title: 7h_rep2

city: Shanghai

first: Pei

last: Hao

state: Shanghai

address: No.320 Yueyang Road

department: Bioinformatics Platform

institute: Institut Pasteur of Shanghai

data_processing:
The RNA sequencing reads were first processed to remove adaptors using Trim_galore and then trimmed from both the 5' and 3' ends, with a quality score of 20 using Trimmomatic.
Evaluate the clean datasets with FastQC
RNA sequencing reads were mapped to human reference genome hg19 using TopHat v2.0.11
The mapping files were processed with Cufflinks (Version: 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: comma separated values (CSV) file includes FPKM values for each Sample

source_name: A549 cell

growth_protocol: A549 cells were maintained in DMEM medium containing 10% FBS

extract_protocol:
Total RNA was isolated from the infected cells using the RNeasy RNA extraction Mini-Kit (Qiagen)
The sequencing library was prepared using the TruSeq RNA sample preparation kit v2 (Illumina))

treatment_protocol: Compounds were diluted with DMEM containing 2% FBS into indicated concentrations. Cells were washed with PBS for 3 times before adding compounds.

tag: virus subtype

tag: virus dose(moi)

tag: infection time


title: 7h_rep1

status: Public on Apr 22 2017

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: 3h_rep2


title: SSF1163_A10_Vehicle_1_KP2311_P3

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

country: USA

institute: DFCI

data_processing:
Sequenced reads were mapped to the mouse genome (mm10) by Tophat
Estimated transcript counts were retrieved via the Cufflinks suite version 2.2.1.
Only single cell samples with at least 100.000 paired-end reads and a minimum of 20% aligning to the transcriptome were retained for further analysis.
Processed counts only show samples that passed the minimum reads and alignment criteria.
Genome_build: mm10
Supplementary_files_format_and_content: processed_counts.txt: txt file with processed counts after cufflinks

organism: Mus musculus

source_name: Lung tumor Macrophage Vehicle

growth_protocol: Genetically engineered mouse model (GEMM) of conditional activating mutation that harboring endogenous Kras (KrasLSL-G12D/+) were crossed with p53 conditional knockout Trp53fl/fl. CRE recombinase was induced through intranasal inhalation of 5x106 p.f.u. adeno-Cre (University of Iowa adenoviral core).

extract_protocol:
Viable CD45+CD3+ T cells  or CD45+CD11c+CD11blo macrophages were sorted from tumor cell suspensions into 2ul of Qiagen TCL buffer in 96-well plates
SmartSeq2 protocol with modifications (Trombetta et al., 2014)

treatment_protocol: Ricolinostat, 50 mg/kg, IP, QD

tag: position

tag: tissue

value: Lung tumor

tag: strain

value: Mixed background

tag: gemm model

value: Macrophage

tag: treatment

value: Vehicle


title: embryo_45_90_min_miCLIP

city: New York

first: Eric

last: Lai

state: New York

address: 430 E 67th Street

department: Department of Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Read processing. Fastq files for six embryo timepoints were adapter trimmed and demultiplexed with a custom pipeline using Flexbar (https://github.com/seqan/flexbar), and pyBarcodeFilter.py from the pyCRAC software suite, respectively. PCR duplicates in the dataset were removed and the read headers were then altered to be compatible with the CIMS software package using methods previously described in Linder et al. 2014. Paired-end RNA-seq data from control mRNA and miCLIP for six embryo developmental timepoints were mapped to the Drosophila reference genome sequence (version r5.45) with Subread-align package from the Subread software suite. Read counts for each gene was extracted from the RNA-seq bam files using featureCounts package from the Subread software. The read counts per gene were then normalized to obtain FPKM values using DEseq package from R Bioconductor.
miCLIP analysis and mutation calling. The reads were mapped to the Drosophila reference genome sequence (version r5.45) with Novoalign (Novocraft) or the Subread-align package from the Subread software suite. For the Novoalign alignment, a maximum alignment score of 85 was allowed and the parameters were adjusted to map short reads. For alignment using the subread-align, the alignment was performed using default parameters for mapping paired-end RNA sequence data. Positions of C to T transitions from the mapped data were identified using the CIMS software package as described in Linder et al. 2014.
Genome_build: r5.45
Supplementary_files_format_and_content: bigWig, matrix.txt: FPKM

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: We mass-collected Canton S embryos across these developmental timepoints: 0-45', 45-90', 1.5-6 hr, 6-12 hr, 12-18 hr and 18-24 hr. In principle, zygotic transcription does not initiate until ~2 hr. However, due to variability in time of egg laying after fertilization, it can be difficult for early timepoints to be staged precisely. Therefore, we changed egg laying plates frequently when collecting the earliest timepoints, and split these into two stages that should both reflect the maternal transcriptome.

extract_protocol:
Linder et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. 2015. Nature Methods 12:767-772.
miCLIP: Reads were sequenced in paired-end mode with 50 bases. All samples were sequenced together on one flowcell lane. Sequencing was performed on an Illumina HiSeq 2500 instrument at Weill Cornell Medicine Epigenomics Core
mRNA: RNA samples were subjected to Illumina mRNA TruSeq Stranded library Prep and sequenced on HiSeq 2500, 2x50, High Output at the New York Genome Center.

tag: developmental stage

tag: tissue type

value: embryo

value: yw

tag: antibody

value: Abcam anti-m6A (ab151230)

tag: iclip barcode

value: NNNTTAG


title: embryo_0_45_min_miCLIP

value: NNNCCGG


title: SSF1163_A1_Vehicle_1_KP2311_P3

source_name: Lung tumor Tcell Vehicle

value: Tcell


title: 1.5h_rep2


title: embryo_1.5_6_hr_mRNA


title: SSF1163_A1_ACY1215_1_KP2313_P3

source_name: Lung tumor Tcell ACY1215


title: male_63a_non-obese_t2d_1h

city: Gothenburg

first: Leif

last: Väremo

address: Kemivägen 10

department: Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
Basecalling, demultiplexing and conversion using CASAVA v1.8.2.
The reads were trimmed from adapter sequences and aligned to the human genome (Ensembl GRCh37.73, DNA primary assembly) using STAR 2.3.1u and the Homo_sapiens.GRCh37.73.gtf-file. The following additional flags were used: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outStd SAM --outFilterType BySJout
Samtools 0.1.18 was used for indexing and sorting
Gene counts were calculated using HTSeq-count 0.5.4p3
Genome_build: Ensembl GRCh37.73
Supplementary_files_format_and_content: The count files contain the gene counts for each sample, as output by HTSeq-count.

source_name: vastus lateralis muscle

growth_protocol: Muscle precursor cells (satellite cells) were isolated from human skeletal muscle biopsies obtained from the vastus lateralis muscle using a biopsy needle with suction (Bergström, 1975) as described in detail previously (Broholm et al., 2012). Isolated satellite cells were cultured in growth media 1 (HAM/F10 supplied with 20% Fetal Bovine Serum and 1% penicillin/streptomycin) and plated in 6-well plates. Upon 70-80% confluence, the media was changed to differentiation media 1 (DMEM 4.5 g/L glucose supplied with 10% FBS and 1% penicillin/streptomycin) for two-three days, until the myoblasts were completely confluent and had lined up. Hereafter, media was changed to differentiation media 2 (DMEM 4.5 g/L glucose supplied with 2% horse serum and 1% penicillin/streptomycin) thereby initiating fusion into myotubes. Cultures were fully differentiated by day 5 as determined by visual confirmation of myotube formation (>3 nuclei per myotube in ~70% of the cells). At day 5, media was changed to DMEM 1.0 g/L glucose without any supplements for two hours and the myotubes were subsequently stimulated with insulin (100nM). Cells were harvested before insulin stimulation, 30 minutes, one hour or two hours after insulin stimulation and total RNA was extracted using Trizol® (Life Sciences) according to the manufactures’ instructions.

extract_protocol:
Total RNA was extracted using Trizol® (Life Sciences) according to the manufactures’ instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA kit

treatment_protocol: The myotubes were stimulated with insulin (100nM) before harvesting.

tag: sample id

tag: cell id

tag: disease

tag: weight

value: non-obese

tag: gender

value: male

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: cell-a

tag: virus subtype

tag: virus dose(moi)

tag: infection time


title: male_119a_non-obese_t2d_0h

treatment_protocol: No treatment.

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: time after insulin, h


title: 3h_rep1


title: 1.5h_rep1


title: female_23a_non-obese_ngt_2h

value: ngt

value: female

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l


title: female_23a_non-obese_ngt_0.5h

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: cell-b

tag: virus subtype

tag: virus dose(moi)

tag: infection time


title: male_59a_obese_ngt_0h

tag: sample id

tag: cell id

tag: disease

tag: weight

value: obese

tag: gender

tag: free fatty acids (2h), mmol/l


title: female_23a_non-obese_ngt_1h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l


title: embryo_12_18_hr_miCLIP

tag: developmental stage

tag: tissue type

tag: strain

tag: antibody

tag: iclip barcode

value: NNNGGTC


title: male_53a_obese_t2d_2h

tag: sample id

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: male_53a_obese_t2d_1h

tag: cell id

tag: disease

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: free fatty acids (2h), mmol/l


title: male_119a_non-obese_t2d_0.5h

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l


title: male_53a_obese_t2d_0.5h

tag: sample id

tag: insulin (2h), pmol/l

tag: homa-ir


title: female_127a_non-obese_t2d_0.5h

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: 24hInd COPR5 ChIP

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: COPR5 ChIP

library_source: genomic

data_processing:
The libraries were run on Illumina NextSeq500 instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Genomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the KSHV genome databaseto determine the DNA bound by specific targets
ChIP peaks were calculated using CLC workbench ChiP-peak tool using input as reference
Genome_build: NCBI genome build of KSHV sequence accession# NC_009333
Supplementary_files_format_and_content: ChIp peaks on the viral genomes are in wig file (CLC workbench)

molecule: genomic DNA

organism: Human gammaherpesvirus 8

source_name: cells were induced with doxycycline for 24h

growth_protocol: TRExBCBL1-Rta  cells were grown in RPMI medium with 10% FBS. Uninduced samples were grown with Tet-Free 10%FBS.

