title: Kidney at adulthood (7 years)

description:
Baboon_Kidney_Adult_3
Gene expression data from Papio hamadryas whole kidney at adulthood.

value: 7 years


title: Sample 10_n199-infected MRC5 cells_8h

status: Public on Jan 20 2018

type: SRA

city: Pittsburgh

first: Neal

last: DeLuca

state: PA

address: 450 Technology Dr

country: USA

institute: Univ. of Pittsburgh

description:
8n199_S4_L006_R1_001
processed data file: n199 2.xlsx

library_source: transcriptomic

data_processing:
reads were trimmed, and mapped to the HSV genome using the RNA seq software in the CLC workbench V9
RNA seq experiments were exported from CLC workbench to Excell
raw read totals were normalized to total read count and size in excell and graphs were made for the abundance of selected IE, E, BG, and L genes
graphs were combined into a single figure using Adobe Illustrator
Genome_build: Herpes simplex virus type 1
Supplementary_files_format_and_content: KOS 2.xlsx is an exported CLC workbench RNAseq experiment giving the raw data for samples 1-6 (sheet 1), normalization factor for total reads (sheet 2), normalized reads (sheet 3), and graphs of reads adjusted to gene size for HSV IE, E, BG, and late genes along with graphic representation of the knietics of expression (sheets 4-7).
Supplementary_files_format_and_content: n199 2.xlsx is an exported CLC workbench RNAseq experiment giving the raw data for samples 7-12 (sheet 1), normalization factor for total reads (sheet 2), normalized reads (sheet 3), and graphs of reads adjusted to gene size for HSV IE, E, BG, and late genes along with graphic representation of the kinetics of expression(sheets 4-7).

molecule: total RNA

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: n199-infected MRC5 cells

extract_protocol: 1 ug of total RNA from each sample was used to create sequencing libraries using the TruSeq RNA Sample Prep kit (Illumina).

tag: cell line

tag: infected with

value: n199 (ICP22 mutant)

tag: time post infection


title: Kidney at 125 days gestation, biological replicate 3

type: RNA

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

description:
Baboon_Kidney_125dG_3
Gene expression data from Papio hamadryas whole kidney at 125 days gestation.

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16hr at 45oC to Affymetrix Human Genome U133A Arrays (adult samples) or to Affymetrix Human Genome U133A 2.0 Arrays (gestational samples). Arrays were washed and stained with phycoerythrein-conjugated streptavidin (Molecular Probes) using a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures.

scan_protocol: GeneChips were scanned using the GCS 3000 high-resolution confocal laser scanner (Affymetrix).

data_processing: The scanned images were analyzed using programs resident in GeneChip Operating System v1.4 (GCOS; Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250 for all arrays used. The expression data were analyzed by statistical algorithms resident in GCOS; in short, the signal intensity for each gene was calculated as the average intensity difference, represented by [Σ(PM - MM)/(number of probe pairs)], where PM and MM denote perfect-match and mismatch probes (Lockhart et al., 1996, Nat. Biotechnol. 14:1675-1680; Liu et al., 2002, Bioinformatics 18:1593-9; Hubbell et al., 2002, Bioinformatics 18(12):1585-92). GCOS-generated detection and change calls were used to identify robust expression changes. Array data were all-median normalized using GeneSifter software (GeneSifter.Net, VizX Labs, Seattle, WA).

label: biotin

organism: Papio hamadryas

source_name: whole kidney at 125 days gestation

label_protocol: Biotinylated cRNA were prepared using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) and Bioarray™ HighYield™ RNA Transcript Labeling Kit (ENZO Diagnostics Inc.) as per the manufacturer’s instructions from 6 ug total RNA.

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

tag: tissue

value: whole kidney

tag: age


title: Sample 9_n199-infected MRC5 cells_6h

description:
6n199_S3_L006_R1_001
processed data file: n199 2.xlsx


title: Kidney at 160 days gestation, biological replicate 3

description:
Baboon_Kidney_160dG_3
Gene expression data from Papio hamadryas whole kidney at 160 days gestation.

source_name: whole kidney at 160 days gestation


title: Kidney at adulthood (6 years)

description:
Baboon_Kidney_Adult_1
Gene expression data from Papio hamadryas whole kidney at adulthood.

source_name: whole kidney at adulthood

value: 6 years


title: human primary OA chondrocyte transfected with siRNA against a-Klotho

status: Public on Jan 21 2018

city: MONTPELLIER

first: Paul

last: CHUCHANA

address: 80 rue Augustin Fliche

country: France

institute: CNRS

description: pool of 3 independent equimolar RNA samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on the Affymetrix® MG-430v2. StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system with HWS kit.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The files were generated with the "rma-alt-splicing" algorithm. Only transcripts having opposite sign between chondrocytes treated with Klotho (normalized to untreated chondrocytes) and chondrocytes transfected with siRNA Klotho (normalized relative to the control siRNA) were selected.

organism: Homo sapiens

source_name: OA patients

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT Express protocol from 100 ng total RNA (GeneAtlas 3'IVT ExpressTechnical Manual, 2010, P/N702833 Rev4 Affymetrix).

growth_protocol: DMEM + 10% Fetal calf serum in monolayer culture

extract_protocol: RNA was isolated from 5x10^5 chondrocytes  with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: double transfection of siRNA or 7 days treatment with recombinant protein with changes every 2 days.

value: cartilage

tag: disease status

value: osteoarthritis


title: Kidney at 160 days gestation, biological replicate 2

description:
Baboon_Kidney_160dG_2
Gene expression data from Papio hamadryas whole kidney at 160 days gestation.


title: human primary OA chondrocyte treated with 40ng/ml recombinant a-Klotho for 7 days


title: Kidney at 160 days gestation, biological replicate 1

description:
Baboon_Kidney_160dG_1
Gene expression data from Papio hamadryas whole kidney at 160 days gestation.


title: TCEP 250uM rep2

city: Antwerp

first: Boris

last: Krivoshiev

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

data_processing:
Alignment, mapping, and annotation steps were performed with CLC Genomics Workbench (CLC Bio, DEN) using default parameters.
Samples were normalized by quantile normalization before being mapped.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with Expression values|Normalized expression values|Gene name|Transcripts annotated|Detected transcripts|Exon length|Gene ID|Unique gene reads|Total gene reads|Unique exon reads|Total exon reads|Unique exon-exon reads|Total exon-exon reads|Unique intron reads|Total intron reads |Exons|RPKM|Chromosome|Chromosome region start|Chromosome region end.

source_name: Human Hepatocellular Carcinoma Cell Line (HepG2)

growth_protocol: HepG2 cells (ATCC HB-8065) were cultured in minimum essential medium supplemented with Earle's salts (Gibco, Carlsbad, CA, USA), 1 mm sodium pyruvate, 4 mm l-glutamine, 1% non-essential amino acids, 50 IU ml–1penicillin, 50 mg ml–1 streptomycin and 10% heat-inactivated fetal bovine serum. Cells were not allowed to exceed maximum of 25 passages.

extract_protocol:
To ensure for high quality and good yield of RNA, the combined TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy (Qiagen, Hilden, Germany) approach was adopted. Briefly, this involved lysing cells and extracting total RNA by phase separation using TRIzol as per the manufacturer's instructions. The aqueous phase containing the crude total RNA extraction was then subjected to clean up using the RNeasy kit according to the manufacturer's instructions, resulting in pure total RNA.
The TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA, USA) was used following the manufacturer's protocol to construct sequencing libraries. Briefly, 4 μg total RNA was subjected to purification using poly-T oligo-attached magnetic beads to purify for poly-A containing mRNA. mRNA was then fragmented using divalent cations and exposure to high temperatures. Fragments were then reverse transcribed into first-strand cDNA using random hexamer primers followed by second-strand cDNA synthesis to create blunt-ended, double-stranded cDNA. Unconverted RNA was then depleted by RNase H incubation. Fragment 3′ ends were then adenylated to prevent ligation to one another during adaptor ligation. Successful adaptor-ligated fragments were purified and enriched by means of PCR using primers that annealed to adaptors to create the final cDNA library.
Constructed sequencing libraries were then paired-end sequenced (2 × 50 bp) using the Illumina HiSeq 1500 platform (Illumina).

treatment_protocol: HepG2 cells were seeded in six-well plates and allowed to culture for 72 hours for acclimatization after detachment/reattachment. Cells were treated with TCEP at concentrations 25 or 250 μm, or to TCIPP at concentrations 2.5 or 25 μm (assigned as low- and high-dose TCEP or TCIPP, respectively, from here on out). Negative controls were treated with 0.1% DMSO only. Treatments were conducted for 72 hours. Treatments were done in triplicate for each condition involving separate cell seeding, cell growth, treatments and RNA extractions per triplicate.

tag: cell type

value: Hepatocellular carcinoma cell line

tag: treatment

value: TCEP

tag: concentration

tag: treatment duration

tag: passages


title: Kidney at 90 days gestation, biological replicate 3

description:
Baboon_Kidney_90dG_3
Gene expression data from Papio hamadryas whole kidney at 90 days gestation.

source_name: whole kidney at 90 days gestation


title: Clostridium difficile - BHIS+DP - 7 hours - Replicate 3

city: Silver Spring

last: Carlson

state: MD

address: 10903 New Hampshire Ave

department: DBPAP

institute: Food and Drug Administration

hyb_protocol: Agilent manufacturer protocols were followed using supplied reagents.

data_processing: Data were median normalized and log2 transformed.

organism: Clostridioides difficile 630

source_name: Clostridium difficile in vitro culture

extract_protocol: RNA was extracted using hot phenol extraction methodology. RNA was treated with DNase prior to use.

treatment_protocol: C. difficile was grown in BHIS broth or BHIS broth with 75uM dipridyl.

tag: strain

tag: culture type

value: in vitro

tag: condition

value: BHIS+DP

tag: time

value: 7 hours


title: Clostridium difficile - BHIS+DP - 7 hours - Replicate 2

scan_protocol: Agilent manufacturer protocols were followed using supplied reagents.


title: Kidney at 90 days gestation, biological replicate 2

description:
Baboon_Kidney_90dG_2
Gene expression data from Papio hamadryas whole kidney at 90 days gestation.


title: Kidney at 125 days gestation, biological replicate 1

description:
Baboon_Kidney_125dG_1
Gene expression data from Papio hamadryas whole kidney at 125 days gestation.


title: Sample 8_n199-infected MRC5 cells_4h

description:
4n199_S2_L006_R1_001
processed data file: n199 2.xlsx


title: Clostridium difficile - BHIS+DP - 7 hours - Replicate 1

label_protocol: Agilent manufacturer protocols were followed using supplied reagents.


