title: SAM19448034

description: Mouse ID: 365; Tissue: Blood; Treatment: Cytoxan

source_name: Mouse 365 Blood Cytoxan


title: DLYM-1202_PD05_valspodar_Post

status: Public on Apr 06 2017

type: SRA

city: Minneapolis

first: Milcah

last: Scott

state: MN

address: 2101 6th Street Se

department: Department of Microbiology and Immunology

country: USA

institute: University of Minnesota

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (v0.33) with the optional "--qualitycontrol" option; 3bp sliding-window trimming from 3' end requiring minimum Q16).
A HISAT2 index for the canine reference genome  (canFam3) was used for mapping sequences with the HISAT2 aligner (2.0.2-beta) using default parameters. After mapping each bam file was sorted and indexed.
Insert size metrics calculated for each sample usng Picard.
Abundance files were generated with Cuffquant (Cufflinks (v2.2.1)).
Cuffnorm used to generate a table of FPKM expression data using the classic-fpkm normalization method.
Genome_build: canFam3
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

molecule: total RNA

organism: Canis lupus familiaris

source_name: lymphoma

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit.
Sequencing libaries were prepared using Illumina TruSeq Library Preparation Kits

treatment_protocol: Lymph node biopsy samples were obtained from dogs newly diagnosed with diffuse large B-cell lymphoma. Dogs were then randomized to receive oral valspodar(7.5 mg/kg) or placebo twice a day for 4 days, at which time lymph node biopsies were obtained again prior to initiation of doxorubicin chemotherapy. The goal was to determine potential effects of ABC transporter inhibition on overall gene expression by lymphoma cells, and specifically on the possibility to detect alterations in gene expression of rare CD34+/CD117+ lymphoid progenitor cells.

tag: treatment group

value: valspodar

tag: time of sample

value: post-treatment

tag: breed

value: Golden Retriever

tag: gender (neuter status)

value: M(N)

tag: age (yr)

tag: duration of remission (days)

tag: overall surival (days)


title: SAM19448004

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description: Mouse ID: 371; Tissue: Blood; Treatment: Ad5 IFNa TD day 21

data_processing:
The libraries were multiplexed (five per lane) and sequenced on Illumina HiSeq2500 (Illumina) to generate 30 million of single end 50 base pair reads for each sample.
50bp Illumina single end reads were processed using the HTSeqGenie Bioconductor package (Pau and Reeder, 2014). RNA-sequencing reads were aligned to release 37 of the reference mouse genome (MGSCv37) using GSNAP (Genomic Short-read Nucleotide Alignment Program) version '2013-10-10' (Wu and Nacu, 2010). QC of RNA-seq samples after alignment resulted in removal of one naïve spleen sample and one sample treated with P505-15.
We filtered out genes with low expression, retaining genes that had at least 10 reads in at least 4 of the samples.
The Bioconductor package, DESeq2 (version 1.4.5) (Love et al., 2014), was used to normalize expression across samples and identify genes that were significantly differentially expressed using the default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

organism: Mus musculus

source_name: Mouse 371 Blood Ad5 IFNa TD day 21

extract_protocol:
The spleen and kidney tissues were disrupted in RLT buffer using a tissue lyser and RNA was extracted using the Qiagen RNeasy mini kit as per manufacturer’s protocol including the on-column DNase digestion. Blood RNA was isolated using Paxgene RNA isolation kit from Qiagen as per manufacturer’s instructions. Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of total RNA samples was determined using NanoDrop 8000 (Thermo Scientific). The integrity of RNA samples was tested using Fragment Analyzer and High Sensitivity RNA kit (Advanced Analytical).
1ug of total RNA was input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Generated libraries were amplified with 8 cycles of PCR. Size of the libraries was confirmed using Fragment Analyzer and High Sensitivity DNA NGS kit (Advanced Analytical) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were first multiplexed (five per lane) and then sequenced on Illumina HiSeq2500 (Illumina) to generate 30 million of single end 50 base pair reads for each sample.

treatment_protocol: The mice were treated with vehicle or Btk SMI G7744 SMI, Syk SMI, G955 SMI, anti-ragweed IgG2a, mBR3-IgG2a and cytoxan in 100ul saline for eight weeks.

tag: strain

value: pre-clinical mouse lupus model (NZB/W F1)

tag: mouse id

tag: primary tissue

value: Blood

tag: treatment name

value: Ad5 IFNa TD day 21


title: 120h Macrophage LPS Rep 2 ATAC-seq

city: Irvine

first: Ricardo

middle: Noel

last: Ramirez

address: 2300 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California Irvine

library_source: genomic

data_processing:
Library strategy: ATAC-seq
ATAC-seq reads were mapped to the hg38 reference genome using bowtie (Langmead et al., 2009). Using parameters (bowtie -S --trim3 7 --chunkmbs 3000 -p 32 -m 3 -v 2 --best --strata -X 3000)
[bed]
HOMER was used to call ATAC-seq peaks. Using parameters (findPeaks Mapp.dir -size 500 -minDist 50 -fdr 0.01) and findPeaks Mapp.dir -minDist 50 -fdr 0.01 -style factor). ‘Narrow’ and ‘broad’ regions were then merged into a single bed file for each replicate.
Counts were normalized for batch effects using Combat (Johnson et al., 2007).
[bigWig]
BAM was generated from SAM file using samtools/0.1.18
BedTools genomeCoverageBed was used to convert BAM to bedGraph with hg38 chromosome sizes.
bedGraphToBigWig from UCSC was used to generate bigWig files.
Genome_build: hg38
Supplementary_files_format_and_content: bed, bigWig

molecule: genomic DNA

organism: Homo sapiens

source_name: Macrophage

growth_protocol: HL-60 cells (ATCC) were grown in Modified Dulbecco's Medium in a final concentration of 20% FBS with penicillin antibiotics (1%). Cells were routinely cultured at a density of 1x10^6 cells/ml.

extract_protocol: Approximately 50,000 HL-60 and differentiated cells were collected for ATAC-seq. ATAC-seq was performed as previously described (Buenrostro et al., 2013) with one amendment. DNA size exclusion was utilized after library generation to enrich for accessible chromatin ranging from 100-400bp.

treatment_protocol: Differentiation of HL-60 cells into macrophage (Murao et al., 1983), monocytes (Mangelsdorf et al., 1984) and neutrophils (Breitman et al., 1980) was performed as previously described. Additionally, monocytes (120 hours post-differentiation) were stimulated with PMA to induce differentiation into monocyte-derived macrophages. LPS stimulation at 48, 120, and 168 hours for specific cell-types was induced at a final concentration of 100ng/ml for ~3h, immediately followed by expression analysis.

tag: induction

value: PMA+LPS

tag: time


title: SAM19448029

description: Mouse ID: 364; Tissue: Blood; Treatment: mBR3 IgG2a

source_name: Mouse 364 Blood mBR3 IgG2a

value: mBR3 IgG2a


title: 120h Macrophage LPS Rep 3 ATAC-seq


title: DLYM-1202_PD05_valspodar_Pre

value: pre-treatment


title: SAM19447999

description: Mouse ID: 437; Tissue: Blood; Treatment: Naive

source_name: Mouse 437 Blood Naive

value: Naive


title: DLYM-1119_PENN04_placebo_Pre

value: placebo

value: NR


title: SAM19448023

description: Mouse ID: 272; Tissue: Blood; Treatment: Anti ragweed IgG2a

source_name: Mouse 272 Blood Anti ragweed IgG2a

value: Anti ragweed IgG2a


title: 120h Macrophage LPS Rep 1 ATAC-seq


title: SAM19448031

description: Mouse ID: 373; Tissue: Blood; Treatment: mBR3 IgG2a

source_name: Mouse 373 Blood mBR3 IgG2a


title: 120h Macrophage Rep 2 ATAC-seq

value: PMA


title: DLYM-1207_MN08_placebo_Post

value: Beagle

value: F(S)


title: 120h Macrophage Rep 3 ATAC-seq


title: DLYM-1119_PENN04_placebo_Post


title: SAM19575191

description: Mouse ID: 419; Tissue: Blood; Treatment: mBR3 IgG2a

source_name: Mouse 419 Blood mBR3 IgG2a


title: SAM19448015

description: Mouse ID: 381; Tissue: Blood; Treatment: Btki

source_name: Mouse 381 Blood Btki

value: Btki


title: 120h Macrophage Rep 1 ATAC-seq


title: DLYM-1204_PD04_placebo_Pre


title: SAM19448010

description: Mouse ID: 391; Tissue: Blood; Treatment: Vehicle HPMC in citrate

source_name: Mouse 391 Blood Vehicle HPMC in citrate

value: Vehicle HPMC in citrate


title: DLYM-1207_MN08_placebo_Pre


title: SAM19448014

description: Mouse ID: 376; Tissue: Blood; Treatment: Btki

source_name: Mouse 376 Blood Btki


title: 96h Macrophage Rep 3 ATAC-seq

value: 96 hr


title: SAM19448035

description: Mouse ID: 369; Tissue: Blood; Treatment: Cytoxan

source_name: Mouse 369 Blood Cytoxan

value: Cytoxan


title: Ep400ciMut1_H2AZChIP

city: Worcester

first: Thomas

last: Fazzio

state: MA

address: 364 Plantation street

institute: UMMS

description: Untreated, Ep400 mutant lacking catalytic activity

data_processing:
Single-end raw FastQ reads were collapsed, adaptor sequence were removed, and reads were mapped to the mouse mm10 genome using bowtie, allowing one mismatch. Aligned reads were used for downstream analysis using the “annotatePeaks” command in HOMER (Heinz et al., 2010) to make 20 bp bins over promoter proximal regions and summing the reads within each bin. Experiments were aligned over high quality (peak score > 6) promoter-proximal Tip60 peaks called from (Ravens et al., 2015). After anchoring mapped reads over the reference site, heatmaps for biological replicates were generated using Java Treeview.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol:
For ChIPseq, cells were crosslinked with 1% formaldehyde. Crosslinking was quenched with 125mM glycine, and the cell pellets were sonicated for ChIP.
ChIP samples were end-repaired, A-tailed, and barcoded adaptors were ligated. DNA purified using EconoSpin column on every steps.  The adaptor ligated DNA was PCR amplified for 16 cycles with Phusion polymerase.

tag: passage

tag: cell line

tag: genotype/variation

value: Ep400 mutant lacking catalytic activity

tag: treatment

value: untreated

tag: chip antibody

value: anti-H2AZ (Abcam, Cat # ab4174, Lot # GR216098-1)


title: E_G

city: Cincinnati

first: Douglas

last: Millay

state: OH

address: 240 Albert Sabin Way  MLC 7020

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequence reads were aligned using Strand NGS Software (Ver. 2.6) against Mouse mm10 (UCSC) using Ensembl transcript annotations ((2013.04.03)
Quantification using known annotation with Normalization Type: RPKM; Threshold for normalization =1;
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: txt

source_name: 10T1/2 fibroblasts

growth_protocol: 10T 1/2 fibroblasts (purchased from American Type Culture Collection) were propagated in DMEM containing 10% heat-inactivated bovine growth serum (BGS), supplemented with antibiotics.

extract_protocol:
Total RNA was ectracted from 10T 1/2 cells infected with empty virus using Trizol (Life Technologies), RNA quality and yield determined using Agilent Bioanalyzer and submitted for RNA-seq analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10T 1/2 cells were plated on 10 cm culture dishes (400,000 cells/plate). Cells were infected with retrovirus generated using an empty pBabe-X retroviral vector 16-18 hours after seeding. Infection was allowed to proceed for 18-hours, after which virus was removed, cells washed with PBS and propagated.

