title: RPL5 MO [mRNA]

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

institute: Beijing Institute of Genomics

data_processing:
TopHat for mapping of Hiseq 2000 RNA-Seq data
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
DAVID and the Gene Ontology for functional analysis of specific genes
Genome_build: Zv9
Supplementary_files_format_and_content: FPKM

source_name: embryo

growth_protocol: Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf

extract_protocol:
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the Illumina mRNA-Seq library preparation kit according to the manufacturer’s instructions.

treatment_protocol: Zebrafish embryos at the one-cell stage were injected with the MOs using an Microinjector (WPI SYS-PV830). Based on initial injection trials, 2-5 ng MO and control MO was chosen as the optimal concentration.

value: RPL5 morpholino knockdown

tag: developmental stage


title: EGFP_2

status: Public on Feb 10 2017

type: SRA

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

library_source: transcriptomic

data_processing:
Paired-end sequencing (150 x 2) was performed using a Nextseq-500 (Illumina).
Reference genome sequence data from Rattus norvegicus were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: rn4). The reference genome index was built using SAMtools (v. 0.1.19) and the Bowtie2-build component of Bowtie2 (v. 2.1.0). Reads were mapped to the reference genome using Tophat2 (v. 2.0).
The number of fragments per kilobase per million mapped reads (fpkm) for each gene of 17,066 RefSeq (UCSC rn4) gene models was calculated using Cufflinks (v. 2.2.1).
Heat maps were constructed using Mev (v. 4.9.0). Statistical analyses and graph construction were performed using R (v. 3.1.0) and PYTHON (v. 2.7.6).
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

molecule: total RNA

organism: Rattus norvegicus

source_name: EGFP, hippocampus from E18 embryos

growth_protocol: Hippocampal neuron cultures were prepared from E18 Sprague-Dawley (SD) rat embryos and maintained for 14-15 days in vitro (DIV) in Neurobasal media containing B27 supplements.

extract_protocol:
Total RNA was isolated from the infected cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.
The sequencing library was prepared using the Illumina TruSeqStranded mRNA Sample Preparation Kits (Illumina).

treatment_protocol: Cultured hippocampal neurons were infected with lentivirus expressing EGFP, CCNY-WT-EGFP or CCNY-shRNA-EGFP at DIV5 or 6.

tag: strain

value: Sprague-Dawley

tag: age

tag: cell type

value: primary culture of hippocampal neurons

tag: genotype/variation

value: control


title: RPL5 MO [miRNA]

city: Beijing

country: China

data_processing:
FASTX-Toolkit clipper was used to remove sequencing adapters.
The .fastq file was converted to a tab-delimited file which held only the unique sequence read and its corresponding number of copies.
The files were uploaded to DSAP (http://dsap.cgu.edu.tw/index.htm) for clustering of tags, classification of non-coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively.
The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP.
Genome_build: Zv9

organism: Danio rerio

extract_protocol:
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
small RNA libraries were constructed using the Illumina miRNA-Seq library preparation kit according to the manufacturer’s instructions.


title: wt_control_rep1

first: Shouyu

last: Yan

address: 5#, Yiheyuan Road

department: Institution of Molecular Medicine

institute: Peking University

data_processing:
raw reads were aligned by Tophat v2.0.8
RPKM values were calculated by in-house perl scripts
Genome_build: danRer7
Supplementary_files_format_and_content: chromosome, start, end, RefseqID,  RPKM Values, strand, geneName, Number of Mapped Reads, Total Length of Exon

molecule: polyA RNA

source_name: zebrafish embryo

extract_protocol:
Total RNA of 36 hpf embryos were isolated by Trizol reagent (Sigma).  Each sample contained 30 embryos.
A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

value: TL

tag: genotype

value: wildtype

tag: library type

value: strand-specific, dUTP protocal

tag: subcellular component

value: whole cell


title: Day 42 Heat Stress Pituitary 981

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

country: USA

institute: University of Delaware

data_processing:
Bowtie
TopHat
Cufflinks
Genome_build: Gallus gallus ver 4

organism: Gallus gallus

source_name: Pituitary Gland Tissue

growth_protocol: Birds were raised following grower standards outlined by our AACUC protocol (#(27)03-12-14R). Briefly, birds were raised on litter with ad libitum access to feed and water. First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. Thermoneutral/Control house maintained this temperature through completion of the trial while heat stress (experimental) house began a cyclical heat stress scheme detaield below through completion of the trial at day 42 (typical market age). Both houses received 23 hours of light and 1 hour of dark for the entirety of the study. Necropsies were performed on Day 21 (prior to treatment), Day 22 (8 hours of treatment), Day 26 (2 hours acute treatment), Day 32 (4 hours acute treatment) and Day 42 (3 weeks of cyclical heat stress). Matched controls were collected at each time point.

extract_protocol:
Birds were euthanized via cervical dislocation and necropsied on each day listed above. Whole pituitary glands were collected and flash frozen with liquid nitrogen.
Libraries were constructed using the Illumina Stranded RNA-seq kit according to manufacturers instructions.

treatment_protocol: Temperature in the experimental house was increased each day from 25 degrees celsius to approximately 35-37 degrees celsius from 7 am to 3 pm each day starting on day 21. This cyclical heat stress scheme continued through day 42, completion of the trial.

tag: tissue

value: Pituitary


title: 6180_RNAseq_dccpA3

city: Houston

first: Samuel

last: Shelburne

state: TX

address: 1515 Holcombe Blvd

department: Infectious Diseases

institute: MD Anderson Cancer Center

data_processing:
FASTQ library was first processed by FASTX (version 0.0.6) to remove low complexity and low quality reads. EDGE-pro v1.3 software, was then used to align the reads using Bowtie2 v2.1.0 and estimate gene expression directly from the alignment output.
For MGAS5005 and MGAS6180 strains, FASTA of the references genome sequences (.fna), protein translation table with coordinates of protein coding genes (.ptt), and a table containing coordinates of tRNA and rRNA genes for each strain was obtained from the NCBI database (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptococcus_pyogenes_MGAS6180_uid58335/; ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptococcus_pyogenes_MGAS5005_uid58337/). For the MGAS10870 strain, the .ptt and .rnt files were generated from an in house genome assembly and were used as inputs into EDGE-pro.  Gene names in MGAS10870 correspond to the previously defined open reading frames from the fully sequenced strains MGAS315. EDGE-pro was run with default parameters to generate a RPKM value table, except for defining the read length as 50 bp and using 64 threads (-t 32) on a Dell PowerEdge R910 (32-Core, 1Tb ram). RSeQC program was used for QC metrics and alignment statistics6. Samples were concatenated through edgeToDeseq.perl script provided by EDGE-pro. DESeq7 was used to identify the gene expression level (http://www.r-project.org). Differentially expressed genes between the wild-type and ΔccpA strains were considered significant based on a p-value ≤ 0.01.
A negative binomial generalized linear model was fit to each gene expression with strain type as covariates. Then a likelihood-ratio test was applied to examine if there is any difference in the expression of a gene among six strains. The Benjamini-Hochberg method was used to control false discovery rate (FDR). The pairwise comparisons were performed to compare the gene expressions between WT vs any other strain using Wald's tests. The Holm's method was used to calculate adjusted p-value to correct for multiple testing. The calculation was conducted using R (version 3.0.1) with the package of DESeq2 (version 1.2.10)
Genome_build: MGAS5005, MGAS10870 and MGAS6180
Supplementary_files_format_and_content: excel file with normalize counts

organism: Streptococcus sp. 'group A'

source_name: 6180-delta-ccpA_bacteria grown in THY

growth_protocol: GAS strains grown in THY to mid-exponential phase

extract_protocol:
Cells were lysed using a fast FastPrep approach and RNA was isolated from ruptured cell using an RNeasy Kit (Qiagen)
cDNA was fragmented to 200 bp (mean fragment size) with the S220 Focused-ultrasonicator (Covaris) and used to make barcoded sequencing libraries on the SPRI-TE Nucleic Acid Extractor (Beckman-Coulter).

treatment_protocol: RNA protect was added at 2x volumes to cells and then cells were harvested by centrifugation, snap frozen, and stored at -80 C.

tag: strain background

tag: molecule type

value: RNA after rRNA depletion


title: 6180_RNAseq_dccpA1


title: CCNYshRNA_2

source_name: CCNYshRNA, hippocampus from E18 embryos

value: CCNY knockdown


title: 6180_RNAseq_wt4

source_name: MGAS6180_bacteria grown in THY

value: wild type


title: 6180_RNAseq_dccpA4


title: morpholino control [miRNA]

value: control morpholino


title: morpholino control [mRNA]


title: 6180_RNAseq_wt1


title: CCNY-WT_1

source_name: CCNY-WT, hippocampus from E18 embryos

value: CCNY overexpression


title: 6180_RNAseq_wt3


title: 6180_RNAseq_wt2


title: 6180_RNAseq_dccpA2


title: 10870_RNAseq_dccpA4

source_name: 10870-delta-ccpA_bacteria grown in THY


title: 10870_RNAseq_dccpA3


title: 10870_RNAseq_dccpA1


title: 10870_RNAseq_wt3

source_name: MGAS10870_bacteria grown in THY


title: 2221_RNAseq_dccpA4

source_name: 2221-delta-ccpA_bacteria grown in THY


title: 2221_RNAseq_wt4

source_name: MGAS2221_bacteria grown in THY


title: 2221_RNAseq_dccpA1


title: 2221_RNAseq_wt2


title: 10870_RNAseq_wt4


title: 2221_RNAseq_dccpA2


title: 10870_RNAseq_wt1


title: SUP-26_CLIP_repC

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

description:
CLIP
BarcodeC
Processed data file: SUP-26_CLIP_Peaks.bed

data_processing:
Library strategy: CLIP-Seq
Basecalls performed using Basespace (raw fastq files from each lane, not yet separated by barcode nor filtered nor trimmed.)
3' ends were then trimmed for PolyA/T tails (minimum length 1), and reads shorter than 27bp after trimming were discarded.
The FASTQ was converted to FASTA, and sequences were collapsed into unique reads. The 3bp randomer was trimmed from the 5' end, and the file was converted back to FASTQ.
Reads were separated according to barcode, resulting in 8.1M, 2.1M, 3.2M, and 2.5M unique high-quality reads for replicates A, B, C and D, respectively (fastq files).
The UMass Biocore Seqmapping 1.2 pipeline was then used for mapping using Bowtie2 and Tophat2. First, Bowtie2 was used to align the reads to index files containing rRNA, miRNA, tRNA and snRNA and rmsk sequences allowing 2 mismatches (parameters -N 2 -v). Reads that aligned to the common RNA index files were separated into an annotated read count file. The remaining reads were aligned to the genome using Tophat2 (parameters --library-type fr-secondstrand -g 1) (bam files).
As a control for input RNA abundance, an RNA-seq dataset generated using poly(A) selection from a similar sample (accession number GSM1290044) was processed in the same way, except Tophat2, which was adjusted for the unstranded nature of the library (parameters -g 1).
Plus and minus strands from alignment file were separated into two files for each alignment using samtools view. Files were converted from BAM to BED using bamtools convert. BED files were used as input for Piranha version 1.2.0, with binning of 100nt or 200nt (-z 100 or -z 200), and using the RNA-seq sample (accession number GSM1290044) as the covariate. Peaks that were called using 100nt or 200nt binning were combined, and plus and minus strand files were rejoined into a single BED (see bed file containing peaks identified in 3 or 4 replicates.)
Bedtools intersect was used to identify overlap between CLIP peaks and Ensembl 3'UTR annotations. Peaks that did not intersect with Ensembl 3'UTRs were intersected with Modencode, Targetscan, and Wormbase 3'UTR annotations, and other Ensembl gene features, and curated by hand (Mangone et al. 2010; Jan et al. 2011). Gene ontology analysis was performed using DAVID (Dennis et al. 2003).
Genome_build: ce10/WS220
Supplementary_files_format_and_content: SUP-26_CLIP_Peaks.bed: Bed file containing coordinates of peaks that were called by Piranha in 3 or more out of 4 replicates (ce10/WS220).

