title: D.melanogaster input DNA (with transgenic D.virilis roX1)

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

description:
Trans-VIR-roX1-input.bedGraph
Trans-VIR-roX1-input.bw

data_processing:
Data processing was performed following the ChIRP-seq pipeline (Chue et al., 2011). Reads were trimmed for adaptor sequence, mapped using bowtie to the respective Drosophila spp. genome, and Even and Odd pairs were merged. ChIRP-seq peaks were called using MACS2.
Fastq > bedGraph > bigWig
Genome_build: multiple: melanogaster = dm3, willistoni = dwil_r1.3, virilis = dvir-all-r1.2, busckii = Dbus_genome_assembly.fa; see Supplementary Information
Supplementary_files_format_and_content: Processed merged and input ChIRP-seq tracks (bedGraph and bigWig)
Supplementary_files_format_and_content: Called ChIRP-seq peaks (roX binding sites; bed format)
Supplementary_files_format_and_content: Genome assembly (fasta format) and genome annotation (bed format) are included for D.busckii
Supplementary_files_format_and_content: Müller element (chromosome arm) assignments for genome assemblies are included for all species
Supplementary_files_format_and_content: all roX1 and roX2 sequences used in this analysis are included in text format

source_name: D.melanogaster mixed-sex wandering 3rd instar larvae

growth_protocol: Larvae were raised at room temperature on standard cornmeal molasses or Wheeler-Clayton medium. Larvae were collected at wander third instar larval stage.

extract_protocol:
DNA was extracted from recovered chromatin fraction by ChIRP by gentle elution with Rnase A and H, proteinase K digestion, and phenol-chloroform extraction.
ChIRP-seq libraries were prepared using NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina with standard TruSeq adapters.

value: whole larvae

tag: developmental stage

value: third instar larval stage

tag: gender

value: mixed


title: Sample 25

status: Public on Jan 25 2016

type: SRA

city: Tjelle

first: Tina

middle: Sorensen

last: Dalgaard

address: Blichers Allé 20

department: Department of Animal Science

country: Denmark

institute: Aarhus University

library_source: transcriptomic

data_processing:
Initial control quality was assessed by the FastQC software version 0.11.3
Raw reads were than trimmed for low quality bases using the Trimmomatic tool version 0.32 applying minimum Phred quality score >10 averaged across the sliding window of five bases. Furthermore, all reads with the length below 40 bp were removed.The following settings for Trimmomatic were used:SLIDING WINDOW:5:10 MINLEN:40
The trimmed reads were mapped to the Gallus gallus reference genome (Gallus_gallus-4.0, release 80 ) using a spliced aligner TopHat2 version 2.014. The Gallus gallus gene annotation used for mapping was retrieved from Ensembl database version 80 (www.ensembl.org). The mapping quality was assessed using a set of Python scripts within the RSeQC toolkit.
Gene count estimation was performed using the HTSeq-count tool in ‘union’ mode. The HTSeq-count is a Python script within the HTSeq framework, version 0.7.1, which is an open source toolkit that allows the input of raw counts from aligned reads to be annotated with gene names based on genomic features.
The read counts obtained were used to estimate gene expression and identify differentially expressed (DE) genes. This was achieved using Bioconductor package edgeR version 3.10.0 and limma version 3.24.5 following a previously described protocol Anders et al. 2013 (Nature Protocols)
Genome_build: Gallus_gallus-4.0, release 80
Supplementary_files_format_and_content: tab-delimited text files include raw gene count values for Sample

molecule: total RNA

organism: Gallus gallus

source_name: L10H_6 wks old_infected bird_spleen

extract_protocol:
Tissue samples were homogenized on a TissueLyzer LT (Qiagen, Hilden, Germany). Total RNA was extracted with the Qiagen RNAeasy Kit (Catalog ID 74104, Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions. The quality of the 64 total RNA samples was verified using a 2200 TapeStation RNA Screen Tape device (Agilent, Santa Clara, CA, USA) and the concentration ascertained using an ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). Libraries were prepared with the Illumina TruseqRNA sample prep kit (Catalog ID FC-122-1001, Illumina, San Diego, USA) following the manufacturer’s protocol and evaluated with the Agilent Tape Station 2200. Libraries were quantified by Picogreen and then normalized to 10 nM as recommended by Illumina for cluster generation on the Hiseq2000. Equimolar amounts of each library were mixed before NaOH denaturation. The Illumina Truseq PE cluster kit v3 (Catalog ID PE-401-3001) was used to generate clusters on the grafted Illumina Flowcell and the hybridized libraries were sequenced on six lines of a Flowcell on the Hiseq2000 with 100 cycles of a paired-end sequencing module using the Truseq SBS kit v3 (Catalog ID FC-401-3001).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: chicken line

tag: genotype/variation

value: high serum concentration of mannose-binding lectin (MBL)

tag: infected with

value: infectious bronchitis virus (IBV) at age of 3 wks

tag: time point

value: 6 weeks old (3 wks post infection)

tag: tissue

value: spleen


title: Sample 14

source_name: L10H_4 wks old_infected bird_spleen

value: 4 weeks old (1 wk post infection)


title: Sample 23

source_name: L10H_6 wks old_uninfected bird_spleen

value: none (uninfected control)


title: D.melanogaster input DNA (with transgenic D.melanogaster roX2 with mutated stem-loops)

city: Stanford

state: CA

country: USA

institute: Stanford University

description:
Trans-MEL-roX2mut-input.bedGraph
Trans-MEL-roX2mut-input.bw

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster


title: Sample 12


title: D.melanogaster roX2-mutated (Odd) ChIRP-seq  (with transgenic D.melanogaster roX2 with mutated stem-loops)

description:
Trans-MEL-roX2mut-merge.bedGraph
Trans-MEL-roX2mut-merge.bw


title: Sample 11


title: D.melanogaster roX2-mutated (Even) ChIRP-seq  (with transgenic D.melanogaster roX2 with mutated stem-loops)


title: Sample 10


title: Sample 9


title: Sample 8

source_name: L10H_4 wks old_uninfected bird_spleen


title: Sample 7


title: D.melanogaster roX2 (Odd) ChIRP-seq (with transgenic D.melanogaster roX2)

description:
Trans-MEL-roX2-merge.bedGraph
Trans-MEL-roX2-merge.bw


title: Sample 5


title: Sample 4


title: Sample 1


title: D.melanogaster roX2 (Even) ChIRP-seq (with transgenic D.melanogaster roX2)


title: D.melanogaster input DNA (with transgenic D.melanogaster roX1)

description:
Trans-MEL-roX1-input.bedGraph
Trans-MEL-roX1-input.bw


title: Sample 3


title: Control patient 5

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

data_processing:
Sequence data quality check was performed using fastqc (v1.0.0). The RNA-seq data were mapped to the hg19 reference genome using Tophat for Illumina15 (v1.5) with default options.
Assembly of transcripts and estimation of their abundance (FPKM: fragments per kilobase of exon per million fragment mapped) were calculated using Cufflinks software (v0.0.6).
Genome_build: hg19
Supplementary_files_format_and_content: Output files from Cufflinks include FPKM values (tabulated text files)

organism: Homo sapiens

source_name: small intestine

extract_protocol:
Preterm patients who underwent bowel resection for stage III acute NEC were referred to as NEC, and preterm patients who underwent resection for diseases other than NEC were included as control patients. Fresh resected intestinal tissues were conserved in RNAlater (ambion). RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries according to the manufacturer instructions..

value: ileum

tag: gestational age

value: 39 weeks

tag: pathology

value: Small intestinal atresia


title: Control patient 4

value: 33 6/7 weeks

value: Bowel obstruction


title: Control patient 3

value: 26 5/7 weeks

value: Meconiumileus


title: D.melanogaster roX1 (Odd) ChIRP-seq (with transgenic D.melanogaster roX1)

description:
Trans-MEL-roX1-merge.bedGraph
Trans-MEL-roX1-merge.bw


title: Control patient 2

value: 26 6/7 weeks

value: Milk curd syndrome


title: Sample 6


title: Sample 13


title: Sample 2


title: D.melanogaster roX1 (Even) ChIRP-seq (with transgenic D.melanogaster roX1)

value: whole larvae

value: third instar larval stage


title: D.melanogaster input DNA (with transgenic D.busckii roX2)

description:
Trans-BUS-roX2-input.bedGraph
Trans-BUS-roX2-input.bw

value: mixed


title: D.melanogaster input DNA (with transgenic D.melanogaster roX2)

description:
Trans-MEL-roX2-input.bedGraph
Trans-MEL-roX2-input.bw


title: sRNAs from HeLa cells transfected with (siDIS3L2 + siTUT1) and antimiR-67

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description: Samples 5 to 10 were prepared and sequenced at the same time

data_processing:
Base calling was performed using CASAVA 1.8.2
Sequencing reads were first preprocessed using the Dustmasker program and FASTX-Toolkit to filter out low complexity reads and remove instances of the 3' adapter, respectively.
Before further analysis, reads corresponding to the exogenous siRNA and antimiR sequences were also excluded.
Remaining reads of at least 15 nt in length were then mapped to the human genome using Bowtie 1.0.0, by permitting up to 1 mismatch in the first 15 nucleotides of each read. Only alignments from the lowest mismatch-stratum were recorded provided they didn't exceed a total number of 9 mismatches and reads that could map to more than 50 loci were discarded.
From there, all known human miRNAs (miRBase v.20) were annotated using BEDTools 2.16.2 by comparing their genomic coordinates to those of the aligned reads, and by keeping reads with at least 80 % of their length inside the genomic feature.
By doing so, we were able to inventory and quantify all miRNA isoforms. During the quantification process, multiple mapped reads were weighted by the number of mapping sites in miRNAs and the annotations of miR-27a-3p and miR-27b-3p were manually curated to redistribute the few sequences that were initially misattributed between the two (most probably due to the loose constraints applied on the 3' read ends during the mapping step).
To further characterize the TIMD mechanism of miR-27a and b, only isoforms corresponding to the wild-type (WT) mature sequence (as defined in miRBase) of these miRNAs, as well as the ones presenting with shifted 3' extremities were taken into account, providing that they showed a 5' genome matched component and a potential 3' tail (addition of non-templated nucleotides).
These sequences were classified as: WT, trimming, tailing, trimming+tailing, cleavageshift, and cleavageshift+tailing.
We then computed a tailing ratio by dividing all tailed sequences (tailing, trimming+tailing, cleavageshift+tailing) by the number of WT sequences, and a trimming ratio by dividing all trimmed sequences (trimming and trimming+tailing) by the number of WT sequences for each isoform.
We then calculated the fold change of the tailing ratio of cells transfected with the antimiR-27 to the one of cells transfected with the control antimiR-67. This fold change was then normalized to the control siRNA (against RLUC) condition, which was set to 1.
The same was done for the trimming ratio.
Genome_build: GRCh37/hg19 (UCSC repository)
Supplementary_files_format_and_content: Annotation files of miR-27a-3p and miR-27b-3p are provided in tab-delimited format for each sample (*-miR-27-annot.txt: MiR, KeptForTIMD, Read#, FullSeq (=Full Sequence), FullLg (=Full Sequence Length), 5GMSeq (=5' Genome Matched Sequence), 3TailSeq (=3' Tail Sequence), TrimLg (=Trimming Length), 3TailLg (=3' Tail Length), Category)

source_name: HeLa cell line

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% (v/v) fetal calf serum at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using Tri-Reagent Soluction (MRC, Inc) according to the manufacturer's instruction except the precipitation step, which is done in presence of 3 volumes absolute ethanol and 0.05 volumes 3M NaAc [pH 5]. RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent), and samples with an RNA integrity number higher than 8 were used for the study.
The Illumina's Truseq small RNA protocol (# 15004197 Rev. C) was used to generate small RNA libraries directly from total RNAs, suitable for subsequent high throughput sequencing. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNAs ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 15 sec at 72°C] x 13 cycles; 10 min at 72°C) to create cDNA constructs. This process selectively enriched those fragments that have adapter molecules on both ends. The last step was an acrylamide gel purification of the 140-150 nt amplified cDNA constructs (corresponding to cDNA inserts from small RNAs + 120 nt from the adapters). Small RNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

treatment_protocol: 0.5x10^6 HeLa cells were seeded in 6-well plates and transfected twice (at day 1 and day 2) with 50 nM of each siRNA using Dharmafect-3 (Dharmacon). On day 3, cells were re-seeded in 6-well plates to be at 50% confluence and allowed to adhere during 10 hours. Then, HeLa cells were transfected with 5 nM antimiR using lipofectamine 2000. Samples were collected 16 hours after the antimiR transfection.

