title: E18.5_2

description: 3'-RNA-seq amplified from 1ng RNA

source_name: Prospermatogonia


title: P5_1

status: Public on Sep 30 2021

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: 3'-RNA-seq amplified from 1ng RNA

library_source: transcriptomic

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_GRCm38.p6, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Spermatogonia

growth_protocol: Generation and Culture of Reconstituted Testes (rTestis)  To isolate E12.5 mouse male gonads (fetal testes), pregnant ICR females were sacrificed by cervical dislocation, and the embryos were isolated in chilled Dulbecco's Modified Eagle Medium (DMEM) (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 10 mM HEPES (GIBCO, #15630-106), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Fetal testes were identified by their appearance, and the mesonephroi were dissected out with tungsten needles.  The isolated fetal testes were dissociated into single cells, and endogenous mouse germ cells were selected out by magnetic-activated cell sorting (MACS).  Compared to FACS, MACS requires much less time and less physical stress to collect the cells for the rTestis formation.  The mPGCLCs (10,000 cells/well) and the fetal testes somatic cells (when using frozen stocks, 20,000 cells/well) (total 30,000 cells/well) were mixed and plated on the wells of a Nunclon Sphera 96-well Microplate (#174925; Thermo Fisher Scientific) and cultured under a floating condition in GK10+FR10 medium (GK10, 10 μM forskolin and 10 μM rolipram).  After a period of 2 days for the floating culture, using a glass capillary, the rTestes were transferred onto ThinCert™Cell Culture Inserts for 24-Well Plates (Greiner #662610) soaked in alpha-Minimum Essential Medium (GIBCO, #32561-037) containing 10% FCS (Hyclone), 55 μM 2-mercaptoethanol (GIBCO, 21985-023), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  Half the medium was changed every two days.  All rTestes were cultured for a gas-liquid interphase culture at 37℃ under an atmosphere of 5% CO2 in air.    Derivation of GSCLCs from rTestis  For the derivation of GSCLCs, VR+; CD9-APC+ cells in rTestes (m14) were sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ).  For deriving GSCLCs from all VR+; CD9-APC+ cells/rTestis, 24-well culture dishes (Falcon, #353047) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, seeded with mouse embryonic feeders (MEF) for at least 6 h prior to the plating of mPGCLC-derived cells, and then VR+; CD9-APC+ cells (derived from 1 rTestis)/well were seeded and cultured with GSCs/GSCLCs medium.  For deriving GSCLCs from single VR+; CD9-APC+ cells, 96-well culture dishes (Falcon, #353072) were coated with PBS supplemented with 0.1% gelatin for at least 30 min, then seeded with MMC-treated MEF for at least 6 h prior to the plating of an mPGCLC-derived cell.  A single VR+; CD9-APC+ cell was then seeded using a FACS Automated Cell Deposition Unit (ACDU) system and cultured with GSCs/GSCLCs medium.The GSC/GSCLC medium was as described previously (Kanatsu-Shinohara et al., 2003), with some modifications (Ishikura et al., 2016).  StemPro-34 SFM (GIBCO, #10639011) was supplemented with StemPro supplement (GIBCO, #10639011), 0.1 mM 2-mercaptoethanol (GIBCO, 21985-023), 1% FCS (Hyclone), 1 × minimal essential medium (MEM) Vitamin Solution (GIBCO, # 11120-052), 5.0 mg/mL AlbuMAXⅠ (GIBCO, #11020-021), 0.1 mM NEAA (GIBCO, #11140-050), 1 mM sodium pyruvate (GIBCO, 11360-070), 100 U/mL penicillin, 0.1 mg/mL streptomycin (GIBCO, #15070), 2 mM GlutaMAX (GIBCO, #35050-061), 1 × Insulin-Transferrin-Selenium (ITS-G) (GIBCO, #41400045), 10 ng/mL bFGF Recombinant Human Protein (Life Technologies, #13256029), 20 ng/mL GDNF Rat Recombinant (RSD, #512GF050), 20 ng/mL EGF Mouse Recombinant Carrier-free (RSD, #2028EG200), and 1000 U/mL LIF (Merk, ESG1107).  Half the medium was changed every two or three days.  All GSCs/GSCLCs were cultured at 37℃ under an atmosphere of 5% CO2 in air.

extract_protocol:
The cells were lysed and the total RNAs were purified using a NucleoSpin RNA XS (Takara Bio, #U0902A) according to the manufacturer’s instructions.  1 ng of total RNAs from each sample was used for the synthesis and amplification of cDNAs.
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).

treatment_protocol: Isolation of Germ Cells  To isolate germ cells for the RNA-seq analysis, ICR females were crossed with C57BL/6N; mvh-RFPTg/Tg males.  The embryonic gonads/postnatal testis fragments at E12.5–P7.5 were dissociated into single cells by incubating with 0.05% Trypsin-EDTA (GIBCO, #15400-054) for 10 min at 37℃, and were quenched with an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, #35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, #15070).  Large clumps of cells were removed using a nylon cell strainer (FALCON, #352350), and cells were centrifuged at 1,200 rpm for 5 min.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, 1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037), and sorted with a flow cytometer (BD Biosciences, FACS Aria Ⅲ)    Fluorescence-activated Cell Sorting (FACS)  The d4 floating aggregates of EpiLCs and d4c5 mPGCLCs were incubated in TrypLE express for 10 min at 37℃, with periodical pipetting, and the dissociates were quenched with a 5 × volume of DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, # 15260037) and DNase I (Sigma, DN25), followed by pipetting to generate a single cell suspension.  After centrifugation at 1,200 rpm for 5 min, the supernatant was discarded.  The cell pellet was re-suspended with DMEM/F12 medium (GIBCO, #1130-082) containing 0.1% BSA fraction V (Life Technologies, #15260037), the cell suspension was filtered through a nylon cell strainer (FALCON, #352350), and BV+ d4 mPGCLCs or BV+; SC+ d4c5 mPGCLCs were sorted by a flow cytometer (BD Biosciences, FACSAria III) and collected in the GK10+FR10 medium.  The rTestes at various culture periods were peeled off from the cell insert membrane using a P1000 pipette tip and incubated in 0.25% Trypsin-EDTA in PBS (GIBCO, #15400-054) for 5~15 min, with periodical intermittent pipetting, and the dissociates were quenched by an equal volume of DMEM medium (GIBCO, #10313-021) containing 10% FCS (Hyclone), 2 mM GlutaMAX (GIBCO, 35050-061), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (GIBCO, 15070).  The resultant cell pellet was resuspended with PBS containing 0.1% BSA fraction V (Life Technologies, # 15260037), and large clumps of cells were removed using a nylon cell strainer (FALCON, #352350).  The BV+; SC+ and Ddx4/mvh-RFP-positive (BV+; SC+; VR+) cells (mPGCLC-derived cells in rTestes: m0, m3, m5, m7, m10), VR+ and CD9-APC-positive (VR+; CD9-APC+) cells (mPGCLC-derived cells in rTestes: m12, m14), and VR+ cells in embryonic gonads/postnatal testes were sorted by the FACSAria III (BD Biosciences) cell sorter, and were collected in CELLOTION (Nippon Zenyaku Kogyo, CB051).  For RNA/DNA extraction, the sorted cells were centrifuged at 500G for 10 min, and the cell pellets were frozen down by liquid N2, and preserved at −80℃.

tag: genotype

tag: cell type

value: Germ cells

tag: strtain

value: ICR x B6C3(Cg)B6F1(5N)


title: E17.5_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_AGGCTTAG-CTCTCTAC

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: smart-seq2 protocol

data_processing:
For non-allele resulotion analyses, reads were mapped to the mouse reference genome (mm10) using STAR 2.5.3a (Dobin et al. 2013) and GENCODE vM16 annotation file. Alignment was performed with default parameters and --sjdbOverhang set to 74 and output to sorted BAM files. Uniquely aligned reads were quantified using the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019).
For allele resolution analyses, reads processed as previously described in (Janiszewski, talon et al). Briefly, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) (Krueger and Andrews 2016) supplied with the list of strain-specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout the entire genome of 20,563,466 SNP positions unique for either strain, of which 634,730 on the X Chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then split into two BAM files containing only strain-specific reads (on average 10.95% for Mus and 10.25% for Cast of total mapped reads) using SNPsplit (version 0.3.4). Unclassified reads were not used for subsequent allele-specific analysis. Using the allelic BAM files, variant calling files (VCF) were generated using samtools’ mpilup command (version 1.7) (ref), and merged using bcftools (ref)(version 1.5). An allelic count matrix was created by retaining counts from SNP positions and annotating these positions with their respective genes, where only genes covered by 4 SNPs or more are kept. Allelic data was size factor normalised by dividing allele-specific gene counts by total counts of that cell, this was then multiplied by 10000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: smartseq_norm_counts.csv: text file containing normalized read counts
Supplementary_files_format_and_content: smartseq_annotation.xlsx: spreadsheet containing additional metadata information
Supplementary_files_format_and_content: loom_XCR_5runs.loom: loom file containing both expression and gene regulatory network data together with tSNE embeddings

molecule: polyA RNA

source_name: MEF to iPSC reprogramming timecourse

growth_protocol: MEFs were cultured in MEF medium [DMEM (Gibco, 41966-554 052) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10270-106), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140-122), 1% (v/v) GlutaMAX (Gibco, 35050-061), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140-050), and 0.008% (v/v) beta-mercaptoethanol (Sigma-Aldrich, M7522)].   Cells undergoing reprogramming, and iPSCs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (50 μg/ml final).

