title: SMMC7721-shPFKFB3

city: Zhengzhou

first: Wen-Kai

last: Shi

state: Henan

address: Jianshedong Road No.1

department: Department of hepatopancreatobiliary surgery

institute: The first affiliated hospital of Zhengzhou university

description:
7721-KD
gene expression after transfected with lentiviral

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE 8x60K array(Agilent) 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

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: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

treatment_protocol: SMMC7721 cells were transfected with lentiviral, then cultured in DMEM medium supplemented with 10% fetal bovine serum. The cultures were incubated 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: genotype/variation

value: PFKFB3 KD


title: 33_Pol2_Input

status: Public on Feb 28 2018

type: SRA

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

country: USA

institute: Hospital for special surgery

library_source: genomic

data_processing:
Single-end sequencing was performed at the Weill Cornell Epigenomics Core using HiSeq2500.  Overall sequence quality was evaluated using FASTQC.
50 bp single-end reads were aligned to the  mouse genome (mm10) with bowtie2.
The quality of Chip-seq experiments was assessed using ChIPQC package. Cross-correlation analysis, Relative Strand Correlation (RSC) and Normalized Strand Cross-correlation coefficient (NSC) for all ChIP-seq datasets used in this study were calculated with CLC BIO genomics workbench
Peak calling was performed with CLC Bio Genomics Workbench (Pol 2) or MACS2 (--gsize 2150570000 --bw=300 --ratio 1.0 --slocal 1000 --llocal 10000 --keep-dup 1 --bdg --qvalue 0.05) with a matching input file to estimate background read distribution. For BRD4 CjipSeq peak calling inputread ditribution  from p65 chipseq was used as a background control.
Peak annotation relative to known genomics features was performed using ChIPpeakAnno package (R, Bioconductor)  with TxDb.Mmusculus.UCSC.mm10.knownGene annotation (2016-09-29 04:05:09 +000).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: C57BL/6 mice (NCI, Charles River Laboratories)  were maintained in the Hospital for Special Surgery Animal Facility in full compliance with institutional guidelines approved by the HSS Animal Care and Use Committee.

extract_protocol:
For GR (Santa Cruz Biotech, sc-1004X), BRD4 (Abcam, ab84776) and p65 (Santa Cruz Biotech, sc-372X) ChIP-seq, nuclei were sonicated with Covaris S220 sonicator according to manufacturer’s instructions (130 μl shearing buffer, 200 cycles/burst, 120 sec, DF 10). For Pol 2 (Santa Cruz Biotech, sc-9001X) and NELF-E (Proteintech, 10705-1-AP) ChIP-seq, cells were formaldehyde cross-linked and nuclei were sonicated as above to obtain fragments in 150-500 bp range. Input DNA was prepared from sonicated material saved prior to IP. Lysates were cleared by centrifugation at 14,000 rpm, 20 min, 4°C, and then incubated with respective antibodies using 40 μl of 50% protein A/G PLUS agarose beads (for GR, BRD4 and Pol 2) or 60 μl of Dynabeads (Invitrogen) (for p65) per reaction at 4°C overnight. GR, BRD4 and Pol 2 IP beads were washed 4x with RIPA buffer and once with TE buffer. p65 IPs were washed 6x with modified RIPA buffer containing 100 mM LiCl on a magnetic stand and once with TE buffer+50 mM NaCl. Each reaction was then incubated in TE+0.5% SDS+200 μg/ml proteinase K (Invitrogen, 25530049) for 2 h at 55°C, followed by 6 h at 65°C to reverse crosslinks. DNA was purified using phenol-chloroform extraction and ethanol precipitation or using Qiagen PCR purification kit. The efficiency of ChIP was assessed by qPCR. The integrity and quality of DNA was evaluated with Bionalyzer 2100 (Agilent Technologies)
The integrity and quality of DNA was evaluated with Bionalyzer 2100 (Agilent Technologies) before using 10 ng of material to prepare Illumina-compatible sequencing libraries using Illumina Truseq ChIP sample prep kit. Library preparation and sequencing was performed by Weill Cornell Epigenomics Core. Libraries were sequenced by a HiSeq 2500 (50 bp, single-end).

treatment_protocol: BMMF were isolated from 8-12 week old male mice and  cultured in DMEM-20% FBS supplemented with the L1-cell conditioned media  for the 6-day MF expansion; cells were then scraped, incubated in DMEM-20% FBS overnight and were treated with 100 nM Dex, 10 ng/ml LPS or LPS+Dex for  45 minutes

tag: strain

tag: age

value: 8-12 weeks

tag: Sex

value: male

tag: cell type

value: bone-marrow derived macrophages (BMMF)

tag: chip antibody

value: none (input)


title: 31_GR_Input


title: 28_Pol2_LD_Rep2

tag: treated with

value: LPS+Dex for  45 minutes

value: Pol 2 (Santa Cruz Biotech, sc-9001X)


title: 29_Pol2_U_Rep1

value: none (untreated)


title: Patient 1 1T_1N

status: Public on Mar 01 2018

type: RNA

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

description:
in the raw data file, rProcessedSignal represented Normal
in the raw data file, gProcessedSignal represented Tumor

hyb_protocol: 27.5 μL of labeled samples were dissolved in 82.5 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a the CapitalBio circRNA Human Gene Expression Microarray V1.0 (4x90K, CapitalBio, Beijing). Arrays hybridization were performed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2565CA (Agilent, Santa Clara, CA). Acquired array images were analyzed by Agilent Feature Extraction (v10.7) software.

data_processing: Microarray data was extracted using Agilent Feature Extraction software. Data summarization, quantile normalization, quality control and most of the subsequent data processing were executed using GeneSpring software V12.0 (Agilent, Santa Clara, CA) or R software package.

molecule: total RNA

organism: Homo sapiens

source_name: adjacent normal

label_protocol: 5ug isolated total RNA was treated with Rnase R (Epicentre, Madison, WI) to remove linear RNA. cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction41, and the procedure has been improved by using CapitalBio circRNA Amplification and Labeling Kit (CapitalBio, Beijing) for producing higher yields of labeled cDNA. In detail, double-stranded cDNAs (containing the T7 RNA polymerase promoter sequence) were synthesized from 0.2 μg total RNA using the CbcScript reverse transcriptase with cDNA synthesis system according to the manufacturer’s protocol (Capitalbio, Beijing) with the T7 Oligo (dN). After completion of double-stranded cDNA (dsDNA) synthesis using DNA polymerase and RNase H, the dsDNA products about 12.5μL were subjected to 40μL in vitro transcription reactions at 37℃ for 14 h using a T7 Enzyme Mix. The amplified cRNA was purified using the RNA Clean-up Kit (MACHEREY - NAGEL, Germany). Klenow enzyme labeling strategy was adopted after reverse transcription using reverse transcriptase. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MACHEREY - NAGEL, Germany) and re-suspended in elution buffer.

extract_protocol: UHRR was bought from Agilent,HBRR was bought from Ambion.tumor samples and normal tissues were collected from the Oncology Department of the Second Affiliated Hospital of Zhen Zhou University by related surgeons. Plasma samples were isolated by EDTA and centrifuged at 820 ×g for 10 min. The postoperative samples were collected 2 to 34 days after surgery.

tag: tissue

value: adjacent normal

value: cervical tumor


title: 25_Pol2_L_Rep1

value: 10 ng/ml LPS for  45 minutes


title: 27_Pol2_LD_Rep1


title: 32_p65_Input


title: 26_Pol2_L_Rep2


title: 30_Pol2_U_Rep2


title: 23_p65_U_rep1

value: p65 (Santa Cruz Biotech, sc-372X)


title: 24_p65_U_rep2


title: 22_p65_LD_rep2


title: 21_p65_LD_rep1


title: 19_p65_L_rep1

value: NELF-E (Proteintech, 10705-1-AP)


title: 18_Nelf3_LD_1h

value: LPS+Dex for  1hr


title: 20_p65_L_rep2


title: 16_Nelf1_LPS1h

value: 10 ng/ml LPS for 1h


title: 12_GR_LD_rep2

value: GR (Santa Cruz Biotech, sc-1004X)


title: 15_Nelf1_LPS0h

value: 10 ng/ml LPS for 0h


title: 13_GR_U_rep1


title: 14_GR_U_rep2


title: 10_GR_L_rep2


title: 11_GR_LD_rep1


title: 08_GR_D_rep2

value: 100 nM Dex for  45 minutes


title: 07_GR_D_rep1

value: 8-12 weeks


title: 09_GR_L_rep1

value: male


title: 04_BRD4_LD_rep2

value: bone-marrow derived macrophages (BMMF)

value: BRD4 (Abcam, ab84776)


title: 05_BRD4_U_rep1


title: 06_BRD4_U_rep2


title: 03_BRD4_LD_rep1

value: LPS+Dex for  45 minutes


title: 01_BRD4_L_rep1


title: 17_Nelf1_LPS3h

value: 10 ng/ml LPS for 3h


title: COLO205.xenograft.hFc.72hr.mm10

city: Tarrytown

first: Qi

last: Zhao

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals Inc

library_source: transcriptomic

data_processing:
The Cell Ranger Suite version 1.1.0 was used to perform sample de-multiplexing, barcode processing and single cell gene UMI (unique molecular index)
Genome_build: mm10 for mouse cells and B37 for human cells
Supplementary_files_format_and_content: tab-delimited text files include UMI values for samples/cells

organism:
Homo sapiens
Mus musculus

source_name: tumor

growth_protocol: 2x10^6 COLO205 human colon carcinoma cells were grown s.c. in male CB.17/SCID mice (Taconic).