organism: Caenorhabditis elegans

source_name: whole mixed-stage animals, SUP-26::FLAG strain VT3121, FLAG IP

growth_protocol: Mixed-stage animals were grown until just starved.

extract_protocol:
Pellets were thawed in cold homogenization buffer [100mM NaCl, 25mM HEPES pH=7.5, 250µM EDTA, 2mM DTT, 25U/ml RNAse inhibitor (ThermoFisher RiboLock), protease inhibitors (Complete Mini, Roche)] at 4°C. Samples were sonicated on ice at 30W using 20s pulses with 60s rest intervals (Branson SLPe). Sonication continued until pellet was nearly completely homogenized (such that only small volume pellet, ~50µl, was visible after the sample settles). Samples were centrifuged at 16000rcf at 4°C for 15min, and supernatant was moved to a fresh tube. Protein was quantified, and concentration was adjusted to 3mg/ml in homogenization buffer.
CLIP libraries were prepared as in Zisoulis et al., 2011, with cloning steps modified from Gu et al., 2011. See supplemental methods in McJunkin & Ambros, "A microRNA family exerts maternal control on sex determination in C. elegans".

treatment_protocol: Recently-starved plates were irradiated with 3kJ/m2 in a Stratagene UV Stratalinker 1800. Worms were washed 3 times in M9 buffer, and pellets were stored at -80°C until use. Biological replicates were collected on different days.

tag: strain/background

value: mixed-stage animals

value: whole body

tag: ip antibody

value: Anti-FLAG M2 (Sigma-Aldrich, cat.# M8823, lot# SLBJ3044V)


title: 2221_RNAseq_dccpA3


title: SUP-26_CLIP_repA

description:
CLIP
BarcodeA
Processed data file: SUP-26_CLIP_Peaks.bed


title: 2221_RNAseq_wt1


title: SUP-26_CLIP_repB

description:
CLIP
BarcodeB
Processed data file: SUP-26_CLIP_Peaks.bed


title: D (replicate 1)

city: Göttingen

first: Carsten

last: Lueder

address: Kreuzbergring 57

country: Germany

institute: Institut für Medizinische Mikrobiologie

data_processing:
Illumina Casava 1.8.2 software was used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
Read alignment was performed using STAR v2.3.0.
Data were converted and sorted by samtools 1.2 and reads per gene were counted via  htseq version 0.6.
Data analysis was performed using R (3.2.1) - differential gene expression  was performed using DESeq2 (v1.8.1).
Candidate genes were filtered to a minimum of 2-fold  change and FDR-corrected p < 0.05 (p adjusted).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files includes information on number of reads, logFC or FC

organism: Mus musculus

source_name: RAW264.7 monocytic cell

extract_protocol:
RNA was isolated using GenElute Total RNA Miniprep kit (Sigma-Aldrich) according to instructions
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

tag: mouse strain

value: BALB/c

tag: treatment 1

tag: treatment 2

value: 100 U/ml IFN-g

tag: duration

value: 24 hours post infection


title: E (replicate 2)

tag: infection

value: T. gondii, strain NTE, MOI 6:1


title: F2 21 h aerobic

city: Bielefeld

first: Felix

middle: Gregor

last: Eikmeyer

address: Universitaetsstrasse 25

department: Center for Biotechnology

institute: Bielefeld University

data_processing:
Illumina CASAVA 1.7 software used for basecalling, MID separation and MID trimming.
Mapping of RNA-Seq data onto reference genome sequences by means of bwa. Further processing with samtools.
RPKM value calculation within ReadXplorer
Differential analysis within ReadXplorer by means of DeSeq
Genome_build: CP003043.1;JN084215.1; JN084214.1; CP003044.1
Supplementary_files_format_and_content: tab-delimited text file including RPKM values and DeSeq results for each sample and each CDS of the reference genome

organism: Lentilactobacillus buchneri subsp. silagei CD034

source_name: bacterial cells

growth_protocol: Cells were grown in controlled fermentations in MRS medium.

extract_protocol:
Cells were mechanically lyzed using Lysing Maxtrix B lysis tubes (MP Biomedicals). RNA was extracted applying the QIAGEN RNeasy kit. mRNA was enriched applying the RiboZero Bacteria kit.
Libraries were created applying the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturers protocol.

treatment_protocol: Cells were harvested under anaerobic conditions. Then aerobic conditions were again created and cells were again harvested.

tag: fermenter

tag: time of sampling

tag: conditions

value: aerobic


title: 2221_RNAseq_wt3

tag: genotype/variation


title: C (replicate 2)

value: DMSO (vehicle)


title: D (replicate 2)


title: F1 18.5 h anaerobic

value: anaerobic


title: C (replicate 1)


title: F2 18.5 h anaerobic


title: SUP-26_CLIP_repD

description:
CLIP
BarcodeD
Processed data file: SUP-26_CLIP_Peaks.bed

tag: developmental stage


title: E (replicate 1)


title: F1 21 h aerobic


title: 10870_RNAseq_wt2


title: A (replicate 1)


title: A (replicate 2)


title: E14 back Axin2-neg

city: New York

first: Catherine

middle: Pei-ju

last: Lu

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
RNA reads were aligned to the mm9 build of the mouse genome using Tophat
Transcript assembly and differential expression was done using Cufflinks with Refseq mRNAs to guide assembly
Genome_build: mm9
Supplementary_files_format_and_content: Cufflinks output

source_name: dorsal back skin

growth_protocol: dissect out skin tissues directly from mouse embryos

extract_protocol:
Cells were FACS sorted into Trizol-LS and RNA were extracted using Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions.
Library preparation using Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility, and RNAs were sequenced on Illumina HiSeq 2000 machines.

treatment_protocol: The dermal tissues were digested in Hanks Balanced Salt Solution (Lonza) with 1000 U/ml collagenase and 300 U/ml hyaluronadase (Sigma) and washed and re-suspended in PBS with 4%FBS to make single cell suspension for FACS sorting.

tag: organ

value: dorsal back

value: skin

tag: cell type

value: dermal cells

tag: transgenic

value: Axin2-LacZ neg


title: E14 back Axin2-pos

tag: tissue

value: Axin2-LacZ pos


title: s38 Older Woman

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

description: lin−/CD34−/CD31− cells

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: h19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each Sample

organism: Homo sapiens

source_name: Bone Marrow Aspirate

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared according to the manufacturer’s instructions for the NuGen Ovation RNA-Seq version 2 and Encore NGS Library Systems (San Carlos, CA).

tag: group

value: Older Woman

value: Bone biopsy

tag: age

value: 64-88 years


title: s39 Older Woman

description: lin−/CD34−/CD31− cells


title: s28 Older Woman

description: lin−/CD34−/CD31− cells


title: s32 Older Woman

description: lin−/CD34−/CD31− cells


title: Vav KO 2_C

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

description:
Vav_KO_4_C
Vav_KO_4_C_CAGATC_L008_R1

data_processing:
quality assessment of the raw data using fastqc v0.11.1
filtering and trimming of adapter residues and low quality reads with the FASTX toolkit v0.0.14
Sequenced reads were mapped to the Ensembl whole genome using tophat v2.4.2a with parameter -g 1
mapped reads were sorted and indexed using samtools v1.2
Counting the mapped reads on the gene level using featureCounts v1.4.6
Differentail expression analysis was done using the R package DESeq2 v1.8.2
Count data were normalized using the size factor to estimate the effective library size
Genome_build: NCBI37
Supplementary_files_format_and_content: tab delimited text files including log2fold change values, pval and padj as calculated by DESeq2

source_name: dendritic cells

growth_protocol: BMDCs were derived from bone marrow as previously described (Nature. 2006 Aug 10;442(7103):651-6.)

extract_protocol:
Total RNA was purified using TRIzol Reagent (Invitrogen) and the RNeasy Mini kit (QIAGEN) with on-column DNase treatment.
Purified RNA was subjected to library preparation using the Illumina TruSeq RNA sample preparation kit v2.

