title: ChIP-seq from OCI-LY3 (ENCLB180QZZ)

description:
https://www.encodeproject.org/experiments/ENCSR584ATA/
***************
biological replicate number: 2
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: ENCLB180QZZ
size range: 200-600
nucleic acid starting quantity: 24
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY3 immortalized 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

value: B cell lymphoma

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: ChIP-seq from MCF-7 (ENCLB950AHW)

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/ENCSR560BUE/
***************
biological replicate number: 1
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: ENCLB950AHW
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens MCF-7 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

tag: antibody

value: CTCF

tag: line

value: cell line

tag: description

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

tag: biosample encode accession

tag: age

value: 69 year

tag: dev stage

tag: Sex

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: passage number

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/

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: brain control rep 4

type: RNA

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

description:
IL_MNR_4
replicate 4

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).

label: biotin

molecule: total RNA

organism: Papio hamadryas

source_name: brain control

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

tag: developmental stage

value: 165 dGa

tag: tissue

value: brain (frontal cortex)

tag: mother's pregnancy condition

value: control


title: E15T1

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: Not Responder T1 patient2

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

value: Whole blood cells collected from patient after septic shock

tag: patient

tag: timepoint

tag: clinical classification

value: NR


title: E04T2

description: Ribo and Globin depleted library

source_name: Responder T2 patient1

value: R


title: brain control rep 3

description:
IL_MNR_3
replicate 3

value: male


title: brain control rep 1

description:
IL_MNR_1
replicate 1


title: ChIP-seq from SK-N-SH (ENCLB937OXB)

description:
https://www.encodeproject.org/experiments/ENCSR541AMF/
***************
biological replicate number: 2
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: ENCLB937OXB
size range: 200-600

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

tag: antibody

value: CTCF

tag: line

value: SK-N-SH

value: cell line

value: 4 year

value: child

value: ENCBS500EWH at ENCODE; https://www.encodeproject.org/ENCBS500EWH/

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 HepG2 (ENCLB607ICN)

description:
https://www.encodeproject.org/experiments/ENCSR508LMH/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB607ICN
size range: 300-600

source_name: Homo sapiens HepG2 immortalized cell line

tag: description

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.

tag: biosample encode accession

value: Bradley Bernstein, Broad

value: hepatocellular carcinoma

value: 15 year

value: ENCBS289AAB at ENCODE; https://www.encodeproject.org/ENCBS289AAB/

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


title: brain control rep 2

description:
IL_MNR_2
replicate 2

value: female

value: 165 dGa

value: brain (frontal cortex)

value: control


title: Jon_M1_2011_Cy5

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: Jonagold apple fruit flesh, 1 month after cold storage, 2011

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: Jonagold

tag: genotype

value: Wild-type

tag: developmental stage at harvest

value: Harvested at optimum maturity

tag: treatment

value: Cold storage for 30 days after harvest


title: Jon_M1_2011_Cy3


title: Fuj_M2_2012_Cy5

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

value: Fuji

value: Cold storage for 60 days after harvest


title: Fuj_M1_2011_Cy3

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


title: 4-2 Th1 [M5323]

city: Hannover

first: Chittappen Kandiyil

last: Prajeeth

address: Carl-Neuberg Str 1

department: Neurology

country: Germany

institute: Hannover Medical School

description: Experiment 4 Gene expression after 16h treatment with Th1 culture supernatants

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
In order to comparatively analyze this dataset with a previously generated, published microglia dataset (Gene Expression Omnibus (GEO) accession number GSE45384) raw data from both studies were reprocessed and normalized together, as follows:   Starting with the main output of the Feature Extraction Software (txt-files), measurements of contained on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  Averaged gPS values were normalized by quantile normalization followed by global linear scaling. For the latter approach, all quantile normalized gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array i’ in the formula shown below). Accordingly, finally normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   Finally normalized gPSArray i = quantile normalized gPSArray i  x (1500 / 75th PercentileArray i)     Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 finally normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.
Normalized processed signal intensity values (non-log), averaged across on-chip replicates. Measurements of control features were removed.

organism: Mus musculus

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) using 500ng of total RNA as input and according to the manufacturer’s recommendations, except that reaction volumes were halved. cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

growth_protocol: Primary cultures of mixed glial cells were prepared from brains of neonatal 1-3 days (P1-P3) old C57BL/6 neonatal mice. Contaminating Microglia and oligodendrocyte precursor cells were eliminated by overnight shaking at 37oC and 170 rpm in an orbital shaker, followed by cytosine arabinoside (AraC; 10 µM; Sigma Aldrich) treatment for three days. Astrocytes were harvested and replated in 6-well plates and the cells were maintained in curlture medium untill they became confluent

extract_protocol: RNA was isolated from astrocytes using the RNeasy Micro kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Confluent astrocyte cultures were treated with T cell culture medium (complete IMDM), Th1 or Th17 culture supernatants diluted in equal volume of mixed glial culture medium (DMEM 10% FCS) for 16h and 37oC

tag: strain

tag: age

value: neonatal brain

tag: cell type

value: Astrocytes

tag: treated with

value: Th1 culture supernatants


title: 4-3 Th17 [M5324]

description: Experiment 4 Gene expression after 16h treatment with Th17 culture supernatants

tag: tissue

value: Th17 culture supernatants


title: E04T1

description: Ribo and Globin depleted library

source_name: Responder T1 patient1

value: Whole blood cells collected from patient after septic shock

tag: patient

value: R


title: ChIP-seq from HepG2 (ENCLB767BZM)

description:
https://www.encodeproject.org/experiments/ENCSR508LMH/
***************
biological replicate number: 1
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: ENCLB767BZM
size range: 300-600

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.

tag: Sex

value: male

tag: lab

value: Bradley Bernstein, Broad

tag: passage number

tag: health state

value: hepatocellular carcinoma

value: 15 year

tag: dev stage

value: child

tag: link

value: ENCBS289AAB at ENCODE; https://www.encodeproject.org/ENCBS289AAB/

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


title: Jon_M2_2012_Cy3

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

value: Fruit

tag: tissue compartment

value: Parenchyma

value: Jonagold

value: Wild-type

value: Harvested at optimum maturity


title: Fuj_M2_2012_Cy3

tag: cultivar

value: Fuji

value: Cold storage for 60 days after harvest


title: 3-3 Th17 [M5321]

description: Experiment 3 Gene expression after 16h treatment with Th17 culture supernatants

value: neonatal brain

value: Astrocytes

value: Th17 culture supernatants


title: ChIP-seq from HCT116 (ENCLB742VES)

description:
https://www.encodeproject.org/experiments/ENCSR240PRQ/
***************
biological replicate number: 1
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: ENCLB742VES
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

tag: antibody

value: CTCF

tag: line

value: cell line

tag: description

value: cells obtained from ATCC

tag: biosample encode accession

value: unknown

value: male

value: colorectal carcinoma

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: 3-2 Th1 [M5320]

description: Experiment 3 Gene expression after 16h treatment with Th1 culture supernatants

tag: strain

tag: age

value: Th1 culture supernatants


title: Diff_S9

city: Houston

first: Annie

middle: W.

last: Shieh

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: Jon_M2_2012_Cy5

tag: tissue

value: Fruit

value: Parenchyma

value: Jonagold

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 Loucy (ENCLB415QBM)

description:
https://www.encodeproject.org/experiments/ENCSR464DKE/
***************
biological replicate number: 2
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: ENCLB415QBM
size range: 200-600

source_name: Homo sapiens Loucy immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eaafee87-23f3-4bb4-adb1-585af01db120/@@download/attachment/ChIP%20New%20General%20ChIP%20Protocol%20041510%20v05.pdf

value: CTCF

value: Loucy

value: cell line

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.

tag: dev stage

value: adult

tag: Sex

value: female

value: 38 year

tag: health state

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

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS080PZG at ENCODE; https://www.encodeproject.org/ENCBS080PZG/

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 OCI-LY1 (ENCLB202LHA)

description:
https://www.encodeproject.org/experiments/ENCSR072EUE/
***************
biological replicate number: 1
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: ENCLB202LHA
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: antibody

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

tag: link

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: 4-1 Medium [M5322]

description: Experiment 4 Gene expression after 16 Medium treatment

value: neonatal brain

value: Astrocytes

tag: treated with

value: T cell culture medium (complete IMDM),


title: Fuj_M2_2011_Cy5

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

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Fuji

value: Wild-type

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: Jon_M2_2011_Cy3

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

value: Jonagold


title: EphrinA1

city: Hangzhou

first: Tianhua

last: Zhou

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

description: Gene expression after transfection with  pcDNA-3.1-EphrinA1 plasmid for 48h

