title: Lef1-CON_P22 rep3 (12400X5)

city: Salt Lake City

first: Yuanyuan

last: Xie

state: Utah

address: 20 South 2030 East, Bldg. 570 BPRB, Rm. 456

institute: University of Utah

description:
12400X5
12400R_counts.txt
12400R_FPKM.txt

data_processing:
sequencing by HiSeq 50 Cycle Single-Read Sequencing version 3 (zebrafish) or version 4 (mouse)
A transcriptome reference was created by combining GRCz10 (zebrafish) or GRCm38 (mouse) chromosome sequences with Ensembl build 84 splice junction sequences generated with USeq (v8.8.8) MakeTranscriptome.
RNA-seq reads were mapped to the GRCz10 (zebrafish) or GRCm38 (mouse) transcriptome reference using Novoalign (v2.08.03).
Splice junction alignments were converted back to genomic space using USeq SamTranscriptomeParser.
USeq DefinedRegionDifferentialSeq was used to generate per gene read counts, which were used in DESeq2 to determine differential expression.
Genome_build: GRCz10 (zebrafish); GRCm38 (mouse)
Supplementary_files_format_and_content: counts, FPKMs

source_name: Lef1-CON, P22, Hypothalamus

extract_protocol:
Zebrafish: Embryos were fixed for 1.5 hours in 4% PFA/5% sucrose in PBS at RT, followed by whole hypothalamus dissection with super fine forceps (FST, 11252-00). For each biological replicate, 28-38 dissected hypothalami were pooled for lef1 mutant and control samples from at least one single-pair breeding. RNA was extracted using a RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Ambion, AM1975) according to the manufacturer’s instructions. Three biological replicates were obtained on different days from offspring of different breedings. A total of 300 ng RNA per sample was submitted for RNA-seq.
Mouse: E14.5 and P22 non-weaned male Lef1-CON and Lef1-CKO hypothalami were dissected using a fluorescent microscope in ice-cold PBS while tail tissue was retained for genotyping. E14.5 tissues were immediately immersed in RNAlater (Thermo Fisher) and stored at 4 °C. P22 tissues dissected from at least 2 litters were immediately homogenized in TRIzol (Thermo Fisher) and stored at -80 °C. Three biological replicates were prepared from either 5 pooled hypothalami (E14.5) or a single hypothalamus (P22) from Lef1-CON and Lef1-CKO mice, and RNA was extracted on the same day using TRIzol followed by an RNeasy Mini Kit (Qiagen) with on-column DNase digestion (Sigma). 1 µg of RNA per sample was submitted for RNA-seq.
Illumina TruSeq Stranded RNA Kit with Ribo-Zero Gold

value: Nkx2-1Cre/+;Lef1flox/+; RosatdTomato/+

value: Hypothalamus


title: MRC-5 mock rep1 24hpi

status: Public on Aug 24 2017

type: SRA

city: Chicago

first: Adam

last: Oberstein

state: IL

address: 835 South Wolcott Ave.

department: Microbiology and Immunology

country: USA

institute: University of Illinois

description: processed data column header: AO.5

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Concatenated human/HCMV fasta and annotation (.gtf) files were created for mapping and feature counting by combining sequences and annotations from gencode human genome Release 24 (GRCh38.p5) and TB40E-BAC4 (EF999921.1).
Align sequencing fragments were mapped to the concatenated genome using HISAT2 version 2.0.3 (Kim et al., 2015)
Strand-specific fragment counts were generated at the gene level using featureCounts (Liao et al., 2014), requiring a minimum mapping quality score of 10 and concordantly mapped fragment ends on the same chromosome.
In order to eliminate compositional bias, HCMV counts were removed prior to normalization and ratio determination.
Ratio determination and significance calling was performed using DESeq2 (Love et al., 2014) with dispersion estimates fit with local regression.
Genome_build: gencode human genome Release 24 (GRCh38.p5) and TB40E-BAC4 (EF999921.1).
Supplementary_files_format_and_content: rawdata_table.tab: Tab-delimited count matrix (gene.id vs. Sample) containing gene-level summarized raw counts from featureCounts. This file contains human and HCMV counts.

molecule: total RNA

organism: Homo sapiens

source_name: embryonic lung

growth_protocol: DMEM supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, 2 mM glutamax (Gibco), 10 mM Hepes pH 7.4, 0.1 mM MEM Non-Essential Amino Acids (Gibco), 100 units/ml Penicillin G, and 100 μg/ml Streptomycin Sulfate.

extract_protocol:
Trizol fractionation followed by Rneasy column and Dnase treatment.
According to manufacturer's instructions using a KAPA Stranded RNA-Seq Kit with RiboErase (Kappa Biosytems).

treatment_protocol: 2h infection at 3 MOI based on IE1-titering (fluorescent focus assay) on each cell type.

tag: cell type

value: fibroblast

tag: treatment

value: mock

tag: replication

value: biological replicate 1


title: Lef1-CON_P22 rep2 (12400X3)

description:
12400X3
12400R_counts.txt
12400R_FPKM.txt

organism: Mus musculus

tag: strain

tag: age

tag: genotype

tag: tissue


title: Lef1-CKO_P22 rep2 (12400X4)

description:
12400X4
12400R_counts.txt
12400R_FPKM.txt

source_name: Lef1-CKO, P22, Hypothalamus


title: ARPE-19 mock rep2 24hpi

description: processed data column header: AO.6

source_name: adult retina

value: epithelial

value: biological replicate 2


title: MRC-5 TB40epi rep2 24hpi

description: processed data column header: AO.4

value: HCMV-infected


title: Lef1-CKO_P22 rep1 (12400X2)

description:
12400X2
12400R_counts.txt
12400R_FPKM.txt


title: Lef1-CON_P22 rep1 (12400X1)

description:
12400X1
12400R_counts.txt
12400R_FPKM.txt


title: MRC-5 mock rep2 24hpi

description: processed data column header: AO.2


title: ARPE-19 mock rep1 24hpi

description: processed data column header: AO.1


title: NH4

city: Shanghai

first: NASHAT

last: ABUMARIA

address: 130 Dong An Road

department: Institute of Brain Science and Department of Laboratory Animal Science

country: China

institute: Fudan University

data_processing:
image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR (version 2.42a) [ref: STAR: ultrafast universal RNA-seq aligner.]
Stringtie version 1.2.3 [ref: Stringtie enables improved reconstruction of a transcriptome from RNA-seq reads.] were implemented for assembly of RNA sequencing reads into transcripts for each sample, then StringTie was run with "--merge" mode to generate a non-redundant set of transcripts observed in all the RNA-seq samples. The Cufflinks program [ref: Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation.] was used to produce expression levels for the merged transcriptome in each sample at both gene and transcript level in FPKM units (FPKM = Fragments Per Kilobase of transcript per Million mapped reads)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina VazymeVAHTSTM Total RNA-seq Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The learned helplessness paradigm in mice that we used has been described previously(Beurel et al., 2013). Mice were induced by exposing to 180 inescapable foot shocks (0.4 mA). The foot shocks were unpredictable with varying duration (1-5 s, average 3 s) and interval-episodes was 17 s, amounting to a total session duration was approximately 1 h. 24 h after the induction session, test session was assessed by shuttle box (14 inches× 7 inches×12 inches; Coulbourn Instruments) performance using Graphic State 4.0 software (Coulbourn Instruments). Mice were in the one side of the shuttle box 3 min for habituation. During the test animals were received 30 trials of escapable foot shock (0.4 mA, 10 s duration, inter-shock intervals of 1-24 s, average 10 s), and the door was open. If mouse successfully shuttled during the 10 s shock, escape latency was measured as the time animal used to shuttle the door. If no shuttling was made during the 10 s shock, the failure was recorded and escape latency was recorded as 10 s. According to testing results, mice can be devided into non-learned helplessness (NLH), learned helplessness (LH) and Ctrl group (only experience escapable shock test without induction session), and the Homecage group was just in their cages without experience induction session and escapable shock. A k–means (k=2) clustering analysis was applied to a database consisting of 31 mice subjected to the learned helplessness procedure. We used failure number and escape latency, the most commonly reported indices of helplessness as parameters for classification. We further performed a linear discriminant analysis on our clustering results, with the number of failures and escape latency as predictor variables, to obtain classification equations for new formula as follows:  "NLH=-15.33667+(-2.7855×Failure number)+(10.30663×Escape latency)"   "LH=-24.75286+" ("0.23071×Failures number" )"+" ("4.78622×Escapse latency" )  Mouse is classified as being non-learned helplessness if NLH > LH, or learned helplessness if LH > NLH (Chourbaji et al., 2005; Wang et al., 2014).

tag: genotype/variation

value: wild type

value: 3 month

tag: sample group

value: nonlearned helplessness (NLH) group

value: hippocampus


title: Lef1-CON_E14.5 rep3 (12313X5)

description:
12313X5
12313R_counts.txt
12313R_FPKM.txt

source_name: Lef1-CON, E14.5, Hypothalamus


title: Lef1-CKO_E14.5 rep2 (12313X4)

description:
12313X4
12313R_counts.txt
12313R_FPKM.txt

source_name: Lef1-CKO, E14.5, Hypothalamus


title: Lef1-CKO_E14.5 rep3 (12313X6)

description:
12313X6
12313R_counts.txt
12313R_FPKM.txt


title: MRC-5 TB40epi rep1 24hpi

description: processed data column header: AO.3


title: NH2


title: Lef1-CKO_E14.5 rep1 (12313X2)

description:
12313X2
12313R_counts.txt
12313R_FPKM.txt


title: ARPE-19 TB40epi rep2 24hpi

description: processed data column header: AO.8


title: Lef1-CKO_P22 rep3 (12400X6)

description:
12400X6
12400R_counts.txt
12400R_FPKM.txt


title: LH4

value: learned helplessness (LH) group


title: NH1


title: Lef1-CON_E14.5 rep1 (12313X1)

description:
12313X1
12313R_counts.txt
12313R_FPKM.txt


title: Lef1-CON_E14.5 rep2 (12313X3)

description:
12313X3
12313R_counts.txt
12313R_FPKM.txt


title: AE1_18

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 1610

department: Biostatistics and Data Science

institute: Tulane University School of Public Health and Tropical Medicine

data_processing:
For the raw fastq files from each sample, we performed alignment to the Human Reference Genome (hg19) using TopHat to generate the BAM files.
We then used a number of Bioconductor packages to process the BAM files into gene count matrix following the procedures listed under http://www.bioconductor.org/help/workflows/rnaseqGene/.
Specifically, we used “BamFileList” function from the “Rsamtools” package to specify the number of reads (2,000,000 reads in our study) to be processed at a time.
We then used “makeTrascriptDbFromGFF” from the “GenomicFeatures” package to generate a database object that contains annotation information of exons, transcripts and genes from the UCSC Genome Browser. The “summarizeOverlaps” function from the “GenomicAlignments” package was then used to annotate the bam files and generate an object that is the gene count matrix containing the gene count for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes gene count values for each sample

source_name: airway epithelial cells

growth_protocol: Human bronchial epithelial cells (BEAS-2B cells), purchased from American Type Culture Collection (ATCC, Wiltshire, USA), were cultured following standard guidelines. Thawed cells were initially grew in a pre-coated flask containing fibronectin (0.01g/ml), bovine collagen type 1 (0.03mg/ml), and bovine serum albumin (0.01mg/ml). Following overnight growth in this pre-coated flask, the cells were sub-cultured in Dulbecco's Modified Eagle Medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin and 100U/ml streptomycin (Invitrogen, Carlsbad, CA). Cells were cultured at 37 ºC in a 100% humidified atmosphere of 5% CO2 in air. A single clone of BEAS-2B was grown to homogenize genomic variation between cultured cells. The cells were divided equally into separate flasks and grown under treatment or no treatment conditions (controls) for 22 passages (P22) for ~ 2.5 months.