treatment_protocol: WT and Vav1/2/3-/- BMDCs were stimulated with Curdlan (200 mg/ml) for 3 hours, or were left untreated

tag: strain

value: BMDC

tag: stimulation time

value: 3 hours

value: Curdlan-stimulated


title: Vav KO 3

description:
Vav_KO_5
Vav_KO_5_ACTGAT_L006_R1

value: unstimulated


title: Vav KO 3_C

description:
Vav_KO_5_C
Vav_KO_5_C_ACTGAT_L008_R1


title: s29 Older Woman

description: lin−/CD34−/CD31− cells


title: s25 Older Woman

description: lin−/CD34−/CD31− cells


title: s30 Older Woman

description: lin−/CD34−/CD31− cells


title: Vav KO 1_C

description:
Vav_KO_2_C
Vav_KO_2_C_TGACCA_L008_R1


title: s24 Older Woman

description: lin−/CD34−/CD31− cells


title: WT 2_C

description:
Vav_WT_2_C
Vav_WT_2_C_GATCAG_L007_R1

value: wild type


title: WT 3_C

description:
Vav_WT_4_C
Vav_WT_4_C_CCGTCC_L007_R1


title: E17 paw Axin2-neg

source_name: ventral foot skin

value: ventral foot


title: Vav KO 2

description:
Vav_KO_2
Vav_KO_2_GAGTGG_L006_R1


title: s21 Older Woman

description: lin−/CD34−/CD31− cells


title: 10870_RNAseq_dccpA2

tag: strain background

tag: molecule type

value: RNA after rRNA depletion


title: Vav KO 1

description:
Vav_KO_1
Vav_KO_1_TGACCA_L006_R1


title: B (replicate 2)

tag: mouse strain

value: BALB/c

tag: treatment 1

value: DMSO (vehicle)

tag: treatment 2

value: 100 U/ml IFN-g

tag: duration

value: 24 hours post infection


title: B (replicate 1)


title: WT 1_C

description:
Vav_WT_1_C
Vav_WT_1_C_TTAGGC_L007_R1


title: s36 Older Woman

description: lin−/CD34−/CD31− cells


title: s20 Young Woman

description: lin−/CD34−/CD31− cells

value: Young Woman

value: 22-40 years


title: WT 3

description:
Vav_WT_4
Vav_WT_4_ACTGAT_L005_R1


title: E17 paw Axin2-pos

value: skin

value: dermal cells

value: Axin2-LacZ pos


title: s19 Young Woman

description: lin−/CD34−/CD31− cells

value: Bone biopsy


title: s17 Young Woman

description: lin−/CD34−/CD31− cells


title: s23 Older Woman

description: lin−/CD34−/CD31− cells

value: Older Woman

value: 64-88 years


title: WT 2

description:
Vav_WT_2
Vav_WT_2_CAGATC_L005_R1

value: BMDC

value: 3 hours


title: s22 Older Woman

description: lin−/CD34−/CD31− cells


title: s14 Young Woman

description: lin−/CD34−/CD31− cells


title: WT 1

description:
Vav_WT_1
Vav_WT_1_TGACCA_L005_R1

value: wild type

value: unstimulated


title: s13 Young Woman

description: lin−/CD34−/CD31− cells


title: s11 Young Woman

description: lin−/CD34−/CD31− cells


title: s9 Young Woman

description: lin−/CD34−/CD31− cells


title: s6 Young Woman

description: lin−/CD34−/CD31− cells


title: s7 Young Woman

description: lin−/CD34−/CD31− cells


title: 43-1_rnaseq

city: bethesda

first: Jack

last: Shern

address: 10 Center drive

institute: NCI

description: Resistent Clone

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 mm10 whole genome using Tophat(2.0.8)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the Cufflink
Genome_build: mm10
Supplementary_files_format_and_content: Cufflink output files include RPKM values for each Sample ...

source_name: A murine pre-B ALL carrying the human E2a:PBX transgene crossed to a CD3ɛ-/-  was generously provided by Dr. Janetta Bijl. These cells were developed into a stable cell line expressing pre-B markers.

growth_protocol: Leukemia cells were cultured in 10% complete mouse media (CMM)

extract_protocol:
Cells were pelleted and RNA was harvested using Qiagen Allprep kit according to the manufactures instructions. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: parental line

tag: transgene

value: Human E2a:PBX

tag: sample type

value: Resistent


title: 38-1_rnaseq

description: Resistent Clone


title: 44-6_rnaseq

description: Resistent Clone


title: s8 Young Woman

description: lin−/CD34−/CD31− cells


title: TF47-24_rnaseq

description: Resistent Clone


title: 32-2_rnaseq

description: Resistent Clone


title: s5 Young Woman

description: lin−/CD34−/CD31− cells


title: 30-4_rnaseq

description: Resistent Clone


title: s3 Young Woman

description: lin−/CD34−/CD31− cells


title: AY01_rnaseq

description: Resistent Clone


title: TF5961_rnaseq

description: Resistent Clone


title: input DNA 5

description: genomic DNA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using bwa mem program
Data were sorted, indexed, and deleted/marked duplicate
peaks were called using MAC2 program with the following setting: -m 7 70; -p 0.00001;
peaks were annotated using HOMER annotatePeaks.pl program
Genome_build: mm10
Supplementary_files_format_and_content: HOMER annotated peaks files

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: subcloned line

value: pre-B


title: s10 Young Woman

description: lin−/CD34−/CD31− cells


title: s4 Young Woman

description: lin−/CD34−/CD31− cells


title: E2a-PBX_rnaseq

description: Resistent Clone


title: input DNA 4

description: genomic DNA


title: H3K27ac_ChIPSeq 5

description: genomic DNA


title: 25-2_rnaseq

description: Resistent Clone


title: Combination 3

city: Philadelphia

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd, BRB 653

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Sequencing reads were aligned to the UCSC hg19 using RUM pipeline and differential gene expression analysis were performed using edgeR.
As an unbiased interrogation of gene regulation, differentially expressed genes (FDR < 0.0001, no fold-change cut off) between any pair of conditions were selected for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: prostate

growth_protocol: Cells were cultured in RPMI-containing Charcoal dextran treated serum. Treatments were added on cells for 24 hours before harvesting RNA

extract_protocol:
RNA was extracted using TRIzol reagent
Illumina’s TruSeq RNA sample preparation v2 kit

treatment_protocol: Samples were treated with vehicle control, ACLY inhibitor alone (10uM), Enzalutamide alone (20uM), and ACLY-inhibitor (10uM) and Enzalutamide (20uM) combined together

tag: tag

value: Cell line

value: Prostate Cancer Cell line

value: C4-2 cell line


title: s1 Young Woman

description: lin−/CD34−/CD31− cells

value: Young Woman

value: 22-40 years


title: s12 Young Woman

description: lin−/CD34−/CD31− cells


title: Combination 2


title: 30-42_rnaseq

description: Resistent Clone


title: ENZ 2


title: ACLYi 2


title: Control 2


title: H3K27ac_ChIPSeq 2

description: genomic DNA


title: H3K27ac_ChIPSeq 3

description: genomic DNA


title: ENZ 3


title: E8

city: Beibei

first: Zhi-Liang

last: Zheng

state: Chongqing

address: 15 Ganjuchun

department: Citrus Research Institute

institute: Southwest University

description: Rep. 2

data_processing:
Basecalls performed by BGI company.
Raw data were preprocessed by removing adaptor sequences and/or low quality reads, resulting in clean reads data.
These clean reads data were then mapped to the Arabidopsis thaliana reference sequences.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel files were generated with geneID and raw count.

organism: Arabidopsis thaliana

source_name: shoot_cae2-1 CA1-1

growth_protocol: Seedlings were grown vertically for 7 days on the MS agar plate, with 16 hr light and 8 hr dark.

extract_protocol:
Shoots were harvested, and total RNA was extracted using the TRizol-based protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: shoot


title: E2a-D3_rnaseq

description: Resistent Clone


title: input DNA 3

description: genomic DNA


title: H3K27ac_ChIPSeq 4

description: genomic DNA


title: Combination 1


title: input DNA 2

description: genomic DNA


title: 24-6_rnaseq

description: Resistent Clone


title: E7

description: Rep. 1

tag: tissue


title: ACLYi 3


title: input DNA 1

description: genomic DNA


title: ENZ 1


title: ACLYi 1


title: E6

description: Rep. 2


title: Control 3


title: H3K27ac_ChIPSeq 1

description: genomic DNA


title: MN.Δ5|6:7|9

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

data_processing:
Genome was constructed from all possible forward-reverse primer concatenated sequence pairs
Bowtie v1 was used to align reads to reference genome of concatenated primer sequences
Spurious high-frequency ligation events were filtered from the dataset
Data was normalized according to sequencing depth.
Genome_build: mm9

source_name: Motor Neuron

growth_protocol: mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). ESCs were differentiated  in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
50 million cells were trypsinized and crosslinked in1% formaldehyde for 10 min at room  temperature. The primary restriction enzyme used was HinDIII. Ligation and xLink reversal was performed and DNA purified for prep of 5C library.
5C primers were annealed at 48C for 16hrs atop 2 biological replicates of 3C libraries from each sample. 1fmol of each primer was used in the annealing reaction with 1ug of 3C template and 500ng of salmon sperm DNA. 16 separate annealing reactions were performed per sample, along with control reactions with individual components removed. Forward and reverse primers that annealed to adjacent regions of the 3C template were ligated with 10U of Taq ligase for 60’ at 48C. Successfully ligated forward-reverse primer pairs were then amplified in 5 separate PCR reactions per annealing reaction, using primers specific to the T7 and T3 overhangs. PCR reactions from the equivalent initial sample were then pooled, purified and run on a gel to ensure the control reactions did not show an amplification product. Libraries were then generated from the purified PCR product as described above to allow for deep sequencing.


title: E5

description: Rep. 1


title: E3

description: Rep. 1


title: E4

description: Rep. 2


title: MN.WT

value: WT


title: P002_OLP mRNA-Seq

first: Wen

last: Shi

state: Outside the US or Canada

address: Beijing, Haidian

department: Oral & Maxillofacial Surgery

institute: Peking University School and Hospital of  Stomatology

data_processing:
Primary sequencing data that produced by Illumina HiSeq 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAP2
QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis.
If alignment result passes QC, we will proceed with downstream analysis including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and SNP detection.
Results of gene expression include gene expression levels and differential expression analysis.
Genome_build: hg18
Supplementary_files_format_and_content: excel file includes RPKM valus of each samples and comparison between each two samples of the same patien

source_name: oral cavity

extract_protocol:
Total RNA, including miRNA, was isolated from premalignant, tumor or normal tissue samples by using TRIzol reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions. The RNA for Next generation sequencing was evaluated with an Agilent 2100Bioanalyzer.
Libraries were prepared for sequencing using standard Illumina protocols

tag: patient

tag: disease

value: oral lichen planus tissue


title: P002_Nor mRNA-Seq

value: normal oral mucosa tissue


title: P001_OLP mRNA-Seq


title: Control 1


title: ESC.Δ5|6:7|9

source_name: mESC


title: E1

description: Rep. 1

value: Col


title: P001_OSCC mRNA-Seq

value: oral squamous cell carcinoma tissue


title: ESC.WT


title: TAM_1

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were mapped to the mouse genome (mm9) using TopHat.  Mapped reads were assigned to Ensembl v63 annotated genes using htseq-count.  Differential expression was assessed using edgeR with TMM normalization.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include normalized cpm values for all samples.

growth_protocol: Cells were cultured at 3% oxygen, 5% carbon dioxide, balanced with nitrogen at 37 degrees celcius.  The culture media consisted of DMEM+10% non-heat-inactivated FBS with 1% penicillin/streptomycin.

