title: 5_dop-1

description: Synchronized embryos were hatched on NGM plates and grown at 20°C until 48 h after the L4 stage of development


title: YAP_Knockdown_rep2

status: Public on Apr 30 2016

type: SRA

city: Jupiter

first: Joseph

last: Kissil

state: Florida

address: 130 Scripps Way

department: Cancer Biology

country: USA

institute: The Scripps Research Institute

description: Mouse cells isolated from Nf2-null schwannoma

library_source: transcriptomic

data_processing:
Adaptor trimming was performed by 'flexbar 2.41 beta' for csfasta files and using an internal perl script for qual files
Quality trimming was performed using an internal perl script
Reads were aligned to mm9 reference genome using 'Tophat 2.0.9'
Raw read counts generated using HTSeq 0.6.1
Normalized counts and a list of differentially expressed genes generated using DESeq 1.14.0
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file is a text file and contains normalized counts obtained from DESeq 1.14.0

molecule: total RNA

organism: Mus musculus

source_name: Nf2-null Schwann cells treated with YAP pooled siRNA

growth_protocol: SC4 cells were maintained in DMEM media with 10% FBS at 37 degrees C, and 5% CO2.  Standard cell culture techniques were employed.

extract_protocol:
Media was aspirated and cells were washed twice with sterile PBS.  0.5 ml of Trizol reagent (Life Technologies) was added to each well.  Cell lysates were collected and frozen immediately and stored at -80 degrees C overnight.
For RNA-Seq analysis, 5-10 μg of total RNA was used to isolate poly(A) RNA using the micropoly(A)purist kit (Ambion). The whole transcriptome library kit (Life Technologies) was used to prepare paired-end sequencing libraries. Briefly, 100 ng of poly(A)+ RNA was enzymatically fragmented to an average size of 150 nt, ligated to directional adapters and reverse-transcribed, and the cDNA was size-selected on denaturing 6% TBE-Urea polyacrylamide gels, amplified for 15 cycles with barcoded primers and purified using AmpPure XP beads. The resulting libraries were quantified using Bioanalyzer (Agilent) and Taqman (Life Technologies) assays. Barcoded libraries from each sample were combined at equimolar amounts and the mixture was used at a final concentration of 0.4 pM in emulsion PCR to link the libraries to the sequencing beads.

treatment_protocol: SC4 cells were passaged into 6-well plates at a concentration of 5.0 x 10^4 cells/well and were grown for 24 hours before treatment.  siRNAs were transfected in OptiMem(Life Technologies) using Lipofectamine 2000 reagent(Life Technologies) at a final concentration of 40 nL of siRNA .  Transfected cells were grown for 48 hours before RNA extraction.

tag: tissue

value: Nf2-null schwannoma

tag: cell line

value: SC4 Schwann cells

tag: treatment

value: YAP Smartpool siRNA (GE Life Sciences)


title: 3_odIs77

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Road

department: Department of Genetics

institute: Waksman Institute, Rutgers The State University of New Jersey

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run Mode, resulting in high quality sequence reads (FAST QC Phred score average of 40 out to the full 50 bp length).
Reads (45-49 million per genome and replicate) were analyzed using Geospiza Genesifter, with alignment to the C. elegans genome (WS220) via Illumina WTS BWA (GATKv3).
From 89-90% of reads mapped to the genome (72-74% mapped to annotated ORFs).
Normalization and statistical analysis was performed with EdgeR with a Benjamini and Hochberg correction.

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to release embryos. Synchronized embryos were hatched on NGM plates and grown at 20°C until 48 h after the L4 stage of development. Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood

extract_protocol:
For each RNA-seq experiment, populations for odIs77[Pcol-19::UbG76V-GFP] and dop-1(vs100); [Pcol- 19::UbG76V-GFP] were grown simultaneously under the same conditions. Total RNA was isolated from animals using trizol (Invitrogen) combined with Bead Beater lysis in 3 biological replicates
mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection. Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run Mode, resulting in high quality sequence reads (FAST QC Phred score average of 40 out to the full 50 bp length).

value: whole animals

tag: genotype/variation


title: 2_odIs77


title: 4_dop-1


title: wildtype male fly head

city: Berkeley

first: Qingqing

last: Wang

state: CA

address: 161 Koshland Hall, UC Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

description: processed data files: Dataset S1-S4

data_processing:
Read alignment: RNA-seq samples using STAR 2.5.0, map to Drosophila dm3 genome
Differential alternative splicing analyses: used MISO, JuncBase, and the Junction Usage Model (author-developed method, see associated manuscript)
Differential overall gene expression level analyses: used DESeq2
genome build: dm3
processed data files format and content: Dataset S1: txt format; Junction Usage Model output for differential AS analyses of PSIΔAB and full-length PSI male fly heads; Dataset S2: txt format; MISO output for differential AS analysis of PSIΔAB and full-length PSI male fly heads; Dataset S3: txt format; JuncBase output for differential AS analysis of PSIΔAB and full-length PSI male fly heads; Dataset S4: txt format; DESeq2 output for differential overall gene expression level analysis of PSIΔAB and full-length PSI male fly heads

organism: Drosophila melanogaster

source_name: wildtype male fly head

extract_protocol:
For RNA-seq, Drosophila heads were isolated from 50mL of manually sorted and frozen males from the v16/v16 PSI mutant fly strain (PSI-null) carrying either the PSI genomic-cDNA wild-type or PSIΔAB transgenes.  Total RNA was isolated using Qiagen RNA Easy kits and polyA (+) RNA was purified using oligo (dT) Dynabeads (Life Technologies).  For iCLIP, Nuclei were isolated from suspension cultures of S2 cells by hypotonic lysis and Dounce homogenization.  Nuclei were resuspended in isotonic buffer and irradiated on ice with 150 mJ/cm2 at 254 nm in a Stratalinker 2400.
NEBNext® mRNA Sample Prep kit (cat # E6110S; New England Biolabs)

tag: genotype

value: wildtype

value: head

tag: gender

value: male


title: SC4_Control_rep3

source_name: Nf2-null Schwann cells treated with Control siRNA

value: Control siRNA (GE Life Sciences)


title: PSIΔAB male fly head rep1

description: processed data files: Dataset S1-S4

source_name: mutant male fly head rep1

value: PSIdeltaAB


title: 24h RN TCDD

city: East Lansing

first: Norb

last: Kaminski

state: MI

institute: MSU

data_processing:
FASTQC v0.11.2 was used for quality control
FASTX v0.0.14 and Cutadapt 1.4.1 was used for adaptor removal and removal of low-complexity reads
TopHat v1.4.1 was used for alignment
SAMTools v0.1.19 was used for file conversion
HTSeq v0.6.1 was used to count feature aligned reads
DESeq was used to transform counts
Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81 (mouse), Rn5 release 76 (rat), GRch38 release 76 (human)
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

organism: Rattus norvegicus

source_name: primary B cell

growth_protocol: Primary mouse and rat B cells were isolated from spleens (female mice and rats 6-9 weeks old) using Miltenyi untouched Mouse/Rat B cell isolation kit. Primary human B cells were isolated from leukopaks donated by anonymous  female donors using Miltenyi naive human B cell isolation kit. After isolation cells were cultured in RPMI1640 medium supplemented with 10% serum.

extract_protocol:
B cells vere collected 4, 8 and 24h pot-treatment, preserved in RNA later stabilization reagent QIAGEN , and RNA was harvested using RNeasy Plus Mini kit (QIAGEN) according to manufacturer's instructions. RNA was quantified and examined for purity and quality by nanodrop, Qubit and Bioanalyzer.  Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Isolated priary cells were activated with 15 ug/ml pokeweed mitogen (PWM) and  treated with either vehicle (0.02%) DMSO or 30 nM TCDD and incubated for 4, 8 and 24h.

tag: strain

value: Sprague-Dawley

tag: Sex

value: Female

tag: age

value: 6-9 weeks

value: TCDD

tag: concentration

tag: concentration unit

value: nM

tag: duration

tag: duration unit

value: hours

tag: replicate

tag: activation method

value: pokeweed mitogen


title: YAP_Knockdown_rep1


title: 4h RN VH

value: DMSO Vehicle


title: 24h RN VH


title: Akt1F/F;Akt2-/-;Alb-Cre

city: Chicago

first: Nissim

last: Hay

state: IL

address: 900 South Ashland Ave

department: BMG

institute: University of Illinois Chicago

data_processing:
Outline of analysis performed  1. Data obtained from University of Chicago server  a. Condition “NH1” (Akt1F/F;Akt2-/-): 51 bp each, 1 biological sample  b. Condition “NH2” (Akt1F/F;Akt2-/-;Alb-Cre): 51 bp each, 1 biological sample  c. FastQC reports for each lane of each sample are provided in the folder QC_reports  2. Alignment to genome using Tophat 2.0.8  a. Standard UCSC mm10 reference genome and annotation  b. Non-default parameters: minimum intron size 70 bp (default is 50 bp)  c. Retain unique alignments with ≤ 2 mismatches  d. Results:  Table 1.1: Alignment statistics  Sample Raw reads (M) Alignments (M) %  NH1 231 197 85.1  NH2 224 194 86.6    3. Differential expression analysis using Cuffdiff 2.1.1  a. Compared NH1 vs NH2, standard mm10 annotation  b. Default parameters  c. Per-gene and per-isoform results (log-fold change, p-value, q-value) are reported in gene.diff.xlsx and isoform.diff.xlsx  i. 100 differentially expressed genes and 84 differentially expressed isoforms at an FDR o f 0.05
Genome_build: mm10
Supplementary_files_format_and_content: cuffdiff

source_name: Livers of 6 month old male mice

extract_protocol: RNA libraries were generated from the livers of 4 six-month-old Akt2-/- male mice and 4 six-month-old Akt1hep-/-Akt2-/- male mice after liver perfusion. Multiplex RNA library sequencing was performed by the University of Chicago Genomics Core. Bioinformatics analysis was carried out by UIC RRC bioinformatics.

value: liver


title: 4h RN TCDD


title: 8h RN VH


title: SC4_Control_rep1

value: Nf2-null schwannoma

value: SC4 Schwann cells


title: 8h RN TCDD


title: 6_dop-1

value: whole animals


title: Akt1F/F:Akt2-/- liver


title: PSIΔAB male fly head rep2

description: processed data files: Dataset S1-S4

source_name: mutant male fly head rep2


city: Houston

first: Jian

last: Chen

state: Texas

address: 1515 Holcombe Blvd.

