title: brain-microglia-S5-1114544 [RNA-seq]

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

description:
brain microglia biological replicate 2
S5
RNA-Seq (300-500bp size fractionation)

data_processing:
Basecalls performed using CASAVA version 1.7.0
Aligned with TopHat 1.3.1, Bowtie 0.12.7 and Ensembl 58 annotation (-G param)
FPKM calculated per sample with Cufflinks 1.0.3
Normalized expression calculated per sample by Alexa-Seq 1.17
Genome_build: mm9
Supplementary_files_format_and_content: Matrix_GeneExpression_v60_S1-6.txt, a tab delimited file with columns for gene ID and the normalized expression values per sample name
Supplementary_files_format_and_content: 11881_gene_fpkm.tsv, a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: brain-microglia

extract_protocol:
Total RNA was isolated from snap-frozen sorted cell pellets using TRIzol-chloroform extraction, resuspended in 10µl Ambion Nuclease-free water (Life Technologies).
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: Tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.

value: brain

value: microglia

value: 6 weeks

tag: gender


title: brain-microglia-S6-1114545 [RNA-seq]

status: Public on Nov 13 2013

type: SRA

country: USA

description:
brain microglia biological replicate 3
S6
RNA-Seq (300-500bp size fractionation)

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: strain

tag: age

value: Female


title: brain-microglia-S4-1114543 [RNA-seq]

description:
brain microglia biological replicate 1
S4
RNA-Seq (300-500bp size fractionation)

value: Male


title: Bxa4_Non_Stimulated

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

country: United Kingdom

institute: University of Edinburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were mapped to mm9 whole genome using Tophat 2.0.4 with the following parameters --min-anchor-length 4  --splice-mismatches 0 --min-intron-length 50 --max-intron-length 1000000   --no-novel-juncs --no-novel-indels --library-type fr-unstranded
Gene expression was calculated as Fragments per Kilobase of modeled exon per Million mapped reads (FPKM) using Cufflinks v2.0.0.
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

source_name: BMDM

growth_protocol: Bone marrow cells were cultured in cell culture medium conditioned with 20% L929 for 7 days before havensting and freezing in liquid nitrogen until use. Cell were pre-plated in the same L929 conditioned medium overnight prior to stimulation or infection.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA (Qiagen RNeasy Plus kit) was isolated from the non-stimulated cells (plated overnight), stimulated and infected cells and the integrity, size, and concentration of RNA checked (Agilent 2100 Bioanalyser). The mRNA was then purified by polyA-tail enrichment (Dynabeads mRNA Purification Kit; Invitrogen), fragmented into 200╨400 base-pair, and reverse transcribed into cDNA before Illumina sequencing adapters were added to each end. Libraries were barcoded, multiplexed into 4 samples per sequencing lane in the Illumina HiSeq 2000

treatment_protocol: BMDMs were left unstimulated, stimulated with IFN/TNF, or CpG for 18 hrs or infected for 8 hrs.

value: BMDM

value: 10 weeks

tag: genotype

value: wild type

tag: treatment


title: bonemarrow-monocyte-S1-1114540 [RNA-seq]

description:
bone marrow monocyte biological replicate 1
S1
RNA-Seq (300-500bp size fractionation)

source_name: bonemarrow-monocyte

value: bone marrow

value: monocyte


title: bonemarrow-monocyte-S3-1114542 [RNA-seq]

description:
bone marrow monocyte biological replicate 3
S3
RNA-Seq (300-500bp size fractionation)


title: bonemarrow-monocyte-S2-1114541 [RNA-seq]

description:
bone marrow monocyte biological replicate 2
S2
RNA-Seq (300-500bp size fractionation)


title: MZdicer 6h miR-430_Ago_hairpin_PS_bond

city: New Haven

first: Antonio

last: Giraldez

state: CT

address: 333 Cedar street

department: Genetics

institute: Yale

data_processing:
Base calling was performed using CASAVA-1.8.2.
For mRNA-Seq, raw reads were aligned strand-specific to the Zebrafish Zv9 (UCSC danRer7) genome sequence using Tophat v2.0.8 with default parameters. RPKMs for gene exons are calculated based on joined Ensembl r70 annotations for uniquely, aligned twice and without limit aligning reads, normalizing against the total number of aligned exonic reads in the sample.
Genome_build: Ensembl 70 / UCSC danRer7
Supplementary_files_format_and_content: Count (uniquely map reads: “count_1”; max twice mapped reads “count_2”; all reads mapped: “count_all”) and RPKM tables (uniquely map reads: “rpkm_1”; max twice mapped reads “rpkm_2”; all reads mapped: “rpkm_all”)

molecule: polyA RNA

organism: Danio rerio

source_name: MZdicer mutant micoinjected with miR-430 (Ago2-haripin 3xPhosphorothioate)

growth_protocol: Embryos are incubated at 28C

extract_protocol:
Total RNA from 15 embryos was extracted using Trizol (Invitrogen) for each experimental condition.
TruSeq strand-specific libraries were constructed according to standard protocols. For mRNA-Seq, polyA+ RNA was selected with oligodT beads.

treatment_protocol: Treated MZdicer embryos were injected at 1-cell with 1 nl of a 25 microMolar stock solution of miR-430 duplex, miR-430 (Ago2-haripin) and miR-430 (Ago2-hairpin 3xPhosphorothioate)

value: Whole embryo

value: MZdicer (hu896/hu896)

tag: Stage

value: 6-hpf (shield)


title: Spombe_Exp1 paired-end

status: Public on Nov 12 2013

city: Evanston

first: Ji-Ping

last: Wang

address: 2006 Sheridan Road

institute: Northwestern University

description: KGY425 (ATCC 96155) (h- his3-D1 leu1-32 ura4-D18 ade6-M210)

library_source: genomic

data_processing:
barcodes were removed first.
Paired-end reads were aligned by allowing for 0 to 3 mismatches progressively. If any read was aligned for the given mismatch tolerance, it was not re-aligned in the following steps.
For unaligned reads, we trimmed the last four bases, and repeated last step.
For unaligned reads, we aligned each end (untrimmed) separately by allowing 0 to 2 mismatches progressively.
For unaligned reads, we further trimmed the last four bases, and repeated the single-end alignment by allowing up to 1 mismatch
The alignment results from above steps were combined.
Genome_build: PomBase version 16.28, released on 03-10-2012
Supplementary_files_format_and_content: tab delimited text file

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Nucleosomal DNA

growth_protocol: The H4S48C S. pombe strain was grown at 30 degrees Celcius in YES medium (5 g/L yeast extract, 30 g/L glucose and 225 mg/L adenine, histidine, leucine, racil and lysine hydrochloride) to mid log phase (OD600 0.7).

extract_protocol: DNA was purified by phenol-chloroform extraction and subsequent ethanol precipitation. The sample was RNased (1mg/ml final) overnight at 42oC and run on a 2% agarose gel.  The shortest DNA band, corresponding to the center-to-center distance of two nucleosome neighbors, was cut out of gel and the DNA was extracted.  The ends of the chemically mapped DNA were blunted using first NEB’s Klenow Polymerase large fragment (cat # M0210L) then processed further using Lucigen’s DNATerminator End Repair Kit (cat # 40035-2). ABI SOLiD adapters were ligated to the blunted and phosphorylated DNA ends. Nick translation and PCR amplification were completed following ABI’s SOLiD Fragment Preparation protocol. All samples were sequenced with ABI’s SOLiD next generation sequencing system.

treatment_protocol: For a 500mL culture, cells were collected and quickly washed twice with water followed by a 10 minute incubation at 30 degrees Celcius in pre-incubation buffer (20 mM citric acid, 20 mM Na2HPO4, 30 mM β- mercaptoethanol (BME), 40 mM EDTA). Cells were centrifuged and resuspended in permeabilizing buffer (1M sorbitol, 50 mM Tris/HCl pH7.4, 5mM BME with 5mg of lyticase (Sigma, L5263vc-200KU) using 10 ml per gram of original cell pellet and spheroplasted at 30 °C with gentle shaking. Spheroplast formation was terminated at an OD600 of 30–40% of the original value by centrifugation at 4°C. Spheroplasts were washed twice in 5mL of 1M sorbitol, 50 mM Tris/HCl and resuspended in 2mL of labeling buffer (1M sorbitol, 50mM NaCl, 10mM Tris-HCl pH 7.5, 5mM MgCl2, 0.5mM spermidine, 0.15mM spermine, 0.075% NP-40). The thiol reactive label - N(1,10 phenanthroline- 5-yl) iodoacetamide  (Biotium cat# 92015), was dissolved in DMSO to a concentration of 7mM and added to the cells for a final concentration of 1.4mM of label and 20% total volume of DMSO.  The light-sensitive labeling reaction was incubated at room temperature, with rotation for 2 hours. This reaction was then washed 2x in 10mL of 1M sorbitol and 0.1% NP-40, then resuspended in 1.5mL mapping buffer (1M sorbitol, 2.5mM NaCl, 50mM Tris-HCl pH 7.5, 5mM MgCl2, 0.5mM spermidine, 0.15mM spermine and 0.1% NP-40).  Cupric chloride (CuCl2) was added to a final concentration of 150mM and incubated for 5min.  The cells were washed 2x in 10mL of mapping buffer and resuspended in 1.5mL mapping buffer. Beta-mercaptopropionic acid (MPA) was added to a final concentration of 6mM, and incubated for 5min, reducing the copper to cuprous chloride.  The chemical mapping reaction was then initiated by the addition of hydrogen peroxide to a final concentration of 6mM.  The reaction was mixed well and incubated for 20 minutes.  The mapping reaction was quenched by the addition of Neocuprine (Sigma), 2.8mM final.  Once quenched the cells were spun down and resuspended in 1mL of 1mM Tris-HCl pH 7.5 and 0.1mM EDTA.  To disrupt histone-DNA contacts, SDS and NaCl were added to a final concentration of 2% and 2M respectively and incubated for 1 hour.

