title: RiboSeq rep3

city: Boston

first: Harleen

last: Saini

address: 240 Longwood Avenue

institute: Harvard Medical School

data_processing:
Genome build: rnor6
Library strategy: Ribosome profiling
Reads in raw data were trimmed to remove a 7nt long barcode sequence from the 5'ends. The adapter was trimmed from each read and reads >= 24 nt were retained. Reads aligning completely to rRNA, tRNA, repeat elements (catalogued by RepeatMasker), and mitochondrial genome were removed prior to alignment to the rat genome using TopHat version 2.0.14:  $ tophat -p 4 --library-type fr-secondstrand --b2-sensitive -g 10 --keep-tmp -G <genes.gtf> -o <output_directory> <genome_index_base> <filtered_reads.fastq>
The alignments are provided as bigwig files. They were prepared using bamCoverage from deepTools version 2.2.2:  bamCoverage --binSize 10 -p 2 -b <input.bam> -o <output.bw>
Please note: If the insert is too small in polyA+ RNAseq or ribosome profiling raw data, then reads would be expected to contain the adaptor sequence "TGGAATTCTCGGGTGCCAAGG". We recommend removing the adaptor and any trailing sequence prior to genome alignment. One way to do so is by using the cutadapt program (Martin, 2011):  $ cutadapt -a TGGAATTCTCGGGTGCCAAGG -o outputfile inputfile

organism: Rattus norvegicus

source_name: RiboSeq

growth_protocol: Hippocampal neurons were extracted from embryos of pregnant rats at 19 days of gestation and maintained in culture for 14 days. To separate projections from cell bodies, neurons were cultured on poly-L-lysine coated semipermeable membranes with 1 μm holes. For cytoplasmic fractionation, neurons were cultured on 6-cm poly-L-lysine coated, standard tissue culture plates. Cells were maintained in Neurobasal media (Invitrogen 21102-049), supplemented with glutamax (Gibco™ 35050061), antibiotic/antimycotic (Gibco™ 15240062), and B27 (Gibco™ 17504001). On day three, Cytosine beta-D-arabinofuranoside (Sigma-Aldrich #C1768), a DNA replication inhibitor, was added to the media to inhibit glial cell division. On day six and day twelve of neuron culture, half of the Neurobasal media was replaced with fresh media. On day 14, cells were harvested for sequencing library preparation.

extract_protocol:
Library preparation method: Ricci E.P., … Moore M.J. (Nat. Struct. Mol. Biol., 2014)
Cyclohexamide was added to the media to inhibit translation and stall ribosomes. The plates were placed on ice, media was removed and the cells were rinsed with ice-cold PBS (containing cyclohexamide). Cells were lysed using lysis buffer (10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 100 mM KCl, 1% Triton™ X-100, 2 mM DTT, 100 μg/ml cycloheximide, protease inhibitor (Complete, EDTA-free, Roche)) and centrifuged to pellet the nuclei. The supernatant was recovered to prepare ribosome profiling and polyA+ RNA-seq libraries.    To purify ribosome occupied RNA, the lysate was treated with RNase T1 (Fermentas) and RNase A (Ambion) to break down polysomes into monosomes, followed by density gradient ultracentrifugation. A gradient fractionator (Brandel) was used to identify and collect the monosome enriched fraction. RNA was subsequently isolated from the monosome enriched fraction for library preparation. Polyadenylated RNA from the cytoplasmic fraction was also sequenced. To extract RNA for ribosome profiling and polyA+ RNAseq, SDS and proteinase K was added to the lysate and samples were incubated at 42°C for 45 minutes. One volume of acid phenol/chlorofom (Ambion AM9720, pH 4.5) was added and the samples were vortexed for 30 seconds followed by centrifugation at 12,000 x g for 15 minutes. The supernatant was transferred to a clean microcentrifuge tube and 0.1 volume of sodium acetate (3 M, pH 5.2) and 10 mM final concentration of MgCl2 were added. To precipitate RNA, 1 volume of 100% isopropanol was added to the solution and centrifuged at 12,000 x g for 35 minutes. The precipitated RNA was rinsed with 70% ethanol, air dried, and reconstituted in water.

tag: tissue source

value: Embryonic day 19 rat hippocampus

value: Primary hippocampal neurons

tag: days in vitro

tag: cell culture platform

value: Standard 6 cm culture dish

tag: cellular fraction

value: Cytoplasm

tag: molecule subtype

value: Ribosome occupied RNA fragments


title: cyto polyA RNAseq rep3

status: Public on Apr 18 2019

type: SRA

state: MA

country: USA

library_source: transcriptomic

molecule: polyA RNA

source_name: cyto polyA RNAseq

extract_protocol:
Library preparation method: Heyer E.E., … Moore M.J. (Nucleic Acids Res., 2015)
Cyclohexamide was added to the media to inhibit translation and stall ribosomes. The plates were placed on ice, media was removed and the cells were rinsed with ice-cold PBS (containing cyclohexamide). Cells were lysed using lysis buffer (10 mM Tris-HCl pH 7.5, 5 mM MgCl2, 100 mM KCl, 1% Triton™ X-100, 2 mM DTT, 100 μg/ml cycloheximide, protease inhibitor (Complete, EDTA-free, Roche)) and centrifuged to pellet the nuclei. The supernatant was recovered to prepare ribosome profiling and polyA+ RNA-seq libraries.    To purify ribosome occupied RNA, the lysate was treated with RNase T1 (Fermentas) and RNase A (Ambion) to break down polysomes into monosomes, followed by density gradient ultracentrifugation. A gradient fractionator (Brandel) was used to identify and collect the monosome enriched fraction. RNA was subsequently isolated from the monosome enriched fraction for library preparation. Polyadenylated RNA from the cytoplasmic fraction was also sequenced. To extract RNA for ribosome profiling and polyA+ RNAseq, SDS and proteinase K was added to the lysate and samples were incubated at 42°C for 45 minutes. One volume of acid phenol/chlorofom (Ambion AM9720, pH 4.5) was added and the samples were vortexed for 30 seconds followed by centrifugation at 12,000 x g for 15 minutes. The supernatant was transferred to a clean microcentrifuge tube and 0.1 volume of sodium acetate (3 M, pH 5.2) and 10 mM final concentration of MgCl2 were added. To precipitate RNA, 1 volume of 100% isopropanol was added to the solution and centrifuged at 12,000 x g for 35 minutes. The precipitated RNA was rinsed with 70% ethanol, air dried, and reconstituted in water.

tag: cell type

value: polyA RNA


title: cyto polyA RNAseq rep1


title: RiboSeq rep2

molecule: total RNA


title: cyto polyA RNAseq rep2


title: F49CA1

city: Riversidy

first: Giovanna

last: Pozuelos

state: California

address: 3401 Watkins Drive

institute: University of California, Riverside

description:
F49CA1: Female, age 49, before clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

data_processing:
Libraries were sequenced as single-end 75 base pair reads using an Illumina NextSeq500 following the manufacturer's instructions.
The RNA-Seq analysis workflow implemented by systemPipeR was used to perform all the downstream data processing.
Adapter sequences and low quality tails were removed from the raw reads using the Trimmomatic package
The preprocessed reads were then aligned against the UCSC hg19 human reference genome using Tophat2 package (Version 2.0.14)
Read counting was performed with the summarizeOverlaps function of the GenomicsAlignment package
Using a cut-off value of at least 1 RPKM average in all the samples, the raw expression counts of the remaining 10,938 genes passing this filter were used for differential gene expression analysis using EdgeR29
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts, RPKM, CPM values and edgeR differential gene expression calls for every gene in each Sample.

organism: Homo sapiens

source_name: Nasal Epithelium

extract_protocol:
RNA was isolated from human nasal scrapes using RNeasy micro kits (Catalogue #74034, Germantown, MD) and the isolated RNA was stored at -80oC untill further processing
Libraries were sequenced as single-end 75 base pair reads using an Illumina NextSeq500 following the manufacturer's instruction
poly-A RNA-Seq

treatment_protocol: Four non-smoker females were individually exposed to clean air using a helmet for a total of ~3 hours. The same individuals returned after ~21 days or more, and were exposed to THS using the same laboratory conditions (wearing the helmet). Nasal scrapes were collected before and after each with the end goal to peform RNAseq.

tag: tissue

value: Nasal Epithelium

tag: gender

value: female

tag: age

tag: exposure

value: before clean air exposure


title: P1A8_THP_and_AGN_2

city: Cambridge

first: Moran

last: Dvela Levitt

address: 415 Main Street

institute: Broad Institute

data_processing:
Illumina HiSeq2500 sequencing system (2x101 Bp Reads) software used for basecalling. The provided data from Sequencing platform  are de-multiplexed and aggregated Picard Bam files.
Bam files received from sequencing platform were reverted to fastq files followed by alignment of paired end reads  to the mm10 mouse or hg19 human reference genome using STAR v2.5.2b.
Quality Control metrics were obtained using RNA-SeQC v2.3.1.
Expression levels were estimated by running RSEM v1.3.0 with default parameters on these alignments.
Genome_build: hg19
Supplementary_files_format_and_content: Raw expression levels produced by RSEM

growth_protocol: 200,000 cells/well were plated on 12-well plate.

extract_protocol:
RNaesy- Qiagen kit-(#74106) was used for RNA extraction
Concentrations of purified RNA were measured with the QuantiTTM RiboGreen® RNA Assay Kit  and normalized to 5 ng/μL. An automated variant of the Illumina TruSeqTM Stranded mRNA Sample Preparation Kit was used for library preparation from a 200 ng aliquot of RNA. This method preserves strand orientation of the RNA transcript and uses oligo dT beads to select mRNA from the total RNA sample. Following cDNA synthesis and enrichment, cDNA libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.

treatment_protocol: 48 hours following plating, 1uM of BRD4780 was added for 24 hours. Then, 100nM of thapsigargin was added for 12 hours.

value: MUC1 kidney disease patient derived kidney epithelial cells

tag: treament

value: ER stress (thapsigargin) +  BRD4780


title: N1H1_Pool_No_Dox_3

growth_protocol: 200,000 cells/well were plated on 12-well filter plates, cells were grown for 4 days before RNA extraction

value: normal kidney cells


title: RiboSeq rep1


title: HMO_Treated_Rep1

type: RNA

city: Fermoy

first: Rita

last: Hickey

state: County Cork

address: Moorepark

department: Food Bioscience

country: Ireland

institute: Teagasc Food Research Centre

description: Gene expression in HT29 cells exposed to 3' Siallylactose

hyb_protocol: 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs to an Agilent Human GE 8x60k Microarray. Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile.

