title: total RNA-seq from gastrocnemius (ENCLB836GZU)

description:
https://www.encodeproject.org/experiments/ENCSR502ORP/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 18-20 months Female
experiment encode accession: ENCSR502ORP
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB836GZU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female gastrocnemius tissue

value: gastrocnemius

value: tissue

tag: description

value: gastrocnemius_B6Cast F1 PND 18-20 months_Female 03_ENC4_cDNA491

value: unknown

value: not collected

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS216EDC at ENCODE; https://www.encodeproject.org/ENCBS216EDC/


title: total RNA-seq from gastrocnemius (ENCLB731AVX)

status: Public on Nov 04 2021

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR502ORP/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 18-20 months Female
experiment encode accession: ENCSR502ORP
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB731AVX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

value: gastrocnemius_B6Cast F1 PND 18-20 months_Female 04_ENC4_cDNA492

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

tag: age

tag: lab

value: ENCBS655BBB at ENCODE; https://www.encodeproject.org/ENCBS655BBB/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from layer of hippocampus (ENCLB272HRQ)

description:
https://www.encodeproject.org/experiments/ENCSR421HSE/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6CastF1 PND14 3x male
experiment encode accession: ENCSR421HSE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB272HRQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (14 days) layer of hippocampus tissue

value: layer of hippocampus

value: male

value: 14 day

value: ENCBS642ONZ at ENCODE; https://www.encodeproject.org/ENCBS642ONZ/


title: ATAC-seq from natural killer cell (ENCLB686CLI)

description:
https://www.encodeproject.org/experiments/ENCSR044ATC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR044ATC
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB686CLI
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

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

value: natural killer cell

value: primary cell

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS834TFI at ENCODE; https://www.encodeproject.org/ENCBS834TFI/

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


title: R6443

city: Los Angeles

first: Richard

middle: Sungho

last: Ahn

address: 611 Charles E. Young Drive East, UCLA, Boyer Hall, 510C

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

data_processing:
Read quality was checked using FastQC 0.11.8
Reads aligned using STAR 2.7.2a
Count table generated using featureCounts 2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file containing a matrix of counts

molecule: polyA RNA

source_name: Whole Blood

extract_protocol:
RNA was isolated from 1 mL RBC-lysed whole blood samples stored in RNAlater (500 μl). Globin RNA was removed using the GLOBINCLEAR kit.
Libraries were prepared for samples that passed quality control using the KAPA stranded mRNA kit.

tag: subject id

tag: timepoint

tag: cmv dnaemia


title: total RNA-seq from left cerebral cortex (ENCLB027SFK)

description:
https://www.encodeproject.org/experiments/ENCSR496PRU/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 2 months Male L. cortex
experiment encode accession: ENCSR496PRU
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB027SFK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (2 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND 2 months Male 03 left cerebral cortex for Wold biobank

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS350BQS at ENCODE; https://www.encodeproject.org/ENCBS350BQS/


title: R6221


title: R6139


title: DNase-seq from head of caudate nucleus (ENCLB865OBD)

description:
https://www.encodeproject.org/experiments/ENCSR042DVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR042DVU
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB865OBD
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens female adult (74 years) with Alzheimer's disease; head of caudate nucleus tissue

value: head of caudate nucleus

value: female

value: 74 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS465FCE at ENCODE; https://www.encodeproject.org/ENCBS465FCE/

value: Derived from ENCODE donor ENCDO907CMO; https://www.encodeproject.org/ENCDO907CMO/


title: R6089


title: total RNA-seq from left cerebral cortex (ENCLB551WTE)

description:
https://www.encodeproject.org/experiments/ENCSR496PRU/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 2 months Male L. cortex
experiment encode accession: ENCSR496PRU
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB551WTE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND 2 months Male 04 left cerebral cortex for Wold biobank

value: male

value: ENCBS790MBN at ENCODE; https://www.encodeproject.org/ENCBS790MBN/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: DNase-seq from activated regulatory T cell (ENCLB284KBF)

description:
https://www.encodeproject.org/experiments/ENCSR242CLA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR242CLA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB284KBF

source_name: Homo sapiens female adult (21 years) activated regulatory T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: activated regulatory T cell

value: primary cell

value: adult

value: 21 year

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;

value: ENCBS378AUF at ENCODE; https://www.encodeproject.org/ENCBS378AUF/

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


title: total RNA-seq from heart (ENCLB688GAA)

description:
https://www.encodeproject.org/experiments/ENCSR496EJP/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND10 Female heart
experiment encode accession: ENCSR496EJP
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB688GAA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (10 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND10 Female 04 heart for Wold biobank

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS726RAM at ENCODE; https://www.encodeproject.org/ENCBS726RAM/


title: R6078


title: BruUV-seq from HCT116 (ENCLB862VXE)

description:
https://www.encodeproject.org/experiments/ENCSR037CVT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR037CVT
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB862VXE
size range: 400-500

source_name: Homo sapiens HCT116 cell line

tag: line

value: cell line

value: male

value: 48 year

value: Mats Ljungman, UMichigan

value: ATCC

tag: health state

value: colorectal carcinoma

value: ENCBS420EHG at ENCODE; https://www.encodeproject.org/ENCBS420EHG/

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


title: total RNA-seq from heart (ENCLB439QLJ)

description:
https://www.encodeproject.org/experiments/ENCSR496EJP/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND10 Female heart
experiment encode accession: ENCSR496EJP
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB439QLJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: B6Cast F1 PND10 Female 03 heart for Wold biobank

value: ENCBS661GMI at ENCODE; https://www.encodeproject.org/ENCBS661GMI/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: CC003_rep5

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

data_processing:
The PEPATAC pipeline with default parameters was used to perform adapter trimming, alignment, and peaking calling.
Sequenced reads were aligned to CC strain-specific pseudogenomes (Build 37, http://csbio.unc.edu/CCstatus/index.py?run=Pseudo).
Uniquely mapped reads were converted to mm9 genome coordinates, to allow for cross-strain comparisons, and alignments overlapping regions in the mm9 blocklist were removed.
Final alignments were converted to BED format and shifted by -5 and +5 base pairs for the negative and positive strain alignments, respectively.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BED files containing ATAC-seq sequence read alignments to the mm9 genome.

source_name: Airway macrophages

growth_protocol: Female and male CC mice were obtained from the UNC Systems Genetics Core Facility as weanlings and aged on investigator's racks. All experiments were performed when animals were between 10-12 weeks of age.

extract_protocol:
Airway macrophage pellets were gently lysed to release nuclei, which were pelleted by centrifugation and used directly for transposition reaction.
PCR amplification of the transposed DNA fragments was performed to add custom indexing primers. Final libraries were purified by double-sided size selection using Agencourt AMPure XP magnetic beads.

treatment_protocol: Mice were exposed to filtered air or 2 ppm ozone for 3 hours in individual wire-mesh cages without access to food or water, then returned to their home cages for 21 hours before necropsy.

