title: WT dendritic cell, Expt2_replicate 3

source_name: Dendritic cells, stimulated with anti-CD40

value: Dendritic cells

value: stimulated with anti-CD40


title: WT CD8+ Dendritic cells_replicate 4

status: Public on Jun 08 2018

type: RNA

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Place, MS 1135

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

hyb_protocol: Six micrograms (6 ug) of cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip array.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing:
Signals were summarized using the Robust Multichip Algorithm (RMA) using Partek Genomics Suite software v6.6 (Partek, Inc). The data from each experiment was summarized as two independent groups.
Performed batch effects removal after combining all together

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CD8+ Dendritic cells

label_protocol: One to five nanograms (1-5 ng) of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were freshly sorted from spleen of mice by FACS

extract_protocol: RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted DCs were lysed with lysis buffer from Rneasy Micro kit from Qiagen

tag: expid

tag: strain

tag: genotype/variation

value: WT

tag: cell type

value: CD8+ Dendritic cells

tag: group


title: WT CD8+ Dendritic cells_replicate 3


title: Rag1-ko dendritic cell, Expt2_replicate 1

tag: stimulatation

value: totalDC


title: Rag1-ko dendritic cell, Expt2_replicate 3


title: Rag1-ko/p38-ko dendritic cell, Expt1_replicate 3


title: A5_Microglia depleted [M397]

type: SRA

city: Boston

first: Stephen

last: Rubino

state: MA

address: 60 Fenwood Road, 10032

institute: Brigham and Women's Hospital

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned using Tophat and RSEM-based quantification using known transcripts,
followed by further processing using the Bioconductor package DESeq in R.
Genome_build: mm9
Supplementary_files_format_and_content: The data was normalized using TMM normalization. The TMM method estimates scale factors between samples that can be incorporated into currently used statistical methods for DE analysis. Post-processing and statistical analysis was carried out in R. Differentially expressed genes were defined using the differential expression pipeline on the raw counts with a single call to the function DESeq (adjusted p value<0.1).

source_name: Brain cortex

extract_protocol:
RNA was extracted from brain tissue using Trizol extraction.
Libraries were constructed using Illumina's TruSeq kit with Poly A selection with 1 microgram of RNA/sample

treatment_protocol: Brain cortical tissue was extracted from mice

tag: strain background

value: microglia-depleted

tag: tissue

value: Brain cortex


title: A4_Microglia depleted [M396]


title: A6_Microglia depleted [M398]


title: Rag1-ko/p38-ko dendritic cell, Expt1_replicate 2


title: Rag1-ko dendritic cell, Expt1_replicate 4


title: Rag1-ko/p38-ko dendritic cell, Expt1_replicate 1


title: A3_Control [C395]

value: control


title: A2_Control [C394]


title: Rag1-ko dendritic cell, Expt1_replicate 2


title: Rag1-ko dendritic cell, Expt1_replicate 1


title: TgP_20WO_VAT_rep1

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

library_source: genomic

data_processing:
Base calling was performed with Real-Time Analysis v2.4.11
ATAC-seq reads from two replicates per sample were filtered for quality using sickle v1.2 (default settings for PE reads), adapter-trimmed using cutadapt v1.8.3 (`-e 0.1, -m 20`), and mapped to mm9 using Bowtie v2.2.4, keeping only mate pairs that mapped to a single best location using samtools v1.3, and were non-duplicates using Picard v1.130.
To generate bigWig files, filtered and mapped reads were used to generate tag directories in HOMER v4.6 (`makeTagDirectory -tbp 1 -checkGC -illuminaPE`), followed by bedGraph files (HOMER  `makeUCSCfile -fsize 1e50 -norm 1e6`), which were then used to generate bigWig files using UCSC-tools (`bedGraphToBigWig`).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: Epididymal adipose tissue

extract_protocol:
10,000 cells were sorted into collection buffer (PBS, 0.5% BSA, 2mM EDTA), pelleted and lysed in hypotonic buffer (10mM Tris-HCl (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% NP-40). Nuclei were pelleted by centrifugation for 30 min. at 500g, 4oC.
The ATAC-seq protocol was adapted from Buenrostro et al., 2013 and Lara-Astiaso et al., 2014. Nuclear pellets were re-suspended in 5uL of transposition mix (1uL Tagment DNA Enzyme, 2.5uL Tagment DNA Buffer from Nextera DNA Sample Prep Kit, 1.5uL H2O), and incubated at 37C for 60min. Two sequential PCR reactions were performed. After the first PCR, libraries were selected for small fragments (< 600bp) using SPRI beads followed by a second round of PCR with the same conditions, and a final SPRI bead purification to capture all fragments for the final library. Paired-end sequencing was performed on an Illumnina NextSeq 500 (50,10,0,31).

tag: age (weeks-old)

value: Epididymal adipose tissue


title: TgP_20WO_Sp_rep2

source_name: Spleen

value: Spleen


title: Rag1-ko dendritic cell, Expt1_replicate 3


title: A1_Control [C393]


title: TgP_10WO_VAT_rep2


title: TgP_10WO_SpPparNeg_rep1


title: TgP_10WO_SpPparLo_rep1


title: TgP_10WO_SpPparNeg_rep3


title: TgP_10WO_SpPparLo_rep2


title: TgP_10WO_VAT_rep1


title: TgP_03WO_Thy_rep2

source_name: Thymus

value: Thymus


title: TgP_03WO_Thy_rep1


title: TgP_10WO_Sp_rep1


title: TgP_03WO_Sp_rep2


title: TgP_10WO_SpPparNeg_rep2


title: TgP_03WO_Sp_rep1


title: TgN_20WO_VAT_rep1


title: TgP_20WO_Sp_rep1


title: TgN_20WO_Sp_rep1


title: TgN_10WO_Sp_rep1


title: TgN_03WO_Thy_rep2


title: TgN_03WO_Thy_rep1


title: TgN_03WO_Sp_rep1


title: TgP_20WO_VAT_rep2


title: 8w_Tg-_Pparg+_Spl_Treg#1

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: PPARg+ Treg

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

tag: genotype

value: vTreg53 Tg-

value: PPARg+ Treg


title: 8w_Tg-_Pparg-_Spl_Treg#3

source_name: PPARg- Treg

value: PPARg- Treg


title: 8w_Tg-_Pparg-_Spl_Treg#2


title: 8w_Tg-_Pparg+_Spl_Treg#2


title: 8w_Tg-_Pparg-_Spl_Treg#1


title: 8w_Tg+_Pparg+_Spl_Treg#4

value: vTreg53 Tg+


title: 8w_Tg+_Pparg+_Spl_Treg#1


title: 8w_Tg+_Pparg-_Spl_Treg#4


title: 8w_Tg+_Pparg+_Spl_Treg#3


title: 8w_Tg+_Pparg-_Spl_Treg#3


title: TgN_10WO_VAT_rep1


title: 8w_Tg+_Pparg+_Spl_Treg#2


title: Tg+_Foxp3-transduced_VAT_Tconv#1

source_name: Foxp3-transduced Tconv

value: visceral adipose tissue

value: Foxp3-transduced Tconv


title: Tg+_Foxp3-transduced_Spl_Tconv#1


title: 8w_Tg+_Pparg-_Spl_Treg#2


title: 8w_Tg+_Pparg-_Spl_Treg#1


title: TgN_20WO_Sp_rep2


title: Tg+_Ctl-transduced_Spl_Tconv#1

source_name: control-transduced Tconv

value: control-transduced Tconv


title: Tg+_Foxp3-transduced_Spl_Tconv#2


title: 10w_Tg+_VAT_Tconv#3

source_name: Tconv

value: Tconv


title: Tg+_Ctl-transduced_Spl_Tconv#2


title: 10w_Tg+_VAT_Tconv#2


title: 10w_Tg+_VAT_Tconv#1


title: 8w_Tg-_Pparg+_Spl_Treg#3


title: 10w_Tg+_Spl_Tconv#3


title: TgN_03WO_Sp_rep2


title: 10w_Tg+_Spl_Tconv#2


title: Tg+_Foxp3-transduced_VAT_Tconv#2


title: 10w_Tg+_Spl_Tconv#1


title: 20w_Tg-_Spl_Treg#3

source_name: Treg

value: Treg


title: 20w_Tg+_Spl_Treg#2


title: 20w_Tg+_Spl_Treg#1


title: 20w_Tg-_Spl_Treg#1


title: 20w_Tg+_VAT_Treg#3


title: 20w_Tg+_VAT_Treg#2


title: 20w_Tg-_Spl_Treg#2


title: 20w_Tg+_Spl_Treg#3


title: 20w_Tg+_VAT_Treg#1


title: 10w_Tg-_VAT_Treg#2


title: 10w_Tg+_VAT_Treg#2


title: 10w_Tg+_VAT_Treg#1


title: 10w_Tg-_VAT_Treg#3


title: 10w_Tg+_VAT_Treg#3


title: 10w_Tg+_Spl_Treg#3


title: 10w_Tg-_VAT_Treg#1


title: 20w_Tg-_VAT_Treg#2


title: 10w_Tg-_Spl_Treg#3


title: 10w_Tg-_Spl_Treg#2


title: 2w_Tg+_Spl_Treg#1


title: 10w_Tg+_Spl_Treg#1


title: 10w_Tg-_Spl_Treg#1


title: 2w_Tg+_Spl_Treg#2


title: 2w_Tg-_Spl_Treg#3


title: 2w_Tg-_Spl_Treg#2


title: 20w_Tg-_VAT_Treg#3


title: 2w_Tg-_Spl_Treg#1


title: 2w_Tg+_Thy_Treg#3


title: 20w_Tg-_VAT_Treg#1


title: 2w_Tg-_Thy_Treg#3


title: 2w_Tg+_Thy_Treg#1


title: 2w_Tg+_Thy_Treg#2


title: 2w_Tg+_Spl_Treg#3


title: Sorted_HSCs_47bpKO_FPRDM16KO_SPRDM16only_fetal_liver_replicate_3

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 W. 168th Street, BB816

department: Medicine

institute: Columbia University Medical Center

description:
47bpFL_KO3
47bpFL_RNAseq_Counts.txt

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
We mapped the reads to a reference genome (mouse UCSC/mm9) using Tophat with 4 mismatches and 10 maximum multiple hits
We test for differentially expressed genes under various conditions using DEseq
Genome_build: UCSC/mm9
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Isolated HSCs (Lin-cKit+Sca1+CD48-)

growth_protocol: Cells were not grown

extract_protocol:
Trizol (Ambion, Austin TX) extraction followed by isopropanol precipitation and ethanol wash
Libraries were generated using Illumina TruSeq RNA prep kit after poly-A pull-down to enrich mRNAs from total RNA samples. For groups 2-4, the RNA library was amplified using the Clontech SMARTer Low Input RNA kit v4

treatment_protocol: Cells were not grown/treated, they were in all cases sorted from murine bone marrow or fetal liver

value: Sorted HSCs

value: PRDM16-KO murine HSCs (expressing s-PRDM16 only)


title: 2w_Tg-_Thy_Treg#2


title: Sorted_HSCs_47bpKO_FPRDM16KO_SPRDM16only_fetal_liver_replicate_1

description:
47bpFL_KO1
47bpFL_RNAseq_Counts.txt


title: Sorted_HSCs_47bpWT_FPRDM16WT_fetal_liver_replicate_1

description:
47bpFL_WT1
47bpFL_RNAseq_Counts.txt

value: wild type


title: Sorted_HSCs_47bpWT_FPRDM16WT_fetal_liver_replicate_3

description:
47bpFL_WT3
47bpFL_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_fetal_liver_replicate_3