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 4 for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 4 for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then slowly remove the slide rack minimizing droplets on the slides.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set high to 100% and low to 10%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, genes have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: HGC-27 cell transfected with pcDNA3.1-EphrinA1 plasmid for 48h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.Total RNA was Clean-up using RNasey Mini Kit(Qiagen p/n 74104) and Base-ZERO Dnase(EPICENTRE, Cat. Nos.DB0711K). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: HGC-27 gastric cancer cell was transfected with pcDNA3.1 control vector or pcDNA3.1-GMAN or pcDNA3.1-EphrinA1 for 48h

tag: disease state

value: gastric cancer

tag: cell line

tag: transfection

value: pcDNA3.1-EphrinA1 plasmid for 48h


title: 2-2 Th1 [M5317]

description: Experiment 2 Gene expression after 16h treatment with Th1 culture supernatants

tag: strain

tag: age

tag: cell type

value: Th1 culture supernatants


title: HL60_S4_ATRA: ctrl_1_HiC

status: Public on Dec 02 2018

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

data_processing:
Read quality was confirmed with FastQC v0.11.4
Reads were aligned and filtered with HiCUP
Aligned reads were converted to .cool format with cooler, and ICE-normalized at multiple resolutions
Hic_breakfinder used raw aligned reads to identify structural variants
Genome_build: hg38
Supplementary_files_format_and_content: Multi-resolution ICE-normalized cooler file for use with HiGlass, .cool file; hic_breakfinder summarized breaks file, .txt

source_name: Myeloid leukaemia

growth_protocol: HL-60/S4 cells were maintained in RPMI 1640 medium, plus 10% fetal calf serum and 1% penicillin, streptomycin, and l‐glutamine at 37°C in a humid incubator purged with 5% CO2/95% air

extract_protocol:
15x107 cells were crosslinked with Formaldehyde (2% FC, 10 min, RT), quenched with Glycine (125mM, 5 min, RT) and scraped from the plate. Cells were lysed on ice in lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% NP-40 and 50 μl protease inhibitors, 15 min) and disrupted using a Dounce homogenizer (10X, 1 min on ice, 10X). Lysed cells were pelleted (4°C, 5,000rpm, 3 min), wash twice in 1X restriction enzyme buffer, suspend in 1X buffer and divided into five tubes with a final volume of 362μl. SDS was added (1% FC), incubated (65°C, 10 min), place back on ice and Quenched with Triton X-100 (10% FC). Chromatin was digested with HindIII (400U, 37OC, 16 h with rotation). Restriction site overhangs were filled in with biotin labeled Cytosine (1.5 μl 10 mM dATP, 1.5 μl 10 mM dGTP, 1.5 μl 10 mM dTTP, 37.5 μl 0.4 mM biotin-14-dCTP, and 50U Klenow), mixed carefully and incubated (45 min, 37°C). Tubes were placed on ice and the enzyme inactivated by SDS (10%), incubated (65°C, exactly 30 min) and placed back on ice immediately. Biotinylated fragments were ligated by adding 7.61 ml ligation mix (745 μl 10% Triton X-100, 745 μl 10x ligation buffer [500 mM Tris-HCl pH 7.5, 100 mM MgCl2, 100 mM DTT], 80 μl 10 mg/ml BSA, 80 μl 100 mM ATP and 5.96 ml water), T4 DNA ligase (50U), mixed and incubated (4 h, 16°C). Crosslinks were reversed and protein degraded by Proteinase K (25 μl, 12 mg/ml) and incubation (16 h, 65°C). After 16 h, additional Proteinase K (25 μl 20 mg/ml) was added and further incubated (2 h, 65°C). The reactions were cooled to RT and DNA was purified by phenol (1X) and phenol:chloroform (1:1, 1X) extraction. The aqueous phase was transferred to high-speed centrifugation tubes (oakridge). The DNA was ethanol precipitated (2.5 volumes 100% Ethanol and 1/10th volume 3M Sodium Acetate), mixed by inversion, chilled (>30 min, -80°C), centrifuged (20 min, 10,000g, 4°C) and the DNA pellet dissolved in 450 μl 1x TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The DNA was phenol:chloroform (1:1) extracted twice more with centrifugation (5 min, 14,000rpm, RT). The DNA was ethanol precipitated (2.5 volumes 100% Ethanol and 1/10th volume 3M Sodium Acetate), mixed by inversion, chilled (>30 min, -80°C) and centrifuged (20 min, 10,000g, 4°C). The DNA pellet was washed with ice-cold 70% ethanol, centrifuged (10 min, >10,000g, 4°C), dried (~10 min) and suspended in 25 μl 1x TE. RNA was degraded by the addition of RNase A (1 μl 1 mg/ml), incubation (30 min, 37°C) and then the Hi-C libraries were pooled. Biotin was removed from unligated ends using T4 DNA polymerase. Mixed ~5μg of Hi-C library with T4 DNA polymerase reaction buffer (1 μl 10 mg/ml BSA, 10 μl 10x NEBuffer 2, 1 μl 10mM dATP, 1 μl 10mM dGTP) and T4 DNA polymerase (5U) in a total volume of 100 μl. Incubated the mixture (2 h, 12°C). Multiple 5 μg reactions were performed. Reactions were stopped by the addition of EDTA (2 μl 0.5M EDTA pH 8.0). Multiple 5 μg reactions were pooled and the DNA purified by three phenol pH 8.0:chloroform (1:1) extractions with centrifugation (5 min, 14,000 rpm, RT). The DNA was Ethanol precipitated (2.5 volumes 100% Ethanol and 1/10th volume 3M Sodium Acetate), mixed by inversion, chilled (>30 min, -80°C) and centrifuged (20 min, 10,000g, 4°C). The DNA pellet was washed with 70% Ethanol, dried, suspended and pooled in a total volume of 100 μl H2O. The DNA was sheared to a size of 300-500bp using a Covaris S2 instrument (duty cycle 5, intensity 5, cycles/burst 200, time 60 secs for 4 cycles). The sheared DNA ends were repaired (14 μl 10x ligation buffer, 14 μl 2.5 mM dNTP mix, 5 μl T4 DNA polymerase, 5 μl T4 polynucleotide kinase, 1 μl Klenow DNA polymerase and 1μl H2O) and incubated (30 min, RT). DNA was purified using a Qiagen MinElute column according to manufacturer's recommendations and the DNA eluted twice with Tris-Low-EDTA (TLE: 15 μl 1x [10 mM Tris pH 8.0, 0.1 mM EDTA]). An ‘A’ tail was added to the DNA fragments using Klenow (5 μl [10x NEBuffer2, 10 μl 1 mM dATP, 2 μl H2O and 3 μl Klenow (exo-)]) and incubation (30 min, 37°C). The Klenow was inactivated (20 min, 65°C) and the reaction was cooled on ice. The reaction volume was reduced to 20 μl using a speedvac, the DNA loaded on a 1.5% agarose gel with 1X TAE, run for 3 hours at 80V and DNA fragments between 300 and 500 bp were excised. The DNA was purified using a Qiagen gel extraction kit according to manufacturers recommendations and the DNA eluted with 50 μl 1x TLE. Combined the purified DNA in a final volume of 300 μl 1x TLE and determined the DNA concentration by QuBit. To enrich for biotin-labeled fragments magnetic streptavidin beads (100 μl) were washed twice with Tween Buffer (TB: 400 μl [5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween]) and suspended in a volume of 2x No Tween Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl) equivalent to the remaining Hi-C library volume. All subsequent steps were performed in DNA LoBind tubes. Combined the beads with Hi-C DNA and incubated (15 min, RT, slow rotation). Placed the tubes on a magnetic particle concentrator, removed the supernatant, washed the beads in NTB (NTB: 400 μl [5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl]) and then with ligation buffer (100 μl 1x). Suspend the beads in ligation buffer (30 μl 1x) and transferred to a new tube. The DNA bound to the streptavidin beads (~100 ng) was used for sequencing library preparation according to Illumina instructions. Resuspention buffer (2.5 µl), DNA adaptor index (2.5 µl) and Ligation Mix 2 (2.5 µl) were added to the tube, and incubated (30°C, 2 h). To stop the reaction Stop Ligation buffer (5 µl) was added to the tube. Removed non-ligated adapters by placing the tube on a magnetic particle concentrator and washing the beads twice with TB (400 μl 1x), once with NTB (200 μl 1x) and twice with NEBuffer 2 (200 μl and 50 μl 1x). Suspended the beads in 50 μl 1x NEBuffer 2 and transfered to a new tube. Determined the number of PCR cycles necessary to generate enough product for sequencing; set up four PCR reactions with 6, 9, 12 or 15 cycles (9 µl of sample [8 µl 1x NEBuffer2 + 1 µl DNA bound beads], 9 µl Enhancer PCR mix and 2 µl PCR cocktail. Run PCR: 95°C – 3 min, {98°C – 20 sec, 60°C – 15 sec, 6-15 cycles 72°C – 30 sec} 6-15 cycles, 72°C – 5 min, 4°C – forever. Determined the optimal cycle number by running the PCR reactions on a 5% polyacrylamide gel (60 min, 80 V). Amplified the remainder of the Hi-C-library-bound streptavidin beads in a large-scale PCR with the optimal number of PCR cycles. Pooled the PCR products from the separate wells and reclaimed the beads. Kept 1% of the large-scale PCR product separate to run on a gel and purify the remainder of the PCR product with Ampure beads (1.8x volume) according to the manufacturer's recommendations. Eluted the DNA with TLE (50 μl 1x) and compared 1% of the Ampure bead purified PCR product to the 1% aliquot of original PCR product on a 5% polyacrylamide gel to insure the successful removal of the PCR primers. Sequenced the Hi-C library with Illumina paired end sequencing (50 bp).
Illumina TruSeq® Nano DNA LT Sample Preparation Kit