value: H4S48C:hhf1S48C, hhf2S48C

tag: growth phase

value: Mid log phase growth


title: MZdicer 6h miR-430_Ago_hairpin

source_name: MZdicer mutant micoinjected with miR-430 (Ago2-haripin)


title: 60 hr workers 1

city: Dunedin

first: Peter

middle: Kenneth

last: Dearden

address: 710 Cumberland St

department: Department of Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
The sequencing was done using the Illumina HiSeq2000 technology, generating 49 bp reads.
The Illumina Genome Analyzer Pipeline Version 1.5 software was used to qualify reads based on the quality scores assigned to each base call. The qualified reads were exported to the CLC Genomic Workbench for the RNA-Seq algorithm followed by Expression analysis.
Low quality reads were discarded.  High quality reads were mapped to the Amel_4.5 genome using the RNA-seq algorthim implemented in CLC genomics Create fusion gene table = No, Create report = Yes, Create list of unmapped reads = Yes, Additional downstream bases = 500, Exon discovery = Yes, Minimum read count fusion gene table = 5, Minimum length of putative exons = 50, Minimum number of reads = 10, Maximum number of mismatches (short reads) = 2, Organism type = Eukaryote, Use annotations for gene and transcript identification = Yes, Expression level possible values: Genes, Transcripts = Genes, Use strand specific assembly = No, Unspecific match limit = 10, Additional upstream bases = 500, Use colorspace encoding = No, Minimum exon coverage fraction = 0.2, Minimum length fraction (long reads) = 0.9, Minimum similarity fraction (long reads) = 0.8, Expression value = Read Per Kilobase of exon Model value.
Data was normalized using the scaling method ( Normalization method = Scaling,  Scaling method = Median, Reference value = Median of medians,  Trimming = 5%,  Normalized data = Original expression values) and data was transformed by adding a constant of 1.
Differential gene expression was determined using Baggerleys test with a false discovery rate correction
Genome_build: Apis mellifera Amel_4.5 (http://www.ncbi.nlm.nih.gov/genome/48?project_id=13343)

organism: Apis mellifera

source_name: Workers

growth_protocol: Queen larvae were produced by grafting newly hatched diploid larvae into queen cells which were then placed in a queen-less hive.  Worker larvae were left in their original cells and placed in another hive.

extract_protocol:
Total RNA was extracted using TRIZOL (Invitogen) and purified with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Upon collection in the feild larvae were stored in liquid nitrogen then later transferred to -80 untill RNA was extracted

tag: developmental stage

value: 60 hr larval sample raised as workers

value: Whole larvae


title: WT 6h

source_name: wild type

value: TU/AB/TL/TLF


title: MZdicer 6h

source_name: MZdicer mutant


title: 60 hr queens 2

source_name: Queens

value: 60 hr larval sample raised as queens


title: 60 hr queens 1


title: Stage6_RiboZero

city: Nijmegen

first: Gert Jan

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: Depleted for rRNA with Epicentre Ribo-Zero rRNA removal kit

data_processing:
For RPKM counts reads were aligned to the genome using bwa 0.6.1 and the RPKM was calculated based on JGI 7.2 gene annotation
Genome_build:   Xtropicalis_v7
Supplementary_files_format_and_content: The file RPKM.csv contains the genomic location (scaffold, start, end strand) of all genes (JGI 7.2) for the JGI 7.1 genome together with the RPKM values for each gene.

organism: Xenopus tropicalis

source_name: whole embryo

extract_protocol:
X.tropicalis embryos were obtained with in vitro fertilization, dejellied in 3% cysteine and collected at indicated Nieuwkoop-Faber stages. Stage VI oocytes were harvested by treating ovarian follicles with collagenase (Clostridium type I collagenase). Oocytes and embryos from stage 6 - 30 were collected and total RNA was isolated using Trizol and the QIAGEN RNeasy Kit. Subsequently polyadenylated RNA was selected by enriching with the Oligotex mRNA kit (QIAGEN). To ensure complete removal of ribosomal RNA (rRNA), polyadenylated mRNA was subjected to an additional round of Oligotex treatment. Total RNA was subjected to depletion of rRNA using Ribozero Epicentre low input kit.
cDNA was prepared with random hexamer primers using Superscript III (Invitrogen) and the second strand was made with DNA polymerase I, DNA ligase and T4 DNA polymerase. The purified double-stranded cDNA was used for Illumina sample preparation.


title: Stage30_polyA

description: polyA RNA was selected with Oligotex mRNA kit (QIAGEN)


title: Stage16_polyA


title: Oocyte_RiboZero

source_name: oocyte

value: oocyte


title: MZdicer 6h 430_duplex

source_name: MZdicer mutant micoinjected with miR-430 duplex


title: Oocyte_polyA


title: Stage6_polyA


title: MP109

city: La Jolla

first: John

last: Ravits

state: CA

department: Neuroscience

institute: UCSD

description: RNA extracted by Trizol reagent and isolated with cloroform.

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Adapters trimmed using Cutadapt v1.2.1. Command: cutadapt -O 5 -a GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
Trimmed reads mapped to mouse genome (mm9) using the GSNAP aligner (part of GMAP package, version 2012-07-20). Command: gsnap -Q -n 10  --quality-protocol="sanger" -t 4 -N 1 -A sam -B 5 -s mm9 -d mm9
Mapped reads assigned to coding regions of Ensembl mouse genes
Supplementary_files_format_and_content: tab-delimited text file containing RPKM values for each gene

source_name: C57Bl/6 mice

growth_protocol: Not applicable

extract_protocol:
Spinal cord tissues were dissected 2 weeks after treatment and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for strand specific RNA sequencing using the published protocol (Parkhomchuk et al. Nucleic Acid Research. 2009 37(18):e123)

treatment_protocol: Intracerebroventricular stereotactic injection of saline, or 500 ug of a control ASO or an ASO targeting mouse C9orf72.

value: Spinal cord

value: Female

value: wild-type

tag: drug treatment

value: Treatment with 500 ug of a mouse C9orf72 ASO (#571883) - 10ul of ASO solution was injected in the right lateral ventricle


title: Stage9_polyA


title: 60 hr workers 2


title: MP108

value: 10 weeks


title: MP103

value: Treatment with 500 ug of a control ASO (#456835) - 10ul of ASO solution was injected in the right lateral ventricle


title: MP102


title: MP107


title: MP100

value: No ASO Treatment - 10ul of saline was injected in the right lateral ventricle


title: MP101


title: MP99


title: TCDD

city: Singapore

first: Zhiyuan

last: Gong

address: Kent Ridge

country: Singapore

institute: National University of Singapore

data_processing:
The SOLiD-generated RNA-Seq reads was in 27 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches.
The expression levels of mapped transcripts were normalized into transcript per million (TPM) to faciliate comparison among different samples.
Supplementary_files_format_and_content: The mapped transcripts were listed with GI and expression levels in TPM.

source_name: liver

extract_protocol: Library construction was conducted by Mission Biotech (Taiwan) following standard ABI SOLiD protocol.

treatment_protocol: 3-month old wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3-L tanks with around 15 adult and water was changed every day.

value: liver

value: wildtype sibling

value: TCDD


title: MP98


title: Stage9_RiboZero


title: Kin4ALS6-Tx

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexing based on index sequences
Sequenced reads were mapped to Refseq RNA sequences using bowtie v0.12.7 with parameters -q -e 100 -m 10 --best --strata
Count reads for each genes
Supplementary_files_format_and_content: tab-delimited text files include counts for each genes in each samples.

organism: Homo sapiens

source_name: Primary fibroblast cell cultures

growth_protocol: Fibroblasts were derived from patient biopsy samples, grown in high glucose DMEM (D5796) with 20% FBS, 2% Pen/Strep, and 1% Fungizone reagent, at 37C 5%CO2, and passaged using 0.05% Trypsin EDTA.

extract_protocol:
Cells were extracted using Trizol reagent and total RNA was isolated and extracted from chloroform layer.
RNA libraries were prepared for sequencing using the published protocol (Genomics. 2011 ;98(4):266-71)

treatment_protocol: Cells were trypsinized, counted, and plated into 6-well plates. 24 hours later media was removed, cells were washed in PBS, and placed in the presence of Cytofectin reagent (1:1000) and 25nM ASO (or water in the case of control treatments, or a non-targeted ASO at 25nM in the case of Mock treatments) in Opti-MEM media for four hours before being washed with PBS and transferred back to normal passage media described previously. Cells were harvested with Trizol 24 hours post-treatment.

value: Fibroblast

value: Male

value: 55 Years

value: No Known Relevant Mutations

tag: diagnosis

value: Non-Neurologic Control

tag: disease onset

tag: disease course

value: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.


title: Kin2ALS6-Tx

value: 56 Years


title: Kin4ALS6-Ctrl

value: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO


title: Kin1ALS6-Ctrl

value: Female

value: 83 Years


title: Stage12_polyA


title: Kin1ALS17-Tx

value: 52 Years


title: C9-4-Tx

value: C9orf72 Intron 1 Hexanucleotide Expansion

value: Familial ALS

value: Leg

value: 2 years at time of biopsy


title: Kin1ALS17-Ctrl


title: Kin2ALS6-Ctrl


title: DMSO

value: liver

value: wildtype sibling

value: DMSO


title: C9-4-Mock

value: Fibroblast

value: Male

value: Transfection Control - Cells were treated with a control ASO which does not have any human genomic target.


title: C9-3-Tx

value: 55 Years

value: Unknown

value: 14 years at time of biopsy


title: C9-2-Tx

value: Sporadic ALS (C9orf72 expansion)

value: Distal UE

value: 1 year at time of biopsy

value: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.


title: C9-3-Mock

value: C9orf72 Intron 1 Hexanucleotide Expansion


title: C9-4-Ctrl

value: Familial ALS

value: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO


title: C9-3-Ctrl


title: C9-2-Mock

value: 52 Years


title: C9-1-Mock

value: Familial ALS and Dementia

value: Bulbar

value: 4 years at time of biopsy


title: C9-2-Ctrl

value: Fibroblast


title: C9-1-Tx

value: Male


title: ALS20

value: 54 Years

value: Unknown Mutation

value: Sporadic ALS

value: Arm

value: 10 months at time of biopsy


title: ALS14

value: 46 Years

value: 6 years at time of biopsy


title: ALS25

value: 2 years at time of biopsy


title: Spombe_Exp2 paired-end

value: H4S48C:hhf1S48C, hhf2S48C

value: Mid log phase growth


title: Diabetes

city: Shanghai

first: Qiwei

last: Zhai

address: 294 Taiyuan Road

country: China

institute: Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: Sample 2

data_processing:
The high-quality reads were screened from the raw data, and the adaptors were removed from each sequence. Subsequently, high quality clean tags were compared with RefSeq database and the expression level of each gene was normalized to transcripts per million (TPM).
Genome_build: mm9
Supplementary_files_format_and_content: the expression level of each gene normalized to transcripts per million (TPM).

