title: total RNA-seq from H1 (ENCLB029TLD)

description:
https://www.encodeproject.org/experiments/ENCSR588EJX/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP_H1ES
experiment encode accession: ENCSR588EJX
assay title: total RNA-seq
encode release date: 2021-10-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB029TLD
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

source_name: Homo sapiens H1 cell line

tag: line

value: cell line

value: male

value: healthy

value: embryonic

value: unknown

value: René Maehr

value: ENCBS872CFG at ENCODE; https://www.encodeproject.org/ENCBS872CFG/

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


title: Histone ChIP-seq from motor neuron (ENCLB329VIY)

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/ENCSR312HLG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR312HLG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR175HRD
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB329VIY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens male child (6 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

tag: antibody

value: motor neuron

value: in vitro differentiated cells

tag: description

value: iPSC-derived motor neuron

tag: biosample encode accession

tag: Sex

tag: dev stage

value: child

tag: age

value: 6 year

tag: lab

value: Michael Snyder, Stanford

tag: source

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

tag: health state

value: Healthy donor

tag: link

value: ENCBS409BIE at ENCODE; https://www.encodeproject.org/ENCBS409BIE/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: GM DNase-seq from K562 (ENCLB513FIZ)

description:
https://www.encodeproject.org/experiments/ENCSR529ATP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR529ATP
assay title: GM DNase-seq
assembly: GRCh38
encode release date: 2019-01-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB513FIZ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens K562 cell line genetically modified (deletion) using TALEN

value: cell line

value: TALEN-mediated homozygous DHS deletion in K562.

value: female

value: adult

value: 53 year

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: chronic myelogenous leukemia (CML)

value: ENCBS031FXR at ENCODE; https://www.encodeproject.org/ENCBS031FXR/

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


title: total RNA-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB891JBP)

description:
https://www.encodeproject.org/experiments/ENCSR538FRP/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD8+ cell, activated Day 7
experiment encode accession: ENCSR538FRP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB891JBP
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

molecule: total RNA

source_name: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell

value: primary cell

value: Memory CD8+ cell, activated Day 7

value: male

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS015SJV at ENCODE; https://www.encodeproject.org/ENCBS015SJV/

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


title: RNA-DNA SPRITE 028

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

description:
RNA and genomic DNA
Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing
HL522DSXX.all.20190924.clusters.gz

data_processing:
Adapters were trimmed from raw paired-end fastq files using Trim Galore! v0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and assessed with Fastqc v0.11.9. Subsequently, the DPM (GATCGGAAGAG) and RPM (ATCAGCACTTA) sequences are trimmed using Cutadapt v2.5 from the 5’ end of Read 1 along with the 3’ end DPM sequences that result from short reads being read through into the barcode (GGTGGTCTTT, GCCTCTTGTT, CCAGGTATTT, TAAGAGAGTT, TTCTCCTCTT, ACCCTCGATT). The additional trimming helps improve read mapping in the end-to-end alignment mode. The SPRITE barcodes of trimmed reads are identified with Barcode ID v1.2.0 (https://github.com/GuttmanLab/sprite2.0-pipeline) and the ligation efficiency is assessed. Reads with an RPM or a DPM barcode are split into two separate files, to process RNA and DNA reads individually downstream, respectively.
RNA reads were aligned to GRCm38.p6 with the Ensembl GRCm38 v95 gene model annotation using Hisat2 v2.1.01 with a high penalty for soft-clipping --sp 1000,1000. Unmapped and reads with a low MapQ score (samtools view -bq 20) were filtered out for downstream realignment. Mapped reads were annotated for gene exons and introns with the featureCounts tool from the subread package v1.6.4 using Ensembl GRCm38 v95 gene model annotation and the Repeat and Transposable element annotation from the Hammel lab. Filtered reads were subsequently realigned to our custom collection of repeat sequences using Bowtie v2.3.5, only keeping mapped and primary alignment reads.
DNA reads were aligned to GRCm38.p6 using Bowtie2 v2.3.5, filtering out unmapped and reads with a low MapQ score (samtools view -bq 20). Data generated in F1 hybrid cells (pSM33: C57BL/6 × 129SV-Jae or pSM44: 129 × castaneous) were assigned the allele of origin using SNPsplit v0.3.4. RepeatMasker defined regions with milliDev <= 140 along with blacklisted v2 regions were filtered out using Bedtools v2.29.0.
RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. MultiQC v1.6 was used to aggregate all reports.
Genome_build: mm10
Supplementary_files_format_and_content: RNA and DNA reads were merged, and a cluster file was generated for all downstream analysis. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments.

organism: Mus musculus

source_name: Mouse Embryonic Stem cells

growth_protocol: All mouse ES cell lines were cultured in serum-free 2i/LIF medium

extract_protocol:
Cells were lifted using trypsinization and were crosslinked in suspension at room temperature with 2mM disuccinimidyl glutarate (DSG) for 45 minutes followed by 3% Formaldehyde for 10 minutes to preserve RNA and DNA interactions in situ.
After lysis of cells, nuclei were lightly sonicated. DNA was DNAse digested to an average size of approximately 150-1000 bp in length. Crosslinked complexes of interacting DNA, RNA, and protein were isolated on NHS beads, RNA and DNA ends were repaired, DNA was dA-tailed to generate a protruding 3’ A-base for ligation of barcodes, RNA was ligated with a partially ssRNA-dsDNA adaptor for ligation of barcodes, and were then split-pool tagged with a series of barcodes over multiple rounds of split-and-pool tagging. A distinct RNA adaptor was ligated to RNA to flag a molecule as RNA rather than DNA. This adaptor contains a shared overhang that allows for simultaneous tagging of RNA and DNA during the split-and-pool tagging process. Reverse transcription was performed to convert RNA into cDNA. After split-and-pool tagging, crosslinks were reversed, the DNA/RNA was isolated, was amplified 8-12 cycles using standard Illumina library prep (dual index), and purified using SPRI beads and gel cut. Libraries were sequenced on a NovaSeq S4 chip (150x150 read length).