treatment_protocol: Cells were differentiated into the granulocytic form with 1µM all-trans retinoic acid for four days

value: Myeloid leukaemia

tag: differentiation

value: neutrophil-like (4 days all-trans retinoic acid)


title: Jon_M2_2011_Cy5

tag: tissue

tag: genotype

tag: developmental stage at harvest

tag: treatment


title: TIL_Bulk_P1_TIM_S3

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
TIL_Bulk_P1_TIM_S3
processed data file: TIL_BulkPD1_TIM_0.001_peaks.narrowPeak

data_processing:
Quality trimming of Fastqs was performed using Trimmomatic
Trimmed reads were aligned to the mm9 mouse genome using Bowtie2
Aligned reads were sorted and biological replicates were merged for peak-calling with samtools
Peak-calling was performed on merged bams using MACS2
Union and merging of peaks across all condition was done using BEDtools
BEDtools was used to quantify raw ATAC cut-sites within each peak in universe for each biological replicate to obtain a raw counts matrix
Library size normalization was performed using DESeq2 to obtain a final normalized counts matrix
Genome_build: mm9

growth_protocol: For LCMV experiments, C57BL/6 mice were infected with 2 x 10^6 pfu LCMV Clone 13 via IV injection. On day 30 after infection, mice were sacrificed and spleens removed for CD8+ T cell isolation. For tumor experiments, C57BL/6 mice were injected subcutaneously with 3 x 10^5 B16-ova cells. Tumors were harvested on day 22 after implantation for CD8+ T cell isolation

extract_protocol:
CD8+ T cells were isolated from LCMV-infected mice by CD8+ MACS negative selection performed on single-cell suspensions of splenocytes, followed by FACS. CD8+ T cells were isolated from B16-ova tumors by dissecting tumors from the surrounding fascia, mechanically mincing and treating with collagenase P and DNAse I for 10 minutes at 37C. Tumor-infiltrating leukocytes were enriched by CD8+ MACS positive selection (Miltenyi) and FACS isolation. In both contexts, cells were sorted directly into PBS with 2% FBS.
Library construction was performed as per standard ATAC-seq protocol, as outlined in Corces et al., Nature Genetics 2016

treatment_protocol: LCMV-infected mice were not treated. Tumor inoculated mice were treated with 100mcg anti-PD-1 or isotype control antibody on days 9 and 12 after implantation

tag: strain background

value: CD8+ T-cells

tag: cell subtype

value: Slamf6-Tim3+SIINFEKL Tetramer+ CD44+PD-1+CD8+ T cells isolated from  B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12

tag: isolation of cd8+ t cells

value: CD8+ MACS negative selection (Miltenyi) followed by FACS


title: 3-1 Medium [M5319]

description: Experiment 3 Gene expression after 16 Medium treatment

value: neonatal brain

value: Astrocytes

tag: treated with


title: TIL_Bulk_P1_Slam_S7

description:
TIL_Bulk_P1_Slam_S7
processed data file: TIL_BulkPD1_Slam_0.001_peaks.narrowPeak

value: Slamf6+Tim3-SIINFEKL Tetramer+ CD44+PD-1+CD8+ T cells isolated from  B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12


title: TIL_Bulk_P2_Slam_S8

description:
TIL_Bulk_P2_Slam_S8
processed data file: TIL_BulkPD1_Slam_0.001_peaks.narrowPeak


title: 2-3 Th17 [M5318]

description: Experiment 2 Gene expression after 16h treatment with Th17 culture supernatants

value: Th17 culture supernatants


title: GMAN

description: Gene expression after transfection with  pcDNA-3.1-GMAN plasmid for 48h

source_name: HGC-27 cell transfected with pcDNA3.1-GMAN plasmid for 48h

value: pcDNA3.1-GMAN plasmid for 48h


title: TIL_Bulk_C2_TIM_S2

description:
TIL_Bulk_C2_TIM_S2
processed data file: TIL_Bulk_TIM_0.001_peaks.narrowPeak

value: Slamf6-Tim3+SIINFEKL Tetramer+ CD44+PD-1+CD8+ T cells isolated from  B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12


title: Control

description: Gene expression after transfection with  pcDNA-3.1 control vector for 48h

source_name: HGC-27 cell transfected with pcDNA3.1 control vector for 48h

value: pcDNA3.1 control vector for 48h


title: 1-2 Th1 [M5314]

description: Experiment 1 Gene expression after 16h treatment with Th1 culture supernatants


title: TIL_Bulk_P2_TIM_S4

description:
TIL_Bulk_P2_TIM_S4
processed data file: TIL_BulkPD1_TIM_0.001_peaks.narrowPeak


title: TIL_Bulk_C2_Slam_S6

description:
TIL_Bulk_C2_Slam_S6
processed data file: TIL_Bulk_Slam_0.001_peaks.narrowPeak

value: Slamf6+Tim3-SIINFEKL Tetramer+ CD44+PD-1+CD8+ T cells isolated from  B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12


title: siEphrinA1

description: Gene expression after transfection with  siRNA targeting EphrinA1 for 48h

source_name: BGC-823 cell transfected with siRNA targeting EphrinA1 for 48h

treatment_protocol: BGC-823 gastric cancer cell was transfected with siRNA control or siRNAs targeting GMAN or EphrinA1 for 48h

value: siRNA targeting EphrinA1 for 48h


title: siGMAN

description: Gene expression after transfection with  siRNA targeting GMAN for 48h

source_name: BGC-823 cell transfected with siRNA targeting GMAN for 48h

value: gastric cancer

value: siRNA targeting GMAN for 48h


title: siControl

description: Gene expression after transfection with  siRNA control for 48h

source_name: BGC-823 cell transfected with siRNA control for 48h

value: siRNA control for 48h


title: 1-1 Medium [M5313]

description: Experiment 1 Gene expression after 16 Medium treatment

value: T cell culture medium (complete IMDM),


title: 1-3 Th17 [M5315]

description: Experiment 1 Gene expression after 16h treatment with Th17 culture supernatants


title: TIL_Bulk_C1_Slam_S5

description:
TIL_Bulk_C1_Slam_S5
processed data file: TIL_Bulk_Slam_0.001_peaks.narrowPeak


title: 3h

type: SAGE

anchor: NlaIII

city: Kitakami

first: Yuichi

last: Sakamoto

state: Iwate

department: Department of Bioresource

country: Japan

institute: Iwate Biotechnology Research Center

data_processing: Matching of tag sequence to the C. cinerea predicted transcripts and to the genome of the strain #326 (http://genome.jgi.doe.gov/Copci_AmutBmut1 was performed with the blastn algorithm. The tag counts that matched to same gene were incremented using a script written in Perl. Fisher’s exact test of every tag count of the genes was performed by using IDEG6

organism: Coprinopsis cinerea

source_name: 3h after light exposure (after 6-days cultivation in dark)

growth_protocol: Coprinopsis cinerea strain #326 was inoculated on edge of petri dish, and cultured on MY1/2G (Molt extract, Yeast extract, 0.2% glucose) for 6 day in dark at 28˚C.

extract_protocol: The total RNAs for Super-SAGE were obtained from these mycelia using RNeasy Plant Mini kit (QIAGEN GmbH, Germany). The reagent of the kit (Buffer RLC) was added first to the frozen tissue, and the tissue was crushed in liquid nitrogen. The remaining procedure for total RNA extraction was performed as per the manufacturer’s instruction. Super-SAGE analysis was performed following the method of Matsumura et al. (Plos One 2010:5(8)e12010).

treatment_protocol: Fluorescent light was exposed to mycelia for 0.5, 1 and 3h. The mycelia were harvested by excising the mycelial colony edge with a knife and scraping it gently off the cellophane sheet. Then immediately freezing them in liquid nitrogen. The collection of mycelia at the hyphal knot region was carried out under red light.

