title: dsIrd5 CrPV 6h replicate 1

description:
Gene expression of S2 cells knocked down for Ird5 and 6h after CrPV induction
dslrd5-CrPV6h1


title: Patient 70

status: Public on Aug 14 2018

type: RNA

city: Aarhus N

first: Karina

middle: Dalsgaard

last: Sørensen

state: Aarhus N

address: Palle Juul-Jensens Boulevard 99

department: Molecular Medicine

country: Denmark

institute: Aarhus University

hyb_protocol: 40 ng of total RNA was reversed transcribed in 40 µl reactions using the miRCURY LNATM miRNA PCR, polyadenylation and cDNA synthesis kit II (Exiqon). cDNA was diluted x100 and analysed in 10 µl PCR reactions. Negative controls (no template in reverse transcription reaction) were run in parallel.

scan_protocol: Amplification was performed using the LightCycler® 480 Real-Time PCR System (Roche) and ExiLENT SYBR® Green Master mix (Qiagen). Amplification curves and melting curves were analysed for quantification cycles (Cq) using the Roche LC software

data_processing:
Background substraction, for ratio model training the raw data Cq values were used
normalized Cq values (Cq Global mean - Cq miRNA)

label: SYBR® Green

molecule: total RNA

organism: Homo sapiens

source_name: prostate

label_protocol: The ExiLENT SYBR Green master mix was used.

extract_protocol: Total RNA was isolated from 1.5mm punch biopsies from the FFPE tissue samples using miRNeasy FFPE Kit (Qiagen), according to manufacturer's instructions. The 260/280 mm absorbance ratio (optimal ratio: 2.0) was used as quality assurance for the RNA samples. RNA samples with a ratio <1.75 were excluded from further analysis. The purified RNA was stored at -80C.

tag: tissue

value: radical prostatectomy


title: BRBS306_F02_P2

type: SRA

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

description:
PolyA RNA
processed data file: CAS_Seurat_norm_n3_5000g.txt

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to human genome hg38 using STAR version 2.2.1 with default parameters except --sjdbOverhang 49 --outSAMstrandField intronMotif --outFilterMultimapNmax 1 (The max number of multiple alignments allowed for a read is 1. If exceeded, the read is considered unmapped).
Read counting was performed using HTSeq-Count (version 0.9.1) with parameters --stranded=no -m union, and using the annotations of human genome hg38 release 87 downloaded from the ENSembl website. In short, our RNA-Seq data has not been made with a strand-specific protocol. When a read was mapped to more than one gene, it was considered as ambiguous and assigned to none of them.
Raw counts were normalized using the Setup fonction of the Seurat package (version 1.4.0.16) with the following parameters : min.cells = 3, do.logNormalize=T, total.expr = 1e6, min.genes=5000, is.expr = 0. We thus selected the cells expressing at least 5000 genes (86), and selected the genes expressed in at least 3 selected cells (18017).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CAS_Seurat_norm_n3_5000g.txt: Text file with tab delimiters including normalized gene counts for each sample.

source_name: Cord blood CD34+ cell-derived dendritic cell cultures

growth_protocol: CD34+ progenitor cells, isolated from human cord blood, were expanded with Flt3L, SCF, TPO and IL7 for 7 days and then induced to differentiation upon plating on OP9+OP9_DLL1 stromal cells for additional 18 days in the presence of Flt3L, TPO and IL7.

extract_protocol:
Cells from cord blood CD34+ hematopoietic progenitor cultures were FACS sorted in 96-well plates (single cell sorted) containing lysis buffer (TCL together with 1% of 2-Mercaptoethanol).
Single cell RNA-sequencing libraries were generated using an adaptation of Smart-Seq2 (Villani et al., Science, 2017) and the Illumina Nextera XT DNA library preparation kit. Full-length RNA-sequencing was performed.

tag: cell type

value: Putative pDC

tag: phenotype


title: BRBS305_E02_P1

value: Cord blood CD34+ cell-derived dendritic cell cultures

value: Putative cDC1


title: Patient 69


title: BRBS304_D02_P4

value: Putative cDC2


title: Patient 68


title: BRBS303_C02_P3

value: Putative pre-cDC2


title: dsIrd5 CrPV 2h replicate 2

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

institute: CNRS

description:
Gene expression of S2 cells knocked down for Ird5 and 2h after CrPV induction
dslrd5-NI2

hyb_protocol: Following fragmentation, labeled cRNA were hybridized on Agilent “Drosophila (V2) Gene Expression Microarray” 4x44K (Design ID 021791), for 17 hrs, at 65°C under 10 rpm.

scan_protocol: Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 5 µm resolution in a 20-bit scan mode, according to the “AgilentHD_GX_1Color” protocol

data_processing:
Raw .tif images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol.
Median raw expression values where further normalized by quantile method

organism: Drosophila melanogaster

source_name: S2 cells

label_protocol: Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 100 ng of total RNA.

growth_protocol: S2 cells were cultured at 25 °C in Schneider's medium (Biowest) supplemented with 10% fetal calf serum (FCS), penicillin/streptomycin (50 μg/ml of each) and 2 mM glutamax.

extract_protocol: RNA was extracted and treated with DNAse, using RNA Spin kit (Macherey Nagel). RNA quality was checked by Eukaryote Total RNA Pico assay (Agilent) and validated. 200 ng of RNA were used to perform micro-array (Agilent DNA microarrays Drosophila).

treatment_protocol: To perform micro-array, 2x10^6 S2 cells (10^6/mL) were seeded in 6-wells plates in serum-free medium and mixed with 30 μg of dsRNAs against GFP or Ird5. After 2h, the medium was supplemented with 10% FCS. Four days after dsRNA soaking, the cells were infected by CrPV for 2h or 6h or non-infection (NI). The cells were collected for total RNA extraction.

tag: strain

tag: genotype/variation

value: IKKb (Ird5) knockdown

tag: infection

value: CrPV

tag: time

tag: replicate

tag: cell line

value: S2 cells


title: MEF_control_rep1

city: New Haven

first: David

middle: Aaron

last: Schoenfeld

state: CT

address: 20 York Street

department: Medical Oncology

country: USA

institute: Yale Cancer Center

hyb_protocol: End labeled cDNA was hybridized to GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix, #902118) for 16h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturer´s protocol.

scan_protocol: GeneChip Scanner 3000 7G and AGCC (Affymetrix)

data_processing: All analysis was done in R. Standard quality control checks were performed, including: checking raw images and RNA degradation plots; confirming that hybridization of probes was uniform, and that correlations and signal intensities across chips were similar; and performing PCA analysis. Normalization was performed using the “gcrma” package. For analysis, post-normalization relative expression values were used.  probe group file: MoGene-2_0-st.pgf  meta-probeset file: MoGene-2_0-st.mps

label: Biotin

organism: Mus musculus

source_name: MEF, control, GFP adenovirus infected

label_protocol: The Ambion WT Expression Kit (#4411973) was used to generate amplified sense-strand cDNA, and fragmentation and labeling was performed with the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, #901525). Microarray expression analysis was performed using GeneChip Mouse Gene 2.0 ST Arrays (Affymetrix, #902118) following the manufacturer’s instructions.

growth_protocol: We isolated murine embryonic fibroblasts (MEFs) using standard protocols from conditional Pbrm1 mice we had generated, where Cre-mediated recombination would cause a frame-shift mutation of the Pbrm1 allele and loss of Pbrm1 expression. MEFs were cultured in DMEM (Cellgro) supplemented with 10% (v/v) fetal bovine serum and 1 mM glutamine.

extract_protocol: Total RNA was collected for microarray analysis using the Qiagen RNeasy kit according to the manufacturer´s protocol.

treatment_protocol: MEFs were infected with either control GFP adenovirus (Vector Biolabs, #1060) or Cre adenovirus (Vector Biolabs, #1045) in 6-well plates. MEFs were passaged 3 times after infection before RNA collection.

value: MEF

tag: adenovirus

value: GFP

value: control


title: Patient 67


title: BRBS302_B02_P2


title: MEF_control_rep3


title: Patient 66


title: Patient 65


title: BRBS301_A02_P1


title: BRBS299_G01_P3


title: dsIrd5 CrPV 2h replicate 1

description:
Gene expression of S2 cells knocked down for Ird5 and 2h after CrPV induction
dslrd5-NI1


title: Patient 64


title: dsGFP CrPV 2h replicate 2

description:
Gene expression of S2 cells knocked down for GFP and 2h after CrPV induction
dsGFP-CrPV6h2


title: BRBS298_F01_P4


title: dsGFP CrPV 6h replicate 1

description:
Gene expression of S2 cells knocked down for GFP and 6h after CrPV induction
dslrd5-CrPV2h1


title: Patient 63


title: Patient 62


title: MEF_KO_rep1

source_name: MEF, KO, Cre adenovirus infected

value: Cre

value: loss of Pbrm1 expression


title: Patient 61


title: Patient 60


title: HSA2/N+

city: Würzburg

first: Christian W.

last: Remmele

address: Am Hubland

department: Department of Bioinformatics

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
Adapter and low quality sequences were trimmed from RRBS reads by trim_galore_v0.4.0 (parameters: --rrbs --stringency 1 -e 0.2 -a GATCGGAAGAGCA)
Curated reads were mapped in a directional manner using bismark_v0.14.5 with default parameters on the hg19 or the panTro4 genome respectively
CpG positions in the chimpanzee genome were transferred onto the human genome via liftover
Genome_build: hg19 and panTro 4
Supplementary_files_format_and_content: csv files contain chromosome name, coordinate, fraction of methylated nucleotides (percent), number of methylated nucleotides, number of unmethylated nucleotides

molecule: genomic DNA

source_name: human_neuronal cells of Brodmann area 10 (Cortex)

extract_protocol:
Genomic DNA from sorted cell fractions was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).
Genomic DNA was digested with the methylation sensitive restriction enzyme MspI (New England BioLabs, Frankfurt a. M., Germany). End repair of the resulting 3’ overhangs and A-tailing were performed to enable adaptor ligation. After purification with AMPure XP beads (Beckmann Coulter, Krefeld, Germany) and ligation of the methylated universal adaptors (Illumina, San Diego, USA), an additional bead wash step was conducted. Bisulfite conversion was performed with the EpiTect Bisulfite Kit (Qiagen, Hilden, Germany), followed by a wash step using the MinElute PCR Purification Kit (Qiagen). After barcoding of the bisulfite treated samples two additional rounds of bead clean-up were performed. The final libraries were sequenced (single end 76 bp) with the Illumina Genome Analyzer II (Illumina, San Diego, USA) according to the manufacturer’s instructions.

treatment_protocol: Cortex tissue was fluorescence-activated cell sorted into neuronal and non-neuronal cells using a NeuN-specific antibody, as described previously (Wagner et al., 2015).

tag: gender

value: female

value: Fresh-frozen frontal cortex sample (Brodmann area BA10)

value: neuronal cells


title: HSA3/N+


title: HSA2/N-

source_name: human_non-neuronal cells of Brodmann area 10 (Cortex)

value: non-neuronal cells


title: HSA3/N-


title: HSA1/N-


title: HSA1/N+


title: Patient 59

value: radical prostatectomy


title: Patient 57


title: Patient 58


title: ash-1(Y888F) H3K27ac ChIPseq

city: Eugene

first: Vincent

middle: T

last: Bicocca

state: OR

address: 1229 University of Oregon

department: Biology

institute: University of Oregon

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011) and bigwig files were generated using DeepTools (Ramirez et al., 2016) using a window size of 20 -200bp (tdf and bigwig files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).
Supplementary_files_format_and_content: For Poly-A mRNA files: Text files contain counts for every gene as outlined in process above.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: none provided by the submitter

value: conidium


title: dsIrd5 replicate 2

description:
Gene expression of S2 cells knocked down for Ird5 and non immune-challenged
dsGFP-CrPV2h2

value: control (non immune-challenged)


title: dsGFP CrPV 2h replicate 1

description:
Gene expression of S2 cells knocked down for GFP and 2h after CrPV induction
dsGFP-CrPV6h1


title: dsGFP replicate 2

description:
Gene expression of S2 cells knocked down for GFP and non immune-challenged
dsGFP-NI2


title: d3EB_Smad23DKO_clone_KT15.1F6

city: Oxford

first: Anna

middle: Dorothea

last: Senft

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: d3EB_Smad23DKO_biological replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Bead-Station data were extracted using the Gene Expression Analysis Module V1.6.0 of GenomeStudio V2009.2 (Illumina) and imported into the R-based Illumina pre-processing module (http://www.arrayanalysis.org/  (Eijssen et al., 2015)). Hierarchical clustering identified three outlier samples in ESCs that were excluded from subsequent analysis.

