title: Heart_Fibroblasts_LCMVd8_RNA_3


title: Heart_Endothelium_SteadyState_RNA_3

status: Public on Jun 30 2020

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: SMART-seq sample of Heart GP38negCD31pos cells

library_source: transcriptomic

data_processing:
Adapter trimming with trimmomatic (version 0.32) with settings: SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:30
Genome alignment using HISAT (2.1.0) with default parameters
Filtered reads to primary alignments (excluding secondary alignments) to exons (defined by Ensembl, genome-build GRCm38.p6 in the GENCODE Basic set)  using the GenomicAlignments package in R (3.2.3)
Counted reads in genes over all samples using the package GenomicAlignments in R (3.2.3)
Normalized to counts per million (CPM) and transformed to log2(CPM) using Limma Voom in R
Regressed out immune cell signatures using Limma removeBatchEffect in R
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of read counts (CSV), read counts of each gene for each sample
Supplementary_files_format_and_content: Matrix of log2(CPM) values (CSV), log2(CPM) after regressing out immune signatures of each gene

molecule: polyA RNA

organism: Mus musculus

source_name: Murine structural cells

growth_protocol: C57BL/6J mice, bred and maintained under specific pathogen free conditions at the Insti-tute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences in Vienna, Austria. 8 to 12 week old mice (males only) were used for the steady state characterization

extract_protocol:
Organs were digested with Accumax and structural cells isolated using FACS
For each individual assay, a maximum of 200 cells were sort-purified and deposited in 96-well plates con-taining 4 μl lysis buffer (1:20 solution of RNase Inhibitor (Clontech) in 0.2% v/v Triton X-100 (Sigma-Aldrich)), spun down, and immediately frozen at -80ºC. Reverse transcription and PCR were performed as described (Picelli et al., 2014). Library preparation was conducted on 1 ng of cDNA using the Nextera XT DNA Sample Preparation Kit (Illumina) followed by SPRI (Beckman Coulter) size selection. Sequencing was performed by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50-bp single-end configuration.

treatment_protocol: For the infection experiments, mice were intravenously infected with 2x106 focus-forming units of lym-phocytic choriomeningitis virus (LCMV) strain Clone 1343 and sacrificed 8 days after infection.

tag: organ

value: Heart

tag: cell type

tag: condition

tag: age

value: 8 to 12 weeks

tag: strain


title: FGFR2_N550K_Fulv.Palbo.FGF2..S159

city: Cambridge

first: Ofir

last: Cohen

state: Massachusetts

address: 415 Main St, Cambridge, MA 02142

department: Cancer Program

country: USA

institute: Broad Institute

description:
FGFR.Rescue.seq.tpm.normalized.QC.csv
FGFR.Rescue.seq.counts.QC.csv

data_processing:
mRNA-seq libraries were sequenced on an Illumina NextSeq 500 sequencer, V2 75 cycle kits
Reads were mapped with STAR aligner (Dobin et al. 2013)
Genome_build: hg19 of the human genome and build 12 of the GENCODE human genome annotation

molecule: total RNA

organism: Homo sapiens

source_name: Breast Cancer

growth_protocol: T47D cells were infected de novo with lentivirus encoding FGFR1, FGFR2 mutants, FGF3  and controls  in the pLX307 plasmid.  Cells were plated in 96-well plates in for 48 hours.

extract_protocol:
Plates with cell lysates were thawed and purified with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics). The RNA captured beads were air-dried and processed immediately for RNA secondary structure denaturation (72˚C for three minutes) and cDNA synthesis. We performed SMART-Seq2 following the published protocol
Smart-seq 2

treatment_protocol: Cell were then treated with DMSO, fulvestrant (100 nM), palbociclib (1 uM), FIIN-3 (100 nM), and trametinib (500 nM) as single agent and in combinations for 24 hours

tag: cell line

tag: lentivirus

tag: replicate

tag: treatment


title: FGFR2_N550K_Fulv.FGF2..S168


title: FGFR2_N550K_Fulv.FGF2.Tram..S158


title: FGFR2_M538I_Fulv.FGF2..S156


title: FGFR2_N550K_Fulv.FGF2.Tram..S157


title: Heart_Endothelium_SteadyState_RNA_1


title: Kidney_Epithelium_LCMVd8_RNA_2

description: SMART-seq sample of Kidney EPCAMpos cells

value: Kidney

value: EPCAMpos


title: FGFR2_M538I_FGF2..S154


title: FGFR2_M538I_FGF2..S153


title: Heart_Fibroblasts_LCMVd8_RNA_1

description: SMART-seq sample of Heart GP38posCD31neg cells


title: FGFR2_M538I_DMSO..S150

value: DMSO


title: GFP_Fulv..S15

value: GFP

value: Fulv


title: Heart_Epithelium_SteadyState_RNA_1

description: SMART-seq sample of Heart EPCAMpos cells


title: Heart_Epithelium_SteadyState_RNA_3


title: Heart_Epithelium_LCMVd8_RNA_1


title: Heart_Epithelium_LCMVd8_RNA_3


title: FGFR2_M538I_DMSO..S149


title: Heart_Epithelium_SteadyState_RNA_2


title: Heart_Epithelium_LCMVd8_RNA_2


title: FGFR2_M538I_Fulv.Palbo.FGF2..S148


title: FGFR2_M538I_Fulv.Palbo.FGF2..S147


title: Caecum_Fibroblasts_SteadyState_RNA_3

description: SMART-seq sample of Caecum GP38posCD31neg cells

value: Caecum


title: Caecum_Fibroblasts_SteadyState_RNA_1


title: Heart_Endothelium_SteadyState_RNA_2


title: FGFR2_M538I_Fulv.FGF2.Tram..S146


title: Caecum_Fibroblasts_SteadyState_RNA_2


title: FGFR2_M538I_Fulv.FGF2..S155


title: FGFR2_M538I_Fulv.FGF2.Tram..S145


title: FGFR2_WT_Fulv.FGF2..S144


title: Caecum_Fibroblasts_LCMVd8_RNA_1


title: Heart_Endothelium_LCMVd8_RNA_1


title: Heart_Endothelium_LCMVd8_RNA_2


title: Caecum_Fibroblasts_LCMVd8_RNA_3


title: FGFR2_M538I_Fulv..S152


title: Heart_Endothelium_LCMVd8_RNA_3


title: FGFR2_WT_FGF2..S142


title: Caecum_Fibroblasts_LCMVd8_RNA_2


title: FGFR2_M538I_Fulv..S151


title: FGFR2_WT_FGF2..S141


title: Caecum_Endothelium_SteadyState_RNA_2

description: SMART-seq sample of Caecum GP38negCD31pos cells


title: FGFR2_WT_Fulv..S140


title: FGFR2_WT_Fulv..S139


title: GFP_DMSO..S14


title: FGFR2_WT_DMSO..S138


title: Caecum_Endothelium_SteadyState_RNA_1


title: Caecum_Endothelium_LCMVd8_RNA_2


title: Caecum_Endothelium_LCMVd8_RNA_3


title: FGFR2_WT_Fulv.Palbo.FGF2..S135


title: FGFR2_WT_Fulv.FGF2..S143


title: FGFR2_WT_Fulv.Palbo.FGF2..S136


title: Caecum_Epithelium_LCMVd8_RNA_1

description: SMART-seq sample of Caecum EPCAMpos cells


title: Caecum_Epithelium_SteadyState_RNA_2


title: Caecum_Endothelium_SteadyState_RNA_3


title: FGFR2_WT_Fulv.FGF2.Tram..S133


title: FGFR1_Fulv.FGF2..S132


title: FGFR2_WT_Fulv.FGF2.Tram..S134


title: Caecum_Epithelium_LCMVd8_RNA_2


title: FGFR1_Fulv.FGF2..S131


title: Caecum_Epithelium_SteadyState_RNA_3


title: Brain_Fibroblasts_SteadyState_RNA_2

description: SMART-seq sample of Brain GP38posCD31neg cells

value: Brain


title: Brain_Fibroblasts_SteadyState_RNA_1


title: FGFR1_FGF2..S130


title: Brain_Fibroblasts_SteadyState_RNA_3


title: GFP_DMSO..S13


title: FGFR1_FGF2..S129


title: Caecum_Endothelium_LCMVd8_RNA_1


title: FGFR1_Fulv..S128


title: FGFR2_WT_DMSO..S137


title: Brain_Fibroblasts_LCMVd8_RNA_2


title: FGFR1_DMSO..S126


title: Caecum_Epithelium_SteadyState_RNA_1


title: FGFR1_Fulv..S127


title: Brain_Endothelium_SteadyState_RNA_2

description: SMART-seq sample of Brain GP38negCD31pos cells


title: FGFR1_DMSO..S125


title: Brain_Fibroblasts_LCMVd8_RNA_1


title: Brain_Endothelium_SteadyState_RNA_3


title: FGFR1_Fulv.Palbo.FGF2..S124


title: Brain_Endothelium_SteadyState_RNA_1


title: FGFR1_Fulv.FGF2.Tram..S122


title: FGFR1_Fulv.FGF2.Tram..S121


title: parental_Fulv.FGF2.FIIN.3..S12

value: parental


title: Brain_Epithelium_SteadyState_RNA_2

description: SMART-seq sample of Brain EPCAMpos cells


title: GFP_Fulv.FGF2..S119


title: Brain_Endothelium_LCMVd8_RNA_3


title: GFP_FGF2..S118


title: GFP_FGF2..S117


title: Brain_Fibroblasts_LCMVd8_RNA_3


title: Brain_Epithelium_SteadyState_RNA_3


title: Brain_Epithelium_SteadyState_RNA_1


title: Brain_Epithelium_LCMVd8_RNA_2


title: Brain_Epithelium_LCMVd8_RNA_3


title: GFP_Fulv.Palbo.FGF2..S111


title: GFP_Fulv..S115


title: GFP_DMSO..S113


title: GFP_Fulv.Palbo.FGF2..S112


title: Brain_Epithelium_LCMVd8_RNA_1


title: Thymus_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Thymus GP38negCD31pos cells

library_source: genomic

data_processing:
Adapter trimming with trimmomatic (version 0.32) with settings LEADING:3 TRAILING:3 SLIDINGWINDOW:4:10 MINLEN:36
Genome alignment using bowtie (2.2.4) with settings --very-sensitive
Filtered reads to primary alignments with MAPQ > 30 using sambamba (0.7.0)
Called peaks using MACS2 (2.7.6)
Counted reads in consensus peak set over all samples using GenomicAlignments in R (3.2.3)
Normalized to counts per million (CPM) and transformed to log2(CPM) using Limma Voom in R
Regressed out immune cell signatures using Limma removeBatchEffect in R
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of read counts (CSV), read counts of each peak in the consensus peak set for each sample
Supplementary_files_format_and_content: Matrix of log2(CPM) values (CSV), log2(CPM) after regressing out immune signatures of each peak in the consensus peak set for each sample

