title: Histone ChIP-seq from uterus (ENCLB785VDS)

description:
https://www.encodeproject.org/experiments/ENCSR189JIH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR189JIH
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR859LXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB785VDS
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) uterus tissue

value: uterus

value: female

value: 51 year

tag: link

value: ENCBS443NGH at ENCODE; https://www.encodeproject.org/ENCBS443NGH/


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB919ASQ)

status: Public on Jan 06 2020

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR200AFX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR200AFX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB919ASQ
fragmentation methods: sonication (generic)
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

value: esophagus muscularis mucosa

value: tissue

tag: description

value: EnTEX:Esophagus - Muscularis

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

tag: age

tag: lab

value: Bradley Bernstein, Broad

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

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


title: ra1612_091

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
102939-001-091
Mild asthmatic (after RV16)

library_source: transcriptomic

data_processing:
The reference of ‘Homo_sapiens.GRCh37.75’ was used to align the reads. The mapping to the reference sequence was done using a short reader aligner based on Burrows-Wheeler transform.
Clustering and DNA sequencing were performed according to the manufacturer’s protocol using the Illumina NextSeq 500.
The reads were trimmed for adapter sequences using Trimmomatic v0.30 before the alignment.
The read counts were loaded into the DESeq2 package, a statistical package within the R/BioConductor platform to determine the differentially expressed genes (paired).
Image analysis, base calling and quality check were performed with Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include curated counts of genes in each sample.

molecule: total RNA

source_name: primary bronchial epithelial cells

extract_protocol:
The pellet was dissolved in 1 ml of TRIzol™ and stored at -80°C until RNA was isolated. After all samples were obtained, they were thawed at room temperature, and after 200 µl of chloroform was added, shaken vigorously for 30 seconds. The samples were kept at RT for 10 mins and centrifuged at 16,000g for 15 mins at 4°C. The aqueous phase was cleaned up and concentrated with protocol 5.3 using the Nucleospin® RNA XS extraction kit (Macherey-Nagel). No carrier RNA was added as it would interfere with RNA sequencing.
The NEBNext Ultra Directional RNA library prep kit for Illumina was used to process the samples. The samples preparation was performed according to the protocol “NEBNext Ultra Directional RNA Library Prep Kit for Illumina” (NEB #7420S/L). Briefly, oligo-dT magnetic beads were used to isolate mRNA from total RNA. cDNA synthesis was performed after fragmentation of this mRNA. This was used for ligation with sequencing adapters followed by PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the fragment analyser. The size of the resulting products was consistent with the expected size distribution between 300-500 base pairs. To evaluate the quality of the library preparation and kits used, the raw data was sampled and mapped to annotated genomic references. Mapping positions were classified as intragenic, exonic, intergenic, intronic and rRNA. Clustering and DNA sequencing were performed according to the manufacturer’s protocol using the Illumina NextSeq 500. A concentration of 1.6pM was used as input. The reads were trimmed for adapter sequences using Trimmomatic v0.30 before the alignment. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12.

tag: cell type

value: primary bronchial epithelial cells

tag: collection method

value: direct bronchoscopy

tag: disease status

value: Mild asthmatic

tag: infection

value: rhinovirus (RV16)


title: Histone ChIP-seq from uterus (ENCLB197BQD)

description:
https://www.encodeproject.org/experiments/ENCSR189JIH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189JIH
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR859LXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197BQD
fragmentation methods: sonication (generic)
size range: 200-600


title: ra1612_089

description:
102939-001-089
Mild asthmatic (after RV16)


title: ra1612_087

description:
102939-001-087
Mild asthmatic (after RV16)


title: ra1612_048

description:
102939-001-048
Mild asthmatic (after RV16)


title: ra1612_050

description:
102939-001-050
Mild asthmatic (after RV16)


title: ra1612_046

description:
102939-001-046
Mild asthmatic (after RV16)


title: TF ChIP-seq from stomach (ENCLB953WBV)

description:
https://www.encodeproject.org/experiments/ENCSR185CCV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR185CCV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB953WBV
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens stomach tissue female adult (53 years)

value: CTCF

value: stomach

value: 53 year

value: ENCBS642ZQR at ENCODE; https://www.encodeproject.org/ENCBS642ZQR/

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


title: ra1612_044

description:
102939-001-044
Mild asthmatic (after RV16)


title: ra1612_040

description:
102939-001-040
Mild asthmatic (after RV16)


title: ra1612_042

description:
102939-001-042
Mild asthmatic (after RV16)


title: TF ChIP-seq from stomach (ENCLB586MBJ)

description:
https://www.encodeproject.org/experiments/ENCSR185CCV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR185CCV
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR539HNK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB586MBJ
fragmentation methods: sonication (generic)
size range: 200-600

value: female


title: Histone ChIP-seq from tibial nerve (ENCLB987VKV)

description:
https://www.encodeproject.org/experiments/ENCSR176ZMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR176ZMW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB987VKV
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) tibial nerve tissue

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: 51 year

tag: source

value: Kristin Ardlie

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/


title: ra1612_058

description:
102939-001-058
Mild asthmatic (after RV16)


title: Histone ChIP-seq from sigmoid colon (ENCLB781LZT)

description:
https://www.encodeproject.org/experiments/ENCSR172LVU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR172LVU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781LZT
fragmentation methods: none
size range: 200-600

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

value: sigmoid colon

value: tissue

value: EnTEX:Colon - Sigmoid

value: male

value: adult

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/

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


title: Histone ChIP-seq from sigmoid colon (ENCLB865SXK)

description:
https://www.encodeproject.org/experiments/ENCSR172LVU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR172LVU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB865SXK
fragmentation methods: sonication (generic)
size range: 200-600


title: ra1612_036

description:
102939-001-036
Mild asthmatic (after RV16)

value: primary bronchial epithelial cells

value: direct bronchoscopy

value: Mild asthmatic

value: rhinovirus (RV16)


title: Histone ChIP-seq from tibial nerve (ENCLB504YJO)

description:
https://www.encodeproject.org/experiments/ENCSR176ZMW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR176ZMW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB504YJO
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: female

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


title: ra1612_032

description:
102939-001-032
Mild asthmatic (after RV16)


title: Histone ChIP-seq from stomach (ENCLB169UXZ)

description:
https://www.encodeproject.org/experiments/ENCSR158WBG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR158WBG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB169UXZ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) stomach tissue

value: stomach

value: Kristin Ardlie

value: ENCBS443LLE at ENCODE; https://www.encodeproject.org/ENCBS443LLE/


title: ra1612_098

description:
102939-001-098
Mild asthmatic (before RV16)


title: Histone ChIP-seq from stomach (ENCLB472FIU)

description:
https://www.encodeproject.org/experiments/ENCSR158WBG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR158WBG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB472FIU
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male


title: ra1612_096

description:
102939-001-096
Mild asthmatic (before RV16)


title: Control ChIP-seq from coronary artery (ENCLB595GZD)

description:
https://www.encodeproject.org/experiments/ENCSR163XFK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR163XFK
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB595GZD
size range: 200-600

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

value: coronary artery

value: EnTEX:Artery - Coronary

value: adult

value: 51 year

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


title: ra1612_090

description:
102939-001-090
Mild asthmatic (before RV16)

value: primary bronchial epithelial cells

value: direct bronchoscopy


title: ra1612_088

description:
102939-001-088
Mild asthmatic (before RV16)

value: Mild asthmatic


title: ra1612_086

description:
102939-001-086
Mild asthmatic (before RV16)


title: Control ChIP-seq from tibial nerve (ENCLB895TVG)

description:
https://www.encodeproject.org/experiments/ENCSR152HLZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR152HLZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB895TVG
size range: 200-600

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

value: tibial nerve

value: 54 year

value: Bradley Bernstein, Broad

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

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


title: Control ChIP-seq from gastrocnemius medialis (ENCLB384WZQ)

description:
https://www.encodeproject.org/experiments/ENCSR138WRC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR138WRC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB384WZQ
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: Kristin Ardlie

