title: GHA507

status: Public on Nov 28 2016

city: Geneva

first: Antonio

last: Frandi

address: rue michel servet 1

department: Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

data_processing:
Library strategy: REC-Seq
genome build: NC_000913.3
To remove contaminating sequences, the reads were split according to the HinfI consensus motif (5’-  G^ANTC-3’) considered as a barcode sequence using fastx_toolkit  (http://hannonlab.cshl.edu/fastx_toolkit/) (fastx_barcode_splitter.pl --bcfile barcodelist.txt --bol --  exact). Most of the reads (more than 90%) were rejected, and the reads kept were remapped to the  reference genomes with bwa mem and samtools to generate a sorted bam file.  The bam file was further filtered to remove low mapping quality reads (keeping AS >= 45) and split  by orientation (alignmentFlag 0 or 16) with bamtools. The reads were counted at 5' positions  using Bedtools (bedtools genomecov -d -5). Both orientation count files were combined into a  bed file at each identified 5’-GANTC-3’ motif (where reverse counts >=1 at position N+1 and forward  counts >=1 at position N-1) using a home-made PERL script. The HinfI positions in the bed file were  associated with the closest gene using Bedtools closest and the gff3 file of the reference genomes  . The final bed file was converted to an MS Excel sheet (S1 and S2 Tables) with a homemade  script. For the MboI-based REC-Seq, the strategy was identical except that a different adaptor was  used for ligation after cleavage and the MboI consensus motif (5’-^GATC-3’) was used as barcode for  filtering of V. cholerae O1 biovar El Tor and E. coli K12 Ec100D gDNA mapped onto the  MG1655 genome.
Supplementary_files_format_and_content: tab delimited text files, with feature annotation, REC_seq score, gene name and description

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or LB

extract_protocol:
For REC-Seq (restriction enzyme cleavage–sequencing) 1 ug of genomic DNA from C.  crescentus NA1000 and S. meliloti Rm2011 was cleaved with HinfI, a blocked (5’biotinylated)  specific adaptor was ligated to the ends and the ligated fragments were then sheared to an average size  of 150-400 bp (Fasteris SA, Geneva, CH). Illumina adaptors were then ligated to the sheared ends  followed by deep-sequencing using a Hi-Seq Illumina sequencer, and the (50 bp single end) reads  were quality controlled with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland

value: wild type


title: CONVD.8 CD8+ T cell

type: SRA

city: St. Louis

first: Jeffrey

last: Gordon

state: MO

address: 4515 McKinley Research Building

department: Center for Genome Sciences & Systems Biology

country: USA

institute: Washington University

library_source: genomic

data_processing:
Data were analyzed as described in the associated manuscript, Semenkovich et. al., 2016 (in submission).
In brief, Illumina reads were trimmed, then mapped to mm10 using bowtie2 with the parameters: --end-to-end --sensitive --no-unal --no-discordant.
Using samtools, low mapping quality reads were filtered (>=10), reads mapping to chrM were removed, and duplicates were then filtered.
Peaks were called using macs14 (with p = 1e-9), and overlapping peaks were used to generate merged .bed files.
Genome_build: mm10
Supplementary_files_format_and_content: .bed files: Per-sample .bed files identifying peaks identified from macs1.4, as described in the methods of the associated manuscript.

molecule: genomic DNA

organism: Mus musculus

source_name: Peripheral blood lymphocyte

growth_protocol: Mice were fed a sterilized low fat, plant polysaccharide rich chow (B&K Universal, Product 7378000, East Yorkshire, UK) that was provided ad lib.

extract_protocol:
Peripheral T cells and IELs were isolated by FACS, with a target maximum of 50,000 cells per transposition reaction. Nuclei were isolated and prepared as described in Buenrostro et al., Nature Methods, 2013.
Libraries were prepared using a modified version of the Illumina Nextera DNA Sample kit, based on the work of Buenrostro et al., Nature Methods, 2013 and outlined in the associated manuscript, Semenkovich et. al., 2016 (in submission).

treatment_protocol: C57BL/6 mice were maintained as sterile (germ-free), conventionally-raised, or colonized with the gut microbiota of a C57BL/6 donor mouse.

tag: microbial colonization state

value: conventionalized

tag: cell type

value: Peripheral blood lymphocyte

tag: strain

tag: tissue origin

value: Peripheral blood


title: CONVD.8 CD4+ T cell


title: CONVD.8 TCR γδ+ IEL

source_name: Intraepithelial lymphocyte

value: Intraepithelial lymphocyte

value: Intestine


title: CONVD.8 TCR αβ+ IEL


title: MucR1_ChIP_exo_T40

description: ChIP-Exo

data_processing:
Base calling: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3, CASAVA-1.8.2
Alignment: Bowtie-0.12.9, samtools-0.1.18
Caulobacter WT cells for ChIP-Exo were taken at different time points after synchronization (10, 40, 70 and 100 minutes). After cross-linking, chromatin was prepared as for qChIP assay. ChIP-Exo was performed with 2 ml of polyclonal antibodies to MucR1 at Peconic LCC (http://www.peconicgenomics.com) (State College, PA), which provided standard genomic position format files (BAM). A custom perl script was then used to obtain the per-base coverage from the total number of mapped reads for each ChIP-Exo experiment. To compute the enrichment for each promoter region, an enrichment ratio (ER) was calculated. To this purpose the script extracted the per-base coverage of a 600 bp region for each ORF (from -500 to +100 from the start codon for each ORF annotated in C. crescentus genome) and calculated the average coverage for each of these regions. The obtained value was then normalized with respect to the coverage of all the intergenic regions: to this purpose the script selected all the intergenic regions in the C. crescentus genome, merged them and extracted the per-base coverage. The coverage was averaged for windows of 600 bp, shifting each window by 100 bp, and the mean of all the values obtained was computed. The ER for each promoter region was therefore calculated as the ratio between the average coverage of the promoter region divided by the mean obtained for the intergenic regions.
Sequences generated by the Pacific Bioscience RSII  were aligned to the C. crescentus NA1000 genome using Blasr  (https://github.com/PacificBiosciences/blasr) and the modification and associated motifs patterns  were identified applying the RS_Modification_and_Motif_Analyisis protocol in SMRT Analysis  (https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Analysis-Software-Installation  v2.2.0). For each aligned base, a statistics measured as interpulse duration (IPD) combined with a  modification quality value (QV) would mark the methylation status. On the one hand, a minimum QV  of 45 is required for a position to be marked as methylated; on the other hand, a maximum QV  between 10 and 30 (depending on the observed kinetic detections background in the sample), coupled  with the requirement that such a score is observed on both strands, would mean that a position, in an  otherwise methylated motif, is unmethylated.
Genome_build: C. crescentus NA1000 : NC_011916.1
Supplementary_files_format_and_content: .txt file reports abundance measurements, peaks annotation (Columns: [0] Enrichment Ratio; [1] from; [2] to; [3] location; [4] strand; [5] length; [6] ID; [7] name; [8] gene_ID; [9] syn; [10] COG; [11] description)
Supplementary_files_format_and_content: .gff file reports list of putatively modified sites
Supplementary_files_format_and_content: .csv file reports complete list of all Interpulse durations at all loci

organism: Caulobacter vibrioides NA1000

growth_protocol: Caulobacter crescentus and derivatives were grown at 30°C in PYE (Peptone yeast extract) or M2G

extract_protocol:
Mid-log phase cells were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1%  formaldehyde at room temperature for 10 min and on ice for 30 min thereafter, washed  thrice in phosphate buffered saline (PBS) and lysed in a Ready-Lyse lysozyme solution  (Epicentre, Madison, WI) according to the manufacturer`s instructions. Lysates were  sonicated (Sonifier Cell Disruptor B-30; Branson Sonic Power. Co., Danbury, CT) on ice  using 10 bursts of 20 sec at output level 4.5 to shear DNA fragments to an average length  of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. Lysates were  normalized by protein content, diluted to 1 mL using ChIP buffer (0.01% SDS, 1.1%  Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl plus protease  inhibitors (Roche) and pre-cleared with 80 μL of protein-A agarose (Roche, Switzerland)  and 100 uμg BSA. Ten % of the supernatant was removed and used as total chromatin  input DNA as described before (Radhakrishnan et al., 2008).  Two microliters of polyclonal antibodies to MucR1 (Josmann Llc, NAPA, CA, USA) were added to the remains of the  supernatant, incubated overnight at 4°C with 80 μL of protein-A agarose beads pre  saturated with BSA, washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2  mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt buffer (0.1% SDS, 1%  Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl) and LiCl buffer  (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH  8.1) and twice with TE buffer (10 mM Tris-HCl (pH 8.1) and 1 mM EDTA). The  protein•DNA complexes were eluted in 500 μL freshly prepared elution buffer (1% SDS,  0.1 M NaHCO3), supplemented with NaCl to a final concentration of 300 mM and  incubated overnight at 65°C to reverse the crosslinks. The samples were treated with 2 μg  of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA  extracted using phenol:chloroform:453 isoamyl alcohol (25:24:1), ethanol-precipitated  using 20 ug glycogen as carrier and re-suspended in 100uL of water. For deep  sequencing (ChIP-seq) total chromatin input DNA was not saved.
DNA libraries were prepared for sequencing using standard Illumina protocols by FASTERIS SA, Switzerland

tag: genotype/variation

tag: protocol

value: synchronization

tag: time

value: 40 minues

tag: chip antibody

value: polyclonal antibodies to MucR1


title: CONVD.7 CD4+ T cell


title: CONVD.6 CD4+ T cell


title: CONVD.6 CD8+ T cell


title: MucR1_ChIP_exo_T70

description: ChIP-Exo

value: 70 minues


title: CONVD.5 TCR αβ+ IEL


title: CONVD.7 TCR αβ+ IEL


title: CONVD.5 CD8+ T cell


title: CONVD.5 CD4+ T cell


title: CONVD.4 CD4+ T cell


title: CONVD.4 CD8+ T cell


title: CONVD.3 CD8+ T cell


title: CONVD.3 TCR γδ+ IEL


title: CONVD.3 CD4+ T cell


title: CONVD.4 TCR αβ+ IEL


title: CONVD.4 TCR γδ+ IEL


title: AB912

status: Public on Nov 29 2016

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

description: polyA+ RNA

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
the R2 sequences, used solely for barcode extraction, were not included.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: umitab.txt.gz: single cell expression matrix: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: Liver cells

growth_protocol: C57bl6 male mice age 2 month were housed under reverse phase cycle, and fasted for 5 hours starting at 7AM.

extract_protocol:
Mouse hepatocytes were isolated by a modification of the two-step collagenase perfusion method of Seglen. Digestion step was performed with Liberase Blendzyme 3 recombinant collagenase (Roche Diagnostics) according to the manufacturer’s instruction.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

treatment_protocol: Mice were anesthetized with an intraperitoneal injection of a ketamine (100 mg/kg) and xylazine (10 mg/kg) mixture.

