title: TK_OVOL2_rep2 [CAGE]

description: processed data file: CAGE_EdgeR.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using BWA.
Mapped CAGE tags were counted with respect to the FANTOM5-CAT TSSs (Hon et al., Nature 2017) to give a unit of CAGE tag start site (CTSS).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: CAGE_EdgeR.txt contains results from edgeR.

growth_protocol: Primary fibroblasts were grown in αMEM medium.

extract_protocol:
Total RNA was extracted by Qiagen miRNeasy Mini Kit (QIAGEN Inc.) according to the manufacturer’s instructions.
CAGE libraries were prepared as previously described (Murata et al., Methods Mol Biol 2014). Briefly, 3 μg of total RNA from each sample was subjected to reverse transcription using SuperScript III Reverse Transcriptase (Life Technologies, Carlsbad, CA, USA) with random primers. The 5-end cap structure were biotinylated by sequential oxidation with NaIO4 and biotinylation with biotin hydrazide (Vector Laboratories, Burlingame, CA, USA). After RNase I treatment (Promega, Madison, WI, USA), the biotinylated cap structure was captured with streptavidin-coated magnetic beads (Life Technologies). After ligation of 5’ and 3’ adaptors, second-strand cDNAs were synthesized with DeepVent (exo−) DNA polymerase (New England BioLabs, Ipswich, MA, USA). The double-stranded cDNAs were treated with exonuclease I (New England BioLabs) and purified.

treatment_protocol: After infection and selection with Puromycin, DOX treatment (500ng/mL) was started at day0 for 5 days (until day5). At day2, medium was changed to KGM medium. RNA samples were collected at day7.


title: MCS_OVOL2_rep1 [ATAC-seq]

status: Public on May 17 2019

type: SRA

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

description:
Transposed chromatin
processed data file: ATAC_count_annotated.txt

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Kundajelab pipeline for ATAC-seq (https://github.com/kundajelab/atac_dnase_pipelines) was used for read processing, peak calling, and quality control.
A reference peak file was created by merging all pooled peaks from all four conditions and then merging peaks closer than 100 bp.
Raw reads falls in the reference peak regions were counted individually for each sample by using bedtools multicov.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: ATAC_count_annotated.txt contains read counts for reference peaks.

molecule: genomic DNA

organism: Homo sapiens

source_name: Dermal fibroblast

growth_protocol: Primary fibroblasts were grown in αMEM medium and primary keratinocytes were grown in KGM medium.

extract_protocol:
After defreezing, viability and cell number were quantified with Countes (Invitrogen), and nuclei were extracted from approximately 25,000 live cells with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100) on ice for 5 min. Transposase reaction was then carried out.
Illumina adaptors were introduced by 9 to 12 total cycles PCR reaction. Amplified DNA fragments were then purified with QIAGEN MinElute PCR Purification Kit and size selected twice with Agencourt AMPure XP (1:1.5 and 1: 0.5 sample to beads; Beckman Coulter, Fullerton, CA, USA).

treatment_protocol: After infection and selection with Puromycin, DOX treatment (500ng/mL) was started at day0 for 5 days (until day5). At day2, medium was changed to KGM medium. Cells were collected at day7 and stored at -80 degree in cell banker solution before usage.

tag: cell type

value: Fibroblast

tag: transgene

tag: passages


title: MCS_MCS_rep1 [ATAC-seq]

value: empty vector


title: TK_OVOL2_rep1 [CAGE]

description: processed data file: CAGE_EdgeR.txt

library_source: transcriptomic

molecule: total RNA

value: TP63, KLF4, OVOL2


title: A1847 DMSO 48h 1

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

country: USA

institute: Fox Chase Cancer Center

description:
WT A1847 treated with DMSO.
DMSO Replicate 1.
mRNA enriched

data_processing:
Illumina basespace for RNA alignment.
Cufflink and Cuffdiff.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: DMSO-GSK_gene.txt: Tab-delimited text file with log2 fold change, p and q values, gene_id.

source_name: Ovarian cancer cell line

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS, 1x Penicillin/Streptomycin, 2mM L-Glutamine, and 5 ug/mL Insulin in a 37C incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using a GeneJet RNA Purification Kit (Thermo Scientific) according to manufacturer's instructions.
TruSeq stranded mRNA library kit (Cat# 20020595).

treatment_protocol: Cells were treated with DMSO or 10 nM trametinib (GSK212) for 48 hours. Media was changed and fresh drug was added 4 hours prior to collection.

tag: cell line

value: Ovarian cancer cell line

tag: treatment

value: DMSO


title: TK_MCS_rep1 [CAGE]

description: processed data file: CAGE_EdgeR.txt

value: TP63, KLF4


title: MCS_MCS_rep2 [CAGE]

description: processed data file: CAGE_EdgeR.txt


title: MCS_OVOL2_rep2 [CAGE]

description: processed data file: CAGE_EdgeR.txt


title: MCS_OVOL2_rep1 [CAGE]

description: processed data file: CAGE_EdgeR.txt


title: MCS_MCS_rep1 [CAGE]

description: processed data file: CAGE_EdgeR.txt


title: SLE969.SM [RRBS-seq]

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome (hg19) using Bismark with the Bowtie2 option.  Binary Alignment Map (BAM) files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages (available upon request)  Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix of methylated and unmethylated reads for each CpG covered by a minimum of 10 reads within each group.  For each CpG there is the chromosome location and for each sample there are three columns of data containing the sample name followed by the following extensions: ".meth", % of reads methylated; ".u", number of reads unmethylated; ".m", number of reads methylated.

source_name: SLE_Circulating B cells

extract_protocol:
DNA was extracted from FACS isolated cell populations using the AllPrep DNA/RNA Mini Kit (Qiagen).
Two aliquots of DNA were separately digested with either TaqI or MspI restriction enzymes over night and subsequently pooled for all downstream processing.  Digested DNA was end-repaired, A-tailed, and adapters containing methylated cytosines ligated on using the KAPA HyperPrep kit according to the manufacturers instructions.  Adapter-ligated DNA was bisulfite converted over using the EpiTech Bisulfite kit (Qiagen, Inc).  Bisulfite treated libraries were PCR amplified using indexed primers and the HiFi HotStart Uracil+ polymerase (KAPA Biosystems).

tag: subject status

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells

tag: cell subtype

value: Switched Memory B cells (SM)

tag: sorting markers


title: SLE969.rN [RRBS-seq]

value: Resting Naive B cells (rN)


title: SLE969.PB.PC [RRBS-seq]

value: Antigen Secreting Cell (ASC)


title: SLE969.aN [RRBS-seq]

value: Activated Naive B cells (aN)


title: fibroblasts from unaffected ctrl female

status: Public on May 18 2019

type: genomic

city: Toronto

first: James

last: Ellis

state: ON

address: 686 Bay St

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

description: Hybridized to CytoScanHD

hyb_protocol: Hybridization was performed by staff at The Centre for Applied Genomics at The Hospital for Sick Children

scan_protocol: Scanning was performed by staff at The Centre for Applied Genomics at The Hospital for Sick Children

data_processing:
The data was processed using Affymetrix Chromosome Analysis Suite (ChAS) version 3.1.0.15 (r9069)
.cychp files contain genome wide copy number data; thresholds for duplications and deletions: 10 kb or greater, containing at least 10 probes

label: biotin

source_name: primary fibroblasts 001

label_protocol: Labelling was performed by staff at The Centre for Applied Genomics at The Hospital for Sick Children

growth_protocol: iPS cells were grown in mTeSR1 medium on matrigel-coated plates

extract_protocol: Qiagen DNeasy blood and tissue kit

value: primary fibroblasts

tag: gender

value: female

tag: diagnosis

value: normal (unaffected)


title: SLE497.rN [RRBS-seq]


title: SLE497.PB.PC [RRBS-seq]


title: TK_MCS_rep2 [CAGE]

description: processed data file: CAGE_EdgeR.txt


title: SLE497.aN [RRBS-seq]


title: SLE280.SM [RRBS-seq]


title: SLE969.DN [RRBS-seq]

value: Double negative B cells (DN2)


title: SLE280.T3 [RRBS-seq]

value: Transitional 3 B cells (T3)


title: SLE497.T3 [RRBS-seq]


title: SLE280.rN [RRBS-seq]


title: SLE280.DN [RRBS-seq]


title: SLE280.PB.PC [RRBS-seq]


title: SLE233.T3 [RRBS-seq]


title: SLE233.DN [RRBS-seq]


title: SLE233.SM [RRBS-seq]


title: SLE497.DN_2 [RRBS-seq]


title: SLE280.aN [RRBS-seq]


title: SLE233.rN_2 [RRBS-seq]


title: iPS cells from unaffected control female, line 2.14

description: Hybridized to CytoScanHD

source_name: iPS cell line 001-2.14

value: iPS cells


title: SLE233.aN [RRBS-seq]


title: iPS cells from unaffected control female, line 2.6

description: Hybridized to CytoScanHD

source_name: iPS cell line 001-2.6


title: fibroblasts from male proband with ASD

description: Hybridized to CytoScanHD

source_name: primary fibroblasts 004

value: male

value: ASD


title: iPS cells from male proband with ASD, line 2.27

description: Hybridized to CytoScanHD

source_name: iPS cell line 004-2.27


title: SLE223.rN [RRBS-seq]


title: SLE969.T3 [RRBS-seq]


title: SLE223.SM [RRBS-seq]


title: SLE223.T3 [RRBS-seq]


title: SLE223.PB.PC [RRBS-seq]


title: SLE497.SM [RRBS-seq]


title: SLE223.DN [RRBS-seq]


title: SLE.603.T3 [RRBS-seq]


title: SLE.658.rN [RRBS-seq]


title: SLE.665.SM [RRBS-seq]


title: SLE223.aN [RRBS-seq]


title: SLE.658.SM [RRBS-seq]


title: SLE.658.aN [RRBS-seq]


title: SLE.665.T3 [RRBS-seq]


title: SLE.662.T3 [RRBS-seq]


title: SLE.662.aN [RRBS-seq]


title: SLE.662.rN [RRBS-seq]


title: SLE.658.DN [RRBS-seq]


title: SLE.662.SM [RRBS-seq]


title: SLE.665.DN [RRBS-seq]


title: SLE.603.rN [RRBS-seq]


title: SLE.603.aN [RRBS-seq]


title: HC917.T3 [RRBS-seq]

source_name: healthy control_Circulating B cells

value: Healthy


title: HC917.SM [RRBS-seq]


title: SLE.603.SM [RRBS-seq]


title: SLE.603.DN [RRBS-seq]


title: HC917.DN [RRBS-seq]


title: HC917.aN [RRBS-seq]


title: SLE.665.aN [RRBS-seq]


title: iPS cells from male proband with ASD, line 2.22

description: Hybridized to CytoScanHD

source_name: iPS cell line 004-2.22


title: HC917.rN [RRBS-seq]


title: SLE.662.DN [RRBS-seq]


title: SLE.658.T3 [RRBS-seq]


title: HC774.T3 [RRBS-seq]


title: HC774.DN [RRBS-seq]


title: HC774.PB.PC [RRBS-seq]


title: HC774.aN [RRBS-seq]


title: HC774.rN [RRBS-seq]


title: HC774.SM [RRBS-seq]


title: HC660.rN [RRBS-seq]


title: HC660.SM [RRBS-seq]


title: HC917.PB.PC [RRBS-seq]


title: HC643.T3 [RRBS-seq]


title: HC660.aN [RRBS-seq]


title: HC643.rN [RRBS-seq]


title: SLE.665.rN [RRBS-seq]


title: HC660.T3 [RRBS-seq]


title: HC660.DN_2 [RRBS-seq]


title: HC.650.rN [RRBS-seq]


title: HC.650.SM [RRBS-seq]


title: HC.650.T3 [RRBS-seq]


title: HC.181.T3 [RRBS-seq]


title: HC643.SM [RRBS-seq]


title: HC643.PB.PC [RRBS-seq]


title: HC.181.SM [RRBS-seq]


title: HC643.aN_2 [RRBS-seq]


title: HC643.DN [RRBS-seq]


title: HC.650.aN [RRBS-seq]


title: HC.181.rN [RRBS-seq]


title: HC.181.aN [RRBS-seq]


title: HC.181.DN [RRBS-seq]


title: HC.120.T3 [RRBS-seq]


title: HC.144.aN [RRBS-seq]


title: HC.144.SM [RRBS-seq]


title: HC.144.rN [RRBS-seq]


title: HC.144.T3 [RRBS-seq]


title: SLE.969.T3 [RNA-seq]

data_processing:
Raw sequencing reads were mapped to the hg19 version of the mouse genome using Tophat2 and the UCSC hg19 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique RefSeq gene using the summarizeOverlaps function of GenomicRanges 1.28.6 R package.
Genes were filtered for detection based on having greater than 3 reads per million (rpm) in at least 1 cell type and resulted in the expression of 11284 genes.
Genome_build: hg19
Supplementary_files_format_and_content: Annotation file containing FPKM normalized read counts for each sample.