tag: strain

tag: cell type

value: Airway macrophages

tag: treatment

value: 2 ppm ozone for 3 hours


title: CC003_rep3


title: R9414

value: Longterm


title: total RNA-seq from adrenal gland (ENCLB399PGB)

description:
https://www.encodeproject.org/experiments/ENCSR414YUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND14_3x Females 03_ENC4_cDNA448
experiment encode accession: ENCSR414YUZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB399PGB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (14 days) adrenal gland tissue

value: adrenal gland

value: tissue

tag: description

value: B6Cast F1 PND14 3x Females 03 adrenal gland for Wold core

value: female

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS403EIL at ENCODE; https://www.encodeproject.org/ENCBS403EIL/


title: CC003_rep4


title: CC003_rep6


title: R9372


title: BruUV-seq from HCT116 (ENCLB854EKU)

description:
https://www.encodeproject.org/experiments/ENCSR037CVT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR037CVT
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR799MPW
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB854EKU
size range: 400-500

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

tag: source

value: ATCC

value: ENCBS856UHU at ENCODE; https://www.encodeproject.org/ENCBS856UHU/

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


title: CC017_rep1

value: Airway macrophages

value: filtered air for 3 hours


title: CC003_rep2


title: total RNA-seq from adrenal gland (ENCLB599CNL)

description:
https://www.encodeproject.org/experiments/ENCSR414YUZ/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND14_3x Females 03_ENC4_cDNA448
experiment encode accession: ENCSR414YUZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB599CNL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

value: B6Cast F1 PND14 Female 04 adrenal gland for Wold core

value: female

tag: link

value: ENCBS232UIC at ENCODE; https://www.encodeproject.org/ENCBS232UIC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: R9355

value: Longterm


title: TF ChIP-seq from WTC11 (ENCLB365EUQ)

description:
https://www.encodeproject.org/experiments/ENCSR231CZR/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-SOX15 ChIP-seq on human WTC11
experiment encode accession: ENCSR231CZR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB365EUQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SOX15

tag: antibody

value: cell line

tag: biosample encode accession

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS683JWW at ENCODE; https://www.encodeproject.org/ENCBS683JWW/

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


title: 5052_AM

description: total RNA-seq

data_processing:
Sequenced reads were filtered for quality using the FASTX-Toolkit (quality score ≥ 20 for ≥ 90% of bases). Subsequently, TagDust was used to remove adapter contamination.
Sequenced reads were aligned to CC strain-specific pseudogenomes (Build 37, http://csbio.unc.edu/CCstatus/index.py?run=Pseudo) or the C57BL/6J reference genome (mm9), where appropriate, using STAR and quantified with RSEM.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: RNA_results.txt: Tab-delimited text files containing gene abundance estimates; each row provides the gene symbol and transcript ID, while the columns provide various metrics of gene abundance.
Supplementary_files_format_and_content: summary_count_matrix.txt: Tab-delimited text file containing gene abundance estimates, summarized as counts across all samples.

growth_protocol: Female and male mice from 5 CC strains were obtained from the UNC Systems Genetics Core Facility as weanlings and aged on investigator's racks. C57BL/6J mice were purchased from the Jackson Laboratory at 6 weeks of age. All experiments were performed when animals were between 10-12 weeks of age.

extract_protocol:
Pelleted airway macrophages were directly lysed with 350 μL of Buffer RLT, and total RNA was isolated using the Qiagen RNeasy Micro Kit per manufacturer's instructions.
Stranded libraries were prepared using 10 ng of total RNA with the NuGEN Ovation SoLo RNA-Seq Library Preparation Kit.

tag: Sex

value: Male

value: Adult

tag: strain pair

value: C


title: total RNA-seq from adrenal gland (ENCLB646DHH)

description:
https://www.encodeproject.org/experiments/ENCSR495QVE/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND25_ Female 03_ENC4_cDNA452
experiment encode accession: ENCSR495QVE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-10-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB646DHH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (25 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND25 Female 03 adrenal gland for Wold core

tag: dev stage

value: unknown

tag: age

value: 25 day

tag: lab

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS430IOM at ENCODE; https://www.encodeproject.org/ENCBS430IOM/


title: DNase-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB944QVQ)

description:
https://www.encodeproject.org/experiments/ENCSR232FAS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR232FAS
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB944QVQ

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

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS507ZTM at ENCODE; https://www.encodeproject.org/ENCBS507ZTM/

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


title: total RNA-seq from adrenal gland (ENCLB734LZZ)

description:
https://www.encodeproject.org/experiments/ENCSR495QVE/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND25_ Female 03_ENC4_cDNA452
experiment encode accession: ENCSR495QVE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-10-11
lab: Barbara Wold, Caltech
library encode accession: ENCLB734LZZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: B6Cast F1 PND25 Female 04 adrenal gland for Wold core

value: female

value: ENCBS214IJR at ENCODE; https://www.encodeproject.org/ENCBS214IJR/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: R9351

tag: subject id

tag: timepoint

value: Longterm

tag: cmv dnaemia


title: TF ChIP-seq from WTC11 (ENCLB167ESC)

description:
https://www.encodeproject.org/experiments/ENCSR231CZR/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-SOX15 ChIP-seq on human WTC11
experiment encode accession: ENCSR231CZR
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB167ESC
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: line

value: cell line

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS787LWW at ENCODE; https://www.encodeproject.org/ENCBS787LWW/

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


title: total RNA-seq from layer of hippocampus (ENCLB213PFX)

description:
https://www.encodeproject.org/experiments/ENCSR390XPU/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6Cast F1 18 - 20 months female
experiment encode accession: ENCSR390XPU
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB213PFX
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (18-20 months) layer of hippocampus tissue

value: layer of hippocampus

value: hippocampus_B6Cast F1_18 - 20 months_female_6_ENC4_cDNA513

value: unknown

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS528DMR at ENCODE; https://www.encodeproject.org/ENCBS528DMR/


title: 5051_AM

description: total RNA-seq

tag: strain

value: Male

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

value: C


title: CC003_rep1

tag: cell type

value: filtered air for 3 hours


title: R9347

value: Longterm


title: TF ChIP-seq from WTC11 (ENCLB395PRK)

description:
https://www.encodeproject.org/experiments/ENCSR027BEE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CDX4 ChIP-seq on human WTC11
experiment encode accession: ENCSR027BEE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615YWF
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB395PRK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens CDX4

value: cell line

value: male

value: adult

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS376SWR at ENCODE; https://www.encodeproject.org/ENCBS376SWR/


title: 5045_AM

description: total RNA-seq

value: Female

tag: treatment

value: A


title: total RNA-seq from adrenal gland (ENCLB872BDH)

description:
https://www.encodeproject.org/experiments/ENCSR301QXH/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND36_ Male 03_ENC4_cDNA454
experiment encode accession: ENCSR301QXH
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB872BDH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (36 days) adrenal gland tissue

value: adrenal gland

value: tissue

tag: description

value: B6Cast F1 PND36 Male 04 adrenal gland for Wold core

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS414TUZ at ENCODE; https://www.encodeproject.org/ENCBS414TUZ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: TF ChIP-seq from WTC11 (ENCLB476UHF)

description:
https://www.encodeproject.org/experiments/ENCSR027BEE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-CDX4 ChIP-seq on human WTC11
experiment encode accession: ENCSR027BEE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615YWF
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB476UHF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