description:
VAVFL_KO3
VAVFL_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_fetal_liver_replicate_1

description:
VAVFL_KO1
VAVFL_RNAseq_Counts.txt


title: 10w_Tg+_Spl_Treg#2


title: Sorted_HSCs_PRDM16WT_fetal_liver_replicate_2

description:
VAVFL_WT2
VAVFL_RNAseq_Counts.txt


title: Sorted_HSCs_47bpKO_FPRDM16KO_SPRDM16only_fetal_liver_replicate_2

description:
47bpFL_KO2
47bpFL_RNAseq_Counts.txt


title: Sorted_HSCs_47bpWT_FPRDM16WT_fetal_liver_replicate_2

description:
47bpFL_WT2
47bpFL_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16WT_fetal_liver_replicate_1

description:
VAVFL_WT1
VAVFL_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_adultBM_replicate_4

description:
VAVBM_KO4
VAVBM_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16WT_fetal_liver_replicate_3

description:
VAVFL_WT3
VAVFL_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_fetal_liver_replicate_2

description:
VAVFL_KO2
VAVFL_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_adultBM_replicate_3

description:
VAVBM_KO3
VAVBM_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_adultBM_replicate_2

description:
VAVBM_KO2
VAVBM_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16KO_adultBM_replicate_1

description:
VAVBM_KO1
VAVBM_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16WT_adultBM_replicate_4

description:
VAVBM_WT4
VAVBM_RNAseq_Counts.txt


title: 2w_Tg-_Thy_Treg#1


title: Sorted_HSCs_PRDM16WT_adultBM_replicate_2

description:
VAVBM_WT2
VAVBM_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16WT_adultBM_replicate_1

description:
VAVBM_WT1
VAVBM_RNAseq_Counts.txt


title: Sorted_HSCs_PRDM16WT_adultBM_replicate_3

description:
VAVBM_WT3
VAVBM_RNAseq_Counts.txt


title: VSMC_shH2AZ_Med1_part2

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

description:
processed data file:
shH2AZ_Med1_merge.bigWig

data_processing:
Basecalls performed using bcl2fastq version v2.18.0.12
For single cell RNA-seq analysis,reads were filtered by cutadapt with phred score threshold 20 and trimmed Ns. Then the reads were mapped to human genome (hg38, UCSC) via STAR (2.5.2b). Reads with same UMI were combined and then annotated to ensemble genes by featureCounts. Only cells expressed more than 500 genes were kept for t-SNE analysis with R package Seurat (2.0.1).
For bulk RNA-seq analysis, the reads were aligned to genomes of hg19 and mm9 by subread (R version 1.24.2). Uniq reads were kept and assigned to in-build refseq gene annotation of rsubread using featureCounts. Differential analysis was conducted with limma
For ChIP-seq, reads were mapped by subread and called peaks with MACS2 (2.1.1). All factor peaks were called using narrow mode of MACS2 and filtered by p value of 1e-6 except Med1, which using broad mode of MACS2 and q valule of 0.1.
For MNase seq data, the reads were mapped as ChIP-seq. The neucleosome enrichment score is defined as the read intensity ratio of a sliding window (each 200bp long, from -800 to 800 around TSS) to the neuclosome-free window (-200 to TSS site).
bigWig files were produced by HOMER v4.9.1
Genome_build: mm9
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, read intensity of samples
Supplementary_files_format_and_content: txt, log fold change of rna-seq
Supplementary_files_format_and_content: csv, single cell UMI data

growth_protocol: For isolation of primary mouse vascular smooth muscle cells, six-week C57BL/6 mice were sacrificed, and aorta were removed to PBS containing heparin sodium (1000 units in 50 ml PBS). After removing the surrounding adipose tissues and para-aortic lymph nodes, aorta were chopped into small pieces and digested with Aorta Dissociation Enzyme stock solution (125 mg/ml Collagenase type I in high glucose DMEM) for 3-4 hour at 37°C. After incubation, the digested aorta were rigorously pipetted up and down for several times, and then filtered through a 70-μm cell strainer into 15ml tubes. Then, isolated cells were spun down (100 rpm, 10 minutes, 4°C), and seeded into 0.1% gelatin-coated plates in high-glucose DMEM containing 20% FBS.Isolated mouse VSMCs were maintained in 10% FBS/DMEM, and P4-P8 cells were used in our study unless otherwise specified.

extract_protocol:
RNA-Seq: Total RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific) 4 days after infection. One ?g of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturerЎЇs instructions.
ChIP-Seq: Mouse VSMCs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop fixation. Cells were harvested, and DNA was fragmented to 300ЁC500 bp by sonication with Covaris S220 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads Protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.
MNase-Seq: Cultured mouse vascular smooth muscle cells were trypsinized and washed twice with PBS. Then, mononucleosomes were prepared using the EZ nucleosomal DNA Prep Kit (D5220, Zymo Research) according to manufacturerЎЇs instructions. Briefly, 1ЎБ106 cells were incubated with 100 ?l Nuclei Prep Buffer for 5 minutes on ice, followed by one wash with 100 ?l Atlantis Digestion Buffer. Isolated nuclei were incubated with 0.5 U Atlantis ds DNase at 42ЎгC for 20 minutes to react, and stopped by adding 5 ЎБ MN Stop Buffer. Nucleosomal DNA was purified with Zymo-SpinIIC column. To obtain mononucleosome, purified nucleosomal DNA was first incubated with 0.8ЎБ Agencourt AMPure XP beads (Beckman Coulter), and supernatant was kept. Afterwards, the collected supernatant was purified with 1.8ЎБ beads, and nucleosomal DNA was evaluated and quantitated by Agilent 2100 Bioanalyzer (Agilent).Nucleosomal sequencing library was prepared using KAPA HyperPlus Kit (Kapa Biosystems) according to manufacturerЎЇs instructions.

value: primary vascular smooth muscle cell

tag: chip antibody

tag: chip antibody info

value: Bethyl; Cat#A300-793A;


title: VSMC_shH2AZ_Med1_part1


title: VSMC_shH2AZ_SMAD3_part2

description:
processed data file:
shH2AZ_Smad3_merge.bigWig


title: VSMC_shH2AZ_SRF_2

description:
processed data file:
shH2AZ_SRF.bigWig

value: SRF

value: SantaCruz; Cat#sc-335; lot#I1014


title: VSMC_shH2AZ_Input_1

description:
processed data file:
shH2AZ_Input.bigBig


title: VSMC_shH2AZ_SMAD3_part1


title: VSMC_shH2AZ_SRF_1

description:
processed data file:
shH2AZ_SRF.bigWig


title: VSMC_shH2AZ_Input_2


title: VSMC_shNT_SMAD3_part2

description:
processed data file:
shNT_Smad3_merge.bigWig


title: VMSC_shNT_Med1_part1

description:
processed data file:
shNT_Med1_merge.bigWig


title: VSMC_P1_MNase

description: processed data file:


title: VSMC_shNT_SMAD3_part1


title: VMSC_shNT_Med1_part2


title: VSMC_shNT_SRF_1

description:
processed data file:
shNT_SRF.bigWig


title: VSMC_P10_MNase

description: processed data file:


title: VSMC_shNT_Input_1

description:
processed data file:
shNT_Input.bigBig


title: VSMC_P10_1

description:
processed data file:
VSMC_P10_RNAseq.bigWig

molecule: polyA RNA


title: VSMC_shH2AZ_MNase

description: processed data file:


title: VSMC_shNT_SRF_2

description:
processed data file:
shNT_SRF.bigWig


title: VSMC_P10_2


title: VSMC_NT_MNase

description: processed data file:


title: VSMC_P1_2

description:
processed data file:
VSMC_P1_RNAseq.bigWig


title: VSMC_P1_1


title: VSMC_P1_Input

description: processed data file:


title: VSMC_P10_Input

description: processed data file:


title: VSMC_P10_SRF

description: processed data file:


title: VSMC_P1_SRF

description: processed data file:


title: VSMC_P10_H2AZ

description: processed data file:

value: Active Motif; Cat#39113; lot#00913003


title: VSMC_P1_H2AZ

description: processed data file:


title: VSMC_STARVE_1

description:
processed data file:
VSMC_FBS_starve_rna_logFC.txt


title: VSMC_FBS_2


title: VSMC_shNT_Input_2

description:
processed data file:
shNT_Input.bigBig


title: VSMC_FBS_1


title: VSMC_Med1

description: processed data file:


title: VSMC_H3K27ac

description: processed data file:


title: VSMC_SRF

description: processed data file:


title: VSMC_H3K27me3

description: processed data file:

value: Active Motif; Cat#39155; lot#06517018


title: VSMC_Input_1

description:
processed data file:
VSMC_H2AZ_Input.bigWig


title: VSMC_Input_2


title: VSMC_H4K4me1

description: processed data file:

value: Active Motif; Cat#39297; lot#01714002


title: VSMC_H2azKD_1

description:
processed data file:
H2AZKD_mm9_rnaseq.bigWig


title: VSMC_H2AZ_1

description:
processed data file:
VSMC_H2AZ_ChIP.bigWig


title: VSMC_H4K4me3

description: processed data file:

value: Active Motif; Cat#39159; lot#06217005


title: VSMC_H2AZ_2


title: VSMC_NT_1

description:
processed data file:
NT_mm9_rnaseq.bigWig


title: VSMC_H2azKD_2


title: RNA-seq-FL-ProB-WT #2

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

description:
Analyze-repeats-FL-ProB-WT-EKO-PKO-mm10-count-exons-Condense-genes-with-adjust.txt
Up_PKO_vs_WT.txt
Up_EKO_vs_WT.txt
Down_PKO_vs_WT.txt
Down_EKO_vs_WT.txt
Peak-list-EBF-1-JEM-WT1-peaks-on-genes-sign-UP-wt-vs-EKO.txt
Peak-list-EBF-1-JEM-WT1-peaks-on-genes-sign-down-wt-vs-EKO.txt
Peak-list-Pax-BIO-Peaks-on-genes-sign-up-WT-vs-PKO.txt
Peak-list-Pax-BIO-Peaks-on-Genes-sign-down-WT-vs-PKO.txt

data_processing:
RNA-Sequencing and data analysis: Each biological sample was processed and sequenced in triplicate.  Libraries  were single-end sequenced on a NexSeq500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using TopHat with single read, standard settings. If not indicated, further  analyses were performed using the HOMER platform (Heinz et al. 2010). For further analyses we used normalization to 10M mapped reads by the analyzeRepeats.pl command with the  option –count exons condeseGenes. For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option followed by the getDiffExpression.pl  command using edgeR or DEseq2.
Processed data files format and content: Processed files include txt files of RNA-seq expressionmatrix. All genomic coordinates are relative to mm10 mouse assembly.

source_name: Wt FL

growth_protocol:
[ProB-cell isolation / culture protocol/Facs staining]
Cell culture: Fetal liver cells were purified from wild-type, Ebf1 deficient, or Pax5 deficient fetus, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol.