molecule: genomic DNA

growth_protocol: C57BL/6J mice , bred and maintained under specific pathogen free conditions at the Insti-tute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences in Vienna, Austria. 8 to 12 week old mice (males only  ) were used for the steady state characterization

extract_protocol:
Organs were digested with Accumax and structural cells isolated using FACS
ChIPmentation was carried out as previously described (Gustafsson et al., 2019; Schmidl et al., 2015), with minor adaptions. Briefly, 50,000 cells (or a lower number of cells for particularly rare cell populations) were washed once with PBS. Cells were fixed and sonicated (Covaris S220) as described (Schmidl et al., 2015). Following sonication, the lysate was brought to RIPA buffer conditions (final concentration: 10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 1x protease inhibitors (Sigma) and 1 mM PMSF) to a volume of 200 µl per immunoprecipitation.  For each immunoprecipitation, 10 µl magnetic Protein A (Life Technologies) were washed twice and resus-pended in PBS supplemented with 0.1% BSA. 1 µg of antibody recognizing H3K4me2 (MerckMillipore, clone AW30) was added and bound to the beads by rotating over night at 4 °C. Beads were added to the sonicated lysate and incubated for 2 h at 4 °C on a rotator followed by washing the beads and tagmenting the bead-bound chromatin as described (Gustafsson et al., 2019).  After tagmentation, the beads were washed once with RIPA and once with cold Tris-Cl pH 8. Bead bound tagmented chromatin was than resuspended in 10.5 µl 20 mM EDTA and incubated for 30 min at 50 °C. Then, 10.5 µl 20 mM MgCl2 as well as 25 µl of pre-activated 2x KAPA HiFi HotStart Ready Mix (incubation at 98 °C for 45 s) are added and incubated for 5 min at 72 °C followed by incubation for 10 min at 95 °C. Beads are magnetized and 2 µl of each library were amplified in a 10 µl qPCR reaction containing 0.8 mM primers, SYBR Green and 5 µl Kapa HiFi HotStart ReadyMix to estimate the optimum number of enrichment cycles with the following program: 72 °C for 5 min, 98 °C for 30 s, 24 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 30 s, and a final elongation at 72 °C for 1 min. Kapa HiFi HotStart ReadyMix was incubated at 98 °C for 45 s before preparation of all PCR reactions (qPCR and final enrichment PCR), to activate the hot-start enzyme for successful nick translation at 72 °C in the first PCR step.  Final enrichment of the libraries was performed in a 50 µl reaction using 0.75 mM primers (custom Nextera primers as described for ATAC-seq) and 25 ml Kapa HiFi HotStart ReadyMix. Libraries were amplified for the rounded-down Cq value determined in the qPCR reaction. Enriched libraries were purified using SPRI AMPure XP beads. For preparation of compatible input controls, 3 μl of 50 mM MgCl2 was added to 15 μl sonicated lysate (pool of 5 μl of endothelium, epithelium and fibroblasts lysates form the same organ) to neutralize the EDTA in the SDS lysis buffer. 20 μl of tagmentation buffer and 1 μl transposase (Nextera, Illumina) was added, and samples were incubated at 37 °C for 10 min. Input control chromatin was purified with MinElute PCR purification kit (Qiagen) and 22.5 μl of the purified transposition reaction were combined with 25 μl of PCR master mix and 0.75 mM primers (custom Nextera). Libraries were subsequently amplified as described above. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 50-bp single-end configuration

value: Thymus


title: Thymus_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Thymus GP38posCD31neg cells


title: GFP_DMSO..S114


title: Thymus_Endothelium_SteadyState_CHIP_1


title: GFP_Fulv.FGF2.Tram..S110


title: Thymus_Fibroblasts_SteadyState_CHIP_1


title: GFP_Fulv..S116


title: Thymus_Epithelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Thymus EPCAMpos cells


title: Thymus_Epithelium_SteadyState_CHIP_1


title: parental_Fulv.FGF2.FIIN.3..S11


title: GFP_Fulv.FGF2.Tram..S109


title: Spleen_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Spleen GP38posCD31neg cells

value: Spleen


title: parental_Fulv.FGF2..S108


title: Spleen_Fibroblasts_SteadyState_CHIP_1


title: Spleen_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Spleen GP38negCD31pos cells


title: Brain_Endothelium_LCMVd8_RNA_2


title: Brain_Endothelium_LCMVd8_RNA_1


title: GFP_Fulv.FGF2..S120


title: Spleen_Epithelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Spleen EPCAMpos cells


title: parental_FGF2..S106


title: Spleen_Endothelium_SteadyState_CHIP_1


title: parental_Fulv.FGF2..S107


title: Spleen_Epithelium_SteadyState_CHIP_1


title: parental_FGF2..S105


title: parental_Fulv..S104


title: SmallIntestine_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of SmallIntestine GP38posCD31neg cells

value: SmallIntestine


title: parental_DMSO..S102

description:
FGFR.Rescue.seq.tpm.normalized.QC.csv
FGFR.Rescue.seq.counts.QC.csv


title: SmallIntestine_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of SmallIntestine GP38negCD31pos cells


title: SmallIntestine_Fibroblasts_SteadyState_CHIP_1


title: SmallIntestine_Endothelium_SteadyState_CHIP_1


title: SmallIntestine_Epithelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of SmallIntestine EPCAMpos cells


title: SmallIntestine_Epithelium_SteadyState_CHIP_1


title: parental_FIIN.3.FGF2..S10


title: parental_DMSO..S101


title: parental_DMSO..S1


title: Skin_Endothelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Skin GP38negCD31pos cells

value: Skin


title: Skin_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Skin GP38posCD31neg cells


title: HCT116 cells, GPS167

city: Sherbrooke

first: Philippe

last: Thibault

state: Quebec

address: 3201, Jean-Mignault

department: faculty of medecine and health sciences

country: Canada

institute: Université de Sherbrooke

data_processing:
Data was preprocessed using Trimmomatic
Reads were aligned on a transcriptome reference sequence database (GRCh38 GENCODE V24) using Bowtie2 aligner (Langmead B, Salzberg S. Nature Methods. 2012, 9:357-359).
Gene abundance quantified in transcript-per-million (TPM) using RSEM (Li and Dewey, BMC Bioinfomatics 2011, 12: 323)
Alternative splicing was quantified using percent spliced-in (PSI) calculated from transcript expression data and based on alternative splicing event annotation database extracted from GENCODE V24 annotations.
Genome_build: GRCh38 GENCODE V24
Supplementary_files_format_and_content: Excel sheets containing log2-ratios or delta-PSI values.

source_name: Colon

growth_protocol: HCT116 cells were obtained from ATCC (Manassas, VA, USA) and were grown in the recommended media.

extract_protocol:
Total RNA was extracted using RNAeasy kit from Qiagen.
Poly-A RNA libraries were prepared according to Illumina's instructions.

treatment_protocol: HCT116 cells were treated with DMSO, GPS167 or GPS192.


title: HCT116 cells, GPS192


title: parental_Fulv..S103


title: Skin_Endothelium_SteadyState_CHIP_2


title: Skin_Fibroblasts_SteadyState_CHIP_1


title: parental_Fulv.Palbo.FGF2..S100


title: Skin_Epithelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Skin EPCAMpos cells


title: Lymphnode_Endothelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Lymphnode GP38negCD31pos cells

value: Lymphnode


title: Lymphnode_Epithelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Lymphnode EPCAMpos cells


title: Lymphnode_Endothelium_SteadyState_CHIP_2


title: Skin_Epithelium_SteadyState_CHIP_1


title: Lung_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Lung GP38posCD31neg cells

value: Lung


title: Lymphnode_Epithelium_SteadyState_CHIP_2


title: Lymphnode_Fibroblasts_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Lymphnode GP38posCD31neg cells


title: HCT116 cells, GPSC

value: Mock


title: Lung_Fibroblasts_SteadyState_CHIP_1


title: Lung_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Lung GP38negCD31pos cells


title: Lung_Endothelium_SteadyState_CHIP_1


title: Lung_Epithelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Lung EPCAMpos cells


title: Lung_Epithelium_SteadyState_CHIP_2


title: Liver_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Liver GP38posCD31neg cells

value: Liver


title: Liver_Fibroblasts_SteadyState_CHIP_1

value: 8 to 12 weeks


title: Liver_Endothelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Liver GP38negCD31pos cells


title: Liver_Endothelium_SteadyState_CHIP_2


title: Liver_Epithelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Liver EPCAMpos cells


title: Liver_Epithelium_SteadyState_CHIP_2


title: LargeIntestine_Epithelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of LargeIntestine EPCAMpos cells

value: LargeIntestine


title: LargeIntestine_Endothelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of LargeIntestine GP38negCD31pos cells


title: LargeIntestine_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of LargeIntestine GP38posCD31neg cells


title: Kidney_Fibroblasts_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Kidney GP38posCD31neg cells

value: Kidney


title: LargeIntestine_Fibroblasts_SteadyState_CHIP_1


title: LargeIntestine_Endothelium_SteadyState_CHIP_2


title: LargeIntestine_Epithelium_SteadyState_CHIP_2

value: EPCAMpos


title: Kidney_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Kidney GP38negCD31pos cells


title: Kidney_Fibroblasts_SteadyState_CHIP_2


title: Kidney_Epithelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Kidney EPCAMpos cells


title: Kidney_Endothelium_SteadyState_CHIP_1


title: Kidney_Epithelium_SteadyState_CHIP_2


title: Heart_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Heart GP38posCD31neg cells

value: Heart


title: Heart_Endothelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Heart GP38negCD31pos cells


title: Heart_Fibroblasts_SteadyState_CHIP_1


title: Heart_Epithelium_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Heart EPCAMpos cells


title: Heart_Endothelium_SteadyState_CHIP_2


title: UPOP_R1

city: Pittsburgh

first: Rajneesh

last: Srivastava

state: Pennsylvania

address: 450 Technology Dr

department: Surgery, University of Pittsburgh

institute: McGowan Institute for Regenerative Medicine

description: Ultra violet crosslinked POP-seq_Replicate_1

data_processing:
POP-seq reads were pre-processed using FASTX toolkits for trimming adaptor sequence ("TGGAATTCTCGGGTGCCAAGG"), and low-quality read fragments. Then the sequence reads were mapped to hg38 (Homo_sapiens.GRCh38.97) reference genome using hisat 0.1.6 with default parameters. Reads mapped onto Human ribosomal DNA complete repeating unit (U13369.1) were discarded.
Aligned reads were post-processed using samtools version 1.2 and formatted for peak calling using bedtools version 2.18.1
Peaks were called using Piranha version 1.2.1 with default parameters
Peaks were merged for the two replicates of each POP-seq variant and used for downstream data analysis
Genome_build: hg38 (Homo_sapiens.GRCh38.97)
Supplementary_files_format_and_content: tsv.gz

source_name: K562 cells

growth_protocol: K562 cells were obtained from the American Type Culture Collection (ATCC). Cells were cultured in Dulbecco’s minimal essential medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Atlanta Biologicals) along with 1% antibiotics (penicillin 5000 Units/ml, Streptomycin 5000 μg/ml). All cells were maintained at 37°C and 5% CO2 in a humidified incubator and fresh media was replenished every alternate day until confluent.