institute: The University of Texas M.D. Anderson Cancer Center

data_processing:
The raw data quality was assessed using a FastQC software.
Adaptor presence was tested using Trimmomatic.
The readings were then aligned to the NCBI mouse  chromosome genome build 37.2 using  the splice-aware aligner Tophat2 v2.0.10.
Transcript quantification was carried using HTSeq
A gene model gtf file corresponding to the NCBI mouse reference genome build 37.2 was used in the quantification.
DESeq2 was used to identify significant differences in gene expression profiles between the MEF cells.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with raw counts

source_name: mouse normal liver from β2SP+/- ; SMAD3+/- mouse

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: beta-2SP+/- ; SMAD3+/-

tag: disease status

value: normal


title: liver tumor2

source_name: mouse liver tumors from β2SP+/- ;SMAD3+/- mouse

value: tumor


title: liver tumor1


title: SC4_Control_rep2

value: Control siRNA (GE Life Sciences)


title: SMAD3-/- MEF

description: SMAD3 homozygous knockout

data_processing:
Whole-transcriptome RNA sequencing of  wild type and β2SP knockout (β2SP+/-, β2SP-/-, SMAD3 +/-, SMAD3-/- and β2SP+/- / SMAD3+/- ) mouse embryonic fibroblasts was carried out on an Illumina HiSeq 2000 sequencer.
The raw data quality was assessed using a FastQC software.
Adaptor presence was tested using Trimmomatic.
The readings were then aligned to the NCBI mouse reference genome build 37.2 using the splice-aware aligner Tophat2 v2.0.10.
Transcript quantification was carried using HTSeq
A gene model gtf file corresponding to the NCBI mouse reference genome build 37.2 was used in the quantification.
DESeq2 was used to identify significant differences in gene expression profiles between the MEF cells.
Genome_build: mm9
Supplementary_files_format_and_content: Raw counts text file

source_name: Mouse embryonic fibroblast

growth_protocol: Sptbn1+/−  and SMAD3 +/- mice were mated, and the females were euthanized by cervical dislocation when the embryos reached E13.5. Primary MEFs were generated and plated.  After the MEFs’ genotype was confirmed and the cells reached confluence, the MEFs were trypsinized and replated. MEFs were cultured in DMEM/F12 medium (D5671; Sigma Aldrich, St Louis, MO) supplemented with 10% fetal bovine serum.

tag: cell type

value: embryonic fibroblast


title: β2SP+/- ; SMAD3+/- MEF

description: Sptbn1 heterozygous and SMAD3 heterozygous knockout


title: β2SP-/- MEF

description: Sptbn1 homozygous knockout


title: 24h MU TCDD


title: β2SP+/- MEF

description: Sptbn1 heterozygous knockout


title: 24h MU VH


title: 8h MU TCDD


title: 8h MU VH


title: SMAD3+/- MEF

description: SMAD3 heterozygous knockout


title: normal liver from wild type mouse

source_name: mouse normal liver from wild type mouse

value: wild type

tag: tissue


title: Lsd1 mko/wt two-cell embyo 5 RNA seq

status: Public on May 01 2016

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Quality control: Reads characterized by at least one of the following criteria were discarded from the analysis i) >50% of low quality bases (Phred score <5) ii) >5% of N bases iii) >80% of AT rate iv) ≥30% of continuous A and/or T
Gene analysis: Reads were aligned to the mouse mm10 genome using the TopHat software v2.0.6. Count tables of gene expression were then generated using HTSeq v0.6.1 software. The DESeq R package v1.16.0 was used to normalize and identify the differentially expressed genes between control and mutant embryos.
Repeats analysis: Reads were aligned to the mouse mm10 genome using the Bowtie v1.0.0 software. Aligned reads were then annotated and intersected with repeats annotation from the repeatMasker database. The number of reads falling in repeats were counted and normalized by the total number of reads aligned on repeats. Differential analysis was performed using the limma R package v3.20.4 .
Genome_build: mm10
Supplementary_files_format_and_content: excel files with 2 sheets: Count read tables i) for each gene ii) for each repeat family

source_name: Lsd1 mat ko/wt_two-cell stage embryo

extract_protocol:
two-cell stage embryos were recovered and flash frozen;reverse transcription was carried out directly on the whole  embryos lysate, and total cDNA were then prepared according to Tang et al Nature Protocol  2010 to be used to  construct sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

tag: developmental stage

value: mouse preimplantation two-cell stage embryos

value: Lsd1 mat ko/wt


title: wild type MEF

description: wild type

value: wt


title: 4h MU TCDD

value: Female

value: 6-9 weeks

tag: treatment

value: TCDD

value: nM


title: 4h MU VH

value: DMSO Vehicle

value: hours

value: pokeweed mitogen


title: GM-CSF(-)-3

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

country: Japan

institute: AIST

data_processing:
Basecalls performed using bcl2fastq 1.8.4
RNA-seq reads were aligned to the UCSC mm10 Refseq assembly using TopHat with --no-novel-juncs switch.
FPKM values were calculated using Cufflinks and the refernce transcriptome used for alignment.
Annotations were appended using Cuffcompare.
Genome_build: mm10
Supplementary_files_format_and_content: tmap files generated using TopHat2/Cufflinks/Cuffcompare

source_name: small intestinal eosinophils not treated

extract_protocol:
RNA samples were isolated from small intestinal eosinophils using Trizol reagent (Invitrogen)
libraries were prepared using Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina)

treatment_protocol: Small intestinal eosinophils of BALB/c mice were cultured with or without 10 ng/ml GM-CSF for 4 hours.

value: not treated

tag: tag

value: small intestinal eosinophils

value: BALB/c


title: GM-CSF(+)-2

source_name: small intestinal eosinophils treated

value: GM-CSF


title: GM-CSF(-)-2


title: 24h HU VH rep3

organism: Homo sapiens


title: GM-CSF(+)-3


title: GM-CSF(-)-1


title: 8h HU TCDD rep3


title: 4h HU TCDD rep3


title: 8h HU VH rep3


title: 4h HU VH rep3


title: 24h HU VH rep2


title: 24h HU TCDD rep2


title: 8h HU VH rep2


title: 4h HU TCDD rep1


title: 4h HU TCDD rep2


title: 8h HU TCDD rep1


title: GM-CSF(+)-1


title: 8h HU VH rep1


title: 24h HU TCDD rep1


title: 4h HU VH rep1


title: 24h HU TCDD rep3


title: normal fibroblast

data_processing:
Whole-transcriptome RNA sequencing of the one norma; fibroblast cell line from normal pople and the 3 different cell lines established from BWS patients: CDKN1C+ (patient with CDKN1C mutation), KvDMR+ (patient with loss of methylation in the KCNQ1OT1 region) and KvDMR- (patient with unknown molecular etiology). The sequencing was carried out on an Illumina HiSeq2000 sequencer.
The raw data quality was assessed using a FastQC software.
Adaptor presence was tested using Trimmomatic.
The readings were then aligned to the NCBI Human  chromosome genome build 37.2 using  the splice-aware aligner Tophat2 v2.0.10.
Transcript quantification was carried using HTSeq
A gene model gtf file corresponding to the NCBI human reference genome build 37.2 was used in the quantification.
DESeq2 was used to identify significant differences in gene expression profiles between the MEF cells.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM available in csv file on series record.

source_name: Human Cell line established from normal people

tag: genotype

value: healthy

value: fibroblast


title: capture in-situ Hi-C

first: Noboru

middle: Jo

last: Sakabe

address: 920 E 58th st

department: Human Genetics

institute: University of Chicago

description: interacting chromatin

library_source: genomic

data_processing:
library strategy: HiC-seq
Basecalls performed with Illumina bcl2fastq2-v2.17.1.14 by the Functional Genomics Facility at the University of Chicago
Read mates were independently aligned to hg19 with bowtie2-2.2.3 with --local --mm --very-sensitive-local
Reads with MAPQ < 10 were filtered out
Reads were paired using a custom script
Cis interactions were called using HOMER with -res 2000 and -superRes 10000, -superRes 20000
Genome_build: hg19
Supplementary_files_format_and_content: interactions identified by HOMER

molecule: genomic DNA

source_name: lymphoblastoid cell line

growth_protocol: LCL's were grown according to Battle et al (2015) [PMID: 25657249]

extract_protocol: In situ Hi-C was performed as described in Rao et al (2014) [PMID: 25497547] using MboI to digest the chromatin. The Hi-C library was amplified directly from the T1 beads with 9 cycles of PCR, using Illumina primers and protocol (Illumina, 2007). To capture promoter interactions, the Hi-C library was hybridyzed to 81,735 biotinylated 120 bp custom RNA probes (Custom Array) targeting the 4 nearest MboI restriction fragment ends (restriction fragments longer than 200 bp) around human RefSeq promoters in hg19. Twelve cycles of PCR were performed in the captured library.

value: lymphoblastoid cell line

tag: passages

tag: iPSc source individual id

tag: restriction enzyme

value: MboI


title: CDKN1C+

source_name: Human Cell line established from BWS patient

value: BWS


title: KvDMR-

value: KvDMR-


title: KvDMR+

value: KvDMR+


title: FLAG-MBTD1

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

data_processing:
Raw reads were mapped on the human genome build hg19 using Burrows-Wheeler Aligner (bwa http://bio-bwa.sourceforge.net/). Uniquely mapped reads were kept for further analysis. Samtools and the script genomeCoverageBed were used to produce bedgraph files. The final bigWig files were generated using the program bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bw

source_name: Human lymphoblast

growth_protocol: RPMI, 10% FBS, 25mM Hepes, 1Xglutamax, 1ug/ml puromycine

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: no treatment

tag: cell line

value: Human lymphoblast

tag: growth conditions

value: untreated cells, normal growth conditions

tag: chip antibody

value: ANTI-FLAG® M2 antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat.#

tag: chip antibody lot #


title: FLAG-EPC1


title: FLAG-EPC1 581


title: Infected

city: Xi'an

first: Li

last: Guo

state: Shaanxi

address: 28 Xianning West Road

country: China

institute: Xi'an Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
DATA FILTERING: java -jar trimmomatic-0.32.jar PE -phred33 control_a.fq.gz control_b.fq.gz control_aPaired.fq.gz control_aUnpaired.fq.gz control_bPaired.fq.gz control_bUnpaired.fq.gz LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36
Data Merging: cat control_1aPaired.fq.gz infected_1aPaired.fq.gz > left.fq.gz ; cat control_1bPaired.fq.gz infected_1bPaired.fq.gz > right.fq.gz
ASSEMBLY: Trinity.pl --JM 40G --CPU 20 --seqType fq --left left.fq.gz --right right.fq.gz --output Pooled_Reference
RSEM: run_RSEM_align_n_estimate.pl --transcripts Pooled_Reference/Trinity.fasta --seqType fq --left control_aP.fq.gz --right control_bP.fq.gz --prefix control --thread_count 10 -- --bowtie-chunkmbs 512
Genome_build: de novo assemby

organism:
Ocimum basilicum
Peronospora belbahrii

source_name: basil leaves

growth_protocol: Sweet basil ‘Genovese’ seed (Johnny’s Seeds, Lot 48104) was germinated in soilless growing media (Premier Tech Horticulture PRO-MIX® BX Mycorrhizae™) in a greenhouse propagation room (75℉, 50-60% humidity). Seedlings were transplanted into 4” pots. Peronospora belbahrii was maintained by inoculating basil plants weekly.

extract_protocol:
Total RNAs were extracted from leaves of healthy and infected basil plants using Trizol reagent (Thermo Fisher Scientific, MA) following manufacturer’s protocol. After removal of genomic DNA by DNase I (New England Biolabs, MA) treatment, RNA samples were quantified using NanoDrop 1000 (Thermo Fisher Scientific, MA) and assessed for integrity using Agilent Bioanalyzer 2100 (Agilent, MA).
Library construction was conducted using Illumina TruSeq mRNA library preparation kit (Illumina, CA)

treatment_protocol: Basil plants with three sets of true leaves (4-6 weeks old) were inoculated by spraying the leaves thoroughly with water and brushing fresh sporangia from diseased plants onto the wetted abaxial leaf surfaces of new plants. Uninoculated plants were sprayed with distilled water only. Plants were then subjected to 100% humidity by enclosing individual plants in thin plastic for 48 hours or until sporulation was visible on inoculated plants. One inoculated plant and one uninoculated plant were randomly selected for RNA-seq analysis.

