSR492GGN/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human omental fat pad
experiment encode accession: ENCSR492GGN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB221DDF
size range: 200-750

source_name: Homo sapiens male adult (54 years) omental fat pad tissue

value: omental fat pad

tag: Sex

value: 54 year

value: ENCODE Consortium

value: LEIDOS

tag: collection date

value: not applicable

tag: link

value: ENCBS210YON at ENCODE; https://www.encodeproject.org/ENCBS210YON/


title: F1_HFLF4_LIV_s


title: 2d5_Participant_130_week_6

tag: age

value: M

tag: timepoint

value: Peripheral blood


title: 2d3_Participant_064_week_6

value: F


title: Secondary_root

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Read alignment + counting; Cell Ranger count; version 6.1.2
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: h5 file containing raw and filtered count matrix (output Cell Ranger count)
Supplementary files format and content: Seurat file in .rds format

organism: Arabidopsis thaliana

source_name: Secondary root

growth_protocol: The seeds were kept in dark at 4 °C for two days and then plated on half-strength Murashige and Skoog growth medium (1/2 GM) supplemented with 2.2 g/L MS salt mixture with vitamins (Duchefa), 1% sucrose, 0.5 g/L MES and 0.8% agar (pH 5.8). The seedlings were transferred to soil around day 7. We utilized 30-day-old pPXY: erYFP grown on soil to isolate protoplasts for single cell analysis.

extract_protocol:
Their roots within 2 cm below the root-hypocotyl junction were harvested (lateral roots were removed) and washed with tap water and then Milli Q water. The roots were longitudinally dissected with a razor blade under a stereo microscope and put into the protoplast isolation solution (1.5% (w/v) cellulase-R10 (Yakult), 0.4% (w/v) macerozyme-R10 (Yakult), 0.4 M mannitol (sigma), 20 mM MES (Duchefa), 20 mM KCl (1 M stock in Milli Q water?), 0.1% (w/v) BSA (sigma) and 10 mM CaCl2 (1 M stock in Milli Q water?)). The samples were incubated at room temperature under the dark condition with gentle shaking (75 rpm) for one hour. After the incubation, the solution was filtered once with the 70 µm cell strainer and the flow-through was centrifuged at 400 g for 6 min. The supernatant was gently removed, and the protoplasts were resuspended in the buffer (the protoplast isolation solution without enzymes). The resuspended protoplast solution was filtered three times with the 40 µm cell strainer. Protoplasts were stained with 14 µM 4’,6-diamidino-2-phenylindole (DAPI) in PBS and the DAPI negative cells were sorted by BD Aria II.
Cell suspensions were loaded into a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (V3 chemistry, 10X Genomics) according to the manufacturer’s instructions.

value: Secondary root

tag: ecotype


title: snATAC-seq from lower leg skin (ENCLB448FLU)

description:
https://www.encodeproject.org/experiments/ENCSR474TGL/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human lower leg skin
experiment encode accession: ENCSR474TGL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB448FLU
size range: 200-750

source_name: Homo sapiens female adult (51 years) lower leg skin tissue

value: lower leg skin

value: tissue

value: female

tag: dev stage

tag: geographic location

value: ENCBS007KAH at ENCODE; https://www.encodeproject.org/ENCBS007KAH/


title: F1_LF2_eWAT_s

value: eWAT

tag: genotype

value: WT

tag: age weeks

tag: diet

value: LFD

value: male


title: 2d2_Participant_104_week_7

tag: sample number

tag: tissue


title: snATAC-seq from uterus (ENCLB859JTQ)

description:
https://www.encodeproject.org/experiments/ENCSR455CVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human uterus
experiment encode accession: ENCSR455CVZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB859JTQ
size range: 200-750

source_name: Homo sapiens female adult (51 years) uterus tissue

value: uterus

value: adult

value: 51 year

tag: lab

tag: source

value: ENCBS468RPZ at ENCODE; https://www.encodeproject.org/ENCBS468RPZ/


title: 9-NGS126_S21_L001, embryo, BHB

city: Québec

first: Ricardo

middle: Perecin

last: Nociti

state: Québec

address: 2425, Rue de l'Agriculture

department: Animal Science

country: Canada

institute: Université Laval

data_processing:
STAR
featurecounts
DESEQ2
PCIT / CETF
Raw counts for each sample in .csv file
Assembly: ARS-UCD 1.3 from NCBI
Supplementary files format and content: .CSV raw_couts and DEGs table

molecule: polyA RNA

organism: Bos taurus

source_name: embryo

extract_protocol:
The total RNA from pools of bovine blastocyst embryos produced in-vitro and treated with or wothout BHB  were extrated with Tryzol  following the manufacturer’s instructions. The total RNA was treated with DNase I (Invitrogen; Carlsbad, CA) to avoid DNA contamination.
The RNA library preparation from pools of  bovine blastocyst embryos produced in-vitro and treated (n=3) with or wothout BHB (n=3)  were performed with 0.1- 4 µg the total RNA using Illumina TruSeq Stranded mRNA Sample Prep kit. The libraries were quantified by qPCR using the KAPA Library Quantification kit (Illumina; KAPA Biosystems). The sequencing was performed in 1 lane of Hiseq 2500 V4 (2x100pb).
PolyA

value: embryo

tag: cell type

value: BHB


title: 8-NGS126_S20_L001, embryo, BHB

tag: treatment


title: 2d1_Participant_104_week_6

source_name: Peripheral blood

tag: Sex

value: M

value: Peripheral blood


title: snATAC-seq from esophagus squamous epithelium (ENCLB069ZXU)

