title: Mouse 4 Thalamus IL-33 pos astrocytes

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

data_processing:
Read quality was assessed using fastqc.
First 5 bases of each read were trimmed and aligned to the Mus Musculus genome (Ensembl GRCm38) using TopHat2 (version 2.0.11) with bowtie2 (version 2.2.3).
TopHat2 was run with the following arguments “--no-coverage-search --segment-length 20 --segment-mismatches 1” with the genes.gtf file from Ensembl GRCm38.
Gene counts were created from the alignment files using htseq-count (version 0.6.1p1) with default parameters.
FPKM values were generated using cuffquant and cuffnorm from the cufflinks suite of software tools. Quantile normalized FPKM values are reported.
From raw count files, DESeq2 was used to detect differentially expressed genes with cooksCutoff=False.
Consensus list of 444 candidates was obtained with the following filters: 1) Significant in the combined differential expression analysis (pAdj<0.01). 2) Moderately expressed (mean FPKM > 20 in at least one condition/region of the IL33-mCherry+ or IL33-mCherry- samples), 3) astrocyte-enriched (2-fold in Aldh1l1+/Aldh1l1- based on an unpublished data set of P9 forebrain astrocytes available upon request).
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with FPKM or DESeq2 output

source_name: Mouse 4 Thalamus IL-33 pos astrocytes

extract_protocol:
FACS isolated IL-33pos/neg astrocytes from thalamus and spinal cord were lysed with RLT+, RNA was isolated using Qiagen RNeasy plus micro kit.
cDNA was made and library prep was performed with NuGEN RNA-Seq V2.

tag: mouse number

value: Thalamus

tag: cell type

value: astrocytes

value: IL-33-mCherry (het)/Aldh1l1-GFP+


title: Mouse 3 Thalamus IL-33 pos astrocytes

status: Public on Feb 05 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Mouse 3 Thalamus IL-33 pos astrocytes

tag: strain

tag: tissue

tag: age

tag: genotype


title: Mouse 3 Spinal cord IL-33 pos astrocytes

value: Spinal cord


title: Mouse 4 Spinal cord IL-33 neg astrocytes


title: Mouse 3 Spinal cord IL-33 neg astrocytes


title: P5A1_ANC-H-un-2

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: Blood per person

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were nomalized by RMA with Parteck Genomic Suit 7.1

label: biotin

organism: Homo sapiens

source_name: human blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tissues from human peripheral blood, granulocytes obtained from density gradient centrifugation (Ficoll), and red cell lysis by ACK lysis buffer

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Two types of samples from individuals with neutrophil counts <1500 as ANC-L and individuals with neutrophil counts >4000 as ANC-H

tag: phenotype

value: ANC-H


title: P8A1_ANC-H-un-3

description: Blood per person


title: DW-M-ANC-H-Un1

description: Blood per person


title: P3A1_ANC-L-un-1

description: Blood per person

value: ANC-L


title: P4A1_ANC-H-un-1

description: Blood per person


title: P18A1_ANC-L-un-2

description: Blood per person


title: Mouse 4 Thalamus IL-33 neg astrocytes

source_name: Mouse 4 Thalamus IL-33 neg astrocytes


title: AK-M-ANC-L-Un4

description: Blood per person


title: MM-M-ANC-L-Un5

description: Blood per person


title: TH-F-ANC-H-Un2

description: Blood per person


title: HY-M-ANC-L-Un3

description: Blood per person


title: Mouse 2 Thalamus IL-33 neg astrocytes

source_name: Mouse 2 Thalamus IL-33 neg astrocytes


title: Mouse 1 Thalamus IL-33 pos astrocytes

source_name: Mouse 1 Thalamus IL-33 pos astrocytes


title: Mouse 2 Spinal cord IL-33 pos astrocytes


title: Mouse 1 Spinal cord IL-33 neg astrocytes


title: Mouse 3 Thalamus IL-33 neg astrocytes

source_name: Mouse 3 Thalamus IL-33 neg astrocytes


title: Mouse 2 Spinal cord IL-33 neg astrocytes


title: Mouse 2 Thalamus IL-33 pos astrocytes

source_name: Mouse 2 Thalamus IL-33 pos astrocytes


title: CJ-F-ANC-L-Un1

description: Blood per person


title: Mouse 1 Thalamus IL-33 neg astrocytes

source_name: Mouse 1 Thalamus IL-33 neg astrocytes


title: Mouse 1 Spinal cord IL-33 pos astrocytes


title: CG-F-ANC-L-Un2

description: Blood per person


title: Naïve T-injected moderately inflamed colon tissue, biological rep1

city: CAMBRIDGE

first: Jesse

last: Lyons

state: Ma

address: 77 Massachusetts Ave 16-343

department: Bioengineering

institute: Massachusetts Institute of Technology

description: Gene expression data from moderately inflamed colons

hyb_protocol: Following labeling, biotinylated cRNA was hybridized to the Mouse Genome 430 2.0 GeneChips®  for 16 hr at 45C in an Affymetrix HybridizationOven 645. GeneChips® were washed and stained in the Affymetrix Fluidics Station 450 using the GeneChip® Hybridization, Wash, and Stain Kit.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the Affymetrix expression console with RMA processing.

source_name: colon tissue from Naïve T-injected mice

label_protocol: The targets were prepared using the Affymetrix 3'IVT assay and labeled by biotinylation.

growth_protocol: Animals were injected with Tregs or naïve T cells at 10 weeks of age and sacrificed 2-3 months after injection.

treatment_protocol: Colons were excised and distal colon tissue (from rectum to proximal/distal junction) was snap frozen.

value: colon

tag: injected cell type

value: Naïve T

value: 4-5 mos

tag: inflammation level

value: moderate


title: EVSAT_siCtrl_BV6_rep1

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

description:
EVSAT 1 siCtrl BV6
Array ID: 200155180027

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

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

growth_protocol: Cell were grown in DMEM (Dulbecco´s modified eagle medium, Life Technologies Inc) supplemented with 10% FCS (Biochrom), 1% penicillin/streptomycin (Invitrogen) and 1% Sodium pyruvate (Invitrogen) at 37°C, 5% CO2. Identity of cell lines was verified by authentication at DSMZ

extract_protocol: Total RNA was isolated using the PeqGold total RNA kit and the PeqGOLD DNAse digest kit (Peqlab Biotechnologie GmbH) according to the manufacturer’s protocol.

treatment_protocol: Cells were transfected with 5nM control siRNA or siRNA directed at TNFR1 for 36hrs using Lipofectamine RNAiMax (invitrogen), then treated with 5nM BV6 (EVSA-T) or 50nM BV6 (MDA-MB-231) for 9hrs. For kinetic MDA-MB-231 were treated with 50nM BV6 for 3, 6, 9, 12, or 15 hours.

tag: cell line

value: EVSA-T

tag: sirna

value: control

tag: treatment

tag: time after stimulation

tag: replicate


title: EVSAT_TNFR1_UT_rep2

description:
EVSAT 2 siTNFR1 UT
Array ID: 200155180027


title: EVSAT_TNFR1_UT_rep1

description:
EVSAT 1 siTNFR1 UT
Array ID: 200155180027


title: MDA_BV6_9h_rep2

description:
MDA 2 BV6 9h
Array ID: 200155180027


title: MDA_BV6_15h_rep2

description:
MDA 2 BV6 15h
Array ID: 200155180027


title: MDA_BV6_6h_rep1

description:
MDA 1 BV6 6h
Array ID: 200144140172


title: MDA_BV6_12h_rep2

description:
MDA 2 BV6 12h
Array ID: 200155180027


title: EVSAT_siCtrl_BV6_rep2

description:
EVSAT 2 siCtrl BV6
Array ID: 200155180027


title: MDA_UT_15h_rep2

description:
MDA 2 UT 15h
Array ID: 200144140172


title: EVSAT_siCtrl_UT_rep1

description:
EVSAT 1 siCtrl UT
Array ID: 200155180027


title: MDA_TNFR1_BV6_rep3

description:
siTNFR1_BV6_3
Array ID: 9985187158


title: MDA_BV6_3h_rep2

description:
MDA 2 BV6 3h
Array ID: 200144140172


title: MDA_BV6_12h_rep1

description:
MDA 1 BV6 12h
Array ID: 200144140172


title: MDA_UT_0h_rep1

description:
MDA 1 UT 0h
Array ID: 200144140172


title: MDA_TNFR1_UT_rep3

description:
siTNFR1_UT_3
Array ID: 9985187158


title: MDA_BV6_9h_rep1

description:
MDA 1 BV6 9h
Array ID: 200144140172


title: MDA_UT_15h_rep1

description:
MDA 1 UT 15h
Array ID: 200144140172


title: MDA_BV6_6h_rep2

description:
MDA 2 BV6 6h
Array ID: 200155180027


title: MDA_UT_9h_rep1

description:
MDA 1 UT 9h
Array ID: 200144140172


title: EVSAT_siCtrl_UT_rep2

description:
EVSAT 2 siCtrl UT
Array ID: 200155180027


title: MDA_UT_9h_rep2

description:
MDA 2 UT 9h
Array ID: 200144140172


title: MDA_IRF1_BV6_rep3

description:
siIRF1_BV6_3
Array ID: 9985187158


title: EVSAT_TNFR1_BV6_rep2

description:
EVSAT 2 siTNFR1 BV6
Array ID: 200155180027


title: MDA_BV6_3h_rep1

description:
MDA 1 BV6 3h
Array ID: 200144140172


title: EVSAT_TNFR1_BV6_rep1

description:
EVSAT 1 siTNFR1 BV6
Array ID: 200155180027


title: MDA_UT_0h_rep2

description:
MDA 2 UT 0h
Array ID: 200144140172


title: MDA_BV6_15h_rep1

description:
MDA 1 BV6 15h
Array ID: 200144140172


title: MDA_IRF1_UT_rep3

description:
siIRF1_UT_3
Array ID: 9985187158


title: MDA_RELA_UT_rep3

description:
sip65_UT_3
Array ID: 9985187158

value: RELA


title: Aldh1l1-GFP+ astrocytes from IL-33 WT replicate 1

data_processing:
Read quality was assessed using fastqc.
First 5 bases of each read were trimmed and aligned to the Mus Musculus genome (Ensembl GRCm38) using TopHat2 (version 2.0.11) with bowtie2 (version 2.2.3).
TopHat2 was run with the following arguments “--no-coverage-search --segment-length 20 --segment-mismatches 1” with the genes.gtf file from Ensembl GRCm38.
Gene counts were created from the alignment files using htseq-count (version 0.6.1p1) with default parameters.
From raw count files, DESeq2 was used to detect differentially expressed genes with cooksCutoff=False and (pAdj<0.05) as significant.
FPKM values were generated using cuffquant and cuffnorm from the cufflinks suite of software tools. Quantile normalized FPKM values are reported.
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with FPKM and DESeq2 output

source_name: Aldh1l1-GFP+ astrocytes from IL-33 WT

extract_protocol:
RNA was extracted from FACS sorted astrocytes and microglia using TRIZOL reagent (Invitrogen), DNAse digested to remove genomic DNA contamination, and further purified using the RNAeasy Kit (Qiagen).
cDNA was made and library prep was performed with NuGEN RNA-Seq V2.

