title: Kc, GFP RNAi, Replicate2 (START-Seq)

description: nuclear total RNA


title: HDAC2 5-2

status: Public on Oct 31 2017

type: SRA

city: Davis

first: Paul

last: Knoepfler

state: CA

address: 1 Shields Ave

department: Cell Biology and Human Anatomy

country: USA

institute: UC Davis School of Medicine

library_source: transcriptomic

data_processing:
 illumina bclfastq 2.16.0 version for pipeline
TopHat v2.0.14, library-type fr-firststrand
Reads were counted and organized into a matrix using bioconductor package "summarizeOverlaps"
EdgeR (edgeR_3.14.0) was used to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Text files with differentially expressed genes, log fold change, p-value, and FDR

molecule: total RNA

organism: Homo sapiens

source_name: 293FT HEK cells

growth_protocol: Cells were grown using standard cell culture techniquesin DMEM supplemented with 10% FBS and 1% L-glutamine

extract_protocol:
Total RNA was isolated from cells at 60-70% confluence utilizing the Nucleospin RNA kit (Macherey-Nagel, Ref #740955.5)
KAPA mRNA stranded kit (KK8401, Roche Catalog07962169001) for library preparation with poly-A enrichment

treatment_protocol: 293FT cells were transfected with guide RNA expressing plasmids targeting the first ATG of the HDAC2 gene, followed by puromycin selection to obtain clonal lines of HDAC2-null cells.

tag: cell line


title: Kc, CLAMP RNAi, Replicate2 (START-Seq)

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description: nuclear total RNA

data_processing:
Library strategy: Start RNA-seq
Analysis for Start-seq was performed as previously described (REF# 24: Science 2010;327: 335–8)
Alignment: Sequence reads were obtained, trimmed to 26nt starting at the 5'-most nucleotide and mapped to the Drosophila melanogaster DM3 genome using the MOM maximum oligonucleotide mapping tool.
All unique reads mapping with two or fewer mismatches were retained. Reads from biological replicates were merged and formatted to .bedgraph format for Forward and Reverse stands.
Genome_build: dm3
Supplementary_files_format_and_content: Reads from biological replicates were merged and formatted to .bedgraph format for Forward and Reverse stands.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Kc, CLAMP RNAi

growth_protocol: Drosophila S2 and Kc cells were maintained at 25°C in Gibco Schnieder’s Drosophila media supplemented with 10% heat-inactivated Fetal Bovine Serum and 1.4X Antibiotic-Antimycotic. Cells were passaged every 2-3 days to maintain appropriate cell density.

extract_protocol:
Total RNA was extracted from isolated nuclei using a standard TRIzol extraction following the manufacturer's directions.
Sequencing libraries were prepared generally according to the Ilumina TruSeq small RNA kit. A detailed protocol is available in Nechaev, S. et al. (2010).

treatment_protocol: RNAi for gfp or clamp was performed in T75 tissue culture flasks using a total of either 1.2x10^7 S2 or Kc cells. The cells were first suspended in 6mLs of Gibco Schenieder’s Drosophila media without FBS and added to a T75 tissue culture flask containing 135μg dsRNA in 3mL ultra pure water. The cells were serum starved at room temperature for 45 minutes before the addition 6mLs of Gibco Schneider’s Drosophila media supplemented with 10% FBS to the flask containing the dsRNA and cells. Cells were incubated for 6 days and upon collection efficiency of the RNAi treatment was determined before performing Start-sequencing.

tag: genotype

value: wild type

tag: treatment

value: clamp RNAi

tag: time

value: 6 days post RNAi incubation

tag: cell type

value: Kc


title: S000980.l.rs.lib

city: Lund

first: Carlos

last: Rovira

address: Medicon Village, Byggnad 404

department: Department of Clinical Sciences, Lund

country: Sweden

institute: Lund University

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard.
Alignment was done against hg38 using Novoalign with settings -a TGGAATTCTCGGGTGCCAAGG -l 14 -h -1 -1 -t 90 -g 50 -x 15 -o SAM -o FullNW -r All 51 -e 51
MicroRNA expression was analyzed using custom Perl scripts and calculated as counts per million miRNA reads (cpm).
FusionCatcher version 0.99.4b16 was used to search RNA-seq data for chimeric transcripts with the --highly-sensitive option and all aligners (blat, star, bowtie2, and bwa)
Genome_build: Human genome reference GRCh38/hg38.

source_name: Primary breast tumour

extract_protocol:
TRIzol LS
Small RNA sequencing libraries were prepared from 500 ng total RNA using a protocol analogous with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), but with custom adapters to incorporate dual indexes. Pooled libraries were sequenced on a NextSeq 500 with High Output v2 75 cycle-kits (Illumina)

tag: scan-b external id

tag: sample fullname

tag: er-status

value: ER+


title: HDAC2 5-1


title: EC_DSS_TSO_3

city: Zurich

first: Isabelle

last: Frey-Wagner

address: Raemistr. 100

department: Division of Gastroenterology

country: Switzerland

institute: University hospital Zurich

description:
6-3_EC
EC_DSS_TSO_3
result--EC_DSS_TSO--over--EC_Control.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Quality assessment based on the remaining reads using the FASTQC quality control tool version 0.10.
Genome_build: Ensembl OryCun2.0
Supplementary_files_format_and_content: tab-delimited text file include Identifier log2 Ratio pValue fdr for each group
Supplementary_files_format_and_content: normalized abundance measurement

organism: Oryctolagus cuniculus

source_name: Epithelial cells

extract_protocol:
Caecal lamina propria mononuclear cells (LPMC) and epithelial cells (EC) were isolated for RNA extraction. Total RNA was isolated with the Qiacube system using the RNeasy Mini Kit with DNase digestion
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-polyA-unstranded. Read type: single-end-100bp

value: TSO

tag: colitis

value: DSS

tag: time point


title: S001090.l.rs.lib

value: ER-


title: 293FT WT-3


title: S000824.l.rs.lib


title: 293FT WT-2


title: EC_DSS_TSO_2

description:
6-2_EC
EC_DSS_TSO_2
result--EC_DSS_TSO--over--EC_Control.txt


title: EC_DSS_TSO_1

description:
6-11_EC
EC_DSS_TSO_1
result--EC_DSS_TSO--over--EC_Control.txt


title: S000642.l.rs.lib


title: 293FT WT-1


title: EC_DSS_Vehicle_3

description:
6-7_EC
EC_DSS_3
result--EC_DSS--over--EC_Control.txt

value: Vehicle


title: S000297.l.rs.lib


title: S000416.l.rs.lib


title: EC_DSS_Vehicle_1

description:
6-1_EC
EC_DSS_1
result--EC_DSS--over--EC_Control.txt


title: S000264.l.rs.lib


title: S000365.l.rs.lib


title: EC_Control_Vehicle_3

description:
6-8_EC
EC_Control_3
result--EC_DSS--over--EC_Control.txt

value: Control


title: EC_Control_Vehicle_2

description:
6-4_EC
EC_Control_2
result--EC_DSS--over--EC_Control.txt


title: S000342.l.rs.lib


title: EC_DSS_Vehicle_2

description:
6-12_EC
EC_DSS_2
result--EC_DSS--over--EC_Control.txt


title: EC_Control_Vehicle_1

description:
6-15_EC
EC_Control_1
result--EC_DSS--over--EC_Control.txt


title: S000039.l.rs.lib


title: S000036.l.rs.lib


title: Kc, GFP RNAi, Replicate1 (START-Seq)

description: nuclear total RNA

source_name: Kc, GFP RNAi

value: gfp RNAi


title: Root replicate 3

city: Vestec

first: Derek

last: Wilkinson

address: Prumyslova 595

department: Genetics and Microbiology

country: Czech Republic

institute: Charles University

data_processing:
Reads mapped to custom transcriptome (created by combining loci from S. cerevisiae build R64 [Ensembl release 76, (Yates et al., 2016)] and lncRNA loci from Xu et al. (2009), Yassour et al. (2010), Lardenois et al. (2011), Van Dijk et al. (2011) and Neil et al. (2009)) and to the yeast genome  using TopHat v2.0.14 (Trapnell et al., 2012)
Reads mapping to indivual loci counted using the feature Counts (Liao et al., 2014) function from the Rsubread package, v1.22.2, from Bioconductor
Differential expression analysis carried out using DESeq2 v1.12.3 (Love et al., 2014), within the R environment, version 3.3.1
Further analysis carried out in Excel
Genome_build: R64 [Ensembl release 76, (Yates et al., 2016)]
Supplementary_files_format_and_content: text (tab-delineated) : raw read counts per locus and per sample replicate

organism: Saccharomyces cerevisiae

source_name: biofilm colonies_root cell subpopulation

growth_protocol: Cells of the BR-F strain were spread over a 47 mm pore, polycarbonate membrane laid over low-agar  GMA (3 % glycerol, 1 % yeast extract, 0.3 % agar)  at densities of 2x103-3x103 per plate and microcolonies were grown at 28 °C for 3 days.

extract_protocol:
Membrane removed gently and aerial cells frozen in liquid nitrogen. Root cells plus contaminating agar vortexed and centrifuged in 1.5 mL tubes at 20,000 g at 22 °C for 5 min then cells harvested by snipping off bottom of tube. Cell pellet frozen in liquid nitrogen. Biomass suspended in 400 μl TES buffer (10 mM Tris pH 7.5, 10 mM EDTA, 0.5% SDS) and total RNA extracted by hot phenol method.
rRNA depleted using Ribo-zero Gold (yeast) kit and rRNA-depleted RNA purified using Agencourt RNA CleanXP kit. cDNA library prepared using Truseq stranded total RNA library prep kit with 15 cycles of PCR and clean-up steps using Agencourt AMPure XP beads.

tag: strain

value: BR-F

value: differentiated yeast biofilm colonies

tag: cell subtype

value: root cell subpopulations

tag: age

value: 3 day old colonies


title: S000034.l.rs.lib


title: S004462.l.rs.lib


title: S000009.l.rs.lib


title: S004446.l.rs.lib


title: Aerial replicate 2

source_name: biofilm colonies_aerial cell subpopulation

value: aerial cell subpopulations


title: Aerial replicate 1


title: S001609.l.rs.lib


title: S001471.l.rs.lib


title: S001210.l.rs.lib


title: WT-rep3

city: Shanghai

first: Zhe

last: Xie

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiaotong University

data_processing:
Illumina HCS (1.5.15.1) software and RTA (1.13.48.0) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WP3 whole genome using SOAPaligner/soap2 (Release 2.21)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Audic, S. et al., Genome Res Research, 1997.
Genome_build: ASM1488v1
Supplementary_files_format_and_content: abundance measurements

organism: Shewanella piezotolerans WP3

source_name: WP3_ancestor wild type

growth_protocol: Grow culture under 4˚С and 20 MPa till maximum growth yield with three replicates. Harvest cells via centrifugation at 4˚С. Remove the residual liquid by pipetting. Cell pellets were immediately stored in RNAlater.

