title: total RNA-seq from HFFc6 (ENCLB155ODR)

description:
https://www.encodeproject.org/experiments/ENCSR841QAC/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 900 ng
experiment encode accession: ENCSR841QAC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB155ODR
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 900
nucleic acid starting quantity units: ng

tag: description

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

tag: Sex

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: TF ChIP-seq from HepG2 (ENCLB937BLY)

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/ENCSR605KVV/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR605KVV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB937BLY
fragmentation methods: sonication (generic)

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF251

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: health state

value: hepatocellular carcinoma

tag: link

value: ENCBS297GRM at ENCODE; https://www.encodeproject.org/ENCBS297GRM/

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


title: Histone ChIP-seq from motor neuron (ENCLB848WMF)

description:
https://www.encodeproject.org/experiments/ENCSR680IWU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR680IWU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255MIG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB848WMF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (55 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: adult

value: 55 year

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS346LNG at ENCODE; https://www.encodeproject.org/ENCBS346LNG/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: RNA-DNA SPRITE 063

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 HFFc6 (ENCLB775QVD)

description:
https://www.encodeproject.org/experiments/ENCSR841QAC/
***************
biological replicate number: 1
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 900 ng
experiment encode accession: ENCSR841QAC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB775QVD
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 900
nucleic acid starting quantity units: ng

library_source: transcriptomic

molecule: total RNA

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

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

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 (ENCLB203FXI)

description:
https://www.encodeproject.org/experiments/ENCSR841QAC/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 900 ng
experiment encode accession: ENCSR841QAC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB203FXI
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 900
nucleic acid starting quantity units: ng

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


title: DNase-seq from posterior cingulate gyrus (ENCLB511UQB)

description:
https://www.encodeproject.org/experiments/ENCSR433NEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR433NEX
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB511UQB
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens female adult (90 or above years) with mild cognitive impairment; posterior cingulate gyrus tissue

value: posterior cingulate gyrus

value: tissue

value: female

value: adult

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS117HVD at ENCODE; https://www.encodeproject.org/ENCBS117HVD/

value: Derived from ENCODE donor ENCDO557QXE; https://www.encodeproject.org/ENCDO557QXE/


title: RNA-DNA SPRITE 062

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: ATAC-seq from memory B cell (ENCLB806QFC)

description:
https://www.encodeproject.org/experiments/ENCSR610AQP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR610AQP
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-09-09
lab: Michael Snyder, Stanford
library encode accession: ENCLB806QFC
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

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

value: memory B cell

value: primary cell

value: male

value: 40 year

value: Michael Snyder, Stanford

value: StemExpress

value: ENCBS010BKY at ENCODE; https://www.encodeproject.org/ENCBS010BKY/

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


title: Histone ChIP-seq from motor neuron (ENCLB901ZLW)

description:
https://www.encodeproject.org/experiments/ENCSR680IWU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR680IWU
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR255MIG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB901ZLW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: adult

value: 55 year

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

value: Healthy donor

value: ENCBS259EPB at ENCODE; https://www.encodeproject.org/ENCBS259EPB/

value: Derived from ENCODE donor ENCDO371BAE; https://www.encodeproject.org/ENCDO371BAE/


title: RNA-DNA SPRITE 061

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 060


title: GM DNase-seq from K562 (ENCLB406ZQY)

description:
https://www.encodeproject.org/experiments/ENCSR903BAY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR903BAY
assay title: GM DNase-seq
assembly: GRCh38
encode release date: 2019-01-08
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB406ZQY

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

value: cell line

value: TALEN-mediated heterozygous DHS deletion in K562.

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: John Stamatoyannopoulos, UW

value: John Stamatoyannopoulos

value: ENCBS901ASD at ENCODE; https://www.encodeproject.org/ENCBS901ASD/

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


title: Histone ChIP-seq from motor neuron (ENCLB482KKH)

description:
https://www.encodeproject.org/experiments/ENCSR540KQC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR540KQC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR201VAH
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB482KKH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (47 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS309GBV at ENCODE; https://www.encodeproject.org/ENCBS309GBV/

value: Derived from ENCODE donor ENCDO908CUN; https://www.encodeproject.org/ENCDO908CUN/


title: total RNA-seq from HFFc6 (ENCLB528QMN)

description:
https://www.encodeproject.org/experiments/ENCSR841QAC/
***************
biological replicate number: 3
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 900 ng
experiment encode accession: ENCSR841QAC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB528QMN
fragmentation methods: chemical (NEBNext Ultra II Directional)
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 900
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: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/

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


title: RNA-DNA SPRITE 059

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from PC-9 (ENCLB117IVW)

description:
https://www.encodeproject.org/experiments/ENCSR743GKS/
***************
biological replicate number: 2
technical replicate number: 1
description: PC-9 for bru-seq comparison
experiment encode accession: ENCSR743GKS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB117IVW
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 PC-9 cell line

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS021NLC at ENCODE; https://www.encodeproject.org/ENCBS021NLC/

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


title: Patient255

type: RNA

city: MIAMI

first: Xi

last: CHEN

state: FL

address: 1120 NW 14th Street

institute: University of Miami

data_processing: We normalized the raw data at the gene level using Robust MultiChip Averaging (RMA) algorithm as implemented in the Affymetrix® Expression ConsoleTM Software 1.3.

