title: P1228

city: Beijing

first: zemin

last: zhang

address: Yiheyuan Road

department: BIOPIC

institute: Peking University

data_processing:
Sequencing data from Illumina 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 (CRC.TCell.S11138.count.txt.gz).
Low-quality cells were filtered if cell library sizes (column sum of the count table) or the numbers of expressed genes (counts > 0) were smaller than the median of all cells minus 3×MAD (Median Absolute Deviation), or if the mitochondrial gene count proportion of a cell was larger than 10%. Only cells with the average TPM of CD3D, CD3E and CD3G larger than 10 were kept in the data. Based on the transcriptome data, we identify CD4, CD8, double negative (DN) and double positive (DP) T cells. Given the average TPM of CD8A and CD8B, one cell was considered as CD8 positive or negative if the value was larger than 30 or less than 3 respectively; given the TPM of CD4, one cell was considered as CD4 positive or negative if the value was larger than 30 or less than 3 respectively. Hence the cells can be classified as CD4+CD8-, CD4-CD8+, CD4+CD8+, CD4-CD8- and other cells cannot be clearly defined. If the transcriptome data based classification conflict with the FACS based classification, the cells were filtered out.The count table of cells passing the above filtration was processed to keep only genes with the average count > 1,  than The counts were normalized by scran method(L. Lun et al., 2016) and centered by patient (CRC.TCell.S10805.norm.centered.txt.gz）.
The TCR sequence were assemblyed by TraCer pipeline (Stubbington et al., 2016), only alpha chain had TPM larger than 10 and beta chain had TPM larger than 15 were kept. If the alpha chain of one cell was rearranged by V segment TRAV1-2, one of J segment TRAJ33, TRAJ20 and TRAJ12, the cell was classified as MAIT cell. If the alpha chain of one cell was rearranged by V segment TRAV10 and J segment TRAJ18, the cell was classified as iNKT cell. Other cells were classified as cells with "diverse" TCR. The cells with diverse TCR were clustered using SC3 (Kiselev et al., 2017), and then the cells were assigned a major cluster label. CD8 MAIT cells were assigned label "CD8_C08-SLC4A10" because these cells have strong specific gene expression signatue. For completeness, other cells with non-diverse TCR or filtered cells were also annotated using the information of CD4/CD8 expression and TCR in the "majorCluster" label.
Genome_build: hg19 downloaded from UCSC

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).

tag: patient

value: T cells from colorectal cancer (CRC) patient


title: P1207

status: Public on Oct 29 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: SK-MSC-hyb1

type: RNA

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’, except that the minimal number of replicates used to calculate population outliers was set to 5. Measurements of on-chip replicates were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling. For this, all gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be scaled (‘Array i’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  A lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.
Normalized processed signal intensity values (non-log), averaged across on-chip replicates / quintuplicate measurements. Measurements of control features were removed.

source_name: SK-OV-3/MSC derived ovarian cancer hybrids

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.


title: P1212


title: Intermediate subiculum_i3_2

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
Trim input file and remove adapters.
Tag reads with cell barcode and UMI
Align reads to PhiX, then to mouse.
Aggregate reads and de-duplicate UMIs.
Post-processing in R with custom scripts and Seurat.
Genome_build: NCBIM37
Supplementary_files_format_and_content: Tab delimited file containing count values.

organism: Mus musculus

source_name: Intermediate subiculum

extract_protocol:
Microdissect and dissociate cells from acute brain slices in B6 mice
As in Cembrowski et al., Cell 173, 1-13

tag: strain

tag: tissue

value: brain (slices)

tag: tissue subtype

value: Intermediate subiculum

value: subiculum pyramidal cell


title: P1012


title: Intermediate subiculum_i2_2


title: SK-MSC-hyb2

value: SK-OV-3/MSC derived ovarian cancer hybrids


title: P0909


title: Intermediate subiculum_i3_1


title: P0825


title: SK-OV-3-cherry P95

source_name: human SK-OV-3 ovarian carcinoma cell line

value: SK-OV-3 ovarian carcinoma cell line


title: F994#3_1_A8886

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

country: USA

institute: National Institute of Allergy and Infectious Diseases

description: spleen RNA 24 hr post infection with strain F994#3,mouse replicate 1, RNAsampleID=A8886

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan-SQ

data_processing: Raw data filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from Genome Studio, cutoff is 0.1; Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

label: biotin

molecule: polyA RNA

source_name: spleen

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

growth_protocol: Inbred female C57BL/6 mice, aged 6–8 weeks, were purchased from Charles River Laboratory.

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 Bioanalyzer or TapeStation.

treatment_protocol: An inoculum containing 10×106 iRBC suspended in 100 ml of phosphate-buffered saline, pH 7.4, from donor mice was injected intravenously into each experimental C57BL/6 mouse to initiate infection. Naive mice receiving an equivalent number of uninfected RBCs served as a negative control group. Three to six mice as a group were infected with each parasite, and parasitemia were monitored by microscopic examination of Giemsa-stained thin tail blood smears.

value: spleen

tag: Sex

value: female

tag: parasite strain

tag: replicate mouse

tag: rna sample id


title: F994#3_2_A8887

description: spleen RNA 24 hr post infection with strain F994#3,mouse replicate 2, RNAsampleID=A8887


title: MSC081113-GFP P6

source_name: human mesenchymal stem/stroma cell

value: mesenchymal stem/stroma cell (MSC)


title: F994#3_3_A8888

description: spleen RNA 24 hr post infection with strain F994#3,mouse replicate 3, RNAsampleID=A8888


title: E995#3_3_A8882

description: spleen RNA 24 hr post infection with strain E995#3,mouse replicate 3, RNAsampleID=A8882


title: E995#3_2_A8881

description: spleen RNA 24 hr post infection with strain E995#3,mouse replicate 2, RNAsampleID=A8881


title: Intermediate subiculum_i2_1


title: Intermediate subiculum_i1_2


title: Intermediate subiculum_i1_1


title: MCF7_SatE2_R1: 3e Hi-C human Saturated E2 MCF7 cell rep.1

first: Daniel

middle: R

last: Larson

state: Maryland

address: 41 Medlars Dr

institute: National Institutes of Health

description: 3e Hi-C

library_source: genomic

data_processing:
Reads were mapped to hg19 with bowtie 2-2.3.4 and output into a sam file using the following command : "bowtie2 -p 10 -3 0 --local -x genome"
Mapped reads were then processed with Homer 4.8.2 initially with the following command: "makeTagDirectory unfiltered_sample samfile_read1,samfile_read2 -tbp 1"
Unfiltered Homer output was then coped to filtered_sample folders and filtered with the following command: "makeTagDirectory filtered_sample -update -genome hg19 -removePEbg -removeSpikes 10000 5"
Matrices were extracted by using the following Homer command: "analyzeHiC filtered_sample -res resolution -raw -cpu 16 -pos chr:s-e" Where resolution was 100000 or 1000, and chr=chromosome, s=start, e=end coordinates depending on the region analyzed.  Visualization for chromosome 21 interaction map was extracted with the -norm option.
Entropy was calculated on specific chromosome or enhancer coordinate raw count matrices using a perl script.
Genome_build: hg19
Supplementary_files_format_and_content: The final datatype is Shannon entropy.  To compute  entropy for the 3eHi-C data, we used specific chromosome 100kb binned matrices or 1kb extracted slices of individual enhancer contact matrices and counted the number of contacts in each segment-segment bin to obtain a contact probability between each segment.  The Shannon entropy of a contact given dose d is given by -sum pi(d)logpi(d) where pi(d) is the probability of a contact “bin” at a given dose d and the sum is over all bins.  This measure is output into 6 tab delimited columns where each column is a sample, and each row is a chromosome bin or enhancer.

molecule: genomic DNA

source_name: MCF7 breast cancer cells

growth_protocol: MCF7 cells in 10cm dishes were grown in MEM media (Corning) supplemented with 2mM Glutamine (Hyclone SH30034), 1X Penicillin/Strep (100units/mL Penicillin, 100micrograms/mL Streptomycin), and 10% FBS (Sigma). This media is denoted in the text as complete media or Saturated E2.

extract_protocol:
fresh MCF7 cells were cross-linked with 1% formaldehyde for 10 minutes at 25°C.  2-5 X 106 cells were lysed in 10 ml lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP40; 10 μl protease inhibitors (Sigma)) with rotation at 4°C for 60 minutes. The cells were then treated with 400 μl 1X NEB cutsmart buffer with 0.1% SDS at 65°C for 10 minutes, followed by addition of 44 μl 10% Triton X-100 to quench SDS. Chromatin was subsequently digested with 20 Units CviQ I (NEB), and 20 Units CviA II (NEB) at 25°C for 20 minutes, then with 20 Units Bfa I (NEB) at 37°C for 20 minutes. The reaction was stopped by washing the cells twice with 600 l wash buffer (10mM NaCl, 1mM EDTA, 0.1% triton-100). The DNA ends were blunted and labeled with biotin by Klenow enzyme in the presence of dCTP, dGTP, dTTP, biotin-14-dATP, followed by ligation using T4 DNA ligase. After reverse crosslinking, the samples were treated with T4 DNA polymerase to remove biotin labels at the DNA ends.
DNA was fragmented to 300-500 bp by sonication with a Bioruptor sonicator (Diagenode UCD-200). Next, The DNA was end-repaired, followed by A-addition as described previously (Lieberman-Aiden et al., 2009). The remaining biotinylated DNA fragments were then captured using Dynabeads MyOne Streptavin C1 Beads (Invitrogen) by incubating for 30 minutes at 25°C with rotation. The DNA on beads was ligated to the Illumina Paired End Adaptors. Following PCR-amplification of the libraries, DNA fragments from 300 to 700 bp were purified from 2% E-gel and sequenced on Hi-Seq 3000.

treatment_protocol: Cells were hormone depleted by washing cells twice in Phenol free media supplemented with 10% Charcoal/Dextran Treated FBS (Atlanta Biologicals), 2mM Glutamine and 1X Penstrep (hormone depleted media). Cells were returned to incubator and an hour later hormone depleted media was replaced. This step was performed again. After 4 days, media was replaced with hormone depleted media supplemented with the specific concentration of E2 or complete media for the Saturated E2 sample. Cells were allowed to reach steady state for 3 days.

tag: cell line

value: breast cancer

tag: gender


title: MCF7_SatE2_R2: 3e Hi-C human Saturated E2 MCF7 cell rep.2

description: 3e Hi-C


title: MCF7_0.05nM_R2: 3e Hi-C human 0.05 nM MCF7 cell rep.2

description: 3e Hi-C


title: MCF7_0nM_R2: 3e Hi-C human 0 nM MCF7 cell rep.2

description: 3e Hi-C


title: MCF7_0.05nM_R1: 3e Hi-C human 0.05 nM MCF7 cell rep.1

description: 3e Hi-C


title: P0701


title: MCF7_0nM_R1: 3e Hi-C human 0 nM MCF7 cell rep.1

description: 3e Hi-C


title: Ventral subiculum_v5_1

source_name: Ventral subiculum

value: Ventral subiculum


title: naive_1_A8955_2

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 1, RNAsampleID=A8955

value: naive


title: 17XNL_1_A8949_2

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 1, RNAsampleID=A8949


title: P0413


title: Ventral subiculum_v4_2


title: E995#3_1_A8880

description: spleen RNA 24 hr post infection with strain E995#3,mouse replicate 1, RNAsampleID=A8880


title: Ventral subiculum_v5_2


title: P0123


title: P0411


title: P0309


title: Ventral subiculum_v3_2


title: G001#5_3_A8903

description: spleen RNA 24 hr post infection with strain G001#5,mouse replicate 3, RNAsampleID=A8903


title: Ventral subiculum_v4_1


title: P0215


title: N67_1_A8952_2

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 1, RNAsampleID=A8952


title: Ventral subiculum_v3_1


title: Ventral subiculum_v2_2


title: G001#5_2_A8902

description: spleen RNA 24 hr post infection with strain G001#5,mouse replicate 2, RNAsampleID=A8902


title: G001#5_1_A8901

description: spleen RNA 24 hr post infection with strain G001#5,mouse replicate 1, RNAsampleID=A8901


title: Ventral subiculum_v2_1


title: Ventral subiculum_v1_2


title: 17XNL_3_A8951_2

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 3, RNAsampleID=A8951


title: Ventral subiculum_v1_1


title: Dorsal subiculum_d4_2

source_name: Dorsal subiculum

value: Dorsal subiculum


title: naive_3_A8957_2

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 3, RNAsampleID=A8957


title: N67_3_A8954_2

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 3, RNAsampleID=A8954


title: Col-0 endosperm 7 DAP rep 2

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were trimmed for QC with Trim_galore v 0.4.1 using the command " trim_galore -q 25 --phred64   --fastqc  --stringency 5 --length 18"
Aligned to TAIR10 genome with TOPHAT v2.1.1 using the command tophat  "-i 30 -I 3000 --b2-very-sensitive --solexa1.3-quals -p 5 --segment-mismatches 1 --segment-length 18 "
Cuffdiff v 2.2.1 was used with default settings to identify differentially expressed genes. The ARAPORT11 genome annotation was used. BAM files were the input for CuffDiff.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: endosperm at 7 days after pollination

growth_protocol: Plants were grown in a greenhouse with a controlled 16 hour light cycle at ~22C.