tag: plant

tag: age

tag: infected with

value: Peronospora belbahrii

tag: time point

value: 5 days post inoculation


title: Control

organism: Ocimum basilicum

value: Sweet basil ‘Genovese’ seed (Johnny’s Seeds, Lot 48104)

value: three sets of true leaves (4-6 weeks old)

value: distilled water (uninfected control)


title: D5 beta4

status: Public on Apr 29 2016

city: Philadelphia

first: Jonathan

last: Schug

state: Pennsylvania

address: 12-156 Smilow Ctr Trans Research

department: School of Medicine

institute: University of Pennsylvania

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to human genome build hg19 and Refseq transcriptome for transcript quantitation.
Differential gene expression was assessed using the edgeR and glm package to consider both the donor and beta cell subtype when comparing different subtypes.
Genome_build: hg19
Supplementary_files_format_and_content: reads.tsv: Tab delimited file of raw read counts, ST8pm.tsv (subtypes 3 and 4 combined vs subtypes 1 and 2 combined) and CD9pm.tsv (subtypes 2 and 4 combined vs subtypes 1 and 3 combined): Differential expression comparison with FC (fold change), CPM (counts per million), LR (likelihood ratio), PValue, FDR columns.

source_name: Pancreas

extract_protocol:
After Trizol extraction, RNA was extracted with a Qiagen Rneasy micro kit
RNA was amplified using the NuGEN Ovation kit.  The resulting cDNA was converted to an Illumina library using the truSeq non-stranded RNA-Seq kit.

treatment_protocol: Islet cells were enzymatically dispersed with trypsin and labeled with a combination of surface-marking monoclonal antibodies. The desired populations of live individual cells were collected by FACS directly into Trizol for RNA collection.

tag: subtype

tag: donor

tag: tissue

value: Pancreas

tag: cell type

value: beta cell


title: 8h HU TCDD rep2

tag: Sex

value: Female

tag: treatment

value: TCDD

tag: concentration

tag: concentration unit

value: nM

tag: duration

tag: duration unit

value: hours

tag: replicate

tag: activation method

value: pokeweed mitogen


title: D4 beta4


title: D5 beta3


title: D4 beta3


title: 24h HU VH rep1

value: DMSO Vehicle


title: 4h HU VH rep2


title: D5 beta2


title: D4 beta2


title: D4 beta1


title: D3 beta4_2


title: D3 beta3_1


title: D3 beta2_1


title: D2 beta4_1


title: D3 beta3_2


title: D3 beta2_2


title: D2 beta3_2


title: D2 beta4_2


title: D3 beta1_1


title: FLAG-Mock

tag: cell line

value: Human lymphoblast

tag: growth conditions

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat.#

tag: chip antibody lot #


title: D3 beta4_1

tag: subtype

tag: donor


title: D2 beta3_1

tag: tissue

tag: cell type


title: D5 beta1


title: D2 beta1_2


title: D1 beta4_2


title: D2 beta2_1


title: D2 beta1_1


title: D1 beta4_1


title: D1 beta2_2


title: D1 beta2_1


title: D1 beta3_2


title: D1 beta1_2


title: D1 beta1_1


title: YoungLens_H3K4me2_Rep2

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

data_processing:
reads were filtered using the quality of multiplexing indices before mapping to prevent contaminations by erroneous de-multiplexing. Reads with average index quality below 30 were discarded (Kircher et al., 2012). The reads were then mapped to mouse genome (mm9) by Bowtie allowing 2 mismatches per read. Only uniquely mapped reads were retained. The mapped reads were further mapped to carrier genome or biotin-DNA sequences by Bowtie allowing 3 mismatches, and reads mapped to the carrier genome or biotin-DNA were discarded.
H3K4me3 peaks of LT-HSC, ST-HSC, or MPPs are called by MACS with p-value threshold of 10-5 and parameter “llocal=100000” to enable broad peak calling. Then the six sets of peaks (two replicates for LT-HSC, ST-HSC, and MPP each) were merged to obtain a complete peak set, and the numbers of reads were counted for each peak region. We used edgeR (Robinson et al., 2010) to call differentially enriched H3K4me3 peaks between LT-HSC versus ST-HSC and between ST-HSC versus MPP data using standard edgeR  procedure. GO-term was determined by DAVID (Huang da et al., 2009).  For lens data, peaks for Young and old lens were called by MACS. Then all peaks were merged and the number of readsfalling on to merged peaks were counted for each sample. Differential peaks were called using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph file for genome browser view

extract_protocol: mESCs (500 or 1000) or sorted HSC subtypes were mixed with ~5x108 DH5a E.coli and fixed in 1% formaldehyde for 10 min at room temperature. After fixation and washes, the mixtures were sonicated with a 1/16-inch probe for 15 min at 3 watts using a tip sonicator (Misonix sonicator 3000). The lysates were incubated with 2 microliter H3K27me3 antibody (Millipore 07-449) or 1 microliter H3K4me3 antibody (Cell Signaling 9751S) overnight at 4oC. To block any non-specific chromatin absorption, 60 microliter protein G magnetic beads (Life Technologies 10004D) or 10 microliter M-280 streptavidin beads (Life Technologies 11206D) were pre-incubated with ~5x108 fixed and sonicated E.coli lysate or the same E.coli lysate plus 5 ng carrier biotin-DNA, respectively, at 4oC overnight. These treated beads were combined and used to ChIP H3K27me3 or H3K4me3 in the sonicated E.coli+mESC or E.coli+HSC lysates for 4 h at 4oC. The beads were then recovered using a magnetic stand. All washing, de-crosslinking, and library building steps were performed following Illumina True-Seq protocol with 12 PCR amplification cycles. After end repair, A-tailing, and adapter ligation steps, 0.25 micro-M blocker oligo was added during final library amplification. The Ocular lenses from P30 and P800 C57/BL6 mice were dissected out and fixed in 1% formaldehyde for 10 min at room temperature. A fixed lens was mixed with ~5x107 formaldehyde-fixed yeast and sonicated using a tip sonicator (Misonix sonicator 3000) to shear genomic DNA to an average fragment size of 150 to 250 bp. The mixture was then used for RP-ChIP-seq following the standard ChIP-seq procedure.

tag: strain

tag: age

value: young; 1 month

value: lens epithelial cell

value: H3K4me3 (Cell Signaling, 9751)


title: OldLens_H3K4me2_Rep1


title: male WT rep1

city: Bethesda

first: Anand

last: Merchant

address: 41 Center Dr

institute: NIH

data_processing:
Trimmed by Trimmomatic v0.30, the reads were aligned with reference mouse mm9 genome and ensemble v70 transcripts using Tophat v2.0.8 to generate a BAM file for each sample.
The sample BAM files were then uploaded onto Partek Genome Studio 6.6 (v6.14.006) and analyzed using the RNA-Seq workflow.
The aligned reads were then taken through a quantification process using a modified Expectation-Maximization (E/M) algorithm and assigned read counts at the level of gene and transcripts.
The scaling method of reads per kilo-base of million mapped reads (RPKM) (70) was applied to obtain scaled counts.
Genome_build: mouse mm9 genome and ensemble v70 transcripts
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values

source_name: male WT

extract_protocol:
Liver tissues were excised from ARE-Del-/- mice immediately upon sacrifice and frozen in liquid nitrogen. The frozen liver was ground with a pestle and mortar chilled with liquid nitrogen. RNA was extracted 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: Liver

value: 20 wk old

tag: gender

value: male

tag: genotype/variation

value: WT


title: male WT rep2


title: D2 beta2_2


title: siWT-2

city: San Diego

first: brian

last: james

address: 10901 North Torrey Pines Road

institute: Sanford Burnham

data_processing:
basecalling from AmpliSeq Platform
data pre-processing (5' trimming or low qulaity filter?)
two step alignment integrated with Tophat2 and Bowtie2
count reads (HT-Seq v0.6.0)
read count normalization by edgeR v3.8.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM  and raw count values for each Sample.

source_name: H3A cells

extract_protocol:
Total RNA from tumors was extracted using TRIzol (Ambion, CA, USA). Total RNA from cell lines was extracted using a total RNA miniprep kit (Sigma-Aldrich)
Protocol outlined in Ion AmpliSeq Transcriptome Human Gene Expression Kit from ThermoFisher Scientific
Ampliseq RNA-Seq

value: human melanocytes

tag: sirna


title: YoungLens_H3K4me2_Rep1


title: siWT-1


title: male WT rep3


title: male ARE-Del rep2

source_name: male ARE-Del

value: ARE-Del


title: male ARE-Del rep3


title: siSV5-2


title: female WT rep3

source_name: female WT

value: female


title: D1 beta3_1

value: Pancreas

value: beta cell


title: siSV5-1


title: siCT-1

value: control


title: female WT rep2


title: female ARE-Del rep3

source_name: female ARE-Del


title: OldLens_H3K4me2_Rep2


title: female ARE-Del rep1


title: f/wt two cell embryo 3 RNA seq

source_name: Lsd1/Kdm1a flox/wt_two-cell stage embryo

tag: stain

tag: developmental stage

value: mouse preimplantation two-cell stage embryos

value: Lsd1/Kdm1a flox/wt


title: Valproate

status: Public on Apr 28 2016

city: Pocatello

first: Michael

last: Thomas

state: ID

address: 921 S. 8th Avenue

department: Biological Sciences Department

institute: Idaho State University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to hg19 reference genomic sequence using Tophat version 2.0.11 with default parameters
The number of reads in each sample that can map to hg19 was calculated using summarizeOverlop function in GenomicAlignments R package
Differentially expressed genes were detected using DESeq2 R package version 1.6.1
Gene set enrichment analysis was carried out using GAGE R package version 2.14.4
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample ...

source_name: SK-N-SH neuronal cells

extract_protocol: Illumina sequencing protocol

treatment_protocol: After differentiation for two weeks, cells were treated with a mixture composed of (MIX: FLX 10μg/l; VNX 50μg/l; CBZ 100μg/l), and Valproate (VPA: 0.035mM). Control cells were treated with DMSO (vehicle) only

tag: treatment


title: female WT rep1


title: male ARE-Del rep1


title: Patient 2 (S2)

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Basecalling, demultiplexing, and QC were performed by the Cologne Center for Genomics at the University of Cologne.
Reads were aligned to the human genome reference sequence (GRCh38) with HISAT 0.1.6, with parameters –-fr –-rna-strandness RF (spliced alignment is enabled by default).
Mitochondrially-aligning reads, and multimapping reads with alignments to the mitochondrial genome and numtS regions (as determined by the hg19 numtS track after converting to the hg38 assembly with the UCSC liftOver program), were extracted and converted to fastq format with samtools and picard tools 1.134. Mitochondrial reads that were orphaned in this process (i.e. with mates mapped to the nuclear genome) were excluded.
Mitochondrial reads and rescued numtS reads were realigned to the mitochondrial genome with HISAT 0.1.6 with parameters –-fr –-rna-strandness RF -–no-spliced-alignment, and the resulting alignments merged with the spliced nuclear alignment (which has been filtered of the numtS-rescued reads). The merged alignment files containing spliced, nuclear alignments and unspliced, mitochondrial alignments were used for normalisation calculations.
Normalised strand-specific coverage profiles were generated in per-base depth format with bedtools genomecov, with parameters -d -split -scale [1000000/total mapped reads], and subsequenctly converted to bedGraph format.
Genome_build: GRCh38
Supplementary_files_format_and_content: Strand-specific per-base bedGraph files with normalised coverage for each sample.