molecule: polyA RNA

extract_protocol:
RNA was extracted from FACS isolated cell populations using the AllPrep DNA/RNA Mini Kit (Qiagen).
50 pg of total RNA was used as input for the SMART-seq v3 cDNA synthesis kit (Takara).  1 ng of cDNA was used as input for the NexteraXT kit (Illumina).


title: HC.120.aN [RRBS-seq]


title: HC.120.rN [RRBS-seq]


title: HC.120.DN [RRBS-seq]


title: SLE.969.SM [RNA-seq]


title: HC.650.DN [RRBS-seq]


title: SLE.662.SM [RNA-seq]


title: SLE.665.rN [RNA-seq]


title: SLE.662.rN [RNA-seq]


title: SLE.969.rN [RNA-seq]


title: SLE.658.T3 [RNA-seq]


title: SLE.969.aN [RNA-seq]


title: SLE.969.PbPc [RNA-seq]


title: SLE.662.T3 [RNA-seq]


title: SLE.662.DN [RNA-seq]


title: RM5-5

city: Berlin

first: Bastiaan

last: Spanjaard

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrück Center

description: barcode: 1--96

data_processing:
Library strategy: Targeted DNA-seq
Align to h2afv-GFP using bwa mem
We only consider reads for which the left mate is mapped in the forward and reverse direction, for which the left mate contains a correct barcode (a list of barcodes can be found in the file cel-seq_barcodes.csv), and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate.
To identify different scars, we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment, combined with the 3’ location of the right mate.
Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library, and those sequences that make up at least 5% of all reads in its CIGAR-class.
Genome_build: Custom
Supplementary_files_format_and_content: Abundance file of each scar in each barcode present in the library

organism: Danio rerio

source_name: Single embryos

extract_protocol:
Extraction with SEL buffer + Proteinase K (50 mM KCl, 2.5 mM MgCl2, 10 mM Tris pH 8.3, 0.045% Igepal, 0.045% Tween-20, 0.05% Gelatine and 0.1 mg/ml Proteinase K). Samples were incubated for 1 h at 60 °C and 15 min at 95 °C
GFP sequences were amplified by PCR with primers complementary to GFP, including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup (AMPure XP beads – Beckman Coulter). Finally, sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.

treatment_protocol:
Embryos were injected at the 1-cell stage with 1 nl mRNA (final concentration 300 ng/μl) in combination with an sgRNA targeting GFP (final concentration 25 ng/μl, sequence: GGTGTTCTGCTGGTAGTGGT).
A mature male zebrafish that was injected with Cas9 mRNA as embryo was mated with a wild-type male; the resulting embryos were collected.

tag: developmental stage


title: RM5-4

description: barcode: 1--96


title: HC.120.SM [RRBS-seq]


title: HC.144.DN [RRBS-seq]


title: SLE.969.DN [RNA-seq]


title: RM5-2

description: barcode: 1--96


title: SLE.658.SM [RNA-seq]


title: RM5-1

description: barcode: 1--96


title: SLE.658.aN [RNA-seq]


title: RF8-4

description: barcode: 1--96

treatment_protocol:
Embryos were injected at the 1-cell stage with 1 nl mRNA (final concentration 300 ng/μl) in combination with an sgRNA targeting GFP (final concentration 25 ng/μl, sequence: GGTGTTCTGCTGGTAGTGGT).
A mature female zebrafish that was injected with Cas9 mRNA as embryo was mated with a wild-type male; the resulting embryos were collected.


title: SLE.603.T3 [RNA-seq]


title: SLE.658.DN [RNA-seq]


title: SLE.603.SM [RNA-seq]


title: RF8-3

description: barcode: 1--96


title: RF8-2

description: barcode: 1--96


title: RF8-5

description: barcode: 1--96


title: SLE.603.DN [RNA-seq]


title: SLE.603.aN [RNA-seq]


title: RM7-2

description: barcode: 1--96


title: RM5-3

description: barcode: 1--96


title: SLE.497.T3 [RNA-seq]


title: RM7-3

description: barcode: 1--96


title: RM1

description: barcode: 1--96


title: SLE.658.rN [RNA-seq]


title: SLE.497.SM [RNA-seq]


title: SLE.603.rN [RNA-seq]


title: RF8-1

description: barcode: 1--96


title: RM7-1

description: barcode: 1--96


title: SLE.497.PbPc [RNA-seq]


title: zf1fin3-E

description: barcode: 55--66

source_name: Sectioned caudal fin pieces

treatment_protocol: Embryos were injected at the 1-cell stage with 1 nl mRNA (final concentration 300 ng/μl) in combination with an sgRNA targeting GFP (final concentration 25 ng/μl, sequence: GGTGTTCTGCTGGTAGTGGT).

value: Mature


title: zf1fin3-C

description: barcode: 20--31


title: SLE.497.aN [RNA-seq]


title: SLE.497.DN [RNA-seq]


title: SLE.497.rN [RNA-seq]


title: zf1fin3-B

description: barcode: 60--71


title: SLE.280.T3 [RNA-seq]


title: SLE.280.rN [RNA-seq]


title: zf1fin3-A

description: barcode: 30--41


title: SLE.280.SM [RNA-seq]


title: CtrlRNAP

description: barcode: 63--74

data_processing:
Align to h2afv-GFP using bwa mem
We only consider reads for which the left mate is mapped in the forward and reverse direction, for which the left mate contains a correct barcode (a list of barcodes can be found in the file cel-seq_barcodes.csv), and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate.
To identify different scars, we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment, combined with the 3’ location of the right mate.
Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library, and those sequences that make up at least 5% of all reads in its CIGAR-class.
Genome_build: Custom
Supplementary_files_format_and_content: Abundance file of each scar in each barcode present in the library

extract_protocol:
TRIzol extraction
GFP sequences were amplified by PCR with primers complementary to GFP, including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup (AMPure XP beads – Beckman Coulter). Finally, sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.

treatment_protocol: Embryos were injected at the 1-cell stage with 1 nl Cas9 protein (final concentration 1590 ng/ul)


title: CtrlDNAR

description: barcode: 75--86

treatment_protocol: Embryos were injected at the 1-cell stage with 1 nl mRNA (final concentration 300 ng/μl)


title: zf1fin3-G

description: barcode: 85--96


title: SLE.280.DN [RNA-seq]


title: SLE.280.PbPc [RNA-seq]


title: CtrlDNAP

description: barcode: 32, 33, 87--96


title: zf1fin3-F

description: barcode: 70--81


title: SLE.280.aN [RNA-seq]


title: SLE.233.T3 [RNA-seq]


title: dynamics-48h

description: barcode: 67


title: dynamics-RNA

description: barcode: 91


title: WGS-1

data_processing:
Library strategy: Whole-genome DNA-seq
For samples 1-32
Align to h2afv-GFP using bwa mem
We only consider reads for which the left mate is mapped in the forward and reverse direction, for which the left mate contains a correct barcode (a list of barcodes can be found in the file cel-seq_barcodes.csv), and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate.
To identify different scars, we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment, combined with the 3’ location of the right mate.
Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library, and those sequences that make up at least 5% of all reads in its CIGAR-class.
Genome_build: Custom
Supplementary_files_format_and_content: Abundance file of each scar in each barcode present in the library
Sample 33: WGS-1
We modified the genome sequence danRer10 by adding a sequence for the histone-GFP fusion gene, and removing chromosome five, the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome.
We use bwa mem to align the reads to this modified genome, selected reads for which both mates align, and remove duplicate reads.
We bin these reads into bins of 1,000 bases
Genome_build: danRer10, modified as indicated above
Supplementary_files_format_and_content: Abundance file of reads in each 1kb bin

source_name: Whole zebrafish

extract_protocol:
Genomic DNA from a homozygotic histone-GFP fish was extracted using DNeasy Blood & Tissue Kit (Qiagen). Following extraction, the DNA was fragmented using an S2 Focused-ultrasonicator (Covaris) with a target peak of 500 bp
For library preparation we used the NEBNext Ultra library preparation kit for Illumina (E7370S) and NEB Multiplex Oligos for Illumina (E7500L).


title: SLE.233.aN [RNA-seq]


title: SLE.233.rN [RNA-seq]


title: SLE.233.SM [RNA-seq]


title: Fin1-2 2

description: barcode: 48--85, 87--96; see Fin_barcodes.xlsx for barcode designation

data_processing:
Library strategy: Targeted DNA-seq
For samples 1-32
Align to h2afv-GFP using bwa mem
We only consider reads for which the left mate is mapped in the forward and reverse direction, for which the left mate contains a correct barcode (a list of barcodes can be found in the file cel-seq_barcodes.csv), and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate.
To identify different scars, we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment, combined with the 3’ location of the right mate.
Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library, and those sequences that make up at least 5% of all reads in its CIGAR-class.
Genome_build: Custom
Supplementary_files_format_and_content: Abundance file of each scar in each barcode present in the library
Sample 33: WGS-1
We modified the genome sequence danRer10 by adding a sequence for the histone-GFP fusion gene, and removing chromosome five, the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome.
We use bwa mem to align the reads to this modified genome, selected reads for which both mates align, and remove duplicate reads.
We bin these reads into bins of 1,000 bases
Genome_build: danRer10, modified as indicated above
Supplementary_files_format_and_content: Abundance file of reads in each 1kb bin


title: SLE.223.T3 [RNA-seq]


title: SLE.223.SM [RNA-seq]


title: CtrlRNAR

description: barcode: 51--62


title: SLE.223.rN [RNA-seq]


title: Fin1-1 1

description: barcode: 11--52; see Fin_barcodes.xlsx for barcode designation


title: SLE.223.PbPc [RNA-seq]


title: Fin1-1 2

description: barcode: 53--94; see Fin_barcodes.xlsx for barcode designation


title: Fin1-0 3

description: barcode: 49--96; see Fin_barcodes.xlsx for barcode designation


title: SLE.223.aN [RNA-seq]


title: Fin1-0 2

description: barcode: 77--82; see Fin_barcodes.xlsx for barcode designation


title: Fin1-0 1

description: barcode: 71--76; see Fin_barcodes.xlsx for barcode designation


title: PF1-4 D

description: barcode: 48--85, 87--96

treatment_protocol:
Embryos were injected at the 1-cell stage with 1 nl Cas9 protein (final concentration 1590 ng/ul) in combination with an sgRNA targeting GFP (final concentration 25 ng/μl, sequence: GGTGTTCTGCTGGTAGTGGT).
A mature female zebrafish that was injected with Cas9 protein as embryo was mated with a wild-type male; the resulting embryos were collected.


