title: DNase-seq from liver (ENCLB477KQW)

description:
https://www.encodeproject.org/experiments/ENCSR809OXS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR809OXS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB477KQW

value: tissue

tag: age

value: virgin

value: not applicable

value: ENCBS568EST at ENCODE; https://www.encodeproject.org/ENCBS568EST/


title: H9, AAV-CRISPR/Cas9, biological replicate 1

status: Public on Jan 14 2025

type: SRA

city: Charlestown

first: Ryuji

last: Morizane

state: MA

address: 149 13th Street

country: USA

institute: Massachusetts General Hospital

description: Library name: H9_Cas9_1

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 and X-Plus Sequencing Platform of 150 bp pair-ended reads (Novogene), alignment and reference genome indexed via STAR (v2.5), and data supplied as fastq files. Visualization of differentially expressed genes was performed using OmicsBox Transcriptomics module, employing HTSeq (v0.6.1) for read number.
Alignment and annotation were conducted with OmicxBox.
Assembly: hg19
Supplementary files format and content: Processed data contains raw expression values of genes.

molecule: total RNA

organism: Homo sapiens

source_name: Kidney organoids

growth_protocol: The directed differentiation of hPSCs into kidney organoids is covered in detail elsewhere (Morizane et al, Nature Biotech, 2015; Morizane et al, Nature Protocols, 2017). Briefly, hPSCs were differentiated into metanephric mesenchyme cells which include nephron progenitor cells, with approximately 80-90% efficiency, by a 3-step directed differentiation protocol. Metanephric mesenchyme cells, arising on day 8 of differentiation, were transferred into suspension culture in 96-well ultra-low adhesion plates (Corning) and further differentiated into kidney organoids through intermediate stages of pre-tubular aggregates (day 11) and renal vesicles (day 14) as previously reported. Quality control measures of SIX2 immunostaining on differentiation day 8 and CDH1, LTL, and PODXL immunostaining on day 17 were performed on all batches of kidney organoids to limit batch-to-batch heterogeneity.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen #15596026, per the manufacturer’s protocol) from triplicate samples of 3-4 kidney organoids for each of CRISPR, AAV, and Control samples on differentiation day 28, following 7 days of treatment with AAV2-saCas9 + AAV2-gRNA, AAV2-GFP, or vehicle control, respectively.
RNA was quantified (Thermo Scientific Nanodrop One spectrophotometer) and its integrity assessed (RNA Nano 6000 Assay Kit, Bioanalyzer 2100, Agilent Technologies, CA). cDNA was synthesized from 500 ng of RNA using a High-capacity cDNA Reverse Transcription kit (Applied Biosystems).

treatment_protocol: In the AAV2-saCas9 plasmid, saCas9 is expressed under the control of the CMV promoter. In the AAV2-gRNA plasmid, each of the two gRNA2 is expressed under the U6 promoter, and mCherry is expressed under the CMV promoter. VectorBuilder has provided stored catalog numbers for re-ordering these vectors (AAV2-saCas9, VB180125-1089ffa; AAV2-gRNA, VB210506-1386zxe). During the co-infection of these vectors in samples denoted ‘CRISPR’, a cumulative MOI of 10^5 vg/cell was employed in 100uL total volume of media, similar to the AAV-GFP serotype testing.

tag: tissue

value: Kidney organoids

tag: cell line

tag: cell type

value: Kidney


title: GN.IL6.Sp_1

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Mus musculus

source_name: Peritoneal Cavity

extract_protocol:
At 2 hours post-injection, 1,000 cells of the 14 immune cell-types from spleen and peritoneal cavity were double-sorted in 5uL of TCL Buffer (QIAGEN) containing 1% 2-mercaptoethanol (Sigma) by BD FACS Aria
Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf)

treatment_protocol: 5-8 week old C57Bl/6J mice shipped from the Jackson Laboratory, Bar Harbor. Mice were injected intravenously with either a free cytokine (5ug of IL1b, IL6 or TNFa in 120uL of PBS)  or PBS (120uL).

value: Peritoneal Cavity

value: GN

tag: strain

tag: treatment


title: 701126331

city: Doha

first: Darawan

last: Rinchai

state: Qatar

address: Al Gharrafa St

department: Research

country: Qatar

institute: Sidra Medicine

data_processing:
All FASTQ passed QC and were aligned to the reference genome GRChg38 using STAR 2.7.9a. BAM files were converted to a raw count expression matrix using HTSeq-count
Assembly: GRChg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
RNA was extracted using the Tempus Spin RNA Isolation Kit (ThermoFisher), which was adapted for the handling of small blood volumes. Contaminating DNA was removed using the TurboDNAse kit (ThermoFisher), and RNA was quantitated on a Qubit instrument (ThermoFisher) and QCed using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).
mRNA-sequencing was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (75 single-end)

tag: time

tag: vaccine dose

value: THIRD

tag: source

value: Fingerstick

value: blood


title: GN.TNFa.Sp_2

value: TNFa


title: DNase-seq from liver (ENCLB491OXG)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR809OXS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR809OXS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491OXG

library_source: genomic

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

molecule: genomic DNA

source_name: Mus musculus strain C57BL/6NJ embryo (13.50 days) liver tissue

value: liver

tag: biosample encode accession

tag: Sex

value: not collected

tag: dev stage

value: embryonic

tag: lab

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

tag: collection date

tag: geographic location

tag: link

value: ENCBS643XHG at ENCODE; https://www.encodeproject.org/ENCBS643XHG/


title: GN.IL1b.Sp_3


title: BJFF, AAV-GFP, biological replicate 1

description: Library name: BJFF_GFP_1

value: BJFF


title: 701126321


title: DNase-seq from liver (ENCLB777NKQ)

description:
https://www.encodeproject.org/experiments/ENCSR809OXS/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR809OXS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB777NKQ

value: tissue

tag: age

value: virgin

value: not applicable

value: ENCBS352XXH at ENCODE; https://www.encodeproject.org/ENCBS352XXH/


title: GN.IL1b.Sp_1

tag: tissue

value: Peritoneal Cavity


title: 701126311


title: 701126301


title: DNase-seq from liver (ENCLB314CYD)

description:
https://www.encodeproject.org/experiments/ENCSR809OXS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR809OXS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB314CYD

value: ENCBS951ESO at ENCODE; https://www.encodeproject.org/ENCBS951ESO/


title: BJFF, AAV-CRISPR/Cas9, biological replicate 2

description: Library name: BJFF_Cas9_2

value: Kidney organoids

tag: cell line

value: Kidney


title: GN.PBS.Sp_5

tag: cell type

value: GN

value: PBS


title: BJFF, AAV-CRISPR/Cas9, biological replicate 1

description: Library name: BJFF_Cas9_1


title: DNase-seq from liver (ENCLB515QRJ)

description:
https://www.encodeproject.org/experiments/ENCSR809OXS/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR809OXS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB515QRJ

value: liver

value: ENCBS521DNT at ENCODE; https://www.encodeproject.org/ENCBS521DNT/


title: 701126291

value: THIRD

value: Fingerstick

value: blood


title: GN.PBS.Sp_4

tag: strain


title: 701126281


title: BJFF, untreated control, biological replicate 3

description: Library name: BJFF_0_3


title: DNase-seq from natural killer cell (ENCLB870FSH)

description:
https://www.encodeproject.org/experiments/ENCSR573LKK/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR573LKK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB870FSH

source_name: Mus musculus strain B6CASTF1/J male adult (2 months) natural killer primary cell

value: natural killer cell

value: primary cell

value: male

value: adult

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: ENCBS476CES at ENCODE; https://www.encodeproject.org/ENCBS476CES/


title: BJFF, untreated control, biological replicate 2

description: Library name: BJFF_0_2

value: Kidney organoids

value: BJFF


title: GN.PBS.Sp_3

value: Peritoneal Cavity

value: GN

tag: treatment


title: BJFF, untreated control, biological replicate 1

description: Library name: BJFF_0_1

value: Kidney


title: DNase-seq from natural killer cell (ENCLB590FSO)

description:
https://www.encodeproject.org/experiments/ENCSR573LKK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR573LKK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB590FSO

value: virgin

value: not applicable

value: ENCBS204YQV at ENCODE; https://www.encodeproject.org/ENCBS204YQV/


title: 701126261

tag: time

value: THIRD

value: Fingerstick

value: blood


title: DNase-seq from natural killer cell (ENCLB634QKN)

description:
https://www.encodeproject.org/experiments/ENCSR803VYN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR803VYN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB634QKN