source_name: Smad2/3 KO day 3 embryonic bodies

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

growth_protocol:
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)
ESCs (see ESC samples) were trypsinized, resuspended in ESC medium (see ESC samples) without LIF (EB medium), pelleted, washed in PBS (w/o MgCl2) and counted. A single-cell solution of 4 x 10^4 cells/ml in EB medium was pipetted into 10μl drops onto square 12cm plates and the plates carefully inverted onto lids containing a 3cm dish filled with PBS (w/o MgCl2) to maintain humidity of hanging drops. Cells were left to form embryoid bodies for 48h after which EBs were harvested in EB medium and  kept in suspension for another 24h.
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)

extract_protocol: RNA was extracted with QIAGEN Rneasy micro kit and DNase I treatment on-column in accordance with the prescribed protocol provided with the kit.

treatment_protocol: ~5000 EBs were collected in EB medium, washed once in PBS (w/o MgCl2) and RNA isolated.

value: Smad2/3 KO day 3 embryonic bodies


title: dsGFP replicate 1

description:
Gene expression of S2 cells knocked down for GFP and non immune-challenged
dsGFP-NI1


title: d3EB_Smad23DKO_clone_KT15.2G9

description: d3EB_Smad23DKO_biological replicate 1


title: Patient 56


title: set-2; ash-1(Y888F) H3K36me2 ChIPseq


title: Patient 55


title: d3EB_Smad23DKO_clone_KT15.2D5

description: d3EB_Smad23DKO_biological replicate 2


title: dsIrd5 replicate 1

description:
Gene expression of S2 cells knocked down for Ird5 and non immune-challenged
dsGFP-CrPV2h1


title: d2EB_Smad23DKO_clone_KT15.1F6

description: d2EB_Smad23DKO_biological replicate 1

source_name: Smad2/3 KO day 2 embryonic bodies

growth_protocol:
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)
ESCs (see ESC samples) were trypsinized, resuspended in ESC medium (see ESC samples) without LIF (EB medium), pelleted, washed in PBS (w/o MgCl2) and counted. A single-cell solution of 4 x 10^4 cells/ml in EB medium was pipetted into 10μl drops onto square 12cm plates and the plates carefully inverted onto lids containing a 3cm dish filled with PBS (w/o MgCl2) to maintain humidity of hanging drops. Cells were left to form embryoid bodies for 48h
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)

value: Smad2/3 KO day 2 embryonic bodies


title: d2EB_Smad23DKO_clone_KT15.1F11

description: d2EB_Smad23DKO_biological replicate 3


title: d2EB_Smad23DKO_clone_KT15.2D5

description: d2EB_Smad23DKO_biological replicate 4


title: ESC_Smad23DKO_clone_KT15.2D5

description: ESC_Smad23DKO_biological replicate 4

source_name: feeder-free Smad2/3 KO embryonic stem cells (serum + LIF)

growth_protocol:
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)
Undifferentiated ESCs were grown in in serum-containing media containing DMEM (Gibco, Cat#11960-085) supplemented with 15% FBS (Gibco Cat#10500-062, Lot: 07Q3446K), 1% PEN/STREP, 1% glutamine, 1% NEAA, 1mM sodium pyruvate, 100μM β-mercaptopethanol and 1000 U/ml LIF.
Embryonic Stem Cells were maintained in ES cell medium + LIF. Embryoid bodies (EBs) were differentiated from 100 ESCs each in the absence of LIF for two or three days (d2 and d3 EBs)

treatment_protocol: ~5x10^6 ESCs were trypsinized and collected in serum-containing medium, washed once in PBS (w/o MgCl2) and RNA isolated.


title: ash-1(Y888F) H3K27me2/3 ChIPseq


title: ESC_Smad23DKO_clone_KT15.1F6

description: ESC_Smad23DKO_biological replicate 3

value: feeder-free Smad2/3 KO embryonic stem cells (serum + LIF)


title: d3EB_Smad3KO_clone_CCE.2B7

description: d3EB_Smad3KO_biological replicate 2

source_name: Smad3 KO day 3 embryonic bodies

treatment_protocol: ~1250 EBs were collected in EB medium, washed once in PBS (w/o MgCl2) and RNA isolated.

value: Smad3 KO day 3 embryonic bodies


title: d3EB_Smad3KO_clone_CCE.2H2

description: d3EB_Smad3KO_biological replicate 4


title: d2EB_Smad23DKO_clone_KT15.2G9

description: d2EB_Smad23DKO_biological replicate 2

treatment_protocol: ~2500 EBs were collected in EB medium, washed once in PBS (w/o MgCl2) and RNA isolated.


title: ESC_Smad23DKO_clone_KT15.2G9

description: ESC_Smad23DKO_biological replicate 2


title: d2EB_Smad3KO_clone_CCE.2B7

description: d2EB_Smad3KO_biological replicate 4

source_name: Smad3 KO day 2 embryonic bodies

value: Smad3 KO day 2 embryonic bodies


title: d3EB_Smad3KO_clone_CCE.1H1

description: d3EB_Smad3KO_biological replicate 3


title: Patient 54


title: d3EB_Smad3KO_clone_CCE.2E7

description: d3EB_Smad3KO_biological replicate 1


title: d2EB_Smad3KO_clone_CCE.2E7

description: d2EB_Smad3KO_biological replicate 2


title: ash-1-3xflag H3K27me2/3 ChIPseq


title: d2EB_Smad3KO_clone_CCE.1H1

description: d2EB_Smad3KO_biological replicate 3


title: ESC_Smad3KO_clone_CCE.2B7

description: ESC_Smad3KO_biological replicate 4

source_name: feeder-free Smad3 KO embryonic stem cells (serum + LIF)


title: Patient 53


title: ESC_Smad3KO_clone_CCE.1H1

description: ESC_Smad3KO_biological replicate 2

value: feeder-free Smad3 KO embryonic stem cells (serum + LIF)


title: d2EB_Smad3KO_clone_CCE.2H2

description: d2EB_Smad3KO_biological replicate 1


title: IN05_PC3_ERb5_1_RNA-seq

city: Houston

first: Anders

middle: Mikael

last: Strom

state: Texas

address: 3517 Cullen Blvd Bldg 545 room 3018

department: Biology & Biochemistry

institute: University od Hpuston

data_processing: The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0  and the gene expression level was estimated using RSEM v1.2.15, TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed.

source_name: PC3 cells

extract_protocol:
RNA was prepared using the Qiagen RNA-easy kit
For library preparation, Truseq stranded mRNA (Illumina) was used. The sequencing was performed on Illumina Hiseq 2000 with 50bp single read.

value: Prostate

tag: ar status

value: Negative


title: IN06_PC3_ERb5_2_RNA-seq


title: npf H3K27me3 ChIPseq


title: Patient 52


title: IN04_PC3_ERb2_2_RNA-seq


title: Patient 3, cell06

type: genomic

city: Regensburg

first: Giancarlo

last: Feliciello

address: Am Biopark 1

institute: Fraunhofer ITEM

description: Genomic profiling of single white blood cells (WBCs). WBCs were used as control samples to validate the assay and to select the most optimal settings to process single-cells extracted from the CellSearch System

hyb_protocol: Array CGH was performed on oligonucleotide-based SurePrint G3 Human CGH 4x180K microarray slides (design code: 022060) according the protocol provided by the manufacturer (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.1, December 2011) with slight modifications. The hybridization mix consisted of 5.0 µg of Cot1-DNA (Roche Diagnostics), 12 µl of 10x Blocking Reagent (Agilent Technologies), 60 µl of 2x Hi RPM Hybridization Buffer, 1% (v/v) of both Tween20 and Igepal and 19 µl of test and reference DNA. For each hybridization 100 µl of the hybridization mix was applied on the array and hybridized at 65◦C for 24 h. Following the hybridization, the slides were washed sequentially: twice for 2:30 min in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technologies) at room temperature and twice for 30 sec min in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technologies) at 37◦C. Washed slides were immersed in acetonitrile to remove all remaining traces of the wash buffers.

scan_protocol: Scanned on an Agilent G2565CA scanner (Dye channel: R+G; Scan resolution: 2.5µm, double pass; Tiff file dynamic range: 16 Bit; Red PMT gain: 100%; Green PMT gain: 100%; No XDR)

data_processing:
Microarray TIFF image files were processed with the Agilent Genomic Feature Extraction Software (version 10.7.3.1). The resulting text files were imported and analyzed with Agilent Genomic Workbench Software (version 6.5.0.18 Lite). Aberrant regions were recognized using ADM-2 algorithm with threshold set to 8.0. Centralization algorithm was set to a threshold of 6.0 and bin size of 10. To avoid false positive aberration calls, aberration filters were applied to define the minimum log2 ratio (minAvgAbsLogRatio = 0.30) and the minimum number of probes in an aberrant interval (minimum number of probes in an interval = 200).
log2 ratio = Normalized log2 ratios (Cy5/Cy3) representing test/reference. The log2 ratios were obtained using the Agilent Genomic Workbench 6.5.0.18; Average log2 value of a genomic interval = average log2 ratios calculated for entire aberrant genomic intervals (0 indicates balance copy number state)

source_name: Disseminated cancer cells collected from sentinel lymph nodes, single-cell DNA (WGA product)

label_protocol: Single-cell WGA samples were labeled using a previously published PCR-based approach. The primary WGA products were labeled as decribed by Czyz ZT et al., PLoS One. 2014 Jan 21;9(1):e85907.

growth_protocol: Not applicable. Samples for the analysis were collected from sentinel lymph nodes. No cell culture protocols were applied on the isolated cells prior to sample processing.

extract_protocol: Cancer patients: following the enrichment with the ParsortixTM System single cells were collected and transferred on chamber slides, enabling manual isolation of single cells . Subsequently, DNA from single-cells were amplified using the Ampli1 WGA Kit. The quality of the resulting WGA products was assessed using the Ampli1 QC Kit. Healthy donors: single-cell were collected in non-automatized manner using an inverted microscope equipped with a micromanipulator. Single-cell specimens were processed using the Ampli1 WGA Kit. The quality of the resulting WGA products was assessed using the Ampli1 QC Kit.

treatment_protocol: Cancer patients: Single cell suspensions of LN samples were prepared as previously described (Ulmer A et al., Clin Cancer Res. 2005 Aug 1;11(15):5425-32.) and filtrated with a 100 µm cell strainer. Cells were resuspended in a total volume of 100 µl PBS/2% FCS and stained with anti-MCSP-PE antibody (clone EP-1 from Miltenyi Biotec, Germany) for 20 minutes as recommended by the manufacturer. An equivalent of 200 MCSP-stained cells were resuspended in a volume of 4 ml in PBS/2% FCS for subsequent enrichment with ParsortixTM system . Briefly, for processing lymph node, 6.5 µm cassettes were primed containing either BSA (2%) alone or a combination EDTA (2mM) with 0.5% BSA. In the first step, cells were enriched based on their size and deformability (capture) and collected in the second step (harvest) in a well of a 48 well plate.  Healthy donor: 10 mL of peripheral blood was collected from a healthy male donor. Mononuclear cell fraction was enriched using centrifugation in density gradient of Percoll. Single-cell were picked in a manual fashion using the micromanipulator and subjected to whole genome amplification using the Ampli1 WGA Kit. The quality of the resulting WGA products was assessed using the Ampli1 QC Kit. Four high quality single-cell WGA products were pooled and used as reference sample for array CGH.