description:
https://www.encodeproject.org/experiments/ENCSR453TVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus squamous epithelium
experiment encode accession: ENCSR453TVZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB069ZXU
size range: 200-750

source_name: Homo sapiens female adult (51 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

tag: biosample encode accession

value: ENCODE Consortium

value: LEIDOS

tag: collection date

value: not applicable

value: ENCBS294BEQ at ENCODE; https://www.encodeproject.org/ENCBS294BEQ/


title: 2e2_Participant_098_week_7

tag: age

value: F


title: F1_HFLF1_LIV_s

value: liver

tag: strain

value: WT

tag: generation

value: HFLFD


title: 7-NGS126_S19_L001, embryo, BHB


title: F1_HF6_LIV_s

value: HFD

value: male


title: 2c5_Participant_052_week_6

tag: timepoint


title: 6-NGS126_S18_L001, embryo, CTRL

value: CTRL


title: snATAC-seq from tibial nerve (ENCLB078EPH)

description:
https://www.encodeproject.org/experiments/ENCSR453BVR/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human tibial nerve
experiment encode accession: ENCSR453BVR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB078EPH
size range: 200-750

source_name: Homo sapiens male adult (54 years) tibial nerve tissue

value: tibial nerve

value: tissue

tag: dev stage

value: adult

value: 54 year

tag: geographic location

tag: link

value: ENCBS773MXP at ENCODE; https://www.encodeproject.org/ENCBS773MXP/


title: 2c4_Participant_038_week_7

value: M

value: Peripheral blood


title: snATAC-seq from vagina (ENCLB289GMK)

description:
https://www.encodeproject.org/experiments/ENCSR441ZWO/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human vagina
experiment encode accession: ENCSR441ZWO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB289GMK
size range: 200-750

source_name: Homo sapiens female adult (53 years) vagina tissue

value: vagina

value: female

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

value: ENCBS293EHK at ENCODE; https://www.encodeproject.org/ENCBS293EHK/


title: F1_HF5_LIV_s

value: liver

tag: genotype

value: WT

tag: age weeks

tag: diet


title: snATAC-seq from breast epithelium (ENCLB857DKE)

description:
https://www.encodeproject.org/experiments/ENCSR438ETW/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human breast epithelium
experiment encode accession: ENCSR438ETW
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB857DKE
size range: 200-750

source_name: Homo sapiens female adult (53 years) breast epithelium tissue

value: breast epithelium

tag: lab

value: not applicable

value: ENCBS869MIO at ENCODE; https://www.encodeproject.org/ENCBS869MIO/


title: 5-NGS126_S17_L001, embryo, CTRL

tag: tissue

value: embryo

value: CTRL


title: F1_HF4_LIV_s

value: HFD

value: male


title: 2c3_Participant_038_week_6

value: M

tag: sample number


title: F1_HFLF3_LIV_s

value: HFLFD


title: F1_HF3_LIV_s


title: 4-NGS126_S16_L001, embryo, CTRL

tag: cell type

tag: treatment


title: F1_HFLF2_LIV_s

tag: Sex


title: 2c2_Participant_096_week_7

value: Peripheral blood


title: snATAC-seq from transverse colon (ENCLB537SOG)

description:
https://www.encodeproject.org/experiments/ENCSR434SXE/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC of human colon transverse
experiment encode accession: ENCSR434SXE
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB537SOG
size range: 200-750

source_name: Homo sapiens male adult (37 years) transverse colon tissue

value: transverse colon

value: tissue

tag: biosample encode accession

value: adult

value: 37 year

tag: source

tag: collection date

value: ENCBS579CDZ at ENCODE; https://www.encodeproject.org/ENCBS579CDZ/


title: F1_HF2_LIV_s

value: liver

tag: strain

tag: generation


title: 2c1_Participant_096_week_6

tag: age

tag: timepoint


title: X15

description:
CG_contralateral
Rosa_etal_2024_Raw_count_table.csv
Rosa_etal_2024_Raw_count_table.csv

data_processing:
FASTQC
TRIMMOMATIC
STAR
DESEQ2
CLUSTERPROFILER
Assembly: ARS UCD 1.2 ENSEMBL
Supplementary files format and content: Raw count table in csv file

source_name: granulosa cells

extract_protocol:
miRNeasy Mini Kit (QIAGEN, Hilden, Germany) / RNase-Free DNase Set (QIAGEN, Hilden, Germany)
SMART-Seq HT Kit (Takara Bio Inc, Kusatsu, Kansai, Japan).
Nextera XT DNA Library Prep (Illumina, San Diego, CA, USA) and sequenced on a NextSeq 550 (Illumina) considering 75-bp single-end reads.

value: granulosa cells

value: contralateral


title: 2c6_Participant_052_week_7


title: snATAC-seq from thoracic aorta (ENCLB653CJO)

description:
https://www.encodeproject.org/experiments/ENCSR402SNA/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human thoracic aorta
experiment encode accession: ENCSR402SNA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB653CJO
size range: 200-750

source_name: Homo sapiens male adult (37 years) thoracic aorta tissue

value: thoracic aorta

tag: dev stage

value: ENCODE Consortium

value: LEIDOS

value: not applicable

tag: geographic location

tag: link

value: ENCBS027MVW at ENCODE; https://www.encodeproject.org/ENCBS027MVW/


title: F1_HF1_LIV_s

source_name: liver

tag: genotype

value: WT

tag: age weeks

tag: diet

value: HFD

value: male


title: X14

tag: tissue


title: 2b6_Participant_114_week_7

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: F

tag: sample number

value: Peripheral blood


title: snATAC-seq from lower leg skin (ENCLB627ZUW)