label: biotin

source_name: Human Colorectal cancer tissue

label_protocol:
According to the GeneChip™ Human Transcriptome Array 2. 0 (Affymetrix, Santa Clara, CA) protocol.
The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin

extract_protocol:
Archived CRC FFPE samples used in this study were stored at room temperature until sectioned for RNA extraction. The first 10µm of the tissue was discarded before cutting sections for RNA extraction. Five-micron sections were mounted on uncharged glass slides. Separate tissue sections from the top and bottom of the serial sections used for RNA extraction were stained with H&E for quality control from each tissue block. RNA was purified from 5µm thick tissue sections containing greater than 80% tumor using High Pure FFPE RNA Micro Kit (Roche) according to manufacturer’s instructions. A minimum of 4 sections per sample were required.
At least 20% of the RNA sample contain fragments of 300 base pairs or longer in length

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: No

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

tag: disease status

value: DOC


title: Patient171

hyb_protocol: According to the GeneChip™ Human Transcriptome Array 2. 0 (Affymetrix, Santa Clara, CA) protocol.

value: FOLFOX

value: AWD


title: Patient256

scan_protocol: According to the GeneChip™ Human Transcriptome Array 2. 0 (Affymetrix, Santa Clara, CA) protocol.

value: DOD


title: Patient252

value: NED


title: TF ChIP-seq from HepG2 (ENCLB717DCI)

description:
https://www.encodeproject.org/experiments/ENCSR600SCF/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR600SCF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB717DCI
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens SCMH1

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS300BIC at ENCODE; https://www.encodeproject.org/ENCBS300BIC/

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


title: total RNA-seq from CD4-positive naive resting alpha-beta T cell (ENCLB631BOC)

description:
https://www.encodeproject.org/experiments/ENCSR911XSA/
***************
biological replicate number: 1
technical replicate number: 1
description: naïve CD4+ T cell(CD45RO- RA+CCR7+)
experiment encode accession: ENCSR911XSA
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB631BOC
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 naive resting alpha-beta T primary cell

value: primary cell

tag: description

value: naïve CD4+ T cell(CD45RO- RA+CCR7+)

value: adult

tag: age

value: 43 year

tag: lab

value: Barbara Wold, Caltech

tag: source

value: AllCells

tag: link

value: ENCBS042IEB at ENCODE; https://www.encodeproject.org/ENCBS042IEB/

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


title: total RNA-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB712WUB)

description:
https://www.encodeproject.org/experiments/ENCSR820IIL/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD8+ cell, activated Day 2
experiment encode accession: ENCSR820IIL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB712WUB
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: naive CD8+ cell, activated Day 2

value: 30 year

value: ENCBS454GLZ at ENCODE; https://www.encodeproject.org/ENCBS454GLZ/

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


title: TF ChIP-seq from HepG2 (ENCLB711CAS)

description:
https://www.encodeproject.org/experiments/ENCSR600SCF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR600SCF
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB711CAS
fragmentation methods: sonication (generic)

value: cell line

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

tag: health state

value: ENCBS516MHX at ENCODE; https://www.encodeproject.org/ENCBS516MHX/


title: total RNA-seq from PC-9 (ENCLB736LNA)

description:
https://www.encodeproject.org/experiments/ENCSR743GKS/
***************
biological replicate number: 1
technical replicate number: 1
description: PC-9 for bru-seq comparison
experiment encode accession: ENCSR743GKS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB736LNA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: not collected

value: unknown

value: Mats Ljungman, UMichigan

value: Sigma

value: ENCBS511ZVG at ENCODE; https://www.encodeproject.org/ENCBS511ZVG/

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


title: WGBS from kidney (ENCLB816IMB)

description:
https://www.encodeproject.org/experiments/ENCSR749COU/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse kidney
experiment encode accession: ENCSR749COU
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB816IMB
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: kidney

value: tissue

value: Kidney 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: ENCBS492BCR at ENCODE; https://www.encodeproject.org/ENCBS492BCR/

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


title: RNA-DNA SPRITE 056

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: Histone ChIP-seq from motor neuron (ENCLB807DXQ)

description:
https://www.encodeproject.org/experiments/ENCSR595HWK/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR595HWK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR744SMV
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB807DXQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

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

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: female

value: not collected

value: Michael Snyder, Stanford

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

value: Healthy donor

value: ENCBS152AIM at ENCODE; https://www.encodeproject.org/ENCBS152AIM/

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


title: total RNA-seq from activated CD8-positive, alpha-beta memory T cell (ENCLB447NDB)

description:
https://www.encodeproject.org/experiments/ENCSR817WHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD8+ cell, activated Day 2
experiment encode accession: ENCSR817WHQ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB447NDB
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 2

value: male

value: adult

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS167CNH at ENCODE; https://www.encodeproject.org/ENCBS167CNH/

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


title: RNA-DNA SPRITE 058

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: Patient249

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

tag: recurrence

tag: disease free survival (days)

tag: death

tag: overall survival (days)

value: DOD


title: Patient253

value: FOLFOX

tag: disease status

value: NED


title: WGBS from kidney (ENCLB749SVZ)

description:
https://www.encodeproject.org/experiments/ENCSR749COU/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse kidney
experiment encode accession: ENCSR749COU
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB749SVZ
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: kidney

value: tissue

tag: description

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

tag: biosample encode accession

tag: Sex

value: pooled male and female

value: healthy

tag: dev stage

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS754XTZ at ENCODE; https://www.encodeproject.org/ENCBS754XTZ/