value: IL-33 WT


title: MDA_siCtrl_UT_rep3

description:
siCtrl_UT_3
Array ID: 9985187158


title: MDA_TNFR1_BV6_rep2

description:
siTNFR1_BV6_2
Array ID: 9985187158


title: CD11b+ microglia from IL-33 WT replicate 1

source_name: CD11b+ microglia from IL-33 WT

value: microglia


title: Aldh1l1-GFP+ astrocytes from IL-33 WT replicate 2


title: Aldh1l1-GFP+ astrocytes from IL-33 WT replicate 3


title: CD11b+ microglia from IL-33 WT replicate 2


title: CD11b+ microglia from IL-33 KO replicate 3

source_name: CD11b+ microglia from IL-33 KO

value: IL-33 KO


title: MDA_RELA_BV6_rep3

description:
sip65_BV6_3
Array ID: 9985187158


title: MDA_IRF1_BV6_rep2

description:
siIRF1_BV6_2
Array ID: 9985187158


title: CD11b+ microglia from IL-33 KO replicate 2


title: MDA_siCtrl_BV6_rep3

description:
siCtrl_BV6_3
Array ID: 9985187158


title: CD11b+ microglia from IL-33 KO replicate 1


title: CD11b+ microglia from IL-33 WT replicate 3


title: MDA_siCtrl_BV6_rep2

description:
siCtrl_BV6_2
Array ID: 9985187138


title: MDA_RELA_BV6_rep1

description:
sip65_BV6_1
Array ID: 9985187138


title: MDA_TNFR1_UT_rep1

description:
siTNFR1_UT_1
Array ID: 9985187138


title: MDA_TNFR1_BV6_rep1

description:
siTNFR1_BV6_1
Array ID: 9985187138


title: MDA_RELA_BV6_rep2

description:
sip65_BV6_2
Array ID: 9985187138


title: MDA_siCtrl_UT_rep1

description:
siCtrl_UT_1
Array ID: 9985187138


title: MDA_IRF1_UT_rep2

description:
siIRF1_UT_2
Array ID: 9985187158


title: MDA_IRF1_UT_rep1

description:
siIRF1_UT_1
Array ID: 9985187138


title: MDA_RELA_UT_rep2

description:
sip65_UT_2
Array ID: 9985187138


title: MDA_IRF1_BV6_rep1

description:
siIRF1_BV6_1
Array ID: 9985187138


title: MDA_siCtrl_UT_rep2

description:
siCtrl_UT_2
Array ID: 9985187138


title: MDA_TNFR1_UT_rep2

description:
siTNFR1_UT_2
Array ID: 9985187158


title: MDA_RELA_UT_rep1

description:
sip65_UT_1
Array ID: 9985187138


title: MDA_siCtrl_BV6_rep1

description:
siCtrl_BV6_1
Array ID: 9985187138


title: Aldh1l1-GFP+ astrocytes from IL-33 KO replicate 3

source_name: Aldh1l1-GFP+ astrocytes from IL-33 KO


title: Aldh1l1-GFP+ astrocytes from IL-33 KO replicate 4


title: Aldh1l1-GFP+ astrocytes from IL-33 KO replicate 2


title: Aldh1l1-GFP+ astrocytes from IL-33 KO replicate 1


title: iBrca2 iWapl BG3 replicate 2

status: Public on Feb 04 2018

city: Saint Louis

first: Dale

last: Dorsett

state: MO

address: 1100 South Grand Boulevard

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using the default settings
Alignment to Drosophila melanogaster genome sequence was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
The total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Expression values in RNAi-treated BG3 replicates were averaged and compared to the average of six mock treated BG3 replicates published in Pherson et al. 2017 Sci Adv 3:e1700944 [GSE100548 (GSM2686307, GSM2686308, GSM2686309, GSM2686310, GSM2686311, GSM2686312)]. Expression values in wing discs with mutant brca2 alleles (brca2[56e/ko], brca2[ko]) were averaged and compared to the averaged expression values from wing discs with wild type brca2 alleles (Canton S, y w).
Genome_build: Drosophila melanogaster release 5 (April 2006) with chrU and U_extra sequences removed
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of all annotated genes and statistical comparison of expression in RNAi treated cells to mock RNAi control cells and between wing discs with wild type brca2  to wing discs with mutant brca2 (brca2[56e/ko], brca2[ko]).

organism: Drosophila melanogaster

source_name: ML-DmBG3-c2 cultured cells

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin. Drosophila were grown at 25 degrees on cornmeal-molasses-yeast based food.

extract_protocol:
Total RNA was extracted using the Zymo Research Quick-RNA MicroPrep Kits with DNaseI treatment following the manufacturer's directions.
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total v2 kits (Life Technologies) according to the manufacturer's directions.

treatment_protocol: For RNAi treatment of BG3 cells, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

tag: RNAi treatment

value: Brca2 Wapl

value: CNS-derived cell-line


title: yw wing disc replicate 2

source_name: third instar larval wing discs

value: wild type

value: wing disc


title: Wapl mock replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Wapl.BG3.mock.log.enrichment.sgr

library_source: genomic

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using default settings
Aligmentment to the Drosophila release 5 genome sequence was performed using the TMAP map4 algorithm without soft clipping (-g 3 option)
Genome coverage at each base pair for Input and each ChIP sample was calcluted using BEDtools genomecoveragebed (-d option)
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts as described in Dorsett and Misulovin Methods Mol Biol. 2017;1515:125-139. Input file used for each sample is indicated above. Coverage in each window was normalized to total genome coverage prior to normalization to Input.
ChIP enrichment was averaged for all replicates to generate final processed data files
Genome_build: Drosophila melanogaster Release 5 (April 2006) with ChrU and Uextra removed
Supplementary_files_format_and_content: sgr text graph file with ChIP enrichment averaged for all replicates. These files are available in a tar archive on the series record.

molecule: genomic DNA

growth_protocol: BG3 cells were cultured in Schneider's media with 10% FCS and 10 μg per ml insulin.

extract_protocol:
BG3 cells were grown to a concentration of 5E6 per mL, then crosslinked by addition of 36% formaldehyde directly to the cell culture media to a final concentration of 1%, and incubation for 10 minutes at room temperature on a rocking platform. The reaction was stopped by addition of glycine pH 7.0 to a final concentration of 0.125 M. Cells were washed once with 1x PBS and once each with Wash Buffers A (10 mM HEPES pH 7.6; 10 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.25% Triton X100) and B (10 mM HEPES pH 7.6; 200 mM NaCl; 1 mM EDTA pH 8.0; 0.5 mM EGTA pH 8.0; 0.01% Triton X-100) for 10 minutes each. Cells were resuspended in sonication buffer to a concentration of 1x109/3 mL, and sonicated using a BioRuptor Sonicator for 14-20 cycles of 30 s on, 30 s off. Na-lauroylsarcosine was added to 0.5% and incubated for 10 minutes, rotating. Chromatin was centrifuged at 12,000g for 5 minutes at 4°C to pellet insoluble material, and 200 uL chromatin aliquots, each representing ~50x106 cells, were snap frozen on dry ice. For immunoprecipitation, aliquots of chromatin (10 - 20 x 106 BG3 cells) were adjusted to RIPA buffer in a final volume of 500 μL. Adjusted chromatin was pre-cleared for 2 hours with Protein A agarose beads, then incubated with primary antibody overnight at 4°C. Antibody-chromatin complexes were pulled down by incubation with Protein A agarose beads for 4 hours at 4°C, and beads were washed consecutively with RIPA, LiCl buffer, and TE. Samples were treated with RNAse A for 30 minutes at 37°C, then DNA crosslinks were reversed by overnight treatment at 65°C with Proteinase K, and DNA was recovered using Qiagen MinElute columns or phenol/choloroform extraction and ethanol precipitation.
Ion Torrent IonXpress barcoded sequencing libraries were constructed using the Ion Xpress Plus Fragment Library Kit (Life Technologies) according to the manufacturer's directions except that size selection was performed using Beckman Agencourt magnetic beads.

treatment_protocol: For RNAi, media was replaced with 1 ml of Express Five SFM (Invitrogen) with 1% FCS, (and 10 μg per ml insulin for BG3 cells), for 3 hours. For RNAi of all factors, from 0.7 to 40 μg of dsRNA was added per well of a 6-well plate. Media was adjusted to 3 ml and 10% FCS with Schneider's media after 2 hrs of RNAi treatment. Cells were replated as needed. Templates for dsRNA synthesis were made by PCR from cDNA or genomic DNA templates using primers with T7 promoters. In most experiments, equal amounts of two dsRNAs against each target were used. Both individual dsRNAs knocked down the targets, but knockdown was generally more efficient with a mixture. Templates were designed to avoid off-target matches of ≥19 nucleotides using Drosophila RNAi Screening Center (http://www.flyrnai.org/) online tools.

tag: antibody

value: Wapl

tag: antibody source

value: Judy Kassis, NICHD


title: iPds5 BG3 replicate 1


title: GSM2686223_re-used_input


title: yw wing disc replicate 3


title: GSM2224492_re-used_input


title: Mock Replicate 2_RNA-seq

value: Mock


title: Wapl iPds5 replicate 1

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Wapl.BG3.iPds5.log.enrichment.sgr


title: GSM2224493_re-used_input


title: Wapl iBrca2 replicate 2

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Wapl.BG3.iBrca2.log.enrichment.sgr


title: Wapl iPds5 replicate 2


title: Wapl mock replicate 1


title: Mock Replicate 3_RNA-seq


title: SA iWapl replicate 5

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
SA.BG3.iWapl.log.enrichment.sgr

value: SA

value: Dale Dorsett


title: SA iWapl replicate 3


title: SA iWapl replicate 6


title: SA iWapl replicate 7


title: Wapl iBrca2 replicate 1


title: SA iPds5 replicate 3

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
SA.BG3.iPds5.log.enrichment.sgr


title: SA iPds5 replicate 2


title: SA iWapl replicate 1


title: SA iWapl replicate 4


title: SA iPds5 replicate 1


title: SA iWapl replicate 2


title: SA iPds5 iWapl replicate 3

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
SA.BG3.iPds5.iWapl.log.enrichment.sgr


title: SA iPds5 iBrca2 replicate 2

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
SA.BG3.iPds5.iBrca2.log.enrichment.sgr


title: Mouse 4 Spinal cord IL-33 pos astrocytes

tag: mouse number

value: Spinal cord

value: astrocytes

value: IL-33-mCherry (het)/Aldh1l1-GFP+


title: Rad21 mock replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Rad21.BG3.mock.log.enrichment.sgr


title: SA iBrca2 replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
SA.BG3.iBrca2.log.enrichment.sgr


title: SA iBrca2 replicate 1


title: SA iPds5 iBrca2 replicate 1


title: Pds5 iWapl replicate 1

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Pds5.BG3.iWapl.log.enrichment.sgr


title: Pds5 mock replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Pds5.BG3.mock.log.enrichment.sgr


title: SA iPds5 iWapl replicate 2


title: Rad21 iPds5 replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Rad21.BG3.iPds5.log.enrichment.sgr


title: Pds5 mock replicate 5

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Pds5.BG3.mock.log.enrichment.sgr


title: Pds5 iWapl replicate 3


title: Pds5 mock replicate 4


title: Pds5 mock replicate 1


title: Rad21 iPds5 replicate 1


title: SA iPds5 iWapl replicate 1


title: Pds5 iNipped-B replicate 3

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Pds5.BG3.iNipB.log.enrichment.sgr