extract_protocol:
Total RNA was extracted at Omega Bio-Tek, Inc (Norcross, GA) using the E.Z.N.A Total RNA kit II produced by the company (Omega Bio-Tek, Inc, Norcross, GA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the oil treatment, we used WAF of crude oil (3%) dilution. For the dispersant treatment, we used Corexit 9500 or Corexit 9527 at 300ppm. For the oil-dispersant mixture treatment, we used WAF-dispersed oil at 300ppm. For controls, we added the equivalent volume of water to the medium, which is the same water solution that was used to dilute the oil or dispersants. For each treatment, including the control, three independent replicate cell samples were used.

tag: cell line

value: lung/bronchus

value: control


title: AE1_17


title: LH2


title: AE1_16


title: NH3


title: KO4

city: St. Louis

first: Jean

middle: E

last: Schaffer

state: MO

address: 660 S Euclid Ave # 8125

institute: Washington University School of Medicine

description: run_1958_s_5_withindex_sequence.txt_CAATATC.fq.gz

data_processing:
Import raw data in fastq file format from sequencing center into Partek Flow software system.
Trim Adaptor sequence "AGATCGGAAGAGCGGTTCAG" from 3' end (Partek Flow)
Align Reads to mouse genome mm9 using Star Aligner Version 2.4.1 with the following parameters: Assembly mouse mm9,Generate unaligned reads false, Max buffers size 150000000, Max junctions 1000000,Type of filtering Normal,Multimap score range 1,Max read mapping 2 (Default: 10),Max mismatches 4 (Default: 10),Mismatch mapped ratio 0.3,Mismatch read ratio 0.3 (Default: 1.0),Min score 0,Normalized min score 0.66,Min matched bases 0,Normalized min matched bases 0.66,Filter alignment using their motifs None,Collapsed splice junctions reads All, Max junction gap 50000 100000 200000, Non-canonical motifs true, Min overhang length for splice junctions 30, Min unique map read count per junction 3, Min total read count per junction 3 ,Min distance to other junctions' donor/acceptor 10
Quantify to Transcriptome using Assembly mouse mm9, RefSeq Annotation Model  (Partek Flow)
Generate Gene Counts (Partek Flow)
Normalize Counts using "Recommended" Settings (Partek Flow)
Generate Gene Analysis (Partek Flow)
Filter by FDR step-up 0.05, fold change <-2 or >2, require  >1 read/million total reads per gene (Partek Flow; Microsoft Excel)
Genome_build: Mouse mm9
Supplementary_files_format_and_content: Fastq, txt

source_name: Pancreatic Islets

extract_protocol:
High quality total RNA (RIN ≥ 8.5) was prepared from hand-picked islets (n = 4 mice/genotype) using TRIZOL reagent and treated with Turbo DNAse (Thermo Fisher).
SeqPlex RNAseq (Sigma) libraries were prepared according to the manufacturer's protocol.

value: Pancreatic Islets

value: 8 week old

value: RpL13a snoRNA knockout on C57BL/6  background


title: LH1


title: KO3

description: run_1958_s_5_withindex_sequence.txt_ACCCACT (1).fq.gz


title: AE1_15


title: Set 1 shTon_TNF

city: Philadelphia

first: Makarand

last: Risbud

state: PA

address: 1015 Walnut St.

department: Orthopaedic Surgery

institute: Thomas Jefferson University

description: processed data file: PLKO_TNF_vs_shTon_TNF.xlsx

data_processing:
Rn5 ensembl annotations (build 75) were downloaded and converted to genePred format.  Splice junction sequences were generated using USeq’s (v8.8.8) MakeTranscriptome application using a radius of 46.  These splice junction sequences were added to the rn5 chromosome sequences and run through novoindex (v2.8) to create the transcriptome index.
Reads were aligned to the transcriptome reference index described above using Novoalign (v2.08.01), allowing up to 50 alignments for each read.  USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application.  These counts were used in DESeq2 to measure the differential expression between each condition, controlling for sample preparation batch.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text file containing EnsemblGeneId, Gene Name, Log2 Fold Change, Adjusted P-value, and DESeq2 normalized counts.

organism: Rattus norvegicus

source_name: Rat nucleus pulposus

growth_protocol: Primary rat nucleus pulposus (NP) cells were dissected from Wistar rat spines, expanded from explant tissues, and maintained in DMEM containing 10% FBS and antibiotics

extract_protocol: Total mRNA was extracted using Qiagen Rneasy mini columns and treated with DNAse1

treatment_protocol: Rat NP cells were transduced with lentivirally-delivered control (PLKO) or TonEBP-specific (shTon) shRNA. 24 h before collection of total mRNA, cells were either left untreated or treated with 50ng/mL TNF-a.

value: Wistar

value: nucleus pulposus

tag: transduced with

value: shTonEBP-transduced

tag: condition

value: TNF-a-treated


title: Homecage4

value: homecage group


title: Set 2 shTon_TNF


title: AE1_14

value: epithelial

value: oil


title: Homecage3

value: wild type


title: Set 2 shTon_CTR

description: processed data file: PLKO_CTR_vs_shTon_CTR.xlsx


title: AE1_13


title: KO2

description: run_1958_s_5_withindex_sequence.txt_TCAACTG.fq.gz


title: KO1

description: run_1958_s_5_withindex_sequence.txt_TTTAACT.fq.gz


title: Set 3 shTon_CTR


title: AE1_12


title: LH3

value: 3 month


title: N15-(DM1)

city: ILLKIRCH

first: nicolas

last: charlet

address: 1 Rue laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA and CASAVA 1.8.
Alternative splicing analysis using MISO software, which computes the fraction of mRNA that includes a given cassette alternative exon
Genome_build: hg19
Supplementary_files_format_and_content: xls files from MISO analysis containing either alternative splicing measurement and pairwise comparison between all samples (consolidated) or alternative splicing comparison between control and DM1 samples with Z-score (monotonic)

molecule: polyA RNA

source_name: disease (DM1)_skeletal muscle

extract_protocol:
Total RNA extraction using Trizol
After isolation of total cellular RNA from human skeletal muscles samples, libraries of template molecules suitable for high throughput DNA sequencing were created using TruSeq RNA Sample Preparation v2 Kit (ref. RS-122-2001, Illumina) with modifications in the manufacturer’s protocol. Briefly, mRNA was purified from 1 µg total RNA using oligo-dT magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers, then the second strand of the cDNA was synthesized using Polymerase I and RNase H. The next steps of RNA-Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit (ref. A84801, Beckman Coulter) with the SPRI-TE instrument (Beckman Coulter). In this system double stranded cDNA fragments were blunted, phosphorylated and ligated to Illumina indexing adapters and fragments in the range of ~200-400 bp were size selected. The automated steps were followed by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C), and then surplus PCR primers and adapter dimers were removed by purification using AMPure XP beads (Beckman Coulter). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

tag: subject status

value: myotonic dystrophy type I (DM1) patient

tag: subject id

value: DM1 patient 15

value: skeletal muscle


title: Set 3 shTon_TNF


title: wT4

description: run_1958_s_5_withindex_sequence.txt_GCTTAGA.fq.gz

value: wildtype C57BL/6


title: Homecage2

value: hippocampus


title: Set 1 shTon_CTR

value: control


title: AE1_11

value: lung/bronchus


title: Homecage1


title: Set 3 PLKO_TNF

description: processed data file: PLKO_CTR_vs_PLK_TNF.xlsx, PLKO_TNF_vs_shTon_TNF.xlsx

value: PLKO-transduced


title: wT3

description: run_1958_s_5_withindex_sequence.txt_GTCGATA.fq.gz

value: Pancreatic Islets

value: 8 week old


title: Ctrl4

value: control group


title: AE1_10


title: Set 2 PLKO_TNF

value: Wistar

value: nucleus pulposus

value: TNF-a-treated


title: wT2

description: run_1958_s_5_withindex_sequence.txt_AGATACT.fq.gz


title: AE1_9

value: epithelial


title: wT1

description: run_1958_s_5_withindex_sequence.txt_GGGTCAA.fq.gz


title: Ctrl2

value: wild type


title: Ctrl3

value: 3 month


title: AE1_8


title: Set 3 PLKO_CTR

description: processed data file: PLKO_CTR_vs_PLK_TNF.xlsx, PLKO_CTR_vs_shTon_CTR.xlsx


title: Set 1 PLKO_TNF


title: AE1_7


title: Set 2 PLKO_CTR


title: Ind_Z 3

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

data_processing:
Reads were trimmed according to varying GC-content at the 5´ and, and a quality cut-off (Q < 20).
Trimmed reads were mapped to the reference genome of Saccharomyces cerevisiae s288c (v. EF4, Ensembl), using Tophat (v2.0.9) (Kim et al. 2013)
Transcripts were quantified on a count basis using HTSeq (v0.6.0) (Anders et al. 2014) with “intersection-strict” mode for overlapping reads.
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: Tab-delimited text file with raw counts for all samples

organism: Saccharomyces cerevisiae

growth_protocol: Cells were recycled for five rounds of fed-batch fermentations in a sugar cane molasses based medium, with acid treatment between the cycles, similar to the industrial process employed in Brazil. Samples where collected after 4 hours of the last fermentation

extract_protocol:
Biomass samples were lysed on a Fastprep instrument (Lysing Matrix Y from MP Biomedicals (cat. no. 116960050), and total RNA extracted according to the manufacturers recommendations (Invitrogen TRIzol Plus RNA purification kit (cat. no. 12183 − 555))
Libraries were prepared using Illumina TruSeq [high sample] kit (cat. no. RS − 122 − 2001) with enzymatic rRNA depletion

value: anti-foam


title: A549 9h Lipofectamine 2000

city: Princeton

first: Alexei

last: Korennykh

address: Schultz Laboratory, Washington Road

institute: Princeton University

description:
A549 cells were grown to ~80% confluence and treated with mock (Lipofectamine 2000 + Opti-MEM) or 2-5A transfection complexes.  Cells were harvested 9h post-transfection in Buffer RLT from the Qiagen Rneasy kit.
A549_25A.txt