tag: cell line

tag: cell type

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: total RNA-seq from gastrocnemius (ENCLB131QOY)

description:
https://www.encodeproject.org/experiments/ENCSR791UVS/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 2 months Female
experiment encode accession: ENCSR791UVS
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB131QOY
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) gastrocnemius tissue

value: gastrocnemius

value: tissue

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

value: female

value: unknown

value: 2 month

value: The Jackson Laboratory

value: ENCBS821KNX at ENCODE; https://www.encodeproject.org/ENCBS821KNX/

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


title: Histone ChIP-seq from motor neuron (ENCLB251MOA)

description:
https://www.encodeproject.org/experiments/ENCSR312HLG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR312HLG
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR175HRD
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB251MOA
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS182GDQ at ENCODE; https://www.encodeproject.org/ENCBS182GDQ/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: total RNA-seq from gastrocnemius (ENCLB948STB)

description:
https://www.encodeproject.org/experiments/ENCSR791UVS/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 2 months Female
experiment encode accession: ENCSR791UVS
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB948STB
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 PND 2 months Female 04 gastrocnemius for Wold core

value: female

value: Barbara Wold, Caltech

value: ENCBS523ZPG at ENCODE; https://www.encodeproject.org/ENCBS523ZPG/


title: WGBS from large intestine (ENCLB848OOV)

description:
https://www.encodeproject.org/experiments/ENCSR784VGW/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse large intestine
experiment encode accession: ENCSR784VGW
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB848OOV
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: large intestine

value: Large intestine tissue from 8 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

value: healthy

value: ENCBS118OIK at ENCODE; https://www.encodeproject.org/ENCBS118OIK/

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


title: total RNA-seq from H1 (ENCLB824TWV)

description:
https://www.encodeproject.org/experiments/ENCSR588EJX/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP_H1ES
experiment encode accession: ENCSR588EJX
assay title: total RNA-seq
encode release date: 2021-10-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB824TWV
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: cell line

value: male

value: embryonic

value: not collected

value: René Maehr

value: ENCBS667PZC at ENCODE; https://www.encodeproject.org/ENCBS667PZC/

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


title: ATAC-seq from motor neuron (ENCLB851BFG)

description:
https://www.encodeproject.org/experiments/ENCSR410DWV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR410DWV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB851BFG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iNPC-derived motor neuron

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS435KUD at ENCODE; https://www.encodeproject.org/ENCBS435KUD/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: total RNA-seq from heart (ENCLB712KKN)

description:
https://www.encodeproject.org/experiments/ENCSR791IFR/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND36 Female heart
experiment encode accession: ENCSR791IFR
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB712KKN
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) heart tissue

value: heart

value: tissue

value: B6Cast F1 PND36 Female 04 heart for Wold biobank

value: female

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS578XBR at ENCODE; https://www.encodeproject.org/ENCBS578XBR/

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


title: total RNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB974ZSN)

description:
https://www.encodeproject.org/experiments/ENCSR533TOW/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ T cells, activated day 2
experiment encode accession: ENCSR533TOW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB974ZSN
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: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS223BQO at ENCODE; https://www.encodeproject.org/ENCBS223BQO/

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


title: ATAC-seq from motor neuron (ENCLB679CNG)

description:
https://www.encodeproject.org/experiments/ENCSR410DWV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR410DWV
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB679CNG
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: motor neuron

value: in vitro differentiated cells

value: iNPC-derived motor neuron

value: Healthy donor

value: child

value: 6 year

value: Michael Snyder, Stanford

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

value: ENCBS942UWC at ENCODE; https://www.encodeproject.org/ENCBS942UWC/

value: Derived from ENCODE donor ENCDO022IAQ; https://www.encodeproject.org/ENCDO022IAQ/


title: TF ChIP-seq from HepG2 (ENCLB058JGQ)

description:
https://www.encodeproject.org/experiments/ENCSR488ZNK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR488ZNK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB058JGQ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF646

value: cell line

value: male

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS464SUO at ENCODE; https://www.encodeproject.org/ENCBS464SUO/

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


title: total RNA-seq from heart (ENCLB763YLJ)

description:
https://www.encodeproject.org/experiments/ENCSR791IFR/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND36 Female heart
experiment encode accession: ENCSR791IFR
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB763YLJ
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 PND36 Female 03 heart for Wold biobank

value: female

value: unknown

value: 36 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS170UDX at ENCODE; https://www.encodeproject.org/ENCBS170UDX/

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


title: total RNA-seq from H1 (ENCLB919QDK)

description:
https://www.encodeproject.org/experiments/ENCSR588EJX/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP_H1ES
experiment encode accession: ENCSR588EJX
assay title: total RNA-seq
encode release date: 2021-10-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB919QDK
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: cell line

value: male

value: embryonic

value: not collected

value: René Maehr

value: healthy

value: ENCBS664DSZ at ENCODE; https://www.encodeproject.org/ENCBS664DSZ/

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


title: WGBS from large intestine (ENCLB397CLV)

description:
https://www.encodeproject.org/experiments/ENCSR784VGW/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse large intestine
experiment encode accession: ENCSR784VGW
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB397CLV
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: large intestine

value: tissue

value: Large intestine tissue from 8 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

value: ENCBS254UEN at ENCODE; https://www.encodeproject.org/ENCBS254UEN/

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


title: TF ChIP-seq from HepG2 (ENCLB686CNP)

description:
https://www.encodeproject.org/experiments/ENCSR488ZNK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR488ZNK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB686CNP
fragmentation methods: sonication (generic)

value: cell line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS354GCS at ENCODE; https://www.encodeproject.org/ENCBS354GCS/

