title: S185_266

status: Public on Jul 31 2020

type: SRA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38 Ensemble release 100)  genomic reference with STAR (v2.7.3a) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: GRCh38 Ensemble release 100: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.100.gtf
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Total RNA was purified using the Qiagen miRNeasy Mini Kit
cDNA was generated using the Clontech SMARTseq v4 Ultra Low Input kit and libraries were prepared for sequencing using the Illumina NexteraXT DNA kit

tag: gender

value: F

tag: disease state

value: Healthy

tag: severity

tag: geographical location

value: Atlanta, GA, USA

tag: cell type

value: PBMC


title: S186_SHXA14

molecule: total RNA

organism: Homo sapiens

value: M


title: ovary-tumor-1 [ID1011]

status: Public on Aug 20 2020

type: RNA

city: Kensington

first: Susan

last: Ramus

state: NSW

address: High Street

department: School of Women's and Children's Health

country: Australia

institute: UNSW Sydney

description:
ID1011
FFPE-derived total RNA

hyb_protocol: 500 ng of total RNA was mixed with hybridization buffer and hybridized at 65°C overnight.

scan_protocol: The sample, wash reagents and imaging cartridges were processed on the nCounter Prep Station and imaged on the Digital Analyzer.

data_processing: We used batch effects adjustment, quality control, and normalisation techniques that are applied one patient at a time, single-patient processing [Talhouk et al. 2016]. After quality control assessments, the count data were log2 transformed and centered by the arithmetic mean of the selected housekeeping genes, RPL19, ACTB, PGK1, SDHA, and POLR1B.

label: barcode

label_protocol: Proprietary 'barcode' for each target sequence.

extract_protocol: RNA was extracted from FFPE tumor samples using the Qiagen miRNeasy FFPE kit.

tag: diagnosis

value: High-grade serous ovarian cancer (HGSOC)

tag: Sex

value: Female

tag: tissue

value: presumed adnexal

tag: status

tag: Stage

tag: signature

tag: age

tag: site

value: NCO


title: ovary-tumor-1 [ID1007]

description:
ID1007
FFPE-derived total RNA

value: adnexal

value: DOV


title: S183_263


title: S184_SHXA18


title: ovary-tumor-1 [ID1002]

description:
ID1002
FFPE-derived total RNA

value: TRI


title: other-tumor-1 [ID1001]

description:
ID1001
FFPE-derived total RNA

value: peritoneal

value: AOC


title: S182_SHXA10


title: S071_280


title: 2G

status: Public on Aug 01 2020

city: chapel hill

first: Seth

last: Weir

address: 115 mason farm rd

institute: UNC Chapel Hill

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Genechip Mouse Gene 2.1 ST arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with partek Genomics Suite version using RMA normalization method.

label: biotin

organism: Mus musculus

source_name: G-Smo medulloblastoma

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

growth_protocol: pups raised frm birth to P15 then tumors harvested

extract_protocol: total RNA extracted using Qiagen kit (QIAGEN, cat#74104) according to the manufacturers protocol.

treatment_protocol: Mice were decapitated under anesthesia and medullblastomas were rapidly dissected free and snap frozen in a dry ice-ethanol bath. Frozen tisue was homogenized while frozen and processed for RNAextraction. Samples 1-12 no treatment, samples 13-24 10gy x-ray radiation 2 hr prior to harvesting tumors.

value: freshly harvested tumor

tag: strain

tag: genotype

value: G-Smo

tag: developmental stage

tag: treatment


title: S070_279

tag: gender


title: 2M

source_name: M-Smo medulloblastoma

value: M-Smo


title: 6M


title: 3M


title: 5M


title: 5G


title: 4M


title: 1M


title: S069_273

value: F

tag: disease state


title: S067_270

value: Healthy

tag: severity


title: S066_265

tag: geographical location

value: Atlanta, GA, USA


title: S068_272

tag: cell type

value: PBMC


title: 6G


title: 3G


title: 1G


title: S065_261


title: S064_260

value: M


title: S063_259


title: S062_258


title: S061_257


title: S180_nCoV034EUHM-Draw-1

value: Moderate


title: S181_255


title: S179_nCoV033EUHM-Draw-1

value: Severe


title: S178_nCoV028EUHM-Draw-1


title: S177_nCoV025EUHM-Draw-2

value: ICU


title: S157_nCOV0029EUHM


title: S176_nCoV025EUHM-Draw-1


title: S175_nCoV024EUHM-Draw-2


title: S153_nCoV007EUHM-Draw-1


title: S147_nCoV001EUHM-Draw-1


title: S149_nCoV002EUHM-Draw-2


title: S154_nCoV0010EUHM-Draw-1


title: S152_nCoV006EUHM-Draw-1


title: S150_nCoV003EUHM-Draw-1


title: S151_nCoV004EUHM-Draw-1


title: S155_nCOV021EUHM


title: S145_nCOV001_C

value: Convalescent


title: Baboon Endometrium Individual 3

status: Public on Jul 28 2020

city: Chicago

first: Katelyn

last: Mika

email: kmmika12@gmail.com, kmmika@uchicago.edu

state: IL

address: 1025 E. 57th Street

department: Organismal Biology; Genetic Medicine

institute: University of Chicago

data_processing:
Kallisto version 0.42.4 was used to pseudo-align the raw RNA-Seq reads to genomes
'kallisto index' with default parameters was used to build the genome index for each species
'kallisto quant' with the added parameters of 100 bootstraps, bias correction, and a flag for single end data with a !Sample_data_processing = fragment length of 50 and a standard deviation of 1 were used to quantify expression for each sample
Genome_build: Baboon (PapAnu2.0); Hamster (MesAur1.0); Bat (MyoLuc2.0); Squirrel (SpeTri2.0); Mouse (GRCm38)
Supplementary_files_format_and_content: Kallisto gene counts

organism: Papio anubis

source_name: Pregnant Baboon

extract_protocol:
Total RNA was extracted from the remaining tissue using the RNeasy Plus Mini Kit
Endometrial tissue samples from the pregnant uteri of baboon (x3), hamster (x3), bat (x2), and squirrel (x2) were dissected and mailed to the University of Chicago in RNA-Later. These samples were further dissected to remove myometrium, luminal epithelium, and extra-embryonic tissues, and then washed 3x in ice cold PBS to remove unattached cell debris and red blood cells. Total RNA was extracted from the remaining tissue using the RNeasy Plus Mini Kit (74134, QIAGEN) per manufacturer’s instructions. RNA concentrations were determined by Nanodrop 2000 (Thermo Scientific). A total amount of 2.5μg of total RNA per sample was submitted to the University of Chicago Genomics Facility for Illumina Next Gen RNA sequencing. Quality was assessed with the Bioanalyzer 2100 (Agilent). A total RNA library was generated using the TruSEQ stranded mRNA with RiboZero depletion (Illumina) for each sample. The samples were fitted with one of six different adapters with a different 6-base barcode for multiplexing. Completed libraries were run on an Illumina HiSEQ2500 with v4 chemistry on 2 replicate lanes for hamster and 1 lane for other species, of an 8 lane flow cell, generating 30-50 million 50bp single-end reads per sample.

value: endometrium


title: Hamster Endometrium Individual 2 Replicate 2

organism: Mesocricetus auratus

source_name: Pregnant Hamster


title: Hamster Endometrium Individual 1 Replicate 2


title: Baboon Endometrium Individual 1


title: Hamster Endometrium Individual 1 Replicate 1


title: Hamster Endometrium Individual 3 Replicate 1


title: Hamster Endometrium Individual 2 Replicate 1


title: Squirrel Endometrium Individual 1

organism: Ictidomys tridecemlineatus

source_name: Pregnant Squirrel


title: Bat Endometrium Individual 1

organism: Carollia perspicillata

source_name: Pregnant Bat


title: Squirrel Endometrium Individual 2


title: Bat Endometrium Individual 2


title: Ets1_shEts1_2-1

status: Public on Jul 07 2020

city: Ann Arbor

first: Mark

middle: Yat-fung

last: Chiang

state: MI

address: 109 Zina Pitcher Place

department: Internal Medicine/Heme-onc

institute: University of Michigan

library_source: genomic

data_processing:
ChIP-Seq: Reads were aligned to the hg19 genome assembly using bwa-aln and bwa-sampe (bwa version 0.7.12)
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: Data were filtered to remove PCR duplicates and reads mapping to >2 genomic sites. Then bigwig display files were generated with deepTools bamCoverage and UCSC wigToBigWig, and bed peak files were generated with Homer findPeaks (“style -factor” for transcription factors and “style -histone” for H3K27ac).

molecule: genomic DNA

source_name: THP-6 T-ALL cell line

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Cells were crosslinked for most samples by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. For Ets1,  Cells were crosslinked with 2 mM DSG and 1% formaldehyde. For H3K27ac, cells were crosslinked with 1% formaldehyde at room temperature. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples, 1:8diluted sonicated chromatin (whole cell extract; wce), was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced (38 bp x 2) on illumina NextSeq.

treatment_protocol: THP-6 T-ALL cells were lentivirally transduced with pLKO.1-type shRNA for 2 days  and then selected with puromycin for 2 days prior to harvesting.

tag: cell line

value: THP-6 T-ALLs

tag: transduction

value: Ets1-silencing shRNA

tag: disease

value: T lymphoblastic leukemia/lymphoma

value: T lymphocyte

tag: antibody

value: ETS1 (Santa Cruz sc-350)


title: Ets1_shEts1_2-2


title: Ets1_shEts1_3-2


title: Ets1_shEts1_3-1


title: S156_nCOV024EUHM-Draw-1


title: Ets1_shControl-2

value: non-silencing shRNA


title: Baboon Endometrium Individual 2

tag: tissue


title: Hamster Endometrium Individual 3 Replicate 2


title: 4G

value: freshly harvested tumor

value: G-Smo


title: PHH_D3_HCV6h

status: Public on Jul 02 2020

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

country: Germany

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

description:
processed data file: Expression Browser PHH 6hrs.xlsx
HCVJc1MOI1_E269-RNA4_R1

data_processing:
Transcriptomic analyses were performed using CLC Genomics Workbench (Qiagen, Aarhaus)
Generated Fastq files were mapped against the hg19 human reference genome with annotated gene and mRNA tracks.
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx documents include total counts & RPKM values for each gene and each condition and additionally, fold change and statistical values

extract_protocol:
PHH were lysed in 1 ml Trizol reagent (Invitrogen) and lysates stored at -80°C until processing. We extracted the total RNA and DNA according to the manufacturer's instructions and added 10-20 µg glycogen per sample to facilitate RNA precipitation. Total RNA of other cells than PHH was extracted from living cells scrapped in RA1 Lysis buffer 1% beta Mercaptoethanol and isolated using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer's instructions.
RNA sequencing library generated with ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Illumina)

tag: subject status

value: donor undergoing partial hepatectomy

tag: phh donor

value: primary human hepatocytes (PHH)

value: infected


title: PHH_D1_mock72h

description:
processed data file: Expression Browser PHH 72hrs.xlsx
E313_8_Mock72h

value: mock control, conditioned medium


title: PHH_D2_mock6h

description:
processed data file: Expression Browser PHH 6hrs.xlsx
E321_RNA6Mockinfection6h_CTCAGA_L005


title: PHH_D2_HCV6h

description:
processed data file: Expression Browser PHH 6hrs.xlsx
E321_RNA5HCVinfection6h_CTATAC_L005


title: PHH_D2_mock72h

description:
processed data file: Expression Browser PHH 72hrs.xlsx
E321_RNA8Mockinfection72h_TAATCG_L008


title: PHH_D3_mock72h

description:
processed data file: Expression Browser PHH 72hrs.xlsx
Mockinfection_E269-RNA8_R1


title: PHH_D1_HCV72h

description:
processed data file: Expression Browser PHH 72hrs.xlsx
E313_7_HCV72h


title: PHH_D3_HCV72h

description:
processed data file: Expression Browser PHH 72hrs.xlsx
HCVJc1MOI1_E269-RNA7_R1


title: PHH_D3_mock6h

description:
processed data file: Expression Browser PHH 6hrs.xlsx
Mockinfection_E269-RNA_R1


title: PHH_D2_HCV72h

description:
processed data file: Expression Browser PHH 72hrs.xlsx
E321_RNA7HCVinfection72h_GACGAC_L008