tag: source

value: ENCBS848ZMN at ENCODE; https://www.encodeproject.org/ENCBS848ZMN/

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


title: 5044_AM

description: total RNA-seq

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

value: D


title: R9340

value: Longterm


title: DNase-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB810ELL)

description:
https://www.encodeproject.org/experiments/ENCSR154NYM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154NYM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB810ELL

source_name: Homo sapiens male adult (36 years) activated CD8-positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 72 hours, 100 ng/mL Interleukin-15 for 72 hours

value: primary cell

value: adult

value: 36 year

value: John Stamatoyannopoulos, UW

value: StemExpress

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:72; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:72; duration_units:hour;

tag: link

value: ENCBS431ENV at ENCODE; https://www.encodeproject.org/ENCBS431ENV/

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


title: total RNA-seq from adrenal gland (ENCLB344FQP)

description:
https://www.encodeproject.org/experiments/ENCSR301QXH/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND36_ Male 03_ENC4_cDNA454
experiment encode accession: ENCSR301QXH
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB344FQP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

value: B6Cast F1 PND36 Male 03 adrenal gland for Wold core

tag: biosample encode accession

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS758KRR at ENCODE; https://www.encodeproject.org/ENCBS758KRR/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: R8942

value: Longterm


title: 5042_AM

description: total RNA-seq

tag: Sex

value: Female

value: Adult

value: Airway macrophages

value: filtered air for 3 hours

value: D


title: 5036_AM

description: total RNA-seq

value: Male

tag: strain pair


title: total RNA-seq from layer of hippocampus (ENCLB800KWO)

description:
https://www.encodeproject.org/experiments/ENCSR292LSH/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6CastF1 PND25 male
experiment encode accession: ENCSR292LSH
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB800KWO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (25 days) layer of hippocampus tissue

value: layer of hippocampus

value: male

tag: dev stage

value: 25 day

value: ENCBS609MWU at ENCODE; https://www.encodeproject.org/ENCBS609MWU/


title: Bru-seq from PC-9 (ENCLB975DQC)

description:
https://www.encodeproject.org/experiments/ENCSR223GHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR223GHJ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB975DQC
size range: 400-500

source_name: Homo sapiens PC-9 cell line

value: cell line

value: not collected

value: unknown

tag: age

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS923VFG at ENCODE; https://www.encodeproject.org/ENCBS923VFG/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: ATAC-seq from HCT116 (ENCLB687QNM)

description:
https://www.encodeproject.org/experiments/ENCSR135OML/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR135OML
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB687QNM
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: adult

value: 48 year

tag: lab

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

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

tag: health state

value: colorectal carcinoma

value: ENCBS621BTW at ENCODE; https://www.encodeproject.org/ENCBS621BTW/

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


title: R8500

source_name: Whole Blood

tag: subject id

tag: timepoint

value: Longterm


title: 5035_AM

description: total RNA-seq

value: Male

value: Adult

value: Airway macrophages

value: filtered air for 3 hours

value: C


title: ATAC-seq from HCT116 (ENCLB511AHV)

description:
https://www.encodeproject.org/experiments/ENCSR135OML/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR135OML
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB511AHV
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

tag: line

value: cell line

value: male

value: ENCBS561ALW at ENCODE; https://www.encodeproject.org/ENCBS561ALW/


title: total RNA-seq from adrenal gland (ENCLB983TRB)

description:
https://www.encodeproject.org/experiments/ENCSR288BJQ/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 2 months_Female 03 _ENC4_cDNA460
experiment encode accession: ENCSR288BJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB983TRB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (2 months) adrenal gland tissue

value: adrenal gland

value: tissue

value: B6Cast F1 PND 2 months Female 03 adrenal gland for Wold core

value: female

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS393LTW at ENCODE; https://www.encodeproject.org/ENCBS393LTW/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: 5034_AM

description: total RNA-seq

tag: strain

value: Female

value: Adult

value: B


title: R8247

value: Longterm

tag: cmv dnaemia


title: ATAC-seq from motor neuron (ENCLB334FVD)

description:
https://www.encodeproject.org/experiments/ENCSR131HOY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR131HOY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB334FVD
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens female adult with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iNPC-derived motor neuron

value: adult

value: not collected

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS460SWY at ENCODE; https://www.encodeproject.org/ENCBS460SWY/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: R8052


title: total RNA-seq from adrenal gland (ENCLB209VXH)

description:
https://www.encodeproject.org/experiments/ENCSR288BJQ/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 2 months_Female 03 _ENC4_cDNA460
experiment encode accession: ENCSR288BJQ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB209VXH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

value: B6Cast F1 PND 2 months Female 04 adrenal gland for Wold core

value: female

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS838VBH at ENCODE; https://www.encodeproject.org/ENCBS838VBH/


title: R8515

value: Longterm


title: R9088


title: R8974


title: total RNA-seq from heart (ENCLB171XWQ)

description:
https://www.encodeproject.org/experiments/ENCSR201FJT/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 2 months Male heart
experiment encode accession: ENCSR201FJT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB171XWQ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (2 months) heart tissue

value: heart

value: B6Cast F1 PND 2 months Male 03 heart for Wold biobank

value: male

value: ENCBS154PWG at ENCODE; https://www.encodeproject.org/ENCBS154PWG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: ATAC-seq from regulatory T cell (ENCLB942JVL)

description:
https://www.encodeproject.org/experiments/ENCSR159GFS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR159GFS
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB942JVL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: regulatory T cell

value: primary cell

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS080WVB at ENCODE; https://www.encodeproject.org/ENCBS080WVB/

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


title: R8955


title: total RNA-seq from adrenal gland (ENCLB547CYZ)

description:
https://www.encodeproject.org/experiments/ENCSR300EHA/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND25_Male 03_ENC4_cDNA450
experiment encode accession: ENCSR300EHA
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB547CYZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (25 days) adrenal gland tissue

value: adrenal gland

value: tissue

value: B6Cast F1 PND25 Male 04 adrenal gland for Wold core

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: ENCBS536PZT at ENCODE; https://www.encodeproject.org/ENCBS536PZT/


title: total RNA-seq from adrenal gland (ENCLB269LOP)

description:
https://www.encodeproject.org/experiments/ENCSR300EHA/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND25_Male 03_ENC4_cDNA450
experiment encode accession: ENCSR300EHA
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB269LOP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND25 Male 03 adrenal gland for Wold core

value: male

value: The Jackson Laboratory

value: ENCBS798KOH at ENCODE; https://www.encodeproject.org/ENCBS798KOH/


title: R8002

value: Longterm


title: R8625


title: 5049_AM

description: total RNA-seq

source_name: Airway macrophages

value: Male

value: Adult

tag: cell type

value: Airway macrophages

tag: treatment

value: 2 ppm ozone for 3 hours

value: B


title: total RNA-seq from layer of hippocampus (ENCLB275TNO)

description:
https://www.encodeproject.org/experiments/ENCSR292LSH/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6CastF1 PND25 male
experiment encode accession: ENCSR292LSH
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB275TNO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

tag: description

tag: source

value: ENCBS049EMJ at ENCODE; https://www.encodeproject.org/ENCBS049EMJ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from layer of hippocampus (ENCLB032DWG)

description:
https://www.encodeproject.org/experiments/ENCSR390XPU/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6Cast F1 18 - 20 months female
experiment encode accession: ENCSR390XPU
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB032DWG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: tissue