tag: cell type

value: HeLa

tag: sirna treatment

value: siDIS3L2 + siTUT1, 100 nM

tag: antimirna treatment

value: control antimiR (antimiR-67), 5 nM


title: NEC patient 7

value: 25 4/7 weeks

value: acute preterm NEC


title: NEC patient 9

value: ileum

value: 29 2/7 weeks


title: sRNAs from HeLa cells transfected with siDIS3L2 and antimiR-67

treatment_protocol: 0.5x10^6 HeLa cells were seeded in 6-well plates and transfected twice (at day 1 and day 2) with 100 nM siRNA using Dharmafect-3 (Dharmacon). On day 3, cells were re-seeded in 6-well plates to be at 50% confluence and allowed to adhere during 10 hours. Then, HeLa cells were transfected with 5 nM antimiR using lipofectamine 2000. Samples were collected 16 hours after the antimiR transfection.

value: siDIS3L2, 100 nM


title: sRNAs from HeLa cells transfected with (siDIS3L2 + siTUT1) and (antimiR-27 + antimiR-16)

value: antimiR-27 + antimiR-16, 5 nM


title: sRNAs from HeLa cells transfected with siDIS3L2 and (antimiR-27 + antimiR-16)


title: sRNAs from HeLa cells transfected with siRLuc and (antimiR-27 + antimiR-16) 2

value: control siRNA (siRLuc), 100 nM


title: NEC patient 8

value: 29 6/7 weeks


title: NEC patient 5

value: 24 6/7 weeks


title: NEC patient 4

value: 27 2/7 weeks


title: sRNAs from HeLa cells transfected with siRLuc and antimiR-67 2


title: NEC patient 6

value: 26 2/7 weeks


title: NEC patient 2

value: 25 3/7 weeks


title: MT2

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

country: China

institute: Huazhong Agricultural University

data_processing:
Small RNA library construction and deep sequencing was as described previously [PMID 18766170]. Briefly, after PAGE purification of small RNA molecules (18-30 bases) and ligation of a pair of Solexa adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 17 cycles and fragments of around 90 bp (small RNA + adaptors) were isolated from agarose gels. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. The image files generated by the sequencer were then processed to produce digital-quality data. After masking of adaptor sequences and removal of contaminated reads, clean reads were processed for computational analysis.
README.txt available on a Series records

organism: Citrus trifoliata

source_name: MT_shoot meristems_adult

growth_protocol: Precocious trifoliate orange and its wild-type samples were collected in the experiment fields of the National Citrus Breeding Center at Huazhong Agricultural University. The seeds of the mutant and its wild-type were planted in 20-cm pots containing a potting mix of a commercial medium (PeiLei, China) and perlite at a ratio of 3:1. The juvenile potted seedlings were then transplanted and grown under field conditions. These juvenile trees were watered regularly with nutrient solution. Shoot meristems of the juvenile mutant trees and its wild-type were collected in June. Lateral buds of spring shoot (in citrus, there are three flushes during the growing season, and the spring flush is the most important one for growth and flower formation, these buds develop to a spring shoot in the next year) of the mutant and its wild-type trees were collected after self-pruning in April next year. All materials were collected from three individual plants and immediately frozen in liquid nitrogen and stored at –80 °C until analyzed.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, USA). A 1.2% agarose gel, stained by ethidium bromide, was run to preliminarily indicate the integrity of the RNA. All RNA samples were quantified and examined for protein contamination (A260/280) and reagent contamination (A260/230) by a Nanodrop ND 1000 spectrophotometer. In addition, the RIN (RNA integrity number) determined by the Agilent Technologies 2100 Bioanalyzer was greater than 8.5 for all samples.Small RNA library construction and deep sequencing was as described previously [PMID 18766170]. Briefly, after PAGE purification of small RNA molecules (18-30 bases) and ligation of a pair of Solexa adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 17 cycles and fragments of around 90 bp (small RNA + adaptors) were isolated from agarose gels. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. The image files generated by the sequencer were then processed to produce digital-quality data. After masking of adaptor sequences and removal of contaminated reads, clean reads were processed for computational analysis.

value: early flowering mutant

tag: sample collection time

value: April following year

value: Shoot meristems

value: adult stage


title: sRNAs from HeLa cells transfected with siTUT1 and (antimiR-27 + antimiR-16)

description: Samples 1 to 4 were prepared and sequenced at the same time

value: HeLa

value: siTUT1, 100 nM


title: NEC patient 3

value: acute preterm NEC


title: Control patient 1

value: ileum

value: 33 5/7 weeks

value: Small intestinal perforation


title: WT1

department: College of Horticulture and Forestry Science

source_name: WT_shoot meristems_juvenile

value: wild type

value: June

value: shoot meristems

value: juvenile stage


title: WT2

source_name: WT_shoot meristems_adult


title: MT1

source_name: MT_shoot meristems_juvenile


title: D.busckii roX2 (Odd) ChIRP-seq (with transgenic D.busckii roX2)

description:
Trans-BUS-roX2-merge.bedGraph
Trans-BUS-roX2-merge.bw

organism: Drosophila busckii

source_name: D.busckii mixed-sex wandering 3rd instar larvae

value: whole larvae

value: third instar larval stage

value: mixed


title: sRNAs from HeLa cells transfected with siTUT1 and antimiR-67

value: control antimiR (antimiR-67), 5 nM


title: NEC patient 1

value: 32 weeks


title: sRNAs from HeLa cells transfected with siRLuc and (antimiR-27 + antimiR-16)

value: control siRNA (siRLuc), 100 nM

value: antimiR-27 + antimiR-16, 5 nM


title: sRNAs from HeLa cells transfected with siRLuc and antimiR-67

value: HeLa


title: D.busckii input DNA

data_processing:
Data processing was performed following the ChIRP-seq pipeline (Chue et al., 2011). Reads were trimmed for adaptor sequence, mapped using bowtie to the respective Drosophila spp. genome, and Even and Odd pairs were merged. ChIRP-seq peaks were called using MACS2.
Fastq > bedGraph > bigWig
Genome_build: multiple: melanogaster = dm3, willistoni = dwil_r1.3 (Flybase), virilis = dvir-all-r1.2 (Flybase), busckii = Dbus_genome_assembly.fa; see Supplementary Information
Supplementary_files_format_and_content: Processed merged and input ChIRP-seq tracks (bedGraph and bigWig)
Supplementary_files_format_and_content: Called ChIRP-seq peaks (roX binding sites; bed format)
Supplementary_files_format_and_content: Genome assembly (fasta format) and genome annotation (bed format) are included for D.busckii
Supplementary_files_format_and_content: Müller element (chromosome arm) assignments for genome assemblies are included for all species
Supplementary_files_format_and_content: all roX1 and roX2 sequences used in this analysis are included in text format


title: D.busckii roX1 (Odd) ChIRP-seq

description:
BUS-roX1.merge.bedGraph
BUS-roX1.merge.bw


title: D.virilis roX1 (Odd) ChIRP-seq (with transgenic D.virilis roX1)

description:
Trans-VIR-roX1-merge.bedGraph
Trans-VIR-roX1-merge.bw

organism: Drosophila virilis

source_name: D.virilis mixed-sex wandering 3rd instar larvae


title: D.melanogaster roX2 (Odd) ChIRP-seq

description:
MEL-roX2.merge.bedGraph
MEL-roX2.merge.bw
Dmel.293_peaks-500bp.bed


title: D.melanogaster roX1 (Even) ChIRP-seq

description:
MEL-roX1.merge.bedGraph
MEL-roX1.merge.bw


title: D.melanogaster roX1 (Odd) ChIRP-seq


title: D.melanogaster input DNA


title: D.busckii roX2 (Even) ChIRP-seq

description:
BUS-roX2.merge.bedGraph
BUS-roX2.merge.bw
Dbus.269_peaks-500bp.bed


title: D.busckii roX2 (Odd) ChIRP-seq


title: D.melanogaster roX2 (Even) ChIRP-seq


title: D.virilis roX1 (Even) ChIRP-seq (with transgenic D.virilis roX1)


title: D.busckii roX1 (Even) ChIRP-seq


title: D.virilis input DNA


title: D.willistoni roX2/3 (Odd) ChIRP-seq

description:
WIL-roX2.merge.bedGraph
WIL-roX2.merge.bw
Dwil.528_peaks-500bp.bed

organism: Drosophila willistoni

source_name: D.willistoni mixed-sex wandering 3rd instar larvae


title: D.virilis roX2 (Odd) ChIRP-seq

description:
VIR-roX2.merge.bedGraph
VIR-roX2.merge.bw
Dvir.309_peaks-500bp.bed


title: D.willistoni input DNA


title: D.willistoni roX1 (Odd) ChIRP-seq

description:
WIL-roX1.merge.bedGraph
WIL-roX1.merge.bw


title: D.virilis roX2 (Even) ChIRP-seq


title: D.willistoni roX1 (Even) ChIRP-seq


title: D.virilis roX1 (Odd) ChIRP-seq

description:
VIR-roX1.merge.bedGraph
VIR-roX1.merge.bw


title: D.busckii roX2 (Even) ChIRP-seq (with transgenic D.busckii roX2)