extract_protocol:
Latent and lytic cells were cross-linked using formaldehyde to fix the protein-DNA for ChIP assay
Chromatins were immunoprecipitated using specific listed antibody by following standard ChIP protocol

treatment_protocol: Cells were induced for lytic reactivation by Doxycycline for 12h or 24h.

tag: tissue

value: KSHV infected Body Cavity Based Lymphoma Cells

tag: genotype/variation

value: RTA protein is under tet-inducible promoter

tag: antibody

value: COPR5 Antibody:Novus Biologicals #NBP2-30884


title: female_127a_non-obese_t2d_0h

tag: cell id

tag: disease

tag: weight

tag: gender

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: female_85a_obese_t2d_2h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: free fatty acids (2h), mmol/l


title: 24hInd IgG ChIP

description: Control IgG ChIP

value: Control IgG Antibody:Cell Signaling Technology, catalog #2729, lot# 7


title: 24hInd Input

description: DNA extracted from the sonicated chromatin

value: none (input)


title: 24hInd PRMT5 ChIP

description: PRMT5 ChIP

value: PRMT5 Antibody:Active Motif #61001


title: female_85a_obese_t2d_1h

tag: sample id

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l


title: 24hInd ORF59 ChIP

description: ORF59 ChIP

tag: tissue

tag: genotype/variation

tag: antibody

value: ORF59 Antibody:Custom synthesized for our lab - anti-KSHV-ORF59 antibody from GenScript


title: male_56a_obese_ngt_0h

tag: cell id

tag: disease

tag: weight

tag: gender

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l


title: 12hInd ORF59 ChIP

description: ORF59 ChIP

source_name: cells were induced with doxycycline for 12h


title: 12hInd PRMT5 ChIP

description: PRMT5 ChIP


title: female_85a_obese_t2d_0.5h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: free fatty acids (0h), mmol/l


title: Und COPR5 ChIP

description: COPR5 ChIP

source_name: Induced cells


title: male_96a_obese_t2d_2h

tag: sample id

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: free fatty acids (2h), mmol/l


title: male_96a_obese_t2d_0.5h

tag: cell id

tag: disease

tag: cholesterol (hdl), mmol/l


title: Und Input

tag: tissue

tag: genotype/variation

tag: antibody


title: SU-DIPG-VI panobinostat_input

status: Public on Apr 21 2017

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

description: whole cell input DNA control

data_processing:
Mapping: ChIP-seq with bowtie2, RNA-seq with tophat2. Default parameters were used against hg19 reference genome
Deduplication: Duplicates were removed using PicardTools 1.128 MarkDuplicates
Bed files generated using bedtools bamtobed
bedGraph files were generated using bedtools genomecov, then converted to bigWig using UCSC bedGraphToBigWig
Gene expression: For RNA-seq, gene expression was counted using featureCounts against an RefSeq hg19 GTF without miRNA or snoRNA
Peak calling: For ChIP-seq, H3K27Ac peaks were called over input controls using macs2 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: bigwig for merged biological replicates, normalized to reads per million
Supplementary_files_format_and_content: allNormCounts.erccPseudo1.txt: raw counts of gene expression abundance for SU-DIPG-VI and SU-DIPG-XIII, ERCC spike-in normalized
Supplementary_files_format_and_content: dipg4-polyA.counts.txt: raw counts of gene expression abundance or SU-DIPG-IV
Supplementary_files_format_and_content: dipg17-polyA.counts.txt: raw counts of gene expression abundance for SU-DIPG-XVII

source_name: patient-derived cell culture

growth_protocol:
Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin.
Cells are grown in Tumor Stem Media (TSM), consisting of Neurobasal (-A), DMEM F12, B27 (-A), bFGF, EGF, PDGF-AB, and heparin. See Grasso et al 2015.

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated. ChIP-seq samples were fixed in 1% formaldehyde for 10 min before glycine quench and freezing at -80C. ChIP-seq pellets were lysed in LB1 Buffer before beginning ChIP protocol.
After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. ChIP-seq libraries were prepared directly from DNA isolated following IP. Libraries for ChIP-seq and RNA-seq were end-repaired using T4 DNA Polymerase, E. coli Klenow fragment, and T4 polynucleotide kinase. DNA was then A-tailed using exo(-) Klenow fragment and ligated to adaptors from NEBNext MultiPlex Oligos or TruSeq Preindexed Adaptors using New England BioLabs Quick Ligase.
Libraries were sequeced at 1x75 (RNA-seq) or 2x75 (ChIP-seq) on either Illumina HiSeq or NextSeq

treatment_protocol: SU-DIPG-VI and SU-DIPG-XIII were treated with DMSO (1%), panobinostat (0.1uM), JQ1 (1uM), THZ1 (0.1uM), or combination for 24 hours in growth media. SU-DIPG-IV and SU-DIPG-XVII were not treated.

tag: cell type

value: Diffuse intrinsic pontine glioma (DIPG) cells

tag: treated with

tag: molecule subtype

value: precipitated DNA


title: SU-DIPG-XIII panobinostat_input

description: whole cell input DNA control


title: SU-DIPG-XIII panobinostat_ChIP-seq

description: H3K27Ac ChIP-seq, cells treated with 0.1uM panobinostat for 24 hours

value: 0.1uM panobinostat for 24 hours

tag: chip antibody

value: Active Motif #39133

value: immunoprecipitated DNA


title: SU-DIPG-XVII_RNA-seq

description: poly(A)+ RNA-seq

value: poly(A)+ RNA


title: male_53a_obese_t2d_0h

tag: weight

tag: gender

value: male

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SU-DIPG-XVII_input

description: whole cell input DNA control


title: SU-DIPG-IV_ChIP-seq

description: untreated H3K27Ac ChIP-seq


title: SU-DIPG-VI panobinostat_ChIP-seq


title: SU-DIPG-IV_input

description: whole cell input DNA control


title: SU-DIPG-XVII_ChIP-seq

description: untreated H3K27Ac ChIP-seq


title: female_109a_non-obese_t2d_2h

tag: sample id

tag: cell id

tag: disease

value: non-obese

value: female

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: Und PRMT5 ChIP

description: PRMT5 ChIP

tag: tissue

tag: genotype/variation

tag: antibody


title: nonhair_rep1_dsRNase_protein

city: Philadelphia

first: Shawn

last: Foley

state: PA

address: 433 S. University Ave

institute: University of Pennsylvania

description:
processed data file:
nonhair_rep1_dsRNase_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
nonhair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt

data_processing:
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed using an in-house perl (version 5.8.8) script
Trimmed and untrimmed reads were aligned to the Arabidopsis thaliana genome (TAIR10) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
PPS files - Reads mapping to the annotated ribosomal RNA (rRNA) genes, as well as mitochondria or chloroplast genomes were discarded and protein-protected sites (PPSs) were identified using a modified version of the CSAR software package (Muino et al. 2011). Specifically, read coverages were calculated for each base position in the genome and a Poisson test was used to compute an enrichment score for ‘protected’ versus ‘unprotected’ libraries. PPSs were then called as described (Muino et al. 2011) with an false discovery rate (FDR) of 5%. These are presented as BED6 files indicating where each PPS maps to across the genome
Structure score files - For every base of detectable transcripts, we calculated the dsRNA-seq and ssRNA-seq coverages from the structure only samples, then calculated the structure score as described previously (Li et al., 2012). The total coverage length was used as the normalization constant instead of the total number of mapped reads used previously, because we believe it is a more reasonable assumption for the transcriptome to have comparable levels of paired/unpaired regions. It is of note that we used a generalized log ratio (glog) instead of normal log-odds because it can tolerate 0 values (positions with no dsRNA or ssRNA read coverage) as well as being asymptotically equivalent to the standard log ratio when the coverage values are large.
Structure scores were calculated for every nucleotide of annotated TAIR10 mRNAs genes. They were standardized such that the sum of the structure scores across each chromosome totals to zero. The unspliced structure scores scores are represented in a BED12 file with a 13th column consisting of a comma separated list of scores corresponding to each nucleotide in the pre-mRNA gene.
An in house python (v2.7) script was used to remove structure scores corresponding to annotated introns from the unspliced structure score file, to generate the spliced structure score file. This is a BED12 file with a thirteenth column comprised of a comma separated list of structure scores that correspond to every nucleotide of the MATURE, SPLICED mRNA.
Genome_build: TAIR10
Supplementary_files_format_and_content: BED format of protein protected sites (PPSs)

organism: Arabidopsis thaliana

growth_protocol: The purified nuclei used in this study were extracted from 10-day-old seedlings of ADF8:NTF/ACT2p:BirA (hair cells) or GL2:NTF/ACT2p:BirA (nonhair cells) Columbia-0 (Col-0) ecotype of Arabidopsis thaliana using the INTACT methodology. All plants were grown at 20°C, in a 16 h light/8 h dark cycle on 0.5x MS plates

extract_protocol:
~Two million INTACT purified nuclei were lysed in 850 ml RIP buffer (25 mM Tris-HCl, pH = 7.4; 150 mM KCl, 5 mM EDTA, pH = 7.5; 0.5% NP40; 10 mM DTT; 1 tablet protease inhbitors and 0.5ml/ml RNaseOUT (Life Technologies; Carlsbad, CA)) by manual grinding. The resulting cell lysate was treated with RNase-free DNase (Qiagen; Valencia, CA). The lysates were then split and treated with either 100 U/ml of a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI)) with 200 μg/ml BSA in 1X RNaseONE buffer for 1 hour at room temperature (RT), or 2.5 U/ml of a double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX)) in 1X RNA structure buffer for 1 hour at 37°C as previously described (Silverman, 2014). See Figure 1A for a schematic representation of library preparation. Proteins were then denatured and digested by treatment with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) for 15 minutes at RT. Proteinase digestion was followed by a 2 hour incubation at 65°C to reverse the RNA-protein cross-links. To determine whether nuclease resistant regions in RNAs are due to protein binding or specific secondary structures, we also determined the digestion patterns of ds- and ssRNases immediately following protein digestion. To do this, we performed the identical treatments as described above except that the cross-linked nuclear lysates were treated with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) and ethanol precipitated prior to being treated with the two RNases. In this way, the SDS and Proteinase K solubilized and digested the proteins allowing us to deduce PPSs within all detectable RNAs in the cells of interest (see Figure 1A for schematic).The digested RNA was then isolated using the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
Purified RNA was used as the substrate for strand-specific sequencing library preparation (TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Zheng et al. 2010; Li et al. 2011), with the exception that we also include DSN library normalization per manufacturer instructions (Illumina; San Diego, CA).

