title: PT6_MPNST_D

status: Public on Feb 11 2020

city: Iowa City

first: Benjamin

middle: W

last: Darbro

state: IA

address: 200 Hawkins Drive

institute: University of Iowa

data_processing:
RNA-Seq reads were processed with the pseudoalignment tool Kallisto
Differential expression was analyzed with the statistical R package Sleuth
Default settings were used with the exception that fold change values were calculated using a log2 and not natural log transformation
Samples with less than 10 million mapping reads were excluded from further analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample

source_name: MPNST

extract_protocol:
Total RNA was extracted using the RNeasy FFPE Kit (Qiagen, Valencia, CA) and its quality assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Agilent SureSelect RNA Direct protocol with the SureSelect Human All Exon V6 + COSMIC enrichment library
Sequencing was performed on the Illumina HiSeq 4000 genome sequencer (Illumina, San Diego, CA) using a 150 bp paired-end sequencing-by-synthesis chemistry

treatment_protocol: The plexiform and MPNST tissues used for extraction and subsequent RNA sequencing were 1.0-mm cores taken from formalin fixed paraffin embedded tissue

tag: disease state

value: Malignant Peripheral Nerve Sheath Tumor

tag: patient

value: Patient 6


title: PT6_PNF_C

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: PNF

value: Plexiform Neurofibroma


title: TF ChIP-seq from HEK293 (ENCLB847ZIR)

status: Public on Feb 12 2020

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR185QFX/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF549 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR185QFX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR300VIY, ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX, ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2018-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB847ZIR
size range: 450-650

library_source: genomic

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

molecule: genomic DNA

source_name: Homo sapiens HEK293 cell line genetically modified (insertion) using site-specific recombination targeting eGFP-ZNF549 originated from HEK293

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: Sex

value: female

tag: health state

value: unknown

tag: dev stage

value: embryonic

tag: age

tag: lab

value: Michael Snyder, Stanford

tag: link

value: Derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/

value: ENCBS716EYG at ENCODE; https://www.encodeproject.org/ENCBS716EYG/

value: ENCODE dbxrefs Cellosaurus CVCL_0045; https://web.expasy.org/cellosaurus/CVCL_0045


title: TF ChIP-seq from HEK293 (ENCLB196JIW)

description:
https://www.encodeproject.org/experiments/ENCSR146NLL/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-REPIN1 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR146NLL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-03-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB196JIW
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-REPIN1 fusion protein

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-REPIN1 under the control of a CMV promoter.

value: ENCBS440JWN at ENCODE; https://www.encodeproject.org/ENCBS440JWN/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: TF ChIP-seq from HEK293 (ENCLB853TZR)

description:
https://www.encodeproject.org/experiments/ENCSR443MVV/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-PRDM4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR443MVV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB853TZR
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-PRDM4 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-PRDM4 under the control of a CMV promoter.

value: ENCBS090OPS at ENCODE; https://www.encodeproject.org/ENCBS090OPS/


title: TF ChIP-seq from HEK293 (ENCLB949YFY)

description:
https://www.encodeproject.org/experiments/ENCSR443MVV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-PRDM4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR443MVV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR598OXI, ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-02-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB949YFY
size range: 450-650

value: ENCBS269DNN at ENCODE; https://www.encodeproject.org/ENCBS269DNN/


title: ChIP-seq from sigmoid colon (ENCLB680QMR)

description:
https://www.encodeproject.org/experiments/ENCSR338PIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR338PIQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR236MWZ
encode release date: 2016-07-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB680QMR
size range: 450-650

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

extract_protocol: not provided

value: sigmoid colon

value: tissue

value: 53 year

value: adult

value: ENCBS835BNK at ENCODE; https://www.encodeproject.org/ENCBS835BNK/

value: derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: PT4_MPNST_A

value: Malignant Peripheral Nerve Sheath Tumor

value: Patient 4


title: PT4_PNF_A

value: Plexiform Neurofibroma


title: PT10_PNF_B

value: Patient 10


title: PT8_MPNST_B

value: Patient 8


title: PT2_PNF_C

value: Patient 2


title: PT12_MPNST_A

value: Patient 12


title: PT14_MPNST_A

value: Patient 14


title: PT15_MPNST_B

value: Patient 15


title: PT1_MPNST_A

value: Patient 1


title: PT13_PNF_A

value: Patient 13


title: PT6_PNF_B

value: Patient 6


title: PT5_MPNST_A

value: Patient 5


title: PT1_PNF_C


title: PT8_PNF_A


title: PT7_MPNST_A

value: Patient 7


title: PT1_PNF_B


title: PT10_PNF_A


title: PT10_MPNST_E


title: PT6_MPNST_C


title: wnt4CD24l_3

status: Public on Feb 22 2020

type: RNA

city: Lausanne

first: Giovanna

last: Ambrosini

address: Station 19

country: Switzerland

institute: EPFL

description: Wnt-4 fl/fl CD24 Low

hyb_protocol: Fluidics protocol FS450_0007

scan_protocol: GeneChip® Scanner 3000 7G  and Power Tools software package (Affymetrix)

data_processing:
Normalized expression signals were calculated from Affymetrix CEL files by the Robust Multi-array Average algorithm (RMA) using the Affymetrix Expression Console Software (version 1.1.2800)
GeneSpring GX 7.3.1

label: biotin

organism: Mus musculus

source_name: Mammary glands

label_protocol: Ovation® Pico WTA System V2 and FL-Ovation cDNA Biotin module V2 (Nugen)

growth_protocol: Conditionally Wnt4 deleted (MMTV::Cre+.Wnt4fl/fl.mT/mG) and control (MMTV::Cre+.Wnt4wt/wt.mT/mG) 10 to 14-week-old female mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The concentration and purity of cRNA was verified on the Bioanalyzer

treatment_protocol: At sacrifice, mammary grafts were mechanically and enzymatically digested, and total cell population was labeled with CD24. Subsequently, cells were FACSsorted based on GFP into CD24 high (Luminal) and CD24 low (myoepithelial) cells, which were then lysed, RNA was extracted, and analyzed by microarray analysis.

tag: genotype

value: Wnt4 deletion


title: PT4_PNF_C


title: PT11_MPNST_B

value: Patient 11


title: PT2_PNF_B


title: PT10_MPNST_C


title: PT14_MPNST_B


title: PT11_MPNST_A


title: PT10_MPNST_B


title: Input_ChIP-Seq_WT_rep2

status: Public on Feb 18 2020

city: Granada

first: Carlos

last: Cordon-Obras

address: Av del Conocimiento

country: Spain

institute: Instituto Parasitologia Lopez Neyra

description:
Input_ChIP-Seq_WT_rep2
A11_HP1_2_FE.bigWig

data_processing:
Demultiplexing with bcl2fastq (Illumina) software v2.19.1.403
ChIP-Seq reads aligned to the genome using BWA v0.7.10-r789 with default parameters
Data sorted, indexed and PCR duplicates filteres using samtools v1.3
Peak calling (callpeak option) and calculation of fold enrichment over input (bdgcmp option) performed with MACS2 (v2.1.1.20160309) software using -BAMPE and --SPMR options.
Genome_build: PlasmoDB-29_Pfalciparum3D7
Supplementary_files_format_and_content: BigWig files obtained using bedGraphToBigWig software v4

organism: Plasmodium falciparum

source_name: In vitro cultured blood stage cells

growth_protocol: Blood stage P. falciparum parasites were cultured in human O+ red blood cells in RPMI-1640 medium supplemented with Albumax II (10% v/v), hypoxanthine (200 μM) and gentamycin (50 μg/ml) in 3% CO2 and 5% O2 at 37 °C.

extract_protocol:
ChIP was performed as previously described (Zanghi et al, 2018 Cell. Rep.) with parasites synchronised at 36 hpi. Sonicated chromatin (500 ng DNA content) was immunoprecipitated overnight with 0.5 μg of anti-HP1 polyclonal rabbit antibodies. and incubated after with 25 μl of Dynabeads Protein G (Invitrogen) for two hours. Subsequent washing, cross-link reversion and DNA extraction were carried out as described before.
Sequencing libraries were produced with the immunoprecipitated DNA using the MicroPlex Library Preparation Kit v2 (Diagenode) with the KAPA HiFi polymerase (Kapa Biosystems) for the PCR amplification. For each ChIP sample, a control DNA corresponding to the ChIP input was processed in parallel.

