title: Female 103d gonad sorted with INTa6/EpCAM RNA-seq

source_name: 103d female fetal gonad

value: 103d female fetal gonad


title: 14 - ALV-J-susceptible chicken

status: Public on Nov 10 2018

type: SRA

city: Guangzhou

first: Xinheng

last: Zhang

state: Guangdong

address: No.483, Wushan Road, Tianhe District

department: Animal Science

country: China

institute: South China Agricultural University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software. Raw junction reads for all samples were normalized by total mapped reads number and log2 transformed.
Differentially expressed circRNAs were identified by ttest between two groups.
Genome_build: galGal4
Supplementary_files_format_and_content: excel format; Number of raw and normalized junction reads.

molecule: total RNA

organism: Gallus gallus

source_name: liver

extract_protocol:
Total RNA from each sample was used to prepare the circRNA sequencing library. 5 μg total RNA were pretreated to enrich circRNA using CircRNA Enrichment Kit (Cloud-seq Inc, China).
RNA libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

tag: phenotype

value: ALV-J-susceptible chicken

tag: age for circrna-sequencing

value: post infection 10 weeks

tag: infection

value: ALV-J NX0101

tag: the date of infection alv-j nx0101

value: post natal day 1

tag: tissue

value: liver


title: 9 - ALV-J-susceptible chicken


title: 8 - ALV-J-susceptible chicken


title: Male 59d gonad sorted with TNAP/cKIT RNA-seq

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

data_processing:
Raw reads in qseq format obtained from sequencer were first converted to fastq format with customized perl script. Reads quality were controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). High quality reads were then aligned to hg19 reference genome using Tophat (Trapnell et al., 2009, v 2.0.13) by using ‘-no-coverage-search’ option, allowing up to two mismatches and only keeping reads that mapped to one location. Basically, reads were first mapped to hg19 gene annotation with known splice junction. When reads did not map to the annotated genes, the reads were mapped to hg19 genome. Number of reads mapping to genes were calculated by HTseq49 (v 0.5.4) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads) in R using customized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: RNASeq:raw reads count of all samples

molecule: polyA RNA

organism: Homo sapiens

source_name: 59d male fetal gonad

extract_protocol:
Sorted cells or cell pellets were lysed in 350uL of RLT buffer (QIAGEN) and total RNA was extracted with RNeasy micro kit (QIAGEN, 74004). Total RNA was reverse transcribed and cDNA was amplified using Ovation RNA-Seq System V2 (Nugen, 7102-32) according to manufacturer’s instructions. Amplified cDNA was fragmented into ~200bp by Covaris S220 Focused-ultrasonicators.
RNA-seq libraries were generated using Ovation® Rapid Library Systems (Nugen, 0319-32 for index 1-8 and 0320-32 for index 9-16) and quantified by KAPA library quantification kit (Illumina, KK4824).
Library type = Ovation RNASeq System V2

tag: cell type

value: 59d male fetal gonad

tag: passage number

value: Not Available


title: UCLA2 hESC replicate 2 RNA-seq

description: UCLA2 hESC replicate 2 RNA-seq

source_name: UCLA2 hESCs

value: UCLA2 hESCs

value: Passage 14


title: UCLA2 hESC replicate 1 RNA-seq

description: UCLA2 hESC replicate 1 RNA-seq

value: Passage 13


title: Fibroblast-young-1

status: Public on Nov 09 2018

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

description: ATAC-seq

library_source: genomic

data_processing:
Sequencing reads were trimmed using Trimmomatic to remove Illumina adapters and low quality base calls on both ends (Phred < 3).  Trimmed reads were mapped to the reference human genome assembly GRCh37 (hg19) using Bowtie2, allowing fragments up to 2kb to be aligned (“-X 2000”).  The alignment result was further processed by SAMtools to remove low quality alignments (mapping quality > 10), duplicate reads, reads mapped to mitochondria, and reads mapped to ENCODE blacklisted genomic regions.  All mapped reads were offset by +4 bp for the +strand and -5 bp for the -strand.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using BEDtools and UCSC command line utilities, for which purpose the visualization tracks were normalized to one million reads per sample.

molecule: genomic DNA

source_name: primary cells

growth_protocol: DMEM/F12, 10%FBS, 37C, 5% CO2, media change every 3 days

extract_protocol:
protocol described in Curr Protoc Mol Biol. 2015; 109: 21.29.1–21.29.9.
protocol described in Curr Protoc Mol Biol. 2015; 109: 21.29.1–21.29.9.

value: primary fibroblasts

tag: passages

value: skin


title: Fibroblast-old-3

description: ATAC-seq


title: Fibroblast-young-2

description: ATAC-seq


title: ASC-young-3

description: ATAC-seq

value: Adipose derived stem cells

value: Adipose


title: ASC-young-2

description: ATAC-seq


title: Fibroblast-old-1

description: ATAC-seq


title: Female 89d gonad sorted with TNAP/cKIT RNA-seq

source_name: 89d female fetal gonad

value: 89d female fetal gonad


title: ASC-young-6

description: ATAC-seq


title: ASC-young-4

description: ATAC-seq


title: Fibroblast-old-2

description: ATAC-seq


title: Fibroblast-young-3

description: ATAC-seq


title: ASC-young-1

description: ATAC-seq


title: Fibroblast-young-4

description: ATAC-seq


title: ASC-old-2

description: ATAC-seq


title: ASC-old-3

description: ATAC-seq


title: ASC-old-7

description: ATAC-seq


title: ASC-old-1

description: ATAC-seq


title: ASC-old-4

description: ATAC-seq


title: ASC-old-6

description: ATAC-seq


title: ASC-old-5

description: ATAC-seq


title: D3C421

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Islets were cultured for 3 days prior to RNA isolation

data_processing:
Quality control: quality of the sequencing reads was ascertained via FASTQC tool
Alignment: Sequencing reads were then mapped to the mouse reference genome (mm10) using STAR alignment tool (version 2.5.1b). Only uniquely mapped reads were reported from STAR by setting the parameter —outFilterMulrimapNmax 1
Computation of FPKM and gene counts: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and gene counts were computed with Cufflinks (version 2.1.1). From Cufflinks output, only genes with status “OK” were selected in every sample. Missing values (corresponding to Cufflinks status “FAIL”, 23 values in total) were imputed by using the function pca from the R package pcaMethods (version 1.60.0)5. This data imputation was performed in both FPKM and gene raw counts expression matrices separately by setting the nPcs parameter to the number of samples (n=21). After this, gene counts were rounded by using the R function round
Genome_build: mm10 (mouse reference genome)
Supplementary_files_format_and_content: FPKM_islets.txt: tab separated file with FPKM values for each gene and sample; Raw_counts_islets.txt: tab separated file with raw gene expression counts for each gene and sample

organism: Mus musculus

source_name: pancreatic islets_laminin-421_3 days

growth_protocol: Isolated mouse pancreatic islets were cultured in triplicate wells precoated with different laminin matrices (5ug/cm2) in medium containing 50% RPMI1640 and 50% CMRL1066, 10% FBS, 10mM HEPES, 1% Glutamax, and 0.5% Penicillin/Streptomycin. Medium was changed every 3 days.

extract_protocol:
RNA was isolated with Norgen Biotek's Single-cell RNA-isolation kit according to manufacturer's protocol. 2 ng of total RNA was used for library construction.
Libraries were constructed with NuGEN's Ovation Single-cell RNA-seq system using 2 ng of total RNA. RNA-seq, barcoded libraries were multiplexed and sequenced as paired-end 75 bp reads on Illumina HiSeq2000 platform in three batches.

treatment_protocol: Day 0 samples were not cultured in wells prior to RNA extraction. All other samples were cultured for 3 or 12 days in wells precoated with different laminins prior to RNA isolation.

tag: strain

value: pancreatic islets

tag: day

value: cultured for 3 days

tag: culture condition

value: grown on laminin-421

tag: extracellular matrix coating

value: human recombinant LN-421 (BioLamina)


title: D3A521

source_name: pancreatic islets_laminin-521_3 days

value: grown on laminin-521

value: human recombinant LN-521 (BioLamina)


title: D3B421


title: D3A421


title: D3C111

source_name: pancreatic islets_laminin-111_3 days

value: grown on laminin-111

value: human recombinant LN-111 (BioLamina)


title: D3B521


title: D3B111


title: D3C521


title: ASC-young-5

description: ATAC-seq


title: Fibroblast-old-4

description: ATAC-seq


title: D12B421

description: Islets were cultured for 12 days prior to RNA isolation

source_name: pancreatic islets_laminin-421_12 days

value: cultured for 12 days


title: D12C521

source_name: pancreatic islets_laminin-521_12 days


title: D12B521


title: D12C421


title: D12A421


title: D12C111

source_name: pancreatic islets_laminin-111_12 days


title: D0A

description: Islets were not cultured (day 0) prior to RNA isolation

source_name: pancreatic islets_not seeded to wells_0 days

value: cultured for 0 days

value: not seeded to wells

value: not applicable


title: D0B


title: Col-0 x Ler-1_rep1

status: Public on Nov 08 2018

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

description: polyA RNA isolated

data_processing:
We mapped Col RNA-seq reads to the TAIR10 genome using HISAT2 [39] with parameter --novel-splicesite-outfile. Only uniquely mapped reads were retained for subsequent analyses. Bur-0, C24, Kro-0 and Ler-1 RNA-seq reads were mapped to the corresponding reference guided assembled genomes from The 1001 Genomes Project, respectively [38]. For increased reliability, only genes that were highly conserved among Col-0, Bur-0, C24, Kro-0 and Ler-1 were analyzed. We used BLAT [64] to align the genomic sequences of TAIR10 genes to the C24 and Ler genomes. Genes with >80% nucleotide identity in >80% of genic regions were retained for further analysis. The UCSC liftover software was used to transform genome positions between Col-0 and other four accessions. For F1 hybrids, we aligned RNA-seq reads to TAIR10 and another parent genome. Reads were assigned to an allele based upon the highest quality alignment and then used to calculate divergence of allelic alternative splicing. To calculate gene expression differences, reads for each hybrid sample that mapped to the Col and another parent genomes were merged without replication. Differential expression between accessions was statistically assessed using the R/Bioconductor package edgeR (V3.0.8) [65], and normalization was performed by trimmed mean of M values (TMM). Genes with FDR < 0.05 by edgeR were identified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include PSI values for each Sample.

organism: Arabidopsis thaliana

source_name: 14 day old seedling

growth_protocol: Arabidopsis accessions Col-0, Bur-0, C24, Kro-0, Ler-1 and their F1 hybrids Col-0   Bur-0, Col-0   C24, Col-0   Kro-0, Col-0   Ler-1 were grown on Murashige and Skoog plates containing 1% (wt/vol) sucrose under long-day conditions (16h 100 ?mol m-2 s-1 white light at 22?C and 8h dark at 18 ?C). Experiments were performed using the first leaf of 14-day-old seedlings.