source_name: human mitochondria_biallelic TRMT10C variants

growth_protocol: Fibroblasts were cultured at 37˚C under humidified 95% air/5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, Life Technologies) containing glucose (4.5 g l−1), 1 mM pyruvate, 2 mM glutamine, penicillin (100 U ml−1 ), streptomycin sulfate (100 µg ml−1 ) and 10% fetal bovine serum (FBS).

extract_protocol:
RNA was isolated from mitochondria using the miRNeasy RNA extraction kit (Qiagen) according to the manufacturers instructions.
RNA from mitochondria  was isolated and the concentration, purity, and integrity were confirmed using a BioAnalyser. The libraries were constructed using the Illumina TruSeq LT Sample Prep Kit and deep sequencing of the mitochondrial RNAs was performed by the Cologne Center for Genomics at the University of Cologne on an Illumina MiSeq according to the manufacturer’s instructions.

value: fibroblasts

tag: molecule subtype

value: mitochondrial RNA


title: Control


title: Patient 1 (S1)


title: Control 2 (C2)

source_name: human mitochondria_wild type

value: wild type


title: siCT-2


title: Control 1 (C1)


title: f/wt two cell embryo 5 RNA seq


title: female ARE-Del rep2


title: Mixture

value: FLX 10μg/l; VNX 50μg/l; CBZ 100μg/l


title: WT_1_RNAseq

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: transcript RNA

data_processing:
Basecalls performed with CASAVA 1.8.2
RNA-seq reads were aligned to the KM923925 viral reference genome with bowtie2 (version 2.1.0). Command: bowtie2 --end-to-end -q <genome file> -U <reads.fastq.gz> -S <out.sam>
Genome_build: The dsRNA viral genome sequence, Accession KM923925, isolated from Colletotrichum higginsianum IMI 349063A
Supplementary_files_format_and_content: gff3 format; includes alignment and count values for each RNAseq aligned to the virus genome KM923925
Supplementary_files_format_and_content: dUTP method results in complementary strand being sequenced; strand reported in gff3 file is the strand that the read came from, which is the reverse complement of the read sequence.

organism: Colletotrichum higginsianum IMI 349063

source_name: Mycelia

extract_protocol:
Total RNA isolated from 4 day old mycelia using Trizol reagent. 10 µg of total RNA was treated with TURBO DNase I (Ambion). 1.5 µg of DNase-treated RNA was treated with RiboZero Magnetic Gold Kit-Yeast (Epicentre) to deplete ribosomal RNAs.
Libraries were prepared according to Wang et al. (2011, PLoS One 6:e26426) and Carbonell et al. (2012, The Plant Cell Sep;24(9):3613-29). Briefly, 70 ng of RiboZero-treated RNA were fragmented at 94ºC for 7 min and reverse-transcribed using Superscript II (Invitrogen). Second strand synthesis was done using DNA-polymerase I (Enzymatics) in the presence of d-UTP for strand-specificity, and DNA was end-repaired using the End-Repair Mix (Enzymatics). The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo) (Enzymatics) and dATP to leave a protruding 3’A for ligation of Y-adaptors. DNA adaptor 1 (ACACTCTTTCCCTACACGACGCTCTTCCGATC*T) and DNA adaptor 2 (G*ATCGGAAGAGCGGTTCAGCAGGAATGCCGAG) were annealed to generate the Y-shape adaptors, and ligated to the 3’ end. Before PCR amplification, dUTPs were degraded with Uracil DNA Glycosilase (Enzymatics). Twelve cycles of PCR amplification using the oligonucleotides PE-Primer-F (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and PE-Primer-R (series N701-N710) was performed to add index sequences the samples. DNA amplicons were analyzed with a Bioanalyzer (DNA HS Kit, Agilent) to ensure the PCR amplicon was ~250 nt then quantified using the Qubit HS Assay Kit (Invitrogen).
PE-Primer-R Series N701-N710:  N701, CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTGACTGGAGTTCAGACGTGT; N702, CAAGCAGAAGACGGCATACGAGATCTAGTACGGTGACTGGAGTTCAGACGTGT; N703, CAAGCAGAAGACGGCATACGAGATTTCTGCCTGTGACTGGAGTTCAGACGTGT; N704, CAAGCAGAAGACGGCATACGAGATGCTCAGGAGTGACTGGAGTTCAGACGTGT; N705, CAAGCAGAAGACGGCATACGAGATGGACTCCTGTGACTGGAGTTCAGACGTGT; N706, CAAGCAGAAGACGGCATACGAGATTAGGCATGGTGACTGGAGTTCAGACGTGT; N707, CAAGCAGAAGACGGCATACGAGATCTCTCTACGTGACTGGAGTTCAGACGTGT; N708, CAAGCAGAAGACGGCATACGAGATCAGAGAGGGTGACTGGAGTTCAGACGTGT; N709, CAAGCAGAAGACGGCATACGAGATGCTACGCTGTGACTGGAGTTCAGACGTGT; N710, CAAGCAGAAGACGGCATACGAGATCGAGGCTGGTGACTGGAGTTCAGACGTGT

value: mycelia

tag: genotype

value: wild-type


title: dcl1dcl2_4_RNAseq

description: transcript RNA


title: dcl1dcl2_1_RNAseq

description: transcript RNA


title: rdr3_2_RNAseq

description: transcript RNA


title: rdr2_1_RNAseq

description: transcript RNA


title: dcl2_1_RNAseq

description: transcript RNA


title: rdr1_4_RNAseq

description: transcript RNA


title: rdr3_3_RNAseq

description: transcript RNA


title: dcl1dcl2_3_RNAseq

description: transcript RNA


title: rdr2_2_RNAseq

description: transcript RNA


title: dcl2_3_RNAseq

description: transcript RNA


title: plasmid_1_RNAseq

description: transcript RNA

value: wild-type + pGKO2


title: dcl2_2_RNAseq

description: transcript RNA


title: rdr2_3_RNAseq

description: transcript RNA


title: rdr1_3_RNAseq

description: transcript RNA


title: dcl1dcl2_2_RNAseq

description: transcript RNA


title: WT_2_RNAseq

description: transcript RNA


title: dcl2_4_RNAseq

description: transcript RNA


title: rdr3_1_RNAseq

description: transcript RNA


title: rdr1_1_RNAseq

description: transcript RNA


title: rdr2_4_RNAseq

description: transcript RNA


title: rdr1_2_RNAseq

description: transcript RNA


title: plasmid_2_RNAseq

description: transcript RNA


title: plasmid_3_RNAseq

description: transcript RNA


title: dcl1_4_RNAseq

description: transcript RNA


title: dcl1_3_RNAseq

description: transcript RNA


title: dcl1_2_RNAseq

description: transcript RNA


title: dcl1_1_RNAseq

description: transcript RNA


title: ago2_4_RNAseq

description: transcript RNA


title: 6F3H-AGO1_2_IP

description: small RNA; IP fraction

data_processing:
Library strategy: smallRNA-Seq
Basecalls performed with CASAVA 1.8.2
The 3' adaptor was parsed from the small RNA sequences by the identification of the 5' end: CTGTAG
Small RNA sequences containing 1 or more N's were excluded from analysis
Small RNA sequences shorter than 18 nt were excluded from analysis
Small RNA sequences were aligned to the KM923925 viral reference genome using bowtie (version 0.12.8) (Langmead et al., Genome Biology 2009) with the following flags: -v 0 -a -S
Genome_build: The dsRNA viral genome sequence, Accession KM923925, isolated from Colletotrichum higginsianum IMI 349063A
Supplementary_files_format_and_content: gff3 format; includes alignment and count values for each small RNA aligned to the virus genome KM923925

source_name: Mycelia, IP fraction

extract_protocol:
1 gram of mycelia tissue was used for preparation of total and IP RNA fractions.   Small RNAs were isolated from Total RNA using size fractionantion following the protocol described in Gilbert et al., (2014, Preparation of Multiplexed Small RNA Libraries from Plants. Bio-protocol 4(20): e1275).   Immunoprecipitated small RNAs were prepared by treating clarified lysates with 4 µg/ml of Monoclonal ANTI-FLAG M2 Antibody (Sigma) for 3 h at 4ºC, followed by the addition of 100 µl Protein-G agarose beads (Roche) per milliliter of extract for 30 min at 4ºC. The entire small RNA fraction isolated from the immunoprecipation was used as input into the small RNA library protocol.
Small RNA libraries were prepared following the detailed protocol described in Gilbert et al., (2014, Preparation of Multiplexed Small RNA Libraries from Plants. Bio-protocol 4(20): e1275). Modifications: 5 µl of size fractionated small RNAs were used as starting material from input fractions and the entire immunoprecipitated fraction was used for the IP libraries; 3' ligation was performed for 2 hr.


title: ago1_1_RNAseq

description: transcript RNA


title: 6F3H-AGO2_2_IP

description: small RNA; IP fraction


title: ago1_3_RNAseq

description: transcript RNA


title: 6F3H-AGO2_1_IP

description: small RNA; IP fraction


title: ago1_4_RNAseq

description: transcript RNA


title: 6F3H-AGO2_1_input

description: small RNA; input fraction

source_name: Mycelia, input fraction


title: ago2_3_RNAseq

description: transcript RNA


title: plasmid_2_smRNA

description: small RNA

data_processing:
Library strategy: smallRNA-Seq
Basecalls performed with CASAVA 1.8.2
The 3' adaptor was parsed and removed from the small RNA sequences by the identification of the 5' end CTGTAG
Small RNA sequences containing 1 or more N's were excluded from analysis
Small RNA sequences shorter than 18 nt were excluded from analysis
Small RNA sequences were aligned to the KM923925 viral reference genome using bowtie (version 0.12.8) (Langmead et al., Genome Biology 2009) with the following flags: -v 0 -a -S
Genome_build: The dsRNA viral genome sequence, Accession KM923925, isolated from Colletotrichum higginsianum IMI 349063A
Supplementary_files_format_and_content: gff3 format; includes alignment and count values for each small RNA aligned to the virus genome KM923925

extract_protocol:
Total RNA was isolated from 4 day old mycelia using Trizol reagent. Small RNAs were isolated from 40 µg of total RNA, and size fractionated following the protocol described in Gilbert et al., (2014, Preparation of Multiplexed Small RNA Libraries from Plants. Bio-protocol 4(20): e1275)
Libraries were prepared following the detailed protocol described in Gilbert et al., (2014, Preparation of Multiplexed Small RNA Libraries from Plants. Bio-protocol 4(20): e1275); Modifications: 5 µl of size fractionated small RNAs were used as input material; 3' ligation was performed for 2 hr.