value: NF54 A11 parental wildtype

tag: chip antibody


title: PT5_PNF_A


title: PT3_PNF_A

value: Patient 3


title: PT6_MPNST_B

value: Malignant Peripheral Nerve Sheath Tumor


title: PT12_MPNST_B


title: PT2_PNF_A

value: Plexiform Neurofibroma


title: PT15_MPNST_A


title: PT9_PNF_A

value: Patient 9


title: PT10_MPNST_A

value: Patient 10


title: PT1_PNF_A


title: PT8_MPNST_A

value: Patient 8


title: PT9_MPNST_A


title: PT4_PNF_B

value: Patient 4


title: PSC-to-Pancreatic-Islet-Cell

status: Public on Feb 10 2020

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

source_name: Microwell-seq analysis

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

value: Not determined

tag: tissue

value: Cultured-Cell-from-PSC


title: PT3_MPNST_A


title: Placenta1

value: Placenta


title: Neonatal-Adrenal-Gland1-1

value: Female

value: Adrenal-Gland


title: Neonatal-Adrenal-Gland1-2


title: iPS-to-EB_18Day

value: Cultured-Cell-from-iPS


title: PT6_PNF_A

value: Patient 6


title: iPS-to-EB_9Day


title: PT11_PNF_A


title: Fetal-Stomach2

value: Stomach


title: iPS-to-EB_20Day


title: Fetal-Thymus2

value: Male

value: Thymus


title: iPS

value: male

value: iPS


title: Fetal-Rib3

value: Rib


title: Fetal-Skin3

value: Skin


title: Fetal-Spinal-Cord1

value: Spinal-Cord


title: Fetal-Skin2


title: Fetal-Rib2


title: Fetal-Pancreas3

value: Pancreas


title: Fetal-Pancreas2


title: Fetal-Pancreas1


title: Fetal-Male-Gonad2

value: Fetal-Gonad


title: Fetal-Muscle1

value: Muscle


title: Fetal-Male-Gonad1


title: Fetal-Lung2

value: Lung


title: Fetal-Lung1


title: Fetal-Thymus1


title: Fetal-Stomach1


title: Fetal-Liver1-2

value: Liver


title: Fetal-Kidney3

value: Kidney


title: Fetal-Intestine4

value: Female

value: Intestine


title: Fetal-Intestine3


title: Fetal-Kidney4


title: Fetal-Kidney6


title: Fetal-Kidney5


title: Fetal-Intestine5


title: Fetal-Heart1

value: Heart


title: Fetal-Heart2


title: Fetal-Intestine2


title: Fetal-Intestine1


title: Fetal-Female-Gonad1


title: Fetal-Eyes1

value: Eyes


title: Fetal-Calvaria1

value: Calvaria


title: Fetal-Brain4

value: Brain


title: Fetal-Adrenal-Gland4

value: Male

value: Adrenal-Gland


title: Fetal-Brain3


title: Fetal-Adrenal-Gland3


title: Fetal-Liver1-1


title: Embryonic-Stem-Cell

value: female


title: Cord-Blood2-CD34P2-2

value: Not determined

value: Cord-Blood


title: Cord-Blood-CD34P1


title: Cord-Blood2-CD34P2-1


title: Cord-Blood2-2


title: Cord-Blood2-1


title: Adult-Uterus1

value: Uterus


title: Chorionic-Villus1

value: Chorionic-Villus


title: Cord-Blood1


title: Fetal-Female-Gonad2

value: Fetal-Gonad


title: Adult-Trachea2

value: Trachea


title: Adult-Temporal-Lobe1-3


title: Adult-Temporal-Lobe1-2


title: Fetal-Brain6


title: Fetal-Brain5


title: Adult-Temporal-Lobe1-1


title: Adult-Spleen1-2

value: Spleen


title: Adult-Spleen1-1


title: Adult-Peripheral-Blood4-3

value: Peripheral-Blood


title: Adult-Pleura1

value: Pleura


title: Fetal-Adrenal-Gland2


title: Adult-Peripheral-Blood4-2


title: Adult-Peripheral-Blood3-2


title: Adult-Peripheral-Blood2


title: Adult-Peripheral-Blood1


title: Adult-Omentum3

value: Omentum


title: Adult-Ureter1

value: Female

value: Ureter


title: Adult-Omentum2


title: Adult-Muscle1

value: Muscle


title: Adult-Kidney4-2

value: Kidney


title: Adult-Kidney4-1

value: Male


title: Adult-Kidney3


title: Adult-Heart2

data_processing:
Base-calls were performed with Illumina bcl2fastq
The cell barcode can be found in read1, the bases 1-6,22-27,43-48 merge (18bp); UMI: In read1, the bases 49-54 (6bp)
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

value: Heart


title: Adult-Kidney2


title: Adult-Heart1


title: Adult-Bone-Marrow2

value: Bone-Marrow


title: Adult-Fallopian-Tube1

value: Fallopian-Tube


title: Adult-Cerebellum1

value: Brain


title: Adult-Cervix1

value: Cervix


title: Adult-Peripheral-Blood4-1


title: Adult-Artery1

value: Artery


title: Adult-Epityphlon1

value: Intestine


title: Adult-Peripheral-Blood3-1


title: Adult-Adrenal-Gland3

value: Adrenal-Gland


title: Adult-Bone-Marrow1

data_processing:
Base-calls were performed with Illumina bcl2fastq
The cell barcode can be found in read1, the bases 1-6,22-27,43-48 merge (18bp); UMI: In read1, the bases 49-54 (6bp)
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Homo_sapiens. GRCh38 assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Homo_sapiens. GRCh38
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

value: Bone Marrow


title: mTECs_Chd4cKO_3_RNA-seq

status: Public on Feb 07 2020

city: bunkyo

first: Yoshihiko

last: Tomofuji

state: Tokyo

address: hongo 7-3-1

department: Immunology

country: Japan

institute: University of Tokyo

description:
mTECs_Chd4cKO_3
mTECs from Chd4 flox/flox Foxn1-Cre mice
processed data file: RNA_seq_data_summary.txt

data_processing:
Data was trimmed and mapped to reference Mus musculus (mm10) genome by using CLC genomics Workbench v.9.0 (CLC).
RPKM was calculated by using CLC genomics Workbench v.9.0 (CLC).
log(RPKM) was calculated and DEGs were detected from total exon reads by using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RNA_seq_data_summary.txt
Supplementary_files_format_and_content: Aire_KO_RNA_seq.csv, Chd4_cKO_RNA_seq.csv, Fezf2_KO_RNA_seq.csv

source_name: mTECs

extract_protocol:
Total RNA from sorted mTECs is extracted by Maxwell® 16 Automated Purification System (Promega).
Library for sequencing was synthesized using SMART-seq v4 Ultra Low Input RNA Kit.

tag: strain

tag: genotype/variation

tag: cell type

value: TECs


title: PT10_MPNST_D

tag: disease state

value: Malignant Peripheral Nerve Sheath Tumor

tag: patient

value: Patient 10


title: Adult-Adipose1

value: Adipose


title: Adult-Adrenal-Gland2


title: mTECs_Chd4cKO_2_RNA-seq

description:
mTECs_Chd4cKO_2
mTECs from Chd4 flox/flox Foxn1-Cre mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_Chd4cKO_1_RNA-seq

description:
mTECs_Chd4cKO_1
mTECs from Chd4 flox/flox Foxn1-Cre mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_Chd4CTL_2_RNA-seq

description:
mTECs_Chd4CTL_2
mTECs from Chd4 flox/flox mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_Chd4CTL_1_RNA-seq

description:
mTECs_Chd4CTL_1
mTECs from Chd4 flox/flox mice
processed data file: RNA_seq_data_summary.txt


title: mTECs_Chd4CTL_3_RNA-seq

description:
mTECs_Chd4CTL_3
mTECs from Chd4 flox/flox mice
processed data file: RNA_seq_data_summary.txt


title: 3.D 72h.2

status: Public on Feb 06 2020

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Fastq files were quality-checked using FastQC v0.10.1
Reads were aligned to the human genome (GRCh38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9 allowing two mismatches and five multihits
Transcript quantification was calculated with htseq and differential expression was calculated with DEseq2
using the human GRCh38 transcript annotations
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text file includes normalized counts for each sample

source_name: Pancreatic cancer

growth_protocol:
Panc-163 and Panc-410 cell lines were grown in DMEM 10% pen/strep 10% FBS
Panc-215 cell line was grown in RPMI 10% pen/strep 10% FBS