title: Rad21 mock replicate 1


title: Pds5 mock replicate 3


title: Pds5 iNipped-B replicate 1


title: Pds5 iWapl replicate 2


title: Pds5 iRad21 replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Pds5.BG3.iRad21.log.enrichment.sgr


title: Pds5 iRad21 replicate 3


title: Pds5 iNipped-B replicate 2


title: Nipped-B iWapl replicate 2

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
NipB.BG3.iWapl.log.enrichment.sgr

value: Nipped-B


title: Pds5 iBrca2 replicate 2

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Pds5.BG3.iBrca2.log.enrichment.sgr


title: Nipped-B iWapl replicate 1


title: Pds5 iBrca2 replicate 1


title: Nipped-B iPds5 replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
NipB.BG3.iPds5.log.enrichment.sgr


title: Pds5 iRad21 replicate 1


title: Nipped-B iPds5 replicate 3


title: Brca2 mock replicate 2

description:
normalization input samples:
GSE100548, GSM2686223
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Brca2.BG3.mock.log.enrichment.sgr


title: Brca2 iPds5 replicate 2

description:
normalization input samples:
GSE83959, GSM2224492, GSM2224493
For completeness, these input samples are available in this series as GSM2941913 (GSM2224492), GSM2941914 (GSM2224493), and GSM2941915 (GSM2686223).
processed data file:
Brca2.BG3.iPds5.log.enrichment.sgr


title: Brca2 mock replicate 1


title: Brca2 iPds5 replicate 1


title: Nipped-B iPds5 replicate 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 4µM, 24mM HU, replicate 1, dye-swap 1

type: genomic

city: Bordeaux

first: Pei-Yun Jenny

last: Wu

address: 1 Rue Camille Saint Saens

country: France

institute: Institute of Biochemistry and Cellular Genetics

hyb_protocol: Labeled samples from before and after S phase entry were added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18-21 hours, and washes were performed for 5 min at room temperature (wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine (twice), wash 2: 0.06x SSPE).

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1).

label: Alexa 555

organism: Schizosaccharomyces pombe

source_name: Cdc13-Cdc2, G1 block

label_protocol: Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) with either Alexa 555 or Alexa 647 dyes.

growth_protocol: Cdc13-Cdc2 cells were grown in EMM6S at 32°C, synchronized in G2 by adding 1µM 3-MBPP1 for 2 h 45 min, treated with 2µM 3-MBPP1 16 min after the release from the G2 block for 30 min and then subsequently treated with 20µM inhibitor for 150min, resulting in a long G1 block. Cells were then released by washing off the inhibitor with EMM6S containing various concentrations inhibitor: 1, 2.5, 4 or 6 µM.

extract_protocol: Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987.

treatment_protocol: Cells were treated with 24 mM hydroxyurea (HU) 10 min before the release. Cells were harvested at the time of release as well as during S phase: 1µM, 30 min after release; 2.5µM, 40 min after release; 4µM, 45 min after release; 6µM, 60 min after release.

tag: strain/background

tag: cell type

tag: phase

value: G1 block

tag: time

value: 0 (unreplicated)

label: Alexa 647

source_name: Cdc13-Cdc2, G1 block - S phase

value: G1 block - S phase

value: 45 min (S phase)


title: Origin mapping Cdc13-Cdc2, G2B, 24mM HU, 70min, replicate 2, dye-swap 2

hyb_protocol: Labeled samples from before and after S phase entry were added to hybridization buffer (50 mM MES pH 6.7, 500 mM NaCl, 6 mM EDTA, 0.5% Sarcosine, 30% Formamide, 1.5 ng/µl herring sperm DNA, 0.8 µg/µl yeast tRNA, 0.05µg/µl Cot1 DNA). Samples were incubated in an Agilent hybridization oven at 42ºC for 18-21 hours, and washes were performed for 5 min at room temperature (wash 1: 6xSSPE, 0.005% N-Lauroylsarcosine (twice), wash 2: 0.06x SSPE)

data_processing: Agilent Feature Extraction Software (v 8.5.1.1)

source_name: G2 block

label_protocol: Genomic DNA samples were labeled using the BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen) with either Alexa 555 or Alexa 647 dyes

growth_protocol: Cells were grown in EMM6S at 32°C, treated with 1µM 3-MBPP1 for 2 h 45 min, which results in G2 arrest, then synchronously re-entered in cell cycle by washing off the inhibitor through filtration with EMM6S.

extract_protocol: Genomic DNA extraction was performed as in Hoffman and Winston, Gene, 1987

treatment_protocol: Cells were treated with 24mM hydroxyurea (HU) 10 min after the release for Cdc13-Cdc2 cells arrested in G2. Cells were harvested at the time of release as well as during S phase: 60 minutes after addition of HU.

tag: strain

value: G2 block

value: Time 0 (unreplicated)

source_name: G2 block - S phase

value: G2 block - S phase

value: Time 70 min (S phase)


title: Origin mapping Cdc13-Cdc2, G2B, 24mM HU, 70min, replicate 1, dye-swap 2


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 2.5µM, 24mM HU, replicate 2, dye-swap 1

value: 40 min (S phase)


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 4µM, 24mM HU, replicate 2, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 2.5µM, 24mM HU, replicate 1, dye-swap 2


title: Origin mapping Cdc13-Cdc2, G2B+30, 24mM HU, 100min, replicate 1, dye-swap 2

treatment_protocol: Cells were treated with 24mM hydroxyurea (HU) 10 min after the release for Cdc13-Cdc2 cells arrested in G2. Cells were harvested at the time of release as well as during S phase: 90 minutes after addition of HU.

value: Time 100 min (S phase)


title: Origin mapping Cdc13-Cdc2, G2B+30, 24mM HU, 100min, replicate 1, dye-swap 1


title: Origin mapping Cdc13-Cdc2, G2B, 24mM HU, 70min, replicate 2, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 4µM, 24mM HU, replicate 1, dye-swap 2


title: Origin mapping Cdc13-Cdc2, G2B+30, 24mM HU, 100min, replicate 2, dye-swap 1


title: Origin mapping Cdc13-Cdc2, G2B, 24mM HU, 70min, replicate 1, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 4µM, 24mM HU, replicate 2, dye-swap 2


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 1µM, 24mM HU, replicate 2, dye-swap 2

value: 30 min (S phase)


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 6µM, 24mM HU, replicate 2, dye-swap 1

value: 60 min (S phase)


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 6µM, 24mM HU, replicate 1, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 2.5µM, 24mM HU, replicate 1, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 1µM, 24mM HU, replicate 1, dye-swap 2


title: Origin mapping Cdc13-Cdc2, G2B+30, 24mM HU, 100min, replicate 2, dye-swap 2


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 6µM, 24mM HU, replicate 2, dye-swap 2


title: G1_15_Replicate1

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1)

label_protocol: RNA was amplified and labeled as described in Wu, Nurse 2014. Labelling was performed with Cy3/Cy5 dyes (using the Amersham CyDye Post-Labelling Reactive Dye pack).

growth_protocol: S. pombe cells were grown to exponential phase in EMM6S at 32˚C. Synchronization was performed in cells operating with the analog-sensitive CDK fusion protein (Cdc13-Cdc2) .

extract_protocol: RNA extraction as described

treatment_protocol: For the G2 block, cells were treated with 1μM 3-MBPP1 for 2h45 min . For the G1 +15 minutes extension, cells were synchronized as in the G2 block, and then treated with 2μM 3-MBPP1 16 min after the release from the G2 block. This treatment arrests cells in G1. The release from the G1 arrest was achieved by washing off the inhibitor after 30 min of treatment (which corresopnds to a 15 min extension of G1). 3-MBPP1 inhibitor was washed out by rapid filtration of the cultures.

tag: sample type

value: input

tag: Stage

value: IP


title: G2B_Replicate2


title: Origin mapping Cdc13-Cdc22, G1 delay 15 min, 24mM HU, replicate 2, dye-swap 2

growth_protocol: Cdc13-Cdc2 cells were grown in EMM6S at 32°C, synchronized in G2 by adding 1µM 3-MBPP1 for 2 h 45 min and then treated with 2µM 3-MBPP1 16 min after the release from the G2 block, resulting in G1 arrest. Cells were then released by washing off the inhibitor with EMM6S, 20 or 30 min after addition of 2µM 3-MBPP1, corresponding respectively to 5 and 15 min G1 delay.

treatment_protocol: Cells were treated with 24 mM hydroxyurea (HU) 10 min before the release. Cells were harvested at the time of release as well as during S phase: 60 minutes after release.


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 6µM, 24mM HU, replicate 1, dye-swap 2


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 1µM, 24mM HU, replicate 2, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 2.5µM, 24mM HU, replicate 2, dye-swap 2


title: G1_15_Replicate2


title: Origin mapping Cdc13-Cdc22, G1 delay 165 min, release in 1µM, 24mM HU, replicate 1, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 15 min, 24mM HU, replicate 2, dye-swap 1


title: G2B_Replicate1


title: BJ H3K27ac Unind Rep2

status: Public on Feb 03 2018

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

data_processing:
Sequencing read were aligned to human genome (hg19) using bowtie with default parameters
Peaks for TF ChIPs were called using MACS2 and IDR framework.
IDR called FOXA2 peaks from several tissues were further processed using in-house pipeline. Peaks from different cells were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for all TFs, histone marks as well as ATAC signal
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with coordinates and RPKM.

source_name: BJ Fibroblasts

growth_protocol: Clonal FOXA2 doxycycline inducible cells lines were derived from an immortalized BJ foreskin fibroblast cell line from ATCC (BJ-5ta; CRL-4001).  Cells were cultured in MEM-Alpha (Life technologies: 32561-037) with 10% FBS, 1% pen-strep, .01mg/mL hygromycin B and 5ng/mL bFGF.  Derived BJFOXA2 lines were grown in the same conditions plus .5ug/mL Puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

treatment_protocol: To induce FOXA2, doxycycline was added at .5ug/mL. Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night.

value: BJ Fibroblast

tag: chip antibody

tag: chip antibody info.

value: Active Motif, 39133


title: BJ H3K27ac Unind Rep1

tag: cell line


title: BJ_ChIP_FOXA2_Unind


title: BJ_FOXA2_Mimo_Release


title: BJ_ChIP_FoxHnf1aCoExp_FOXA2


title: BJ_ChIPBS_FOXA2_WT


title: BJ_ChIPBS_FOXA2_DeltaN_Rep2


title: BJ H3K27me3 Unind Rep1

value: Active Motif, 39155


title: BJ_ChIPBS_FOXA2_DeltaN_Rep1


title: BJ_ChIPBS_FOXA2_DeltaC_Rep2


title: Origin mapping cdc25-22, 12mM HU, replicate 2, dye-swap 2

source_name: cdc25-22, G2 block

growth_protocol: cdc25-22: cells were grown in EMM6S to exponential phase at 25ºC, shifted to 36.5ºC for 4 h to arrest cells in G2, then returned to 25ºC for synchronous mitotic cycles. Cdc13-Cdc2: cells were grown in EMM6S at 32°C, treated with 1µM 3-MBPP1 for 2 h 45 min, which results in G2 arrest, then synchronously re-entered in cell cycle by washing off the inhibitor through filtration with EMM6S.

