title: ana_p8_2

city: Durham

first: Jia Wern

last: Pan

state: NC

address: French Family Science Center, Science Drive

department: Biology

institute: Duke University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for the adaptor sequence, and then mapped to each species’ transcriptome that was downloaded from FlyBase (FB2014_6 release) using bwa-0.7.8
Count tables for each sample were generated using a customized python script, and each transcript ID was given a gene identifier based on ortholog calls from FlyBase. The count tables were then consolidated into matrices containing transcript ID and read counts from all genotypes for each stage using a Ruby script.
Matrices of gene counts were normalized for each species’ developmental time points in R using the DESeq2 suite
Genome_build: FlyBase dsec-r1.3, dere-r1.3, dvir-r1.2, dana-r1.05, dsim-r2.02
Supplementary_files_format_and_content: Comma-separated-values file (.csv) containing normalized transcript counts (baseMean) from DESeq2 for each gene and species for each developmental time point

organism: Drosophila ananassae

source_name: 8hr APF pupal antennal disc

growth_protocol: All flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20°C

extract_protocol:
Dissected tissue was stored in Trizol reagent for pooling. RNA was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions, including an on-column DNase digestion (Qiagen).
RNA concentrations were measured and 700ng RNA was diluted to 60ul total volume with H2O. RNA sequencing libraries were prepared with TruSeq Stranded mRNA Sample Prep Kit (Illumina) according to manufacturer’s instructions. For the RNA fragmentation step, 94˚C, 2min was used with the intention to obtain a median size ~185bp. PCR amplification was done with 15 cycles. A total of 24 multiplexed libraries (barcoded) were accessed for quality and combined together before separation into two identical pooled libraries, which were then subjected to cluster generation followed by Illumina 50bp paired-end sequencing by the UNC High-Throughput Sequencing Facility (HTSF).

value: Antennal disc

value: 8hrs after pupal formation

tag: number of pooled individuals

tag: strain

value: wild-type


title: ana_p40_2

status: Public on Dec 01 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: 40hr APF pupal antenna

tag: tissue

value: Antenna

tag: developmental stage

value: 40hrs after pupal formation


title: ana_p8_1


title: ana_3L_2

source_name: 3rd instar larvae antennal disc

value: 3rd instar larvae


title: ana_p40_1


title: HJ2 rep2

city: Hangzhou

first: Xiong-wei

last: Li

state: Zhejiang

address: Yuhangtang Road866

department: Department of Horticulture

country: China

institute: Zhejiang University

data_processing:
Raw data of fastq format were processed through in-house Perl scripts to obtain clean data by removing reads containing adapter or ploy-N and low quality reads.
Reference genome and gene model annotation files were downloaded from the genome website (http://www.rosaceae.org/species/prunus_persica/genome_v1.0) directly. The index of the reference genome was built using Bowtie v0.12.8, and paired-end clean reads were aligned to the reference genome using TopHat v1.4.0. We selected TopHat as the mapping tool as it can generate a database of splice junctions based on the gene model annotation file, so giving better mapping results than other non-splice mapping tools (Trapnell et al. 2009).
HTSeq v0.5.3 was used to count the reads mapped to each gene, and the RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two biological replicates per sample was performed using the DESeq R package (1.10.1) (Wang et al. 2010; Robinson et al. 2010). The P values were adjusted using the Benjamini & Hochberg method (Robinson et al. 2010; Benjamini et al. 1995)
Genome_build: Prunus persica Whole Genome v1.0 Assembly & Annotation
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Prunus persica

source_name: fruit mesocarp

extract_protocol:
Total RNA for each sample was isolated from 1g frozen fruit tissue, according to Zhang (2010). Contaminating genome DNA was removed by RNase-free DNase I (Fermentas, Vilnius, Lithuania). RNA integration and quantification was by agarose electrophoresis at an absorbance of 260nm (A260) using the NanoDrop® ND-3300 Fluorospectrometer with Quant-iT™ RiboGreen® RNA Reagent (Invitrogen, USA). First-strand cDNA was synthesized using 2.0 μl DNA-free RNA with the PrimeScript RT reagent Kit with gDNA Eraser, following the manufacturer’s instructions (Takara), and was diluted for RT-qPCR using a CFX 96 real-time PCR detection system (Bio-Rad, Hercules, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: fruit mesocarp

tag: aromatic strength

value: strong

tag: flesh texture

value: soft melting

tag: brix

tag: cultivar

value: Hu Jing Mi Lu


title: HJ1 rep1

value: slight


title: HJ2 rep1


title: ana_3L_1


title: HJ1 rep2


title: ana_AA_2

source_name: adult antenna

value: Adult


title: ana_AA_1


title: vir_p40_2

organism: Drosophila virilis

source_name: 48hr APF pupal antenna

value: 48hrs after pupal formation


title: vir_p40_1


title: vir_p8_2

source_name: 10hr APF pupal antennal disc

value: 10hrs after pupal formation


title: sec_3L_2

organism: Drosophila sechellia


title: sec_p8_1


title: sec_3L_1


title: vir_3L_2


title: sec_AA_2


title: vir_AA_1


title: sec_p40_1


title: sec_p40_2


title: ere_p40_2

organism: Drosophila erecta


title: vir_p8_1


title: ere_p8_2


title: vir_AA_2


title: vir_3L_1


title: ere_p8_1


title: ere_AA_2


title: S2753 stat C bio1

city: Kgs. Lyngby

first: Sonia

last: Giubergia

address: Matematiktorvet 301

country: Denmark

institute: Technical University of Denmark

data_processing:
Data received from BGI were already sorted according to their respective adaptor sequences, and linker sequences had already been removed. RNA seq data was analyzed using the CLC genomics workbench software (CLC Aarhus, version 8.5). Quality and quantity of RNA sequence data was evaluated by the number of reads, GC%, PHRED-score, nucleotide contribution, quality distribution and enriched 5mers sequences. Reads were trimmed removing the first 15 nucleotides when nucleotide contribution was not normally distributes. Reads were then mapped to the reference genomes and expression values were calculated as RPKM. Gene expression profiles of biological samples were merged and, for each strain at each time point, the profiles deriving from the two media were compared. The quality of the transcriptomic data was evaluated using hierarchical clustering and principal component analysis. Statistically significant gene expression differences were assesses through a Baggerley's test using p-value<0.05 and q-values<0.05
Genome_build: P. galatheae genome (JMIB01)
Supplementary_files_format_and_content: xslx files including total gene reads, RPKM values etc. for each sample

organism: Photobacterium galatheae

source_name: Photobacterium galatheae

growth_protocol: Strains were inoculated in 10 ml of ½ YTSS in a 50 ml Erlenmeyer flasks and grown aerated (200 rpm) at 25 degrees for 24 hours. 100 ul of the 24 hours cultures were used to inoculate 10 ml of fresh ½ YTSS, and these cultures were grown for 24 hours, 200 rpm at 25 degrees. 50 ml of the glucose containing medium (SSBG, 2% Sigma Sea Salts, 0.3% casamino acids, 40mM MOPS, 0.2% glucose) and of the chitin containing medium (SSBC, 2% Sigma Sea Salts, 0.3% casamino acids, 0.2% colloidal chitin) were inoculated at a cell density of  approximately 10^3 CFU/ml. Cultures were run in 250 ml Erlenmeyer flasks, 200 rpm, 25 degrees. Samples for gene expression and bacterial counts were taken in the late exponential phase (cell density 10^8 CFU/ml) and in the stationary phase (24 hours old cultures, approx 10^9 CFU/ml)

extract_protocol:
RNA was extracted using the RNeasy kit(Qiagen), following manufacturer's instructions. DNA was removed on column with the Rnase-free Dnase set (Qiagen). Integrity and  quality of total RNA were assesses with a NanoDrop spectrometer and an Agilent 2100 Bioanalyzer. Total RNA samples were sent to the Beijing Genome Institute (BGI, Hong Kong), where rRNA was removed using the Ribo-Zero rRNA removal kit
Library where constructed by BGI with the TruSeq RNA Library Preparation kit (Illumina) and 100 bp paired-enf sequenced on a HiSeq 2000

treatment_protocol: At the harvesting time points, subsamples of the bacterial cultures were taken and mixed with 0.2 volumes of ice-cold STOP solution (95% [v/v] ethanol, 5% [v/v] phenol), incubated for 5 minutes on ice and pelleted by centrifugation. Cell pellets were stored at -80 degrees until RNA extraction.

tag: carbon source

value: Growth on chitin

tag: growth phase

value: Stationary phase


title: S2753 stat G bio2

value: Growth on glucose


title: ere_3L_2

value: Antennal disc


title: ere_3L_1


title: sec_AA_1


title: sec_p8_2

value: 8hrs after pupal formation


title: sim_p40_2

organism: Drosophila simulans

value: wild-type


title: ere_AA_1

value: Antenna


title: S2753 stat G bio3


title: S2753 stat G bio1


title: sim_p40_1

value: 40hrs after pupal formation


title: S2753 stat C bio2


title: S2753 exp C bio3

value: Exponential phase


title: S2753 exp C bio2


title: S2753 exp C bio1


title: S2753 exp G bio3


title: sim_3L_2

value: 3rd instar larvae


title: ere_p40_1


title: sim_AA_2


title: sim_AA_1


title: S2753 exp G bio2


title: SK-N-SH_EBF3_P177L_4

status: Public on Nov 30 2016

city: Huntsville

first: Richard

middle: M

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
PolyA RNA
SK-N-SH EBF3 p.P177L transfected RNA-Seq.
EBF3_P177L_4
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt

data_processing:
RNA-seq paired-end FASTQ files were aligned to hg19 using STAR 2.5.
RNA-seq counts were merged into a single count table and filtered to remove any gene with no counts in any sample.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt: Tab-delimited text file containing raw read counts for all genes with at least one read in any sample.

organism: Homo sapiens

source_name: SK-N-SH, p.P177L EBF3

growth_protocol: SK-N-SH (ATCC HTB-11) cells were obtained from ATCC and grown under recommended growth conditions.

extract_protocol:
Total RNA was harvested using the Norgen Total RNA Preparation Kit (Norgen Biotek). cDNA was prepared using the ThemoFisher High-Capacity RNA-to-cDNA Kit (ThermoFisher).
RNA-seq was performed as previously described (Gertz et al. 2012).

treatment_protocol: 5 ug of EBF3-WT or EBF3-P177L vector per 1x10e6 cells were transfected into SK-N-SH cell using Nucleofection (Lonza) kit V using manufacturer's instructions. Cells were selected with 400 ug/mL G418 (Invitrogen, 10131035) for two weeks and then with 200 ug/mL for a further 2-3 weeks to generate SK-N-SH cells with stable EBF3-3xFlag expression.