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


title: RNA-DNA SPRITE 057


title: WGBS from kidney (ENCLB831TCW)

description:
https://www.encodeproject.org/experiments/ENCSR749COU/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse kidney
experiment encode accession: ENCSR749COU
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB831TCW
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: adult

tag: age

tag: lab

tag: source

tag: link


title: Patient119


title: total RNA-seq from HFFc6 (ENCLB718KRD)

description:
https://www.encodeproject.org/experiments/ENCSR735JKB/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 7 minute fragmentation
experiment encode accession: ENCSR735JKB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB718KRD
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

tag: health state

value: normal

tag: passage number

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

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


title: Histone ChIP-seq from motor neuron (ENCLB145TGW)

description:
https://www.encodeproject.org/experiments/ENCSR595HWK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR595HWK
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR744SMV
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB145TGW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: female

value: Healthy donor

value: unknown

value: Michael Snyder, Stanford

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

value: ENCBS733MQS at ENCODE; https://www.encodeproject.org/ENCBS733MQS/

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


title: Patient132_RDB124

tag: subject status

value: colorectal cancer (CRC) patient

tag: clinical stage

value: FOLFOX

tag: recurrence

value: DOD


title: WGBS from kidney (ENCLB310OUE)

description:
https://www.encodeproject.org/experiments/ENCSR749COU/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse kidney
experiment encode accession: ENCSR749COU
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB310OUE
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: kidney

value: tissue

value: Kidney 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: ENCBS492BCR at ENCODE; https://www.encodeproject.org/ENCBS492BCR/

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


title: Histone ChIP-seq from motor neuron (ENCLB866BTV)

description:
https://www.encodeproject.org/experiments/ENCSR540KQC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR540KQC
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR201VAH
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB866BTV
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: 47 year

value: Michael Snyder, Stanford

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS545YIS at ENCODE; https://www.encodeproject.org/ENCBS545YIS/

value: Derived from ENCODE donor ENCDO908CUN; https://www.encodeproject.org/ENCDO908CUN/


title: RNA-DNA SPRITE 055

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 HFFc6 (ENCLB606IZW)

description:
https://www.encodeproject.org/experiments/ENCSR735JKB/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 7 minute fragmentation
experiment encode accession: ENCSR735JKB
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB606IZW
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

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: DNase-seq from T-helper 17 cell (ENCLB632HUD)

description:
https://www.encodeproject.org/experiments/ENCSR537TXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR537TXP
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB632HUD

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

value: T-helper 17 cell

value: primary cell

value: male

tag: dev stage

value: adult

tag: age

value: 50 year

tag: lab

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS686XJY at ENCODE; https://www.encodeproject.org/ENCBS686XJY/

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


title: RNA-DNA SPRITE 054

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from left cerebral cortex (ENCLB211CTN)

description:
https://www.encodeproject.org/experiments/ENCSR946YUY/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND36 Female L. cortex
experiment encode accession: ENCSR946YUY
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB211CTN
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) left cerebral cortex tissue

value: left cerebral cortex

value: tissue

value: B6Cast F1 PND36 Female 03 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 36 day

value: Barbara Wold, Caltech

tag: source

value: The Jackson Laboratory

tag: link

value: ENCBS527XPI at ENCODE; https://www.encodeproject.org/ENCBS527XPI/

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


title: Histone ChIP-seq from motor neuron (ENCLB476NNQ)

description:
https://www.encodeproject.org/experiments/ENCSR672RKZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR672RKZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR124KQG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB476NNQ
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: adult

value: 47 year

value: Michael Snyder, Stanford

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

tag: health state

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS038RNY at ENCODE; https://www.encodeproject.org/ENCBS038RNY/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: Histone ChIP-seq from motor neuron (ENCLB779NIK)

description:
https://www.encodeproject.org/experiments/ENCSR425FUS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR425FUS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR663GIS
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB779NIK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (49 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

tag: antibody

value: 49 year

value: ENCBS980NQQ at ENCODE; https://www.encodeproject.org/ENCBS980NQQ/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: Histone ChIP-seq from motor neuron (ENCLB479IRY)

description:
https://www.encodeproject.org/experiments/ENCSR672RKZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR672RKZ
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR124KQG
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB479IRY
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS238JUI at ENCODE; https://www.encodeproject.org/ENCBS238JUI/


title: Histone ChIP-seq from motor neuron (ENCLB159MRF)

description:
https://www.encodeproject.org/experiments/ENCSR425FUS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human motor neuron
experiment encode accession: ENCSR425FUS
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR663GIS
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB159MRF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS855DRG at ENCODE; https://www.encodeproject.org/ENCBS855DRG/


title: total RNA-seq from CD8-positive naive resting alpha-beta T cell (ENCLB501SKY)

description:
https://www.encodeproject.org/experiments/ENCSR473XAP/
***************
biological replicate number: 1
technical replicate number: 1
description: naïve CD8+ T cell(CD45RO-CCR7+)
experiment encode accession: ENCSR473XAP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB501SKY
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) CD8-positive naive resting alpha-beta T primary cell

value: primary cell

value: naïve CD8+ T cell(CD45RO-CCR7+)

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS048QUB at ENCODE; https://www.encodeproject.org/ENCBS048QUB/

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


title: total RNA-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB470QSP)

description:
https://www.encodeproject.org/experiments/ENCSR996OED/
***************
biological replicate number: 1
technical replicate number: 1
description: Naïve CD4+ T cell, activated Day 2
experiment encode accession: ENCSR996OED
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB470QSP
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: Naïve CD4+ T cell, activated Day 2

value: male

value: adult

value: 43 year

value: ENCBS211PXT at ENCODE; https://www.encodeproject.org/ENCBS211PXT/

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


title: total RNA-seq from left cerebral cortex (ENCLB746ULA)

description:
https://www.encodeproject.org/experiments/ENCSR946YUY/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND36 Female L. cortex
experiment encode accession: ENCSR946YUY
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB746ULA
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 PND36 Female 04 left cerebral cortex for Wold biobank

value: female

value: unknown

value: 36 day

value: The Jackson Laboratory

value: ENCBS888DCZ at ENCODE; https://www.encodeproject.org/ENCBS888DCZ/

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


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB633TIE)

description:
https://www.encodeproject.org/experiments/ENCSR899IVV/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ T cells, activated day 7
experiment encode accession: ENCSR899IVV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB633TIE
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 10 ng/mL Interleukin-2 , anti-CD3 and anti-CD28 coated beads

value: primary cell

value: 20 year

value: Yijun Ruan, JAX

value: AllCells

tag: treatments

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: ENCBS081TPG at ENCODE; https://www.encodeproject.org/ENCBS081TPG/