extract_protocol:
Following the trizol lysis, interphase pellet was subjected to RNase A/T1 (thermo scientific) degradation in RNase buffer (10 mM Tris-HCl, pH 7.5, 300 mM NaCl and 5 mM EDTA, pH 7.5). 2 µg of RNase A/T1 mix was added to the interphase pellet, mixed by pipetting and incubated at 37° C for 15 min. Interphase-RNase mixture was resolubilized in trizol reagent to recover the RNA-protein complexes. After addition of chloroform, tubes were incubated at room temperature for 5 min, vortexed and centrifuged at 12000 g for 10 min. This results in protein bound RNA at the interphase, unbound RNA in the aqueous phase while the unbound proteins in the organic phase. The aqueous and organic layers were discarded as described previously. Interphase pellet was precipitated in 1 ml methanol and spun down to remove the methanol. Next, the interphase was mixed with Proteinase K in appropriate buffer (0.1M NaCl, 10 mM Tris-HCl, pH 8, 1 mM EDTA, 0.5% SDS and 200 µg/ml proteinase K). Samples were incubated at 50° C for 2 hours. After proteinase K digestion, free RNA was recovered from the aqueous layer by trizol extraction as described previously.  Samples were cooled and the released RNA was purified by standard trizol extraction. The upper aqueous layer containing the free RNA fragments (previously bound to proteins) was transferred to new tube and precipitated with isopropanol as per the manufacturer instructions.   Protein bound RNA’s concentration was estimated using Nanodrop and up to 1 µg of RNA was incubated with DNase I, 1U (thermo scientific) at 37° C for 30 min to remove any traces of DNA contamination. 1 µl of 50 mM EDTA was added to the reaction mixture and incubated at 65° C for 10 min to terminate the reaction. RNA was purified using conventional trizol extraction from the aqueous layer. At this point, r-RNA depletion was performed with 1 µg input RNA using Ribo-cop kit (Lexogen) as per manufacturer instructions. Further, the ends of r-RNA depleted RNA were modified by treating with Calf intestine alkaline phosphatase (CIAP, Invitrogen) and T4 polynucleotide kinase (T4 PNK, thermo scientific) as per manufacturer protocol.  The end modification enabled the library preparation of these RNA fragments.
RNA purity and concentration were assessed at each step using Nanodrop (thermo scientific) based on the absorbance ratio 260/280 >2. RNA integrity was evaluated using Agilent 2100 bioanalyser system. At least 50 ng of r-RNA depleted POP-seq RNA was used to generate sequencing libraries using the True-seq small RNA library prep kit (Illumina). All libraries were barcoded and sequenced in parallel on a Next-seq platform for 400 million reads to obtain 75 bp single end reads.
POP-seq libraries prepared using Illumina True seq small RNA library preparation kit

treatment_protocol: Cells were cultured in T-175 flask until a maximum of 90% confluency was reached. A total of 100 million cells per replicate of each sample were used for UV, formaldehyde and no-crosslinking control. Cell were washed twice with 1X PBS, the supernatant was removed by pipetting and cells were resuspended in 1X PBS. For UV crosslinking, cells in PBS suspension were transferred to 100 mm dishes and UV irradiated at 254 nm with 400 mJ/cm2 dosage (UV Stratalinker 1800). Immediately after crosslinking, cells were collected in 15 ml tubes and pelleted at 1500 rpm for 5 min. Supernatant was discarded and cells were lysed in 8 ml trizol reagent (Life Technologies) by pipetting up and down to obtain a homogenous cell lysate.    Formaldehyde crosslinking was achieved by pelleting 100 million cells and washing in 1X PBS twice until all the media is discarded. Cells were resuspended in 30 ml PBS in 50 ml tubes and crosslinked with 0.5% formaldehyde (405 µl) for 10 min by gentle shaking at room temperature. Formaldehyde crosslinking was stopped by adding 1 M Glycine (3.75 ml) to the cell suspension for 5 min by gentle shaking at room temperature. Cells were pelleted down at 1500 rpm for 5 min, lysed in 8 ml trizol and homogenized by pipetting up and down. For non-crosslinked samples, cells were pelleted down, washed in 1X PBS and subsequently lysed in trizol for phase separation.

value: K562 cells

tag: experiment

value: UPOP-seq (UV-crosslinking)


title: UPOP_R2

description: Ultra violet crosslinked POP-seq_Replicate_2


title: Heart_Epithelium_SteadyState_CHIP_2


title: Caecum_Fibroblasts_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Caecum GP38posCD31neg cells

value: Caecum


title: Caecum_Fibroblasts_SteadyState_CHIP_1


title: Caecum_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Caecum GP38negCD31pos cells


title: FPOP_R2

description: Formaldehyde crosslinked POP-seq_Replicate_2

value: FPOP-seq (Formaldehyde crosslinking)


title: NPOP_R1

description: Non-crosslinked POP-seq_Replicate_1

value: NPOP-seq (no crosslinking)


title: FPOP_R1

description: Formaldehyde crosslinked POP-seq_Replicate_1


title: NPOP_R2

description: Non-crosslinked POP-seq_Replicate_2


title: Caecum_Epithelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Caecum EPCAMpos cells


title: Caecum_Endothelium_SteadyState_CHIP_1


title: Brain_Endothelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Brain GP38negCD31pos cells

value: Brain


title: Brain_Fibroblasts_SteadyState_CHIP_1

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Brain GP38posCD31neg cells


title: Brain_Epithelium_SteadyState_CHIP_2

description:
H3K4me2 bound DNA fragments (ChIPmentation)
ChIPmentation sample of Brain EPCAMpos cells


title: Thymus_Fibroblasts_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Thymus GP38posCD31neg cells

growth_protocol: C57BL/6J mice, bred and maintained under specific pathogen free conditions at the Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences in Vienna, Austria. 8 to 12 week old mice (males only  ) were used for the steady state characterization

extract_protocol:
Organs were digested with Accumax and structural cells isolated using FACS
Chromatin accessibility mapping by ATAC-seq was performed as previously described (Buenrostro et al., 2013; Corces et al., 2016), with minor adaptations. In each experiment, a maximum of 50,000 sort-purified cells were collected at 300 g for 5 min at 4 °C. After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 µl 2xTD buffer, 2 µl TDE1 (Illumina), 10.25 µl nuclease-free water, and 0.25 µl 1% digitonin (Promega)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 11 µl, 1 µl of the eluted DNA was used in a quantitative PCR reaction to estimate the optimum number of amplification cycles. The remaining 10 μl of each library were amplified for the number of cycles corre-sponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) from the qPCR (rounded up). Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluo-rometer (Life Technologies). Library amplification was performed using custom Nextera primers (Buenrostro et al., 2013). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50-bp single-end configuration.

treatment_protocol: not applicable

value: Thymus


title: Caecum_Epithelium_SteadyState_CHIP_1


title: Caecum_Fibroblasts_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Caecum GP38posCD31neg cells


title: Caecum_Endothelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Caecum GP38negCD31pos cells


title: Brain_Endothelium_SteadyState_CHIP_1


title: Thymus_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Thymus EPCAMpos cells


title: Lymphnode_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Lymphnode EPCAMpos cells


title: Brain_Fibroblasts_SteadyState_CHIP_2


title: Spleen_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Spleen EPCAMpos cells

value: Spleen


title: Brain_Epithelium_SteadyState_CHIP_1


title: Caecum_Fibroblasts_SteadyState_ATAC_2


title: Spleen_Epithelium_SteadyState_ATAC_1


title: Spleen_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Spleen GP38negCD31pos cells


title: Thymus_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Thymus GP38negCD31pos cells


title: Lymphnode_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Lymphnode GP38negCD31pos cells

value: Lymphnode


title: Spleen_Endothelium_SteadyState_ATAC_2


title: Spleen_Fibroblasts_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Spleen GP38posCD31neg cells


title: Thymus_Epithelium_SteadyState_ATAC_1


title: Thymus_Endothelium_SteadyState_ATAC_2


title: SmallIntestine_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of SmallIntestine EPCAMpos cells

value: SmallIntestine


title: SmallIntestine_Epithelium_SteadyState_ATAC_1


title: SmallIntestine_Endothelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of SmallIntestine GP38negCD31pos cells


title: SmallIntestine_Endothelium_SteadyState_ATAC_1


title: SmallIntestine_Fibroblasts_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of SmallIntestine GP38posCD31neg cells


title: Spleen_Fibroblasts_SteadyState_ATAC_1


title: Skin_Fibroblasts_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Skin GP38posCD31neg cells

value: Skin


title: Skin_Fibroblasts_SteadyState_ATAC_2


title: SmallIntestine_Fibroblasts_SteadyState_ATAC_1


title: Lymphnode_Fibroblasts_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Lymphnode GP38posCD31neg cells


title: Skin_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Skin EPCAMpos cells


title: Skin_Epithelium_SteadyState_ATAC_1


title: Lymphnode_Epithelium_SteadyState_ATAC_1


title: Skin_Endothelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Skin GP38negCD31pos cells


title: PC-3 siELL2-2: siRNA knockdown of ELL2 gene

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
The quality reads were first aligned to hg38 Human Ensembl reference genome using Hisat2 v2.1.0
The abundance of reads was measured using HTSeq v0.9.0
Genome_build: hg38
differential expression analysis was perfromed by using edgeR
Supplementary_files_format_and_content: tab-delimited text files for each sample as provided by HTSeq

