title: ret_sema3d_double_null_female_2

city: Houston

first: Ashish

last: Kapoor

state: TX

address: 1825 Pressler St. Rm SRB 530C

institute: University of Texas Health Science Center at Houston

description:
DESeq_doublenull_combined_GLM_results.txt
DESeq_interaction_term_combined_GLM_results.txt

data_processing:
Illumina RNA-seq paired-end read fastq files were quality checked using FASTQC (version: 0.11.5) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Processed using Trimmomatic (version: 0.36), for removing adapters and other Illumina-specific sequences from the reads, and, for performing a sliding-window based trimming of low quality bases from each read (ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
For estimating gene and isoform expression levels, we first extracted reference transcript sequences from the mouse genome (GRCm38, primary assembly) based on the GENCODE (http://www.gencodegenes.org/mouse_releases/current.html) primary assembly gene annotation (release M10) and built STAR aligner indices using the RSEM software package (version: 1.2.31).
Trimmed paired-end reads from each sample were then aligned to the reference transcript sequences by calling the STAR aligner within RSEM and using alignment parameters from the ENCODE STAR-RSEM long RNA-seq pipeline (--outSAMunmapped Within --outFilterType BySJout  --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --quantMode TranscriptomeSAM).
Gene and isoform expression levels were then estimated in each sample from these transcriptome alignments using RSEM keeping in mind the strandedness of the prepared RNA-seq libraries (--forward-prob 0.0).
Gene-level read count data generated by RSEM was compared between various wildtype and mutant mice to assess differential gene expression using the DESeq software (version: 1.24.0).  Only those genes where the sum of read counts across the 12 samples in each comparison (three male and three female wildtype and the three male and three female mutant replicates) was >1, were retained for differential gene expression analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include differential gene expression results from DESeq based on comparing gene-level read count data between various wildtype and mutant mice

source_name: E12.5 gut

extract_protocol:
Total RNA was isolated from each E12.5 gut using RNeasy Mini Kit following manufacturers’ recommendations (Qiagen, CA) that included the on-column DNase digestion using RNase-Free DNase set (Qiagen, CA).  The quantity and quality of total RNA was assessed by NanoDrop spectrophotometer (Thermo Scientific, DE).
KAPA Stranded mRNA-Seq kit (KAPA Biosystems, MA) was used to generate indexed Illumina platform sequencing libraries.  Briefly, polyA RNA was captured from 1 µg total RNA using magnetic oligo-dT beads.  After elution from the magnetic beads, polyA RNA was fragmented to generate inserts ranging in size from 100-200 bp, followed by random priming and reverse transcription to generate double-stranded cDNA.  Next, after performing a 1.8× SPRI cleanup using AMPure XP beads (Agencourt, MA), dAMP was added to 3’-ends of the cDNA fragments followed by ligation with indexed 3’-dTMP Illumina TruSeq adapters.  Ligated fragments were subsequently size selected using PEG/NaCl SPRI solution and underwent PCR amplification (12 cycles) to generate the sequencing libraries.  After performing a 1× SPRI cleanup using AMPure XP beads (Agencourt, MA), a sample from each library was used to assess library fragment size distribution by electrophoresis using BioAnalyzer High Sensitivity DNA Assay (Agilent Technologies, CA) and to assess library concentration by qPCR using KAPA library quantification kit (KAPA Biosystems, MA).  Equimolar amounts of libraries were pooled and sequenced on an Illumina HiSeq 2500 instrument using standard protocols for paired end 100 bp sequencing with a desired sequencing depth of ~30 million paired end reads per library.

tag: strain

value: C57BL/6, 129/Sv and C3H

value: gut

value: embryonic day 12.5

tag: genotype/variation

value: female


title: KO Male 4 RNAseq

status: Public on Mar 28 2017

type: SRA

city: New York

first: Joseph

middle: M

last: Luna

state: NY

address: 1230 York Ave #64

country: USA

institute: The Rockefeller University

library_source: transcriptomic

data_processing:
Alignment: Fastq files were processed with kallisto on an index built from Ensembl release 85 mm10 trancripts;  kallisto -b 100 --single -l 100 -s 25; pachterlab.github.io/kallisto/
Expression testing: kallisto output was processed with sleuth for expression testing between WT and KO samples; http://pachterlab.github.io/sleuth/
Transcript with highest mean expression across all sample was selected as representative per gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes sleuth output, gene symbol, and pseudocount matrix per sample

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was extracted from tissue using Trizol
RNAseq libraries were prepared for sequencing using standard Illumina protocols with Poly-A selection

treatment_protocol: Flash frozen mouse livers were pulverzied in liquid nitrogen. Two-thirds of powder was UV crosslinked at 254nM for CLIP. Remaining third was left uncrosslinked for RNAseq.

tag: mir122 status

value: KO

tag: Sex

value: Male

tag: mouse id

tag: sample type

value: RNAseq


title: sema3d_null_male_2

description:
DESeq_sema3dnull_combined_GLM_results.txt
DESeq_interaction_term_combined_GLM_results.txt

molecule: total RNA

tag: tissue

tag: age

value: male


title: sema3d_null_female_3


title: sema3d_null_male_1


title: sema3d_null_male_3


title: sema3d_null_female_1


title: ret_sema3d_double_null_male_3


title: ret_sema3d_double_null_female_3


title: ret_sema3d_double_null_male_2


title: ret_sema3d_double_null_female_1


title: ret_sema3d_double_null_male_1


title: sema3d_null_female_2


title: ret_null_male_1

description:
DESeq_retnull_combined_GLM_results.txt
DESeq_interaction_term_combined_GLM_results.txt


title: ret_null_male_2


title: ret_null_female_3


title: ret_null_female_2


title: wildtype_male_2

description:
DESeq_retnull_combined_GLM_results.txt
DESeq_sema3dnull_combined_GLM_results.txt
DESeq_doublenull_combined_GLM_results.txt
DESeq_interaction_term_combined_GLM_results.txt

value: wildtype


title: wildtype_female_3


title: wildtype_male_1


title: WT Male 5 CLIP

data_processing:
quality filtering: minimum quality filter applied for barcode and insert; fastq_filter.pl; -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ;github.com/chaolinzhanglab/ctk/tree/v1.0.3
collapse exact sequences: exact duplicate sequences removed; fasta2collapse.pl; ;github.com/chaolinzhanglab/ctk/tree/v1.0.3
trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing); fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs; stripBarcode.pl; -linker 5 ; github.com/chaolinzhanglab/ctk/tree/v1.0.3
remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped; fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/
Groomed reads aligned to mm10 with bowtie2 using defaults
Collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated; tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; github.com/chaolinzhanglab/ctk/tree/v1.0.3
Collapsed mapped reads were clustered, where the peak cluster coordinate +/- 32 nt was searched for the presence of miRNA 6-8mers, for those miRNAs with CLIP evidence.
Fold changes were calculated by adding a psuedocount of 1 to every cluster, normalizing each cluster for read depth (reads per million mapped), and dividing by condition.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes CLIP-seq cluster definition and locations, miRNA seed search results, and genomic annotations

extract_protocol:
UV crosslinked cells were lysed in 1x PXL buffer, lysates were Dnase treated, partially RnaseI digested, clarified by centrifugation, and Argonaute-mRNA complexes isolated with pan-Ago 2A8 antibody.
CLIP libraries were prepared as in Luna, JM et al (2015). 1st PCR Products were amplified in a second round of PCR that added a 4 nt index (for multiplexing) and a 16 nt common primer sequence. Raw files are demultiplexed on the basis of this index, but have not been further modified.
CLIPseq

value: WT

value: CLIP


title: wildtype_male_3


title: ret_null_female_1


title: wildtype_female_2


title: wildtype_female_1


title: ret_null_male_3


title: Sample_GFPAGO2-1-RIP-small

city: Lund

first: Rebecca

last: Petri

address: Sölvegatan 17

country: Sweden

institute: Lund University

description: OB tissue was collected 8 weeks after viral vecor injection for AGO2-RIPseq

data_processing:
Adaptor sequences were removed using cutadapt
Reads from samples  were mapped to the mm10 mouse genome using STAR  (2 mismatches per 20nt were allowed)
Reads were quantified using the Rsubread package for R using miRbase annotation (miRNAs).
Genome_build: mm10
Supplementary_files_format_and_content: txt files containing abundance measurements of miRNA features from miRBase  Whitespace separated. Columns: [Geneid- Chr- Start- End- Strand- Length - #reads mapping to feature]

source_name: freshly dissected mouse olfactory bulb tissue

extract_protocol:
RNA was extracted using the miRNAeasy Micro Kit from Qiagen
NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: The olfactory bulb was quickly dissected from decapitated viral vector-/ sham-injected mice (8 weeks after injection), and immedeately  homogenised in Tissue LyserLT (50 Hz, 2min).

tag: viral vector

tag: time after injection

value: 8 weeks


title: Sample_Control-1-RIP-small


title: Sample_Control-3-RIP-small


title: Sample_GFPAGO2-3-RIP-small


title: 9A Old Resistance PreTraining

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed to remove adapter sequence and aligned using MapRSeq pipeline (Kalari et al; BMC Bioinformatics. 2014 Jun 27;15:224) using default configuration.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of raw reads per gene in each sample.

organism: Homo sapiens

source_name: vastus lateralis muscle biopsy

extract_protocol: We measured mRNA expression as previously described (Lanza et al., Cell Metab. 16 (2012), pp. 777–788) with slight modifications. In brief, total RNA was isolated from the biopsy collected at 1000 hr, and sequencing libraries were prepared with TruSeq RNA Sample Prep Kit v2. Libraries were sequenced on a HiSeq 2000 sequencer using TruSeq SBS sequencing kit version 3 and HCS version 2.0.12.0 software. Genes with a FDR-corrected p value of ≤0.05 and an absolute log2 fold change of ≥0.5 (where 0.0 signifies no change) were considered for further analysis.

value: Old

tag: exercise type

value: Resistance

tag: biopsy timepoint

value: PreTraining


title: 9B Old Resistance PostTraining

value: PostTraining


title: 8A Old Resistance PreTraining


title: 8B Old Resistance PostTraining


title: 53B Old HIIT PostTraining

value: HIIT


title: 6A Young HIIT PreTraining

value: Young


title: 51B Old HIIT PostTraining


title: 51A Old HIIT PreTraining


title: 7C Old Combined PostTraining

value: Combined


title: 6B Young HIIT PostTraining


title: 50A Old Resistance PreTraining


title: 49A Old Resistance PreTraining


title: 49B Old Resistance PostTraining


title: 5C Old Combined PostTraining


title: 5B Old Combined PreTraining


title: 53A Old HIIT PreTraining


title: 7B Old Combined PreTraining


title: 52B Old HIIT PostTraining


title: 50B Old Resistance PostTraining


title: 52A Old HIIT PreTraining


title: 46C Old Combined PostTraining


title: HeLa_NTC Replicate 2

city: Galveston

first: Mariano

last: Garcia-Blanco

address: 301 University Blvd

institute: The University of Texas Medical Branch

data_processing:
Illumina bcl2fastq-1.8.4 used for base calling
Alignment to known splicing events database vastdb.hsa.7.3.14 using Vast-tools version 0.2.1 align function with default parameters.   Irimia, M., Weatheritt, R.J., Ellis, J.D., Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallieres, M., Tapial, J., Raj, B., O'Hanlon, D., et al. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 159, 1511-1523
Differential splicing analysis using Vast-tools diff function with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: Inclusion levels tab delimited file is the Vast-tools full output reporting the number of reads in each sample supporting each alternative splicing event. Xls files report the significant differences between experiment conditions and the pdf files provide visual output of the significant differences. In each file NS is the NSC control siRNA, D11 is the DDX_3 siRNA and D13 is the DDX_4 siRNA.

source_name: HeLa cell line

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations
Strand specific RNA polyA+ libraries were prepared from 1 ug of total RNA using Illumina's True_Seq RNA kit using standard protocols
RNA-Seq , paired end 100 bases on an Illumina HiSeq 1500. Technical replicates of each sample were run on lanes 1 and 2 of two separate HiSeq Rapid-Run flow cells.