tag: cell line

value: SK-N-SH (ATCC HTB-11)

tag: stable expression

value: p.P177L EBF3


title: SK-N-SH_EBF3_P177L_1

description:
PolyA RNA
SK-N-SH EBF3 p.P177L transfected RNA-Seq.
EBF3_P177L_1
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: SK-N-SH_EBF3_P177L_2

description:
PolyA RNA
SK-N-SH EBF3 p.P177L transfected RNA-Seq.
EBF3_P177L_2
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: SK-N-SH_EBF3_WT_3

description:
PolyA RNA
SK-N-SH EBF3 WT transfected RNA-Seq.
EBF3_WT_3
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt

source_name: SK-N-SH, WT EBF3

value: WT EBF3


title: sim_p8_2


title: SK-N-SH_Control_2

description:
PolyA RNA
SK-N-SH Control RNA-Seq.
SKNSH_WT_2
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt

source_name: SK-N-SH, control


title: SK-N-SH_Control_1

description:
PolyA RNA
SK-N-SH Control RNA-Seq.
SKNSH_WT_1
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: SK-N-SH_Control_3

description:
PolyA RNA
SK-N-SH Control RNA-Seq.
SKNSH_WT_3
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: SK-N-SH_EBF3_WT_1

description:
PolyA RNA
SK-N-SH EBF3 WT transfected RNA-Seq.
EBF3_WT_1
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: Sample36900 (RNA-Seq)

city: Duarte

first: Susan

last: Neuhausen

state: California

address: 1500 E duarte road

department: Population Sciences

institute: City of hope

description: RNA-Seq data, FFPE samples with metadata indicate in 'characteristics'

data_processing:
Basecalls performed CASAVA
RNA-Seq reads were aligned using TopHat2
Genome_build: hg19
Supplementary_files_format_and_content: read counts produced using findOverlaps/GenomicRanges, using RefSeq exon annotations downloaded 9/11/12 (either raw counts or Read-Per-Kilobase-per-Million / RPKM)

source_name: FFPE prostatectomy

growth_protocol: clinical samples

extract_protocol:
RecoverAll™ Total Nucleic Acid Isolation kit (Life Technology Inc.)
Illumina TruSeq,Total RNA

treatment_protocol: untreated

tag: age

value: tumor

tag: patient id

tag: Stage

tag: gleason

tag: psa

tag: race

value: White

tag: ethnicity

value: Non-Hispanic

tag: batch


title: Sample36852 (RNA-Seq)

tag: tissue


title: Sample36885 (RNA-Seq)

value: African-American


title: Sample36967 (RNA-Seq)


title: sim_p8_1

tag: developmental stage

tag: number of pooled individuals

tag: strain


title: Sample36861 (RNA-Seq)


title: Sample36916 (RNA-Seq)


title: Sample36908 (RNA-Seq)


title: Sample36867 (RNA-Seq)

value: Asian


title: sim_3L_1


title: Sample36918 (RNA-Seq)


title: Sample36883 (RNA-Seq)

value: Hispanic


title: Sample36897 (RNA-Seq)


title: Sample36929 (seq)

description: miRNA-Seq data, FFPE samples

data_processing:
Basecalls performed CASAVA
miRNA-Seq reads were aligned using Bowtie
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] read counts produced using findOverlaps/GenomicRanges, using miRbase 18 annotations

extract_protocol:
RecoverAll™ Total Nucleic Acid Isolation kit (Life Technology Inc.)
Illumina TruSeq Small RNA

tag: patientid

value: normal


title: S2753 exp G bio1

tag: carbon source

value: Growth on glucose


title: Sample36889 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36928 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36890 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36922 (seq)

description: miRNA-Seq data, FFPE samples


title: SK-N-SH_EBF3_P177L_3

description:
PolyA RNA
SK-N-SH EBF3 p.P177L transfected RNA-Seq.
EBF3_P177L_3
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: Sample36923 (seq)

description: miRNA-Seq data, FFPE samples


title: SK-N-SH_EBF3_WT_2

description:
PolyA RNA
SK-N-SH EBF3 WT transfected RNA-Seq.
EBF3_WT_2
Processed data file: SK-N-SH_EBF3_RNA-Seq_Count_Table.txt


title: Sample36903 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36863 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36904 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36925 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36864 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36948 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36924 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36854 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36853 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36973 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36855 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36851 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36974 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36947 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36861 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36926 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36915 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36914 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36967 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36969 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36869 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36927 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36870 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36902 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36860 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36862 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36857 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36858 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36900 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36852 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36856 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36961 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36959 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36867 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36950 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36873 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36871 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36872 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36874 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36876 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36875 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36906 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36930 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36881 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36935 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36918 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36882 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36953 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36942 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36919 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36956 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36958 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36866 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36934 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36943 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36933 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36921 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36908 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36920 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36907 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36932 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36880 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36917 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36901 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36877 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36916 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36878 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36931 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36905 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36955 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36910 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36884 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36909 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36887 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36886 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36894 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36893 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36885 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36888 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36939 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36965 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36891 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36895 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36892 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36941 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36898 (seq)

description: miRNA-Seq data, FFPE samples


title: piwi heterozygote smRNA

city: Providence

first: Jason

middle: G

last: Wood

state: RI

address: 185 Meeting St.

department: MCB

institute: Brown University

description:
piwi.het
Small RNA-seq
Processed data file: piwi.pirna.repenrich.antisense.rawcounts.txt
Processed data file: piwi.pirna.repenrich.antisense.normalized.log2FC.txt

data_processing:
Basecalling performed with Illumina CASAVA 1.8.
Adapter sequences trimmed using cutadapt.
RNA-seq reads aligning to rRNA were removed using bowtie2 alignment to known dm3 rRNA sequences.
RNA-seq reads aligned to dm3 genome using Tophat 2.0.10.
Small RNA-seq reads aligned to dm3 genome using bowtie1 -v 1.
Count tables and RPKM values performed using easyRNASeq Bioconductor package, with geneModels summarization parameter. Normalized easyRNASeq RPKM values are reported in head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt.
Transposable element quantification performed using RepEnrich software (Criscione et al., BMC Genomics 15:583), using RepBase transposable element annotation.
RNA-seq transposable element normalization, log2 fold change calculation, and differential expression testing was performed using edgeR package, with correction for batch effects as described in edgeR vignette. Normalized counts and log2 Fold Changes are reported in piwi.rnaseq.repenrich.edgeR.txt.
Small RNA-seq transposable element counts were normalized to reads mapping to cisNATs and structured loci, described in Malone et al., Cell 137:522-35. Normalized read counts and log2 fold changes are reported in piwi.pirna.repenrich.antisense.normalized.log2FC.txt.
Rawcounts txt files contain raw read counts output from easyRNASeq or RepEnrich as appropriate.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include Count/RPKM tables.

organism: Drosophila melanogaster

source_name: fat body, piwi2/CyO

growth_protocol: Female flies grown on 15% dextrose, 15% yeast, 2% agar food for 10days post eclosion, passed to new food vials every 2-3 days.

extract_protocol:
Total RNA was isolated using the protocol from the mirVana kit (Ambion).
RNA-seq: 100ng total RNA used as input for Nugen Universal RNA-seq kit, prepped as per manufacturer's instructions using Drosophila rRNA depletion module.
Small RNA-seq: 1ug of total RNA was oxidized with 200mM sodium periodate per Zamore lab protocol (http://www.umassmed.edu/zamore/resources/protocols/), purified with Zymo RNA Minelute cleanup kit, then used as input for NEBNext Multiplex Small RNA Library Prep kit (NEB catalog #7300S) per manufacturer's instructions.

treatment_protocol: Relevant body parts dissected from 25-100 flies. For fat bodies, abdominal cavity was cut open and fat tissue scraped from inside of body wall after discarding ovaries and gut.

tag: genotype/variation

value: fat body

tag: Sex

value: female


title: piwi homozygote smRNA

description:
piwi.hom
Small RNA-seq
Processed data file: piwi.pirna.repenrich.antisense.rawcounts.txt
Processed data file: piwi.pirna.repenrich.antisense.normalized.log2FC.txt

source_name: fat body, piwi2/piwi2


title: Sample36883 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36966 (seq)

description: miRNA-Seq data, FFPE samples


title: WT smRNA

description: Small RNA-seq

source_name: fat body, wild-type

tag: strain/background

value: Canton S

value: wild-type


title: piwi homozygote, rep3

description:
hom.r3
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt
Processed data file: piwi.rnaseq.repenrich.counts.txt
Processed data file: piwi.rnaseq.repenrich.edgeR.txt

tag: age


title: piwi heterozygote, rep3

description:
het.r3
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt
Processed data file: piwi.rnaseq.repenrich.counts.txt
Processed data file: piwi.rnaseq.repenrich.edgeR.txt


title: piwi homozygote, rep1

description:
hom.r1
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt
Processed data file: piwi.rnaseq.repenrich.counts.txt
Processed data file: piwi.rnaseq.repenrich.edgeR.txt


title: piwi homozygote, rep2

description:
hom.r2
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt
Processed data file: piwi.rnaseq.repenrich.counts.txt
Processed data file: piwi.rnaseq.repenrich.edgeR.txt


title: piwi heterozygote, rep1

description:
het.r1
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt
Processed data file: piwi.rnaseq.repenrich.counts.txt
Processed data file: piwi.rnaseq.repenrich.edgeR.txt


title: Sample36896 (seq)

description: miRNA-Seq data, FFPE samples


title: Sample36897 (seq)

description: miRNA-Seq data, FFPE samples


title: Abdomen, rep1

description:
abdomen.r1
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt

source_name: eviscerated abdomen, wild-type

value: eviscerated abdomen


title: ovary, rep3

description:
ovary.r3
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt

source_name: ovary, wild-type

value: ovary


title: Abdomen, rep3

description:
abdomen.r3
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: Head, rep1

description:
heads.r1
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt

source_name: head, wild-type

value: head


title: Sample36938 (seq)

description: miRNA-Seq data, FFPE samples


title: Thorax, rep2

description:
thorax.r2
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt

source_name: thorax, wild-type

value: thorax


title: ovoD1 smRNA

description: Small RNA-seq

source_name: fat body, ovoD1


title: Thorax, rep3

description:
thorax.r3
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: ovary, rep1

description:
ovary.r1
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: Sample36936 (seq)

description: miRNA-Seq data, FFPE samples


title: ovary, rep2

description:
ovary.r2
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: Thorax, rep1

description:
thorax.r1
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: Head, rep3

description:
heads.r3
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: Head, rep2

description:
heads.r2
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: Female round worm of dog

city: Rongchang

first: Guangxu

last: Ma

state: Chongqing

address: xueyuan road 160#

department: veterinary medicine

institute: Southwest university

data_processing:
Illumina Casava1.7 software used for basecalling,dirty raw reads are discarded using a internal software developped by BGI.
Transcriptome de novo assembly is carried out with short reads assembling program - Trinity
The calculation of Unigene expression uses FPKM (RPKM) method (Fragments Per kb per Million reads)
Differentially expressed genes were identified using internal software FPKM and SOAP release 2.21.
Supplementary_files_format_and_content: Microsoft excel files include mRNA number, raw reads counts and normalized mRNA abundance measurements of male and female adult toxocara canis.