title: PHH_D1_mock6h

description:
processed data file: Expression Browser PHH 6hrs.xlsx
E313_6_Mock6h


title: PHH_D1_HCV6h

description:
processed data file: Expression Browser PHH 6hrs.xlsx
E313_5_HCV6h


title: Huh-7.5_hIRF1_2

description:
processed data file: Expression Browser_EMPTYvsIRF1.xlsx
hIRF1_P11_S31_L003

value: hepatocellular carcinoma cell line

tag: ectopic expression


title: Huh-7.5_HCV2

description:
processed data file: Expression Browser_EMPTYvsHCV.xlsx
19_72hr_empty_HCV_S9_L002


title: Huh-7.5_HCV1

description:
processed data file: Expression Browser_EMPTYvsHCV.xlsx
2b_Empty_HCV_S18_L004


title: Huh-7.5_HCV3

description:
processed data file: Expression Browser_EMPTYvsHCV.xlsx
L470_EMPTYplusHCV_A_S37


title: Huh-7.5_mock3

description:
processed data file: Expression Browser_EMPTYvsHCV.xlsx
Empty_S8_L002

value: mock control


title: Huh-7.5_mock2

description:
processed data file: Expression Browser_EMPTYvsHCV.xlsx
1b_Empty_Un_S17_L003


title: Huh-7.5_mock1

description:
processed data file: Expression Browser_EMPTYvsHCV.xlsx
1a_Empty_Un_S12_L003


title: Gcn5_60sec_ChEC

status: Public on Jul 01 2020

city: Geneva

first: Maria

middle: Jessica

last: Bruzzone

address: 30, quai Ernest-Ansermet

department: Molecular Biology Department

country: Switzerland

institute: Univeristy of Geneva

data_processing:
Library strategy: ChEC-Seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive" through HTSStation (http://htsstation.epfl.ch)
Data were filtered to retain only the mapped reads with at most 5 hits in the reference
The mapped reads were extended by 1 bp only to indicate cut sites
All densities were normalized by total number of reads (in units of 10 millions)
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: cells were grown at 30 degrees in YPAD to OD600=0.6

extract_protocol:
DNA was prepared as described in Kubik S. et al., 2018 (PMID: 29979971 )
Libraries were constructed as described in Kubik S. et al., 2018 (PMID: 29979971 )

treatment_protocol: At OD600 ~0.6, cells were washed and resuspended in a buffer containing 15 mM Tris, pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1× Roche EDTA-free mini protease inhibitors, 1 mM PMSF and 0.1% digitonin and incubated for 5 min at 30°C. CaCl2 was added to the final concentration of 5 mM and reactions were stopped after 10, 30, 60 seconds for Esa1 and Gcn5 ChEC, 60 seconds for Sfp1 ChEC and 20 minutes for free MNase ChEC by adding EGTA to a final concentration of 50 mM.

tag: strain

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 GCN5-3XFLAG-MNase::HIS3


title: Gcn5_30sec_ChEC

tag: genotype


title: Gcn5_10sec_ChEC


title: Esa1_30sec_ChEC

value: W303 mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ESA1-3XFLAG-MNase::HIS3


title: Esa1_60sec_ChEC


title: Esa1_10sec_ChEC


title: Hi-C H1 replicate 6

status: Public on Jun 26 2020

city: Cleveland

first: Xiaoxiao

last: Liu

state: Ohio

address: 10900 Euclid Ave

department: Genetics and Genomes Sciences

institute: Case Western Reserve University

description:
anchor_2_anchor.loop.H1.txt.gz
H1.loops.txt.gz

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. Easy Hi-C reads were mapped to hg19 using BOWTIE. Because nearly all the mappable reads start with HindIII sequence AGCTT, we trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases.
For Hi-C, we focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria. For eHi-C library, the only type of invalid cis- pairs are self-circles with two ends within the same HindIII fragment facing each other
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~335k anchors after short fragments (<5kb) are merged into neighboring anchors. For every anchor, we first count Hi-C/eHi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content, and visibility. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
Genome_build: hg19
Supplementary_files_format_and_content: For each Hi-C and easy Hi-C data set, the fragment-to-fragment frequency are provided in the txt file (columns 3 to 5: observed_reads, expected_reads, and p_value). For each Chip-Seq replicate, peak-calling results are provided in the bed file.

source_name: embroynic stem cells

growth_protocol: Fibroblasts were grown in DMEM medium supplemented with 10% FBS (Hyclone), Glutamax (Thermo Fisher Scientific) and NEAA (Thermo Fisher Scientific) and subcultured at a ratio of 1:3 when they reach 90% confluence. H1 cells were cultured on the hESC-qualified Matrigel (Corning, #354277) coated plates in mTeSR1 medium (StemCell Technologies, #05850). iPS cells were cultured on Matrigel with a daily change of E8 medium and passaged by collagenase. To generate iPSC-derived NPCs, detached iPSC colonies were suspended in embryoid body (EB) medium (DMEM:F12 with 20% KOSR, 2?M dorsomorphin and 2 ?M A 83-01) for 7 days. Floating EBs were attached on Matrigel and cultured in NPC medium (DMEM/F12, N2 supplement, NEAA and 2 uM cyclopamine). After 14 days, neural tube-like rosettes were mechanically picked and dissociated into single NPCs by Accutase. NPCs were maintained as monolayer in NPC medium with medium change every two days. For neuronal differentiation, NPCs were plated on Matrigel and cultured in Neurobasal medium supplemented with 2%B27, 2 mM L-glutamine, 10 ng/ml BDNF and 10 ng/ml GDNF.

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

value: no treat

tag: chip antibody

value: no

tag: restriction enzyme

value: HindIII


title: Hi-C H1 replicate 5

tag: treatment


title: Huh-7.5_hIRF1_1

description:
processed data file: Expression Browser_EMPTYvsIRF1.xlsx
hIRF1_P9_S30_L003


title: Huh-7.5_hIRF1_3

description:
processed data file: Expression Browser_EMPTYvsIRF1.xlsx
hIRF1_S9_L002


title: Hi-C H1 replicate 3


title: Hi-C H1 replicate 4


title: prostate_tissue-L-replicate_RIB0034401

status: Public on Jun 17 2020

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate RP tissue specimen (prostate cancer)

hyb_protocol: We used 1.65 µg of labeled cRNA for hybridization with the custom microarray following manufacturer's instructions.

scan_protocol: After hybridization the arrays were washed according to the manual and scanned using the Agilent G2565CA Microarray Scanner System with Agilent Scan Control Software (Version A851) and following settings for scanning: Profile: AgilentG3_GX_1Color; Channels: Green; Scan Region: Agilent HD (61x 21,6 mm); Resolution: 3 µm double pass; Tiff: 20 bit; Green PMT Gain: 100 %. We extracted the result tables after grid placement using Agilent Feature Extraction Software (Version 11.5.1.1).

data_processing: Three microarray were excluded from further processing due to scratches on array slides (data not included in GEO series). Quality control of remaining arrays (N=255) was performed by checking distribution of ``bright corner'', ``dark corner'' probes, and relative spike-in concentration versus normalized signal. Quality control confirmed high quality of the results and consequently all remaining microarray data were included in the downstream analysis. To retrieve a set of probes mapping to unique genomic positions in hg19 we used BLAT v35 with the parameter -minIdentity=95 allowing to detect probes spanning splice sites. All probes mapping to more than one distinct genomic region were discarded. Normalization between arrays was done by using quantile normalization. In order to reduce the number of univariate t-tests nonspecific filtering was applied as follows: The expression of a probe must be larger than background expression in at least 20 arrays. Background expression was defined by the mean intensity plus three times the standard deviation of negative control spots (Agilent's 3xSLv spots). In addition, a probe must exhibit a nonspecific change of expression, which was assessed by an interquartile range of at least 0.5. Finally, a linear model to detect expression variation between BPH and tumor specimens adjusted for array processing batches was fitted using limma v3.24.15 and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate (FDR) was controlled by Benjamini-Hochberg adjustment.

source_name: prostate

label_protocol: We prepared all samples assembled for expression analysis with the custom microarray using the Agilent Quick Amp Labeling Kit for single color following the manufacturer's instructions. Instead of the Oligo-dT/T7-primer delivered with the Quick Amp Labeling Kit, we used 120 pmol of a random N6/T7 primer synthesized by Metabion (Planegg, Germany) and used 200 ng RNA as input for the labeling procedure. cRNA quantity was checked using a NanoDrop ND-1000 UV-VIS Spectrophotometer, as enlisted in the manufacturer's instructions.

extract_protocol: Stacks of consecutive cryosections were generated from frozen RP tissue samples and immediately transferred to 1ml Qiazol (Qiagen, Hilden, Germany). A pathologist evaluated HE-stained cryosections flanking the stacks concerning tumor and stroma cell content (Supplementary Figure S1). Only PCa tissue stacks, which were flanked on either side by sections containing at least 50% tumor cells underwent RNA isolation. In case of insufficient RNA quantity, we combined multiple tissue stacks with suitable tumor cell content. We isolated total RNA using the miRNeasy Mini Kit on the QIAcube (Qiagen) followed by manual DNase I digestion. After determining the RNA concentration with a NanoDrop 1000 (Peqlab, Erlangen, Germany), we verified the RNA integrity on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). RNA samples with an RNA-Integrity-Number (RIN) of at least six passed for further processing.