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner

data_processing: Data was extracted from the scanned image using Feature Extraction 10.7 (Agilent Technologies)

source_name: Human colon adenocarcinoma cell line HT-29 exposed to 4mg/ml 3'-Siallylactose for 24hrs

label_protocol: 200 ng of total RNA were converted into labelled complementary RNA with nucleotides coupled to fluorescent dye Cy3 using the Low-Input QuickAmp kit (Agilent) following the manufacturer’s protocol. The purity and quantity of each sample were again determined by spectroscopy (A260/A280) and the size distribution was assessed using an Agilent Bioanalyzer

growth_protocol: Human colon adenocarcinoma cell line HT-29 cells were fgrown in McCoy's 5A modified medium supplemented with 10% fetal bovine serum in 75 cm2 tissue culture flasks at 37 degrees celsium in 5% CO2.The medium was changed every other day and the cells were passaged at 80% confluency.

extract_protocol: Following treatment, the culture medium was removed from the cells which were washed twice with Phosphate buffered saline (PBS) and the cells detached from the flask using a cell scraper. The suspended cells were centrifuged in a microcentrifuge (14,000 rpm). The resulting cell pellets (10 per flask) were stored at -80 degrees celsius until required. Total RNA was extracted from the frozen pellets using a HighPure RNA isolation kit (Roche). The quality and quantity of each RNA sample was determind on a BioAnalyser (Agilent Technologies). Only samples with an A260/A280 ratioo > 1.8 were used for analysis.

treatment_protocol: 24 hours prior to treatment the culture medium was replaced with McCoy's 5A medium supplemented with 2% Fetal bovine serum. To begin the treatment the culture medium was removed and replaced with McCoys 5A medium supplemented with  Bovine Colostrum Oligosaccharides (BCO) at 4 mg/ml or Human Milk Oligosaccharides (HMO) at 4mg/ml or 3' - Siallylactose at 4mg/ml . Cells in nonsupplemented McCoy's 5A medium were used as a control.

tag: cell line

value: human epithelial adenocarcinoma cell line

tag: treatment


title: BCF_Treated_Rep1

description: Gene expression in HT29 cells exposed to Bovine Colostrum Fraction

source_name: Human colon adenocarcinoma cell line HT-29 exposed to 4mg/ml Bovine Colostrum Fraction for 24hrs


title: whole-cell total RNAseq rep3

data_processing:
Genome build: rnor6
Reads aligning completely to rRNA, repeat elements (catalogued by RepeatMasker), 7sl (or SRP), and mitochondrial genome were removed using bowtie2 version 2.2.3:  $ bowtie2 -p 2 -N 1 --no-unal --un-conc <output_unaligned.fastq> --al-conc <output_aligned.fastq> -1 <input_R1.fastq> -2 <input_R2.fastq> -S <output_alignments.sam>
Filtered reads were mapped to the rat genome (Ensembl release 81, Rnor_6.0, annotation downloaded on July 24, 2015) with TopHat version 2.1.1 using the following command:   $ tophat -p 6 --library-type fr-firststrand --b2-sensitive --mate-inner-dist 100 -i 30 -g 10 --max-coverage-intron 5000000 -G <genes.gtf> -o <output_directory> <genome_index_base> <input_filtered.R1.fastq> <input_filtered.R2.fastq>
The alignments are provided as bigwig files. They were prepared using bamCoverage from deepTools version 2.2.2:  bamCoverage --binSize 10 -p 2 -b <input.bam> -o <output.bw>

source_name: whole-cell total RNAseq

extract_protocol:
Library preparation method: Zhang Z., … Zamore P.D. (Silence, 2012).
RNA extraction: For neurons cultured on semipermeable membranes, RNA was extracted following the steps recommended by TRIzol® reagent (ThermoFisher #15596018) manual with minor modifications. Briefly, media was removed and TRIzol® was applied to the projections-side, the surface was scraped using a cell-scraper and lysate was gently pippeted and transferred into a clean tube. Lysate was similarly collected from the cell body side of the membrane. The lysate was vortexed briefly and kept at room temperature for 5 minutes. 200 μl of chloroform per 1 ml of TRIzol® was added for phase separation. The tubes were vigorously shaken by hand and centrifuged at 12,000 x g for 15 min at 4°C. The aqueous phase was transferred to fresh tubes and the chloroform wash was repeated two more times. RNA was precipitated by adding 100% isopropanol. Samples were incubated at room temperature for 15 min, and centrifuged at 12,000 x g at 4°C for 15 min. The supernatant was removed without disturbing the precipitated RNA. The RNA precipitate was rinsed two times 75% ethanol and finally dissolved in RNase-free water by incubating for 10 min at 55-60°C.

value: Semipermeable membrane with 1 μm holes

value: Whole-cells

value: Total RNA, rRNA depleted


title: Untreated_Rep1

description: Gene expression in untreated HT29 cells

source_name: Human colon adenocarcinoma cell line HT-29 Untreated

value: untreated


title: BCF_Treated_Rep2

value: exposed to 4mg/ml Bovine Colostrum Fraction for 24hrs


title: F44CA2

description:
F44CA2: Female, age 47, after clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

value: after clean air exposure


title: projections total RNAseq rep2

source_name: projections total RNAseq

value: Embryonic day 19 rat hippocampus

value: Primary hippocampal neurons

value: Projections


title: projections total RNAseq rep3


title: P1A8_THP_and_AGN_1


title: whole-cell total RNAseq rep2


title: Untreated_Rep2

description: Gene expression in untreated HT29 cells


title: F44CA1

description:
F44CA1: Female, age 47, before clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt


title: whole-cell total RNAseq rep1


title: HMO_Treated_Rep3

value: exposed to 4mg/ml 3'-Siallylactose for 24hrs


title: BCF_Treated_Rep3


title: Untreated_Rep3

description: Gene expression in untreated HT29 cells


title: P1A8_THP_and_AGN_3


title: BMDMs-EVs-miR-93

first: Yang

last: Jin

address: 72 E Concord St, R304

institute: Boston University Medical Campus

description:
BMDMs were exposed to epithelial EVs transfected with miR-93 mimics
2194_BMDM-4

data_processing:
After completion of the proton run, the raw sequence files were aligned to the mouse genome (MM10) reference sequence by the alignment plugin tool in Ion Torrent Suite software using the default parameters.
The genes and transcripts annotations that were used were retrieved from the Ensembl database. Aligned BAM files were used for further analysis.
Quality control was assessed by the Strand NGS program, which determined the pre- and post-alignment quality of the reads for each sample.
The aligned reads were then filtered based on alignment score (≥90), match count (≤1), mapping quality (≥25) and reads that failed vendors QC were removed.
After filtering, the aligned reads were normalized and quantified using the DEseq algorithm by the Strand NGS program.
DEGs were determined for each group and Fold change analysis was completed by comparing specific samples.
Genome_build: MM10
Supplementary_files_format_and_content: xls file includes raw counts of sequencing reads, normalized abundance measurements and fold changes for each sample.

organism: Mus musculus

source_name: Bone marrow-dervide macrophages

growth_protocol: Isolated bone marrow cells were cultured with 30 % of L929-conditioned medium for 5 to 7 days to induce differentiation of the bone marrow monocyte/macrophage progenitors into BMDMs

extract_protocol:
Total RNAs were extracted from the treated BMDMs (n = 4 biological replicates were pooled) using MiRNeasy Mini Kits (Qiagen, Valencia, CA).
cDNA libraries were constructed using Ion Total RNA-Seq Kit v2 from Life Technologies (Cat# 4479789) and manufacturer's recommended protocol.

treatment_protocol: BMDMs were treated with lung epithelial Beas2B cell-derived EVs transfected with scrambled control RNA, miR-17 mimics, or miR-93 mimics for 16 h.

tag: strain

tag: source

value: bone marrow

value: 6 - 8 weeks

tag: transfection

value: miR-93 mimics


title: P1A8_THP_3

value: MUC1 kidney disease patient derived kidney epithelial cells

value: ER stress (thapsigargin)


title: HMO_Treated_Rep2


title: P1A8_THP_2


title: F48CA2

description:
F48CA2: Female, age 48, after clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

value: Nasal Epithelium

value: female


title: projections total RNAseq rep1

value: Semipermeable membrane with 1 μm holes


title: BMDMs-EVs

description:
BMDMs were exposed to epithelial EVs transfected with scrambled control RNAs
2192_BMDM-2

value: scrambled control RNAs


title: P1A8_THP_1


title: WT BMDMs

description:
WT BMDMs
2191_BMDM-1

value: WT


title: P1A8_DMSO_3

value: DMSO


title: P1A8_DMSO_2


title: Retina_P7_CTL

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

data_processing:
Basecalls performed using Illumina RTA 2.4.11
Samples demultiplexed using bcl2fastq 2.20
For miRNA entries with identical or near-identical sequences in the miRBase mature  database, a manual calibration was created and a new, combined miRNA entry was  made for each particular miRNA set. For example, the sequence of hsa-miR-151b is  entirely contained within the sequence of hsa-miR-151a-5p. As a result, the miRNA  entry is hsa-miR-151b/151a-5p.
Reads are first processed by trimming off the 3’ adapter and low-quality bases using cutadapt (cutadapt.readthedocs.io/en/stable/guide.html). Reads with no adapter sequence are tallied (no_adapter_reads).
Following trimming, the insert sequences and UMI sequences are identified. Reads with less than 16 bp insert sequences (too_short_reads) or less than 10 bp UMI sequences (UMI_defective_reads) are discarded.
To annotate the insert sequences, a unique sequence set is made for all readsets/samples in a submitted job. Following this, a sequential alignment strategy is followed to map to different databases (perfect match to miRBase mature, miRBase hairpin, noncoding RNA, mRNA and otherRNA, and ultimately a second mapping to miRBase mature, where up to two mismatches are tolerated) using bowtie (bowtie-bio.sourceforge.net/index.shtml). At each step, only unmapped sequences pass to the next step. Read counts for each RNA category (miRBase mature, miRBase hairpin, piRNA, tRNA, rRNA, mRNA and otherRNA) are calculated from the mapping results (miRNA_Reads, hairpin_Reads, piRNA_Reads, etc.). miRBase V21 is used for miRNA, and piRNABank is used for piRNA.
A species-specific miRBase mature database is then used, and all remaining unmapped sequences are aligned to the respective genome (RGSC Rnor_6.0) to identify possible novel miRNA molecules.
For each sample, all reads assigned to a particular miRNA or piRNA ID are counted, and the associated UMIs are aggregated to count unique molecules. Read counts and UMI counts are presented in the output Excel ® file “miR_piRNA” sheet. For sequences aligned with tRNAs or otherRNAs, these results are displayed in the “tRNA” or “otherRNA” sheet, respectively. For sequences aligned to genome at the last alignment step, the same information (read counts and clustered UMIs) are output to “notCharacterized_mappable” sheet. Remaining reads are also tallied (notCharacterized_notMappable).
Genome_build: RGSC Rnor_6.0
Supplementary_files_format_and_content: Excel files generated from the pipeline contains a summary tab as well as UMI and read counts for the various miRNAs, pi_RNAs, tRNAs and other small RNAs identified.

source_name: eye

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
Qiaseq miRNA

value: retina

tag: condition

value: normoxic (CTL)

value: Sprague Dawley


title: Retina_p17_ROI

value: hyperoxic (OIR)


title: Retina_P7_ROI


title: Retina_p14_ROI


title: Retina_p14_CTL


title: F27CA2

description:
F27CA2: Female, age 27, after clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

value: after clean air exposure


title: F48CA1

description:
F48CA1: Female, age 48, before clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

value: before clean air exposure


title: Retina_p17_CTL


title: choroid_P7_ROI

value: choroid


title: P1A8_DMSO_1


title: choroid_P7_CTL


title: choroid_p17_ROI


title: BMDMs-EVs-miR-17

description:
BMDMs were exposed to epithelial EVs transfected with miR-17 mimics
2193_BMDM-3

value: bone marrow

value: 6 - 8 weeks

value: miR-17 mimics


title: MCF10A cells_RUNX1 ChIPseq

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

library_source: genomic

data_processing:
Base calling was done using Illumina RTA 2.4.6
Reads were aligned to human genome hg38 using Bowtie2 alignment.
Peaks were called using the MACS algorithm with setting: callpeak -t CHNM36.bam.sorted.bam -c CHNM35.bam.sorted.bam -f BAM -n RUNX1ChIP_MCF10AOEq0.05 -g hs -B -q 0.05
Genome_build: hg38
Supplementary_files_format_and_content: peaks

molecule: genomic DNA

source_name: Engineered MCF10A cells (ATCC® CRL-10317)

growth_protocol: MCF10A cells were cultured in DMEM/F12 media supplemented with 5% horse serum, 10 µg/ml human recombinant insulin, 20 ng/ml human EGF, 500 ng/ml Hydrocortisone, 100ng/ml Cholera toxin and antibiotics.