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) natural killer primary cell

value: natural killer cell

value: primary cell

value: female

value: ENCBS914PIY at ENCODE; https://www.encodeproject.org/ENCBS914PIY/


title: BJFF, AAV-CRISPR/Cas9, biological replicate 3

description: Library name: BJFF_Cas9_3


title: DNase-seq from natural killer cell (ENCLB716COJ)

description:
https://www.encodeproject.org/experiments/ENCSR573LKK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR573LKK
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB716COJ

value: male

value: adult

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: ENCBS962SKT at ENCODE; https://www.encodeproject.org/ENCBS962SKT/


title: GN.PBS.Sp_1

value: Peritoneal Cavity

value: GN

value: PBS


title: GN.IL1b.Sp_2


title: Mo.6C+.TNFa.Sp_3

value: Mo

value: TNFa


title: 701126271

tag: vaccine dose

value: THIRD

value: Fingerstick


title: DNase-seq from natural killer cell (ENCLB982LEO)

description:
https://www.encodeproject.org/experiments/ENCSR803VYN/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR803VYN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB982LEO

value: natural killer cell

tag: source

value: virgin

value: not applicable

value: ENCBS140KQO at ENCODE; https://www.encodeproject.org/ENCBS140KQO/


title: A549 cells, MI-3, H3K4me3 (ChIP), biolRep2

city: Xiamen

first: junbo

last: yuan

state: Fujian

address: Xiang'an South Road

country: China

institute: Xiamen university

description: Library name: A549, MI-3, H3K4me3, biolRep2

data_processing:
Image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument.
Pass filter data of fastq format were processed by Cutadapt (version 1.9.1) to be high quality clean data.
Clean data is aligned to reference genome via software Bowtie2 (version 2.2.6).
MACS (2.1.1) software was used for peak quality control, peak calling, and peak annotation.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak of each sample

source_name: Lung adenocarcinoma

growth_protocol: Cells were cultured at 37℃ with 5% CO2, following sterile techniques. All culture media contained 10% FBS, 100 U/ml penicillin-streptomycin, and 2 mM glutamine.

extract_protocol:
Approximately 2 million cells were used for each ChIP sample. The cells were cross-linked with 1% formaldehyde at room temperature for 10 min. After quenching and cell lysis,chromatin was sonicated at 20% power for 3 min using a sonicator (SONICS, VCX150).
For each sample, ChIP product was used for library preparation. The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptorligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer. Then libraries with different indices were multiplexed and loaded on an Illumina NovaSeq 6000 instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: Lung adenocarcinoma

value: Human alveolar basal epithelial cells

tag: chip antibody

value: H3K4me3 (Millipore, #17-614)


title: GN.PBS.Sp_2


title: Mo.6C+.TNFa.Sp_2


title: 701125921

value: blood


title: DNase-seq from natural killer cell (ENCLB305ZQY)

description:
https://www.encodeproject.org/experiments/ENCSR803VYN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR803VYN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB305ZQY

value: primary cell

tag: biosample encode accession

tag: Sex

value: female

value: adult

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: ENCBS786LPI at ENCODE; https://www.encodeproject.org/ENCBS786LPI/


title: 701125931

value: THIRD


title: 701125911

value: Fingerstick


title: A549 cells, control, INPUT

description: Library name: A549, control, INPUT

value: DMSO


title: A549 cells, MI-3, H3K4me3 (ChIP), biolRep1

description: Library name: A549, MI-3, H3K4me3, biolRep1


title: 701125901


title: DNase-seq from natural killer cell (ENCLB125NCI)

description:
https://www.encodeproject.org/experiments/ENCSR803VYN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR803VYN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB125NCI

value: natural killer cell

tag: dev stage

tag: lab

value: virgin

value: ENCBS273SLZ at ENCODE; https://www.encodeproject.org/ENCBS273SLZ/


title: Mo.6C+.IL6.Sp_3

value: Peritoneal Cavity

value: Mo


title: 701125891


title: Mo.6C+.IL6.Sp_2


title: DNase-seq from liver (ENCLB716OQQ)

description:
https://www.encodeproject.org/experiments/ENCSR541RQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541RQH
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB716OQQ

source_name: Mus musculus strain C57BL/6N,129 (b-thallasemia globin locus deletion, HOM globin mutation, multiple YAC copy) embryo (13.50 days) liver tissue

value: liver

value: tissue

value: not collected

value: embryonic

tag: model organism mating status

tag: collection date

value: not applicable

value: ENCBS599YUD at ENCODE; https://www.encodeproject.org/ENCBS599YUD/


title: Mo.6C+.IL6.Sp_1


title: A549 cells, control, H3K4me3 (ChIP), biolRep2

description: Library name: A549, control, H3K4me3, biolRep2

value: Lung adenocarcinoma

value: Human alveolar basal epithelial cells

value: H3K4me3 (Millipore, #17-614)


title: 701125881

value: THIRD

value: blood


title: 701125871

value: Fingerstick


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB522TGQ)

description:
https://www.encodeproject.org/experiments/ENCSR300SJS/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR300SJS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB522TGQ

source_name: Mus musculus strain B6CASTF1/J male adult (2 months) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: male

value: adult

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: geographic location

tag: link

value: ENCBS522WDQ at ENCODE; https://www.encodeproject.org/ENCBS522WDQ/


title: 701125851

tag: tissue


title: Control eCLIP from K562 (ENCLB075BPY)

description:
https://www.encodeproject.org/experiments/ENCSR937QWU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against APEX1
experiment encode accession: ENCSR937QWU
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-09-12
lab: Gene Yeo, UCSD
library encode accession: ENCLB075BPY
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

tag: line

value: cell line

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: age

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

tag: passage number

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: Control eCLIP from K562 (ENCLB676JLI)

description:
https://www.encodeproject.org/experiments/ENCSR937QWU/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against APEX1
experiment encode accession: ENCSR937QWU
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-09-12
lab: Gene Yeo, UCSD
library encode accession: ENCLB676JLI
fragmentation methods: see document
size range: 175-300

value: not applicable

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: A549 cells, control, H3K4me3 (ChIP), biolRep1

description: Library name: A549, control, H3K4me3, biolRep1

value: Lung adenocarcinoma

tag: cell line

tag: cell type

value: Human alveolar basal epithelial cells

tag: treatment

value: DMSO

value: H3K4me3 (Millipore, #17-614)


title: 701125861

tag: time

tag: vaccine dose

value: THIRD

tag: source

value: Fingerstick

value: blood


title: A549 cells, MI-3, INPUT

description: Library name: A549, MI-3, INPUT

tag: chip antibody


title: Mo.6C+.IL1b.Sp_3

value: Peritoneal Cavity

value: Mo

tag: strain


title: Mo.6C+.IL1b.Sp_1


title: Mo.6C+.TNFa.Sp_1

value: TNFa


title: Mo.6C+.PBS.Sp_5

value: PBS


title: DNase-seq from B cell (ENCLB180EXJ)

description:
https://www.encodeproject.org/experiments/ENCSR499UQO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR499UQO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB180EXJ

source_name: Mus musculus strain B6CASTF1/J male adult (2 months) B primary cell

value: B cell

value: primary cell

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 2 month

tag: lab

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

value: virgin

value: ENCBS511GYY at ENCODE; https://www.encodeproject.org/ENCBS511GYY/


title: Control eCLIP from K562 (ENCLB998HLJ)

description:
https://www.encodeproject.org/experiments/ENCSR856KEU/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against FMR1
experiment encode accession: ENCSR856KEU
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB998HLJ
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: DNase-seq from monocyte (ENCLB787TIX)

description:
https://www.encodeproject.org/experiments/ENCSR526NSY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR526NSY
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB787TIX

source_name: Mus musculus strain B6CASTF1/J male adult (2 months) monocyte primary cell

value: monocyte

tag: age

value: ENCBS617IKX at ENCODE; https://www.encodeproject.org/ENCBS617IKX/


title: 701125841

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: 701125831


title: Control eCLIP from K562 (ENCLB686XOV)

description:
https://www.encodeproject.org/experiments/ENCSR856KEU/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against FMR1
experiment encode accession: ENCSR856KEU
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB686XOV
fragmentation methods: see document
size range: 175-300

tag: health state

value: adult

tag: passage number

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: DNase-seq from B cell (ENCLB544SID)

description:
https://www.encodeproject.org/experiments/ENCSR499UQO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR499UQO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB544SID

value: B cell

value: primary cell

value: male

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: ENCBS116UIT at ENCODE; https://www.encodeproject.org/ENCBS116UIT/


title: DNase-seq from B cell (ENCLB172PRA)

description:
https://www.encodeproject.org/experiments/ENCSR499UQO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR499UQO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB172PRA

value: not applicable

value: ENCBS025CQK at ENCODE; https://www.encodeproject.org/ENCBS025CQK/


title: DNase-seq from CD8-positive naive resting alpha-beta T cell (ENCLB755IMB)

description:
https://www.encodeproject.org/experiments/ENCSR300SJS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR300SJS
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB755IMB

value: ENCBS407WVW at ENCODE; https://www.encodeproject.org/ENCBS407WVW/


title: Mo.6C+.PBS.Sp_3

value: Peritoneal Cavity

tag: cell type

value: Mo

tag: treatment

value: PBS


title: DNase-seq from B cell (ENCLB849FEM)

description:
https://www.encodeproject.org/experiments/ENCSR499UQO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR499UQO
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB849FEM

value: adult

tag: source

value: ENCBS566KPN at ENCODE; https://www.encodeproject.org/ENCBS566KPN/


title: DNase-seq from HCT116 (ENCLB030BUB)

description:
https://www.encodeproject.org/experiments/ENCSR823GSV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR823GSV
assay title: DNase-seq
assembly: GRCh38
encode release date: 2023-01-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB030BUB