value: hippocampus_B6Cast F1_18 - 20 months_female_7_ENC4_cDNA514

value: female

value: unknown

value: 18-20 month

tag: link

value: ENCBS953PDK at ENCODE; https://www.encodeproject.org/ENCBS953PDK/


title: 5043_AM

description: total RNA-seq

value: Female

value: A


title: total RNA-seq from heart (ENCLB351BOU)

description:
https://www.encodeproject.org/experiments/ENCSR201FJT/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 2 months Male heart
experiment encode accession: ENCSR201FJT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB351BOU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: B6Cast F1 PND 2 months Male 04 heart for Wold biobank

tag: biosample encode accession

value: male

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS297GPP at ENCODE; https://www.encodeproject.org/ENCBS297GPP/


title: R8781

value: Longterm


title: total RNA-seq from gastrocnemius (ENCLB731MQB)

description:
https://www.encodeproject.org/experiments/ENCSR095VGF/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 18-20 months Male
experiment encode accession: ENCSR095VGF
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB731MQB
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male gastrocnemius tissue

value: gastrocnemius

value: gastrocnemius_B6Cast F1 PND 18-20 months_Male 03_ENC4_cDNA489

tag: Sex

value: ENCBS752ONG at ENCODE; https://www.encodeproject.org/ENCBS752ONG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: DNase-seq from central memory CD8-positive, alpha-beta T cell (ENCLB126RNI)

description:
https://www.encodeproject.org/experiments/ENCSR160VHJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR160VHJ
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB126RNI

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

value: primary cell

value: adult

value: 36 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS963HDP at ENCODE; https://www.encodeproject.org/ENCBS963HDP/

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


title: 5030_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

tag: strain pair

value: A


title: 5031_AM

description: total RNA-seq

value: B


title: 5040_AM

description: total RNA-seq

value: Male

value: D


title: Bru-seq from OCI-LY7 (ENCLB412YRW)

description:
https://www.encodeproject.org/experiments/ENCSR121MLV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR121MLV
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB412YRW
size range: 400-500

source_name: Homo sapiens OCI-LY7 cell line

value: cell line

value: male

tag: dev stage

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

value: B cell lymphoma

value: ENCBS199KYH at ENCODE; https://www.encodeproject.org/ENCBS199KYH/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: ATAC-seq from motor neuron (ENCLB163ZBP)

description:
https://www.encodeproject.org/experiments/ENCSR131HOY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR131HOY
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB163ZBP
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iNPC-derived motor neuron

value: female

value: Healthy donor

value: adult

tag: age

value: unknown

value: Michael Snyder, Stanford

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

value: ENCBS927HHK at ENCODE; https://www.encodeproject.org/ENCBS927HHK/

value: Derived from ENCODE donor ENCDO689YDN; https://www.encodeproject.org/ENCDO689YDN/


title: 5029_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

value: filtered air for 3 hours

value: A


title: R7832

value: Longterm


title: 5039_AM

description: total RNA-seq

value: Male

value: 2 ppm ozone for 3 hours

value: C


title: R7830


title: Bru-seq from OCI-LY7 (ENCLB944LIB)

description:
https://www.encodeproject.org/experiments/ENCSR121MLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121MLV
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB944LIB
size range: 400-500

value: cell line

value: male

value: B cell lymphoma

value: 48 year

tag: lab

value: Mats Ljungman, UMichigan

value: DSMZ

value: ENCBS749YAG at ENCODE; https://www.encodeproject.org/ENCBS749YAG/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: 5027_AM

description: total RNA-seq

value: D


title: total RNA-seq from gastrocnemius (ENCLB714CQR)

description:
https://www.encodeproject.org/experiments/ENCSR095VGF/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 18-20 months Male
experiment encode accession: ENCSR095VGF
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB714CQR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: tissue

value: gastrocnemius_B6Cast F1 PND 18-20 months_Male 04_ENC4_cDNA490

value: unknown

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS861KNF at ENCODE; https://www.encodeproject.org/ENCBS861KNF/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from gastrocnemius (ENCLB810ZHG)

description:
https://www.encodeproject.org/experiments/ENCSR102ZZC/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND4 Male
experiment encode accession: ENCSR102ZZC
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB810ZHG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (4 days) gastrocnemius tissue

value: B6Cast F1 PND4 Male 04 gastrocnemius for Wold core

value: 4 day

value: ENCBS659ATN at ENCODE; https://www.encodeproject.org/ENCBS659ATN/


title: R7293

value: Longterm


title: 5025_AM

description: total RNA-seq

value: Male

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours


title: BruUV-seq from PC-3 (ENCLB482CLD)

description:
https://www.encodeproject.org/experiments/ENCSR331BIC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR331BIC
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB482CLD
size range: 400-500

source_name: Homo sapiens PC-3 cell line

value: cell line

value: male

value: adult

value: 62 year

value: Mats Ljungman, UMichigan

value: ATCC

tag: health state

value: grade IV, adenocarcinoma

value: ENCBS301NVX at ENCODE; https://www.encodeproject.org/ENCBS301NVX/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/


title: R7135

tag: subject id


title: total RNA-seq from heart (ENCLB417RBF)

description:
https://www.encodeproject.org/experiments/ENCSR095TCB/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND4 Male heart
experiment encode accession: ENCSR095TCB
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB417RBF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (4 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND4 Male 04 heart for Wold biobank

value: unknown

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS987ISY at ENCODE; https://www.encodeproject.org/ENCBS987ISY/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: DNase-seq from brain (ENCLB794TNI)

description:
https://www.encodeproject.org/experiments/ENCSR330JXM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330JXM
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB794TNI
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens male adult (53 years) brain organoid, 90 days post differentiation, preserved by cryopreservation

value: brain

value: organoid

value: PGP1 derived brain organoid 90 days

value: 53 year

value: Bradley Bernstein, Broad

value: Paola Arlotta

value: ENCBS247YMQ at ENCODE; https://www.encodeproject.org/ENCBS247YMQ/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: R7007

tag: timepoint

value: Longterm


title: BruUV-seq from PC-3 (ENCLB190KCF)

description:
https://www.encodeproject.org/experiments/ENCSR331BIC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR331BIC
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR622SUM
encode release date: 2021-01-14
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB190KCF
size range: 400-500

tag: line

value: cell line

value: male

value: adult

value: 62 year

value: Mats Ljungman, UMichigan

value: ATCC

value: grade IV, adenocarcinoma

value: ENCBS618SEN at ENCODE; https://www.encodeproject.org/ENCBS618SEN/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/


title: 5023_AM

description: total RNA-seq

tag: strain

value: Female

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

value: A


title: 5022_AM

description: total RNA-seq

value: filtered air for 3 hours


title: total RNA-seq from adrenal gland (ENCLB681ZHU)

description:
https://www.encodeproject.org/experiments/ENCSR195UUB/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND10_Female 03_ENC4_cDNA444
experiment encode accession: ENCSR195UUB
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB681ZHU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (10 days) adrenal gland tissue

value: adrenal gland

value: tissue

value: B6Cast F1 PND10 Female 03 adrenal gland for Wold core

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS824HLN at ENCODE; https://www.encodeproject.org/ENCBS824HLN/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: total RNA-seq from heart (ENCLB409RTS)