title: Sample 5_KOS-infected MRC5 cells_12h

description:
12KOS_S11_L006_R1_001
processed data file: KOS 2.xlsx

source_name: KOS-infected MRC5 cells

value: KOS (wt)


title: Sample 4_KOS-infected MRC5 cells_8h

description:
8KOS_S10_L006_R1_001
processed data file: KOS 2.xlsx


title: Kidney at 125 days gestation, biological replicate 2

description:
Baboon_Kidney_125dG_2
Gene expression data from Papio hamadryas whole kidney at 125 days gestation.


title: mdmxER-Cre;C463A/WT MEFs treated with EtOH, biological rep1

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: Goldenson Building, Long wood Ave.

department: School of Public Health

institute: Harvard University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array

label: Biotin

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured at 37°C and 5% CO2 in DMEM medium (Corning, Cat.No 10013CV) with 10% fetal bovine serum (Gibco, Cat.No 10082147) and 1% penicillin-streptomycin until about 80% confluent.

extract_protocol: Followed standard  manufacturer's instructions of RNeasy MinElut kit

treatment_protocol: EtOH or 4OHT were added into the media for 24 hours. After replaced with fresh medium for 48 hours, cells were harvested.

value: Mouse Embryonic Fibroblasts

tag: genotype/varation

tag: treated with

value: EtOH for 24hrs


title: Sample 7_n199-infected MRC5 cells_2h

description:
2n199_S1_L006_R1_001
processed data file: n199 2.xlsx

tag: cell line


title: Clostridium difficile - BHIS - 7 hours - Replicate 1

value: BHIS


title: Clostridium difficile - BHIS - 7 hours - Replicate 2


title: Kidney at 60 days gestation, biological replicate 2

description:
Baboon_Kidney_60dG_2
Gene expression data from Papio hamadryas whole kidney at 60 days gestation.

source_name: whole kidney at 60 days gestation


title: Kidney at 90 days gestation, biological replicate 1

description:
Baboon_Kidney_90dG_1
Gene expression data from Papio hamadryas whole kidney at 90 days gestation.


title: Clostridium difficile - BHIS - 7 hours - Replicate 3


title: Sample 3_KOS-infected MRC5 cells_6h

description:
6KOS_S9_L006_R1_001
processed data file: KOS 2.xlsx

tag: infected with


title: Kidney at 60 days gestation, biological replicate 1

description:
Baboon_Kidney_60dG_1
Gene expression data from Papio hamadryas whole kidney at 60 days gestation.


title: H9-TCF7L1_+PS Medium_rep3

city: Irvine

first: Peter

middle: J

last: Donovan

state: CA

address: Gross Hall, Rm 3006, 845 Health Sciences Road

institute: University of California, Irvine

hyb_protocol: Following the recommended procedure, 2 ug of this fragmented target single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Human Gene 1.0 ST Array

scan_protocol: Arrays were scanned using the GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3.to produce .CEL intensity files.

data_processing: These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). (Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile).

source_name: H9-TCF7L1, 48hr PS differentiation medium

label_protocol: The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 70 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChipÒ WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

extract_protocol: Total RNA was isolated according to the Qiagen RNeasy instructions.


title: H9-TCF7L1_+PS Medium_+Dox_rep1

source_name: H9-TCF7L1, 48hr PS differentiation medium + 48hr Dox (1 ug/ml)


title: H9-TCF7L1_+PS Medium_+Dox_rep2


title: Sample 6_KOS-infected MRC5 cells_16h

description:
16KOS_S12_L006_R1_001
processed data file: KOS 2.xlsx

tag: time post infection


title: H9-TCF7L1_Untreated_rep1

source_name: H9-TCF7L1, mTeSR1 medium


title: H9-TCF7L1_Untreated_rep2


title: H9-TCF7L1_Untreated_rep3


title: Clostridium difficile - BHIS+DP - 5 hours - Replicate 3

value: 5 hours


title: H9-TCF7L1_+PS Medium_rep2


title: H9-TCF7L1_+PS Medium_+Dox_rep3


title: Sample 2_KOS-infected MRC5 cells_4h

description:
4KOS_S8_L006_R1_001
processed data file: KOS 2.xlsx


title: Clostridium difficile - BHIS+DP - 5 hours - Replicate 2


title: Clostridium difficile - BHIS+DP - 5 hours - Replicate 1


title: Sample 1_KOS-infected MRC5 cells_2h

description:
2KOS_S7_L006_R1_001
processed data file: KOS 2.xlsx


title: Clostridium difficile - BHIS - 5 hours - Replicate 2


title: Clostridium difficile - BHIS - 5 hours - Replicate 3


title: H9_TCF7L1 siRNA_Day 3_rep2

source_name: H9, transfected with TCF7L1 siRNA

value: embryonic stem cell


title: H9_TCF7L1 siRNA_Day 3_rep1


title: H9_TCF7L1 siRNA_Day 3_rep3


title: H9-TCF7L1_+PS Medium_rep1


title: human primary OA chondrocyte untreated

description: pool of 3 independent equimolar RNA samples

tag: tissue


title: N33_NB2i rep2

city: Tianjin

first: Renpeng

last: Guo

address: Weijin Road 94th, Nankai District, Tianjin, China

country: China

institute: Nankai University

data_processing:
Basecalls performed using the software Zebra call
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2.
Fragments Per Kilobase per Million is calculated to represent the gene expression level. FPKM = numFragments / ( geneLength/1000 * totalNumFragments /1,000,000). numFragments - number of fragments mapped to a gene sequence. geneLength - length of the gene sequence. totalNumFragments - total number of mapped fragments of a sample.
Functional enrichment (GO annotation, KEGG) of gene sets with different expression patterns was performed using clusterProfiler. The heat maps were drawn by the function ‘pheatmap’ of R packages ‘pheatmap’ and correlation coefficients were calculation by the function ‘cor’ in R. Scatter plots were generated using the ‘ggplot2’ package to graphically reveal genes that differ significantly between two samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited FPKM files include FPKM values for each Sample.

source_name: mouse ESCs

growth_protocol: For routine feeder culture condition, ESCs were cultured under 5% CO2 at 37 °C on mitomycin C-treated MEF feeder in ES cell culture medium consisting of knockout DMEM supplemented with 20% fetal bovine serum (FBS, ES quality, Hyclone), 1,000 U/ml leukemia inhibitory factor (LIF)(ESGRO, Chemicon), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, and penicillin (100 U/ml) and streptomycin (100 µg/ml). For feeder-free culture (serum condition), plates were pre-coated with gelatin. Chemically defined serum and feeder-free culture conditions (N2B27+2i): ESCs were cultured on poly-L-ornithine and laminin-coated plates using N2B27 medium (DMEM/F12 and Neurobasal medium mixed at a ratio of 1:1, 1xN2 supplement, 1xB27 supplement, 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 0.1 mM nonessential amino acids, 100 units/ml penicillin, 100 μg/ml streptomycin) supplemented with Gsk3β inhibitor (CHIR99021, 3 μM) and Mek inhibitor (PD0325901, 1 μM) and 1,000 U/ml LIF.

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen), according to manufacturer’s instructions.
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Then the selected RNA was fragmented and copied into first strand cDNA, which was followed by second strand cDNA synthesis. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched with PCR amplification. PCR yield was quantified and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: ESCs were washed by PBS and trypsinized to single cells. ESCs cultured with feeders were removed off feeders twice based on their differences in the adherence to the bottom of dish.

value: ESC

tag: culture condition


title: N33_NB2i rep1


title: Non-tumor of Patient 1

city: Guangzhou

first: Feng

last: He

state: Guangdong

address: 1# Panfu Road

department: Department of General Surgery

institute: Guangzhou First People's Hospital, the Second Affiliated Hospital of South China University of Technology

description:
Gene expression of non-tumor colorectal tissue from patient1
D653416N

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Patient1: Male, 55yrs, TNM stage : II

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) and purified using the RNeasy Mini Kit (Qiagen). Complementary DNA was synthesized, labeled, purified, and hybridized to the microarray (Arraystar).

treatment_protocol: Fresh colorectal tumor samples and matched non-tumor samples (obtained from unaffected colorectal at least 5 cm from the tumor) from 6 colorectal cancer patients were individually profiled.

tag: individual

value: Colorectal tissue

tag: gender

value: Male

tag: age

tag: tnm stage

value: II


title: Clostridium difficile - BHIS - 5 hours - Replicate 1


title: Clostridium difficile - BHIS+DP - 3 hours - Replicate 3

value: 3 hours


title: H9_Non-Silencing siRNA_Day 3_rep2

source_name: H9, transfected with non-silencing siRNA

tag: cell type


title: H9_Non-Silencing siRNA_Day 3_rep3


title: N33_F2i rep1

value: serum with feeder and 2i


title: N33_F2i rep2


title: N33_F rep1

value: serum with feeder


title: H9_No siRNA_Day 3_rep2

source_name: H9, untreated


title: N33_F rep2


title: Clostridium difficile - BHIS+DP - 3 hours - Replicate 2


title: N33_G rep2

value: serum without feeder


title: N33_G rep1

data_processing:
Basecalls performed using the software Zebra call
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2.
Fragments Per Kilobase per Million is calculated to represent the gene expression level. FPKM = numFragments / ( geneLength/1000 * totalNumFragments /1,000,000). numFragments = number of fragments mapped to a gene sequence. geneLength = length of the gene sequence. totalNumFragments = total number of mapped fragments of a sample.
Functional enrichment (GO annotation, KEGG) of gene sets with different expression patterns was performed using clusterProfiler. The heat maps were drawn by the function ‘pheatmap’ of R packages ‘pheatmap’ and correlation coefficients were calculation by the function ‘cor’ in R. Scatter plots were generated using the ‘ggplot2’ package to graphically reveal genes that differ significantly between two samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited FPKM files include FPKM values for each Sample.


