title: C99F5: PHF6 C99F rep5

city: SAINT LOUIS

first: Daofeng

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Technical replicate fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart.  RPKM calculated from gene counts with standard RPKM transformation with custom R scripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in txt format

source_name: cortex

extract_protocol:
Retinas were removed, flash frozen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cortex

tag: genotype

value: PHF6 C99F


title: C99F4: PHF6 C99F rep4

status: Public on Oct 30 2018

type: SRA

last: Li

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age


title: 454161_A02

type: genomic

city: Philadelphia

first: Jay

middle: S

last: Schneider

state: PA

address: 1020 Locust St

department: Anatomy,Pathology and Cell biology

institute: Thomas Jefferson University

description:
LPN - 750ppm - Methylation
MeDIP_Hippocampus

hyb_protocol: The immunoprecipitated CpG-methylated DNA (test, experimental samples) and the untreated, sonicated DNA (input DNA) were differentially labeled and hybridized to a single array as a two-color experiment (Rat DNA Methylation 3 × 720 K CpG Island Plus RefSeq Promoter Array (GPL 18610) for 20 h at 42°C, followed by washing with the Nimblegen Wash Kit.

scan_protocol: Scanning was performed with 100% gain and double pass for optimal sensitivity and scanning accuracy.

data_processing:
Raw data were extracted as pair files by NimbleScan software.  The intensity ratio of immunoprecipitated to control DNA was plotted versus genomic position to identify regions where increased signal (i.e. DNA fragment enrichment) was present relative to the control sample. The R/Bioconductor package Ringo was utilized to extract the green (Cy3, 532nm, associated to total DNA) and red (Cy5, 635nm, associated to MeDIP fraction) channels from the provided pair files.  Normalization of the probe intensities was carried out by applying the Nimblegen algorithm, following the recommendation of Adriaens et al. for ChIP-on-chip and DNA methylation microarrays (Adriaens et al., 2012).
Signals from the two channels were then summarized by calculating the log2 ratio of the MeDIP and input channels.  Being log2-ratios, a value of 1 corresponds to a two-fold enrichment of the MeDIP signal relative to total DNA, while a value of -1 is interpreted as a MeDIP signal two times smaller than the input channel. The normalized data for the control "RANDOM" probes are available on the series record.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: MeDIP DNA_LPN - 750ppm - Methylation

label_protocol: Experimental (IP) samples were labeled with Cy5 and control (input) samples with Cy3.

extract_protocol: Genomic DNA was extracted from hippocampus tissue samples using PureGene DNA isolation kits.

tag: Sex

value: Male

value: hippocampus

value: Long-Evans

source_name: Input DNA_LPN - 750ppm - Methylation


title: Nhp10_YPD30_Nhp10-A_3426_input

city: Seattle

first: Sam

last: Cutler

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch Cancer Research Center

library_source: genomic

data_processing:
Align with bowtie: $ bowtie2 -x <reference-genome> -U <file>.fastq -S <file>-mapped.sam
Filter and sort with samtools: $ samtools view -S -b -o <file>mapped_unique.bam -F 256 <file>mapped.sam       $ samtools sort <file>unique.bam <file>mapped_unique_sorted
Generate coverage file with genomecoveragebed: $ genomeCoverageBed -d -ibam <file>sorted.bam -g <file>.fastq > <file>coverage.sgr    --> .sgr coverage file has 3 columns, column 1 = chromosome (chrI, chrVI, etc.), column 2 = basepair, column 3 = signal at that basepair
Custom Python script that calculates the average read depth at each base pair in the genome, and divides the signal at each base pair by that value, thus normalizing each sample for read depth.
Custom Python script that calculates the ratio between the normalized signal at each base pair in the IP sample relative to the matched input sample.
Genome_build: Saccharomyces_cerevisiae.EF4.65.gtf

organism: Saccharomyces cerevisiae

source_name: Asynchronous growth in liquid YPD

growth_protocol: Saturated YPD cultures were inoculated into 70 ml fresh YPD and then shaken overnight at 180 RPM at 30 degrees C, and then cells were collected at mid-log phase, OD660 ~ 0.5-0.8.

extract_protocol:
Cells were broken by bead-beating, chromatin was sonicated, stored in FA buffer.
Libraries prepared with Nugen Ovation Ultralow System V2 (catalog # 0344-32).

treatment_protocol: Collected cells were formaldehyde cross-linked, washed in TBS.

tag: chip antibody

value: none (input)


title: 454256_A01


title: C99F3: PHF6 C99F rep3


title: C99F2: PHF6 C99F rep2


title: BALF_IMM2

city: San Francisco

first: Heather

middle: H

last: Pua

state: CA

address: 513 Parnassus Ave, HSE-201, Box 0997

institute: UCSF

data_processing:
data filtering step: Data was demultiplexed and adapters trimmed using FastX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and cutadapt (Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10.)
alignment: Sequence alignment and small RNA read counts were obtained using the exceRpt small RNA-seq Pipeline (v4) (https://www.genboree.org/epigenomeatlas/genboreeWorkbench.rhtml).
expression analysis: Comparative expression analysis was performed with DESeq2 (PMID:25516281)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain raw read counts from the exceRpt small RNA-seq Pipeline. The supplementary file DESeq2norm_AAexRNA_rpm contains DESeq2 normalized rpm counts for each sample.

source_name: Bronchoalveolar Lavage Fluid

extract_protocol:
Bronchoalveolar lavages were performed with 1 ml of cold PBS. BAL fluid was centrifuged at 500 g for 5 minutes to separate cell free BALF supernatant
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
Biofluids were lysed in Trizol LS and cells lysed in Trizol, and total RNA collected by precipitation.
20-65ng of total RNA was used to build miRNA librarires as previously described (PMID 23440203) with slight modification. Five random nucleotides were added to the 5’ end of the 3’ oligodeoxynucleotide adapterto reduce ligation bias. A mix of calibrators 1, 2, 3, 4 and 7 from the orginal publication were used at a final combined concentration of 0.025nM in the 3’ ligation reaction.

treatment_protocol: Mice were injected intraperitoneally weekly for 3-4 weeks with 50 ug ovalbuminin 100 ul of PBS plus 100 ul of Imject alum. Starting 7 days after the last injection, mice were challenged daily by oropharyngeal aspiration of 20 ul of PBS alone for three consecutive days. Specimens were collected on day 4 after the first lung challenge.

value: Lung

tag: tissue biofluid

value: Bronchoalveolar Lavage Fluid

tag: treatment group

value: intrapertioneal immunization


title: WT-KI5: WT for C99F rep5

value: WT for C99F


title: 454145_A01

value: Female


title: WT-KI4: WT for C99F rep4


title: WT-KI3: WT for C99F rep3


title: WT-KI1: WT for C99F rep1


title: Isw2_YPD30_Isw2-B_1997_IP

value: Sigma anti-FLAG monoclonal (F3165)


title: E11.5 Cont heart, Biological Rep 6

type: RNA

city: London

first: Timothy

middle: J

last: Mohun

address: The Ridgeway, Mill Hill,

department: Developmental Biology Division

country: United Kingdom

institute: MRC National Institute for Medical Research

description: Gene expression data from a single heart from Nkx2-5+/IRES-CRE mouse (Sibling control)

hyb_protocol: As per standard Affymetrix protocol for the Mouse Gene 1.0 ST Array.

scan_protocol: Arrays were scanned using the Affymetrix Scanner 3000.

data_processing: Log2 transformation and Robust Multichip Average (RMA) normalization method was applied using Expression Console software using the following parameters: affymetrix-algorithm-param-apt-opt-analysis-spec=rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, subsetmd5=79d5db3133f5267f6c61d65ecbaaf825,pm-only,med-polish, expon=false, attenuate=true, l=0.005, h=-1,expr, genotype=false, strand=false.

label: biotin

source_name: E11.5 heart, Nkx2-5+/IRES-CRE

label_protocol: 100ng of total RNA was labeled and hybridized to Affymetrix mouse GeneChip® Mouse Gene 1.0 ST Array as per manufacturer's instructions.

extract_protocol: Total RNA was extracted from individual hearts using Trizol according to the manufacter's instructions (Invitrogen).

tag: organ

value: heart

value: cardiac

tag: developmental stage


title: E11.5 Cont heart, Biological Rep 4


title: WT-KI2: WT for C99F rep2


title: KO4: PHF6 KO rep4

value: PHF6 KO


title: 454198_A02


title: E11.5 Cont heart, Biological Rep 3


title: C99F1: PHF6 C99F rep1


title: KO3: PHF6 KO rep3


title: 454144_A03


title: 454008_A03

description:
LPN- Control - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_LPN- Control - Methylation

source_name: Input DNA_LPN- Control - Methylation


title: 453950_A01


title: KO1: PHF6 KO rep1


title: E11.5 Cont heart, Biological Rep 5


title: KO2: PHF6 KO rep2


title: WT3: WT rep3

value: WT


title: WT2: WT rep2


title: E11.5 hypo heart, Biological Rep 6

description: Gene expression data from a single heart from hypomorphic Nkx2-5 mouse (Nkx2-5gfp/IRES-CRE)

source_name: E11.5 heart, Nkx2-5gfp/IRES-CRE


title: E11.5 Cont heart, Biological Rep 1


title: WT1: WT rep1


title: E11.5 hypo heart, Biological Rep 5


title: WT4: WT rep4


title: E11.5 Cont heart, Biological Rep 2


title: CD45+ cells from tumor microenvironment of aPD1 and aCTLA4 treated mice

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v1.3.1)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v1.3.1)
barcode processing, Cell Ranger Single Cell Software Suite (v1.3.1)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v1.3.1)
alignment, Cell Ranger Single Cell Software Suite (v1.3.1)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: CD45+ cells from tumor microenvironment of aPD1-aCTLA4 treated mice

extract_protocol:
Mice were treated intraperitoneally with 200 μg anti-PD-1 (RMP1-14) or anti-CTLA-4 (9D9), used alone or in combination on days 3, 6, and 9 post-tumor transplant.  For controls, mice were injected with 200 μg of rat IgG2a isotype control antibody. Established tumors were excised from mice, minced and treated with 1 mg/ml type IA collagenase (Sigma) in HBSS (Hyclone) for 1 h at 37 °C.  Cells were washed thrice.  Red blood cells were lysed using red blood cell lysis buffer (Sigma).  To remove aggregates and clumps, cells were filtered through a 40-micron strainer. Antibodies were diluted in PBS prior to injection for a total volume of 0.5 ml per mouse. For sorting of intratumoral CD45+ cells, single cell suspensions of digested tumor were stained for 5 minutes at room temperature with 500 ng of Fc block (anti-CD16/32) and then stained with anti-CD45-PerCP/Cy5.5 (Biolegend) (1:400) plus Zombie NIR Viability dye (Biolegend) (1:500) in 100 µl of staining buffer (PBS with 2% FCS) for 30 minutes at 4 °C.  Sorting of live CD45+ cells was performed on a BD FACSAria II (BD Biosciences). The purity of the sorted cells for single cell RNA sequencing was greater than 96% as assessed during post-sort cellular analysis.
Droplet-based 3′ end massively parallel single-cell RNA sequencing (scRNAseq) was performed by encapsulating sorted live CD45+ tumor infiltrating cells into droplets and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v1 according to manufacturer’s protocol (10x Genomics).  The generated scRNAseq libraries were sequenced using an Illumina HiSeq2500. 14x98nt read lengths were used.