description:
https://www.encodeproject.org/experiments/ENCSR095TCB/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND4 Male heart
experiment encode accession: ENCSR095TCB
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB409RTS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: B6Cast F1 PND4 Male 03 heart for Wold biobank

value: male

value: 4 day

value: ENCBS148ESM at ENCODE; https://www.encodeproject.org/ENCBS148ESM/


title: R6855

value: Longterm

tag: cmv dnaemia


title: 5048_AM

description: total RNA-seq

value: Male

value: Adult

tag: cell type

value: Airway macrophages

value: filtered air for 3 hours

value: B


title: 5021_AM

description: total RNA-seq

value: Female

tag: treatment


title: 5020_AM

description: total RNA-seq

value: C


title: Bru-seq from PC-9 (ENCLB236ZZL)

description:
https://www.encodeproject.org/experiments/ENCSR223GHJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR223GHJ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB236ZZL
size range: 400-500

source_name: Homo sapiens PC-9 cell line

value: cell line

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS934UTA at ENCODE; https://www.encodeproject.org/ENCBS934UTA/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/


title: ATAC-seq from HCT116 (ENCLB400CYG)

description:
https://www.encodeproject.org/experiments/ENCSR328JGW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR328JGW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB400CYG
fragmentation methods: chemical (Tn5 transposase)
size range: 250-450

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

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS952SXX at ENCODE; https://www.encodeproject.org/ENCBS952SXX/

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


title: total RNA-seq from layer of hippocampus (ENCLB708VBR)

description:
https://www.encodeproject.org/experiments/ENCSR280DCZ/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6CastF1 PND36 female
experiment encode accession: ENCSR280DCZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB708VBR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (36 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

tag: description

value: female

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS151TGO at ENCODE; https://www.encodeproject.org/ENCBS151TGO/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: ATAC-seq from HCT116 (ENCLB980HNB)

description:
https://www.encodeproject.org/experiments/ENCSR328JGW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR328JGW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB980HNB
fragmentation methods: sonication (Bioruptor Pico)
size range: 150-1000

value: cell line

tag: source

value: ENCBS417MYJ at ENCODE; https://www.encodeproject.org/ENCBS417MYJ/


title: ATAC-seq from activated T-helper 17 cell (ENCLB192DWS)

description:
https://www.encodeproject.org/experiments/ENCSR115OIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR115OIV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB192DWS
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: activated T-helper 17 cell

value: primary cell

value: male

value: 50 year

value: Michael Snyder, Stanford

value: StemExpress

tag: link

value: ENCBS269GXO at ENCODE; https://www.encodeproject.org/ENCBS269GXO/

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


title: 5019_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

value: B


title: total RNA-seq from adrenal gland (ENCLB704RAM)

description:
https://www.encodeproject.org/experiments/ENCSR195UUB/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND10_Female 03_ENC4_cDNA444
experiment encode accession: ENCSR195UUB
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB704RAM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

value: B6Cast F1 PND10 Female 04 adrenal gland for Wold core

tag: biosample encode accession

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS622FYD at ENCODE; https://www.encodeproject.org/ENCBS622FYD/


title: R6601

source_name: Whole Blood

value: Longterm


title: ATAC-seq from activated T-helper 17 cell (ENCLB737FLH)

description:
https://www.encodeproject.org/experiments/ENCSR115OIV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR115OIV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB737FLH
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: activated T-helper 17 cell

value: primary cell

tag: Sex

value: male

value: adult

value: 50 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS929WKP at ENCODE; https://www.encodeproject.org/ENCBS929WKP/


title: R6731


title: R6713


title: total RNA-seq from layer of hippocampus (ENCLB213EDM)

description:
https://www.encodeproject.org/experiments/ENCSR280DCZ/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6CastF1 PND36 female
experiment encode accession: ENCSR280DCZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB213EDM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

value: 36 day

value: ENCBS574NYN at ENCODE; https://www.encodeproject.org/ENCBS574NYN/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: WGBS from cerebral cortex (ENCLB136VVL)

description:
https://www.encodeproject.org/experiments/ENCSR277BIL/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse cerebral cortex
experiment encode accession: ENCSR277BIL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB136VVL
fragmentation methods: shearing (Covaris S2)
size range: 180-500

source_name: Mus musculus strain B6NCrl mixed sex adult (54-61 days) cerebral cortex tissue

value: cerebral cortex

value: Cerebral cortex tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS792RNB at ENCODE; https://www.encodeproject.org/ENCBS792RNB/

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


title: 5018_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

tag: strain pair

value: C


title: R6511

value: Longterm


title: WGBS from cerebral cortex (ENCLB706JOT)

description:
https://www.encodeproject.org/experiments/ENCSR277BIL/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse cerebral cortex
experiment encode accession: ENCSR277BIL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB706JOT
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: tissue

tag: dev stage

value: adult


title: 5017_AM

description: total RNA-seq

value: Male

tag: age

value: filtered air for 3 hours

value: B


title: R6233


title: WGBS from cerebral cortex (ENCLB019CMU)

description:
https://www.encodeproject.org/experiments/ENCSR277BIL/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse cerebral cortex
experiment encode accession: ENCSR277BIL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB019CMU
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: cerebral cortex

value: Cerebral cortex tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

tag: lab

value: ENCBS980GHA at ENCODE; https://www.encodeproject.org/ENCBS980GHA/


title: 5016_AM

description: total RNA-seq

value: D


title: R5950


title: ATAC-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB710RYZ)

description:
https://www.encodeproject.org/experiments/ENCSR326ESM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR326ESM
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB710RYZ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (42 years) activated CD8-positive, naive alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads for 24 hours, 50 U/mL Interleukin-2 for 24 hours, 100 ng/mL Interleukin-15 for 24 hours

value: primary cell

value: male

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P60568; treatment_term_name:Interleukin-2; treatment_type:protein; duration:24; duration_units:hour; treatment_term_id:UniProtKB:P40933; treatment_term_name:Interleukin-15; treatment_type:protein; duration:24; duration_units:hour;

value: ENCBS337FXX at ENCODE; https://www.encodeproject.org/ENCBS337FXX/

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


title: BruUV-seq from OCI-LY7 (ENCLB476QUY)

description:
https://www.encodeproject.org/experiments/ENCSR114UOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR114UOQ
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB476QUY
size range: 400-500

value: cell line

value: adult

value: 48 year

value: Mats Ljungman, UMichigan

value: DSMZ

tag: health state

value: B cell lymphoma

value: ENCBS184QSB at ENCODE; https://www.encodeproject.org/ENCBS184QSB/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/


title: BruUV-seq from OCI-LY7 (ENCLB589BVB)

description:
https://www.encodeproject.org/experiments/ENCSR114UOQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR114UOQ
assay title: BruUV-seq
assembly: GRCh38
possible controls: ENCSR121MLV
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB589BVB
size range: 400-500

value: ENCBS389QNU at ENCODE; https://www.encodeproject.org/ENCBS389QNU/


title: R9430

tag: subject id

tag: timepoint

value: Longterm


title: WGBS from cerebral cortex (ENCLB084WKH)

description:
https://www.encodeproject.org/experiments/ENCSR277BIL/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse cerebral cortex
experiment encode accession: ENCSR277BIL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB084WKH
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: cerebral cortex

value: tissue

value: Cerebral cortex tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS980GHA at ENCODE; https://www.encodeproject.org/ENCBS980GHA/