extract_protocol:
Cells were isolated from dorsal skin by removal of skin followed by enzymatic digestion using collagenase (2 mg/ml) and hyaluronidase (1 mg/ml) in DMEM at 37 degrees for 4 hours.  Following digest, cells were plated on tissue culture plates, allowed to sit for 24 hours and then washed with PBS and fresh media supplied.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with either tamoxifen or ethanol (vehicle) as noted above in "Samples" section

tag: strain

value: FVB/N

value: skin

tag: treatment

value: 10uM tamoxifen


title: TAM_2


title: Plasma_2h

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

data_processing:
Basecalling was performed using Illumina CASAVA version1.8.2.
CLC genomics version 5.5.1 was used for alignment, normalization (RPKM) and for differential gene expression calculation.
Kal’s statistical test, with false discovery rate, was applied to identify statistically significant alterations in the transcriptome of BRC incubated with whole blood, PMN or MN cells, plasma and TSB as compared with the control (bacteria before the assay - T0h)
Genes with P values above 0.05 and fold changes below 3 were discarded.
Having to consider that bacteria may change their transcriptome, in a nonspecific manner, after being transferred in to a new environment, the transcriptomic alterations detected on BRC incubated with blood and its components (as compared with T0h) were compared with those observed in the presence of TSB. All the genes that were common to BRC incubated with human blood components and TSB were discarded.However, genes with opposite regulation in human blood and its components were maintained (to add this sentence). Hence, the final list only presents the alterations which are particular to each of the condition tested.
Genome_build: NC_002976.3
Supplementary_files_format_and_content: Tab-delimited text files with gene locus tag and respective fold change values regarding the control (T0h).

organism: Staphylococcus epidermidis

source_name: Bacteria

growth_protocol: BRC were grown as described in Franca et al., 2016, AMB Express 6(1): 23. In brief, 24 hours biofilms, grown in a fed-batch system in the presence of Tryptic Soy Broth supplemented with 0.65% G (TSBG) and incubated at 37C and shaking at 120 rpm, were washed twice with saline solution, fresh TSBG was added and biofilms were allowed to grow for additional 24 hours, under the same temperature and shaking conditions. The cells in the biofilm-bulk fluid (BRC, released from the biofilm by both dispersion and detachment processes) were collected and harvested by centrifugation.

extract_protocol:
BRC total RNA was extracted using RNeasy mini kit (QIAGEN) with minor alterations as described in FranÃ§a et al., 2012, PLoS One 7 (5): e37480. In brief, BRC were suspended in 500 µL of lysis buffer provided by the kit plus 500 µL of phenol. This suspension was transferred into BeadBug tubes (1.0 mm Zirconium beads, triple-pure, high impact, Sigma) and using a MPBio 24 (MPBio) the cells were lysed (3 cyles at 6.5 meter/second for 35 seconds.Between each cycle samples were placed on ice for 5 minutes). Finally, the tubes were centrifuged and the suspension transferred into a new tube. An equal volume of 70 % of ethanol was added. The suspension was transferred in to the RNeasy mini kit columns and the manufacturer's instructions were strickly followed. Total RNA, eluted in 50 µL, was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to degrade and isolate, respectively, genomic DNA. Additionally, total RNA was treated with MICROBEnrichTM (Ambion) and Ribo-ZeroTM rRNA removal kit for Gram-positive bacteria (Epicentre) in order to remove eukaryotic RNA and bacterial ribosomal RNA, respectively.
Libraries were constructed using ScriptSeq RNAseq Library preparation kit (low input) and strictly following the manufacturer's indications.

treatment_protocol: BRC concentration was ajusted to 1E9 cells/mL with saline solution and 100 µL of this suspension was incubated with 900 µL of whole human blood, 1E6 PMN or MN cells, plasma and TSB for 2 hours at 37C. BRC were then collected by centrifugation and immediately suspended in 1 mL of RNA protect bacteria reagent (Qiagen) diluted 2:1 in RNase-free water as indicated by the manufacturer. After 5 minutes incubation at room temperature BRC were harvested by centrifugation at 5000 gduring 10 minutes.

value: interaction with plasma for 2h


title: MN_2h

value: interaction with MN for 2h


title: TAM_3


title: EtOH_3

value: vehicle (ethanol)


title: PMN_2h

value: interaction with PMN for 2h


title: P002_OSCC miRNA-Seq

data_processing:
The 50nt sequence tags from HiSeq sequencing will go through the data cleaning first, which includes getting rid of the low quality tags and several kinds of contaminants from the 50nt tags. Length distribution of clean tags are then summarized.
Afterwards, the standard bioinformatics analysis will annotate the clean tags into different categories and take those which can not be annotated to any category to predict the novel miRNA and base edit of potential known miRNA.
Genome_build: hg18
Supplementary_files_format_and_content: excel file includes the standard expression values of all samples and comparisons between each two samples of the same patient


title: P002_OSCC mRNA-Seq


title: Blood_2h

value: interaction with blood for 2h


title: P002_OLP miRNA-Seq


title: TSB_2h


title: P002_Nor miRNA-Seq


title: E2

description: Rep. 2


title: EtOH_1


title: T0h_2h


title: P001_OSCC miRNA-Seq


title: P001_OLP miRNA-Seq


title: EtOH_2


title: P001_Nor mRNA-Seq


title: TT2_Input

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

data_processing:
BAM file: Sequence reads were mapped to mm9 using BWA (Li & Durbin, 2009) using default parameters. File includes unique and multiple aligned reads.
BigWig: Reads having identical coordinates were collapsed into a single read and reads with mapQ >=5 passed to FindPeaks 3.1 (Fejes et a;., 2008) for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: embryonic stem cell

growth_protocol: ES cells were maintained in DMEM supplemented with 15% fetal bovine serum, 20mM HEPES, 2mML-glutamine, 0.1mM non-essential amino acids, 0.1mM 2-betamercaptoetahnol, 100U/mL penicillin, 0.05mM streptomycin and leukemia inhibitory factor on gelatinized plates.

extract_protocol:
Cells were crosslinked and digested with microccocal nuclease, then protein:DNA complexes were immunoprecipitated with specific antibodies. Eluted DNA underwent crosslink reversal and phenol:choloroform cleanup.
Adaptor ligation based library construction for paired-end Illumina sequencing

tag: cell type

value: ES


title: Amp Rep 1

city: Hangzhou

first: Bin

last: Li

state: Zhejiang

address: Zijingang Campus, Nongshenghuan Building, C702

department: College of Agriculture and Biolechnology

institute: Zhejiang 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 Acidovorax avenae subsp. avenae strain ATCC 19860 whole genome using tophat 2.0.8b with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1.
Genome_build: Accession Number CP002521
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Paracidovorax avenae

source_name: A. avenae RS-1_Amp+

growth_protocol: Aaa strain under Amp of final concentration of 100 µg/ml for 48 h incubation.

extract_protocol:
RNA extraction and puriﬁcation were performed with RNeasy Mini Kit (Qiagen). RNA samples were treated with DNaseI and puriﬁed by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. In order to remove rRNA and polyadenylated mRNA, ten micrograms from each total RNA sample was subsequently treated with the MICROB Express Bacterial mRNA Enrichment kit (Ambion), RiboMinus Transcriptome Isolation Kit (Bacteria) (Invitrogen) and the Sera-mag Magnetic Oligo(dT) Beads (Thermo) following the manufacturer’s instructions.
Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.

value: strain RS-1

tag: treated with

value: 100 µg/ml Ampicillin for 48 h


title: P001_Nor miRNA-Seq

city: Beijing


title: Amp Rep 2


title: In vitro degradation of randomized RNA substrate_16548

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description: 30-40 nt size selection

data_processing:
The adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG) was cut once with cutadapt (v1.2.1). The random 4mers on the 3' were removed with fastx_trimmer of the fastx-toolkit (v0.0.13). Sequences with exact 4nt length were counted and the reads per million for each 4mer was calculated.
library strategy: synthetic RNA seq
Genome_build: Flybase r5.57
Supplementary_files_format_and_content: TXT (RPM): tab separated text containing 4mer and it's RPM (read per million); TXT (SEQCNT) tab separated text file containing alignment position, feature, tail statistics and count; XLSX: Excel file containing summary statistics (length, nt count, nt count from 3' to 5')

organism: synthetic construct

source_name: synthetic RNA oligo NNNN-3´

extract_protocol: 2 min sec treatment with FLAG-dmDis3l2, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

tag: sample group

value: 2 min sec treatment with FLAG-dmDis3l2

tag: molecule subtype

value: synthetic randomized RNA NNNN3´


title: TT2_HP1b

tag: antibody


title: In vitro degradation of randomized RNA substrate_16547

description: 30-40 nt size selection

extract_protocol: 30 sec treatment with FLAG-dmDis3l2, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

value: 30 sec treatment with FLAG-dmDis3l2


title: In vitro degradation of randomized RNA substrate_16546

description: 30-40 nt size selection

extract_protocol: Input,  Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

value: Input


title: neg1_46668_A

city: Berlin

first: Dubravka

last: Vučićević

address: Ihnestraße 63-73

institute: Max Planck Institute for Molecular Genetics

data_processing:
Data was processed using TRAP pipeline  (Fernandez-Cuesta et al, 2015).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig and rpkm files from total RNA-seq in HeLa.

source_name: HeLa

extract_protocol: none provided

tag: knock-down of enst00000046668 (parrot)

value: cervical cancer

tag: cell line

value: HeLa


title: neg2_46668_C


title: neg1_46668_C


title: 46668_si2C


title: neg2_46668_A


title: In vitro degradation of randomized RNA substrate_16558

description: 30-40 nt size selection

extract_protocol: 10 sec treatment with ecoRNaseR, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

value: 10 sec treatment with ecoRNaseR


title: In vitro degradation of randomized RNA substrate_16557

description: 30-40 nt size selection

extract_protocol: 5 sec treatment with ecoRNaseR, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

value: 5 sec treatment with ecoRNaseR


title: 46668_si2A


title: 46668_si1C


title: In vitro degradation of randomized RNA substrate_15485

description: 30-40 nt size selection

extract_protocol: 10 min treatment with FLAG-dmDis3l2, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

value: 10 min treatment with FLAG-dmDis3l2


title: In vitro degradation of randomized RNA substrate_16549

description: 30-40 nt size selection


title: In vitro degradation of randomized RNA substrate_16556

description: 30-40 nt size selection

extract_protocol: Input, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced


title: 46668_si1A


title: 2850LN_MBDcap-seq

city: New Lambton Heights

first: Kelly

last: Avery-Kiejda

state: NSW

address: Kookaburra Circuit

department: Medical Genetics

country: Australia

institute: Hunter Medical Research Institute

description: MBDCap-seq

data_processing:
Sequenced reads were aligned to hg19 genome assembly using bowtie. Reads with more than three mismatches and reads mapping to multiple positions were removed. Finally, multiple reads mapping to exactly the same genomic coordinate were eliminated and only one read was retained for downstream analysis.
For each MBDCap-Seq sample, fragment length was estimated using HOMER software, sequenced tags were shifted to the middle of estimated fragment length. Genes used in this analysis were broken into 1kb tiles beginning 2kb upstream of the first transcription start site associated with that gene and continued untill the end of the gene. The number of sequenced tags overlapping differentially expressed gene regions was then computed.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing a table of overlapping sequence tags (rows) for each sample (columns).
Supplementary_files_format_and_content: table of counts for all samples and at all regions of interest

growth_protocol: DNA was extracted from cells microdissected from human tissue samples representing normal breast and tumor breast tissue.