tag: phenotype

value: DDX39B Control

tag: cell line

value: HeLa


title: HeLa_DDX_4 Replicate 2

value: DDX39B DDX_4 siRNA Knockdown


title: 4B Old HIIT PostTraining


title: 48C Old Combined PostTraining


title: HeLa_DDX_3 Replicate 1

value: DDX39B DDX_3 siRNA Knockdown


title: 46B Old Combined PreTraining


title: 4A Old HIIT PreTraining


title: HeLa_NTC Replicate 1


title: 48B Old Combined PreTraining


title: 47B Old HIIT PostTraining


title: HeLa_DDX_3 Replicate 2


title: HeLa_DDX_4 Replicate 1


title: 45B Old HIIT PostTraining


title: 45A Old HIIT PreTraining


title: 43A Old Resistance PreTraining


title: 44B Old Resistance PostTraining


title: adulttom_1

first: Yariv

last: Houvras

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Alignment: STAR v2.3
Read Counting: htseq-count (v0.6.0, parameters -t exon, Ensembl transcriptome v70)
Genome_build: zv9
Supplementary_files_format_and_content: raw reads mapped to Ensembl transcriptome v70

organism: Danio rerio

source_name: transgenic adult fish

extract_protocol:
RNA was extracted using TRIzol (Life Technologies) followed by RNeasy Mini spin column
RNA libraries were prepared for sequencing using standard Illumina protocol

value: TdTOM dissected thyroid

tag: developmental stage

value: adult zebrafish

tag: genotype

value: transgenic tg-TOM zebrafish


title: 47A Old HIIT PreTraining


title: adulttom_2


title: 43B Old Resistance PostTraining


title: adulttom_3


title: 41C Young Combined PostTraining


title: 42A Old HIIT PreTraining


title: adultbraf_5

value: transgenic tg-TOM;tg-BRAF zebrafish


title: adultbraf_4


title: adultbraf_3


title: TOM_3

source_name: transgenic embryos

value: embryo

tag: cell type

value: TdTOM+ cells FACS sorted

value: 5dfp embryos


title: 42B Old HIIT PostTraining

value: Old


title: 40B Young HIIT PostTraining


title: 44A Old Resistance PreTraining

value: Resistance

value: PreTraining


title: 40A Young HIIT PreTraining

value: HIIT


title: 41B Young Combined PreTraining

value: Young


title: TOM_2


title: adultbraf_2


title: 3B Young Resistance PostTraining

value: PostTraining


title: TOM_1


title: adultbraf_1


title: 3A Young Resistance PreTraining


title: 39B Young HIIT PostTraining


title: BRAF_3


title: BRAF_2


title: 39A Young HIIT PreTraining


title: BRAF_1


title: 38B Young Resistance PostTraining


title: L1 dmMagoh repB

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
5’-barcode: ACTTG, 3’-barcode: YRRY
L1_dmMagoh_repB_dm3.bed
L1_dmMagoh_dm3_minus.bigWig
L1_dmMagoh_dm3_plus.bigWig
L1_dmMagoh_dm3.narrowPeak

data_processing:
Barcodes and random tags were extracted using custom fastqpl scripts (Horton P. fastapl – a utility for versatile and easy processing of fasta format data (and fastqpl for fastq files). F1000Posters 2011, 2:1197 (poster)).
Adapters were trimmed and the library was demultiplexed using Flexbar (v2.32).
Possible readthroughs into the barcoded regions were removed by clipping 10 and 5 nt from the 3’-ends of first and second mate reads.
Reads were mapped to the reference genomes (hg19, mm10, dm3) using bowtie2 (v2.2.0) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant and --maxins=200.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)).
Crosslinking events of M and L size fractions were combined for each biological replicate.
Peaks were called with JAMM (version 1.0.7rev1, parameters "-d y -t paired -b 50 -w 1 -m normal") on crosslinked nucleotides of the two replicates for each pulldown condition as foreground and the control condition as background.
Genome_build: hg19, dm3 or mm10 as indicated
Supplementary_files_format_and_content: bed files of crosslinking event alignments with random tag in name column and number of merged PCR-duplicates in score column; bigWig profiles of combined L and M fractions for both strands; JAMM peaks in narrowPeak format.

organism: Drosophila melanogaster

extract_protocol:
The cells are rinsed with PBS and crosslinked with 0.15mJ/cm2 UV-C light. After crosslinking, the cells are pelleted by centrifugation, snap-frozen in liquid nitrogen and kept at -80˚C until use. Cells are lysed with 0.5mL of lysis buffer, mildly sonicated and immunoprecipitated with anti-FLAG beads for 1hr at ˚C. The beads are washed with lysis buffer and bound material is eluted with 3xFLAG peptide (250µg/mL). The eluate is then incubated with MyONEC1 beads to collect biotinylated target protein, after which the beads are washed with high-stringency buffers (0.1%SDS, 1M NaCl, 0.5% LiDS, 0.5M LiCl and 1% SDS, 0.5M LiCl) to aggressively remove non-specific interactors. 3’-linkers are then ligated with T4 RNA Ligase 1, excess adapters are washed away and 3’-tagged, cross-linked RNA is released with proteinase K digestion and column purification (Zymo DNA Clean & Concentrator).
Reverse transcription is carried out with SuperScript III and barcoded reverse-transcription primers. After reverse transcription, relevant samples are mixed and the cDNA is separated on a 6% 6M Urea PAA gel. Size fractionated cDNA is then processed essentially as described in the iCLIP protocol to generate sequencing libraries (König, J. et al. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J. Vis. Exp. (2011). doi:10.3791/2638). uvCLAP reads contain two custom barcodes adjacent to the 5'- and 3'-adapters. The 5 nt 5'-barcodes are flanked by 5 random nt according to the pattern NNNTTTTTNN (N: random nucleotide, T: barcode nucletide) and specify the pulldown condition. The 5 nt semi-random 3'-barcodes DRYYR and DYRRY (D: not C, R: purine, Y: pyrimidine) are used to distinguish the two replicates of each experiment. The 5'-barcodes are located at the first 10 nucleotides of the first mate reads. The read pairs align forward/reverse, thus the reverse complement of the 3'-barcodes is located at the first 5 nucleotides of the second mate reads.

tag: expression vector

value: dmMagoh

tag: clip antibody

value: Anti-FLAG® M2 Magnetic Beads (M8823 Sigma)


title: 37C Old Combined PostTraining

value: Combined


title: 38A Young Resistance PreTraining


title: L1 dmMagoh repA

description:
5’-barcode: ACTTG, 3’-barcode: RYYR
L1_dmMagoh_repA_dm3.bed
L1_dmMagoh_dm3_minus.bigWig
L1_dmMagoh_dm3_plus.bigWig
L1_dmMagoh_dm3.narrowPeak


title: 37B Old Combined PreTraining


title: K1 dmMLE-wt repB

description:
5’-barcode: CGGCG, 3’-barcode: YRRY
processed data file: K1_dmMLE-wt_dm3_plus.bigWig
processed data file: K1_dmMLE-wt_dm3_minus.bigWig
processed data file: K1_dmMLE-wt_dm3.narrowPeak

data_processing:
Barcodes and random tags were extracted using custom fastqpl scripts (Horton P. fastapl – a utility for versatile and easy processing of fasta format data (and fastqpl for fastq files). F1000Posters 2011, 2:1197 (poster)).
Adapters were trimmed and the library was demultiplexed using Flexbar (v2.32).
Possible readthroughs into the barcoded regions were removed by clipping 10 and 5 nt from the 3’-ends of first and second mate reads.
Reads were mapped to the reference genomes (hg19, mm10, dm3) using bowtie2 (v2.2.0) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant and --maxins=200.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156173 (2013)).
Crosslinking events of M and L size fractions were combined for each biological replicate.
Genome_build: hg19, dm3 or mm10 as indicated
bed files of crosslinking event alignments with random tag in name column and number of merged PCR-duplicates in score column; bigWig profiles of combined L and M fractions for both strands; JAMM peaks in narrowPeak format. BigWig and narrowPeak files are available in a tar archive on the series record. Bed files are available on the sample records.

source_name: K1 dmMLE-wt

value: dmMLE

value: Anti-FLAG M2 Magnetic Beads (M8823 Sigma)


title: 36C Young Combined PostTraining


title: K1 dmMLE-wt repA

description:
5’-barcode: CGGCG, 3’-barcode: RYYR
processed data file: K1_dmMLE-wt_dm3_plus.bigWig
processed data file: K1_dmMLE-wt_dm3_minus.bigWig
processed data file: K1_dmMLE-wt_dm3.narrowPeak


title: K1 control repB

description:
5’-barcode: GTATG, 3’-barcode: YRRY
processed data file: K1_control_dm3_plus.bigWig
processed data file: K1_control_dm3_minus.bigWig

source_name: K1 control

value: eGFP


title: 34A Old Resistance PreTraining


title: 34B Old Resistance PostTraining


title: 35A Young HIIT PreTraining


title: 35B Young HIIT PostTraining


title: 32A Young HIIT PreTraining


title: 33B Young Resistance PostTraining


title: 32B Young HIIT PostTraining


title: 30A Young Resistance PreTraining


title: 31B Young Combined PreTraining


title: 30B Young Resistance PostTraining


title: 2C Young Combined PostTraining


title: 2B Young Combined PreTraining


title: 31C Young Combined PostTraining


title: 29B Young Resistance PostTraining


title: 29A Young Resistance PreTraining


title: 27B Young Combined PreTraining


title: 28A Old Resistance PreTraining


title: 26B Young HIIT PostTraining


title: 28B Old Resistance PostTraining


title: 24B Young HIIT PostTraining


title: 25A Young Resistance PreTraining


title: 26A Young HIIT PreTraining


title: 23B Young HIIT PostTraining


title: 36B Young Combined PreTraining


title: 23A Young HIIT PreTraining


title: K1 control repA

description:
5’-barcode: GTATG, 3’-barcode: RYYR
processed data file: K1_control_dm3_plus.bigWig
processed data file: K1_control_dm3_minus.bigWig


title: 25B Young Resistance PostTraining


title: 22B Old HIIT PostTraining


title: 33A Young Resistance PreTraining


title: 22A Old HIIT PreTraining


title: 21B Young Combined PreTraining


title: 20B Old Combined PreTraining


title: 19A Young Resistance PreTraining


title: 1B Old Combined PreTraining


title: 18A Young HIIT PreTraining


title: HFD2

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

library_source: genomic

data_processing:
Raw reads were processed with trim galore to obtain clean data
Clean reads were mapped to mm10 using Bismark
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files

molecule: genomic DNA

growth_protocol: Mice received an injection of hCG 2 days after PMSG priming and were then mated overnight with males of proven fertility. Zygotes from normal and HFD mice were harvested by flushing the oviducts 24h and 45h post-hCG, respectively.

extract_protocol:
Denuded zygotes (30 zygotes from 5 mice for each sample) were collected following removal of the zona pellucida with acidic Tyrode’s solution and removal of polar bodies following a Piezo pulse. Samples were lysed in lysis buffer (10 mM Tris-Cl pH 7.4 and 2% SDS) with 0.5 μl protease K for 1 h at 37 °C.
Bisulfite conversion was performed on cell lysates using EZ DNA Methylation-Gold Kit (Zymo). Purification was performed and DNA was eluted in 10 mM Tris-Cl and combined with oligo 1. Klenow were added and incubated at 4 °C for 5 min, 37 °C for 30 min. Following incubation at 95 °C for 1 min, samples were transferred to ice before addition of fresh oligo 1. This random priming and extension was repeated a further three times. Samples were then incubated with 40 U exonuclease I and M-280 Streptavidin Dynabeads. After washes and resuspension in oligo 2 and Blue Buffer, samples were incubated at 95 °C for 45 s, transferred immediately to ice before addition of 100 U Klenow. Libraries were amplified by PCR, and assessed for quality and quantity using Agilent Bioanalyzer and StepOnePlus Real-Time PCR System. Libraries were prepared for 125-bp paired-end sequencing on a HiSeq2500.