data_processing:
Reads were filtered so every base in the read had a quality score >=30
Reads were Reverse complemented and trimmed of Illumina adaptor sequences using Custom software
For small RNAs, reads were mapped the Hg19 transcriptome and uniquely mapping reads were kept for analysis
For mRNAs, reads were mapped to Hg19 using TopHat2 and reads mapping to protein coding genes were quantitated with HTSeq-Count
Genome_build: Hg19 transcriptome

source_name: A549 9h Lipofectamine 2000

growth_protocol:
Standard tissue culture methods.
HeLa were grown in MEM + 10% FBS, T47D and A549 cells were grown in RPMI + 10% FBS.  Hap1 were grown in IMDM + 10% FBS

extract_protocol:
small RNA were purified by miRNA.
mRNAs were purified by Rneasy followed by oligo-dT pulldown
RNA quality was assessed by RNA 6000 NanoChip or by 8M urea 10% PAGE
Libraries for small RNA were made following a custom protocol.
Barcodes are in a separate text file (barcodes.txt)

value: wild-type


title: Ctrl1


title: Set 1 PLKO_CTR


title: AE1_5


title: AE1_6


title: Ind_Z 2


title: untreated A549; control for DTT

description:
A549 cells were grown to ~80% confluence and treated with 2 mM DTT or vehicle (water) for 3 hours.  Cells were harvested by Trypisinization.
Dataset_S1.xlsb

source_name: untreated A549; control for DTT


title: AE1_4


title: Ind_Z 1


title: Ind_B 3


title: 2328912_TimePoint4_BoneMarrow

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T04YSMmCoDaBM_TGACCAL001R1_2328912.fastq.gz
Raw File 2: E03T04YSMmCoDaBM_TGACCAL001R2_2328912.fastq.gz

data_processing:
A combined reference index was built which includes the parasite and host genomes. Bowtie2-build (vesion 2.1.0) takes the merged *.fasta file and makes a reference index where default parameters are used.
The transcriptome annotation index is made using gffread. The *.gff gene annotations files for both the host and the parasite are obtained from the iRODS server. tophat2 (v2.0.10) is used to build the transcriptome index by supplying the -G. The parameter passed to the -G option is the merged gtf file. Default parameters are used.
The raw fastq files from each library (one library per sample) are mapped to a combined reference genome index using tophat2 (v2.0.10). Default options for tophat2 are used with the following exceptions: -p 8 : this option is used to increase the speed of the mapping step by using multiple threading.
htseq (version 0.5.4) was used to quantify the number of reads mapping to each gene in the reference annotation file, which was made in the previous step. The two required parameters are the bam file (sorted by name) and the *.gtf (gene annotation) file. Default parameters are used with the following exception: -s reverse : this parameter is used since the Illumina protocol to preserved strandedness uses the second (reverse) strand. The mapping input is the sam file sorted by read name (and not by chromosomal location). The reference annotation is the same as that from the read mapping step.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under accession  PRJNA214746. Parasite: Plasmodium coatneyi strain Hackeri genome assembly was used. The assembly has been deposited in GenBank under the accession PRJNA329102.
Supplementary_files_format_and_content: Excel files contain normalized transcript abundances at the gene level, for each individual.  Abundances are further classified by experimental Time Point (1-7), and Specimen Type (Bone Marrow). Gene expression normalization is performed using the gene level expression files with DESeq (version 1.28.0). Default parameters were used. Normalized parasite results should be used with caution since host were not infected at all time points. See supplementary readme for details. Note that raw counts are also provided as supplementary files.
Supplementary_files_format_and_content: LibSizeNormCounts Column headers are defined as follows:
Supplementary_files_format_and_content: 'Gene ID':  Identifiers of all Genes in the annotation.
Supplementary_files_format_and_content: 'Gene Symbol': Symbols of all Genes in the annotation.
Supplementary_files_format_and_content: 'Raw File 1 / Raw File 2 / Abundances': Library size normalized read counts of all genes, from the raw files listed in the column header. The raw file names contain information regarding Specimen Type, NHP ID, and Time Point
Supplementary_files_format_and_content: There will be one read count column per specimen per NHP  (Non-Human-Primate) per Time Point. So, 1 * 5 * 7 = 35 columns with read counts.
Supplementary_files_format_and_content: There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.

organism:
Macaca mulatta
Plasmodium coatneyi

source_name: Bone Marrow

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Bone marrow (1ml) was collected into 1.5 ml tubes with EDTA, and the mononuclear cells were purified by density gradient centrifugation on Lymphoprep (Stem Cell Technologies) solution and preserved in RLT buffer (Qiagen) to stabilize mRNA.  Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted from the BM samples using Qiagen RNEasy Mini-Plus kits following the manufacturer-recommended procedures, and from PB samples using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq1000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: The NHPs were given sub-curative treatment with Artemether during the experiment. After the 101-day experimental period, NHPs were treated with blood-stage curative doses of Artemether.

tag: time point

tag: gender

value: Male

tag: non human primate individual id

tag: parasite strain

value: P. coatneyi strain Hackeri


title: 2328910_TimePoint4_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T04YSMmCoDaBM_GTCCGCL008R1_2328910.fastq.gz
Raw File 2: E03T04YSMmCoDaBM_GTCCGCL008R2_2328910.fastq.gz


title: AE1_3

tag: cell type

tag: treatment

value: oil


title: 2328909_TimePoint7_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T07YSMmCoDaBM_ACAGTGL008R1_2328909.fastq.gz
Raw File 2: E03T07YSMmCoDaBM_ACAGTGL008R2_2328909.fastq.gz


title: A549 9h 2-5A


title: Ind_B 2


title: AE1_2


title: T47D 3 min +2-5A


title: AE1_1


title: 2328908_TimePoint1_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T01YSMmCoDaBM_ATGTCAL008R1_2328908.fastq.gz
Raw File 2: E03T01YSMmCoDaBM_ATGTCAL008R2_2328908.fastq.gz


title: Ind_B 1


title: T47D 1 min +2-5A


title: Control 3

value: control


title: A549 3h 2 mM DTT

source_name: A549 3h 2 mM DTT


title: 2328892_TimePoint5_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T05YSMmCoDaBM_CTTGTAL008R1_2328892.fastq.gz
Raw File 2: E03T05YSMmCoDaBM_CTTGTAL008R2_2328892.fastq.gz


title: WT-3 DNase-seq

city: Ann Arbor

first: Anthony

last: Antonellis

state: MI

address: 1241 E Catherine St.

department: Human Genetics

institute: University of Michigan

library_source: genomic

data_processing:
Read Trimming: Adapter or linker DNA sequences were removed from each read, resulting 18~26nt left at the 5’ end of each read. The trimmed reads which are shorter than 18nt were discarded.
Read quality assessment by FastQC
Alignment: The raw reads were aligned uniquely to Rn5 assembly by Bowtie. Up to two mismatches were allowed.
Peak Calling: Peaks were called using F-seq with default parameters.
Peak annotation: Peaks annotated by Homer.
BigWig File Generation: Wig files generated from F-seq were convereted into BigWig files.
Genome_build: rn5
Supplementary_files_format_and_content: BigWig files of DNase HSS peaks.

molecule: genomic DNA

source_name: Myelinating Schwann Cell

growth_protocol: S16 cells were cultured using standard growth media supplemented with L-glutamine. The cells were cultured in a T-75 flask and passaged every 2-3 days.

extract_protocol:
Approximately 20 million cells per sample were used to extract genomic DNA. Extraction and preparation were performed according to Song and Crawford, DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells, 2010.
Libraries were prepared for sequencing according to Song and Crawford, DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells, 2010.

value: Schwann cell line S16

value: WT

tag: passage


title: T47D 3 min -2-5A


title: 2328870_TimePoint5_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T05YSMmCoDaBM_CAGATCL007R1_2328870.fastq.gz
Raw File 2: E03T05YSMmCoDaBM_CAGATCL007R2_2328870.fastq.gz


title: WT-1 DNase-seq


title: Control 1


title: 2328868_TimePoint7_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T07YSMmCoDaBM_ACAGTGL007R1_2328868.fastq.gz
Raw File 2: E03T07YSMmCoDaBM_ACAGTGL007R2_2328868.fastq.gz


title: T47D 1 min -2-5A


title: untreated RNase L -/- Hap1

source_name: untreated RNase L -/- Hap1

value: RNase L -/-


title: Control 2


title: untreated T47D

description:
This section applies to all T47D cells. Cells were trypsinized, washed with complete media, then PBS, aliquoted, and pelleted.  Cell pellets were immediately lysed in miRVana lysis buffer (untreated) or resuspended in a digitonin semi-permeabilization buffer lacking or containing 2-5A to activate RNase L.  Aliquots were withdrawn and added to miRVana lysis buffer at 1 and 3 minutes.
Dataset_S1.xlsb

source_name: untreated T47D


title: untreated WT Hap1

description:
Hap1 cells were grown to ~80% confluence and harvested by trypsinization
Dataset_S1.xlsb

source_name: untreated WT Hap1


title: Rat Sperm MRE-seq

city: SAINT LOUIS

first: Daofeng

last: Li

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
Sequencing reads were aligned to rat rn4 or mouse mm9 with BWA
For MeDIP-seq, redandunt reads were discard
For MRE-seq, reads were filtered by MRE recognization site in genome.
Aligned results were further processed by methylQA (http://methylqa.sourceforge.net/) to get bigWig files
Genome_build: rn4, mm9
Supplementary_files_format_and_content: bigWig

source_name: Rat Sperm

extract_protocol:
For MeDIP, 5–15 μg DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA), than DNA was sonicated to ~100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2–5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg ml−1, Eurogentec. Catalog No. BI-MECY-0100). For this, DNA was heat-denatured at 95 °C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl primary antibody per microgram of DNA overnight at 4 °C with rocking agitation in 500 μl immunoprecipitation buffer (10 mM sodium phosphate buffer, pH 7.0, 140 mM NaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 4 μl of rabbit anti-mouse IgG secondary antibody (2.5 mg ml−1, Jackson Immunoresearch. Catalog No. 315-005-008) and 100 μl Protein A/G beads (Pierce Biotechnology. Catalog No. PI20421) were added and incubated for an additional 2 h at 4 °C with agitation. After immunoprecipitation a total of six immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg ml−1proteinase K for 2 h at 55 °C and then allowed to cool to room temperature. MeDIP DNA were purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen).
Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.
For MRE:  DNA isolated using the DNeasy Tissue kit (Qiagen, Valencia, CA). Three parallel digests were performed (HpaII, AciI and Hin6I; Fermentas), each with 1μg of DNA. Five units of enzyme per microgram DNA were added and incubated at 37 °C in Fermentas Tango buffer for 3 h. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube. Combined DNA was size-selected by electrophoresis on a 1% agarose TBE gel. A 100–300 bp gel slice was excised using a sterile scalpel and gel-purified using Qiagen QIAquick columns, eluting in 30 µl of Qiagen EB buffer.
Library construction was performed using the Illumina Genomic DNA Sample Kit (Illumina) with single-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the Klenow DNA polymerase was diluted 1:5 in water and 1 µl used per reaction. For single-end oligo adaptor ligation, adapters were diluted 1:10 in water and 1 μl used per reaction. Fifteen cycles of PCR were performed using the single-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (220-520 bp) was performed by electrophoresis in DNA was eluted in 36 μl EB buffer using Qiagen QIAquick columns. After cleanup with Qiagen MinElute columns, each library was examined by spectrophotometry (Nanodrop, Thermo Scientific) and Agilent DNA Bioanalyzer (Agilent).2% agarose. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis.