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


title: R5925


title: total RNA-seq from heart (ENCLB218MIN)

description:
https://www.encodeproject.org/experiments/ENCSR083OKX/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND4 Female heart
experiment encode accession: ENCSR083OKX
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB218MIN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (4 days) heart tissue

value: heart

value: B6Cast F1 PND4 Female 03 heart for Wold biobank

value: female

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS502QND at ENCODE; https://www.encodeproject.org/ENCBS502QND/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: 5009_AM

description: total RNA-seq

source_name: Airway macrophages

tag: strain

value: Female

value: Adult

value: Airway macrophages

value: filtered air for 3 hours

value: A


title: 5012_AM

description: total RNA-seq

value: Male

value: 2 ppm ozone for 3 hours

value: B


title: 5008_AM

description: total RNA-seq

value: C


title: R9428

value: Longterm

tag: cmv dnaemia


title: [DRIP-Seq] Human brain pericytes_Ct

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney

description: MACS2 peaks of ChIP-seq data

data_processing:
Library strategy: DRIP-seq
Hisat2 was used to map the data to human reference genome (hg38).
Mapped read were filtered based on a phred scale>=30 and duplicate reads were removed.
Peak calling was performed using MACS2.
Genome_build: Homo sapiens hg38
Supplementary_files_format_and_content: Tabular xls files generated using MACS2.

source_name: Human brain pericytes

growth_protocol: Human neural pericytes were purchased from ScienCell (Carlsbad, CA; #1200). Human neural pericytes were cultured in Dulbecco's Modified Eagle Medium/F12 (DMEM/F12) supplemented with 10% fetal calf serum, recombinant human FGF‐2 20 ng/ml (R&D Systems, 233‐FB), and Antibiotic‐Antimycotic (100×, Life Technologies).

extract_protocol:
After fixation, chromatin was immunoprecipitated using anti-S9.6 (Abcam) and protein G-coated Sepharose beads.
Pure DNA was isolated using the ISOLATE II Genomic DNA Kit and 15–30 ng of size selected DNA fragments were used to produce ChIP-seq libraries (Illumina TruSeq ChIP Library Preparation Kit).

treatment_protocol: In order to simulate the combined effect of absence of mechanical cues and enhanced reductive stress on induction of pro-neural transcription factors, we cultured pericytes in serum-free neurobasal medium (Gibco) containing the reductive N2 supplement (0.25mM transferrin-bound Fe3+, redox potential of Fe3+/Fe2+: +0.77 volts, Gibco) and GlutaMAX (Gibco).

tag: group

value: Control

tag: time

value: 0 min

value: Growth medium


title: total RNA-seq from gastrocnemius (ENCLB686PJU)

description:
https://www.encodeproject.org/experiments/ENCSR367VMG/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND4 Female
experiment encode accession: ENCSR367VMG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB686PJU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (4 days) gastrocnemius tissue

value: gastrocnemius

value: tissue

tag: description

value: B6Cast F1 PND4 Female 04 gastrocnemius for Wold core

value: female

value: unknown

value: 4 day

value: Barbara Wold, Caltech

value: ENCBS519KGT at ENCODE; https://www.encodeproject.org/ENCBS519KGT/


title: [DRIP-Seq] Human brain pericytes_T10

description: MACS2 peaks of ChIP-seq data

value: Transdifferentiating

value: 10 min

tag: treatment

value: N2 medium


title: 5007_AM

description: total RNA-seq

value: Female

value: Adult

tag: cell type

value: Airway macrophages

value: 2 ppm ozone for 3 hours


title: [ChIP-Seq] Human brain pericytes_T10

description: MACS2 peaks of ChIP-seq data

data_processing:
Hisat2 was used to map the data to human reference genome (hg38).
Mapped read were filtered based on a phred scale>=30 and duplicate reads were removed.
Peak calling was performed using MACS2.
Genome_build: Homo sapiens hg38
Supplementary_files_format_and_content: Tabular xls files generated using MACS2.

extract_protocol:
After fixation, chromatin was immunoprecipitated using anti-γH2AX (Abcam) and protein G-coated Sepharose beads.
Pure DNA was isolated using the ISOLATE II Genomic DNA Kit and 15–30 ng of size selected DNA fragments were used to produce ChIP-seq libraries (Illumina TruSeq ChIP Library Preparation Kit).

tag: antibody


title: R9412

value: Longterm


title: R9378


title: 5006_AM

description: total RNA-seq

tag: Sex

value: A


title: [ChIP-Seq] Human brain pericytes_Ct

description: MACS2 peaks of ChIP-seq data

value: Control

value: 0 min

value: Growth medium


title: R9362


title: R9345


title: 5005_AM

description: total RNA-seq

value: Male

value: filtered air for 3 hours

tag: strain pair

value: B


title: 5014_AM

description: total RNA-seq

value: D


title: total RNA-seq from heart (ENCLB491ZYG)

description:
https://www.encodeproject.org/experiments/ENCSR363LZO/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND36 Male heart
experiment encode accession: ENCSR363LZO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB491ZYG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (36 days) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND36 Male 03 heart for Wold biobank

tag: biosample encode accession

value: male

tag: dev stage

value: unknown

value: 36 day

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS001UUS at ENCODE; https://www.encodeproject.org/ENCBS001UUS/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: [ATAC-Seq] Human brain pericytes_T10 replicate

description: MACS2 peaks of ATAC-seq data

data_processing:
Data were analysed using the pipeline for analysis of ATAC-seq in galaxy server with a slight modification.
Hisat2 was used to map the data to human reference genome (hg38).
Mapped read were filtered based on a phred scale>=30 and duplicate reads were removed.
Peak calling was performed using MACS2 and plotHeatmap was used to generated heatmaps of chromatin accesibility landscape.
Genome_build: Homo sapiens hg38
Supplementary_files_format_and_content: Tabular xlsx files generated using MACS2.

extract_protocol:
50,000 nuclei from control and transdifferentiating pericytes were used for ATAC-seq with a slight modification. Due to rapid pace of TD and a requirement for sampling at short intervals (2 min), cell lysis and crude nuclei preparation were done on culture plates and without harvesting the adherent cells.
Transposition Reaction, Purification, and PCR amplification were performed as per method developed by Buenrostro et al (Curr Protoc Mol Biol 2015).
Libraries were prepared using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits.