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

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


title: Control ChIP-seq from tibial nerve (ENCLB259GZE)

description:
https://www.encodeproject.org/experiments/ENCSR152HLZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR152HLZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB259GZE
size range: 200-600

value: tissue

value: EnTEX:Nerve - Tibial

value: male

value: adult


title: Control ChIP-seq from gastrocnemius medialis (ENCLB145HFT)

description:
https://www.encodeproject.org/experiments/ENCSR138WRC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR138WRC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB145HFT
size range: 200-600

value: 51 year


title: Control ChIP-seq from gastrocnemius medialis (ENCLB060GAC)

description:
https://www.encodeproject.org/experiments/ENCSR138WRC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR138WRC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060GAC
size range: 200-600

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

value: ENCBS640TBC at ENCODE; https://www.encodeproject.org/ENCBS640TBC/


title: ra1612_047

description:
102939-001-047
Mild asthmatic (before RV16)

value: primary bronchial epithelial cells

value: direct bronchoscopy

value: Mild asthmatic


title: ra1612_049

description:
102939-001-049
Mild asthmatic (before RV16)


title: ra1612_045

description:
102939-001-045
Mild asthmatic (before RV16)


title: Histone ChIP-seq from testis (ENCLB304UZU)

description:
https://www.encodeproject.org/experiments/ENCSR136ZQZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR136ZQZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB304UZU
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) testis tissue

value: testis

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/

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


title: ra1612_043

description:
102939-001-043
Mild asthmatic (before RV16)


title: ra1612_039

description:
102939-001-039
Mild asthmatic (before RV16)


title: ra1612_041

description:
102939-001-041
Mild asthmatic (before RV16)


title: Histone ChIP-seq from testis (ENCLB012TKK)

description:
https://www.encodeproject.org/experiments/ENCSR136ZQZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136ZQZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB012TKK
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: Control ChIP-seq from Peyer's patch (ENCLB621RVK)

description:
https://www.encodeproject.org/experiments/ENCSR118FQN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR118FQN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB621RVK
size range: 200-600

source_name: Homo sapiens male adult (54 years) Peyer's patch tissue

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: 54 year

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/

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


title: ra1612_035

description:
102939-001-035
Mild asthmatic (before RV16)


title: ra1612_031

description:
102939-001-031
Mild asthmatic (before RV16)


title: ra1612_022

description:
102939-001-022
Healthy (after RV16)

value: Healthy

value: rhinovirus (RV16)


title: ra1612_037

description:
102939-001-037
Mild asthmatic (before RV16)


title: Control ChIP-seq from prostate gland (ENCLB888GHQ)

description:
https://www.encodeproject.org/experiments/ENCSR113QDZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR113QDZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB888GHQ
size range: 200-600

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

value: prostate gland

value: tissue

value: male

value: adult

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


title: Histone ChIP-seq from uterus (ENCLB495SXU)

description:
https://www.encodeproject.org/experiments/ENCSR111DTF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR111DTF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB495SXU
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (53 years) uterus tissue

value: uterus

value: female

value: 53 year

value: ENCBS754FVJ at ENCODE; https://www.encodeproject.org/ENCBS754FVJ/

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


title: ra1612_057

description:
102939-001-057
Mild asthmatic (before RV16)

value: primary bronchial epithelial cells

value: direct bronchoscopy

value: Mild asthmatic


title: ra1612_020

description:
102939-001-020
Healthy (after RV16)


title: Histone ChIP-seq from uterus (ENCLB885YOB)

description:
https://www.encodeproject.org/experiments/ENCSR111DTF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR111DTF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB885YOB
fragmentation methods: sonication (generic)
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: ra1612_038

description:
102939-001-038
Mild asthmatic (after RV16)


title: Histone ChIP-seq from sigmoid colon (ENCLB769SND)

description:
https://www.encodeproject.org/experiments/ENCSR104CCB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR104CCB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB769SND
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) sigmoid colon tissue

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 51 year

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: ra1612_010

description:
102939-001-010
Healthy (after RV16)

value: Healthy

value: rhinovirus (RV16)


title: Histone ChIP-seq from sigmoid colon (ENCLB926WOZ)

description:
https://www.encodeproject.org/experiments/ENCSR104CCB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR104CCB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB926WOZ
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: adult


title: Control ChIP-seq from Peyer's patch (ENCLB764FSP)

description:
https://www.encodeproject.org/experiments/ENCSR118FQN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR118FQN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB764FSP
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: male

value: 54 year

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/

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


title: Control ChIP-seq from prostate gland (ENCLB334TAP)

description:
https://www.encodeproject.org/experiments/ENCSR113QDZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR113QDZ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB334TAP
size range: 200-600

value: prostate gland

value: Bradley Bernstein, Broad

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


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB241ZZW)

description:
https://www.encodeproject.org/experiments/ENCSR101KMF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR101KMF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB241ZZW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: female

value: Kristin Ardlie

value: ENCBS821VGX at ENCODE; https://www.encodeproject.org/ENCBS821VGX/


title: ra1612_006

description:
102939-001-006
Healthy (after RV16)

value: primary bronchial epithelial cells

value: direct bronchoscopy

value: Healthy

value: rhinovirus (RV16)


title: ra1612_021

description:
102939-001-021
Healthy (before RV16)


title: ra1612_009

description:
102939-001-009
Healthy (before RV16)


title: GAc3

type: RNA

city: Boston

first: Doaa

middle: AS

last: Megahed

state: MA

address: 200 Longwood Avenue, Harvard Medical schooL, WaB 536D

department: Systems Biology

institute: Harvard Medical School

description:
barcode: 8090936087_C
control

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalized in Genome Studio's Gene expression module

label: biotin

organism: Mus musculus

source_name: GA muscle from control countralateral leg

label_protocol: Biotinylated cRNA was prepared using the Illumina® TotalPrep™-96 RNA Amplification Kit (Life technologies) according to the manufacturer's directions starting with ?100 ng total RNA

extract_protocol: Tissue was homogenized with a homogenizer in trizol (Invitrogen), extracted with chloroform, precipitated in ethanol, and dissolved in nuclease-free water

tag: tissue

value: Gastrocnemius muscle


title: GAd2

description:
barcode: 8090936087_E
denervated

source_name: GA muscle 14 days after schiatic nerve damage


title: ra1612_005

description:
102939-001-005
Healthy (before RV16)


title: GAc2

description:
barcode: 8090936087_B
control


title: OT1_Q4-IL15-T140_rep3

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, followed by 5 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0782

hyb_protocol: Total samples were hybridized to GeneChip HT MG-430 PM arrays (Thermo Fisher Scientific). Washing, staining and scanning was performed using the GeneTitan Wash, and Stain Kit for 3' IVT Array Plates, and the GeneTitan Instrument (Thermo Fisher Scientific).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol

data_processing: Expression data (cel files) were normalized with the rma.sketch algorithm (target signal = 100) using APT powertools (Affymetrix)

source_name: OT-1 cells, Q4/IL-15 stimulated, 140h

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 100 ng total RNA was amplified using the GeneChip 3' IVT Plus Reagent kit (Thermo Fisher Scientific) generating biotinylated complementary RNA. Sample quality was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies)  after fragmentation.

growth_protocol: OT-1 T cells were purified by magnetic cell separation (Miltenyi Biotec). Cells were cultured at 37C at 5% CO2 in RPMI 1640 medium (PAN-Biotech), supplemented with 10% FCS (PAN-Biotech) and 2-ME (Sigma-Aldrich).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer`s protocol, followed by an additional sodium acetate purification step.

treatment_protocol: Cells were stimulated in U-bottom 96 well plates (Cellstar) with 1ng/ml SIINFELK or SIIQFEKL peptides (Genscript), washed and cultured for an additional 5 days with 50 ng/ml IL-15 or 100ng/ml IL-2 (PreproTech).

value: CD8 T cells

tag: background strain

tag: genotype

value: Tg(TcraTcrb)1100Mjb/J (OT-1)

value: 8 wk


title: OT1_Q4-IL15-T140_rep2

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, followed by 5 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0781


title: Histone ChIP-seq from transverse colon (ENCLB820OPP)

description:
https://www.encodeproject.org/experiments/ENCSR101EEJ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR101EEJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB820OPP
fragmentation methods: sonication (generic)
size range: 200-600