tag: strain

value: Holtzman

value: Sperm


title: HeLa H672N RNase L overexpression

description:
HeLa cells in 10 cm dish transfected with 10 ug plasmid for RNase L overexpression.  Media was changed 4h post-transfection and cells were harvested by trypsinization 24h post-treatment
Dataset_S1.xlsb

source_name: HeLa H672N RNase L overexpression

value: HeLa

tag: genotype


title: 2328866_TimePoint2_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T02YSMmCoDaBM_CGATGTL007R1_2328866.fastq.gz
Raw File 2: E03T02YSMmCoDaBM_CGATGTL007R2_2328866.fastq.gz


title: Rat Brain MRE-seq

source_name: Rat Brain

tag: tissue

value: Brain


title: control_3 dpf rep3 (10688X5)

description:
10688X5
10688R_counts.txt
10688R_FPKM.txt

organism: Danio rerio

source_name: control, 3 dpf, Hypothalamus

value: *AB

tag: age

value: 3 dpf

value: lef1+/- or lef1+/+

value: Hypothalamus


title: 2328864_TimePoint1_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T01YSMmCoDaBM_ACAGTGL006R1_2328864.fastq.gz
Raw File 2: E03T01YSMmCoDaBM_ACAGTGL006R2_2328864.fastq.gz


title: HeLa WT RNase L overexpression

source_name: HeLa WT RNase L overexpression


title: Rat Blood MRE-seq

source_name: Rat Blood

value: Blood


title: lef1-/-_3 dpf rep2 (10688X4)

description:
10688X4
10688R_counts.txt
10688R_FPKM.txt

source_name: lef1-/-, 3 dpf, Hypothalamus


title: 2328863_TimePoint2_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T02YSMmCoDaBM_CGATGTL006R1_2328863.fastq.gz
Raw File 2: E03T02YSMmCoDaBM_CGATGTL006R2_2328863.fastq.gz


title: control_3 dpf rep2 (10688X3)

description:
10688X3
10688R_counts.txt
10688R_FPKM.txt


title: HeLa 8h Lipofectamine

description:
Mock transfection complex containing Lipofectamine 2000 + Opti-MEM was added to cells in 10 mL final volume.  Cell were harvested by trypsinization 8h post-transfection
Dataset_S1.xlsb

source_name: HeLa 8h Lipofectamine

value: wild-type


title: WT-2 DNase-seq

tag: genotype/variation


title: lef1-/-_3 dpf rep1 (10688X2)

description:
10688X2
10688R_counts.txt
10688R_FPKM.txt


title: HeLa 8h poly-IC

description:
Transfection complex containing Lipofectamine 2000 + Opti-MEM + poly-IC was added to cells in 10 mL final volume. Final poly-IC concetration after adding it cells was 1 ug/mL. Cell were harvested by trypsinization 8h post-transfectionby trypsinization
Dataset_S1.xlsb

source_name: HeLa 8h poly-IC

tag: cell line


title: Rat Brain MeDIP-seq


title: 2328862_TimePoint2_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T02YSMmCoDaBM_GTGAAAL006R1_2328862.fastq.gz
Raw File 2: E03T02YSMmCoDaBM_GTGAAAL006R2_2328862.fastq.gz

value: Male


title: 2328867_TimePoint2_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T02YSMmCoDaBM_TGACCAL007R1_2328867.fastq.gz
Raw File 2: E03T02YSMmCoDaBM_TGACCAL007R2_2328867.fastq.gz

value: P. coatneyi strain Hackeri


title: Rat Blood MeDIP-seq


title: 2328861_TimePoint3_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T03YSMmCoDaBM_GTCCGCL006R1_2328861.fastq.gz
Raw File 2: E03T03YSMmCoDaBM_GTCCGCL006R2_2328861.fastq.gz


title: 2319023_TimePoint3_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T03YSMmCoDaBM_AGTTCCL005R1_2319023.fastq.gz
Raw File 2: E03T03YSMmCoDaBM_AGTTCCL005R2_2319023.fastq.gz


title: control_3 dpf rep1 (10688X1)

description:
10688X1
10688R_counts.txt
10688R_FPKM.txt


title: lef1-/-_3 dpf rep3 (10688X6)

description:
10688X6
10688R_counts.txt
10688R_FPKM.txt


title: BGA0201_447_L7.D706

city: Charlottesville

first: Mark

middle: Jon

last: Lawson

state: Virginia

address: 501 Locust Avenue, Suite 301

department: Computational Biology

institute: HemoShear Therapeutics

data_processing:
reads were pseudoaligned to the human transcriptome (GRCh38), and transcripts were quantified using kallisto
Transcript abundances were pooled into gene-level estimates using the tximport package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene abundance estimates in tab-delimited text file

source_name: HEP Cell

extract_protocol:
Hepatocyte cell pellets were collected following cessation of experiments at day 10, and RNA isolated using the Invitrogen Purelink RNA Mini kit (12183018A) according to manufacturer’s instructions
Libraries were constructed according to Illumina Protocols

tag: media

value: NASH

value: Hepatocyte


title: BGA0201_446_L7.D705

value: LGLI


title: 2328860_TimePoint7_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T07YSMmCoDaBM_ATGTCAL005R1_2328860.fastq.gz
Raw File 2: E03T07YSMmCoDaBM_ATGTCAL005R2_2328860.fastq.gz


title: BGA0201_445_L8.D704


title: Gsk3a-/-;Gsk3b-/-_ESC_2

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

data_processing:
RNA-Seq reads mapped to the reference mouse genome (mm10) using STAR with the option --alignSJoverhangMin 8
Counts of STAR-aligned reads that overlapped transcript exons (used Ensembl relase 82 annotation) were quantified with the GenomicRanges package in R (count mode: Union)
Counts were then normalized and differentially expressed genes between WT and GSK3 DKO were identified using default parameters with DESeq in R
mgi_symbol and gene_biotype columns were added to the deseq_res table using biomaRt in R
Genome_build: mm10
Supplementary_files_format_and_content: deseq_res.txt is a tab-delim table of results from DESeq including mgi_symbol and gene_biotype columns

source_name: Mouse Embryonic Day 16 Stem Cells

growth_protocol: 37 °C in 5% CO₂ in DMEM supplemented with 15% FBS, 0.1mM MEM, 2mM Glutamax, 0.055mM β-mercaptoethanol, and 1000 units/mL LIF on 0.1% gelatin-coated plates with irradiated mouse embryonic fibroblasts.

extract_protocol:
Total RNA extracted with TRIzol using manufacturer's instructions
RNA QC and TruSeq stranded library construction were carried out by  the Genomics Division of the Iowa Institute of Human Genetics which is supported, in part, by the University of Iowa Carver College of Medicine.

value: Embryonic Stem Cells

value: Embryonic Day 16


title: Gsk3a-/-;Gsk3b-/-_ESC_1


title: Wild Type_ESC_2


title: 2319022_TimePoint4_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T04YSMmCoDaBM_CAGATCL005R1_2319022.fastq.gz
Raw File 2: E03T04YSMmCoDaBM_CAGATCL005R2_2319022.fastq.gz

source_name: Bone Marrow


title: 2319021_TimePoint6_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T06YSMmCoDaBM_CTTGTAL005R1_2319021.fastq.gz
Raw File 2: E03T06YSMmCoDaBM_CTTGTAL005R2_2319021.fastq.gz


title: Wild Type_ESC_1


title: Rat Sperm MeDIP-seq

value: Holtzman


title: BGA0201_305_L6.D707


title: BGA0201_448_L3.D707


title: 2319020_TimePoint6_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T06YSMmCoDaBM_AGTTCCL004R1_2319020.fastq.gz
Raw File 2: E03T06YSMmCoDaBM_AGTTCCL004R2_2319020.fastq.gz


title: BGA0201_304_L5.D706


title: 2319019_TimePoint5_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T05YSMmCoDaBM_CTTGTAL004R1_2319019.fastq.gz
Raw File 2: E03T05YSMmCoDaBM_CTTGTAL004R2_2319019.fastq.gz


title: 2319018_TimePoint6_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T06YSMmCoDaBM_AGTCAAL004R1_2319018.fastq.gz
Raw File 2: E03T06YSMmCoDaBM_AGTCAAL004R2_2319018.fastq.gz


title: 2319017_TimePoint2_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T02YSMmCoDaBM_GCCAATL004R1_2319017.fastq.gz
Raw File 2: E03T02YSMmCoDaBM_GCCAATL004R2_2319017.fastq.gz


title: BGA0201_303_L5.D705


title: 2319016_TimePoint1_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T01YSMmCoDaBM_CGATGTL004R1_2319016.fastq.gz
Raw File 2: E03T01YSMmCoDaBM_CGATGTL004R2_2319016.fastq.gz


title: 2319015_TimePoint7_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T07YSMmCoDaBM_GCCAATL003R1_2319015.fastq.gz
Raw File 2: E03T07YSMmCoDaBM_GCCAATL003R2_2319015.fastq.gz


title: BGA0201_301_L2.D703


title: 5GB1_FM_88_TR1

city: Seattle

first: Mitchell

middle: William

last: Pesesky

state: WA

address: 616 NE Northlake Place

institute: University of Washington

data_processing:
Alignment was performed using BWA version 0.7.12-r1044 using the BWA-MEM algorithm and default parameters
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.8.0 in the ‘intersection-nonempty’ mode
Differential abundance analysis was performed with DESeq2 1.2.10 and R 3.3.1.
Protein gene identifiers in the processed data files are located at https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=proteinCodingGenes&taxon_oid=2516653075
Genome_build: AOTL01000000

organism: Methylotuvimicrobium buryatense

source_name: Bioreactor culture

growth_protocol: M. buryatense 5GB1C and its derivatives were grown in a modified NMS medium with methane at 30°C, as previously described (Puri, Owen et al. 2015). Bioreactor experiments were carried out in a New Brunswick BioFlo 310 bioreactor (Eppendorf, Inc. Enfield, CT, USA), and off gas samples were measured using Shimadzu gas chromatograph GC2014 (Shimadzu Scientific Instruments, Inc. Columbia, MD, USA) as described previously (Gilman et al., 2015), using premixed gas tanks (20% CH4, 5% O2, 75% N2) and a dilution rate of 0.03 hr-1.