title: D.virilis roX1 (Even) ChIRP-seq


title: YY super-males

status: Public on Jan 24 2016

city: Wuhan

first: Jie

last: Mei

state: Hubei

address: No.7, Donghu South Road, Wuchang District

department: Institute of Hydrobiology

institute: Chinese Academy of Sciences

data_processing:
The raw sequenced sequences (sequ-seqs) were subjected to Illumina pipeline filter.
After removing adapter sequences and low-quality reads, high-quality reads between 16 and 30 nt in length were processed for bioinformatics analysis with a proprietary software package: ACGT101-miR v4.2 (LC Sciences, Houston, USA).
The sequencing sequences (sequ-seqs) were searched against pre-miRNA (pre-miR) and mature miRNA (miR) sequences from selected species (Deuterostoma) listed in the miRBase v20.0 (http://www.mirbase.org/).  The selected species are:  Danio rerio; Cyprinus carpio; Fugu rubripes; Mus musculus; Homo sapiens; Canis familiaris; Xenopus tropicalis; Taeniopygia guttata; Monodelphis domestica; Equus caballus; Gallus gallus; Tetraodon nigroviridis; Anolis carolinensis; Sus scrofa; Ornithorhynchus anatinus; Bos Taurus; Pan troglodytes; Cricetulus griseus; Oryzias latipes; Rattus norvegicus; Petromyzon marinus; Gorilla gorilla; Macaca mulatta; Pongo pygmaeus; Sarcophilus harrisii; Paralichthys olivaceus; Branchiostoma florida; Branchiostoma belcheri; Ciona intestinalis; Xenopus laevis; Hippoglossus hippoglossus; Ovis aries; Ciona savignyi; Saccoglossus kowalevsk; Strongylocentrotus purpu; Pan paniscus; Ateles geoffroyi; Macaca nemestrina; Saguinus labiatus; Oikopleura dioica; Lemur catta; Lagothrix lagotricha; Artibeus jamaicensis; Xenoturbella bocki.
Reads mapped to mRNA in NCBI Genebank, non-coding RNAs (rRNA, tRNA, snoRNA, snRNA and others) in Rfam (http://rfam.janelia.org) and repetitive sequence elements in RepBase (www.girinst.org/repbase) were removed before further analysis.
Flanking sequences from each mapping locus were subjected to secondary structure analysis using RNAfold (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi) with the default folding criteria.
Genome_build: miRBase v20.0
Supplementary_files_format_and_content: txt files include abundance measurements for each sample

organism: Tachysurus fulvidraco

source_name: gonad

extract_protocol:
Gonad tissues were taken from each individual of XX females, XY males, YY super-males. Total RNA was isolated from each sample by a Qiagen miRNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol and standardized to a concentration of 1 μg/μL. RNA from the same type tissues was combined into one RNA pool, whose quality and quantity was measured with NanoDrop 2000 and Agilent 2100 Bioanalyzer.
Three small RNA libraries were constructed with these three RNA pools using the TruSeq Small RNA Sample Preparation Kits. Briefly, total RNA was ligated with a 3' RNA adaptor and then with a 5' RNA adaptor. PCR amplification after reverse transcription was performed to enrich the fragments that had adaptors on both ends. Subsequently, the cDNA constructs were purified and enriched with 6% denaturing polyacrylamide gel electrophoresis to isolate the expected size fractions and eliminate dimerized adaptors. Finally, these three RNA libraries were sequenced using an Illumina/Solexa Genome Analyzer

tag: age

value: one-year-old

value: testis

value: YY


title: XY males

value: XY


title: Biorep_2_48_hours paired-end

status: Public on Jan 23 2016

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

description: This sample was sequenced twice to increase the number of reads.  Only reads that map to the viral genome are reported here.

data_processing:
filtering using Trimmomatic V0.30 to remove adaptor sequences and low quality reads.  Parameters: -phred33 ILLUMINACLIP:truseqv2_sequences.fa:2:40:15 LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:55
Perform RNAseq analysis using CLC Genomics Workbench 8.0 and the MacoNPV-A 90/2 (genbank accession U59461 AF467808 GI:20043274) reference genome. Use the paired reads from both runs.  Parameters:  Mapping type="map to gene regions only"; Mismatch cost=2; Insertion cost=3, Deletion cost=3; length fraction=0.8; similarity fraction=0.8; Global Alignment = no; Strand specific=Both; Count Paired Reads as 2 = No; calculate RPKM for genes without transcripts=Yes.  this calculates the RPKM values relative to the number of firal reads (as opposed to the total number of reads in the library.  This was done because the majority of the sequence reads came from the insect host).
Extract the reads that mapped to the viral genome using the CLC Genomics Workbench 8.0.  This results in 4 files:  paired reads from sequencing run 1, single reads (where the pair didn't map to the viral genome) from sequencing run 1, paired reads from sequencing run 2, and single reads from sequencing run 2.  I'm submitting these reads as the raw data, as we prefer not to release the associated M. configurata reads just yet (they will be released in a future publication).
Genome_build: genbank accession U59461 AF467808 GI:20043274
Supplementary_files_format_and_content: Export the alignment of the reads to the genome as a .bam file for each sample.  Export a table of the RNAseq results for each biorep as a .xls file.

molecule: polyA RNA

organism: Mamestra configurata nucleopolyhedrovirus A

source_name: infected midgut

growth_protocol: Preparation of viral stocks: The MacoNPV-A strain 90/2 was produced by oral infection of 4th instar Mamestra configurata (bertha armyworm) larvae. Occlusion bodies (OB) were harvested from larval cadavers, purified by centrifugation on sucrose gradients and quantified by using a hemocytometer.  Insect culture: A laboratory culture of M. configurata was maintained on a semi-synthetic diet {Bucher, 1976 #22} and larvae were reared at 21oC, 60% relative humidity and a 18:6 light/dark photoperiod.

extract_protocol:
Following removal of the peritrophic matrix and food bolus, the midgut tissue was directly immersed in 0.5 ml of TRIzol (Life Technologies). The midgut samples in TRIzol samples were stored at -70oC until tissue collection was complete. Total RNA was extracted from each pool of 5-6 midguts by homogenizing in 1.0 ml of TRIzol reagent according to the manufacturer’s protocol (Invitrogen). Total RNA was resuspended in 100 µl of sterile DEPC-treated H2O and quantified by measuring absorbance at 260 and 280 nm using a Nanodrop spectrophotometer (Fisher-Thermo). The quality of the RNA was assessed using an RNA 6000 Nano Kit and a Bioanalyzer 2100 instrument (Agilent).
Libraries were synthesized and sequencing performed at the National Research Council, Saskatoon, Canada. Briefly, libraries were prepared from 1 ug total RNA, representing 6 MacoNPV-A 90/2 infected BAW midguts as pooled samples. For each pooled sample treatment, there were two  biological replicates representing separate infection events collected at 6 time points post-infection plus two controls, water and 0.5% fluorescent brightener 28 (Sigma Chemicals). The TruSeq RNA Sample Prep Kit v2 (Illumina) was used to generate cDNA libraries for polyA-selected RNA from each time point.  The quality of each library was checked on a DNA 1000 chip on the 2100 Bioanalyzer (Agilent Technologies Inc.) and the concentration was determined by qPCR using the KAPA SYBR®FAST qPCR Kit (Kapa Biosystems) on the StepOnePlus Real-Time PCR System (Applied Biosystems). The cDNA library insert sizes ranged from 200-600 bp with an average size of 275 bp, including the adapter sequences (126 bp), therefore the insert size range was ~75-475 bp. The samples were multiplexed at 14 libraries/lane.  Equimolar concentrations of the libraries were pooled and a final concentration of 10 pM was used for clustering in one lane of a flowcell on a cBOT (Illumina).   The samples were sequenced (2 x 101 cycles, paired-end reads) on the HiSeq2500 (Illumina) using the TruSeq SBS Kit v3-HS 200 cycles Kit (Illumina). Each cDNA library was sequenced in two separate sequencing runs to increase the number of reads.

treatment_protocol: M. configurata 4th instar larvae were infected with MacoNPV-A OB using the canola leaf disc method. Briefly, 2 µl of inoculum, 5.0x107 OB/mL suspension containing 0.5% Fluorescent Brightener #28 (Sigma), or brightener alone as a control, was pipetted onto 3.1 mm2 canola leaf discs placed in each well of a 24-well NuTrend plate containing 1.0 ml of solidified 1.0% agar per well. Larvae were starved for 12 h prior to being placed individually on leaf discs; larvae that consumed the entire disc within 90 min were deemed to have consumed a 1.0x105 OB/larva dose. This time point was set at 0 hours post-inoculation (hpi) because most of the treated larvae required the entire 90 min to completely consume the leaf disc and acquire the full dose of virus OBs. In addition, at 6, 12, 18, 24 and 48 h afterward, 5-6 larvae were randomly selected and their midguts dissected.  Independent bioassay infections were carried out to provide two bio-replicates for cDNA library synthesis and RNA-Seq Illumina sequencing.

value: 48 hours post-infection

tag: biological replicate


title: Biorep_2_24_hours paired-end

value: 24 hours post-infection


title: XX females

value: ovary

value: XX


title: Biorep_2_24_hours single


title: Biorep_2_12_hours paired-end

value: 12 hours post-infection


title: Biorep_2_12_hours single


title: Biorep_1_24_hours paired-end


title: D.willistoni roX2/3 (Even) ChIRP-seq

value: whole larvae


title: Biorep_2_6_hours single

value: 6 hours post-infection


title: Biorep_1_48_hours single


title: Biorep_2_6_hours paired-end


title: Biorep_2_0_hours single

value: 0 hours post-infection


title: Biorep_2_0_hours paired-end


title: Biorep_2_18_hours single

value: 18 hours post-infection


title: Biorep_1_18_hours single


title: Biorep_1_12_hours paired-end


title: Biorep_2_18_hours paired-end


title: Biorep_1_12_hours single


title: Biorep_1_6_hours paired-end


title: Biorep_1_6_hours single


title: Biorep_1_48_hours paired-end


title: Biorep_1_0_hours paired-end


title: Biorep_1_0_hours single


title: WT_rep2_hiseq

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
WT_rep2
Merged processed data files:
8613_5CYoung-HEK239T-WT-R2.matrix.gz (not merged)
8616_5CYoung-HEK239T-WT__20000__8___6344_2MbHindIIILmo2__cis.matrix.gz
8616_5CYoung-HEK239T-WT__20000__8___6343_2MbHindIIITal1__cis.matrix.gz
8616_5CYoung-HEK239T-WT.matrix.gz

data_processing:
library strategy: 5C
Sequencing data was obtained from both an Illumina MiSeq and an Illumina HiSeq 2000 machine and was processed by a custom pipeline to map and assemble 5C interactions to hg19. We used an updated version of the Novoalign mapping algorithm (V3.02.00).  Data from the two biological replicates were pooled, producing a single interaction map for the wild type (wt), TAL1-deletion (TAL-ΔCTCF), and LMO2-deletion (LMO2-ΔCTCF) samples. The summary statistics and the read depth of each 5C libraries can be found in Table S7.
We merged primer interactions from the same fragments and binned the data using a binsize=20 kb, binstep=2.5kb, binmode=median.  We calculated the difference of the z-score matrices to quantify the amount of the differential interactions observed between the WT and deletion datasets.
Genome_build: hg19
Supplementary_files_format_and_content: *cis.matrix.gz [binned_interaction_matrix], *subtract.matrix.gz [log2_distadj_comparison], all other *.matrix.gz [raw_interaction_matrix]

source_name: WT

growth_protocol: For each 5C library, 50 million cells were resuspended in 40 mL DMEM (high glucose, pyruvate; Invitrogen, 11995-073) followed by the addition of 4 mL 11% formaldehyde solution (11% formaldehyde, 50 mM HEPES pH 7.3, 100 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0). Cells were cross-linked for 10 minutes with gentle agitation every 2 minutes. Cross-linking was quenched by the addition of 2 ml 2.5M glycine followed by two washes with ice cold PBS. Crosslinked cells were snap-frozen in liquid nitrogen and stored at -80oC until further processing.