source_name: siRNA knockdown of ELL2

extract_protocol:
Total RNA was isolated with Trizol reagent (15596018, Invitrogen) according to the instruction. cDNA was synthesized with PrimeScript™ RT Master Mix  (RR036A, Takara Bio). Quantitative RT-PCR was conducted to amplify ELL2, STAT1, IRF1 and GAPDH with Real-time qPCR Master Mix (639676, Takara Bio) on ABI Step-One Plus (Applied Biosystems, Foster City, CA).
RNA Seq libraries were prepared using Illumina TruSEQ Stranded mRNA kit

tag: tissue

value: prostate cancer cell line

value: siRNA knockdown


title: Lung_Fibroblasts_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Lung GP38posCD31neg cells

value: Lung

value: 8 to 12 weeks


title: Lung_Endothelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Lung GP38negCD31pos cells


title: Lung_Fibroblasts_SteadyState_ATAC_1


title: PC-3 siELL2-1: siRNA knockdown of ELL2 gene


title: PC-3 siNC2: control

source_name: control

value: control


title: PC-3 siELL2-3: siRNA knockdown of ELL2 gene


title: PC-3 siNC1: control


title: PC-3 siNC3: control


title: Skin_Endothelium_SteadyState_ATAC_1


title: Lymphnode_Fibroblasts_SteadyState_ATAC_1


title: Lung_Epithelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Lung EPCAMpos cells

value: EPCAMpos


title: Lung_Endothelium_SteadyState_ATAC_1


title: Liver_Fibroblasts_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Liver GP38posCD31neg cells

value: Liver


title: Liver_Epithelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Liver EPCAMpos cells


title: LargeIntestine_Fibroblasts_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of LargeIntestine GP38posCD31neg cells

value: LargeIntestine


title: Liver_Fibroblasts_SteadyState_ATAC_2


title: LargeIntestine_Fibroblasts_SteadyState_ATAC_1


title: Liver_Epithelium_SteadyState_ATAC_2


title: Liver_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Liver GP38negCD31pos cells


title: LargeIntestine_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of LargeIntestine EPCAMpos cells


title: LargeIntestine_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of LargeIntestine GP38negCD31pos cells


title: Kidney_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Kidney GP38negCD31pos cells

value: Kidney


title: Kidney_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Kidney EPCAMpos cells


title: Kidney_Fibroblasts_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Kidney GP38posCD31neg cells


title: Heart_Endothelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Heart GP38negCD31pos cells

value: Heart


title: Caecum_Endothelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Caecum GP38negCD31pos cells

value: Caecum


title: Heart_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Heart EPCAMpos cells


title: Liver_Endothelium_SteadyState_ATAC_2


title: Patient A2

city: Irvine

first: Trina

middle: M.

last: Norden-Krichmar

state: CA

address: School of Medicine

institute: University of California, Irvine

data_processing:
fastq files were examined for quality using FastQC then aligned to the human genome hg19 using TopHat2
DE analysis was performed with the Cufflinks software using upper quartile normalization between the data files.
Genome_build: version 19 of human reference genome hg19
Supplementary_files_format_and_content: [gene_exp.diff]  cuffdiff output file. q1=donor, q2=control, q3=patient.

source_name: human dermal fibroblasts

growth_protocol: Cells were grown to confluency in a T-25 flasks

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared at DNA-Link using poly A RNA enrichment

treatment_protocol: Fibroblasts were harvested using TrypLE enzymatic digestion

tag: group

value: Patient

tag: genotype

value: LMNA +/-

value: dermal fibroblasts


title: Kidney_Fibroblasts_SteadyState_ATAC_1


title: Kidney_Epithelium_SteadyState_ATAC_1


title: Caecum_Epithelium_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Caecum EPCAMpos cells


title: Kidney_Endothelium_SteadyState_ATAC_2


title: LargeIntestine_Epithelium_SteadyState_ATAC_1


title: Lung_Epithelium_SteadyState_ATAC_2


title: Heart_Fibroblasts_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Heart GP38posCD31neg cells


title: Heart_Endothelium_SteadyState_ATAC_1


title: LargeIntestine_Endothelium_SteadyState_ATAC_2


title: Brain_Fibroblasts_SteadyState_ATAC_1

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Brain GP38posCD31neg cells

value: Brain


title: Heart_Epithelium_SteadyState_ATAC_1


title: Brain_Fibroblasts_SteadyState_ATAC_2


title: Control A3

value: Control

value: LMNA +/+


title: Brain_Endothelium_SteadyState_ATAC_1

description: open chromatin (ATAC-seq)


title: Brain_Endothelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Brain GP38negCD31pos cells


title: Heart_Fibroblasts_SteadyState_ATAC_2


title: Caecum_Epithelium_SteadyState_ATAC_2


title: Patient A3


title: Brain_Epithelium_SteadyState_ATAC_2

description:
open chromatin (ATAC-seq)
ATAC-seq sample of Brain EPCAMpos cells


title: Donor 4

value: Donor


title: Brain_Epithelium_SteadyState_ATAC_1


title: Control A1


title: Donor 2


title: D14_M3_Ca

city: Bonn

first: Branko

last: Cirovic

address: Carl-Troll Str 31

country: Germany

institute: LIMES

data_processing:
raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to human reference transcriptome hg38 from UCSC and transcript abundance quantified using kallisto (v0.440) with default parameters.
abundance measurements were imported into R using tximport (v1.8.0).
for further filtering transcripts were removed not matching HGNC gene symbols, read sum lower than 10 across all samples or corresponding antisense, LINC or pseudogenes.
filtered data was imported into the DESeq2 package (v1.20.0) in R to generated a normalized expression table.
Genome_build: hg38
Supplementary_files_format_and_content: normalised expression table from DESeq2 containing all samples

source_name: cultured PBMC

extract_protocol:
total RNA from PBMC cultures was isolated using Qiazol (QIAGEN GmbH, Germany) and the miRNeasy Micro Kit (QIAGEN GmbH, Germany).
libraries were constructed following the SMART-seq2 protocol.

value: cultured PBMC

tag: timepoint

value: C.albicans treated

tag: donor


title: Donor 3


title: D14_D0_Ca


title: D09_D0_Ca


title: D12_M3_Ca


title: Control A2


title: D08_M3_Ca


title: Patient A1


title: mouse_9_IR_14d

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads were mapped with STAR v2.7.1a against the GRCm38/mm10 reference genome using the ensembl gene annotations
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Readcounts of genes are present in a matrix format, with rows being genes and columns being individual mice.

growth_protocol: Mouse were kept unde normal housing conditions

extract_protocol:
RNA was collected using TRIzol reagent according to manufacturer's protocol
Illumina sequencing libraries were prepared using Illumina truseq stranded total RNA with ribo-zero

treatment_protocol: All mice underwent either ischemia-reperfusion (IR) or a sham surgery. IR was performed by a 1-hour temporal ligation of the left anterior descending (LAD) artery. Cardiac tissue was collected at several time points post surgery.

value: Cardiac (left ventricle - infarcted region)

value: 8 weeks

tag: Sex

value: Male


title: D08_D0_Ca


title: mouse_8_IR_14d


title: mouse_7_IR_14d


title: mouse_6_IR_24hr


title: D16_M3_Ca


title: D16_D0_Ca


title: mouse_5_IR_24hr


title: D09_M3_Ca


title: mouse_3_Sham

source_name: sham


title: D12_D0_Ca


title: mouse_1_Sham


title: ST486_mZIP-SCR_Ago2-T_replicate

type: RNA

city: Groningen

first: Fubiao

last: Niu

address: Hanzeplein 1

department: Pathology and Medical Biology

institute: University Medical Center of Groningen

hyb_protocol: According to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: ST486 mZIP-SCR Ago2 Total fraction labeled with Cy3

label_protocol: Cy3 and Cy5 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3 CTP Dye Pack, Cyanine 5 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

growth_protocol: BL cell lines were cultured in RPMI-1640 medium at 37℃ in an atmosphere containing 5% CO2.

extract_protocol: Standard Trizol RNA isolation (Life Technologies)

value: Burkitt lymphoma cell line

tag: antibody

value: total fraction

tag: genotype/variation

value: mZIP-SCR


title: ST486_mZIP-SCR_Ago2-T

tag: cell type


title: mouse_4_IR_24hr


title: EGFP+ macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves, rep3

city: PARIS

first: Alexandre

last: Boissonnas

address: 91 Boulevard de l'hopital

department: CIMI

country: France

institute: INSERM

description: EGFP+ CD64+ CD11b+ SiglecF- Ly6G- macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves. rep3.

data_processing:
Quality of raw data has been evaluated with FastQC. Poor quality sequences have been trimmed or removed with Trimmomatic software to retain only good quality paired reads.
Star v2.5.3a has been used to align reads on mm10 reference genome using standard options. Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalization on library size with DESEq2 bioconductor package.
Finally, differential analysis has been conducted with edgeR bioconductor package. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with fpkm values for every gene and every sample

source_name: Res 3, Sciatic Nerve

extract_protocol:
Sorted cells were lysed in 100µl of RA1/TCEP buffer (NucleoSpin RNA XS, Macherey-Nagel), snap frozen in liquid nitrogen and stored at -80C until RNA extraction. Input cell numbers were adjusted to be the same for all samples, around 400 cells. All samples were processed in parallel and RNA extraction (without Carrier RNA but with on-column DNase treatment) was performed according to manufacturer's instructions (NucleoSpin RNA XS, Macherey-Nagel). RNA was eluted in RNAse-free water.
Preparation of cDNA libraries for RNAseq was done using the SmartSeq method according to manufacturer's instructions (SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, Clontech/TaKaRa). Due to the low number of cells, the total amount of eluted RNA was used as starting material for reverse transcription, followed by 18 cycles of pre-amplification. 1ng of cDNA were used for RNAseq sequencing library preparation, according to manufacturer's instructions (Nextera XT DNA Library Preparation, Illumina). Final samples pooled library prep were sequenced on a Nextseq 500 ILLUMINA with MidOutPut cartridge (2x130Millions of 75 bases reads) with 2 runs (4plex and 5plex), corresponding to 2x30Millions of (paired-end) reads per sample after demultiplexing.

treatment_protocol: CCI

value: Sciatic Nerve

value: D14 after CCI

value: Macblue x Cx3cr1egfp/+

value: CCI


title: EGFP+ macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves, rep2

description: EGFP+ CD64+ CD11b+ SiglecF- Ly6G- macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves. rep2.

source_name: Res 2, Sciatic Nerve


title: ST486_mZIP-378a-3p_Ago2-IP_replicate

source_name: ST486 mZIP-378a-3p Ago2 IP fraction labeled with Cy3

value: Ago2 IP


title: ECFP+ macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves, rep1

description: ECFP+ CD64+ CD11b+ SiglecF- Ly6G- macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves. rep1.