extract_protocol:
Total RNA were extracted using TRIzol Reagent according the manufacturer’s instructions (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: ancestor WT strain


title: OE100-rep1

source_name: WP3_evolved H2O2-stressed strain OE100

value: evolved H2O2-stressed strain OE100


title: OE100-rep2


title: OE100-rep3


title: S001224.l.rs.lib


title: S000544.l.rs.lib


title: S000524.l.rs.lib


title: S001054.l.rs.lib


title: EC_Control_TSO_1

description:
6-10_EC
EC_TSO_1
result--EC_TSO--over--EC_Control.txt


title: WT-rep2


title: Root replicate 2


title: Root replicate 1


title: Aerial replicate 3


title: S000397.l.rs.lib


title: S000316.l.rs.lib


title: S001394.l.rs.lib2


title: S001394.l.rs.lib


title: S000019.l.rs.lib


title: WT-rep1


title: S001197.l.rs.lib


title: S000928.l.rs.lib


title: S001200.l.rs.lib


title: S002193.l.rs.lib


title: S000373.l.rs.lib


title: Kc, CLAMP RNAi, Replicate1 (START-Seq)

description: nuclear total RNA

value: wild type

value: clamp RNAi


title: S000359.l.rs.lib2


title: S000275.l.rs.lib


title: S000359.l.rs.lib


title: S000045.l.rs.lib


title: S000046.l.rs.lib


title: S004308.l.rs.lib


title: S000109.l.rs.lib


title: Control #4 WGBS

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive, ASRC 164

department: Animal Sciences

institute: University of Missouri, Columbia

description: Day ~105 Bos indicus taurus × Bos taurus taurus F1 fetal skeletal muscle

library_source: genomic

data_processing:
The Cutadapt program (version: 1.9.1) was used to remove the adaptor sequences in the read pairs.  For base quality trimming, DynamicTrim (version 3.1) was used to obtain the longest segment of the read in which each base has <1% error rate.
WGBS read pairs were aligned to the bovine reference genome assembly UMD3.1 and the Lambda genome using Bismark (version: 0.15.0) with default parameters. Only uniquely aligned read pairs that had the expected read mate orientation and expected ranges of insert size were retained for further analyses.
Bis-SNP (version: 0.82.2) was used to perform the SNP calling using the WGBS data. Only CpG site that show consensus CpG context for both parental alleles (i.e., do not overlap any SNPs identified by Bis-SNP) were used for the subsequent analyses.
As CpG methylation is symmetric, the methylation level was determined using the reads from both forward and reverse strands covering the same symmetric CpG site.  The methylation level was calculated as: (number of “C” reads)/(number of “C” reads + number of “T” reads).
For most analyses, only CpGs covered by at least by five reads were used for the calculation of the methylation level.  The exception is the allele-specific methylation analyses, in which only CpGs covered at least by 8 reads (four reads per parental allele) were included for the statistical test.  For reads with PCR duplicates, only one of them was randomly choosed for the determination of the methylation level.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Bigwig files were generated using "bedGraphToBigWig" from UCSC genome browser. Scores represent the ratios of methylated CpGs except for the "Fisher_exact_test_p-value.bw" which represent the significance of allele-sepcific DNA methylation

molecule: genomic DNA

organism: Bos indicus x Bos taurus

source_name: Control, day ~105 conceptus

extract_protocol:
DNA were isolated using the phenol-chrolorform method
For whole genome bisulfite sequencing (WGBS) library preparation, 1μg bovine DNA was subject to sodium bisulfite mutagenesis using NEB EpiMark Bisulfite Conversion Kit (NEB E3318) according to the manufacturer’s instructions.  Prior to the sodium bisulfite reaction, 5ng (0.5%) unmethylated cl857 Sam7 Lambda DNA (48,502bp, Promega D1521) was combined with bovine DNA to act as an internal control to monitor the bisulfite conversion rate. The WGBS libraries were generated using the NEBNext Ultra DNA library Prep Kit for Illumina (NEB E7370) as per the manufacturer’s instructions.

tag: tissue

value: fetal skeletal muscle

tag: condition


title: S000062.l.rs.lib


title: S004321.l.rs.lib


title: S002573.l.rs.lib


title: S002607.l.rs.lib


title: S002712.l.rs.lib

value: ER+


title: S004225.l.rs.lib


title: S002493.l.rs.lib


title: S002559.l.rs.lib


title: S002276.l.rs.lib


title: S001152.l.rs.lib


title: S001385.l.rs.lib


title: S002353.l.rs.lib


title: S002448.l.rs.lib


title: S002463.l.rs.lib


title: S000695.l.rs.lib


title: S002065.l.rs.lib


title: S001151.l.rs.lib


title: S001168.l.rs.lib


title: S001118.l.rs.lib


title: S004562.l.rs.lib


title: S000927.l.rs.lib2


title: E234P_a

city: Wuhan

first: Tao

last: Liu

state: Hubei

address: Shizishang Street No.1

institute: State Key Laboratory of Agricultural Microbiology

description:
Processed data file: fpkm.xls
Processed data file: OE3avsE234p_up.xls
Processed data file: OE3avsE234p_down.xls

data_processing:
Illumina Casava HiSeqX HD 3.4.0.38 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the cleandata were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S.L. Salzberg, 2012).
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: S. islandicus REY15A (accession no. NC_017276.1)
Supplementary_files_format_and_content: fpkm.xls: Excel file includes FPKM values for each sample.
Supplementary_files_format_and_content: OE3a_vs_E234p_up.xls: Excel file
Supplementary_files_format_and_content: OE3a_vs_E234p_down.xls: Excel file
Supplementary_files_format_and_content: Dcas1OE3a_vs_Dcas1P_up.xls: Excel file
Supplementary_files_format_and_content: Dcas1OE3a_vs_Dcas1P_down.xls: Excel file
Supplementary_files_format_and_content: Dcas3cmr2alphacmr2betaOE3a_vs_Dcas3cmr2alphacmr2betaP_up.xls: Excel file
Supplementary_files_format_and_content: Dcas3cmr2alphacmr2betaOE3a_vs_Dcas3cmr2alphacmr2betaP_down.xls: Excel file

organism: Saccharolobus islandicus REY15A

source_name: wild type, pSeSD plasmid

growth_protocol: Strains were cultured in ACVy medium at 78°C to log phase (OD600=0.3).

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. rRNA is removed using a specialized kit that leaves the mRNA. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 μl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.

value: wild type with pSeSD plasmid

tag: cell growth phase

value: log phase


title: E234P_b


title: OE3a_b

source_name: wild type, pCsa3a plasmid

value: wild type with pCsa3a plasmid


title: S000927.l.rs.lib

value: ER-


title: S000893.l.rs.lib


title: OE3a_a


title: S001544.l.rs.lib


title: S000861.l.rs.lib


title: S000969.l.rs.lib


title: S000832.l.rs.lib


title: S000802.l.rs.lib


title: S000590.l.rs.lib


title: S000520.l.rs.lib


title: S000352.l.rs.lib


title: S000357.l.rs.lib


title: S000629.l.rs.lib


title: S000017.l.rs.lib


title: S001130.l.rs.lib


title: S000606.l.rs.lib


title: S002373.l.rs.lib


title: S001095.l.rs.lib


title: S000304.l.rs.lib


title: S000127.l.rs.lib


title: S001459.l.rs.lib


title: S001167.l.rs.lib


title: S000131.l.rs.lib


title: S000950.l.rs.lib


title: S000633.l.rs.lib


title: S000561.l.rs.lib


title: s067r

city: Hamburg

first: Stefan

last: Scholten

address: Ohnhorststrasse 18

department: Biocenter Klein Flottbek

country: Germany

institute: University of Hamburg

description: sRNA_115maize_lines_rpmqn_min1_line1.csv

data_processing:
Illumina software used for basecalling and demultiplexing
Sequenced reads were trimmed for adaptor sequence with trimgalore using the following parameters. trim_galore --clip_R1 4 --three_prime_clip_R1 4.
After adapter removal the reads were trimmed to 99.9% sequencing quality and all sequence reads ranging from 15-nt to 40-nt were retained.
The raw read counts were quantile normalized according to Bolstad et al. (2003,Bioinformatics 19, 185–193) with a modification preventing the allocation of read counts to sequence tags not expressed in the sample.
The normalized read counts were scaled to one million reads per library resulting in read counts per million quantile normalized (rpmqn) reads
Supplementary_files_format_and_content: space-delimited text file include rpmqn values for each sample

organism: Zea mays

source_name: whole seedling

growth_protocol: Seeds of all lines were laid out in a completely randomized design with one seed per entry and grown for seven days under controlled conditions (25°C 16 h day, 21°C 8 h night, 70% air humidity) in a climate chamber. For each entry four biological replicates were grown.

extract_protocol:
Total RNA was isolated with mirVana miRNA isolation kit (Ambion, Thermo Scientific).
Illumina-compatible sequencing libraries were generated using the NEXTflex Small RNA Sequencing Kit v2 (BIOO SCIENTIFIC) and following the manufacturers recommendations with 1 µg total RNA. Libraries were sequenced on an Illumina HiSeq 4000 with 50 bp single end reads.

treatment_protocol: All plants were grown in identical conditions. The biological replicates were pooled before homogenization.