extract_protocol:
For the isolation of Day 0 time point of single-cell transcriptome analysis, 96 Xi-GFP cells were sorted into a 96-well multiwell plate with 2 µl lysis buffer, followed by initial steps of smart-seq2 protocol (see below). Remaining cells were plated for reprogramming directly after sorting, 50.000 cells per one well of a 12 well plate. Reprogramming was induced by doxycycline (2 μg/ml final) in mouse ESC medium in the presence of ascorbic acid (50 μg/ml final). The medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with dox and AA withdrawal after picking. Next, FUT4+ reprogramming intermediates were sorted into single wells, each with 2 µl of the lysis buffer [0,2% Triton X100, 1:20 RRI (Recombinant RNase Inhibitor Takara)] and snap-frozen in -80°C until cells from all timepoints were collected.
All samples were processed following the smart-seq2 protocol (Picelli et al). cDNA synthesis was done starting from 500 pg of input RNA, followed by library preparation from 80 pg of cDNA using the Nextera XT kit (Illumina, FC-131-1096). Indexing was performed with the Nextera XT index Kit V2 (Illumina, FC-131-2003). The quality of cDNA and individual libraries was assessed using an Agilent 2100 Bioanalyzer system.

treatment_protocol: Reprogramming experiments, unless stated otherwise, were performed by conditional induction of lentivirally delivered reprogramming factors. First, passage 1 MEFs at around 70% confluency were transduced with concentrated lentiviral supernatants. Lentiviruses were generated using HEK cells separately for two constructs: tetO-FUW-OSKM, Addgene cat. 20321 (Carey et al. 2009) and FUW-M2rtTA, Addgene cat. 20342 (Hockemeyer et al. 2008) with the calcium precipitation method. Supernatants with lentiviral particles were concentrated using lenti-X-concentrator (Takara, 631231) in 1:100 ratios. Infection with a pool of equal volumes of both constructs was carried out overnight, followed by 12 hours culture in MEF medium and 1:6 split. Cells were then sorted using FACS (described below) in order to isolate homogeneous population with regard to allelic inactivation of the X-GFP transgene (either Xi-GFP or Xa-GFP).

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K107713_RNASeq

city: Indianapolis

first: Natascia

last: Marino

state: IN

address: 980 W. Walnut St, R3-C238

department: Hematology/Oncology Division

country: USA

institute: Indiana University School of Medicine

description:
transcriptome profile
K107713_RNASeq

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.36 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the human genome reference, GRCh38.p12 using STAR (version STAR_2.5.2b) (Dobin et al. 2013).
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes from gencode v.28 using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Wiggle files containing deduplicated insert coverage

organism: Homo sapiens

source_name: Breast

growth_protocol: The breast tissue cores are collected by using a needle biopsy needle (Hologic, Marlborough, MA). The skin is cleaned, then numbed with lidocaine. The physician nicks the skin with a scalpel, usually in the upper-outer quadrant of the breast, and the needle is inserted into this incision. From this single incision, five sample cores are removed from the breast (approximately 200mg). A nurse/surgeon’s assistant holds pressure on the incision for 10 full minutes, then applies a pressure bandage. An ice pack is immediately placed on the breast. Within 10 min from collection the tissue cores are fresh frozen in liquid nitrogen

extract_protocol:
Total RNA was extracted using the Allprep DNA/RNA/miRNA Universal Kit (QIAGEN, Germantown, MD).
The concentration and quality of total RNA and DNA samples was first assessed using Agilent 2100 Bioanalyzer. For the RNAsequencing: cDNA library was prepared using the TruSeq Stranded Total RNA Kit (Illumina) and sequenced using Illumina HiSeq4000. For the DNA methylation analysis: Library was generated using MethylCap Library Kit (Diagenode, Denville NJ, US) according to the manufacturer′s protocols followed by single-end 75-bp sequencing on Illumina Nextseq4000

tag: age

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

tag: race

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: P1_2

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_AGGCTTAG-GGACTCCT

description: smart-seq2 protocol


title: P5_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K107731_RNASeq

description:
transcriptome profile
K107731_RNASeq

value: Post


title: GC071398_AGGCTTAG-GCTCATGA

description: smart-seq2 protocol


title: E16.5_1

description: 3'-RNA-seq amplified from 1ng RNA


title: P0_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K107658_RNASeq

description:
transcriptome profile
K107658_RNASeq


title: GC071398_AGGCTTAG-CGATCAGT

description: smart-seq2 protocol

value: iPSCs


title: E15.5_1

description: 3'-RNA-seq amplified from 1ng RNA


title: K107628_RNASeq (second donation from K106641)

description:
transcriptome profile
K107628_RNASeq

value: AFRNAMER


title: E17.5_1

description: 3'-RNA-seq amplified from 1ng RNA


title: GC071398_AGGCTTAG-CCTAAGAC

description: smart-seq2 protocol


title: K107572_RNASeq

description:
transcriptome profile
K107572_RNASeq


title: GC071398_AGGCTTAG-GCGTAGTA

description: smart-seq2 protocol


title: GC071398_AGGCTTAG-ATGCGCAG

description: smart-seq2 protocol


title: E15.5_2

description: 3'-RNA-seq amplified from 1ng RNA


title: K107659_RNASeq

description:
transcriptome profile
K107659_RNASeq

value: Average


title: K107661_RNASeq

description:
transcriptome profile
K107661_RNASeq


title: E18.5_1

description: 3'-RNA-seq amplified from 1ng RNA


title: K107842_RNASeq (second donation from K107545)

description:
transcriptome profile
K107842_RNASeq


title: 96CC

city: New York

first: Fatemeh

last: Haghighi

state: NY

address: 1425 Madison Ave, 9-20D

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Alignment of sequenced reads was done with STAR 2.4.2a. STAR index was created using splice junction annotation database for guidance and both genome sequence and annotation files of Ensembl Rnor 6.0.
Quantification of gene expression was achieved through featureCounts 1.4.3-p1 with Ensembl Rnor 6.0 annotation.
Genome_build: Ensembl rnor 6.0 (Rnor_6.0)
Supplementary_files_format_and_content: featureCounts.txt: Tab-delimited text file includes raw counts.

organism: Rattus norvegicus

source_name: Brain

growth_protocol: 11 adult male Sprague-Daley rats (275–320 g) were maintained on a 12:12 light:dark cycle for at least two weeks, then were randomized to PBBI (n=6) or sham (n=5) groups.

extract_protocol: Brains were harvested, underwent sectioning and cortical tissue samples were stored. RNA were isolated from tissue samples.

treatment_protocol:
Penetrating Ballistic Brain Injury (PBBI). Following a recovery period of approximately 2–3 days after EEG/implantation, animals received a right unilateral frontal PBBI injury. This penetrating injury was a model of a shockwave with a ballistic component that created a brain cavity. A computer-controlled simulated ballistic injury device with an attached custom-designed 20 G stainless steel tubular probe. Along one end of this probe were fixed holes covered by airtight elastic tubing. Following unilateral (right) frontal pole craniectomy (+4.5mm anteroposterior, +2mm medio-lateral from bregma), the probe was inserted at an angle of 50° from the vertical axis and 25° counter-clockwise from the anterior-posterior axis to a distance of 1.2 cm from the dural surface of the brain. An automated pulse-generator was used to quickly (< 40 ms) inflate/deflate the elastic tubing into an elliptical balloon to a size roughly equal to 10% brain volume. Sham animals were subjected to identical procedures but without probe insertion.
Sleep-Wake Assessment. Twenty-four hour continuous EEG/EMG data were collected (n=11). EG electrodes were implanted using a flexible shielded cable and multipin connector equipped with multichannel gold contact swivel commutator (Dragonfly Inc., Ridgeley, WV). All EEG/EMG/ECG signals were continuously monitored at a sampling frequency of 400 Hz using a computerized Grass Technologies LTM Monitoring amplifier and data acquisition system (Natus Neurology Incorporated - Grass Products, Warwick, RI). EEG and EMG signals were used to objectively classify 1-second epochs into vigilance states (wakefulness, slow-wave sleep, and REM sleep) using a computerized algorithm based on EEG and EMG amplitudes and frequencies as well as the probability that the subject will transition from a given stage to another (Neuroscore 3.0 software, Data Sciences International, St Paul, MN). The sleep score for a given 10-second period was based on the summary of 1-second epochs. Epochs were assigned to a specific vigilance state when < 50% of the epoch fulfilled the criteria for a sleep stage.
The time spent in vigilance states (minutes/hour) was calculated for the entire 12-hour period. All 10-second epochs were summed into 60-minute bins and group-averaged to examine the amount of time spent in wake, SWS, and REM sleep. Polysomnograms of each hemisphere (contralateral and ipsilateral to injury) were scored separately. Sleep-wake parameters used in these analyses included latency (onset) to SWS or REM sleep (defined as the time interval to the first six consecutive SWS or REM 10-second epochs), and duration of sleep/wake states.