treatment_protocol: The mice were randomly divided into two diet groups, one group receiving a high‐fat diet (D12492, Research Diets Inc., New Brunswick, NJ) and the other group received a normal diet (D1415, Beijing HFK Bioscience Co. LTD) for 16 weeks.

tag: strain background

value: ICR

tag: mice group

value: high‐fat diet (HFD)

value: zygote


title: 1C Old Combined PostTraining


title: 19B Young Resistance PostTraining


title: 18B Young HIIT PostTraining


title: HFD1


title: 17B Young HIIT PostTraining


title: 17A Young HIIT PreTraining


title: Ctrl1

value: normal diet


title: Ctrl2


title: 24A Young HIIT PreTraining


title: Ern1f/fLyz2-Cre IL-4-rep2

city: Wuhan

first: Yong

last: Liu

state: Hubei

address: Wuhan 430072, China

institute: Wuhan University

data_processing:
RNA-seq data were uniquely mapped  to  mm10  reference  genome  by  TopHat  v1.4.1
Expression  values  were  assigned  to gene  level  by  Cufflinks  v1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values of expressed genes

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow cells were isolated from the femur and tibia of male C57BL/6J mice or age-matched Ern1f/f and Ern1f/fLyz2-Cre mice. Cells were maintained in L929 cell-derived differentiation medium for 7 days to differentiate into mature macrophages.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) from BMDMs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Alternative activation of BMDMs was induced with IL-4 (20 ng/ml) for 24 hours.

tag: strain

value: macrophage

value: 8 weeks


title: 16B Young Resistance PostTraining

value: Resistance


title: Ern1f/fLyz2-Cre control-rep2


title: 21C Young Combined PostTraining


title: Ern1f/f IL-4-rep2


title: Ern1f/fLyz2-Cre IL-4-rep1


title: Ern1f/f control-rep2


title: 15A Young Resistance PreTraining

value: PreTraining


title: 14C Young Combined PostTraining


title: 20C Old Combined PostTraining

value: Old


title: Ern1f/f IL-4-rep1


title: Ern1f/fLyz2-Cre control-rep1


title: 14B Young Combined PreTraining

value: Young


title: 11A Young HIIT PreTraining

value: HIIT


title: Ern1f/f control-rep1


title: 11B Young HIIT PostTraining

value: PostTraining


title: 13A Young Resistance PreTraining


title: 10B Young Combined PreTraining


title: Lung_14wk_M0520522

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
RRBS and ChIP-BS-Seq: Trimmed sequences were mapped to the mouse GRCm38 genome using Bismark (Krueger and Andrews, 2011) (v0.16.3); CpG methylation calls were extracted and analysed using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and custom R scripts. For details, see Stubbs et al.
Genome_build: GRCm38
The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol:
All tissues were snap frozen directly after isolation. Genomic DNA was isolated from ~10mg frozen tissue using the DNeasy Blood & Tissue Kit (Qiagen).
RRBS libraries were prepared from isolated DNA following published protocols (Smallwood et al.,2011). Briefly, RRBS libraries were prepared by MspI digestion of 100-500ng genomic DNA, followed by end-repair and T-tailing using Klenow Exo- (Fermentas). Adapter ligation was performed overnight (homemade adapters) using T4 DNA Ligase (NEB), followed by a cleanup step using AMPure XP beads (Agencourt, 0.9x). Subsequently, libraries were bisulfite treated according to the manufactures instructions (Sigma Imprint Kit; 2 step protocol) and purified using an automated liquid handling robotic system (Agilent Bravo). The libraries were amplified using KAPA HiFi Uracil HotStart DNA Polymerase (KAPA Biosystems), indexing the samples with individual primers. All amplified libraries were purified (AMPure XP beads, 0.8x) and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing of all libraries was carried out with a 75 bp paired-end protocol on a HiSeq 2000 instrument (Illumina).

value: Lung

value: C57BL/6 BABR


title: Cortex_14wk_M0520522

value: Cortex


title: Heart_14wk_M0520522

value: Heart


title: Liver_14wk_M0520522

value: Liver


title: 15B Young Resistance PostTraining


title: Liver_27wk_M0512375


title: 16A Young Resistance PreTraining


title: Heart_27wk_M0512375


title: G2 hKHDRBS2-fixed repB

description:
5’-barcode: AGAAT, 3’-barcode: YRRY
G2_hKHDRBS2-fixed_hg19_minus.bigWig
G2_hKHDRBS2-fixed_hg19_plus.bigWig
G2_hKHDRBS2-fixed_hg19.narrowPeak

value: Anti-FLAG® M2 Magnetic Beads (M8823 Sigma)


title: G2 hKHDRBS1-Y440F repB

description:
5’-barcode: CGGCG, 3’-barcode: YRRY
G2_hKHDRBS1-Y440F_hg19_minus.bigWig
G2_hKHDRBS1-Y440F_hg19_plus.bigWig
G2_hKHDRBS1-Y440F_hg19.narrowPeak


title: Cortex_27wk_M0512375


title: G2 hKHDRBS2-fixed repA

description:
5’-barcode: AGAAT, 3’-barcode: RYYR
G2_hKHDRBS2-fixed_hg19_minus.bigWig
G2_hKHDRBS2-fixed_hg19_plus.bigWig
G2_hKHDRBS2-fixed_hg19.narrowPeak


title: G2 hKHDRBS1-Y440F repA

description:
5’-barcode: CGGCG, 3’-barcode: RYYR
G2_hKHDRBS1-Y440F_hg19_minus.bigWig
G2_hKHDRBS1-Y440F_hg19_plus.bigWig
G2_hKHDRBS1-Y440F_hg19.narrowPeak


title: Liver_1wk_M04NB


title: F1 hMagoh repA

description:
5’-barcode: GCTGA, 3’-barcode: RYYR
F1_hMagoh_repA_hg19.bed
F1_hMagoh_hg19_minus.bigWig
F1_hMagoh_hg19_plus.bigWig
F1_hMagoh_hg19.narrowPeak

value: hMagoh


title: Heart_1wk_M04NB


title: 13B Young Resistance PostTraining


title: Lung_1wk_M04NB


title: F1 hMagoh repB

description:
5’-barcode: GCTGA, 3’-barcode: YRRY
F1_hMagoh_repB_hg19.bed
F1_hMagoh_hg19_minus.bigWig
F1_hMagoh_hg19_plus.bigWig
F1_hMagoh_hg19.narrowPeak


title: 10C Young Combined PostTraining

value: Combined


title: Cortex_1wk_M04NB


title: G1 hKHDRBS3 repA

description:
5’-barcode: TCACG, 3’-barcode: RYYR
processed data file: G1_hKHDRBS3_hg19_plus.bigWig
processed data file: G1_hKHDRBS3_hg19_minus.bigWig
processed data file: G1_hKHDRBS3_hg19.narrowPeak

data_processing:
Barcodes and random tags were extracted using custom fastqpl scripts (Horton P. fastapl – a utility for versatile and easy processing of fasta format data (and fastqpl for fastq files). F1000Posters 2011, 2:1197 (poster)).
Adapters were trimmed and the library was demultiplexed using Flexbar (v2.32).
Possible readthroughs into the barcoded regions were removed by clipping 10 and 5 nt from the 3’-ends of first and second mate reads.
Reads were mapped to the reference genomes (hg19, mm10, dm3) using bowtie2 (v2.2.0) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant and --maxins=200.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)).
Crosslinking events of M and L size fractions were combined for each biological replicate.
Peaks were called with JAMM (version 1.0.7rev1, parameters "-d y -t paired -b 50 -w 1 -m normal") on crosslinked nucleotides of the two replicates for each pulldown condition as foreground and the control condition as background.
Genome_build: hg19, dm3 or mm10 as indicated
Supplementary_files_format_and_content: bed files of crosslinking event alignments with random tag in name column and number of merged PCR-duplicates in score column; bigWig profiles of combined L and M fractions for both strands; JAMM peaks in narrowPeak format. BigWig and narrowPeak files are available in a tar archive on the series record. Bed files are available on the sample records.


title: G1 hKHDRBS3 repB

description:
5’-barcode: TCACG, 3’-barcode: YRRY
processed data file: G1_hKHDRBS3_hg19_plus.bigWig
processed data file: G1_hKHDRBS3_hg19_minus.bigWig
processed data file: G1_hKHDRBS3_hg19.narrowPeak


title: G1 hKHDRBS2 repB

description:
5’-barcode: AGAAT, 3’-barcode: YRRY
processed data file: G1_hKHDRBS2_hg19_plus.bigWig
processed data file: G1_hKHDRBS2_hg19_minus.bigWig
processed data file: G1_hKHDRBS2_hg19.narrowPeak


title: Lung_27wk_M0512375


title: Lung_14wk_M0420527


title: Liver_14wk_M0420527


title: Heart_14wk_M0420527


title: G1 hKHDRBS1 repA

description:
5’-barcode: CGGCG, 3’-barcode: RYYR
processed data file: G1_hKHDRBS1_hg19_plus.bigWig
processed data file: G1_hKHDRBS1_hg19_minus.bigWig
processed data file: G1_hKHDRBS1_hg19.narrowPeak


title: G1 hKHDRBS1 repB

description:
5’-barcode: CGGCG, 3’-barcode: YRRY
processed data file: G1_hKHDRBS1_hg19_plus.bigWig
processed data file: G1_hKHDRBS1_hg19_minus.bigWig
processed data file: G1_hKHDRBS1_hg19.narrowPeak


title: Cortex_14wk_M0420527


title: Lung_14wk_M0420525


title: G2 hnRNP-K repB

description:
5’-barcode: TCACG, 3’-barcode: YRRY
processed data file: G2_hnRNP-K_hg19_plus.bigWig
processed data file: G2_hnRNP-K_hg19_minus.bigWig
processed data file: G2_hnRNP-K_hg19.narrowPeak

value: hnRNP-K


title: G2 hnRNP-K repA

description:
5’-barcode: TCACG, 3’-barcode: RYYR
processed data file: G2_hnRNP-K_hg19_plus.bigWig
processed data file: G2_hnRNP-K_hg19_minus.bigWig
processed data file: G2_hnRNP-K_hg19.narrowPeak


title: G2 control repA

description:
5’-barcode: ACTTG, 3’-barcode: RYYR
processed data file: G2_control_hg19_plus.bigWig
processed data file: G2_control_hg19_minus.bigWig

value: HBH tag


title: G2 control repB

description:
5’-barcode: ACTTG, 3’-barcode: YRRY
processed data file: G2_control_hg19_plus.bigWig
processed data file: G2_control_hg19_minus.bigWig


title: G2 heIF4A1 repB

description:
5’-barcode: GAGGT, 3’-barcode: YRRY
processed data file: G2_heIF4A1_hg19_plus.bigWig
processed data file: G2_heIF4A1_hg19_minus.bigWig
processed data file: G2_heIF4A1_hg19.narrowPeak


title: G2 heIF4A1 repA

description:
5’-barcode: GAGGT, 3’-barcode: RYYR
processed data file: G2_heIF4A1_hg19_plus.bigWig
processed data file: G2_heIF4A1_hg19_minus.bigWig
processed data file: G2_heIF4A1_hg19.narrowPeak


title: Liver_14wk_M0420525


title: L1 dmeIF4A3 repA

description:
5’-barcode: TGATA, 3’-barcode: RYYR
processed data file: L1_dmeIF4A3_dm3_plus.bigWig
processed data file: L1_dmeIF4A3_dm3_minus.bigWig
processed data file: L1_dmeIF4A3_dm3.narrowPeak

source_name: L1 dmeIF4A3

value: Anti-FLAG M2 Magnetic Beads (M8823 Sigma)