treatment_protocol: Cells were treated with 12 mM hydroxyurea (HU) at the time of release from restrictive temperature for cdc25-22 or 10 min after the release for Cdc13-Cdc2 cells arrested in G2. Cells were harvested at the time of release as well as during S phase: cdc25-22, 90 minutes after return to permissive temperature; Cdc13-Cdc2, 60 minutes after addition of HU.

source_name: cdc25-22, G2 block - S phase

value: 90 min (S phase)


title: Origin mapping Cdc13-Cdc22, G1 delay 15 min, 24mM HU, replicate 1, dye-swap 1

value: G1 block

value: 0 (unreplicated)


title: Origin mapping cdc25-22, 12mM HU, replicate 1, dye-swap 2


title: Origin mapping Cdc13-Cdc2, 12mM HU, replicate 2, dye-swap 1

source_name: Cdc13-Cdc2, G2 block

source_name: Cdc13-Cdc2, G2 block - S phase

value: 70 min (S phase)


title: Origin mapping Cdc13-Cdc22, G1 delay 15 min, 24mM HU, replicate 1, dye-swap 2

value: G1 block - S phase


title: Origin mapping Cdc13-Cdc2, 12mM HU, replicate 2, dye-swap 2

value: G2 block


title: Origin mapping Cdc13-Cdc2, 12mM HU, replicate 1, dye-swap 1

value: G2 block - S phase


title: Origin mapping Cdc13-Cdc22, G1 delay 5 min, 24mM HU, replicate 1, dye-swap 2


title: Origin mapping cdc25-22, 12mM HU, replicate 2, dye-swap 1


title: BJ H3K27me3 Unind Rep2


title: BJ H3K4me2 Unind Rep2

value: Active Motif, 39141


title: BJ H3K4me2 Unind Rep1


title: BJ_WCE_Rep1


title: BJ_FOXA2_Mimo


title: BJ_FOXA2CDT1_Mimo_FOXA2


title: BJ_H3K27me3_1dFOXA2_Rep1


title: Origin mapping Cdc13-Cdc22, G1 delay 5 min, 24mM HU, replicate 1, dye-swap 1


title: Origin mapping Cdc13-Cdc22, G1 delay 5 min, 24mM HU, replicate 2, dye-swap 2

source_name: G1 block

value: Time 0 (unreplicated)

source_name: G1 block - S phase

value: Time 60 min (S phase)


title: hESC_ATAC

source_name: hESC

extract_protocol:
Tagmentation was performed on whole nuclei at 37C for 45 minutes as previously described in (Buenrostro et al., 2013).  DNA was isolated on PCR min-elute columns (Qiagen) and a small amount of the DNA was amplified for 9, 12 and 15 cycles to determine optimal cycling conditions.
Nextera amplified

treatment_protocol: To induce FOXA2, doxycycline was added at .5ug/mL. Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night. For Co-expression we infected BJFOXA2 with a second lentiviral construct containing constitutively expressed V5-tagged GATA4, induced simultaneous expression of both factors.

tag: cell line background

value: immortalized BJ foreskin fibroblast cell line

tag: genotype/variation

value: wildtype


title: Origin mapping Cdc13-Cdc2, 12mM HU, replicate 1, dye-swap 2


title: BJ_ChIPBS_FOXA2_DeltaC_Rep1


title: BJ_H3K27me3_1dFOXA2_Rep2


title: BJ_ChIP_cTermCDT1_FOXA2_Rep3


title: A549_WCE_Rep1


title: P21_4

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description: single cell isolation by Indrops

data_processing: Transcripts were processed according to the pipeline in Macosko et al. (2015). Briefly, this pipeline was used to build a custom transcriptome from Ensembl GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1, after filtering the annoatation gtf file (gencode.v17.annotation.gtf filtered for feature_type=îgeneî, gene_type="protein_coding" and gene_status="KNOWN"). Read quality control and mapping against this transcriptome was performed. Unique molecular identifiers (UMIs) were used to link sequence reads back to individual captured molecules. All steps of the pipeline were run using default parameters unless explicitly stated.

source_name: Lateral geniculte nucleus

extract_protocol:
Mice were euthanized on postnatal days 5, 10, 16, and 21. Each time point includes data from eight mice total processed as four independent samples of two mice each.  After isoflurane anesthetization, mice were decapitated and the brain was isolated. Mouse brains were dissected and 300 _m coronal sections were made on a Leica VT1000S vibratome. The dorsal LGN were then microdissected in ice cold PBS after visual identification using a Nikon SMZ-10A brightfield dissection microscope. LGNs from four animals were pooled to create one replicate per time point. LGN tissue was transferred to dissociation media: HBSS (Life Technologies), 10mM HEPES (Sigma), 172mg/l kynurenic acid (Sigma), 0.86 g/l MgCl2o6H2O (Sigma), 6.3 g/l D-glucose (Sigma). This solution was saturated with 95% oxygen and 5% CO2 and was pH adjusted to 7.35 prior to use. Papain (20U/ml, Worthington), Pronase from Streptomyces griseus (1 mg/ml, Sigma), proteinase XXIII from Aspergillus melleus (3 mg/ml, Sigma) and DNAse (2mg/ml, Worthington) were added to the dissociation media. Dissociation was carried out at 37¡ C for 1h. The samples were then triturated, filtered, and spun at 300 x g for five minutes. The pellet was resuspended in trypsin inhibitor solution (dissociation media with 1% BSA and 1% ovomucoid). Following gradient centrifugation, the cells were washed in dissociation media containing 0.04% BSA and resuspended in dissociation media containing 0.04% BSA and 15% Optiprep (Sigma).
Individual cells were captured and barcoded using the inDrops platform as previously described. Briefly, single-cell suspensions were fed into a microfluidic device that packaged the cells with barcoded hydrogel microspheres and reverse transcriptase/lysis reagents. After cell encapsulation, primers were photo-released by UV exposure. Two libraries of approximately 3000 cells each were collected for each sample. Indexed libraries were pooled and sequenced on a Nextseq 500 (Illumina).

tag: tissue

value: Lateral geniculte nucleus

tag: age

value: Post-natal day 21


title: P21_2

description: single cell isolation by Indrops


title: pHep_1

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

description: gene expression data from primary murine hepatocytes

hyb_protocol: Labeled cRNA was hybridized to Agilent´s murine 4x44k V2 microarrays for 16h at 68°C.

scan_protocol: Scanning was performed using Agilent DNA Microarray Scanner.

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Extracted microarray raw data (txt-files from Feature Extraction) were imported into Omics Explorer software v3.0 (Qlucore) under default import settings for Agilent One Color mRNA Microarrays. Accordingly, data processing steps were: 1) removal of control measurements, 2) log base 2 transformation, 3) normalization of non-control values by shifting to 75 Percentile, 4) averaging of values from on-chip replicates, 5) baseline transformation to the median.

source_name: primary hepatocytes, replicate 1

label_protocol: 50ng of total RNA were applied for Cy3-labelling reaction using the one color Quick Amp Labeling protocol (Agilent Technologies; Waldbronn, Germany).

extract_protocol: Extraction of total RNA was done using RNeasy Mini Kit (Qiagen) in combination with QIAschredder (Qiagen) according to the manufacturer's instructions.

tag: cell source

value: primary murine hepatocytes


title: P21_3

description: single cell isolation by Indrops


title: MEF_1

description: gene expression data from murine fibroblasts

source_name: Mouse embryo fibroblasts, replicate 1

value: murine fibroblasts


title: 5500024016480061506625_F11

city: Atlanta

first: Hanjoong

last: Jo

state: GA

address: 1760 Haygood Drive, Health Sciences Research Bldg E170

department: Coulter Department of Biomedical Engineering

institute: Georgia Tech and Emory Univ

hyb_protocol: Biotin-labeled cRNA was generated from the cDNA and used to probe a Human Genome HT_HG-U133A plate (Affymetrix, Sunnyvale, CA, USA), consisting of 96 single U133AAOFAV2 arrays in a 96-well plate. Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

data_processing: CEL files from the Affymetrix Array Station were processed and normalized by the Robust Multi-Array Average (RMA) algorithm.

source_name: peripheral blood mononuclear cells (PBMCs)

label_protocol: Double-stranded cDNAs were synthesized from 1 µg of total RNA through reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter and converted to double-strand using the cDNA Synthesis System (Invitrogen). Biotin-labeled cRNA was generated from the cDNA. All cDNA and cRNA target preparation steps were processed on a Caliper GeneChip Array Station from Affymetrix.

extract_protocol: RNA was isolated using the Qiagen RNeasy isolation kit according to manufacturer’s instructions.

treatment_protocol: Cells were cultured at 5 million lymphocytes/well of a 96-well flat-bottom block plate (Qiagen, Hilden, Germany) in 500 µl assay media (RPMI-1640 with GlutaMAX, 10% charcoal-stripped fetal bovine serum; Gibco Laboratories, Gaithersburg, MD, USA). Cells were cultured for 6 hours with either dimethyl sulfoxide (DMSO) vehicle or 1 μM prednisolone. After 6 hours, cells were pelleted and resuspended in 1 ml nucleic acid purification lysis solution (Applied Biosystems, Foster City, CA, USA) diluted 1:2 with calcium-free and magnesium-free phosphate-buffered saline (Invitrogen, Carlsbad, CA, USA). Cells were incubated in lysis buffer for 10 minutes at room temperature followed by storage at –80°C.

tag: donor

tag: treatment

value: Pred

tag: dose

tag: batch

value: PBMCs were isolated from the blood of 2 independent donors using Ficoll gradient centrifugation. Samples were collected and profiled in 5 batches as indicated in the experimental design.


title: MEF_2

source_name: Mouse embryo fibroblasts, replicate 2


title: e-mHepA2D_2

description: gene expression data from immortalized murine hepatocyte cell line e-mHepA cultivated in 2D

source_name: immortalized hepatocyte cell line e-mHepA; cultivated in 2D replicate 2

value: e-mHepA


title: P21_1

description: single cell isolation by Indrops


title: pHep_2

source_name: primary hepatocytes, replicate 2


title: e-mHepA2D_1

source_name: immortalized hepatocyte cell line e-mHepA; cultivated in 2D replicate 1


title: Hepa1-6_2

description: gene expression data from murine hepatocyte cell line Hepa1-6

source_name: hepatocyte cell line Hepa1-6, replicate 2

value: murine hepatocyte cell line


title: 5500024016480061506625_G02

scan_protocol: Array hybridization, washing, and scanning were performed according to the manufacturer’s recommendations.

value: DMSO


title: e-mHepA3D_1

description: gene expression data from immortalized murine hepatocyte cell line e-mHepA cultivated in 3D

source_name: immortalized hepatocyte cell line e-mHepA; cultivated in 3D replicate 1


title: 5500024016480061506625_F10


title: Origin mapping cdc25-22, 12mM HU, replicate 1, dye-swap 1

source_name: cdc25-22, G2 block

tag: strain/background

tag: cell type

tag: phase

value: 0 (unreplicated)

value: 90 min (S phase)


title: Wild-type VNO at P17, biological rep1

city: Albany

first: Paolo

middle: E

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: Unversity at Albany

description: Gene expression data in wild-type VNOs

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene ST 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing: Data analysis was performed using Transcriptome Analysis Console (TAC 4.0) Software, Applied Biosystems. CEL files were quantile-normalized with Gene Level - RMA and differential analysis was done using Anova (p<0.05) and a fold change filter of 1.5

source_name: wild-type VNOs

label_protocol: Biotinylated cRNA were prepared from 100ng total RNA according to the standard Affymetrix WT Plus protocol

growth_protocol: Mice were raised in a normal 12hr light/dark cycle until collection.