tag: patient id

tag: origin

value: Clinical Sample

tag: disease state

value: nodular melanoma

value: male

tag: enrichment/isolation procedure

value: ParsortixTM system

value: circulating tumor cell (ctc)

tag: Stage

tag: expressed markers

value: MCSP (+)

tag: single-cell wga product/mix of 4 single-cell wga products/cell pool wga product

value: Single-cell WGA product

tag: method of whole genome amplification (wga)

value: Ampli1™ WGA Kit (Silicon Biosystems)

source_name: White blood cells (WBCs) collected from peripheral blood of a healthy male individual, single-cell DNA (WGA product)

value: Reference

value: healthy donor

value: Male

value: Percoll density centrifugation/Manual isolation of single cells

value: white blood cell (wbc)

value: Mix of 4 single-cell WGA products


title: Patient 51

source_name: prostate

tag: tissue

value: radical prostatectomy


title: ESC_Smad3KO_clone_CCE.2E7

description: ESC_Smad3KO_biological replicate 3

tag: strain

value: feeder-free Smad3 KO embryonic stem cells (serum + LIF)


title: set-2 H3K36me2 ChIPseq

tag: cell type

value: conidium


title: IN03_PC3_ERb2_1_RNA-seq

value: Prostate

value: Negative


title: Patient 1, cell07

value: Clinical Sample

value: acral lentiginous melanoma

value: male


title: d3EB_Smad2KO_clone_KT12

description: d3EB_Smad2KO_biological replicate 4

source_name: Smad2 KO day 3 embryonic bodies

value: Smad2 KO day 3 embryonic bodies


title: Patient 50


title: Patient 1, cell05

value: ParsortixTM system

value: circulating tumor cell (ctc)

value: MCSP (+)

value: Single-cell WGA product


title: WT H3K27ac ChIPseq


title: IN02_PC3_GFP_2_RNA-seq


title: Patient 49


title: IN01_PC3_GFP_1_RNA-seq


title: WT H3K27me3 ChIPseq


title: WT(mus-52, his-) RNAseq


title: WT H3K27me2/3 ChIPseq


title: Patient 47


title: WT (his-) RNAseq


title: Patient 46


title: Patient 3, cell09

value: nodular melanoma

value: Ampli1™ WGA Kit (Silicon Biosystems)

value: Reference

value: healthy donor

value: Male


title: set-2 RNAseq


title: Patient 45

value: radical prostatectomy


title: Patient 44


title: Patient 48


title: Smad23DKO_EpiLC_clone_KT15.1F6_differentiation2 (RNA-seq)

description:
RNA-seq_EpiLC_Smad23DKO_biological replicate 2
d2EpiLC_15.1F6_RNA_MERGED_FORWARD.bw
d2EpiLC_15.1F6_RNA_MERGED_REVERSE.bw
Smad23DKO_EpiLC_DESeq.Result.Table_FULL.DEDUP.txt.gz
Smad23DKO_EpiLC_DESeq.Counts.Table_FULL.DEDUP.txt.gz

data_processing:
RNA-seq reads were initially aligned using bowtie2 against the rRNA genomic sequence (GenBank: BK000964.3) to filter out rRNA fragments, prior to alignment against the mm10 genome using the STAR RNA-seq aligner with default parameters (Dobin et al., 2012). PCR duplicates were removed using Samtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate, and merged to create a representative genome track using DANPOS2 (Chen et al., 2013).
mm10 refGene gene bodies were annotated with biological replicate read counts and gene expression changes were identified with DESeq2 (Love et al., 2014). A padj<0.05 and a fold change > 1.5 was deemed a significant change
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] stranded bigWig represent genome coverage for merged biological triplicates. [.txt] ReadCounts and DESeq2 results

source_name: day 2 epiblast-like cells

growth_protocol: EpiLCs were induced from ESCs grown in N2B27 (NDiff®227, Cat#Y40002) supplemented with 1μM PD0325091 and 3μM CHIR99021 and 1000 U/ml LIF as previously described (Hayashi et al., 2011). In brief, 2.33 x 10^5 ESCs were washed and resuspended in N2B27 supplemented with 12ng/ml Fgf2 (R&D, Cat#314-BP-050, Lot: BEM10214113), 20ng/ml Activin A (Peprotech, Cat#120-14E, Lot: 1115478-1) and 1% KSR (Gibco, Cat#10828, Lot:1508151) and grown on fibronectin-coated (5μg/cm^2, Millipore Cat#FC010) 6cm dishes. Medium was exchanged daily and cells grown for 48h to form EpiLCs.

extract_protocol:
Total RNA was isolated from ~1.5 x10^6 Smad2/3 DKO and wild type EpiLCs from three independent EpiLC differentiations per genotype. These cell samples were taken from the same cells that were also used for ATAC-seq (see below). Total RNA was normalised to 800ng per sample, depleted of cytoplasmic and mitochondrial ribosomal RNA sequences (Ribo-Zero Gold rRNA Removal Kit (H/M/R), Cat: #MRZG12324) and used for library preparation
Libraries were constructed using the Illumina TruSeq Stranded Total RNA Library Prep (H/M/R), Cat: #20020597) followed by sequencing (75-cycle paired end) on the Illumina HiSeq4000 platform.

tag: genotype

value: day 2 epiblast-like cells


title: Smad23DKO_EpiLC_clone_KT15.1F6_differentiation3 (RNA-seq)

description:
RNA-seq_EpiLC_Smad23DKO_biological replicate 3
d2EpiLC_15.1F6_RNA_MERGED_FORWARD.bw
d2EpiLC_15.1F6_RNA_MERGED_REVERSE.bw
Smad23DKO_EpiLC_DESeq.Result.Table_FULL.DEDUP.txt.gz
Smad23DKO_EpiLC_DESeq.Counts.Table_FULL.DEDUP.txt.gz


title: Patient 43


title: Patient 42


title: Patient 41


title: wildtype_EpiLC_clone_CCE_differentiation2 (RNA-seq)

description:
RNA-seq_EpiLC_wildtype_biological replicate 2
d2EpiLC_CCE.1_RNA_MERGED_FORWARD.bw
d2EpiLC_CCE.1_RNA_MERGED_REVERSE.bw
Smad23DKO_EpiLC_DESeq.Result.Table_FULL.DEDUP.txt.gz
Smad23DKO_EpiLC_DESeq.Counts.Table_FULL.DEDUP.txt.gz

value: wildtype


title: wildtype_EpiLC_clone_CCE_differentiation3 (RNA-seq)

description:
RNA-seq_EpiLC_wildtype_biological replicate 3
d2EpiLC_CCE.1_RNA_MERGED_FORWARD.bw
d2EpiLC_CCE.1_RNA_MERGED_REVERSE.bw
Smad23DKO_EpiLC_DESeq.Result.Table_FULL.DEDUP.txt.gz
Smad23DKO_EpiLC_DESeq.Counts.Table_FULL.DEDUP.txt.gz


title: wildtype_EpiLC_clone_CCE_differentiation1 (RNA-seq)

description:
RNA-seq_EpiLC_wildtype_biological replicate 1
d2EpiLC_CCE.1_RNA_MERGED_FORWARD.bw
d2EpiLC_CCE.1_RNA_MERGED_REVERSE.bw
Smad23DKO_EpiLC_DESeq.Result.Table_FULL.DEDUP.txt.gz
Smad23DKO_EpiLC_DESeq.Counts.Table_FULL.DEDUP.txt.gz


title: Patient 39


title: d3EB_Smad2KO_clone_KT11

description: d3EB_Smad2KO_biological replicate 3


title: Tn5_control_wildtype_EpiLC_rep1 (ATAC-seq)

description:
Tn5_control_ATAC-seq_EpiLC_wildtype_biological replicate 1
genomic DNA

data_processing:
Paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “--no-mixed” and “--no-discordant” options. Non-uniquely mapping reads and reads mapping to a custom “blacklist” of artificially high regions of the genome were discarded. PCR duplicates were removed using Samtools (Li et al. 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate, and merged to create a representative genome track using DANPOS2 (Chen et al., 2013) with the Tn5 control provided as background.
ATAC hypersensitive sites in both wild type and SMAD2/3-null EpiLCs were identified using the DANPOS2 dpeak function with biological triplicates and a Tn5 genomic DNA control as background. Significant changes in ATAC-seq datasets were identified using the DiffBind package (Stark and Brown, 2011). A FDR<0.05 and a fold change > 1.5 was deemed a significant change.
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] bigWig represent genome coverage (with background subtracted) for merged biological triplicates were generated using DANPOS2. [.txt] DiffBind results

growth_protocol: EpiLCs were induced from embryonic stem cells  grown in N2B27 (NDiff®227, Cat#Y40002) supplemented with 1μM PD0325091 and 3μM CHIR99021 and 1000 U/ml LIF as previously described (Hayashi et al., 2011). In brief, 2.33 x 10^5 ESCs were washed and resuspended in N2B27 supplemented with 12ng/ml Fgf2 (R&D, Cat#314-BP-050, Lot: BEM10214113), 20ng/ml Activin A (Peprotech, Cat#120-14E, Lot: 1115478-1) and 1% KSR (Gibco, Cat#10828, Lot:1508151) and grown on fibronectin-coated (5μg/cm^2, Millipore Cat#FC010) 6cm dishes. Medium was exchanged daily and cells grown for 48h to form EpiLCs.

extract_protocol:
Two technical replicates of 75,000 wild type or Smad2/3 DKO single-cell suspensions of day 2 epiblast-like cells were harvested and washed with PBS (w/o MgCl2/CaCl2). Three independent differentiations per genotype were used a biological replicates. Nuclei were isolated using 50ul of cold lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl2, 3mM MgCl2, 0.1% IGEPAL CA-630), spun down immediately at 500g for 10min, 4C, washed once with 50ul cold PBS buffer and spun down (500g for 10min, 4C). Supernatant was discarded and the pellet resuspended in transposition reaction mix (for each reaction: 2.5ul Tn5 transposase (Illumina, Cat#FC-121-1030), 25ul 2xTD buffer (Illumina, Cat#FC-121-1030), 22.5ul nuclease-free water) and incubated at 30C for 30min before purification of tagmented DNA using a Qiagen MinElute Kit (Qiagen, Cat# 28004). 100ng genomic DNA of wild type day 2 epiblast-like cells were also treated with transposition reaction mix and treated as above as a control reaction (Tn5control).
ATAC-seq libraries were prepared by PCR amplification using custom Nextera index primers Ad2.1-2.13 (Supplementary Table 1 in Buenrostro et al. (2013)) with NEBNext High-Fidelity 2x PCR master mix (NEB, Cat#M0541) with 11 cycles and purified using a Qiagen MinElute Kit (Qiagen, Cat# 28004) prior to sequencing (75bp paired-end) on the Illumina HiSeq4000 platform.