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

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: male

value: adult

value: 54 year

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

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


title: OT1_N4-IL15-T140_rep1

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 5 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0777

source_name: OT-1 cells, N4/IL-15 stimulated, 140h


title: GAc1

description:
barcode: 8090936087_A
control


title: OT1_N4-IL15-T140_rep2

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 5 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0778


title: GAd1

description:
barcode: 8090936087_D
denervated


title: OT1_N4-IL15-T140_rep3

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 5 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0779


title: ra1612_019

description:
102939-001-019
Healthy (before RV16)

source_name: primary bronchial epithelial cells


title: Histone ChIP-seq from transverse colon (ENCLB911PQY)

description:
https://www.encodeproject.org/experiments/ENCSR101EEJ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR101EEJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB911PQY
fragmentation methods: sonication (generic)
size range: 200-600

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS633KVX at ENCODE; https://www.encodeproject.org/ENCBS633KVX/


title: OT1_Q4-IL15-T72_rep3

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, followed by 2 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0776

source_name: OT-1 cells, Q4/IL-15 stimulated, 72h


title: Histone ChIP-seq from transverse colon (ENCLB340GKS)

description:
https://www.encodeproject.org/experiments/ENCSR101EEJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR101EEJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340GKS
fragmentation methods: sonication (generic)
size range: 200-600


title: 106_RRn16R_NK_Grp3_W4

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Sorted peripheral cells

extract_protocol:
RNA was purified using QIAGEN RNeasy Micro columns, and RNA quality assessed using Agilent Bioanalyzer.
1 ng of total RNA was used as input for cDNA amplification using 5’ template-switch PCR with the Clontech SMART-Seq v4 Ultra Low Input RNA kit, according to manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual indexed bar codes using Illumina NexteraXT DNA Library Prep kits. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq 3000 using (101 bp SR) at an average read depth of 23 million reads/sample.

treatment_protocol: CD8 depletion administered subcutaneously to the whole animal at 50 mg/kg on day 0. N-803 was administered in four weekly subcutaneous injections of 100 µg/kg. Blood was collected in EDTA tubes and PBMCs were isolated. PBMCs were stained using fluorescent antibodies and CD4+ T cells +/- CD8+ T cells and NK cells were FACS sorted. Sorted cells were resuspended in 350 uL RLT+BME and frozen in -80.

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type

value: Bulk NK


title: OT1_Q4-IL15-T140_rep1

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, followed by 5 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0780


title: Histone ChIP-seq from transverse colon (ENCLB454KSS)

description:
https://www.encodeproject.org/experiments/ENCSR101EEJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101EEJ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB454KSS
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

tag: description

tag: biosample encode accession

tag: link


title: OT1_Q4-IL15-T72_rep1

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, followed by 2 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0774

tag: age


title: 98_RIt16R_NK_Grp3_W4


title: Histone ChIP-seq from testis (ENCLB564ZNF)

description:
https://www.encodeproject.org/experiments/ENCSR091MNT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR091MNT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR385ODY
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB564ZNF
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) testis tissue

value: testis

tag: Sex

tag: dev stage

tag: lab

value: ENCBS849BBS at ENCODE; https://www.encodeproject.org/ENCBS849BBS/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB533SBT)

description:
https://www.encodeproject.org/experiments/ENCSR101KMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR101KMF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB533SBT
fragmentation methods: none
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: female

value: 51 year

value: ENCBS821VGX at ENCODE; https://www.encodeproject.org/ENCBS821VGX/

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


title: OT1_N4-IL15-T72_rep3

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 2 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0773

source_name: OT-1 cells, N4/IL-15 stimulated, 72h

tag: cell type

value: CD8 T cells

value: Tg(TcraTcrb)1100Mjb/J (OT-1)

value: 8 wk


title: GAd3

description:
barcode: 8090936087_F
denervated

value: Gastrocnemius muscle


title: Histone ChIP-seq from testis (ENCLB146PUD)

description:
https://www.encodeproject.org/experiments/ENCSR091MNT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091MNT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR385ODY
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB146PUD
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male

value: adult

value: 54 year

value: Bradley Bernstein, Broad

tag: source

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


title: OT1_Q4-IL15-T72_rep2

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, followed by 2 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0775


title: 94_REi16R_NK_Grp3_W4

value: ALT-803 Only=Grp3

value: Bulk NK


title: OT1_N4-IL15-T72_rep2

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 2 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0771


title: AP_cIN_R4

city: Saint Louis

first: Kristen

middle: L

last: Kroll

state: MO

address: 320 McDonnell Sciences/660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to hg38 using STAR_2.5.4b with gencode v27 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
gene counts file from feature counts was scaled to RPKM using R version 3.5.1.
Genome_build: hg38
Supplementary_files_format_and_content: gene counts and RPKM text files

source_name: Neural progenitor cells

extract_protocol:
Total RNA was collected from iPSC-derived day 12 cExN and cIN NPCs using the NucleoSpin RNA II kit (Takara) per the manufacturer’s instructions. RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific), and the integrity of RNA was confirmed with an Agilent Bioanalyzer 2100 to ensure a RIN value above 8.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Genome Technology Access Center at Washington University. RNA depletion was performed using Ribo-Zero.

value: iPSC-derived cortical inhibitory neural progenitor cells

tag: iPSc source

value: Affected proband (AP)

tag: passage


title: 102_RBn16R_NK_Grp3_W4


title: OT1_N4-IL2-T72_rep1

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 2 days of 100ng/ml IL-2. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0768

source_name: OT-1 cells, N4/IL-2 stimulated, 72h

tag: background strain

tag: genotype


title: 90_RAf16R_NK_Grp3_W4

tag: animalid

tag: group


title: OT1_N4-IL2-T72_rep2

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 2 days of 100ng/ml IL-2. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0770


title: OT1_Q4-T30_rep3

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0767

source_name: OT-1 cells, Q4 stimulated, 30h


title: 80_RRn16R_CD8_Grp3_W4

tag: time point

tag: specific cell type

value: Bulk CD8


title: Histone ChIP-seq from tibial nerve (ENCLB929SRG)

description:
https://www.encodeproject.org/experiments/ENCSR091KXI/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR091KXI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB929SRG
fragmentation methods: sonication (generic)
size range: 200-600

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

tag: antibody

value: tibial nerve

tag: description

value: EnTEX:Nerve - Tibial

value: Kristin Ardlie

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


title: OT1_N4-T30_rep3

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0764

source_name: OT-1 cells, N4 stimulated, 30h

value: CD8 T cells

value: Tg(TcraTcrb)1100Mjb/J (OT-1)

value: 8 wk


title: OT1_N4-T30_rep1

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0762


title: OT1_T0_rep2

description:
Unstimulated OT-1 cells, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0760

source_name: OT-1 cells, unstimulated


title: Histone ChIP-seq from tibial nerve (ENCLB485WAA)

description:
https://www.encodeproject.org/experiments/ENCSR091KXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091KXI
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB485WAA
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

tag: biosample encode accession

value: male

tag: link


title: OT1_T0_rep3

description:
Unstimulated OT-1 cells, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0761

tag: age


title: AP_cIN_R2


title: OT1_N4-T30_rep2

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0763


title: OT1_T0_rep1

description:
Unstimulated OT-1 cells, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0759


title: IS_cIN_R4

value: Intermediate phenotype sister (IS)


title: OT1_N4-IL2-T72_rep3

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 2 days of 100ng/ml IL-2. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0772


title: 76_RBn16R_CD8_Grp3_W4


title: OT1_N4-IL15-T72_rep1

description:
OT-1 cells stimulated for 30h with N4 peptides and anti-CD28, followed by 2 days of 50ng/ml IL-15. Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0769


title: IS_cIN_R3


title: Histone ChIP-seq from adrenal gland (ENCLB923ALY)

description:
https://www.encodeproject.org/experiments/ENCSR086QZY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR086QZY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB923ALY
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) adrenal gland tissue

value: adrenal gland

value: EnTEX:Adrenal Gland

tag: Sex

value: female

tag: dev stage

value: adult

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS458UEH at ENCODE; https://www.encodeproject.org/ENCBS458UEH/