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations.
Library construction protocol: RNA-Seq Libraries were constructed using NuGEN’s  Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of single read NextSeq500 sequencing (Illumina, San Diego,CA).

treatment_protocol: Cultured in Optimem +10% FBS, FL, KL, IL7 on OP9

tag: genotype / variation

value: Wild type

value: ProB


title: RNA-seq-FL-ProB-WT #3


title: RNA-seq-FL-ProB-WT #1


title: RNA-seq-FL-ProB-PAX-KO #1

source_name: Pax5-/- FL

value: Pax5 knock out


title: RNA-seq-FL-ProB-PAX-KO #2


title: VSMC_STARVE_2


title: RNA-seq-FL-ProB-EBF-KO #3

source_name: Ebf1-/- FL

value: Ebf1 knock out


title: RNA-seq-FL-ProB-EBF-KO #1


title: RNA-seq-FL-ProB-PAX-KO #3


title: RNA-seq-FL-ProB-EBF-KO #2


title: VSMC_NT_2


title: ATAC-seq-FL-ProB Wt #2

description:
Annotattion-ATAC-signal-on-Pax-BIO-EBF1-overlapping-peaks.txt
Annotattion-ATAC-signal-on-Pax-BIO-NOT-EBF-bound-peaks.txt
Annotattion-ATAC-signal-on-EBF1-NOT-PAX-BIO-Bound-peaks.txt
Ghist-WT-Ebf1-ChIP-WT-EKO-ATAC-and-EKO-pMig-MigEBF-Mig-Pax-and-PKO-mig-MigEBF-on-EBF1-peaks.txt
Ghist-WT-PAx5-BIO-ChIP-WT-PKO-ATAC-and-PKO-pMig-MigEBF-MigPax-and-EKO-mig-MigPax-on-Pax5-BIO-peaks.txt
Ghist-WT-Ebf1-PAx-BIO-Chip-WT-ATAC-and-EKO-PKO-MiGR1-exp-on-Ebf1-Pax5-BIO-overlapping-peaks.txt
Hist-ATAC-signal-on-Pax-peaks-on-genes-sign-UP-or-DOWN-WT-vs-PKO.txt
Hist-ATAC-tags-on-sign-positive-or-negative-EBF-peaks.txt
Combined-ATAC-FL-WT.ucsc.bedGraph

data_processing:
ATAC-Sequencing and data analysis:Libraries  were single-end sequenced on a NexSeq500. Each biological sample was processed  for ATAC-Seq and sequenced in triplicate. The data was mapped to mm10 using Bowtie2 with standard single end  settings. Tag directories with reads mapped to the mitochondrial chromosome filtered  out were created using HOMER.  ATAC-seq peaks were identified using findPeaks.pl in HOMER with the settings: -style histone -size 75 -minDist 75 -minTagThreshold 6 -L 8 -F 8.  BED files were created from Tag directories using the HOMER package. Annotation of ATAC-seq peaks on ChIP-seq Peaks was done in HOMER using the annotatePeaks.pl command.
Processed data files format and content: Processed files include bedGraph files and txt files with ATAC data on annotated peak positions.

extract_protocol:
For ATAC-seq: Cells were washed in ice cold PBS prior to Assay for Transposase Accessible Chromatin  (ATAC-seq) library preparation as described in (Buenrostro et al. 2013).
Library construction protocol: ATAC-Seq ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers Libraries were run single read on the Illumina NexSeq500.


title: ATAC-seq-FL-ProB Wt #1


title: ATAC-seq-FL-ProB Wt #3


title: ATAC-seq-FL-ProB Pax5-/- #3

description:
Annotattion-ATAC-signal-on-Pax-BIO-EBF1-overlapping-peaks.txt
Annotattion-ATAC-signal-on-Pax-BIO-NOT-EBF-bound-peaks.txt
Annotattion-ATAC-signal-on-EBF1-NOT-PAX-BIO-Bound-peaks.txt
Ghist-WT-Ebf1-ChIP-WT-EKO-ATAC-and-EKO-pMig-MigEBF-Mig-Pax-and-PKO-mig-MigEBF-on-EBF1-peaks.txt
Ghist-WT-PAx5-BIO-ChIP-WT-PKO-ATAC-and-PKO-pMig-MigEBF-MigPax-and-EKO-mig-MigPax-on-Pax5-BIO-peaks.txt
Ghist-WT-Ebf1-PAx-BIO-Chip-WT-ATAC-and-EKO-PKO-MiGR1-exp-on-Ebf1-Pax5-BIO-overlapping-peaks.txt
Hist-ATAC-signal-on-Pax-peaks-on-genes-sign-UP-or-DOWN-WT-vs-PKO.txt
Hist-ATAC-tags-on-sign-positive-or-negative-EBF-peaks.txt
Combined-ATAC-FL-Pax5-KO.ucsc.bedGraph


title: ATAC-seq-FL-ProB Pax5-/- #2


title: ATAC-seq-FL-ProB Ebf1-/- #1

description:
Annotattion-ATAC-signal-on-Pax-BIO-EBF1-overlapping-peaks.txt
Annotattion-ATAC-signal-on-Pax-BIO-NOT-EBF-bound-peaks.txt
Annotattion-ATAC-signal-on-EBF1-NOT-PAX-BIO-Bound-peaks.txt
Ghist-WT-Ebf1-ChIP-WT-EKO-ATAC-and-EKO-pMig-MigEBF-Mig-Pax-and-PKO-mig-MigEBF-on-EBF1-peaks.txt
Ghist-WT-PAx5-BIO-ChIP-WT-PKO-ATAC-and-PKO-pMig-MigEBF-MigPax-and-EKO-mig-MigPax-on-Pax5-BIO-peaks.txt
Ghist-WT-Ebf1-PAx-BIO-Chip-WT-ATAC-and-EKO-PKO-MiGR1-exp-on-Ebf1-Pax5-BIO-overlapping-peaks.txt
Hist-ATAC-signal-on-Pax-peaks-on-genes-sign-UP-or-DOWN-WT-vs-PKO.txt
Hist-ATAC-tags-on-sign-positive-or-negative-EBF-peaks.txt
Combined-ATAC-FL-Ebf1-KO.ucsc.bedGraph


title: TgN_20WO_VAT_rep2

value: Epididymal adipose tissue


title: ATAC-seq-FL-ProB Ebf1-/- #3


title: ATAC-seq-FL-ProB Pax5-/- #1


title: ATAC-seq-FL-ProB Ebf1-/- #2


title: Control stroke B2

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Motor cortical neurons in adult C57 mice

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Motor cortical neurons

tag: condition


title: STR_DRE_CRE_SAL_1


title: Control stroke B1


title: STR_DRE_CRE_CNO_1


title: GCB_KO_SRBC_3: SRBC-immunized miR-146a KO GC B cells

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

description: total RNA (including small RNAs)

data_processing:
Reads from all libraries were mapped to the mouse genome (mm9) using STAR (v2.2.0c). To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: rpkm.txt.gz - tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq transcripts

source_name: B220+PNA+GL7+ GC B cells

extract_protocol:
total RNA (including small RNAs) was extracted with the miRNeasy kit (Qiagen) from FACS-sorted B220+ B cells or B220+PNA+GL7+ GC B cells isolated from indicated mice
Multiplexed libraries were constructed using the Illumina TruSeq RNA Sample Prep Kit. Libraries were sequenced on the Illumina HiSeq 2500 according to the manufacturer's instructions.

value: miR-146a KO

value: GC B cells


title: STR_DRE_CRE_CNO_2


title: DRE_CREB_SALINE_2


title: CREB stroke B4


title: DRE_CREB_SALINE_1


title: Control stroke B3


title: CREB stroke B1


title: DRE_CREB_CNO_1


title: Control stroke B4


title: Control stroke A2


title: CREB stroke B2


title: STR_DRE_CRE_SAL_2


title: CREB2

value: CREB


title: CREB stroke A2


title: GCB_KO_SRBC_2: SRBC-immunized miR-146a KO GC B cells

description: total RNA (including small RNAs)


title: Control stroke A1


title: DRE_CREB_CNO_2


title: CREB stroke A1


title: CREB stroke B3


title: CREB1


title: BALF_exosome_poly(I:C)_inoculation_72h_rep2

city: Madison

first: Tadashi

last: Maemura

state: Wisconsin

address: 575 Science Drive

institute: Influenza Research Institute

description: miRNA expression in BALF exosome in poly(I:C) inoculation at 72 h

hyb_protocol: Cy3-pCp-labelled RNA was resuspended in hybridization master mix and was hybridized on the Agilent SurePrint G3 Mouse miRNA 8 × 60 K V19 at 55°C for 20 h.

scan_protocol: The microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (Agilent Technologies), and image data were processed by using Agilent Feature Extraction software ver. 10.7.3.1.

data_processing: All data were subsequently uploaded into GeneSpring GX ver. 13.0 for data analysis. We selected miRNAs that were filtered on Expression (20–100th) percentile in the Normalized data and were flagged as Detected. Then, we selected miRNAs whose expression was statistically significantly different by moderated t-test (naive vs. 48 hpi, and naive vs. 72 hpi) and 2-fold higher than those in the naive mice group.

source_name: poly(I:C) inoculation, 72h, BALF exosome, replicate 2

label_protocol: One hundred nanograms of total RNA was used for miRNA microarray by using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies) according to the manufacturer’s instructions. Cy3-pCp-labelled RNA was dried by a vacuum concentrator at 40°C for 2 h.

extract_protocol: The total RNA from the exosomes was isolated by using the miRNeasy Serum/Plasma Kit (QIAGEN). Isolated total RNA integrity was evaluated by using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and by examining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer (Agilent Technologies) according to the manufacturer’s instructions. We confirmed that the RNA isolated from the exosomes did not contain ribosomal RNAs.

treatment_protocol: Mouse lungs were lavaged with 1 ml of phosphate-buffered saline (PBS). Lavage fluid (800 µl) was collected by gentle aspiration. This procedure was repeated three times. BALF was centrifuged at 1,100 × g for 15 min at 4°C, and the cells and supernatants were collected.  BALF was centrifuged at 16,000 × g for 60 min at 4°C. To remove cellular debris, the recovered supernatants were filtered through a 0.22-μm Millex-GV (Millipore, MA, USA). The supernatant was then ultracentrifuged at 100,000 × g for 90 min at 4°C. The pellets containing the exosomes were resuspended in 100 µl of PBS.

value: Blonchoalveolar lavage fluid exosome

tag: stimulant

value: poly(I:C) inoculation at 72 h


title: BALF_exosome_poly(I:C)_inoculation_72h_rep3

source_name: poly(I:C) inoculation, 72h, BALF exosome, replicate 3


title: BALF_exosome_poly(I:C)_inoculation_72h_rep1

source_name: poly(I:C) inoculation, 72h, BALF exosome, replicate 1


title: BALF_exosome_PR8_infection_72hpi_rep3

description: miRNA expression in BALF exosome in PR8 infection at 72 hpi

source_name: PR8 infection, 72hpi, BALF exosome, replicate 3

value: PR8 infection at 72 hpi


title: Control 2

value: TOMATO


title: B_KO_nonimm_3: non-immunized miR-146a KO B cells

description: total RNA (including small RNAs)

source_name: B220+ B cells

value: B cells


title: Control 1


title: B_KO_nonimm_2: non-immunized miR-146a KO B cells

description: total RNA (including small RNAs)


title: GCB_WT_SRBC_3: SRBC-immunized WT GC B cells

description: total RNA (including small RNAs)

value: WT


title: BALF_exosome_PR8_infection_48hpi_rep2

description: miRNA expression in BALF exosome in PR8 infection at 48 hpi

source_name: PR8 infection, 48hpi, BALF exosome, replicate 2

value: PR8 infection at 48 hpi


title: BALF_exosome_PR8_infection_48hpi_rep1

source_name: PR8 infection, 48hpi, BALF exosome, replicate 1


title: BALF_exosome_PR8_infection_72hpi_rep1

source_name: PR8 infection, 72hpi, BALF exosome, replicate 1


title: BALF_exosome_PR8_infection_72hpi_rep2

source_name: PR8 infection, 72hpi, BALF exosome, replicate 2


title: GCB_WT_SRBC_2: SRBC-immunized WT GC B cells

description: total RNA (including small RNAs)


title: BALF_exosome_PR8_infection_24hpi_rep2

description: miRNA expression in BALF exosome in PR8 infection at 24 hpi

source_name: PR8 infection, 24hpi, BALF exosome, replicate 2

value: PR8 infection at 24 hpi


title: GCB_WT_SRBC_1: SRBC-immunized WT GC B cells

description: total RNA (including small RNAs)


title: BALF_exosome_PR8_infection_24hpi_rep3

source_name: PR8 infection, 24hpi, BALF exosome, replicate 3


title: BALF_exosome_naive_rep2

description: miRNA expression in BALF exosome in naive condition

source_name: naive mice, BALF exosome, replicate 2

value: naive condition


title: BALF_exosome_PR8_infection_24hpi_rep1

source_name: PR8 infection, 24hpi, BALF exosome, replicate 1


title: BALF_exosome_naive_rep3

source_name: naive mice, BALF exosome, replicate 3


title: B_WT_nonimm_3: non-immunized WT B cells

description: total RNA (including small RNAs)


title: BALF_exosome_naive_rep1

source_name: naive mice, BALF exosome, replicate 1


title: B_WT_nonimm_2: non-immunized WT B cells

description: total RNA (including small RNAs)


title: MM_BMSC_12_exo

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

data_processing:
ath-miR-159 were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).
Fold Change worksheet reports test/control ratios.