source_name: Diabetic liver

extract_protocol:
About 3 h after the beginning of light cycle, 9-week-old mice were sacrificed, and the livers were immediately removed and snap-frozen in liquid nitrogen. Total RNA was extracted from liver samples with Trizol reagent (Invitrogen), according to the manufacturer's instruction.
The Solexa sequencing procedure was conducted by using the manufacturer’s protocol. Briefly, magnetic oligo(dT) beads were used to isolate poly(A) mRNA from the total RNA samples. cDNA was synthesized from the isolated mRNA using random hexamer primers. Then the cDNA was digested with Dpn II, and the standard Solexa protocol for digital gene expression-tag profiling was followed thereafter to create cDNA libraries.

tag: strain background

tag: genotype/variation

value: db/db (type 2 diabetic)

value: male

value: adult, 9 weeks

value: liver


title: Kin1ALS6-Tx

value: Female

value: 83 Years

value: No Known Relevant Mutations

value: Non-Neurologic Control

value: ASO Treatment - Cells were transfected with a nuclear RNase-H dependent antisense oligonucleotide targeting Exon 2 of Hs C9orf72. This ASO has been shown in previous work to efficiently knockdown all known isoforms of C9orf72.


title: SigX_wildtype_sample1

status: Public on Nov 11 2013

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

description:
deletion control rep1
SigX_differential_expression_knockout_vs_wild_type.txt

data_processing:
Sequenced ChIP-seq reads were trimmed for adaptor sequence allowing for a minimal quality of 10 at their ends, then mapped to the PA14 genome using bowtie v0.12.7 with default parameters
RNA-seq reads were mapped to the PA14 genome using the stampy aligner with default settings. We ommitted the read trimming step since the read length was 36bp
ChIP-seq peaks were called using the MACS algorithm with the following options: -g 5200000 –nomodel --shiftsize=30 -p 0.05
Differential expression was estimated using the DESeq R library using a pre-filtering step. The overexpressing samples were used together with the empty vector controls for negative binomial test. Similarly, the relevant controls for the knockout mutant were the wildtype samples.
For detection of the differentially expressed genes, both replicates for each condition were used, thus the corresponding processed data files were generated on the basis of 4 samples each. The ChIP-seq peaks were detected superposing the treated against the control samples in 2 separate calculations. Only promoters [-500,+100] having ChIP-seq peaks with p-values below 0.01 and fold change at least 3 in both calculations were considered to be bound by SigX.
Genome_build: ASM1462v1 [gi|116048575|ref|NC_008463.1|]
Supplementary_files_format_and_content: Tab-delimited text files (*.txt) containing the detected ChIP-seq peaks as reported by the MACS algorithm and the differential expression output as generated by the DESEQ R library after performing a negative binomial test. All files contain p-values and log2FoldChanges over the relevant controls.

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: PA14 strains in LB medium containing 8 mM NaCl at 37°C and 180 r.p.m. until OD600=0.5. After a cultivation for 45 minutes under same conditions, cells were harvested.

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Briefly, rRNA depletion using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmentation by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.


title: SigX_control_sample2

description: ChIP-seq control rep2

growth_protocol: PA14 strains in LB medium containing 8 mM NaCl at 37°C and 180 r.p.m. until OD600=0.5. Induction of sigX expression by adding L-arabinose to a final concentration of 0.5% for 45 minutes.

extract_protocol:
Polyhistidine-tagged sigma-factors were isolated by using anti6Xhis-antibodies (abcam) and magnetic beads coupled with protein-G (Invitrogen) on a rotator.
Immunoprecipitated DNA was linear amplified similar to the LinDA-ChIP-seq protocol published by Shankaranarayanan et al., Nature potocols, 2012. Library was constructed using the TruSeq DNA sample preparation kit according to the low-throughput protocol (Illumina).

treatment_protocol: DNA-protein crosslinking was performed by addition of formaldehyde to a final concentration of 0.5% for 5 minutes at ambient temperature. Reaction was quenched by addition of glycine to a final concentration of 137 mM. Cells were lysed in lysis buffer containing EDTA and lysozyme. Cells were disrupted and DNA was sheared by sonication.

tag: antibody

value: none, input


title: SigX_wildtype_sample2

description:
deletion control rep2
SigX_differential_expression_knockout_vs_wild_type.txt


title: SigX_knockout_mutant_sample2

description:
deletion mutant rep2
SigX_differential_expression_knockout_vs_wild_type.txt


title: SigX_knockout_mutant_sample1

description:
deletion mutant rep1
SigX_differential_expression_knockout_vs_wild_type.txt


title: SigX_empty_vector_sample1

description:
overexpressing control rep1
SigX_differential_expression_overexpressed_vs_empty_vector.txt


title: SigX_overexpressed_sample2

description:
overexpressing wildtype rep2
SigX_differential_expression_overexpressed_vs_empty_vector.txt


title: SigX_overexpressed_sample1

description:
overexpressing wildtype rep1
SigX_differential_expression_overexpressed_vs_empty_vector.txt


title: SigX_chip_sample1

description:
ChIP-seq treated rep1
SigX_MACS_peaks_sample1.txt

value: anti6Xhis (abcam)


title: SigX_control_sample1

description: ChIP-seq control rep1


title: SigX_empty_vector_sample2

description:
overexpressing control rep2
SigX_differential_expression_overexpressed_vs_empty_vector.txt


title: RNA-seq of PolyA minus from  Mouse Ter119+ erythroid  cells

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

institute: University of Oxford

data_processing:
Reads were mapped to the mm9 mouse genome build using TopHat 1.1.4b
Read coverage was calculated genome-wide to produce a UCSC Wig file
Genome_build: mm9
Supplementary_files_format_and_content: wig file of read densities from tophat coverage output.

growth_protocol: Mouse primary erythroid cells were sorted from the spleens of acetylphenylhydrazine-treated mice based on the expression of Ter119 (Spivak et al., 1973; Vernimmen et al., 2009).

extract_protocol:
RNA was isolated with Tri-Reagent (Sigma). The RNA quality was assessed using Agilent Bioanalyser. Only RNA with overall RIN score >9 was used for further procedures. Subsequently, RNA was treated with DNAseI (DNA-free, Ambion) according to the manufacturer’s protocol kit according to the protocol. Good quality and DNA-free RNA was subjected to polyA fractionation using PolyA selection kit (Promega) using the standard kit protocol.  The RNA fraction was precipitated overnight and resuspended with water. The quality of obtained RNA samples was assessed using PicoChip (Agilent). A Paired sequencing library was generated using the standard Illumina prtocol.
For RNA-Seq libraries, total RNA was split into poly(A)+ and poly(A)- RNA using the PolyATract mRNA isolation system (Promega).  Poly(A)- RNA libraries were generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre), after depletion of ribosomal transcripts with RiboMi- nus Eukaryote Kit for RNA sequencing (Invitrogen and sequenced on Illumina  GA-IIx.

tag: rna subtype

value: PolyAMinus  RNA

value: Ter119+ erythroid  cells


title: brat adult heads_replicate 3

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Basecalling was performed with RTA Version 1.6.32.0
The strand specific paired-end reads were screened for ribosomal RNA by alignment (max. 3 mismatches) against known rRNA sequences (RefSeq) using Bowtie.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.2.0) against the Drosophila melanogaster genome (release 5). Introns of 30–150,000 bp were allowed based on FlyBase statistics. Maximum multihits was set to 1, and microexon-search was enabled. Additionally, a gene model was provided as GTF (Ensembl BDGP5.25.60).
Aligned reads in valid pairs were subjected to FPKM estimation using Cufflinks (v1.0.2). In this step, bias detection and correction was performed. Furthermore, only those fragments compatible with Ensembl annotation (BDGP5.25.60) were allowed and counted towards the number of mapped hits used in the FPKM denominator.
Genome_build: FlyBase dmel_r5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks);

organism: Drosophila melanogaster

source_name: female heads

growth_protocol: Flies heads were maintained and crossed according to standard procedures, and female flies were collected 2-4 days after hatching

extract_protocol:
Total RNA was isolated from adult fly heads by TRIzol purification (Invitrogen)
Total RNA(~1µg) was enriched for polyA mRNA (Dynabeads, Invitrogen), fragmented and first strand and second strand (dUTP, instead dTTP was used) was generated. Library preparation was done using a modified protocol from Illumina with NEBNext DNA sample Prep Reagent kits (NEB), and UGDase treatment was done to confer strand specificity.

