title: Liver-Male-IRLWT_ZT8-Rep5


title: Liver-Male-IRLKO_ZT16-Rep6

status: Public on Jan 01 2023

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 icroarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 29 out of 36 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 35450 spots out of 62976 were selected.  The mean signal of the 11 first samples, 12 next and 13 last ones were substracted to individuals signals to correct the batch effect of the 3 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32801 rows each corresponding to a unique ProbeName (provided as data Matrix).

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: All mice were fed a standard rodent diet (Safe 04 U8220G10R), and housed under controlled temperature (21-23°C) and light (12-h light/12-h dark) conditions : lights were turned on at Zeitgeber time (ZT) 0 and turned off at ZT12.

extract_protocol: Total liver RNA was extracted using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA)

treatment_protocol: Mice did not receive any treament and were fed ad libitum.

tag: genotype

value: IRLKO

tag: time

tag: gender

value: Male

tag: washbatch

tag: age

value: 11 weeks old mice

tag: feeding

value: AdLib


title: ZnSO4 dose level 7 bio rep 7 [Zn_P1_G8_S61]

type: SRA

city: Cincinnati

first: John

middle: Walter

last: Martinson

state: Ohio

address: 26 W. Martin L. King Drive

department: ORD

country: USA

description:
96 well plate
Zn_P1_G8_S61_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

library_source: transcriptomic

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads from each sample's RNA-Seq fastq(.gz) file were mapped with STAR (Dobin, et. al) v2.7.1a to indexed FHM genome with 26,150 gene models loaded within the genome (WIOS00000000; BioSample SAMN12875914). STAR "--quantMode GeneCounts" was used to produce raw counts from the mapping; reverse strand count column was used as dictated by sequencing protocol. Genomic gene and transcript coordinates and associated annotations are contained in files WIOS01.1.gbff.gz, WIOS01.2.gbff.gz and WIOS01.3.gbff.gz available at https://www.ncbi.nlm.nih.gov/Traces/wgs/WIOS01?display=contigs. Uniprot accessions associated with gene models are available from the authors.
Samples with <2 million raw counts and/or less than 50% unique mapping rate were removed, and within-chemical features (genes) with mean raw counts <5 across all samples were filtered from respective raw counts matrices.
For each chemical, the raw counts for the remaining features were normalized to counts per million reads (CPM), and after adding a pseudo-count of 1 to prevent taking log of zero counts, log2 transformed.
For each chemical, an MDS plot of the normalized data was generated. Individual samples separated from all remaining samples on either principle component #1 (PC1) or principle component #2 (PC2) by >2x the span of all other samples on the corresponding PC were removed from further analysis. Qualitative assessment was applied and samples with a relatively large Euclidean distance from all other remaining samples on MDS plots were also excluded, along with samples especially distant from corresponding replicates within dose.
Assembly: EPA_FHM_2.0.b
Supplementary files format and content: For each chemical, tab delimited text matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: For each sample, tab delimited text matrix table with normalized expression values for every gene and every sample that passed all filtering.

organism: Pimephales promelas

source_name: whole body

extract_protocol:
Larvae remained in their 1 mL deep wells, exposure solution was removed and replaced with lysis buffer, a bead was added to each well, and subjects were homogenized in their wells.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

treatment_protocol: For ten different chemicals, 24h post-hatch individual fathead minnow larvae were statically exposed in 96 deep well plates to controls and a half-log dilution series of treatment concentrations. Exposures were for 24 hours. Subjects from all doses that did not exhibit excessive levels of mortality were further processed.

tag: tissue

value: whole body

tag: developmental stage

value: larva

value: 5 dpf/24 hr post hatch

tag: Sex

tag: treatment

tag: concentration

tag: time point

value: 24 hr


title: Liver-Male-IRLKO_ZT8-Rep2


title: ZnSO4 control bio rep 8 [Zn_P1_H1_S57]

description:
96 well plate
Zn_P1_H1_S57_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: Liver-Male-IRLKO_ZT12-Rep3


title: ZnSO4 dose level 6 bio rep 7 [Zn_P1_G7_S60]

description:
96 well plate
Zn_P1_G7_S60_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: ZnSO4 dose level 5 bio rep 7 [Zn_P1_G6_S59]

description:
96 well plate
Zn_P1_G6_S59_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: ZnSO4 dose level 4 bio rep 7 [Zn_P1_G5_S66]

description:
96 well plate
Zn_P1_G5_S66_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: ZnSO4 dose level 2 bio rep 7 [Zn_P1_G3_S64]

description:
96 well plate
Zn_P1_G3_S64_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: ZnSO4 dose level 1 bio rep 7 [Zn_P1_G2_S63]

description:
96 well plate
Zn_P1_G2_S63_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: ZnSO4 dose level 3 bio rep 7 [Zn_P1_G4_S65]

description:
96 well plate
Zn_P1_G4_S65_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 48H_PBS18: PBS, 48h, replicate2

city: Sapporo

first: Takashi

last: Teramura

address: North 15 West 7, Kita-ku

country: Japan

institute: Hokkaido University

description: Gene expression after 48hrs in topical treatment of PBS on to the skin surface.

hyb_protocol: Cy3-labelled cRNA  2x Agilent hybridization buffer was added to the Cy3-labbelled cRNA and hybridized to SurePrint G3 Mouse GE 8x60K Microarray v2 (Agilent) for 17 hours.  After hybridization, microarrays were washed 1 minute at room temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan.

data_processing: The scanned images were analyzed with Feature Extraction Software v.10.7.3.1 (Agilent)

source_name: PBS, 48h, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Samples were homogenized with BioMasher II (Nippi)and total RNA was extracted from the epidermis using the SV Total RNA Isolation system(Promega). The quantitative and qualitative evaluation of extracted RNA was performed with Agilent Bioanalyzer 2100 (Agilent).

treatment_protocol: Female hairless mice (Hos:HR-1) aged 5 to 7 weeks were used in this study. A total of 250 µL of 3% (w/v) SLS prepared in PBS was applied cotton pad, which was then attached onto the side of the abdomen for 30 min.

value: Epidermis

value: Female


title: 48H_PBS17: PBS, 48h, replicate1


title: 24H_PBS14: PBS, 24h, replicate2

description: Gene expression after 24hrs in topical treatment of PBS on to the skin surface.

source_name: PBS, 24h, replicate1


title: 06H_PBS08: PBS, 6h, replicate2

description: Gene expression after 6hrs in topical treatment of PBS on to the skin surface.