tag: mouse genotype

value: wt

value: Cd45+ cells


title: CD45+ cells from tumor microenvironment of aCTLA4 treated mice


title: 453777_A03


title: CD45+ cells from tumor microenvironment of IgG2a isotype control antibody treated mice


title: E11.5 hypo heart, Biological Rep 4


title: 453916_A01

description:
LPN - Control - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_LPN - Control - Methylation

source_name: Input DNA_LPN - Control - Methylation


title: 454074_A01


title: 453954_A01


title: Tumor2-spleen

city: Charlestown

first: Jin Mo

last: Park

state: MA

address: 149 Thirteenth Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description: Splenic erythroid cells

data_processing:
The splice-aware alignment program STAR was used to map the sample sequencing reads to a mus musculus (assembly mm10) reference genome file.
Gene expression counts in counts per million were calculated using the program HTSEQ based on the most current Ensembl annotation file for mm10 .
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for control versus duplicated test groups

source_name: Tumor-bearing mouse rep2

growth_protocol: Bone marrow from untreated mice and spleens from UVB-irradiated or tumor-bearing mice were used for isolating erythroid cell purification.

extract_protocol:
mRNA was isolated from erythroid cells using Trizol reagent and polyA selection. An Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The mice were left untreated (steady-state bone marrow), irradiated with topical UVB (50 mJ/cm2), or subjected to subcutaneous injection of B16 melanoma cells for tumor formation.

tag: cell type

value: Erythroid cells

value: Spleen


title: 454148_A03

description:
EPN - 150ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_EPN - 150ppm - Methylation

value: hippocampus

source_name: Input DNA_EPN - 150ppm - Methylation


title: UVB2-spleen

description: Splenic erythroid cells

source_name: UVB-irradiated mouse rep2


title: Tumor1-spleen

description: Splenic erythroid cells

source_name: Tumor-bearing mouse rep1


title: 454199_A02

value: Long-Evans


title: UVB1-spleen

description: Splenic erythroid cells

source_name: UVB-irradiated mouse rep1


title: 454432_A01

value: Male


title: Control_BM

description: Bone marrow erythroid cells

source_name: Steady-state control mouse

value: Bone marrow


title: E11.5 hypo heart, Biological Rep 1


title: d14-2

city: TianJin

first: Hua

middle: Jin

last: Liu

address: 288 Nanjing Road

department: State Key Laboratory of Experimental Hematology

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use HISAT2  to map clean reads to genome reference and transcript  references
genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by STRINGTIE
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: erythroid differentiation at day 14

growth_protocol: CD34+ cells cultured in IMDM medium supplemented with 20% BIT,5ng/ml IL-3, 100 ng/ml  SCF ,10^-6 M Hydrocortisone and 3 U/ml human EPO for 8 days. From days 8 through 14, SCF and EPO were included in the culture medium

extract_protocol:
CD34+ drived erythroid cells  cells was collected and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source cell type

value: CD34+ cells

tag: culture day

value: cord blood CD34+ derived erythroid cells


title: 453955_A02


title: d11-2

source_name: erythroid differentiation at day 11


title: CD45+ cells from tumor microenvironment of aPD1 treated mice


title: 454151_A01


title: d14-1


title: d11-1


title: 454008_A02


title: 453902_A02


title: d8-2

source_name: erythroid differentiation at day 8


title: d8-1


title: 454148_A02


title: E11.5 hypo heart, Biological Rep 2


title: d4-1

source_name: erythroid differentiation at day 4


title: d4-2


title: 454259_A03


title: HeLa-NaBH4 treated-smRNA-rep3

city: Copenhagen N

first: Jeppe

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

description:
Small RNA libraries were prepared using “The NEBNext Multiplex Small RNA” kit according to manufactures protocol
human_tRNA_out.txt

data_processing:
Sequencing reads were processed with Cutadapt (version 1.14) to remove adapter sequences using the setting -a AGATCGGAAGAGCACACGTCT. For reads generated nextseq platform, the option --nextseq-trim=20” was included.
All samples (except small RNA-Seq experiments): The RNAProbR preprocessing.sh script (http://people.binf.ku.dk/~jvinther/data/rna_probing/) was used to remove the 7 base barcode from the sequencing read using the options “-b NNNNNNN -t 9”
Reads were aligned with bowtie2 (version 2.2.3) using high sensitivity options “--local -N 1 -D 20 -R 3 -L 15”
All samples (except small RNA-Seq experiments): Potential PCR duplicates among the sequencing reads were removed by discarding all but one of the reads having identical barcode and mapping to the same position using the collapse.sh script (available at http://people.binf.ku.dk/jvinther/data/RNA-seq).
The mapped reads for the control and NaBH4 treated samples were processed with the mpileup tool from the samtools package (version 1.7).
Genome_build: E. coli strain bw25113 (ensembl cDNA release 87), S. cerevisiae (ensembl cDNA release 84). rRNA sequences were obtained were obtained from the CRW database (http://www.rna.ccbb.utexas.edu). tRNA sequences were obtained from the genomic tRNA database (http://gtrnadb.ucsc.edu/index.html).
Supplementary_files_format_and_content: The mutation frequency file is the output from the GetFreq function (available at https://github.com/jeppevinther/m7g_map_seq) includes a number of statistics for each position, including coverage,  mutation frequency for the treated and control samples and the mutation rate difference between the treated and control samples. It includes p-values for the observed mutation rates being different in the treated and the control samples and for the replicate samples being different.

source_name: HeLa

extract_protocol:
Hot acid phenol extraction
RNA-seq: Methods in molecular biology, 1038, 213-231 (2013) with RNA fragmentation step included.  Small RNA-seq: NEBNext Multiplex Small RNA Kit.

value: HeLa

tag: nabh4 treatment

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: HeLa-NaBH4 treated-smRNA-rep2


title: HeLa-untreated-smRNA-rep2


title: HeLa-NaBH4 treated-smRNA-rep1


title: HeLa-untreated-smRNA-rep3


title: AT-MSC-3

city: Helsinki

first: Sippy

last: Kaur

address: PO Box 63

department: Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.).
Reads were mapped using Bowtie 2 software according to the Exiqon NGS Service microRNA/smallRNA pipeline. First, reads aligned to spike-ins or abundant sequences were discarded. Second, reads were aligned to miRBase 20. Third, unaligned reads were aligned to miRNA and smRNA loci in GRCh37 reference genome. Reads aligned to miRNA loci were combined with reads aligned to miRBase.
Genome_build: GRCh37
Supplementary_files_format_and_content: mirna_raw_counts.txt: tab-delimited text file including miRNA raw counts for all samples, smrna_raw_counts.txt: tab-delimited text file including other smRNA raw counts for all samples

source_name: Mesenchymal stem cell extracellular vesicles

extract_protocol:
EVs were isolated from 3 ml conditioned cell culture media using miRCURY™ Exosome Isolation kit (Exiqon A/S) followed by RNA isolation using miRCURY™ RNA Isolation Kits - Cell & Plant (Exiqon A/S).
The library preparation was done using the NEBNext® Small RNA Library preparation kit (New England Biolabs). A total of 6 μl isolated RNA was converted into microRNA NGS libraries. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent). Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The pool was then size selected using the LabChip XT (PerkinElmer) aiming to select the fraction with the size corresponding to microRNA libraries (~ 145 nt). The library pool were then sequenced on a NextSeq 500 sequencing instrument according to the manufacturer instructions.

tag: sex/karyotype

value: XX

tag: passage

tag: source/details

value: Adipose tissue (Thigh)

tag: bmi


title: 453902_A01

tag: tissue

tag: strain


title: 454199_A01

tag: Sex


title: 454431_A03

value: Female


title: HeLa-untreated-smRNA-rep1


title: AT-MSC-2

value: Adipose tissue (Abdominal flanks)

tag: age


title: E11.5 hypo heart, Biological Rep 3

source_name: E11.5 heart, Nkx2-5gfp/IRES-CRE

value: heart

value: cardiac

tag: genotype


title: hPSC-2

source_name: Induced pluripotent stem cell extracellular vesicles

value: Skin/Sendai


title: AT-MSC-1


title: hPSC-1

source_name: Embryonic stem cell extracellular vesicles

value: Blastocyst


title: 454008_A01


title: LM.sh2187_hypoxia/low glucose, 48hr [8508853080_F]

city: Memphis

first: Meiyun

last: Fan

address: 19 S. Manassas Street

institute: University of Tennessee

hyb_protocol: Biotinylated cRNA were hybridized to the Illumina array per manufacturer's instructions

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina Genome Studio software was used for data processing: background subtraction and Quantile normalization

label: Biotin

source_name: LM.sh2187_hypoxia/low glucose, 48hr

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: cells were maintained in in DMEM/F12 medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% FBS, 100 units/ml penicillin, 100 µg/ml streptomycin, 10 mg/ml fungin (InvivoGen, San Diego, CA) and 2 ug/ml puromycin.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: cells were untreated or exposed to hypoxia (1% O2)/low glucose (1 mg/ml) for 6 or 48 hr.

tag: cell line

value: LM

value: lung metastatic subline of MDA-MB-231

tag: transfected with

value: MISSION shRNA (TRCN0000232187) to knockdown BHLHE40

tag: treated with

value: hypoxia/low glucose, 48hr


title: LM.sh2187_untreated [8508853080_D]

value: none (untreated)


title: 454201_A01

description:
EPN - 375ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_EPN - 375ppm - Methylation

value: hippocampus

value: Long-Evans

source_name: Input DNA_EPN - 375ppm - Methylation


title: 454199_A03

value: Male


title: 454431_A02

source_name: MeDIP DNA_EPN - 150ppm - Methylation

source_name: Input DNA_EPN - 150ppm - Methylation


title: LM_hypoxia/low glucose, 48hr [8508853080_C]

source_name: LM_hypoxia/low glucose, 48hr

value: control vector


title: 454157_A03


title: LM.sh2187_hypoxia/low glucose, 6hr [8508853080_E]

source_name: LM.sh2187_hypoxia/low glucose, 6hr

value: hypoxia/low glucose, 6hr


title: 453902_A03


title: 454202_A02


title: LM_hypoxia/low glucose, 6hr [8508853080_B]

source_name: LM_hypoxia/low glucose, 6hr


title: 454436_A02


title: PCOS, biological rep1

city: Shanghai

first: Jun

last: Zhao

address: 845 Lingshan Road

department: Renji Hospital, School of medicine

institute: Shanghai Jiao Tong university

description: Gene expression data from granulosa cells of PCOS patients

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

data_processing: The data were analyzed by the Expression Console software of Affymetrix at gene level and exon level respectively.

source_name: granulosa cells from PCOS patients

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Ovarian stimulation and oocyte retrieval were performed under gonadotropin-releasing hormone (GnRH) antagonist protocol. After adequate follicle development (detecting by ultrasound scan and serum estradiol assay), human chorionic gonadotropin (Lvzhu, Zhuhai, China) was administered to trigger ovulation. Ultrasound-guided oocytes retrieval was performed 36 hours later.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The follicular fluid was pooled and centrifuged at 2500 rpm for 15 minutes, then the pellet were resuspended in PBS and dispersed in 0.1% hyaluronidase (Sigma Chemical Co, St-Louis, MO) at 37°for 15 minutes. After that, granulosa cells were purified by Ficoll-Paque (GE-Health Care Bio-Science, Uppsala, Sweden), and rudimental red blood cells were removed by lysis buffer.