extract_protocol:
Total RNA was isolated from the first leaf of 14-day-old Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal).
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the standard Illumina protocol.

tag: ecotype

value: Col-0 x Ler-1

value: the first leaf


title: Col-0 x Ler-1_rep2

description: polyA RNA isolated


title: Col-0 x Kro-0_rep1

description: polyA RNA isolated

value: Col-0 x Kro-0


title: D0C


title: D12B111


title: Col-0 x Kro-0_rep2

description: polyA RNA isolated


title: C24_rep1

description: polyA RNA isolated


title: Kro-0_rep1

description: polyA RNA isolated


title: Kro-0_rep2

description: polyA RNA isolated


title: Col-0 x Bur-0_rep2

description: polyA RNA isolated

value: Col-0 x Bur-0


title: Col-0_rep2

description: polyA RNA isolated


title: Col-0 x C24_rep1

description: polyA RNA isolated

value: Col-0 x C24


title: Bur-0_rep2

description: polyA RNA isolated


title: Col-0 x C24_rep2

description: polyA RNA isolated


title: D12A521

value: pancreatic islets


title: D12A111


title: Bur-0_rep1

description: polyA RNA isolated


title: D3A111

value: cultured for 3 days


title: C24_rep2

description: polyA RNA isolated


title: Ler-1_rep2

description: polyA RNA isolated


title: Col-0_rep1

description: polyA RNA isolated


title: Col-0 x Bur-0_rep1

description: polyA RNA isolated


title: undiff-1

city: Berlin

first: Nancy

last: Mah

address: Augustenburger Platz 1

department: Berlin-Brandenburger Centrum für Regenerative Therapien (BCRT)

country: Germany

institute: Charité - Universitätsmedizin Berlin

description: T315615; C1-undiff i PSC

data_processing:
Gapped alignment of reads was performed by TopHat using default parameters. Transcript abundance (FPKM) was performed by Cufflinks v2.1.1 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: processed data file contains FPKM values calculated by Cufflinks v2.1.1

source_name: iPS cells

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen). Contaminating DNA was degraded with the use of the DNase I, RNase-free kit (Fermentas, EN0521).
RNA-Seq library preparation and NGS: cDNA libraries from poly-A-tail enriched RNA were prepared using TruSeq mRNA sample prep kit v.2 (Illumina).
unstranded library construction

treatment_protocol: Confluent PSC were dissociated with Accutase (Life Technologies) and 10,000 cells/cm2 seeded in stem cell culture medium containing 10 µM Y27632 (Wako) for 24 h. At 75% confluency, induction factors were applied in STEMdiff APEL Medium (Stemcell Technologies) for specified time periods . During Stage I, 10 ng/ml Activin A (Peprotech), 30 ng/ml recombinant human (rh) BMP-4; Peprotech) with 10 µM all-trans-retinoic acid (RA; Sigma-Aldrich)  was added to APEL base. Stage II medium was composed of 150 ng/ml GDNF (Peprotech) in APEL medium. During the course of differentiation, medium was replenished every 48 h . For terminal differentiation, cells obtained at the end of day 8 were replated on Laminin521 (BioLamina) with 50 ng/ml rhHGF (Peprotech) in APEL medium.

value: iPS cells from IMR-90

tag: timepoint

tag: treatment

value: no treatment


title: undiff-3

description: T315817; C3-undiff i PSC


title: D8-5

description: T316019; U2-Strati-II

source_name: nephron cell induction from iPS cells

value: IPS-derived renal-like cells

value: Day 8 of nephron cell induction

value: IPS cells exposed to 4 days of ActivinA,BMP4,Retinoic acid and 4 days of GDNF


title: D8-4

description: T315918; U1-Strati-I


title: D8-3


title: D6-1

value: Day 6 of nephron cell induction

value: IPS cells exposed to 4 days of ActivinA,BMP4,Retinoic acid and 2 days of GDNF


title: H1_d8-2

source_name: nephron cell induction from H1 ESC cells

value: ESC-derived renal-like cells

value: ESC cells exposed to 4 days of ActivinA,BMP4,Retinoic acid and 4 days of GDNF


title: D4-3

value: Day 4 of nephron cell induction

value: IPS cells exposed to 4 days of ActivinA,BMP4,Retinoic acid


title: D8-6

description: T316120; U3-Strati-V


title: D8-2


title: D2-2

value: Day 2 of nephron cell induction

value: IPS cells exposed to 2 days of ActivinA,BMP4,Retinoic acid


title: D4-1


title: D6-2


title: D8-1


title: D2-3


title: undiff-2

description: T315716; C2-undiff i PSC


title: Ler-1_rep1

description: polyA RNA isolated

value: the first leaf


title: D14-1_TEC

growth_protocol: Confluent PSC were dissociated with Accutase (Life Technologies) and 10,000 cells/cm2 seeded in stem cell culture medium containing 10 µM Y27632 (Wako) for 24 h. At 75% confluency, induction factors were applied in STEMdiff APEL Medium (Stemcell Technologies) for specified time periods . During Stage I, 10 ng/ml Activin A (Peprotech), 30 ng/ml recombinant human (rh) BMP-4; Peprotech) with 10 µM all-trans-retinoic acid (RA; Sigma-Aldrich)  was added to APEL base. Stage II medium was composed of 150 ng/ml GDNF (Peprotech) in APEL medium. During the course of differentiation, medium was replenished every 48 h . For terminal differentiation, cells obtained at the end of day 8 were replated on Laminin521 (BioLamina) with 50 ng/ml rhHGF (Peprotech) in APEL medium.

value: Day 14 of nephron cell induction, tubular epithelial cell

value: IPS cells exposed to 4 days of ActivinA,BMP4,Retinoic acid, 4 days of GDNF and 6 days of Renal Epithelial Growth Medium.


title: Syl4 (SYZLO-EUCGR)

city: montpellier

first: Laurent

last: Maggia

address: TA A-108 / 03 Av. Agropolis

department: BIOS

country: France

institute: Cirad

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl4_ACTTGA_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (Hisat 2.04)
Differential Gene Expression analysisof infected SYL13 and SYL15 (considered as susceptible) versus healthy SYL2, SYL4, SYL7, SYL10 and SYL18 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:8], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: GCF_000612305.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene

organism: Syzygium longifolium

source_name: leaf

extract_protocol:
CTAB RNA extraction protocol
Illumina Truseq RNA Sample Preparation Kit

treatment_protocol: Liquid nitrogen conservation

value: leaf

tag: leaf age

value: young leaf

tag: rust phenotype

value: healthy

tag: sampling site

value: nursery

tag: bioanalyzeur rna concentration ng/µl

tag: rrna ratio [25s/18s]

tag: rin

tag: illumina adaptator


title: D14-2_TEC

tag: cell type

value: IPS-derived renal-like cells


title: D14-3

value: Day 14 of nephron cell induction

value: IPS cells exposed to 4 days of ActivinA,BMP4,Retinoic acid, 4 days of GDNF and 6 days of HGF


title: Syl7 (SYZLO-EUCGR)

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl7_GATCAG_L003

tag: tissue


title: D2-1


title: D4-2


title: D14-1


title: H1_d8-1

value: Day 8 of nephron cell induction


title: D6-3

value: Day 6 of nephron cell induction

value: IPS cells exposed to 4 days of ActivinA,BMP4,Retinoic acid and 2 days of GDNF


title: Syl18 (SYZLO-EUCGR)

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl18_GGCTAC_L003


title: Syl18 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl18_GGCTAC_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (bwa 0.7.12)
Differential Gene Expression analysis of infected SYL13 and SYL15 (considered as susceptible) versus healthy SYL2, SYL4, SYL7, SYL10 and SYL18 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:8], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: Mapping (bwa 0.7.12) on de novo transcriptome assembled with Trinity
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene


title: Syl15 (SYZLO-EUCGR)

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl15_AGTCAA_L003

value: infected


title: Syl4 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl4_ACTTGA_L003


title: Syl7 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl7_GATCAG_L003


title: Syl15 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl15_AGTCAA_L003


title: Syl2 (SYZLO-EUCGR)

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl2_CAGATC_L003


title: Syl13 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl13_CTTGTA_L003


title: Tg5 (TRIGL-FAR-EUCGR)

description:
Tristaniopsis glauca Farino
TRIGL-FAR-EUCGR_readcount.tsv
TRIGL-FAR-EUCGR_RPKM.tsv
TRIGL-FAR-EUCGR_edgeR.tsv
Tg5_GTGGCC_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (Hisat 2.04)
Differential Gene Expression analysis of infected TG5 and TG6 (considered as susceptible) versus healthy TG3 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:4], group=conds); y <- estimateTagwiseDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: GCF_000612305.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene

organism: Tristaniopsis glauca

value: Mature leaf


title: Tg6 (TRIGL-FAR-EUCGR)

description:
Tristaniopsis glauca Farino
TRIGL-FAR-EUCGR_readcount.tsv
TRIGL-FAR-EUCGR_RPKM.tsv
TRIGL-FAR-EUCGR_edgeR.tsv
Tg6_GTTTCG_L003


title: Syl10 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl10_TAGCTT_L003


title: Syl10 (SYZLO-EUCGR)

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl10_TAGCTT_L003


title: Tg3 (TRIGL-FAR-EUCGR)

description:
Tristaniopsis glauca Farino
TRIGL-FAR-EUCGR_readcount.tsv
TRIGL-FAR-EUCGR_RPKM.tsv
TRIGL-FAR-EUCGR_edgeR.tsv
Tg3_ATGTCA_L003


title: Tg5 (TRIGL-FAR-DENOVO)

description:
Tristaniopsis glauca Farino
TRIGL-far-denovo_readcount.tsv
TRIGL-far-denovo_RPKM.tsv
TRIGL-FAR-denovo_edgeR.tsv
Tg5_GTGGCC_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (bwa 0.7.12)
Differential Gene Expression analysis of infected TG5 and TG6 (considered as susceptible) versus healthy TG3 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:4], group=conds); y <- estimateCommonDisp(y); y <- estimateTagwiseDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="tagwise"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: Mapping (bwa 0.7.12) on de novo transcriptome assembled with Trinity
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene

tag: bioanalyzer rna concentration ng/µl


title: Tg6 (TRIGL-FAR-DENOVO)

description:
Tristaniopsis glauca Farino
TRIGL-far-denovo_readcount.tsv
TRIGL-far-denovo_RPKM.tsv
TRIGL-FAR-denovo_edgeR.tsv
Tg6_GTTTCG_L003


title: Tg3 (TRIGL-FAR-DENOVO)

description:
Tristaniopsis glauca Farino
TRIGL-far-denovo_readcount.tsv
TRIGL-far-denovo_RPKM.tsv
TRIGL-FAR-denovo_edgeR.tsv
Tg3_ATGTCA_L003


title: Tg2 (TRIGL-FAR-DENOVO)

description:
Tristaniopsis glauca Farino
TRIGL-far-denovo_readcount.tsv
TRIGL-far-denovo_RPKM.tsv
TRIGL-FAR-denovo_edgeR.tsv
Tg2_AGTTCC_L003


