title: ChIP-seq from MM.1S (ENCLB340JFO)

description:
https://www.encodeproject.org/experiments/ENCSR894QWM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR894QWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB340JFO
size range: 300-600
nucleic acid starting quantity: 13
nucleic acid starting quantity units: ng

source_name: Homo sapiens MM.1S immortalized cell line

tag: line

value: cell line

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

value: 42 year

tag: health state

value: immunoglobulin A lambda myeloma

value: ENCBS241TLI at ENCODE; https://www.encodeproject.org/ENCBS241TLI/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: ChIP-seq from GM12878 (ENCLB508FEM)

status: Public on Dec 03 2018

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/ENCSR933EYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR933EYC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2017-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB508FEM
size range: 200-600
nucleic acid starting quantity: 9
nucleic acid starting quantity units: ng

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens GM12878 immortalized cell line

tag: antibody

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: unknown

tag: passage number

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

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


title: ChIP-seq from MM.1S (ENCLB430LJZ)

description:
https://www.encodeproject.org/experiments/ENCSR894QWM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR894QWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB430LJZ
size range: 300-600
nucleic acid starting quantity: 9
nucleic acid starting quantity units: ng

tag: description


title: HuBM_CD19+_CD20+_9-16

type: RNA

city: Gaithersburg

first: Christopher

last: Groves

state: MD

address: One MedImmune Way

institute: MedImmune

description: Gene expression data from FACS purified human bone-marrow CD19+/CD20+ cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HGU133 Plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were processed and analyzed in R with frma package

label: biotin

molecule: total RNA

source_name: FACS purified human bone marrow CD19+/CD20+ cells

label_protocol: Biotinylated cRNA were prepared according MessageAmp™ Premier RNA Amplification Kit procedure

extract_protocol: Zymo miniprep kit

treatment_protocol: Untreated BM cells were stained w mAbs and sorted by FACS. The populations from BM were identified by CD27, CD38, CD19, CD20, and CD138. ASC were defined as CD38hiCD27+CD138+ and either CD19+ or CD19-. B cells were non-ASC CD19+ and either CD20+ or CD20-.

tag: marker

tag: tissue

value: Bone Marrow


title: W05_M2_2012_Cy3

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

country: France

institute: IRHS

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532 and 635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. Pair-data files were extracted from the scanned images using DEVA 1.2.1 software (Roche).

data_processing: Statistical analyses were performed using R version 2.14.1 (R Development Core Team, 2011) and the package LIMMA 3.10.1 (Smyth G.K., 2005) from the Bioconductor project. Data were normalized by the lowess method from LIMMA.

organism: Malus domestica

source_name: W055 apple fruit flesh, 2 months after cold storage, 2012

label_protocol: 200ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized.

growth_protocol: Fruits were harvested at INRA, Angers (Experimental unit of Bois L'Abbé-La Rétuziére).

extract_protocol: Derived from the apple tissues RNA extraction method (Gasic et al., 2004) and pine tree RNA isolation method (Chang et al., 1993)

treatment_protocol: Cold storage at 1°C, after harvest.

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Hybride W055

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

tag: treatment

value: Cold storage for 60 days after harvest


title: ChIP-seq from OCI-LY1 (ENCLB703PKH)

description:
https://www.encodeproject.org/experiments/ENCSR768JED/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR768JED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB703PKH
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: line

value: cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: male

tag: health state

value: B cell lymphoma

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from OCI-LY1 (ENCLB540NIM)

description:
https://www.encodeproject.org/experiments/ENCSR768JED/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR768JED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB540NIM
size range: 200-600
nucleic acid starting quantity: 5
nucleic acid starting quantity units: ng

tag: antibody

tag: biosample encode accession

value: adult

value: Bradley Bernstein, Broad

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/


title: H07_M2_2012_Cy5

source_name: H074 apple fruit flesh, 2 months after cold storage, 2012

value: Fruit

value: Hybride H074


title: H07_M2_2012_Cy3

value: Parenchyma


title: H07_M2_2011_Cy3

source_name: H074 apple fruit flesh, 2 months after cold storage, 2011

value: Wild-type


title: ChIP-seq from MM.1S (ENCLB677WIS)

description:
https://www.encodeproject.org/experiments/ENCSR894QWM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR894QWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB677WIS
size range: 300-600
nucleic acid starting quantity: 11
nucleic acid starting quantity units: ng

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

tag: dev stage

tag: Sex

value: female

value: 42 year

value: immunoglobulin A lambda myeloma

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: W05_M2_2011_Cy5

source_name: W055 apple fruit flesh, 2 months after cold storage, 2011

value: Hybride W055

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: W05_re_2012_Cy5

source_name: W055 apple fruit flesh, at harvest, 2012


title: W05_M2_2012_Cy5


title: ChIP-seq from OCI-LY1 (ENCLB081OPA)

description:
https://www.encodeproject.org/experiments/ENCSR768JED/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR768JED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB081OPA
size range: 200-600

value: cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

tag: age

value: 44 year

value: adult

value: male

value: B cell lymphoma

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: H07_re_2012_Cy3

source_name: H074 apple fruit flesh, at harvest, 2012

value: Fruit

value: Parenchyma

value: Hybride H074

value: Wild-type


title: ChIP-seq from OCI-LY1 (ENCLB853KNU)

description:
https://www.encodeproject.org/experiments/ENCSR768JED/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR768JED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB853KNU
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/


title: H07_M2_2011_Cy5

value: Harvested at optimum maturity


title: W05_M2_2011_Cy3

value: Hybride W055

value: Cold storage for 60 days after harvest


title: T17p1_H1

city: Spring House

first: K

last: Li

state: PA

address: 1400 McKean Road

institute: Janssen R&D

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 9.

source_name: tissue biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

treatment_protocol: Mucosal biopsies (n=162) were collected 15 to 20 cm from the anal verge at screening during endoscopies from a subset of 87 patients who participated in the PURSUIT study. The Mayo score ranges from 0-12, with higher scores indicating more severe disease. More information on the score can be found at: http://www.globalrph.com/mayo_clinic_score.htm  Independent of the PURSUIT study , biopsies were also collected from 21 healthy normal subjects to serve as control.  Biopsies were immediately placed in RNAlater and subsequently stored at –80oC until RNA preparation.