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

value: cell line

value: colorectal carcinoma

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS662EON at ENCODE; https://www.encodeproject.org/ENCBS662EON/


title: Mo.6C+.PBS.Sp_2

tag: strain


title: DNase-seq from adrenal gland (ENCLB166KJB)

description:
https://www.encodeproject.org/experiments/ENCSR756AFB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR756AFB
assay title: DNase-seq
assembly: mm10
encode release date: 2023-01-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB166KJB

source_name: Mus musculus strain B6CASTF1/J female adult (13 months) adrenal gland tissue

value: adrenal gland

value: tissue

tag: biosample encode accession

value: female

value: 13 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS947INP at ENCODE; https://www.encodeproject.org/ENCBS947INP/


title: Mo.6C+.IL1b.Sp_2

value: Peritoneal Cavity

value: Mo


title: 701126131

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: DNase-seq from adrenal gland (ENCLB397IDR)

description:
https://www.encodeproject.org/experiments/ENCSR756AFB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR756AFB
assay title: DNase-seq
assembly: mm10
encode release date: 2023-01-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB397IDR

source_name: Mus musculus strain B6CASTF1/J female adult (9-13 months) adrenal gland tissue

tag: Sex

tag: dev stage

value: adult

value: 9-13 month

tag: lab

value: not applicable

value: ENCBS526DLN at ENCODE; https://www.encodeproject.org/ENCBS526DLN/


title: 701126121


title: Mo.6C+.PBS.Sp_1

value: PBS


title: MFrp.TNFa.Sp_3

value: MFrp

value: TNFa


title: 701126111


title: eCLIP from K562 (ENCLB899KZX)

description:
https://www.encodeproject.org/experiments/ENCSR554UVB/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against FMR1
experiment encode accession: ENCSR554UVB
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR856KEU
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB899KZX
fragmentation methods: see document
size range: 175-300

tag: antibody

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

tag: collection date

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: DNase-seq from liver (ENCLB189RFP)

description:
https://www.encodeproject.org/experiments/ENCSR260SFQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR260SFQ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB189RFP

source_name: Mus musculus strain C57BL/6N,129 (HS1 HS4 M deletion, HOM globin mutation) embryo (13.50 days) liver tissue

value: liver

value: tissue

value: not collected

value: embryonic

tag: age

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: geographic location

tag: link

value: ENCBS200QNF at ENCODE; https://www.encodeproject.org/ENCBS200QNF/


title: 701126101

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: DNase-seq from liver (ENCLB968MXH)

description:
https://www.encodeproject.org/experiments/ENCSR740PXN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR740PXN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB968MXH

source_name: Mus musculus strain C57BL/6N,129 (LCR deletion, HET globin mutation) embryo (13.50 days) liver tissue

value: not applicable

value: ENCBS325FQF at ENCODE; https://www.encodeproject.org/ENCBS325FQF/


title: Mo.6C+.PBS.Sp_4

value: Peritoneal Cavity

tag: cell type

value: Mo

tag: treatment

value: PBS


title: MFrp.TNFa.Sp_1

value: MFrp

tag: strain

value: TNFa


title: 701126091

tag: source


title: eCLIP from K562 (ENCLB828AGB)

description:
https://www.encodeproject.org/experiments/ENCSR554UVB/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FMR1
experiment encode accession: ENCSR554UVB
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR856KEU
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB828AGB
fragmentation methods: see document
size range: 175-300

value: cell line

tag: biosample encode accession

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

tag: passage number

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: DNase-seq from B cell (ENCLB035CZI)

description:
https://www.encodeproject.org/experiments/ENCSR224YYX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR224YYX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB035CZI

source_name: Mus musculus strain B6CASTF1/J female adult (2 months) B primary cell

value: B cell

value: primary cell

tag: Sex

tag: dev stage

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: ENCBS202HBA at ENCODE; https://www.encodeproject.org/ENCBS202HBA/


title: MFrp.TNFa.Sp_2

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: MFrp

value: TNFa


title: DNase-seq from liver (ENCLB613MVK)

description:
https://www.encodeproject.org/experiments/ENCSR740PXN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR740PXN
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB613MVK

value: liver

value: tissue

value: not collected

value: embryonic

tag: lab

value: not applicable

value: ENCBS542NOP at ENCODE; https://www.encodeproject.org/ENCBS542NOP/


title: eCLIP from K562 (ENCLB421YPG)

description:
https://www.encodeproject.org/experiments/ENCSR256NCI/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against APEX1
experiment encode accession: ENCSR256NCI
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR937QWU
encode release date: 2022-09-12
lab: Gene Yeo, UCSD
library encode accession: ENCLB421YPG
fragmentation methods: see document
size range: 175-300

tag: antibody

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: 701126081

source_name: blood

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: MFrp.IL6.Sp_2

value: Peritoneal Cavity

value: MFrp


title: eCLIP from K562 (ENCLB838QKG)

description:
https://www.encodeproject.org/experiments/ENCSR256NCI/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against APEX1
experiment encode accession: ENCSR256NCI
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR937QWU
encode release date: 2022-09-12
lab: Gene Yeo, UCSD
library encode accession: ENCLB838QKG
fragmentation methods: see document
size range: 175-300

tag: age

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: 701126071


title: DNase-seq from B cell (ENCLB759BYU)

description:
https://www.encodeproject.org/experiments/ENCSR224YYX/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR224YYX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB759BYU

value: B cell

value: primary cell

value: 2 month

value: John Stamatoyannopoulos, UW

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS303RPE at ENCODE; https://www.encodeproject.org/ENCBS303RPE/


title: 701126141

tag: tissue


title: MFrp.IL6.Sp_1

tag: cell type

tag: strain

tag: treatment


title: eCLIP from K562 (ENCLB680CKP)

description:
https://www.encodeproject.org/experiments/ENCSR248TXP/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP experiment on K562 against FXR1
experiment encode accession: ENCSR248TXP
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR111UKN
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB680CKP
fragmentation methods: see document
size range: 175-300

value: cell line

tag: biosample encode accession

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

tag: source

value: ATCC


title: DNase-seq from B cell (ENCLB805DTL)

description:
https://www.encodeproject.org/experiments/ENCSR224YYX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224YYX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB805DTL

tag: Sex

tag: dev stage

tag: lab

value: ENCBS448RUP at ENCODE; https://www.encodeproject.org/ENCBS448RUP/


title: 701126061

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: MFrp.IL1b.Sp_3

value: Peritoneal Cavity

value: MFrp


title: 701126051


title: 701126041


title: MFrp.IL6.Sp_3


title: PRO-cap from K562 (ENCLB967SPT)

description:
https://www.encodeproject.org/experiments/ENCSR220XSM/
***************
biological replicate number: 1
technical replicate number: 2
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in K562 cells.
experiment encode accession: ENCSR220XSM
assay title: PRO-cap
assembly: GRCh38
encode release date: 2024-10-26
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB967SPT

tag: line

tag: age

value: Haiyuan Yu, Cornell

value: ENCBS165TOO at ENCODE; https://www.encodeproject.org/ENCBS165TOO/


title: MFrp.IL1b.Sp_2


title: DNase-seq from activated T-cell (ENCLB023BVZ)

description:
https://www.encodeproject.org/experiments/ENCSR300NZA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR300NZA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB023BVZ

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

value: activated T-cell

value: primary cell

value: male

value: 43 year

value: John Stamatoyannopoulos, UW

value: StemExpress

tag: treatments

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

tag: collection date

value: not applicable

tag: geographic location

value: ENCBS148PXX at ENCODE; https://www.encodeproject.org/ENCBS148PXX/


title: 701168491

tag: tissue


title: MFrp.IL1b.Sp_1

tag: cell type

tag: strain


title: DNase-seq from B cell (ENCLB314JDJ)

description:
https://www.encodeproject.org/experiments/ENCSR224YYX/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR224YYX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB314JDJ

value: B cell

tag: biosample encode accession

value: female

value: adult

value: 2 month

value: Mark Groudine

tag: model organism mating status

value: virgin

tag: link

value: ENCBS285UFZ at ENCODE; https://www.encodeproject.org/ENCBS285UFZ/


title: Control eCLIP from K562 (ENCLB289ZTR)

description:
https://www.encodeproject.org/experiments/ENCSR111UKN/
***************
biological replicate number: 2
technical replicate number: 1
description: eCLIP control experiment on K562 against FXR1
experiment encode accession: ENCSR111UKN
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB289ZTR
fragmentation methods: see document
size range: 175-300