extract_protocol: 3C was performed with HindIII restriction enzyme as previously described with some minor modifications. Ligation was performed in a final volume of 1,200 µL with 10 U of T4 ligase (Invitrogen) and 1% of triton X-100. For 50 million cells, 10 ligation reactions were performed, and pooled after DNA purification. The 3C libraries were then interrogated by 5C.  The multiplex annealing reaction was performed overnight at 50°C.  Pairs of annealed 5C primers were ligated at the same temperature using Taq DNA ligase for 1 h. 7 independent ligation reactions were performed for each 5C library, each containing an amount of 3C template that represents 600,000 genome equivalents and 0.3 fmol of each primer. Ligated 5C primer pairs, which represent a specific ligation junction in the 3C library and thus a long-range interaction between the two corresponding loci, were then amplified using 20 cycles of PCR with T7 and T3R universal tail primers that recognize the common tails of the 5C forward and reverse primers. Four separate amplification reactions were carried out for each of 7 annealing reactions described above and all the PCR products were pooled together. This pool constitutes the 5C library. The libraries were concentrated using Amicon Ultra Centrifugal filters - 0.5ml 30K (Millipore) and purified with Qiaquick PCR purification kit. Index adaptors (Illumina) were ligated to the 5C library using the Illumina protocol (TruSeq Nano DNA sample Prep kit). The linkered 5C libraries were then amplified by PCR (6 cycles), using the Illumina PCR mix. The 5C libraries were gel purified and sequenced on the Illumina HiSeq 2000 platform, generating 50-bp paired-end reads. The indexed adapter was AD005 for WT, AD006 for TAL1 deletion and AD015 for LMO2 deletion.

tag: cell line

value: Human embryonic kidney cell line HEK293T

value: WT


title: WT_rep1_hiseq

description:
WT_rep1
Merged processed data files:
8619_5CYoung-HEK239T-WT-R1.matrix.gz
8616_5CYoung-HEK239T-WT__20000__8___6344_2MbHindIIILmo2__cis.matrix.gz
8616_5CYoung-HEK239T-WT__20000__8___6343_2MbHindIIITal1__cis.matrix.gz
8616_5CYoung-HEK239T-WT.matrix.gz


title: Biorep_2_48_hours single


title: Lmo2Del_rep1_hiseq

description:
Lmo2Del_rep1
Merged processed data files:
8617_5CYoung-HEK239T-Lmo2Del-R1.matrix.gz
8614_5CYoung-HEK239T-Lmo2Del__20000__8___6343_2MbHindIIITal1__cis.matrix.gz
8614_5CYoung-HEK239T-Lmo2Del__20000__8___6344_2MbHindIIILmo2__cis.matrix.gz
8614_5CYoung-HEK239T-Lmo2Del.matrix.gz
distance-adjusted__LMO2__Lmo2Del__WT.subtract.matrix.gz
distance-adjusted__TAL1__Lmo2Del__WT.subtract.matrix.gz

value: Lmo2 deletion


title: Tal1Del_rep2_hiseq

description:
Tal1Del_rep2
Merged processed data files:
8612_5CYoung-HEK239T-Tal1Del-R2.matrix.gz (not merged)
8615_5CYoung-HEK239T-Tal1Del__20000__8___6343_2MbHindIIITal1__cis.matrix.gz
8615_5CYoung-HEK239T-Tal1Del__20000__8___6344_2MbHindIIILmo2__cis.matrix.gz
8615_5CYoung-HEK239T-Tal1Del.matrix.gz
distance-adjusted__LMO2__Tal1Del__WT.subtract.matrix.gz
distance-adjusted__TAL1__Tal1Del__WT.subtract.matrix.gz

value: Tal1 deletion


title: Biorep_1_18_hours paired-end


title: Tal1Del_rep1_hiseq

description:
Tal1Del_rep1
Merged processed data files:
8618_5CYoung-HEK239T-Tal1Del-R1.matrix.gz
8615_5CYoung-HEK239T-Tal1Del__20000__8___6343_2MbHindIIITal1__cis.matrix.gz
8615_5CYoung-HEK239T-Tal1Del__20000__8___6344_2MbHindIIILmo2__cis.matrix.gz
8615_5CYoung-HEK239T-Tal1Del.matrix.gz
distance-adjusted__LMO2__Tal1Del__WT.subtract.matrix.gz
distance-adjusted__TAL1__Tal1Del__WT.subtract.matrix.gz


title: Biorep_1_24_hours single


title: 2540.Scalp

city: Baltimore

first: Andrew

last: Jaffe

state: MD

address: 855 N Wolfe St, Ste 300

department: Clinical Sciences

institute: Lieber Institute for Brain Development

data_processing:
Reads were mapped to the genome using TopHat2 [Kim et al, Genome Biology 2013] using the paired-ends procedure (we used the option --library-type fr-firststrand).
Gene counts relative to the UCSC hg19 knownGene annotation were calculated using featureCounts in the subread package (version 1.4.6). There were 23,710 genes in this annotation, and we dropped 305 genes that were annotated to more than 1 chromosome.
We used the Sailfish software, version 0.7.6, to quantify isoforms from our RNA-seq reads. As a result, we obtained TPM (transcripts per million) values for each isoform.
Genome_build: hg19
Supplementary_files_format_and_content: (1) geneCounts.csv: gene count matrix, obtained from RNA-Seq data. [CSV file] (2) sailfish_transcriptTPM.csv: matrix of transcript TPM values. [CSV file]

source_name: Scalp fibroblasts

growth_protocol: Scalp and Dura Tissue Cultures: The dura culture medium was prepared out of 1X DMEM (Ref#11960-044, GIBCO) with 10% by volume fetal bovine serum, 2% by volume 100X GlutaMAX (Cat#: 35050, GIBCO), 1% by volume Penicillin-Streptomycin/Amphotercin solution (Ref# 15140-122, GIBCO), and 1% by volume Gentamicin solution (Cat# 17105-041, Quality Biological). This culture medium was used in all subsequent steps of the dura culturing procedure. The scalp culture medium used for all subsequent steps of the scalp culturing procedure was made the same way except without the 1% Gentamycin. A rinsing solution was prepared out of 1X PBS (pH 7.2) (Ref# 21-040-CV, Corning Life Sciences), 1% by volume Penicillin-Streptomycin/Amphotericin solution (Ref# 15140-122, GIBCO), and 1% by volume Gentamicin (Cat# 17105-041, Quality Biological). The dissected scalp sample was washed with the rinsing solution three times, the fat tissues were cut away, and all hair was plucked out with forceps. The scalp sample was then placed epidermis side down on a dish and floated with Dispase II enzyme solution (2.4 units of the Dispase II enzyme per mL of PBS, Dispase II enzyme: Cat#17105-041, GIBCO). The dish was covered with parafilm and foil, and placed in a 37 deg. C incubator for 24 hours. After the 24-hour period, the epidermis was peeled away from the dermis. The dermis was washed with the rinsing solution, dried, and cut into 2-3 mm^2 pieces. The pieces were placed in a Falcon Easy Grip tissue culture 35×10 mm dish and one drop of scalp culture medium was added to each piece of scalp. The dish was placed in the incubator at 37 deg. C and 5% CO2 for culturing. A similar procedure was followed for the dura samples. Dura samples were washed with the rinsing solution three times. Then, a few 2-3 mm^2 pieces were cut from the dura mater and placed together in an Easy Grip cell culture 35×10 mm dish. One drop of dura culture medium was added to each dura piece. The culture dish was then placed in an incubator (at 37 deg. C and 5% CO2) for culturing. The medium of each culture was changed to fresh medium 2-3 times per week to promote growth of the fibroblasts. On average, fibroblast cells started to proliferate at 7-14 days, however some samples took longer (up to 3 weeks).   Fibroblast Cell Cultures: The dura and scalp tissue cultures were monitored under a phase-contrast microscope. When the fibroblast growth reached 90-95% confluence, 1 mL of a 0.25% trypsin solution (Cat#T4049, Sigma) was added to each culture dish, and the cells were incubated for 5 to 8 min. Then, 1mL of media was added to each dish stop the enzymatic reaction. Next, the contents of each culture dish were transferred into separate 15 mL Falcon conical tubes and 8mL of media was added to each tube. The conical tubes were centrifuged for 5 min at 1100 rpm. The supernatant was discarded, 5mL of fresh media was added to each conical tube, and the contents of the tubes were transferred onto separate 25 cm^3 cell culture Easy Flasks (Thermo Scientific, Cat# 156367), where they were kept in cultures for 3-5 days in an incubator (at 37 deg. C and 5% CO2). When the cells reached 90-95% confluence, the cells from each 25 cm^3 flask were transferred onto two 75 cm^3 cell culture easy flasks (Thermo Scientific, Cat# 156499) and kept in cultures for continued growth. When the cells reached 90-95% confluence, they were incubated with 3 mL of 0.25% trypsin solution for 5 to 8 min, after which 3mL of fresh culture media was added to stop the enzymatic reaction. Then, the contents of the flasks were transferred into separate 15 mL Falcon conical tube and 4mL of media was added to each tube. The tubes were centrifuged (5 min, 1100 rpm), the supernatant was discarded and the pellets containing the fibroblasts were removed from the centrifuge tubes and transferred to cryoTube vials (Cat#375418, Thermo Scientific). 0.5 mL of recovery cell culture freezing medium (Cat#12648-010, GIBCO) was added to each vial, after which the vials were insulated with Styrofoam and placed into a -80 deg. C freezer. Later, the tubes were transferred to a -152 deg. C liquid nitrogen freezer. These frozen dura and scalp fibroblast cells were then used generate RNA-Seq data.

extract_protocol:
RNA was extracted from the cultured dura and scalp fibroblasts with the RNeasy kit (Qiagen), in accordance with the manufacturer’s protocol. RNA molecules were treated with Dnase and polyadenylated (polyA+) RNA was isolated.
Sequencing libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit (v2). The resulting libraries were sequenced on an Illumina HiSeq 2000. We note that while all samples were run on the same flow cell, the samples were somewhat imbalanced by lane – however, the first PC of the expression data did separate perfectly by sampling location. Sample-specific information on reads and alignments are available in S1 Table.
2x100 base pair paired-end reads using the Illumina TruSeq strand specific protocol

tag: Sex

value: M

tag: race

value: Cauc


title: 2540.Dura

source_name: Dura mater fibroblasts


title: 2533.Dura


title: 5008.Dura


title: 2533.Scalp


title: 2328.Scalp


title: 5054.Dura

value: F


title: 2328.Dura


title: 5054.Scalp


title: Lmo2Del_rep2_hiseq

description:
Lmo2Del_rep2
Merged processed data files:
8611_5CYoung-HEK239T-Lmo2Del-R2.matrix.gz (not merged)
8614_5CYoung-HEK239T-Lmo2Del__20000__8___6343_2MbHindIIITal1__cis.matrix.gz
8614_5CYoung-HEK239T-Lmo2Del__20000__8___6344_2MbHindIIILmo2__cis.matrix.gz
8614_5CYoung-HEK239T-Lmo2Del.matrix.gz
distance-adjusted__LMO2__Lmo2Del__WT.subtract.matrix.gz
distance-adjusted__TAL1__Lmo2Del__WT.subtract.matrix.gz


title: 2371.Scalp


title: 2385.Scalp

value: AA


title: 2371.Dura


title: 2435.Dura


title: 2429.Dura

value: HISP


title: 2520.Scalp


title: 2429.Scalp


title: 2520.Dura


title: 2385.Dura


title: 5008.Scalp


title: 2468.Scalp


title: CB2_MPP--

city: Toronto

first: Sasan

last: Zandi

state: Ontario

address: 101 college St

institute: UHN

description: flow sorted

data_processing:
Alignment by STAR.
Expression analysis by cufflinks.
Genome_build: hg19