tag: strain

value: Sprague-Daley

tag: Sex

value: Male

value: Adult

tag: tissue

value: Brain

tag: hemisphere

value: CONTRA

tag: treatment

value: PBBI

tag: animal id


title: E14.5_2

description: 3'-RNA-seq amplified from 1ng RNA

tag: genotype

tag: cell type

value: Germ cells

tag: strtain

value: ICR x B6C3(Cg)B6F1(5N)


title: 91CI

tag: age

value: IPSI

value: SHAM


title: 90CI


title: K107509_RNASeq

description:
transcriptome profile
K107509_RNASeq

tag: age of menarche

tag: menopausal status

value: No

tag: blood relatives cancer

value: Yes


title: E16.5_2

description: 3'-RNA-seq amplified from 1ng RNA


title: 90CC


title: P0_1

description: 3'-RNA-seq amplified from 1ng RNA


title: 96CI


title: K107545_RNASeq

description:
transcriptome profile
K107545_RNASeq

tag: race

tag: hispanic

tag: bmi


title: 94CC


title: 94CI


title: GC071398_AGGCTTAG-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: E14.5_1

description: 3'-RNA-seq amplified from 1ng RNA


title: 88CI

tag: strain

tag: Sex


title: GC071398_AGGCTTAG-ACTGAGCG

description: smart-seq2 protocol


title: K107540_RNASeq

description:
transcriptome profile
K107540_RNASeq

value: Pre

value: WHITE

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071398_AGGCTTAG-ACTCGCTA

description: smart-seq2 protocol

value: iPSCs


title: GC071398_AGGCTTAG-CGAGGCTG

description: smart-seq2 protocol


title: 91CC

tag: tissue

tag: hemisphere

tag: treatment

tag: animal id


title: 85CI

tag: age


title: 86CC


title: K107467_RNASeq

description:
transcriptome profile
K107467_RNASeq

tag: age of menarche

tag: menopausal status

value: Average


title: K107454_RNASeq

description:
transcriptome profile
K107454_RNASeq

tag: blood relatives cancer

tag: race

value: ASIAN


title: 86CI

value: Sprague-Daley

value: Male


title: 84CC

value: Adult

value: Brain


title: GC071398_AGGCTTAG-ATCTCAGG

description: smart-seq2 protocol


title: GC071398_AGGCTTAG-AGGCAGAA

description: smart-seq2 protocol


title: GC071398_AGCTAGAA-TGCAGCTA

description: smart-seq2 protocol

value: Cast


title: K107456_RNASeq

description:
transcriptome profile
K107456_RNASeq

tag: hispanic

tag: bmi


title: 88CC

value: CONTRA

value: PBBI


title: K107480_RNASeq

description:
transcriptome profile
K107480_RNASeq

value: Post


title: 83CC-T2-3


title: GC071398_AGGCTTAG-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: 85CC

tag: strain

tag: Sex


title: GC071398_AGCTAGAA-TCGACGTC

description: smart-seq2 protocol


title: K107439_RNASeq

description:
transcriptome profile
K107439_RNASeq

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)


title: 84CI

tag: tissue

value: IPSI

value: SHAM


title: 82PFC-C-3

tag: hemisphere


title: K107448_RNASeq (second donation from K106629)

description:
transcriptome profile
K107448_RNASeq

value: No

tag: risk category


title: GC071398_AGCTAGAA-GGAGCTAC

description: smart-seq2 protocol


title: 81PFC-C

tag: treatment

tag: animal id


title: GC071398_AGCTAGAA-TAGCGCTC

description: smart-seq2 protocol


title: 83CI

tag: age


title: 82CI-3


title: GC071398_AGCTAGAA-TACGCTGC

description: smart-seq2 protocol


title: K107435_RNASeq

description:
transcriptome profile
K107435_RNASeq

tag: age of menarche

tag: menopausal status

value: Yes

value: High


title: GC071398_AGCTAGAA-CGGAGCCT

description: smart-seq2 protocol


title: GC071398_AGCTAGAA-CCTAAGAC

description: smart-seq2 protocol


title: 81PFC-I


title: GC071398_AGCTAGAA-GCGTAGTA

description: smart-seq2 protocol


title: GC071398_AGCTAGAA-CGATCAGT

description: smart-seq2 protocol


title: K107359_RNASeq

description:
transcriptome profile
K107359_RNASeq

tag: blood relatives cancer

tag: race

value: WHITE


title: K107341_RNASeq

description:
transcriptome profile
K107341_RNASeq

value: Pre

tag: hispanic

tag: bmi


title: K107389_RNASeq

description:
transcriptome profile
K107389_RNASeq

value: Average


title: Lung tissue_surgery_rep5-2

type: RNA

city: Nanjing

first: Chen

last: Wang

state: Jiangsu

address: 163 Xianlin Avenue

department: Life Sciences

country: China

institute: Nanjing University

description: LncRNA and mRNA expresssion data from matched nontumor tissues in NSCLC patients

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change filtering or Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Matched nontumor tissues, rep5-2

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Lung cancer tissues and matched nontumor tissues from NSCLC patients

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

treatment_protocol: Lung tissues from NSCLC surgery were instantly immersed in liquid nitrogen and preserved at -80 °C.

value: Lung

tag: disease state

value: matched non-tumor

tag: gender

value: female

tag: patient id


title: K107339_RNASeq

description:
transcriptome profile
K107339_RNASeq

tag: ever pregnant


title: Sandhoff 2

city: Sevilla

first: Alejandro

last: Rubio

state: Sevilla

address: C/Utrera, Km1

department: Genética

country: Spain

institute: Universidad Pablo de Olavide

description: Gene expression data from Sandhoff patient

hyb_protocol: 100 ng of total RNA was hybridized to 5.2 μg of labelled cDNA

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

data_processing: Array data were processed using Affymetrix® Genechip® Command Console® 2.0 with respect to background subtraction and normalization. We used the Affymetrix Microarrays ClariomTM D Arrays Human and Mouse, which includes 65956 genes. The raw data were analysed by the Affymetrix software Trancriptome Analysis Console (TAC) which analyse and visualize global expression patterns of genes, exons, pathways, and alternative splicing events.

label: biotin

source_name: Patient fibroblasts with Sandhoff

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

growth_protocol: After approval of the local ethics committee and informed consent forms form the patients were obtained, patient fibroblasts with Tay-Sachs and Sandhoff were isolate from skin patient’s biopsies. They were obtained according to the Helsinki Declarations of 1964, as revised in 2001. Skin biopsies were placed in 10ml of transport media (PBS1X and antibiotics) and transported at RT. Individual samples were transferred to a sterile 35mm Petri dish and cut in a 5-10mm2 piece of tissue. Then, it was dissociated with forceps and scalpel transferring to a new 35mm Petri dish with the dermis upside down. The dish was placed inside the culture hood during 5-10 minutes to let the pieces of tissue dry and attach to the dish surface. After that, the samples were covered with DMEM culture 20% FBS and placed in the incubator 37ºC and 5% of CO2 until the fibroblast were propagated. Fibroblasts were cultured in high glucose media DMEM (Dulbeccoo`s modified media) (Gibco, Invitrogen, Eugene, OR, USA) supplemented with 20% fetal bovine serum (FBS) (Gibco, Invitrogen, Eugene, OR, USA) and 1% antibiotics (Sigma ChemicalCo., St Louis, MO, USA). Cells were incubated at 37ºC in a 5% CO2 atmosphere.