extract_protocol:
Tissues were minced, enzymatically digested for 10 minutes using 2.5 mg/ml collagenase Type II, 2.5 mg/ml collagenase Type IV (Gibco), and 0.5 mg/ml DNase (Sigma) in PBS / 1% BSA at 37°C, treated with DMEM containing 10% FBS and filtered (70-µm nylon filter; Falcon). Single cell suspensions were subjected to 1X PharMLyse for 4 (tumor) or 10 (heart) minutes, washed and subjected to dead cell removal kit (130-090-101, Miltenyi). The remaining cells were used for single cell sequencing.
Tumor single cell suspensions underwent a depletion step using the following FITC conjugated Abs: COLO205 cells were incubated with anti-CD24 (11-0247-42, eBioscience) and anti-E-Cadherin (324104, Biolegend) using 10 µl anti-FITC-beads for 1x10^6 total cells. The remaining cells were used for single cell sequencing.
Cellular suspensions (~6000 cells) were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single cell GEMs. Single-cell RNAseq libraries were prepared using version 1 Chromium Single cell 3’ Library, Gel beads & Mutiplex kit (10X Genomics).

treatment_protocol: When tumors reached 100-150 mm3, mice remained untreated or were treated by s.c. injection with hFc (control protein, 25 mg/kg), aflibercept (VEGF Trap, ziv-aflibercept, 25 mg/kg), a DLL4 blocker (REGN 1035, 10 mg/kg) or a combination (combo) of aflibercept plus anti-Dll4 antibody. 24hr and 72hr post treatment heart and tumor tissues were harvested.

tag: treatment

value: COLO205 tumor

value: CB.17/SCID (Taconic)

value: tumor

value: adult

tag: genotype

value: WT

tag: gender


title: COLO205.xenograft.aflibercept.72hr.mm10


title: COLO205.xenograft.combo.mm10


title: heart.aflibercept.72hr.mm10

source_name: heart

value: normal heart

value: heart


title: COLO205.xenograft.aflibercept.24hr.mm10


title: heart.combo.72hr.mm10


title: COLO205.xenograft.combo.24hr.mm10


title: COLO205.xenograft.anti-Dll4-Ab.mm10


title: COLO205.xenograft.anti-Dll4-Ab.24hr.mm10


title: heart.anti-Dll4-Ab.72hr.mm10


title: heart.hFc.72hr.mm10


title: SMMC7721-shVector

country: China

description:
7721-NC
gene expression after transfected with lentiviral

value: control


title: heart.combo.24hr


title: heart.anti-Dll4-Ab.24hr


title: heart.aflibercept.24hr


title: heart.hFc.24hr


title: 02_BRD4_L_rep2

value: 10 ng/ml LPS for  45 minutes


title: COLO205.xenograft.hFc.24hr.mm10


title: HL-1_siAirn-001.2.2

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

description: siAirn-001.2-transfected, biological rep2

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained in the Affymetrix Fluidics Station 400 according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol.

data_processing: The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de). After the normalization by Robust Multi-array Average (RMA) and the application of moderate t-statitsics via the limma package, Transcript Cluster IDs that do not match to a gene or that match to multiple genes were discarded. Then, a standard deviation is calculated across samples. For a gene that matches to multiple Transcript Cluster IDs, the Transcript Cluster ID with the highest standard deviation was kept for further analysis.

label: biotin

source_name: HL-1 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HL-1 cells are gift from Prof. Dr. William C. Claycomb (Louisiana State University Health Sciences Center). The cells were cultured according to the protocol by Dr. Claycomb using Claycomb Medium (Sigma-Aldrich, #51800C) supplemented with 10% fetal bovine serum (Sigma-Aldrich, #F2442; batch approved by Dr. Claycomb), 2mM L-glutamine (Sigma-Aldrich, #G7513), 0.1mM Norepienphrine (Sigma-Aldrich, #A0937), and antibiotics.

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

treatment_protocol: Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol.


title: HL-1_siAirn-001.2.3

description: siAirn-001.2-transfected, biological rep3


title: HL-1_siScr.5

description: siScramble-transfected, biological rep5


title: HL-1_siScr.2

description: siScramble-transfected, biological rep2


title: HL-1_siAirn-001.2.1

description: siAirn-001.2-transfected, biological rep1


title: HL-1_siScr.3

description: siScramble-transfected, biological rep3


title: HL-1_siAirn-001.1.4

description: siAirn-001.1-transfected, biological rep4


title: HL-1_siScr.4

description: siScramble-transfected, biological rep4


title: HL-1_siAirn-001.2.4

description: siAirn-001.2-transfected, biological rep4


title: HL-1_siScr.1

description: siScramble-transfected, biological rep1


title: HL-1_siAirn-001.1.2

description: siAirn-001.1-transfected, biological rep2


title: HL-1_siAirn-001.1.1

description: siAirn-001.1-transfected, biological rep1


title: HL-1_siScr.6

description: siScramble-transfected, biological rep6


title: HL-1_siAirn_IgG.2

description: siAirn-001.1-transfected, anti-IgG RIP, biological rep2

data_processing: The data were analyzed using noncoder web interface (http://noncoder.mpi-bn.mpg.de).

treatment_protocol: Transient siRNA transfection (10nM final concentration) was carried out using RNAiMax (Life Technologies) according to the manufacturer’s protocol. RIP assay was performed using Magna RIP Kit (Millipore) following manufacturer's protocol.


title: HL-1_siScr_IgG.1

description: siScramble-transfected, anti-IgG RIP, biological rep1


title: HL-1_siAirn_Igf2bp2.2

description: siAirn-001.1-transfected, anti-Igf2bp2 RIP, biological rep2


title: HL-1_siAirn_Igf2bp2.1

description: siAirn-001.1-transfected, anti-Igf2bp2 RIP, biological rep1


title: HL-1_siScr_Igf2bp2.2

description: siScramble-transfected, anti-Igf2bp2 RIP, biological rep2


title: HL-1_siScr_Igf2bp2.1

description: siScramble-transfected, anti-Igf2bp2 RIP, biological rep1


title: hyl1

status: Public on Feb 27 2018

city: Shanghai

first: Zhenfei

last: Sun

address: Dongchuan Road 500

institute: Shanghai Jiaotong University

data_processing:
base-calling performed using HCS,RTA and OLB 1.9.4
Data were filtered by the following steps:   1) Getting rid of low quality reads (The criteria for this is listed in the explanation of meaning of each row in the result table)   2) Getting rid of reads with 5' primer contaminants   3) Getting rid of reads without 3' primer   4) Getting rid of reads without the insert tag   5) Getting rid of reads with poly A   6) Getting rid of reads shorter than 18nt
Map the small RNA tags to genome by SOAP2.20 to analyze their expression and distribution on the genome.   Program and Parameters:   soap -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
Alignments to mirbase, Genbank, Rfam performed by blastn:  blastall -p blastn -F F -e 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: counts

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: plants were grown in soil at 16 hr light/8 hr dark photoperiod

extract_protocol:
Small RNAs were isolated using mirVana™miRNA Isolation Kit (Ambion, AM1561)
Small RNA libraries were prepared and sequenced by Illumina high-throughput sequencing
The small RNA reads were trimmed for adaptor sequence using Perl scripts and mapped to miRNA hairpin sequences downloaded from mirRBase version 15.0 using the Bowtie program

treatment_protocol: no treatment


title: WT


title: HL-1_siAirn_IgG.1

description: siAirn-001.1-transfected, anti-IgG RIP, biological rep1


title: pif4


title: HL-1_siAirn-001.1.3

description: siAirn-001.1-transfected, biological rep3


title: INOF_FRT

status: Public on Feb 13 2018

city: Sherbrooke

first: Michelle

middle: S

last: Scott

state: Quebec

address: 3201 Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

description: Total RNA ribodepleted, fragmented (200nt)

data_processing:
Reads were treated with Cutadapt (using parameters -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG --minimum-length 2) and Trimmomatic (with TRAILING:30)
The resulting reads were aligned to the build hg38 using STAR (--outSAMprimaryFlag AllBestScore, --alignIntronMax 1250000), unmapped reads being re-aligned with Bowtie2 (-q -I 13).
CoCo (http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco) was used to produce read counts per genes and associated CPM and TPM values from the Ensembl (v87) annotation modified with CoCo.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated-value (csv) file holding the name of every gene and their abundance value (raw counts, CPM or TPM) for each dataset

source_name: INOF cell line

growth_protocol: grown in OSE medium, supplemented with 10 % Hyclone fetal bovine serum and L-glutamine. Cell propagation and passaging occured once per week or as needed. Cells were trypsinized and collected in 5X10^6 pellets resuspended in 700ul TRIzol (Ambion) and kept at -80°C until RNA extraction

extract_protocol:
cDNA library produced with TGIRT
RNA was isolated and DNase treated using RNEasy mini kit (Qiagen 74106) according to the manufacturer protocol. 5ug DNA-free total RNA was then ribodepleted using Ribo-zero Gold (Illumina RZG1224 ) according to the manufacturer protocol and purified using a modified ZYMO RNA Clean and Concentrator (R1016) protocol where 8 volumes EtOH instead of 4. rRNA depleted RNA was fragmented with NEBNext Magnesium RNA Fragmentation Module (E6150) followed by dephosphorylation using T4PNK (mandel  ) and purified by same modified ZYMO protocol.
cDNAs were synthesized via TGIRT template-switching with 1µM TGIRT-III reverse transcriptase (Ingex, LLC) for 15 min at 60o C, during which a DNA oligonucleotide containing the complement of an Illumina Read 2 sequencing primer-binding site becomes seamlessly linked to the 5’ cDNA end. After reaction cleanup (Qiagen MinElute Reaction cleanup 28206), a 5’ adenylated DNA oligonucleotide containing the complement of an Illumina Read 1 sequencing primer-binding site is then ligated to the 3’ cDNA end with Thermostable 5’ AppDNA / RNA Ligase (New England Biolabs M0319). Properly ligated cDNAs were amplified by PCR (12 cycles) to synthesize the second strand and add Illumina flowcell capture and index sequences. Library was size-selected with Ampure XP beads (Beckman-Coulter) and quantified with Qubit and evaluated on an Agilent 2100 Bioanalyzer.