treatment_protocol: Fly heads were isolated by shaking and sieving in liquid nitrogen

value: brat mutant

value: 1-3 days


title: brat adult heads_replicate 1


title: w- adult heads_replicate 3

value: control


title: C9-1-Ctrl

tag: tissue

value: Fibroblast

tag: gender

value: Male

value: 52 Years

value: C9orf72 Intron 1 Hexanucleotide Expansion

value: Familial ALS and Dementia

value: Bulbar

value: 4 years at time of biopsy

value: No ASO Treatment - Cells were exposed to cytofectin transfection reagent for four hours, but were not transfected with an ASO


title: ALS2

value: 54 Years

value: Unknown Mutation

value: Sporadic ALS

value: 2.5 years at time of biopsy


title: Strand Specific, Paired end NanoCage analysis of Total RNA from Mouse Ter119+ erythroid  cells

data_processing:
The 21 bp Nanocage primer was trimmed from the Read 1 fastq file.  Reads were mapped to the mm9 mouse genome build using TopHat 1.1.4b
Aligned reads were splits into forward and reverse strands using samtools.  The position of the first mapped based on read 1 was then used to generate the density of transcription start site positions in a moving window of 100 bp with a 10bp increment of movement.
Genome_build: mm9
Supplementary_files_format_and_content: wig files of strand specific start site density in a moving window of 100bp with and moving increment of 10 bp

source_name: Ter119+ erythroid  cells

extract_protocol:
RNA was isolated with Tri-Reagent (Sigma). The RNA quality was assessed using Agilent Bioanalyser. Only RNA with overall RIN score >9 was used for further procedures. Subsequently, RNA was treated with DNAseI (DNA-free, Ambion) according to the manufacturer’s protocol kit according to the protocol.  The RNA fraction was precipitated overnight and resuspended with water. The quality of obtained RNA samples was assessed using PicoChip (Agilent). A Paired-End Nancage library was commercially generated via Source Bioscience.
The library was constructed commericailly via the company Source Bioscience as laid out in the publication "NanoCAGE: A High-Resolution Technique to Discover and Interrogate Cell Transcriptomes" Salimullah et al Cold Spring Harb. Protoc. 2011

tag: strain


title: brat adult heads_replicate 2

tag: age


title: RNA-seq of mRNA from  Mouse Ter119+ erythroid  cells

extract_protocol:
RNA was isolated with Tri-Reagent (Sigma). The RNA quality was assessed using Agilent Bioanalyser. Only RNA with overall RIN score >9 was used for further procedures. Subsequently, RNA was treated with DNAseI (DNA-free, Ambion) according to the manufacturer’s protocol kit according to the protocol. Good quality and DNA-free RNA was subjected to polyA fractionation using PolyA selection kit (Promega) using the standard kit protocol.  The RNA fraction was precipitated overnight and resuspended with water. The quality of obtained RNA samples was assessed using PicoChip (Agilent). A Paired sequencing library was generated using the standard Illumina prtocol.
Total RNA quantity and integrity were assessed, using Quant-IT RiboGreen RNA Assay Kit (Invitrogen, Carlsbad, CA, USA) and Agilent Tapestation 2200 R6K. mRNA enrichment was achieved by processing 5µg of total RNA using the Magnetic mRNA Isolation Kit from NEB (S1550S) with minor modifications.  Generation of double stranded cDNA and library construction were performed using NEBNext® mRNA Sample Prep Reagent Set 1 (E6100L) according to manufacturer specifications.  Upon ligation of Illumina Adapters (Multiplexing Sample Preparation Oliogonucleotide Kit) each library was size selected with two Ampure Bead bindings (firstly, 1:0.7x volume and secondly, the supernatant from the first bind was taken for a 1:1.7x volume clean-up).   The following custom primers (25 µM each) were used for the PCR enrichment step:  Multiplex PCR primer 1.05'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'  Index primer5'-CAAGCAGAAGACGGCATACGAGAT[INDEX]CAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'   Indices were according to the eight bases tags developed by WTCHG (manuscript in preparation).  For libraries that were run as pools:  Amplified libraries were analysed for size distribution using the Agilent Tapestation 2200 D1K. Libraries were quantified by quantitative RT-PCR using Agilent qPCR Library Quantification Kit and a MX3005P instrument (Agilent) and relative volumes were pooled accordingly. Finally, a second quantitative RT-PCR was performed to measure the relative concentration of the pool compared to a previously sequenced mRNA library in order to determine the volume to use for sequencing.  Sequencing was performed as 50bp paired end read on a HiSeq2000 according to Illumina specifications.  For non-pooled libraries:  Amplified libraries were analysed for size distribution using the Agilent Tapestation 2200 D1K. Quantitative RT-PCR was performed to measure the relative concentration of the library compared to a previously sequenced mRNA library in order to determine the volume to use for sequencing. Sequencing was performed as 50bp Paired End read on a HiSeq2000 according to Illumina specifications.

tag: cell type

value: PolyA+ RNA


title: Normal

description: Sample 1

source_name: Wild type liver

value: wild type

value: male

value: adult, 9 weeks

value: liver


title: w- adult heads_replicate 2

value: control

value: 1-3 days


title: H3K4me3_Ter119_Positive

description: ChIP-Seq

data_processing:
Paired-end reads from ChIP-Seq and input samples were aligned to the mouse genome build using Bowtie (version 0.12.3) using standard parameters
Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments
Genome_build: MM9
Supplementary_files_format_and_content: Wig files of genomic distribution of aligned reads

extract_protocol:
ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, Ter119+ cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Immunoprecipitations were performed after an overnight incubation with the appropriate antibody with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Input and immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation. Subsequently the material was analysed by real time PCR (ABI Prism 7000 Sequence Detection System, Applied Biosystems) using a series of PCR amplicons and 5'FAM-3'TAMRA probes across the alpha-globin locus.
Samples were quantified using the High Sensitivity Qubit system (Invitrogen) and distribution of fragments was determined using Agilent High Sensitivity DNA Kit and a 2100 Bioanalyzer Instrument system (Agilent).  Libraries were constructed using the NEBNext DNA Sample Prep Kit (NEB) with the following modifications: End Repair was performed with 1µl of Enzyme mix and adapters were ligated using 4µl of Ligase. We used 10µl of a 1 in 100 dilution of Illumina Adapters (Multiplexing Sample Preparation Oliogonucleotide Kit) for 10ng of DNA and amplified with 25 µM each of the following custom primers:  PCR primer 1.0  5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’  Index primer  5’-CAAGCAGAAGACGGCATACGAGAT[INDEX]CAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’  *Indexes were according to the six bases tags developed by Illumina.  The amplified libraries were purified using Ampure beads and size selected using 2% E-Gel® EX (Invitrogen), the distribution of fragments in the purified fraction was determined using a High Sensitivity Bioanalyzer kit and a 2100 Bioanalyzer Instrument system (Agilent). For equimolar pooling of the libraries, the relative concentration of the libraries was determined by realtime using Agilent QPCR Library Quantification Kit and a MX3005P instrument (Agilent). Finally, in order to determine the volume to use for sequencing, a second realtime was performed to measure the relative concentration of the pool compared to a previously sequenced ChIP library. Sequencing was performed as 50bp paired end on a GAIIx according to Illumina specifications using Cluster Generation Kit v4 and Sequencing Kit v4 in combination with illumina SCS 2.6/ RTA 1.6 software.

treatment_protocol: Mouse primary erythroid cells were sorted from the spleens of acetylphenylhydrazine-treated mice based on the expression of Ter119 (Spivak et al., 1973; Vernimmen et al., 2009).

value: Millipore, 05-745R clone 15-10C-E4

value: Ter119+ Cells


title: DHS_Ter119_Positive

description: DNase-seq

data_processing:
Paired-end reads from DNase-Seq  were aligned to the mouse genome build using Bowtie (version 0.12.3) using standard parameters
Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments
Genome_build: MM9
Supplementary_files_format_and_content: Wig files of genomic distribution of aligned reads

source_name: Ter119+ Cells

extract_protocol:
DNase I assays were performed using ,56107 cells. Nuclei from mainly terminally differentiated erythroblast (,60–80% cells) were digested with eight different concentrations of DNase I (0ice,037,0.5,1,2,4,8,16,32,64mlof10U/mlDNaseIin1ml reaction volume) at 37uC (except 0ice) until the sample containing 16 ml reached water-like viscosity. The digestions were stopped instantly by transferring the tubes to an ice box followed by transferring the reactions into lysis buffer. DNA was extracted using a phenol/chloroform mix and ethanol precipitated. Since DHS represent a spectrum of signal intensities, and the optimal sample should include material from different DNase I concen- tration digestions, the mid phase of digestions were selected for library preparation by qPCR (see below). Based on the principle that DNase I may cut more than once across DHS, generating small DNA fragments that can be amplified.
Samples were quantified using the High Sensitivity Qubit system (Invitrogen) and distribution of fragments was determined using Agilent High Sensitivity DNA Kit and a 2100 Bioanalyzer Instrument system (Agilent). DNA (2–4 mg) was blunt- ended with T4 DNA Polymerase (NEB), adenine overhangs were added using Klenow 59-39 exo-minus, Illumina Solexa sequencing adapters were ligated using T4 DNA ligase (NEB) and amplifi- cation was carried with 10 PCR cycles (15 sec extension time) using Phusion DNA polymerase (Finnzymes) and Illumina Solexa sequencing primers 1.1 and 2.1 (Illumina). Finally, libraries were size selected by electrophoresis and sequenced on an Illumina Genome Analyzer  HiSeq2000.


title: H3K4me1_Ter119_Positive

description: ChIP-Seq

value: Millipore, 07-436


title: G0 in vivo CSF

status: Public on Nov 10 2013

city: Durham

last: Perfect

state: NC

address: 0557 Duke South, blue zone

department: Division of Infectious Disease

institute: Duke University Medical Center

data_processing:
Sequencing reads of each sample were mapped to C. neoformans var. grubii H99 (2012 release; http://www.ncbi.nlm.nih.gov/assembly/GCA_000149245.2/) using Tophat 2.0.0
HT-Seq count 0.5.3 (http://www-huber.embl.de/users/anders/HTSeq) was used to convert the mapped reads to read counts per gene.
DESeq package was used to normalize the read count for each gene among different samples
Genome_build: C. neoformans var. grubii H99 (2012 release; http://www.ncbi.nlm.nih.gov/assembly/GCA_000149245.2/)
Supplementary_files_format_and_content: tab-delimited text files include normlized expression level values for each Sample

organism: Cryptococcus neoformans

source_name: yeast cells

growth_protocol: The in vivo CSF pellets were obtained from yeast cells directly harvested from patients' cerebrospinal fluid (CSF) by centrifugation and stored at -80C until RNA extraction.  These samples were part of the Duke IRB approved Database and Specimen Repository for Infectious Disease Related Studies (PR0005314) in which patients are de-identified and clinical information is limited in collection. HC1 strain is from a patient in USA and strain G0 is from an Uganda patient. YPD broth (1% yeast extract, 1% Bacto Peptone, 2% dextrose) and sterile human CSF (pool of 10 -20 individuals) as previously described (59) were used for in vitro or ex vivo exposure of the strains. The strains were grown in YPD broth for 16 hours at 37¼C and then harvested. Additionally, yeast cells that reached stationary phase by culture in YPD overnight at 37¼C were then exposed to human CSF for 9 hours (CSF replenished every 3 hours) and then harvested. All harvested cells were snap frozen and lyophilized for total RNA isolation.

