title: LNCaP xenograft tumor [LNCaP_Xeno_8]

status: Public on Mar 17 2020

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
LNCaP_Xeno_8
LNCaP human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to grid and extract the data using the GE2-v5_95_Feb07 protocol with default settings. We normalized the raw data within arrays using loess and normexp background correction with offset 50, removed control probes, averaged duplicate probes, and assigned a value of null to spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers. Data was further normalized using between-array quantile normalization in three batches specific to cell line. All normalizations were performed using the Limma package in R.

source_name: HGS

label_protocol: Amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol:
To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNase using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.
Total RNA was extracted using the Qiagen RNeasy Kit, (Qiagen Inc.) according to the manufacturer's protocol with on-column DNase digestion followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: sample type

value: Reference

value: Pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: gender

value: Male

value: Prostate tumor cells grown as 3-dimensional xenografts

value: LNCaP (ATCC CRL-1740)


title: P20P-405265-T-RNA [S141]

status: Public on Mar 10 2020

type: SRA

city: Durham

first: David

last: Kirsch

state: NC

address: PO Box 96100

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Base-calling was done on the instrument using RTA v3.3.3.
Demultiplexing was done using bcl2fatq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to mouse mm10 genome using STAR v5.5.4b and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with read counts per gene

molecule: total RNA

organism: Mus musculus

growth_protocol: Primary p53/MCA sarcomas were generated in mice between 6-10 weeks old by  intramuscular Adeno-Cre injection into the gastrocnemius of p53FL/FL mice, followed by injection of 300 µg MCA (Sigma-Aldrich) resuspended in sesame oil (SigmaAldrich) at 6 µg/µl. Allograft p53/MCA sarcomas were generated by injecting 50,000 cells resuspended in 100 uL DMEM (Gibco) and Corning matrigel from cell line 402230 into the gastrocnemius muscle of syngeneic mice.

extract_protocol:
Tumor specimens and matched liver control were harvested and stored in RNALater at -80° until all samples were collected. DNA and RNA extractions from each sample were performed using AllPrep DNA/RNA Mini Kit (Qiagen). Extracted total RNA quality and concentration was assessed on a 2100 Bioanalyzer (Agilent Technologies) and Qubit 2.0 (ThermoFisher Scientific), respectively. Only extracts with RNA Integrity Number (RIN) greater than 7 were processed for sequencing. DNA extraction was followed by RNAse treatment (Qiagen). Genomic DNA samples were quantified using fluorometric quantitation on the Qubit 2.0 (ThermoFisher Scientific). For each sample, 200 ng of DNA was sheared using focused-ultrasonicators (Covaris) to generate DNA fragments of about 300 bp in length.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit (Roche) following the manufacturer’s protocol. In brief, mRNA transcripts were first captured using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed using random priming. During the 2nd strand synthesis, the cDNA:RNA hybrid was converted into to double-stranded cDNA (dscDNA) and dUTP incorporated into the 2nd cDNA strand, effectively marking the second strand. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. The strand marked with dUTP was not amplified, allowing strand-specificity sequencing.
Libraries were indexed using a dual indexing approach allowing for multiple libraries to be pooled and sequenced on the same sequencing Illumina sequencing flow cell.

treatment_protocol: Tumors were treated when volume reached ~150 mm3 and harvested 3 days later. Mice received  200 ug IP of either muDX400 (Merck, murine anti-PD-1) or isotype control followed immediately by 0 or 20 Gy radiation. For mice receiving radiation, the tumor-bearing hind limb of the mice was irradiated with 20 Gy using the X-RAD 225Cx small animal image-guided irradiator (Precision X-Ray). The irradiation field included the whole left hind limb and was defined using fluoroscopy with 40 kVp, 2.5 mA X-rays using a 2 mm Al filter. Irradiations were performed using parallel-opposed anterior and posterior fields with an average dose rate of 300 cGy/min prescribed to midplane with 225 kVp, 13 mA X-rays using a 0.3 mm Cu filter.

tag: strain background

tag: replicate group

tag: barcode

value: TCTCGCGC+ATAGAGGC

tag: tumor type

value: Primary

tag: radiation dose

tag: treatment


title: 22Rv1 xenograft tumor [22Rv1_Xeno_3]

type: RNA

description:
22Rv1_Xeno_3
22Rv1 human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.

organism: Homo sapiens

tag: cell line


title: P20P-405241-T-RNA [S142]

value: CTGAAGCT+TATAGCCT


title: 22Rv1 human prostate tumor cell line [22Rv1_Cells_C]

description:
22Rv1_Cells_C
22Rv1 (ATCC-CRL-2505) cells were cultured in RMPI-1640 (Life Technologies) supplemented with 10% FCS (Life Technologies).

value: Prostate tumor cells grown in vitro (2-dimensional)


title: HepG2_Fr-5_Seq

city: Wako

first: Itoshi

last: Nikaido

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

library_source: genomic

data_processing:
(Fr-1 ~ Fr-5, and RNA) Sequenced reads were trimmed with retaining last 50 bps using fastx_trimmer (-l 50).
(Fr-1 ~ Fr-5) Sequenced reads were mapped to hg38 whole genome using hisat2 v2.0.4 (samtools 0.1.19)  with parameters -p 24, then sorted and converted to bed.
(Fr-1 ~ Fr-5) Sequence reads were scaled to their read counts using wiggletools "scale".
(Fr-1 ~ Fr-5) Bam data were converted to wig (bam2wig.py -t 8500000000 -u -s hg38.chrom.sizes) and evaluate Fr-5/Fr-1 ratio using wiggletools "ratio" and "log 2"
(RNA-seq) TPM of each gene was evaluated using sailfish (SailfishBeta-0.10.0_CentOS5) quant -p 20 -l SR, and -i "hg38 gene of ensembl76"
Genome_build: hg38
Supplementary_files_format_and_content: wig format data and tab-delimited text files include TPM of each gene

molecule: genomic DNA

source_name: HepG2 cells

growth_protocol: HepG2 cells were cultured in a minimum essential medium with alpha-modification supplemented with 10% fetal bovine serum.

