title: D-6.Cortex.HI.P20

description: Gene expression data from rat microglia


title: D-4.Cortex.HI.P20

status: Public on Jan 13 2020

type: RNA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: Gene expression data from rat microglia

hyb_protocol: The labeled, fragmented cDNA (5.5µg ) was hybridized to the GeneChip Rat Transcriptome Array 1.0 (Affymetrix, Santa Clara, CA) for 16 hours in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) at 45° C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA)

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed with the R/Bioconductor package oligo. The function rma was used for array normalization. The package affycoretools was used for probe annotation. Only unique probe sets with an ENTREZ ID were retained for further analysis. In case of several probe sets mapping to the same ENTREZID the one with the highest variance as measured by the interquartile range was retained.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Rat microglia from cortex region Cortex

label_protocol: Biotin labeling was performed using the GeneChip WT Pico Kit (Affymetrix, Santa Clara, CA), according to the manufacturer's protocol from 500 pg total RNA per sample.

extract_protocol: Total RNA was extracted from CD11b+ purified cells with the Arcturus PicoPure RNA isolation kit (ThermoFisher Scientific, Waltham, MA) including DNAse treatment. The concentration, purity and integrity of RNA were assessed for each sample using the  2100 Bioanalyzer with the RNA 6000 Pico LabChips (Agilent, Santa Clara, CA). In sample CH14DIVUSBR100337 and CH50DIVUSBR100077, RIN values could repeatedly not been calculated (RIN value: “NA”), but the graphical assessment of the electropherogram indicated a similar RNA integrity as compared to samples with RIN > 8.4).

treatment_protocol: P7 Sprague-Dawley rats were subjected to sham surgery (exposure of the right [ipsilateral] common carotid artery) or HI surgery (temporary occlusion of the ipsilateral common carotid artery and exposure to hypoxia). Animals were transcardially perfused with NaCl 0.9% at either P10 or P20. The anterior dorsolateral SVZ (ipsilateral in HI animals, ipsi- and contralateral in sham animals) and the contralateral M2 supplementary motor cortex (CX) were microdissected. SVZ and CX tissue was collected separately in individual rats and dissociated by papain / DNAse treatment. Microglia were purified by anti-CD11b magnetic bead sorting (Miltenyi Biotec, San Diego, CA).

tag: animal id

tag: tissue

value: Cortex

tag: treatment

value: HI

tag: age

tag: rin


title: B-5.SVZ.Sham.P20

description: Gene expression data from rat microglia

source_name: Rat microglia from cortex region SVZ

value: SVZ

value: Sham


title: A-1.Cortex.Sham.P10

description: Gene expression data from rat microglia


title: E-2.Cortex.HI.P10

description: Gene expression data from rat microglia


title: A-4.SVZ.Sham.P10

description: Gene expression data from rat microglia


title: A-4.Cortex.Sham.P10

description: Gene expression data from rat microglia


title: A-6.SVZ.Sham.P10

description: Gene expression data from rat microglia


title: B-6.Cortex.Sham.P20

description: Gene expression data from rat microglia


title: D-2.SVZ.HI.P20

description: Gene expression data from rat microglia


title: B-4.Cortex.Sham.P20

description: Gene expression data from rat microglia


title: B-2.SVZ.Sham.P20

description: Gene expression data from rat microglia


title: D-6.SVZ.HI.P20

description: Gene expression data from rat microglia


title: C-5.SVZ.HI.P10

description: Gene expression data from rat microglia


title: D-1.Cortex.HI.P20

description: Gene expression data from rat microglia


title: A-1.SVZ.Sham.P10

description: Gene expression data from rat microglia


title: E-2.SVZ.HI.P10

description: Gene expression data from rat microglia


title: C-5.Cortex.HI.P10

description: Gene expression data from rat microglia


title: A-6.Cortex.Sham.P10

description: Gene expression data from rat microglia


title: E-1.Cortex.HI.P10

description: Gene expression data from rat microglia


title: D-4.SVZ.HI.P20

description: Gene expression data from rat microglia


title: A-3.Cortex.Sham.P10

description: Gene expression data from rat microglia


title: C-1.SVZ.HI.P10

description: Gene expression data from rat microglia


title: D-3.Cortex.HI.P20

description: Gene expression data from rat microglia


title: A-5.Cortex.Sham.P10

description: Gene expression data from rat microglia


title: D-5.Cortex.HI.P20

description: Gene expression data from rat microglia


title: TH1 CD4+ T cells replicate 2

status: Public on Dec 04 2019

type: SRA

description: tagmented DNA

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (UCSC version mm10) with bowtie2 (version 2.3.2) using options "--maxins 2000 --no-mixed --no-discordant --local --mm".
The output was sorted and indexed with samtools (version 1.7) and duplicated reads were marked with picard (version 2.9.2).
The read and alignment quality was evaluated using the qQCReport function of the bioconductor package QuasR (R version 3.5.2; Bioconductor version 3.8).
Coverage tracks per sample were generated by tiling the genome in 20bp windows and counting 5'end of reads per window using the function bamCount from the bioconductor package bamsignals.
These window counts were scaled to RPKM values and exported in bigWig format using the bioconductor package rtracklayer.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: memory CD4+ T cells from pooled mice splenic extracts

growth_protocol: Mice were bred and kept in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
Single cells were extracted from suspensions of spleen from 4 male and 2 female individual mice that were pooled for sorting TH1 and TFH cells or one individual female litter-mate mice for naive CD4 T cells
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for dump-CD4+CD44+gp66+ expression and either Ly6C+ PSGL-1+ (Th1) Ly6C-PSGL-1- (TFH) or dump- CD4+ CD44- CD62L+ for naive CD4 T cells.
The sorted cell suspension from each sample were prepared according to Omni ATAC protocol that was previously published
In brief, DNA was isolated, tagmented with a transposase, amplified by PCR and purified

tag: cell type

value: memory CD4+ T cells

tag: strain

value: T-bet ZSGREEN

tag: Sex

value: pooled male and female


title: TFH  CD4+ T cells replicate 1

description: tagmented DNA


title: D-1.SVZ.HI.P20

description: Gene expression data from rat microglia


title: TFH  CD4+ T cells replicate 2

description: tagmented DNA


title: Naive  CD4+ T cells replicate 1

description: tagmented DNA

source_name: memory CD4+ T cells from one mouse splenic extracts

value: naive CD4 T cells

value: female


title: C-2.Cortex.HI.P10

description: Gene expression data from rat microglia


title: Treat_10

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR (version 2.7.0c) with default parameters, except reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”).
Sequencing and mapping quality was assessed by the qQCReport function of the R package QuasR (version 1.18) and with FastQC (version 0.11.4).
Gene expression was quantified by featureCounts (Subread version 1.6.4) using an exon-union model of Ensembl 84 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: text file with comma-separated counts for each gene; each row contains the annotation and raw counts per gene as indicated in file header

source_name: memory TFH cells sorted from a single mouse splenic extract

extract_protocol:
Single cells were extracted from suspensions of spleen from individual mice.
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for dump-CD4+CD44+gp66+ Ly6C-PSGL-1- (TFH) cells
Total RNA was isolated with PicoPure RNA isolation kit
cDNA and library preparation were performed with SMART-Seq v4 Ultra Low Input RNA Sequencing kit

treatment_protocol: Anti-ICOSL treatment was performed starting at day 50 after infection, 4 injections every 72 hours and spleens were harvested day 61 p.i.