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Taxol was added during 24 hours and then washed it out
Palbociclib treatment started 24 hours later and was maintained until the indicated time points
Combination: Taxol 24 hours followed by Palbociclib maintained until the indicated time points
DMSO was added during 24 hours

tag: cell line

value: Pancreatic cancer cell line

tag: treatment

value: Combination

tag: time-point

value: 72 hours


title: Adult-Esophagus1

tag: Sex

value: Male

value: Esophagus


title: 3.D 48h.2

value: 48 hours


title: 3.D 48h.1


title: mTECs_from_Chd4cKO_mice_ATAC-seq_2

description:
ATAC_Chd4cKO_2
ATAC-seq for mTECs from Chd4 fl/fl Foxn1 Cre mice
processed data file: ATAC_Chd4cKO.bw

data_processing:
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 ver2.3.2.
Duplicates were removed through command line interface.
Generated sam files were converted to bamfiles by using samtools.
bamfiles were converted to bigwig files by using deeptools.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files

extract_protocol:
5×10e4 mTEChi from 3- to 4-week-old male WT mice, Fezf2fl/fl Foxn1-Cre mice, or Chd4fl/fl Foxn1-Cre mice were used for preparation of ATAC-seq libraries.
Cells were suspended in 100 µl of cold hypotonic lysis buffer [10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP40], followed by immediate centrifugation at 550 g for 30 min. The pellet was re-suspended in 5 µl of transposition reaction mix [1 µl of Tagment DNA Enzyme and 2.5 µl of Tagment DNA Buffer from Nextera DNA Sample Prep Kit (Illumina), 1.5 µl H2O], and was incubated for 60 min at 37 °C for DNA to be fragmented and tagged. For library preparation, two sequential seven-cycles of PCR were performed to enrich small tagmented DNA fragments. After the PCR, the libraries were selected for large fragments (more than 100 bp) using AMPure XP.


title: 3.D 36h.2

value: 36 hours


title: 3.C 72h.1

value: Palbociclib


title: 3.C 72h.2


title: 3.C 48h.1


title: 3.C 48h.2


title: 3.C 36h.2


title: Adult-Esophagus2


title: 3.D 72h.1


title: 3.C 36h.1


title: 3.D 36h.1


title: 3.B 72h.2

value: Taxol


title: 3.B 36h.1


title: 3.B 48h.1


title: 3.B 36h.2


title: 3.A 24h.2

value: DMSO

value: 24 hours


title: 3.B 24h.2


title: 3.B 24h.1


title: mTECs_from_Chd4cKO_mice_ATAC-seq_1

description:
ATAC_Chd4cKO_1
ATAC-seq for mTECs from Chd4 fl/fl Foxn1 Cre mice
processed data file: ATAC_Chd4cKO.bw


title: 3.A 24h.1


title: 2.D 72h.2


title: 2.D 48h.2


title: 2.D 72h.1


title: 2.D 36h.1


title: 2.D 36h.2


title: 2.C 72h.2


title: 2.C 72h.1


title: 2.C 48h.2


title: 3.B 48h.2


title: 3.B 72h.1


title: 2.C 48h.1


title: 2.B 72h.1

description:
2.B 72h.1
processed data file: ALLsamples.normalizedCounts.xls

data_processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Fastq files were quality-checked using FastQC v0.10.1.
Reads were aligned to the human genome (GRCh38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9 allowing two mismatches and five multihits.
Transcript quantification was calculated with htseq and differential expression was calculated with DEseq2 using the human GRCh38 transcript annotations.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: ALLsamples.normalizedCounts.xls: Excel file includes normalized counts for each sample.

growth_protocol:
Panc-163 and Panc-410 cell lines were grown in DMEM 10% pen/strep 10% FBS.
Panc-215 cell line was grown in RPMI 10% pen/strep 10% FBS.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Life Technologies) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol:
Taxol was added during 24 hours and then washed out.
Palbociclib treatment started 24 hours later and was maintained until the indicated time points.
Combination: Taxol 24 hours followed by Palbociclib maintained until the indicated time points.
DMSO was added during 24 hours.


title: 2.B 72h.2

description:
2.B 72h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 2.B 48h.1

description:
2.B 48h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 2.B 36h.1

description:
2.B 36h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 2.C 36h.1

description:
2.C 36h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 2.B 36h.2

description:
2.B 36h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 2.D 48h.1

description:
2.D 48h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 2.C 36h.2

description:
2.C 36h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 2.B 24h.2

description:
2.B 24h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 2.B 24h.1

description:
2.B 24h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 2.B 48h.2

description:
2.B 48h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 2.A 24h.1

description:
2.A 24h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.D 72h.2

description:
1.D 72h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.D 72h.1

description:
1.D 72h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.C 72h.1

description:
1.C 72h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.C 72h.2

description:
1.C 72h.2
processed data file: ALLsamples.normalizedCounts.xls


title: PT6_MPNST_A

value: Patient 6


title: PT7_PNF_A

value: Plexiform Neurofibroma

value: Patient 7


title: 1.B 72h.2

description:
1.B 72h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.B 72h.1

description:
1.B 72h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.D 48h.1

description:
1.D 48h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.D 48h.2

description:
1.D 48h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.B 48h.2

description:
1.B 48h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.B 48h.1

description:
1.B 48h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.C 48h.2

description:
1.C 48h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.D 36h.2

description:
1.D 36h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.D 36h.1

description:
1.D 36h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.C 36h.2

description:
1.C 36h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 2.A 24h.2

description:
2.A 24h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.C 36h.1

description:
1.C 36h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.B 36h.1

description:
1.B 36h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.A 24h.2

description:
1.A 24h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.B 24h.1

description:
1.B 24h.1
processed data file: ALLsamples.normalizedCounts.xls


title: 1.B 24h.2

description:
1.B 24h.2
processed data file: ALLsamples.normalizedCounts.xls


title: 1.A 24h.1

description:
1.A 24h.1
processed data file: ALLsamples.normalizedCounts.xls


title: Allowtwaplko3 [Sample_116515]

status: Public on Feb 01 2020

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
reads aligned  to the reference mRNA transcriptome with TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
Differential expression Cufflinks/CuffDiff (version 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKMs

source_name: Donor Splenic Pan-T-cells from recipient spleen 7 days post HSCT

growth_protocol: Eight to 12 week-old female B6.SJL-Ptprca Pepcb/BoyJ (H-2b, CD45.1) and CByJ.SJL(B6)-Ptprca/J (H-2d, CD45.1) recipient mice were purchased from Jackson Laboratories.  Eight to twelve week-old female C57BL/6 (CD45.2) donor mice were purchased from Jackson Laboratories.  Animals were house under specific pathogen-free conditions.  All animal studies were approved by the University Committee on Use and Care of Animals of the University of Michigan, based on University Laboratory Animal Medicine guidelines. Naive WT and Wapl KO splenic T cells were isolated and processed for RNA isaolation and sequencing. Donor T cells (WT and Wapl KO) were iwssoalted from reciepients and sorted as we described. The sorted T cells were processed for RNA isolation and sequencing.

extract_protocol:
On day +7 post HSCT, donor splenic T-cells were harvested and enriched using the Pan T-cell Isolation Kit II (Miltenyi Biotec).  Live donor T-cells were subsequently flow sorted (LiveDead NearIR-/CD3-PE+/CD45.2-APC+).  RNA was extracted using the AllPrep DNA/RNA Mini Kit with on-column DNaseI digestion from Qiagen.
Libraries were constructed using 100ng of total RNA and the KAPA RNA HyperPrep Kit with  RiboErase per manufacturer instruction.

treatment_protocol: Murine bone marrow transplantation was performed on 8-12 week-old animals.  Splenic T-cells from donor mice were enriched using the Pan T-cell Isolation Kit II (Miltenyi Biotec), while bone marrow (BM) cells were depleted of T cells by using CD90.2 magnetic beads (Miltenyi Biotec).  B6.SJL-Ptprca Pepcb/BoyJ (syngeneic) and CByJ.SJL(B6)-Ptprca/J  (allogeneic) recipient mice were irradiated with 9.5 or 8 (dose split equally 3-4 hours apart) Gy from a 137Cs source, respectively, on day -1.  On day 0, recipient mice received via tail vein injection 5 x 10^6 T cell depleted (TCD) BM as well as 8.5 (syngeneic recipients) or 1 x 10^6 (allogeneic recipients) splenic T-cells from C57BL/6 donor mice.  All recipients received pH 3.0 water starting day -1.