source_name: PBS, 6h, replicate1


title: ZnSO4 dose level 10 bio rep 7 [Zn_P1_G11_S56]

description:
96 well plate
Zn_P1_G11_S56_L003
Zn.raw.counts.txt
na


title: ZnSO4 dose level 9 bio rep 7 [Zn_P1_G10_S55]

description:
96 well plate
Zn_P1_G10_S55_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 06H_PBS07: PBS, 6h, replicate1


title: ZnSO4 dose level 8 bio rep 6 [Zn_P1_F9_S29]

description:
96 well plate
Zn_P1_F9_S29_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 96H_SLS24: SLS, 96h, replicate3

description: Gene expression after 96hrs in topical treatment of 3%SLS on to the skin surface.

source_name: 3% SLS, 96h, replicate1


title: ZnSO4 control bio rep 7 [Zn_P1_G1_S45]

description:
96 well plate
Zn_P1_G1_S45_L003
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: ZnSO4 dose level 7 bio rep 6 [Zn_P1_F8_S23]

description:
96 well plate
Zn_P1_F8_S23_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 1444 [202193490121_R06C01]

type: genomic

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

description: DNA methylation

hyb_protocol: standard protocol

scan_protocol: The BeadChip was then coating-protected and scanned on iScan (Illumina) to generate methylation raw data

data_processing:
Data quality was checked via Illumina standard QC analysis, which showed high quality. Locus-specific probes on the array report fluorescent signals from both methylated (Cy5) and unmethylated (Cy3) alleles, and average methylation level (β) is derived from replicate methylation measurements, where β = (max(Cy5, 0))/ (|Cy3| + |Cy5| + 100). Beta (β) = 1 indicates complete methylation; β = 0 represents no methylation. Raw methylation array data was preprocessed using the ENmix package, which included quality control, background correction, color bias correction and probe design bias correction. Relative leukocyte fractions were estimated using the minfi package. Beta estimates were adjusted for surrogate variables to account for potential batch effect and other sources of unwanted variation using the ENmix package
matrix processed value definition: Average Beta

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral Blood

label_protocol: Using Infinium MethylationEPIC BeadChip kit, the bisulfite converted DNA was denatured, isothermally amplified, enzymatically fragmented and precipitation recovered. The re-suspended DNA fragments was then hybridized onto the chip with the beads attached to specific probes. Samples underwent stratified randomization of BeadChip position to help mitigate batch effects17. After washing, a single-base extension was added to differentiate methylated C (unchaged) or unmethylated C (converted to T) followed by staining of the BeadChip.

extract_protocol: DNA was extracted from peripheral blood using the QIAamp DNA Blood Maxi kit (Qiagen) and bisulfite-modified using the Zymo EZ DNA methylation kit (Irvine, CA) under the manufacturer's recommended conditions

tag: year

value: M

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: 96H_SLS22: SLS, 96h, replicate2

tag: tissue

tag: gender


title: 96H_SLS21: SLS, 96h, replicate1


title: 24H_PBS13: PBS, 24h, replicate1


title: ZnSO4 dose level 6 bio rep 6 [Zn_P1_F7_S24]

description:
96 well plate
Zn_P1_F7_S24_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: age

tag: Sex

tag: treatment

tag: concentration

tag: time point


title: Liver-Male-IRLWT_ZT12-Rep4

tag: genotype

value: IRLWT

tag: time

tag: washbatch

tag: feeding


title: Tumor

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

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

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

data_processing: GenomeStudio

source_name: FFPE ZFTA-fusion-positive ependymoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor sample using MagPurix according to standard instructions for automatic extraction of genomic DNA

treatment_protocol: Formaline fixing and paraffine inclusion

value: male

value: 6 months

value: non-hemispheric transtentorial ZFTA-fusion-positive ependymoma


title: ZnSO4 dose level 5 bio rep 6 [Zn_P1_F6_S25]

description:
96 well plate
Zn_P1_F6_S25_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 1444 [202193490121_R05C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: fibrinogen

tag: insulin


title: Liver-Male-IRLWT_ZT8-Rep2

tag: gender

tag: age


title: Liver-Male-IRLWT_ZT16-Rep6


title: Liver-Male-IRLKO_ZT16-Rep3


title: 1407 [202128330052_R02C01]

description: DNA methylation

tag: Sex

tag: ldl

tag: crp

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: 48H_SLS20: SLS, 48h, replicate3

description: Gene expression after 48hrs in topical treatment of 3%SLS on to the skin surface.

source_name: 3% SLS, 48h, replicate1

tag: tissue


title: 1407 [202128330052_R01C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr


title: 1396 [202128330052_R04C01]

description: DNA methylation

tag: sbp

tag: dbp

tag: triglyceride


title: 48H_SLS19: SLS, 48h, replicate2


title: ZnSO4 dose level 4 bio rep 6 [Zn_P1_F5_S26]

description:
96 well plate
Zn_P1_F5_S26_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 1396 [202128330052_R03C01]

description: DNA methylation

tag: age

tag: Sex

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin


title: 48H_SLS18: SLS, 48h, replicate1

tag: tissue

tag: gender


title: 1379 [202163550104_R03C01]

description: DNA methylation

tag: year

value: F

tag: bmi

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: 24H_SLS15: SLS, 24h, replicate3

description: Gene expression after 24hrs in topical treatment of 3%SLS on to the skin surface.

source_name: 3% SLS, 24h, replicate1


title: ZnSO4 dose level 3 bio rep 6 [Zn_P1_F4_S34]

description:
96 well plate
Zn_P1_F4_S34_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment


title: ZnSO4 dose 1 bio rep 6 [Zn_P1_F2_S36]

description:
96 well plate
Zn_P1_F2_S36_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: concentration

tag: time point


title: ZnSO4 dose level 2 bio rep 6 [Zn_P1_F3_S35]

description:
96 well plate
Zn_P1_F3_S35_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: Sex


title: 1270 [202193490125_R08C01]

description: DNA methylation

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: crp


title: 1320 [202128330052_R05C01]

description: DNA methylation

tag: year

tag: bmi

tag: fibrinogen

tag: insulin

tag: glucose


title: 1270 [202193490125_R07C01]

description: DNA methylation

tag: uric acid

tag: creatinin

tag: calcium


title: 24H_SLS14: SLS, 24h, replicate2

tag: tissue

tag: gender


title: 1255 [202163550105_R07C01]

description: DNA methylation

tag: age

tag: Sex

tag: whr


title: 1255 [202163550105_R08C01]

description: DNA methylation

tag: sbp

tag: dbp

tag: triglyceride


title: 24H_SLS13: SLS, 24h, replicate1


title: 1216 [202123800036_R02C01]

description: DNA methylation

tag: hdl

tag: ldl

tag: crp


title: 12H_SLS12: SLS, 12h, replicate3

description: Gene expression after 12hrs in topical treatment of 3%SLS on to the skin surface.