title: L1 dmeIF4A3 repB

description:
5’-barcode: TGATA, 3’-barcode: YRRY
processed data file: L1_dmeIF4A3_dm3_plus.bigWig
processed data file: L1_dmeIF4A3_dm3_minus.bigWig
processed data file: L1_dmeIF4A3_dm3.narrowPeak


title: G1 hQKI-B repA

description:
5’-barcode: GCTGA, 3’-barcode: RYYR
processed data file: G1_hQKI-B_hg19_plus.bigWig
processed data file: G1_hQKI-B_hg19_minus.bigWig
processed data file: G1_hQKI-B_hg19.narrowPeak

source_name: G1 hQKI-B

value: hQKI-B


title: Heart_14wk_M0420525


title: L1 control repB

description:
5’-barcode: GTTCT, 3’-barcode: YRRY
processed data file: L1_control_dm3_plus.bigWig
processed data file: L1_control_dm3_minus.bigWig

source_name: L1 control

value: eGFP


title: Cortex_14wk_M0420525


title: G1 hQKI-A repB

description:
5’-barcode: GAGGT, 3’-barcode: YRRY
processed data file: G1_hQKI-A_hg19_plus.bigWig
processed data file: G1_hQKI-A_hg19_minus.bigWig
processed data file: G1_hQKI-A_hg19.narrowPeak

source_name: G1 hQKI-A

value: hQKI-A


title: G1 hQKI-A repA

description:
5’-barcode: GAGGT, 3’-barcode: RYYR
processed data file: G1_hQKI-A_hg19_plus.bigWig
processed data file: G1_hQKI-A_hg19_minus.bigWig
processed data file: G1_hQKI-A_hg19.narrowPeak


title: L1 control repA

description:
5’-barcode: GTTCT, 3’-barcode: RYYR
processed data file: L1_control_dm3_plus.bigWig
processed data file: L1_control_dm3_minus.bigWig


title: G1 control repB

description:
5’-barcode: ACTTG, 3’-barcode: YRRY
processed data file: G1_control_hg19_plus.bigWig
processed data file: G1_control_hg19_minus.bigWig

source_name: G1 control


title: Heart_1wk_M03NB


title: Cortex_1wk_M03NB


title: Lung_1wk_M03NB


title: G1 control repA

description:
5’-barcode: ACTTG, 3’-barcode: RYYR
processed data file: G1_control_hg19_plus.bigWig
processed data file: G1_control_hg19_minus.bigWig


title: G1 hKHDRBS2 repA

description:
5’-barcode: AGAAT, 3’-barcode: RYYR
processed data file: G1_hKHDRBS2_hg19_plus.bigWig
processed data file: G1_hKHDRBS2_hg19_minus.bigWig
processed data file: G1_hKHDRBS2_hg19.narrowPeak


title: Lung_1wk_M02NB


title: F1 heIF4A3 repB

description:
5’-barcode: GCTGA, 3’-barcode: YRRY
processed data file: F1_heIF4A3_hg19_plus.bigWig
processed data file: F1_heIF4A3_hg19_minus.bigWig
processed data file: F1_heIF4A3_hg19.narrowPeak

source_name: F1 heIF4A3


title: F1 heIF4A3 repA

description:
5’-barcode: GCTGA, 3’-barcode: RYYR
processed data file: F1_heIF4A3_hg19_plus.bigWig
processed data file: F1_heIF4A3_hg19_minus.bigWig
processed data file: F1_heIF4A3_hg19.narrowPeak


title: F1 hDHX9 repB

description:
5’-barcode: TGATA, 3’-barcode: YRRY
processed data file: F1_hDHX9_hg19_plus.bigWig
processed data file: F1_hDHX9_hg19_minus.bigWig
processed data file: F1_hDHX9_hg19.narrowPeak

source_name: F1 hDHX9


title: Cortex_1wk_M02NB


title: G1 hQKI-B repB

description:
5’-barcode: GCTGA, 3’-barcode: YRRY
processed data file: G1_hQKI-B_hg19_plus.bigWig
processed data file: G1_hQKI-B_hg19_minus.bigWig
processed data file: G1_hQKI-B_hg19.narrowPeak


title: F1 control repB

description:
5’-barcode: CTCTC, 3’-barcode: YRRY
processed data file: F1_control_hg19_plus.bigWig
processed data file: F1_control_hg19_minus.bigWig

source_name: F1 control


title: F1 hDHX9 repA

description:
5’-barcode: TGATA, 3’-barcode: RYYR
processed data file: F1_hDHX9_hg19_plus.bigWig
processed data file: F1_hDHX9_hg19_minus.bigWig
processed data file: F1_hDHX9_hg19.narrowPeak


title: Heart_1wk_M01NB


title: F1 control repA

description:
5’-barcode: CTCTC, 3’-barcode: RYYR
processed data file: F1_control_hg19_plus.bigWig
processed data file: F1_control_hg19_minus.bigWig


title: Lung_1wk_M01NB


title: Lung_27wk_M0112371


title: Heart_27wk_M0112371


title: Liver_27wk_M0112371


title: C106

city: Lyon

first: Anamaria

last: Necsulea

address: 43 Bd. du 11 Novembre 1918

department: Laboratoire de Biométrie et Biologie Evolutive

country: France

institute: CNRS, Université Claude Bernard Lyon 1

description:
UniqueReadCounts.txt
RawRPKM_UniqueReads.txt
NormalizedRPKM_UniqueReads.txt
CufflinksFPKM.txt
Cufflinks_AllAssembledTranscripts.gtf
CombinedAnnotations_Ensembl82_Cufflinks.gtf
CombinedAnnotations_Ensembl82_Cufflinks_WithoutOverlappingRegions.gtf
Selected_Candidate_LncRNAs.txt

data_processing:
RNA-seq reads were trimmed to remove 3’ end adapter sequences, keeping a maximum read length of 81 bp.
The reads were aligned on the hg38 primary assembly (excluding patches and haplotypic sequences) of the human genome, downloaded from the Ensembl database release 76, using TopHat release 2.0.10 and Bowtie release 2.1.0. We allowed intron sizes between 40 bp and 1 million bp for spliced read alignments, with a minimum anchor size of 8 bp and a maximum of 1 mismatch for each aligned read segment.
We used Cufflinks release 2.2.1 to reconstruct de novo gene models from TopHat unique read alignments. Reads with multiple reported alignments were excluded from the dataset prior to de novo reconstruction. We kept isoforms with a minimum frequency above 0.05. Intra-intronic transcripts (corresponding to retained introns or unspliced pre-mRNAs) were kept if their frequency was above 0.25. We allowed intron sizes between 40 bp and 500,000 bp. Neighboring transcribed regions were collapsed if they were closer than 40 bp. We performed the gene model reconstruction separately for each RNA-seq sample and then merged them into a single set of gene models using the cuffmerge tool in Cufflinks.
We computed gene expression levels for protein-coding genes and candidate long non-coding RNAs derived from Ensembl annotations or predicted de novo with RNA-seq. For genes that had multiple annotated or predicted isoforms, we combined exon coordinates from all isoforms into a single “flattened” gene model and computed a single expression level for each gene. We used two approaches to estimate gene expression levels. First, we estimated gene-based RPKM (reads per kilobase of exon per million mapped reads) values by counting uniquely mapped RNA-seq reads that overlapped with exon coordinates over at least 5 bp. RNA-seq reads that were mapped to sense-overlapping exonic regions were added to the read count of all corresponding genes. The total number of mapped reads for each sample (corresponding to the M denominator in the RPKM computation) was computed after discarding ambiguously mapped reads and reads that aligned to the mitochondrial genome. Second, we used Cufflinks to estimate gene expression levels using all TopHat-aligned reads, assigning reads with multiple alignments to each gene depending on gene expression levels estimated with unique reads (default multiple read correction procedure in Cufflinks).
Genome_build: hg38
Supplementary_files_format_and_content: We provide tab-delimited .txt files containing the number of unique reads mapped on each gene, the raw and normalized RPKM values computed based on the uniquely mapped reads and the Cufflinks FPKM values. We also provide GTF files with the coordinates of the de novo annotated genes and transcripts and a tab-delimited .txt file containing the list of transcripts annotated as candidate lncRNAs in this study.  File list: 1) UniqueReadCounts.txt (unique read counts), 2) RawRPKM_UniqueReads.txt (raw RPKM values computed with unique reads); 3) NormalizedRPKM_UniqueReads.txt (RPKM values, normalized based on the 200 least-varying genes (Brawand et al., 2011)); 4) Cufflinks_FPKM.txt (RPKM/FPKM expression values computed with Cufflinks on all mapped reads); 5) Cufflinks_AllAssembledTranscripts.gtf (Results of the de novo transcript assembly procedure with Cufflinks); 6) CombinedAnnotations_Ensembl82_Cufflinks.txt (Combined annotations, starting from Ensembl82 and adding all non-overlapping transcripts de novo annotated with Cufflinks); 7) CombinedAnnotations_Ensembl82_Cufflinks_WithoutOverlappingRegions.gtf (Combined Ensembl82/Cufflinks annotations, excluding sense-overlapping exonic regions for expression computations); 8)Selected_Candidate_LncRNAs.txt (Information for the Ensembl/de novo genes annotated as candidate lncRNAs in this study.

source_name: liver biopsy

extract_protocol:
Total RNA was extracted from fresh-frozen bulk liver biopsy tissue using Trizol reagent (Invitrogen) and subsequently subjected to DNase treatment using DNA-free™ DNA Removal Kit (Ambion) according to manufacturer’s instructions. RNA concentration was determined using NanoDrop 2000 spectrophotometer (Thermo Scientific) and RNA quality/integrity was assessed in an Agilent 2100 bioanalyzer using RNA 6000 Nano Kit (Agilent Technologies). All 46 RNA samples included in this study had RNA integrity number (RIN) values of >7 (7.1-9.4; median 8.9), with 42 out of 46 samples having RIN values ≥8.
RNA sequencing libraries were constructed with the TruSeq Stranded mRNA protocol, with polyA selection.

value: liver

tag: infection status

value: HCV

value: high ISG

tag: treatment


title: C186

tag: tissue


title: C71


title: Cortex_27wk_M0112371

tag: age


title: C250a

value: non-HCV


title: Lung_27wk_M00018754

value: Lung

value: C57BL/6 BABR


title: Liver_1wk_M02NB


title: Heart_27wk_M00018754

value: Heart


title: C173


title: C369


title: Cortex_27wk_M00018754

value: Cortex


title: Liver_27wk_M00018754

value: Liver


title: C51a


title: Liver_1wk_M01NB


title: B986


title: B929


title: Liver_27wk_M00018752


title: Cortex_1wk_M01NB


title: B371

value: pegIFNa/ribavirin 144h


title: Lung_27wk_M00018752


title: B247

value: low ISG


title: Cortex_27wk_M00018752


title: C145


title: Heart_27wk_M00018752


title: Lung_27wk_M00018724


title: Liver_27wk_M00018724


title: A707_2


title: Cortex_27wk_M00018724


title: B178

value: pegIFNa/ribavirin 96h


title: B304


title: A616_B2


title: Heart_27wk_M00018724


title: Patient 9 Tumor 1

data_processing:
quality filtering: minimum quality filter applied for barcode and insert; fastq_filter.pl; -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ;github.com/chaolinzhanglab/ctk/tree/v1.0.3
collapse exact sequences: exact duplicate sequences removed; fasta2collapse.pl; ;github.com/chaolinzhanglab/ctk/tree/v1.0.3
trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing); fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/
strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs; stripBarcode.pl; -linker 5 ; github.com/chaolinzhanglab/ctk/tree/v1.0.3
remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped; fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/
Groomed reads aligned to hg38 with bowtie2 using defaults
Collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated; tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; github.com/chaolinzhanglab/ctk/tree/v1.0.3
Collapsed mapped reads were clustered, where the peak cluster coordinate +/- 32 nt was searched for the presence of miRNA 6-8mers, for those miRNAs with CLIP evidence.
Fold changes were calculated by adding a psuedocount of 1 to every cluster, normalizing each cluster for read depth (reads per million mapped), and dividing by condition.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes CLIP-seq cluster definition and locations, miRNA seed search results, and genomic annotations

source_name: Liver

extract_protocol:
UV crosslinked pulverized tissue was lysed in 1x PXL buffer, lysates were Dnase treated, partially RnaseI digested, clarified by centrifugation, and Argonaute-mRNA complexes isolated with pan-Ago 2A8 antibody.
CLIP libraries were prepared as in Luna, JM et al (2015). 1st PCR Products were amplified in a second round of PCR that added a 4 nt index (for multiplexing) and a 16 nt common primer sequence. Raw files are demultiplexed on the basis of this index, but have not been further modified.
CLIPseq

treatment_protocol: Flash frozen human liver resections were pulverzied in liquid nitrogen. Pulverzized tissue powder was UV crosslinked at 254nM for CLIP.