treatment_protocol: Immediately before nuclei purification, the fully differentiated root tissue was excised from 10-day-old seedling and was crosslinked in nuclear purification buffer (20 mM MOPS (pH 7), 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA) plus 1% (vol/vol) formaldehyde under vacuum for 10 minutes, followed by a five minute quench with 125 mM Glycine under vacuum for an additional five minutes.  Crosslinked seedlings then underwent INTACT purification as previously described (Deal, 2010).

tag: ecotype background

value: Columbia-0 (Col-0)

tag: age

value: 10-day-old seedlings

tag: sample type

value: Nuclei (of root nonhair cells)

tag: crosslinker

value: formaldehyde

tag: rnase

value: dsRNase (Rnase V1)

tag: protein-bound

value: yes


title: nonhair_rep1_ssRNase_noprotein

description:
processed data file:
nonhair_rep2_dsRNase_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
nonhair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt

value: ssRNase (Rnase ONE)

value: no


title: nonhair_rep2_dsRNase_protein

description:
processed data file:
nonhair_rep1_ssRNase_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
nonhair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt


title: nonhair_rep2_dsRNase_noprotein


title: nonhair_rep2_ssRNase_protein

description:
processed data file:
nonhair_rep2_ssRNase_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
nonhair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
nonhair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt


title: hair_rep2_ssRNase_protein

description:
processed data file:
hair_rep2_ssRNase_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
hair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt

value: Nuclei (of root hair cells)


title: male_96a_obese_t2d_1h

tag: sample id

tag: cell id

tag: weight

value: obese

tag: gender

tag: time after insulin, h

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: hair_rep2_ssRNase_noprotein

tag: ecotype background

tag: genotype/variation


title: nonhair_rep2_ssRNase_noprotein

tag: age

tag: sample type


title: SU-DIPG-IV_RNA-seq

description: poly(A)+ RNA-seq

tag: cell type

value: Diffuse intrinsic pontine glioma (DIPG) cells

tag: treated with

tag: molecule subtype


title: hair_rep2_dsRNase_noprotein

description:
processed data file:
hair_rep2_dsRNase_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
hair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt

tag: crosslinker

tag: rnase

tag: protein-bound


title: hair_rep1_dsRNase_noprotein

description:
processed data file:
hair_rep1_dsRNase_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
hair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt


title: hair_rep1_ssRNase_protein

description:
processed data file:
hair_rep1_ssRNase_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_merged_merged.CSAR_PPS_FDR05.bed
hair_rep1and2_noprotein_NR_structure_unspliced_std_filtered.bed12.txt
hair_rep1and2_noprotein_NR_structure_spliced_std_filtered.bed12.txt


title: iOL_219mimic_2

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 or rn4 whole genome using TopHat using default options.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files.
Genome_build: rn4 (RGSC_v3.4)
Supplementary_files_format_and_content: *.fpkm_tracking: Cufflinks output: Tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: Oligodendrocyte, miR-219 mimic transduction

extract_protocol:
Cells and optic nerves were collected, flash frozen on dry ice, and total RNA was extracted using Trizol reagent.
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).

value: Oligodendrocyte


title: OPC_219mimic_Pulldown

source_name: Oligodendrocyte, biotin-miR-219 pull down


title: iOL_Ctrl_1_genes

source_name: Oligodendrocyte, control


title: iOL_219mimic_1


title: nonhair_rep1_ssRNase_protein


title: OPC_219mimic_1_genes


title: nonhair_rep1_dsRNase_noprotein


title: iOL_Ctrl_2_genes


title: OPC_219mimic_2_genes


title: OPC_Ctrl_2_genes


title: hair_rep2_dsRNase_protein


title: OPC_Ctrl_1_genes


title: PR2_A

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description:
Ponatinib resistant LC-2/ad cells cultured in 200 nM ponatinib
Barcode: CTTGTA

data_processing:
Tophat (version 2.0.14) used to map reads to human genome
Cufflinks (version 2.2.1) used to assemble transcripts
Cuffdiff (version 2.2.1) used to identify differenentially expressed genes
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text file includes normalized expression levels

source_name: PR2 cells

extract_protocol:
RNeasy kit (Qiagen)
RNAlibraries were prepared for sequencing using TruSEQ RNA Sample Prep v4 using standard Illumina protocols.

tag: cell line

value: PR2 cells


title: PR2_C

description:
Ponatinib resistant LC-2/ad cells cultured in 200 nM ponatinib
Barcode: AGTCAA


title: PR1_B

description:
Ponatinib resistant LC-2/ad cells cultured in 200 nM ponatinib
Barcode: CAGATC

source_name: PR1 cells

value: PR1 cells


title: hair_rep1_dsRNase_protein


title: PR2_B

description:
Ponatinib resistant LC-2/ad cells cultured in 200 nM ponatinib
Barcode: CCGTCC


title: LC2_A

description:
Parental LC-2/ad cells
Barcode: ACAGTG

source_name: LC/2-AD cells

value: LC/2-AD cells


title: OPC_Ctrl_Pulldown

source_name: Oligodendrocyte, control pull down


title: hair_rep1_ssRNase_noprotein


title: post10

first: Anthony

last: Oro

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

data_processing:
alignment was performed to mouse genome build NCBI/build37.2 using Tophat. Differential expression analysis for RNASeq was performed using DESeq.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: RNASeq normalized counts, text file

source_name: AA patient_post-treatment

extract_protocol:
poly-A pull-down
library preparation using Illumina TruSeq RNA prep kit

tag: subject status

value: patients with Alopecia Areata

tag: time point

value: at 8 weeks of treatment with Tofacitinib Citrate 5 mg BID

tag: tissue

value: scalp biopsy


title: PR1_A

description:
Ponatinib resistant LC-2/ad cells cultured in 200 nM ponatinib
Barcode: GCCAAT


title: post28


title: post2


title: PR1_C

description:
Ponatinib resistant LC-2/ad cells cultured in 200 nM ponatinib
Barcode: GTGAAA


title: LC2_C

description:
Parental LC-2/ad cells
Barcode: TGACCA


title: LC2_B

description:
Parental LC-2/ad cells
Barcode: CGATGT


title: post17


title: post15


title: post1


title: post16


title: post13


title: post18


title: post14


title: post21


title: post5


title: post26


title: post19


title: post4


title: post20


title: post9


title: post24


title: post3


title: post6


title: post8


title: pre13

source_name: AA patient_pre-treatment

value: before treatment


title: post23


title: post12


title: post25


title: pre5


title: post27


title: post11


title: post22


title: pre14


title: pre20


title: pre19


title: pre15


title: post7


title: pre17


title: pre21


title: pre18


title: pre26


title: pre8


title: pre25


title: pre22


title: pre11


title: pre4


title: LIV NOMET Rep5

city: Athens

first: Samuel

middle: E

last: Aggrey

state: GA

address: 110 Cedar Street

department: Poultry Science

institute: University of Georgia

data_processing:
Read alignment software, version, parameters: Tophat version 2.0.9 in conjunction with Bowtie version 1.0.0. Mapping is carried out with unfiltered reads.  Segment-mismatches parameter value set to 2.
Cufflinks version 2.1.1 and Cuffdiff version 2.1.1 to collect FPKM expression values across all samples, both at the Gene- (G) and transcript “gene Isoform”.
Genome_build: Galgal4 (Gallus_gallus-4.0; Ensembl v74)
Supplementary_files_format_and_content: The cufflinks *.isoforms and *.genes files include RPKM values for each sample.

organism: Gallus gallus

source_name: Liver (LIV), L-Methionine-deficient diet

extract_protocol:
Pectoralis major and liver were removed, snapped frozen in liquid nitrogen and stored at -86C. RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep 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.

treatment_protocol: Gallus gallus males were fed either control (L-Methionine) or L-Methionine-deficient diet (5 control and 5 treatment) from 3-5 weeks of age.

tag: breed

value: Ross 708

tag: gender

value: Male

value: Post-hatch day 35

value: Liver (LIV)

tag: treatment

value: L-Methionine-deficient diet


title: LIV NOMET Rep2


title: LIV NOMET Rep3


title: pre16


title: pre7


title: pre12


title: pre23


title: LIV LMET Rep4

source_name: Liver (LIV), control diet

value: Control diet


title: pre27


title: LIV LMET Rep3


title: pre2


title: pre24


title: pre6


title: LIV LMET Rep1


title: pre9


title: pre1


title: LIV LMET Rep2


title: pre10


title: BRE NOMET Rep4

source_name: Pectoralis major (BRE), L-Methionine-deficient diet

value: Pectoralis major (BRE)


title: BRE NOMET Rep5


title: BRE NOMET Rep3


title: pre3


title: pre28


title: LIV LMET Rep5


title: LIV NOMET Rep4


title: BRE LMET Rep3

source_name: Pectoralis major (BRE), control diet


title: BRE NOMET Rep2


title: BRE NOMET Rep1


title: BRE LMET Rep5


title: BRE LMET Rep4


title: SU-DIPG-XIII panobinostat + THZ1_RNA-seq

description:
poly(A)+ RNA-seq, cells treated with 0.1uM panobinostat and 0.1uM THZ1 for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt

value: poly(A)+ RNA


title: FS022

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

data_processing:
RTA (Illumina) for base calling
bcl2fastq (version 1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat 1 with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks 2 with default settings. We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: sampleName.counts.txt were generated containing number of counts for each gene

source_name: Renal graft

growth_protocol: Mouse ebryonic fibroblasts were generated by dissociating E13.5 mebryos and cultured in 10%FBS/DMEM media. Induced epithelial cells were generated by primed conversion of fibroblasts in basal epithelial media.