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


title: total RNA-seq from endothelial cell of umbilical vein (ENCLB585VAC)

description:
https://www.encodeproject.org/experiments/ENCSR993JMV/
***************
biological replicate number: 1
technical replicate number: 1
description: HUVEC for bru-seq comparison
experiment encode accession: ENCSR993JMV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB585VAC
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 newborn endothelial of umbilical vein primary cell

value: endothelial cell of umbilical vein

value: not collected

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS820SXP at ENCODE; https://www.encodeproject.org/ENCBS820SXP/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: RNA-DNA SPRITE 047

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

source_name: Mouse Embryonic Stem cells

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 051


title: RNA-DNA SPRITE 048


title: RNA-DNA SPRITE 049


title: total RNA-seq from activated CD4 positive, naive alpha-beta T cell (ENCLB427PTN)

description:
https://www.encodeproject.org/experiments/ENCSR458FZP/
***************
biological replicate number: 1
technical replicate number: 1
description: Naïve CD4+ T cell, activated Day 7
experiment encode accession: ENCSR458FZP
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB427PTN
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: Naïve CD4+ T cell, activated Day 7

value: male

value: adult

value: 43 year

value: Barbara Wold, Caltech

value: ENCBS917XRI at ENCODE; https://www.encodeproject.org/ENCBS917XRI/

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


title: TF ChIP-seq from A549 (ENCLB583VNP)

description:
https://www.encodeproject.org/experiments/ENCSR590IHT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF302 ChIP-seq on human A549
experiment encode accession: ENCSR590IHT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR365RFY, ENCSR928HJI
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB583VNP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens A549 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZNF302

tag: line

value: cell line

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS888PZM at ENCODE; https://www.encodeproject.org/ENCBS888PZM/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: total RNA-seq from adrenal gland (ENCLB930KYN)

description:
https://www.encodeproject.org/experiments/ENCSR920ABO/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND4_Male 03_ENC4_cDNA438
experiment encode accession: ENCSR920ABO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB930KYN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: adrenal gland

value: tissue

value: unknown

value: 4 day

value: The Jackson Laboratory

value: ENCBS886OBH at ENCODE; https://www.encodeproject.org/ENCBS886OBH/

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


title: total RNA-seq from endothelial cell of umbilical vein (ENCLB751ROJ)

description:
https://www.encodeproject.org/experiments/ENCSR993JMV/
***************
biological replicate number: 2
technical replicate number: 1
description: HUVEC for bru-seq comparison
experiment encode accession: ENCSR993JMV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB751ROJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: endothelial cell of umbilical vein

value: primary cell

value: not collected

value: newborn

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS023JCN at ENCODE; https://www.encodeproject.org/ENCBS023JCN/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/


title: RNA-DNA SPRITE 052

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 053


title: total RNA-seq from adrenal gland (ENCLB414TCN)

description:
https://www.encodeproject.org/experiments/ENCSR920ABO/
***************
biological replicate number: 2
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND4_Male 03_ENC4_cDNA438
experiment encode accession: ENCSR920ABO
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB414TCN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adrenal gland

value: tissue

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

value: male

value: Barbara Wold, Caltech

value: ENCBS623ZPY at ENCODE; https://www.encodeproject.org/ENCBS623ZPY/


title: RNA-DNA SPRITE 050


title: total RNA-seq from left cerebral cortex (ENCLB753RLT)

description:
https://www.encodeproject.org/experiments/ENCSR841KGE/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND4 Male L. cortex
experiment encode accession: ENCSR841KGE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB753RLT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Mus musculus strain B6CASTF1/J male (4 days) left cerebral cortex tissue

value: left cerebral cortex

value: B6Cast F1 PND4 Male 03 left cerebral cortex for Wold biobank

value: unknown

value: 4 day

value: The Jackson Laboratory

value: ENCBS398MXZ at ENCODE; https://www.encodeproject.org/ENCBS398MXZ/

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


title: total RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB059VWM)

description:
https://www.encodeproject.org/experiments/ENCSR989IFF/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD8+ (CD3+CD8+CD45RO+ and CD45RO-CCR7-)
experiment encode accession: ENCSR989IFF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB059VWM
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) CD8-positive, alpha-beta memory T primary cell

value: CD8-positive, alpha-beta memory T cell

value: primary cell

value: adult

value: 30 year

value: AllCells

value: ENCBS107RWR at ENCODE; https://www.encodeproject.org/ENCBS107RWR/

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


title: TF ChIP-seq from A549 (ENCLB419OJX)

description:
https://www.encodeproject.org/experiments/ENCSR590IHT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF302 ChIP-seq on human A549
experiment encode accession: ENCSR590IHT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR365RFY, ENCSR928HJI
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB419OJX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

value: 58 year

value: Michael Snyder, Stanford

value: Michael Snyder

value: ENCBS108ZNW at ENCODE; https://www.encodeproject.org/ENCBS108ZNW/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: total RNA-seq from layer of hippocampus (ENCLB762AYJ)

description:
https://www.encodeproject.org/experiments/ENCSR912TCG/
***************
biological replicate number: 2
technical replicate number: 1
description: hippocampus B6Cast F1 2 months female
experiment encode accession: ENCSR912TCG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB762AYJ
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) layer of hippocampus tissue

value: layer of hippocampus

value: tissue

value: female

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS912RBR at ENCODE; https://www.encodeproject.org/ENCBS912RBR/


title: total RNA-seq from layer of hippocampus (ENCLB285MCK)

description:
https://www.encodeproject.org/experiments/ENCSR912TCG/
***************
biological replicate number: 1
technical replicate number: 1
description: hippocampus B6Cast F1 2 months female
experiment encode accession: ENCSR912TCG
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB285MCK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: ENCBS422YFH at ENCODE; https://www.encodeproject.org/ENCBS422YFH/