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


title: RNA-DNA SPRITE 026

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 032


title: WGBS from large intestine (ENCLB899MHU)

description:
https://www.encodeproject.org/experiments/ENCSR784VGW/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse large intestine
experiment encode accession: ENCSR784VGW
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB899MHU
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: large intestine

value: tissue

value: Large intestine tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: healthy

value: ENCBS118OIK at ENCODE; https://www.encodeproject.org/ENCBS118OIK/


title: M33

city: Chengdu

first: Chen

last: Haining

address: Renminnan Road

country: China

institute: Sichuan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using STAR(2.7.3a)
Raw counts were calculated using featureCounts(v1.5.3)
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNAs were extracted by TRIzol Reagent (Thermo Fisher Scientific, 15596018) following acquirement of MDR cancer cells and MDR persister cancer cells. Subsequently, RNA samples were sent to Novogene Technology Co., Ltd. (Beijing, P.R. China) for high-throughput sequencing analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human multi-drug resistant cancer cell line

tag: cell state

value: persister

tag: serial number

value: Repeat samples in parallel #3


title: total RNA-seq from HFFc6 (ENCLB807RXC)

description:
https://www.encodeproject.org/experiments/ENCSR420ZKB/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 13 minute fragmentation
experiment encode accession: ENCSR420ZKB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB807RXC
fragmentation methods: chemical (NEBNext Ultra II Directional)
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: Homo sapiens HFFc6 cell line, preserved by flash-freezing

extract_protocol:
extraction method: Animal tissue kit (Norgen Biotek cat#: 25700)
extraction protocol: https://www.encodeproject.org/documents/33482357-bcb8-43d0-ac76-d58ff785b710/@@download/attachment/Norgen_Animal-Tissue-RNA-Purification-Kit-Insert-PI25700-8-M14.pdf, general protocol: https://www.encodeproject.org/documents/01a7807d-0d18-4a4a-ac90-f4056a25a681/@@download/attachment/manualE7760_Directional_RNA_library_kit_October30_2018.pdf

tag: line

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: normal

tag: passage number

value: ENCBS252IDB at ENCODE; https://www.encodeproject.org/ENCBS252IDB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: RNA-DNA SPRITE 025

description:
RNA and genomic DNA
Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing
HL522DSXX.all.20190924.clusters.gz

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 027


title: M32

value: Repeat samples in parallel #2


title: WGBS from large intestine (ENCLB865DZQ)

description:
https://www.encodeproject.org/experiments/ENCSR784VGW/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse large intestine
experiment encode accession: ENCSR784VGW
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB865DZQ
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: large intestine

value: tissue

tag: description

value: Large intestine tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

tag: biosample encode accession

value: pooled male and female

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS254UEN at ENCODE; https://www.encodeproject.org/ENCBS254UEN/

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


title: WGBS from spleen (ENCLB438MLC)

description:
https://www.encodeproject.org/experiments/ENCSR662VFL/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse spleen
experiment encode accession: ENCSR662VFL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB438MLC
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: spleen

value: Spleen tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

tag: Sex

tag: dev stage

value: ENCBS750WUM at ENCODE; https://www.encodeproject.org/ENCBS750WUM/


title: WGBS from spleen (ENCLB377XYE)

description:
https://www.encodeproject.org/experiments/ENCSR662VFL/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse spleen
experiment encode accession: ENCSR662VFL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB377XYE
fragmentation methods: shearing (Covaris S2)
size range: 180-500

tag: age

tag: lab

value: ENCBS721KBQ at ENCODE; https://www.encodeproject.org/ENCBS721KBQ/


title: M02

value: human multi-drug resistant cancer cell line

value: normal


title: total RNA-seq from HFFc6 (ENCLB468ASC)

description:
https://www.encodeproject.org/experiments/ENCSR420ZKB/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 13 minute fragmentation
experiment encode accession: ENCSR420ZKB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB468ASC
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: newborn

value: 0 year

value: Job Dekker, UMass

tag: source

value: Job Dekker

tag: health state

value: ENCBS508JLR at ENCODE; https://www.encodeproject.org/ENCBS508JLR/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: WGBS from spleen (ENCLB369LKS)

description:
https://www.encodeproject.org/experiments/ENCSR662VFL/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse spleen
experiment encode accession: ENCSR662VFL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB369LKS
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: tissue

value: pooled male and female

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

tag: link


title: M31

tag: cell line

tag: cell type

value: human multi-drug resistant cancer cell line

value: persister

value: Repeat samples in parallel #1


title: total RNA-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB921ZBJ)

description:
https://www.encodeproject.org/experiments/ENCSR415SXI/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD8+ cell, activated Day 2
experiment encode accession: ENCSR415SXI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB921ZBJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: primary cell

value: Memory CD8+ cell, activated Day 2

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS347MCB at ENCODE; https://www.encodeproject.org/ENCBS347MCB/

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


title: RNA-DNA SPRITE 021

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 022


title: M01

tag: cell state

value: normal


title: RNA-DNA SPRITE 023


title: RNA-DNA SPRITE 020


title: D33

tag: serial number

value: Repeat samples in parallel #3


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB393DZF)

description:
https://www.encodeproject.org/experiments/ENCSR501DTN/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ T cells (CD3+CD8+)
experiment encode accession: ENCSR501DTN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB393DZF
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: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: male

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: ENCBS222RFX at ENCODE; https://www.encodeproject.org/ENCBS222RFX/

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


title: WGBS from cerebellum (ENCLB152BBV)

description:
https://www.encodeproject.org/experiments/ENCSR893RHD/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse cerebellum
experiment encode accession: ENCSR893RHD
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB152BBV
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: cerebellum

value: tissue

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

value: pooled male and female

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS358CVB at ENCODE; https://www.encodeproject.org/ENCBS358CVB/

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


title: WGBS from spleen (ENCLB329CRE)

description:
https://www.encodeproject.org/experiments/ENCSR662VFL/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse spleen
experiment encode accession: ENCSR662VFL
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB329CRE
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: spleen

value: Spleen tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: ENCBS750WUM at ENCODE; https://www.encodeproject.org/ENCBS750WUM/


title: total RNA-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB448YHB)

description:
https://www.encodeproject.org/experiments/ENCSR409UYW/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD8+ cell, activated Day 2
experiment encode accession: ENCSR409UYW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB448YHB
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: Homo sapiens male adult (30 years) activated CD8-positive, naive alpha-beta T primary cell

value: primary cell

value: naive CD8+ cell, activated Day 2

value: male

value: adult

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS966KLV at ENCODE; https://www.encodeproject.org/ENCBS966KLV/

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


title: RNA-DNA SPRITE 019

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB543FSB)

description:
https://www.encodeproject.org/experiments/ENCSR401DHH/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD4+ T cell, activated Day 7
experiment encode accession: ENCSR401DHH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB543FSB
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: Homo sapiens male adult (43 years) activated CD4-positive, alpha-beta memory T primary cell

value: Memory CD4+ T cell, activated Day 7

value: 43 year

value: ENCBS318AWH at ENCODE; https://www.encodeproject.org/ENCBS318AWH/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: WGBS from cerebellum (ENCLB336HAE)

description:
https://www.encodeproject.org/experiments/ENCSR893RHD/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse cerebellum
experiment encode accession: ENCSR893RHD
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB336HAE
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: cerebellum

value: tissue

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

value: pooled male and female

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS588RGY at ENCODE; https://www.encodeproject.org/ENCBS588RGY/