title: single fibroblast from donor RA8 (RA8_H9)

status: Public on Jan 19 2018

city: Charlestown

first: Kamil

last: Slowikowski

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

description:
singlecell_rnaseq_gene_counts.tsv.gz
singlecell_rnaseq_transcript_counts.tsv.gz
singlecell_rnaseq_gene_tpm.tsv.gz
singlecell_rnaseq_transcript_tpm.tsv.gz

data_processing:
kallisto-0.42.4
Genome_build: Ensembl 83
Supplementary_files_format_and_content: tab-delimited text files with pseudocounts or transcripts per million (TPM) for each transcript or gene reported by kallisto
singlecell_rnaseq_gene_counts.tsv.gz (pseudocounts of each gene)
singlecell_rnaseq_transcript_counts.tsv.gz (pseudocounts of each transcript)
singlecell_rnaseq_gene_tpm.tsv.gz (transcripts per million (TPM) of each gene)
singlecell_rnaseq_transcript_tpm.tsv.gz (transcripts per million (TPM) of each transcript)

molecule: polyA RNA

source_name: fibroblasts from athroplasty

extract_protocol:
We digested tissues with 4 mg/ml collagenase type 4 (Worthington, NJ), 0.8 mg/ml Dispase II, 0.1 mg/ml DNaseI (Roche) in DMEM at 37Â°C. After 15 minutes, we collected the supernatant and replaced with fresh enzyme mix. We repeated these procedures every 15 minutes for total 1 hour. We digested tissues with 0.2 mg/ml Liberase TL (Roche), 0.1 mg/ml DNaseI in RPMI at 37Â°C for 20 minutes to minimize the cleavage of surface markers of lymphocytes during the enzymatic digestion. After lysing red blood cells with ACK-lysing buffer, we stained cells with antibodies, and sorted by FACSAria Fusion (BD) with 100 um nozzle at 20 psi. The cells were stained with antibodies and directly sorted into 5 ul of TCL buffer (QIAGEN) with 1% 2-mercaptoethanol (SIGMA) in 96 well plates.
Smart-Seq2

tag: donor

tag: disease state

value: RA

tag: Sex

value: Female

tag: joint

value: Knee


title: H9_No siRNA_Day 3_rep3


title: H9_Non-Silencing siRNA_Day 3_rep1


title: Clostridium difficile - BHIS+DP - 3 hours - Replicate 1

tag: strain

tag: culture type

value: in vitro

tag: condition

value: BHIS+DP

tag: time


title: Clostridium difficile - BHIS - 3 hours - Replicate 2


title: Clostridium difficile - BHIS - 3 hours - Replicate 1


title: Clostridium difficile - BHIS - 3 hours - Replicate 3


title: single fibroblast from donor RA8 (RA8_H7)


title: single fibroblast from donor RA8 (RA8_H6)


title: single fibroblast from donor RA8 (RA8_H8)


title: single fibroblast from donor RA8 (RA8_H5)


title: single fibroblast from donor RA8 (RA8_H4)


title: single fibroblast from donor RA8 (RA8_H12)


title: single fibroblast from donor RA8 (RA8_H11)


title: H9_No siRNA_Day 3_rep1

tag: cell line


title: single fibroblast from donor RA8 (RA8_H2)


title: single fibroblast from donor RA8 (RA8_G8)


title: single fibroblast from donor RA8 (RA8_H3)


title: single fibroblast from donor RA8 (RA8_G9)


title: single fibroblast from donor RA8 (RA8_G6)


title: single fibroblast from donor RA8 (RA8_H10)


title: single fibroblast from donor RA8 (RA8_G7)


title: single fibroblast from donor RA8 (RA8_H1)


title: single fibroblast from donor RA8 (RA8_G5)


title: single fibroblast from donor RA8 (RA8_G3)


title: single fibroblast from donor RA8 (RA8_G2)


title: single fibroblast from donor RA8 (RA8_G12)


title: single fibroblast from donor RA8 (RA8_G1)


title: single fibroblast from donor RA8 (RA8_F6)


title: single fibroblast from donor RA8 (RA8_G4)


title: single fibroblast from donor RA8 (RA8_F8)


title: single fibroblast from donor RA8 (RA8_F7)


title: single fibroblast from donor RA8 (RA8_F9)


title: single fibroblast from donor RA8 (RA8_F3)


title: single fibroblast from donor RA8 (RA8_G10)


title: single fibroblast from donor RA8 (RA8_G11)


title: single fibroblast from donor RA8 (RA8_F12)


title: single fibroblast from donor RA8 (RA8_F4)


title: single fibroblast from donor RA8 (RA8_F2)


title: single fibroblast from donor RA8 (RA8_F5)


title: single fibroblast from donor RA8 (RA8_F1)


title: single fibroblast from donor RA8 (RA8_F10)


title: single fibroblast from donor RA8 (RA8_E1)


title: single fibroblast from donor RA8 (RA8_E2)


title: single fibroblast from donor RA8 (RA8_F11)


title: single fibroblast from donor RA8 (RA8_E6)


title: single fibroblast from donor RA8 (RA8_E10)


title: single fibroblast from donor RA8 (RA8_E3)


title: single fibroblast from donor RA8 (RA8_E11)


title: single fibroblast from donor RA8 (RA8_E9)


title: single fibroblast from donor RA8 (RA8_E4)


title: single fibroblast from donor RA8 (RA8_E7)


title: single fibroblast from donor RA8 (RA8_E5)


title: single fibroblast from donor RA8 (RA8_D9)


title: single fibroblast from donor RA8 (RA8_E12)


title: single fibroblast from donor RA8 (RA8_D3)


title: single fibroblast from donor RA8 (RA8_E8)


title: single fibroblast from donor RA8 (RA8_D7)


title: single fibroblast from donor RA8 (RA8_D8)


title: single fibroblast from donor RA8 (RA8_D10)


title: single fibroblast from donor RA8 (RA8_C8)


title: single fibroblast from donor RA8 (RA8_D11)


title: single fibroblast from donor RA8 (RA8_C7)


title: single fibroblast from donor RA8 (RA8_C5)


title: single fibroblast from donor RA8 (RA8_C6)


title: single fibroblast from donor RA8 (RA8_D5)


title: single fibroblast from donor RA8 (RA8_D2)


title: single fibroblast from donor RA8 (RA8_D6)


title: single fibroblast from donor RA8 (RA8_D4)


title: single fibroblast from donor RA8 (RA8_C9)


title: single fibroblast from donor RA8 (RA8_D1)


title: single fibroblast from donor RA8 (RA8_C4)


title: single fibroblast from donor RA8 (RA8_D12)


title: single fibroblast from donor RA8 (RA8_C11)


title: single fibroblast from donor RA8 (RA8_C10)


title: single fibroblast from donor RA8 (RA8_C12)


title: single fibroblast from donor RA8 (RA8_B9)


title: single fibroblast from donor RA8 (RA8_B12)


title: single fibroblast from donor RA8 (RA8_B3)


title: single fibroblast from donor RA8 (RA8_B10)


title: single fibroblast from donor RA8 (RA8_B1)


title: single fibroblast from donor RA8 (RA8_A9)


title: single fibroblast from donor RA8 (RA8_A8)


title: single fibroblast from donor RA8 (RA8_B2)


title: single fibroblast from donor RA8 (RA8_C2)


title: single fibroblast from donor RA8 (RA8_A4)


title: single fibroblast from donor RA8 (RA8_B11)


title: single fibroblast from donor RA8 (RA8_B4)


title: single fibroblast from donor RA8 (RA8_A3)


title: single fibroblast from donor RA8 (RA8_C1)


title: single fibroblast from donor OA5 (OA5_H8)

value: OA


title: single fibroblast from donor OA5 (OA5_H9)


title: single fibroblast from donor OA5 (OA5_H7)


title: single fibroblast from donor OA5 (OA5_H5)


title: single fibroblast from donor OA5 (OA5_H12)


title: single fibroblast from donor RA8 (RA8_A6)


title: single fibroblast from donor OA5 (OA5_H4)


title: single fibroblast from donor RA8 (RA8_C3)


title: single fibroblast from donor OA5 (OA5_H10)


title: single fibroblast from donor RA8 (RA8_A2)


title: single fibroblast from donor RA8 (RA8_B5)


title: single fibroblast from donor RA8 (RA8_B7)


title: single fibroblast from donor RA8 (RA8_B8)


title: single fibroblast from donor OA5 (OA5_G9)


title: single fibroblast from donor OA5 (OA5_G8)


title: single fibroblast from donor RA8 (RA8_A11)


title: single fibroblast from donor RA8 (RA8_B6)


title: single fibroblast from donor OA5 (OA5_G7)


title: single fibroblast from donor OA5 (OA5_H11)


title: single fibroblast from donor OA5 (OA5_G6)


title: single fibroblast from donor RA8 (RA8_A5)


title: single fibroblast from donor OA5 (OA5_H2)


title: single fibroblast from donor RA8 (RA8_A1)


title: single fibroblast from donor RA8 (RA8_A7)


title: single fibroblast from donor RA8 (RA8_A10)


title: single fibroblast from donor OA5 (OA5_G4)


title: single fibroblast from donor OA5 (OA5_G3)


title: single fibroblast from donor RA8 (RA8_A12)


title: single fibroblast from donor OA5 (OA5_F9)


title: single fibroblast from donor OA5 (OA5_G12)


title: single fibroblast from donor OA5 (OA5_F5)


title: single fibroblast from donor OA5 (OA5_F8)


title: single fibroblast from donor OA5 (OA5_G10)


title: single fibroblast from donor OA5 (OA5_H3)


title: single fibroblast from donor OA5 (OA5_H1)


title: single fibroblast from donor OA5 (OA5_F12)


title: single fibroblast from donor OA5 (OA5_F2)


title: single fibroblast from donor OA5 (OA5_E8)


title: single fibroblast from donor OA5 (OA5_E7)


title: single fibroblast from donor OA5 (OA5_F1)


title: single fibroblast from donor OA5 (OA5_G2)


title: single fibroblast from donor OA5 (OA5_F4)


title: single fibroblast from donor OA5 (OA5_F7)


title: single fibroblast from donor OA5 (OA5_D8)


title: single fibroblast from donor OA5 (OA5_E11)


title: single fibroblast from donor OA5 (OA5_G1)


title: single fibroblast from donor OA5 (OA5_D6)


title: single fibroblast from donor OA5 (OA5_F6)


title: single fibroblast from donor OA5 (OA5_E6)


title: single fibroblast from donor OA5 (OA5_F3)


title: single fibroblast from donor OA5 (OA5_E12)


title: single fibroblast from donor OA5 (OA5_D5)


title: single fibroblast from donor OA5 (OA5_G5)


title: single fibroblast from donor OA5 (OA5_D4)


title: single fibroblast from donor OA5 (OA5_D2)


title: single fibroblast from donor OA5 (OA5_G11)


title: single fibroblast from donor OA5 (OA5_D7)


title: single fibroblast from donor OA5 (OA5_E1)


title: single fibroblast from donor OA5 (OA5_E10)


title: single fibroblast from donor OA5 (OA5_E4)


title: single fibroblast from donor OA5 (OA5_E9)


title: single fibroblast from donor OA5 (OA5_C8)


title: single fibroblast from donor OA5 (OA5_C9)


title: single fibroblast from donor OA5 (OA5_E2)


title: single fibroblast from donor OA5 (OA5_C6)


title: single fibroblast from donor OA5 (OA5_D9)


title: single fibroblast from donor OA5 (OA5_F11)


title: single fibroblast from donor OA5 (OA5_C5)


title: single fibroblast from donor OA5 (OA5_F10)


title: single fibroblast from donor OA5 (OA5_E5)


title: single fibroblast from donor OA5 (OA5_D3)