tag: hsct type

value: Allogeneic (Wapl KO)

value: Donor sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic Wapl KO T-cells 7 days post allogeneic HSCT into BALB/c


title: Allowtwaplko1 [Sample_116513]


title: Allowtwaplko2 [Sample_116514]


title: Allowt1 [Sample_116510]

value: Allogeneic (WT control)

value: Donor sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic T-cells 7 days post allogeneic HSCT into BALB/c Recipients


title: Allowt2 [Sample_116511]


title: 1.C 48h.1

description:
1.C 48h.1
processed data file: ALLsamples.normalizedCounts.xls

value: Pancreatic cancer cell line


title: synwaplko1 [Sample_116507]

value: Syngeneic (Wapl KO)

value: Donor sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic Wapl KO T-cells 7 days post syngeneic HSCT into CByJ.SJL(B6)-Ptprca/J


title: synwaplko2 [Sample_116508]


title: Synwt3 [Sample_116506]

value: Syngeneic (WT control)

value: Donor sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic T-cells 7 days post syngeneic HSCT into B6.SJL-Ptprca Pepcb/BoyJ Recipients


title: Allowt3 [Sample_116512]


title: synwaplko3 [Sample_116509]


title: Synwt1 [Sample_116504]


title: Synwt2 [Sample_116505]


title: waplko3 [Sample_116503]

source_name: Spleen Pan-T-cells

value: Wapl KO

value: Naive sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic Walp KO T-cells


title: waplko2 [Sample_116502]

value: Naive sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic Wapl KO T-cells


title: waplko1 [Sample_116501]


title: wt3 [Sample_116500]

value: WT control

value: Naive sorted LiveDead Near IR-,CD3+,CD45.2+ C57BL/6 Splenic T-cells


title: wt2 [Sample_116499]


title: wt1 [Sample_116498]


title: 1.B 36h.2

description:
1.B 36h.2
processed data file: ALLsamples.normalizedCounts.xls

value: Taxol

value: 36 hours


title: ppp-1(wrm15) monosomal RNA replicate 3

city: Cologne

first: Martin

last: Denzel

address: Joseph-Stelzmann-Str. 9b

country: Germany

institute: Max Planck Institute for Biology of Ageing

description:
mutB_Mono_3
Monosome associated RNA

data_processing:
For data analysis, raw reads from all RNAseq, monosome and polysome sequencing replicates were mapped to the C. elegans reference genome (ENSEMBL 91) using HISAT2 (v2.1.0).
After guided transcriptome assembly with StringTie (v1.3.4d), transcriptomes were merged with Cuffmerge and quantification was performed with Cuffquant (Cufflinks v2.2.1).
The analysis for differential gene expression was performed with Cuffdiff (Cufflinks v2.2.1).
Genome_build: C. elegans reference genome (ENSEMBL 91) WBcel235
Supplementary_files_format_and_content: Tab separated file containing differential gene expression data

organism: Caenorhabditis elegans

source_name: Monosomal fraction of total worm lysis

growth_protocol: Synchronized worms were grown on regular NGM plates seeded with OP50 until day 1 of adulthood and then collected.

extract_protocol:
Synchronized gravid day 1 adults were grown on NGM plated seeded with OP50. Per genotype and replicate, ~12000 worms were harvested and washed twice with M9, once with M9 supplemented with 1 mM cycloheximide (Sigma) and once with lysis buffer (20 mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 0.5 % Nonidet P40, 1 mM DTT, 1 mM cycloheximide). Worms were pelleted and resuspended in 350 µL cold lysis buffer supplemented with 1% sodiumdeoxycholate (DOC, Sigma). Resuspended worms were lysed using a chilled Dounce homogenizer. Ribonuclease inhibitor RNasin (Promega) was added to samples at a concentration of 0,4 U/µL. Samples were then mixed and incubated on ice for 30 min, followed by a centrifugation step (12000 g, 10 minutes, 4°C) for clearance. The pellet was discarded and the RNA concentration of the supernatant was estimated by absorbance measurement at 260 nm.  To prepare sucrose gradients, 15% (w/v) and 60% (w/v) sucrose solutions were prepared in basic lysis buffer (20mM Tris pH 8.5, 140 mM KCl, 1.5 mM MgCl2, 1mM DTT, 1mM cycloheximide). Linear sucrose gradients were produced using a Gradient Master (Biocomp). Equivalent amounts of sample (around 400 µg RNA) were loaded on the gradient and centrifuged at 39000 g for 3 h at 4°C, using an Optima L-100 XP Ultracentrifuge (Beckman Coulter) and the SW41Ti rotor. To analyze the sample on the gradient during fractionation, absorbance at 254 nm was measured and recorded (Econo UV monitor EM-1, Biorad) using the Gradient Profiler software (version 2.07). Gradient fractionation was performed from the top down using a Piston Gradient Fractionator (Biocomp) and a fraction collector (Model 2110, Biorad). For precise analysis of ribosomal fractions, they were collected by hand according to their absorbance profile; for RNAseq and qPCR analyses, one fraction for 80S ribosomes and one for polysomes (excluding disomes) was collected per sample. RNA extraction from total lysates and from each fraction was performed using the Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer´s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols with a ribosomal RNA depletion method by Cologne Center for Genomics.

treatment_protocol: No treatment.

tag: strain/genotype

tag: age

value: Day 1 adults


title: ppp-1(wrm15) monosomal RNA replicate 1

description:
mutB_Mono_1
Monosome associated RNA


title: ppp-1(wrm15) polysomal RNA replicate 4

description:
mutB_Poly_4
Polysome associated RNA

source_name: Polysomal fraction of total worm lysis


title: ppp-1(wrm15) polysomal RNA replicate 3

description:
mutB_Poly_3
Polysome associated RNA


title: ppp-1(wrm15) monosomal RNA replicate 2

description:
mutB_Mono_2
Monosome associated RNA


title: ppp-1(wrm15) monosomal RNA replicate 4

description:
mutB_Mono_4
Monosome associated RNA


title: ppp-1(wrm15) polysomal RNA replicate 2

description:
mutB_Poly_2
Polysome associated RNA


title: ppp-1(wrm15) total RNA replicate 4

description:
mutB_Total_4
Total RNA

source_name: Total worm lysis


title: ppp-1(wrm15) polysomal RNA replicate 1

description:
mutB_Poly_1
Polysome associated RNA


title: ppp-1(wrm15) total RNA replicate 3

description:
mutB_Total_3
Total RNA


title: ppp-1(wrm10) monosomal RNA replicate 4

description:
mutA_Mono_4
Monosome associated RNA


title: ppp-1(wrm10) polysomal RNA replicate 1

description:
mutA_Poly_1
Polysome associated RNA


title: ppp-1(wrm10) polysomal RNA replicate 3

description:
mutA_Poly_3
Polysome associated RNA


title: ppp-1(wrm10) polysomal RNA replicate 4

description:
mutA_Poly_4
Polysome associated RNA


title: ppp-1(wrm15) total RNA replicate 2

description:
mutB_Total_2
Total RNA


title: ppp-1(wrm15) total RNA replicate 1

description:
mutB_Total_1
Total RNA


title: Wild type monosomal RNA replicate 4

description:
wt_Mono_4
Monosome associated RNA

value: Wild type (Bristol N2)


title: ppp-1(wrm10) monosomal RNA replicate 1

description:
mutA_Mono_1
Monosome associated RNA


title: ppp-1(wrm10) total RNA replicate 2

description:
mutA_Total_2
Total RNA


title: Wild type monosomal RNA replicate 2

description:
wt_Mono_2
Monosome associated RNA


title: Wild type monosomal RNA replicate 3

description:
wt_Mono_3
Monosome associated RNA


title: ppp-1(wrm10) total RNA replicate 4

description:
mutA_Total_4
Total RNA


title: ppp-1(wrm10) total RNA replicate 3

description:
mutA_Total_3
Total RNA


title: Wild type monosomal RNA replicate 1

description:
wt_Mono_1
Monosome associated RNA


title: Wild type polysomal RNA replicate 4

description:
wt_Poly_4
Polysome associated RNA


title: ppp-1(wrm10) total RNA replicate 1

description:
mutA_Total_1
Total RNA


title: ppp-1(wrm10) monosomal RNA replicate 3

description:
mutA_Mono_3
Monosome associated RNA


title: Wild type polysomal RNA replicate 3

description:
wt_Poly_3
Polysome associated RNA


title: ppp-1(wrm10) polysomal RNA replicate 2

description:
mutA_Poly_2
Polysome associated RNA


title: Wild type polysomal RNA replicate 2

description:
wt_Poly_2
Polysome associated RNA


title: Wild type polysomal RNA replicate 1

description:
wt_Poly_1
Polysome associated RNA


title: ppp-1(wrm10) monosomal RNA replicate 2

description:
mutA_Mono_2
Monosome associated RNA


title: Wild type total RNA replicate 4

description:
wt_Total_4
Total RNA


title: Wild type total RNA replicate 1

description:
wt_Total_1
Total RNA


title: Wild type total RNA replicate 3

description:
wt_Total_3
Total RNA


title: HCO4_T75

city: Tampa

first: Rays HY

last: Jiang

state: FL

address: 3720 Spectrum Blvd, Suite 304

department: Department of Global Health

institute: University of South Florida

description: HC04 cells collected 4 days post-seed from Corning® BioCoat™ Collagen I 75cm² Rectangular Canted Neck Cell Culture Flask with Vented Cap

data_processing:
RNAseq reads from each sample were aligned to human reference genome (GRCh38.p10) using Tophat2, allowing a maximum of one mismatch per read.
The mapped reads were used to assemble known transcripts from the reference and their abundances were estimated using Cufflinks 2.2.1. The expression level of each gene was normalized as FPKM (fragments per kilobase of exon per million mapped reads).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HC04 Cell Line