tag: tumor status

value: Tumor

tag: Sex

value: F

tag: tech replicate

tag: batch

tag: sample type

value: CLIP


title: Lung_41wk_M00018381


title: B284

value: pegIFNa/ribavirin 48h


title: A727_2


title: Patient 8 Tumor 1

value: M


title: Heart_41wk_M00018381


title: Patient 7 Tumor 1


title: B401

value: liver


title: Cortex_41wk_M00018381


title: A748_2

value: HCV


title: Patient 6 Tumor 1


title: C591

value: pegIFNa/ribavirin 16h


title: Patient 5 Tumor 2


title: A991_2

value: high ISG


title: Liver_41wk_M00018381


title: B217


title: Lung_41wk_M00018363

value: Lung


title: Patient 5 Tumor 1


title: A972_2


title: Heart_41wk_M00018363

value: C57BL/6 BABR


title: Patient 4 Tumor 1


title: Patient 4 Tumor 2


title: A720_2

value: pegIFNa/ribavirin 4h


title: Patient 3 Tumor 2


title: A609_2


title: Liver_41wk_M00018363


title: Patient 3 Tumor 1


title: Lung_41wk_M00018362


title: A764_2


title: Cortex_41wk_M00018363

value: Cortex


title: A584_2


title: Heart_41wk_M00018362

value: Heart


title: Patient 2 Tumor 2


title: B346


title: B320


title: Patient 2 Tumor 1


title: Lung_41wk_M00018359


title: B215


title: Patient 1 Tumor 2


title: Patient 1 Tumor 1


title: A972


title: A707


title: Heart_41wk_M00018359


title: Patient 9 Normal 1

value: Normal


title: Liver_41wk_M00018359

value: Liver


title: Patient 8 Normal 1


title: Liver_41wk_M00018362


title: F3 mmMSL2-mESC repB

description:
5’-barcode: GTTCT, 3’-barcode: YRRY
processed data file: F3_mmMSL2-mESC_mm10_plus.bigWig
processed data file: F3_mmMSL2-mESC_mm10_minus.bigWig
processed data file: F3_mmMSL2-mESC_mm10.narrowPeak

source_name: neural precursor cells

value: neural precursor cells

value: Anti-FLAG® M2 Magnetic Beads (M8823 Sigma)


title: B136

value: low ISG


title: B283


title: F3 mmMSL2-mESC repA

description:
5’-barcode: GTTCT, 3’-barcode: RYYR
processed data file: F3_mmMSL2-mESC_mm10_plus.bigWig
processed data file: F3_mmMSL2-mESC_mm10_minus.bigWig
processed data file: F3_mmMSL2-mESC_mm10.narrowPeak


title: Patient 5 Normal 2

value: CLIP


title: Patient 6 Normal 1

value: F


title: B254


title: A727


title: F3 mmMSL1-mESC repA

description:
5’-barcode: ATCGT, 3’-barcode: RYYR
processed data file: F3_mmMSL1-mESC_mm10_plus.bigWig
processed data file: F3_mmMSL1-mESC_mm10_minus.bigWig
processed data file: F3_mmMSL1-mESC_mm10.narrowPeak


title: F3 mmMSL1-mESC repB

description:
5’-barcode: ATCGT, 3’-barcode: YRRY
processed data file: F3_mmMSL1-mESC_mm10_plus.bigWig
processed data file: F3_mmMSL1-mESC_mm10_minus.bigWig
processed data file: F3_mmMSL1-mESC_mm10.narrowPeak


title: Patient 4 Normal 2

value: M


title: Cortex_41wk_M00018362


title: A748

value: liver


title: RVKB022B_flaA_WT_RNA

city: Seattle

first: Kevin

last: Barry

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description: total RNA

data_processing:
Basecalling and separation of multi-plexed runs with Illumina Casava  v1.8.0
Filtering for high quality reads with the fastq_illumina_filter-0.1.
RNAseq: Trimming of 10-15 nucleotides with the FastX-toolkit.
RNAseq: 3' adapter clipping with the FastX-toolkit.
RNAseq: Transcriptome alignment with TopHat2 v2.0.13
RNAseq: Read quantification using custom scripts.
Ribosome profiling: Filtering for high quality reads with the fastq_illumina_filter-0.1.
Ribosome profiilng: 3' adapter clipping with the FastX-toolkit.
Ribosome profiling: Deletion of first nucleotide of 5' end with the FastX-toolkit
Ribosome profiling: rRNA alignment with bowtie v1.0.0
Ribosome profiling: Transcriptome alignment with Tophat v2.0.10
Ribosome profiling: Read quantification using custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delmited text files contain read count values for each sample

source_name: Bone Marrow Macrophages

growth_protocol: Macrophages were derived from the bone marrow of C57BL/6J (Jackson Laboratory) and Myd88–/– (Hou et al., 2008, PMID: 18656388) mice on the B6 background. Macrophages were derived by 8 days of culture in RPMI supplemented with 10% serum, 100μM streptomycin, 100U/mL penicillin, 2mM L-glutamine and 10% supernatant from 3T3-macrophage-colony stimulating factor cells, with feeding on day 5. Cells were re-plated in antibiotic free media 24hrs prior to infection with L. pneumophila. All L. pneumophila strains were derived from LP02, a streptomycin-resistant thymidine auxotroph derived from L. pneumophila LP01. The ΔdotA, ΔflaA, and Δ7ΔflaA strains were generated on the LP02 background and have been described previously (Barry et al., 2013, PMID: 23686480; Fontana et al., 2011, PMID: 21390206; Ren et al., 2006, PMID: 16552444). 2-fold dilutions of Legionella pneumophila strains used for infections were grown overnight in liquid buffered-yeast-extract culture and, at the time of infection, cultures with an optical density (600 nm) greater than 4.0 were selected.

extract_protocol:
Ribosome profiling experiments were undertaken essentially as previously described (Ingolia et al., 2012, PMID: 22836135). For all experiments cells were lysed by flash freezing and thawed in the presence of lysis buffer as previously described (Ingolia et al., 2012, PMID: 22836135). Clarified lysates were split and some was used to generate ribosome footprints while some was used to isolate total RNA for RNA sequencing. For RNAseq libraries 300μL of clarified lysate was mixed with 900μL of Trizol LS (Life Technologies) and RNA was isolated following the manufacturer’s guidelines.
Ribosome profiling libraries were generated as previously described (Ingolia et al., 2012, PMID: 22836135). All RNA and DNA gel extractions were performed overnight as previously described (Ingolia et al., 2012, PMID: 22836135). The Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to remove rRNA from ribosome profiling samples before the dephosphorylation and linker ligation steps described (Ingolia et al., 2012, PMID: 22836135). For RNAseq libraries total RNA was submitted to the University of California, Berkeley Functional Genomics Laboratory. There the Ribo-Zero Gold rRNA Removal Kit (Illumina) was used to remove rRNA. RNA integrity was measured utilizing the RNA Pico method on the Agilent 2100 Bioanalyzer at the University of California, Berkeley Functional Genomics Laboratory. High quality RNA with a RNA integrity number (RIN) >8 (Agilent Technologies) was used to generate libraries following standard Illumina protocols for single read 100 (RS100) sequencing. Final ribosome profiling libraries were sequenced on a HiSeq2000 System (Illumina) with single read 50 (SR50) read lengths and final RNAseq libraries were sequenced on a HiSeq2000 System (Illumina) with SR100 read lengths by the Vincent J. Coates Genomics Sequencing Laboratory at UC, Berkeley.

treatment_protocol: Bone marrow derived macrophages were plated in tissue culture treated 6-well plates or 75cm2 flasks at a density of approximately 1.56e5 cells per cm2 (1.5e6 macrophages per well of a 6-well plate or 1.2e7 macrophages per 75cm2 flask). Macrophages were infected with the indicated strains of L. pneumophila at an MOI=3, or left untreated, spun at 400 xg for 10 min and allowed to infect at 37°C in 5% CO2 for 1hr. After 1hr incubation media was replaced and the cells were incubated for an additional 5hrs at 37°C in 5% CO2. When used, harringtonine treatment was performed as previously described (Ingolia et al., 2012, PMID: 22836135). Harringtonine (LKT Laboratories) was added at a final concentration of 2 μg/mL for 120 seconds at the end of the 6hr infection. 100 μg/mL of cycloheximide (Sigma) was added to freeze ribosomes after the 120-second harringtonine treatment.

value: Bone Marrow Macrophages

tag: strain/genotype

tag: l. pneumophila infection

value: flaA

tag: drug treatment


title: RVKB022C_dotflaA_WT_RNA

description: total RNA

tag: cell type

value: dotflaA


title: RVKB022A_uninf_WT_RNA

description: total RNA

value: uninfected


title: C552

value: HCV


title: Patient 4 Normal 1


title: Patient 3 Normal 2


title: A991

value: high ISG


title: B199


title: Cortex_41wk_M00018359

value: Cortex

value: C57BL/6 BABR


title: RVKB021B_flaA_Myd88_RNA

description: total RNA


title: RVKB021C_dotflaA_Myd88_RNA

description: total RNA


title: Patient 3 Normal 1

value: Normal


title: A616_OCT


title: Patient 7 Normal 1


title: Patient 2 Normal 1


title: Patient 2 Normal 2


title: A720


title: A764


title: RVKB021A_uninf_Myd88_RNA

description: total RNA


title: A609


title: Patient 1 Normal 1


title: Patient 1 Normal 2


title: Patient 5 Normal 1


title: RVKB020B_flaA_WT

description: ribosome footprints


title: RVKB020C_dotflaA_WT

description: ribosome footprints


title: XL2 IgG-mouse-HEK rep B

description: 3'-tag: GTGGAA, 3'-RY-space tag: YY

data_processing:
Adapters were trimmed using Flexbar (v2.5).
Libraries were demultiplexed using bctools (https://github.com/dmaticzka/bctools, v0.2.0) and Flexbar (v2.5).
Possible readthroughs into the barcoded regions were removed by clipping 13 nt from the 3'-ends of first mate reads.
Reads were mapped to reference genome hg19 using bowtie2 (v2.2.6) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant --maxins 500.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)) with bctools (https://github.com/dmaticzka/bctools, v0.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing coordinates of crosslinking event alignments with id of a representative read in name column and number of merged PCR-duplicates in score column. bigWig profiles of crosslinking event alignments for each strand.

extract_protocol:
Cells are crosslinked with 0.15mJ/cm2 UV-C irradiation, lysed with 1xNLB and homogenized by waterbath-sonication. Target protein of interest is pulled-down with paramagnetic beads pre-coupled to antibodies against the protein of interest.
After a brief RNAseI-digestion, RNA 3'-ends are healed with T4 PNK. Custom-made, barcoded adapters are ligated using T4 RNA Ligase 1 or T4 RNA Ligase 2KQ (if pre-adenylated adapters are used) for 1 hr at 25˚C. Custom FLASH adapters contained two barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNBBNTTTTTTNN (N: random tag nucleotide, T: tag nucleotide, B: RY-space tag nucleotide). Random tags are used to merge PCR-duplicates, regular tags are used to specify the pulldown condition, and semi-random RY-space tags are used to distinguish the biological replicates (RR: replicate A, YY: replicate B, R: purine, Y: pyrimidine). Excess adapters are washed away, negative controls (IgG) are mixed with experimental controls and RNA is isolated with Proteinase K treatment and column purification. Isolated RNA is reverse-transcribed and RNaseH-treated. cDNA is column-purified and circularized with CircLigase for 2-16hrs. Circularized cDNA is directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode.