source_name: neonatal cord blood

extract_protocol:
RNA was isolated using mirVana RNA isolation kit and then subjected to SMARTseq.
Nextera

value: MPP--

value: neonatal cord blood


title: CB2_MPP++

description: flow sorted

value: MPP++


title: CB2_MEP--

description: flow sorted

value: MEP--


title: CB2_GMP

description: flow sorted

value: GMP


title: CB1_MPP--

description: flow sorted


title: CB2_MEP++

description: flow sorted

value: MEP++


title: WT_rep1_miseq


title: CB1_MPP++

description: flow sorted


title: CB1_MEP--

description: flow sorted


title: 2435.Scalp


title: CB1_MEP++

description: flow sorted


title: 2468.Dura


title: Tal1Del_rep1_miseq


title: CB1_GMP

description: flow sorted


title: CB1_CMP+-

description: flow sorted

value: CMP+-


title: CB2_MLP

description: flow sorted

value: MLP


title: CB2_MPP+-

description: flow sorted

value: MPP+-


title: CB2_MEP+-

description: flow sorted

value: MEP+-


title: CB2_HSC

description: flow sorted

value: HSC


title: CB2_CMP--

description: flow sorted

value: CMP--


title: CB2_CMP++

description: flow sorted

value: CMP++


title: Control-2788, CD19+ cultured 24h with anti-CD40 & -IgM rep1

city: Boston

first: Baochun

last: Zhang

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
ABC 1
KR_DC_015

data_processing:
Illumina TrueSeq mRNA-seq libraries were prepared from total RNA according to the manufacturer's instructions (Illumina). All libraries were sequenced in 6-plex pools, two lanes per pool, for 1x101 cycles on an Illumina HiSeq2000 instrument. An average of 65,061,816 single-end 101bp reads were generated per sample, of which ~93.37% on average could be mapped onto the ENSEMBL NCBIM37.67 mouse reference genome sequence using TopHat (Trapnell et al., 2009). An average of 72.59% of all mapped bases per sample were aligned within ENSEMBL gene bodies. For expression analysis, reads uniquely mapping to individual ENSEMBL genes were counted using htseq-count (http://www-huber.embl.de/users/anders/HTSeq). Gene expression was quantified using edgeR based on a negative binomial generalized log-linear model (Robinson et al., 2010). Biological reproducibility between the replicates was excellent (Pearson correlation: 0.990899). For classification of the mouse DLBCLs, hierarchical clustering was applied based on the expression of all genes. Euclidean distance and complete linkage was used to assess the similarity between individual DLBCL samples and GC B cells (GCB), resting B cells (Resting B), or in vitro activated B cells (ABC) prepared using anti-CD40 and anti-IgM antibodies. Sequence variants were detected within the mRNA-seq reads using VarScan (Koboldt et al., 2009). A minimum coverage of 10 uniquely mapping reads in each sample was required in order to call a variant. Variants with alternative allele frequencies between 8% and 75% were defined as being heterozygous. Sequence variants were annotated with their predicted effect on protein coding sequence using snpEff (PMID: 22728672) based on ENSEMBL NCBIM37.67 gene models. Somatic variants and loss-of-heterozygosity events were extracted from the total list of variants by comparing each tumor sample to the resting B-cell control samples. The VarScan probability of a variant to be somatic was thresholded at a 5% false-positive rate.
Genome_build: ENSEMBL NCBIM37.67; mm9
Supplementary_files_format_and_content: Excel; contains variant calling and gene expression

organism: Mus musculus

source_name: activated B-cell control (ABC)

extract_protocol:
QIAGEN AllPrep DNA/RNA mini kit for RNA extraction (following manufacturer's instructions)
Illumina TrueSeq mRNA-seq libraries were prepared from total RNA according to the manufacturer's instructions (Illumina)

tag: strain background

value: Spleen

value: activated B-cell control (ABC)


title: Control-2822, cg1-cre/YFP GCB cells (YFP+), d10 rep2

description:
GCB 2
KR_DC_018

source_name: germinal center B cell control (GCB)

value: germinal center B cell control (GCB)


title: Control-2788, CD19+ cultured 24h with anti-CD40 & -IgM rep2

description:
ABC 2
KR_DC_016


title: Control-2822, cg1-cre/YFP GCB cells (YFP+), d10 rep1

description:
GCB 1
KR_DC_017


title: CB1_MPP+-

description: flow sorted


title: Lmo2Del_rep1_miseq

value: Human embryonic kidney cell line HEK293T

value: Lmo2 deletion


title: OMV RNA seq.

city: Tsukuba

first: Masanori

last: Toyofuku

address: Tennoudai 1-1-1

country: Japan

institute: University of Tsukuba

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing reads were mapped to the PAO1 genome (RefSeq NC_002516.2) using CLC Genomics Workbench v4.9 (CLCbio) allowing up to 2 mismatches per read.
RNA-Seq count data were analyzed for differential transcript expressionby the R package DESeq (version 1.6.1, Anders and Huber, 2010).
Supplementary_files_format_and_content: RPKM

organism: Pseudomonas aeruginosa PAO1

source_name: OMV

growth_protocol: P. aeruginosa was grown in LB

extract_protocol:
RNA was extracted by the hot phenol method from the cell or purifed OMV
RNA libraries were prepared for sequencing according to the Illumina TruSeq RNA preparation guide

value: membrane vesicle

tag: media

value: complex medium LB


title: PAO1 Cell RNA seq.

source_name: Cell

value: whole cell


title: OMV DNA seq.

description: control


title: Control-2788, cg1-cre/+, spl CD19+ rep1

description:
resting B-cell 1
KR_DC_013

source_name: resting B cell control

tag: genotype/variation

value: resting B cell control


title: CB2_CMP+-

description: flow sorted

value: neonatal cord blood


title: CB1_MLP

description: flow sorted


title: Control-2788, cg1-cre/+, spl CD19+ rep2

description:
resting B-cell 2
KR_DC_014


title: Tumor-1128

description:
Mouse #12
KR_DC_012

source_name: Lymphoma B cells

value: Lymphoma B cells


title: CB1_MEP+-

description: flow sorted


title: CB1_HSC

description: flow sorted


title: CB1_CMP++

description: flow sorted


title: Tumor-920

description:
Mouse #10
KR_DC_010


title: Tumor-818

description:
Mouse #9
KR_DC_009


title: CB1_CMP--

description: flow sorted


title: Tumor-776

description:
Mouse #7
KR_DC_007


title: Tumor-604

description:
Mouse #2
KR_DC_002


title: Tumor-775

description:
Mouse #6
KR_DC_006


title: Tumor-603

description:
Mouse #1
KR_DC_001


title: 49_min

status: Public on Jan 22 2016

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

description: RNA isolated from bacteria 49 min post-infection

data_processing:
Clean and merge reads using the adapter sequences and discarding the shortest ones; TOOL=SeqPrep; VERSION=v0.4-5-gb62f433; PARAMETERS=-f reads_1.fq -r reads_2.fq -1 reads_adapterClean_1.fq.gz -2 reads_adapterClean_2.fq.gz -s reads_adapterClean_pairedSingle.fq.gz -L 35 -y I -A CTGTCTCTTATAC -B CTGTCTCTTATAC
Filter out reads with homopolymers (>70% read length) and trim the bases at the end of the read with lower quality values (<20); TOOL=At-home perl script; PARAMETERS=--quality_threshold 20 --homopolymer_threshold 70
mapping to the host and phage genomes was done using the CLC Genomics Workbench v7.5.1
the processed data files were done by including all the Total Gene Reads (TGR) for each annotated gene feature at each time point
Genome_build: Yersinia enterocolitica subsp. palearctica Y11 (FR729477) and phiR1-37 (AJ972879)

organism:
Yersinia enterocolitica
Yersinia phage phiR1-37

source_name: bacterium and bacteriophage

growth_protocol: Overnight cultures were diluted in fresh sterile LB broth and pre-incubated at 22 degrees. Subsequently, the bacteriophage was added (MOI = 10).

extract_protocol:
The total RNA was isolated using the SV Total RNA Isolation System (Promega). The qualities of the isolated RNA, as well as the rRNA profiles were determined using Bioanalyzer (Agilent).
The ribosomal RNA was removed using Ribo-ZeroTM rRNA Removal Kit for Gram-negative Bacteria (Epicentre); RNA libraries were prepared for sequencing using standard Illumina protocols

tag: bacterial strain

value: rough derivative of the serotype O:3

tag: growth phase

value: logarythmic phase


title: 42_min

description: RNA isolated from bacteria 42 min post-infection


title: 35_min

description: RNA isolated from bacteria 35 min post-infection


title: 21_min

description: RNA isolated from bacteria 21 min post-infection


title: 15_min

description: RNA isolated from bacteria 15 min post-infection


title: 10_min

description: RNA isolated from bacteria 10 min post-infection


title: 5_min

description: RNA isolated from bacteria 5 min post-infection


title: 2_min

description: RNA isolated from bacteria 2 min post-infection


title: control mimic_4

city: San Francisco

first: Heather

middle: H

last: Pua

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

data_processing:
Base calling: Illumina Casava1.8 software used for basecalling.
Sequence alignment: Sequence alignment and splice junction estimation was performed using Bowtie2(Langmead and Salzberg, 2012) and TopHat(Trapnell et al., 2009), respectively. Genome alignments were restricted to those reads that map uniquely to an annotated transcriptome provided by Ensembl (Flicek et al., 2014).
Expression Analysis: Mappings were aggregated on a per-gene basis as raw input for the program DESeq(Anders and Huber, 2010). Data from one control mimic sample (cont_1) was excluded for low total read counts (203,495). Data from two of the miR-27 mimic transfections (mir27a_1 and mir27a_2) were combined into a single biologic replicate (mir27a_agg) (9+6 = 15 million total reads) to obtain a total of 11-31 million unique reads per sample. Analysis was performed on batch normalized data sets based on principle component analysis (sort 1 and 2 were similar, sort 3 and 4 were similar). Expression values were analyzed as log2(fold change) of cells transfected with each miRNA mimic compared with control mimic.
Genome_build: mm10

source_name: CD4+ T cells

growth_protocol: CD4+ T cells from the spleen and lymph nodes of mice were enriched by Dynabead positive selection (Invitrogen, L3T4).  Cells were stimulated with anti-CD3 and anti-CD28 in the presence of 10 units/ml IL-4 (supernatant from I3L6 cells) for 3 days then rested with 20 units/ml recombinant IL-2 (National Cancer Institute) for an additional 2 days.

extract_protocol:
150,000-800,000 live RosaYFP+CD4+ Dgcr8f/f Tbx21-/- Cd4-cre cells were sorted directly into Trizol LS (Life Technologies) and RNA isolated using a miRNeasy Micro Kit (QIAGEN) with on-column DNase digestion.
RNA sequencing libraries were generated using 1ng of total RNA and the Ovation RNA-Seq System V2 and Ultralow Library Construction System sample prep kits (NuGEN). Libraries were multiplexed at a density of 4 per flow-cell lane and sequenced on the HiSeq 2500 to generate single end 50bp reads per the manufacturer’s instructions (Illumina). The following barcodes were used: 23a_1=AAGGGA, 23a_2=AAGACG, 23a_3=ACACGA, 23a_4=ACAAAC, 24_1=CCTTCA, 24_2=CCTCGG, 24_3=CACACA, 24_4=CACCTC, 27a_1=GGACCC, 27a_2=GGATGT, 27a_3=GTGTTA, 27a_4=GTGGCC, cont_1=TTCAGC, cont_2=TTCGCT, cont_3=TGTGAA, cont_4=TGTTGC.