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


title: RNA-DNA SPRITE 018


title: D32

value: human multi-drug resistant cancer cell line

value: persister

value: Repeat samples in parallel #2


title: M03

value: normal

value: Repeat samples in parallel #3


title: RNA-DNA SPRITE 024

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from HFFc6 (ENCLB248MCB)

description:
https://www.encodeproject.org/experiments/ENCSR420ZKB/
***************
biological replicate number: 3
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 13 minute fragmentation
experiment encode accession: ENCSR420ZKB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB248MCB
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

tag: line

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: male

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: D31

value: human multi-drug resistant cancer cell line

value: Repeat samples in parallel #1


title: RNA-DNA SPRITE 017


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB285QIM)

description:
https://www.encodeproject.org/experiments/ENCSR385KVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ T cells, activated day 2
experiment encode accession: ENCSR385KVQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB285QIM
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: Homo sapiens male adult (20 years) activated CD4-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: primary cell

value: adult

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS883EPS at ENCODE; https://www.encodeproject.org/ENCBS883EPS/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: WGBS from cerebellum (ENCLB707QAI)

description:
https://www.encodeproject.org/experiments/ENCSR893RHD/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse cerebellum
experiment encode accession: ENCSR893RHD
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB707QAI
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: cerebellum

value: tissue

tag: description

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

value: pooled male and female

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS358CVB at ENCODE; https://www.encodeproject.org/ENCBS358CVB/

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


title: RNA-DNA SPRITE 016

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: D03

value: human multi-drug resistant cancer cell line

value: normal

value: Repeat samples in parallel #3


title: WGBS from cerebellum (ENCLB532KID)

description:
https://www.encodeproject.org/experiments/ENCSR893RHD/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse cerebellum
experiment encode accession: ENCSR893RHD
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB532KID
fragmentation methods: shearing (Covaris S2)
size range: 180-500

tag: biosample encode accession

value: adult

value: ENCBS588RGY at ENCODE; https://www.encodeproject.org/ENCBS588RGY/


title: D02

value: Repeat samples in parallel #2


title: total RNA-seq from CD4-positive, alpha-beta T cell (ENCLB998TIL)

description:
https://www.encodeproject.org/experiments/ENCSR411MUF/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ T cells (CD3+CD4+)
experiment encode accession: ENCSR411MUF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB998TIL
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: Homo sapiens male adult (20 years) CD4-positive, alpha-beta T primary cell

value: CD4-positive, alpha-beta T cell

value: primary cell

tag: Sex

value: male

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS984FMU at ENCODE; https://www.encodeproject.org/ENCBS984FMU/

value: Derived from ENCODE donor ENCDO394DKX; https://www.encodeproject.org/ENCDO394DKX/


title: RNA-DNA SPRITE 015

description:
RNA and genomic DNA
Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing
HL522DSXX.all.20190924.clusters.gz

value: Female ES cells


title: total RNA-seq from HFFc6 (ENCLB220BDN)

description:
https://www.encodeproject.org/experiments/ENCSR381OTM/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF
experiment encode accession: ENCSR381OTM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB220BDN
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

tag: dev stage

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

tag: passage number

value: ENCBS508JLR at ENCODE; https://www.encodeproject.org/ENCBS508JLR/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: D01

value: human multi-drug resistant cancer cell line

value: normal

value: Repeat samples in parallel #1


title: RNA-DNA SPRITE 013

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 014


title: WGBS from lung (ENCLB038SIN)

description:
https://www.encodeproject.org/experiments/ENCSR728AGC/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse lung
experiment encode accession: ENCSR728AGC
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB038SIN
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: lung

value: tissue

value: Lung tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: adult

tag: age

tag: lab

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS211WSV at ENCODE; https://www.encodeproject.org/ENCBS211WSV/

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


title: total RNA-seq from left cerebral cortex (ENCLB092UVH)

description:
https://www.encodeproject.org/experiments/ENCSR996TVY/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Male L. cortex
experiment encode accession: ENCSR996TVY
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB092UVH
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 adult (18-20 months) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 DPN18-20months

value: male

value: 18-20 month

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

value: ENCBS321KXV at ENCODE; https://www.encodeproject.org/ENCBS321KXV/

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


title: total RNA-seq from HFFc6 (ENCLB440BJO)

description:
https://www.encodeproject.org/experiments/ENCSR381OTM/
***************
biological replicate number: 3
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF
experiment encode accession: ENCSR381OTM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB440BJO
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

tag: health state

value: normal

tag: link

value: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: total RNA-seq from HFFc6 (ENCLB442LLX)

description:
https://www.encodeproject.org/experiments/ENCSR381OTM/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF
experiment encode accession: ENCSR381OTM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB442LLX
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS252IDB at ENCODE; https://www.encodeproject.org/ENCBS252IDB/


title: total RNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB247XFI)

description:
https://www.encodeproject.org/experiments/ENCSR282GZU/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ T cells, activated day 7
experiment encode accession: ENCSR282GZU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB247XFI
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: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: adult