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


title: total RNA-seq from left cerebral cortex (ENCLB270TSD)

description:
https://www.encodeproject.org/experiments/ENCSR841KGE/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND4 Male L. cortex
experiment encode accession: ENCSR841KGE
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB270TSD
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 PND4 Male 04 left cerebral cortex for Wold biobank

value: 4 day

value: ENCBS178USG at ENCODE; https://www.encodeproject.org/ENCBS178USG/


title: ATAC-seq from motor neuron (ENCLB023QZM)

description:
https://www.encodeproject.org/experiments/ENCSR516YAD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR516YAD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB023QZM
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

source_name: Homo sapiens male adult (47 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

value: male

value: adult

value: 47 year

value: Michael Snyder, Stanford

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

value: Donor with Amyotrophic Lateral Sclerosis

value: ENCBS038RNY at ENCODE; https://www.encodeproject.org/ENCBS038RNY/

value: Derived from ENCODE donor ENCDO565NIZ; https://www.encodeproject.org/ENCDO565NIZ/


title: RNA-DNA SPRITE 046

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: ATAC-seq from motor neuron (ENCLB524ECH)

description:
https://www.encodeproject.org/experiments/ENCSR516YAD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR516YAD
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB524ECH
fragmentation methods: chemical (Tn5 transposase)
size range: 200-7000

value: ENCBS238JUI at ENCODE; https://www.encodeproject.org/ENCBS238JUI/


title: Bru-seq from mammary epithelial cell (ENCLB653HRM)

description:
https://www.encodeproject.org/experiments/ENCSR419IWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR419IWZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB653HRM
size range: 400-500

source_name: Homo sapiens female mammary epithelial primary cell

value: mammary epithelial cell

value: primary cell

value: female

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS438MAO at ENCODE; https://www.encodeproject.org/ENCBS438MAO/

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


title: RNA-DNA SPRITE 044


title: WGBS from heart (ENCLB854DQE)

description:
https://www.encodeproject.org/experiments/ENCSR899RXH/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse heart
experiment encode accession: ENCSR899RXH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB854DQE
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: heart

value: tissue

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

value: pooled male and female

value: healthy

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS881SQY at ENCODE; https://www.encodeproject.org/ENCBS881SQY/

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


title: TF ChIP-seq from K562 (ENCLB028HYC)

description:
https://www.encodeproject.org/experiments/ENCSR419CNA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR419CNA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR516XLO
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB028HYC
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ZC3H4

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS838UVE at ENCODE; https://www.encodeproject.org/ENCBS838UVE/

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


title: Bru-seq from mammary epithelial cell (ENCLB349PAI)

description:
https://www.encodeproject.org/experiments/ENCSR419IWZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR419IWZ
assay title: Bru-seq
assembly: GRCh38
encode release date: 2021-09-30
lab: Mats Ljungman, UMichigan
library encode accession: ENCLB349PAI
size range: 400-500

value: mammary epithelial cell

value: primary cell

value: unknown

value: not collected

value: Mats Ljungman, UMichigan

value: Lonza

value: ENCBS348PER at ENCODE; https://www.encodeproject.org/ENCBS348PER/

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


title: total RNA-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB294NEQ)

description:
https://www.encodeproject.org/experiments/ENCSR957WSE/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD8+ cell, activated Day 7
experiment encode accession: ENCSR957WSE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB294NEQ
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: naive CD8+ cell, activated Day 7

value: male

value: adult

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS900CSN at ENCODE; https://www.encodeproject.org/ENCBS900CSN/

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


title: WGBS from heart (ENCLB218DPS)

description:
https://www.encodeproject.org/experiments/ENCSR899RXH/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse heart
experiment encode accession: ENCSR899RXH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB218DPS
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: heart

value: tissue

value: Heart 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: ENCBS427EAY at ENCODE; https://www.encodeproject.org/ENCBS427EAY/

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


title: total RNA-seq from heart (ENCLB467OTI)

description:
https://www.encodeproject.org/experiments/ENCSR838GNN/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND25 Male heart
experiment encode accession: ENCSR838GNN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB467OTI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: B6Cast F1 PND25 Male 03 heart for Wold biobank

value: unknown

value: 25 day

value: The Jackson Laboratory

value: ENCBS139NCJ at ENCODE; https://www.encodeproject.org/ENCBS139NCJ/

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


title: RNA-DNA SPRITE 043

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: total RNA-seq from CD8-positive, alpha-beta memory T cell (ENCLB406YSY)

description:
https://www.encodeproject.org/experiments/ENCSR446LDS/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD8+ (CD3+CD8+CD45RO+ and CD45RO-CCR7-)
experiment encode accession: ENCSR446LDS
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB406YSY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: CD8-positive, alpha-beta memory T cell

value: primary cell

value: male

value: adult

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS706HGH at ENCODE; https://www.encodeproject.org/ENCBS706HGH/