extract_protocol:
Total RNAs of the two strains (HC1 and G0) under the various treatments were extracted using TRI-zol (Invitrogen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: in vivo cerebrospinal fluid (CSF)

value: yeast cells


title: w- adult heads_replicate 1


title: G0 YPD

value: YPD


title: SigX_chip_sample2

description:
ChIP-seq treated rep2
SigX_MACS_peaks_sample2.txt

value: anti6Xhis (abcam)


title: HC1 in vivo CSF


title: mRNAs from Fusarium graminearum Z-3639 flbD deletion mutant after 6 h after induction of conidiogenesis

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

country: South Korea

institute: Seoul National University

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample

organism: Fusarium graminearum

source_name: Fungal culture

growth_protocol: Each fungal strain was grown on YMA medium for induction of condiogensis for 0h, 6h, and 12h

extract_protocol: Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

value: flbD deletion mutant

tag: time point

value: 6 h after induction of conidiogenesis


title: mRNAs from Fusarium graminearum Z-3639 flbD deletion mutant after 12 h after induction of conidiogenesis

value: 12 h after induction of conidiogenesis


title: HC1 YPD


title: G0 ex vivo CSF

value: ex vivo cerebrospinal fluid (CSF)


title: mRNAs from Fusarium graminearum Z-3639 flbD deletion mutant after 0 h after induction of conidiogenesis

value: 0 h after induction of conidiogenesis


title: HC1 ex vivo CSF


title: mRNAs from Fusarium graminearum Z-3639 wetA deletion mutant after 12 h after induction of conidiogenesis

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32 (ftp://ftpmips.gsf.de/fungi/FGDB/v32/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
wetA_12h_processed.txt: FGDB_v32

source_name: Fungi culture

extract_protocol:
Total RNAs were extracted with Easy Spin Total RNA Extraction Kit (Intron Biotech, Seongnam, Korea).
Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

value: wetA deletion mutant


title: mRNAs from Fusarium graminearum Z-3639 wetA deletion mutant after 6 h after induction of conidiogenesis

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32 (ftp://ftpmips.gsf.de/fungi/FGDB/v32/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
wetA_6h_processed.txt: FGDB_v32


title: mRNAs from Fusarium graminearum Z-3639 wetA deletion mutant after 0 h after induction of conidiogenesis

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32 (ftp://ftpmips.gsf.de/fungi/FGDB/v32/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
wetA_0h_processed.txt: FGDB_v32


title: Co-culture_RNASeq_02

city: Taichung

first: Li-Ching

last: Hsieh

address: 145 Xingda Rd.

department: Graduate Institute of Genomics and Bioinformatics

country: Taiwan

institute: National Chung Hsing University

description: MAT-a type

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
RNA-seq reads were analyzed by ASAP (“Allele-Specific Alignment Pipeline”). To determine whether a given sequence matches one of the two reference genomes specifically, it performs alignments against both sequences in parallel using the Bowtie program (Langmead et al. 2009). In our analysis, the seed length was set to 40 and the maximum number of mismatches permitted in the seed was set to 2.
Genome_build: SGD (version R58-1-1) & RM11-la Database (BROAD Inst.)
Supplementary_files_format_and_content: each tab-delimited text file includes counts of reads mapped on SNPs of each of the orthologous gene pairs

organism: Saccharomyces cerevisiae

source_name: Cell

growth_protocol: Overnight subcultures were used to prepare four technical replicates each of BYxRM hybrid (WL201) cultures and BY+RM co-cultures with starting OD600 at 0.1 and harvested overnight subcultures were used to prepare four technical replicates each of hybrid (WL201) cultures and BY+RM co-cultures with starting OD600 at 0.1 and harvested when cell density reached OD600=1.0 at 30'C, 250rpm

extract_protocol:
Each of the replicated subcultures of BYxRM hybrid and BY+RM co-culture harvested at OD600=1.0 was used to extract total RNA by the hot acid phenol method (Kohrer and Domdey 1991)
mRNA-seq library preparation used the Illumina TruSeq mRNA-seq Sample Prep kit with some modifications. Briefly, 5 μg of total RNA from each sample was used to purify for polyA-RNA, and the mRNA was fragmented by heat at 94℃ for 8 min. Double-stranded cDNA was synthesized by random priming, end repaired, and ligated to the Y-shaped TruSeq adaptors. Samples were cleaned by AMPure beads (Agencourt) and split into two halves, which were independently assembled into two PCR reactions, one using the PCR reagents provided in the Illumina kit, and the other using the KAPA PCR reagent (KAPA HiFi HotStart ReadyMix). All reactions went through 12 cycles of PCR amplifications, and were cleaned by AMPure beads to remove primer dimers. The purified products were quantified by Qubit (Invitrogen) and BioAnalyzer 2100 High Sensitivity DNA Assay (Agilent).

value: MAT-a type


title: Co-culture_RNASeq_01

description: MAT-a type


title: Hybrid_RNASeq_02

description: a/alpha diploid

value: a/alpha diploid


title: mRNAs from Fusarium graminearum Z-3639 wild type after 12 h after induction of conidiogenesis

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Locus_tags in the processed data files (e.g. FGSG_00001, FGSG_00002 etc) are available in mips Fusarium graminearum genome database (http://mips.helmholtz-muenchen.de/genre/proj/fusarium)
Genome_build: FGDB_v32 (ftp://ftpmips.gsf.de/fungi/FGDB/v32/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample

source_name: WT_fungi culture

value: wild type


title: mRNAs from Fusarium graminearum Z-3639 AbaA deletion mutant after 0 h after induction of conidiogenesis

source_name: mutant_fungi culture

value: AbaA deletion mutant


title: mRNAs from Fusarium graminearum Z-3639 wild type after 0 h after induction of conidiogenesis


title: mRNAs from Fusarium graminearum Z-3639 wild type after 6 h after induction of conidiogenesis


title: mRNAs from Fusarium graminearum Z-3639 AbaA deletion mutant after 12 h after induction of conidiogenesis


title: Hybrid_RNASeq_01

description: a/alpha diploid


title: RNA-seq_palmitate_control_rep3

status: Public on Nov 09 2013

city: Cambridge

first: Kinyui Alice

last: LO

state: MA

address: 77 Massachusetts Ave.

department: Biological Engineering

institute: MIT

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
palm_cont3_accepted_hits.bw: mm9

growth_protocol: 3T3-L1 cells (ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine serum (Invitrogen), 100 units/ml penicillin, and 100µg/ml streptomycin.  Two days after confluence (Day 0), cells were induced to differentiate with DMEM containing 10% fetal bovine serum (FBS) , 1µM dexamethasone, 10 µg/ml insulin and 0.5mM  3-isobutyl-1-methyxanthine for 2 days.  Cells were then incubated in DMEM containing 10% FBS and 10 µg/ml insulin for 2 more days.  After Day 4, Cells were maintained in DMEM containing 10% FBS, with medium change every other day.  Experiments were done on Day 8 to Day12 mature adipocytes.

extract_protocol: For each insulin resistance-inducing condition and the control condition, RNA-Seq experiments on biological triplicates were performed.  10ug of total RNA was used for each RNA-Seq library preparation according to the manufacturer's instructions (Illumina).  Quality of RNA was verified using bioanalyzer (Agilent); only RNA with a RIN > 9 was used for RNA-Seq.  cDNA libraries were prepared according to Illumina's instructions and sequenced by Illumina GAII or HiSeq.

treatment_protocol:
Before starting any insulin resistance-inducing treatment, cells were washed with PBS and changed to serum-free, low-glucose (1g/L) DMEM with 0.5% BSA.   Insulin resistance was induced with one of the following: 2.5 nM of TNF-α (R&D Systems) for 24 hr; incubation in a 1% oxygen chamber for 24 hr; treatment with both 2.5 nM TNF-α and 1% oxygen for 24 hr; 1 μM dexamethasone (Sigma-Aldrich) for 24 hr; 100 nM insulin (Sigma-Aldrich) in high-glucose (4.5 g/l) medium for 24 hr; or 800 μM of palmitate (dissolved in 70% ethanol) for 48 hr in DMEM containing 1% serum and 2% BSA.
Before starting any insulin resistance-inducing treatment, cells were washed with PBS and changed to serum-free, low-glucose (1g/L) DMEM with 0.5% BSA.  For the TNFα treatment, cells were treated with 2.5µM of TNFα (R & D Systems) for 24h.  For hypoxia treatments, cells were incubated in a 1% oxygen chamber (Powers, Millman et al. 2010) for 24h.  Two types of hormonal stress were used to induce insulin resistance: dexamethasone treatment consisted of 24h incubation with 1µM dexamethasone (Sigma); high-insulin treatment consisted of 24h incubation of 100nM insulin (Sigma) in high glucose (4.5g/L) medium.