extract_protocol:
Renal grafts derived from tissue recombination assays of induced epithelial cells with rat urogenital mesenchyme were harvested after 6 weeks of growth in nude mice,  flash frozen in liquid nitrogen, and RNA was harvested using Rneasy Mini Kit from Qiagen. Mouse prostate were dissected out, flash frozen in liquid nitrogen, and RNA was harvested using Rneasy Mini Kit from Qiagen. Pellets of mouse embryonic fibroblasts were flash frozen in liquid nitrogen, and RNA was harvested using Rneasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq RNA Sample Prep Kit vs 2 (cat# RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain

tag: growth duration

value: 6 weeks

value: induced mouse epithelial cells and rat urogenital mesenchyme


title: FS023


title: LIV NOMET Rep1

tag: age


title: BRE LMET Rep2


title: FS020

data_processing:
RTA (Illumina) for base calling
bcl2fastq (version 1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat 1 with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks 2 with default settings. We test for differentially expressed genes under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Raw RNAseq counts were normalized (variance stabilization) using DESeq package in R-studio Version 0.99.484
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text or xls files include DESeq normalized values for each Sample

source_name: Fibroblasts

growth_protocol: Mouse embryonic fibroblasts were generated by dissociating E13.5 mebryos and cultured in 10%FBS/DMEM media. Induced epithelial cells were generated by primed conversion of fibroblasts in basal epithelial media.

value: mouse embryonic fibroblasts

value: Nkx3-1tm2(LacZ)Mms /+


title: BRE LMET Rep1


title: SU-DIPG-XIII THZ1_RNA-seq

description:
poly(A)+ RNA-seq, cells treated with 0.1uM THZ1 for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: 0.1uM THZ1 for 24 hours


title: SU-DIPG-VI panobinostat + THZ1_RNA-seq

value: 0.1uM panobinostat and 0.1uM THZ1 for 24 hours


title: SU-DIPG-XIII panobinostat + JQ1_RNA-seq

description:
poly(A)+ RNA-seq, cells treated with 0.1uM panobinostat and 1uM JQ1 for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt


title: FS019


title: SU-DIPG-VI THZ1_RNA-seq


title: FS017


title: FS016


title: FS014

source_name: Prostate

value: Prostate


title: FS018


title: SU-DIPG-VI JQ1_RNA-seq

description:
poly(A)+ RNA-seq, cells treated with 1uM JQ1 for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt

source_name: patient-derived cell culture

value: 1uM JQ1 for 24 hours


title: SU-DIPG-XIII panobinostat_RNA-seq

description:
poly(A)+ RNA-seq, cells treated with 0.1uM panobinostat for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt

value: 0.1uM panobinostat for 24 hours


title: FS015


title: SU-DIPG-XIII DMSO_input

description: whole cell input DNA control

value: precipitated DNA


title: FS013


title: SU-DIPG-XIII DMSO_RNA-seq

description:
poly(A)+ RNA-seq, cells treated with 1% DMSO for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt

value: 1% DMSO for 24 hours


title: FS012


title: FS008


title: FS011


title: FS009


title: SU-DIPG-XIII DMSO_ChIP-seq

description: H3K27Ac ChIP-seq, cells treated with 1% DMSO for 24 hours

tag: chip antibody

value: Active Motif #39133

value: immunoprecipitated DNA


title: FS010

tag: cell type


title: FS007


title: FS003


title: SU-DIPG-VI DMSO_input

description: whole cell input DNA control

tag: treated with


title: SU-DIPG-VI panobinostat_RNA-seq

tag: molecule subtype


title: dCKO1

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm9 or rn4 whole genome using TopHat using default options.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.fpkm_tracking: Cufflinks output: Tab-delimited text files include FPKM values for each Sample.

source_name: Optic nerve, miR-219 dCKO

tag: genotype/variation

value: Postnatal day 12

value: Optic nerve


title: CapStarr-seq HeLa replicate 2

city: Marseille

first: Salvatore

last: Spicuglia

state: PACA

address: 163, Avenue de Luminy

department: TAGC U1090

country: France

institute: INSERM

description: CapStarr-seq

data_processing:
Libraries were sequenced on the FlowCell Hight Output 75 cycles v2 (single-end 75bp) using the NextSeq500 (Illumina), according to manufacturer’s instructions.
Reads were mapped to the Huma genome (HG19) using Bowtie (v2).
Reads were elongated to the mean fragment size (314bp), and converted to wig format
Wiggle files were then normalized by the number of mapped reads in the samples.
Genome_build: HG19
Supplementary_files_format_and_content: Wiggle files were generated using a developed in-house tool.

source_name: HeLa cell line

extract_protocol:
Total RNA CapStarr-seq transfected library from given cell line was extracted using RNeasy miniprep kit (Qiagen) with the on-column DNaseI treatment. The PolyA RNA fraction was isolated using µMACS mRNA isolation kit (Miltenyi) following manufacturer’s instructions. PolyA RNA was treated with Ambion turboDNase (Ambion) and purified with RNeasy Minelute kit (Qiagen). Finally, mRNA was quantified with Qubit RNA HS Kit (Life technologies). 1st strand cDNA synthesis was performed with superscript III (Life technologies) using a reporter-RNA specific primer (CAAACTCATCAATGTATCTTATCATG) and 0.2 to 0.3 µg of polyA RNA per reaction for a total of 10 reactions. cDNA was purified with QIAquick PCR purification kit and concentration was determined with Qubit ssDNA Kit (Life Technologies).
Libraries were prepared follow NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB, E6000S). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo-) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 7 cycles and library fragments of ~400 bp (insert plus adaptors and PCR primer sequences) were cleaned up using AMPure XP beads (ratio bead/PCR = 1.2). Libraries were then processed follow CapStarr-seq procedure. Total RNA was isolated as described above. cDNA was amplified by a 2-step nested PCR using the KAPA Hifi Hot Start Ready Mix. In the first PCR (98°C for 2 minutes; followed by 15 cycles of 98°C for 20s, 65°C for 20s, 72°C for 30s), 5 ng of cDNA per reaction were amplified using 2 reporter-specific primers (fw: GGGCCAGCTGTTGGGGTG*T*C*C*A*C and rw: CTTATCATGTCTGCTCGA*A*G*C), one of which spans the splice junction of the synthetic intron, in a total of 10 reactions. The PCR product was then clean-up with QIAquick minelute PCR purification kit (Qiagen). To generate the Illumina libraries, the purified PCR product was used as template for the second PCR (2ng/PCR, for a total of 10 PCR; 98°C for 2 minutes; followed by 10 cycles of 98°C for 20s, 65°C for 20s, 72°C for 30s), with Universal primer and Index Primer (Illumina) using the KAPA Hifi Hot Start Ready Mix. To generate the INPUT control, ten reactions with 5 ng of reporter constructs (library) per reaction were amplified using the same conditions as above, at the exception of the forward primer in the 1st PCR (fw: GGGCCAGCTGTTGGGGTG*A*G*T*A*C).
The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. Libraries were run on Illumina NextSeq500.

value: HeLa


title: Ctrl2

source_name: Optic nerve, control


title: FS005

value: 6 weeks


title: SU-DIPG-VI DMSO_ChIP-seq

description: H3K27Ac ChIP-seq, cells treated with 1% DMSO

value: 1% DMSO


title: SU-DIPG-XIII JQ1_RNA-seq

value: poly(A)+ RNA


title: CapStarr-seq K562 replicate 1

description: CapStarr-seq

source_name: K562 cell line


title: CapStarr-seq HeLa replicate 1

description: CapStarr-seq


title: FS002

value: induced mouse epithelial cells and rat urogenital mesenchyme


title: CapStarr-seq K562 replicate 2

description: CapStarr-seq


title: dCKO2


title: Ctrl1


title: Th17_Rep3

status: Public on Apr 20 2017

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

data_processing:
library strategy: ATAC-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard. Peaks were called using the MACS2 algorithm, which was first applied to each dataset independently. Mapped reads from each group of samples were merged to call peaks using MACS2, and highquality peaks were filtered using FDR < 10E-7. The peak sets from each sample group were then merged using ZIMBA to generate a merged peak list.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: Peak files are in tab seperated format, which includes the following columns: chromosome, start, stop, name, number of reads in peak, strand, arbitary score

source_name: human Th17 cell

growth_protocol: Donors were recruited under a Stanford University IRB-approved protocol. Volunteer patients with CTCL were recruited from Stanford Hospital. Informed consent was obtained. Standard blood draws in green-top tube were obtained for each time point. 1-5mL of whole blood was enriched for CD4+ cells using RosetteSep Human CD4+ T Cell Enrichment Cocktail (StemCell Technology)

extract_protocol:
CD4+ T cells were isolated from 5 ml of blood using negative selection. Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: For patients diagnosed with CTCL were treated with either Vorinostat of Romidepsin, based on their clinical tests.

value: Normal Donor

value: human Th17 cell


title: Th2_Rep3

source_name: human Th2 cell

value: human Th2 cell


title: Th17_Rep2


title: SU-DIPG-VI DMSO_RNA-seq

description:
H3K27Ac ChIP-seq, cells treated with 1% DMSO for 24 hours
processed data file:
allNormCounts.erccPseudo1.txt