title: single fibroblast from donor OA5 (OA5_C2)


title: single fibroblast from donor OA5 (OA5_E3)


title: single fibroblast from donor OA5 (OA5_C1)


title: single fibroblast from donor OA5 (OA5_D12)


title: single fibroblast from donor OA5 (OA5_D11)


title: single fibroblast from donor OA5 (OA5_C3)


title: single fibroblast from donor OA5 (OA5_C11)


title: single fibroblast from donor OA5 (OA5_D10)


title: single fibroblast from donor OA5 (OA5_C10)


title: single fibroblast from donor OA5 (OA5_C12)


title: single fibroblast from donor OA5 (OA5_C7)


title: single fibroblast from donor OA5 (OA5_C4)


title: single fibroblast from donor OA5 (OA5_D1)


title: single fibroblast from donor OA5 (OA5_B6)


title: single fibroblast from donor OA5 (OA5_B5)


title: single fibroblast from donor OA5 (OA5_B7)


title: single fibroblast from donor OA5 (OA5_B8)


title: single fibroblast from donor OA5 (OA5_B2)


title: single fibroblast from donor OA5 (OA5_B11)


title: single fibroblast from donor OA5 (OA5_B12)


title: single fibroblast from donor OA5 (OA5_B1)


title: single fibroblast from donor OA5 (OA5_A9)


title: single fibroblast from donor OA5 (OA5_A8)


title: single fibroblast from donor OA5 (OA5_B4)


title: single fibroblast from donor OA5 (OA5_B10)


title: single fibroblast from donor OA5 (OA5_B9)


title: single fibroblast from donor OA5 (OA5_A7)


title: single fibroblast from donor OA5 (OA5_A6)


title: single fibroblast from donor OA5 (OA5_A5)


title: single fibroblast from donor OA5 (OA5_A4)


title: single fibroblast from donor OA5 (OA5_A2)


title: single fibroblast from donor OA5 (OA5_A3)


title: single fibroblast from donor OA5 (OA5_A12)


title: single fibroblast from donor OA5 (OA5_B3)


title: single fibroblast from donor OA5 (OA5_A1)


title: single fibroblast from donor OA5 (OA5_A10)


title: single fibroblast from donor OA5 (OA5_A11)


title: single fibroblast from donor RA9 (RA9_H7)

value: Elbow


title: single fibroblast from donor RA9 (RA9_H5)


title: single fibroblast from donor RA9 (RA9_H9)


title: single fibroblast from donor RA9 (RA9_H6)


title: single fibroblast from donor RA9 (RA9_H2)


title: single fibroblast from donor RA9 (RA9_H10)


title: single fibroblast from donor RA9 (RA9_G9)


title: single fibroblast from donor RA9 (RA9_H1)


title: single fibroblast from donor RA9 (RA9_H4)


title: single fibroblast from donor RA9 (RA9_H12)


title: single fibroblast from donor RA9 (RA9_G6)


title: single fibroblast from donor RA9 (RA9_G5)


title: single fibroblast from donor RA9 (RA9_G2)


title: single fibroblast from donor RA9 (RA9_G8)


title: single fibroblast from donor RA9 (RA9_H11)


title: single fibroblast from donor RA9 (RA9_G4)


title: single fibroblast from donor RA9 (RA9_G12)


title: single fibroblast from donor RA9 (RA9_G3)


title: single fibroblast from donor RA9 (RA9_G7)


title: single fibroblast from donor RA9 (RA9_H3)


title: single fibroblast from donor RA9 (RA9_G1)


title: single fibroblast from donor RA9 (RA9_F9)


title: single fibroblast from donor RA9 (RA9_F4)


title: single fibroblast from donor RA9 (RA9_H8)


title: single fibroblast from donor RA9 (RA9_G10)


title: single fibroblast from donor RA9 (RA9_F10)


title: single fibroblast from donor RA9 (RA9_F12)


title: single fibroblast from donor RA9 (RA9_F1)


title: single fibroblast from donor RA9 (RA9_F6)


title: single fibroblast from donor RA9 (RA9_G11)


title: single fibroblast from donor RA9 (RA9_E6)


title: single fibroblast from donor RA9 (RA9_E5)


title: single fibroblast from donor RA9 (RA9_E8)


title: single fibroblast from donor RA9 (RA9_E3)


title: single fibroblast from donor RA9 (RA9_F7)


title: single fibroblast from donor RA9 (RA9_F5)


title: single fibroblast from donor RA9 (RA9_F2)


title: single fibroblast from donor RA9 (RA9_F8)


title: single fibroblast from donor RA9 (RA9_F3)


title: single fibroblast from donor RA9 (RA9_E4)


title: single fibroblast from donor RA9 (RA9_E11)


title: single fibroblast from donor RA9 (RA9_D8)


title: single fibroblast from donor RA9 (RA9_E7)


title: single fibroblast from donor OA5 (OA5_H6)


title: single fibroblast from donor RA9 (RA9_F11)


title: single fibroblast from donor RA9 (RA9_E2)


title: single fibroblast from donor RA9 (RA9_D6)


title: single fibroblast from donor RA9 (RA9_E1)


title: single fibroblast from donor RA9 (RA9_E12)


title: single fibroblast from donor RA9 (RA9_D5)


title: single fibroblast from donor RA9 (RA9_D2)


title: single fibroblast from donor RA9 (RA9_D7)


title: single fibroblast from donor RA9 (RA9_D3)


title: single fibroblast from donor RA9 (RA9_D9)


title: single fibroblast from donor RA9 (RA9_C6)


title: single fibroblast from donor RA9 (RA9_E9)


title: single fibroblast from donor RA9 (RA9_E10)


title: single fibroblast from donor RA9 (RA9_D1)


title: single fibroblast from donor RA9 (RA9_C8)


title: single fibroblast from donor RA9 (RA9_D10)


title: single fibroblast from donor RA9 (RA9_C11)


title: single fibroblast from donor RA9 (RA9_D4)


title: single fibroblast from donor RA9 (RA9_D12)


title: single fibroblast from donor RA9 (RA9_C9)


title: single fibroblast from donor RA9 (RA9_C7)


title: single fibroblast from donor RA9 (RA9_D11)


title: single fibroblast from donor RA9 (RA9_C2)


title: single fibroblast from donor RA9 (RA9_C12)


title: single fibroblast from donor RA9 (RA9_C5)


title: single fibroblast from donor RA9 (RA9_B6)


title: single fibroblast from donor RA9 (RA9_B9)


title: single fibroblast from donor RA9 (RA9_B2)


title: single fibroblast from donor RA9 (RA9_B11)


title: single fibroblast from donor RA9 (RA9_C4)


title: single fibroblast from donor RA9 (RA9_B4)


title: single fibroblast from donor RA9 (RA9_C3)


title: single fibroblast from donor RA9 (RA9_B3)


title: single fibroblast from donor RA9 (RA9_B1)


title: single fibroblast from donor RA9 (RA9_C1)


title: single fibroblast from donor RA9 (RA9_B5)


title: single fibroblast from donor RA9 (RA9_A7)


title: single fibroblast from donor RA9 (RA9_A4)


title: single fibroblast from donor RA9 (RA9_B8)


title: single fibroblast from donor RA9 (RA9_A9)


title: single fibroblast from donor RA9 (RA9_A3)


title: single fibroblast from donor RA9 (RA9_A5)


title: single fibroblast from donor RA9 (RA9_C10)


title: single fibroblast from donor RA9 (RA9_A10)


title: single fibroblast from donor RA9 (RA9_A1)


title: single fibroblast from donor OA4 (OA4_H9)


title: single fibroblast from donor RA9 (RA9_B7)


title: single fibroblast from donor RA9 (RA9_A11)


title: single fibroblast from donor OA4 (OA4_H8)


title: single fibroblast from donor OA4 (OA4_H6)


title: single fibroblast from donor RA9 (RA9_A6)


title: single fibroblast from donor OA4 (OA4_H10)


title: single fibroblast from donor OA4 (OA4_H12)


title: single fibroblast from donor RA9 (RA9_B10)


title: single fibroblast from donor OA4 (OA4_H11)


title: single fibroblast from donor OA4 (OA4_H1)


title: single fibroblast from donor OA4 (OA4_H7)


title: single fibroblast from donor RA9 (RA9_B12)


title: single fibroblast from donor RA9 (RA9_A2)


title: single fibroblast from donor OA4 (OA4_G9)


title: single fibroblast from donor RA9 (RA9_A12)


title: single fibroblast from donor OA4 (OA4_G5)


title: single fibroblast from donor OA4 (OA4_G8)


title: single fibroblast from donor RA9 (RA9_A8)


title: single fibroblast from donor OA4 (OA4_G4)


title: single fibroblast from donor OA4 (OA4_G3)


title: single fibroblast from donor OA4 (OA4_H4)


title: single fibroblast from donor OA4 (OA4_G10)


title: single fibroblast from donor OA4 (OA4_H2)


title: single fibroblast from donor OA4 (OA4_H3)


title: single fibroblast from donor OA4 (OA4_F8)


title: single fibroblast from donor OA4 (OA4_G7)


title: single fibroblast from donor OA4 (OA4_G12)


title: single fibroblast from donor OA4 (OA4_H5)


title: single fibroblast from donor OA4 (OA4_F6)


title: single fibroblast from donor OA4 (OA4_G2)


title: single fibroblast from donor OA4 (OA4_G1)


title: single fibroblast from donor OA4 (OA4_F1)


title: single fibroblast from donor OA4 (OA4_E9)


title: single fibroblast from donor OA4 (OA4_G11)


title: single fibroblast from donor OA4 (OA4_F4)


title: single fibroblast from donor OA4 (OA4_E7)


title: single fibroblast from donor OA4 (OA4_F11)


title: single fibroblast from donor OA4 (OA4_F3)


title: single fibroblast from donor OA4 (OA4_F10)


title: single fibroblast from donor OA4 (OA4_F5)


title: single fibroblast from donor OA4 (OA4_F12)


title: single fibroblast from donor OA4 (OA4_F9)


title: single fibroblast from donor OA4 (OA4_E6)


title: single fibroblast from donor OA4 (OA4_E5)


title: single fibroblast from donor OA4 (OA4_F2)


title: single fibroblast from donor OA4 (OA4_E10)


title: single fibroblast from donor OA4 (OA4_E12)


title: single fibroblast from donor OA4 (OA4_E4)


title: single fibroblast from donor OA4 (OA4_E1)


title: single fibroblast from donor OA4 (OA4_E3)


title: single fibroblast from donor OA4 (OA4_D9)


title: single fibroblast from donor OA4 (OA4_E11)


title: single fibroblast from donor OA4 (OA4_F7)


title: single fibroblast from donor OA4 (OA4_D5)