extract_protocol:
The MethylMinerTM Methylated DNA Enrichment Kit (Invitrogen) was used to isolate methylated DNA from 500 ng – 1 μg of genomic FFPET DNA.
10ng DNA of MBDCap enriched DNA was prepared for Ilumina sequencing using the Illumina ChIP-Seq DNA sample prep kit (IP-102-1001) according to the manufacturer’s instructions.  The library preparation was analyzed on Agilent High Sensitivity DNA 1000 Chip.

value: lymph node metastatic breast tumour tissue


title: 2532LN_MBDcap-seq

description: MBDCap-seq


title: CACO-2 cells incubated with HMO-grown B. breve, replicate 3

city: Davis

first: Danielle

middle: G

last: Lemay

state: CA

address: 451 Health Sciences Dr

department: Genome Center

institute: University of California Davis

data_processing:
Reads were demultiplexed and imported into CLC-Bio Genomics Workbench Version 5.5.1
The following criteria were used to filter the unique sequence reads:  minimum length fraction of 0.9; minimum similarity fraction of 0.8; maximum number of two mismatches.
Reads were mapped to the human reference genome, build 37.1
Data were normalized by calculating the reads per kilo base per million mapped reads (RPKM=total exon reads/mapped reads in millions x exon length in kb) for each gene
Gene annotations were based on the Ensembl human genome assembly GRCh37.p11
Genome_build: Homo sapiens, Build 37.1
Supplementary_files_format_and_content: tab-delimited text files contain abundance measurements as RPKM and counts

source_name: CACO-2 cells

growth_protocol: B. infantis ATCC 15697 and B. breve SC 95 from the exponentially grown 48h-old cultures supplemented with HMO, GLU or LAC were collected by centrifugation (4000g for 10 min), washed, and resuspended in DMEM. For reference purposes (100% values), 1 ml aliquots of the original bacterial cell suspensions used in the adhesion assay were centrifuged, the cells resuspended in 200 μl trypsin/EDTA plus 200 μl PBS and then frozen and stored at ‑20°C until quantification of the bacteria.  B. infantis ATCC 15697 and B. breve SC 95 bacterial suspensions were carefully washed twice with sterile phosphate-buffered saline (PBS; pH 7.3) and approximately 1 x 108 cells of each strain were incubated at 37°C, 5% CO2 for 2h with a monolayer of fully differentiated Caco-2 cells. All incubations were performed in biologically independent triplicates. After 2 hours of incubation, cell monolayers were gently washed three times with PBS, to remove unbound bacteria.

extract_protocol:
Caco-2 cell monolayers were gently washed three times with PBS and RNA was extracted from Caco-2 cells using the Trizol method according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA).
Sequencing libraries of mRNA were prepared using the Illumina TruSeq RNA Sample Prep Kit v2
Pooled libraries were sequenced on an Illumina HiSeq 2000. Sequencing was run for 100 cycles, with read length of 100 bp (single reads).

value: HMO-grown B. breve

tag: replicate


title: CACO-2 cells incubated with HMO-grown B. breve, replicate 2


title: 20578LN_MBDcap-seq

description: MBDCap-seq


title: 12627LN_MBDcap-seq

description: MBDCap-seq


title: CACO-2 cells incubated with HMO-grown B. breve, replicate 1


title: In vitro degradation of randomized RNA substrate_15484

description: 30-40 nt size selection


title: 3050LN_MBDcap-seq

description: MBDCap-seq


title: 1138LN_MBDcap-seq

description: MBDCap-seq


title: In vitro degradation of randomized RNA substrate_15482

description: 30-40 nt size selection

extract_protocol: Input, Substrate RNA was gelpurified,  ligated to 3´ adapter and product was PCR amplified and sequenced


title: 214LN_MBDcap-seq

description: MBDCap-seq


title: In vitro degradation of randomized RNA substrate_16559

description: 30-40 nt size selection

extract_protocol: 30 sec treatment with ecoRNaseR, residual Substrate RNA was gelpurified, ligated to 3´ adapter and product was PCR amplified and sequenced

value: 30 sec treatment with ecoRNaseR


title: CACO-2 cells incubated with glucose-grown B. breve, replicate 3

value: glucose-grown B. breve


title: In vitro degradation of randomized RNA substrate_15483

description: 30-40 nt size selection


title: CACO-2 cells incubated with glucose-grown B. breve, replicate 2


title: CACO-2 cells incubated with lactose-grown B. breve, replicate 3

value: lactose-grown B. breve


title: CACO-2 cells incubated with lactose-grown B. breve, replicate 1


title: CACO-2 cells incubated with glucose-grown B. breve, replicate 1


title: CACO-2 cells incubated with lactose-grown B. breve, replicate 2


title: CACO-2 cells incubated with glucose-grown B. infantis, replicate 2

source_name: CACO-2 cells_glucose-grown B. infantis

growth_protocol: B. infantis ATCC 15697  from the exponentially grown 48h-old cultures supplemented with HMO, GLU or LAC were collected by centrifugation (4000g for 10 min), washed, and resuspended in DMEM. For reference purposes (100% values), 1 ml aliquots of the original bacterial cell suspensions used in the adhesion assay were centrifuged, the cells resuspended in 200 μl trypsin/EDTA plus 200 μl PBS and then frozen and stored at ‑20°C until quantification of the bacteria.  B. infantis ATCC 15697 bacterial suspensions were carefully washed twice with sterile phosphate-buffered saline (PBS; pH 7.3) and approximately 1 x 108 cells of each strain were incubated at 37°C, 5% CO2 for 2h with a monolayer of fully differentiated Caco-2 cells. All incubations were performed in biologically independent triplicates. After 2 hours of incubation, cell monolayers were gently washed three times with PBS, to remove unbound bacteria.

tag: incubated with

value: glucose-grown B. infantis


title: CACO-2 cells incubated with HMO-grown B. infantis, replicate 2

source_name: CACO-2 cells_HMO-grown B. infantis

value: HMO-grown B. infantis


title: CACO-2 cells incubated with glucose-grown B. infantis, replicate 3


title: CACO-2 cells incubated with lactose-grown B. infantis, replicate 3

source_name: CACO-2 cells_lactose-grown B. infantis

value: lactose-grown B. infantis


title: CACO-2 cells incubated with glucose-grown B. infantis, replicate 1


title: CACO-2 cells incubated with lactose-grown B. infantis, replicate 2


title: CACO-2 cells incubated with lactose-grown B. infantis, replicate 1


title: CACO-2 cells incubated with HMO-grown B. infantis, replicate 3


title: BMDM_WT_HP_720min_rep2

city: Blacksburg

first: Monica

last: Viladomiu

state: VA

address: 1015 Life Science Circle

department: Virginia Bioinformatics Institute

institute: Nutritional Immunology and Molecular Medicine Laboratory

data_processing:
Adapter trimming
Bowtie was used to map the reads to RefSeq sequences of mouse (downloaded from UCSC), and RSEM was used to calculate expression values for each gene. FPKM-transformed values were log-transformed followed by normal quantile transformation. Two methods of P-value adjustment (FDR & Bonferroni) were used. Kolmogorov-Smirnov test was used to test normality, followed by parametric 3-way ANOVA to obtain differential expression.
Genome_build: mm9

growth_protocol: femur and tibia were excised, washed in 70% EtOH and cold 1xPBS. BM progenitors were flushed out with cRPMI_M (RPMI 1640, 10% FBS, 2.5% Hepes, 1% Sodium pyruvate, 1% Pen/Strep, 1% L-Glutamine, 50uM 2-mercaptoethanol),  filtered through a 100µm cell strainer and centrifuged for 8 min at 1,200 rpm at 4°C. Red blood cells were eliminated by osmotic lysis and cell suspensions were filtered and centrifuged again as described above. BM progenitors were adjusted to 1x106 cells/mL with cRPMI_M containing 35ng/mL recombinant mouse M-CSF (Peprotech). Cells were plated in 100mm petri dishes and incubated at 37°C, 95% humidity and 5% CO2. Fresh media containing M-CSF was added on day 3. On day 6, non-adherent cells were removed and bone marrow derived macrophages (BMDM) were detached by incubation in ice cold 1xPBS at 4°-8°C for 10 minutes.  Cells were carefully removed from the dish by flushing them off the culture dish. BMDM were centrifuged, resuspended in fresh cRPMI_M without antibiotics and used for the Gentamicin infiltration assay.

extract_protocol:
After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
infection protocol: BMDM cell suspensions were resuspended in cRPMI_M without antibiotics and plated in triplicate in 12-well plates (2.5x105 for re-isolation experiments, 1x106 cells for RNA isolation). Cells were left to adhere overnight at 37°C, 95% humidity and 5% CO2. The following day, H. pylori SS1 was harvested from Columbia blood agar plates and resuspended in cRPMI_M w/o Ab to a concentration of 1x108 CFU/mL. H. pylori were added to BMDM at MOI 10 and plates were quick spun to ensure immediate contact. For iNOS inhibition experiments, cells were incubated with the selective iNOS inhibitor L-N6-(1-Iminoethyl)lysine dihydrochloride (L-NIL) at 100µM for 30 min. In some experiments, WT BMDM were treated with the PPARγ antagonist GW9662 (10µM) for 2 hours prior to bacterial co-culture. In the case of M1 induction BMDM were pre-treated with LPS (100ng/ml) and rIFN-γ (100ng/ml) overnight.   After 15 minutes of bacteria-macrophage co-culture at 37°C, 95% humidity, 5% CO2, the culture supernatant was removed and cells were washed three times with PBS/5% FBS/100ng/ml Gentamicin. Cells for time-point 0 were washed with 1xPBS and immediately collected for downstream assays.  The cells allocated for the remaining time points (15 min to 24 hours) were covered with culture media supplemented with 100ng/ml Gentamicin to kill extracellular H. pylori. Cells were incubated for the indicated time-points and then collected as described below.
BMDM were isolated from WT and PPARg-/- mice and cultured with M-CSF for 7 days to promote macrophage differentiation. Fully differentiation macrophages were challenged with H. pylori strains SS1 at an MOI of 10 for 15 minutes. Extracellular bacteria was then eliminated by gentamycin treatment. Cells were collected at 0, 60, 120, 240, 360 and 720 minutes post gentamycin treatment to ascertain whole transcriptome differential gene expression during infection.