title: Syl2 (SYZLO-DENOVO)

description:
sampling: liquid nitrogen and CTAB RNA extraction protocol
SYZLO-denovo_readcount.tsv
SYZLO-denovo_RPKM.tsv
SYZLO-denovo_edgeR.tsv
Syl2_CAGATC_L003


title: V6 (TRIGL-BDS-EUCGR)

description:
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V6_ACTGAT_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (Hisat 2.04)
Differential Gene Expression analysis of infected V1, V2, V6 and V7 (considered as susceptible) versus healthy V3 and V4 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:7], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: GCF_000612305.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene

value: Young leaf

value: natural field


title: V7 (TRIGL-BDS-EUCGR)

description:
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V7_ATTCCT_L003


title: Tg2 (TRIGL-FAR-EUCGR)

description:
Tristaniopsis glauca Farino
TRIGL-FAR-EUCGR_readcount.tsv
TRIGL-FAR-EUCGR_RPKM.tsv
TRIGL-FAR-EUCGR_edgeR.tsv
Tg2_AGTTCC_L003


title: V7 (TRIGL-BDS-DENOVO)

description:
Tristaniopsis glauca Bois du sud
TRIGL-bds-denovo_readcount.tsv
TRIGL-bds-denovo_RPKM.tsv
TRIGL-bds-denovo_edgeR.tsv
V7_ATTCCT_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (bwa 0.7.12)
Differential Gene Expression analysis of infected V1, V2, V6 and V7 (considered as susceptible) versus healthy V3 and V4 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:7], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: Mapping (bwa 0.7.12) on de novo transcriptome assembled with Trinity
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene


title: V1 (TRIGL-BDS-EUCGR)

description:
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V1_CGTACG_L003


title: V2 (TRIGL-BDS-EUCGR)

description:
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V2_GAGTGG_L003


title: V3 (TRIGL-BDS-EUCGR)

description:
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V3_GTCCGC_L003


title: V4 (TRIGL-BDS-EUCGR)

description:
Tristaniopsis glauca Bois du sud
TRIGL-BDS-EUCGR_readcount.tsv
TRIGL-BDS-EUCGR_RPKM.tsv
TRIGL-BDS-EUCGR_edgeR.tsv
V4_GTGAAA_L003


title: V6 (TRIGL-BDS-DENOVO)

description:
Tristaniopsis glauca Bois du sud
TRIGL-bds-denovo_readcount.tsv
TRIGL-bds-denovo_RPKM.tsv
TRIGL-bds-denovo_edgeR.tsv
V6_ACTGAT_L003


title: Syl13 (SYZLO-EUCGR)

description:
SYZLO-EUCGR_readcount.tsv
SYZLO-EUCGR_RPKM.tsv
SYZLO-EUCGR_edgeR.tsv
Syl13_CTTGTA_L003


title: V4 (TRIGL-BDS-DENOVO)

description:
Tristaniopsis glauca Bois du sud
TRIGL-bds-denovo_readcount.tsv
TRIGL-bds-denovo_RPKM.tsv
TRIGL-bds-denovo_edgeR.tsv
V4_GTGAAA_L003


title: Tg4 (TRIGL-FAR-EUCGR)

description:
Tristaniopsis glauca Farino
TRIGL-FAR-EUCGR_readcount.tsv
TRIGL-FAR-EUCGR_RPKM.tsv
TRIGL-FAR-EUCGR_edgeR.tsv
Tg4_CCGTCC_L003


title: V2 (TRIGL-BDS-DENOVO)

description:
Tristaniopsis glauca Bois du sud
TRIGL-bds-denovo_readcount.tsv
TRIGL-bds-denovo_RPKM.tsv
TRIGL-bds-denovo_edgeR.tsv
V2_GAGTGG_L003


title: V3 (TRIGL-BDS-DENOVO)

description:
Tristaniopsis glauca Bois du sud
TRIGL-bds-denovo_readcount.tsv
TRIGL-bds-denovo_RPKM.tsv
TRIGL-bds-denovo_edgeR.tsv
V3_GTCCGC_L003


title: V1 (TRIGL-BDS-DENOVO)

description:
Tristaniopsis glauca Bois du sud
TRIGL-bds-denovo_readcount.tsv
TRIGL-bds-denovo_RPKM.tsv
TRIGL-bds-denovo_edgeR.tsv
V1_CGTACG_L003


title: Ag6 (ARIGU-EUCGR)

description:
ARIGU-EUCGR_readcount.tsv
ARIGU-EUCGR_RPKM.tsv
ARIGU-EUCGR_edgeR.tsv
Ag6_TGACCA_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (Hisat 2.04)
Differential Gene Expression analysis of infected Ag19, Ag28 and Ag6 (considered as susceptible) versus healthy Ag2, Ag3 and Ag4 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:7], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: GCF_000612305.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene

organism: Arillastrum gummiferum


title: Ag4 (ARIGU-EUCGR)

description:
ARIGU-EUCGR_readcount.tsv
ARIGU-EUCGR_RPKM.tsv
ARIGU-EUCGR_edgeR.tsv
Ag4_TTAGGC_L003


title: Ag3 (ARIGU-EUCGR)

description:
ARIGU-EUCGR_readcount.tsv
ARIGU-EUCGR_RPKM.tsv
ARIGU-EUCGR_edgeR.tsv
Ag3_CGATGT_L003


title: Ag3 (ARIGU-DENOVO)

description:
ARIGU-denovo_readcount.tsv
ARIGU-denovo_RPKM.tsv
ARIGU-denovo_edgeR.tsv
Ag3_CGATGT_L003

data_processing:
Raw data quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Cleaning reads (remove adapters, over represented sequences and quality trimming; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_1_cutadapt_in_chain.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Mean quality score filter (remove bad quality reads, <35 bp reads; https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_2_filter_fastq_on_mean_quality.pl)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_htc_0_fastq_in_chains.pl)
Paired reads synchronization (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_3_synchronized_paired_fastq_end5.sh)
Quality control (https://github.com/SouthGreenPlatform/arcad-hts/tree/master/scripts/arcad_hts_0_fastq_in_chains.pl)
Mapping (bwa 0.7.12)
Differential Gene Expression analysis of infected Ag19, Ag28 and Ag6 (considered as susceptible) versus healthy Ag2, Ag3 and Ag4 (considered as resistant; EdgeR 3.14.0; command line: y <- DGEList(counts=countDF[,2:7], group=conds); y <- estimateCommonDisp(y); et <- exactTest(y, pair=c("resistant", "susceptible"), dispersion="common"); https://github.com/SouthGreenPlatform/Myrtaceae-RNASeq-scripts/blob/master/edger_script_for_github.R)
Genome_build: Mapping (bwa 0.7.12) on de novo transcriptome assembled with Trinity
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values  for each sample and logFC, Pvalue and FDR for each gene


title: Ag6 (ARIGU-DENOVO)

description:
ARIGU-denovo_readcount.tsv
ARIGU-denovo_RPKM.tsv
ARIGU-denovo_edgeR.tsv
Ag6_TGACCA_L003


title: Ag4 (ARIGU-DENOVO)

description:
ARIGU-denovo_readcount.tsv
ARIGU-denovo_RPKM.tsv
ARIGU-denovo_edgeR.tsv
Ag4_TTAGGC_L003


title: Ag28 (ARIGU-EUCGR)

description:
ARIGU-EUCGR_readcount.tsv
ARIGU-EUCGR_RPKM.tsv
ARIGU-EUCGR_edgeR.tsv
Ag28_GCCAAT_L003


title: Ag2 (ARIGU-DENOVO)

description:
ARIGU-denovo_readcount.tsv
ARIGU-denovo_RPKM.tsv
ARIGU-denovo_edgeR.tsv
Ag2_ATCACG_L003


title: siCTRL_2

status: Public on Nov 07 2018

city: Shenzhen

first: Qiangzu

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

data_processing:
Illumina hiseq4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software
mapping QC by samtools and picard software
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MCF-7 cells were treated with 50nM siControl

growth_protocol: cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the qiagen RNA exaction kit
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: cells were treated with 50nM siRNF168 or siControl

tag: cell line

value: breast cancer cell line

tag: tumor stage

value: 15-18 passage


title: Ag28 (ARIGU-DENOVO)

description:
ARIGU-denovo_readcount.tsv
ARIGU-denovo_RPKM.tsv
ARIGU-denovo_edgeR.tsv
Ag28_GCCAAT_L003


title: Ag19 (ARIGU-DENOVO)

description:
ARIGU-denovo_readcount.tsv
ARIGU-denovo_RPKM.tsv
ARIGU-denovo_edgeR.tsv
Ag19_ACAGTG_L003


title: siCTRL_3


title: siRNF168_1

source_name: MCF-7 cells were treated with 50nM siRNF168


title: Tg4 (TRIGL-FAR-DENOVO)

description:
Tristaniopsis glauca Farino
TRIGL-far-denovo_readcount.tsv
TRIGL-far-denovo_RPKM.tsv
TRIGL-FAR-denovo_edgeR.tsv
Tg4_CCGTCC_L003


title: pool T1_9

city: Shanghai

first: Weijie

last: Yin

address: 320 Yue Yang Road

institute: Shanghai Institutes for Biological Sciences

description:
10,000 cell RNA
TPM-pool.txt

data_processing:
Quality control was executed using fastqc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase Million (RPKM) were calculated using Cufflinks with default parameters.
RPKM was transformed into Transcripts Per Million (TPM) according to Wagner GP, Kin K, Lynch VJ. Theory Biosci. 2012.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: 10,000 pooled cells

growth_protocol: CD4+ T cells were purified from spleen of C57BL/6 mice. Purified CD4+ T cells were activated with plate-bound anti-Hamster IgG and soluble anti-CD3 + anti-CD28 in T cell medium. For TH2 differentiation, anti-IFNγ and IL-4 were add. 2 days later, cells were suspended from plate and IL-2 were added. Cells were cultured for 5 days.

extract_protocol:
56 Single cells were isolated with a Fluidigm C1 system. For bulk RNA-seq, pooled 10,000 cells was prepared.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Differentiated Th2 cells were restimulated with anti-CD3 and anti-CD28.