tag: age

value: post natal two months


title: CONVD.3 TCR αβ+ IEL


title: CONVD.2 CD4+ T cell


title: Root control

city: Passo Fundo

first: Jorge

middle: Fernando

last: Pereira

state: RS

address: Rodovia BR-285, Km 294

country: Brazil

institute: Embrapa Trigo

description:
Root_Profiling.xlsx
Root_Total_GOAnalysis.xlsx
Root_Leaf_Differential_Expression.xlsx

data_processing:
De novo assembly performed with software GS De Novo Assembler (v 2.6). Assembly parameter: seed step (default value: 12), seed length (default value: 16), seed count (default value: 1), minimum overlap length (default value: 40), minimum overlap identity (default value: 90), alignment identity score (default value: 2), alignment difference score (default value: -3).
cDNA / Transcriptome options: isogroup threshold (default value: 500 contigs), isotig threshold (default value: 100 isotigs), isotig contig count threshold (default value: 100 contigs), isotig contig length threshold (default value: 3 base pairs)
Singletons cleaning: software SeqClean, Lucy (parameter: minimum length 100 bp)
Blast (Basic Local Alignment Search Tool) (E-value: 1.0E-3)
GO assignment
Genome_build: see Leaf_Total.fasta and Root_Total.fasta linked as supplementary files on the Series record.
Supplementary_files_format_and_content: [Root_Profiling.xlsx] Excel sheet containing the number of transcripts detected in roots under control and drought conditions
Supplementary_files_format_and_content: [Leaf_Profiling.xlsx] details of the isotigs detected in leaves
Supplementary_files_format_and_content: [Root_Total_GOAnalysis.xlsx] Excel sheet containing the GO analysis of the root-derived transcripts detected in control and stressed conditions
Supplementary_files_format_and_content: [Leaf_Total_GOAnalysis.xlsx] Excel sheet containing the GO analysis of the leaf-derived transcripts detected in control and stressed conditions
Supplementary_files_format_and_content: [Root_Leaf_Differential_Expression.xlsx] Excel sheet containing the statistical analysis to detect the differentially expressed transcripts under drought in roots and leaves

molecule: total RNA

organism: Triticum aestivum

source_name: Wheat root system with 5 weeks-old.

growth_protocol: Germinated seeds were transferred to pots (3 seeds per pot) containing 6.5 kg of a mixture of soil, sand and vermiculite (2:1:1) and incubated in a glasshouse with natural light at 22 ± 4°C. Plants were watered daily. Control plants were grown for five weeks at 100% of field capacity.

extract_protocol:
Total RNA was extracted with TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions, and purified using an RNeasy Mini Kit (Qiagen). During the purification, one DNase digestion step was performed with an RNase-free DNase Set (Qiagen).
Total RNA was sent to Macrogen Inc (South Korea) for construction of cDNA libraries.

treatment_protocol: Germinated seeds were transferred to pots (3 seeds per pot) containing 6.5 kg of a mixture of soil, sand and vermiculite (2:1:1) and incubated in a glasshouse with natural light at 22 ± 4°C. Plants were watered daily. In the stress treatment, plants were watered for 2 weeks at 75% of field capacity followed by 3 weeks of water deprivation.

tag: cultivar

value: MGS1 Alianca

tag: growth stage

value: Tillering stage

tag: stress

value: control

tag: tissue

value: root


title: MucR1_ChIP_exo_T100

description: ChIP-Exo

value: 100 minues


title: CONVD.7 CD8+ T cell


title: CONVD.7 TCR γδ+ IEL


title: MucR1_ChIP_exo_T10

description: ChIP-Exo

value: 10 minutes


title: CONVD.2 TCR γδ+ IEL


title: CONVD.1 CD8+ T cell


title: CONVD.2 TCR αβ+ IEL


title: CONVR.8 TCR γδ+ IEL

value: conventionally-raised


title: CONVD.1 CD4+ T cell

value: conventionalized


title: CONVR.7 CD4+ T cell

value: Peripheral blood lymphocyte


title: CONVR.7 CD8+ T cell

value: Peripheral blood


title: CONVD.1 TCR αβ+ IEL

value: Intraepithelial lymphocyte


title: CONVD.1 TCR γδ+ IEL

value: Intestine


title: CONVR.6 CD4+ T cell


title: CONVR.7 TCR αβ+ IEL


title: CONVR.6 TCR γδ+ IEL


title: CONVR.7 TCR γδ+ IEL


title: CONVR.6 TCR αβ+ IEL


title: CONVR.5 CD4+ T cell


title: CONVR.5 TCR αβ+ IEL


title: CONVR.5 CD8+ T cell


title: CONVR.5 TCR γδ+ IEL


title: CONVR.8 CD4+ T cell


title: GF.8 TCR γδ+ IEL

value: germ-free


title: GF.8 TCR αβ+ IEL


title: GF.8 CD8+ T cell


title: GF.6 CD8+ T cell


title: GF.8 CD4+ T cell


title: GF.7 TCR γδ+ IEL


title: GF.7 TCR αβ+ IEL


title: CONVR.8 TCR αβ+ IEL


title: GF.7 CD4+ T cell


title: GF.7 CD8+ T cell


title: GF.6 CD4+ T cell


title: CONVR.6 CD8+ T cell


title: GF.6 TCR γδ+ IEL


title: GF.5 CD4+ T cell


title: GF.5 CD8+ T cell


title: GHA510

data_processing:
Library strategy: REC-Seq
genome build: NC_011916.1
To remove contaminating sequences, the reads were split according to the HinfI consensus motif (5’-  G^ANTC-3’) considered as a barcode sequence using fastx_toolkit  (http://hannonlab.cshl.edu/fastx_toolkit/) (fastx_barcode_splitter.pl --bcfile barcodelist.txt --bol --  exact). Most of the reads (more than 90%) were rejected, and the reads kept were remapped to the  reference genomes with bwa mem and samtools to generate a sorted bam file.  The bam file was further filtered to remove low mapping quality reads (keeping AS >= 45) and split  by orientation (alignmentFlag 0 or 16) with bamtools. The reads were counted at 5' positions  using Bedtools (bedtools genomecov -d -5). Both orientation count files were combined into a  bed file at each identified 5’-GANTC-3’ motif (where reverse counts >=1 at position N+1 and forward  counts >=1 at position N-1) using a home-made PERL script. The HinfI positions in the bed file were  associated with the closest gene using Bedtools closest and the gff3 file of the reference genomes  . The final bed file was converted to an MS Excel sheet (S1 and S2 Tables) with a homemade  script. For the MboI-based REC-Seq, the strategy was identical except that a different adaptor was  used for ligation after cleavage and the MboI consensus motif (5’-^GATC-3’) was used as barcode for  filtering of V. cholerae O1 biovar El Tor and E. coli K12 Ec100D gDNA mapped onto the  MG1655 genome.
Supplementary_files_format_and_content: tab delimited text files, with feature annotation, REC_seq score, gene name and description

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus

value: {delta}mucR1 {delta}mucR2


title: GF.5 TCR αβ+ IEL


title: GHA505

value: wild type


title: GF.5 TCR γδ+ IEL


title: CONVR.4 CD8+ T cell


title: CONVR.4 CD4+ T cell


title: CONVR.4 TCR γδ+ IEL


title: DAC+ProsA_3

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: YB5 is a colon cancer cell line derived from the SW48 colon cancer cell line and contains a DNA methylated and silenced CMV promoter driving GFP expression

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the reads in fastq files to hg19 and generating BAM files
ht-seq-count  with default settings to generate counts of each gene
edgeR to generate RPKM and fold change of each condition compared to control, only keep genes with at least one read in one of the samples
export fold change of each inhibitor vs. control into a text file, then import all the fold changes into one excel file
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are in excel format. The first 12 columns are the RPKMs of the individual samples. The following columns are the fold change, p-value, and FDR of the triplicates of each condition compared against the triplicates of control samples

organism: Homo sapiens

source_name: YB5 colon cancer cell line

growth_protocol: YB5 cell line was cultured in L-15 medium with 10% fetal bovine serum

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen)
Strand-specific RNA libraries were generated from 1μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina)

treatment_protocol: Cells were treated daily with 100nM decitabine (5-aza-CdR) for 48h, then with or without 50nM proscillaridin A for an additional 48h

tag: cell line

value: colon cancer cell line

value: Dukes' type C, grade IV, colorectal adenocarcinoma

tag: gender

value: female


title: CONVR.3 TCR γδ+ IEL


title: CONVR.3 CD8+ T cell


title: CONVR.3 TCR αβ+ IEL


title: CONVR.3 CD4+ T cell


title: CONVR.2 CD8+ T cell


title: CONVR.2 CD4+ T cell


title: ProsA_3


title: DAC_3


title: GF.6 TCR αβ+ IEL


title: CONVR.2 TCR αβ+ IEL


title: DAC+ProsA_2


title: Cntrl_3


title: CONVR.1 CD4+ T cell


title: ProsA_2


title: DAC_2


title: CONVR.2 TCR γδ+ IEL


title: CONVR.1 CD8+ T cell


title: CONVR.1 TCR αβ+ IEL


title: CONVR.1 TCR γδ+ IEL


title: Cntrl_2


title: DAC+ProsA_1


title: GF.4 CD8+ T cell


title: DAC_1


title: ProsA_1


title: Cntrl_1


title: GF.4 TCR αβ+ IEL


title: GF.3 CD4+ T cell


title: GF.3 CD8+ T cell


title: GF.3 TCR γδ+ IEL


title: ST 4

city: NEW YORK

first: Piali

last: Mukherjee

state: New York

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Basecalling performed by CASAVA version 1.8.2
filtered for pass filter reads by unix tool grep with a command:  zcat sample_R1.fastq.gz | grep --no-group-separator -A 3 '^@.* [^:]*:N:[^:]*:' > sample_R1_PF.fastq
adaper trimming performed by Flexbar v2.4 with command:  flexbar -r sample_R1_PF.fastq -p sample_R2_PF.fastq -t sample_trimmed -a peadapters.fa -f i1.5 -ao 6 -m 21 -at 2 -ae RIGHT -n 10 -u 2 -j -am 3 -ai -3 -ag -20
align to human genome hg18 performed by Bismark v0.5.4, Bowtie v0.12.7 with command:  bismark -q -un -X 400 -l 100 --phred33-quals --directional hg19 -1 sample_trimmed_1.fastq -2 sample_trimmed_2.fastq
methylation extraction by custom PERL script
Genome_build: hg18
Supplementary_files_format_and_content: Tab delimited CpG methylcall files (text/tsv) with coverage of 10 or more. Columns are as follows:  chromosome, base, strand, coverage, frequency C, and frequency T

source_name: Supratentorial Ependymoma

extract_protocol:
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
ERRBS libraries were prepared by digesting 75 ng of DNA with restriction enzyme MspI, followed by post end-repair, A-tailing, and adapter ligation with Illumina TruSeq adapters. The region corresponding to 84-334bp was size-selected as two fractions, and each fraction was subjected to overnight bisulfite conversion (55 cycles of 95 °C for 30 sec, 50 °C for 15 min) using EZ DNA methylation kit (Cat # D5002, Zymo Research, Irvine CA). Purified bisulfite converted DNA was PCR amplified (using TruSeq primers, Illumina Inc. San Diego, CA) for 18 cycles of denaturing, annealing and extension/elongation steps using Roche FastStart (cat # 03 553 361 001):  94 °C for 20 secs, 65 °C for 30 secs, 72 °C for 1 min, followed by 72 °C for 3 min. The resulting libraries were normalized to 2nM and pooled at the same molar ratio.