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

tag: passage number

value: Gene Yeo, UCSD

tag: source

value: ATCC

value: ENCBS177POD at ENCODE; https://www.encodeproject.org/ENCBS177POD/


title: PRO-cap from K562 (ENCLB682NEV)

description:
https://www.encodeproject.org/experiments/ENCSR220XSM/
***************
biological replicate number: 1
technical replicate number: 1
description: A run-on assay that precisely maps the transcription start sites genome-wide with high sensitivity and specificity in K562 cells.
experiment encode accession: ENCSR220XSM
assay title: PRO-cap
assembly: GRCh38
encode release date: 2024-10-26
lab: Haiyuan Yu, Cornell
library encode accession: ENCLB682NEV

tag: Sex

tag: dev stage

tag: lab

value: Haiyuan Yu, Cornell

value: ENCBS165TOO at ENCODE; https://www.encodeproject.org/ENCBS165TOO/


title: 701168481

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

value: blood


title: DNase-seq from kidney (ENCLB590ERB)

description:
https://www.encodeproject.org/experiments/ENCSR218AFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR218AFD
assay title: DNase-seq
assembly: mm10
encode release date: 2023-01-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB590ERB

source_name: Mus musculus strain 5xFAD/CAST (B6SJL-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax x CAST/EiJ) male adult (11 months) kidney tissue

value: kidney

value: tissue

value: male

tag: age

value: 11 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: not applicable

value: ENCBS035LBJ at ENCODE; https://www.encodeproject.org/ENCBS035LBJ/


title: DNase-seq from heart (ENCLB982QGK)

description:
https://www.encodeproject.org/experiments/ENCSR231NBX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR231NBX
assay title: DNase-seq
assembly: mm10
encode release date: 2022-10-04
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB982QGK

source_name: Mus musculus strain 5xFAD/CAST (B6SJL-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax x CAST/EiJ) male adult (11 months) heart tissue

value: heart

value: adult

tag: collection date

value: ENCBS792PFU at ENCODE; https://www.encodeproject.org/ENCBS792PFU/


title: DNase-seq from liver (ENCLB579RGC)

description:
https://www.encodeproject.org/experiments/ENCSR146KDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR146KDZ
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB579RGC

source_name: Mus musculus strain C57BL/6N,129 (HS1 HS4 F deletion, HOM globin mutation) embryo (13.50 days) liver tissue

value: liver

value: not collected

value: embryonic

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

tag: geographic location

value: ENCBS953ORY at ENCODE; https://www.encodeproject.org/ENCBS953ORY/


title: DNase-seq from liver (ENCLB726DUK)

description:
https://www.encodeproject.org/experiments/ENCSR102OZE/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR102OZE
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB726DUK

source_name: Mus musculus strain C57BL/6N,129 (WT with A20 YAC, single YAC copy) embryo (13.50 days) liver tissue

value: tissue

value: ENCBS476ZYM at ENCODE; https://www.encodeproject.org/ENCBS476ZYM/


title: MFrp.PBS.Sp_4

tag: tissue

value: Peritoneal Cavity

value: MFrp

tag: treatment

value: PBS


title: Control eCLIP from K562 (ENCLB118BRD)

description:
https://www.encodeproject.org/experiments/ENCSR111UKN/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on K562 against FXR1
experiment encode accession: ENCSR111UKN
assay title: Control eCLIP
assembly: GRCh38
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB118BRD
fragmentation methods: see document
size range: 175-300

tag: line

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: 701168471

value: THIRD

value: Fingerstick

value: blood


title: 701168461


title: DNase-seq from liver (ENCLB690HQO)

description:
https://www.encodeproject.org/experiments/ENCSR102OZE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR102OZE
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB690HQO

value: liver

tag: biosample encode accession

value: not collected

value: embryonic

value: John Stamatoyannopoulos, UW

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS432ODQ at ENCODE; https://www.encodeproject.org/ENCBS432ODQ/


title: DNase-seq from T-cell (ENCLB057ITN)

description:
https://www.encodeproject.org/experiments/ENCSR101RCL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101RCL
assay title: DNase-seq
assembly: GRCh38
encode release date: 2023-01-27
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB057ITN

source_name: Homo sapiens male adult (43 years) T-cell primary cell

value: T-cell

value: primary cell

value: male

value: adult

value: 43 year

value: StemExpress

value: ENCBS199BPV at ENCODE; https://www.encodeproject.org/ENCBS199BPV/


title: DNase-seq from liver (ENCLB249HPU)

description:
https://www.encodeproject.org/experiments/ENCSR102OZE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR102OZE
assay title: DNase-seq
assembly: mm10
encode release date: 2022-12-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB249HPU

value: tissue

tag: model organism mating status

value: ENCBS243JKS at ENCODE; https://www.encodeproject.org/ENCBS243JKS/


title: MFrp.PBS.Sp_2

value: Peritoneal Cavity

tag: cell type

value: MFrp

tag: strain

value: PBS


title: 701125511

value: THIRD

value: Fingerstick

value: blood


title: eCLIP from K562 (ENCLB237AAC)

description:
https://www.encodeproject.org/experiments/ENCSR248TXP/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP experiment on K562 against FXR1
experiment encode accession: ENCSR248TXP
assay title: eCLIP
assembly: GRCh38
possible controls: ENCSR111UKN
encode release date: 2022-07-19
lab: Gene Yeo, UCSD
library encode accession: ENCLB237AAC
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens K562 cell line

tag: antibody

value: cell line

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

tag: passage number

tag: link

value: ENCBS344MAK at ENCODE; https://www.encodeproject.org/ENCBS344MAK/

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


title: DNase-seq from T-cell (ENCLB138IBS)

description:
https://www.encodeproject.org/experiments/ENCSR035JYT/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR035JYT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB138IBS

source_name: Mus musculus strain B6CASTF1/J male adult (2 months) T-cell primary cell

value: T-cell

value: primary cell

tag: Sex

value: male

tag: dev stage

value: adult

value: 2 month

tag: lab

value: John Stamatoyannopoulos, UW

tag: source

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS875SWF at ENCODE; https://www.encodeproject.org/ENCBS875SWF/


title: A549 cells, shMEN1, rep3

data_processing:
Raw reads of fastq format were firstly processed using fastp (Version 0.20.1) and the low quality reads were removed to obtain the cleanreads using fastqc (Version 0.11.9).
The clean reads were mapped to the reference genome using HISAT2 (Version 2.0.5).
FPKM of each gene was calculated and the read counts of each gene were obtained by featureCounts (Version 1.5.0-p3 ).
Differential expression analysis of two groups (three biological replicates per group) was performed using the DESeq2 R package (1.20.0).
Assembly: Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
RNA was harvested using Total RNA Extraction Reagent (Yeasen, 10606ES60). 2 μg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: cell line

value: Lung adenocarcinoma cells

tag: genotype

value: MEN1 knockdown


title: 701125501

tag: time

tag: vaccine dose

value: THIRD

value: Fingerstick

tag: tissue

value: blood


title: MFrp.PBS.Sp_5

value: Peritoneal Cavity

value: MFrp

tag: treatment

value: PBS


title: MFrp.PBS.Sp_1


title: DNase-seq from T-cell (ENCLB882KAY)

description:
https://www.encodeproject.org/experiments/ENCSR035JYT/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR035JYT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB882KAY

value: T-cell

value: primary cell

tag: biosample encode accession

tag: age

tag: model organism mating status

tag: collection date

tag: geographic location

value: ENCBS760YTO at ENCODE; https://www.encodeproject.org/ENCBS760YTO/


title: A549 cells, shMEN1, rep1

tag: cell type


title: A549 cells, shMEN1, rep2


title: 701125481


title: A549 cells, shNC, rep3

value: Control


title: DNase-seq from T-cell (ENCLB852TIF)

description:
https://www.encodeproject.org/experiments/ENCSR035JYT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR035JYT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB852TIF

value: male

value: adult

value: 2 month

value: John Stamatoyannopoulos, UW

tag: link

value: ENCBS931QNH at ENCODE; https://www.encodeproject.org/ENCBS931QNH/


title: Treg.TNFa.Sp_3

value: Treg

tag: strain

value: TNFa


title: F0_HFLF4_sperm_s

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: Library name: Sample117543

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: sperm

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.