extract_protocol: Extraction of total RNA was performed according to manufacturer instructions of the PureLink™ RNA Mini Kit

treatment_protocol: Mice were euthanized by CO2 at P17 and immediately put on ice for immediate VNO extraction.

value: Vomeronasal Organ

tag: genotype

value: wild-type


title: AP2e-null VNO at P17, biological rep2

description: Gene expression in AP-2e null VNOs

source_name: AP-2e null VNOs

value: AP-2e null


title: P16_4

description: single cell isolation by Indrops

tag: strain

value: Post-natal day 16


title: AP2e-null VNO at P17, biological rep3

description: Gene expression in AP-2e null VNOs


title: Origin mapping Cdc13-Cdc22, G1 delay 5 min, 24mM HU, replicate 2, dye-swap 1

value: G1 block

tag: time

value: Time 0 (unreplicated)

value: G1 block - S phase

value: Time 60 min (S phase)


title: P16_3

description: single cell isolation by Indrops

value: Lateral geniculte nucleus


title: P10_4

description: single cell isolation by Indrops

value: Post-natal day 10


title: P16_1

description: single cell isolation by Indrops


title: P16_2

description: single cell isolation by Indrops


title: P10_2

description: single cell isolation by Indrops


title: P10_1

description: single cell isolation by Indrops


title: P10_3

description: single cell isolation by Indrops


title: Hepa1-6_1

source_name: hepatocyte cell line Hepa1-6, replicate 1


title: BJ_ATAC_FOXA2_10dExp_12dWD_Rep2

source_name: BJ Fibroblasts

value: immortalized BJ foreskin fibroblast cell line

value: FOXA2 doxycycline inducible


title: Wild-type VNO at P17, biological rep2

description: Gene expression data in wild-type VNOs


title: P5_3

description: single cell isolation by Indrops

value: Post-natal day 5


title: P5_4

description: single cell isolation by Indrops


title: P5_2

description: single cell isolation by Indrops


title: BJ_ATAC_FOXA2GATA4CoExp_2d_Rep1

value: FOXA2 doxycycline inducible with GATA4 co-expressed


title: 5500024016480061506625_F03

value: DMSO

value: PBMCs were isolated from the blood of 2 independent donors using Ficoll gradient centrifugation. Samples were collected and profiled in 5 batches as indicated in the experimental design.


title: BJ_ATAC_FOXA2GATA4CoExp_2d_Rep2


title: 5500024016480061506625_A03

value: Pred


title: 5500024016480061506625_F07


title: Wild-type VNO at P17, biological rep3

description: Gene expression data in wild-type VNOs

value: Vomeronasal Organ


title: In vitro Rep2

city: Athens

middle: H

last: Kvitko

state: GA - Georgia

address: 120 Carlton St

department: Plant Pathology

institute: University of Georgia

description: processed files .rpkm_0, .rpkm_1, and .rpkm_1 correspond to abundance measurments for NC_004278.1, NC_004632.1, and NC_004633.1 respectively

data_processing:
Illumina BaseSpace Sequence Hub used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v.032
Trimmed reads were aligned to the P. syringae pv. tomato DC3000 reference genome (NC_004278.1, NC_004632.1, NC_004633.1) using EDGE-pro v.1.3.1
Counts of RNA-Seq fragments were computed for each annotated gene from RPKM values using the egdeToDeseq.perl script within EDGE-pro.
Genome_build: NC_004278.1, NC_004632.1, NC_004633.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene for each sample

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: Starting inoculum

growth_protocol: Pseudomonas syringae pv. tomato DC3000 was streaked from a single colony onto King’s B media and grown overnight at room temperature. Bacterial inoculum was smeared into a lawn using liquid media and incubated overnight at room temperature. For individual inoculations, bacteria were harvested from plates, suspended in 0.25 mM MgCl2, and diluted to an OD600 of 0.8 (~1X10^9 CFU/mL)

extract_protocol:
Leaves from each treatment were arranged on two sheets of parafilm, rolled and inserted into the barrel of a two 20 mL syringes. A RNAlater-like RNA stabilizing buffer pH 5.2, was poured into each syringe, sealed, and vacuum infiltrated at 95 kPa for 2 min followed by a slow release of the vacuum.  Vacuum-infiltration with RNA stabilizing buffer was conducted twice on inoculated leaves. Excess RNA stabilizing buffer was decanted and the syringes were placed into 50 mL conical tubes and centrifuged at 1000 g for 10 min at 4°C to recover the intercellular wash fluid.  The flow-through was pooled for each treatment and concentrated by syringe filtration using a 0.20 µm Micropore Express Plus membrane placed within a removable filtering syringe tip adapter. Filters were placed in homogenization tubes and flash frozen in liquid nitrogen. The filter membranes were homogenized in Trizol Reagent for 1 min at 1750Hz using a GenoGrinder followed by the Direct-Zol Miniprep Plus kits, which included an on-column DNAse I treatment (30 U/column for 15 minutes). RNA samples were additionally treated with TURBO DNase to eliminate DNA contamination. Total RNA underwent RiboZero treatment to remove bacterial rRNA.
Illumina TruSeq Stranded Total RNA Sample Prep Kit was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four marked leaves each on plants (24-31 per time point per treatment) were treated with either 1 mM flg22 in 0.1% DMSO or with 0.1% DMSO (mock) by infiltration with a 1 mL blunt syringe on the abaxial surface.  Plants were kept uncovered in the growth room for 20 hours prior to bacterial inoculation.

tag: time of collection

value: 0 hour post inoculation

tag: host plant tissue

tag: host plant treatment

tag: time post infection


title: In vitro Rep3


title: P5_1

description: single cell isolation by Indrops

tag: tissue


title: dEN_ATAC

source_name: dEN

tag: cell line background

value: Definitive Endoderm (ES derived)

tag: genotype/variation

value: wildtype


title: 5500024016480061506625_C04

tag: donor


title: Flg22 5hpi Rep2

source_name: Flg22-treated Arabidopsis leaves

value: 5 hours post inoculation

value: leaves

value: 5 hours


title: BJ_ATAC_FOXA2_10dExp_12dWD_Rep1


title: Flg22 5hpi Rep3


title: Flg22 5hpi Rep1


title: Flg22 3hpi Rep1

value: 3 hours post inoculation

value: 3 hours


title: Flg22 3hpi Rep2


title: Flg22 3hpi Rep3


title: Mock 5hpi Rep1

source_name: Mock-treated Arabidopsis leaves

value: mock


title: 5500024016480061506625_B04

tag: treatment


title: e-mHepA3D_2

source_name: immortalized hepatocyte cell line e-mHepA; cultivated in 3D replicate 2

tag: cell source

tag: cell line

value: e-mHepA


title: AP2e-null VNO at P17, biological rep1

description: Gene expression in AP-2e null VNOs

value: AP-2e null


title: Mock 3hpi Rep3


title: Mock 3hpi Rep2


title: Mock 1hpi Rep1

value: 1 hour post inoculation

value: 1 hour


title: In vitro Rep1


title: Flg22 1hpi Rep1


title: Mock 1hpi Rep2


title: Flg22 1hpi Rep3


title: Isotype [Single Cell RNA-seq]

status: Public on Feb 02 2018

city: New York

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Sequencing data was processed using version 1.2.1 of the Cell Ranger Single-Cell Software Suite provided by 10X Genomics: https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. This pipeline includes read alignment and barcode demultiplexing using the cellranger mkfastq function, followed by UMI and barcode filtering and correction using the cellranger count function. Default parameters are used.
Genome_build: mm10
Supplementary_files_format_and_content: The matrix.mtx files are gene-barcode matrices containing UMI counts, generated and filtered using the cellranger count function. These are stored in market exchange (MEX) format. The barcodes.tsv files correspond to the matrix columns, and the genes.tsv file correspond to the matrix rows, for each respective sample.

source_name: Lung

extract_protocol: 5,000 cells from isotype or 7C6-mIgG2a groups were targeted for the 10X Genomics 3’ V2 single cell assay (10X Genomics). Reverse transcription, cDNA amplification and library preparation were all performed according to the manufacturer’s instructions. Libraries were sequenced using an MiSeq on rapid-run mode, which yielded >25,000 reads per cell.

tag: inoculation

value: Mice inoculated with B16-MICA

value: Mice treated with an isotype control

value: lung CD45+, CD3e-, TCRb-, NK1.1+, NKp46+ cells


title: Normal [Single Cell RNA-seq]

value: Naïve mice

tag: cell type


title: Mock 5hpi Rep3


title: Mock 5hpi Rep2


title: 7C6-mIgG2a [Single Cell RNA-seq]

value: Mice treated with 7C6-mIgG2a antibody


title: Macx

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: processed data file: Expression_Count_Matrix.txt

data_processing:
Raw sequence reads (.fastq) per sample were pre-processed, mapped against MM10, and the number of mapped reads per gene enumerated (exon+intron) by nuclei (umi) using commands described in the "Drop-Seq Alignment Cookbook" (http://mccarrolllab.com/dropseq/).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Expression_Count_Matrix.txt: Tab-delimited text file containing read counts for each gene (exon+intron) by sample in matrix format.

source_name: Brain

growth_protocol: Male and female ICR/CD-1 mice, between 8-11 weeks old, were used.

extract_protocol:
Protocol was adapted from (Halder et al., 2015). Mice were euthanized by CO2 inhalation, the lumbar spinal cord was then rapidly dissected, and the dorsal root ganglia removed. Cords were dounced in 500ul sucrose buffer (0.32M sucrose, 10mM HEPES pH 8.0, 5mM CaCl2, 3mM Mg-Acetate, 0.1mM EDTA, 1mM DTT) with 0.1% Triton X-100 using five strokes with the “A” pestle (Kontes Dounce Tissue Grinder), followed by five strokes with the “B” pestle. The lysate was then diluted with 3 mL sucrose buffer and was centrifuged at 3,200xg for 10 minutes. The supernatant was removed and 3 mL of sucrose buffer was added to the pellet and incubated for 1-2 minutes and the loosened pellet was then transferred to an Oak Ridge centrifuge tube. The pellet was then homogenized using an Ultra-Turrax on setting “1” for one minute. 12mL of density buffer (1M sucrose, 10mM HEPES pH 8.0, 3mM Mg-Acetate, 1mM DTT) was then added carefully below the nuclei layer and the tube was centrifuged at 3,200xg for 20 minutes. The supernatant was then rapidly poured off and the nuclei on the walls of the tube were collected with 1mL of PBS with 0.01% BSA and spun at 3,200xg for 10 minutes. Nuclei were then resuspended in PBS with 0.01% BSA.
Drop-Seq was performed as previously described (Macosko et al., 2015) with the following modifications. Nuclei in 1mL of PBS with 0.01% BSA were counted with a hemocytometer and adjusted to a final concentration of 225 nuclei/ul. Beads were prepared at a concentration of 250 beads/ul in a lysis buffer that contained 0.7% sarkosyl. The following flow rates were used: beads (35ul/min), nuclei (35ul/min), oil (200ul/min). Ten PCR reactions were performed for each sample, and these were pooled, purified with AMPure beads (0.6X), quantified with Qubit 3.0, and analyzed on a High Sensitivity DNA Bioanalyzer chip. Multiple tagmentation and library preparation reactions were performed for each sample, each with 600pg input. Parallel reactions were then pooled, double purified with AMPure beads (0.8X), quantified with Qubit 3.0, and analyzed on a High Sensitivity DNA Bioanalyzer chip. Libraries were sequenced at a minimum depth of 20,000 reads per nucleus using HiSeq 2500 Rapid Mode with the following parameters: Read 1 25bp, index, custom primer; Read 2 50bp, Illumina primer. Each sample was produced from the lumbar cords of a pair of ICR mice, ages 8-11 weeks old. There were six independent samples for baseline, prepared on four different days (three male and three female), five independent samples for formalin treatment, prepared on three different days (three male and two female), and five independent samples for rotarod behavior, prepared on two different days (three male and two female). For all formalin samples, a second round of sequencing was performed, producing ten sequencing reactions for the five biological replicates.