tag: developmental stage

value: 7 days after sowing

tag: genotype

value: whole seedling


title: S000391.l.rs.lib


title: s067


title: FUS_P525L_6

city: Rome

first: Alessandro

last: Rosa

address: P.le Aldo Moro 5

department: Biology and Biotechnology Charles Darwin

country: Italy

institute: Sapienza University of Rome

data_processing:
Base-Calling with Casava.
RNA-Seq reads were initially trimmed using the Trimmomatic software to remove adapter sequences and poor quality bases; the minimum read length after trimming was set to 18.
Bowtie 2 was used to align reads to human rRNA sequences; reads mapping to these sequences were filtered out. In order to calculate the distribution of the inner distance between mate pairs, reads were aligned to a non-redundant set of human RNA sequences derived from Ensembl 77 gene annotation  using BWA software. Mean and variance of inner distance distribution were estimated from aligned read pairs whose inner distance was within interval [Q1-2(Q3-Q1),[Q3+2(Q3-Q1)]] (Q1=first quartile, Q3=third quartile). TopHat2 was employed to align reads to GRCh38 human genome and Ensembl transcriptome using parameters -i 50 -r -32 --mate-std-dev  58 --library-type fr-firststrand.
Read counts for Ensembl 77 human genes were calculated using htseq-count software, specifying the intersection-strict option. edgeR software was used to find differentially expressed genes in GFP-positive vs GFP-negative and FUS_WT vs FUS_P525L comparisons. In both cases, TMM normalization was applied to read counts after filtering genes with a CPM (Count Per Million) value less than 1 in at least three (in GFP-positive vs GFP-negative comparison) or four (in  FUS_WT vs FUS_P525L comparison) samples. For FUS_WT vs FUS_P525L comparison an additive model was fitted to adjust for baseline differences between the three independent differentiation experiments: design <- model.matrix (~ experiment + condition). Model fitting and testing was performed using glmFIT and glmLRT functions.
Genome_build: GRCh38
Supplementary_files_format_and_content: text files containg per sample gene RPKMs
Base-Calling with Casava.
mirPRo software was used to remove adapter sequences, map reads to human pre-miRNA sequences downloaded from mirBase v21 using NovoAlign, and calculate read counts for mature miRNAs.
Starting from the raw counts, sample clustering and differential expression of mature miRNAs were performed using the same procedure adopted for FUS_WT vs FUS_P525L comparison.
Genome_build: miRBase v21 human miRNAs.
Supplementary_files_format_and_content: text files containg per sample miRNA CPMs

source_name: Motoneurons day12+7

growth_protocol: Generation of iPSCs is described in Lenzi et al. (2015; Disease Models and Mechanisms 8:755-766)

extract_protocol:
TruSeq Small RNA Library Prep Kit
Total RNA was extracted with the Quick RNA MiniPrep (Zymo Research)

treatment_protocol: Cells were differentiated to motoneurons in presence of RA and SAG for 12 days (day12), then sorted according to an Hb9::GFP reporter and cultured for additional 7 days (day12+7)

value: iPSC-derived motoneurons

tag: days of differentiation


title: s058r


title: FUS_P525L_4

tag: cell type


title: FUS_P525L_5


title: S004350.l.rs.lib

tag: scan-b external id


title: S000251.l.rs.lib

tag: sample fullname


title: s058


title: s050


title: S002657.l.rs.lib

tag: er-status


title: S002554.l.rs.lib


title: s049


title: FUS_WT_5

value: FUS-WT


title: FUS_WT_6


title: S002498.l.rs.lib


title: FUS_WT_4


title: S002296.l.rs.lib


title: S002473.l.rs.lib


title: s046


title: FUS_P525L_3

extract_protocol:
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero treatment
Total RNA was extracted with the Quick RNA MiniPrep (Zymo Research)


title: S002245.l.rs.lib


title: FUS_P525L_2


title: s044


title: s036


title: S002117.l.rs.lib


title: S000057.l.rs.lib


title: FUS_P525L_1


title: S002116.l.rs.lib


title: s028


title: s018


title: S001555.l.rs.lib


title: FUS_WT_1


title: s049r


title: FUS_WT_3


title: FUS_WT_GFP-Negative_2

source_name: Neuronal cells Hb9::GFP negative day15

value: iPSC-derived neuronal cells (non-motoneurons)


title: s002


title: S001554.l.rs.lib


title: FUS_WT_2


title: s016


title: FUS_WT_GFP-Negative_1

source_name: Neuronal cells Hb9::GFP negative day14


title: S001467.l.rs.lib


title: s015


title: p312


title: FUS_WT_GFP-Positive_1

source_name: Motoneurons Hb9::GFP positive day12


title: S001437.l.rs.lib


title: p330


title: p302


title: S001380.l.rs.lib


title: S001207.l.rs.lib


title: Wild type differentiation day 4

city: Bethlehem

first: Ashvin

last: Iyer

state: Pennsylvania

address: 1325B Johnston Drive

department: Pharmaceutical Sciences

institute: University of the Sciences

description:
[processed data files:]
WT vs Emerin null day 4 differentiation.xlsx
WT differentiation day 3 to 4 transition.diff
WT proliferation vs day 4 differentiation.diff

data_processing:
Quality control of raw sequence was performed with FastQC.
Reads were mapped to the mouse genome (mm10) with Tophat according to established protocols
Differential expression analysis was done using Cuffdiff according to established protocols.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files include expression values for individual genes for Wildtype and emerin-null myogenic precursor cells during proliferation and different days of differentiaton. They also include log2 fold change value for each gene in emerin-null myogenic precursors compared with respect to wildtype myogenic precursor cells and P-values for statistical significance. Cuffdiff files contain similar information using different samples for each analysis.

organism: Mus musculus

source_name: Wildtype H2K myogenic precursor cells

growth_protocol: Proliferating myogenic progenitors  were cultured in plates coated with gelatin at 37°C and 10% CO2 in DMEM containing 20% HI-FBS, 2% L-glutamine, 2% Chick embryo extract , 1% Pen/Strep and 20 units/ml γ-interferon . Differentiating cells were cultured in plates coated with gelatin in proliferative conditions for 24 h, then switched to differentiation media consisting of DMEM supplemented with 5% horse serum and 2% L-glutamine and grown at 37°C and 5% CO2.

extract_protocol:
Qiagen miRNeasy mini kit/ Qiazol according to manufacterer's instructions
Library construction and sequencing was performed using the Illumina HiScan-SQ  at Functional Genomics Facility at The University of Chicago.

treatment_protocol: Cells were collected according to miRNeasy mini kit/ Qiazol protocol

tag: cell line

value: myogenic precursor cells

value: wildtype


title: FUS_WT_GFP-Positive_2

source_name: Motoneurons Hb9::GFP positive day13


title: S001206.l.rs.lib

source_name: Primary breast tumour


title: S001192.l.rs.lib


title: p291


title: p299


title: p290


title: S001505.l.rs.lib


title: Wild type differentiation day 3

description:
[processed data files:]
WT vs Emerin null day 3 differentiation.xlsx
WT differentiation day 2 to 3 transition.diff
WT differentiation day 3 to 4 transition.diff
WT proliferation vs day 3 differentiation.diff


title: Wild type differentiation day 2

description:
[processed data files:]
WT vs Emerin null day 2 differentiation.xlsx
WT differentiation day 1 to 2 transition.diff
WT differentiation day 2 to 3 transition.diff
WT proliferation vs day 2 differentiation.diff


title: Wild type differentiation day 1

description:
[processed data files:]
WT vs Emerin null day 1 differentiation.xlsx
WT differentiation day 0 to 1 transition.diff
WT differentiation day 1 to 2 transition.diff
WT proliferation vs day 1 differentiation.diff


title: S001146.l.rs.lib


title: p284


title: S001122.l.rs.lib


title: Wild type differentiation day 0

description:
[processed data files:]
WT vs Emerin null day 0  differentiation.xlsx
WT proliferation to day 0 differentiation transition.diff
WT differentiation day 0 to 1 transition.diff


title: S001080.l.rs.lib


title: Wild type proliferation

description:
[processed data files:]
WT vs Emerin null day Proliferation.xlsx
WT proliferation to day 0 differentiation transition.diff
WT proliferation vs day 1 differentiation.diff
WT proliferation vs day 2 differentiation.diff
WT proliferation vs day 3 differentiation.diff
WT proliferation vs day 4 differentiation.diff


title: p271


title: Emerin null differentiation day 4

description:
[processed data files:]
WT vs Emerin null day 4 differentiation.xlsx
Emerin null differentiaton day 3 to 4 transition.diff
Emerin null proliferation vs day 4 differentiation.diff

source_name: Emerin-null H2K myogenic precursor cells

value: Emerin-null


title: Emerin null differentiation day 3

description:
[processed data files:]
WT vs Emerin null day 3 differentiation.xlsx
Emerin null differentiation day 2 to 3 transition.diff
Emerin null differentiaton day 3 to 4 transition.diff
Emerin null proliferation vs day 3 differentiation.diff


title: p261


title: S001056.l.rs.lib


title: S001031.l.rs.lib


title: Emerin null differentiation day 2

description:
[processed data files:]
WT vs Emerin null day 2 differentiation.xlsx
Emerin null differentiaton day 1 to 2 transition.diff
Emerin null differentiation day 2 to 3 transition.diff
Emerin null proliferation vs day 2 differentiation.diff


title: Emerin null differentiation day 0

description:
[processed data files:]
WT vs Emerin null day 0  differentiation.xlsx
Emerin null proliferation to day 0 differentiation transition.diff
Emerin null  differentiaton day 0 to 1 transition.diff


title: S001045.l.rs.lib


title: S000965.l.rs.lib


title: p235


title: Emerin null differentiation day 1

description:
[processed data files:]
WT vs Emerin null day 1 differentiation.xlsx
Emerin null  differentiaton day 0 to 1 transition.diff
Emerin null differentiaton day 1 to 2 transition.diff
Emerin null proliferation vs day 1 differentiation.diff


title: p210


title: p209


title: S000901.l.rs.lib


title: Purified splenic CD4 T cells  number 3 activated with anti-CD3/CD28 + Salp15 day 4

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

description:
4S153
4SC_vs_4S15

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) to account for spliced reads alignments, allowing two  mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the SAM files of the samples in each comparative. These tables are in tab separated plain text format.

source_name: Purified splenic CD4 T cells, activated with anti-CD3/CD28 + Salp15 day 4

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol:
RNA was extracted from CD4 T cells using PureLink RNA Micro Scale Kit (Thermo Fisher Scientific)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)

value: 8 weeks

value: Blood

value: CD4 T cells

tag: treatment

tag: time

value: day 4


title: p204


title: S000869.l.rs.lib

value: ER+


title: p245


title: p223


title: S000792.l.rs.lib


title: p165


title: Purified splenic CD4 T cells  number 2 activated with anti-CD3/CD28 + Salp15deltaP11 day 4

description:
4SC2
4SC_vs_4S15

source_name: Purified splenic CD4 T cells, activated with anti-CD3/CD28 + Salp15deltaP11 day 4

tag: strain


title: S000666.l.rs.lib


title: Purified splenic CD4 T cells  number 3 activated with anti-CD3/CD28 + Salp15deltaP11 day 4

description:
4SC3
4SC_vs_4S15

tag: age


title: p214


title: p211


title: Purified splenic CD4 T cells  number 3 activated with anti-CD3/CD28 + Salp15 day 2

description:
2S153
2SC_vs_2S15

source_name: Purified splenic CD4 T cells, activated with anti-CD3/CD28 + Salp15 day 2

value: day 2


title: S000651.l.rs.lib


title: S000658.l.rs.lib


title: p154


title: S000925.l.rs.lib


title: Purified splenic CD4 T cells  number 2 activated with anti-CD3/CD28 + Salp15 day 4

description:
4S152
4SC_vs_4S15


title: Purified splenic CD4 T cells  number 1 activated with anti-CD3/CD28 + Salp15 day 4

description:
4S151
4SC_vs_4S15


title: p150


title: Purified splenic CD4 T cells  number 2 activated with anti-CD3/CD28 + Salp15 day 2

description:
2S152
2SC_vs_2S15


title: S000573.l.rs.lib


title: p140


title: Purified splenic CD4 T cells  number 1 activated with anti-CD3/CD28 + Salp15 day 2

description:
2S151
2SC_vs_2S15


title: p167


title: Purified splenic CD4 T cells  number 3 activated with anti-CD3/CD28 + Salp15deltaP11 day 2