title: HC.917.T3 [RNA-seq]


title: HC.917.rN [RNA-seq]


title: PF1-4 C

description: barcode: 48--85, 87--96


title: HC.917.SM [RNA-seq]


title: SLE.233.DN [RNA-seq]


title: PF1-4 B

description: barcode: 48--83


title: HC.917.PbPc [RNA-seq]


title: PF1-4 A

description: barcode: 48--59, 84, 85, 87--96


title: Fin1-2 1


title: HC.917.DN [RNA-seq]


title: HC.917.aN [RNA-seq]


title: dCas9 injections 2

description: barcode: 10--14, 16

treatment_protocol: Embryos were injected at the 1-cell stage with 1 uCas9 (final concentration 300 ng/µl) in combination with an sgRNA targeting GFP (final concentration 25 ng/µl, sequence: GGTGTTCTGCTGGTAGTGGT).


title: HC.774.T3 [RNA-seq]


title: PF1-3 PB

description: barcode: 1--96


title: PF1-3 fast

description: barcode: 21--43


title: Fin1-0 4

description: barcode: 11--34; see Fin_barcodes.xlsx for barcode designation


title: dCas9 injections 1

description: barcode: 17--21, 26


title: HC.774.SM [RNA-seq]


title: HC.774.rN [RNA-seq]


title: Protein injections

description: barcode: 1--12

data_processing:
For samples 1-32
Align to h2afv-GFP using bwa mem
We only consider reads for which the left mate is mapped in the forward and reverse direction, for which the left mate contains a correct barcode (a list of barcodes can be found in the file cel-seq_barcodes.csv), and for which the right mate starts with the primer sequence and has a length of 76 nucleotides. The PCR primer locations were chosen such that the scar can be found in the right mate.
To identify different scars, we first classify right mate reads using the CIGAR string that describes length and position of insertions and deletions in the alignment, combined with the 3’ location of the right mate.
Within each CIGAR string we perform a subclassification based on which sequences it contains. We retain those CIGAR strings for which we see at least 20 reads in a library, and those sequences that make up at least 5% of all reads in its CIGAR-class.
Genome_build: Custom
Supplementary_files_format_and_content: Abundance file of each scar in each barcode present in the library
Sample 33: WGS-1
We modified the genome sequence danRer10 by adding a sequence for the histone-GFP fusion gene, and removing chromosome five, the location of the h2afv histone to minimize the number of reads both mapping to the fusion gene and the fifth chromosome.
We use bwa mem to align the reads to this modified genome, selected reads for which both mates align, and remove duplicate reads.
We bin these reads into bins of 1,000 bases
Genome_build: danRer10, modified as indicated above
Supplementary_files_format_and_content: Abundance file of reads in each 1kb bin

extract_protocol:
RNA was extracted from homogenized zebrafish samples with TRIzol reagent (Ambion).
GFP sequences were amplified by PCR with primers complementary to GFP, including an 8 bp barcode sequence and adapter sequences for Illumina sequencing. Samples were then pooled and subjected to magnetic bead cleanup (AMPure XP beads – Beckman Coulter). Finally, sequenceable libraries were generated by a second round of PCR with indexed primers from Illumina’s TruSeq Small RNA Sample Prep Kit.

treatment_protocol: Embryos were injected at the 1-cell stage with 1 nl Cas9 protein (final concentration 1590 ng/ul) in combination with an sgRNA targeting GFP (final concentration 25 ng/μl, sequence: GGTGTTCTGCTGGTAGTGGT).


title: HC.774.PbPc [RNA-seq]


title: HC.774.DN [RNA-seq]


title: Dynamics experiment 4: 48h

description: barcode: 51--60


title: HC.774.aN [RNA-seq]


title: Untreated ST2- Treg rep2 [HT2]

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
The ion-torrent reads were trimmed for quality using Cutadapt
These quality reads were first aligned to GRCm38 mouse Ensembl reference genome using Tophat v2.0.9, then alignment for unmapped reads using bowtie v2.1.0 in local mode
Cufflinks v2.2.1 was used to assemble the transcripts and estimate their abundances.
Cuffdiff v2.2.1 was used to perform differential gene expression between the sample sets
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample as provided by Cufflinks

organism: Mus musculus

source_name: Untreated ST2- Treg

extract_protocol:
Splenic CD4+ T cells were obtained from B6 FIR mice using negative depletion with Dynabeads (Life Technologies) . These cells were cultured for 5 days with BALB/c CD11c+ bone marrow derived dendritic cells generated as we have described (52) in media supplemented with rIL-33 (20 ng/ml; Biolegend). Cultured cells were then stained with anti-CD4 and -ST2, and the CD4+ Foxp3+ (RFP+) ST2+ population FACS sorted. Sorted cells were rested for 15-18 h in complete RPMI at 5% CO2 and 37℃, followed by a 6 hours period where they remained untreated or were stimulated with 100 ng/ml mouse rIL-33. Cells were collected and RNA extracted after lysing in TRIzol reagent (ThermoFisher).
RNA-seq libraries were prepared using Ion Total RNA-Seq Kit (Life Technologies) with GeneRead rRNA Reduction kit (Qiagen).

tag: strain

value: C57BL/6 FIR

tag: tissue

value: Spleen

value: ST2- Treg cells

value: Untreated


title: rIL-33 treated ST2- Treg [HT7]

source_name: rIL-33 treated ST2- Treg

value: rIL-33 6 hr


title: rIL-33 treated ST2+ Treg rep1 [HT8]

source_name: rIL-33 treated ST2+ Treg

value: ST2+ Treg cells


title: ST2- natural Treg [HT11]

source_name: ST2- natural Treg

value: ST2- natural Treg cells


title: rIL-33 treated ST2+ Treg rep2 [HT9]


title: Untreated ST2+ Treg rep2 [HT4]

source_name: Untreated ST2+ Treg


title: Untreated ST2+ Treg rep1 [HT3]


title: Dynamics experiment 4: 6d

description: barcode: 41--50


title: Dynamics experiment 4: 72h

description: barcode: 61--70


title: HC.660.aN [RNA-seq]

value: Circulating B cells

value: Activated Naive B cells (aN)


title: HC.660.rN [RNA-seq]

value: Resting Naive B cells (rN)


title: HC.660.DN [RNA-seq]

value: Double negative B cells (DN2)


title: HC.650.aN [RNA-seq]


title: HC.660.SM [RNA-seq]

value: Switched Memory B cells (SM)


title: HC.650.SM [RNA-seq]


title: HC.643.SM [RNA-seq]


title: HC.643.T3 [RNA-seq]

value: Transitional 3 B cells (T3)


title: HC.650.T3 [RNA-seq]


title: HC.643.rN [RNA-seq]


title: TOMO-3

description: barcode: 1--48

source_name: Sectioned embryo


title: Dynamics experiment 3: 4h, 6h, 6d

description: barcode: 4h: 11, 6h: 12, 6d: 75--80, 82--83

source_name: Pooled (4h, 6h) and single (6d) embryos


title: Dynamics experiment 4: 8h

description: barcode: 71,78--86


title: Dynamics experiment 4: 24h

description: barcode: 87--96


title: Dynamics experiment 3: 72h

description: barcode: 51--55, 84--88


title: Dynamics experiment 3: XX

description: barcode: 2h: 7, 8h: 15, 22, 24h: 32, 42, 32h: 69, 6d: 81

source_name: Pooled (2h) and single embryos


title: Dynamics experiment 4: 32h

description: barcode: 31--40


title: Dynamics experiment 3: 32h

description: barcode: 14, 47, 59, 60, 68, 70--73


title: Dynamics experiment 3: 48h

description: barcode: 56--58, 61--67


title: HC.660.T3 [RNA-seq]


title: Dynamics experiment 4: 2h, 4h, 6h

description: barcode: 2h: 76,77; 4h: 74,75; 6h: 72,73

source_name: Pooled embryos


title: Dynamics experiment 3: 24h

description: barcode: 27, 31, 33, 36, 37, 41, 43, 45


title: Untreated ST2- Treg rep1 [HT1]


title: HC.643.PbPc [RNA-seq]

value: Antigen Secreting Cell (ASC)


title: ST2+ natural Treg [HT10]

source_name: ST2+ natural Treg

value: ST2+ natural Treg cells


title: HC.643.aN [RNA-seq]

value: Healthy


title: HC.643.DN [RNA-seq]


title: HC.181.T3 [RNA-seq]


title: TOMO-2

description: barcode: 1--48


title: HC.181.SM [RNA-seq]


title: HC.181.DN [RNA-seq]


title: HC.181.rN [RNA-seq]


title: Testis S16

city: COLLEGE STATION

first: SHER AFZAL

last: KHAN

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

data_processing: HiSat2 software version 2.0.5 (Kim et al. 2015) was used to align  reads to the Tribolium genome (GCA_000002335.3_Tcas5.2_genomic_RefSeqIDs.gff, obtained from www.ncbi.nlm.nih.gov) using default parameters. Edge R software (McCarthy 2012) in “R” package was used to normalized the libraries using the trimmed mean of M-values method and for differential gene expression analysis. Lowly expressed transcripts were removed from the analysis if the counts per million (CPM) was less than five in 3 samples.

organism: Tribolium castaneum

source_name: Testes day 4 adults

growth_protocol: Beetles were reared on flour medium (95% flour, 5% yeast by weight), and caged in glass jars with tight-fitting fine mesh closures. Beetles were housed in a growth chamber at 25°C with 60-80% relative humidity and 12/12 hour light cycling

extract_protocol:
Embryos were collected at 0-5 hours and 6-11 hours respectively in three replicates (each replicate has 80-100 Embryos). Similarly, ovary, testis and carcasses from adult beetles at four days post eclosion (30 beetles in each replicate) were collected to evaluate transcriptional activity. Total RNA from these tissues was extracted with Trizol (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. After total RNA extraction, RNA was treated with Turbo DNase (Ambion/Applied Biosystems, Austin, TX).
RNAseq library was prepared using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490) for mRNA isolation and NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7530S) for library preparation according to the manufacturing instructions. Each library had a peak size of approximately 300 base pairs. cDNA library quality was assessed on an Agilent 2200 TapeStation using a High Sensitivity D1000 tape. Libraries were quantified using the Invitrogen Qubit 2.0 Fluorometer High Sensitivity dsDNA assay. All libraries were normalized to a 4 nM concentration and then pooled in equal volumes for denaturing and diluting for sequencing. The library pool was denatured and diluted to a final concentration of 1.8 pM following the Illumina NextSeq Denature and Dilution protocol including a 1% PhiX DNA spike in

value: Testes

tag: genotype

value: Wild type


title: Testis S17


title: Ovary  S15

source_name: Ovaries day4 adults

value: Ovaries


title: Male carcass S12

source_name: Male carcass lack testis

value: Male carcass


title: Noncancerous liver, JPLT08-13N

type: RNA

city: Hiroshima

first: Eiso

last: Hiyama

state: Hiroshima

address: 1-2-3, Kasumi, Minami-ku

department: Natural Science Center for Basic Research and Deve

institute: Hiroshima University

description: noncancerous liver tissue sample

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console version1.1 (RMA)  using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Noncancerous liver tissue resected at surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Total RNA was extracted by the acid guanidinium–phenol–chloroform method

treatment_protocol: Fresh tissue specimens were frozen in liquid nitrogen and stored at -80C.