tag: risk group

value: L

value: prostate

tag: follow-up time in months

tag: gender

value: male

tag: gleason score

tag: diagnosis

value: prostate cancer


title: prostate_tissue-Ms-replicate_RIB0034497

value: Ms


title: prostate_tissue-Md-replicate_RIB0034485

value: Md


title: prostate_tissue-Ms-replicate_RIB0034818


title: prostate_tissue-H+dt-replicate_RIB0034276

value: H+dt


title: prostate_tissue-L-replicate_RIB0034340


title: prostate_tissue-H+dt-replicate_RIB0034323


title: prostate_tissue-L-replicate_RIB0034779


title: prostate_tissue-H-st-replicate_RIB0034819

value: H-st


title: prostate_tissue-H+st-replicate_RIB0034315

value: H+st


title: prostate_tissue-Ms-replicate_RIB0034372


title: prostate_tissue-V-replicate_RIB0034777

value: V


title: prostate_tissue-V-replicate_RIB0034409


title: prostate_tissue-H+st-replicate_RIB0034794


title: prostate_tissue-L-replicate_RIB0034383


title: prostate_tissue-H+st-replicate_RIB0034830


title: prostate_tissue-H+st-replicate_RIB0034972


title: prostate_tissue-V-replicate_RIB0034227


title: prostate_tissue-L-replicate_RIB0034403


title: prostate_tissue-H-dt-replicate_RIB0034767

value: H-dt


title: prostate_tissue-V-replicate_RIB0034780


title: prostate_tissue-H-dt-replicate_RIB0034239


title: prostate_tissue-L-replicate_RIB0034415


title: prostate_tissue-H-st-replicate_RIB0034864


title: prostate_tissue-H-st-replicate_RIB0034326


title: prostate_tissue-L-replicate_RIB0034826


title: prostate_tissue-H-st-replicate_RIB0034984


title: prostate_tissue-L-replicate_RIB0034886


title: prostate_tissue-L-replicate_RIB0034683


title: prostate_tissue-L-replicate_RIB0034458


title: prostate_tissue-H+st-replicate_RIB0034254


title: prostate_tissue-H+st-replicate_RIB0034479


title: prostate_tissue-V-replicate_RIB0034457


title: prostate_tissue-Ms-replicate_RIB0034964


title: prostate_tissue-V-replicate_RIB0034484


title: prostate_tissue-Ms-replicate_RIB0034459


title: prostate_tissue-V-replicate_RIB0034942


title: prostate_tissue-H-st-replicate_RIB0034882


title: prostate_tissue-V-replicate_RIB0034961


title: prostate_tissue-V-replicate_RIB0034353


title: prostate_tissue-V-replicate_RIB0034976


title: prostate_tissue-Ms-replicate_RIB0034378


title: prostate_tissue-H-st-replicate_RIB0034361


title: prostate_tissue-H+dt-replicate_RIB0034858


title: prostate_tissue-V-replicate_RIB0034959


title: prostate_tissue-H+st-replicate_RIB0034434


title: prostate_tissue-L-replicate_RIB0034904


title: prostate_tissue-Ms-replicate_RIB0034822


title: prostate_tissue-H-dt-replicate_RIB0034986


title: prostate_tissue-V-replicate_RIB0034483


title: prostate_tissue-H+st-replicate_RIB0034878


title: prostate_tissue-H-st-replicate_RIB0034414


title: prostate_tissue-H+st-replicate_RIB0034841


title: prostate_tissue-L-replicate_RIB0034833


title: prostate_tissue-H+dt-replicate_RIB0034733


title: prostate_tissue-H+st-replicate_RIB0034989


title: prostate_tissue-H-st-replicate_RIB0034914


title: prostate_tissue-L-replicate_RIB0034880


title: prostate_tissue-H-st-replicate_RIB0034751


title: prostate_tissue-H-st-replicate_RIB0034776


title: prostate_tissue-Ms-replicate_RIB0034849


title: prostate_tissue-L-replicate_RIB0034462


title: prostate_tissue-V-replicate_RIB0034496


title: prostate_tissue-L-replicate_RIB0034928


title: prostate_tissue-V-replicate_RIB0034957


title: prostate_tissue-V-replicate_RIB0034747


title: prostate_tissue-H+dt-replicate_RIB0034202


title: prostate_tissue-H-st-replicate_RIB0034208


title: prostate_tissue-H-dt-replicate_RIB0034464


title: prostate_tissue-V-replicate_RIB0034470


title: prostate_tissue-H-dt-replicate_RIB0034918


title: prostate_tissue-H-st-replicate_RIB0034423


title: prostate_tissue-H-st-replicate_RIB0034875


title: prostate_tissue-L-replicate_RIB0034500


title: prostate_tissue-H+dt-replicate_RIB0034422


title: prostate_tissue-Md-replicate_RIB0034448


title: prostate_tissue-L-replicate_RIB0034478


title: prostate_tissue-L-replicate_RIB0034486


title: prostate_tissue-Ms-replicate_RIB0034425


title: prostate_tissue-H+st-replicate_RIB0034432


title: prostate_tissue-V-replicate_RIB0034985


title: prostate_tissue-V-replicate_RIB0034939


title: prostate_tissue-Ms-replicate_RIB0034941


title: prostate_tissue-Md-replicate_RIB0034731


title: ovary-tumor-1 [ID1038]

description:
ID1038
FFPE-derived total RNA

value: High-grade serous ovarian cancer (HGSOC)

tag: Sex

value: Female

value: adnexal

tag: status

tag: Stage

tag: signature

tag: age

tag: site

value: DOV


title: prostate_tissue-V-replicate_RIB0034762

tag: tissue


title: prostate_tissue-H-st-replicate_RIB0034471


title: prostate_tissue-H+dt-replicate_RIB0034727


title: prostate_tissue-H+dt-replicate_RIB0034429


title: prostate_tissue-Ms-replicate_RIB0034408


title: prostate_tissue-V-replicate_RIB0034979


title: prostate_tissue-L-replicate_RIB0034489


title: prostate_tissue-H+dt-replicate_RIB0034370


title: prostate_tissue-L-replicate_RIB0034946


title: prostate_tissue-V-replicate_RIB0034998


title: prostate_tissue-H-dt-replicate_RIB0034491


title: prostate_tissue-V-replicate_RIB0034711


title: prostate_tissue-Ms-replicate_RIB0034759


title: prostate_tissue-H+st-replicate_RIB0034303


title: prostate_tissue-L-replicate_RIB0034954


title: prostate_tissue-H+st-replicate_RIB0034736


title: prostate_tissue-H+st-replicate_RIB0034783


title: prostate_tissue-Ms-replicate_RIB0034702


title: prostate_tissue-H+st-replicate_RIB0034233


title: prostate_tissue-Ms-replicate_RIB0034772


title: prostate_tissue-L-replicate_RIB0034271


title: prostate_tissue-V-replicate_RIB0034282


title: prostate_tissue-H-st-replicate_RIB0034342


title: prostate_tissue-V-replicate_RIB0034944


title: prostate_tissue-L-replicate_RIB0034269


title: prostate_tissue-V-replicate_RIB0034729


title: prostate_tissue-L-replicate_RIB0034258


title: prostate_tissue-H+dt-replicate_RIB0034927


title: prostate_tissue-V-replicate_RIB0034265


title: prostate_tissue-L-replicate_RIB0034812


title: prostate_tissue-L-replicate_RIB0034274


title: prostate_tissue-L-replicate_RIB0034244


title: prostate_tissue-L-replicate_RIB0034242


title: prostate_tissue-V-replicate_RIB0034223


title: prostate_tissue-L-replicate_RIB0034312


title: prostate_tissue-H-st-replicate_RIB0034224


title: prostate_tissue-L-replicate_RIB0034373


title: prostate_tissue-Ms-replicate_RIB0034214


title: prostate_tissue-H+st-replicate_RIB0034388


title: prostate_tissue-H+dt-replicate_RIB0034827


title: prostate_tissue-V-replicate_RIB0034821


title: prostate_tissue-H-dt-replicate_RIB0034469


title: prostate_tissue-V-replicate_RIB0034321


title: prostate_tissue-V-replicate_RIB0034392


title: prostate_tissue-H+st-replicate_RIB0034450


title: prostate_tissue-H-st-replicate_RIB0034289


title: prostate_tissue-L-replicate_RIB0034359


title: prostate_tissue-V-replicate_RIB0034360


title: prostate_tissue-H-st-replicate_RIB0034455


title: prostate_tissue-L-replicate_RIB0034356


title: prostate_tissue-V-replicate_RIB0034390


title: prostate_tissue-V-replicate_RIB0034204


title: prostate_tissue-L-replicate_RIB0034428


title: prostate_tissue-H-dt-replicate_RIB0034385


title: prostate_tissue-H+st-replicate_RIB0034921


title: prostate_tissue-H+dt-replicate_RIB0034938


title: prostate_tissue-L-replicate_RIB0034320


title: prostate_tissue-V-replicate_RIB0034475


title: prostate_tissue-H-st-replicate_RIB0034966


title: prostate_tissue-H+dt-replicate_RIB0034377


title: prostate_tissue-Ms-replicate_RIB0034480


title: prostate_tissue-H-st-replicate_RIB0034477


title: A375-Input-H3K27me3-shU7-EZH2

status: Public on May 01 2020

city: Beijing

first: Lin

last: Shan

address: 10 You’anmen Outer West 1st Street

country: China

institute: Capital Medical University

data_processing:
ChIP-seq reads quality control performed using FastQC v0.11.5 and  cutadapt v1.8.3
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2
ChIP-seq peaks were called using macs2
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq  bw files were generated using bamCoverage

source_name: A375 cells

growth_protocol: A375 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Approximately 5X107 cells were used for each ChIP-seq assay. The chromatin DNA precipitated by polyclonal antibodies against USP7, EZH2 or H3K27me3. The DNA samples were purified with the Qiagen PCR purification kit before in-depth whole genome DNA sequencing was performed by BGI (Wu Han, China).
The raw sequencing image data were examined by the Illumina analysis pipeline, aligned to the unmasked human reference genome (hg19) using Bowtie2, and further analyzed by MACS (Model-based Analysis for ChIP-seq).

treatment_protocol: Infection with EZH2 or shRNA against USP7 were performed using polybrene reagent according to the manufacturer's insturctions.

tag: cell type

value: knockdown of USP7 combined with EZH2 overexpression

tag: antibodies


title: A375-H3K27me3-ChIP-seq-shU7

value: knockdown of USP7


title: A375-H3K27me3-ChIP-seq-shU7-EZH2


title: prostate_tissue-H+dt-replicate_RIB0034913


title: A375-Input-H3K27me3-shU7


title: A375-Input-H3K27me3-Control

value: untreated


title: prostate_tissue-Ms-replicate_RIB0034905

value: prostate


title: prostate_tissue-Ms-replicate_RIB0034983

value: male


title: A375-H3K27me3-ChIP-seq-Control


title: A375-Input-EZH2


title: A375-Input-USP7


title: A375-EZH2-ChIP-seq


title: A375-USP7-ChIP-seq


title: prostate_tissue-L-replicate_RIB0034956

value: L

value: prostate cancer


title: A38N

status: Public on Apr 15 2020

city: Chengdu

first: Qian

last: Bu

address: No.24 South Section 1, Yihuan Road

department: Department of food and Technology

institute: Sichuan University

description: Read 2 fastq file was not provided

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: hg19

source_name: Brain tissue

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Cystic hemangioblastoma


title: prostate_tissue-L-replicate_RIB0034900


title: prostate_tissue-Ms-replicate_RIB0034207

value: Ms


title: non_int_rep3

status: Public on Mar 20 2020

city: Oklahoma

first: David

middle: J

last: Forsthoefel

state: OK

address: 825 NE 13th St

department: Genes and Human Disease Research Program

institute: Oklahoma Medical Research Foundation

description: laser captured tissue

data_processing:
Basecalling: Demultiplexing:
Adapters and low quality reads were trimmed from fastq sequence files with BBDuk (https://sourceforge.net/projects/bbmap/) using Lexogen data analysis recommendations (https://www.lexogen.com/quantseq-data-analysis/): k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20.
Sequence quality was assessed before and after trimming using FastQC.
Reads were mapped to the dd_Smed_v6 transcriptome (restricted to 28,069 unique transcripts) using Bowtie2 (v2.3.1) with default settings.
Resulting SAM files were converted to BAM files, sorted, and indexed using Samtools (v1.3).
Raw read counts per transcript were then generated for each BAM file using the “idxtats” command in Samtools.
The resulting read counts matrix was imported into R, then analyzed in edgeR v3.8.6. Data were normalized with the trimmed mean of M-values (TMM) method, and differentially expressed genes were identified using the generalized linear models (GLM) approach.
Genome_build: Dresden S. mediterranea transcriptome dd_Smed_v6 (http://planmine.mpi-cbg.de/) (Brandl et al, Nucleic Acids Res 2016)
Supplementary_files_format_and_content: Processed data are in two tab-delimited .txt files. Readcounts includes geneID, length, and readcounts. Processed data includes geneID, length, log2 Fold Changes, logCPM, likelihood ratio (LR), P value, and FDR-adjusted P value for medial/lateral intestine vs. non-intestine, plus CPM, RPKM and TPM for all samples.

organism: Schmidtea mediterranea

source_name: Whole animal

growth_protocol: Asexual Schmidtea mediterranea (clonal line CIW4) were maintained in 0.5 g/L Instant Ocean salts with 0.0167 g/L sodium bicarbonate dissolved in Type I water, and fed with beef liver paste. For all experiments, planarians were starved seven days prior to fixation. For LCM, planarians were 6-9 mm in length.

extract_protocol:
Frozen, stained PEN slides were warmed to room temperature in 100% ethanol to maintain RNAse inactivation during thawing, then air dried for 2-3 minutes. Tissue was captured using a Leica LMD7 laser microdissection microscope at 10X magnification using the following parameters: Power-30; Aperture-20; Speed-5; Specimen Balance-1; Head Current-100%; Pulse Frequency-392 Hz. Regions were dissected into empty RNAse-free 0.5 ml microcentrifuge caps. After capture, 20 µl Buffer XB (Arcturus PicoPure RNA Isolation Kit) was added to captured tissue, then tubes were immediately frozen on dry ice and stored at -80°C prior to RNA extraction. Total RNA was extracted using the Arcturus PicoPure RNA Isolation Kit, quantified using a Denovix UV Spectrophotometer, and analyzed using Agilent HS RNA ScreenTape on an Agilent TapeStation 2200.
Libraries were generated using the Lexogen Quantseq 3’ mRNA Library Prep Kit according to the manufacturer’s protocol, with 5 ng total RNA input for each sample. Briefly, first-strand cDNA was generated using 5’-tagged poly-T oligomer primers. Following RNase digestion, second strand cDNA was generated using 5’-tagged random primers. A subsequent PCR step with additional primers added the complete adapter sequence to the initial 5’ tags, added unique indices for demultiplexing of samples, and amplified the library. Final libraries for each sample were assayed on the Agilent Tapestation for appropriate size and quantity.