extract_protocol: Total RNA from fibroblasts were extracted using the RNeasy kit (RNeasy, QIAGEN, Valencia, CA) and then the quality of total RNA for array analysis was determined using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

tag: group

value: Sandhoff


title: Tay-Sachs Infantile, Infantile 3

description: Gene expression data from Tay-Sachs infantile patient

source_name: Patient fibroblasts with Tay-Sachs Infantile

value: TS Infantile


title: Tay-Sachs Infantile, Infantile 4


title: K107298_RNASeq

description:
transcriptome profile
K107298_RNASeq

tag: life time risk (tyrer-cuzick score)


title: GC071398_AGCTAGAA-ATGCGCAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Cast


title: K107299_RNASeq

description:
transcriptome profile
K107299_RNASeq

tag: risk category


title: GC071398_AGCTAGAA-ACTGAGCG

description: smart-seq2 protocol


title: Tay-Sachs Juvenile, Juvenile 3

description: Gene expression data from Tay-Sachs juvenile patient

source_name: Patient fibroblasts with Tay-Sachs Juvenile

value: TS Juvenile


title: K107324_RNASeq

description:
transcriptome profile
K107324_RNASeq


title: K107325_RNASeq

description:
transcriptome profile
K107325_RNASeq


title: K107284_RNASeq (second donation from K106008)

description:
transcriptome profile
K107284_RNASeq


title: GC071398_AGCTAGAA-ACTCGCTA

description: smart-seq2 protocol


title: Lung tissue_surgery_rep5-1

description: LncRNA and mRNA expresssion data from lung cancer tissues in NSCLC patients

source_name: Lung cancer tissues, rep5-1

tag: tissue

value: non-small cell lung cancer (NSCLC)


title: Lung tissue_surgery_rep4-2

source_name: Matched nontumor tissues, rep4-2

value: male

tag: age


title: K107266_RNASeq

description:
transcriptome profile
K107266_RNASeq

tag: age of menarche

value: Don‚Äôt know


title: GC071398_AGAGGATA-TCGACGTC

description: smart-seq2 protocol

value: iPSCs

value: Mus


title: K107264_RNASeq

description:
transcriptome profile
K107264_RNASeq

tag: menopausal status

value: No

value: Yes

value: AFRNAMER


title: 779_pe_astrocyte

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

data_processing:
Basecalls and demultiplexing performed with bcl2fastq2 (Illumina)
alignment to mouse GRCm38 and human GRCh38 Ensembl release 76 with STAR v2.5.1a1
Gene counts derived using Subread::featureCount v1.4.6-p52
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: raw counts file in .tsv format

source_name: astrocyte

growth_protocol: mice were aged to 3.8 months

extract_protocol:
Total RNA was extracted from FACS-isolated microglia and astrocytes using miRNeasy Micro Kit (Qiagen, 1071023), following the manufacture's instructions. During the purification, DNase was utilized to ensure the total RNA was free of genomic DNA.
After determining the integrity on an Agilent Bioanalyzer, extracted total RNA was prepared using the Takara-Clontech SMARTer library preparation method in the GTAC at Washington University.

treatment_protocol: 2 dose of tamoxifen were administered i.p. 100 mg/kg to remove astroycte APOE4 in Aldh1l1-Cre+ mice

tag: mouse genotype

tag: cell type

value: astrocyte

tag: treatment

value: tamoxifen


title: Healthy, HDFN3

description: Gene expression data from healthy patient

source_name: Healthy patient

value: HDFN


title: Tay-Sachs Infantile, Infantile 1


title: Lung tissue_surgery_rep3-2

source_name: Matched nontumor tissues, rep3-2

value: Lung

value: matched non-tumor


title: Lung tissue_surgery_rep3-1

source_name: Lung cancer tissues, rep3-1


title: Healthy, HDFN2


title: Sandhoff 1

value: Sandhoff


title: 779_cy7_microglia

source_name: cortex, hippocampus, thalamus microglia

value: microglia


title: Lung tissue_surgery_rep2-2

source_name: Matched nontumor tissues, rep2-2


title: 774_pe_astrocyte

source_name: cortex, hippocampus, thalamus astrocyte


title: Lung tissue_surgery_rep4-1

source_name: Lung cancer tissues, rep4-1


title: K107251_RNASeq

description:
transcriptome profile
K107251_RNASeq

value: Pre

tag: blood relatives cancer

tag: race

value: WHITE

tag: hispanic

tag: bmi

value: High


title: Tay-Sachs Juvenile, Juvenile 1

value: TS Juvenile


title: GC071398_AGAGGATA-TAGGCATG

description: smart-seq2 protocol

source_name: MEF to iPSC reprogramming timecourse


title: 774_cy7_microglia


title: GC071398_AGAGGATA-TCCTGAGC

description: smart-seq2 protocol


title: Healthy, HDFN1


title: GC071398_AGAGGATA-TAGCGCTC

description: smart-seq2 protocol


title: 759_pe_astrocyte


title: Tay-Sachs Infantile, Infantile 2

value: TS Infantile


title: K107244_RNASeq

description:
transcriptome profile
K107244_RNASeq

source_name: Breast

tag: ever pregnant

value: Average


title: Lung tissue_surgery_rep1-2

source_name: Matched nontumor tissues, rep1-2

tag: disease state

tag: gender

value: male

tag: patient id


title: GC071398_AGAGGATA-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Tay-Sachs Juvenile, Juvenile 2

tag: group


title: Lung tissue_surgery_rep1-1

source_name: Lung cancer tissues, rep1-1

tag: tissue

value: non-small cell lung cancer (NSCLC)

tag: age


title: DNA_METHYLATION_15-492/005_BENIGN

type: genomic

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-492/005
A10-177-5_BENIGN

hyb_protocol: Bisulfite converted DNA was fragmented and hybridized to Illumina EPIC arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScanSQ using standard recommended Illumina scanner setting

data_processing:
IDAT files were processed using Minfi (R version 4.1) using the preprocessRaw and preprocessSWAN functions. Methyated and unmethylated intensity values were acquired using the getMeth and getUnmeth functions. Detection P values were acquired using the detectionP function. SWAN-normalized beta values were acquired using the ratioConvert and getBeta functions.
matrix_processed.txt:  SWAN normalized Average Beta
matrix_signal_intensities.txt:  Unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA was purifed from ribbons of FFPE tissues using the QIAamp DNA FFPE Tissue Kit, or from buffy coat aliquots using the DNeasy Blood and Tissue Kit, according to the manufacturer's instructions.

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Blood was drawn into EDTA tubes prior to surgery. Prostate tissues were grossed, accessioned, fixed in formalin, and embedded in paraffin.

value: prostate cancer

tag: patientid

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type

value: normal

value: prostate tissue


title: DNA_METHYLATION_15-492/005_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-492/005
A10-178-35_TUMOR

tag: race

value: cancer


title: DNA_METHYLATION_15-492/006_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-492/006
A10-177-6_BENIGN

value: remission


title: DNA_METHYLATION_15-492/006_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-492/006
A10-178-36_TUMOR


title: Lung tissue_surgery_rep2-1

source_name: Lung cancer tissues, rep2-1

value: Lung


title: K107241_RNASeq

description:
transcriptome profile
K107241_RNASeq

tag: age of menarche

tag: menopausal status

value: Post

value: No

tag: blood relatives cancer

tag: hispanic

tag: bmi

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071398_AGAGGATA-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071398_AGAGGATA-TACGCTGC

description: smart-seq2 protocol

value: iPSCs


title: GC071398_AGAGGATA-GGACTCCT

description: smart-seq2 protocol


title: 475_pe_astrocyte

tag: mouse genotype

tag: cell type

value: astrocyte

tag: treatment

value: tamoxifen


title: GC071398_AGAGGATA-TGCAGCTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-492/004_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-492/004
A10-178-34_TUMOR

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: age

tag: tissue


title: 475_cy7_microglia

value: microglia


title: K107225_RNASeq

description:
transcriptome profile
K107225_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

value: WHITE

tag: ever pregnant

value: Average


title: DNA_METHYLATION_15-492/006_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-492/006
A10-172-20_BUFFYCOAT

value: prostate cancer

value: white

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: buffy coat


title: K107188_RNASeq (second donation from K105894)

description:
transcriptome profile
K107188_RNASeq

tag: hispanic

tag: bmi

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-492/005_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-492/005
A10-172-19_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

value: recurrence

value: normal


title: GC071398_AGAGGATA-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071398_AGAGGATA-GCTCATGA

description: smart-seq2 protocol


title: 469_cy7_microglia

tag: mouse genotype

tag: cell type

tag: treatment


title: 460_pe_astrocyte


title: GC071398_AGAGGATA-CGTACTAG

description: smart-seq2 protocol


title: K107257_RNASeq

description:
transcriptome profile
K107257_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race


title: K107214_RNASeq

description:
transcriptome profile
K107214_RNASeq

value: Post

tag: hispanic

tag: ever pregnant


title: 759_cy7_microglia


title: GC071398_AGAGGATA-CGGAGCCT

description: smart-seq2 protocol


title: K107092_RNASeq

description:
transcriptome profile
K107092_RNASeq

value: No

tag: bmi

tag: life time risk (tyrer-cuzick score)


title: DNA_METHYLATION_15-492/004_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-492/004
A10-172-18_BUFFYCOAT

tag: disease state

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue


title: 465_pe_astrocyte

tag: mouse genotype

tag: cell type

tag: treatment


title: 469_pe_astrocyte


title: 459_pe_astrocyte


title: GC071398_AGAGGATA-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

value: iPSCs

tag: initially inactive x allele


title: K107172_RNASeq

description:
transcriptome profile
K107172_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

value: Yes

tag: risk category


title: K107170_RNASeq

description:
transcriptome profile
K107170_RNASeq

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

value: High


title: DNA_METHYLATION_15-492/003_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-492/003
A10-177-4_BENIGN