value: Immortalized normal ovarian fibroblast


title: Wildtype 2

status: Public on Feb 11 2018

city: Montreal

first: Przemyslaw

last: Sapieha

address: 5345 Assumption Blvd

institute: Maisonneuve-Rosemont Research Center

data_processing:
Analysis was performed using the Torrent Suite software v4.4 (Thermo Fisher) and the whole Transcriptome Analysis Plugin v 4.2-r7 (Thermo Fisher)
The whole Transcriptome Analysis Plugin aligns reads on mouse reference genome (mm10) using Tophat2 then unmapped reads are aligned using Bowtie2 and merged together.
FPKM are calculated using Cufflinks.
Genome_build:  mm10
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: Peritoneal macrophage

growth_protocol: F12 DMEM growth medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from macrophages using the RNeasy Mini Kit (QIAGEN). The mRNA was then purified from 1μg of total RNA using the Dynabeads® mRNA DIRECT™ Micro Kit (Thermo Fisher). Whole transcriptome libraries were prepared using the Ion Total RNA-seq Kit v2. The yield and size distribution of the amplified libraries were assessed with an Agilent Bioanalyzer using a DNA 1000 Kit. Sequencing was performed on an Ion Chef™ Instrument (Ion Torrent™, Thermo Fisher).
Analysis was performed using the Torrent Suite software v4.4 (Thermo Fisher) and the whole Transcriptome Analysis Plugin v 4.2-r7 (Thermo Fisher). The whole Transcriptome Analysis Plugin aligns reads on mouse reference genome (mm10) using Tophat2 then unmapped reads are aligned using Bowtie2 and merged together. FPKM are calculate using Cufflinks.

value: Wildtype

value: Peritoneal macrophage


title: Wildtype 1


title: HL-1_siScr_IgG.2

description: siScramble-transfected, anti-IgG RIP, biological rep2


title: NRP1_KO 1


title: P8 Wild type GCP-hemisphere_rep 1

status: Public on Feb 22 2018

city: New York

first: Alexandra

last: Joyner

state: NY

department: Developmental Biology

institute: Sloan Kettering Institute

description: Gene expression data from P8 wild type GCPs isloated from the lateral cerebellum

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing:
Feature intensity was extracted by Affymetrix GeneChip Command Console as CEL files.
Microarray expression analysis was performed using Partek Genomic Suite. Probe intensities were imported and the Robust Multi-Array Average (RMA) procedure was used for background correction. Quantile normalization and Median Polish probeset summarization were subsequently conducted.

source_name: postnatal day 8 wild type mouse cerebella

label_protocol: 500 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.

tag: developmental stage

value: postnatal day 8

value: cerebella

tag: background strain

value: mixed background containing C57BL/6 and Swiss Webster

tag: cerebellar region

value: hemisphere

value: wildtype


title: P8 Wild type GCP-hemisphere_rep 3


title: P8 Wild type GCP-vermis_rep 1

description: Gene expression data from P8 wild type GCPs isloated from the medial cerebellum

value: vermis


title: KO3

status: Public on Jan 31 2018

city: Columbia

first: Jing

last: Fang

state: SC

address: 715 Sumter Street

department: Drug Discovery and Biomedical Sciences

institute: University of South Carolina

data_processing:
Sequence reads were aligned to the reference genome using the TopHat aligner.
Reads aligning to each known transcript were counted using Bioconductor packages for next-generation sequencing data analysis.
The differential expression analysis between different sample types was performed using the negative binomial statistical model of read counts as implemented in the edgeR Bioconductor package.
The cluster analysis of all genes differentially expressed in individual comparisons was performed using the Bayesian infinite mixture models.
The pathway enrichment analysis was performed using the LRpath methodology as implemented in the CLEAN package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include NCBI Gene IDs and RPKM values.

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
Total RNA was extracted and purified with Quick-RNA MiniPrep Kit (Zymogen). RNA quality was determined using the Agilent Bioanalyzer 2100 (Hewelett Packard).
100 ng total RNA was used for enrichment of poly A RNA with the Apollo 324 (WaferGen, Fremont, CA). Poly A RNA was further fragmented (RNase III), adaptor-ligated, and reverse transcribed (Superscript III reverse transcriptase, Lifetech, Grand Island, NY), followed by purification using Agencourt AMPure XP beads (Beckman Coulter, Indianapolis IN). To prepare libraries, universal and index-specific primers, and sample-specific index were added to each adaptor-ligated cDNA sample to amplify the library, followed by purification using AMPure XP beads. The quality and yield of the libraries were assessed on the Bioanalyzer (Agilent, Santa Clara, CA). Libraries at the final concentration of 15 pM were clustered onto a PE flow cell using Illumina's TruSeq PE Cluster kit v3, and sequenced using TruSeq SBS kit on the Illumina HiSeq system.

value: Lineage-Sca1+Kit+ (LSK) cells

value: C57BL/6, after transplantation

value: Traf6 knockout


title: NRP1_KO 2


title: P8 SmoM2 GCP-vermis_rep 2

description: Gene expression data from P8 SmoM2-mutant GCPs isloated from the medial cerebellum

source_name: postnatal day 8 mutant mouse cerebella


title: P8 Wild type GCP-hemisphere_rep 2


title: P8 Wild type GCP-vermis_rep 2


title: P8 Wild type GCP-vermis_rep 3


title: P8 SmoM2 GCP-hemisphere_rep 2

description: Gene expression data from P8 SmoM2-mutant GCPs isloated from the lateral cerebellum


title: KO4


title: P8 SmoM2 GCP-vermis_rep 1


title: P8 SmoM2 GCP-hemisphere_rep 3


title: P8 SmoM2 GCP-hemisphere_rep 1


title: Esophageal mucosae with intermediate risk (pool2)

type: genomic

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description: SAMPLE 3

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
Genome Studio software was used.  Beta values were obtained after background correction and normalization to internal controls.
the non_normalized.txt contains unmethylated and methylated signal intensities.

label: Cy5 and Cy3

source_name: Esophageal mucosae_intermediate risk

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA samples were isolated using Phenol-chloroform extraction protocol.  The same amount of genomic DNA samples from 4 (or 8) individuals were pooled.

tag: subject status

value: Non-cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking

tag: gender in each pool

tag: age (yrs)

value: biopsy, esophageal mucosa


title: KO1


title: WT2

value: wild type


title: P8 SmoM2 GCP-vermis_rep 3


title: WT1


title: Esophageal mucosae with intermediate risk (pool3)

description: SAMPLE 4


title: 11_at1Rsm22

status: Public on Jan 30 2018

first: Josephine

last: Galatioto

address: 1468 Madison Avenue

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: processed data file: At1aR_data.csv

data_processing:
Sequencing reads were aligned to the mouse reference genome 'mm9' using Tophat 2.0.8, samtools-0.1.7 and bowtie 2.1.0.
DEGs were identified with cufflinks 1.3.0. Tophat was used with the Ensembl GTF file as a gene annotation reference and the option ’no-novel-juncs’.
Output BAM files were directly subjected to differential gene expression identification using Cufflinks with the options ’multi-read-correct’, ’upper-quartile-norm’ and ’frag-bias-correct’ against the mm9 genome.
DEGs in wildtype (at1Rfl) versus knockout at1Rcdh5 and at1Rsm22 aortas were identified based on a false discovery rate (FDR) of 10% and a minimum fold change (log2((FPKMcondition1+1)/(FPKMcondition2 + 1)) ≥ ± log2(1.3)).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: At1aR data.csv: Cufflinks output text file.

source_name: Aorta

extract_protocol:
RNA was purified from frozen aortic tissues using the RNeasy Fibrous Tissue Kit (Qiagen). RNA amounts were quantitated by Qubit fluorometer (Life Technologies) and RNA quality was assessed using an Agilent 2100 Bioanalyzer. Total RNA preparations with ribosomal integrity numbers >8 were used for RNA-Seq experiments.
Libraries were prepared from 1μg of total RNA using TruSeq Stranded mRNA kit protocol (Illumina®) according to the supplier’s recommendation. Briefly, poly-A RNA was isolated using oligo-dTs attached to magnetic beads, fragmented into ~300 bp-long pieces using divalent cations under elevated temperature, used as template for double-stranded cDNA synthesis, Illumina adapters ligation and PCR-mediated cDNA library amplification. Sequencing of random paired-end 75 bp molecules was carried out on Illumina HiSeq4000.

tag: strain/background

tag: genotype/variation

value: AT1ar floxed; SM22 cre

tag: cre transgene

value: 90 days

value: male

value: Aorta


title: 12_at1Rsm22

description: processed data file: At1aR_data.csv

tag: age


title: WT4

tag: cell type

tag: strain


title: Esophageal mucosae with high risk (pool1)

description: SAMPLE 6

source_name: Esophageal mucosae_high risk

value: Cancer patients, with alcohol drinking, betel nuts chewing and cigarette smoking

value: Male6, Female2


title: 10_at1Rsm22

description: processed data file: At1aR_data.csv


title: WT3


title: KO2


title: Esophageal mucosae with high risk (pool4)

description: SAMPLE 9


title: Esophageal mucosae with high risk (pool3)

description: SAMPLE 8


title: 8_at1Rcdh5

description: processed data file: At1aR_data.csv

value: AT1ar floxed; CDH5 cre


title: 7_at1Rcdh5

description: processed data file: At1aR_data.csv


title: 3_at1Rfl

description: processed data file: At1aR_data.csv

value: AT1ar floxed


title: 2_at1Rfl

description: processed data file: At1aR_data.csv


title: 1_at1Rfl

description: processed data file: At1aR_data.csv


title: Esophageal mucosae with intermediate risk (pool1)

description: SAMPLE 2


title: Esophageal mucosae with intermediate risk (pool4)

description: SAMPLE 5


title: Esophageal mucosae with high risk (pool5)

description: SAMPLE 10


title: Esophageal mucosae with low risk (pool)

description: SAMPLE 1

source_name: Esophageal mucosae_low risk

value: Non-cancer patients, no alcohol drinking, no betel nuts chewing, no cigarette smoking

value: Male1, Female3


title: Esophageal mucosae with high risk (pool2)

description: SAMPLE 7


title: 9_at1Rcdh5

description: processed data file: At1aR_data.csv


title: Fetal Fibroblasts

status: Public on Dec 31 2017

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

state: MD

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description: Individual sample

hyb_protocol: All arrays were hybridized at 55ºC for 20 hours followed by wash procedure according to the miRNA Microarray System Protocol, Version 1.5, December 2007 (Agilent Technologies).