organism: Toxocara canis

source_name: round worm of dog

extract_protocol:
High-quality total RNA were extracted from the entire body of a male and a female adult worms using Trizol reagent (Invitrogen, Carlsbad, CA, USA), respectively.
The Illumina RNA-Seq library preparation protocol includes poly-A RNA isolation, RNA fragmentation, reverse transcription to cDNA using random primers, adapter ligation, size-selection from a gel and PCR enrichment

value: Rongchang

value: adult

value: whole body


title: Male round worm of dog

value: male


title: Sodium Acetate Replicate 1

city: Emeryville

first: Ankita

last: Kothari

state: CA

address: 5885 Hollis Str

institute: Lawrence Berkeley National Lab

data_processing:
The resultant bclfiles were converted to Fastq files and demultiplexed using the Illumina CASAVA software v1.18.
The A. venetianus RAG-1 genome (NCBI accession number APPO00000000.1) was uploaded to RAST(26–28) server for annotation. The trimmed and rRNA-depleted RNA-Seq reads were mapped against the RAST-annotated A. venetianus genome using the CLC Bio Genomics Workbench 8.0.2 software (http://www. clcbio. com/products/clcgenomicsworkbench), which re-implemented EdgeR RNA quantification workflow(29).
The reads per kilobase of exon model per million mapped reads (RPKM) method was used to normalize expression of each gene(30). The differential gene expression tests were conducted with tagwise dispersion with the following parameters: length fraction cutoff=0.95, similarity fraction cutoff=0.8, exact test=”all pairs,” reads count filter=5, max P-value=0.01, and minimum fold change value=2.

organism: Acinetobacter venetianus RAG-1 = CIP 110063

source_name: Bacterial

growth_protocol: Acinetobacter venetianus RAG-1 (ATCC 31012) was obtained from ATCC and maintained on E2 medium(23) with either 1 % v/v dodecane(13)  or 0.01 % v/v ethanol(24). Our preliminary data indicated that replacement of the trace metal solution in E2 medium with ferrous chloride lead to increased growth rates and hence E2 medium was supplemented with freshly prepared ferrous chloride (0.05 mg/ml final volume).

extract_protocol:
The extracted RNA was subjected to Turbo DNAse to get rid of any DNA contamination. The RNA obtained was analyzed using Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit. The RIN (RNA Integrity Number) values of all samples were above 9.6 indicating high quality RNA. The total RNA samples were prepared for Illumina Next-Generation Sequencing at the Functional Genomics Lab (FGL, QB3-Berkeley Core Research Facility at University of California, Berkeley). RiboZero kit (Illumina) was used to deplete ribosomal RNA. The treated RNA was re-checked on Bioanalyzer for integrity.
The library preparation was performed on the Apollo 324TM with PrepXTM RNA-Seq Library Preparation Kit (WaferGen Biosystems, Fremont, CA) according to the manufacturer’s recommendation. The resulting samples were quantified using fluorimetry (Qubit, ThermoFischer) and PCR amplified for 18 cycles to incorporate indexes and flow cell-binding regions.
Final libraries were quantified by Qubit, Bioanalyzer and qPCR, pooled at 14 picomolar concentration and sequenced on an Illumina HiSeq2000 using 50 base single read version 3 chemistry.

treatment_protocol: A. venetianus RAG-1 was grown in presence of three different carbon sources, specifically, dodecane (1 % v/v), dodecanol (5mM) and sodium acetate (0.2 %) in triplicates, in 250 ml Erlenmeyer flasks with 50 ml of E2 media. The cells were harvested at mid-log phase, frozen in liquid nitrogen and stored at -80 °C. Total RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

value: Mid log phase cells

value: sodium acetate


title: Dodecanol Replicate 3

value: dodecanol


title: Sodium Acetate Replicate 2


title: Sodium Acetate Replicate 3


title: piwi heterozygote, rep2

description:
het.r2
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt
Processed data file: piwi.rnaseq.repenrich.counts.txt
Processed data file: piwi.rnaseq.repenrich.edgeR.txt


title: Dodecanol Replicate 2


title: Dodecanol Replicate 1


title: Dodecane Replicate 1

value: dodecane


title: Dodecane Replicate 2


title: Dodecane Replicate 3


title: Abdomen, rep2

description:
abdomen.r2
Processed data file: head.thorax.abdomen.ovary.rawcounts.txt
Processed data file: head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt


title: gDNA_ATAC-seq_rep2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

library_source: genomic

data_processing:
library strategy: FANS-ATAC-seq
maize_B73_overground_part_FANS-ATAC-seq_1million_reads were mapped to maize B73_5a and the others to the TAIR 10
Regulatory regions were called by HOTSPOT and footprints identified by pyDNase
Genome_build: TAIR 10
Supplementary_files_format_and_content: *BED file, the identified regulatory regions
Supplementary_files_format_and_content: *BW file, the genome coverage of each sample, BigWig format

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: The Arabidopsis thaliana accession Col-0 and 35S:H2AX-GFP transgenic plants were grown on a vertical plate with ½ LS media and 1% sugar in long day light conditions (16 hours light / 8 hours dark) for 7-8 days.

extract_protocol: Nuclei were isolated by chopping fresh whole seedlings or roots, density gradient centrifugation and then FANS. Tn5 integration were  performed with 50,000 or as less as 500 purified nuclei. Libraries were constructed with 10-13 cycles amplafication of the Tn5 integration products.

tag: ecotype background

value: wild type

value: whole seedlings


title: H2AX-GFP_50k_nuclei_FANS-ATAC-seq_rep2

value: 35S:H2AX-GFP transgenic line


title: Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep2


title: Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep1


title: Col-0_50k_crude_nuclei_FANS-ATAC-seq_rep1


title: Col-0_500_seedling_nuclei_FANS-ATAC-seq_rep2


title: Col-0_50k_root_nuclei_FANS-ATAC-seq_rep1

value: roots


title: Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep1


title: H2AX-GFP_50k_nuclei_FANS-ATAC-seq_rep1


title: gDNA_ATAC-seq_rep1


title: Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2


title: BY_YEPD_PLUS_2

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

data_processing:
Bases were called using HiSeq 2500 Control Software
Quality control was peformed using FastQC options -t 2 -f fastq
Adaptors were trimmed with trimmomatic. LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were alligned to the SGDv4 reference genome using Bowtie.  Options -S -p 30 -v 2 -a
Reads were counted using htseq-count options -f sam -s reverse and differential expression was assessed by DESeq
Genome_build: SGD S288C Reference Genome
Supplementary_files_format_and_content: .txt file of normalized read counts

organism: Saccharomyces cerevisiae

source_name: yeast NAD-RNA

growth_protocol: YEPD- 2% dextrose, minimal- yeast nitrogen base, 1X complete amino acid mixture, 2% dextrosegrown until mid-log; e.g, OD600 ~0.5

extract_protocol:
RNA used for library preparation was treated with Turbo DNase prior to any downstream manipulations.  Total RNA was not depleted of rRNA nor fragmented. Total RNA was either incubated with ADP-ribosylcyclase (or mock-treated as a control) in the presence of the alkyne 4-pentynol.  RNA was re-extracted with phenol:chloroform and ethanol precipitated.  This RNA was then biotinylated using copper sulfate and biotin-peg3-azide, and next extracted and precipitated as before.  Next this RNA-biotin was coupled to magnetic streptavidin beads.
Library preparation was initiated by first strand cDNA synthesis on biotinylated RNA that was coupled to streptavidin beads.  Downstream library preparation was carried out using adaptors/primers described in Zhang et al, 2012 using standard Illumina protocols.

tag: media

value: YEPD media

tag: pulldown method

value: with ADPRC


title: BY_YEPD_PLUS_1


title: BY_YEPD_MINUS_1

source_name: yeast mock RNA control

value: without ADPRC


title: BY_YEPD_PLUS_3


title: Col-0_50k_seedling_nuclei_FANS-ATAC-seq_rep2


title: BY_YEPD_MINUS_3


title: BY_MINIMAL_MINUS_3

value: minimal media


title: BY_YEPD_MINUS_2


title: BY_MINIMAL_MINUS_2


title: BY_MINIMAL_PLUS_2


title: BY_MINIMAL_PLUS_1


title: BY_MINIMAL_PLUS_3


title: Col-0_50k_seedling_nuclei_FANS-ATAC-seq_1million_reads


title: sec63mVenusBirA_deltaSND3_chx_2minBiotin_pulldown

city: Cambridge

first: Jonathan

middle: S

last: Weissman

state: MA

address: 455 Main St

department: HHMI, Biology

institute: Whitehead Institute for Biomedical Research, MIT

description: ribosome protected mRNA fragment

data_processing:
library strategy: ribosome profiling
base calls were called with Illumina CASAVA software
3' adaptor was trimmed using a custom python script
reads were aligned sequentially first to rRNA, then unaligned reads were aligned to tRNA, then unaligned reads were aligned to a genomic index (sacCer3)
expression was quantitated using custom scripts after P-site mapping
Genome_build: sacCer3
Supplementary_files_format_and_content: tab delimited file containing count and rpkm data

growth_protocol: Yeast cells were grown in SD media containing 0.125 ng/ml D-biotin to OD600 .4-.6.

extract_protocol:
Yeast cells were harvested by filtration, flash frozen, and cryogenically pulverized in a Retsch mixer-mill.
Footprinting was performed with RNase I, monosomes purified on 10-50% sucrose gradients and biotinylated ribosomes purified on streptavidin dynabeads. RNA was extracted with trizol and protected fragments gel purified. Ends were repaired with T4 PNK and ligated to a pre-adenylated linker with T4 RNA Ligase 2.  Ligated fragments were gel purified, reverse transcribed and gel purified.  The cDNA was circularized then PCR amplified.