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: Yes

tag: mayo score


title: ChIP-seq from OCI-LY3 (ENCLB996JGZ)

description:
https://www.encodeproject.org/experiments/ENCSR756ZKG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR756ZKG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB996JGZ
size range: 300-600

source_name: Homo sapiens OCI-LY3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

value: CTCF

value: cell line

tag: description

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: adult

value: male

value: B cell lymphoma

tag: link

value: ENCBS757GPD at ENCODE; https://www.encodeproject.org/ENCBS757GPD/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: H07_re_2012_Cy5

tag: tissue

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Hybride H074

tag: genotype

value: Wild-type

value: Harvested at optimum maturity


title: ChIP-seq from cardiac muscle cell (ENCLB138FBA)

description:
https://www.encodeproject.org/experiments/ENCSR713SXF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR713SXF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB138FBA
size range: 200-600

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

value: cardiac muscle cell

value: in vitro differentiated cells

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS343AKO at ENCODE; https://www.encodeproject.org/ENCBS343AKO/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: ChIP-seq from OCI-LY3 (ENCLB920GBI)

description:
https://www.encodeproject.org/experiments/ENCSR756ZKG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR756ZKG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB920GBI
size range: 200-600

value: CTCF

tag: line

value: cell line

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: adult

value: male

tag: health state

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS018GXW at ENCODE; https://www.encodeproject.org/ENCBS018GXW/


title: T17p1_E3

value: colon mucosa

value: Ulcerative Colitis (UC)

tag: treatment

value: golimumab

value: Week 0

value: Yes


title: T17p2_C6


title: T17p1_E7

value: No


title: ChIP-seq from PC-3 (ENCLB406GAH)

description:
https://www.encodeproject.org/experiments/ENCSR617RSQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR617RSQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406GAH
size range: 300-600
nucleic acid starting quantity: 22
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

tag: antibody

value: prostate cancer cell line

tag: biosample encode accession

tag: dev stage

value: 62 year

value: grade IV, adenocarcinoma

tag: passage number

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from A673 (ENCLB659PZY)

description:
https://www.encodeproject.org/experiments/ENCSR611JJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR611JJS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR196CXJ
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB659PZY
size range: 200-600

source_name: Homo sapiens A673 immortalized cell line

value: CTCF

value: cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

tag: Sex

value: female

tag: age

value: 15 year

tag: lab

value: ENCBS615MBV at ENCODE; https://www.encodeproject.org/ENCBS615MBV/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: T17p1_E12

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: No

tag: mayo score


title: W05_re_2012_Cy3

tag: tissue

value: Fruit

tag: tissue compartment

value: Parenchyma

value: Hybride W055

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity


title: H07_re_2011_Cy5

source_name: H074 apple fruit flesh, at harvest, 2011

tag: cultivar

value: Hybride H074

tag: genotype


title: W05_re_2011_Cy5

source_name: W055 apple fruit flesh, at harvest, 2011

tag: treatment


title: Ari_M4_2011_Cy5

source_name: Ariane apple fruit flesh, 4 months after cold storage, 2011

value: Ariane

value: Cold storage for 120 days after harvest


title: T17p2_H7


title: Gre_M4_2011_Cy5

source_name: Greensleeves  apple fruit flesh, 4 months after cold storage, 2011

value: Greensleeves


title: T17p2_D3


title: Gre_M4_2011_Cy3


title: H07_re_2011_Cy3


title: T17p1_A12


title: T17p1_B5


title: Gra_M4_2012_Cy5

source_name: Granny Smith apple fruit flesh, 4 months after cold storage, 2012

value: Granny Smith


title: ChIP-seq from OCI-LY3 (ENCLB346BZD)

description:
https://www.encodeproject.org/experiments/ENCSR584ATA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR584ATA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB346BZD
size range: 200-600
nucleic acid starting quantity: 19
nucleic acid starting quantity units: ng

tag: antibody

tag: line

value: cell line

tag: description

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: adult

value: male

tag: health state

value: B cell lymphoma

value: Bradley Bernstein, Broad

tag: link

value: ENCBS757GPD at ENCODE; https://www.encodeproject.org/ENCBS757GPD/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: Gre_M2_2011_Cy5

source_name: Greensleeves  apple fruit flesh, 2 months after cold storage, 2011

value: Fruit

value: Parenchyma

value: Wild-type

value: Cold storage for 60 days after harvest


title: T17p1_G9

value: colon mucosa

value: Ulcerative Colitis (UC)

tag: age

value: golimumab

value: Week 0

value: No


title: Gre_M2_2011_Cy3

value: Greensleeves

value: Harvested at optimum maturity


title: ChIP-seq from MM.1S (ENCLB485LRQ)

description:
https://www.encodeproject.org/experiments/ENCSR542YRH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR542YRH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-10-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB485LRQ
size range: 300-600
nucleic acid starting quantity: 60
nucleic acid starting quantity units: ng

source_name: Homo sapiens MM.1S immortalized cell line

value: cell line

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

value: 42 year

value: immunoglobulin A lambda myeloma

tag: lab

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: W05_re_2011_Cy3

value: Fruit

value: Parenchyma

value: Hybride W055

value: Wild-type


title: ChIP-seq from MCF-7 (ENCLB808LCF)

description:
https://www.encodeproject.org/experiments/ENCSR560BUE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR560BUE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB808LCF
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

value: CTCF

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: breast cancer (adenocarcinoma)

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: Ari_M4_2011_Cy3

tag: tissue

value: Ariane

value: Harvested at optimum maturity

value: Cold storage for 120 days after harvest


title: T17p2_A2

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: Yes

tag: mayo score


title: Ari_M2_2011_Cy5

source_name: Ariane apple fruit flesh, 2 months after cold storage, 2011

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

tag: genotype

value: Wild-type

tag: developmental stage at harvest

tag: treatment

value: Cold storage for 60 days after harvest


title: Gol_M4_2012_Cy3

source_name: Golden delicious apple fruit flesh, 4 months after cold storage, 2012

value: Golden delicious


title: T17p2_F7


title: ChIP-seq from MM.1S (ENCLB252IMH)

description:
https://www.encodeproject.org/experiments/ENCSR542YRH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR542YRH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-10-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB252IMH
size range: 300-600
nucleic acid starting quantity: 113
nucleic acid starting quantity units: ng

tag: antibody

tag: line

value: cell line

tag: description

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

value: adult

value: female

value: 42 year

tag: health state

value: immunoglobulin A lambda myeloma

value: Bradley Bernstein, Broad

tag: link

value: ENCBS241TLI at ENCODE; https://www.encodeproject.org/ENCBS241TLI/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: Ari_M2_2011_Cy3

value: Ariane

value: Harvested at optimum maturity


title: T17p1_G3

value: colon mucosa

value: Ulcerative Colitis (UC)

tag: age

value: golimumab

value: Week 0

value: Yes


title: Gol_M4_2012_Cy5

value: Fruit

value: Parenchyma

value: Golden delicious

value: Wild-type

value: Cold storage for 120 days after harvest


title: Gra_M4_2011_Cy5

source_name: Granny Smith apple fruit flesh, 4 months after cold storage, 2011

value: Granny Smith


title: Gra_M4_2012_Cy3


title: ChIP-seq from SK-N-SH (ENCLB471RHA)

description:
https://www.encodeproject.org/experiments/ENCSR541AMF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541AMF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471RHA
size range: 200-600

source_name: Homo sapiens SK-N-SH immortalized cell line

value: CTCF

value: SK-N-SH

value: cell line

tag: biosample encode accession

value: 4 year

tag: dev stage

value: child

tag: Sex

value: female

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS324TZB at ENCODE; https://www.encodeproject.org/ENCBS324TZB/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531


title: ChIP-seq from ovary (ENCLB802SAA)

description:
https://www.encodeproject.org/experiments/ENCSR509SEX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR509SEX
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB802SAA
size range: 200-600