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), HLD (18 weeks) or HFD (9 weeks) followed by LFD (9 weeks).

value: sperm

value: WT

tag: generation

tag: age weeks

tag: diet

value: HFLFD

tag: Sex


title: 701125461

value: THIRD

tag: source

value: Fingerstick

value: blood


title: Treg.IL6.Sp_3

value: Peritoneal Cavity


title: Treg.IL6.Sp_2


title: DNase-seq from T-cell (ENCLB143ZQX)

description:
https://www.encodeproject.org/experiments/ENCSR035JYT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR035JYT
assay title: DNase-seq
assembly: mm10
encode release date: 2022-11-01
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB143ZQX

value: T-cell

value: primary cell

tag: dev stage

tag: lab

value: Mark Groudine

value: virgin

value: not applicable

value: ENCBS990XZR at ENCODE; https://www.encodeproject.org/ENCBS990XZR/


title: 701125451

tag: time

tag: vaccine dose

tag: tissue


title: MFrp.PBS.Sp_3

value: MFrp

tag: treatment

value: PBS


title: Treg.TNFa.Sp_2

value: Treg


title: F0_HFLF3_sperm_s

description: Library name: Sample117542

tag: genotype

value: male


title: gastric cancer [G30T]

city: Fukuoka

first: Naoki

last: Katayama

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics)
Output files were analyzed with the R v4.2.1 package "Seurat v4.3.0".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

source_name: LOW

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1 the Chromium Next GEM Single Cell 5′ Kit v2 for Dual Index (10x Genomics). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct the 3’ and 5’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

tag: tissue type

value: gastric cancer

value: stomach

tag: age

tag: gender

value: Female


title: Treg.TNFa.Sp_1

tag: cell type

value: TNFa


title: 701125471

value: THIRD

value: Fingerstick


title: A549 cells, shNC, rep2

tag: cell line

value: Lung adenocarcinoma cells

value: Control


title: Treg.IL6.Sp_1

value: Peritoneal Cavity

tag: strain


title: 701125491

value: blood


title: 701125431


title: A549 cells, shNC, rep1


title: F0_HFLF1_sperm_s

description: Library name: Sample117540

value: sperm

value: WT

tag: generation

tag: age weeks

value: HFLFD


title: Treg.IL1b.Sp_3


title: F0_HFLF5_sperm_s

description: Library name: Sample117544

tag: diet

tag: Sex


title: Treg.IL1b.Sp_2


title: 701125441

tag: source


title: F0_HFLF6_sperm_s

description: Library name: Sample117526


title: gastric cancer [G29T]

source_name: MID

value: Male


title: 701125421


title: F0_HF6_sperm_s

description: Library name: Sample117524

value: HFD


title: F0_HFLF2_sperm_s

description: Library name: Sample117541


title: W111Control, non IBD

city: Dublin

first: Patrick

last: Walsh

address: Trinity Centre for Health Sciences,, Trinity College Dublin, the University of Dublin,, St. James’s Hospital

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

data_processing:
featureCounts v1.5.0-p3
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: tab-delimited text file contains raw counts of each Sample

source_name: rectal biopsy

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: rectal biopsy

tag: disease

value: non IBD


title: U101Control, non IBD


title: 701125411

tag: time


title: F0_HF5_sperm_s

description: Library name: Sample117522

value: male


title: Treg.IL1b.Sp_1

value: Treg


title: T96Control, non IBD


title: 701125401

tag: vaccine dose


title: Treg.PBS.Sp_4

tag: tissue

value: PBS


title: Treg.PBS.Sp_3

tag: treatment


title: F0_HF4_sperm_s

description: Library name: Sample117520

tag: genotype


title: 701125381


title: F0_HF3_sperm_s

description: Library name: Sample117518


title: R86Control, non IBD


title: Treg.PBS.Sp_2


title: F0_HF2_sperm_s

description: Library name: Sample117516


title: Q81Control, CD

value: CD


title: Treg.PBS.Sp_1


title: 701125361

value: THIRD


title: F0_HF1_sperm_s

description: Library name: Sample117514


title: Tgd.TNFa.Sp_3

value: Tgd

value: TNFa


title: P76Control, CD


title: V106Control, non IBD


title: 701125351

value: Fingerstick


title: Treg.PBS.Sp_5

value: Peritoneal Cavity


title: O71Control, CD


title: F0_LF6_sperm_s

description: Library name: Sample117512

value: LFD


title: 701125391

value: blood


title: F0_LF5_sperm_s

description: Library name: Sample117510

value: sperm

value: WT


title: 701125341


title: Tgd.TNFa.Sp_2


title: Tgd.TNFa.Sp_1


title: 701125331


title: F0_LF4_sperm_s

description: Library name: Sample117508


title: M61Control, CD


title: Tgd.IL6.Sp_3


title: S91Control, non IBD


title: 701125321


title: Tgd.IL6.Sp_2


title: L56Control, CD


title: F0_LF3_sperm_s

description: Library name: Sample117506


title: 701125371


title: 701125311


title: F0_LF2_sperm_s

description: Library name: Sample117504


title: K51Control, CD


title: Tgd.IL6.Sp_1


title: F0_LF1_sperm_s

description: Library name: Sample117502


title: J46Control, CD


title: 701125301


title: I41Control, UC

value: UC


title: Tgd.IL1b.Sp_3


title: N66Control, CD


title: 701125281


title: F0_HFLF6_eWAT_s

description: Library name: Sample7722

source_name: eWAT

value: eWAT

value: HFLFD


title: Tgd.IL1b.Sp_2


title: H36Control, UC

value: rectal biopsy


title: Tgd.IL1b.Sp_1


title: F0_HFLF5_eWAT_s

description: Library name: Sample7721

value: male


title: 701125291


title: 701125271


title: 701125261


title: Tgd.PBS.Sp_5


title: F0_HFLF4_eWAT_s

description: Library name: Sample7720


title: G31Control, UC


title: 701125251


title: Tgd.PBS.Sp_3


title: F0_HFLF2_eWAT_s

description: Library name: Sample7718


title: F26Control, UC


title: F0_HFLF3_eWAT_s

description: Library name: Sample7719


title: E21Control, UC


title: 701125241


title: F0_HFLF1_eWAT_s

description: Library name: Sample7717


title: 701125231


title: D16Control, non IBD

value: non IBD


title: Tgd.PBS.Sp_1

value: PBS


title: Tgd.PBS.Sp_4


title: F0_HF6_eWAT_s

description: Library name: Sample7716

value: HFD


title: C11Control, CD

value: CD


title: 701125221

value: THIRD


title: F0_HF5_eWAT_s

description: Library name: Sample7715


title: 701125211


title: B6Control, non IBD


title: NK.TNFa.Sp_3

value: NK

value: TNFa


title: A1Control, non IBD


title: 701125201

value: Fingerstick


title: F0_HF3_eWAT_s

description: Library name: Sample7713


title: NK.TNFa.Sp_1

value: Peritoneal Cavity


title: F0_HF2_eWAT_s

description: Library name: Sample7712


title: 701125191

value: blood


title: 701125181


title: 4h6_Participant_032_week_7

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

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

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.