tag: cell type

value: fibroblasts

value: non-fusogenic cells

tag: transduced with

value: retrovirus carrying empty retroviral vector


title: SAM19448017

description: Mouse ID: 414; Tissue: Blood; Treatment: Btki

source_name: Mouse 414 Blood Btki

value: pre-clinical mouse lupus model (NZB/W F1)

value: Blood


title: 96h Macrophage Rep 2 ATAC-seq


title: 96h Macrophage Rep 1 ATAC-seq


title: Input_H2AZChIP

description: Untreated E14 ES cells

value: WT


title: SAM19448005

description: Mouse ID: 274; Tissue: Blood; Treatment: Ad5 IFNa TD day 21

source_name: Mouse 274 Blood Ad5 IFNa TD day 21

value: Ad5 IFNa TD day 21


title: Tip60ciMut2_H4acChIP

description: Untreated, Tip60 mutant lacking KAT (lysine acetyltransferase) activity

value: anti-H4ac (Millipore, Cat # 06-598, Lot # 2510372)


title: SAM19448013

description: Mouse ID: 363; Tissue: Blood; Treatment: Btki

source_name: Mouse 363 Blood Btki


title: 48h Macrophage LPS Rep 2 ATAC-seq

value: PMA+LPS

value: 48 hr


title: 48h Macrophage LPS Rep 1 ATAC-seq


title: 48h Macrophage LPS Rep 3 ATAC-seq


title: SAM19448021

description: Mouse ID: 356; Tissue: Blood; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 356 Blood SYK SMI G955 60 mg/kg

value: SYK SMI G955 60 mg/kg


title: WT_H2AZChIP

description: Untreated E14 ES cells


title: Tip60ciMut1_H4acChIP

value: Tip60 mutant lacking KAT (lysine acetyltransferase) activity


title: 48h Macrophage Rep 3 ATAC-seq

value: PMA


title: WT_H4acChIP

description: Untreated E14 ES cells


title: SAM19448000

description: Mouse ID: 438; Tissue: Blood; Treatment: Naive

source_name: Mouse 438 Blood Naive

value: Naive


title: 48h Macrophage Rep 2 ATAC-seq

source_name: Macrophage


title: IgG_H4acChIP

description: Untreated E14 ES cells

value: anti-IgG (Abcam, Cat # ab37415, Lot # GR90135-1)


title: 48h Macrophage Rep 1 ATAC-seq


title: KO-GP

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: experimental

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed with adaptor sequence using cutadapt v1.2.1  and mapped to mm10 reference with corresponding RefGene GTF annotation using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 and RPKM estimation using edgeR_3.12.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with RPKM values of each sample

source_name: bone marrow

growth_protocol: cells purified by flow cytometry directly from bone marrow of the indicated groups

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: female

tag: mouse model

value: IRF8-deficient mice

tag: tissue

value: bone marrow

value: purified granulocyte progenitors


title: 4T1-GP

description: experimental

value: F1 semi-syngeneic (H-2b/d)

value: 4T1 tumor-bearing mice


title: Ep400ciMut2_H2AZChIP

value: Ep400 mutant lacking catalytic activity

value: untreated

value: anti-H2AZ (Abcam, Cat # ab4174, Lot # GR216098-1)


title: 24h Macrophage Rep 2 ATAC-seq

value: 24 hr


title: 24h Macrophage Rep 3 ATAC-seq


title: SAM19448001

description: Mouse ID: 439; Tissue: Blood; Treatment: Naive

data_processing:
The libraries were multiplexed (five per lane) and sequenced on Illumina HiSeq2500 (Illumina) to generate 30 million of single end 50 base pair reads for each sample.
!Sample_data_processing = 50bp Illumina single end reads were processed using the HTSeqGenie Bioconductor package (Pau and Reeder, 2014). RNA-sequencing reads were aligned to release 37 of the reference mouse genome (MGSCv37) using GSNAP (Genomic Short-read Nucleotide Alignment Program) version '2013-10-10' (Wu and Nacu, 2010). QC of RNA-seq samples after alignment resulted in removal of one naïve spleen sample and one sample treated with P505-15.
We filtered out genes with low expression, retaining genes that had at least 10 reads in at least 4 of the samples.
The Bioconductor package, DESeq2 (version 1.4.5) (Love et al., 2014), was used to normalize expression across samples and identify genes that were significantly differentially expressed using the default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

source_name: Mouse 439 Blood Naive

value: pre-clinical mouse lupus model (NZB/W F1)

value: Blood


title: 24h Macrophage Rep 1 ATAC-seq


title: mc6-1

city: Beijing

first: Hongkui

last: Deng

address: this is for reviewer only

country: China

institute: Peking University

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using RPKM for mouse samples and FPKM for human samples respectively.
Genome_build: hg19 for human and GRCm38/mm10 for mouse
Supplementary_files_format_and_content: Excel files include the expression values for each sample

source_name: Mouse extended pluripotent stem cells

growth_protocol: Human primed pluripotent stem cells were maintained in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells in conventional human embryonic stem cell medium.Human extended pluripotent stem cells were cultured in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells. Mouse extended pluripotent stem cells were maintained in serum-free LCDM medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or Matrigel-coated plates. Mouse embryonic stem cells were maintained in serum-free 2i medium in 20% O2, 5% CO2 conditions on mitomycin C-inactivated MEF feeder cells or or Matrigel-coated plates.

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Mouse extended pluripotent stem cells


title: 12h Macrophage Rep 3 ATAC-seq

value: 12 hr


title: OG6-3


title: NTB-GP

description: control

value: non-tumor-bearing mice


title: 12h Macrophage Rep 2 ATAC-seq

value: PMA


title: OG-2i

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells


title: mc2i


title: 6h Macrophage Rep 2 ATAC-seq

value: 6 hr


title: 6h Macrophage Rep 3 ATAC-seq


title: 6h Macrophage Rep 1 ATAC-seq


title: shMP2-2

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

institute: Chinese Academic of Science

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat
Genome_build: mm9
Supplementary_files_format_and_content: mRNA expression analysis

molecule: polyA RNA

source_name: cortical neurons isolated from E14.5 embryonic cortex

growth_protocol: cortical neurons were isolated from E14.5 embryonic cortex and cultured in vitro for 5-7 days

extract_protocol:
total RNAs were isolated using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cultured cortial neurons were infected with lentivirus expressing either shMeCP2 or scrambled shRNA at DIV2 and cultured for another 3-5 days

value: cultured cortical neurons

tag: developmental stage

tag: infection

value: lentivirus expressing shRNA against mouse MeCP2


title: GFP-3

value: lentivirus expressing scrambled shRNA


title: shMP2-3


title: shMP2-1


title: 3h Macrophage Rep 1 ATAC-seq

value: 3 hr


title: SAM19448019

description: Mouse ID: 252; Tissue: Blood; Treatment: SYK SMI G955 60 mg/kg

source_name: Mouse 252 Blood SYK SMI G955 60 mg/kg

tag: strain

tag: mouse id

value: SYK SMI G955 60 mg/kg


title: GFP-2


title: 12h Macrophage Rep 1 ATAC-seq


title: 3h Macrophage Rep 2 ATAC-seq


title: HL60 Rep 3 ATAC-seq

value: 0 hr


title: HL60 Rep 2 ATAC-seq


title: Immune activated gut tissue

city: Washington

first: Katherine

middle: Michele

last: Buckley

state: DC

address: 800 22nd St NW

department: Department of Biological Sciences

institute: The George Washington University

description: Gut tissue collected from an adult S. purpuratus 12 hr after immune challenge

data_processing:
Low-quality reads were filtered using the Fastx-toolkit and mapped to the S. purpuratus genome, v43.1 using Bowtie (v0.12.7) with the following parameters: -k 50 -m 50 -n 3 -e 900 --snpfrac 0.4.
RPKM values were determined for each gene using the methods outlined in Mortazavi et al., 2008.
Genome_build: Spur3.1
Supplementary_files_format_and_content: RPKM

organism: Strongylocentrotus purpuratus

source_name: Gut tissue

extract_protocol:
Whole RNA was extracted from Trizol preparations using manufacturers instructions. Polyadenylated RNA was purified using the Poly(A)Purist Kit (Ambion).
Libraries were prepared for SOLiD sequencing using standard ABI protocols.

value: Gut

tag: age

value: Adult

tag: tissue preparation

value: Gut tissue was carefully dissected from an adult S. purpuratus animal.  Tissue was washed in ASW to remove fecal matter and stored in Trizol prior to homogenization.


title: GFP-1


title: Immune activated phagocytic coelomocytes

description: Coelomocytes collected from an adult S. purpuratus 12 hr after immune challenge

source_name: Coelomocytes

value: Coelomocytes

value: Whole coelomocytes were harvested from an adult S. purpuratus animal and diluted 1:1 in calcium, magnesium-free sea water (CMFSW).  The phagocytic coelomocytes were isolated on a discontinuous density centrifugation using Optiprep.  Isolated phagocytes were washed three times in CMFSW, pelleted by centrifugation and stored in Trizol.


title: HL60 Rep 1 ATAC-seq

tag: induction

tag: time


title: DGRP-900_Male_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate5

status: Public on Apr 05 2017

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description:
HTSeq_raw_read_counts_matrix.txt
DESeq2_normalized_read_counts_matrix.txt

data_processing:
We performed base-calling using CASAVA v1.8.2 (Illumina, San Diego, CA), converted BCL to FASTQ files and demultiplexed reads by barcode using bcl2fastq v1.8 (Illumina, San Diego, CA). We mapped demultiplex reads to the Drosophila genome assembly release 6 plus ISO1 MT with appended ERCC sequences using STAR v2.5.1b (Dobin et al, 2015, PMID: 23104886). To generate indexes files for STAR we provided a GTF file with the gene models FlyBase r6.09 and appended ERCC in the ‘–sjdbGTFfile’ option. We used SAMtools v1.3.1 (Li et al., Bioinformatics, 2009, PMID 19505943) to index chromosomes and sort the alignments. Mapped reads were counted at the gene level using HTseq v0.6.1p1 (Anders et al., 2014. PMID: 25260700) with parameters ‘–s reverse’ to get strand specific read counts and normalized using DESeq2 v1.10.1 (Love et al. 2014, PMID: 25516281).
Genome_build: Drosophila genome assembly release 6 plus ISO1 MT
Supplementary_files_format_and_content: Tab limited text files contain transcript abundance information, generated using HTseq and normalized by DESeq2.

organism: Drosophila melanogaster

growth_protocol: We reared Drosophila melanogaster (genotype DGRP-900, FlyBase line ID: FBst0028261) on Chemical Defined Food (CDF, Lee W-C. & Micchelli C., 2013, PMID: 23844001) at 25°C, 60% humidity, and constant light. CDF was prepared according to the protocol (Lee W-C. & Micchelli C., 2013, PMID: 23844001) and drugs were added from the concentrated water solution stocks before food solidification. Concentrated stocks were stored at -80C.

extract_protocol:
We isolated total RNA with RNeasy Plus Micro Kit (Qiagen, Valencia, CA) according to the manufacturer's protocol. First we homogenized brains using a Pellet Pestle Cordless Motor (Kimble®/Kontes, Rockwood, TN) for 2 min, and then we cleaned the pestle with 300 ul of RLT buffer to collect remaining cells and proceeded to the homogenization step using QIAshredder columns (Qiagen, Valencia, CA). RNA quantity was measured with Quant-iT™ RiboGreen® RNA Assay Kit (Molecular Probes, Eugene, OR) and 30ng of total RNA was used for library preparation. Total RNA was eluted from the column with RNAse free water from the Kit and stored at -80C.
Stranded PolyA+ RNA libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, San Diego, CA). On the fragmentation step we added 10 pg of ERCC (External RNA Controls Consortium) spike-ins sequences, which were used for libraries preparation quality check, to the Fragment-Prime-Finish Mix. We utilized spike-ins pools 78A/78B (Zook et al., 2012. PMID: 22859977). Annotations of these pools have been recently modificated (Pine et al, 2016, http://dx.doi.org/10.1101/034868): seven ERCC RNA sequences were reverse-complimented and ERCC 00085 was reassigned to subpool C. Both FASTA and GTF files of ERCC sequences used in the analysis are available as supplementary files in this GEO entry. The cDNA libraries were multiplexed using 24 different barcoded adapters from TruSeq (Illumina, San Diego, CA). Index sequences are available in the characteristics field of each sample. We measured quantity of cDNA libraries with Quant-iTª PicoGreen (Molecular Probes, Eugene, OR). We visually inspected elecrophoregrams of the cDNA libraries to check for a maximum peak around 300bp using Agilent Bioanalyzer High Sensitivity DNA chips on the 2100 Bioanalyzer system (Agilent, Santa Clara, CA). We performed multiplexed single-end 75bp sequencing on an Illumina HiSeq2500.