extract_protocol:
RNA was extracted as previously described (Chu and Lidstrom, 2016).
RNA sequencing and library construction was performed by GENEWIZ (South Plainfield, NJ, USA) using Illumina HiSeq2500 1x50 (single ended) reads.

tag: condition

value: O2 limiting, slow growth conditions; terminal oxidase knockout


title: 5GB1_FM_90_TR1


title: 5GB1_FM_87_TR1

value: O2 limiting, slow growth conditions


title: 2319013_TimePoint7_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T07YSMmCoDaBM_GTGAAAL003R1_2319013.fastq.gz
Raw File 2: E03T07YSMmCoDaBM_GTGAAAL003R2_2319013.fastq.gz


title: BGA0201_444_L8.D703


title: 2319012_TimePoint3_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T03YSMmCoDaBM_GTCCGCL003R1_2319012.fastq.gz
Raw File 2: E03T03YSMmCoDaBM_GTCCGCL003R2_2319012.fastq.gz


title: BGA0201_376_L6.D706


title: BGA0201_378_L12


title: BGA0201_377_L1.D707


title: Pn_AL

city: Trivandrum

first: Soniya

last: E V

state: KERALA

department: Plant Molecular Biology

country: India

institute: Rajiv gandhi Centre for Biotechnology

description: small RNA

data_processing:
Illumina HiSeq Sequencing-By-Synthesis (SBS) technology at the Beijing Genomics Institute (Shenzhen, China).
Sequenced reads were trimmed for 5'  and 3' adaptor sequence, and masked for low-quality sequence.
Using software developed by BGI, the raw data from HiSeq sequencing are processed to remove low quality reads, 5' and 3' adapter contaminants, small quality tags  (<18nt) and poly A reads.
Each processed file contains clean tags of 18-30 nt length and their corresponding sequence counts and each small RNA  is represented with unique sequence ID.
mirBase v20 was used to identify miRNAs.
Genome_build: de novo transcriptome assembly was used for mapping the reads. The FASTA file of assembled sequences is available on the series record. The file "match_genome_Pn_Cl.txt" contains the ids of the small RNAs and the assembled sequence from which it was identified.
Supplementary_files_format_and_content: Counts of small RNA sequence. The processed data files are in fasta format with the small RNA ID and count available on the description line followed by the sequence of the small RNA.

organism: Piper nigrum

source_name: Leaves from drought stressed plants

extract_protocol:
Small RNA enriched total RNA  was isolated using miRVana miRNA isolation kit (Life Technologies).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: Pathogen stress is given to black pepper plants by artificially inoculating the cultures of  Phytophthora capsici. Control uninfected leaves, Leaves and roots from P. capsici infected black pepper plant (variety –Panniyur 1) (24hpi) were used for extraction of total RNA.  For abiotic stress, plants were treated for drought stress and total RNA enriched  small RNAs were isolated from leaves  of drought stressed plants.

tag: cultivar

value: Panniyur 1

value: Leaf

tag: stress status

value: leaves from drought stressed plants


title: Pn_IR

description: small RNA

source_name: Roots from Phytophthora capsici infected plants

value: Root

value: Roots from P. capsici infected plants (24hpi)


title: Pn_CL

description: small RNA

source_name: Control Leaf

value: control uninfected leaf


title: BGA0201_300_L1.D702


title: BGA0201_375_L6.D705


title: 5GB1_FM22_TR3_UW

value: O2 limiting, fast growth conditions


title: 5GB1_FM_86_TR1


title: 5GB1_FM22_TR3


title: 2319011_TimePoint1_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T01YSMmCoDaBM_CCGTCCL003R1_2319011.fastq.gz
Raw File 2: E03T01YSMmCoDaBM_CCGTCCL003R2_2319011.fastq.gz

tag: time point

value: Male


title: Pn_IL

description: small RNA

source_name: Leaves from Phytophthora capsici infected plants

value: leaves from P. capsici infected plants (24hpi)


title: 2319010_TimePoint3_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T03YSMmCoDaBM_GCCAATL002R1_2319010.fastq.gz
Raw File 2: E03T03YSMmCoDaBM_GCCAATL002R2_2319010.fastq.gz

tag: gender

value: P. coatneyi strain Hackeri


title: BGA0201_302_L2.D704

value: Hepatocyte


title: BGA0201_372_L10

value: LGLI


title: 2319008_TimePoint5_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T05YSMmCoDaBM_TGACCAL002R1_2319008.fastq.gz
Raw File 2: E03T05YSMmCoDaBM_TGACCAL002R2_2319008.fastq.gz

tag: non human primate individual id


title: 2319014_TimePoint1_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T01YSMmCoDaBM_ACAGTGL003R1_2319014.fastq.gz
Raw File 2: E03T01YSMmCoDaBM_ACAGTGL003R2_2319014.fastq.gz

tag: parasite strain


title: 5GB1_FM19_TR3


title: 2319006_TimePoint4_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T04YSMmCoDaBM_GTGAAAL002R1_2319006.fastq.gz
Raw File 2: E03T04YSMmCoDaBM_GTGAAAL002R2_2319006.fastq.gz


title: 5GB1_FM19_TR1_UW


title: WIN-rep3

city: New York

first: Philippe

last: Melas

address: 1051 Riverside Drive

institute: Columbia University

data_processing:
Sequencing was performed on a HiSeq 3000/HiSeq 4000 System (Illumina; Illumina Inc., San Diego, CA, USA) for a paired-end 150 bp run. Data quality check was done on the Sequencing Analysis Viewer (SAV, Illumina). Demultiplexing was performed with the bcl2fastq2 v 2.17 program (Illumina).
Reads were first mapped to the latest UCSC transcript set using STAR version 2.4.1d and the gene expression level was quantified to annotation model (Partek E/M). Gene expression levels were normalized to total counts.
Differentially expressed genes were identified using the differential gene expression (GSA) algorithm (Partek; Partek Inc., St. Louis, MO, USA).
Genes showing altered expression with FDR < 0.05 and more than 2-fold changes were considered differentially expressed (Table S2; first worksheet).
Genome_build: RGSC 6.0/ rn6
Supplementary_files_format_and_content: tab-delimited text file  includes  normalized counts for each sample

source_name: PC-12 cell line

growth_protocol: PC12 cells were maintained in BioCoat™ Collagen IV 75cm² culture flasks (Corning; Corning Inc., Corning, NY, USA) to facilitate attachment and were incubated at 37°C in an atmosphere containing 5% CO2. During maintenance, PC12 cells were grown in 1X cellgro™ RPMI 1640 medium with L-Glutamine (Corning), supplemented with 10% horse serum (SIGMA), 5% fetal bovine serum (Gibco; Thermo Fisher Scientific, Waltham, MA, USA) and 1X Pen Strep Glutamine (Gibco). All drug-treatment experiments, unless otherwise noted, were performed using NGF-differentiated PC12 cells, of passage (P) ~10-20, plated on BioCoat™ Collagen IV multiwell plates (Corning). For differentiation, PC12 cells were maintained in 1X cellgro™ RPMI 1640 medium with L-Glutamine (Corning), supplemented with 1% horse serum (SIGMA), 1X Pen Strep Glutamine (Gibco) and 100ng/ml of recombinant murine β-NGF (Peprotech; PeproTech Inc., Rocky Hill, NJ, USA), for seven days according to the literature.

extract_protocol:
Total RNA was isolated using the Direct-zol™ RNA MiniPrep Plus w/ TRI Reagent® kit
KAPA Stranded RNA-Seq Kit

treatment_protocol: For stimulation of cannabinoid receptors 1 and 2, the full CB1/CB2 receptor agonist WIN 55,212-2 mesylate (Tocris; Tocris Bioscience, Minneapolis, MN, USA) was used at 5μM. For stimulation of Dopamine 1 (D1) receptors, a D1 agonist was used (SKF 81297 hydrobromide; Tocris) for ~30 minutes at 1μM. All drugs were dissolved in dimethyl sulfoxide (DMSO).

tag: passages

tag: differentiation

value: NGF-differentiated


title: WIN-rep2


title: 5GB1_FM19_TR1


title: 2319005_TimePoint5_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T05YSMmCoDaBM_CAGATCL001R1_2319005.fastq.gz
Raw File 2: E03T05YSMmCoDaBM_CAGATCL001R2_2319005.fastq.gz


title: WIN-rep1


title: N7-(CTRL)

source_name: control_skeletal muscle

tag: subject status

value: control patient

tag: subject id

value: Control patient 7

value: skeletal muscle


title: N32-(DM1)

source_name: disease (DM1)_skeletal muscle

value: myotonic dystrophy type I (DM1) patient

value: DM1 patient 32


title: 5GB1_FM14_TR2

tag: strain

value: CH4 limiting, fast growth conditions


title: 2319004_TimePoint4_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T04YSMmCoDaBM_GTCCGCL001R1_2319004.fastq.gz
Raw File 2: E03T04YSMmCoDaBM_GTCCGCL001R2_2319004.fastq.gz


title: 2319003_TimePoint6_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T06YSMmCoDaBM_CCGTCCL001R1_2319003.fastq.gz
Raw File 2: E03T06YSMmCoDaBM_CCGTCCL001R2_2319003.fastq.gz


title: DMSO-rep3


title: N22-(DM1)

value: DM1 patient 22

tag: tissue


title: 5GB1_FM14_TR1


title: 5GB1_FM12_TR2


title: 5GB1_FM22_TR1


title: N33-(CTRL)

value: Control patient 33


title: BGA0201_374_L4.D704

tag: cell type


title: 2319002_TimePoint3_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T03YSMmCoDaBM_CGATGTL001R1_2319002.fastq.gz
Raw File 2: E03T03YSMmCoDaBM_CGATGTL001R2_2319002.fastq.gz


title: DMSO-rep1


title: DMSO-rep2


title: 5GB1_FM12_TR1


title: Biliatresone 1

status: Public on Aug 23 2017

first: Xiao

last: Zhao

address: 411 Curie Blvd, Rm 1126

department: Medicine/DIgestive Diseases

data_processing:
Hiseq control software (HCS) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to zv9 whole genome using STAR.
Python Htseq script was used to count the number of reads.
Genome_build: zv9
Supplementary_files_format_and_content: tab-delimited text files include htseq-count output.

source_name: liver

extract_protocol:
Livers were dissected directly in to the lysis buffer (RLT) and RNA was harvested using the standard Qiagen protocol (RNeasy Mini Kit).
1 ug of total RNA was used for sequecning library construction and the libraries were prepared using the Truseq Stranded Ribo-Zero Library Prep Kit.

treatment_protocol: Zebrafish larvae were treated with biliatresone (0.5 ug/ml) for four hours.