value: memory TFH cells


title: Naive CD4+ T cells replicate 2

description: tagmented DNA


title: D-5.SVZ.HI.P20

description: Gene expression data from rat microglia


title: B-3.Cortex.Sham.P20

description: Gene expression data from rat microglia


title: Treat_9


title: A-3.SVZ.Sham.P10

description: Gene expression data from rat microglia


title: C-2.SVZ.HI.P10

description: Gene expression data from rat microglia


title: TH1 CD4+ T cells replicate 1

description: tagmented DNA


title: A-2.Cortex.Sham.P10

description: Gene expression data from rat microglia


title: B-4.SVZ.Sham.P20

description: Gene expression data from rat microglia


title: E-3.Cortex.HI.P10

description: Gene expression data from rat microglia


title: B-6.SVZ.Sham.P20

description: Gene expression data from rat microglia


title: D-2.Cortex.HI.P20

description: Gene expression data from rat microglia


title: Ctrl_5


title: Ctrl_4


title: Treat_8


title: Ctrl_3


title: Ctrl_1


title: B-5.Cortex.Sham.P20

description: Gene expression data from rat microglia


title: E-3.SVZ.HI.P10

description: Gene expression data from rat microglia


title: D-3.SVZ.HI.P20

description: Gene expression data from rat microglia


title: E-1.SVZ.HI.P10

description: Gene expression data from rat microglia


title: Treat_7


title: spleen_2

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.1.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.5.3a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
For spleen_0 sample, using cells from a mouse strain including a fluorescent ZSGREEN reporter gene construct, we added the sequence obtained at https://www.ncbi.nlm.nih.gov/nuccore/6090872 to the reference transcriptome before mapping.
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R and the cellrangerRkit package version 2.0.0. The UMI matrix was filtered to keep only cells with log library size > 2.8, log number of features > 2.6, % mitochondrial reads >= 6, % ribosomal protein reads >= 20. Genes with average counts < .005 were removed.  We retained a total of 3096 cells and 9853 genes. The UMI counts matrix is provided as files UMImatrix_NICD_protector.tsv.gz and UMImatrix_no_NICD_protector.tsv.gz.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAACCTGAGCCAGTAG-Spleen_0")

source_name: memory CD4+ T cells from a single mouse splenic extract

extract_protocol:
Single cells were extracted from suspensions of spleen from 3 female individual litter-mate mice that were pooled for spleen_0 sample and individual female litter-mate mice for spleen_1 and spleen_2 sample  (1 per sample)
For Spleen_1 and Spleen_2 samples, mice were intravenously injected with 25μg of commercial (BioLegend, #149802) NICD-protector 15 minutes prior to organ harvest.
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for dump-CD4+CD44+gp66+ expression.
The sorted cell suspension from each sample was loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: No treatment was performed


title: spleen_0


title: spleen_1


title: Pons P3

status: Public on Nov 19 2019

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

description:
C57BL6-P3-pons
single cell RNA-Seq
processed data file: Pons_join.2D.tsv

data_processing:
Read1 (26nt) contains the barcode and the UMI
Read2 (98nt) contains the biological information
Cell Ranger v2.0.1 for E12.5, E15.5 and P0 samples and Cell Ranger v2.1.1 for P3 and P6 samples was used with default parameters to demultiplex and align sequencing reads, to distinguish cells from background, and to obtain gene read counts per cell
The gtf from the Ensembl release 84 was used as gene reference
Genome_build: mm10
Supplementary_files_format_and_content: filtered gene matrix from Cell Ranger.
Supplementary_files_format_and_content: See GSE133531_metadata.info_README.txt for a description of the metadata.tsv, Forebrain_join.2D.tsv, and Pons_join.2D.tsv files.

source_name: Pons, fresh tissue

extract_protocol:
Mouse embryonic and postnatal brain structures were dissected from the gestational timepoints E12.5 and E15.5 and from postnatal timepoints P0, P3 and P6. Dissections were performed under a Leica stereoscope with a pair of Moria ultra fine forceps (Fine Science Tools), in a PBS solution. The tissue was transferred into ice cold Leibovitz’s medium, followed by single cell dissociation with the Papain System Dissociation.
The concentration of the single cell suspension was assessed with a Trypan blue count. Approximately 10,000 cells per sample were loaded on the Chromium Single Cell 3’ (10X Genomics) system V2 protocol. GEM-RT, DynaBeads cleanup, PCR amplification and SPRIselect beads cleanup were performed using Chromium Single Cell 3’ Gel Bead kit. Indexed single cell libraries were generated using the Chromium Single Cell 3’ Library kit and the Chromium i7 Multiplex kit

value: Pons, fresh tissue

tag: method of dissociation

value: Worthington Papain Dissociation System

tag: phenotype

value: Normal mouse

tag: developmental stage


title: meningioma [18-43]

status: Public on Nov 13 2019

city: Houston

first: Tiemo

middle: J

last: Klisch

state: Texas

address: 1250 Moursund Street, N1370.08

department: Department of Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description:
18-43
Primary tumor

data_processing:
Individual libraries within the samples were demultiplexed using CASAVA 1.8.2 (CASAVA, RRID:SCR_001802).
TopHat2 (RRID:SCR_013035) was used for read alignment.
FastQC (RRID:SCR_014583) and RSeQC (RRID:SCR_005275) were used for read and alignment quality assessment.
HTSeq (RRID:SCR_005514) was used for expression count.
The reads were aligned to GRCh37 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: GRCh37
Supplementary_files_format_and_content: *_htseq.counts.txt: Tab-delimited text files include expression count values for each Sample.

organism: Homo sapiens

source_name: meningioma, WHO II, Validation

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
Illumina, using SOP from BCM-HGSC (https://www.hgsc.bcm.edu).

tag: cohort

value: Validation

value: Meningioma

tag: pathology

value: WHO II

tag: gender

value: Male

tag: wes

value: Y


title: Forebrain E12.5

description:
ET_CT_12
single cell RNA-Seq
processed data file: Forebrain_join.2D.tsv

source_name: Forebrain, fresh tissue

value: Forebrain, fresh tissue


title: Pons P6

description:
C57BL6-P6-pons
single cell RNA-Seq
processed data file: Pons_join.2D.tsv


title: meningioma [18-33]

description:
18-33
Primary tumor

source_name: meningioma, WHO I, Validation

value: WHO I

value: Female


title: meningioma [18-48]

description:
18-48
Primary tumor


title: Forebrain E15.5

description:
ET_CT_15
single cell RNA-Seq
processed data file: Forebrain_join.2D.tsv


title: Forebrain P6

description:
C57BL6-P6-cortex
single cell RNA-Seq
processed data file: Forebrain_join.2D.tsv


title: Forebrain P3

description:
C57BL6-P3-cortex
single cell RNA-Seq
processed data file: Forebrain_join.2D.tsv


title: meningioma [18-03]

description:
18-03
Primary tumor


title: Hindbrain E12.5

description:
ET_PO_12
single cell RNA-Seq
processed data file: Pons_join.2D.tsv

source_name: Hindbrain, fresh tissue

value: Hindbrain, fresh tissue


title: meningioma [18-24]

description:
18-24
Primary tumor


title: MEP_E12_1

status: Public on Nov 29 2019

description:
BSSE_QGF_39309
MEP_SclCre;Exon12 (E12)_1

data_processing:
Reads were mapped against the mouse genome (version GRCm38/mm10) using the spliced-read aligner STAR.
Raw reads and mapping quality was assessed by the qQCReport function from the R/Bioconductor software package QuasR.
Expression of RefSeq genes (annotation downloaded from UCSC 2015-12-18) was quantified by counting reads mapping into exons using the qCount function of QuasR.
For gene expression visualization the resulting count table was normalized using function voom from the R/Bioconductor software package limma, including a quantile normalization to adjust for library composition biases.
Genome_build: mm10
Supplementary_files_format_and_content: gene_counts.tsv.gz: text file with tab separated values; each row contains the annotation and raw counts per gene; columns correspond to: 1. ENTREZID, 2. gene symbol, 3. gene name, 4. gene length (exon union model), 5.-13. gene counts per sample;
Supplementary_files_format_and_content: gene_expression_levels.tsv.gz: text file with tab separated values; each row contains the annotation and the limma-voom estimated gene expression levels per gene; columns correspond to: 1. ENTREZID, 2. gene symbol, 3. gene name, 4.-12. gene expression levels per sample;

source_name: MEP_SclCre;Exon12 (E12)

growth_protocol: JAK2 mutations were induced with 5 consecutiveinjections of tamoxifen everyday (i.p.)