scan_protocol: Fluorescent signals were obtained by scanning with an Agilent scanner controlled by Agilent Scan Control 7.0 software.

data_processing: Data were acquired with Agilent Feature Extraction 9.5.3.1 software for miRNA microarray. MicroRNA Expression data were extracted from Agilent miRNA Kits by Agilent Feature Extraction software and then Partek and Spotfire were employed for their normalization and analysis. The fluorescent signal data were imported into Partek where duplicate probe information was merged and were then normalized to the 75th percentile. The 75th percentile normalization process is similar to median normalization, above, except that each gene’s 75th percentile value is subtracted rather than its median. (Agilent recommends the 75th percentile based on the observation that about half the microRNAs are not expressed, so the 75th percentile is near the median for those that are).

source_name: Fetal Fibroblasts

label_protocol: 150 ng total RNA from each sample was labeled using the miRNA Labeling Reagent & Hybridization Kit (Agilent Technologies, Santa Clara, CA) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the miRNeasy Mini Kit (Qiagen) with on-column DNase I digestion.

value: Fetal Fibroblasts

tag: cell line


title: Rpl22_Hippocampus_WT_BiologicalReplicate2_TechnicalReplicate1

status: Public on Jan 05 2018

first: Ruteja

middle: A

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

description:
mRNA
WT mouse #133544 sample #21736

hyb_protocol: Then, the labeled cDNAs were hybridized to Agilent Technologies mouse SurePrint G3 Mouse Gene Expression 8x60k microarrays according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent Technologies SureScan microarray scanner to detect fluorescence.

data_processing: Gridding and analysis of images were performed using Agilent Technologies Feature Extraction software version 11.5. Normalization was performed using IRON-Iterative rank-order normalization of gene expression microarray data (Welsh et al. 2013 (PMID 23647742)).

source_name: Ribotag hipppocampus, WT

label_protocol: RNA was amplified and reverse transcribed to cDNA with the WTA2 Complete Whole Transcriptome Amplification Kit from Sigma, then fluorescently labeled with the Kreatech ULS kit from Kreatech Diagnositcs. Labeled cDNAs were purified on QIAquick PCR purification columns and quantified with a NanoDrop spectrophotometer.

growth_protocol: Adult (at least 3 months of age) mice of both sexes, of either genotype Ctcf loxP/loxP; Camk2a-Cre; Rpl22-tsam1.1Psam/J or Ctcf wild type; Camk2a-Cre; Rpl22-tsam1.1Psam/J.

extract_protocol: Hippocampus was dissected rapidly from naive adult mice (3 males and 1 females, each at least 3 months old) and homogenized in polysome buffer consisting of 50 mM Tris, pH 7.5, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/ml Rnasin Plus (Promega), 200 U/ml Superasin (Life Technologies), 100 microg/ml cyclohexamide, 1 mg/ml heparin, and 1x complete protease inhibitor tablet mixture (Sigma-Aldrich). Samples were centrifuged at 10,000 g for 10 min at 4°C. The supernatants were collected and immunoprecipitated with anti-HA antibody (HA.11, BioLegend catalog #901502, RRID: AB_2565007) overnight at 4°C, and the next day, antibody-antigen-RNA complexes were recovered with Dynabeads protein G. The beads were washed 3 times for 5 min each in high-salt buffer consisting of 50 mM Tris, pH 7.5, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, and 100 microg/ml cyclohexamide. Then, the antigen–antibody–RNA complexes were eluted with RA1 buffer (Machery-Nagel) containing 1:100 beta-mercaptoethanol. RNA was recovered from the eluate using NucleoSpin RNA columns (Machery-Nagel) with on-column DNase digestion. RNA concentration was determined using a NanoDrop (Thermo Scientific) and RNA integrity was verified using an Agilent Technologies bioanalyzer and either RNA 6000 nano or pico chips, depending on the concentration of the sample.

treatment_protocol: Mice were naïve and untreated prior to tissue collection.

value: Ctcf wild type; Camk2a-Cre positive; Ribotag positive

value: adult (at least 3 months)

tag: tissue

value: Hippocampus

tag: antibody

value: anti-HA


title: Rpl22_Hippocampus_WT_BiologicalReplicate1_TechnicalReplicate1

description:
mRNA
WT mouse #133545 sample #21738


title: Rpl22_Hippocampus_CKO_BiologicalReplicate4_TechnicalReplicate1

description:
mRNA
CKO mouse #134191 sample #21720

source_name: Ribotag hipppocampus, Ctcf CKO

value: Ctcf loxP/loxP; Camk2a-Cre positive; Ribotag positive


title: Rpl22_Hippocampus_CKO_BiologicalReplicate3_TechnicalReplicate1

description:
mRNA
CKO mouse #134906 sample #21724


title: Hippocampus_CKO_BiologicalReplicate1_TechnicalReplicate2

description:
Sample 12027
Sex distribution: 2 females; 1 male; 19-23 weeks

hyb_protocol: Then, the labeled cDNAs were hybridized to Agilent Technologies mouse GE 4x44k v2 microarrays according to the manufacturer’s instructions.

source_name: Hippocampus, Ctcf CKO

label_protocol: RNA was amplified and reverse transcribed to cDNA with the MessageAmpII kit from LifeTechnologies, then fluorescently labeled with the Kreatech ULS kit from Kreatech Diagnositcs. Labeled cDNAs were purified on QIAquick PCR purification columns and quantified with a NanoDrop spectrophotometer.

growth_protocol: Adult (3-6 months of age) mice of both sexes, of either genotype Ctcf loxP/loxP, or Ctcf loxP/loxP;Camk2a-Cre.

extract_protocol: Brain regions were harvested and snap frozen in liquid nitrogen. Tissues were homogenized in Trizol using a bullet blender. The Trizol procedure was performed and RNA was then purified on NucleoSpin RNA columns with on-column DNase digestion. RNA concentration was determined with a NanoDrop and RNA integrity was verified on an Agilent bioanalyzer.

treatment_protocol: Mice were exposed to behavioral testing in the open field, sensorimotor battery, Morris water maze, and social approach test.

value: Ctcf loxP/loxP; Camk2a-Cre positive

value: pooled male and female

value: 19-23 weeks


title: Hippocampus_CKO_BiologicalReplicate2_TechnicalReplicate1

description:
Sample 12028
Sex distribution: 3 females; 0 male; 18-19 weeks

value: female

value: 18-19 weeks


title: Rpl22_Hippocampus_WT_BiologicalReplicate3_TechnicalReplicate1

description:
mRNA
WT mouse #133547 sample #21742


title: Rpl22_Hippocampus_WT_BiologicalReplicate4_TechnicalReplicate1

description:
mRNA
WT mouse #134259 sample #21740

value: male


title: Hippocampus_WT_BiologicalReplicate3_TechnicalReplicate1

description:
Sample 12026
Sex distribution: 0 females; 3 males; 15-17 weeks

source_name: Hippocampus, WT

value: Ctcf loxP/loxP; Camk2a-Cre negative

value: 15-17 weeks


title: Rpl22_Hippocampus_CKO_BiologicalReplicate1_TechnicalReplicate1

description:
mRNA
CKO mouse #133448 sample #21722


title: Rpl22_Hippocampus_CKO_BiologicalReplicate2_TechnicalReplicate1

description:
mRNA
CKO mouse #134909 sample #21726


title: Hippocampus_CKO_BiologicalReplicate3_TechnicalReplicate1

description:
Sample 12029
Sex distribution: 0 females; 3 males; 15-17 weeks


title: Hippocampus_WT_BiologicalReplicate1_TechnicalReplicate1

description:
Sample 12024
Sex distribution: 2 females; 1 male; 19-23 weeks


title: Hippocampus_WT_BiologicalReplicate2_TechnicalReplicate1

description:
Sample 12025
Sex distribution: 3 females; 0 male; 18-19 weeks


title: Hippocampus_CKO_BiologicalReplicate1_TechnicalReplicate1


title: Hippocampus_WT_BiologicalReplicate1_TechnicalReplicate2


title: GEO-8

status: Public on Dec 16 2017

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

data_processing:
STAR v2.5.1b used for sequence alignment with hg19 genome build
STAR v2.5.1b used for second pass alignment with hg19 genome build along with pooled splice junciton information
Picard v1.136.0 used for merging properly paired and discordant paired reads
HTSeq Count v0.6.0 used for gene counts
All gene expression variables were scaled to a mean value of 0 and variance equal to 1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including gene counts
Supplementary_files_format_and_content: Raw data: German law does not allow raw data to be submitted for public access

molecule: polyA RNA

source_name: bone marrow or peripheral blood mononuclear cells

extract_protocol:
Mononuclear cells from peripheral blood (PB) or bone marrow (BM) were enriched by Ficoll gradient centrifugation.
RNAseq libraries were prepared using the Sense mRNA Seq Library Prep Kit V2 (Lexogen, n=238) and the TruSeq RNA Library Preparation V2 Kit (Illumina, n=12, GEO-1 to 12) following the manufractur´s instruction. Between 500-1000 ng total RNA (RNA integrity number [RIN] >7) were used as input material. All sequencing was paired end and performed using polyadenylated-selected and, in case of the Lexogen libraries, stranded RNA sequencing.

treatment_protocol: Pretreatment bone marrow mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML)

tag: diagnosis

value: Acute Myeloid Leukemia

tag: age (years)

tag: response

value: sensitive

tag: overall survival (days)

tag: life status

value: dead

tag: predicted ps29mrc group

value: predicted sensitive

value: No


title: GEO-11

value: bone marrow or peripheral blood mononuclear cells

tag: gender

value: predicted refractory


title: GEO-10


title: GEO-9


title: GEO-6


title: GEO-12


title: GEO-7


title: GEO-5

value: alive


title: VECs cultured alone rep2

status: Public on Dec 30 2017

city: Xi'an

first: Jinqing

state: Shaanxi Province

address: 569 Xinsi Road

department: Department of Plastic and Burn Surgery

institute: Tangdu Hospital, Fourth Military Medical University

description:
VEC6
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R.