treatment_protocol: Transfections with 500nM miRIDIAN miRNA mimics (Dharmacon) were performed on day 1 and day 4 of the culture using the Neon Transfection System (Invitrogen).

tag: strain

tag: genotype

value: Dgcr8f/f Tbet-/- CD4-cre

tag: miRNA mimic

value: control


title: Tumor-817

description:
Mouse #8
KR_DC_008

tag: tissue

tag: cell type


title: 0_min

description: RNA isolated from uninfected bacteria (negative control)


title: Tumor-1078

description:
Mouse #11
KR_DC_011


title: control mimic_2


title: miR27a_4


title: control mimic_1


title: control mimic_3


title: miR27a_3


title: Tumor-773

description:
Mouse #5
KR_DC_005


title: THC 2

city: New Orleans

first: Liz

last: Simon

state: Louisiana

address: 1901 Perdido Street

department: Physiology

institute: Louisiana State University Health Sciences Center

data_processing:
Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis
base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70)
ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis
genome build: Mmul_051212.
Supplementary_files_format_and_content: raw counts

organism: Macaca mulatta

source_name: striatum

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using Norgen RNA extraction kit. Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: agent


title: Tumor-611

description:
Mouse #4
KR_DC_004


title: miR27a_2


title: miR27a_1


title: THC/SIV 1

value: SIV-infected + delta9-THC


title: Tumor-607

description:
Mouse #3
KR_DC_003

value: Spleen


title: THC 1


title: VEH/SIV 2

value: SIV-infected + vehicle


title: VEH/SIV 1


title: miR24_3


title: miR24_2


title: VEH 1

value: vehicle


title: VEH 2


title: miR23a_4


title: miR24_1


title: miR23a_2


title: miR23a_3


title: 28_min

description: RNA isolated from bacteria 28 min post-infection


title: THC/SIV 2


title: wt_NSC_Lsd1

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

description: ChIP-seq sample of Rcor2Flag NSC using LSD1 antibody

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2(v 2.0.10.20131216) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --nomodel --broad --shiftsize=73 --SPMR" relative to input samples for H3K4me1 samples.
Peaks were called using masc2(v 2.0.10.20131216) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --nomodel--shiftsize=73 --SPMR" relative to input sample for Rcor2 & Lsd1 samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: neural stem cell

growth_protocol: Rcor2Flag mice were generated by knocking in 3×Flag sequences adjacent to the start codon ATG of Rcor2 gene locus by CRISPR/Cas9.

extract_protocol:
Cross-linking, chromatin isolation, sonication and immunoprecipitation were performed using MAGnifyTM Chromatin Immunoprecipitation System (Invitrogen) following the manufacturer’s instructions.
Library was constructed using KAPA HyperPlus Library Preparation Kit (Cat. No. kk8510)

treatment_protocol: Embryonic cortex were isolated from Rcor2Flag and Rcor2cko embryos at E13.5 respectively.

tag: development stage

tag: chip antibody


title: ko_NSC_Lsd1

description: ChIP-seq sample of Rcor2cko NSC using LSD1 antibody


title: wt_NSC_Input

description: Input sample of Rcor2Flag NSC


title: miR23a_1


title: E13.5_Rcor2

description: ChIP-seq sample of Rcor2Flag NSC using Flag M2 antibody

source_name: embryonic brain


title: E13.5_Input

description: Input sample of Rcor2Flag cortex


title: ko_NSC_H3K4me1

description: ChIP-seq sample of Rcor2cko cortex using H3K4me1 antibody


title: miR24_4


title: ko_NSC_Input

description: Input sample of Rcor2cko NSC


title: root_drought

city: Beijing

first: Xu

middle: Zhao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ZmB73 whole genome using tophat with parameters -p -r -G -o genome C1_R1_1.fq C1_R1_2.fq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.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: ZmB73
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Zea mays

extract_protocol:
The total RNA was isolated from plant leaves, stems and roots using an RNeasy Plant Mini Kit followed by RNase-Free DNase Set (Qiagen, Hilden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: age

value: 2-3 leaf stage

value: wild type


title: Down’s syndrome

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: Bisulphite treated

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Two reference sequences were prepared based on the HG19 reference
The alignment was performed using the bowtie alignment software version  0.12.8
Methylation calls files for C's in the bowtie alignment files were generated using Bismark software
Genome_build: HG19
Supplementary_files_format_and_content: Methylation calls files

source_name: Brain

growth_protocol: N/A. Primary patient samples.

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C.

treatment_protocol: Untreated

value: brain Grey matter

tag: condition

value: Down’s syndrome

tag: sample type

value: Primary


title: Alzheimer's disease

description: Bisulphite treated

value: Alzheimer's disease


title: Parkinson's disease

description: Bisulphite treated

value: Parkinson's disease


title: Dementia of Lewy bodies

description: Bisulphite treated

value: Dementia of Lewy bodies


title: H

city: Nanjing

first: Lingfei

last: Shangguan

state: Jiangsu

address: 1 Weigang Rd

department: Horticultural Department

institute: Nanjing Agri. University

description: H_vs_Q_CG.DMR_Gene, H_vs_Q_CHG.DMR_Gene, H_vs_Q_CHH.DMR_Gene, H_vs_X_CG.DMR_Gene, H_vs_X_CHG.DMR_Gene, H_vs_X_CHH.DMR_Gene

data_processing:
Vitis vinifera genome sequences were downloaded from EnsemblPlants database (http://plants.ensembl.org/Vitis_vinifera, verison  IGGP_12x), and used as the reference to align the methylation data.
Reads were mapped using BSMAP software version 2.73 (Xi and Li 2009).
Methylation ratios were determined using a Python script (methratio.py) distributed together with the BSMAP package.
Only cytosines in a CpG context with sufficient sequencing depth (defined here as greater than or equal to 10× coverage) were retained for further analysis.
Supplementary_files_format_and_content: txt

organism: Vitis vinifera

source_name: mature stage

growth_protocol: Berries from Vitis vinifera (cv. ‘Fujiminori’) were sampled at the first growth (after flowering 40 days), véraison (after flowering 65 days), and mature (after flowering 90 days) stages throughout the growing season.

extract_protocol:
Furthermore, in order to capture a representative biological selection of transcripts at each time-point, RNA for Illumina sequencing was purified from tissue consisting of 20 berries collected from 10 bunches. Total DNA was extracted from the fruits collected from our experiments. Total DNA was prepared by proteinase K/phenol extraction following the manufacturer’s instructions.
The DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of ~250bp, followed by the blunt ending, dA addition to 3’-end, and adaptor addition following the manufacturer’s protocol. The bisulfite conversion of the adaptor-added DNA was performed as described previously (Hayatsu, Tsuji et al. 2006). Ultra-high-throughput pair-end sequencing was performed using the Hiseq 2000 according to the manufacturer’s instructions. Raw data were processed using Illumina base-calling pipeline.

tag: developmental stage

value: mature stage

tag: cultivar

value: Fujiminori


title: stem_drought

value: stem


title: 60min_IP

city: Sao Paulo

first: Paulo

last: Lee Ho

state: SP

address: 1500 Vital Brazil

department: Centro de Biotecnologia

country: Brazil

institute: Instituto Butantan

data_processing:
alignment with Bowtie2 to the genome of Leptospira interrogans serovar Copenhageni strain FioCruz L1-130, default parameters, allowing no mismatches. Resulting files are ".sam".
number of reads at each chromosomal position was normalized to the total number of reads of the sample
peak-calling in CisGenome: -e 250 -b 5 -c 2 -maxgap 25 –minlen 50 –bw 2, using total samples as background controls. We only considered peaks with fold change greater than 2
Genome_build: accession numbers NC_005823.1 and NC_005824 (chromosome 1 and chromosome 2, respectively).

source_name: L. interrogans crosslinked lysate

growth_protocol: Cells, from up to the third passage after isolation from hamsters kidneys, were grown in supplemented EMJH medium at 30 C, without agitation.

extract_protocol:
DNA in total lysates and immunoprecipitated samples was sheared by sonication, yielding fragments between 200 to 600bp and visualized in a BioAnalyzer 2100 (Agilent) after extraction  with Qiagen Gel extraction kit.
Samples were handed to MicroBio Center, in the Department of Biology in MIT for sequencing.

treatment_protocol: Cells in the fifth day of growth in liquid medium were harvested by centrifugation, washed and resuspended in formaldehyde (2% final concentration). After 40 or 60min incubation at room temperature, glycine was added and cross-linked cells were lysed.

tag: crosslink


title: siCon1

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

description: RNA-seq

data_processing:
Illumina Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.4
cufflinks v2.0.2 was used to identify expression level (fpkm) for each gene
Genes with maximum fpkm < 0.2 in all samples were removed. fpkm were taken log2 with adding a psuedo count of 0.1
Genome_build: hg19
Supplementary_files_format_and_content: text file of log2fpkm for each gene

source_name: Prostate cancer cell line LNCaP-abl_control_si_1

growth_protocol: The prostate cancer cell line LNCaP-abl cells were maintained in phenol-red-free RPMI 1640 medium supplemented with 10% charcoal stripped fetal bovine serum (CDT), 2mM glutamine, 100 U/mL penicillin and 100 mg/mL streptomycin.

extract_protocol:
After 72hrs of siRNA transfection, RNA was extracted using Qiagen Rneasy Mini Kit following manufacturer's instruction
Libraries were prepared according toIllumina TruSeq RNA Sample Prep Kit v2

treatment_protocol: LNCaP-abl cells were transfected with control siRNAs or target gene siRNAs (ON-target smart pool from Thermo Scientifc ) using Lipofectamine RNAiMAX from Life Technologies.

value: prostate

value: LNCaP-abl

tag: passage


title: wt_NSC_H3K4me1

description: ChIP-seq sample of Rcor2Flag cortex using H3K4me1 antibody


title: siE2F1

description: RNA-seq

source_name: Prostate cancer cell line LNCaP-abl_E2F1_si


title: siCon0

description: RNA-seq

source_name: Prostate cancer cell line LNCaP-abl_control_si_0


title: stem_control


title: 60min_total

organism: Leptospira interrogans serovar Copenhageni


title: root_control


title: leaf_drought

value: leaf


title: X

description: Q_vs_X_CG.DMR_Gene, Q_vs_X_CHG.DMR_Gene, Q_vs_X_CHH.DMR_Gene, H_vs_X_CG.DMR_Gene, H_vs_X_CHG.DMR_Gene, H_vs_X_CHH.DMR_Gene

source_name: first growth stage

treatment_protocol: Berries from Vitis vinifera (cv. ‘Fujiminori’) were sampled at the first growth (after flowering 40 days), véraison (after flowering 65 days), and mature (after flowering 90 days) stages throughout the growing season.

value: first growth stage


title: Q

description: Q_vs_X_CG.DMR_Gene, Q_vs_X_CHG.DMR_Gene, Q_vs_X_CHH.DMR_Gene, H_vs_Q_CG.DMR_Gene, H_vs_Q_CHG.DMR_Gene, H_vs_Q_CHH.DMR_Gene

source_name: véraison stage

value: veraison


title: 40min_IP


title: wt rna-seq

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v1.3.3 with default parameters.
Gene expression for each sample was quantified to RPKM using Cufflinks(v 1.2.0).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each transcript.