extract_protocol:
Seeds from crosses 7 days after pollination were dissected to isolate endosperm. RNA was isolated from endosperm using the Ambion RNAaqueous Micro Kit. RNA was treated with DNase and was submitted for library preparation at the Genome Technology Core of The Whitehead Institute.
SMARTerUltra-lowPOLYA-V4

tag: genotype

value: endosperm

tag: developmental stage

value: 7 days after pollination


title: patient 8 liver donor - whole liver tissue mRNA mRNA-DON-8

city: Cagliari

first: Giacomo

last: Diaz

address: Via Porcell 4

department: Dept Biomedical Sciences

country: Italy

institute: University of Cagliari

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

label: Biotin

source_name: specimen obtained from explanted liver of patient 8

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

value: whole liver

tag: source

value: liver donor


title: patient 69 with liver angioma - whole liver tissue mRNA mRNA-DON-69

source_name: specimen obtained from explanted liver of patient 69

tag: disease state

value: liver angioma


title: Dorsal subiculum_d4_1

value: brain (slices)


title: patient 56 with liver angioma - whole liver tissue mRNA mRNA-DON-56

source_name: specimen obtained from explanted liver of patient 56


title: patient 62 with liver angioma - whole liver tissue mRNA mRNA-DON-62

source_name: specimen obtained from explanted liver of patient 62


title: F120#5_2_A8908

description: spleen RNA 24 hr post infection with strain F120#5,mouse replicate 2, RNAsampleID=A8908


title: Dorsal subiculum_d3_2


title: G004#2_3_A8906

description: spleen RNA 24 hr post infection with strain G004#2,mouse replicate 3, RNAsampleID=A8906


title: F120#5_1_A8907

description: spleen RNA 24 hr post infection with strain F120#5,mouse replicate 1, RNAsampleID=A8907


title: patient 37 with liver angioma - whole liver tissue mRNA mRNA-DON-37

source_name: specimen obtained from explanted liver of patient 37


title: F120#5_3_A8909

description: spleen RNA 24 hr post infection with strain F120#5,mouse replicate 3, RNAsampleID=A8909


title: genomic DNA from Psoriatic tissue 24

type: genomic

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

description:
Psoriasis disease skin sample
Sample name: 114D

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 BeadArray Reader using standard recommended Illumina scanner setting

data_processing: IDAT files were processed using ChAMP pipeline for data processing. We used BMIQ Normal skinization. After Normal skinization and quality control checking, the signal intesities along with the detection P-values are calculated for each CpG probes. Normal skinized average beta values are calculated using ChAMP software implemented in R software.

label: Cy5 and Cy3

source_name: Psoriatic skin 24

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from Psoriasis and adjacent Normal skin samples using Qiagen Tissue & Blood DNA Kit according to manufacturer's protocols

value: skin

tag: age

tag: age of psoriasis onset

value: Male

tag: sample type

value: Psoriasis lesion

value: Normal

tag: batch

value: Batch 1


title: Mac_sSiglec-14(+)_24h

city: Taipei

first: Takashi

last: Angata

address: 128, Section 2, Academia Road, Nangang District

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16.5h at 45 degreeC on GeneChip HG-U133_Plus_2. GeneChips were washed and stained in the Affymetrix Fluidic Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

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

source_name: Human macrophages, treated with soluble Siglec-14 (1 ug/ml), for 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip Expression Analysis Technical Manual rev5, Affymetrix).

growth_protocol: Monocytes were cultured in the presence of M-CSF (10 ng/ml) for 7 days, and further incubated in the presence or absence of recombinant soluble Siglec-14 (1 ug/ml).

extract_protocol: Total RNA was extracted with RNeasy Plus Mini Kit (Qiagen)

tag: cell type

value: In vitro-differentiated macrophages

tag: agent

value: soluble Siglec-14


title: G004#2_1_A8904

description: spleen RNA 24 hr post infection with strain G004#2,mouse replicate 1, RNAsampleID=A8904

tag: tissue

value: spleen

value: female

tag: strain


title: Mac_sSiglec-14(-)_24h

description: Macrophage control

source_name: Human macrophages, treated without soluble Siglec-14, for 24h

value: control


title: genomic DNA from Adjacent Normal skin 24

description:
Adjacent Normal sample
Sample name: 114N

source_name: Normal skin 24

value: Adjacent Normal

value: Disease


title: patient 36 with liver angioma - whole liver tissue mRNA mRNA-DON-36

source_name: specimen obtained from explanted liver of patient 36


title: Dorsal subiculum_d3_1

tag: tissue subtype

value: Dorsal subiculum

value: subiculum pyramidal cell


title: Dorsal subiculum_d2_2


title: patient 29 with liver angioma - whole liver tissue mRNA mRNA-DON-29

source_name: specimen obtained from explanted liver of patient 29

value: whole liver

value: liver donor


title: G004#2_2_A8905

description: spleen RNA 24 hr post infection with strain G004#2,mouse replicate 2, RNAsampleID=A8905

source_name: spleen

tag: Sex

tag: parasite strain

tag: replicate mouse


title: F995#4_3_A8885

description: spleen RNA 24 hr post infection with strain F995#4,mouse replicate 3, RNAsampleID=A8885

tag: rna sample id


title: genomic DNA from Psoriatic tissue 22

description:
Psoriasis disease skin sample
Sample name: 71D

source_name: Psoriatic skin 22

tag: gender


title: Dorsal subiculum_d2_1

value: brain (slices)


title: F995#4_2_A8884

description: spleen RNA 24 hr post infection with strain F995#4,mouse replicate 2, RNAsampleID=A8884


title: genomic DNA from Psoriatic tissue 23

description:
Psoriasis disease skin sample
Sample name: 108D

source_name: Psoriatic skin 23

value: skin


title: patient 25 with liver angioma - whole liver tissue mRNA mRNA-DON-25

source_name: specimen obtained from explanted liver of patient 25

value: liver angioma


title: patient 18 with liver angioma - whole liver tissue mRNA mRNA-DON-18

source_name: specimen obtained from explanted liver of patient 18


title: Dorsal subiculum_d1_1

source_name: Dorsal subiculum


title: Dorsal subiculum_d1_2


title: genomic DNA from Psoriatic tissue 21

description:
Psoriasis disease skin sample
Sample name: 68D

source_name: Psoriatic skin 21

value: Male

value: Psoriasis lesion


title: Blood_treatment_3

city: Burnaby

first: Amy

middle: H.

last: Lee

address: 8888 University Drive

department: Molecular Biology and Biochemistry

institute: Simon Fraser University

data_processing:
Base-calling and de-multiplexing were performed on the Illumina instrument.
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
FASTQ files were aligned to the Ensembl murine reference genome using STAR aligner (version 2.5.2B).
Read count tables were generated using HTSeq-count (version 0.6.1p1)
Genome_build: GRCm38.p5 (build 86)
Supplementary_files_format_and_content: The .count files were generated using HTSeq-count and represent read counts.

source_name: Blood

extract_protocol:
Lung samples were collected in RNAlater (Qiagen) and blood samples were collected in RNAprotect animal blood tubes (Qiagen), both according to the manufacturer protocols. Total RNA was isolated using the RNAeasy Plus Mini kit (Qiagen). An enrichment with poly d(T) beads (New England Biolabs) was used to isolate polyA RNA. A KAPA Stranded Total RNA-Seq kit (Kapa Biosystems) was used to create the cDNA libraries.
The cDNA libraries were made according to the manufacturer protocol. In brief, first strand cDNA was synthesized, following by second strand synthesis and blunt-end formation. After 3’ adenylation, adapters (Bioo Scientific) for multiplexing were ligated, followed by amplification and then purification using Agencourt Ampure XP beads (Beckman Coulter).

value: blood

tag: treatment


title: F995#4_1_A8883

description: spleen RNA 24 hr post infection with strain F995#4,mouse replicate 1, RNAsampleID=A8883


title: genomic DNA from Adjacent Normal skin 22

description:
Adjacent Normal sample
Sample name: 71N

source_name: Normal skin 22

value: Batch 1


title: Blood_treatment_2


title: E890#3_3_A8879

description: spleen RNA 24 hr post infection with strain E890#3,mouse replicate 3, RNAsampleID=A8879


title: genomic DNA from Adjacent Normal skin 21

description:
Adjacent Normal sample
Sample name: 68N

source_name: Normal skin 21


title: patient 68 with liver angioma - whole liver tissue mRNA mRNA-ANG-68

source_name: specimen obtained from explanted liver of patient 68

tag: source

value: hepatic resection for liver angioma


title: Blood_treatment_1


title: naive_3_A8957_1

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 3, RNAsampleID=A8957

value: spleen

value: naive


title: patient 86 with liver angioma - whole liver tissue mRNA mRNA-ANG-86

source_name: specimen obtained from explanted liver of patient 86

tag: disease state


title: patient 16 with liver angioma - whole liver tissue mRNA mRNA-DON-16

source_name: specimen obtained from explanted liver of patient 16


title: E890#3_1_A8877

description: spleen RNA 24 hr post infection with strain E890#3,mouse replicate 1, RNAsampleID=A8877

value: female


title: Blood_PA103_4


title: patient 65 with liver angioma - whole liver tissue mRNA mRNA-ANG-65

source_name: specimen obtained from explanted liver of patient 65


title: Blood_PA103_3


title: genomic DNA from Adjacent Normal skin 19

description:
Adjacent Normal sample
Sample name: 57N

source_name: Normal skin 19

tag: age

value: Female

value: Adjacent Normal


title: genomic DNA from Psoriatic tissue 20

description:
Psoriasis disease skin sample
Sample name: 69D

source_name: Psoriatic skin 20

tag: age of psoriasis onset

value: Normal

value: Batch 2


title: Blood_PA103_2


title: E890#3_2_A8878

description: spleen RNA 24 hr post infection with strain E890#3,mouse replicate 2, RNAsampleID=A8878


title: genomic DNA from Adjacent Normal skin 18

description:
Adjacent Normal sample
Sample name: 84N

source_name: Normal skin 18

tag: sample type

value: Disease


title: Blood_PA103_1


title: genomic DNA from Psoriatic tissue 18

description:
Psoriasis disease skin sample
Sample name: 84D

source_name: Psoriatic skin 18

tag: batch


title: patient 55 with liver angioma - whole liver tissue mRNA mRNA-ANG-55

source_name: specimen obtained from explanted liver of patient 55

value: whole liver


title: genomic DNA from Adjacent Normal skin 23

description:
Adjacent Normal sample
Sample name: 108N

source_name: Normal skin 23


title: genomic DNA from Psoriatic tissue 19

description:
Psoriasis disease skin sample
Sample name: 57D

source_name: Psoriatic skin 19


title: patient 23 with liver angioma - whole liver tissue mRNA mRNA-ANG-23

source_name: specimen obtained from explanted liver of patient 23


title: N67_1_A8952_1

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 1, RNAsampleID=A8952

source_name: spleen


title: patient 64 with liver angioma - whole liver tissue mRNA mRNA-ANG-64

source_name: specimen obtained from explanted liver of patient 64


title: naive_2_A8956_1

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 2, RNAsampleID=A8956


title: naive_1_A8955_1

description: spleen RNA 24 hr post infection with strain naive,mouse replicate 1, RNAsampleID=A8955