tag: treatment

value: control

tag: cell line

tag: passage

value: less than 10


title: RNA-seq_palmitate_rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
palm3_accepted_hits.bw: mm9

value: Palmitate


title: RNA-seq_palmitate_control_rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
palm_cont2_accepted_hits.bw: mm9


title: RNA-seq_palmitate_rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
palm1_accepted_hits.bw: mm9


title: RNA-seq_palmitate_rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
palm2_accepted_hits.bw: mm9


title: RNA-seq_palmitate_control_rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
palm_cont1_accepted_hits.bw: mm9


title: RNA-seq_cotreat_rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
cotreatment2_accepted_hits.bw: mm9

value: TNFalpha and hypoxia


title: RNA-seq_cotreat_rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
cotreatment4_accepted_hits.bw: mm9


title: RNA-seq_cotreat_rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).  For the cotreatment, palmitate and palmiate control samples, single-end, 50-bp reads were aligned.
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome_build: mm9
Genome Build:
cotreatment5_accepted_hits.bw: mm9


title: mRNAs from Fusarium graminearum Z-3639 AbaA deletion mutant after 6 h after induction of conidiogenesis


title: Male adults (MA)

city: Kunming

first: Pu

last: Yang

address: Bailongsi

institute: Insect

data_processing:
The raw reads obtained from Illumina HiSeq™ 2000
Clean reads were obtained after reads with adaptors, those with more than 10% unknown bases, and low-quality reads were removed before data analysis
Clean reads were mapped to reference sequences using SOAPaligner/soap
Sequences were assessed by read quality, statistics of alignment analysis, sequencing saturation analysis, distribution of reads on reference unigene genes
Statistics regarding gene expression level, screening of differentially expressed genes, and analysis of expression patterns
Genome_build: n/a
Supplementary_files_format_and_content: The txt file including RPKM values for each sample

organism: Ericerus pela

source_name: Male adults

extract_protocol:
washed in three times in DEPC-treated (diethypyrocarbonate) water, and homogenized in TRIZOL (Invitrogen, U.S.). Total RNA from each sample was extracted separately according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stages

value: adults

value: male


title: Female early-stage adults (FA1)

source_name: Female adults

value: female


title: Female later-stage adults (FA3)


title: Female middle-stage adults (FA2)


title: Male second-instar larvae (MS)

source_name: Male larvae

value: second-instar larvae


title: Male first-instar larvae (MF)

value: first-instar larvae


title: Female first-instar larvae (FF)

source_name: Female larvae


title: NBS2

status: Public on Nov 08 2013

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 Eye Street NW

department: Biochemistry and Molecular Medicine

institute: GWU

data_processing:
Illumina pipeline version 1.3.2 was used for basecalling
The paired end reads were aligned using TopHat allowing two mismatches in the alignment. The aligned reads were assembled into transcripts using cufflinks.
Cuffcompare program was used to identify transcripts that were identical to the reference human genome for further analysis and cuffdiff was used for identifying differentially expressed genes and alternatively spliced genes. High confidence transcripts associated with FPKMs above 0.01 in all of the samples were used for further analysis.
Samtools mpileup utitlity was used for identifying variants in our dataset, which were annotated using SeattleSeq v. 8.01, dbSNP build 137.
Refer to PMIDs: 22355776, 23604310 and 23884293 for a detailed description of the data processing and analysis steps.
Genome_build: hg19
Supplementary_files_format_and_content: transcripts.gtf for each sample generated from cufflinks tool (reference based and non-reference based (RABT method,denovo). The vcf file generated from mpileup utility of samtools.

source_name: normal human breast organoids

extract_protocol:
Whole transcriptome RNA was extracted from total RNA by removing large and small ribosomal RNA (rRNA) using RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA). Five micrograms of total RNA was hybridised to rRNA-specific biotin labelled probes at 70°C for 5 minutes. The rRNA-probe complexes were then removed by streptavidin-coated magnetic beads. The rRNA-free transcriptome RNA was concentrated by ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor type

value: Normal Breast Organoids


title: NBS1


title: NBS3


title: UGA076_RNAseq

city: Bethesda

first: Francis

middle: S

last: Collins

state: MD

address: 1 Center Drive, Rm 126

department: Genome Technology Branch

institute: NHGRI

description: PolyA RNA

data_processing:
Base calling was performed by CASAVA version 1.8.
Reads that fail Illumina chastity filter were removed, and reads were trimmed to 76bp, to match ENCODE data sets and prevent bias due to mappability issues.
Reads were mapped to hg19 using STAR version 2.1.1a_r109 with default parameters.
Duplicate reads were removed using samtools rmdup.
Reads from all four islets were combined prior to counting reads overlapping features.
Gene-level counts were calculated using only uniquely-mapped (MAPQ=255) reads with HTSeq, with parameters --stranded=no, with Ensembl 68 annotations.
Standard RPKMs (not quantile-normalized) were calculated using the CQN R library.
Only RPKMs for protein-coding genes present in the Gene Ontology Database are included in the final table.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for combined samples; see Islets column for results from this dataset.

source_name: pancreatic islets

growth_protocol: Fresh human pancreatic islets were obtained from the Islet Cell Resource (ICR) and National Disease Research Interchange (NDRI). Upon receipt, islets were warmed to 37 C in CMRL shipping medium for 1-2 hours. After equilibration, islets were washed with calcium- and magnesium-free Dulbecco's phosphate-buffered saline (Invitrogen, Carlsbad, CA).

extract_protocol:
Total RNA was extracted and purified using Trizol (Invitrogen, Carlsbad, CA).
Non-directional RNA-seq libraries were prepared using standard Illumina protocol, and run on Illumina HiSeq 2000 as 101bp paired-end reads.

value: pancreatic islets

tag: Sex

value: M

tag: purity

tag: viability

tag: rin


title: UG3350_RNAseq

description: PolyA RNA

value: F


title: ULI102_RNAseq

description: PolyA RNA


title: HER2-3

source_name: Primary Tumor

value: HER2 Positive Breast Tumor


title: HER2-4


title: HER2-2


title: Non-TNBC3

value: Non-TNBC Breast Tumor


title: Non-TNBC4


title: Non-TNBC6


title: HER2-1


title: Non-TNBC5


title: Non-TNBC1


title: Female second-instar larvae (FS)


title: Non-TNBC2


title: TNBC4

value: TNBC Breast Tumor


title: TNBC6


title: TNBC5


title: TNBC3


title: TNBC2


title: UFK467_RNAseq

description: PolyA RNA


title: VAS050_H3K4me3

data_processing:
Base calling was performed by CASAVA version 1.8.
Reads that fail Illumina chastity filter were removed.
Reads were mapped to hg19 using BWA version 0.5.8c with default parameters.
Duplicate reads were removed using samtools rmdup.
Reads from all islets were combined for each epitope prior to running ChromHMM analysis.
Chromatin states were learned jointly by applying the ChromHMM (version 1.02) hidden Markov model (HMM) algorithm at 200 bp resolution to seven data tracks (Input, CTCF, K27ac, K27me3, K36me3, K4me1, K4me3) from each of the ten cell types, as previously described in Ernst J et al. (Nature, 2011).
We ran ChromHMM with a range of possible states, and settled on a 12 state model as it accurately captured information from higher state models and provided sufficient resolution to identify biologically meaningful patterns in a reproducible way.
Genome_build: GRCh37
Supplementary_files_format_and_content: Integrated chromHMM BED file.

source_name: pancreatic islets, H3K4me3 ChIP

extract_protocol:
Crosslinked chromatin was prepared and immunoprecipitated as described in Stitzel ML, et al. (Cell Metab, 2010).
Libraries were prepared and sequenced using standard Illumina protocols for GAII.

treatment_protocol: 12,000-16,000 islet equivalents (12-16 million cells) from each sample were crosslinked in 1% formaldehyde for 20 minutes at room temperature, flash frozen in liquid nitrogen, and stored at -80 C.

tag: chip antibody

value: mouse anti-H3K4me3 (Abcam ab12209; lot 738622)


title: VAS050_Input

source_name: pancreatic islets, input

tag: tissue


title: VAS050_H3K27ac

source_name: pancreatic islets, H3K27ac ChIP

value: rabbit anti-H3K27ac (Abcam ab4729, lots 961080, GR45851-1)


title: WBB020_Input


title: TNBC1


title: ULI102_Input


title: HER2-5


title: ULI102_H3K27ac


title: UG3360_Input


title: HTE-B2

city: Chicago

first: Ann

last: Harris

state: IL

address: 2430 N Halsted Street Box 211

institute: Lurie Children's Hospital of Chicago Research Center

description: DNase-seq data biological replicate 2

data_processing:
Data processing is described in detail at http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=346639599&c=chr21&g=wgEncodeOpenChromDnase and is briefly summarized below.
Sequences from each experiment were aligned to the genome using BWA (Li et al., 2008) for the GRCh37 (hg19) assembly. The command used for these alignments was: > bwa aln -t 8 genome.fa s_1.sequence.txt.bfq > s_1.sequence.txt.sai where genome.fa is the whole genome sequence and s_1.sequence.txt.bfq is one lane of sequences converted into the required bfq format.
Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Input data was generated for several cell lines. These were used directly to create a control/background model used for F-Seq when generating signal annotations for these cell lines. These models were meant to correct for sequencing biases, alignment artifacts, and copy number changes in these cell lines. Input data was not generated directly for other cell lines. For cell lines for which there is no input experiment available, the peaks were generated using the control of generic_male or generic_female, as an attempt to create a general background based on input data from several cell types. These files are in "iff" format, which is used when calling peaks with F-seq software, and can be downloaded from the production lab directly from under the section titled "Copy number / karyotype correction." Using a general background model derived from the available Input data sets provided corrections for sequencing biases and alignment artifacts, but did not correct for cell type-specific copy number changes. The exact command used for this step was: > fseq -l 600 -v -f 0 -b <bff files> -p <iff files> aligments.bed where the bff files are the background files based on alignability, the iff files are the background files based on the Input experiments, and alignments.bed is a bed file of filtered sequence alignments.
Discrete DNaseI HS sites (peaks) were identified from DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. Contiguous regions where p-values were below a 0.05/0.01 threshold were considered significant.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: TE_finalPeaks.npf contains the combined peak calls for HTE B1 and B2.

source_name: Human tracheal epithelial cells

growth_protocol: Growth conditions as described in Davis PB, Silski CL, Kercsmar CM, et al. Beta-adrenergic receptors on human tracheal epithelial cells in primary culture. Am J Physiol 1990;258:C71–6.