value: liver

tag: treatment

value: Biliatresone


title: LNCaP Bag-1L CMut DHT rep2

city: Boston

first: Laura

last: Cato

state: MA

address: 450 Brookline Ave., D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.7
Alignment of the reads using TopHat2 version 2.0.11
Raw count calculation using HTSeq version 0.5.3p3
Genome_build: Homo sapiens GRCh37.75
Supplementary_files_format_and_content: Raw count file generated with HTSeq

source_name: LNCaP Bag-1L C-terminal mutant (K231A, K232A, K279A) cells

growth_protocol: Routinely cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/ml), streptomycin (100 units/ml) and L-glutamine (2 mM), at 37 °C with an atmosphere of 5% CO2. For experimental conditions, cells were grown under hormone-starvation conditions for 72 h using the same media composition, but substituting FBS for charcoal/dextran-treated FBS (CDT).

extract_protocol:
RNA extraction was carried out using the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.
The libraries were prepared using the TruSeq mRNA stranded kit (Illumina). Using poly-dT beads, mRNA was purified prior to the library preparation.

treatment_protocol: Cells were grown under hormone-starvation conditions for 72 h using the same media composition, but substituting FBS for charcoal/dextran-treated FBS (CDT). Cells were then treated with vehicle (ETOH) or 10 nM DHT for 16 h.

value: LNCaP

tag: genotype/variation

value: C-terminal mutant (K231A, K232A, K279A)

tag: culture conditions

value: Hormone starvation + 16 h DHT


title: Biliatresone 2


title: 2319007_TimePoint6_BoneMarrow

description:
E03M99FGMmCoDaBM_Coatneyi-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
E03M99FGMmCoDaBM_Mulatta-Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx
To interpret the *Genes-LibSizeNormalized-Results_MULTIPL_GEO.xlsx files, please use the following raw file names:
Raw File 1: E03T06YSMmCoDaBM_CTTGTAL002R1_2319007.fastq.gz
Raw File 2: E03T06YSMmCoDaBM_CTTGTAL002R2_2319007.fastq.gz

value: Male

value: P. coatneyi strain Hackeri


title: LNCaP Bag-1L CMut ETOH rep2

value: Hormone starvation + 16 h EtOH


title: Control 2

value: DMSO


title: LNCaP Bag-1L CMut DHT rep1


title: LNCaP Bag-1L CMut ETOH rep1


title: Control 1


title: LNCaP Bag-1L WT DHT rep2

source_name: LNCaP Bag-1L wild-type cells

value: wildtype


title: LNCaP Bag-1L WT DHT rep1


title: LN Talen Bag-1L KO DHT rep2

data_processing:
Basecalls performed using CASAVA version 1.7
Alignment of the reads using TopHat2 version 2.0.11
Raw count calculation using HTSeq version 0.5.3p3
Genome_build: Homo sapiens v75
Supplementary_files_format_and_content: Raw count file generated with HTSeq

source_name: LNCaP Bag-1L KO cell line

growth_protocol: Routinely cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/ml), streptomycin (100 units/ml) and L-glutamine (2 mM), at 37 °C with an atmosphere of 5% CO2. For experimental conditions, cells were grown either under the conditions described or under hormone-starvation conditions  for 72 h using the same media composition, but substituting FBS for charcoal/dextran-treated FBS (CDT).

extract_protocol:
RNA extraction was carried out using the RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.
The libraries were prepared using the TruSeq mRNA stranded kit (Illumina).
Using poly-dT beads, mRNA was purified prior to the library preparation.

treatment_protocol: Cells were grown either under the conditions described above or under hormone-starvation conditions  for 72 h using the same media composition, but substituting FBS for charcoal/dextran-treated FBS (CDT). Cells were then treated with vehicle (ETOH) or 10 nM DHT for 16 h.

value: LNCaP-Talen cell line

value: Bag-1L KO


title: LNCaP Bag-1L WT ETOH rep1


title: LN Talen Ctr DHT rep2

source_name: LNCaP control cell line

value: Control


title: LN Talen Bag-1L KO EtOH rep1


title: LN Talen Ctr DHT rep1


title: N27-(CTRL)

value: control patient

value: Control patient 27

value: skeletal muscle


title: LNCaP Bag-1L WT ETOH rep2


title: LN Talen Ctr EtOH rep2


title: LN Talen Bag-1L KO EtOH rep2


title: LN Talen Bag-1L KO FM rep2

value: Full media


title: LN Talen Ctr EtOH rep1


title: S_cerevisiae.WT.MM.R2

city: Newark

first: Bin

last: Tian

state: NEW JERSEY

address: 205 South Orange Ave., CC-F1230

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

data_processing:
The details of the method was described previously (Hoque, et al., 2014). Briefly, the 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT). Reads were mapped to yeast genomes (S. cerevisiae: EF4, Ensembl v16; S. pombe: ASM294v2, Ensembl v17) using Bowtie2 (local mode). 5' four random nucleotides were removed before mapping using "-5 4" parameter in bowtie2. Reads with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.
Genome_build: Two yeast genomes (S. cerevisiae: EF4, Ensembl v16; S. pombe: ASM294v2, Ensembl v17)
Supplementary_files_format_and_content: tab delimited file containing information of Chr., Strand, pA coordinates, read number of pAs in different samples

source_name: minimal media, wild type, replicate 2

extract_protocol:
Library construction protocol is explained in Hoque et al (2014) Methods  Mol Biol.
Specific protocol was used to amplify the 3'Ends of polyA+ RNA

tag: genotype

value: wild type


title: LN Talen Ctr FM rep2


title: LN Talen Ctr FM rep1


title: S_cerevisiae.WT.RM.R2

source_name: rich media, wild type, replicate 2


title: LN Talen Bag-1L KO FM rep1


title: S_cerevisiae.WT.MM.R1

source_name: minimal media, wild type, replicate 1


title: LN Talen Bag-1L KO DHT rep1


title: Mot2∆ Rep 1

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

data_processing:
Illumina Casava1.8.2 software used for basecalling
Data were trimmed using cutadapt-1.3 with default settings
Data were mapped to the ASM294v2.23 S.pombe genome (pombase.org) using bowtie2 with the -N 1 parameter
Number of reads per transcript were calculated using HT-seq with the following parameters: htseq-count -i external_name -t transcript -s yes sam_file.sam GFF_file.gff
Genome_build: ASM294v2.23
Supplementary_files_format_and_content: Number of mapped reads per transcript. Data is output by ht-seq count, it consists of a tab separated matrix containing genes names (external_name in the gff) and the read count.

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: S. pombe strains were grown in minimal medium (EMM0,5X; Formedium) and harvested during exponential phase (OD between 0,8 and 1,0)

extract_protocol:
Total RNAs were extracted with hot acid phenol and treated with DNaseI.
1 ug of total RNA was used for the construction of libraries, which were prepared for sequencing using Illumina TruSeq SBS Kit v3 Kit - HS 50 cycles (FC-401-3002, Illumina).

value: h90, ura4-DS/E, leu1-32, mat3M::gfp+::natRMX, mot2::kanRMX


title: Rrp6∆ Rep 2

value: h90, ura4-DS/E, leu1-32, mat3M::gfp+::natRMX, rrp6::kanRMX


title: Mot2∆ Rep 2


title: WT Rep 3

value: h90, ura4-DS/E, leu1-32, mat3M::gfp+::natRMX


title: WT Rep 2


title: Rrp6∆ Rep 1


title: WT Rep 1


title: B_84

city: Madrid

first: Inglada

last: Lucía

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: CNIO

description: small RNA-seq

data_processing:
Read files were quality-checked with FastQC.
Adapter sequences were removed with cutadapt v1.2.1 and only those reads longer than 15bp and shorter than 35bp were kept for further analysis.
Reads were aligned to the human genome (GRCh37/hg19) with Bowtie 0.12.7 and Samtools 0.1.18 allowing no mismatches and a maximum of 1 alignment per read.
Raw counts for miRNAs were obtained with HTSeq v0.5.3p9, using the miRBase v20 annotation for hg19
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Normalized expression (read counts) for miRNAs obtained with DESeq

source_name: ccRCC

extract_protocol:
Hematoxylin and eosin stained sections of the FFPE tumor samples were examined by a pathologist to confirm the diagnosis and to estimate tumor content. Tumor content was above 90% in 71 cases and was 70% in 3 cases. Total RNA was isolated with the Recover All Total Nucleic Acid Isolation kit (Ambion) using 4-6 whole 10-μm sections of the FFPE tumor samples.
Total RNA samples were provided by the user. Sample RNA Integrity Numbers were in the range 1.7 to 2.5 when assayed on an Agilent 2100 Bioanalyzer. Sample amounts used ranged between 200 and 500ng of total RNA. They were processed with kit "NEBNext Multiplex Small RNA Library Prep Set for Illumina" (NEB part # E7300 v2.1) by following manufacturer instructions. Briefly, samples were sequentially ligated to 3' and 5' adapters, with the truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with ProtoScript II Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by PCR with LongAmp Taq DNA polymerase mix (12 cycles). Amplified barcoded cDNA from different samples was pooled, and a polyacrylamide gel electrophoresis fraction of 140 to 150 bases -expected to include both miRNA and piRNA libraries- was extracted. The purified fraction was applied to an Illumina flow cell for cluster generation, and sequenced on an Illumina instrument (see below) by following manufacturer's protocols. Sequencing read ends are expected to contain a variable length of the 3' adaptor, whose sequence is AGATCGGAAGAGCACACGTCTGAACTCC.