value: granulosa cells

value: female

tag: diagnosis

value: Polycystic Ovary Syndrome (PCOS)


title: Normal, biological rep3

description: Gene expression data from granulosa cells of non-PCOS patients

source_name: granulosa cells from normal patients

tag: cell type

value: healthy control


title: LM_untreated [8508853080_A]


title: 454157_A02


title: 453903_A01

value: Female


title: 454139_A01


title: Normal, biological rep2


title: 454436_A01


title: 454197_A02

description:
EPN - 750ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_EPN - 750ppm - Methylation

source_name: Input DNA_EPN - 750ppm - Methylation


title: 453955_A01


title: 454201_A03


title: Osteoblasts_2

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
Fastq files were aligned to the mouse reference (GRCm38) using HISAT2 v 2.0.5 (https://ccb.jhu.edu/software/hisat2/index.shtml) with an SNP aware reference index (genome_snp).
SAM files were sorted and converted to BAM files using samtools v 1.7 -sort (http://samtools.sourceforge.net/)
Gene-level quanitification was performed using an Ensembl GTF with Stringtie v1.3.3.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text file for each sample contains the following columns 1) Ensembl gene ID, 2) Gene name, 3) Reference, 4) Strand, 5) Start, 6) End, 7) Coverage, 8) FPKM, and 9) TPM

source_name: bone marrow-derived osteoblasts

growth_protocol: One or both femurs from a given mouse were aseptically isolated, denuded of soft tissue and the marrow extracted by removing the proximal end of each bone and centrifuging at 2000 xg for 30 s such that the marrow collects into 25 µl of fetal bovine serum (FBS). Exudates from a single femur were dispersed, via trituration, in 5ml complete media (MEM-alpha, 10% FBS, 100U penicillin/100ug Streptomycin per ml, 2 mM glutamine). Cells were manually counted where upon 4 million were used to seed a 10 cm dish for CFU-F determination and the remainder were applied to a 60mm dish. Media on the 60 mm dishes was changed on day 2 with cells removed via trypsin/EDTA (Gibco) digestion on day 4.  Detached cells were triturated in 5 ml complete media, pelleted at 1000 xg for 5 min., re-suspended in 1 ml complete media and counted where upon 150,000 cells were used to seed a well of a 12 well dish.  A minimum of 2 wells per sample were obtained for all samples reported here in.  Osteoblast differentiation was initiated 3 days after plating (7 days after bone marrow isolation) by replacing the media with complete media supplemented with 50 µg/ml ascorbic acid, 10 mM beta-glycerophosphate and 10 nM dexamethasone. Media was changed every other day for 8 days at which time cells were either used as a source for RNA (mirVana, Thermo Fisher) or used to determine the amount of hydroxyapatite formed during differentiation.

extract_protocol:
Total RNA was then isolated from bone and BMSC-derived osteoblasts using RNeasy Plus Mini Kit (Qiagen) .
RNA-Seq libraries were constructed using TruSeq RNA Library Prep Kit v2 sample prep kits (Illumina).

tag: strain info

value: osteoblasts


title: Osteoblasts_3


title: 454201_A02


title: LM.sh2187_hypoxia/low glucose, 48hr [8508853057_J]


title: 454257_A01


title: 454145_A03


title: Bone_3

source_name: cortical bone from femur minus marrow

value: bone


title: Bone_1


title: LM_hypoxia/low glucose, 48hr [8508853057_I]

value: LM


title: Bone_2


title: 454120_A03


title: 454145_A02


title: LM_hypoxia/low glucose, 6hr [8508853057_E]

value: lung metastatic subline of MDA-MB-231


title: HeLa-NaBH4 treated

description:
Libraries were prepared from polyA enriched RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The
hela_wt_rrna_out.txt

source_name: HeLa

value: HeLa

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: mESC_3'SS library_SF3B1-K700K_RNA-seq_ALL

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

description:
mESC_SF3B1_K700E_RNA_ALL
processed data file:
A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI.MATS.ReadsOnTargetAndJunctionCounts.txt
SE.MATS.ReadsOnTargetAndJunctionCounts.txt

data_processing:
For 293T files, A reference minigene file were made using the R1 and barcoded R2 reads from the DNA seq
The fastq files (Wildtype,Mutant) generated from RNA sequencing were locally aligned using blastn 2.6.0+  with the reference sequence file to get the splice junctions in each minigenes
A single file was created combining the witltype and mutatnt alignemnt results, the splice positions and Splicing fraction was determined fro SA1,SA2,SA_cryptic
Kmers were generated (n=6) of all possible combination and the odds ratio of these Kmers were predicted using custom made scripts
The branch point prediction was done by RNAcofold(ViennaRNA-2.3.5 suit)/LaBrachoR/RNAhybrid-2.1.2
mESC_RNA samples were aligned to mm9 using STAR Aligner
Aligned bam files were used for differential splicing analysis using rMATS
Supplementary_files_format_and_content: tab seperated text files were generated for Human and Mouse

source_name: mouse embryonic stem cells

growth_protocol: HEK293T cells were grown in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1X penicillin/streptomycin (Gibco). mESC were grown in DMEM (Gibco 11965) supplemented with 15% FBS (Gemini Bio) and 1x penicillin/streptomycin (Gibco) in tissue culture dishes coated with 0.1% gelatin.

extract_protocol:
For RNA-seq cells were harvested 48 hr of transfection using RNAEasy kit (Quiagen) followed by DNAse digestion (Ambion, Turbo) as per manufacturer's instructions. For protein cells were lysed in 1X RIPA buffer ( 10mM Tris-Cl(pH 8.0), 1mM EDTA, 0.5 mM EGTA, 1% Triton X-100. 0.1% sodium deoxycholate) supplemented wuth protease inhibitor ( Roche).
Illumina compatible RNA and DNA  libraries were generated using custom primers specific to mini-gene library using 1X NEB high fidelity master mix.

treatment_protocol: HEK293t cells were transiently co-transfected with mini-gene plasmid library along with either SF3B1-WT or SF3B1-K700E plasmid. Mini-gene plasmid library were transiently transfected in isogenic cell lines of mouse embryonic stem cell generated using crispr-cas9.

tag: cell line/type

value: mouse embryonic stem cells

tag: minigene library

value: 3'SS library

tag: sf3b1 mutation


title: HeLa-untreated

tag: nabh4 treatment


title: Osteoblasts_1


title: LM.sh2187_hypoxia/low glucose, 6hr [8508853057_F]

value: MISSION shRNA (TRCN0000232187) to knockdown BHLHE40


title: 453903_A03

value: hippocampus

value: Long-Evans


title: PCOS, biological rep2


title: PCOS, biological rep3


title: 454197_A01

value: Male


title: Control (miRNA-seq)

city: Bangalore

first: Nisha

state: Karnataka

address: EPIP Zone, Whitefield

department: Department of Periodontics

country: India

institute: Vydehi Institute of Dental sciences and Research Centre

data_processing:
Illumina Casava1.9 software used for basecalling.
Alignment of clean reads for both case & control with RNAcentral (non-coding RNA sequence database) release 7 database was done separately using blast algorithm.
Data were filtered using the following specifications…
The blast alignment result was filtered using parameters such as reads with read length <= 26bp, should have query coverage of 100% with < 2nt mismatch & 0nt gap whereas reads with read length > 26bp should have query coverage of 100% with <= 3nt mismatch & < 2nt gap to get annotated as other small RNA type.The unaligned and blast result filtered out reads were considered as putative candidate for miRNA identification.
The putative miRNA reads with read length 16-28 bp were used for known & novel miRNA identification. Both the sample (case & control) putative miRNA reads (16-28bp) were aligned with mature (animal) miRNAs sequence using java-based UEA Small RNA Workbench version 2.4 analysis tool mirProf for known miRNA identification & mirCat for Novel miRNA prediction using standard default animal parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content:
[miRNA-Expression.txt]  miRNA Expression Case & Control
[Known-miRNA-Case-vs-Control.txt]  Differential analysis of salivary microRNA profiles in healthy and chronic periodontitis patients.

source_name: Saliva

extract_protocol:
Saliva was collected from patient diagnosed with chronic periodontitis and an age and sex-matched healthy individual which served as the control using passive drool method. Total RNA was isolated from the two saliva (human) sample case & control using Trizol (Invitrogen,CA, USA) according to the manufacturer’s protocol.
The RNA quality was evaluated by electrophoresis on a 1% agarose gel. RNA quantity and quality were examined using Nanodrop spectrophotometer and Agilent 2100 bioanalyzer system respectively. All materials and solutions were handled in RNase-free conditions. All solutions were prepared in RNase-free water. The purified RNA from both the sample was used to prepare small RNA libraries separately according to the TruSeq Small RNA Sample preparation kit (Illumina) instructions. Fifty base pair (bp), single end sequencing was performed using the HiSeq 2000 instrument (Illumina).

tag: disease state

value: control

tag: rna source

value: saliva


title: 293T_3'SS library_SF3B1-K700E_RNA-seq_selected

description:
293T_SF3B1_WT_RNA_SELECTED
processed data file:
Minigenes_List.txt.gz


title: LM.sh2187_untreated [8508853057_B]

value: none (untreated)


title: 453903_A02

tag: tissue


title: LM_untreated [8508853057_A]

value: control vector


title: Normal, biological rep1

value: granulosa cells

value: female

value: healthy control


title: AFB208

city: Paris

first: Lucas

middle: Theo

last: Husquin

state: --- Select a state ---

address: 28 rue du docteur Roux

department: Genetics and Genomics

country: France

institute: Institut Pasteur

description: SAMPLE 156

hyb_protocol: Bisulfite converted DNAs were hybridized to beadchips provided the Illumina Infinium MethylationEPIC BeadChip Kit

scan_protocol: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus

source_name: CD14+ Monocytes, resting cells

label_protocol: Sample barcoding and staining were carried out by following the instructions of Illumina provided in the Infinium MethylationEPIC BeadChip Kit

growth_protocol: Monocyte DNA samples were obtained from PBMCs frozen in 90% fetal calf serum (FCS) and 10% dimethyl sulfoxide  dimethyl sulfoxid

extract_protocol: Each DNA sample was extracted from 2x106 primary monocytes by a standard phenol/chloroform protocol followed by ethanol precipitation. Prior to DNA methylation profiling, DNAs were then bisulfite converted and processed using the Illumina Infinium MethylationEPIC BeadChip Kit, according to the manufacturer's instructions  followed by ethanol precipitation

treatment_protocol: Primary monocytes were positively selected with magnetic CD14 microbeads from Miltenyi Biotec, according to the manufacturer's instructions

tag: gender

tag: batch

tag: ethnicity

value: African descent


title: EUB073

description: SAMPLE 155

data_processing: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus

tag: age

value: European descent


title: 454256_A03

tag: Sex

tag: strain


title: 293T_3'SS library_SF3B1-WT_RNA-seq_selected

description:
293T_SF3B1_K700E_RNA_SELECTED
processed data file:
Minigenes_List.txt.gz