The 37701-row Sample data tables are focused on the gene level, and the supplementary 48803-row normalized data matrix is focused on the probe level. The gene-level data are obtained from the probe-level data after processing with GenomeStudio software (V2011.1).

source_name: Human umbilical vein

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

growth_protocol: CFs were cultured in DMEM (high glucose, serum free) for 20-22 days and then were purified for further experiments; VECs were cultured in ECM medium (SciCell Corp., Cat # 1002), and cells of passage 4 were used for experiments.

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

treatment_protocol: CFs or VECs were either cultured alone or co-cultured in Transwell in the medium of DMEM serum free and ECM medium (mixed 1:1) for 24 hours, and then were lysed using TRIZOL.

value: vascular endothelial cells (VECs)


title: CFs co-cultured with VECs rep2

description:
P2
Replicate 2

source_name: Human peripheral blood

value: circulating fibrocytes (CFs) cocultured with vascular endothelial cells (VECs)


title: GEO-4


title: CFs co-cultured with VECs rep1

description:
P1
Replicate 1


title: VECs cultured alone rep3

description:
VEC7
Replicate 3


title: CFs cultured alone rep3

description:
P13
Replicate 3

value: circulating fibrocytes (CFs)


title: VECs co-cultured with CFs rep1

description:
V1
Replicate 1

value: vascular endothelial cells (VECs) co-cultured with circulating fibrocytes (CFs)


title: CFs cultured alone rep1

description:
P4
Replicate 1


title: VECs co-cultured with CFs rep3

description:
V3
Replicate 3


title: GEO-3

value: female

value: Yes


title: GEO-1


title: GEO-258


title: VECs cultured alone rep1

description:
VEC5
Replicate 1


title: GEO-2


title: CFs cultured alone rep2

description:
P5
Replicate 2


title: GEO-256


title: GEO-257


title: CFs co-cultured with VECs rep3

description:
P3
Replicate 3


title: GEO-253


title: GEO-255


title: GEO-254

value: male


title: GEO-252


title: GEO-250


title: GEO-251


title: GEO-249


title: GEO-248


title: VECs co-cultured with CFs rep2

description:
V2
Replicate 2


title: GEO-245

value: resistant


title: GEO-244


title: GEO-243


title: GEO-242


title: TP5A

city: New York City

first: Ricky

middle: Shantilal

last: Joshi

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference human genome hg18 (NCBI36) using BLAT, allowing up to 2 mismatches and 1 gap. Beta values from the autosomal probes were quantile normalized using lumi package in R.

label: Cy3, Cy5

source_name: Fibroblast, No media change, harvest at 240 hours

label_protocol: Standard Illumina labelling protocol

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
No change of initial media and then harvested after 240 hours

extract_protocol: DNA was extracted using the Qiagen DNeasy blood and tissue kit

value: Fibroblast

value: Female


title: TP4A

source_name: Fibroblast, No media change, harvest at 192 hours

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
No change of initial media, harvested after 192 hours


title: TP3

source_name: Fibroblast, Fresh media at 48 and 96 hrs, harvest at next 48 hrs

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
Fresh media given at 48 and 96 hours and then harvested after a further 48 hours


title: GEO-240

value: Acute Myeloid Leukemia


title: GEO-238

value: dead


title: GEO-239

value: predicted sensitive


title: GEO-237

value: No


title: GEO-247

value: bone marrow or peripheral blood mononuclear cells


title: GEO-246


title: GEO-233

value: sensitive


title: TP1

source_name: Fibroblast, Harvested after 48 hrs

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
Harvested after 48 hours


title: GEO-235


title: TP5

source_name: Fibroblast, Fresh media at 48, 96, 144 and 192 hrs, harvest at next 48 hours

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
Fresh media given at 48, 96, 144 and 192 and then harvested after a further 48 hours


title: GEO-232

value: alive


title: GEO-234


title: GEO-236


title: GEO-241

value: predicted refractory


title: TP2A

source_name: Fibroblast, No media change, harvest at 96 hours

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
No change of initial media, harvested after 96 hours


title: GEO-230


title: GEO-229


title: TP4

source_name: Fibroblast, Fresh media at 48, 96 and 144 hrs,harvest at next 48 hrs

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
Fresh media given at 48, 96 and 144, and then harvested after a further 48 hours


title: GEO-231


title: GEO-227


title: TP2

source_name: Fibroblast, Fresh media at 48 hrs, harvest at next 48 hrs

growth_protocol:
A growing culture of human skin fibroblasts from a normal male individual was obtained from Coriell Institute for Medical Research (Camden, NJ). Cells were grown in RPMI1640 media supplemented with 1mM L-glutamine, 10% FBS and 100u/L each of penicillin and streptomycin. A single vial of fibroblasts was initially grown in a 2ml culture plate, with media changed every 24 hours. Once the cells attained 80% confluency they were trypsinized and split equally into two T25 flasks. Each flask was treated identically, with media changed every 24 hours until the cells achieved 80% confluency (approximately 7 days after seeding). Both cultures were then trypsinized and seeded equally into a total of nine T25 flasks, which were then harvested at set time points
Fresh media given at 48 hours and then harvested after a further 48 hours


title: GEO-225


title: GEO-221


title: GEO-223


title: GEO-224


title: GEO-222


title: GEO-220


title: GEO-219


title: GEO-228


title: GEO-226


title: GEO-218


title: GEO-216


title: GEO-217


title: GEO-213


title: GEO-214


title: GEO-215


title: GEO-210


title: GEO-212


title: GEO-207


title: GEO-208


title: GEO-204


title: GEO-205


title: GEO-196


title: GEO-206


title: GEO-199


title: GEO-203


title: GEO-201


title: GEO-197


title: GEO-191


title: GEO-189


title: GEO-194


title: GEO-195


title: GEO-192


title: GEO-193


title: GEO-188


title: GEO-187


title: GEO-185


title: GEO-211


title: GEO-183


title: GEO-200


title: GEO-202


title: GEO-198


title: GEO-182


title: GEO-190


title: GEO-181


title: GEO-184


title: GEO-186


title: GEO-177


title: GEO-171


title: GEO-174


title: GEO-172


title: GEO-166


title: GEO-179


title: GEO-163


title: GEO-175


title: GEO-167


title: GEO-164


title: GEO-168


title: GEO-165


title: GEO-173


title: GEO-176


title: GEO-161


title: GEO-162


title: GEO-180


title: GEO-160


title: GEO-158


title: GEO-159


title: GEO-157


title: GEO-178


title: GEO-156


title: GEO-155


title: GEO-170


title: GEO-153


title: GEO-154


title: GEO-169


title: GEO-152


title: GEO-151


title: GEO-150


title: GEO-146


title: GEO-144


title: GEO-145


title: GEO-147


title: GEO-143


title: GEO-139


title: GEO-137


title: GEO-136


title: GEO-138


title: GEO-134


title: GEO-149


title: GEO-140


title: GEO-142


title: GEO-129


title: GEO-128


title: GEO-131


title: GEO-127


title: GEO-133


title: GEO-132


title: GEO-130


title: GEO-126


title: GEO-122


title: GEO-124


title: GEO-123


title: GEO-125


title: GEO-121


title: GEO-141


title: GEO-120


title: GEO-148


title: GEO-117


title: GEO-119


title: GEO-115


title: GEO-118


title: GEO-114


title: GEO-116


title: GEO-110


title: GEO-112


title: GEO-108


title: GEO-109


title: GEO-105


title: GEO-113


title: GEO-104


title: GEO-107


title: GEO-101


title: GEO-99


title: GEO-98


title: GEO-102


title: GEO-100


title: GEO-103


title: GEO-97


title: GEO-96


title: GEO-95


title: GEO-94


title: GEO-93


title: GEO-92


title: GEO-91


title: GEO-90


title: GEO-111


title: GEO-89


title: GEO-87


title: GEO-86


title: GEO-83


title: GEO-84


title: GEO-82


title: GEO-80


title: GEO-79


title: GEO-78


title: GEO-73


title: GEO-74


title: GEO-72


title: GEO-71


title: GEO-69


title: GEO-70


title: GEO-63


title: GEO-62


title: GEO-65


title: GEO-66


title: GEO-64


title: GEO-67


title: GEO-59


title: GEO-60


title: GEO-61


title: GEO-85


title: GEO-81


title: GEO-55


title: GEO-56


title: GEO-54


title: GEO-77


title: GEO-53


title: GEO-58


title: GEO-57


title: GEO-48


title: GEO-52


title: GEO-50


title: GEO-45


title: GEO-44


title: GEO-46


title: GEO-47


title: GEO-76


title: GEO-41


title: GEO-39


title: GEO-35


title: GEO-36


title: GEO-40


title: GEO-33


title: GEO-42


title: GEO-37


title: GEO-38


title: GEO-30


title: GEO-43


title: GEO-32


title: GEO-31


title: GEO-51


title: GEO-28


title: GEO-24


title: GEO-25


title: GEO-26


title: GEO-23


title: GEO-29


title: GEO-22


title: GEO-27


title: GEO-20


title: GEO-19


title: GEO-17


title: GEO-14


title: GEO-16


title: GEO-18


title: GEO-13


title: Heart_human_right atrial tissue_POAF_sample-3

status: Public on Oct 30 2017

city: Lille

first: Lefebvre

last: Philippe

state: Nord

address: Blvd Pr. J.Leclerc

country: France

institute: Inserm

description: Right atrial tissue gene expression data from human diabetic patient in whom POAF developed

hyb_protocol: 600ng 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 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_sept09 and Grid: 03949_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.   The processed data is available on the series level and contains the normalized signal intensity values.