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


title: OT1_Q4-T30_rep1

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0765

tag: cell type


title: Histone ChIP-seq from adrenal gland (ENCLB245VYO)

description:
https://www.encodeproject.org/experiments/ENCSR086QZY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR086QZY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB245VYO
fragmentation methods: none
size range: 200-600

tag: lab

tag: source


title: OT1_Q4-T30_rep2

description:
OT-1 cells stimulated for 30h with Q4 peptides and anti-CD28, Total RNA was isolated and analyzed on Affymetrix GeneTitan to generate expression profile
ext0766


title: 68_REi16R_CD8_Grp3_W4

value: ALT-803 Only=Grp3

value: Bulk CD8


title: 72_RIt16R_CD8_Grp3_W4


title: IS_cIN_R2

value: iPSC-derived cortical inhibitory neural progenitor cells

tag: iPSc source

tag: passage


title: UM_cIN_R3

value: Unaffected mother (UM)


title: 64_RAf16R_CD8_Grp3_W4


title: IS_cIN_R1


title: Histone ChIP-seq from transverse colon (ENCLB951EIZ)

description:
https://www.encodeproject.org/experiments/ENCSR083DXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR083DXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB951EIZ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) transverse colon tissue

value: transverse colon

value: EnTEX:Colon - Transverse

value: 37 year

value: Kristin Ardlie

value: ENCBS816BKF at ENCODE; https://www.encodeproject.org/ENCBS816BKF/

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


title: Histone ChIP-seq from transverse colon (ENCLB694KKN)

description:
https://www.encodeproject.org/experiments/ENCSR083DXD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR083DXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB694KKN
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male


title: UM_cIN_R2


title: UM_cIN_R4


title: 40_RRn16R_CD4_Grp3_W4

value: Bulk CD4


title: UC_cIN_R4

value: Unaffected control (UC)


title: UC_cIN_R3


title: Histone ChIP-seq from transverse colon (ENCLB532TVC)

description:
https://www.encodeproject.org/experiments/ENCSR083DXD/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR083DXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB532TVC
fragmentation methods: sonication (generic)
size range: 200-600

extract_protocol: not provided

value: adult

value: Bradley Bernstein, Broad

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/


title: UM_cIN_R1


title: TF ChIP-seq from esophagus muscularis mucosa (ENCLB473DVO)

description:
https://www.encodeproject.org/experiments/ENCSR073TPC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR073TPC
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777AJC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB473DVO
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: 54 year

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

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


title: 32_RBn16R_CD4_Grp3_W4

value: ALT-803 Only=Grp3


title: UC_cIN_R2

value: iPSC-derived cortical inhibitory neural progenitor cells


title: 16_REi16R_CD4_Grp3_W4


title: TF ChIP-seq from esophagus muscularis mucosa (ENCLB872CYR)

description:
https://www.encodeproject.org/experiments/ENCSR073TPC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR073TPC
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777AJC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872CYR
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: AP_cExN_R2

value: iPSC-derived cortical excitatory neural progenitor cells

value: Affected proband (AP)


title: AP_cExN_R1


title: AP_cExN_R4


title: UC_cIN_R1


title: AP_cExN_R3


title: Histone ChIP-seq from transverse colon (ENCLB676ITU)

description:
https://www.encodeproject.org/experiments/ENCSR069EGE/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB676ITU
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: male

value: ENCBS633KVX at ENCODE; https://www.encodeproject.org/ENCBS633KVX/


title: 8_RAf16R_CD4_Grp3_W4

value: Bulk CD4


title: Histone ChIP-seq from transverse colon (ENCLB897GLA)

description:
https://www.encodeproject.org/experiments/ENCSR069EGE/
***************
biological replicate number: 1
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: ENCLB897GLA
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: IS_cExN_R4

value: Intermediate phenotype sister (IS)


title: Histone ChIP-seq from thyroid gland (ENCLB274VUZ)

description:
https://www.encodeproject.org/experiments/ENCSR064LHU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR064LHU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR475NOQ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB274VUZ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens thyroid gland tissue female adult (53 years)

value: thyroid gland

value: 53 year

value: female

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/

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


title: IS_cExN_R3


title: 105_RRn16R_NK_Grp3_W2

value: ALT-803 Only=Grp3

value: Bulk NK


title: IS_cExN_R2

value: iPSC-derived cortical excitatory neural progenitor cells


title: IS_cExN_R1


title: 101_RBn16R_NK_Grp3_W2


title: UM_cExN_R4

value: Unaffected mother (UM)


title: Histone ChIP-seq from thyroid gland (ENCLB841TEA)

description:
https://www.encodeproject.org/experiments/ENCSR064LHU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR064LHU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR475NOQ
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB841TEA
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: 97_RIt16R_NK_Grp3_W2


title: 24_RIt16R_CD4_Grp3_W4


title: UM_cExN_R3


title: UM_cExN_R1


title: UC_cExN_R4

value: Unaffected control (UC)


title: UC_cExN_R3


title: UM_cExN_R2


title: Control ChIP-seq from tibial nerve (ENCLB890JJG)

description:
https://www.encodeproject.org/experiments/ENCSR059VTG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR059VTG
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB890JJG
size range: 200-600

source_name: Homo sapiens female adult (51 year) tibial nerve tissue

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: 51 year

value: Kristin Ardlie

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/

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


title: UC_cExN_R2


title: Control ChIP-seq from tibial nerve (ENCLB959VKK)

description:
https://www.encodeproject.org/experiments/ENCSR059VTG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059VTG
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB959VKK
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from upper lobe of left lung (ENCLB794QIP)

description:
https://www.encodeproject.org/experiments/ENCSR050LBS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR050LBS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB794QIP
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: male

value: 54 year

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/

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


title: 83_REf16R_NK_Grp3_W2

value: ALT-803 Only=Grp3

value: Bulk NK


title: 89_RAf16R_NK_Grp3_W2


title: 79_RRn16R_CD8_Grp3_W2

value: Bulk CD8


title: UC_cExN_R1

value: iPSC-derived cortical excitatory neural progenitor cells

value: Unaffected control (UC)


title: Histone ChIP-seq from upper lobe of left lung (ENCLB357OQF)

description:
https://www.encodeproject.org/experiments/ENCSR050LBS/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR050LBS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB357OQF
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Histone ChIP-seq from upper lobe of left lung (ENCLB725SPY)

description:
https://www.encodeproject.org/experiments/ENCSR050LBS/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR050LBS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB725SPY
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from upper lobe of left lung (ENCLB435AET)

description:
https://www.encodeproject.org/experiments/ENCSR050LBS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR050LBS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB435AET
fragmentation methods: sonication (generic)
size range: 200-600


title: 75_RBn16R_CD8_Grp3_W2


title: 71_RIt16R_CD8_Grp3_W2


title: 86_RVz15R_NK_Grp3_W2


title: 67_REi16R_CD8_Grp3_W2


title: 63_RAf16R_CD8_Grp3_W2


title: Histone ChIP-seq from transverse colon (ENCLB781XYA)

description:
https://www.encodeproject.org/experiments/ENCSR047JMV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR047JMV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB781XYA
fragmentation methods: sonication (generic)
size range: 200-600

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

value: transverse colon

value: EnTEX:Colon - Transverse

value: 53 year

value: female

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/

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


title: Histone ChIP-seq from transverse colon (ENCLB913MCD)

description:
https://www.encodeproject.org/experiments/ENCSR047JMV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR047JMV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB913MCD
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: 60_RVz15R_CD8_Grp3_W2


title: 57_REf16R_CD8_Grp3_W2


title: Histone ChIP-seq from vagina (ENCLB703FEC)

description:
https://www.encodeproject.org/experiments/ENCSR046OON/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR046OON
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB703FEC
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) vagina tissue

value: vagina

value: 51 year

value: Kristin Ardlie

value: ENCBS468YOF at ENCODE; https://www.encodeproject.org/ENCBS468YOF/

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


title: wholeblood__CRC305E9229_120h

city: London

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: whole blood gene expression of participant CRC305E9229 at 120 hours post immunization