description:
https://www.encodeproject.org/experiments/ENCSR397ODX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human lower leg skin
experiment encode accession: ENCSR397ODX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB627ZUW
size range: 200-750

source_name: Homo sapiens male adult (37 years) lower leg skin tissue

value: lower leg skin

value: tissue

tag: lab

value: ENCBS380GWR at ENCODE; https://www.encodeproject.org/ENCBS380GWR/


title: F1_LF6_LIV_s

value: LFD

tag: Sex


title: X13

tag: cell type

tag: treatment


title: snATAC-seq from suprapubic skin (ENCLB255AXX)

description:
https://www.encodeproject.org/experiments/ENCSR397LYX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human suprapubic skin
experiment encode accession: ENCSR397LYX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB255AXX
size range: 200-750

source_name: Homo sapiens female adult (51 years) suprapubic skin tissue

value: suprapubic skin

tag: biosample encode accession

value: female

value: adult

value: 51 year

tag: source

tag: collection date

value: ENCBS825XXY at ENCODE; https://www.encodeproject.org/ENCBS825XXY/


title: 2b5_Participant_114_week_6

tag: age


title: F1_LF5_LIV_s

value: liver

tag: strain

tag: generation


title: 2b4_Participant_073_week_7

value: M

tag: timepoint


title: snATAC-seq from sigmoid colon (ENCLB236ZWD)

description:
https://www.encodeproject.org/experiments/ENCSR388NCA/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human colon sigmoid
experiment encode accession: ENCSR388NCA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB236ZWD
size range: 200-750

source_name: Homo sapiens female adult (53 years) sigmoid colon tissue

value: sigmoid colon

tag: dev stage

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

value: not applicable

tag: geographic location

tag: link

value: ENCBS696LTC at ENCODE; https://www.encodeproject.org/ENCBS696LTC/


title: X11

description:
CG_ipsilateral
Rosa_etal_2024_Raw_count_table.csv
Rosa_etal_2024_Raw_count_table.csv

value: granulosa cells

value: ipsilateral


title: X12


title: snATAC-seq from sigmoid colon (ENCLB340WTO)

description:
https://www.encodeproject.org/experiments/ENCSR367GKP/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human colon sigmoid
experiment encode accession: ENCSR367GKP
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB340WTO
size range: 200-750

source_name: Homo sapiens male adult (37 years) sigmoid colon tissue

value: tissue

value: male

value: 37 year

value: ENCODE Consortium

value: LEIDOS

value: ENCBS630RYD at ENCODE; https://www.encodeproject.org/ENCBS630RYD/


title: 2b3_Participant_073_week_6

value: Peripheral blood


title: snATAC-seq from suprapubic skin (ENCLB304ZBR)

description:
https://www.encodeproject.org/experiments/ENCSR364GEA/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human suprapubic skin
experiment encode accession: ENCSR364GEA
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB304ZBR
size range: 200-750

source_name: Homo sapiens female adult (53 years) suprapubic skin tissue

value: suprapubic skin

value: female

value: adult

value: ENCBS407MSH at ENCODE; https://www.encodeproject.org/ENCBS407MSH/


title: F1_LF3_LIV_s

value: liver

tag: genotype

value: WT

tag: age weeks

tag: diet

value: LFD


title: 2b2_Participant_081_week_7

value: M

tag: sample number

tag: tissue


title: X10

value: granulosa cells

tag: cell type


title: snATAC-seq from ascending aorta (ENCLB114EJJ)

description:
https://www.encodeproject.org/experiments/ENCSR411MLR/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human ascending aorta
experiment encode accession: ENCSR411MLR
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB114EJJ
size range: 200-750

source_name: Homo sapiens female adult (51 years) ascending aorta tissue

value: ascending aorta

tag: Sex

value: 51 year

tag: lab

value: not applicable

value: ENCBS220XWH at ENCODE; https://www.encodeproject.org/ENCBS220XWH/


title: X16

tag: treatment

value: contralateral


title: F1_LF4_LIV_s

value: male


title: F1_LF2_LIV_s


title: X9

value: ipsilateral


title: 2b1_Participant_081_week_6

value: Peripheral blood


title: snATAC-seq from transverse colon (ENCLB444VLF)

description:
https://www.encodeproject.org/experiments/ENCSR349XKD/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human transverse colon
experiment encode accession: ENCSR349XKD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB444VLF
size range: 200-750

source_name: Homo sapiens male adult (54 years) transverse colon tissue

value: transverse colon

value: tissue

tag: biosample encode accession

value: 54 year

value: Bing Ren, UCSD

tag: source

value: Kristin Ardlie

tag: collection date

value: ENCBS609JJK at ENCODE; https://www.encodeproject.org/ENCBS609JJK/


title: 2a6_Participant_120_week_7

tag: age

value: F


title: snATAC-seq from adrenal gland (ENCLB841ODN)

description:
https://www.encodeproject.org/experiments/ENCSR302LEY/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human adrenal gland
experiment encode accession: ENCSR302LEY
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB841ODN
size range: 200-750

source_name: Homo sapiens female adult (53 years) adrenal gland tissue

value: adrenal gland

value: female

value: adult

value: 53 year

value: ENCBS648XAU at ENCODE; https://www.encodeproject.org/ENCBS648XAU/


title: X7

description:
CC_contralateral
Rosa_etal_2024_Raw_count_table.csv
Rosa_etal_2024_Raw_count_table.csv

source_name: cumulus cells

value: cumulus cells


title: X6

value: contralateral


title: snATAC-seq from tibial artery (ENCLB191DJV)

description:
https://www.encodeproject.org/experiments/ENCSR302CMX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human tibial artery
experiment encode accession: ENCSR302CMX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB191DJV
size range: 200-750

source_name: Homo sapiens male adult (54 years) tibial artery tissue

value: tibial artery

value: male

value: ENCODE Consortium

value: LEIDOS

value: not applicable

value: ENCBS851KVK at ENCODE; https://www.encodeproject.org/ENCBS851KVK/


title: F0_HFLF5_eWAT

source_name: eWAT

growth_protocol: C57BL/6 male F0 mice were fed with chow diet from weaning to 6-week-old and then kept with specific diet until 24-week-old.