label: TaqMan probe (FAM-MGB)

organism: Homo sapiens

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

growth_protocol: BMSCs were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2, and the adherent cells were collected after two or three passages for subsequent analysis.

extract_protocol: Total RNA was isolated with the miRNeasy mini kit (Qiagen).

treatment_protocol: The exosomes from culture medium of BMSCs were isolated by Exoquick-TC (SBI).

tag: subject status

value: MM patient

tag: age

value: 74 years

value: Bone marrow stromal cells (BMSCs)

tag: sample type

value: test


title: MM_BMSC_14_exo

value: 68 years


title: MM_BMSC_4_exo


title: MM_BMSC_5_exo

value: 81 years


title: GCB_KO_SRBC_1: SRBC-immunized miR-146a KO GC B cells

description: total RNA (including small RNAs)

tag: strain

value: miR-146a KO

value: GC B cells


title: B_WT_nonimm_1: non-immunized WT B cells

description: total RNA (including small RNAs)

tag: genotype/variation


title: B_KO_nonimm_1: non-immunized miR-146a KO B cells

description: total RNA (including small RNAs)

tag: cell type


title: MM_BMSC_2_exo

value: 82 years


title: BALF_exosome_PR8_infection_48hpi_rep3

source_name: PR8 infection, 48hpi, BALF exosome, replicate 3

value: Blonchoalveolar lavage fluid exosome


title: npr1-1_npr4-4D_untreated_2

city: Vancouver

first: Yuelin

last: Zhang

state: BC

address: 6270 University Blvd

department: Department of Botany

country: Canada

institute: University of British Columbia

description:
countDFeByg_paired.txt
sample name: sorted_paired_Zhang_08.bam.bam

data_processing:
Reads were aligned to TAIR10 using HISAT2 version 2.0.4 on default parameters
SAMtools version 0.1.12  was used to convert SAM files, sort and index BAM files
Read counts were generated for each gene using summarizeOverlaps (R package GenomicAlignments) with the following settings: mode = "Union", ignore.strand = TRUE, inter.feature  = FALSE, singleEnd = TRUE
Genome_build: Tair10
Supplementary_files_format_and_content: Matrix containing counts for each sample

organism: Arabidopsis thaliana

source_name: two-week old seedling tissue

growth_protocol: two-week-old seedlings of npr1-1, npr4-4D and wild- type plants grown on  ½ MS media

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen) with on-column DNase digestion, following the manufacturer’s instructions.
Libraries were prepared using standard Illumina protocols

treatment_protocol: 50μM SA was sprayed on seedlings

tag: ecotype

value: Col

tag: treatment

value: Untreated

value: npr1-1 npr4-4D

value: seedling

value: 2 weeks old


title: MGUS_BMSC_13_exo

value: MGUS patient

value: 72 years


title: npr1-1_npr4-4D_untreated_1

description:
countDFeByg_paired.txt
sample name: sorted_paired_Zhang_07.bam.bam


title: npr1-1_npr4-4D_treated_2

description:
countDFeByg_paired.txt
sample name: sorted_paired_Zhang_16.bam.bam

value: Treated


title: MGUS_BMSC_1_exo

value: 53 years


title: MM_BMSC_20_exo

value: MM patient

value: 74 years

value: Bone marrow stromal cells (BMSCs)


title: Ex_vivo_AF9_cells_KO-PRDM16+SPRDM16_replicate_1

description:
AF9_KOSL_1
AF9_RNAseq_Counts.txt

source_name: Ex vivo MLL-AF9 cells from moribund mice

value: Leukemic MLL-AF9 cells

value: PRDM16-KO overexpressing either s-PRDM16

tag: group


title: npr1-1_npr4-4D_treated_1

description:
countDFeByg_paired.txt
sample name: sorted_paired_Zhang_15.bam.bam

tag: tissue


title: normal_BMSC_2_exo

value: elderly donors

value: control


title: MM_BMSC_20_cell

data_processing:
RNU6B were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
Fold Change worksheet reports test/control ratios.

source_name: MM patient (age of donor: 74 years)

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA).

tag: disease status

value: Multiple myeloma (MM)

value: test


title: Ex_vivo_AF9_cells_KO-PRDM16+SPRDM16_replicate_2

description:
AF9_KOSL_2
AF9_RNAseq_Counts.txt


title: Ex_vivo_AF9_cells_KO-PRDM16+FPRDM16_replicate_3

description:
AF9_KOFL_3
AF9_RNAseq_Counts.txt

value: PRDM16-KO overexpressing either f-PRDM16


title: MGUS_BMSC_2_exo

value: 78 years


title: MM_BMSC_14_cell

source_name: MM patient (age of donor: 68 years)

value: 68 years


title: npr4-4D_untreated_1

description:
countDFeByg_original.txt
sample name: sorted_39_1.bam.bam

value: Col

value: Untreated

tag: genotype

value: seedling

value: 2 weeks old


title: MM_BMSC_12_cell


title: npr4-4D_treated_2

description:
countDFeByg_original.txt
sample name: sorted_46_1.bam.bam

value: Treated


title: MM_BMSC_4_cell


title: Ex_vivo_AF9_cells_KO-PRDM16+FPRDM16_replicate_1

description:
AF9_KOFL_1
AF9_RNAseq_Counts.txt


title: normal_BMSC_1_exo


title: Ex_vivo_AF9_cells_KO-PRDM16+FPRDM16_replicate_2

description:
AF9_KOFL_2
AF9_RNAseq_Counts.txt


title: npr4-4D_treated_1

description:
countDFeByg_original.txt
sample name: sorted_45_1.bam.bam


title: MM_BMSC_2_cell

source_name: MM patient (age of donor: 82 years)

value: 82 years


title: Ex_vivo_AF9_cells_KO-PRDM16+SPRDM16_replicate_3

description:
AF9_KOSL_3
AF9_RNAseq_Counts.txt


title: Ex_vivo_AF9_cells_KO-PRDM16+EV_replicate_3

description:
AF9_KOEV_3
AF9_RNAseq_Counts.txt


title: MGUS_BMSC_13_cell

source_name: MGUS patient (age of donor: 72 years)

value: Monoclonal gammopathy of undetermined significance (MGUS)

value: 72 years


title: npr1-1_untreated_2

description:
countDFeByg_original.txt
sample name: sorted_38_1.bam.bam


title: MGUS_BMSC_2_cell

source_name: MGUS patient (age of donor: 78 years)

value: Bone marrow stromal cells (BMSCs)


title: Ex_vivo_AF9_cells_KO-PRDM16+EV_replicate_2

description:
AF9_KOEV_2
AF9_RNAseq_Counts.txt

value: Leukemic MLL-AF9 cells


title: MGUS_BMSC_1_cell

source_name: MGUS patient (age of donor: 53 years)

value: 53 years


title: npr1-1_untreated_1

description:
countDFeByg_original.txt
sample name: sorted_37_1.bam.bam


title: Ex_vivo_AF9_cells_KO-PRDM16+EV_replicate_1

description:
AF9_KOEV_1
AF9_RNAseq_Counts.txt


title: npr1-1_treated_2

description:
countDFeByg_original.txt
sample name: sorted_42_1.bam.bam


title: npr4-4D_untreated_2

description:
countDFeByg_original.txt
sample name: sorted_40_1.bam.bam


title: npr1-1_treated_1

description:
countDFeByg_original.txt
sample name: sorted_41_1.bam.bam


title: Ex_vivo_AF9_cells_WT-PRDM16+EV_replicate_3

description:
AF9_WTEV_3
AF9_RNAseq_Counts.txt

value: wild type


title: MM_BMSC_5_cell

source_name: MM patient (age of donor: 81 years)

value: Multiple myeloma (MM)

value: 81 years


title: normal_BMSC_2_cell

source_name: Elderly donors (age of donor: 72 years)

value: Healthy

value: control


title: Ex_vivo_AF9_cells_WT-PRDM16+EV_replicate_1

description:
AF9_WTEV_1
AF9_RNAseq_Counts.txt


title: WT_untreated_2

description:
countDFeByg_original.txt
sample name: sorted_36_1.bam.bam

value: WT


title: normal_BMSC_1_cell

source_name: Elderly donors (age of donor: 68 years)

value: 68 years


title: Ex_vivo_AF9_cells_WT-PRDM16+EV_replicate_2

description:
AF9_WTEV_2
AF9_RNAseq_Counts.txt


title: WT_treated_1

description:
countDFeByg_original.txt
sample name: sorted_43_1.bam.bam

value: Col


title: WT_treated_2

description:
countDFeByg_original.txt
sample name: sorted_44_1.bam.bam

value: seedling


title: input DNA

city: Tel Aviv

first: Yuval

last: Ebenstein

address: Haim Levanon

department: Physical Chemistry

country: Israel

institute: Tel Aviv University

description: input sample for hMeDIP-seq

data_processing:
Library strategy: hMeDIP-seq
Sequencing reads were aligned to the hg19 genome assembly using Bowtie2 version 2.2.6 with default parameters.
reads with MAPQ less than 30 were filtered with SAMtools, and the remaining reads were de-duplicated with Picard to eliminate PCR duplication bias.
Reads from the pull-down data set were extended in the 3' direction to a total length of 200 bp, in order to account for insert size.
Genomic coverage of 5-hmC and input DNA was calculated using BEDTools version 2.25.0.
All regions where the 5-hmC signal was lower than 7 were set to zero based on the signal extraction scaling method. Additionally, ENCODE-defined signal artifact regions were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig and bedGraph files contain the 5-hmC and input coverage in each genomic position

source_name: Peripheral blood mononuclear cells

extract_protocol:
Samples were prepared according to the IrysPrep™ Plug Lysis Long DNA Isolation Protocol (Bionano Genomics Inc.)
Libraries were prepared by Epigentek Inc.