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

data_processing:
The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.
Quantile normalized signal intensity using limma 3.38.3,  read.maimages source = agilent, backgroundCorrect method= normexp, normalizeBetweenArrays method= quantile

source_name: whole blood,PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA extracted from the whole blood in PaxGene tubes or the muscle biopsies stored in RNAlater using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: protocol

tag: treatment

value: FLUADE

tag: day

tag: hour

tag: tissue

value: whole blood

tag: participant

tag: gender

value: male

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: 54_RRn16R_CD4_Grp3_W2

source_name: Sorted peripheral cells

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type

value: Bulk CD4


title: muscle_immunized_CRC305E95729_24h

description: immunized muscle biopsy gene expression of participant CRC305E95729 at 24 hours post immunization

source_name: muscle,RNAlater

value: PLACEBOE

tag: injected leg

value: right

value: muscle

tag: biopsied leg

tag: biopsy site treatment

value: immunized

tag: biopsy comments

value: muscle tissue+++

tag: age


title: wholeblood__CRC305E9761034_24h

description: whole blood gene expression of participant CRC305E9761034 at 24 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

value: hispanic or latino


title: wholeblood__CRC305E9761034_0h

description: whole blood gene expression of participant CRC305E9761034 at 0 hours post immunization

tag: day

tag: hour


title: muscle_notimmunized_CRC305E9021_72h

description: not immunized muscle biopsy gene expression of participant CRC305E9021 at 72 hours post immunization

value: left

tag: tissue

value: not immunized

value: 1st biopsy sample too little. 2nd sample all muscle adequate no connective tissue or adipose seen.

tag: participant


title: wholeblood__CRC305E95227_120h

description: whole blood gene expression of participant CRC305E95227 at 120 hours post immunization

tag: gender

tag: race


title: wholeblood__CRC305E97445_120h

description: whole blood gene expression of participant CRC305E97445 at 120 hours post immunization

tag: ethnicity


title: wholeblood__CRC305E9091012_0h

description: whole blood gene expression of participant CRC305E9091012 at 0 hours post immunization

value: FLUADE


title: wholeblood__CRC305E97843_72h

description: whole blood gene expression of participant CRC305E97843 at 72 hours post immunization

value: whole blood


title: Histone ChIP-seq from transverse colon (ENCLB812XOG)

description:
https://www.encodeproject.org/experiments/ENCSR047JMV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR047JMV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB812XOG
fragmentation methods: sonication (generic)
size range: 200-600

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

tag: antibody

value: transverse colon

value: tissue

tag: description

value: EnTEX:Colon - Transverse

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

value: adult

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS280DYM at ENCODE; https://www.encodeproject.org/ENCBS280DYM/

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


title: wholeblood__CRC305E93544_168h

description: whole blood gene expression of participant CRC305E93544 at 168 hours post immunization

tag: protocol

value: PLACEBOE

value: male

tag: age

value: white


title: wholeblood__CRC305E9091012_24h

description: whole blood gene expression of participant CRC305E9091012 at 24 hours post immunization

tag: treatment

tag: day

value: not hispanic or latino


title: 47_RBn16R_CD4_Grp3_W2

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type

value: Bulk CD4


title: Histone ChIP-seq from vagina (ENCLB732WKH)

description:
https://www.encodeproject.org/experiments/ENCSR046OON/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR046OON
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB732WKH
fragmentation methods: sonication (generic)
size range: 200-600

value: vagina

value: 51 year

value: ENCBS468YOF at ENCODE; https://www.encodeproject.org/ENCBS468YOF/

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


title: wholeblood__CRC305E93544_0h

description: whole blood gene expression of participant CRC305E93544 at 0 hours post immunization

tag: hour

tag: tissue

value: whole blood

tag: participant

tag: gender

tag: race

tag: ethnicity

value: hispanic or latino


title: 93_REi16R_NK_Grp3_W2

value: Bulk NK


title: wholeblood__CRC305E97042_24h

description: whole blood gene expression of participant CRC305E97042 at 24 hours post immunization

value: FENDRIXE


title: wholeblood__CRC305E97843_0h

description: whole blood gene expression of participant CRC305E97843 at 0 hours post immunization


title: wholeblood__CRC305E97445_0h

description: whole blood gene expression of participant CRC305E97445 at 0 hours post immunization


title: wholeblood__CRC305E95729_24h

description: whole blood gene expression of participant CRC305E95729 at 24 hours post immunization


title: TF ChIP-seq from stomach (ENCLB968HCM)

description:
https://www.encodeproject.org/experiments/ENCSR037GKL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR037GKL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB968HCM
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) stomach tissue

tag: antibody

value: CTCF

value: stomach

value: tissue

tag: description

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS443LLE at ENCODE; https://www.encodeproject.org/ENCBS443LLE/

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


title: Histone ChIP-seq from uterus (ENCLB536UHG)

description:
https://www.encodeproject.org/experiments/ENCSR035ONO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR035ONO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB536UHG
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (53 years) uterus tissue

value: uterus

value: female

tag: age

value: 53 year

tag: source

tag: link

value: ENCBS754FVJ at ENCODE; https://www.encodeproject.org/ENCBS754FVJ/

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


title: 39_RIt16R_CD4_Grp3_W2

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

value: Bulk CD4


title: 31_REi16R_CD4_Grp3_W2

tag: specific cell type


title: wholeblood__CRC305E97042_0h

description: whole blood gene expression of participant CRC305E97042 at 0 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

tag: day

tag: hour

tag: tissue

value: whole blood

tag: participant

value: male

value: white

value: hispanic or latino


title: wholeblood__CRC305E94341_3h

description: whole blood gene expression of participant CRC305E94341 at 3 hours post immunization

tag: gender

tag: race

tag: ethnicity

value: not hispanic or latino


title: wholeblood__CRC305E93439_120h

description: whole blood gene expression of participant CRC305E93439 at 120 hours post immunization

value: PLACEBOE


title: 15_RVz15R_CD4_Grp3_W2


title: 23_RAf16R_CD4_Grp3_W2


title: 7_REf16R_CD4_Grp3_W2


title: wholeblood__CRC305E94341_0h

description: whole blood gene expression of participant CRC305E94341 at 0 hours post immunization


title: 104_RRn16R_NK_Grp3_D3

value: Bulk NK


title: wholeblood__CRC305E97940_0h

description: whole blood gene expression of participant CRC305E97940 at 0 hours post immunization


title: TF ChIP-seq from stomach (ENCLB149XWT)

description:
https://www.encodeproject.org/experiments/ENCSR037GKL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR037GKL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB149XWT
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

value: CTCF

value: stomach

value: tissue

tag: description

tag: biosample encode accession

tag: Sex

tag: dev stage

value: adult

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS443LLE at ENCODE; https://www.encodeproject.org/ENCBS443LLE/


title: wholeblood__CRC305E97940_24h

description: whole blood gene expression of participant CRC305E97940 at 24 hours post immunization

tag: age


title: Histone ChIP-seq from ovary (ENCLB291XEE)

description:
https://www.encodeproject.org/experiments/ENCSR029TTW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR029TTW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509SEX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB291XEE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (53 years) ovary tissue

value: ovary

value: female

value: 53 year

tag: source

tag: link

value: ENCBS760QKF at ENCODE; https://www.encodeproject.org/ENCBS760QKF/

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


title: Histone ChIP-seq from ovary (ENCLB708IKO)

description:
https://www.encodeproject.org/experiments/ENCSR029TTW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR029TTW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509SEX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB708IKO
fragmentation methods: sonication (generic)
size range: 200-600


title: wholeblood__CRC305E95838_72h

description: whole blood gene expression of participant CRC305E95838 at 72 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

value: whole blood

value: male

value: white


title: Histone ChIP-seq from uterus (ENCLB146RNR)

description:
https://www.encodeproject.org/experiments/ENCSR035ONO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR035ONO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB146RNR
fragmentation methods: sonication (generic)
size range: 200-600

value: uterus

value: ENCBS754FVJ at ENCODE; https://www.encodeproject.org/ENCBS754FVJ/


title: 100_RBn16R_NK_Grp3_D3

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type

value: Bulk NK


title: Histone ChIP-seq from stomach (ENCLB615RGF)