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: Treg_Rep1

source_name: human Treg cell

value: human Treg cell


title: Th2_Rep1


title: Th1_Rep3

source_name: human Th1 cell

value: human Th1 cell


title: Th2_Rep2


title: Naive_Rep4

source_name: human Naïve T cell

value: human naive T cell


title: Treg_Rep2


title: Capstarr Input

description: Plasmid library

source_name: Peripheral blood mononuclear cell

value: PMBC


title: Naive_Rep3


title: Naive_Rep2


title: Naive_Rep1


title: Leukemic_Patient1424_Romi_Day35

value: patiet with cutaneous T cell leukemia (CTCL)

tag: subject gender

value: Female

value: human CD4+ T cell

tag: cell subtype

value: Leukemic Cells


title: Leukemic_Patient1424_Romi_Day0


title: Leukemic_Patient1424_Romi_Day14


title: Leukemic_Patient1424_Romi_Day28


title: Leukemic_Patient1366_Romi_Day0


title: Leukemic_Patient62_Romi_Day0_Rep2


title: Leukemic_Patient62_Romi_Day0_Rep1


title: Leukemic_Patient59_Romi_Day7_Rep2


title: Leukemic_Patient39_Romi_Day7_Rep2


title: Leukemic_Patient60_Romi_Day7

value: Male


title: Leukemic_Patient60_Romi_Day0


title: Leukemic_Patient39_Romi_Day0_Rep2


title: Leukemic_Patient59_Romi_Day7_Rep1


title: Leukemic_Patient39_Romi_Day7_Rep1


title: Leukemic_Patient20_Romi_Day7


title: Leukemic_Patient11_Romi_Day7_Rep2


title: Leukemic_Patient11_Romi_Day14_Rep1


title: Th1_Rep1


title: Leukemic_Patient1424_Romi_Day7


title: Leukemic_Patient11_Romi_Day7_Rep1


title: SU-DIPG-VI panobinostat + JQ1_RNA-seq

value: 0.1uM panobinostat and 1uM JQ1 for 24 hours


title: Host_Patient1424_Vori_Day7

value: Host Cells


title: Leukemic_Patient11_Romi_Day0_Rep2


title: Leukemic_Patient11_Romi_Day0_Rep1


title: Host_Patient1424_Vori_Day35


title: Host_Patient1424_Vori_Day21


title: Host_Patient1424_Vori_Day28


title: Host_Patient1424_Vori_Day14


title: Host_Patient1424_Vori_Day0


title: Host_Patient1366_Romi_Day0


title: Leukemic_Patient1424_Romi_Day21


title: Leukemic_Patient61_Romi_Day0


title: Th1_Rep2


title: Host_Patient62_Romi_Day0_Rep2


title: Leukemic_Patient39_Romi_Day0_Rep1


title: Leukemic_Patient11_Romi_Day14_Rep2


title: Host_Patient59_Romi_Day7


title: Host_Patient11_Romi_Day14_Rep2


title: Host_Patient11_Romi_Day0


title: Host_Patient62_Romi_Day0_Rep1


title: Host_Patient11_Romi_Day14_Rep1


title: Host_Patient59_Romi_Day0


title: BulkCTCL_Patient1424_Vori_Day7

value: Bulk Cells


title: BulkCTCL_Patient1409_Romi_Day0


title: BulkCTCL_Patient1409_Romi_Day28


title: Host_Patient39_Romi_Day7


title: BulkCTCL_Patient1424_Vori_Day21


title: BulkCTCL_Patient1424_Vori_Day15


title: BulkCTCL_Patient1424_Vori_Day28


title: BulkCTCL_Patient1424_Romi_Day7


title: BulkCTCL_Patient1424_Vori_Day0


title: BulkCTCL_Patient1424_Vori_Day35


title: BulkCTCL_Patient1424_Romi_Day0


title: BulkCTCL_Patient1366_Romi_Day7


title: BulkCTCL_Patient1366_Romi_Day14


title: Host_Patient20_Romi_Day7


title: BulkCTCL_Patient1482_Romi_Day0


title: BulkCTCL_Patient1482_Romi_Day14


title: BulkCTCL_Patient1461_Romi_Day7


title: BulkCTCL_Patient1461_Romi_Day0Post1Hour


title: BulkCTCL_Patient1461_Romi_Day0


title: BulkCTCL_Patient1482_Romi_Day7


title: BulkCTCL_Patient1461_Romi_Day35


title: BulkCTCL_Patient1461_Romi_Day28


title: BulkCTCL_Patient5_Vori_Day14


title: BulkCTCL_Patient5_Vori_Day21


title: BulkStage3_Patient30_Vori_Day0

value: patient with cutaneous T cell leukemia (CTCL) State III


title: BulkStage3_Patient30_Vori_Day21


title: BulkCTCL_Patient20_Vori_Day14


title: BulkCTCL_Patient5_Vori_Day7


title: BulkStage3_Patient30_Vori_Day14


title: BulkStage3_Patient30_Vori_Day7


title: BulkCTCL_Patient11_Vori_Day21


title: BulkCTCL_Patient20_Vori_Day7


title: BulkCTCL_Patient5_Vori_Day0


title: BulkCTCL_Patient11_Vori_Day14


title: BulkCTCL_Patient1366_Romi_Day28


title: BulkCTCL_Patient20_Vori_Day0


title: BulkCTCL_Patient11_Romi_Day14


title: BulkCTCL_Patient11_Vori_Day7


title: BulkCTCL_Patient11_Romi_Day7


title: Normal_Donor9_Day38_Rep1

value: normal/healthy donor


title: Normal_Donor4_Day224_Rep2


title: BulkCTCL_Patient20_Vori_Day21


title: BulkCTCL_Patient11_Vori_Day0


title: BulkCTCL_Patient11_Romi_Day0


title: Normal_Donor4_Day107_Rep1


title: Normal_Donor33_Day224_Rep2


title: Normal_Donor4_Day37_Rep1


title: Normal_Donor33_Day224_Rep1


title: Normal_Donor32_Day224_Rep2


title: Normal_Donor32_Day224_Rep1


title: Normal_Donor2_Day224_Rep2


title: Normal_Donor3_Day37_Rep1


title: Normal_Donor1_Day224_Rep2


title: Normal_Donor2_Day224_Rep1


title: Normal_Donor31_Day192_Rep1


title: Normal_Donor1_Day224_Rep1


title: Normal_Donor31_Day192_Rep2


title: Normal_Donor10_Day224_Rep2


title: Normal_Donor7_Day38_Rep1


title: Normal_Donor1_Day38_Rep1


title: Normal_Donor10_Day38_Rep1


title: Normal_Donor1_Day37_Rep2


title: Normal_Donor4_Day107_Rep2


title: Normal_Donor4_Day224_Rep1


title: Normal_Donor1_Day39_Rep1


title: Normal_Donor1_Day37_Rep1


title: Normal_Donor1_Day38_Rep2


title: Normal_Donor1_Day2_Rep2


title: Normal_Donor1_Day1_Rep2


title: Normal_Donor1_Day2_Rep1


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_96]

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw data files were trimmed using Reaper with a quality cutoff of 53 (length 20 bp, prefix 50 bp) and a minimum clean read length of 50 bp.
Reads were then mapped to the genome (mm10) using STAR.
FeatureCounts was used to assign reads to genes from the Gencode vM6 annotation.
Genes with less than 50 counts across all cells were discarded prior to normalization.
The knn.error.models function from SCDE59 was used to construct cell-specific error models by evaluating the gene counts for a observed cell vs. the expected gene counts from the k most similar cells. The parameter k was chosen to resemble roughly three subpopulations.
Estimated fragments per million mapped reads (FPM, in log scale) were then obtained using the scde.expression.magnitude function.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

source_name: aortal smooth muscle cells

extract_protocol:
Single-cell transcriptome analysis was performed on a C1 Autoprep station (Fluidigm) using 5-10µm mRNA Arrays and standard protocols. 15.000 events sorted on a JSAN swift  sorter were suspended in 10 µl resuspension buffer (PBS + 0.5% bovine serum albumin + 2nM EDTA, sterile filtered) and further diluted (6:4) in suspension buffer. 3µl were loaded to the C1 Array while remaining cells (~10.000) were used for total RNA isolation using µRNeasy micro kit (Qiagen) combined with on-column DNase digest (Qiagen). RNA was quantified by Qubit HS RNA Assay (Thermo Fisher) and used for tube control. Pre-amplification and cDNA synthesis were done with Smarter ultra-low RNA Kit (Clontech) without changes to the standard protocol.
cDNA obtained from C1 system was quantified using PicoGreen assay (Thermo Fisher) and diluted to 0.1–0.3 ng/μl. Picking of positive cDNA samples and library preparation were done with NGS Express pipetting robot (Perkin Elmer) using custom made protocols. Barcoded and amplified libraries were pooled in groups of 16 libraries for final SRRI-bead based cleanup and quantified by Qubit HS dsDNA Assay (Thermo Fisher) and BioAnalyzer 2100 HS DNA Assay (Agilent).
Sequencing was performed on Nextseq500 Sequencer (Illumina) using v2 chemistry and High Output Flow Cell with 75bp single end protocol.

treatment_protocol: Smooth muscle-specific EGFP reporter mice (Myh11-CreERT2pos;dTom/EGFP-reporter) were sacrificed and perfused with PBS. The aorta including common carotid arteries was dissected, minced, and enzymatically digested for 90-120 minutes while shaking at 37°C in a digestion mix containing collagenase II (2 mg/ml; Worthington), elastase-I (0.04 mg/ml; Sigma), and DNase1 (5 U/ml; New England Biolabs). Cell suspensions were serially filtered through 70µm and 40µm cell strainers followed by washing twice with PBS. Aortic smooth muscle cells were sorted on a JSAN cell sorter (Bay Biosciences, Japan) based on their EGFP expression.