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: black

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: prostate tissue


title: K107216_RNASeq

description:
transcriptome profile
K107216_RNASeq

tag: age

tag: age of menarche

value: WHITE


title: 465_cy7_microglia

tag: mouse genotype

tag: cell type

value: microglia

tag: treatment

value: tamoxifen


title: GC071398_AGAGGATA-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071398_AGAGGATA-CTCTCTAC

description: smart-seq2 protocol


title: 460_cy7_microglia


title: K107203_RNASeq

description:
transcriptome profile
K107203_RNASeq

tag: menopausal status

tag: blood relatives cancer

tag: race

tag: hispanic

tag: bmi

tag: ever pregnant

tag: risk category

value: Average


title: DNA_METHYLATION_15-492/002_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-492/002
A10-178-31_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: tissue


title: DNA_METHYLATION_15-492/003_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-492/003
A10-178-33_TUMOR

tag: age

tag: 5-year disease status

value: recurrence

tag: sample type

value: cancer


title: 458_pe_astrocyte

tag: mouse genotype

tag: cell type

value: astrocyte

tag: treatment


title: GC071398_AGAGGATA-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-492/004_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-492/004
A10-177-7_BENIGN

tag: race

value: white

value: normal


title: DNA_METHYLATION_15-492/002_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-492/002
A10-172-16_BUFFYCOAT

value: remission

value: buffy coat


title: DNA_METHYLATION_15-492/002_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-492/002
A10-178-32_TUMOR


title: DNA_METHYLATION_15-492/003_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-492/003
A10-172-17_BUFFYCOAT


title: K107140_RNASeq

description:
transcriptome profile
K107140_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: 458_cy7_microglia


title: K107043_RNASeq

description:
transcriptome profile
K107043_RNASeq

tag: age

value: Yes

value: WHITE


title: K107041_RNASeq

description:
transcriptome profile
K107041_RNASeq

value: Post


title: 459_cy7_microglia

value: microglia

value: tamoxifen


title: GC071398_AGAGGATA-ATCTCAGG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-492/001_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-492/001
A10-178-30_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: tissue

value: prostate tissue


title: GC071398_AGAGGATA-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: 447_cy7_microglia

tag: mouse genotype

tag: cell type

tag: treatment


title: DNA_METHYLATION_15-492/001_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-492/001
A10-172-15_BUFFYCOAT

tag: race

value: white

tag: sample type


title: GC071398_AGAGGATA-CCTAAGAC

description: smart-seq2 protocol

value: iPSCs


title: GC071398_AGAGGATA-ATGCGCAG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U47_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U47
A10-178-27_BENIGN

value: remission

value: normal


title: K107050_RNASeq

description:
transcriptome profile
K107050_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: K106979_RNASeq (second donation from K107339)

description:
transcriptome profile
K106979_RNASeq

tag: age

value: No


title: DNA_METHYLATION_15-008/U47_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U47
A10-172-12_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: tissue

value: buffy coat


title: DNA_METHYLATION_15-492/001_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-492/001
A10-178-29_BENIGN

tag: race

tag: sample type


title: 447_pe_astrocyte

tag: mouse genotype

tag: cell type

value: astrocyte

tag: treatment


title: K106980_RNASeq

description:
transcriptome profile
K106980_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

value: High


title: 443_pe_astrocyte

value: tamoxifen


title: K107021_RNASeq (second donation from K106734)

description:
transcriptome profile
K107021_RNASeq

tag: age

value: Post

value: Don‚Äôt know

value: AFRNAMER

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071398_AGAGGATA-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: 443_cy7_microglia

value: microglia


title: K107062_RNASeq

description:
transcriptome profile
K107062_RNASeq


title: GC071398_ACTCTAGG-TCGACGTC

description: smart-seq2 protocol

value: Cast


title: DNA_METHYLATION_15-008/U47_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U47
A10-178-28_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

value: cancer

tag: tissue

value: prostate tissue


title: K107016_RNASeq

description:
transcriptome profile
K107016_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

tag: race

value: Average


title: DNA_METHYLATION_15-008/U46_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U46
A10-178-25_BENIGN

tag: age

tag: sample type

value: normal


title: GC071398_AGAGGATA-ACTCGCTA

description: smart-seq2 protocol

value: iPSCs


title: GC071398_AGAGGATA-AAGAGGCA

description: smart-seq2 protocol


title: K107069_RNASeq

description:
transcriptome profile
K107069_RNASeq

value: Yes

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071398_ACTCTAGG-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: 439_pe_astrocyte

tag: mouse genotype

tag: cell type

value: astrocyte

tag: treatment

value: tamoxifen


title: DNA_METHYLATION_15-008/U46_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U46
A10-178-26_TUMOR

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

tag: tissue


title: GC071398_ACTCTAGG-TAGCGCTC

description: smart-seq2 protocol

value: Cast


title: 26_pe_astrocyte


title: GC071398_ACTCTAGG-GGAGCTAC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U45_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U45
A10-177-8_BENIGN

value: prostate cancer

tag: race

tag: age

tag: sample type


title: K106889_RNASeq

description:
transcriptome profile
K106889_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Asian

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: B3

city: Xi'an

first: Feng

last: Zhang

address: Changle west Road

department: Department of Pathology

institute: Fourth Military Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；mRNA-seq reads were aligned to the mmu10 genome assembly using Hisat2 version 2.1.0 .
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression were analysed  using edgeR package in R program version 3.4.3
Genome_build: mmu10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: postnatal day 6 mice

growth_protocol: All the mice were maintained in pathogen-free conditions

extract_protocol:
Total RNA was extracted from.Cartilaginous tissues using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hbb were conditionally knockout in cartilage in experiment groups.Cartilaginous tissues of knee joint of P6 mice were collected

value: knee joint cartilaginous tissues

tag: genotype

value: wildtype


title: K106766_RNASeq

description:
transcriptome profile
K106766_RNASeq

value: Post


title: K106801_RNASeq

description:
transcriptome profile
K106801_RNASeq


title: DNA_METHYLATION_15-008/U44_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U44
A10-178-23_TUMOR

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

value: unknown

value: remission

value: cancer

value: prostate tissue


title: K106863_RNASeq (second donation from K106169)

description:
transcriptome profile
K106863_RNASeq

value: Pre

value: No

value: Average


title: K106845_RNASeq

description:
transcriptome profile
K106845_RNASeq

value: WHITE

value: Yes


title: B1

tag: tissue


title: DNA_METHYLATION_15-008/U46_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U46
A10-172-11_BUFFYCOAT

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: normal

value: buffy coat


title: 22_cy7_microglia

tag: mouse genotype

tag: cell type

value: microglia

tag: treatment

value: tamoxifen


title: K106734_RNASeq

description:
transcriptome profile
K106734_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Don‚Äôt know

value: AFRNAMER

tag: hispanic

tag: bmi


title: GC071398_ACTCTAGG-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Cast


title: GC071398_ACTCTAGG-CCTAAGAC

description: smart-seq2 protocol


title: K106733_RNASeq

description:
transcriptome profile
K106733_RNASeq

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: GC071398_ACTCTAGG-CGATCAGT

description: smart-seq2 protocol


title: GC071398_ACTCTAGG-CGGAGCCT

description: smart-seq2 protocol


title: A3

tag: tissue

value: knee joint cartilaginous tissues

tag: genotype

value: Hbb conditional knockout in chondrocytes


title: A2


title: GC071398_ACTCTAGG-ATGCGCAG

description: smart-seq2 protocol


title: 26_cy7_microglia


title: K106757_RNASeq

description:
transcriptome profile
K106757_RNASeq

tag: race

value: High


title: B2

value: wildtype


title: DNA_METHYLATION_15-008/U45_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U45
A10-178-24_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

value: prostate tissue


title: GC071398_ACTCTAGG-ACTGAGCG

description: smart-seq2 protocol


title: GC071398_ACTCTAGG-GCGTAGTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U44_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U44
A10-170-45_BUFFYCOAT

value: unknown

tag: age


title: K106841_RNASeq

description:
transcriptome profile
K106841_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

value: No

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

tag: bmi


title: K106684_RNASeq

description:
transcriptome profile
K106684_RNASeq

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: DNA_METHYLATION_15-008/U42_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U42
A10-178-19_TUMOR

tag: disease state

tag: race

value: white

tag: tissue


title: DNA_METHYLATION_15-008/U44_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U44
A10-178-22_BENIGN

tag: patientid

tag: gender

tag: preoperative psa

value: normal


title: DNA_METHYLATION_15-008/U45_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U45
A10-170-46_BUFFYCOAT