title: single fibroblast from donor OA4 (OA4_D7)


title: single fibroblast from donor OA4 (OA4_E2)


title: single fibroblast from donor OA4 (OA4_D4)


title: single fibroblast from donor OA4 (OA4_D11)


title: single fibroblast from donor OA4 (OA4_D8)


title: single fibroblast from donor OA4 (OA4_G6)


title: single fibroblast from donor OA4 (OA4_D12)


title: single fibroblast from donor OA4 (OA4_D1)


title: single fibroblast from donor OA4 (OA4_D2)


title: single fibroblast from donor OA4 (OA4_C9)


title: single fibroblast from donor OA4 (OA4_C7)


title: single fibroblast from donor OA4 (OA4_D3)


title: single fibroblast from donor OA4 (OA4_C8)


title: single fibroblast from donor OA4 (OA4_C6)


title: single fibroblast from donor OA4 (OA4_C12)


title: single fibroblast from donor OA4 (OA4_D10)


title: single fibroblast from donor OA4 (OA4_C2)


title: single fibroblast from donor OA4 (OA4_D6)


title: single fibroblast from donor OA4 (OA4_C3)


title: single fibroblast from donor OA4 (OA4_B8)


title: single fibroblast from donor OA4 (OA4_C4)


title: single fibroblast from donor OA4 (OA4_B4)


title: single fibroblast from donor OA4 (OA4_E8)


title: single fibroblast from donor OA4 (OA4_C5)


title: single fibroblast from donor OA4 (OA4_C10)


title: single fibroblast from donor OA4 (OA4_B7)


title: single fibroblast from donor OA4 (OA4_B9)


title: single fibroblast from donor OA4 (OA4_B6)


title: single fibroblast from donor OA4 (OA4_C1)


title: single fibroblast from donor OA4 (OA4_B1)


title: single fibroblast from donor OA4 (OA4_B11)


title: single fibroblast from donor OA4 (OA4_B2)


title: single fibroblast from donor OA4 (OA4_A6)


title: single fibroblast from donor OA4 (OA4_A8)


title: single fibroblast from donor OA4 (OA4_B10)


title: single fibroblast from donor OA4 (OA4_B5)


title: single fibroblast from donor OA4 (OA4_A7)


title: single fibroblast from donor OA4 (OA4_B12)


title: single fibroblast from donor OA4 (OA4_B3)


title: single fibroblast from donor OA4 (OA4_A9)


title: single fibroblast from donor OA4 (OA4_A4)


title: single fibroblast from donor OA4 (OA4_C11)


title: single fibroblast from donor OA4 (OA4_A12)


title: single fibroblast from donor OA4 (OA4_A2)


title: fibroblasts gated by flow cytometry from donor RA7 (RA7_CD34L_CD90L_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA7_CD34L_THY1L_CDH11L

data_processing:
kallisto-0.42.4
Genome_build: Ensembl 83
Supplementary_files_format_and_content: tab-delimited text files with pseudocounts or transcripts per million (TPM) for each transcript or gene reported by kallisto
rnaseq_gene_counts.tsv.gz (pseudocounts of each gene)
rnaseq_transcript_counts.tsv.gz (pseudocounts of each transcript)
rnaseq_gene_tpm.tsv.gz (transcripts per million (TPM) of each gene)
rnaseq_transcript_tpm.tsv.gz (transcripts per million (TPM) of each transcript)

source_name: fibroblasts gated by flow cytometry

extract_protocol:
We digested tissues with 4 mg/ml collagenase type 4 (Worthington, NJ), 0.8 mg/ml Dispase II, 0.1 mg/ml DNaseI (Roche) in DMEM at 37Â°C. After 15 minutes, we collected the supernatant and replaced with fresh enzyme mix. We repeated these procedures every 15 minutes for total 1 hour. After lysing red blood cells with ACK-lysing buffer, we stained cells with antibodies, and sorted by FACSAria Fusion (BD) with 100 um nozzle at 20 psi. The cells were sorted into 2% FBS HBS+ buffer, spun down, and lysed with TRIzol (Invitrogen). We extracted RNA and cleaned up by RNeasy micro kit (QIAGEN) with DNaseI treatment.
Smart-Seq2

value: Foot

value: fibroblasts


title: single fibroblast from donor OA4 (OA4_A1)


title: single fibroblast from donor OA4 (OA4_A11)


title: single fibroblast from donor OA4 (OA4_A3)


title: single fibroblast from donor OA4 (OA4_A5)


title: single fibroblast from donor OA4 (OA4_A10)


title: fibroblasts gated by flow cytometry from donor RA6 (RA6_CD34H_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA6_CD34H_THY1H_CDH11H

value: Wrist


title: fibroblasts gated by flow cytometry from donor RA7 (RA7_CD34H_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA7_CD34H_THY1H_CDH11H


title: fibroblasts gated by flow cytometry from donor RA7 (RA7_CD34L_CD90L_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA7_CD34L_THY1L_CDH11H


title: fibroblasts gated by flow cytometry from donor RA7 (RA7_CD34L_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA7_CD34L_THY1H_CDH11H


title: fibroblasts gated by flow cytometry from donor RA6 (RA6_CD34L_CD90L_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA6_CD34L_THY1L_CDH11L


title: fibroblasts gated by flow cytometry from donor RA7 (RA7_CD34L_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA7_CD34L_THY1H_CDH11L


title: fibroblasts gated by flow cytometry from donor RA6 (RA6_CD34L_CD90L_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA6_CD34L_THY1L_CDH11H


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34H_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34H_THY1H_CDH11L


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34H_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34H_THY1H_CDH11H


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34H_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34H_THY1H_CDH11L


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34L_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34L_THY1H_CDH11H


title: fibroblasts gated by flow cytometry from donor RA6 (RA6_CD34H_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA6_CD34H_THY1H_CDH11L


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34L_CD90L_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34L_THY1L_CDH11H


title: fibroblasts gated by flow cytometry from donor RA6 (RA6_CD34L_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA6_CD34L_THY1H_CDH11L


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34L_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34L_THY1H_CDH11L


title: H1299.175R.2

city: Philadelphia

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: H1299 cell line, P72R variant R, p53 mutant R175H, batch b2

data_processing:
RNA-Seq data was aligned using bowtie2 against hg38 version of genome and rsem (ver. 1.2.12) with Ensemble v84 transcriptome information used for gene count
DESeq2 was used for differentail expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: R variant, p53 mutant R175H, batch b2

growth_protocol: H1299 cell lines were obtained from the ATCC and used  at early passage

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with Lexogen  QuantSeq 3’mRNA-Seq library prep kit at the Wistar Institute Genomics Facility and subjected to a 75 bp single-end sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.

treatment_protocol: Cells were  transfected with the constructs of interest (5ugs of DNA) with Fugene and selected in  Neomycin 800ugs/ml for 14 days to make stable isogenic cell lines

value: R

tag: hotspot

tag: batch


title: H1299.175R.1

description: H1299 cell line, P72R variant R, p53 mutant R175H, batch b1

source_name: R variant, p53 mutant R175H, batch b1


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34L_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34L_THY1H_CDH11H


title: fibroblasts gated by flow cytometry from donor RA6 (RA6_CD34L_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA6_CD34L_THY1H_CDH11H


title: H1299.273P.2

description: H1299 cell line, P72R variant P, p53 mutant R273H, batch b1

source_name: P variant, p53 mutant R273H, batch b1

value: P


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34H_CD90L_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34H_THY1L_CDH11H


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34H_CD90L_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34H_THY1L_CDH11H


title: H1299.175R.4


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34H_CD90H_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34H_THY1H_CDH11H


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34L_CD90L_Cad11H)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34L_THY1L_CDH11H


title: H1299.273P.3


title: fibroblasts gated by flow cytometry from donor RA5 (RA5_CD34L_CD90L_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA5_CD34L_THY1L_CDH11L


title: H1299.273P.4


title: H1299.273R.3

description: H1299 cell line, P72R variant R, p53 mutant R273H, batch b2

source_name: R variant, p53 mutant R273H, batch b2


title: H1299.175P.4

description: H1299 cell line, P72R variant P, p53 mutant R175H, batch b2

source_name: P variant, p53 mutant R175H, batch b2


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34L_CD90H_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34L_THY1H_CDH11L


title: fibroblasts gated by flow cytometry from donor RA4 (RA4_CD34L_CD90L_Cad11L)

description:
rnaseq_gene_counts.tsv.gz
rnaseq_transcript_counts.tsv.gz
rnaseq_gene_tpm.tsv.gz
rnaseq_transcript_tpm.tsv.gz
Sample name: RA4_CD34L_THY1L_CDH11L


title: H1299.273P.1

description: H1299 cell line, P72R variant P, p53 mutant R273H, batch b2

source_name: P variant, p53 mutant R273H, batch b2


title: H1299.175P.2


title: H1299.175P.1


title: B12-IP2

city: Poznan

first: Agnieszka

last: Dzikiewicz-Krawczyk

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B12_AGO2IP fraction_2

hyb_protocol: Overnight hybridization at 65oC on Agilent-050524 SurePrint G3 Custom Human 8x60K according to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: BL case B12

label_protocol: Cy5 labeled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 5 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies). Each sample was labeled and hybridized in duplicate.

extract_protocol: miRNeasy Micro/Mini Kit (Qiagen)

treatment_protocol: CD19+ B cells were sorted by magnetic-activated cell sorting (MACS) from tonsil tissue samples of three donors between three and nine years old. Briefly, a freshly prepared tonsillar cell suspension was prepared and enriched for CD19+ cells using CD19-beads and LS columns (both Miltenyi Biotec, Leiden, The Netherlands). For BL tumor tissues, immunoprecipitation of AGO2-containing RISC complexes was performed on fifty 10 uM tissue sections of two fresh-frozen primary BL tumors.

tag: tissue

value: Fresh-frozen primary BL tumor tissue

value: male


title: B12-total2

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B12_total fraction_2


title: CD19-1-total2

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-1_total fraction_2

source_name: CD19+ cells from tonsil 1

value: CD19+ cells sorted from tonsil tissue obtained during routine tonsillectomy


title: 598_liver_chow_18wk

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

country: Netherlands

institute: TNO

data_processing:
Quality filtering of the NextSeq 500 fastq files was not required
Reads of the fastq files were aligned to the reference sequence using Tophat 2.0.14 combined with Bowtie 2.1.0 (yielding 93.4 - 95.7 % aligned reads/sample). The default mismatch rate of 2% was used (3 mismatches in a read of 150 bases). The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package.
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files. The amount of reads mapped on genes was 69.9-78.6 %/sample (as a % of all reads initially aligned to the genome).
Genome_build: Mus_musculus.GRCm38.dna.primary_assembly (.fa and .gtf files)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample).