tag: cell line

tag: clip antibody

value: IgG (mouse) (Santa Cruz, cat#:sc-2025, lot:K1814)


title: shALKBH5-rep1-IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: RIP-seq

data_processing:
All samples were sequenced by Illumina HiSeq 2500 with single-end 50-bp read length. The deep sequencing data were mapped to human genome version 38 (GRCh38).
Data analysis for each experiment: (1) for m6A-seq, reads were aligned to the reference genome using Tophat v2.0.14 with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene had multiple isoforms. Aligned reads were extended to 150 bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from introns in peak calling. The peak calling method was modified from published work (Dominissini et al., 2012). To call m6A peaks, the longest isoform of each gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with read counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the read counts in each window were normalized by the median count of all windows of that gene. A Fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the FDR < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP samples in the current peak/window (a), median read counts of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c), and median read counts of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c). (2) for mRNA-seq (the input samples of m6A-seq), reads were mapped with Tophat and Cufflink (v2.2.1) was used to calculate the FPKM of each gene to represent their mRNA expression level.
Genome_build: hg38
Supplementary_files_format_and_content: excel file containing processed FPKM from input samples and m6A peak list from IP samples

source_name: human cell line

extract_protocol:
total RNA was extracted using Direct-zol (Zymo) from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: shRNA knockdown

value: ALKBH5 shRNA

value: glioblastoma stem-like cells

tag: antibody

value: m6A antibody (Synaptic Systems, 202003)


title: RVKB019C_dotflaA_Myd88

description: ribosome footprints


title: shALKBH5-rep2-IP

description: RIP-seq


title: XL2 IgG-mouse-HEK rep A

description: 3'-tag: GTGGAA, 3'-RY-space tag: RR


title: shCont-rep1-IP

description: RIP-seq

value: control shRNA


title: XL2 hnRNPC-mAb-HEK rep B

description: 3'-tag: TTAGCC, 3'-RY-space tag: YY

value: hnRNPC(4F4) (Santa cruz, cat#:sc-32308, lot:D2914)


title: XL2 hnRNPC-mAb-HEK rep A

description: 3'-tag: TTAGCC, 3'-RY-space tag: RR


title: RVKB019A_uninf_Myd88

description: ribosome footprints


title: shCont-rep2-IP

description: RIP-seq


title: RVKB019B_flaA_Myd88

description: ribosome footprints


title: RVKB018D_7flaA_RNA

description: total RNA


title: shALKBH5-rep1-input

description: This sample was used for both RNA-seq analysis and as input for RIP-seq analysis.


title: shALKBH5-rep2-input


title: A584

tag: infection status

value: low ISG


title: shCont-rep2-input


title: XL1 IgG-Rb rep A

description: 3'-tag: GTGGAA, 3'-RY-space tag: RR

data_processing:
Adapters were trimmed using Flexbar (v2.5).
Libraries were demultiplexed using bctools (https://github.com/dmaticzka/bctools, v0.2.0) and Flexbar (v2.5).
Possible readthroughs into the barcoded regions were removed by clipping 13 nt from the 3'-ends of first mate reads.
Reads were mapped to reference genome hg19 using bowtie2 (v2.2.6) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant --maxins 500.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)) with bctools (https://github.com/dmaticzka/bctools, v0.2.0).
Peaks for DHX9-Rb and DHX9-mAb were with PEAKachu (https://github.com/tbischler/PEAKachu/, v0.0.1alpha2) using parameters --pairwise_replicates, --max_insert_size 100, -m 0, -n manual, and --size_factors 1 1 0.75 0.75, with the IgG control as experimental background.
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing coordinates of crosslinking event alignments with id of a representative read in name column and number of merged PCR-duplicates in score column. bigWig profiles of crosslinking event alignments for each strand. PEAKachu peaks in gff format.

source_name: HEK293_XL1 IgG-Rb

value: IgG-Rb


title: XL1 DHX9-Rb rep B

description:
3'-tag: CAAGTG, 3'-RY-space tag: YY
processed data file: XL1_DHX9_Rb_peakachu.gff

source_name: HEK293_XL1 DHX9-Rb

tag: clip antibody info.


title: XL1 IgG-Rb rep B

description: 3'-tag: GTGGAA, 3'-RY-space tag: YY


title: RVKB020A_uninf_WT

description: ribosome footprints

value: Bone Marrow Macrophages


title: RVKB018A_uninf_RNA

description: total RNA


title: shCont-rep1-input


title: XL1 DHX9-Rb rep A

description:
3'-tag: CAAGTG, 3'-RY-space tag: RR
processed data file: XL1_DHX9_Rb_peakachu.gff


title: RVKB017C_7flaA

description: ribosome footprints


title: XL1 DHX9-mAb repB

description:
3'-tag: TTAGCC, 3'-RY-space tag: YY
processed data file: XL1_DHX9_mAb_peakachu.gff

source_name: HEK293_XL1 DHX9-mAb


title: RVKB017D_7flaA_harr

description: ribosome footprints

value: harringtonine


title: H3K79me3 ChIP-seq of parental SPH colorectal cancer cell line

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

description: SPH (mesenchymal-like DLD1 derivative)  colorectal cancer cell line

data_processing:
CLC Genomics Workbench 7.5 software was used
The raw reads were cleaned by trimming of adaptor sequences.
Sequenced reads were mapped to hg19 genome using CLC Workbench default parameters
Peaks were called with the ChIP-seq analysis module of the CLC Genomics Workbench software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with peak coordinates and number of reads under the peak

source_name: colorectal cancer cell line

growth_protocol: Colorectal cancer cell line DLD1 and its derivatives were maintained in McCoy`s 5A Medium (Invitrogen) containing 10% fetal bovine serum (FBS, Invitrogen), 100 units/ml penicillin and 0.1 mg/ml streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were precipitated with indicated histone antibodies using the Diagenode iDeal ChIP-seq & library preparation kit according to manufacturers instructions
Libraries were prepared  with Diagenode iDeal ChIP-seq & library preparation kit according to manufacturers instructions

value: colorectal cancer cell line

tag: cell characteristics

value: mesenchymal, derived from colonospheres

tag: chip antibody


title: XL1 DHX9-mAb repA

description:
3'-tag: TTAGCC, 3'-RY-space tag: RR
processed data file: XL1_DHX9_mAb_peakachu.gff


title: H3K79me3 ChIP-seq of parental SA colorectal cancer cell line

description: SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line

value: mesenchymal, derived from soft agar colonies


title: RVKB017B_dotflaA_harr

description: ribosome footprints

value: dotflaA


title: RVKB017A_dotflaA

description: ribosome footprints


title: H3K79me3 ChIP-seq of parental DLD1 colorectal cancer cell line

value: epithelial, parental


title: H3K27me3 ChIP-seq of parental METS colorectal cancer cell line

description: METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line

value: epithelial, derived from xenograft lung metastasis


title: polyA_plus_HEK_s4020_3

description: Poly-A plus RNA

data_processing:
Read trimming for Illumina adapters using Cutadapt (v-1.8.1)
Read mapping to genome using TopHat2 (v2.0.13) with bowtie2 (v2.2.3)
Generating coverage signal tracks (bigWigs) from all mapped alignments using Samtools (v1.2) and DeepTools2 (v2.0.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: .bigWig files, containing coverage signals from TopHat alignments

growth_protocol: DMEM-Glutamax supplemented with sodium pyruvate, glucose and 10% FBS

extract_protocol:
Total RNA with Zymo Quick RNA kit
TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: 5nM of Silencer Select siRNAs transfected with RNAiMAX

tag: condition

value: DHX9 knockdown with s4020


title: RVKB018C_dotflaA_RNA

description: total RNA

value: dotflaa


title: polyA_plus_HEK_s4020_4

description: Poly-A plus RNA


title: RVKB018B_flaA_RNA

description: total RNA

value: flaA


title: H3K27me3 ChIP-seq of parental SPH colorectal cancer cell line


title: polyA_plus_HEK_s4020_1

description: Poly-A plus RNA


title: RVKB016D_flaA_harr

description: ribosome footprints


title: RVKB016B_uninf_harr

description: ribosome footprints

value: uninfected


title: H3K27me3 ChIP-seq of parental SA colorectal cancer cell line


title: H3K79me3 ChIP-seq of parental METS colorectal cancer cell line


title: RVKB016C_flaA

description: ribosome footprints


title: RVKB010D_7flaA_RNA

description: total RNA


title: RVKB016A_uninf

description: ribosome footprints


title: H3K4me3 ChIP-seq of parental METS colorectal cancer cell line


title: polyA_plus_HEK_s4019_4

description: Poly-A plus RNA

value: DHX9 knockdown with s4019


title: polyA_plus_HEK_s4019_2

description: Poly-A plus RNA


title: RVKB010C_dotflaA_RNA

description: total RNA


title: H3K27me3 ChIP-seq of parental DLD1 colorectal cancer cell line


title: H3K4me3 ChIP-seq of parental SA colorectal cancer cell line


title: polyA_plus_HEK_s4019_1

description: Poly-A plus RNA


title: H3K4me3 ChIP-seq of parental SPH colorectal cancer cell line


title: polyA_plus_HEK_ctrl_4

description: Poly-A plus RNA

value: scrambled control


title: polyA_plus_HEK_s4019_3

description: Poly-A plus RNA


title: polyA_plus_HEK_ctrl_3

description: Poly-A plus RNA


title: polyA_plus_HEK_s4020_2

description: Poly-A plus RNA


title: H3K4me3 ChIP-seq of parental DLD1 colorectal cancer cell line


title: RVKB010A_uninf_RNA

description: total RNA


title: RVKB008D_dotflaA_Myd88

description: ribosome footprints


title: total RNA DNA from SPH (mesenchymal-like DLD1 derivative)  colorectal cancer cell line

description:
SPH (mesenchymal-like DLD1 derivative)  colorectal cancer cell line
SPH

data_processing:
CLC Genomics Workbench 7.5 software was used
Sequenced reads were mapped to hg19 genome using CLC Workbench default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total RNA from cell lines was isolated using the Total RNA Isolation Kit (Roche)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: parental cell line

value: colorectal cancer cell line DLD1


title: polyA_plus_HEK_ctrl_2

description: Poly-A plus RNA


title: total RNA DNA from SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line

description:
SA (mesenchymal-like DLD1 derivative) colorectal cancer cell line
SA


title: total RNA DNA from METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line

description:
METS (metastasis-derived DLD1 derivative)  colorectal cancer cell line
METS