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

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

value: ENCBS809ILB at ENCODE; https://www.encodeproject.org/ENCBS809ILB/

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


title: total RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB063JCU)

description:
https://www.encodeproject.org/experiments/ENCSR297AZN/
***************
biological replicate number: 1
technical replicate number: 1
description: memory CD4+ T cell (CD45RO+CCR7+/-)
experiment encode accession: ENCSR297AZN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB063JCU
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: Homo sapiens male adult (43 years) CD4-positive, alpha-beta memory T primary cell

value: CD4-positive, alpha-beta memory T cell

value: memory CD4+ T cell (CD45RO+CCR7+/-)

value: male

value: 43 year

value: Barbara Wold, Caltech

value: ENCBS010ART at ENCODE; https://www.encodeproject.org/ENCBS010ART/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ATAC-seq from natural killer cell (ENCLB661NPT)

description:
https://www.encodeproject.org/experiments/ENCSR305QTE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR305QTE
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB661NPT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (47 years) natural killer primary cell

value: natural killer cell

value: 47 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS415BNN at ENCODE; https://www.encodeproject.org/ENCBS415BNN/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: DNase-seq from middle frontal area 46 (ENCLB792DFB)

description:
https://www.encodeproject.org/experiments/ENCSR306LNA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR306LNA
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB792DFB

source_name: Homo sapiens male adult (73 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: adult

value: 73 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS198CUA at ENCODE; https://www.encodeproject.org/ENCBS198CUA/

value: Derived from ENCODE donor ENCDO059BOC; https://www.encodeproject.org/ENCDO059BOC/


title: WGBS from lung (ENCLB449AON)

description:
https://www.encodeproject.org/experiments/ENCSR728AGC/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse lung
experiment encode accession: ENCSR728AGC
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB449AON
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: lung

value: Lung tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS610BKN at ENCODE; https://www.encodeproject.org/ENCBS610BKN/

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


title: RNA-DNA SPRITE 011

source_name: Mouse Embryonic Stem cells

tag: cell line

tag: cell type

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from endodermal cell (ENCLB465SZM)

description:
https://www.encodeproject.org/experiments/ENCSR266XAJ/
***************
biological replicate number: 2
technical replicate number: 1
description: LRGASP_H1_endo
experiment encode accession: ENCSR266XAJ
assay title: total RNA-seq
encode release date: 2021-10-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB465SZM
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

source_name: Homo sapiens male embryo endodermal in vitro differentiated cells

value: endodermal cell

value: in vitro differentiated cells

value: male

value: embryonic

value: not collected

value: Barbara Wold, Caltech

value: René Maehr

value: ENCBS012DYC at ENCODE; https://www.encodeproject.org/ENCBS012DYC/

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


title: RNA-DNA SPRITE 012

tag: protocol

tag: treatment


title: total RNA-seq from endodermal cell (ENCLB295LUF)

description:
https://www.encodeproject.org/experiments/ENCSR266XAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: LRGASP_H1_endo
experiment encode accession: ENCSR266XAJ
assay title: total RNA-seq
encode release date: 2021-10-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB295LUF
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: ENCBS464AKI at ENCODE; https://www.encodeproject.org/ENCBS464AKI/


title: total RNA-seq from endodermal cell (ENCLB686DGB)

description:
https://www.encodeproject.org/experiments/ENCSR266XAJ/
***************
biological replicate number: 3
technical replicate number: 1
description: LRGASP_H1_endo
experiment encode accession: ENCSR266XAJ
assay title: total RNA-seq
encode release date: 2021-10-08
lab: Barbara Wold, Caltech
library encode accession: ENCLB686DGB
spikeins used: Lexogen set 4 reference spike-ins used for long-read RNA-seq, including the longSIRVs and SIRVs. Note that this does NOT contain the ERCCs that are a part of this mix.
nucleic acid starting quantity: 400
nucleic acid starting quantity units: ng

value: unknown

value: ENCBS971DDS at ENCODE; https://www.encodeproject.org/ENCBS971DDS/


title: DNase-seq from activated T-cell (ENCLB797DMN)

description:
https://www.encodeproject.org/experiments/ENCSR303JDG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR303JDG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB797DMN

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

value: activated T-cell

value: primary cell

value: female

value: adult

value: 21 year

value: John Stamatoyannopoulos, UW

value: StemExpress

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: ENCBS213FCL at ENCODE; https://www.encodeproject.org/ENCBS213FCL/

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


title: WGBS from lung (ENCLB531WVT)

description:
https://www.encodeproject.org/experiments/ENCSR728AGC/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse lung
experiment encode accession: ENCSR728AGC
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB531WVT
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: lung

value: tissue

value: Lung tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: healthy

value: ENCBS211WSV at ENCODE; https://www.encodeproject.org/ENCBS211WSV/

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


title: total RNA-seq from left cerebral cortex (ENCLB294YAR)

description:
https://www.encodeproject.org/experiments/ENCSR996TVY/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Male L. cortex
experiment encode accession: ENCSR996TVY
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB294YAR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: B6Cast F1 DPN18-20months

value: male

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS972OCB at ENCODE; https://www.encodeproject.org/ENCBS972OCB/

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


title: RNA-DNA SPRITE 009

description:
RNA and genomic DNA
Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing
HL522DSXX.all.20190924.clusters.gz

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: WGBS from lung (ENCLB040TPX)

description:
https://www.encodeproject.org/experiments/ENCSR728AGC/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse lung
experiment encode accession: ENCSR728AGC
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB040TPX
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: lung

value: tissue

value: Lung tissue from 8 adult P54-61 day old mice. C57BL/6 from Charles River

value: pooled male and female

value: adult

value: ENCBS610BKN at ENCODE; https://www.encodeproject.org/ENCBS610BKN/


title: RNA-DNA SPRITE 010


title: ATAC-seq from activated memory B cell (ENCLB697NYQ)

description:
https://www.encodeproject.org/experiments/ENCSR302PTB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR302PTB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB697NYQ
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: activated memory B cell

value: primary cell

value: 40 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS478HFG at ENCODE; https://www.encodeproject.org/ENCBS478HFG/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: ATAC-seq from natural killer cell (ENCLB853QZF)

description:
https://www.encodeproject.org/experiments/ENCSR305QTE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR305QTE
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB853QZF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: natural killer cell

value: male

value: 47 year

value: ENCBS090OSL at ENCODE; https://www.encodeproject.org/ENCBS090OSL/

value: Derived from ENCODE donor ENCDO311UBW; https://www.encodeproject.org/ENCDO311UBW/


title: total RNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB993QYJ)

description:
https://www.encodeproject.org/experiments/ENCSR264VJN/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ T cells, activated day 2
experiment encode accession: ENCSR264VJN
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB993QYJ
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: Homo sapiens male adult (21 years) activated CD8-positive, alpha-beta T primary cell treated with anti-CD3 and anti-CD28 coated beads