tag: strain background

tag: genotype/variation

value: Wild-type

value: Bone marrow-derived macrophages (BMDM)

tag: infection status

value: H.pylori SS1-infected (MOI 10)

tag: collection time-point

value: 720min post gentamycin treatment


title: BMDM_WT_HP_720min_rep3


title: BMDM_LYS_uninfected_720min_rep3

value: PPARgfl/fl:LysCre+ (R2+)

value: Negative control (uninfected)


title: BMDM_LYS_HP_720min_rep3


title: BMDM_LYS_uninfected_720min_rep2


title: BMDM_LYS_uninfected_720min_rep1


title: BMDM_WT_uninfected_720min_rep3


title: CACO-2 cells incubated with HMO-grown B. infantis, replicate 1


title: BMDM_WT_uninfected_720min_rep2


title: BMDM_WT_uninfected_720min_rep1


title: BMDM_LYS_HP_360min_rep2

value: 360min post gentamycin treatment


title: BMDM_LYS_HP_360min_rep3


title: BMDM_LYS_HP_360min_rep1


title: BMDM_LYS_HP_720min_rep1


title: BMDM_LYS_HP_720min_rep2


title: BMDM_WT_HP_360min_rep3


title: BMDM_WT_HP_360min_rep1


title: BMDM_WT_HP_360min_rep2


title: BMDM_LYS_uninfected_360min_rep2


title: BMDM_WT_uninfected_360min_rep3


title: BMDM_LYS_uninfected_360min_rep3


title: MDA-231_pcDNA_vector_mRNA.A_121024_Miller_pool1_7_CAGATC_L001_R1

city: New Orleans

first: Bridgette

last: Collins-Burow

state: LA

address: 1430 Tulane Ave, SL-78

department: Medicine

institute: Tulane University

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for quality and adaptor sequence, then mapped to hg19 whole genome using tophat2 (version 2.0.6) with parameters --b2-very-sensitive --read-edit-dist 2 --max-multihits 100 --library-type.  Gencode version 13 was used as the reference annotation.  Mapped reads were associated with genes using custom perl scripts.
Differential gene expression was determined using using the edgeR software (version 2.6.0) by supplying raw gene counts as input.
Genome_build: hg19

source_name: triple-negative breast carcinoma from pleural effusion

growth_protocol: cells were grown in normal growth media (DMEM supplemented with 10% FBS) on plastic culture dishes to ~70% confluence. Pellets were harvested using PBS/EDTA.

extract_protocol:
Total RNA was extracted using a modified version of the Qiagen  RNeasy AllPrep method (Qiagen Sciences, Valencia, CA 91355, cat. no. 80004). Methods are described in detail in our article "A New Method for Stranded Whole Transcriptome RNA-seq" in Methods, 2013.
Libraries were prepared according to Illumina's instructions and as described in  "A New Method for Stranded Whole Transcriptome RNA-seq" in Methods, 2013.

tag: plasmid

value: pcDNA-Vector


title: MDA-231_pcDNA_LKB1_fmRNA.D_121024_Miller_pool4_8_ACTTGA_L003_R1

value: pcDNA-FLAG-LKB1 wildtype


title: MDA-231_pcDNA_LKB1_fmRNA.C_121112_3D2_7_CAGATC_L001_R1


title: MDA-231_pcDNA_vector_mRNA.B_121024_Miller_pool2_8_ACTTGA_L002_R1


title: BMDM_LYS_uninfected_360min_rep1


title: BMDM_WT_uninfected_360min_rep2


title: BMDM_WT_HP_720min_rep1


title: BMDM_WT_uninfected_360min_rep1


title: BMDM_LYS_HP_240min_rep3

value: 240min post gentamycin treatment


title: BMDM_WT_HP_240min_rep3


title: BMDM_LYS_HP_240min_rep1


title: BMDM_LYS_HP_240min_rep2


title: BMDM_LYS_HP_60min_rep2

value: 60min post gentamycin treatment


title: BMDM_WT_HP_60min_rep1


title: BMDM_LYS_uninfected_120min_rep2

value: 120min post gentamycin treatment


title: BMDM_WT_uninfected_120min_rep2


title: BMDM_LYS_HP_120min_rep3


title: BMDM_WT_HP_120min_rep1


title: BMDM_LYS_HP_60min_rep1


title: BMDM_WT_uninfected_120min_rep3


title: BMDM_WT_uninfected_240min_rep1


title: BMDM_LYS_HP_120min_rep2


title: BMDM_WT_HP_240min_rep1


title: BMDM_WT_HP_240min_rep2


title: BMDM_LYS_uninfected_240min_rep1


title: BMDM_WT_uninfected_120min_rep1


title: BMDM_WT_HP_60min_rep2


title: BMDM_LYS_HP_60min_rep3


title: BMDM_WT_HP_60min_rep3


title: BMDM_LYS_uninfected_120min_rep3


title: BMDM_WT_HP_120min_rep3


title: BMDM_LYS_uninfected_60min_rep3


title: BMDM_WT_uninfected_240min_rep2


title: BMDM_WT_HP_120min_rep2


title: BMDM_LYS_uninfected_60min_rep1


title: BMDM_LYS_uninfected_240min_rep2


title: BMDM_LYS_uninfected_240min_rep3


title: BMDM_LYS_uninfected_60min_rep2


title: BMDM_LYS_uninfected_120min_rep1


title: 3A-144-R2

city: Fargo

first: Shaobin

last: Zhong

state: ND

address: 306 Walster Hall

department: Plant Pathology

institute: North Dakota State University

data_processing:
Mapping of sequence reads to reference genome, and analyses of transcript abundance and differential gene expression were performed as described by Trapnell et al. (2012).
The trimmed reads (37 bases) were then aligned to the F. graminearum reference genome downloaded from the Broad  using Bowtie v0.12.5 and TopHat v2.0. with default settings. Cufflinks v0.9.3 was used to calculate transcript abundance based on fragments per kilobase of transcript per million fragments mapped (FPKM) using all parameters on default settings.
The pairwise comparisons of gene expression profiles between the two populations were done using the Cuffdiff program of the Cufflinks version 1.3.0 (Trapnell et al, 2010).
Principal component analysis (PCA) was performed using JMP Genomics v 6.0 (SAS Institute Inc., Cary, NC) for all genes (except novel transcripts).
The differently expressed genes (DEGs) were functionally categorized online for all pairwise comparisons according to the Munich Information Center for Protein Sequences (MIPS) functional catalogue (Ruepp et al. 2004). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed using interface on Blast2GO.
Genome_build: The trimmed reads (37 bases) were then aligned to the F. graminearum reference genome downloaded from the Broad Institute.
Supplementary_files_format_and_content: File includes total number of reads, number of reads mapped to the reference genome, differently expressed genes in all pairwise comparisons.

organism: Fusarium graminearum

source_name: Infected plant tissue_3A-144

extract_protocol:
Total RNA was extracted using Promega SV total RNA isolation kit. Extracted RNA was converted dscDNA and used for library preparation and sequencing using TruSeq RNA sample preparation kit from Illumina.
The library was constructed using TruSeq RNA sample preparation kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. Briefly, the poly-A containing mRNA was purified from the total RNA using the poly-T oligo-attached to the magnetic beads. After purifications, mRNA was fragmented into small pieces using divalent cations under elevated temperature. The fragmented mRNA was converted to first strand cDNA using reverse transcriptase and random primers. Single strand cDNA was further converted to double strand (ds) cDNA using DNA polymerase I and RNase H. Then, the ds cDNA fragments were end repaired, ligated with indexing adapters, purified and enriched with PCR to develop the library. The prepared libraries were sent to Huntsman Cancer Institute, the University of Utah (Salt Lake City, UT) for generating 50bp single-end reads with the Illumina HiSeq 2000 sequencing system

tag: experiment type

value: in-planta inoculations

tag: infection in

value: spring wheat cultivar- Briggs

tag: inoculated with

value: 3ADON isolate population

tag: tissue

value: Inoculated Spikelet

tag: time point

value: 144 HAI

tag: sequence id


title: 3A-48-R2

source_name: Infected plant tissue_3A-48

value: 48 HAI


title: 15A-144-R2

source_name: Infected plant tissue_15A-144

value: 15ADON isolate population


title: 3A-96-R1

source_name: Infected plant tissue_3A-96

value: 96 HAI


title: Adipocyte_RNA-seq

city: seoul

first: yoosik

last: yoon

address: Heukseok-street 47,Dongjak-gu

institute: chungang university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

growth_protocol: Cell culture. 3T3-L1 cells were purchased from the American Type Culture Collection (Manassas, VA, USA) and maintained in Dulbecco’s modiﬁ ed Eagle’s medium (DMEM) supplemented with 10% calf serum, 100 μg/mL streptomycin and 100 units/mL penicillin  at   37 ºC in 5% CO2. The cells were subcultured after reaching a conﬂ uence of 80%. To induce adipogenesis, 3T3-L1 cells were cultured until conﬂ uent, and 2 days after reaching conﬂ uence, called day 0, the culture medium was changed into a differentiation/induction medium containing 1 μg/mL insulin, 0.25 μm dexamethasone and 0.5 mm 3-isobutyl-1-methylxanthine in DMEM with 10% fetal bovine serum for 2 days. Next, the cells were maintained in a differentiation maintenance medium containing 1 μg/mL insulin in DMEM with 10% fetal bovine serum.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: test the effects of DF-GA70 on adipogenesis, it was added to the medium until the cells were harvested.

tag: cell type

value: Adipocyte

tag: passages

tag: treated with

value: none (control)


title: F-15A-R2

source_name: Mycelia in growth media_F-15A

value: in-vitro inoculations

value: Mung Bean Media

value: Mycelia

value: 5 DAI


title: 15A-144-R1


title: 3A-48-R1


title: F-15A-R1


title: F-3A-R1

source_name: Mycelia in growth media_F-3A


title: 3A-96-R2


title: 3A-144-R1


title: 15A-96-R1

source_name: Infected plant tissue_15A-96


title: F-3A-R2


title: BMDM_LYS_uninfected_0min_rep3

value: PPARgfl/fl:LysCre+ (R2+)

value: Bone marrow-derived macrophages (BMDM)

value: Negative control (uninfected)

value: 0min post gentamycin treatment


title: BMDM_LYS_uninfected_0min_rep1


title: BMDM_WT_HP_0min_rep2

value: Wild-type

value: H.pylori SS1-infected (MOI 10)


title: BMDM_WT_HP_0min_rep1


title: BMDM_WT_uninfected_0min_rep2


title: DF-GA70_RNA-seq

tag: cell line

value: DF, an anti-obesity multi-herbal composition


title: BMDM_WT_uninfected_0min_rep3


title: BMDM_WT_uninfected_60min_rep2

value: 60min post gentamycin treatment


title: BMDM_LYS_HP_0min_rep2


title: BMDM_LYS_uninfected_0min_rep2


title: BMDM_WT_uninfected_60min_rep1


title: BMDM_WT_uninfected_60min_rep3


title: BMDM_LYS_HP_0min_rep1


title: BMDM_WT_uninfected_0min_rep1


title: 15A-96-R2

value: in-planta inoculations

value: spring wheat cultivar- Briggs

value: Inoculated Spikelet


title: 15A-48-R2

source_name: Infected plant tissue_15A-48

value: 15ADON isolate population

value: 48 HAI


title: Mouse_d18.1

city: Madison

first: Christopher

middle: A

last: Barry

state: WI

address: 330 N. Orchard St.