tag: strain

tag: age

value: 8 weeks

value: spleen

tag: genotype/variation

value: wild type


title: single cell T5_11

description:
single cell RNA
TPM-56cells.txt

source_name: single cell


title: siCTRL_1


title: siRNF168_2

source_name: MCF-7 cells were treated with 50nM siRNF169


title: single cell T5_10

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_9

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_8

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_12

description:
single cell RNA
TPM-56cells.txt


title: Ag2 (ARIGU-EUCGR)

description:
ARIGU-EUCGR_readcount.tsv
ARIGU-EUCGR_RPKM.tsv
ARIGU-EUCGR_edgeR.tsv
Ag2_ATCACG_L003

value: leaf

value: healthy


title: single cell T5_6

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_5

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_1

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_4

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_2

description:
single cell RNA
TPM-56cells.txt


title: Ag19 (ARIGU-EUCGR)

description:
ARIGU-EUCGR_readcount.tsv
ARIGU-EUCGR_RPKM.tsv
ARIGU-EUCGR_edgeR.tsv
Ag19_ACAGTG_L003

value: nursery


title: single cell T4_11

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_10

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_9

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_12

description:
single cell RNA
TPM-56cells.txt


title: siRNF168_3

source_name: MCF-7 cells were treated with 50nM siRNF170


title: single cell T4_7

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_6

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_5

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_4

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_2

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_3

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_1

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_12

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_11

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_10

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_9

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_3

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_4

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_5

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_8

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_6

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_7

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_2

description:
single cell RNA
TPM-56cells.txt


title: single cell T3_3

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_7

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_9

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_11

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_8

description:
single cell RNA
TPM-56cells.txt


title: single cell T4_8

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_1

description:
single cell RNA
TPM-56cells.txt


title: single cell T5_7

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_2

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_6

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_5

description:
single cell RNA
TPM-56cells.txt


title: single cell T1_8

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_4

description:
single cell RNA
TPM-56cells.txt


title: single cell T1_6

description:
single cell RNA
TPM-56cells.txt


title: single cell T1_4

description:
single cell RNA
TPM-56cells.txt


title: single cell T1_3

description:
single cell RNA
TPM-56cells.txt


title: single cell T2_12

description:
single cell RNA
TPM-56cells.txt


title: Aged DN rep1

status: Public on Nov 06 2018

city: Washington

first: Brett

middle: Adam

last: Shook

state: DC

address: 2300 I St NW

department: Biochemistry & Molecular Medicine

institute: George Washington University

description: wound bed day 5

data_processing:
Illumina HiSeq2500 software used for basecalling.
Tophat (Version 2.1.1) to align reads to mm10 using default parameters
Cuffdiff (version 2.2.1) to quantify differential expression using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Cuffdiff output

source_name: Dermis

extract_protocol:
Extraction of RNA was performed using Absolutely RNA Nanoprep Kit from Agilent
SMARTer Ultra Low RNA Kit (Clonetech) was used with 500pg-1ng RNA.

tag: Sex

value: male

value: >24 months old


title: single cell T3_1

description:
single cell RNA
TPM-56cells.txt


title: Aged DN rep2

description: wound bed day 5


title: Aged AP - CD9High rep2

description: wound bed day 5


title: Aged CD29 rep2

description: wound bed day 5


title: Aged CD29 rep1

description: wound bed day 5


title: single cell T2_3

description:
single cell RNA
TPM-56cells.txt


title: single cell T1_1

description:
single cell RNA
TPM-56cells.txt


title: Aged AP - CD9Low rep2

description: wound bed day 5


title: CD301b mphage rep1

description: wound bed day 5

data_processing:
Illumina HiSeq2000 software used for basecalling.
Tophat (Version 2.0.2) to align reads to mm9 using default parameters
Cuffmerge (Version 2.0.2) to assemble the final transcriptome using default parameters
Cuffdiff (version 2.0.2) to quantify differential expression using default parameters
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output

extract_protocol:
Extraction of RNA was performed using a combination of Trizol and the RNEasy Plus Micro Kit from Qiagen
illumina Truseq mRNA library prep protocol

value: 7 week old


title: single cell T1_5

description:
single cell RNA
TPM-56cells.txt


title: single cell T1_7

description:
single cell RNA
TPM-56cells.txt


title: CD301b mphage rep2

description: wound bed day 5


title: single cell T1_2

description:
single cell RNA
TPM-56cells.txt


title: Young DN rep1

description: wound bed day 5


title: F4/80neg rep1

description: wound bed day 5


title: Young AP - CD9High rep2

description: wound bed day 5


title: Young CD29 rep1

description: wound bed day 5


title: WB AP rep1

description: wound bed day 5


title: Young AP - CD9Low rep1

description: wound bed day 5


title: Nonwounded AP rep6

description: dorsal skin


title: single cell T2_10

description:
single cell RNA
TPM-56cells.txt


title: Nonwounded AP rep5

description: dorsal skin


title: WB AP rep2

description: wound bed day 5


title: Nonwounded AP rep4

description: dorsal skin


title: Nonwounded AP rep2

description: dorsal skin


title: Nonwounded AP rep3

description: dorsal skin


title: adult lung

city: Melbourne

first: Amit

last: Kumar

state: VIC

address: 2 St Andrews Place, East Melbourne, Victoria

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Paired end raw RNA-seq read were cleaned by removing reads with adaptors, with unknown nucleotides larger than 5% and reads with low quality.
samtools-0.1.18
bowtie2-2.0.0-beta6
Cufflinks2.1.1.1
The RNA-seq data was investigated using SeqMonk (version 0.24.1)
Genome_build: monodelphis_domestica_broad05_67
Supplementary_files_format_and_content: text file with log 2 transformed FPKM values from cufflinks.

organism: Monodelphis domestica

source_name: lung tissue

growth_protocol: natural growth of captive animal

extract_protocol:
The RNA isolation from whole individual lungs was performed using an RNA isolation kit (Ambion), and the quality and integrity was confirmed using the Agilent 2100 Bioanalyser RNA Nano Chip.
RNA samples were sequenced using the Illumina Hiseq 2000 RNA-seq sequencing platform at BGI-HongKong Co., Ltd.

treatment_protocol: Lungs were collected from neonates at day 1, 3, 6, 8, 12, 14, 18, 24, 29, 35, 41, 51, 61, 100 of age and from an adult

value: lung


title: Aged AP - CD9Low rep1

description: wound bed day 5


title: Nonwounded AP rep1

description: dorsal skin


title: Young CD29 rep2

description: wound bed day 5


title: Aged AP - CD9High rep1

description: wound bed day 5


title: Young DN rep2

description: wound bed day 5


title: day 29 lung


title: day 35 lung


title: Young AP - CD9High rep1

description: wound bed day 5


title: Young AP - CD9Low rep2

description: wound bed day 5


title: day 61 lung


title: day 14 lung


title: day 3 lung


title: day 8 lung


title: F4/80neg rep2

description: wound bed day 5


title: PBS-1

status: Public on Nov 05 2018

city: Beer-Sheva

first: Nir

last: Bujanover

address: Ben Gurion 1

department: Immunology

country: Israel

institute: Ben-Gurion University

data_processing:
Base calling- Illumina's bcl2fastq v2.17
Illuminas Cufflinks Assembly & DE (BaseSpace Workflow) v2.0.0:  Isis (Analysis Software) 2.6.25.12  TopHat (Aligner) 2.1.0  Bowtie2 (Aligner) 2.2.6  BEDTools 2.17.0  Cufflinks 2.2.1  BLAST 2.2.26+
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking file contains FPKM of all samples. generated by the cufflinks algorithm in the BaseSpace workflow

source_name: Hematopoietic Stem Cells

extract_protocol:
Tרeated mice where euthanized, femur and tibia extracted, crashed in sample medium (PBSx1, EDTA 2mM, serum 2%) and loaded on Histopaq1083. this mononuclear enriched population was stained and sorted for LSK150+mC+ cell, 1000 cells from each sample, to SMARTseq buffer. library construction and sequencing was performed by the INCPM facility (Rehovot)
SMARTSeq Ultra Low Input RNA V4 kit from Clontech (polyA based capture), with 14 cycles of cDNA amplification. The amplified cDNA was fragmented using the Covaris machine to around 450bp. Illumina libraries were constructed using the End repair, A base addition and adapter ligation (TruSeq like adapters:GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCGCCTTATCTCGTATGCCGTCTTCTG) and amplified using 13 PCR cycles

treatment_protocol: poly-Inosinic-poly-Cytidine (pIC, Sigma-Aldrich cat:P1530, lot:122M4002v)) intraperitoneally (i.p.) 200ugr per mouse

value: C57BL/6 Fgd5-mCherry

tag: treatment

value: PBS, control

value: bone marrow Lineage-Sca1+cKit+CD150+mCherry+ cells


title: PBS-2


title: pIC-2

value: poly-Inosinic-poly-Cytidine (pIC, Sigma-Aldrich cat:P1530, lot:122M4002v)) intraperitoneally (i.p.) 200ugr per mouse


title: WT_HC_rep3

city: Strasbourg

first: Anne-Laurence

last: Boutillier

address: 12 rue Goethe

department: LNCA

description:
Home_Cage (no training)_S
processed data file: S15010_genesdiff_HS179_HS190.txt

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Alignment : Reads were mapped onto the mm9 assembly of mouse genome using Tophat v2.0.10 (Kim et al., 2013) and the bowtie v2.1.0 aligner.
Quantification : Gene expression was quantified from uniquely aligned reads using HTSeq v0.5.4p3 (Anders et al., 2013) and gene annotations from Ensembl release 67.
Normalization : Read counts were normalized across libraries with the method proposed by Anders and Huber (2010). Statistical analysis was performed with the method proposed by Love et al. (2014) implemented in the DESeq2 Bioconductor library (v1.0.19).
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing raw read counts, and normalized read counts.

source_name: dorsal hippocampus

extract_protocol: RNA-Seq libraries were generated from 300 ng of total RNA Illumina® TruSeq® RNA Sample Preparation Kit v2 (Part Number RS-122-2001). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis followed, using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman Coulter) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Sequencing was performed on the Illumina Genome Hiseq2500 as single-end 50 base reads following Illumina’s instructions.

treatment_protocol: Total RNA was extracted from the dorsal hippocampal tissues using TRizol reagent (Invitrogen). Freshly dissected tissues were chopped with a razor blade and 400μl of TRizol reagent were added on half hippocampus. The tissues were homogenized and frozen (20min at -80°C), followed by 3min centrifugation at 14000g to remove cellular debris before chloroform/isoamyl extraction. DNA precipitation was performed on the supernatant using isopropanol and RNAse free glycogen (10min at RT). The pellet was washed once with 70% ethanol and resuspended in milliQ water for DNAse treatment (30min at 37°C). RNA samples were further purified using a phenol/chloroform extraction, followed by a new precipitation (overnight at -20°C, with 100% ethanol, 3M NaOAC and Glycogen RNAse free). The next day two last 70% ethanol washes were done before air drying the resulting RNA pellet. The pellets were resuspended in 30μl nuclease-free milliQ water.