treatment_protocol: Planarians were relaxed in 0.66 M MgCl2 for 1 minute, fixed in methacarn for 10 min at room temperature, then rinsed 3 times in methanol. After rehydration, samples were incubated in sucrose/PBS (5%, 15%, 30%), mounted and frozen in OCT medium, and cryosectioned at 20 µm thickness onto PEN membrane slides. Slides were quickly stained in alcoholic Eosin Y (5 min total), then stored on dry ice prior to laser capture the same day.

tag: strain

value: clonal line CIW4

value: non-intestinal tissue (anterior)

tag: developmental stage

value: uninjured adult


title: non_int_rep4

description: laser captured tissue


title: non_int_rep2

description: laser captured tissue


title: prostate_tissue-V-replicate_RIB0034916

value: V


title: prostate_tissue-V-replicate_RIB0034299


title: non_int_rep1

description: laser captured tissue


title: prostate_tissue-Ms-replicate_RIB0034306


title: lateral_int_rep4

description: laser captured tissue

value: lateral intestine (anterior)


title: prostate_tissue-L-replicate_RIB0034798


title: prostate_tissue-V-replicate_RIB0034226


title: prostate_tissue-V-replicate_RIB0034810


title: lateral_int_rep3

description: laser captured tissue


title: prostate_tissue-L-replicate_RIB0034756


title: lateral_int_rep1

description: laser captured tissue


title: medial_int_rep4

description: laser captured tissue

value: medial intestine (anterior)


title: prostate_tissue-H+st-replicate_RIB0034235

value: H+st


title: 4C_P0_cortex_HS7_HS5-1del_rep2

status: Public on Mar 06 2020

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Reads were aligned to the reference mouse genome (NCBI37/mm9) or Homo sapien genome(UCSC hg19) using the Bowtie program (version 1.2.2)
File format is  transformed to BAM using samtools version 1.9
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: zipped bedGraph files include RPM values for each Sample

source_name: cortex neuron

extract_protocol:
P0 mouse brain was dissected, and the tissue from cerebral cortex was digested with 0.013% of collagenase in Neurobasal Medium (Gibco) at 37℃ for 3 min. The collagenase was neutralized by adding excess amount of Neurobasal Medium. Single-cell suspension was made by gentle pipetting, and then filtered through 100-μm cell strainers (BD Biosciences). For HEC-1-B cells, trypsin was added to the culture dish and the single cells were suspended in the culture medium. Single cells were then picked under the microscope by using a micro capillary pipette into the thin-walled PCR tube containing 2 µl of cell lysis buffer, 1 µl of oligo-dT primer and 1 µl of dNTP mix.
The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions.  The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).
4C-seq

tag: line

tag: genotype


title: lateral_int_rep2

description: laser captured tissue


title: prostate_tissue-V-replicate_RIB0034387

tag: risk group

tag: follow-up time in months


title: medial_int_rep1

description: laser captured tissue


title: 4C_P0_cortex_HS7_HS5-1inv_rep2


title: prostate_tissue-V-replicate_RIB0034297

tag: gender

tag: gleason score


title: 4C_P0_cortex_HS7_HS5-1inv_rep1

value: HS5-1binv -/-


title: 4C_P0_cortex_b4_HS5-1inv_rep1


title: 4C_P0_cortex_b4_HS5-1del_rep2


title: 4C_P0_cortex_b4_HS5-1inv_rep2


title: 4C_P0_cortex_b4_HS5-1del_rep1


title: 4C_P0_cortex_b4_HS5-1binv_rep1


title: 4C_P0_cortex_b4_HS5-1bdel_rep2

value: HS5-1bdel -/-


title: 4C_P0_cortex_b4_HS5-1bdel_rep1


title: 4C_P0_cortex_b4_HS5-1adel_rep2

value: HS5-1adel -/-


title: 4C_P0_cortex_HS7_HS5-1del_rep1


title: 4C_P0_cortex_b3_HS5-1inv_rep2


title: 4C_P0_cortex_b3_HS5-1del_rep1


title: 4C_P0_cortex_ac1_WT_rep2

value: WT


title: 4C_P0_cortex_b3_HS5-1del_rep2


title: 4C_P0_cortex_b3_HS5-1inv_rep1


title: 4C_P0_cortex_b3_HS5-1binv_rep2


title: prostate_tissue-L-replicate_RIB0034951

value: prostate

tag: diagnosis


title: 4C_P0_cortex_b4_HS5-1binv_rep2


title: 4C_P0_cortex_ac1_HS5-1inv_rep1


title: 4C_P0_cortex_ac1_HS5-1del_rep1


title: 4C_P0_cortex_ac1_HS5-1del_rep2


title: prostate_tissue-L-replicate_RIB0034936

value: male


title: 4C_P0_cortex_ac1_HS5-1bdel_rep2


title: 4C_P0_cortex_ac1_HS5-1bdel_rep1


title: 4C_P0_cortex_a12_WT_rep2


title: 4C_P0_cortex_a12_WT_rep1


title: 4C_P0_cortex_ac1_WT_rep1


title: 4C_P0_cortex_a12_HS5-1inv_rep1


title: 4C_P0_cortex_a12_HS5-1del_rep2


title: 4C_P0_cortex_ac1_HS5-1inv_rep2


title: 4C_P0_cortex_a12_HS5-1adel_rep2


title: 4C_P0_cortex_ac1_HS5-1adel_rep1


title: 4C_P0_cortex_a12_HS5-1del_rep1


title: 4C_P0_cortex_b3_HS5-1binv_rep1


title: 4C_P0_cortex_a12_HS5-1bdel_rep2


title: 4C_P0_cortex_a12_HS5-1bdel_rep1


title: 4C_P0_cortex_ac1_HS5-1adel_rep2


title: 4C_P0_cortex_a12_HS5-1adel_rep1


title: 4C_P0_cortex_a9_WT_rep2


title: 4C_P0_cortex_a9_WT_rep1


title: 4C_P0_cortex_a12_HS5-1inv_rep2


title: 4C_P0_cortex_b4_HS5-1adel_rep1


title: 4C_P0_cortex_a9_HS5-1inv_rep2


title: 4C_P0_cortex_a9_HS5-1inv_rep1


title: 4C_P0_cortex_a9_HS5-1del_rep1


title: 4C_P0_cortex_a9_HS5-1bdel_rep2


title: 4C_P0_cortex_a9_HS5-1bdel_rep1


title: 4C_P0_cortex_a9_HS5-1del_rep2


title: 4C_P0_cortex_a4_WT_rep2


title: 4C_P0_cortex_a4_WT_rep1


title: 4C_P0_cortex_a4_HS5-1inv_rep2


title: 4C_P0_cortex_a4_HS5-1del_rep2


title: 4C_P0_cortex_a4_HS5-1inv_rep1


title: 4C_P0_cortex_a4_HS5-1del_rep1


title: 4C_P0_cortex_a4_HS5-1bdel_rep1


title: 4C_P0_cortex_a4_HS5-1adel_rep2


title: 4C_P0_cortex_a4_HS5-1adel_rep1


title: Regen_56 DPA_scRNA-seq

status: Public on Nov 15 2019

city: Toronto

first: Freda

middle: D

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

country: Canada

institute: The Hospital For Sick Children

data_processing:
FASTQ sequencing reads were processed, aligned to the mouse genome (mm10) and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite.
The number of cell barcodes per sample was identified by calculating the cumulative fraction of reads attributable to each individual cell barcode and arranging these in decreasing order.
Genome_build: mm10
Supplementary_files_format_and_content: The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.

source_name: Adult regenerated digit tip

extract_protocol:
Tissue was dissected from the region of the digit/limb as indicated in the source name, at the specific timepoint indicated in the sample title. Freshly dissected tissue was digested in Liberase (280ug/mL) at 37°C for 1 - 4hr, with constant aggitation. Cells were mechanically dissociated with a small-bore-hole glass pipette, filtered through a 20um cell strainer and pelleted by centrifugation at 1000 rpm for 5 min. The cell pellet was then washed in 1X HBSS and cells were counted with a haemocytometer and pelleted again by centrifugation at 1000 rpm for 5 min. The cell pellet was re-suspended in a solution containing 0.04% BSA in 1X HBSS at a concentration of 500-700 cells/ul, prior to collection of single cell transcriptomes.
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit.

value: Adult regenerated digit tip

tag: regeneration time point

value: 56 Days

tag: number of digits

value: 10 - 12 Weeks

tag: time spent in enzymatic digestion


title: control

status: Public on Jan 08 2020

city: Oklahoma City

first: Rafal

last: Donczew

department: Cell Cycle and Cancer Biology

description: Library strategy: ChEC-Seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

growth_protocol: 30 degrees in synthetic medium to mid-log phase

extract_protocol:
ChEC-seq was performed as previously described (Grünberg et al., 2016; PMID: 27797823; Zentner et al., 2015; PMID: 26490019) with following modifications. The final calcium concentration in the reaction mixture was 0.2 mM (2 mM in the original protocol) and MNase digestion was done for 5 min for all collected samples. Stop buffer was supplemented with D. melanogaster MNase-digested DNA (1 ng/ml stock concentration) in the amount calculated based on S. cerevisiae culture A600 measurement (volume = A600 x 8 ul).
Sequencing libraries were prepared similarly as described (Warfield et al., 2017; PMID: 28918900) with several modifications. 1/6 vol of the final ChEC DNA sample was used as an input. Final adapter concentration during ligation was 6.5 nM. Following ligation, two-step cleanup was performed using 0.25X vol AMPure XP reagent in the first step and 1.1X vol in the second step. 18 cycles were used for library amplification.

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 [P_Bdf2-3xFlag-Mnase HIS3]::BDF2


title: 4C_P0_cortex_a9_HS5-1adel_rep2

tag: age


title: 4C_P0_cortex_a9_HS5-1adel_rep1


title: AG15486_HDAC2_K562_ChIP

status: Public on Feb 17 2020

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
Basecalling, RTA v1.13
Alignments to GRCh38, BWA v0.7.12
Read processing, Samtools v1.2
Read density, Bedops v2.4.15
MAC2 FDR 5% combined replicate peak calls
Genome_build: hg38
Supplementary_files_format_and_content: normalized density bigWig file, combined replicate mac2 peaks bed file

growth_protocol: Grown in IMDM, supplemented with 10%Fetal Bovine Serum (PAA), sodium pyruvate (GIBCO), L-glutamine (GIBCO), penicillin and streptomycin (GIBCO). dBET1 (Tocris) was dissolved in DMSO (Sigma Aldrich) to a concentration of 10mM and cells were treated at a concentration of 1uM for the time indicated.

extract_protocol:
https://elifesciences.org/articles/21856
Low-input single-stranded library construction protocol as per PMIDs 23493070 & 26771485

tag: cell

tag: antibody lot number

value: Active Motif 39533

tag: dilution

value: mouse mAb 2:100

tag: hdac2, active motif 39533, mouse mab, 2


title: 4C_P0_cortex_a4_HS5-1bdel_rep2


title: Subject # 46, day 7

status: Public on Sep 05 2019

city: Palo Alto

first: Dmitri

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

hyb_protocol: Samples were hybridized on HG-133 plus 2.0  chips

scan_protocol: Plates were scanned on GeneTitan multichannel instrument (Affymetrix)