source_name: 3% SLS, 12h, replicate1


title: ZnSO4 control bio rep 6 [Zn_P1_F1_S37]

description:
96 well plate
Zn_P1_F1_S37_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 1216 [202123800036_R01C01]

description: DNA methylation

tag: year

tag: bmi

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid

tag: creatinin


title: 1210 [202123800146_R05C01]

description: DNA methylation

tag: age

tag: Sex

tag: whr

tag: sbp

tag: calcium


title: 12H_SLS11: SLS, 12h, replicate2

tag: tissue

tag: gender


title: ZnSO4 dose level 9 bio rep 6 [Zn_P1_F10_S28]

description:
96 well plate
Zn_P1_F10_S28_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment


title: ZnSO4 dose level 8 bio rep 5 [Zn_P1_E9_S32]

description:
96 well plate
Zn_P1_E9_S32_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: concentration

tag: time point


title: ZnSO4 dose level 10 bio rep 6 [Zn_P1_F11_S27]

description:
96 well plate
Zn_P1_F11_S27_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 1210 [202123800146_R06C01]

description: DNA methylation

tag: year

tag: bmi

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: crp


title: 1179 [202775280053_R07C01]

description: DNA methylation

tag: age

tag: Sex

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid

tag: creatinin


title: 1320 [202128330052_R06C01]

description: DNA methylation

tag: whr

tag: sbp

tag: calcium


title: 1178 [202123800272_R04C01]

description: DNA methylation

tag: year


title: 06H_SLS08: SLS, 6h, replicate3

description: Gene expression after 6hrs in topical treatment of 3%SLS on to the skin surface.

source_name: 3% SLS, 6h, replicate1

tag: tissue

tag: gender


title: 1178 [202123800272_R03C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: triglyceride


title: ZnSO4 dose level 7 bio rep 5 [Zn_P1_E8_S33]

description:
96 well plate
Zn_P1_E8_S33_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 1121 [202193490102_R08C01]

description: DNA methylation

tag: age

tag: Sex

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin


title: 1133 [202193490101_R08C01]

description: DNA methylation

tag: year

tag: whr

tag: sbp

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: 1133 [202193490101_R07C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: triglyceride


title: 1379 [202163550104_R04C01]

description: DNA methylation

tag: age


title: 06H_SLS07: SLS, 6h, replicate2

tag: tissue

tag: gender


title: ZnSO4 dose level 5 bio rep 5 [Zn_P1_E6_S41]

description:
96 well plate
Zn_P1_E6_S41_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: Sex

tag: treatment

tag: concentration

tag: time point


title: 06H_SLS06: SLS, 6h, replicate1


title: 1179 [202775280053_R08C01]

description: DNA methylation

tag: year

tag: whr

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin


title: 1052 [202060330182_R07C01]

description: DNA methylation

tag: bmi

tag: sbp

tag: dbp

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: 1052 [202060330182_R08C01]

description: DNA methylation

tag: age

tag: Sex

tag: triglyceride


title: 1028 [202775280082_R08C01]

description: DNA methylation

tag: year


title: 01H_SLS04: SLS, 1h, replicate3

description: Gene expression after 1hr in topical treatment of 3%SLS on to the skin surface.

source_name: 3% SLS, 1h, replicate1

tag: tissue

tag: gender


title: 01H_SLS02: SLS, 1h, replicate2


title: ZnSO4 dose level 4 bio rep 5 [Zn_P1_E5_S44]

description:
96 well plate
Zn_P1_E5_S44_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 1028 [202775280082_R07C01]

description: DNA methylation

tag: bmi

tag: whr

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin


title: 983 [202193490121_R08C01]

description: DNA methylation

tag: sbp

tag: dbp

tag: crp

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: 01H_SLS01: SLS, 1h, replicate1

tag: tissue

tag: gender


title: 12H_SLS09: SLS, 12h, replicate1


title: ZnSO4 dose level 3 bio rep 5 [Zn_P1_E4_S43]

description:
96 well plate
Zn_P1_E4_S43_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: age

tag: Sex

tag: treatment

tag: concentration


title: 983 [202193490121_R07C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr

tag: triglyceride

tag: hdl

tag: ldl


title: ZnSO4 dose level 6 bio rep 5 [Zn_P1_E7_S42]

description:
96 well plate
Zn_P1_E7_S42_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: time point


title: 1121 [202193490102_R07C01]

description: DNA methylation

tag: sbp

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid


title: 926 [202123800146_R04C01]

description: DNA methylation

tag: age

tag: crp

tag: creatinin

tag: calcium


title: 903 [202128330134_R06C01]

description: DNA methylation

tag: year

tag: Sex


title: 903 [202128330134_R05C01]

description: DNA methylation

tag: bmi

tag: whr


title: ZnSO4 control bio rep 5 [Zn_P1_E1_S40]

description:
96 well plate
Zn_P1_E1_S40_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration


title: 962 [202775280082_R05C01]

description: DNA methylation

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl


title: ZnSO4 dose level 10 bio rep 5 [Zn_P1_E11_S30]

description:
96 well plate
Zn_P1_E11_S30_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: time point


title: ZnSO4 dose level 1 bio rep 5 [Zn_P1_E2_S38]

description:
96 well plate
Zn_P1_E2_S38_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 962 [202775280082_R06C01]

description: DNA methylation

tag: fibrinogen

tag: crp

tag: insulin

tag: glucose

tag: uric acid

tag: creatinin


title: PDNC4, Clone C3, Input

city: Pittsburgh

first: Megan

last: Mahlke

state: Pennsylvania

address: 5115 Centre Ave

institute: UPMC

description: CENP-A Input

library_source: genomic

data_processing:
Reads generated from PD-NC4 CENP-A ChIP-seq were assessed for quality using FastQC (https://github.com/s-andrews/FastQC), trimmed with Sickle (https://github.com/najoshi/sickle; v1.33) to remove low-quality 5′ and 3′ end bases, and trimmed with Cutadapt (v.2.10) to remove adapters.
Processed CENP-A ChIP reads were aligned to the CHM13 whole-genome assembly v1.1 using BWA (v0.7.17) with the following parameters: bwa mem -k 50 -c 1000000 [index] [read1.fastq] [read2.fastq] for paired-end data.
SAM files were filtered using SAMtools47 with FLAG score 2308 to prevent multi-mapping of reads.
High-confidence CENP-A positions were identified with mapping scores (MAPQ: 20, or the probability of correctly mapping to another location is 0.01) to identify reads that aligned uniquely to low-frequency repeat variants.
Alignments were normalized with deepTools77 (v.3.3.0) bamCompare with the following parameters: bamCompare -b1 [ChIP.bam] -b2 [Input.bam] --operation ratio --binSize 50 -o [output.bw].
Assembly: CHM13 v1.1
Supplementary files format and content: Processed data are bigwig tracks of CENP-A position at all sites or at high-confidene (MAPQ20) sites.