extract_protocol:
Bone marrow MEPs were FACS sorted and total RNA was extraced with PicoPure RNA preparation kit (invitrogen)
SmartSeq 2

treatment_protocol: 6-12 weeks post tamoxifen induction

tag: strain background

tag: genotype/variation

value: SclCre;Exon12 (E12)

value: Bone marrow

tag: cell population

value: MEP

tag: time point

value: 6 weeks after tamoxifen induction


title: MEP_WT_50

description:
BSSE_QGF_52894
MEP_WT_50

value: WT

tag: tissue

value: 12 weeks after tamoxifen induction


title: MEP_WT_51

description:
BSSE_QGF_52895
MEP_WT_51


title: MEP_E12_5

description:
BSSE_QGF_39311
MEP_SclCre;Exon12 (E12)_5


title: MEP_VF_2

description:
BSSE_QGF_39295
MEP_SclCre;V617F (VF)_2

source_name: MEP_SclCre;V617F (VF)

value: SclCre;V617F (VF)


title: MEP_VF_3

description:
BSSE_QGF_39296
MEP_SclCre;V617F (VF)_3


title: meningioma [18-42]

description:
18-42
Primary tumor

tag: age


title: Forebrain P0

description:
PT_CT_0
single cell RNA-Seq
processed data file: Forebrain_join.2D.tsv

value: Worthington Papain Dissociation System

value: Normal mouse


title: MEP_VF_1

description:
BSSE_QGF_39294
MEP_SclCre;V617F (VF)_1


title: meningioma [18-34]

description:
18-34
Primary tumor

value: Validation

value: Meningioma


title: MEP_E12_2

description:
BSSE_QGF_39310
MEP_SclCre;Exon12 (E12)_2


title: MEP_WT_52

description:
BSSE_QGF_52896
MEP_WT_52


title: meningioma [17-35]

description:
17-35
Primary tumor


title: Pons P0

description:
PT_PO_0
single cell RNA-Seq
processed data file: Pons_join.2D.tsv

value: Pons, fresh tissue


title: meningioma [17-30]

description:
17-30
Primary tumor

value: WHO II

value: Male

value: Y


title: meningioma [17-09]

description:
17-09
Primary tumor

value: Female


title: Pons E15.5

description:
ET_PO_15
single cell RNA-Seq
processed data file: Pons_join.2D.tsv


title: meningioma [18-40]

description:
18-40
Primary tumor

value: WHO I


title: meningioma [18-38]

description:
18-38
Primary tumor


title: meningioma [18-45]

description:
18-45
Primary tumor


title: meningioma [18-13]

description:
18-13
Primary tumor


title: meningioma [17-23]

description:
17-23
Primary tumor


title: meningioma [17-29]

description:
17-29
Primary tumor


title: meningioma [18-08]

description:
18-08
Primary tumor


title: meningioma [17-34]

description:
17-34
Primary tumor


title: A-5.SVZ.Sham.P10

description: Gene expression data from rat microglia

tag: animal id

value: SVZ

tag: treatment

value: Sham

tag: rin


title: meningioma [18-50]

description:
18-50
Primary tumor


title: meningioma [18-26]

description:
18-26
Primary tumor


title: meningioma [18-35]

description:
18-35
Primary tumor


title: meningioma [18-15]

description:
18-15
Primary tumor


title: meningioma [18-17]

description:
18-17
Primary tumor


title: meningioma [18-30]

description:
18-30
Primary tumor


title: meningioma [18-07]

description:
18-07
Primary tumor


title: meningioma [18-18]

description:
18-18
Primary tumor


title: meningioma [18-39]

description:
18-39
Primary tumor


title: meningioma [18-49]

description:
18-49
Primary tumor


title: meningioma [18-29]

description:
18-29
Primary tumor


title: meningioma [18-28]

description:
18-28
Primary tumor


title: meningioma [18-05]

description:
18-05
Primary tumor


title: meningioma [17-33]

description:
17-33
Primary tumor


title: meningioma [17-28]

description:
17-28
Primary tumor


title: meningioma [17-24]

description:
17-24
Primary tumor


title: meningioma [17-22]

description:
17-22
Primary tumor


title: meningioma [17-25]

description:
17-25
Primary tumor


title: meningioma [18-41]

description:
18-41
Primary tumor


title: meningioma [18-20]

description:
18-20
Primary tumor


title: meningioma [18-14]

description:
18-14
Primary tumor


title: meningioma [DCC37]

description:
DCC37
Primary tumor

source_name: meningioma, WHO II, Discovery

value: Discovery


title: meningioma [17-13]

description:
17-13
Primary tumor

source_name: meningioma, WHO I, Discovery


title: meningioma [DCC34]

description:
DCC34
Primary tumor


title: meningioma [17-20]

description:
17-20
Primary tumor


title: meningioma [17-01]

description:
17-01
Primary tumor


title: meningioma [DCC40]

description:
DCC40
Primary tumor


title: meningioma [DCC35]

description:
DCC35
Primary tumor


title: meningioma [DCC33]

description:
DCC33
Primary tumor


title: meningioma [DCC43]

description:
DCC43
Primary tumor


title: meningioma [16-02]

description:
16-02
Primary tumor


title: meningioma [DCC53]

description:
DCC53
Primary tumor


title: meningioma [15-17]

description:
15-17
Primary tumor


title: meningioma [DCC23]

description:
DCC23
Primary tumor


title: meningioma [DCC36]

description:
DCC36
Primary tumor


title: meningioma [DCC13]

description:
DCC13
Primary tumor


title: meningioma [DCC31]

description:
DCC31
Primary tumor


title: meningioma [DCC06]

description:
DCC06
Primary tumor


title: meningioma [DCC27]

description:
DCC27
Primary tumor


title: meningioma [DCC19]

description:
DCC19
Primary tumor


title: meningioma [DCC22]

description:
DCC22
Primary tumor


title: meningioma [DCC10]

description:
DCC10
Primary tumor


title: meningioma [DCC18]

description:
DCC18
Primary tumor


title: meningioma [DCC09]

description:
DCC09
Primary tumor


title: meningioma [17-12]

description:
17-12
Primary tumor


title: meningioma [DCC21]

description:
DCC21
Primary tumor


title: meningioma [16-28]

description:
16-28
Primary tumor


title: meningioma [17-10]

description:
17-10
Primary tumor


title: meningioma [DCC38]

description:
DCC38
Primary tumor


title: meningioma [DCC32]

description:
DCC32
Primary tumor


title: meningioma [17-11]

description:
17-11
Primary tumor


title: meningioma [17-08]

description:
17-08
Primary tumor


title: meningioma [16-14]

description:
16-14
Primary tumor


title: meningioma [16-49]

description:
16-49
Primary tumor


title: meningioma [DCC25]

description:
DCC25
Primary tumor


title: meningioma [17-19]

description:
17-19
Primary tumor


title: meningioma [17-02]

description:
17-02
Primary tumor


title: meningioma [16-47]

description:
16-47
Primary tumor


title: meningioma [16-50]

description:
16-50
Primary tumor


title: meningioma [DCC07]

description:
DCC07
Primary tumor


title: meningioma [17-04]

description:
17-04
Primary tumor


title: meningioma [15-23]

description:
15-23
Primary tumor


title: meningioma [15-18]

description:
15-18
Primary tumor


title: meningioma [DCC51]

description:
DCC51
Primary tumor


title: meningioma [16-51]

description:
16-51
Primary tumor


title: meningioma [15-35]

description:
15-35
Primary tumor


title: meningioma [DCC30]

description:
DCC30
Primary tumor


title: meningioma [DCC28]

description:
DCC28
Primary tumor


title: meningioma [DCC12]

description:
DCC12
Primary tumor


title: meningioma [15-13]

description:
15-13
Primary tumor


title: meningioma [DCC29]

description:
DCC29
Primary tumor


title: meningioma [17-15]

description:
17-15
Primary tumor


title: meningioma [17-05]

description:
17-05
Primary tumor


title: meningioma [17-03]

description:
17-03
Primary tumor


title: meningioma [16-44]

description:
16-44
Primary tumor


title: meningioma [15-25]

description:
15-25
Primary tumor


title: meningioma [16-41]

description:
16-41
Primary tumor


title: meningioma [16-35]

description:
16-35
Primary tumor


title: meningioma [15-24]

description:
15-24
Primary tumor


title: meningioma [16-06]

description:
16-06
Primary tumor


title: meningioma [14-04]

description:
14-04
Primary tumor


title: meningioma [DCC42]

description:
DCC42
Primary tumor


title: meningioma [15-32]

description:
15-32
Primary tumor


title: VBB_Gard_2

status: Public on Aug 22 2019

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

data_processing:
Illumina adapters and low-quality score (<20) bases were removed from the raw reads using TrimGalore! (V.0.2.7). Trimmed reads were mapped to the rhesus macaque genome (MacaM v7.6.8) using the STAR 2-pass method, and collated the number of reads that mapped uniquely to each annotated MacaM gene using HTSeq-count (v0.6.1) with the option “intersection-nonempty”.
Prior to RNA-seq data analysis, we first filtered out genes that were very lowly or not detectably expressed in our samples. Specifically, we removed genes that exhibited low median RPKM (≤ 2) in all three conditions (Gard, reported here, and control and LPS, available in GSE83304), which resulted in a final set of read counts for 9,088 genes.
We then normalized gene expression levels across samples using the TMM algorithm (weighted trimmed mean of M-values), implemented in the R package edgeR. Finally, we log-transformed the data using the voom function in R package limma.
Genome_build: MacaM
Supplementary_files_format_and_content: SGE_Gard_read_counts.txt

molecule: polyA RNA

organism: Macaca mulatta

source_name: Whole blood

extract_protocol:
We separated the serum and cellular fractions, lysed and discarded the red cells from the cell pellet with red blood cell lysis buffer (RBC lysis solution, 5 Prime Inc.), and lysed the remaining white blood cell fraction in Qiazol for storage at -80°C. We extracted total RNA from each sample using the Qiagen miRNAEASY kit.
Each RNA-sequencing library was prepared from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following the manufacturer’s instructions and selecting for ~350 bp size fragments. Libraries were amplified via PCR for 13 cycles, barcoded, and pooled into sets of 10-12 samples for sequencing on an Illumina HiSeq 2500.