title: d3EB_Smad2KO_clone_KT15

description: d3EB_Smad2KO_biological replicate 2


title: d3EB_Smad2KO_clone_KT17

description: d3EB_Smad2KO_biological replicate 1


title: d2EB_Smad2KO_clone_KT11

description: d2EB_Smad2KO_biological replicate 3

source_name: Smad2 KO day 2 embryonic bodies

value: Smad2 KO day 2 embryonic bodies


title: d2EB_Smad2KO_clone_KT17

description: d2EB_Smad2KO_biological replicate 4


title: d2EB_Smad2KO_clone_KT12

description: d2EB_Smad2KO_biological replicate 1


title: Smad23DKO_EpiLC_clone_KT15.1F6_differentiation1 (RNA-seq)

description:
RNA-seq_EpiLC_Smad23DKO_biological replicate 1
d2EpiLC_15.1F6_RNA_MERGED_FORWARD.bw
d2EpiLC_15.1F6_RNA_MERGED_REVERSE.bw
Smad23DKO_EpiLC_DESeq.Result.Table_FULL.DEDUP.txt.gz
Smad23DKO_EpiLC_DESeq.Counts.Table_FULL.DEDUP.txt.gz


title: Patient 38


title: d2EB_Smad2KO_clone_KT15

description: d2EB_Smad2KO_biological replicate 2


title: ESC_Smad2KO_clone_KT17

description: ESC_Smad2KO_biological replicate 4

source_name: feeder-free Smad2 KO embryonic stem cells (serum + LIF) (Tremblay et al. 2000)


title: Patient 37


title: d3EB_wildtype_clone_CCH

description: d3EB_wildtype_biological replicate 3

source_name: day 3 wild type embryoid bodies

value: day 3 wild type embryoid bodies


title: ESC_Smad2KO_clone_KT12

description: ESC_Smad2KO_biological replicate 2

value: feeder-free Smad2 KO embryonic stem cells (serum + LIF) (Tremblay et al. 2000)


title: ESC_Smad2KO_clone_KT15

description: ESC_Smad2KO_biological replicate 3


title: Patient 36


title: Patient 40


title: d3EB_wildtype_clone_CCB

description: d3EB_wildtype_biological replicate 2


title: d3EB_wildtype_clone_CCE

description: d3EB_wildtype_biological replicate 1


title: Smad23DKO_EpiLC_clone_KT15.1F6_differentiation3 (ATAC-seq)

description:
d2EpiLC_15.1F6_ATAC.bgsub.Fnor.smooth.wig.bw
Smad23DKO.EpiLC.ATAC.DiffBind.ResultTable.txt.gz
ATAC-seq_EpiLC_Smad23DKO_biological replicate 3
nuclear chromatin


title: Smad23DKO_EpiLC_clone_KT15.1F6_differentiation2 (ATAC-seq)

description:
d2EpiLC_15.1F6_ATAC.bgsub.Fnor.smooth.wig.bw
Smad23DKO.EpiLC.ATAC.DiffBind.ResultTable.txt.gz
ATAC-seq_EpiLC_Smad23DKO_biological replicate 2
nuclear chromatin


title: d3EB_wildtype_clone_CCF

description: d3EB_wildtype_biological replicate 4


title: DU145-SRRM4_2

city: Vancouver

first: Xuesen

last: Dong

state: British Columbia

address: 2660 Oak Street

department: Department of Urologic sciences, Vancouver Prostate Centre

country: Canada

institute: University of British Columbia

data_processing:
Primary analysis and normalization were performed using the AmpliSeq RNA plugin available through the Ion Torrent™ suite Software (Li et al., 2015; PMID 26673413).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text file includes the values of normalized reads for each sample

source_name: Metastatic prostate cancer cells from brain

growth_protocol: Cells were cultured in Dulbecco Modified Eagle Medium/High Glucose with 10% fetal bovine serum with a subcultivation ratio of 1:10. Medium renewed every 2-3 days.

extract_protocol:
Total RNA was extracted by using the mirVana RNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Three independently repeated experiments were performed for each cell line condition. The quantity and quality of the RNA samples were assessed by Nanodrop 2000 as well as Agilent 2100 Bioanalyzer before sent for AmpliSeq Transcriptome Sequencing.
cDNA was synthesized from 100 ng of total RNA using the SuperScript® VILOTM cDNA Synthesis kit and amplified with Ion AmpliSeq™ technology. Barcoded cDNA libraries were diluted to 100pM, equally pooled, and amplified on Ion Torren OneTouch2 instrument using emulsion PCR. Then, templated libraries were subjected for sequencing of > 20,000 RefSeq transcripts using the Ion Torrent Proton™ sequencing system.

treatment_protocol: Lentiviral constructs encoding Flag-SRRM4 were constructed by using the FUGWBW vector as the backbone. Invitrogen gateway system was used to package lentivirus. Briefly, 12μg of each lentiviral vector (pFUGWBW control vector or Flag-SRRM4) together with 9μg of R8.9 and 3μg of VSV-G were transfected into 293T cells, using Lipofectamine 3000 at 37°C and 5% CO2. Lentiviral particles were harvested by removing medium 48 hours after transfection and used to infect DU145 cells. Lentivirus-infected cells were exposed to 5μg/μl blasticidin to select stably infected cells for 3 weeks. Polyclonal and antibiotic resistant cells were pooled and labeled as CTL or SRRM4.

value: Prostate cancer

tag: treatment

value: Lentiviral transduction of SRRM4


title: DU145-SRRM4_3


title: DU145-SRRM4_1


title: Patient 35


title: Patient 34


title: wildtype_EpiLC_clone_CCE_differentiation3 (ATAC-seq)

description:
d2EpiLC_CCE.1_ATAC.bgsub.Fnor.smooth.wig.bw
Smad23DKO.EpiLC.ATAC.DiffBind.ResultTable.txt.gz
ATAC-seq_EpiLC_wildtype_biological replicate 3
nuclear chromatin


title: Smad23DKO_EpiLC_clone_KT15.1F6_differentiation1 (ATAC-seq)

description:
d2EpiLC_15.1F6_ATAC.bgsub.Fnor.smooth.wig.bw
Smad23DKO.EpiLC.ATAC.DiffBind.ResultTable.txt.gz
ATAC-seq_EpiLC_Smad23DKO_biological replicate 1
nuclear chromatin


title: DU145-CTL_2

value: Lentiviral transduction of empty vector


title: Patient 33


title: DU145-CTL_3


title: wildtype_EpiLC_clone_CCE_differentiation2 (ATAC-seq)

description:
d2EpiLC_CCE.1_ATAC.bgsub.Fnor.smooth.wig.bw
Smad23DKO.EpiLC.ATAC.DiffBind.ResultTable.txt.gz
ATAC-seq_EpiLC_wildtype_biological replicate 2
nuclear chromatin


title: wildtype_EpiLC_clone_CCE_differentiation1 (ATAC-seq)

description:
d2EpiLC_CCE.1_ATAC.bgsub.Fnor.smooth.wig.bw
Smad23DKO.EpiLC.ATAC.DiffBind.ResultTable.txt.gz
ATAC-seq_EpiLC_wildtype_biological replicate 1
nuclear chromatin


title: Patient 32


title: Patient 31


title: total culture

data_processing:
NextSeq data were demultiplexed using the 10x Genomics suite Cell Ranger 1.3.1 and specifically the function mkfastq. This first level of analysis generates quality metrics (Q30, number of reads by sample,...) and FASTQ files. Then Cell Ranger 1.3.1 count was performed on each library (sample) that was demultiplexed by Cell Ranger 1.3.1 mkfastq. Finally, Cell ranger 1.3.1 count was performed against human reference genome, detecting the number of cells and the number of genes per cell, quantifying gene expression (count tables) and performing t-SNE analysis.
Raw counts were normalized using the Setup fonction of the Seurat package (version 1.4.0.16) with the following parameters : min.cells = 3, do.logNormalize=T, total.expr = 1e6, min.genes=200, is.expr = 0. We thus selected the cells expressing at least 200 genes, and selected the genes expressed in at least 3 selected cells. Then,cells in which mitochondrial genes represented more than 10 % of all detected genes were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file with tab delimiters including normalized gene counts for each sample

source_name: in vitro culture of CD34+ cord blood cells

extract_protocol:
PBMCs from a healthy blood donor were separated by density gradient centrifugation, enriched by magnetic bead-based sorting using the pan-DC enrichment kit from Miltenyi, and stained with aqua dead fixable kit, FITC-lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56), BV785-HLA-DR, APC-BDCA2 and V450-CD11c. Live Lineage(negative) HLA-DR(positive) cells were then sorted by flow cytometry before loading into the Chromium Single Cell Controller apparatus. For the in vitro cultures, purified CD34+ human cord blood cells were thawed and expanded for 7 days, at 5% CO2 and +37°C, in α-MEM glutamax (Life Technologies), 10% FCS (Biowest), Penicillin / Streptomycin, 1mM sodium pyruvate, 50μM β-mercaptoethanol, 25ng/ml hFLT3L, 5ng/ml hIL7, 5ng/ml hTPO and 2.5ng/ml hSCF (cytokines from Peprotech or R&D). Expanded cells were then differentiated for 14 to 21 days on a mixed feeder layer of OP9 and OP9_DLL1 cells in α-MEM, 20% FCS, Penicillin / Streptomycin, 1mM sodium pyruvate, 50μM β-mercaptoethanol, 15ng/ml hFLT3L, 5ng/ml hIL7 and 2.5ng/ml hTPO, with replacement of half of the medium on day7 and 14 with medium supplemented with 2x concentrated cytokines. Cells were harvested at the end of the culture by pipetting and filtered through a 30μm nylon mesh. Live [Live dead staining(negative)] total hematopoietic [CD45(positive)] or Lineage(negative) HLA-DR(positive) cells were sorted by flow cytometry before loading into the Chromium Single Cell Controller apparatus.
Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with the Chromium Single Cell Controller(10X genomics), where all generated cDNA share a common 10x Barcode. Libraries were generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions. Analysis using molecular indexing information provides an absolute digital measurement of gene expression levels. Sequencing was performed using a NextSeq500 sequencer (Illumina).

value: Cells from total culture of CD34+ cord blood cells


value: Lineage- HLA-DR+ cells sorted from culture of CD34+ cord blood cells


title: ATACseq_subject2_GF_rep2

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: ATAC-seq analysis of preadipocytes cultured from abdominal adipose tissue obtained from premenopausal apple-shaped women - Subject 2_rep2

data_processing:
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
‘Peaks’ were predicted using the Model-based Analysis of ChIP-Seq (MACS2) tool (v2.0.10)
bedgraph generation with homer v4.2 makeUCSCfile using -fsize 1e50 -norm parameters
Genome_build: human hg19
Supplementary_files_format_and_content: bedgraph

growth_protocol: Stromal-vascular fractions were isolated from scWAT abdominal and GF depot, plated and grown in aMEM media, 2.5% FBS with addition of hEGF and hFGF (10µg/ml and 4µg/ml respectively). At confluence, cells were harvested and used for ATACseq

extract_protocol:
After trypsinisation, abdominal and GF preadipocytes nuclei were isolated
Nuclei were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina). After tagmentation DNA was purified with MinElute PCR Purification Kit (Qiagen). Tagmented DNA was amplified with Kapa Hifi Hot Start Kit (Kapa Biosystems) using 16 PCR cycles. Amplified libraries were purified with Agencourt AMPure XP (Beckman Coulter)

tag: individual

value: subject 2

value: adipose

value: gluteo-femoral

value: preadipocytes

tag: passage


title: Patient 28


title: DU145-CTL_1


title: Patient 30


title: TRP47

city: Galveston

first: Clayton

middle: Eugene

last: Kibler

state: TX

address: 301 University Blvd

department: Pathology

institute: UTMB

data_processing:
Sequence reads were analyzed by base calling and sequence quality filtering scripts with Illumina Pipeline software.
Sequences were aligned to the human genome (UCSC hg38) using bowtie v2.3.2, default parameters.
Alignment files were processed by removing PCR duplicates using Picard tools, reads mapping to multiple genomic locations using Linux grep command, and reads with low mapping scores using Samtools.
MACS v2.1.1.20160309 with default parameters was used to call peaks ranked by significance.
Downstream analyses included identifying binding peak-gene associations with GREAT and DNA binding motif with MEME-ChIP.
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated by MACS. For each peak, column 5 has the integer score calculated as int(-10*log10qvalue), column 7 has fold-change, column 8 has -log10pvalue, column 9 has -log10qvalue, and column 10 has relative summit position to peak start.