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish

label: Biotin

label_protocol: Fragemented cRNA was lebeled with biotin

extract_protocol: RNA was isolated from isolated PBMCs using RNAeasy kit (Quagen)

tag: tissue

value: PBMC

tag: days after vaccination

value: day 7

tag: antibiotic treatment

value: No


title: Subject # 33, day 1

value: day 1


title: Subject # 47, day 0

value: day 0

value: Yes


title: Subject # 33, day -21 (Screening)

value: day -21 (Screening)


title: medial_int_rep3

description: laser captured tissue

tag: strain

value: clonal line CIW4

value: medial intestine (anterior)

tag: developmental stage

value: uninjured adult


title: medial_int_rep2

description: laser captured tissue


title: Subject # 31, day 7


title: Subject # 47, day 1


title: Subject # 47, day 7


title: Subject # 33, day 0


title: Subject # 47, day 3

value: day 3


title: Subject # 46, day 1


title: Subject # 44, day 3


title: Subject # 46, day 0


title: Subject # 44, day 1


title: Subject # 44, day 7


title: Subject # 47, day -3 (Screening)

value: day -3 (Screening)


title: Subject # 33, day 3


title: Subject # 44, day -21 (Screening)


title: Subject # 43, day 1


title: Subject # 44, day 0


title: Subject # 46, day -21 (Screening)


title: Subject # 43, day 7


title: Subject # 31, day 3


title: Subject # 43, day -21 (Screening)


title: Subject # 38, day 7


title: Subject # 43, day 0


title: Subject # 38, day 3


title: Subject # 38, day 1


title: Subject # 43, day 3


title: Subject # 38, day -21 (Screening)


title: Subject # 36, day 1


title: Subject # 37, day 3


title: Subject # 37, day 1


title: Subject # 38, day 0


title: Subject # 37, day 0


title: Subject # 35, day 0


title: Subject # 37, day -3 (Screening)


title: Subject # 36, day 3


title: Subject # 31, day 1


title: Subject # 29, day 1


title: Subject # 37, day 7


title: Subject # 35, day 3


title: Subject # 34, day -3 (Screening)


title: Subject # 31, day 0


title: Subject # 36, day -21 (Screening)


title: Subject # 29, day 3


title: Subject # 04, day 3


title: Subject # 34, day 1


title: Subject # 34, day 3


title: Subject # 35, day 7


title: Subject # 35, day -3 (Screening)


title: Subject # 35, day 1


title: Subject # 33, day 7


title: Subject # 29, day 0


title: Subject # 34, day 0


title: Subject # 34, day 7


title: Subject # 36, day 7


title: Subject # 36, day 0


title: Subject # 31, day -3 (Screening)


title: Subject # 24, day 7


title: Subject # 24, day 1


title: Subject # 24, day -21 (screening)

value: day -21 (screening)


title: Subject # 29, day -21 (screening)


title: Subject # 04, day 1


title: Subject # 24, day 3


title: Subject # 24, day 0


title: Subject # 27, day 3


title: Subject # 27, day 0


title: Subject # 27, day -21 (screening)


title: Subject # 19, day 0


title: Subject # 25, day 3


title: Subject # 25, day 7


title: Subject # 04, day 0


title: Subject # 04, day -21 (screening)


title: Subject # 19, day 7


title: Subject # 19, day 1


title: Subject # 27, day 1


title: Subject # 17, day 1


title: Subject # 17, day 3


title: Subject # 17, day 0


title: Subject # 25, day -21 (screening)


title: Subject # 17, day 7


title: Subject # 25, day 1


title: Subject # 19, day -21 (screening)


title: Subject # 17, day -21 (screening)


title: Subject # 26, day 7


title: Subject # 25, day 0


title: Subject # 26, day 3


title: Subject # 19, day 3


title: Subject # 26, day 0


title: Subject # 26, day -21 (screening)


title: Subject # 26, day 1


title: Subject # 23, day 7


title: Subject # 23, day 0


title: Subject # 22, day 0


title: Subject # 20, day -21 (screening)


title: Subject # 02, day 7


title: Subject # 11, day 7


title: Subject # 22, day 1


title: Subject # 11, day 1


title: Subject # 22, day 7


title: Subject # 23, day 1


title: Subject # 22, day 3


title: Subject # 20, day 3


title: Subject # 20, day 0


title: Subject # 20, day 1


title: Subject # 20, day 7


title: Subject # 07, day 1


title: Subject # 11, day 0


title: Subject # 02, day 3


title: Subject # 11, day -21 (screening)


title: Subject # 23, day 3


title: Subject # 11, day 3


title: Subject # 22, day -21 (screening)


title: Subject # 23, day -21 (screening)


title: Subject # 07, day 7


title: Subject # 07, day 3


title: Subject # 07, day 0


title: Subject # 02, day 1


title: Subject # 15, day 7


title: Subject # 15, day 3


title: Subject # 15, day 1


title: Subject # 10, day 3


title: Subject # 15, day 0


title: Subject # 15, day -21 (screening)


title: Subject # 02, day 0


title: Subject # 12, day 3


title: Subject # 12, day -21 (screening)


title: Subject # 14, day -21 (screening)


title: Subject # 10, day 7


title: Subject # 12, day 0


title: Subject # 10, day -21 (screening)


title: Subject # 14, day 0


title: Subject # 10, day 0


title: Subject # 09, day 7


title: Subject # 14, day 3


title: Subject # 10, day 1


title: Subject # 12, day 7


title: Subject # 14, day 1


title: Subject # 02, day -21 (screening)


title: Subject # 12, day 1


title: Subject # 09, day 3


title: Subject # 09, day 0


title: Subject # 09, day -21 (screening)


title: Subject # 05, day 7


title: Subject # 05, day 3


title: Subject # 27, day 7


title: Subject # 14, day 7


title: Subject # 09, day 1


title: Subject # 05, day 0


title: Uwt22018_RNA

status: Public on Jul 01 2019

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: RNA library. Second flow cell. Cells from pooled mice.

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned mm10 genome assembly, indexed to GENCODE (vM16) GFF3 annotation with flag ‘--sjdbOverhang 74’ equivalent to (read length – 1), via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting. Lexogen SIRVome was independently aligned and quantified for qualitative assessment of library concordancy.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons within flow cells (i.e. respective wild-type samples were used). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: mm10 indexed to GENCODE (vM16) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output) and non-thresholded DESeq2 differential-expression analysis.

source_name: endometrial epithelium

growth_protocol: Mice were housed at the Van Andel Research Institute Animal Facility and the Michigan State University Grand Rapids Research Center in accordance with protocols approved by the Van Andel Research Institute and Michigan State University, under AUF# 01/16-099-00.

extract_protocol:
Endometrial epithelial cells were magnetically sorted using EpCAM-PE and anti-PE microbeads. RNA was collected using the Arcturus PicoPure RNA Isolation Kit (ThermoFisher).
Lexogen SIRV-set2 RNAs were spiked into RNA prior to library preparation at a concentration of 1% by mass. RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq Kit from 100 ng of total RNA material.

treatment_protocol: Mouse uteri were surgically removed and minced using scissors. Tissues were digested using the MACS Multi Tissue Dissociation Kit II (Miltenyi Biotec).

value: EPCAM+ endometrial epithelium

tag: genotype

value: Control wild-type

tag: phenotype

value: normal healthy


title: Uwt32018_RNA


title: Uwt12018_RNA


title: Subject # 04, day 7

source_name: PBMC


title: Subject # 05, day 1


title: Subject # 30, day 0


title: Subject # 30, day -21 (screening)


title: hSKP-HPC_'NASH'_2

status: Public on Jun 01 2019

city: Brussels

first: Joost

last: Boeckmans

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-Cosmetology (IVTD)

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

hyb_protocol: 1) 11 µg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 chips with hybridization cocktail solution.  2) Chips were incubated in an Genechip Hybridization Oven-645 (Affymetrix) (60 RPM / 45 °C /16h)  3) Chips were washed on a Genechip Fluidics Station-450 (Affymetrix)  4) Chips were stained with the Affymetrix HWS kit

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G.

data_processing: Robust Multichip Average (RMA) Express was used for normalization and summarization.

source_name: foreskin

label_protocol: RNA (100 ng) was amplified using the GeneChip 3' IVT PLUS Reagent Kit (Affymetrix). The amplified RNA was purified using magnetic beads and treated with fragmentation reagent.

growth_protocol: hSKP were isolated, cultivated and differentiated towards hepatic cells according to Rodrigues et al. (2014) (DOI: 10.1089/scd.2013.0157).

extract_protocol: Total RNA was extracted using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich).

treatment_protocol: See SAMPLES section.

tag: treatment

value: No treatment (dimethylsulfoxide)


title: Subject # 18, day -21 (screening)

value: PBMC


title: Subject # 05, day -21 (screening)


title: Subject # 30, day 1


title: hSKP-HPC_'NASH'_3


title: hSKP-HPC_'NASH'_1


title: hSKP-HPC_control_1


title: hSKP-HPC_control_2


title: Subject # 30, day 3


title: Subject # 29, day 7

value: day 7


title: hSKP-HPC_control_3


title: Subject # 07, day -21 (screening)


title: Subject # 30, day 7


title: day8_RNASeq [d8_2_1]

status: Public on Jan 29 2019

city: Cologne

first: Leo

last: Kurian

state: I am not in the U.S. or Canada

address: Kurian lab,Center for Molecular Medicine, Robert-Koch-Str. 21

department: Center for Molecular Medicine

institute: University of Cologne Germany

data_processing:
Illumina HiSeq 2000 Platform was used
Sequenced reads were trimmed for adaptor sequence and their quality was assessed using Flexbar 2.5, and the reads were mapped to hg38 whole genome using STAR  (2.5.0). Cufflinks software suite (version 2.2.1) was used for the downstream analysis.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated.
The counts of the aligned reads of all samples for known genes from Gencode annotation and the yylncRNAs which we identified in this study.
Genome_build: hg38
Supplementary_files_format_and_content: counts

molecule: polyA RNA

source_name: H1 ES cells

growth_protocol: ES cells were routinely cultured in FTDA media. Please refer PMID:22860038 for more information.

extract_protocol:
Cell were collected as pellets and were immediately resuspended in cold TriZol for RNA isolation.
Standard illumina library preparation protocol

treatment_protocol: ES cells protocol was used as discussed in detail in PMID: 26748419

tag: cell type

value: ES-derived early cardiomyocytes

tag: passages


title: day6_RNASeq [d6_2_1]

value: ES-derived cardiac progenitor cells


title: day6_RNASeq [d6_1_1]


title: day4_RNASeq [d4_2_1]

value: ES-derived cardiac mesoderm cells


title: day8_RNASeq [d8_1_1]


title: day2_RNASeq [d2_2_1]

value: ES-derived late mesoderm cells


title: day4_RNASeq [d4_1_1]


title: day2_RNASeq [d2_1_1]


title: day14_RNASeq rep3

description:
D004270063_39866_21_d14_3_1
late cardiomyocytes
D004270063_39866_21_d14_3_1

data_processing:
Illumina HiSeq 2000 Platform was used
Sequenced reads were trimmed for adaptor sequence and their quality was assessed using Flexbar 2.5, and the reads were mapped to hg38 whole genome using STAR  (2.5.0). Cufflinks software suite (version 2.2.1) was used for the downstream analysis.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated.
Genome_build: hg38
Supplementary_files_format_and_content: The counts of the aligned reads of all samples for known genes from Gencode annotation and the yylncRNAs which we identified in this study.

growth_protocol: ES cells were routinely cultured in FTDA media. For detailed composition, please refer PMID:22860038

value: ES-derived late cardiomyocytes


title: C29

status: Public on Mar 20 2019

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

description:
sample name:
201050360042_R02C01

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing: Raw data files generated by the iScan array scanner were read and preprocessed using minfi Bioconductor package (Aryee et al., 2014). With the minfi package the same preprocessing steps as in Illumina's Genomestudio software were performed. In addition, the following filtering criteria were applied: Removal of probes targeting the X and Y chromosomes, removal of probes containing-nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, and probes not mapping uniquely to the human reference genome (hg19) allowing for one mismatch. In total 394,848 common probes of Illumina 450K and EPIC arrays were kept for clustering analysis.