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide for 2 minutes prior to biotin induction with 10 nM biotin for 2 minutes.

tag: strain background

tag: strain info.

value: snd3Δ::NAT sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3Δ0 met15Δ0 his3Δ1


title: sec63mVenusBirA_deltaSND2_chx_2minBiotin_pulldown

description: ribosome protected mRNA fragment

value: snd2Δ::NAT sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3Δ0 met15Δ0 his3Δ1


title: sec63mVenusBirA_deltaSND3_chx_2minBiotin_input

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_deltaSND2_chx_2minBiotin_input

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_deltaSND1_chx_2minBiotin_pulldown

description: ribosome protected mRNA fragment

value: snd1Δ::NAT sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3Δ0 met15Δ0 his3Δ1


title: sec63mVenusBirA_chx_2minBiotin_pulldown

description: ribosome protected mRNA fragment

value: sec63::SEC63-mVenus-BirA::HIS5 rpl16a::RPL16a-HA-TEV-AVI rpl16b::RPL16b-HA-TEV-AVI ura3Δ0 met15Δ0 his3Δ1


title: sec63mVenusBirA_chx_2minBiotin_input

description: ribosome protected mRNA fragment


title: sec63mVenusBirA_deltaSND1_chx_2minBiotin_input

description: ribosome protected mRNA fragment


title: CH-S11

first: Conrad

last: Hodgkinson

address: 210 Research Dr, GSRBII, Box 3718

data_processing:
RNA-seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low quality bases and Illumina sequencing adaptors from the 3’ end of the reads.
Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the GRCm38v68 version of the mouse genome and transcriptome using the STAR RNA-seq alignment tool.
Reads were kept for further analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTseq tool.
Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package with the R statistical programming environment.
Genome_build: GRCm38v68
Supplementary_files_format_and_content: Excel spreadsheet containing Gene ID, Gene Name, Number of reads

organism: Mus musculus

source_name: c-Kit(+) cells from the heart

extract_protocol:
Eight week C57BL6 c-KitCreERT2/mTeG mice were injected for 14 consecutive days with tamoxifen (0.5 mg/day by i.p) to induce Cre expression and to label c-Kit(+) cells with eGFP. Mice underwent MI and two days later were treated with vehicle or Sfrp2. C-Kit(+) cells were isolated one day prior to MI, one day post-MI and 12 days post-MI (vehicle and Sfrp2). Cardiac biopsies were isolated for c-Kit(+) cells.
Total RNA from the purified c-Kit(+) population was isolated using a PicoPure Arcturus kit (Invitrogen). Complimentary cDNA was generated with an Ovation Pico WTA System V2 kit (NuGEN).

value: C57BL/6 c-KitCreERT2/mTeG

value: Heart

tag: time

value: c-Kit(+) cells 1 day post-MI vehicle group_N2


title: CH-S9

value: c-Kit(+) cells 12 days post-MI vehicle group_N3


title: CH-S10

value: c-Kit(+) cells 1 day post-MI vehicle group_N1


title: CH-S8

value: c-Kit(+) cells 12 days post-MI vehicle group_N2


title: CH-S6

value: c-Kit(+) cells 12 days post-MI vehicle group_N1


title: CH-S7

value: c-Kit(+) cells 12 days post-MI Sfrp2 group_N3


title: CH-S5

value: c-Kit(+) cells 12 days post-MI Sfrp2 group_N2


title: BY_MINIMAL_MINUS_1


title: CH-S4

value: c-Kit(+) cells 12 days post-MI Sfrp2 group_N1


title: CH-S3

value: c-Kit(+) cells prior to myocardial infarction (MI)_N3


title: CH-S1

value: c-Kit(+) cells prior to myocardial infarction (MI)_N1


title: RNA-seq_shNTplus 3

first: Aikaterini

last: Nanou

state: Attiki

address: Soranou Efessiou 4

department: Hematology

country: Greece

institute: Biomedial Research Foundation Academy of Athens

description: 1 out of 5 biological replicates

data_processing:
Primer and adapter sequencing were removed, and reads were trimmed if necessary using Trimmomatic (version 0.30).
RNA-seq reads were aligned to mm10 genome assembly using Tophat2 (version 2.0.10) with the following parameters: --b2-very-sensitive, --read-realign-edit-dist 0, -g 2, -G mm10.gtf, -M.
Number of reads per gene were counted using the Htseq-count (version 0.5.4p5) with the following parameters: --mode=intersection-nonempty
DESeq2 (version 1.2) was used for differential expression analysis and libraries were corrected for batch effect (according to their culture dates).
Genome_build: mm10
Supplementary_files_format_and_content: Number of reads per gene were generated using Htseq-count (txt files) and differential expression was performed using DESeq2 (excel files).

molecule: polyA RNA

growth_protocol: Mouse pro-B Ba/F3 cells were routinely cultured in RPMI (with 10% FBS and 1% penicillin-streptomycin) medium supplemented with IL3 at a concentration of 1ng/mL. For IL3 deprivation conditions, cells were cultured with no IL3 for 6 hours, and for IL3 stimulation conditions, cells were cultured with no IL3 for 6 hours and then cultured with 10ng/mL IL3 for 30 minutes.

extract_protocol:
Cells were lysed using Tri Reagent (Sigma T9424) and total RNA was extracted.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation kit v2 (Illumina RS-122-2001) using 1.5ug total RNA according to manufacturer’s instructions.

treatment_protocol: Cells were transduced with lentiviruses expressing different short-hairpin constructs and maintained under puromycin selection (3um/mL) for a minimum of 1 week.

tag: cell line

value: pro-B Ba/F3 cell line

tag: condition

value: IL3 deprivation for 6h and IL3 stimulation for 30min

tag: treatment

value: lentivirus expressing No-Target short hairpin construct


title: CH-S2

tag: tissue

value: c-Kit(+) cells prior to myocardial infarction (MI)_N2


title: RNA-seq_shNTplus 5

description: 1 out of 5 biological replicates


title: RNA-seq_shNTplus 4

description: 1 out of 5 biological replicates


title: RNA-seq_shSTAT5Bplus 3

description: 1 out of 3 biological replicates

value: lentivirus expressing shSTAT5b construct


title: RNA-seq_shNTplus 2

description: 1 out of 5 biological replicates


title: RNA-seq_shNTplus 1

description: 1 out of 5 biological replicates


title: RNA-seq_shLSD1plus 3

description: 1 out of 3 biological replicates

value: lentivirus expressing shLSD1 construct


title: RNA-seq_shLSD1plus 1

description: 1 out of 3 biological replicates


title: RNA-seq_shHDAC3plus 2

description: 1 out of 3 biological replicates

value: lentivirus expressing shHDAC3 construct


title: RNA-seq_shHDAC3plus 3

description: 1 out of 3 biological replicates


title: CH-S12

source_name: cardiomyocytes from the heart

tag: strain

value: C57BL/6 c-KitCreERT2/mTeG

value: Heart

value: Cardiomyocytes sham mice


title: RNA-seq_shSTAT5Aplus 1

description: 1 out of 3 biological replicates

value: lentivirus expressing shSTAT5a construct


title: RNA-seq_shHDAC3plus 1

description: 1 out of 3 biological replicates


title: RNA-seq_shSTAT5Aplus 2

description: 1 out of 3 biological replicates


title: RNA-seq_shSTAT5Bplus 1

description: 1 out of 3 biological replicates


title: RNA-seq_wtBaFplus 5

description: 1 out of 5 biological replicates

value: no treatment


title: RNA-seq_wtBaFplus 4

description: 1 out of 5 biological replicates


title: RNA-seq_wtBaFminus 5

description: 1 out of 5 biological replicates

value: IL3 deprivation for 6h


title: RNA-seq_wtBaFplus 1

description: 1 out of 5 biological replicates


title: RNA-seq_wtBaFminus 3

description: 1 out of 5 biological replicates


title: RNA-seq_wtBaFminus 4

description: 1 out of 5 biological replicates


title: RNA-seq_wtBaFminus 1

description: 1 out of 5 biological replicates


title: input DNA

description: one sample

data_processing:
Primer and adapter sequencing were removed, and reads were trimmed if necessary using Trimmomatic (version 0.30).
ChIP-seq reads were aligned to mm10 genome assembly using Bowtie2 (version 2.1.0) with the following parameters: --end-to-end, --very-sensitive, ---no-unal
Duplicate sequences (which arise from PCR reactions) were removed using Picard (version 1.92).
HOMER suite (version 4.8) was used for creating bedgraph files (for UCSC visualization), peak calling (bed peak files) and peak annotation (excel file containing annotated peaks) at default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files are included for UCSC visualisation, bed files contain the singificant binding events with binding scores and excel files show the annotation details per binding event.

source_name: pro-B Ba/F3_input DNA

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 minutes, lysates were clarified from sonicated nuclei, and protein-DNA complexes were isolated with antibodies.
Library construction was performed as described in Ford et al, 2014. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 5-15 cycles and library fragments of ~250-450 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 Sequencing System.

value: IL3 maintenance

tag: chip antibody


title: RNA-seq_shSTAT5Bplus 2

description: 1 out of 3 biological replicates


title: RNA-seq_shLSD1plus 2

description: 1 out of 3 biological replicates


title: ChIP_HDAC3plus 2

description: per sample 2 biological replicates, and 1 merged library processed and annotated

source_name: pro-B Ba/F3_ChIP_HDAC3plus

value: HDAC3 (Santa Cruz, sc11417X)


title: ChIP_LSD1plus 2

source_name: pro-B Ba/F3_ChIP_LSD1plus

value: LSD1 (Abcam, ab17721)


title: ChIP_HDAC3minus 2

source_name: pro-B Ba/F3_ChIP_HDAC3minus


title: RNA-seq_wtBaFplus 2

description: 1 out of 5 biological replicates


title: ChIP_LSD1plus 1


title: ChIP_HDAC3minus 1


title: RNA-seq_shSTAT5Aplus 3

description: 1 out of 3 biological replicates


title: RNA-seq_wtBaFminus 2

description: 1 out of 5 biological replicates


title: ChIP_LSD1minus 2

source_name: pro-B Ba/F3_ChIP_LSD1minus


title: ChIP_LSD1minus 1


title: RNA-seq_wtBaFplus 3

description: 1 out of 5 biological replicates


title: early G1 rep1

city: Stanford

first: Ansuman

middle: T

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University

description: nascent RNA

data_processing:
Illumina HiSeq 2500 used for basecalling.
Sequenced reads were mapped to mm9 whole genome using BWA v0.7.12 with default parameters.
Convergent transcription peaks were identified using HOMER findPeaks with parameters -style groseq -o auto -uniqmap. Quantification of convergent transcription in these regions was performed as described in (Meng et al., 2014).
Genome_build: mm9
Supplementary_files_format_and_content: BED files include peak regions and levels of convergent transcription

source_name: Primary B cell

growth_protocol: Splenic B cells were purified from Fucci-EGFP+ mouse spleens and activated in vitro by LPS, IL4, and Rp105.

extract_protocol:
Nuclei were extracted from approximately 20 million sorted live B cells in early G1 or non-synchronized cells.
Global run-on and following library preparation for sequencing were done as described with minor modifications (Kaikkonen et al., 2013).