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: buffy coat


title: DNA_METHYLATION_15-008/U43_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U43
A10-178-21_TUMOR

tag: age

value: recurrence

tag: sample type


title: DNA_METHYLATION_15-008/U42_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U42
A10-178-18_BENIGN


title: 439_cy7_microglia

tag: mouse genotype

tag: cell type

value: microglia

tag: treatment

value: tamoxifen


title: K106713_RNASeq

description:
transcriptome profile
K106713_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

value: High


title: GC071398_ACTCTAGG-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Cast


title: LSK from EC-Spred1 KO CML mice [44219_24]

city: Duarte

first: Hsun

middle: Teresa

last: Ku

state: CA

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: LSK from EC-Spred1 KO CML mice

extract_protocol: Total RNA was extracted from Lin-Sca-1+c-Kit+ (LSK) cells sorted from the BM of Spred1HSCΔ/ΔSCLtTA/BCR-ABL (HSC KO) and Spred1HSCwt/wtSCLtTA/BCR-ABL (HSC wt) (n=5 mice per group, both group given 7 doses of 250μg poly(I:C), ip, every two days, to activate Mx1-cre), Spred1ECΔ/ΔSCLtTA/BCR-ABL (EC KO) and Spred1ECwt/wtSCLtTA/BCR-ABL (EC wt) (n=5 mice per group) mice using the miRNeasy micro Kit (Qiagen, Valencia, CA)

value: leukemic stem cells (LSK)

tag: strain background

tag: genotype/variation

value: EC-Spred1 KO CML mice


title: DNA_METHYLATION_15-008/U42_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U42
A10-170-43_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

value: remission

tag: tissue


title: DNA_METHYLATION_15-008/U43_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U43
A10-170-44_BUFFYCOAT

tag: age

tag: 5-year disease status

tag: sample type


title: GC071392_TCTTACGC-TAGGCATG

description: smart-seq2 protocol

value: Mus


title: LSK from EC-Spred1 KO CML mice [44221_26]

tag: cell type


title: LSK from EC-Spred1 KO CML mice [44217_22]


title: 22_pe_astrocyte

tag: mouse genotype

value: astrocyte

tag: treatment


title: GC071392_TCTTACGC-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106655_RNASeq

description:
transcriptome profile
K106655_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: A1

tag: tissue

value: knee joint cartilaginous tissues

tag: genotype

value: Hbb conditional knockout in chondrocytes


title: DNA_METHYLATION_15-008/U41_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U41
A10-178-17_TUMOR

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: cancer

value: prostate tissue


title: K106695_RNASeq (second donation from K104949

description:
transcriptome profile
K106695_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Average


title: LSK from EC-Spred1 KO CML mice [44218_23]

tag: cell type

value: leukemic stem cells (LSK)

tag: strain background

tag: genotype/variation


title: LSK from EC-Spred1 KO CML mice [44220_25]

value: EC-Spred1 KO CML mice


title: GC071392_TCTTACGC-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/U41_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U41
A10-170-42_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: sample type

value: normal

tag: tissue

value: buffy coat


title: K106642_RNASeq

description:
transcriptome profile
K106642_RNASeq

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: LSK from HSC-Spred1 wt CML mice [44215_20]

source_name: LSK from HSC-Spred1 wt CML mice

value: HSC-Spred1 wt CML mice


title: GC071392_TCTTACGC-TCGACGTC

description: smart-seq2 protocol

value: Mus


title: DNA_METHYLATION_15-008/U40_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U40
A10-178-15_TUMOR

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission


title: LSK from HSC-Spred1 wt CML mice [44213_18]

tag: cell type

tag: strain background

tag: genotype/variation


title: K106730_RNASeq (second donation from K106642)

description:
transcriptome profile
K106730_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: WHITE

value: Yes


title: K106641_RNASeq

description:
transcriptome profile
K106641_RNASeq

value: AFRNAMER

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

value: High


title: DNA_METHYLATION_15-008/U43_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U43
A10-178-20_BENIGN

tag: disease state

tag: patientid

value: white

value: recurrence

tag: sample type

tag: tissue

value: prostate tissue


title: DNA_METHYLATION_15-008/U40_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U40
A10-178-14_BENIGN

tag: gender

tag: preoperative psa

tag: gleason score

tag: race


title: K106620_RNASeq

description:
transcriptome profile
K106620_RNASeq

tag: age

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_TCTTACGC-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_TCTTACGC-GGACTCCT

description: smart-seq2 protocol


title: GC071392_TCTTACGC-TAGCGCTC

description: smart-seq2 protocol


title: LSK from HSC-Spred1 wt CML mice [44212_17]

tag: cell type

value: leukemic stem cells (LSK)

tag: strain background

tag: genotype/variation


title: K106678_RNASeq

description:
transcriptome profile
K106678_RNASeq

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant


title: K106656_RNASeq

description:
transcriptome profile
K106656_RNASeq


title: LSK from HSC-Spred1 wt CML mice [44214_19]


title: LSK from HSC-Spred1 wt CML mice [44216_21]


title: DNA_METHYLATION_15-008/U39_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U39
A10-178-13_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue


title: K106647_RNASeq

description:
transcriptome profile
K106647_RNASeq

tag: age

tag: race

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/U41_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U41
A10-178-16_BENIGN

tag: gleason score

value: normal


title: K106597_RNASeq

description:
transcriptome profile
K106597_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer


title: GC071392_TCTTACGC-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: LSK from HSC-Spred1 KO CML mice [44209_14]

source_name: LSK from HSC-Spred1 KO CML mice

tag: cell type

tag: strain background

tag: genotype/variation

value: HSC-Spred1 KO CML mice


title: GC071392_TCTTACGC-CTCTCTAC

description: smart-seq2 protocol


title: K106629_RNASeq

description:
transcriptome profile
K106629_RNASeq

value: Pre

tag: hispanic

tag: bmi

tag: ever pregnant


title: LSK from HSC-Spred1 KO CML mice [44208_13]


title: DNA_METHYLATION_15-008/U40_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U40
A10-170-41_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue

value: buffy coat


title: GC071392_TCTTACGC-GGAGCTAC

description: smart-seq2 protocol


title: K106531_RNASeq (second donation from K105926)

description:
transcriptome profile
K106531_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: No

tag: race

value: AFRNAMER

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/U39_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U39
A10-178-12_BENIGN

tag: gleason score

value: white


title: GC071392_TCTTACGC-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106609_RNASeq

description:
transcriptome profile
K106609_RNASeq

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant


title: LSK from HSC-Spred1 KO CML mice [44211_16]

tag: cell type

tag: strain background

tag: genotype/variation


title: K106517_RNASeq

description:
transcriptome profile
K106517_RNASeq

value: High


title: GC071392_TCTTACGC-GCTCATGA

description: smart-seq2 protocol


title: GC071392_TCTTACGC-CGGAGCCT

description: smart-seq2 protocol


title: GC071392_TCTTACGC-GCGTAGTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U38_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U38
A10-170-39_BUFFYCOAT

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: DNA_METHYLATION_15-008/U38_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U38
A10-178-10_BENIGN

tag: gleason score

tag: race

tag: age

value: prostate tissue


title: GC071392_TCTTACGC-CGTACTAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/U38_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U38
A10-178-11_TUMOR


title: K106578_RNASeq

description:
transcriptome profile
K106578_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: LSK from HSC-Spred1 KO CML mice [44207_12]

tag: cell type

value: leukemic stem cells (LSK)

tag: strain background

tag: genotype/variation


title: DNA_METHYLATION_15-008/U39_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U39
A10-170-40_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: K106481_RNASeq

description:
transcriptome profile
K106481_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

tag: race

value: Average


title: LSK from Spred1 wt CML mice [44205_10]

source_name: LSK from Spred1 wt CML mice

value: Spred1 wt CML mice


title: LSK from HSC-Spred1 KO CML mice [44210_15]


title: LSK from Spred1 wt CML mice [44206_11]


title: LSK from Spred1 wt CML mice [44204_9]


title: DNA_METHYLATION_15-008/U37_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U37
A10-178-8_BENIGN

tag: gleason score

value: unknown

value: normal


title: K106507_RNASeq

description:
transcriptome profile
K106507_RNASeq

value: Pre

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/U37_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U37
A10-178-9_TUMOR

tag: disease state

tag: patientid

tag: gender

value: male

value: cancer


title: GC071392_TCTTACGC-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/U37_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U37
A10-170-38_BUFFYCOAT

tag: preoperative psa

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue

value: buffy coat


title: GC071392_TCTTACGC-CGAGGCTG

description: smart-seq2 protocol


title: GC071392_TCTTACGC-CCTAAGAC

description: smart-seq2 protocol


title: K106301_RNASeq

description:
transcriptome profile
K106301_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: No

tag: race

value: AFRNAMER

value: Yes


title: DNA_METHYLATION_15-008/U36_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U36
A10-180-12_TUMOR

tag: gleason score

value: white

value: prostate tissue


title: LSK from Spred1 wt CML mice [44202_7]