value: wild-type


title: 293T_3'SS library_SF3B1-WT_RNA-seq_ALL

description:
293T_SF3B1_K700E_RNA_ALL
processed data file:
Minigenes_List.txt.gz


title: mESC_3'SS library_SF3B1-K700E_RNA-seq_ALL

description:
mESC_SF3B1_K700K_RNA_ALL
processed data file:
A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
RI.MATS.ReadsOnTargetAndJunctionCounts.txt
SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: 453954_A03


title: Case (miRNA-seq)

value: chronic periodontitis


title: 454202_A01

source_name: MeDIP DNA_EPN - 375ppm - Methylation


title: AFB211

description: SAMPLE 153


title: Carnegie stage 22 _HET haplotype Rep 2

city: Baltimore

first: Sumantra

last: Chatterjee

state: MD

address: 733 N Broadway, Room 572

department: Institute of Genetic Medicine

institute: Johns Hopkins University School of Medicine

data_processing:
Trimmomatic was used to trim Illumina adaptor sequences from the fastq files
The files were then mapped to the human genome hg19 index file uisng Tophat2 with the following attributes --library-type fr-unstranded -G (unstranded and pair end)
Successfully mapped reads were used to assemble transcripts using UCSC annotations and estimate their abundances ((FPKM) using Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: Cufflink output file  showing FPKM values for each gene for all 3 haplotypes. Replicates have been merged

source_name: Gut (stomach and intestine)

extract_protocol:
Guts were dissected out, from tissues donated to Human Developmental Biology Resource (HDBR) and RNA was extracted and cleaned using a Trizol-Rneasy column hybrid method
cDNA  was prepared  by oligo dT beads to select mRNA from the total RNA sample followed by heat fragmentation and cDNA synthesis from the RNA template as part of the Illumina Tru Seq™ RNA Sample Preparation protocol. The resultant cDNA then was used for library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using standard Illumina protocols.

value: Gut (stomach and intestine)

tag: developental stage

value: Carnegie stage 22

tag: ret haplotype

value: Heterozygous (RS haplotype)


title: EUB014

description: SAMPLE 152


title: Carnegie stage 22 _HET haplotype Rep 1


title: EUB088

description: SAMPLE 151


title: Carnegie stage 22 _NULL haplotype Rep 1

value: Null (SS haplotype)


title: Carnegie stage 22 _WT haplotype Rep 2

value: Wildtype (RR haplotype)


title: Carnegie stage 22 _WT haplotype Rep 1


title: EUB156

description: SAMPLE 150

value: Male


title: EUB067

description: SAMPLE 154


title: Carnegie stage 22 _NULL haplotype Rep 2


title: AFB163

description: SAMPLE 149


title: 453955_A03

description:
EPN - Control - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_EPN - Control - Methylation

value: Female

value: hippocampus

value: Long-Evans

source_name: Input DNA_EPN - Control - Methylation


title: 293T_3'SS library_SF3B1-K700E_RNA-seq_ALL

description:
293T_SF3B1_WT_RNA_ALL
processed data file:
Minigenes_List.txt.gz

value: 3'SS library


title: AFB026

description: SAMPLE 148


title: 454139_A03


title: AFB192

description: SAMPLE 143


title: 453899_A03


title: 454151_A03

description:
Perinatal - 150ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_Perinatal - 150ppm - Methylation

source_name: Input DNA_Perinatal - 150ppm - Methylation


title: EUB081

description: SAMPLE 142


title: EUB062

description: SAMPLE 147


title: EUB166

description: SAMPLE 145


title: 454436_A03


title: AFB018

description: SAMPLE 141


title: 454139_A02


title: 453914_A03


title: 454149_A02


title: AFB070

description: SAMPLE 146


title: EUB176

description: SAMPLE 140


title: AFB170

description: SAMPLE 144


title: wt2_unstim_rep. 2

city: Vienna

first: Alexander

last: Swoboda

state: Vienna

address: Waehringer Strasse 13a

country: Austria

institute: Ludwig Boltzmann Institute for Cancer Research

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions, by the Core Facility Genomics, Medical University Vienna, Vienna, Austria.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: murine melanoma cell line, unstim, 2h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA, by the Core Facility Genomics, Medical University Vienna, Vienna, Austria.

growth_protocol: Cells were grown in standard DMEM medium, containing 10% FBS and 1% penicillin and streptomycin.

extract_protocol: Total RNA was isolated by trizol extraction from murine melanoma cells followed by purification facilitating a RNeasy Plus Mini kit both performed according to the manufacturer's instructions.

treatment_protocol: Cells were serum starved over night and stimulated with 5ng/ml IL-6 or 10ng/ml OSM for two hours.

value: lymph node derived melanoma cell line

tag: treatment


title: AFB161

description: SAMPLE 139


title: wt2_unstim_rep. 1


title: wt2_OSM_rep. 2

source_name: murine melanoma cell line, OSM stim, 2h

value: OSM


title: wt2_OSM_rep. 1


title: 454428_A02

first: Jay

institute: Thomas Jefferson University

data_processing:
Raw data were extracted as pair files by NimbleScan software.  The intensity ratio of immunoprecipitated to control DNA was plotted versus genomic position to identify regions where increased signal (i.e. DNA fragment enrichment) was present relative to the control sample. The R/Bioconductor package Ringo was utilized to extract the green (Cy3, 532nm, associated to total DNA) and red (Cy5, 635nm, associated to MeDIP fraction) channels from the provided pair files.  Normalization of the probe intensities was carried out by applying the Nimblegen algorithm, following the recommendation of Adriaens et al. for ChIP-on-chip and DNA methylation microarrays (Adriaens et al., 2012).
Signals from the two channels were then summarized by calculating the log2 ratio of the MeDIP and input channels.  Being log2-ratios, a value of 1 corresponds to a two-fold enrichment of the MeDIP signal relative to total DNA, while a value of -1 is interpreted as a MeDIP signal two times smaller than the input channel. The normalized data for the control "RANDOM" probes are available on the series record.

extract_protocol: Genomic DNA was extracted from hippocampus tissue samples using PureGene DNA isolation kits.


title: wt2_IL-6_rep. 2

source_name: murine melanoma cell line, IL-6 stim, 2h


title: wt2_IL-6_rep. 1


title: EUB078

description: SAMPLE 138


title: EUB122

description: SAMPLE 137


title: AFB053

description: SAMPLE 136


title: 454149_A01


title: 454006_A01


title: 454146_A02


title: del2_IL-6_rep. 2


title: del2_unstim_rep. 2


title: del2_OSM_rep. 1


title: del2_IL-6_rep. 1


title: del2_unstim_rep. 1


title: 454151_A02


title: EUB083

description: SAMPLE 135


title: del1_unstim_rep. 2


title: del2_OSM_rep. 2


title: del1_unstim_rep. 1


title: AFB126

description: SAMPLE 134


title: del1_OSM_rep. 2


title: 454146_A01


title: del1_OSM_rep. 1


title: del1_IL-6_rep. 2


title: 454428_A01


title: EUB061

description: SAMPLE 132


title: AFB038

description: SAMPLE 131


title: wt1_OSM_rep. 2


title: EUB035

description: SAMPLE 133


title: 454150_A01

description:
Perinatal - 375ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_Perinatal - 375ppm - Methylation

source_name: Input DNA_Perinatal - 375ppm - Methylation


title: EUB052

description: SAMPLE 130


title: del1_IL-6_rep. 1


title: 454074_A03


title: wt1_unstim_rep. 2


title: wt1_unstim_rep. 1


title: wt1_IL-6_rep. 2


title: wt1_OSM_rep. 1


title: EUB047

description: SAMPLE 129


title: wt1_IL-6_rep. 1


title: 454202_A03


title: AFB193

description: SAMPLE 128


title: H7

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

description: miRNA raw reads file

data_processing:
sRNAbench: expression profiling of microRNAs based on genome mappings generated by Bowtie aligner
edgeR: differntially expressed microRNA identification, differentially expressed microRNA were defined from edgeR output table with FDR < 10%
miRanda and PITA: consensus microRNA target prediction, using miRanda and PITA
Functional anlaysis for target genes with Ingenuity Pathway Anlaysis
Genome_build: BosTau7
Supplementary_files_format_and_content: excel file including counts of each microRNA identified in each tissue of each animal

organism: Bos taurus

source_name: Descending colon

extract_protocol:
Two 2 cm2 biopsies of intestinal tissues were collected from each animal and immediately snap frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina TruSeq Small RNA Sample Preparation kit

treatment_protocol: Cattle with two phenotypes, control group was catlle negative for fecal E. coli O157, experimental group was cattle shedding > 104 CFU E. coli O157/g of feces

tag: sample type

value: super-shedder

value: Descending colon tissue


title: 453912_A03

city: Philadelphia

last: Schneider

address: 1020 Locust St


title: G7

description: miRNA raw reads file


title: 453913_A01


title: F7

description: miRNA raw reads file


title: J7

description: miRNA raw reads file


title: 454434_A01


title: AFB105

description: SAMPLE 127

value: African descent


title: 454253_A01


title: 454432_A03


title: B7

description: miRNA raw reads file

value: negative for E. coli O157


title: AFB057

description: SAMPLE 126


title: EUB173

description: SAMPLE 125

value: European descent


title: I7

description: miRNA raw reads file


title: 453913_A03


title: C7

description: miRNA raw reads file


title: 454159_A01


title: 454074_A02


title: 453956_A03


title: A. thaliana-NaBH4 treated

description:
Libraries were prepared from polyA enriched RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The
ara_wt_rrna_out.txt

organism: Arabidopsis thaliana

source_name: Arabidopsis, Col-0 genotype

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: 3'SS plasmid DNA library_seq

description:
3SS_plasmid_DNA
processed data file:
Minigenes_List.txt.gz

organism: synthetic construct

source_name: plasmid library

tag: molecule subtype

value: Plasmid Library


title: A7

description: miRNA raw reads file


title: 454159_A02


title: A. thaliana-untreated


title: EUB161

description: SAMPLE 122


title: EUB100

description: SAMPLE 123


title: H6

description: miRNA raw reads file

source_name: Spiral colon

value: Spiral colon tissue


title: 453913_A02


title: I6

description: miRNA raw reads file


title: G6

description: miRNA raw reads file


title: E7

description: miRNA raw reads file


title: 454149_A03


title: J6

description: miRNA raw reads file


title: EUB197

description: SAMPLE 120


title: AFB040

description: SAMPLE 121


title: D7

description: miRNA raw reads file


title: EUB124

description: SAMPLE 124


title: F6

description: miRNA raw reads file


title: EUB033

description: SAMPLE 119


title: 454257_A03

description:
Perinatal - 750ppm - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_Perinatal - 750ppm - Methylation

source_name: Input DNA_Perinatal - 750ppm - Methylation


title: EUB080

description: SAMPLE 117

source_name: CD14+ Monocytes, resting cells


title: 454198_A01


title: AFB093

description: SAMPLE 116


title: C6

description: miRNA raw reads file


title: B6

description: miRNA raw reads file


title: EUB032

description: SAMPLE 114


title: A6

description: miRNA raw reads file


title: EUB082

description: SAMPLE 118


title: 454197_A03


title: D6

description: miRNA raw reads file


title: J5

description: miRNA raw reads file

source_name: Distal jejunum

value: Distal jejunum tissue


title: Experimental Ovaries Ectopic JAK/STAT and EGFR Rep2

city: Princeton

first: Julia

last: Wittes

state: New Jersey

address: Lewis Thomas Lab, Washington Road

department: Department of Molecular Biology

institute: Princeton University

description:
Biological replicate 2 of 3. RNA from experimental condition ovaries of genotype GAL80TS/+ ; GR1-GAL4/UAS-Unpaired, UAS-lambdatorpedo.
Expt-rep2

hyb_protocol: Labeled cRNA was hybridized for 17 hours at 65°C. Hybridization and washes were performed according to Quick Amp kit protocols.