tag: light length

value: #326 (AmutBmut)

tag: developmental stage

value: mycelia


title: LCMV_Round3_S2_TIM_S8

description:
LCMV_Round3_S2_TIM_S8
processed data file: LCMV_Round3_TIM_0.001_peaks.narrowPeak

value: CD8+ T-cells

value: Slamf6-Tim3+GP33 Tetramer+ CD44+PD-1+ CD8+ T cells isolated from spleens of LCMV Cl13 infected mice 28 days post-infection


title: Fuj_M2_2011_Cy3

value: Fruit

tag: tissue compartment

value: Parenchyma

tag: cultivar

value: Fuji

value: Wild-type

value: Harvested at optimum maturity

value: Cold storage for 60 days after harvest


title: LCMV_Round3_S1_TIM_S6

description:
LCMV_Round3_S1_TIM_S6
processed data file: LCMV_Round3_TIM_0.001_peaks.narrowPeak

value: CD8+ MACS negative selection (Miltenyi) followed by FACS


title: LCMV_Round3_S2_Slam_S7

description:
LCMV_Round3_S2_Slam_S7
processed data file: LCMV_Round3_Slam_0.001_peaks.narrowPeak

value: Slamf6+Tim3-GP33 Tetramer+ CD44+PD-1+ CD8+ T cells isolated from spleens of LCMV Cl13 infected mice 28 days post-infection


title: LCMV_Round3_S1_Slam_S5

description:
LCMV_Round3_S1_Slam_S5
processed data file: LCMV_Round3_Slam_0.001_peaks.narrowPeak


title: Tumor_P2_tet_Tim3_E09_TechRep3

data_processing:
Quality trimming of Fastqs was performed using Trimmomatic
Trimmed reads were aligned to the mm10 mouse genome using Bowtie2
HTSeq was used to map aligned reads to genes and quanitfy gene counts for each technical replicate
Counts for technical replicates were averaged and rounded to the nearest integer to obtain a raw counts matrix (rawCount_cleaned_merged.txtt)
Library size normalization was performed using DESeq2 to obtain a final normalized counts matrix (normalizedCount_cleaned_merged.txt)
Genome_build: mm10

extract_protocol:
CD8+ T cells were isolated from LCMV-infected mice by CD8+ MACS negative selection performed on single-cell suspensions of splenocytes, followed by FACS. CD8+ T cells were isolated from B16-ova tumors by dissecting tumors from the surrounding fascia, mechanically mincing and treating with collagenase P and DNAse I for 10 minutes at 37C. Tumor-infiltrating leukocytes were enriched by CD8+ MACS positive selection (Miltenyi) and FACS isolation. In both contexts, cells were sorted directly into RLT buffer + 1% BME in 96 well plates.
Library construction was performed according to a modified Smart-Seq2 protocol as described in Yates et al., PNAS, 2018.

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #3

value: CD8+ MACS positive selection (Miltenyi) followed by FACS


title: 1h

source_name: 1h after light exposure (after 6-days cultivation in dark)


title: TIL_Bulk_C1_TIM_S1

description:
TIL_Bulk_C1_TIM_S1
processed data file: TIL_Bulk_TIM_0.001_peaks.narrowPeak

value: Slamf6-Tim3+SIINFEKL Tetramer+ CD44+PD-1+CD8+ T cells isolated from  B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12


title: Tumor_P2_tet_Tim3_E08_TechRep2

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P2_DP_Tim3_E01_TechRep1

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, , technical replicate #1


title: Tumor_P2_DP_Tim3_E03_TechRep3

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #3


title: Tumor_P2_tet_Slam_D01_TechRep2

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P1_tet_Tim3_C06_TechRep3

value: CD8+ T-cells

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #3


title: 0.5h

source_name: 0.5h after light exposure (after 6-days cultivation in dark)

value: #326 (AmutBmut)

value: mycelia


title: Tumor_P2_DP_Slam_E05_TechRep2

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P2_DP_Slam_E06_TechRep3

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #3


title: Tumor_P2_DP_Tim3_E02_TechRep2

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: 0h

source_name: mycelia just before light exposure (after 6-days cultivation in dark)

value: 0h (without light treatment)


title: Tumor_P2_tet_Slam_C01_TechRep1

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1


title: Tumor_P1_tet_Slam_C03_TechRep2

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P1_DP_Tim3_B03_TechRep3

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #3


title: Tumor_P2_DP_Slam_E04_TechRep1

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1

value: CD8+ MACS positive selection (Miltenyi) followed by FACS


title: Tumor_P1_tet_Tim3_C04_TechRep1

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1


title: Tumor_P1_DP_Tim3_B02_TechRep2

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P2_tet_Tim3_E07_TechRep1

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1


title: Tumor_P1_tet_Slam_C02_TechRep1

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1


title: Tumor_P1_DP_Tim3_B01_TechRep1

value: CD8+ T-cells

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1


title: Tumor_P1_DP_Slam_B06_TechRep3

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #3


title: Tumor_P1_tet_Tim3_C05_TechRep2

value: SIINFEKL-Tetramer+ CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P1_DP_Slam_B05_TechRep2

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #2


title: Tumor_P1_DP_Slam_B04_TechRep1

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with anti-PD-1 on days 9 and 12, technical replicate #1


title: Tumor_C2_tet_Tim3_A09_TechRep3

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #3


title: Tumor_C2_tet_Tim3_A08_TechRep2

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: Tumor_C2_tet_Tim3_A07_TechRep1

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C2_DP_Tim3_A03_TechRep3

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #3


title: Tumor_C2_tet_Slam_B08_TechRep1

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C2_DP_Tim3_A02_TechRep2

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: Tumor_C2_DP_Slam_A06_TechRep3

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #3

value: CD8+ MACS positive selection (Miltenyi) followed by FACS


title: Tumor_C2_DP_Slam_A04_TechRep1

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C2_DP_Slam_A05_TechRep2

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: Tumor_C1_tet_Tim3_D04_TechRep1

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C2_DP_Tim3_A01_TechRep1

value: CD8+ T-cells

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C1_DP_Tim3_C07_TechRep1

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C1_tet_Tim3_D06_TechRep3

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #3


title: Tumor_C1_DP_Slam_D09_TechRep3

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #3


title: Tumor_C1_DP_Slam_D08_TechRep2

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: LCMV_Cp2_Tim3_D11_TechRep2

value: GP33-Tetramer+CD44+CD8+Slamf6-Tim-3+ T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #2

value: CD8+ MACS negative selection (Miltenyi) followed by FACS


title: Tumor_C1_DP_Tim3_C08_TechRep2

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: Tumor_C1_DP_Slam_D07_TechRep1

value: CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C1_DP_Tim3_C09_TechRep3

value: CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #3


title: Tumor_C1_tet_Slam_D02_TechRep1

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #1


title: Tumor_C1_tet_Tim3_D05_TechRep2

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6-Tim-3+ CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: LCMV_Cp2_Tim3_D10_TechRep1

value: GP33-Tetramer+CD44+CD8+Slamf6-Tim-3+ T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #1


title: LCMV_Cp2_Tim3_E11_TechRep3

value: GP33-Tetramer+CD44+CD8+Slamf6-Tim-3+ T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #3


title: LCMV_Cp2_Slamf6_E10_TechRep3

value: GP33-Tetramer+CD44+CD8+Slamf6+Tim-3- T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #3


title: Tumor_C2_tet_Slam_B09_TechRep2

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #2 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2

value: CD8+ MACS positive selection (Miltenyi) followed by FACS


title: LCMV_Cp2_Slamf6_C11_TechRep2

value: CD8+ T-cells

value: GP33-Tetramer+CD44+CD8+Slamf6+Tim-3- T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #2


title: LCMV_Cp2_Slamf6_C10_TechRep1

value: GP33-Tetramer+CD44+CD8+Slamf6+Tim-3- T cells isolated from biologic replicate #2 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #1


title: LCMV_Cp1_Tim3_B11_TechRep2

value: GP33-Tetramer+CD44+CD8+Slamf6-Tim-3+ T cells isolated from biologic replicate #1 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #2


title: Tumor_C1_tet_Slam_D03_TechRep2

value: SIINFEKL-tetramer+CD44+PD-1+ Slamf6+Tim-3- CD8+ T cells isolated from biologic replicate #1 of B16-ova tumors 22 days post-inoculation after treatment with isotype control antibody on days 9 and 12, technical replicate #2


title: LCMV_Cp1_Tim3_B10_TechRep1

value: GP33-Tetramer+CD44+CD8+Slamf6-Tim-3+ T cells isolated from biologic replicate #1 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #1


title: LCMV_Cp1_Slamf6_A11_TechRep2

value: GP33-Tetramer+CD44+CD8+Slamf6+Tim-3- T cells isolated from biologic replicate #1 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #2

value: CD8+ MACS negative selection (Miltenyi) followed by FACS


title: LCMV_Cp1_Slamf6_A10_TechRep1

value: GP33-Tetramer+CD44+CD8+Slamf6+Tim-3- T cells isolated from biologic replicate #1 of spleens of LCMV Cl13 infected mice 30 days post-infection, technical replicate #1


title: WT_Treg_untreated_4

city: San Francisco

first: Kelly

last: Remedios

address: 513 Parnassus Ave, HSW1201B

institute: UCSF

data_processing:
Using an Illumina RNASeq, cDNA was sequenced to a 25M read depth.
Reads were aligned to Ensembl mg GRCm38.p4 reference genome using TopHat (v. 2. 0. 12).
After alignment, SAM files were generated using SAMtools.
Htseq-count (0. 6. 1p1, with union option) was used to obtain read counts.
Differentially expressed genes between paired samples was determined using the R/Bioconducter package DESeq2.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: comma separated value file contains raw counts for each sample

source_name: Tregs

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using QIAGEN Rneasy Spin Columns and quality was checked using an Agilent Bioanalyzer Pico Chip.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Standed mRNA sample preparation kit.