extract_protocol:
ChIP DNA was extracted by standard phenol approach.
TruSeq ChIP Library Prep Kit (IP-202-1012)

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 24 hours before ChIPseq

tag: genotype

value: RUNX1-deleted MCF10A cell line

value: transduced RUNX1-KO MCF10A cells with lentiviruses that inducibly express RUNX1; treated RUNX1-inducible MCF10A cells with doxycycline

tag: chip antibody


title: MCF10A cells_Input DNA


title: choroid_p17_CTL


title: HEK293T_IP (RIP-seq)

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

description: Reads were recommended to trim to 50 to get rid of bad quality bases

data_processing:
Basecalls performed using illumina bcl2fastq2.
Adapters were trimmed with cutadapt.
Clean reads were mapped to the reference genome with Tophat2
m5C peak analysis was then performed. Each gene was split into the 100-nucleotide sliding windows and an enrichment fold (winscore) was calculated for each window
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: HEK293T, cell line

extract_protocol:
Total RNA was isolated from cultured cells using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
Polyadenylated mRNA was first fragmented with Magnesium RNA Fragmentation Module and then cleaned up using ethanol precipitation. 100ng RNA was saved to serve as input control and the rest was incubated with 5ug anti-m5C antibody in IPP buffer overnight at 4℃. 60μl Protein-G magnetic beads was pre-blocked with 0.5mgml-1 BSA at 4℃ for 2h and then added for immunoprecipitating m5C-Ab mixture at 4℃ for another 2h. After washing with IPP buffer 3 times, RNA was competitively eluted from the beads with 20mM 5-Methylcytosine hydrochloride , followed by ethanol precipitation. RNA was resuspended in 8μl water. VAHTS Stranded mRNA-seq library prep kit (Vazyme) was used for library construction of both IP and input RNAs.

tag: rip antibody

value: 5-mC antibody, Diagenode, catalog:C15200003, lot:003


title: RUNX1 KO1, repeat4 [RSNM21]

description:
RSNM21_S52
processed data file: matrix_RUNX1.xlsx, RUNX1_KO1vsWT.csv

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome (Human - hg19) and the annotated  transcripts using STAR to make bam files.
Both the normalized count and the raw count are provided as part of the data delivery.  The read count matrix files were obtained from the bam files using the R package GenomicAlignments in the Bioconductor. The differentially expressed genes were obtained by using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: matrix file of unnormalized counts for each transcript of each sample; Differential expression of CBFB KO vs. WT, CBFB KO1 vs. WT, CBFB KO2 vs. WT

source_name: MCF10A_RUNX1 KO1

extract_protocol:
RNA were extracted with Trizol followed by cleanup using the Qiagen's Rneasey kit .
TruSeq mRNA Prep Kit  RS-122-2101
illumina TruSeq mRNA Prep Kit RS-122-  2101

treatment_protocol: No treatment

value: MCF10A cells (ATCC CRL-10317)

tag: genotype/variation

value: RUNX1 KO1

tag: passages

value: less than 30


title: RUNX1 KO2, repeat4 [RSNM23]

description:
RSNM23_S50
processed data file: matrix_RUNX1.xlsx, RUNX1_KO2vsWT.csv

source_name: MCF10A_RUNX1 KO2

value: RUNX1 KO2


title: choroid_p14_ROI


title: projections PASseq rep3

data_processing:
Genome build: rnor6
Reads were trimmed using cutadapt version 1.7.1 to remove a 7nt barcode sequence from the 5' end and stretches of As from the 3' end. The reads were further selected for > 35 quality and minimum 25 nt length. Filtered reads were aligned to rnor6 genome using the following TopHat2 parameters:  $ tophat/2.1.1/tophat -p 4 --library-type fr-secondstrand --b2-very-sensitive --no-novel-juncs -i 30 -g 10 -G <genes.gtf> -o <output_directory> <genome_index_base> <PASseq_reads.fastq>. PolyA sites were identified using CleanUpdTseq (Sheppard et al., 2013), and read coverage on statistically significant polyA sites is provided as a bigwig file.

source_name: projections PASseq

extract_protocol:
Library preparation method: Ashar-Patel A., … Moore M.J. (Scientific Reports, 2017).
RNA extraction: For neurons cultured on semipermeable membranes, RNA was extracted following the steps recommended by TRIzol® reagent (ThermoFisher #15596018) manual with minor modifications. Briefly, media was removed and TRIzol® was applied to the projections-side, the surface was scraped using a cell-scraper and lysate was gently pippeted and transferred into a clean tube. Lysate was similarly collected from the cell body side of the membrane. The lysate was vortexed briefly and kept at room temperature for 5 minutes. 200 μl of chloroform per 1 ml of TRIzol® was added for phase separation. The tubes were vigorously shaken by hand and centrifuged at 12,000 x g for 15 min at 4°C. The aqueous phase was transferred to fresh tubes and the chloroform wash was repeated two more times. RNA was precipitated by adding 100% isopropanol. Samples were incubated at room temperature for 15 min, and centrifuged at 12,000 x g at 4°C for 15 min. The supernatant was removed without disturbing the precipitated RNA. The RNA precipitate was rinsed two times 75% ethanol and finally dissolved in RNase-free water by incubating for 10 min at 55-60°C.

tag: tissue source

value: Embryonic day 19 rat hippocampus

tag: cell type

value: Primary hippocampal neurons

tag: days in vitro

tag: cell culture platform

value: Semipermeable membrane with 1 μm holes

tag: cellular fraction

value: Projections

tag: molecule subtype

value: polyA RNA


title: choroid_p14_CTL

tag: tissue

value: normoxic (CTL)

value: Sprague Dawley


title: CBFB_KO, poly, rep2

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome (Human - hg19) and the annotated  transcripts using STAR.
Both the normalized count and the raw count are provided as part of the data delivery.
Genome_build: hg19
Supplementary_files_format_and_content: The gene expression quantification analysis (RSEM) was performed for all samples using STAR/RSEM tools.
Supplementary_files_format_and_content: expected_count  TPM     FPKM

source_name: MCF10A cells (ATCC® CRL-10317)

extract_protocol:
RNA were extracted with Trizol followed by cleanup using the Qiagen's Rneasey kit .
TruSeq mRNA Prep Kit  RS-122-2101

treatment_protocol: Two million WT and CBFB_KO MCF10A cells were treated with 100 µg/ml of cycloheximide at 37°C for 30 min. Afterwards, cells were washed with chilled PBS and harvested with trypsin. Subsequently, cells were lysed in polysome lysis buffer (20mM Tris, pH7.2, 130 mM KCl, 15 mM MgCl2, 2.5 mM DTT, 0.5% NP-40, 0.2mg/ml Heparin, 0.5% deoxycholic acid, 100µg/ml cycloheximide supplemented with protease inhibitors and RNase inhibitors) for 20 min at 4°C. Cleared lysate was prepared by centrifuging samples at 8000g for 10 min. Further, lysate was carefully layered upon 10-50% linear sucrose gradient and ultracentrifuged at 100,000g at 4°C for 2 hr. After centrifuging, fractions were obtained using fractionator (Biocomp Instruments, Fredericton, Canada).

value: less than 20

tag: cell line

value: CBFB knockout

tag: fraction

value: polyribosomal


title: projections PASseq rep2


title: F27CA1

description:
F27CA1: Female, age 27, before clean air exposure
Final_supplemental_counts_rpkm_cpm_edger_ClearAir.txt

value: Nasal Epithelium

tag: gender

value: female

tag: age

tag: exposure

value: before clean air exposure


title: projections PASseq rep1


title: RUNX1 KO2, repeat3 [RSNM17]

description:
RSNM17_S56
processed data file: matrix_RUNX1.xlsx, RUNX1_KO2vsWT.csv

value: MCF10A cells (ATCC CRL-10317)


title: CBFB_KO, free, rep2

value: free


title: RUNX1 KO1, repeat3 [RSNM15]

description:
RSNM15_S58
processed data file: matrix_RUNX1.xlsx, RUNX1_KO1vsWT.csv

value: RUNX1 KO1

value: less than 30


title: CBFB_KO, mono, rep2

value: mono


title: WT, repeat3 [RSNM13]

description:
RSNM13_S60
processed data file: matrix_RUNX1.xlsx

value: WT


title: whole-cell PASseq rep1

source_name: whole-cell PASseq

value: Embryonic day 19 rat hippocampus

value: Primary hippocampal neurons

value: Semipermeable membrane with 1 μm holes

value: Whole-cells


title: whole-cell PASseq rep2

value: polyA RNA


title: E.coli stationary B

city: Rehovot

first: yitzhak

last: Pilpel

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Read were trimmed using homerTool
Alignment was done to the genome concatenate with mature tRNA (Chan, P.P. & Lowe, T.M. (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucl. Acids Res. 44(Database issue):D184-D189.) using Bowtie2 with parameters --very-sensitive-local -a. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were randomly assigned when mapping to identical anticodon, and discarded from the analysis if aligned to different anticodon.
Read count was done using BedTools-coverage count.
Genome_build: ASM584v2
Supplementary_files_format_and_content: read counts of mature tRNA and total genome of all samples

organism: Escherichia coli

source_name: E.coli culture growth

growth_protocol: cells were grown in of 3ml of modified MOPS rich defined medium made with the following recipe: 10X MOPS rich buffer, 10X ACGU nucleobase stock and 100X 0.132M K2HPO4 (Teknova, Cat. No. M2105) were used at 1X final concentration. Medium was supplemented with 0.25% glucose as carbon source, 10−4% thiamine, 17.2mM Serine, 640µM Lysine, 661µM Arginine, 592µM Histidine, 464µM Tyrosine and 800µM of all 15 remaining amino acids. pH was adjusted to 7.4 using 1M NaOH . Cultures were grown at 37°C until reaching stationary phase. Cells were then diluted 1:1000 into  and grown at 37°C  to OD values roughly corresponding to early exponential phase, late exponential phase, and stationary phase

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. 0.1uM yeast PhetRNA was added to 4ug total RNA as a spike-in. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

treatment_protocol: cells were centrifuged at 12,000 rpm for 1 min, frozen in liquid nitrogen and stored at -80 ̊C until RNA extraction.

tag: strain

tag: culture stage

value: stationary


title: whole-cell PASseq rep3


title: CBFB_KO, poly, rep1

value: less than 20

value: CBFB knockout


title: LDO 18

city: West Lafayette

first: Maria

last: Sepulveda

state: Indiana

address: 195 Marsteller St.