title: 6F3H-AGO2_2_input

description: small RNA; input fraction


title: WT_1_IP

description: small RNA; IP fraction


title: 6F3H-AGO1_3_input

description: small RNA; input fraction


title: ago2_2_RNAseq

description: transcript RNA


title: rdr3_3_smRNA

description: small RNA


title: WT_3_smRNA

description: small RNA


title: 6F3H-AGO1_2_input

description: small RNA; input fraction


title: WT_1_smRNA

description: small RNA


title: rdr3_4_smRNA

description: small RNA


title: ago1_2_RNAseq

description: transcript RNA


title: WT_1_input

description: small RNA; input fraction


title: 6F3H-AGO1_1_input

description: small RNA; input fraction


title: plasmid_1_smRNA

description: small RNA


title: 6F3H-AGO1_3_IP

description: small RNA; IP fraction


title: ago2_1_RNAseq

description: transcript RNA


title: WT_2_smRNA

description: small RNA


title: 6F3H-AGO1_1_IP

description: small RNA; IP fraction


title: plasmid_3_smRNA

description: small RNA


title: rdr3_2_smRNA

description: small RNA


title: rdr3_1_smRNA

description: small RNA


title: rdr2_4_smRNA

description: small RNA


title: rdr2_1_smRNA

description: small RNA


title: rdr2_3_smRNA

description: small RNA


title: rdr1_4_smRNA

description: small RNA


title: rdr2_2_smRNA

description: small RNA


title: rdr1_3_smRNA

description: small RNA


title: FLAG-Tip60

tag: cell line

value: Human lymphoblast

tag: growth conditions

value: untreated cells, normal growth conditions

tag: chip antibody

value: ANTI-FLAG® M2 antibody

tag: chip antibody vendor

value: Sigma


title: rdr1_1_smRNA

description: small RNA


title: dcl2_3_smRNA

description: small RNA


title: dcl2_2_smRNA

description: small RNA


title: dcl2_4_smRNA

description: small RNA


title: dcl1dcl2_2_smRNA

description: small RNA


title: dcl1dcl2_4_smRNA

description: small RNA


title: dcl2_1_smRNA

description: small RNA


title: dcl1dcl2_1_smRNA

description: small RNA


title: ago2_4_smRNA

description: small RNA


title: dcl1_4_smRNA

description: small RNA


title: dcl1_1_smRNA

description: small RNA


title: dcl1dcl2_3_smRNA

description: small RNA


title: ago2_2_smRNA

description: small RNA


title: ago2_3_smRNA

description: small RNA


title: dcl1_2_smRNA

description: small RNA


title: ago2_1_smRNA

description: small RNA


title: ago1_3_smRNA

description: small RNA


title: ago1_2_smRNA

description: small RNA


title: D3 beta1_2

tag: subtype

tag: donor


title: ago1_4_smRNA

description: small RNA

tag: tissue


title: rdr1_2_smRNA

description: small RNA

tag: strain


title: POB_input 2

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome reference sequence mm9 by bowtie aligner
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the input control
Genome_build: mm9
Supplementary_files_format_and_content: .bed file reports peaks

source_name: Primary osteoblasts

growth_protocol: Primary osteoblasts were isolated from P1 calvaria. In vitro cultured osteoblasts were isolated from MC3T3E1 cells cultured for 1 week

extract_protocol:
Cells were isolated by 1 unit/ml Liberase TM (05401119001, Roche), Protein-DNA complexes were crosslinked with 1% formaldehyde, Lysates were clarified from sonicated nuclei and Protein-DNA complexes were purified with FLAG antibody.
Libraries were prepared ThruPLEX®-FD Prep Kit (R40012, Rubicon Genomics) according to manufacturer’s instruction

treatment_protocol: In in vitro culture, osteogenic media contained 10% FBS/alpha-MEM supplemented with 50 ug/mL ascorbic acid phosphate, 10 mM b-glycerophosphate and 10 ng/ml recombinant human BMP‑2 (rhBMP-2, 355-BM, R&D)

tag: cell type

value: Calvarial osteoblasts

tag: age


title: dcl1_3_smRNA

description: small RNA


title: ago1_1_smRNA

description: small RNA


title: MC3_input

source_name: In vitro cultured osteoblasts

value: osteoblastic cell line MC3T3-E1

tag: protocol

value: cultured for 1 week in osteogenic medium

tag: passages


title: MC3_Sp7mut-FLAG1

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome build 37 by the ELAND aligner
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the input control
Genome_build: mm9
Supplementary_files_format_and_content: .bed file reports peaks

value: FLAG M2 antibody (Sigma, F1804)


title: MC3_FLAG-Sp7

value: FLAG M2 antibody (Sigma, catalog# F1804, lot# SLBK1346V)


title: MC3_input2

description:
input DNA
This is used for peak calling for MC3_Sp1-FLAG1, MC3_Sp1-FLAG2, MC3_Sp7mut-FLAG1 and MC3_Sp7mut-FLAG2

value: none (input)


title: MC3_Sp7-BioFLAG


title: Nod2-/-, IL-13 treated, rep 5

first: Mei San

last: Tang

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

data_processing:
FASTQ files were generated by CASAVA 1.8.4 with bcl2fastq function
Alignment was performed with TopHat2 (v2.0.12) to the reference genome mm10 and the reference transcriptome annotated by RefSeq using the parameter --library-type fr-firststrand.
Aligned reads with MAPQ score <30 were filtered. Mitochondrial reads and chromosome Y reads were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Reads were counted at gene level (i.e. total exon reads for each gene) with HTSeq using the parameters --stranded=reverse --mode=union.

source_name: Small intestine

extract_protocol:
RNA was extracted from small intestinal tissue using the RNeasy kit.
Library was constructed using the TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Nod2-/- mice were injected I.P. with a complex of 25ug of anti-IL13 (eBio1316H) and 5ug of recombinant IL-13 (Peprotech cat#210-13) for 21 days. Control mice were injected with PBS. Small intestinal tissue was collected from control and rIL13 treated mice on day 21.

tag: mouse genotype

value: small intestine


title: Nod2-/-, IL-13 treated, rep 2


title: MC3_GFP-FLAG


title: Nod2-/-, IL-13 treated, rep 4


title: MC3_input1

description:
input DNA
This is used for peak calling for MC3_Sp7-FLAG1, MC3_Sp7-FLAG2, MC3_Dlx5-FLAG1 and MC3_Dlx5-FLAG2


title: Nod2-/-, untreated, rep 4


title: MC3_Sp7mut-FLAG2


title: Nod2-/-, IL-13 treated, rep 3


title: MC3_Sp1-FLAG1


title: MC3_Sp1-FLAG2


title: Nod2-/-, IL-13 treated, rep 1


title: MC3_Dlx5-FLAG1


title: Nod2-/-, untreated, rep 2


title: Nod2-/-, untreated, rep 1


title: Nod2-/-, untreated, rep 5


title: WT, untreated, rep 5


title: POB_Sp7Ab-ChIP

description: Sp7 antibody ChIP-seq

value: Sp7 antibody (Abcam, catalog #ab22552, lot# GR193738-1)


title: WT, untreated, rep 3


title: MC3_Sp7-FLAG1


title: WT, untreated, rep 2


title: WT, untreated, rep 1


title: POB_input

description:
input DNA
This is used for peak calling for POB_Sp7-FLAG1, POB_Sp7-FLAG2 and POB_WT-FLAG


title: Cho_rep3

description:
Cho_WT3
HH_Rib_3

data_processing:
The raw reads were first subjected to pre-alignment Quality Assurance and Quality Control (QA/QC).
Any base below a Phred value of 20 was trimmed from either side of the read and reads shorter than 25 nt length were removed.
The processed reads were aligned by Tophat2-2.0.8 (Kim et al., 2013) to mm9 reference genome.
The mapping quality and coverage were checked by post-alignment QA/QC.
Aligned reads were quantified by an expectation maximization algorithm (Xing et al., 2006), followed by a normalization of mapped reads per kilo base length of transcript per million reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports abundance measurements

source_name: Primary chondrocyte

growth_protocol: Primary osteoblasts were isolated P1 mouse calvaria and primary chondrocytes were isolated from P1 mouse rib cartilage

extract_protocol:
Primary osteoblasts were isolated by 1 unit/ml Liberase TM (05401119001, Roche). Primary chondrocytes were isolated by 2 mg/mL PRONASE Protease (53702, EMD Millipore Corporation)  and 0.2% Collagenase D (1088858; Roche Applied Science)
RNA libraries were constructed by Tru-Seq Illumina kit (RS-122-2001, illumina) with some modifications

value: Chondorocytes

tag: isolated from

value: rib

value: WT


title: Cho_rep2

description:
Cho_WT2
HH_Rib_2


title: POB_Sp7-FLAG1


title: Cho_rep1

description:
Cho_WT1
HH_Rib_1


title: MC3_Dlx5-FLAG2


title: POB_Sp7-FLAG2


title: POB_WT-FLAG

value: wild-type


title: Control Biological Rep3

city: Madison

first: Yan

last: Zhang

state: WI

address: 425 Henry Mall Room 5240

department: Genetics

institute: UW-Madison

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNAseq analysis involved alignment using TopHat and assembly and expression estimation by Cufflinks
Genome_build: GRCm38
Supplementary_files_format_and_content: DIFF file

source_name: E13.5 lung

extract_protocol:
Lung were dissected, flash frozen in liquid nitrogen, and RNA was harvested using Qiagen Miniprep Kit. Illumina TruSeq RNA Sample Prep Kit was used with 2ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

tag: development stage

value: Embyonic day 13.5

value: Shhcre;Rfwd2 F/+


title: Mutant Biological Rep1

value: Shhcre;Rfwd2 F/D


title: Mutant Biological Rep3


title: Mutant Biological Rep2


title: Control Biological Rep1


title: Control Biological Rep2


title: WT, untreated, rep 4


title: MC3_Sp7-FLAG2


title: WT_044

city: Cuernavaca

first: Jose

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autonoma de México

data_processing:
Alignment with Bowtie1.
The obtained reads were mapped to the E. coli MG1655 genome (NC_000913.2) using the short-read aligner Bowtie  25 with two mismatches allowed per read alignment.
To estimate gene expression FPKM values were calculated using cufflinks tool 2.0.2
Genome_build: NC_000913.2
Supplementary_files_format_and_content: .txt files with fpkm values of each condition

organism: Escherichia coli str. K-12 substr. MG1655

source_name: WT strain

growth_protocol: Cultures were grown in batch or chemostat mode, M9 minimal media or LB complex media. Samples for Batch mode were taken from mid-log phase, samples from chemostat were taken once the steady state was achieved

extract_protocol:
RNA was extracted by
Ribosomal RNA was substracted and dUTP method was used for library preparation

treatment_protocol: Samples were taken with 2 volumes of RNAprotect reagent (quiagen)

tag: genotype/variation

value: wild type

tag: media

value: M9 minimal

tag: growth mode

value: Chemostat

tag: carbon source

value: glucose


title: rpoB_546_044

source_name: rpoBE546V mutant

value: rpoBE546V mutant


title: rpoB_546_M9

value: Batch


title: Input

city: Boston

first: Peter

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description: Cross-linked, sonicated genomic input DNA

data_processing:
First the reads with aligned to hg19 using bowtie2 with -M 1 option.
Aligned reads were processed and filtered using the spp R package to filter out low quality reads.
ChIP-seq and input reads were mapped to RefSeq annotated genes calculating the background-subtracted RNA Polymerase II density at the TSS and gene body of each gene
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated files (CSV) of each RefSeq isoform with library-size and length normalized read density of ChIP or Input reads mapping to the TSS or gene body of each annotated isoform

source_name: MCF7 cell line

growth_protocol: MCF7 was cultured in DMEM with 10% FBS

extract_protocol:
MCF7 were crosslinked with 1% formaldehyde for 10min and then incubated with nuclear extraction buffer (20mM Hepes-KOH ph7.5, 10mM KCl, 1mM EDTA, 0.2% NP40, 1mM DTT and 10% glycerol) to isolate nuclei. The nulei  in sonication buffer (20mM Tris-HCl pH8, 150mM NaCl, 2mM EDTA, 0.1% SDS, 1% TritonX-100) was sheared in Misonix Sonicator. The further chromatin immunoprecipitation was implimented with RNAP2 antibody (05-623 Millipore) .
The library construction followed the protocol in kit of NEBNext® ChIP-Seq Library Prep Reagent Set (E6200, New England Biolab) with the modfication that single index primer in place of dual primers was used in the final step of PCR amplication.
The libraries were indexed with Illumina barcode. Five indexed libraries were finally pooled into one lane and sequenced in Hiseq2500.