description:
https://www.encodeproject.org/experiments/ENCSR009RJD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR009RJD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB615RGF
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) stomach tissue

value: stomach

value: tissue

value: adult

value: 51 year

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/

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


title: AP_cIN_R1

source_name: Neural progenitor cells

tag: cell type

value: iPSC-derived cortical inhibitory neural progenitor cells

tag: iPSc source

value: Affected proband (AP)

tag: passage


title: wholeblood__CRC305E96637_0h

description: whole blood gene expression of participant CRC305E96637 at 0 hours post immunization

tag: day

tag: hour

tag: tissue

tag: participant

tag: gender

tag: race

tag: ethnicity

value: not hispanic or latino


title: 96_RIt16R_NK_Grp3_D3


title: wholeblood__CRC305E96536_3h

description: whole blood gene expression of participant CRC305E96536 at 3 hours post immunization

value: FENDRIXE

tag: age


title: wholeblood__CRC305E96637_168h

description: whole blood gene expression of participant CRC305E96637 at 168 hours post immunization

tag: protocol

value: whole blood


title: wholeblood__CRC305E95335_3h

description: whole blood gene expression of participant CRC305E95335 at 3 hours post immunization

tag: treatment

value: PLACEBOE

value: male


title: wholeblood__CRC305E95838_0h

description: whole blood gene expression of participant CRC305E95838 at 0 hours post immunization

value: white


title: 85_RVz15R_NK_Grp3_D3

tag: animalid


title: 92_REi16R_NK_Grp3_D3

tag: group


title: Histone ChIP-seq from stomach (ENCLB302NEB)

description:
https://www.encodeproject.org/experiments/ENCSR007GED/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR007GED
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB302NEB
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

tag: description

tag: biosample encode accession

tag: Sex

tag: dev stage

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS443LLE at ENCODE; https://www.encodeproject.org/ENCBS443LLE/

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


title: Histone ChIP-seq from stomach (ENCLB148LPW)

description:
https://www.encodeproject.org/experiments/ENCSR009RJD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR009RJD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB148LPW
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: tissue

value: female

value: adult


title: wholeblood__CRC305E93439_0h

description: whole blood gene expression of participant CRC305E93439 at 0 hours post immunization

tag: day

tag: hour

tag: tissue

tag: participant


title: wholeblood__CRC305E92633_168h

description: whole blood gene expression of participant CRC305E92633 at 168 hours post immunization

tag: gender

tag: age

tag: race

tag: ethnicity


title: 88_RAf16R_NK_Grp3_D3

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type

value: Bulk NK


title: wholeblood__CRC305E92432_120h

description: whole blood gene expression of participant CRC305E92432 at 120 hours post immunization

tag: protocol

tag: treatment

value: asian

value: not hispanic or latino


title: 82_REf16R_NK_Grp3_D3


title: Histone ChIP-seq from stomach (ENCLB358YCU)

description:
https://www.encodeproject.org/experiments/ENCSR007GED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR007GED
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB358YCU
fragmentation methods: sonication (generic)
size range: 200-600

tag: antibody

tag: description

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: lab


title: wholeblood__CRC305E96536_0h

description: whole blood gene expression of participant CRC305E96536 at 0 hours post immunization

value: FENDRIXE

tag: day

tag: hour

tag: tissue

value: whole blood

tag: participant


title: Histone ChIP-seq from adrenal gland (ENCLB880OJG)

description:
https://www.encodeproject.org/experiments/ENCSR006TUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR006TUH
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB880OJG
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) adrenal gland tissue

value: adrenal gland

value: EnTEX:Adrenal Gland

tag: age

value: 51 year

tag: source

tag: link

value: ENCBS458UEH at ENCODE; https://www.encodeproject.org/ENCBS458UEH/

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


title: wholeblood__CRC305E92633_0h

description: whole blood gene expression of participant CRC305E92633 at 0 hours post immunization

value: PLACEBOE

tag: gender

value: male

tag: race

value: white

tag: ethnicity


title: 78_RRn16R_CD8_Grp3_D3

tag: animalid

tag: group

tag: time point

tag: specific cell type

value: Bulk CD8


title: wholeblood__CRC305E95335_0h

description: whole blood gene expression of participant CRC305E95335 at 0 hours post immunization

tag: protocol

tag: treatment


title: wholeblood__CRC305E91030_3h

description: whole blood gene expression of participant CRC305E91030 at 3 hours post immunization


title: Histone ChIP-seq from adrenal gland (ENCLB143YEF)

description:
https://www.encodeproject.org/experiments/ENCSR006TUH/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR006TUH
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB143YEF
fragmentation methods: none
size range: 200-600

tag: antibody

value: tissue

tag: description

tag: biosample encode accession

tag: Sex

value: female

tag: dev stage

tag: lab

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: wholeblood__CRC305E92432_0h

description: whole blood gene expression of participant CRC305E92432 at 0 hours post immunization

tag: day

tag: hour

tag: tissue

tag: participant

tag: age

value: asian


title: wholeblood__CRC305E95931_72h

description: whole blood gene expression of participant CRC305E95931 at 72 hours post immunization

tag: gender

tag: race

tag: ethnicity

value: not hispanic or latino


title: wholeblood__CRC305E91030_0h

description: whole blood gene expression of participant CRC305E91030 at 0 hours post immunization


title: wholeblood__CRC305E95227_0h

description: whole blood gene expression of participant CRC305E95227 at 0 hours post immunization

value: FENDRIXE


title: wholeblood__CRC305E93728_72h

description: whole blood gene expression of participant CRC305E93728 at 72 hours post immunization

value: whole blood


title: wholeblood__CRC305E95931_0h

description: whole blood gene expression of participant CRC305E95931 at 0 hours post immunization


title: 74_RBn16R_CD8_Grp3_D3

tag: animalid

tag: group

value: ALT-803 Only=Grp3

tag: time point

tag: specific cell type


title: Histone ChIP-seq from tibial artery (ENCLB907HCS)

description:
https://www.encodeproject.org/experiments/ENCSR000SNM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000SNM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR714GXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB907HCS
fragmentation methods: none
size range: 200-600

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

tag: antibody

value: tibial artery

tag: description

value: EnTEX:Artery - Tibial

value: adult

tag: source

tag: link

value: ENCBS636NCW at ENCODE; https://www.encodeproject.org/ENCBS636NCW/


title: wholeblood__CRC305E95729_0h

description: whole blood gene expression of participant CRC305E95729 at 0 hours post immunization

tag: protocol

tag: treatment

value: PLACEBOE


title: 66_REi16R_CD8_Grp3_D3


title: 70_RIt16R_CD8_Grp3_D3


title: wholeblood__CRC305E92725_3h

description: whole blood gene expression of participant CRC305E92725 at 3 hours post immunization

value: FLUADE

tag: day

tag: hour

value: male


title: wholeblood__CRC305E95426_0h

description: whole blood gene expression of participant CRC305E95426 at 0 hours post immunization

tag: tissue

tag: participant

value: white


title: Histone ChIP-seq from tibial artery (ENCLB607NMP)

description:
https://www.encodeproject.org/experiments/ENCSR000SNM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR000SNM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR714GXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB607NMP
fragmentation methods: none
size range: 200-600

value: tissue

tag: biosample encode accession

tag: Sex

tag: dev stage

tag: age

value: 51 year

tag: lab

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


title: 62_RAf16R_CD8_Grp3_D3

tag: animalid

tag: group

tag: time point

value: Bulk CD8


title: AP_cIN_R3

tag: cell type

value: iPSC-derived cortical inhibitory neural progenitor cells

tag: iPSc source

value: Affected proband (AP)

tag: passage


title: GBM1-selinexor  rep1

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

institute: University of Colorado

description:
G1-3
(one of two replicates; samples G1-3, G1-4)
GBM1_all_genes_FDR.csv

data_processing:
Data were trimmed using trimmomatic
Data were mapped to the human genome (hg38) by gSNAP
Expression (FPKM) was derived by Cufflinks
Genome_build: hg38
Supplementary_files_format_and_content: FPKMs