value: Transdifferentiating

value: 10 min

value: N2 medium


title: [ATAC-Seq] Human brain pericytes_T10

description: MACS2 peaks of ATAC-seq data


title: 5004_AM

description: total RNA-seq

value: Male

tag: age

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours


title: total RNA-seq from adrenal gland (ENCLB523DKI)

description:
https://www.encodeproject.org/experiments/ENCSR270SAI/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND36_Female 03_ENC4_cDNA456
experiment encode accession: ENCSR270SAI
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB523DKI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (36 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND36 Female 03 adrenal gland for Wold core

value: female

tag: lab

value: ENCBS681BGW at ENCODE; https://www.encodeproject.org/ENCBS681BGW/


title: total RNA-seq from heart (ENCLB573SNK)

description:
https://www.encodeproject.org/experiments/ENCSR083OKX/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND4 Female heart
experiment encode accession: ENCSR083OKX
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB573SNK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: tissue

value: B6Cast F1 PND4 Female 04 heart for Wold biobank

value: unknown

value: 4 day

value: ENCBS430MXC at ENCODE; https://www.encodeproject.org/ENCBS430MXC/


title: R9180

tag: subject id

tag: timepoint

value: Longterm


title: R9047

tag: cmv dnaemia


title: 5001_AM

description: total RNA-seq

tag: strain

value: D


title: [ATAC-Seq] Human brain pericytes_T8 replicate

description: MACS2 peaks of ATAC-seq data

tag: group

value: Transdifferentiating

tag: time

value: 8 min

value: N2 medium


title: total RNA-seq from adrenal gland (ENCLB306YZC)

description:
https://www.encodeproject.org/experiments/ENCSR270SAI/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND36_Female 03_ENC4_cDNA456
experiment encode accession: ENCSR270SAI
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB306YZC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: description

value: B6Cast F1 PND36 Female 04 adrenal gland for Wold core

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS668OIM at ENCODE; https://www.encodeproject.org/ENCBS668OIM/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: 5000_AM

description: total RNA-seq

value: Male

value: Adult

tag: cell type

value: Airway macrophages

tag: treatment

value: filtered air for 3 hours


title: total RNA-seq from gastrocnemius (ENCLB745VFE)

description:
https://www.encodeproject.org/experiments/ENCSR367VMG/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND4 Female
experiment encode accession: ENCSR367VMG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB745VFE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: tissue

value: B6Cast F1 PND4 Female 03 gastrocnemius for Wold core

tag: Sex

value: female

value: unknown

value: 4 day

value: ENCBS559PTX at ENCODE; https://www.encodeproject.org/ENCBS559PTX/


title: [ATAC-Seq] Human brain pericytes_T6 replicate

description: MACS2 peaks of ATAC-seq data

value: Transdifferentiating

value: 6 min

value: N2 medium


title: R7797

value: Longterm


title: total RNA-seq from layer of hippocampus (ENCLB965UVE)

description:
https://www.encodeproject.org/experiments/ENCSR338WMA/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6CastF1 PND25 female
experiment encode accession: ENCSR338WMA
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB965UVE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (25 days) layer of hippocampus tissue

value: layer of hippocampus

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS690ORU at ENCODE; https://www.encodeproject.org/ENCBS690ORU/


title: WGBS from olfactory bulb (ENCLB240OWU)

description:
https://www.encodeproject.org/experiments/ENCSR334YHO/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse olfactory bulb
experiment encode accession: ENCSR334YHO
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB240OWU
fragmentation methods: shearing (Covaris S2)
size range: 180-500

source_name: Mus musculus strain B6NCrl mixed sex adult (54-61 days) olfactory bulb tissue

value: olfactory bulb

value: Olfactory bulb tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River.

value: pooled male and female

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

tag: health state

value: healthy

value: ENCBS363WHQ at ENCODE; https://www.encodeproject.org/ENCBS363WHQ/

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


title: 4999_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

value: filtered air for 3 hours

tag: strain pair

value: C


title: [ATAC-Seq] Human brain pericytes_T8

description: MACS2 peaks of ATAC-seq data

value: Transdifferentiating

value: 8 min

value: N2 medium


title: [ATAC-Seq] Human brain pericytes_T6

description: MACS2 peaks of ATAC-seq data

value: 6 min


title: total RNA-seq from layer of hippocampus (ENCLB898RCS)

description:
https://www.encodeproject.org/experiments/ENCSR338WMA/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6CastF1 PND25 female
experiment encode accession: ENCSR338WMA
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB898RCS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: layer of hippocampus

value: tissue

tag: biosample encode accession

value: female

tag: dev stage

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS369QTC at ENCODE; https://www.encodeproject.org/ENCBS369QTC/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: 4998_AM

description: total RNA-seq

value: Female

value: Adult

value: A


title: total RNA-seq from heart (ENCLB697VFI)

description:
https://www.encodeproject.org/experiments/ENCSR363LZO/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND36 Male heart
experiment encode accession: ENCSR363LZO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB697VFI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: heart

value: B6Cast F1 PND36 Male 04 heart for Wold biobank

value: male

value: 36 day

tag: source

tag: link

value: ENCBS378WXL at ENCODE; https://www.encodeproject.org/ENCBS378WXL/


title: WGBS from olfactory bulb (ENCLB334PBJ)

description:
https://www.encodeproject.org/experiments/ENCSR334YHO/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse olfactory bulb
experiment encode accession: ENCSR334YHO
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB334PBJ
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: olfactory bulb

value: Olfactory bulb tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River.

value: pooled male and female

value: healthy

value: adult

tag: age

tag: lab

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS910QRJ at ENCODE; https://www.encodeproject.org/ENCBS910QRJ/

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


title: [ATAC-Seq] Human brain pericytes_T4 replicate

description: MACS2 peaks of ATAC-seq data

value: Transdifferentiating

value: N2 medium


title: 4995_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

value: 2 ppm ozone for 3 hours

value: A


title: 4997_AM

description: total RNA-seq

value: C


title: R7389

tag: subject id

tag: timepoint

value: Longterm


title: R7205

tag: cmv dnaemia


title: WGBS from olfactory bulb (ENCLB247AFU)

description:
https://www.encodeproject.org/experiments/ENCSR334YHO/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse olfactory bulb
experiment encode accession: ENCSR334YHO
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB247AFU
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: olfactory bulb

value: tissue

value: Olfactory bulb tissue from 16 adult P54-61 day old mice. C57BL/6 from Charles River.

value: ENCBS363WHQ at ENCODE; https://www.encodeproject.org/ENCBS363WHQ/


title: R7277


title: WGBS from olfactory bulb (ENCLB738NJW)

description:
https://www.encodeproject.org/experiments/ENCSR334YHO/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse olfactory bulb
experiment encode accession: ENCSR334YHO
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB738NJW
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: pooled male and female

value: healthy

value: adult

value: Len Pennacchio, LBNL


title: [ATAC-Seq] Human brain pericytes_T4

description: MACS2 peaks of ATAC-seq data

tag: group

value: Transdifferentiating


title: 4988_AM

description: total RNA-seq

tag: strain

value: Male

value: filtered air for 3 hours

value: B


title: [ATAC-Seq] Human brain pericytes_T2 replicate

description: MACS2 peaks of ATAC-seq data

tag: time

value: 2 min

value: N2 medium


title: R7867


title: R7140


title: 4986_AM

description: total RNA-seq

value: Adult

tag: cell type

value: Airway macrophages

value: 2 ppm ozone for 3 hours


title: R7086

value: Longterm


title: total RNA-seq from left cerebral cortex (ENCLB161LOR)

description:
https://www.encodeproject.org/experiments/ENCSR248KDJ/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND25 Female L. cortex
experiment encode accession: ENCSR248KDJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB161LOR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (25 days) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