treatment_protocol: For H2A.Z knockdown experiments, 10umol/l scramble and H2A.Z siRNA were used to transfect MCF7.

tag: cell line

value: breast cancer cells


title: WT_LB

value: LB complex media


title: RMA_MNase-Seq

city: Ottawa

first: Andrew

last: Makrigiannis

state: Ontario

address: 451 Smyth Rd

department: Microbiology & Immunology

country: Canada

institute: University of Ottawa

data_processing:
Reads were mapped to mm10 by Genome Quebec and provided to us as a single BAM file
For the Ly49 region of interest, BAM file was converted to nucleosome positions using the R package, PING, obtained from bioconductor
BED file from PING was compared with previous NuPoP predictions to generate true and false positive nucleosome maps of Ly49 cluster
Genome_build: mm10
Supplementary_files_format_and_content: Nucleosome positions stored as BED file from PING

source_name: RMA cell line

growth_protocol: Cells were maintained in RPMI supplemented with 5% FBS and antibiotics, and passsaged when 80% confluent.

extract_protocol:
Nuclei were isolated by centrifugation, and single-nucleosome fragments were isolated by formaldehyde crosslinking followed by micrococcal nuclease digestion, then purified by crosslink reversal and proteinase K digestion
Library was prepared by Genome Quebec using Illumina technology for ChIP-Seq. Illumina TruSeq DNA v1 was used as the adaptor.

value: RMA

value: NK-T cell lymphoma


title: rpoB_546_031


title: MDA231_IgG

city: Milan

first: Marco

middle: J.

last: Morelli

address: via Adamello 16

department: Center for Genomic Science of IIT@SEMM

country: Italy

institute: Istituto Italiano di Tecnologia

description: no processed data file;  The IgG sample was only used for local reads quantification.

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Significant peaks call using the Model-based Analysis of ChIP-Seq (MACS) pvalue cutoff 1e-5, fold enrichment cutoff 10
Genomic Regions Enrichment of Annotations Tool (GREAT, version 2.0.2) to associate MACS peaks to nearby genes within a distance of +/-500 bp from peaks to gene TSS
Genome_build: hg19 genome
Supplementary_files_format_and_content: BED file with annotation

growth_protocol: Human cell line MDA-MB-231 (p53 R280K)  were cultured in DMEM medium (Sigma) supplemented with 10% FCS (ECS0180L, Euroclone), and antibiotics (DE17-602E, Lonza) until 80% confluence.

extract_protocol:
Cells on six 15 cm plates of MDA-MB-231 per IP were fixed with 1% formaldehyde for 20 min., washed with PBS, scraped and lysed in Lysis Buffer - 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, nuclei spun down, washed in 10 mM Tris-HCl, pH 7.5, 200 mM NaCl, 1mM EDTA and resuspended in Sheraing Buffer - 0.1% SDS, 1mM EDTA, 10 mM Tris, pH 7.5. Samples were sonicated using Bioruptor sonicator (Diagenode) for the total time of 30 min., to achieve average size of 250-300 bp of the sonicated chromatin fragments. The Shearing Buffer was then supplemented to RIPA buffer and the rest of the protocol followed as described in Girardini et al, Cancer Cell, 2011.
2–10 ng DNA resulting form the ChIP procedure was prepared for HiSeq2000 sequencing with TruSeq ChIP Sample Prep Kit (Illumina) following the manufacturer’s instructions

treatment_protocol: The chromatin solution was immunoprecipitated with mouse anti-p53 DO1 or with mouse unspecific IgG antibody.

value: triple negative breast cancer cells

tag: chip antibody

value: Mouse normal IgG

tag: chip antibody vendor

value: Santa Cruz Biotech.

tag: chip antibody cat. #

tag: chip antibody vendor lot #


title: Myc ChIP sample 1 Lane 1 and Lane 2

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

description: myc chip sample

data_processing:
Base-calls were made using RTA  version 1.12.4.2
Reads were aligned to mouse genome mm9 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Sequences for each replicate were combined from the two lanes
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using macs14
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: mouse mm9
Supplementary_files_format_and_content: Bed files from MACS, containing chromosome and coordinates of peak locations

source_name: mouse corneal epithelium

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. 24 ug of sonicated chromatin was used for each IP.
Sequencing libraries were generated for the two replicate chip samples using Illumina Tru-Seq ChIP-Seq kit, multiplexed to be sequenced in a single lane, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library [Schmidt D, Methods, 2009]. Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer. Two lanes of the multiplexed replicates were sequenced, and sequences from the two lanes were combined after alignment for each replicate.

treatment_protocol: Corneal epithelium was isolated by digestion in 50% EMEM/dispase II with 50 mM sorbitol and 10 ml/ml bME for two hours at 37°C, prior to fixation for ChIP.

value: Myc (Invitrogen 46-0603, Lot no. 1141786)

value: P7 K14 DN-Clim


title: Myc ChIP sample 2 Lane 1 and Lane 2

description: myc chip sample


title: WT_031


title: WT_M9


title: MDA231_Input

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Significant peaks call using the Model-based Analysis of ChIP-Seq (MACS) pvalue cutoff 1e-5, fold enrichment cutoff 10
Genomic Regions Enrichment of Annotations Tool (GREAT, version 2.0.2) to associate MACS peaks to nearby genes within a distance of +/-500 bp from peaks to gene TSS
Genome_build: hg19
Supplementary_files_format_and_content: BED file with annotation

source_name: triple negative breast cancer

extract_protocol:
Cells on six 15 cm plates of MDA-MB-231 per IP were fixed with 1% formaldehyde for 20 min., washed with PBS, scraped and lysed in Lysis Buffer - 50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, nuclei spun down, washed in 10 mM Tris-HCl, pH 7.5, 200 mM NaCl, 1mM EDTA and resuspended in Sheraing Buffer - 0.1% SDS, 1mM EDTA, 10 mM Tris, pH 7.5. Samples were sonicated using Bioruptor sonicator (Diagenode) for the total time of 30 min., to achieve average size of 250-300 bp of the sonicated chromatin fragments. The Shearing Buffer was then supplemented to RIPA buffer and the rest of the protocol followed as described in Girardini et al, Cancer Cell, 2011.
2–10 ng DNA resulting form the ChIP procedure was prepared for HiSeq2000 sequencing with TruSeq ChIP Sample Prep Kit (Illumina) following the manufacturer’s instructions
50 base pair single reads

value: tumor-derived cancer cells

value: IgG


title: rpoB_546_LB


title: rpoB_672_LB

source_name: rpoBE672K mutant

value: rpoBE672K mutant


title: rpoB_672_M9

value: M9 minimal


title: Pol II H2AZ knockdown

description: Cross-linked, sonicated genomic DNA with RNA Polyermase II ChIP-seq pulldown with H2A.Z siRNA

tag: treated with

value: siRNA against H2A.Z

value: RNAP2 antibody

value: Millipore


title: MDA231_DO-1

tag: cell type

value: sc-126, Santa Cruz


title: Pol II Control

description: Cross-linked, sonicated genomic DNA with RNA Polyermase II ChIP-seq pulldown with control siRNA

value: breast cancer cells

value: scramble siRNA


title: MSI2  shRNA knock down - expt 1

status: Public on Apr 27 2016

city: Montreal

first: Brian

last: Wilhelm

address: 2950 Chemin Polytechnique

institute: University of Montreal

data_processing:
Reads for all samples were mapped to the human genome using Casava (Ver 1.8.2) with default paramters
RPKM values and reads counts were calculated using Casava
Analysis of differntial gene expression was performed thorugh ratio analysis and R (Deseq package)
Genome_build: hg19
Supplementary_files_format_and_content: KH_ratios_results.xlsx: This file contains the results of a ratio analysis of gene expression
Supplementary_files_format_and_content: KH_DESeq_results.xlsx: This file contains the results of a gene expression analysi performed using the DEseq R package

source_name: Cord blood stem cells

growth_protocol: Human lineage depleted CD34+ cord blood cells were FACS purified and cultured for 12 hours cells in StemSpan medium (Stem Cell Techonologies) supplemented with growth factors Interleukin 6 (20 ng/ml), Stem cell factor (100 ng/ml), Flt3 ligand (100 ng/ml) and Thrombopoietin (20 ng/ml). Lentivirus (Musashi-2 overexpression or knockdown) was then added in the same medium at a multiplicity of infection of 30–100 for 24 hours.  Cells were given 2 days post transduction before flow-sorting for GFP expression.

extract_protocol:
Total RNA from transduced cells (~1x10^5) was isolated using TRIzol LS as recommended by the manufacturer (Invitrogen) and then further purified using RNeasy columns (Qiagen). Libraries were subjected to standard Illumina sequencing protocols.
standard Illumina Truseq RNA-seq protocol followed

tag: treatment

value: MSI2 knockdown

value: Cord blood stem cells


title: MSI2 over expression samples - expt 2

treatment_protocol: Human lineage depleted CD34+ cord blood cells were FACS purified and cultured for 12 hours cells in StemSpan medium (Stem Cell Techonologies) supplemented with growth factors Interleukin 6 (20 ng/ml), Stem cell factor (100 ng/ml), Flt3 ligand (100 ng/ml) and Thrombopoietin (20 ng/ml). Lentivirus (Musashi-2 overexpression or knockdown) was then added in the same medium at a multiplicity of infection of 30–100 for 24 hours.  Cells were given 2 days post transduction before flow-sorting for GFP expression.

value: MSI2 over-expression


title: MSI2 over expression samples - expt 1


title: MSI2 over expression control - expt 2

value: control


title: MSI2 Rep 1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Sequencing reads from CLIP-seq and RIP-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
Reads that were PCR replicates were removed from each CLIP-seq library using a custom script. Briefly one read was kept at each nucleotide position when more than one read’s 5' end was mapped
Clusters were then assigned using the CLIPper software with parameters --bonferroni --superlocal --threshold- software (Lovci et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted MSI2 binding

source_name: NB4 cell line

growth_protocol: Human NB4 cells were cultured in RPMI supplemented with 10% FBS and grown at 37 deg C and 5% CO2.

extract_protocol:
25 million NB4 cells were subjected to UV cross-linking at 400mJ/cm^2 on ice.
CLIP-seq libraries for MSI2 were constructed as previously described (Yeo et al. 2009) using anti-MSI2 (Abcam) antibody. Libraries were subjected to standard Illumina sequencing protocols.