extract_protocol:
Total RNA samples for RNA sequencing were extracted from PHHs cultured in the μHEP slides and a variety of commercial microtiter plates (Corning® BiocoatTM collagen-coated 384-well plate, Cat No: Cat No: 356664, Corning; Falcon® 24-well Clear Flat Bottom Tissue Culture-treated Multiwell Cell Culture Plate, Cat No: 353047, Corning; and a 12 Well glass bottom plate with high performance #1.5 cover glass, Cat No: P12-1.5H-N, In Vitro Scientific, CA, USA). Trizol was added to each sample, incubated for 5 minutes and stored at -80 °C until further isolation. Total RNA was isolated using TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s instructions using chloroform, isopropanol, and 75% ethanol. The resulting RNA pellet was resuspended in DEPCtreated water. RNA quantification was performed by Qubit (Thermo Fisher Scientific), RIN values were determined using a TapeStation 2200 (Agilent Technologies, Santa Clara, CA) and A260/280 and A260/230 ratios were assessed using the NanoDrop® Spectrophotometer ND-1000 (Thermo Fisher Scientific). For each sample, 0.5-1.0 μg total RNA with a RIN value greater than 7.0, A260/280 ratio greater than 1.8, and A260/230 ratio greater than 2.0 was used for library preparation.
0.5 μg - 1.0 μg total RNA of each sample was used for library preparation. Libraries were prepared by using KAPA Stranded RNA-Seq Kit. Library quantification was conducted by qPCR and TapeStation (Agilent Technologies) measurements. Libraries were subsequently pooled and sequenced on Illumina HiSeq 4000 with a 150bp pair-end run.

tag: culture platform

value: Corning BioCoat Collagen I 75cm2 Rectangular Canted Neck Cell Culture Flask with Vented Cap

value: Day 4


title: PDC_12well_Glass

description: PHH collected 3 days post-seed from 12 Well glass bottom plate with high performance #1.5 cover glass

source_name: Cultured Primary Human Hepatocyte

value: Day 3


title: PDC_2_384well_Corning

description: PHH collected 3 days post-seed from Corning® BiocoatTM collagen-coated 384-well plate

value: Corning BioCoat collagen-coated 384-well plate


title: PDC_24well_Polyst

description: PHH collected 3 days post-seed from Falcon® 24-well Clear Flat Bottom Tissue Culture-treated Multiwell Cell Culture Plate

value: Falcon 24-well Clear Flat Bottom Tissue Culture-treated Multiwell Cell Culture Plate


title: PDC_Day14

description: PHH collected 14 days post-seed from the 48 well μHEP Slide

value: uHEP Slide

value: Day 14


title: PDC_1_384well_Corning


title: PDC_Day8.3

description: PHH collected 8 days post-seed from the 48 well μHEP Slide

value: Day 8


title: PDC_Day8.2


title: PDC_Day8.1


title: Ethanol_CTR #3_ATAC-seq

status: Public on Jan 31 2020

city: Indianapolis

first: Duojiao

last: Chen

state: INDIANA

address: 410 W. 10th Street

department: Departments of Medical and Molecular Genetics

institute: Indiana University

data_processing:
For ATAC-seq: Illumina adapter sequences and low-quality base calls were trimmed off the paired-end reads with Trim Galore v0.4.3. Sequence reads were aligned to human reference genome hg19 using bowtie2 with default settings. Duplicate reads were discarded with Picard. Reads mapped to mitochondrial DNA together with low mapping quality reads were excluded from further analysis. Two rounds of sequencing were conducted and the bam files of same sample from two rounds were mergred into one. MACS2 was used for peak calling.
For RNA-seq:  sequence reads were aligned to human reference genome hg19 with STAR. featureCounts was used to quantify gene expression (parameters applied: "“–Q 10")
For ATAC-seq: differential chromatin accessibility analysis was performed using edgeR.
For RNA-seq: differential expression analysis was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: For ATAC-seq: bigwig file and tab-delimited file includes log2 fold change values, p-values and FDR for all samples; for RNA-seq: tab-delimited file includes raw counts, log2 fold change values, p-values and FDR for all samples

growth_protocol: MCF-7 cells maintained in phenol red free MEM plus 5% charcoal-dextran treated fetal bovine serum for three days were treated with either ethanol or 0.1 nM E2 for indicated time

extract_protocol: Total RNA was prepared using RNAeasy kit from Qiagen

treatment_protocol: Ethanol or estradiol (0.1 nM) were added for indicated time

value: estrogen receptor-positive (ER+) breast cancer cell line

value: vehicle (ethanol)


title: Ethanol_CTR #2_ATAC-seq


title: Ethanol_CTR #1_ATAC-seq


title: MCF7_Ethanol #1_RNA-seq


title: E2_TX_3HRS #1_ATAC-seq


title: MCF7_E2_3hrs #1_RNA-seq


title: E2_TX_3HRS #3_ATAC-seq


title: MCF7_E2_3hrs #3_RNA-seq


title: MCF7_Ethanol #2_RNA-seq


title: MCF7_E2_3hrs #2_RNA-seq


title: MCF7_Ethanol #3_RNA-seq


title: E2_TX_1HRS #3_ATAC-seq


title: Wild type total RNA replicate 2

description:
wt_Total_2
Total RNA


title: E2_TX_1HRS #1_ATAC-seq


title: Ulcerative Colitis sample 13

status: Public on Jan 18 2020

city: Tromso

first: Christopher

last: Fenton

state: Norge

address: MH bygget

department: GSCT

country: Norway

institute: Universiry of Tromso

description:
UC_13
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab

data_processing:
Aligned with STAR-2.5.2b against UCSC_HG38.
Gene counting with HTSeq counts (STAR option).
Genome_build: UCSC_Hg38 (GRCh38)
Supplementary_files_format_and_content: *.ReadsPerGene.out.tab: Tab-delimited text files
Supplementary_files_format_and_content: raw_counts.tab: Tab-delimited text file includes the raw count matrix.
Supplementary_files_format_and_content: DESeq2_normalized_counts.tab: Tab-delimited text file includes the DESeq2 normalized counts (not log2).

source_name: Colon biopsy

extract_protocol:
RNA was extracted using the Allprep DNA/RNA mini kit from Qiagen (cat no: 80204).
Whole transcriptome libraries were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina, cat no: RS-122-2203), using 1ug of total RNA as input.

value: Mucosal biopsy

tag: disease status

value: Ulcerative colitis


title: Ulcerative Colitis sample 14

description:
UC_14
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: E2_TX_1HRS #2_ATAC-seq


title: Ulcerative Colitis sample 12

description:
UC_12
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 11

description:
UC_11
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 10

description:
UC_10
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 9

description:
UC_09
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 8

description:
UC_08
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 7

description:
UC_07
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: PDC_Day0

description: PHH collected prior to seeding on the plates.

source_name: Cryopreserved Primary Human Hepatocyte

value: Day 0


title: Ulcerative Colitis sample 6

description:
UC_06
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 3

description:
UC_03
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 4

description:
UC_04
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: E2_TX_3HRS #2_ATAC-seq


title: Ulcerative Colitis sample 5

description:
UC_05
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 2

description:
UC_02
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Ulcerative Colitis sample 1

description:
UC_01
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 13

description:
R_13
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab

value: Remission


title: Remission sample 3

description:
R_03
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 7

description:
R_07
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 9

description:
R_09
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 12

description:
R_12
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 6

description:
R_06
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 4

description:
R_04
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 10

description:
R_10
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 8

description:
R_08
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 14

description:
R_14
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 11

description:
R_11
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 13

description:
N_13
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab

value: Healthy


title: Normal sample 14

description:
N_14
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 15

description:
N_15
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 1

description:
R_01
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 16

description:
N_16
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 2

description:
R_02
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 9

description:
N_09
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 10

description:
N_10
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 11

description:
N_11
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 6

description:
N_06
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 8

description:
N_08
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 5

description:
N_05
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 4

description:
N_04
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 3

description:
N_03
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Remission sample 5

description:
R_05
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Normal sample 1

description:
N_01
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: A3_NL43_CD4

status: Public on Jan 14 2020

city: Cambridge

first: Silvi

last: Rouskin

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: DMS-modified RNA

data_processing:
Library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1).
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8).
DREEM Clustering (custom code available at https://gitlab.com/Corbin-Rouskin/RNA_structure/tree/gpu).
RNAstructure (v6.0.1) folding and VARNA (v3.93) visualization.
.sam files generated with bowtie2, .dot files generated by RNAstucture, _Mu.txt files produced by DREEM clustering algorithm.
GRCh38; HIV-1NL4-3 (Genbank accession number AF324493.1); HIV-1NHG(Genbank accession number JQ585717.1)
Supplementary_files_format_and_content: *_Clusters_Mu.txt files produced by DREEM clustering algorithm.