department: Forestry and Natural Resources

institute: Purdue University

description:
Whole body (n = 2)
20° C, 30 ppt, 2 ppm DO, 15 ppb PAH

data_processing:
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to F. heteroclitus genome using Tophat
Transcript assembly, read counts, and normalization of fragments per kilobase of transcript per million fragments mapped (FPKM) was done using Cufflinks
Significant differential gene expression changes between groups was determined by one-way ANOVA with Benjamini Hochberg multiple testing corrections
Genome_build: F. heteroclitus genome (NCBI genome ID 743). The file GEO_seq_Fundulusgrandis_Annotations.xlsx contains the gene annotation and chromosome location information for each entry in the processed data files.
Supplementary_files_format_and_content: .COUNT files including read counts

organism: Fundulus grandis

growth_protocol: Animals were maintained  in 30 ppt artificial sea water at 30 °C for duration of experiment.

extract_protocol:
Qiagen RNEasy, according to manufacturer's protocol
Illumina TruSeq Stranded mRNA kit to construct polyA libraries

treatment_protocol: F. grandis from 1 life stage (larval) were subjected to oil exposure (15 ppb HEWAF) under normoxic (≥ 5 mg/L oxygen)  hypoxic ( ≤ 2 mg/L oxygen) high salinity ( 30 ppt) low salinity (3 ppt) high temperature (30C) low temperature (20C) for 48 hours.

value: whole body

value: 48 h post hatch

tag: oil concentrtation

value: 15 ppb

tag: oxygen concnetration

value: ≤ 2 mg/L


title: HEK293T_input (RIP-seq)

tag: rip antibody


title: RUNX1 KO2, repeat2 [RSNM11]

description:
RSNM11_S38
processed data file: matrix_RUNX1.xlsx, RUNX1_KO2vsWT.csv

value: MCF10A cells (ATCC CRL-10317)

tag: genotype/variation

value: RUNX1 KO2

tag: passages


title: CBFB_KO, mono, rep1


title: E.coli mid-log C

value: mid-log


title: RUNX1 KO1, repeat2 [RSNM9]

description:
RSNM9_S40
processed data file: matrix_RUNX1.xlsx, RUNX1_KO1vsWT.csv

value: RUNX1 KO1

value: less than 30


title: WT, repeat4 [RSNM19]

description:
RSNM19_S54
processed data file: matrix_RUNX1.xlsx

value: WT


title: CBFB_KO, free, rep1

value: free


title: LDO 16


title: E.coli exponential growth C

value: exponential


title: WT, poly, rep2

value: wild type

value: polyribosomal


title: LDO 15

description:
Whole body (n = 3)
20° C, 30 ppt, 2 ppm DO, 0 ppb PAH


title: RUNX1 KO2, repeat1 [RSNM5]

description:
RSNM5_S44
processed data file: matrix_RUNX1.xlsx, RUNX1_KO2vsWT.csv


title: WT, repeat2 [RSNM7]

description:
RSNM7_S42
processed data file: matrix_RUNX1.xlsx


title: E.coli exponential growth B


title: E.coli mid-log B


title: WT, mono, rep2

value: mono


title: RUNX1 KO1, repeat1 [RSNM3]

description:
RSNM3_S46
processed data file: matrix_RUNX1.xlsx, RUNX1_KO1vsWT.csv


title: LDO 14


title: WT, repeat1 [RSNM1]

description:
RSNM1_S48
processed data file: matrix_RUNX1.xlsx


title: WT, free, rep2

value: less than 20


title: E.coli exponential growth A


title: LDO 13


title: E.coli stationary A

value: stationary


title: LDO 12

description:
Whole body (n = 3)
20° C, 3 ppt, 2 ppm DO, 15 ppb PAH

value: whole body


title: WT, poly, rep1


title: W2mef suspended rep8

city: Accra

first: Prince

middle: Berko

last: Nyarko

state: Greater Accra

address: WACCBIP, Volta Road, University Of Ghana

department: Department of Biochemistry, Cell and Molecular Biology

country: Ghana

institute: West African Centre for Cell Biology of Infectious Diseases, University of Ghana

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

data_processing:
Bases were called and adaptor sequences were removed using the Illumina MiSeq software
Sequence reads were mapped to the P. falciparum 3D7 May 2015 v3.1 reference genome using hisat2 version 2.0.4 with parameters -p 16 -t -q --dta-cufflinks --phred33 -x.  Duplicate reads were marked and removed using Picard. Samtools was used to convert reads into BAM files.
Resulting bam files were filtered  to exclude reads with MAPQ scores < 60.
Reads were counted against the GTF_VarRifStev_filtered out.gtf annotation file and summarized, using the genomicAligments package in R (with the following settings: mode="Union", singleEnd=FALSE,ignore.strand=TRUE,fragments=FALSE).  Read counts were extracted from the assays accessor of the summarized experiment.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using the FPKM function of the DESeq2 package in R
Genome_build: P. falciparum 3D7 v3 reference genome
Supplementary_files_format_and_content: Comma-separated values files for raw counts and FPKM values.  Supplied as matricies with all samples in each file.

organism: Plasmodium falciparum

source_name: In vitro cultured cells

growth_protocol: All parasites were cultured at 37C in RPMI 1640 supplemented with 0.5% albumax, 20mg hypoxanthine, 2g sodium bicarbonate and 50µg/ml gentamicin sulfate using human group O+ erythrocytes in blood gas. Suspended cultures were rotated horizontally at 44rpm.

extract_protocol:
Schizonts were purified by percoll-alanine gradient centrifugation, lysed in TRIzol and RNA extracted by the TRIzol protocol
Stranded mRNA TruSeq libraries were prepared for sequencing using the standard Illumina protocol for this library type with a MiSeq sequencer

treatment_protocol: Purified schizonts were allowed to mature for 6 hours in the presence of 10µM E64 to block merozoite egress

tag: condition

value: Suspended

tag: time-point

value: Week 8

tag: Stage

value: Schizonts

tag: purification

value: Percoll-alanine


title: LDO 17

description:
Whole body (n = 3)
20° C, 30 ppt, 2 ppm DO, 15 ppb PAH

tag: tissue

value: 48 h post hatch

value: 15 ppb

value: ≤ 2 mg/L


title: WT, mono, rep1

tag: cell line


title: W2mef suspended rep7

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: LDO 11


title: Frontal_cortex_N1 (human_BS)

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: hg19

source_name: Frontal cortex

extract_protocol:
Total RNA was isolated from tissues or cultured cells using chloroform and isopropanol following the manufacturer’s protocol. Polyadenylated RNA was separated from total RNA using either GenElute mRNA miniprepKit (Sigma-Aldrich) or Oligo dT Magnetic Beads (Vazyme).
Bisulfite treatment was performed using the EZ RNA methylation kit (Zymo Research) with some modifications. In brief, 1μg of polyadenylated RNA was converted using three different conversion conditions. The quantity of the converted RNA was determined by Qubit. Libraries were then constructed using VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). In short, 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 3min in 2× frag/prime buffer. The fragmented RNA was then used for library construction, following the manufacturer’s protocol.

value: Frontal cortex


title: LDO 10


title: WT, free, rep1

tag: fraction


title: W2mef suspended rep6

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: WT, repeat3 [RS162]

description:
RS162_S16
processed data file: matrix_CBFB.xlsx, CBFB_KOvs_WT.csv

value: MCF10A cells (ATCC CRL-10317)

value: WT

value: less than 30


title: W2mef suspended rep5

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: CBFB KO, repeat2 [RS160]

description:
RS160_S2
processed data file: matrix_CBFB.xlsx, CBFB_KOvs_WT.csv

source_name: MCF10A_CBFB KO

value: CBFB KO


title: shRNA control

city: Shanghai

first: Tao

last: Yue

address: 540 Xinhua Road

department: Department of Rheumatology

institute: ShangHai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine

data_processing:
Adapters and reads with lower mapping quility were trimed by trim_galore.
Reads were aligned to the human hg38 reference genomes using the Hisat2.
Raw counts were quantified against Ensemble transcript and annotated by featureCount.
Differentially expressing genes were detected by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count for each sample.

source_name: FLS from rheumatoid arthritis patient

growth_protocol: RA FLS was cultured in 90% Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, USA) under 95% air and 5% CO2 at 37 ℃. FLS from passages 5–8 monolayer culture were used for the following experiments in this study.

extract_protocol:
Total RNA were extracted by using Trizol reagent (Invitrogen, USA), the concentration (>= 500ng/ul is qualified), purity (OD260/OD280 range from 1.8 to 2.2) and integrity (28S:18S >=1.5) were detected using Qubit® RNA Assay Kit with Qubit® 2.0 Flurometer (Life Technologies, USA), NanoPhotometer® spectrophotometer (IMPLEN, USA) and RNA Nano 6000 Assay Kit with Bioanalyzer 2100 system (Agilent Technologies, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pGPU6 and pEX-2 plasmids were used for establishment of control overexpression, lnc-ITSN1-2 overexpression, control shRNA, and lnc-ITSN1-2 shRNA plasmids by Shanghai Gene Bio-Tech Company (Shanghai, China).

tag: shRNA

value: shRNA control

value: synovial tissue


title: LDO 9

description:
Whole body (n = 3)
20° C, 3 ppt, 2 ppm DO, 0 ppb PAH

tag: age


title: WT, repeat2 [RS158]

description:
RS158_S4
processed data file: matrix_CBFB.xlsx, CBFB_KOvs_WT.csv


title: LDO 8


title: CBFB KO, repeat1 [RS156]

description:
RS156_S6
processed data file: matrix_CBFB.xlsx, CBFB_KOvs_WT.csv


title: W2mef suspended rep3

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: Lnc-ITSN1-2 shRNA

value: Lnc-ITSN1-2 shRNA


title: W2mef static rep6

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Static


title: CBFB KO, repeat3 [RS164]

description:
RS164_S14
processed data file: matrix_CBFB.xlsx, CBFB_KOvs_WT.csv


title: WT, repeat1 [RS154]

description:
RS154_S8
processed data file: matrix_CBFB.xlsx, CBFB_KOvs_WT.csv


title: overexpression control

value: overexpression control


title: LDO 7

value: whole body


title: HDO 23

description:
Whole body (n = 3)
20° C, 30 ppt, 6 ppm DO, 15 ppb PAH

tag: oxygen concentration

value: greater than or equal to 6 mg/L


title: VX_SHU4

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: processed data header: DPT16

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Gonadal fat

growth_protocol: Lean male mice maintained in standard chow diet.

extract_protocol:
RNA was extracted using RNAqueous-micro kit (Thermo Fisher from frozen samples homogenized using TissueLyser (Qiagen). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lean mice received either subdiaphragmatic vagotomy (sDVX) or sham-operated surgery. 4 weeks later, they received intracerebroventricular infusion of either vehicle or SHU9119 (1nmol/day) for 2 weeks using osmotic minipumps. During that period, all mice were fed isocalorically. Gonadal fat depots were weighed, frozen inmediately and stored at -80℃ prior RNA extraction.