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog#

value: NB4 (Human Acute Promyelocytic Leukemia Cells)


title: MSI2  shRNA knock down - expt 2


title: MSI2  shRNA knock down - control 1


title: Montelukast - Rep 1

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description:
A549 human cells not infected, treated with Montelukast Sodium. Biological replicate 1
A549_MK-R1

data_processing:
Basecalls performed using Illumina pipeline v1.9
Short reads (fastq) were quality-checked with FastQC. No additional filters were applied.
Short reads were aligned against human genome with TopHat2 considering intron sizes between 50nt and 100.000nt (parameters -i and -I)
Gene reads were quantified with htseq-count using gene annotations from Ensembl in gtf format.
Normalized counts were obtained by DESeq2 package from www.bioconductor.org. Default parameters for stimating size factors were used.
Genome_build: GRCh38.76
Supplementary_files_format_and_content: text-tabulated files with three columns: COLUMN 1: GeneID (Ensembl); COLUMN 2: raw counts (htseq-count output); COLUMN 3: normalized counts (DESeq2 output)

source_name: A549 cells

growth_protocol: Cells were cultivated in Dulbecco's modified Eagles medium (DMEM) supplemented with 10% foetal bovine serum and non-essential amino acids. The cells were subcultured by trypsin 0.25%-EDTA 0.02% treatment. The cells were cultivated at 37ºC and 5% CO2.

extract_protocol:
Cell pellets containing 2.5 106 cells were resuspended in 1 ml of TRIZOL reagent (Invitrogen) and the RNA was purified as recommended by the manufacturer. The RNA was digested with RNAse-free DNAse (1 u/mg) for 1 h at 37ºC, extracted with phenol-chloroform-isoamylalcohol and precipitated with ethanol.  The purified RNA was resuspended in nuclease free water and the absorbance was measured at 260 nm (NanoDrop ND-1000).
Ribosomal RNA was removed using the Ribo-Zero Removal Kits purchased to Illumina (RZH1046). Each RNA preparation was monitored using the Agilent 2100 Bioanalyzer (Agilent technologies). Ribosomal-depleted RNA was fragmented to approximately 300bp. cDNA was synthesized using reverse transcriptase (SuperScript II, ref. 18064-014, Invitrogen) and random primers. The second strand of the cDNA incorporated dUTP instead of dTTP. Double-stranded DNA was subjected to A-tailing and ligation of the bar-coded Truseq adapters. Purification steps were done using Ampure XP Beads. Library amplification was performed by PCR using the primer cocktail supplied in the kit. Final libraries were analysed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot.

treatment_protocol: For infection with influenza viruses the cells were washed with PBS and virus inoculum prepared in PBS containing bovine serum albumin at 5µg/ml and added to the cultures. After 1 hour at room temperature, the inocula were removed and the cells were incubated with DMEM supplemented with 5% foetal bovine serum. At this time, chemical compounds were added at a final concentration of 50 µM and maintained for the infection period.

value: A549 cells

tag: infected

value: Not infected

tag: treated

value: Treated with Montelukast Sodium


title: MSI2 Rep 2


title: Infected+Montelukast - Rep 2

description:
A549 human cells infected with influenza virus, treated with Montelukast Sodium. Biological replicate 2
A549_I_MK-R2

value: Infected with Influenza virus


title: Montelukast - Rep 2

description:
A549 human cells not infected, treated with Montelukast Sodium. Biological replicate 2
A549_MK-R2


title: Not infected. Not treated - Rep 2

description:
A549 human cells not infected. Biological replicate 2
A549-R2

value: Not treated


title: Infected - Rep 1

description:
A549 human cells infected with influenza virus. Biological replicate 1
A549_I-R1


title: MDAMB231_siCtrl_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

data_processing:
RNA-seq quality control executed with FastQC
Tuxedo software suite (Trapnell, 2012) implemented in Galaxy workflow manager
The mapping was performed by Tophat2
Cufflinks was used to find out differential expressed genes.
Genome_build: hg19

source_name: MDA-MB-231 control siRNA

growth_protocol: Human cell lines MDA-MB-231 (R280K)  were cultured in DMEM medium (Sigma) supplemented with 10% FCS (ECS0180L, Euroclone), and antibiotics (DE17-602E, Lonza).

extract_protocol:
RNA was extracted with Qiazol reagent (Qiagen), following the protocol provided by the manufacturer. RNA integrity was checked by formaldehyde agarose gel electrophoresis. Purity and concentration were determined on a Nanodrop spectrophotometer.
Libraries were constructed with the Illumina TruSeq RNA kits. 100 base pair reads (pair ends).

treatment_protocol: All cells lines were transfected at 50-70% confluence two times with 24h interval (to increase efficiency of silencing), with 50 nM siRNA oligonucleotides using Lipofectamine RNAiMax (Invitrogen), following manufacturer’s instructions. After 48 hr of the second silencing, cells were processed.

tag: sirna

value: siCTRL

tag: tissue

value: Breast Cancer


title: MDAMB231_siCtrl_rep1


title: MDAMB231_siCtrl_rep2


title: Infected - Rep 2

description:
A549 human cells infected with influenza virus. Biological replicate 2
A549_I-R2


title: MDAMB231_siTP53_rep3

source_name: MDA-MB-231 p53 siRNA


title: MSI2 over expression control - expt 1


title: B. pseudomallei K96243 WT replicate 1

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

institute: Monash University

data_processing:
Reads were mapped with CLC genomics workbench v7.0
Mapped reads were convted to counts with CLC genomics workbench v7.0
Genome_build: K96243
Supplementary_files_format_and_content: CSV file containing raw read counts per CDS feature

organism: Burkholderia pseudomallei K96243

source_name: Cell

growth_protocol: B. pseudomallei parent strain K96243 and the directed bprS, bprR and bprRS  mutants were grown overnight at 37 °C in LB with appropriate antibiotics (K96243 in gentamicin 64 µg/ml; mutants in gentamicin 64 µg/ml and tetracycline 25 µg/ml). Strains were subcultured 1/50 into fresh antibiotic-free medium and grown at 37 °C with shaking (200 rpm) to an OD600 of 0.5.

extract_protocol:
Strains were subcultured 1/50 into fresh antibiotic-free medium and grown at 37 °C with shaking (200 rpm) to an OD600 of 0.5. The cells were harvested by centrifugation, and RNA purified using Trizol reagent (Gibco/BRL) as specified by the manufacturer. RNA was DNase treated using the TURBO DNA-free kit (Ambion), followed by processing with a QIAGEN RNeasy kit clean-up with on-column DNase digestion as per the manufacturer’s instructions. RNA samples were quantified and analysed for DNA contamination using the Qubit kit (Invitrogen) and visualised by gel electrophoresis.
The construction of the cDNA library from purified RNA samples was performed using the Truseq RNA Preparation Kit (Illumina). Ribosomal RNA (rRNA) was removed from the samples using the Ribozero kit (Epicentre).

treatment_protocol: All strains were grown in LB and 37 °C with shaking to an optical density of 0.5 at 600 nm and samples taken without further treatment.

tag: genotype

value: WT


title: B. pseudomallei K96243 WT replicate 3


title: B. pseudomallei K96243 bprRS mutant replicate 3

value: bprRS mutant


title: B. pseudomallei K96243 bprRS mutant replicate 2


title: MSI2  shRNA knock down - control 2


title: B. pseudomallei K96243 bprRS mutant replicate 1


title: B. pseudomallei K96243 WT replicate 2


title: B. pseudomallei K96243 bprS mutant replicate 2

value: bprS mutant


title: B. pseudomallei K96243 bprS mutant replicate 3


title: Infected+Montelukast - Rep 1

description:
A549 human cells infected with influenza virus, treated with Montelukast Sodium. Biological replicate 1
A549_I_MK-R1


title: B. pseudomallei K96243 bprS mutant replicate 1


title: Not infected. Not treated - Rep 1

description:
A549 human cells not infected. Biological replicate 1
A549-R1


title: B. pseudomallei K96243 bprR mutant replicate 3

value: bprR mutant


title: MDAMB231_siTP53_rep1


title: B. pseudomallei K96243 bprR mutant replicate 2


title: MDAMB231_siTP53_rep2


title: M59_Transgenic_line_a_day_538

city: Okazaki

first: Yasuhiro

last: Go

address: 38 Nishigonaka Myodaiji

department: Department of Brain Sciences, Center for Novel Science Initiatives

institute: National Institutes of Natural Sciences

data_processing:
Mouse reference genome was complemented with the human genomic region inserted into GLUD2 transgenic mice to construct a custom reference genome
STAR was used to align the reads to the reference genome with parameters: --outFilterMultimapNmax 1 --outFilterMatchNmin 95 --outFilterMismatchNmax 1 --outFilterIntronMotifs RemoveNoncanonical
Reads per kilobase per million mapped reads (RPKM) was calculated for each gene based on mapping alignments and mouse GENCODE vM1 gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample

molecule: polyA RNA

source_name: Transgenic, line a, day 538

extract_protocol:
The poly(A)+ RNA fraction was isolated and processed for sequencing
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A human bacterial artificial chromosome containing the GLUD2 gene (RP11-610G22) was linearized by NotI and injected into the male pronucleus of C57Bl/6 mice.