treatment_protocol: Nocodazole (100 ng/ml) was added at 42 hours after isolation. After six hours, synchronized cells were collected and sorted. Sorted EGFP+ cells (mostly G2/M) were put back into culture. After 1.5 hours at 37 °C, cells were collected for sorting early G1 cells.

tag: cell-type

value: in vitro activated primary B cells

value: early G1

tag: genotype

value: Fucci-EGFP+


title: total cell control rep2

description: nascent RNA

value: unsynchronized


title: total cell control rep1

description: nascent RNA


title: ChIP_STAT5Aplus 1

source_name: pro-B Ba/F3_ChIP_STAT5Aplus

value: pro-B Ba/F3 cell line

value: IL3 deprivation for 6h and IL3 stimulation for 30min

value: STAT5a (Santa Cruz, sc1081X)


title: ChIP_STAT5Aminus 2

source_name: pro-B Ba/F3_ChIP_STAT5Aminus


title: ChIP_STAT5Aminus 1


title: ChIP_HDAC3plus 1


title: KO_YAsample2

city: Jena

first: Friedrich

last: Becker

state: Thuringia

address: Beutenberg Strasse 11

department: Stem cell aging

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

description: Gene expression 3 days after injury

data_processing:
Sequencing reads were filtered out for low quality sequences and trimmed of low quality bases by using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit
TopHat software (Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111, doi:10.1093/bioinformatics/btp120 (2009)) was used for mapping sequencing reads to mm9 genome.
Gene quantification was performed by using HT-Seq and differentially expressed genes (DEGs) were estimated by using DESEQ2 (Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169, doi:10.1093/bioinformatics/btu638 (2015); Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15, 550, doi:10.1186/s13059-014-0550-8 (2014))
Genome_build: mm9
Supplementary_files_format_and_content: RefSeq genes were used for annotation. Tab-delimited text files include gene name and read numbers for each sample

source_name: skeletal muscle from hindlimbs

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol:
Total RNA was isolted using the MagMAX 96 total RNA Isolation Kit (Ambion)
Libraries were generated with the TruSeq Stranded Total RNA (RiboZero Gold).

treatment_protocol: Mice were anaesthetized using isoflurane in air and oxygen through a nose cone. For satellite cell activation, muscles were injured by injecting a total volume of 50 µl of 1.2% BaCl2 into approximately 20 sites in the hindlimb muscles

value: Hoxa9 knock-out

value: satellite cells

value: 3-4 months


title: KO_YAsample1

description: Gene expression 3 days after injury


title: Pancreas_i4F_replicate3

city: Madrid

first: Lluc

last: Mosteiro

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

data_processing:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
For RNA-seq total RNA was extracted using the AGPC method (acid guanidinium thiocyanate-phenol-chloroform)
1 µg of total RNA sample was used as provided by the user. Sample RNA Integrity Numbers were in the range 7.4 to 9.4 (average 8.0) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: We treated 5 mice of each strain with 0.2 mg/ml of doxycycline in the drinking water for 7 days

tag: genotype/variation

value: Pancreas


title: KO_OAsample3

description: Gene expression 3 days after injury

value: 22-28 months


title: Pancreas_i4F_replicate5


title: Pancreas_i4F_replicate4


title: Pancreas_i4F_replicate2


title: KO_YAsample3

description: Gene expression 3 days after injury


title: KO_OAsample2

description: Gene expression 3 days after injury


title: Pancreas_i4F_replicate1


title: KO_OAsample1

description: Gene expression 3 days after injury


title: WT_YAsample2

description: Gene expression 3 days after injury

value: wildtype


title: WT_YAsample3

description: Gene expression 3 days after injury


title: WT_YAsample1

description: Gene expression 3 days after injury


title: early G1 rep2

description: nascent RNA


title: Pancreas_p53_KO_replicate5


title: ChIP_STAT5Aplus 2


title: WT_OAsample2

description: Gene expression 3 days after injury


title: WT_OAsample3

description: Gene expression 3 days after injury


title: Pancreas_p53_KO_replicate2


title: Pancreas_p53_KO_replicate1


title: Pancreas_i4F_Ink4a/Arf_KO_replicate5


title: Pancreas_i4F_Ink4a/Arf_KO_replicate4


title: WT_OAsample1

description: Gene expression 3 days after injury


title: KO_FL-HSC(LSK)_rep2

city: new york

first: Xufeng

last: Chen

state: NY

address: 550 First Avenue, Smilow 1307

institute: NYU Langone Medical Center

data_processing:
Base-calls performed using Illumina data processing pipeline (version 1.8)
High-quality, clean reads were generated using the FASTX toolkit pipeline (version 0.0.13), and the resulting high-quality reads were then mapped onto the UCSC using TopHat (version 2.0.9)
The differentially expressed genes were analyzed by using Cufflinks (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: combined matrix table include raw counts and FPKM values for all Samples

source_name: FL-HSC(LSK)

extract_protocol:
FL-HSCs(LSKs) (approximately10,000 cells) were isolated from WT and Uhrf1-/- fetal livers by cell sorting (double sort, purity > 95%). RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US).
Libraries were generated for sequencing using the TruSeq RNA sample preparation kit (Illumina)

value: fetal liver

tag: cell type

value: HSC(LSK)


title: Pancreas_i4F_Ink4a/Arf_KO_replicate3


title: WT_FL-HPC(LK)

source_name: FL-HPC(LK)

value: HPC(LK)

tag: age

value: wild type


title: KO_FL-HSC(LSK)_rep3


title: KO_FL-HSC(LSK)_rep1


title: Kidney_i4F_replicate3

value: Kidney


title: Kidney_i4F_replicate4


title: Pancreas_i4F_Ink4a/Arf_KO_replicate1


title: WT_FL-HSC(LSK)_rep2


title: WT_FL-HSC(LSK)_rep1


title: Pancreas_i4F_Ink4a/Arf_KO_replicate2


title: WT_FL-HSC(LSK)_rep3


title: Kidney_i4F_replicate5


title: Pancreas_p53_KO_replicate3


title: Kidney_i4F_replicate2


title: Kidney_i4F_p53_KO_replicate5


title: Kidney_i4F_replicate1


title: Pancreas_p53_KO_replicate4


title: Kidney_i4F_p53_KO_replicate4


title: rdr6_rep2

city: Nankang

first: Ho-Ming

state: Taipei

address: No. 128, Sec. 2, Academia Road

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
Illumina Casava v1.8  was used for basecalling with default parameters
Sequenced reads were trimmed for adapter sequence using FASTX-Toolkit and raw abundance was counted and included in processed data files if the length of trimmed sequences is over 15 nt.
Supplementary_files_format_and_content: Text files containing trimmed sequences and raw abundance separately by tab

growth_protocol: Arabidopsis thaliana was grown in soil or on 0.8% Bacto-agar plates containing half-strength Murashige and Skoog (MS) medium (pH 5.7) and 1% sucrose under a 16/8-h light/dark cycle at 22°C.

extract_protocol:
Total RNA was extracted from the powder of frozen plant tissues by PureLink Plant RNA Reagent (Thermo Fisher) and MaxTract high-density gel tubes (Qiagen).
PARE libraries were constructed from 80 μg total RNA following the protocol described previously ( Zhai J, Arikit S, Simon SA, Kingham BF, Meyers BC: Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods 2014, 67:84-90).

tag: ecotype background

tag: growth medium

value: soil

value: rdr6 mutant

value: inflorescence


title: ago7_rep2

value: ago7 mutant


title: ago7_rep1


title: WT_rep2

value: wild-type


title: rdr6_rep1


title: Kidney_i4F_p53_KO_replicate3


title: Kidney_i4F_p53_KO_replicate2


title: WT_rep1


title: Kidney_i4F_p53_KO_replicate1


title: inflorescence

source_name: inflorescence

tag: ecotype


title: 11-day-old seedling

source_name: seedling

value: seedling

value: 0.8% Bacto-agar plates containing half-strength Murashige and Skoog (MS) medium (pH 5.7) and 1% sucrose


title: Kidney_i4F_Ink4a/Arf_KO_replicate5


title: Kidney_i4F_Ink4a/Arf_KO_replicate4


title: SK-N-SH_EBF3_WT_FLAG_RXL

description:
ChIP DNA
Wild-type EBF3-FLAG ChIP-Seq (Reverse Crosslink Control).
Processed data file: SKNSH_WT_FLAG_1_peaks.narrowPeak
Processed data file: SKNSH_WT_FLAG_2_peaks.narrowPeak

data_processing:
ChIP-seq reads were aligned using the BWA aligner to hg19.
Peaks were called for each replicate using MACS2.1.03 and parameters --keep-dup 1 --extsize 100 --verbose 3 --down-sample --seed 1 --fix-bimodal --qvalue 0.01 --bw 200 --mfold 10 30 --gsize 2790000000
Overlapping peaks in each replicate peak files for each construct (EBF3 WT or EBF3 P177L) were merged using BedTools overlap.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *peaks.narrowPeak: MACS2.1.03 peak files containing peak location, peak summit position, pileup height at peak summit, and -log10(pvalue) and -log10(qvalue) for the peak.
Supplementary_files_format_and_content: *FLAG_Peaks_overlap_merge.bed: Overlapping peaks determined by BedTools for EBF3 WT or EBF3 P177L.

source_name: SK-N-SH, WT EBF3-FLAG, FLAG ChIP (Reverse Crosslink Control)

extract_protocol:
20x10e6 cells for two biological replicates for each vector were crosslinked in 1% formaldehyde, sonicated to fragment chromatin using the BioRuptor Twin Sonicator (Diagenode), and immunoprecipitated using monoclonal anti-FLAG M2 antibody (Sigma). Samples were reverse-crosslinked and recovered DNA was used as input for Illumina sequencing library preparation.
ChIP-seq was performed as previously described (Reddy et al. 2009).