extract_protocol:
Cell extracts for the chromatin fractionation were prepared as follows: treatment with formaldehyde, solubilization, and fragmentation by sonication. Total RNA was prepared using an RNeasy MinElute Cleanup Kit (#74204, Qiagen).
The DNA in the fractions was sheared with an LE220 Focused-ultrasonicator (Covaris), and converted to a sequence library using a KAPA Hyper Library Preparation Kit (KAPA Biosystems). Total RNA from HepG2 cells was converted to a sequence library using a KAPA Stranded mRNA-seq Kit (KAPA Biosystems).

tag: cell type

value: hepatocyte carcinoma

tag: fractional distribution

value: the lowermost fraction


title: 22Rv1 human prostate tumor cell line [22Rv1_Cells_B]

description:
22Rv1_Cells_B
22Rv1 (ATCC-CRL-2505) cells were cultured in RMPI-1640 (Life Technologies) supplemented with 10% FCS (Life Technologies).


title: P20P-405134-T-RNA [S140]

value: ATTCAGAA+GGCTCTGA


title: VCaP human prostate tumor cell line [VCaP_Cells_B2]

description:
VCaP_Cells_B2
VCaP (ATCC-CRL-2876) cells were cultured in DMEM/F12 (Life Technologies) supplemented with 10% FCS (Life Technologies).

value: VCaP  (ATCC CRL-2876)


title: VCaP human prostate tumor cell line [VCaP_Cells_A1]

description:
VCaP_Cells_A1
VCaP (ATCC-CRL-2876) cells were cultured in DMEM/F12 (Life Technologies) supplemented with 10% FCS (Life Technologies).


title: VCaP xenograft tumor [VCaP_Xeno_7]

description:
VCaP_Xeno_7
VCaP human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: 22Rv1 xenograft tumor [22Rv1_Xeno_5]

description:
22Rv1_Xeno_5
22Rv1 human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: LNCaP human prostate tumor cell line [LNCaP_Cells_A]

description:
LNCaP_Cells_A
LNCaP clone FGC (ATCC-CRL-1740) cells were cultured in RMPI-1640 (Life Technologies) supplemented with 10% fetal calf serum (FCS, Life Technologies).


title: LNCaP xenograft tumor [LNCaP_Xeno_10]

description:
LNCaP_Xeno_10
LNCaP human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: LNCaP xenograft tumor [LNCaP_Xeno_3]

description:
LNCaP_Xeno_3
LNCaP human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: 22Rv1 xenograft tumor [22Rv1_Xeno_4]

description:
22Rv1_Xeno_4
22Rv1 human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: VCaP xenograft tumor [VCaP_Xeno_8]

description:
VCaP_Xeno_8
VCaP human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: LNCaP human prostate tumor cell line [LNCaP_Cells_B]

description:
LNCaP_Cells_B
LNCaP clone FGC (ATCC-CRL-1740) cells were cultured in RMPI-1640 (Life Technologies) supplemented with 10% fetal calf serum (FCS, Life Technologies).


title: 22Rv1 human prostate tumor cell line [22Rv1_Cells_A]

description:
22Rv1_Cells_A
22Rv1 (ATCC-CRL-2505) cells were cultured in RMPI-1640 (Life Technologies) supplemented with 10% FCS (Life Technologies).


title: VCaP xenograft tumor [VCaP_Xeno_1a]

description:
VCaP_Xeno_1a
VCaP human prostate cancer mouse xenograft tumors were propagated as previously described (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677971/). Briefly, two million prostate cancer cells were first aggregated with matrigel (BD Biosciences) and then injected subcutaneously into flanks of male NOD Scid mice (Taconic Farms). The tumor’s size was measured daily and tumors were harvested after eight to ten weeks in biological triplicates.


title: HepG2_Fr-1_Seq

value: the uppermost fraction


title: P20P-405264-T-RNA [S143]

value: CGGCTATG+AGGCGAAG


title: P20P-405050-T-RNA [S139]

value: GAGATTCC+GTACTGAC


title: P20P-405003-T-RNA [S137]

value: CGCTCATT+CAGGACGT


title: P20I-405208-T-RNA [S136]

value: AGCGATAG+AGGCGAAG

value: Isotype


title: P20I-405223-T-RNA [S135]

value: TAATGCGC+CCTATCCT


title: P20I-405242-T-RNA [S133]

value: CGGCTATG+TATAGCCT


title: P20I-405312-T-RNA [S132]

value: GAATTCGT+GTACTGAC


title: P0P-520068-T-RNA [S127]

value: CTGAAGCT+ATAGAGGC


title: P0P-405310-T-RNA [S128]

value: TCTCGCGC+TATAGCCT

value: Primary


title: P20I-520063-T-RNA [S130]

value: ATTCAGAA+CAGGACGT


title: P0P-405253-T-RNA [S125]

value: TAATGCGC+GTACTGAC


title: P0P-405156-T-RNA [S122]

value: GAATTCGT+CCTATCCT


title: P0P-405227-T-RNA [S123]

value: ATTACTCG+CAGGACGT


title: P20I-405226-T-RNA [S131]

value: TCCGGAGA+GGCTCTGA


title: P0P-405206-T-RNA [S124]

value: CGCTCATT+TAATCTTA


title: P0I-405251-T-RNA [S117]

value: CTGAAGCT+GGCTCTGA


title: P0I-405263-T-RNA [S120]

value: TAATGCGC+ATAGAGGC


title: P20P-405122-T-RNA [S138]

value: ATTACTCG+TAATCTTA


title: P0I-405123-T-RNA [S113]