tag: strain

tag: genotype/variation

value: Transgenic

tag: line

value: a

tag: age

value: day 538

tag: Sex

value: M

value: prefrontal cortex


title: M56_Transgenic_line_b_day_316

source_name: Transgenic, line b, day 316

value: b

value: day 316

value: F


title: M57_Transgenic_line_a_day_318

source_name: Transgenic, line a, day 318

value: day 318


title: M54_Transgenic_line_b_day_232

source_name: Transgenic, line b, day 232

value: day 232


title: M51_Transgenic_line_a_day_111

source_name: Transgenic, line a, day 111

value: day 111


title: M49_Transgenic_line_a_day_82

source_name: Transgenic, line a, day 82

value: day 82


title: M52_Transgenic_line_a_day_170

source_name: Transgenic, line a, day 170

value: day 170


title: B. pseudomallei K96243 bprR mutant replicate 1


title: M48_Transgenic_line_b_day_79

source_name: Transgenic, line b, day 79

value: day 79


title: M50_Transgenic_line_b_day_111

source_name: Transgenic, line b, day 111


title: M47_Transgenic_line_a_day_58

source_name: Transgenic, line a, day 58

value: day 58


title: M45_Transgenic_line_a_day_34

source_name: Transgenic, line a, day 34

value: day 34


title: M44_Transgenic_line_b_day_32

source_name: Transgenic, line b, day 32

value: day 32


title: M43_Transgenic_line_a_day_24

source_name: Transgenic, line a, day 24

value: Transgenic

value: day 24


title: M41_Transgenic_line_a_day_21

source_name: Transgenic, line a, day 21

value: a

value: day 21


title: M38_Transgenic_line_a_day_10

source_name: Transgenic, line a, day 10

value: day 10

value: M

value: prefrontal cortex


title: M40_Transgenic_line_b_day_12

source_name: Transgenic, line b, day 12

value: b

value: day 12


title: M37_Transgenic_line_a_day_10

value: F


title: M36_Transgenic_line_a_day_10


title: M35_Transgenic_line_b_day_7

source_name: Transgenic, line b, day 7

value: day 7


title: M58_Transgenic_line_b_day_319

source_name: Transgenic, line b, day 319

value: day 319


title: M32_Transgenic_line_b_day_3

source_name: Transgenic, line b, day 3

value: day 3


title: M34_Transgenic_line_a_day_6

source_name: Transgenic, line a, day 6

value: day 6


title: M42_Transgenic_line_b_day_23

source_name: Transgenic, line b, day 23

value: day 23


title: M39_Transgenic_line_b_day_12


title: M31_Transgenic_line_b_day_3


title: M55_Transgenic_line_a_day_262

source_name: Transgenic, line a, day 262

value: day 262


title: M29_Control_line_a_day_538

source_name: Control, line a, day 538

value: Control

value: day 538


title: M26_Control_line_b_day_316

source_name: Control, line b, day 316

value: day 316


title: M53_Transgenic_line_b_day_176

source_name: Transgenic, line b, day 176

value: Transgenic

value: day 176


title: M28_Control_line_b_day_319

source_name: Control, line b, day 319


title: M33_Transgenic_line_b_day_6

source_name: Transgenic, line b, day 6


title: M25_Control_line_a_day_265

source_name: Control, line a, day 265

value: a

value: day 265


title: M23_Control_line_a_day_210

source_name: Control, line a, day 210

value: day 210

value: M

value: prefrontal cortex


title: M24_Control_line_b_day_233

source_name: Control, line b, day 233

value: b

value: day 233

value: F


title: M27_Control_line_a_day_318

source_name: Control, line a, day 318

value: day 318


title: M46_Transgenic_line_b_day_55

source_name: Transgenic, line b, day 55

value: day 55


title: IS22330_DS_2

city: Piacenza

first: Alessandra

last: Fracasso

state: Piacenza

address: via Emilia Parmense 84

department: DiProVeS

institute: Università Cattolica del Sacro Cuore

description: processed data file: Genotype2-treatment.Gene.rpkm.xls

data_processing:
OLB-1.9.4 software was used for basecalling
Raw reads were filtered to remove the sequence of adapter, content of unknown bases higher than 10% per reads, and low quality reads. After filtering, the remaining reads are called "clean reads" and used for downstream bioinformatics analysis.
Clean reads are mapped to a reference sequences using SOAPaligner/SOAP2. No more than 5 mismatches are allowed in the alignment
Gene expression levels were calculated by using the RPKM method (Reads per kilobase transcriptome per million mapped reads) according to Mortazavi, A., B. A. Williams, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008.5(7): 621-8.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-20/fasta/sorghum_bicolor/dna/
Supplementary_files_format_and_content: Genotype1-control.Gene.rpkm.xls: the excel file include the number of unique mappede reads, lenght and RPKM for each gene found in the genotype IS20351 under well-watered conditions.
Supplementary_files_format_and_content: Genotype1-treatment.Gene.rpkm.xls:  the excel file include the number of unique mappede reads, lenght and RPKM for each gene found in the genotype IS20351 under drought-stressed conditions
Supplementary_files_format_and_content: Genotype2-control.Gene.rpkm.xls:  the excel file include the number of unique mappede reads, lenght and RPKM for each gene found in the genotype IS22330 under well-watered conditions
Supplementary_files_format_and_content: Genotype2-treatment.Gene.rpkm.xls:  the excel file include the number of unique mappede reads, lenght and RPKM for each gene found in the genotype IS22330 under drought-stressed conditions

organism: Sorghum bicolor

source_name: Leaf of IS22330 drought-stressed condition

growth_protocol: Germination of seeds was carried out in Petri dishes at 25 °C and in dark conditions for 3 days. Five germinated seeds were planted in plastic pots (16 L capacity), filled with a base layer of sand to guarantee drainage and 8 kg of a soil mixture (24% clay, 64% silt, and 12% sand), that had been previously sieved, dried and homogenized. At the 4th leaf stage, plants were thinned in order to have one healthy plant per pot. Plants were grown under well-water conditions until they reached the 6th leaf stage. At this moment, all the plants were irrigated until FC, the soil surface was covered by a thin layer of perlite, and the top of the pot was covered with PVC bags. A little slit was made in the bottom of the plastic bag to allow the sorghum plant to grow through. The slit was sealed with adhesive packing tape to minimise water loss by evaporation. Following the protocol of the dry-down experiment (Fracasso et al., 2016) a decrease of pot weight between two consecutive weight determinations is only attributed to plant transpiration.

extract_protocol:
Three biological replicates were used for all RNA-Seq experiments from each genotypes and water treatment. The total RNA from the leaf meristem was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) and purified using the RNeasy Plant Mini kit (Qiagen, Valencia, CA). On column DNase digestion was performed according to the manufacturer’s protocol (Qiagen, Valencia, CA). RNA quality and integrity was verified using a 2100 Bioanalyzer RNA Nanochip (Agilent, Santa Clara, CA) and all three samples had RNA Integrity Number (RIN) value more than 8.5. The quantification of the total RNA was checked by a NanoDropND-1000 Spectrophotometer (Nano-Drop, Wilmington, DE) and agarose gel electrophoresis.
Illumina sequencing using the GAII platform was performed at Beijing Genomics Institute (BGI-Shenzhen, Shenzhen, China http://www.genomics.cn/index.php) according to the manufacturer’s instructions (Illumina, San Diego, CA). Briefly, poly-A RNA was isolated from 20 μg of total RNA using Magnetic Oligo (dT) Beads (Illumina) and digested in short fragment. First and second strand synthesis were followed by end repair, and adenosines were added to the 3’ ends. Adapters were ligated to the cDNA and fragments (200 ± 25 bp) were purified by agarose gel electrophoresis and amplified by PCR. Finally, after validating on an Agilent Technologies 2100 Bioanalyzer using the Agilent DNA 1000 chip kit, the cDNA library was sequenced on a PE flow cell using Illumina Genome AnalyzerIIx, and the workflow was as follows: template hybridization, isothermal amplification, linearization, blocking, sequencing primer hybridization, and sequencing on the sequencer for Read 1

treatment_protocol: Forty plants were divided in two groups: the well-watered (WW) and the drought stressed (DS) plants. Irrigation was withheld for half of them (the DS ones) till the FTSW value reached 0.2. This value was kept constant for nine days by re-integrating water losses of the DS plants day by day, while the WW plants were irrigated daily to maintain soil water content close to 0.7 FTSW. After nine days had passed, the plants were harvested in order to perform physiological and transcriptomic analysis

value: Leaf

tag: irrigation status

value: drought-stressed


title: IS22330_DS_1


title: M22_Control_line_b_day_176

source_name: Control, line b, day 176

value: Control


title: M21_Control_line_a_day_170

source_name: Control, line a, day 170

value: day 170


title: IS22330_WW_2

description: processed data file: Genotype2-control.Gene.rpkm.xls

source_name: Leaf of IS22330 well-watered condition

value: well-watered


title: M19_Control_line_a_day_82

source_name: Control, line a, day 82

value: day 82


title: M18_Control_line_b_day_80

source_name: Control, line b, day 80

value: day 80


title: M30_Transgenic_line_a_day_3

source_name: Transgenic, line a, day 3

value: Transgenic

value: a

value: day 3


title: IS20351_DS_2

description: processed data file: Genotype1-treatment.Gene.rpkm.xls

source_name: Leaf of IS20351 drought-stressed condition


title: M17_Control_line_b_day_55

source_name: Control, line b, day 55


title: IS20351_DS_1


title: IS20351_DS_3


title: IS22330_WW_1


title: IS20351_WW_2

description: processed data file: Genotype1-control.Gene.rpkm.xls

source_name: Leaf of IS20351 well-watered condition


title: M16_Control_line_a_day_34

source_name: Control, line a, day 34

value: day 34


title: IS20351_WW_3


title: IS22330_DS_3


title: M12_Control_line_b_day_12

source_name: Control, line b, day 12

value: day 12

value: M

value: prefrontal cortex


title: M15_Control_line_b_day_32

source_name: Control, line b, day 32

value: b

value: day 32


title: M10_Control_line_a_day_11

source_name: Control, line a, day 11

value: day 11


title: M14_Control_line_b_day_23

source_name: Control, line b, day 23

value: day 23

value: F


title: M11_Control_line_b_day_12

value: Control


title: M7_Control_line_a_day_6

source_name: Control, line a, day 6

value: day 6


title: M20_Control_line_a_day_111

source_name: Control, line a, day 111

value: day 111


title: M13_Control_line_a_day_21

source_name: Control, line a, day 21

value: day 21


title: M6_Control_line_a_day_6


title: M8_Control_line_b_day_7

source_name: Control, line b, day 7

value: day 7


title: M5_Control_line_b_day_6

source_name: Control, line b, day 6


title: Dsim_YVF_repC

city: Göttingen

first: Nico

last: Posnien

address: Justus-von-Liebig-Weg 11

department: Department of Developmental Biology

country: Germany

institute: University of Göttingen

description:
Counts_Length_Published_DmauDsim.txt
Counts_Length_Direct_DmauDsim.txt
Counts_Length_Reciprocal_DmauDsim.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
100 bp PE RNA-seq reads (from D. mauritiana replicates D, E and F and from D. simulans A, B and C) were split into two 50 bp reads each. Left and right reads were merged into a single fastq file to be equivalent to single-end reads.
Bowtie2 with parameters –very-sensitive-local –N 1 was used to map the RNA-seq reads to the respective references: D. melanogaster reads were mapped to the published CDS set (Flybase, r5.55, only longest transcript) and to our novel reciprocally re-annotated transcript set. D. mauritiana and D. simulans reads were mapped to the respective published transcript sets, to the directly re-annotated transcript sets and to the reciprocally re-annotated transcript sets.
The number of reads mapping to each transcript were summarized using samtools v0.1.19. Transcript length was also obtained using samtools.
Genome_build: This study was perfomed with the aim of showing the bias introduced to differential expression analysis by using non-comparable species-specific mapping references. Therefore the RNA-seq reads were mapped to different transcriptomic references already published or generated in this study. D. melanogaster reads were mapped to the published CDS set (Flybase, r5.55, only longest transcript) and to our novel reciprocally re-annotated transcript set. D. mauritiana and D. simulans reads were mapped to the respective published transcript sets (Nolte, V. et al. 2013 and Hu, T.T. et al. 2013, respectively), to the directly re-annotated transcript sets and to the reciprocally re-annotated transcript sets. All re-annotated references are available upon request.
Supplementary_files_format_and_content: Files are in tab-delimited text format. The row names are the FlyBase ID of all orthologs present in the annotated transcript set for each pair of species (D. mauritiana and D. melanogaster or D. mauritiana and D. simulans). The first three columns contain the raw counts of mapped reads to the D. mauritiana references (replicates A, B and C for the comparison to D. melanogaster and replicates D, E and F for the comparison to D. simulans). Columns four to six contain the raw counts of mapped reads to D. melanogaster or D. simulans references. Column seven contains the length (in bp) of the transcript in the D. mauritiana reference and column eight contains the length (in bp) of the transcript in the D. melanogaster or D. simulans reference.

organism: Drosophila simulans

source_name: eye-antennal imaginal disc

growth_protocol: flies were raised at 25ºC and 12h:12h dark/light cycle in density‐controlled conditions (30 freshly hatched LI larvae per vial).

extract_protocol:
Female LIII larvae were dissected and eye-antennal imaginal discs were stored in RNALater at 120 h after egg laying. 40-50 discs were dissected per sample. Total RNA was isolated using the Trizol  and the samples were DNAse I treated in order to remove DNA contamination.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit starting from 500 ng of total RNA. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™dsDNA System . The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). cDNA libraries were amplified and sequenced by using cBot and HiSeq 2000 (Illumina):single-end reads were generated for D. mauritiana (replicates A, B and C) and for D. melanogaster samples (1x50 bp) and paired-end reads were generated for D. mauritiana (replicates D, E and F) and for D. simulans samples (2x100 bp).

value: YVF

tag: species

value: Drosophila simulans

value: female

tag: developmental stage

value: late L3 larva

value: eye-antennal imaginal disc


title: IS20351_WW_1

value: Leaf

value: well-watered


title: M3_Control_line_b_day_3

source_name: Control, line b, day 3

value: b

value: day 3

value: M

value: prefrontal cortex


title: IS22330_WW_3

source_name: Leaf of IS22330 well-watered condition


title: Dsim_YVF_repB


title: Dsim_YVF_repA


title: M1_Control_line_a_day_3

source_name: Control, line a, day 3

value: a


title: M2_Control_line_a_day_3

value: Control

value: F


title: Dmel_OreR_repA

description:
Counts_Length_Published_DmauDmel.txt
Counts_Length_Direct_DmauDmel.txt
Counts_Length_Reciprocal_DmauDmel.txt

value: OreR

value: Drosophila melanogaster


title: Dmel_OreR_repB


title: Dmel_OreR_repC