scan_protocol: Slide were scanned on an Agilent G2505C scanner at a 5µm resolution. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Bioconductor's Limma package for R was used to Loess normalize, background correct and quantile normalize raw data.

organism: Drosophila melanogaster

source_name: Wildtype OreR ovaries (reference)

label_protocol: Each labeling reaction was performed with 322 ng of RNA. Universal reference RNA was labeled with Cy3-CTP and all other RNA samples were labeled with Cy5-CTP. Labeling was performed with the Quick Amp two-color labeling kit. Labeled cRNA was purified by RNeasy column. Dye incorporation and cRNA yield were determined by NanoDrop.

growth_protocol: OreR (Wildtype) flies were raised at room temperature. Adult females were fed yeast and placed at 25°C for two days before dissecting out whole ovaries

extract_protocol: RNA was extracted from ovaries using TRIzol reagent and further purified with Qiagen RNeasy columns. It was then treated with TURBO DNase.

value: Whole ovaries

value: OreR

tag: genotype

value: Wildtype

source_name: Ovaries with ectopic JAK/STAT and EGFR expression in the follicle cells

growth_protocol: Crosses were carried out at 18°C. Adult females of specified genotypes were fed yeast for two days prior to dissection. Transgene expression was induced by incubating flies at 29°C for 16 hours before dissecting out whole ovaries.


title: 453914_A02

value: Female

value: hippocampus


title: 454144_A02

value: Long-Evans


title: AFB147

description: SAMPLE 113

value: Male


title: AFB175

description: SAMPLE 115


title: 454257_A02


title: Experimental Ovaries Ectopic JAK/STAT and EGFR Rep1

description:
Biological replicate 1 of 3. RNA from experimental condition ovaries of genotype GAL80TS/+ ; GR1-GAL4/UAS-Unpaired, UAS-lambdatorpedo.
Expt-rep1


title: I5

description: miRNA raw reads file


title: AFB203

description: SAMPLE 112


title: 454253_A03


title: E6

description: miRNA raw reads file


title: EUB138

description: SAMPLE 111


title: Control Ovaries Rep2

description:
Biological replicate 2 of 3. RNA from control ovaries of genotype GAL80TS/+ ; GR1-GAL4/TM6B.
Ctrl-rep2

source_name: Control ovaries

value: GAL80TS/+ ; GR1-GAL4/TM6B


title: H3K4me3 ChiPSeq Crohn's 7

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Histone H3 lysine 4 trimethylation modifications in intestinal epithelial cells obtained from ileal endoscopic biopsy in Crohn's patient

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were mapped to human genome hg19 or mouse genome mm9 with Bowtie
Global sequencing data was analyzed with Biowardrobe and average tag density profiles of each sample confirmed H3K4me3 enrichment and effective ChIP-seq before inclusion.
Differential ChIP-seq data was analyzed with replicates in THOR. Sample signal was normalized based on peaks at housekeeping genes and differential peaks between CD and control groups with all replicates are detected using a Hidden Markov Model approach.
Significant differential enrichment was defined as a BH-corrected p <0.05 and fold change ≥1.75.
Genome_build: Hg19

source_name: Ileal endoscopic biopsy

growth_protocol: Epithelial cells obtained from ileal biopsies were stored at -80C.

extract_protocol:
Fresh formaldehyde was added to each IEC sample for a final concentration of 1% and mixed end over end at room temperature for 10min to crosslink proteins to DNA. Cells were lysed with a Triton X-100 and Igepal buffer (0.25% Triton C-100, 0.5% Igepal, 10% glycerol, 1mM EDTA, 140mM NaCl, 50mM Hepes). Nuclei were then washed and chromatin sheared in a 0.1%SDS in TE buffer using a S220 Covaris Sonicator to 150-500 bp size. Immunoprecipitation was carried out with a SX-8G IP-STAR robot and an antibody optimized for histone H3 lysine 4 trimethylation (H3K4me3) as described previously.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Sequencing was performed using Illumina HiSeq 2500.

tag: cell type

value: Intestinal epithelial cells

tag: diagnosis

value: Newly-diagnosed Crohn's Disease

value: 12-18 years

tag: chip antibody

value: Histone H3 lysine 4 trimethylation


title: H5

description: miRNA raw reads file

value: super-shedder


title: 453950_A03


title: 454253_A02


title: Experimental Ovaries Ectopic JAK/STAT and EGFR Rep3

description:
Biological replicate 3 of 3. RNA from experimental condition ovaries of genotype GAL80TS/+ ; GR1-GAL4/UAS-Unpaired, UAS-lambdatorpedo.
Expt-rep3


title: H3K4me3 ChiPSeq Crohn's 6


title: Control Ovaries Rep1

description:
Biological replicate 1 of 3. RNA from control ovaries of genotype GAL80TS/+ ; GR1-GAL4/TM6B.
Ctrl-rep1

growth_protocol: OreR (Wildtype) flies were raised at room temperature. Adult females were fed yeast and placed at 25°C for two days before dissecting out whole ovaries.


title: Control Ovaries Rep3

description:
Biological replicate 3 of 3. RNA from control ovaries of genotype GAL80TS/+ ; GR1-GAL4/TM6B.
Ctrl-rep3


title: H3K4me3 ChiPSeq Crohn's 5


title: EUB036

description: SAMPLE 109

value: European descent


title: F5

description: miRNA raw reads file


title: G5

description: miRNA raw reads file


title: H3K4me3 ChiPSeq Crohn's 4


title: E5

description: miRNA raw reads file

value: negative for E. coli O157


title: EUB060

description: SAMPLE 108


title: H3K4me3 ChiPSeq Crohn's 3


title: EUB049

description: SAMPLE 107


title: AFB101

description: SAMPLE 106

value: African descent


title: H3K4me3 ChiPSeq Crohn's 2


title: Cells with ADT in hypoxia, biological rep 2

city: Portland

first: David

last: Qian

address: 3303 SW Bond Ave, CH14R

institute: Oregon Health & Science University

description: Gene expression due to androgen in hypoxia

hyb_protocol: Following fragmentation, 6.5ug of cRNA were hybridized for 18 hr at 45C to GeneChip Human PrimeView Arrays. GeneChips were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip 3000 Scanner with the 7G upgrade.  Image processing was performed using Affymetrix Command Console (AGCC) v.3.1.1 software

data_processing: The data files were processed using Expression Console Software build 1.4.1.46 and RMA without normalization

label: Biotinylated-labeled cRNA

source_name: androgen + hypoxia

label_protocol: Biotinylated-labeled cRNA were prepared using the Applied Biosystems 3'IVT Plus protocol with 100ng of total RNA input.

treatment_protocol: RPMI media with 5% charcoal-stripped FBS, with or without 1 nM R1881, with or without hypoxia for 24 hours.

value: prostate cancer cell line

tag: cell line

value: LNCaP


title: D5

description: miRNA raw reads file

tag: tissue

value: Distal jejunum tissue


title: H3K4me3 ChiPSeq Crohn's 1


title: 453914_A01


title: C5

description: miRNA raw reads file


title: Cells with ADT in hypoxia, biological rep 3


title: A5

description: miRNA raw reads file


title: 453950_A02


title: B5

description: miRNA raw reads file


title: 453899_A02

description:
Perinatal - Control - Methylation
MeDIP_Hippocampus

source_name: MeDIP DNA_Perinatal - Control - Methylation

source_name: Input DNA_Perinatal - Control - Methylation


title: EUB003

description: SAMPLE 105

tag: gender


title: 454144_A01


title: H3K4me3 ChiPSeq Control 8

description: Histone H3 lysine 4 trimethylation modifications in intestinal epithelial cells obtained from ileal endoscopic biopsy in a healthy control

value: Healthy control


title: Cells with R1881 in hypoxia, biological rep 3

description: Gene expression due to ADT/castration in hypoxia

source_name: ADT + hypoxia


title: EUB091

description: SAMPLE 104

tag: batch


title: Cells with R1881 in hypoxia, biological rep 1


title: 454432_A02

value: Female


title: AFB207

description: SAMPLE 103

tag: ethnicity


title: J3

description: miRNA raw reads file

source_name: Proximal jejunum

value: Proximal jejunum tissue


title: H3K4me3 ChiPSeq Control 7

tag: age


title: H3K4me3 ChiPSeq Control 6


title: I3

description: miRNA raw reads file


title: H3K4me3 ChiPSeq Control 5


title: H3

description: miRNA raw reads file


title: Cells with R1881, biological rep 3

description: Gene expression due to androgen

source_name: androgen


title: Cells with R1881, biological rep 2

description: Gene expression due to androgen


title: EUB076

description: SAMPLE 100


title: EUB106

description: SAMPLE 101


title: AFB028

description: SAMPLE 102


title: H3K4me3 ChiPSeq Control 3


title: 453912_A01

tag: Sex

value: hippocampus

value: Long-Evans


title: 453956_A02

tag: strain


title: 453912_A02


title: EUB119

description: SAMPLE 99

value: Male


title: F3

description: miRNA raw reads file


title: EUB039

description: SAMPLE 110


title: H3K4me3 ChiPSeq Control 4

value: Intestinal epithelial cells


title: E3

description: miRNA raw reads file


title: EUB118

description: SAMPLE 98


title: Cells with R1881 in hypoxia, biological rep 2


title: H3K4me3 ChiPSeq Control 2


title: G3

description: miRNA raw reads file


title: Cells with ADT, biological rep 3

description: Gene expression due to ADT/castration

source_name: ADT


title: Cells with ADT, biological rep 2

description: Gene expression due to ADT/castration


title: Cells with R1881, biological rep 1

description: Gene expression due to androgen


title: AFB084

description: SAMPLE 97


title: D3

description: miRNA raw reads file


title: Cells with ADT, biological rep 1

description: Gene expression due to ADT/castration


title: H3K4me3 ChiPSeq Control 1


title: AFB048

description: SAMPLE 96


title: B3

description: miRNA raw reads file


title: EUB101

description: SAMPLE 95


title: 453956_A01


title: CD5 IECs

description: intestinal epithelial cells obtained from an ileal endoscopic biopsy from a newly-diagnosed Crohn's disease

data_processing:
Sequence reads were aligned to the Hg19 genome by using Illumina sequence analysis pipeline.
Sequence reads were aligned to the reference genome using the TopHat2 aligner, and reads aligning to each known transcript were counted using Bioconductor packages for next-generation sequencing data analysis.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: ileal endoscopic biopsy

growth_protocol: Epithelial cells obtained from ileal biopsies were stored at -80C in RNAlater.