tag: disease state

value: clear cell renal cell carcinoma (ccRCC)

value: tyrosine kinase inhibitors (TKIs)

tag: tki best response

value: Progression of the disease


title: B_8

description: small RNA-seq

value: Stable disease, Partial response or complete response


title: S_cerevisiae.WT.RM.R1

source_name: rich media, wild type, replicate 1


title: B_81

description: small RNA-seq


title: B_80

description: small RNA-seq


title: B_82

description: small RNA-seq


title: B_83

description: small RNA-seq


title: B_7

description: small RNA-seq


title: B_78

description: small RNA-seq


title: B_79

description: small RNA-seq


title: B_75

description: small RNA-seq


title: B_76

description: small RNA-seq


title: B_73

description: small RNA-seq


title: B_74

description: small RNA-seq


title: B_72

description: small RNA-seq


title: B_77

description: small RNA-seq


title: B_9

description: small RNA-seq


title: B_68

description: small RNA-seq


title: B_69

description: small RNA-seq


title: B_66

description: small RNA-seq


title: B_65

description: small RNA-seq


title: B_67

description: small RNA-seq


title: B_64

description: small RNA-seq


title: B_61

description: small RNA-seq


title: B_63

description: small RNA-seq


title: B_60

description: small RNA-seq


title: B_62

description: small RNA-seq


title: B_59

description: small RNA-seq


title: B_58

description: small RNA-seq


title: B_55

description: small RNA-seq


title: B_56

description: small RNA-seq


title: B_57

description: small RNA-seq


title: B_53

description: small RNA-seq


title: B_5

description: small RNA-seq


title: B_54

description: small RNA-seq


title: B_6

description: small RNA-seq


title: B_49

description: small RNA-seq


title: B_51

description: small RNA-seq


title: B_52

description: small RNA-seq


title: B_4

description: small RNA-seq


title: B_45

description: small RNA-seq


title: B_43

description: small RNA-seq


title: B_46

description: small RNA-seq


title: B_44

description: small RNA-seq


title: B_41

description: small RNA-seq


title: B_42

description: small RNA-seq


title: B_3

description: small RNA-seq


title: B_40

description: small RNA-seq


title: B_39

description: small RNA-seq


title: B_38

description: small RNA-seq


title: B_36

description: small RNA-seq


title: B_35

description: small RNA-seq


title: B_34

description: small RNA-seq


title: B_33

description: small RNA-seq


title: B_32

description: small RNA-seq


title: B_28

description: small RNA-seq


title: B_25

description: small RNA-seq


title: B_26

description: small RNA-seq


title: B_24

description: small RNA-seq


title: B_29

description: small RNA-seq


title: B_23

description: small RNA-seq


title: B_27

description: small RNA-seq


title: B_21

description: small RNA-seq


title: B_18

description: small RNA-seq


title: B_20

description: small RNA-seq


title: B_17

description: small RNA-seq


title: B_15

description: small RNA-seq


title: B_10

description: small RNA-seq


title: B_16

description: small RNA-seq


title: B_12

description: small RNA-seq


title: B_11

description: small RNA-seq


title: NAC CTRL female 9

first: Eddie

last: Loh

address: 1425 Madison Avenue

department: Department of Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ and FASTX-toolkit were used to examine the sequencing quality and trim reads. Paired-end reads for the mouse data were aligned to the MM10 and GENCODE vM2 version of the human genome and annotation using TopHat, using the comprehensive gene annotation on the reference chromosome only.
Reads were counted using HTSeq. A gene was considered the union of all its exons in any known isoforms. Any reads that fell in multiple genes were excluded from the analysis. Threshold for filtering out low expressed genes was set to >5 reads in at least 80% of the samples.
Differentially expressed genes (DEGs) between groups of samples were determined using linear models implemented in the ‘limma’ package of Bioconductor.
Genome_build: mm10
Supplementary_files_format_and_content: text file of fpkm matrix

source_name: Nucleus Accumbens (Nac)

extract_protocol:
RNA was extracted using Trizol Reagents from flash frozen mouse brain samples. 300ng of RNA for mouse samples was used, every samples got spike-in ERCC control 1. Libraries were created using the Epicenter (Illumina) Gold Kit with ribosomal depletion
Libraries for RNAseq were created using the Epicenter (Illumina) Gold Kit with a ribosomal depletion.

value: Nucleus Accumbens (Nac)

value: Female

tag: Cause of death

tag: age

tag: pmi

tag: ph

tag: phenotype

value: CTRL

tag: alcool

tag: drugs

tag: drug type

tag: medication

tag: medication type

tag: smoking

tag: rin


title: NAC CTRL female 10

tag: tissue

tag: gender


title: NAC CTRL female 8


title: NAC CTRL female 7


title: NAC CTRL female 6


title: B_30

description: small RNA-seq

tag: treatment


title: B_37

description: small RNA-seq

tag: disease state


title: NAC CTRL female 5


title: NAC CTRL female 2


title: NAC CTRL female 4


title: NAC CTRL female 1


title: NAC CTRL female 3


title: B_1

description: small RNA-seq

tag: tki best response


title: B_22

description: small RNA-seq


title: NAC CTRL male 7

value: Male

tag: Cause of death


title: NAC CTRL male 6

tag: age


title: NAC CTRL male 5

tag: pmi


title: NAC CTRL male 8

tag: ph


title: NAC CTRL male 3

tag: phenotype


title: NAC CTRL male 2

tag: alcool


title: NAC CTRL male 9

tag: drugs


title: NAC CUS female 9

value: Stress

tag: drug type


title: NAC CUS female 10

tag: medication


title: NAC CUS female 7

tag: medication type


title: NAC CUS female 8

tag: smoking


title: NAC CUS female 6

tag: rin


title: NAC CUS female 5

tag: tissue


title: NAC CUS female 4

tag: gender


title: NAC CUS female 3


title: NAC CUS female 2


title: NAC CTRL male 1


title: NAC CUS female 1


title: NAC CUS male 10


title: NAC CUS male 9


title: NAC CUS male 7


title: NAC CUS male 8


title: NAC CUS male 4


title: NAC CTRL male 10


title: NAC CUS male 6


title: NAC CUS male 3


title: NAC CTRL male 4


title: NAC CUS male 2


title: NAC CUS male 5


title: PFC CTRL female 10

source_name: prefrontal cortex (PFC)

value: prefrontal cortex (PFC)


title: NAC CUS male 1


title: PFC CTRL female 5


title: PFC CTRL female 6


title: PFC CTRL female 7


title: PFC CTRL male 10


title: PFC CTRL female 1


title: PFC CTRL male 9


title: PFC CTRL female 2


title: PFC CTRL female 3


title: PFC CTRL male 5


title: PFC CTRL male 6


title: PFC CTRL male 4


title: PFC CTRL male 3


title: PFC CTRL male 2


title: PFC CUS female 10


title: PFC CUS female 9


title: PFC CTRL male 1


title: PFC CUS female 5


title: PFC CUS female 7


title: PFC CUS female 6


title: PFC CUS female 8


title: PFC CUS female 3


title: PFC CTRL female 9


title: PFC CUS female 2


title: PFC CTRL female 4


title: PFC CUS female 4


title: PFC CUS female 1


title: Plasmid_replicate1

city: Beijing

first: Xiaoyue

last: Wang

address: 5 Dongdansantiao, Dongcheng District

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina HCS 2.2.68 used for basecalling.
The raw reads were mapped to human reference genome hg19 using BWA version 0.7.12-r1039 with the parameters:bwa mem -M
Fragments of a size ranging from 400bp to 600 bp and overlapped with at least one selected SNP were kept for further analysis using an in-house perl script.
Count the number of fragments overlapped with each SNP site by an in-house perl script.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files including the counts of fragments overlapped with each SNP site for each Sample.

molecule: other

organism: synthetic construct

source_name: plasmid DNA

extract_protocol: 1ng plasmid library was amplified with PCR using primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (universal primer) and CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCAGACGTG (Illumina index 7 primer).  The PCR products were purified using 0.8 X Agencourt AMPureXP DNA beads, quantified with Agilent DNA1000 Chip (Agilent, 5067-1504) and then sequenced on a HiSeq 2500 (Illumina) with 250bp pair-end sequencing.

tag: sample type

value: Input plasmid library before transfection


title: Plasmid_replicate2


title: PFC CUS male 10


title: PFC CTRL male 7


title: Body, mutant, replicate 1

data_processing:
The details of the method was described previously (Hoque et al., 2014). Briefly, the 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT). Reads were mapped to the Fly genome (BDGP5, Ensembl v70) using Bowtie2 (local mode). 5' four random nucleotides were removed before mapping using "-5 4" parameter in bowtie2. Reads with a mapping quality score (MAPQ) ≥10 were selected for further analysis. Reads with ≥2 non-genomic As after alignment were called polyA site supporting (PASS) reads.
All PASS reads mapped to the 3’-most exons of a gene were used to calculate the expression level of the gene, shown as the reads per million total PASS reads (RPM) value.
Genome_build: Drosophila melanogaster (BDGP5, Ensembl v70).
Supplementary_files_format_and_content: *pA.read_counts.txt: Tab-delimited files containing information of Chr., Strand, pA coordinates, read number of pAs in different samples.

organism: Drosophila melanogaster

source_name: Body, mutant

extract_protocol:
Library construction protocol is explained in Hoque et al. (2014) Methods Mol Biol and Zheng et al. (2016) RNA.
Specific protocol was used to amplify the 3'Ends of polyA+ RNA.

tag: strain

tag: genotype/variation

value: Mutant (RNA Pol II 215 C4 allele)

value: Body


title: Body, mutant, replicate 2


title: PFC CTRL male 8

tag: Cause of death


title: PFC CUS male 8

tag: age


title: Body, wild type, replicate 4

source_name: Body, wild type

value: Wild type


title: Head, mutant, replicate 2

source_name: Head, mutant

value: Head


title: Body, wild type, replicate 3


title: PFC CUS male 7

tag: pmi


title: Head, mutant, replicate 1


title: PFC CUS male 6

tag: ph


title: Head, wild type, replicate 3

source_name: Head, wild type


title: Head, wild type, replicate 4


title: PFC CUS male 5

tag: phenotype


title: S_Pombe.mPAB2.RM

source_name: rich media, PAB2 mutant

tag: genotype

value: PAB2 mutant


title: S_Pombe.mPCF11.MM

source_name: minimal media, PCF11 mutant

value: PCF11 mutant


title: PFC CUS male 3

tag: alcool

tag: drugs


title: S_Pombe.WT.MM

source_name: minimal media, wild type

value: wild type


title: PFC CUS male 2

tag: drug type

tag: medication


title: PFC CUS male 1

tag: medication type

tag: smoking


title: S_Pombe.WT.RM

source_name: rich media, wild type


title: Head, wild type, replicate 2

tag: tissue


title: Body, wild type, replicate 2


title: Body, wild type, replicate 1


title: Sample_C6706-3

city: Göteborg

first: Sergiu

last: Netotea

address: Chalmersplatsen 4

country: Sweden

institute: Chalmers tekniska högskola AB

data_processing:
QC using FASTQC
Index the transcriptome using hg19 reference genome from iGenomes: tophat/2.0.12, bowtie2/2.2.3, samtools/0.1.19
Read alignment with tophat2 using hg19 as genome reference and as source for the transcriptome index: tophat/2.0.12, bowtie2/2.2.3, samtools/0.1.19
Transcript assembly with cufflinks: cufflinks/2.2.1
Merge transcripts with cuffmerge: cufflinks/2.2.1
Estimate counts with HTSEQ: htseq/0.6.1
Genome_build: HG19: ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
Supplementary_files_format_and_content: raw counts

source_name: colon carcinoma cells

growth_protocol: Human ileocecal colorectal adenocarcinoma (HCT8) cells were cultured in RPMI 1640 (GIBCO) medium, supplemented with 10% heat-inactivated fetal bovine serum and penicillin/streptomycin at 37°C in a humid 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the total RNA isolation kit according to the manufacturer’s protocol (RNeasy Mini Kit, Qiagen). Sequencing libraries were prepared from 1 μg total RNA using the TruSeq stranded mRNA library preparation kit (Illumina Inc) including poly-A selection.
Libraries were prepared according to Illimina's protocol (#15021047, rev E)
HiSeq2500 rapid mode,single read, 50 bp read length

treatment_protocol: Cells were seeded 16 h prior the infection, medium was changed and MVs or control (20mM Tris-HCl) were incubated with HCT8 cells for 5 hours.