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: NK.IL6.Sp_3


title: 4h4_Participant_054_week_7

tag: age


title: F0_HF1_eWAT_s

description: Library name: Sample7711

value: WT


title: Tgd.PBS.Sp_2

tag: cell type

value: Tgd


title: NK.IL6.Sp_1


title: 4h3_Participant_054_week_6


title: F0_LF6_eWAT_s

description: Library name: Sample7710

value: eWAT

value: LFD


title: 701125171


title: F0_LF5_eWAT_s

description: Library name: Sample7709

value: male


title: 4h2_Participant_132_week_7

value: F


title: NK.IL1b.Sp_3


title: 4h1_Participant_132_week_6


title: NK.IL1b.Sp_2


title: 701125161


title: F0_LF4_eWAT_s

description: Library name: Sample7708


title: F0_HF4_eWAT_s

description: Library name: Sample7714


title: 701125151


title: NK.TNFa.Sp_2


title: 4g6_Participant_127_week_7


title: F0_LF3_eWAT_s

description: Library name: Sample7707


title: 4g5_Participant_127_week_6


title: F0_LF2_eWAT_s

description: Library name: Sample7706


title: NK.PBS.Sp_5

value: PBS


title: NK.IL1b.Sp_1


title: 701125131


title: 4g4_Participant_026_week_7


title: NK.PBS.Sp_4


title: 701125121


title: F0_LF1_eWAT_s

description: Library name: Sample7705


title: 701125111


title: NK.PBS.Sp_2


title: F0_HFLF6_LIV_s

description: Library name: Sample7704

source_name: liver

value: liver

value: HFLFD


title: F0_HFLF5_LIV_s

description: Library name: Sample7703


title: 701125101

value: THIRD


title: 4g2_Participant_103_week_7


title: 4g1_Participant_103_week_6


title: F0_HFLF4_LIV_s

description: Library name: Sample7702


title: NK.PBS.Sp_1

source_name: Peritoneal Cavity

value: NK


title: 701125141

source_name: blood


title: 701125081


title: DC.8+.TNFa.Sp_3

value: TNFa


title: F0_HFLF3_LIV_s

description: Library name: Sample7701


title: 4f6_Participant_019_week_7


title: F0_HFLF2_LIV_s

description: Library name: Sample7700


title: 701125091

value: Fingerstick


title: 701125071


title: F0_HFLF1_LIV_s

description: Library name: Sample7699


title: 4f4_Participant_113_week_7


title: 701125061


title: 4f3_Participant_113_week_6


title: NK.PBS.Sp_3

value: Peritoneal Cavity


title: DC.8+.IL6.Sp_3


title: F0_HF6_LIV_s

description: Library name: Sample7698

value: HFD


title: 4g3_Participant_026_week_6


title: DC.8+.IL6.Sp_2


title: F0_HF5_LIV_s

description: Library name: Sample7697


title: 701125051

value: blood


title: DC.8+.IL6.Sp_1


title: 701125041


title: 4f5_Participant_019_week_6

value: Peripheral blood


title: 4e6_Participant_138_week_7


title: DC.8+.TNFa.Sp_2


title: DC.8+.IL1b.Sp_3


title: 701125021


title: DC.8+.TNFa.Sp_1


title: 4e5_Participant_138_week_6


title: F0_HF3_LIV_s

description: Library name: Sample7695

value: WT


title: DC.8+.IL1b.Sp_2


title: 4e3_Participant_090_week_6

value: M


title: 701125011


title: 701125001


title: 4f2_Participant_137_week_7


title: F0_HF1_LIV_s

description: Library name: Sample7693


title: F0_HF2_LIV_s

description: Library name: Sample7694


title: DC.8+.PBS.Sp_5


title: 4e2_Participant_051_week_7


title: 701124991


title: DC.8+.PBS.Sp_4


title: 4e1_Participant_051_week_6


title: F0_LF6_LIV_s

description: Library name: Sample7692


title: 4f1_Participant_137_week_6


title: F0_LF5_LIV_s

description: Library name: Sample7691


title: 701124981


title: F0_HF4_LIV_s

description: Library name: Sample7696


title: 4d6_Participant_093_week_7


title: DC.8+.PBS.Sp_2


title: 701125031


title: DC.8+.PBS.Sp_1


title: 701124961


title: 4d5_Participant_093_week_6


title: 701124951


title: MC.TNFa.PC_3

value: MC


title: F0_LF3_LIV_s

description: Library name: Sample7689

value: LFD


title: 701124941


title: 4d4_Participant_107_week_7


title: MC.TNFa.PC_2


title: F0_LF2_LIV_s

description: Library name: Sample7688

value: male


title: F0_LF1_LIV_s

description: Library name: Sample7687


title: MC.IL6.PC_3


title: 4d2_Participant_034_week_7


title: 701124931


title: 4d3_Participant_107_week_6

value: F


title: C3

city: Guangzhou

first: Yanteng

last: Xu

state: Guangdong

address: 600# Tianhe Road

department: Centre for Nanomedicine

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Library name: Control3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/mus musculus c57bl6nj/dna/) to map reads to the reference genome of mus musculus Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mus_musculus Ensembl_v112
Supplementary files format and content: tab-delimited text files include FPKM and count values for each sample

source_name: Tumor

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Tumor

value: untreated control group


title: 701124921


title: MC.IL6.PC_1


title: 4d1_Participant_034_week_6


title: 701124911


title: 4c6_Participant_014_week_7


title: 701124901


title: F0_LF4_LIV_s

description: Library name: Sample7690

value: liver


title: MC.IL1b.PC_3


title: 701124891

value: THIRD


title: C1

description: Library name: Control1


title: MC.IL1b.PC_1


title: 4c5_Participant_014_week_6


title: T3

description: Library name: Treat3

value: treatment group receiving a 12-h MS-DF-MS therapy


title: 4c4_Participant_003_week_7


title: MC.PBS.PC_5

value: PBS


title: T2

description: Library name: Treat2


title: MC.PBS.PC_4


title: 4c3_Participant_003_week_6


title: 701124881

value: Fingerstick


title: T1

description: Library name: Treat1


title: MC.TNFa.PC_1

value: Peritoneal Cavity

value: TNFa


title: 4c2_Participant_009_week_7


title: MC.PBS.PC_3


title: C2

description: Library name: Control2


title: 4c1_Participant_009_week_6


title: MC.PBS.PC_2


title: F1_HFLF6_eWAT

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.

growth_protocol: C57BL/6 male F1 mice were fed with chow diet from weaning to 6-week-old and then kept with LFD 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 RNA-seq were prepared using NovaSeq 6000 SP Reagent Kit.

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

value: eWAT

value: HFLFD


title: F1_HFLF5_eWAT

value: WT


title: 701124851

value: blood


title: 4b6_Participant_095_week_7

value: M

value: Peripheral blood


title: F1_HFLF4_eWAT

value: male


title: 4b5_Participant_095_week_6


title: MFpc.TNFa.PC_2

value: MFpc


title: 701124831


title: F1_HFLF3_eWAT


title: F1_HFLF2_eWAT


title: 701124841


title: 4b4_Participant_125_week_7


title: 701124821


title: MFpc.TNFa.PC_1


title: F1_HFLF1_eWAT


title: 701124871


title: 701124801


title: F1_HF6_eWAT

value: HFD


title: 4b2_Participant_008_week_7


title: 701124811


title: MFpc.IL6.PC_2


title: MFpc.IL6.PC_1


title: 701124861


title: F1_HF5_eWAT


title: 701124781


title: F1_HF4_eWAT


title: 4b1_Participant_008_week_6


title: 4a6_Participant_119_week_7

value: F


title: MFpc.TNFa.PC_3


title: 701124771


title: 4b3_Participant_125_week_6


title: MFpc.IL1b.PC_2


title: F1_HF3_eWAT


title: 4a4_Participant_061_week_7


title: MFpc.IL1b.PC_3


title: MFpc.IL1b.PC_1


title: 701125701


title: F1_HF2_eWAT


title: 4a3_Participant_061_week_6


title: MFpc.IL6.PC_3


title: MFpc.PBS.PC_5


title: F1_HF1_eWAT


title: 4a2_Participant_094_week_7


title: MFpc.PBS.PC_4


title: F1_LF6_eWAT

value: LFD


title: 701125681

value: THIRD


title: 701124791


title: 4a1_Participant_094_week_6


title: MFpc.PBS.PC_3


title: F1_LF5_eWAT


title: 701125671


title: 701125661


title: 3h4_Participant_122_week_7


title: MFpc.PBS.PC_2


title: 4a5_Participant_119_week_6


title: 3h6_Participant_083_week_7


title: MFpc.PBS.PC_1


title: 701125651


title: F1_LF2_eWAT


title: zmlx181_Eosinophil deficient

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v. 3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Bbrowser (3.5.26) for quality filtering, dimensionality reduction (tsne), analysis of features
Seurat (4.3.0) - visualization of feature and comparative analysis
Assembly: mm10-2.1.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Lung tissue was minced and digested by IMDM medium containing collagenase II and DNAse for 35 minutes at 37°C in a shaker. The digested lung tissue was passed through a 70-μm cell strainer and treated with ACK lysing buffer to remove red cell contamination.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3, 10X Genomics)

treatment_protocol: We transplanted Balb/c left lung to C57BL/6iPHIL recipient with co-stimulatory blockade, then administrate either Diphtheria Toxin or Saline since 30days post-engraftment. Harvest the lung allografts after 3-4 weeks eosinophil depletion period.

value: lung

value: C57BL/6iPHIL (eosinophil DTR mice)

value: Iphil

value: saline


title: 3h3_Participant_122_week_6


title: 3h2_Participant_055_week_7


title: zmlx180_Eosinophil deficient

description: 10x Genomics


title: 701125691

value: Fingerstick


title: 3h1_Participant_055_week_6


title: F1_LF3_eWAT

value: eWAT


title: 701125621


title: F1_HFLF4_LIV

value: liver

value: HFLFD


title: zmlx176_Eosinophil deficient

description: 10x Genomics

value: Diphtheria toxin


title: F1_HFLF3_LIV

value: WT


title: 3g6_Participant_064_week_7

value: Peripheral blood


title: 701125611

value: blood


title: zmlx175_Eosinophil deficient

description: 10x Genomics

value: male


title: 701125601


title: F1_HFLF2_LIV


title: 701125591


title: 3g4_Participant_013_week_7

value: M


title: F1_HFLF1_LIV


title: 3g3_Participant_013_week_6


title: 701125641


title: amnios37

type: RNA

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: gene expression after in vitro expansion

hyb_protocol: 1.65 µg of Cy3-labeled fragmented cRNA during 17 hours at 65°C

scan_protocol: Agilent Microarray Scanner System

data_processing: Agilent Feature Extraction Software for image processing and Rosetta Resolver for gene expression analysis