label: Cy5, Cy3

source_name: astroblastomas

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

value: astroblastomas


title: day6_RNASeq rep2

description:
SN7640334_39859_14_d6_2_1
cardiac progenitor cells
SN7640334_39859_14_d6_2_1


title: day8_RNASeq rep1

description:
SN7640334_39861_16_d8_1_1
early cardiomyocytes
SN7640334_39861_16_d8_1_1


title: day6_RNASeq rep3

description:
SN7640334_39860_15_d6_3_1
cardiac progenitor cells
SN7640334_39860_15_d6_3_1


title: day6_RNASeq rep1

description:
SN7640334_39858_13_d6_1_1
cardiac progenitor cells
SN7640334_39858_13_d6_1_1


title: day14_RNASeq rep2

description:
D004270063_39865_20_d14_2_1
late cardiomyocytes
D004270063_39865_20_d14_2_1


title: day8_RNASeq rep3

description:
SN7640334_39863_18_d8_3_1
early cardiomyocytes
SN7640334_39863_18_d8_3_1


title: C30

description:
sample name:
201533640031_R08C01


title: C6

description:
sample name:
201050360042_R06C01


title: day14_RNASeq rep1

description:
D004270063_39864_19_d14_1_1
late cardiomyocytes
D004270063_39864_19_d14_1_1


title: day4_RNASeq rep3

description:
SN7640334_39857_12_d4_3_1
cardiac mesoderm cells
SN7640334_39857_12_d4_3_1


title: C12

description:
sample name:
201050360090_R01C01


title: C19

description:
sample name:
201533610029_R06C01


title: C14

description:
sample name:
201533610029_R05C01


title: day4_RNASeq rep2

description:
SN7640334_39856_11_d4_2_1
cardiac mesoderm cells
SN7640334_39856_11_d4_2_1


title: C5

description:
sample name:
201050360040_R05C01


title: C20

description:
sample name:
201533610029_R08C01


title: C1

description:
sample name:
201557510028_R06C01


title: C3

description:
sample name:
201050360040_R07C01


title: day4_RNASeq rep1

description:
SN7640334_39855_10_d4_1_1
cardiac mesoderm cells
SN7640334_39855_10_d4_1_1


title: day2_RNASeq rep3

description:
SN7640334_39854_9_d2_3_1
late mesoderm cells
SN7640334_39854_9_d2_3_1


title: day1_RNASeq rep2

description:
SN7640334_39850_5_d1_2_1
early mesoderm cells
SN7640334_39850_5_d1_2_1

value: ES-derived early mesoderm cells


title: day2_RNASeq rep2

description:
SN7640334_39853_8_d2_2_1
late mesoderm cells
SN7640334_39853_8_d2_2_1


title: day1_RNASeq rep3

description:
SN7640334_39851_6_d1_3_1
early mesoderm cells
SN7640334_39851_6_d1_3_1


title: day1_RNASeq rep1

description:
SN7640334_39849_4_d1_1_1
early mesoderm cells
SN7640334_39849_4_d1_1_1


title: day0_RNASeq rep3

description:
SN7640334_39848_3_d0_3_1
embryonic stem cells
SN7640334_39848_3_d0_3_1

value: embryonic stem cells


title: day0_RNASeq rep2

description:
SN7640334_39847_2_d0_2_1
embryonic stem cells
SN7640334_39847_2_d0_2_1


title: C9

description:
sample name:
201050360042_R08C01


title: E9.5_2_RNASeq

description:
E95_2
cardiogenic regions were dissected

data_processing:
Illumina HiSeq 2000 Platform was used
Sequenced reads were trimmed for adapter sequences and the  qualtiy of the reads were  assessed using Flexbar 2.5. The reads were mapped to hg38 whole genome using STAR  (2.5.0). Cufflinks software suite (version 2.2.1) was used for the downstream analysis.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated.
The counts of the aligned reads of all samples for known genes from Gencode annotation and the yylncRNAs which we identified in this study.
Genome_build: Mm10 (GRCm38)
Supplementary_files_format_and_content: counts

source_name: mouse embryo

extract_protocol:
Tissues were collected and immediately resuspended in cold TriZol for RNA isolation.
Standard illumina library preparation protocol

value: cardiogenic region


title: E9.5_3_RNASeq

description:
E95_3
cardiogenic regions were dissected


title: C11

description:
sample name:
201050360042_R05C01


title: day0_RNASeq rep1

description:
SN7640334_39846_1_d0_1_1
embryonic stem cells
SN7640334_39846_1_d0_1_1


title: C33

description:
sample name:
201533610029_R03C01


title: day8_RNASeq rep2

description:
SN7640334_39862_17_d8_2_1
early cardiomyocytes
SN7640334_39862_17_d8_2_1


title: C7

description:
sample name:
201557510028_R07C01


title: C23

description:
sample name:
201050360042_R04C01


title: C32

description:
sample name:
201533610029_R07C01


title: E8.5_3_RNASeq

description:
E85_3
cardiogenic regions were dissected


title: C34

description:
sample name:
201533610029_R02C01


title: E8.5_2_RNASeq

description:
E85_2
cardiogenic regions were dissected


title: E8.5_1_RNASeq

description:
E85_1
cardiogenic regions were dissected


title: E8_2_RNASeq

description:
E8_2
cardiogenic regions were dissected


title: C24

description:
sample name:
201050360090_R02C01


title: CUMC_S97

status: Public on Nov 27 2018

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used to convert BCL to fastq format, coupled with adaptor trimming
Tophat (version 2.0.4) was used for mapping reads to the reference genome.
HTSeq was used to count raw reads per gene.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited text file containing raw read count values for each sample

source_name: PDAC

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2

tag: patient id

tag: compartment

value: Stroma

tag: library

value: NuGEN


title: CUMC_S100


title: CUMC_S101


title: CUMC_S99


title: CUMC_S98


title: E8_3_RNASeq

description:
E8_3
cardiogenic regions were dissected


title: E14_2_RNASeq

description:
E14_2
cardiogenic regions were dissected


title: CUMC_S96


title: CUMC_S95


title: CUMC_S94


title: C10

description:
sample name:
201050360040_R08C01


title: C13

description:
sample name:
201050360042_R03C01


title: CUMC_S93


title: C22

description:
sample name:
201050360042_R07C01


title: CUMC_S89


title: CUMC_S87


title: CUMC_S88


title: CUMC_S83


title: CUMC_S82


title: CUMC_S84


title: CUMC_S81


title: CUMC_S78


title: CUMC_S76


title: CUMC_S92


title: CUMC_S80


title: CUMC_S74


title: CUMC_S73


title: CUMC_S90


title: CUMC_S91


title: E9.5_1_RNASeq

description:
E95_1
cardiogenic regions were dissected


title: CUMC_S72


title: CUMC_S70


title: CUMC_S85


title: CUMC_S71


title: CUMC_S69


title: CUMC_S67


title: CUMC_S68


title: CUMC_B21

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used to convert BCL to fastq format, coupled with adaptor trimming
Tophat (version 2.0.4) was used for mapping reads to the reference genome.
HTSeq was used to count raw reads per gene.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited text file containing raw read count and TPM values for each sample

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2 for LCM as well as bulk samples and Illumina TruSeq RNA prep kit for bulk samples, respectively. See characteristics 'Library_method'.

value: Bulk

value: TruSeq


title: CUMC_S79


title: CUMC_S77


title: CUMC_B23


title: CUMC_B20


title: CUMC_B22


title: CUMC_B18


title: CUMC_S75


title: day2_RNASeq rep1

description:
SN7640334_39852_7_d2_1_1
late mesoderm cells
SN7640334_39852_7_d2_1_1


title: CUMC_B19


title: CUMC_B17


title: CUMC_E66

value: Epithelium


title: CUMC_S66


title: CUMC_S65


title: CUMC_S63


title: CUMC_E64


title: CUMC_E63


title: CUMC_E62


title: CUMC_E61


title: CUMC_B10


title: CUMC_B9


title: E14_3_RNASeq

description:
E14_3
cardiogenic regions were dissected


title: CUMC_S61


title: CUMC_B8


title: E14_1_RNASeq

description:
E14_1
cardiogenic regions were dissected


title: CUMC_B6


title: CUMC_B7


title: CUMC_S60


title: CUMC_B5


title: CUMC_S59


title: CUMC_S58


title: CUMC_E59


title: CUMC_E58


title: CUMC_E65


title: CUMC_E57


title: CUMC_S64


title: CUMC_S56


title: CUMC_E56


title: CUMC_S62


title: CUMC_S54


title: CUMC_E55


title: CUMC_E54


title: CUMC_E53


title: CUMC_S53


title: CUMC_S52


title: CUMC_E52


title: CUMC_S51


title: CUMC_E51


title: CUMC_S50


title: CUMC_E60


title: CUMC_E50


title: CUMC_S57


title: CUMC_E49


title: CUMC_S48


title: CUMC_E48


title: CUMC_S49


title: CUMC_S47


title: CUMC_E47


title: CUMC_S46


title: CUMC_S45


title: CUMC_S55


title: CUMC_S44


title: CUMC_E45


title: CUMC_E44


title: CUMC_E43


title: CUMC_S42


title: CUMC_S43


title: CUMC_S41


title: CUMC_E41


title: CUMC_E40


title: CUMC_E42


title: CUMC_S39


title: CUMC_S38


title: CUMC_S40


title: CUMC_S37


title: CUMC_E37


title: CUMC_E36


title: CUMC_S35


title: CUMC_E35


title: CUMC_S34


title: CUMC_S36


title: CUMC_E46


title: CUMC_E34


title: CUMC_S33


title: CUMC_S32


title: CUMC_E33


title: CUMC_E38


title: CUMC_E32


title: CUMC_S31


title: CUMC_S30


title: CUMC_S29


title: CUMC_E30


title: CUMC_E29


title: CUMC_E39


title: CUMC_E27


title: CUMC_S28


title: CUMC_S24


title: CUMC_S86


title: CUMC_S26


title: CUMC_E26


title: CUMC_E25


title: CUMC_S23


title: CUMC_E23


title: CUMC_S22


title: CUMC_S25


title: CUMC_S21


title: CUMC_E21


title: CUMC_S20


title: CUMC_E20


title: CUMC_E31


title: CUMC_E22


title: CUMC_S19


title: CUMC_E19


title: CUMC_E18


title: CUMC_S17


title: CUMC_S18


title: CUMC_E28


title: CUMC_E17


title: CUMC_S16


title: CUMC_S27


title: CUMC_S14


title: CUMC_S15


title: CUMC_E15


title: CUMC_E16


title: CUMC_E14


title: CUMC_S13


title: CUMC_E13


title: CUMC_S12


title: CUMC_E24


title: CUMC_E12


title: CUMC_B2


title: CUMC_S123


title: CUMC_E5


title: CUMC_B1


title: CUMC_S122


title: CUMC_E4


title: CUMC_S121


title: CUMC_S3


title: CUMC_S120


title: CUMC_S119


title: CUMC_E3


title: CUMC_S118


title: E8_1_RNASeq

description:
E8_1
cardiogenic regions were dissected


title: CUMC_S2


title: CUMC_E2


title: CUMC_S116


title: CUMC_S11


title: CUMC_S117


title: CUMC_S115


title: CUMC_E11


title: CUMC_S114


title: CUMC_S1


title: CUMC_S112


title: CUMC_E10


title: CUMC_S113


title: CUMC_S111


title: CUMC_S9


title: CUMC_S110


title: CUMC_S4


title: CUMC_S8


title: CUMC_S108


title: CUMC_E8


title: CUMC_S109


title: CUMC_S7


title: CUMC_E7


title: CUMC_S107


title: CUMC_S105


title: CUMC_S106


title: CUMC_S6


title: CUMC_S104


title: CUMC_S103


title: CUMC_S102


title: CUMC_S5


title: CUMC_E1


title: P7_CD-1_OSNs

status: Public on Oct 03 2018

city: Kansas City

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research

data_processing:
Raw sequencing data were processed using 10x Genomics Cell Ranger pipeline (version 2.1.1).
Reads were demultiplexed into Fastq file format using cellranger mkfastq.
The first 16 bp of R1 is the cell barcode whereas the following 10 bp is the UMI.
Genome index was built by cellranger mkref using genome mm10, ensembl 87 gene model.
Cell counts tables were generated using cellranger count function with default parameters.
Final expression matricies were generated via seurat's read10x function of the filtered_gene_bc_matrices.
Genome_build: genome mm10, ensembl 87 gene model.
Supplementary_files_format_and_content: Tab delimited file with gene expression counts;  genes as rows and cells as columns.

source_name: Olfactory epithelium

extract_protocol:
Papain cell extraction
Single cell RNA-Seq was performed using Chromium Single Cell Controller (10X Genomics). The maximum allowable volume of cells for each sorted sample was added to the Chromium system targeting ~2,000-3,000 cells each. Libraries were prepared using Chromium Single Cell 3' Library & Gel Bead Kit v2. All four libraries were sequenced on an Illumina HiSeq 2500 as paired end using SBS v2 Rapid flowcells and following read lengths were generated: 26 bp Read1, 8 bp I7 Index and 98 bp Read2. Approximately 1,400 to 3,000 cells were captured for each sample and 20,000-50,000 reads were obtained per cell.