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

value: Control

value: ovary

value: tissue

value: adult

value: 53 year

tag: source

value: Kristin Ardlie

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

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


title: Gol_M4_2011_Cy3

source_name: Golden delicious apple fruit flesh, 4 months after cold storage, 2011

tag: tissue

value: Fruit

value: Parenchyma

value: Golden delicious

value: Wild-type

value: Harvested at optimum maturity

value: Cold storage for 120 days after harvest


title: ChIP-seq from HepG2 (ENCLB897HJX)

description:
https://www.encodeproject.org/experiments/ENCSR508LMH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR508LMH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR055XHN
encode release date: 2017-11-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB897HJX
size range: 200-600
nucleic acid starting quantity: 11
nucleic acid starting quantity units: ng

source_name: Homo sapiens HepG2 immortalized cell line

value: cell line

value: Hep G2 (Hepatocellular carcinoma, human) Hep G2 is a perpetual cell line which was derived from the liver tissue of a 15-year-old Caucasian American male with a well-differentiated hepatocellular carcinoma. These cells are epithelial in morphology, have a model chromosome number of 55, and are not tumorigenic in nude mice.

value: male

value: Bradley Bernstein, Broad

tag: passage number

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS011BYX at ENCODE; https://www.encodeproject.org/ENCBS011BYX/

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


title: Gol_M4_2011_Cy5

tag: tissue compartment

tag: cultivar


title: ChIP-seq from Loucy (ENCLB938OTD)

description:
https://www.encodeproject.org/experiments/ENCSR464DKE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR464DKE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB938OTD
size range: 200-600

source_name: Homo sapiens Loucy immortalized cell line

value: CTCF

value: Loucy

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: adult

value: female

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: ENCBS170DPY at ENCODE; https://www.encodeproject.org/ENCBS170DPY/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: ChIP-seq from KMS-11 (ENCLB582DBY)

description:
https://www.encodeproject.org/experiments/ENCSR430YRJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR430YRJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR720GSE
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB582DBY
size range: 200-600

source_name: Homo sapiens KMS-11 immortalized cell line

value: cell line

value: multiple myeloma

value: 67 year

value: Bradley Bernstein, Broad

value: ENCBS682HMC at ENCODE; https://www.encodeproject.org/ENCBS682HMC/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: T17p1_C7

source_name: tissue biopsy

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: No

tag: mayo score


title: Gra_M4_2011_Cy3

value: Fruit

value: Parenchyma

value: Granny Smith

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

tag: treatment

value: Cold storage for 120 days after harvest


title: T17p2_F6

tag: age

value: Yes


title: T17p1_C10


title: Gra_M1_2011_Cy5

source_name: Granny Smith apple fruit flesh, 1 month after cold storage, 2011

value: Cold storage for 30 days after harvest


title: T17p2_B1


title: Gra_M1_2012_Cy3

source_name: Granny Smith apple fruit flesh, 1 month after cold storage, 2012


title: T17p2_B6


title: Gra_M1_2012_Cy5


title: Gol_M1_2011_Cy3

source_name: Golden delicious apple fruit flesh, 1 month after cold storage, 2011

value: Golden delicious


title: Gra_re_2012_Cy5

source_name: Granny Smith apple fruit flesh, at harvest, 2012


title: Gol_re_2012_Cy3

source_name: Golden delicious apple fruit flesh, at harvest, 2012


title: Gol_M1_2012_Cy5

source_name: Golden delicious apple fruit flesh, 1 month after cold storage, 2012


title: Gol_M1_2011_Cy5


title: T17p1_C3


title: ChIP-seq from HCT116 (ENCLB779MQU)

description:
https://www.encodeproject.org/experiments/ENCSR429CLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR429CLV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779MQU
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

tag: antibody

tag: line

value: cell line

tag: description

value: cells obtained from ATCC; http://www.ncbi.nlm.nih.gov/pubmed?cmd=Retrieve&list_uids=7214343&dopt=AbstractPlus

tag: biosample encode accession

value: unknown

value: male

tag: health state

value: colorectal carcinoma

value: Bradley Bernstein, Broad

tag: link

value: ENCBS851PYB at ENCODE; https://www.encodeproject.org/ENCBS851PYB/

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

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: T17p2_G5

tag: tissue

value: colon mucosa

value: Ulcerative Colitis (UC)

value: golimumab

value: Week 0

value: No


title: Gra_M1_2011_Cy3

value: Fruit

tag: tissue compartment

value: Parenchyma

value: Granny Smith

value: Wild-type

value: Harvested at optimum maturity


title: T17p2_A1


title: Gol_re_2012_Cy5

tag: cultivar

value: Golden delicious


title: Gra_re_2012_Cy3


title: ChIP-seq from PC-3 (ENCLB324KFH)

description:
https://www.encodeproject.org/experiments/ENCSR359LOD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR359LOD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB324KFH
size range: 300-600
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

value: CTCF

value: cell line

value: prostate cancer cell line

tag: dev stage

value: adult

tag: Sex

value: male

value: 62 year

value: grade IV, adenocarcinoma

tag: passage number

tag: lab

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: T17p1_B1

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: Yes

tag: mayo score


title: Gra_re_2011_Cy5

source_name: Granny Smith apple fruit flesh, at harvest, 2011

value: Fruit

value: Parenchyma

value: Granny Smith

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

tag: treatment


title: ChIP-seq from HCT116 (ENCLB817UGL)

description:
https://www.encodeproject.org/experiments/ENCSR429CLV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR429CLV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB817UGL
size range: 200-600

tag: antibody

tag: line

value: cell line

tag: description

value: cells obtained from ATCC

tag: biosample encode accession

tag: age

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from PC-3 (ENCLB622RIN)

description:
https://www.encodeproject.org/experiments/ENCSR359LOD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR359LOD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622RIN
size range: 300-600
nucleic acid starting quantity: 5
nucleic acid starting quantity units: ng

value: CTCF

value: prostate cancer cell line

value: adult

value: 62 year

tag: health state

value: grade IV, adenocarcinoma

tag: link

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: Gol_re_2011_Cy3

source_name: Golden delicious apple fruit flesh, at harvest, 2011

tag: tissue

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Golden delicious

value: Wild-type

value: Harvested at optimum maturity


title: Gol_re_2011_Cy5


title: Gol_M1_2012_Cy3

value: Cold storage for 30 days after harvest


title: ChIP-seq from KMS-11 (ENCLB285XYV)

description:
https://www.encodeproject.org/experiments/ENCSR430YRJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR430YRJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR720GSE
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB285XYV
size range: 200-600
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: multiple myeloma

tag: dev stage

tag: Sex

value: female

value: 67 year

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS987CHP at ENCODE; https://www.encodeproject.org/ENCBS987CHP/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from PC-3 (ENCLB804PBP)

description:
https://www.encodeproject.org/experiments/ENCSR218QFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR218QFN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2017-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB804PBP
size range: 300-600
nucleic acid starting quantity: 6
nucleic acid starting quantity units: ng

value: prostate cancer cell line

value: adult

value: male

value: 62 year

value: grade IV, adenocarcinoma

tag: passage number

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

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


title: ChIP-seq from PC-3 (ENCLB230LLA)

description:
https://www.encodeproject.org/experiments/ENCSR218QFN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR218QFN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2017-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB230LLA
size range: 300-600
nucleic acid starting quantity: 30
nucleic acid starting quantity units: ng