tag: developmental stage

value: healthy adult

value: aorta

value: aortal smooth muscle cells


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_95]

value: Smooth muscle-specific EGFP reporter mice


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_91]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_93]


title: Normal_Donor1_Day1_Rep1

tag: subject status


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_94]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_88]


title: Normal_Donor10_Day224_Rep1


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_83]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_82]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_85]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_75]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_81]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_69]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_68]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_65]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_58]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_62]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_59]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_56]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_54]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_48]


title: Th17_Rep1

value: Normal Donor

value: human Th17 cell


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_47]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_39]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_46]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_42]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_36]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_33]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_86]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_35]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_26]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_30]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_61]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_79]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_23]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_55]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_21]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_90]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_16]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_22]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_38]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_10]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_11]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_95]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_05]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_32]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_40]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_43]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_01]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_24]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_45]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_03]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_41]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_19]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_31]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_27]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_09]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_23]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_34]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_28]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_32]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_24]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_06]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run2_15]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_30]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_27]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_29]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_28]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_26]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_20]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_18]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_17]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_10]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_02]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_19]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_25]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_03]


title: EGFR- from Glioblastoma replicate3

city: NEW YORK

first: NADEJDA

middle: M

last: TSANKOVA

state: NEW YORK

address: 1425 MADISON AVENUE 9TH FLOOR

department: PATHOLOGY

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

description: GBM3 EGFRN

data_processing:
Samples were run on the HiSeq2500 System, and base calling and Q-scoring was performed with Illumina’s Real-Time Analysis (RTA) version 1.18.64. bcl2fastq 1.8.3 was used to demulitplex and convert files to the fastq format
Read alignment was done using STAR v 2.5.2b with default parameters.
Gene counts were obtained using the featureCount utility of the subread package V. 1.5.0.
Differential expression analysis on the RNAseq data was performed using the DESeq2 R package V. 1.14.1
In summary, Illumina sequencer output FASTQ files for each sample were subjected to a quality control assessment using the FASTQC package. RNAseq reads were aligned to the human genome (GENCODE GRCh38) using STAR with default settings. Gene counts were obtained using the featureCount utility of the subread package. Differential expression analysis on the RNAseq data was performed using the DESeq2 R package, which models the data with a negative binomial distribution and uses Empirical Bayes shrinkage for 5 dispersion and fold-change estimation. Gene set enrichment analysis was done utilizing the HOMER tool. The gene background set for the enrichment analysis was defined as the set of genes passing the independent filtering low expression threshold by DESeq2. All RNAseq tests were FDR adjusted for multiple testing correction.
Genome_build: Genome Reference Consortium Human Build 38 (GRCh38)
Supplementary_files_format_and_content: Microsoft Excel file containing normalized abundance measurements as outputs from DESeq2 R package.

source_name: Glioblastoma

extract_protocol:
EGFR+ and EGFR– cell populations were directly isolated from fresh GM and GBM tissues using FACS, without any prior culturing.  Upon FACS isolation, cells were collected in Trizol reagent (15596-026, Life Technologies) and flash-frozen on dry ice. Total RNA was obtained following manufacturer’s protocol, including a DNAse digestion step (Zymo Research). cDNA was generated using Clontech SMART-seq v4 (634888). Briefly, 150pg of RNA were converted to cDNA by introducing 3’ SMART-Seq CDS Primer II A and the SMART-Seq v4 Oligonucleotide. cDNA was subsequently amplified in 10-11 cycles by LD PCR and purified by Agencourt AMPure XP Kit (Beckman Coulter A63880).
Libraries were prepared using Nextera XT (FC-131-1024). Briefly, 1ng of pre-amplified cDNA was tagmented for 5 mins and subsequently amplified adding Index1 (i7) and Index2 (i5) adapters for 12 cycles. Libraries were then cleaned up using AMPure XP and pooled in equimolar conditions. Regular QC assays were applied before sequencing.

treatment_protocol: Tissues were in PIPES solution for a variable time from 1-3hours since the extraction from the patient to the tissue processing. The time from tissue dissociation to FACS isolation was approximately 3 hours.

tag: developmental stage/tumor stage

value: Glioblastoma EGFR amplification/EGFR vIII mutation


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_12]

tag: tissue


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_09]


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_04]


title: EGFR- from Germinal Matrix replicate2

description: GM2 EGFRN

source_name: Germinal Matrix

growth_protocol: EGFR+ and EGFR– cell populations were directly isolated from fresh GM and GBM tissues using FACS, without any prior culturing.

value: 19 gestational weeks


title: EGFR+ from Germinal Matrix replicate1

description: GM1 EGFRP

value: 21 gestational weeks


title: EGFR+ from Glioblastoma replicate3

description: GBM3 EGFRP


title: Improved total RNA extraction

city: Sapporo

first: Tetsuro

last: Hirose

state: Hokkaido

address: Kita-15-jo Nishi-7-chome, Kita-Ku

department: Institute for Genetic Medicine

country: Japan

institute: Hokkaido University

data_processing:
Basecalling was performed using Hiseq Control Software (version 2.0.12.0), Real Time Analysis (version 1.17.21.3), and bcl2fastq (version 1.8.3).
Sequenced reads were trimmed for adaptor sequence using cutadapt (version 1.1), then mapped to GRCh37 release 66 whole genome using TopHat (version 2.0.9) designating the library type as fr-firststrand and using parameters in default setting.
Transcripts were assembled using Cufflinks for each sample designating the library type as --library-type fr-firststrand and parameters in default setting. Transcripts from two samples were integrated by Cuffmerge with default parameters.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using Cuffdiff using parameters --max-bundle-frags 100000000 / --library-type fr-firststrand.
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include gene short name, locus, and FPKM values for each sample.

source_name: HeLa cells

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
TRI Reagent (MRC) was added to cells at a ratio of one ml reagent to 1×106 cells. Cell/reagent solution was (improved method) or was not (conventional method) put through 20 G needle for 100 times. Subsequently, total RNA was extracted according to manufacturer’s instruction.
Ribosomal RNA was depleted with Ribo-Zero Gold Kit (Epicentre). Libraries were prepared using Illumina TruSeq Stranded RNA Sample Prep Kit, according to manufacturer's instructions.

tag: extraction method

value: improved AGPC method


title: EGFR- from Glioblastoma replicate2

description: GBM2 EGFRN


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_13]


title: EGFR+ from Glioblastoma replicate1

description: GBM1 EGFRP


title: EGFR- from Glioblastoma replicate1

description: GBM1 EGFRN


title: EGFR+ from Glioblastoma replicate2

description: GBM2 EGFRP


title: Single-cell sequencing of individual murine aortal smooth muscle cells [Harmandeep_SMC_run1_11]


title: 63b_A

city: Copenhagen

first: Kristoffer

last: Vitting-Seerup

address: Ole Maaløes Vej 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

data_processing:
RNA-seq reads were aligned to hg19 with tophat2
quantification were performed with FeatureCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including raw count-values for each sample

source_name: non-responding_before treatment

extract_protocol:
RNA was extracted from 3*10 micron thick FFPE sections using Deparaffinization Solution (Qiagen, Ca. No. 19093) and RNAeasy FFPE kit (Qiagen, Ca. No. 73504).
Library preparation was carried out using the strand-specific Ovation Human FFPE RNA-seq Library System from Nugen according to the instructions from the manufacturer. 250 ng of total RNA was used for library construction.

value: glioblastoma patient

tag: subject id

tag: subject group

value: non-responding

tag: batch

tag: time point

value: before bevacizumab combination treatment

tag: gender

value: male

tag: age (yrs)

tag: first-line therapy

value: RT/TMZ+TMZ

tag: sample from primary gbm diagnosis

value: no

tag: diagnosis

value: GBM

tag: overall survival (months)

tag: rna-extraction date

tag: library preperation date


title: 5a_B

source_name: responding_after treatment

value: responding

value: after bevacizumab combination treatment


title: 63b_B

source_name: non-responding_after treatment


title: EGFR- from Germinal Matrix replicate3

description: GM3 EGFRN

value: 22 gestational weeks


title: 5a_A

source_name: responding_before treatment


title: EGFR+ from Germinal Matrix replicate3

description: GM3 EGFRP


title: EGFR+ from Germinal Matrix replicate2

description: GM2 EGFRP


title: 2000_B


title: 35_B


title: 3021_A

value: female


title: 32_A

value: yes


title: TNFa 4h Rep 1

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

data_processing:
Quality control was performed using FastQC
Reads were mapped using STAR aligner v2.5.0c
Mapped reads were counted using subread featureCounts
Read counts were normalised using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimeted file of DESeq2 normalised read counts

growth_protocol: HEK293∆RAF1:ER cells were cultured in DMEM w/o phenol red supplemented with 10% fetal calf serum, 1% pen/strep and 1% Ultraglutamine.

extract_protocol:
Total RNA was extraced with Qiagen RNeasyMini Kit
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: Before treatment, cells were starved with serum-free medium over night. Cells were then treated with 4-hydroxy tamoxifen (Sigma-Aldrich H7904, 0.5µM), Ly29002 (lifetechnologies, PHZ1144, 10µM), TNFalpha (Peprotech, 20ng/ml), TGF1beta (Pepprotech, 10ng/ml) or IFNgamma (Peprotech, 50ng/ml)

tag: cell type

value: HEK293 delta-RAF1:ER cells

tag: treated with

value: TNFa

tag: treatment duration


title: EGFR- from Germinal Matrix replicate1

description: GM1 EGFRN

tag: developmental stage/tumor stage


title: 3020_B

tag: subject status


title: TNFa 1h Rep 2


title: TNFa 4h Rep 2


title: Conventional total RNA extraction

tag: extraction method

value: conventional AGPC method


title: 3019_B

tag: subject id

tag: subject group


title: 3019_A

tag: batch

tag: time point


title: TGF1b 4h Rep 2


title: 3010_A

tag: gender

tag: age (yrs)


title: TNFa 1h Rep 1


title: AV macrophage, Transcriptome 8

first: Matthias

last: Nahrendorf

state: MA

address: 185 Cambridge St.