extract_protocol:
Extraction was performed according to the protocol at http://genome.ucsc.edu/ENCODE/protocols/general/Duke_DNase_protocol.pdf
Library Construction was performed according to the protocol at http://genome.ucsc.edu/ENCODE/protocols/general/Duke_DNase_protocol.pdf

treatment_protocol: No treatment

tag: developmental stage

value: adult

value: trachea

value: epithelia


title: HTE-B1

description: DNase-seq data biological replicate 1


title: UG3360_H3K36me3

source_name: pancreatic islets, H3K36me3 ChIP

value: rabbit anti-H3K36me3 (Abcam ab9050; lots 446805, 572220)


title: mRNARP-Dark_2

city: Taipei

first: Ming-Jung

last: Liu

address: 128 Sec. 2, Academia Rd, Nankang

institute: Academia sinica

data_processing:
Adaptor sequences (5'CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTT
GGCACCCGAGAATTCCAATTGATGGTGCCTACAG3') were trimmed from the sequence reads
Only the unique reads with 95% and above identity were aligned to the representative gene models.
The 15th nucleotide of aligned reads was assigned for the calculation of the read count for every nucleotide of each individual transcript.
RPKM (reads per kilobase per million mapped reads) were used to represent the read intensity in 5' UTR, CDS and 3' UTR.
Genome_build: Reference transcript datasets including the 5’ UTRs, CDS and 3’ UTRs for 27,416 annotated protein-coding gene models were retrieved from The Arabidopsis Information Resources (TAIR10; http://www.arabidopsis.org). We have updated gene models of 3,111 genes originally lacking 5’/3’ UTRs in Tair10 with the use of our sequencing datasets.
Supplementary_files_format_and_content: The "Processed data_Whole_genome" contains the length, read counts and RPKM of 5' UTR, CDS and 3' UTR for 27,416 represent gene models in 4 samples (mRNASS_Dark, mRNASS_L4h, mRNARP_Dark, mRNARP_L4h).

organism: Arabidopsis thaliana

source_name: ribosome-protectedl mRNAs from 4-day old etiolated seedling, repeat2

growth_protocol: Col-0 were grown on 1/2 MS medium in darkness for 4 days

extract_protocol:
Seedlings were quickly harvested in liquid nitrogen. The Arabidopsis polysome complexes were extracted with polysome extraction buffer and digested with RNase I. The ribosome protected fragments were purified with SDS/phenol method. Messenger RNAs purified with Illustra mRNA purification kit were fragmented with NEBNext RNA Fragmentation Reaction Buffer (NEB, MA, USA) at 940C for 40 min.
RNA libraries were prepared for deep sequencing using a protocol from Ingolia et al., Cell, 2011.

treatment_protocol: 4-day-old dark-grown seedlings illuminated with/without 4-h white light (80 mmole m-1 sec-1)

tag: ecotype

tag: sample type

value: ribosome-protected mRNA

value: without light


title: 8) b-PDGFR fl/fl, GFAP Cre +/-, 72h pHx

city: New York

first: Peri

last: Kocabayoglu

state: NY

address: 1425 Madison Avenue

department: Liver Diseases

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The 100 nucleotide single end sequencing was done on an Illumina HiSeq 2000.
Transcripts expression levels were quantified as Fragments Per Kilobase per Megabase (FPKM) using the TopHat and Cufflinks pipeline, as described in Trapnell, Cole, et al. ("Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks." Nature protocols 7.3 (2012): 562-578.)
Expression of genes with multiple transcripts was obtained as the sum of the FPKM values of each transcript.
Genome_build: mm9 (NCBIM37)
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM values for each gene (in rows) and for each Sample (in columns). A separate tab-delimited text file includes the transcript level FPKM values.

source_name: Liver

extract_protocol:
Livers were removed, and RNA was extracted using Trizol reagent, followed by purification using Quiagen Spin Column and on-column DNAse digestion. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-930-2002) was used with 2.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 3 months

tag: genotype/variation

value: b-PDGFR fl/fl, GFAP-Cre pos

value: partial hepatectomy 72h


title: 7) b-PDGFR fl/fl, GFAP Cre +/-, 72h pHx

tag: treatment


title: 6) b-PDGFR fl/fl, GFAP Cre -/-, 72h pHx

value: b-PDGFR fl/fl, GFAP-Cre neg


title: mRNARP-L4h_2

source_name: ribosome-protectedl mRNAs from 4-day old etiolated seedling with 4-h light treatment, repeat2

value: with 4h light


title: mRNASS-Dark_2

source_name: steady-state mRNA from 4-day old etiolated seedling, repeat2

value: steady-state mRNA


title: mRNASS-L4h_2

source_name: steady-state mRNA from 4-day old etiolated seedling with 4-h light treatment, repeat2


title: WBB020_H3K36me3

value: pancreatic islets

value: M


title: 3) b-PDGFR fl/fl, GFAP Cre +/-, sham

value: sham


title: mRNARP-L4h

data_processing:
Adaptor sequences (5'CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTT
CCTTGGCACCCGAGAATTCCAATTGATGGTGCCTACAG3') were trimmed from the sequence reads
Only the unique reads with 95% and above identity were aligned to the representative gene models.
The 15th nucleotide of aligned reads was assigned for the calculation of the read count for every nucleotide of each individual transcript.
RPKM (reads per kilobase per million mapped reads) were used to represent the read intensity in 5' UTR, CDS and 3' UTR.
Genome_build: Reference transcript datasets including the 5’ UTRs, CDS and 3’ UTRs for 27,416 annotated protein-coding gene models were retrieved from The Arabidopsis Information Resources (TAIR10; http://www.arabidopsis.org). We have updated gene models of 3,111 genes originally lacking 5’/3’ UTRs in Tair10 with the use of our sequencing datasets.
Supplementary_files_format_and_content: The "Processed data_Whole_genome" contains the length, read counts and RPKM of 5' UTR, CDS and 3' UTR for 27,416 represent gene models in 4 samples (mRNASS_Dark, mRNASS_L4h, mRNARP_Dark, mRNARP_L4h).

source_name: ribosome-protectedl mRNAs from 4-day old etiolated seedling with 4-h light treatment


title: mRNARP-Dark

source_name: ribosome-protectedl mRNAs from 4-day old etiolated seedling


title: 2) b-PDGFR fl/fl, GFAP Cre -/-, sham


title: mRNASS-Dark

source_name: steady-state mRNA from 4-day old etiolated seedling


title: 1) b-PDGFR fl/fl, GFAP Cre -/-, sham


title: mRNASS-L4h

source_name: steady-state mRNA from 4-day old etiolated seedling with 4-h light treatment


title: Ter119+ poly(A)- RNA

status: Public on Nov 07 2013

first: Harvey

middle: F.

last: Lodish

address: 9 Cambridge Center

institute: Whitehead Institute

description: poly(A)- RNA

data_processing:
The resulting directional 100 bp paired-end reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and low quality reads and adapters were removed using the fastq_quality_trimmer (“-t 20” parameter) and the fastx_clipper tools  from FASTX-Toolkit (  http://hannonlab.cshl.edu/fastx_toolkit/index.html). Only perfect paired reads were mapped to mm9 using TopHat v1.3.2 (PMID: 19289445) (default parameters and “--min-anchor 5”). To construct transcript models, we took the mapped reads from total RNA data and performed de novo assembly using Cufflinks v1.3.0 (PMID: 20436464) (default parameters and “-p 4 --min-frags-per-transfrag 0”) considering annotations from RefSeq, Ensembl and UCSC to maximize assembly accuracy.
Genome_build: mm9
Supplementary_files_format_and_content: mapped reads in bigwig

source_name: fetal liver

extract_protocol:
E14.5 mouse fetal liver cells were separated into TER119+ and TER119- fractions via magnetic-assisted cell sorting. Total RNA was isolated from these cells using the QIAGEN miRNeasy Kit according to the manufacturer’s instructions. Ribosomal RNA was depleted from 4 ug total RNA using the Ribo-Zero Gold Kit from Epicentre.
Strand-specific sequencing libraries were generated following a previously described protocol (PMID: 21943893) from the total RNA (TER119- and TER119+ cells) or from the poly(A)+ and poly(A)- fractions (TER119+ cells). The latter fractions were separated using the Solexa kit (Illumina) according to the manufacturer’s instructions. cDNA fragments of 400-600 bp from these libraries were selected by gel purification and then sequenced on a Illumina HiSeq2000 sequencer.

value: fetal liver


title: Ter119+ poly(A)+ RNA

description: poly(A)+ RNA


title: Ter119+ total RNA minus rRNA

description: total RNA minus rRNA


title: GATA4_ChIP-seq

city: Philadelphia

first: Rena

last: Zheng

state: PA

address: 3615 Civic Center Blvd. Abramson Research Center 315A

institute: Children's Hospital of Philadelphia

data_processing:
ChIP-seq reads were aligned to the canonical mm9 reference genome with  bowtie v.0.12.7 available as the "Map with Bowtie for Illumina" tool on  http://usegalaxy.org. Default parameters were used, except for the following options: -e 80, -y  "Try hard",  -k 1, --best "use best", and --maxbts 800
Peaks were called with SPP and MACS v.2.0.10 following the Irreproducible Discovery Rate (IDR) pipeline described at https://sites.google.com/site/anshulkundaje/projects/idr. Settings per program were used as described in the protocol, and in addition MACS2 -B option was used to generate the pooled samples BedGraph files
SPP and MACS2 peaks were intersected with Bedtools v2.16.1. The following options were used: intersectBed -u -a SPP_peaks -b MACS2_peaks > common_peaks
BigWIg files were generated by converting the BedGraph files with the Wig/BedGraph-to-bigWig tool available at http:// usegalaxy.org
Genome_build: canonical mm9 (available at http://usegalaxy.org)
Supplementary_files_format_and_content: UCSC track files in BED format containing peak regions andpooled samples signal in BedGraph format

extract_protocol:
Liver tissue was fixed with formaldehyde, lysed, sonicated, and GATA4-DNA complexes were isolated with antibody.  DNA was purified using phenol/chloroform extraction and ethanol precipitation.
Libraries were prepared with Illumina ChIP-Seq DNA Sample Prep kit Cat # IP-102-1001.  The input (liver) and ChIP DNA fragments were repaired to generate blunt ends, with a single adenine added to each end. Illumina genomic adaptors were ligated to both ends of the fragments, ligation products were amplified by 18 cycles of PCR, and the PCR products between 250 and 450 bp were gel purified according to standard Illumina protocols. The quantity and quality of each library was evaluated by qPCR and Bioanalyzer (Agilent Technologies, Santa Clara, CA). Cluster generation and sequencing chemistry were performed using Illumina-supplied kits as appropriate. The ChIP DNA library was sequenced in single-read mode on the Illumina HiSeq 2000 platform.