tag: strain

value: 16 weeks old

tag: vagotomy

value: sDVX

tag: icv infusion

value: SHU


title: W2mef baseline rep8

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Baseline

value: Week 0

value: Schizonts

value: Percoll-alanine


title: VX_SHU3

description: processed data header: DPT15


title: W2mef baseline rep7

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: HDO 22

value: 48 h post hatch

tag: oil concentrtation

value: 15 ppb


title: HDO 21


title: VX_SHU2

description: processed data header: DPT14


title: W2mef baseline rep6

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: HDO 20

description:
Whole body (n = 3)
20° C, 30 ppt, 6 ppm DO, 0 ppb PAH


title: VX_SHU1

description: processed data header: DPT13


title: VX_Veh4

description: processed data header: DPT12

value: Veh


title: HDO 19


title: W2mef baseline rep4

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: WT_05_5.5months

city: Munich

first: Anja

last: Capell

state: Bavaria

address: Feodor-Lynen Str 17

department: Biomedical Center (BMC)

country: Germany

institute: Ludwig-Maximilians-University

description: MG534 panel

data_processing: NanoString data were normalized and analyzed using nSolver™ software version 3.0 (NanoString Technologies, Inc.).  RNA n counts were normalized using the geometric mean of five (Grn Ko study) to six (TremKO study) housekeeping genes including Cltc, Gapdh, Gusb, Hprt1 , Tubb5 and additionally Pgk1 for the Trem2KO study

source_name: microglia

growth_protocol: Housing conditions included standard pellet food and water provided ad libitum, 12-hour light-dark cycle at temperature of 22 °C with maximal 5 mice per cage and cage replacement once per week and regular health monitoring.

extract_protocol: Total RNA was isolated using mirVanaTM miRNA isolation kit (Ambion) according to the manufacturer's protocol

tag: gender

value: male

value: wildtype


title: WT_03_5.5months

description: MG534 panel

tag: genotype/variation


title: W2mef baseline rep3

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: HDO 18


title: VX_Veh3

description: processed data header: DPT11


title: W2mef static rep4

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Week 8


title: Lnc-ITSN1-2 overexpression

value: Lnc-ITSN1-2 overexpression

value: synovial tissue


title: HDO 17

description:
Whole body (n = 2)
20° C, 3 ppt, 6 ppm DO, 15 ppb PAH

value: whole body


title: VX_Veh2

description: processed data header: DPT10


title: WT_02_5.5months

description: MG534 panel


title: WT_01_5.5months

description: MG534 panel


title: HDO 16

description:
Whole body (n = 3)
20° C, 3 ppt, 6 ppm DO, 15 ppb PAH

value: greater than or equal to 6 mg/L


title: GrnKO_05_5.5months

description: MG534 panel

value: Grn knockout


title: VX_Veh1

description: processed data header: DPT9

value: 16 weeks old

value: sDVX


title: HDO 15


title: W2mef baseline rep1

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Baseline


title: W2mef baseline rep5

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Week 0


title: GrnKO_03_5.5months

description: MG534 panel


title: Sham_SHU3

description: processed data header: DPT7

value: Sham

value: SHU


title: GrnKO_04_5.5months

description: MG534 panel


title: GrnKO_02_5.5months

description: MG534 panel


title: HDO 14

description:
Whole body (n = 3)
20° C, 3 ppt, 6 ppm DO, 0 ppb PAH

value: 48 h post hatch


title: Sham_SHU4

description: processed data header: DPT8


title: Sham_SHU2

description: processed data header: DPT6


title: GrnKO_01_5.5months

description: MG534 panel


title: HDO 13


title: WT_04_5.5months

description: MG534 panel


title: Sham_SHU1

description: processed data header: DPT5


title: W2mef baseline rep2

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Schizonts

value: Percoll-alanine


title: M- DMAD embryos(3h) (replicate 1)

city: Beijing

first: Shunmin

last: He

address: 1 Beichen West Road,  Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
FastQC was used to make sure that the sequencing data were high quality
Reads were aligned to the dm6 genome assembly using Tophat2/STAR
Differential expression analysis was carried out by cuffdiff
Genome_build: dm6

organism: Drosophila melanogaster

source_name: 3h M- DMAD rep 1

extract_protocol:
Total RNAs were isolated from embryos at indicated stages using TRIzol reagent (Invitrogen) and mRNAs were then purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module according to the user manual.
Illumina sequencing libraries were constructed according to the manufacturer’s instructions. The libraries were then sequenced using the Illumina Hiseq2500 V4 and NovaSeq platform

value: M- DMAD

value: embryo


title: Dd2 suspended rep8

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Suspended

value: Week 6


title: Sham_Veh4

description: processed data header: DPT4

value: Veh


title: wild type embryos(3h) (replicate 2)


title: HDO 11

description:
Whole body (n = 2)
30° C, 30 ppt, 6 ppm DO, 15 ppb PAH

value: whole body

value: 15 ppb


title: HDO 10

value: greater than or equal to 6 mg/L


title: Dd2 suspended rep6

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: M- DMAD embryos(3h) (replicate 2)

source_name: 3h M- DMAD rep 2


title: Sham_Veh3

description: processed data header: DPT3

value: 16 weeks old


title: Dd2 suspended rep4

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: wild type embryos(3h) (replicate 1)


title: Dd2 suspended rep3

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: Dd2 suspended rep7

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: jumu mutant ovary (replicate 2)

source_name: jumu mutant ovary rep 2

value: jumu mutant

value: ovary


title: Dd2 suspended rep2

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: Sham_Veh2

description: processed data header: DPT2


title: Sham_Veh1

description: processed data header: DPT1


title: Dd2 suspended rep1

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: HDO 8

description:
Whole body (n = 3)
30° C, 30 ppt, 6 ppm DO, 0 ppb PAH


title: jumu mutant ovary (replicate 1)

source_name: jumu mutant ovary rep 1


title: Dd2 suspended rep5

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: HDO 7


title: HDO 12


title: wild type ovary (replicate 2)

source_name: w1118 ovary   rep 2


title: projections total RNAseq rep5

source_name: projections total RNAseq

tag: tissue source

value: Embryonic day 19 rat hippocampus

tag: cell type

value: Primary hippocampal neurons

tag: days in vitro

tag: cell culture platform

value: Semipermeable membrane with 1 μm holes

tag: cellular fraction

value: Projections

tag: molecule subtype

value: Total RNA, rRNA depleted


title: Dd2 static rep2

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

tag: condition

value: Static

tag: time-point

tag: Stage

value: Schizonts

tag: purification

value: Percoll-alanine


title: wild type ovary (replicate 1)

source_name: w1118 ovary  rep 1

tag: tissue

value: embryo

tag: age


title: whole-cell total RNAseq rep5

source_name: whole-cell total RNAseq

value: Whole-cells


title: projections total RNAseq rep4


title: Dd2 baseline rep8

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

tag: strain

value: Baseline

value: Week 0


title: Dd2 static rep7

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Week 6


title: HDO 6

description:
Whole body (n = 3)
30° C, 3 ppt, 6 ppm DO, 15 ppb PAH

value: whole body

value: 48 h post hatch

value: 15 ppb

tag: oxygen concentration

value: greater than or equal to 6 mg/L


title: 3h M-,Z- jumu embryos (replicate 1)

source_name: 3h M-,Z- jumu rep 1

value: M-,Z- jumu


title: HDO 9

tag: oil concentrtation


title: Dd2 baseline rep7

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: 3h M-,Z- jumu embryos (replicate 2)

source_name: 3h M-,Z- jumu rep 2


title: HDO 3

description:
Whole body (n = 3)
30° C, 3 ppt, 6 ppm DO, 0 ppb PAH


title: HDO 4


title: Dd2 baseline rep6

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: SSP-25 rep3

city: Chongqing

first: lei

last: Zhou

address: No.55, South University Road, Shapingba District

institute: Chongqing University

data_processing:
RNA-seq reads were aligned to the reference genome WBcel235 using Tophat v.2.0.6
meta-transcript and by the size of the library.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) was calculated, and the differential gene and transcript expression analysis was performed using Cufflinks tools
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Synchronized L1 worms were cultured on NGM plates seeded with OP50 bacteria.

extract_protocol:
Total RNA was extracted using Trizol reagent.
Sequencing libraries were generated using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina.

treatment_protocol: Growing the worms at 15°C and 25°C, respectively.

tag: developmental stage

tag: culture temperature

tag: e. coli b strain for diet


title: whole-cell total RNAseq rep4

data_processing:
Genome build: rnor6
Reads aligning completely to rRNA, repeat elements (catalogued by RepeatMasker), 7sl (or SRP), and mitochondrial genome were removed using bowtie2 version 2.2.3:  $ bowtie2 -p 2 -N 1 --no-unal --un-conc <output_unaligned.fastq> --al-conc <output_aligned.fastq> -1 <input_R1.fastq> -2 <input_R2.fastq> -S <output_alignments.sam>
Filtered reads were mapped to the rat genome (Ensembl release 81, Rnor_6.0, annotation downloaded on July 24, 2015) with TopHat version 2.1.1 using the following command:   $ tophat -p 6 --library-type fr-firststrand --b2-sensitive --mate-inner-dist 100 -i 30 -g 10 --max-coverage-intron 5000000 -G <genes.gtf> -o <output_directory> <genome_index_base> <input_filtered.R1.fastq> <input_filtered.R2.fastq>
The alignments are provided as bigwig files. They were prepared using bamCoverage from deepTools version 2.2.2:  bamCoverage --binSize 10 -p 2 -b <input.bam> -o <output.bw>

extract_protocol:
Library preparation method: Zhang Z., … Zamore P.D. (Silence, 2012).
RNA extraction: For neurons cultured on semipermeable membranes, RNA was extracted following the steps recommended by TRIzol® reagent (ThermoFisher #15596018) manual with minor modifications. Briefly, media was removed and TRIzol® was applied to the projections-side, the surface was scraped using a cell-scraper and lysate was gently pippeted and transferred into a clean tube. Lysate was similarly collected from the cell body side of the membrane. The lysate was vortexed briefly and kept at room temperature for 5 minutes. 200 μl of chloroform per 1 ml of TRIzol® was added for phase separation. The tubes were vigorously shaken by hand and centrifuged at 12,000 x g for 15 min at 4°C. The aqueous phase was transferred to fresh tubes and the chloroform wash was repeated two more times. RNA was precipitated by adding 100% isopropanol. Samples were incubated at room temperature for 15 min, and centrifuged at 12,000 x g at 4°C for 15 min. The supernatant was removed without disturbing the precipitated RNA. The RNA precipitate was rinsed two times 75% ethanol and finally dissolved in RNase-free water by incubating for 10 min at 55-60°C.

tag: tissue source

value: Embryonic day 19 rat hippocampus

tag: cell type

value: Primary hippocampal neurons


title: 3h M-,Z+ jumu embryos (replicate 2)

source_name: 3h M-,Z+ jumu rep 2

value: M-,Z+ jumu


title: SSP-25 rep2


title: HDO 2


title: Dd2 baseline rep5

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

source_name: In vitro cultured cells


title: 3h M-,Z+ jumu embryos (replicate 1)

source_name: 3h M-,Z+ jumu rep 1


title: E.coli stationary C

data_processing:
Read were trimmed using homerTool
Alignment was done to the genome concatenate with mature tRNA (Chan, P.P. & Lowe, T.M. (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucl. Acids Res. 44(Database issue):D184-D189.) using Bowtie2 with parameters --very-sensitive-local. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were randomly assigned when mapping to identical anticodon, and discarded from the analysis if aligned to different anticodon.
Read count was done using BedTools-coverage count.
Genome_build: ASM584v2
Supplementary_files_format_and_content: read counts of mature tRNA and total genome of all samples

organism: Escherichia coli BW25113

source_name: E.coli culture growth

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

tag: culture stage

value: stationary


title: HDO 1


title: Dd2 baseline rep4

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: SSP-15 rep3


title: 3h wild type embryos (replicate 2)


title: SSP-25 rep1


title: HDO 5


title: Dd2 baseline rep3

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: 3h wild type embryos (replicate 1)


title: SSP-15 rep2


title: Dd2 baseline rep2

description:
Counts_all_raw.csv
Counts_all_FPKM.csv


title: 3h zld overexpression embryos (replicate 2)

source_name: 3h zld overexp rep 2

value: zld overexpression


title: E.coli mid-log A

value: mid-log


title: SSP-15 rep1


title: LEC-enriched hepatic non-parenchymal cells (Non-Diseased, rep 2)