treatment_protocol: 6-week-old mice were fed with LFD (18 weeks), HLD (18 weeks) or HFD (9 weeks) followed by LFD (9 weeks).

value: eWAT

tag: strain

value: WT

tag: generation

value: HFLFD


title: 2a4_Participant_036_week_7

source_name: Peripheral blood

value: F

tag: timepoint

value: Peripheral blood


title: snATAC-seq from omental fat pad (ENCLB805IZY)

description:
https://www.encodeproject.org/experiments/ENCSR274HQD/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human omental fat pad
experiment encode accession: ENCSR274HQD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB805IZY
size range: 200-750

source_name: Homo sapiens female adult (53 years) omental fat pad tissue

value: omental fat pad

value: tissue

value: female

tag: dev stage

value: Bing Ren, UCSD

value: Kristin Ardlie

tag: geographic location

tag: link

value: ENCBS524PHY at ENCODE; https://www.encodeproject.org/ENCBS524PHY/


title: F0_HFLF4_eWAT

tag: genotype

tag: age weeks

tag: diet


title: X5

tag: tissue

value: cumulus cells

tag: cell type

value: contralateral


title: 2a3_Participant_036_week_6

tag: Sex

tag: sample number


title: X4

description:
CC_ipsilateral
Rosa_etal_2024_Raw_count_table.csv
Rosa_etal_2024_Raw_count_table.csv

tag: treatment

value: ipsilateral


title: F0_HFLF3_eWAT

value: male


title: F0_HFLF2_eWAT


title: snATAC-seq from body of pancreas (ENCLB059DGS)

description:
https://www.encodeproject.org/experiments/ENCSR261TQO/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human body of pancreas
experiment encode accession: ENCSR261TQO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB059DGS
size range: 200-750

source_name: Homo sapiens female adult (51 years) body of pancreas tissue

value: body of pancreas

tag: biosample encode accession

value: adult

value: 51 year

tag: lab

value: ENCODE Consortium

tag: source

value: LEIDOS

value: not applicable

value: ENCBS853AVG at ENCODE; https://www.encodeproject.org/ENCBS853AVG/


title: 2a2_Participant_129_week_7

tag: age

value: F

value: Peripheral blood


title: snATAC-seq from gastrocnemius medialis (ENCLB335IUJ)

description:
https://www.encodeproject.org/experiments/ENCSR244GZL/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastrocnemius medialis
experiment encode accession: ENCSR244GZL
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB335IUJ
size range: 200-750

source_name: Homo sapiens female adult (53 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

value: tissue

value: female

value: 53 year

tag: collection date

value: ENCBS254RFH at ENCODE; https://www.encodeproject.org/ENCBS254RFH/


title: 2a1_Participant_129_week_6

tag: timepoint


title: F0_HFLF1_eWAT

value: eWAT

tag: strain

value: WT

tag: generation

value: HFLFD


title: 1h6_Participant_002_week_7

value: M


title: X2

value: cumulus cells

value: ipsilateral


title: snATAC-seq from body of pancreas (ENCLB395JZU)

description:
https://www.encodeproject.org/experiments/ENCSR234CRD/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human body of pancreas
experiment encode accession: ENCSR234CRD
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB395JZU
size range: 200-750

source_name: Homo sapiens male adult (54 years) body of pancreas tissue

value: body of pancreas

value: male

tag: dev stage

value: adult

value: 54 year

value: ENCODE Consortium

tag: geographic location

tag: link

value: ENCBS692CGI at ENCODE; https://www.encodeproject.org/ENCBS692CGI/


title: F0_HFLF6_eWAT

tag: genotype

tag: age weeks

tag: diet


title: F0_HF6_eWAT

tag: tissue

value: HFD

tag: Sex


title: F1_LF1_LIV_s

source_name: liver

value: liver

value: LFD


title: X1

tag: cell type

tag: treatment


title: 2a5_Participant_120_week_6

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

value: F

tag: sample number

value: Peripheral blood


title: 1h5_Participant_002_week_6


title: X8

value: contralateral


title: snATAC-seq from gastroesophageal sphincter (ENCLB292IVR)

description:
https://www.encodeproject.org/experiments/ENCSR215BTH/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastroesophageal sphincter
experiment encode accession: ENCSR215BTH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB292IVR
size range: 200-750

source_name: Homo sapiens female adult (53 years) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: tissue

tag: biosample encode accession

value: female

value: 53 year

tag: lab

value: Bing Ren, UCSD

tag: source

value: Kristin Ardlie

value: not applicable

value: ENCBS181ZFU at ENCODE; https://www.encodeproject.org/ENCBS181ZFU/


title: F0_HF5_eWAT

value: eWAT

value: WT

value: male


title: gDNA_quant_MPRA_9

city: Boston

first: James

middle: Christopher

last: Taggart

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

data_processing:
Barcodes were counted by directly parsing the single-end sequencing reads derived from both gDNA and RNA in a FASTQ format, with the barcode appearing at a fixed position within the read. As before, any variant with mutations in the constant sequence proceeding the barcode was discarded. Additionally, any two barcodes of identical sequence and unique molecular identifier were counted as a single read. The number of unique reads mapping to each variant barcode was calculated for both the RNA and gDNA-derived samples, and the ratio of RNA to gDNA-derived reads was calculated to extract the relative accumulation of processed mRNA for each variant. Barcodes can then be grouped by associated mutations, thresholded based on read count, and normalized to the median wild-type barcode’s ratio.
Assembly: N/A
Supplementary files format and content: .txt files are tab-separated tables summarizing data including counts for each detected variant, integrating information from all three datasets (barcode-to-sequence mapping, RNA quantification, and gDNA quantification).