value: Tregs

tag: culture conditions

value: IL6, IL23, IL1B

value: Treated - FcCD70


title: WT_Treg_untreated_3

tag: strain


title: Adult_Skin_Treg_2

data_processing:
The primary sequencing output ( FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools. Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis)
Reads were then mapped to mm10 using the UCSC refFlat gene model
Reads were mapped using Tophat (v2.0.12) with Bowtie2 (2.1.0.0) and sorted with Samtools (0.1.19.0).
Reads were counted with HTSeq (0.6.1) using the settings union and stranded=no
Genome_build: mm10
Supplementary_files_format_and_content: comma separated value file contains raw counts for each sample

source_name: Skin

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using by column purification.
RNA samples were converted into cDNA libraries using the Illumina SMARTer Ultra Low Input sample preparation kit.

value: Skin Tregs

tag: age

value: 6 weeks

value: Skin

tag: characteristics


title: Adult_Skin_Treg_4

tag: cell type


title: WT_Treg_untreated_2


title: WT_Treg_FcCD70_2

value: Untreated


title: WT_Treg_FcCD70_4


title: WT_Treg_FcCD70_3


title: WT_Treg_untreated_1


title: WT_Treg_FcCD70_1


title: Adult_Skin_Teff_1

value: Skin Teffs

tag: tissue


title: Adult_Skin_Treg_1


title: Akita rep3

city: Jerusalem

first: Yael

last: Riahi

address: Ein Kerem

country: Israel

institute: Hadassah Medical Center

data_processing:
Raw reads were processed with cutadapt, v1.12, with parameters -q 15, -m 15, -a <adapter sequence>.
Processed reads were aligned to the mouse genome, version GRCm38, using STAR (v2.5.2b), with default parameters.
Quantification of read counts per gene was performed using htseq-count (version 0.7.2) with parameter -s 'no', and differentially expressed genes were identified using DESeq2 package (version 1.12.4), with default parameters, after removing genes with less than 10 counts in all samples.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel sheet with columns for gene details, raw counts, normalized counts and the DESeq2 results, as specified by column headers.

source_name: whole islets

growth_protocol: whole islets from WT and Akita mice were extracted by ductal perfusion of collagenase P.

extract_protocol:
RNA was extracted using TRI Reagent and an RNeasy Micro Kit
RNA sequencing libraries were constructed from 120 ng of total RNA using the TruSeq RNA V2 sample prep kit (Illumina).

treatment_protocol: Hand-picked islets were plated for overnight recovery in RPMI-1640 medium containing 11.1 mmol/l glucose supplemented with 10% FBS, L-glutamine and penicillin-streptomycin in a 37°C, 5% CO2 incubator before RNA extraction

value: whole islets

tag: genotype

value: Akita (Ins2(WT/C96Y))

value: postnatal day 19-21

tag: number of animals pooled


title: Akita rep2


title: Akita rep1


title: WT rep2

value: WT


title: WT rep1


title: Stroma_wound_MMC_3

status: Public on Dec 01 2018

city: Bethesda

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

institute: NIAMS NIH

data_processing:
BCL Conversion and Demultiplex bcl2fastq
Map to mm10 using Tophat 2.1.0
Calculate RPKM using Partek GS 6.6
ANOVA comparison using Partek GS 6.6
Genome_build: mm10
Supplementary_files_format_and_content: Excel, RPKM and ANOVA results

molecule: polyA RNA

source_name: Stroma Wounded MMC

extract_protocol:
For RNA-seq studies, epithelium was isolated from mouse corneas. After limbal to limbal debridement, eyes were removed, corneas dissected to yield clear stromal buttons. For both epithelium and stroma, 4 variables were tested (Control, Mitomycin C Control, Wound, Mitomycin C Wound). RNA was extracted using Arcturus Picopure RNA isolation kit (Applied Biosystems).
cDNA libraries were generated using NEBnext and NuGen kits. Sequencing was performed on the HiSeq3000

value: cornea

value: Stroma

tag: wound status

value: Wounded

tag: treatment

value: MMC


title: Stroma_wound_MMC_2


title: Stroma_wound_untx_4

source_name: Stroma Wounded untreated

value: untreated


title: Stroma_wound_untx_3


title: Stroma_wound_MMC_4


title: Stroma_wound_untx_2


title: Stroma_wound_MMC_1


title: Stroma_wound_untx_1


title: Stroma_ctrl_MMC_3

source_name: Stroma Unwounded MMC

value: Unwounded


title: WT rep3


title: Stroma_ctrl_MMC_1


title: Stroma_ctrl_untx_4

source_name: Stroma Unwounded untreated


title: Stroma_ctrl_MMC_4


title: Stroma_ctrl_MMC_2


title: Stroma_ctrl_untx_3


title: hrr25is_CMK_pThr4

type: genomic

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

description:
SAMPLE_12
pThr4 ChIP-chip from hrr25is treated with CMK

hyb_protocol: 24 pmol of ChIP DNA and an equivalent mass of input DNA were mixed in a speedvac on medium heat for 30 min. The samples were resuspended in 18 uL of hybrdization buffer and loaded using NimbleGen X1 mixers and hybridzed on a MAUI instrument.

scan_protocol: Arrays were scanned on a GenePix 4000B instrument as previously described (Tietjen, et al., 2010).

data_processing:
Probe intensities were extracted with NimbleScan using the .ndf file. Global and local normalization was performed using in-house R code available upon request, log2-transformed and averaged with a five-probe moving average to smooth the data.
Global and local normalization was performed using in-house R code available upon request, log2-transformed and averaged with a five-probe moving average to smooth the data.

organism: Saccharomyces cerevisiae

source_name: pThr4 input DNA from hrr25is treated with CMK

label_protocol: ChIP DNA was end-repaired, linkers were ligated and ligation-mediated PCR was performed as previously described (Tietjen, et al., 2010).

growth_protocol: grow in YPD to OD600=0.3 at 30°C

extract_protocol: For every immunoprecipitation, 50 ul of protein G conjugated Dynabeads (Life Technologies), pre-washed with lysis buffer (50mM HEPES-KOH [pH 7.5], 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 1mM, Aprotinin, 1mM Leupeptin, 1mM PMSF, 1mM Benzamidine, 1.45mM Pepstatin, 1mM NaN3, 1mM Na3VO4, 1mM NaF), were mixed with the whole cell extract-antibody mixture to pulldown Pol II complexes. Washes and elution were performed as previously described (Tietjen et al., 2010).

tag: strain info.

value: his3Δ leu2Δ ura3Δ Hrr25Δ::kanMX4 pRS315-hrr25-I82G,I23C

value: CMK for 1h

tag: sample type

value: input DNA

source_name: pThr4 IP DNA from hrr25is treated with CMK

growth_protocol: grown in YPD to OD600=0.3 at 30°C

tag: antibody

value: pThr4 - 1G7 - gift from Dirk Eick


title: rtt103tap_hrr25is_DMSO_Rtt103

description:
SAMPLE_13
Rtt103 ChIP-chip from rtt103tap_hrr25is treated with DMSO

source_name: Rtt103 input DNA from rtt103tap_hrr25is treated with DMSO

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Rtt103-TAP::His3 Hrr25Δ::URA3 pRS315-hrr25-HA

tag: treated with

value: DMSO for 1h

source_name: Rtt103 IP DNA from rtt103tap_hrr25is treated with DMSO

value: TAP - CAB1001 - Thermo Fisher


title: rtt103tap_hrr25is_CMK_Rtt103

description:
SAMPLE_14
Rtt103 ChIP-chip from rtt103tap_hrr25is treated with CMK

source_name: Rtt103 input DNA from rtt103tap_hrr25is treated with CMK

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Rtt103-TAP::His3 Hrr25Δ::URA3 pRS315-hrr25-HA (I82G, I23C)

source_name: Rtt103 IP DNA from rtt103tap_hrr25is treated with CMK


title: 2-1 Medium [M5316]