treatment_protocol: We drew 1 mL of whole blood from each female (in Phase 2 only) directly into a TruCulture tube (Myriad RBM) that contained cell culture media plus 1 μg/ml of the TLR7 agonist Gardiquimod (Gard), a synthetic ligand that mimics infection with a single-stranded RNA virus. Paired samples treated with either media only (control) or Lipopolysaccharide (1 μg/mL ultra pure LPS from the E. coli 0111:B4 strain) were processed in two additional tubes per subject (see GSE83304). Samples in the three conditions were incubated in parallel for 4 hours at 37°C.

tag: cell type

value: White blood cells

tag: subject id

value: VBB

tag: study phase

value: phase 2

tag: study group

tag: condition

value: Gard

tag: current rank (elo)

tag: past rank (elo)

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: WXC_Gard_2

tag: cell type

tag: subject id

value: WXC

tag: study phase

tag: age


title: RVe12_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RUf11_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RWu12_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RVw12_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RZe12_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: RVb12_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RTf12_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RUd14_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RSu12_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RSu10_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: RSh11_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RSi10_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RPy12_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RPs7_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RPq11_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: RPp10_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RZq10_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RPm4_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RVq13_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RNi12_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: ROv12_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RPj10_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: ROn5_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RJl11_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RJs11_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: RJj10_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RJf7_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RQp9_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RIb12_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RIe12_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: RFm12_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: REg12_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RBc8_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: RFq9_Gard_2

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: RCy13_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: age


title: 482_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)


title: RAa11_Gard_2

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: RIa13_Gard_2

tag: cd14-act. mon.

tag: helper t cells

tag: cytotoxic t cells

tag: double+ t cells


title: IL-94

status: Public on Jul 26 2019

description:
mRNA
processed data file: normalized_expr.valerie_celiac.human.csv

data_processing:
Adaptor sequences and low quality score bases (Phred score < 20) were first trimmed using Trim Galore (version 0.2.7).
The resulting reads were then mapped to the human genome reference sequence (Ensembl GRCh37 release 75) using Kallisto v0.43 with a GRch38 transcript annotation GTF file downloaded from Ensembl rel 87.
Gene expression was normalized across samples using the weighted trimmed mean of M-values algorithm (TMM), as implemented in the R package edgeR.
After normalization, we log-transformed the data using the voom function in the limma package.
For all downstream analyses, we excluded non-coding and lowly expressed genes with a median read count lower than 20 in all samples.
Following this pre-processing of the data, we fitted the log-transformed expression estimates to linear models using the lmFit function from the limma package to look at differences in gene expression between control and celiac disease patients, while taking into account variation in sex and age of the donors.
Genome_build: Ensembl GRCh37
Supplementary_files_format_and_content: normalized_expr.valerie_celiac.human.csv: Comma-separated text file; Gene by sample expression matrix.

source_name: duodenum

extract_protocol:
One duodenal biopsy was obtained from ninety-six individuals undergoing upper gastrointestinal endoscopy during diagnostic work-up at the University of Chicago Medicine and at Mayo Clinic, including forty-five non-celiac controls and fifty-one untreated CeD patients (active CeD) for subsequent RNA-sequencing. Control subjects included 29 females and 16 males and underwent upper gastrointestinal endoscopy during a diagnostic work-up for anemia, failure to thrive or other intestinal disorders not associated with CeD. All controls had normal small intestinal histology, no family history of CeD, no significant levels of anti-TG2 IgA antibodies in the serum. Active CeD patients included 31 females and 20 males, all had positive anti-TG2 antibodies and small intestinal enteropathy with increased infiltration of IELs, crypts hyperplasia and villous atrophy, according to currently accepted diagnostic guidelines. A single duodenal bioptic fragment was directly submerged in RNA-later (QIAGEN), kept at 4°C for 24 hours and then frozen at -80°C upon RNA later removal until processing. Defrost tissues were homogenized using magnetic beads and a Cell Tissue Homogenizer (Bullet blender by Next Advance) and RNA was extracted using RNeasy columns (QIAGEN). RNA integrity was assessed by Bioanalyzer (Agilent).
RNA-sequencing libraries were prepared using the SMARTer® Stranded Total RNA Sample Prep Kit-HI Mammalian by Clontech Laboratories (Takara), according to manufacturer’s instructions.
Libraries quality was checked by Bioanalyzer (Agilent) prior to pooling and sequencing. Indexed cDNA libraries were pooled in equimolar amounts and sequenced with single-end 50bp reads with a high output Flow Cell (8 lane flow cell) on an Illumina HiSeq4000 at the University of Chicago Genomic Facility.

tag: tissue

value: Duodenum

tag: diagnosis

value: CONTROL

tag: Sex


title: IL-91


title: IL-95


title: IL-99

value: ACTIVE CELIAC


title: IL-83


title: IL-85


title: IL-8


title: IL-81


title: IL-80


title: IL-249


title: IL-84


title: IL-245


title: IL-243


title: IL-97


title: IL-242


title: IL-241


title: IL-79


title: RCw10_Gard_2

tag: cell type

tag: subject id

tag: study phase

tag: cd8- b cells

tag: cd8+ b cells

tag: nk t cells

tag: nk cells cd3- cd16+ (%)


title: IL-7

tag: age


title: IL-24


title: IL-236


title: IL-23


title: IL-244


title: IL-228


title: IL-231


title: IL-226


title: IL-234


title: IL-225


title: IL-223


title: IL-224


title: IL-218


title: IL-219


title: IL-215


title: IL-217


title: IL-22


title: IL-221


title: IL-206


title: IL-207


title: IL-227


title: IL-230


title: IL-210


title: IL-202


title: IL-204


title: IL-2


title: IL-205


title: IL-191


title: IL-184


title: IL-185


title: IL-187


title: IL-18


title: IL-178


title: IL-192


title: IL-190


title: IL-211


title: IL-196


title: IL-195


title: IL-173


title: IL-171


title: IL-165


title: IL-169


title: IL-203


title: IL-159


title: IL-168


title: IL-174


title: IL-151


title: IL-150


title: IL-193


title: IL-179


title: IL-164


title: IL-158


title: IL-136


title: IL-133


title: IL-146


title: IL-13


title: IL-155


title: IL-142


title: IL-147


title: IL-115


title: IL-116


title: IL-112


title: IL-156


title: IL-121


title: IL-111


title: IL-157


title: IL-122


title: IL-106


title: IL-107


title: IL-1


title: J4679_BI00853520_50mgkg_5d

status: Public on Jul 19 2019

description: Sample 8

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm9, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in July 2013) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm9
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: 4T1 primary tumor

growth_protocol: 1,000,000 4T1 cells suspended in 100µl sterile PBS were injected into mammary fat pad number nine of anaesthetized, six to ten week- old female BALB/c mice.

extract_protocol:
Snap-frozen 4T1 mouse tumor pieces were homogenized in Trizol (Sigma-Aldrich) and total RNA was isolated with the RNeasy Lipid Tissue Mini Kit (Qiagen).
Approximately 80 ng of total RNA were subsequently used for TruSeq Stranded mRNA Library preparation on the NeoPrep System (Illumina, San Diego, CA, USA) and sequenced on the HiSeq1500 with the paired-end 50 cycle protocol and the fast-output mode (Illumina, San Diego, CA, USA).

treatment_protocol: BI 853520 was administered from day 15 post injection for five consecutive days.