title: patient 2 with liver angioma - whole liver tissue mRNA mRNA-ANG-2

source_name: specimen obtained from explanted liver of patient 2


title: patient 32 with ALF - whole liver tissue mRNA mRNA-ALF-32-4

source_name: specimen obtained from explanted liver of patient 32

value: from OLT of HBV-associated acute liver failure

value: acute liver failure


title: genomic DNA from Psoriatic tissue 17

description:
Psoriasis disease skin sample
Sample name: 113D

source_name: Psoriatic skin 17

value: skin


title: Blood_IDR1002_2

source_name: Blood


title: N67_2_A8953_1

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 2, RNAsampleID=A8953


title: Blood_IDR1002_3


title: patient 32 with ALF - whole liver tissue mRNA mRNA-ALF-32-3


title: patient 32 with ALF - whole liver tissue mRNA mRNA-ALF-32-2


title: 17XNL_3_A8951_1

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 3, RNAsampleID=A8951


title: 17XNL_2_A8950_1

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 2, RNAsampleID=A8950


title: Blood_control_3


title: 17XNL_1_A8949_1

description: spleen RNA 24 hr post infection with strain 17XNL,mouse replicate 1, RNAsampleID=A8949


title: patient 32 with ALF - whole liver tissue mRNA mRNA-ALF-32-1


title: Blood_control_2


title: genomic DNA from Adjacent Normal skin 17

description:
Adjacent Normal sample
Sample name: 113N

source_name: Normal skin 17

value: Male


title: N67_3_A8954_1

description: spleen RNA 24 hr post infection with strain N67,mouse replicate 3, RNAsampleID=A8954


title: genomic DNA from Psoriatic tissue 16

description:
Psoriasis disease skin sample
Sample name: 79D

source_name: Psoriatic skin 16

value: Psoriasis lesion


title: genomic DNA from Adjacent Normal skin 16

description:
Adjacent Normal sample
Sample name: 79N

source_name: Normal skin 16


title: genomic DNA from Adjacent Normal skin 20

description:
Adjacent Normal sample
Sample name: 69N

source_name: Normal skin 20


title: patient 31 with ALF - whole liver tissue mRNA mRNA-ALF-31-3

source_name: specimen obtained from explanted liver of patient 31


title: patient 31 with ALF - whole liver tissue mRNA mRNA-ALF-31-4


title: E891#5_3_A8948

description: spleen RNA 24 hr post infection with strain E891#5,mouse replicate 3, RNAsampleID=A8948


title: Blood_control_1

value: blood


title: patient 31 with ALF - whole liver tissue mRNA mRNA-ALF-31-2


title: E891#5_2_A8947

description: spleen RNA 24 hr post infection with strain E891#5,mouse replicate 2, RNAsampleID=A8947


title: genomic DNA from Psoriatic tissue 14

description:
Psoriasis disease skin sample
Sample name: 55D

source_name: Psoriatic skin 14


title: U2OS cells control (replicate 2)

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

data_processing:
Reads were mapped against the human genome (GRCh38) and rRNA sequences using ContextMap 2.7.9 with BWA as internal alignment program.
To calculate FPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped) values, fragment counts per gene (from Gencode version 25) were calculated using the featureCounts program from the subread package (v1.4.6-p3).
Genome_build: GRCh38
Supplementary_files_format_and_content: read counts for genes

source_name: U2OS cells

extract_protocol:
After thawing RNA was extracted from 0.4ml of TriZol lysate using the direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) as described in the manufacturer’s protocol. RNA was assessed for purity by UV-vis spectrometry (Nanodrop) and for integrity by Bioanalyzer (Agilent Bioanalyzer 2100, Agilent, Santa Clara USA)). RNA was of high purity (abs. 260/280 >1.9, abs 269/239>2.1) and integrity (Bioanalyzer RIN>9 ) and thus used for further processing.
For production of RNA-seq libraries total RNA was DNAse treated (dsDNAse, Fermentas) and 100 ng of this RNA was processed with a strand-specific protocol (RNA-seq complete kit, NuGEN, San Carlos, USA). In brief the RNA was reverse transcribed to cDNA with a reduced set of hexamer primers, avoiding excessive representation of rRNA in the cDNA. Second strand cDNA synthesis was done in presence of dUTP. After ultrasonic fragmentation of the cDNA and end repair, Illumina-compatible adapter were ligated. Adapters contained uracil in one strand, allowing complete digestion of the second-strand derived DNA. After strand selection the libraries were amplified, assessed for correct insert size on the Agilent Bioanalyser and diluted to 10nM. Barcoded libraries were mixed in equimolar amounts and sequenced on an Illumina HiSeq1500 in single-read mode with a read length of 100 bp.

treatment_protocol: Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-terminal zinc finger of ZNF768 for 12h. For preparation of total RNA cells were resuspended in TRIzol reagent (Life Technologies) at 0.9Mio/ml and snap-frozen.

value: control


title: patient 31 with ALF - whole liver tissue mRNA mRNA-ALF-31-1


title: genomic DNA from Psoriatic tissue 15

description:
Psoriasis disease skin sample
Sample name: 83D

source_name: Psoriatic skin 15


title: genomic DNA from Adjacent Normal skin 13

description:
Adjacent Normal sample
Sample name: 101N

source_name: Normal skin 13

value: Batch 1


title: U2OS cells control (replicate 1)


title: genomic DNA from Adjacent Normal skin 14

description:
Adjacent Normal sample
Sample name: 55N

source_name: Normal skin 14


title: genomic DNA from Adjacent Normal skin 15

description:
Adjacent Normal sample
Sample name: 83N

source_name: Normal skin 15


title: U2OS cells ZNF768-DN (replicate 4)

value: ZNF768 inhibition


title: patient 241 with ALF - whole liver tissue mRNA mRNA-ALF-241-4

source_name: specimen obtained from explanted liver of patient 241


title: patient 241 with ALF - whole liver tissue mRNA mRNA-ALF-241-3


title: U2OS cells control (replicate 3)


title: patient 241 with ALF - whole liver tissue mRNA mRNA-ALF-241-2


title: U2OS cells ZNF768-DN (replicate 3)


title: genomic DNA from Psoriatic tissue 12

description:
Psoriasis disease skin sample
Sample name: 98D

source_name: Psoriatic skin 12


title: patient 241 with ALF - whole liver tissue mRNA mRNA-ALF-241-1


title: patient 219 with ALF - whole liver tissue mRNA mRNA-ALF-219-5

source_name: specimen obtained from explanted liver of patient 219


title: U2OS cells ZNF768-DN (replicate 1)


title: Raji total RNA (replicate 4)

source_name: Raji cells

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS), 100U/ml penicillin, 100mg/ml streptomycin and 2mM L-glutamine (Gibco/Invitrogen) at 37°C and 5% CO2.

extract_protocol:
Illumina's Small RNA Library Prep Kit by using a modified protocol described in Mol Cell. 2018 Jan 4;69(1):48-61
Cells were harvested and total RNA was extracted using protocols described in Shah et al, Mol Cell. 2018 Jan 4;69(1):48-61.

tag: cell type

value: Raji B cell


title: U2OS cells ZNF768-DN (replicate 2)


title: genomic DNA from Psoriatic tissue 13

description:
Psoriasis disease skin sample
Sample name: 101D

source_name: Psoriatic skin 13


title: Raji total RNA (replicate 3)


title: U2OS cells control (replicate 4)


title: Cu_Whole_Cell_Extract_replicate3

city: Durham

first: John

middle: R.

last: Perfect

state: North Carolina

address: 303 Research Drive, Rm.337

department: Division of Infectious Diseases

institute: Duke University School of Medicine

data_processing:
read alignment were performed by Bowtie2.
Reads were aligned to the C. neoformans var. grubii H99  reference genome using Bowtie 2. Approximately 75 – 83% reads aligned uniquely to the reference.
THOR tool was used to detect and analyze differential signal peaks between control and treated samples with replicates.
The Integrative Genomics Viewer were used to visualize and compare peak differences between control and treatment replicate samples.
Genome_build: CNA3
Supplementary_files_format_and_content: narrowPeak

organism: Cryptococcus neoformans H99

source_name: Yeast

growth_protocol: An overnight C. neoformans culture of a cuf1Δ complemented with Cuf1-2xFLAG strain in synthetic complete (SC) medium (MP Biomedicals) was back-diluted to an OD600 of 0.2 in a 50 ml volume of SC media and grown for three hours at 30˚C, corresponding to ~one population doubling. At this time point, cells were treated as described below.

extract_protocol:
After 3 hours of treatment, formaldehyde was added and cells incubated for 20 minutes for crosslinking and crosslinking quenched with glycine for 5 minutes. Cells were pelleted and washed once in 10 mL of PBS containing glycine. The washed pellets were resuspended in 1 mL ChIP lysis buffer and lysed by bead beating three times 1 minute with a Mini Bead Beater 16 (BioSpec). The lysate was aspirated added to a 15 ml conical tube with 1 ml of ChIP lysis buffer and sonicated 40 seconds, 20 seconds on, 20 seconds off. Lysates were cleared by two successive centrifugations for 10 minutes at 20,000 x g at 4˚C. The resulting supernatant is now the input for the ChIP experiment. 30 µl were transferred to a new tube as the Whole Cell Extract (WCE). To prepare immunoprecipitation samples 250 µl lysate was added to 250 µl ChIP lysis buffer and 120 µl 3.6 M NaCl. To these samples, protein A agarose beads (Protein A Plus Agarose, Pierce) were added and incubated for 1 hour at 4˚C with rotation to clear protein that non-specifically binds beads. Lysates with agarose beads were then centrifuged at 10,000 x g for 1 minute at 4˚C, the supernatant transferred to a new tube and FLAG antibody beads (EZview Red Anti-FLAG M2 Affinity Gel, Sigma) blocked in PBS with 5% milk for 1 hour and washed in ChIP lysis buffer were added to the lysates and incubated for 16 hours at 4˚C while rotating. After beads washed several times, The immunoprecipitated Cuf1-2xFLAG was eluted by adding 150 µl of ChIP elution buffer and incubated for 10 minutes at 65˚C, centrifuged at 10,000 x g for 1 minute and 125 µl of the supernatant was transferred to a new tube. 95 µl of ChIP elution buffer was added to 30 ul WCE. The IP and WCE tubes were incubated at 65˚C overnight to reverse formaldehyde crosslinks, treated with 5 µl of proteinase K (BioLine) at 37˚C for 90 minutes and samples purified using a Qiagen PCR purification kit as per manufacturer’s instructions and eluted in 50 µl of water.
Libraries were prepared using the Kapa BioSystem HyperPrep Library Kit. libraries were cleaned using SPRI beads, quantified using Qubit 2.0 and size checked using the Agilent Bioanalyzer. Four libraries of replicate 1 were pooled together and sequenced by Illumina HiSeq 2000 sequencer at 100 bp single end. the other eight files from replicate 2 and 3 were sequenced by Illumina HiSeq 4000 sequencer at 51 bp single end.

treatment_protocol: Cells were treated with 1 mM CuSO4 or 1 mM BCS for three hours at 30˚C.

tag: media

value: SC media with 1 mM CuSO4

tag: genotype

value: Cuf1(del) complemented with Cuf1-2xFLAG

tag: chip antibody


title: Raji total RNA (replicate 2)

extract_protocol:
Epicenter's ScriptSeq V2 library preparation protocol according to manufacturer's instructions
Cells were harvested and total RNA was extracted using protocols described in Shah et al, Mol Cell. 2018 Jan 4;69(1):48-61.