value: ATTACTCG+CCTATCCT


title: P0I-404904-T-RNA [S114]

value: CGCTCATT+AGGCGAAG

value: Isotype


title: P0I-405137-T-RNA [S115]

value: GAATTCGT+TAATCTTA


title: P0P-405077-T-RNA [S121]

value: TCCGGAGA+AGGCGAAG


title: P0I-404905-T-RNA [S116]

value: TCCGGAGA+CAGGACGT


title: P0I-405313-T-RNA [S118]

value: GAGATTCC+AGGCGAAG


title: P20I-405319-T-RNA [S134]

value: TCCGCGAA+ATAGAGGC

value: Primary


title: A20P-500589-T-RNA [S111]

value: TCCGCGAA+GTACTGAC

value: Allograft


title: A20I-405292-T-RNA [S108]

value: GAGATTCC+CCTATCCT


title: A20P-405222-T-RNA [S109]

value: AGCGATAG+CAGGACGT


title: A20I-405246-T-RNA [S107]

value: ATTCAGAA+AGGCGAAG


title: A20P-500615-T-RNA [S110]

value: ATTACTCG+TATAGCCT


title: A20I-405225-T-RNA [S105]

value: GAATTCGT+ATAGAGGC


title: A20I-500610-T-RNA [S106]

value: TCCGGAGA+TATAGCCT


title: P0I-405204-T-RNA [S119]

value: AGCGATAG+TATAGCCT


title: P0P-405309-T-RNA [S126]

value: AGCGATAG+GGCTCTGA


title: P20I-405140-T-RNA [S129]

value: GAGATTCC+TAATCTTA

value: Isotype


title: A20P-500591-T-RNA [S112]

value: CGGCTATG+GGCTCTGA


title: A0P-405173-T-RNA [S102]

value: CGGCTATG+CAGGACGT


title: A0P-520232-T-RNA [S104]

value: CTGAAGCT+GTACTGAC


title: A0P-500553-T-RNA [S101]

value: TCCGCGAA+TAATCTTA


title: A0I-500596-T-RNA [S100]

value: ATTACTCG+AGGCGAAG


title: A0I-500551-T-RNA [S99]

value: CGCTCATT+CCTATCCT


title: A0I-500595-T-RNA [S97]

value: ATTCAGAA+TATAGCCT

value: Allograft


title: A0I-500545-T-RNA [S98]

value: GAGATTCC+ATAGAGGC


title: 5_CS_mammary

status: Public on Mar 05 2020

city: Hangzhou

first: Diming

last: Wang

address: 866 yuhangtang RD

country: China

institute: Zhejiang University

data_processing:
Alignment to Genome with Tophat2
Alignment output piped to Ht-seq-count
Reads mapped were normlized into counts per million
Differential analysis was performed using edgeR and SAS
Functional anlaysis with Ingenuity Pathway Anlaysis, David and Panther
Genome_build: umd3.1
Supplementary_files_format_and_content: text file with CPM, content is normalized expressional abundance of each gene each animal

organism: Bos taurus

source_name: mammary gland

extract_protocol:
After feeding trail, cows were slaughtered and duodenum, jejunum, liver and mammary gland epithelial samples were collected from each animal and immediately flash frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina truseq_stranded_total_rna_sample_preparation kit

treatment_protocol: Cattle with three diet (Alfalfa hay, rice straw or corn stover)