value: noncancerous liver tissue

tag: age(month)

tag: Sex

value: Female

tag: histologic type

value: Well differentiated

tag: stage (pretext)

tag: chic risk   stratificationb

tag: ctnnbi gene alteration

tag: event

tag: clinical course

tag: distant metastasis


title: Ovary S13


title: Ovary S14


title: Noncancerous liver, LB6N

description: noncancerous liver tissue sample

value: Male


title: HC.144.T3 [RNA-seq]

source_name: healthy control_Circulating B cells

tag: subject status

tag: cell type

value: Circulating B cells

tag: cell subtype


title: Noncancerous liver, LB44N

description: noncancerous liver tissue sample


title: Noncancerous liver, LB11N

description: noncancerous liver tissue sample


title: Male carcass S11


title: Noncancerous liver, JPLT09-32N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT10-31N

description: noncancerous liver tissue sample


title: Noncancerous liver, LB5N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT09-35N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT08-07N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT11-01N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT10-11N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT08-12N

description: noncancerous liver tissue sample


title: zf1fin3-D

description: barcode: 40--51

source_name: Sectioned caudal fin pieces

value: Mature


title: HC.144.SM [RNA-seq]

tag: sorting markers


title: HC.144.rN [RNA-seq]

value: Resting Naive B cells (rN)


title: Tumor, JPLT08-09

description: tumor tissue sample

source_name: Tumor resected before chemotherapy

value: tumor tissue

value: Standard

value: Free

value: Alive


title: Male carcass S10


title: Noncancerous liver, JPLT07-06N

description: noncancerous liver tissue sample


title: Noncancerous liver, JPLT09-08N

description: noncancerous liver tissue sample


title: Tumor, JPLT10-11T

description: tumor tissue sample

value: Poorly differentiated

value: Deletion


title: Female carcass S9

source_name: Female carcass lack ovary

value: Female carcass


title: HC.120.T3 [RNA-seq]

value: Healthy

value: Transitional 3 B cells (T3)


title: Tumor, JPLT11-01T

description: tumor tissue sample


title: Tumor, JPLT03-11T

description: tumor tissue sample

value: Wild Type


title: Tumor, LB6T

description: tumor tissue sample

value: High

value: positive


title: Female carcass S8

value: Wild type


title: Tumor, JPLT02-09

description: tumor tissue sample

value: Female

value: Dead


title: Female carcass S7


title: HC.120.DN [RNA-seq]

value: Circulating B cells

value: Double negative B cells (DN2)


title: Embryo 6-11 hrs S6

source_name: Embryos

value: Embryos


title: HC.120.aN [RNA-seq]

value: Activated Naive B cells (aN)


title: SLE.969.T3 [ATAC-seq]

description:
SLE969_T3
SLE.969.T3.rppm

data_processing:
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Read counts for each peak were summarized using GenomicRanges and normalized to reads per peak per million and peaks annotated using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rppm) using R/Bioconductor

source_name: SLE_Circulating B cells

extract_protocol:
2000-10000 cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C.
DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

value: Systemic lupus erythematosus (SLE)


title: Embryo 6-11 hrs S5


title: SLE.969.SM [ATAC-seq]

description:
SLE969_SM
SLE.969.SM.rppm

value: Switched Memory B cells (SM)


title: HC.120.SM [RNA-seq]


title: Embryo 6-11 hrs S4


title: Embryo 0-5hrs S2


title: SLE.223.DN [RNA-seq]


title: SLE.969.Pc [ATAC-seq]

description:
SLE969_Pc
SLE.969.Pc.rppm

value: Antigen Secreting Cell (ASC)


title: SLE.969.DN [ATAC-seq]

description:
SLE969_DN
SLE.969.DN.rppm


title: Tumor, JPLT10-20T

description: tumor tissue sample

value: tumor tissue

value: Poorly differentiated

value: Alive


title: Tumor, JPLT07-01T

description: tumor tissue sample

value: Male

value: Standard

value: Free


title: Tumor, JPLT09-03T

description: tumor tissue sample

value: Well differentiated

value: Wild Type


title: Tumor, JPLT07-03

description: tumor tissue sample

value: Other


title: Hand2 cKO 1

city: Nanjing

first: Meng

last: Xia

state: JiangSu

address: XueFu Road 12

department: Model Animal Research Center

country: China

institute: Nanjing unversity

data_processing:
Base CaIllumina bcl2fastq version 2.18 were used to the basecalling
Sequenced reads with 10% low quality bases, adapters and artificial sequences (including UP1, UP2, polyA sequences) introduced during the experimental processes were trimmed by in house scripts.
The trimmed clean reads were aligned to the mm8 reference using STAR (v2.5.1b) with default settings (Trapnell et al., 2009).
Cufflinks (v2.2.1) with defualt settings was used to quantify transcription levels of annotated genes (Trapnell et al., 2010), and FPKM were calculated
FPKM values were log2-transformed with an offset value of 1.0.
Genome_build: mm8
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample

source_name: embryos

extract_protocol:
aDPW and OFTs were dissected from embryos and pooled. RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aDPW+OFT

tag: developmental stage

tag: genotype/variation

value: Hand2flox/flox; Mef2c-AHF-Cre


title: Tumor, JPLT00-26

description: tumor tissue sample

tag: tissue

value: High

value: Deletion

value: Dead

value: positive


title: Tumor, JPLT08-18T

description: tumor tissue sample

value: Female


title: Tumor, JPLT13-22T

description: tumor tissue sample


title: Tumor, JPLT01-20T

description: tumor tissue sample


title: Hand2 cKO 3

tag: strain


title: Embryo 0-5hrs S1

value: Embryos

tag: genotype

value: Wild type


title: Hand2 cKO 2


title: Control2

value: control


title: SLE.969.aN [ATAC-seq]

description:
SLE969_aN
SLE.969.aN.rppm

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells

value: Activated Naive B cells (aN)


title: Control3


title: Embryo 0-5hrs S3


title: Control1


title: RA_stroma_sample

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
The Cell Ranger Single Cell Software Suite 2.0.2 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Cell Ranger commands used to produce this aggregated dataset:
cellranger count --id=RA_stroma_sample  --transcriptome=refdata-cellranger-mm10-1.2.0  --expect-cells=3000 ...
Genome_build: mm10
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcode information for each read, stored as TAG fields; h5: aggregated count matrix of 1167 cells in hdf5 format.

source_name: Bone Marrow

growth_protocol: ex vivo FACS sorted VCAM-1+CD45-Ter119-CD31- BM cells

extract_protocol: 10X Genomics platform using the Single Cell 3’ Reagent Kit V2 (10x Genomics) following the manufacturer’s instructions


title: SLE.280.SM [ATAC-seq]

description:
SLE280_SM
SLE.280.SM.rppm

value: Switched Memory B cells (SM)


title: Tumor, JPLT08-12T

description: tumor tissue sample

value: tumor tissue

tag: age(month)

tag: Sex

value: Male

value: Poorly differentiated

value: Standard

value: Free

value: Alive


title: Tumor, JPLT08-11

description: tumor tissue sample

tag: histologic type

tag: stage (pretext)

value: Intermediate


title: SLE.280.DN [ATAC-seq]

description:
SLE280_DN
SLE.280.DN.rppm

value: Double negative B cells (DN2)


title: Isl4-Teff-Lo

city: Houston

first: Maria

last: Bettini

address: 1102 Bates St

institute: Baylor College of Medicine

data_processing:
NextSeq Control Software v2.0 used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using TopHat Alignment v1.0.0
Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0
Genome_build: RefSeq mm10
Supplementary_files_format_and_content: abundance measurements

source_name: CD5 low effector T cells

extract_protocol:
TritonX-100 cell lysis, reverse transcription, cDNA amplification
Nextera XT

value: NOD

value: pancreatic islets and spleen

tag: age

value: 6-9 wks


title: Isl3-Teff-Lo


title: Isl4-Teff-Hi

source_name: CD5 high effector T cells


title: Isl3-Teff-Hi


title: SLE.233.SM [ATAC-seq]

description:
SLE233_SM
SLE.233.SM.rppm


title: SLE.233.T3 [ATAC-seq]

description:
SLE233_T3
SLE.233.T3.rppm

value: Transitional 3 B cells (T3)


title: female_40d_C

city: Jupiter

first: Ronald

middle: L

last: Davis

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: The Scripps Research Institute - Scripps Florida

data_processing:
Paired-end sequencing reads were trimmed to remove adapter sequences and low-quality base reads using Trimmomatic (v0.35) with standard settings.
Samples were aligned against the full D. melanogaster genome using the splice-aware STAR aligner.
The HTSeq-count script was used in “union” mode to count reads that mapped unambiguously to annotated features on the assembled genome.
Genome_build: dm6 (UCSC)
Supplementary_files_format_and_content: Tab-delimited text file contains read counts/gene

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
RNA was isolated from each sample using the Qiagen RNeasy Plus Micro Kit (Qiagen, Venlo, Netherlands) and treated with DNaseI using the TURBO DNA-free kit (Life Technologies, Carlsbad, CA), according to the manufacturers’ instructions.
Twenty-five nanograms of RNA from each sample was used to generate cDNA libraries using the Ovation Universal RNA Seq V2 Kit for Drosophila (Nugen, San Carlos, CA) according to manufacturer’s instructions.

value: Canton-S

value: female

value: 40 days

value: brain


title: male_40d_B

value: male


title: male_40d_A


title: Tumor, LB11T

description: tumor tissue sample

value: tumor tissue

value: Well differentiated

tag: chic risk   stratificationb

tag: ctnnbi gene alteration

value: Deletion

tag: event


title: SLE.233.DN [ATAC-seq]

description:
SLE233_DN
SLE.233.DN.rppm

tag: subject status

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells


title: Tumor, JPLT08-07

description: tumor tissue sample

value: Male

value: Standard

value: Wild Type

tag: clinical course

value: Dead

tag: distant metastasis


title: P53_WWOX_DKO_4 (4470)

city: Jerusalem

first: Suhaib

middle: Khaled

last: Abdeen

address: Ein kerem

department: Immunology and cancer research

country: Israel

institute: Hebrew Univeristy

description: DESeq2_final 14-7-2018

data_processing:
Trimming and filtering of raw reads  The NextSeq basecalls files were converted to fastq files using the bcl2fastq (v2.17.1.14) program with default parameters. The provided SampleSheet.csv file contained samples' names and barcodes only, so  no trimming or filtering was done at this stage and a fastq file was created for each sample separately.  Raw reads (fastq files) were inspected for quality issues with FastQC (v0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). According to the FastQC report, reads were quality-trimmed at both ends, using in-house Perl scripts, with a quality threshold of 32. In short, the scripts use a sliding window of 5 bases from the read's end and trim one base at a time until the average quality of the window passes the given threshold. Following quality-trimming, adapter sequences were removed with cutadapt (version 1.7.1, http://cutadapt.readthedocs.org/en/stable/), using a minimal overlap of 1 (-O parameter), allowing for read wildcards, and filtering out reads that became shorter than 15 nt (-m parameter). The remaining reads were further filtered to remove very low quality reads, using the fastq_quality_filter program of the FASTX package (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/), with a quality threshold of 20 at 90 percent or more of the read's positions.
Mapping and differential expression analysis  The processed fastq files were mapped to the mouse transcriptome and genome using TopHat (v2.0.13). The genome version was GRCm38, with annotations from Ensembl release 84. Mapping allowed up to 5 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 10 (full command: tophat -G genes.gtf -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 20 --read-realign-edit-dist 3 --library-type fr-firststrand genome processed.fastq).  For the statistics file, quantification was done using htseq-count (version 0.6.0, http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). Strand information was set to 'reverse', and an annotation file that lacked information for genes of type IG, TR, Mt, rRNA, tRNA, miRNA, misc_RNA, scRNA, snRNA, snoRNA, sRNA, scaRNA, piRNA, vaultRNA, ribozyme, artifact and LRG_gene, was used.  For further analysis, quantification was done with the Cufflinks package (v2.2.1), using the cuffquant program with the genome bias correction (-b parameter), multi-mapped reads assignment algorithm (-u parameter) and masking for genes of the same types as above (IG, TR, etc.) (-M parameter). Strand directionallity was given by the --library-type fr-firststrand parameter. Raw counts were obtained by running cuffnorm on the cuffquant output.  Normalization and differential expression were done with the DESeq2 package (version 1.10.1). Genes with a sum of counts less than 2 over all samples were filtered out prior to normalization, then dispersion and size factors were calculated. Differential expression was calculated using a design which included the genotype factor, compensating for any run effects (both P53_WWOX_DKO and WWOX_KO_T genotypes included samples from 2 different runs). Calculations were performed with default parameters. All required comparisons were performed with a significance threshold of padj<0.1, using default parameters. Comparisons between normal  and cancer samples were performed with the lfcThreshold (changing the default testing for any change to such that is above a given threshold), setting its value to 0.7 (~1.6 fold). Several quality control assays, such as counts distributions and principal component analysis, as well as differential expression results, were calculated and visualized in R (version 3.2.1, with packages 'RColorBrewer_1.1-2', 'pheatmap_1.0.8' and 'ggplot2_2.1.0').  The principle component analysis showed that sample P53_WWOX_DKO_4 harbored an additional, unknown, source of variation, thus might be an outlier. Hence, an analysis which excluded this sample (using the same parameters otherwise) was also performed (termed All_noDKO4).  In addition, samples in this experiment came from two different mice strains, introducing a source of variation which might not be directly related to the different genotypes. For each strain, an analysis was performed which included only its own samples, calculating the intra-strain comparisons (using the same parameters as above).  Results (for all analyses) were then combined with gene details (such as symbol, Entrez accession, etc.) taken from the results of a BioMart query (Ensembl, release 84) to produce the final Excel file.
Genome_build: mm10
Supplementary_files_format_and_content: Normalization and differential expression were done with the DESeq2 package (version 1.10.1).