title: patient 219 with ALF - whole liver tissue mRNA mRNA-ALF-219-4

tag: tissue


title: patient 219 with ALF - whole liver tissue mRNA mRNA-ALF-219-2


title: Cu_Whole_Cell_Extract_replicate2

tag: strain


title: patient 219 with ALF - whole liver tissue mRNA mRNA-ALF-219-3


title: patient 219 with ALF - whole liver tissue mRNA mRNA-ALF-219-1


title: Raji total RNA (replicate 1)


title: BCS_Whole_Cell_Extract_replicate3

value: SC media with 1 mM BathoCuproinediSulfonate


title: genomic DNA from Psoriatic tissue 10

description:
Psoriasis disease skin sample
Sample name: 87D

source_name: Psoriatic skin 10

value: Normal


title: BCS_Whole_Cell_Extract_replicate2


title: Cu_IP_Cuf1_replicate3

value: EZview Red Anti-FLAG (Sigma)


title: genomic DNA from Adjacent Normal skin 12

description:
Adjacent Normal sample
Sample name: 98N

source_name: Normal skin 12

value: Adjacent Normal

value: Disease

value: Batch 2


title: genomic DNA from Psoriatic tissue 8

description:
Psoriasis disease skin sample
Sample name: 106D

source_name: Psoriatic skin 8


title: Cu_IP_Cuf1_replicate2


title: Blood_IDR1002_1

source_name: Blood


title: BCS_IP_Cuf1_replicate3


title: E891#5_1_A8946

description: spleen RNA 24 hr post infection with strain E891#5,mouse replicate 1, RNAsampleID=A8946

source_name: spleen

value: spleen

tag: Sex

value: female

tag: parasite strain


title: genomic DNA from Adjacent Normal skin 7

description:
Adjacent Normal sample
Sample name: 100N

source_name: Normal skin 7

value: skin

value: Male


title: genomic DNA from Adjacent Normal skin 8

description:
Adjacent Normal sample
Sample name: 106N

source_name: Normal skin 8


title: genomic DNA from Adjacent Normal skin 11

description:
Adjacent Normal sample
Sample name: 85N

source_name: Normal skin 11


title: 32D MPL-HA Jak2VF IFNa treated

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

description: JAK2VF +

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 18 hours at 60 rpm; Fluidics Station Program FS_450_0007

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with robust multiarray average algorithm (Affymetrix): RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: Myoblast-like cell line 32D MPL-HA

label_protocol: Fragmented, biotinylated cDNAs were prepared from 300 ng total RNA using  the WT Plus Reagent Kit of Affymetrixaccording to the manufacturers instructions.

growth_protocol: cells were cultivated in RPMI - 10%FCS - PS - IL3

extract_protocol: Total RNA was isolated using the Trizol-Choroform method.

treatment_protocol: Cells were either treated with 100IU murine IFNa or 4h (+) or mock treated (wo)

tag: cell line

value: 32D MPL-HA

value: Jak 2 V617F

value: 100IU IFNa treated for 4 hrs


title: 32D MPL-HA Jak2VF mock treated

description: JAK2VF wo

value: mock treated for 4 hrs


title: genomic DNA from Psoriatic tissue 7

description:
Psoriasis disease skin sample
Sample name: 100D

source_name: Psoriatic skin 7

tag: gender

value: Psoriasis lesion


title: BCS_IP_Cuf1_replicate2


title: 32D MPL-HA Calr del 52 mock treated

description: del 52 wo

value: Calr del 52

tag: treatment


title: genomic DNA from Psoriatic tissue 11

description:
Psoriasis disease skin sample
Sample name: 85D

source_name: Psoriatic skin 11


title: genomic DNA from Adjacent Normal skin 9

description:
Adjacent Normal sample
Sample name: 104N

source_name: Normal skin 9


title: genomic DNA from Psoriatic tissue 9

description:
Psoriasis disease skin sample
Sample name: 104D

source_name: Psoriatic skin 9


title: genomic DNA from Psoriatic tissue 5

description:
Psoriasis disease skin sample
Sample name: 96D

source_name: Psoriatic skin 5

value: Batch 1


title: AH6

status: Public on Oct 28 2018

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped with STAR (DOI: 10.1002/0471250953.bi1114s51) to assembly hg38.
Counting proceeded over genes annotated in RefSeq release for  hg38  (igenomes) using STAR (DOI: 10.1002/0471250953.bi1114s51).
Genome_build: hg38
Supplementary_files_format_and_content: MCF7.xlsx Excel file containing  raw gene counts for MCF7 cell line samples
Supplementary_files_format_and_content: ZR75_OE.xlsx Excel file containing  raw gene counts for ZR75-1 cell line AH samples
Supplementary_files_format_and_content: ZR75.xlsx Excel file containing  raw gene counts for ZR75-1 cell line KWZ samples

source_name: ZR75-1 cell line

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel) or RNeasy Microkit (Qiagen).
For RNA-seq analysis, 500ng of total RNA was fragmented, followed by reverse transcription and second strand cDNA synthesis. The double stranded cDNA was subjected to end repair, A base addition, adapter ligation and PCR amplification to create libraries. Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of multiple samples over 3 lanes.

tag: replicate


title: AH3


title: AH1

value: vector (control)


title: KWMC9

source_name: MCF7 cell line


title: KWMC5


title: KWZ15


title: AH4


title: KWMC6


title: KWMC4

value: siControl


title: KWZ14


title: KWMC8


title: genomic DNA from Adjacent Normal skin 5

description:
Adjacent Normal sample
Sample name: 96N

source_name: Normal skin 5

tag: disease state


title: KWZ13


title: KWZ12


title: genomic DNA from Adjacent Normal skin 6

description:
Adjacent Normal sample
Sample name: 72N

source_name: Normal skin 6

tag: age


title: genomic DNA from Psoriatic tissue 6

description:
Psoriasis disease skin sample
Sample name: 72D

source_name: Psoriatic skin 6

tag: age of psoriasis onset

value: Normal


title: KWZ11


title: AH5


title: KWZ10


title: KWZ8


title: KWZ7


title: KWZ9


title: genomic DNA from Psoriatic tissue4

description:
Psoriasis disease skin sample
Sample name: 97D

source_name: Psoriatic skin 4

tag: sample type


title: L1-21

data_processing:
Reads were mapped using STAR (DOI: 10.1002/0471250953.bi1114s51) to mm10 assembly and quantified with STAR using mm10 refSeq annotation (igenomes).
Genome_build: mm10
Supplementary_files_format_and_content: LATS-CKO-PyMT-RNAseq.xlsx contains raw sequence counts per gene (STAR quantification)

source_name: mammary tumor

extract_protocol:
RNA was isolated using the NucleoSpin kit (Macherey Nagel) or RNeasy Mini kit (Qiagene)
RNA was isolated from Lats1-CKO and Lats2-CKO PyMT tumors. For each genotype, the corresponding wt littermate controls were used. For RNA-seq analysis, 500ng of total RNA was processed using the TruSeq RNA Sample Preparation Kit v2 protocol (Illumina) (Part # 15026495). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 7 samples per lane (3 wt tumors and 4 Lats-CKO tumors).

value: mammary tumor

tag: batch

tag: histology

value: adenosquamous carcinoma


title: genomic DNA from Adjacent Normal skin 3

description:
Adjacent Normal sample
Sample name: 91N

source_name: Normal skin 3

value: Adjacent Normal


title: genomic DNA from Psoriatic tissue 3

description:
Psoriasis disease skin sample
Sample name: 91D

source_name: Psoriatic skin 3

value: Disease


title: genomic DNA from Adjacent Normal skin 2

description:
Adjacent Normal sample
Sample name: 80N

source_name: Normal skin 2

value: Female


title: genomic DNA from Adjacent Normal skin 4

description:
Adjacent Normal sample
Sample name: 97N

source_name: Normal skin 4

value: skin


title: L1-14

value: carcinoma


title: L1-18


title: genomic DNA from Psoriatic tissue 2

description:
Psoriasis disease skin sample
Sample name: 80D

source_name: Psoriatic skin 2


title: PB-58 26hpi rep3

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

hyb_protocol: Cy3 labeled cDNA was allowed to hybridize for 17 h to a custom Agilent microarray (GPL22280)  at 65°C at 10 rpm

scan_protocol: The microarray image was taken using a 2 μM scanner and probe intensity values were obtained using Agilent Feature Extraction software.

data_processing: Probe intensities for all samples were quantile normalized. Samples were visualized using Principle Component Analysis. Combat and SVA packages in R were used to remove batch effects due to RNA processing, cDNA creation, cDNA labeling and microarray hybridization. Transcript expression levels were summarized for each gene by averaging the batch corrected processed signal intensity of all the probes across its exons.

organism: Plasmodium falciparum

label_protocol: 1µg of cDNA was labeled with Cy3 dye using 65% AT rich pre-labeled random hexamers as primers for cDNA synthesis by Klenow fragment of DNA polymerase I.

growth_protocol: The parasite strains NF54 and PB58 were maintained in identical standard culture conditions in human red blood cells (Indiana Regional Blood Center, Indianapolis, Indiana) suspended in complete medium (CM) containing RPMI 1640 with L-glutamine (Invitrogen Corp.), 50 mg/L hypoxanthine (Sigma-Aldrich), 25 mM HEPES (Cal Biochem), 0.5% Albumax II (Invitrogen Corp.), 10 mg/L gentamicin (Invitrogen Corp.) and 0.225% NaHCO3 (Biosource) at 5% hematocrit. Cultures were grown separately in sealed flasks at 37˚C under an atmosphere of 5% CO2, 5% O2, and 90% N2. Three replicated cultures were thawed and triple sorbitol synchronized. The time points collected were 6 (n=3), 26 (n=5),  and 38 (n=3) hours post invasion (hpi).

extract_protocol: RNA was extracted using TriZol reagent (Invitrogen, Carlsbad, CA) and the quality and quantity determined by NanoDrop (NanoDrop Technologies). 300ng of RNA was used as starting material for cDNA synthesis using the Sigma WTA2 whole transcriptome amplification kit (Sigma Aldrich, St Louis, MO).

treatment_protocol: Culture were maintained under standard culture conditions.

value: Isogenic mutant of NF54

tag: time point (hours post invasion)


title: L1-27

value: adenoma

tag: genotype


title: PB-58 26hpi rep2


title: PB-58 38hpi rep1


title: PB-58 38hpi rep2


title: WT-17

value: WT


title: WT-20


title: PB-58 26hpi rep1


title: genomic DNA from Adjacent Normal skin 10

description:
Adjacent Normal sample
Sample name: 87N

source_name: Normal skin 10

value: Male

value: Batch 2


title: WT-22


title: PB-58 6hpi rep2


title: L2-8


title: PB-58 6hpi rep3


title: L2-16


title: PB-58 6hpi rep1


title: L2-7


title: NF54 38hpi rep3

value: Parent


title: L2-1


title: KWMC7


title: WT-1


title: AH2


title: NF54 38hpi rep1


title: genomic DNA from Adjacent Normal skin 1

description:
Adjacent Normal sample
Sample name: 14N

source_name: Normal skin 1

value: Batch 1


title: NF54 26hpi rep3


title: genomic DNA from Psoriatic tissue 1

description:
Psoriasis disease skin sample
Sample name: 14D

source_name: Psoriatic skin 1

value: Psoriasis lesion


title: NF54 38hpi rep2


title: WT-2


title: WT-14


title: NF54 26hpi rep2


title: NF54 6hpi rep3


title: 32D MPL-HA Calr del 52 IFNa treated

description: del52 +

source_name: Myoblast-like cell line 32D MPL-HA

value: 32D MPL-HA

value: Calr del 52

value: 100IU IFNa treated for 4 hrs


title: NF54 26hpi rep1


title: EXP-17-AD3951 MM11

status: Public on Oct 27 2018

city: South San Francisco

first: Manu

last: Kumar

state: California

address: 650 Gateway Blvd Suite 100

institute: Asher Biotherapeutics

data_processing:
FASTQ files were processed with the CellRanger software (10x Genomics, Inc., version 2.0).
Files containing read 1 FC_xxxxx_Sx_Sx_R1_00x.fastq contain 26 base pair reads. The first 16 are the cell barcode and the next 10are the UMI. Files containing read 2 FC_xxxxx_Sx_Sx_R2_00x.fastq contain 98 base pair reads of the biological transcript.
Mouse genome 10-1.2.0 was used as the reference genome (10x Genomics, Inc.) to generate the matrix files containing cell barcodes and transcript counts.
To distinguish true cells from dead cells, debris or background, we used a cut-off of 1,500 on the number of genes detected per barcode, resulting in 10,573 true cells.
After conversion to transcript-per-million (TPM) values, we computed expression levels as Ei,j=log2(TPMi,j+1), where TPMi,j refers to the TPM for gene i in sample j.
We then normalized each cell to its average expression level of 3559 housekeeping genes by adding the average log-normalized housekeeping expression value (equivalent to scaling first) (Eisenberg & Levanon, 2013)
Genome_build: Mouse genome 10-1.2.0
Supplementary_files_format_and_content: The processed data file, compressed_syngeneic.tar.gz is a compressed version of three files. 1) sygeneic expression.csv contains the expression matrix aggregated across all samples. Each row represents a single cell and each column corresponds to a gene. 2) syngeneic_row_data.csv contains the gene symbols and ENSEMBL IDs corresponding to each colum of the expression matrix 3) syngeneic_columnd_data.csv contains the Sample_ID, isolation protocol, syngeneic tumor model, and experiment ID for each cell corresponding to the rows of the expression matrix

source_name: tumor

growth_protocol: For our tumor models, we used six different syngeneic mouse tumor cell lines. Cell lines were implanted into mice subcutaneously.