value: dorsal hippocampus

value: 8 months

tag: genotype

value: WT


title: THY-Tau22_train_T_rep2

description:
Spatial training (MWM)_T
processed data file: S15010_genesdiff_HS179_HS190.txt


title: pIC-1


title: dHIP_TAU CSP_H3k27ac

description: dHIP_TAU CSP_H3k27ac

data_processing:
Illumina Casava1.8 software was used for basecalling.
Reads were mapped onto Mouse reference assembly mm9/ NCBI37 using Bowtie v0.12.7 aligner.
Peak detection of H2Bac and H3K27ac was performed using SICER v1.1  with the following parameters: window size: 200; gap size: 1000 for H2Bac and 600 for H3K27Ac. Peaks were annotated relative to genomic features using Homer  with annotation from Ensembl v67.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

extract_protocol: ChIP-seq libraries were prepared using NEXTflex ChIPSeq Kit (#5143-02, Bioo Scientific) following the manufacturer’s protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP-enriched DNA or Input DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3′ ends of the blunt DNA fragments with a Klenow fragment (3′ to 5′exo minus). The ends of the DNA fragments were ligated to double-stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes-6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR [2 min at 98°C; (30 s at 98°C, 30 s at 65°C, 60 s at 72°C) x 14 cycles; 4 min at 72°C] and cleanedup using Agencourt AMPure XP beads.

treatment_protocol: dorsal hippocampi from 8 mice were pooled (sex-matched between THY-Tau22 and WT animals), cut into small fragments, fixed in 1% formaldehyde and incubated for 10 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. Tissue samples were sonicated with a Diagenode Bioruptor (35 cycles with 30sec ON/30sec OFF on High Power). Sonicated chromatin was centrifuged 10min at 14000g, then the supernatant was collected and diluted 10 times in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-Cl, pH 8.1, 167mM NaCl). A fraction of supernatant (50μl) from each sample was saved before IP and served as ‘total input chromatin’. Supernatants were incubated overnight (4°C) with primary antibody (H2Bac (ab1759; 07-382), H3K27ac (ab4729), followed by protein A Dynabeads (Invitrogen) for 2h at RT. After several wash steps (with low salt, high salt, LiCl and TE buffers), complexes were eluted in 300μl Elution buffer (1% SDS, 0.1 M NaHCO3). The crosslinking was reversed (overnight at 65°C) and the DNA was subsequently purified with RNAse (30min, 37°C), proteinase K (2h, 45°C), phenol/chloroform and chloroform/isoamyl extractions. After overnight ethanol precipitation, two last 70% ethanol washes were done before air drying the resulting DNA pellet. The pellets were resuspended in 30μl nuclease-free milliQ water and the supernatant was transferred in low binding tubes and brought to the sequencing platform for DNA concentration estimation (Qubit fluorometric quantitation).

tag: chip antibody

value: H3k27ac:Abcam, ab4729


title: WT_HC_rep1


title: dHIP_TAU CSPTTK21_H2Bac_rep2

description: dHIP_TAU CSPTTK21_H2Bac_rep2

value: H2Bac:Abcam, ab1759; Millipore, 07-382


title: THY-Tau22_train_C_rep2

description:
Spatial training (MWM)_C
processed data file: S15010_genesdiff_HS179_HS190.txt


title: THY-Tau22_rep2

description:
basal (resting)_TAU
processed data file: S14061_mm9_genesdiff_groups.txt


title: THY-Tau22_train_T_rep1


title: THY-Tau22_rep1


title: dHIP_WT_H3k27ac


title: THY-Tau22_train_C_rep1


title: WT_rep2

description:
basal (resting)_WT
processed data file: S14061_mm9_genesdiff_groups.txt


title: WT_train_rep2

description:
Spatial training (MWM)_S
processed data file: S15010_genesdiff_HS179_HS190.txt


title: WT_rep1


title: dHIP_TAU CSP_H2Bac_rep2

description: dHIP_TAU CSP_H2Bac_rep2


title: dHIP_WT_H2Bac_rep2


title: WT_train_rep1


title: dHIP_TAU CSPTTK21_Input_rep2

description: dHIP_TAU CSPTTK21_Input_rep2

value: No antibody


title: WT_rep3


title: Sox21a-n2

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

institute: Menzies Institute for Medical Research

description: DamID

data_processing:
Library strategy: DamID
FASTQ files were processed with damidseq_pipeline, version 1.4.  Biological replicates in gatc.bedgraph format were averaged, and the averaged binding tracks used for further analysis.
Genes with significant RNA pol II occupancy were called via polii.gene.call v1.0.3
Peaks were called via find_peaks v1.0.2, default options
Genome_build: DMBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised log2(Dam-fusion/Dam) enrichment.  Processed files are provided as both raw data and scaled data.

organism: Drosophila melanogaster

source_name: dissected adult midgut

extract_protocol:
DNA was extracted from dissected midguts via Qiagen Blood and Tissue kits as per manufacturers' instructions, digested with DpnI, DamID adaptors ligated, digested with DpnII and amplified via PCR.
DNA was sonicated to an average size of 300bp using a Diagenode Bioruptor and DamID adaptors removed via AlwI digestion.  Sonnicated material was end-repaired, A-tailed, sequencing adaptors ligated and PCR amplified.

value: gut

tag: developmental stage

value: adult


title: Sox21a-n3

description: DamID


title: RUX3165

city: Nashville

first: Justin

middle: M.

last: Balko

state: TN

address: 2220 Pierce Avenue

department: Cancer Biology

institute: Vanderbilt University Medical Center

description:
NA
rux_TPM.txt
3574-JMB-18_S23

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads quality was checked by fastqc.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR_2.5.2a with twopassMode.
Transcripts Per Kilobase Million of library size (TPM) were calculated using htseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Tumor

extract_protocol:
10um slides were macrodissected to enrich for tumor regions, followed by RNA isolation using the Promega Maxwell simplyRNA kit according to manufacturer's recommended protocol
Illumina RNAaccess

tag: patient #

value: Baseline

tag: tissue site

value: Ipsilateral breast


title: dHIP_TAU CSP_Input_rep2

description: dHIP_TAU CSP_Input_rep2


title: Sox21a-n1

description: DamID


title: dHIP_TAU CSPTTK21_H3k27ac

description: dHIP_TAU CSPTTK21_H3k27ac


title: RUX3330

description:
Single cluster of 25 tumor cells, rest normal liver
rux_TPM.txt
3574-JMB-17_S22

value: Liver


title: polII-n2-myo

description: DamID


title: WT_HC_rep2

value: male


title: dHIP_WT_Input_rep2


title: polII-n2-esg

description: DamID


title: RUX3269

description:
60% necrosis
rux_TPM.txt
3574-JMB-16_S21


title: polII-n1-myo

description: DamID


title: Dam-n2-esg

description: DamID


title: RUX3185

description:
NA
rux_TPM.txt
3574-JMB-14_S19

value: Cycle 2

value: Skin


title: Dam-n3-sox21a

description: DamID


title: dHIP_WT_H2Bac_rep1


title: dHIP_TAU CSPTTK21_H2Bac_rep1

description: dHIP_TAU CSPTTK21_H2Bac_rep1


title: RUX3255

description:
NA
rux_TPM.txt
3574-JMB-15_S20

value: Lymph node


title: Dam-n2-myo

description: DamID


title: Dam-n2-sox21a

description: DamID


title: dHIP_TAU CSP_Input_rep1

description: dHIP_TAU CSP_Input_rep1


title: Dam-n1-esg

description: DamID


title: Dam-n1-sox21a

description: DamID


title: dHIP_TAU CSPTTK21_Input_rep1

description: dHIP_TAU CSPTTK21_Input_rep1


title: polII-n1-esg

description: DamID


title: dHIP_WT_Input_rep1


title: RUX3159

description:
Very scant tissue
rux_TPM.txt
3574-JMB-11_S17


title: RUX3162

description:
Mostly normal liver
rux_TPM.txt
3574-JMB-12_S18


title: Dam-n1-myo

description: DamID


title: RUX2988

description:
NA
rux_TPM.txt
3574-JMB-7_S13


title: RUX3040

description:
NA
rux_TPM.txt
3574-JMB-8_S14

value: Inguingal node


title: RUX3054

description:
NA
rux_TPM.txt
3574-JMB-9_S15


title: RUX2985

description:
NA
rux_TPM.txt
3574-JMB-6_S12

value: Soft tissue


title: RUX3060

description:
NA
rux_TPM.txt
3574-JMB-10_S16


title: input DNA

city: Sendai

first: Kazuhiko

last: Igarashi

address: Seiryo 2-1

country: Japan

institute: Tohoku University

description: genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using bwa version 0.7.10
bwa data (bam) were merged for each experiment
peaks were called using MACS2 version 2.1.0 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file format is TXT containing peaks generated using MACS2.

growth_protocol: M1 cells were cultured on TC-non-trreated plastic dosh (CORNING) in RPMI-1640 medium (Sigma-Aldrich) supplemented with 10% FBS and penicilli/streptmycin (typically 0.5–1 × 106 cells)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared from 1~3 ng of ChIP DNA with the use of Ovation Ultralow DR Multiplex System (Nugen). The DNA libraries were clonally amplified on a flow cell and sequenced on HiSeq2500 (HiSeq Control Software v2.2.38, Illumina) with 51-mer paired-end sequence. Image analysis and base calling were performed using Real-Time Analysis Software (v1.18.61, Illumina).

treatment_protocol: no treatment

value: Myeloid leukemia cell line M1

value: No stimulation


title: Mafk_ChIPSeq

description: genomic DNA

value: NF-E2 p18 (c-16) (Santa Cruz, catalog# sc-477, lot# C0606)


title: Bach2_ChIPSeq

description: genomic DNA

value: Bach2 (Bach2N2; made in-house)


title: Bach1_ChIPSeq

description: genomic DNA

value: Bach1 (A1-6; made in-house)


title: RUX3092

description:
NA
rux_TPM.txt
3574-JMB-5_S11

value: Contralateral Breast


title: RUX3339

description:
Touch prep
rux_TPM.txt
3574-JMB-4_S10

value: Pleural effusion


title: dHIP_TAU CSP_H2Bac_rep1

description: dHIP_TAU CSP_H2Bac_rep1

value: dorsal hippocampus

value: H2Bac:Abcam, ab1759; Millipore, 07-382


title: RUX3283

description:
NA
rux_TPM.txt
3574-JMB-3_S9

value: Baseline

value: Ipsilateral breast


title: RUX2989

description:
NA
rux_TPM.txt
3574-JMB-1_S7

value: Neck lymph node


title: patient_16_High_Pain_mRNA

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Mapping and feature quantification for RNA-seq performed with RSEM v.1.2.18 using the ensembl 75 annotations
Mapping and feature quantification performed with ncPRO-seq for small RNA-seq
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited raw counts

extract_protocol:
Synovial tissues were collected from knees of OA patientsat the time of the join-replacement surgery and total RNA was extracted according to the modified Chomczynski and Sacchi protocol,by using TRIzol Reagent (ThermoFisher)
For mRNA sequencing, the Illumina TruSeq® Stranded total RNA protocol with the TruSeq Stranded total RNA Sample Preparation Kit. For small RNA sequencing, libraries were produced by NEBNext® Small RNA Library Prep Set for Illumina® (NEB #E7330S/L)