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen). Directional polyA RNA-seq was performed by the Genomics, Epigenomics and Sequencing Core (GESC) at the University of Cincinnati. NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) was used for polyA RNA purification with the Apollo 324 system (WaferGen) and PrepX PolyA script for automated polyA RNA isolation.
To study differential gene expression, individually indexed and compatible libraries were proportionally pooled (~25 million reads per sample in general) for clustering in cBot system (Illumina). Libraries at the final concentration of 15 pM were clustered onto a single read (SR) flow cell using Illumina NEBNext Ultra Directional RNA Library Prep Kit.

value: intestinal epithelial cells

value: newly-diagnosed Crohn's disease


title: CD6 IECs

value: 12-18 years


title: C3

description: miRNA raw reads file


title: CD4 IECs


title: A3

description: miRNA raw reads file


title: AFB169

description: SAMPLE 94


title: CD3 IECs


title: AFB108

description: SAMPLE 93


title: 872/6 (B)

first: Genotypic

last: technology

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

hyb_protocol: 2000ng ng of labeled cRNA sample were fragmented at 60° C and hybridized on to a Agilent custom Microarray Gene expression 8x15k Array (AMADID: 027511). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65° C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2505C).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift .Gene based analysis was performed.

organism: Leishmania donovani

source_name: Leishmania donovani promastigote

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligodT primer with T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Leishmania donovani parasite isolated from bone marrow aspirate of VL patients before miltefosine treatment (xxx/0), one month after treatment (xxx/1) and patient that relapsed after miltefosine treatment (xxx/4 and xxx/6).

extract_protocol: Total parasite RNA was extracted using Trizol regent according to manufacturer's instructions.

treatment_protocol: L. donovani parasite derived from bone marrow aspirate of VL patient was grown in vitro as promastigote and maintined in medium 199 supplemented with 10%FCS.

tag: isolate


title: CD2 IECs


title: 902/1 (C)

value: one month after treatment


title: 872/6 (A)

value: patient that relapsed after miltefosine treatment


title: J2

description: miRNA raw reads file

source_name: Cecum

value: super-shedder

value: Cecum tissue


title: CD1 IECs


title: 902/1 (B)


title: 902/1 (A)


title: AFB017

description: SAMPLE 91

value: African descent


title: H2

description: miRNA raw reads file


title: EUB141

description: SAMPLE 92

value: European descent


title: 902/0 (C)

value: bone marrow aspirate of VL patients before miltefosine treatment


title: CTL7 IECs

description: intestinal epithelial cells obtained from an ileal endoscopic biopsy from a healthy control

value: healthy control


title: I2

description: miRNA raw reads file


title: G2

description: miRNA raw reads file


title: 902/0 (B)


title: AFB047

description: SAMPLE 89


title: CTL6 IECs


title: F2

description: miRNA raw reads file


title: 902/0 (A)


title: CTL5 IECs


title: AFB087

description: SAMPLE 88


title: E2

description: miRNA raw reads file

value: negative for E. coli O157


title: 1062/4 (B)


title: H3K4me3 ChiPSeq Crohn's 8

value: Newly-diagnosed Crohn's Disease

value: Histone H3 lysine 4 trimethylation


title: Cells with ADT in hypoxia, biological rep 1

value: prostate cancer cell line

value: LNCaP


title: CTL4 IECs


title: D2

description: miRNA raw reads file


title: AFB013

description: SAMPLE 87

value: Male


title: 1062/4 (A)


title: 994/1 (C)


title: CTL3 IECs

value: intestinal epithelial cells


title: CTL2 IECs


title: 994/1 (B)


title: C2

description: miRNA raw reads file


title: B2

description: miRNA raw reads file


title: EUB157

description: SAMPLE 90


title: AFB165

description: SAMPLE 85


title: AFB190

description: SAMPLE 86


title: EUB065

description: SAMPLE 84


title: CTL1 IECs


title: EUB153

description: SAMPLE 83


title: J1

description: miRNA raw reads file

source_name: Duodenum

value: Duodenum tissue


title: 994/1 (A)


title: S. cerevisiae-WT-NaBH4 treated-mRNA-exp1-rep3

description:
Libraries were prepared from polyA enriched RNA. Briefly, after NaBH4/mock treatment the RNA was reverse transcribed to cDNA using a random primer with Illumina overhang, and an adapter was ligated to the 3'-end of the cDNA. The
yeast_wt_rrna_out.txt

data_processing:
Sequencing reads were processed with Cutadapt (version 1.14) to remove adapter sequences using the setting -a AGATCGGAAGAGCACACGTCT. For reads generated nextseq platform, the option --nextseq-trim=20” was included.
All samples (except small RNA-Seq experiments): The RNAProbR preprocessing.sh script (http://people.binf.ku.dk/~jvinther/data/rna_probing/) was used to remove the 7 base barcode from the sequencing read using the options “-b NNNNNNN -t 9”
Reads were aligned with bowtie2 (version 2.2.3) using high sensitivity options “--local -N 1 -D 20 -R 3 -L 15”
All samples (except small RNA-Seq experiments): Potential PCR duplicates among the sequencing reads were removed by discarding all but one of the reads having identical barcode and mapping to the same position using the collapse.sh script (available at http://people.binf.ku.dk/jvinther/data/RNA-seq).
The mapped reads for the control and NaBH4 treated samples were processed with the mpileup tool from the samtools package (version 1.7).
Genome_build: E. coli strain bw25113 (ensembl cDNA release 87), S. cerevisiae (ensembl cDNA release 84). rRNA sequences were obtained were obtained from the CRW database (http://www.rna.ccbb.utexas.edu). tRNA sequences were obtained from the genomic tRNA database (http://gtrnadb.ucsc.edu/index.html).
Supplementary_files_format_and_content: The mutation frequency file is the output from the GetFreq function (available at https://github.com/jeppevinther/m7g_map_seq) includes a number of statistics for each position, including coverage,  mutation frequency for the treated and control samples and the mutation rate difference between the treated and control samples. It includes p-values for the observed mutation rates being different in the treated and the control samples and for the replicate samples being different.

source_name: yeast

tag: nabh4 treatment

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: 994/0 (C)


title: I1

description: miRNA raw reads file


title: AFB154

description: SAMPLE 82

source_name: CD14+ Monocytes, resting cells


title: H1

description: miRNA raw reads file


title: EUB093

description: SAMPLE 81


title: S. cerevisiae-WT-NaBH4 treated-mRNA-exp1-rep2


title: 994/0 (B)


title: S. cerevisiae-WT-NaBH4 treated-exp1-mRNA-rep1


title: AFB215

description: SAMPLE 80


title: ICb-1078MB-22241-digoxin-bio_S13_L003

city: Houston

first: LEI

last: HUANG

state: TX

department: Systems medicine and Bioengineering

institute: Houston Methodist Research Institute

data_processing:
Illumina CASAVA v1.8.2 software was used for basescalling.
Fragment reads were mapped to the UCSC mouse genome (hg38) using Tophat2.
Raw counts for each gene were obtained by HTSeq2, and we also obatined the FPKMs (Fragments Per Kilobase of transcript per Million mapped reads) of raw counts using Cufflinks and scaled via the median of the genomic means for each gene across all libraries as described (Anders and Huber, 2010 [PMID 20979621]).
Adjusted p values for each gene were obtained by R package Deseq2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file includes rawcounts for each Sample.

source_name: Brain

growth_protocol: ICb-2555MB in vivo passage 2 or ICb-1078MB in vivo passage 2 were suspended in 2 µL of culture medium and injected into the right cerebellar hemisphere via a 10-µL 26-gauge Hamilton Gastight 1701 syringe needle.

extract_protocol:
RNA was extracted from tumor cells using TRIzol reagent and mRNAs were selected using Poly (A) Purist MAG kit (Thermofisher).  The RNA library prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England lab, NEB) and sequenced using NextSeq 500/550 v2 Kits (high output 150 cycle, Illumina) on a HiSeq 2500 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: digoxin intermittent (2 cycles of daily treatment for 14 days, separated by 21 days)

value: Brain

tag: treatment

value: Treat with digoxin

tag: group

tag: disease state

value: medulloblastoma


title: ICb-1078MB-22241-digoxin-bio_S13_L002


title: ICb-1078MB-22241-digoxin-bio_S13_L004


title: ICb-1078MB-22241-digoxin-bio_S13_L001


title: ICb-1078MB-22234-digoxin-bio_S12_L004


title: A2

description: miRNA raw reads file

tag: sample type

value: Cecum tissue


title: G1

description: miRNA raw reads file

value: super-shedder


title: EUB075

description: SAMPLE 79

value: European descent


title: EUB004

description: SAMPLE 78


title: S. cerevisiae-WT-untreated-mRNA-exp1-rep3

first: Jeppe

institute: University of Copenhagen

extract_protocol:
Hot acid phenol extraction
RNA-seq: Methods in molecular biology, 1038, 213-231 (2013) with RNA fragmentation step included.  Small RNA-seq: NEBNext Multiplex Small RNA Kit.


title: S. cerevisiae-WT-untreated-mRNA-exp1-rep2


title: ICb-1078MB-22234-digoxin-bio_S12_L003


title: F1

description: miRNA raw reads file


title: ICb-1078MB-22234-digoxin-bio_S12_L002


title: S. cerevisiae-WT-untreated-mRNA-exp1-rep1


title: AFB171

description: SAMPLE 77

value: African descent


title: ICb-1078MB-22234-digoxin-bio_S12_L001


title: AFB043

description: SAMPLE 76


title: C1

description: miRNA raw reads file


title: B1

description: miRNA raw reads file


title: ICb-1078MB-18343-Control_S9_L004

value: No treatment


title: 994/0 (A)

value: bone marrow aspirate of VL patients before miltefosine treatment


title: D1

description: miRNA raw reads file

value: negative for E. coli O157


title: AFB082

description: SAMPLE 74


title: A1

description: miRNA raw reads file


title: ICb-1078MB-18343-Control_S9_L003


title: AFB129

description: SAMPLE 72


title: AFB055

description: SAMPLE 71


title: ICb-1078MB-18343-Control_S9_L001


title: E1

description: miRNA raw reads file


title: 116-B (miRNA-Seq)

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

data_processing:
Sequence reads were trimmed and filtered with Trimmomatic [v0.36] to remove adaptor sequences , low quality reads and reads shorter than 16 nucleotides.
The sRNAbench module from the sRNAtoolbox program was applied to map sequences to the reference genome, to profile the expression of known small RNAs from miRBase sheep miRNAs and to predict novel miRNAs. Rfam data was used to identify other small RNAs originating from rRNA, tRNA, snRNA and snoRNA and exclude them from the analysis.
The predicted new miRNAs were searched in the RNACentral database with blastn [v2.7.1] to known if they have been previously identified and to try to annotate them.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Tab-delimited text file matrix with the raw counts of sequencing reads for miRNAs. The miRNAs are identified with the miRBase ID and the samples are identified by the name of the title column of the SAMPLES section.

organism: Ovis aries

source_name: Blood

growth_protocol: The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the EthicalCommittee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.