source_name: Pre-operative right atrial tissue from human diabetic patient in whom POAF developed

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Absolutely RNA Nanoprep kit (Stratagene).  Dye incorpor

growth_protocol: Prospective study. Right atrial appendage were processes immediately after collection in ice cold oxygenated buffer to extract RNA

extract_protocol: Extract-All extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: individual_time of day

value: Patient 14_AM

value: Heart_right atrial tissue


title: Heart_human_right atrial tissue_POAF_sample-7

value: Patient 8_PM


title: Heart_human_right atrial tissue_POAF_sample-2


title: Heart_human_right atrial tissue_POAF_sample-6

value: Patient 10_AM


title: Heart_human_right atrial tissue_SR_sample-8

description: Right atrial tissue gene expression data from human diabetic patient in sinus rhythm (SR)

source_name: Pre-operative right atrial tissue from human diabetic patient in sinus rhythm (SR)

value: Patient 9_PM


title: Heart_human_right atrial tissue_SR_sample-7

value: Patient 10_PM


title: Heart_human_right atrial tissue_SR_sample-9

value: Patient 9_AM


title: Heart_human_right atrial tissue_SR_sample-4

value: Patient 13_AM


title: Heart_human_right atrial tissue_POAF_sample-4


title: Heart_human_right atrial tissue_POAF_sample-5

value: Patient 11_AM


title: Heart_human_right atrial tissue_SR_sample-6

value: Patient 12_AM


title: Heart_human_right atrial tissue_SR_sample-5

value: Patient 11_PM


title: GEO-21

value: Acute Myeloid Leukemia

value: male

value: resistant

value: dead

value: predicted sensitive


title: Heart_human_right atrial tissue_POAF_sample-1

value: Patient 12_PM


title: Heart_human_right atrial tissue_SR_sample-1

value: Patient 17_AM


title: Heart_human_right atrial tissue_SR_sample-2

value: Patient 16_AM

value: Heart_right atrial tissue


title: Heart_human_right atrial tissue_SR_sample-3

value: Patient 15_AM


title: GEO-15

value: bone marrow or peripheral blood mononuclear cells

value: female

value: No

value: Yes


title: P0322

status: Public on May 17 2017

city: Beijing

first: zemin

last: zhang

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

description: Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001002072

data_processing:
Sequencing data from Illumina Hiseq2500 or Hiseq4000 sequencer were first processed to filter out low quality reads which were defined as: 1) “N” bases account for 10% reads’ length; 2) bases with quality < 5 account for 50% reads’ length; 3) contain adapter sequence.
Reads were then aligned to ribosomal RNA sequences download from RFam using the GSNAP alignment tool.
Next the unmapped reads were mapped with GSNAP to reference sequences, containing human genome reference sequence version 19 (hg19) downloaded from UCSC and 92 ERCC spike-in RNA sequences obtained from the datasheet of the External RNA Controls Consortium kit. In addition, a gene model file named knownGene.txt was downloaded from UCSC and used to define known exon-exon junctions with the adjustable parameters “--novelsplicing 1 -n 10 -i 1 -M 2” except other default parameters.
After retrieving reads overlapping with genes defined in the gene model file with R function findOverlaps, the read counts of each gene were obtained.
Genome_build: hg19 downloaded from UCSC
Supplementary_files_format_and_content: compressed txt file. Each row is one gene. The first column is the Entrez ID and the second column is the HGNC gene symbol, other columns are cell names.
Supplementary_files_format_and_content: HCC.TCell.S5063.TPM.txt: Tab-delimited text file includes gene expression measured in TPM.
Supplementary_files_format_and_content: gene.length.txt: Tab-delimited text file; each row is one gene; lengths can be used to calculate FPKM or TPM from count.

source_name: T cells

extract_protocol:
Based on FACS analysis, single cells of different subtypes, including CD8+ T cells (CD3+ and CD8+), T helper cells (CD3+, CD4+ and CD25-), and regulatory T cells (CD3+, CD4+ and CD25high), were sorted into wells of 96-well plates (Axygen) with lysis buffer, which contained 1 µl 10 mM dNTP mix (Fermentas), 1 µl 10 µM Oligo dT primer, 1.9 µl 1% Triton X-100 (Sigma) plus 0.1 µl 40 U/µl RNase Inhibitor (Takara). The sealed plates were stored frozen at −80 ℃. Single cell transcriptome amplifications were performed following the Smart-Seq2 protocol. The amplified cDNA products were purified with 1x Agencourt XP DNA beads (Beckman). Following the first round of beads purification, the cDNA of each single cell was quantified with qPCR of CD3D, and fragment analysis (using fragment analyzer AATI).
For those single cell samples with high quality, the DNA products were further cleaned with 0.5x Agencourt XP DNA beads (Beckman) to eliminate short fragments (less than 500 bp). At this step, the concentration of each sample was quantified with Qubit HsDNA kits (Invitrogen), and libraries were then constructed with the TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme). Constructed libraries derived from patients P0205, P0508 and P0322 were analyzed by an Illumina HiSeq2500 sequencer with 100 bp pair-end reads, and for patients P0407 and P1116, libraries were analyzed by an Illumina Hiseq 4000 sequencer with 150 bp pair-end reads.

tag: patient

value: T cells from HCC patient


title: P0407


title: P0205


title: LS292 Ground control 3C

status: Public on Mar 01 2017

city: Dalian

first: Ying

last: Gao

state: Liaoning

address: Linghai Road 1

institute: Dalian Maritime university

description:
This sample is of ced-1 mutant Caenorhabditis elegans. The sample was treated with ground control condition.
sample name in raw and processed data: 3C

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.11.0) (Exiqon) according to array manual in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities >= 50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans LS292, Ground 1g

label_protocol: One µg total RNA from each samplewas labeled with Hy3™  fluorescent label using the miRCURY™  Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) following the procedure described by the manufacturer.

growth_protocol: Worms were cultured on Nematode Growth Medium (NGM) at 23°C and synchronized to dauer larvae by 1% sodium dodecyl sulfonate (SDS) (Sangon Biotec, Shanghai, China) according to the protocols in Wormbook (Stiernagle 2006).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Shenzhou-8 was launched in the Jiuquan Satellite Launch Center on 1 November 2011. About 10 h before the launch, fresh solid NGM and approximately 100,000 dauer worms were successively loaded in the containers.Containers were settled into the centrifugal and static slots of BIOBOX. The Shenzhou-8 mission was ﬂown from 1 – 17 November 2011, with a total mission time of 16.5 days. Throughout the duration of the experiment, the containers maintained a temperature of 23 0.5℃. G-force peaks did not exceed levels of 0.01 g, while most of the time values oscillated between 0.005 g. Space radiations dose was measured in the static slot (1.92 mGy) and centrifuge slot (2.27 mGy), respectively. Seven hours after landing, worms were collected and kept in liquid nitrogen. The corresponding ground controls of the experiment were performed in parallel at the Payload Integration Test Center in Beijing 2 days later. Here, the samples were kept in a static slot in BIOBOX and temperature was maintained at 23 0.5°C. The ground group was stopped after 16.5 days and  the samples were collected after 7 h later.

tag: genotype

tag: condition

value: Ground control condition

tag: major environmental factor


title: N2 Ground control 3A

description:
This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was treated with ground control condition.
sample name in raw and processed data: 3A

source_name: Caenorhabditis elegans N2, Ground 1g

value: Wild-type


title: P0508


title: P1202t


title: P1116


title: LS292 Spaceflgiht 1g-centrifugal 2C

description:
This sample is of ced-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight 1g-centrifugal condition, which supplied the spaceflight condition without microgravity.
sample name in raw and processed data: 2C

source_name: Caenorhabditis elegans LS292,Space radiation+1g

value: Spaceflight 1g-centrifugal condition

value: Space radiation+1g


title: N2 Spaceflgiht Static 1A

description:
This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was treated with spaceflight static condition .
sample name in raw and processed data: 1A

source_name: Caenorhabditis elegans N2, Space radiation+μg

value: Spaceflight static condition

value: Space radiation+μg


title: LS292 Spaceflgiht Static 1C

description:
This sample is of ced-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight static condition.No replicate used in this experiment.
sample name in raw and processed data: 1C

source_name: Caenorhabditis elegans LS292, Space radiation+μg


title: N2 Transport control con

description:
This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was kept in a incubator at Dalian Maritime University as a transport-control group.
sample name in raw and processed data: 4A

source_name: Caenorhabditis elegans N2, Ground 1g,No transport

value: Ground condition without transport to the launch lad at Jiuquan,China


title: LS292 Transport control con

description:
This sample is of dys-1 mutant Caenorhabditis elegans. The sample was kept in a incubator at Dalian Maritime University as a transport-control group.
sample name in raw and processed data: 4B