value: SK-N-SH (ATCC HTB-11)

tag: stable expression

value: WT EBF3-FLAG

value: anti-FLAG(M2) (Sigma-1804, Lot# SLBK1346V)


title: Kidney_i4F_Ink4a/Arf_KO_replicate3


title: Kidney_i4F_Ink4a/Arf_KO_replicate1


title: SK-N-SH_EBF3_P177L_FLAG_Rep_2

description:
ChIP DNA
p.P177L EBF3-FLAG ChIP-Seq.
Processed data file: SKNSH_P177L_FLAG_2_peaks.narrowPeak
Processed data file: SKNSH_EBF3_P177L_FLAG_Peaks_overlap_merge.bed

source_name: SK-N-SH, p.P177L EBF3-FLAG, FLAG ChIP

value: p.P177L EBF3-FLAG


title: SK-N-SH_EBF3_WT_FLAG_Rep_1

description:
ChIP DNA
Wild-type EBF3-FLAG ChIP-Seq.
Processed data file: SKNSH_WT_FLAG_1_peaks.narrowPeak
Processed data file: SKNSH_EBF3_WT_FLAG_Peaks_overlap_merge.bed

source_name: SK-N-SH, WT EBF3-FLAG, FLAG ChIP


title: SK-N-SH_EBF3_P177L_FLAG_Rep_1

description:
ChIP DNA
p.P177L EBF3-FLAG ChIP-Seq.
Processed data file: SKNSH_P177L_FLAG_1_peaks.narrowPeak
Processed data file: SKNSH_EBF3_P177L_FLAG_Peaks_overlap_merge.bed


title: SK-N-SH_EBF3_WT_FLAG_Rep_2

description:
ChIP DNA
Wild-type EBF3-FLAG ChIP-Seq.
Processed data file: SKNSH_WT_FLAG_2_peaks.narrowPeak
Processed data file: SKNSH_EBF3_WT_FLAG_Peaks_overlap_merge.bed


title: Kidney_i4F_Ink4a/Arf_KO_replicate2


title: AR1_651

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

description: transfected with AR1-651 plasimd

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and then mapped to hg19 reference genome using BWA(v0.7.10-r789) with parameters: -o 1 -e 50 -i 50 -L -k 2 -l 31 -t 4 -q 10
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each gene.

source_name: Prostate cancer cell line

growth_protocol: LNCaP prostate cancer cells were cultured in RPMI 1640 (GBICO). Media were supplemented with 10% FBS (BioWest, cat. no. S1580-500) and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (Qiagen). High quality (Agilent Bioanalyzer RIN >7.0) total RNAs were employed for the preparation of sequencing libraries using Illumina TruSeq Stranded Total RNA/Ribo-Zero Sample Prep Kit.
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo (dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: LNCaP cells were transfected with AR1-651 or empty vector as control for 24 hours and cells were treated with or without AIL for the next 12 hours.

value: LNCaP

value: Prostate

value: transfected with AR1-651 plasimd


title: AR1_651_AIL

description: transfected with AR1-651 plasimd and treated with AIL


title: Empty_vector

description: transfected with Empty vector plasimd

value: transfected with Empty vector plasimd


title: AIL

description: transfected with Empty vector plasimd and treated with AIL


title: Activin A +Wnt3a 2h input ChIP-seq

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

description: ChIP DNA

data_processing:
For RNA-seq, paired-end reads were first trimmed the first 15 bps for each end and then mapped to human genome (hg19) using STAR (v2.4.0d), with the following options: --outFilterMultimapNmax 1, --outFilterMismatchNmax 7, --outFilterMismatchNoverLmax0.1, --outFilterMatchNminOverLread 0.4, --alignEndsType EndToEnd. Gene expression was estimated and normalized with Cuffnorm from the Cufflinks package (v2.2.1) into FPKM matrix using default parameters for the annotations GTF file downloaded from GENCODE (v19).
For ChIP-seq, reads were mapped into human genome (hg19) using bowtie (v1.1.0) with the options: -y –k 1 -m 1 –-best –-chunkmbs 200.  MACS (v2.1.0) was used to identity significant binding events for each ChIP-seq data with options: -nomodel -extsize 75 - keep-dup 1 -broad. The bigWig profile fies wre generated by MACS with the setting  -B --SPMR  -g hs --nomodel --extsize 75 --fix-bimodal.
Genome_build: hg19
Supplementary_files_format_and_content: The bigWig profile fies were generated by MACS with the setting  -B --SPMR  -g hs --nomodel --extsize 75 --fix-bimodal. The gene.attr_table.txt and genes.fpkm_table.txt were generated by Cuffnorm using the GENCODE (v19) annotations.

growth_protocol: H1 cells cultured in N2B27-Chemical defined meiudm on matrigel

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 and H3K4me3  antibody.
libraries were set up by Berry Genomics BeiJing

treatment_protocol: And treated with  25ng/ml Activin A, 25ng/ml Wnt3a and both of them for 2h and 6h in B27-Chemical defined medium for H3K27me3, H3K4me3 ChIP-seq.

value: Activin A + Wnt3a 2h

tag: antibody


title: Activin A +Wnt3a 6h input ChIP-seq

description: ChIP DNA

value: Activin A + Wnt3a 6h


title: Control input ChIP-seq

description: ChIP DNA


title: Activin A + Wnt3a 6h  H3K4me3 ChIP-seq

description: ChIP DNA


title: Activin A + Wnt3a 2h  H3K4me3 ChIP-seq

description: ChIP DNA


title: Control H3K27me3 ChIP-seq

description: ChIP DNA


title: Activin A +Wnt3a 24h RNA-seq

description: polyA mRNA

extract_protocol:
H1 cells were lysised with TriZol regent to get RNA
libraries were set up by Berry Genomics BeiJing

treatment_protocol: H1 cells treated with 25ng/ml Activin A, 25ng/ml Wnt3a and both of them for 6h or 24h in B27-Chemical defined medium for 6h and 24h

value: Activin A + Wnt3a 24h


title: Control H3K4me3 ChIP-seq

description: ChIP DNA


title: Wnt3a 24h RNA-seq

description: polyA mRNA

value: Wnt3a 24h


title: Activin A 24h RNA-seq

description: polyA mRNA

value: Activin A 24h


title: Activin A + Wnt3a 6h  H3K27me3 ChIP-seq

description: ChIP DNA


title: SK-N-SH_EBF3_P177L_FLAG_RXL

first: Richard

address: 601 Genome Way

description:
ChIP DNA
p.P177L EBF3-FLAG ChIP-Seq (Reverse Crosslink Control).
Processed data file: SKNSH_P177L_FLAG_1_peaks.narrowPeak
Processed data file: SKNSH_P177L_FLAG_2_peaks.narrowPeak

source_name: SK-N-SH, p.P177L EBF3-FLAG, FLAG ChIP (Reverse Crosslink Control)


title: Wnt3a 6h RNA-seq

description: polyA mRNA

value: Wnt3a 6h


title: Control RNA-seq

description: polyA mRNA


title: Activin A 6h RNA-seq

description: polyA mRNA

value: Activin A 6h


title: YFP+ NKT liver rep3

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

description: DP-specific conditional Rag2-deficient mouse

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using tophat2 (version 2.8.0) with default parameters.
Aligned seqeunces were converted relative expression using cufflinks (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: liver DN invariant NKT

extract_protocol:
Before FACS staining, DN thymocytes were highly purified by depletion of CD4+ and CD8+ and DP thymocytes with AutoMACS. Then, DN NKT cells were FACS sorted using BD FACS Aria, and RNA was prepared using RNeasy Micro Plus kit containing gDNA eliminator columns (Qiagen). RNA was analyzed for quantity and quality using Agilent Bioanalyzer 2100 or Agilent 2200 TapeStation equipment, and 10 ng of total RNA was used with SMARTer Ultra Low Input RNA Kit v3 for Illumina Sequencing (Clontech) for cDNA synthesis.
Illumina TruSeq RNA Sample Prep Kit v2 (Illumina) or ThruPLEX DNA-seq Kit (RUBICON GENOMICS) were used for the construction of sequencing libraries.

value: liver

tag: developmental stage

value: mature invariant NKT cell


title: YFP+ NKT liver rep2


title: YFP+ NKT liver rep1


title: cKO DN NKT liver rep3

description: NKT cells from YFP+ mouse


title: CHLA25-WNT3A_RSPO _Top10percent_2

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

data_processing:
Three biological replicates per sample were used and further three technical replicates for each of the biological sample were sequenced on the Illumina HiSeq 2000 instrument (50 cycle single read). Fastq generation was performed using Illumina’s CASAVA-1.8.2 software. Quality control (QC) analyses were done on the fastq files using FASTQC. The fastq sequences that passed the QC were then aligned to Human genome (Ensembl GRCh37) using Tophat (v.2.0.5) embedded with Bowtie (v.2.2.0) with a maximum number of 2 mismatches. The RNA-seq data was aligned using Sailfish, a rapid alignment-free isoform quantification software. The transcript coverage is accurately estimated using counts of k-mers occurring in reads instead of alignments of reads. The criterion for considering a transcript as expressed was that more than one replicate from at least one sample group have RPKM (reads per kilobase per million mapped reads) greater than 1
Genome_build: (Ensembl GRCh37
Supplementary_files_format_and_content: An excel file with RPKM values

source_name: CHLA25 cells stably transduced with 7TGP vector

growth_protocol: Cells were cultured in RPMI 1640 media (Gibco) supplemented with 10% fetal bovine serum (FBS)(Atlas Biologicals) and 2mM L-glutamine (Life Technologies);  grown on plates coated with 0.2% gelatin.

extract_protocol:
RNA extraction was done using Qiagen's RNEasy kit according to manufacturer's instructions.
RNA-seq libraries were prepared according to Illumina TruSeq standard procedures.
Single end, 50bp length

treatment_protocol: Stably transduced CHLA25-7TGP cells were stimulated with 1:1 RPMI1640 supplemented with 5% FBS and 1% L-glutamine and CM +/- RSPO2 for 48 hours

value: respondin

value: CHLA25-WNT3A Top10 percent

tag: cell line

value: CHLA25 Ewing sarcoma cell line


title: CHLA25-WNT3A_RSPO _Top10percent_3


title: CHLA25-WNT3A_Top10percent_2


title: cKO DN NKT liver rep1

description: NKT cells from YFP+ mouse


title: Activin A + Wnt3a 2h  H3K27me3 ChIP-seq

description: ChIP DNA


title: cKO DN NKT rep3

source_name: thymic DN invariant NKT

value: thymus


title: cKO DN NKT liver rep2

description: NKT cells from YFP+ mouse


title: CHLA25L-CELL_3

value: control


title: cKO DN NKT rep1


title: CHLA25-WNT3A_Top10percent_1


title: YFP+ NKT rep3

description: NKT cells from YFP+ mouse


title: CHLA25L-CELL_1


title: Activin A +Wnt3a 6h RNA-seq

description: polyA mRNA


title: YFP+ NKT rep2

description: NKT cells from YFP+ mouse


title: CHLA25L-CELL_2


title: CC Rice

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
Raw reads were trimmed using trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) with the --clip_R1 9 parameter
Trimmed reads were aligned to their respective reference genomes (TAIR10/MSU7 including mitochondira and chloroplast contigs) using Bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) with the --non_directional parameter
CG/CHG/CHH Methylation was extracted from the bismark BAM file using the bismark_methylation_extractor command using the following parameters; --comprehensive --cytosine_report --bedGraph --CX
Single_C: We used a Perl script to convert the extracted methylation from bismark_methylation_extrator into single-c files for each sequence context (CG, CHG, CHH)
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: MSU7 (Oryza sativa)
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

organism: Oryza sativa

source_name: central cell

growth_protocol: Oryza sativa L. cv. Nipponbare was grown in environmental chambers (K30-7248, Koito Industries, Yokohama, Japan) at 26 °C in a 13/11h light/dark cycle.