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from HCT116 (ENCLB670RPO)

description:
https://www.encodeproject.org/experiments/ENCSR240PRQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR240PRQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670RPO
size range: 200-600

value: CTCF

value: cell line

value: cells obtained from ATCC

value: unknown

value: colorectal carcinoma

value: ENCBS847SOB at ENCODE; https://www.encodeproject.org/ENCBS847SOB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: T17p2_A6

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: No

tag: mayo score


title: ChIP-seq from ovary (ENCLB489NOE)

description:
https://www.encodeproject.org/experiments/ENCSR149EOW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR149EOW
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB489NOE
size range: 200-600

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

tag: antibody

value: Control

value: ovary

value: tissue

value: female

value: adult

value: 51 year

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

value: ENCBS423EPK at ENCODE; https://www.encodeproject.org/ENCBS423EPK/

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


title: T17p1_D5

tag: treatment


title: ChIP-seq from neural progenitor cell (ENCLB449ICV)

description:
https://www.encodeproject.org/experiments/ENCSR125NBL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR125NBL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB449ICV
size range: 200-600

source_name: Homo sapiens neural progenitor in vitro differentiated cells female embryo (5 days) derived from H9

value: CTCF

value: neural progenitor cell

value: in vitro differentiated cells

tag: description

value: Frozen or fixed, in vitro differentiated neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

tag: biosample encode accession

tag: age

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: Gre_M4_2012_Cy3

source_name: Greensleeves  apple fruit flesh, 4 months after cold storage, 2012

tag: tissue

value: Fruit

value: Parenchyma

value: Greensleeves

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

value: Cold storage for 120 days after harvest


title: Ari_M2_2012_Cy5

source_name: Ariane apple fruit flesh, 2 months after cold storage, 2012

tag: tissue compartment

tag: cultivar

value: Ariane

value: Cold storage for 60 days after harvest


title: Gra_re_2011_Cy3

value: Granny Smith


title: T17p1_E6

value: colon mucosa

value: Ulcerative Colitis (UC)

value: golimumab

value: Week 0

value: No


title: Ari_M4_2012_Cy5

source_name: Ariane apple fruit flesh, 4 months after cold storage, 2012


title: Ari_M4_2012_Cy3


title: Gre_M2_2012_Cy3

source_name: Greensleeves  apple fruit flesh, 2 months after cold storage, 2012


title: Ari_M1_2012_Cy5

source_name: Ariane apple fruit flesh, 1 month after cold storage, 2012

value: Cold storage for 30 days after harvest


title: T17p2_G1

source_name: tissue biopsy

value: Yes


title: Gre_M4_2012_Cy5


title: T17p2_E1


title: Ari_M2_2012_Cy3


title: T17p1_A4


title: T17p2_G3


title: ChIP-seq from neural progenitor cell (ENCLB054TGL)

description:
https://www.encodeproject.org/experiments/ENCSR125NBL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125NBL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB054TGL
size range: 200-600

value: CTCF

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

tag: dev stage

value: embryonic

tag: Sex

value: female

tag: health state

value: healthy

tag: lab

value: Richard Myers, HAIB

tag: link

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from neural progenitor cell (ENCLB525MCC)

description:
https://www.encodeproject.org/experiments/ENCSR125NBL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR125NBL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2017-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB525MCC
size range: 200-600
nucleic acid starting quantity: 8
nucleic acid starting quantity units: ng

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/


title: Gre_M1_2012_Cy5

source_name: Greensleeves apple fruit flesh, 1 month after cold storage, 2012

value: Fruit

value: Parenchyma

value: Greensleeves

value: Wild-type

value: Harvested at optimum maturity


title: Gre_M1_2012_Cy3

value: Cold storage for 30 days after harvest


title: Ari_M1_2011_Cy5

source_name: Ariane apple fruit flesh, 1 month after cold storage, 2011

value: Ariane


title: Gre_M1_2011_Cy3

source_name: Greensleeves apple fruit flesh, 1 month after cold storage, 2011


title: Gre_M1_2011_Cy5


title: ChIP-seq from GM12878 (ENCLB008SEC)

description:
https://www.encodeproject.org/experiments/ENCSR091BOQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091BOQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR142REC
encode release date: 2018-01-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB008SEC
size range: 200-600
nucleic acid starting quantity: 11
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

tag: line

value: cell line

value: adult

value: unknown

tag: passage number

value: Bradley Bernstein, Broad

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

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


title: Ari_M1_2012_Cy3


title: ChIP-seq from OCI-LY1 (ENCLB063SGX)

description:
https://www.encodeproject.org/experiments/ENCSR072EUE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR072EUE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB063SGX
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: antibody

value: CTCF

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: male

value: B cell lymphoma

value: ENCBS899DSB at ENCODE; https://www.encodeproject.org/ENCBS899DSB/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: T17p1_B2

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

tag: treatment

value: golimumab

tag: visit

value: Week 0

value: Yes

tag: mayo score


title: T17p2_C3

tag: tissue

tag: age

value: No


title: Ari_M1_2011_Cy3

value: Fruit

tag: tissue compartment

value: Parenchyma

value: Ariane

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

value: Cold storage for 30 days after harvest


title: Ari_re_2012_Cy5

source_name: Ariane apple fruit flesh, at harvest, 2012

tag: cultivar


title: Gre_re_2012_Cy5

source_name: Greensleeves  apple fruit flesh, at harvest, 2012

value: Greensleeves


title: ChIP-seq from neural progenitor cell (ENCLB918MIT)

description:
https://www.encodeproject.org/experiments/ENCSR069DPL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR069DPL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2017-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB918MIT
size range: 200-600
nucleic acid starting quantity: 6
nucleic acid starting quantity units: ng

value: neural progenitor cell

value: in vitro differentiated cells

tag: description

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

tag: biosample encode accession

value: 5 day

tag: dev stage

value: embryonic

tag: Sex

value: female

tag: health state

value: healthy

value: Richard Myers, HAIB

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: T17p1_F2

value: colon mucosa

value: Ulcerative Colitis (UC)

value: golimumab

value: Week 0

value: No


title: T17p1_A10


title: T17p1_G1


title: Ari_re_2011_Cy5

source_name: Ariane apple fruit flesh, at harvest, 2011

value: Fruit

value: Parenchyma

value: Ariane

value: Wild-type

value: Harvested at optimum maturity


title: T17p2_H4


title: Gre_re_2012_Cy3

value: Greensleeves


title: ChIP-seq from neural progenitor cell (ENCLB664GYK)

description:
https://www.encodeproject.org/experiments/ENCSR069DPL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR069DPL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2017-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB664GYK
size range: 200-600

tag: antibody

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

tag: lab

tag: link

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/


title: ChIP-seq from HCT116 (ENCLB647FMG)

description:
https://www.encodeproject.org/experiments/ENCSR046HGP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR046HGP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB647FMG
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

tag: line

value: cell line

value: cells obtained from ATCC

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS847SOB at ENCODE; https://www.encodeproject.org/ENCBS847SOB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: Ari_re_2012_Cy3