extract_protocol:
For isolation of ovine peripheral blood mononuclear cells (PBMCs), blood was collected from the jugular vein of 6 Rasa sheep. The blood was collected into heparinised Vacutainer tubes (Becton, Dickinson and Company, Sparks, MD), transferred into 50-ml centrifuge tubes and diluted 1∶2 in HBSS. Twenty-five millilitres of blood:HBSS were layered over 10 ml of Ficoll-Paque (1.084 g/cm3) (GE HealthCare Bio-Sciences, Uppsala, Sweden) in 50-ml centrifuge tubes. Cells were centrifuged at 900×g for 30 min to separate erythrocytes and polymorphonuclear cells from PBMCs. PBMCs were collected from the HBSS-Ficoll-Paque interface, washed with HBSS by centrifugation at 400×g for 10 min, lysed in 1 ml of Trizol and storage at -80 ⁰C until used. Total RNA was extracted from PBMCs using RNA Clean & Concentrator™-5 kit (Zymo Research, Irvine, CA, USA) following manufacturer’s instructions and stored at -80 ⁰C. The TruSeq Small RNA library prep kit (Illumina, San Diego, CA, USA) was used for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The animals were treated with two different treatments: one group was inoculated with nine different commercial vaccines and the other one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium. Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and April of 2106, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.

tag: cell type

value: PBMC

value: Adjuvant

tag: time

value: tf

tag: sample source


title: AFB061

description: SAMPLE 69

value: Male


title: 125-B (miRNA-Seq)

value: Vaccine


title: ICb-1078MB-18342-Control_S8_L003


title: ICb-1078MB-18342-Control_S8_L004


title: AFB083

description: SAMPLE 70


title: 114-B (miRNA-Seq)


title: ICb-1078MB-18342-Control_S8_L001


title: 111-B (miRNA-Seq)


title: AFB213

description: SAMPLE 75


title: 124-B (miRNA-Seq)


title: 121-B (miRNA-Seq)


title: ICb-1078MB-18342-Control_S8_L002


title: 116-A (miRNA-Seq)


title: ICb-2555MB-21659-digoxin-bio_S14_L004


title: 114-A (miRNA-Seq)


title: EUB058

description: SAMPLE 66


title: AFB079

description: SAMPLE 68


title: AFB022

description: SAMPLE 67


title: ICb-1078MB-18343-Control_S9_L002


title: AFB095

description: SAMPLE 65


title: ICb-2555MB-21659-digoxin-bio_S14_L002


title: EUB164

description: SAMPLE 73


title: ICb-2555MB-21659-digoxin-bio_S14_L003


title: ICb-2555MB-21659-digoxin-bio_S14_L001


title: 111-A (miRNA-Seq)


title: 125-A (miRNA-Seq)


title: AFB168

description: SAMPLE 64


title: Icb-2555MB-20908_S23_L004


title: EUB010

description: SAMPLE 63


title: 124-A (miRNA-Seq)


title: 121-A (miRNA-Seq)


title: EUB034

description: SAMPLE 61


title: EUB070

description: SAMPLE 62


title: Icb-2555MB-20908_S23_L001


title: Icb-2555MB-20908_S23_L002


title: AFB091

description: SAMPLE 59


title: EUB174

description: SAMPLE 58


title: EUB030

description: SAMPLE 57


title: VR.5

city: Ames

first: Lindsay

last: Rutter

state: IA

address: 2014 Molecular Biology Building

department: Bioinformatics and Computational Biology Program

institute: Iowa State University

data_processing:
Reads were aligned using the programs GMAP and GSNAP
Feature read counts were obtained using HTSeq-count-0.6.1
Genome_build: BeeBase Version 3.2 genome from the Hymenoptera Genome Database
Supplementary_files_format_and_content: Tab-delimited text file containing read counts for each sample

organism: Apis mellifera

source_name: Whole body tissue

extract_protocol:
Whole body RNA from each pool was extracted using Qiagen RNeasy MiniKit followed by Qiagen DNase treatment.
A standard Illumina mRNA library was prepared for Illumina HiSeq Sequencing

value: Whole body

tag: virus

value: Infected with IAPV

tag: diet

value: Rockrose


title: VC.6

tag: tissue

value: Chestnut


title: VR.4


title: AFB151

description: SAMPLE 60

tag: gender

tag: batch


title: VR.2


title: EUB121

description: SAMPLE 56

tag: age

tag: ethnicity


title: VR.3


title: VR.1


title: VC.5


title: RNAPII_ChIP

city: London

first: Timothy

last: Mohun

address: The Ridgeway, Mill Hill,

department: Developmental Biology Division

institute: MRC National Institute for Medical Research

description:
RNAPII ChIP Biological Rep 1-3
Two of the raw data files (GSM444366_CS21.CEL and GSM444366_CS26.CEL) are identical to those (GSM444365_CS21.CEL and GSM444365_CS26.CEL) for sample GSM444365.

hyb_protocol: 5 micrograms of DNA was hybridized per array using the Affymetrix hybridization kit.  The arrays were hybridized for 16hr at 45C at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing:
The enriched transcription factor binding regions were detected by analysis of three independent biological repeats using the Model-based Analysis of Tiling-array (MAT) algorithm (Johnson et al. 2006) using a bandwidth of 300bp and a P-value cutoff of 1e-5 (.bed files)(BPMAP =  Mm_PromPF_v02-1_NCBI35.NR.bpmap).

bed files were generated using the Model-based Analysis of Tiling-array (MAT) algorithm using three biological repeats of specific antibody ChIP versus three biological repeats of input.

source_name: RNAPII ChIP DNA from E11.5 heart

label_protocol: Immunoprecipitated DNA and 10ng of input genomic DNA was amplified using ligated-mediated PCR (LM_PCR) and then enzymatically fragmented and labeled with biotin using the WT Labeling Kit (Affymetrix).

extract_protocol: Chromatin was prepared from 20-25 mouse embryonic hearts at stage E11.5. Tissue was fixed for 3 hours at room temperature in buffer (50mM HEPES pH7.9, 1mM EDTA, 1mM EGTA, 100mM NaCl, 0.07% butryric acid) containing 1.8% formaldehyde. The tissue homogenized using an Ultra-Turrax, T25 basic (IKA-Werke), and pelleted at low speed. Samples were washed twice with ice-cold PBS with freshly added EDTA-free protease inhibitors (PI) (Roche). Samples were resuspended in 1.5ml lysis buffer (25mM Tris pH 7.5, 150mM NaCl, 1% Triton X100, 1% SDS, 2.5mM Sodium deoxycholate, PI) and transferred to RNAse-free, non-stick microfuge tubes (Ambion). Samples sonicated for 15 x 30 seconds on ice using a Branson Digital Sonicator with a 2.5mm stepped probe tip. Samples were spun at 15K using a bench top centrifuge for 15 minutes at 4ºC. The supernatant was then pre-blocked with protein A/G sepharose (Perbio), pre-treated with BSA (Biorad) and Poly (dI-dC)-poly (dI-dC) (GE Healthcare). A proportion of the sample was kept at this stage as an input control. 150μl of chromatin was diluted 10 fold in ChIP dilution buffer (16.7mM Tris pH7.5, 0.01% SDS, 1.1% Triton, 1.2mM EDTA, 167mM NaCl) and specific antibody was added and incubated overnight at 4ºC with rotation. The antibody:protein:DNA complexes were captured using pre-blocked protein A/G sepharose for 2 hours rotating at 4ºC. The beads were then spun down and washed twice in wash buffer A (10mM HEPES pH 7.6, 1mM EDTA, 0.5mM EGTA, 0.25% Triton X100) and twice with wash buffer B (10mM HEPES pH7.6, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.01% Triton X100. The beads were resuspended in TE and cross-links reversed overnight at 65ºC. Samples were adjusted to 0.1% SDS, digested with 10μg Proteinase K (Roche) at 50ºC for 3 hours and extracted twice with phenol/chloroform. Samples were ethanol precipitated and resuspended in 100μl TE. To generate sufficient material for hybridization to the Affymetrix GeneChIP® Mouse Promoter 1.0R Array, immunoprecipitated DNA from three ChIP experiments or 10ng of input DNA as control, were amplified using ligated-mediated PCR (LM-PCR). The ChIP-chip assay was performed using a minimum of three biologically independent samples.

tag: organ

value: heart

value: cardiac

tag: developmental stage

tag: antibody

value: RNA polymerase II

source_name: Input DNA from E11.5 hearts


title: AFB060

description: SAMPLE 54


title: Icb-2555MB-20908_S23_L003

value: Brain

tag: treatment

value: medulloblastoma


title: Nkx2-5_ChIP

description: Nkx2-5 ChIP Biological Rep 1-3

source_name: Nkx2-5 ChIP DNA from E11.5 heart


title: SRF_ChIP

description:
SRF ChIP Biological Rep 1-3
Two of the raw data files (GSM444365_CS21.CEL and GSM444365_CS26.CEL) are identical to those (GSM444366_CS21.CEL and GSM444366_CS26.CEL) for sample GSM444366.

source_name: SRF ChIP DNA from E11.5 heart

value: SRF


title: VR.6


title: EUB162

description: SAMPLE 52

value: European descent


title: AFB132

description: SAMPLE 53

value: African descent


title: VC.3


title: AFB067

description: SAMPLE 51


title: VC.2


title: AFB068

description: SAMPLE 55


title: AFB197

description: SAMPLE 48


title: AFB204

description: SAMPLE 50


title: EUB175

description: SAMPLE 49


title: NR.6

value: Not infected with IAPV


title: NR.5


title: VC.4


title: BC3 Cells-Italy

city: Chapel Hill

first: Dirk

last: Dittmer

state: North Carolina

address: 450 West Dr

department: Microbiology and Immunology

institute: University of North Carolina at Chapel Hill

hyb_protocol: The array oligos are hybridized to a biotin-labeled target and is stained with a florescent dye coniugated to strepavidin

scan_protocol: Command Console Software

data_processing:
Expression value are calculated based on the difference of the perfect match signal and mismatch signal at each probe pairs using the Affimetrix Command Console system
The initial data are black and white pixelated images of each hybridization. The more useful data are files containing the numeric summaries of these pixelated images

source_name: PEL cell line, parental

label_protocol: biotin-label

growth_protocol: cells were grown in RPMI 10% FBS, 1% L-Glutamine, 100 IU penicillin and 100 μg/mL streptomycin

extract_protocol: RNA extraction by Trizol

tag: condition

value: parental, KSHV infected

tag: cell line

value: PEL


title: CRO6_cl2_EBV+ Cells

source_name: PEL cell line, EBV infected

value: KSHV and EBV infected


title: AFB075

description: SAMPLE 46

value: Male


title: BC3_cl10_EBV+ Cells


title: CRO6_cl3_EBV+ Cells


title: BC3 Cells-USA


title: CRO6 Cells


title: NR.3

value: Whole body


title: EUB134

description: SAMPLE 45


title: NR.2


title: NR.1


title: AFB146

description: SAMPLE 44


title: VC.1

value: Infected with IAPV


title: NC.6


title: EUB139

description: SAMPLE 47


title: NR.4

value: Rockrose


title: NC.5

value: Chestnut


title: AFB062

description: SAMPLE 43


title: NC.4


title: EUB072

description: SAMPLE 41


title: EUB028

description: SAMPLE 40


title: EUB160

description: SAMPLE 39


title: NC.3


title: EUB031

description: SAMPLE 38


title: AFB209

description: SAMPLE 37


title: NC.1


title: NC.2


title: EUB137

description: SAMPLE 36


title: AFB081

description: SAMPLE 42


title: AFB035

description: SAMPLE 35


title: IP_3567

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

institute: INSA

description:
Total reads :  31 822 212 ; average fragment size : 296
DLT3567_Rox.fasta