source_name: Cultured tumor cells

growth_protocol: Cells were grown as neurospheres in serum-free growth medium

extract_protocol:
Qiagen RNAEASY kit
Library preparation was performed using the TruSeq Library Preparation Kit v2 (Agilent) to obtain an mRNA-focused sequencing library

treatment_protocol: Cells were treated for 16 hours with selinexor

tag: tumor type

value: Pediatric high grade glioma

tag: cell line

value: selinexor 307 nM


title: wholeblood__CRC305E93728_0h

description: whole blood gene expression of participant CRC305E93728 at 0 hours post immunization

tag: protocol

tag: treatment

tag: day

value: whole blood

tag: gender

tag: race

tag: ethnicity

value: not hispanic or latino


title: GBM1-vehicle  rep2

description:
G1-2
(one of two replicates; samples G1-1, G1-2)
GBM1_all_genes_FDR.csv

value: control


title: 56_REf16R_CD8_Grp3_D3

value: ALT-803 Only=Grp3

tag: specific cell type


title: GBM1-vehicle  rep1

description:
G1-1
(one of two replicates; samples G1-1, G1-2)
GBM1_all_genes_FDR.csv


title: GBM1-selinexor  rep2

description:
G1-4
(one of two replicates; samples G1-3, G1-4)
GBM1_all_genes_FDR.csv


title: wholeblood__CRC305E95426_168h

description: whole blood gene expression of participant CRC305E95426 at 168 hours post immunization

value: FENDRIXE

tag: hour

tag: tissue

tag: participant

tag: age


title: DIPG7-selinexor  rep2

description:
D7-4
(one of two replicates; samples D7-3, D7-4)
DIPG7_all_genes_FDR.csv

value: Diffuse intrinsic pontine glioma

value: selinexor 535 nM


title: 53_RRn16R_CD4_Grp3_D3

tag: animalid

tag: group

tag: time point

value: Bulk CD4


title: DIPG7-selinexor  rep1

description:
D7-3
(one of two replicates; samples D7-3, D7-4)
DIPG7_all_genes_FDR.csv


title: 46_RBn16R_CD4_Grp3_D3


title: 59_RVz15R_CD8_Grp3_D3


title: 30_REi16R_CD4_Grp3_D3


title: DIPG7-vehicle  rep2

description:
D7-2
(one of two replicates; samples D7-1, D7-2)
DIPG7_all_genes_FDR.csv


title: DIPG7-vehicle  rep1

description:
D7-1
(one of two replicates; samples D7-1, D7-2)
DIPG7_all_genes_FDR.csv


title: wholeblood__CRC305E94223_120h

description: whole blood gene expression of participant CRC305E94223 at 120 hours post immunization

value: FLUADE

value: male

value: other


title: 22_RAf16R_CD4_Grp3_D3


title: DIPG4-selinexor  rep2

description:
D4-4
(one of two replicates; samples D4-3, D4-4)
DIPG4_all_genes_FDR.csv

value: selinexor 610 nM


title: wholeblood__CRC305E95124_168h

description: whole blood gene expression of participant CRC305E95124 at 168 hours post immunization

value: white


title: wholeblood__CRC305E91922_72h

description: whole blood gene expression of participant CRC305E91922 at 72 hours post immunization

value: PLACEBOE

value: hispanic or latino


title: wholeblood__CRC305E93921_24h

description: whole blood gene expression of participant CRC305E93921 at 24 hours post immunization


title: wholeblood__CRC305E94223_0h

description: whole blood gene expression of participant CRC305E94223 at 0 hours post immunization


title: wholeblood__CRC305E91922_0h

description: whole blood gene expression of participant CRC305E91922 at 0 hours post immunization


title: wholeblood__CRC305E93921_0h

description: whole blood gene expression of participant CRC305E93921 at 0 hours post immunization


title: wholeblood__CRC305E95124_0h

description: whole blood gene expression of participant CRC305E95124 at 0 hours post immunization


title: wholeblood__CRC305E91420_72h

description: whole blood gene expression of participant CRC305E91420 at 72 hours post immunization


title: 14_RVz15R_CD4_Grp3_D3


title: wholeblood__CRC305E92725_0h

description: whole blood gene expression of participant CRC305E92725 at 0 hours post immunization


title: wholeblood__CRC305E91218_0h

description: whole blood gene expression of participant CRC305E91218 at 0 hours post immunization


title: DIPG4-selinexor  rep1

description:
D4-3
(one of two replicates; samples D4-3, D4-4)
DIPG4_all_genes_FDR.csv


title: wholeblood__CRC305E91420_0h

description: whole blood gene expression of participant CRC305E91420 at 0 hours post immunization


title: wholeblood__CRC305E95016_0h

description: whole blood gene expression of participant CRC305E95016 at 0 hours post immunization


title: wholeblood__CRC305E93817_168h

description: whole blood gene expression of participant CRC305E93817 at 168 hours post immunization

value: asian


title: wholeblood__CRC305E94819_120h

description: whole blood gene expression of participant CRC305E94819 at 120 hours post immunization


title: wholeblood__CRC305E92315_3h

description: whole blood gene expression of participant CRC305E92315 at 3 hours post immunization


title: DIPG4-vehicle  rep2

description:
D4-2
(one of two replicates; samples D4-1, D4-2)
DIPG4_all_genes_FDR.csv


title: wholeblood__CRC305E94819_0h

description: whole blood gene expression of participant CRC305E94819 at 0 hours post immunization


title: wholeblood__CRC305E91218_3h

description: whole blood gene expression of participant CRC305E91218 at 3 hours post immunization


title: wholeblood__CRC305E92315_0h

description: whole blood gene expression of participant CRC305E92315 at 0 hours post immunization


title: wholeblood__CRC305E93614_168h

description: whole blood gene expression of participant CRC305E93614 at 168 hours post immunization


title: wholeblood__CRC305E93614_0h

description: whole blood gene expression of participant CRC305E93614 at 0 hours post immunization


title: wholeblood__CRC305E93817_0h

description: whole blood gene expression of participant CRC305E93817 at 0 hours post immunization


title: wholeblood__CRC305E91513_0h

description: whole blood gene expression of participant CRC305E91513 at 0 hours post immunization


title: wholeblood__CRC305E95016_24h

description: whole blood gene expression of participant CRC305E95016 at 24 hours post immunization


title: 52_RVe16R_CD4_Grp2_D3

value: CD8 depletion Only=Grp2


title: 45_RSt15R_CD4_Grp2_D3


title: BT-245-selinexor  rep2

description:
245-4
(one of two replicates; samples 245-3, 245-4)
BT245_all_genes_FDR.csv

value: Diffuse midline glioma (thalamus)

value: selinexor 365 nM


title: wholeblood__CRC305E93011_120h

description: whole blood gene expression of participant CRC305E93011 at 120 hours post immunization

value: whole blood

value: not hispanic or latino


title: DIPG4-vehicle  rep1

description:
D4-1
(one of two replicates; samples D4-1, D4-2)
DIPG4_all_genes_FDR.csv

value: control


title: 37_REs16R_CD4_Grp2_D3


title: BT-245-selinexor  rep1

description:
245-3
(one of two replicates; samples 245-3, 245-4)
BT245_all_genes_FDR.csv


title: 6_REf16R_CD4_Grp3_D3

value: ALT-803 Only=Grp3


title: BT-245-vehicle rep2

description:
245-2
(one of two replicates; samples 245-1, 245-2)
BT245_all_genes_FDR.csv


title: BT-245-vehicle rep1

description:
245-1
(one of two replicates; samples 245-1, 245-2)
BT245_all_genes_FDR.csv


title: 21_RKs15R_CD4_Grp2_D3


title: 13_ROr15R_CD4_Grp2_D3


title: wholeblood__CRC305E9229_0h

description: whole blood gene expression of participant CRC305E9229 at 0 hours post immunization


title: 5_RNz15R_CD4_Grp2_D3


title: wholeblood__CRC305E91110_0h

description: whole blood gene expression of participant CRC305E91110 at 0 hours post immunization


title: wholeblood__CRC305E93011_0h

description: whole blood gene expression of participant CRC305E93011 at 0 hours post immunization