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: treatment_term_name:anti-CD3 and anti-CD28 coated beads; treatment_type:antibody;

value: ENCBS520WQB at ENCODE; https://www.encodeproject.org/ENCBS520WQB/

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


title: RNA-DNA SPRITE 007

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from CD4-positive, alpha-beta memory T cell (ENCLB635CAH)

description:
https://www.encodeproject.org/experiments/ENCSR177XCG/
***************
biological replicate number: 1
technical replicate number: 1
description: memory CD4+ T cell (CD45RO+CCR7+/-)
experiment encode accession: ENCSR177XCG
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB635CAH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: CD4-positive, alpha-beta memory T cell

value: primary cell

value: memory CD4+ T cell (CD45RO+CCR7+/-)

value: adult

value: 43 year

value: Barbara Wold, Caltech

value: ENCBS009MRL at ENCODE; https://www.encodeproject.org/ENCBS009MRL/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: ATAC-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB709ZZG)

description:
https://www.encodeproject.org/experiments/ENCSR392YGP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR392YGP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB709ZZG
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: male

value: 33 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS035CTF at ENCODE; https://www.encodeproject.org/ENCBS035CTF/

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


title: ATAC-seq from activated memory B cell (ENCLB589BZH)

description:
https://www.encodeproject.org/experiments/ENCSR302PTB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR302PTB
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB589BZH
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: activated memory B cell

value: 40 year

value: ENCBS288RHU at ENCODE; https://www.encodeproject.org/ENCBS288RHU/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: total RNA-seq from gastrocnemius (ENCLB354IFV)

description:
https://www.encodeproject.org/experiments/ENCSR486QNN/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND36 Female
experiment encode accession: ENCSR486QNN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB354IFV
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) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6Cast F1 PND36 Female 03 gastrocnemius for Wold core

value: female

value: unknown

value: 36 day

value: The Jackson Laboratory

value: ENCBS342UJO at ENCODE; https://www.encodeproject.org/ENCBS342UJO/

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


title: total RNA-seq from heart (ENCLB684MYS)

description:
https://www.encodeproject.org/experiments/ENCSR484UKA/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND10 Male heart
experiment encode accession: ENCSR484UKA
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB684MYS
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 (10 days) heart tissue

value: heart

value: B6Cast F1 PND10 Male 03 heart for Wold biobank

value: male

value: 10 day

value: Barbara Wold, Caltech

value: ENCBS840HGS at ENCODE; https://www.encodeproject.org/ENCBS840HGS/


title: ATAC-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB465KZM)

description:
https://www.encodeproject.org/experiments/ENCSR392YGP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR392YGP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB465KZM
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: primary cell

value: adult

value: 33 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS407SBU at ENCODE; https://www.encodeproject.org/ENCBS407SBU/

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


title: total RNA-seq from heart (ENCLB244ZAK)

description:
https://www.encodeproject.org/experiments/ENCSR484UKA/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND10 Male heart
experiment encode accession: ENCSR484UKA
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB244ZAK
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 PND10 Male 04 heart for Wold biobank

value: unknown

value: ENCBS734HOK at ENCODE; https://www.encodeproject.org/ENCBS734HOK/


title: RNA-DNA SPRITE 005

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 006


title: total RNA-seq from layer of hippocampus (ENCLB148NJB)

description:
https://www.encodeproject.org/experiments/ENCSR893IBO/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6Cast F1 PND10 3x female
experiment encode accession: ENCSR893IBO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB148NJB
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) layer of hippocampus tissue

value: layer of hippocampus

value: female

value: 10 day

value: The Jackson Laboratory

value: ENCBS286DXZ at ENCODE; https://www.encodeproject.org/ENCBS286DXZ/

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


title: ATAC-seq from HCT116 (ENCLB729PGH)

description:
https://www.encodeproject.org/experiments/ENCSR389WJO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR389WJO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB729PGH
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

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS899HWT at ENCODE; https://www.encodeproject.org/ENCBS899HWT/

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


title: ATAC-seq from HCT116 (ENCLB348ZOF)

description:
https://www.encodeproject.org/experiments/ENCSR389WJO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR389WJO
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB348ZOF
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: ENCBS209CFY at ENCODE; https://www.encodeproject.org/ENCBS209CFY/


title: total RNA-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB935HOR)

description:
https://www.encodeproject.org/experiments/ENCSR152FDX/
***************
biological replicate number: 1
technical replicate number: 1
description: Naïve CD4+ T cell, activated Day 7
experiment encode accession: ENCSR152FDX
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB935HOR
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: Homo sapiens male adult (43 years) activated CD4 positive, naive alpha-beta T primary cell

value: primary cell

value: Naïve CD4+ T cell, activated Day 7

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS125FDB at ENCODE; https://www.encodeproject.org/ENCBS125FDB/

value: Derived from ENCODE donor ENCDO791UJG; https://www.encodeproject.org/ENCDO791UJG/


title: RNA-DNA SPRITE 008

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from layer of hippocampus (ENCLB997TYH)

description:
https://www.encodeproject.org/experiments/ENCSR893IBO/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6Cast F1 PND10 3x female
experiment encode accession: ENCSR893IBO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB997TYH
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: female

value: unknown

value: 10 day

value: The Jackson Laboratory

value: ENCBS739AAH at ENCODE; https://www.encodeproject.org/ENCBS739AAH/

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


title: RNA-DNA SPRITE 003

description:
RNA and genomic DNA
Female ES cells (pSM44 ES cell line) derived from a 129 × castaneous F1 mouse cross. These cells express Xist from the endogenous locus under control of a tetracycline-inducible promoter. The dox-inducible Xist gene is on the 129 allele, enabling allele-specific analysis of Xist induction and X chromosome silencing
HL522DSXX.all.20190924.clusters.gz


title: total RNA-seq from gastrocnemius (ENCLB894UAD)

description:
https://www.encodeproject.org/experiments/ENCSR486QNN/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND36 Female
experiment encode accession: ENCSR486QNN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB894UAD
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: B6Cast F1 PND36 Female 04 gastrocnemius for Wold core

value: 36 day

value: ENCBS062SUO at ENCODE; https://www.encodeproject.org/ENCBS062SUO/


title: ATAC-seq from HCT116 (ENCLB771JTO)

description:
https://www.encodeproject.org/experiments/ENCSR302NVX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR302NVX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB771JTO
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 SMARCA5