organism: Bacillus subtilis

source_name: bacterial cell

growth_protocol: To collect samples, a single cryovial of a B. subtilis library was thawed, washed twice with 10 mL LB to remove glycerol, and grown overnight in 200 mL of LB at 37°C in a 2.8 L flask with vigorous shaking. These cultures were then back-diluted to an OD600 of 0.0003 in 200 mL LB with library inducer and grown at 37°C until an OD600 of 0.3, at which point samples were harvested.

extract_protocol:
RNA was extracted from frozen cell pellets with gDNA depletion using an RNeasy Plus Mini Kit (Qiagen). gDNA was prepared from a frozen cell pellet using the Wizard Genomic DNA Purification Kit (Promega).
For RNA-derived libraries from experiments 1a, 1b, 2a, 2b, and 9 (see Table S7), 40 µg of total RNA was reverse transcribed using primer oJT442 and SuperScript III. This cDNA was then run on a 6% TBE-Urea gel, and the following size selection ranges were gel purified: 300-500 nt for full-length cggR and glnR constructs (experiments 1a, 2a, 9) and 100-250 nt for cleaved cggR constructs (experiments 1b and 2b). For the remaining experiments, cleaved RNA was isolated by size selection of RNAs ranging from 200-400 nt for tetM-cggR sites, 150-300 nt for aprE-cggR sites, and 150-350 nt for aprE-glnR sites on a 6% TBE-Urea gel (Novex). The size selected product was reverse transcribed using primer oJT442 and SuperScript III (Thermo Fisher) and size selected on 6% TBE-Urea gel, extracting approximately 120 to 200 nucleotides for cggR libraries and 100 to 200 for glnR. For all experiments, size-selected cDNA was amplified using Phusion DNA polymerase (NEB), adding a barcode and Illumina adapters with a Truseq indexing primer and an isoform-specific primer (see Table S2 for primer sequences). These isoform-specific primers were oJT441/oJT1290 for cleaved/full-length products from cggR constructs or oJT890/oJT1291 for cleaved/full-length products from glnR constructs. gDNA-derived libraries were generated using a two-step Phusion PCR protocol. An initial amplicon was performed generated through 2 cycles of PCR using from 4 µg of purified nucleic acid per 50 µL PCR reaction (reaction scaled up as needed to minimize UMI collapse in more complex libraries) with primers oJT444/445 for cggR upstream mutations, oJT1125/445 for cggR downstream mutations, and oJT891/445 for glnR downstream mutations. The untranslated cggR library required a longer amplicon to capture the upstream stop codon and was instead amplified with oJT942 and oJT445. This first PCR reaction was cleaned up with a double-sided Select-a-Size DNA Clean & Concentrator column (Zymo) and a DNA Clean & Concentrator 5 column (Zymo). A quarter of this reaction was then used for the second round of PCR, using the same primers as used for quantifying cleaved RNA abundance (oJT441 or oJT890 with our Truseq indexing primer) and size selected on an 8% TBE gel.

treatment_protocol: For all MPRA experiments, cells were grown in LB medium with an inducer (20 ng/mL anhydrotetracycline or 2% xylose) when noted. For all experiments in an inducible RNase J1 background, 2% xylose was consistently used to maintain RNase J1 expression, which was substituted for 2% glucose when RNase J1 depletion was required.

value: bacterial cell

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

value: 2% xylose (RNase J1 induction)


title: RNA_quant_MPRA_9


title: 1h4_Participant_089_week_7

tag: age

value: F

tag: timepoint


title: F0_HF4_eWAT

tag: strain

tag: generation

value: HFD


title: snATAC-seq from tibial nerve (ENCLB125GDB)

description:
https://www.encodeproject.org/experiments/ENCSR205TUH/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human tibial nerve
experiment encode accession: ENCSR205TUH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB125GDB
size range: 200-750

source_name: Homo sapiens female adult (51 years) tibial nerve tissue

value: tibial nerve

tag: dev stage

value: adult

value: 51 year

value: ENCODE Consortium

value: LEIDOS

tag: collection date

tag: geographic location

value: ENCBS131WCD at ENCODE; https://www.encodeproject.org/ENCBS131WCD/


title: snATAC-seq from stomach (ENCLB285NUQ)

description:
https://www.encodeproject.org/experiments/ENCSR266ZPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human stomach
experiment encode accession: ENCSR266ZPZ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB285NUQ
size range: 200-750

source_name: Homo sapiens male adult (37 years) stomach tissue

value: stomach

value: tissue

value: 37 year

tag: link

value: ENCBS962QGQ at ENCODE; https://www.encodeproject.org/ENCBS962QGQ/


title: snATAC-seq from upper lobe of left lung (ENCLB023IVJ)

description:
https://www.encodeproject.org/experiments/ENCSR182PJN/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human upper lobe of left lung
experiment encode accession: ENCSR182PJN
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB023IVJ
size range: 200-750