extract_protocol:
Each mouse tumor was harvested when the tumor size reached 100 – 200 mm3. Each sample was minced and digested with reagents from Mouse Tumor Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. Cells were resuspended at 2x105 cells/mL in PBS-0.04% BSA.
Single cell suspensions of all samples were resuspended in PBS-0.04% BSA at 5x105 cells/mL and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells for each sample was subsequently reverse-transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10x Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina HiSeq according to the manufacturer’s instructions (Illumina).

tag: model

tag: protocol

value: fresh


title: EXP-17-AD3951 MM8

tag: strain

value: A/J


title: EXP-17-AD3951 MM9


title: EXP-17-AD3951 MM12


title: EXP-17-AD3951 MM15


title: EXP-17-AD3951 MM14

value: BALB/c


title: EXP-17-AD3951 MM13


title: EXP-17-AD3951 MM10


title: NF54 6hpi rep1


title: NF54 6hpi rep2


title: EXP-17-AD3951 MM5


title: EXP-17-AD3951 MM6


title: EXP-17-AD3951 MM4


title: EXP-17-AD3951 MM1


title: EXP-17-AD3950 S8

value: overnight


title: EXP-17-AD3951 MM2


title: EXP-17-AD3951 MM3


title: EXP-17-AD3950 S6


title: EXP-17-AD3950 S3


title: EXP-17-AD3950 S7


title: EXP-17-AD3950 S4


title: EXP-17-AD3950 S5


title: EXP-17-AD3951 MM7


title: EXP-17-AD3950 S1


title: PB-58 38hpi rep3


title: EXR-SADAS1119a-BS

city: Boston

first: Saumya

last: Das

address: 185 Cambridge Street Suite 3201

department: Cardiovascular Research Center

institute: Massachusetts General Hospital

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Plasma

extract_protocol:
Plasma was collected from patients approximately 4 weeks post-myocardial infarction at Brigham and Women's Hospital, Massachusetts General Hospital, and Beth Israel Deaconess Medical Centre. Blood was obtained by peripheral venous cannula insertion into the forearm and collected in EDTA tubes.  Samples were processed within two hours of the initial blood collection. Tubes were centrifuged at 1200xg for 10 minutes and then the plasma was pipetted in 500-1000 uL aliquots into labeled 2.0 mL sterile conical screw cap tubes. Samples were then placed immediately into a secure -80o C freezer for storage. RNA isolation kit was miRcury biofluids (Exiqon). Proteinase K Treatment was performed (0.1 mg/ml proteinase K concentration, 0.5% SDS concentration, 55 C incubation temperature, 20 minute incubation time). Enzymatic treatment of purified exRNA was performed (T4 polynucleotide kinase treatment (10 units, NEB) at 37 C for 30 minutes).
Library construction kit was NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1). Standard protocol, with the exception that all adaptors were diluted 1:6 and gel purification was performed using a 10% TBE gel run for 100 min. Samples were multiplexed. Type of starting material was total RNA.

tag: condition

value: Myocardial Infarction

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: miRcury biofluids (Exiqon)


title: EXR-SADAS1062A-BS


title: EXR-SADAS1074A-BS


title: EXP-17-AD3950 S2


title: EXR-SADAS1106-BS


title: EXR-SADAS1010A-BS


title: EXR-SADAS1286A-BS


title: EXR-SADAS1251A-BS


title: EXR-SADAS1064B-BS


title: EXR-SADAS1044A-BS


title: EXR-SADAS1261A-BS


title: EXR-SADAS1120a-BS


title: EXR-SADAS1034A-BS


title: EXR-SADAS1035B-BS


title: EXR-SADAS1269A-BS


title: EXR-SADAS1049B-BS


title: EXR-SADAS1024A-BS


title: EXR-SADAS1066A-BS


title: EXR-SADAS1100A-BS


title: EXR-SADAS1113a-BS


title: EXR-SADAS1215B-BS


title: EXR-SADAS1219A-BS


title: EXR-SADAS1083B-BS


title: EXR-SADAS1225A-BS


title: EXR-SADAS1175A-BS


title: EXR-SADAS1253A-BS


title: EXR-SADAS1002A-BS


title: EXR-SADAS1M071B-BS


title: EXR-SADAS1257A-BS


title: EXR-SADAS1050A-BS


title: EXR-SADAS1004B-BS


title: EXR-SADAS1147B-BS


title: EXR-SADAS1025A-BS


title: EXR-SADAS1095A-BS


title: EXR-SADAS1103A-BS


title: EXR-SADAS1234A-BS


title: EXR-SADAS1196a-BS


title: EXR-SADAS1290A-BS


title: 012_EX_PK_CACTCA

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of TGGAATTCTCGGGTGCCAAGG. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

extract_protocol:
RNA isolation kit was MiRVana Paris (Ambion) with phenol–chloroform extractions.
Library construction kit was TruSeq Small RNA library prep kit (Illumina). Samples were multiplexed. Type of starting material was total RNA.

value: Healthy Control

value: Entire body system

value: MiRVana Paris (Ambion)