growth_protocol: Cells were maintained in DMEM medium (Gibco) containing 10% fetal bovine serum (Omega Scientific), 100U/ml penicillin, 100U/ml streptomycin and 2mM l-glutamine at 37oC in a 5% CO2 atmosphere with 21% oxygen.

extract_protocol:
Chromatin was extracted Nuclei from 1×108 nuclei of PD-NC4 cells as previously described (Nechemia-Arbely et al., 2019).
ChIP libraries were prepared using NEB Ultra II (Cat # E7103L) following NEBNext protocols with minor modifications (please see associated manuscript for details).

tag: cell line

tag: cell type

value: Fibroblast

tag: antibody


title: PDNC4, Clone C2, Input

description: CENP-A Input


title: 901 [202772890063_R03C01]

description: DNA methylation

tag: year

tag: Sex

tag: bmi

tag: whr

tag: calcium


title: ZnSO4 dose level 9 bio rep 5 [Zn_P1_E10_S31]

description:
96 well plate
Zn_P1_E10_S31_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration


title: 926 [202123800146_R03C01]

description: DNA methylation

tag: age

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen


title: 893 [202193490123_R05C01]

description: DNA methylation

tag: insulin

tag: glucose

tag: uric acid

tag: creatinin


title: 892 [202128330134_R04C01]

description: DNA methylation

tag: year

tag: Sex

tag: bmi

tag: whr

tag: crp


title: 893 [202193490123_R06C01]

description: DNA methylation

tag: calcium


title: 892 [202128330134_R03C01]

description: DNA methylation

tag: age


title: 872 [202193490121_R01C01]

description: DNA methylation

tag: sbp


title: 872 [202193490121_R02C01]

description: DNA methylation

tag: dbp


title: PDNC4, Clone C2, CENP-A

description: CENP-A IP

tag: cell line

tag: cell type

tag: antibody

value: Abcam ab13939


title: ZnSO4 dose level 2 bio rep 5 [Zn_P1_E3_S39]

description:
96 well plate
Zn_P1_E3_S39_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 867 [202193490037_R08C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid

tag: creatinin


title: PDNC4, Clone C3, CENP-A

description: CENP-A IP

tag: cell line


title: ZnSO4 dose level 7 bio rep 4 [Zn_P1_D8_S9]

description:
96 well plate
Zn_P1_D8_S9
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: Sex


title: ZnSO4 dose level 8 bio rep 4 [Zn_P1_D9_S6]

description:
96 well plate
Zn_P1_D9_S6
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue


title: ZnSO4 dose level 6 bio rep 4 [Zn_P1_D7_S8]

description:
96 well plate
Zn_P1_D7_S8
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage


title: 901 [202772890063_R04C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: crp

tag: calcium


title: PDNC4, Parental cells, Input

description: CENP-A Input

tag: cell type

tag: antibody


title: 867 [202193490037_R07C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin


title: 810 [202128330024_R02C01]

description: DNA methylation

tag: age

tag: Sex

tag: glucose

tag: uric acid

tag: creatinin


title: 810 [202128330024_R01C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp


title: ZnSO4 dose level 5 bio rep 4 [Zn_P1_D6_S3]

description:
96 well plate
Zn_P1_D6_S3
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 802 [202193490123_R07C01]

description: DNA methylation

tag: year

tag: dbp

tag: triglyceride

tag: hdl

tag: calcium


title: ZnSO4 dose level 4 bio rep 4 [Zn_P1_D5_S2]

description:
96 well plate
Zn_P1_D5_S2
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: Sex


title: 802 [202193490123_R08C01]

description: DNA methylation

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: 779 [202775280053_R02C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: creatinin


title: ZnSO4 dose level 3 bio rep 4 [Zn_P1_D4_S5]

description:
96 well plate
Zn_P1_D4_S5
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: ZnSO4 dose level 1 bio rep 4 [Zn_P1_D2_S16]

description:
96 well plate
Zn_P1_D2_S16
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age


title: 774 [202775280026_R06C01]

description: DNA methylation

tag: year

tag: Sex

tag: dbp

tag: triglyceride

tag: hdl

tag: calcium


title: 801 [201502880027_R08C01]

description: DNA methylation

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: CNE2 p53WT

city: Houston

first: An

last: Xu

state: TX

institute: UThealth Houston

data_processing:
QC: FastQC v0.11.5. Sequenced reads were then trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNAeq Alignment: RNAStar for RNASeq, Bowtie2 for ChIPseq
RNAseq normalization: Featurecounts
ChIPseq sorting, normalization, and visualization: MACS2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .csv; ChIPSeq: genome browser tracks in .bigwig

growth_protocol: CNE2 cells were cells were grown in RPMI 1640 medium supplemented with 10% (vol/vol) fetal bovine serum (FBS) (Opti-Gold performance enhanced F0900-050, GenDEPOT, Barker, TX), L-glutamine, and penicillin/streptomycin.

extract_protocol:
For RNAseq, cells samples were lysed in Trizol reagent (Invitrogen, 10296010).ChIP-seq, cells were fixed, quenched, sonicated to ~250 bp in 1% SDS lysis buffer, and incubated with Protein A/G Dynabeads and 5 µg of the indicated antibody. 2% pre-cleared chromatin prior to primary antibody addition was kept as input DNA. After wash, treatment with RNAse A and Proteinase K, DNA was eluted and purified with Qiagen's PCR purification kit (28106).
For RNASeq, library construction was performed using PE150 high-throughput sequencing. For ChIPSeq, library construction was performed using PE75 high-throughput sequencing.

tag: cell line

tag: cell type

value: Nasopharyngeal carcinoma (NPC)

value: Yes

tag: chip antibody

value: p53 (Santa Cruz  Technology,sc-126)

tag: genotype

value: NPC cell with WT-p53 expression

tag: disease state

value: NPC


title: PDNC4, Parental cells, CENP-A

description: CENP-A IP

tag: antibody


title: 774 [202775280026_R05C01]

description: DNA methylation

tag: year

tag: age

tag: Sex

tag: bmi

tag: whr

tag: sbp

tag: creatinin


title: 761 [202163550105_R01C01]

description: DNA methylation

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: calcium


title: 761 [202163550105_R02C01]

description: DNA methylation

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: 739 [202128330024_R04C01]

description: DNA methylation

tag: year


title: ZnSO4 dose level 10 bio rep 4 [Zn_P1_D11_S1]

description:
96 well plate
Zn_P1_D11_S1
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

value: whole body

tag: developmental stage

value: larva

tag: age

value: 5 dpf/24 hr post hatch

tag: treatment

tag: concentration

tag: time point


title: ZnSO4 dose level 9 bio rep 4 [Zn_P1_D10_S7]

description:
96 well plate
Zn_P1_D10_S7
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: Sex

value: 24 hr


title: CNE2 p53KO

tag: cell line

tag: cell type

tag: chip antibody

tag: genotype

value: NPC cell with p53 depletion

tag: disease state


title: P4_cite

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: cite-seq data result is included in scRNA-seq result. Tag information: 1_Treg_library.csv