source_name: Res 1.1, Sciatic Nerve


title: mouse_2_Sham


title: ST486_mZIP-378a-3p_Ago2-T_replicate

source_name: ST486 mZIP-378a-3p Ago2 Total fraction labeled with Cy3


title: ST486_mZIP-SCR_Ago2-IP_replicate

source_name: ST486 mZIP-SCR Ago2 IP fraction labeled with Cy3


title: noEC 1h challenge rep 2

city: Palo Alto

first: Samuel

last: Yang

address: 1201 Welch Road

department: Emergency Medicine

institute: Stanford University School of Medicine

data_processing:
RNA-seq reads were aligned to hg19 using HISAT2 in a strand specific manner and counts were generates using Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt file with the raw RNA-seq counts

source_name: Healthy untreated neutrophils, 1 hour

extract_protocol:
RNA was extracted from isolated neutrophils after the 1- and 4-hour EC challenges as well untreated controls using the miRNeasy Micro kit
Libraries generated using KAPA PolyA enrichment mRNA library prep

treatment_protocol: Neutrophils from healthy female voulnteers betewen 31-40 were challenged with 6 pathogen mimicking ligands and whole blood from vounteers were challenged with 2 whole organisms.

value: neutrophils

tag: time

value: 1 hour


title: ST486_pCDH-EV_Ago2-IP_replicate

source_name: ST486 pCDH-EV Ago2 IP fraction labeled with Cy5

value: pCDH-EV


title: ECFP+ macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves, rep2

description: ECFP+ CD64+ CD11b+ SiglecF- Ly6G- macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves. rep2.

source_name: Res 2.1, Sciatic Nerve

tag: age


title: ST486_pCDH-EV_Ago2-IP


title: ST486_mZIP-378a-3p_Ago2-T


title: ST486_pCDH-EV_Ago2-T

source_name: ST486 pCDH-EV Ago2 Total fraction labeled with Cy5


title: noEC 1h challenge rep 1


title: ST486_pCDH-378a_Ago2-IP

source_name: ST486 pCDH-378a Ago2 IP fraction labeled with Cy5


title: noEC 4h challenge rep 2

source_name: Healthy untreated neutrophils, 4 hours

value: 4 hours


title: ST486_pCDH-378a_Ago2-T_replicate

source_name: ST486 pCDH-378a Ago2 Total fraction labeled with Cy5


title: ST486_mZIP-SCR_Ago2-IP


title: ST486_mZIP-378a-3p_Ago2-IP


title: noEC 4h challenge rep 1


title: ECFP+ macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves, rep3

description: ECFP+ CD64+ CD11b+ SiglecF- Ly6G- macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves. rep3.

source_name: Res 3.1, Sciatic Nerve

tag: strain


title: EGFP+ macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves, rep1

description: EGFP+ CD64+ CD11b+ SiglecF- Ly6G- macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves. rep1.

source_name: Res 1, Sciatic Nerve


title: EC 4h challenge rep 2

source_name: Escherichia coli challenged neutrophils, 4 hour


title: Non-2

city: Fukuoka

first: Kei

last: Miyamoto

address: 744 Moto-oka, Nishi-ku

department: Faculty of Agriculture

country: Japan

institute: Kyushu University

description:
Non_Non2_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis

data_processing:
Fastq files from Illumina sequencing were filtered for low quality reads by sliding window trimming (window size 10, <QV20), and low quality bases were trimmed from the ends of the reads (<QV20) using Trimmomatic. Reads less than 20 bases and unpaired reads were removed. Furthermore, adaptor, polyA, polyT and polyG sequences were removed using trim_galore and cutadapt.
The sequencing reads were then mapped to the mouse genome (mm10) using STAR. Reads on annotated genes were counted using featureCounts. FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: 2-cell stage embryos_non-injected

growth_protocol: After in vitro fertilization, embryos were cultured in potassium simplex optimized medium (KSOM) at 37°C under 5% CO2 until 2-cell stage (32 hours post insemination: 32 hpi).

extract_protocol:
After the removal of zona pellucida, embryos were washed with PBS containing 0.1% BSA, and then transferred to a 0.2 ml tube containing 9.5 μl of reaction buffer to make a final volume of 10.5 μl. After cell lysis in the buffer, 1 μl of the solution was removed and, instead, 1 μl of the diluted ERCC RNA Spike-In Mix was added (1:40,000 dilution; Thermo Fisher Scientific, 4456740). The lysed RNA solution with the spike-in RNA were subjected to reverse transcription.
The produced cDNA was amplified by PCR with 13 cycles. The amplified cDNA was purified using AMPure XP beads (BECKMAN COULTER, A63882). The purified cDNA was measured on the Bioanalyzer (Agilent) using High Sensitivity DNA Kit (5067-4626) and the normalized volume of DNA was subjected to library preparation using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) by following the vendor’s instruction. The obtained library was quality-checked by Bioanalyzer and quantified using Qubit (Thermo Scientific).
Paired end sequencing (50 bp + 25 bp) was carried out using the Illumina NextSeq system.

treatment_protocol: After insemination, fertilized embryos were collected at 2 hpi for mRNA injection. mRNAs were injected using a piezo manipulator (Prime Tech, Tsukuba, Japan).

value: ICR

tag: mrna injected

value: Non-injected

tag: developmental stage

value: 2-cell stage

value: embryos


title: EC 4h challenge rep 1


title: Non-3

description:
Non_Non3_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis


title: ST486_pCDH-378a_Ago2-T

tag: cell line


title: ST486_pCDH-EV_Ago2-T_replicate


title: G15S-3

description:
G15S_G15S3_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis

source_name: 2-cell stage embryos_G15S


title: ST486_pCDH-378a_Ago2-IP_replicate


title: EC 1h challenge rep 1

source_name: Escherichia coli challenged neutrophils, 1 hour


title: Non-1

description:
Non_Non1_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis


title: 3 weeks MM rep 2a

first: Mark

last: Mercola

address: 1651 Page Mill Road

department: Department of Medicine

data_processing:
FastQC (v0.11.5) and MultiQC (v1.3) were used to assess read quality.
Adapter and quality trimming of reads were performed with trimmomatic (v0.36).
Reads were mapped to genome GRCh37 (hg19) using STAR (v2.5.3a) with UCSC gene annotations.
Uniquely mapped reads were quantified with featureCounts (v1.28.1) from the Rsubread module.
The DESeq2 Bioconductor package (v1.17.39) was used to identify genes that were differentially expressed between groups. Pairwise comparison between groups were conducted by applying the Wald test of the negative binomial distribution to the log2 gene counts and then Benjamini–Hochberg correction was applied.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: counts.csv

source_name: iPSC-derived cells

growth_protocol: hiPSC-derived cardiomyocytes were cultured in either RMPI or MM based media for 3 weeks (RMPI or MM, ie W3RC or W3MC), or harvest immediately after differentiation (baseline, ie D0).

extract_protocol:
miRVana isolation kit (Ambion)
Conducted by Novogene

tag: treatment

value: 3 weeks MM


title: EC 1h challenge rep 2


title: 3 weeks MM rep 3


title: 3 weeks RMPI rep 3

value: 3 weeks RMPI


title: 3 weeks MM rep 2b


title: 3 weeks RMPI rep 1


title: 3 weeks MM rep 1


title: Exp6+R62D-3

description:
Exp-plus-R62D_ER3_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis

source_name: 2-cell stage embryos_Exp6+R62D

value: mCherry-Exp6 and actinR62D-HA-NLS


title: Baseline cardiomyocyte rep 3

value: baseline


title: G15S-2

description:
G15S_G15S2_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis


title: Control 28d rep 4

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
small RNA
normalized_count_data_filtered.txt
225_S11_L001_R1_001

data_processing:
The generated reads were checked for quality and trimmed of adapter sequence (minimum read length =15, adapter trim stringency = 0.9) using the Illumina BaseSpace Application. The processed FastQ files were analyzed using the Partek Flow (version 6.0) software program (Partek, St. Louis, MO). Samples with less than a million reads were filtered out at this step (Samples 57, 80, 81, 118 & 121)
Remaining sequences of 18 bp or greater were retained and trimmed from both 5’ and 3’ ends if the Phred quality score was less than 20.
Samples were aligned with Bowtie version 1.0.0 to the mm10 reference index using up to a 1 base pair mismatch and seed length of 10.
Aligned sequences were then annotated to miRBase mature miRNA v21 with the Partek E/M (expectation maximum) algorithm. Samples that exhibited less than 10% annotated miRNA counts were filtered out at this step (Samples 51, 56, 119, 123, 152 & 177). Features (miRNAs) were excluded if the geometric mean across all samples was less than or equal to 10.
MiRNA counts were normalized with TMM (trimmed mean of M-values) and 0.0001 count was added to all features.
Negative binomial regression was used to model the normalized count data when determining differentially expressed miRNAs (DEmiRs). Significance testing was corrected for multiple tests and was determined by a Storey q-value of p ≤0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file contains TMM normalized count values for all samples and mapped featues.

source_name: liver

extract_protocol:
Total RNA was isolated from approximately 20 mg of frozen liver tissue homogenized in RNAzol RT (Molecular Research Center, Cincinnati, Ohio) followed by purification with the RNeasy MinElute column protocol modified to retain the small RNA (Qiagen GmbH, Hilden, Germany). Initial yield was quantified by the NanoDrop spectrophotometer (NanoDrop Technologies, Wilmington, Delaware.) RNA quality was assessed by the Agilent RNA6000 kit assay on the Agilent 2100 Bioanalyzer (Agilent Technologies, Berlin, Germany). The RNA was DNase-treated using a Turbo DNase treatment (ThermoFisher Scientific, Waltham, Massachusetts) followed by Qiagen MinElute cleanup. Total RNA was quantitated using the Qubit Broad Range RNA assay (ThermoFisher Scientific).
The CleanTag Small RNA Library Prep Kit (TriLink Biotechnologies, San Diego, CA) and protocol was used to prepare the sequencing library. For the liver samples, 500ng of total RNA was used as input. All reaction parameters were set as described in the protocol, including use of Illumina small RNA index primers in the library amplification. After amplification, the library was bead-purified according to manufacturer’s instructions. Purified library quality was assessed using the High Sensitivity DNA kit on the Agilent 2100 Bioanalyzer, and concentration was determined by the Qubit dsDNA High Sensitivity Assay (ThermoFisher Scientific).