tag: tissue

value: mammary gland

tag: diet

value: cows fed corn stover diet


title: 6_CS_mammary


title: 4_CS_mammary


title: 5_RS_mammary

value: cows fed rice straw diet


title: 2_CS_mammary


title: 2_RS_mammary


title: 3_CS_mammary


title: 3_RS_mammary


title: 1_CS_mammary


title: 6_RS_mammary


title: 4_RS_mammary


title: 1_RS_mammary


title: 4_AL_mammary

value: cows fed alfalfa hay diet


title: 3_AL_mammary


title: 6_CS_liver

source_name: liver tissue

value: liver


title: 4_CS_liver


title: 2_AL_mammary


title: 1_AL_mammary


title: 3_CS_liver


title: 5_CS_liver


title: 2_CS_liver


title: 1_CS_liver


title: 6_RS_liver


title: 3_RS_liver


title: 4_RS_liver


title: 2_RS_liver


title: 1_RS_liver


title: 5_AL_liver


title: 6_AL_liver


title: 3_AL_liver


title: 1_AL_liver


title: 5_AL_mammary


title: 6_CS_jejunum

source_name: jejunum tissue

value: jejunum


title: 5_CS_jejunum


title: 4_CS_jejunum


title: 6_AL_mammary


title: 4_AL_liver


title: 2_AL_liver


title: 1_CS_jejunum


title: 3_CS_jejunum


title: 2_CS_jejunum


title: 2_RS_jejunum


title: 3_RS_jejunum


title: 6_RS_jejunum


title: 5_RS_jejunum


title: 4_RS_jejunum


title: 6_AL_jejunum


title: 1_RS_jejunum


title: 3_AL_jejunum

value: jejunum epithelial


title: 5_RS_liver


title: 4_AL_jejunum


title: 5_AL_jejunum


title: 6_CS_duodenum

source_name: duodenum tissue

value: duodenum


title: 2_AL_jejunum


title: 5_CS_duodenum


title: 6_RS_duodenum


title: 2_RS_duodenum


title: 1_RS_duodenum


title: 2_CS_duodenum


title: 3_RS_duodenum


title: 1_CS_duodenum


title: 4_RS_duodenum


title: 3_CS_duodenum


title: 5_AL_duodenum


title: 4_CS_duodenum


title: 6_AL_duodenum


title: 1_AL_jejunum


title: 3_AL_duodenum


title: 1_AL_duodenum

source_name: Duodenum

value: Duodenum


title: 2_AL_duodenum


title: RNA_seq_aly_mutant_rep1

status: Public on Feb 27 2020

city: Stanford

first: Margaret

last: Fuller

state: California

address: 279 Campus Drive, Beckman Center B301

department: Developmental Biology

institute: Stanford University

description:
total RNA with rRNA depletion
RNA-seq for aly mutant replicate 1

data_processing:
trim adaptors and low quality bases. trim_galore/0.4.1
map with STAR/2.5.1b (RNA-seq), bwa/0.7.10 (ATAC-seq), STAR/2.5.4b (CAGE)
count reads for each gene or promoter STAR (RNA-seq and CAGE)
create bigwig files with deepTools/2.5.4 (RNA-seq), bedtools/2.25.0 and bedGraphToBigWig (ATAC-seq and CAGE)
call peaks with MACS2/2.1.1 (ATAC-seq)
call nucleosomes with NucleoATAC/0.3.2 (ATAC-seq)
Genome_build: dm6
Supplementary_files_format_and_content: raw_counts.txt are raw read counts by STAR; MACS2_ATAC.narrowPeak were peaks called by MACS2; .bw files were bigwig files normalized by library sizes for visualization in genomic viewer.

organism: Drosophila melanogaster

source_name: testis

growth_protocol: in molasses medium, 25C for 10 days

extract_protocol:
100 pairs of testes from < 2 day old male flies were used per replicate. The testis were dissected in PBS on ice. Total RNA was extracted using RNeasy Mini Kit (Qiagen 74104).
Ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kit (Illumina MRZH116). Library preparation was then carried out using SMARTer Stranded RNA-Seq Kit (Clonetech 634839).

value: testis

tag: developmental stage enriched

value: mature spermaocyte

tag: time post heat shock

value: no heat shock

tag: genotype

value: aly -/-


title: RNA_seq_aly_mutant_rep2

description:
total RNA with rRNA depletion
RNA-seq for aly mutant replicate 2


title: 4_AL_duodenum


title: 5_RS_duodenum


title: RNA_seq_72hrPHS_rep1

description:
total RNA with rRNA depletion
RNA-seq for 72hr post heat shock replicate 1

growth_protocol: in molasses medium, 22C for 9 days, heat shock, then 25C for 72hr

value: bam -/- with heat shock promoter driven Bam

value: heat shock at 37C for 30min


title: RNA_seq_72hrPHS_rep2

description:
total RNA with rRNA depletion
RNA-seq for 72hr post heat shock replicate 2


title: RNA_seq_48hrPHS_rep2

description:
total RNA with rRNA depletion
RNA-seq for 48hr post heat shock replicate 2

growth_protocol: in molasses medium, 22C for 9 days, heat shock, then 25C for 48hr

value: young spermatocyte


title: RNA_seq_bam_mutant_rep2

description:
total RNA with rRNA depletion
RNA-seq for bam mutant replicate 2

growth_protocol: in molasses medium, 22C for 12 days

value: spermatogonia

value: bam -/-


title: A0P-500550-T-RNA [S103]

value: TCTCGCGC+GGCTCTGA

value: Allograft


title: ATAC_seq_topi_mutant_rep1b

description: ATAC-seq for topi mutant replicate 1, technical replicate b

extract_protocol:
No extraction was done prior to library construction.
For each technical replicate, 10~20 pairs of testes from < 1 day old male flies were dissected in PBS on ice, and immediately digested for 8 minutes at room temperature in 0.5mg/ml of dispase (Worthington LS02109) and 0.5mg/ml of collagenase XI (Sigma C7657) dissolved in PBS with 0.3mM of CaCl2. Testis were washed once in cold PBS and broken open by pipetting 7 ~ 10 times in 50ul of cold PBS. Cells were spun down at 2000rpm for 1min, cold lysis buffer (Buenrostro et al. 2015) added, and the pellet gently resuspended by flicking the tube. After another 2000rpm 2min spin, 20ul of transposase mix from the Nextera Kit (Illumina, cat. no. FC-121-1030) was added and the pellet gently resuspended by flicking the tube. The reaction was incubated at 30oC for 25min with the tube flicked once during incubation. The DNA was purified using Qiagen MinElute column (Qiagen 28004) and the entire sample used for PCR with NEBNext (NEB M0541S) for a total of 8~9 amplification cycles.

value: mature spermatocyte

value: topi -/-


title: ATAC_seq_aly_mutant_rep2a

description: ATAC-seq for aly mutant replicate 2, technical replicate a


title: ATAC_seq_aly_mutant_rep3a

description: ATAC-seq for aly mutant replicate 3, technical replicate a


title: ATAC_seq_aly_mutant_rep1b

description: ATAC-seq for aly mutant replicate 1, technical replicate b


title: ATAC_seq_aly_mutant_rep3b

description: ATAC-seq for aly mutant replicate 3, technical replicate b


title: CAGE_bam_mutant_rep2

description: CAGE for bam mutant, replicate 2

extract_protocol:
300 pairs of testes from < 2 day old male flies were used per replicate. Testis were dissected in PBS on ice. RNA was extracted and purified with Trizol (Invitrogen 15596026) and Qiagen RNeasy Mini Kit (Qiagen 74104).
20~50ug of total RNA was sent to DNAform (https://www.dnaform.jp/en/products/library/cage/) for CAGE library preparation using published protocol nAnTi-CAGE (non-amplifying-non-tagging illumina CAGE) (Murata et al. 2014).