source_name: amnios human

label_protocol: T7 RNA based amplification for 1µg of total RNA, production of Cy3-labeled cRNA (Agilent Quick Amp Labeling Kit (low input)

growth_protocol: MSCs were amplified and freezed in MEMa medium + 10% human serum albumin + 10% dimethylsulfoxide (Sigma-Aldrich) during three passages

extract_protocol: Total RNA NucleoSpin RNA II Macherey Nagel, Control quality on Agilent 2100 Bioanalyzer

treatment_protocol: Basal condition no treatment

value: mesenchymal stromal cells

tag: sample  id

value: sample id 37


title: amnios27

value: sample id 27


title: F1_HFLF6_LIV

tag: strain


title: 701125581

value: THIRD


title: amnios66

value: sample id 66


title: F1_HF6_LIV

tag: generation

value: HFD


title: F1_HFLF5_LIV

tag: age weeks


title: 3g2_Participant_031_week_7

value: F


title: 701125571

value: Fingerstick


title: 701125631


title: F1_HF5_LIV

tag: diet


title: 3g1_Participant_031_week_6

tag: Sex


title: 701125561

tag: source


title: 3f6_Participant_048_week_7


title: F1_HF3_LIV


title: chorion37

source_name: chorion human


title: 701125551


title: F1_HF2_LIV


title: chorion66


title: 3g5_Participant_066_week_6


title: 3f4_Participant_012_week_7


title: 3f3_Participant_012_week_6


title: F1_HF1_LIV


title: chorion27


title: 701125531


title: cordon66

source_name: cord blood human


title: F1_LF3_LIV

value: LFD


title: cordon27


title: 701125521


title: 3f2_Participant_111_week_7


title: iCLIP from K562 (ENCLB166UXA)

description:
https://www.encodeproject.org/experiments/ENCSR984SOD/
***************
biological replicate number: 2
technical replicate number: 1
description: iCLIP experiment in K562 cells against FUBP1
experiment encode accession: ENCSR984SOD
assay title: iCLIP
assembly: hg19
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB166UXA
fragmentation methods: see document
size range: 159-196

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: female

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 year

tag: passage number

tag: lab

value: Gene Yeo, UCSD

value: ATCC

tag: url

tag: collection date

value: not applicable

tag: geographic location

tag: link

value: ENCBS209FBZ at ENCODE; https://www.encodeproject.org/ENCBS209FBZ/


title: cordon37

tag: cell type

value: mesenchymal stromal cells

tag: sample  id

value: sample id 37


title: F1_LF2_LIV

tag: tissue

value: liver

tag: strain

tag: genotype

value: WT

tag: generation

tag: age weeks

value: male


title: 701124971

tag: time

tag: vaccine dose

value: THIRD

tag: source

value: blood


title: 3f1_Participant_111_week_6

tag: age

tag: Sex

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: iCLIP from K562 (ENCLB407DGT)

description:
https://www.encodeproject.org/experiments/ENCSR984SOD/
***************
biological replicate number: 1
technical replicate number: 1
description: iCLIP experiment in K562 cells against FUBP1
experiment encode accession: ENCSR984SOD
assay title: iCLIP
assembly: hg19
encode release date: 2016-10-31
lab: Gene Yeo, UCSD
library encode accession: ENCLB407DGT
fragmentation methods: see document
size range: 165-203

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: female

tag: health state

tag: dev stage

tag: passage number

tag: lab

tag: url

tag: collection date

value: ENCBS809CIO at ENCODE; https://www.encodeproject.org/ENCBS809CIO/


title: NSC siPQBP1_2

city: Strasbourg

first: Amélie

last: Piton

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Mapping using Tophat 2.0.14 and bowtie version 2-2.1.0
Quantification of gene expression has been performed using HTSeq-0.6.1 with annotations coming from Ensembl 85
Checking of the normalization process by drawing Relative Log Expression (RLE) plots
Quantification of expression using DESeq2
Assembly: hg38

extract_protocol:
Trizol
Librairies prepared from the KAPA mRNA HyperPrep Kit (Roche)

tag: cell type

value: human neural stem cells (hNSCs)

tag: genotype


title: F1_LF6_LIV

tag: tissue

tag: strain

tag: generation

tag: age weeks

tag: diet

value: LFD


title: 701125541

tag: time

tag: vaccine dose

tag: source

value: Fingerstick


title: 3e6_Participant_133_week_7

tag: age

tag: Sex

value: F

tag: timepoint

tag: sample number


title: F1_LF1_LIV


title: iCLIP from K562 (ENCLB198MDG)

description:
https://www.encodeproject.org/experiments/ENCSR961WWI/
***************
biological replicate number: 1
technical replicate number: 1
description: iCLIP experiment in K562 cells against EIF4G1
experiment encode accession: ENCSR961WWI
assay title: iCLIP
assembly: hg19
encode release date: 2015-05-18
lab: Gene Yeo, UCSD
library encode accession: ENCLB198MDG
fragmentation methods: see document
size range: 169-225

tag: antibody

tag: line

tag: biosample encode accession

tag: health state

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 year

tag: passage number

tag: lab

value: Gene Yeo, UCSD

value: ATCC

value: not applicable

tag: geographic location

tag: link

value: ENCBS704IXT at ENCODE; https://www.encodeproject.org/ENCBS704IXT/


title: 3e4_Participant_020_week_7

tag: tissue


title: 3e3_Participant_020_week_6


title: NSC siPQBP1_1

source_name: Librairies prepared from the KAPA mRNA HyperPrep Kit (Roche)

tag: cell type

tag: genotype


title: YM

city: shanghai

first: Yaohui

last: Liu

address: 500 Zhennan Road，Putuo District

department: School of Medicine

institute: Tongji University

description:
Library name: sample 2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rnor6.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Meniscus

extract_protocol:
Meniscal tissues were processed as described previously. Briefly, tissues were minced into ~1 mm³ pieces, digested with 4 mg/mL protease for 1 hour, followed by 0.25 mg/mL collagenase P for 4-6 hours. After washing with 0.04% bovine serum albumin (BSA) in phosphate-buffered saline (PBS), the cells were resuspended in 0.04% BSA and filtered through a 35 µm cell strainer. Viable cells were visually inspected, sorted via flow cytometry, and collected. Flow cytometry sorting ensured a viability threshold of >85% for downstream analyses.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Meniscus

value: young


title: PeWA_Let7d4

growth_protocol: Primary epidydimal SVF cells were cultured in DMEM/Ham’s F12 supplemented with 0.1% Biotin/D-Pantothenate (33mM/17mM), 1% penicillin-streptomycin, and 20% FBS.

treatment_protocol:
Until reaching 80% confluency, primary cells were induced by induction medium with 1 µM rosiglitazone, 850 nM insulin, 1 µM dexamethasone, 250 µM 3-isobutyl-1-methyl-xanthin (IBMX) and 10% FBS. Subsequently, the medium was changed every other day by a differentiation medium containing 1 µM rosiglitazone, 850 nM insulin and 10% FBS.
Negative control and mmu-miR-let-7-d/e-5p mimics were reversely transfected using Lipofectamine RNAiMAX (Thermo Fisher Scientific) at day 4 after induction. Completely differentiated cells were harvested at 7 days after induction for further analysis.

value: eWAT

tag: strain

value: WT

tag: age weeks

tag: diet

value: chow

tag: treatment

value: male


title: PeWA_Let7d3

tag: Sex


title: 3e1_Participant_070_week_6

tag: age

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: iCLIP from K562 (ENCLB912JMG)

description:
https://www.encodeproject.org/experiments/ENCSR096IJV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR096IJV
assay title: iCLIP
assembly: hg19
encode release date: 2014-09-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB912JMG
fragmentation methods: see document
size range: 200-650

source_name: Homo sapiens K562 cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: female

tag: health state

tag: source

tag: url

tag: collection date

value: ENCBS005ZXA at ENCODE; https://www.encodeproject.org/ENCBS005ZXA/


title: AM

description:
Library name: sample 1
10x Genomics

tag: tissue

value: aged


title: Control eCLIP from HepG2 (ENCLB394UKC)

description:
https://www.encodeproject.org/experiments/ENCSR188OHK/
***************
biological replicate number: 1
technical replicate number: 1
description: eCLIP control experiment on HepG2 against TNRC6A
experiment encode accession: ENCSR188OHK
assay title: Control eCLIP
assembly: GRCh38, hg19
encode release date: 2017-11-28
lab: Gene Yeo, UCSD
library encode accession: ENCLB394UKC
fragmentation methods: see document
size range: 175-300

source_name: Homo sapiens HepG2 immortalized cell line

tag: dev stage

value: child

value: 15 year

tag: passage number

tag: lab

value: hepatocellular carcinoma

tag: link

value: ENCBS362ASG at ENCODE; https://www.encodeproject.org/ENCBS362ASG/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/Products/All/HB-8065.aspx


title: 3f5_Participant_048_week_6

value: F


title: iCLIP from K562 (ENCLB576NYG)

description:
https://www.encodeproject.org/experiments/ENCSR096IJV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR096IJV
assay title: iCLIP
assembly: hg19
encode release date: 2014-09-03
lab: Gene Yeo, UCSD
library encode accession: ENCLB576NYG
fragmentation methods: see document
size range: 200-650