tag: agent


title: J4680_BI00853520_50mgkg_5d

description: Sample 9


title: RAc8_Gard_2

tag: study group

tag: condition

tag: current rank (elo)

tag: past rank (elo)

tag: flowcell

tag: pmn cells (%)

tag: class. mon.

tag: cd14+ act. mon.


title: IL-152

tag: tissue

tag: diagnosis

tag: Sex


title: IL-144


title: J4678_BI00853520_50mgkg_5d

description: Sample 7


title: J4677_BI00853520_50mgkg_5d

description: Sample 6


title: IL-163


title: IL-109


title: IL-14


title: IL-110


title: J4676_BI00853520_50mgkg_5d

description: Sample 5


title: J4675_BI00853520_50mgkg_5d

description: Sample 4


title: J4674_Natrosol_0.5perc_5d

description: Sample 3

value: Natrosol


title: J4672_Natrosol_0.5perc_5d

description: Sample 1


title: J4673_Natrosol_0.5perc_5d

description: Sample 2


title: 201228790040_R03C01

status: Public on Jun 06 2019

type: genomic

city: Atlanta

first: Alicia

last: Smith

address: 101 Woodruff Circle

institute: Emory University

description: HumanMethylationEPIC BeadChip - standard protocol

hyb_protocol: HumanMethylationEPIC BeadChip

scan_protocol: BeadStudio

data_processing: non-normalized, background subtracted beta-values

label: cy3, cy5

source_name: Whole Blood

label_protocol: Illumina Protocol

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA)
EZ DNA Methylation-GoldTM Kit (Zymo Research, Irvine, CA)

tag: gender

tag: race

tag: nk

tag: bcell

tag: mono

tag: neu

tag: age acceleration


title: 201228780147_R07C01

tag: age

value: AA


title: 201228790040_R07C01


title: 201228780147_R05C01


title: 201228790040_R04C01


title: 201228790010_R07C01


title: 201228790041_R01C01


title: 201228780147_R06C01

value: Other


title: 201228790041_R06C01


title: 201228790040_R01C01


title: 201228790010_R08C01


title: 201228790010_R06C01


title: 201228790041_R03C01


title: 201228790040_R02C01


title: 201228790010_R02C01


title: 201228780147_R04C01


title: 201228790041_R05C01


title: 201228780147_R02C01


title: 201228780147_R03C01


title: 201228790010_R05C01


title: IL-143


title: 201228780145_R08C01


title: 201228780147_R08C01


title: 201228780145_R06C01


title: 201228790041_R02C01


title: 201228790041_R04C01


title: 201228780147_R01C01


title: 201228790010_R01C01


title: 201228780145_R04C01


title: 201228780145_R03C01


title: 201228780145_R05C01


title: 201228780138_R05C01


title: 201228780145_R02C01


title: 201228780138_R07C01


title: 201228780138_R02C01


title: 201228780140_R03C01


title: 201228780139_R02C01


title: 201228780138_R03C01


title: 201228780140_R07C01


title: 201228780140_R02C01


title: 201228780140_R04C01


title: 201228780138_R04C01


title: 201228780138_R06C01


title: 201228780145_R01C01


title: 201228780137_R08C01


title: 201228780137_R05C01


title: 201228780137_R07C01


title: 201228780137_R03C01


title: 201228780138_R08C01


title: 201228780137_R02C01


title: 201228780136_R07C01


title: 201228780137_R01C01


title: 201228780137_R06C01


title: 201228780136_R02C01


title: 201228780133_R08C01


title: 201228780133_R07C01


title: 201228780138_R01C01


title: 201228780133_R06C01


title: 201228780133_R05C01


title: 201228780133_R01C01


title: 201228780133_R04C01


title: 201228780132_R07C01


title: 201228780137_R04C01


title: 201228790010_R03C01


title: 201228780131_R05C01


title: 201228780132_R05C01


title: 201228780132_R01C01


title: 201228780131_R07C01


title: 201228780131_R04C01


title: 201228780132_R06C01


title: IL-135

value: Male


title: 201228780131_R06C01

value: Female


title: 201228780129_R08C01


title: 201228780132_R04C01


title: 201228780132_R02C01


title: 201228780132_R03C01


title: 201228780131_R03C01


title: 201228780129_R06C01


title: 201228780129_R07C01


title: 201228780129_R05C01


title: 201228780129_R04C01


title: 201228780129_R02C01


title: 201228780129_R03C01


title: 201228780129_R01C01


title: 201228780127_R07C01


title: 201228780127_R06C01


title: 201228780127_R08C01


title: 201228780131_R08C01


title: 201228780127_R03C01


title: 201228780127_R05C01


title: 201228780127_R04C01


title: 201228780127_R02C01


title: 201228780122_R07C01


title: 201228780122_R02C01


title: 201228780118_R08C01


title: 201228780101_R05C01


title: 201228780118_R02C01


title: 201228780118_R05C01


title: 201228780101_R06C01


title: 201228780101_R01C01


title: 201228780118_R03C01


title: 201228780101_R08C01


title: 201228780118_R06C01


title: 201228780100_R02C01


title: 201228780118_R04C01


title: 201228780118_R01C01


title: 201228780118_R07C01


title: 201228780100_R04C01


title: 201228780100_R03C01


title: 201228780098_R08C01


title: 201228780098_R07C01


title: 201228780098_R05C01


title: 201228780098_R02C01


title: 201228780089_R08C01


title: 201228780089_R07C01


title: 201228780101_R07C01


title: 201228780098_R01C01


title: 201228780085_R03C01


title: 201228780089_R02C01


title: 201228780089_R01C01


title: 201228780100_R01C01


title: 201228780085_R02C01


title: 201228780074_R04C01


title: 201228780074_R08C01


title: 201228780074_R02C01


title: 201228780073_R04C01


title: 201228780073_R01C01


title: 201228780074_R01C01


title: 201228780073_R02C01


title: 201228780035_R08C01


title: 201228780035_R07C01


title: 201228780035_R04C01


title: 201228780074_R03C01


title: 201228780035_R03C01


title: 201228780035_R06C01


title: 201228780098_R06C01


title: 201228780035_R05C01


title: 201228780035_R02C01


title: 201228780098_R04C01


title: 201228780035_R01C01


title: 201228780030_R08C01


title: 201228780080_R06C01


title: 201228780030_R06C01


title: 201228780030_R05C01


title: 201228780030_R04C01


title: 201228780030_R03C01


title: 201228780030_R01C01


title: 201228780061_R02C01


title: 201228780030_R02C01


title: 201228780029_R08C01


title: 201228780073_R08C01


title: 201228780025_R08C01


title: 201228780025_R07C01


title: 201228780029_R07C01


title: 201228780025_R05C01


title: 201228780018_R07C01


title: 201228780025_R02C01


title: 201228780025_R03C01


title: 201228780025_R01C01


title: 201228780018_R02C01


title: 201228780025_R06C01


title: 201228780013_R01C01


title: 201220980060_R07C01


title: 201228780013_R06C01


title: 201228780030_R07C01


title: 201220980060_R06C01


title: 201220980060_R01C01


title: 201228780018_R01C01


title: 201228780027_R08C01


title: 201220980052_R08C01


title: 201220980060_R02C01


title: 201220980056_R02C01


title: 201220980052_R07C01


title: 201228780025_R04C01


title: 201228780018_R03C01


title: 201220980049_R06C01


title: 201220980052_R02C01


title: 201220980052_R03C01


title: 201220980049_R08C01


title: 201220980052_R04C01


title: 201220980049_R04C01


title: 201220980049_R07C01


title: 201220980049_R03C01


title: 201220980049_R02C01


title: 201220980048_R08C01


title: 201220980049_R01C01


title: 201220980048_R06C01


title: 201220980048_R04C01


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title: 200928190033_R07C01


title: 200930750006_R08C01


title: 200928190033_R03C01


title: CBX8-HS

status: Public on May 31 2019

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
Sequencing reads were aligned to the human genome hg19 using bwa and bam2bw was used for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (bw) files

growth_protocol: The (human) erythromyeloblastoid leukemia cell line K562 was cultured in RPMI 1640 (containing L-glutamine) supplemented with 10% FCS and 1% penicillin/streptomycin (PAA Laboratories).