treatment_protocol: Mice were habituated to the environment prior to formalin-administration or rotarod resting for one hour. Formalin administration was by injection, 30ul of 2% paraformaldehyde, into the plantar surface of both hindpaws. Rotarod challenge involved a standard acceleration program going from 0 to 40 rotations per minute over five minutes.

tag: group

value: Control

value: Brain


title: facx


title: fbcx


title: Mock 3hpi Rep1


title: Flg22 1hpi Rep2


title: rotarod4

value: rotarod-challenged


title: rotarod3


title: rotarod2


title: rotarod5


title: Mock 1hpi Rep3

value: leaves


title: form10

value: formalin-administered


title: rotarod1


title: form7


title: form5


title: form4


title: form6


title: F4


title: form1


title: form8


title: form2


title: M5


title: F3


title: M4


title: m1


title: f1


title: form9


title: form3


title: KK1GFP(+)

city: St. Louis

first: David

last: Spencer

address: 660 South Euclid Avenue

department: Department of Medicine

institute: Washington University in St. Louis

data_processing:
Tuxedo pipeline was used for generation of CuffDiff output files in the following steps: (1) mapping single-end reads for reference genome using TopHat v2.0.13 (options: -g 1), (2) Transcript assembly using cufflinks v2.2.1, (3) Transcriptome  assembly using cuffmerge v2.2.1, (4) Quantification of differential expression using cuffdiff v2.2.1. All pipeline was performed using default parameters, unless specified.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample and Log ratio for differential expression

source_name: KK1GFP ( subclone of KK1 ATL cell line)

growth_protocol: MT1GFP cell line is maintained in RPMI + 10% FBS + Penicillin/Streptomycin + 0.5 μg/mL G418. KK1GFP cell line is maintained in RPMI + 20% FBS + Penicillin/Streptomycin + 0.5 μg/mL G418 + IL-2 200 U/ml

extract_protocol:
For Both Cell lines (MT1GFP and KK1GFP), FACS sorting was performed to isolate d2EGFP(-) and d2EGFP(+) populations. Cells were sorted directly into RLT buffer from RNeasy Mini Kit (QIAGEN). Subsequently, Total RNA was extracted for cDNA library construction according to manufacturer protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T-cell

tag: tax expression status

value: Tax(+)

tag: clone

value: KK1GFP clone 11


title: KK1GFP(-)

value: Tax(-)


title: MT1GFP(+)

source_name: MT1GFP ( subclone of MT-1 ATL cell line)

value: MT1GFP clone 5-43


title: MT1GFP(-)


title: B. subtilis YK240 Day 3

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: Hybridization, washing, and scanning was performed as described in the Two-Color Microarray-Based Gene Expression Analysis manual (Version 6.6, Agilent Technologies). Briefly, hybridization mixtures were made by combining 300 ng test (Cy3) and 300 ng common reference (Cy5) material and were subsequently hybridized to the Agilent SurePrint Custom 8x15k microarrays G2509F (Agilent Technologies).

scan_protocol: The slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche Nimblegen).

data_processing: Feature extraction was performed with NimbleScan v2.5 (Roche Nimblegen).

organism: Bacillus subtilis

source_name: B. subtilis YK240 Day 3

label_protocol: Labeling was performed by reverse transcription using random octamers, incorporating Cy3 for the test samples and Cy5 for the common reference

growth_protocol: B. subtilis strains were grown at 30°C or 37°C in Nutrient broth (Oxoid), LB or competence medium (78 mM K2HPO4, 42.8 mM KH2PO4, 14.7 mM (NH4)2SO4, 6.6 mM MgSO4, 3.3 mM Na3-citrate, 26.9 mM glucose, 95 μM tryptophan, 4.2 μM ferric ammonium citrate, 0.02% casaminoacids).

extract_protocol: To isolate RNA, cell pellets were flash frozen in liquid nitrogen immediately after harvesting and stored at -80°C. Frozen pellets were grounded and subjected to RNA extraction

treatment_protocol: DNA manipulations were carried by standard techniques, chromosomal DNA was purified using a phenol chloroform extraction. Transformations of cells were carried out as described previously {Inoue, 1990 #1033;Anagnostopoulos, 1961 #1416;Hamoen, 2002 #1417}, and plated on nutrient agar supplemented with ampicillin (100 ug/ml), chloramphenicol (5 ug/ml), erythromycin (1 ug/ml), glucose (0.4 0.8%), kanamycin (5 ug/ml), spectinomycin (50 ug/ml), tetracycline (12 ug/ml), X gal (160 mg/ml), IPTG (0.5 1 mM), xylose (0.025 1 %).

tag: strain

tag: time (day)

source_name: Pool of all samples

tag: sample type

value: Pool of different samples of different B. subtilis strains


title: Ezh2Δ/Δp53Δ/Δ-ETP-ALL_13

city: Kumamoto

first: Goro

last: Sashida

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

department: IRCMS

country: Japan

institute: Kumamoto University

description: Gene expression in Ezh2Δ/Δp53Δ/Δ ETP-ALL DN2 cells

hyb_protocol: 600 ng of the labeled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray. The process of hybridization and washing was performed using a Hi-RPM Gene Expression Hybridization Kit (Large) (Agilent) and a Gene Expression Wash Pack (Agilent), respectively.

scan_protocol: GeneChips were scanned using a DNA microarray scanner and Feature Extraction ver 10.7.1.1 (Agilent Technologies)

data_processing: Standard Agilent protocol using GeneSpringGX12.0 (Agilent Technologies): Threshold raw signals to 1.0. Normalizsation algorithm, Pertentile Shift. Shift to percentile, 75.

source_name: Thymus DN2 cells, Ezh2Δ/Δp53Δ/Δ, ETP-ALL_13, replicate 1

label_protocol: 20 ng of total RNA was mixed with spike-in controls using an Agilent One Color Spike Mix Kit (Agilent), amplified and labeled with Cyanine 3 using a Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, which generated single-color labeled cRNA.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Freshly isolated bone marrow cells were stained by appropriate antibodies, and then sorted on FACSAriaII (BD).

tag: genotype

tag: cells

tag: leukemia

value: ETP-ALL


title: Ezh2Δ/Δ-DN3

description: Gene expression in Ezh2Δ/Δ DN3 cells at 3 months post transplantation

source_name: Thymus DN3 cells, Ezh2Δ/Δ, replicate 1

value: NO


title: Ezh2Δ/Δ-DN1

description: Gene expression in Ezh2Δ/Δ DN1 cells at 3 months post transplantation

source_name: Thymus DN1 cells, Ezh2Δ/Δ, replicate 1


title: Ezh2Δ/Δ-DN2

description: Gene expression in Ezh2Δ/Δ DN2 cells at 3 months post transplantation

source_name: Thymus DN2 cells, Ezh2Δ/Δ, replicate 1


title: p53Δ/Δ-DN2

description: Gene expression in p53Δ/Δ DN2 cells at 3 months post transplantation

source_name: Thymus DN2 cells, p53Δ/Δ, replicate 1


title: p53Δ/Δ-DN1

description: Gene expression in p53Δ/Δ DN1 cells at 3 months post transplantation

source_name: Thymus DN1 cells, p53Δ/Δ, replicate 1


title: Ezh2Δ/Δp53Δ/Δ-DN2

description: Gene expression in Ezh2Δ/Δp53Δ/Δ DN2 cells at 3 months post transplantation

source_name: Thymus DN2 cells, Ezh2Δ/Δp53Δ/Δ, replicate 1


title: B. subtilis YK240 Day 4

source_name: B. subtilis YK240 Day 4


title: Ezh2Δ/Δp53Δ/Δ-ETP-ALL_19

source_name: Thymus DN2 cells, Ezh2Δ/Δp53Δ/Δ, ETP-ALL_19, replicate 1


title: WT-DN3

description: Gene expression in WT DN3 cells at 3 months post transplantation

source_name: Thymus DN3 cells, WT, replicate 1

value: WT


title: Ezh2Δ/Δp53Δ/Δ-DN1

description: Gene expression in Ezh2Δ/Δp53Δ/Δ DN1 cells at 3 months post transplantation

source_name: Thymus DN1 cells, Ezh2Δ/Δp53Δ/Δ, replicate 1


title: p53Δ/Δ-DN3

description: Gene expression in p53Δ/Δ DN3 cells at 3 months post transplantation

source_name: Thymus DN3 cells, p53Δ/Δ, replicate 1


title: Ezh2Δ/Δp53Δ/Δ-DN3

description: Gene expression in Ezh2Δ/Δp53Δ/Δ DN3 cells at 3 months post transplantation

source_name: Thymus DN3 cells, Ezh2Δ/Δp53Δ/Δ, replicate 1


title: WT-DN1

description: Gene expression in WT DN1 cells at 3 months post transplantation

source_name: Thymus DN1 cells, WT, replicate 1


title: B. subtilis YK240 Day 1

source_name: B. subtilis YK240 Day 1


title: AM73 treated, technical rep2

city: Stockholm

first: Amanda

middle: Tove

last: Klein

address: von Eulers väg 8

department: Dept of Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

description:
Gene expression data from AM73 treated brown fat cells
AM73-2

hyb_protocol: 2.5ug of ss DNA target was hybridized for 18h at 48C° to a Mouse Gene 2.1 ST Array Plate, washed and stained in the Gene Titan Instrument 400.

scan_protocol: Standard Affymetrix protocol

data_processing:
Analysis Software = Expression Console (V.1.41), Method = med-polish (rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false)
Data was log2 transformed. Statistical analysis for comparisons of different treatment groups: Student's t-test, unpaired, 2-sided.

source_name: Brown fat cells treated with AM73 8h

label_protocol: 100ng of total RNA was used to generate amplified sense strand DNA targets with Affymetrix WT Plus Reagent Kit followed by fragmentation and biotinylation with Affymetrix WT Terminal Labeling Kit.