treatment_protocol: The experimental design and treatment protocols have been described previously (Lake et al., 2016). Briefly, weanling male B6C3F1 mice were obtained at approximately 21 days from Charles River Laboratories (Raleigh, NC) and cared for under protocols approved by the Institutional Animal Care and Use Committee of the U.S. Environmental Protection Agency (EPA). Body weight and food and water consumption were monitored throughout this period to ensure similar treatment group starting conditions. When the mice reached a minimum of 65 days of age, they were dosed for 7 days with either control diet or diet containing DEHP (750, 1500, 3000, and 6000ppm), DNOP (1250, 2500, 5000, and 10000ppm), or BBP (1500, 3000, 6000, and 12000 ppm). Mice were monitored throughout dosing for food and water uptake. On the day of sacrifice, body and liver weights were recorded, and liver tissue was immediately flash frozen in liquid nitrogen and stored at -80°C until further processing. Serum samples were processed from blood obtained via cardiac puncture and stored at -80°C.

tag: exposure

value: control feed

tag: dose

value: 0 ppm

tag: exposure length

tag: gender

value: male


title: 3 weeks RMPI rep 2


title: 6K DEHP 28d rep 4

description:
small RNA
normalized_count_data_filtered.txt
210_S8_L001_R1_001

value: di(2-ethylhexyl) phthalate


title: 6K DEHP 28d rep 3

description:
small RNA
normalized_count_data_filtered.txt
209_S16_L001_R1_001


title: G15S-1

description:
G15S_G15S1_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis

tag: tissue


title: 7375: Healthy.15

city: San Francisco

first: Hsin-Wen

last: Chang

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

data_processing:
Sequencing reads were mapped to human genome (GRCh38, GENCODE release 25) by using STAR (v. 2.4.2a).
BAM files resulting from the alignments were summarized to genes using HTSeq-count (v. 0.6.0)
Expression data was normalized by DEseq2 package
Genome_build: GRCh38, GENCODE release 25
Supplementary_files_format_and_content: tab-delimited text files generated by HTSeq-count, which includes gene counts for each gene(rows) and each sample (columns).

source_name: sigmoidal biopsies

growth_protocol: two snip biopsies from the sigmoidal colon and preserved in RNAlater solution at -80C prior to RNA extraction

extract_protocol:
RNA was isolated using the RNeasy Plus Universal Kits (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA Library Prep kit (Illumina) with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: disease state

value: healthy

tag: pasi

value: M

value: sigmoidal colon


title: 7376: Healthy.16

value: F


title: 7371: Healthy.12


title: 7368: Healthy.10


title: Exp6+R62D-1

description:
Exp-plus-R62D_ER1_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis


title: Exp6+R62D-2

description:
Exp-plus-R62D_ER2_R1_val_1-pw1_10-cN10-pq20w10m20
processed data file: gene-FPKM_name-2.xlsx
A pool of 5 embryos at the 2-cell stage were subjected to cDNA synthesis


title: Control 28d rep 3

description:
small RNA
normalized_count_data_filtered.txt
224_S14_L001_R1_001


title: 7374: Healthy.14


title: Control 28d rep 2

description:
small RNA
normalized_count_data_filtered.txt
223_S18_L001_R1_001


title: 7369: Healthy.11


title: Baseline cardiomyocyte rep 2


title: 7365: Healthy.9


title: Baseline cardiomyocyte rep 1


title: 6K DEHP 28d rep 1

description:
small RNA
normalized_count_data_filtered.txt
207_S4_L001_R1_001


title: 7360: Healthy.7


title: 7364: Healthy.8


title: 0.75K 7d DEHP rep 8

description:
small RNA
normalized_count_data_filtered.txt
155_S19_L001_R1_001

value: 750 ppm

value: 7 d


title: Control 7d rep 8

description:
small RNA
sample dropped
177_S1_L001_R1_001


title: Control 28d rep 1

description:
small RNA
normalized_count_data_filtered.txt
222_S7_L001_R1_001


title: 7372: Healthy.13


title: Control 7d rep 7

description:
small RNA
normalized_count_data_filtered.txt
176_S12_L001_R1_001


title: 7358: Healthy.6


title: 6K DEHP 7d rep 8

description:
small RNA
sample dropped
152_S13_L001_R1_001


title: 0.75K 7d DEHP rep 7

description:
small RNA
normalized_count_data_filtered.txt
154_S17_L001_R1_001


title: 7355: Healthy.5


title: 7351: Healthy.3


title: 7350: Healthy.2


title: 7353: Healthy.4


title: 3K DEHP 7d rep 8

description:
small RNA
normalized_count_data_filtered.txt
150_S24_L001_R1_001


title: 1.5K DEHP 7d rep 8

description:
small RNA
normalized_count_data_filtered.txt
148_S22_L001_R1_001


title: 7331: PSO.25

value: psoriasis


title: Control 7d rep 6

description:
small RNA
normalized_count_data_filtered.txt
145_S21_L001_R1_001


title: 1.5K DEHP 7 d rep 7

description:
small RNA
normalized_count_data_filtered.txt
146_S9_L001_R1_001


title: 6K DEHP 28d rep 2

description:
small RNA
normalized_count_data_filtered.txt
208_S1_L001_R1_001


title: 7327: PSO.22


title: Control 7d rep 5

description:
small RNA
normalized_count_data_filtered.txt
144_S19_L001_R1_001


title: 0.75K 7d DEHP rep 6

description:
small RNA
sample dropped
123_S5_L001_R1_001


title: 6K DEHP 7d rep 6

description:
small RNA
normalized_count_data_filtered.txt
120_S20_L001_R1_001


title: 7328: PSO.23


title: 0.75K 7d DEHP rep 5

description:
small RNA
sample dropped
121_S16_L001_R1_001


title: 7325: PSO.21


title: 7330: PSO.24


title: 7324: PSO.20


title: 6K DEHP 7d rep 7

description:
small RNA
normalized_count_data_filtered.txt
151_S9_L001_R1_001


title: 6K DEHP 7d rep 5

description:
small RNA
sample dropped
119_S17_L001_R1_001


title: 7323: PSO.19


title: 7332: PSO.26


title: 7314: PSO.14


title: 7315: PSO.15


title: 1.5K DEHP 7 d rep 5

description:
small RNA
normalized_count_data_filtered.txt
114_S10_L001_R1_001


title: 7322: PSO.18


title: 3K DEHP 7d rep 6

description:
small RNA
sample dropped
118_S23_L001_R1_001


title: 7320: PSO.17


title: 3K DEHP 7d rep 7

description:
small RNA
normalized_count_data_filtered.txt
149_S2_L001_R1_001


title: 7312: PSO.12


title: 7317: PSO.16


title: 7311: PSO.11


title: 7310: PSO.10


title: 0.75K 7d DEHP rep 4

description:
small RNA
normalized_count_data_filtered.txt
90_S11_L001_R1_001


title: 3K DEHP 7d rep 5

description:
small RNA
normalized_count_data_filtered.txt
116_S23_L001_R1_001


title: 7309: PSO.9


title: 3K DEHP 7d rep 4

description:
small RNA
normalized_count_data_filtered.txt
86_S2_L001_R1_001


title: 3K DEHP 7d rep 3

description:
small RNA
normalized_count_data_filtered.txt
85_S5_L001_R1_001


title: 7306: PSO.6


title: 1.5K DEHP 7d rep 6

description:
small RNA
normalized_count_data_filtered.txt
115_S18_L001_R1_001


title: Control 7d rep 4

description:
small RNA
normalized_count_data_filtered.txt
113_S12_L001_R1_001


title: 7313: PSO.13


title: 0.75K 7d DEHP rep 3

description:
small RNA
normalized_count_data_filtered.txt
89_S4_L001_R1_001


title: Control 7d rep 3

description:
small RNA
normalized_count_data_filtered.txt
112_S22_L001_R1_001


title: 6K DEHP 7d rep 4

description:
small RNA
normalized_count_data_filtered.txt
88_S14_L001_R1_001


title: 6K DEHP 7d rep 3

description:
small RNA
normalized_count_data_filtered.txt
87_S6_L001_R1_001


title: 7307: PSO.7


title: 7304: PSO.4


title: 1.5K DEHP 7 d rep 3

description:
small RNA
normalized_count_data_filtered.txt
82_S24_L001_R1_001


title: 1.5K DEHP 7d rep 4

description:
small RNA
normalized_count_data_filtered.txt
84_S3_L001_R1_001


title: Control 7d rep 2

description:
small RNA
sample dropped
81_S15_L001_R1_001


title: 7303: PSO.3


title: 7308: PSO.8


title: 7301: PSO.2


title: Control 7d rep 1

description:
small RNA
sample dropped
80_S13_L001_R1_001


title: 0.75K 7d DEHP rep 2

description:
small RNA
normalized_count_data_filtered.txt
58_S20_L001_R1_001


title: 0.75K 7d DEHP rep 1

description:
small RNA
sample dropped
57_S7_L001_R1_001


title: NC-5

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

country: China

institute: The Affiliated People’s Hospital of Jiangsu University

data_processing:
After Illumina sequencing, image analysis, and base recognition, the original reads after quality control were harvested. First use Q30 for quality control. Use cutadapt software (v1.9.3) to de-join the original reads, remove low-quality reads, and keep the reads with length> = 15 nt to get the de-connected reads (ie trimmed reads).
Then, the trimmed reads of all samples were combined, and new miRNA prediction was performed using miRDeep2 software (v2.0.0.5). Use Novoalign software (v3.02.12) to compare the trimmed reads of each sample to the combined human pre-miRNAs database (miRBase pre-miRNAs (v21) + newly predicted pre-miRNAs), allowing up to 1 mismatch.
Statistically compare the number of tags on each mature miRNA as the original expression level of the miRNA, and use TPM (tag counts per million aligned miRNAs) method for standardization. Calculate the Fold change between the two samples and screen for differentially expressed miRNAs. Calculate the P-value and Fold Change between the two groups of samples (with duplicates), and screen for differentially expressed miRNAs.
Genome_build: human NBCI genobuild 36
Supplementary_files_format_and_content: Number of alignment tags per mature miRNA

source_name: peripheral blood mononuclear cells

extract_protocol:
Human PBMCs were isolated by density-gradient
centrifugation over Ficoll-Hypaque solution (Tianjin Haoyang Biological Technology Co., Tianjin, China) according to the manufacturer’s instructions and stored at -80 °C   until use for miRNA sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adult female