value: ERRBS

tag: sample type

value: ST


title: ST 3


title: GF.3 TCR αβ+ IEL


title: ST 2


title: ST 1


title: GF.2 CD8+ T cell


title: GF.2 CD4+ T cell


title: PF positive 3

source_name: Posterior Fossa Ependymoma

value: PF positive


title: PF positive 1


title: GF.2 TCR γδ+ IEL


title: PF positive 2


title: PF negative 8

value: PF negative


title: GF.4 TCR γδ+ IEL


title: GF.4 CD4+ T cell


title: GF.2 TCR αβ+ IEL


title: PF negative 6


title: GF.1 CD8+ T cell


title: PF negative 4


title: PF negative 7


title: GF.1 CD4+ T cell


title: GF.1 TCR γδ+ IEL


title: PF negative 3


title: PF negative 5


title: PF negative 2


title: TSPAN8-low subpopulation of P6 ID4-EGFP+ - sample 2

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

data_processing:
Resulting FASTQ files from each sample were merged, trimmed, and quality was confirmed with FASTQC.
Reads in trimmed FASTQs were aligned to the mouse genome (mm9) with TopHat v2.0.12 and Bowtie v2.2.3.0.
Transcript abundance was determined with Cufflinks (Trapnell et al., 2012).
Fragments per kilobase of transcript per million mapped reads (FPKM) transcript abundance values for each gene in each sample were normalized and used for differential gene expression analysis as described (Dozmorov and Lefkovits, 2009), producing normalized counts.
Genome_build: mm9
Supplementary_files_format_and_content: Three csv matrix files with either Raw FPKM or normalized expression counts (Log or NOT log) for each gene (rows) and one column per sample.

source_name: P6 ID4-EGFP+ spermatogonia from mouse testes

growth_protocol: LT-11B6 (Id4-eGfp transgenic mice on C57BL/6 background) from Jon Oatley (Washington State University; Chan et al., 2014 Genes & Development 28: 1351-1362) were bred to produce pup male mice. Testes from postnatal day 6 (P6)  pups were used to produce testis cell suspensions that were stained with antibodies against TSPAN8, EPHA2 or PVR and subsequently used for FACS. For the "high" subpopulations of ID4-EGFP+ spermatogonia (based on EPHA2, PVR or TSPAN8 antibody labeling), the top 1/3 most robustly stained cells were sorted, while for the low subpopulations, the bottom 1/3 most weak positive stained cells were selected.  Three replicate preparations of cells are included for each sample type.

extract_protocol:
Sorted P6 ID4-EGFP+ spermatogonia and subpopulations defined by antibody labeling for TSPAN8, EPHA2, or PVR were used for RNA-seq analysis of transcriptomes. For this purpose, sorted cells were pelleted, counted and subjected to direct cDNA synthesis using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories, Mountain View, CA) per manufacturer recommendations and 9 cycles of amplification. Amplified cDNAs from each sample were purified using Agencourt AMPure XP Pure magnetic beads (Beckman Coulter Life Sciences, Indianapolis, IN) and pre-qualified for library construction using a 2100 Bioanalyzer and High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA).
Using 250pg input cDNA, we performed Nextera XT dual-index library preparation with modifications from manufacturer recommendations. Specifically, tagmentation was performed with 2.5ul Tagment DNA buffer, 1.25ul Amplification Tagment Mix, and 1.25ul cDNA for exactly 10 minutes at 55°C, ramp to 10°C, and immediate addition of 1.25ul NT buffer.  Additionally, PCR amplification with index primers (separate index per sample) was performed with the entire 6.25ul of Tagmentation reaction mix plus 3.75ul Nextera PCR Mix using the recommended cycling conditions except that the extension time was 60 seconds. Libraries were quantified with Qubit fluorometry (ThermoFisher Scientific) and qualified for fragment size and distribution by 2100 Bioanalyzer with High-sensitivity DNA reagents (522 ± 6 bp). Libraries were pooled at equal concentrations and subjected to four lanes of rapid mode Illumina HiSeq2500 sequencing (paired-end 100bp) at the University of Texas Southwestern Medical Center Genomics and Microarray Core.

tag: label

tag: subpopulation

value: low


title: PF negative 1


title: TSPAN8-high subpopulation of P6 ID4-EGFP+ - sample 3

value: high


title: TSPAN8-low subpopulation of P6 ID4-EGFP+ - sample 1


title: PF positive 4


title: Myceliophthora_thermophila_flax_45C

city: Montreal

first: Ian

last: Reid

state: QC

address: 7141 Sherbrooke West

department: Biology

country: Canada

institute: Concordia University

data_processing:
Reads were aligned to the M thermophila genome using tuqueMap version 1.0.4 (http://sourceforge.net/projects/tuque/) with default parameters
The reads that mapped within each annotated transcript were counted and the counts were converted to Fragments per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: JGI Myceliophthora thermophila (Sporotrichum thermophile) v2.0
Supplementary_files_format_and_content: A tab-delimited text file with a column for each Sample and a row of FPKM values for each transcript. The annotation is publicly available, along with the genome sequence, at http://genome.jgi-psf.org/pages/dynamicOrganismDownload.jsf?organism=Spoth2

organism: Thermothelomyces thermophilus

source_name: Mycelium

growth_protocol: Spores were inoculated at a final concentration of 10^6/mL into 10x Trametes Defined Medium containing 2% carbon source and incubated at 45 °C with shaking at 150 rpm

extract_protocol:
RNA was extracted with Trizol (Invitrogen, Carlsbad CA, USA) according to the manufacturer's protocol.
Libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq Sample Prep Kit

tag: carbon source

value: flax straw

tag: growth temperature

tag: hours


title: Myceliophthora_thermophila_canola_45C

value: canola straw


title: TSPAN8-high subpopulation of P6 ID4-EGFP+ - sample 2

tag: strain


title: TSPAN8-high subpopulation of P6 ID4-EGFP+ - sample 1


title: P6 ID4-EGFP+ sample 3

value: GFP


title: Myceliophthora_thermophila_oat_45C

value: oat straw


title: GF.1 TCR αβ+ IEL

tag: microbial colonization state

tag: cell type

value: Intraepithelial lymphocyte

tag: tissue origin

value: Intestine


title: P6 ID4-EGFP+ sample 1


title: P6 ID4-EGFP+ sample 2


title: Myceliophthora_thermophila_triticale_45C

value: triticale straw


title: WT

city: Pittsburgh

first: Igor

last: Nasonkin

state: Pennsylvania

address: 200 Lothrop street

institute: University of Pittsburgh

data_processing:
Raw sequencing reads were aligned to the Mus musculus genome (mm10) by TopHat 2.0.8
Fragments per kilobase of transcript per million mapped reads (FPKM) values were calculated by using Cuffdiff (v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include differential expression values of Control and Triple mutant samples.

source_name: Control Retina

extract_protocol:
Retinas were dissected from P15 pups and stored in RNA later. Total RNA was isolated with Qiagen Allprep DNA/RNA mini kit.
RNA libraries were prepared using standard Illumina protocols by Genewiz.

value: Retina

tag: age

value: Post natal day 15

tag: genotype

value: Dnmt1 flox/flox, Dnmt3a Flox/flox, Dnmt3b Flox/flox, Rx-Cre negative


title: Triple Mutant

source_name: Mutant retina

value: Dnmt1 flox/flox, Dnmt3a Flox/flox, Dnmt3b Flox/flox, Rx-Cre positive


title: ZI418RT3

city: Planegg-Martinsried

first: Stephan

last: Hutter

state: Bavaria

address: Grosshaderner Strasse 2

department: Department of Biology II

country: Germany

institute: University of Munich

data_processing:
Standard Illumina pipeline using Bustard for basecalling
Illumina sequence reads were mapped to the reference D. melanogaster transcriptome (FlyBase release 5.57) using NextGenMap (version 0.4.12) and requiring a minimum of 40 mapped residues (option –R 40)
Expression was quantified on a “per gene” basis. For this, if a sequence read mapped to one or more transcripts of the same gene, it was counted as one “hit” for that gene and all subsequent analyses were performed at the gene level
Genome_build: dmel_r5.57
Supplementary_files_format_and_content: tab-delimited text files include gene specific read counts for each sample

organism: Drosophila melanogaster

source_name: whole flies

growth_protocol: All flies were maintained on standard cornmeal-molasses medium at 22° with a 14 h light:10 h dark cycle

extract_protocol:
Total RNA extraction and DNase I digestion were performed using the MasterPure RNA Purification Kit (Epicentre)
Poly-A mRNA was purified and fragmented by sonication. First strand single end cDNA was synthesized using random primers. Tagged libraries were generated, pooled and run on a HiSeq 2000 sequencer (Illumina) to generate single reads of 51 bases

treatment_protocol: Flies were exposed to a 0°C cold shock for 7h and then brought back to room temperature for recovery

tag: Sex

value: male

tag: population

value: Africa

tag: line

tag: condition

value: room temperature


title: ELK1_TKOMEF_and_ELK1FW_TPA

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

description: ChIP-seq

data_processing:
ChipSeq SRF ELK1: Each fastq file have been aligned to the mm9 genome using BWA
genome build: MM9
processed data files format and content: Wig files are those generated by MACS at 1bp resolution and a set normalised to 30 million mapped reads are additionally provided.

source_name: Cultured MEFs (Mouse Embryonic fibroblasts)

growth_protocol: The different types of MEFs were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.

extract_protocol: Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow size select on 2%Agarose gel.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip. Samples have been multiplexed and run on Hi-seq 2000/1000 (6 samples per multiplexed lane).

treatment_protocol: Cells were  starved for 48h in 0.3%FCS. Where indicated, cells were stimulated for 30 minutes with 12-O-tetradecanoyl phorbol-13-acetate (Sigma TPA, 50 ng/ml).

value: TKO recon pMY Elk-1 FW mutant

tag: chip antibody

value: ELK1 in house antibody

tag: scaling factor used

value: (total mapped reads normalised to 30MM reads)


title: ZI418rec90_3

value: recovery (90 minutes)


title: ELK1_TKOMEF_and_ELK1NONA_03

description: ChIP-seq

value: Cultured MEFs (Mouse Embryonic fibroblasts

value: TKO recon pMY Elk-1 nonA mutant


title: TSPAN8-low subpopulation of P6 ID4-EGFP+ - sample 3

tag: label

value: low


title: ZI418RT1


title: ZI418rec90_1


title: ELK1_TKOMEF_and_ELK1NONA_TPA

description: ChIP-seq


title: ZI418rec15_3

value: recovery (15 minutes)


title: ELK1_TKOMEF_and_ELK1FW_03

description: ChIP-seq


title: ZI418CS3

value: cold shock (3.5h)


title: ZI418CS1


title: ELK1_TKOMEF_and_ELK1WT_TPA

description: ChIP-seq

value: TKO recon pMY Elk-1 wt


title: ZI216RT3


title: ZI216RT1


title: ZI216rec90_3


title: ELK1_TKOMEF_and_EMPTY_03

description: ChIP-seq

value: TKO recon pMY Empty


title: ELK1_TKOMEF_and_EMPTY_TPA

description: ChIP-seq


title: ZI216rec90_1


title: SRF_TKOMEF_TPA_replicate2

description: ChIP-seq

value: TCF KO (TKO)


title: SRF_TKOMEF_TPA_replicate1

description: ChIP-seq


title: ZI418rec15_1


title: SRF_TKOMEF_03_replicate2

description: ChIP-seq


title: ZI216rec15_3


title: ZI216CS1


title: ZI216rec15_1


title: ZI197RT3


title: SRF_WTMEF_TPA_replicate2

description: ChIP-seq

value: wildtype


title: SRF_WTMEF_03_replicate2

description: ChIP-seq


title: ZI216CS3


title: ZI197RT1


title: SRF_WTMEF_TPA_replicate1

description: ChIP-seq


title: SRF_WTMEF_03_replicate1

description: ChIP-seq


title: ZI197rec90_1


title: RNA_TKOMEF_and_ELK1NONA_TPA_replicate2

description: RNA-seq


title: ELK1_TKOMEF_and_ELK1WT_03

description: ChIP-seq


title: ZI197rec15_3


title: ZI197CS3


title: RNA_TKOMEF_and_ELK1NONA_03_replicate1

description: RNA-seq

data_processing:
RNASeq: Alignments were performed using bwa
genome build: MM9
processed data files format and content: wig files generated by MACS at 1bp resolution and a set of normalised wig files is provided.