tag: age

value: Olfactory epithelium


title: CUMC_E6


title: P0_CD-1_OSNs


title: P21_CD-1_OSNs


title: CUMC_E9


title: Limbs_E12_Wt_RAD21

status: Public on Dec 22 2017

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

institute: Université de Genève

description: Whole forelimb and hindlimb mouse E12.5_Wt_RAD21_ChIP-seq

data_processing:
adapters and bad quality bases were removed with cutadapt (ref Martin et al 2011 version 1.8 options -m 15 -q 30 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for ChIP and -a CTGTCTCTTATACACATCTGACGCTGCCGACGA for ChIPmentation).
Then reads were mapped using bowtie2 on the mm10 genome (ref Langmead et al. 2012 version 2.2.4 default parameters).
Bam files were merged when replicates or resequencing were done.
The peaks and the coverage were obtained as the output of MACS2 (ref Zhang et al 2008 version 2.1.1.20160309 command line: macs2 callpeak -t input.bam --call-summits -B). By default, MACS2 only kept one tag at the same location (the same coordinates and the same strand), which would remove all potential contaminants from 4C experiments.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak contains the peak calling; BedGraph contains the coverage from macs2

source_name: Whole Forelimbs and Hindlimbs

growth_protocol: Heterozygous mutant mice were crossed in order to obtain Wt and homozygous mutant embryos.

extract_protocol:
E12.5 limb tissue was micordissected from wild type or HoxD mutants embryos and used for ChIP experiments. Samples were fixed in 1% formaldehyde/PBS for 10 (CTCF, H3K27ac, RAD21) or 25 (RAD21, SMC1) minutes at room temperature, washed three times with col
For ChIP-seq, 5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

value: Whole Forelimbs and Hindlimbs

value: wild type

tag: embryonic day

tag: antibody

value: anti-RAD21 (abcam, ab992)


title: Limbs_E12_Wt_CTCF

description: Whole forelimb and hindlimb mouse E12.5_Wt_CTCF_ChIP-seq

extract_protocol:
E12.5 limb tissue was micordissected from wild type or HoxD mutants embryos and used for ChIP experiments. Samples were fixed in 1% formaldehyde/PBS for 10 (CTCF, H3K27ac, RAD21) or 25 (RAD21, SMC1) minutes at room temperature, washed three times with cold PBS containing protease inhibitor (and, for H3K27ac, deacetylase inhibitor) and stored at -80°C. For ChIP-seq samples, around, one hundred milligrams of tissue were used. Nuclei were extracted by incubating them in a cell lysis buffer provided in the ChIP IT high sensitivity kit (Active motif) during at least 10 minutes and with the aid of a Dounce homogenizer type B (Active motif). The isolated nuclei were pelleted and lysed in sonication buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH=8.0, protease inhibitor and, for the case of H3K27ac, deacetylase inhibitor) for 10 min on ice, and fragmented to a range of 200-500 bp using a Vibracell tip sonicator or a Diagenode Bioruptor pico waterbath device. DNA concentration was estimated using the Qubit ds DNA HS assay kit following manufacturer instruction and 25-30ug of chromatin were diluted ten times in ChIP dilution buffer (20mM HEPES, 150mM NaCl, 0.1% NP40) and incubated overnight at 4ºC with 4ug of anti-CTCF antibody (Active motif, 61311, 61312), anti-SMC1 (Bethyl, A300-055A), anti-RAD21 (abcam, ab992) or 2ug of anti-H3K27ac (abcam, ab4729) on a rotating platform. For ChIP-seq samples, the next day chromatin-antibody complexes were incubated with protein A/G agarose beads during 3h at 4ºC and successively washed following manufacturer instructions. Finally they were eluted and purified by phenol:chlorophorm extraction and precipitation. Between 5 to 10ng of immunoprecipitated DNA were sequenced with a 50bp single-end Illumina HiSeq flow cell.
For ChIP-seq, 5-10 ng of purified DNA were used to make libraries according to the manufacturer’s protocol (Illumina). The material was sequenced with 50 bp single-end reads on the Illumine HiSeq according to the manufacturer’s specifications.

value: anti-CTCF (Active motif, 61311, 61312)


title: CUMC_S10


title: X129S6.SVEV_male_S23098

status: Public on Dec 05 2017

data_processing:
Basecalls performed using HiSeq Control Software (v2.2.58) and the fastq files were generated using 'bcl2fastq'.
Sequenced reads were trimmed for adaptor and low-quality sequences using Trim Galore
Trimmed Sequences were aligned to mm10 genome using STAR aligner with ensembl reference version 87 for annotation. Uniquely mapped reads were quantified using "--quantMode GeneCounts" and extracted from 4th column of output matching orientation of True-seq stranded preparation.
Differential Expression Analysis was performed using R package DESeq2 resulting in contrast results and normalized counts matrix
Genome_build: mm10
Supplementary_files_format_and_content: STAR generated raw counts table with ensembl annotations is provided in tsv format
Supplementary_files_format_and_content: DESeq2 normalized counts table with ensembl annotations is provided in tsv format

extract_protocol:
Total RNA was isolated from VNO epithelia of individual mouse using Trizol solution followed by spin column purification. Ribodepletion was performed before sequencing libraries were generated using TruSeq Stranded Total RNA Kit.
RNA libraries were prepared for sequencing using Illumina protocols

tag: Sex

value: male

value: Vomeronasal epithelial tissue

tag: molecule subtype

value: Ribo depleted total RNA


title: SJL.J_female_S23110

value: SJL/J

value: female

tag: tissue


title: SJL.J_male_S23106


title: X129S6.SVEV_female_S23102


title: P3_CD-1_OSNs


title: SWR.J_female_S23086

value: SWR/J


title: C57.BL6_female_S23094


title: SWR.J_male_S23082


title: SJL.J_female_S23109


title: C57.BL6_male_S23090


title: SJL.J_male_S23105


title: X129S6.SVEV_female_S23101


title: X129S6.SVEV_male_S23097


title: C57.BL6_female_S23093


title: C57.BL6_male_S23089


title: SWR.J_female_S23085


title: SWR.J_male_S23081


title: SJL.J_female_S23108


title: SJL.J_male_S23104


title: X129S6.SVEV_male_S23096


title: C57.BL6_female_S23092


title: C57.BL6_male_S23088


title: X129S6.SVEV_female_S23100


title: SJL.J_male_S23103


title: SJL.J_female_S23107


title: SWR.J_male_S23080


title: SWR.J_female_S23084


title: X129S6.SVEV_female_S23099


title: C57.BL6_female_S23091


title: X129S6.SVEV_male_S23095


title: SWR.J_female_S23083


title: SWR.J_male_S23079


title: C57.BL6_male_S23087


title: HIPCVAX005_ZV228_D7_PBMC

status: Public on Aug 18 2017

city: Atlanta

first: Thomas

last: Hagan

address: 954 Gatewood Road

department: Emory Vaccine Center

institute: Emory University

hyb_protocol: Samples were hybridized on  HG-133-plus-PM plates

data_processing: Probe level processing was done by RMA with log2 transform and probe summary by median polish (using the rma function in the affy package v1.44.0 in R v3.1.3).

source_name: elderly_subject_Visit 4

extract_protocol: RNA was isolated from whole blood Paxgene tubes using RNAeasy kit (Quagen)