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v3.1.0)
Background and non-cellular barcodes are removed
Genome_build: GRCh38
Supplementary_files_format_and_content: .tsv: barcodes, genes, .mtx: count matrix, .csv: tcr sequence

source_name: Treg and CD4 T cell

extract_protocol:
Single-cell sequencing libraries were prepared using Chromium 10x Genomics platform with a V(D)J Enrichment Kit and 5’ Library and Gel Bead Kit (10x Genomics, Pleasanton, CA, USA, PN-1000005, PN-1000006) according to the manufacturer’s instructions
The single-cell suspension of CD4+CD25hiCD127lo T-Tregs, B-Tregs, and CD4+CD45RA+CCR7+CD25loCD127hi B-naïve Tconvs from paired tumor and blood sorted using FACS Aria II was diluted in nuclease-free water and then combined with Single-Cell 5’ Gel Beads, a master mix, and Partitioning Oil on Chromium Chip A, found in the aforementioned kit. RNA transcripts were uniquely barcoded and reverse-transcribed within nanoliter-scale droplets containing barcoded beads. 10x barcoded full-length cDNA were then pooled and enriched via PCR. For V(D)J Enriched Library, the enriched cDNA pool was amplified using primers specific to TCR. For 5’Gene Expression (GEX) library, the cDNA pool underwent an end repair process, A-tailing, adaptor ligation, and sample index PCR. Both libraries for scRNA-seq and scTCR-seq were sequenced using the HiSeqX platform (Illumina).

value: Treg and CD4 T


title: CNE2 p53R280T

value: NPC cell with p53 mutation (p53R280T)


title: 739 [202128330024_R03C01]

description: DNA methylation

value: M

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: creatinin

tag: calcium


title: ZnSO4 control bio rep 4 [Zn_P1_D1_S17]

description:
96 well plate
Zn_P1_D1_S17
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: treatment

tag: concentration

tag: time point


title: 737 [202163550104_R08C01]

description: DNA methylation

tag: year

tag: Sex

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: P4_vdj

tag: cell type


title: 801 [201502880027_R07C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride


title: ZnSO4 dose level 8 bio rep 3 [Zn_P1_C9_S12]

description:
96 well plate
Zn_P1_C9_S12
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage


title: 779 [202775280053_R01C01]

description: DNA methylation

tag: age

tag: hdl

tag: ldl

tag: fibrinogen

tag: creatinin

tag: calcium


title: ZnSO4 dose level 2 bio rep 4 [Zn_P1_D3_S4]

description:
96 well plate
Zn_P1_D3_S4
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: Sex

tag: treatment

tag: concentration

tag: time point


title: 733 [202193490101_R06C01]

description: DNA methylation

tag: year

tag: bmi

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: 722 [201502880056_R06C01]

description: DNA methylation

tag: whr

tag: sbp

tag: dbp

tag: triglyceride


title: 733 [202193490101_R05C01]

description: DNA methylation

tag: age

tag: hdl

tag: ldl

tag: fibrinogen


title: ZnSO4 dose level 7 bio rep 3 [Zn_P1_C8_S13]

description:
96 well plate
Zn_P1_C8_S13
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: Sex

tag: treatment


title: P4_gex

tag: cell type


title: ZnSO4 dose level 6 bio rep 3 [Zn_P1_C7_S10]

description:
96 well plate
Zn_P1_C7_S10
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: concentration

tag: time point


title: 722 [201502880056_R05C01]

description: DNA methylation

tag: year

tag: bmi

tag: insulin

tag: glucose

tag: creatinin

tag: calcium


title: 710 [202193490037_R03C01]

description: DNA methylation

tag: age

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: uric acid


title: ZnSO4 dose level 5 bio rep 3 [Zn_P1_C6_S11]

description:
96 well plate
Zn_P1_C6_S11
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: Sex


title: P3_vdj

tag: cell type


title: P3_gex


title: P3_cite


title: ZnSO4 dose level 4 bio rep 3 [Zn_P1_C5_S21]

description:
96 well plate
Zn_P1_C5_S21
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: treatment

tag: concentration

tag: time point


title: P2_cite


title: 664 [202128330134_R02C01]

description: DNA methylation

tag: year

tag: bmi

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin


title: 674 [202772890063_R01C01]

description: DNA methylation

tag: age

tag: whr

tag: sbp

tag: dbp

tag: glucose

tag: creatinin

tag: calcium


title: ZnSO4 dose level 3 bio rep 3 [Zn_P1_C4_S22]

description:
96 well plate
Zn_P1_C4_S22
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: Sex

tag: treatment


title: 674 [202772890063_R02C01]

description: DNA methylation

tag: year

tag: bmi

tag: triglyceride

tag: uric acid


title: P2_vdj

tag: cell type


title: 676 [202772890063_R07C01]

description: DNA methylation

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin


title: ZnSO4 dose level 2 bio rep 3 [Zn_P1_C3_S19]

description:
96 well plate
Zn_P1_C3_S19
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: concentration

tag: time point


title: 737 [202163550104_R07C01]

description: DNA methylation

tag: whr

tag: sbp

tag: dbp

tag: glucose

tag: creatinin

tag: calcium


title: 664 [202128330134_R01C01]

description: DNA methylation

tag: year

tag: Sex

tag: bmi


title: 646 [202163550104_R02C01]

description: DNA methylation

tag: triglyceride

tag: crp

tag: uric acid


title: P2_gex

tag: cell type


title: 646 [202163550104_R01C01]

description: DNA methylation

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin


title: ZnSO4 dose level 1 bio rep 3 [Zn_P1_C2_S20]

description:
96 well plate
Zn_P1_C2_S20
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: treatment

tag: concentration

tag: time point


title: 614 [202193490125_R04C01]

description: DNA methylation

tag: year

tag: whr

tag: sbp

tag: dbp

tag: glucose

tag: creatinin

tag: calcium


title: 620 [202772890063_R05C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: triglyceride

tag: hdl

tag: uric acid


title: P1_cite

tag: cell type


title: 620 [202772890063_R06C01]

description: DNA methylation

tag: age

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin


title: ZnSO4 control bio rep 3 [Zn_P1_C1_S18]

description:
96 well plate
Zn_P1_C1_S18
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: P1_vdj


title: 710 [202193490037_R04C01]

description: DNA methylation

tag: year

tag: whr

tag: sbp

tag: dbp

tag: glucose

tag: creatinin

tag: calcium


title: 599 [202123800146_R02C01]

description: DNA methylation

tag: age

tag: Sex

tag: bmi

tag: triglyceride

tag: hdl

tag: uric acid


title: P1_gex

tag: cell type


title: ZnSO4 dose level 10 bio rep 3 [Zn_P1_C11_S14]

description:
96 well plate
Zn_P1_C11_S14
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment


title: 614 [202193490125_R03C01]

description: DNA methylation

tag: year

tag: ldl

tag: fibrinogen

tag: insulin


title: 676 [202772890063_R08C01]

description: DNA methylation

tag: whr

tag: sbp

tag: dbp

tag: crp

tag: glucose


title: ZnSO4 dose level 9 bio rep 3 [Zn_P1_C10_S15]

description:
96 well plate
Zn_P1_C10_S15
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: Sex

tag: concentration

tag: time point


title: IGSF3_GOF_replicate3

first: Akdes

last: Serin Harmanci

address: One Baylor Plaza

institute: Baylor College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: glioma

extract_protocol:
Mouse gliomas were dissociated into single cells. RNA was extracted using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.  RNA libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3, 10x Genomics).