extract_protocol: RNA-seq libraries were prepared using directional mRNA-Seq Library Prep v1.0 Protocol from Illumina with minor adjustments. The samples were collected using GenElute Mammalian Total RNA Miniprep Kit and DNA contaminants were removed by treating the samples with DNaseI (see section above). To reduce the ribosomal rRNA in the libraries, samples were processed using the Ribo-zero rRNA removal kit (Epicentre). The Kapa HiFi HotStart ready mix, which reduced the overall volume of the PCR, was substituted to the Illumina kit Phusion enzyme and the ratio for the Agencourt AMPure XP beads was adjusted accordingly. The standard PCR cycle suggested by the Illumina protocol was changed to match the quantity of the total RNA measured initially with the Bioanalyser.


title: RNA_TKOMEF_and_ELK1NONA_03_replicate2

description: RNA-seq


title: SRF_TKOMEF_03_replicate1

description: ChIP-seq


title: ZI197rec15_1


title: ZI197rec90_3


title: RNA_TKOMEF_and_ELK1FW_TPA_replicate2

description: RNA-seq


title: ZI197CS1


title: SU58RT3

value: Europe


title: RNA_TKOMEF_and_ELK1FW_TPA_replicate1

description: RNA-seq


title: SU58rec90_3

value: male


title: SU58RT1


title: RNA_TKOMEF_and_ELK1FW_03_replicate2

description: RNA-seq


title: RNA_TKOMEF_and_ELK1FW_03_replicate1

description: RNA-seq


title: SU58rec90_1


title: RNA_TKOMEF_and_ELK1WT_TPA_replicate2

description: RNA-seq


title: RNA_TKOMEF_and_ELK1WT_03_replicate2

description: RNA-seq


title: SU58rec15_3


title: RNA_TKOMEF_and_EMPTY_TPA_replicate2

description: RNA-seq


title: RNA_TKOMEF_and_ELK1NONA_TPA_replicate1

description: RNA-seq


title: RNA_TKOMEF_and_ELK1WT_03_replicate1

description: RNA-seq


title: SU58CS3


title: SU58rec15_1


title: SU08RT1


title: RNA_TKOMEF_and_EMPTY_03_replicate1

description: RNA-seq


title: RNA_TKOMEF_and_EMPTY_TPA_replicate1

description: RNA-seq


title: RNA_TKOMEF_TPA_replicate3

description: RNA-seq


title: SU08rec90_3


title: RNA_TKOMEF_TPA_replicate2

description: RNA-seq


title: SU08rec90_1


title: RNA_TKOMEF_TPA_replicate1

description: RNA-seq


title: SU08rec15_1


title: RNA_TKOMEF_03_replicate3

description: RNA-seq


title: SU08CS3


title: RNA_TKOMEF_03_replicate2

description: RNA-seq


title: SU08CS1


title: RNA_TKOMEF_03_replicate1

description: RNA-seq


title: SU07RT3


title: SU58CS1


title: SU08RT3


title: SU07RT1


title: RNA_TKOMEF_and_ELK1WT_TPA_replicate1

description: RNA-seq


title: RNA_WTMEF_TPA_replicate1

description: RNA-seq


title: RNA_WTMEF_TPA_replicate3

description: RNA-seq


title: SU07rec15_3


title: SU07rec90_1


title: RNA_WTMEF_03_replicate3

description: RNA-seq


title: RNA_WTMEF_TPA_replicate2

description: RNA-seq


title: SU07rec90_3


title: RNA_TKOMEF_and_EMPTY_03_replicate2

description: RNA-seq


title: SU08rec15_3


title: SU07rec15_1


title: tnpo3 mutant rep3

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

department: Immunology

institute: MPI-IE Freiburg

description:
processed data file: diff_gene_expr_tnpo3.mutant-vs-wild-type.tsv.gz
processed data file: retained_introns_tnpo3.tsv.gz
processed data file: skipped_exons_tnpo3.tsv.gz

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA version 1.18.64.
Reads were aligned to the Zv9 genome assembly using TopHat 2.0.13 with the following settings: transcriptome alignment to Ensembl release 78 gene annotation first, library type fr-firststrand, fragment length mean and standard deviation set to sample-specific values. The fragment length metrics was determined by mapping a 1 million read pair subsample to the zebrafish transcriptome using Bowtie 2 version 2.2.3.
The number of reads per annotated gene (based on Ensembl 78 zebrafish gene annotation) were counted with featureCounts version 1.4.5-p1. Fragments were only counted if both ends aligned on the same chromosome with a minimum mapping quality of 10 and in agreement with the strand orientation of the annotated gene.
Differential gene expression analysis was performed with Bioconductor package limma version 3.26.3. Genetic background was explicitly omitted from the linear regression formula (~condition) due to low statistical power with the given number of replicates. Differentially expressed genes were filtered at absolute logFC >=1 and FDR < 5%.
Differential alternative splicing events were analysed with rMATS 3.0.9 separately for the three mutants. Aligned reads were filtered to include only reads overlapping with annotated transcripts in the same strand orientation. Zebrafish gene and transcript annotations from Ensembl 78 were used. Fragment size mean and standard deviation were set to sample-specific values obtained during alignment of a read subsamble. Alternative splicing events supported by reads spanning splice junctions were reported.
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include differential gene expression results generated by limma for the three mutants, separately. Tab-delimited text files include significant alternative splicing events generated by rMATS for the three mutants samples, separately.

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma) following the  manufacturer's instructions. After treatment with Cloned DNaseI (Takara),  RNA extraction using TRI Reagent was repeated. RNA quality was determined using the 2100 Bioanalyzer instrument (Agilent) and RNA concentration was determined using Qbit 2.0 Fluorometer (Life Technologies).
RNA libraries were prepared for sequencing using the TruSeq stranded total RNA sample preparation with Ribo-Zero Human/Mouse/Rat (RS-122-2203).

value: mixed background C

tag: surface phenotype


title: tnpo3 mutant rep2


title: lsm8 mutant rep3

description:
processed data file: diff_gene_expr_lsm8.mutant-vs-wild-type.tsv.gz
processed data file: skipped_exons_lsm8.tsv.gz
processed data file: retained_introns_lsm8.tsv.gz

data_processing:
Basecalling was performed with Illumina HiSeq Control Software/RTA version 1.18.64.
Reads were aligned to the Zv9 genome assembly using TopHat 2.0.13 with the following settings: transcriptome alignment to Ensembl release 78 gene annotation first, library type fr-firststrand, fragment length mean and standard deviation set to sample-specific values. The fragment length metrics was determined by mapping a 1 million read pair subsample to the zebrafish transcriptome using Bowtie 2 version 2.2.3.
The number of reads per annotated gene (based on Ensembl 78 zebrafish gene annotation) were counted with featureCounts version 1.4.5-p1. Fragments were only counted if both ends aligned on the same chromosome with a minimum mapping quality of 10 and in agreement with the strand orientation of the annotated gene
Differential gene expression analysis was performed with Bioconductor package limma version 3.26.3. Genetic background was explicitly omitted from the linear regression formula (~condition) due to low statistical power with the given number of replicates. Differentially expressed genes were filtered at absolute logFC >=1 and FDR < 5%.
Differential alternative splicing events were analysed with rMATS 3.0.9 separately for the three mutants. Aligned reads were filtered to include only reads overlapping with annotated transcripts in the same strand orientation. Zebrafish gene and transcript annotations from Ensembl 78 were used. Fragment size mean and standard deviation were set to sample-specific values obtained during alignment of a read subsamble. Alternative splicing events supported by reads spanning splice junctions were reported.
genome build: Zv9
Tab-delimited text files include differential gene expression results generated by limma for the three mutants, separately. Tab-delimited text files include significant alternative splicing events generated by rMATS for the three mutants samples, separately.

tag: tissue

value: whole embryo

value: mixed background B


title: RNA_WTMEF_03_replicate2

description: RNA-seq


title: lsm8 mutant rep2


title: lsm8 mutant rep1


title: SU07CS3


title: control rep3

description:
processed data file: diff_gene_expr_snapc3.mutant-vs-wild-type.tsv.gz
processed data file: diff_gene_expr_lsm8.mutant-vs-wild-type.tsv.gz
processed data file: diff_gene_expr_tnpo3.mutant-vs-wild-type.tsv.gz
processed data file: skipped_exons_snapc3.tsv.gz
processed data file: skipped_exons_lsm8.tsv.gz
processed data file: skipped_exons_tnpo3.tsv.gz
processed data file: retained_introns_snapc3.tsv.gz
processed data file: retained_introns_lsm8.tsv.gz
processed data file: retained_introns_tnpo3.tsv.gz

value: wt


title: E14RT1

value: room temperature


title: snapc3 mutant rep3

description:
processed data file: diff_gene_expr_snapc3.mutant-vs-wild-type.tsv.gz
processed data file: skipped_exons_snapc3.tsv.gz
processed data file: retained_introns_snapc3.tsv.gz

value: mixed background A


title: RNA_WTMEF_03_replicate1

description: RNA-seq

value: Cultured MEFs (Mouse Embryonic fibroblasts


title: snapc3 mutant rep1


title: control rep1


title: SU07CS1


title: E14rec90_1

value: recovery (90 minutes)


title: E14RT3


title: tnpo3 mutant rep1


title: A157RT3

value: Africa


title: E14rec15_1

value: recovery (15 minutes)


title: control rep2


title: A157rec90_3


title: snapc3 mutant rep2


title: E14CS3

value: cold shock (3.5h)


title: A157rec90_1


title: E14rec15_3


title: E14CS1


title: E14rec90_3


title: A157RT1


title: A157rec15_1


title: A157rec15_3


title: CaulobacterCrescentusNA1000

description:
Pacific Biosciences SMRTcell data
Pacific Biosciences 10Kb with size selection

extract_protocol:
Sequencing libraries were prepared from gDNA extracted from the two samples (C.  crescentus WT and mucR mutant strains) using the DNA Template Prep Kit 2.0 (250bp  - 3Kb, Pacific Biosciences p/n 001-540-726).
DNA Template Prep Kit 2.0 (250bp - 3Kb, Pacific Biosciences p/n 001-540-726)

tag: genotype/variation

value: wild type


title: HUVEC_RNA-Seq_Histamine-7h_rep1

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description: Histamine 7h

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove 3' A-stretches originating from the library preparation and poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10).
Reads were aligned to the hg19 genome using Tophat.
Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://homer.salk.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values (RPKM) and UCSC Bedgraphs are provided

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were cultured in Endothelial Cell Growth medium (EGM; Thermo Scientific) on fibronectin-gelatin coated surfaces (10 µg/ml, 0.05%; Sigma-Aldrich).

extract_protocol:
RNA was purified using RNeasy Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Confluent cultures of HUVECs were washed with PBS, followed by starvation of cells for 16 hrs with EGM medium supplemented with 0.5 % FBS. The cells were stimulated with VEGF-A165 (100 ng/ml) or histamine (20 µM) for 7 hrs.