value: Fruit

value: Parenchyma

value: Ariane

value: Wild-type

value: Harvested at optimum maturity

tag: treatment


title: ChIP-seq from HCT116 (ENCLB216HEW)

description:
https://www.encodeproject.org/experiments/ENCSR046HGP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR046HGP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216HEW
size range: 200-600

value: cells obtained from ATCC; http://www.ncbi.nlm.nih.gov/pubmed?cmd=Retrieve&list_uids=7214343&dopt=AbstractPlus

value: ENCBS851PYB at ENCODE; https://www.encodeproject.org/ENCBS851PYB/


title: Ari_re_2011_Cy3


title: Cox_M4_2012_Cy3

source_name: Cox apple fruit flesh, 4 months after cold storage, 2012

value: Cox

value: Cold storage for 120 days after harvest


title: Gre_re_2011_Cy3

source_name: Greensleeves  apple fruit flesh, at harvest, 2011

value: Greensleeves


title: T17p2_B5

value: colon mucosa

tag: subject

tag: disease

value: Ulcerative Colitis (UC)

value: golimumab

tag: visit

value: Week 0

value: No

tag: mayo score


title: G51T2

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: Ribo and Globin depleted library

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15
Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58906 genes (rows) [counts matrix]

source_name: Responder T2 patient17

extract_protocol:
Peripheral blood was collected in EDTA tubes at T1 and T2 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5
Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA

tag: tissue

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: R


title: Gre_re_2011_Cy5

value: Fruit

tag: tissue compartment

tag: cultivar

tag: genotype

tag: developmental stage at harvest


title: G51T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient17


title: Cox_M4_2012_Cy5

value: Parenchyma


title: GO-treated cells exposed to H2O2_rep8

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 8 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA).Microarray data were extracted, the background subtracted and normalisation performed using the standard miRNA procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Equus caballus

source_name: satellite cells isolated from musculus semitendinosus

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling.

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB).

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation equine satellite cells were pre-incubated with GO for 24h (0.125 µM ) and exposed to hydrogen peroxide (3mM, 1h during 24h pre-incubation with GO).

tag: age

value: 3rd day of differentiation

value: m. semitendinosus


title: Gal_M4_2011_Cy5

source_name: Gala apple fruit flesh, 4 months after cold storage, 2011

value: Gala

value: Wild-type

value: Harvested at optimum maturity


title: GO-treated cells exposed to H2O2_rep6

description: Biological replicate 6 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: Gal_M4_2012_Cy3

source_name: Gala apple fruit flesh, 4 months after cold storage, 2012


title: T17p1_E10

source_name: tissue biopsy


title: GO-treated cells exposed to H2O2_rep4

description: Biological replicate 4 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: GO-treated cells exposed to H2O2_rep5

description: Biological replicate 5 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: GO-treated cells exposed to H2O2_rep7

description: Biological replicate 7 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: Cox_M4_2011_Cy3

source_name: Cox apple fruit flesh, 4 months after cold storage, 2011

value: Cox


title: T17p1_H4

value: Yes


title: Cox_M4_2011_Cy5

value: Cold storage for 120 days after harvest


title: T17p2_A7

value: colon mucosa


title: T17p1_D4

value: Ulcerative Colitis (UC)


title: T17p2_A4

value: golimumab


title: Cox_M2_2012_Cy5

source_name: Cox apple fruit flesh, 2 months after cold storage, 2012

value: Cold storage for 60 days after harvest


title: T17p1_C8

value: Week 0


title: T17p2_C1


title: GO-untreated cells exposed to H2O2_rep8

description: Biological replicate 7 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)


title: Gal_M2_2012_Cy5

source_name: Gala apple fruit flesh, 2 months after cold storage, 2012


title: GO-treated cells exposed to H2O2_rep3

description: Biological replicate 3 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: GO-treated cells exposed to H2O2_rep2

description: Biological replicate 2 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: T17p2_B7

value: No


title: Gal_M4_2011_Cy3


title: Cox_M2_2012_Cy3


title: GO-treated cells exposed to H2O2_rep1

description: Biological replicate 1 of 8. Gamma-oryzanol treated equine satellite cells exposed to hydrogen peroxide (EXPERIMENTAL)


title: T17p2_B8


title: Gal_M2_2012_Cy3


title: Gal_M2_2011_Cy5

source_name: Gala apple fruit flesh, 2 months after cold storage, 2011


title: T17p2_F4


title: T17p1_A11


title: GO-untreated cells exposed to H2O2_rep6

description: Biological replicate 6 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)


title: Cox_M2_2011_Cy3

source_name: Cox apple fruit flesh, 2 months after cold storage, 2011


title: GO-untreated cells exposed to H2O2_rep7

description: Biological replicate 8 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)


title: Cox_M2_2011_Cy5


title: Gre_M2_2012_Cy5

source_name: Greensleeves  apple fruit flesh, 2 months after cold storage, 2012

value: Greensleeves


title: GO-untreated cells exposed to H2O2_rep5

description: Biological replicate 5 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)


title: GO-untreated cells exposed to H2O2_rep4

description: Biological replicate 4 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)


title: T17p1_A8


title: Brown adipose tissue_interleukin-18 knockout_12w-biological rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: whole brown adipose tissue derived from 12 week-old IL-18KO strain

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 3µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for data processing.

organism: Mus musculus

source_name: whole brown adipose tissue derived from 12w IL-18KO strain

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNAs were extracted from whole brown adipose tissues stored in RNA later (Ambion), derived from wild type and interleukin-18 knockout mice using miRNeasy extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: no teatment

tag: strain

value: BALB/c

tag: organ

value: Brown adipose tissue

value: interleukin-18 knockout

value: 12 week-old


title: G41T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient12

value: Whole blood cells collected from patient after septic shock

value: R


title: Disome5_RPF

city: Boston

first: James

middle: Christopher

last: Taggart

state: MA

address: 200 Longwood Avenue

department: Systems Biology

institute: Harvard Medical School

description: ribosome protected mRNA

data_processing:
Library strategy: Ribo-Seq
Raw fastq files were trimmed of poly(A) or adapter sequences using Cutadapt with parameters –u 1 (or -u 3 for samples prepared with SMARTer smRNA-seq kit) and –m 24. Nucleotides are removed from the 5' end of reads to address non-template addition during reverse transcription and template switching.
Trimmed reads were aligned to reference transcriptome using tophat v1.4.1 using parameters –G --no_novel-juncs --transcriptome-only –N 1
Genome_build: sacCer3
Supplementary_files_format_and_content: wiggle files contain positions offset by +13 nucleotides and counts of mapped 5' ends.

organism: Saccharomyces cerevisiae

source_name: Budding yeast

growth_protocol: Overnight cultures were grown from a single colony in selective synthetic complete medium and back-diluted to OD590 = 0.002 in 500 mL YPD. Culture were grown in shaking 2.8L flasks at 30°C until OD590 reached 0.5.

extract_protocol:
Ribosome protected fragments were dephosphorylated at the 3’ end and depleted of rRNA by selective hybridization to biotinylated oligonucleotides. The fragments were then ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified.
Cell lysis was performed as described in detail previously (Li et al., Cell 2014), with the following modifications. 500 mL of cell culture was rapidly filtered at 30C by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal spatula, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 25 mL canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4C. Lysates were treated with RNase I and ribosome protected fragments were isolated by hot phenol extraction. Ribosome protected fragments were size selected by gel extraction.