tag: cell line

tag: treatment

value: treated with V. cholerae membrane vesicles


title: Sample_MC1061-3

value: treated with E. coli membrane vesicles


title: Sample_MC1061-1


title: Sample_MC1061-2


title: ChIP_Bcells_ZBTB17

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_quality_trimmer -Q33 -t 20 -l 10 -v -i ; fastq_masker -Q33 -q 20 -r -N -v -i
Reads were aligned to the reference mouse genome (NCBI37, mm9) using bwa software (version 0.6.2-r126) with standard parameters.
ChIP-seq narrow peaks were called against the input using MACS2 software (version 2.0.9, p-value threshold = 1e-5, --mfold=7,30). For RNAPII samples, MACS2 was also used to call broad peaks.
Genome_build: mm9
Supplementary_files_format_and_content: text files with peaks identified by the macs2 software. For each peak, genomic coordinates (chromosome, start, end, length, summit), number of tags falling within, and confidence scores (-10*log10(pvalue), fold_enrichment and FDR(%)) are reported

source_name: Primary B-cells

growth_protocol: Splenic B-cells were isolated from young 6-8 weeks old animal by incubation with B220 MicroBeads (Miltenyi Biotech) and enriched by magnetic cell sorting (MACS), according to the manufacturer’s instructions (Miltenyi Biotech).

extract_protocol:
Cells were washed in PBS and fixed for 15 min in 1% of formaldehyde (Sigma) in PBS. Glycin was added (125 mM glycin) and cells were incubated for 5 min. Cells were washed with PBS and scraped in SDS buffer (100mM NaCl, 50mM Tris pH 8.1, 5mM EDTA, 0.2% NaN3, 0.5% (w/v) SDS). Cells were cleared by centrifugation and the pellet resuspended in cold ChIP buffer (100mM NaCl, 133mM Tris pH 8.0, 5 mM EDTA, 0.2% NaN3, 0.67% SDS, 1.67% Triton X-100) supplemented with protease inhibitors (cOmplete Protease Inhibitor Cocktail Tablets, Roche) and phosphatase inhibitors (50 mM NaF, 1 mM β-GP, 1 mM NaV). All following steps were performed on ice, if not specified differently. Chromatin was sonicated to an average length of 200-400bp, pre-cleared with proteinG-sepharose beads (blocked with 0.5% E. coli tRNA (Sigma) and 0.5% BSA).
10µg of antibodies were used per ChIPseq reaction. The antibody was incubated overnight with 500-1000µl of chromatin. Blocked proteinG-sepharose beads were added, incubated for 2-3h and washed as follows: 3x mixed micelle buffer (150 mM NaCl, 20 mM Tris pH 8.1, 5 mM EDTA, pH 8.0, 5.2% sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), 2x buffer 500 (50 mM HEPES pH 7.5, 0.1% sodium deoxycholate, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.2% NaN3), 2x LiCl/detergent buffer (10 mM Tris pH 8.0, 0.5% sodium deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.2% NaN3) and once in TE. DNA:protein crosslinking was reverted overnight (2% SDS in TE, 65°C), DNA purified using QiaQuick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
2-5 ng of ChIP DNA were used for ChIPseq library preparation as described in (Blecher-Gonen et al., Nat Protoc, 2013) and sequenced with the Illumina HiSeq sequencer according to the manufacturer.

tag: strain

tag: cell type

value: B cells from spleen

value: WT

tag: chip antibody

value: anti-Miz (10E2) (home-made)


title: Sample_control-3

value: no treatment


title: Sample_C6706-1


title: Sample_control-2


title: ChIP_RNAPII_2h

source_name: embryonic fibroblasts, E13.5

growth_protocol: 3T9MycER fibroblasts were cultured in DMEM medium, supplemented with 10% fetal bovine serum, 2 mM L-glutamine and penicillin/streptomycin. Cells were used at sub-confluent cell densities for all experiments. Due to infection with the pBabe bleomycin MycER construct, cells are resistant for zeocin. Upon thawing, cells were maintained for 7-10 days in zeocin-containing medium (100µg/ml), but grown without zeocin for subsequent experiments.

extract_protocol:
Cells were washed in PBS and fixed for 15 min in 1% of formaldehyde (Sigma) in PBS. Glycin was added (125 mM glycin) and cells were incubated for 5 min. Cells were washed with PBS and scraped in SDS buffer (100mM NaCl, 50mM Tris pH 8.1, 5mM EDTA, 0.2% NaN3, 0.5% (w/v) SDS). Cells were cleared by centrifugation and the pellet resuspended in cold ChIP buffer (100mM NaCl, 133mM Tris pH 8.0, 5 mM EDTA, 0.2% NaN3, 0.67% SDS, 1.67% Triton X-100) supplemented with protease inhibitors (cOmplete Protease Inhibitor Cocktail Tablets, Roche) and phosphatase inhibitors (50 mM NaF, 1 mM β-GP, 1 mM NaV). All following steps were performed on ice, if not specified differently. Chromatin was sonicated to an average length of 200-400bp, pre-cleared with proteinG-sepharose beads (blocked with 0.5% E. coli tRNA (Sigma) and 0.5% BSA).
10µg of the following antibodies were used per ChIPseq reaction: Myc N262 (Santa Cruz, sc-764), RNAPII N20 (Santa Cruz, sc-899). The antibody was incubated overnight with 500-1000µl of chromatin. Blocked proteinG-sepharose beads were added, incubated for 2-3h and washed as follows: 3x mixed micelle buffer (150 mM NaCl, 20 mM Tris pH 8.1, 5 mM EDTA, pH 8.0, 5.2% sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), 2x buffer 500 (50 mM HEPES pH 7.5, 0.1% sodium deoxycholate, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.2% NaN3), 2x LiCl/detergent buffer (10 mM Tris pH 8.0, 0.5% sodium deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.2% NaN3) and once in TE. DNA:protein crosslinking was reverted overnight (2% SDS in TE, 65°C), DNA purified using QiaQuick columns (Qiagen) and quantified using PicoGreen (Invitrogen).
2-5 ng of ChIP DNA were used for ChIPseq library preparation as described in (Blecher-Gonen et al., Nat Protoc, 2013) and sequenced with the Illumina HiSeq sequencer according to the manufacturer.

treatment_protocol: MycER activation was achieved by addition of 400nM of the synthetic 4-hydroxytamoxifen (OHT; Sigma-Aldrich)

value: 3T9 fibroblasts

value: c-mycflox/flox; in vitro infected with MycER

value: RNAPII N20 (Santa Cruz, sc-899)


title: ChIP_RNAPII_4h


title: ChIP_RNAPII_30min


title: Starr-seq_293T_replicate2

source_name: Human embryonic kidney

growth_protocol: HEK293T cells were cultured in DMEM medium (Hyclone) supplemented with 10% heat-inactivated FBS (Gibco) at 37℃.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy maxi prep kit 24 hours after transfection and reverse transcribed using a reporter RNA specific primer (5’ CAAACTCATCAATGTATCTTATCATG) and 450~500ng mRNA per reaction for a total of 30 reactions.
The cDNA was amplified in 120 PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix (NEB, M0541L), each started with 5μL cDNA product with primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (universal primer) and CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCAGACGTG (Illumina index 8 primer), or CAAGCAGAAGACGGCATACGAGATTACGTACGGTGACTGGAGTTCAGACGTG (Illumina index 22 primer). The PCR products were pooled and purified by 0.8X Agencourt AMPureXP DNA beads, eluted in 20μL H2O and quantified by Agilent DNA1000 Chip (Agilent, 5067-1504). The output library was sequenced on an Illumina HiSeq 2500 using paired-end 250bp reads.

treatment_protocol: Library transfection was performed using Neon Transfection System. Each 5×106 cells were transfected with 30μg library plasmids, then electroporation at the condition of 1260V-20ms-2pulses.

value: HEK 293T


title: PFC CUS male 4

value: prefrontal cortex (PFC)

tag: gender

value: Male

tag: Cause of death

tag: age

value: Stress

tag: rin


title: Head, wild type, replicate 1

tag: genotype/variation

value: Wild type

value: Head


title: ChIP_RNAPII_20min

tag: genotype


title: ChIP_3T9MycER_ZBTB17


title: Starr-seq_293T_replicate1


title: ChIP_RNAPII_0min


title: empty vector, minus dox  [P70_MINUS]

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

institute: Cleveland Clinic

data_processing:
Raw reads in the fastq format were aligned to Human Genome HG19 using the RNAseq STAR aligner version 2.4.0d.
Mapped reads for each sample were counted for each gene in annotation files in GTF format (gencode.v19.annotation.gtf available for download from GENECODE website using the  FeatureCounts read summarization program
Genome_build: HG19
Supplementary_files_format_and_content: raw feature counts

source_name: immortalized human astrocytes

growth_protocol: Inducible astrocytes were grown in DMEM + Tetracycline-free FBS (10%) and IDH1 R132H expression was induced with the addition of 1 ug/ml of doxycycline. Tumorspheres were grown in NeuroCult NS-A Proliferation media (STEMCELL Technologies) with EGF and FGF.

extract_protocol:
RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
RNA-seq (Ribo-deplete protocol); Libraries were prepared according to Illumina's instructions.

value: immortalized human astrocytes

value: empty vector

tag: dox

value: minus

tag: passage

value: 40 passages from baseline (passage 30)


title: TS543 [TS_543]

source_name: glioma tumorsphere

value: glioma tumorsphere

value: IDH1 R132H wild-type


title: TS603  [TS_603]

value: IDH1 R132H


title: empty vector, off dox [P70_OFF]

value: withdrawn

value: off 40 passages from baseline (P30)


title: ChIP_Myc_4h

value: 3T9 fibroblasts

value: c-mycflox/flox; in vitro infected with MycER

value: Myc N262 (Santa Cruz, sc-764)


title: ChIP_Myc_2h


title: TS667 [TS_667]


title: empty vector, plus dox [P31_PLUS]

value: plus

value: baseline (passage 30)


title: ChIP_Myc_30min


title: empty vector, minus dox [P31_MINUS]


title: IDH1 R132H, plus dox [M70_PLUS]

value: IDH1 R132H (off)


title: Sample_control-1

value: no treatment


title: IDH1 R132H, off dox [M70_OFF]

value: IDH1 R132H (induced)


title: IDH1 R132H, minus dox [M70_MINUS]

value: immortalized human astrocytes

value: IDH1 R132H (not induced)


title: IDH1 R132H, plus dox [M31_PLUS]


title: ChIP_Myc_0min


title: ChIP_input


title: IDH1 R132H, minus dox [M31_MINUS]

value: minus