value: Peripheral blood mononuclear cells

tag: antibody


title: SC_92558_2

description:
processed data file:
VSMC_sc_umi.csv

source_name: Human carotid artery

value: Human carotid artery


title: SC_92558_1

description:
processed data file:
VSMC_sc_umi.csv


title: SC_92467_2

description:
processed data file:
VSMC_sc_umi.csv


title: hnRNPA1_si_rep1

city: Berkeley

first: Yeon

last: Lee

address: 1 Barker Hall

institute: UC Berkeley

data_processing:
For JUM analysis, RNA-seq reads were mapped to hg38 using STAR (v2.5.2) (Dobin et al., 2013) with the 2-pass mode (Dobin et al. 2013) for junction discovery. Only unique mapped reads were considered in the downstream JUM (v1.3.7) (Wang et al., 2016) analysis. Only splice junctions that received more than 5 reads in each of the replicates of the RNAi and the control knockdown samples are considered as valid junctions for downstream analysis. A p-value of 0.05 is used as the statistical cutoff for differentially spliced AS events.
For MISO (v0.5.4) analysis (Katz et al. 2010), the reads from replicate samples were mapped to hg19 genome using Tophat (v2.0.8) (--library-type fr-firststrand) (Trapnell et al. 2009) for stranded RNA-seq libraries, then merged for differential splicing analysis. The duplicate sample reads were merged then sorted using SAMtools (Li et al. 2009) for MISO analysis. The minimum number of inclusion and exclusion RNA-seq reads over each detected splicing junction was set to 10, and differential splicing events were detected using the following options using MISO: filter_events.py --num-inc 1 --num-exc 1 --num-sum-inc-exc 10 --delta-psi --bayes-factor 10.

source_name: Myeloid leukemia cell line

growth_protocol: Human K562 cells (American Type Culture Collection, Manassas, VA, USA) were maintained at 37◦C in RPMI media, supplemented with 15% FBS, 1 mM sodium pyruvate (Gibco, Life Technologies), and 1X nonessential amino acids (Gibco, Life Technologies).

extract_protocol:
After RNA isolation using RNeasy Mini Kit (Qiagen #74104), followed by 30 min DNase treatment (Ambion AM2238) at 37°C.
Poly(A)+ RNA transcript was isolated (NEBNext Poly(A) mRNA Magnetic Isolation Module - NEB #E7490) from 1 microgram of total RNA for RNA library preparation and sequencing using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB # E7420S) according to the manufacture’s instruction.

treatment_protocol: siRNA duplexes (Ambion, Life Technologies) were generated against the following target sequences or commercially purchased: hnRNPA1 siRNA 1: CAGCTGAGGAAGCTCTTCA (sequence provided by Dr. James Manley); hnRNPA1 siRNA 2 (s6710; Ambion, Life Technologies); DDX5 siRNA 1 (s4009; Ambion, Life Technologies); and DDX5 siRNA 2 (s4008; Ambion, Life Technologies). Non-specific control siRNA duplexes 1 [scrambled siRNA (scr si)] were purchased from Life Technologies (4390843). For all knockdown experiments, combinations of hnRNPA1 siRNA 1 and 2 (hnRNPA1 combo siRNA) or DDX5 siRNA 1 and siRNA 2 (DDX5 combo siRNA) were used.

tag: cell line

value: human myeloid leukemia cell line


title: SC_92467_1

description:
processed data file:
VSMC_sc_umi.csv


title: hnRNPA1_si_rep2


title: scr_si_rep4


title: DDX5_si_rep2


title: scr_si_rep3


title: DDX5_si_rep1


title: scr_si_rep1


title: scr_si_rep2


title: RIF woman serum  Replicate 3

city: lanzhou

first: lin

last: liu

address: chengguanqu donggangxilu 1 hao

country: China

institute: lanzhou university

description: serum were obtained from women who had experienced RIF after ovarian stimulation and IVF-ET. RIF was defined as women who had undergone≥3 failed cycles with high-grade embryos were transferred.

hyb_protocol: Each array was hybridized with 100 ng of Cy3-labelled RNA using the miRNA Complete Labeling and Hyb Kit (Exiqon) in a hybridization oven that was set at 55 ℃ and 20 r.p.m for 20 h according to the manufacturers’ instructions.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.
Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: RIF woman serum  Replicate 3

label_protocol: The miRCURY LNA Array system (Exiqon, Vedbaek, Denmark)  was used according to the manufacturer’s guideline for miRNA labelling. 1, After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:    a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture          was incubated for 30 min at 37°C.      b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of          fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling          reaction was incubated for 1 h at 16°C    c, Terminated by incubation for 15 min at 65°C.     2, After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.    a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first          denatured for 2 min at 95°C, incubated on ice for 2 min    b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization          System - Nimblegen Systems, Inc., Madison, WI, USA)      c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

growth_protocol: 10 ml of venous blood was withdrawn into anticoagulant-free tubes.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.  miRNA labeling and array hybridization

treatment_protocol: After 1 h incubation, serum was separated by centrifugation, aliquoted and stored at −70 °C until further analyses.

tag: Sex

value: female


title: fertile woman serum  Replicate 3

description: serum were obtained from fertile women who had given birth at least once

source_name: fertile woman serum  Replicate 3


title: WT_untreated_1

description:
countDFeByg_original.txt
sample name: sorted_35_1.bam.bam

value: Untreated

value: 2 weeks old


title: RIF woman serum  Replicate 2

source_name: RIF woman serum  Replicate 2


title: RIF woman serum  Replicate 1

source_name: RIF woman serum  Replicate 1


title: hMeDIP-seq

value: 5-hmC monoclonal antibody


title: fertile woman serum  Replicate 2

source_name: fertile woman serum  Replicate 2


title: fertile woman serum  Replicate 1

source_name: fertile woman serum  Replicate 1


title: RNA-seq_SB-treated_rep4

city: Chicago

first: He

last: Huang

institute: The University of Chicago

data_processing:
RNA-seq reads were mapped to reference genome of Illumina iGenomes UCSC hg38 using TopHat version 2.1.0.
Mapped reads were summarized for each gene using featureCounts version 1.5.0.
Differential expression analysis was implemented using edgeR version 3.16.5.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR version 3.16.5.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: Cultured cells

growth_protocol: Cells were cultured in DMEM with 10% FBS

extract_protocol:
Total RNAs were extracted from cells using the RNeasy Mini Kit (QIAGEN Inc, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: In the treatment group, cells were treated with 10 mM sodium benzoate for 24 hours before harvesting


title: RNA-seq_SB-treated_rep1


title: RNA-seq_SB-treated_rep3


title: RNA-seq_control_rep4


title: D458Med_shRNA_Ctrl_rep2

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: The D458Med cell line has been infected with lentivirus encoding shRNA control or targeting NRL. Transcriptome of Control vs NRL knock-down cells has bee studied.

value: Ctrl


title: RNA-seq_control_rep3


title: RNA-seq_control_rep2


title: D458Med_shRNA_NRL_rep3

value: downregulated NRL


title: D458Med_shRNA_NRL_rep2


title: D458Med_shRNA_NRL_rep1


title: D458Med_shRNA_Ctrl_rep1


title: D458Med_shRNA_Ctrl_rep3


title: C (control, non stretched sample) rep 3

city: Pisa

first: Vittoria

last: Raffa

state: Please Select

address: S.S. 12 Abetone e Brennero, 4

department: Department of Biology

country: Italy

institute: Università di Pisa

data_processing:
Conventional base calls Sanger / Illumina 1.9
Trimming: cutadapt 1.9.dev3 with Python 2.7.10. Reads have been trimmed for contaminating sequence adapters and low quality bases. The parameters for quality trimming are: i) bases are trimmed if the Phred score falls below 25, ii) reads are removed if the length of the reads is trimmed to less than 54 bp and iii) if the sequence data is paired end then the pair is also removed.
Abundance measurament: kallisto 0.43.0
Differential gene expression analysis: Deseq2
Genome_build: rn6
Supplementary_files_format_and_content: abundance measurament and files generated by Deseq2

organism: Rattus norvegicus

source_name: ATCC® CRL-1721™

growth_protocol: Rat pheochromocytoma PC12 cells obtained from American Type Culture Collection (ATCC) were cultured in Dulbecco’s modified Eagle’s medium with 10% horse serum, 5% fetal bovine serum (FBS), 100 IU/ml penicillin, 100 µgml−1 streptomycin and 2 mM L-glutamine. Cells were cultured in Petri dishes coated with poly-l-lysine 10 µgml−1 (PLL, Sigma, P1274) and maintained at 37°C in a saturated humidity atmosphere of 95% air and 5% CO2.

extract_protocol:
Cell pellets were killed in liquid nitrogen and RNA was extracted according to micro RNeasy Kit (Qiagen). Homogenization step was performed with QIAshredder columns (Qiagen). Quality check (QC) was performed (RIN=10).
RNAseq was performed with the platform Illumina NextSeq500. RNA library was prepared by using polyA selection library (TruSeq stranded mRNA sample prep kit was used with 1 ug of total RNA for the construction of sequencing libraries) and sequencing mode: PE 2x75bp, 33M.

treatment_protocol: 500,000 cells were seeded in 35 mm Petri dishes (pre-coated with PLL 1 µg/ml). Cells were used at passage 6. 24 h later, cells were incubated in differentiation medium, i.e. in reduced serum medium (1% FBS) supplemented with NGF 100 ng/ml and MNP 10 µg/ml. MNP used in this experiments were deeply described in (J. Mater. Chem. B, 2013,1, 3607-3616, doi: 10.1039/C3TB20336K). 18 h later, one group (sample, S) was placed in a toroidal magnet (the magnet described in https://doi.org/10.1016/j.nano.2013.12.008). 9 h later, stretched groups (S, sample) and non stretched groups (C, control) were chilled in N2 and the RNA extracted.

tag: passage

value: non stretched


title: C (control, non stretched sample) rep 2


title: C (control, non stretched sample) rep 1


title: S (stretched sample) rep 3

value: stretched


title: BM-MSC donor 7

city: Edegem

first: Steffi

last: Matthyssen

state: Antwerpen

address: Wilrijkstraat 10, UZA/CCRG U113

country: Belgium

institute: University of Antwerp

description: control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using the CFX Manager software Gene Study (http://www.bio-rad.com/en-be/product/cfx-manager-software?ID=aed9803d-cb4d-4ecb-9263-3efc9e650edb)
For the normalization it uses the average of three housekeeping genes: TBP, HPRT1 and GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The CFX manager software automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (CS-MSCs/BM-MSCs) ratios.

label: SYBR Green

source_name: bone marrow

label_protocol: qRT-PCR assays were prepared in triplicate in 96-well PrimePCR plates for human MSCs (Mesenchymal stem cells, SAB Target List, Bio-Rad Laboratories, Temse, Belgium). From the purified RNA, 10ng was used per sample to synthesize cDNA using the iScript Advanced cDNA synthesis kit (Bio-Rad Laboratories, Temse, Belgium) following the protocol supplied by the manufacturer. Quantitative real-time PCR were performed (CFX96 Real-Time System – C1000 Thermal Cycler, Bio-Rad) with 40 cycles at 95°C for 5 seconds and 60°C for 30 seconds.

growth_protocol: CS-MSCs from six donors were seeded after isolation in both Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), as the standard culture condition, and in DMEM supplemented with 10% Human Platelet Lysate (HPL), following our optimized xeno-free culture protocol reported previously (Matthyssen et al. IOVS 2017). BM-MSCs from a single donor were expanded in DMEM + 10% FBS. When 80% to 90% confluence was reached, cells were passaged using TrypLE (Life Technologies, Gent, Belgium) for 5 minutes. All cells were used in the experiments before the 6th passage.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: bone marrow mesenchymal stem cells


title: RNA-seq_control_rep1


title: ChIP-seq_SB-treated_Kbz

data_processing:
ChIP-seq reads were mapped to reference genome of Illumina iGenomes UCSC hg38 using Bowtie (version 2.2.6), and only the uniquely mapped reads were retained
SAMtools (version 0.1.19) was then used to convert files to bam format, sort, and remove PCR duplicates
Peaks were called using MACS2 (version 2.1.1) with FDR = 0.01
Genome_build: hg38
Supplementary_files_format_and_content: text file with called peaks.