value: Liver

value: postnatal 2-3 months

value: GATA4 C-20 (Santa Cruz sc-1237)


title: Ter119- total RNA minus rRNA

description: total RNA minus rRNA


title: input DNA


title: Me-RIP, DAA3

city: Manchester

first: Jean-Michel

last: Fustin

state: England

address: Faculty of Biology, Medicine and Health, , Oxford road

department: Centre for Biological Timing

institute: University of Manchester

description: m6A-immunoprecipitated mRNA

data_processing:
Library strategy: MeRIP-Seq
Basecalls performed using CASAVA version 1.8.
38bp reads aligned to genome using BWA with default settings on TopHat 2.0, filtered with low Phred score(< 25),  converted to BED files using SamTools, filtered rRNAs and tRNAs annotations using IntersectBed command in BEDtools.
For identification of Me-RIP regions, non-IP background subtraction from MeRIP sample was performed by original Perl program.
Gene annotations were found using edgeR program on Genomatix Genome Analyzer, inputting BED files, processed across 3 replicates for identification of differentially expressed genes between DAA and Ctrl
Genome_build: hg19
Supplementary_files_format_and_content: BED files

source_name: U2OS + 3-Deazaadenosine (Me-RIP)

growth_protocol: All cells were grown in 20 cm Petri dishes until confluence (3-4 days) in standard DMEM-F12 containing 10% FBS and 1xPSA.

extract_protocol:
Medium was removed and cells were lysed directly on the dish with 3 ml Sepasol (Nacalai Tesque, Japan). Total RNA was then extracted following standard protocol with Sepasol. mRNA was further purified using two rounds of Oligotex-dT30 mRNA Purification Kit (Takara Bio, Japan). mRNA was fractionnated using NEBNext Magnesium RNA Fragmentation Module (NEB, Japan) following manufacturer's protocol. All mRNA samples were checked by Bioanalyzer 2100 (Agilent Technologies) to confirm size and quality. In addition to the extraction steps common to all samples, Me-RIP samples were further processed according to the following method. 500 ng fragmented mRNA was incubated in 250 ml of 20% protein A- or G-Agarose slurry in PBS 0.1M, 0.01% Triton X-100, 0.1 mg/ml BSA, 1mM DTT, 0.4 U/ml RNase inhibitor (Toyobo) for 1 h at 4°C for background removal. The RNA/beads slurry was then centrifuged at 700xg, 4°C for 2 min, the RNA supernatant (~200 ml) was used in the next step and the agarose beads pellet discarded. 50% protein A-Agarose slurry in the same buffer was conjugated with anti-m6A rabbit polyclonal antibody (Synaptic Systems, 30 mg antibody/ml slurry) for 3 h at 4°C. Beads were then washed by 5 cycles of re-suspension with >2 volumes of buffer, then centrifugation (700xg, 4°C for 2 min). The final 50% beads-antibody conjugate slurry was then aliquoted into 1.5 ml tubes, 100 ml/tubes; tubes were centrifuged at 700xg, 4°C for 2 min and beads (~50 ml) were re-suspended with the RNA supernatant from the previous step and incubated at 4°C overnight in a tube rotator, with 0.5 mM random decamers (Invitrogen, Japan) in the incubation buffer as blocking reagent. The tubes were then centrifuged at 700xg, 4°C for 2 min. Pellets (methylated RNA) were washed by 5 cycles of re-suspension with at least 10 volumes of buffer and centrifugation at 700xg, 4°C for 2 min. The final pellet (~50 ml) was homogenized with 1 ml Sepasol RNA I super G by vortexing at full speed then kept at -80°C until processed further. RNA was then extracted with a combination of Qiazol/RNeasy micro kit following Qiagen protocol, with Sepasol instead of Qiazol. The RNA eluate (~14 ml) was then used for RNA quantification by Nanodrop and reverse-transcribed using VILO (Invitrogen, Japan).
Sequencing libraries were prepared using the NEBNext® Ultra RNA Library Prep Kit with partially modified steps in random primer annealing condition as 65 °C for 15 min.

treatment_protocol: Culture medium was removed and replaced with new medium containing 100 mM deazaadenosine or vehicle (0.01x PBS). Cells were then incubated at 37°C, 5% CO2 for 24 hours before extraction.

tag: cell line


title: Me-RIP, CTL3

description: m6A-immunoprecipitated mRNA

source_name: U2OS + Vehicle (Me-RIP)


title: Me-RIP, DAA2

description: m6A-immunoprecipitated mRNA


title: 4) b-PDGFR fl/fl, GFAP Cre +/-, sham


title: 5) b-PDGFR fl/fl, GFAP Cre -/-, 72h pHx


title: Me-RIP, CTL2

description: m6A-immunoprecipitated mRNA


title: DAA3

description: mRNA

source_name: U2OS + 3-Deazaadenosine (input)


title: Me-RIP, CTL1

description: m6A-immunoprecipitated mRNA


title: CTL2

description: mRNA

source_name: U2OS + Vehicle (input)


title: DAA2

description: mRNA


title: CTL3

description: mRNA


title: DAA1

description: mRNA


title: CTL1

description: mRNA


title: 3T3 cells co-transfected with pCAG-EGFP_MosIR and pEF-1_mDcrS expressing a somatic form of a murine Dicer.

city: Prague 4

first: Radek

last: Malik

address: Videnska 1083

department: Dep. of Epigenetics Regulations

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
The given adapters were trimmed, and the raw files were filtered by quality using the cutadapt tool with the following command line: cutadapt -m 15 -e 0.1 -o fastq -c -z -a adapter csfastq csqual
All fastq files were mapped in colorspace using the Shrimp short read aligner using following command line: shrimp -o 4 --strata -N 1 -L genome.index.i input.file
The *.bed files were constructed using the bamToBed command from the bedtools toolkit.
Genome_build: NCBI37/mm9 (without the chromosome containing "random" in their names) + pCAG-EGFP_MosIR plasmid sequence (available upon request).
Supplementary_files_format_and_content: *.bed file format

source_name: cell line

growth_protocol:
3T3 cells were grown under standard tissue culture conditions in DMEM supplemented with 10% FCS.
Mouse embryonic stem cells were cultured on gelatin-coated plastic in 2i-LIF medium: Knockout D-MEM (Invitrogen) containing 15% FCS (Sigma), 1× NEAA, 1 mM sodium pyruvate, 2 mM L-glutamine, 50 µM 2-mercaptoethanol, supplemented with mouse LIF (1,000 U/mL), 3μM CHIR99021, and 1 μM PD0325901 (Sellect Chemicals).

extract_protocol: Samples processing and SOLiD sequencing was performed by Seqomics Ltd. (Hungary). Briefly, samples were depleted of ribosomal RNA using RiboMinus rRNA Removal Kit, eluted twice into 15 ul and treated with DNase I (5 ul 10x DNase I buffer, 2.5 U DNase I and water up to 50 ul reaction) 20 min at 37°C. Samples were ethanol-precipitated, eluted into 10 ul TE buffer and fragmented by RNase III treatment (1 ul 10x RNaseIII buffer, 8 ul sample, 1 ul RNaseIII) 10 min at 37°C. Fragmented samples were precipitated by ethanol and eluted into 4 ul. Adaptor was hybridized and ligated to each sample (10 ul 2x ligase buffer, 2 ul Adaptor mix, 3 ul hybridization solution, 2 ul ligation enzyme) by incubating O.N. at 16°C. Adaptor-ligated RNA was subjected to reverse transcription (4 ul 10x RT buffer, 2 ul dNTP mix, 2 ul RT primer, 1 ul ArrayScript RT, 13 ul water) for 40 min at 42°C. Resulting cDNA was purified using PCR Purification kit (Qiagen) and eluted into 10 ul. cDNA was run on 6% TBE-Urea gel and fragments 150-250 nt in length were excised. Isolated cDNA was amplified for 15 cycles using AmpliTaq DNA polymerase and purified by PCR Purification kit (elution twice in 10 ul). Second round of size selection on PAGE gel was performed and PCR products 110-130 nt in length were excised from gel and isolated.  Purified amplicons were sequenced using ABI SOLiD 4 platform.

treatment_protocol:
NIH3T3 were co-transfected with pCAG-EGFP_MosIR and pcDNA4-DicerS-myc-His or pcDNA4-DicerS-myc-His (1.5 µg each per well in 6 well-plate). Cells were processed 48 hours post-transfection.
Mouse embryonic stem cell lines were transfected with pCAG-EGFP_MosIR plasmid (3 µg per well in 6 well-plate). Cells were processed 48 hours post-transfection.

tag: passages

tag: transfected plasmid

value: pCAG-EGFP_MosIR + pcDNA4-DicerS-myc-His


title: Dicer -/- mESCs, clone O3 transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene

value: Dicer -/- mouse embryonic stem cells


title: 3T3 cells co-transfected with pCAG-EGFP_MosIR and pEF-1_mDcrO expressing an oocyte form of a murine Dicer

value: pCAG-EGFP_MosIR + pcDNA4-DicerO-myc-His


title: Dicer -/- mESCs, clone O2 transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene


title: 3T3 cells transfected with pCAG-EGFP_MosIR expressing long hairpin derived from mouse Mos gene


title: Dicer -/- mESCs, clone S11 transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene


title: Dgcr8 -/- mESCs transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene

value: Dgcr8 -/- mouse embryonic stem cells


title: Dicer -/- mESCs, clone S4 transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene


title: Dicer flox/- mESCs transfected with pCAG-EGFP_MosIR expressing long hairpin derived from Mos gene

value: Dicer flox/- mouse embryonic stem cells


title: Dicer -/- (mESCs) transfected with pEF-1_mDcO plasmid; clone O4


title: Me-RIP, DAA1

description: m6A-immunoprecipitated mRNA


title: Dicer -/- (mESCs) transfected with pEF-1_mDcO plasmid; clone O3


title: Dicer -/- (mESCs) transfected with pEF-1_mDcrS plasmid; clone S11


title: Dicer -/- (mESCs) transfected with pEF-1_mDcO plasmid; clone O2


title: Dgcr8 -/- (mESCs)


title: Dicer -/- (mESCs); this cell line was used for all transfection experiments


title: Dicer -/- (mESCs) transfected with pEF-1_mDcrS plasmid; clone S4