department: Center for Systems Biology

institute: Massachusetts General Hospital

data_processing:
transcriptome mapping: STAR version 2.3.0 using the Ensembl 67 release exon/splice-junction annotations
feature counting: HTSeq v.0.6.0 with unstranded count parameter. The 76 samples with the most reads (260K to 6.3M, median 2.1M) weres selected for further analysis.
selection of detected genes: clean.counts() routine within SCDE (Single Cell Differential Expression)
quantification of overdispersion: pagoda.varnorm() routine within SCDE. 9235 total genes were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: MHa10.cpm.txt

source_name: AV node macrophage

extract_protocol:
AV node macrophages were FACS-purified from whole AV node tissue as described above. Single macrophages were then captured using the Fluidigm C1 microfluidic chip designed for 5- to 10-µm cells according to the manufacturer’s protocol. A concentration of 1.8x105 cells per ml was used for chip loading. After cell capture, chips were examined visually to identify empty chambers, which were excluded from later analysis. Cell lysis and cDNA synthesis were performed on-chip with Clontech SMARTer Ultra Low RNA kit for the Fluidigm C1 system. Amplified cDNA was validated and quantified on an Agilent Bioanalyzer with the High Sensitivity DNA chip.
Illumina libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a modified protocol supplied by Fluidigm. Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip, and subsequently normalized and pooled to equal concentrations. The pooled libraries were quantified by qPCR using KAPA Library Quantification kit (Kapa Biosystems).

treatment_protocol: For AV node harvest, C57BL6/J mice were perfused through the left ventricle with 10 ml of ice-cold PBS. Hearts were then excised and subjected to AV node microdissection. In detail, the triangle of Koch, which contains the AV node, was excised by using the following landmarks: ostium of the coronary sinus, tendon of Todaro and septal leaflet of the tricuspid valve. After harvest, AV nodes were minced into small pieces and subjected to enzymatic digestion with 450 U/ml collagenase I, 125 U/ml collagenase XI, 60 U/ml DNase I, and 60 U/ml hyaluronidase (all Sigma) for 20 minutes at 37°C under agitation. Tissues were then triturated and cells filtered through a 40-μm nylon mesh (BD Falcon), washed and centrifuged to obtain single-cell suspensions. To purify macrophages from AV node tissue, digested samples were stained with hematopoietic lineage markers, CD11b, CD45, F4/80 and Ly6C, and macrophages were FACS-sorted using a FACSAria II cell sorter (BD Biosystems). DAPI was used as a cell viability marker. AV node macrophages were identified as (B220/CD49b/CD90.2/CD103/Ly6G/NK1.1/Ter119)low (CD45/CD11b)high Ly6Clow/int F4/80high.

tag: strain

value: AV node macrophage

tag: genotype

value: WT


title: AV macrophage, Transcriptome 9


title: AV macrophage, Transcriptome 84


title: 3005_B

value: glioblastoma patient

tag: first-line therapy

tag: sample from primary gbm diagnosis

tag: diagnosis

tag: overall survival (months)


title: 35_A

tag: rna-extraction date

tag: library preperation date


title: TGF1b 1h Rep 2

tag: cell type

tag: treated with

tag: treatment duration


title: TGF1b 4h Rep 1


title: AV macrophage, Transcriptome 83


title: AV macrophage, Transcriptome 82


title: 2000_A

tag: subject status

tag: subject id

value: non-responding


title: 3005_A

tag: subject group

tag: batch

value: before bevacizumab combination treatment


title: AV macrophage, Transcriptome 81


title: 3020_A

tag: time point

tag: gender


title: AV macrophage, Transcriptome 7

tag: strain


title: AV macrophage, Transcriptome 77

tag: genotype


title: AV macrophage, Transcriptome 78


title: 3004_B

tag: age (yrs)

tag: first-line therapy


title: TGF1b 1h Rep 1


title: Ly29002 4h Rep 2


title: Ly29002 1h Rep 2


title: AV macrophage, Transcriptome 70


title: AV macrophage, Transcriptome 71


title: AV macrophage, Transcriptome 73


title: AV macrophage, Transcriptome 76


title: 3004_A

tag: sample from primary gbm diagnosis

tag: diagnosis


title: Ly29002 1h Rep 1


title: 3003_B

tag: overall survival (months)

tag: rna-extraction date


title: AV macrophage, Transcriptome 6

tag: cell type


title: AV macrophage, Transcriptome 68


title: 3003_A

tag: library preperation date


title: AV macrophage, Transcriptome 69


title: IFNg 4h Rep 2

tag: treated with

value: IFNg

tag: treatment duration


title: IFNg 4h Rep 1


title: AV macrophage, Transcriptome 67


title: AV macrophage, Transcriptome 64


title: AV macrophage, Transcriptome 63


title: AV macrophage, Transcriptome 66


title: Ly29002 4h Rep 1


title: AV macrophage, Transcriptome 75


title: AV macrophage, Transcriptome 61


title: AV macrophage, Transcriptome 60


title: 22a_B

tag: subject status

tag: subject id

value: RT/TMZ+TMZ


title: 22a_A

tag: subject group

tag: batch


title: 1326_A

tag: time point

tag: gender


title: AV macrophage, Transcriptome 5

tag: strain

tag: genotype


title: IFNg 1h Rep 2


title: AV macrophage, Transcriptome 58


title: AV macrophage, Transcriptome 56


title: AV macrophage, Transcriptome 57


title: BSA 4h Rep 2

value: BSA


title: 1314_A

value: male

tag: age (yrs)

tag: first-line therapy

value: no

value: GBM


title: 3002_A

value: responding

tag: sample from primary gbm diagnosis

tag: diagnosis


title: AV macrophage, Transcriptome 55


title: AV macrophage, Transcriptome 54


title: BSA 4h Rep 1


title: AV macrophage, Transcriptome 53


title: 1306_B

value: after bevacizumab combination treatment

tag: overall survival (months)

tag: rna-extraction date


title: BSA 1h Rep 1

tag: cell type


title: AV macrophage, Transcriptome 52


title: IFNg 1h Rep 1

tag: treated with


title: 4OHT 4h Rep 2

tag: treatment duration


title: 1306_A

tag: subject status

value: yes

tag: library preperation date


title: AV macrophage, Transcriptome 50


title: AV macrophage, Transcriptome 4


title: 3002_B

tag: subject id

tag: subject group


title: AV macrophage, Transcriptome 51


title: 1314_B

tag: batch

tag: time point


title: AV macrophage, Transcriptome 49

tag: strain


title: 1305_B

tag: gender

value: female


title: 4OHT 4h Rep 1

value: HEK293 delta-RAF1:ER cells


title: 119b_A

tag: age (yrs)

value: RT + TMZ


title: AV macrophage, Transcriptome 44

value: AV node macrophage

tag: genotype


title: AV macrophage, Transcriptome 46

value: WT


title: AV macrophage, Transcriptome 45


title: 102b_B

value: glioblastoma patient

tag: first-line therapy

tag: sample from primary gbm diagnosis


title: 4OHT 1h Rep 1


title: AV macrophage, Transcriptome 47


title: AV macrophage, Transcriptome 48


title: 4OHT 1h Rep 2


title: 1305_A

value: non-responding

tag: diagnosis

tag: overall survival (months)


title: AV macrophage, Transcriptome 41

tag: cell type


title: AV macrophage, Transcriptome 43


title: 119b_B

tag: rna-extraction date


title: BSA 1h Rep 2

tag: treated with

tag: treatment duration


title: 102b_A

tag: subject status

value: before bevacizumab combination treatment

tag: library preperation date


title: AV macrophage, Transcriptome 34


title: AV macrophage, Transcriptome 3


title: AV macrophage, Transcriptome 33


title: AV macrophage, Transcriptome 37


title: AV macrophage, Transcriptome 35


title: AV macrophage, Transcriptome 36


title: AV macrophage, Transcriptome 38


title: AV macrophage, Transcriptome 32


title: AV macrophage, Transcriptome 39


title: AV macrophage, Transcriptome 29


title: CC rep2

city: San Francisco

first: Steven

last: Van Dyken

address: 513 Parnassus Ave

institute: University of California, San Francisco

data_processing:
Sequence alignment and splice junction estimation was performed using STAR_2.4.2a (Dobin et al., 2013)
Mappings were restricted to those that were uniquely assigned to the mouse transcriptome, as provided by Ensembl (Flicek, et al., 2014) and aggregated on a per-gene basis
Variance and differential expression assessed using DESeq2 (Anders and Huber, 2010)
Genome_build: Ensembl Mouse GRCh38.78

source_name: ChiaRed+ EpCAM+CD45- lung cells

extract_protocol:
total RNA isolated using miRNeasy micro kit (Qiagen) with on-column DNAse treatment
RNA sequencing libraries generated using Illumina TruSeq stranded mRNA kit (Illumina)

tag: tissue

value: Lung

value: C/C

tag: age

value: 14 weeks


title: AV macrophage, Transcriptome 40


title: WT rep1

source_name: EpCAM+CD45- lung cells


title: C+ rep1


title: AV macrophage, Transcriptome 28


title: C+ rep2


title: WT rep2


title: AV macrophage, Transcriptome 27


title: CC rep1


title: AV macrophage, Transcriptome 31


title: AV macrophage, Transcriptome 42


title: AV macrophage, Transcriptome 30


title: AV macrophage, Transcriptome 2


title: C+ rep3


title: WT rep3


title: AV macrophage, Transcriptome 26


title: AV macrophage, Transcriptome 22


title: AV macrophage, Transcriptome 25


title: AV macrophage, Transcriptome 20


title: AV macrophage, Transcriptome 24


title: AV macrophage, Transcriptome 23


title: LIII36

city: Durham

first: Yuan

last: Zhuang

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

data_processing:
Raw reads in fastq format 2 were masked for Illumina adapter sequences, barcodes, and Phred-scaled base qualities of 10 and less using GATK
Reads were aligned to mouse genome using default settings in Tophat for paired end sequences, which were output as BAM files and merged using Picard (http://picard.sourceforge.net/)
Fragments per kilobase of transcript per million reads (FPKM) values and differential expression analysis were done using TopHat and Cufflinks from Biospace
Broad filtering criteria were used to remove genes with below baseline levels of expression using cutsom R scripts
Z scores were calculated using Microsoft excel
Genome_build: mm9
Supplementary_files_format_and_content: excel file with FPKM values and z scores for each sample

source_name: Lymphoma cells from CD1dTet- tumor in thymus of 30 week old mouse

extract_protocol:
Total RNA was extracted from lysed tumor tissue using an RNAqueous Kit (Life Technology) according to manufacturer’s protocol
mRNA library was prepared using a TruSeq RNA Stranded mRNA kit (Illumina) according to manufacturer's protocol

value: L-DKO


title: LV69

source_name: Lymphoma cells from CD1dTet- tumor in payer's patch of 26 week old mouse


title: AV macrophage, Transcriptome 21

city: Boston


title: AV macrophage, Transcriptome 19


title: AV macrophage, Transcriptome 1


title: seminal_vesicles_rep_1

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Sequencing and base calling: RNA-seq libraries were sequenced on an Illumina HiSeq 2500 machine (Illumina, San Diego, CA, USA) with base calling by CASAVA software (version 1.8.2, Illumina, San Diego, CA, USA).
Read alignment: RNA-seq library reads were mapped to the Flybase Drosophila melanogaster release 6.06 genome with TopHat (version 2.1.0,  ‘--library-type fr-firststrand’ options, Trapnell et al., 2009).
Gene specific read counts: Gene specific read counts were determined with HTSeq-count (version 0.6.1p1, Anders et al., 2015).
Genome_build: Flybase Drosophila melanogaster release 6.06.
Supplementary_files_format_and_content: Reads are in .fastq format and contain the raw base calls from sequencing.  Alignment files are in .bam format and contain mapped reads.  Gene counts are in .txt format and contain the number of counts mapped to each gene.