tag: pre-purification of extracellular vesicles

value: no


title: EXR-SADAS1M073B-BS


title: 013_EX_BL_GAGTGG


title: EXR-SADAS1256A-BS


title: EXR-SADAS1M025A-BS


title: 010_EX_BL_CTTGTA


title: EXR-SADAS1161A-BS


title: 029_EX_PK_CTAGCT


title: 019_EX_PK_ATGAGC


title: 077_Ex_PK_GTGAAA


title: 031_EX_PK_CCAACA


title: 078_Ex_BL_ATGTCA


title: 032_EX_BL_ATGTCA


title: EXR-SADAS1272A-BS


title: 030_EX_PK_GACGAC


title: EXR-SADAS1159A-BS


title: 044_BL_Vs_ATCACG

value: extracellular vesicle

value: yes


title: 006_EX_PK_CAGGCG


title: 018_EX_PK_TTAGGC


title: 019_EX_BL_GATCAG


title: 007_EX_BL_ATCACG


title: 029_EX_BL_CGATGT


title: 028_EX_PK_CTCAGA


title: 004_EX_BL_TAGCTT


title: 026_EX_BL_GCCAAT


title: 006_EX_BL_ACTTGA


title: 007_EX_PK_GGCTAC


title: 031_EX_BL_GTCCGC


title: 032_EX_PK_CATTTT


title: 070_Ex_PK_GTCCGC


title: 028_EX_BL_AGTTCC


title: 027_EX_PK_CACGAT


title: 030_EX_BL_CGTACG


title: 004_EX_PK_CGGAAT


title: 024_EX_PK_CTATAC


title: 026_EX_PK_CATGGC


title: 018_EX_BL_GTGAAA


title: 068_PK_Vs_CAGATC


title: 059_EX_PK_TAATCG


title: 070_PK_Vs_ACTTGA


title: 070_Ex_BL_AGTCAA


title: 077_BL_Vs_TGACCA


title: 059_EX_BL_CACCGG


title: 014_EX_PK_GTAGAG


title: 012_EX_BL_ACTGAT


title: 027_EX_BL_GTGGCC


title: 014_EX_BL_ACAGTG


title: 077_PK_Vs_GATCAG


title: 077_Ex_BL_AGTTCC


title: 003_EX_PK_CAACTA


title: 023_EX_PK_TGACCA


title: 078_PK_Vs_TAGCTT


title: 024_EX_BL_AGTCAA


title: 025_EX_PK_CCGTCC


title: 044_Ex_PK_CCGTCC


title: 068_Ex_PK_GTAGAG


title: 078_Ex_PK_GTGGCC


title: 070_BL_Vs_TTAGGC


title: 010_EX_PK_CAAAAG


title: 023_EX_BL_GTTTCG


title: 044_Ex_BL_GGCTAC


title: 044_PK_Vs_GCCAAT


title: 078_BL_Vs_ACAGTG


title: 003_EX_BL_CAGATC


title: 013_EX_PK_ATTCCT


title: 025_EX_BL_GGTAGC


title: 068_Ex_BL_CTTGTA


title: GCS-B3-4

city: Los Angeles

first: David

last: Wong

state: CA

address: 10833 Le Conte, CHS - Box 951668

institute: UCLA

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Saliva

extract_protocol:
This study followed the principle of prospective specimen collection and retrospective blind evaluation (PRoBE) design. All subjects were recruited from Samsung Medical Hospital (South Korea). Approximately 5mL of  saliva samples were collected in a 50 ml Falcon tube on ice. The whole saliva sample was centrifuged at 2600xg for 15 minutes and then the suppernant was pipetted in 1mL aliquots into labeled 2.0 mL sterile conical screw cap tubes (Fisherbrand). Then 1 uL of Superase-In was added to each aliguot. Samples were placed immediately into a secure -80 degree C freezer for storage. RNA was isolated using miRNeasy (Qiagen) Micro Kit. Qiazol:saliva ratio was 3:1, 20uL chloroform for every 100uL Qiazol used. exRNA quantification method was Ribogreen with Bioanalyzer Pico6000 RNA Chip for quality. RNA integrity method was Bioanalyzer (Agilent 2100). The following spike-in sequences were used: >1|5012815 TGACATGGGACTGCCTAAGCTA, >2|4430506 GATGGATATGTCTTCAAGGAC, >3|3920531 TCATGGTCAGATCCGTCATCC, >4|3474759 TACCAACCTTTCATCGTTCCC, >5|2772989 TAAGATCCGGACTACAACAAAG, >6|2099198 TGATTGGAAATTTCGTTGACT, >7|1932106 TCCCAAATGTAGACAAAGCA, >8|844587 TTGAATTGAAGTGCTTGAATT, >9|722119 TTCTTCGTGAATATCTGGCAT, >10|655988 TTAGATGACCATCAACAAACT, >11|363690 TAATTTGGTGTTTCTTCGATC, >12|331387 TGTTTGTTGTACTCGGTCTAGT, >13|321657 AGCTCTGATACCAAATGATGGAAT, >14|311970 TCGCTCTGATACCAAATTGATG, >15|200063 CGAAACTGGTGTCGACCGACA, >16|131490 TTCGATGTCTAGCAGTGCCA, >17|113465 TCTAGCAGCTGTTGAGCAGGT, >19|106634 GGTTCGTACGTACACTGTTCA, >20|99631 TCCGGCAAGTTGACCTTGGCT, >21|84955 TTATGTCTTGTTGATCTCAAT, >22|70769 TGAGCCTCTGTGGTAGCCCTCA, >23|65795 TCCTGTGTTTCCTTTGATGCGTGG, >25|56250 TTGGCATTCTGTCCACCTCC, >28|36527 ATGAATTTGGATCTAATTGAG, >30|33572 ATCAGTTTCTTGTTCGTTTCA, >35|29397 TTGATTCCCAATCCAAGCAAG, >36|26252 TACGCATTGAGTTTCGTTGCTT, >37|24916 TAAACTAATCACGGAAATGCA, >38|22984 CCTTGGAGAAATATGCGTCAA, >39|22435 TTTGCTTCCAGCTTTTGTCTC, >54|13534 TCTAAGTCTTCTATTGATGTT, >57|12681 TGATCTCTTCGTACTCTTCTTG, >61|12170 TTCTTGCATATGTTCTTTATC, >67|11555 TGTGTTCTCAGGTCACCCCTT, >75|10105 TGGCTTGGTTTATGTACACCG, >90|7532 TAATCCTACCAATAACTTCAGC, >93|7348 TAAAGTCAATAATACCTTGAAG, >96|7247 TGAAGCTGCCAGCATGATCTA, >105|6953 TAGAATGCTATTGTAATCCAG, >110|6652 TTGGTTACCCATATGGCCATC, >132|4738 CAGCCAAGGATGACTTGCCGG, >176|3027 TAACTAAACATTGGTGTAGTA, >194|2697 TTCGAGGCCTATTAAACCTCTG, >237|2044 TAGTCCGGTTTTGGATACGTG, >247|1894 ACAAACACCTTGGATGTTCTT, >254|1851 TTCTGCTATGTTGCTGCTCAT, >312|1402 ATTGGTTCAATTCTGGTGTTG, >368|1146 AGAATCTTGATGATGCTGCAT, >511|775 TTTTGGAAATTTGTCCTTACG, >515|765 CCCCAAATGTAGACAAAGCA, >1406|143 TTTTTCCTCAAATTTATCCAA, >1596|112 TCTTGCTTAAATGAGTATTCCA, >3275|34 CAGCCAAGGATGACTTGCCGA, >6870|13 TGTGTTCTCAGGTCACCCCTG, >13326|8 TTTGATTCCAGCTTTTGTCTC
NEBNext small RNA library prep (NEB) was used. Samples were not multiplexed. Strand specificity is non-stranded. Type of starting material is total RNA.

value: Entire oral cavity

value: miRNeasy (Qiagen)


title: GCS-B12-7

value: Gastric Cancer Pathologic TNM Finding v7


title: GCS-B11-5


title: GCS-B2-2


title: GCS-B16-1


title: GCS-B17-3


title: GCS-B25-4


title: 068_BL_Vs_CGATGT


title: GCS-B1-2


title: GCS-B20-8


title: GCS-B11-6


title: GCS-B14-1


title: GCS-B10-5


title: GCS-B11-7


title: GCS-B22-2


title: GCS-B23-4


title: GCS-B2-4


title: GCS-B24-3


title: GCS-B19-8


title: GCS-B10-6


title: GCS-B9-4


title: GCS-B1-3


title: GCS-B18-7


title: GCS-B21-1


title: GCS-B22-3


title: GCS-B9-6


title: GCS-B21-3


title: GCS-B8-5


title: GCS-B15-7


title: GCS-B17-8


title: GCS-B6-4


title: GCS-B20-2


title: GCS-B2-3


title: GCS-B5-3


title: GCS-B14-6


title: GCS-B19-2


title: GCS-B16-2


title: GCS-B13-6


title: GCS-B4-3


title: GCS-B25-3


title: GCS-B18-1


title: GCS-B3-2


title: GCS-B1-1


title: GCS-B21-8


title: GCS-B24-2


title: GCS-B23-2


title: GCS-B17-6


title: GCS-B9-5


title: GCS-B18-8


title: GCS-B22-1


title: GCS-B23-3


title: GCS-B21-2


title: EXP-17-AD3951 MM16

value: fresh


title: GCS-B19-7


title: GCS-B7-3


title: GCS-B4-8


title: GCS-B2-7


title: GCS-B8-4


title: GCS-B16-5


title: GCS-B12-5


title: GCS-B16-6


title: GCS-B17-7


title: GCS-B7-2


title: GCS-B25-8


title: GCS-B20-1


title: GCS-B15-1


title: GCS-B1-6


title: GCS-B2-8


title: GCS-B6-2


title: GCS-B7-4


title: GCS-B8-3


title: GCS-B10-4


title: GCS-B15-5


title: GCS-B19-1


title: GCS-B13-5


title: GCS-B6-3


title: GCS-B24-8


title: GCS-B14-4


title: GCS-B4-2


title: GCS-B15-6


title: GCS-B1-8


title: GCS-B23-7


title: GCS-B3-1


title: GCS-B12-4


title: GCS-B21-7


title: GCS-B23-1


title: GCS-B25-2


title: GCS-B10-3


title: GCS-B20-7


title: GCS-B5-8


title: GCS-B2-1


title: GCS-B18-6


title: GCS-B19-6


title: GCS-B9-3


title: GCS-B4-7


title: GCS-B16-7


title: GCS-B6-1


title: GCS-B15-4


title: GCS-B8-2


title: GCS-B22-8


title: GCS-B3-7


title: GCS-B14-3


title: GCS-B1-7


title: GCS-B3-8


title: GCS-B2-6


title: GCS-B17-5


title: GCS-B11-4


title: GCS-B23-6


title: GCS-B13-3


title: GCS-B14-5


title: GCS-B5-1


title: GCS-B22-6


title: GCS-B5-2


title: GCS-B24-7


title: GCS-B7-8


title: GCS-B10-1


title: GCS-B4-1


title: GCS-B13-4


title: GCS-B21-5


title: GCS-B11-3


title: GCS-B12-2


title: GCS-B9-8


title: GCS-B22-7


title: GCS-B23-8


title: GCS-B20-6


title: GCS-B25-1


title: GCS-B24-1


title: GCS-B9-2


title: GCS-B6-8


title: GCS-B6-6


title: GCS-B8-1


title: GCS-B10-2


title: GCS-B3-6


title: GCS-B18-5


title: GCS-B17-4


title: GCS-B11-8


title: GCS-B7-1


title: GCS-B25-7


title: GCS-B2-5


title: GCS-B16-4


title: GCS-B1-5


title: GCS-B15-3


title: GCS-B13-2


title: GCS-B10-8


title: GCS-B9-7


title: GCS-B12-1


title: GCS-B24-6


title: GCS-B21-4


title: GCS-B20-4


title: GCS-B5-7


title: GCS-B12-3


title: GCS-B11-1


title: GCS-B14-8


title: GCS-B5-5


title: GCS-B8-8


title: GCS-B21-6


title: GCS-B6-7


title: GCS-B11-2


title: GCS-B19-3


title: GCS-B20-5


title: GCS-B4-4


title: GCS-B13-7


title: GCS-B18-3


title: GCS-B19-4


title: GCS-B19-5


title: GCS-B5-6


title: GCS-B4-6


title: GCS-B9-1


title: GCS-B22-5


title: GCS-B17-2


title: GCS-B18-4


title: GCS-B8-7


title: GCS-B3-5


title: GCS-B10-7


title: GCS-B1-4


title: GCS-B7-6


title: GCS-B12-8


title: GCS-B25-6


title: GCS-B15-2


title: GCS-B24-4


title: GCS-B24-5


title: GCS-B23-5


title: GCS-B13-1


title: GCS-B14-2


title: GCS-B16-3


title: GCS-B22-4


title: GCS-B20-3


title: GCS-B16-8


title: GCS-B7-5


title: GCS-B6-5


title: GCS-B18-2


title: GCS-B14-7


title: GCS-B4-5


title: GCS-B5-4


title: GCS-B12-6


title: GCS-B3-3


title: GCS-B17-1


title: GCS-B13-8


title: ULMC135_PLASUNTR_2

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Place

department: Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with an adapter sequence of TGGAATTCTCGGGTGCCAAGG. exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data archive contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

extract_protocol:
Within 3hrs of collection, blood specimens preserved in EDTA  are processed using serial centrifugation to yield cell-free plasma. After gently resuspending the blood cells, tubes are centrifuged at 3,400xg for 10 min at 22C, setting acceleration and deceleration to the maximum setting. Upper plasma layers are immediately transferred to clean tubes, and spun at 1,940xg for 10min at 22C, with Acceleration and braking set to maximum and minimum levels, respectively. The cell-free supernatat is transferred to a fresh tube and stored at -80C.
High speed centrifugation was used. RNA was isolated with the miRNeasy (Qiagen) kit, following manufaturer's recommendations with minor modifications. Pre-purification of extracellular vesicles was not performed.
TruSeq Small RNA library prep kit (Illumina) was used. Samples were multiplexed. Strand specificity was stranded. Starting material was total RNA. Primer sequence was GCCTTGGCACCCGAGAATTCCA.

tag: enzymatic treatment of purified exrna

value: No (No treatment performed)


title: ULMC134_PLASUNTR_5


title: ULMC134_PLASPNK_6

value: Yes (RNA was treated with PNK followed by column-based enzymatic reaction cleanup (Qiagen))


title: GCS-B8-6


title: ULMC135_PLASPNK_3


title: ULMC209_PLASUNTR_5


title: ULMC148_PLASPNK_9


title: ULMC157_PLASUNTR_9


title: ULMC202_SERUNTR_5

source_name: Serum

extract_protocol:
1x10ml of venus blood is drawn into BD Vacutainer SST Plus Blood Collection Tubes and allowed to clot for 45 minutes at room temperature. Serum processing begins within 1 hour of collection ( 4 hours, if stored at 4C ). SST tubes are centrifuged 1200xg for 15 min at room temperature. The liquid supernatant is transferred to 1.5 ml screw cap tubes, making sure to leave at least 0.5 cm layer of serum behind without disturbing the pellet. Samples are stored at -80C.
High speed centrifugation was used. RNA was isolated with the miRNeasy (Qiagen) kit, following manufaturer's recommendations with minor modifications. Pre-purification of extracellular vesicles was not performed.
TruSeq Small RNA library prep kit (Illumina) was used. Samples were multiplexed. Strand specificity was stranded. Starting material was total RNA. Primer sequence was GCCTTGGCACCCGAGAATTCCA.