value: cell line

value: male

value: colorectal carcinoma

value: adult

value: 48 year

value: Erez Aiden, Baylor

value: Dr. Masato Kanemaki

value: ENCBS993RWC at ENCODE; https://www.encodeproject.org/ENCBS993RWC/

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


title: total RNA-seq from CD8-positive, alpha-beta T cell (ENCLB246DIJ)

description:
https://www.encodeproject.org/experiments/ENCSR151FXS/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ T cells (CD3+CD8+)
experiment encode accession: ENCSR151FXS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB246DIJ
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: Homo sapiens male adult (21 years) CD8-positive, alpha-beta T primary cell

value: CD8-positive, alpha-beta T cell

value: primary cell

value: 21 year

value: Yijun Ruan, JAX

value: AllCells

value: ENCBS547LLS at ENCODE; https://www.encodeproject.org/ENCBS547LLS/

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


title: RNA-DNA SPRITE 004

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: ATAC-seq from HCT116 (ENCLB388VPL)

description:
https://www.encodeproject.org/experiments/ENCSR302NVX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR302NVX
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB388VPL
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

value: cell line

value: male

value: colorectal carcinoma

value: ENCBS104UKW at ENCODE; https://www.encodeproject.org/ENCBS104UKW/


title: total RNA-seq from heart (ENCLB200RXP)

description:
https://www.encodeproject.org/experiments/ENCSR984JDC/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 2 months Female heart
experiment encode accession: ENCSR984JDC
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB200RXP
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) heart tissue

value: heart

value: tissue

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

value: female

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS353NKX at ENCODE; https://www.encodeproject.org/ENCBS353NKX/

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


title: RNA-DNA SPRITE 002

value: Female ES cells


title: RNA-DNA SPRITE 001

value: RNA-DNA SPRITE


title: total RNA-seq from HFFc6 (ENCLB172FDA)

description:
https://www.encodeproject.org/experiments/ENCSR146ZSP/
***************
biological replicate number: 3
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 600 ng
experiment encode accession: ENCSR146ZSP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB172FDA
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 600
nucleic acid starting quantity units: ng

source_name: Homo sapiens HFFc6 cell line, preserved by flash-freezing

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: normal

value: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: DNase-seq from middle frontal area 46 (ENCLB921BFJ)

description:
https://www.encodeproject.org/experiments/ENCSR386XPD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR386XPD
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-06-30
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB921BFJ

source_name: Homo sapiens female adult (82 years) middle frontal area 46 tissue

value: middle frontal area 46

value: tissue

value: female

value: adult

value: 82 year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS863VRT at ENCODE; https://www.encodeproject.org/ENCBS863VRT/

value: Derived from ENCODE donor ENCDO377QXX; https://www.encodeproject.org/ENCDO377QXX/


title: total RNA-seq from heart (ENCLB174ECJ)

description:
https://www.encodeproject.org/experiments/ENCSR984JDC/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 2 months Female heart
experiment encode accession: ENCSR984JDC
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB174ECJ
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 Female 03 heart for Wold biobank

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS759GYL at ENCODE; https://www.encodeproject.org/ENCBS759GYL/

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


title: total RNA-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB453HJH)

description:
https://www.encodeproject.org/experiments/ENCSR240JQW/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD8+ cell, activated Day 7
experiment encode accession: ENCSR240JQW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB453HJH
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: Homo sapiens male adult (30 years) activated CD8-positive, alpha-beta memory T primary cell

value: primary cell

value: Memory CD8+ cell, activated Day 7

value: male

value: 30 year

value: AllCells

value: ENCBS737GYC at ENCODE; https://www.encodeproject.org/ENCBS737GYC/

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


title: total RNA-seq from gastrocnemius (ENCLB296APF)

description:
https://www.encodeproject.org/experiments/ENCSR886CRW/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND14 3x Females
experiment encode accession: ENCSR886CRW
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB296APF
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) gastrocnemius tissue

value: gastrocnemius

value: tissue

value: B6Cast F1 PND14 Female 04 gastrocnemius for Wold core

value: female

value: 14 day

value: ENCBS838OKI at ENCODE; https://www.encodeproject.org/ENCBS838OKI/


title: DNase-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB130RQG)

description:
https://www.encodeproject.org/experiments/ENCSR386BOX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR386BOX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB130RQG

source_name: Homo sapiens male adult (48 years) activated CD4 positive, naive alpha-beta T primary cell treated with 50 U/mL Interleukin-2 for 72 hours, anti-CD3 and anti-CD28 coated beads for 72 hours

value: adult

value: 48 year

value: John Stamatoyannopoulos, UW

value: StemExpress

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: ENCBS996KNW at ENCODE; https://www.encodeproject.org/ENCBS996KNW/

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


title: R9332

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: TF ChIP-seq from WTC11 (ENCLB571BRO)

description:
https://www.encodeproject.org/experiments/ENCSR110QIL/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-RORB ChIP-seq on human WTC11
experiment encode accession: ENCSR110QIL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB571BRO
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

tag: antibody

value: RORB

tag: line

value: cell line

value: male

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS563AAL at ENCODE; https://www.encodeproject.org/ENCBS563AAL/

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


title: R9302


title: total RNA-seq from HFFc6 (ENCLB890KDJ)

description:
https://www.encodeproject.org/experiments/ENCSR146ZSP/
***************
biological replicate number: 1
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 600 ng
experiment encode accession: ENCSR146ZSP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB890KDJ
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 600
nucleic acid starting quantity units: ng

tag: description

value: Clonal line 6 derived from hTert immortalized HFF parental line

tag: biosample encode accession

tag: Sex

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: normal

value: ENCBS252IDB at ENCODE; https://www.encodeproject.org/ENCBS252IDB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: total RNA-seq from HFFc6 (ENCLB318NXK)

description:
https://www.encodeproject.org/experiments/ENCSR146ZSP/
***************
biological replicate number: 3
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 600 ng
experiment encode accession: ENCSR146ZSP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB318NXK
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 600
nucleic acid starting quantity units: ng

tag: dev stage

tag: age

tag: passage number

value: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/


title: total RNA-seq from HFFc6 (ENCLB726FWA)

description:
https://www.encodeproject.org/experiments/ENCSR146ZSP/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 600 ng
experiment encode accession: ENCSR146ZSP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB726FWA
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 600
nucleic acid starting quantity units: ng