source_name: mammary tumor

extract_protocol:
RNA extracted from tumors using TRI reagent (Biolab), then chloroform was added. The upper layer was taken and washed with isopropanol and then with ethanol 75%. The RNA was eluted using DPEC water
Libraries were made using KAPA Single-Indexed Adapter Kit (Illumina, Massachusetts, USA)

value: Mixed background

tag: genotyping

value: Wwox fl/fl Trp53 fl/fl MMTV-cre +

value: 270 days


title: Tumor, JPLT07-10

description: tumor tissue sample

value: Alive


title: SLE.233.aN [ATAC-seq]

description:
SLE233_aN
SLE.233.aN.rppm

tag: cell type

tag: cell subtype

value: Activated Naive B cells (aN)

tag: sorting markers


title: Tumor, JPLT99-15T

description: tumor tissue sample

tag: tissue

value: Free


title: P53_WWOX_DKO_3 (4524)

description: DESeq2_final 14-7-2018

tag: strain

value: 225 days


title: Tumor, JPLT06-24T

description: tumor tissue sample

tag: age(month)

value: Poorly differentiated


title: Tumor, LB5T

description: tumor tissue sample

value: tumor tissue

tag: Sex


title: male_40d_C

value: Canton-S

value: male

value: 40 days

value: brain


title: Tumor, JPLT07-25

description: tumor tissue sample

value: Male

tag: histologic type

value: Well differentiated

value: Deletion


title: SLE.223.T3 [ATAC-seq]

description:
SLE223_T3
SLE.223.T3.rppm

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells

value: Transitional 3 B cells (T3)


title: Tumor, JPLT09-35T

description: tumor tissue sample

value: Female

tag: stage (pretext)

value: Standard


title: Tumor, JPLT02-06

description: tumor tissue sample

value: Wild Type

value: Dead


title: P53_WWOX_DKO_2 (4257)

description: DESeq2_final 14-7-2018

value: Mixed background

value: Wwox fl/fl Trp53 fl/fl MMTV-cre +

tag: age

value: 150 days


title: Tumor, JPLT08-39T

description: tumor tissue sample

value: tumor tissue

tag: chic risk   stratificationb

value: Alive


title: male_20d_B

value: Canton-S

value: male

value: 20 days


title: female_40d_B

value: female

value: 40 days

value: brain


title: P53_WWOX_DKO_1 (4382)

description: DESeq2_final 14-7-2018

value: 225 days


title: SLE.223.DN [ATAC-seq]

description:
SLE223_DN
SLE.223.DN.rppm

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells

value: Double negative B cells (DN2)


title: SLE.223.SM [ATAC-seq]

description:
SLE223_SM
SLE.223.SM.rppm

value: Switched Memory B cells (SM)


title: P53_KO_2 (4465)

description: DESeq2_final 14-7-2018

value: Wwox +/+ Trp53 fl/fl MMTV-cre +

value: 245 days


title: Tumor, JPLT10-31T

description: tumor tissue sample

value: Female

value: Well differentiated

value: Standard

tag: ctnnbi gene alteration

value: Free


title: P53_KO_1 (4552)

description: DESeq2_final 14-7-2018

value: Mixed background

value: 235 days


title: HC.917.T3 [ATAC-seq]

description:
HC917_T3
HC.917.T3.rppm

value: Healthy

value: Transitional 3 B cells (T3)


title: WWOX_KO_T_4 (5663)

description: DESeq2_final 14-7-2018

value: Wwox fl/fl MMTV-cre +

value: 240 days


title: female_20d_C

value: Canton-S

value: female

value: 20 days

value: brain


title: SLE.223.aN [ATAC-seq]

description:
SLE223_aN
SLE.223.aN.rppm

value: Systemic lupus erythematosus (SLE)

value: Circulating B cells

value: Activated Naive B cells (aN)


title: female_40d_A

value: 40 days


title: female_20d_B


title: Tumor, JPLT08-14

description: tumor tissue sample

value: tumor tissue

value: Male

value: Poorly differentiated

value: High

tag: event

value: Dead

value: positive


title: WWOX_KO_T_3 (5616)

description: DESeq2_final 14-7-2018

value: 190 days


title: HC.917.SM [ATAC-seq]

description:
HC917_SM
HC.917.SM.rppm

tag: subject status

value: Healthy

value: Switched Memory B cells (SM)


title: Tumor, JPLT08-13T

description: tumor tissue sample

value: Female

value: Well differentiated

value: Standard

value: Deletion

value: Free

tag: clinical course

value: Alive


title: female_20d_A

value: Canton-S

value: female

value: 20 days

value: brain


title: HC.917.Pc [ATAC-seq]

description:
HC917_Pc
HC.917.Pc.rppm

value: Circulating B cells

value: Antigen Secreting Cell (ASC)


title: male_20d_C

value: male


title: WWOX_KO_T_2 (5540)

description: DESeq2_final 14-7-2018

value: Wwox fl/fl MMTV-cre +

value: 270 days


title: male_30d_C

value: 30 days


title: HC.917.DN [ATAC-seq]

description:
HC917_DN
HC.917.DN.rppm

value: Healthy

value: Double negative B cells (DN2)


title: male_20d_A


title: WWOX_KO_T_1 (5528)

description: DESeq2_final 14-7-2018

value: 280 days


title: male_30d_B


title: Tumor, JPLT09-31T

description: tumor tissue sample

value: tumor tissue

value: Female

value: Poorly differentiated

value: Intermediate

tag: distant metastasis


title: female_30d_B

value: Canton-S


title: female_30d_C

value: female


title: HC.917.aN [ATAC-seq]

description:
HC917_aN
HC.917.aN.rppm

value: Activated Naive B cells (aN)


title: HC.774.T3 [ATAC-seq]

description:
HC774_T3
HC.774.T3.rppm

value: Transitional 3 B cells (T3)


title: WWOX_KO_N_2 (5713)

description: DESeq2_final 14-7-2018

source_name: normal mammary epithelial cells

tag: genotyping

value: 150 days


title: WWOX_KO_N_3 (5715)

description: DESeq2_final 14-7-2018


title: female_30d_A

value: brain


title: WT_N_3 (5711)

description: DESeq2_final 14-7-2018

value: Wild type


title: WWOX_KO_N_1 (5712)

description: DESeq2_final 14-7-2018

value: Wwox fl/fl MMTV-cre +


title: Tumor, JPLT09-15T

description: tumor tissue sample

value: Well differentiated

value: Standard

value: Deletion

value: Free

value: Alive


title: WT_N_2 (5699)

description: DESeq2_final 14-7-2018

value: 260 days


title: male_5d_B

value: male

value: 5 days


title: Tumor, JPLT01-03

description: tumor tissue sample

value: tumor tissue

value: Female

value: High

value: Dead

value: positive


title: Tumor, LB44T

description: tumor tissue sample

value: Poorly differentiated

value: Intermediate

value: Wild Type


title: WT_N_1 (5698)

description: DESeq2_final 14-7-2018

value: Wild type


title: Tumor, JPLT02-11

description: tumor tissue sample

value: Male

value: Well differentiated


title: male_5d_C

value: Canton-S

value: brain


title: male_5d_A


title: HC.660.T3 [ATAC-seq]

description:
HC660_T3
HC.660.T3.rppm

value: Healthy

tag: cell type

value: Circulating B cells

value: Transitional 3 B cells (T3)


title: Tumor, JPLT09-08T

description: tumor tissue sample

value: Deletion

value: Free

value: Alive


title: Tumor, JPLT08-21T

description: tumor tissue sample

value: tumor tissue

value: High


title: HC.774.DN [ATAC-seq]

description:
HC774_DN
HC.774.DN.rppm

tag: cell subtype

value: Double negative B cells (DN2)


title: HC.774.Pc [ATAC-seq]

description:
HC774_Pc
HC.774.Pc.rppm

value: Antigen Secreting Cell (ASC)

tag: sorting markers


title: HC.774.SM [ATAC-seq]

description:
HC774_SM
HC.774.SM.rppm

value: Switched Memory B cells (SM)


title: HC.660.Pc [ATAC-seq]

description:
HC660_Pc
HC.660.Pc.rppm


title: female_5d_C

value: female

value: 5 days

tag: tissue


title: HC.660.SM [ATAC-seq]

description:
HC660_SM
HC.660.SM.rppm


title: female_5d_B

tag: strain


title: Tumor, JPLT12-24T

description: tumor tissue sample

tag: age(month)

value: Male

value: Wild Type

value: Dead

value: positive


title: HC.660.aN [ATAC-seq]

description:
HC660_aN
HC.660.aN.rppm

value: Healthy

value: Activated Naive B cells (aN)


title: female_5d_A

value: Canton-S

tag: Sex

value: brain


title: HC.643.T3 [ATAC-seq]

description:
HC643_T3
HC.643.T3.rppm

value: Circulating B cells

value: Transitional 3 B cells (T3)


title: DDX3_P_2

city: Lund

first: Göran

last: Jönsson

address: Medicon Village

country: Sweden

institute: Lund University

data_processing:
Raw sequencing read data were demultiplexed and collated by library barcode into sample data sets.
TopHat 2 was used to align reads to the human reference genome hg38 together with transcript annotations from the UCSC knownGenes table.
Cufflinks 2.2.1 was used to calculate FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file containing FPKM values per transcript.