description: Experiment 2 Gene expression after 16 Medium treatment

value: neonatal brain

value: Astrocytes

value: T cell culture medium (complete IMDM),


title: Stroma_ctrl_untx_1

value: cornea


title: hrr25is_DMSO_pThr4

description:
SAMPLE_11
pThr4 ChIP-chip from hrr25is treated with DMSO

source_name: pThr4 input DNA from hrr25is treated with DMSO

source_name: pThr4 IP DNA from hrr25is treated with DMSO


title: WT_CMK_pThr4

description:
SAMPLE_10
pThr4 ChIP-chip from WT treated with CMK

source_name: pThr4 input DNA from WT treated with CMK

value: his3Δ leu2Δ ura3Δ Hrr25Δ::kanMX4 pRS316-HRR25

source_name: pThr4 IP DNA from WT treated with CMK


title: Epi_wound_MMC_2

source_name: Epidermis Wounded MMC

value: Epidermis

value: Wounded


title: Epi_wound_MMC_1

value: MMC


title: Epi_wound_untx_3

source_name: Epidermis Wounded untreated

value: untreated


title: Epi_wound_untx_4


title: Epi_wound_untx_1


title: hrr25is_CMK_Hrr25

description:
SAMPLE_8
Hrr25 ChIP-chip from hrr25is treated with CMK

source_name: Hrr25 input DNA from hrr25is treated with CMK

value: his3Δ leu2Δ ura3Δ Hrr25Δ::kanMX4 pRS315-hrr25-I82G,I23C

source_name: Hrr25 IP DNA from hrr25is treated with CMK

value: HA - ab9110 - Abcam


title: Epi_ctrl_MMC_4

source_name: Epidermis Unwounded MMC

value: Unwounded


title: hrr25is_DMSO_Hrr25

description:
SAMPLE_7
Hrr25 ChIP-chip from hrr25is treated with DMSO

source_name: Hrr25 input DNA from hrr25is treated with DMSO

value: input DNA

source_name: Hrr25 IP DNA from hrr25is treated with DMSO


title: Epi_wound_MMC_4


title: Epi_ctrl_MMC_3


title: WT_DMSO_pThr4

description:
SAMPLE_9
pThr4 ChIP-chip from WT treated with DMSO

source_name: pThr4 input DNA from WT treated with DMSO

source_name: pThr4 IP DNA from WT treated with DMSO

value: pThr4 - 1G7 - gift from Dirk Eick


title: Epi_ctrl_MMC_2


title: Epi_ctrl_MMC_1


title: hrr25is_DMSO_Rpb3

description:
SAMPLE_3
Rpb3 ChIP-chip from hrr25is treated with DMSO

source_name: Rpb3 input DNA from hrr25is treated with DMSO

value: DMSO for 1h

source_name: Rpb3 IP DNA from hrr25is treated with DMSO

value: Rpb3 - 1Y26 - Biolegend


title: WT_DMSO_Hrr25

description:
SAMPLE_5
Hrr25 ChIP-chip from WT treated with DMSO

source_name: Hrr25 input DNA from WT treated with DMSO

source_name: Hrr25 IP DNA from WT treated with DMSO


title: Epi_ctrl_untx_4

source_name: Epidermis Unwounded untreated


title: Epi_ctrl_untx_3


title: Epi_ctrl_untx_2


title: Stroma_ctrl_untx_2

source_name: Stroma Unwounded untreated

value: Stroma


title: Epi_wound_untx_2


title: WT_CMK_Hrr25

description:
SAMPLE_6
Hrr25 ChIP-chip from WT treated with CMK

source_name: Hrr25 input DNA from WT treated with CMK

value: CMK for 1h

source_name: Hrr25 IP DNA from WT treated with CMK


title: Epi_ctrl_untx_1


title: hrr25is_CMK_Rpb3

description:
SAMPLE_4
Rpb3 ChIP-chip from hrr25is treated with CMK

source_name: Rpb3 input DNA from hrr25is treated with CMK

source_name: Rpb3 IP DNA from hrr25is treated with CMK


title: WT_CMK_Rpb3

description:
SAMPLE_2
Rpb3 ChIP-chip from WT treated with CMK

source_name: Rpb3 input DNA from WT treated with CMK

source_name: Rpb3 IP DNA from WT treated with CMK


title: WT_DMSO_Rpb3

description:
SAMPLE_1
Rpb3 ChIP-chip from WT treated with DMSO

source_name: Rpb3 input DNA from WT treated with DMSO

source_name: Rpb3 IP DNA from WT treated with DMSO


title: 5_10_Cd.GeneExp.txt

city: Muenster

first: Ruediger

middle: J

last: Paul

address: Schlossplatz 8

department: Institute of Zoophysiology

institute: University of Muenster

description: 10 µM CdCl2 in the NGM medium for the contrasts 10_Cd_vs_HT115_2 and 10_Cd_vs_0.1_Cd. See additional processed data files.

data_processing:
Using Illumina HiSeq2000 technology, samples were sequenced at the BGI with a minimum of 10 megareads per sample and a sequencing quality of more than 98% clean reads. Sequences were mapped to Wormbase release WS257. Mean expression intensities of genes (i.e., means from the three biological replicates per experimental condition, after checking for substantial deviations between corresponding data; see below) and differential gene expression were calculated with the FPKM method (fragments per kilobase of exon per million fragments mapped) to normalize for sequencing depth and gene length. The NOISeq method was used to determine the threshold of P (diverge probability ≥ 0.8) for the differentially expressed genes (DEGs).
In case of OP50, HT115_2, 0.1 Cd, and 10 Cd, the three biological replicates at each test condition showed a high degree of similarity with regard to the expression intensity of corresponding genes, and mean expression intensities were calculated using the data from all three biological replicates. In case of HT115_1, however, one biological replicate differed significantly from the two others regarding the expression intensity of corresponding genes, and mean expression intensities were calculated here using the data from only two biological replicates.
Genome_build: Wormbase release WS257
Supplementary_files_format_and_content: Tab-delimited text files which include: GeneID: identity of gene; TranscriptID(s): identity of transcript(s); Means: group: mean expression (FPKM) of group; KEGG Orthology: KEGG annotation; GO Component: GO Component annotation; GO Function: GO Function annotation; GO Process: GO Process annotation; Blast nr: NR annotation
Additional processed data files which include: GeneID: identity of gene; geneLength: gene length; Means: groupA: mean expression (FPKM) of groupA; Means: groupB: mean expression (FPKM) of groupB; Ratio(s2/s1): mean expression in two groups [Ratio(s2/s1)]; log2 Ratio(s2/s1): Log2(folds of mean expression in two groups); Probability: probability of significant differential gene expression between two experimental conditions (from NOISeq, diverge probability ≥ 0.8); KEGG Orthology: KEGG annotation; GO Component: GO Component annotation; GO Function: GO Function annotation; GO Process: GO Process annotation; Blast nr: NR annotation
The additional processed data files (linked at the foot of the Series record) are:
A_HT115_1_vs_OP50.GeneExp.txt (2 different E. coli strains as feed)
B_0.1_Cd_vs_HT115_2.GeneExp.txt (0.1 µM CdCl2 vs control)
C_10_Cd_vs_HT115_2.GeneExp.txt (10 µM CdCl2 vs control)
D_10_Cd_vs_0.1_Cd.GeneExp.txt (10 µM CdCl2 vs 0.1 µM CdCl2)

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Worms were incubated for three weeks on NGM plates seeded with E. coli HT115 (HT115_2) suspension and containing 10 µmol/L of CdCl2 (abbr. 10 Cd). The worms were transferred onto new NGM plates twice a week. Subsequently, synchronized L1 larvae were transferred onto 15 different NGM plates per experimental condition.

extract_protocol:
RNAiso-G (Segenetic, Borken, Germany) was added to the samples, before they were frozen in liquid nitrogen. After thermal disruption of worms (liquid nitrogen, 35°C; three repetitions), chloroform extraction on ice (10 min), and centrifugation (12.000 × g, 4°C, 15 min), DNA was digested and RNA purified with a RNase-free DNase set and RNeasy® mini kit (Qiagen, Hilden, Germany). Quality control was performed using an Agilent Bioanalyzer® (Agilent Technologies, Böblingen, Germany). After adding the samples to RNAstableTM matrix (Biomatrica, San Diego, CA, USA) and a subsequent vacuum centrifigution for drying (2 h), the samples from three experimental approaches were sent to the Beijing Genomics Institute (BGI) for RNA-Seq analysis.
RNA libraries were prepared for sequencing using standard Illumina HiSeq2000 protocols.

treatment_protocol: After reaching adulthood, worms were washed off from the NGM plates and cleaned several times using purified water to get rid of bacteria. Five plates per experimental condition were combined to one biological sample. Thus, three biological replicates per experimental condition were further prepared for RNA-Seq.

value: N2 Bristol variety

tag: developmental stage

value: synchronized adult worms

value: 10 µM CdCl2


title: 4_0.1_Cd.GeneExp.txt

description: 0.1 µM CdCl2 in the NGM medium for the contrasts 0.1_Cd_vs_HT115_2 and 10_Cd_vs_0.1_Cd. See additional processed data files.

growth_protocol: Worms were incubated for three weeks on NGM plates seeded with E. coli HT115 (HT115_2) suspension and containing 0.1 µmol/L of CdCl2 (abbr. 0.1 Cd). The worms were transferred onto new NGM plates twice a week. Subsequently, synchronized L1 larvae were transferred onto 15 different NGM plates per experimental condition.