title: ATAC_seq_topi_mutant_rep1a

description: ATAC-seq for topi mutant replicate 1, technical replicate a


title: ATAC_seq_topi_mutant_rep2b

description: ATAC-seq for topi mutant replicate 2, technical replicate b


title: ATAC_seq_aly_mutant_rep2b

description: ATAC-seq for aly mutant replicate 2, technical replicate b


title: CAGE_bam_mutant_rep1

description: CAGE for bam mutant, replicate 1


title: ATAC_seq_topi_mutant_rep2a

description: ATAC-seq for topi mutant replicate 2, technical replicate a


title: ATAC_seq_72hrPHS_rep3

description: ATAC-seq for 72hr post heat shock, replicate 3


title: ATAC_seq_aly_mutant_rep1a

description: ATAC-seq for aly mutant replicate 1, technical replicate a


title: ATAC_seq_48hrPHS_rep2

description: ATAC-seq for 48hr post heat shock, replicate 2


title: ATAC_seq_72hrPHS_rep1

description: ATAC-seq for 72hr post heat shock, replicate 1


title: ATAC_seq_ctrl_48hrPHS_rep2

description: ATAC-seq for 48hr post heat shock control, with no heat shock driven Bam, replicate 2

value: bam -/- (as control for effect of heat shock)


title: ATAC_seq_48hrPHS_rep1

description: ATAC-seq for 48hr post heat shock, replicate 1


title: ATAC_seq_ctrl_48hrPHS_rep1

description: ATAC-seq for 48hr post heat shock control, with no heat shock driven Bam, replicate 1


title: RNA_seq_bam_mutant_rep1

description:
total RNA with rRNA depletion
RNA-seq for bam mutant replicate 1


title: CAGE_72hrPHS_rep2

description: CAGE for 72hr post heat shock, replicate 2


title: ATAC_seq_bam_mutant_rep1

description: ATAC-seq for bam mutant replicate 1


title: CAGE_72hrPHS_rep1

description: CAGE for 72hr post heat shock, replicate 1


title: ATAC_seq_72hrPHS_rep2

description: ATAC-seq for 72hr post heat shock, replicate 2


title: ATAC_seq_48hrPHS_rep3

description: ATAC-seq for 48hr post heat shock, replicate 3


title: ATAC_seq_bam_mutant_rep2

description: ATAC-seq for bam mutant replicate 2


title: Swarna.Drought.4

status: Public on Feb 25 2020

city: Los Banos

first: Jeshurun Asher

middle: Marayag

last: Tarun

state: Laguna

address: Pili Drive

department: Plant Breeding

country: Philippines

institute: International Rice Research Institute

data_processing:
The Illumina Hiseq 4000 generates raw images utilizing HCS (HiSeq Control Software v3.3) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v2.5.2). The BCL (base calls) binary is converted into FASTQ utilizing Illumina package bcl2fastq (v2.16.0.10). Adapters are not trimmed away from the reads.
The raw fasta reads were filtered using trimmomatic (RRID: SCR_011848; http://www.usadellab.org/cms/index.php?page=trimmomatic) with mostly default settings (ILLUMINACLIP:./TruSeq3-PE-2.fa:2:30:15 TRAILING:28 LEADING:28 MINLEN:30).
A transcriptome fasta file of the rice japonica genome fasta file and gff3 annotations downloaded from RGAP (MSUv.7) was made using the gffread function under Cufflinks (version 2.2.1) software.
Using the converted transcriptome fasta file, the Salmon software (version 0.7.2) indexed the transcriptome (Patro et al., 2017).
We then used Salmon to quantify transcript abundance in quassi-mapping mode directly using the indexed transcriptome, and the trimmed high-quality paired-end reads. The parameters -l A, -seqBias and -gcBias was provided to allow Salmon to automatically infer library type, to enable Salmon to learn and correct for sequence-specific and fragment-level GC content biases, respectively. Gene expression levels were then normalized using the transcripts per million mapped reads (TPM) method.
The estimated transcript abundance from Salmon was imported and aggregated to the gene level using the Bioconductor package tximport (version 1.2.0) (Soneson et al., 2016) complemented with the reader package (version 1.1.1) through R (version 3.3.3) software. Principal component analysis (PCA) was performed using ggplot2 (version 2.2.1) and gplots package (version 3.0.1) to determine relationships between samples.
DESeq2 software (version 1.14.1) was used in R to identify DEGs in pairwise comparisons (Love et al., 2014). Two series of differential expression (DE) analysis using the contrast argument was performed for the reference assembly approach in flag-leaf and panicle samples. Firstly, the contrasts of the condition effect for each genotype, i.e., IL_D vs IL_C, and SWA_D vs SWA_C. Secondly, the contrasts of the genotypic effect for each condition, i.e., IL_C vs SWA_C and IL_D vs SWA_D. Only genes that have at least ten reads total were used for DE analysis. The pre-filtered raw counts of the flag-leaf datasets were used for the transformation on the log2 scale, which has been normalized concerning library size using vst function in the DESeq2 package. Differentially expressed genes (DEGs) were defined as those presenting an absolute fold change (FC) ≥2 and an adjusted P-value (FDR) ≤ 0.05 in any pairwise comparison.
Genome_build: Rice Genome Annotation version 7
Supplementary_files_format_and_content: csv file in matrix table of the aggregated raw gene counts and csv files (four pairwise comparisons) with genes that passed the adjusted p-value < 0.05 correction without the log2-fold change filtering:
Supplementary_files_format_and_content: Aggregated gene counts_flag-leaf.csv: Raw gene counts of sequencing reads in comma-separated text format.
Supplementary_files_format_and_content: ILDroughtvsSwarnaDrought_gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.
Supplementary_files_format_and_content: ILControlvsSwarnaControl_gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.
Supplementary_files_format_and_content: SwarnaDroughtvsSwarnaControl_gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.
Supplementary_files_format_and_content: ILDroughtvsILControl_gene-level_ressig-padjat0.05_vsd_filtered.csv: Gene DE analysis that passed the adjusted p-value < 0.05 correction.