treatment_protocol: On day 1 we collected 120 virgin male and 120 virgin female flies (30 animals per vial) and fed them on 400 k-Cal/L CDF. On day 4 we transferred flies to new vials with CDF containing 0.5 g/L Sulforhodamine B sodium salt (Sigma, Saint Louis, CA, #S1402-5G), a non-toxic dye for fly food (Amrein H. & Thorne N., 2005, PMID: 16139201, Bahadorani S. & Hilliker A., 2008, PMID: 19083435), and one of the tested drugs to the final concentrations of: 1) Control – 0mM (no drug), 2) 7 mM Chlorpromazine 3) 0.5 mM Trifluoperazine2HCl, or 4) 60 mM Sodium Salycilate. We exposed flies to the drugs for 24 hours and then dissected 5 brains per sample. To allow all flies to be exposed equal amount of time due to time consumed by the dissection step we transferred females to the vials with drugs 2 hours earlier than males. We dissected brains in Phosphate Buffer Saline (PBS) buffer and transferred them using a needle to eppendorf tubes with 50 ul RLT lysis buffer from RNeasy Plus Micro Kit (Qiagen, Valencia, CA) on ice. Brains were frozen at -80C until RNA extraction. Only flies with pink abdomens (due to ingesting Sulforhodamine B) were dissected.

tag: genotype

value: DGRP-900 (FlyBase line ID:FBst0028261)

value: adult

tag: Sex

value: Male

tag: replicate

value: GAGTGG


title: DGRP-900_Male_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate6

tag: treatment

value: ACTGAT


title: DGRP-900_Male_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate4

value: CGTACG


title: DGRP-900_Male_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate2

value: GTGGCC


title: DGRP-900_Male_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate1

value: GTGAAA


title: DGRP-900_Male_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate3

value: GTTTCG


title: DGRP-900_Male_brain_treated_with_SodiumSalicylate_for_24 hours_replicate4

value: SodiumSalicylate

value: TAGCTT


title: 3h Macrophage Rep 3 ATAC-seq

value: PMA

value: 3 hr


title: DGRP-900_Male_brain_treated_with_SodiumSalicylate_for_24 hours_replicate6

value: CTTGTA


title: DGRP-900_Male_brain_treated_with_SodiumSalicylate_for_24 hours_replicate1

value: CAGATC


title: DGRP-900_Male_brain_treated_with_SodiumSalicylate_for_24 hours_replicate3

value: GATCAG


title: DGRP-900_Male_brain_treated_with_Control_for_24 hours_replicate6

value: Control


title: DGRP-900_Male_brain_treated_with_Control_for_24 hours_replicate1

value: DGRP-900 (FlyBase line ID:FBst0028261)


title: DGRP-900_Male_brain_treated_with_Chlorpromazine_for_24 hours_replicate6

value: adult

value: Chlorpromazine


title: DGRP-900_Male_brain_treated_with_Control_for_24 hours_replicate2

value: Male


title: DGRP-900_Male_brain_treated_with_Control_for_24 hours_replicate5

value: GAGTGG


title: DGRP-900_Male_brain_treated_with_SodiumSalicylate_for_24 hours_replicate2

value: ACTTGA


title: DGRP-900_Male_brain_treated_with_Control_for_24 hours_replicate3


title: DGRP-900_Male_brain_treated_with_Control_for_24 hours_replicate4

value: CGTACG


title: DGRP-900_Male_brain_treated_with_Chlorpromazine_for_24 hours_replicate4


title: DGRP-900_Male_brain_treated_with_Chlorpromazine_for_24 hours_replicate3


title: DGRP-900_Male_brain_treated_with_Chlorpromazine_for_24 hours_replicate5

value: GGCTAC


title: DGRP-900_Male_brain_treated_with_Chlorpromazine_for_24 hours_replicate2


title: DGRP-900_Female_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate6

value: Female

value: GTCCGC


title: DGRP-900_Male_brain_treated_with_Chlorpromazine_for_24 hours_replicate1


title: DGRP-900_Female_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate5

value: ATTCCT


title: DGRP-900_Female_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate3

value: ATGTCA


title: DGRP-900_Female_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate1

value: AGTCAA


title: DGRP-900_Female_brain_treated_with_SodiumSalicylate_for_24 hours_replicate6

value: SodiumSalicylate

value: GCCAAT


title: DGRP-900_Female_brain_treated_with_SodiumSalicylate_for_24 hours_replicate3

value: TTAGGC


title: DGRP-900_Female_brain_treated_with_SodiumSalicylate_for_24 hours_replicate4

value: TGACCA


title: DGRP-900_Female_brain_treated_with_SodiumSalicylate_for_24 hours_replicate2

value: DGRP-900 (FlyBase line ID:FBst0028261)

value: CGATGT


title: DGRP-900_Female_brain_treated_with_Control_for_24 hours_replicate4

value: adult

value: Control

value: CCGTCC


title: DGRP-900_Female_brain_treated_with_Control_for_24 hours_replicate5


title: DGRP-900_Female_brain_treated_with_Control_for_24 hours_replicate2

value: AGTTCC


title: DGRP-900_Female_brain_treated_with_Control_for_24 hours_replicate3


title: DGRP-900_Female_brain_treated_with_SodiumSalicylate_for_24 hours_replicate1

value: ATCACG


title: DGRP-900_Female_brain_treated_with_Chlorpromazine_for_24 hours_replicate3

value: Chlorpromazine


title: DGRP-900_Female_brain_treated_with_Chlorpromazine_for_24 hours_replicate2

value: Female


title: DGRP-900_Female_brain_treated_with_Control_for_24 hours_replicate6

value: GTCCGC


title: Small RNAs from embryos of Misy R strain

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requirement of perfect matching.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files include the raw counts of clipped read occurrences in each library.

source_name: 0-2h embryo, Misy R strain

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogen) and size-fractioned by PAGE (19-29 nt).
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012).

value: 0-2h embryos

tag: strain/background

value: Misy


title: DGRP-900_Female_brain_treated_with_Chlorpromazine_for_24 hours_replicate5

value: ACAGTG


title: DGRP-900_Female_brain_treated_with_Chlorpromazine_for_24 hours_replicate6


title: DGRP-900_Female_brain_treated_with_Chlorpromazine_for_24 hours_replicate1


title: Small RNAs from ovaries of Zola R strain 2

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect mathcing.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files include the raw counts of clipped read occurrences in each library.

source_name: ovaries

extract_protocol:
Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt)
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)

value: ovaries

value: Zola


title: DGRP-900_Female_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate4


title: Small RNAs from ovaries of Zola R strain

source_name: ovaries, Zola R strain

value: female


title: Small RNAs from embryos of Paris R strain

source_name: 0-2h embryo, Paris R strain

value: Paris


title: DGRP-900_Female_brain_treated_with_Trifluoperazine2HCl_for_24 hours_replicate2

value: DGRP-900 (FlyBase line ID:FBst0028261)


title: Small RNAs from ovaries of Misy R strain

source_name: ovaries, Misy R strain


title: Small RNAs from ovaries of Paris R strain

source_name: ovaries, Paris R strain


title: HMTS30_F_Sib.3

city: Canberra

first: Li

last: Wang

state: ACT

address: North-Science Road, Acton ACT 2601

country: Australia

institute: CSIRO

description: Barcode: TAGCTT

data_processing:
The quality of raw data (.fastq files) was assessed by FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped against the TAIR10 reference genome using Biokanga (sourceforge.net/projects/biokanga/)under default settings.
The DEseq package was used to determine significant differences in gene expression between samples. Normalization was performed on aligned reads across all the samples based on the size of each library.
To identify the differentially expressed genes between two samples, non-expressed genes (genes with reads < 100 in every sample) were filtered. A threshold of p ≤ 0.05 was applied for differentially expressed gene.
Genome_build: TAIR10
Supplementary_files_format_and_content: Table 1. Sequencing depth; raw and mapped sequenced counts of two parents, F1 hybrids and F6 plant lines at 15 DAS.xlsx
Supplementary_files_format_and_content: Raw_counts_HMTS_2016.txt

organism: Arabidopsis thaliana

source_name: Med-F Sib.3

growth_protocol: Seeds of C24/Ler hybrids were produced by hand-pollination between Arabidopsis accessions C24 and Landsberg erecta (Ler). Seeds of C24/Ler Hybrid Mimic lines (HM-W, HM-S, and HM-G) and three other F6 plant lines (Med-E, Med-F, and Sml-D) were produced from the recurrent selection protocol.  Surface sterilized seeds were sown on Murashige and Skoog (MS) medium supplemented with 1% (wt/vol) sucrose and 0.8% wt/vol agar. After stratification at 4 ºC for three days, plants were grown under 16h light (22°C)/8h dark (18°C). Light intensity was controlled at 130 - 150μmol photons m-2·s-1 under fluorescent light tubes (OSRAM L 36W/865 LumLux Daylight).

extract_protocol:
The aerial tissues of 15 day seedlings were sampled. Total RNA was isolated using QIAGEN RNeasy MiniKitTM following the product instructions.
illumina True-seq kit

treatment_protocol: No treatment

tag: line

value: Med-F

value: Whole aerial tissue

value: 15 day old

value: seedling


title: DGRP-900_Female_brain_treated_with_Chlorpromazine_for_24 hours_replicate4

value: adult

value: TGACCA


title: HMTS29_F_Sib.2

description: Barcode: GATCAG

source_name: Med-F Sib.2


title: HMTS28_F_Sib.1

description: Barcode: ACTTGA

source_name: Med-F Sib.1


title: HMTS27_D_Sib.3

description: Barcode: CAGATC

source_name: Sml-D Sib.3

value: Sml-D


title: HMTS25_D_Sib.1

description: Barcode: ACAGTG

source_name: Sml-D Sib.1


title: DGRP-900_Female_brain_treated_with_Control_for_24 hours_replicate1

value: Female

value: Control

value: AGTCAA


title: HMTS26_D_Sib.2

description: Barcode: GCCAAT

source_name: Sml-D Sib.2


title: DGRP-900_Female_brain_treated_with_SodiumSalicylate_for_24 hours_replicate5

value: SodiumSalicylate


title: HMTS23_S_Sib.2

description: Barcode: TTAGGC

source_name: HM-S Sib.2

value: HM-S


title: HMTS22_S_Sib.1

description: Barcode: CGATGT

source_name: HM-S Sib.1


title: HMTS21_W_Sib.3

description: Barcode: ATCACG

source_name: HM-W Sib.3

value: HM-W


title: HMTS20_W_Sib.2

description: Barcode: ATTCCT

source_name: HM-W Sib.2


title: HMTS17_G_Sib.2

description: Barcode: CGTACG

source_name: HM-G Sib.2

value: HM-G


title: HMTS18_G_Sib.3

description: Barcode: GAGTGG

source_name: HM-G Sib.3


title: HMTS13_E_Sib.1

description: Barcode: GTCCGC

source_name: Med-E Sib.1

value: Med-E


title: Small RNAs from ovaries of cn bw; e R strain

source_name: ovaries, cn bw; e R strain

value: ovaries

value: cn bw; e

value: female


title: HMTS15_E_Sib.3

description: Barcode: GTGGCC

source_name: Med-E Sib.3

value: Whole aerial tissue


title: HMTS12_LerXC24_RepC

description: Barcode: CCGTCC

source_name: LerXC24 RepC

value: 15 day old


title: HMTS16_G_Sib.1

description: Barcode: GTTTCG

source_name: HM-G Sib.1

value: seedling


title: HMTS11_LerXC24_RepB

description: Barcode: ATGTCA

source_name: LerXC24 RepB


title: HMTS07_C24XLer_RepA

description: Barcode: GGCTAC

source_name: C24XLer RepA


title: HMTS10_LerXC24_RepA

description: Barcode: AGTTCC

source_name: LerXC24 RepA


title: DGRP-900_Male_brain_treated_with_SodiumSalicylate_for_24 hours_replicate5

value: DGRP-900 (FlyBase line ID:FBst0028261)

value: adult

value: Male

value: GGCTAC


title: HMTS08_C24XLer_RepB

description: Barcode: CTTGTA

source_name: C24XLer RepB


title: HMTS05_Ler_RepB

description: Barcode: GATCAG

source_name: Ler RepB

value: Ler


title: HMTS06_Ler_RepC

description: Barcode: TAGCTT

source_name: Ler RepC


title: HMTS04_Ler_RepA

description: Barcode: ACTTGA

source_name: Ler RepA


title: HMTS09_C24XLer_RepC

description: Barcode: AGTCAA

source_name: C24XLer RepC


title: HMTS01_C24_RepA

description: Barcode: ACAGTG

source_name: C24 RepA


title: HMTS03_C24_RepC

description: Barcode: CAGATC

source_name: C24 RepC


title: HMTS24_S_Sib.3

description: Barcode: TGACCA

source_name: HM-S Sib.3


title: HMTS19_W_Sib.1

description: Barcode: ACTGAT

source_name: HM-W Sib.1


title: 3_2_ContrSmall

city: Marburg

first: Gerhard

last: Schratt

address: Karl-von-Frisch-Straße n.1

department: Institute for Physiological Chemistry

country: Germany

institute: Philipps-University Marburg

description: Sample 13

data_processing:
For initial processing of the smallRNA data the online tool www.usegalaxy.org was used.
www.usegalaxy.org:    3'adapter-AGATCGGAAGAGCACACGTCT- was removed and reads were filtered by quality (quality cut-off:30; Minimum percentage:90
www.usegalaxy.org:  after removing the sequencing artefacts and short reads (<15 nucleotides), sequences were collapsed
The reads were aligned to the miRNAs using miraligner software (3 nucleotides freedom at 5' and 3'end; 1 mismatch)
genome build: miRBase v19
processed data files format and content: tab delimited; 1st column_Gene-name; 2nd column_miRBase_mature_miRNA accession number; 3rd column_read counts

organism: Rattus norvegicus

source_name: Primary HC cells (neuronal enriched)

growth_protocol: Primary cultures of Sprague–Dawley rats embryonic hippocampal (E18) were prepared. RNA was extracted at 20DIV

extract_protocol:
RNA was extracted with peqGOLD TriFast™.
RNA libraries were prepared for sequencing using standard Illumina protocols - polyA RNA, Ribominus RNA, smallRNA

treatment_protocol: Samples 1-18  neuronal enriched HC cultures. Samples 19-26 "normal" HC cultures. Vehicle or picrotoxin was applied at 18DIV for 48h.