tag: cell collection details

value: Sample from 1 individual

tag: passage

value: passage 5

tag: replicate

value: biological replicate #1

tag: treatment

value: Histamine 7h

value: HUVEC


title: HUVEC_RNA-Seq_VEGFA-7h_rep1

description: rVEGFA 7h

value: rVEGFA 7h

tag: cell type


title: HUVEC_RNA-Seq_Histamine-7h_rep2

description: Histamine 7h

value: Pool of at least 3 individuals

value: passage 9

value: biological replicate #2


title: CaulobacterCrescentus4171

tag: strain

value: {delta}mucR1 {delta}mucR2


title: A157CS3

value: male


title: GHA508

data_processing:
Library strategy: REC-Seq
genome build: chr1 NC_002505.1, chr2 NC_002506.1
To remove contaminating sequences, the reads were split according to the HinfI consensus motif (5’-  G^ANTC-3’) considered as a barcode sequence using fastx_toolkit  (http://hannonlab.cshl.edu/fastx_toolkit/) (fastx_barcode_splitter.pl --bcfile barcodelist.txt --bol --  exact). Most of the reads (more than 90%) were rejected, and the reads kept were remapped to the  reference genomes with bwa mem and samtools to generate a sorted bam file.  The bam file was further filtered to remove low mapping quality reads (keeping AS >= 45) and split  by orientation (alignmentFlag 0 or 16) with bamtools. The reads were counted at 5' positions  using Bedtools (bedtools genomecov -d -5). Both orientation count files were combined into a  bed file at each identified 5’-GANTC-3’ motif (where reverse counts >=1 at position N+1 and forward  counts >=1 at position N-1) using a home-made PERL script. The HinfI positions in the bed file were  associated with the closest gene using Bedtools closest and the gff3 file of the reference genomes  . The final bed file was converted to an MS Excel sheet (S1 and S2 Tables) with a homemade  script. For the MboI-based REC-Seq, the strategy was identical except that a different adaptor was  used for ligation after cleavage and the MboI consensus motif (5’-^GATC-3’) was used as barcode for  filtering of V. cholerae O1 biovar El Tor and E. coli K12 Ec100D gDNA mapped onto the  MG1655 genome.
Supplementary_files_format_and_content: tab delimited text files, with feature annotation, REC_seq score, gene name and description

organism: Vibrio cholerae O1 biovar El Tor

source_name: Vibrio cholerae O1 biovar El Tor


title: GHA511

data_processing:
Library strategy: REC-Seq
genome build: chr NC_003047.1, pSymA NC_003037.1, pSymB NC_003078.1
To remove contaminating sequences, the reads were split according to the HinfI consensus motif (5’-  G^ANTC-3’) considered as a barcode sequence using fastx_toolkit  (http://hannonlab.cshl.edu/fastx_toolkit/) (fastx_barcode_splitter.pl --bcfile barcodelist.txt --bol --  exact). Most of the reads (more than 90%) were rejected, and the reads kept were remapped to the  reference genomes with bwa mem and samtools to generate a sorted bam file.  The bam file was further filtered to remove low mapping quality reads (keeping AS >= 45) and split  by orientation (alignmentFlag 0 or 16) with bamtools. The reads were counted at 5' positions  using Bedtools (bedtools genomecov -d -5). Both orientation count files were combined into a  bed file at each identified 5’-GANTC-3’ motif (where reverse counts >=1 at position N+1 and forward  counts >=1 at position N-1) using a home-made PERL script. The HinfI positions in the bed file were  associated with the closest gene using Bedtools closest and the gff3 file of the reference genomes  . The final bed file was converted to an MS Excel sheet (S1 and S2 Tables) with a homemade  script. For the MboI-based REC-Seq, the strategy was identical except that a different adaptor was  used for ligation after cleavage and the MboI consensus motif (5’-^GATC-3’) was used as barcode for  filtering of V. cholerae O1 biovar El Tor and E. coli K12 Ec100D gDNA mapped onto the  MG1655 genome.
Supplementary_files_format_and_content: tab delimited text files, with feature annotation, REC_seq score, gene name and description

organism: Sinorhizobium meliloti

source_name: Sinorhizobium meliloti


title: A157CS1


title: GHA506


title: HUVEC_RNA-Seq_notx_rep2

description: no treatment control

value: no treatment control


title: HUVEC_RNA-Seq_notx_rep1

description: no treatment control


title: Celera_ringgland_C

status: Public on Nov 27 2016

city: Parkville

first: Trent

last: Perry

state: Victoria

address: 30 Flemington Road

department: Biosciences

country: Australia

institute: The University of Melbourne

description: ~80 ring glands pooled

data_processing:
Raw RNA-seq reads for the central nervous system (to be used for differential expression analysis) were downloaded in SRA format from the modMINE database (accession: SRX029398) then converted to paired end fastq format using the fastq-dump utiliy included in the NCBI SRA toolkit.
Reads were aligned to the D. melanogaster reference genome (BDGP release 5) using Tophat 2.0.13.
Expression levels and differential expression was calculated using Cufflinks 2.2.1 with options to enable reference annotation based transcript assembly (-g), fragment bias correction (-b), multiread correction (-u) and increased maximum fragment alignment (-max-bundle-frags).
Genome_build: BDGP release 5
Supplementary_files_format_and_content: gene_exp.diff was generated by Cuffdiff. The FPKM values for each sample are listed. P-values are given for three differential expression analyses: Celera ring gland vs central nervous system, Armenia-14 ring gland vs central nervous system, Celera ring gland vs Armenia-14 ring gland.

source_name: ring gland

growth_protocol: Larvae reared on normal media.

extract_protocol:
Approximately 80 ring glands were pooled. Total RNA was extracted using the Reliaprep RNA Cell Miniprep System (Promega) then stored at -80degreesC.
RNA libraries were prepared for sequencing using standard Illumina protocols by the Australian Genome Research Facility (AGRF).

value: Celera

tag: developmental stage

value: Wandering 3rd instar larvae

value: ring gland


title: Celera_ringgland_A

description: ~80 ring glands pooled


title: Celera_ringgland_B

description: ~80 ring glands pooled


title: Armenia_ringgland_B

description: ~80 ring glands pooled


title: Armenia_ringgland_A

description: ~80 ring glands pooled


title: Armenia_ringgland_C

description: ~80 ring glands pooled


title: HUVEC_RNA-Seq_VEGFA-7h_rep2

description: rVEGFA 7h


title: 34_CAR_AI_90

status: Public on Nov 26 2016

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
Base-calling was performed by Casava v1.8.2
Sequences were aligned to the cattle (Bos taurus) genome (Btau4) using the TopHat software, allowing for 2 mismatches for each block of 25 nucleotides. The unaligned sequences were trimmed at the 3’ end to 75 nt and realigned; the process was then repeated once more, with unaligned reads trimmed to 50 nt in length.
The three files with aligned sequences were merged, and the sequences were filtered to retain those matched to a unique position in the reference genome, with mapping quality greater than 30 and containing up to 3 mismatches.
Duplicate reads were removed by Picard tools
Sequence reads were counted according to overlaps on exon models obtained from the ensGene database from the UCSC genome browser. The database was downloaded in January 2011 using R software and processed using the Bioconductor packages rtracklayer, Rsamtools, GenomicRanges and GenomicFeatures. A set of genes that was not annotated in the Ensembl database but that was annotated in the refGene database from the UCSC genome browser was analyzed in conjunction with the Ensembl annotation. The reads that overlapped to an exon model were used for downstream analyses.
Genome_build: btau4
Supplementary_files_format_and_content: unfiltered_reads_count_EET.txt: reads count for extra-embryonic tissues and exon length
unfiltered_reads_count_END.txt: reads count for endometrial tissues and exon length

organism: Bos taurus

extract_protocol:
Total RNA was extracted from snap frozen tissues using the guanidinium thiocyanate-phenol-chloroform method (Chomczynski and Sacchi, 2006) (TRIzol® Reagent, Invitrogen, Carlsbad, CA) following the manufacturer’s instructions with slight modifications. A purification with acid phenol:chloroform (pH 4.5, Ambion) was added prior to RNA precipitation with isopropanol. RNA samples were purified with the RNeasy® Mini Kit (Qiagen, Boston, MA), quantified, and assayed for purity on a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
Three µg of total RNA was used for the polyA+ library construction using a TruSeq SBS Sequencing Kit Version 3

tag: tissue source

value: Endometrium

value: Caruncle

tag: gestation day

tag: group

value: artificial insemination (AI)


title: 34_CAR_AI_82


title: 34_ICAR_AI_81

value: Inter-caruncle


title: 34_ICAR_AI_91


title: 34_ICAR_AI_83


title: 34_ICAR_AI_85


title: 34_CAR_AI_84


title: Sample_CB-9_L001_1

city: Medford

first: Eric

middle: R

last: Reed

state: MA

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

data_processing:
Samples were run across four lanes on 4 different flow cells and 50bp reads for each sample were generated via the Illumina HiSeq 4000.
Fastq files are quality checked with FastQC (v0.11.3).
Single-end reads were mapped to the mouse genome (mm10) using tophat (v2.1.0). Per gene read counts were computed using HTSeq (v0.6.1p1).  Count normalization was carried out with weighted trimmed mean of M-values (TMM) using edgeR (v3.8.6) R package. Differential gene expression was carried out using the Limma (v3.22.7) R package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab Delimited file of read counts per gene from HTSeq

source_name: mutant B6NJ allele_male_striatum

extract_protocol:
Striatum punches were harvested on Day 24 immediately following the 5-min behavioral test on the EPM, stored in RNAlater for 48 h, blotted dry with a kimwipe, and transferred to -80ºC.
Total RNA was isolated  and shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (50 bp single-end reads). Samples were sequenced using the Illumina HiSeq 4000 with 16 samples per lane over four lanes (technical quadruplicates).

tag: strain background

value: C57BL/6NJ (B6NJ) x C57BL/6J (B6J)

value: homozygous for mutant B6NJ allele (binge-prone; N/N)

tag: age

value: 69-100 days old at the time of sacrifice

tag: Sex

value: Striatum

tag: sampleID

tag: lane

tag: cage #


title: Sample_CB-9_L003_2

tag: genotype/variation

tag: tissue


title: Sample_CB-9_L001_2


title: 34_ICAR_SCNT_71

value: somatic cell nuclear transfer (SCNT)


title: Sample_CB-9_L002_2


title: Sample_CB-8_L003_2

source_name: wild-type B6J allele_male_striatum

value: homozygous for wild-type B6J allele (binge-resistant; J/J)


title: 34_ICAR_SCNT_69


title: 34_CAR_SCNT_70


title: Sample_CB-8_L001_2


title: Sample_CB-8_L001_1


title: 34_ICAR_SCNT_65


title: Sample_CB-7_L002_2

source_name: wild-type B6J allele_female_striatum

value: female


title: 34_ICAR_SCNT_67


title: 34_CAR_SCNT_66


title: Sample_CB-7_L003_2


title: 34_CAR_SCNT_64


title: Sample_CB-7_L001_2


title: 34_ICAR_AI_77


title: Sample_CB-7_L001_1


title: 34_ICAR_SCNT_63


title: Sample_CB-6_L002_2


title: Sample_CB-6_L001_2


title: 34_CAR_SCNT_62


title: 34_CAR_AI_76


title: 34_CAR_AI_80


title: 34_CAR_SCNT_60


title: 34_ICAR_SCNT_57


title: 34_ICAR_SCNT_61


title: Sample_CB-6_L003_2


title: 34_CAR_SCNT_68


title: Sample_CB-6_L001_1


title: 34_CAR_SCNT_56


title: Sample_CB-5_L002_2


title: Sample_CB-8_L002_2


title: Sample_CB-5_L003_2


title: Sample_CB-5_L001_2


title: Sample_CB-5_L001_1


title: 18_ICAR_SCNT_49


title: Sample_CB-4_L003_2

source_name: mutant B6NJ allele_female_striatum


title: 18_ICAR_SCNT_51


title: Sample_CB-4_L002_2


title: 18_CAR_SCNT_50


title: Sample_CB-4_L001_2


title: Sample_CB-4_L001_1


title: 18_CAR_SCNT_46


title: Sample_CB-3_L002_2


title: 18_ICAR_SCNT_45


title: Sample_CB-3_L001_2


title: 18_ICAR_SCNT_53


title: 18_CAR_SCNT_44


title: 18_CAR_SCNT_42


title: CONVR.4 TCR αβ+ IEL

data_processing:
Data were analyzed as described in the associated manuscript, Semenkovich et. al., 2016 (in submission).
In brief, Illumina reads were trimmed, then mapped to mm10 using bowtie2 with the parameters: --end-to-end --sensitive --no-unal --no-discordant.
Using samtools, low mapping quality reads were filtered (>=10), reads mapping to chrM were removed, and duplicates were then filtered.
Peaks were called using macs14 (with p = 1e-9), and overlapping peaks were used to generate merged .bed files.
Genome_build: mm10
Supplementary_files_format_and_content: .bed files: Per-sample .bed files identifying peaks identified from macs1.4, as described in the methods of the associated manuscript.