extract_protocol: RNA was extracted by Isol reagent according to manufacturer's protocol

tag: tissue

value: Brown fat

tag: agent


title: AM80 treated, technical rep3

description:
Gene expression data from AM80 treated brown fat cells
AM80-3

source_name: Brown fat cells treated with AM80 8h


title: AM80 treated, technical rep1

description:
Gene expression data from AM80 treated brown fat cells
AM80-1


title: AM73 treated, technical rep3

description:
Gene expression data from AM73 treated brown fat cells
AM73-3


title: WT-DN2

description: Gene expression in WT DN2 cells at 3 months post transplantation

source_name: Thymus DN2 cells, WT, replicate 1


title: DMSO treated, technical rep2

description:
Gene expression data from DMSO treated brown fat cells
DMSO-2

source_name: Brown fat cells treated with DMSO 8h

value: control


title: T47D_PRA8_R_rep 2

city: los Angeles

first: Hany

middle: A

last: Abdel-Hafiz

address: 110 N George Burns RD, DRoom 3057

department: Medicine/ Medical Oncology

institute: Cedars-Sinai Medical Center

description:
PRA8_R_002
Gene expression

hyb_protocol: Hybridization to Affymetrix U133 Plus 2 microarrays was performed at the Genomics and Microarray Core at the University of Colorado Denver.

scan_protocol: Initial analyses were performed at the Genomics and Microarray Core at the University of Colorado Denver.

data_processing: The data were filtered and any probes with a detection P-value less than 0.05 were removed from the normalized dataset. The data was then normalized using log2 transformation and quantile normalization using Partek® Genomics Suite™ 6.6.

source_name: T47D-PRAK388R, R5020, replicate 2

label_protocol: Labeling was performed at the Genomics and Microarray Core at the University of Colorado Denver.

growth_protocol: Cells were maintained in Dulbecco's modified eagle medium (DMEM, Life Technologies) containing 5% charcoal stripped fetal bovine serum (FBS, Japan Serum) in the presence or absence of 10 nM synthetic progestin R5020.

extract_protocol: Total RNA was extracted (PicoPure; Arcturus) following the manufacturer's recommendations.

treatment_protocol: Cells were treated with ethanol or 10 nM synthetic progestin R5020.

tag: originating cell line

value: breast cancer cell line

tag: genotype/variation

value: SUMOylation-deficient PR-AK388R mutant

value: synthetic progestin R5020


title: T47D_Y_C_rep 1

description:
Y_C_001
Gene expression

source_name: T47D-Y, control, replicate 1

value: PR-negative

tag: treatment

value: ethanol control


title: AM80 treated, technical rep2

description:
Gene expression data from AM80 treated brown fat cells
AM80-2


title: T47D_Y_C_rep 2

description:
Y_C_002
Gene expression

source_name: T47D-Y, control, replicate 2


title: DMSO treated, technical rep3

description:
Gene expression data from DMSO treated brown fat cells
DMSO-3


title: ATAC_SLE413-PD1hi

city: Farmington

first: Diogo

middle: F

last: Troggian Veiga

state: Connecticut

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Reads were trimmed using trimmomatic v.0.33
Alignment to the GRCh37/hg19 assembly of the human genome using bwa-mem v.7.12
Duplicate reads were removed and technical replicates merged using samtools v. 0.1.19
Peak calling was performed using MACS2 v. 2.1.0.20151222 with “--nomodel --shift 37 --extsize 73 --broad” parameters, and only peaks with q-value < 0.05 were selected
Peaks overlapping blacklisted regions as defined by the ENCODE project were discarded
Coverage of consensus peaks present in at least two samples was obtained using the DiffBind R package v. 2.2.12
Peaks were annotated to the closest transcription start sites in the UCSC hg19 knownGene transcriptome using the ChIPSeeker R package v.1.5.1
Differential chromatin accessibility was performed using EdgeR v. 3.18.1
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-delimited text file – columns: peak_chromosome, peak_start, peak_end, width, geneChr, geneStart, geneEnd, geneLength, geneStrand, NCBI_geneID, Symbol, Gene_name, ENSEMBL, UCSC_transcriptId, distanceToTSS, annotation, SLE392.PD1hi.counts, SLE413.PD1hi.counts, SLE298.PD1hi.counts, SLE456.PD1hi.counts, SLE392.Tfh.counts, SLE298.Tfh.counts

source_name: Sorted CXCR3+ PD1hi CD4+ T cells from PBMCs of SLE patient

extract_protocol:
For blood CD4+ T cell subset sorting, frozen PBMCs from SLE patients were stained with anti-CD4 PE-Cy7, anti-CXCR5 AlexaFluor 647, anti-CD45RA APC-H7, anti-PD1 Brilliant Violet 421, anti-CD3 V500 and anti-CXCR3 Brilliant Violet 785. CXCR3- PD1hi CD4+ T cells were sorted from the CD3+ CD4+ CD45RA- CXCR5- cells fraction, and Tfh cells (CD3+ CD4+ CD45RA− CXCR5+ CD4+ T cells) were also sorted for comparison.
ATAC-seq was performed as previously described (Buenrostro et al., 2013). 20,000 unfixed nuclei were tagged using Tn5 transposase (Nextera DNA sample prep kit; Illumina) for 30 min at 37°C, and the resulting library fragments were purified using a Qiagen MinElute kit. Libraries were amplified by 10–12 PCR cycles, purified using a Qiagen PCR cleanup kit, and sequenced on an Illumina HiSeq 2500 with 75 bp paired-end reads and average depth of 79 million reads per sample.

tag: donor

tag: diagnosis

value: systemic lupus erythematosus (SLE)

value: CD4+ T cell

tag: cell population


title: ATAC_SLE392-Tfh

source_name: Sorted Tfh cells from PBMCs of SLE patient

tag: cell type

value: Tfh


title: ATAC_SLE298-Tfh


title: ATAC_SLE392-PD1hi


title: ATAC_SLE456-PD1hi


title: ATAC_SLE298-PD1hi


title: Yy1-KO rep3

city: Madison

first: Xuan

last: Pan

state: Wisconsin

address: 2015 Linden Drive

institute: University of Wisconsin-Madison

data_processing:
Sequencing reads were mapped to the genome using Subjunc aligner from subread package  (verion 1.5.0-p1).
Quantification of expression for each gene was calculated using the featureCounts tool from subread. RPKM values were calculated using R edgeR package.
Differential gene expression was detected using  the R Limma package. The raw gene counts data were normalized using voom method first.
GSEA analysis was performed using gsea version 2-2.2.2 and mouse gene sets from http://baderlab.org/GeneSets.
Genome_build: mm10
Supplementary_files_format_and_content: YY1_vs_WT.csv

source_name: HSC (Lin-Sca1+c-Kit+CD150+)

extract_protocol:
Total RNA was purified from bone marrow HSCs (Lin-Sca1+c-Kit+ CD48-CD150+and Lin-Sca1+c-Kit+CD48-CD150-) sorted from Yy1-/- versus Yy1+/+ mice using RNeasy Micro kit (Qiagen).
Sequencing libraries were prepared by using Ovation RNA-Seq System V2 (NuGen) according to the manufacturer’s specifications and were sequenced by an Illumina HiSeq 2000.

value: bone marrow

tag: age

value: 6-8 weeks old


title: WT rep2


title: Yy1-KO rep1


title: T47D_PRA8_C_rep 1

description:
PRA8_C_001
Gene expression

source_name: T47D-PRAK388R, control, replicate1


title: T47D_PRA_R_rep 1

description:
PRA_R_001
Gene expression

source_name: T47D-PRA, R5020, replicate 1

value: WT PR-A


title: AM73 treated, technical rep1

description:
Gene expression data from AM73 treated brown fat cells
AM73-1


title: Yy1-KO rep2


title: T47D_PRA_C_rep 2

description:
PRA_C_002
Gene expression

source_name: T47D-PRA, control, replicate 2


title: T47D_PRA_C_rep1

description:
PRA_C_001
Gene expression

source_name: T47D-PRA, control, replicate 1


title: T47D_PRA8_C_rep 2

description:
PRA8_C_002
Gene expression

source_name: T47D-PRAK388R, control, replicate 2


title: WT rep3


title: DMSO treated, technical rep1

description:
Gene expression data from DMSO treated brown fat cells
DMSO-1


title: T47D_PRA8_R_rep 1

description:
PRA8_R_001
Gene expression

source_name: T47D-PRAK388R, R5020, replicate 1


title: T47D_PRA_R_rep 2

description:
PRA_R_002
Gene expression

source_name: T47D-PRA, R5020, replicate 2


title: WT rep1


title: genomic DNA from labial salivary gland 26

city: Berkeley

first: Michael

middle: B

last: Cole

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

description:
control labial salivary gland sample
SAMPLE 30

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner

data_processing: The 3,091 CpH (non‐CpG) probes and 65 SNP probes were removed prior to analysis. We also removed 16,177 cross‐reactive CpG probes 20. In order to avoid direct effects of genotype variation, we removed 1,213 CpG probes targeting variable SNPs genotyped in our study sample. We identified and removed 62,220 CpG probes neighboring SNPs. An additional 3,392 CpG probes were removed from the analysis due to high‐detection P values (P > 0.05) in 1 or more samples, as computed by Illumina's GenomeStudio software.

label: Cy5 and Cy3

source_name: labial salivary gland 26

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from LSG samples using Qiagen DNeasy Kit according to standard instructions

value: Negative

value: Missing-Skip


title: genomic DNA from labial salivary gland 24

description:
control labial salivary gland sample
SAMPLE 29

source_name: labial salivary gland 24


title: genomic DNA from labial salivary gland 17

description:
control labial salivary gland sample
SAMPLE 28

source_name: labial salivary gland 17


title: genomic DNA from labial salivary gland 21

description:
other labial salivary gland sample
SAMPLE 13

source_name: labial salivary gland 21

value: negative

value: other


title: genomic DNA from labial salivary gland 9

description:
case labial salivary gland sample
SAMPLE 27

source_name: labial salivary gland 9

value: positive

value: case


title: genomic DNA from labial salivary gland 6

description:
case labial salivary gland sample
SAMPLE 5

source_name: labial salivary gland 6

value: Positive


title: genomic DNA from labial salivary gland 19 replicate 2

description:
case labial salivary gland sample
SAMPLE 22

source_name: labial salivary gland 19


title: genomic DNA from labial salivary gland 15

description:
control labial salivary gland sample
SAMPLE 17

source_name: labial salivary gland 15

value: control


title: genomic DNA from labial salivary gland 18

description:
other labial salivary gland sample
SAMPLE 19

source_name: labial salivary gland 18


title: genomic DNA from labial salivary gland 16

description:
case labial salivary gland sample
SAMPLE 18

source_name: labial salivary gland 16


title: genomic DNA from labial salivary gland 27

description:
control labial salivary gland sample
SAMPLE 15

source_name: labial salivary gland 27


title: genomic DNA from labial salivary gland 13

description:
control labial salivary gland sample
SAMPLE 12

source_name: labial salivary gland 13


title: genomic DNA from labial salivary gland 10

description:
control labial salivary gland sample
SAMPLE 8

source_name: labial salivary gland 10


title: genomic DNA from labial salivary gland 11 replicate 2

description:
control labial salivary gland sample
SAMPLE 9

source_name: labial salivary gland 11


title: genomic DNA from labial salivary gland 7

description:
case labial salivary gland sample
SAMPLE 24

source_name: labial salivary gland 7


title: genomic DNA from labial salivary gland 22

description:
control labial salivary gland sample
SAMPLE 16

source_name: labial salivary gland 22


title: genomic DNA from labial salivary gland 25

description:
case labial salivary gland sample
SAMPLE 23

source_name: labial salivary gland 25


title: ATM-HF-lard_60_exp4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).