extract_protocol:
Rice central cells were isolated according to (Uchiumi et al. 2006 Sex Plant Reprod 19:37-45) with a small modification. Central cells were collected from rice ovules with an incision in the peripheral region. Ovules were incubated in 650 mOsmol/kg H2O mannitol solution containing enzymes (Uchiumi et al. 2006 Sex Plant Reprod 19:37-45) for 30 min to 1 hr at room temperature until the central cell was released from the embryo sac. Central cells with visible polar nuclei and large vacuoles were collected. Rice egg cells were isolated according to (Abiko et al. 2013 J Exp Bot 64:1927-1940). Egg cells released from ovaries with an incision in the basal portion were collected and washed in 370 mOsmol/kg H2O mannitol solution without enzymes.
Bisulfite sequencing libraries were constructed as described in (Smallwood et al. 2014 Nat Methods 11:817-820). We followed the single-cell library preparation protocol using Klenow exo- from Enzymatics (Beverly, MA, USA). Library amplification was performed with 13 PCR cycles using the EPIK Amplification Kit (Bioline GmbH, Germany).

value: central cell

tag: cultivar

value: Nipponbare


title: 60mg_arm_3

city: Dunedin

first: Julia

last: Horsfield

address: 58 Hanover Street

department: Department of Pathology

country: New Zealand

institute: University of Otago

data_processing:
Sequence reads were filtered for quality using trimgalore.
Reads were then mapped to the zebrafish genome using tophat v2.0.9, then assembled and merged with cufflinks v2.2.0 and cuffmerge, respectively.
Differentially expressed transcripts were determined using cuffdiff v2.2.0.
Gene ontology was assessed using BinGO 3.0.3, a plugin for cytoscape v3.3.0.
Genome_build: Zv9

organism: Danio rerio

source_name: Unfertilized eggs

growth_protocol: Zebrafish were maintained under standard conditions

extract_protocol:
The eggs were transferred to tube containing RA1 buffer (Macherey-Nagel, cat. 740955.250) with b-mercaptoethanol, and stored at -80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit (Macherey-Nagel, cat. 740955.250) and bound and eluted with columns (17 - 23,000 nt size range) from the RNA clean and concentrator kit (Zymo cat. no. R1017).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.

value: In house AB/Pet shop

value: Unfertilized eggs

tag: FISH age

value: 9 mpf

tag: treatment arm

value: 60 mg


title: 60mg_arm_2

tag: strain

tag: tissue


title: EC Rice

source_name: egg cell

value: egg cell


title: 5mg_arm_3

value: 5 mg


title: 5mg_arm_2


title: 60mg_arm_1


title: CHLA25-WNT3A_RSPO _Top10percent_1

tag: treatment


title: CHLA25-WNT3A_Top10percent_3


title: 5mg_arm_1


title: DsBgDicer-1_2

city: Barcelona

first: Guillem

last: Ylla

state: Catalonia

address: Passeig Marítim de la Barceloneta, 37

institute: Institute of Evolutionary Biology

data_processing:
Quality control with FastQC
Read filtering and trimming with Trimmomatic
Reads mapping with Bowtie
miRNA counts with FeatureCounts
Genome_build: v1 (Bger_1.0)
Supplementary_files_format_and_content: [.csv] file reports miRNA counts

organism: Blattella germanica

growth_protocol: Blattella germanica specimens used for the whole transcriptome analysis were obtained from a population reared at the Institut de Biologia Evolutiva (CSIC-UPF). Conditions were 70% humidity at 30 ºC and a commercial dog food diet.

extract_protocol:
miRNeasy Mini Kit (Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina®

treatment_protocol: 5-day-old fifth instar female nymphs were treated with a 3µg of dsBgDicer-1 twice, first just after the emergency and secondly 3 days later, and were dissected 2 days after molting to the last (sixth) nymphal instar (Lozano et al 2015). As control we followed the same protocol but injecting dsPolyhedrin.

value: Nymph 6 day 2

value: Whole body


title: cKO DN NKT rep2


title: Control_1

source_name: dsPolyhedrin


title: Control_2


title: DsBgDicer-1_1


title: D.sim smRNA

city: Providence

first: Jason

last: Wood

state: RI

address: 185 Meeting St.

institute: Brown University

description: Small RNA-seq

data_processing:
Basecalling performed with Illumina CASAVA 1.8.
Adapter sequences trimmed using cutadapt.
RNA-seq reads aligning to rRNA were removed using bowtie2 alignment to known dm3 rRNA sequences.
RNA-seq reads aligned to dm3 genome using Tophat 2.0.10.
Small RNA-seq reads aligned to dm3 genome using bowtie1 -v 1.
Count tables and RPKM values performed using easyRNASeq Bioconductor package, with geneModels summarization parameter. Normalized easyRNASeq RPKM values are reported in head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt.
Transposable element quantification performed using RepEnrich software (Criscione et al., BMC Genomics 15:583), using RepBase transposable element annotation.
RNA-seq transposable element normalization, log2 fold change calculation, and differential expression testing was performed using edgeR package, with correction for batch effects as described in edgeR vignette. Normalized counts and log2 Fold Changes are reported in piwi.rnaseq.repenrich.edgeR.txt.
Small RNA-seq transposable element counts were normalized to reads mapping to cisNATs and structured loci, described in Malone et al., Cell 137:522-35. Normalized read counts and log2 fold changes are reported in piwi.pirna.repenrich.antisense.normalized.log2FC.txt.
Rawcounts txt files contain raw read counts output from easyRNASeq or RepEnrich as appropriate.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include Count/RPKM tables.

source_name: fat body, wild-type

extract_protocol:
Total RNA was isolated using the protocol from the mirVana kit (Ambion).
RNA-seq: 100ng total RNA used as input for Nugen Universal RNA-seq kit, prepped as per manufacturer's instructions using Drosophila rRNA depletion module.
Small RNA-seq: 1ug of total RNA was oxidized with 200mM sodium periodate per Zamore lab protocol (http://www.umassmed.edu/zamore/resources/protocols/), purified with Zymo RNA Minelute cleanup kit, then used as input for NEBNext Multiplex Small RNA Library Prep kit (NEB catalog #7300S) per manufacturer's instructions.

value: wild-type

value: fat body

tag: Sex

value: female


first: Robert

last: Schmitz

address: B416 Davison Life Sciences

institute: University of Georgia

data_processing:
library strategy: FANS-ATAC-seq
maize_B73_overground_part_FANS-ATAC-seq_1million_reads were mapped to maize B73_5a and the others to the TAIR 10
Regulatory regions were called by HOTSPOT and footprints identified by pyDNase
Genome_build: TAIR 10
Supplementary_files_format_and_content: *BED file, the identified regulatory regions
Supplementary_files_format_and_content: *BW file, the genome coverage of each sample, BigWig format

organism: Zea mays subsp. mays

extract_protocol: Nuclei were isolated by chopping fresh whole seedlings or roots, density gradient centrifugation and then FANS. Tn5 integration were  performed with 50,000 or as less as 500 purified nuclei. Libraries were constructed with 10-13 cycles amplafication of the Tn5 integration products.

tag: genotype/variation

value: wild type

value: overground parts


title: YFP+ NKT rep1

description: NKT cells from YFP+ mouse

value: thymus

value: mature invariant NKT cell


title: CC Wt Rep 2

growth_protocol: A. thaliana plants homozygous for the DD7:NTF transgene were grown on soil in either a greenhouse or in an environment-controlled room with a long-day photoperiod (16 hr light, 8 hr dark).

extract_protocol:
We emasculated stage 12 A. thaliana flowers, which have yellow anthers that have not dehisced. The emasculated plants were then incubated in an environment-controlled room or in a growth chamber with a long-day photoperiod for 24 hours. Pistils were dissected, opened, and ovules exposed to a protoplasting enzyme solution in a vacuum based on methods described in (Yoo et al. 2007 Nature Protocols 2:1565-1572). Protoplasts were gently pelleted by centrifugation, the supernatant was removed, and the pellet was resuspended in protoplast lysis buffer adapted from (Sheen 1993 Embo Journal 12:3497-3505). Modified procedures based on the INTACT method (Deal and Henikoff 2011 Nat Protoc 6:56-68) were used to purify central cell nuclei. To remove cell debris, samples were pre-incubated with Dynal Protein-G magnetic beads (Invitrogen: 100-03D), which were pelleted by exposure to a magnetic field. The supernatant was removed and incubated with anti-GFP antibodies (Invitrogen: G10362), which were precipitated with Protein-G magnetic beads. Central cell nuclei were dissociated from the anti-GFP beads and stored at -80C.
Bisulfite sequencing libraries were constructed as described in (Smallwood et al. 2014 Nat Methods 11:817-820). We followed the single-cell library preparation protocol using Klenow exo- from Enzymatics (Beverly, MA, USA). Library amplification was performed with 13 PCR cycles using the EPIK Amplification Kit (Bioline GmbH, Germany).

value: central cell

value: Wild-type


title: CC DME

value: DEMETER loss of function mutant


title: D.yak smRNA

description: Small RNA-seq

organism: Drosophila yakuba


title: CC Wt Rep 1


title: NPC_XY8 ATAC-seq

status: Public on Nov 29 2016

first: Howard

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Dermatology

data_processing:
library strategy: ATAC-seq
ATAC adapters and barcodes were trimmed using CutAdapt Software
Sequences were aligned to the mm9 genome using Bowtie2 software
Non-concordant reads and reads mapping to the mm9 blacklist were filtered out
Peaks were called using Macs2 software with a no-shifting model - peaks were called separately for the X chromosome and the autosomes and then merged
Peaks were filtered using IDR software with a  cutoff of 0.05.
Number of allelic reads (SNP-containing reads) per peak was quantified and added to the peak file
Genome_build: mm9
Supplementary_files_format_and_content: mNPC_ATACseq_peaks.bed is the global peak set for all NPC samples combined.  All sequencing reads from NPCs were combined and peaks were called using MACS2 with q>0.001 and enrichment score >5.  Peaks in the mm9 blacklist were removed.