extract_protocol:
RNA was extracted from either total RNA, or from the fraction of polysomal RNA isolated by sucrose gradient fractionation
RNA libraries were prepared for sequencing using standard Illumina protocols
Paired end sequencing of 75 bp reads on an Illumina NextSeq 500 instrument

value: Melanoma cell line

tag: cell line

tag: sirna

tag: replicate experiment

tag: rna fraction

value: polysomal RNA


title: DDX3_TOT_2

value: total RNA


title: Tumor, JPLT06-23

description: tumor tissue sample

value: tumor tissue

tag: histologic type

value: Poorly differentiated

tag: stage (pretext)

tag: chic risk   stratificationb

value: Intermediate

tag: ctnnbi gene alteration

value: Deletion


title: Tumor, JPLT00-32-2

description: tumor tissue sample

value: Female

value: Well differentiated

value: High

tag: event

tag: clinical course

tag: distant metastasis


title: Tumor, JPLT07-26

description: tumor tissue sample

value: Male

value: Standard

value: Free

value: Alive


title: Tumor, JPLT00-19

description: tumor tissue sample

value: Wild Type

value: Dead


title: DDX3_P_1

tag: cell type


title: HC.643.SM [ATAC-seq]

description:
HC643_SM
HC.643.SM.rppm

tag: subject status

value: Healthy

value: Circulating B cells

tag: cell subtype

value: Switched Memory B cells (SM)

tag: sorting markers


title: HC.643.Pc [ATAC-seq]

description:
HC643_Pc
HC.643.Pc.rppm

value: Antigen Secreting Cell (ASC)


title: CTRL_TOT_2

value: Melanoma cell line

value: Control

value: total RNA


title: CTRL_P_2

value: polysomal RNA


title: DDX3_TOT_1


title: HC.1646.T3 [ATAC-seq]

description:
HC1646_T3_S30
HC.1646.T3.rppm

value: Transitional 3 B cells (T3)


title: Tumor, JPLT08-05P

description: tumor tissue sample

source_name: Tumor resected after chemotherapy

tag: tissue

value: tumor tissue

tag: age(month)

value: Female

value: Well differentiated

value: Deletion


title: HC.1646.rN [ATAC-seq]

description:
HC1646_rN_S29
HC.1646.rN.rppm

value: Resting Naive B cells (rN)


title: HC.643.DN [ATAC-seq]

description:
HC643_DN
HC.643.DN.rppm

value: Double negative B cells (DN2)


title: Tumor, JPLT08-35

description: tumor tissue sample

tag: Sex

value: Male

value: Standard

value: Free

value: Alive


title: CTRL_P_1

tag: cell line

tag: sirna


title: S3_PEBL

city: Singapore

first: Dario

last: Campana

address: 14 medical drive, MD6 #09-02

department: Pediatrics

country: Singapore

institute: National University of Singapore

data_processing:
Reads were mapped to human genome reference hg19 using STAR
Reads aligned to each were counted using featureCounts
Expression level was calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
The expression levels were log transformed, followed by batch effect correction using ComBat of sva package
The expression levels of 44 selected genes were reported
Genome_build: hg19
Supplementary_files_format_and_content: The processed data "expression" is the excel sheet containing the normalized expression of the 44 selected genes in the 6 samples.
Supplementary_files_format_and_content: The processed data "expressionall" is the excel sheet containing the normalized expression of all genes in the 6 samples.

source_name: peripheral blood NK cells from healthy donor

growth_protocol: NK cells were grown in Stem Cell Growth Medium (SCGM) from CellGenix

extract_protocol:
Trizol extraction
Whole transcriptome mRNA sequencing library preparation was performed using TruSeq stranded mRNA library prep kit (Illumina).

treatment_protocol: NKG2A+ NK cells were isolated and subsequently transduced with MSCV-GFP (Mock) and MSCV-PEBL-GFP

tag: donor id

tag: sample type

value: PEBL


title: Tumor, JPLT12-12T

description: tumor tissue sample

tag: histologic type

tag: stage (pretext)

value: High

value: positive


title: HC.1646.PbPc [ATAC-seq]

description:
HC1646_PbPc_S33
HC.1646.PbPc.rppm

value: Healthy

value: Circulating B cells

value: Antigen Secreting Cell (ASC)


title: Tumor, JPLT07-06T

description: tumor tissue sample

value: Poorly differentiated

tag: chic risk   stratificationb

value: Intermediate

tag: ctnnbi gene alteration

value: Wild Type


title: S3_Control

value: Control


title: S2_Control


title: Tumor, JPLT01-01T

description: tumor tissue sample

value: tumor tissue

value: Female

tag: event

tag: clinical course


title: CTRL_TOT_1

tag: cell type

value: Melanoma cell line

tag: replicate experiment

tag: rna fraction

value: total RNA


title: HC.1252.T3 [ATAC-seq]

description:
HC1252_T3_S41
HC.1252.T3.rppm

tag: subject status

tag: cell subtype

value: Transitional 3 B cells (T3)

tag: sorting markers


title: HC.1252.SM [ATAC-seq]

description:
HC1252_SM_S43
HC.1252.SM.rppm

value: Switched Memory B cells (SM)


title: HC.1252.rN [ATAC-seq]

description:
HC1252_rN_S40
HC.1252.rN.rppm

value: Resting Naive B cells (rN)


title: S1_Control


title: HC.1252.DN [ATAC-seq]

description:
HC1252_DN_S44
HC.1252.DN.rppm

value: Double negative B cells (DN2)


title: HC.1252.PbPc [ATAC-seq]

description:
HC1252_PbPc_S45
HC.1252.PbPc.rppm


title: Tumor, JPLT10-05

description: tumor tissue sample

tag: tissue

tag: age(month)

tag: Sex

value: Other

value: High

value: Deletion

value: Dead

tag: distant metastasis


title: S1_PEBL

tag: donor id

tag: sample type

value: PEBL


title: Tumor, JPLT11-14T

description: tumor tissue sample

value: Male

tag: histologic type

value: Well differentiated

tag: stage (pretext)

value: Standard

value: Free

value: Alive


title: Tumor, JPLT07-27

description: tumor tissue sample

value: tumor tissue

tag: chic risk   stratificationb

tag: ctnnbi gene alteration


title: BMSC2_RNA-seq

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

description:
stable cell line
BMSC2.fq.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

source_name: human bone marrow MSC line 2

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 2000.

value: human bone marrow MSC line 2


title: S2_PEBL


title: Tumor, JPLT09-32T

description: tumor tissue sample

value: Female

value: Wild Type

tag: event

tag: clinical course


title: HC.1252.aN [ATAC-seq]

description:
HC1252_aN_S42
HC.1252.aN.rppm

value: Healthy

tag: cell type

value: Circulating B cells

value: Activated Naive B cells (aN)


title: HC.1141.rN [ATAC-seq]

description:
HC1141_rN_S24
HC.1141.rN.rppm

value: Resting Naive B cells (rN)


title: Tumor, JPLT09-34

description: tumor tissue sample


title: Tumor, JPLT00-15T

description: tumor tissue sample

value: Poorly differentiated


title: HC.1141.PbPc [ATAC-seq]

description:
HC1141_PbPc_S28
HC.1141.PbPc.rppm

value: Antigen Secreting Cell (ASC)


title: hiPSC-NMP-MSC_RNA-seq

description:
stable cell line
other RNA-Seq data.fq.xls

source_name: hiPSC-NMP-derived MSC

value: hiPSC-NMP-derived MSC


title: H9-NMP-MSC2_RNA-seq

source_name: H9-NMP-derived MSC line 2

value: H9-NMP-derived MSC line 2


title: D_Fibroblast_chemo_1.

city: Los Angeles

first: Xiaojiang

last: Cui

state: CA

address: 3884 Fredonia  Dr#F

department: Surgery Dept

institute: Cedars Sinai Medical Center

data_processing:
Tophat2 (2.0.7) [1] was applied to align sequencing reads to the reference mouse genome (GRCm38/mm10).
The relative gene expression RPKM and read counts were estimated using SAMMate (2.7.4) and Ensembl database (Mus Musculus.GRCm38.82).
Protein coding genes with at least 2 RPKM on average in either condition were used to perform the differential gene expression analysis ( fibroblast ctrl vs fibroblast chemo ) using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: File includes RPKM values for each Sample

source_name: mouse lung fibrolasts

extract_protocol:
RNA was isolated from the  using RNeasy Mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: BALB/c

tag: genotype

value: wild-type

value: lung

value: fibrolasts

tag: age

value: 4 weeks

tag: treatment

value: chemokines CXCL1/2/8


title: E_Fibroblast_chemo_2.

tag: tissue


title: B_Fibroblast_ctrl_2

value: control


title: H9-NMP-MSC1_RNA-seq

source_name: H9-NMP-derived MSC line 1

value: H9-NMP-derived MSC line 1


title: HC.1085.T3 [ATAC-seq]

description:
HC1085_T3_S35
HC.1085.T3.rppm

source_name: healthy control_Circulating B cells

tag: subject status

tag: cell subtype

value: Transitional 3 B cells (T3)

tag: sorting markers


title: Soleus-Wild-Type

city: Los angeles

first: Xiangming

last: Ding

address: 650 Charles E Young Dr S, Los Angeles, CA 90095

institute: UCLA

data_processing:
Bowtie was used fo the alignment and RSEM was used for the gene counting. TMM method in the edgeR package was used for the gene expression normalization
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements

source_name: Soleus from aged wildtype mice

extract_protocol:
RNA was extracted form tissue using the Qiagen Rneasy mini kit
library was constructed using the Kapa strand mRNA library kit

value: WT

value: Soleus

value: 11-12 months


title: Soleus-EXOs

source_name: Soleus from aged mdx mice treated with Exosomes

value: mdx


title: Soleus-Vehicle

source_name: Soleus from aged mdx mice treated with vehicle


title: H1-NMP-MSC_RNA-seq

source_name: H1-NMP-derived MSC

value: H1-NMP-derived MSC


title: HC.1085.SM [ATAC-seq]

description:
HC1085_SM_S37
HC.1085.SM.rppm

value: Healthy

value: Circulating B cells

value: Switched Memory B cells (SM)


title: Soleus-CDCs

source_name: Soleus from aged mdx mice treated with CDCs


title: hiPSC-NMP-PM_RNA-seq

source_name: hiPSC-NMP-derived paraxial mesoderm cells


title: H9-NMP-PM_RNA-seq

source_name: H9-NMP-derived paraxial mesoderm cells

value: H9-NMP-derived paraxial mesoderm cells


title: Heart-Wild-Type

source_name: heart from aged wildtype mice

value: Heart


title: A_Fibroblast_ctrl_1

value: BALB/c

value: wild-type

value: lung


title: BMSC1_RNA-seq

description:
stable cell line
BMSC1.fq.xlsx

source_name: human bone marrow MSC line 1

value: human bone marrow MSC line 1


title: HC.1085.rN [ATAC-seq]

description:
HC1085_rN_S34
HC.1085.rN.rppm

value: Resting Naive B cells (rN)


title: HC.1085.PbPc [ATAC-seq]

description:
HC1085_PbPc_S39
HC.1085.PbPc.rppm

value: Antigen Secreting Cell (ASC)


title: H1-NMP-PM_RNA-seq

source_name: H1-NMP-derived paraxial mesoderm cells

value: H1-NMP-derived paraxial mesoderm cells


title: Heart-EXOs

source_name: heart from aged mdx mice treated with Exosomes


title: hiPSC_RNA-seq

description:
stable cell line
hiPSC.fq.xlsxhiPSC.fq.xlsx

source_name: undifferentiated hiPSC

value: undifferentiated hiPSC


title: HC.1141.DN [ATAC-seq]

description:
HC1141_DN_S27
HC.1141.DN.rppm

value: Double negative B cells (DN2)


title: HC.1085.DN [ATAC-seq]

description:
HC1085_DN_S38
HC.1085.DN.rppm


title: HC.1085.aN [ATAC-seq]

description:
HC1085_aN_S36
HC.1085.aN.rppm

value: Activated Naive B cells (aN)


title: Heart-CDCs

source_name: heart from aged mdx mice treated with CDCs

value: mdx

value: 11-12 months


title: H9_RNA-seq

source_name: undifferentiated H9 embryonic stem cells


title: JHUEM14_Veh_input

city: Brisbane

first: Tracy

last: O'Mara

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
Mapping and analysis of ChIP-seq reads were performed using the ENCODE analysis pipeline, Histone ChIP-seq Unary Control (GRCh37), with DNAnexus software tools (https://dnanexus.com)
Bed files contain replicated peaks across biological replicates p<0.1 with fold change >1.15
Genome_build: GRCh37
Supplementary_files_format_and_content: broadpeak bed files

growth_protocol: Cell lines were authenticated using STR profiling and confirmed to be negative for mycoplasma contamination. Ishikawa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies #1195-065) with 10% fetal bovine serum (FBS) and antibiotics (100 IU/ml penicillin and 100 ug/ml streptomycin). JHUEM-14 cells were cultured in DMEM/F12 medium (Life Technologies #11320-033) with 10% FBS and antibiotics.