value: glioma


title: 592 [202775280082_R04C01]

description: DNA methylation

value: F

tag: bmi

tag: triglyceride

tag: hdl

tag: uric acid

tag: creatinin

tag: calcium


title: ZnSO4 dose level 7 bio rep 2 [Zn_P1_B8_S14]

description:
96 well plate
Zn_P1_B8_S14_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment


title: ZnSO4 dose level 8 bio rep 2 [Zn_P1_B9_S5]

description:
96 well plate
Zn_P1_B9_S5_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 592 [202775280082_R03C01]

description: DNA methylation

tag: year

tag: whr

tag: sbp

tag: ldl

tag: fibrinogen

tag: insulin


title: 591 [202123800272_R08C01]

description: DNA methylation

tag: age

tag: Sex

tag: dbp

tag: crp

tag: glucose


title: 591 [202123800272_R07C01]

description: DNA methylation

tag: bmi

tag: triglyceride

tag: hdl

tag: uric acid


title: IGSF3_GOF_replicate1

description: 10x Genomics

tag: tissue


title: 590 [202128330052_R07C01]

description: DNA methylation

tag: creatinin

tag: calcium


title: ZnSO4 dose level 6 bio rep 2 [Zn_P1_B7_S13]

description:
96 well plate
Zn_P1_B7_S13_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 590 [202128330052_R08C01]

description: DNA methylation

tag: year

tag: whr

tag: sbp

tag: ldl

tag: fibrinogen

tag: insulin


title: 589 [202775280062_R04C01]

description: DNA methylation

tag: age

tag: Sex

tag: crp

tag: glucose


title: 589 [202775280062_R03C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: triglyceride

tag: hdl

tag: uric acid


title: Control_replicate3

description: 10x Genomics

tag: tissue


title: ZnSO4 dose level 5 bio rep 2 [Zn_P1_B6_S12]

description:
96 well plate
Zn_P1_B6_S12_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 573 [201502880056_R02C01]

description: DNA methylation

tag: year

tag: whr

tag: sbp

tag: ldl

tag: creatinin

tag: calcium


title: Control_replicate2

description: 10x Genomics


title: ZnSO4 dose level 4 bio rep 2 [Zn_P1_B5_S11]

description:
96 well plate
Zn_P1_B5_S11_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age

tag: Sex


title: 573 [201502880056_R01C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose


title: ZnSO4 dose level 3 bio rep 2 [Zn_P1_B4_S10]

description:
96 well plate
Zn_P1_B4_S10_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage


title: Control_replicate1

description: 10x Genomics


title: 599 [202123800146_R01C01]

description: DNA methylation

tag: triglyceride

tag: hdl

tag: uric acid


title: 560 [201502880056_R08C01]

description: DNA methylation

tag: year

tag: whr

tag: crp


title: 556 [202193490076_R02C01]

description: DNA methylation

tag: sbp

tag: ldl

tag: creatinin


title: IGSF3_LOF_replicate3

description: 10x Genomics


title: 548 [201502880027_R04C01]

description: DNA methylation

tag: age

tag: Sex

tag: calcium


title: ZnSO4 dose level 2 bio rep 2 [Zn_P1_B3_S9]

description:
96 well plate
Zn_P1_B3_S9_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: treatment

tag: concentration

tag: time point


title: ZnSO4 dose level 1 bio rep 2 [Zn_P1_B2_S8]

description:
96 well plate
Zn_P1_B2_S8_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue


title: 560 [201502880056_R07C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose


title: IGSF3_LOF_replicate1

description: 10x Genomics


title: 556 [202193490076_R01C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: uric acid


title: 536 [202128330134_R08C01]

description: DNA methylation

tag: age

tag: sbp

tag: ldl

tag: crp

tag: creatinin


title: 536 [202128330134_R07C01]

description: DNA methylation

tag: Sex

tag: calcium


title: ZnSO4 control bio rep 2 [Zn_P1_B1_S7]

description:
96 well plate
Zn_P1_B1_S7_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 512 [202193490107_R04C01]

description: DNA methylation

tag: year

tag: bmi

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose


title: ZnSO4 dose level 10 bio rep 2 [Zn_P1_B11_S6]

description:
96 well plate
Zn_P1_B11_S6_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age


title: 512 [202193490107_R03C01]

description: DNA methylation

tag: whr

tag: sbp

tag: triglyceride

tag: hdl

tag: ldl

tag: uric acid


title: IGSF3_GOF_replicate2

description: 10x Genomics

tag: tissue


title: GL26110_CD3posP1_C12_R1

first: Elizabeth

last: Perez

address: 30 Fruit Street

institute: MGH

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie mapping to UCSC mm10 mouse transcriptome with parameters `-n 0 -m 10`
RSEM v1.2.8
Supplementary files format and content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each cell (columns)

source_name: brain

extract_protocol:
Dissociated individual cells
Full length scRNA-seq (Smart-Seq2)

value: brain

tag: cell type

value: Tcell

tag: treatment


title: 511 [202775280062_R02C01]

description: DNA methylation

tag: Sex

tag: crp

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_E07_R1


title: ZnSO4 dose level 9 bio rep 2 [Zn_P1_B10_S4]

description:
96 well plate
Zn_P1_B10_S4_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 511 [202775280062_R01C01]

description: DNA methylation

tag: year

tag: age

tag: bmi

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose


title: 509 [202775280060_R05C01]

description: DNA methylation

tag: whr

tag: sbp

tag: triglyceride

tag: hdl

tag: ldl

tag: uric acid


title: 509 [202775280060_R06C01]

description: DNA methylation

tag: Sex

tag: crp

tag: creatinin

tag: calcium


title: ZnSO4 dose level 8 bio rep 1 [Zn_P1_A9_S20]

description:
96 well plate
Zn_P1_A9_S20_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: ZnSO4 dose level 6 bio rep 1 [Zn_P1_A7_S18]

description:
96 well plate
Zn_P1_A7_S18_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age