value: Sprague-Dawley

value: hippocampus

tag: rna fraction

value: Small RNA

tag: extraction stage

tag: sample origin


title: 3_2_PtxSmall

description: Sample 16

tag: tissue

tag: developmental stage


title: 10_2_PtxSmall

description: Sample 17

tag: strain


title: HMTS14_E_Sib.2

description: Barcode: GTGAAA

source_name: Med-E Sib.2


title: 20_2_Contr_polyA

description: Sample 3

data_processing:
Mapping: STAR version 2.3.1z12; -limitOutSJoneRead 10 -outSAMstrandField intronMotif -outSAMattributes All -outFilterMultimapNmax 2 -outFilterMismatchNmax 5 -outFilterIntronMotifs RemoveNoncanonicalUnannotated
Cuffquant (Cufflinks version 2.2.1)
cuffdiff (Cufflinks version 2.2.1)
cuffnorm (Cufflinks version 2.2.1)
UTR analysis: IsoSCM (version: IsoSCM-2.0.7), bedtools intersect (bedtools version 2.22.1), python script to filter and calculate length.
genome build: Rn5, ensembl version: 79
processed data files format and content: *differential_gene_expression.txt (tab delimited, cuffdiff output) ; *.gene_expression.txt (tab delimited, cuffnorm output) ; utr_length (tab delimited, estimated UTR length).

value: polyA RNA


title: 10_2_Contr_polyA

description: Sample 2


title: 10_2_Ptx_polyA

description: Sample 5


title: 3_2_Ptx_polyA

description: Sample 4


title: DA-2-CD4

city: shanghai

first: wang

last: yujie

state: Shanghai

address: Chi Feng road No:65

institute: Shanghai JiaYin Biological technology co., LTD

description:
Paired sample with BA-2-CD4.
mRNA-seq
Processed data file: expression_level_all.txt
Processed data file: Treat_vs_control_diff.txt

data_processing:
Reads were aligned to the human genome (hg19 assembly) using STAR Aligner.
Exons from all isoforms of a gene were merged to create one meta-gene.
The number of reads falling in the exons of this meta-gene was counted using HTSeq-count, and differential expression analysis was performed using DESeq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: expression_level_all.txt: Tab-delimited text file
Supplementary_files_format_and_content: Treat_vs_control_diff.txt: Tab-delimited text file

source_name: CD4 T cells, decidua

growth_protocol: The separation of decidual tissues and mononuclear cells was performed according to the procedure of nonenzymatic leukocytes separation. Briefly, vacuum-aspirated abortion tissues were washed in sterile PBS, and decidual tissue was macroscopically separated from fetal tissue and placenta, which was then cut into small pieces using ocular scissors and filtered by a 74-μm nylon mesh filter to obtain a single cell suspension. Both decidual mononuclear cells (DMCs) and peripheral blood mononuclear cells (PBMCs) were isolated and purified by density gradient centrifugation using LymphoprepTM.

extract_protocol:
Total RNA was extracted by using Trizol Reagent, and was purified by RNeasy Micro Kit.
Library preparation was performed as previously described (Zhang et al., 2014). We used 200 ng RNA per sample as input material for the RNA sample preparations. cDNA libraries were constructed by using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instruction, and the products were purified by AMPure XP system and library quality was determined on the Agilent Bioanalyzer 2100 system.

tag: gender

tag: disease status

value: healthy

tag: stage of pregnancy

value: early

value: decidual tissues

tag: cell type

value: CD4+ T cells


title: 3_2_Contr_polyA

description: Sample 1


title: 6dCD4

description:
Paired sample with 6xue CD4.
mRNA-seq
Processed data file: expression_level_all.txt
Processed data file: Treat_vs_control_diff.txt

value: female


title: 20_2_ContrSmall

description: Sample 15


title: 6xue CD4

description:
Paired sample with 6dCD4.
mRNA-seq
Processed data file: expression_level_all.txt
Processed data file: Treat_vs_control_diff.txt

source_name: CD4 T cells, peripheral blood

value: peripheral blood


title: 7xueCD4

description:
Paired sample with 7dCD4.
mRNA-seq
Processed data file: expression_level_all.txt
Processed data file: Treat_vs_control_diff.txt


title: 20_2_Ptx_polyA

description: Sample 6


title: HMTS02_C24_RepB

description: Barcode: GCCAAT

source_name: C24 RepB

value: Whole aerial tissue

tag: age

value: 15 day old


title: P48_H1_bulk_296

city: Gainesville

first: Rhonda

last: Bacher

state: FL

address: 2004 Mowry Rd.

institute: University of Florida

description: H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequencing reads were mapped to hg19 using bowtie 0.12.8. Single cell samples were mapped to hg19 + ERCC spike-ins.
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: hg19
Supplementary_files_format_and_content: Bacher.RSEM.xlsx: Excel spreadsheet reporting RSEM Expected Counts expression estimation on five tabs, corresponding to different sample types and multiplexing levels.

source_name: undifferentiated human embryonic stem cells

growth_protocol: Undifferentiated H1 hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance.

extract_protocol:
Cells were washed with 1xPBS and lysed with 350 μl RLT Buffer.  Cell lysates were vortexed and stored at -80 °C.  RNA was isolated from the cell lysates using the RNeasy Mini Isolation Kit (Qiagen), performed according to the manufacturer’s instructions. cDNA libraries were generated by the Ligation Mediated (LM-Seq) Protocol (Hou et al, 2015).
Poly-A-tailed mRNA was isolated from 100 ng/μl total RNA using oligo-dT beads.  Purified mRNA was then fragmented and first strand cDNA was synthesized using random hexamer oligos.  Next RNA was removed and the 5' adapter was ligated.  The cDNA library was amplified and cleaned.  The H1 cDNA Libraries were multiplexed at 48 libraries per lane, and single-end reads of 51-bp sequencing was performed on an Illumina HiSeq 2500 system.

tag: cell line

value: human embryonic stem cells

tag: passage

value: passage 16

tag: multiplexing


title: P48_H1_bulk_293


title: P48_H1_bulk_292


title: P48_H1_bulk_294


title: P48_H1_bulk_295


title: P48_H1_bulk_291


title: P48_H1_bulk_290


title: 20_2_PtxSmall

description: Sample 18


title: P48_H1_bulk_287


title: P48_H1_bulk_289


title: 10_2_ContrSmall

description: Sample 14


title: 7dCD4

description:
Paired sample with 7xueCD4.
mRNA-seq
Processed data file: expression_level_all.txt
Processed data file: Treat_vs_control_diff.txt


title: P48_H1_bulk_286


title: P48_H1_bulk_283


title: P48_H1_bulk_285


title: P48_H1_bulk_282


title: P48_H1_bulk_281


title: BA-2-CD4

description:
Paired sample with DA-2-CD4.
mRNA-seq
Processed data file: expression_level_all.txt
Processed data file: Treat_vs_control_diff.txt


title: P48_H1_bulk_280


title: P48_H1_bulk_284


title: P48_H1_bulk_279


title: P48_H1_bulk_275


title: P48_H1_bulk_276


title: P48_H1_bulk_274


title: P48_H1_bulk_273


title: P48_H1_bulk_277


title: P48_H1_bulk_288


title: P48_H1_bulk_268


title: P48_H1_bulk_269


title: P48_H1_bulk_267


title: P48_H1_bulk_272


title: P48_H1_bulk_266


title: P48_H1_bulk_264


title: P48_H1_bulk_263


title: P48_H1_bulk_262


title: Dehy 3h rep2

city: NEW YORK

first: Nam-Hai

last: Chua

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: dehydration stress for 3 h (Dehy_3h)

data_processing:
Strand-specific RNA-seq reads were mapped to the Arabidopsis genome (TAIR10) using TopHat (version 2.0.8) with parameters “--library-type=fr-firststrand -i 40 -I 5000 -g 1 --segment-length=20”.
The mapped reads were assembled using Cufflinks (v2.1.1) with parameters “--library-type=fr-firststrand -I 5000 --min-intron-length=40” and with TAIR10 annotation as the reference.
The assembled transcripts of each ssRNA-seq sample were merged and annotated using Cuffcompare (v2.1.1) with TAIR10 annotation as the reference.
The expression levels of each gene were then calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using Cuffdiff with parameter “--library-type=fr-firststrand”.
A 2-fold variance in FPKM, a P value less than 0.05, and an adjusted P value less than 0.1 were used as cutoffs to define differentially expressed genes. The P value and adjusted P value were calculated using DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited Excel files include FPKM values (of 22,526 protein coding genes detected by RNA-seq) and raw read counts (of 22,526 protein coding genes detected by RNA-seq) for each sample

source_name: 14d-old seedlings_dehydration_3hrs

growth_protocol: The Arabidopsis thaliana ecotype Columbia (Col-0) was used as wild type in this study. For all experiments, sterilized and stratified seeds were grown on Murashige and Skoog (MS) medium (pH 5.7) with 1% sucrose (Fisher Scientific) and 0.8% (wt/vol) Bacto-Agar (Becton, Dickinson and company), and were grown at 22°C under 16 hour light / 8 hour dark condition with a light intensity of 40 µmol m-2 s-1. (±)-Abscisic acid (ABA, Sigma) stock solution was prepared in methanol.