tag: subject id

tag: vaccine

value: VZV

tag: cohort

value: Denver

tag: visit

value: Visit 4; days 7 post-vaccination

tag: age group

value: elderly

tag: race

value: white

tag: ethnicity

value: non-hispanic

tag: tissue/cell type

value: PBMC


title: HIPCVAX005_ZV227_D7_PBMC

source_name: young_subject_Visit 4

value: young

value: asian


title: HIPCVAX005_ZV238_D7_PBMC


title: HIPCVAX005_ZV214_D7_PBMC


title: HIPCVAX005_ZV233_D7_PBMC

value: black


title: HIPCVAX005_ZV208_D7_PBMC

value: mixed race

value: hispanic


title: HIPCVAX005_ZV230_D7_PBMC


title: HIPCVAX005_ZV222_D7_PBMC

value: male


title: HIPCVAX005_ZV212_D7_PBMC


title: HIPCVAX005_ZV215_D7_PBMC


title: HIPCVAX005_ZV239_D7_PBMC


title: HIPCVAX005_ZV220_D7_PBMC


title: HIPCVAX005_ZV226_D7_PBMC


title: HIPCVAX005_ZV207_D7_PBMC


title: HIPCVAX005_ZV235_D7_PBMC


title: HIPCVAX005_ZV216_D7_PBMC


title: HIPCVAX005_ZV232_D7_PBMC


title: HIPCVAX005_ZV223_D7_PBMC


title: HIPCVAX005_ZV209_D7_PBMC


title: HIPCVAX005_ZV210_D7_PBMC


title: HIPCVAX005_ZV224_D7_PBMC


title: HIPCVAX005_ZV231_D7_PBMC


title: HIPCVAX005_ZV206_D7_PBMC


title: HIPCVAX005_ZV219_D7_PBMC


title: HIPCVAX005_ZV236_D7_PBMC


title: HIPCVAX005_ZV225_D7_PBMC


title: HIPCVAX005_ZV234_D7_PBMC


title: HIPCVAX005_ZV221_D7_PBMC


title: HIPCVAX005_ZV217_D7_PBMC


title: HIPCVAX005_ZV211_D7_PBMC


title: HIPCVAX005_ZV203_D7_PBMC


title: HIPCVAX005_ZV205_D7_PBMC


title: HIPCVAX005_ZV201_D7_PBMC


title: HIPCVAX005_ZV143_D7_PBMC

value: Atlanta


title: HIPCVAX005_ZV204_D7_PBMC


title: HIPCVAX005_ZV139_D7_PBMC


title: HIPCVAX005_ZV132_D7_PBMC


title: HIPCVAX005_ZV138_D7_PBMC


title: HIPCVAX005_ZV137_D7_PBMC


title: HIPCVAX005_ZV122_D7_PBMC


title: HIPCVAX005_ZV127_D7_PBMC


title: HIPCVAX005_ZV134_D7_PBMC


title: HIPCVAX005_ZV142_D7_PBMC


title: HIPCVAX005_ZV120_D7_PBMC


title: HIPCVAX005_ZV117_D7_PBMC


title: HIPCVAX005_ZV202_D7_PBMC


title: HIPCVAX005_ZV116_D7_PBMC


title: HIPCVAX005_ZV131_D7_PBMC


title: HIPCVAX005_ZV144_D7_PBMC


title: HIPCVAX005_ZV135_D7_PBMC


title: HIPCVAX005_ZV119_D7_PBMC


title: HIPCVAX005_ZV121_D7_PBMC


title: HIPCVAX005_ZV125_D7_PBMC


title: HIPCVAX005_ZV115_D7_PBMC


title: HIPCVAX005_ZV128_D7_PBMC


title: HIPCVAX005_ZV133_D7_PBMC


title: HIPCVAX005_ZV126_D7_PBMC


title: HIPCVAX005_ZV129_D7_PBMC


title: HIPCVAX005_ZV136_D7_PBMC


title: HIPCVAX005_ZV118_D7_PBMC


title: HIPCVAX005_ZV101_D7_PBMC


title: HIPCVAX005_ZV103_D7_PBMC


title: HIPCVAX005_ZV104_D7_PBMC


title: HIPCVAX005_ZV114_D7_PBMC


title: HIPCVAX005_ZV105_D7_PBMC


title: HIPCVAX005_ZV238_D3_PBMC

source_name: elderly_subject_Visit 3

value: Visit 3; days 3 post-vaccination


title: HIPCVAX005_ZV226_D3_PBMC

value: female


title: HIPCVAX005_ZV110_D7_PBMC


title: HIPCVAX005_ZV111_D7_PBMC


title: HIPCVAX005_ZV112_D7_PBMC


title: HIPCVAX005_ZV233_D3_PBMC


title: HIPCVAX005_ZV109_D7_PBMC


title: HIPCVAX005_ZV234_D3_PBMC


title: HIPCVAX005_ZV236_D3_PBMC


title: HIPCVAX005_ZV230_D3_PBMC


title: HIPCVAX005_ZV239_D3_PBMC


title: HIPCVAX005_ZV227_D3_PBMC

source_name: young_subject_Visit 3


title: HIPCVAX005_ZV219_D3_PBMC


title: HIPCVAX005_ZV113_D7_PBMC


title: HIPCVAX005_ZV228_D3_PBMC


title: HIPCVAX005_ZV106_D7_PBMC


title: HIPCVAX005_ZV108_D7_PBMC


title: HIPCVAX005_ZV225_D3_PBMC


title: HIPCVAX005_ZV223_D3_PBMC


title: HIPCVAX005_ZV231_D3_PBMC


title: HIPCVAX005_ZV235_D3_PBMC


title: HIPCVAX005_ZV232_D3_PBMC


title: HIPCVAX005_ZV221_D3_PBMC


title: HIPCVAX005_ZV222_D3_PBMC


title: HIPCVAX005_ZV224_D3_PBMC


title: HIPCVAX005_ZV220_D3_PBMC


title: HIPCVAX005_ZV208_D3_PBMC


title: HIPCVAX005_ZV216_D3_PBMC


title: HIPCVAX005_ZV214_D3_PBMC


title: HIPCVAX005_ZV212_D3_PBMC


title: HIPCVAX005_ZV210_D3_PBMC


title: HIPCVAX005_ZV143_D3_PBMC


title: HIPCVAX005_ZV215_D3_PBMC


title: HIPCVAX005_ZV203_D3_PBMC


title: HIPCVAX005_ZV217_D3_PBMC


title: HIPCVAX005_ZV207_D3_PBMC


title: HIPCVAX005_ZV138_D3_PBMC


title: HIPCVAX005_ZV144_D3_PBMC


title: HIPCVAX005_ZV142_D3_PBMC


title: HIPCVAX005_ZV209_D3_PBMC


title: HIPCVAX005_ZV211_D3_PBMC


title: HIPCVAX005_ZV204_D3_PBMC


title: HIPCVAX005_ZV202_D3_PBMC


title: HIPCVAX005_ZV135_D3_PBMC


title: HIPCVAX005_ZV134_D3_PBMC


title: HIPCVAX005_ZV126_D3_PBMC


title: HIPCVAX005_ZV205_D3_PBMC


title: HIPCVAX005_ZV127_D3_PBMC


title: HIPCVAX005_ZV136_D3_PBMC


title: HIPCVAX005_ZV131_D3_PBMC


title: HIPCVAX005_ZV139_D3_PBMC


title: HIPCVAX005_ZV137_D3_PBMC


title: HIPCVAX005_ZV201_D3_PBMC


title: HIPCVAX005_ZV132_D3_PBMC


title: HIPCVAX005_ZV129_D3_PBMC


title: HIPCVAX005_ZV128_D3_PBMC


title: HIPCVAX005_ZV206_D3_PBMC


title: HIPCVAX005_ZV125_D3_PBMC


title: HIPCVAX005_ZV116_D3_PBMC


title: HIPCVAX005_ZV119_D3_PBMC


title: HIPCVAX005_ZV117_D3_PBMC


title: HIPCVAX005_ZV133_D3_PBMC


title: HIPCVAX005_ZV121_D3_PBMC


title: HIPCVAX005_ZV118_D3_PBMC


title: HIPCVAX005_ZV114_D3_PBMC


title: HIPCVAX005_ZV113_D3_PBMC


title: HIPCVAX005_ZV115_D3_PBMC


title: HIPCVAX005_ZV109_D3_PBMC


title: HIPCVAX005_ZV111_D3_PBMC


title: HIPCVAX005_ZV103_D3_PBMC


title: HIPCVAX005_ZV120_D3_PBMC


title: HIPCVAX005_ZV112_D3_PBMC


title: HIPCVAX005_ZV238_D1_PBMC

source_name: elderly_subject_Visit 2

value: Visit 2; day 1 post-vaccination


title: HIPCVAX005_ZV108_D3_PBMC

value: VZV


title: HIPCVAX005_ZV104_D3_PBMC


title: HIPCVAX005_ZV105_D3_PBMC


title: HIPCVAX005_ZV239_D1_PBMC

value: Denver


title: HIPCVAX005_ZV106_D3_PBMC


title: HIPCVAX005_ZV101_D3_PBMC


title: HIPCVAX005_ZV235_D1_PBMC


title: HIPCVAX005_ZV226_D1_PBMC


title: HIPCVAX005_ZV122_D3_PBMC


title: HIPCVAX005_ZV233_D1_PBMC


title: HIPCVAX005_ZV110_D3_PBMC


title: HIPCVAX005_ZV234_D1_PBMC


title: HIPCVAX005_ZV236_D1_PBMC


title: HIPCVAX005_ZV232_D1_PBMC


title: HIPCVAX005_ZV230_D1_PBMC


title: HIPCVAX005_ZV219_D1_PBMC


title: HIPCVAX005_ZV224_D1_PBMC

source_name: young_subject_Visit 2


title: HIPCVAX005_ZV231_D1_PBMC


title: HIPCVAX005_ZV222_D1_PBMC


title: HIPCVAX005_ZV225_D1_PBMC


title: HIPCVAX005_ZV220_D1_PBMC


title: HIPCVAX005_ZV228_D1_PBMC


title: HIPCVAX005_ZV217_D1_PBMC


title: HIPCVAX005_ZV223_D1_PBMC


title: HIPCVAX005_ZV208_D1_PBMC


title: HIPCVAX005_ZV216_D1_PBMC


title: HIPCVAX005_ZV214_D1_PBMC


title: HIPCVAX005_ZV221_D1_PBMC


title: HIPCVAX005_ZV211_D1_PBMC


title: HIPCVAX005_ZV227_D1_PBMC


title: HIPCVAX005_ZV215_D1_PBMC


title: HIPCVAX005_ZV202_D1_PBMC


title: HIPCVAX005_ZV204_D1_PBMC


title: HIPCVAX005_ZV201_D1_PBMC


title: HIPCVAX005_ZV210_D1_PBMC


title: HIPCVAX005_ZV206_D1_PBMC


title: HIPCVAX005_ZV212_D1_PBMC


title: HIPCVAX005_ZV143_D1_PBMC


title: HIPCVAX005_ZV144_D1_PBMC


title: HIPCVAX005_ZV127_D1_PBMC


title: HIPCVAX005_ZV138_D1_PBMC


title: HIPCVAX005_ZV134_D1_PBMC


title: HIPCVAX005_ZV131_D1_PBMC


title: HIPCVAX005_ZV205_D1_PBMC


title: HIPCVAX005_ZV122_D1_PBMC


title: HIPCVAX005_ZV136_D1_PBMC


title: HIPCVAX005_ZV125_D1_PBMC


title: HIPCVAX005_ZV128_D1_PBMC


title: HIPCVAX005_ZV139_D1_PBMC


title: HIPCVAX005_ZV142_D1_PBMC


title: HIPCVAX005_ZV137_D1_PBMC


title: HIPCVAX005_ZV121_D1_PBMC


title: HIPCVAX005_ZV132_D1_PBMC


title: HIPCVAX005_ZV120_D1_PBMC


title: HIPCVAX005_ZV119_D1_PBMC


title: HIPCVAX005_ZV135_D1_PBMC


title: HIPCVAX005_ZV126_D1_PBMC


title: HIPCVAX005_ZV133_D1_PBMC


title: HIPCVAX005_ZV115_D1_PBMC


title: HIPCVAX005_ZV203_D1_PBMC


title: HIPCVAX005_ZV116_D1_PBMC


title: HIPCVAX005_ZV129_D1_PBMC


title: HIPCVAX005_ZV118_D1_PBMC


title: HIPCVAX005_ZV106_D1_PBMC


title: HIPCVAX005_ZV114_D1_PBMC


title: HIPCVAX005_ZV110_D1_PBMC


title: HIPCVAX005_ZV111_D1_PBMC


title: HIPCVAX005_ZV108_D1_PBMC


title: HIPCVAX005_ZV109_D1_PBMC


title: HIPCVAX005_ZV113_D1_PBMC


title: HIPCVAX005_ZV234_D0_PBMC

source_name: elderly_subject_Visit 1

value: Visit 1; baseline


title: HIPCVAX005_ZV101_D1_PBMC


title: HIPCVAX005_ZV117_D1_PBMC


title: HIPCVAX005_ZV232_D0_PBMC

value: elderly


title: HIPCVAX005_ZV239_D0_PBMC

value: white


title: HIPCVAX005_ZV105_D1_PBMC

value: non-hispanic


title: HIPCVAX005_ZV236_D0_PBMC

value: PBMC


title: HIPCVAX005_ZV103_D1_PBMC


title: HIPCVAX005_ZV231_D0_PBMC


title: HIPCVAX005_ZV238_D0_PBMC


title: HIPCVAX005_ZV225_D0_PBMC


title: HIPCVAX005_ZV112_D1_PBMC

value: young


title: HIPCVAX005_ZV230_D0_PBMC


title: HIPCVAX005_ZV226_D0_PBMC


title: HIPCVAX005_ZV233_D0_PBMC


title: HIPCVAX005_ZV219_D0_PBMC


title: HIPCVAX005_ZV104_D1_PBMC


title: HIPCVAX005_ZV227_D0_PBMC

source_name: young_subject_Visit 1

value: asian


title: HIPCVAX005_ZV235_D0_PBMC


title: HIPCVAX005_ZV220_D0_PBMC


title: HIPCVAX005_ZV223_D0_PBMC


title: HIPCVAX005_ZV228_D0_PBMC


title: HIPCVAX005_ZV215_D0_PBMC


title: HIPCVAX005_ZV209_D0_PBMC


title: HIPCVAX005_ZV207_D1_PBMC


title: HIPCVAX005_ZV221_D0_PBMC


title: HIPCVAX005_ZV212_D0_PBMC


title: HIPCVAX005_ZV224_D0_PBMC


title: HIPCVAX005_ZV217_D0_PBMC


title: HIPCVAX005_ZV208_D0_PBMC


title: HIPCVAX005_ZV222_D0_PBMC


title: HIPCVAX005_ZV205_D0_PBMC


title: HIPCVAX005_ZV214_D0_PBMC


title: HIPCVAX005_ZV210_D0_PBMC


title: HIPCVAX005_ZV216_D0_PBMC


title: HIPCVAX005_ZV209_D1_PBMC


title: HIPCVAX005_ZV202_D0_PBMC


title: HIPCVAX005_ZV144_D0_PBMC


title: HIPCVAX005_ZV207_D0_PBMC


title: HIPCVAX005_ZV211_D0_PBMC


title: HIPCVAX005_ZV139_D0_PBMC


title: HIPCVAX005_ZV138_D0_PBMC


title: HIPCVAX005_ZV206_D0_PBMC


title: HIPCVAX005_ZV201_D0_PBMC


title: HIPCVAX005_ZV142_D0_PBMC

value: black


title: HIPCVAX005_ZV204_D0_PBMC


title: HIPCVAX005_ZV203_D0_PBMC


title: HIPCVAX005_ZV143_D0_PBMC


title: HIPCVAX005_ZV137_D0_PBMC


title: HIPCVAX005_ZV131_D0_PBMC


title: HIPCVAX005_ZV136_D0_PBMC


title: HIPCVAX005_ZV132_D0_PBMC


title: HIPCVAX005_ZV127_D0_PBMC


title: HIPCVAX005_ZV126_D0_PBMC


title: HIPCVAX005_ZV114_D0_PBMC


title: HIPCVAX005_ZV122_D0_PBMC


title: HIPCVAX005_ZV134_D0_PBMC


title: HIPCVAX005_ZV121_D0_PBMC


title: HIPCVAX005_ZV120_D0_PBMC


title: HIPCVAX005_ZV104_D0_PBMC


title: HIPCVAX005_ZV118_D0_PBMC


title: HIPCVAX005_ZV116_D0_PBMC

value: mixed race


title: HIPCVAX005_ZV105_D0_PBMC


title: HIPCVAX005_ZV125_D0_PBMC


title: HIPCVAX005_ZV135_D0_PBMC


title: HIPCVAX005_ZV113_D0_PBMC


title: HIPCVAX005_ZV133_D0_PBMC


title: HIPCVAX005_ZV129_D0_PBMC


title: HIPCVAX005_ZV119_D0_PBMC


title: HIPCVAX005_ZV106_D0_PBMC


title: HIPCVAX005_ZV112_D0_PBMC


title: HIPCVAX005_ZV117_D0_PBMC


title: HIPCVAX005_ZV109_D0_PBMC


title: HIPCVAX005_ZV110_D0_PBMC


title: HIPCVAX005_ZV108_D0_PBMC


title: HIPCVAX005_ZV115_D0_PBMC