source_name: THP-1 cells

growth_protocol: Ehrlichia chaffensis (Arkansas strain) was propagated in a human monocytic cell line (THP-1). THP-1 cells were maintained in RPMI 1640 (HyClone, Logan, UT) supplemented with 5% fetal bovine serum (FBS; HyClone), 2.05 mM L-glutamine, 1 mM sodium pyruvate, and 2.5 g/L glucose at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Cells were cross-linked using a final concentration of 1% formaldehyde for 10 min. Cells were then pelleted and lysed with lysis buffer and a dounce homogenizer. Lysate was sonicated on ice using Sonics Vibra-Cell (20 cycles, 30 sec at 5 W output, 30 sec rest) to generate chromatin fragments around 300 bp in length. TRP47 was immunoprecipitated using rabbit anti-TRP47 at optimized concentration and pre-immune serum was used as a control. Washing of IP reactions and reversal of crosslinks were performed according to Magna ChIP protocol, and nucleic acid was purified and quantified using a Qubit fluorometer.
Preparation of indexed DNA sample libraries involving PCR amplification with adapter ligation was performed by the UTMB Next Generation Sequencing Core using the NEBNext Ultra II DNA Library Kit. Library quality and quantity was evaluated using Agilent Bioanalyzer. Samples were sequenced using an Illumina HiSeq 1500 to generate about 40 million single-end 50 base pair sequence reads per sample.

treatment_protocol: THP-1 cells were infected with E. chaffeensis 48 hours prior to harvesting.

tag: e. chaffensis strain

value: Arkansas

tag: hours post infection

tag: chip antibody

value: rabbit anti-TRP47


title: ATACseq_subject2_abd_rep2

description: ATAC-seq analysis of preadipocytes cultured from abdominal adipose tissue obtained from premenopausal apple-shaped women - Subject 1_rep2

value: subject 1

tag: origin


title: Patient 27

value: radical prostatectomy


title: Serum

description: processed data available on GSM3330435.

value: rabbit pre-immune serum


title: Patient 29


title: ATACseq_subject1_GF_rep2


title: ATACseq_subject1_GF_rep1

description: ATAC-seq analysis of preadipocytes cultured from abdominal adipose tissue obtained from premenopausal apple-shaped women - Subject 2_rep1

value: abdominal


title: Lineage- HLA-DR+ cells sorted from DC-enriched PBMCs

source_name: adult peripheral blood from a healthy donor


title: ATACseq_subject2_abd_rep1

description: ATAC-seq analysis of preadipocytes cultured from abdominal adipose tissue obtained from premenopausal apple-shaped women - Subject 1_rep1


title: ATACseq_subject2_GF_rep1


title: ATACseq_subject1_abd_rep2


title: Patient 26


title: 20170921_run55_universal_R64-1-1_13

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: yCP50 library, D.m. histones, 10 nM remodeler S.c. INO80 (HSAɑ1), reaction time 60 min.

data_processing:
Sequencing reads were aligned to S. cerevisiae genome ENSEMBL R64-1-1 using bowtie2 (v2.2.9).
Non-uniquely mapped reads were removed using samools (v1.3.1).
Reads were shifted 73 bases towards the dyad and reduced to 1 base width.
Dyad coverage was exported to bedgraph file.
Genome_build: R64-1-1
Supplementary_files_format_and_content: *_dyad.bedgraph: bedGraph files describing coverage of nucleosome dyads.

organism: Saccharomyces cerevisiae

source_name: in vitro reconstitution

growth_protocol: Saccharomyces cerevisiae (sc) genes coding for all 15 subunits and respective mutants were combined in two separate pFBDM vector using the MultiBac system. Integration of genes from the pFBDM vector into the baculoviral genome was performed in DH10MultiBac cells, baculovirus generation in Spodoptera frugiperda Sf21 insect cells (IPLB-Sf21AE) and proteins co-expression in Trichoplusia ni High Five insect cells (Invitrogen) according to a published protocol. High Five cells were transfected 1/100 (v/v) with baculovirus. Cells were cultured for 60 h at 27°C until they were harvested by centrifugation.

extract_protocol:
Recombinant remodeler were purified via affinity tag purification and ion exchange chromatography. The yeast genome plasmid library used was derived from Sa3A digested yeast genome fragments and ligated via BamHI into the YCp50 plasmid. Chromatin was reconstituted via salt gradient dialysis. Remodeling reactions were started with adding 10 nM of protein to 90 nM chromatin and stopped via apyrase treatment. After MNase treatment, mononucleosomes were isolated and sequencing libraries prepared according to NEBNext Multiplex Oligos for Illumina protocols.
The NEBNext Multiplex Oligos for Illumina were used to generate sequencing libraries. Approximately 50 ng of purified mononucleosomal DNA after MNase digest was incubated with 1.25 U Taq polymerase (NEB), 3.75 U T4 DNA polymerase (NEB) and 12.5 U T4-PNK (NEB) in 1x ligation buffer (B0202S, NEB) for 15 min at 12°C, 15 min at 37°C and 20 min at 72°C. To ligate NEBNext Adaptors (0.75 µM final concentration, NEB) to the DNA, samples were incubated with T4 DNA ligase (NEB) at 25°C for 10 min, followed by incubation with 2 U USER enzyme (NEB) for 10 min at 37°C. Fragments were purified using AMPure XP beads (Beckman Coulter) and amplified for 10-12 cycles using NEBNext Universal Primer and NEBnext Index Primer, Phusion High-Fidelity DNA Polymerase (1 U, NEB), deoxynucleotide solution mix (dNTP, 2.5 mM, NEB) and Phusion HF Buffer (1x, NEB). The following protocol was applied for amplification: 98°C for 30 s, 98°C for 10 s, 65°C for 30 s, 72°C for 30 s (repeated for 12 cycles) with a final amplification step at 72°C for 5 min. The Qubit dsDNA HS Assay Kit (Invitrogen) was used to assess the DNA content of 1 µL PCR reaction. Adaptor-ligated mono-nucleosomal DNA was purified from agarose gels via Freeze N Squeeze DNA Gel Extraction Spin Columns (Biorad), ethanol precipitated and resuspended in 15 µL 0.1x TE buffer. DNA was measured with Qubit dsDNA HS Assay Kit and diluted to final concentration of 10 nM (calculation based on the assumption that the DNA fragment length is 272 bp, i. e., 147 bp nucleosomal DNA and 122 bp sequencing adaptor). 10 nM samples were pooled according to sequencing lane requirements. The final pool was quantified by BioAnalyzer (Agilent) and analyzed on an Illumina HiSeq 1500 in the 50 bp single-end mode (Laboratory for Functional Genome Analysis, LAFUGA, LMU Munich).

tag: histone source

value: Drosophila melanogaster

tag: chromatin remodeler

value: S.c. INO80 (HSAalpha1)


title: 20170921_run55_universal_R64-1-1_15

description: yCP50 library, D.m. histones, 10 nM remodeler S.c. INO80 (HSAɑ2), reaction time 60 min.

value: S.c. INO80 (HSAalpha2)


title: 20170921_run55_universal_R64-1-1_18

description: yCP50 library, D.m. histones, 10 nM remodeler S.c. INO80 (HSAɑ1/ɑ2), reaction time 60 min.

value: S.c. INO80 (HSAalpha1/alpha2)


title: 20170921_run55_universal_R64-1-1_20

description: yCP50 library, D.m. histones, no remodeler added, reaction time 60 min.

value: Salt gradient dialysis, no remodeler


title: Patient 25


title: Patient 24


title: Patient 23


title: 20170921_run55_universal_R64-1-1_11

description: yCP50 library, D.m. histones, 10 nM remodeler S.c. INO80 (WT), reaction time 60 min.

value: S.c. INO80 (WT)


title: d2EB_wildtype_clone_CCB

description: d2EB_wildtype_biological replicate 2

source_name: day 2 wild type embryoid bodies

value: day 2 wild type embryoid bodies


title: d2EB_wildtype_clone_CCH

description: d2EB_wildtype_biological replicate 3


title: Patient 22


title: ATACseq_subject1_abd_rep1


title: Patient 21


title: RNAseq_subject2_abd

description:
RNAseq analysis of preadipocytes cultured from abdominal adipose tissue obtained from premenopausal apple-shaped women - Subject 2
Sub2Abd vs GF_gene_exp_RPKM

data_processing:
Samples were aligned with TopHat v2.0.7 using default parameters.
FPKM values were calculated by cufflinks v2.0.2 using default parameters.
Genome_build: human hg19
Supplementary_files_format_and_content: table, normalized FPKM values.  Value_1=ABD, value_2=GF.

growth_protocol: Stromal-vascular fractions were isolated from scWAT abdominal and GF depot, plated and grown in aMEM media, 2.5% FBS with addition of hEGF and hFGF (10µg/ml and 4µg/ml respectively). At confluence, cells were harvested and used for RNA extraction.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen) from abdominal and GF preadipocytes
Approximately 2 ug RNA was used for library preparation with TruSeq RNA Sample Preparation Kit (Illumina).

value: subject 2


title: RNAseq_subject2_GF

description:
RNAseq analysis of preadipocytes cultured from gluteal adipose tissue obtained from premenopausal apple-shaped women - Subject 2
Sub2Abd vs GF_gene_exp_RPKM

value: adipose


title: 20170725_run51_universal_R64-1-1_15


title: RNAseq_subject1_GF

description:
RNAseq analysis of preadipocytes cultured from gluteal adipose tissue obtained from premenopausal apple-shaped women - Subject 1
Sub1Abd vs GF_gene_exp_RPKM

value: gluteo-femoral


title: 20170725_run51_universal_R64-1-1_20 `


title: Patient 19

data_processing:
Background substraction, for ratio model training the raw data Cq values were used
normalized Cq values (Cq Global mean - Cq miRNA)

extract_protocol: Total RNA was isolated from 1.5mm punch biopsies from the FFPE tissue samples using miRNeasy FFPE Kit (Qiagen), according to manufacturer's instructions. The 260/280 mm absorbance ratio (optimal ratio: 2.0) was used as quality assurance for the RNA samples. RNA samples with a ratio <1.75 were excluded from further analysis. The purified RNA was stored at -80C.


title: Patient 20


title: d2EB_wildtype_clone_CCF

description: d2EB_wildtype_biological replicate 4


title: RNAseq_subject1_abd

description:
RNAseq analysis of preadipocytes cultured from abdominal adipose tissue obtained from premenopausal apple-shaped women - Subject 1
Sub1Abd vs GF_gene_exp_RPKM

value: preadipocytes


title: 20170725_run51_universal_R64-1-1_11


title: 20170725_run51_universal_R64-1-1_9


title: d2EB_wildtype_clone_CCE

description: d2EB_wildtype_biological replicate 1


title: Patient 17


title: ESC_wildtype_clone_CCF

description: ESC_wildtype_biological replicate 4

source_name: feeder-free wild type embryonic stem cells (serum + LIF)


title: ESC_wildtype_clone_CCH

description: ESC_wildtype_biological replicate 3

value: feeder-free wild type embryonic stem cells (serum + LIF)


title: Patient 16


title: ESC_wildtype_clone_CCB

description: ESC_wildtype_biological replicate 2


title: WT_bapta_Inj2

city: IRAPUATO

first: ALFREDO

last: HERRERA ESTRELLA

state: GUANAJUATO

address: 9.6 KM CARR IRAPUATO LEON

department: LANGEBIO

country: Mexico

institute: CINVESTAV

data_processing:
A Pseudo-aligned to the T. atroviride V2 transcripts, using kallisto.
For the differential gene expression analysis, using the edgeR package.
Genome_build: Trichoderma atroviride v2: https://genome.jgi.doe.gov/Triat2/Triat2.home.html
Supplementary_files_format_and_content: raw_counts matrix.txt includes count values for each Sample. Additional text files with differential expression analysis are included.