value: 0.1 µM CdCl2


title: 3_HT115_2.GeneExp.txt

description: E. coli strain HT115 (HT115_2) as feed for the contrasts 0.1 µM CdCl2 vs. E.c. HT115_2 (0.1_Cd_vs_HT115_2) and 10 µM CdCl2 vs. E.c. HT115_2 (10_Cd_vs_HT115_2). See additional processed data files.

growth_protocol: Worms were incubated for three weeks on NGM plates seeded with E. coli HT115 suspension (abbr. HT115_2). The worms were transferred onto new NGM plates twice a week. Subsequently, synchronized L1 larvae were transferred onto 15 different NGM plates per experimental condition.

value: E. coli strain HT115 (HT115_2) as feed


title: 1_HT115_1.GeneExp.txt

description: E. coli strain HT115 (HT115_1) as feed for the contrast HT115_1_vs_OP50. See additional processed data files.

growth_protocol: Worms were incubated for three weeks on NGM plates seeded with E. coli HT115 suspension (abbr. HT115_1). The worms were transferred onto new NGM plates twice a week. Subsequently, synchronized L1 larvae were transferred onto 15 different NGM plates per experimental condition.

value: E. coli strain HT115 (HT115_1) as feed


title: 2_OP50.GeneExp.txt

description: E. coli strain OP50 as feed for the contrast HT115_1_vs_OP50. See additional processed data files.

growth_protocol: Worms were incubated for three weeks on NGM plates seeded with E. coli OP50 suspension (abbr. OP50). The worms were transferred onto new NGM plates twice a week. Subsequently, synchronized L1 larvae were transferred onto 15 different NGM plates per experimental condition.

value: E. coli strain OP50 as feed


title: Array14_Rosco_tumor_Apr_25_2015

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

country: Canada

institute: University of Saskatchewan

description: Gene expression: from tumor

hyb_protocol: .5ug of Cy3-labeled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 2.2ul Agilent fragmentation buffer and 11ul of 10X Agilent blocking agent following the manufacturers’ instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Canine Gene Expression Microarray v2 (AMDID 021193) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried for 1min in acetonitrile.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution

data_processing: Data was processed with Agilent Feature Extraction 11.0.1.1.

organism: Canis lupus familiaris

source_name: Canine tumor lymphoma

label_protocol: Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0

growth_protocol: Tumor samples were obtained initially using a biopsy, with repeated samples obtained non-invasively using fine needle aspirates.

extract_protocol: Total RNA quality was assessed with the Agilent 2100 bioanalyzer prior to microarray analysis.  Samples with a RIN value of greater than or equal to 8.0 were deemed to be acceptable for microarray analysis.

tag: subject id

value: Rosco

tag: condition

value: Second original drug resistant lymphoma tumor obtained by FNA

value: Canine tumor lymphoma


title: Array10_Rosco_tumor_remission

description: Gene expression: from remission

source_name: Canine tumor tissue following remission

treatment_protocol: Tumor samples were obtained initially using a biopsy, with repeated samples obtained non-invasively using fine needle aspirates.

value: Drug resistant lymphoma tumor in remission after metformin treatment obtained by fine needle aspirate (FNA)

value: Canine tumor tissue following remission


title: Array11_Rosco_tumor_no_remission1

description: Gene expression: from tumor after failing remission 1

source_name: Canine tumor lymphoma relapse 1

value: FNA aspirate of tumor after metformin, after relapse

value: Canine tumor lymphoma relapse 1


title: Array8_Rosco_tumor_postmortem

description: Gene expression: from tumor post mortem

source_name: Canine tumor lymphoma post mortem

value: Tumor sample retrieved after death

value: Canine tumor lymphoma post mortem


title: Array2_MalcolmX_tumor_after

description: Gene expression: drug resistant tumor

value: MalcolmX

value: Drug resistant lymphoma tumor after metformin treatment obtained by fine needle aspirate (FNA)


title: Array7_Dog_Y_tumor

description: Gene expression: from tumor before treatment

value: Dog Y

value: Original drug resistant lymphoma tumor obtained by biopsy


title: Array15_Thai_tumor_naive

description: Gene expression: from tumor

value: Thai

value: Original drug sensitive lymphoma tumor obtained by biopsy


title: Array3_MalcolmX_tumor_before

description: Gene expression: original drug resistant lymphoid tumor


title: Array4_Jake_tumor

value: Jake


title: Array6_Rosco_tumor


title: Array13_Rosco_tumor_no_remission3

description: Gene expression: from tumor after failing remission 3

source_name: Canine tumor lymphoma relapse 3

value: Third FNA aspirate of tumor after metformin, after relapse

value: Canine tumor lymphoma relapse 3


title: Array1_MalcolmX_control

description: Gene expression: skin biopsy

source_name: Canine control tissue

value: Skin biopsy

value: Canine control tissue (skin)


title: Array12_Rosco_tumor_no_remission2

description: Gene expression: from tumor after failing remission 2

source_name: Canine tumor lymphoma relapse 2

value: Rosco

value: Second FNA aspirate of tumor after metformin, after relapse

value: Canine tumor lymphoma relapse 2


title: Array9_Rosco_tumor_resistant_failed_chop

description: Gene expression: from tumor following restistance

source_name: Canine tumor lymphoma failing chemo

value: FNA of tumor before metformin after failing chemo

value: Canine tumor lymphoma failing chemo


title: OP8

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software was used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.4.4), Trimmomatic (ver. 0.36) and cutadapt (ver. 1.16) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.91) using STAR (ver. 2.6.1a).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.1)
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include featureCount values for each sample

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the Magnosphere™ UltraPure mRNA Purification Kit (Clontech). Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for five days on mNGM plates covered with OP50 (control-fed group) or CBM 588 (CBM 588-fed group).

value: Bristol N2

value: wild-type

tag: Sex

value: hermaphrodite

value: eight-day-old


title: Array5_Rosco_control

description: Gene expression: skin biopsy


title: CBM8

tag: strain

value: CBM 588


title: Control_CMs_day21_1

first: Takeshi

last: Hatani

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: Gene expression at day21 after cardiomyocyte differentiation

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

label_protocol: Manufature's protocol

growth_protocol: For iPSCs, ReproCELL supplemented with bFGF at 37 ºC in a humidified incubator with 5% CO2. For cardiomyocytes, undifferentiated iPSCs were dissociated, and then suspended in StemPro-34 media supplemented with Y-27632 and BMP4, and allowed to form EBs by being placed into 96-well plates. On day 1, media, containing activin A, BMP4 and bFGF, were added into the wells. On day 3, EBs were collected and dissociated, and 20000 cells were put in each 96-wells to form EBs in differentiation media supplemented with VEGF and IWP-3. On day 7, the media were changed to StemPro-34 media supplemented with VEGF and bFGF. For the maintenance of iPSC-CMs, the culture media were exchanged every 2-3 days.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: iPSCs were differentiated to cardiac lineage cells using ActivinA and BMP4. iPSC-derived cardiomyocytes were sorted for EGFP using FACS.

value: iPSC derived cariomyocyte


title: Control_CMs_day21_4


title: Control_CMs_day14_4

description: Gene expression at day14 after cardiomyocyte differentiation


title: Control_CMs_day14_1


title: Control_CMs_day21_3


title: Control_CMs_day7_4

description: Gene expression at day7 after cardiomyocyte differentiation


title: Control_CMs_day14_3


title: Control_CMs_day21_2


title: Control_CMs_day14_2


title: Control_CMs_day7_3


title: Control_iPSCs_1

description: Gene expression before cardiomyocyte differentiation

value: iPS cell


title: Control_iPSCs_4


title: Control_CMs_day7_2


title: APEX2_CMs_day7_1


title: APEX2_CMs_day7_2


title: Control_CMs_day7_1


title: APEX2_CMs_day7_4


title: APEX2_CMs_day14_3


title: APEX2_CMs_day14_4


title: APEX2_CMs_day21_4


title: APEX2_CMs_day14_2


title: APEX2_CMs_day21_3


title: APEX2_CMs_day21_1


title: Control_iPSCs_2


title: Control_iPSCs_3


title: Endo_STZ3

city: New York

first: Chengguo

last: Wei

state: NY

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

description: STZ DM model

data_processing:
The RNA-seq data was analyzed by following the procedure described here. Briefly, after sequence quality filtering at a cutoff of a minimum quality score Q20 in ≥90% bases, the good quality reads were aligned to the University of California Santa Cruz’s Mus musculus reference genome and transcriptome (build mm10) using the Burrows-Wheeler Aligner.43 The reads that are uniquely aligned to the exon and splicing-junction sites for each transcript were combined to calculate as expression level for a corresponding transcript and further normalized based on reads per kilobase per million reads44 in order to compare transcription levels among samples. The transcripts with a low raw read count <100 in all the samples were excluded for downstream analysis. Gene expression value was transformed to the log2 base scale. Principal component analysis was first performed to assess the sample correlations using the expression data of all the genes. The DEGs in diabetic mice versus control mice were identified by the R package DEGseq for sorted GECs, and we selected the genes based on DEGseq adjusted P < 0.05 and 1.5-fold change. The limma test45 was applied for analysis of data in isolated glomeruli with a cutoff of P < 0.05 and 1.5-fold change. The Gene Ontology and pathway analysis for the differentially expressed genes were then performed using INGENUITY IPA (http://www.ingenuity.com/products/ipa) and online tool Enrichr.19 The read coverage of gene functional elements was also visualized by IGV tool (Integrative Genome Viewer; http://www.broadinstitute.org/igv/) from the genome alignment file. Heat map analysis was performed for the top 50 fold-changed DEGs with DEGseq test after median center transformed using Multiple Experiment Viewer (Web MEV) software (mev.tm4.org).46
Genome_build: mm10
Supplementary_files_format_and_content: text file with abundance measurements