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

description:
count_matrix.tsv.gz
cell_metadata.tsv.gz
nd2

data_processing:
UMI count matrices were generated using the 10x genomics CellRanger count (3.0.1) pipeline with default parameters.
The count matrices were combined and normalized using Seurat.
The combined matrix was then further filtered to exclude cells not passing the following QC measures: at least 250 genes detected (UMI > 0) and proportion of UMIs derived from mitochondia less than 20%. Genes were also excluded  if they were not expressed in at least  3 cells (UMI count > 0).
After filtering, this matrix was used for tSNE projection and graph based clustering. Following cell-embeddings and clustering, the original non-downsampled UMI data was used for all analysis and is provided as the count_matrix.tsv.gz.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix

source_name: LEC-enriched hepatic non-parenchymal cells (Non-Diseased)

growth_protocol: Transplanted livers were harvested and non-parenchymal cells (NPCs) were isolated and frozen in a single cell suspension as previously described. Additionally, non-diseased NPCs were purchased from Triangle research laboratories.

extract_protocol:
To enrich LECs from hepatic NPCs we thawed frozen samples in RPMI containing 10% Human Serum AB (Gemini Bio-products, West Sacramento, CA) and 1% DNASE (MP Biomedicals, Santa Ana, CA). Cells were washed 2x with PBS containing 2% FBS (Atlas Biologicals, Fort Collins, CO) and stained with antibodies against CD45 (clone HI30), CD31 (PECAM1, clone WM59), Podoplanin (clone NC-08) and CD146 (clone P1H12) from Biolegend (San Diego, CA) and CD68 (clone KP1) from abcam (San Francisco, CA). Cells from either Non-diseased, NASH or HCV were sorted using an Aria Fusion sorter (BD Biosciences, Franklin lakes, NJ) and enriched LECs were sorted into RPMI containing 50% human serum AB. Approximately 10,000 LEC-enriched hepatic NPCs were loaded onto a 10x genomics (San Francisco, CA) controller per manufacturer instructions to generate barcoded single cell GEMs using the 10x genomics 3’ kit.
10x Genomics 3' end library kit

tag: disease state

value: Non-diseased

value: liver


title: LEC-enriched hepatic non-parenchymal cells (NASH)

description:
count_matrix.tsv.gz
cell_metadata.tsv.gz
nash

value: NASH


title: Dd2 baseline rep1

description:
Counts_all_raw.csv
Counts_all_FPKM.csv

value: Baseline

value: Schizonts

value: Percoll-alanine


title: 17ab_rep3

status: Public on Apr 17 2019

city: East Lansing

first: Yan

last: Bao

address: 603 Wilson Road

institute: MIchigan State University

description: 170115_I137_FCHF7KVBBXX_L1_WHMUSqphRAAORAAPEI-201

data_processing:
All data with read length 250 bp were aligned to Arabidopsis TAIR10 genome, using STAR (version 2.4.0 with parameters “--outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.10”)
Subsequently, reads count of each annotated gene was calculated by htseq-count (version 0.6.0 with parameters “-t mRNA -m intersection-nonempty --stranded no”).
Next, significantly differently expressed genes (DEGs) between each two samples were extracted with cutoff FDR (false discovery rate) < 0.01 using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with gene_id. transcript_id(s), length, expected_count and FPKM data

organism: Arabidopsis thaliana

source_name: 17ab mutat_10-days Seedlings

growth_protocol: Seeds from WT and 17ab were germinated and vertically grown on 100 mm × 100 mm square plates (Fisher Scientific) with 1/2 MS-0 media for 10 days.

extract_protocol: Samples were harvested and immediately ground into powder in liquid nitrogen. Total RNA extraction was extracted by using RNeasy Plant Mini Kit (QIAGEN, Cat. No. 74904).

treatment_protocol: Seedlings with similar size were picked up and frozen in liquid nitrogen immediately.

tag: genotype/variation

value: mutant 17ab

value: 10-days Seedlings


title: 17ab_rep2

description: 170115_I137_FCHF7KVBBXX_L1_WHMUSqphRAANRAAPEI-225


title: WT_rep3

description: 170115_I137_FCHF7KVBBXX_L1_WHMUSqphRAACRAAPEI-211

source_name: WT_10-days Seedlings

value: wild type


title: 17ab_rep1

description: 170115_I137_FCHF7KVBBXX_L1_WHMUSqphRAAMRAAPEI-223


title: WT_rep1

description: 170115_I137_FCHF7KVBBXX_L1_WHMUSqphRAAARAAPEI-209


title: WT_rep2

description: 170115_I137_FCHF7KVBBXX_L1_WHMUSqphRAABRAAPEI-210


title: RNA-seq of dbr1-2 with Rnase R digestion replication 2

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

description:
dbr1-2_r2_RnaseR_plus
zheng_m55_2_rRNA_mRNA_removal_Rnase_20140509_ATTCCT_L006

data_processing:
TopHat (v2.0.13) was used to aligned the obtained reads to the genome of Arabidopsis (TAIR10).
Cufflinks (v2.2.1) was used to obtain the genes and transcripts and genes with the TAIR10 annotation.
Cuffmerge (v1.0.0) was used to merge the assembled genes and transcripts from individual libraries.
CuffCompare (v2.2.1) was used to compare the merged genes and transcripts to the annotated genes and transcripts in the TAIR10 database.
Cuffquant (v2.2.1) was used to quantify the expression levels (FPKM) values of genes and transcripts.
Cuffnorm (v2.2.1) was used to normalize the FPKM values of genes and transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values of genes

source_name: dbr1-2 with Rnase R digestion

growth_protocol: Total RNA extracted from inflorescences of Col-0 and dbr1-2, which are grown in 16/8 hr ligh/dark cycle, 22 ℃.

extract_protocol:
Total RNA were extracted with Trizol (Amion)
Total RNA isolated from Col-0 and dbr1-2 was treated with a Ribo Zero kit (Epicenter) to obtain a ribosomal RNA-depleted RNA (ribo- RNA). Then ribo- RNA was incubated with RNase R (Epicentre) and then subjected to phenol:chloroform purification. Purified RNAs were further used for library preparation with Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N15031048), and then subjected to deep sequencing with Illumina HiSeq 2000 at Genergy (Shanghai, China).

treatment_protocol: Total RNA were first treated by rRNA removal using Ribo-Zero kit (epicenter), and the rRNA-depleted RNA were then treated by Rnase R for 2 hr at 37℃, and RNA recovered by phenol:chloroform purification for library construction.

tag: ecotype background

value: Columbia

value: dbr1-2 mutant

value: inflorescences

tag: molecule subtype

value: total RNA with RNase R treatment


title: RNA-seq of dbr1-2 with Rnase R digestion replication 1

description:
dbr1-2_r1_RnaseR_plus
zheng_m55_2_rRNA_removal_Rnase_20140509_ACTGAT_L006


title: RNA-seq of dbr1-2 without Rnase R digestion replication 2

description:
dbr1-2_r2_RnaseR_minus
zheng-m55-2-removemRNArRNA_20150106B_TTAGGC_L001

source_name: dbr1-2 without Rnase R digestion

value: total RNA


title: RNA-seq of dbr1-2 without Rnase R digestion replication 1

description:
dbr1-2_r1_RnaseR_minus
zheng_m55_2_rRNA_mRNA_removal_20140509_TTAGGC_L006


title: 3h zld overexpression embryos (replicate 1)

source_name: 3h zld overexp rep 1

value: embryo


title: RNA-seq of Col-0 with Rnase R digestion replication 2

description:
col_r2_RnaseR_plus
zheng-col-1-removemRNArRNARnaseR_20150108B_CGATGTAT_L001

source_name: Col-0 with Rnase R digestion


title: RNA-seq of Col-0 without Rnase R digestion replication 1

description:
col_r1_RnaseR_minus
zheng_col_1_rRNA_mRNA_removal_20140509_TGACCA_L006

source_name: Col-0 without Rnase R digestion


title: RNA-seq of Col-0 with Rnase R digestion replication 1

description:
col_r1_RnaseR_plus
zheng-col-1-removemRNArRNARnaseR_20150106B_CGATGT_L001


title: RNA-seq of Col-0 without Rnase R digestion replication 2

description:
col_r2_RnaseR_minus
zheng-col-1-removemRNArRNA_20150106B_ATCACG_L001


title: RNA-seq in Col

city: San Diego

first: Bing

state: CALIFORNIA

address: 9500 Gilman Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
ChIP-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10 release) using Bowtie 2 with default parameters and the local alignment model. Duplicated reads and low mapping quality reads (MAQ<30) were identified and removed using Samtools.
Enriched intervals were identified using MACS with default parameters. Density maps of reads for visualization were based on counts of the 200-bp extension of sequencing reads in the 3’ direction followed with RPGC (Reads Per Genomic Content) normalization.
Hypermethylation of H3K4me3 between the jmj16 mutant and wild type were detected using the ChIPDiff program with a 1.5-fold change as described previously. Significant enriched regions of JMJ16 were identified by 2-fold change comparing to wild type.
RNA-seq reads were firstly aligned to the Arabidopsis thaliana transcriptome (based on the TAIR10 annotation) using Tophat 2 with default parameters for further visualization in IGB (Integrated Genome Browser from BioViz) with ChIP-seq data.
Meanwhile, RNA-seq reads were remapped and quantitatively evaluated by Salmon. Differentially expressed genes between the jmj16-1 mutant and wild type were identified with1.5-fold change as cut-off.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were normalized and generated by deepTools; RNA quantifications are evaluated by Salmon.

source_name: Rosette Leaf 5 and 6 in 5 weeks Arabidopsis under LD

growth_protocol: All Arabidopsis thaliana lines used in this research were in the Col-0 background. Col-0 and  jmj16-1 (SAIL_535_F09), Surface-sterilized seeds were imbibed for 3 d at 4°C, plated on MS medium, left to grow for 6 days, and then transferred to soil and grown in a culture room at 22°C under a 16-h-light/8-h-dark cycle.

extract_protocol:
Total RNA was extracted from 5-6 rosette leaves with TRIZOL (RNAiso Plus TaKaRa). 1 g of leaves 5 and 6 of indicated developmental stages of Col-0, jmj16-1 and transgenic jmj16-1 plants expressing JMJ16 full length driven by its own promoter were harvested and ground in liquid nitrogen and then cross-linked with formaldehyde. Anti-HA (Sigma H6908) and anti-H3K4me3 (Millipore 07-473)  were used for immunoprecipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols using 1 mg RNA. A ChIP-seq library was constructed using the NEBNext® DNA Library Prep Master Mix Set for Illumina® (NEB, E6040S).