title: 505 [202193490125_R06C01]

description: DNA methylation

tag: year

tag: bmi

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose


title: IGSF3_LOF_replicate2

description: 10x Genomics


title: 548 [201502880027_R03C01]

description: DNA methylation

tag: whr

tag: sbp

tag: triglyceride

tag: hdl

tag: ldl

tag: uric acid


title: 498 [202193490125_R02C01]

description: DNA methylation

tag: Sex

tag: crp

tag: creatinin

tag: calcium


title: 505 [202193490125_R05C01]

description: DNA methylation

tag: age


title: GL26110_CD3posP1_H10_R1

tag: tissue

tag: cell type

tag: treatment


title: GL26110_CD3posP1_A11_R1


title: GL26110_CD3posP1_C04_R1


title: ZnSO4 dose level 5 bio rep 1 [Zn_P1_A6_S17]

description:
96 well plate
Zn_P1_A6_S17_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: ZnSO4 dose level 4 bio rep 1 [Zn_P1_A5_S16]

description:
96 well plate
Zn_P1_A5_S16_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt


title: 495 [202163550169_R04C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr

tag: dbp

tag: fibrinogen

tag: insulin

tag: glucose


title: ZnSO4 dose level 3 bio rep 1 [Zn_P1_A4_S15]

description:
96 well plate
Zn_P1_A4_S15_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: Sex


title: GL26110_CD3posP1_A02_R1


title: 493 [202193490076_R08C01]

description: DNA methylation

tag: sbp

tag: triglyceride

tag: hdl

tag: ldl

tag: crp

tag: uric acid

tag: creatinin


title: 494 [202163550035_R03C01]

description: DNA methylation

tag: age

tag: calcium


title: 495 [202163550169_R03C01]

description: DNA methylation

tag: year


title: 494 [202163550035_R04C01]

description: DNA methylation

tag: bmi


title: GL26110_CD3posP1_G03_R1

tag: tissue

tag: cell type

tag: treatment


title: GL26110_CD3posP1_H01_R1


title: 485 [202772890073_R04C01]

description: DNA methylation

tag: whr

tag: dbp

tag: fibrinogen

tag: insulin


title: 485 [202772890073_R03C01]

description: DNA methylation

tag: Sex

tag: sbp

tag: triglyceride

tag: glucose


title: GL26110_CD3posP1_C03_R1


title: ZnSO4 control bio rep 1 [Zn_P1_A1_S3]

description:
96 well plate
Zn_P1_A1_S3_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: ZnSO4 dose level 10 bio rep 1 [Zn_P1_A11_S22]

description:
96 well plate
Zn_P1_A11_S22_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: age


title: 479 [202193490123_R01C01]

description: DNA methylation

tag: year

tag: hdl

tag: ldl

tag: uric acid

tag: creatinin

tag: calcium


title: 498 [202193490125_R01C01]

description: DNA methylation

tag: bmi

tag: whr

tag: dbp


title: 463 [202775280060_R08C01]

description: DNA methylation

tag: Sex

tag: fibrinogen

tag: crp

tag: insulin


title: 463 [202775280060_R07C01]

description: DNA methylation

tag: sbp

tag: triglyceride

tag: glucose


title: ZnSO4 dose level 9 bio rep 1 [Zn_P1_A10_S21]

description:
96 well plate
Zn_P1_A10_S21_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: treatment

tag: concentration

tag: time point


title: 460 [202772890073_R02C01]

description: DNA methylation

tag: year

tag: hdl

tag: ldl

tag: uric acid

tag: creatinin

tag: calcium


title: 460 [202772890073_R01C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: whr

tag: dbp

tag: fibrinogen


title: Sertraline dose level 10 bio rep 8 [Ser_P2_H11_S4]

description:
96 well plate
Ser_P2_H11_S4_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

value: Sertraline


title: 447 [202775280062_R08C01]

description: DNA methylation

tag: sbp

tag: triglyceride

tag: crp

tag: insulin

tag: glucose


title: GL26110_CD3posP1_H03_R1

tag: cell type

tag: treatment


title: GL26110_CD3posP1_F07_R1


title: Sertraline dose level 9 bio rep 8 [Ser_P2_H10_S1]

description:
96 well plate
Ser_P2_H10_S1_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: age

tag: concentration

tag: time point


title: 447 [202775280062_R07C01]

description: DNA methylation

tag: year

tag: Sex

tag: hdl

tag: ldl

tag: uric acid

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_E08_R1

tag: tissue


title: 493 [202193490076_R07C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: fibrinogen


title: GL26110_CD3posP1_H04_R1

tag: cell type

tag: treatment


title: 445 [201502880027_R05C01]

description: DNA methylation

tag: age

tag: insulin

tag: glucose


title: 438 [202775280053_R04C01]

description: DNA methylation

tag: year

tag: Sex

tag: hdl

tag: crp


title: 445 [201502880027_R06C01]

description: DNA methylation

tag: ldl

tag: uric acid

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_C02_R1

tag: tissue


title: Sertraline dose level 7 bio rep 8 [Ser_P2_H08_S2]

description:
96 well plate
Ser_P2_H08_S2_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 438 [202775280053_R03C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: fibrinogen


title: 479 [202193490123_R02C01]

description: DNA methylation

tag: year

tag: age

tag: Sex

tag: insulin

tag: glucose


title: GL26110_CD3posP1_E03_R1

tag: cell type

tag: treatment


title: ZnSO4 dose level 1 bio rep 1 [Zn_P1_A2_S1]

description:
96 well plate
Zn_P1_A2_S1_L002
Zn.raw.counts.txt
Zn.sansG11H11.filtered.normFinal.txt

tag: tissue


title: 432 [202123800272_R02C01]

description: DNA methylation

tag: hdl

tag: ldl

tag: crp

tag: uric acid

tag: creatinin

tag: calcium


title: Sertraline dose level 5 bio rep 8 [Ser_P2_H06_S8]

description:
96 well plate
Ser_P2_H06_S8_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 430 [202775280060_R04C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: fibrinogen


title: GL26110_CD3posP1_H11_R1

tag: tissue

tag: cell type

tag: treatment


title: GL26110_CD3posP1_B07_R1


title: 430 [202775280060_R03C01]

description: DNA methylation

tag: age

tag: Sex

tag: hdl

tag: ldl

tag: insulin

tag: glucose


title: Sertraline dose level 4 bio rep 8 [Ser_P2_H05_S7]

description:
96 well plate
Ser_P2_H05_S7_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 432 [202123800272_R01C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr

tag: uric acid

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_G12_R1

tag: tissue

tag: cell type


title: 423 [201502880056_R04C01]

description: DNA methylation

tag: age

tag: sbp

tag: dbp

tag: triglyceride

tag: fibrinogen

tag: crp


title: Sertraline dose level 3 bio rep 8 [Ser_P2_H04_S6]