extract_protocol:
Control and HS K562 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature at a concentration of 15x106 cells/ml. The fixed cells were sonicated for 4 minutes (30 sec on; 30 sec off) using the Diagnode Bioruptor and centrifuged at maximum speed for 10 minutes. Chromatin of about 5x105 cells was incubated overnight in dilution buffer (167mM NaCl, 16,7 mM Tris (pH 8), 1,2mM EDTA, 1% Triton X-100) with 1 µg antibody at 4C. ProtA/G beads were blocked and incubated with the chromatin-Ab for one hour at 4C. Beads were washed with three different wash buffers and chromatin was eluted from the beads. DNA-proteins were de-crosslinked (200mM NaCl and 4 µl proteinase K (10mg/ml)), by incubation for four hours at 65C and samples were purified using the Qiaquick MinElute PCR purification kit according manufacturer’s protocol.
Sequencing samples were prepared according to the manufacturer's protocol (Illumina). End repair was performed using the precipitated DNA using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adapters were ligated. The DNA was loaded on gel and a band corresponding to ~300 bp (ChIP fragment + adapters) was excised. The DNA was isolated, amplified by PCR and used for cluster generation on the NextSeq500 genome analyzer. The 50 bp tags were mapped to the human genome HG19 using BWA (Li and Durbin, 2009). For processing and manipulation of SAM/BAM files SAMtools was used (Li et al., 2009). For each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window and visualized in the UCSC genome browser (Kent et al., 2002).

treatment_protocol: Cells were heat shocked  for 1 hour at 44C

tag: antibody

value: anti-CBX8 (C15410333, Diagenode)

tag: treatment

tag: sample collection (day)

tag: cell line


title: GFP-CBX2-HS

value: anti-GFP (ab290, Abcam)


title: Sca_rep2

status: Public on May 16 2019

description: Sample 13

data_processing:
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for allowing only unique hits to genome (outFilterMultimapNmax=1) and  filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw counts for Entrez Genes , 1.column is EntrezGeneID, 2. column is length of all exons in nt, 3. and remaining columns contain raw counts

source_name: Forelimbs E10.5

growth_protocol: not applicable

extract_protocol:
Rneasy micro Kit (Qiagen)
NEBNext Poly(A) mRNA Magnetic Isolation Module; NEBNext Ultra II RNA Library Prep; NEBNext Multiplex Oligos for Illumina Index Primes set 1

treatment_protocol: not applicable

tag: populations phenotype

tag: gating strategy

value: 7AAD- (CD31 Ter119 CD45 EpCam Gr1 CD11b)- Sox9-JAG1-SCA-1+

tag: replicate

tag: developmental stage


title: Sca_rep3

description: Sample 14


title: Jagged_rep2

description: Sample 11

value: 7AAD- (CD31 Ter119 CD45 EpCam Gr1 CD11b)- Sox9-JAG1+SCA-1-


title: 200928190033_R08C01


title: Jagged_rep3

description: Sample 12


title: 200928190033_R05C01


title: Jagged_rep1

description: Sample 10


title: PDGFRa_rep3

description: Sample 9

value: 7AAD- (CD31 Ter119 CD45 EpCam Gr1 CD11b)- Sox9-JAG1-SCA-1-PDGFRαhi


title: 200928190033_R04C01


title: 200928190096_R08C01


title: PDGFRa_rep2

description: Sample 8


title: CB_rep2

description: Sample 5

source_name: Forelimbs E11.5

value: 7AAD- (CD31 Ter119 CD45 EpCam Gr1 CD11b)- Sox9+PDGFRαhi


title: GFP-CBX2-untreated

value: untreated


title: CBX8-untreated


title: OCP_rep2

description: Sample 2


title: 201113990023_R04C01


title: CB_rep3

description: Sample 6


title: PDGFRa_rep1

description: Sample 7


title: OCP_rep3

description: Sample 3


title: 200928190033_R02C01


title: Nlrp6 knock out, host 1

status: Public on May 08 2019

description:
Nlrp6ko_1
BSSE_QGF_65656_H5TY3BGX3_1_7_6_Nlrp6ko_1_GCCAATA_S5

data_processing:
Reads were aligned to the mouse genome (mm10) using the spliced read aligner STAR. Sequencing and mapping quality was assessed by the
qQCReport function of the R package QuasR. Gene expression was quantified by the qCount function of QuasR using an exon-union model
of mm10 known genes (downloaded from UCSC 2015-12-18).
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab separated values; each row contains the annotation and raw counts per gene; columns correspond to: 1. ENTREZID, 2. gene symbol, 3. gene name, 4. gene length (exon union model), 5.-12. gene counts per sample

source_name: Nlrp6 knock out_CD4+ T cells from host spleen

extract_protocol:
T cells were isolated from the colonic lamina propria, and RNA isolated with the Direct-zol MiniPrep Kit (Zymo Research). Liberaries were prepared with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and sequenced by Single-reads 81 bases using the NextSeq 500 High Output Kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: host strain genotype

value: RAG-/-

tag: host id

tag: transferred with

value: Nlrp6-/- CD4 T cells

tag: cell type

value: CD4+ T cells from host spleen


title: Nlrp6 knock out, host 5

description:
Nlrp6ko_5
BSSE_QGF_65659_H5TY3BGX3_1_8_2_Nlrp6ko_5_TAGCTTA_S8


title: Nlrp6 knock out, host 2

description:
Nlrp6ko_2
BSSE_QGF_65657_H5TY3BGX3_1_7_7_Nlrp6ko_2_CAGATCA_S6


title: Nlrp6 wild type, host 5

description:
WT_5
BSSE_QGF_65655_H5TY3BGX3_1_7_5_WT_5_ACAGTGA_S4

source_name: Nlrp6 wild type_CD4+ T cells from host spleen

value: Wild Type CD4 T cells


title: Nlrp6 knock out, host 4

description:
Nlrp6ko_4
BSSE_QGF_65658_H5TY3BGX3_1_8_1_Nlrp6ko_4_GATCAGA_S7


title: 200928190114_R03C01

tag: gender

tag: race

tag: nk

tag: bcell

tag: mono


title: Nlrp6 wild type, host 4

description:
WT_4
BSSE_QGF_65654_H5TY3BGX3_1_7_4_WT_4_TGACCAA_S3


title: Nlrp6 wild type, host 1

description:
WT_1
BSSE_QGF_65652_H5TY3BGX3_1_7_1_WT_1_ATCACGA_S1


title: RUNX1wt_ChIP_16172

status: Public on Apr 24 2019

data_processing:
Sequenced reads were aligned against the UCSC human reference genome (GRCh37/hg19) with Burrows-Wheeler Aligner (BWA) program with default parameters. The resultant BAM files were subjected to removal of potential PCR and optical duplicates using Picard MarkDuplicates option. The peak calling algorithm MACS2 was used to detect the RUNX1 binding sites at p-value of 10e-6. Peaks overlapping with the consensus excludable ENCODE blacklist and on sex chromosomes were discarded to avoid confounding by repetitive regions and gender-specific bias. All alignment files were extended to the estimated fragment length and scaled to RPKM-normalized read coverage files using deepTools for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using deepTools by scaling read depth to RPKM-normalized coverage

source_name: AML

extract_protocol:
Purified cells were fixed with 1% formaldehyde (Sigma) at a concentration of approximately 10 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x10 minutes (30 seconds on; 30 seconds off). 67µl of chromatin (1 million cells) was incubated with 229µl dilution buffer, 3µl protease inhibitor cocktail and 0.5-1µg of RUNX1 antibody (Abcam: ab23980) and incubated overnight at 4ºC with rotation. Protein A/G magnetic beads were washed in dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 minutes at 4°C. Beads were washed with 400µl buffer for 5 minutes at 4°C with five rounds of washes. After washing chromatin was eluted using elution buffer for 20 minutes. Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C.Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C. Subsequently adapters were ligated by adding 30µl ligation buffer, 10 Kapa l DNA ligase, 5µl diluted adaptor in a total volume of 110µl and incubated for 15 minutes at 15°C. Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis. Sequencing was performed using Illumina NextSeq 500 machines and generated 43bp paired-end reads.

tag: antibody

value: RUNX1 antibody (Abcam:ab23980)

value: AML


title: RUNX1wt_ChIP_16171


title: CB_rep1

description: Sample 4


title: OCP_rep1

description: Sample 1


title: 200928190096_R05C01

tag: age

value: AA

tag: neu

tag: age acceleration


title: Nlrp6 wild type, host 2

description:
WT_2
BSSE_QGF_65653_H5TY3BGX3_1_7_2_WT_2_CGATGTA_S2


title: 200928190096_R07C01


title: spleen_0ppm_FB1_Ctrl_rep2

status: Public on Apr 15 2019

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

description: 4 weeks diet

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to GPL19893 microarray (Agilent 8X60K, Design 037880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 8 out of 10 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 37571 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 37570 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Sus scrofa

source_name: spleen

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: 12 crossbred weanling piglets housed in floored indoor pens were used in this study. The piglets were weaned at the age of 28 days and transported to the animal facility of the INRA Research Center in Food Toxicology (Toxalim, Toulouse, France).