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings using TRIzol reagent (Ambion), treated with TURBO DNase (Ambion) and purified using RNeasy mini spin column (Qiagen). The quality of purified RNA was assessed using an Agilent 2100 Bioanalyzer.
The cDNA libraries for ssRNA-seq were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to the low sample protocol guidelines. The quality and size of each sample library was assessed using an Agilent High Sensitivity D1K ScreenTape System. The average sizes of the enriched cDNA fragments were between 272 and 300 bp. The three biological replicates for each condition (negative control, ABA 1 h, ABA 3 h, dehydration 1 h and dehydration 3 h) were pooled into one well, and sequenced on an Illumina HiSeq 2500 with 100-cycle single reads per multiplexed sample.

treatment_protocol: For ABA and dehydration treatment, 13-day-old seedlings grown on MS solid medium were transferred to MS liquid medium (pH 5.7) with 1% sucrose and grown under same condition for an additional day before treatments. For ABA treatment, 14-day-old seedlings were treated with 20 µM ABA in MS liquid medium under light condition (40 µmol m-2 s-1) and seedlings were harvested at 1 and 3 hours after application. For dehydration treatment, 14-day-old seedlings were removed from MS liquid medium and left on filter papers (Fisher Scientific) under light condition (40 µmol m-2 s-1) for up to 1 and 3 hours before harvesting. The negative control samples were harvested before ABA and dehydration treatment.

tag: ecotype

value: Columbia (Col-0)

value: 14-day-old seedlings

tag: treated with

value: dehydration (left on filter papers) for 3hrs


title: P48_H1_bulk_265


title: P48_H1_bulk_270


title: P48_H1_bulk_271


title: Dehy 3h rep1

description: dehydration stress for 3 h (Dehy_3h)


title: P48_H1_bulk_278


title: Dehy 3h rep3

description: dehydration stress for 3 h (Dehy_3h)


title: Dehy 1h rep1

description: dehydration stress for 1 h (Dehy_1h)

source_name: 14d-old seedlings_dehydration_1hr

value: dehydration (left on filter papers) for 1hr


title: P48_H1_bulk_260


title: P48_H1_bulk_259


title: P48_H1_bulk_257


title: ABA 3h rep2

description: ABA treatment for 3 h (ABA_3h)

source_name: 14d-old seedlings_ABA 3hrs

value: 20 µM ABA for 3hrs


title: ABA 3h rep3

description: ABA treatment for 3 h (ABA_3h)


title: Dehy 1h rep3

description: dehydration stress for 1 h (Dehy_1h)


title: ABA 3h rep1

description: ABA treatment for 3 h (ABA_3h)


title: ABA 1h rep3

description: ABA treatment for 1 h (ABA_1h)

source_name: 14d-old seedlings_ABA 1h

value: 20 µM ABA for 1hr


title: P48_H1_bulk_255


title: ABA 1h rep1

description: ABA treatment for 1 h (ABA_1h)


title: ABA 1h rep2

description: ABA treatment for 1 h (ABA_1h)


title: NC rep3

description: normal condiction (NC)

source_name: 14d-old seedlings_control

value: none (control)


title: P48_H1_bulk_254


title: P48_H1_bulk_252


title: P48_H1_bulk_261


title: NC rep1

description: normal condiction (NC)


title: P48_H1_bulk_249


title: Dehy 1h rep2

description: dehydration stress for 1 h (Dehy_1h)


title: P48_H1_bulk_251


title: P48_H1_bulk_256


title: P24_H9b3s_095

description: H9 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel

growth_protocol: Undifferentiated H9 hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). The H9 single-cell cDNA libraries were multiplexed at 24 libraries per lane, and single-end reads of 51-bp sequencing was performed on an Illumina HiSeq 2500 system.

value: passage 25-35


title: KD2_H3K27me3

city: Los Angeles

first: Ranjani

last: Lakshminarasimhan

address: 1441 Eastlake ave NOR7336

department: Urology

institute: University of Southern California

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Non-unique reads were filtered out and reads were mapped to hg19 using BWA
Reads were extended to 200bp, duplicates removed.
Peaks were called using MACS algorithm with a p-value cut-off of 10^-10. Read-count quantification was perfomed then log2 transformed -- corrected for total read count of the largest datastore, only reads within peaks were counted, and corrected for peak length.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with peak list and read-count quantification

source_name: Endometriosis

extract_protocol:
Nuclei were fixed, lysed, and chromatin was sonicated. Histone-DNA complexes were isolated with antibody. Genomic DNA was isolated by standard phenol-chloroform extraction and ethanol precipitation
Libraries were prepared according to Illumina's instructions and sequenced on either HiSeq-2000 or NextSeq 500 platforms.

value: hTERT immortalized endometriosis cells

tag: genotype/variation

value: ARID1A Knockdown

tag: antibody


title: KD2_H3K27ac


title: P48_H1_bulk_258


title: KD2_H3K4me3


title: P24_H9b3s_094


title: P24_H9b3s_093


title: SCR_rep2_H3K27ac

value: Control


title: SCR_rep2_H3K27me3


title: KD2_H3K4me1


title: P24_H9b3s_091


title: P48_H1_bulk_253


title: P24_H9b3s_084


title: NC rep2

description: normal condiction (NC)


title: P24_H9b3s_083


title: P24_H9b3s_096


title: P48_H1_bulk_250


title: P24_H9b3s_082


title: P24_H9b3s_081


title: SCR_rep2_H3K4me3


title: MOLM13-sgENL-DMSO-2

first: Liling

last: Wan

address: 1230 York Avenue, Box 78

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
Raw reads were mapped to human reference genome (hg19) and transcriptome using the the TopHat2 package. Transcript abundances were quantified using htseq-count v0.6.0
Differentially expressed genes were determined using DESeq2 for MOLM13 RNA-seq samples, and EdgeR for MV411 RNAseq-samples.
Genome_build: hg19
Supplementary_files_format_and_content: raw count files were generated using htseq-count v0.6.0

growth_protocol: Cells were cultured in RPMI with 10% FBS.

extract_protocol:
RNA was isolated from iCas9-MOLM-13 and MV411 cells using the RNeasy Mini Kit (Qiagen, Gaithersburg, MD).
Samples were prepared as instructed using the TruSeq mRNA Sample Preparation Kit v2 (Illumina, San Diego, CA) in accordance with the manufacturer's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles, DNA fragments were sequenced using single-end sequencing technology on Illumina NextSeq 500 platform (MOLM-13) or pair sequencing technology on Illumina HiSeq 2000 platform (MOLM-13)

treatment_protocol: ICas9-MOLM-13 Cells were treated with doxycyline for indicated time before RNA collection; MV411 cells were transduced with shRNA followed by drug selection, and RNA was collected at 6 days post infection for RNA-seq

tag: cell

value: iCas9-MOLM-13 cells

tag: treatment

value: DMSO 24hour, ENL Knock Down

tag: batch


title: MOLM13-sgENL-JQ1-50nM-1

value: JQ1 50nM 24hour, ENL Knock Down


title: SCR_rep2_H3K4me1


title: P24_H9b3s_080


title: P24_H9b3s_079


title: MOLM13-sgENL-DMSO-1


title: P24_H9b3s_072


title: MOLM13-sgGFP-DMSO-2

value: DMSO 24hour, Control


title: MOLM13-sgGFP-DMSO-1


title: P24_H9b3s_071

value: human embryonic stem cells


title: MOLM13-sgGFP-JQ1-50nM-1

value: JQ1 50nM 24hour, Control


title: P24_H9b3s_068


title: P24_H9b3s_067


title: MOLM13-sgENL-Y78A-1

value: doxycyline 4 days, ENL Knock Down plus  Y78A mutant rescue


title: P24_H9b3s_070


title: P24_H9b3s_092


title: MOLM13-sgENL-F59A-2

value: doxycyline 4 days, ENL Knock Down plus  F59A mutant rescue


title: P24_H9b3s_059


title: MOLM13-sgENL-F59A-1


title: MOLM13-sgENL-JQ1-50nM-2


title: P24_H9b3s_058


title: MOLM13-sgENL-WT-2

value: doxycyline 4 days, ENL Knock Down plus WT rescue


title: MOLM13-sgENL-WT-1


title: P24_H9b3s_057


title: P24_H9b3s_056


title: MOLM13-sgENL-vec-1

value: doxycyline 4 days, ENL Knock Down


title: MOLM13-sgGFP-JQ1-50nM-2


title: P24_H9b3s_090


title: MOLM13-sgLuc-vec-1

value: doxycyline 4 days, Control


title: P24_H9b3s_088


title: MOLM13-sgENL-Y78A-2


title: MOLM13-sgGFP-day5-2

value: doxycyline 5 days, Control


title: P24_H9b3s_087


title: MOLM13-sgGFP-day5-1


title: P24_H9b3s_085


title: MOLM13-sgGFP-day3-1

value: doxycyline 3 days, Control


title: P24_H9b3s_078

value: passage 25-35


title: P24_H9b3s_060


title: P24_H9b3s_086


title: MOLM13-sgENL5-day5-2

value: doxycyline 5 days, ENL Knock Down


title: P24_H9b3s_076


title: P24_H9b3s_077


title: MOLM13-sgENL5-day5-1


title: P24_H9b3s_075


title: MOLM13-sgENL5-day3-1

value: doxycyline 3 days, ENL Knock Down


title: MOLM13-sgENL5-day3-2


title: MOLM13-sgENL-vec-2


title: MOLM13-sgENL1-day5-2


title: MOLM13-sgLuc-vec-2


title: P24_H9b3s_073


title: P24_H9b3s_089


title: MOLM13-sgENL1-day3-2


title: MOLM13-sgENL1-day5-1


title: P24_H9b3s_055


title: P24_H9b3s_074


title: P24_H9b3s_066


title: MOLM13-sgENL1-day3-1


title: P24_H9b3s_065


title: P24_H9b3s_064


title: MOLM13-sgAF9-day5-1

value: doxycyline 5 days, AF9 Knock Down


title: MOLM13-sgAF9-day5-2

value: iCas9-MOLM-13 cells


title: P24_H9b3s_063


title: MOLM13-sgAF9-day3-2

value: doxycyline 3 days, AF9 Knock Down


title: P24_H9b3s_062


title: MOLM13-sgAF9-day3-1


title: P24_H9b3s_052


title: P24_H9b3s_053


title: P24_H9b3s_054


title: SCR_CONTROL

data_processing:
Sequencing reads were mapped to hg19 and methylation levels of CpG and GpC dinucleotides determined using the previously described pipeline (Lay et al Genome Res. 2015, Kelly et al. et al. Genome Res. 2012)
Base calling (Illumina Real-time analysis), alignment and mapping (BSMAP), and methylation levels (Bis-SNP) were performed.
Genome_build: hg19
Supplementary_files_format_and_content: GCH: accessibility
Supplementary_files_format_and_content: HCG: methylation

extract_protocol:
Nuclei isolated from exponentially growing cells were lysed and treated with M.CviPI GpC methyltransferase. Genomic DNA was isolated by standard phenol-chloroform extraction and ethanol precipitation.
GpC enzyme (M.CviPI) treated DNA was fragmented to ∼200-bp, END-repaired (Epicenter), methylated adaptors ligated (Illumina), bisulfite-converted (Zymo EZ DNA methylation), and PCR-amplified

value: hTERT immortalized endometriosis cells

tag: arid1a status

value: Control


title: ARID1A_KD

value: Knockdown


title: KD_input

value: ARID1A Knockdown

value: input


title: P24_H9b3s_050

value: human embryonic stem cells


title: P24_H9b3s_051


title: KD1_H3K27me3


title: KD1_H3K4me3


title: KD1_H3K27ac


title: P24_H9b3s_049


title: P24_H9b3s_048


title: KD1_H3K4me1


title: P24_H9b3s_047


title: P24_H9b3s_046


title: P24_H9b3s_045


title: SCR_rep1_H3K27ac


title: SCR_input


title: SCR_rep1_H3K4me3


title: P24_H9b3s_044


title: P24_H9b3s_036


title: P24_H9b3s_043


title: SCR_rep1_H3K4me1


title: P24_H9b3s_035


title: MV411.shNT_rep3

value: MV411 cells


title: MV411.shNT_rep2


title: P24_H9b3s_034


title: MV411.shNT_rep1


title: MV411.shENL_rep3

value: shENL Knock Down


title: MV411.shENL_rep2


title: P24_H9b3s_032


title: P24_H9b3s_031


title: P24_H9b3s_033


title: MV411.shENL_rep1


title: P24_H9b3s_024


title: IRF1-deficient T cells-Th9 rep3

first: Lucia

last: Campos Carrascosa

address: Hans-Meerwein-Straße 2

institute: Institute of Medical Microbiology

description: IRF1-deficient T cells cultured for 2 days under Th9-polarising conditions in the presence of IFN-gamma