tag: genotype/variation


title: GO-untreated cells exposed to H2O2_rep3

description: Biological replicate 2 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)

value: 3rd day of differentiation

value: m. semitendinosus


title: Gal_M2_2011_Cy3

value: Fruit

value: Parenchyma

value: Gala

value: Wild-type

value: Harvested at optimum maturity

tag: treatment


title: G41T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient12


title: DisomeWT_rep1_RPF

description: ribosome protected mRNA

value: DisomeWT


title: Gal_M1_2012_Cy5

source_name: Gala apple fruit flesh, 1 month after cold storage, 2012

value: Cold storage for 30 days after harvest


title: GO-untreated cells exposed to H2O2_rep2


title: Cox_M1_2012_Cy3

source_name: Cox apple fruit flesh, 1 month after cold storage, 2012

value: Cox


title: Brown adipose tissue_interleukin-18 knockout_12w-biological rep1


title: Brown adipose tissue_interleukin-18 knockout_6w-biological rep3

description: whole brown adipose tissue derived from 6 week-old IL-18KO strain

source_name: whole brown adipose tissue derived from 6w IL-18KO strain

value: 6 week-old


title: GO-untreated cells exposed to H2O2_rep1

description: Biological replicate 1 of 8. Gamma-oryzanol untreated equine satellite cells exposed to hydrogen peroxide (CTRL)

source_name: satellite cells isolated from musculus semitendinosus


title: fgf3 sibling

city: Kansas City

first: Tatjana

last: Piotrowski

state: MO

institute: Stowers Institute

data_processing:
Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome (GRCz10) using the Cell Ranger (version 2.1.1) pipeline from 10x genomics using the default settings.
Genome_build: danRer10
Supplementary_files_format_and_content: h5 files contain the UMI counts for each cell.

organism: Danio rerio

source_name: neuromast

extract_protocol:
Presumptive neuromast cells (GFP+) were isolated by FACS.
Standard 10x genomics scRNA-seq protocol using v2 chemistry
Droplet based scRNA-seq

value: neuromast


title: WT

value: WT


title: Gal_M1_2012_Cy3


title: Brown adipose tissue_interleukin-18 knockout_6w-biological rep1

value: BALB/c

value: Brown adipose tissue

value: interleukin-18 knockout


title: Cox_M1_2012_Cy5


title: G39T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient11

value: Whole blood cells collected from patient after septic shock

value: R


title: fgf3 mutant

value: fgf3^t26212;ET(krt4:EGFP)SqGw57A;Tg(pou4f3:GAP-GFP)s356t (screened for mutants)


title: Brown adipose tissue_wild type_12w-biological rep3

description: whole brown adipose tissue derived from 12 week-old wild type strain

source_name: whole brown adipose tissue derived from 12w wild type strain

value: wild type

value: 12 week-old


title: G39T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient11


title: Gal_M1_2011_Cy5

source_name: Gala apple fruit flesh, 1 month after cold storage, 2011

value: Fruit

value: Parenchyma

value: Gala


title: Brown adipose tissue_interleukin-18 knockout_12w-biological rep2


title: Cox_M1_2011_Cy3

source_name: Cox apple fruit flesh, 1 month after cold storage, 2011

value: Wild-type

value: Harvested at optimum maturity


title: Brown adipose tissue_interleukin-18 knockout_6w-biological rep2


title: G34T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient10


title: Gal_M1_2011_Cy3

value: Cold storage for 30 days after harvest


title: Cox_M1_2011_Cy5

value: Cox


title: Brown adipose tissue_wild type_12w-biological rep1


title: Gal_re_2012_Cy5

source_name: Gala apple fruit flesh, at harvest, 2012


title: Brown adipose tissue_wild type_12w-biological rep2


title: G34T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient10


title: Brown adipose tissue_wild type_6w-biological rep3

description: whole brown adipose tissue derived from 6 week-old wild type strain

source_name: whole brown adipose tissue derived from 6w wild type strain

value: 6 week-old


title: D10P_S15

city: Houston

first: Annie

middle: W.

last: Shieh

state: Texas

address: 1825 Pressler St

department: Brown Foundation Institute Of Molecular Medicine

institute: University of Texas Health Science Center

data_processing:
Sequenced reads were mapped to hg19 genome with gencode v19 transcript model using TopHat v2.1.1
Uniquely mapped reads were identified with the NH:i:1 flag and quantified using FeatureCount of the Subread v1.5.2 package
Genome_build: hg19
Supplementary_files_format_and_content: table of counts

source_name: hESC derived muscle progenitor cells

growth_protocol: Human ESC line (H9 from WiCell) was maintained on Matrigel-coated dishes (BD Biosciences) in mTeSR1 medium (STEMCELL Technologies).

extract_protocol:
1 x 106 cells were harvested / sorted at each time- point and RNA extracted using QIAGEN miRNeasy RNA isolation kit (217004, QIAGEN) according to manufacturer’s protocol.
Each RNA sample was converted to cDNA using oligo-dT primers and was further converted into indexed sequencing libraries using Illumina TruSeq kit.

treatment_protocol: For skeletal muscle differentiation, human pluripotent stem cells were harvested using Accutase (Stem Cell Technologies) and seeded on Matrigel-coated plates (10,000 cells/cm2) in myogenic differentiation medium-I (MDM-I) and maintained for 4 days. MDM-I medium consisted of IMDM supplemented with 5% horse serum, 3 μM CHIR99021 (Selleck Chemical LLC), 2 μM SB431542 (Selleck Chemical LLC), 10 ng/ml hr-EGF (PeproTech Inc), 10 μg/ml insulin (Sigma- Aldrich), 0.4 mg/ml dexamethasone (Sigma-Aldrich) and 200 μM L- ascorbic acid (Sigma-Aldrich). After 4 days of induction, cells were harvested using Accutase and seeded on Matrigel-coated plates (10,000 cells/cm2) in myogenic differentiation medium-II (MDM-II). MDM-II medium contained IMDM supplemented with 5% horse serum, 10 μg/ml insulin (Sigma- Aldrich), 10 ng/ml hr-EGF (Pepro Tech Inc), 20 ng/ml hr-HGF (Pepro Tech Inc), 20 ng/ml hr-FGF (Pepro Tech Inc), 10 ng/ml IGF-1 (Pepro Tech Inc), 2 μM SB431542 (Selleck Chemical LLC), 0.5 μM LDN193189 (Stemgent), 200 μM L-ascorbic acid (Sigma-Aldrich). The cells were cultured in MDM-II medium for 6-11 days. At day 10 to 15 of differentiation (4 + 6-11), the cells were harvested and sorted for EGFP or surface markers. Sorted fractions were seeded on Matrigel-coated plates with similar densities (300,000/well of a 6 well plate) and expanded in MDM-II medium for an additional 2-3 days (or longer for expansion time-course experiments). For terminal myotube differentiation, once cells reached appropriate confluency (80-90%), the medium was switched to MDM-III medium. MDM-III medium consisted of IMDM (Invitrogen), 15% knockout serum replacement (Invitrogen), 100mM MEM non-essential amino acids (Invitrogen) and 10 ng/ml IGF-1.