source_name: Homo sapiens female adult (53 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: female

value: 53 year

value: Bing Ren, UCSD

value: Kristin Ardlie

value: not applicable

value: ENCBS573MMI at ENCODE; https://www.encodeproject.org/ENCBS573MMI/


title: 1h3_Participant_089_week_6

value: F

value: Peripheral blood


title: F0_HF3_eWAT

value: eWAT

tag: genotype

value: WT

tag: age weeks

tag: diet

value: HFD

value: male


title: X3

tag: tissue

value: cumulus cells

tag: cell type

value: ipsilateral


title: 1h2_Participant_139_week_7

tag: Sex

tag: sample number


title: F0_HF2_eWAT


title: snATAC-seq from omental fat pad (ENCLB586VVD)

description:
https://www.encodeproject.org/experiments/ENCSR181XXQ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human omental fat pad
experiment encode accession: ENCSR181XXQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB586VVD
size range: 200-750

source_name: Homo sapiens female adult (51 years) omental fat pad tissue

value: omental fat pad

value: tissue

tag: biosample encode accession

value: adult

value: 51 year

tag: lab

value: ENCODE Consortium

value: LEIDOS

value: ENCBS614VNG at ENCODE; https://www.encodeproject.org/ENCBS614VNG/


title: 1h1_Participant_139_week_6

tag: age


title: RNA_quant_MPRA_8b

value: bacterial cell

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

tag: treatment

value: 2% glucose (RNase J1 depletion)


title: F0_HF1_eWAT

tag: strain


title: 1g6_Participant_057_week_7

value: F

tag: timepoint

value: Peripheral blood


title: snATAC-seq from esophagus squamous epithelium (ENCLB128TZP)

description:
https://www.encodeproject.org/experiments/ENCSR164GSH/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus squamous epithelium
experiment encode accession: ENCSR164GSH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB128TZP
size range: 200-750

source_name: Homo sapiens female adult (53 years) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: female

tag: dev stage

value: 53 year

value: Bing Ren, UCSD

tag: source

value: Kristin Ardlie

value: not applicable

value: ENCBS088TRE at ENCODE; https://www.encodeproject.org/ENCBS088TRE/


title: snATAC-seq from esophagus muscularis mucosa (ENCLB632TLT)

description:
https://www.encodeproject.org/experiments/ENCSR168TFI/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human esophagus muscularis mucosa
experiment encode accession: ENCSR168TFI
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB632TLT
size range: 200-750

source_name: Homo sapiens female adult (53 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: tissue

value: adult

tag: collection date

tag: geographic location

value: ENCBS718DCV at ENCODE; https://www.encodeproject.org/ENCBS718DCV/


title: RNA_quant_MPRA_8a

tag: genotype

value: 2% xylose (RNase J1 induction)


title: F0_LF6_eWAT

value: eWAT

value: WT

tag: generation

tag: age weeks

value: LFD

value: male


title: 1g5_Participant_057_week_6

value: F

tag: tissue

value: Peripheral blood


title: F0_LF5_eWAT

tag: diet


title: snATAC-seq from gastrocnemius medialis (ENCLB749XLV)

description:
https://www.encodeproject.org/experiments/ENCSR139TIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastrocnemius medialis
experiment encode accession: ENCSR139TIQ
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB749XLV
size range: 200-750

source_name: Homo sapiens male adult (54 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

tag: Sex

value: 54 year

tag: link

value: ENCBS187FIA at ENCODE; https://www.encodeproject.org/ENCBS187FIA/


title: 1g4_Participant_112_week_7

value: M

tag: sample number


title: F0_LF4_eWAT


title: snATAC-seq from Peyer's patch (ENCLB180HSZ)

description:
https://www.encodeproject.org/experiments/ENCSR101JHK/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human Peyer's patch
experiment encode accession: ENCSR101JHK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB180HSZ
size range: 200-750

source_name: Homo sapiens female adult (53 years) Peyer's patch tissue

value: Peyer's patch

tag: biosample encode accession

value: female

value: 53 year

tag: lab

value: Bing Ren, UCSD

value: Kristin Ardlie

value: not applicable

value: ENCBS047QJO at ENCODE; https://www.encodeproject.org/ENCBS047QJO/


title: RNA_quant_MPRA_7

tag: cell type

value: bacterial cell


title: 1g3_Participant_112_week_6

tag: age


title: gDNA_quant_MPRA_7

tag: strain


title: snATAC-seq from upper lobe of left lung (ENCLB250JVF)

description:
https://www.encodeproject.org/experiments/ENCSR089CGX/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human upper lobe of left lung
experiment encode accession: ENCSR089CGX
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB250JVF
size range: 200-750

source_name: Homo sapiens male adult (54 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: tissue

tag: dev stage

value: adult

value: ENCODE Consortium

value: LEIDOS

value: ENCBS965VNB at ENCODE; https://www.encodeproject.org/ENCBS965VNB/


title: RNA_quant_MPRA_6


title: F0_LF2_eWAT

source_name: eWAT

value: eWAT

value: WT

value: LFD

value: male


title: gDNA_quant_MPRA_8a

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

tag: treatment

value: 2% xylose (RNase J1 induction)


title: F0_LF3_eWAT


title: 1g2_Participant_035_week_7

source_name: Peripheral blood

value: M

tag: timepoint

value: Peripheral blood


title: gDNA_quant_MPRA_8b

value: 2% glucose (RNase J1 depletion)


title: F0_LF1_eWAT


title: gDNA_quant_MPRA_5


title: snATAC-seq from uterus (ENCLB458SNN)