organism: Oryza sativa

source_name: flag-leaf tissue

growth_protocol: A pot experiment was arranged in a randomized complete block design with two treatments (well-watered and 2-weeks drought-stressed), two genotypes, and six replications or pots in a greenhouse at the International Rice Research Institute (Los Banos, Philippines). For reproductive-stage drought stress (RDS), water was withheld at reproductive (R2) stage on discrete morphological criteria as described by Counce et al. (2000) until the soil moisture level progressively dropped to 75% field capacity (FC) and was maintained for nine days, whereas control plants were well-watered. After the 10th day, the FC was brought down and maintained at 50% for three more days. During the drought stress period, the pots were weighed daily, and the difference in weight on subsequent days was corrected by adding water to maintain the required FC. Flag-leaf samples of well-watered and drought-stressed treatments were collected at the R3 stage on the 12th day of RDS and immediately flash-frozen in liquid nitrogen. Four independent biological replicates for each tissue sample were harvested.

extract_protocol:
Flag-leaf tissue under control and drought-stress conditions were removed, flash frozen on dry liquid nitrogen, and total RNA was extracted using TRIzol reagent and isolated using the Qiagen RNeasy Plant Mini Kit (Qiagen, Limburg, Netherlands). The total RNA concentration was quantified using Nanodrop spectrophotometer (ND-1000; Nanodrop Technologies, Wilmington, DE), with absorbance at 260 nm. RNA purity and integrity were examined using an Agilent 2100 BioAnalyzer RNA 6000 Kit (Agilent Technologies). 2 ug of total RNA was submitted and Illumina library preparation and sequencing were completed following the standard protocols of Macrogen INC (Seoul, Korea).
RNA libraries were prepared for sequencing using standard Illumina protocols as per Macrogen Korea specifications.

value: Flag-leaf

tag: developmental stage

value: Reproductive-stage

value: Swarna (recipient parent)

tag: phenotype

value: Drought-sensitive

value: Drought


title: Swarna.Control.2

value: Control


title: IL.Control.4

value: IL (introgression line)

value: Drought-tolerant


title: Swarna.Control.3


title: Swarna.Control.4


title: IL.Control.2


title: IL.Drought.2


title: IL.Drought.1


title: Swarna.Control.1


title: IL.Drought.4


title: IL.Control.3


title: IL.Control.1


title: IL.Drought.3


title: 1001200522_P8

status: Public on Feb 18 2020

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

country: Sweden

institute: University of Gothenburg

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Genome_build: GRCh38

source_name: pancreatic islets

extract_protocol:
SmartSeq2 (21X-23X PCR cycles)
SmartSeq2 (21X-23X PCR cycles)

tag: cryopreserved

value: No

tag: diabetes

tag: Sex

value: M

tag: patched

value: FACS


title: 1001200522_P9


title: 1001200522_P7


title: non-AMD Patient 2 iPS RPE

status: Public on Feb 26 2020

city: New Haven

first: Hui

middle: Cong

last: Cai

state: CT

address: 300 George St, Suite 8100

institute: Yale University

hyb_protocol: All reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S arrays (Thermo Fisher Scientific) were washed using the GeneChip® Fludics Station 450 (Thermo Fisher Scientific)

scan_protocol: Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing:
Raw data were processed to perform gene-level normalization and quality control using Affymetrix Expression Console Software (Thermo Fisher Scientific). RMA expression value derived from Expression Console software Transcriptome Analysis Console (TAC) 4.0.1 (Applied Biosystems)
Clariom_S_Human.r1.pgf
Clariom_S_Human.r1.na36.hg38.a1.transcript.csv
Normal vs AMD,  Normal: 3 samples, AMD: 4 samples; Filter criteria:  Fold Change: > 2 or < -2; Total number of genes: 21448

label: biotin

source_name: non-AMD patient donor derived

label_protocol: GeneChip® WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.

growth_protocol: Fibroblasts from 4 donors with age-related macular degeneration and 3 controls with no history of AMD were grown and treated with modified messenger ribonucleic acid (mRNA) encoding reprogramming factors, Oct3/4, Sox-2, Klf4, and c-Myc, nanog and Lin28. Newly generated iPSC colonies were picked and expanded using Nutristem medium (Stemgent, Reprocell, MD, USA) or MTeSR™1 media. iPSC colonies were detached and grown as embryoid bodies (EB) in EB formation medium and STEMdiff™ Neural Induction Medium and RPE differentiation medium containing DMEM/F12, 2% B-27 supplement, minimum essential media, non-essential amino acids and antibiotics. At ~45 days, pigmented iPSC-derived RPE cells appeared in the cultures. Patches of pigmented iPSC-derived RPE cells were micro-dissected, dissociated with trypsin-ethylenediaminetetraacetic acid (EDTA, 0.05%), and plated onto laminin-coated plates until confluent as previously described.

extract_protocol: Total RNA was isolated from differentiated iPSC-derived RPE cells using Aurum™ Total RNA Mini Kit (Bio-Rad Laboratories, CA, USA) according to the manufacturer’s instructions, with Dnase I treatment. RNA quantity and quality were assessed by micro-volume spectrophotometry on the Nanodrop 2000 (Thermo Fisher Scientific) and by on-chip capillary electrophoresis on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: no special treatment

tag: donor id

value: non-AMD Patient 6

tag: donor status

value: non-AMD Patient

value: iPS-derived retinal pigment epithelial (RPE) cells


title: non-AMD Patient 3 iPS RPE

value: non-AMD Patient 3


title: AMD Patient 1 iPS RPE

description: RMA expression value derived from Expression Console software Transcriptome Analysis Console (TAC)  4.0.1 (Applied Biosystems)