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


title: RNA-DNA SPRITE 045


title: total RNA-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB191PAE)

description:
https://www.encodeproject.org/experiments/ENCSR856VAD/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD4+ T cell, activated Day 7
experiment encode accession: ENCSR856VAD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB191PAE
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: ENCBS707KPO at ENCODE; https://www.encodeproject.org/ENCBS707KPO/

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


title: total RNA-seq from heart (ENCLB622UER)

description:
https://www.encodeproject.org/experiments/ENCSR838GNN/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND25 Male heart
experiment encode accession: ENCSR838GNN
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB622UER
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 PND25 Male 04 heart for Wold biobank

value: unknown

value: 25 day

value: The Jackson Laboratory

value: ENCBS857DKA at ENCODE; https://www.encodeproject.org/ENCBS857DKA/

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


title: TF ChIP-seq from K562 (ENCLB268IBX)

description:
https://www.encodeproject.org/experiments/ENCSR419CNA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR419CNA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR516XLO
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB268IBX
fragmentation methods: sonication (generic)

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS944EOM at ENCODE; https://www.encodeproject.org/ENCBS944EOM/

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


title: total RNA-seq from HFFc6 (ENCLB331EOB)

description:
https://www.encodeproject.org/experiments/ENCSR636LEU/
***************
biological replicate number: 1
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 300 ng
experiment encode accession: ENCSR636LEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB331EOB
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

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 042

tag: cell line

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from HFFc6 (ENCLB699NAA)

description:
https://www.encodeproject.org/experiments/ENCSR636LEU/
***************
biological replicate number: 3
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 300 ng
experiment encode accession: ENCSR636LEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB699NAA
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: ENCBS249LEB at ENCODE; https://www.encodeproject.org/ENCBS249LEB/


title: WGBS from heart (ENCLB869FAJ)

description:
https://www.encodeproject.org/experiments/ENCSR899RXH/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse heart
experiment encode accession: ENCSR899RXH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB869FAJ
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: heart

value: tissue

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

value: pooled male and female

value: healthy

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS881SQY at ENCODE; https://www.encodeproject.org/ENCBS881SQY/

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


title: RNA-DNA SPRITE 041

tag: cell type


title: DNase-seq from head of caudate nucleus (ENCLB068KJR)

description:
https://www.encodeproject.org/experiments/ENCSR511PFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR511PFY
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-08-31
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB068KJR
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 4000

source_name: Homo sapiens male adult (90 or above years) with Alzheimer's disease; head of caudate nucleus tissue

value: head of caudate nucleus

value: male

value: 90 or above year

value: John Stamatoyannopoulos, UW

value: Rush University

value: ENCBS116GVY at ENCODE; https://www.encodeproject.org/ENCBS116GVY/

value: Derived from ENCODE donor ENCDO287LNQ; https://www.encodeproject.org/ENCDO287LNQ/


title: total RNA-seq from adrenal gland (ENCLB860TKG)

description:
https://www.encodeproject.org/experiments/ENCSR748DUR/
***************
biological replicate number: 1
technical replicate number: 1
description: adrenal gland_B6Cast F1 PND 18-20 months_Male 03_ENC4_cDNA462
experiment encode accession: ENCSR748DUR
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB860TKG
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 (18-20 months) adrenal gland tissue

value: adrenal gland

value: unknown

value: 18-20 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS999WBI at ENCODE; https://www.encodeproject.org/ENCBS999WBI/

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


title: total RNA-seq from HFFc6 (ENCLB913AQA)

description:
https://www.encodeproject.org/experiments/ENCSR636LEU/
***************
biological replicate number: 2
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 300 ng
experiment encode accession: ENCSR636LEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB913AQA
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

value: normal

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

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


title: RNA-DNA SPRITE 040

value: Female ES cells

tag: protocol

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from HFFc6 (ENCLB526VPN)

description:
https://www.encodeproject.org/experiments/ENCSR636LEU/
***************
biological replicate number: 1
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 300 ng
experiment encode accession: ENCSR636LEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB526VPN
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: male

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


title: WGBS from liver (ENCLB760KHX)

description:
https://www.encodeproject.org/experiments/ENCSR733ZTZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse liver
experiment encode accession: ENCSR733ZTZ
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB760KHX
fragmentation methods: shearing (Covaris S2)
size range: 180-500

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

value: liver

value: tissue

value: Liver 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: ENCBS702AET at ENCODE; https://www.encodeproject.org/ENCBS702AET/

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


title: WGBS from heart (ENCLB626OSX)

description:
https://www.encodeproject.org/experiments/ENCSR899RXH/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse heart
experiment encode accession: ENCSR899RXH
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB626OSX
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: heart

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

value: ENCBS427EAY at ENCODE; https://www.encodeproject.org/ENCBS427EAY/


title: total RNA-seq from gastrocnemius (ENCLB958XPL)

description:
https://www.encodeproject.org/experiments/ENCSR809JHL/
***************
biological replicate number: 1
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 2 months Male
experiment encode accession: ENCSR809JHL
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB958XPL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

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

value: gastrocnemius

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

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS258UBR at ENCODE; https://www.encodeproject.org/ENCBS258UBR/

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


title: ATAC-seq from regulatory T cell (ENCLB669MTR)

description:
https://www.encodeproject.org/experiments/ENCSR504OUW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR504OUW
assay title: ATAC-seq
assembly: GRCh38
encode release date: 2021-10-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB669MTR
fragmentation methods: chemical (Tn5 transposase)
size range: 150-1000

source_name: Homo sapiens male adult (38 years) regulatory T primary cell

value: regulatory T cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS739HXE at ENCODE; https://www.encodeproject.org/ENCBS739HXE/