title: RVKB008B_dotflaA_WT

description: ribosome footprints


title: RKVB008C_flaA_Myd88

description: ribosome footprints


title: polyA_minus_HEK_s4020_4

description:
Poly-A minus RNA
Ribo-Zero Treated after mRNA depletion


title: polyA_plus_HEK_ctrl_1

description: Poly-A plus RNA


title: RVKB008A_flaA_WT

description: ribosome footprints


title: polyA_minus_HEK_s4020_3


title: RVKB007C_7flaA

description: ribosome footprints


title: polyA_minus_HEK_s4020_1


title: RVKB007B_dotflaA

description: ribosome footprints

value: dotAflaA


title: total RNA from parental DLD1 colorectal cancer cell line

description:
parental DLD1 colorectal cancer cell line
DLD1


title: polyA_minus_HEK_s4020_2


title: polyA_minus_HEK_s4019_4


title: RVKB007A_flaA

description: ribosome footprints


title: polyA_minus_HEK_s4019_3


title: polyA_minus_HEK_s4019_2


title: polyA_minus_HEK_s4019_1


title: RVKB005C_dotflaA_WT_RNA

description: total RNA


title: RVKB010B_flaA_RNA

description: total RNA


title: RVKB005B_flaA_WT_RNA

description: total RNA


title: polyA_minus_HEK_ctrl_3


title: RVKB005A_uninf_WT_RNA

description: total RNA


title: RVKB006A_uninf_Myd88_RNA

description: total RNA


title: polyA_minus_HEK_ctrl_4


title: D CCB604 (W168 [delta]yacP + pDG-yacP) + IPTG

city: Paris

first: Ciaran

last: Condon

address: 13 rue Pierre et Marie Curie

institute: CNRS

description:
SLX085-02-v4.604p_complete.xls
SLX085-02-v4.604mvs604p.complete.xls

data_processing:
Reads were demultiplexed and adapters trimmed (https://demult.web.pasteur.fr/ and Casava 1.8 version (Consensus Assessment of Sequence and Variance software, Illumina).
Quality control checks were performed before and after trimming by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Fifty-nt reads were mapped by Bowtie (Langmead et al, 2009) and yielded about 107 aligned reads per sample.
Data analysis was performed using the R software, Bioconductor (Gentleman et al, 2004) packages including DESeq2 (Anders & Huber, 2010; Love et al, 2014) and the PF2tools package (version 1.2.3) developed at PF2 (Institut Pasteur).
Normalization and differential analysis were carried out according to the DESeq2 model and package (version 1.6.2).
Supplementary_files_format_and_content: Excel files

organism: Bacillus subtilis

source_name: cell culture

growth_protocol: Cultures were grown at 37°C  in 2xYT in the presence of appropriate antibiotics (mls or kan) with shaking +/- 1 mM IPTG. Cells were harvested by centrifugation at OD600 = 0.6

extract_protocol:
Total RNA was isolated from 20 mL culture (pelleted and frozen) by the glass beads/phenol method described previously (Bechhofer et al, 2008). RNA samples were treated with RQ DNase Promega (37°C for 20 minutes) to remove potential contaminating chromosomal DNA.
Ribosomal RNA was removed from 5 mg total RNA using RiboZero kit from Epicenter, according to the manufacturer's instructions. Ribosomal RNA depletion and overall RNA quality was analysed by Bioanalyser (Agilent). cDNA libraries were prepared using the Smarter Stranded RNA-Seq Kit (Clontech) with adapters for multiplexing, according to manufacturer's instructions. RNA concentration and quality was checked by Bioanalyser (Agilent).
The 12 samples were normalized to 2nM, multiplexed and denatured at a concentration of 1nM using 0.1N NaOH (5 minutes at room temperature) before dilution to 10pM and loading on a HiSeq2000 flowcell.

tag: strain


title: D CCB375 (W168 [delta]yacP)

description:
SLX085-02-v4.375_complete.xls
SLX085-02-v4.1002vs375.complete.xls

value: CCB375 (W168 [delta]yacP)


title: polyA_minus_HEK_ctrl_1


title: polyA_minus_HEK_ctrl_2


title: F3 mmDHX9-mNPC repA

description:
5’-barcode: CTACA, 3’-barcode: RYYR
processed data file: F3_mmDHX9-mNPC_mm10_plus.bigWig
processed data file: F3_mmDHX9-mNPC_mm10_minus.bigWig
processed data file: F3_mmDHX9-mNPC_mm10.narrowPeak

source_name: F3 mmDHX9-mNPC

value: neural precursor cells

tag: expression vector

value: Anti-FLAG M2 Magnetic Beads (M8823 Sigma)


title: F3 mmDHX9-mESC repB

description:
5’-barcode: GAGGT, 3’-barcode: YRRY
processed data file: F3_mmDHX9-mESC_mm10_plus.bigWig
processed data file: F3_mmDHX9-mESC_mm10_minus.bigWig
processed data file: F3_mmDHX9-mESC_mm10.narrowPeak

source_name: F3 mmDHX9-mESC

value: embryonic stem cells


title: D SSB1002 (W168 wild-type)

description:
SLX085-02-v4.1002_complete.xls
SLX085-02-v4.1002vs375.complete.xls

value: SSB1002 (W168 wild-type)


title: F3 mmDHX9-mNPC repB

description:
5’-barcode: CTACA, 3’-barcode: YRRY
processed data file: F3_mmDHX9-mNPC_mm10_plus.bigWig
processed data file: F3_mmDHX9-mNPC_mm10_minus.bigWig
processed data file: F3_mmDHX9-mNPC_mm10.narrowPeak


title: KO_rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Filtered on quality using sickle1.2: sickle pe -f R1.fastq -r R2.fastq -o filtered_R1.fastq -p filtered_R2.fastq -t sanger -s filtered_singles.fastq
Mapping to the mouse mm9 genome: bowtie2 -p 2 -x mm9 -X 1000 –fr -1 clean_R1.fastq -2 clean_R2.fastq  -S btout2.sam
Multiple location mapping filtering: sed ‘/XS:/d’ mapped.sam > mapped_1alignmentonly.sam
PCR duplicates removal using Picard tools 1.130: java -Xms1024m -jar /opt/picard-1.130/picard.jar MarkDuplicatesWithMateCigar INPUT = mapped_1align.sorted.bam OUTPUT=$prefix.sorted.uniq.bam METRICS_FILE = metrics.txt REMOVE_DUPLICATES = true ASSUME_SORTED = true SKIP_PAIRS_WITH_NO_MATE_CIGAR = true
Nucleosome-free fragments (<120 bp) isolation: samtools view -h $prefix.sorted.uniq.bam | awk ‘ ^/ @/ { print $0 >> “nuc120.sam” ; next } { if ($9 <120 && $9 > -120) {print $0 >> “nuc120.sam”} }’
Peak calling using Homer 4.6: findPeaks homer_tagdir_nuc120/ -o $prefix.nuc120.peaks_size250mindist500.txt -region -size 250 -minDist 500
Differential peak analysis was performed using DiffBind
Genome_build: mm9
Supplementary_files_format_and_content: bed: chromosome, start, end, name, score, strand, RPKM

source_name: spleen + LN

extract_protocol:
Cells were isolated form 8-10 week-old NOD mice and double sorted by flow cytometry for DAPI- CD4+ TCRb+ CD25hi (top 50%) Tregs
50,000 CD4+TCRβ+CD25hi (top 50%) Tregs were sorted and lysed. After transposition and PCR, a final bead purification and selection (100–600 bp) was performed twice using 0.6× and  1.6× SPRI beads. Libraries were paired-end sequenced using a 75-bp kit on an Illumina NextSeq high-throughput sequencing system.

value: NOD

tag: genotype

value: Flicr KO

value: Treg


title: F3 mmDHX9-mESC repA

description:
5’-barcode: GAGGT, 3’-barcode: RYYR
processed data file: F3_mmDHX9-mESC_mm10_plus.bigWig
processed data file: F3_mmDHX9-mESC_mm10_minus.bigWig
processed data file: F3_mmDHX9-mESC_mm10.narrowPeak


title: B CCB604 (W168 [delta]yacP + pDG-yacP) - IPTG

description:
SLX085-02-v4.604m_complete.xls
SLX085-02-v4.604mvs604p.complete.xls


title: RVKB006C_dotflaA_Myd88_RNA

description: total RNA

value: Bone Marrow Macrophages

tag: strain/genotype

value: dotflaA


title: F3 control-mNPC repB

description:
5’-barcode: CTCTC, 3’-barcode: YRRY
processed data file: F3_control-mNPC_mm10_plus.bigWig
processed data file: F3_control-mNPC_mm10_minus.bigWig

source_name: F3 control-mNPC

value: eGFP


title: D CCB604 (W168 [delta]yacP + pDG-yacP) - IPTG


title: WT_rep2

value: Flicr WT


title: B CCB604 (W168 [delta]yacP + pDG-yacP) + IPTG


title: WT_rep1


title: RVKB006B_flaA_Myd88_RNA

description: total RNA

tag: l. pneumophila infection

value: flaA


title: B SSB1002 (W168 wild-type)


title: A CCB604 (W168 [delta]yacP + pDG-yacP) - IPTG


title: F3 control-mESC repA

description:
5’-barcode: GTATG, 3’-barcode: RYYR
processed data file: F3_control-mESC_mm10_plus.bigWig
processed data file: F3_control-mESC_mm10_minus.bigWig

source_name: F3 control-mESC


title: F3 control-mESC repB

description:
5’-barcode: GTATG, 3’-barcode: YRRY
processed data file: F3_control-mESC_mm10_plus.bigWig
processed data file: F3_control-mESC_mm10_minus.bigWig


title: XL8 IgG-Rb ESC repB

description: 3'-tag: TTAGCC, 3'-RY-space tag: YY

data_processing:
Adapters were trimmed using Flexbar (v2.5).
Libraries were demultiplexed using bctools (https://github.com/dmaticzka/bctools, v0.2.0) and Flexbar (v2.5).
Possible readthroughs into the barcoded regions were removed by clipping 13 nt from the 3'-ends of first mate reads.
Reads were mapped to reference genome hg19 using bowtie2 (v2.2.6) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant --maxins 500.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)) with bctools (https://github.com/dmaticzka/bctools, v0.2.0).
Peaks for DHX9-Rb were called with PEAKachu (https://github.com/tbischler/PEAKachu/, v0.0.1alpha2) using parameters --pairwise_replicates, --max_insert_size 100, -m 0, -n manual, and --size_factors 1 1 0.75 0.75, with the IgG control as experimental background.
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing coordinates of crosslinking event alignments with id of a representative read in name column and number of merged PCR-duplicates in score column. bigWig profiles of crosslinking event alignments for each strand. PEAKachu peaks in gff format.

source_name: embryonic stem cells

treatment_protocol: The feeder-independent mouse male ES cell line WT26 (a kind gift from the lab of T. Jenuwein), was grown on gelatin-coated dishes in ES cell culture media KnockOut-DMEM supplemented with 1% L-glutamine, 1% penicillin/streptavidin, 1% Non- essential amino acids, 1% Sodium Pyruvate, 1% 2-mercaptoethanol. All ESC media contained 15% FBS and 1000 U/ml (for feeder free) or 2000U/ml (for feeder-dependent) of leukemia inhibitory factor (LIF).

value: IgG-Rb (Santa Cruz, sc-2027m lot H2814)


title: A SSB1002 (W168 wild-type)


title: F3 control-mNPC repA

description:
5’-barcode: CTCTC, 3’-barcode: RYYR
processed data file: F3_control-mNPC_mm10_plus.bigWig
processed data file: F3_control-mNPC_mm10_minus.bigWig

data_processing:
Barcodes and random tags were extracted using custom fastqpl scripts (Horton P. fastapl – a utility for versatile and easy processing of fasta format data (and fastqpl for fastq files). F1000Posters 2011, 2:1197 (poster)).
Adapters were trimmed and the library was demultiplexed using Flexbar (v2.32).
Possible readthroughs into the barcoded regions were removed by clipping 10 and 5 nt from the 3’-ends of first and second mate reads.
Reads were mapped to the reference genomes (hg19, mm10, dm3) using bowtie2 (v2.2.0) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant and --maxins=200.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156173 (2013)).
Crosslinking events of M and L size fractions were combined for each biological replicate.
Genome_build: hg19, dm3 or mm10 as indicated
bed files of crosslinking event alignments with random tag in name column and number of merged PCR-duplicates in score column; bigWig profiles of combined L and M fractions for both strands; JAMM peaks in narrowPeak format. BigWig and narrowPeak files are available in a tar archive on the series record. Bed files are available on the sample records.