extract_protocol:
Chromatin was prepared by MNase digestion and isolated with antibody.
ChIP-seq libraries were prepared following the TruSEq Chip-SEQ kit (Illumina, San Diego, CA) as per manufacturer’s instruction.

tag: chip antibody

value: Anti-Pan Kbz (manufacturer:PTM Biolabs; not commercially available now)


title: RNA-seq_SB-treated_rep2


title: S (stretched sample) rep 2


title: ChIP-seq_SB-treated_Kac

value: Anti-Pan Kac (manufacturer:PTM Biolabs; catalog number:PTM-101; lot number:01BC08M02)


title: CS-MSC donor 6 FBS

description: test

source_name: corneal stroma

value: corneal stromal mesenchymal stem cells

tag: supplements

value: FBS


title: S (stretched sample) rep 1


title: ChIP-seq_SB-treated_input


title: CS-MSC donor 6 HPL

description: test

value: HPL


title: ChIP-seq_control_Kbz

description: No peaks were identified in the peak calling for this sample, therefore there is no associated processed data file.


title: CS-MSC donor 5 FBS

description: test


title: CS-MSC donor 5 HPL

description: test


title: ChIP-seq_control_Kac


title: CS-MSC donor 4 FBS

description: test


title: ChIP-seq_control_input


title: CS-MSC donor 4 HPL

description: test


title: CS-MSC donor 3 FBS

description: test


title: CS-MSC donor 3 HPL

description: test


title: CS-MSC donor 2 FBS

description: test


title: CS-MSC donor 1 HPL

description: test


title: CS-MSC donor 1 FBS

description: test


title: CS-MSC donor 2 HPL

description: test


title: U937_ATAC-seq

status: Public on Jun 07 2018

city: Cambridge

first: Sharon

middle: R

last: Grossman

address: 415 Main Street

institute: Broad Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the hg19 genome assembly using Bowtie2 version 2.1.0 with the parameter --maxins 1000
Data were filtered using MAPQ>30
Peaks were called using using MACS2 (95) with the standard parameters used by the Epigenomics Roadmap Project.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain significant peaks

source_name: U937 cells

extract_protocol: Cells were washed with ice cold FACS Buffer and kept on ice until cell sorting. 25,000 live cells from each condition were sorted in to FACS Buffer and pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed angle centrifuge. Cell lines were then tagmented according to the previously described Fast-ATAC protocol (92). Briefly, all supernatant was removed being careful to not disturb the not visible cell pellet. 50 ul transposase mixture (25 ul of 2x TD, 2.5 ul of TDE1, 0.5 ul of 1% digitonin, 22 ul of nuclease-free water) (Cat# FC-121-1030, Illumina; Cat# G9441, Promega) was added to the cells, the pellet was dissociated by pipetting. Transposition reactions were incubated at 37C for 30 minutes in an Eppendorf ThermoMixer with agitation at 300 RPM. Transposed DNA was purified using a QIAgen MinElute Reaction Cleanup kit (Cat# 28204) and purified DNA was eluted in 12 ul elution buffer (10 mM Tris-HCl, pH 8). Transposed fragments were amplified and purified as described previously (93) with modified primers (94). Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on a NextSeq with 76x8x8x76 cycle reads at an average read depth of 30 million reads per sample.

value: U937 myeloid lymphocyte


title: Jurkat_ATAC_seq

source_name: Jurkat cells

growth_protocol: Cells were washed with ice cold FACS Buffer and kept on ice until cell sorting. 25,000 live cells from each condition were sorted in to FACS Buffer and pelleted by centrifugation at 500 RCF for 5 minutes at 4C in a pre-cooled fixed angle centrifuge.

value: Jurkat T lymphocytes


title: GM12878-DNA-SPRITE01

city: Princeton

first: Sofia

middle: Agustina

last: Quinodoz

state: NJ

address: 25 William St

department: CBE

institute: Princeton University

description:
The reads have the following structure: Read 1 contains genomic DNA positional information and the DPM tag, and Read 2 has the remaining tags.
Processed data files:
human.mapq-ge10.clusters.gz
human.mapq-ge30.clusters.gz

data_processing:
Library strategy: DNA SPRITE
SPRITE barcodes were identified by parsing the first DNA tag sequence from the beginning of Read 1 (DPM) and the remainder of the tags were parsed from Read 2. We identified these tag sequences corresponding to the DPM, Odd, Even, and Terminal tags that were added to these samples. The tags and their sequences were identified by software available at: https://github.com/GuttmanLab/sprite-pipeline/wiki/1.-Barcode-Identification. The configuration files required for this software are available on the series record.
We aligned each read to the appropriate reference genome (mm9 for mouse; hg19 for human) using Bowtie2 (v2.3.1). We trimmed the 11 base pair tag sequence (DPM) from Read 1 using the --trim5 11 parameter and used a local alignment search (--local).
We filtered the alignments for low quality reads, multimappers, and repetitive sequences. First, we removed all alignments with a MAPQ score less than 10 or 30. Second, we removed all reads that had >2 mismatches to the reference genome. Third, we removed all alignments that overlapped a region that was masked by Repeatmasker (UCSC, milliDiv < 140) using bedtools (v2.26.0). Fourth, we removed any read that aligned to a non-unique region of the genome by excluding alignments mapping to regions generated by the ComputeGenomeMask program in the GATK package (readLength=35nt mask).
To define SPRITE clusters, all reads that have the same barcode sequence were grouped into a single cluster. To remove possible PCR duplicates, all reads starting at the same genomic position with identical barcodes were removed.
Genome_build: mm9 (mouse), hg19 (human)
Supplementary_files_format_and_content: Cluster files were generated for the F1-21 mES cell and GM12878 lymphoblast DNA-SPRITE samples for all reads with MAPQ scores greater than 10 or 30. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments. When multiple positions are listed, these regions are in physical contact with each other. If only one position is listed, either that fragment exists on its own as a singleton, or the other constituent pieces were not sequenced.

source_name: B-lymphoblastoids

growth_protocol: Cell lines were cultured according to manufacturers instructions

extract_protocol: Cells were crosslinked with 3%FA-DSG and then lysed with nuclei isolated. DNA was then lightly sonicated and DNAse digested to an average size of approximately 150-1000 bp in length. Crosslinked protein-DNA complexes were isolated on NHS beads, DNA ends were repaired, dA-tailed to generate a protruding 3’ A-base for ligation of barcodes, and were then split-pool tagged with a series of barcodes over multiple rounds of split-and-pool tagging. For DNA-RNA SPRITE, a distinct RNA adaptor was ligated to RNA to flag a molecule as RNA rather than DNA. This adaptor contains a shared overhang that allows for simultaneous tagging of RNA and DNA during the split-and-pool tagging process. Reverse transcription was performed to convert RNA into cDNA. After split-and-pool tagging, crosslinks were reversed, the DNA/RNA was isolated, was amplified 8-12 cycles using standard Illumina library prep (single index), and purified using SPRI beads. Libraries were sequenced on the HiSeq2500 or NextSeq 500 following the manufacturer's protocols.

tag: protocol

value: DNA SPRITE


title: mES-DNA-SPRITE04

description:
The reads have the following structure: Read 1 contains genomic DNA positional information and the DPM tag, and Read 2 has the remaining tags.
Processed data files:
mouse.mapq-ge10.clusters.gz
mouse.mapq-ge30.clusters.gz

source_name: Mouse Embryonic Stem cells

growth_protocol: Mouse ES cell lines were cultured in serum-free 2i/LIF medium and maintained at an exponential growth phase


title: mES-DNA-SPRITE02


title: mES-DNA-SPRITE05


title: mES-DNA-SPRITE06


title: mES-DNA-SPRITE03


title: GM12878-DNA-SPRITE10


title: mES-DNA-SPRITE01


title: PDX tumor rep2

city: Clevleand

first: Mohamed

middle: E.

last: Abazeed

state: OH

department: Radiation Oncology/Translational Hematology Oncology Research

institute: Cleveland Clinic

description:
Sample 4
replicate 2

data_processing: Remove bad or no match probes; remove probes that are not expressed above control (FDR >=5%) in at least 3 arrays; quantile normalize and log2 transform data

source_name: human tumor grown in NSG mouse

tag: source gender

value: female

tag: host strain

value: NSG mouse

tag: tumor type

value: patient derived xenografts (PDX)  tumor


title: PDX tumor rep1

description:
Sample 3
replicate 1


title: CyrKOCdr1as671_cerebellum_smallRNA_1

first: David

middle: P

last: Bartel

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute / MIT

description:
29978029
DESeq2_CyrKOCdr1as671_cerebellum_smallRNA.txt

data_processing:
Reads were trimmed of adaptor sequence using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters "-q 30 -p 100" to ensure that all bases have an accuracy of 99.9%.
To count miRNAs in each library, the first 18 nts of each read were string-matched to a dictionary of miRNA sequences. Mouse and human dictionaries were based on annotations in miRbase_v20 and miRbase_v21, respectively. Matching to the first 18 nt had the advantage of combining all miRNA isoforms into a single count but also can result in ambiguous read assignments for mature miRNAs from distinct loci that are identical for the first 18 nt but differ at one or more positions closer to their 3′ ends (such as let-7a-5p and let-7c-5p). To avoid this ambiguity, these miRNAs (<5% of all annotations) were removed from the dictionary.
Count files were merged to generate tables of counts for each tissue organized by genotype. Differential expression was determined using DESeq2 v1.10-v1.18 (Love et al, Genome Biol 2014) with the parameter “betaPrior = FALSE” and with no lfcShrink function.
Genome_build: miRbase_v20 (mouse) or miRbase_v21 (human)
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 v1.10-v1.18 contain normalized counts for each library, log2-fold changes, and p-values

source_name: cerebellum

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Small-RNA sequencing libraries were prepared as described (Fang and Bartel, 2015), except for size selection, which was for small RNAs from 18–32 nts (instead of 18–30 nts). A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from 5 ug total RNA from tissues of 1-month-old male mice on a C57Bl/6J background.

tag: strain

value: cerebellum

tag: age

value: 1 month

value: male

value: CyrKO; Cdr1as 671 18 nt del

tag: rin


title: Primary tumor rep1

description:
Sample 1
replicate 1

source_name: human tumor

value: primary tumor of endometrial origin, metastasis


title: CyrKOCdr1as671_cerebellum_smallRNA_3

description:
23477689
DESeq2_CyrKOCdr1as671_cerebellum_smallRNA.txt


title: Incubated with Cocoa Extract for 24h -rep1

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description:
Gene expression data from treated control
CE-1

hyb_protocol: Hybridaztion was performed using GeneChip HT 3’IVT Express Kit

scan_protocol: GeneChips were scanned using Genechip scanner 3000(Affymetrix)

data_processing: Data was processed using Genespring v13 software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale, using a baseline transformation to the median of control samples

label: Biotin

source_name: Incubated with Cocoa Extract for 24h

label_protocol: RNA samples were processed in the automated  Biomek FX System (Beckman Coulter), where  cRNA was produced, and labeled with Biotin

growth_protocol: HT29 colorectal adenocarcinoma cells were seeded in 100 mm plates, grown in F12 + 7%FBS

extract_protocol: RNAeasy mini kit, extraction performed according to user's protocol.