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


title: total RNA-seq from HFFc6 (ENCLB677SFX)

description:
https://www.encodeproject.org/experiments/ENCSR636LEU/
***************
biological replicate number: 3
technical replicate number: 2
description: Clonal line 6 derived from hTert immortalized HFF 300 ng
experiment encode accession: ENCSR636LEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB677SFX
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

value: normal

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 gastrocnemius (ENCLB930KUU)

description:
https://www.encodeproject.org/experiments/ENCSR809JHL/
***************
biological replicate number: 2
technical replicate number: 1
description: gastrocnemius B6Cast F1 PND 2 months Male
experiment encode accession: ENCSR809JHL
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB930KUU
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 Male 04 gastrocnemius for Wold core

value: unknown

value: 2 month

value: Barbara Wold, Caltech

value: The Jackson Laboratory

value: ENCBS689CSE at ENCODE; https://www.encodeproject.org/ENCBS689CSE/

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


title: RNA-DNA SPRITE 038

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

source_name: Mouse Embryonic Stem cells

value: Female ES cells

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: WGBS from liver (ENCLB438NFH)

description:
https://www.encodeproject.org/experiments/ENCSR733ZTZ/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse liver
experiment encode accession: ENCSR733ZTZ
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB438NFH
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: liver

tag: description

value: Liver 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: ENCBS702AET at ENCODE; https://www.encodeproject.org/ENCBS702AET/

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


title: TF ChIP-seq from K562 (ENCLB821FEZ)

description:
https://www.encodeproject.org/experiments/ENCSR415NNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-THAP12 ChIP-seq on human K562
experiment encode accession: ENCSR415NNQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR334KTB
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB821FEZ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens THAP12

value: cell line

tag: biosample encode accession

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: ENCBS982PFW at ENCODE; https://www.encodeproject.org/ENCBS982PFW/

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


title: Histone ChIP-seq from motor neuron (ENCLB357VKI)

description:
https://www.encodeproject.org/experiments/ENCSR503HWR/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR503HWR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR663GIS
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB357VKI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens male adult (49 years) with amyotrophic lateral sclerosis; motor neuron in vitro differentiated cells

value: motor neuron

value: in vitro differentiated cells

value: iPSC-derived motor neuron

tag: Sex

value: male

value: Donor with Amyotrophic Lateral Sclerosis

value: 49 year

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

value: ENCBS855DRG at ENCODE; https://www.encodeproject.org/ENCBS855DRG/

value: Derived from ENCODE donor ENCDO272LDF; https://www.encodeproject.org/ENCDO272LDF/


title: total RNA-seq from A673 (ENCLB800GHN)

description:
https://www.encodeproject.org/experiments/ENCSR558SEE/
***************
biological replicate number: 1
technical replicate number: 1
description: A673 for bru-seq comparison
experiment encode accession: ENCSR558SEE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB800GHN
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 A673 cell line

value: cell line

tag: dev stage

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ENCBS119CST at ENCODE; https://www.encodeproject.org/ENCBS119CST/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: Histone ChIP-seq from motor neuron (ENCLB847IWX)

description:
https://www.encodeproject.org/experiments/ENCSR503HWR/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on human motor neuron
experiment encode accession: ENCSR503HWR
assay title: Histone ChIP-seq
assembly: GRCh38
possible controls: ENCSR663GIS
encode release date: 2021-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB847IWX
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: adult

tag: age

value: Michael Snyder, Stanford

value: ENCBS980NQQ at ENCODE; https://www.encodeproject.org/ENCBS980NQQ/


title: WGBS from liver (ENCLB506AYR)

description:
https://www.encodeproject.org/experiments/ENCSR733ZTZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on 8 week adult mouse liver
experiment encode accession: ENCSR733ZTZ
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB506AYR
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: liver

value: tissue

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

value: pooled male and female

value: healthy

tag: lab

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS986WRA at ENCODE; https://www.encodeproject.org/ENCBS986WRA/

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


title: RNA-DNA SPRITE 036

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: DNase-seq from effector memory CD8-positive, alpha-beta T cell (ENCLB531DOW)

description:
https://www.encodeproject.org/experiments/ENCSR582MYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR582MYC
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-02
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB531DOW

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

value: primary cell

value: male

value: 36 year

value: John Stamatoyannopoulos, UW

tag: source

value: StemExpress

value: ENCBS996ZCK at ENCODE; https://www.encodeproject.org/ENCBS996ZCK/

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


title: total RNA-seq from activated CD4-positive, alpha-beta memory T cell (ENCLB883TLN)

description:
https://www.encodeproject.org/experiments/ENCSR777TBF/
***************
biological replicate number: 1
technical replicate number: 1
description: Memory CD4+ T cell, activated Day 2
experiment encode accession: ENCSR777TBF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB883TLN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: Memory CD4+ T cell, activated Day 2

value: adult

value: 43 year

value: Barbara Wold, Caltech

value: AllCells

tag: link

value: ENCBS655INE at ENCODE; https://www.encodeproject.org/ENCBS655INE/

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


title: RNA-DNA SPRITE 037

value: Female ES cells


title: total RNA-seq from HFFc6 (ENCLB699ONZ)

description:
https://www.encodeproject.org/experiments/ENCSR636LEU/
***************
biological replicate number: 2
technical replicate number: 1
description: Clonal line 6 derived from hTert immortalized HFF 300 ng
experiment encode accession: ENCSR636LEU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB699ONZ
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