treatment_protocol: Mature stage leaves indicate fully expanded leaves 5 and 6 of plants without a visible yellowing phenotype were collected for RNA-seq and ChIP-seq. Around 5 weeks under our growth condition.

tag: genotype

value: 4 weeks


title: ChIP-seq of HA in JMJ16-HA

value: JMJ16-HA rescued jmj16

tag: antibody

value: HA


title: ChIP-seq of HA in Col


title: HD-CAF484: High desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

institute: University Health Network

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using robust spline normalisation using lumi in R

source_name: NSCLC primary tumor

label_protocol: CY3-HYB cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The primary lung cancer associated fibroblasts were resected from NSCLC patients and were cultured in complete DMEM. Passage 2 of these cells used in the experiments.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The primary NSCLC cancer associated fibroblasts were cultured in complete DMEM. Passage 2 of these cells used in the experiments.

tag: tissue

value: NSCLC primary tumor

value: Primary carcinoma associated fibroblast


title: HD-CAF487: High desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours


title: HD-CAF482: High desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours


title: LD-CAF485: Low desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours


title: LD-CAF481: Low desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours


title: LD-CAF466: Low-desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours


title: ChIP-seq of H3K4me3 in Col

tag: age


title: Nontargetting siRNA 2 biological rep2

city: Istanbul

first: Sema

last: Sirma Ekmekci

address: Vakif Gureba cad

department: Genetics

country: Turkey

institute: Istanbul University, Aziz Sancar Institute of Experimental Medicine

description: Gene expression data from control cells.

hyb_protocol: Fragmented end-labeled cDNA was hybridized to the Affymetrix's GeneChip® HG-U133 Plus2.0 Array according to Affymetrix's standard procedure.

scan_protocol: The array was scanned with GeneChip Scanner 3000 7G.

data_processing:
The expression data were generated by Affymetrix Expression Console software version 1.1 (Affymetrix).
Expression signals were extracted and normalized by means of the Expression Console software (Affymetrix) applying the Robust Multichip Average (RMA) normalization method.

label: Biotin

source_name: Nontargetting siRNA transfected cells (control)

label_protocol: RNAs were amplified and labeled using Affymetrix's GeneChip® 3' IVT Express kit.

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium that contained 10% FBS, 100 U/ml penicillin, 100 mg/ml streptomycin and 2mM L-glutamine at 37°C with 5% CO2.

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

treatment_protocol: Jurkat cells were transfected with 100nM LEF1 siRNA (Smartpool on-target plus siRNA, Dharmacon) or 100nM non-targeting siRNA (Smartpool on-target plus siRNA, Dharmacon) with HiPerFect transfection reagent (Qiagen) according to the manufacturer's protocol and cultured for 24 hours.

tag: cell line

value: Jurkat (T-ALL cell line)

tag: sirna

value: Non-targetting


title: Nontargetting siRNA 1 biological rep1


title: LEF1 siRNA 1 biological rep1

description: Gene expression data from LEF1 knockdown cells.

source_name: LEF1 siRNA transfected cells


title: LEF1 siRNA 2 biological rep2


title: Human stimluated T rep3

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

data_processing:
RNA-seq reads were aligned to reference genome sequences using STAR(Dobin et al., 2013) aligner software. Mapped reads were assigned to genomic features using Rsubread(Liao et al., 2013)  R package(Team, 2014).
Genes that were differentially expressed (>4 fold, P<0.01, FDR<0.05) between conditions and their normalised expression values, were generated with Partek® Flow®, an online analysis platform for Next Generation Sequencing data (http://www.partek.com/partek-flow/).
Supplementary_files_format_and_content: counts

source_name: PBMC

extract_protocol:
Cells were lysed in RLT buffer (Qiagen Ltd., UK), tthen RNA extracted using the Qiagen's RNA Mini Kit according to the manufacturer’s instructions.
Briefly, RNA quality and quantity were assessed using the Bioanalyzer 2100 RNA pico kit (Agilent technologies). The input total RNA was normalized to 100 pg per sample and >9 RIN. RNA was reverse transcribed and cDNA amplified by in vitro transcription with the standard PolyA selection at the Wellcome Trust Human Genomics Centre, Oxford. Following first strand synthesis, cDNA was amplified 12 cycles by LD PCR using blocked PCR primers. Amplified cDNA was purified using AMPure XP prior to QC using the bioanalyser 2100 HS DNA kit (Agilent technologies).
Library preparation of purified amplified cDNA was performed using Nextera XT library preparation (Illumina). Following QC, 100 pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposons. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalization and pooling before loading onto the HiSeq 4000 (Illumina, Oxford) for paired end sequencing.

treatment_protocol: Human PBMC: Magnetically enriched CD8+cells were stained with surface antibodies (CD161-PE, TCR Va7.2-FITC) and live/dead dye SYTOX blue for 15 mins on ice. Cells were sorted immediately into ice cold PBS with 10% FCS using a Beckman Coulter MoFlo XDP cell sorter selecting live CD161++Va7.2+ (MAIT) cells from the positive fraction. Following sorting cells were stimulated by T, C, or TC, or left in the media unstimulated for 20 hours. The next day, cells were centrifuged at 1800rpm for 5 mins then resuspended in 100 uL of RNA lysis buffer (Qiagen Ltd., UK) stored at -20'C.

value: Live CD3+CD8+TCR-Valpha7.2

tag: individual

value: Healthy volunteer #43

tag: treatment

value: T(anti-CD3/CD28 beads only)


title: Human stimluated TC rep1

value: Healthy volunteer #32

value: TC(beads+cytokines)


title: Human stimluated C rep3


title: Human stimluated C rep2

value: Healthy volunteer #42


title: Human stimluated TC rep3


title: Human stimluated TC rep2


title: Human stimluated C rep1


title: RNA-seq in jmj16


title: LD-CAF458: Low desmoplaisa-carcinoma associated fibroblast_embedded in Collagen gel for 24 hours


title: Human unstimulated UT rep3

value: Unstimulated


title: Human stimluated T rep1


title: Human unstimulated UT rep2


title: Human unstimulated UT rep1


title: MDA231: IVMS2

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

institute: Shantou University Medical College

description: miRNA profiling by RNA sequencing

data_processing:
Libraries were sequenced using the Illumina HiSeqTM 2500.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, and mapped to human genome using BWA. Clean reads were compared with a miRBase database (version 21) . The analysis was performed by the Guangzhou RiboBio co. Ltd in Guangzhou, China.
Supplementary_files_format_and_content: Excel files include RPM values for each Sample

growth_protocol: MDA231 Cells were cultured in cultured DMEM supplemented with 10% fetal bovine serum, 100 U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol:
MDA231 Cells were lysed in an ice-cold lysis buffer (20 mM Tris•Cl pH7.5, 50 mM NaCl, 5 mM MgCl2, 0.5% NP-40) containing protease inhibitors and RNasin (200 U/mL). Lysates were centrifuged at 12,000 rpm at 4°C for 15 minutes to remove cell debris. Cell lysates were incubated with RNA conjugated Amylose resin at 4°C for 5 h with gentle rotation. After washed with wash buffer, the Amylose resin complexes  were eluted with 100 μl lysis buffer containing 10 mmol/L maltose. The eluted samples were further subject to RNA purification for miRNA-seq.
Libaries were prepared for sequencing according to Illumina's protocol. The experiment was performed by the Guangzhou RiboBio co. Ltd in Guangzhou, China.

treatment_protocol: LncRNA MACC1-AS1-MS2 was in vitro transcribed using T7 RNA polymerase transcription system. RNA was incubated with Amylose resin attached MBP-MCP (MS2 coat protein) at 4°C for 3 h with gentle rotation

value: MDA231  (parental)

value: breast cancer cells

tag: rna substrate

value: lncRNA MACC1-AS1-MS2


title: ChIP-seq of H3K4me3 in jmj16

value: 4 weeks


title: 6 day_Fn3NC_rep1

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

description:
DG48
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx

data_processing:
Reads were mapped onto the human genome (GRCh37, version 19 (Ensembl 74) and its corresponding GENCODE annotation file, version 2013-12-05) using STAR with the outFilterMatchNminOverLread parameter set to 0.4. Expression values given as fragments per kilo base per million mapped reads (FPKM) and expected counts per transcript were then calculated using rsem-calculate-expression from RSEM-1.3.0 software. Only mRNAs with an FPKM above 1 were kept for further analysis.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx: Excel file includes matrix tables with counts and processed FPKM for all samples.

source_name: Human embryonic kidney-293

growth_protocol: Cells were grown on plates at 37°C in DMEM supplemented with 10% tetracycline-free FBS (BioConcept) for inhibition of leaky recombinant protein synthesis in the absence of doxycycline.

extract_protocol:
Total RNA was extracted from all samples simultaneously using the “RNeasy Mini kit” (Qiagen) according to the manufacturer’s recommendations.
Poly (A)-containing mRNA from each sample was used to prepare libraries using NEXTflex qRNA-seq Kit for 125 nucleotide single-end sequencing by Illumina HiSeq 2500.

treatment_protocol: Synthesis of recombinant proteins was induced with 1 μg/ml doxycycline in the medium.

tag: transgene

value: Flag-Cherry-HCF-2 Fn3nc*

tag: day after addition of doxycycline

tag: experiment

value: RNA-seq


title: 2 day_Fn3NC_rep2

description:
DG35
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 2 day_Fn3NC_rep1

description:
DG36
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 1 day_Fn3NC_rep2

description:
DG37
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 1 day_Fn3NC_rep1

description:
DG38
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 6 day_WT_rep2

description:
DG39
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx

value: Flag-Cherry-HCF-2 WT


title: Human stimluated T rep2

tag: cell type


title: 6 day_WT_rep1

description:
DG40
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 4 day_WT_rep2

description:
DG27
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 2 day_WT_rep2

description:
DG31
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 4 day_WT_rep1

description:
DG28
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 1 day_WT_rep1

description:
DG21
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: MDA231: IVCON

description: miRNA profiling by RNA sequencing

value: MDA231 (parental)


title: 2 day_WT_rep1

description:
DG32
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: 1 day_WT_rep2

description:
DG22
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: AD 13-45

city: South San Francisco

first: Brad

middle: A

last: Friedman

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: repeated in GSE95587: NA

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from fusiform gyrus

extract_protocol: RNA was extracted from frozen tissue sections.