tag: disease state

value: osteoarthritis

value: synovial tissue from knee

tag: pain

value: High

tag: gender

value: Female


title: patient_17_High_Pain_mRNA

source_name: Synovial tissues were collected from knees

tag: tissue


title: patient_18_High_Pain_mRNA


title: patient_22_Low_Pain_mRNA

value: Low


title: patient_22_Low_Pain_sRNA

description: small RNA


title: patient_12_High_Pain_mRNA


title: patient_21_Low_Pain_sRNA

description: small RNA


title: RUX3114

description:
DCIS also present, approx 40% of tumor
rux_TPM.txt
3574-JMB-2_S8

value: Cycle 2


title: patient_16_High_Pain_sRNA

description: small RNA


title: patient_18_High_Pain_sRNA

description: small RNA


title: patient_19_High_Pain_sRNA

description: small RNA


title: patient_19_High_Pain_mRNA


title: patient_14_Low_Pain_mRNA


title: patient_21_Low_Pain_mRNA


title: patient_15_Low_Pain_mRNA


title: patient_17_High_Pain_sRNA

description: small RNA


title: patient_13_Low_Pain_mRNA


title: patient_14_Low_Pain_sRNA

description: small RNA


title: patient_12_High_Pain_sRNA

description: small RNA


title: patient_13_Low_Pain_sRNA

description: small RNA


title: untreated SSCs rep3 (A3)

status: Public on Nov 04 2018

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq reads for each sample were first cleaned using Seqtk (https://github.com/lh3/seqtk)
RNA-seq reads were aligned to the mouse genome (mm10, Genome Reference Consortium Mouse Build 38) using TopHat 2.0.9 software
The number of reads mapped to each of the Ensembl genes (release 85) was counted using the HTSeq python package
The normalization was carried out using TMM (trimmed mean of M values) and the FPKM(Fragments Per Kilobase of exon model per Million mapped reads) was calculated by Perl script
Genome_build: mm10

source_name: Spermatogonial stem cell

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit (Qiagen,217004),and further purified by RNAClean XP Kit (Beckman Coulter,A63987) and RNase-Free DNase Set(QIAGEN,79254).
Sequencing libraries were constructed using TruSeq RNA Sample Pre Kit v2–Set B(Illumina,RS-122-2002),according to the manufacturers’ instructions.

treatment_protocol: Bisphnel A was added in complete medium at a concentration of 100μM, and cultures were treated for about 4 days.

value: DBA/2J X c57BL/6J

value: post natal day 6

tag: passages

value: Spermatogonial stem cell


title: untreated SSCs rep1 (A1)


title: untreated SSCs rep2 (A2)


title: Bisphnel A-treated SSCs rep3 (B3)


title: Bisphnel A-treated SSCs rep2 (B2)


title: cytokines

city: Hangzhou

first: Mengmeng

last: Jiang

address: Yuhangtang Road 866, Xihu Distric

data_processing:
Basecalls performed using Illumina Casava1.7 software
Sequenced reads were trimmed for adaptor sequence,then mapped to hg38 human genome using STAR v2.5.1b
All multi-aligned reads were removed and GTF annotation files from Gencode were used to tag aligned reads. For UMI count, molecular barcodes with one edit distance were merged to one within a gene. For the cell quality control,cells which less than 500 genes were expressed.
Dimension reduction and clustering were generated using Seurat.The most 501 variable genes were selected after calculating the average expression and dispersion for each gene.
Genome_build: hg38
Supplementary_files_format_and_content: txt files were generated using …; Scores represent …

source_name: CD34+ cells

growth_protocol: human CD34+ cells were cultured in IMDM supplemented with serum substitute.

extract_protocol:
Single cells and barcoded beads were blocked in an array of agarose microwells, enabling efficient cell lysis and transcript capture.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human mobilized peripheral blood

value: cytokines

tag: incubation time

value: 7 days


title: CFO + cytokines

value: CFO+cytokines


title: control


title: CFO

value: CFO


title: patient_15_Low_Pain_sRNA

description: small RNA


title: 4004_35d_vernalization-2

status: Public on Nov 02 2018

city: Deajeon

first: Won Yong

last: Jung

state: N/A = Not Applicable

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: Korea Research Institute Bioscience and Biotechnology(KRIBB)

description: vernalization for 35day-2nd

data_processing:
Trimming - SolexaQA package
Transcriptome reference-based assemble
Read mapping - bowtie2
DEG - R (EdgeR)
Genome_build: Brapa_sequence_v1.5.fasta; B.rapa - Brassica Database (http://brassicadb.org/brad)

organism: Brassica rapa subsp. pekinensis

source_name: shoot tissue

growth_protocol: 23°C, 16 h light/8 h dark, for 2 weeks

extract_protocol:
Total RNAs were extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA), and were then treated with DNase I (Fermentas, Pittsburgh, PA, USA) according to the manufacturers’ instructions.
Following the Illumina protocol(TruSeq RNA Library Prep Kit, TruSeq Stranded mRNA Sample Prep Kit)

treatment_protocol: cold (5±1°C), 12 h light/12 h dark, for 35 days

tag: cultivar

value: shoot

value: 7-week-old plants

value: cold 35 days


title: uncultured cells

institute: Zhejiang University

value: unculture


title: 4004_0d_control-1

description: 0day (non treatment-1st)

value: 2-week-old plants

value: cold 0 days


title: Bisphnel A-treated SSCs rep1 (B1)

tag: strain


title: 4004_0d_control-2

description: 0day (non treatment-2nd)


title: RNAseq_LN95_shARfl_1nM_DHT_2; Sample 44

city: Boston

first: Myles

last: Brown

state: MA

address: 450 Brookline Ave., D730

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Differential gene expression was determined using the Visualization Pipeline for RNA-seq (https://bitbucket.org/cfce/viper/) and DEseq {Anders, 2010 #64}
Genome_build: hg19
Supplementary_files_format_and_content: Differential expression tables produced by Deseq

growth_protocol: LNCaP95 cells maintained in phenol red-free RPMI 1640 medium with supplemented 10% charcoal/dextran-treated FBS, 1% L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
TRIzol (Thermo Fisher Scientific) and RNeasy Mini Kit (Qiagen)
Generated by the Center for Functional Cancer Epigenetics at the Dana Farber Cancer Institute using 1 ug total RNA and the Illumina TruSeq stranded mRNA sample kit. Libraries were sequenced on the Illumina NextSeq 500 platform

treatment_protocol: Cells were treated with 0.1nM, 1nM and 10nM DHT or the equivalent volume of ETOH for 24h.

tag: cell line

tag: transfection

value: shARfl

value: 1nM DHT

tag: batch date (d.m.y)


title: RNAseq_LN95_shARfl_1nM_DHT_1; Sample 43

tag: treatment


title: RNAseq_LN95_shARfl_0.1nM_DHT_1; Sample 40

value: 0.1nM DHT


title: RNAseq_LN95_shGFP_10nM_DHT_3; Sample 36

value: shGFP

value: 10nM DHT


title: RNAseq_LN95_shARfl_1nM_DHT_3; Sample 45


title: RNAseq_LN95_shARfl_0.1nM_DHT_2; Sample 41


title: RNAseq_LN95_shARfl_10nM_DHT_2; Sample 47


title: RNAseq_LN95_shARfl_10nM_DHT_1; Sample 46


title: RNAseq_LN95_shARfl_0.1nM_DHT_3; Sample 42


title: RNAseq_LN95_shGFP_10nM_DHT_2; Sample 35


title: RNAseq_LN95_shARfl_ETOH_2; Sample 38

value: ETOH


title: RNAseq_LN95_shARfl_10nM_DHT_3; Sample 48


title: RNAseq_LN95_shGFP_1nM_DHT_1; Sample 31


title: RNAseq_LN95_shGFP_1nM_DHT_2; Sample 32


title: RNAseq_LN95_shGFP_1nM_DHT_3; Sample 33


title: RNAseq_LN95_shGFP_10nM_DHT_1; Sample 34


title: RNAseq_LN95_shGFP_0.1nM_DHT_3; Sample 30


title: RNAseq_LN95_shGFP_0.1nM_DHT_2; Sample 29


title: 4004_35d_vernalization-1

description: vernalization for 35day-1st


title: RNAseq_LN95_shGFP_ETOH_2; Sample 26


title: RNAseq_LN95_shARfl_ETOH_3; Sample 39


title: RNAseq_LN95_shGFP_ETOH_1; Sample 25


title: RNAseq_LN95_shGFP_0.1nM_DHT_1; Sample 28


title: RNAseq_LN95_shARv7_10nM_DHT_3; Sample 24


title: RNAseq_LN95_shGFP_ETOH_3; Sample 27


title: RNAseq_LN95_shARfl_ETOH_1; Sample 37


title: RNAseq_LN95_shARv7_10nM_DHT_2; Sample 23


title: RNAseq_LN95_shARv7_10nM_DHT_1; Sample 22


title: RNAseq_LN95_shARv7_1nM_DHT_2; Sample 20


title: RNAseq_LN95_shARv7_0.1nM_DHT_3; Sample 18


title: RNAseq_LN95_shARv7_0.1nM_DHT_1; Sample 16


title: RNAseq_LN95_shARv7_1nM_DHT_3; Sample 21


title: RNAseq_LN95_shGFP_10nM_DHT_2; Sample 11


title: RNAseq_LN95_shARv7_ETOH_1; Sample 13


title: RNAseq_LN95_shGFP_10nM_DHT_1; Sample 10


title: RNAseq_LN95_shARv7_1nM_DHT_1; Sample 19


title: RNAseq_LN95_shARv7_0.1nM_DHT_2; Sample 17


title: RNAseq_LN95_shARv7_ETOH_2; Sample 14


title: RNAseq_LN95_shGFP_1nM_DHT_2; Sample 08


title: RNAseq_LN95_shGFP_10nM_DHT_3; Sample 12


title: RNAseq_LN95_shGFP_1nM_DHT_1; Sample 07


title: RNAseq_LN95_shGFP_0.1nM_DHT_1; Sample 04


title: RNAseq_LN95_shGFP_ETOH_3; Sample 03


title: RNAseq_LN95_shGFP_0.1nM_DHT_3; Sample 06


title: RNAseq_LN95_shGFP_ETOH_2; Sample 02


title: RNAseq_LN95_shGFP_ETOH_1; Sample 01


title: ChIP_LN95_parental_DHT_ARN20; Sample 52

data_processing:
BWA reads mapping/MAPQ filter as part of the ChiLin pipeline
MACS2 peak calling as part of the ChiLin pipeline
SAMtools to downsample and sort bam files
Bamliquidator to calculated normalized read counts for peaks
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using Chilin; Bamliquidator counts were generate using Bamliquidator

extract_protocol:
Approximately 10^7 cells were cross-linked with 1% formaldehyde for 10min. Lysed cells were sonicated in a Covaris E210 sonicator. Sheared chromatin was incubated with antibodies over night and immunoprecipitated using Dynabeads Protein A (Life Technologies). Chromatin was treated with RNaseA and Protease K and purified using phenol-chloroform extraction.
Sequencing libraries were generated according to manufacturer's instructions (ThruPLEX DNA-seq Kit, Rubicon Genomics) and then sequenced on the Illumina NextSeq 500 platform

treatment_protocol: Cells were treated with 10nM DHT or the equivalent volume of ETOH for 4h.