treatment_protocol: 24 hours with either saline or  500 µg PCE (Polyphenolic cocoa extract)

tag: cancer type

value: colon

value: HT29 colorectal adenocarcinoma cells

tag: agent

value: cocoa


title: Cdr1as671_cerebellum_smallRNA_2

description:
23894453
DESeq2_Cdr1as671_cerebellum_smallRNA.txt

tag: tissue

value: Cdr1as 671 18nt del


title: Cdr1as671_cerebellum_smallRNA_3

description:
29626594
DESeq2_Cdr1as671_cerebellum_smallRNA.txt

tag: genotype


title: Primary tumor rep2

description:
Sample 2
replicate 2

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: Incubated with Cocoa Extract for 24h -rep2

description:
Gene expression data from treated control
CE-2


title: Untreated control, rep 2

description:
Gene expression data from untreated control
CNT-2

source_name: Untreated control

value: control


title: Untreated control, rep 3

description:
Gene expression data from untreated control
CNT-3


title: Incubated with Cocoa Extract for 24h -rep3

description:
Gene expression data from treated control
CE-3


title: Cdr1as671_cerebellum_smallRNA_1

description:
27341432
DESeq2_Cdr1as671_cerebellum_smallRNA.txt


title: CyrKO_hippocampus_smallRNA_3

description:
37816041
DESeq2_CyrKO_hippocampus_smallRNA.txt

source_name: hippocampus

value: hippocampus

value: CyrKO


title: CyrKO_hippocampus_smallRNA_1

description:
47904982
DESeq2_CyrKO_hippocampus_smallRNA.txt


title: CyrKO_hippocampus_smallRNA_2

description:
29261295
DESeq2_CyrKO_hippocampus_smallRNA.txt


title: WT_hippocampus_smallRNA_3

description:
36223454
DESeq2_CyrKO_hippocampus_smallRNA.txt

value: WT


title: WT_hippocampus_smallRNA_2

description:
33947634
DESeq2_CyrKO_hippocampus_smallRNA.txt


title: mES-RNA-DNA-SPRITE01

description:
genomic DNA, nuclear RNA
SPRITE RNA-DNA maps were generated in the pSM33 ES cell line (provided by K. Plath), a male ES cell line derived from the V6.5 ES cell line, which expresses Xist from the endogenous locus under the transcriptional control of a tet-inducible promoter and the Tet transactivator (M2rtTA) from the Rosa26 locus. We induced Xist expression in these cells using doxycycline (Sigma, D9891) at a final concentration of 2 µg/mL for 6-24 hours.
The reads have the following structure: Read 1 contains genomic DNA positional information and the DPM or cDNA tag, and Read 2 has the remaining tags.
Processed data files:
RNA_DNA_20160522_5p2.mapq-ge10.clusters.gz
RNA_DNA_20160522_5p2.mapq-ge30.clusters.gz

data_processing:
Library strategy: DNA-RNA SPRITE
SPRITE barcodes were identified by parsing the first DNA tag sequence from the beginning of Read 1 (DPM) and the remainder of the tags were parsed from Read 2. We identified these tag sequences corresponding to the DPM, Odd, Even, and Terminal tags that were added to these samples. The tags and their sequences were identified by software available at: https://github.com/GuttmanLab/sprite-pipeline/wiki/1.-Barcode-Identification. The configuration files required for this software are available on the series record.
We aligned each read to the appropriate reference genome (mm9 for mouse; hg19 for human) using Bowtie2 (v2.3.1). We trimmed the 11 base pair tag sequence (DPM) from Read 1 using the --trim5 11 parameter and used a local alignment search (--local).
We filtered the alignments for low quality reads, multimappers, and repetitive sequences. First, we removed all alignments with a MAPQ score less than 10 or 30. Second, we removed all reads that had >2 mismatches to the reference genome. Third, we removed all alignments that overlapped a region that was masked by Repeatmasker (UCSC, milliDiv < 140) using bedtools (v2.26.0). Fourth, we removed any read that aligned to a non-unique region of the genome by excluding alignments mapping to regions generated by the ComputeGenomeMask program in the GATK package (readLength=35nt mask).
To define SPRITE clusters, all reads that have the same barcode sequence were grouped into a single cluster. To remove possible PCR duplicates, all reads starting at the same genomic position with identical barcodes were removed.
Genome_build: mm9 (mouse), hg19 (human)
Supplementary_files_format_and_content: Cluster files were generated for the F1-21 mES cell and GM12878 lymphoblast DNA-SPRITE samples for all reads with MAPQ scores greater than 10 or 30. Each cluster, containing all reads with a shared series of tags, occupies one line of the resulting text file and contains the barcode name and genomic alignments. When multiple positions are listed, these regions are in physical contact with each other. If only one position is listed, either that fragment exists on its own as a singleton, or the other constituent pieces were not sequenced.

value: RNA-DNA SPRITE

tag: treatment

value: 24hr doxycycline for Xist induction


title: CyrKOCdr1as671_cerebellum_smallRNA_2

description:
29279727
DESeq2_CyrKOCdr1as671_cerebellum_smallRNA.txt


title: WT_hippocampus_smallRNA_1

description:
32129858
DESeq2_CyrKO_hippocampus_smallRNA.txt


title: CyrKO_cerebellum_smallRNA_1

description:
24462470
DESeq2_CyrKO_cerebellum_smallRNA.txt


title: CyrKO_cerebellum_smallRNA_3

description:
25539726
DESeq2_CyrKO_cerebellum_smallRNA.txt


title: WT_cerebellum_smallRNA_3

description:
25036114
DESeq2_CyrKO_cerebellum_smallRNA.txt
DESeq2_Cdr1as671_cerebellum_smallRNA.txt
DESeq2_CyrKOCdr1as671_cerebellum_smallRNA.txt


title: CyrKO_cerebellum_smallRNA_2

description:
36238934
DESeq2_CyrKO_cerebellum_smallRNA.txt


title: Untreated control, rep 1

description:
Gene expression data from untreated control
CNT-1

tag: cell line


title: WT_cerebellum_smallRNA_1

description:
27875118
DESeq2_CyrKO_cerebellum_smallRNA.txt
DESeq2_Cdr1as671_cerebellum_smallRNA.txt
DESeq2_CyrKOCdr1as671_cerebellum_smallRNA.txt

tag: Sex


title: Mir7DKO_cortex_Expt2_1

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR v2.4 (Dobin et al, Bioinformatics 2013) with the parameters “--outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate”.
Aligned reads were assigned to genes using annotations from Ensembl (Mus_musculus.GRCm38.73.gtf; downloaded October 15, 2014) and htseq-count v0.6.1p1 (Anders et al, Bioinformatics 2015) with the parameters “-m union -s no” for unstranded libraries and “-m union -s reverse” for stranded libraries.
Count files were merged to generate tables of counts for each tissue organized by genotype. Differential expression was determined using DESeq2 v1.10-v1.18 (Love et al, Genome Biol 2014) with the parameter “betaPrior = FALSE” and with no lfcShrink function.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 v1.10-v1.18 contain counts and normalized counts, log2-fold changes, and p-values for protein-coding and noncoding genes including Cyrano (1700020I14Rik) and Cdr1as

source_name: cortex

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. The Bioo Scientific NEXTflex RNA-Seq Kit (Cat#5138-10) was used with 4 ug of total RNA to construct polyA-selected stranded sequencing libraries.
RNA libraries were prepared for sequencing using standard Bioo Scientific protocols

value: cortex

tag: number of reads


title: WT_cortex_Expt2_3


title: Mir7DKO_cortex_Expt2_3


title: WT_cortex_Expt2_2


title: WT_cortex_Expt2_4


title: Mir7DKO_cerebellum_Expt2_3


title: WT_cortex_Expt2_1


title: WT_cerebellum_Expt2_3


title: WT_cerebellum_Expt2_4


title: Mir7DKO_cerebellum_Expt2_1


title: WT_cerebellum_Expt2_1


title: Mir7DKO_cerebellum_Expt1B_4


title: WT_cerebellum_Expt2_2


title: Mir7DKO_cerebellum_Expt1B_3


title: Mir7DKO_cerebellum_Expt1B_1


title: CyrKO_cerebellum_Expt1B_3


title: CyrKO_cerebellum_Expt1B_4


title: CyrKO_cerebellum_Expt1B_2


title: CyrKO_cerebellum_Expt1B_1


title: WT_cerebellum_smallRNA_2

description:
29884960
DESeq2_CyrKO_cerebellum_smallRNA.txt
DESeq2_Cdr1as671_cerebellum_smallRNA.txt
DESeq2_CyrKOCdr1as671_cerebellum_smallRNA.txt


title: Mir7DKO_cortex_Expt2_2


title: WT_cerebellum_Expt1B_3

description:
DESeq2_Expt2_CyrKO_cerebellum.txt
DESeq2_Expt2_Mir7DKO_cerebellum.txt


title: WT_cerebellum_Expt1B_4


title: WT_cerebellum_Expt1B_1


title: WT_cerebellum_Expt1B_2


title: CyrMut_cerebellum_Expt1A_4

value: CyrMut


title: CyrMut_cerebellum_Expt1A_3

value: cerebellum


title: Mir7DKO_cerebellum_Expt2_2

value: 1 month


title: CyrMut_cerebellum_Expt1A_2

value: male


title: WT_cerebellum_Expt1A_3


title: WT_cerebellum_Expt1A_2


title: CyrMut_cerebellum_Expt1A_1


title: Mir7DKO_cerebellum_Expt1B_2


title: CyrKO_striatumthalamus_3

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR v2.4 (Dobin et al, Bioinformatics 2013) with the parameters “--outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate”.
Aligned reads were assigned to genes using annotations from Ensembl (Mus_musculus.GRCm38.73.gtf; downloaded October 15, 2014) and htseq-count v0.6.1p1 (Anders et al, Bioinformatics 2015) with the parameters “-m union -s no” for unstranded libraries and “-m union -s reverse” for stranded libraries.
Count files were merged to generate tables of counts for each tissue organized by genotype. Differential expression was determined using DESeq2 v1.10-v1.18 (Love et al, Genome Biol 2014) with the parameter “betaPrior = FALSE” and with no lfcShrink function.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 v1.10-v1.18 contain counts and normalized counts, log2-fold changes, and p-values for protein-coding genes and Cyrano (1700020I14Rik)

source_name: striatum/thalamus

extract_protocol:
Tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. The Illumina TruSeq RNA Library Prep Kit v2 (Cat#RS-122-2001) was used with 4 ug of total RNA to construct polyA-selected unstranded sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: striatum/thalamus