title: ULMC148_PLASUNTR_8


title: GCS-B15-8


title: ULMC202_PLASPNK_2


title: ULMC202_SERUNTR_6


title: ULMC209_PLASPNK_8


title: ULMC209_PLASUNTR_6


title: ULMC209_SERPNK_5


title: ULMC123_PLASUNTR_2


title: ULMC215_PLASPNK_6


title: ULMC134_PLASUNTR_6


title: ULMC215_PLASUNTR_7


title: ULMC215_PLASPNK_8


title: ULMC202_PLASUNTR_3


title: ULMC209_SERPNK_7


title: ULMC148_PLASUNTR_2


title: ULMC215_PLASUNTR_9


title: ULMC215_SERPNK_1


title: ULMC202_PLASPNK_7


title: ULMC148_PLASPNK_3


title: ULMC209_SERUNTR_5


title: ULMC123_PLASPNK_4


title: ULMC135_PLASPNK_9


title: ULMC157_PLASUNTR_3


title: ULMC135_PLASPNK_8


title: ULMC148_PLASPNK_2


title: ULMC148_PLASPNK_1


title: ULMC135_PLASUNTR_1


title: ULMC134_PLASPNK_8


title: ULMC123_PLASPNK_6


title: ULMC209_SERUNTR_6


title: ULMC148_PLASUNTR_6


title: ULMC202_SERUNTR_4


title: ULMC215_PLASUNTR_1


title: ULMC202_PLASUNTR_8


title: ULMC157_PLASPNK_9


title: ULMC123_PLASUNTR_1


title: ULMC202_SERPNK_8


title: ULMC148_PLASUNTR_7


title: ULMC135_PLASUNTR_3


title: ULMC135_PLASUNTR_9


title: ULMC209_PLASUNTR_4


title: ULMC202_PLASUNTR_2


title: ULMC157_PLASPNK_4


title: ULMC215_SERPNK_7


title: ULMC148_PLASPNK_8


title: ULMC202_SERPNK_9


title: ULMC157_PLASUNTR_1


title: ULMC157_PLASUNTR_2


title: ULMC157_PLASPNK_2


title: ULMC202_PLASPNK_5


title: ULMC209_PLASPNK_7


title: ULMC215_SERUNTR_2


title: ULMC157_PLASPNK_3


title: ULMC202_SERUNTR_9


title: ULMC134_PLASUNTR_9


title: ULMC135_PLASUNTR_8


title: ULMC135_PLASPNK_2


title: ULMC202_SERPNK_2


title: ULMC202_PLASUNTR_7


title: ULMC123_PLASUNTR_7


title: ULMC215_SERPNK_6


title: ULMC157_PLASUNTR_6


title: ULMC135_PLASPNK_1


title: ULMC148_PLASPNK_6


title: ULMC123_PLASPNK_5


title: ULMC157_PLASUNTR_8


title: ULMC148_PLASUNTR_5


title: ULMC134_PLASPNK_3


title: ULMC209_SERUNTR_4


title: ULMC202_SERUNTR_3


title: ULMC134_PLASPNK_5


title: ULMC209_PLASPNK_5


title: ULMC215_SERUNTR_4


title: ULMC215_SERUNTR_9


title: ULMC215_PLASPNK_3


title: ULMC148_PLASPNK_7


title: ULMC202_SERPNK_7


title: ULMC215_PLASUNTR_4


title: ULMC215_PLASPNK_5


title: ULMC209_SERUNTR_9


title: ULMC134_PLASUNTR_3


title: ULMC123_PLASPNK_9


title: ULMC209_PLASUNTR_3


title: ULMC209_SERPNK_4


title: ULMC215_PLASUNTR_6


title: ULMC135_PLASUNTR_6


title: ULMC157_PLASPNK_1


title: ULMC202_PLASUNTR_1


title: ULMC209_PLASPNK_6


title: ULMC123_PLASUNTR_6


title: ULMC209_PLASUNTR_9


title: ULMC209_SERUNTR_3


title: ULMC202_PLASPNK_4


title: ULMC202_SERPNK_1


title: ULMC148_PLASUNTR_4


title: ULMC209_SERPNK_9


title: ULMC157_PLASPNK_6


title: ULMC157_PLASUNTR_7


title: ULMC134_PLASUNTR_8


title: ULMC202_PLASUNTR_5


title: ULMC123_PLASPNK_3


title: ULMC157_PLASPNK_7


title: ULMC135_PLASUNTR_7


title: ULMC134_PLASUNTR_2


title: ULMC215_SERUNTR_3


title: ULMC202_SERUNTR_2


title: ULMC215_SERPNK_5


title: ULMC157_PLASPNK_8


title: ULMC135_PLASPNK_7


title: ULMC215_PLASPNK_4


title: ULMC202_SERPNK_6


title: ULMC134_PLASPNK_4


title: ULMC215_SERUNTR_8


title: ULMC148_PLASPNK_5


title: ULMC209_PLASUNTR_1


title: ULMC209_SERPNK_3


title: ULMC215_PLASUNTR_5


title: ULMC209_PLASPNK_4


title: ULMC123_PLASPNK_8


title: ULMC209_SERUNTR_1


title: ULMC135_PLASUNTR_5


title: ULMC135_PLASPNK_6


title: ULMC209_SERUNTR_2


title: ULMC215_SERPNK_4


title: ULMC202_PLASPNK_3


title: ULMC202_PLASUNTR_4


title: ULMC215_SERUNTR_1


title: ULMC215_SERPNK_3


title: ULMC209_SERPNK_8


title: ULMC209_SERUNTR_8


title: ULMC134_PLASUNTR_7


title: ULMC202_SERUNTR_8


title: ULMC209_PLASUNTR_8


title: ULMC148_PLASPNK_4


title: ULMC209_SERPNK_1


title: ULMC202_PLASPNK_9


title: ULMC134_PLASPNK_9


title: ULMC215_PLASPNK_9


title: ULMC215_SERUNTR_6


title: ULMC209_SERPNK_2


title: ULMC123_PLASUNTR_4


title: ULMC215_PLASPNK_2


title: ULMC209_PLASPNK_3


title: ULMC123_PLASUNTR_9


title: ULMC202_PLASUNTR_6


title: ULMC134_PLASPNK_2


title: ULMC123_PLASPNK_2


title: ULMC157_PLASUNTR_5


title: ULMC215_PLASUNTR_3


title: ULMC134_PLASUNTR_1


title: ULMC123_PLASUNTR_5


title: ULMC209_PLASPNK_2


title: ULMC148_PLASUNTR_9


title: ULMC135_PLASUNTR_4


title: ULMC209_PLASUNTR_2


title: ULMC123_PLASPNK_7


title: ULMC134_PLASUNTR_4


title: ULMC123_PLASUNTR_3


title: ULMC215_PLASUNTR_8


title: ULMC148_PLASUNTR_1


title: ULMC123_PLASPNK_1


title: ULMC215_SERPNK_9


title: ULMC209_PLASUNTR_7


title: ULMC215_PLASPNK_7


title: ULMC202_PLASPNK_1


title: ULMC135_PLASPNK_4


title: ULMC134_PLASPNK_1


title: ULMC157_PLASPNK_5


title: ULMC209_SERPNK_6


title: ULMC157_PLASUNTR_4


title: ULMC135_PLASPNK_5


title: ULMC215_SERPNK_2


title: ULMC148_PLASUNTR_3


title: ULMC202_PLASPNK_8


title: ULMC215_SERPNK_8


title: ULMC209_SERUNTR_7


title: ULMC202_SERUNTR_1


title: ULMC123_PLASUNTR_8


title: ULMC202_PLASUNTR_9


title: ULMC134_PLASPNK_7


title: ULMC202_SERPNK_5


title: ULMC209_PLASPNK_1


title: ULMC209_PLASPNK_9


title: ULMC202_SERPNK_3


title: ULMC215_SERUNTR_5


title: ULMC215_PLASUNTR_2


title: ULMC215_PLASPNK_1


title: 2D09BLO

city: Phoenix

first: Kendall

last: Van Keuren-Jensen

state: AZ

address: 445 N. Fifth Street

institute: The Translational Genomics Research Institute

extract_protocol:
RNA was isolated using MiRVana Paris (Ambion).
TruSeq Small RNA library prep kit (Illumina) was used. Samples were not multiplexed. Strand specificity is non-stranded. Type of starting material is total RNA.