description:
2SC3
2SC_vs_2S15

source_name: Purified splenic CD4 T cells, activated with anti-CD3/CD28 + Salp15deltaP11 day 2


title: Purified splenic CD4 T cells  number 1 activated with anti-CD3/CD28 + Salp15deltaP11 day 4

description:
4SC1
4SC_vs_4S15


title: p135


title: S000559.l.rs.lib


title: p159


title: Purified splenic CD4 T cells  number 1 activated with anti-CD3/CD28 + Salp15deltaP11 day 2

description:
2SC1
2SC_vs_2S15


title: S000948.l.rs.lib


title: S000518.l.rs.lib


title: Purified splenic CD4 T cells  number 2 activated with anti-CD3/CD28 + Salp15deltaP11 day 2

description:
2SC2
2SC_vs_2S15


title: p092


title: S000366.l.rs.lib


title: p083


title: Purified splenic CD4 T cells  number 3 unstimulated

description:
3C
C_vs_2SC
C_vs_4SC

source_name: Purified splenic CD4 T cells, unstimulated

value: Non activated

value: control


title: p084


title: Purified splenic CD4 T cells  number 2 unstimulated

description:
2C
C_vs_2SC
C_vs_4SC


title: S000371.l.rs.lib


title: S000330.l.rs.lib


title: p081


title: KMM-KSHV_BAC36-latent-input-R3

city: Xuzhou

first: Hui

state: Jiangsu

address: #1 Daxue Road

institute: China University of Mining and Technology

data_processing:
Library strategy: MeRIP-seq
Fastq file generated with CASAVA
m6A-seq reads were aligned to the corresponding genome (human / rat / KSHV_BAC16 / KSHV_BAC36) using Tophat 2.
m6A peaks called by exomePeak.
Differential m6A peaks was detected by the differential peak discovery algorithm bltest.
Motif analysis of m6A peaks was performed using the MEME package.
The expression of transcripts and isoforms were calculated using cufflinks based on the input samples.
The differential expression of transcripts and isoforms were calculated using cuffdiff, based on the input samples.
Genome_build: hg19, rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: polyA RNA

organism: Rattus norvegicus

source_name: MM Cells

growth_protocol: Cells were grown at 37C, 5% CO2 in their respective growth media

extract_protocol:
Total RNA was extracted with Trizol and mRNA was purified using polydT beads. m6A-IP was then performed using an anti-m6A antibody from Synaptic Systems. The immunoprecipitated RNA (IP) and input for each sample was used to generate libraries.
10-25ng of mRNA was used for library preparation using the Illumina TruSeq stranded mRNA kit according to manufacturer’s protocol with two modifications. First, the elute-frag-prime stage was done at 80°C for 2 min to allow annealing without causing fragmentation. RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random primers. Then, the second strand cDNA was synthesized using DNA Polymerase I and RNase H. The cDNA fragments then went through an end repair process with the addition of a single ‘A’ base followed by ligation of the adapters. The products were then purified and enriched by PCR amplification for 10 cycles to generate the final RNA-Seq library. The second modification was done to adjust the bead-DNA ratio to preserve smaller fragments during the adapter ligation double beads clean up step. A beads:DNA ratio of 1:3 instead of 1:1 was used. cDNA libraries were quantified and pooled for cBot amplification and subsequent sequencing on an Illumina HiSeq 2000.

treatment_protocol: See samples section

tag: infection status

value: latent

value: MM

tag: antibody


title: Purified splenic CD4 T cells  number 1 unstimulated

description:
1C
C_vs_2SC
C_vs_4SC

tag: tissue


title: p080

value: 7 days after sowing

value: whole seedling


title: S000309.l.rs.lib


title: KMM-KSHV_BAC36-latent-ip-R3

value: SYSY


title: p074


title: MM-uninf-input-R3

value: Not infected


title: S000267.l.rs.lib


title: p072


title: S000156.l.rs.lib

value: ER-


title: p070


title: KMM-KSHV_BAC36-latent-input-R2


title: p068


title: S000141.l.rs.lib


title: MM-uninf-ip-R3


title: S004724.l.rs.lib


title: KMM-KSHV_BAC36-latent-ip-R2


title: eHiC_9

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

description: We added A before the first 34 bases, and the 35 base were mapped to hg18 using bowtie. Identical reads should NOT be treated as PCR duplicates.

data_processing:
library strategy: easy Hi-C (eHi-C)
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE.  The two reads were mapped independently and then merged into pairs using in-house script. After mapping, we further filter the reads requiring the positions of both ends to be exactly at the HindIII cutting sites.
The deep sequenced eHi-C library (eHiC_10) was prepared with UMI adapter, and the UMI barcode are includeded in the fastq files. PCR duplications were defined as identical PE reads also with the same UMI barcode. The eHi-C libraries sequenced on MiSeq (eHiC1~9) were not intended for deep sequencing and therefore were prepared without UMI barcode. We assume no PCR duplication in those libraries.
Genome_build: hg18
Supplementary_files_format_and_content: For each Hi-C replicate, the fragment-to-fragment frequency are provided in the txt file. The location of each fragment are provided in bed file (not included in the GEO records). More details in the 'README.txt'

source_name: fetal lung fibroblast

growth_protocol: IMR90 cells were grown as instructed by ATCC

extract_protocol:
After confluence, the cells were detached with trypsin and collected by spinning down at 900g for 5 minutes. Then the cells were fixed in 1% formaldehyde for 15 minutes at 37ºC, followed by 1/20 volume of 2.5M glycine at room temperature for 5 minutes to quench formaldehyde. The fixed cells were scrapped, washed in PBS and pelleted before stored in -80C.
In easy Hi-C, we begin with the in situ proximity ligation procedure and perform HindIII digestion and proximity ligation while keeping nuclei intact. Lligation was performed directly after HindIII digestion without end repair, leading to HindIII-digestible junction products. After nuclear lysis and reverse crosslink, the DNA are digested with more frequent 4-base cutter DpnII before self-ligation. The samples are next treated with exonuclease to remove DNA that failed to form self-circles, and contaminations from un-ligated ends and other linear DNA species. In order to enrich the ligation junction products, we then cut the self-circularized DNA again with HindIII, and only re-linearized junction DNA will be amplified during the library generation. Libraries were prepared according to Illumina's instruction or cited literatures.

value: fetal lung fibroblast

tag: experiment

value: easy Hi-C (eHi-C)

value: no

tag: restriction enzyme

value: HindIII


title: p066r

tag: developmental stage


title: S004512.l.rs.lib


title: S002451.l.rs.lib


title: p065

tag: genotype


title: MM-uninf-ip-R2


title: S000310.l.rs.lib


title: eHiC_7


title: p066


title: S002637.l.rs.lib


title: MM-uninf-input-R2


title: eHiC_6


title: KMM-KSHV_BAC36-latent-ip

description:
PolyA RNA
Processed data file: KMM-KSHV_BAC16-latent_input.genes.fpkm_tracking

data_processing:
Library strategy: MeRIP-Seq
Fastq files generated with CASAVA.
m6A-seq reads were aligned to the corresponding genome (human / rat / KSHV_BAC16 / KSHV_BAC36) using Tophat 2.
m6A peaks called by exomePeak.
Differential m6A peaks were detected by the differential peak discovery algorithm bltest.
Motif analysis of m6A peaks was performed using the MEME package.
The expression of transcripts and isoforms were calculated using cufflinks based on the input samples.
The differential expression of transcripts and isoforms were calculated using cuffdiff, based on the input samples.
Genome_build: hg19 (GRCh37), rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *fpkm_tracking: Tab-delimited text files include RPKM values for each Sample.

source_name: MM cells, latent, no treatment, m6A IP

growth_protocol: Cells were grown at 37C, 5% CO2 in their respective growth media.

extract_protocol:
Total RNA was extracted with Trizol and mRNA was purified using polydT beads. m6A-IP was then performed using an anti-m6A antibody from Synaptic Systems. The immunoprecipitated RNA (IP) and input for each sample was used to generate libraries.
10-25ng of mRNA was used for library preparation using the Illumina TruSeq stranded mRNA kit according to manufacturer’s protocol with two modifications. First, the elute-frag-prime stage was done at 80°C for 2 min to allow annealing without causing fragmentation. RNA was reverse transcribed into first strand cDNA using reverse transcriptase and random primers. Then, the second strand cDNA was synthesized using DNA Polymerase I and RNase H. The cDNA fragments then went through an end repair process with the addition of a single 'A' base followed by ligation of the adapters. The products were then purified and enriched by PCR amplification for 10 cycles to generate the final RNA-Seq library. The second modification was done to adjust the bead-DNA ratio to preserve smaller fragments during the adapter ligation double beads clean up step. A beads:DNA ratio of 1:3 instead of 1:1 was used. cDNA libraries were quantified and pooled for cBot amplification and subsequent sequencing on an Illumina HiSeq 2000.

treatment_protocol: 1ug/ml doxycycline for 24 hours or 48 hours, or no treatment.

value: Latent

value: anti-m6A (SYSY)


title: p064

source_name: whole seedling


title: KMM-KSHV_BAC36-latent-input

source_name: MM cells, latent, no treatment, input


title: eHiC_5


title: MM-uninf-input

description:
PolyA RNA
Processed data file: MM_input.genes.fpkm_tracking

source_name: MM cells, not infected, no treatment, input


title: eHiC_4


title: eHiC_8


title: S002338.l.rs.lib


title: p060


title: S002322.l.rs.lib

value: ER+


title: eHiC_3


title: p272


title: MM-uninf-ip

source_name: MM cells, not infected, no treatment, m6A IP


title: eHiC_2


title: S001570.l.rs.lib2


title: S001570.l.rs.lib


title: p048


title: eHiC_1


title: p047


title: S001051.l.rs.lib


title: S002102.l.rs.lib


title: S001564.l.rs.lib


title: p063


title: p046


title: p045


title: S001524.l.rs.lib


title: S001421.l.rs.lib


title: S001164.l.rs.lib


title: p042


title: S002470.l.rs.lib


title: p048r


title: p027


title: p034


title: p036


title: S001485.l.rs.lib


title: p033


title: S001205.l.rs.lib


title: S001419.l.rs.lib


title: p024


title: total RNA-seq in Ovary [MO_RNA-seq]

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

description: total RNA-seq

data_processing:
3' adapter sequences were  trimmmed using Trimmomatic-0.36
Total RNA-seq paired-end reads from four datasets to UCSC Drosophila melanogaster (dm6) genome assembly using HISAT2
Supplementary_files_format_and_content: The mapping alignments in bam format and counts of genes and 3'UTR extension were generated
dm6flybase_3seq_genePlus3ext_counts.tab: 3'-seq raw counts on gene and 3'UTR extension
dm6flybase_RNAseq_genePlus3ext_counts.tab: RNA-seq raw counts on gene and 3'UTR extension
dyak3_3seq_genePlus3ext_counts.tab: 3'-seq raw counts on gene and 3'UTR extension
dyak3_RNAseq_genePlus3ext_counts.tab: RNA-seq raw counts on gene and 3'UTR extension
dvir3_3seq_genePlus3ext_counts.tab: 3'-seq raw counts on gene and 3'UTR extension
dvir3_RNAseq_genePlus3ext_counts.tab: RNA-seq raw counts on gene and 3'UTR extension

source_name: Ovary

extract_protocol:
3'-seq libraries were prepared and sequenced as described (Sanfilippo P, Miura P, Lai EC: Genome-wide profiling of the 3' ends of polyadenylated RNAs. Methods 2017, 75:in press.), using 2 μg of total RNA as starting material.  Total RNA-seq libraries were prepared starting with 1 μg of total RNA in water.
The 3p-seq libraries were sequenced using a hiseq-1000 with SE-50 mode at the genomics core facility at MSKCC.  Total RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit (cat. No. RS-122-2201).  The protocol was followed exactly as per manufacturer's instructions. The libraries were sequenced on a hiseq-1000 sequencer at the genomics core facility at MSKCC.
3p-seq hiseq-1000 with SE-50; Total RNA-seq paired-end PE75

value: Ovary


title: total RNA-seq in Testis [MT_RNA-seq]

description: total RNA-seq

source_name: Testis

value: Testis


title: S000800.l.rs.lib


title: p006


title: S001105.l.rs.lib


title: S001444.l.rs.lib


title: p040


title: total RNA-seq in Female Head [MH_RNA-seq]

description: total RNA-seq

source_name: Female Head

value: Female Head


title: l043


title: S000913.l.rs.lib

source_name: Primary breast tumour


title: S000572.l.rs.lib


title: l041


title: l043r


title: S001144.l.rs.lib


title: l035


title: 3'-seq in Female Head [H]


title: 3'-seq in Ovary [O]


title: S000628.l.rs.lib


title: l024r


title: 3'-seq in Embryo 18-24h [dme_18_24h]

source_name: Embryo 18-24h

value: Embryo 18-24h


title: S000602.l.rs.lib


title: l024


title: l005


title: S000618.l.rs.lib


title: S000271.l.rs.lib


title: S000525.l.rs.lib


title: 3'-seq in Embryo 90-6h [dme_90_6h]

source_name: Embryo 90-6h

value: Embryo 90-6h


title: 3'-seq in Embryo 6-12h [dme_6_12h]

source_name: Embryo 6-12h

value: Embryo 6-12h


title: 3'-seq in Embryo 0-45' [dme_0_45]

source_name: Embryo 0-45'

value: Embryo 0-45'


title: f161

value: 7 days after sowing

value: whole seedling


title: f162


title: S000324.l.rs.lib


title: S000323.l.rs.lib


title: S000295.l.rs.lib

value: ER-


title: 3'-seq in Carcass Male [adM_carcass]

source_name: Carcass Male

value: Carcass Male


title: 3'-seq in Testis [T]


title: 3'-seq in Carcass Female [adF_carcass]

source_name: Carcass Female

value: Carcass Female


title: 3'-seq in Embryo 12-18h [dme_12_18h]

source_name: Embryo 12-18h

value: Embryo 12-18h


title: l007


title: f159


title: f160


title: S000306.l.rs.lib


title: 3'-seq in Whole body Male 2-5d [adM_2_5d]

source_name: Whole body Male 2-5d

value: Whole body Male 2-5d


title: f169


title: Biofilm 3

city: Penang

first: Jason

last: Chin

state: Penang

address: Jalan Inovasi

department: INFORMM

country: Malaysia

institute: Universiti Sains Malaysia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to S. Typhi ct18 whole genome using bowtie2 v2.2.6
Differential gene expression was calculated and reported by Cufflinks v 2.2.1
Genome_build: S. Typhi ct18 Accession number: NC_003198.1
Supplementary_files_format_and_content: Tab delimited Excel file format

organism: Salmonella enterica subsp. enterica serovar Typhi

source_name: biofilm cells

growth_protocol: Planktonic cells are grown in normal nutrient broth. Biofilm cells are grown in enriched nutrient broth containing ox-bile.

extract_protocol:
RNA extraction was done using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ATCC 7251

tag: condition

value: Biofilm


title: 3'-seq in Embryo 45-90' [dme_45_90]

source_name: Embryo 45-90'

value: Embryo 45-90'


title: S000617.l.rs.lib

value: ER+


title: Biofilm 1


title: Biofilm 2


title: S000553.l.rs.lib2


title: 3'-seq in S2R+ cell line [S2Rplus]

source_name: S2R+ cell line

value: S2R+ cell line


title: f157

source_name: whole seedling


title: f154


title: 3'-seq in OSS cell line [OSS]

source_name: OSS cell line

value: OSS cell line


title: Planktonic 3

source_name: planktonic cells

value: Planktonic


title: f151


title: Planktonic 2


title: Emerin null proliferation

description:
[processed data files:]
WT vs Emerin null day Proliferation.xlsx
Emerin null proliferation to day 0 differentiation transition.diff
Emerin null proliferation vs day 1 differentiation.diff
Emerin null proliferation vs day 2 differentiation.diff
Emerin null proliferation vs day 3 differentiation.diff
Emerin null proliferation vs day 4 differentiation.diff

source_name: Emerin-null H2K myogenic precursor cells

tag: cell type

value: myogenic precursor cells

value: Emerin-null


title: S000553.l.rs.lib

tag: scan-b external id


title: S000276.l.rs.lib

tag: sample fullname


title: 3'-seq in Dmd32 cell line [163_Dmd32]

source_name: Dmd32 cell line

value: Dmd32 cell line


title: f138

value: 7 days after sowing


title: 3'-seq in Dmd4 cell line [139_Dmd4]

source_name: Dmd4 cell line

value: Dmd4 cell line


title: Dcas3cmr2αcmr2βP_b

description:
cas3,cmr2α,cmr2β deletion with pSeSD plasmid
Processed data file: fpkm.xls
Processed data file: Dcas3cmr2alphacmr2betaOE3a_vs_Dcas3cmr2alphacmr2betaP_up.xls
Processed data file: Dcas3cmr2alphacmr2betaOE3a_vs_Dcas3cmr2alphacmr2betaP_down.xls

source_name: cas3,cmr2-alpha,cmr2-beta deletion, pSeSD plasmid

tag: genotype/variation

value: cas3,cmr2-alpha,cmr2-beta deletion with pSeSD plasmid

tag: cell growth phase

value: log phase


title: f137

description: sRNA_115maize_lines_rpmqn_min1_line1.csv

value: whole seedling


title: 3'-seq in Dmd20 cell line [189_Dmd20]

source_name: Dmd20 cell line

tag: cell line

value: Dmd20 cell line


title: f145


title: Planktonic 1


title: S000386.l.rs.lib

source_name: Primary breast tumour

tag: er-status


title: 3'-seq in mldmd16_c3  cell line [137_mldmd16_c3]

source_name: mldmd16_c3  cell line

value: mldmd16_c3  cell line


title: S000349.l.rs.lib


title: 3'-seq in Whole body female 2-5d [adF_2_5d]

source_name: Whole body female 2-5d

value: Whole body female 2-5d


title: S000272.l.rs.lib


title: f136


title: Dcas3cmr2αcmr2βP_a


title: 3'-seq in BG3 cell line [125_BG3]

source_name: BG3 cell line

value: BG3 cell line


title: 3'-seq in cmel1 cell line [87_cmel1]

source_name: cmel1 cell line

value: cmel1 cell line


title: PAM_24H_rep5

first: Pablo

last: Peña-Martínez

address: Klinikgatan 28

department: Clinical Genetics

data_processing:
Bcl2FastQ software was used for basecalling.
Sequenced reads were mapped to the hg19 reference genome using Tophat 2.0.13 with parameters -p 2 --keep-fasta-order --bowtie1 --no-coverage-search
BAM files were imported to the Qlucore Omics Explorer 3.0 software and normalized using the TMM (Trimmed Mean of M-values) method. Features with less than 5 reads in at least 6 samples were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized abundance measurements (TMM factor) for all samples

source_name: PAM_24H, MLL-AF9 tranduced cord blood cells

growth_protocol: The MA9 cells were cultured in IMDM containing 15% fetal bovine serum, 1% penicillin and streptomycin, 1% L-glutamine, and 0.1 μM 2-mercaptoethanol (Sigma Aldrich). The MA9 medium was supplemented with hTPO, hFLT3L, hSCF, all at 10 ng/mL (Peprotech Inc).

extract_protocol:
RNA was extracted using the QIAshredder and RNeasy Microkit (QIAgen, Hilden, Germany).
Illumina TruSeq RNA Sample Prep Kit v2 (Cat#RS-122-2001) was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The treated grouped was cultured in the presence of 1 ug/mL of PAM3CSK4 in addition to the baseline conditions for 3 or 24 hours.

value: Cord blood stem cells

tag: cell line name

value: MA9 cells

tag: treatment

value: PAM

tag: time


title: PAM_24H_rep4


title: Dcas3cmr2αcmr2βOE3a_b

description:
cas3,cmr2α,cmr2β deletion with pCsa3a plasmid
Processed data file: fpkm.xls
Processed data file: Dcas3cmr2alphacmr2betaOE3a_vs_Dcas3cmr2alphacmr2betaP_up.xls
Processed data file: Dcas3cmr2alphacmr2betaOE3a_vs_Dcas3cmr2alphacmr2betaP_down.xls

source_name: cas3,cmr2-alpha,cmr2-beta deletion, pCsa3a plasmid

value: cas3,cmr2-alpha,cmr2-beta deletion with pCsa3a plasmid


title: f117


title: f124


title: PAM_24H_rep3


title: Dcas3cmr2αcmr2βOE3a_a


title: f104


title: Dcas1P_b

description:
Processed data file: fpkm.xls
Processed data file: Dcas1OE3a_vs_Dcas1P_up.xls
Processed data file: Dcas1OE3a_vs_Dcas1P_down.xls

source_name: cas1 deletion, pSeSD plasmid

value: cas1 deletion with pSeSD plasmid


title: Control_24H_rep5

source_name: Control_24H, MLL-AF9 tranduced cord blood cells

value: Control


title: Control_24H_rep4


title: PAM_24H_rep1


title: LOS #3 WGBS

description: Day ~105 Bos indicus taurus × Bos taurus taurus F1 fetal skeletal muscle

source_name: LOS, day ~105 conceptus

value: fetal skeletal muscle

value: LOS


title: 3'-seq in mbn2 cell line [43_mbn2]

source_name: mbn2 cell line

value: mbn2 cell line


title: f134

source_name: whole seedling

value: 7 days after sowing


title: Dcas1P_a

value: log phase


title: LOS #4 WGBS


title: Dcas1OE3a_b

source_name: cas1 deletion, pCsa3a plasmid

value: cas1 deletion with pCsa3a plasmid


title: f090

value: whole seedling


title: 3'-seq in gm2 cell line [9_gm2]

source_name: gm2 cell line

value: gm2 cell line


title: f103


title: Dcas1OE3a_a


title: f099


title: LOS #2 WGBS


title: total RNA-seq in Ovary [VO_RNA-seq]

description: total RNA-seq

organism: Drosophila virilis

source_name: Ovary

value: Ovary


title: Control_24H_rep2


title: total RNA-seq in Female Head [VH_RNA-seq]

description: total RNA-seq

source_name: Female Head

value: Female Head


title: Control #3 WGBS

source_name: Control, day ~105 conceptus


title: Control_24H_rep3


title: LOS #1 WGBS


title: PAM_24H_rep2


title: f072


title: Control #2 WGBS


title: Control_24H_rep1


title: PAM_3H_rep5

source_name: PAM_3H, MLL-AF9 tranduced cord blood cells


title: f055


title: f062


title: f047r


title: PAM_3H_rep4


title: 3'-seq in Ovary [VO]


title: 3'-seq in Embryo 36-48h [Virilis_36_48hr_embryos]

source_name: Embryo 36-48h

value: Embryo 36-48h


title: PAM_3H_rep2

value: Cord blood stem cells


title: Control #1 WGBS


title: f087


title: total RNA-seq in Testis [VT_RNA-seq]

description: total RNA-seq

source_name: Testis

value: Testis


title: 3'-seq in Testis [VT]


title: PAM_3H_rep1

value: MA9 cells

value: PAM


title: PAM_3H_rep3


title: 3'-seq in Female Head [VH]


title: f045


title: f047


title: f043


title: S001028.l.rs.lib

source_name: Primary breast tumour

extract_protocol:
TRIzol LS
Small RNA sequencing libraries were prepared from 500 ng total RNA using a protocol analogous with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), but with custom adapters to incorporate dual indexes. Pooled libraries were sequenced on a NextSeq 500 with High Output v2 75 cycle-kits (Illumina)

value: ER+


title: 3'-seq in Embryo 0-12h [Virilis_0_12hr_embryos]

source_name: Embryo 0-12h

value: Embryo 0-12h


title: Control_3H_rep4

source_name: Control_3H, MLL-AF9 tranduced cord blood cells

value: Control


title: f040


title: 3'-seq in Embryo 24-36h [Virilis_24_36hr_embryos]

source_name: Embryo 24-36h

value: Embryo 24-36h


title: Control_3H_rep5


title: Control_3H_rep3


title: Control_3H_rep2


title: 3'-seq in Embryo 12-24h [Virilis_12_24hr_embryos]

source_name: Embryo 12-24h

value: Embryo 12-24h


title: f037r

value: 7 days after sowing


title: total RNA-seq in Ovary [YO_RNA-seq]

description: total RNA-seq

organism: Drosophila yakuba


title: f039r


title: f039


title: total RNA-seq in Testis [YT_RNA-seq]

description: total RNA-seq


title: total RNA-seq in Female Head [YH_RNA-seq]

description: total RNA-seq


title: Control_3H_rep1


title: f030


title: S001032.l.rs.lib


title: f037


title: f013


title: 3'-seq in Embryo 12-24h [Yakuba_12_24hr_embryos]


title: f012


title: f034


title: f023


title: 3'-seq in Testis [YT]


title: 3'-seq in Female Head [YH]


title: 3'-seq in Ovary [YO]


title: P2B_H

city: Parkville

first: christophe

last: lefevre

state: VIC

address: 1 G Royal Parade

department: Bioinformatics Division

institute: Walter Eliza Hall Institute of Medical Research

data_processing:
fastQC
alignments with Tophat 2.0.5(Langmead and Salzberg, 2012, Kim and Salzberg, 2011)
transcripts assembled using Cufflinks (Trapnell et al., 2010)
final transcriptome assembly was performed by merging assembled transcripts using Cuffmerge and SAMtools (Li et al., 2009)
differential expression determined using Cuffdiff
Genome_build: Macropus_eugenii.Meug_1
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample (cuffdiff output)

organism: Notamacropus eugenii

source_name: mammary epithelial cells

growth_protocol: MID lactation mammary epithelial cells (WallMEC) were cultured on MID or LATE lactation ECM

extract_protocol:
RNA was extracted using the RNeasy Lipid Tissue (Qiagen) protocol
library construction protocol not provided.

treatment_protocol: Cells were grown in the presence or absence of  lactogenic hormones ( 1 μg/ml cortisol, 1 μg/ml insulin, 0.2μg/ml prolactin, 650pg/ml triodothyronine and 1 pg/ml estradiol)

value: mammary gland

value: mammary epithelial cells

tag: source of ecm

value: MID lactation mammary gland

tag: hormones


title: P3_NH

tag: tissue

value: LATE lactation mammary gland

value: No hormones


title: 3'-seq in Embryo 0-12h [Yakuba_0_12hr_embryos]


title: P3_H


title: P2B_NH

value: No hormone


title: ControlTGIRTInputRep2 input

status: Public on Oct 30 2017

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Reads were aligned to the human genome (hg19) using STAR aligner with default parameters
An in house script was used to merge left and right reads into a single bam file spanning the full interval from the beginning of the 'left' read to the end of the 'right' read
Strand specific bedgraph files were generated quantifying the number of reads beginning at each position, using bedtools genomecov (activating the '-5' and '-strand' flags
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: HEK293T cells

growth_protocol: Human HEK293T cells were plated in 6-well plates at 20% confluence.

extract_protocol:
Briefly, 40 μl of protein-G magnetic beads were washed and resuspended in 200 μl of IPP buffer, and tumbled with 5 μl of affinity purified anti-m1A polyclonal antibody (Synaptic Systems) at room temperature for 30 minutes. RNA was added to the antibody-bead mixture, and incubated for 2 h at 4°C. The RNA was then washed twice in 200 μl of IPP buffer, twice in low-salt IPP buffer (50 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5), and twice in high-salt IPP buffer (500 mM NaCl, 0.1% NP-40, 10 mM Tris-HCl, pH 7.5), and eluted in 30 μl RLT (Qiagen). To purify the RNA, 20 μl MyOne Silane Dynabeads (Life Technologies) were washed in 100 μl RLT, resuspended in 30 μl RLT, and added to the eluted RNA. 60 μl 100% ethanol was added to the mixture, the mixture attached to the magnet and the supernatant discarded. Following two washes in 100 μl of 70% ethanol, the RNA was eluted from the beads in 10 μl H20.
RNA was first subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by a 3’ ligation of an RNA adapter using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed either using SuperScript-III (Invitrogen) or using TGIRT-III (InGex), and the cDNA was subjected to a 3’ ligation with a second adapter using T4 ligase. The single-stranded cDNA product was then amplified for 9-12 cycles in a PCR reaction. Libraries were sequenced on Illumina Nextseq platforms generating short paired end reads, ranging from 25-55 bp from each end.

treatment_protocol: For overexpression, plasmids encoding full length of TRMT6/TRMT61A under CMV promoter were obtained from ORIGENE. The plasmids were transfected into HEK293T cell using PolyJet (SignaGene) with one boost of the plasmid at 24 hours. Cells were harvested 48 hours following transfection.

value: input


title: f005

value: whole seedling


title: ControlTGIRTInputRep1 M1A IP

value: M1A IP


title: SuperScriptRep2 M1A IP


title: SuperScriptDimrothRep2 M1A IP


title: ControlTGIRTInputRep2 M1A IP


title: SuperScriptDimrothRep1 M1A IP


title: SuperScriptRep1 input


title: OverXTGIRTRep1 input


title: TGIRTDimrothRep2 M1A IP


title: TGIRTDimrothRep1 M1A IP


title: SuperScriptRep1 M1A IP


title: TGIRTRep2 M1A IP


title: TGIRTRep1 input


title: TGIRTRep1 M1A IP


title: ControlTGIRTInputRep1 input


title: OverXTGIRTRep1 M1A IP


title: OverXTGIRTRep2 M1A IP


title: OverXTGIRTRep2 input


title: CTCF_ChIP-nexus Rep2

city: Shang Hai

first: Zhang

last: Mo

address: Dong Chuan Road 800

institute: SJTU

data_processing:
About 20 million reads were needed for motif analyses.
Remove adaptor using cutadapt and then map reads to hg19 with Bowtie2
MACS was used to peakcall and obtain CTCF  binding position MACE  was  used  for  CTCF  occupancy border  (footprint) measure
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using MACE software, and  this bw files represent forward and reverse border of CTCT binding  sites in genome

source_name: 293T cells

growth_protocol: HEK293T cells were cultured in DMEM (Hyclone) medium supplemented with 10% (v/v) FBS (Gibco) and 1% penicillin-streptomycin. Cells were grown in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
ChIP-nexus  experiments were  performed according to  the  published protocol50  with modifications.  Briefly,  HEK293T  cells  (~2x107)  were  crosslinked  with  1%  (v/v) formaldehyde for 10 min at room temperature (20-25°C), and then quenched by 125 mM glycine (final concentration). Crosslinked cells were lysed and washed twice using the ChIP  buffer  (10  mM  Tris  pH7.5,  1  mM  EDTA,  1%  Triton  X-100,  0.1%  Sodium deoxycholate, 0.1% SDS, 1x protease inhibitors, 0.15 M NaCl) to obtain nuclei. Nuclear samples were sonicated using Bioruptor Sonicator to fragmentize DNA to sizes ranging from 100 bp to 10,000 bp. Chromatins were then immunoprecipitated with 5-10 μl CTCF antibody (Millipore, 07-729) by slow rotation at 4°C for overnight. The mixture was then incubated with 50 μl Protein G Magnetic beads (life technologies, 10004D) for another 3 hours at 4°C. The magnetic beads with enriched chromatin were then sequentially washed with the washing buffer A (10 mM TE, 0.1% Triton X-100), washing buffer B (150 mM NaCl, 20 mM Tris-HCl pH 8.0, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100, 0.2% SDS), washing buffer C (250 mM NaCl, 5 mM Tris-HCl pH 8.0, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate, 0.5 mM EDTA), washing buffer D (250 mM LiCl, 0.5% NP-40, 10 mM Tris-HCl pH 8.0, 0.5% sodium deoxycholate, 10 mM EDTA), and the Tris buffer (10 mM Tris-HCl pH 7.5). The chromatin ends were repaired with 2 μl end-repair enzyme mixture (NEB, E6050S) in 50 μl 1x buffer for 30 min at 20°C and then washed again with the buffers A-D. The chromatin ends were dA-tailed by adding 3 μl Klenow exo- (NEB, M0212S) and 10 μl 1 mM dATP (NEB, N0440S) in 50 μl 1x NEB Buffer 2 at 37°C for 30 min. The Nexus adaptors (5' phosphate GATCG GAAGA GCACA CGTCT GGATC CACGA CGCTC TTCC, 5'  phosphate TCAGA GTCGA GATCG  GAAGA GCGTC  GTGGA TCCAG ACGTG TGCTC TTCCG ATCT) were added by incubating with 50 μl 1x Ligase mix (NEB, M0367S) for 1h at 25°C. The ends were filled with 1 μl Klenow exo- and then with  1.5  μl  T4  DNA  polymerase  (NEB,  M0203S)  to  generate  blunt-ended  DNAs. Beads-DNA samples were then treated with 20 U Lambda Exonuclease (NEB, M0262S) with the Exonuclease buffer (0.2% Triton-X and 1% DMSO in 100 μl 1x Lambda) by incubation at 37°C for 1h with 1000 rpm on thermomixer. Samples were then digested by 75 U RecJf exonuclease (NEB, M0264S) with 0.2% Triton-X and 1% DMSO in 100 μl 1x NEB Buffer 2 at 37°C for 1h with 1000 rpm on thermomixer, and then washed three times  with  the  RIPA buffer  (50  mM  HEPES  pH  7.5,  1  mM  EDTA,  0.7%  sodium deoxycholate, 1% NP-40, 0.5 M LiCl). To elute DNA, incubate samples with 200 μl elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS) at 65°C for 30 min on thermomixer of 1000 rpm. The samples were reverse-crosslinked at 65°C for overnight, and then incubated with 2 μl RNase A (Thermo, EN0531) at 37°C for 2h, and then with 8μl proteinase K (NEB, P8107S) at 55°C for 4 h. The ssDNAs were extracted with 400 μl phenol:chloroform:isopentanol, and then precipitated with ethanol and sodium acetate. The precipitated DNAs were resuspended with 10 μl nuclease-free water.
The ssDNA was incubated at 95°C for 5 min and then chill on ice immediately to denature single strand DNA. The ssDNA was circularized with 75 U ssDNA Ligase (Epicentre, CL4111K), 0.05 mM ATP, 2.5 mM MnCl2 in 15 μl 1x CircLigase Buffer at 60°C for 1h. The samples were incubated with 0.2 μM cut-oligo (GAAGA GCGTC GTGGA  TCCAG  ACGTG)  in  50  μl  1x  FastDigest  Buffer  (Thermo,  FD0054)  in thermocycler with the annealing program: 95°C for 1 min, slowly cool down at 1% ramp to 25°C for 1 min, hold at 25°C for 30min. Add 3 μl FastDigest BamHI and incubate at 37°C for 30 min to linearize DNA. Precipitate DNA using ethanol and sodium acetate, and resuspend DNA with 20 μl water. To PCR amplify samples, add 25 μl Q5 polymerase (NEB, M0543S), 2.5 μl 10 mM Illumina universal primer and index primer and follow the PCR program: 98°C for 30 sec to denature DNA, followed by 16 cycles of 98°C for 10 sec and 65°C for 75 sec, with a final extension at 65°C for 5 min. PCR products of sizes range about 150-300 bp were purified from 2% agarose gel using QIAquick gel extraction kit (Qiagen, 28604). Purified DNA samples were sequenced on an Illumina HiSeq platform.

value: HEK 293T cells

value: wide type

tag: chip antibody

value: CTCF (Millipore, 07-729)


title: SuperScriptRep2 input


title: CTCF_ChIP-nexus Rep1


title: NXF3 pulldown 2

city: Indianapolis

first: Scot

middle: J

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: Small RNA, 30-375 nucleotides

data_processing:
Sequencing was performed using an Illumina HiSeq 2500. Demultiplexed data were analyzed using Partek Flow (build version 6.0.17.0305 Copyright ©; 2017 Partek Inc., St. Louis, MO, USA). Sequences were evaluated for quality and trimmed to remove adapter sequence. A custom Linux script was used to remove murine ribosomal sequences according to the Illumina iGenome murine genome annotation. Remaining sequences were aligned to the murine genome (mm9 Refseq Transcript 2016-08-01, Bowtie for Illumina, default settings) and aligned reads were quantified, normalized and annotated. Analysis was limited to genes with >100 aligned reads.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include read counts.

source_name: NIH 3T3 mouse fibroblast, transfected

growth_protocol: 3T3 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 10% calf serum (NIH3T3).

extract_protocol:
Input and immunoprecipitated RNA from 3 independent experiments were isolated and concentrated using RNA Clean & Concentrator-5 (Zymo Research).
Indexed RNA-sequencing libraries were made using the Illumina TruSeq small RNA kit. Libraries were amplified with 14 cycles of PCR, pooled, and separated by PAGE. Products with sizes 30-375 nucleotides were excised and collected from the gel.

value: NIH 3T3

value: fibroblast cell line

tag: transfection

value: pEGFP-NXF3 plasmid

tag: ip antibody

value: anti-GFP (Abcam, #ab290)


title: Input 2

description: Small RNA, 30-375 nucleotides


title: NXF3 pulldown 3

description: Small RNA, 30-375 nucleotides


title: NXF3 pulldown 1

description: Small RNA, 30-375 nucleotides


title: 8A_ILL13_SRL_RNAseq

city: New York

first: Jeremiah

last: Faith

state: NY

address: One Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Transcript expression values were obtained by mapping to the Mus musculus mm10 genome (http://genome.ucsc.edu/) using HISAT and StringTie.
FPKM was exported with the ballgown R package.
Genome_build: mm10

source_name: C57BL/6 Mouse Colon

extract_protocol:
10-30mg of tissue from the proximal colon was placed into an RNAlater (Qiagen). RNA was extracted with an RNeasy Kit (Qiagen) using 1mm zirconia/silica beads (BioSpec).
mRNA Illumina libraries were generated by the NYU Genome Technology Center and sequenced to a depth of 43 ± 3 million (mean ±  std) 50nt paired-end reads/sample (Illumina HiSeq).

treatment_protocol: Diet was given a week prior to starting 3% DSS or maintaining water and mice were sacrificed after 3 days of DSS/water.

value: Colon

tag: diet

tag: condition

value: DSS


title: 7B_ILL13_SRL_RNAseq


title: 8B_ILL13_SRL_RNAseq


title: 7C_ILL13_SRL_RNAseq


title: TGIRTRep2 input


title: 7A_ILL13_SRL_RNAseq


title: 8C_ILL13_SRL_RNAseq


title: 6A_ILL13_SRL_RNAseq


title: 6B_ILL13_SRL_RNAseq


title: 4C_ILL13_SRL_RNAseq

value: Water


title: 4B_ILL13_SRL_RNAseq


title: CK

city: Chengdu

first: li

middle: li

last: qin

state: sichuan province

address: wenjiang district huiming 211road

institute: Sichuan Agricultural University

data_processing:
Statistical analysis of the quality information was performed and the raw sequence reads were cleaned using fastx (version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/index.html). Bases with low quality at 3'3 end and fuzzy N bases in reads were removed from raw sequences. All low quality reads, such as short reads (<20 nt), empty reads, and ncRNA reads, were removed
A total Pool of Reads was generated with each samples’ reads and de novo assembly was performed using the Scaffolding Contig Algorithm of CLC GenomicsWorkbench (version 5.5).
Statistical analysis was performed to identify differentially expressed genes between the two libraries. RPKM (Reads perKilo bases per Million reads) quantitative criteria was applied to calculate the expressed amount of the reads coverage
Fisher’s test for difference was conducted according to the RPKM of the contigs and internal reference of the total expression amount in each sample
we used a stringent FDR value <0.05 and the fold change ≥2 or ≤0.5 as a threshold to judge the significant difference of gene expression. The DEGseq analysis was performed to count the differential gene expression.
Supplementary_files_format_and_content: RPKM values for each Sample and comparison between two samples; details in 'readme.txt'

organism: Nicotiana tabacum

growth_protocol: The tobacco seeds were surface sterilized and germinated on MS medium for 20 days,

extract_protocol:
Total RNA was isolated from roots of alligator weed using Trizol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: then transfer to low potassium medium for, 6h, 12h and 24h treatment.

value: seedings

tag: growth condition

value: control


title: LK

source_name: tobacco_low potassium

value: low potassium treatment for 6h,12h, and 24h


title: Input 3

description: Small RNA, 30-375 nucleotides

tag: cell type


title: 3C_ILL13_SRL_RNAseq


title: Input 1

description: Small RNA, 30-375 nucleotides


title: 3B_ILL13_SRL_RNAseq


title: 2B_ILL13_SRL_RNAseq


title: 2A_ILL13_SRL_RNAseq


title: 2C_ILL13_SRL_RNAseq


title: 3A_ILL13_SRL_RNAseq


title: OP9 Flat2

city: Edinburgh

first: Alexander

last: Medvinsky

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequencing reads were processed using the RNA-seq analysis pipelines of Geneprof  (Halbritter et al., 2012)
Sequencing reads were aligned with TopHat (Trapnell et al., 2009) v1.2.0 (2012-11-14).
The mRNA levels per gene were quantified by a custom script in Geneprof which accounts for multi-mapping reads. Briefly, all uniquely mapped reads overlapping with each annotated gene (Ensembl 58 Mouse Genes, NCBIM37) were summed, while ambiguously mapped genes were divided into fractions, weighted proportionally to the number of uniquely mapped genes in each possible gene assignment.
Read counts were then scaled per million (RPM)
Differential expression was with DESeq (Anders and Huber, 2010) (2011-03-15)
Genome_build: mm9
Supplementary_files_format_and_content: matrix contains normalised sequencing reads per million (RPM), the log2 fold change and adjusted p-value (output of DESeq) from comparisons between groups

source_name: OP9 Flat

extract_protocol:
RNA was extracted from these samples with Qiagen RNeasy minikit (QIAGEN) including DNase I treatment (QIAGEN).
RNA sequencing libraries were prepared with a TruSeq RNA Library Preparation Kit (Illumina) and multiplexed.