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0b)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (Marini et al., 2016)
Differential expression analysis was performed with DESeq2 (version 1.12.3), setting the False Discovery Rate to 0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts from DESeq2 for each sample

source_name: IRF1-deficient T lymphocyte

growth_protocol: For the generation of Th9 cells, mice were sacrificed by cervical dislocation. Spleen and lymph nodes were removed and T cells were isolated by magentic negative selection. Th9 cell cultures were cultured in RPMI supplemented with 10% FCS in the presence of IL-2, IL-4, TGF-b and IFN-g,

extract_protocol:
Th9 cell total RNA was isolated using Trizol
Barcoded mRNA-seq cDNA libraries were prepared from 400ng of total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to the manual. Quantity was assessed using Invitrogen’s Qubit HS assay kit and library size was determined using Agilent’s 2100 Bioanalyzer HS DNA assay.  Barcoded RNA-Seq libraries were onboard clustered using HiSeq® Rapid SR Cluster Kit v2 using 8pM and 59bps were sequenced on the Illumina HiSeq2500 using HiSeq® Rapid SBS Kit v2 (59 Cycle). The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol

tag: strain background

value: T lymphocyte


title: IRF1-deficient T cells-Th9 rep2


title: SCR_rep1_H3K27me3


title: P24_H9b3s_020


title: P24_H9b3s_023


title: P24_H9b3s_022


title: WT T cells-Th9 rep3

description: WT T cells cultured for 2 days under Th9-polarising conditions in the presence of IFN-gamma

source_name: T lymphocyte

value: WT


title: IRF1-deficient T cells-Th9 rep1


title: WT T cells-Th9 rep2


title: WT T cells-Th9 rep1


title: P24_H9b3s_019


title: R3B

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

data_processing:
Illumina Basespace RNA-Seq Alignment application Version: 1.0.0 was used to trim adapters and align reads
Illumina Basespace Cufflinks Assembly & DE application Version: 2.0.0 was used to calculate FPKM values and identify differentially abundant mRNAs
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values in Excel file

source_name: Olfactory mucosa tissue

extract_protocol:
Olfactory mucosa were removed and immediately processed for collection of total RNA by Qiagen Rneasy micro kit
TruSeq

tag: strain

value: post natal day 11

tag: genotype

value: wild type

tag: tissue

value: open nostril


title: P24_H9b3s_010

tag: cell type

value: passage 25-35


title: P24_H9b3s_012


title: P24_H9b3s_011


title: P24_H9b3s_008


title: R3A

tag: age

value: closed nostril


title: P24_H9b3s_007

tag: cell line


title: R2A


title: R1B


title: P24_H9b3s_042

tag: passage


title: R1A


title: P24_H9b3s_041

tag: multiplexing


title: P24_H9b3s_039


title: P24_H9b3s_038


title: Hippo_rep2_sh34

city: Stanford

first: Marius

last: Wernig

state: CA

address: 265 Campus Drive, Rm. G3145

department: Institute for Stem Cell Biology & Regenerative Medicine

institute: Stanford University

description: processed data file: genes_Hippo.fpkm_tracking

data_processing:
Reads were aligned to GRCm38/mm10 using TopHat2 (version 2.1.1) and the transcripts were assempled using cufflinks & cuffdiff (version 2.2.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-seq: cuffdiff output

source_name: Primary hippocampal neurons_sh34

growth_protocol: For primary neuronal cultures the hippocampus of P0 wild-type mouse pups was isolated and cultured on Matrigel-coated plates (Corning) in MEM supplemented with B27, glucose, transferrin and 5% FBS. 2 days after plating the medium was supplemented with 2 mM Ara-C (Sigma) as published previously (Maximov et al., 2007). For Myt1l knock-down cells were infected with shRNA-expressing lentiviruses on third day of in vitro culture and analysed 11 days later by RNA sequencing.

extract_protocol: RNA was isolated using Trizol (Invitrogen) and treated with DNase (NEB) prior to library prepartion using the Illumina RNA TruSeq RNA Library Prep Kit.

treatment_protocol: Lentivirus was produced by transfection of TetO-FUW lentiviral backbones containing the indicated transgenes together with third-generation packaging plasmids into HEK293 cells following the Trono laboratory protocol (Dull et al., 1998). Virus was concentrated from culture supernatant by ultra-centrifugation (23000 rpm, 2 h, 4 °C) and cells were infected with three different viral titers. Infected cell populations that were used for reprogramming and genomic analysis were verified by immunofluorescence to contain approximately 70%-90% transgene-positive cells two days after induction based on immunofluorescence microscopy.

tag: tissue/cell type

value: Primary hippocampal neurons

tag: overexpressed proteins

value: Myt1L shRNA hairpin #2 (sh34)


title: P24_H9b3s_040


title: P24_H9b3s_037


title: P24_H9b3s_030


title: Hippo_rep1_sh34

source_name: Primary hippocampal neurons


title: P24_H9b3s_029


title: Hippo_rep2_sh0

value: Control shRNA hairpin (sh0)


title: Hippo_rep1_sh33

data_processing:
eads were aligned to GRCm38/mm10 using TopHat2 (version 2.1.1) and the transcripts were assempled using cufflinks & cuffdiff (version 2.2.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-seq: cuffdiff output

value: Myt1L shRNA hairpin #1 (sh33)


title: P24_H9b3s_028


title: P24_H9b3s_027


title: Hippo_rep1_sh0


title: Myt1L_rep2

description: processed data file: genes_Monly.fpkm_tracking

source_name: TauEGFP MEFs_Myt1L

growth_protocol: Passage three heterozygous TauEGFP knock-in MEFs were infected with indicated lentivirus in (DMEM; Invitrogen) containing 10% cosmic calf serum (CCS; Hyclone), beta mercaptoethanol (Sigma), non-essential amino acids, sodium pyruvate and penicillin/streptomycin (all from Invitrogen) media containing 8 μg/ml polybrene (Sigma) for 16-20 h. Cells were switched into fresh MEF media containing 2 μg/ml doxycycline (Sigma) to induce transgene expression for 2 days followed by RNA sequencing.

value: embryonic fibroblasts

value: rtTA + Myt1L + GFP


title: Myt1L_rep3


title: R2B


title: P24_H9b3s_018


title: rtTA_rep3

source_name: TauEGFP MEFs_rtTA

value: rtTA + GFP


title: P24_H9b3s_017

value: human embryonic stem cells


title: P24_H9b3s_025


title: rtTA_rep2

growth_protocol: MEFs were grown in DMEM with 10% Serum, b-mercaptoethanol, NEAA, sodium pyruvate and penicillin/streptomycin with 2 µg/ml doxycycline to induce overexpression. Mouse neurons were cultured in PO-laminin coated tissue culture dishes with DMEM/F12 containing N2 or B27 supplement, penicillin/streptomycin, and 20 ng/ml EGF, 10 ng/ml FGF.


title: P24_H9b3s_016


title: P24_H9b3s_015


title: Hippo_rep2_sh33

source_name: Primary hippocampal neurons_sh33


title: P24_H9b3s_014


title: P24_H9b3s_013


title: MIPSL3

city: Boston

first: Daniel

middle: Adam

last: Petkovich

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Genetics

institute: Brigham and Women's Hospital

data_processing:
Basecalls performed usingbcl2fastq 1.8.3.
Adapter removal and quality trimming were performed by using Trim Galore! v.0.4.0
Aligment performed by Bismark v0.14.0 with Bowtie 2. (-q -n 1 -k 2 --best --chunkmbs 512)
Methylation levels were determined as suggested by the Bismark program manual using the following parameters: bismark_methylation_extractor -p --multicore 10 --bedGraph --ample_memory --cytosine_report --genome_folder ./ $Sample.R1_val_1.fq.gz_bismark_pe.bam
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files of methylation status

source_name: iPSCs from lung fibroblasts

growth_protocol: Isolated fibroblasts were grown in DMEM with 20% FBS (37C, 5% CO2). IPSCs were grown with LIF and DMEM with 20% FBS (37C, 5% CO2)

extract_protocol:
Whole blood was harvested, mixed with K2EDTA, mixed with lysis buffer and DNA was isolated from lysate. Fibroblasts and IPSCs were lysed and DNA was isolated from lysate.
Libraries were prepared using Reduced Representation Bisulfite Sequencing. Six to seven samples were pooled together using Illumina's TrueSeq Nano DNA LT adaptors.

treatment_protocol: Isolated fibroblasts were transformed into iPSCs by lenti-viral vector (OKSM).

value: iPSCs from lung fibroblasts

value: Derived from L3

tag: age (years)

value: 2.5 (at isolation)

tag: gender

value: Male

tag: genetic condition

value: Wild Type

tag: diet

value: standard


title: MIPSL2

value: Derived from L2


title: MIPSL1

value: Derived from L1


title: MIPSK2

source_name: iPSCs from kidney fibroblasts

value: iPSCs from kidney fibroblasts

value: Derived from K2


title: MIPSK1

value: Derived from K1


title: P24_H9b3s_005

source_name: undifferentiated human embryonic stem cells

value: passage 25-35


title: P24_H9b3s_006


title: P24_H9b3s_003


title: P24_H9b3s_002


title: M3503R

source_name: Whole Blood

value: whole blood


title: M3502R


title: M3502


title: P24_H9b3s_004


title: P96_H9b3s_096

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). The H9 single-cell cDNA libraries were multiplexed at 96 libraries per lane, and single-end reads of 51-bp sequencing was performed on an Illumina HiSeq 2500 system.


title: M3501R


title: P96_H9b3s_095


title: P96_H9b3s_094


title: M3410


title: M3501


title: P96_H9b3s_093


title: M3409


title: MIPSK3

value: Derived from K3


title: P96_H9b3s_092


title: M3408


title: M3406


title: P96_H9b3s_091


title: M3405


title: P96_H9b3s_083


title: P24_H9b3s_001


title: P96_H9b3s_081


title: M3401


title: M3402


title: M3403


title: M3210


title: M3404


title: P96_H9b3s_079


title: M3209


title: P96_H9b3s_072


title: M3208


title: P96_H9b3s_071


title: M3207


title: M3503


title: P96_H9b3s_070


title: P96_H9b3s_067


title: P96_H9b3s_084


title: M3206


title: M3205


title: P96_H9b3s_082


title: P96_H9b3s_060


title: P96_H9b3s_068


title: M3009


title: P96_H9b3s_080


title: P96_H9b3s_059


title: M3204


title: M3010


title: P96_H9b3s_058


title: P96_H9b3s_057


title: M3006


title: M3005


title: P96_H9b3s_056


title: M3004


title: P96_H9b3s_090


title: M3003


title: P96_H9b3s_055


title: M3002


title: M3001


title: P96_H9b3s_087


title: P96_H9b3s_088


title: M2810


title: P96_H9b3s_086


title: M3007


title: P96_H9b3s_085


title: M2806


title: P96_H9b3s_078


title: M2808


title: P96_H9b3s_077


title: M2805


title: P96_H9b3s_074


title: P96_H9b3s_076


title: M2809


title: P96_H9b3s_075


title: M2802


title: M2804


title: P96_H9b3s_089


title: P96_H9b3s_073


title: M2801


title: P96_H9b3s_066


title: P96_H9b3s_063


title: M2608


title: M2607


title: P96_H9b3s_062


title: M2610


title: P96_H9b3s_064


title: P96_H9b3s_054


title: M2606


title: M2807


title: M2605


title: P96_H9b3s_053


title: M2601


title: M2602


title: P96_H9b3s_049


title: M2603


title: P96_H9b3s_050


title: M2609


title: M2604


title: M2411


title: P96_H9b3s_047


title: P96_H9b3s_046


title: M2409


title: P96_H9b3s_051


title: P96_H9b3s_065


title: M2408


title: M2407


title: P96_H9b3s_048


title: P96_H9b3s_045


title: M2405


title: M2401


title: M2403


title: P96_H9b3s_036


title: P96_H9b3s_043


title: P96_H9b3s_034


title: P96_H9b3s_052


title: M2402


title: P96_H9b3s_035


title: P96_H9b3s_033


title: M2210


title: M2206


title: P96_H9b3s_032


title: M2208


title: P96_H9b3s_024


title: P96_H9b3s_031


title: M2201


title: M2205


title: M2204


title: M2202


title: P96_H9b3s_044


title: P96_H9b3s_019


title: M2203


title: M2404


title: P96_H9b3s_022


title: P96_H9b3s_012


title: P96_H9b3s_011


title: P96_H9b3s_008


title: P96_H9b3s_010


title: P96_H9b3s_007


title: P96_H9b3s_020


title: P96_H9b3s_042


title: M2007


title: P96_H9b3s_023


title: M2209


title: M2010


title: M2005


title: P96_H9b3s_040


title: M2004


title: P96_H9b3s_038


title: M2001


title: M1610


title: M2008


title: P96_H9b3s_028


title: P96_H9b3s_039


title: P96_H9b3s_030


title: M1608


title: P96_H9b3s_027


title: M2006


title: M2009


title: M2003


title: P96_H9b3s_025


title: M1606


title: M1609


title: P96_H9b3s_037


title: P96_H9b3s_029


title: M1607


title: M1602


title: P96_H9b3s_018


title: P96_H9b3s_017


title: M1603


title: P96_H9b3s_041


title: P96_H9b3s_016


title: M1601


title: M1210


title: P96_H9b3s_014


title: P96_H9b3s_015


title: M1209


title: M1208


title: P96_H9b3s_013


title: P96_H9b3s_006


title: M1605


title: P96_H9b3s_005


title: P96_H9b3s_004


title: M1205


title: M1204


title: P96_H9b3s_003


title: P96_H9b3s_002


title: M1206


title: M1201


title: M1203


title: M10_7510


title: P96_H9b3s_001


title: M1207


title: M1202


title: P24_H1b5s_093

growth_protocol: Undifferentiated H1 hESCs were cultured in E8 medium on Matrigel-coated tissue culture plates with daily media feeding at 37 °C. Cells were split every 3-4 days with 0.5 mM EDTA in 1xPBS for standard maintenance