tag: cell type

value: leukemic stem cells (LSK)

tag: strain background

tag: genotype/variation


title: GC071392_TCTTACGC-ATGCGCAG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U36_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U36
A10-178-7_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender


title: LSK from global Spred1 KO CML mice [44200_5]

source_name: LSK from global Spred1 KO CML mice

value: global Spred1 KO CML mice


title: GC071392_TCTTACGC-ATCTCAGG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/U36_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U36
A10-170-37_BUFFYCOAT

tag: preoperative psa

tag: pathologic stage

tag: 5-year disease status


title: K106221_RNASeq

description:
transcriptome profile
K106221_RNASeq

tag: age

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: LSK from Spred1 wt CML mice [44203_8]

tag: cell type

value: Spred1 wt CML mice


title: K106208_RNASeq

description:
transcriptome profile
K106208_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

value: WHITE

value: High


title: LSK from global Spred1 KO CML mice [44201_6]

tag: strain background

tag: genotype/variation


title: GC071392_TCTTACGC-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/U35_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U35
A10-177-9_BENIGN

tag: disease state

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: pathologic stage

value: remission

tag: sample type

value: normal

tag: tissue


title: LSK from global Spred1 KO CML mice [44197_2]

tag: cell type


title: LSK from global Spred1 KO CML mice [44199_4]


title: LSK from global Spred1 KO CML mice [44198_3]


title: K106169_RNASeq

description:
transcriptome profile
K106169_RNASeq

tag: age

tag: age of menarche

value: No

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: DNA_METHYLATION_15-008/U35_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U35
A10-170-36_BUFFYCOAT

tag: race

tag: 5-year disease status

value: buffy coat


title: LSK from global Spred1 KO CML mice [44196_1]

tag: strain background

tag: genotype/variation


title: GC071392_TCTTACGC-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K106201_RNASeq

description:
transcriptome profile
K106201_RNASeq

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes


title: DNA_METHYLATION_15-008/U34_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U34
A10-178-5_TUMOR

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: K106295_RNASeq

description:
transcriptome profile
K106295_RNASeq

tag: age

tag: age of menarche

value: Don‚Äôt know

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: K106157_RNASeq

description:
transcriptome profile
K106157_RNASeq

tag: menopausal status

tag: race

value: Average


title: K106060_RNASeq

description:
transcriptome profile
K106060_RNASeq

tag: blood relatives cancer


title: K106139_RNASeq

description:
transcriptome profile
K106139_RNASeq


title: K106071_RNASeq

description:
transcriptome profile
K106071_RNASeq


title: GC071392_TCTTACGC-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_TCTTACGC-AGGCAGAA

description: smart-seq2 protocol


title: GC071392_TCGCATAA-TGCAGCTA

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U35_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U35
A10-178-6_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: 5-year disease status


title: GC071392_TCGCATAA-TCCTGAGC

description: smart-seq2 protocol


title: GC071392_TCGCATAA-TCGACGTC

description: smart-seq2 protocol


title: 1362InputwInhibOcto

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description: AllExpressed_InhibitorExperiment_070721.txt

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (v4.0) (Strand Life Sciences).
Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 2bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Normalization was performed with the DESeq2 algorithm.
Transcripts with an average read count value >5 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
For statistical analysis of differential expression, a one-way ANOVA or two-way ANOVA with the factors of TRAP fraction and treatment and a Benjamini-Hochberg Multiple Testing Correction followed by Student-Newman Keuls post hoc test were used (FDR<0.1). For those transcripts meeting this statistical criterion, a fold change >|2| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable due to their very small magnitude of change.
Genome_build: Mm10 build of the mouse genome (2014.11.26)
Supplementary_files_format_and_content: Data matrix with raw and normalized counts of all expressed genes.

source_name: brain

extract_protocol:
Purification of ribosomal-bound, microglial-specific RNA was performed as previously described (Chucair-Elliott et al., 2020; Kang et al., 2018; Roh et al., 2018) with slight modifications. For TRAP from whole tissue, a hemisected half-brain was minced into small pieces and homogenized in 1.5 ml ice-cold complete homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/ml sodium heparin; 1 mM DTT; 100 µg/mL cycloheximide (#C4859-1ML, Millipore Sigma); 200 units/ml RNaseOUT Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher); 0.5 mM Spermidine (#S2626, Sigma), 1X complete EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma)) with a glass dounce tissue grinder set (#D8938; 15 times with pestle A). For TRAP from cells, microglial cells were sorted by a variety of methods (FACSAria, AutoMACS, Tyto, AutoMACS to Tyto). After pelleting cells at 1000 x g for 10 min at 4°C, cells were resuspended in 400 ul of complete ice-cold homogenization buffer, transferred to a glass dounce tissue grinder set, and homogenized 15 times with pestle A. Volume was brought up to 1.5 mL with complete homogenization buffer. Homogenates (from tissue or cells) were transferred to 2 mL round-bottom tubes and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 100 µL of the supernatant was saved as “RNA” input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 µg/µl of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for one hour. Dynabeads Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 ml ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 ml round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C with end-over-end rotation overnight. Magnetic beads were collected using a DynaMag-2 magnet and the unbound- ribosomes and associated RNA discarded. Beads and GFP-bound polysomes were then washed three times with 0.5 ml of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 2mM DTT). Following the last wash, 350 µL of Buffer RLT (Qiagen) supplemented with 3.5 µl 2-β mercaptoethanol (#444203, Sigma) was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound polysomes and associated RNA was transferred to a new tube. 350 µl of 100% ethanol was added to the tube (“TRAP” fraction: enriched in transcriptome associated to EGFP-tagged ribosomes) and then loaded onto a RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies).
Directional RNA-Seq libraries were made from 5-100 ng RNA, as previously described (Chucair-Elliott et al., 2020; Chucair-Elliott et al., 2019). Briefly, poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (#NEBE7490L; New England Biolabs, Ipswich, MA) and then processed using NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs) for the creation of cDNA libraries, according to the manufacturer’s instruction. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies) and libraries were quantified by Qubit HSDNA (#Q32851, Thermo). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system (SP PE50bp) at the Oklahoma Medical Research Foundation Clinical Genomics Center.

treatment_protocol: At ~3 months of age, Cx3cr1-NuTRAP mice received a daily intraperitoneal (ip) injection of tamoxifen (Tam) solubilized in 100% sunflower seed oil by sonication (100 mg/kg body weight) to induce cre recombination in microglia (Cx3cr1+).

tag: genotype

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

value: TRAP Input

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: Transcription/Translation Inhibitors

tag: tissue

value: brain


title: 1362PoswInhibOcto

value: TRAP Pos Fraction


title: 1362PosOcto


title: DNA_METHYLATION_15-008/U33_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U33
A10-178-3_TUMOR

value: male

tag: gleason score

value: unknown

tag: pathologic stage

tag: age

value: remission

tag: sample type


title: K106008_RNASeq

description:
transcriptome profile
K106008_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: race

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: K106009_RNASeq

description:
transcriptome profile
K106009_RNASeq

value: Yes


title: DNA_METHYLATION_15-008/U33_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U33
A10-178-2_BENIGN

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: 5-year disease status

value: normal

value: prostate tissue


title: GC071392_TCGCATAA-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/U34_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U34
A10-170-35_BUFFYCOAT

value: prostate cancer

tag: gleason score

value: white

tag: pathologic stage

tag: age

tag: sample type

tag: tissue

value: buffy coat


title: 1361PoswInhibOcto

tag: genotype

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: Transcription/Translation Inhibitors


title: GC071392_TCGCATAA-TACGCTGC

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U34_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U34
A10-178-4_BENIGN

tag: disease state

value: male

tag: race


title: 1361PosOcto

value: TRAP Pos Fraction

value: brain


title: K106020_RNASeq

description:
transcriptome profile
K106020_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_TCGCATAA-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K105980_RNASeq

description:
transcriptome profile
K105980_RNASeq

tag: age

value: Don‚Äôt know

value: AFRNAMER

value: No


title: GC071392_TCGCATAA-TAGCGCTC

description: smart-seq2 protocol


title: GC071392_TCGCATAA-TAGGCATG

description: smart-seq2 protocol


title: DNA_METHYLATION_15-008/U32_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U32
A10-178-1_TUMOR

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue


title: DNA_METHYLATION_15-008/U32_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U32
A10-177-60_BENIGN

tag: disease state

tag: race

value: normal

value: prostate tissue


title: DNA_METHYLATION_15-008/U33_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U33
A10-170-34_BUFFYCOAT

value: prostate cancer

value: unknown


title: 1362InputOcto

tag: genotype

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

value: TRAP Input

tag: experiment

tag: inhibitors


title: K105970_RNASeq

description:
transcriptome profile
K105970_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: WHITE

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: K106006_RNASeq (second donation from K104932)

description:
transcriptome profile
K106006_RNASeq

tag: age


title: K105938_RNASeq

description:
transcriptome profile
K105938_RNASeq


title: DNA_METHYLATION_15-008/U32_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U32
A10-170-33_BUFFYCOAT