tag: cell type

value: in vitro differentiation

tag: parent cell line

value: H9 from WiCell

tag: passage


title: Cox_re_2012_Cy3

source_name: Cox apple fruit flesh, at harvest, 2012


title: Brown adipose tissue_wild type_6w-biological rep2

value: BALB/c

value: Brown adipose tissue


title: D10P_S14


title: D10N_S12


title: ESC_GO_H2O2_4

description: Biological replicate 4 of 4. GO pre-incubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1

hyb_protocol: On each two-colour microarray 825 ng of cRNA from GO pre-incubated and hydrogen peroxide exposed cells (Cy5) and 825 ng of cRNA from control cells-exposed to hydrogen peroxide without GO pre-incubation (Cy3) were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and Linar & LOWESS normalization.

source_name: GO and H2O2-treated equine satellite cells_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluency proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9.2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation equine satellite cells were pre-incubated with GO (0.125 µM ) for 24h and exposed to hydrogen peroxide (3mM, last hour during 24h pre-incubation with GO).

value: satellite cells

value: 3rd day of differentiation

tag: satellite cell origin

value: m. semitendinosus


title: D10P_S13


title: Cox_re_2012_Cy5

tag: tissue


title: ESC_GO_H2O2_3

description: Biological replicate 3 of 4. GO-preincubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1


title: Non-tumor6(matched Tumor6)

city: Hangzhou

first: Tianhua

last: Zhou

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

description: Tumor tissue and its matched non-tumor tissue  from separate patients

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labelled ds-cDNA in NimbleGen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software.

source_name: gastric cancer non-tumor tissue6

label_protocol: For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). 1 μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA was extracted and clean-up using the kit (TRIzol® Reagent,Invitrogen life technologies; RNasey Mini Kit,Qiagen; Dnase,EPICENTRE) following the manufacturer's recommendations.Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Six fresh human gastric cancer tissues and their matched non-tumor tissues

value: stomach

tag: disease state

value: non-tumor


title: D10N_S11


title: G23T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient6

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

value: R


title: D10N_S10


title: G23T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient6

tag: clinical classification


title: Diff_S8


title: ESC_GO_H2O2_1

description: Biological replicate 1 of 4. GO pre-incubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1


title: ESC_GO_H2O2_2

description: Biological replicate 2 of 4. GO pre-incubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without GO treatment_Cy3_rep1


title: DU145 cell line_scr mimic

city: Toronto

first: Stanley

middle: K

last: Liu

state: Ontario

address: 2075 Bayview Avenue

department: Radiation Oncology

country: Canada

institute: Sunnybrook Research Institute

hyb_protocol: 16hr at 45°C

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Expression Console

label: Biotin

source_name: DU145 scr

label_protocol: Biotin Allonamide Triphosphate

growth_protocol: DU145 cells were cultured in DMEM (1X) GlutaMAX containing 4.5g/L glucose (Invitrogen, Canada), 10% FBS (Invitrogen), and penicillin (100U/mL, Invitrogen) - streptomycin (100 ug/mL, Invitrogen). Cells were maintained in humidified 37°C incubator with 5% CO2

extract_protocol: Cells were lysed and total RNA was collected using RNAeasy Mini Kit (Qiagen, Canada)

treatment_protocol: DU145 cells were transfected with control(scr) or miR-106a-5p mimic with Lipofectamine 2000 Reagent (Invitrogen) and Opti-MEM I (1X) reduced serum media (Invitrogen)

tag: cell line

value: Prostate cancer cell line

tag: cell line info.

value: AR neg, CNS metastasis

tag: transfected with

value: scr mimic


title: Gal_M4_2012_Cy5

source_name: Gala apple fruit flesh, 4 months after cold storage, 2012

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Gala

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

value: Cold storage for 120 days after harvest


title: DU145 cell line_miR-106a mimic

value: has-miR-106a-5p mimic


title: Gal_re_2011_Cy5

source_name: Gala apple fruit flesh, at harvest, 2011

tag: treatment


title: Diff_S7

tag: cell type

value: in vitro differentiation

value: H9 from WiCell


title: Gal_re_2012_Cy3


title: Brown adipose tissue_wild type_6w-biological rep1

tag: strain

value: BALB/c

tag: organ

value: Brown adipose tissue

value: wild type

tag: age

value: 6 week-old


title: Cox_re_2011_Cy3

source_name: Cox apple fruit flesh, at harvest, 2011

tag: tissue

value: Cox


title: Fuj_re_2012_Cy5

source_name: Fuji apple fruit flesh, at harvest, 2012

value: Fuji


title: D4_S6

tag: parent cell line

tag: passage


title: Jon_re_2012_Cy3

source_name: Jonagold apple fruit flesh, at harvest, 2012

value: Jonagold


title: Gal_re_2011_Cy3


title: D4_S4


title: D4_S5


title: Cox_re_2011_Cy5


title: ESC_S2

source_name: hESC

value: embryonic stem cells


title: Fuj_re_2012_Cy3

value: Fruit


title: Jon_re_2012_Cy5

value: Parenchyma


title: Fuj_re_2011_Cy5

source_name: Fuji apple fruit flesh, at harvest, 2011


title: ESC_S1


title: Jon_re_2011_Cy3

source_name: Jonagold apple fruit flesh, at harvest, 2011


title: ESC_S3


title: ChIP-seq from H1-hESC (ENCLB732BPF)

description:
https://www.encodeproject.org/experiments/ENCSR850KIP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR850KIP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2017-11-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB732BPF
size range: 300-600

source_name: Homo sapiens H1-hESC stem cell male embryo

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: dev stage

value: embryonic

tag: Sex

value: male

value: unknown

tag: health state

value: healthy

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS364BFI at ENCODE; https://www.encodeproject.org/ENCBS364BFI/

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


title: E33T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient6

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: NR


title: ChIP-seq from H1-hESC (ENCLB843EWE)

description:
https://www.encodeproject.org/experiments/ENCSR850KIP/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR850KIP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2017-11-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB843EWE
size range: 300-600


title: E33T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient6


title: Jon_re_2011_Cy5

tag: tissue compartment

tag: cultivar

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

tag: treatment


title: Fuj_re_2011_Cy3

tag: tissue

value: Fuji


title: Fuj_M4_2012_Cy5

source_name: Fuji apple fruit flesh, 4 months after cold storage, 2012

value: Cold storage for 120 days after harvest


title: ChIP-seq from H1-hESC (ENCLB102BNU)

description:
https://www.encodeproject.org/experiments/ENCSR814KIO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR814KIO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB102BNU
size range: 300-1000

tag: antibody

tag: age


title: Jon_M4_2012_Cy3

source_name: Jonagold apple fruit flesh, 4 months after cold storage, 2012

value: Jonagold


title: Fuj_M4_2012_Cy3

value: Fruit


title: ChIP-seq from H1-hESC (ENCLB254JND)