source_name: Intraepithelial lymphocyte

extract_protocol:
Peripheral T cells and IELs were isolated by FACS, with a target maximum of 50,000 cells per transposition reaction. Nuclei were isolated and prepared as described in Buenrostro et al., Nature Methods, 2013.
Libraries were prepared using a modified version of the Illumina Nextera DNA Sample kit, based on the work of Buenrostro et al., Nature Methods, 2013 and outlined in the associated manuscript, Semenkovich et. al., 2016 (in submission).

tag: microbial colonization state

value: conventionally-raised

value: Intraepithelial lymphocyte

tag: tissue origin

value: Intestine


title: 18_CAR_SCNT_40


title: 18_ICAR_SCNT_41


title: Sample_CB-2_L002_2


title: Sample_CB-3_L001_1

value: male


title: Sample_CB-2_L003_2


title: Sample_CB-2_L001_2


title: 18_CAR_SCNT_52


title: Sample_CB-1_L003_2


title: Sample_CB-2_L001_1


title: 18_ICAR_SCNT_39


title: 18_CAR_SCNT_38


title: 18_CAR_SCNT_48


title: Sample_CB-1_L002_2


title: Sample_CB-1_L001_1


title: 18_CAR_SCNT_36


title: 18_ICAR_AI_18


title: Sample_CB-1_L001_2


title: 18_ICAR_SCNT_47


title: Sample_CB-3_L003_2


title: Sample_CB-16_L003_2


title: 18_ICAR_SCNT_43


title: Sample_CB-16_L001_2


title: Sample_CB-16_L002_2


title: 18_CAR_AI_15


title: 18_CAR_AI_17


title: Sample_CB-16_L001_1


title: 18_ICAR_AI_10


title: 18_ICAR_AI_16


title: Sample_CB-15_L002_2


title: Sample_CB-15_L003_2


title: Sample_CB-15_L001_1


title: Sample_CB-15_L001_2


title: 18_ICAR_AI_4


title: 18_ICAR_AI_2


title: 18_CAR_AI_1


title: Sample_CB-14_L003_2


title: 18_CAR_AI_9


title: Sample_CB-14_L002_2


title: 18_ICAR_SCNT_37


title: Sample_CB-14_L001_2


title: Sample_CB-14_L001_1


title: 34_ALL_SCNT_18

value: Conceptus

value: Allantois


title: Sample_CB-13_L003_2


title: 34_ALL_SCNT_28


title: Input_WT_Veh_2

city: Boston

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
ChIP-seq peaks were called using HOMER. Peaks above  4-fold over KO and above 1rpm were kept.
RNAseq normalized counts were generated using Htseq and differential gene expression was found using DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: bed file with called peaks; Excel file with DESeq output.

source_name: Isolated islets

extract_protocol:
Islets were isolated and processed immdiately for RNA extraction with Trizol, or fixed with 1% formaldehyde for ChIP.
Libraries were prepared using standard Illumina protocols

treatment_protocol: C57BL6/J mice on normal chow were gavaged tamoxifen (2mg/day) or corn oil vehicle daily for 5 days 2 weeks prior to islet isolation.

value: islets

value: 10 weeks

tag: genotype


title: 34_ALL_SCNT_42


title: Input_KO_1


title: Input_KO_2


title: Sample_CB-13_L002_2


title: 18_CAR_AI_3

value: Endometrium

value: Caruncle

value: artificial insemination (AI)


title: 34_ALL_SCNT_25


title: Sample_CB-13_L001_2

value: C57BL/6NJ (B6NJ) x C57BL/6J (B6J)

value: homozygous for mutant B6NJ allele (binge-prone; N/N)


title: Input_WT_Veh_1


title: HDAC3_KO_2


title: Sample_CB-13_L001_1

value: 69-100 days old at the time of sacrifice

value: Striatum


title: 34_ALL_AI_12


title: 34_ALL_AI_15


title: Sample_CB-12_L003_2


title: HDAC3_WT_Veh_3


title: 34_ALL_AI_38


title: HDAC3_KO_1


title: Sample_CB-12_L001_2


title: 34_CHO_SCNT_23

value: Chorion

value: somatic cell nuclear transfer (SCNT)


title: Sample_CB-12_L001_1


title: HDAC3_WT_Veh_1


title: 34_CHO_SCNT_31


title: HDAC3_KO_3


title: 34_CHO_SCNT_16


title: Control5b


title: Sample_CB-11_L002_2

value: female


title: Control4b


title: Sample_CB-12_L002_2


title: 34_CHO_SCNT_32


title: 34_ALL_SCNT_14


title: Sample_CB-11_L001_2


title: 34_ALL_AI_17


title: Control3b


title: 34_CHO_SCNT_11


title: 34_CHO_SCNT_43


title: Control2b


title: Sample_CB-10_L003_2

value: homozygous for wild-type B6J allele (binge-resistant; J/J)


title: Control1b


title: Sample_CB-10_L002_2


title: 34_CHO_SCNT_49


title: KO5b


title: 34_CHO_AI_4


title: KO4b


title: Sample_CB-10_L001_2


title: 34_CHO_AI_8


title: 34_CHO_AI_27


title: KO3b


title: Control3a


title: 18_EET_SCNT_39

value: Extra-embryonic tissue


title: Control1a


title: 34_CHO_AI_30


title: KO2b


title: KO3a


title: KO1b


title: Sample_CB-11_L001_1


title: 18_EET_SCNT_41


title: Control2a


title: 18_EET_SCNT_53


title: KO2a


title: 18_EET_SCNT_40


title: 18_EET_SCNT_37


title: 18_EET_SCNT_48


title: KO1a


title: 18_EET_SCNT_26


title: 18_EET_SCNT_21


title: 18_EET_SCNT_54


title: 18_EET_AI_52

source_name: Conceptus_Extra-embryonic tissue_AI_18d


title: 18_EET_AI_35


title: IMR-32 cells with GAS5 siRNA

city: Orlando

first: Joseph

last: Mazar

state: FL

address: 13535 Nemours Parkway

department: Research

institute: Nemours Children's Hospital

data_processing:
The raw reads (fastq files) from Illumina HiSeq1500 were aligned to the reference genome using TopHat version 1.4.1 (http://www.ncbi.nlm.nih.gov/pubmed/19289445) with RefSeq annotations and the “—no-novel-juncs” option.
Ambiguous reads that mapped to more than one region in the genome and reads with MAPQ score less than 10 were removed.  The UCSC human genome version 19 (hg19) and corresponding RefSeq annotations were used for reference and mRNA transcript quantification.
The bed coordinates of lncRNAs from the Dinger Lab were applied for lncRNA transcript quantification. Transcript quantification was performed using Partek Genomics Suite (version 6.4, Partek Inc, St. Louis MI), and the raw read counts and normalized read counts (RPKM: reads per kilobase per million mapped reads, http://www.ncbi.nlm.nih.gov/pubmed/18516045) were obtained.
The raw count information for all the mRNA and lncRNA transcripts was first filtered, with transcripts that did not produce read counts in all the samples filtered from further analyses. The remaining transcripts were analyzed using the BioConductor DESeq package (http://www.ncbi.nlm.nih.gov/pubmed/20979621) to detect differential expression between GAS5 knockdowns and negative control cells.  Transcripts detected in at least one sample (RPKM>1), fold change over 1.5, and with a p-value less than 0.05 were considered significantly differentially expressed.
Genome_build: hg19

source_name: IMR-32 cells with GAS5 siRNA

growth_protocol: IMR-32 cells were purchased from ATCC and were cultured in Minimum Essential Medium (MEM) Alpha + GlutaMAX™ [Gibco Life Sciences] supplemented with 10% fetal bovine serum [FBS]

extract_protocol:
Total RNA was isolated using Trizol reagent (Ambion, Foster City, CA) and quantified with a ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE). The quality of Total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies).
RNA-Seq library was constructed using the Truseq Stranded Total RNA library preparation instruction from Illumina using 1ug of Total RNA. Shortly, the total RNA is Ribo-depleted using Ribo-Zero Gold kit to remove rRNA from total RNA and then fragmented into small pieces using divalent cations under elevated temperature. Following fragmentation, the first strand cDNA were synthesized using random primers and followed by second strand synthesis using DNA Polymerase I. The cDNA is then ligated with index adapters for each sample followed by purification and then enriched with PCR to create the final library. The quality and quantity of the libraries were detected by Agilent Bioanalyzer and Kapa Biosystems qPCR.
Multiplexed libraries are pooled and single-end 50-bp sequencing was performed on one flow-cell of an Illumina Hiseq 1500.

treatment_protocol: IMR-32 cells were trypsinized and reverse transfected using Lipofectamine® RNAiMax (Life Technologies) and 50 µM of the following siRNAs (Life Technologies):  GAS5 Silencer® Select siRNA (cat #: n272331) and Silencer®  Select negative control #1 (cat #: 4390843). Cells were seeded into 6-well plates at a density of 2.5 x 105 cells per well. Cells were incubated for 24 or 48 hours at 37°C in a CO2 incubator. Once the transfection period was complete, cells were harvested and counted for use in cell biology assays. The efficiency of gene knockdown was assessed by quantitative real-time PCR (qRT-PCR).

tag: cell line


title: 18_EET_AI_9


title: Sample_CB-10_L001_1


title: 34_CHO_AI_29


title: 18_EET_AI_20


title: 18_EET_AI_13


title: 6h trophic withdrawal 2

status: Public on Nov 25 2016

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

data_processing:
Reads were processed by GERALD and mapped to mm10 using Tophat v2.0.10
Gene quantification was done using HTSeq  against RefSeq annotation
Normalized counts and log expression values (rld) were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing for each gene the expression value

source_name: DRG neurons -NGF 6h

growth_protocol: E13.5 DRG sensory neurons were grown for 36h before treatment

extract_protocol:
RNA was isolated using the Qiagene RNeasy Plus Micro Kit (Qiagene, Hilden, Germany) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trophic Withdrawal for 1h, 3h, 6h

tag: strain

value: ICR

tag: cell type

value: DRG neurons

tag: time point

value: 6h trophic withdrawal


title: 6h trophic withdrawal 1


title: 1h trophic withdrawal

source_name: DRG neurons -NGF 1h

value: 1h trophic withdrawal


title: Control 6h no trophic withdrawal

source_name: DRG neurons +NGF

value: 6h no trophic withdrawal


title: pEGFP replicate 2

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Libraries were run on an Illumina MiSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing gene symbol and raw read numbers for each gene in each sample

source_name: HEK 293T Dicer -/- cells

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: HEK 293T Dicer -/-

tag: transfection

value: pEGFP


title: pEGFP-VP55 replicate 2


title: pEGFP replicate 1


title: PAX8-NFE2L2 fusion+ rep2

status: Public on Nov 24 2016

city: Göteborg

first: Erik

last: Larsson Lekholm

address: Box 440

department: Institute of biomedicine

country: Sweden

institute: University of Gothenburg

data_processing:
reads were aligned to the GRCm38 reference genome using STAR with default parameters.
Gene read counts were quantified using HTSeq, against the GENCODE M7 reference annotation (using the options “–s no” and “-m intersection-strict” for htseq-count).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample ...