value: Parental (none)

tag: antibody

value: AR N-20 (Santa-Cruz Biotechnology)


title: ChIP_LN95_parental_DHT_Input; Sample 46

value: INPUT


title: ChIP_LN95_parental_ETOH_ARv7; Sample 47

value: ARv7 (H6 253 Epitomics)


title: ChIP_LN95_parental_DHT_ARv7; Sample 48


title: RNAseq_LN95_shARv7_ETOH_3; Sample 15


title: ChIP_LN95_parental_ETOH_Input; Sample 49


title: ChIP_LN95_parental_ETOH_ARN20; Sample 51


title: ChIP_LN95_parental_DHT_Input; Sample 50


title: ChIP_LN95_parental_ETOH_Input; Sample 45


title: RNAseq_LN95_shGFP_1nM_DHT_3; Sample 09


title: ChIP_LN95_parental_DHT_ARfl; Sample 44

value: ARfl (Clone SP242; Spring Bioscience)


title: ChIP_LN95_shGFP_DHT_ARfl; Sample 36


title: ChIP_LN95_shARv7_ETOH_Input; Sample 41


title: ChIP_LN95_shARv7_DHT_ARfl; Sample 38


title: ChIP_LN95_shARv7_ETOH_ARfl; Sample 37


title: ChIP_LN95_shGFP_ETOH_Input; Sample 39


title: ChIP_LN95_shGFP_DHT_Input; Sample 40


title: ChIP_LN95_shGFP_ETOH_ARfl; Sample 35


title: ChIP_LN95_shARfl_ETOH_Input; Sample 33


title: RNAseq_LN95_shGFP_0.1nM_DHT_2; Sample 05


title: ChIP_LN95_shARfl_DHT_ARfl; Sample 32


title: ChIP_LN95_shARfl_ETOH_ARfl; Sample 31


title: ChIP_LN95_shARfl_DHT_Input; Sample 30


title: ChIP_LN95_shARv7_DHT_Input; Sample 29


title: ChIP_LN95_shGFP_DHT_Input; Sample 28


title: ChIP_LN95_shARfl_ETOH_Input; Sample 27


title: ChIP_LN95_shARv7_ETOH_Input; Sample 26


title: ChIP_LN95_shGFP_ETOH_Input; Sample 25


title: ChIP_LN95_shARv7_DHT_Input; Sample 42


title: ChIP_LN95_shARfl_DHT_ARv7; Sample 24


title: ChIP_LN95_shARv7_DHT_ARv7; Sample 23


title: ChIP_LN95_shGFP_ETOH_ARv7; Sample 19


title: ChIP_LN95_shARv7_ETOH_ARv7; Sample 20


title: ChIP_LN95_parental_ETOH_ARfl; Sample 43


title: ChIP_LN95_shARfl_ETOH_ARv7; Sample 21


title: ChIP_LN95_shARfl_ETOH_Input; Sample 17


title: ChIP_LN95_shARfl_DHT_Input; Sample 34


title: ChIP_LN95_shARv7_ETOH_Input; Sample 15


title: ChIP_LN95_shARfl_ETOH_H3k27ac; Sample 11


title: ChIP_LN95_shARv7_ETOH_H3k27ac; Sample 9


title: ChIP_LN95_shARfl_DHT_H3k27ac; Sample 12


title: ChIP_LN95_shGFP_ETOH_Input; Sample 13


title: ChIP_LN95_shARv7_DHT_Input; Sample 16


title: ChIP_LN95_shARfl_ETOH_HOXB13; Sample 6


title: ChIP_LN95_shGFP_ETOH_H3k27ac; Sample 7


title: ChIP_LN95_shGFP_DHT_Input; Sample 14


title: ChIP_LN95_shARv7_DHT_H3k27ac; Sample 10


title: ChIP_LN95_shARv7_ETOH_FOXA1; Sample 2

value: FOXA1 (Abcam)


title: ChIP_LN95_shGFP_ETOH_HOXB13; Sample 4


title: ChIP_LN95_shGFP_ETOH_FOXA1; Sample 1


title: ChIP_LN95_shGFP_DHT_ARv7; Sample 22


title: E15_B7

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Library strategy: Rainbow-seq
Map reads with STAR version 2.5.1b
Count reads for each gene with htseq-count
Calculate gene expression in FPKM
Count reads for each transposon with htseq-count
Calculate transposon expression in FPKM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: pre-implantation embryo

extract_protocol:
single cells were lysed (0.1% Triton X100)
Nextera XT

treatment_protocol: Two-cell embryos were collected 46hpi and treated in vitro with 4-Hydroxytamoxifen for two hours, followed by in vitro culture in KSOM media (37°C, 5%CO2, 100% humidity). Embryos were cultured until developed to 4-cell, 8-cell or early blastocyst stages

value: pre-implantation embryo

tag: embryo identifier

tag: cell identifier

tag: cell stage

tag: cell label


title: E15_B8

value: B


title: ChIP_LN95_shARfl_ETOH_FOXA1; Sample 3


title: E15_B2

value: A


title: E14_B8


title: E15_B1


title: E15_B5


title: ChIP_LN95_shGFP_DHT_H3k27ac; Sample 8


title: ChIP_LN95_shARv7_ETOH_HOXB13; Sample 5


title: E14_B6


title: E14_B2


title: E14_B5


title: E14_B7


title: E13_B8


title: E14_B1


title: E13_B5


title: E13_B6


title: E13_B4


title: E13_B3


title: E14_B3


title: E15_B4


title: E12_B7


title: E13_B1


title: E13_B2


title: E13_B7


title: E14_B4


title: E12_B6


title: E12_B4


title: E12_B5


title: E15_B6


title: E12_B1


title: E12_B2


title: E11_B6

description: This sample was not included in the publication analysis


title: E11_B4


title: E10_B5


title: E11_B1


title: E11_B2


title: E10_B4


title: E11_B3


title: E10_B1


title: ChIP_LN95_shARfl_DHT_Input; Sample 18


title: E9_B3


title: E10_B2


title: E9_B4


title: E9_B2


title: E10_B3


title: E11_B5


title: E8_B2


title: E8_B1


title: E12_B3


title: E8_B4


title: VEC_A_1 MPRA_control

city: Cambridge

first: Abbie

last: Groff

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

institute: Harvard University

description: C2C12_lincmRNA_combined_Jan2017_hiseq.tab

data_processing:
Custom python scripts were used to count barcodes in MPRA experiments.
In RNA seq experiments, reads were aligned to mm10 and quantified using rsem. For mESC samples, reads were first trimmed to 50bp.
Differential analysis was performed using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: counts

organism: synthetic construct

extract_protocol:
Embryonic organs were harvested and homogenized in TRIzol. Cells were cultured and harvested directly in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)
RNA-seq or plasmid-sequencing (For MPRA Vector DNA libraries)

tag: lncrna previous name

tag: background

tag: official strain name

tag: genotype

tag: Sex

tag: sample type

value: Vector DNA


title: VEC_B_2 MPRA_control


title: VEC_B_1 MPRA_control


title: VEC_A_3 MPRA_control


title: VEC_A_2 MPRA_control


title: E7_B3

tag: tissue


title: E7_B4


title: E6_B4


title: E7_B1


title: E6_B3


title: E6_B2


title: E6_B1


title: E5_B4


title: E9_B1


title: E4_B2


title: E4_B3


title: E8_B3


title: E5_B1


title: E3_B3


title: E7_B2


title: E3_B1


title: E5_B3


title: E2_B4


title: E2_B3


title: E2_B2


title: E2_B1


title: Peritoneal - BCL2+ 3

city: Palo Alto

first: Kristopher

middle: David

last: Marjon

state: CA

address: 265 Campus

department: ISCBRM

institute: Stanford

data_processing:
altanalyze version 2.0 was used to handle all processing of RNAseq samples
used standard program settings for RNASeq and Mus Musculus for Processing of RNA-Seq reads of the FASTA files
use multithreading for read genomic annotation, removed genes with RPKM less than 1, used Benjamini-Hochberg false discovery rate statistic.

source_name: macrophages

extract_protocol:
Cells were extracted from the peritoneal cavity and bone marrow of each mouse in PBS and 5mM EDTA. These cells were FACS sorted directly into Trizol prior to total RNA extraction with chloroform and purification with the Qiagen RNEasy MinElute Cleanup Kit
For library preparation we used the NEBNext Ultra RNA Library Prep Kit for Illumina, using Illumina TruSeq Adapters for barcoding. Depending on the concentration of adaptor-ligated cDNA, as determined by Qubit quantitation, 6-15 PCR cycles were carried out to amplify the libraries.

treatment_protocol: Mice were injected with 2ml of Thoglycolalte i.p.. Bones and peritoneal levage was conduceted 6 hours after injection.

value: peritoneal cavity

tag: strain

value: fvb


title: Peritoneal - WT - 2

value: wild type


title: BM - WT - 3

value: bone marrow


title: Peritoneal - WT - 3


title: Peritoneal - BCL2+ 2


title: E5_B2


title: BM - WT - 2


title: E4_B4


title: BM - WT - 1


title: E4_B1


title: E1_B4


title: E1_B2


title: Peritoneal - BCL2+ 1


title: BM - BCL2+ 3


title: BM - BCL2+ 1


title: E1_B1


title: C2C12_B_3 MPRA_sample

value: GFP-RNA


title: E3_B4


title: Peritoneal - WT - 1


title: C2C12_A_2 MPRA_sample


title: C2C12_B_1 MPRA_sample


title: C2C12_A_1 MPRA_sample


title: E1_B3


title: C2C12_B_2 MPRA_sample


title: Peril N3 mesc WT4 rep2

source_name: mESC

value: Peril

value: WT

value: M

value: polyA RNA


title: Peril N3 mesc WT4 rep1


title: Peril N3 mesc KO6 rep2

value: KO


title: Peril L43 E14.5 kidney kof9

source_name: kidney

value: F


title: BM - BCL2+ 2


title: MB231_p0#27_ADI48h_rep2

city: Duarte

first: David

middle: K.

last: Ann

address: 1500 E Duarte Rd

institute: City of Hope

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 hg19 whole genome using bowtie.
ReadReads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using software Partek.
Genome_build: hg19

source_name: breast cancer cells

growth_protocol: DMEM (high glucose) supplemented with 10% FBS and pen/strep.

extract_protocol:
RNA was extracted using Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Arginine deiminase (ADI, 0.3 µg/mL 48h) was added to MDA-MB-231 full growth medium.