department: Regenerative Biology

institute: Morgridge Institute for Research

description:
Mouse EpiSC teratoma day d18 rep1
Teratoma.RSEM.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 1.0 --seed-length 28 "
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Excel Spreadsheets containing RSEM-calculated Gene Expression Estimates in both Expected Counts (EC) and Transcripts Per Million (TPM)

source_name: Teratoma time course

growth_protocol: In vitro cells were differentiated in DF3S+N2 supplement + B27 supplement + 100 ng/mL Noggin.  EGFP-positive cells for tertomas were injected in a 1.8:1 ratio of either TSS:Matrigel+3uM Y-27632 (mEpiSC) or E8:Matrigel (H1).  Dissected teratomas were digested with Dispase/Collagenase (Roche) for single cell suspensions for FACS sort.

extract_protocol:
RNA was extracted using the Rneasy plus mini kit (Qiagen)
cDNA libraries were prepped using the LM-Seq protocol described in  Hou et al 2015 (PMID 25831155).

treatment_protocol: Each sample was lysed in RLT plus buffer and stored at -80C until multiple samples could be processed in parallel.

value: EpiSC

tag: time course


title: Mouse_d9.2

description:
Mouse EpiSC teratoma day d9 rep2
Teratoma.RSEM.xlsx


title: Mouse_d14.1

description:
Mouse EpiSC teratoma day d14 rep1
Teratoma.RSEM.xlsx


title: Mouse_d21.1

description:
Mouse EpiSC teratoma day d21 rep1
Teratoma.RSEM.xlsx


title: Mouse_d11.1

description:
Mouse EpiSC teratoma day d11 rep1
Teratoma.RSEM.xlsx


title: Mouse_d4.2

description:
Mouse EpiSC teratoma day d4 rep2
Teratoma.RSEM.xlsx


title: Mouse_d10.1

description:
Mouse EpiSC teratoma day d10 rep1
Teratoma.RSEM.xlsx


title: Mouse_d2.2

description:
Mouse EpiSC teratoma day d2 rep2
Teratoma.RSEM.xlsx


title: Mouse_d9.1

description:
Mouse EpiSC teratoma day d9 rep1
Teratoma.RSEM.xlsx


title: Mouse_d16.1

description:
Mouse EpiSC teratoma day d16 rep1
Teratoma.RSEM.xlsx


title: Mouse_d8.1

description:
Mouse EpiSC teratoma day d8 rep1
Teratoma.RSEM.xlsx


title: Mouse_d4.1

description:
Mouse EpiSC teratoma day d4 rep1
Teratoma.RSEM.xlsx


title: P. chlororaphis_PCA_AB_rep2

city: Vernon Hills

first: DONGPING

last: WANG

state: IL

address: 777 Forest Edge Dr

department: Amlan

institute: OilDri Corporation of America

description:
strain: Pseudomonas chlororaphis 30-84 genotype: mutant, growing condition: AB minimal medium, Stage: late logarithm phase
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

data_processing:
Paired-end sequencing was carried out by the Otogenetic company. Targeted sequencing depth was ten-million paired-end reads per sample.
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Based on gene annotation information, the pipeline produced genome alignment results as a compressed binary version of the Sequence Alignment Map (BAM files).
Mapped reads were visualized using BamView in Artemis 13.2.0 (Rutherford et al. 2000).
The number of reads per kb of transcript per million mapped reads (RPKM) was used to normalize the raw data (Mortazavi et al., 2008), and mean RPKM values were determined for both the wild-type and mutant samples.
Genome_build: GenBank Accession #: PRJNA67533
Supplementary_files_format_and_content: Excel file containing the RPKM values for each gene

organism: Pseudomonas chlororaphis subsp. aureofaciens 30-84

source_name: mutant bacterial cells

growth_protocol: Two biological replicates of every strain were started from single colonies located on two separate plates containing AB + 2% CAA and then transferred to 1.5 ml AB + 2% CAA broth. All cultures were grown at 28˚C in static plates to an approximate OD600 = 1.8.

extract_protocol:
Transfer 700 μl lysate into RNeasy Mini column place in a 2 ml collection tube and centrifuge for 30 s at highest speed. Add 350 μl Buffer RW1 to the column and centrifuge for 30 s. Discard flow-through and reuse the collection tube. Add 10 μl DNase stock solution to 70 μ l RDD Buffer. Add the DNase I solution into the column and incubate at RT for 15 min. Add 350 μl Buffer RW1 to the column and wait for 5 min, centrifuge for 30 s. Discard the flow-through and collection tubes. Place the RNeasy Mini spin column in a new 2 ml collection tube. Add 500 μl Buffer RPE to the column. Centrifuge for 30 s. Place the column in a new 1.5 ml tube, and centrifuge for 1 min to eliminate any residue ethanol. Place the column in a new collection tube. Add 50 μl RNase free water, centrifuge for 1 min. Store RNA samples at -20°C
Strand-specific cDNA libraries were constructed using Illumina TruSeq RNA Sample Preparation Kits.

treatment_protocol: wild type and mutant strains

tag: strain

value: PCA strain


title: P. chlororaphis_O_AB_rep1

value: O star straiin


title: Mouse_d2.1

description:
Mouse EpiSC teratoma day d2 rep1
Teratoma.RSEM.xlsx


title: P. chlororaphis_WT_AB_rep2 (phenazine)

description:
strain: Pseudomonas chlororaphis 30-84 genotype: wild type, growing condition: AB minimal medium, Stage: late logarithm phase
Strand-specific cDNA libraries were constructed using the SOLiD Total RNA-Seq kit according to the manufacturer’s instructions with the following modifications: 1) For RNA fragmentation, 300 ng of rRNA-depleted RNA were incubated at 95˚C for 5 min. Bioanalyzer traces were used to confirm that the largest proportion of RNA fragments were around 200 bp. 2) Bioanalyzer traces following reverse transcription were used to confirm that hybrization and ligation of RNA adapters and subsequent reverse transcription of the RNA to cDNA was successful. 3) Amplification of cDNA was carried out following reverse transcription, but preceding the size-selection step. Samples were barcoded by replacing the SOLiD 3’ primer with the appropriate barcoding primer as directed in the SOLiD instructions. Size selection of DNA amplicons ranging from 200-300 bp was performed using an E-Gel iBase system (SYBR Safe 2% SizeSelect gel) (Life Technologies, Carlsbad, CA).  This step was repeated to ensure that adapter-adapter dimers were fully eliminated before sequencing. Paired-end sequencing was carried out by the University of Texas Genomic Sequencing and Analysis Facility (UTGSAF: http://www.ti3d.utexas.edu/facilities/gene-expression) on a Life Technologies SOLiD 5500xl sequencing system. Targeted sequencing depth was six-million paired-end reads per sample.

source_name: wild type bacterial cells

value: wild type


title: P. chlororaphis_Z_AB_rep1

value: ZN mutant


title: P. chlororaphis_O_AB_rep2


title: P. chlororaphis_WT_AB_rep1 (phenazine)


title: P. chlororaphis_PCA_AB_rep1


title: P. chlororaphis_Z_AB_rep2


title: D161_miRNA

city: Guangzhou

first: Fan

last: Wu

state: Guangdong

address: Wushan Road

institute: South China Agricultral University

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: Ensembl release 73 for sus scrofa and mirBase 20.0
Supplementary_files_format_and_content: output from ACGT101-miR (LC Sciences, Houston, Texas, USA)

organism: Sus scrofa

source_name: psoas major muscle

growth_protocol: The muscle samples for different libraries were obtained from different stages of porcine psoas major muscle (D63, D98 and D161).

extract_protocol: Total RNA was isolated with the Total RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada) according to the manufacturer’s instructions. Small RNA libraries were generated from the two samples using the Illumina Truseq Small RNA Preparation kit according to Illumina’s TruSeq Small RNA Sample Preparation Guide. The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina HiSeq 2000 following vendor’s instruction for running the instrument. Raw sequencing reads were obtained using Illumina’s Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Degradome library was constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of known and novel miRNA.

tag: development status

value: fattening pig

value: psoas major muscle

tag: days


title: Mouse_d1.1

description:
Mouse EpiSC teratoma day d1 rep1
Teratoma.RSEM.xlsx


title: mEpi_d21

description:
47875_Mouse EpiSC day 21 in vtro
mEpiVH1.RSEM.xlsx

source_name: In Vitro Neural Differentiation


title: D98_miRNA


title: D63_miRNA


title: 15A-48-R1


title: mEpi_d20

description:
47874_Mouse EpiSC day 20 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d18

description:
47873_Mouse EpiSC day 18 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d16

description:
47872_Mouse EpiSC day 16 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d14

description:
47870_Mouse EpiSC day 14 in vitro
mEpiVH1.RSEM.xlsx


title: Mouse_d0.1

description:
Mouse EpiSC teratoma day d0 rep1
Teratoma.RSEM.xlsx


title: Xa leaves

city: Fuzhou

first: Chen

last: Lisong

address: Shangdian street NO.15

institute: Fujian Agriculture and Forestry University

data_processing:
Basecalls performed
Get rid of some contaminant reads from the fq file and get the final clean reads.
The clear reads were mapped to Citrus clementina genome (JGI version 1.1, http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Csinensis) using SOAP, only perfectly mapped sequences were retained and analyzed further. rRNAs, tRNAs, snRNAs and snoRNAs were removed from the sRNAs sequences through BLASTn search using NCBI Genebank database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi/) and Rfam (12.0) database (http://www.sanger.ac.uk/resources/databases/rfam.html) (e = 0.01). The remaining sequences were aligned with known plant miRNAs from miRBase 21 (http://www.mirbase.org/).
Reads that were not annotated were used to predict novel miRNAs using a prediction software Mireap (http://sourceforge.net/projects/mireap/), which was developed by the BGI
Supplementary_files_format_and_content: abundance

organism: Citrus sinensis

source_name: boron-deficiect leaves

growth_protocol: 5-week-old seedlings of ‘Xuegan’ [Citrus sinensis (L.) Osbeck] were transplanted into 6 L pots containing fine river sand. Ten weeks after transplanting, each pot was supplied every other day with B-deficient (0 μM H3BO3) or B-sufficient (10 μM H3BO3, control) nutrient solution for 15 weeks. There were 10 replications per B treatment with 2 pots in a completely randomized design.