data_processing:
Basecalls and alignment performed using Torrent_Suite 5.0.4
ChIP-seq reads were aligned to the N16961 genome
Genome_build: Escherichia coli str. K-12 substr. MG1655 ASM584v2, DLT2075_converted.fasta, DLT3548_SopC_nosopB_pJYB294.fasta, DLT3567_Rox.fasta/DLT2075_converted.fasta  DLT3548_SopC_nosopB_pJYB294.fasta  DLT3567_Rox.fastahome_net/labourd/projets/ChipSeq_Roxanne/Geo_deposit/labour_addsamples/labour_aaddsamples_ref
Supplementary_files_format_and_content: The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the option –d and –fs

organism: Escherichia coli

source_name: bacteria

growth_protocol: Samples were prepared from exponential growing phase cultures at 37°C in LB media (OD = 0.5) in the presence of IPTG (where indicated)

extract_protocol:
Lysates were clarified from sonicated cell and protein-DNA complexes were isolated with anti ParBF antibody
A maximum of 2 ng of ChIP DNA was used to synthetize the library as described in manufacturer’s instructions (Ion ChIP-Seq Library Preparation on the Ion Proton™ System - revision B - Step10). The last size selection was modified by a double size selection (0.55X/0.25X) of binding to AMPure® XP beads followed by a step of wash and elution. Then, qualification and quantification were made with the Bioanalyzer - Agilent, Santa Clara, CA

treatment_protocol: Cells were treated with formalhedyde (1 %)

tag: strains

tag: parsf location

value: E.coli xylE::parSF

tag: iptg induction (um)

tag: parbf allele

value: wild type; in trans

value: anti ParBF


title: Input_3567

description:
Total reads :  4 500 397; average fragment size : 274
DLT3567_Rox.fasta


title: IP_3548-LB

description:
Total reads : 16 608 073 ; average fragment size : 223
DLT3548_SopC_nosopB_pJYB294.fasta

value: ParBF-mVenus


title: input_2075-100

description: Total reads : 2 749 708 ; average fragment size : 221

data_processing:
Basecalls and alignment performed using Torrent_Suite 5.0.4
ChIP-seq reads were aligned to the N16961 genome
Genome_build: Escherichia coli str. K-12 substr. MG1655 ASM584v2
Supplementary_files_format_and_content: The counting of reads over the genomic sequences was performed using bedtools 2.26.0 with the tool genomecov and the option –d and –fs

tag: strain

tag: iptg induction (µm)

value: wild type

value: input


title: IP_2075-0

description: Total reads :  19 383 231 ; average fragment size : 227


title: Input_3548-LB

description:
Total reads :  4 708 965 ; average fragment size : 229
DLT3548_SopC_nosopB_pJYB294.fasta


title: ATCC-DYR0103hiPSc (II), biological rep2

city: Setagaya

first: Takuya

last: Kuroda

state: Tokyo

address: 1-18-1 Kamiyoga

department: Division of cell-based therapeutic products

country: Japan

institute: National Institute of Health and Sciences

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The TGT value is 500.

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy  Mini Kit, Qiagen)


title: 454E2 (II), biological rep3


title: EUB084

first: Lucas

institute: Institut Pasteur

description: SAMPLE 32

data_processing: Signal intensity is measured with the Illumina HiScan system to generate beta values, a measure of the degree of methylation at a locus

extract_protocol: Each DNA sample was extracted from 2x106 primary monocytes by a standard phenol/chloroform protocol followed by ethanol precipitation. Prior to DNA methylation profiling, DNAs were then bisulfite converted and processed using the Illumina Infinium MethylationEPIC BeadChip Kit, according to the manufacturer's instructions  followed by ethanol precipitation

value: European descent


title: AFB136

description: SAMPLE 33

value: African descent


title: AFB144

description: SAMPLE 34


title: ATCC-DYR0103hiPSc (II), biological rep1


title: IP_2075-500

description: Total reads :  18 640 299 ; average fragment size : 236


title: 454E2 (II), biological rep1


title: IP_2075-100

description: Total reads :  28 121 778 ; average fragment size : 232


title: ATCC-DYR0100hiPSc (II), biological rep2


title: mc-iPS (II), biological rep3

source_name: mc-iPS

value: mc-iPS


title: ATCC-DYR0100hiPSc (II), biological rep3


title: ATCC-DYR0100hiPSc (II), biological rep1


title: IP_2075-Rif-R1

description:
Total reads :   18 807 472  ; average fragment size : 220
DLT2075_converted.fasta


title: AFB090

description: SAMPLE 31


title: neonatal_rat_cardiacfibroblast_yap_2

city: Wauwatosa

first: Michael

middle: Andrew

last: Flinn

state: WI

address: 8701 W Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

data_processing:
Primary sequencing data was conducted with a BGISEQ-500 50SE at 20M reads per sample.
Raw reads are subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which are aligned to the reference sequences.
"Dirty" raw reads are reads which contain the sequence of adaptor, high content of unknown bases and low quality reads, and are removed before analysis.
Bowtie2 was used to map clean reads to reference gene, and HISAT used to reference genome.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM)  method is used to calculated expression level.
Genome_build: rn6
Supplementary_files_format_and_content: Excel files containing FKPM values for expression levels.

source_name: neonatal rat, cardiac fibroblast, yap siRNA, replicate 2

growth_protocol: Fibroblasts or myocytes were incubated in DMEM supplemented with 15% FBS and penicillin-streptomycin.

extract_protocol:
RNA was extracted using Trizol (Thermo Fisher Scientific) phenol cholorform extraction.
RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low-input poly-A BGISEQ-500RSRNASeq(Transcriptome) protocol.

treatment_protocol: After 16 hours, the cells were transfected using mission siRNA transfection reagent (Sigma) with two different siRNAs each at a concentration of 25 nM designed against the target gene of interest. Forty-eight hours post transfection cells were collected in Trizol for RNA extraction.

value: Sprague Dawley

tag: cell type

value: cardiac fibroblast

tag: sirna treatment

value: yap siRNA


title: ATCC-DYR0103hiPSc (II), biological rep3


title: EUB140

last: Husquin

description: SAMPLE 30

tag: gender

value: Male

tag: batch


title: input_2075-Rif-R1

description:
Total reads :  2 584 320  ; average fragment size : 218
DLT2075_converted.fasta


title: mc-iPS (II), biological rep1


title: IP_3548-M9

description: Total reads :  32 487 616 ; average fragment size : 207

growth_protocol: Samples were prepared from exponential growing phase cultures at 37°C in M9 glucose supplemented with casamino acids


title: EUB046

description: SAMPLE 29

tag: age

tag: ethnicity


title: 454E2 (II), biological rep2


title: neonatal_rat_cardiacfibroblast_neg_3

source_name: neonatal rat, cardiac fibroblast, negative siRNA, replicate 3

value: negative siRNA


title: neonatal_rat_cardiacfibroblast_yap_3

source_name: neonatal rat, cardiac fibroblast, yap siRNA, replicate 3


title: input_3548-M9

description: Total reads :  3 428 361 ; average fragment size : 232


title: HiPS-RIKEN-2A (II), biological rep3


title: AFB155

description: SAMPLE 28


title: mc-iPS (II), biological rep2


title: neonatal_rat_cardiacfibroblast_neg_2

source_name: neonatal rat, cardiac fibroblast, negative siRNA, replicate 2


title: EUB155

description: SAMPLE 27


title: HiPS-RIKEN-2A (II), biological rep2


title: IP_3651-R2

description: Total reads :  20 019 051 ; average fragment size : 196

value: E.coli xylE::parSF delta(locus A)


title: neonatal_rat_cardiacfibroblast_yap_1

source_name: neonatal rat, cardiac fibroblast, yap siRNA, replicate 1


title: neonatal_rat_cardiacfibroblast_neg_1

source_name: neonatal rat, cardiac fibroblast, negative siRNA, replicate 1


title: HiPS-RIKEN-12A (II), biological rep3


title: HiPS-RIKEN-1A (II), biological rep3


title: input_3651-R2

description: Total reads :  4 846 778 ; average fragment size : 210


title: AFB077

description: SAMPLE 26

source_name: CD14+ Monocytes, resting cells


title: AFB031

description: SAMPLE 25


title: neonatal_rat_cardiomyocyte_yap_3

source_name: neonatal rat, cardiomyocyte, yap siRNA, replicate 3

value: cardiomyocyte


title: HiPS-RIKEN-12A (II), biological rep1


title: neonatal_rat_cardiomyocyte_yap_2

source_name: neonatal rat, cardiomyocyte, yap siRNA, replicate 2


title: IP_2075-Stat

description: Total reads :  17 421 430 ; average fragment size : 221


title: IP_2075-Rif

description: Total reads : 17 497 222 ; average fragment size : 235


title: HiPS-RIKEN-12A (II), biological rep2


title: HiPS-RIKEN-1A (II), biological rep2


title: neonatal_rat_cardiomyocyte_yap_1

source_name: neonatal rat, cardiomyocyte, yap siRNA, replicate 1


title: HiPS-RIKEN-2A (II), biological rep1


title: input_2075-Rif

description: Total reads :  4 701 941 ; average fragment size : 245


title: AFB138

description: SAMPLE 23


title: neonatal_rat_cardiomyocyte_neg_3

source_name: neonatal rat, cardiomyocyte, negative siRNA, replicate 3


title: EUB048

description: SAMPLE 22


title: neonatal_rat_cardiomyocyte_neg_2

source_name: neonatal rat, cardiomyocyte, negative siRNA, replicate 2


title: IP_3566

description: Total reads :  19 729 447 ; average fragment size : 217


title: input_3566

description: Total reads :  5 643 898 ; average fragment size : 231


title: EUB146

description: SAMPLE 21


title: S. cerevisiae-WT-NaBH4 treated-smRNA-rep3

city: Copenhagen N

last: Vinther

address: Ole Maaloes Vej 5

department: Biology

description:
Small RNA libraries were prepared using “The NEBNext Multiplex Small RNA” kit according to manufactures protocol
yeast_tRNA_out.txt

source_name: yeast

tag: nabh4 treatment

value: 0.3 M NaBH4, incubated at 0 C for 30 minutes in darkness


title: AFB140

city: Paris

address: 28 rue du docteur Roux

description: SAMPLE 20


title: neonatal_rat_cardiomyocyte_neg_1

source_name: neonatal rat, cardiomyocyte, negative siRNA, replicate 1


title: EUB038

description: SAMPLE 24


title: IP_3726

description: Total reads :  14 936 423  ; average fragment size : 298

value: E.coli xylE::parSF

tag: antibody


title: S. cerevisiae-WT-NaBH4 treated-smRNA-rep2


title: 409B2 (II), biological rep1


title: input_3726

description: Total reads :  2 510 131; average fragment size : 303


title: AFB195

description: SAMPLE 19


title: S. cerevisiae-WT-NaBH4 treated-smRNA-rep1


title: EUB107

description: SAMPLE 18


title: IP_3509

description: Total reads :  11 726 332 ; average fragment size : 207


title: 409B2 (II), biological rep2