source_name: glomerular endothelial cells

extract_protocol: Total RNA was isolated from either isolated glomeruli or sorted GECs by using RNeasy mini kit (74104; Qiagen, Hilden, Germany) according to the manufacturer’s protocol. RNAs of 4 mice were pooled per sample. RNA concentrations were quantified using a NanoDrop Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) at a wavelength of 260 nm. RNA samples were then analyzed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) at a concentration of 100 to 200 ng/μl to verify the concentration and the purity of samples. Only the samples with RNA integrity values >7.5 were used for mRNA sequencing at the CLC Genomics and Epigenomics Core Facility at Weill Cornell Medical College (New York, NY).

treatment_protocol: Glomeruli were isolated by Dynabead perfusion and cells were dissociated as described previously.10 Briefly, animals were perfused with 8-ml bead solution and 2-ml bead solution with enzymatic digestion buffer containing collagenase type II 300 U/ml, pronase E (1 mg/ml), and Dynase I (50 μg/ml), which was prewarmed at 37 °C. At the end of perfusion, kidneys were removed, decapsulated, minced into 1- mm3 pieces, and digested in 3 ml digestion buffer at 37 °C for 15 minutes on a rotator (100 rpm). Digested tissue was then passed through a 100-μm cell strainer and collected by centrifugation. The pellet was resuspended in 2  ml of Hanks buffered salt solution and glomeruli were washed 3 times and collected using a magnet. Separated glomeruli were resuspended in 2 ml digestion buffer and incubated at 37 °C for additional 40 minutes at 1400 rpm/min on a thermomixer. During the digestion period, the solution was vortexed every 10 minutes and sheared with a 27G needle every 15 minutes. The solution was then put on magnetic particle concentrator, and supernatants were pooled. The suspension was sieved through 40-μm cell strainer and centrifuged at 1500 rpm for 5 minutes at 4 °C. After the 2-step approach for primary cell purification, single cells were resuspended in 0.5 ml of Hanks buffered salt solution supplemented with 2% fetal bovine serum, 25 mmol/l N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid and 4',6-diamidino-2-phenylindole. Single-cell suspension was then sorted into EYFP+ and EYFP– population with a BD Aria II cell sorter (BD Biosciences, San Jose, CA) with a laser excitation at 488 nm and a sheath pressure of 30 psi. On average, 200,000 sorted GECs were obtained per mouse.

value: glomerular endothelial cells

value: eNOS-null

value: STZ treatment


title: Endo_STZ1

description: STZ DM model


title: Endo_STZ2

description: STZ DM model


title: APEX2_CMs_day7_3


title: APEX2_CMs_day21_2


title: Endo_Con2

description: Control

value: no treatment


title: Endo_Con3

description: Control


title: Endo_Con1

description: Control


title: APEX2_iPSCs_4


title: APEX2_CMs_day14_1


title: APEX2_iPSCs_2


title: APEX2_iPSCs_1


title: Ezh2KO h3k27me3 rep1

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

data_processing:
Low quality reads were trimmed and filtered with Trimmomatic
Alignment to the mm10 genome was done using Bowtie2
Enriched domains were detected using Macs2
Enriched peaks and domains were detected using hiddenDomains
Peak annotation was created by ChIPseeker
Reads at promoters (+/- 1kb around the most 5' transcription start site) were counted with HTseq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files that contain the enriched peaks and domains

source_name: E14 Embryonic Stem Cells

extract_protocol: ChIP-seq libraries were prepared according to Illumina instructions

value: Ezh2-knock out of exon14

value: E14 Embryonic Stem Cells


title: Ezh2KO Input


title: WT ezh2 rep1


title: Ezh2KO h3k27me3 rep2


title: WT ezh2 rep2


title: WT h3k27me3 rep1


title: WT h3k27me3 rep2


title: APEX2_iPSCs_3


title: Ezh2KO ezh2 rep2


title: Epi_wound_MMC_3

source_name: Epidermis Wounded MMC

value: cornea

tag: tissue compartment

value: Epidermis

value: Wounded

value: MMC


title: WT Inupt


title: H3K27Ac

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Adapter trimming using cutadapt (default parameters for single-end)
Genome alignment using bowtie2 (version 2.2.5) against the mm10 genome build (params: -k 50 --non-deterministic)
Peak calling using MACS2 against input (params: -f BAM -g 1.87e9 -B -p 10e-10 --nomodel)
Genome_build: mm9
Supplementary_files_format_and_content: bed files

source_name: granulosa cells

growth_protocol: 21 days old mice

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Chromatin was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: mice were injected with 5 IU eCG, following by 5 IU hCG after 46 hours. After 6 hours of hCG mice were culled for granulosa cell collection.

value: peri-ovulatory granulosa cells

value: CBA x C57BL/6 F1

tag: age

value: 21 days

value: H3K27ac (39133, Active Motif)


title: Pooled_Input

tag: cell type


title: Foxk1_replicate3_knockdown_RNA-seq

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1KD_r3

data_processing:
Obtained raw reads were aligned using HISAT2 v2.1.0 aligner against mm10 as reference genome with default parameters
Insert size calculations are done using CollectInsertSizeMetrics from Picard v1.141
Quantification for transcripts from GENCODE vM10 was done using featureCounts from Subread v1.5.1 package
Considered only uniquely mapped exonic reads while quantification (mapping quality MAPQ, 40)
Quantified reads are RPKM normalized using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: Matrix containing tab-delimited data includes normalized expression RPKM values for transcripts in each Sample.

source_name: 3T3-L1 adipocytes

growth_protocol: 3T3-L1 cells were growth and differentiated into adipocytes using standard protocol. Differentiation medium contained 1 µM dexamethasone, 0.5 mM isobutyl methylxanthine, 5 µg/ml insulin, 10 µM troglitazone. Cells were cultured in medium containing only 5 µg/ml insulin from day 4. From day 6 the cells were kept in growth medium

extract_protocol:
Total RNA from cells was extracted using TRI reagent and isolated using RNeasy mini kit (Quagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ectopic overexpression or downregulation of Foxk1 and Foxk2 in 3T3-L1 adipocytes

tag: cell line

value: adipocytes

value: Swiss mouse

tag: expression construct

value: Foxk1 shRNA


title: Foxk1_replicate1_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1KD_r1


title: PR4

value: PGR (sc-7208, Santa Cruz)


title: Foxk1_Control_replicate1_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1_ControlKD_r1

value: scrambled shRNA control


title: Foxk1_replicate3_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1OE_r3

value: constituent overexpression of FOXK1


title: Ezh2KO ezh2 rep1

tag: genotype


title: Foxk1_replicate1_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1OE_r1


title: Foxk1_Control_replicate3_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1_ControlOE_r3

value: empty vector control


title: PR1-2


title: RNA-seq_NT-Rep1

first: Mahesh

last: Bachu

email: bmahesh07@gmail.com, bachum@hss.edu

state: New York

address: 535 E 70th St 6th Floor

institute: Hospital For Special Surgery

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using tophat/2.0.13 with the following parameters --no-novel-juncs --b2-sensitive
Read Counts were calculated using Htseq tool (0.7.2)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample.

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEF cells were cultured in 6-well plates in the presence of DMEM containing 10% FBS containing antibiotics and  treated with 100 units/mL of murine recombinant IFNβ (PBL IFN Source) for 6h , and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEF cells were either treated with 100 units/mL of murine recombinant IFNβ (PBL IFN Source) for 6h or left untreated

tag: strain background

value: Murine embryonic fibroblasts (MEFs)

tag: passages

value: wild type

value: none (untreated)

tag: chip antibody


title: Foxk1_replicate2_overexpression_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1OE_r2


title: RNA-seq_NT-Rep2

tag: treatment


title: Foxk1_Control_replicate3_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk1_ControlKD_r3


title: RNA-seq_IFNB-6h-Rep2

value: IFN-Beta


title: RNA-seq_IFNB-6h-Rep1


title: Foxk2_Control_replicate2_knockdown_RNA-seq

description:
Complete_gencode_expression_profile_RPKM_matrix.txt
Foxk2_ControlKD_r2