growth_protocol: Flies were raised on Drosophila food (Labexpress, Ann Arbor, Michigan) (For 1 liter: yeast 15 gm, cornmeal 27 gm, sucrose 43 gm, agar 8 gm, 0.4% propionic acid and 0.15% tegosept).  at 25°C under constant light.  Males were separated from females one day after eclosion and aged for 3-4 days en masse.

extract_protocol:
Drosophila melanogaster testes/seminal vesicles were dissected from flies in phosphate buffered saline (PBS).  Testes were then separated from the basal testes terminal epithelium transition zone/seminal vesicles.  This point can roughly be considered the diameter of the dorsal to ventral axis of the seminal vesicle, anterior to the zone at which the testes and seminal vesicles meet.  Dissected samples were then stored in ice cold PBS.  Total RNA was then extracted using a Qiagen RNeasy Mini Kit (Qiagen, Valencia, Ca, USA) according to the manufacturers protocol.
200 ng of total RNA was used to prepare RNA-seq libraries with a TruSeq Stranded mRNA Library Prep Kit, using half volumes for all reactions according to the manufacturers protocol (Illumina, San Diego, CA, USA).  External RNA Control Consortium (ERCC) RNA spike-ins were added to each sample (1 pmol/sample, Pool 78B-Testes, Pool 78A-Seminal Vesicles) before poly-A RNA fragmentation (Jiang et al., 2011, Zook et al., 2012, updated ERCC information can be found in Pine et al., 2016).

value: 4-5 days

tag: Sex

value: Male

tag: developmental stage

value: Adult

value: seminal vesicles


title: AV macrophage, Transcriptome 17

tag: strain


title: AV macrophage, Transcriptome 16


title: AV macrophage, Transcriptome 18


title: testes_rep_2

source_name: testes

value: testes


title: AV macrophage, Transcriptome 15


title: testes_rep_1


title: seminal_vesicles_rep_2


title: MCF-7 siDDX54 replicate 2 IR 0h

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrueck Center

data_processing:
Basecalls were performed using CASAVA 1.8.2 or bcl2fastq v2.16.0.10. Demultiplexing and adapter removal of raw reads were performed using Flexbar (v2.5) utilizing Illumina RPI index barcodes. Reads were simultaneously filtered for quality (cutoff Phred+ 10) and length (cutoff 18 nucleotides).
We used Tophat2 (v2.1.0) (Kim et al., 2013) to align reads to the common reference composed of human genome (version hg19) and 92 sequences corresponding to synthetic RNAs in the ERCC Spike in Control (Thermo Fisher). Reads were counted in Gencode v19 exons and ERCC spike-in sequences using HTSeq-count (Anders et al., 2015). Pairwise differential expression analyses were performed by DESeq2 (Love et al., 2014) using default parameters. Normalization of read counts was performed using size factors obtained from ERCC spike-in read counts from HTSeq-count output. Transcripts with p adjusted value lower than 0.10 were considered differentially expressed.
We quantified pre-mRNA and mRNA levels by RSEM (v.1.2.20) (Li and Dewey, 2011) using bowtie (v.1.1.2) (Langmead et al., 2009) as read alignment program. We first prepared a custom annotation file by adding whole gene loci as “transcript” category in the Gencode v19 annotation GTF file (i.e. all rows with the “gene” category were modified to “transcript”). Bowtie/RSEM index was then obtained by rsem-prepare-reference program using default settings with the modified GTF file. Pre-mRNA abundance metrics (expected counts, TPM and FPKM) were considered only for genes with more than one exon and were derived from reads that mapped to the entire gene locus only (ENSG* id*s in the transcript_id column of *.isoform.expression files). For mRNA abundance we computed the sum of metrics for all annotated transcripts within the annotated gene.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (HTSeq-count read counts; RSEM read counts, TPMs and FPKMs)

source_name: MCF-7 siDDX54 IR 0h

growth_protocol: MCF-7 Flp-In cells were cultured in high glucose Dulbeco’s modified Eagle’s medium (DMEM, Thermo Fisher), supplemented with 10% (v/v) fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin/streptomycin (all from Gibco).

extract_protocol:
Cells were harvested at different time periods after irradiation (0h, 1h, 2h and 6h) by removing the media and adding 1ml Trizol (Thermo Fisher) per well. RNA was then extracted by miRNAeasy kit (Qiagen) according to manufacturer's protocol. Next, 2 µg of total RNA were treated with 0.4 U Turbo DNase (Thermo Fisher) for 30 min at 37 ºC, phenol-chlorotorm extracted, ethanol-precipitated and resuspended in water.
Equal amounts of total RNA (1 µg) and 2 µl of 1:100 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher) were mixed, adjusted to 50 µl final volume with water, and input into the Truseq unstranded mRNA kit v2 (Illumina) using 2 rounds of oligo-dT enrichment. Manufacturer's instructions were followed in all subsequent steps. cDNA libraries from different samples were multiplexed using Illumina RPI oligonucleotides and sequenced by multiplexing 6 samples per lane on a HiSeq 2000 instrument using 1x101+7 cycles.
Illumina Truseq RNA v2 kit (unstranded)

treatment_protocol: MCF-7 Flp-in cells were reverse-transfected in a 6-well format using 2 different siRNAs (1 and 3). We plated 0.5 ml Optimem per well, followed by the addition of 60 pmol siRNA and 5 µl Lipofectamine RNAimax. After a 15-20 min incubation, 2.5x105 cells in 2.5 ml of supplemented DMEM (final volume was thus 3 ml per well) were added, incubated for 48 hours and irradiated (10Gy).

tag: cell line

value: breast carcinoma epithelial cell line

tag: transfected with

tag: time point

value: 2h post irradiation

tag: barcode

value: TGACCA


title: MCF-7 siDDX54 replicate 2 IR 2h

source_name: MCF-7 siDDX54 IR 2h

value: GCCAAT


title: MCF-7 siDDX54 replicate 2 IR 6h

source_name: MCF-7 siDDX54 IR 6h

value: CTTGTA


title: AV macrophage, Transcriptome 12

value: AV node macrophage

tag: genotype

value: WT


title: AV macrophage, Transcriptome 10


title: MCF-7 siDDX54 replicate 1 IR 6h

value: 1h post irradiation

value: CAGATC


title: Cd11b-DTR_AV_7

data_processing:
transcriptome mapping: STAR version 2.3.0 using the Ensembl 67 release exon/splice-junction annotations
feature counting: HTSeq v.0.6.0 with unstranded count parameter
differential expression: exactTest routine of the edgeR R package. Read counts were normalized to counts per million and genes were excluded if (cpm) < 1 for eight or nine sample
Genome_build: mm9
Supplementary_files_format_and_content: MHa1.cpm.txt: each row shows the CPM values for all nine (9) samples for one gene

source_name: Macrophage-depleted

extract_protocol:
Total RNA was extracted with QIAzol reagent, followed by clean-up and DNase I treatment with Qiagen RNeasy Micro kit according to the manufacturer’s protocol. The RNA quality was assessed with the RNA 6000 Pico assay kit using the Agilent Bioanalyzer.
Sequencing-ready cDNA libraries were prepared using the NEBNext Ultra RNA Directional Library Prep kit for Illumina (New England BioLabs) following the manufacturer’s protocol. Bioanalyzer traces were used to confirm library size distribution. The libraries were quantified by qPCR using KAPA Library Quantification kit (Kapa Biosystems).

value: Microdissected AV node


title: Cd11b-DTR_AV_9


title: Cd11b-DTR_AV_8


title: MCF-7 siDDX54 replicate 1 IR 2h

value: ACAGTG


title: MCF-7 siDDX54 replicate 1 IR 0h

value: CGATGT


title: Cx3cr1_Cx43ko_AV_4

source_name: Cx3cr1 Cx43-/- AV node


title: Cx3cr1_Cx43ko_AV_6


title: MCF-7 mock replicate 2 IR 6h

source_name: MCF-7 mock IR 6h

value: mock

value: GTGAAA


title: Control_AV_2

source_name: Control AV node

value: Control


title: Cx3cr1_Cx43ko_AV_5


title: Control_AV_3


title: Control_AV_1


title: MCF-7 mock replicate 2 IR 2h

source_name: MCF-7 mock IR 2h

value: GTCCGC


title: MCF-7 mock replicate 2 IR 0h

source_name: MCF-7 mock IR 0h

value: AGTTCC


title: AV macrophage, Transcriptome 14


title: MCF-7 mock replicate 1 IR 2h

value: breast carcinoma epithelial cell line

value: ATGTCA