extract_protocol:
tissues were removed, flash frozen on dry ice, and RNA  was purified using an RNA Purification Method/Kit (RNABee, Machery Nagel).
Strand-specific mRNA-seq libraries for the Illumina platform were generated using Illumina protocols and sequenced at BaseClear BV (Leiden, The Netherlands).

tag: strain background

tag: genotype/variation

value: LDLr-/-.Leiden mouse deficient for LDLreceptor

tag: treatment diet

value: chow

tag: treatment week

tag: treatment group (diet_week)

tag: treatment group #

value: liver


title: 596_liver_chow_18wk


title: 600_liver_chow_00wk


title: 586_liver_HFD_24wk

value: HFD


title: 599_liver_chow_18wk


title: 583_liver_HFD_24wk


title: 585_liver_HFD_24wk


title: 579_liver_chow_12wk


title: 581_liver_chow_00wk


title: CD19-3-IP1

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-3_AGO2IP fraction_1

source_name: CD19+ cells from tonsil 3

tag: age

tag: gender

value: female


title: CD19-3-total1

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-3_total fraction_1


title: CD19-2-IP1

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-2_AGO2IP fraction_1

source_name: CD19+ cells from tonsil 2


title: B17-IP2

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B17_AGO2IP fraction_2

source_name: BL case B17


title: B17-total1

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B17_total fraction_1


title: CD19-1-IP1

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-1_AGO2IP fraction_1


title: B17-IP1

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B17_AGO2IP fraction_1


title: 597_liver_chow_18wk


title: CD19-2-total1

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-2_total fraction_1


title: CD19-1-total1

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-1_total fraction_1


title: CD19-3-total2

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-3_total fraction_2


title: B12-IP1

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B12_AGO2IP fraction_1


title: B17-total2

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B17_total fraction_2


title: CD19-3-IP2

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-3_AGO2IP fraction_2


title: CD19-2-IP2

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-2_AGO2IP fraction_2


title: CD19-2-total2

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-2_total fraction_2


title: CD19-1-IP2

description:
AGO2-RIP was performed on CD19+ B cells sorted by magnetic-activated cell sorting (MACS) using CD19-beads and LS columns
mRNA and lncRNA expression analysis_tonsil-1_AGO2IP fraction_2


title: B12-total1

description:
AGO2-RIP was performed on fifty 10 uM tissue sections
mRNA and lncRNA expression analysis_BL case B12_total fraction_1


title: 574_liver_chow_06wk


title: 575_liver_chow_06wk


title: 569_liver_HFD_18wk


title: 564_liver_chow_00wk


title: 572_liver_HFD_18wk


title: 563_liver_chow_24wk


title: 578_liver_chow_12wk


title: 562_liver_chow_24wk


title: 556_liver_HFD_24wk


title: 558_liver_HFD_24wk


title: 553_liver_HFD_24wk


title: 570_liver_HFD_18wk


title: 571_liver_HFD_18wk


title: 576_liver_chow_12wk


title: 577_liver_chow_06wk


title: 557_liver_HFD_24wk


title: 540_liver_HFD_12wk


title: 541_liver_HFD_12wk


title: 537_liver_HFD_18wk


title: 560_liver_HFD_24wk


title: 552_liver_HFD_24wk


title: 536_liver_HFD_18wk


title: 535_liver_HFD_18wk


title: 549_liver_HFD_12wk


title: 533_liver_HFD_18wk


title: 568_liver_HFD_18wk


title: 565_liver_chow_24wk


title: 539_liver_HFD_12wk


title: 546_liver_chow_24wk


title: 550_liver_HFD_24wk


title: 561_liver_HFD_24wk


title: 507_liver_HFD_06wk


title: 515_liver_HFD_12wk


title: 503_liver_HFD_06wk


title: 505_liver_HFD_06wk


title: 499_liver_HFD_06wk


title: 525_liver_chow_18wk


title: 551_liver_HFD_24wk


title: 532_liver_HFD_18wk


title: 524_liver_chow_18wk


title: 506_liver_HFD_06wk


title: 516_liver_HFD_12wk


title: 518_liver_HFD_12wk


title: 500_liver_HFD_06wk


title: 548_liver_HFD_12wk


title: 487_liver_HFD_18wk


title: 484_liver_HFD_18wk


title: 485_liver_HFD_12wk


title: 519_liver_HFD_12wk


title: 489_liver_HFD_12wk


title: 477_liver_chow_06wk


title: 490_liver_chow_24wk


title: 496_liver_HFD_06wk


title: 497_liver_HFD_06wk


title: 482_liver_HFD_06wk


title: 480_liver_HFD_06wk


title: 474_liver_chow_06wk


title: 495_liver_chow_24wk


title: 481_liver_HFD_06wk


title: 486_liver_HFD_12wk


title: 478_liver_HFD_06wk


title: 466_liver_chow_00wk


title: 473_liver_chow_12wk


title: 476_liver_chow_06wk


title: 472_liver_chow_12wk


title: 475_liver_chow_12wk


title: 471_liver_chow_00wk


title: Lib 1 viral RNA rep 3

city: Strasbourg

first: Redmond

middle: P

last: Smyth

state: Alsace

address: 15 rue Rene Descartes

department: Architecture et Réactivité de L'ARN

institute: IBMC CNRS

description: viral RNA

data_processing:
Demultiplex reads using novobarcode (Novocraft) using parameters -F ILMFQ -l 6
Trim reads using trim galore! (Babraham Bioinformatics) with the parameters -q 30 --phred64 --paired
Trimmed reads we aligned to the HIV-1 genome using novoalign (Novocraft) with the parameters -F STDFQ -o SAM -o SoftClip -r None
Data processing was performed using a Python script using the Numpy, Pysam and Numba (Continuum Analytics) modules. Briefly, this script parses SAM files containing reads aligned to the reference sequence. It fetches alignment matches by decoding the CIGAR and reads are translated into sequence matches or mismatches in comparison to the reference sequence. It then merges match patterns derived from aligned paired-end reads removing redundancy and sequencing errors where overlapping paired reads disagree. Absolute nucleotide occurrences are counted using one of the three modes: The ‘1d’ mode counts the number of A, C, G, U at each position, the ‘2d’ mode is used for inferring the effect of single mutations on protein binding. It counts all non-redundant combinations of two positions (i,j); i ∈I,j ∈J;I={1…532}; J=I \j; and fills an array containing the number of dinucleotide occurrences for each pair of positions [number of AA,AC,…TG,TT]. Results are serialized to a binary .npy file. A separate script converts these numpy arrays into text files compatible with statistical tools written in MATLAB (MathWorks).
Genome_build: HIV-1 NL4-3
Supplementary_files_format_and_content: 1D processed text file list genome position and the number of A, T, C, and G nucleotide found at that position. 2D list non redundant pairs of genome positions and the number of dinucleotides (AA, AT, AC…) found at these positions

organism: Human immunodeficiency virus 1

source_name: viral RNA

extract_protocol:
Trizol extraction of RNA
RNA was reverse transcribed into cDNA and a specific region of the RNA was PCRed into dsDNA. This dsDNA was then randomly fragmented before library construction for sequencing on the Illumina HiSeq2000 in 100 paired end read mode. Libraries were prepared by ligating preanneled Illumina multiplex adaptors P-GATCGGAAGAGCACACGTCT and ACACTCTTTCCCTACACGACGCTCTTCCGATCT to the blunted and A-tailed dsDNA. This was then amplified using primer PCR1.0 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and an index containing primer CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where NNNNNN is replaced with one of the Illumina TruSeq indexes

tag: library

value: Lib 1

tag: population

value: viral RNA

tag: replicate


title: Lib 2 viral RNA rep 3

description: viral RNA

value: Lib 2


title: S1 bZIP knockdown + Est replicate 3

city: Wuerzburg

first: Wolfgang

last: Droege-Laser

address: Julius-von-Sachs Platz 2

department: Julius-von-Sachs Institute

country: Germany

data_processing:
High-throughput sequencing was performed on an Illumina GAIIx platform following the manufacturer’s instructions.
Quality control of the sequencing data was done using fastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Mapping of the reads was performed using Bowtie 0.12.8 (Lawrence et al., 2009) onto the A. thaliana genome release TAIR10.
The resulting BAM files were then sorted and indexed using samtools 0.1.18.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown in a plant growth incubator (BINDER, Tuttlingen, Germany) in a 12 h light (120 µmol/s·m²) / 12 h dark photoperiod, at 22°C/20°C and a relative humidity of 60%.

extract_protocol:
Total plant RNA was cleaned-up using a RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's protocol. 5 μg of total RNA was used for library preparation.
cDNA library was prepared using the NEBNext mRNA Library Prep Master Mix Set for Illumina (New England BioLabs) in combination with the NEBNext Multiplex Oligos for Illumina (New England BioLabs).

treatment_protocol: 14d-old WT and snrk1α1/α2 plants were pre-treated with Est for 6 d, whereas WT and bzipS1 plants were grown for further 5 d on MS and subsequently transferred to medium with Est for 1d. Afterwards, all plants were cultured for 6 h in extended night and harvested simultaneously.

tag: ecotype

value: 3 weeks old

tag: genotype

value: bZIP1/bZIP53 ko + inducible group bZIP2/-11/-44 knockdown


title: WT + Est replicate 3 for S1

value: wild-type


title: Lib 1 cellular RNA rep 3

description: cellular RNA

source_name: cellular RNA

value: cellular RNA


title: WT + Est replicate 1 for S1


title: Lib 2 cellular RNA rep 3

description: cellular RNA


title: WT + Est replicate 2 for S1


title: S1 bZIP knockdown + Est replicate 2


title: WT viral RNA rep 3

description: viral RNA

value: WT


title: Lib 1 DNA rep 3

description: plasmid DNA

library_source: genomic

molecule: genomic DNA

source_name: DNA

value: DNA


title: 468_liver_chow_00wk


title: SnRK knockdown + Est replicate 3

value: snrk1-alpha-1 ko + inducible snrk1-alpha-2 knockdown


title: WT DNA rep 3

description: plasmid DNA


title: Lib 2 viral RNA rep 2

description: viral RNA


title: SnRK knockdown + Est replicate 1


title: SnRK knockdown + Est replicate 2


title: S1 bZIP knockdown + Est replicate 1


title: WT + Est replicate 3 for SnRK


title: WT + Est replicate 2 for SnRK


title: Lib 1 viral RNA rep 2

description: viral RNA


title: Lib 2 DNA rep 3

description: plasmid DNA


title: WT viral RNA rep 2

description: viral RNA


title: WT + Est replicate 1 for SnRK


title: Lib 2 cellular RNA rep 2

description: cellular RNA


title: WT cellular RNA rep 3

description: cellular RNA


title: Lib 1 DNA rep 2

description: plasmid DNA


title: WT cellular RNA rep 2

description: cellular RNA


title: Lib 1 cellular RNA rep 2

description: cellular RNA


title: Lib 2 viral RNA rep 1

description: viral RNA


title: Lib 2 DNA rep 2

description: plasmid DNA


title: Chlorine-exposed mouse 5

city: Louisville

first: Gary

last: Hoyle

state: KY

address: EOHS Lab 701 HSC-A

institute: University of Louisville

description: Gene expression data from tracheal mesenchymal tissue, chlorine-exposed