extract_protocol:
Cells were washed twice with PBS and fixed at room temperature in 1% formaldehyde in PBS. After 10 min, cells were placed on ice and washed twice with ice-cold PBS. The reaction was quenched with 10 mM DTT in 100 mM Tris.HCl (pH 9.4) and cells removed from the dish with a cell scraper. Cells were incubated at 30oC for 15 min then spun for 5 min at 2,000 g. Cells were washed sequentially with ice cold PBS, Buffer I (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5) and Buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH6.5) and centrifuged for 5 min at 2,000 g at 4 oC. Cells were resuspended in 300-750 ul of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris.HCl, pH 8.1, with complete protease inhibitor cocktail (Sigma Aldrich #11836145001). Ishikawa cells were sonicated for eight cycles (10s) and JHUEM-14 cells for 20 cycles using the highest power setting of a Branson Digital Sonifier SLPt. After chromatin shearing was confirmed by agarose gel electrophoresis, samples were centrifuged for 10 min at 4 oC. Samples were diluted 10-fold in 1% Triton X-100, 2 mM EDTA, 20 mM Tris.HCl (pH 8.1) and 150 mM NaCl with complete protease inhibitor cocktail. Magna ChIP protein A/G magnetic beads (EMD Millipore #16-663) were added to 500 ul of diluted chromatin and incubated with 5 ug of antibody overnight at 4 oC. Antibodies to H3K4Me1 (Abcam #ab8895), H3K4Me3 (Abcam #ab8580) and H3K27Ac (Abcam #ab4729) were used. The next day supernatant was removed and the beads washed three times with the following ice-cold buffers: RIPA 150 (0.1% SDS, 1% Triton X-100, 1 mM EDTA, 50 mM Tris.HCl (pH 8.10, 150 mM NaC1, 0.1% sodium deoxycholate), RIPA 500 (0.1% SDS, 1% Triton X-100, 1 mM EDTA, 50 mM Tris.HCl (pH 8.10, 500 mM NaC1, 0.1% sodium deoxycholate), LiCl RIPA (500 mM LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 50 mM Tris.HCl (pH 8.1) and TE buffer. Chromatin was then eluted by incubating beads overnight at 60 oC with 100 ul of elution buffer (1% SDS, 100 mM NaHCO3) and 0.5 mg/ml proteinase K. The next day beads were incubated at 95 oC for 10 min and supernatant removed. Chromatin was purified using the QIAquick Spin kit (QIAGEN) and eluted from columns using 50 ul of QIAGEN EB buffer. DNA was quantified using a Qubit dsDNA HS Assay kit (ThermoFisher Scientific).
Libraries were prepared by the Australian Genomic Research Facility for library preparation and sequencing on the Illumina HiSeq 2500

treatment_protocol: Ishikawa and JHUEM-14 cells were plated on to 10 cm tissue culture dishes in phenol red-free DMEM (Sigma Aldrich #D1145) supplemented with L-glutamine, sodium pyruvate and 10% charcoal-dextran stripped FBS. Three days later media were replaced and cells incubated with fresh medium containing either 10 nM estradiol or DMSO (vehicle control) for 3h.

tag: cell line

value: endometrial cancer cell line

value: 10nM DMSO

tag: chip antibody


title: H1_RNA-seq

source_name: undifferentiated H1 embryonic stem cells


title: plasma_mid_exp_rep1

city: Davis

first: Zeljka

last: Smit-McBride

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

hyb_protocol: Affymetrix GeneTitan Chips were run at Genomics Services offered at Institute for Human Genetics at UCSF following manufactureres protocol.

scan_protocol: MicroRNA GeneChips were scanned using the Affymetrix GeneTitan Scanner as a part of Genomics Services offered at Institute for Human Genetics at UCSF.

data_processing: The data was analyzed with Expression Console (Affymetrix) and Transcriptome Analysis Console (Affymetrix) using GCRMA  miRNA arrays.

organism: Macaca mulatta

label_protocol: The miRNA samples (10-20 nanograms) were labeled as probes using FlashTag kit.

growth_protocol: Primates were kept at UCRP at UC Davis Primate Center

extract_protocol: MiRNAs was isolated from each of the individual samples using Exiqon RNA isolation kit for fluids, quantified and quality checked on BioAnalyzer small RNA chips.

treatment_protocol: Animals were sacrificed with phenobarbitol injection by CNPRC stuff, eyes were disected, and aqueous and vitreous collected with syringe.  Blood was collected in purple top tube, spun down in Accuspin tube,  and plasma collected. Samples were stored at -80C till the RNA isolation step.

tag: exp. group

value: Group 3

value: plasma

tag: gender

value: female


title: plasma_mid_exp_rep4


title: plasma_mid_exp_rep3


title: Heart-Vehicle

source_name: heart from aged mdx mice treated with vehicle

value: Heart


title: RNAseq_subconfluentHFF-RH_rep3

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

data_processing:
for subconfluent samples: remove adapter sequences with CLIP tool from FASTX toolkit as implemented through usegalaxy.org platform
for confluent samples: remove adapter sequences with TrimGalore! (v0.4.3.1) as implemented through usegalaxy.org platform
alignment to human and Toxoplasma gondii genomes independently with HISAT2 (v2.1.0) using standard options as implemented through usegalaxy.org platform
feature counts obtained with htseq-count (v0.9.1) with standard options as implemented through usegalaxy.org platform
differential expression obtained with DESeq2 (v2.11.40.2) with standard options as implemented through usegalaxy.org platform
Genome_build: Toxoplasma gondii (ME49) v37 on ToxoDB.org and Homo sapiens v37 on HostDB.org
Supplementary_files_format_and_content: tab-delimited files with gene counts obtained with htseq-count

organism:
Homo sapiens
Toxoplasma gondii RH

source_name: Human Foreskin Fibroblasts and RH Toxoplasma

growth_protocol: parasites routinely subcultured in HFFs in DMEM supplemented with 1% heat-inactivated FBS w/o antibiotic; HFFs routinely subcultured in DMEM supplemented with 10% heat-inactivated FBS w/o antibiotics

extract_protocol:
cytoplasmic lysate was collected and an aliquot was immediately stored in Trizol for RNA-seq samples.  The rest was digested with RNaseI and monosomes were collecte by ultracentrifugation on a sucrose gradient. Ribosome-protected fragments (RFP) were purified after gel electrophoresis
RNA-seq and Ribo-seq samples of confluent samples were processed with the TruSeq Ribo Profile kit (Illumina) as per manufacturer. Subconfluent samples: total RNA was fragmented by alkaline hydrolysis. Fragments were purfied by gel electrophoresis. fragments were dephosphorylated, ligated at 5' end with barcoded adapter, rRNA removal with RiboZero mammalian kit (Illumina), phosphorylated, ligated at 3' end with SR-adapter, reverse transcribed & PCR with NEBnext barcoded adapters

treatment_protocol: HFFs were split, allowed to grow for 24 hours then infected with RH strain T. gondii for 24 hours in DMEM supplemented with 10% heat-inactivated FBS w/o antibiotic

tag: host cell type

value: human foreskin fibroblasts

tag: parasite

value: Toxoplasma gondii RH

tag: host growth

value: subconfluent


title: plasma_mid_pre_rep4


title: RNAseq_subconfluentHFF-RH_rep2


title: RNAseq_subconfluentHFF-RH_rep1


title: JHUEM14_Veh_H3K4Me1

value: H3K4Me1 (Abcam #ab8895)


title: JHUEM14_Veh_H3K4Me3

value: H3K4Me3 (Abcam #ab8580)


title: RNAseq_subconfluentHFF_rep3

source_name: Human Foreskin Fibroblasts


title: JHUEM14_Veh_H3K27Ac

value: H3K27Ac (Abcam #ab4729)


title: plasma_mid_pre_rep2


title: plasma_mid_pre_rep3


title: plasma_mid_pre_rep1


title: plasma_mid_rep2


title: Riboseq_subconfluentHFF-RH_rep3

data_processing:
Library strategy: RNA ribosome footprints
for subconfluent samples: remove adapter sequences with CLIP tool from FASTX toolkit as implemented through usegalaxy.org platform
for confluent samples: remove adapter sequences with TrimGalore! (v0.4.3.1) as implemented through usegalaxy.org platform
alignment to human and Toxoplasma gondii genomes independently with HISAT2 (v2.1.0) using standard options as implemented through usegalaxy.org platform
feature counts obtained with htseq-count (v0.9.1) with standard options as implemented through usegalaxy.org platform
differential expression obtained with DESeq2 (v2.11.40.2) with standard options as implemented through usegalaxy.org platform
Genome_build: Toxoplasma gondii (ME49) v37 on ToxoDB.org and Homo sapiens v37 on HostDB.org
Supplementary_files_format_and_content: tab-delimited files with gene counts obtained with htseq-count


title: plasma_mid_exp_rep2


title: RNAseq_subconfluentHFF_rep1


title: RNAseq_subconfluentHFF_rep2


title: JHUEM14_E2_H3K4Me1

value: 10nM estradiol


title: JHUEM14_E2_H3K4Me3


title: plasma_mid_rep3


title: Riboseq_subconfluentHFF-RH_rep1


title: Ishikawa_Veh_input

value: Ishikawa


title: JHUEM14_E2_H3K27Ac


title: Riboseq_subconfluentHFF-RH_rep2


title: JHUEM14_E2_input


title: plasma_mid_rep1


title: AML_1_Lena

city: Barcelona

middle: Belen

last: Lopez-Millan

state: Barcelona

address: Carrer Casanova 143

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Gene expression data from AML bone marrow blasts treated with lenalidomide (10 µM) for 48 h (AML patient 1)

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the GeneChip® Human Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the GeneChip Whole Transcript (WT) Plus Reagent Kit Manual (Affymetrix).

scan_protocol: After hybridation, the chips were stained and washed in a GeneChip Fluidics Station 450 (Affymetrix) and scaned by sing a GeneChip Array scanner 3000 7G (Affimetrix)

data_processing: Expression data were generated by Affymetrix Expression Console software version1.4.1.46. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: AML blasts from patient#1 treated with lenalidomide

label_protocol: 100 ng of total RNA from each sample was converted to double-strand cDNA using a random hexamer incorporating a T7 promoter, amplified RNA (cRNA) was generated from the double-stranded cDNA template though an IVT (in-vitro transcription) reaction and purified with the Affymetrix magnetic beads. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. RNA template was removed with a RNAsa H enzyme. The cDNA was then purified with magnetic beads and, afterwards, fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Purified AML blasts and BM-CD34+ cells cultured were cultured in Stemspam medium (Stem Cell Technologies, Vancouver, Canada) supplemented with the hematopoietic cytokines Stem Cell Factor (100 ng/mL), FLT3 ligand (100 ng/mL), IL3 (10 ng/mL, all from PeproTech) and penicillin-streptomycin-amphotericinB (Gibco). Cells were treated or not with 10 µM lenalidomide for 48h before global gene expression profiling. Cultures were maintained in a humidified atmosphere with 5% CO2 at 37⁰C.

extract_protocol: Total RNA was then extracted using a Maxwell® RSC simplyRNA Cells Kit in a Maxwell® RSC Instrument (Promega) following manuactuer's instructions.