organism: Trichoderma atroviride

extract_protocol:
Mycelia of the _tmk1, _tmk3 and WT strains were collected 30 min after mycelial damage and frozen immediately. The WT strain was previously treated with 10 mM BAPTA or 100 _M ATP for 15 min, as indicated. In all cases, an injured control without chemical treatment and a control without injury were included, and three biological replicates were analyzed per strain and/or treatment. Total RNA was extracted with TRIzol (Invitrogen).
Libraries for RNAseq were prepared using the TruSeq RNA library preparation protocol (Illumina).

tag: background strain

value: WT

value: Mycelium

tag: age

value: Incubated for 36 h before injury and/or chemical treatment


title: PTR3/N-

description: Sample 12

organism: Pan troglodytes

source_name: chimpanzee_non-neuronal cells of Brodmann area 10 (Cortex)

tag: gender

value: female

value: Fresh-frozen frontal cortex sample (Brodmann area BA10)

value: non-neuronal cells


title: WT_bapta_Inj3


title: PTR2/N-

description: Sample 11


title: ATP_3


title: 20170725_run51_universal_R64-1-1_25

value: Drosophila melanogaster


title: Patient 15

value: radical prostatectomy


title: Patient 14


title: ESC_wildtype_clone_CCE

description: ESC_wildtype_biological replicate 1


title: Patient 13


title: PTR2/N+

description: Sample 8

source_name: chimpanzee_neuronal cells of Brodmann area 10 (Cortex)

value: neuronal cells


title: ATP_2


title: PTR3/N+

description: Sample 9


title: PTR1/N-

description: Sample 10


title: Patient 11


title: PTR1/N+

description: Sample 7


title: ATP_1


title: Tmk3_Inj2

value: Tmk3 mutant


title: Patient 18


title: Patient 10


title: WT_bapta_Inj1


title: Tmk3_Inj1


title: Patient 9


title: Tmk3_C3


title: M-ES2

city: beijing

first: Jun

last: Wei

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Plant Molecular Physiology, CAS

country: China

institute: Institute of Botany, CAS

description: Endosperm tissues were collected  from 25 DPA

data_processing:
The raw paired reads were trimmed and quality controlled by Seqprep (https://github.com/jstjohn/SeqPrep ) and Sickle (https://github.com/najoshi/sickle ) with default parameters.
The clean reads were aligned to Chinese Spring genome (TGACv1, ftp: //ftp.ensemblgenomes.org/pub/plants/release-36/fasta/triticum_aestivum; Gff3: ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gff3/triticum_aestivum/) using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009
Differentially expressed genes were identified  using DESeq R package with FDR<0.001  and (|log2(Fold Change)|≥1
Enrichment analysis for GO using topGO R package and GO classification using WEGO 2.0 (wego.genomics.org.cn/)
Venn diagram of GO items  performed using GOView (www.webgestalt.org/GOView/)
Genome_build: TGACv1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Triticum aestivum

source_name: Grain

growth_protocol: Wheat (Triticum aestivum L.) cultivar Zhou 8425B were field cultivated at Beijing during cropping seasons.

extract_protocol:
Embryo or endosperm (0.2g) were grinned under liquid nitrogen to fine powder using cooled mortar and pestle. Samples were placed in 2ml Eppendorf tubes and total RNA was isolated following the protocol of Plant Total RNA Purification Kit (GMbiolab co., Ltd. Taichung, Taiwan).
The twelve RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No

tag: cultivar

value: Zhou 8425B

value: Endosperm (including episperm and pericarp)

tag: developmental stage

value: 25  day post anthesis


title: Test NRP2 KO

city: Omaha

first: Sohini

last: Roy

state: Nebraska

address: 985870 nebraska medical center, DRC1

department: Biochemistry and molecular biology

institute: University of nebraska medical center

data_processing:
CD11b+ cells were isolated from subcutaneous PC tumors using magnetic beads as mentioned. RNA-Seq service was obtained from Kelvin Chan and his team at Seqmatic. Extracted RNA was QC with Agilent TapeStation RNA screentape. The RIN value of the control sample was 9.1 and that of the test was 9.4. A paired end read 2x75bp sequencing run of RNA libraries were performed using the Illumina NextSeq 500 instrument. For analysis, raw reads were demultiplexed by barcode and output into FASTQ format. Cutadapt was used to filter out adapter sequences and low-quality bases. Filtered sequence reads were aligned to mouse reference genome grcm38 using HISAT2 aligner. Reads mapping to exon regions as defined by Ensembl gene annotations were counted using FeatureCounts. Data analysis was performed with the help of Seqmatic, California and the Bioinformatics Core at UNMC. Genes with a cutoff value log fold change (+/- 1) were selected and those with zero counts in either control or test samples were eliminated for stringency.
The Ingenuity Pathway Knowledge Base (IPA) was used to identify the enriched cellular and molecular functions among the differentially expressed transcripts in the two samples. The Database for Annotation, Visualization and Integrated Discovery (DAVID), The Gene Ontology Project, Kegg pathway were used and extensive literature reviewed to annotate differentially regulated transcripts with a GO designation. Among the enriched functional annotation clusters, we selected representative clusters (as mentioned in the Results section) to analyze the effect of NRP2 depletion on phagocytosis, macrophage phenotype and secretion of chemokines and cytokines as well as interaction between macrophages and leucocytes/lymphocytes.
Genome_build: mouse reference genome grcm38
Supplementary_files_format_and_content: processed file containing basemean, log2foldchange, Ifcse, stat, padj values, and p values

source_name: CD11b cells isolated from subcut tumors

growth_protocol: Pancreatic cancer cell lines (mouse) were subcutaneously implanted into the right flanks of NRP2f/fCSF1R-iCRE mice. Once the tumors became palpable, the animals were randomly divided into control and test groups. The test animals received daily intraperitoneal injection of tamoxifen (dose as per Jackson Lab recommendations) to specifically knock out NRP2 in monocytes/macrophages. After 15days, tumors were harvested and CD11b cells isolated from digested tumors using magnetic beads. Trizol was added to the samples for rna isolation and RNA SEQ was performed by Seqmatic.

extract_protocol:
We followed the protocol published by Cassetta et al. 2016. The CD11b cells were isolated from control and test subcutanoeus tumors using magnetic beads. Trizol was added for RNA extraction and sent to Seqmatic for further processing for RNA Sequencing.
Illumina TruSeq stranded mRNA kit

tag: strain

value: NRP2f/flCSF1R-iCRE (BL6 background)

tag: tissue

value: subcutaneous tumors


title: Tmk3_C2

tag: genotype


title: Control


title: Patient 12

source_name: prostate


title: Tmk3_Inj3


title: Patient 7


title: Tmk1_Inj3

value: Tmk1 mutant


title: s2669 (anti-PD1-JQ1)

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
anti-PD-1+JQ1 treatment
counts.raw.csv.gz
counts.normalized.csv.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

molecule: polyA RNA

source_name: Tumor nodules

extract_protocol:
Agencourt RNAadvance kit was used for isolation of nucleic acids from frozen tissue and implemented on a Biomek FXP Laboratory Automation Workstation. Briefly the tissue is lysed, after which the RNA is immobilized onto the magnetic particles. The RNA is then treated with DNase and the contaminants rinsed away using a simple wash procedure. RNA isolates were eluted in a 55ul volume of RNase/DNase-free H2O. All RNA was stored at -80C. RNA quality was assessed by Agilent Bioanalyzer using the RNA 6000 pico kit
TruSeq RNA Access Library Prep Kit was utilized for RNA-seq library prep. 50ng RNA was utilized as input. The method was automated on the Biomek FXP Laboratory Automation Workstation to facilitate enrichment of the coding regions of the transcriptome that are captured using sequence-specific probes to create the final library.

tag: treatment

value: Lung Tumor

value: Mixed background

tag: gemm model


title: Patient 6

city: Aarhus N

first: Karina

last: Sørensen

address: Palle Juul-Jensens Boulevard 99

institute: Aarhus University


title: Patient 5


title: s2625 (JQ1)

description:
JQ1-treatment
counts.raw.csv.gz
counts.normalized.csv.gz


title: Tmk3_C1

value: Mycelium


title: M-ES3


title: G-ES3

description: Endosperm tissues were collected  from 14 DPA


title: s2617 (Vehicle)

description:
Vehicle treatment
counts.raw.csv.gz
counts.normalized.csv.gz

value: Vehicle


title: Tmk1_Inj2

value: Incubated for 36 h before injury and/or chemical treatment


title: M-EB1

description: Embryo tissues were collected  from 25 DPA

value: Embryo

value: 14  day post anthesis


title: Patient 4


title: Patient 3


title: Tmk1_C3


title: G-ES1


title: s2596 (Vehicle)


title: Tmk1_Inj1


title: G-ES2


title: M-ES1


title: Patient 8


title: s2521 (anti-PD1)

description:
anti-PD-1 treatment
counts.raw.csv.gz
counts.normalized.csv.gz


title: Patient 2


title: M-EB2


title: Tmk1_C2


title: M-EB3


title: Patient 1


title: Tmk1_C1


title: s2503 (JQ1)


title: G-EB2

description: Embryo tissues were collected  from 14 DPA


title: s2467 (anti-PD1-JQ1)


title: Hfq_Flag_coIP

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Quality trimming with fastq_quality_trimmer (fastx 0.11.2)
Read mapping with READemption (0.4.3) and segemehl (0.2.)
Coverage plote generation with READemtpoin
Genome_build: CP012199.1
Supplementary_files_format_and_content: wiggle of normalized coverages

organism: Sphingopyxis granuli

source_name: Exponentially growing cells

growth_protocol: Sphingopyxis granuli strains were grown at 30ºC in minimal medium MM supplied with tetralin in the vapor phase or 40 mM β-hydroxybutyrate.

extract_protocol:
Total RNA purification was performed from exponentially-growing TFA cells in β-hydroxybutyrate or tetralin. DNase I treatment was performed with a DNA-free kit (Ambion). Once the absence of contaminating DNA was confirmed by PCR amplification, the samples were purified by using RNeasy columns (Qiagen) and RNA integrity was checked by agarose gel electrophoresis.
For the depletion of processed transcripts, equal amounts of RNA were incubated with Terminator 5'-phosphate-dependent exonuclease (TEX) (Epicentre #TER51020) as previously described (Sharma et al., 2010). The transcripts were not fragmented in order to get mainly sequencing reads of the 5'-end of the transcripts. Libraries for Illumina sequencing of cDNA were constructed by vertis Biotechnology AG, Germany (http://www.vertis-biotech.com/), as described previously for eukaryotic microRNAs (Berezikov et al., 2006) but omitting the RNA size-fractionation step prior to cDNA synthesis. Equal amounts of RNA samples were poly(A)-tailed using poly(A) polymerase. Then, the 5'-triphosphates were removed by applying tobacco acid pyrophosphatase (TAP) resulting in 5'-monophosphat. Afterwards, a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter.

tag: genotype/variation

value: TFA strain with hfq gene exchanged by a hfq::3xFlag tagged version

tag: ip antibody

value: ANTI-FLAG® antibody produced in rabbit (Sigma)

tag: molecule subtype

value: anti-Flag immunoprecipitated RNA


title: G-EB1


title: wt_coIP

value: TFA

value: wild type


title: s1795 (anti-PD1)


title: THN_plus_TEX

tag: carbon source

value: tetralin (THN)


title: WT H3K36me3 ChIPseq

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window TDF or bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: For ChIP-seq files: The tdf files were generated using the "count" function in igvtools (Integrative Genomics Viewer; Broad Institute, Robinson et al, 2011) and bigwig files were generated using DeepTools (Ramirez et al., 2016) using a window size of 20 -200bp (tdf and bigwig files are binary files that shows enrichment peaks for each ChIP sample and have been processed for faster display of the data in IGV).
Supplementary_files_format_and_content: For Poly-A mRNA files: Text files contain counts for every gene as outlined in process above.