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Affymetrix Mouse 430.2 arrays according to the GeneChip array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 4.0 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level, followed by a one-way ANOVA.

source_name: Chlorine-exposed mouse

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix GeneChip WT Plus Reagent Kit from 250 ng total RNA

growth_protocol: Mice were purchased from The Jackson Laboratory at 8 weeks of age and were housed for 1 week at the University of Louisville under SPF barrier conditions before the chlorine exposure protocol was performed.

extract_protocol: RNA was prepared from dissected tissue using Arcturus PicoPure extraction kit according to the manufacturer's instructions.

treatment_protocol: Tracheas were collected from euthanized mice and were flash-frozen in OCT compound.  Frozen sections of trachea were cut and were stained with hematoxylin and eosin.  Laser-capture microdissection was performed to collect subepithelial mesenchymal tissue.  Tissue was pooled from multiple sections from each animal.

tag: strain

value: FVB/NJ

tag: Sex

value: Male

value: 9 weeks

value: Subepithelial mesenchyme from trachea

tag: treatment

value: Whole-body chlorine exposure, 235 ppm for 1 hr


title: Unexposed mouse 4

description: Gene expression data from tracheal mesenchymal tissue, unexposed

source_name: Unexposed mouse

tag: tissue


title: Unexposed mouse 2


title: Unexposed mouse 3


title: Unexposed mouse 5


title: Unexposed mouse 1


title: Chlorine-exposed mouse 3


title: Chlorine-exposed mouse 2


title: Chlorine-exposed mouse 4


title: WT viral RNA rep 1

description: viral RNA


title: WT DNA rep 2

description: plasmid DNA


title: Lib 2 cellular RNA rep 1

description: cellular RNA


title: Lib 1 viral RNA rep 1

description: viral RNA


title: HET1 ThyDP69+ Rep1

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

description: HET1 ThyDP69+

hyb_protocol: Hybridisation to Affymetrix Mouse Gene 2.0 ST arrays was performed for 16 hours at 45C with constant rotation. Samples were hybridised according to the Affymetrix specifications: hybridisation cocktails were heated at 99C for 5 minutes and then at 45C for another 5 minutes. Samples were centrifuged at max speed for 1 minute and 200ul was transferred to each array. Hybridisation was carried out for 16 hours at 45C and 60 rpm. Fluidics washing was FS450_0001.

scan_protocol: Arrays were scanned with an Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalised using rma function from the oligo package in R

source_name: HET_E18.5 DP69+ Thymocytes

label_protocol: Up to 5.5g of total RNA was fragmented and labelled using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay as outlined in the manufacturer's instructions.

extract_protocol: RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher, Cat. KIT0202) performed according to the manufacturer's instructions.

treatment_protocol: Fetal Thymi were dissected from E18.5 embryos for each genotype and stained for surface markers CD4, CD8 and CD69.  DP69- (CD4+CD8+CD69-), DP69+ (CD4+CD8+CD69+) and SP4 (CD4+CD8-) thymocytes were sorted and RNA was extracted from these cells.

tag: developmental stage

value: fetal thymus

tag: cell type

value: thymocytes

tag: cell subtype

value: DP69+ (CD4+CD8+CD69+) cells


title: WT1 ThySP4 Rep1

description: WT1 ThySP4

source_name: WT_E18.5 SP4 Thymocytes

tag: genotype/variation

value: Wildtype

value: SP4 (CD4+CD8-) cells


title: KO2 ThySP4 Rep2

description: KO2 ThySP4

source_name: KO_E18.5 SP4 Thymocytes


title: KO1 ThySP4 Rep1

description: KO1 ThySP4


title: WT cellular RNA rep 1

description: cellular RNA


title: HET1 ThySP4 Rep1

description: HET1 ThySP4

source_name: HET_E18.5 SP4 Thymocytes


title: HET2 ThyDP69+ Rep2

description: HET2 ThyDP69+


title: WT2 ThySP4 Rep2

description: WT2 ThySP4


title: HET2 ThySP4 Rep2

description: HET2 ThySP4


title: KO1 ThyDP69+ Rep1

description: KO1 ThyDP69+

source_name: KO_E18.5 DP69+ Thymocytes


title: Lib 1 cellular RNA rep 1

description: cellular RNA

value: Lib 1


title: Lib 1 DNA rep 1

description: plasmid DNA


title: RBM3KO

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse whole genome using TopHat v2.0.12 and bowtie v1.0.1 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTSeq v0.6.0
Genome_build: mm10 reference sequences were download from http://www.ensembl.org/index.html
Supplementary_files_format_and_content: tab-delimited text files include Normalized Reads Count and  RPKM values for each Sample

source_name: embryonic brain cortex from maternal hypothermia induced condition

growth_protocol: the maternal hypothermia was induced at E14 and embryonic brain cortex was isolated from E16 mice

extract_protocol:
Total RNA was extracted by using Trizol reagent. Total 2ug RNA for the construction of sequencing libraries
mRNA were enriched by Oligo(dT) bread and then fragmented by fragmentation buffer. cDNA was synthesized by reverse transcription using 6bp random primers and purified by QIAQuick PCR kit. After adapter ligation, DNA was PCR amplified sequences and band isolated from an agarose gel.

value: mouse embryonic brain


title: Chlorine-exposed mouse 1


title: WT2 ThyDP69+ Rep2

description: WT2 ThyDP69+

source_name: WT_E18.5 DP69+ Thymocytes


title: KO2 ThyDP69+ Rep2

description: KO2 ThyDP69+


title: WT1 ThyDP69+ Rep1

description: WT1 ThyDP69+


title: KO2 ThyDP69- Rep2

description: KO2 ThyDP69-

source_name: KO_E18.5 DP69- Thymocytes

value: DP69- (CD4+CD8+CD69-) cells


title: KO1 ThyDP69- Rep1

description: KO1 ThyDP69-


title: WT

treatment_protocol: the maternal hypothermia was induced at E14

value: Wild type


title: Lib 2 DNA rep 1

description: plasmid DNA

value: Lib 2


title: WT DNA rep 1

description: plasmid DNA

value: WT

value: DNA


title: WT2 ThyDP69- Rep2

description: WT2 ThyDP69-

source_name: WT_E18.5 DP69- Thymocytes


title: HET1 ThyDP69- Rep1

description: HET1 ThyDP69-

source_name: HET_E18.5 DP69- Thymocytes


title: HET2 ThyDP69- Rep2

description: HET2 ThyDP69-


title: HCC031_non-tumor tissue_SNP

type: genomic

first: Gangqiao

last: Zhou

address: No. 27, Taiping Road, Haidian District

institute: Beijing Institute of Radiation Medicine

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
From raw.CEL file, Copy-number estimation using Robust Multichip Analysis (CRMA) was used to pre-process the probe signal intensities. The procedure included that signal intensities were calibrated for offset and crosstalk between alleles, and normalized for probe sequence effects. After summarizing to probe-set level signals, fragment-length effects were normalized. Next, raw copy numbers was calculated by paired analysis, taking paired tumor-adjacent tissue as a reference for every tumor tissue. Then segmented copy number profiles were analyzed using Circular binary segmentation (CBS) algorithm2 with default parameters in the R package “DNA-copy” (http://www.r-project.org/).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: adjacent non-tumor liver tissues of HCC patient

label_protocol: DNA labeling, hybridization (Genome-Wide Human SNP Array 6.0, Affymetrix®), and data extraction were performed by an Affymetrix service facility (CapitalBio Corporation, China).

extract_protocol: Genomic DNA was extracted from frozen tissues using proteinase K digestion and subsequent phenol/chlororform extraction. DNA concentration and purity were determined using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: For all tumors and non-tumor tissues, samples were snap frozen and stored at -80°C. Tumor sections had to contain more than 70% tumor cell nuclei and less than 20% necrosis in all tumor samples.

tag: subject id

tag: subject status

value: hepatocellular carcinoma (HCC) patient

value: male

tag: tnm staging


title: HCC028_non-tumor tissue_SNP

tag: gender

tag: age


title: HCC029_non-tumor tissue_SNP


title: HCC026_non-tumor tissue_SNP


title: HCC025_non-tumor tissue_SNP


title: HCC024_non-tumor tissue_SNP


title: HCC023_non-tumor tissue_SNP


title: HCC027_non-tumor tissue_SNP


title: WT1 ThyDP69- Rep1

description: WT1 ThyDP69-


title: HCC022_non-tumor tissue_SNP


title: N_sham_220_L_NS

city: JiNan

first: Li

middle: quan

last: Xin

state: Shandong

address: 44#, Wenhua Xi Road

department: Department of Pharmacology

institute: Shandong University

description: Gene expression after 24h in kidney with sham operation.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Kidney with sham operation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All organizations are stored in the -80°C refrigerator before detection.

extract_protocol: Total RNA was isolated from kidney using TRIzol reagent (Invitrogen).

treatment_protocol: Kidney with sham operation or ischemia reperfusion injury.

tag: strain/background

value: 8 weeks

value: kidney

value: sham operation


title: HCC030_non-tumor tissue_SNP

value: female


title: WT_IR48h_18_L_NS

description: Gene expression after 24h in kidney with ischemia reperfusion injury.