tag: cell line

tag: cell type

tag: modification

value: Arginine deiminase (ADI, 0.3 µg/mL 48h)


title: MB231_ADI48h_rep2

value: parental


title: MB231_p0#27_rep2


title: MB231_ADI48h_rep1


title: MB231_p0#27_ADI48h_rep1


title: Peril L43 E14.5 kidney kom7


title: Peril L43 E14.5 kidney  wtf3


title: MB231_p0#27_rep1


title: MB231_rep1


title: Peril L43 E14.5 kidney wtm8


title: Peril L43 E14.5 kidney kof10


title: E3_B2

value: pre-implantation embryo


title: Peril L43 E14.5 kidney wtM1


title: MB231_rep2


title: Peril L46 E14.5 GE + OB kof 7

source_name: GEOB


title: Peril L46 E14.5 GE + OB wtm3


title: Peril L46 E14.5 GE + OB wtm1


title: Peril N3 mesc KO6 rep3


title: Peril N3 mesc WT4 rep3


title: E15_B3

value: B


title: Peril L46 E14.5 GE + OB kof2


title: Peril N3 mesc KO6 rep1


title: Mg7L1

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
base-calling: all reads were acquired by using the Genome Analyzer Data Collection Software SCS version 2.6
alignment: Reads were mapped to the Oryza sativa subsp. Japonica reference genome (build MSU7.0) in two phases using TopHat version 1.3.1 and Cufflinks, version 1.0.3, a detailed description of the workflow and settings used in the data analysis can be found in the description of GEO-submission GSE35843
quantification: Expression was quantified per sample and per annotated or unannotated transcript as the sum of all reads mapped to the respective gene exons with a 16 base pair tolerance on either side to compensate for potential errors in the gene annotation.
Genome_build: Genome_build: MSU7
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab separated values, gene names (known and novel) with location information and number of reads per sample

organism: Oryza sativa Japonica Group

source_name: shoots of Meloidogyne graminicola infected plants 7 dai

growth_protocol: Oryza sativa cv. ‘Nipponbare’ (GSOR-100, USDA) was germinated on wet filter paper for 6 days at 30°C,  transferred to SAP-substrate (Sand Absorbent Polymer; Reversat et al. 1999) and further grown at 26°C under a 16h/8h light-regime.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Mini Kit (Qiagen), with an additional sonication step after addition of buffer RLT. RNA integrity was checked using the Agilent BioAnalyzer 2100 (Agilent).
Approximately two microgram of total RNA was used for mRNA-Seq library construction according to the manufacturer’s recommendations (Illumina). We used the multiplexing sequencing adapters provided in the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection of the library was performed on a 2% agarose gel (Low Range Ultra Agarose, Biorad 161-3107). The denatured library was diluted to a final concentration of 6 pM and loaded on a paired-end read flow cell (TruSeq v5 kit, Illumina).

treatment_protocol: The nematodes were extracted using a Baermann funnel from Meloidogyne graminicola infected rice plants cultured under the same conditions. Five days after transplanting in SAP, the plants were inoculated with 250 nematodes per plant. One day after root-knot nematode inoculation, the plants were transferred to a hydroponic culturing system with Hoagland solution to synchronize the infection process.

value: shoots


title: Mg7L8


title: Mg3L1

source_name: shoots of Meloidogyne graminicola infected plants 3 dai


title: H3K9me3_input_cKO

status: Public on Nov 01 2018

city: London

first: Takayuki

last: Hirota

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The basecalling is done automatically by the sequencer with the illumina software RTA. Conversion to fastq was done with the illumina software bcl2fastq version 2.
RNA-seq: abundance was calculated by running kallisto (Bray et al, Nat Biotech, 2016) using the mouse transcriptome index (GRCm38), with the parameter "-b 150 -l 200 -t 4 -s 20 --single". Normalisation was performed using kallisto to generate transcript-level TPM values which were later aggregated to gene-level TPM values using sleuth (Pimentel et al, Nat Methods, 2017). Differential expression analysis was performed using sleuth. All chromosome and gene Biotype annotations were extracted from Ensembl.
ChIP-seq: alignment was performed by running hisat2 (Kim et al, Nat Methods, 2015) using mouse genome index (GRCm38), with the parameter "-p 6 -t -q --add-chrname -3 0 -5 9 --dta-cufflinks --no-spliced-alignment". Mapping files containing uniquely mapped reads were converted into bam format and sorted using samtools (Li et al, Bioinformatics, 2009). Duplicated reads were removed using picard (http://broadinstitute.github.io/picard). Bigwig file of H3K9me3 occupancy fold-change relative to Setdb1 cKO of wildtype cells was generated by comparing bam files using bamCompare in deeptools2 (Ramirez et al, Nucleic Acids Res, 2016) with the parameter "-bs 100 -bl mm10.blacklist.bed --normalizeTo1x 2150570000 --centerReads --pseudocount 1 --ratio reciprocal_ratio".
Genome_build: GRCm38
Supplementary_files_format_and_content: excel spreadsheet include TPM values and sleuth output values
Supplementary_files_format_and_content: bigwig file showing H3K9me3 occupancy fold-change relative to Setdb1 cKO of wildtype cells

extract_protocol:
RNA-seq: total RNA was extracted from 500 pachytene cells using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher, AM1931) and eluted in 10 µl of elution solution. ChIP-seq: wildtype (3268 cells) and Setdb1 cKO (5203 cells) pachytene cells were used for library prep described below.
RNA-seq: cDNA was amplified from 1 µl of total RNA by using Smart-seq2 protocol (S. Picelli et al., Nat Methods. 10, 1096-8. 2013; 15 amplification cycles). 10 ng of cDNA was sheared using Covaris E220. Libraries of ~300 bp were generated using Ovation Ultralow DR kit (NuGEN, 0330) with 14 PCR cycles. ChIP-seq: Ultra-low-input native ChIP-seq library was prepared by following a published protocol (J. Brind'Amour et al., Nat. Commun. 6, 6033. 2015). 5% of the samples after micrococcal nuclease digestion were taken as input. 6.25 µl of diluted H3K9me3 antibody (1:100; Active Motif, 39161) per reaction was used for ChIP. NEBNext Adapter for Illumina was used as adapters and adapter-ligated DNAs were amplified by 13 PCR cycles using NEBNext Index primers (New England Biolabs, included in E7335 and E7500). The libraries were size-selected (200-500 bp) using E-Gel (ThermoFisher).

treatment_protocol: wildtype and Setdb1 cKO

value: male

tag: genotype/variation

value: Setdb1 cKO

value: testis

value: pachytene spermatocytes


title: H3K9me3_input_WT

value: wildtype


title: H3K9me3_ChIP_WT

tag: chip antibody

value: H3K9me3 antibody (Active Motif, Cat.# 39161)


title: H3K9me3_ChIP_cKO


title: Mg3L2


title: JB-2

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

data_processing:
Adapters were trimmed using cutadapt with default parameters
Trimmed reads were aligned to the mouse reference genome, mm10, using STAR and default parameters
Raw read counts per gene were tabulated using HTSeq count and default parameters
Normalization and Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: normalized reads counts

extract_protocol:
Cells were pelletted down and RNA was harvested using RNAeasy reagent from qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse oviduct

tag: treatment

value: shRNA scramble


title: JB-3


title: JB-6

value: shRNA targeting PTEN


title: JB-4


title: RNAseq-Neuron-TENM1-4

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Data quality was assessed using FastQC v.0.11.2
Trimmed reads were screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.4.3
RSeQC package v.2.3.7 was used to assess read distribution, positional read duplication and confirm strandedness of alignments
Raw trimmed reads were aligned to the reference genome hg19 using Tophat v.2.0.11
Tophat alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Raw gene counts were loaded and sample-normalized using DESeq v.1.18.0
Two-condition differential expression was done with the edgeR R package, v.3.8.6
The method used for normalizing the data was TMM, implemented by the calcNormFactors(y) function
The test for differential expression was done using the quasi-likelihood F-test functionality in edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: glutamatergic NEUROG2-induced neurons

growth_protocol: All iPSC lines were maintained on matrigel coating, with complete media change every day in mTeSR (StemCellTechnologies). Neurons were generated by 7-day overexpression of NEUROG2 followed by 21-day maturation in Neurobasal media (Gibco), 1x B27 (Gibco), 1x glutamax (Gibco), 1x pen/strep (Gibco), laminin (10 μg/ml, Sigma), BDNF (10 ng/μl, Peprotech) and GDNF (10 ng/μl, Peprotech)

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared using NEBNext Ultra RNA Library Preparation kit for Illumina

value: glutamatergic NEUROG2-induced neurons

tag: passages

tag: days of differentiation


title: JB-5


title: WT3

city: New York

first: Yotam

last: Sagi

state: NY

address: 1230 York Ave.

institute: Rockefeller University

description: ribosome bound RNA

data_processing:
The data source for the reference genome mm10 and the genes.gtf file was UCSC.
Alignment to the Mus musculus genome mm10 using Tophat (version 2.0.8). The parameter setting for Tophat was: -g 1 --no-coverage-search -G genes.gtf.
Fragments per kilobase of transcript per million mapped reads (FPKM) values of genes were calculated with Cufflinks (version 2.1.1). The parameter setting for Cufflinks was: -G genes.gtf.
DESeq package (version 1.10.1) with the standard comparison mode between two experimental conditions.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM and DESeq output

source_name: ChAT cells of the striatum

growth_protocol: Male and female mice were maintained on a C57/Bl6N background and were kept on a 12-h light/dark cycle with food and water ad libitum. Mice were housed in groups of up to five animals

extract_protocol:
Freshly harvested 6 striata from 3 mice were subjected to a translating ribosome affinity procedure  The quantity (> 1 ng) and quality (RIN > 6.2) of all RNA samples were validated by Bioanalyzer
1 ng of RNA from ach I.P. sample was reversed transcribed using Ovation RNA-seq V2 kit (Nugen, San Carlos,CA).
cDNA was sheared by Covaris and  150 bp long, single end labeled cDNA libraries were constructed using Truseq RNA sample preparation kit V2 (Illumina, San Diego, CA)

value: ventral striatum, ChAT cells

tag: age

value: 8-12 weeks

value: ChAT TRAP X  p11 fl/fl/ X  WT


title: WT2

description: ribosome bound RNA


title: KO3

description: ribosome bound RNA

value: ChAT TRAP X  p11 fl/fl/ X  ChAT Cre


title: WT1

description: ribosome bound RNA


title: KO4

description: ribosome bound RNA


title: JB-1


title: RNAseq-Neuron-SCN2A-4


title: RNAseq-Neuron-TENM1-5


title: KO2

description: ribosome bound RNA


title: RNAseq-Neuron-ANOS1-3


title: RNAseq-Neuron-ANOS1-4


title: RNAseq-Neuron-ANOS1-2


title: KO1

description: ribosome bound RNA


title: RNAseq-Neuron-SCN2A-3


title: RNAseq-Neuron-SCN2A-2


title: RNAseq-Neuron-KCNQ2-4


title: RNAseq-Neuron-DLGAP2-3


title: RNAseq-Neuron-CHD8-4


title: RNAseq-Neuron-DLGAP2-4