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). The H1 single-cell cDNA libraries were multiplexed at 24 libraries per lane, and single-end reads of 51-bp sequencing was performed on an Illumina HiSeq 2500 system.

value: passage 20-30


title: P24_H1b5s_095


title: M10_7507


title: M10_7508


title: M10_7506


title: P24_H1b5s_092


title: P24_H1b5s_091


title: M10_7505


title: P24_H1b5s_084


title: M10_7504


title: P24_H1b5s_083


title: M10_7501


title: P24_H1b5s_096


title: P24_H1b5s_082


title: P24_H1b5s_094


title: M10_7509


title: P24_H1b5s_081


title: P24_H1b5s_080


title: M0806


title: P24_H1b5s_079


title: P24_H1b5s_070


title: M0808


title: P24_H1b5s_071


title: P24_H1b5s_072


title: M0805


title: P24_H1b5s_069


title: M0804


title: P24_H1b5s_068


title: M0802


title: M0803


title: M0610


title: M0801


title: P24_H1b5s_060


title: P24_H1b5s_059


title: M10_7502


title: P24_H1b5s_067


title: P24_H1b5s_058


title: M0810


title: M0807


title: P24_H1b5s_057


title: M0608


title: M0606


title: P24_H1b5s_090


title: P24_H1b5s_055


title: M0607


title: M0604


title: P24_H1b5s_089


title: P24_H1b5s_056


title: M0605


title: M0603


title: M0409


title: M0410


title: P24_H1b5s_088


title: M0601


title: M0609


title: P24_H1b5s_078


title: P24_H1b5s_085


title: P24_H1b5s_087


title: P24_H1b5s_076


title: M0407


title: P24_H1b5s_075


title: M0406


title: M0403


title: P24_H1b5s_074


title: M0404


title: M0405


title: M0402


title: P24_H1b5s_073


title: P24_H1b5s_066


title: M0401


title: P24_H1b5s_065


title: P24_H1b5s_086


title: P24_H1b5s_063


title: P24_H1b5s_064


title: M0310


title: P24_H1b5s_062


title: P24_H1b5s_054


title: M0309


title: M0306


title: M0308


title: P24_H1b5s_061


title: M0305


title: P24_H1b5s_053


title: M0302


title: P24_H1b5s_051


title: M0304


title: P24_H1b5s_050


title: P24_H1b5s_049


title: M0303


title: P24_H1b5s_052


title: L2

source_name: Lung fibroblasts

value: Primary Lung Fibroblasts

value: Lung Fibroblasts, C57BL/6


title: P24_H1b5s_047

value: human embryonic stem cells


title: M0301


title: L3


title: P24_H1b5s_046


title: P24_H1b5s_045


title: L1


title: K3

source_name: Kidney fibroblasts

value: Primary Renal Fibroblasts

value: Kidney Fibroblasts, C57BL/6


title: K1

value: 2.5 (at isolation)

value: Male


title: K2

value: Wild Type

value: standard


title: P24_H1b5s_036


title: GX2642

value: (C57BL/6J x BALB/cByJ)/F2

value: Female

value: GHRKO


title: P24_H1b5s_035


title: P24_H1b5s_034


title: GX2638

value: GHRKO WT


title: GX2627


title: GX2623


title: P24_H1b5s_033


title: GX2595


title: P24_H1b5s_032


title: P24_H1b5s_024


title: P24_H1b5s_031


title: P24_H1b5s_021


title: P24_H1b5s_022


title: GX2584


title: P24_H1b5s_023


title: P24_H1b5s_019


title: GX2582


title: GX2521


title: GX2522


title: P24_H1b5s_044


title: GX2518


title: P24_H1b5s_020


title: P24_H1b5s_012


title: GX2517


title: GX2519


title: P24_H1b5s_010


title: GX2481


title: GX2479


title: GX2474


title: P24_H1b5s_011


title: GX2483


title: GX2596


title: P24_H1b5s_009


title: GX2472


title: P24_H1b5s_042


title: P24_H1b5s_007


title: P24_H1b5s_041


title: GX2471


title: P24_H1b5s_040


title: GX2468


title: P24_H1b5s_039


title: P24_H1b5s_038


title: GX2467


title: P24_H1b5s_030


title: GX2466


title: P24_H1b5s_029


title: P24_H1b5s_027


title: GX2464


title: DW9

value: (DW/J x C3H/HEJ)/F2

value: Snell Dwarf Control


title: P24_H1b5s_025


title: P24_H1b5s_026


title: DW8

value: whole blood

value: Snell Dwarf


title: P24_H1b5s_018

value: passage 20-30


title: P24_H1b5s_017


title: DW6


title: DW5


title: DW7


title: P24_H1b5s_015


title: P24_H1b5s_016


title: GX2470


title: DW4


title: DW33


title: P24_H1b5s_014


title: P24_H1b5s_013


title: GX2465


title: P24_H1b5s_006


title: P24_H1b5s_005


title: DW31


title: P24_H1b5s_004


title: DW32


title: DW3


title: DW30


title: P24_H1b5s_003


title: GX2455


title: P24_H1b5s_002


title: DW25


title: DW28


title: P24_H1b5s_037


title: P24_H1b5s_001


title: P96_H1b5s_096

extract_protocol:
Single-cell suspensions were loaded onto a medium size (10-17 μm) C1 Single-Cell Auto Prep IFC (Fluidigm), and cell-loading script was performed according to the manufacturer’s instructions. Full-length single-cell cDNA libraries generated by the SMARTer PCR cDNA Synthesis kit (Clontech) and the Advantage 2 PCR kit (Clontech) performed in the C1 system.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina). The H1 single-cell cDNA libraries were multiplexed at 96 libraries per lane, and single-end reads of 51-bp sequencing was performed on an Illumina HiSeq 2500 system.


title: DW27


title: DW23


title: DW24


title: DW34


title: P96_H1b5s_093


title: P96_H1b5s_095


title: P96_H1b5s_094


title: P96_H1b5s_092


title: DW2


title: DW13


title: P96_H1b5s_084


title: DW11


title: DW1


title: B6D2F1_CR2705

value: Calorie Restricted


title: P96_H1b5s_082

value: human embryonic stem cells


title: P96_H1b5s_081


title: P96_H1b5s_080


title: B6D2F1_CR2703


title: B6D2F1_CR2702


title: P96_H1b5s_079


title: P96_H1b5s_072


title: P96_H1b5s_071


title: b6d2f1_CR2107


title: b6d2f1_CR2106


title: P96_H1b5s_070


title: B6D2F1_CR2104


title: P96_H1b5s_069


title: DW12


title: P96_H1b5s_068


title: B6D2F1_CR2105


title: P96_H1b5s_091


title: B6D2F1_CR2103


title: P96_H1b5s_067


title: P24_H1b5s_043


title: P96_H1b5s_083


title: B6D2F1_CR2704


title: B6D2F1_CR2101


title: B6D2F1_2705


title: P96_H1b5s_059


title: B6D2F1_2704


title: P96_H1b5s_060


title: P96_H1b5s_057


title: B6D2F1_2703


title: B6D2F1_CR2701


title: B6D2F1_2702


title: P96_H1b5s_056


title: P96_H1b5s_055


title: B6D2F1_2701


title: P96_H1b5s_090


title: B6D2F1_2005


title: P96_H1b5s_089


title: P96_H1b5s_088


title: P96_H1b5s_087


title: B6D2F1_CR2102


title: B6D2F1_2001


title: P96_H1b5s_086


title: B6D2F1_2002


title: P96_H1b5s_058


title: P96_H1b5s_085


title: P96_H1b5s_078


title: B6D2F1_2003


title: P96_H1b5s_076


title: P96_H1b5s_075


title: B6_CR2704


title: B6_CR2705


title: P96_H1b5s_074


title: B6_CR2703


title: P96_H1b5s_073


title: B6_CR2305


title: B6_CR2304


title: B6D2F1_2004


title: P96_H1b5s_064


title: B6_CR2303


title: SS_5M_HR_DRG_6

city: Minneapolis

first: Kalpna

last: Gupta

address: 14-100 PWB, 516 Delaware Street SE

department: Medicine/HOT

institute: University of Minnesota

data_processing:
Primary analysis and de-multiplexing are performed using Illumina’s CASAVA software 1.8.2. The end result of the CASAVA workflow is de-multiplexed FastQ files that are subjected to subsequent analysis by the mapping software and aligner.
The illumina read files were processed via a pipeline developed by University of Minnesota Informatics Institute (UMII) in collaboration with Minnesota Supercomputing Institute (MSI) and University of Minnesota Genomics Center (UMGC). FastQ files were trimmed via trimmomatic using the following parameters: -phred33 -threads 8, ILLUMINACLIP, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:16 MINLEN:25.
After trimming, mapping was performed via TopHAT (v2.0.13) using bowtie (v2.2.4.0). This mapping results into output of one binary alignment/map (BAM) files for each sample matched to a reference mouse genome – mm10.
Finally, fragments per kilobase of transcript per million mapped reads (FPKM) values was calculated as expression data via cuffquant (--quiet -u --max-bundle-frags 10000000 and cuffnorm).
The primary output files from the analysis pipeline are FastQC files to check the quality of the reads in FastQ files, raw count expression tables as text files and expression data as FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: excel files with raw read count and FPKM values.

source_name: Dorsal root ganglion

extract_protocol:
Hypoxia/reoxygenation treatment: The mice in small rodent cages are placed in a chamber with the atmosphere controlled by a ProOx110 gas controller (BioSpherix, Ltd, Parish, NY). These mice are exposed to hypoxia with 8% O2 and 92% N2 for 3 hours, followed by reoxygenation for 1 hour in the room air (3)
Dorsal root ganglia (DRGs) were removed and preserved in RNA Later, and RNA was harvested using Trizol reagent. The total amount of RNA in each sample is quantified using a fluorimetric RiboGreen assay (R11490 Quant-iT from thermo-fischer) and RIN is generated for each sample by performing capillary electrophoresis using Agilent BioAnalyzer 2100. RNA with RIN score of 8 or more was finally selected for RNA-seq. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. Total RNA samples are converted to Illumina sequencing libraries using Illumina’s Truseq RNA Sample Preparation Kit (Cat.# RS-122-2001). In brief, 1 mg of total RNA from each sample is purified using oligo-dT coated magnetic beads (part of rna prep kit). Next they are fragmented and then reverse transcribed into cDNA. The cDNA is fragmented, blunt-ended, and ligated to indexed (barcoded) adaptors and amplified using 15 cycles of polymerase chain reaction (PCR) (Biorad DNA Engine Tetrad 2). Final library size distribution is validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen) and via qPCR. Indexed libraries are then normalized, pooled and then size selected to 320bp +/- 5% using Caliper’s XT instrument (Perkin Elmer). Truseq libraries are hybridized to a paired end flow cell and individual fragments are clonally amplified by bridge amplification on the Illumina cBot. Once clustering is complete, the flow cell is loaded on the HiSeq 2000 and sequenced using Illumina’s sequencing by synthesis (SBS) chemistry to generate 50 bp paired end reads. Upon completion of read 1, a 7 base pair index read is performed. Finally, the library fragments are resynthesized in the reverse direction and sequenced from the opposite end of the read 1 fragment, thus producing the template for paired end read 2. Base call (.bcl) files for each cycle of sequencing are generated by Illumina Real Time Analysis (RTA) software during the sequencing run on HiSeq 2000. The base call files and run folders are then exported to servers maintained at the Minnesota Supercomputing Institute.