value: 4 months


title: CyrKO_striatumthalamus_4


title: CyrKO_striatumthalamus_5


title: WT_cerebellum_Expt1A_1


title: CyrKO_striatumthalamus_1


title: CyrKO_striatumthalamus_2


title: WT_striatumthalamus_5


title: WT_striatumthalamus_1


title: WT_striatumthalamus_2


title: WT_striatumthalamus_4


title: CyrKO_spleen_4

source_name: spleen

value: spleen


title: WT_striatumthalamus_3


title: CyrKO_spleen_2


title: CyrKO_spleen_1


title: WT_spleen_3


title: CyrKO_spleen_3


title: WT_spleen_2


title: CyrKO_spleen_5


title: WT_spleen_1


title: CyrKO_skeletalmuscle_6

source_name: skeletal muscle

value: skeletal muscle


title: WT_spleen_4


title: CyrKO_skeletalmuscle_3


title: CyrKO_skeletalmuscle_1


title: CyrKO_skeletalmuscle_4


title: CyrKO_skeletalmuscle_5


title: CyrKO_skeletalmuscle_2


title: WT_skeletalmuscle_4


title: WT_skeletalmuscle_5


title: WT_skeletalmuscle_6


title: WT_skeletalmuscle_1


title: WT_skeletalmuscle_3


title: WT_skeletalmuscle_2


title: CyrKO_pituitary_4

source_name: pituitary

value: pituitary


title: WT_pituitary_3


title: WT_pituitary_2


title: CyrKO_pituitary_1


title: WT_pituitary_4


title: CyrKO_pituitary_3


title: CyrKO_islets_4

source_name: islets (pancreas)

value: islets (pancreas)


title: WT_pituitary_1


title: WT_pituitary_5


title: CyrKO_islets_3


title: CyrKO_islets_2


title: WT_islets_3


title: WT_islets_2


title: CyrKO_islets_1


title: WT_islets_1


title: CyrKO_hippocampus_4


title: CyrKO_hippocampus_3


title: WT_islets_4


title: CyrKO_hippocampus_2


title: CyrKO_hippocampus_1


title: WT_hippocampus_6


title: WT_hippocampus_4


title: CyrKO_pituitary_2


title: WT_hippocampus_3


title: WT_hippocampus_2


title: CyrKO_cortex_3


title: CyrKO_cortex_4


title: CyrKO_cortex_1


title: WT_hippocampus_1


title: WT_cortex_4


title: WT_cortex_2


title: CyrKO_cerebellum_3


title: CyrKO_cerebellum_4


title: CyrKO_cerebellum_2


title: WT_cerebellum_4


title: WT_cerebellum_3


title: WT_cerebellum_2


title: WT_hippocampus_5


title: WT_cerebellum_5


title: CyrKO_brownadipose_5

source_name: brown adipose tissue

value: brown adipose tissue


title: CyrKO_brownadipose_2


title: WT_cerebellum_1


title: CyrKO_cerebellum_1


title: CyrKO_brownadipose_1


title: CyrKO_brownadipose_4


title: CyrKO_brownadipose_3


title: WT_brownadipose_4


title: WT_brownadipose_3


title: CyrKO_cortex_2


title: WT_brownadipose_1


title: WT_cortex_3


title: CyrKO_anteriorcortex_5

source_name: anterior cortex

value: anterior cortex


title: WT_cortex_1


title: CyrKO_cerebellum_5

value: CyrKO


title: CyrKO_anteriorcortex_3


title: CyrKO_anteriorcortex_2


title: CyrKO_anteriorcortex_1


title: WT_anteriorcortex_5

value: WT


title: WT_anteriorcortex_4


title: WT_anteriorcortex_2


title: WT_brownadipose_5


title: WT_anteriorcortex_1


title: WT_anteriorcortex_3


title: DamID-seq CBX1

city: Boston

first: Chen-Yu

last: Wang

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Library strategy: DamID-seq
DamID-seq: DamID-seq reads were aligned allele-specifically to 129S1/SvJm (mus) and CAST/Eih (cas) genome using NovoAlign_v3-1.00.02. After removing PCR duplicates, uniquely mapped reads were used to generate log2 ratio tracks by normalizing to the Dam alone sample using all reads (comp), mus-specific (mus) reads, or cas-specific (cas) reads.
genome_build: mm9
Supplementary_files_format_and_content: DamID-seq: Uniquely mapped read pairs were used as input files for damidseq_pipeline to generate log2 ratio tracks by normalizing to the Dam alone sample (in the “kernel density estimation” mode) using all reads (comp), mus-specific (mus) reads, or cas-specific (cas) reads. To match sequencing depths, 45% reads from SMCHD1 rep2 libraries were randomly sampled to generate the normalized log2 ratio profiles.

source_name: mouse embryonic fibroblasts

growth_protocol: ES cell–derived neural progenitor cell clones were cultured on poly-L-ornithine (0.001%) and laminin (1μg/ml) coated plates with N2 media (DMEM/F-12, GlutaMAX™ supplement, 1X N2 supplement, 1X B27 supplement, 1X Pen/Strep) supplemented with FGF2 (20ng/ml), EGF (20ng/ml), laminin (1μg/ml), and heparin (10μg/ml). Undifferentiated ES cells were grown on 0.2% gelatin-coated plates with N2B27 media (mixture of 500ml DMEM/F12 media, 500ml Neurobasal media, 5ml N2 supplement, 10ml B27 supplement, 10ml Pen/Strep, 5ml GlutaMAX, and 2ml 55mM β-mercaptoethanol) supplemented with 1μM PD0325901, 3μM CHIR-99021, and 1000U/ml LIF. Embryoid bodies (EBs) were grown with differentiation media (DMEM, high glucose, GlutaMAX supplement, pyruvate, 15% Hyclone FBS, 25mM HEPES pH 7.2-7.5, 1X MEM non-essential amino acids, 1X Pen/Strep, 0.1mM β-mercaptoethanol) in suspension (D4 EBs) or on gelatin-coated plates (D7 EBs).

extract_protocol:
Total RNA was extracted using standard Trizol protocol. ChIP/CHART-enriched and input DNA were extracted with phenol:chloroform.
RNA-seq libraries were generated by dUTP-mediated directional RNA-seq based on NEBNext Ultra directional RNA library preparation protocol. ChIP-seq and Hi-C libraries were generated by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina. CHART-seq libraries were generated by NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: cell type

value: mouse embryonic fibroblasts


title: DamID-seq SMCHD1 rep2


title: DamID-seq SMCHD1 rep1


title: WT_brownadipose_2


title: 66

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Mice given a single bolus dose by oral gavage

data_processing:
FASTQC v0.11.3 was used for quality control
FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads
TopHat v2.1.0 was used for alignment
SAMTools v0.1.2 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified and examined for purity and quality by nanodrop, Qubit, Bioanalyzer and visualization on a denaturing gel.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Male C57BL/6 mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected at 2, 4, 8, 12, 24, 72, and 168h following gavage.

value: Male

tag: age unit

value: days

value: TCDD

tag: dose

tag: dose unit

value: ug/kg

tag: duration

tag: duration unit

value: hours

tag: replicate


title: 68

tag: strain

tag: age


title: 67


title: 63

value: Vehicle


title: 57


title: 58


title: 61


title: 56


title: 53


title: 62


title: 51


title: 48


title: CyrKO_anteriorcortex_4

value: male

tag: rin


title: 46


title: 47


title: 37


title: 42


title: 38


title: 43


title: 32


title: 33


title: DamID-seq Dam alone


title: 31


title: 52


title: 28


title: 27


title: 26


title: 23


title: Somatostatin+ cell in Subventricular Zone (3rd isolation)

city: Leuven

first: Lynette

last: Lim

address: Herestraat 49, ON5

department: Centre for Brain and Disease

institute: VIB-KUL

description: Svz_r3 (SL45158.bam)

data_processing:
Post processing of the sequencing reads from RNA-seq experiments from each sample was performed as per GSL pipeline. Briefly, quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK).Raw reads were mapped to the reference mouse genome mm9 (UCSD)  using TopHat v1.4 (Langmead et al., 2009; Trapnell et al., 2009) with two mismatches allowed and other default parameters.
The alignment metrics of the mapped reads was estimated using SAMtools (Li et al., 2009). Aligned reads were then imported onto the commercial data analysis platform, Avadis NGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95, and mapping quality less than 40 were removed.
Remaining reads were then filtered on the basis of their read statistics, where missing mates, translocated, unaligned and flipped reads were removed. The reads list was then filtered to remove duplicates.
Samples were grouped as MZ and SVZ identifiers and quantification of transcript abundance was done on this final read list using Trimmed Means of M-values (TMM) as the normalization method using EdgeR software in R (Robinson et al., 2010).
Differential expression of genes was calculated on the basis of observed between defined conditions, and the p-value of the differentially expressed gene list was estimated by Benjamini Hochberg False discovery rate (FDR) correction of 5% (Benjamini and Hochberg, 1995).
Genome_build: mm9
Supplementary_files_format_and_content: raw count value for each transcripts and DEseq2 fold change analyses comparing MZ vs SVZ cells

growth_protocol: Mouse embryonic tissue from SST-cre;Ai9

extract_protocol:
FACS cells were stored in Qiagen RNAeasy extraction kitsbuffer 1 in -80C. RNA containing both mRNA as well as miRNA fractions was extracted from approximately 10,000 to 15,000 SST+ FACS cells of either the MZ or SVZ using Invitroen RNA microKit with DNase treatment according to manufacturer's protocol. Final elution was made in 12 µl RNase free sterile distilled water. The concentration and integrity of the extracted total RNA was estimated by the Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA, USA).  RNA samples with a RNA integrity Number (RIN) value of at least 7.5 or higher was used for further processing.
All RNA-seq library preparation and sequencing were performed by Hudson Alpha Institute of Biotechnology (Huntsville, Alabama).  Briefly, total RNA from each sample was amplified using Ovation® RNA-Seq System V2 (NuGen Technologies, San Carlos, CA) using manufacturer's instructions. The amplified product was purified using QIAquick PCR cleanup column and final elution was made in 30µl Elution (EB) buffer (Qiagen Inc., Valencia, California, USA). Final yield and quality of the amplified product was checked using Qubit® 2.0 Fluorometer and DNA 1000 chip on the Agilent 2100 Bioanalyzer.  The post-ovation double-stranded DNA thus amplified by Ovation® RNA-Seq System V2 kit was ready for the construction of RNA-Seq libraries. Approximately, 2.5 µg amplified DNA from each sample was sheared on a Covaris S200 focused-ultrasonicator (Woburn, MA, USA) at 6°C water bath for 3 minutes with 200 cycles per burst with a target yield of  an average 200bp fragment size. Post shearing material was analyzed on a DNA 1000 chip on Agilent 2100 Bioanalyzer to confirm the targeted fragmentation range. Following this the fragmented DNA was taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA ) with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house Hudson Alpha genomics service lab (GSL) primers and amplified through 8 cycles of PCR using KAPA HiFi HotStart Ready Mix (Kapa Biosystems, Inc., Woburn, MA, USA). The quality of the final libraries were assessed by Qubit® 2.0 Fluorometer , and the concentration of the libraries was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer, respectively.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: embryonic day E17.5

value: brain

tag: tissue subtype

value: Subventricular Zone

value: Somatostatin interneurons


title: 22

tag: treatment


title: Somatostatin+ cell in Marginal zone (1st isolation)

description: Mz_r1 (SL45153.bam)

source_name: Somatostatin+ cell in Marginal zone

tag: tissue

value: Marginal zone


title: Somatostatin+ cell in Subventricular Zone (2nd isolation)

description: Svz_r2 (SL45156.bam)


title: Somatostatin+ cell in Subventricular Zone (1st isolation)

description: Svz_r1 (SL45154.bam)


title: 18

tag: Sex


title: 36


title: 16


title: Somatostatin+ cell in Marginal zone (2nd isolation)

description: Mz_r2 (SL45155.bam)

tag: cell type


title: 13

tag: age unit


title: 14

tag: dose


title: 11

tag: dose unit


title: 21

tag: duration


title: 09

tag: duration unit


title: 06

tag: replicate


title: Somatostatin+ cell in Marginal zone (3rd isolation)

description: Mz_r3 (SL45157.bam)


title: 01

tag: strain


title: 17

tag: age