source_name: Caenorhabditis elegans LS292, Ground 1g,No transport

value: dys-1(cx18) I


title: N2 Ground control con


title: LS292 Ground control con

description:
This sample is of dys-1 mutant Caenorhabditis elegans. The sample was treated with ground control condition.
sample name in raw and processed data: 3B


title: N2 Spaceflgiht 1g -centrifugal 2A

description:
This sample is of wild-type Caenorhabditis elegans N2 Bristol. The sample was treated with spaceflight 1g-centrifugal condition, which supplied the spaceflight condition without microgravity.
sample name in raw and processed data: 2A

source_name: Caenorhabditis elegans N2, Space radiation+1g


title: N2 Spaceflgiht Static  con


title: LS292 Spaceflgiht Static con

description:
This sample is of dys-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight static condition.No replicate used in this experiment.
sample name in raw and processed data: 1B


title: LS292 Spaceflgiht 1g-centrifugal  con

description:
This sample is of dys-1 mutant Caenorhabditis elegans. The sample was treated with spaceflight 1g-centrifugal condition, which supplied the spaceflight condition without microgravity.
sample name in raw and processed data: 2B


title: N2 Spaceflgiht 1g -centrifugal con


title: Batf2_KO_BMDMs_R848_0h

status: Public on Jul 24 2017

city: Kumamoto

first: Hisashi

last: Kanemaru

state: Kumamoto

address: 1-1-1 Honjo Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto University

description:
AR2585_01
Gene expression of Batf2-deficient BMDMs without stimulations.

hyb_protocol: 2 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 8x60K Microarray (Agilent) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Two evaluated signal data (Base and Experiment) were compared and their log2 ratios were calculated. The log2 ratios of the expressed genes in WT BMDMs were listed in descending order (Set04_Log2Ratio).

source_name: bone marrow-derived macrophages (BMDMs), Batf2 KO, untreated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from Total RNA using the Low Input Quick Amp Labeling 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-2000 Spectrophotometer.

growth_protocol: Bone marrow cells were harvested from femurs and differentiated into macrophages in 15-cm non-coated sterile tissue culture dishes in RPMI-1640 with 10% FBS containing 3 ng/ml macrophage colony-stimulating factor (M-CSF, PeproTech). Medium was changed on day 3. On day 5, macrophages were harvested and stimulated.

extract_protocol: RNA was extracted from cells using a High Pure RNA Isolation kit (Roche).

treatment_protocol: BMDMs were stimulated with 100 ng/ml of R848 (InvivoGen).

tag: strain/background

tag: genotype/variation

value: male

tag: cell type

value: bone marrow-derived macrophages (BMDMs)

tag: treatment


title: WT_BMDMs_R848_0h

description:
AR2585_03
Gene expression of WT BMDMs without stimulations.

source_name: bone marrow-derived macrophages (BMDMs), WT, untreated

value: WT


title: WT_BMDMs_R848_8h

description:
AR2585_04
Gene expression after 8hr in R848-stimulated WT BMDMs.

source_name: bone marrow-derived macrophages (BMDMs), WT, R848


title: Batf2_KO_BMDMs_R848_8h

description:
AR2585_02
Gene expression after 8hr in R848-stimulated Batf2-deficient BMDMs.

source_name: bone marrow-derived macrophages (BMDMs), Batf2 KO, R848


title: diabetic with transplantation, biological rep 3

status: Public on Feb 01 2017

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from adult C57Bl6/J mice 6 weeks after STZ diabetes induction treated with islet-cell transplantation and continious insulin releasing pellets for additional 6 weeks

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Mogene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Whole retina from transplantation and insulin releasing pellets treated animals @12 weeks

growth_protocol: Diabetes was induced by intra peritoneal injection of streptozotocin (160 mg/kg/bodyweight; Sigma) in 8-week-old outbred male C57BL6/J mice weighing 24-26 g. After confirmation of stable hyperglycemia (blood glucose >15 mM 7 d after injection), hyperglycemic mice were randomly assigned to receive either standard chow or chow containing benfotiamine (80 mg per kg body weight per day). Non-diabetic animals served as controls. Body weight and blood glucose values were monitored at regular intervals. Animals were housed with a 12-/12-h light/dark cycle with ad libitum access to standard or benfotiamine containing rodent chow. Termination occured at 6 weeks and 12 weeks after diabetes induction.

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

treatment_protocol: Enucleated Eyes were snapp frozen in liquid nitrogen and stored at -80°C till further preperation. Extraction of the retina was performed at 0°C and immediately suspended in Trizol.

tag: background strain

tag: tissue

value: Whole retina

tag: disease

value: diabetic

tag: beta cells transplantation

value: yes

tag: streptozotocin


title: diabetic with transplantation, biological rep 1


title: diabetic with transplantation, biological rep 5


title: diabetic control, biological rep 3

description: Gene expression data from adult C57Bl6/J mice 12 weeks after STZ diabetes induction

source_name: Whole retina from diabetic animals @12 weeks

value: no


title: diabetic with transplantation, biological rep 4

value: Yes


title: diabetic control, biological rep 2


title: diabetic control, biological rep 5


title: diabetic control, biological rep 6


title: diabetic with transplantation, biological rep 2


title: diabetic control, biological rep 1


title: normal control, biological rep 6

description: Gene expression data from normal control C57Bl6/J mice after 12 weeks

source_name: Whole retina from normoglycemic animals @12 weeks

value: normoglycemic

value: Ctrl


title: diabetic control, biological rep 4


title: normal control, biological rep 5


title: normal control, biological rep 4


title: normal control, biological rep 2


title: normal control, biological rep 3


title: normal control, biological rep 1


title: Patient 9, CD56+ cells, before first dose of fingolimod [gene-level]

status: Public on May 20 2016

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

institute: University of Rostock

description: Gene expression data from a multiple sclerosis patient treated with fingolimod

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console (AGCC) software version 4.0. The data were then processed using Expression Console version 1.3.1. The robust multi-array average (RMA) algorithm was applied with the default configuration, which includes a log2 data transformation and quantile normalization. In this step, the measured signal intensities of >6 million probes were summarized into gene level probe sets (n=70523) and exon level probe sets (n=914585). The Transcriptome Analysis Console (TAC) software version 1.0 was utilized to analyze the RNA expression dynamics.

label: Biotin

source_name: Peripheral blood CD56+ cells

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 70 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Patient blood samples were taken immediately before the first dose of fingolimod as well as one day and three months post therapy initiation.

extract_protocol: Peripheral blood CD56+ cells were separated by magnetic-activated cell sorting using Whole Blood CD56 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

treatment_protocol: Patients were treated with fingolimod (Gilenya, Novartis) according to the approved label (0.5 mg orally once-daily) and the guidelines and recommendations of the German Society of Neurology.

tag: patient identifier

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment

value: interferon-beta-1b subcutaneous

tag: treatment gap in months

tag: edss at baseline

tag: edss after 1 year

tag: edss after 2 years

tag: edss after 3 years

tag: edss after 4 years

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: Patient 6, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: gender

value: glatiramer acetate


title: Patient 9, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: patient identifier


title: Patient 8, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: age in years at baseline

value: interferon-beta-1a subcutaneous


title: Patient 10, CD56+ cells, before first dose of fingolimod [gene-level]

tag: disease duration in years at baseline


title: Patient 8, CD56+ cells, before second dose of fingolimod [gene-level]

tag: previous treatment


title: Patient 7, CD56+ cells, before second dose of fingolimod [gene-level]

value: female

tag: treatment gap in months


title: Patient 6, CD56+ cells, before second dose of fingolimod [gene-level]

tag: edss at baseline


title: Patient 4, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

value: interferon-beta-1a intramuscular

tag: edss after 1 year


title: Patient 7, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 2 years


title: Patient 8, CD56+ cells, before first dose of fingolimod [gene-level]

tag: edss after 3 years


title: Patient 6, CD56+ cells, before first dose of fingolimod [gene-level]

tag: edss after 4 years


title: Patient 10, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during the year prior to fingolimod


title: Patient 9, CD56+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 1-year follow-up


title: Patient 7, CD56+ cells, before first dose of fingolimod [gene-level]

tag: relapses during 2-year follow-up


title: Patient 4, CD56+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 3-year follow-up


title: Patient 10, CD56+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 4-year follow-up


title: Patient 4, CD56+ cells, before first dose of fingolimod [gene-level]

tag: completed years of fingolimod therapy


title: Patient 3, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: gender


title: Patient 1, CD56+ cells, after 3 months of fingolimod treatment [gene-level]

tag: patient identifier


title: Patient 1, CD56+ cells, before second dose of fingolimod [gene-level]

tag: age in years at baseline


title: Patient 3, CD56+ cells, before first dose of fingolimod [gene-level]

tag: disease duration in years at baseline


title: Patient 10, CD19+ cells, before second dose of fingolimod [gene-level]

source_name: Peripheral blood CD19+ cells

extract_protocol: Peripheral blood CD19+ cells were separated by magnetic-activated cell sorting using Whole Blood CD19 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

tag: previous treatment


title: Patient 9, CD19+ cells, before second dose of fingolimod [gene-level]

tag: treatment gap in months


title: Patient 3, CD56+ cells, before second dose of fingolimod [gene-level]

tag: edss at baseline


title: Patient 9, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 1 year


title: Patient 8, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 2 years


title: Patient 8, CD19+ cells, before first dose of fingolimod [gene-level]

tag: edss after 3 years


title: Patient 10, CD19+ cells, before first dose of fingolimod [gene-level]

tag: edss after 4 years


title: Patient 1, CD56+ cells, before first dose of fingolimod [gene-level]

tag: relapses during the year prior to fingolimod


title: Patient 9, CD19+ cells, before first dose of fingolimod [gene-level]