source_name: Kidney with ischemia reperfusion injury

value: ischemia reperfusion injury


title: HCC020_non-tumor tissue_SNP


title: N_IR48h_279_R_NS


title: WT_sham_26_R_NS


title: HCC021_non-tumor tissue_SNP


title: 14-1E 3minRep3

city: Leuven

first: Bob

last: Blasdel

state: Vlaams-Brabant

address: Kasteelpark Arenberg 21, bus 2462

institute: KU Leuven

description: Non-ribosomal RNA

data_processing:
After trimming, sequencing reads were aligned separately to both the phage and host genomes with the CLC Genomics workbench v7.5.1 (QIAGEN Bioinformatics, Aarhus, Denmark)
Alignments were then summarized into count tables of Total Gene Reads that map to phage or host gene features respectively. Each statistical comparison presented was performed using the DESeq2 R/Bioconductor package to normalize host transcript populations to host transcript populations, before testing for differential expression as described by Blasdel et al. (2017).
The core analysis compares directional host total gene read counts for four phage negative controls sampled at a point immediately before infection to samples representing the synchronized late infections of LUZ19, YuA, PEV2 and 14-1. The DESeq2 test for the statistical significance of differential expression between the negative controls and phage-infected samples here is used to specifically highlight gene features that are differentially expressed in common between the different phage infections. As the four phages used have radically different metabolisms, genome contents, and methods for coopting host mechanisms, they are unlikely to all mediate differential expression of any given host gene in the same way. Thus, any differential expression of host genes that is common to all of the independent infections is likely to be mediated by the one biological entity all of the infections have in common, the host.
Given that there are two biological entities within the infected cell whose transcripts are sequenced together, and which change in total abundance relative to each other, meaningfully assessing differential expression for host genes becomes non-intuitively complex. Indeed, we observe a global depletion of all host transcripts relative to the total (phage and host) transcript population present in the cell due to the influx of phage transcripts. Therefore, two approaches could theoretically be used to measure the change in the abundance of a host transcript during a phage infection. We could measure changes (1) relative to either only other host transcripts or (2) relative to the total transcript population in the cell, including new phage transcripts. We have here adopted the first, asking which host transcripts are up or down regulated relative to other host transcripts by normalizing host transcripts before infection to host transcripts after infection. This has the effect of artificially enriching host reads in the phage infected condition by normalizing away the influx of phage transcripts, so as to compare it to the uninfected condition as if those phage transcripts were not present. The answer to this question focuses on how the host transcripts are being being targeted for either increased transcription or decreased degradation by at least one of the two biological entities in the cell, by ignoring the replacement of host transcripts with phage transcripts. Analyzing the change in a transcript's abundance relative to the total transcript population could not be addressed analysis of multiple phage infections, since depletion of host transcripts relative to the total happens at different rates during different phage infections. This effectively prevents us from elucidating a transcript's differential ability to compete for ribosome activity through changes relative abundance. For example, as was reported for prophage transcripts by Blasdel et al. (2017) during phage infection, a transcript could be targeted for increased transcription even while the stronger degradation of all non-phage transcripts reduces its abundance relative to the total transcript population in the cell.
Genome_build: Pseudomonas aeruginosa PAO1 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000006765.1)
Supplementary_files_format_and_content: Total gene read counts, Results of differential expression analysis

organism: Pseudomonas aeruginosa

source_name: Cell Lysate

growth_protocol: The Pseudomonas aeruginosa strain PAO1 was used as a host for phages LUZ19, YuA, PEV2, 14-1, and PhiKZ. Cultures were grown to an OD600 0.3 (1.2 x 10^8 / mL) in Lysogeny broth (10 g/L Tryptone, 5 g/L Yeast extract, 5 g/L NaCl) and infected at a multiplicity of infection of 50 to ensure synchronous infection. P. aeruginosa strain PAK was used as a host for phages PAK_P3 and PAK_P4.

extract_protocol:
At time points after the addition of phage chosen to reflect each phase of infection, cells were immediately halted with stop solution (1%, 9% ethanol, 90% sample Blasdel (2018), pelleted, and re-suspended in TRIzol to lyse cells as well as inactivate RNAses and start an organic extraction. The resulting nucleic acid was digested with TURBO DNAse to remove DNA, rRNA was removed with the Ribo-Zero kit.
Stranded cDNA was prepared with the TruSeq Stranded mRNA Library Prep Kit ahead of sequencing according to manufacturers instructions

treatment_protocol: RNA-Sequencing was performed on four phage-negative controls taken immediately before infection. Samples were also taken from synchronized infections by phages LUZ19, YuA, PEV2, and 14-1 to represent early, middle and late transcription as described by Blasdel et al. (2017, 2018). Briefly, synchronicity was controlled for by ensuring that fewer than 5% of host cells still survived before the early time point was taken.

tag: phage

value: Infected by 14-1

tag: time point

tag: phase of infection

value: Early


title: 14-1E 3minRep2

description: Non-ribosomal RNA


title: HepG2 cells with MYH10 shRNAs, biological replicate 1 [shMYH10-1]

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

source_name: HepG2_MYH10 shRNAs

label_protocol: Biotinylated cRNA were performed by CapitalBio Corporation (Beijing, China) according to the manufacturer’s instructions (Affymetrix, USA).

growth_protocol: HepG2 cells were maintained in high-glucose Dulbecco’s modified Eagle’s medium (DMEM; HyClone, USA) supplemented with 10% fetal bovine serum (FBS; HyClone, USA), 100 U/ml penicillin, and 100 μg/ml streptomycin. The cells were incubated at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA was harvested from HepG2 cells with treatment using the RNeasy mini kit (QIAGEN, Germany) according to the manufacturer's instructions.

treatment_protocol: Constructs including MYH10 shRNAs or the control shRNAs were transfected into HepG2 cells separately using Lipofectamine 2000.

tag: cell line

value: immortalized hepatocellular carcinoma (HCC) cell line

tag: transfected with

value: MYH10 shRNAs


title: HCC018_non-tumor tissue_SNP


title: 14-1E 3minRep1

description: Non-ribosomal RNA


title: YuAL 25minRep3

description: Non-ribosomal RNA

value: Infected by YuA

value: Late


title: HepG2 stably expressing of human RRS1 gene, biological replicate 1 [HepG2 NR-1]

description: HepG2 NR-1

hyb_protocol: 750 ng of cRNA were hybridized to Human HT12 v4 Expression BeadChips (Illumina, San Diego, CA, USA)

scan_protocol: and scanned on the Illumina HiScan instrument according to the manufacturer’s specifications

data_processing: Raw data of all probes was extracted by Illumina GenomeStudio without additional background correction. Data was further processed within R / Bioconductor. Expression values were log2-transformed and normalized using RSN. Batch effects of expression BeadChips were corrected using ComBat.

source_name: HepG2 NR

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total 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.

value: empty vector as a control

value: liver cell line


title: HepG2 cells with CEP104 shRNAs, biological replicate 3 [shCEP104-3]

source_name: HepG2_CEP104 shRNAs

treatment_protocol: Constructs including CEP104 shRNAs or the control shRNAs were transfected into HepG2 cells separately using Lipofectamine 2000.

value: CEP104 shRNAs


title: HepG2 cells with MYH10 shRNAs, biological replicate 2 [shMYH10-2]


title: HepG2 cells with MYH10 shRNAs, biological replicate 3 [shMYH10-3]


title: HepG2 cells with control shRNA, biological replicate 3 [shCt-3]

source_name: HepG2_control shRNA

value: control shRNA


title: HepG2 cells with control shRNA, biological replicate 2 [shCt-2]


title: HCC017_non-tumor tissue_SNP

value: hepatocellular carcinoma (HCC) patient


title: HepG2 stably expressing of human RRS1 gene, biological replicate 3 [HepG2 NR-3]

description: HepG2 NR-3


title: HepG2, biological replicate 2 [HepG2 N-2]

description: HepG2 N-2

source_name: HepG2 N

value: stably expressing of human RRS1 gene


title: HCC019_non-tumor tissue_SNP

value: male


title: HepG2 cells with control shRNA, biological replicate 1 [shCt-1]


title: HepG2 cells with CEP104 shRNAs, biological replicate 2 [shCEP104-2]


title: HepG2 stably expressing of human RRS1 gene, biological replicate 2 [HepG2 NR-2]

description: HepG2 NR-2


title: HCC016_non-tumor tissue_SNP


title: YuAL 25minRep2

description: Non-ribosomal RNA


title: HepG2, biological replicate 3 [HepG2 N-3]

description: HepG2 N-3


title: HepG2, biological replicate 1 [HepG2 N-1]

description: HepG2 N-1


title: YuAM 15minRep2

description: Non-ribosomal RNA

value: Middle


title: HepG2 cells with CEP104 shRNAs, biological replicate 1 [shCEP104-1]


title: HCC015_non-tumor tissue_SNP


title: YuAE 5minRep3

description: Non-ribosomal RNA


title: HCC013_non-tumor tissue_SNP


title: HepG2 cells with control shRNA, biological replicate 3 [shCN-3]


title: HCC014_non-tumor tissue_SNP


title: HepG2 cells with control shRNA, biological replicate 1 [shCN-1]


title: LUZ19L 15minRep3

description: Non-ribosomal RNA

value: Infected by LUZ19


title: HepG2 cells with control shRNA, biological replicate 2 [shCN-2]


title: YuAE 5minRep2

description: Non-ribosomal RNA


title: HCC012_non-tumor tissue_SNP


title: sample collected from patient 8C at 3 months after transplantation [Accommodation_PRAGUE_C8]

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: For all samples a total of 750 ng of labeled cRNA was hybridized at 58°C for 16 hours to the Illumina HumanHT-12 v4.0 Expression BeadChips (Illumina) and subsequently washed.

scan_protocol: Fluorescence signals of the hybridized IlLumina Microarrays were detected using BeadStation 500 instrument (Illumina Inc). The raw data were extracted with the BeadStudio Data Analysis Software (Illumina).

data_processing: Bead level data were summarized by Illumina BeadStudio Software v3, imported into R and normalized using the quantile method in the Lumi package.  Please note that only probes with detectable signal intensity in at least five samples were included, resulting in 20,370 data rows. The probes with no signal were excluded from the non_normalized data matrix as well.

source_name: renal graft biopsy

label_protocol: RNA was amplified and biotinylated  for hybridization using Ambion® Illumina® TotalPrep™ RNA Amplification Kit according to manufacturer´s instructions. For all samples 200 ng of total RNA was used for amplification. Yields of labeled cRNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The small portion (2mm) of the  the renal graft biopsy was immediately placed in RNA later (Ambion Corporation, Austin, TX), snap frozen and stored at -80 °C until RNA extraction. RNA was isolated from renal biopsies using the RNeasy Micro Kit (Qiagen, Hilden, Germany).Quality and integrity of PAXgene RNA were determined using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified by measuring absorbance at 260 nm on the ND-1000 Spectrophotometer (NanoDrop Technologies).

treatment_protocol: Whole renal transcriptome was evaluated in 3-months protocol biopsies with isolated C4d staining in otherwise stable ABO incompatible (ABOi) and HLA incompatible DSA positive kidney grafts (HLAi) as well as in C4d negative HLA compatible grafts with normal histological findings (controls) with the aim to elucidate the mechanism of accommodation.

tag: patient id

tag: type of  transplantation (aboincompatible=0, hlaincompatible=1, abocompatible with stable graft function and no dsa=3)

tag: donor specific antibodies positivity 1= yes, 0= no

value: renal graft biopsy


title: HCC011_non-tumor tissue_SNP


title: LUZ19L 15minRep2

description: Non-ribosomal RNA


title: LUZ19L 15minRep1

description: Non-ribosomal RNA


title: sample collected from patient 7C at 3 months after transplantation [Accommodation_PRAGUE_C7]

tag: tissue