description:
https://www.encodeproject.org/experiments/ENCSR814KIO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR814KIO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB254JND
size range: 300-800

tag: line

tag: biosample encode accession

value: ENCBS284CPV at ENCODE; https://www.encodeproject.org/ENCBS284CPV/


title: Jon_M4_2011_Cy3

source_name: Jonagold apple fruit flesh, 4 months after cold storage, 2011

value: Parenchyma


title: Jon_M4_2012_Cy5


title: Fuj_M4_2011_Cy5

source_name: Fuji apple fruit flesh, 4 months after cold storage, 2011


title: E26T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient5


title: ChIP-seq from PC-9 (ENCLB617FIY)

description:
https://www.encodeproject.org/experiments/ENCSR793USK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR793USK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB617FIY
size range: 200-600

source_name: Homo sapiens PC-9 immortalized cell line

value: cell line

tag: description

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

tag: dev stage

tag: Sex

value: not collected

value: ENCBS987JQH at ENCODE; https://www.encodeproject.org/ENCBS987JQH/

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

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: E18T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient2

value: R


title: ChIP-seq from H1-hESC (ENCLB840AVY)

description:
https://www.encodeproject.org/experiments/ENCSR771SNW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR771SNW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB840AVY
size range: 300-800

value: embryonic

value: male

value: unknown

tag: health state

value: healthy

tag: lab

value: Bradley Bernstein, Broad

tag: link

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


title: E26T1

description: Ribo and Globin depleted library

source_name: Not Responder T1 patient5

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: NR


title: Jon_M4_2011_Cy5

value: Fruit

tag: tissue compartment

tag: cultivar

value: Jonagold

tag: genotype

value: Wild-type

value: Harvested at optimum maturity

value: Cold storage for 120 days after harvest


title: ChIP-seq from PC-9 (ENCLB127QTS)

description:
https://www.encodeproject.org/experiments/ENCSR793USK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793USK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB127QTS
size range: 200-600

value: cell line

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

value: not collected

value: ENCBS177ANS at ENCODE; https://www.encodeproject.org/ENCBS177ANS/


title: brain mnr rep 6

city: San Antonio

first: Laura

middle: L

last: Cox

department: Genetics

institute: Texas Biomedical Research Institute

description:
IL_MNR_12
replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected with GenomeStudio v1.9.0. Data was customized to include only probes that were detected at greater than or equal to 95% confidence in all baboon samples of at least one tissue type from previous Illumina gene expression experiments (n=22,148). These included probe signals from fetal baboon brain (n=12), liver (n=12), placenta (n=12), and kidney (n=12). All median normalisation and log2 transformation was performed on the filtered dataset  in Genesifter Analysis Edition (http://www.geospiza.com/Products/AnalysisEdition.shtml).

organism: Papio hamadryas

source_name: brain mnr

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: female

tag: developmental stage

value: 165 dGa

tag: tissue

value: brain (frontal cortex)

tag: mother's pregnancy condition

value: nutrient restricted


title: brain mnr rep 2

description:
IL_MNR_8
replicate 2


title: brain mnr rep 4

description:
IL_MNR_10
replicate 4

value: male


title: brain mnr rep 1

description:
IL_MNR_7
replicate 1


title: brain control rep 6

description:
IL_MNR_6
replicate 6

source_name: brain control

value: control


title: brain mnr rep 3

description:
IL_MNR_9
replicate 3


title: brain mnr rep 5

description:
IL_MNR_11
replicate 5


title: Fuj_M4_2011_Cy3

value: Parenchyma

value: Fuji

tag: developmental stage at harvest

tag: treatment


title: ChIP-seq from OCI-LY1 (ENCLB099QSV)

description:
https://www.encodeproject.org/experiments/ENCSR768JED/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR768JED
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB099QSV
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: antibody

tag: line

tag: description

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

tag: biosample encode accession

tag: age

value: 44 year

tag: dev stage

value: adult

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS899DSB at ENCODE; https://www.encodeproject.org/ENCBS899DSB/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from H1-hESC (ENCLB693NXV)

description:
https://www.encodeproject.org/experiments/ENCSR771SNW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR771SNW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB693NXV
size range: 300-1000

value: cell line

value: embryonic

tag: Sex

value: unknown

tag: health state

value: healthy

tag: lab

tag: link

value: ENCBS364BFI at ENCODE; https://www.encodeproject.org/ENCBS364BFI/

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


title: E18T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient2

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: R


title: Jon_M1_2012_Cy5

source_name: Jonagold apple fruit flesh, 1 month after cold storage, 2012

tag: tissue

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Jonagold

tag: genotype

value: Wild-type

value: Harvested at optimum maturity

value: Cold storage for 30 days after harvest


title: Jon_M1_2012_Cy3

tag: developmental stage at harvest

tag: treatment


title: Fuj_M1_2012_Cy3

source_name: Fuji apple fruit flesh, 1 month after cold storage, 2012

value: Fuji


title: Fuj_M1_2012_Cy5


title: E15T2

description: Ribo and Globin depleted library

source_name: Not Responder T2 patient2

value: NR


title: brain control rep 5

description:
IL_MNR_5
replicate 5

tag: gender

value: female

tag: developmental stage

value: 165 dGa

value: brain (frontal cortex)

tag: mother's pregnancy condition

value: control


title: ChIP-seq from PC-9 (ENCLB696MUZ)

description:
https://www.encodeproject.org/experiments/ENCSR702GMW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR702GMW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB696MUZ
size range: 200-600

tag: antibody

tag: line

value: cell line

tag: description

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

tag: biosample encode accession

tag: dev stage

value: unknown

value: not collected

tag: age

value: Bradley Bernstein, Broad

value: ENCBS987JQH at ENCODE; https://www.encodeproject.org/ENCBS987JQH/

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

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: Fuj_M1_2011_Cy5

source_name: Fuji apple fruit flesh, 1 month after cold storage, 2011

value: Fruit

value: Parenchyma

value: Wild-type


title: ChIP-seq from PC-3 (ENCLB940BKK)

description:
https://www.encodeproject.org/experiments/ENCSR617RSQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR617RSQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB940BKK
size range: 300-600
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

value: prostate cancer cell line

value: adult

tag: Sex

value: male

value: 62 year

tag: health state

value: grade IV, adenocarcinoma

tag: passage number

tag: lab

tag: link

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from A673 (ENCLB352PYX)

description:
https://www.encodeproject.org/experiments/ENCSR611JJS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR611JJS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR196CXJ
encode release date: 2017-11-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB352PYX
size range: 300-800
nucleic acid starting quantity: 2
nucleic acid starting quantity units: ng

source_name: Homo sapiens A673 immortalized cell line

value: CTCF

value: cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: female

value: 15 year

value: ENCBS385OLC at ENCODE; https://www.encodeproject.org/ENCBS385OLC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: ChIP-seq from PC-9 (ENCLB769XHP)

description:
https://www.encodeproject.org/experiments/ENCSR702GMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR702GMW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2018-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB769XHP
size range: 200-600

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

value: not collected

value: Bradley Bernstein, Broad

value: ENCBS177ANS at ENCODE; https://www.encodeproject.org/ENCBS177ANS/

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

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260