extract_protocol: Total RNA was extracted in lysing matrix D tubes (MP Biomedicals, Illkirch, France) containing guanidine thiocyanate-acid phenol (Eurobio, Courtaboeuf, France). Quality of these samples was assessed on Bioanalyzer 2100 (Agilent RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA). All samples had a RIN over 7.5.

treatment_protocol: Animals were 6 weeks old at the begining of the study. Animals had ad libitum access to water and feed for the duration of the trial. The first group of pigs was fed with the control diet while the second group was fed with control diet artificially contaminated with 10 ppm Fumonisin B1. They were fed during 4 weeks prior to sacrifice. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. A portion of the spleen were collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.

tag: diet

value: Ctrl


title: spleen_0ppm_FB1_Ctrl_rep1

description: 4 weeks diet


title: jejunal Peyer's patches_10ppm_FB1_Treat_rep6

description: 4 weeks diet

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 10 out of 12 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 38638 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 38637 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: jejunal Peyer's patches

treatment_protocol: Animals were 6 weeks old at the begining of the study. Animals had ad libitum access to water and feed for the duration of the trial. The first group of pigs was fed with the control diet while the second group was fed with control diet artificially contaminated with 10 ppm Fumonisin B1. They were fed during 4 weeks prior to sacrifice. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. A portion of the jejunum with Jejunal Peyers' patches were collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.

tag: condition

value: Treat


title: spleen_0ppm_FB1_Ctrl_rep5

description: 4 weeks diet


title: spleen_10ppm_FB1_Treat_rep5

description: 4 weeks diet


title: jejunal Peyer's patches_0ppm_FB1_Ctrl_rep5

description: 4 weeks diet


title: spleen_10ppm_FB1_Treat_rep2

description: 4 weeks diet


title: spleen_10ppm_FB1_Treat_rep4

description: 4 weeks diet


title: spleen_0ppm_FB1_Ctrl_rep3

description: 4 weeks diet


title: spleen_10ppm_FB1_Treat_rep1

description: 4 weeks diet


title: spleen_10ppm_FB1_Treat_rep3

description: 4 weeks diet


title: liver_0ppm_FB1_Ctrl_rep5

description: 4 weeks diet

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 9 out of 11 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 36415 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36414 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: liver

treatment_protocol: Animals were 6 weeks old at the begining of the study. Animals had ad libitum access to water and feed for the duration of the trial. The first group of pigs was fed with the control diet while the second group was fed with control diet artificially contaminated with 10 ppm Fumonisin B1. They were fed during 4 weeks prior to sacrifice. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. A portion of the liver were collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.


title: liver_10ppm_FB1_Treat_rep5

description: 4 weeks diet


title: jejunal Peyer's patches_10ppm_FB1_Treat_rep4

description: 4 weeks diet


title: jejunal Peyer's patches_10ppm_FB1_Treat_rep5

description: 4 weeks diet


title: jejunal Peyer's patches_0ppm_FB1_Ctrl_rep1

description: 4 weeks diet


title: jejunal Peyer's patches_0ppm_FB1_Ctrl_rep3

description: 4 weeks diet


title: jejunal Peyer's patches_10ppm_FB1_Treat_rep2

description: 4 weeks diet


title: spleen_0ppm_FB1_Ctrl_rep4

description: 4 weeks diet


title: jejunal Peyer's patches_0ppm_FB1_Ctrl_rep6

description: 4 weeks diet


title: liver_10ppm_FB1_Treat_rep3

description: 4 weeks diet


title: jejunal Peyer's patches_10ppm_FB1_Treat_rep3

description: 4 weeks diet


title: jejunal Peyer's patches_0ppm_FB1_Ctrl_rep2

description: 4 weeks diet


title: jejunal Peyer's patches_10ppm_FB1_Treat_rep1

description: 4 weeks diet


title: liver_10ppm_FB1_Treat_rep4

description: 4 weeks diet


title: liver_0ppm_FB1_Ctrl_rep6

description: 4 weeks diet


title: liver_0ppm_FB1_Ctrl_rep4

description: 4 weeks diet


title: PD_15.0205 (mILC-2 suspension)

status: Public on Mar 22 2019

data_processing:
Bases were called using the Illumina CASAVA 1.8.2
RNA-seq: Tags were mapped using TopHat2 (Bowtie2).
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: Wiggle files were generated by determining the number of overlapping sequence reads for each base pair in the genome, averaged over a 10 bp window.

source_name: invasive lobular carcinoma cell line_suspension

growth_protocol: Cells were seeded into a 6 well plate and grown to 80% confluency. For suspension culture, 200.000 cells were seeded into ultra-low attachment 6 well plates and cultured for 24 hours.

extract_protocol:
After washing in Ca2+/Mg2+ containing PBS, RNA was isolated and purified using the RNAeasy kit (Qiagen) followed by DNase treatment (Qiagen).
For RNA-seq 250 ng of RNA was used for ribosomal RNA depletion with RiboZero (Illumina) and subsequent strand specific (USER) library preparation.

tag: cell line

value: invasive lobular carcinoma cell line

tag: culture condition

value: suspension


title: PD_10.0405 (mILC-1 suspension)


title: PD_02.0405 (mILC-1)

source_name: invasive lobular carcinoma cell line_adherent

value: adherent


title: liver_0ppm_FB1_Ctrl_rep2

description: 4 weeks diet


title: PD_34.2606 (IPH-926)


title: liver_10ppm_FB1_Treat_rep2

description: 4 weeks diet


title: liver_0ppm_FB1_Ctrl_rep3

description: 4 weeks diet


title: PD_35.2505 (IPH-926 suspension)


title: jejunum_0ppm_FB1_Ctrl_rep6

description: 4 weeks diet

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 10 out of 12 microarrays or with a minimal weight of 5 per group from at least one experimental group. At this step, 38204 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 38203 rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: jejunum

treatment_protocol: Animals were 6 weeks old at the begining of the study. Animals had ad libitum access to water and feed for the duration of the trial. The first group of pigs was fed with the control diet while the second group was fed with control diet artificially contaminated with 10 ppm Fumonisin B1. They were fed during 4 weeks prior to sacrifice. They were cared for in accordance with the National Institute of Health Guide and the French Ministry of Agriculture for the Care and Use of Laboratory Animals. At the conclusion of the experiment, immediately after electrical stunning, the piglets were sacrificed by exsanguination. A portion of the jejunum was collected from euthanatized animals, flash-frozen in liquid nitrogen, and stored at -80°C until processed for total RNA extraction.


title: jejunum_10ppm_FB1_Treat_rep1

description: 4 weeks diet


title: jejunum_0ppm_FB1_Ctrl_rep2

description: 4 weeks diet


title: liver_0ppm_FB1_Ctrl_rep1

description: 4 weeks diet


title: liver_10ppm_FB1_Treat_rep1

description: 4 weeks diet


title: jejunum_0ppm_FB1_Ctrl_rep1

description: 4 weeks diet


title: jejunum_10ppm_FB1_Treat_rep2

description: 4 weeks diet


title: ME_IP_GATA2_KD

data_processing:
ChIP-seq: After reads mapping to the hg19 reference genome using BWA14, peak calling of CBFβ-MYH11 fusion, RUNX1, and GATA2 ChIP-seq was conducted using MACS1.3.3 at a p-value cutoff of 10-6. RNA-seq:  RNA-seq reads were uniquely mapped to the hg19 reference genome using STAR, and subsequently normalized to RPKM values for all RefSeq genes using tag counting scripts.
Genome_build: NCBI build37

growth_protocol: ME-1 cells were routinely cultured in RPMI 1640 supplemented with 10% FCS and 1% pen/strep at 37℃. ME-1 shRNA stable cell lines were cultured in tet-free FBS, and shRNA expression was induced for 72 h for ChIP-seq and RNA-seq by adding 600 ng/ml doxycycline (Dox).