source_name: ATM-HF-lard

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: In various experiments male C57Bl/6 mice (Harlan, Germany) were given high-fat diets (HFD) or low-fat diets (LFD) for periods up to 16 weeks. The HFD contained either 45 or 60 kcal% fat (diets D12451 resp. D12492, Research Diets Inc.), and the matched LFD contained 10 kcal% fat (diets D12450B resp. D12450J, Research Diets Inc.). Two versions of the 45 kcal% diet were prepared, one according to formulation D12451 (thus with lard; HF-lard), and a variant in which the lard was completely replaced by safflour oil (HF-saf). Mice had access to feed and water ad libitum throughout the study.

extract_protocol: RNA was purified using TRIzol (Life Technologies, Calsbad, CA, USA) followed by an additional round of purification with RNeasy Microkit columns (Qiagen, Venlo, the Netherlands). RNA quality was assessed using RNA 6000 nanochips on the Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: After the dietary intervention, mice were killed by cervical dislocation, and epididymal adipose tissue (AT) was removed. Next the AT was processed sterile to separate the stromal vascular fraction (SVF) from adipocytes using collagenase digestion as described previously (Stienstra et al., PMID: 25008177). Adipose tissue macrophages (ATMs) were purified from the stromal vascular fraction by F4/80+ positive selection with magnetic beads (Milteny Biotec). Cell pellets were frozen directly for RNA isolation, snap frozen in liquid nitrogen, and stored at -80°C.

tag: Sex

value: male

value: wildtype

tag: experiment

tag: time of dietary intervention (wk)

tag: diet group

value: high fat diet -lard (Research Diets D12492, 60 kcal%)

value: epididymal adipose tissue

value: adipose tissue macrophages (ATM)


title: genomic DNA from labial salivary gland 4

description:
case labial salivary gland sample
SAMPLE 7

source_name: labial salivary gland 4


title: genomic DNA from labial salivary gland 3 replicate 2

description:
case labial salivary gland sample
SAMPLE 3

source_name: labial salivary gland 3


title: genomic DNA from labial salivary gland 1

description:
control labial salivary gland sample
SAMPLE 6

source_name: labial salivary gland 1


title: genomic DNA from labial salivary gland 8

description:
case labial salivary gland sample
SAMPLE 20

source_name: labial salivary gland 8


title: genomic DNA from labial salivary gland 14

description:
control labial salivary gland sample
SAMPLE 25

source_name: labial salivary gland 14


title: genomic DNA from labial salivary gland 23

description:
case labial salivary gland sample
SAMPLE 31

source_name: labial salivary gland 23


title: genomic DNA from labial salivary gland 20

description:
control labial salivary gland sample
SAMPLE 26

source_name: labial salivary gland 20


title: genomic DNA from labial salivary gland 28

description:
case labial salivary gland sample
SAMPLE 21

source_name: labial salivary gland 28


title: genomic DNA from labial salivary gland 19 replicate 1

description:
case labial salivary gland sample
SAMPLE 14

source_name: labial salivary gland 19


title: genomic DNA from labial salivary gland 3 replicate 1

description:
case labial salivary gland sample
SAMPLE 2


title: genomic DNA from labial salivary gland 5

description:
case labial salivary gland sample
SAMPLE 4

source_name: labial salivary gland 5


title: genomic DNA from labial salivary gland 11 replicate 1

description:
control labial salivary gland sample
SAMPLE 11


title: genomic DNA from labial salivary gland 12

description:
control labial salivary gland sample
SAMPLE 10

source_name: labial salivary gland 12


title: genomic DNA from labial salivary gland 2

description:
case labial salivary gland sample
SAMPLE 1

source_name: labial salivary gland 2


title: Roots_MU_2

city: Zürich

first: Laura

last: Montani

state: ZH

address: Otto Stern Weg 7

country: Switzerland

institute: IMHS - ETH Zürich

hyb_protocol: Following fragmentation, 10 ug of cRNA per sample were hybridized for 16 hr at 45C on Affymetrix MG-430 PM Array Strips. Strips were washed and stained using the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: An Affymetrix GeneAtlas Imaging Station was used to measure the fluorescent intensity emitted by the labeled targets.

data_processing: Signal estimates were calculated using RMA in Bioconductor (v.2.11).

label_protocol: Biotinylated cRNA were prepared using the GeneAtlasTM 3’IVT Express Kit (Affymetrix) from 100ng total RNA

extract_protocol: total RNA by Trizol/chloroform/ethanol extraction

treatment_protocol: P60 mice were euthanized and tissue immediately dissected, transferred to eppendorfs and snap frozen in liquid nitrogen. Tissues were stored at -80C to be subsequently processed for total RNA extraction.

tag: strain background

value: mixed

value: FASN Schwann cell-conditional mutant; DhhCre+ Fasn lox/lox

value: Roots


title: htz1Δ replicate3

city: Salamanca

first: Pedro

last: San Segundo

state: Salamanca

address: Instituto de Biología Funcional y Genómica. Zacarías González 2.

department: Unidad II. Dinámica del genoma y epigenética.

country: Spain

institute: University of Salamanca

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G and the images were acquired by Affymetrix default GeneChip® Operating System 1.4.0.036 (GCOS), and converted in .DAT files.

data_processing: The .DAT image files for each array were converted into .CEL files using Affymetrix GCOS software. These .CEL files were further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (affylmGUI interface) of R/Bioconductor project.

organism: Saccharomyces cerevisiae

source_name: htz1 mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Strains were grown in 2xSC for 20 - 24 hours, then transferred to YPDA and incubated to saturation for additional 8 hours. Cells were harvested, washed with 2% potassium acetate (KAc), resuspended into 2% KAc and incubated at 30ºC with vigorous shaking to induce meiosis and sporulation. Both YPDA and 2% KAc were supplemented with 20 mM adenine and 10 mM uracil. Samples for RNA extraction were collected at 15 hours (peak of meiotic prophase in this strain background)

extract_protocol: Rneasy® midi kit (Qiagen) of total RNA was performed according to the manufacturer's instructions.

tag: strain


title: Sciatic nerves_MU_3

source_name: Sciatic nerves_MU

value: Sciatic nerve


title: ATM_LF-lard_10_exp2

value: low fat diet - lard (Research Diets D12450J, 10 kcal %)


title: wt replicate2

source_name: wild type


title: wt replicate3


title: Sciatic nerves_MU_2


title: ATM_LF-lard_10_exp1

value: low fat diet - lard (Research Diets D12450B, 10 kcal%)


title: ATM-LF-lard_10_exp4

source_name: ATM-LF-lard

value: low fat diet -lard (Research Diets D12450J, 10 kcal %)


title: ATM_HF-lard_60_exp2

value: high fat diet - lard (Research Diets D12492, 60 kcal%)


title: ATM_LF_lard_10_exp3


title: htz1Δ replicate2


title: Roots_MU_1


title: ATM_HF-lard_45_exp3

value: high fat diet - lard (Research diets D12451, 45 kcal%)


title: Roots_MU_3


title: Sciatic nerves_MU_1


title: Roots_CT_3

value: control; DhhCre- Fasn lox/lox


title: ATM_HF-lard_45_exp1

value: high fat diet - lard (Research Diets D12451, 45 kcal%)


title: Roots_CT_1


title: Sciatic nerves_CT_2

source_name: Sciatic nerves_CT


title: wt replicate1


title: Fructose_3

city: La Jolla

first: Nathan

last: Lewis

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

hyb_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.

data_processing: Affymetrix CEL files were normalized using GCRMA (version 2.20.0) implemented in R (version 2.11.1)

organism: Escherichia coli

source_name: E. coli K-12 MG1655, aerobic conditions on 0.2% (w/v) fructose M9 minimal media at 37°C

growth_protocol: E. coli K12 MG1655 was grown and expression profiled on 0.2% (w/v) glucose M9 minimal media or 0.2% (w/v) fructose M9 minimal media or 0.2% (w/v) acetate M9 minimal media at 37°C. Each experimental condition was tested in triplicate in the respective carbon sources using independent cultures. Cultures were grown to mid-exponential growth phase aerobically (OD600 = 0.3) in minimal media, supplemented with the appropriate carbon source.

extract_protocol: total RNA

treatment_protocol: Addition of 0.2% v/v carbon source to the M9 media


title: iMEF wt d3 I

city: Regensburg

first: Stefan

last: Dillinger

address: Universitätsstr. 31

institute: University Regensburg

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: The values represent  M-values= log2(R/G), normalized by qspline (a natural cubic spline interpolation method followed by linear interpolation of outlier values, Bioconductor aCGH.Spline_2.2.tar), each array was normalized separately.

source_name: nucleolar DNA

label_protocol: 2µg of DNA were submitted to NimbleGen and steps were performed as service there.

growth_protocol: MEF cells were grown under standard conditions: 37°C, 5 % CO2, DMEM-GlutaMAX, high Glucose (4 g/L), 10 % FCS

extract_protocol: 1x10^8 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. After washing cells 2 times with ice-cold PBS they were scraped off and pooled in 100 mL 1xPBS and centrifuged (750 g, 5 min, 4°C). Supernatant was discarded and cells were resuspended in 1 mL HMg buffer (10 mM Hepes pH 7.4, 0.88 M sucrose, 12 mM MgCl2, 1 mM TCEP, PI). Cells were then sonified with the Bioruptor 30 sec on 30 sec off for 3x5min with high mode. After ceintrifugation the pellet was respuspended in 1mL LMg (10 mM Hepes pH 7.4, 0.88 M sucrose, 1 mM MgCl2, 1 mM TCEP, PI) buffer and sonified again with the same settings. Supernatant was discarded and the pellet was resuspended in 200 µL 20 mM Tris pH 8.1. RNA was digested by adding 3 µL of RNAse A (10 mg/mL) and incubation for 1 h at 37°C. Proteins were digested by adding 5 µL Proteinase K and incubation for 8 h at 37°C and the cross-link was reversed for 8 h at 65°C. Finally DNA was precipitated.

treatment_protocol: For UBF knock-out MEF cells were treated for 4h with 50 nM 4-hydroxytamoxifen.

tag: cell line

value: iMEF UBFwt/wt / ER-Cre+/+ / SvT

value: 72h after UBF ko

tag: molecule type

value: nucleolar DNA

source_name: MEF genomic DNA


title: htz1Δ replicate1


title: iMEF wt d0 I

value: untreated


title: Acetate_3

scan_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.

source_name: E. coli K-12 MG1655, aerobic conditions on 0.2% (w/v) acetate M9 minimal media at 37°C


title: Fructose_2

label_protocol: cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by Affymetrix standard protocol.

value: 0.2% (w/v) fructose M9 minimal media at 37°C


title: Roots_CT_2

tag: tissue


title: Glucose_1

source_name: E. coli K-12 MG1655, aerobic conditions on 0.2% (w/v) glucose M9 minimal media at 37°C


title: Sciatic nerves_CT_3


title: Acetate_2

value: 0.2% (w/v) acetate M9 minimal media at 37°C


title: Glucose_2

value: 0.2% (w/v) glucose M9 minimal media at 37°C


title: Glucose_3


title: Fructose_1