source_name: AMD patient donor derived

value: AMD Patient 1

value: advanced age-related macular degeneration (AMD)-patient


title: Swarna.Drought.3

value: Flag-leaf

tag: treatment


title: non-AMD Patient 1 iPS RPE

value: non-AMD Patient 5


title: AMD Patient 4 iPS RPE

value: AMD Patient 4


title: 1001200522_P6


title: AMD Patient 3 iPS RPE

value: AMD Patient 3


title: AMD Patient 2 iPS RPE

value: AMD Patient 2


title: 1001200522_P5


title: Swarna.Drought.2

value: Reproductive-stage

value: Swarna (recipient parent)

value: Drought-sensitive

value: Drought


title: Swarna.Drought.1


title: 1001200522_P4

value: No

value: M


title: 1001200522_P3

value: FACS


title: 1001200522_P20


title: 1001200522_P23


title: 1001200522_P22


title: 1001200522_P21


title: 1001200522_P17


title: 1001200522_P2


title: 1001200522_P19


title: 1001200522_P16


title: 1001200522_P15


title: 1001200522_P10


title: 1001200522_P11


title: 1001200522_P13


title: 1001200522_P12


title: 1001200522_P14


title: 1001200522_P18


title: 1001200522_O8


title: 1001200522_P1


title: 1001200522_O9


title: 1001200522_O6


title: 1001200522_O7


title: 1001200522_O5


title: 1001200522_O22


title: 1001200522_O4


title: 1001200522_O3


title: 1001200522_O2


title: 1001200522_O20


title: 1001200522_O21


title: 1001200522_O19


title: 1001200522_O18


title: 1001200522_O17


title: 1001200522_O16


title: 1001200522_O13


title: RNA_seq_48hrPHS_rep1

description:
total RNA with rRNA depletion
RNA-seq for 48hr post heat shock replicate 1