title: XL8 IgG-Rb ESC repA

description: 3'-tag: TTAGCC, 3'-RY-space tag: RR


title: Nab2_0_deltaRrp6

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

institute: University of Edinburgh

description: Barcode: NNNACTCAGC

data_processing:
Data was preprocessed using the fastx package. All sequences are of the form:
5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNXXXXXX==INSERT==TGGAATTCTCGGGTGCCAAGGCCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG-3’
where NNN are random nucleotides to assess for duplicates in PCR amplification and XXXXXX is a barcode to allow for multiplexing of different libraries. The barcode used for each sample is listed in the 'description' field.
Fastq files were split by barcode using pyBarcodeFilter.py in the pyCRAC package (Webb, et al, 2014). -m 0
Reads were aligned to the genome using Novoalign. -r Random
Reads were counted using pyReadCounter. --sense
Sequences were plotted along the genome using pyGTF2bedgraph
Genome_build: EF4.68
Supplementary_files_format_and_content: bedgraph or bigwig files showing the distribution of reads across the yeast genome

organism: Saccharomyces cerevisiae

source_name: Nab2 0 deltaRrp6

extract_protocol:
Cells were lysed, followed by stringent, denaturing, two-step affinity purification of the tagged protein. Bound RNA was partially degraded with RNase, radiolabeled, and 5’ and 3’ linkers were added. Finally, covalent RNA-protein complexes were isolated by SDS-PAGE. Following Proteinase K digestion of the bound proteins, RNA fragments were amplified by RT-PCR.
RNA libraries were prepared using the standard CRAC protocol (Tuck and Tollervey, 2013)

tag: sample type

value: crosslinked RNA


title: Nab3_4_replicate1

description: Barcode: NNNATTAGC

source_name: Nab3 4


title: A CCB604 (W168 [delta]yacP + pDG-yacP) + IPTG


title: XL9 DHX9-Rb rep A

description: 3'-tag: CAAGTG, 3'-RY-space tag: RR

source_name: neural progenitor cells

growth_protocol: Mouse ES cells were differentiated into neuronal progenitor cells. In brief, ESC (1x106 cells) were deprived of feeders and plated on 0.1 % gelatin-coated dishes in N2B27 medium and grown for 7 days. During that period of time, the medium was changed every day. Next, cells were dissociated from the plate using accutase and approximately 3 x 10e6 cells were plated in a petri dish to induce formation of embryoid bodies (in N2B27 medium supplemented with 10 ng/ml EGF and FGF2). After 72 hours, embryoid bodies were transferred to 0.1 % gelatin-coated dishes and allowed to attach to the bottom leading to expansion of NPC cells. NPC lines were maintained in N2B27 medium supplemented with EGF and FGF2 (10ng/ml each), on 0.1 % gelatin- coated flasks.

treatment_protocol: The feeder-independent mouse male ES cell line WT26 (a kind gift from the lab of T. Jenuwein), was grown on gelatin-coated dishes in ES cell culture media KnockOut-DMEM supplemented with 1% L-glutamine, 1% penicillin/streptavidin, 1% Non- essential amino acids, 1% Sodium Pyruvate, 1% 2-mercaptoethanol. All ESC media contained 15% FBS and 1000 U/ml (for feeder free) or 2000U/ml (for feeder-dependent) of leukemia inhibitory factor (LIF). NPC lines were derived from previously mentioned ES cell lines and cultured in N2B27 medium (StemCell Sciences) containing 10 ng/mL EGF and FGF (Preprotech) on gelatin-coated flasks. The cells were kept in a humidified incubator at 37°C and 5% CO2 and were passed when reaching 80-90% confluency.

tag: cell type

value: ES-derived neural progenitor cells


title: XL9 IgG-Rb rep A

description: 3'-tag: TTAGCC, 3'-RY-space tag: RR

tag: cell line


title: XL9 DHX9-Rb rep B

description: 3'-tag: CAAGTG, 3'-RY-space tag: YY

tag: clip antibody


title: XL8 DHX9-Rb ESC repA

description: 3'-tag: CAAGTG, 3'-RY-space tag: RR


title: XL9 IgG-Rb rep B

description: 3'-tag: TTAGCC, 3'-RY-space tag: YY


title: Rpo21_4_replicate2

description: Barcode: NNNCTAGC

source_name: Rpo21 4


title: Rpo21_4_replicate1

description: Barcode: NNNTAAGC


title: Rpo21_0_mock

description: Barcode: NNNTCTCTAGC

source_name: Rpo21 0 mock


title: wild type root tip repeat2

first: shaoli

last: zhou

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
For RNA-seq, Tophat (version 2.0.13) was used to align the clean tags filtered by Trimmomatic (version 0.32) to the reference genome of Niponbarre (version 7.0). Cufflink (version 2.2.1) suite was used for identification of differentially expressed genes.
Genome_build: RGAP version 7.0
Supplementary_files_format_and_content: tab-delimited text file of output of Cufflink software. Files with suffix "fpkm_tracking" represent RPKM value of all genes in each sequencing data.

organism: Oryza sativa Japonica Group

source_name: root tip

growth_protocol: Rice (Oryza sativa spp japonica) material for transformation of OsGCN5 RNAi and over-expression vectors used in this study is from ‘ZhongHua11’ (ZH11) background. Transgenic plants of T3 segregating population from multiple lines were used for genotypic and phenotypic analysis. For germination culture, seeds were surface-sterilized and germinated in medium containing 0.8% agar supplemented with 3% (w/v) sucrose at 28°C (in light) and 24°C (in dark) with a 14-h-light/10-h-dark cycle. Whole roots or root tips were harvested at the 5th day (after germination). For growth in field, germinated rice seedling was transplant in field at the beginning of May in Wuhan area, seeds were harvested in September.

extract_protocol:
The total RNA samples of 3-5mm root tip or whole root tip were isolated using TRIzol reagent (Invitrogen) from OsGCN5 RNAi and corresponding wild type Zhonghua11. The total RNA was extracted using TRIzol reagent, purified with phenol chloroform mixture, and precipitated by 2 volume alcohol.
RNA libraries were prepared according to the Illumina RNA-seq library construction protocol strictly.  Briefly, 5 μg of total RNAs was used for mRNA purification, first strand cDNA systhesis, second strand cDNA systhesis, 3' end of blunt double strand cDNA ligated with "A" nuleotide, index primers ligation, low cycle PCR amplyfication, and double-strand DNA purification.

tag: tissue

value: 3-5 mm root tip from 5 day seedling

tag: cultivar


title: B CCB375 (W168 [delta]yacP)

value: CCB375 (W168 [delta]yacP)


title: KO_rep1


title: wild type root tip repeat1


title: OsGCN5 RNAi root tip repeat2


title: OsGCN5 RNAi root tip repeat1


title: XL8 DHX9-Rb ESC repB

description: 3'-tag: CAAGTG, 3'-RY-space tag: YY


title: A CCB375 (W168 [delta]yacP)


title: Nab2_0_wt

description: Barcode: NNNCTAGC

source_name: Nab2 0 wt


title: wild type whole root repeat2

description: GCN5_RNAi_vs_WT_whole_root_gene_exp.diff

source_name: root

value: root from 5 day seedling


title: Mtr4_0_mock

description: Barcode: NNNTAAGC

source_name: Mtr4 0 mock


title: OsGCN5 RNAi whole root repeat1


title: OsGCN5 RNAi whole root repeat2


title: Input control

status: Public on Mar 27 2017

city: Washington

first: Ray-Chang

last: Wu

state: DC

address: 2300 I St, NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm9) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: [.bed] MACS peaks file in text format.

source_name: Testes, input

growth_protocol: standard chow

extract_protocol:
Testis lysates were clarified from sonicated nuclei and the ARID4B-DNA complexes were isolated with the anti-ARID4B antibody (CAT#: A302-233A, LOT#: A302-233A-1, Bethyl Laboratories).
Libraries were prepared for sequencing using standard Illumina protocols

value: hybrid C57BL6/J and 129/SvEv

value: wild type

tag: age

value: postnatal day 1.5

value: Testes


title: ddx39a_24hpf_RNAseq

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

data_processing:
Illumina bcl2fastq2-v 2.16.0.10 software was used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters -q -p 8 --no-novel-juncs -G -o.
Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: embryos

extract_protocol:
24hpf zebrafish embryos were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Magnetic beads with oligo(dT) were used to enrich the mRNAs, and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first-strand cDNA. Then double-stranded cDNA was synthesized by adding buffer solution, dNTPs and DNA polymeraseΙ. The double-stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions, then repaired at the tail ends, poly(A) added and enriched by PCR amplification. Finally, we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.

value: ddx39a mutant

value: embryo

tag: developmental stage


title: WT_24hpf_RIPseq

extract_protocol:
Microinjection ddx39a-Flag mRNA in ddx39a mutant embryos at one-cell stage. Lysates were clarified from 24hpf embryos were isolated with anti-Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
Magnetic beads with oligo(dT) were used to enrich the mRNAs, and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first-strand cDNA. Then double-stranded cDNA was synthesized by adding buffer solution, dNTPs and DNA polymeraseΙ. The double-stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions, then repaired at the tail ends, poly(A) added and enriched by PCR amplification. Finally, we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.


title: BN3

city: Moscow

first: Anastasia

last: Nikitina

address: Malaya Pirogovskaya

department: Department of Molecular Biology and Genetics

country: Russia

institute: Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia

data_processing:
Basecalling was performed by Torrent Suite 5.0 fastqCreator v3.4.56313 BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --phasing-residual-filter=20 -max-phasing-levels 2
Reads filtering was carried out by Cutadapt -q 15 -m 25
Reads were then mapped to human genome version hg19 using STAR.
Genomic coordinates of genes encoding ribosomal RNAs were combined in one .bed file and intersectBed was used to remove from .bam files all aligned reads corresponding to these genes.
HTSeq was used to count the number of reads mapping to a particular gene.
Genome_build: hg19 Gencode Release 19 (GRCh37.p13)
Supplementary_files_format_and_content: *txt: Each tab-delimited text file includes raw read counts corresponding to a particular gene represented by its Ensembl ID (Release 19 (GRCh37.p13)) for a given sample.

source_name: normal prostate tissue, PCa patient

extract_protocol:
AllPrep DNA/RNA FFPE Kit (Qiagen) and RNeasy FFPE kit (Qiagen) were used according to manufacturer's instructions to extract RNA from FFPE samples. DNA contaminations were removed with the use of DNase I (Fermentas) following the manufacturer's recommendations.
Transcriptome libraries were constructed using Ion Total RNA-seq Kit v2 (Life Technologies) with the following modifications of the protocol. For RNA fragmentation, 1 ul of 10x RNase III buffer (Life Technologies) was added to 9 ul of RNA solution and heated for 10 min at 95 ˚С followed by immediate snap-cooling on ice. After that, 1 ul of 10 uM ATP and 1 ul of polynucleotide kinase (Fermentas) were added to the solution from the previous step and the whole mix was incubated at 37˚С for 30 min. The fragmented RNA was cleaned up using Micro Bio-Spin Chromatography Columns (Bio-Rad). Further steps of library preparation including adapter ligation, first-strand cDNA synthesis and amplification were carried out in accordance with the manufacturer's instructions.

tag: diagnosis

value: prostate cancer

value: normal prostate tissue

tag: age at operation

tag: psa level (ng/ml)

tag: gleason sum

tag: primary gleason score

tag: secondary gleason score

tag: extraprostatic invasion

value: no

tag: population

value: Russian

tag: patient identifier


title: WT_24hpf_RNAseq

tag: genotype


title: ARID4B ChIP-Seq

source_name: Testes, ChIP fraction

tag: strain

tag: chip antibody

value: anti-ARID4B antibody (CAT#:A302-233A, LOT#:A302-233A-1,Bethyl Laboratories)


title: BP2

source_name: adenomatous prostate tissue, BPH patient

value: benign prostatic hyperplasia

value: adenomatous prostate tissue

value: not applicable


title: BN1

source_name: normal prostate tissue, BPH patient


title: BP3

source_name: tumorous prostate tissue, PCa patient

value: tumorous prostate tissue


title: BP1


title: CP15


title: CN14


title: CP14


title: CN12

value: yes


title: CP13


title: CN10


title: CP12


title: CP11


title: CP10


title: wild type whole root repeat1

value: root from 5 day seedling


title: CN9


title: CN8


title: CP9


title: CP8


title: CN15


title: CN7


title: CN6


title: CP7


title: CP6


title: CN5


title: CP5


title: CP2