tag: lab

tag: source

tag: health state

value: ENCBS508JLR at ENCODE; https://www.encodeproject.org/ENCBS508JLR/


title: total RNA-seq from left cerebral cortex (ENCLB039EHL)

description:
https://www.encodeproject.org/experiments/ENCSR774DTO/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND14 3x Females L. cortex
experiment encode accession: ENCSR774DTO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB039EHL
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) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND14 3x Females 03 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

tag: link

value: ENCBS374ENP at ENCODE; https://www.encodeproject.org/ENCBS374ENP/

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


title: TF ChIP-seq from WTC11 (ENCLB067TTX)

description:
https://www.encodeproject.org/experiments/ENCSR110QIL/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-RORB ChIP-seq on human WTC11
experiment encode accession: ENCSR110QIL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR049LUW
encode release date: 2021-09-02
lab: Michael Snyder, Stanford
library encode accession: ENCLB067TTX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: RORB

value: cell line

value: male

value: adult

value: 30 year

value: Michael Snyder, Stanford

value: Kevin White

value: ENCBS510ARK at ENCODE; https://www.encodeproject.org/ENCBS510ARK/

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


title: total RNA-seq from HFFc6 (ENCLB557YTP)

description:
https://www.encodeproject.org/experiments/ENCSR146ZSP/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 600 ng
experiment encode accession: ENCSR146ZSP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB557YTP
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 600
nucleic acid starting quantity units: ng

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: normal

value: ENCBS252IDB at ENCODE; https://www.encodeproject.org/ENCBS252IDB/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: R9241


title: total RNA-seq from left cerebral cortex (ENCLB148UKM)

description:
https://www.encodeproject.org/experiments/ENCSR774DTO/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND14 3x Females L. cortex
experiment encode accession: ENCSR774DTO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB148UKM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND14 Female 04 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 14 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS120AVS at ENCODE; https://www.encodeproject.org/ENCBS120AVS/

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


title: ATAC-seq from activated naive B cell (ENCLB380ZTT)

description:
https://www.encodeproject.org/experiments/ENCSR379NMT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR379NMT
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB380ZTT
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: activated naive B cell

value: primary cell

value: male

value: adult

value: 40 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS737YXU at ENCODE; https://www.encodeproject.org/ENCBS737YXU/

value: Derived from ENCODE donor ENCDO512FEI; https://www.encodeproject.org/ENCDO512FEI/


title: total RNA-seq from HFFc6 (ENCLB409RVK)

description:
https://www.encodeproject.org/experiments/ENCSR146ZSP/
***************
biological replicate number: 2
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 600 ng
experiment encode accession: ENCSR146ZSP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB409RVK
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 600
nucleic acid starting quantity units: ng

value: cell line

value: Clonal line 6 derived from hTert immortalized HFF parental line

value: newborn

value: 0 year

value: Job Dekker, UMass

value: Job Dekker

value: normal

value: ENCBS508JLR at ENCODE; https://www.encodeproject.org/ENCBS508JLR/

value: Derived from ENCODE donor ENCDO737WWC; https://www.encodeproject.org/ENCDO737WWC/


title: R9121


title: R9113


title: total RNA-seq from layer of hippocampus (ENCLB481NKO)

description:
https://www.encodeproject.org/experiments/ENCSR976DKW/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6Cast F1 PND10 3x male
experiment encode accession: ENCSR976DKW
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB481NKO
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 (10 days) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: unknown

value: 10 day

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS435SED at ENCODE; https://www.encodeproject.org/ENCBS435SED/

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


title: total RNA-seq from gastrocnemius (ENCLB157JST)

description:
https://www.encodeproject.org/experiments/ENCSR886CRW/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND14 3x Females
experiment encode accession: ENCSR886CRW
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB157JST
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: B6Cast F1 PND14 3x Females 03 gastrocnemius for Wold core

value: female

value: 14 day

value: ENCBS205QFK at ENCODE; https://www.encodeproject.org/ENCBS205QFK/


title: total RNA-seq from layer of hippocampus (ENCLB267YSL)

description:
https://www.encodeproject.org/experiments/ENCSR976DKW/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6Cast F1 PND10 3x male
experiment encode accession: ENCSR976DKW
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB267YSL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: ENCBS426ZTY at ENCODE; https://www.encodeproject.org/ENCBS426ZTY/


title: total RNA-seq from heart (ENCLB131YRA)

description:
https://www.encodeproject.org/experiments/ENCSR465PBJ/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Female heart
experiment encode accession: ENCSR465PBJ
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB131YRA
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 adult (18-20 months) heart tissue

value: heart

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: ENCBS007ZPS at ENCODE; https://www.encodeproject.org/ENCBS007ZPS/


title: Mint-ChIP-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCLB477KHL)

description:
https://www.encodeproject.org/experiments/ENCSR122KBB/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, CD25-positive, alpha-beta regulatory T cell
experiment encode accession: ENCSR122KBB
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR242OUP
encode release date: 2021-09-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB477KHL
fragmentation methods: none

source_name: Homo sapiens CD4-positive, CD25-positive, alpha-beta regulatory T primary cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS764TKE at ENCODE; https://www.encodeproject.org/ENCBS764TKE/

value: Derived from ENCODE donor ENCDO836ICQ; https://www.encodeproject.org/ENCDO836ICQ/


title: total RNA-seq from mammary epithelial cell (ENCLB631HFC)

description:
https://www.encodeproject.org/experiments/ENCSR020YQE/
***************
biological replicate number: 1
technical replicate number: 1
description: HMEC for bru-seq comparison
experiment encode accession: ENCSR020YQE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB631HFC
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: Homo sapiens female mammary epithelial primary cell

value: mammary epithelial cell

value: female

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS996RLF at ENCODE; https://www.encodeproject.org/ENCBS996RLF/

value: Derived from ENCODE donor ENCDO343AAA; https://www.encodeproject.org/ENCDO343AAA/


title: R8971


title: total RNA-seq from mammary epithelial cell (ENCLB349LDR)

description:
https://www.encodeproject.org/experiments/ENCSR020YQE/
***************
biological replicate number: 2
technical replicate number: 1
description: HMEC for bru-seq comparison
experiment encode accession: ENCSR020YQE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB349LDR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS710VQU at ENCODE; https://www.encodeproject.org/ENCBS710VQU/


title: R9091