treatment_protocol: Purified AML blasts and BM-CD34+ cells were treated or not with 10 µM lenalidomide for 48h before global gene expression profiling.

value: Bone marrow


title: BM-CD34+_2_Lena

description: Gene expression data from healthy CD34+ bone marrow cells treated with lenalidomide (10 µM) for 48 h (healthy volunteer 2)

source_name: CD34+ bone marrow cells from healthy volunteer#2 treated with lenalidomide


title: Riboseq_subconfluentHFF_rep3


title: plasma_old_rep4

value: Group 2


title: Ishikawa_Veh_H3K4Me3


title: BM-CD34+_2_Ctrl

description: Gene expression data from CD34+ bone marrow cells without treatment (healthy volunteer 2)

source_name: CD34+ bone marrow cells from healthy volunteer#2 without treatment


title: plasma_old_rep3


title: AML_2_Ctrl

description: Gene expression data from AML bone marrow blasts without treatment (AML patient 2)

source_name: AML blasts from patient#2 without treatment


title: AML_3_Ctrl

description: Gene expression data from AML bone marrow blasts without treatment (AML patient 3)

source_name: AML blasts from patient#3 without treatment


title: AML_2_Lena

description: Gene expression data from AML bone marrow blasts treated with lenalidomide (10 µM) for 48 h (AML patient 2)

source_name: AML blasts from patient#2 treated with lenalidomide


title: Ishikawa_Veh_H3K27Ac


title: Ishikawa_Veh_H3K4Me1


title: AML_1_Ctrl

description: Gene expression data from AML bone marrow blasts without treatment (AML patient 1)

source_name: AML blasts from patient#1 without treatment


title: AML_3_Lena

description: Gene expression data from AML bone marrow blasts treated with lenalidomide (10 µM) for 48 h (AML patient 3)

source_name: AML blasts from patient#3 treated with lenalidomide


title: Ishikawa_E2_input


title: Riboseq_subconfluentHFF_rep2


title: plasma_old_rep2


title: FACS sorted, mouse fore brain OPCs Ep400_cko P6, biological replicate 2

city: Erlangen

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

description: RNAseq data from P6 mouse fore brain OPCs (Ep400 cko)

data_processing:
Sequencing data were pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to mm10 reference genome using STAR (version 2.5.1.b).
Unique maps were generated using HTSeq count relating to Ensembl genes version 85.
Statistical analysis of raw data was done with DESeq2 by R version 1.10.1.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with raw counts, log2 fold change and statistics.

source_name: mouse fore brain P6 (CNP1::Cre, conditional Rosa26stopflox-YFP, conditional Ep400)

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA Kit.

treatment_protocol: Isolated, meninges-free fore brains of ctrl and cko mice wer digested with cysteine, DNAse I and papaine for 30min at 37°C. Digested tissue was drawn by syringe three times through different cannulas (19G, 22G, 24G) to prepare single cell suspensions. After dilution in 10ml DMEM, suspensions were passed through a 40µm strainer. Cells were centrifuged, resuspended in 25ml FACS buffer and nuclei were stained with Hoechst-33342 for 20min. After additional centrifugation, cells were washed with PBS, resuspended in 1ml FACS buffer and sorted by YFP- and Hoechst-fluorescence directly in 100µl RLT buffer from RNeasy Micro Kit (QIAGEN ) to isolate OPCs.

value: mixed 129SvJ/C57Bl/6J background

value: postnatal day 6

value: fore brain OPCs


title: plasma_old_rep1


title: Riboseq_subconfluentHFF_rep1


title: RNAseq_confluentHFF-RH_rep2

value: confluent


title: FACS sorted, mouse fore brain OPCs Ep400_cko P6, biological replicate 3

value: CNP1::Cre, conditional Rosa26stopflox-YFP, conditional Ep400


title: Ishikawa_E2_H3K4Me3

value: endometrial cancer cell line


title: Ishikawa_E2_H3K4Me1


title: FACS sorted, mouse fore brain OPCs Ep400_cko P6, biological replicate 1


title: plasma_yng_rep3

value: Group 1

value: plasma

value: female


title: RNAseq_confluentHFF-RH_rep1

value: human foreskin fibroblasts

value: Toxoplasma gondii RH


title: FACS sorted, mouse fore brain OPCs Ep400_ctrl P6, biological replicate 3

description: RNAseq data from P6 mouse fore brain OPCs (ctrl)

source_name: mouse fore brain P6 (CNP1::Cre, conditional Rosa26stopflox-YFP)


title: BM-CD34+_1_Ctrl

description: Gene expression data from CD34+ bone marrow cells without treatment (healthy volunteer 1)

source_name: CD34+ bone marrow cells from healthy volunteer#1 without treatment


title: Ishikawa_E2_H3K27Ac


title: RNAseq_confluentHFF-RH_rep3


title: RNAseq_confluentHFF_rep3


title: FACS sorted, mouse fore brain OPCs Ep400_ctrl P6, biological replicate 2


title: plasma_yng_rep1


title: plasma_yng_rep2


title: plasma_yng_rep4


title: RNAseq_confluentHFF_rep2


title: RNAseq_confluentHFF_rep1


title: Riboseq differentiating rep4

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

institute: Washington University School of Medicine

description:
mRNA footprints
Ribosome profiling

data_processing:
Trim_galore! was used to remove small RNA adaters
TopHat2 (v 2.1.0) was used to align the reads to the hg38 reference genome
Ribo-seq reads were firstly aligned to a set of known rRNA and tRNAs (selected from the UCSC RepeatMasker tracks), followed by alignment of all unmapped reads to the reference genome.
FeatureCounts were used to count the number of reads per gene
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files containing counts for each gene and sample. For RNA-seq the exon counts, for Ribo-seq the coding sequence (CDS) counts are provided.

source_name: H9 cells

growth_protocol: hESC were maintained in Essential 8 media (Thermo Fisher Scientific) on hESC-Qualified Matrigel (Corning) coated plates at 37°C, 5 % CO2. Cultures were dissociated in clumps using 0.5mM EDTA every 4 days and media was renewed daily.

extract_protocol:
mRNA footprints were prepared according to the ribosomal profilig protocol published by Ingolia et al., while total RNA was extracted using Trizol.
mRNA footprints were Ribozero treated (Illumina) and libraries were prepared using TruSeq Small RNA Preparation Kit (Illumina) according to manufacturer instructions. For RNA-seq, total RNA was treated with the RiboZero Magnetic Kit (Illumina) to remove ribosomal RNA. Libraries for sequencing were prepared using the NEB next Ultra Directional library prep kit for Illumina.

treatment_protocol: Differentiating hESC were cultured in MEF-conditioned KSR media plus 1uM retinoic acid in DMSO, while the control hESC population was maintained in MEF-conditioned KSR media completed with 4 ng/mL FGF2. Self-renewing cells were collected at Day 0, while differentiating cells at day 5 of treatment.

value: human embryonic stem cells


title: Riboseq differentiating rep3

description:
mRNA footprints
Ribosome profiling


title: vitreous_mid_exp_rep4

value: Group 3

value: vitreous humor


title: Tumor, JPLT08-22T

last: Hiyama

address: 1-2-3, Kasumi, Minami-ku

description: tumor tissue sample

data_processing: The data were analyzed with Expression Console version1.1 (RMA)  using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Tumor resected before chemotherapy

extract_protocol: Total RNA was extracted by the acid guanidinium–phenol–chloroform method

value: tumor tissue

tag: age(month)

tag: Sex

value: Male

tag: histologic type

value: Well differentiated

tag: stage (pretext)

tag: chic risk   stratificationb

value: Standard

tag: ctnnbi gene alteration

tag: event

tag: clinical course

value: Dead

tag: distant metastasis


title: vitreous_mid_exp_rep3

tag: tissue

tag: age


title: Riboseq_confluentHFF-RH_rep3


title: vitreous_mid_exp_rep2


title: BM-CD34+_1_Lena

description: Gene expression data from healthy CD34+ bone marrow cells treated with lenalidomide (10 µM) for 48 h (healthy volunteer 1)

source_name: CD34+ bone marrow cells from healthy volunteer#1 treated with lenalidomide

value: Bone marrow


title: Riboseq differentiating rep1

description:
mRNA footprints
Ribosome profiling

tag: cell type


title: GAA-1

city: chengdu

first: wang

middle: yu

last: jie

address: 211 Huimin Road, Wenjiang District, Chengdu

institute: Sichuan Agricultural University

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp)
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM), then standardized by the formula log2 (RPM+1), which allowed unbiased comparison among samples.
Genome_build: Genome database:mouse genome (assembly GCA_000001635.8); miRbase version: V21.0
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

source_name: microRNA derived from myotubes after Guanidineacetic acid supplement (GAA)

growth_protocol: Murine skeletal muscle cell line C2C12 was cultured growth medium that contained high glucose DMEM supplemented with 10% fetal bovine serum, 100000 units/L of penicillin sodium, and 100 mg/L of streptomycin sulfate at 37 ℃ in a humidified atmosphere that contained 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: When the cells density reached about 80 % confluence, the C2C12 myoblasts were induced differentiation by placing  differentiation medium  that contained high glucose DMEM, 2% horse serum and present or absent 20 mM Guanidineacetic acid.

tag: strain background

tag: tissue source

value: myoblast

tag: cell line

value: Murine skeletal muscle cell line

tag: developmental stage

value: 6 days after differentiation


title: Riboseq_confluentHFF-RH_rep2

source_name: Human Foreskin Fibroblasts and RH Toxoplasma

tag: host cell type

tag: parasite

tag: host growth

value: confluent


title: Riboseq self-renewing rep4

description:
mRNA footprints
Ribosome profiling


title: FACS sorted, mouse fore brain OPCs Ep400_ctrl P6, biological replicate 1

tag: strain

value: mixed 129SvJ/C57Bl/6J background

value: postnatal day 6

value: fore brain OPCs

tag: genotype


title: GAA-2


title: vitreous_mid_exp_rep1

tag: exp. group

tag: gender

value: female


title: Riboseq_confluentHFF-RH_rep1

value: human foreskin fibroblasts

value: Toxoplasma gondii RH


title: NC-2

source_name: microRNA derived from negative control (NC) myotubes


title: Wildtype Sample 3

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

institute: Research Institute at Nationwide Children's Hospital

description: valves

data_processing:
50 base paired end reads were performed on an illumina high seq 2500.
Fastq files were aligned to the mouse genome (mm9) using the STAR aligner version 2.4.0 in 2 pass mode using default parameters
Quality Control (QC) was performed on aligned files using RNASeQC and RSeQC to verify alignment quality.
Resulting BAM files were processed using cufflinks pipeline version 2.2.0 (cufflinks, cuffdiff, cuffnorm, and cuffquant) for gene expression and differential expression.
Principal component analysis identified a potential batch effect in sample KI2, as it did not group with other KI samples, and it was therefore removed from the study. All data is available for alll 6 samples for this study, with additional statistics that were performed without K2.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM

source_name: E15.5 Outflow tract valves

extract_protocol:
Norgen Total RNA Extraction Kit
RNA TruSeq Stranded Total RNA LT with Ribo-Zero Gold Set A

value: outflow tract

value: embryonic day 15.5

tag: genotyp

value: Control


title: Wildtype Sample 2

description: valves


title: Riboseq self-renewing rep3

description:
mRNA footprints
Ribosome profiling

value: human embryonic stem cells


title: Riboseq self-renewing rep2

description:
mRNA footprints
Ribosome profiling


title: Riboseq_confluentHFF_rep3

source_name: Human Foreskin Fibroblasts


title: vitreous_mid_rep3

value: Group 3

value: vitreous humor


title: vitreous_old_rep3

value: Group 2


title: Riboseq_confluentHFF_rep1