value: Blood

tag: condition

value: normal control


title: 7300: PSO.1


title: NC-4


title: 6K DEHP 7d rep 1

description:
small RNA
normalized_count_data_filtered.txt
54_S10_L001_R1_001


title: 6K DEHP 7d rep 2

description:
small RNA
sample dropped
56_S21_L001_R1_001


title: NC-3


title: NC-2


title: 1.5K DEHP 7d rep 2

description:
small RNA
normalized_count_data_filtered.txt
50_S8_L001_R1_001


title: 3K DEHP 7d rep 2

description:
small RNA
normalized_count_data_filtered.txt
53_S15_L001_R1_001


title: 1.5K DEHP 7 d rep 1

description:
small RNA
normalized_count_data_filtered.txt
49_S6_L001_R1_001


title: 7305: PSO.5


title: NC-1


title: 3K DEHP 7d rep 1

description:
small RNA
sample dropped
51_S3_L001_R1_001


title: HT-3

value: Hashimoto's Thyroiditis


title: HT-4


title: 6532: Healthy.1


title: HT-2


title: HT-5


title: BDL day 14 [KW101218-12_S12]

city: Los Angeles

first: Celia

middle: Anne

last: Short

address: 4650 Sunset Blvd

department: Pediatric Surgery

institute: Children's Hospital Los Angeles

data_processing:
Sequencing was performed on an Illumina Nextseq Mid-Output flowcell (Illumina, San Diego, CA) at the CHLA sequencing core.
Sequencing analysis was performed with Partek Flow Genomic Analysis software (St. Louis, MO).
Raw reads were trimmed for a minimum quality read of 20, with a minimum length of 25bp.
Reads were aligned and quantified using the Star aligner 2.6.1d (Mm10 GENCODE, release M18).
Normalization was performed with the upper quartile method, with at least ten reads.
Enriched gene cutoff included those genes with a fold change >1.5 and p-value <0.05
Genome_build: Mm10 GENCODE, release M21

source_name: adult hepatic Prom1+ expressing hepatic progenitor cells and their progeny_BDL day 14

growth_protocol: No growth protocol, cells were collected via FACS and then RNA extraction occurred immediately after

extract_protocol:
Livers were harvested, then minced and digested with PBS containing 0.1% collagenase (Sigma), 0.1% pronase (Sigma), and 0.01% DNase (Sigma) for 45min at 37oC. After addition of FBS (10% final concentration), the dissociated cells were strained through a 70 um pore filter and red blood cells were removed with RBC lysis buffer. The resultant cells then underwent serial centrifugation to enrich the nonparenchymal fraction. Cells were incubated with propidium iodide and were analyzed by FACS Aria I (BD) at the CHLA FACS Core. After exclusion of dead cells stained with propidium iodide, expression of GFP were analyzed. Negative gating was set with simultaneously digested wild type livers. For RNA-seq analysis, we sorted 1x10e5 GFP(+) cells directly into Trizol solution. Total RNA were purified using Trizol solution. RNA were further purified with silica bead Microprep columns (Qiagen, Germantown, MD). RNA quality was analyzed with an RNA Bioanalyzer (Agilent, Santa Clara, CA).
Libraries were prepared with a Truseq mRNA library prep and sequencing was performed on an Illumina Nextseq Mid-Output flowcell (Illumina, San Diego, CA) at the CHLA sequencing core.

treatment_protocol: Tamoxifen was injected into all samples 7 days prior to Sham (day 0 collect) vs BDL, then day 3 or day 14 collection of liver samples

tag: strain background

tag: time point

value: Bile duct ligation (BDL) day  14

value: liver

value: FACs sorted GFP+ cells (Prom1+ HPC and progeny =/- Prom1)

tag: genotype/variation


title: Sham day 0 [KW101218-10_S10]

source_name: adult hepatic Prom1+ expressing hepatic progenitor cells and their progeny_Sham day 0

value: Sham day 0

tag: cell type


title: BDL day 3 [KW101218-5_S5]

source_name: adult hepatic Prom1+ expressing hepatic progenitor cells and their progeny_BDL day 3

value: Bile duct ligation (BDL) day  3


title: HT-1

tag: strain


title: BDL day 14 [KW101218-11_S11]


title: BDL day 14 [KW101218-7_S7]

value: Bile duct ligation (BDL) day 14


title: Sham day 0 [KW101218-8_S8]


title: BDL day 14 [KW101218-9_S9]


title: Pt292_3

city: Barcelona

first: Violeta

last: Serra

address: CELLEX C/ Natzaret, 115-117

country: Spain

institute: Vall d Hebron Institute of Oncology

data_processing:
bcbio-nextgen 1.1.6 rnaseq pipeline
Alignment with HiSat2 2.1.0
Quantification of transcript and gene abundance with Salmon 0.14.1
Quality Control with FastQC 0.11.8, Qualimap 2.2.2c, MultiQC 1.7
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file with read abundance per gene

source_name: tumor biopsy

extract_protocol:
Illumina RNAAccess, 25 M 50 bp PE SQ1409 protocol was followed. Total RNA samples were fragmented and converted into indexed cDNA libraries. Resulting cDNA libraries were positively selected for coding RNA using hybrid capture with probes specific for the coding region of the genome.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast

tag: agent

value: Capivasertib


title: Pt320_3


title: Pt292_1


title: BDL day 14 [KW101218-2_S2]


title: BDL day 14 [KW101218-1_S1]


title: BDL day 3 [KW101218-6_S6]


title: Pt320_2


title: Pt320_1


title: BDL day 3 [KW101218-4_S4]

value: Bile duct ligation (BDL) day 3


title: Pt292_2


title: 15-492-002_G3-3 reanalysis

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
15-492-002_G3-3
A3-52-5
reanalysis of GSM3728646

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with TrimGalore.
Trimmed FASTQ files were aligned to hg19 using STAR.
Genomic features were quantified using FeatureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Ensembl gene ID, Log2 counts-per-million (CPM), gene symbol, description

source_name: prostate

extract_protocol:
Total RNA was extracted from cells adhered to caps using the Qiagen RNeasy FFPE kit.
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit.

treatment_protocol: FFPE human prostate tissues were sectioned onto metal frame membrane slides, and regions of interest were excised onto caps using laser capture microdissection.

value: male

tag: patientcode

tag: regionofinterest


title: 15-492-002_G4-1 reanalysis

description:
15-492-002_G4-1
A3-52-6
reanalysis of GSM3728647


title: Sham day 0 [KW101218-3_S3]


title: 15-492-002_IDC-2 reanalysis

description:
15-492-002_IDC-2
A3-52-4
reanalysis of GSM3728644


title: Pt279_3


title: 15-492-002_IDC-1 reanalysis

description:
15-492-002_IDC-1
A3-52-2
reanalysis of GSM3728642


title: 15-492-002_HGPIN-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-7
processed data file: HumanProstateTissue.txt

data_processing:
Base-calling was performed with CASAVA 1.9.
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HumanProstateTissue.txt: Tab-separated values, gene symbol, description, transcripts-per-million (TPM).

value: prostate


title: 15-492-002_G4-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-8
processed data file: HumanProstateTissue.txt


title: Pt279_2


title: Pt279_1


title: 15-492-002_B9-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-9
processed data file: HumanProstateTissue.txt


title: 15-492-002_G3-2 reanalysis

description:
15-492-002_G3-2
A3-52-3
reanalysis of GSM3728643


title: 15-492-002_G3-1 reanalysis

description:
15-492-002_G3-1
A3-52-1
reanalysis of GSM3728641


title: 15-492-002_G3-3

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-5
processed data file: HumanProstateTissue.txt


title: lung, 8wk3

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
align with STAR 2.6.0b-1  using galaxy
raw count generated by featrueCounts  1.6.0.3  using galaxy
counts normalization and differential expression using DESeq2  2.11.40.2 using galaxy
Genome_build: mm10
Supplementary_files_format_and_content: normalized count file generated by DESeq2

source_name: mouse lung

extract_protocol: qiagen mirneasy mini kit

value: lung

tag: treatment

value: tamoxifen

tag: time


title: lung, 6wk2


title: lung, 6wk1


title: lung, 4wk4


title: 15-492-002_G3-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-1
processed data file: HumanProstateTissue.txt


title: lung, 4wk2


title: scRNA_seq_E13.5

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with E13 in the column of processed data file

data_processing:
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=5000 \’.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

source_name: E13.5 XX gonads

extract_protocol:
Gonads were isolated and washed with PBS solution supplemented with 0.04% bovine serum albumin. Then, the gonads were digested with 1X TrypLE™ Express (Cat# 12605010) for 3 min to obtain single cell pellets. The single-cell Gel-Bead in Emulsions (GEMs) were then generated with Chromium 10x Genomics single-cell system by using single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics, Cat#120237). Captured cells were then lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

value: gonads

tag: developmental stage


title: scRNA_seq_E11.5

description: The group information is prefixed with E11 in the column of processed data file

source_name: E11.5 XX gonads


title: 15-492-002_G4-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-6
processed data file: HumanProstateTissue.txt


title: RNA-Seq_HiraKO_2

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
The mouse reference genome (GRCm38) and corresponding gene annotation were obtained from Illumina iGenome.
Reads for ATAC-Seq were first processed using Trim Galore 0.4.5, then aligned to mouse reference genome using bowtie 2-2.2.9.
Peak calling for ATAC-Seq was performed by using MACS 2.1.1 with default settings. To identify differential ATAC-Seq peaks between two conditions, we first called peaks by using MACS 2.1.1 after merging all related data, then counted the number of reads located within +/- 125 bp of peak summit with the multicov function of BEDTools. Finally, differential peak calling were performed by using DESeq2 (Love et al., 2014) with threshold: foldChange>2 and FDR<0.05.
Reads for RNA-Seq were aligned to the reference genome using STAR 2.5.3a with parameters: --outSAMstrandField intronMotif --outFilterType BySJout outFilterIntronMotifs RemoveNoncanonical.
To identify differentially expressed genes, we first obtained the read counts for each gene with htseq-count (Anders et al., 2015), then identified differential genes as foldChange>2 and FDR<0.05 using DESeq2  (Love et al., 2014). To visualize the expression profile of representative genes, we first quantified gene expression using RSEM 1.3.0 with parameters: --bowtie2 --calc-ci --ci-memory 1024. The calculated TPM (transcript per million) values were normalized using trimmed mean of M-values normalization (TMM) method. The normalized TPM values were used for visualization.
Genome_build: GRCm38
Supplementary_files_format_and_content: narrowPeak files for the peak calling results generated by using MACS2 for ATAC-Seq data .
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each gene as generated by using RSEM for RNA-Seq data.