value: fusiform gyrus

tag: case id

tag: diagnosis

value: Alzheimer's disease

tag: Sex

value: M

value: V


title: AD 04-60

description: repeated in GSE95587: NA


title: AD 08-45

description: repeated in GSE95587: GSM2516847

value: VI


title: 6 day_Fn3NC_rep2

description:
DG47
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: AD 07-38

description: repeated in GSE95587: NA

value: F

value: IV


title: AD 03-05

description: repeated in GSE95587: NA


title: CON 08-23

description: repeated in GSE95587: NA

value: control

value: III


title: AD 07-64

description: repeated in GSE95587: NA

value: II


title: AD 03-59

description: repeated in GSE95587: NA


title: CON 00-14

description: repeated in GSE95587: NA


title: CON 10-10

description: repeated in GSE95587: NA


title: 4 day_Fn3NC_rep2

description:
DG33
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: CON 11-60

description: repeated in GSE95587: NA


title: 4 day_Fn3NC_rep1

description:
DG34
Poly(A) RNA
processed data file: Daria_Gudkova_RNAseq_counts_and_fpkm.xlsx


title: AD 98-40

description: repeated in GSE95587: NA


title: CON 05-10

description: repeated in GSE95587: NA


title: AD 11-75

description: repeated in GSE95587: GSM2516830


title: AD 07-42

description: repeated in GSE95587: NA


title: CON 04-05

description: repeated in GSE95587: NA


title: AD 10-23

description: repeated in GSE95587: NA


title: CON 10-74

description: repeated in GSE95587: NA


title: AD 03-27

description: repeated in GSE95587: NA


title: AD 03-36

description: repeated in GSE95587: NA


title: AD 09-54

description: repeated in GSE95587: NA


title: AD 04-29

description: repeated in GSE95587: GSM2516867


title: AD 98-15

description: repeated in GSE95587: NA


title: AD 00-28

description: repeated in GSE95587: GSM2516915


title: AD 13-06

description: repeated in GSE95587: NA


title: AD 04-37

description: repeated in GSE95587: NA


title: AD 04-42

description: repeated in GSE95587: NA


title: AD 03-19

description: repeated in GSE95587: NA


title: AD 10-75

description: repeated in GSE95587: GSM2516835


title: AD 11-14

description: repeated in GSE95587: GSM2516811


title: AD 13-10

description: repeated in GSE95587: NA


title: CON 07-04

description: repeated in GSE95587: NA


title: AD 10-86

description: repeated in GSE95587: NA


title: AD 11-99

description: repeated in GSE95587: NA


title: AD 13-42

description: repeated in GSE95587: NA


title: AD 11-65

description: repeated in GSE95587: NA


title: AD 04-54

description: repeated in GSE95587: GSM2516894


title: AD 00-39

description: repeated in GSE95587: GSM2516910


title: AD 08-22

description: repeated in GSE95587: NA


title: AD 11-02

description: repeated in GSE95587: NA


title: AD 11-38

description: repeated in GSE95587: GSM2516862


title: CON 09-44

description: repeated in GSE95587: GSM2516905


title: AD 06-54

description: repeated in GSE95587: GSM2516866


title: AD 10-53

description: repeated in GSE95587: GSM2516899


title: AD 04-43

description: repeated in GSE95587: NA


title: AD 10-18

description: repeated in GSE95587: GSM2516864


title: CON 01-51

description: repeated in GSE95587: NA


title: AD 05-40

description: repeated in GSE95587: NA


title: AD 12-45

description: repeated in GSE95587: NA


title: AD 10-66

description: repeated in GSE95587: NA


title: AD 11-03

description: repeated in GSE95587: GSM2516829


title: AD 98-05

description: repeated in GSE95587: NA


title: AD 13-15

description: repeated in GSE95587: NA


title: AD 01-30

description: repeated in GSE95587: NA


title: AD 08-29

description: repeated in GSE95587: GSM2516892


title: AD 11-108

description: repeated in GSE95587: GSM2516869


title: AD 12-02

description: repeated in GSE95587: NA


title: AD 99-36

description: repeated in GSE95587: NA


title: AD 08-09

description: repeated in GSE95587: NA


title: AD 03-04

description: repeated in GSE95587: NA


title: CON 07-72

description: repeated in GSE95587: NA


title: CON 07-37

description: repeated in GSE95587: NA


title: AD 04-44

description: repeated in GSE95587: NA


title: AD 03-21

description: repeated in GSE95587: NA


title: CON 06-19

description: repeated in GSE95587: NA


title: AD 98-30

description: repeated in GSE95587: NA


title: CON 09-20

description: repeated in GSE95587: GSM2516825


title: AD 10-92

description: repeated in GSE95587: NA


title: AD 99-53

description: repeated in GSE95587: NA


title: AD 04-55

description: repeated in GSE95587: GSM2516917


title: AD 04-32

description: repeated in GSE95587: NA


title: AD 13-50

description: repeated in GSE95587: NA


title: AD 10-77

description: repeated in GSE95587: NA


title: CON 10-63

description: repeated in GSE95587: GSM2516906


title: AD 13-23

description: repeated in GSE95587: NA


title: CON 09-31

description: repeated in GSE95587: NA


title: AD 09-51

description: repeated in GSE95587: NA


title: CON 03-50

description: repeated in GSE95587: NA


title: CON 08-44

description: repeated in GSE95587: GSM2516842


title: AD 11-42

description: repeated in GSE95587: NA


title: AD 06-39

description: repeated in GSE95587: NA


title: AD 99-48

description: repeated in GSE95587: GSM2516856


title: AD 03-62

description: repeated in GSE95587: GSM2516893


title: AD 07-08

description: repeated in GSE95587: NA


title: AD 03-30

description: repeated in GSE95587: NA


title: AD 11-10

description: repeated in GSE95587: NA


title: AD 04-09

description: repeated in GSE95587: GSM2516882


title: CON 07-10

description: repeated in GSE95587: NA


title: CON 05-61

description: repeated in GSE95587: NA


title: AD 98-06

description: repeated in GSE95587: NA


title: CON 08-83

description: repeated in GSE95587: NA


title: AD 99-18

description: repeated in GSE95587: NA


title: AD 09-36

description: repeated in GSE95587: NA


title: AD 98-07

description: repeated in GSE95587: GSM2516877


title: AD 04-50

description: repeated in GSE95587: NA


title: AD 11-56

description: repeated in GSE95587: GSM2516901


title: AD 07-24

description: repeated in GSE95587: NA


title: AD 03-56

description: repeated in GSE95587: NA


title: AD 12-65

description: repeated in GSE95587: NA


title: AD 01-27

description: repeated in GSE95587: NA

value: I


title: AD 01-32

description: repeated in GSE95587: NA


title: AD 10-36

description: repeated in GSE95587: NA


title: AD 11-51

description: repeated in GSE95587: NA


title: AD 12-61

description: repeated in GSE95587: NA


title: AD 11-105

description: repeated in GSE95587: GSM2516875


title: CON 08-90

description: repeated in GSE95587: GSM2516853


title: AD 08-26

description: repeated in GSE95587: NA


title: AD 99-12

description: repeated in GSE95587: NA


title: AD 05-25

description: repeated in GSE95587: NA


title: CON 04-64

description: repeated in GSE95587: GSM2516904


title: CON 97-19

description: repeated in GSE95587: NA


title: AD 00-01

description: repeated in GSE95587: NA


title: CON 07-58

description: repeated in GSE95587: NA


title: CON 11-102

description: repeated in GSE95587: GSM2516872


title: AD 08-20

description: repeated in GSE95587: GSM2516861


title: AD 07-12

description: repeated in GSE95587: NA


title: CON 06-08

description: repeated in GSE95587: NA


title: AD 12-71

description: repeated in GSE95587: NA


title: AD 99-34

description: repeated in GSE95587: NA


title: CON 06-61

description: repeated in GSE95587: NA


title: AD 08-37

description: repeated in GSE95587: GSM2516907


title: AD 10-93

description: repeated in GSE95587: NA


title: AD 13-48

description: repeated in GSE95587: NA


title: AD 09-01

description: repeated in GSE95587: NA


title: CON 11-15

description: repeated in GSE95587: GSM2516859


title: AD 08-46

description: repeated in GSE95587: GSM2516850


title: AD 10-80

description: repeated in GSE95587: NA


title: AD 10-41

description: repeated in GSE95587: NA


title: AD 12-48

description: repeated in GSE95587: NA


title: AD 10-79

description: repeated in GSE95587: NA


title: AD 09-16

description: repeated in GSE95587: NA


title: AD 13-38

description: repeated in GSE95587: NA


title: AD 13-32

description: repeated in GSE95587: NA


title: AD 12-63

description: repeated in GSE95587: NA


title: AD 11-72

description: repeated in GSE95587: NA


title: AD 99-11

description: repeated in GSE95587: NA


title: CON 02-38

description: repeated in GSE95587: GSM2516819


title: AD 11-85

description: repeated in GSE95587: NA


title: CON 00-30

description: repeated in GSE95587: NA


title: CON 13-43

description: repeated in GSE95587: NA


title: CON 08-35

description: repeated in GSE95587: GSM2516883


title: AD 05-39

description: repeated in GSE95587: GSM2516886


title: AD 11-89

description: repeated in GSE95587: GSM2516919


title: AD 09-22

description: repeated in GSE95587: NA


title: CON 10-94

description: repeated in GSE95587: GSM2516821


title: CON 08-55

description: repeated in GSE95587: NA


title: AD 00-37

description: repeated in GSE95587: GSM2516857


title: AD 13-31

description: repeated in GSE95587: NA


title: AD 03-07

description: repeated in GSE95587: NA


title: AD 11-48

description: repeated in GSE95587: GSM2516898


title: AD 08-54

description: repeated in GSE95587: GSM2516912


title: AD 04-28

description: repeated in GSE95587: GSM2516903


title: AD 11-66

description: repeated in GSE95587: GSM2516887


title: AD 98-26

description: repeated in GSE95587: NA


title: AD 09-09

description: repeated in GSE95587: NA


title: AD 11-49

description: repeated in GSE95587: GSM2516888


title: CON 99-29

description: repeated in GSE95587: GSM2516922


title: AD 07-71

description: repeated in GSE95587: NA


title: AD 00-54

description: repeated in GSE95587: GSM2516840


title: AD 10-68

description: repeated in GSE95587: NA


title: AD 03-35

description: repeated in GSE95587: NA


title: AD 07-15

description: repeated in GSE95587: GSM2516823


title: AD 00-46

description: repeated in GSE95587: NA


title: AD 99-06

description: repeated in GSE95587: NA


title: CON 10-42

description: repeated in GSE95587: GSM2516918


title: CON 98-33

description: repeated in GSE95587: NA


title: CON 10-58

description: repeated in GSE95587: NA


title: AD 99-07

description: repeated in GSE95587: NA


title: AD 12-64

description: repeated in GSE95587: NA


title: CON 04-62

description: repeated in GSE95587: NA


title: CON 03-41

description: repeated in GSE95587: GSM2516852


title: AD 08-62

description: repeated in GSE95587: NA


title: AD 99-03

description: repeated in GSE95587: NA


title: AD 99-60

description: repeated in GSE95587: NA


title: CON 05-36

description: repeated in GSE95587: GSM2516837


title: CON 11-87

description: repeated in GSE95587: GSM2516854


title: AD 03-37

description: repeated in GSE95587: GSM2516855


title: AD 07-34

description: repeated in GSE95587: GSM2516860


title: AD 03-14

description: repeated in GSE95587: NA


title: AD 09-11

description: repeated in GSE95587: GSM2516884


title: CON 06-68

description: repeated in GSE95587: NA


title: AD 13-16

description: repeated in GSE95587: NA


title: CON 13-49

description: repeated in GSE95587: NA


title: CON 02-12

description: repeated in GSE95587: GSM2516827


title: AD 03-38

description: repeated in GSE95587: NA


title: AD 11-101

description: repeated in GSE95587: NA


title: AD 98-09

description: repeated in GSE95587: NA


title: AD 05-52

description: repeated in GSE95587: GSM2516822


title: AD 08-59

description: repeated in GSE95587: GSM2516845


title: AD 07-50

description: repeated in GSE95587: GSM2516828


title: AD 03-54

description: repeated in GSE95587: NA