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue

value: buffy coat


title: GC071392_TCGCATAA-GGACTCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_TCGCATAA-GGAGCTAC

description: smart-seq2 protocol


title: 1361InputwInhibOcto

tag: genotype

tag: sort method

tag: trap fraction

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: Transcription/Translation Inhibitors

value: brain


title: 1361InputOcto


title: 949TissuePositive2

value: Tissue Homogenate (no sort)

value: TRAP Pos Fraction


title: K105926_RNASeq

description:
transcriptome profile
K105926_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

tag: blood relatives cancer

value: No

tag: race

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: DNA_METHYLATION_15-008/U31_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U31
A10-177-59_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: K105906_2_RNASeq

description:
transcriptome profile
K105906_2_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Yes

value: WHITE

value: High


title: GC071392_TCGCATAA-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: DNA_METHYLATION_15-008/U31_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U31
A10-177-58_BENIGN

value: male

tag: race

value: white

value: normal


title: 949TissueInput2

tag: genotype

tag: sort method

value: Tissue Homogenate (no sort)

tag: trap fraction

value: TRAP Input

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: brain


title: 948TissuePositive2

value: TRAP Pos Fraction


title: K105898_RNASeq

description:
transcriptome profile
K105898_RNASeq

value: Pre

value: No

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_TCGCATAA-GCGTAGTA

description: smart-seq2 protocol


title: GC071392_TCGCATAA-CGGAGCCT

description: smart-seq2 protocol


title: 947TissuePositive2

tag: tissue


title: 947TissueInput2


title: DNA_METHYLATION_15-008/U30_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U30
A10-177-57_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: pathologic stage

tag: age

tag: 5-year disease status

value: recurrence

tag: sample type

value: cancer


title: 948TissueInput2

tag: genotype

tag: sort method

tag: trap fraction

tag: experiment


title: 946TissuePositive2

tag: inhibitors


title: DNA_METHYLATION_15-008/U30_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U30
A10-170-31_BUFFYCOAT

tag: race

value: buffy coat


title: DNA_METHYLATION_15-008/U29_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U29
A10-177-55_TUMOR

value: unknown

value: remission

value: prostate tissue


title: DNA_METHYLATION_15-008/U30_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U30
A10-177-56_BENIGN

value: male

value: white


title: K105883_RNASeq

description:
transcriptome profile
K105883_RNASeq

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: Yes

value: ASIAN

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071392_TCGCATAA-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: 946TissueInput2

value: Tissue Homogenate (no sort)

value: TRAP Input

value: Inhibitor Comparison

tag: tissue

value: brain


title: 157PosOcto

tag: genotype

value: Cell suspension (no sort)

value: TRAP Pos Fraction


title: K105727_RNASeq

description:
transcriptome profile
K105727_RNASeq

tag: age

value: Post

value: WHITE

value: No


title: GC071392_TCGCATAA-CTCTCTAC

description: smart-seq2 protocol


title: GC071392_TCGCATAA-CGTACTAG

description: smart-seq2 protocol


title: K105813_RNASeq

description:
transcriptome profile
K105813_RNASeq

value: Pre

value: Average


title: DNA_METHYLATION_15-008/U28_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U28
A10-177-53_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: black

tag: pathologic stage

tag: 5-year disease status

value: recurrence

tag: sample type

value: cancer

value: prostate tissue


title: DNA_METHYLATION_15-008/U31_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U31
A10-170-32_BUFFYCOAT

tag: race

value: white

value: remission

value: normal

value: buffy coat


title: GC071392_TCGCATAA-CGATCAGT

description: smart-seq2 protocol

value: Mus


title: 157InputOcto

description: AllExpressed_InhibitorExperiment_070721.txt

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

value: TRAP Input

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: brain


title: K105717_RNASeq

description:
transcriptome profile
K105717_RNASeq

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: Yes

value: WHITE

tag: hispanic

value: No

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: High


title: GC071392_TCGCATAA-ATGCGCAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: K105437_RNASeq

description:
transcriptome profile
K105437_RNASeq

tag: age

value: Average


title: K105894_RNASeq

description:
transcriptome profile
K105894_RNASeq

value: Pre


title: GC071392_TCGCATAA-CCTAAGAC

description: smart-seq2 protocol


title: 156PoswInhibOcto

tag: genotype

value: TRAP Pos Fraction

value: Transcription/Translation Inhibitors

tag: tissue


title: K105295_RNASeq

description:
transcriptome profile
K105295_RNASeq

tag: race


title: DNA_METHYLATION_15-008/U29_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U29
A10-177-54_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: prostate tissue


title: DNA_METHYLATION_15-008/U29_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U29
A10-170-30_BUFFYCOAT

value: normal

value: buffy coat


title: DNA_METHYLATION_15-008/U28_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U28
A10-170-29_BUFFYCOAT

value: black

value: recurrence


title: 156PosOcto

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

value: brain


title: GC071392_TCGCATAA-AAGAGGCA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_TCGCATAA-AGGCAGAA

description: smart-seq2 protocol


title: K105555_RNASeq

description:
transcriptome profile
K105555_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: No

value: AFRNAMER

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_TCGCATAA-ATCTCAGG

description: smart-seq2 protocol


title: 157InputwInhibOcto

tag: genotype

value: TRAP Input

value: Transcription/Translation Inhibitors

tag: tissue


title: K105643_RNASeq

description:
transcriptome profile
K105643_RNASeq

value: Pre

tag: race

value: WHITE


title: DNA_METHYLATION_15-008/U27_TUMOR

description:
Illumina EPIC array for prostate tissue cancer sample from patient 15-008/U27
A10-180-11_TUMOR

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

value: prostate tissue


title: K105688_RNASeq

description:
transcriptome profile
K105688_RNASeq

tag: age

tag: age of menarche

tag: menopausal status

tag: blood relatives cancer

value: High


title: DNA_METHYLATION_15-008/U28_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U28
A10-177-52_BENIGN

value: black

value: recurrence

value: normal


title: GC071392_TCGCATAA-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: K105278_RNASeq

description:
transcriptome profile
K105278_RNASeq

value: No

tag: hispanic

tag: bmi

tag: ever pregnant

value: Yes

tag: life time risk (tyrer-cuzick score)

tag: risk category


title: 156InputOcto

tag: genotype

tag: sort method

value: Cell suspension (no sort)

tag: trap fraction

value: TRAP Input

tag: experiment

value: Inhibitor Comparison

tag: inhibitors

tag: tissue

value: brain


title: DNA_METHYLATION_15-008/U26_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U26
A10-170-27_BUFFYCOAT

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: buffy coat


title: GC071392_TATGCAGT-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: DNA_METHYLATION_15-008/U27_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U27
A10-177-51_BENIGN

value: male

value: unknown

value: remission


title: K105188_RNASeq

description:
transcriptome profile
K105188_RNASeq

tag: age of menarche

tag: menopausal status

value: Post

tag: blood relatives cancer

value: ASIAN

tag: hispanic

tag: bmi

tag: ever pregnant

tag: life time risk (tyrer-cuzick score)

tag: risk category

value: Average


title: GC071392_TATGCAGT-TAGGCATG

description: smart-seq2 protocol


title: GC071392_TATGCAGT-TAGCGCTC

description: smart-seq2 protocol


title: 156InputwInhibOcto

tag: genotype

tag: sort method

tag: trap fraction

tag: experiment

tag: inhibitors

value: Transcription/Translation Inhibitors

tag: tissue


title: K105282_RNASeq

description:
transcriptome profile
K105282_RNASeq

tag: age

tag: race

value: WHITE


title: GC071392_TATGCAGT-TGCAGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: 949TissuePos

value: Tissue Homogenate (no sort)

value: TRAP Pos Fraction

value: Sort Comparison


title: K105138_RNASeq

description:
transcriptome profile
K105138_RNASeq

tag: age of menarche

tag: menopausal status

value: Pre

value: Yes

value: No

value: High


title: 949TissueInput

value: TRAP Input

value: brain


title: 157PoswInhibOcto

value: Cell suspension (no sort)

value: Inhibitor Comparison


title: DNA_METHYLATION_15-008/U25_BENIGN

description:
Illumina EPIC array for prostate tissue normal sample from patient 15-008/U25
A10-177-48_BENIGN

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: prostate tissue


title: 949OctoPos

tag: genotype

tag: sort method

tag: trap fraction

tag: experiment


title: DNA_METHYLATION_15-008/U25_BUFFYCOAT

description:
Illumina EPIC array for buffy coat normal sample from patient 15-008/U25
A10-170-26_BUFFYCOAT

tag: race

tag: age

tag: tissue

value: buffy coat


title: 991LFACSPos

value: FACSAria FACS

value: TRAP Pos Fraction

tag: inhibitors


title: GC071392_TATGCAGT-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus