title: ZFTMA_untreated_RRBS

city: Ghent

first: Sandra

last: Steyaert

address: Coupure Links 653

country: Belgium

institute: Ghent University

description: Sample 10

data_processing:
For each sample, MethylCap-seq paired-end reads were mapped with Bowtie2 (v2.1.0). The mapping parameters were chosen so that only paired-end reads that mapped uniquely and concordantly on the zebra finch reference genome (assembly taeGut3.2.4, Ensembl release 72) within a maximum of 400 bp of each other were retained. Seed mismatches, length and interval during multiseed alignment were set to the default values. For RRBS, paired-end reads were mapped with Bismark (v0.9.0) in Bowtie2-mode. Again, default values were chosen for the multiseed alignment and only concordantly, uniquely mapped reads with a maximum insert size of 500 bp were withheld. Paired-end RNA-seq reads were mapped with STAR (v2.3.0). Here, reads mapping up to 10 places on the zebra finch genome were allowed with a maximum of 6 mismatches per fragment, i.e. read pair. For MethylCap-seq, duplicate fragments, i.e. fragments with the exact same location of both paired-end reads, were disposed as these are most likely the result of amplification of the same sequence reads during library preparation. As for RNA-seq and RRBS duplicate reads are expected - they arise from both the enzymatic cutting (RRBS)/limited library complexity (RNA-seq) as well as from the PCR step and there is no simple way to distinguish between these two sources of duplicate reads - they were retained for further analysis.
The mapped RNA-seq reads were converted to fragment counts per exon and grouped per gene with the R-package Rsubread (v1.12.0). Gene annotations were obtained from Ensembl (release 72).
In order to summarize the MethylCap-seq reads, it was necessary to first identify all possibly methylated regions in the zebra finch genome (Methylation Peaks). This was done by taking the summed coverage of both ZFTMA and G266 cell line control sample results (i.e. DMSO-treated), and by evaluating different coverage thresholds for “significant” methylation. Assuming that the large majority of methylation events in both cell lines is conserved between both cell lines, the ZFTMA RRBS results were used to select an optimal threshold. Subsequently, Methylation Peaks were defined as all genomic regions where every position has a total coverage larger than or equal to this optimal coverage threshold. Additionally, these regions were trimmed at both ends so that the final regions all start and end with a CpG. Finally, for each sample, the non-duplicate, uniquely mapped MethylCap-seq reads could be summarized into fragment counts per Methylation Peak.
Normalization of the MethylCap-seq counts between the two treatments was performed based on the reads that mapped in non-Methylation Peaks, i.e. the library size of the “noise reads”. The rationale of this in-house method was that despite the performed treatment, the observed noise, i.e. amount of reads between Methylation Peaks, should be similar between the two G266 samples as well as between the two ZFTMA samples. Normalization of the RNA-seq gene counts was performed with the PoissonSeq package implemented in R (v1.1.2).
Genome_build: Taeniopygia_guttata-3.2.4
Supplementary_files_format_and_content: The .txt file reports RRBS counts.
Supplementary_files_format_and_content: The .bedGraph file is a methylation call output file.

organism: Taeniopygia guttata

source_name: ZFTMA cells

growth_protocol: Cells were cultured in DMEM high glucose medium (Life Technologies 41965039) supplemented with 10% heat inactivated fetal bovine serum (Life Technologies 102070106), 2% heat inactivated chicken serum (Life Technologies 15140122). The cultures were maintained at 37°C, 5% CO2 and 95-98% humidity.

extract_protocol:
Bisulfite treatment, library preparation and sequencing of the untreated ZFTMA DNA sample were done by BaseClear, using the Zymo Research EpiQuest bisulfite and library preparation procedures.  For this sample, 500 ng genomic DNA (gDNA) was checked for integrity and lack of degradation by agarose gel electrophoresis and the concentration was measured by a non-UV method. The DNA was subsequently fragmented, size selected (150-450 bp) and a bisulfite conversion was performed. Next, Illumina adapters were added and the fragments amplified with a PCR amplification. The length distribution of the resulting library was checked on a BioAnalyzer (Agilent Technologies G2940CA) and quantified. The quantified and converted DNA libraries were loaded on the Illumina HiSeq2000 platform and a paired-end sequencing run was performed as subscribed in the Illumina protocol ‘performing a multiplexed paired-end run’ (2 times 50 cycles).
Genomic DNA was extracted from an untreated ZFTMA cell line as well as from AZA- and DMSO-treated G266 and ZFTMA cell lines using the DNeasy mini kit (Qiagen 69506) while RNA was extracted from AZA- and DMSO-treated G266 and ZFTMA cell lines using the RNeasy mini kit (Qiagen 74106), both according to the manufacturer’s instructions. DNA and RNA concentrations were measured using Nanodrop 1000 (Thermo Fisher Scientific).

treatment_protocol: Cells were treated for 72 hours with 1 μM concentration of AZA (= demethylation treatment, Sigma-Aldrich A3656), with DMSO as a solvent control, or left untreated. Both AZA and DMSO inductions were repeated every 24 hours, as AZA is known to be relative unstable in aqueous solution. Upon collection, the cells were divided into two halves for which subsequently one half was used for DNA isolation, and the second half for RNA isolation.

tag: cell line

value: ZFTMA

tag: gender

value: female

value: no treatment


title: 311

status: Public on Dec 10 2015

type: SRA

city: Shanghai

first: Xu

last: Zhang

address: 320 Yue Yang Road

department: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

country: China

institute: Institute of neuroscience

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.9 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -m 0 -g 2  --read-realign-edit-dist 1
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed using Fisher-test function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: lumbar DRG neuron

growth_protocol: GFP-labled APL cells were expanded in vivo via transplantation into syngeneic mice.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

tag: strain

tag: tissue

value: dorsal root ganglion (DRG) neurons


title: ZFTMA_AZA_RNAseq

description: Sample 9

data_processing:
For each sample, MethylCap-seq paired-end reads were mapped with Bowtie2 (v2.1.0). The mapping parameters were chosen so that only paired-end reads that mapped uniquely and concordantly on the zebra finch reference genome (assembly taeGut3.2.4, Ensembl release 72) within a maximum of 400 bp of each other were retained. Seed mismatches, length and interval during multiseed alignment were set to the default values. For RRBS, paired-end reads were mapped with Bismark (v0.9.0) in Bowtie2-mode. Again, default values were chosen for the multiseed alignment and only concordantly, uniquely mapped reads with a maximum insert size of 500 bp were withheld. Paired-end RNA-seq reads were mapped with STAR (v2.3.0). Here, reads mapping up to 10 places on the zebra finch genome were allowed with a maximum of 6 mismatches per fragment, i.e. read pair. For MethylCap-seq, duplicate fragments, i.e. fragments with the exact same location of both paired-end reads, were disposed as these are most likely the result of amplification of the same sequence reads during library preparation. As for RNA-seq and RRBS duplicate reads are expected - they arise from both the enzymatic cutting (RRBS)/limited library complexity (RNA-seq) as well as from the PCR step and there is no simple way to distinguish between these two sources of duplicate reads - they were retained for further analysis.
The mapped RNA-seq reads were converted to fragment counts per exon and grouped per gene with the R-package Rsubread (v1.12.0). Gene annotations were obtained from Ensembl (release 72).
In order to summarize the MethylCap-seq reads, it was necessary to first identify all possibly methylated regions in the zebra finch genome (Methylation Peaks). This was done by taking the summed coverage of both ZFTMA and G266 cell line control sample results (i.e. DMSO-treated), and by evaluating different coverage thresholds for “significant” methylation. Assuming that the large majority of methylation events in both cell lines is conserved between both cell lines, the ZFTMA RRBS results were used to select an optimal threshold. Subsequently, Methylation Peaks were defined as all genomic regions where every position has a total coverage larger than or equal to this optimal coverage threshold. Additionally, these regions were trimmed at both ends so that the final regions all start and end with a CpG. Finally, for each sample, the non-duplicate, uniquely mapped MethylCap-seq reads could be summarized into fragment counts per Methylation Peak.
Normalization of the MethylCap-seq counts between the two treatments was performed based on the reads that mapped in non-Methylation Peaks, i.e. the library size of the “noise reads”. The rationale of this in-house method was that despite the performed treatment, the observed noise, i.e. amount of reads between Methylation Peaks, should be similar between the two G266 samples as well as between the two ZFTMA samples. Normalization of the RNA-seq gene counts was performed with the PoissonSeq package implemented in R (v1.1.2).
Genome_build: Taeniopygia_guttata-3.2.4
Supplementary_files_format_and_content: tab-delimited text files containing read counts per Methylation Peak (MethylCap-seq) or per gene (RNA-seq)

molecule: total RNA

extract_protocol:
RNA samples were analyzed with both the Quant-iTTM Ribogreen® RNA Assay Kit (Invitrogen R11491) and the Agilent Eukaryote Total RNA 6000 Pico Chip (Agilent 5067-1513) to ensure adequate quality and quantity of total RNA. Prior to the library preparation, an rRNA depletion step was performed on 3 μg input RNA (Ribogreen® measurement) using the Ribo-ZeroTM Magnetic Kit (Human/Mouse/Rat, Epicentre MRZH11124). Next, cDNA libraries for the ZFTMA and G266 rRNA depleted samples (6 μl/sample) were prepared using the ScriptSeqTM v2 RNA-seq Library Preparation Kit (Epicentre SSV21124) following the manufacturer’s protocol. Library amplification was performed with 15 PCR cycles. Quality control of the libraries was assessed using an Agilent High Sensitivity DNA Chip (Agilent Technologies 5067-4526). The concentration was determined following Illumina’s qPCR Quantification Protocol Guide (Illumina SY-930-1010). After pooling the libraries, paired-end sequencing was performed by BaseClear on one lane (4 samples/lane) of the Illumina HiSeq2000 again following Illumina’s protocol ‘performing a multiplexed paired-end run’ (2 times 50 cycles).
Genomic DNA was extracted from an untreated ZFTMA cell line as well as from AZA- and DMSO-treated G266 and ZFTMA cell lines using the DNeasy mini kit (Qiagen 69506) while RNA was extracted from AZA- and DMSO-treated G266 and ZFTMA cell lines using the RNeasy mini kit (Qiagen 74106), both according to the manufacturer’s instructions. DNA and RNA concentrations were measured using Nanodrop 1000 (Thermo Fisher Scientific).

tag: treatment


title: ZFTMA_DMSO_RNAseq

description: Sample 8

value: dimethyl sulfoxide


title: G266_AZA_RNAseq

description: Sample 7

source_name: G266 cells

value: male


title: 282


title: 281


title: 284


title: 280


title: 279


title: G266_DMSO_RNAseq

description: Sample 6


title: ZFTMA_untreated_MethylCapseq

description:
Sample 5
processed data file: MethylationPeaks_counts.txt

library_source: genomic

molecule: genomic DNA

extract_protocol:
Methyl-CpG binding domain protein sequencing (MethylCap-seq),29 which combines enrichment of methylated DNA fragments by MBD-based affinity purification with massively parallel sequencing, was used to profile the DNA methylation pattern of the DMSO-, AZA- and untreated zebra finch cell lines, i.e. G266 and ZFTMA. The gDNA was sheared using Covaris S2 equipment with following settings: duty cycle 10%, intensity 5, 200 cycles per burst during 190 seconds to obtain fragments with an envisaged average length of 200 bp. The power mode was frequency sweeping, temperature 6-8°C and water level of 12. 2 μg was loaded in 130 μl TE (1:5) in a microtube with AFA intensifier. After DNA fragmentation, the methylated fragments were captured using Diagenode’s MethylCapTM kit (Diagenode AF-100-0048) according to the manufacturer’s instructions starting from a DNA concentration between 250 and 500 ng. Captured DNA was eluted in a 150 μl High Elution buffer and purified with MinElute PCR purification columns (Qiagen 28006). Purified DNA was used for library preparation, which was performed on the Apollo 324TM (IntegenX) using the Multiplexing Sample Preparation Oligonucleotide Kit (Illumina PE-400-1001). Size selection (100-350 bp) was done with Agencourt AMPure XP Beads (Beckman Coulter Inc. (Analis SA) A63882) in combination with polyethylene glycol (PEG). 22 μl of DNA was subjected to PCR following the Illumina Library Amplification Index Protocol (Illumina) with 21 cycles of PCR amplification using Phusion® High-Fidelity PCR Master Mix (New England BioLabs (NEB) M0532L) with primers of the Multiplexing Sample Preparation Oligonucleotide Kit (Illumina). PCR products were purified with the High Pure PCR Cleanup Micro Kit (Roche Applied Science 04983912001). Next, libraries were assessed using an Agilent DNA 1000 Chip (Agilent Technologies 5067-1504). The concentration was determined following Illumina’s qPCR Quantification Protocol Guide (Illumina SY-930-1010). After pooling the libraries, paired-end sequencing was performed by BaseClear on one lane (8 samples/lane) of the Illumina HiSeq2000 following the Illumina protocol ‘performing a multiplexed paired-end run’ (2 times 50 cycles).
Genomic DNA was extracted from an untreated ZFTMA cell line as well as from AZA- and DMSO-treated G266 and ZFTMA cell lines using the DNeasy mini kit (Qiagen 69506) while RNA was extracted from AZA- and DMSO-treated G266 and ZFTMA cell lines using the RNeasy mini kit (Qiagen 74106), both according to the manufacturer’s instructions. DNA and RNA concentrations were measured using Nanodrop 1000 (Thermo Fisher Scientific).


title: 276


title: ZFTMA_AZA_MethylCapseq

description:
Sample 4
processed data file: MethylationPeaks_counts.txt


title: 273


title: 272


title: 270


title: 309


title: 313


title: G266_AZA_MethylCapseq

description:
Sample 2
processed data file: MethylationPeaks_counts.txt


title: G266_DMSO_MethylCapseq

description:
Sample 1
processed data file: MethylationPeaks_counts.txt


title: 271


title: 277


title: 269


title: 310


title: 268


title: 267


title: 266


title: 265


title: 263


title: 232


title: 262


title: 229


title: 224


title: ZFTMA_DMSO_MethylCapseq

description:
Sample 3
processed data file: MethylationPeaks_counts.txt


title: 201


title: 199


title: 347


title: 197


title: 193


title: 191


title: 189


title: 183


title: 187


title: 182


title: 177


title: 171


title: 174


title: 173


title: 169


title: 165


title: 230


title: 166


title: 158


title: 164


title: 157


title: 156


title: 155


title: 194


title: 153


title: 152


title: 142


title: 144


title: 179


title: 141


title: 143


title: 140


title: 128


title: 329


title: 126


title: 167


title: 131


title: 122


title: 124


title: 121


title: 123


title: WQ_T_RNA_TGACCA

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

country: South Korea

institute: Seoul National University

data_processing:
Adaptor sequences and low quality bases with PHERD scores (Q) ≤ 20 were removed. And we employed Trimmomatic for removal of adapter sequences.
we performed assembly and mapping with the following specific parameters: (1) In order to make reference consensus and assemble the transcriptome, we combined left and right reads, respectively, in paired-end reads using 12 whole samples
Using combined left and right reads, we created the assembled transcriptome by Trinity.pl with ‘min_ker_cov_2’ option given the large number of reads
The read mapping into assembled transcriptome was performed using bowtie2 implemented in tophat2;
For the abundance estimation, we employed the RSEM tool, In addition, In order to annotate the genes, we employed TransDecoder.
Genome_build: n/a
Supplementary_files_format_and_content: CSV file including all samples (FPKM)

organism: Coturnix japonica

source_name: WQ breed testis

extract_protocol:
Total RNA was prepared from 4 tissues of 3 phenotypically different Japanese quails. Total RNA was extracted using TRIzol reagent (MRC).
Libraries were prepared using  illimina manual and platform.

tag: breed

value: WQ

value: testis


title: 120


title: WQ_O_RNA_CGATGT

source_name: WQ breed ovary

value: ovary


title: 154


title: 119


title: WQ_MB_RNA_GCCAAT

source_name: WQ breed male brain

value: male brain


title: 118


title: 117


title: 114


title: 116


title: 113


title: 112


title: WQ_FB_RNA_ACAGTG

source_name: WQ breed female brain

value: female brain


title: LQ_T_RNA_CCGTCC

source_name: LQ breed testis

value: LQ


title: 132


title: 111


title: 130


title: 110


title: 109


title: LQ_O_RNA_ATGTCA

source_name: LQ breed ovary


title: 108


title: LQ_MB_RNA_GTGAAA

source_name: LQ breed male brain


title: 106


title: 107


title: LQ_FB_RNA_GTCCGC

source_name: LQ breed female brain


title: 105


title: 103


title: 102


title: HQ_T_RNA_CTTGTA

source_name: HQ breed testis

value: HQ


title: HQ_O_RNA_CAGATC

source_name: HQ breed ovary


title: 100


title: 101


title: HQ_MB_RNA_AGTTCC

source_name: HQ breed male brain


title: 99


title: HQ_FB_RNA_AGTCAA

source_name: HQ breed female brain


title: 97


title: 98


title: Cflo.d1.brain.minor.1pct.linda.t1.mRNA

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

description:
DNA fragments sequenced following RNA isolation, polyA+ purification, and LinDA amplification
Cflor.d1.minor.brain.LinDA.controls.rnaseq.normalized.txt

data_processing:
Base calling was performed using Bcl2FastQ 2.0
All sequenced reads were aligned to the custom diploid C. floridanus reference genome; The diploid reference was first split into two pseudo-haplotypes by randomly partitioning the two alleles at each single nucleotide polymorphism into two haploid genome sequences. Mapping was performed against each refernece haplotype using an updated version of Glimmr with calls to Bowtie2 with options (--end-to-end --very-sensitive) and allowing each read to display valid alignment for up to 10 distinct genomic locations (-k 10). Successfully mapped reads were then merged into a single alignment file by retaining the alignments for a given read that contain fewer mismatches to the particular reference haplotype. For RNA-seq data, remaining unmapped reads were also aligned to a reference transcriptome containing full-length transcripts for annotated genes. Remaining unmapped reads were then trimmed in an iterative manner from full-length 75nt reads, to 55nt reads, to 35nt reads, where the 10 outer bases on either end of the read were removed at each step.
RNA-seq: Relative mRNA transcript abundance Yij for gene i in sample j was estimated as fragments per kilobase per million reads (FPKM) using Cufflinks v2.2.1; with the following flags for strand specificity and multi-read correction (--library-type fr-firststand -u). Expression levels were estimated from FPKM data by log transformation as follows: log2(Yij + 1), where the +1 addend provides a variance stabilizing function for weakly expressed transcripts. Expression levels were then normalized in three steps as follows: (1) quantile normalization; (2) scaling by genes with invariant expression across samples; (3) for scout brain samples only, quantile normalized and corrected data were further scaled by the mean expression of ERCC spike-in oligos. Invariant genes in step (2) were identified as those genes that have non-zero expression in all samples and a standard error of expression among samples was in the bottom 25th percentile (SE < 0.388) of all genes in consideration; in this way a total of 1305 invariant genes v were identified. Actin (Cflo_10344) and GAPDH (Cflo_07234) were always included as known reference genes. Corrected quantile normalized expression levels Q*ij in a given sample j were obtained by subtracting the average expression of invariant genes in sample j relative to their global average expression over all samples; Finally, these corrected values were scaled conservatively using the ERCC spike-in controls, where Eij = log2(Zij + 1) was used for ERCC expression Zij for oligo i in sample j, as this transformation yielded the highest average pairwise Pearson correlation between all 21 samples (0.92). Here, a correction factor was estimated as the relative shift in median expression of sample data Q*ij compared to median expression of corresponding ERCC data; RNA-seq data from one day-old minor and major brains was normalized as above, but without ERCC normalization (step 3); that is, final expression estimates were determined by Q*ij.
ChIP-seq: ChIP-seq alignment maps were quantitated using Glimmr; and normalized using custom software. The posterior probability of binding was computed for every nucleotide in the genome for H3K9ac and H3K27ac by normalizing to input samples, setting the prior probability of binding equal to 0.4 for H3K9ac and H3K27ac samples and 0.5 for input samples and default parameters otherwise. Resulting probability scores Pij for locus i in sample j were converted to a Phred-like enrichment score Eij = -10log10(1 – Pij); and then log transformed and normalized to the 75th percentile of per-nucldeotide enrichment scores genome-wide, Pj(75): Zij = log2(Eij / Pj(75)). H. saltator chromatin spike-in data were analyzed in the same manner, except only full-length reads were mapped to the H. saltator reference genome to maximize specificity. These data were used to identify the normalization method that would minimize the per nucleotide standard error among samples. To this end, upper-quartile normalization was chosen (average technical replicate error = 0.11), and empolyed to normalize C. floridanus data as well.
Genome_build: Custom fork of C. floridanus assembly v3.0 (Bonasio et al, Science 329, 2010), yielding a diploid reference genome
Supplementary_files_format_and_content: ChIP-seq data files are provided in wiggle format at 25bp resolution; RNA-seq data files are provided as normalized FPKM matrices.
Genome_build: cflo.v3.3 http://hymenopteragenome.org/drupal/sites/hymenopteragenome.org.camponotus/files/data/Cflo_3.3_scaffolds.fa.gz, http://hymenopteragenome.org/camponotus/?q=genome_consortium_datasets

organism: Camponotus floridanus

source_name: Central brain from one day-old minor

growth_protocol: Ant colonies have been maintained in a sealed environmental growth chamber kept at a constant temperature of 25°C with constant humidity of 50% and a 12:12 light:dark cycle. Ants are fed twice a week with an ample supply of water, 20% sugar water (sucrose cane sugar), and Bhatkar–Whitcomb diet

extract_protocol:
RNA extract protocol: A 15µL aliquot representing 15% of cells in a single brain was prepared after light sonication; Total RNA was purified by phenol:chloroform extraction and purification using RNAse-free Agencourt AMPure XP beads (Beckman Coulter, Inc.). 1µL of ERCC RNA Spike-In Mix (Ambion) was added to each 15µL aliquot to total RNA to facilitate transcript-level normalization relative to cell number and to control for technical variation during library preparation. The mRNA fraction of RNA was purified by selection for poly adenylated transcripts using oligo(dT)25 Dynabeads (Invitrogen); cDNA was produced from total RNA using SuperScript III Reverse Transcriptase (Invitrogen), and second strand synthesis was performed using dUTP to preserve strand specificity; Strand-specific RNA-seq libraries were subsequently produced for these dUTP incorporated dsDNA libraries after one round of linear amplification (LinDA)
ChIP extract protocol: Chromatin immunoprecipitation (ChIP) was performed on individual scout brains using 45µL of remaining cell material (60e3–75e3 cells) for a subset of the same brains used for RNA-seq according to Simola and Ye, et al, Genome Res 23, 2013; brain tissue was crosslinked with formaldeyde for 5 min.; After mixing C. floridanus (75µg/IP) and H. saltator (1.88µg/IP) chromatin, IPs were performed using 1µg antibody
NEB Next Ultra, NEB Multiplex Barcode Oligos

treatment_protocol: 15 25–30 day-old minors were isolated from the designated colony, placed into a 195c nest box, and provided with 0.5% DMSO, 50µM TSA or 50µM TSA in combination with 50µM or 100µM C646 dissolved in 0.5% DMSO in 20% sugar water; scouts were frozen on dry ice after 45 days of treatment

tag: colony

tag: dev. stage

value: Adult (post-eclosion)

tag: age

tag: morphology

value: Minor worker

tag: behavioral caste

value: Callow

tag: treatment duration

tag: foundress origin

value: Florida Keys, FL, USA

tag: modification

value: dUTP-stranded RNA (polyA+)

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: 95


title: 96


title: Cflo.d1.brain.minor.4pct.linda.t4.mRNA


title: 94


title: 90


title: 93


title: Cflo.d1.brain.minor.4pct.linda.t2.mRNA


title: 91


title: 92


title: Cflo.d1.brain.minor.4pct.linda.t3.mRNA


title: 89


title: 104


title: Cflo.d1.brain.minor.4pct.linda.t1.mRNA


title: 88


title: 85


title: Cflo.d1.brain.minor.75pct.nolinda.t1.mRNA

description:
DNA fragments sequenced following RNA isolation, polyA+ purification
Cflor.d1.minor.brain.LinDA.controls.rnaseq.normalized.txt


title: 86


title: 82


title: 81


title: Cflo.minor.scout.DMSO.b20.Input

description:
Input DNA for ChIP
none

source_name: Central brain from adult minor scout

value: Scout

value: DMSO

value: ad lib feeding in 20% sugar water for 45 days

value: Input


title: Cflo.minor.scout.DMSO.b19.Input

description:
Input DNA for ChIP
none


title: 80

value: dorsal root ganglion (DRG) neurons


title: Cflo.minor.scout.TSA+C646.b15.Input

description:
Input DNA for ChIP
none


title: 78


title: 76


title: Cflo.minor.scout.DMSO.b17.Input

description:
Input DNA for ChIP
none


title: h2b(RNAi)B

city: Dallas

first: James

last: Collins

state: TX

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern

description:
control vs. h2b(RNAi).xls
h2b_9_17_ACTTGA_L006_R1_001

data_processing:
The quality-scores line in fastq files processed with Casava1.8
Reads Per Kilobase of transcript per Million mapped reads were determined using the RNAseq module in CLC Genomics Workbench (version 5) using defult settings.
Samples were mapped to the annotated Schistosoma mansoni genome version 5.  The GFF file used for annotation was downloaded from the Wellcome Trust Sanger Institute Schistosoma mansoni ftp site: ftp://ftp.sanger.ac.uk/pub/pathogens/Schistosoma/mansoni/genome/GFF/
Genome_build: Schistosoma mansoni Version 5
Supplementary_files_format_and_content: An excel speadsheet that includes RPKM values.  Speadsheet also includes mean RPKM values for both control and irradiated samples.

organism: Schistosoma mansoni

source_name: Adult Schistosoma mansoni tissue without head or testes

extract_protocol:
Total RNAi was extracted with Trizol and treated with Dnase.
The RNAseq libraries were prepared with Illumina's 'TruSeq RNAseq Sample Prep kit'

treatment_protocol: Parasites > 6 weeks post-infection were harvested from mice, suspended in Basch media 169, and exposed to 200 Gy of γ-irradiation using a Gammacell-220 Excel with a Co60 source (Nordion, Ottawa, ON, Canada), mock irradiated, or cultured in the presence of dsRNA.  At either 14D following irrdiation or 21D of RNAi treatment, males were separated from female parasites using ethyl 3-aminobenzoate methanesulfonate.  Following separation, the head and testes of males were removed and total RNA was extracted for RNAseq.

value: NMRI

value: h2b RNAi treated


title: 74

source_name: lumbar DRG neuron


title: h2b(RNAi)A

description:
control vs. h2b(RNAi).xls
h2b_8_15_CAGATC_L006_R1_001


title: 72-2


title: fgfrA(RNAi) B

description:
control vs. fgfrA(RNAi).xls
fgfrA_8_30_ACAGTG_L006_R1_001

value: fgfrA RNAi treated


title: fgfrA(RNAi) C

description:
control vs. fgfrA(RNAi).xls
fgfrA_9_17_GCCAAT_L006_R1_001


title: Cflo.minor.scout.TSA.b9.Input

description:
Input DNA for ChIP
none

value: 50µM TSA


title: 72-1


title: Cflo.minor.scout.TSA.b7.Input

description:
Input DNA for ChIP
none


title: fgfrA(RNAi) A

description:
control vs. fgfrA(RNAi).xls
fgfrA_8_15_TGACCA_L006_R1_001


title: 70


title: Cflo.minor.scout.TSA.b3.Input

description:
Input DNA for ChIP
none


title: 71


title: 69


title: Control RNAi B

description:
control vs. fgfrA(RNAi).xls
Control_8_30_CGATGT_L006_R1_001

value: Control RNAi treated


title: Control RNAi C

description:
control vs. fgfrA(RNAi).xls
control vs. h2b(RNAi).xls
Control_9_17_TTAGGC_L006_R1_001


title: Cflo.minor.scout.DMSO.b20.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.DMSO.b20.H3K27ac.wig.txt

value: Abcam


title: 68


title: Cflo.minor.scout.DMSO.b19.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.DMSO.b19.H3K27ac.wig.txt


title: 67


title: Control RNAi A

description:
control vs. fgfrA(RNAi).xls
control vs. h2b(RNAi).xls
Control_8_15_ATCACG_L006_R1_001


title: 200Gy C

description:
Control D14 vs. 200 Gy D14.xls
D14_IRR_200GyC_GGCTAC_L004_R1_001

value: Irradiated with 200 gy


title: 200Gy B

description:
Control D14 vs. 200 Gy D14.xls
D14_IRR_200GyB_TAGCTT_L004_R1_001


title: 38


title: Cflo.minor.scout.TSA+C646.b14.Input

description:
Input DNA for ChIP
none

value: Adult (post-eclosion)


title: Cflo.minor.scout.TSA+C646.b15.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA+C646.b15.H3K27ac.wig.txt

value: Minor worker


title: Cflo.minor.scout.TSA+C646.b14.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA+C646.b14.H3K27ac.wig.txt


title: Cflo.minor.scout.TSA+C646.b13.Input

description:
Input DNA for ChIP
none

value: 50µM TSA + 50µM C646


title: 200Gy A

description:
Control D14 vs. 200 Gy D14.xls
D14_IRR_200GyA_GATCAG_L004_R1_001


title: Cflo.minor.scout.TSA+C646.b13.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA+C646.b13.H3K27ac.wig.txt

value: Florida Keys, FL, USA


title: 35


title: 37


title: 0Gy B

description:
Control D14 vs. 200 Gy D14.xls
D14_0GyB_TTAGGC_L004_R1_001

value: no treatment


title: Cflo.minor.scout.TSA.b7.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA.b7.H3K27ac.wig.txt

value: Scout


title: Cflo.minor.scout.TSA.b9.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA.b9.H3K27ac.wig.txt


title: 0Gy A

description:
Control D14 vs. 200 Gy D14.xls
D14_0GyA_ATCACG_L004_R1_001


title: Cflo.minor.scout.TSA.b3.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA.b3.H3K27ac.wig.txt


title: Cflo.minor.scout.DMSO.b17.H3K9ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.DMSO.b17.H3K9ac.wig.txt

value: DMSO

value: Active Motif


title: Cflo.minor.scout.DMSO.b17.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.DMSO.b17.H3K27ac.wig.txt

value: ad lib feeding in 20% sugar water for 45 days


title: Cflo.minor.scout.TSA+C646.b15.H3K9ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA+C646.b15.H3K9ac.wig.txt


title: 29

value: dorsal root ganglion (DRG) neurons


title: 25


title: 31


title: 27


title: Cflo.minor.scout.TSA.b9.H3K9ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
Cflo.minor.scout.TSA.b9.H3K9ac.wig.txt


title: Cflo.minor.scout.DMSO.b21.mRNA

description:
DNA fragments sequenced following RNA isolation, polyA+ purification, and LinDA amplification
Cflor.minor.scout.brain.rnaseq.normalized.txt

value: dUTP-stranded RNA (polyA+)


title: 23


title: 275


title: 24


title: Cflo.minor.scout.DMSO.b20.mRNA


title: 22


title: 21


title: Cflo.minor.scout.DMSO.b18.mRNA


title: Cflo.minor.scout.DMSO.b17.mRNA


title: Cflo.minor.scout.DMSO.b19.mRNA


title: 34


title: 0Gy C

description:
Control D14 vs. 200 Gy D14.xls
D14_0GyC_ACTTGA_L004_R1_001

value: NMRI


title: 18


title: Cflo.minor.scout.TSA+C646.b16.mRNA


title: Cflo.minor.scout.TSA+C646.b15.mRNA


title: 13


title: Cflo.minor.scout.TSA+C646.b14.mRNA


title: 14


title: 6


title: 5


title: Cflo.minor.scout.TSA+C646.b13.mRNA


title: 4


title: Cflo.minor.scout.TSA+C646.b12.mRNA


title: Cflo.minor.scout.TSA+C646.b11.mRNA


title: 4 SAFB1 iCLIP

city: Bristol

last: Uney

address: Medical School, University Walk

department: School of Clinical Sciences

country: United Kingdom

institute: University of Bristol

description: Stress 42oC

data_processing:
Library strategy: CLIP-Seq
Data was processed using RTA version 1.13.48, with default filter and quality settings.
The reads were demultiplexed (allowing no mismatches in the index sequence) with CASAVA 1.8.2
The random bar-code sequences for the individual experiments were applied using the following RT primers: 5’-phosphate-NNXXXXNNNAGATCGGAAGAGCGTCGTGGATCCTGAACCGC-3’ where the unique experimental identifier (XXXX) was as follows: AACC, ACAC and AGGT for the anti-SafB1 antibody (Bethyl) experiments and CGAC for a no antibody control.
The random barcodes were registered and PCR-duplicates were removed along with any reverse-primer sequences.
The filtered iCLIP tag sequences were mapped to the human genome sequence (version hg19/GRCh37) allowing one mismatch using Bowtie version 1.0.1. Comparing cross-link nucleotide positions from three independent replicates assessed reproducibility, and allowed the z-score analysis of enriched pentamers at cross-link nucleotides to be calculated
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Kmer Z-scores: z-score 1 processed from sample 1 SAFB1 (GSM1954829); z-score 2 processed from sample 2 SAFB1(GSM1954830) etc.

organism: Homo sapiens

growth_protocol: SHSY-5Y cells were grown using standard cell culture techniques in DMEM-F12 media supplemented with 10% FBS (4 SAFB1, 5 SAFB1 & 6SAFB1 were exposed to a heat stress 42 degrees celcius)

extract_protocol:
iCLIP was performed with partial RNase I digestion and following SDS-PAGE analysis of immunoprecipitated SAFB1 the cross-linked RNA was extracted, reverse-transcribed and PCR-amplified. (For detailed protocol see reference Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J: iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. Journal of visualized experiments : JoVE 2011(50))
The iCLIP procedure introduces Illumina sequencing primer sequences into the cDNA libraries (Konig et al. Journal of visualized experiments : JoVE 2011(50)) during the reverse transcription and PCR-amplification steps.
High-throughput sequencing of iCLIP cDNA was performed on a HiSeq 2500 high output mode using v3 Illumina chemistry.

treatment_protocol: SHSY5Y neuroblastoma cells were irradiated once with 400 mJ/cm2 at 254 nm in a Stratalinker 1800 and SAFB1 was immunoprecipitated with protein G Dynabeads (Invitrogen) conjugated to rabbit anti-SafB1 antibody  (Bethyl laboratories Inc., A300-811A). The region corresponding to 140-200 kDa complexes was excised from the membrane to isolate the RNA and high-throughput sequencing of iCLIP cDNA was performed using Illumina GA2

tag: cell type

value: Neuroblastoma

tag: antibody

value: Bethyl SAFB1


title: 5 SAFB1 iCLIP

description: Stress 42oC


title: 6 SAFB1 iCLIP

description: Stress 42oC


title: Cflo.minor.scout.TSA.b10.mRNA

value: 50µM TSA


title: 2

tag: strain


title: 20

tag: tissue


title: Cflo.minor.scout.TSA.b8.mRNA

tag: treatment


title: Cflo.minor.scout.TSA.b9.mRNA


title: sihRRP6_E3

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

country: Germany

institute: MDC-Berlin

description: Differential expression datafile: full_list_edgeR_annotated_RRP6.txt

data_processing:
Sequenced reads were trimmed using fastx-trimmer (fastx version 0.0.13) with options -f 11 -l 110 -Q 33
Reads were mapped to the human hg19 (GrCh37) genome, using tophat version 2.0.10, with the options --library-type fr-firststrand -r -50 --mate-std-dev 40
Raw reads counts were generated using Ensembl 75 (GrCh37.p13) genes annotation and featureCounts (from the subread package, version 1.4.6) with the options -s 2 -p
Differential expression was calculated using the edgeR package (version 3.2.4), removing genes with less than 5 reads across all samples, normalized with the TMM method using "calcNormFactors", calculating dispersion with "estimateTagwiseDisp" and calling the differential expression with "exactTest"
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited Raw count files for each sequence (featureCount output). siNon samples = A3, A5, A7; siDGCR8= B1, B3, B5; sihRRP6=E1,E3,E4
Supplementary_files_format_and_content: edgeR output, annotated with gene names and types in .txt format

growth_protocol: Cells were grown under standard cell culture conditions

extract_protocol:
Isolated RNA was rRNA depleted
Illumina TruSeq V2 stranded Total RNA libraries

treatment_protocol: Depletions were generated by performing two rounds of siRNA knockdown. Cells were collected 72-96hrs after first siRNA transfection

tag: cell line

value: HeLa

value: sihRRP6 knockdown

tag: barcode

value: GTCCGC


title: sihRRP6_E1

value: CCGTCC


title: Cflo.minor.scout.TSA.b6.mRNA

tag: colony

tag: dev. stage

value: Adult (post-eclosion)

value: Minor worker


title: Cflo.minor.scout.TSA.b5.mRNA

tag: age

tag: morphology

value: Florida Keys, FL, USA


title: siDGCR8_B3

description: Differential expression datafile: full_list_edgeR_annotated_DGCR8.txt

value: siDGCR8 knockdown

value: CAGATC


title: siDGCR8_B5

value: GATCAG


title: siDGCR8_B1

value: GCCAAT


title: sihRRP6_E4

value: GTGAAA


title: Cflo.minor.scout.TSA.b4.mRNA

tag: behavioral caste

value: Scout

tag: treatment duration

value: ad lib feeding in 20% sugar water for 45 days

value: dUTP-stranded RNA (polyA+)


title: Cflo.minor.scout.TSA.b3.mRNA

tag: foundress origin

tag: modification


title: siNon_A7

value: control knockdown

value: ACAGTG


title: Cflo.minor.scout.TSA.b2.mRNA

value: 50µM TSA

tag: antibody vendor

tag: antibody catalog #


title: siNon_A5

value: HeLa

value: TGACCA


title: siNon_A3

value: CGATGT


title: ES single cell  47 Lane 002

status: Public on Dec 09 2015

city: boston

first: Luca

last: Pinello

state: MA

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were aligned using the STAR aligner (v2.3.1z12)using the UCSC mm9 genome assembly.
After alignment we counted the fragments for each isoform with the command featureCounts from the SUBREAD package (v1.4.5-p1) using the Refseq mm9 gene annotations from UCSC genome browser as reference.
Genome_build: mm9
Supplementary_files_format_and_content: Table containing fragment counts for each gene (rows) in each single cell (columns).

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured in feeder-free conditions. Cells cultured in serum were grown in Dulbecco’s Modified Eagle Medium (DMEM) + Glutamax (Gibco) + 15% fetal bovine serum (FBS, Gemini) + penicillin/streptomycin (Gibco) + non-essential amino acids (NEAA) (Gibco) + b-mercaptoethanol (EmbryoMax ES cell-qualified, Millipore) + 1,000U/ml  leukaemia inhibitory factor (LIF, Millipore).

extract_protocol:
Direct lysis on C1 ChIP
Single ESCs were captured on a medium-sized (10–17 mm cell diameter) microfluidic RNA-seq chip (Fluidigm) using the Fluidigm C1 system. Whole-transcriptome amplified cDNA was prepared on chip using the SMARTer Ultra Low RNA kit for Illumina (Clontech). Amplified cDNAs were diluted with C1 DNA dilution reagent, quantified using Quant-it HS system, and validated by qPCR with selected primers. Successfully amplified single-cell cDNA samples were selected and diluted to the same concentration. Single-cell libraries were constructed using the Nextera XT DNA Sample Preparation kit (Illumina), pooled using Nextera XT DNA Sample Preparation Index Kit (Illumina) and then sequenced using Hiseq 2500 (Illumina). Each library was sequenced twice on two lanes.

treatment_protocol: Culture with serum

tag: es clone

value: J1 ES cells

tag: passage

tag: sampling

value: Single cell

tag: culture protocol

value: Culture with serum


title: ES single cell  48 Lane 002


title: ES single cell  48 Lane 001


title: ES single cell  47 Lane 001


title: ES single cell  46 Lane 001


title: ES single cell  45 Lane 001


title: Cflo.minor.scout.TSA.b7.mRNA

value: Adult (post-eclosion)

value: Minor worker

tag: treatment

value: Florida Keys, FL, USA

tag: antibody lot #


title: ES single cell  44 Lane 001


title: ES single cell  43 Lane 001


title: ES single cell  42 Lane 001


title: ES single cell  43 Lane 002


title: ES single cell  42 Lane 002


title: ES single cell  41 Lane 002


title: ES single cell  46 Lane 002


title: ES single cell  41 Lane 001


title: ES single cell  39 Lane 002


title: ES single cell  38 Lane 001


title: ES single cell  39 Lane 001


title: ES single cell  38 Lane 002


title: ES single cell  37 Lane 002


title: Cflo.minor.scout.TSA.b1.mRNA


title: ES single cell  36 Lane 001


title: ES single cell  35 Lane 002


title: ES single cell  35 Lane 001


title: ES single cell  44 Lane 002


title: ES single cell  45 Lane 002


title: ES single cell  34 Lane 002


title: ES single cell  40 Lane 002


title: ES single cell  40 Lane 001


title: ES single cell  36 Lane 002


title: ES single cell  33 Lane 001


title: ES single cell  30 Lane 002


title: ES single cell  26 Lane 002


title: ES single cell  31 Lane 002


title: ES single cell  30 Lane 001


title: ES single cell  34 Lane 001


title: ES single cell  27 Lane 002


title: ES single cell  25 Lane 001


title: ES single cell  32 Lane 001


title: ES single cell  28 Lane 001


title: ES single cell  32 Lane 002


title: ES single cell  37 Lane 001


title: ES single cell  23 Lane 002


title: ES single cell  25 Lane 002


title: ES single cell  33 Lane 002


title: ES single cell  24 Lane 002


title: ES single cell  29 Lane 002


title: ES single cell  28 Lane 002


title: ES single cell  26 Lane 001


title: ES single cell  27 Lane 001


title: ES single cell  29 Lane 001


title: ES single cell  24 Lane 001


title: ES single cell  22 Lane 002


title: ES single cell  22 Lane 001


title: ES single cell  31 Lane 001


title: ES single cell  21 Lane 002


title: ES single cell  20 Lane 002


title: ES single cell  21 Lane 001


title: ES single cell  20 Lane 001


title: ES single cell  23 Lane 001


title: ES single cell  19 Lane 002


title: ES single cell  17 Lane 002


title: ES single cell  18 Lane 002


title: ES single cell  18 Lane 001


title: ES single cell  12 Lane 002


title: ES single cell  16 Lane 001


title: ES single cell  14 Lane 002


title: ES single cell  19 Lane 001


title: ES single cell  15 Lane 001


title: ES single cell  17 Lane 001


title: ES single cell  10 Lane 002


title: ES single cell  15 Lane 002


title: ES single cell  13 Lane 001


title: ES single cell  10 Lane 001


title: ES single cell  7 Lane 002


title: ES single cell  11 Lane 002


title: ES single cell  8 Lane 002


title: ES single cell  16 Lane 002


title: ES single cell  12 Lane 001


title: ES single cell  11 Lane 001


title: ES single cell  8 Lane 001


title: ES single cell  7 Lane 001


title: ES single cell  14 Lane 001


title: ES single cell  9 Lane 001


title: ES single cell  13 Lane 002


title: ES single cell  6 Lane 002


title: ES single cell  5 Lane 002


title: ES single cell  6 Lane 001


title: ES single cell  9 Lane 002


title: ES single cell  5 Lane 001


title: ES single cell  4 Lane 002


title: ES single cell  3 Lane 001


title: CiPSC-N6

city: Beijing

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
The transcriptome reads were aligned to the mouse genome using TopHat program
Aligned reads were assembled using Cufflinks program.
The gene expression level was calculated by using FPKM method.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking .txt file includes FPKM values for the analysis of gene expression

source_name: CiPSC cell line N6

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
RNA sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB).

treatment_protocol: Treatment protocol was described in Experimental Procedures section of the paper

tag: strain

tag: cell type

value: CiPSCs


title: ES single cell  3 Lane 002


title: ES single cell  1 Lane 001


title: ESC-1

source_name: Embryonic stem cells derived from mouse E3.5 embryo

value: ESCs


title: ESC-2


title: ES single cell  1 Lane 002


title: eXEN-2

source_name: eXEN cell line (gift from Dr. Rossant's laboratory) maintained in traditional XEN culture medium

value: wild-type ICR

value: eXEN cells


title: eXEN-1

source_name: eXEN cell line (gift from Dr. Rossant's laboratory) maintained in stage 1 medium (with VC6TF plus 20 ng/ml bFGF)


title: ES single cell  2 Lane 001


title: CiPSC-N4

source_name: CiPSC cell line N4


title: Day28

source_name: intermediate cells on day 28 during chemical reprogramming of MEFs

value: intermediate cells during chemical reprogramming of MEFs

tag: time

value: day 28


title: CiPSC-G3

source_name: CiPSC cell line G3


title: CiPSC-C2

source_name: CiPSC cell line C2


title: Day26

source_name: intermediate cells on day 26 during chemical reprogramming of MEFs

value: day 26


title: CiPSC-G1

source_name: CiPSC cell line G1


title: CiPSC-C3

source_name: CiPSC cell line C3


title: CeXEN-rep1

source_name: E3.5 embryo-derived XEN cells (eXENs) using stage 1 medium (with VC6TFAE plus 20 ng/ml bFGF)

value: CeXEN cells


title: Day16_rep2

source_name: intermediate cells on day 16 during chemical reprogramming of MEFs

value: day 16


title: CeXEN-rep2


title: Day20

source_name: intermediate cells on day 20 during chemical reprogramming of MEFs

value: day 20


title: Day16_rep1


title: CiPSC-C1

source_name: CiPSC cell line C1


title: Day12

source_name: intermediate cells on day 12 during chemical reprogramming of MEFs

value: day 12


title: MEFs_rep1

source_name: Mouse embryonic fibroblast cells from E13.5 embyos

value: MEFs


title: ES single cell  4 Lane 001

source_name: Mouse embryonic stem cells

value: J1 ES cells

value: Single cell


title: ES single cell  2 Lane 002

value: Culture with serum


title: MEFs_rep2


title: M_Pod_DZNep_H3K27me3 Chip-seq_3

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

description: Mouse podocytes treated with DZNep biological replicate 3

data_processing:
Basecalls were performed using CASAVA version 1.5.
ChIP-seq reads were aligned to the GRCm38/mm10 genome assembly using Bowtie v2.2.1 alignment software.
Aligned sequence read plots were generated using Integrated Genome Browser
ChIP-seq peak analysis was done using Cis Genome with default parameters
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: wig format

source_name: Terminally Differentiated Podocyte

growth_protocol: Mouse Podocyte were maintined in an undifferetiated state at 33 degrees C in RPMI media conating 10% FCS, 1% penicillin and streptomycin and interferon gamma (IFN g, 10U/mL Sigma-Aldrich, Cat No. I4777, Lot No. 069K1081). To obtain differentiated mouse podocytes, cells were transferred to 37 degrees C and maintained in RPMI media containing 10% FCS, 1% penicillin and streptomycin for 14 days before performing the experiment. Mouse podocytes were cultured in collagen type 1 coated 6 well plates.

extract_protocol:
Cells were processed using Magna ChIP™ A - Chromatin Immunoprecipitation Kit, Millipore,Cat No. 7-408, Lot No.2500615 to obtain the Chip DNA using H3K27me3 antibody
Libraries from the immunoprecipitated and whole cell lysate DNA were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina (NEB, Cat. No. E6200S).  In brief, immunoprecipitated DNA was first end-repaired, followed by a dA-Tailing of End Repaired DNA using NEBNext dA-Tailing reaction mixture (NEB, Cat No. E6053), and ligated to custom adapters with NEBNext adaptor (NEB E7500) having Oligos for Illumina. Fragments of 150 to 700 (+120 bp) bp of adaptor-ligated DNA were size-selected using AMPure XP Beads followed by ligation-mediated PCR amplification of the adaptor-ligated DNA using Phusion DNApolymerase.

treatment_protocol: Mouse Pododcyte were serum starved for overnight and treated either with DMSO or 5microM DZNep for 48 hours and harvested for immunoprecipitation and Chip-seq

value: Immortalized Mouse Podocyte

tag: chip antibody

value: H3K27me3 (Cell Signaling, 9733S, Lot 8)


title: M_Pod_DZNep_H3K27me3 Chip-seq_2

description: Mouse podocytes treated with DZNep biological replicate 2


title: M_Pod_Input_Control

description: Input DNA for control

value: None (input)


title: M_Pod_DZNep_H3K27me3 Chip-seq_1

description: Mouse podocytes treated with DZNep biological replicate 1


title: Male vehicle treatement, biological replicate 3

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: Sample L

data_processing:
Sequenced reads are mapped to Ensembl GRCm38 reference genome using Tophat2 v2.0.9 (default parameters)
The transcripts are assembled using Cufflinks v2.2.1 (default parameters)
The replicates assemblies are merged with the reference transcriptome annotation using Cuffmerge v.2.2.1 (default parameters).
Cuffdiff v2.2.1 (default parameters) is then used to calculate the expression levels and perform differential expression analysis using the merged assembly and the mapped reads.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample as produced by Cuffdiff

growth_protocol: Hypothalamus dissected from embryonic day 14.5 fetal mice were dissociated into single cells and then cultured as neurospheres

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The Ilumina Stranded Total RNA-Seq Kit was used to construct the library per manufactuer's instructions

treatment_protocol: Neurospheres at third passage were treated with 100 nM dexamethasone or equivalent volumes of ethanol vehicle for 4 hours

tag: age

value: embryonic day E14.5

tag: gender

value: Male

value: Vehicle


title: Male dexamethasone treatment, biological replicate 2

description: Sample I

value: Dexamethasone


title: M_Pod_Control_H3K27me3 Chip-seq_1

description: Mouse podocytes treated with DMSO biological replicate 1


title: Male vehicle treatement, biological replicate 2

description: Sample J


title: Female vehicle treatement, biological replicate 3

description: Sampel F

value: Female


title: Male dexamethasone treatment, biological replicate 3

description: Sample K


title: M_Pod_Control_H3K27me3 Chip-seq_2

description: Mouse podocytes treated with DMSO biological replicate 2


title: Female dexamethasone treatment, biological replicate 3

description: Sample E


title: Female vehicle treatement, biological replicate 2

description: Sample D


title: Female dexamethasone treatment, biological replicate 2

description: Sample C


title: Male vehicle treatement, biological replicate 1

description: Sample B


title: Male dexamethasone treatment, biological replicate 1

description: Sample A


title: Female vehicle treatement, biological replicate 1

description: Sample H


title: HCT116_Akti1/2_Replicate2 (RNA-Seq)

city: Boston

first: Ben

middle: S

last: Wittner

address: 185 Cambridge Street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.5 software used for basecalling.
Clipping of contaminating adapter sequences and trimming of low-quality read ends was done with Trimmomatic v0.25.
Average fragment length and its standard deviation were empirically determined for each sample with Bowtie v2.1.0.
Tophat v2.0.8b was used to align the reads to hg19 version of the human genome and transcriptome. Multiple mapping reads were excluded from subsequent analyses.
Fragments per kilobase per million reads (FPKMs) estimations for each annotated genomic feature were obtained with Cufflinks v2.1.1.
Ribosomal, mitochondrial and transfer RNAs were masked in the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Cufflinks v2.0.8b genes.fpkm_tracking output files (tab-delimited)

source_name: HCT116 colon carcinoma cells, Akti-1/2 treated

growth_protocol: MCF7 was maintained in DMEM, 10% FCS, 40mM glutamine, 100 U/mL penicillin, and 100µg/mL streptomycin; HCT116 was maintained in McCoy’s 5α medium supplemented with 10% FCS, 100U/mL penicillin, and 100µg/mL streptomycin. All cells were grown at 37ºC and 5% CO2.

extract_protocol:
Total RNA was purified using RNAeasy miniprep kit (Qiagen) and the RNA integrity was checked using RNA 6000 Nano assay on Agilent 2100 Bioanalyzer. 4µg of total RNA were used for library construction.
Purification, fragmentation and first strand synthesis were performed as described in the Illumina Tru-Seq RNA Sample kit v2. The second strand cDNA synthesis was modified using the dUTP second strand method. End repair, 3’ adenylation and adapter ligation steps were done using Tru-Seq protocol.

treatment_protocol: Cells were treated for 72h with vehicle (DMSO), Akti-1/2 inhibitor (HCT116: 20µM; MCF7: 2µM) (Sigma)

tag: cell line

value: colon carcinoma

tag: cell state

value: AKT1 Low


title: MCF7_DMSO_Replicate1 (RNA-Seq)

source_name: MCF7 breast adenocarcinoma cells, DMSO treated

value: breast adenocarcinoma

value: AKT1 WT


title: MCF7_DMSO_Replicate2 (RNA-Seq)


title: CDP_H3K27me3

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

institute: Institute for Biomedical Engineering

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (version 0.12.8) with the following parameter settings: -m 1 -a - - best - - strata
H3K4me3, H3K27me3 and H3K9me3 peaks were identified using SICER, a spatial clustering approach for the identification of ChIP-enriched regions. H3K4me1 and PU.1 peaks were identified by MACS software (version 1.4.2).
Genome_build: mm9
Supplementary_files_format_and_content: wig files of histone modification and PU.1 profiles were generated by IGVTools (version 2.1.7).

source_name: Common dendritic cell progenitor (CDP)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described before (Dahl and Collas, 2008) with minor modifications. Briefly, sorted cells were cross-linked at a concentration of 2 million cells/ml with 1% formaldehyde for 6 min at room temperature. Cross-linking was stopped with 0.125 M glycine. Chromatin sonification into fragments of 200-400 bp in size was done by Diagenode Bioruptor with cooling device at 4°C for 10 min with 30 s pulse/pause cycles. Sheared lysates were clarified by centrifugation at 12,000g (10 mins, 4°C). 10 µl Dynabeads Protein A (Life Technologies) were preincubated with either 1 µg IgG control (Santa Cruz) or specific antibodies for H3K4me1, H3K4me3, H3K9me3, H3K27me3 or PU.1. For immunoprecipitation sheared chromatin of 1 million cells was added to the preincubated beads over night at 4°C. Chromatin complexes were isolated by magnetic bead selection and washed with RIPA and TE buffer. Chromatin complexes were digested with 50 µg/ml RNase (Roche) at 37°C for 30 min. Immunoprecipitated DNA was purified using QIAquick PCR Purification Kit according to the manufacturer's protocol (Qiagen). DNA concentration of immunoprecipitated DNA was determined by using Qubit dsDNA HS Assay kit (Life Technologies).
Libraries were prepared and subjected to deep-sequencing on the Illunima platform according to then manufacturer's protocols.

value: Common dendritic cell progenitor (CDP)

value: H3K27me3 (Diagenode, pAb-069-050)


title: MPP_H3K4me3

source_name: Multipotent progenitor (MPP)

value: Multipotent progenitor (MPP)

value: H3K4me3 (Diagenode, pAb-003-050)


title: CDP_H3K4me3


title: HCT116_DMSO_Replicate1 (RNA-Seq)

source_name: HCT116 colon carcinoma cells, DMSO treated


title: M_Pod_Control_H3K27me3 Chip-seq_3

description: Mouse podocytes treated with DMSO biological replicate 3


title: HCT116_DMSO_Replicate2 (RNA-Seq)


title: HCT116_Akti1/2_Replicate1 (RNA-Seq)


title: Female dexamethasone treatment, biological replicate 1

description: Sample G


title: B_Veg_t1

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Sequenced reads were mapped to transcript reference sequence (unique sequence for one gene id) for Xenopus tropicalis (source: Mike Gilchrist; http://genomics.nimr.mrc.ac.uk/resources/xenopus/Xt-transcripts-Xenbase-v72b-MJG-27oct11.fasta); using bowtie2 v2.1.0 with local alignment; 6MM for 50bp.  We filled these sequences with annotation and took the longest sequence for one identifier (FullAnnotation5.csv).
Data was preprocessed and analyzed in the R environment (3.0.0) loading edgeR and biomaRt packages. Normalization, estimation of dispersions and testing for differentially expressed genes based on a test assuming negative binomial data distribution was computed via DESeq.
Genome_build: Xt72b [Collart C, Owens ND, Bhaw-Rosun L, Cooper B, De Domenico E, Patrushev I, Sesay AK, Smith JN, Smith JC, Gilchrist MJ. High-resolution analysis of gene activity during the Xenopus mid-blastula transition. Development. 2014 May;141(9):1927-39]
Supplementary_files_format_and_content: counts file includes normalized values for each sample

organism: Xenopus laevis

source_name: vegetal oocyte half

extract_protocol:
Oocyte halves were prepared by manual dissection, flash frozen in liquid nitrogen and RNA was prepared by proteinase K treatment, phenol-chloroform extraction and Lithiumchloride- as well as Ethanol/Ammoniumacetate-precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oocyte

tag: cell region

value: vegetal oocyte half

tag: Stage

value: VI

tag: oocytes taken from frog individual

value: B

tag: animal/vegetal halves from batch


title: A_Veg_t1

value: A


title: B_Veg_t2


title: MCF7_Akti1/2_Replicate1 (RNA-Seq)

source_name: MCF7 breast adenocarcinoma cells, Akti-1/2 treated


title: HCT116_DMSO_Replicate2 (GRO-Seq)

data_processing:
Library strategy: GRO-Seq
Library strategy: GRO-Seq
Illumina Casava1.5 software used for basecalling.
Clipping of contaminating adapter sequences was done with Cutadapt v1.2.1.
Reads with poor overall quality were further removed with fastq_quality_filter v0.0.13.
Reads were aligned to the hg19 human genome with Bowtie v0.12.9, allowing no mismatches and discarding multiple mapping reads
Stranded read counts were obtained using coverageBed v2.17.0. In order to specifically quantify the amount of actively elongated polymerase, the expression level of each gene was quantified based on the number of reads mapping to the region starting at +500 bp downstream the transcription start site (TSS) up to the transcription end site (TES).
Reads per kilobase per million reads (RPKMs) were estimated based on the number of uniquely aligned reads per sample, the number of reads mapping to each gene, and the gene length. The number of reads mapping to each gene and the gene length exclude the 500bp window downstream the TSS.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with a matrix with the RPKMs for each gene and sample, once the 500bp region downstream the TSS has been excluded.

extract_protocol:
Isolation of nuclei and nuclear run-on was carried out as described in Core et al, Science (2008) . Nascent RNAs were on average approximately 100nt long.
The immuno-purified RNA was resuspended in 8.5µl water and 5’- or 3’- adapters ligated using Tru-Seq Small RNA Kit, Illumina. RNAs were reverse transcribed and amplified. The NRO-cDNA libraries were then run on a non-denaturing 1XTBE, 8% acrylamide gel, and cDNAs greater than 90 nucleotides were excised from the gel and eluted, precipitated and sequenced on the HiSeq 2000.


title: A_Veg_t2


title: HCT116_DMSO_Replicate1 (GRO-Seq)


title: MCF7_DMSO_Replicate2 (GRO-Seq)


title: A_An_t1

source_name: animal oocyte half

value: animal oocyte half


title: HCT116_Akti1/2_Replicate1 (GRO-Seq)


title: HCT116_Akti1/2_Replicate2 (GRO-Seq)


title: MPP_H3K27me3


title: A_An_t2


title: MCF7_Akti1/2_Replicate2 (GRO-Seq)


title: MCF7_Akti1/2_Replicate1 (GRO-Seq)


title: HCT116_DMSO_Replicate2 (Microvesicles small RNA-Seq)

data_processing:
Illumina Casava1.9 software used for basecalling.
Clipping of contaminating adapter sequences was done with Cutadapt v1.2.1.
Reads with poor overall quality were further removed from downstream analyses with fastq_quality_filter tool.
Reads were aligned to the hg19 human genome with Bowtie v1.0, allowing no mismatches and discarding multiple mapping reads
For every annotated feature in the GENCODE v19 database (http://www.gencodegenes.org/releases/19.html), read counts were obtained using the HTSeq Python package
Reads normalized per million sequenced reads (RPMs) were subsequently estimated based on the number of million reads sequenced per sample and the number of reads mapping to each gene in that sample.
For each gene, counts coming from each pair of technical replicates were added.
Genome_build: hg19 (GRCh37.p13)
Supplementary_files_format_and_content: Tab-delimited text file with a matrix with the counts for each gene and sample.

extract_protocol:
Exosomal RNA was isolated as per manufacturer’s instructions using the Total Exosome RNA and Protein isolation kit (Invitrogen). RNA recovered was characterized using RNA Pico Kit on Agilent 2100 Bioanalyzer. We used 1µg of total RNA for library construction
The library of microvesicle small RNA was made using Illumina’s Tru-Seq Small RNA kit. The 3’ and 5’ adaptors were ligated and an RT reaction is used to create single stranded cDNA, then PCR amplified using a common primer and one index sequences before size selection on 6% native polyacrylamide gel. Fragment range of 105-150bp corresponding to the small RNA population were excised, eluted, precipitated and resuspended in 20μl of nuclease free water. The size, quality and quantity of the DNA in each final small RNA library were verified using the High Sensitivity kit (Agilent).


title: MCF7_Akti1/2_Replicate2 (RNA-Seq)


title: SC-G37R-11m-1

city: La Jolla

first: Don

middle: W.

last: Cleveland

state: CA

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to mm9 whole genome using tophat-2.0.8b.Linux_x86_64 with parameters --no-coverage-search -G genes.gtf --transcriptome-index=transcriptome_data/known --prefilter-multihits --max-multihits 1 --library-type fr-firststrand -o *_thout genome *.fastq.bz2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks version v2.1.1 with parameters -N -F 0 -G genes.gtf -o *_clout *_thout/accepted_hits.bam
Significant gene expression change between groups has been detected using cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each sample

source_name: Spinal Cord

extract_protocol:
mRNA from specific cell type was isolated by GFP immunoprecipitation and purified by Absolutely RNA Nanoprep kit
Illumina TruSeq mRNA Sample Preparation Kit
RNA-seq, 50nt single end

tag: tissue

value: Spinal Cord

tag: disease stage

value: Early symptomatic stage

tag: genotype

value: SOD1 G37R

value: Male


title: SC-G37R-11m-2

value: Female


title: SC-G37R-11m-3


title: SC-CTRL-11m-2

value: Non-Tg


title: HCT116_Akti1/2_Replicate2 (Microvesicles small RNA-Seq)

value: colon carcinoma

value: AKT1 Low


title: hTert-immortilized dermal fibroblast SW603 , WT, + siPOLA1; poly(dA:dT), 16 h Sample 26

first: Igor

middle: M

last: Dozmorov

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

description: cDNA derived from total polyA-mRNA

data_processing:
Custom programs were used to demuliplex individual samples using their unique index. Approximately 235 Million pass filter reads were achieved per lane. Each sample had close to 19.5 million reads.
We used CLC Genomics Workbench 7 for RNASEQ alignment and statistical analysis of the data. Human HG19 was used as reference sequence. The expression for the genes expressed in all samples was calculated.
Methods for data normalization and analysis are based on the use of “internal standards” (D. M. Rocke, B. Durbin, J Comput Biol 8, 557 (2001)).The comparison of these methods with some other normalization and analysis procedures was previously reported (M. G. Dozmorov, J. M. Guthridge, R. E. Hurst, I. M. Dozmorov, PLoS One 5,  (2010)).  ).  Created initially for the analysis of microarray data, they were slightly modified to the needs of RNA-seq data analysis.
The two-step normalization procedure and the Associative analysis functions were implemented in MatLab (Mathworks, MA). These algorithms are obtainable from an R package diffGeneAnalysis, available as a part of Bioconductor packages (http://www.bioconductor.org/packages/2.5/bioc/html/diffGeneAnalysis.html). Heatmaps were generated with the Spotfire Decision Site 9 (TIBCO, Palo Alto, CA) with gene subsets created from the list of significant genes. Functional analysis of identified genes was performed with Ingenuity Pathway Analysis (IPA; Ingenuity® Systems, Redwood City, CA, http://www.ingenuity.com).
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited Excel files include RPKM values for each Sample

source_name: Derma

growth_protocol: Cells were grown in DMEM, suplemented with 10% FBS and glutamine

extract_protocol:
RNA was extracted using the RNeasy chromatography method (Qiagen), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TNF was added to the culture medium for 2 or 12 hours. Poly(dA:dT) was transfected into cells following manufacturer's recommendation for 16 hours.

tag: status

value: POLA1 deficient

tag: disease model

value: siRNA silencing

value: dermal fibroblast


title: SC-CTRL-11m-1


title: SC-G37R-8m-4

value: Onset


title: hTert-immortilized dermal fibroblast SW603 , WT, + siPOLA1; non stimulated Sample 25

description: cDNA derived from total polyA-mRNA


title: B_An_t2

value: oocyte


title: B_An_t1

value: VI


title: SC-G37R-8m-3


title: HCT116_Akti1/2_Replicate1 (Microvesicles small RNA-Seq)


title: MCF7_DMSO_Replicate1 (GRO-Seq)

value: breast adenocarcinoma

value: AKT1 WT


title: MCF7_DMSO_Replicate2 (Microvesicles small RNA-Seq)


title: SC-G37R-8m-2


title: SC-G37R-8m-1


title: SC-CTRL-8m-3


title: SC-CTRL-8m-4


title: SC-CTRL-8m-2


title: SC-CTRL-8m-1


title: hTert-immortilized dermal fibroblast SW606 from XLPDR patient, POLA1-deficient, non stimulated Sample 23

description: cDNA derived from total polyA-mRNA

value: XLPDR syndrome


title: MCF7_Akti1/2_Replicate2 (Microvesicles small RNA-Seq)


title: hTert-immortilized dermal fibroblast SW603 , WT, + siPOLA1; TNF (1000 U/mL), 12 h Sample 22

description: cDNA derived from total polyA-mRNA


title: SC-CTRL-11m-3

value: Spinal Cord


title: Oligo-G85R-11m-3

source_name: Oligodendrocyte

value: Early symptomatic stage

value: SOD1 G85R


title: HCT116_DMSO_Replicate1 (Microvesicles small RNA-Seq)


title: hTert-immortilized dermal fibroblast SW603 , WT, + siPOLA1; TNF (1000 U/mL), 2 h Sample 21

description: cDNA derived from total polyA-mRNA


title: Oligo-G85R-11m-2


title: MCF7_Akti1/2_Replicate1 (Microvesicles small RNA-Seq)


title: Oligo-G85R-11m-1

value: Male


title: HCT116_DMSO_Replicate2 (Cellular small RNA-Seq)

data_processing:
Illumina Casava1.5 software used for basecalling.
Clipping of contaminating adapter sequences was done with Cutadapt v1.2.1.
Reads with poor overall quality were further removed from downstream analyses with fastq_quality_filter tool.
Reads were aligned to the hg19 human genome with Bowtie v1.0, allowing no mismatches and discarding multiple mapping reads
For every annotated feature in the GENCODE v19 database (http://www.gencodegenes.org/releases/19.html), read counts were obtained using the HTSeq Python package
Reads normalized per million sequenced reads (RPMs) were subsequently estimated based on the number of million reads sequenced per sample and the number of reads mapping to each gene in that sample.
Genome_build: hg19 (GRCh37.p13)
Supplementary_files_format_and_content: Tab-delimited text file with a matrix with the counts for each gene and sample.

extract_protocol:
Total RNA was purified using RNAeasy miniprep kit (Qiagen) and the RNA integrity was checked using RNA 6000 Nano assay on Agilent 2100 Bioanalyzer. 1µg of total RNA were used for library construction.
The library of cellular small RNA was made using Illumina’s Tru-Seq Small RNA kit. The 3’ and 5’ adaptors were ligated and an RT reaction is used to create single stranded cDNA, then PCR amplified using a common primer and one index sequences before size selection on 6% native polyacrylamide gel. Fragment range of 105-150bp corresponding to the small RNA population were excised, eluted, precipitated and resuspended in 20μl of nuclease free water. The size, quality and quantity of the DNA in each final small RNA library were verified using the High Sensitivity kit (Agilent).


title: hTert-immortilized dermal fibroblast SW603 , WT, + siPOLA1; non stimulated Sample 20

description: cDNA derived from total polyA-mRNA


title: Oligo-G37R-11m-2

value: SOD1 G37R

value: Female


title: Oligo-G37R-11m-3


title: hTert-immortilized dermal fibroblast SW606 from XLPDR patient, POLA1-deficient, TNF (1000 U/mL), 12 h Sample 19

description: cDNA derived from total polyA-mRNA


title: Oligo-G37R-11m-1


title: HCT116_DMSO_Replicate1 (Cellular small RNA-Seq)

value: colon carcinoma


title: hTert-immortilized dermal fibroblast SW606 from XLPDR patient, POLA1-deficient, TNF (1000 U/mL), 2 h Sample 18

description: cDNA derived from total polyA-mRNA


title: Oligo-CTRL-11m-4

value: Non-Tg


title: hTert-immortilized dermal fibroblast SW606 from XLPDR patient, POLA1-deficient, poly(dA:dT), 16 h Sample 24

description: cDNA derived from total polyA-mRNA

value: POLA1 deficient


title: Oligo-CTRL-11m-3


title: MCF7_DMSO_Replicate1 (Microvesicles small RNA-Seq)


title: Oligo-CTRL-11m-5


title: hTert-immortilized dermal fibroblast SW606 from XLPDR patient, POLA1-deficient, non stimulated Sample 17

description: cDNA derived from total polyA-mRNA


title: HCT116_Akti1/2_Replicate2 (Cellular small RNA-Seq)

value: AKT1 Low


title: Oligo-CTRL-11m-2


title: Oligo-G37R-8m-4


title: Oligo-CTRL-11m-1


title: hTert-immortilized dermal fibroblast SW606 from XLPDR patient, POLA1-deficient, non stimulated Sample 16

description: cDNA derived from total polyA-mRNA

value: dermal fibroblast


title: Oligo-G37R-8m-2

value: Onset


title: HCT116_Akti1/2_Replicate1 (Cellular small RNA-Seq)


title: Primary dermal fibroblasts SW1756 from XLPDR patient, POLA1-deficient, non stimulated Sample 15

description: cDNA derived from total polyA-mRNA


title: Oligo-G37R-8m-3


title: Oligo-G37R-8m-1


title: hTert-immortilized dermal fibroblast SW603 , WT, + siControl; poly(dA:dT), 16 h Sample 14

description: cDNA derived from total polyA-mRNA

value: healthy


title: MCF7_DMSO_Replicate1 (Cellular small RNA-Seq)


title: Oligo-CTRL-8m-5


title: MCF7_Akti1/2_Replicate2 (Cellular small RNA-Seq)


title: hTert-immortilized dermal fibroblast SW603 , WT, + siControl; non stimulated Sample 13

description: cDNA derived from total polyA-mRNA


title: Oligo-CTRL-8m-2


title: MCF7_DMSO_Replicate2 (Cellular small RNA-Seq)


title: hTert-immortilized dermal fibroblast SW603 , WT, poly(dA:dT), 16 h Sample 12

description: cDNA derived from total polyA-mRNA


title: Oligo-CTRL-8m-4


title: Oligo-CTRL-8m-3


title: MCF7_Akti1/2_Replicate1 (Cellular small RNA-Seq)


title: Oligo-CTRL-8m-1


title: hTert-immortilized dermal fibroblast SW603 , WT, non stimulated Sample 11

description: cDNA derived from total polyA-mRNA


title: Astro-G37R-4

source_name: Astrocyte


title: Astro-G37R-3


title: hTert-immortilized dermal fibroblast SW603 , WT, + siControl; TNF (1000 U/mL), 12 h Sample 10

description: cDNA derived from total polyA-mRNA


title: Astro-G37R-2


title: hMe-Seal combined patient input

city: Chicago

first: Christopher

last: Mariani

state: IL

institute: University of Chicago

description: Input for Samples 8-11

data_processing:
alignment with BWA-backtrack to hg19; peak calling with MACS 1.4
Genome_build: hg19
Supplementary_files_format_and_content: wig outputs from MACS 1.4 for hMe-Seal data; RNA-seq FPKM values outputted by Cufflinks 2.2.1 provided as supplemental information as Excel spreadsheet

source_name: Input from samples 8-11

extract_protocol:
AllPrep RNA/DNA/miRNA Universal Kit (Qiagen)
RNA libraries were built following polyA selection using Illumina kits; DNA libraries were constructed using Illumina kits.  All library construction and sequencing was performed by the University of Chicago NGS core

tag: day of differentiation

tag: normal/tumor


title: hMe-Seal: T2

description: Tumor biopsy; colonocyte fraction

source_name: Primary patient sample

value: Tumor 2


title: hTert-immortilized dermal fibroblast SW603 , WT, + siControl; TNF (1000 U/mL), 2 h Sample 9

description: cDNA derived from total polyA-mRNA

tag: cell type


title: hMe-Seal: N2

description: Adjacent normal biopsy; colonocyte fraction; matched normal for sample 11

value: Normal 2


title: Astro-CTRL-6


title: hMe-Seal: T1

description: Tumor biopsy; colonocyte fraction

value: Tumor 1


title: Astro-G37R-1


title: Astro-CTRL-4


title: hTert-immortilized dermal fibroblast SW603 , WT, TNF (1000 U/mL), 12 h Sample 7

description: cDNA derived from total polyA-mRNA


title: hMe-Seal input

description: Input for Samples 1-4

source_name: Input for samples 1-4

value: input


title: MN-G37R-3

source_name: Motor Neuron

value: Spinal Cord


title: hTert-immortilized dermal fibroblast SW603 , WT, TNF (1000 U/mL), 2 h Sample 6

description: cDNA derived from total polyA-mRNA


title: MN-G37R-2


title: Astro-CTRL-2


title: Astro-CTRL-1


title: MN-G37R-4


title: hTert-immortilized dermal fibroblast SW603 , WT, + siControl; non stimulated Sample 8

description: cDNA derived from total polyA-mRNA


title: MN-G37R-1


title: hMe-Seal: N1

description: Adjacent normal biopsy; colonocyte fraction; matched normal for sample 9

value: Normal 1


title: Astro-CTRL-3


title: hTert-immortilized dermal fibroblast SW603 , WT, non stimulated Sample 5

description: cDNA derived from total polyA-mRNA


title: RNA-Seq: d15

description: RNA-seq of differentiating T84 cells; d15

data_processing:
Alignment with Bowtie2.1.0/Tophat2.0.11; FPKM calculated by Cufflinks v2.2.1; all steps used GTF file from Ensembl
Genome_build: hg19
Supplementary_files_format_and_content: wig outputs from MACS 1.4 for hMe-Seal data; RNA-seq FPKM values outputted by Cufflinks 2.2.1 provided as supplemental information as Excel spreadsheet

source_name: Differentiating T84 Cells


title: hMe-Seal: d15

description: 5-hmC mapping in differentiating T84 cells; d15


title: MN-CTRL-2


title: Astro-CTRL-5


title: MN-CTRL-4


title: Primary dermal fibroblast “C” , WT, non stimulated Sample 3

description: cDNA derived from total polyA-mRNA


title: hTert-immortilized dermal fibroblast SW603 , WT, non stimulated Sample 4

description: cDNA derived from total polyA-mRNA


title: hMe-Seal: d12

description: 5-hmC mapping in differentiating T84 cells; d12


title: MN-CTRL-1


title: cDC_H3K27me3

source_name: Classical dendritic cell (cDC)

value: Classical dendritic cell (cDC)

tag: chip antibody

value: H3K27me3 (Diagenode, pAb-069-050)


title: Primary dermal fibroblast “B” , WT, non stimulated Sample 2

description: cDNA derived from total polyA-mRNA


title: hMe-Seal: d4

description: 5-hmC mapping in differentiating T84 cells; d4


title: RNA-Seq: d0

description: RNA-seq of differentiating T84 cells; d0


title: MN-CTRL-3

value: Male


title: pDC_H3K9me3

source_name: Plasmacytoid dendritic cell (pDC)

value: Plasmacytoid dendritic cell (pDC)

value: H3K9me3 (Diagenode, pAb-056-050)


title: Primary dermal fibroblast “A”, WT, non stimulated Sample 1

description: cDNA derived from total polyA-mRNA


title: cDC_H3K9me3


title: pDC_H3K4me3

value: H3K4me3 (Diagenode, pAb-003-050)


title: CDP_H3K9me3

source_name: Common dendritic cell progenitor (CDP)

value: Common dendritic cell progenitor (CDP)


title: cDC_H3K4me3


title: MPP_H3K9me3

source_name: Multipotent progenitor (MPP)

value: Multipotent progenitor (MPP)


title: hMe-Seal: d0

description: 5-hmC mapping in differentiating T84 cells; d0


title: pDC_H3K27me3


title: 52d_root_stress_br2

city: Stuttgart

first: Christian

last: Grumaz

address: Nobelstr. 12

department: MBT

institute: Fraunhofer IGB

description: Severe stress and re-watering (Day 52), total RNA from J. curcas roots subjected to water withholding (drought stress).

data_processing:
Basecalls were performed using standard software supplied by Illumina for HiSeq 2000 sequencing.
Reads generated with HiSeq 2000 were mapped with NextGenMap v0.4.12 using default settings and producing bam-files.
Gene quantification was calculated with a python script 'rpkmforgenes.py' from the Sandberg laboratory (http://sandberg.cmb.ki.se/rnaseq/) at readcount and RPKM level (=reads per kilobase of exon model per million mapped reads according to Mortazavi et al. (2008)) using uniquely mapped reads.
Genome_build: Jatropha curcas genome version 4.5 as reference (Hirakawi et al., 2012) (ftp://ftp.kazusa.or.jp/pub/jatropha/).
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts which were exclusively taken for differential gene expression profiling [J.curcas_readcounts.txt] and quantile-normalized RPKM values (to each value 1 RPKM was added) [J.curcas_normalized_rpkm.txt.gz].

organism: Jatropha curcas

source_name: root drought stress

growth_protocol: Homogeneous seeds were germinated in clean sand, and 10-day-old homogeneous seedlings were transplanted to 7.5 L pots containing a soil mixture of sand, peat and soil (3:1:1) and supplemented with a commercial fertilizer (Osmocote, Scotts, Netherlands) (5 g/pot) (N:P:K:Mg, 16:9:12:2.5). Plants were daily irrigated until the beginning of the treatments. Experiments were carried out in a greenhouse under natural photoperiod (29 Jun. - 24 Aug. 2011, Oeiras, Portugal) with a day/night temperature of 29±3 to 20±2ºC, day/night relative humidity of 39±8 to 69±4% and an average light intensity at plant level of 411±226 μmol photon m-2 s-1 (11-12 a.m.).

extract_protocol:
Root tips and young leaves were collected along the drought assay and subsequent re-watering period. In detail, one leaf (≤2cm in length) per plant was cut with a scalpel blade from the apical tip of the plants and immediately frozen in liquid nitrogen. For root collection, plants were gently removed from the pot. Root tips (≤ 1 cm in length) were retracted with forceps from different parts of the root system and carefully brushed to remove any attached soil, the process never extended more than 30 seconds until samples were flash-frozen in liquid nitrogen. A pool of six plants for days 0 and 49, and three plants for days 13 and 52 were sampled per treatment and accession. Samples were stored at – 80ºC until further use. Before extraction the frozen material was grind in liquid nitrogen with a mortar and pestle into a fine powder. Total RNA was extracted using the RNeasy plant mini kit (Qiagen, Germany) according to the manufacturer’s instructions, however for leaf samples the lysis buffer was supplemented with 0.2% of PEG 20000, as suggested by Gehrig et al. (2000). After the extraction, samples were treated with DNAse (Turbo DNA-free Kit, AM1907, Ambion, USA) according to the manufacturer’s instructions to minimize genomic contaminants. RNA quality and quantity was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips, following manufacturer’s protocol; RNA integrity numbers (RIN) ranged from 8.3 - 9.9.
cDNA libraries were prepared using an initial amount of 400 ng of total RNA, and the Illumina’s TruSeqTM RNA Sample Preparation v2 protocol. Indexed barcodes were used for pooling, and sequencing was performed on an Illumina HiSeqTM 2000. To assess concentration and ensure an appropriate size distribution (between 200-570 bp) the cDNA libraries were checked using Bioanalyzer DNA 1000 chips. The sequencing run was carried out on a fully loaded flow cell with single-end 50 bp reads following manufacturer’s instructions with a loading amount of 9 pmol cDNA per lane. On average, each sample was covered by about 82 million reads.

treatment_protocol: Potted 36-day-old seedlings (at the five-leaf stage) from both accessions were subjected to drought stress or continuously grown under well-watered conditions (Control). Drought stress was imposed by water withholding for a maximum period of 49 days, followed by a 7-day re-watering period.

tag: strain

value: Cape Verde islands

value: root


title: Non-calcified tricuspid  valve_YBO035

city: Quebec

last: Guauque-Olarte

address: 2725, chemin Sainte-Foy

institute: CRIUCPQ

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to Hg19 whole genome using tophat v2.0.9-1 (-r85 --mate-std-dev 75) and bowtie v1.0.0-1 (Trapnell, Nat Biotechnol. 2013;31:46-53)
The aligned reads were assembled by Cufflinks program to produce transcripts annotated to the same reference genome. The tool Cuffdiff of Cufflinks was utilized to quantify the transcriptomes and compare them across calcified and normal tricuspid valves  (Trapnell, Nat Biotechnol. 2013;31:46-53).
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Human aortic valve leaflet

extract_protocol:
RNA was extracted from 30 mg and 100 mg of normal and calcified tissue, respectively, using a modified TRIzol protocol followed by RNA cleanup using QIAGEN RNeasy Mini Kit. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: gender

value: Non-calcified tricuspid  valve


title: Non-calcified tricuspid  valve_YBO056


title: Non-calcified tricuspid  valve_YBO052


title: Non-calcified tricuspid  valve_YBO048


title: 52d_root_stress_br1


title: Non-calcified tricuspid  valve_YBO051


title: 52d_leaf_stress_br1

description: Severe stress and re-watering (Day 52), total RNA from J. curcas leaves subjected to water withholding (drought stress).

source_name: leaf drought stress

value: leaf


title: 52d_leaf_stress_br2


title: Calcified tricuspid aortic valve_YBO054

value: Calcified tricuspid aortic valve


title: Non-calcified tricuspid  valve_YBO040


title: Non-calcified tricuspid  valve_YBO043


title: Calcified tricuspid aortic valve_YBO046


title: Calcified tricuspid aortic valve_YBO044


title: 49-52d_root_control_br1

description: Control (Day 49/52 pooled), total RNA from J. curcas roots subjected to well watered conditions (control).

source_name: root control


title: Calcified tricuspid aortic valve_YBO062


title: Non-calcified tricuspid  valve_YBO037


title: Non-calcified tricuspid  valve_YBO060


title: 49-52d_leaf_control_br2

description: Control (Day 49/52 pooled), total RNA from J. curcas leaves subjected to well watered conditions (control).

source_name: leaf control


title: Calcified tricuspid aortic valve_YBO058


title: Non-calcified tricuspid  valve_YBO063


title: 49-52d_leaf_control_br1


title: 49-52d_root_control_br2


title: 49d_root_stress_br1

description: Severe stress (Day 49), total RNA from J. curcas roots subjected to water withholding (drought stress).


title: 49d_root_stress_br2


title: 49d_leaf_stress_br2

description: Severe stress (Day 49), total RNA from J. curcas leaves subjected to water withholding (drought stress).


title: Calcified tricuspid aortic valve_YBO042


title: Calcified tricuspid aortic valve_YBO057


title: Calcified tricuspid aortic valve_YBO034


title: Calcified tricuspid aortic valve_YBO050


title: 49d_leaf_stress_br1


title: 13d_root_stress_br1

description: Moderate stress (Day 13), total RNA from J. curcas roots subjected to water withholding (drought stress).


title: 13d_root_control_br2

description: Control (Day 13), total RNA from J. curcas roots subjected to well watered conditions (control).


title: Veg_2

organism: Xenopus tropicalis

source_name: vegetal oocyte half

value: oocyte

value: vegetal oocyte half

value: full grown oocyte


title: 13d_leaf_stress_br1

description: Moderate stress (Day 13), total RNA from J. curcas leaves subjected to water withholding (drought stress).


title: 13d_root_stress_br2


title: 13d_root_control_br1


title: An_1

source_name: animal oocyte half

value: animal oocyte half


title: 0d_leaf_control_br2

description: Beginning of experiment (Day 0), total RNA from J. curcas leaves subjected to well watered conditions (control).


title: 13d_leaf_control_br1

description: Control (Day 13), total RNA from J. curcas leaves subjected to well watered conditions (control).


title: An_2


title: 13d_leaf_stress_br2


title: AMPH hot ID FG204W

status: Public on Dec 08 2015

city: Jefferson

first: John

last: Bowyer

state: AR

address: 3900 NCTR Drive

department: Neurotoxicology

institute: National Center for Toxicological Research FDA

description: Amphetamine Hyperthermic #22

data_processing:
Basecall files were converted to fastq files using CASAVA 1.8.2
Fastq files were clipped using fastq-mcf (parameters: “--max-ns 4 --qual-mean 25 -H -p 5 -q 7 -l 25”)
Fastq files were aligned to rat Ensembl release 70 transcriptome (rn5) using bowtie 0.12.9 (params: “-e 500 –m 100 –chunkmbs 256”)
Alignments were quantified using RSEM v 1.2.0 (no special parameters)
Genome_build: Genome build: rn5
Supplementary_files_format_and_content: Separate count per gene files for each sample. A tab is between the gene and the count. One count per gene on each line.

organism: Rattus norvegicus

source_name: Amphetamine Hyperthermic

growth_protocol: Animals used in these experiments were Charles River male Sprague-Dawley. They were given access to water and food ad lib and kept on a 12 hour light cycle 6:00am to 6:00pm until testing

extract_protocol:
Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).
Alpha and Beta Globin mRNA were substantially depleted from total RNA samples using the GlobinClear-Mouse/Rat Kit (Life Technologies # AM1981) as described by the vendor at EA/Quintiles; 4324 S. Alton Ave. Durham, N.C.  Analysis.
Globin mRNA-depleted RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103). Starting with 300 ng of Globin mRNA-depleted RNA, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads.  Performed at EA/ Quintiles.
Final cDNA libraries were analyzed for size distribution and using an Agilent 2200 TapeStation, quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824) and normalized to 2 nM for sequencing. Performed at EA/Quintiles.
Clusters were generated on an Illumina cBOT using an Illumina TruSeq Paired-End Cluster Kit on an Illumina Paired End Flow Cell. The Flowcell was sequencing through 51 bases, paired end, (8 base index cycle) on an Illumina HiSeq 2000 (HiSeq Control Software v 1.5.15.1). Performed at EA/Quintiles.
Quality control files contained read length and depth results (before and after clipping), presence of artifact/duplicate sequences, distribution of base quality and base frequency by sample.  Also, flow cell total yield, PF reads, barcode quality, alignment summaries and # of genes detected were determined.  FASTQ files for each RNA aliquot were generated.

treatment_protocol: Whole blood was obtained via cardiac puncture at 4:30 to 5:30 pm, and immediately frozen, from adult 85 to 90 day old male Sprague-Dawley rats at 3 hr after four sequential injections of saline, saline in a cool  environmental, saline in a hot envrionment (39°C), amphetamine or amphetamine in a cool environment

value: Sprague-Dawley

value: adult

value: male

tag: sample group

value: Amphetamine Hyperthermic

value: whole blood


title: AMPH hot ID FG199W

description: Amphetamine Hyperthermic #21


title: AMPH hot ID FG198W

description: Amphetamine Hyperthermic #20


title: H30

first: Yue

last: Hao

address: No.2 Yuanmingyuan West Road

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

data_processing:
Raw data (i.e., raw reads) of fastq format were processed into clean data (i.e., clean reads) using Genome Analyzer Pipeline software (Illumina) by removing reads with ploy-N or 5’adapter contaminants; without 3’ adapter or insert tags; and with ploy A, T, G, or C.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Sus scrofa draft genome assembly by Bowtie with no mismatches.Known miRNAs were identified by mapping clean reads to mature miRNAs in miRBase (19.0). Novel miRNAs were identified by miREvo and miRDeep2 by assessing the secondary structures, dicer cleavage sites, and minimum free energy of the small RNA tags unannotated in the initial steps.
Expression levels of miRNAs in CON and H30 were estimated and normalized by TPM (transcript per million). Differential expression analysis between H30 and CON was performed using the DEGseq (2010) R package. A ‘‘normalization reads > 1’’ and ‘‘P < 0.01’’ were used as the criteria for judging the significance of differences in miRNA expression.
Genome_build: Sus scrofa draft genome assembly (Sus_scrofa.Sscrofa10.2.70)
Supplementary_files_format_and_content: read count, TPM

organism: Sus scrofa

source_name: Skeletal muscle

growth_protocol: 16 healthy crossbred barrows (DLY, originating from Duroc boars and Yorkshire-Landrace sows; body weight: 79.0±1.5 kg) from eight litters were selected.

extract_protocol:
Total RNAs were isolated from each sample using Trizol. Then total RNAs were pooled with equal quantities of small RNAs from LD muscles of 8 pigs in each group.
For the small RNA library, 3 μg of total RNA per sample was used. Briefly, RNAs were ligated to a 5’ and a 3’ adapter sequentially, reverse transcribed into cDNA. Using adapter primers, PCR was performed for 12 cycles; the 140–160 bp (the length of small non-coding RNA plus the 3’ and 5’ adapters) DNA fragments were subsequently recovered from the agarose gel. Library quality was assessed with the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: They were raised under constant ambient temperature at 22°C (CON, n = 8) or constant high ambient temperature at 30°C (H30, n = 8) for 21 days

value: Lonissimus dorsi

tag: protocol

value: constant heat stressconstant high ambient temperature at 30 degreeC


title: AMPH hot ID FG189W

description: Amphetamine Hyperthermic #18


title: AMPH hot ID FG197W

description: Amphetamine Hyperthermic #19


title: AMPH hot ID FG184W

description: Amphetamine Hyperthermic #15


title: AMPH hot ID FG185W

description: Amphetamine Hyperthermic #16


title: Control ID FG201W

description: Saline Control #21

source_name: Saline Control

value: Saline Control


title: 13d_leaf_control_br2

value: Cape Verde islands


title: 0d_leaf_control_br1


title: Control ID FG196W

description: Saline Control #19


title: Control ID FG200W

description: Saline Control #20


title: Control ID FG181W

description: Saline Control #18


title: CON

value: ambient temperature at 22 degreeC


title: Control cool ID FG194

description: Saline Control Cool Environment #5

source_name: Saline Control Cool Environment

extract_protocol:
Total RNA was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH) (Chomczynski and Mackey, 1995) with modifications similar to those previously described (Bowyer et al., 2007).
Alpha and Beta Globin mRNA were substantially depleted from total RNA samples using the GlobinClear-Mouse/Rat Kit (Life Technologies # AM1981) as described by the vendor at EA/Quintiles; 4324 S. Alton Ave. Durham, N.C.  Analysis.
Globin mRNA-depleted RNA samples were converted into cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-2103). Starting with 300 ng of Globin mRNA-depleted RNA, polyadenylated RNA (primarily mRNA) was selected and purified using oligo-dT conjugated magnetic beads.  Performed at EA/ Quintiles.
Final cDNA libraries were analyzed for size distribution and using an Agilent 2200 TapeStation, quantitated by qPCR (KAPA Library Quant Kit, KAPA Biosystems # KK4824) and normalized to 2 nM for sequencing. Performed at EA/Quintiles.
Clusters were generated on an Illumina cBOT using an Illumina TruSeq Paired-End Cluster Kit on an Illumina Paired End Flow Cell. The Flowcell was sequencing through 51 bases, paired end, (8 base index cycle) on an Illumina HiSeq 2000  (HiSeq Control Software v 1.5.15.1). Performed at EA/Quintiles.
Quality control files contained read length and depth results (before and after clipping), presence of artifact/duplicate sequences, distribution of base quality and base frequency by sample.  Also, flow cell total yield, PF reads, barcode quality, alignment summaries and # of genes detected were determined.  FASTQ files for each RNA aliquot were generated.

value: Saline Control Cool Environment


title: Control ID FG180W

description: Saline Control #17


title: Control cool ID FG193

description: Saline Control Cool Environment #4


title: AMPH normo ID FG158

description: Amphetamine Noromothermic #14

source_name: Amphetamine Noromothermic

value: Amphetamine Noromothermic


title: Control cool ID FG190

description: Saline Control Cool Environment #1


title: AMPH normo ID FG157

description: Amphetamine Noromothermic #13


title: AMPH hot ID FG188W

description: Amphetamine Hyperthermic #17


title: AMPH normo ID FG148

description: Amphetamine Noromothermic #11


title: AMPH normo ID FG147

description: Amphetamine Noromothermic #10


title: AMPH normo ID FG159

description: Amphetamine Noromothermic #15


title: Control ID FG202W

description: Saline Control #22


title: AMPH normo ID FG134

description: Amphetamine Noromothermic #8


title: AMPH normo ID FG149

description: Amphetamine Noromothermic #12


title: AMPH normo ID FG133

description: Amphetamine Noromothermic #7


title: AMPH normo ID FG145

description: Amphetamine Noromothermic #9


title: AMPH normo ID JB114

description: Amphetamine Noromothermic #4


title: AMPH normo ID JB104

description: Amphetamine Noromothermic #3


title: AMPH normo ID FG132

description: Amphetamine Noromothermic #6


title: AMPH normo ID JB115

description: Amphetamine Noromothermic #5


title: Veg_1

tag: cell region

tag: Stage


title: AMPH normo ID JB103

description: Amphetamine Noromothermic #2


title: AMPH normo ID JB93

description: Amphetamine Noromothermic #1


title: AMPH hot ID FG139

description: Amphetamine Hyperthermic #10


title: AMPH hot ID FG144

description: Amphetamine Hyperthermic #14


title: Control cool ID FG191

description: Saline Control Cool Environment #2


title: AMPH hot ID FG142

description: Amphetamine Hyperthermic #12


title: AMPH hot ID FG143

description: Amphetamine Hyperthermic #13


title: AMPH hot ID FG105

description: Amphetamine Hyperthermic #9


title: AMPH hot ID FG86

description: Amphetamine Hyperthermic #7


title: Control cool ID FG192

description: Saline Control Cool Environment #3


title: AMPH hot ID JB113

description: Amphetamine Hyperthermic #6


title: AMPH hot ID FG140

description: Amphetamine Hyperthermic #11


title: AMPH hot ID JB100

description: Amphetamine Hyperthermic #4


title: AMPH hot ID FG104

description: Amphetamine Hyperthermic #8


title: AMPH hot ID JB97

description: Amphetamine Hyperthermic #3


title: AMPH hot ID JB102

description: Amphetamine Hyperthermic #5


title: AMPH hot ID JB92

description: Amphetamine Hyperthermic #2