source_name: prostate

extract_protocol:
Quick-RNA™ MiniPrep (Zymo Research, Irvine, CA) was used as per the manufacturer’s recommendation to isolate RNA.
The library preparations were done on an Illumina HiSeq 2500. Single end reads (50 bp) were generated per sample at GATC Biotech AG (Konstanz, Germany).

treatment_protocol: PAX8-NFE2L2 fusion gene constructs were synthesized and cloned into the Lv229 lentiviral plasmid vector (GeneCopoeia, Maryland, USA). The plasmid along with a matching empty vector control was transformed into lab propagated Stbl3 cells (Thermo Fisher Scientific, Waltham, MA) made competent using Mix & Go reagent (Zymo Research, Irvine, CA). Plasmids were isolated using Qiagen Plasmid Plus Midi Kit (Qiagen, Germany). TRAMP-C1 cells and HEK-293T cells were purchased from ATCC (Manassas, VA) and cultured using DMEM media from Gibco (Thermo Fisher Scientific, Waltham, MA) supplemented with 10% FBS from HyCLONE (GE Healthcare Life Sciences, USA) and gentamicin and sodium pyruvate (Thermo Fisher Scientific, Waltham, MA). HEK-293T cells were seeded on 10 cm plates (Sarstedt, Germany) one day prior to transfection. Cells were transfected with aforementioned plasmids using Lenti-Pac HIV Expression Packaging Kit (GeneCopoeia,Maryland, USA) and supernatant was collected at 42, 46, 50 and 66 hours post transfection. The virus containing supernatant was passed through 0.45 µm low protein-binding filters (Sarstedt, Germany). For each transduction, 4 ml of filtered supernatant was concentrated by ultra-centrifugation at 50000 x g for 90 minutes at 4°C. Supernatant was carefully discarded and pellet was dissolved in 500 µl of media. TRAMP-C1 cells seeded on 12-well plates (Sarstedt, Germany) were transduced with a 1:1 mixture of media and concentrated virus. 12 h post transduction, fresh media was added and cells were allowed to grow for another 24 h.

tag: overexpression

value: PAX8-NFE2L2 fusion+

value: prostate epithelial


title: IMR-32 cells with Negative Control siRNA


title: Ribosome profiling of wild-type ecotype Landsberg erecta treated with cycloheximide

city: Gent

first: Petra

middle: Van

last: Damme

state: East Flanders

address: Albert Baertsoenkaai 3

department: Department of Biochemistry

country: Belgium

institute: University of Gent

data_processing:
Library strategy: Ribo-Seq
Ribosome profiling sequenced reads were processed using the PROTEOFORMER pipeline (Crappe et al. 2015).
The sequenced reads were trimmed for adaptor sequences using fastx_clipper 0.0.14.
The trimmed reads were then sequentially aligned onto the Arabidopsis thaliana rRNA or tRNA allowing for 2 mismatches using STARv2.5.1b. Reads aligning to these indices were discarded.
The remaining reads were then aligned onto the Arabidopsis thaliana TAIR10 genome using STAR v2.5.1b and allowing for reads with at most 2 mismatches. Reads mapping to a maximum of 16 locations within the genome were allowed at locations.
Ribosome occupancy position was determined by using only reads of length 26-34bps. An offset of +12, +13 and +14 from the 5' end of the reads were used for reads of length 26-30bps, 31-33bps and 34bps, respectively. The positional scores represent the number of reads alignment attributed to each genomic position.
Genome_build: TAIR10
Supplementary_files_format_and_content: BedGraph files were generated by PROTEOFORMER for the sense and antisense separately: The positional scores represent the number of reads aligned to each genomic position.

organism: Arabidopsis thaliana

source_name: Landsberg erecta, WT, stem cells, cycloheximide

growth_protocol: The cells were sub-cultured every week in fresh medium at a 1:10 dilution. After 2 days of culture, 200 ml cell suspensions cultured in 500 ml conical flasks and shaken at 125 rpm at 25°C in an orbital shaker under continuous light (50 μE) were collected.

extract_protocol:
Cells were collected by filtration and washed with ice-cold PBS with 100 µg/ml CHX added. Collected cells were subjected to snap freezing in liquid nitrogen and frozen cell pellets (approx. 400 mg) were ground into a fine powder using a liquid nitrogen cooled pestle and mortar. The frozen pellet was re-suspended and thawed in 1.3 ml ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton X-100, 2 mM dithiothreitol (DTT), 100 µg/ml CHX, 1x complete and EDTA-free protease inhibitor cocktail (Roche)), vortexed and left on ice for 10 min with periodical agitation. Lysates were subsequently passed through QIAshredder spin columns (Qiagen) and cell debris eliminated by centrifugation at 16,000 x g for 10 min at 4°C. The recovered supernatant was subjected to RNase I (Thermo Fisher Scientific Inc.) digestion using 1500 U of enzyme (approx. 200 U per mg total protein content). Digestion of polysomes proceeded for 45 min at 25°C with gentle agitation at 400 rpm and the reaction stopped by addition of 600 U SUPERase•In™ RNase Inhibitor (Thermo Fisher Scientific).
Ribosome protected fragments (RPFs) with sizes ranging from 26-34 nucleotides were extracted from 3 x 20 µg of RNA. Size-selected and dephosphorylated RNA fragments were depleted from ribosomal RNA derived contaminants using the magnetic Ribo-Zero™ rRNA Removal Kits (Plant Leaf, Epicentre) according to the manufacturer's instructions. rRNA depleted using the Ribo-Zero™ Magnetic Kit (Plant Leaf, Epicentre). Samples were amplified by PCR using compatible primers (xxx). The resulting ribosome-profiling libraries were duplexed (samples treated with the same inhibitor, LTM or CHX, were joined) and the obtained cDNA libraries were sequenced on a HiSeq 2000 instrument (Illumina) to yield 50bp single-end reads.

treatment_protocol: 10 ml of the wild-type ecotype Landsberg erecta cell suspensions brought at 4% packed cell volume (PCV) were incubated with either 50 µM lactimidomycin (LTM) or 100 µg/ml cycloheximide (CHX) (Sigma, USA) at 25°C for 5 and 30 min, respectively.

tag: ecotype

value: Landsberg erecta

value: Wild-type

value: Stem explants

tag: treatment

value: Cycloheximide


title: PAX8-NFE2L2 fusion+ rep3


title: pEGFP-VP55 replicate 1


title: Ribosome profiling of wild-type ecotype Landsberg erecta treated with lactimidomycin

source_name: Landsberg erecta, WT, stem cells, lactimidomycin

value: Lactimidomycin


title: Empty vector rep3

value: Empty vector


title: PAX8-NFE2L2 fusion+ rep1


title: WT rep1


title: Empty vector rep1


title: Empty vector rep2


title: tRA_04

city: Stockholm

first: Klementy

last: Shchetynsky

state: Stockholm

address: CMM L8:04 Karolinska University Hospital Solna

department: Medicine, Solna

institute: Karolinska Institutet

data_processing:
Mapping to human referense assembly hg19 was performed with Tophat/1.3.3
Duplicate removal on mapped data was performed with picard-tools/1.29
FPKM values were calculated with cufflinks/1.3.0
The above analysies were performed in complience with the protocol of Science for Life Laboratory, Stockholm, Sweden
hg19
Supplementary_files_format_and_content: Tab-delimited table with merged FPKM values for each sample

source_name: Whole blood cells (PAX)

extract_protocol:
RNA was extracted using PAXgene Blood miRNA kit (QIAGEN) following the manufacturer protocol
RNA libraries were  prepared using standard illumina TruSeq RNA protocol, following PolyA enrichment

tag: clinical status

value: RA patient

tag: dmards treatment

value: YES

tag: group

value: Established RA


title: tRA_06


title: tRA_02


title: tRA_07


title: tRA_03


title: tRA_01


title: 3h trophic withdrawal

city: Rehovot

source_name: DRG neurons -NGF 3h

value: ICR

value: DRG neurons

tag: age

value: 3h trophic withdrawal


title: HC_11

value: Healthy Control

value: NO

value: No RA


title: HC_12


title: HC_09


title: HC_08


title: HC_04


title: HC_05


title: ntRA_05

value: Newly diagnosed RA


title: HC_03


title: HC_07


title: HC_02


title: HC_01


title: HC_06


title: ntRA_01


title: ntRA_04


title: ntRA_02


title: tRA_05


title: ntRA_03


title: G192W-2-d0

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

data_processing:
Clean reads were aligning to human genome (hg19) with TopHat2 (Kim et al., 2013).
Gene expression levels were estimated by Cufflinks (Ghosh and Chan 2016).
Genome DNA sequence and gene annotation were download from UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: PKD-iPSC derived cells

growth_protocol: Neural differentiation of all iPSC lines was performed according to a previously published method for step-wise monolayer neural induction of human pluripotent cells through the synergistic action of two inhibitors of SMAD signaling (Noggin and SB431542) with minor modifications.

extract_protocol:
Total RNA was extract by standard TriZol protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PKD-iPSCs and normal iPSCs were initially cultured in the mTesR1 medium, then disaggregated using Accutase, and plated on Matrigel-coated dishes with the mTesR1 medium containing ROCK-Inhibitor (Y-27632) at a density of 20,000 cells/cm2. Subsequently, cells were cultured to expand in the medium without Y27632 until they were nearly confluent. The initial differentiation medium included the knockout serum replacement (KSR) medium together with 500 ng/ml Noggin and 10 μM SB431542. During day 5-10 of differentiation, increasing amount of N2 medium (25%, 50%, 75%) was added to the KSR medium every 2 days with the maintaining of 10 μM SB431542 and 500 ng/ml Noggin. At 10 days post-induction, SB431542 and Noggin were removed, and then cells were digested into small clumps for the first replating. Later, we picked up rosette-like clumps and plated them onto Matrigel-coated dishes. Cells were dissociated into single cells by 0.05% trypsin. All later passages of NPCs were maintained in the N2B27 medium supplemented with 10 ng/ml of bFGF. On day 30 of differentiation, spontaneously neuronal differentiation was induced by the culture medium consisting of the neurobasal medium supplemented with L-glutamine, B27, BDNF and GDNF.