value: HbSS-BERK (Transgenic sickle cell disease mouse model)

value: Dorsal root ganglion

value: 5 months

tag: treatment

value: Hyoxia/reoxygenation (simulating acute pain condition)


title: P96_H1b5s_065


title: B6_CR2302

value: Male

value: Wild Type


title: P96_H1b5s_063


title: SS_5M_HR_DRG_4


title: SS_5M_HR_DRG_3


title: P96_H1b5s_062


title: SS_5M_HR_DRG_2


title: SS_5M_HR_DRG_1


title: P96_H1b5s_061


title: B6_CR1805


title: B6_CR2301


title: B6_CR2701


title: B6_CR2702


title: P96_H1b5s_066


title: P96_H1b5s_054


title: SS_5M_Norm_DRG_4

value: Normoxia (i.e., no treatment - simulation chronic pain condition)


title: B6_CR1804


title: SS_5M_Norm_DRG_5


title: B6_CR1803


title: P96_H1b5s_053


title: SS_5M_Norm_DRG_3


title: B6_CR1802


title: SS_5M_HR_DRG_5


title: P96_H1b5s_052


title: P96_H1b5s_051


title: SS_2M_HR_DRG_6

value: 2 months


title: SS_5M_Norm_DRG_1


title: B6_CR1801


title: SS_2M_HR_DRG_4


title: SS_2M_HR_DRG_5


title: B6_CR1005


title: SS_2M_HR_DRG_3


title: P96_H1b5s_050


title: SS_5M_Norm_DRG_6


title: SS_2M_HR_DRG_2


title: B6_CR1004


title: P96_H1b5s_049


title: SS_2M_HR_DRG_1


title: P96_H1b5s_047


title: P96_H1b5s_046


title: SS_2M_Norm_DRG_5


title: SS_2M_Norm_DRG_4


title: SS_2M_Norm_DRG_3


title: SS_5M_Norm_DRG_2


title: SS_2M_Norm_DRG_2


title: B6_CR1003


title: P96_H1b5s_044


title: 35D06

value: standard


title: 35D07


title: SS_2M_Norm_DRG_1


title: B6_CR1002


title: AA_5M_HR_DRG_5

value: HbAA-BERK (Control mouse for transgenic sickle cell disease mouse model)


title: P96_H1b5s_043


title: P96_H1b5s_045


title: AA_5M_HR_DRG_6


title: P96_H1b5s_036


title: AA_5M_HR_DRG_3


title: AA_5M_HR_DRG_4


title: AA_5M_HR_DRG_2


title: P96_H1b5s_035


title: 35D04


title: AA_5M_Norm_DRG_6


title: AA_5M_Norm_DRG_4


title: B6_CR1001


title: SS_2M_Norm_DRG_6


title: AA_5M_Norm_DRG_3


title: P96_H1b5s_033


title: P96_H1b5s_034


title: AA_5M_Norm_DRG_2


title: AA_5M_HR_DRG_1


title: 35D05


title: 35D02


title: 35D01


title: AA_5M_Norm_DRG_5


title: AA_2M_HR_DRG_6


title: AA_2M_HR_DRG_3


title: 20D07


title: P96_H1b5s_031


title: P96_H1b5s_032


title: 20D06


title: AA_2M_HR_DRG_1


title: AA_2M_HR_DRG_2


title: AA_5M_Norm_DRG_1


title: AA_2M_Norm_DRG_6


title: AA_2M_Norm_DRG_5


title: AA_2M_HR_DRG_4


title: P96_H1b5s_023


title: AA_2M_Norm_DRG_4


title: 20D03


title: AA_2M_HR_DRG_7


title: P96_H1b5s_022


title: 20D05


title: 20D02


title: P96_H1b5s_021


title: P96_H1b5s_024


title: AA_2M_Norm_DRG_2


title: AA_2M_Norm_DRG_1


title: AA_2M_Norm_DRG_3


title: P96_H1b5s_020


title: P96_H1b5s_019


title: P96_H1b5s_011


title: P96_H1b5s_010


title: P96_H1b5s_012


title: 20D04


title: R_2016_03_15_14_58_59

city: St John's

first: Marc

middle: Patrick

last: Grüll

state: Newfoundland

address: 230 Elizabeth Ave

department: Biology

country: Canada

institute: Memorial University of Newfoundand

data_processing:
In house software used for data processing
In house software sRNA-Detect used to perform genome wide detection of sRNAs

organism: Rhodobacter capsulatus

source_name: Supernatant from anaerobic photosynthetic culture

growth_protocol: R. capsulatus cells were grown aerobically in RCV minimal medium for one day. Cells were then transferred to an anaerobic photosynthetic tube containing YPS medium. The anaerobic cultures were prepared to have an initial optical density of 20 Klett Units (KU). Cultures were grown for 15-16 hours.

extract_protocol:
500μ of culture were transferred into 100μl 95% Ethanol and 5% Phenol. Samples were spun down for 2 minutes and the pellets were stored at -80°C. Small RNA was extracted following the Macherey-Nagel protocol for DNA, RNA, and protein purification kit for small RNA fraction.
Libraries were prepared following the Ion Torrent Ion Total RNA-Seq Kit V2 for Small RNA Libraries protocol

tag: growth phase

value: Early Stationary


title: R_2016_03_15_11_04_56


title: MEF_Sin3b_rep2

description:
ChIP
macs2.con.48h_flM_Sin3b_cat_peaks.narrowPeak

data_processing:
Reads were aligned to GRCm38/mm10 using bowtie2 (version 2.2.3) allowing maximum one mismatch per read (Langmead et al., 2012). Peaks for each sample were called using MACS2 (version 2.0.10.20131216 (Zhang et al., 2008) using shift size values from the run_spp.R script of the SPP peak caller (Kharchenko et al., 2008). The IDR pipeline was run to identify high-quality peaks according to https://sites.google.com/site/anshulkundaje/projects/idr using a cutoff value of 0.02.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: narrowPeak files of idr-processed ChIP peaks

source_name: TauEGFP MEFs

growth_protocol: Passage three heterozygous TauEGFP knock-in MEFs were infected with indicated lentivirus in (DMEM; Invitrogen) containing 10% cosmic calf serum (CCS; Hyclone), beta mercaptoethanol (Sigma), non-essential amino acids, sodium pyruvate and penicillin/streptomycin (all from Invitrogen) media containing 8 μg/ml polybrene (Sigma) for 16-20 h. Cells were switched into fresh MEF media containing 2 μg/ml doxycycline (Sigma) to induce transgene expression for 2 days followed by ChIP sequencing.

extract_protocol: ChIP-seq were carried out following the Farnham protocol (O'Geen et al., 2011). Libraries were generated using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina.

tag: strain background

value: embryonic fibroblasts

value: Brn2, Ascl1, Myt1l, rtTA

tag: chip antibody

value: Sin3b Santa Cruz #sc-996 (rabbit)


title: MEF_Sin3b_rep1


title: MEF_rtTA_Myt1LB_rep1

description:
ChIP
48h_rtTA_Myt1LB.narrowPeak

value: rtTA

value: Myt1lb (rabbit)


title: MEF_rtTA_Myt1LB_rep2

description:
ChIP
48h_rtTA_Myt1LB.narrowPeak


title: MEF_Sin3b_HDAC_Input_rep2

description: ChIP Input


title: MEF_HDAC_rep2

description:
ChIP
macs2.con.48h_flM_HDAC1_cat_peaks.narrowPeak

value: HDAC Abcam #ab7028 (rabbit)


title: P96_H1b5s_009

value: human embryonic stem cells

value: passage 20-30


title: P96_H1b5s_007


title: AA_2M_HR_DRG_5

tag: strain

value: Dorsal root ganglion


title: MEF_truncM_Myt1lb_rep2

description:
ChIP
macs2.con.48h_truncM_Myt1LB_cat_peaks.narrowPeak

tag: tissue


title: MEF_Sin3b_HDAC_Input_rep1

description: ChIP Input


title: P96_H1b5s_042

tag: cell type


title: MEF_truncM_Input_rep2

description: ChIP Input


title: P96_H1b5s_041


title: P96_H1b5s_039


title: P96_H1b5s_038


title: MEF_HDAC_rep1


title: P96_H1b5s_040


title: MEF_flM_Myt1lb_rep2

description:
ChIP
macs2.con.48h_flM_Myt1LB_cat_peaks.narrowPeak

value: Myt1l, rtTA


title: MEF_truncM_Myt1lb_rep1


title: MEF_flM_Input_rep2

description: ChIP Input


title: P96_H1b5s_029


title: MEF_flM_Myt1lb_rep1


title: MEF_flM_Input_rep1

description: ChIP Input


title: MEF_BAtruncM_Myt1lb_rep3

description:
ChIP
macs2.con.48h_BAtruncM_Myt1LAB_cat_peaks.narrowPeak

value: Brn2, Ascl1, Myt1l(200-623), rtTA


title: P96_H1b5s_030


title: P96_H1b5s_027


title: P96_H1b5s_018


title: P96_H1b5s_026


title: MEF_BAtruncM_Input_rep3

description: ChIP Input


title: P96_H1b5s_037


title: Group Control 4

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

country: United Kingdom

institute: Cardiff University

description:
Sample 14
processed data file: Control_v_Novel.csv, Control_v_Familiar.csv

data_processing:
Base calling and trimming of sequences and adapters was performed using the Torrent Suite Software v4.0.2. . For each sample, the data from both chips were pooled before running the analysis pipeline.
Alignment of the sequencing reads was performed via TopHat using the rat reference genome Rnor_6.0 (GenBank Assembly ID GCA_000001895.4). We used default TopHat parameters except for the range of expected intron lengths, which we set to 12-270,000 based on the current reference gene models. Unmapped reads were then re-aligned using Bowtie2 local alignments and combined with the TopHat alignments.
Reads were mapped to rat genes and the relative abundance of each transcript was quantified using the HTSeq package, counting only uniquely mapped reads and allowing for an alignment quality threshold of 10.
We used RUVSeq to adjust read counts in order to mitigate unwanted variation unrelated to treatment groups. Using these counts as input, differential gene expression analysis was performed using edgeR.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: csv files containing output from edgeR after each RUVSeq normalisation step (fold changes, p values) for each Ensembl gene ID.

source_name: No test_Caudal perirhinal cortex

growth_protocol: All rats were kept on a reversed 12-h light/dark cycle (lights on 20.00-08.00 h) and all behavioural testing. Prior to the start of the behavioural experiments, the animals were placed on food restriction with daily access to food for a period of 2 h. The rats were kept at over 85% of their free-feeding weight. Water was available without restriction.

extract_protocol:
Total RNA was extracted from isolated and snap-frozen caudal perirhinal cortex tissue 1h after completion of the behavoural task using TRIzol (Life Technologies) and the Rneasy Mini kit (Qiagen). Samples were selectively depleted of rRNA using the Low Input Ribominus Eukaryote System v2 (Life Technologies).
cDNA libraries were prepared from 250 ng total RNA using the Ion Total RNA-seq Kit v2 in combination with the Ion Xpress RNA-Seq Barcode 1-16 Kit (both kits from Life Technologies).

treatment_protocol: Rats were trained in the bow-tie maze recognition memory task and on the final day were allowed to explore either completely novel objects (Group Novel) or highly familiar objects (Group Familiar). Group Control consisted of naïve rats that had not undergone any behavioural training.

value: Lister Hooded

tag: Sex

value: male

tag: weight

tag: behavioural task

value: Naïve

tag: test condition

value: No test

value: Caudal perirhinal cortex

tag: molecule subtype

value: rRNA-depleted total RNA


title: MEF_BAtruncM_Myt1lb_rep2

value: embryonic fibroblasts

tag: overexpressed proteins


title: P96_H1b5s_025

tag: cell line

tag: passage

tag: multiplexing


title: Group Control 2

description:
Sample 12
processed data file: Control_v_Novel.csv, Control_v_Familiar.csv


title: Group Control 3

description:
Sample 13
processed data file: Control_v_Novel.csv, Control_v_Familiar.csv


title: Group Control 1

description:
Sample 11
processed data file: Control_v_Novel.csv, Control_v_Familiar.csv


title: MEF_BAtruncM_Input_rep2

description: ChIP Input


title: P96_H1b5s_017

description: H1 cells were routinely maintained at the undifferentiated state in E8 medium on Matrigel


title: MEF_BAtruncM_Myt1la_rep1

value: Myt1la (rabbit)


title: MEF_truncM_Input_rep1

description: ChIP Input