value: testis

value: young spermatocyte

value: bam -/- with heat shock promoter driven Bam

value: heat shock at 37C for 30min


title: 1001200522_O10


title: 1001200522_O11


title: 1001200522_O15


title: 1001200522_N9


title: 1001200522_O1


title: 1001200522_O14


title: 1001200522_N7


title: 1001200522_O12


title: 1001200522_N8


title: 1001200522_O23


title: 1001200522_N6


title: 1001200522_N3


title: 1001200522_N5


title: 1001200522_N4


title: 1001200522_N23


title: 1001200522_N20


title: 1001200522_N2


title: 1001200522_N21


title: 1001200522_N22


title: 1001200522_N19


title: 1001200522_N17


title: 1001200522_N16


title: 1001200522_N15


title: 1001200522_N14


title: 1001200522_N11


title: 1001200522_N13


title: 1001200522_M8


title: 1001200522_M7


title: 1001200522_M6


title: 1001200522_M5


title: 1001200522_M3


title: 1001200522_M4


title: 1001200522_M22


title: 1001200522_M20


title: 1001200522_M21


title: 1001200522_M2


title: 1001200522_N18


title: 1001200522_M16


title: 1001200522_M18


title: 1001200522_M19


title: 1001200522_M17


title: 1001200522_M15


title: 1001200522_N12


title: 1001200522_M14


title: 1001200522_M13


title: 1001200522_M12


title: 1001200522_M11


title: 1001200522_N10


title: 1001200522_M10


title: 1001200522_N1


title: 1001200522_L7


title: 1001200522_M1


title: 1001200522_M23


title: 1001200522_L8


title: 1001200522_M9


title: 1001200522_L6


title: 1001200522_L4


title: 1001200522_L22


title: 1001200522_L3


title: 1001200522_L2


title: 1001200522_L16


title: 1001200522_L19


title: 1001200522_L15


title: 1001200522_L17


title: 1001200522_L18


title: 1001200522_L14


title: 1001200522_L13


title: 1001200522_L9


title: 1001200522_L11


title: 1001200522_L10


title: 1001200522_K9


title: 1001200522_L12


title: 1001200522_K8


title: 1001200522_L1


title: 1001200522_K7


title: 1001200522_L20


title: 1001200522_L5


title: 1001200522_L23


title: 1001200522_K5


title: 1001200522_K4


title: 1001200522_L21


title: 1001200522_K22


title: 1001200522_K6


title: 1001200522_K21


title: 1001200522_K19


title: 1001200522_K2


title: 1001200522_K20


title: 1001200522_K3


title: 1001200522_K18


title: 1001200522_K17


title: 1001200522_K13


title: 1001200522_K16


title: 1001200522_K14


title: 1001200522_K12


title: 1001200522_J7


title: 1001200522_J6


title: 1001200522_J5


title: 1001200522_K1


title: 1001200522_J8


title: 1001200522_J9


title: 1001200522_K10


title: 1001200522_K11


title: 1001200522_J3


title: 1001200522_J4


title: 1001200522_J23


title: 1001200522_J2


title: 1001200522_K23


title: 1001200522_J21


title: 1001200522_J19


title: 1001200522_J22


title: 1001200522_J20


title: 1001200522_J18


title: 1001200522_J16


title: 1001200522_J15


title: 1001200522_J13


title: 1001200522_K15


title: 1001200522_J14


title: 1001200522_J10


title: 1001200522_J12


title: 1001200522_I8


title: 1001200522_I7


title: 1001200522_I6


title: 1001200522_I23


title: 1001200522_I21


title: 1001200522_I4


title: 1001200522_I22


title: 1001200522_I5


title: 1001200522_I3


title: 1001200522_I14


title: 1001200522_I12


title: 1001200522_I20


title: 1001200522_J17


title: 1001200522_I2


title: 1001200522_I13


title: 1001200522_I19


title: 1001200522_I17


title: 1001200522_I10


title: 1001200522_I16


title: 1001200522_I18


title: 1001200522_I1


title: 1001200522_I15


title: 1001200522_J11


title: 1001200522_I11


title: 1001200522_J1


title: 1001200522_I9


title: 1001200522_H9


title: 1001200522_H7


title: 1001200522_H6


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title: 1001200522_H3


title: 1001200522_H23


title: 1001200522_H19


title: 1001200522_H20


title: 1001200522_H4


title: 1001200522_H2


title: 1001200522_H22


title: 1001200522_H21


title: 1001200522_H17


title: 1001200522_H15


title: 1001200522_H13


title: 1001200522_H18


title: 1001200522_H12


title: 1001200522_H11


title: 1001200522_H16


title: 1001200522_H14


title: 1001200522_G7


title: 1001200522_G6


title: 1001200522_G8


title: 1001200522_G5


title: 1001200522_H5


title: 1001200522_G9


title: 1001200522_G3


title: 1001200522_G4


title: 1001200522_G23


title: 1001200522_G22


title: 1001200522_G21


title: 1001200522_G20


title: 1001200522_G2


title: 1001200522_G18


title: 1001200522_G19


title: 1001200522_G17


title: 1001200522_G14


title: 1001200522_G16


title: 1001200522_H1


title: 1001200522_G15


title: 1001200522_H10


title: 1001200522_G13


title: 1001200522_G11


title: 1001200522_G12


title: 1001200522_G10


title: 1001200522_F7


title: 1001200522_F8


title: 1001200522_G1


title: 1001200522_F6


title: 1001200522_F9


title: 1001200522_F5


title: 1001200522_F23


title: 1001200522_F20


title: 1001200522_F3


title: 1001200522_F21


title: 1001200522_F22


title: 1001200522_F19


title: 1001200522_F2


title: 1001200522_F4


title: 1001200522_F18


title: 1001200522_F17


title: 1001200522_F16


title: 1001200522_F15


title: 1001200522_F11


title: 1001200522_F14


title: 1001200522_F10


title: 1001200522_F12


title: 1001200522_E8


title: 1001200522_E9


title: 1001200522_F1


title: 1001200522_E7


title: 1001200522_E4


title: 1001200522_E6


title: 1001200522_E23


title: 1001200522_E21


title: 1001200522_E22


title: 1001200522_E5


title: 1001200522_E3


title: 1001200522_E2


title: 1001200522_E17


title: 1001200522_E20


title: 1001200522_E16


title: 1001200522_E13


title: 1001200522_E15


title: 1001200522_E18


title: 1001200522_E14


title: 1001200522_E11


title: 1001200522_E12


title: 1001200522_E10


title: 1001200522_F13


title: 1001200522_D9


title: 1001200522_D6


title: 1001200522_D5


title: 1001200522_D23


title: 1001200522_D22


title: 1001200522_D20


title: 1001200522_E19


title: 1001200522_D2


title: 1001200522_D21


title: 1001200522_D19


title: 1001200522_D18


title: 1001200522_D17


title: 1001200522_D15


title: 1001200522_D12


title: 1001200522_D14


title: 1001200522_D13


title: 1001200522_D10


title: 1001200522_D1


title: 1001200522_C9


title: 1001200522_D11


title: 1001200522_D4


title: 1001200522_C6


title: 1001200522_C8


title: 1001200522_D7


title: 1001200522_C4


title: 1001200522_C5


title: 1001200522_E1


title: 1001200522_C7


title: 1001200522_D8


title: 1001200522_C3


title: 1001200522_C23


title: 1001200522_C22


title: 1001200522_D3


title: 1001200522_D16


title: 1001200522_C19


title: 1001200522_C20


title: 1001200522_C16


title: 1001200522_C2


title: 1001200522_C11


title: 1001200522_C15


title: 1001200522_C14


title: 1001200522_C13


title: 1001200522_C12


title: 1001200522_C10


title: 1001200522_C1


title: 1001200522_B9


title: 1001200522_B8


title: 1001200522_B23


title: 1001200522_B3


title: 1001200522_B7


title: 1001200522_B6


title: 1001200522_B21


title: 1001200522_B2


title: 1001200522_B20


title: 1001200522_B5


title: 1001200522_B19


title: 1001200522_B17


title: 1001200522_B4


title: 1001200522_B22


title: 1001200522_C18


title: 1001200522_C21


title: 1001200522_C17


title: 1001200522_B18


title: 1001200522_B15


title: 1001200522_B14


title: 1001200522_B13


title: 1001200522_B11


title: 1001200522_B16


title: 1001200522_B10


title: 1001200522_B12


title: 1001200522_B1


title: 1001200522_A8


title: 1001200522_A9


title: 1001200522_A7


title: 1001200522_A4


title: 1001200522_A5


title: 1001200522_A3


title: 1001200522_A20


title: 1001200522_A23


title: 1001200522_A22


title: 1001200522_A2


title: 1001200522_A18


title: 1001200522_A17


title: 1001200522_A19


title: 1001200522_A16


title: 1001200522_A15


title: 1001200522_A12


title: 1001200522_A11


title: 1001200522_A14


title: 1001200522_A1


title: 1001200521_P8

value: nondiabetic


title: 1001200521_P9


title: 1001200522_A13


title: 1001200522_A10


title: 1001200521_P7


title: 1001200521_P6


title: 1001200521_P5


title: 1001200521_P3


title: 1001200522_A21


title: 1001200521_P4


title: 1001200521_P23


title: 1001200521_P21


title: 1001200521_P22


title: 1001200521_P2


title: 1001200521_P20


title: 1001200521_P19


title: 1001200521_P18


title: 1001200521_P16


title: 1001200521_P13


title: 1001200522_A6


title: 1001200521_P12


title: 1001200521_P1


title: 1001200521_P11


title: 1001200521_O8


title: 1001200521_P10


title: 1001200521_O7


title: 1001200521_O6


title: 1001200521_O9


title: 1001200521_O4


title: 1001200521_O5


title: 1001200521_O3


title: 1001200521_O23


title: 1001200521_O22


title: 1001200521_P17


title: 1001200521_O2


title: 1001200521_O16


title: 1001200521_P15


title: 1001200521_O17


title: 1001200521_O19


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