tag: description

value: B6Cast F1 PND25 Female 04 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 25 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS168HOX at ENCODE; https://www.encodeproject.org/ENCBS168HOX/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: 4985_AM

description: total RNA-seq

tag: Sex

value: Male

tag: treatment

value: filtered air for 3 hours

value: D


title: [ATAC-Seq] Human brain pericytes_Ct

description: MACS2 peaks of ATAC-seq data

value: Control

value: 0 min

value: Growth medium


title: total RNA-seq from left cerebral cortex (ENCLB760PKR)

description:
https://www.encodeproject.org/experiments/ENCSR248KDJ/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND25 Female L. cortex
experiment encode accession: ENCSR248KDJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB760PKR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND25 Female 03 left cerebral cortex for Wold biobank

value: ENCBS532TZI at ENCODE; https://www.encodeproject.org/ENCBS532TZI/


title: R6893

value: Longterm


title: 4981_AM

description: total RNA-seq

value: Female

value: Adult

value: Airway macrophages

tag: strain pair

value: A


title: [ATAC-Seq] Human brain pericytes_Ct replicate

description: MACS2 peaks of ATAC-seq data


title: total RNA-seq from gastrocnemius (ENCLB714HQJ)

description:
https://www.encodeproject.org/experiments/ENCSR238FNF/
***************
biological replicate number: 2
technical replicate number: 1
description: :gastrocnemius B6Cast F1 PND10 Female
experiment encode accession: ENCSR238FNF
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB714HQJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (10 days) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6Cast F1 PND10 Female 04 gastrocnemius for Wold core

tag: biosample encode accession

value: female

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: ENCBS900JGS at ENCODE; https://www.encodeproject.org/ENCBS900JGS/


title: 4984_AM

description: total RNA-seq

value: Male

value: 2 ppm ozone for 3 hours

value: D


title: R9204

value: Baseline


title: total RNA-seq from adrenal gland (ENCLB906GVH)

description:
https://www.encodeproject.org/experiments/ENCSR158WTT/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND4_Female 03_ENC4_cDNA440
experiment encode accession: ENCSR158WTT
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB906GVH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (4 days) adrenal gland tissue

value: adrenal gland

value: B6Cast F1 PND4 Female 04 adrenal gland for Wold core

tag: dev stage

value: 4 day

value: The Jackson Laboratory

value: ENCBS118MVG at ENCODE; https://www.encodeproject.org/ENCBS118MVG/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: R9146


title: scRNAseq-HL-E125-WT

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

data_processing: No processed data submitted to GEO

source_name: Embryonic Limb Bud

growth_protocol: Limbs from 40-45 somite-stage (E12.5) mouse embryos were microdissected in PBS.

extract_protocol:
Two replicates of fore and hindlimb buds of E12.5 wildtype embryos and hindlimb buds of mutant embryos (Pitx1Pen-/Pen-, Pitx1-/-) were micro-dissected and incubated for 12 minutes in 400ul trypsin-EDTA 0.25% (Thermo Fischer Scientific, 25300062), supplemented with 40ul of 5% BSA. During incubation tissues were disrupted by pipetting after 6 minutes of incubation and at the end of the 12 minutes. Trypsin was then inactivated by adding 2x volume of 5% BSA and single cell suspension was obtained by passing cells in a 40um cell strainer. Cells were then spun at 250g for 5 minutes at 4° and resuspended in 1%BSA in PBS. Cells were then counted using an automatized cell counter and a 1% BSA 700cells/ul suspension was prepared. 10ul of this solution was used as input for the 10X Genomics library preparation.
Single-cell libraries were prepared using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 following the manufacture’s protocol (10X Genomics, PN-1000075). Briefly, Gel beads in EMulsion (GEMs) are generated by combining Single Cell 3ʹ v3 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Chip B. Incubation of the GEMs produced from the poly-adenylated mRNA barcoded, full-length cDNA. Immediately, gel beads are dissolved and cDNA is amplified via PCR followed by library construction and sequencing. Libraries were paired-end sequenced on a HiSeq 4000. On average, 7000 cells were loaded on the Chromium Chip and between 25000-35000 mean reads were obtained.

tag: tissue

value: Embryonic Limb Bud

tag: genotype

value: wildtype


title: 4980_AM

description: total RNA-seq

value: Female

tag: age

value: Adult

value: Airway macrophages

value: A


title: scRNAseq-HL-E125-delPitx1


title: PBMC, VP3

city: nanchang

first: shulan

last: zhang

state: Jiangxi

address: NO.1 minde Road

country: China

institute: The Second Affiliated Hospital of Nanchang University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM for each Sample

source_name: veinal blood

extract_protocol:
After taking venous blood, PBMC was rapidly extracted within 2 hours.Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PBMC

value: veinal blood

tag: condition

value: non-segmental vitiligo

value: 20 years old

value: M


title: PBMC, VP4

value: 32 years old


title: total RNA-seq from gastrocnemius (ENCLB450QYY)

description:
https://www.encodeproject.org/experiments/ENCSR238FNF/
***************
biological replicate number: 1
technical replicate number: 1
description: :gastrocnemius B6Cast F1 PND10 Female
experiment encode accession: ENCSR238FNF
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB450QYY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: gastrocnemius

value: tissue

value: B6Cast F1 PND10 Female 03 gastrocnemius for Wold core

value: female

value: unknown

value: 10 day

tag: lab

value: Barbara Wold, Caltech

tag: source

tag: link

value: ENCBS927BKO at ENCODE; https://www.encodeproject.org/ENCBS927BKO/


title: [ATAC-Seq] Human brain pericytes_T2

description: MACS2 peaks of ATAC-seq data

tag: group

value: Transdifferentiating

value: 2 min

value: N2 medium


title: R9018

tag: subject id

tag: timepoint

value: Baseline

tag: cmv dnaemia


title: PBMC, VP5

tag: cell type

value: PBMC

value: veinal blood

value: 27 years old

value: F


title: R8923


title: PBMC, VP2

value: non-segmental vitiligo

value: 31 years old

tag: Sex


title: total RNA-seq from left cerebral cortex (ENCLB000LSZ)

description:
https://www.encodeproject.org/experiments/ENCSR219ZXZ/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 2 months Female L. cortex
experiment encode accession: ENCSR219ZXZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB000LSZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J female (2 months) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

tag: description

value: B6Cast F1 PND 2 months Female 04 left cerebral cortex for Wold biobank

value: 2 month

value: The Jackson Laboratory

value: ENCBS235YYJ at ENCODE; https://www.encodeproject.org/ENCBS235YYJ/

value: Derived from ENCODE donor ENCDO509HIY; https://www.encodeproject.org/ENCDO509HIY/


title: PBMC, VP1

value: 18 years old

value: M


title: total RNA-seq from left cerebral cortex (ENCLB414FBC)

description:
https://www.encodeproject.org/experiments/ENCSR219ZXZ/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 2 months Female L. cortex
experiment encode accession: ENCSR219ZXZ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB414FBC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: B6Cast F1 PND 2 months Female 03 left cerebral cortex for Wold biobank

value: female

value: unknown

value: Barbara Wold, Caltech

value: ENCBS121OPX at ENCODE; https://www.encodeproject.org/ENCBS121OPX/


title: R6207

source_name: Whole Blood

value: Longterm