organism:
Homo sapiens
Human immunodeficiency virus 1

source_name: HIV-1 NL4-3 infected CD4 + T cells

growth_protocol: CD4+ T cells were grown in T75 flasks and cultured in RPMI1640 + 10%FBS + Penn/strep, maintained at a concentration of ~1-3million/mL. CD4+ T cells were activated with 10ug/mL PHA and 100U/mL IL-2.

extract_protocol:
DMS-treated cells were pelleted and resuspended in 1 mL Trizol, RNA was extracted by phenol-chloroform extraction and isopropanol precipitation.
3' Phosphorylation with rSAP, linker ligation with T4 RNA ligase truncated KQ, excess linker degraded with RecJ and 5'Deadenylase. rRNA was subtracted with RiboZero, and RT was performed with TGIRT-III. cDNAs were isolated by gel extraction on a 10% TBE-Urea gel and extracted by isopropanol precipitation. cDNAs were circularized with circLigase and amplified by PCR with phusion polymerase. PCR products were purified by gel extraction from an 8% TBE gel and isopropanol precipitation. Samples were quantified by Bioanalyzer.

treatment_protocol: DMS-treatment for RNA secondary structure analysis, between 0.5-2% DMS at 37C for 5 minutes. Shake during DMS treatment for suspension cells.

tag: human cell type or cell line

value: CD4+ T cells

tag: infection or transfection

value: infected with HIV-1 NL4-3


title: A3_NHG_293-3

description: DMS-modified RNA

source_name: HEK293t cells transfected with HIV-1 NHG

growth_protocol: HEK293t were grown in T75 and cultured in DMEM+ 10% FBS + Penn/strep. Transfections were done in 6-well plates with X-tremegene9.

value: HEK293t cell line

value: transfected with HIV-1 NHG


title: A3_A3SLMut4_293

description: DMS-modified RNA

source_name: HEK293t cells transfected with HIV-1 NHG A3SLMut4

value: transfected with HIV-1 NHG A3SLMut4


title: Normal sample 12

description:
N_12
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab

tag: tissue


title: TF ChIP-seq from transverse colon (ENCLB651KNW)

status: Public on Jan 06 2020

description:
https://www.encodeproject.org/experiments/ENCSR907BES/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR907BES
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB651KNW
fragmentation methods: sonication (generic)
size range: 200-600

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

tag: antibody

value: CTCF

value: transverse colon

value: tissue

tag: description

value: EnTEX:Colon - Transverse

tag: biosample encode accession

value: male

tag: dev stage

value: adult

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS121FBL at ENCODE; https://www.encodeproject.org/ENCBS121FBL/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB486LBV)

description:
https://www.encodeproject.org/experiments/ENCSR894MOX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR894MOX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB486LBV
fragmentation methods: sonication (generic)
size range: 200-600

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

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: female

value: 51 year

value: ENCBS955ZON at ENCODE; https://www.encodeproject.org/ENCBS955ZON/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from ascending aorta (ENCLB719XOS)

description:
https://www.encodeproject.org/experiments/ENCSR846JKO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR846JKO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR494YJW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB719XOS
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: ascending aorta

value: EnTEX:Artery- Aorta

value: ENCBS273PSC at ENCODE; https://www.encodeproject.org/ENCBS273PSC/


title: Normal sample 7

description:
N_07
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab

value: Mucosal biopsy

value: Healthy


title: A3_A3SLMut1_293

description: DMS-modified RNA

source_name: HEK293t cells transfected with HIV-1 NHG A3SLMut1

value: HEK293t cell line

value: transfected with HIV-1 NHG A3SLMut1


title: A3_NHG_293-1

description: DMS-modified RNA

value: transfected with HIV-1 NHG


title: Normal sample 2

description:
N_02
processed data file: raw_counts.tab
processed data file: DESeq2_normalized_counts.tab


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB330AYL)

description:
https://www.encodeproject.org/experiments/ENCSR805OCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR805OCD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777AJC
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB330AYL
fragmentation methods: sonication (generic)
size range: 200-600

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

value: tissue

value: male

value: adult

value: 54 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS390MKW at ENCODE; https://www.encodeproject.org/ENCBS390MKW/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB428DBT)

description:
https://www.encodeproject.org/experiments/ENCSR708BMV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR708BMV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB428DBT
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: female

value: 51 year

value: ENCBS677JLV at ENCODE; https://www.encodeproject.org/ENCBS677JLV/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from upper lobe of left lung (ENCLB152VDJ)

description:
https://www.encodeproject.org/experiments/ENCSR759RTY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR759RTY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152VDJ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: upper lobe of left lung

value: 53 year

value: ENCBS684YJH at ENCODE; https://www.encodeproject.org/ENCBS684YJH/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Histone ChIP-seq from prostate gland (ENCLB800OJS)

description:
https://www.encodeproject.org/experiments/ENCSR748RBT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR748RBT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800OJS
fragmentation methods: sonication (generic)
size range: 200-600

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

value: prostate gland

value: tissue

value: ENCBS619YXY at ENCODE; https://www.encodeproject.org/ENCBS619YXY/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from prostate gland (ENCLB722RPE)

description:
https://www.encodeproject.org/experiments/ENCSR763IDK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR763IDK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB722RPE
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: adult

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS633UTQ at ENCODE; https://www.encodeproject.org/ENCBS633UTQ/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB012UDF)

description:
https://www.encodeproject.org/experiments/ENCSR708BMV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR708BMV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB012UDF
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: female

value: ENCBS955ZON at ENCODE; https://www.encodeproject.org/ENCBS955ZON/


title: Histone ChIP-seq from prostate gland (ENCLB084BTV)

description:
https://www.encodeproject.org/experiments/ENCSR748RBT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR748RBT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB084BTV
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: Histone ChIP-seq from prostate gland (ENCLB917AIW)

description:
https://www.encodeproject.org/experiments/ENCSR763IDK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR763IDK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR113QDZ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB917AIW
fragmentation methods: sonication (generic)
size range: 200-600


title: TF ChIP-seq from tibial nerve (ENCLB942FVP)

description:
https://www.encodeproject.org/experiments/ENCSR689VEF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR689VEF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB942FVP
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS952IFF at ENCODE; https://www.encodeproject.org/ENCBS952IFF/


title: TF ChIP-seq from ascending aorta (ENCLB916VAO)

description:
https://www.encodeproject.org/experiments/ENCSR555DCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR555DCD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007WYC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB916VAO
fragmentation methods: sonication (generic)
size range: 200-600

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

value: ascending aorta

value: tissue

value: EnTEX:Artery- Aorta

value: 53 year

value: ENCBS801NKM at ENCODE; https://www.encodeproject.org/ENCBS801NKM/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB577CCI)

description:
https://www.encodeproject.org/experiments/ENCSR543UBL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR543UBL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777AJC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB577CCI
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: adult

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS390MKW at ENCODE; https://www.encodeproject.org/ENCBS390MKW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB449YZO)

description:
https://www.encodeproject.org/experiments/ENCSR674WSL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR674WSL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777AJC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB449YZO
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: Kristin Ardlie


title: TF ChIP-seq from thoracic aorta (ENCLB753PDZ)

description:
https://www.encodeproject.org/experiments/ENCSR549TXG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR549TXG
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR158PLZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB753PDZ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: thoracic aorta

value: 37 year

value: ENCBS882JUX at ENCODE; https://www.encodeproject.org/ENCBS882JUX/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: microRNA-seq from C2C12 (ENCLB118NHM)

description:
https://www.encodeproject.org/experiments/ENCSR808LQW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation C2C12 microRNA-seq from Mortazavi
experiment encode accession: ENCSR808LQW
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB118NHM
size range: <30

source_name: Mus musculus C2C12 cell line

tag: line

value: cell line

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: ATCC

tag: strain

value: ENCBS930AJT at ENCODE; https://www.encodeproject.org/ENCBS930AJT/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: microRNA-seq from C2C12 (ENCLB703AFN)

description:
https://www.encodeproject.org/experiments/ENCSR808LQW/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation C2C12 microRNA-seq from Mortazavi
experiment encode accession: ENCSR808LQW
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB703AFN
size range: <30

tag: Sex

value: ENCBS589VFX at ENCODE; https://www.encodeproject.org/ENCBS589VFX/


title: Histone ChIP-seq from heart left ventricle (ENCLB452RFQ)

description:
https://www.encodeproject.org/experiments/ENCSR613PPL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR613PPL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB452RFQ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: heart left ventricle

value: tissue

value: EnTEX:Heart - Left Ventricle

value: female

value: adult

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: A3_NHG_293-2

description: DMS-modified RNA

value: HEK293t cell line

value: transfected with HIV-1 NHG


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB437PDS)

description:
https://www.encodeproject.org/experiments/ENCSR894MOX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR894MOX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB437PDS
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: ENCBS677JLV at ENCODE; https://www.encodeproject.org/ENCBS677JLV/