growth_protocol: Rcor2fl/fl and Rcor2cko mice were generated by crossing Rcor2fl/+NesCre mouse

extract_protocol:
RNA was isolated using RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions
library was constructed using KAPA Stranded mRNA-Seq Kit (Cat. No.kk8420)

treatment_protocol: Embryonic cortex were isolated, and the VZ-SVZ regions were dissected from Rcor2fl/fl and Rcor2cko embryos at E13.5 respectively.


title: 40min_total


title: leaf_control


title: homo rna-seq


title: lsm1a lsm1b-4ºC

status: Public on Jan 21 2016

city: Madrid

first: Carlos

last: Perea-Resa

address: Ramiro de Maeztu,9

institute: CIB-CSIC

data_processing:
RNAseq reads were aligned to the TAIR10 Col-0 reference genome using TopHat2 (Kim et al, 2013) with default parameters
Uniquely mapped reads were counted per representative gene model (excluding introns) according to the TAIR10 annotation using custom R scripts
Differential expression between WT and mutant in each condition was calculated using DEseq2 (Love et al. 2014) following its manual
Genome_build: TAIR10
Supplementary_files_format_and_content: Text files include raw counts for each sample

organism: Arabidopsis thaliana

source_name: leaves from two-week-old plants_cold

growth_protocol: Plants were grown under long-day photoperiod (photon flux of 90µmol m-2 s-1). For cold treatments, plants were grown on soil. For drought and high salt treatments, plants were grown on GM medium plates

extract_protocol:
Stressed plants were colected, inmediately frozen on liquid nitrogen and homogenized. Total RNA was extracted using TRIzol® Reagent (Life Technologies) and cleaned with RNeasy Plant Mini Kit (Quiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cold treatment, plants were exposed to 4ºC for 24h under long-day photoperiod (photon flux of 40µmol m-2 s-1). For drought and high salt treatments, plants were transferred from GM medium to PEG (55%)- or NaCl (150mM)-containning plates for 10h, respectively

value: lsm1a lsm1b

value: two-week-old

value: leaves


title: Col-0-4ºC


title: Am_CK_L

first: Luyang

last: Zhao

address: 28 Fuxing Road, HaiDian District

department: Department of Gynecology and Obstetrics

institute: People’s Liberation Army (PLA) Medical School, Chinese PLA General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SRX381742 using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: Transcriptome assembled using SRX381742
Supplementary_files_format_and_content: xls files include RPKM values for each Sample

organism: Ammopiptanthus mongolicus

source_name: Mesophyll cell

extract_protocol:
Leaves were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mesophyll

value: wild type

tag: treatment


title: Am_Drought stress_L72

value: Drought stress

tag: time


title: Am_Drought stress_L24


title: Am_Drought stress_L1

value: 1 h


title: Am_Cold stress_L72

value: Cold stress


title: Am_Cold stress_L1


title: fiber_MethylC-seq rep2

city: Austin

first: Qingxin

last: Song

state: Texas

address: 3517 North Hills Drive Apt C207

institute: UT austin

data_processing:
Basecalls performed using CASAVA version 1.8
We applied Bismarck software to align reads to reference genome with default parameters. First 75 bases of unmapped reads were extracted and aligned to genome again. Only reads mapped to the unique sites were reserved for further analysis. Reads mapped to the same site were collapsed into a single consensus read to reduce clonal bias. For each cytosine, the binomial distribution was used to identify whether this cytosine was methylated. The probability p in binomial distribution B (n, p) was referred to bisulfite conversion failure rate. The number of trials (n) in the binomial distribution was the read depth. Only cytosines covered by at least three reads in all compared tissues were considered for identification. Cytosines with P-values below 1e–5 were identified as methylcytosines.
Differentially methylated regions (DMRs) for CHH methylation were identified using 100-bp sliding-windows. Mean methylation level was calculated for each window.  Windows containing at least eight cytosines in CHH context covered by at least three reads were selected to identify DMRs. ANOVA test using 2 biological replications (P < 0.05) and difference of methylation levels (> 0.1) were used to determine CHH DMRs when two tissues were compared.
Genome_build: Genome sequences of Gossypium arboreum (Ca_all_Version2) and Gossypium raimondii (v2.1)
Supplementary_files_format_and_content: cytosine_methylation_status.txt.gz: This file is summary about detected C and T number in each cytosine location for all samples.1st column: Chromosome; 2nd column: cytosine location; 3rd column: DNA strand; 4th column: cytosine context; 5th column: number of C in Leaf rep1; 6th column: number of T in Leaf rep1; 7th column: number of C in Leaf rep2; 8th column: number of T in Leaf rep2; 9th column: number of C in ovule rep1; 10th column: number of T in ovule rep1; 11th column: number of C in ovule rep2; 12th column: number of T in ovule rep2; 13th column: number of C in fiber rep1; 14th column: number of T in fiber rep1; 15th column: number of C in fiber rep2; 16th column: number of T in fiber rep2;
The website for D genome (Gossypium raimondii) is: http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Graimondii . The website for A genome (Gossypium arboreum) is: http://cgp.genomics.org.cn/page/species/download.jsp?category=arboreum .

organism: Gossypium hirsutum

source_name: fiber

extract_protocol:
Genomic DNA was isolated from cotton leaves, ovules at 0 DPA and fibers at 14 DPA using CTAB method.
About 5 μg genomic DNA was fragmented to 100-1000 bp using Bioruptor (Diagenode). End repair (NEBNext® End Repair Module) and adding an 'A' base to the 3'end (NEBNext® dA-Tailing Module) were performed on the DNA fragment and then methylated DNA adapter (NEXTflex™ DNA Barcodes) was ligated to the product. The adapter-ligated DNA of 200–400 bp was purified using AMPure beads (Beckman Coulter), followed by sodium bisulfite conversion using MethylCode™ Bisulfite Conversion Kit (Life Technologies). The bisulfite-converted DNA was amplified by 12 cycles of PCR using LongAmp® Taq DNA Polymerase (NEB) and purified using AMPure beads (Beckman Coulter). The Paired-End sequencing of the MethylC-seq libraries was performed for 101 cycles.

value: 14 DPA


title: upf1_2

city: Paris

first: Maxime

last: Wery

address: 26 rue d'Ulm

institute: Institut Curie

description: rRNA-depleted RNA

data_processing:
Reads were mapped to the S. cerevisiae S288C reference genome (retrieved from SGD) using the version 2.0.6 of TopHat, with a tolerance of 3 mismatches and a maximum size for introns of 5 Kb.
All bioinformatics analyses used reads uniquely mapped on the reference genome.
Tags densities were normalized on snoRNAs, that are insensitive to Xrn1.
Genome_build: S. cerevisiae S288C
Supplementary_files_format_and_content: A single tab-delimited text file including normalized tag densities (tag/nt) for each annotated feature (including XUT, SUT and CUT lncRNAs) in each sample

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
Total RNA was extracted using standard hot phenol procedure. rRNAs were depleted from total RNA using the RiboMinus Eukaryote System v2 (Life Technologies). Alternatively, total RNA was treated with Terminator 5'-Phosphate-Dependent Exonuclease (Epicentre) to digest all 5'-monophosphate-ended RNAs.
Strand-specific total RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina), starting from 125 ng of rRNA-depleted RNA or Terminator-treated RNA . Paired-end sequencing (2x50 nt) of the libraries was performed on a HiSeq 2500 sequencer.

tag: genotype/variation

value: YAM202 upf1D strain

tag: background strain

tag: replicate


title: upf1_1

description: rRNA-depleted RNA


title: WT_UPF1_2

description: rRNA-depleted RNA

value: YAM1 wild-type strain


title: ovule_MethylC-seq rep1

source_name: ovule

value: 0 DPA


title: xrn1_W303_1

description: rRNA-depleted RNA

value: YAM97 xrn1D strain


title: WT_UPF1_1

description: rRNA-depleted RNA


title: ovule_MethylC-seq rep2


title: Leaf_MethylC-seq rep2

source_name: leaf

value: young leaves


title: fiber_MethylC-seq rep1


title: fiber_smRNA-seq rep2

data_processing:
Basecalls performed using CASAVA version 1.8
After adapter clipping, smRNA-seq reads (18-30 nt) were mapped to reference genome using Bowtie2 allowing no mismatches and no more than 200 alignments. Multi-mapped smRNA-seq reads were evenly assigned to all locations.
Genome_build: Genome sequences of Gossypium arboreum (Ca_all_Version2) and Gossypium raimondii (v2.1)
Supplementary_files_format_and_content: smRNA_chromosome_distribution.txt: This is smRNA distribution in chromosomes using 100kb window for leaf, ovule and fiber. 1st column:chromosome; 2nd column: start site; 3rd column: stop site; 4th column: smRNA PPM in leaf; 5th column: smRNA PPM in ovule; 6th column: smRNA PPM in fiber.
The website for D genome (Gossypium raimondii) is: http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Graimondii . The website for A genome (Gossypium arboreum) is: http://cgp.genomics.org.cn/page/species/download.jsp?category=arboreum .

extract_protocol:
Total RNA was isolated from cotton leaves, ovules at 0 DPA and fibers at 14 DPA using Plant RNA Reagent (Life Technologies).
By polyacrylamide gel electrophoresis, RNAs corresponding to ～15 to 30 nt in length from 20 μg total RNA were excised and eluted from the gel using 0.3 M NaCl. Small RNAs were precipitated using ethanol and dissolved in 6 μl RNase free water. smRNA-seq libraries with three biological replicates were constructed using NEBNext® Multiplex Small RNA Library Prep Set (NEB) according to the manufacturer’s instructions. smRNA-seq libraries were single-end sequenced for 50 cycles.


title: xrn1_W303_2

description: rRNA-depleted RNA


title: Leaf_MethylC-seq rep1


title: fiber_smRNA-seq rep3


title: WT_W303_1

description: rRNA-depleted RNA

value: YAM92 wild-type strain


title: WT_W303_2

description: rRNA-depleted RNA


title: fiber_smRNA-seq rep1


title: ovule_smRNA-seq rep2


title: dcp2_37C_Ter_1

description: Terminator-treated RNA

value: YAM2283 dcp2-7 strain (37C)


title: dcp2_37C_Ter_2

description: Terminator-treated RNA


title: ovule_smRNA-seq rep1


title: ovule_smRNA-seq rep3


title: WT_37C_Ter_2

description: Terminator-treated RNA

value: YAM1 wild-type strain (37C)


title: Leaf_smRNA-seq rep3


title: WT_37C_Ter_1

description: Terminator-treated RNA


title: Leaf_smRNA-seq rep2


title: xrn1_S288C_Ter_2

description: Terminator-treated RNA

value: YAM6 xrn1D strain


title: WT_S288C_Ter_2

description: Terminator-treated RNA


title: xrn1_S288C_Ter_1

description: Terminator-treated RNA


title: fiber_RNA-seq rep1

data_processing:
Basecalls performed using CASAVA version 1.8
Gene annotation and TE information of Gossypium arboreum and Gossypium raimondii were downloaded from http://cgp.genomics.org.cn and http://phytozome.jgi.doe.gov, respectively. mRNA-seq reads were mapped to reference genome using Tophat{Trapnell, 2009}. Uniquely mapped reads were extracted and analyzed by Cufflinks to determine gene and TE abundance using Gene annotation and TE information{Roberts, 2011}. The up-regulated or down-regulated genes were identified through double filtering with fold change (> 2-fold) and ANOVA tests (P < 0.01).
Genome_build: Genome sequences of Gossypium arboreum (Ca_all_Version2) and Gossypium raimondii (v2.1)
Supplementary_files_format_and_content: 1st column: gene ID; 2nd column: FPKM in leaf rep1; 3rd column: FPKM in leaf rep2; 4th column: FPKM in ovule rep1; 5th column: FPKM in ovule rep2; 6th column: FPKM in fiber rep1; 7th column: FPKM in fiber rep2

extract_protocol:
Total RNA was isolated from cotton leaves, ovules at 0 DPA and fibers at 14 DPA using Plant RNA Reagent (Life Technologies).
After DNase treatment of 5 μg total RNA, Strand-specific mRNA-seq libraries with two biological replications were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB) according to the manufacturer’s instructions. mRNA-seq libraries were single-end sequenced for 150 cycles.