extract_protocol:
About 0.1 g mixed frozen B-sufficient and B-deficient leaves from five replictations were used to extract RNA. Total RNA was extracted from frozen roots using TRIzol reagent (Invitrogen, Carlsbad, CA)
Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina. Two sRNA libraries were constructed, sRNAs were isolated from the total RNA by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). Then the sRNAs were ligated with 5' and 3' adaptor by T4 RNA ligase after being dephosphorylatd by alkaline phosphatase. The adaptor-ligated sRNAs were transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter, the single-stranded cDNA was used as templates for double-stranded synthesis by PCR amplification using the primer designed according to the adapter sequence. The obtained PCR products were sequenced on a Solexa sequencer (Illumina) at the Beijing Genomics Institute (BGI), Shenzhen, China.

treatment_protocol: Xa(B-deficient ,0 μM H3BO3),Xb(B-sufficient ,10 μM H3BO3)

value: Fully expanded Citrus sinensis leaves were excised from the seedlings

tag: treatment

value: boron-deficiect


title: mEpi_d10

description:
47868_Mouse EpiSC day 10 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d12

description:
47869_Mouse EpiSC day 12 in vitro
mEpiVH1.RSEM.xlsx


title: nofix_rep1

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: Microcolonies encapsulated in alginate, no EtOH fixed, not sorted.Barcode in the beginning of the second read - TGCCGA

data_processing:
Base-calling was done during processing of sequencing data with the illumina pipeline casava v1.8.2
Reads were mapped to S. cerevisiae genome (SGD R64-1-1) using the GSNAP version 2012-01-11
Genome_build: R64-1-1 (sacCer3)
Supplementary_files_format_and_content: Count table containing the 3' polyadenylation sites identified.

organism: Saccharomyces cerevisiae

growth_protocol: S. cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% glucose) at 30ºC. Microencapsulation of individual yeast cells in alginate microspheres (no more than one cell per microparticle) was performed using a Cellena microencapsulator (Ingeniatrics), as described (Gómez-Herreros et al, NAR 2011). Encapsulated cells were incubated together in YPD medium under standard culturing conditions. After ethanol fixation, microcolonies were analysed and sorted using a BioSorter large-particle flow cytometer (Union Biometrica). A detailed protocol of the sorting procedures is described in (Delgado-Ramos et al, G3 2014).

extract_protocol:
Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion)
Genome-wide quantification of gene expression and poly(A) site usage was performed using 3’T-fill approach (Wilkening et al 2013; PMID: 23295673). We used 500-3000 ng of total RNA as starting material.

tag: sample type

value: encapsulated cells not fixed with ethanol

tag: genotype/variation

value: Mat a; his3^1leu2^0 ura3^0 met15^0


title: Xb leaves

source_name: boron-sufficient leaves

value: boron-sufficient


title: nofix_rep2

description: Microcolonies encapsulated in alginate, no EtOH fixed, not sorted.Barcode in the beginning of the second read - TGACAT


title: YPD2_rep2

description: Not encapsulated cells. Abs600nm  2Barcode in the beginning of the second read - TATATC

value: without encapsulation grown at cell density YPD2


title: small_rep4

description: Microcolonies encapsulated in alginate, EtOH fixed, small colonies.Barcode in dedicated read - TTAGGC


title: YPD05_rep1

description: Not encapsulated cells. Abs600nm  0.5Barcode in the beginning of the second read - GATCTG

value: without encapsulation grown at cell density YPD05


title: YPD05_rep2

description: Not encapsulated cells. Abs600nm  0.5Barcode in the beginning of the second read - TTAATT


title: mEpi_d8

description:
47867_Mouse EpiSC day 8 in vitro
mEpiVH1.RSEM.xlsx


title: YPD2_rep1

description: Not encapsulated cells. Abs600nm  2Barcode in the beginning of the second read - CCTCCC


title: mEpi_d3

description:
47862_Mouse EpiSC day 3 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d2

description:
47861_Mouse EpiSC day 2 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi3_d1

description:
47860_Mouse EpiSC day 1 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d5

description:
47864_Mouse EpiSC day 5 in vitro
mEpiVH1.RSEM.xlsx


title: big_rep3

description: Microcolonies encapsulated in alginate, EtOH fixed, big colonies.Barcode in the beginning of the second read - ATTGGC

value: big particles


title: big_rep1

description: Microcolonies encapsulated in alginate, EtOH fixed, big colonies.Barcode in the beginning of the second read - TGGTCA


title: mEpi_d6

description:
47865_Mouse EpiSC day 6 in vitro
mEpiVH1.RSEM.xlsx


title: mEpi_d7

description:
47866_Mouse EpiSC day 7 in vitro
mEpiVH1.RSEM.xlsx


title: small_rep2

description: Microcolonies encapsulated in alginate, EtOH fixed, small colonies.Barcode in the beginning of the second read - ACATCG

value: small particles


title: small_rep3

description: Microcolonies encapsulated in alginate, EtOH fixed, small colonies.Barcode in the beginning of the second read - GCCTAA. Excluded due to low quality


title: big_rep2

description: Microcolonies encapsulated in alginate, EtOH fixed, big colonies.Barcode in the beginning of the second read - CACTGT


title: mEpi3_Sorted_d0

description:
47859_Mouse EpiSC day 0 in vitro
mEpiVH1.RSEM.xlsx


title: small_rep1

description: Microcolonies encapsulated in alginate, EtOH fixed, small colonies.Barcode in the beginning of the second read - TACAAG. Excluded due to low quality.


title: total_rep3

description: Microcolonies encapsulated in alginate, EtOH fixed, not sorted.Barcode in the beginning of the second read - GTAGCC

value: non-sorted particles


title: shH3.3A_rep2

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

country: France

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

description: library strategy: Ribo-Zero RNA-seq

data_processing:
Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).
The libraries were loaded in the flow cell at 7 pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads following Illumina's instructions.
Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2.
Reads were mapped onto the mm9 assembly of the mouse genome by using Tophat2 and the bowtie aligner3.
Quantification of gene expression was performed using HTSeq-0.5.4p3 (http://www-huber.embl.de/users/anders/HTSeq) and gene annotations from Ensembl release 67.
Read counts have been normalized across librairies with the statistical method proposed by Anders and Huber4 and implemented in the DESeq Bioconductor library.
Genome_build: mm9
Supplementary_files_format_and_content: Processed expression data were summarized in a single tab-delimited text file containing the following informations: gene name (c1), Gene description (c2), Ensemble_gene_id (c3), shControl_rep1 raw read count (c4), shControl_rep2 raw read count (c5),  shH3.3A_rep1 raw read count (c6),  shH3.3A_rep2 raw read count (c7), shControl_rep1 normalized read count (c8), shControl_rep2 normalized read count (c9), shH3.3A_rep1 normalized read count (c10),  shH3.3A_rep2 normalized read count (c11), log2foldchange (c12), p-value (c13), p-value adjusted for multi-testing (c14).

source_name: Mouse embryonic fibroblasts (MEFs)

growth_protocol: MEFs are grown in glutamine and pyruvate containing DMEM, supplemented with 10% serum, 1% penicillin-streptomycin

extract_protocol:
RNA samples were purified using standard methods from subconfluent MEFs cultures.
Libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” .

treatment_protocol: 293T cells were cotransfected with with pLP1, pLP2, pLP3 and pLKO-shRNA vectors at a ratio of 1:0.5:0.6:2 respectively using Lipofectamine 2000 reagent (Invitrogen). shRNA against H3.3A mRNA (Dharmacon GE, TRCN0000012026) to knock-down H3.3A or a scrambled control shRNA as control (shControl) was used. Transfection medium was replaced the next day with fresh complete medium. Viral supernatant was collected 48hours post transfection and filtered through 0.45um filters. H3.3B-KO MEFs at ~70% confluence were infected with the viral supernatant. Infection medium was replaced the next day and cells were selected with 3μg/ml puromycin. Cells were collected 7 days later.

value: Mouse embryonic fibroblasts (MEFs)

value: shH3.3A expressing H3.3 B KO cells

value: C57BL/6 and 129S mixed genetic background

tag: age

value: MEFs were derived from E13.5 embryos


title: shH3.3A_rep1

description: library strategy: Ribo-Zero RNA-seq


title: shControl_rep2

description: library strategy: Ribo-Zero RNA-seq

value: shControl expressing H3.3 B KO cells


title: total_rep1

description: Microcolonies encapsulated in alginate, EtOH fixed, not sorted.Barcode in the beginning of the second read - CGTGAT


title: total_rep2

description: Microcolonies encapsulated in alginate, EtOH fixed, not sorted.Barcode in the beginning of the second read - AAGCTA


title: PE-22

city: Melbourne

first: Nicole

middle: Margaret

last: Haynes

state: Victoria

address: 305 Grattan Street

department: Sir Peter MacCallum Department of Oncology

institute: Peter MacCallum Cancer Centre

description: AU565(pv) tumour bearing SCID mice treated with Panobinostat + Trastuzumab (Panobinostat 15mg/kg days 0,1; Trastuzumab 10mg/kg days 0)

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the mouse reference genome (mm10) using Tophat2 with default parameters.
Counts per gene were obtained using HTSeq with mode intersection-nonempty and Ensembl gtf.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing transcript counts for each Sample

source_name: AU565(pv) human breast tumor xenograft grown in the mammary fat pad of SCID mice

growth_protocol: 1.5x1E6 AU565(pv) tumor cells were injected into the mammary fat pad of SCID mice.  Established tumours (20-25mm2) were treated as outlined below.

extract_protocol:
Whole tumors were mashed and lysed in QIAzol (Qiagen). Total RNA was extracted using a Qiagen miRNeasy Mini Kit and cleaned and concentrated using a Qiagen RNeasy MinElute Cleanup Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Vehicle and Drug treatments were administered intraperitoneally. Treatment Groups: Vehicle (D5W days 0,1; PBS days 0), Trastuzumab (D5W days 0,1; Trastuzumab 10mg/kg days 0), Panobinostat (Panobinostat 15mg/kg days 0,1; PBS days 0), Panobinostat + Trastuzumab (Panobinostat 15mg/kg days 0,1; Trastuzumab 10mg/kg days 0)

value: Whole AU565(pv) tumor:human tumour cells, mouse stroma, epithelial cells and immune cells

tag: origin

value: Mammary fat pad AU565(pv) xenograft, harvest 2-days post initiation of drug treatment

value: SCID mice


title: PE-16


title: mEpi_d4

description:
47863_Mouse EpiSC day 4 in vitro
mEpiVH1.RSEM.xlsx

value: EpiSC


title: PE-2


title: shControl_rep1

description: library strategy: Ribo-Zero RNA-seq