description:
https://www.encodeproject.org/experiments/ENCSR028RFK/
***************
biological replicate number: 1
technical replicate number: 2
description: snATAC-seq of human uterus
experiment encode accession: ENCSR028RFK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB458SNN
size range: 200-750

source_name: Homo sapiens female adult (53 years) uterus tissue

value: uterus

value: female

value: 53 year

value: Bing Ren, UCSD

tag: source

value: Kristin Ardlie

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS057FDO at ENCODE; https://www.encodeproject.org/ENCBS057FDO/


title: 1f6_Participant_099_week_7

value: F


title: snATAC-seq from tibial artery (ENCLB959OAN)

description:
https://www.encodeproject.org/experiments/ENCSR058XJK/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human tibial artery
experiment encode accession: ENCSR058XJK
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB959OAN
size range: 200-750

source_name: Homo sapiens female adult (53 years) tibial artery tissue

value: tibial artery

value: tissue

value: adult

value: ENCBS595ABE at ENCODE; https://www.encodeproject.org/ENCBS595ABE/


title: snATAC-seq from Peyer's patch (ENCLB352WBS)

description:
https://www.encodeproject.org/experiments/ENCSR052DKH/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human Peyer's patch
experiment encode accession: ENCSR052DKH
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB352WBS
size range: 200-750

source_name: Homo sapiens female adult (51 years) Peyer's patch tissue

value: Peyer's patch

value: 51 year

value: ENCODE Consortium

value: LEIDOS

value: ENCBS324ZYJ at ENCODE; https://www.encodeproject.org/ENCBS324ZYJ/


title: F0_HFLF6_LIV

source_name: liver

value: liver

tag: genotype

value: WT

tag: generation

tag: age weeks

value: HFLFD

value: male


title: gDNA_quant_MPRA_4b

value: bacterial cell

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

value: 2% glucose (RNase J1 depletion)


title: 1f5_Participant_099_week_6

tag: Sex

value: F

tag: tissue

value: Peripheral blood


title: RNA_quant_MPRA_5


title: F0_HFLF4_LIV

tag: diet


title: 1g1_Participant_035_week_6

value: M

tag: sample number


title: snATAC-seq from gastrocnemius medialis (ENCLB691LSC)

description:
https://www.encodeproject.org/experiments/ENCSR023FME/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human gastrocnemius medialis
experiment encode accession: ENCSR023FME
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB691LSC
size range: 200-750

source_name: Homo sapiens female adult (51 years) gastrocnemius medialis tissue

value: gastrocnemius medialis

value: tissue

tag: biosample encode accession

value: female

value: adult

tag: lab

value: Bing Ren, UCSD

value: Kristin Ardlie

value: not applicable

tag: link

value: ENCBS530CJS at ENCODE; https://www.encodeproject.org/ENCBS530CJS/


title: 1f4_Participant_018_week_7

tag: age


title: snATAC-seq from transverse colon (ENCLB373OUN)

description:
https://www.encodeproject.org/experiments/ENCSR007QIO/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of human transverse colon
experiment encode accession: ENCSR007QIO
assay title: snATAC-seq
assembly: GRCh38
encode release date: 2022-03-23
lab: Bing Ren, UCSD
library encode accession: ENCLB373OUN
size range: 200-750

source_name: Homo sapiens female adult (53 years) transverse colon tissue

value: transverse colon

tag: dev stage

value: 53 year

value: ENCBS378RII at ENCODE; https://www.encodeproject.org/ENCBS378RII/


title: gDNA_quant_MPRA_6

source_name: bacterial cell

tag: cell type

value: bacterial cell

tag: strain


title: 1f3_Participant_018_week_6

tag: timepoint


title: icLASER from K562 (ENCLB194OBJ)

description:
https://www.encodeproject.org/experiments/ENCSR623ICN/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 icLASER experiment
experiment encode accession: ENCSR623ICN
assay title: icLASER
assembly: GRCh38
possible controls: ENCSR167VHJ
encode release date: 2020-12-11
lab: Rob Spitale, UCI
library encode accession: ENCLB194OBJ
size range: >200

source_name: Homo sapiens K562 cell line treated with NAz-N3, non-ionizing ultraviolet radiation exposure

extract_protocol:
general protocol: https://www.encodeproject.org/documents/0b5a5970-ad0a-46b3-b02a-80f8eafdea08/@@download/attachment/icLASER_protocol.pdf
extraction method: Trizol

tag: line

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: Rob Spitale, UCI

tag: source

value: ATCC

tag: treatments

value: treatment_term_name:NAz-N3; treatment_type:chemical; treatment_term_id:NTR:0001180; treatment_term_name:non-ionizing ultraviolet radiation exposure; treatment_type:irradiation;

tag: collection date

value: ENCBS486GVG at ENCODE; https://www.encodeproject.org/ENCBS486GVG/


title: RNA_quant_MPRA_4b

tag: genotype

value: W168 amyE::{Pxyl-rnjA Cm} rnjA::spc ganA::{comK kan}

tag: treatment

value: 2% glucose (RNase J1 depletion)


title: 1f2_Participant_033_week_7

description: Total RNA sequenced from infant as part of the AIR study to investigate responses to vaccination

tag: Sex

value: F

tag: tissue

value: Peripheral blood


title: icLASER from K562 (ENCLB564GYL)