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Gene Yeo, UCSD

value: ATCC

value: not applicable

tag: geographic location

value: ENCBS287TWJ at ENCODE; https://www.encodeproject.org/ENCBS287TWJ/


title: PeWA_NegativeControl4

value: eWAT

tag: cell type

tag: strain

tag: genotype

value: WT

tag: age weeks

tag: diet

value: chow

tag: treatment

tag: Sex

value: male


title: 3e2_Participant_070_week_7

tag: age

value: M

tag: timepoint

tag: sample number

value: Peripheral blood


title: PeWA_Let7e4


title: iCLIP from K562 (ENCLB321IJI)

description:
https://www.encodeproject.org/experiments/ENCSR961WWI/
***************
biological replicate number: 2
technical replicate number: 1
description: iCLIP experiment in K562 cells against EIF4G1
experiment encode accession: ENCSR961WWI
assay title: iCLIP
assembly: hg19
encode release date: 2015-05-18
lab: Gene Yeo, UCSD
library encode accession: ENCLB321IJI
fragmentation methods: see document
size range: 170-202

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: female

tag: health state

tag: source

tag: url

tag: collection date

value: ENCBS254KOX at ENCODE; https://www.encodeproject.org/ENCBS254KOX/


title: PeWA_NegativeControl3

tag: tissue

tag: cell type


title: 3d6_Participant_015_week_7

value: F


title: scRNA-seq from forelimb stylopod (ENCLB938HOJ)

description:
https://www.encodeproject.org/experiments/ENCSR847RRR/
***************
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 proximal forelimb
experiment encode accession: ENCSR847RRR
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB938HOJ
size range: 300-600

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

value: forelimb stylopod

value: tissue

tag: note

value: not collected

tag: dev stage

value: embryonic

value: 15 day

tag: lab

value: Barbara Wold, Caltech

value: The Jackson Laboratory

tag: geographic location

tag: link

value: ENCBS854DSW at ENCODE; https://www.encodeproject.org/ENCBS854DSW/


title: scRNA-seq from forelimb (ENCLB042NUM)

description:
https://www.encodeproject.org/experiments/ENCSR792LNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 14.0 day embryonic mouse forelimb
experiment encode accession: ENCSR792LNZ
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB042NUM
size range: 300-600

source_name: Mus musculus strain B6NCrl embryo (14 days) forelimb tissue

value: forelimb

tag: Sex

tag: age

value: 14 day

value: not applicable

value: ENCBS432CRR at ENCODE; https://www.encodeproject.org/ENCBS432CRR/


title: MouseLiver_HFHS_15W

city: Tokyo

first: Nobuhito

last: Goda

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

institute: Waseda University, Faculty of Science and Engineering

description: gene expression after 15 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, 15wks

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: 3d5_Participant_015_week_6

tag: timepoint

tag: sample number

value: Peripheral blood


title: 3d4_Participant_005_week_7

value: M


title: PeWA_Let7e2

source_name: eWAT

value: eWAT

tag: strain

tag: genotype

value: WT

tag: age weeks

tag: diet

value: chow

tag: treatment


title: scRNA-seq from forelimb (ENCLB268GZV)

description:
https://www.encodeproject.org/experiments/ENCSR787QXE/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (version 2 kit) that was sequenced in PE151 format. They are from monocellular suspensions of 8,000 dispersed embryonic limb buds.
experiment encode accession: ENCSR787QXE
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2018-12-19
lab: Barbara Wold, Caltech
library encode accession: ENCLB268GZV
size range: 300-600

source_name: Mus musculus strain B6NCrl embryo (13.5 days) forelimb tissue

value: tissue

tag: biosample encode accession

value: not collected

tag: source

value: Genetically Engineered Mouse Services, California Institute of Technology

tag: collection date

value: ENCBS688AVZ at ENCODE; https://www.encodeproject.org/ENCBS688AVZ/


title: PeWA_Let7e3

tag: tissue

tag: cell type


title: PeWA_Let7e1


title: MouseLiver_HFHS_5W

description: gene expression after 5 wks in HFHS-treated mouse liver

source_name: Liver, 5wks


title: scRNA-seq from forelimb (ENCLB414YSS)

description:
https://www.encodeproject.org/experiments/ENCSR745DNK/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 12.0 day embryonic mouse forelimb
experiment encode accession: ENCSR745DNK
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB414YSS
size range: 300-600

source_name: Mus musculus strain B6NCrl embryo (12 days) forelimb tissue

tag: note

tag: dev stage

value: embryonic

value: 12 day

tag: lab

value: Barbara Wold, Caltech

value: The Jackson Laboratory

tag: geographic location

value: ENCBS958PTQ at ENCODE; https://www.encodeproject.org/ENCBS958PTQ/


title: 3d3_Participant_005_week_6

source_name: Peripheral blood

tag: age

tag: Sex


title: MouseLiver_HFHS_10W

description: gene expression after 10 wks in HFHS-treated mouse liver

source_name: Liver, 10wks

tag: gender


title: PeWA_Let7d2

tag: strain


title: 3d2_Participant_010_week_7

value: F

tag: timepoint

tag: sample number


title: scRNA-seq from forelimb zygopod (ENCLB229VWB)

description:
https://www.encodeproject.org/experiments/ENCSR698TMC/
***************
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 mid forelimb
experiment encode accession: ENCSR698TMC
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB229VWB
size range: 300-600

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

value: forelimb zygopod

value: 15 day

value: not applicable

tag: link

value: ENCBS981UHN at ENCODE; https://www.encodeproject.org/ENCBS981UHN/


title: scRNA-seq from forelimb (ENCLB583JZE)

description:
https://www.encodeproject.org/experiments/ENCSR874BOF/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 10.5 day embryonic mouse forelimb
experiment encode accession: ENCSR874BOF
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB583JZE
size range: 300-600

source_name: Mus musculus strain B6NCrl embryo (10.5 days) forelimb tissue

value: forelimb

value: ENCBS316RLK at ENCODE; https://www.encodeproject.org/ENCBS316RLK/


title: H1299 cells, +rReprimo_0.5 ug/ml, 8 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 7

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

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

tag: treatment

value: recombinant Reprimo protein


title: 3d1_Participant_010_week_6

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

value: Peripheral blood


title: PeWA_NegativeControl2

value: eWAT

tag: genotype

value: WT

tag: age weeks

tag: diet

value: chow

value: male


title: H1299 cells, +rReprimo_0.5 ug/ml, 32 hr

description: Library name: Sample 8


title: PeWA_Let7d1

tag: tissue

tag: cell type


title: scRNA-seq from forelimb (ENCLB635BYD)

description:
https://www.encodeproject.org/experiments/ENCSR642XVO/
***************
biological replicate number: 1
technical replicate number: 1
description: 10X Genomics Chromium 3' single-cell RNA-Seq (v2 kit) of C57Bl6 wild-type 11.0 day embryonic mouse forelimb
experiment encode accession: ENCSR642XVO
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB635BYD
size range: 300-600

source_name: Mus musculus strain B6NCrl embryo (11 days) forelimb tissue

value: tissue

tag: biosample encode accession

tag: note

value: not collected

tag: dev stage

value: embryonic

value: 11 day

tag: source

tag: collection date

value: ENCBS336XKN at ENCODE; https://www.encodeproject.org/ENCBS336XKN/


title: 3c6_Participant_102_week_7

tag: age

tag: Sex

value: F


title: H1299 cells, High cell density, 0 hr

description: Library name: Sample 6


title: PeWA_NegativeControl1

tag: strain


title: scRNA-seq from autopod region (ENCLB428UEV)

description:
https://www.encodeproject.org/experiments/ENCSR416FHN/
***************
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 distal forelimb
experiment encode accession: ENCSR416FHN
assay title: scRNA-seq
assembly: mm10, mm10-minimal
encode release date: 2019-11-14
lab: Barbara Wold, Caltech
library encode accession: ENCLB428UEV
size range: 300-600

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

value: autopod region

value: 15 day

tag: lab

value: Barbara Wold, Caltech

value: The Jackson Laboratory

tag: geographic location

value: ENCBS274QWE at ENCODE; https://www.encodeproject.org/ENCBS274QWE/


title: H1299 cells, Low cell density, 0 hr

description: Library name: Sample 5

tag: cell line


title: 3c5_Participant_102_week_6

tag: timepoint

tag: sample number


title: 3c3_Participant_001_week_6

value: M