title: microRNA-seq from adrenal gland (ENCLB697CJP)

description:
https://www.encodeproject.org/experiments/ENCSR407OAH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation adrenal gland C57BL6 WT female microRNA-seq from Mortazavi
experiment encode accession: ENCSR407OAH
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB697CJP
size range: <30

source_name: Mus musculus strain C57BL/6J adrenal gland tissue

value: adrenal gland

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: The Jackson Laboratory

value: ENCBS162KCU at ENCODE; https://www.encodeproject.org/ENCBS162KCU/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: Histone ChIP-seq from tibial nerve (ENCLB391FHR)

description:
https://www.encodeproject.org/experiments/ENCSR464TRM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR464TRM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB391FHR
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: tissue

value: EnTEX:Nerve - Tibial

value: male

value: adult

value: 54 year

value: Kristin Ardlie

value: ENCBS952IFF at ENCODE; https://www.encodeproject.org/ENCBS952IFF/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: microRNA-seq from adrenal gland (ENCLB063BRO)

description:
https://www.encodeproject.org/experiments/ENCSR407OAH/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation adrenal gland C57BL6 WT female microRNA-seq from Mortazavi
experiment encode accession: ENCSR407OAH
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB063BRO
size range: <30

value: ENCBS525FJF at ENCODE; https://www.encodeproject.org/ENCBS525FJF/


title: microRNA-seq from adrenal gland (ENCLB928NMB)

description:
https://www.encodeproject.org/experiments/ENCSR014LFG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation adrenal gland C57BL6 WT male microRNA-seq from Mortazavi
experiment encode accession: ENCSR014LFG
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB928NMB
size range: <30

value: adrenal gland

value: ENCBS004AHE at ENCODE; https://www.encodeproject.org/ENCBS004AHE/


title: Histone ChIP-seq from gastrocnemius medialis (ENCLB002JAZ)

description:
https://www.encodeproject.org/experiments/ENCSR453MSI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR453MSI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138WRC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB002JAZ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: gastrocnemius medialis

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal also gastrocnemius medialis

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS731GTN at ENCODE; https://www.encodeproject.org/ENCBS731GTN/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: microRNA-seq from adrenal gland (ENCLB828SZQ)

description:
https://www.encodeproject.org/experiments/ENCSR014LFG/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation adrenal gland C57BL6 WT male microRNA-seq from Mortazavi
experiment encode accession: ENCSR014LFG
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB828SZQ
size range: <30

value: tissue

value: not collected

value: unknown

value: Ali Mortazavi, UCI

value: The Jackson Laboratory

value: ENCBS873WBE at ENCODE; https://www.encodeproject.org/ENCBS873WBE/

value: Derived from ENCODE donor ENCDO072AAA; https://www.encodeproject.org/ENCDO072AAA/


title: TF ChIP-seq from transverse colon (ENCLB155CMY)

description:
https://www.encodeproject.org/experiments/ENCSR907BES/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR907BES
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB155CMY
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: CTCF

value: transverse colon

value: EnTEX:Colon - Transverse

value: male

value: adult

value: 54 year

value: Kristin Ardlie

value: ENCBS989UNA at ENCODE; https://www.encodeproject.org/ENCBS989UNA/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: TF ChIP-seq from coronary artery (ENCLB232BAX)

description:
https://www.encodeproject.org/experiments/ENCSR447ANW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR447ANW
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR163XFK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB232BAX
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) coronary artery tissue

value: coronary artery

value: EnTEX:Artery - Coronary

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS984LMH at ENCODE; https://www.encodeproject.org/ENCBS984LMH/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: microRNA-seq from right lobe of liver (ENCLB340XRJ)

description:
https://www.encodeproject.org/experiments/ENCSR783JQT/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W63 right lobe liver microRNA-seq from Mortazavi
experiment encode accession: ENCSR783JQT
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB340XRJ
size range: <30

source_name: Homo sapiens female adult (47 years) right lobe of liver tissue, preserved by flash-freezing

value: right lobe of liver

value: tissue

tag: health state

value: DM:no; HTN:yes; CAD:no

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS768CAB at ENCODE; https://www.encodeproject.org/ENCBS768CAB/

value: Derived from ENCODE donor ENCDO912EIY; https://www.encodeproject.org/ENCDO912EIY/


title: microRNA-seq from heart left ventricle (ENCLB191UFL)

description:
https://www.encodeproject.org/experiments/ENCSR792MDW/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue left ventricle microRNA-seq from Mortazavi
experiment encode accession: ENCSR792MDW
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB191UFL
size range: <30

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

value: heart left ventricle

value: Heart - Left Ventricle

tag: age

value: 53 year

value: adult

value: Barbara Wold, Caltech

value: ENCBS504IQD at ENCODE; https://www.encodeproject.org/ENCBS504IQD/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: TF ChIP-seq from right atrium auricular region (ENCLB503OVA)

description:
https://www.encodeproject.org/experiments/ENCSR401KRN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR401KRN
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR195BZZ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503OVA
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: Bradley Bernstein, Broad

value: female

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/


title: microRNA-seq from HFFc6 (ENCLB269WLX)

description:
https://www.encodeproject.org/experiments/ENCSR750ZGO/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HFFc6 microRNA-seq from Mortazavi
experiment encode accession: ENCSR750ZGO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB269WLX
size range: <30

source_name: Homo sapiens HFFc6 cell line

value: cell line

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

value: male

value: normal

value: newborn

value: 0 year

value: Ali Mortazavi, UCI

value: Job Dekker

tag: passage number

value: ENCBS758GLU at ENCODE; https://www.encodeproject.org/ENCBS758GLU/

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


title: microRNA-seq from HFFc6 (ENCLB380KWO)

description:
https://www.encodeproject.org/experiments/ENCSR750ZGO/
***************
biological replicate number: 3
technical replicate number: 1
description: RNA Evaluation HFFc6 microRNA-seq from Mortazavi
experiment encode accession: ENCSR750ZGO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB380KWO
size range: <30

value: ENCBS917RBN at ENCODE; https://www.encodeproject.org/ENCBS917RBN/


title: microRNA-seq from ovary (ENCLB473OCZ)

description:
https://www.encodeproject.org/experiments/ENCSR684FLE/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 ovary microRNA-seq from Mortazavi
experiment encode accession: ENCSR684FLE
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB473OCZ
size range: <30

source_name: Homo sapiens female adult (41 year) ovary tissue, preserved by flash-freezing

value: ovary

value: tissue

value: DM:no; HTN:no; CAD:no

value: adult

value: 41 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS472VJA at ENCODE; https://www.encodeproject.org/ENCBS472VJA/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: microRNA-seq from GM12878 (ENCLB298VOK)

description:
https://www.encodeproject.org/experiments/ENCSR770HBF/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation GM12878 microRNA-seq from Mortazavi, using 5' adaptor set 1 and 2 for reps 1 and 2.
experiment encode accession: ENCSR770HBF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2018-09-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB298VOK
size range: <30

source_name: Homo sapiens GM12878 cell line

value: cell line

value: CEPH/UTAH PEDIGREE 1463 / B-Lymphocyte / Transformation Type:Epstein-Barr Virus

value: female

value: unknown

value: Coriell

value: ENCBS771XJW at ENCODE; https://www.encodeproject.org/ENCBS771XJW/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: microRNA-seq from GM12878 (ENCLB318HJU)

description:
https://www.encodeproject.org/experiments/ENCSR770HBF/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation GM12878 microRNA-seq from Mortazavi, using 5' adaptor set 1 and 2 for reps 1 and 2.
experiment encode accession: ENCSR770HBF
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2018-09-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB318HJU
size range: <30

value: Ali Mortazavi, UCI

value: ENCBS609AMN at ENCODE; https://www.encodeproject.org/ENCBS609AMN/


title: microRNA-seq from pancreas (ENCLB236IUX)

description:
https://www.encodeproject.org/experiments/ENCSR701ZTJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W80 pancreas microRNA-seq from Mortazavi
experiment encode accession: ENCSR701ZTJ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB236IUX
size range: <30

source_name: Homo sapiens female adult (61 year) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: 61 year

value: ENCBS346NXH at ENCODE; https://www.encodeproject.org/ENCBS346NXH/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: microRNA-seq from HFFc6 (ENCLB347JNS)

description:
https://www.encodeproject.org/experiments/ENCSR750ZGO/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HFFc6 microRNA-seq from Mortazavi
experiment encode accession: ENCSR750ZGO
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB347JNS
size range: <30