description:
https://www.encodeproject.org/experiments/ENCSR623ICN/
***************
biological replicate number: 2
technical replicate number: 1
description: K562 icLASER experiment
experiment encode accession: ENCSR623ICN
assay title: icLASER
assembly: GRCh38
possible controls: ENCSR167VHJ
encode release date: 2020-12-11
lab: Rob Spitale, UCI
library encode accession: ENCLB564GYL
size range: >200

tag: biosample encode accession

value: female

value: adult

tag: geographic location

value: ENCBS633JKZ at ENCODE; https://www.encodeproject.org/ENCBS633JKZ/


title: gDNA_quant_MPRA_4a

value: 2% xylose (RNase J1 induction)


title: RNA_quant_MPRA_4a


title: F0_HFLF2_LIV

value: liver

value: WT

tag: generation

tag: age weeks

tag: diet

value: HFLFD

value: male


title: F0_HFLF1_LIV


title: 1f1_Participant_033_week_6

tag: age

tag: sample number


title: gDNA_quant_MPRA_3

tag: cell type

value: bacterial cell

tag: strain

value: W168 ganA::{comK kan}


title: 1e6_Participant_092_week_7

tag: timepoint


title: icLASER from K562 (ENCLB236IHK)

description:
https://www.encodeproject.org/experiments/ENCSR167VHJ/
***************
biological replicate number: 2
technical replicate number: 1
description: K562 icLASER control experiment
experiment encode accession: ENCSR167VHJ
assay title: icLASER
assembly: GRCh38
encode release date: 2020-12-11
lab: Rob Spitale, UCI
library encode accession: ENCLB236IHK
size range: >200

source_name: Homo sapiens K562 cell line treated with NAz-N3

tag: line

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: 53 year

tag: lab

value: Rob Spitale, UCI

tag: source

value: ATCC

value: not applicable

tag: link

value: ENCBS892ZTL at ENCODE; https://www.encodeproject.org/ENCBS892ZTL/


title: icLASER from K562 (ENCLB214NTF)

description:
https://www.encodeproject.org/experiments/ENCSR167VHJ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562 icLASER control experiment
experiment encode accession: ENCSR167VHJ
assay title: icLASER
assembly: GRCh38
encode release date: 2020-12-11
lab: Rob Spitale, UCI
library encode accession: ENCLB214NTF
size range: >200

tag: Sex

value: female

tag: treatments

tag: collection date

value: ENCBS558VEU at ENCODE; https://www.encodeproject.org/ENCBS558VEU/


title: F0_HF6_LIV

tag: tissue

tag: genotype

tag: generation

value: HFD


title: 1e5_Participant_092_week_6

tag: age

value: F

value: Peripheral blood


title: F0_HFLF5_LIV

value: liver

value: WT

tag: age weeks

tag: diet


title: snATAC-seq from forebrain (ENCLB141KLL)

description:
https://www.encodeproject.org/experiments/ENCSR997YJI/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR997YJI
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB141KLL
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NCrl male adult (2 months) forebrain tissue

value: forebrain

value: tissue

tag: biosample encode accession

value: male

value: adult

value: 2 month

value: Bing Ren, UCSD

value: CRL

tag: geographic location

value: ENCBS116BFK at ENCODE; https://www.encodeproject.org/ENCBS116BFK/


title: F0_HF5_LIV

tag: strain


title: RNA_quant_MPRA_3

tag: cell type

value: bacterial cell

value: W168 ganA::{comK kan}


title: gDNA_quant_MPRA_2a+b

description:
mpra_2a.txt
mpra_2b.txt


title: snATAC-seq from forebrain (ENCLB964AIU)

description:
https://www.encodeproject.org/experiments/ENCSR997YJI/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR997YJI
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB964AIU
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

tag: dev stage

value: not applicable

value: ENCBS940GAF at ENCODE; https://www.encodeproject.org/ENCBS940GAF/


title: F0_HF4_LIV

value: HFD


title: 1e4_Participant_045_week_7

value: F

tag: timepoint

tag: sample number


title: RNA_quant_MPRA_2b


title: 1e3_Participant_045_week_6

value: Peripheral blood


title: snATAC-seq from forebrain (ENCLB001IUG)

description:
https://www.encodeproject.org/experiments/ENCSR978IKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR978IKJ
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB001IUG
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (13.5 days)

tag: description

value: Forebrain from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS273RVL at ENCODE; https://www.encodeproject.org/ENCBS273RVL/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: F0_HF3_LIV

tag: tissue

value: liver

value: WT

tag: Sex

value: male


title: F0_HF2_LIV

tag: genotype

tag: generation


title: 1e2_Participant_079_week_7

tag: age

value: M


title: RNA_quant_MPRA_2a

value: bacterial cell

value: W168 ganA::{comK kan}


title: F0_HFLF3_LIV

tag: age weeks

tag: diet

value: HFLFD


title: snATAC-seq from forebrain (ENCLB563YQU)

description:
https://www.encodeproject.org/experiments/ENCSR978IKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: snATAC-seq of mouse forebrain
experiment encode accession: ENCSR978IKJ
assay title: snATAC-seq
assembly: mm10
encode release date: 2019-04-19
lab: Bing Ren, UCSD
library encode accession: ENCLB563YQU
fragmentation methods: chemical (Nextera tagmentation)
size range: 200-750

value: forebrain

value: tissue

tag: biosample encode accession

value: ENCBS793ZRY at ENCODE; https://www.encodeproject.org/ENCBS793ZRY/


title: RNA_quant_MPRA_1b

tag: strain


title: gDNA_quant_MPRA_1a+b

description:
mpra_1a.txt
mpra_1b.txt

tag: cell type


title: 1e1_Participant_079_week_6

value: Peripheral blood


title: F0_LF6_LIV

value: LFD