tag: relapses during 1-year follow-up


title: Patient 4, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during 2-year follow-up


title: Patient 6, CD19+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 3-year follow-up


title: Patient 10, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during 4-year follow-up


title: Patient 6, CD19+ cells, before first dose of fingolimod [gene-level]

tag: completed years of fingolimod therapy


title: Patient 8, CD19+ cells, before second dose of fingolimod [gene-level]

tag: gender


title: Patient 4, CD19+ cells, before first dose of fingolimod [gene-level]

tag: patient identifier


title: Patient 3, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: age in years at baseline


title: Patient 4, CD19+ cells, before second dose of fingolimod [gene-level]

tag: disease duration in years at baseline


title: Patient 6, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: previous treatment


title: Patient 3, CD19+ cells, before second dose of fingolimod [gene-level]

tag: treatment gap in months


title: Patient 3, CD19+ cells, before first dose of fingolimod [gene-level]

tag: edss at baseline


title: Patient 1, CD19+ cells, before second dose of fingolimod [gene-level]

tag: edss after 1 year


title: Patient 1, CD19+ cells, before first dose of fingolimod [gene-level]

tag: edss after 2 years


title: Patient 10, CD14+ cells, before first dose of fingolimod [gene-level]

source_name: Peripheral blood CD14+ cells

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 200 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

extract_protocol: Peripheral blood CD14+ cells were separated by magnetic-activated cell sorting using Whole Blood CD14 MicroBeads (Miltenyi Biotec) and total RNA was isolated using the mirVana isolation kit (Thermo Fisher Scientific) according to the manufacturers' protocols.

tag: edss after 3 years


title: Patient 10, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 4 years


title: Patient 1, CD19+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during the year prior to fingolimod


title: Patient 10, CD14+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 1-year follow-up


title: Patient 9, CD14+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 2-year follow-up


title: Patient 9, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: relapses during 3-year follow-up


title: Patient 9, CD14+ cells, before first dose of fingolimod [gene-level]

tag: relapses during 4-year follow-up


title: Patient 8, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: completed years of fingolimod therapy


title: Patient 6, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: gender


title: Patient 8, CD14+ cells, before first dose of fingolimod [gene-level]

tag: patient identifier


title: Patient 6, CD14+ cells, before second dose of fingolimod [gene-level]

tag: age in years at baseline


title: Patient 8, CD14+ cells, before second dose of fingolimod [gene-level]

tag: disease duration in years at baseline


title: Patient 4, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: previous treatment


title: Patient 6, CD14+ cells, before first dose of fingolimod [gene-level]

tag: treatment gap in months


title: Patient 4, CD14+ cells, before second dose of fingolimod [gene-level]

tag: edss at baseline


title: Patient 3, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: edss after 1 year


title: Patient 4, CD14+ cells, before first dose of fingolimod [gene-level]

tag: edss after 2 years


title: Patient 3, CD14+ cells, before second dose of fingolimod [gene-level]

tag: edss after 3 years


title: Patient 3, CD14+ cells, before first dose of fingolimod [gene-level]

tag: edss after 4 years


title: Patient 10, CD56+ cells, before second dose of fingolimod [exon-level]

tag: relapses during the year prior to fingolimod


title: Patient 9, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 1-year follow-up


title: Patient 1, CD14+ cells, before second dose of fingolimod [gene-level]

tag: relapses during 2-year follow-up


title: Patient 10, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 3-year follow-up


title: Patient 10, CD56+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 4-year follow-up


title: Patient 1, CD14+ cells, after 3 months of fingolimod treatment [gene-level]

tag: completed years of fingolimod therapy


title: Patient 9, CD56+ cells, before second dose of fingolimod [exon-level]

tag: gender


title: Patient 8, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: patient identifier


title: Patient 1, CD14+ cells, before first dose of fingolimod [gene-level]

tag: age in years at baseline


title: Patient 7, CD56+ cells, before first dose of fingolimod [exon-level]

tag: disease duration in years at baseline


title: Patient 6, CD56+ cells, before first dose of fingolimod [exon-level]

tag: previous treatment


title: Patient 8, CD56+ cells, before first dose of fingolimod [exon-level]

tag: treatment gap in months


title: Patient 7, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss at baseline


title: Patient 6, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 1 year


title: Patient 9, CD56+ cells, before first dose of fingolimod [exon-level]

tag: edss after 2 years


title: Patient 3, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 3 years


title: Patient 3, CD56+ cells, before second dose of fingolimod [exon-level]

tag: edss after 4 years


title: Patient 7, CD56+ cells, before second dose of fingolimod [exon-level]

tag: relapses during the year prior to fingolimod


title: Patient 8, CD56+ cells, before second dose of fingolimod [exon-level]

tag: relapses during 1-year follow-up


title: Patient 6, CD56+ cells, before second dose of fingolimod [exon-level]

tag: relapses during 2-year follow-up


title: Patient 4, CD56+ cells, before second dose of fingolimod [exon-level]

tag: relapses during 3-year follow-up


title: Patient 4, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 4-year follow-up


title: Patient 3, CD56+ cells, before first dose of fingolimod [exon-level]

tag: completed years of fingolimod therapy


title: Patient 4, CD56+ cells, before first dose of fingolimod [exon-level]

tag: gender


title: Patient 1, CD56+ cells, after 3 months of fingolimod treatment [exon-level]

tag: patient identifier


title: Patient 1, CD56+ cells, before second dose of fingolimod [exon-level]

tag: age in years at baseline


title: Patient 1, CD56+ cells, before first dose of fingolimod [exon-level]

tag: disease duration in years at baseline


title: Patient 9, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

tag: previous treatment


title: Patient 10, CD19+ cells, before second dose of fingolimod [exon-level]

tag: treatment gap in months


title: Patient 10, CD19+ cells, before first dose of fingolimod [exon-level]

tag: edss at baseline


title: Patient 8, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 1 year


title: Patient 9, CD19+ cells, before second dose of fingolimod [exon-level]

tag: edss after 2 years


title: Patient 4, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 3 years


title: Patient 4, CD19+ cells, before first dose of fingolimod [exon-level]

tag: edss after 4 years


title: Patient 4, CD19+ cells, before second dose of fingolimod [exon-level]

tag: relapses during the year prior to fingolimod


title: Patient 8, CD19+ cells, before second dose of fingolimod [exon-level]

tag: relapses during 1-year follow-up


title: Patient 6, CD19+ cells, before second dose of fingolimod [exon-level]

tag: relapses during 2-year follow-up


title: Patient 6, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 3-year follow-up


title: Patient 1, CD19+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 4-year follow-up


title: Patient 3, CD19+ cells, before second dose of fingolimod [exon-level]

tag: completed years of fingolimod therapy


title: Patient 8, CD19+ cells, before first dose of fingolimod [exon-level]

tag: gender


title: Patient 10, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

tag: patient identifier


title: Patient 3, CD19+ cells, before first dose of fingolimod [exon-level]

tag: age in years at baseline


title: Patient 10, CD14+ cells, before second dose of fingolimod [exon-level]

tag: disease duration in years at baseline


title: Patient 1, CD19+ cells, before second dose of fingolimod [exon-level]

tag: previous treatment


title: RTK_INI29

status: Public on Mar 08 2016

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

source_name: Rhabdoid Tumor of the Kidney

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

tag: tissue

value: RTK


title: RTK_INI143


title: Patient 6, CD19+ cells, before first dose of fingolimod [exon-level]

tag: treatment gap in months

tag: edss at baseline


title: Patient 9, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

tag: edss after 1 year

tag: edss after 2 years


title: RMC_INI141

source_name: Renal Medullary Carcinoma

value: MRC


title: RTK_INI23


title: RMC_INI95


title: Patient 10, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

value: male

tag: edss after 3 years

tag: edss after 4 years


title: Patient 6, CD14+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up


title: Patient 1, CD19+ cells, after 3 months of fingolimod treatment [exon-level]

tag: relapses during 2-year follow-up

tag: relapses during 3-year follow-up


title: RMC_INI137


title: RMC_INI111


title: Patient 9, CD14+ cells, before first dose of fingolimod [exon-level]

tag: relapses during 4-year follow-up

tag: completed years of fingolimod therapy


title: Patient 10, CD14+ cells, before first dose of fingolimod [exon-level]

tag: patient identifier

tag: gender


title: dkfz_ATRT_32

status: Public on Mar 02 2016

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: Gene expression data from an ATRT tumor sample

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

source_name: Primary ATRT tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from biopsy samples was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using the TRIzol reagent (Invitrogen, Carlsbad, USA), and subsequently passed over a RNeasy Mini Spin Column (Qiagen, Hilden, Germany) for the removal of small fragments. Integrity control and sample quantitation of total extracted RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

tag: age (years)

tag: tumor location

value: Infratentorial


title: Patient 8, CD14+ cells, before second dose of fingolimod [exon-level]

tag: age in years at baseline

tag: disease duration in years at baseline

tag: previous treatment


title: dkfz_ATRT_84

value: M


title: Patient 6, CD14+ cells, before first dose of fingolimod [exon-level]

tag: treatment gap in months

tag: edss at baseline

tag: edss after 1 year


title: dkfz_ATRT_14


title: Patient 6, CD14+ cells, before second dose of fingolimod [exon-level]

tag: edss after 2 years

tag: edss after 3 years

tag: edss after 4 years


title: dkfz_ATRT_165

value: F


title: dkfz_ATRT_85


title: dkfz_ATRT_161

value: Supratentorial


title: Patient 8, CD14+ cells, before first dose of fingolimod [exon-level]

tag: relapses during the year prior to fingolimod

tag: relapses during 1-year follow-up

tag: relapses during 2-year follow-up


title: dkfz_ATRT_90


title: dkfz_ATRT_72


title: dkfz_ATRT_167