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

value: male

value: normal

value: newborn

value: 0 year

value: Job Dekker

value: ENCBS857YWJ at ENCODE; https://www.encodeproject.org/ENCBS857YWJ/

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


title: microRNA-seq from mucosa of descending colon (ENCLB747TVX)

description:
https://www.encodeproject.org/experiments/ENCSR664CDH/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W80 mucosa descending colon microRNA-seq from Mortazavi
experiment encode accession: ENCSR664CDH
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB747TVX
size range: <30

source_name: Homo sapiens female adult (61 year) mucosa of descending colon tissue, preserved by flash-freezing

value: mucosa of descending colon

value: female

value: adult

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS825BLU at ENCODE; https://www.encodeproject.org/ENCBS825BLU/


title: microRNA-seq from adrenal gland (ENCLB688YIP)

description:
https://www.encodeproject.org/experiments/ENCSR649MMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue adrenal gland 1-2 microRNA-seq from Mortazavi
experiment encode accession: ENCSR649MMJ
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB688YIP
size range: <30

source_name: Homo sapiens male adult (37 years) adrenal gland tissue

value: adrenal gland

value: tissue

value: 37 year

value: Ali Mortazavi, UCI

value: Kristin Ardlie

value: ENCBS061XGD at ENCODE; https://www.encodeproject.org/ENCBS061XGD/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: microRNA-seq from myocyte (ENCLB824HZS)

description:
https://www.encodeproject.org/experiments/ENCSR613OJJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation C2C12 differentiated for 72 hours microRNA-seq from Mortazavi
experiment encode accession: ENCSR613OJJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB824HZS
size range: <30

source_name: Mus musculus myocyte in vitro differentiated cells

value: myocyte

value: in vitro differentiated cells

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury; differentiated from C2C12 cells for 72 hours

value: not collected

value: unknown

value: ATCC

value: ENCBS258SSQ at ENCODE; https://www.encodeproject.org/ENCBS258SSQ/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB379ITD)

description:
https://www.encodeproject.org/experiments/ENCSR316LNO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR316LNO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR642QDW
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB379ITD
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) gastroesophageal sphincter tissue

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: female

value: adult

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS617FGB at ENCODE; https://www.encodeproject.org/ENCBS617FGB/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from gastrocnemius medialis (ENCLB521EDV)

description:
https://www.encodeproject.org/experiments/ENCSR283BRU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR283BRU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138WRC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB521EDV
fragmentation methods: sonication (generic)
size range: 200-600

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal also gastrocnemius medialis

value: Kristin Ardlie

value: ENCBS731GTN at ENCODE; https://www.encodeproject.org/ENCBS731GTN/


title: microRNA-seq from K562 (ENCLB339NLX)

description:
https://www.encodeproject.org/experiments/ENCSR569QVM/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation K562 microRNA-seq from Mortazavi, using 5' adaptor sets 3 and 4 for rep 1 and 2.
experiment encode accession: ENCSR569QVM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2018-09-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB339NLX
size range: <30

source_name: Homo sapiens K562 cell line

value: cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Ali Mortazavi, UCI

value: ENCBS567ZFF at ENCODE; https://www.encodeproject.org/ENCBS567ZFF/

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


title: microRNA-seq from K562 (ENCLB136UZC)

description:
https://www.encodeproject.org/experiments/ENCSR569QVM/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation K562 microRNA-seq from Mortazavi, using 5' adaptor sets 3 and 4 for rep 1 and 2.
experiment encode accession: ENCSR569QVM
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2018-09-20
lab: Ali Mortazavi, UCI
library encode accession: ENCLB136UZC
size range: <30

value: female

value: adult

value: ATCC

value: ENCBS870SMK at ENCODE; https://www.encodeproject.org/ENCBS870SMK/


title: microRNA-seq from HL-60 (ENCLB140KJM)

description:
https://www.encodeproject.org/experiments/ENCSR157VHD/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation HL60 microRNA-seq from Mortazavi
experiment encode accession: ENCSR157VHD
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2018-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB140KJM
size range: <30

source_name: Homo sapiens HL-60 cell line

value: Promyelocytic leukemia cells, (PMID:276884)

value: acute promyelocytic leukemia

value: 36 year

value: Sigma

value: ENCBS698WLF at ENCODE; https://www.encodeproject.org/ENCBS698WLF/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: microRNA-seq from myocyte (ENCLB924SYG)

description:
https://www.encodeproject.org/experiments/ENCSR613OJJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RNA Evaluation C2C12 differentiated for 72 hours microRNA-seq from Mortazavi
experiment encode accession: ENCSR613OJJ
assay title: microRNA-seq
assembly: mm10
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB924SYG
size range: <30

value: myocyte

value: in vitro differentiated cells

value: Myoblast cell line derived from thigh muscle of C3H mice after crush injury; differentiated from C2C12 cells for 72 hours

value: not collected

value: unknown

value: ENCBS574BLY at ENCODE; https://www.encodeproject.org/ENCBS574BLY/

value: Derived from ENCODE donor ENCDO321TZV; https://www.encodeproject.org/ENCDO321TZV/


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB906KMI)

description:
https://www.encodeproject.org/experiments/ENCSR316LNO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR316LNO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR642QDW
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB906KMI
fragmentation methods: none
size range: 200-600

value: gastroesophageal sphincter

value: tissue

value: EnTEX:Esophagus - Gastroesophageal Junction

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS910MIF at ENCODE; https://www.encodeproject.org/ENCBS910MIF/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: microRNA-seq from left lung (ENCLB742FBK)

description:
https://www.encodeproject.org/experiments/ENCSR183LLK/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W62 left lung microRNA-seq from Mortazavi
experiment encode accession: ENCSR183LLK
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB742FBK
size range: <30

source_name: Homo sapiens female child (16 years) left lung tissue, preserved by flash-freezing

value: left lung

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS725WGH at ENCODE; https://www.encodeproject.org/ENCBS725WGH/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: microRNA-seq from HL-60 (ENCLB488WWC)

description:
https://www.encodeproject.org/experiments/ENCSR157VHD/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation HL60 microRNA-seq from Mortazavi
experiment encode accession: ENCSR157VHD
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2018-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB488WWC
size range: <30

value: cell line

value: Promyelocytic leukemia cells, (PMID:276884)

value: acute promyelocytic leukemia

value: adult

value: 36 year

value: Ali Mortazavi, UCI

value: Sigma

value: ENCBS880XNW at ENCODE; https://www.encodeproject.org/ENCBS880XNW/

value: Derived from ENCODE donor ENCDO000AAM; https://www.encodeproject.org/ENCDO000AAM/


title: microRNA-seq from colonic mucosa (ENCLB071LJZ)

description:
https://www.encodeproject.org/experiments/ENCSR128VGG/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W61 colon mucosa microRNA-seq from Mortazavi
experiment encode accession: ENCSR128VGG
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB071LJZ
size range: <30

source_name: Homo sapiens female adult (41 year) colonic mucosa tissue, preserved by flash-freezing

value: colonic mucosa

value: tissue

value: female

value: 41 year

value: ENCBS205RQN at ENCODE; https://www.encodeproject.org/ENCBS205RQN/

value: Derived from ENCODE donor ENCDO575WHY; https://www.encodeproject.org/ENCDO575WHY/


title: Histone ChIP-seq from transverse colon (ENCLB928YXJ)

description:
https://www.encodeproject.org/experiments/ENCSR069EGE/
***************
biological replicate number: 3
technical replicate number: 1
description: Pipeline ran using replicate 1 and 3, replicate 2 raw data was archived.
experiment encode accession: ENCSR069EGE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB928YXJ
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: transverse colon

value: EnTEX:Colon - Transverse

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS989UNA at ENCODE; https://www.encodeproject.org/ENCBS989UNA/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: microRNA-seq from spleen (ENCLB102UIZ)

description:
https://www.encodeproject.org/experiments/ENCSR086SWA/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W80 spleen microRNA-seq from Mortazavi
experiment encode accession: ENCSR086SWA
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB102UIZ
size range: <30

source_name: Homo sapiens female adult (61 year) spleen tissue, preserved by flash-freezing

value: spleen

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS150YMA at ENCODE; https://www.encodeproject.org/ENCBS150YMA/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: microRNA-seq from left lung (ENCLB429RSD)

description:
https://www.encodeproject.org/experiments/ENCSR151ZUP/
***************
biological replicate number: 1
technical replicate number: 1
description: RNA Evaluation human tissue W76 left lung microRNA-seq from Mortazavi
experiment encode accession: ENCSR151ZUP
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2019-12-17
lab: Ali Mortazavi, UCI
library encode accession: ENCLB429RSD
size range: <30

source_name: Homo sapiens male adult (40 years) left lung tissue, preserved by flash-freezing

value: left lung

value: tissue

value: DM:no; HTN:yes; CAD:no

value: 40 year

value: ENCBS420JRY at ENCODE; https://www.encodeproject.org/ENCBS420JRY/

value: Derived from ENCODE donor ENCDO392CRK; https://www.encodeproject.org/ENCDO392CRK/