source_name: neural progenitor cells

growth_protocol: NPCs were grown in N2/B27 media supplemented with 10 ng/mL FGF and EGF on 0.2% gelatin coated plates

extract_protocol:
Nuclei were isolated using NP-40-containing buffer and subsequently transposed with adapter-loaded hyperactive Tn5 transposase (Illumina).
Following clean-up transposed fragments were directly amplified and barcoded using Nextera indexes
Libraries were then sequenced using Illumina NextSeq 500 with 2x75 bp reads

tag: strain background

value: 129S1 x Cast:EiJ F1

tag: gender

value: male

tag: cell type

value: clonal hybrid F1 murine neural progenitor cells

tag: cell number

value: 50K per replicate


title: NPC_XY5 ATAC-seq


title: NPC_XY7 ATAC-seq


title: NPC_XY10 ATAC-seq


title: NPC_XY6 ATAC-seq


title: NPC_XY9 ATAC-seq


title: Standard-Low lipid rep4

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Basecalling with Illumina pipeline software (SCS v2.8 / RTA v1.8)
151 bp reads were checked for quality using FastQC.
adapters were clipped with fastx_clipper
bases with quality <30 were removed with fastq_quality_trimmer
de novo assembly with ABySS
reads mapped to the new assembly with BWA-MEM
Reads with mapQ>=20 were counted
Genome_build: de novo assembly with ABySS
Supplementary_files_format_and_content: Matrix of contig methylation enrichment counts

organism: Psammomys obesus

source_name: Hypothalamus Tissue

extract_protocol:
Humane culling, hypothalamus harvest, homogenisation in PBS and trizol extraction followed by column purification.
Methyl Miner enrichment
Illumina ChIP-seq library prep kit

value: hypothalamus

tag: age

value: post natal 16 weeks

tag: diet

value: Standard Lipid


title: Standard-Low lipid rep3


title: Low-Low lipid rep3

value: Low lipid


title: Standard-Low lipid rep1


title: Low-Low lipid rep4


title: Standard-Low lipid rep2


title: Low-Low lipid rep2


title: Low-Low lipid rep1


title: Control 95648

city: Seattle

first: Nathan

middle: J.

last: Sniadecki

state: Washington

address: Box 352600, Mechanical Engineeering

institute: University of Washington

description: Control 95648 95648

data_processing:
raw sequences were aligned to GRC37/hg19 using Tophat
Aligned reads mapping to genes were quantitated with HTseq (http://www-huber.embl.de/HTSeq/doc/overview.html) and converted to count per million (CPM) values using R.
Supplementary_files_format_and_content: CPM

source_name: Non-bone related diseased osteoblasts

growth_protocol: SSC and control osteoblast cell lines were grown from cryogenic vials and cultured in T25 flasks containing Waymouth’s media (Sigma-Aldrich, St Kouism MO, USA) supplemented with 10% fetal bovine serum (Hyclone Laboratories, Logan, UT, USA) and 1% streptomycin/penicillin (Hyclone Laboratories, Logan, UT, USA) in a 37 oC, 5% CO2 incubator. Cells were harvested at 70% confluency for RNA isolation. Next-generation sequencing libraries were prepared from 1.25 µg of total RNA in an automated, high-throughput format using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA).

extract_protocol:
Calvaria samples from craniosynostosis cases were obtained from discarded tissues during surgical reconstructive procedures, whereas control calvaria samples were obtained from discarded tissues from anonymous surgical or autopsy specimens. These samples were then washed with Waymouth media (Sigma-Aldrich, St. Louis, MO, USA) and cleaned of all soft tissue. They were then sliced into thin 3-5 mm diameter pieces and placed in 12-well plates. As the osteoblasts reached confluency, the contents of each 12-well place were trypsinized using 0.05% Trypsin (Gibco Life Technologies, Grand Island, NY, USA) and passaged into T75 flasks. After reaching confluence, the samples were frozen in liquid nitrogen in 90% fetal bovine serum (Gibco Life Technologies, Grand Island, NY, USA) and 10% DMSO (Fisher Scientific, Fair Lawn, NJ, USA).
Illumina stranded, paired end protocol

value: Non-bone related diseased osteoblasts

value: F

tag: age (days)


title: Control 95489

description: Control 95489 95489

value: M


title: Control 95590

description: Control 95590 95590


title: Control 95659

description: Control 95659 95659


title: Control 95541

description: Control 95541 95541


title: Control 95554

description: Control 95554 95554


title: SSC 95581

description: SSC 95581 95581

source_name: Calvarial osteoblast

value: Calvarial osteoblast


title: SSC 95555

description: SSC 95555 95555


title: SSC 95466

description: SSC 95466 95466


title: SSC 95663

description: SSC 95663 95663


title: Control 95692

description: Control 95692 95692


title: SSC 95560

description: SSC 95560 95560


title: SSC 95477

description: SSC 95477 95477


title: SSC 95446

description: SSC 95446 95446


title: SSC 95566

description: SSC 95566 95566


title: SSC 95559

description: SSC 95559 95559


title: SSC 95600

description: SSC 95600 95600


title: SSC 95575

description: SSC 95575 95575


title: SSC 95649

description: SSC 95649 95649


title: NPC_XY14 ATAC-seq

state: CA


title: SSC 95594

description: SSC 95594 95594


title: NPC_XY15 ATAC-seq


title: NPC_XY16 ATAC-seq


title: SSC 95684

description: SSC 95684 95684


title: Control 95465

description: Control 95465 95465


title: NPC_XY13 ATAC-seq


title: SSC 95522

description: SSC 95522 95522


title: NPC_XY11 ATAC-seq


title: Control 95568

description: Control 95568 95568


title: NPC_XX3 ATAC-seq

value: female


title: NPC_XX4 ATAC-seq


title: NPC_XX1 ATAC-seq


title: NPC_XX2 ATAC-seq


title: ESC_XX1 ATAC-seq

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown in medium supplemented with fetal bovine serum (FBS) and mLIF on 0.2% gelatin-coated plates.

value: mouse embryonic stem cells


title: AB630

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description: polyA+ RNA

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
the R2 sequences, used solely for barcode extraction, were not included.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: umitab.txt.gz: single cell expression matrix: Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: Liver cells

growth_protocol: C57bl6 male mice age 2 month were housed under reverse phase cycle, and fasted for 5 hours starting at 7AM.

extract_protocol:
Mouse hepatocytes were isolated by a modification of the two-step collagenase perfusion method of Seglen. Digestion step was performed with Liberase Blendzyme 3 recombinant collagenase (Roche Diagnostics) according to the manufacturer’s instruction.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: Mice were anesthetized with an intraperitoneal injection of a ketamine (100 mg/kg) and xylazine (10 mg/kg) mixture.

value: post natal two months


title: AB1031

description: polyA+ RNA


title: AB1032

description: polyA+ RNA


title: AB1034

description: polyA+ RNA


title: AB942

description: polyA+ RNA


title: AB945

description: polyA+ RNA


title: AB943

description: polyA+ RNA


title: NPC_XY12 ATAC-seq

institute: Stanford University


title: AB1029

description: polyA+ RNA


title: AB631

description: polyA+ RNA


title: AB979

description: polyA+ RNA


title: AB1028

description: polyA+ RNA


title: AB1030

description: polyA+ RNA


title: AB1035

description: polyA+ RNA


title: AB1027

description: polyA+ RNA


title: AB1033

description: polyA+ RNA


title: AB934

description: polyA+ RNA


title: AB932

description: polyA+ RNA


title: AB933

description: polyA+ RNA


title: AB931

description: polyA+ RNA


title: Leaf stressed

city: Passo Fundo

first: Jorge

middle: Fernando

last: Pereira

state: RS

address: Rodovia BR-285, Km 294

country: Brazil

institute: Embrapa Trigo

description:
Leaf_Profiling.xlsx
Leaf_Total_GOAnalysis.xlsx
Root_Leaf_Differential_Expression.xlsx

data_processing:
De novo assembly performed with software GS De Novo Assembler (v 2.6). Assembly parameter: seed step (default value: 12), seed length (default value: 16), seed count (default value: 1), minimum overlap length (default value: 40), minimum overlap identity (default value: 90), alignment identity score (default value: 2), alignment difference score (default value: -3).
cDNA / Transcriptome options: isogroup threshold (default value: 500 contigs), isotig threshold (default value: 100 isotigs), isotig contig count threshold (default value: 100 contigs), isotig contig length threshold (default value: 3 base pairs)
Singletons cleaning: software SeqClean, Lucy (parameter: minimum length 100 bp)
Blast (Basic Local Alignment Search Tool) (E-value: 1.0E-3)
GO assignment
Genome_build: see Leaf_Total.fasta and Root_Total.fasta linked as supplementary files on the Series record.
Supplementary_files_format_and_content: [Root_Profiling.xlsx] Excel sheet containing the number of transcripts detected in roots under control and drought conditions
Supplementary_files_format_and_content: [Leaf_Profiling.xlsx] details of the isotigs detected in leaves
Supplementary_files_format_and_content: [Root_Total_GOAnalysis.xlsx] Excel sheet containing the GO analysis of the root-derived transcripts detected in control and stressed conditions
Supplementary_files_format_and_content: [Leaf_Total_GOAnalysis.xlsx] Excel sheet containing the GO analysis of the leaf-derived transcripts detected in control and stressed conditions
Supplementary_files_format_and_content: [Root_Leaf_Differential_Expression.xlsx] Excel sheet containing the statistical analysis to detect the differentially expressed transcripts under drought in roots and leaves

organism: Triticum aestivum

source_name: Wheat leaves with 5 weeks-old.

growth_protocol: Germinated seeds were transferred to pots (3 seeds per pot) containing 6.5 kg of a mixture of soil, sand and vermiculite (2:1:1) and incubated in a glasshouse with natural light at 22 ± 4°C. Plants were watered daily. Control plants were grown for five weeks at 100% of field capacity.

extract_protocol:
Total RNA was extracted with TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions, and purified using an RNeasy Mini Kit (Qiagen). During the purification, one DNase digestion step was performed with an RNase-free DNase Set (Qiagen).
Total RNA was sent to Macrogen Inc (South Korea) for construction of cDNA libraries.

treatment_protocol: Germinated seeds were transferred to pots (3 seeds per pot) containing 6.5 kg of a mixture of soil, sand and vermiculite (2:1:1) and incubated in a glasshouse with natural light at 22 ± 4°C. Plants were watered daily. In the stress treatment, plants were watered for 2 weeks at 75% of field capacity followed by 3 weeks of water deprivation.

value: MGS1 Alianca

tag: growth stage

value: Tillering stage

tag: stress

value: drought

value: leaf


title: AB914

description: polyA+ RNA


title: Leaf control

tag: cultivar

value: control


title: AB913

description: polyA+ RNA


title: Root stressed

description:
Root_Profiling.xlsx
Root_Total_GOAnalysis.xlsx
Root_Leaf_Differential_Expression.xlsx

source_name: Wheat root system with 5 weeks-old.

value: root


title: ESC_XY2 ATAC-seq

city: Stanford

value: 129S1 x Cast:EiJ F1

value: male

tag: cell line

value: 50K per replicate


title: AB1036

description: polyA+ RNA


title: AB980

description: polyA+ RNA


title: AB944

description: polyA+ RNA


title: AB911

description: polyA+ RNA