title: Leaf_smRNA-seq rep1


title: ovule_RNA-seq rep2


title: fiber_RNA-seq rep2


title: xrn1_SK1_1

description: rRNA-depleted RNA

value: YAM2087 xrn1D strain

value: SK1 haploid


title: xrn1_SK1_2n_2

description: rRNA-depleted RNA

value: YAM2068 xrn1D/xrn1D strain

value: SK1 diploid


title: xrn1_SK1_2n_1

description: rRNA-depleted RNA


title: ovule_RNA-seq rep1


title: Leaf_RNA-seq rep1


title: WT_SK1_1

description: rRNA-depleted RNA

value: YAM1977 wild-type strain


title: Leaf_RNA-seq rep2


title: xrn1_SK1_2

description: rRNA-depleted RNA


title: WT_SK1_2n_1

description: rRNA-depleted RNA

value: YAM2067 wild-type strain


title: MDA-MB231.2

city: Göttingen

first: Tim

last: Beissbarth

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: University Medical Center Göttingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using STAR version 2.4 to human hs38. Data were converted and sorted by samtools 0.1.19 and gene abundances were estimated using RSEM 1.2.19.
Gene Definitions were used from ENSEMBL genome version GRCh38 release 78. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes expected counts (abundance measurements) for each Sample

organism: Homo sapiens

extract_protocol:
Total RNA for array experiments was isolated using TRIZOL reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA). RNA integrity for each sample was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 1000 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.
Non stranded mRNA-Seq

treatment_protocol: The ER+ and PR+ human breast cancer cell line MCF-7 was purchased from DSMZ and the triple-negtaive MDA-MB-231 breast cancer cell war pruchased from ATCC. Both cell lines were maintained in RPMI-1640 medium (PAA Laboratories Inc., Cölbe, Germany) supplemented with 10% heat-inactivated fetal calf serum (FCS, Invitrogen, Karlsruhe, Germany). For gene expression studies, cells were seeded on extracellular matrix (R&D Systems, Wiesbaden, Germany)-coated tissue culture wells.

tag: cell line

value: Triple Negative


title: MDA-MB231.3

tag: cell type


title: dcp2_37C_2

description: rRNA-depleted RNA


title: MDA-MB231.1


title: dcp2_37C_1

description: rRNA-depleted RNA


title: WT_37C_2

description: rRNA-depleted RNA


title: MCF7.2

value: ER+, PR+


title: WT_S288C_Ter_1

description: Terminator-treated RNA


title: xrn1_S288C_2

description: rRNA-depleted RNA


title: WT_37C_1

description: rRNA-depleted RNA


title: siPTBP1/siUPF1 rep2

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were  mapped to hg19 whole genome usingtophat/2.0.10/bowtie2-2.2.0 with parameters -p 8 -g 1 -N 2 -r 200 --no-coverage-search --no-mixed
After downloading 3UTR coordinates bed file from UCSC genome browser table, mapped reads in 3UTR were counted by bedtools coverageBed function.
The reads number in each refSeq transcript 3UTR region were summed and normalized by the library size and length of the 3UTR region to generate RPKM values.
75th percentile normalization and log10 transformation on each sample RPKM dataset
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files listing Refseq IDs, raw read counts, RPKM values

source_name: 293 Tet-off

growth_protocol: 293 Tet-off cells (Clontech) were grown in DMEM supplemented with L-glutamine, penicillin, and streptomycin (Life Technologies).

extract_protocol:
Total RNA was isolated using the Qiagen Rneasy kit, according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for paired-end sequencing.

treatment_protocol: Cells were transfected with indicated siRNAs using RNAiMAX reagent (Life Technologies).


title: siPTBP1/siUPF1 rep1


title: xrn1_S288C_1

description: rRNA-depleted RNA


title: WT_S288C_2

description: rRNA-depleted RNA


title: WT_SK1_2n_2

description: rRNA-depleted RNA


title: WT_SK1_2

description: rRNA-depleted RNA


title: WT_S288C_1

description: rRNA-depleted RNA


title: siPTBP1 rep2


title: siNS rep1

value: siNS


title: siUPF1 rep2


title: siNS rep2


title: TCRgd+NK1.1-_2

city: New York

first: Saida

last: Dadi

state: NY

address: 1275 York Ave

department: Immunology

institute: MSKCC

data_processing:
The raw output BAM files were converted to FASTQ using PICARD Sam2Fastq. Reads were then trimmed using fastq_quality_trimmer with default settings.
The trimmed reads were first mapped to the mouse genome using rnaStar (version 2.3.0e).
The genome assembly mm9 was used with junctions from ENSEMBL (Mus_musculus.NCBIM37.67) and a read overhang of 49.  Then any unmapped reads were mapped to mm9 using BWA MEM (version 0.7.5a).  The two resulting BAM files were merged and gene level counts were computed using htseq-count (options -s y -m intersection-strict) and the same gene models (Mus_musculus.NCBIM37.67).
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file where 1st column contains Ensembl gene ids. Each column after the first one contains the counts for a sample

source_name: Mammary tumors of 20- to 24-week-old PyMT C57BL/6 mice

extract_protocol:
Cells were isolated from pooled tumors of 20- to 24-week-old PyMT mice. Tumors were prepared by mechanical disruption using a razor blade followed by treatment with 280 U/ml Collagenase Type 3 (Worthington Biochemical) and 4 μg/ml DNase I (Sigma) at 37°C for 1 h with periodic short vortexing. Digested tissues were mashed through 70-μm filters, and collected by centrifugation. Cell pellet was resuspended in 44% Percoll, layered on top of 66% Percoll (Sigma), and centrifuged at 1,900 g for 30 min without brake. Cells at the Percoll interface were collected, stained with antibodies and analyzed by flow cytometry. Cells were sorted using FACS Aria-II machines directly in Tri-Reagent (Sigma).
RNA was prepared and complementary DNA (cDNA) libraries were amplified using the SMARTer RACE Amplification Kit (Clontech)

tag: strain

tag: gender

value: female

value: 20- to 24-week-old

tag: tissue

value: mammary tumor

tag: cell population


title: TCRb+CD8a+NK1.1-_2

tag: age


title: siPTBP1 rep1


title: TCRgd+ILTC1_2


title: ML-4

city: Charlotte

first: Adam

middle: Michael

last: Whaley

state: NC

address: 9201 University City Blvd

department: Bioinformatics and Genomics

institute: UNCC

data_processing:
Published Cufflinks analysis pipeline (tophat v.2.0.9, cufflinks v.2.1.1).
Sequences aligned to Glycine max reference genome version 2.75 (available at JGI-phytozome).
Mapping step done with suggested non-mammalian parameters (-I 5000), reference GTF file used (also available at phytozome).
Genome_build: V2.75

organism: Glycine max

source_name: G. Max 5th trifiolate leaf

extract_protocol:
Whole leaf tissue from each of the three leaflets from the  5th trifoliate leafs was extracted using the Qiagen Plant RNAEasy extraction kit (Qiagen, CA) followed by Ambion DNA-free treatment (Life Technologies, NY).
RNA-seq libraries were subsequently created using Illumina TruSeq RNA-seq kit (Illumina, CA).  Each library was quantified on the Bioanalyzer using RNA nano chips (Agilent, CA)

treatment_protocol: High Ozone treatments exposed to 75 ppb ozone atmospheric conditions in CSTR

tag: ozone level

tag: time point


title: MCF7.1


title: FH-4


title: ILC1l_2


title: cNK_2

value: cNK


title: FL-3


title: FL-4


title: TCRb+CD8a+NK1.1-_1


title: siUPF1 rep1


title: FH-3


title: MH-4


title: MH-2


title: MH-3


title: TCRgd+NK1.1-_1


title: TCRab+ILTC1_1


title: ML-2


title: FH-2


title: TCRab+ILTC1_2


title: RNAseq_Atoh1_restoration_rep7

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
For ChIP-Seq, reads were aligned to the murine genome (mm9) with BOWTIE v0.12.8 using either the -m 1, -v 0 options (ChIPs from sorted tumor cells) or standard-options (ChIPs from tumorspheres). For RNA-Seq data, we sequential map reads using an in-house script implementing BWA with default settings, STAR (extra settings: "--outSAMunmapped Within --outSAMstrandField intronMotif") and SIM4 with default settings, followed by a re-implementation of Picard's CleanSam in which we enable trimming for alignments that run off the end of the reference, and in which we also enable extending alignments by identifying soft-clipping that could align in-place.
Peaks were called and wig-files were produced with MACS-1.4.2
All further analysis were performed in R, Excel and Seqminer or with bedtools. For RNA-Seq, reads for each ensembl gene were counted using the summarizeOverlaps {GenomicAlignments} function in R. Weakly expressed genes were removed (read sum of all samples per gene > 18) and differentially expressed genes were called using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: MACS-output files in wig-format or bed-format are provided. For RNA-Seq, matrix file contains read count and edgeR output contains gene name, ensembl ID, Log2 fold change, log2 CPM, p-value and Benjamini-Höchberg-adjusted p-value (FDR).

growth_protocol: The Group3 (G3) medulloblastoma (MB) model relies on enforced expression of c-Myc (Myc) in primary granule neuron progenitors (GNPs) isolated from the cerebella of 7 day-old Trp53-/-;Cdkn2c-/- mice followed by orthotopic transplantation of the transduced cells into the cortices or cerebella of naïve immunocompromised CD-1 nu/nu recipient animals (Kawauchi et al., 2012).

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies).
Libraries forRNA-seq samples were contructed following manufactor's intructions using the TruSeq Stranded Total RNA Kit (Illumina).

treatment_protocol: Three G3 MB tumorsphere lines (#19251, 19554, and 19568) infected with retroviruses encoding Atoh1 followed by cranial implants into the cortices of recipient animals. Tumor cells were dissociated and purified by percoll-gradient.

tag: generation of cells

value: spheres from tumor cells


title: FL-2


title: TCRgd+ILTC1_1


title: cNK_1


title: TCRb+CD8a+PD1-NK1.1-_2


title: RNAseq_Atoh1_restoration_rep5


title: ILC1I_1


title: RNAseq_Atoh1_restoration_rep4


title: TCRb+CD8a+PD1+_2


title: RNAseq_Atoh1_restoration_rep3


title: MH-1


title: FL-1


title: RNAseq_Atoh1_restoration_rep2


title: ML-1


title: RNAseq_Atoh1_restoration_rep6


title: TCRb+CD8a+NK1.1+_2


title: ML-3