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

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


title: RNA-DNA SPRITE 035

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: total RNA-seq from A673 (ENCLB449BKF)

description:
https://www.encodeproject.org/experiments/ENCSR558SEE/
***************
biological replicate number: 2
technical replicate number: 1
description: A673 for bru-seq comparison
experiment encode accession: ENCSR558SEE
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB449BKF
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: female

value: child

value: 15 year

value: Mats Ljungman, UMichigan

value: ATCC

value: ENCBS060KJN at ENCODE; https://www.encodeproject.org/ENCBS060KJN/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/


title: total RNA-seq from activated CD8-positive, alpha-beta T cell (ENCLB531XDR)

description:
https://www.encodeproject.org/experiments/ENCSR552RFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: CD8+ T cells, activated day 7
experiment encode accession: ENCSR552RFJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB531XDR
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: male

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: ENCBS272IFK at ENCODE; https://www.encodeproject.org/ENCBS272IFK/

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


title: TF ChIP-seq from K562 (ENCLB106AWH)

description:
https://www.encodeproject.org/experiments/ENCSR415NNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-THAP12 ChIP-seq on human K562
experiment encode accession: ENCSR415NNQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR334KTB
encode release date: 2021-06-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB106AWH
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

tag: antibody

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS972UYE at ENCODE; https://www.encodeproject.org/ENCBS972UYE/

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


title: DNase-seq from natural killer cell (ENCLB201BKX)

description:
https://www.encodeproject.org/experiments/ENCSR407WGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR407WGG
assay title: DNase-seq
assembly: GRCh38
encode release date: 2021-09-10
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB201BKX

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

value: natural killer cell

value: female

value: 41 year

value: John Stamatoyannopoulos, UW

value: StemExpress

value: ENCBS965EEA at ENCODE; https://www.encodeproject.org/ENCBS965EEA/

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


title: WGBS from liver (ENCLB585SDT)

description:
https://www.encodeproject.org/experiments/ENCSR733ZTZ/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on 8 week adult mouse liver
experiment encode accession: ENCSR733ZTZ
assay title: WGBS
assembly: mm10
encode release date: 2018-03-30
lab: Joe Ecker, Salk
library encode accession: ENCLB585SDT
fragmentation methods: shearing (Covaris S2)
size range: 180-500

value: liver

value: tissue

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

value: pooled male and female

value: healthy

value: adult

value: Len Pennacchio, LBNL

value: Len Pennacchio

value: ENCBS986WRA at ENCODE; https://www.encodeproject.org/ENCBS986WRA/

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


title: RNA-DNA SPRITE 034

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 039


title: total RNA-seq from activated CD8-positive, naive alpha-beta T cell (ENCLB987AXH)

description:
https://www.encodeproject.org/experiments/ENCSR437HKI/
***************
biological replicate number: 1
technical replicate number: 1
description: naive CD8+ cell, activated Day 7
experiment encode accession: ENCSR437HKI
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB987AXH
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: naive CD8+ cell, activated Day 7

value: male

value: 30 year

value: Barbara Wold, Caltech

value: AllCells

value: ENCBS454JUB at ENCODE; https://www.encodeproject.org/ENCBS454JUB/

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


title: TF ChIP-seq from HepG2 (ENCLB111YSW)

description:
https://www.encodeproject.org/experiments/ENCSR414WBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR414WBQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB111YSW
fragmentation methods: sonication (generic)

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

value: NFIB

value: cell line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS410QPV at ENCODE; https://www.encodeproject.org/ENCBS410QPV/

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


title: total RNA-seq from heart (ENCLB196DAW)

description:
https://www.encodeproject.org/experiments/ENCSR795WFC/
***************
biological replicate number: 1
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Male heart
experiment encode accession: ENCSR795WFC
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB196DAW
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) heart tissue

value: heart

value: tissue

value: B6Cast F1 DPN18-20months

value: adult

value: 18-20 month

value: The Jackson Laboratory

value: ENCBS540JOT at ENCODE; https://www.encodeproject.org/ENCBS540JOT/

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


title: RNA-DNA SPRITE 033

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: TF ChIP-seq from HepG2 (ENCLB767WSF)

description:
https://www.encodeproject.org/experiments/ENCSR414WBQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR414WBQ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR661ZUK
encode release date: 2021-08-13
lab: Richard Myers, HAIB
library encode accession: ENCLB767WSF
fragmentation methods: sonication (generic)

value: NFIB

value: cell line

value: male

value: child

value: 15 year

value: ENCBS267GGP at ENCODE; https://www.encodeproject.org/ENCBS267GGP/


title: total RNA-seq from heart (ENCLB497GBO)

description:
https://www.encodeproject.org/experiments/ENCSR795WFC/
***************
biological replicate number: 2
technical replicate number: 1
description: B6Cast F1 PND 18-20 months Male heart
experiment encode accession: ENCSR795WFC
assay title: total RNA-seq
assembly: mm10
encode release date: 2021-08-18
lab: Barbara Wold, Caltech
library encode accession: ENCLB497GBO
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: Barbara Wold, Caltech

value: ENCBS897MIA at ENCODE; https://www.encodeproject.org/ENCBS897MIA/


title: total RNA-seq from activated CD4-positive, alpha-beta T cell (ENCLB036DLQ)

description:
https://www.encodeproject.org/experiments/ENCSR593MZL/
***************
biological replicate number: 1
technical replicate number: 1
description: CD4+ T cells, activated day 7
experiment encode accession: ENCSR593MZL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-06-17
lab: Barbara Wold, Caltech
library encode accession: ENCLB036DLQ
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 10 ng/mL Interleukin-2 , 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_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: ENCBS456ENT at ENCODE; https://www.encodeproject.org/ENCBS456ENT/

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


title: RNA-DNA SPRITE 030

value: Female ES cells

value: RNA-DNA SPRITE

value: 24hr doxycycline for Xist induction


title: RNA-DNA SPRITE 029


title: RNA-DNA SPRITE 031