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
Total RNA was isolated from sorted LSK cells by trizol reagent. The RNA sequencing library was prepared from approximately 50 ng RNA using the Ovation RNA-seq System V2 (NuGEN) and Nextera XT DNA Library Preparation Kit (Illumina), and sequencing was done using an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using NuGEN and Illumina protocols

value: Bone marrow

value: Hematopoietic stem and progenitor cells

tag: genotype

value: Hira conditional KO


title: lung, 8wk2


title: lung, 6wk3


title: lung, 2wk2


title: lung, 8wk1


title: RNA-Seq_WT_2

value: WT


title: RNA-Seq_WT_1


title: 15-492-002_IDC-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-4
processed data file: HumanProstateTissue.txt

tag: gender


title: 15-492-002_G3-2

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-3
processed data file: HumanProstateTissue.txt

tag: tissue


title: 15-492-002_IDC-1

description:
Total RNA was extracted from laser capture microdissected tissue, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility using the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
A3-52-2
processed data file: HumanProstateTissue.txt


title: lung, 4wk3


title: scRNA_seq_E14.5

description: The group information is prefixed with E14 in the column of processed data file

source_name: E14.5 XX gonads


title: lung, 4wk1


title: lung, 2wk3


title: scRNA_seq_E12.5

description: The group information is prefixed with E12 in the column of processed data file

source_name: E12.5 XX gonads


title: RNA-Seq_HiraKO_1


title: AT2 cells, control3

data_processing:
align with STAR 2.6.0b-1 using galaxy
raw count generated by featrueCounts 1.6.0.3 using galaxy
counts normalization and differential expression using DESeq2 2.11.40.2 using galaxy
Genome_build: mm10
Supplementary_files_format_and_content: normalized count file generated by DESeq2

extract_protocol: qiagen mirneasy micro kit

value: control


title: sdGAL4_Dam7

city: Canberra

first: Olga

last: Zaytseva

state: ACT

address: 131 Garran Road

country: Australia

institute: John Curtin School of Medical Research

description: Dam only control

data_processing:
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline v1.4.5, including aligning the reads to the Drosophila BDGP6 genome with Bowtie2, converting to GATC resolution and calculating the log2 ratio between Dam-fusion protein profile and Dam alone
Average enrichment across biological replicates was determined by calculating average coverage at each region flanked by GATC sites, and the average profile was used for further analysis.
Significant peaks were detected at 1% FDR using the find_peaks script
Genome_build: BDGP6
Supplementary_files_format_and_content: Bedgraph file indicating average enrichment at each GATC-flanked genomic fragment. Score represents the normalised log2(Dam-fusion/Dam) enrichment.
Supplementary_files_format_and_content: GFF file containing peak coordinates identified the corresponding bedgraph profile at FDR0.01, the average enrichment across the peak region and the FDR value

organism: Drosophila melanogaster

source_name: imaginal wing disc

growth_protocol: Drosophila melanogaster embryos from parental crosses were collected over the course of <4-hour lays at 25ºC, after which the embryos were placed at the repressive temperature of 18ºC for 7 days until the second larval instar stage. The larvae were then shifted to the permissive temperature of 29ºC for 24h

extract_protocol:
Wing discs from female larvae were collected into cold PBS, genomic DNA was extracted using a Zymo Quick-DNA kit (#D4069). DNA was digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 300bp using Covaris ME200 sonicator and DamID adaptors removed via AlwI digestion.  Sonicated material was end-repaired, adenylated, sequencing adaptors were ligated and samples were PCR amplified.

treatment_protocol: Dam-fusion contructs expressed using scalloped-GAL4 driver in the background of temperature-sensitive GAL80

tag: gal4 driver

value: sdGAL4 ; tsGAL80

tag: stock number

value: mid-third instar larvae

value: wing imaginal disc

tag: Sex

value: female


title: AT2 cells, control2


title: lung, 2wk1


title: lung, control3


title: lung, control2


title: lung, control1


title: AT2 cells, Sin3a-LOF_2wk3


title: AT2 cells, control1


title: sdGAL4_Dam3

description: Dam only control


title: AT2 cells, Sin3a-LOF_2wk2


title: AT2 cells, Sin3a-LOF_2wk1


title: sdGAL4_Dam6

description: Dam only control


title: Fibroblast culture derived from primary tonsil  FST93_

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label: biotin

source_name: derived from primary tonsil

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Fib: IMDM, 20% FCS; bFGF 10ng/ml, 4-6 passages; L-428: RPMI; 10% FCS

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen. 40ng of the total RNA was amplified using the Ovation Pico WTA System V2 from NUGEN.

treatment_protocol: Luteolin working concentration: 30 µM

tag: sample type


title: in vitro culture of KB33 treated with Luteolin Luteolin3_


title: in vitro coculture (KB33 and L-428 cell line) CAF+HRS3_


title: Fibroblast culture derived from foreskin FibP15_

source_name: derived from foreskin


title: in vitro coculture (KB33 and L-428 cell line) CAF+HRS1_


title: Fibroblast culture derived from primary tonsil  FST94_


title: sdGAL4_Dam5

description: Dam only control


title: in vitro culture of KB33 treated with Luteolin Luteolin1_


title: Fibroblast culture derived from foreskin FibP40_


title: Fibroblast culture derived from primary tonsil  FST98_


title: sdGAL4_Dam4

description: Dam only control


title: sdGAL4_Dam1

description: Dam only control


title: sdGAL4_Dam2

description: Dam only control


title: Pol DamID 2

description: Myc RNAi

tag: dam only sample used as control


title: Pol DamID 1

description: Myc RNAi


title: in vitro mock coculture (KB33 and L-428 cell line) mock1_


title: Fibroblast culture derived from primary lymph node FST89_

source_name: derived from primary lymph node


title: in vitro culture of KB33 treated with Luteolin Luteolin2_


title: in vitro mock coculture (KB33 and L-428 cell line) mock2_


title: in vitro coculture (KB33 and L-428 cell line) CAF+HRS2_


title: in vitro mock coculture (KB33 and L-428 cell line) mock3_


title: Fibroblast culture derived from primary lymph node KB39_


title: Fibroblast culture derived from primary lymph node KB30_


title: Fibroblast culture derived from primary lymph node KB29_


title: Fibroblast culture derived from primary lymph node KB33_


title: Fibroblast culture derived from primary lymph node KB40_


title: Fibroblast culture derived from primary lymph node KB12_


title: Pol DamID 3

description: Myc RNAi


title: Fibroblast culture derived from primary lymph node KB22_


title: Fibroblast culture derived from primary lymph node FST124_


title: Fibroblast culture derived from primary lymph node KB37_


title: Myc DamID 2

description: Psi RNAi


title: Myc DamID 3

description: Psi RNAi


title: Myc DamID 1

description: Psi RNAi


title: Psi DamID 3

description: control


title: Fibroblast culture derived from primary lymph node KB16_


title: Fibroblast culture derived from primary lymph node KB32_


title: Fibroblast culture derived from primary lymph node KB20_


title: FGFR1_Fulv.Palbo.FGF2..S123

city: Cambridge

first: Ofir

last: Cohen

address: 415 Main St, Cambridge, MA 02142

institute: Broad Institute

description:
FGFR.Rescue.seq.tpm.normalized.QC.csv
FGFR.Rescue.seq.counts.QC.csv

data_processing:
mRNA-seq libraries were sequenced on an Illumina NextSeq 500 sequencer, V2 75 cycle kits
Reads were mapped with STAR aligner (Dobin et al. 2013)
Genome_build: hg19 of the human genome and build 12 of the GENCODE human genome annotation

source_name: Breast Cancer

extract_protocol:
Plates with cell lysates were thawed and purified with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics). The RNA captured beads were air-dried and processed immediately for RNA secondary structure denaturation (72˚C for three minutes) and cDNA synthesis. We performed SMART-Seq2 following the published protocol
Smart-seq 2

tag: cell line

tag: lentivirus

tag: replicate


title: Fibroblast culture derived from primary lymph node KB5_


title: Psi DamID 2

description: control


title: antiTNF_NONResponder_2 (DAS28 criteria)

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

institute: Vall d'Hebron Hospital Research Institute

description:
antiTNF_NONResponder_2
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE7

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were log2 transformed and quantile normalized using R Bioconductor. Only microarray probes matching curated gene sequences from NCBI RefSeq database (release 51) were selected. A final number of 21,189 curated probes representing the expression of 18,524 different human genes were finally selected for analysis.

extract_protocol: RNA was extracted using Quiagen Mini Kit Protocol in accordance with the described protocol. Dnase I treatment was used to remove genomic DNA traces.

tag: disease

value: Rheumatoid Arthritis fulfilling ACR/EULAR 2010 diagnostic criteria

tag: age

tag: anti-tnf response wk20

value: European League Against Rheumatoid Arthritis (EULAR) none responder


title: Fibroblast culture derived from primary lymph node KB14_


title: Fraction_20

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:
Adaptor clipping:cutadapt
Read mapping:READemption  align and segemehl
coverage calculationREADemption coverage
Genome_build: NC_000913.3
Supplementary_files_format_and_content: wiggle

organism: Escherichia coli

source_name: Clarified whole cell lysate

growth_protocol: Escherichia coli MG1655 was streaked on LB plates and grown overnight at 37°C. Overnight cultures of single colonies were grown in 2 ml LB at 37°C with shaking at 220 rpm. The next day, 1:100 dilutions in fresh LB of the overnight cultures were used to start the cultures for the experiments and grown to an OD600 nm of 2.0 (early stationary phase) at 37°C with shaking at 220 rpm.

extract_protocol:
Clarified lysates were centrifuged on a glycerol gradient, which was subsequently fractionated and the RNA extracted by P/C/I extraction. Input control was isolated using TRIzol reagent.
RNA was fragmented, and the 3' TruSeq adapter ligated to the 3' end. Following cDNA synthesis, the 5' TruSeq adapter was ligated to the 3' end and the resulting cDNA amplified by PCR.

tag: strain

tag: growth phase

value: Early stationary (OD 2.0)

value: wild type


title: Fraction_19


title: pSNL rep3

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were  removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Rattus norvegicus

source_name: dorsal root ganglia

extract_protocol:
DRG were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGIseq500 RNA library kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dorsal root ganglia

tag: treatment

value: post pSNL day 7


title: antiTNF_Responder_7 (DAS28 criteria)

description:
antiTNF_Responder_7
Immediately after arthroscopy biopsy, samples were kept in RNALater preservation agent and stored at -80ÂºC until extraction.
SAMPLE10

scan_protocol: Standard Illumina hybridization protocol

value: European League Against Rheumatoid Arthritis (EULAR) responder


title: Fibroblast culture derived from primary lymph node FST119 _


title: Psi DamID 1

description: control

tag: developmental stage