tag: passages


title: G192W-1-d30


title: G192W-2-d30


title: G192W-2-d5


title: Q163X-2-d30


title: G192W-1-d10


title: G192W-1-d5


title: G192W-2-d10


title: HC_10


title: Q163X-2-d10


title: Q163X-1-d30


title: Q163X-2-d5


title: Q163X-2-d0


title: Q163X-1-d10


title: N2-d30

source_name: normal iPSC derived cells


title: Q163X-1-d5


title: Q163X-1-d0


title: N2-d10


title: G192W-1-d0


title: N2-d5


title: N1-d10


title: N1-d30


title: H3K4me3_ChIPSeq - F11

first: Zhenyang

last: Yu

state: Shanghai

address: Siping Rd 1239

department: College of Environmental Science and Engeering

institute: Tongji University

description:
F11
Peak_Annotation_F11_against Control.xlsx

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
After passing Solexa CHASTITY quality filter, the clean reads were aligned to C. elegans genome (UCSC ce10) using BOWTIE software (V2.1.0).
Aligned reads were used for peak calling of the ChIP regions using MACS 1.4.0rc2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison to a Poisson background model.
The peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
The signal profile (at 10 bp resolution) with UCSC WIG file format was generated from ChIP-seq data, which can be visualized on UCSC genome browser or IGB browser (Integrated Genome Browser, Java Runtime Enviroment needed, http://www.bioviz.org/igb/).
Genome_build: UCSC ce10
Supplementary_files_format_and_content: wig

organism: Caenorhabditis elegans

source_name: nematode whole body

growth_protocol: Briefly, E. coli OP50 was used as the food of nematode, and it was cultured in sterile lysogeny broth (LB) culture medium overnight at 37 ºC. At the same time, the nematode growth medium (NGM) plates were prepared. Next, E. coli OP50 in LB medium was added on NGM plates which were incubated overnight at 37 ºC. Then, the NGM plates with a bacterial lawn were ready to culture the nematodes at 20 ºC.

extract_protocol:
Nematode samples were cross-linked with 2% formaldehyde for 30 min at room temperature. Next, formaldehyde was then quenched by addition of 1M Tris (pH 7.5). After sonication, cell extracts containing DNA fragments with an expected range between 200 and 800 bp were immunoprecipitated using anti-H3K4me3 (Abcam ab8580).
ChIP-Sequencing library preparation was performed according to Illuminas protocol Preparing Samples for ChIP Sequencing of DNA.

treatment_protocol: Nematode eggs (F1) were exposed to sulfomethoxazole via nematode growth medium (NGM) plates for 6 days. Next, the adult nematodes (still in F1) were used to breed eggs (F2) that were transferred on NGM plates with the same SMX concentration. Through the same way, nematodes were exposed for 11 consecutive generations. F11 nematodes and their first non-exposed progeny (F14') were collected and stored at -80 ºC until ChIP-Seq.

value: wild type

tag: exposure

value: SMX in K-medium in NGM plates

tag: chip antibody

value: H3K4me3 (Abcam, catalog# ab8580, lot# 20700500)


title: H3K4me3_ChIPSeq - F14'

description:
F14'
Peak_Annotation_F14'_against Control.xlsx

value: K-medium in NGM plates


title: N1-d5


title: H3K4me3_ChIPSeq - C

description:
C
served as the foundation of comparison


title: Ad_AGGF1

city: Nanjing

first: Bisheng

last: Zhou

state: Jiangsu

address: 140 Hanzhong Rd

department: Department of Pathophysiology

institute: Nanjing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Primary murine hepatic stellate cells were isolated from mice and cultured in DMEM medium.

extract_protocol:
RNA was extracted with the RNeasy RNA isolation kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: primary mouse HSCs were infected with Ad-v or Ad-AGGF1 adenoviral particles by an MOI of 50; cells were harvested and RNAs were extracted at the 8th day

value: Primary hepatic stellate cells

tag: infected with

value: AGGF1 adenovirus particles

value: day 8


title: TT_Rep2

city: Porto Alegre

first: Tatiana

middle: N

last: Basika

state: Rio Grande do Sul

address: Av. Bento Gonçalves 9500, Prédios 43421/43431 - Setor IV

department: Centro de Biotecnologia

institute: Universidade Federal do Rio Grande do Sul

description: small RNA

data_processing:
Small RNA library data were pre-processed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). After adapter trimming, low quality reads and reads <18 nt were removed to obtain clean reads
Identical clean reads were then collapsed into unique sequences with associated read counts. The miRDeep2 (v 0.0.5) software package was used to identify miRNAs from the sRNA libraries. Unique sequences were mapped to the M. corti genome (version 1.0.4). For miRNA predictions with the miRDeep2 core algorithm, all metazoan mature miRNAs and precursor sequences (retrieved from the miRBase 21) were included. E. granulosus s.s., E. canadensis and E. multilocularis mature miRNA and precursor sequences were also used as input, as these cestode parasites are the closest phylogenetically related species to M. corti with available sequences from high throughput analyses (Macchiaroli et al., Parasit. Vectors. 8 (2015) 83.; Cucher et al.,J. Parasitol. 45 (2015) 253–267.; Bai et al., BMC Genomics. 15 (2014) 736).
Genome_build: M. corti draft genome assembly version 1.0.4

organism: Mesocestoides corti

source_name: Parasite in culture, larval stage

growth_protocol: TT samples were cultured for 24 h in modified RPMI 1640 medium with 10 % FBS (McRPMI) at 37°C and 5% CO2. Strobilated worms (ST) were obtained from TT (n = 60) cultured under strobilation-inducing conditions as previously described (Markoski et al., Parasitol. Int. 55 (2006) 51–61 doi:10.1016/j.parint.2005.09.005)

extract_protocol:
RNA extractions were carried out using Trizol according to the manufacturer's instructions. The aqueous phase obtained after the organic phase separation step was enriched in sRNAs (RNAs<200 nt) with the mirVana miRNA Isolation Kit (Ambion).
Libraries were constructed with the TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer´s instructions. Library size selection was performed in order to recover 18 to 30 nt-long sRNAs.

tag: developmental stage

value: parasites in culture, larval stage


title: Ad_NC

value: negative control adenovirus particles


title: GSC-222_si-JAG1_rep1

status: Public on Nov 23 2016

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

description: Gene expression in si-JAG1 treated Giloma sten cell 222

data_processing:
Illumina Casava1.7 software used for basecalling.
RNAseq analysis was conducted by The BaseSpace® RNA Express app (Illumina).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include results of differential expression analysis.

source_name: Giloma sten cell, 222, si-JAG1, replicate 1

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human glioblastoma

tag: gender

value: male


title: ST_Rep1

description: small RNA

source_name: Parasite in culture, adult stage

value: parasites in culture, adult stage


title: ST_Rep2

description: small RNA


title: TT_Rep3

description: small RNA


title: GSC-222_si-NC_rep1

description: Gene expression in si-NC treated Giloma sten cell 222

source_name: Giloma sten cell, 222, si-NC, replicate 1


title: GSC-222_si-Notch1_rep1

description: Gene expression in si-Notch1 treated Giloma sten cell 222

source_name: Giloma sten cell, 222,si-Notch1, replicate 1


title: GSC-1228_si-Notch1_rep1

description: Gene expression in si-Notch1 treated Giloma sten cell 1228

source_name: Giloma sten cell, 1228,si-Notch1, replicate 1


title: GSC-1228_si-JAG1_rep1

description: Gene expression in si-JAG1 treated Giloma sten cell 1228

source_name: Giloma sten cell, 1228, si-JAG1, replicate 1


title: GSC-1228_si-NC_rep1

description: Gene expression in si-NC treated Giloma sten cell 1228

source_name: Giloma sten cell, 1228, si-NC, replicate 1


title: 10-02s-Normal

city: Farmington

first: Allen

last: Mo

state: CT

address: 263 Farmington Avenue

department: Center for Molecular Medicine

institute: UConn Health

description: Each biopsy specimen requires four separate library preps: epithelia, stroma and two RNA Ampliseq Panels

data_processing:
IonTorrent Suite (v4.4) for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to targetted regions using coverageAnalysis plugin and aligned to hg19_RNA_CanTran_v1
Total reads were normalized to one million per panel, and all samples were combined into one large processed datamatrix (possible pseudogenes were removed)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample panel

source_name: Colon tissue biopsy during colonoscopy

extract_protocol:
OCT-embedded colon biopisies were sectioned at 9-um thickness onto PEN membrance slides and subjected to LCM of stromal and epithelial cells onto separate caps. RNA was extracted from caps using Picopure RNA isolation kit following manufacturer's protocols. Half of extracted RNA was used for each library preparation panel
RNA libraries were prepared for sequencing using standard IonTorrent RNA Ampliseq protocols for two separate panels (Apoptosis and custom Senesence). Libraries were barcoded with IonXpress Adapters.
Targetted RNA-seq, Barcoded (provided in the barcode.txt) to run 4 samples per 318 chip
each raw data file is named as 'Patient#-Biopsy#-Epithelia/Stroma-Apoptosis/Senescence Panel-ACF/Normal' and the original file names  (associated with each sample)/their checksums are included in the barcode.txt.

tag: patient #

tag: biopsy #

tag: tissue

value: biopsied normal colon

tag: mutation

value: laser capture microdissected stromal cells


title: 10-01s-ACF-BRAF

value: biopsied proximal colon ACF (aberrant crypt foci)

tag: cell type


title: 09-02s-Normal


title: 09-01s-ACF-BRAF


title: 08-03s-Normal


title: 08-02s-ACF-BRAF


title: N1-d0


title: 07-01s-ACF-KRAS


title: ST_Rep3

description: small RNA


title: 05-02s-Normal


title: 06-02s-Normal


title: 07-02s-Normal


title: 06-01s-ACF-KRAS


title: 05-01s-ACF-KRAS


title: TT_Rep1

description: small RNA


title: 04-02s-ACF-KRAS


title: 03-01s-ACF-APC


title: 02-02s-Normal


title: 02-01s-ACF-APC


title: 04-01s-ACF-APC


title: 01-02s-Normal


title: 04-03s-Normal


title: 03-02s-Normal


title: 01-01s-ACF-APC


title: 10-02-Normal

value: laser capture microdissected epithelial cells


title: 10-01-ACF-BRAF


title: 09-01-ACF-BRAF


title: 09-02-Normal


title: Sample_CB-11_L003_2

source_name: mutant B6NJ allele_female_striatum

tag: strain background

value: C57BL/6NJ (B6NJ) x C57BL/6J (B6J)

tag: genotype/variation

value: homozygous for mutant B6NJ allele (binge-prone; N/N)

value: 69-100 days old at the time of sacrifice

tag: Sex

value: female

value: Striatum

tag: sampleID

tag: lane

tag: cage #


title: 08-01s-ACF-KRAS


title: 08-02-ACF-BRAF


title: 07-02-Normal


title: 08-01-ACF-KRAS


title: 07-01-ACF-KRAS


title: 06-01-ACF-KRAS


title: 04-03-Normal


title: 04-02-ACF-KRAS


title: 05-01-ACF-KRAS


title: 05-02-Normal


title: 03-01-ACF-APC


title: 04-01-ACF-APC


title: 02-01-ACF-APC


title: 01-02-Normal


title: 01-01-ACF-APC


title: 03-02-Normal


title: siControl rep3

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

data_processing:
Basecalling was done by RTA1.18.64
Truseq adapter and polyA were removed
reads were aligned to the human genome by STAR RNAseq read mapper
reads overlapping with annotated genes were counted with HTseq count
variance stabilisation and differential gene expression were done by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count and vst tranformed expression values from DEseq2

source_name: siControl rep3

extract_protocol:
Total RNA was purified using the Trizol standard protocol and treated with heat-labile dsDNAse (Thermo scientific)
libraries were produced from 150ng total RNA with Nugen complete RNAseq library system according to the manufacturers protocol.

value: colon cancer

tag: cell line


title: siADNP rep1

source_name: siADNP rep1


title: siControl rep1

source_name: siControl rep1


title: 02-02-Normal


title: 08-03-Normal


title: siADNP rep3

source_name: siADNP rep3