value: Subarachnoid Hemorrhage

value: Entire brain


title: 10D14CSF

source_name: Cerebrospinal fluid


title: 14D09BLO


title: 01D03CSF


title: 11D01CSF


title: ULMC215_SERUNTR_7

value: Entire cardiovascular system


title: 33D05CSF

value: total cell-free biofluid RNA


title: 33D03BLO


title: 10D12BLO


title: 01D04CSF


title: 13D08CSF


title: 13D03BLO


title: 31D02CSF2


title: 02D04CSF


title: 34D04BLO


title: 14D04BLO


title: 15D05BLO


title: 10D07CSF


title: 20D05CSF


title: 03D05CSF


title: 30D02CSF


title: 12D02BLO


title: 34D06CSF


title: ULMC202_SERPNK_4


title: 13D14BLO


title: 42D04CSF


title: 1D05BLO


title: 21D05CSF


title: 32D04BLO


title: 11D08CSF


title: 16D05BLO


title: 10D02CSF


title: 11D03CSF


title: 11D01BLO


title: 2D06BLO


title: 05D07CSF


title: 33D05BLO


title: 43D04CSF


title: 34D06BLO


title: 17D06BLO


title: 1D03BLO


title: 12D04CSF


title: 16D06BLO


title: 33D00BLO


title: 2D05BLO


title: 02D06CSF


title: 44D03BLO


title: 10D13CSF


title: 12D03CSF


title: 12D01BLO


title: 03D07CSF


title: 3D06BLO


title: 04D08CSF


title: 11D14CSF


title: 04D06CSF


title: 13D02BLO


title: 34D00BLO


title: 30D04CSF


title: 13D04CSF


title: 4D07BLO


title: 14D05CSF


title: 15D04BLO


title: 32D06CSF


title: 14D03BLO


title: 5D08BLO


title: 35D01BLO


title: 05D09CSF


title: 36D02BLO


title: 43D04BLO


title: 20D01CSF


title: 21D02CSF


title: 42D03CSF


title: 17D08CSF


title: 6D09BLO


title: 33D06CSF


title: 10D01CSF


title: 16D07CSF


title: 10D15CSF


title: 44D05BLO


title: 36D07BLO


title: 12D03BLO


title: 01D05CSF


title: 1D04BLO


title: 36D05BLO2


title: 13D04BLO


title: 44D07CSF


title: 11D02CSF


title: 32D00CSF


title: 17D14BLO


title: 02D05CSF


title: 14D05BLO


title: 14D07CSF


title: 10D10CSF


title: 41D04CSF


title: 02D14CSF


title: 42D05CSF


title: 35D03BLO


title: 04D07CSF


title: 15D06BLO


title: 34D02CSF


title: 03D01CSF


title: 11D10CSF


title: 16D07BLO


title: 43D06CSF


title: 16D09CSF


title: 13D10BLO


title: 05D08CSF


title: 10D03CSF


title: 30D06CSF2


title: 1D06BLO


title: 17D08BLO


title: 31D01CSF


title: 16D01BLO


title: 11D04CSF


title: 15D08CSF


title: 43D05CSF


title: 20D14CSF


title: 17D07BLO


title: 32D02CSF


title: 32D00BLO


title: 17D02BLO


title: 21D01CSF


title: 33D01BLO


title: 44D06CSF


title: 01D01CSF


title: 33D03CSF


title: 14D10BLO


title: 06D09CSF


title: 13D06CSF


title: 03D08CSF


title: 34D02BLO


title: 2D01BLO


title: 06D08CSF


title: 35D05CSF


title: 02D02CSF


title: 13D05CSF


title: ULMC202_SERUNTR_7


title: 11D10BLO


title: 2D07BLO


title: 34D01BLO


title: 35D02BLO


title: 35D04CSF


title: 3D02BLO


title: 04D04CSF


title: 20D02CSF


title: 30D00CSF


title: 4D03BLO


title: 16D03BLO


title: 14D01CSF


title: 36D03BLO


title: 21D03CSF


title: 5D04BLO


title: 15D07CSF


title: 43D02CSF


title: 05D04CSF


title: 17D04BLO


title: 16D08CSF


title: 31D00CSF


title: 15D02CSF


title: 4D08BLO


title: 44D01CSF


title: 5D09BLO


title: 17D09CSF


title: 44D03CSF


title: 14D06CSF


title: 06D05CSF


title: 12D01CSF


title: 07D06CSF


title: 1D14BLO


title: 32D01CSF


title: 33D02CSF


title: 05D05CSF


title: 10D11CSF


title: 35D04BLO


title: 16D14BLO


title: 15D09CSF


title: 3D04BLO


title: 08D07CSF


title: 13D02CSF


title: 34D03CSF


title: 36D05BLO


title: 14D03CSF


title: 14D01BLO


title: 4D05BLO


title: 17D10BLO


title: 5D06BLO


title: 36D00BLO


title: 15D04CSF


title: 15D02BLO


title: 31D02CSF


title: 15D01BLO


title: 03D02CSF


title: 14D08CSF


title: 6D07BLO


title: 02D10CSF


title: 06D07CSF


title: 32D03CSF


title: 04D03CSF


title: 16D05CSF


title: 6D06BLO


title: 17D03BLO


title: 1D02BLO


title: 16D02BLO


title: 15D10BLO


title: 02D01CSF


title: 2D14BLO


title: 07D08CSF


title: 16D04CSF


title: 04D02CSF


title: 33D04CSF


title: 7D07BLO


title: 43D01CSF


title: 1D01BLO


title: 20D10CSF


title: 34D05CSF


title: 44D02CSF


title: 2D02BLO


title: 35D06CSF


title: 01D02CSF


title: 9D09BLO


title: 03D04CSF


title: 02D03CSF


title: 13D01CSF


title: 04D05CSF


title: 1D10BLO


title: 14D14CSF


title: 05D06CSF


title: 07D14CSF


title: 17D05CSF


title: 13D10CSF


title: 16D04BLO


title: 43D03CSF


title: 36D01CSF


title: 14D02CSF


title: 15D03CSF


title: 17D05BLO


title: 35D00CSF


title: 06D06CSF


title: 2D04BLO


title: 44D04CSF


title: 07D07CSF


title: 12D02CSF


title: 03D10CSF


title: 3D05BLO


title: 13D03CSF


title: 4D04BLO


title: 21D05CSF2


title: 16D10BLO


title: 5D05BLO


title: 09D09CSF


title: 06D01CSF


title: 14D04CSF


title: 4D06BLO


title: 07D02CSF


title: 5D07BLO


title: 35D02CSF


title: 3D00BLO


title: 15D05CSF


title: 36D03CSF


title: 36D01BLO


title: 01D10CSF


title: 6D08BLO


title: 16D06CSF


title: 2D10BLO


title: 17D07CSF


title: 05D02CSF


title: 07D09CSF


title: 7D08BLO


title: 6D14BLO


title: 17D06CSF


title: 06D03CSF


title: 6D02BLO


title: 33D00CSF


title: 14D10CSF


title: 16D14CSF


title: 35D00BLO


title: 07D04CSF


title: 34D01CSF


title: 15D06BLO2


title: 17D01CSF


title: 7D03BLO


title: 7D09BLO


title: 8D04BLO


title: 15D10BLO2


title: 08D05CSF


title: 09D05CSF


title: 9D05BLO


title: 35D01CSF


title: 34D00CSF


title: 36D02CSF


title: 6D04BLO


title: 06D14CSF


title: 12D04CSF2


title: 16D02CSF


title: 09D06CSF


title: 7D05BLO


title: 06D02CSF


title: 17D03CSF


title: 9D07BLO


title: 14D03BLO2


title: 35D03CSF


title: 07D03CSF


title: 03D00CSF


title: 17D14CSF


title: 3D01BLO


title: 08D04CSF


title: 08D03CSF


title: 4D02BLO


title: 6D10BLO


title: 15D01CSF


title: 17D01CSF2


title: 06D04CSF


title: 20D06CSF2


title: 4D10BLO


title: 17D01BLO


title: 07D05CSF


title: 05D03CSF


title: 16D01CSF


title: 17D02CSF


title: 8D06BLO


title: 08D06CSF


title: 16D10CSF


title: 8D05BLO


title: 06D10CSF


title: 9D06BLO


title: 6D05BLO


title: 09D02CSF2


title: 5D03BLO


title: 16D03CSF


title: 17D04CSF


title: 5D02BLO


title: 7D06BLO


title: 09D01CSF


title: 8D07BLO


title: 7D04BLO


title: 6D03BLO


title: 9D08BLO


title: 09D03CSF


title: 7D01BLO


title: 9D02BLO


title: 10D09BLO


title: 17D10CSF


title: 5D10BLO


title: 17D04CSF2


title: 8D02BLO


title: 20D07BLO


title: 07D01CSF


title: 15D10CSF


title: 7D14BLO


title: 2D01BLO2


title: 20D09BLO


title: 05D10CSF


title: 30D06BLO


title: 09D02CSF


title: 31D07BLO


title: 6D01BLO


title: 7D02BLO


title: 9D10BLO


title: 08D02CSF


title: 9D04BLO


title: 09D04CSF


title: 8D03BLO


title: 9D03BLO


title: 20D08BLO


title: 41D06BLO


title: 09D10CSF


title: 10D05BLO


title: 21D09BLO


title: 02D03CSF2


title: 13D08BLO


title: 07D10CSF


title: 42D07BLO


title: 11D06BLO


title: 10D07BLO


title: 30D07BLO


title: 7D10BLO


title: 20D05BLO


title: 11D08BLO


title: 20D04BLO


title: 21D05BLO


title: 11D14BLO2


title: 20D08CSF


title: 04D03CSF2


title: 10D13BLO


title: 30D02BLO


title: 10D08CSF


title: 08D04CSF2


title: 31D04BLO


title: 10D15BLO


title: 32D05BLO


title: 13D09BLO


title: 11D14BLO


title: 11D07BLO


title: 21D08BLO


title: 35D02BLO2


title: 31D05BLO


title: 10D09CSF


title: 30D04BLO


title: 20D06BLO


title: 33D06BLO


title: 21D09CSF


title: 10D06BLO


title: 11D02BLO


title: 10D08BLO


title: 20D06CSF


title: 10D01BLO


title: 21D07BLO


title: 34D07BLO


title: 42D05BLO


title: 11D09BLO


title: 41D07BLO


title: 21D06BLO


title: 10D03BLO


title: 21D01BLO


title: 43D05BLO


title: 44D06BLO


title: 16D08BLO


title: 15D07BLO


title: 07D07CSF2


title: 09D09CSF2


title: 42D06CSF


title: 41D05CSF


title: 20D14BLO


title: 21D03BLO


title: 11D04BLO


title: 12D04BLO


title: 31D00BLO


title: 20D07CSF


title: 32D06BLO


title: 13D05BLO


title: 42D04BLO


title: 41D03BLO


title: 10D14BLO


title: 21D08CSF


title: 14D06BLO


title: 31D06BLO


title: 20D02BLO


title: 43D07CSF


title: 10D04CSF


title: 31D06CSF


title: 10D16CSF


title: 01D08CSF


title: 17D09BLO


title: 10D16BLO


title: 10D02BLO


title: 1D07BLO


title: 10D11BLO


title: 2D08BLO


title: 20D09CSF


title: 33D02BLO


title: 02D09CSF


title: 42D06BLO


title: 41D07CSF


title: 13D07CSF


title: 15D09BLO


title: 20D04CSF


title: 14D08BLO


title: 41D05BLO


title: 30D06CSF


title: 32D01BLO


title: 10D04BLO


title: 31D02BLO


title: 11D05BLO


title: 10D06CSF


title: 3D09BLO


title: 31D07CSF


title: 30D01CSF


title: 43D07BLO


title: 20D03CSF


title: 11D07CSF


title: 11D03BLO


title: 1D09BLO


title: 34D03BLO


title: 34D03BLO2


title: 20D01BLO


title: 21D04CSF


title: 43D06BLO


title: 14D14BLO


title: 33D04BLO


title: 21D02BLO


title: 13D07BLO


title: 34D05BLO


title: 01D07CSF


title: 13D06BLO


title: 43D01BLO


title: 02D08CSF


title: 13D09CSF


title: 44D07BLO


title: 35D06BLO


title: 44D02BLO


title: 10D10BLO


title: 14D09CSF


title: 10D12CSF


title: 02D07CSF


title: 35D05BLO


title: 20D03BLO


title: 30D01BLO


title: 15D08BLO


title: 13D01BLO


title: 32D03BLO


title: 20D10BLO


title: 36D06BLO


title: 42D03BLO


title: 21D04BLO


title: 41D06CSF


title: 31D04CSF


title: 14D02BLO


title: 42D07CSF


title: 42D02BLO


title: 21D06CSF


title: 16D09BLO


title: 32D03CSF2


title: 14D07BLO


title: 30D00BLO


title: 01D09CSF


title: 15D03BLO


title: 43D03BLO


title: 1D08BLO


title: 32D04CSF


title: 32D02BLO


title: 30D03CSF


title: P22_S02_CSF

extract_protocol:
RNA was isolated using MiRVana Paris (Ambion).
TruSeq Small RNA library prep kit (Illumina) was used. Samples were multiplexed. Strand specificity is non-stranded. Type of starting material is total RNA.

value: Intraventricular Brain Hemorrhage


title: P29_S08_CSF


title: 44D04BLO


title: P22_S01_CSF


title: P33_S01_CSF


title: P23_S01_CSF


title: P10_S02_CSF


title: P17_S01_CSF


title: P04_S02_CSF


title: P04_S01_CSF


title: 31D01BLO


title: 31D03CSF


title: P05_S01_CSF


title: P10_S05_CSF


title: P08_S06_CSF


title: 10D05CSF


title: P28_S04_CSF


title: 21D07CSF


title: P38_S01_CSF


title: P39_S01_CSF


title: P28_S05_CSF


title: P11_S01_CSF


title: P27_S01_CSF


title: P08_S01_CSF


title: P29_S03_CSF


title: P26_S01_CSF


title: P20_S02_CSF


title: P10_S01_CSF


title: P29_S10_CSF


title: P28_S03_CSF


title: P15_S01_CSF


title: P05_S07_CSF


title: P14_S01_CSF


title: P19_S02_CSF


title: P02_S02_CSF


title: P29_S02_CSF


title: P05_S04_CSF


title: P03_S01_CSF


title: P20_S01_CSF


title: P32_S01_CSF


title: P29_S04_CSF


title: P29_S07_CSF


title: P19_S01_CSF


title: P02_S01_CSF


title: P36_S01_CSF


title: P10_S04_CSF


title: P18_S01_CSF


title: P10_S03_CSF


title: P05_S03_CSF


title: P05_S02_CSF


title: P09_S03_CSF


title: P07_S01_CSF


title: P10_S09_CSF


title: P09_S04_CSF


title: P24_S01_CSF


title: P06_S01_CSF


title: HeLa Non Sync Cell 5C R1T1

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description: MO5CM-Hela-NS-C-combined__5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced__15000__6.balanced.matrix

data_processing:
Library strategy: 5C-Seq
Mapping onto custom build genome based on 5C primer.  For more details see supplemental methods of Oomen et al, BioRxiv 2018 (https://www.biorxiv.org/content/early/2018/07/11/365866) and https://github.com/dekkerlab/cworld-dekker
Binning and balancing to obtain contact matrix files. For more details see supplemental methods of Oomen et al, BioRxiv 2018 (https://www.biorxiv.org/content/early/2018/07/11/365866) and https://github.com/dekkerlab/cworld-dekker
Genome_build: Custom built based on 5C primers, originally used in Hnisz et al, Science 2016
Supplementary_files_format_and_content: Insulation score calling and heatmap generation calling using cWorld pipeline (cworlds-dekker : https://github.com/dekkerlab/cworld-dekker). For more details see supplemental methods of Oomen et al, BioRxiv 2018 (https://www.biorxiv.org/content/early/2018/07/11/365866)

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 cells were cultured glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin

extract_protocol:
For each 5C library, 25 million cells or the equivalent in mitotic chromatin clusters from HeLa S3  were used as input. Cells  were crosslinked for 10 minutes at room temperature in a final concentration of 1%  formaldehyde. Glycine was added to quench crosslinking and pellets were frozen at -80C until 5C library generation
5C was performed  according to published protocols (Dostie et al., 2006; Hnisz et al., 2016).

treatment_protocol: Cells were harvested as non-synchrous without treatment or arrested in mitosis using 24hr Thymidine treatment and 12hr Nocodazole (mitotic cells). Mitotic chromatin was purified from mitotic cells using percoll gradients.

tag: enzyme

value: HindIII

tag: cell type

value: Human adenocarcinoma cells

tag: cell line


title: HeLa Non sync Cell 5C R2T1


title: HeLa Mitotic Cell 5C R1T1

description: MO5CM-Hela-M-Cl-combined__5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced__15000__6.balanced.matrix


title: HeLa Mitotic Cell 5C R2T1

description: MO5CM-Hela-M-C-combined__5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced__15000__6.balanced.matrix


title: P27_S03_CSF

value: MiRVana Paris (Ambion)


title: P13_S01_CSF


title: HeLa Mitotic Chromatin 5C R2T1


title: P29_S05_CSF


title: P12_S01_CSF


title: P37_S01_CSF