source_name: germinated conidia

extract_protocol: none provided by the submitter

tag: cell type

value: conidium


title: WT_C2

value: WT


title: ash-1(Y888F) H3K36me3 ChIPseq


title: WT H3K36me2 ChIPseq


title: WT_C1


title: WT_C3


title: WT INPUT


title: G-EB3

value: Zhou 8425B


title: WT_Inj1


title: β-HB_plus_TEX

value: β-hydroxybutyrate (β-HB)


title: β-HB_minus_TEX


title: evo_7

status: Public on Aug 13 2018

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description:
Genomic DNA extracted from blood was genotyped using HumanHap650Yv3 Genotyping BeadChip (HumanHap650Yv3_A) (Illumina).
processed and raw data files:
Tambets_et_al_650k_Matrix_processed.txt; Tambets_et_al_650k_Matrix_signal_intensities.txt

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).
Genotype: AA,AB,BB,or NC (no call)

label: Cy3, Cy5

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Estonians

tag: region

value: Europe

value: blood


title: evo_4


title: evo_6


title: WT_Inj2

tag: background strain

value: Mycelium


title: WT_Inj3

tag: age

value: Incubated for 36 h before injury and/or chemical treatment


title: ash-1(Y888F) H3K36me2 ChIPseq


title: THN_minus_TEX


title: evo_3


title: CMEC1

city: HUNTSVILLE

first: NRIPESH

last: PRASAD

state: AL

address: 601 GENOME WAY

department: GENOMIC SERVICES LABORATORY

institute: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0003

data_processing:
For miRNAseq data, raw reads were imported on Avadis NGS Quality control checks, adapter trimming, and read filtering were performed. Filtered reads were used to extract and count miRNAs which were annotated with miRBase release 21 database. Sample were grouped according to their respective identifiers followed by quantification of miRNA abundance.  Differentially expressed miRNAswere identified based on fold change. Probability values for each differentially expressed miRNA were estimated by z-score calculations using a false discovery rate of 0.05.
miRNA were normalized as Reads per Million (RPM) for a given miRNA target compared to all miR reads in the sample.
Genome_build: canFam3/mIRBase release 21
Supplementary_files_format_and_content: excel with normalized expression.

organism: Canis lupus familiaris

source_name: Exosomal RNA from normal canine mammary cells (biological replicate #1)

growth_protocol: CMT and CMEC cells were grown in 75 cm2 flasks in synthetic Xerum-free® media + DMEM media supplemented with 2X penicillin/streptomycin antibiotics at 37ºC until 70-80% confluence. Media from the first 24 hours of culture was discarded and conditioned media from the second 48 hours was harvested on day 3 of growth prior to trypsinization and subculture.

extract_protocol:
RNA was extracted from 5 mL of cell-free, serum-free conditioned media using the Norgen Biotek Urine/Cell Culture Exosomal RNA Isolation kit (Norgen Biotek, Thorold, ON, Canada) according to manufacturer instructions. After the lysis step, 10 pM final concentration synthetic miRVana cel-miR-39-3p mimic (Thermo Fisher Scientific, Waltham, MA, USA) was spiked into samples as an external control for technical variation. Extracted RNA was stored at -80°C until being shipped on dry ice to the Genomic Services Laboratory at the Hudson Alpha Institute for Biotechnology.
Briefly, total RNA (500 ng) from each sample was used for miRNA library preparation. For miRNAseq, the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs Inc., Ipswich, MA, USA) was followed according to the manufacturer’s protocol. Final  miRNA library quantities were assessed using a Qubit® 2.0 Fluorometer and library quality was determined using a DNA High Sense chip on Agilent 2100 Bioanalyzer. Further library quantification was completed using the qPCR-based KAPA Biosystem Library Quantification kit (Kapa Biosystems Inc., Woburn, MA, USA). For miRNAseq, individual sample libraries were diluted to a final concentration of 1.25 nM. Equimolar amounts of individual barcoded  samples from each group were pooled prior to sequencing. miRNAseq was conducted using an Illumina HiSeq 2500 instrument (Illumina Inc., San Diego, CA, USA) at 50bp Single End condition generating approximately 15 million reads per sample.

tag: cell compartment

value: exosome

tag: cell line

tag: cell source lesion type

value: Normal canine mammary cells

tag: age (days)

value: 3 day conditioned media


title: CMEC2

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0008

source_name: Exosomal RNA from normal canine mammary cells (biological replicate #2)


title: CMT-28

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0002

source_name: Exosomal RNA from CMT-28 cells

value: Mammary carcinoma cells


title: CMT-12

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0005

source_name: Exosomal RNA from CMT-12 cells


title: CMT-119

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0007

source_name: Exosomal RNA from CMT-119 cells


title: CMT-47

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0006

source_name: Exosomal RNA from CMT-47 cells


title: hant7

description:
Genomic DNA extracted from blood was genotyped using Human610-Quad v1.0 BeadChip (Illumina).
processed and raw data files:
Tambets_et_al_610k_Matrix_processed.txt; Tambets_et_al_610k_Matrix_signal_intensities.txt

value: Khanty

value: Siberia

tag: tissue


title: hant6


title: Tatar1003

value: Tatars


title: hant8


title: hant4


title: Tatar1008


title: hant2


title: hant10


title: hant3


title: NST3p_CEF2-VP16_nst1-1_nst3-1_stem_rep4

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes to produce the normalized signal value.

organism: Arabidopsis thaliana

source_name: NST3pro:CEF2-VP16 nst1-1 nst3-1 Arabidopsis Col0 stem, 10cm long

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on soil in greenhouse at 23 Celsius degree in 16h/8h day/night cycle.

extract_protocol: Plant RNeasy Mini kit (QIAGEN) was used to isolate total RNA.

treatment_protocol: None applied

tag: genotype

value: NST3pro:CEF2-VP16:HSP nst1-1 nst3-1

value: stem


title: hant9


title: NST3p_CEF2-VP16_nst1-1_nst3-1_stem_rep3


title: hant1


title: NST3p_CEF2-VP16_nst1-1_nst3-1_stem_rep1


title: CMT-27

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0001

source_name: Exosomal RNA from CMT-27 cells


title: saami4

source_name: Saami from Sweden_Europe

value: Saami from Sweden


title: saami8


title: NST3p_CEF2-VP16_nst1-1_nst3-1_stem_rep2


title: saami12


title: hant5


title: saami9


title: Vehicle treated for 24h

city: Hershey

first: Junxuan

last: Lu

state: Pennsylvania

address: R130 Pharmacology, PO BOX 850

department: Pharmacology

institute: Penn State College of Medicine

description: Vehicle alone

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: Raw data were normalized by rank invariant normalization of Illumina BeadStudio 3.0 software. Data filter was performed on detection P-value (P  0.05) in at least 2/3 of the samples, signal intensity (100.0), and cut-off Fold-change 1.1 and 0.9 between vehicle and bufalin-treated groups. For multiple probes of the same gene, we averaged the ratio of each probe. Thereafter, the normalized and filtered data of 13758 probes were analyzed .

source_name: LNCaP-ethanol for 24h

label_protocol: According to Illumina protocol.

growth_protocol: Human LNCaP prostate cancer cells were maintained in RPMI-1640 medium (Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Flowery Branch, GA) without antibiotics and incubated in standard 37°C and 5% CO2 humidified environment.

extract_protocol: RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA).  Total RNA quality was checked for integrity using Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: LNCaP cells were treated with 0, 10 and 20 nM of bufalin for 24 h for concentration-dependent changes.

value: LNCaP

tag: treatment

value: ethanol for 24h


title: Bufalin 10nM treated for 24h

description: Bufalin 10nM

source_name: LNCaP-Bufalin 10nM for 24h

value: Bufalin 10nM for 24h


title: nst1-1_nst3-1_stem_rep2

source_name: nst1-1 nst3-1 Arabidopsis Col0 stem, 10 cm long

value: nst1-1 nst3-1


title: saami7

value: Europe

value: blood


title: saami6


title: Bufalin 20nM treated for 24h

description: Bufalin 20nM

source_name: LNCaP-Bufalin 20nM for 24h

value: Bufalin 20nM for 24h


title: saami14


title: saami3


title: saami13


title: saami2


title: saami11


title: nst1-1_nst3-1_stem_rep1


title: saami1


title: nst1-1_nst3-1_stem_rep4


title: 400238

value: Estonians


title: 400237


title: 400240


title: 400221


title: 400235


title: 400236


title: 400210


title: 400209


title: saami5


title: 100259


title: 100263


title: 100258


title: 400204


title: 400206


title: 100261


title: 100254


title: 100550


title: 100520


title: 100531


title: 100257


title: 100252


title: 100253


title: 100249


title: 100558


title: 100557


title: 100248


title: 100235


title: 100243


title: HV-132: RNA-seq leukemia KO Rep3

city: Chicago

first: Panagiotis

last: Ntziachristos

state: IL

address: 320 E Superior

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the mm10 genome assembly using Tophat
Reads were counted on the exons of mm10 genes using htseq
Differential gene expression analysis was performed for (WT vs KO T cells) and (WT T cells vs WT T-ALL). Analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values. Bigwig of RNA-seq tracks.

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: CD8+ T cells and T-ALL cells were sorted from spleens and RNA was extracted immediately without culture.

extract_protocol:
RNeasy kit (Qiagen)
SMART-Seq v4 Ultra Low Input RNA Kit was used to generate full-length cDNA and Nextera XT DNA sample preparation kit was used to prepare final library

value: T-cell acute lymphoblastic leukemia

value: HK2 null (KO)


title: H4-388: RNA-seq lymphocytes WT Rep4

source_name: lymphocytes

value: lymphocytes

value: HK2 WT


title: HV-133: RNA-seq leukemia WT Rep3


title: H4-385: RNA-seq lymphocytes KO Rep5


title: HV-128: RNA-seq leukemia WT Rep1


title: HV-89: RNA-seq leukemia KO Rep4


title: HV-127: RNA-seq leukemia KO Rep1


title: HV-130: RNA-seq leukemia KO Rep2


title: H4-380: RNA-seq lymphocytes KO Rep3


title: H4-381: RNA-seq lymphocytes KO Rep4


title: H4-402: RNA-seq lymphocytes WT Rep5


title: HV-84: RNA-seq leukemia WT Rep4


title: HV-133-2: RNA-seq leukemia WT Rep2


title: H4-384: RNA-seq lymphocytes WT Rep3


title: H-132: RNA-seq lymphocytes WT Rep1


title: H-133: RNA-seq lymphocytes WT Rep2


title: 100230


title: 100232


title: 100228


title: 100233


title: 100218


title: C_Russian1006

source_name: Central Russians_Europe

value: Central Russians


title: H4-375: RNA-seq lymphocytes KO Rep1


title: C_Russian1012


title: aavgnp MI MeRIP

first: Susmita

last: Sahoo

address: One Gustave L. Levy Place, Box 1030

department: CVRC

institute: Icahn School of Medicine at Mount Sinai

description:
MI + aavgnp
diff_peak_fto_null.xls

data_processing:
Library strategy: MeRIP-Seq
Libraries were sequenced by the Illumina HiSeq 2500 platform (Illumina) as 50bp single reads
Unaligned reads were mapped to the mm10 reference genome using STAR v2.5.3a at default settings
The total number of MeRIP reads for each group was used for Figure 6A.
For each condition in Figure 6B, total MeRIP reads per transcript were calculated for reads that fully overlapped with a given feature, and were normalized to total non-IP reads per corresponding transcript. This ratio was normalized to corresponding Sham values, and was defined as fold change
Differential peak analysis of m6A MeRIP-Seq datasets were carried out using a modification of exomePeak R/Bioconductor package to compare the ratio of the absolute number of MeRIP reads to non-IP reads at a given peak between two conditions.
Genome_build: mm10
Supplementary_files_format_and_content: Differential peak analysis of m6A MeRIP-Seq datasets

source_name: Left Ventricle

extract_protocol:
LV tissues were harvested from mice post surgeries, snap frozen. For RNA, tissues homigenized in trizol and 200ug RNA was used for MeRIP per group, followed by PolyA and fragmentation steps. RNA was immunipurified using anti-m6A antibody and libraries were prepared using Illumina Truseq kit and samples were sequences in Illumina HiSeq 2500.
For library preparation, polyA and fragmentation steps were eliminated as these were done before MeRIP.