extract_protocol:
ChIP-seq: Purified cells were first cross-linked with 1% formaldehyde for 20 min at room temperature, quenched with 0.125 M glycine and washed with three buffers: (i) PBS, (ii) buffer of composition 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6 and (iii) 0.15 M NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6. Cells were then suspended in ChIP incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 20 mM HEPES pH 7.6) and sonicated using a Diagenode Bioruptor sonicator for 20 min at high power (30 seconds ON and 30 seconds OFF cycle). Sheared chromatin was centrifuged at maximum speed for 10 min and then incubated overnight at 4℃ in incubation buffer supplemented with 0.1% BSA with protein A/G-Sepharose beads (Santa Cruz) and 1 µg of antibody. Beads were washed sequentially with four different wash buffers at 4℃: two times with a solution of composition 0.1% SDS, 0.1% DOC, 1% Triton, 150 mM NaCl, TEE (10 mM Tris pH 8.0, 0.1 mM EDTA and 0.5 mM EGTA), one time with a similar buffer but now with 500 mM NaCl, one time with a solution of composition 0.25 M LiCl, 0.5% DOC, 0.5% NP-40, TEE and two times with TEE. Precipitated chromatin was eluted from the beads with 400 µl of elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature for 20 minutes. Protein-DNA crosslinks were reversed at 65℃ for 4 hours in the presence of 200 mM NaCl, after which DNA was isolated by Qiagen column. RNA-seq: Total RNA was isolated with the RNeasy RNA extraction kit with on-column DNaseI treatment (Qiagen), and the concentration was measured with a Qubit fluorometer (Invitrogen). Ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit (Epicentre) according to manufacturer instructions.
ChIP-seq: ChIP-seq libraries were prepared from precipitated DNA of 5 million cells (5-8 pooled biological replicas) for MLL, or from 1 million cells for the histone tail modifications. End repair was performed using Klenow and T4 PNK. A 3’ protruding A base was generated using Taq polymerase and adaptors were ligated. The DNA was loaded on E-gel and a band corresponding to ~300 bp (ChIP fragment + adaptors) was excised. The DNA was isolated, amplified by PCR and used for cluster generation and sequencing on the HiSeq 2000 or NextSeq (Illumina). RNA-seq: Total RNA was isolated with the RNeasy RNA extraction kit with on-column DNaseI treatment (Qiagen), and the concentration was measured with a Qubit fluorometer (Invitrogen). Ribosomal RNA was removed by Ribo-Zero rRNA Removal Kit (Epicentre) according to manufacturer instructions. 16 µl of purified RNA was fragmented by addition of 4 µl 5× fragmentation buffer (200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate) and incubated at 94℃ for exactly 90 s. After ethanol precipitation, fragmented RNA was mixed with 5 µg random hexamers, followed by incubation at 70℃ for 10 min and chilling on ice. We synthesized the first-strand cDNA with this RNA primer mix by adding 4 µl 5× first-strand buffer, 2 µl 100 mM DTT, 1 µl 10 mM dNTPs, 132 ng of actinomycin D, 200 U SuperScript III, followed by 2 h incubation at 48℃. First strand cDNA was purified by Qiagen mini elute column to remove dNTPs and eluted in 34 µl elution buffer. Second-strand cDNA was synthesized by adding 91.8 µl, 5 µg random hexamers, 4 µl of 5× first-strand buffer, 2 µl of 100 mM DTT, 4 µl of 10 mM dNTPs with dTTP replaced by dUTP, 30 µl of 5× second-strand buffer, 40 U of Escherichia coli DNA polymer¬ase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubated at 16℃ for 2 h followed by incubation with 10 U T4 polymerase at 16℃ for 10 minutes. Double-stranded cDNA was purified by Qiagen mini elute column and used for library preparation as described in the KAPA HyperPrep protocol.

treatment_protocol: shRNA expression to knockdown CBFB-MYH11 was induced for 72 h for ChIP-seq and RNA-seq by adding 600 ng/ml doxycycline (Dox)

value: acute myeloid leukemia (AML) cell line

tag: genotype/variation

value: harbouring a dox inducible CBFB-MYH11 knockdown construct

tag: treatment

value: 600 ng/ml doxycycline

tag: chip antibody

value: GATA-2 (H-116) Santa Cruz


title: ME_IP_GATA2_Control

tag: cell type

value: no dox


title: ME_6_nodox


title: jejunum_10ppm_FB1_Treat_rep5

description: 4 weeks diet


title: jejunum_10ppm_FB1_Treat_rep6

description: 4 weeks diet


title: ME_GATA2


title: jejunum_0ppm_FB1_Ctrl_rep4

description: 4 weeks diet


title: ME_6_dox


title: jejunum_10ppm_FB1_Treat_rep4

description: 4 weeks diet


title: ME_IP_MYH11_Control

value: MYH11 ( Novus Biologicals)


title: PD_07.2505 (mILC-2)


title: jejunum_0ppm_FB1_Ctrl_rep3

description: 4 weeks diet


title: ME_5_dox


title: ME_5_nodox


title: jejunum_0ppm_FB1_Ctrl_rep5

description: 4 weeks diet


title: ME_CM_KD_7days_H3K27ac

value: H3K27ac #A1723-0041d (Diagenode)


title: jejunum_10ppm_FB1_Treat_rep3

description: 4 weeks diet


title: ME_Control_H3K27ac


title: ME_CM_KD_72h_H3K27ac


title: H_TDLN

status: Public on Apr 04 2019

city: San Francisco

first: Joshua

last: Pollack

state: CA

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

description: Sumitter's statement: Raw data (bam) for Human TDLN is being held for institutional IP review.  Will be added as soon as this process is complete.

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v2.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v2.1 using default parameteres.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: sorted myeloid cells (CD45+ CD3- CD19/20- CD56-)

extract_protocol:
Sorted cells were processed using standard protocols associated with 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit V2
Libraries were constructed using standard protocols associated with 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit V2

tag: tissue

value: melanoma-draining lymph node

tag: genetic model


title: ME_IP_MYH11_KD


title: ME_IP_CBFB_Control

value: CBFB sc-20693x (Santa Cruz)


title: ME_IP_RUNX1_KD

value: RUNX1 ab23980 (abcam)


title: ME_IP_CBFB_KD


title: ME_IP_RUNX1_Control


title: RNASeq_d34_DOX_iPSC

status: Public on Feb 06 2019

data_processing:
For expression analyses, the hg19 reference genome index was first generated using STAR aligner with UCSC gene annotation. Paired-end reads were mapped to the indexed genome in two-pass mode with default parameters, to increase alignment accuracy and sensitivity. Stranded gene-level read counts were enumerated at the same time. Expression quantification for each RefSeq gene was performed by Cuffnorm function in Cufflinks, to estimate Fragments Per Kilobase per Million aligned reads value (FPKM). All alignment files were  scaled to RPKM-normalized read coverage files using deepTools for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: Gene-level read counts were enumerated by STAR tool. bigWig files were generated using deepTools by scaling read depth to RPKM-normalized coverage

source_name: iPSC

extract_protocol:
Total RNA was extracted from 1x10e6 iPSC control and RUNX1mut cells using the RNeasy mini kit (Qiagen) and performing on-column DNaseI treatment. Ribosomal RNA was depleted by using the ribo-zero rRNA removal kit (Illumina). RNA was fragmented in 300 bp fragments by incubation for 7.5 minutes in fragmentation buffer (200 mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate (pH 8.2)). First strand cDNA synthesis was performed using superscript III (Life Technologies), followed by synthesis of the second cDNA strand. Libraries were generated using the Kapa hyper prep kit (KAPA Biosystems).
Libraries were generated using the Kapa hyper prep kit. End repair and A-tailing was performed on the double strand DNA using end repair and A-tailing buffer. Subsequently, the adapters were ligated and a post-ligation cleanup was performed using Agencourt AMPure XP reagent. The libraries were amplified by PCR using the Kapa Hifi hotstart readymix and primer mix, 10 cycles. Samples were purified using the Qiaquick MinElute PCR purification kit and 300 bp fragments were selected from E-gel and the size was checked on the agilent bioanalyzer. Samples were sequenced on the Illumina NextSeq 500.

tag: mutation status

value: DOX-induced RUNX1mut

tag: harvest time

value: day 34

value: iPSC


title: RNASeq_d34_CTR_iPSC

value: control


title: RNASeq_d31_DOX_iPSC

value: day 31


title: RNASeq_d26_DOX_iPSC

value: day 26


title: RNASeq_d26_CTR_iPSC


title: RNASeq_d31_CTR_iPSC


title: ME_control_EV


title: RNASeq_RMCO4

value: RUNX1mut transduced

value: Cord blood CD34 cells