tag: strain

value: Foetal calvaria stromal line (de Bruijn lab)

tag: culture conditions

value: Maintained in flat culture submersed below media


title: OP9 Flat4

tag: cell line


title: OP9 Reaggregate6

source_name: OP9 Reaggregate

value: Foetal calvaria stromal line

value: Reaggregated and cultured at the liquid-gas interface on 0.8-μm nitrocellulose filters for 48h with IL3 (200 μg/μl)


title: OP9 Reaggregate5

value: Reaggregated and cultured at the liquid-gas interface on 0.8-μm nitrocellulose filters for 48h


title: OP9 Flat1


title: 6C_ILL13_SRL_RNAseq


title: OP9 Reaggregate3


title: OP9 Reaggregate4


title: OP9 Reaggregate1


title: E10.5 UGR rep1

data_processing:
Sequencing reads were processed using the RNA-seq analysis pipelines of Geneprof  (Halbritter et al., 2012)
Sequencing reads were aligned with Bowtie (Langmead et al., 2009) v0.12.3 (2012-04-10).
The mRNA levels per gene were quantified by a custom script in Geneprof which accounts for multi-mapping reads. Briefly, all uniquely mapped reads overlapping with each annotated gene (Ensembl 58 Mouse Genes, NCBIM37) were summed, while ambiguously mapped genes were divided into fractions, weighted proportionally to the number of uniquely mapped genes in each possible gene assignment.
Read counts were then scaled per million (RPM)
Differential expression was with DESeq (Anders and Huber, 2010) (2011-03-15)
Genome_build: mm9
Supplementary_files_format_and_content: matrix contains normalised sequencing reads per million (RPM), the log2 fold change and adjusted p-value (output of DESeq) from comparisons between groups

source_name: E10.5 UGR

extract_protocol:
Embryonic aorta-gonad-mesonephros regions were subdissected, pooled and total RNA was extracted from these pools with Qiagen RNeasy minikit (QIAGEN) including DNase I treatment (QIAGEN).
RNA sequencing libraries were prepared with a TruSeq RNA Library Preparation Kit (Illumina) and multiplexed.

tag: strain background

tag: developmental stage

value: UGR


title: E10.5 UGR rep3


title: E10.5 UGR rep2


title: E10.5 AoV rep2

source_name: E10.5 AoV

value: AoV


title: E10.5 AoV rep1


title: E10.5 AoD rep3

source_name: E10.5 AoD

value: AoD


title: OP9 Reaggregate2


title: 4A_ILL13_SRL_RNAseq


title: E9.5 AoV rep3

source_name: E9.5 AoV


title: E10.5 AoV rep3


title: E9.5 AoV rep1


title: E10.5 AoD rep2


title: E9.5 AoD rep3

source_name: E9.5 AoD


title: E9.5 AoD rep2


title: p075

data_processing:
Illumina software used for basecalling and demultiplexing
Sequenced reads were trimmed for adaptor sequence with trimgalore using the following parameters. trim_galore --clip_R1 4 --three_prime_clip_R1 4.
After adapter removal the reads were trimmed to 99.9% sequencing quality and all sequence reads ranging from 15-nt to 40-nt were retained.
The raw read counts were quantile normalized according to Bolstad et al. (2003,Bioinformatics 19, 185–193) with a modification preventing the allocation of read counts to sequence tags not expressed in the sample.
The normalized read counts were scaled to one million reads per library resulting in read counts per million quantile normalized (rpmqn) reads
Supplementary_files_format_and_content: space-delimited text file include rpmqn values for each sample

source_name: whole seedling

extract_protocol:
Total RNA was isolated with mirVana miRNA isolation kit (Ambion, Thermo Scientific).
Illumina-compatible sequencing libraries were generated using the NEXTflex Small RNA Sequencing Kit v2 (BIOO SCIENTIFIC) and following the manufacturers recommendations with 1 µg total RNA. Libraries were sequenced on an Illumina HiSeq 4000 with 50 bp single end reads.

value: 7 days after sowing

tag: genotype

value: whole seedling


title: OP9 Flat3


title: E9.5 AoD rep1


title: OEP02_N712_S508

city: Berkeley

first: Diya

last: Das

state: California

address: 265 Life Sciences Addition #3200

department: Molecular & Cell Biology

institute: University of California, Berkeley

description:
processed data file:
oeHBC_Cufflinks_eSet_counts_table.txt
oeHBC_Cufflinks_eSet_fpkm_table.txt
oeHBC_Cufflinks_eSet_tpm_table.txt
oeHBC_RSEM_eSet_expectedCounts_table.txt
oeHBC_RSEM_eSet_fpkm_table.txt
oeHBC_RSEM_eSet_tpm_table.txt
oeHBC_kallisto_eSet_estimatedCounts_table.txt
oeHBC_kallisto_eSet_tpm_table.txt
oeHBC_Cufflinks_eSet.Rda
oeHBC_RSEM_eSet.Rda
oeHBC_kallisto_eSet.Rda
oeHBC_WTKOregen_countsMatrix.txt
oeHBC_diffregen_countsMatrix.txt

data_processing:
Illumina CASAVA bcl2fastq_v2.17 software used for basecalling.
Reads were aligned to the GRCm38.3 (mm10, patch release 3) mouse genome assembly with Tophat2 (Version 2.1.1), and low quality reads were removed with Trimmomatic (Version 0.3.2).
Gene level counts were calculated using Tophat (Version 2.1.1) alignments and featureCounts (Version 1.5.0-p3). TPMs were derived from Cufflinks (Version 2.2.1) FPKMs.
As a second strategy for getting gene level counts, we used RSEM (Version 1.2.31) to get expected counts.
As a third stategy for getting gene level counts, we used kallisto (Version 0.43.0) to obtain estimated counts and RPKMs.
Genome_build: GRCm38.3 (mm10, patch release 3)
Supplementary_files_format_and_content:
tab-delimited text files include gene level count, FPKM, and TPM values for each sample derived from Cufflinks and featureCounts
tab-delimited text files include gene level expected count, FPKM, and TPM values for each sample derived from RSEM
tab-delimited text files include gene level estimated count and TPM values for each sample derived from kallisto
ExpressionSets that include all metadata and the appropriate count data for each of our three alignment and gene level count procedures (oeHBC_Cufflinks_eSet, oeHBC_RSEM_eSet, oeHBC_Kallisto_eSet)
oeHBC_phenoData.txt: metadata on samples including experimental condition and batch; includes samples from GSE95601
oeHBC_Cufflinks_eSet_counts_table.txt: abundance measurements (featureCounts), text file; includes samples from GSE95601
oeHBC_Cufflinks_eSet_fpkm_table.txt: abundance measurements (Cufflinks), text file; includes samples from GSE95601
oeHBC_Cufflinks_eSet_tpm_table.txt: abundance measurements (derived from Cufflinks fpkms), text file; includes samples from GSE95601
oeHBC_Cufflinks_eSet_featureData.txt: information about the genes
oeHBC_Cufflinks_eSet_protocolData.txt: QC metrics, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_expectedCounts_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_fpkm_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_tpm_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_RSEM_eSet_featureData.txt: information about the genes
oeHBC_RSEM_eSet_protocolData.txt: QC metrics, text file; includes samples from GSE95601
oeHBC_kallisto_eSet_estimatedCounts_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_kallisto_eSet_tpm_table.txt: abundance measurements, text file; includes samples from GSE95601
oeHBC_kallisto_eSet_featureData.txt: information about the genes
oeHBC_Cufflinks_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data; includes samples from GSE95601
oeHBC_RSEM_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data; includes samples from GSE95601
oeHBC_kallisto_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data; includes samples from GSE95601
oeHBC_WTregen_countsMatrix.txt: normalized counts matrix (log2), text file
oeHBC_WTKOregen_countsMatrix.txt: normalized counts matrix (log2), text file
oeHBC_diffregen_countsMatrix.txt: normalized counts matrix (log2), text file; includes samples from GSE95601

source_name: Krt5-Rosa-eYFP_Sox2 cKO_72 hrs post tamoxifen_uninjured

extract_protocol:
dissociation protocol: Olfactory epithelium was dissected from transgenic animals; the dorsal region corresponding to the sensory olfactory epithelium was isolated and dissociated with papain for 25 minutes.  Labeled cells were collected by FACS.
single cell isolation, lysis, RT, amplification: The Fluidigm C1 system was used for single cell capture, cell lysis, and reverse transcription to make cDNA, and amplification (C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq; SMARTer Ultra Low RNA Kit for the Fluidigm C1 System). Cell capture was performed at room temperature.
sequencing library synthesis: The Nextera XT DNA Sample Preparation Kit (Illumina cat# FC-131-1096) and Index Kit A-D (cat# FC-131-2001-4) were used to synthesize sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Single-cell RNA-sequencing.  scRNA-Seq was performed on Illumina HISEQ 2500 sequencers; up to 192 samples were sequenced per lane, often in Rapid Run mode.

tag: sex type

value: M

tag: age

value: olfactory epithelium

value: Horizontal basal cell (HBC) stem cell

tag: expt condition

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: MEDIUM

tag: c1 machine id

value: FRODO

tag: ercc spike-in dilution


title: OEP02_N712_S507

tag: strain background

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc


title: OEP02_N712_S504

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set


title: E10.5 AoD rep1

tag: developmental stage


title: OEP02_N712_S506

tag: strain background

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N712_S502

tag: sex type

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: OEP02_N711_S508

tag: strain background

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N712_S503

tag: sex type

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N711_S507

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: OEP02_N712_S505

tag: strain background

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N710_S508

tag: sex type

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N712_S501

tag: age

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id


title: OEP02_N711_S506

tag: strain background

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: E9.5 AoV rep2

tag: developmental stage


title: OEP02_N711_S502

tag: sex type

tag: age

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N711_S501

tag: strain background

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N710_S503

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N710_S505

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N709_S507

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N709_S505

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N709_S502

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N708_S508

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N710_S506

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N709_S503

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N710_S504

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N709_S508

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N710_S502

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N709_S506

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N710_S507

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N709_S504

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N709_S501

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N708_S505

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N708_S504

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N708_S503

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N707_S507

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N707_S504

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N707_S506

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N707_S508

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N707_S502

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N706_S508

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N707_S501

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N708_S507

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N710_S501

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N708_S506

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N706_S506

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N706_S504

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N708_S501

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N707_S503

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N706_S501

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N705_S508

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N705_S505

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N706_S507

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N704_S508

description:
processed data file:
oeHBC_Cufflinks_eSet_counts_table.txt
oeHBC_Cufflinks_eSet_fpkm_table.txt
oeHBC_Cufflinks_eSet_tpm_table.txt
oeHBC_RSEM_eSet_expectedCounts_table.txt
oeHBC_RSEM_eSet_fpkm_table.txt
oeHBC_RSEM_eSet_tpm_table.txt
oeHBC_kallisto_eSet_estimatedCounts_table.txt
oeHBC_kallisto_eSet_tpm_table.txt
oeHBC_Cufflinks_eSet.Rda
oeHBC_RSEM_eSet.Rda
oeHBC_kallisto_eSet.Rda
oeHBC_WTregen_countsMatrix.txt
oeHBC_WTKOregen_countsMatrix.txt
oeHBC_diffregen_countsMatrix.txt

source_name: Krt5-Rosa-eYFP_96 hrs post injury

tag: sex type

value: FF

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

value: SMALL


title: OEP02_N704_S506

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N706_S505

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N704_S502

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N706_S502

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N704_S507

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N706_S503

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N703_S505

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N703_S508

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N708_S502

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id


title: OEP02_N705_S506

tag: strain background

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution


title: OEP02_N705_S507

tag: tissue

tag: cell type

tag: expt condition

tag: number of animals

tag: visual qc

tag: facs selection

tag: c1 batch id

tag: dilution plate coordinate


title: OEP02_N707_S505

tag: sex type

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id