tag: strain

value: Left Ventricle

value: 1 week post MI

value: WT


title: aavFto MI MeRIP

description:
MI + aavFto
diff_peak_fto_null.xls


title: aavFto MI non-IP

description:
MI + aavFto
diff_peak_fto_null.xls


title: H4-379: RNA-seq lymphocytes KO Rep2


title: Mansi2

description:
Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).
processed and raw data files:
Tambets_et_al_660k_Matrix_processed.txt; Tambets_et_al_660k_Matrix_signal_intensities.txt

value: Mansi

value: Siberia


title: Mansi228


title: Mansi24


title: Mansi110


title: Mansi138


title: Mansi128


title: aavgnp MI non-IP

description:
MI + aavgnp
diff_peak_fto_null.xls


title: MI non-IP

description:
MI
diff_peak_mi_sham.xls


title: Mansi172


title: Mansi80


title: Sham non-IP

description:
Sham
diff_peak_mi_sham.xls


title: Sham MeRIP

description:
Sham
diff_peak_mi_sham.xls


title: MI MeRIP

description:
MI
diff_peak_mi_sham.xls


title: buryat_V43501

description:
Genomic DNA extracted from blood was genotyped using Illumina HumanOmni1-Quad BeadChip (Illumina).
processed and raw data files:
Tambets_et_al_1M_Matrix_processed.txt; Tambets_et_al_1M_Matrix_signal_intensities.txt

value: Buryats


title: Mansi3


title: Mansi85


title: E12.5 Batch 2

city: San Francisco

first: Jeremy

last: Reiter

state: California

address: 555 Mission Bay Boulevard South

institute: UCSF

description:
single cell RNA sequencing of E12.5 pancreas (batch 2)
read length: Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with v1.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger v1.1 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: pancreatic cells

extract_protocol:
Pancreata were isolated from Swiss Webster mouse embryos and dissociated in TrypLE Express at 37C with pipet trituration at 5 minute intervals during incubation. E12.5 pancreata were dissociated for 10 minutes, E14.5 pancreata for 15 minutes, and E17.5 pancreata for 30 minutes. Dissociations were neutralized with FACS buffer (10% FBS + 2mM EDTA in phenol-red free HBSS). Dissociated cells were passed through a 30um cell strainer and stained with Sytox live/dead stain (Thermo Fisher). Stained cells were washed twice in FACS buffer and then processed through a BD FACS Aria II; all live cells were collected.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument; droplet-based single cell RNA-Seq

value: Swiss Webster

value: pancreas

tag: developmental stage


title: Mansi17


title: E14.5 Batch 2

description:
single cell RNA sequencing of E14.5 pancreas (batch 2)
read length: Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: E17.5 Batch 2

description:
single cell RNA sequencing of E17.5 pancreas (batch 2)
read length: Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: khanty_V32243

value: Khanty


title: vepsian_V21441

value: Vepsians

value: Europe

value: blood


title: swede_V49245

value: Swedes


title: Mansi1


title: Mansi125


title: E14.5 Batch 1

description:
single cell RNA sequencing of E14.5 pancreas (batch 1)
read length: Read 1= 98, Index read 1 (i7)= 14, Index read 2 (i5)= 8, Read 2= 10


title: Mansi93


title: Mansi25


title: karelian_V11080

value: Karelians


title: karelian_V04898


title: Mansi218


title: ingerian_V22241

source_name: Ingrian Finns_Europe

value: Ingrian Finns


title: Mansi22


title: ingerian_V06336


title: ingerian_V42764


title: ingerian_V33586


title: Mansi211


title: ingerian_V46386


title: ingerian_V24378


title: Mansi15


title: Mansi13


title: Mansi23


title: Mansi19


title: Mansi230


title: vepsa50


title: MDS-L_SIRT1OE-hMeDIP-rep2

city: Duarte

first: Sun

last: Jie

state: CA

address: 1500 East Duarte Road

institute: City of Hope

data_processing:
Illumina bcl2fastq2-2.18 software was used for basecalling
Sequencing reads were aligned to the human genome build GRCh37/hg19 using theBurrows-Wheeler Aligner (BWA, v0.7.5a) (Li and Durbin, 2009).
MACS2 was utilized to define peaks with significantly enriched signals (Zhang et al., 2008).

source_name: MDS-L

growth_protocol: RPMI 1640 medium with 10% FBS and 1% penicillin-streptomycin in the presence of 30 ng/mL human recombinant human IL-3

extract_protocol:
Genomic DNA were sonicated and enriched with anti-5hmC antibody.
KAPA HyperPrep Kits

treatment_protocol: Lentivirous base transduction of SIRT1 overexpression or MOCK vector

value: myelodysplastic syndrome (MDS) cell line MDS-L

tag: transduction

value: SIRT1 overexpression

tag: antibody

value: anti-5hmC antibody


title: MDS-L_SIRT1OE-hMeDIP-rep1


title: Compound_24hr_rep6

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

institute: GSK

hyb_protocol: Labelled cDNA was hybridized onto Mouse Genome 430 2.0  GeneChip oligonucleotide arrays (Affymetrix).

scan_protocol: Standard protocols

data_processing: Data were analysed in R/Bioconductor, normalised by RMA

source_name: S. pneumoniae infected mice_Compound_24hr_whole lung

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

growth_protocol: Standard laboratory conditions

extract_protocol: WT-Ovation Pico RNA Amplification System (NuGen).

treatment_protocol: intranasal

tag: strain C57BL/6Babr

tag: mouse status

value: S. pneumoniae infected mouse

tag: treated with

value: Nemiralisib

tag: time point

value: whole lung


title: Compound_24hr_rep5


title: SaamiKola49

source_name: Saami from Kola Peninsula, Russia_Europe

tag: population

value: Saami from Kola Peninsula, Russia

tag: region


title: Nenets986

value: Maris


title: Compound_24hr_rep3


title: Compound_24hr_rep2


title: Compound_24hr_rep1


title: Compound_24hr_rep4


title: SaamiKola7


title: control_24hr_rep5

source_name: S. pneumoniae infected mice_control_24hr_whole lung

value: control


title: MDS-L_MOCK-hMeDIP-rep1

value: MOCK vector


title: Axial progenitors rep3

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

country: Italy

institute: National Research Council of Italy (CNR)

description:
normalized_counts_matrix.txt
treated3.txt

data_processing:
The quality of raw reads in fastq format was analyzed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Adapter contamination and poor quality ends were removed using Trim Galore v. 0.4.0
Single-end clean reads were aligned to the human reference genome using Tophat2 v2.0.13
Read alignments were sorted with SAMtools v1.1 before being counted to genomic features by HTSeq version 0.6.0 (Anders et al., 2015)
Genome_build: hg38 assembly
Supplementary_files_format_and_content: .txt file reports normalized counts

source_name: human embryonic stem cells

growth_protocol: Feeder-free hESCs were grown in Essential 8 medium on Geltrex

extract_protocol:
Total RNA was harvested using the RNeasy kit (Qiagen) according to the manufacturer’s instructions and digested with DNase I (Qiagen) to remove genomic DNA.
Total RNA was processed according to the TruSeq protocol (Illumina). Three separate RNA libraries (biological replicates) were barcoded and prepared for hESCs and D3 axial progenitors. Library size, purity and concentration were determined using the Agilent Technologies 2100 Bioanalyzer. For sequencing, four samples were loaded per lane on an Illumina Genome Analyzer Hiseq2500.

treatment_protocol: hESCs were treated with bFGF (20 ng/ml) and the WNT agonist/GSK3 inhibitor CHIR99021 for 3 days and cultured on fibronectin to give rise to axial progenitors

tag: cell type

value: in vitro derived axial progenitors


title: MDS-L_SIRT1OE-input

value: input


title: MDS-L_MOCK-Input


title: SaamiKola47

value: Europe


title: Axial progenitors rep2

description:
normalized_counts_matrix.txt
treated2.txt


title: SaamiKola74

value: blood


title: Axial progenitors rep1

description:
normalized_counts_matrix.txt
treated1.txt


title: control_24hr_rep1


title: SaamiKola25


title: Compound_6hr_rep6

source_name: S. pneumoniae infected mice_Compound_6hr_whole lung


title: control_24hr_rep3


title: control_24hr_rep2


title: control_24hr_rep6


title: MDS-L_MOCK-hMeDIP-rep2


title: SaamiKola5


title: SaamiKola40


title: Compound_6hr_rep3


title: Compound_6hr_rep5


title: SaamiKola6


title: hESCs rep1

description:
normalized_counts_matrix.txt
untreated1.txt

value: undifferentiated hESCs


title: Compound_6hr_rep4


title: Finland95

value: Finns


title: control_24hr_rep4


title: hESCs rep2

description:
normalized_counts_matrix.txt
untreated2.txt


title: Finland94


title: Compound_6hr_rep2


title: hESCs rep3

description:
normalized_counts_matrix.txt
untreated3.txt


title: Finland97


title: Finland87


title: Compound_6hr_rep1


title: Finland86


title: control_6hr_rep3

source_name: S. pneumoniae infected mice_control_6hr_whole lung


title: Finland84


title: Finland76


title: control_6hr_rep1


title: control_6hr_rep4


title: Finland78


title: control_6hr_rep2


title: Finland74


title: Finland69


title: Finland65


title: control_6hr_rep5


title: Finland119


title: Finland67


title: control_6hr_rep6


title: Finland118


title: Compound_3hr_rep5

source_name: S. pneumoniae infected mice_Compound_3hr_whole lung


title: Compound_3hr_rep6


title: Compound_3hr_rep3


title: Compound_3hr_rep1


title: Finland117


title: Compound_3hr_rep4


title: control_3hr_rep6

source_name: S. pneumoniae infected mice_control_3hr_whole lung


title: Compound_3hr_rep2


title: control_3hr_rep5


title: Finland109


title: Finland106


title: Finland111


title: Poland151

value: Poles


title: Poland149


title: Poland150


title: Finland101


title: control_3hr_rep3


title: latvian51E3

value: Latvians


title: Poland148


title: control_3hr_rep1


title: control_3hr_rep2


title: Compound_0hr_rep5

source_name: S. pneumoniae infected mice_Compound_0hr_whole lung


title: control_3hr_rep4


title: Compound_0hr_rep6


title: Compound_0hr_rep3


title: CMEC3

description:
Total RNA (kit designed to bias towards exosomal content)
3421-EJF-0009

source_name: Exosomal RNA from normal canine mammary cells (biological replicate #3)

tag: cell compartment

value: exosome

tag: cell line

value: Normal canine mammary cells

value: 3 day conditioned media


title: Compound_0hr_rep2

value: S. pneumoniae infected mouse

value: Nemiralisib


title: Poland135


title: Compound_0hr_rep4

value: whole lung


title: Compound_0hr_rep1


title: Gagauz10

value: Gagauzes