title: wholeblood__CRC305E9448_24h

description: whole blood gene expression of participant CRC305E9448 at 24 hours post immunization

value: FENDRIXE


title: wholeblood__CRC305E9448_0h

description: whole blood gene expression of participant CRC305E9448 at 0 hours post immunization


title: wholeblood__CRC305E9077_0h

description: whole blood gene expression of participant CRC305E9077 at 0 hours post immunization


title: 51_REu16R_CD4_Grp1_D3

value: CD8 depletion + early ALT-803= Grp1

value: Bulk CD4


title: 29_RRb16R_CD4_Grp2_D3


title: 44_RNa16R_CD4_Grp1_D3


title: wholeblood__CRC305E91110_72h

description: whole blood gene expression of participant CRC305E91110 at 72 hours post immunization

value: FLUADE

value: male


title: 36_RAu15R_CD4_Grp1_D3


title: 28_RUa16R_CD4_Grp1_D3


title: RNA-seq_CTCF Y226A, F228A_rep2

first: Angela

last: Sedeno Cacciatore

address: Plesmanlaan 121

department: Gene regulation

institute: Netherlands Cancer Institute

description:
CTCF_103_02
5235_5_CTCF

data_processing:
Reads were mapped to hg19 using TopHat 2.1.1 (Kim et al., 2013) and HTSeq-count (Anders et al., 2015) was used to generate transcript-counts using GENCODE release 19  as reference.
DESeq2 was used to infer differentially expressed genes with an adjusted p-value threshold of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Count table of reads per transcript for all samples and DESeq2 results of differential expression for the CTCF mutant  compared to WT.

molecule: polyA RNA

source_name: CTCF Y226A, F228A

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in IMDM (Invitrogen) supplemented with 10% FCS (Clontech), 1% Penicillin-Streptomycin (Invitrogen) and 0.5% Ultraglutamin (Lonza).

extract_protocol:
Total RNA from cultured cells was extracted using TRIzol reagent (Invitrogen).
Strand-specific libraries were generated using the TruSeq PolyA Stranded mRNA sample preparation kit (iIlumina). In brief, polyadenylated RNA was purified using oligo-dT beads. Following purification, the RNA was fragmented, random-primed and reserve transcribed using SuperScript II Reverse Transcriptase (Invitrogen). The generated cDNA was 3’ end-adenylated and ligated to Illumina Paired-end sequencing adapters and amplified by PCR using HiSeq SR Cluster Kit v4 cBot (Illumina).

treatment_protocol: gRNA targeting exon 1 of CTCF were designed and annealed into pX330 (primer: 5’- CGATTTTGAGGAAGAACAGC-3’). To modify the targeted locus we co-transfected a 120 basepair repair oligo containing the desired mutation and a silent mutation. For oligo sequence, see supplementary file on the GSE126637 SuperSeries record. pBabePuro was co-transfected in a 10:1 ratio to the pX330. Transfected clones were selected using 2 µg/µl puromycin for 2 days. gDNA of clones was isolated and send for Sanger sequencing to check for the desired mutation.

tag: genotype

value: CTCF Y226A, F228A


title: RNA-seq_CTCF Y226A, F228A_rep3

description:
CTCF_103_03
5235_6_CTCF


title: 20_106_13R_CD4_Grp1_D3


title: RNA-seq_WT_rep3

description:
WT_03
5235_3_WT

source_name: WT

value: Wild-type


title: wholeblood__CRC305E91513_72h

description: whole blood gene expression of participant CRC305E91513 at 72 hours post immunization

value: white


title: RNA-seq_CTCF Y226A, F228A_rep1

description:
CTCF_103_01
5235_4_CTCF


title: wholeblood__CRC305E9077_3h

description: whole blood gene expression of participant CRC305E9077 at 3 hours post immunization


title: RNA-seq_WT_rep2

description:
WT_02
5235_2_WT


title: wholeblood__CRC305E9086_0h

description: whole blood gene expression of participant CRC305E9086 at 0 hours post immunization

value: PLACEBOE

value: black or african american


title: wholeblood__CRC305E9285_0h

description: whole blood gene expression of participant CRC305E9285 at 0 hours post immunization


title: 103_RRn16R_NK_Grp3_Pre

value: Pre

value: Bulk NK


title: 12_RHv15R_CD4_Grp1_D3


title: 4_RJt15R_CD4_Grp1_D3


title: wholeblood__CRC305E9053_0h

description: whole blood gene expression of participant CRC305E9053 at 0 hours post immunization


title: wholeblood__CRC305E9285_168h

description: whole blood gene expression of participant CRC305E9285 at 168 hours post immunization


title: wholeblood__CRC305E9086_168h

description: whole blood gene expression of participant CRC305E9086 at 168 hours post immunization


title: wholeblood__CRC305E9042_0h

description: whole blood gene expression of participant CRC305E9042 at 0 hours post immunization


title: wholeblood__CRC305E9053_120h

description: whole blood gene expression of participant CRC305E9053 at 120 hours post immunization


title: wholeblood__CRC305E9064_3h

description: whole blood gene expression of participant CRC305E9064 at 3 hours post immunization

value: asian


title: wholeblood__CRC305E9021_72h

description: whole blood gene expression of participant CRC305E9021 at 72 hours post immunization

value: whole blood


title: RNA-seq_WT_rep1

description:
WT_01
5235_1_WT


title: wholeblood__CRC305E9042_24h

description: whole blood gene expression of participant CRC305E9042 at 24 hours post immunization

value: not hispanic or latino


title: muscle_notimmunized_CRC305E97445_120h

description: not immunized muscle biopsy gene expression of participant CRC305E97445 at 120 hours post immunization

tag: injected leg

value: right

value: muscle

tag: biopsied leg

value: left

tag: biopsy site treatment

value: not immunized

tag: biopsy comments

value: all muscle


title: muscle_immunized_CRC305E95838_72h

description: immunized muscle biopsy gene expression of participant CRC305E95838 at 72 hours post immunization

tag: protocol

tag: treatment

value: FENDRIXE

tag: day

value: immunized


title: muscle_notimmunized_CRC305E95838_72h

description: not immunized muscle biopsy gene expression of participant CRC305E95838 at 72 hours post immunization

tag: gender

value: male

tag: race

tag: ethnicity


title: muscle_notimmunized_CRC305E97940_24h

description: not immunized muscle biopsy gene expression of participant CRC305E97940 at 24 hours post immunization

tag: hour

tag: tissue


title: 99_RBn16R_NK_Grp3_Pre

value: ALT-803 Only=Grp3

tag: specific cell type


title: muscle_notimmunized_CRC305E97843_72h

description: not immunized muscle biopsy gene expression of participant CRC305E97843 at 72 hours post immunization

tag: participant

tag: age

value: white

value: hispanic or latino


title: muscle_notimmunized_CRC305E95931_72h

description: not immunized muscle biopsy gene expression of participant CRC305E95931 at 72 hours post immunization


title: muscle_immunized_CRC305E97843_72h

description: immunized muscle biopsy gene expression of participant CRC305E97843 at 72 hours post immunization

value: PLACEBOE

value: large amount of muscle


title: 95_RIt16R_NK_Grp3_Pre

tag: animalid

tag: group

tag: time point

value: Pre

value: Bulk NK


title: muscle_immunized_CRC305E97940_24h

description: immunized muscle biopsy gene expression of participant CRC305E97940 at 24 hours post immunization

tag: injected leg

tag: biopsied leg

value: large amount of muscle. some blood.


title: muscle_immunized_CRC305E95931_72h

description: immunized muscle biopsy gene expression of participant CRC305E95931 at 72 hours post immunization

tag: biopsy site treatment

tag: biopsy comments

value: asian

value: not hispanic or latino


title: wholeblood__CRC305E9064_0h

description: whole blood gene expression of participant CRC305E9064 at 0 hours post immunization

tag: protocol

tag: treatment

value: whole blood


title: muscle_immunized_CRC305E97445_120h

description: immunized muscle biopsy gene expression of participant CRC305E97445 at 120 hours post immunization

value: left

tag: day

value: muscle

tag: gender


title: 91_REi16R_NK_Grp3_Pre