description:
96 well plate
Ser_P2_H04_S6_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: Sex

tag: treatment


title: 410 [202193490102_R01C01]

description: DNA methylation

tag: year

tag: hdl

tag: ldl

tag: insulin

tag: glucose


title: 407 [202163550105_R03C01]

description: DNA methylation

tag: bmi

tag: whr

tag: uric acid

tag: creatinin

tag: calcium


title: 405 [202123800272_R06C01]

description: DNA methylation

tag: age

tag: sbp

tag: dbp


title: GL26110_CD3posP1_E01_R1

tag: tissue

tag: cell type


title: GL26110_CD3posP1_B02_R1


title: GL26110_CD3posP1_H08_R1


title: Sertraline dose level 6 bio rep 8 [Ser_P2_H07_S3]

description:
96 well plate
Ser_P2_H07_S3_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: Sex

tag: concentration

tag: time point


title: GL26110_CD3posP1_C09_R1

tag: treatment


title: Sertraline dose level 1 bio rep 8 [Ser_P2_H02_S12]

description:
96 well plate
Ser_P2_H02_S12_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: 396 [202775280026_R04C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp

tag: insulin


title: 396 [202775280026_R03C01]

description: DNA methylation

tag: age

tag: bmi

tag: whr

tag: glucose

tag: uric acid

tag: creatinin

tag: calcium


title: Sertraline dose level 10 bio rep 7 [Ser_P2_G11_S10]

description:
96 well plate
Ser_P2_G11_S10_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: Sex

tag: concentration


title: GL26110_CD3posP1_A10_R1

tag: cell type

tag: treatment


title: Sertraline dose level 9 bio rep 7 [Ser_P2_G10_S9]

description:
96 well plate
Ser_P2_G10_S9_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: time point


title: 389 [202163550035_R02C01]

description: DNA methylation

tag: year

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen


title: 385 [201502880027_R02C01]

description: DNA methylation

tag: age

tag: bmi

tag: whr

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: 389 [202163550035_R01C01]

description: DNA methylation

tag: Sex

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_G01_R1

tag: tissue

tag: cell type

tag: treatment


title: 385 [201502880027_R01C01]

description: DNA methylation

tag: year

tag: sbp

tag: dbp

tag: triglyceride


title: 423 [201502880056_R03C01]

description: DNA methylation

tag: age

tag: hdl

tag: ldl

tag: fibrinogen


title: Sertraline dose level 8 bio rep 7 [Ser_P2_G09_S16]

description:
96 well plate
Ser_P2_G09_S16_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 410 [202193490102_R02C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: whr

tag: crp

tag: insulin

tag: glucose

tag: uric acid


title: GL26110_CD3posP1_C06_R1

tag: tissue

tag: cell type

tag: treatment


title: Sertraline dose level 7 bio rep 7 [Ser_P2_G08_S15]

description:
96 well plate
Ser_P2_G08_S15_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: age


title: GL26110_CD3posP1_C10_R1


title: 379 [202775280053_R06C01]

description: DNA methylation

tag: year

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: creatinin

tag: calcium


title: 379 [202775280053_R05C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: ldl

tag: fibrinogen


title: Sertraline dose level 2 bio rep 8 [Ser_P2_H03_S5]

description:
96 well plate
Ser_P2_H03_S5_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 405 [202123800272_R05C01]

description: DNA methylation

tag: whr

tag: insulin

tag: glucose

tag: uric acid


title: 407 [202163550105_R04C01]

description: DNA methylation

tag: year

tag: age

tag: sbp

tag: crp


title: Sertraline control bio rep 8 [Ser_P2_H01_S11]

description:
96 well plate
Ser_P2_H01_S11_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: treatment


title: 371 [202775280082_R02C01]

description: DNA methylation

tag: Sex

tag: dbp

tag: triglyceride

tag: hdl

tag: creatinin

tag: calcium


title: 364 [202193490037_R02C01]

description: DNA methylation

tag: bmi

tag: ldl

tag: fibrinogen


title: GL26110_CD3posP1_F06_R1

tag: cell type


title: 371 [202775280082_R01C01]

description: DNA methylation

tag: whr

tag: insulin

tag: glucose

tag: uric acid


title: 361 [202775280026_R02C01]

description: DNA methylation

tag: year

tag: age

tag: sbp

tag: crp


title: Sertraline dose level 5 bio rep 7 [Ser_P2_G06_S13]

description:
96 well plate
Ser_P2_G06_S13_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: Sex

tag: treatment

tag: concentration

tag: time point


title: GL26110_CD3posP1_B10_R1


title: Sertraline dose level 6 bio rep 7 [Ser_P2_G07_S14]

description:
96 well plate
Ser_P2_G07_S14_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: 361 [202775280026_R01C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: creatinin

tag: calcium


title: 364 [202193490037_R01C01]

description: DNA methylation

tag: year

tag: whr

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid


title: 346 [202193490102_R06C01]

description: DNA methylation

tag: age

tag: Sex

tag: sbp

tag: crp


title: GL26110_CD3posP1_H09_R1

tag: tissue

tag: cell type

tag: treatment


title: Sertraline dose level 3 bio rep 7 [Ser_P2_G04_S19]

description:
96 well plate
Ser_P2_G04_S19_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: Sertraline dose level 4 bio rep 7 [Ser_P2_G05_S20]

description:
96 well plate
Ser_P2_G05_S20_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_B11_R1


title: 342 [202193490107_R06C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: creatinin

tag: calcium


title: 346 [202193490102_R05C01]

description: DNA methylation

tag: year

tag: age

tag: whr

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid


title: 340 [202193490121_R04C01]

description: DNA methylation

tag: Sex

tag: sbp

tag: crp


title: Sertraline dose level 2 bio rep 7 [Ser_P2_G03_S18]

description:
96 well plate
Ser_P2_G03_S18_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 340 [202193490121_R03C01]

description: DNA methylation

tag: bmi

tag: dbp

tag: triglyceride

tag: hdl

tag: ldl

tag: creatinin


title: Sertraline dose level 1 bio rep 7 [Ser_P2_G02_S17]

description:
96 well plate
Ser_P2_G02_S17_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: age


title: GL26110_CD3posP1_D09_R1

tag: cell type


title: 342 [202193490107_R05C01]

description: DNA methylation

tag: year

tag: whr

tag: fibrinogen

tag: insulin

tag: glucose

tag: uric acid

tag: calcium


title: 315 [202163550105_R06C01]

description: DNA methylation

tag: Sex

tag: sbp

tag: crp


title: 315 [202163550105_R05C01]

description: DNA methylation

tag: bmi

tag: dbp


title: 308 [202775280026_R08C01]

description: DNA methylation

tag: triglyceride

tag: hdl


title: GL26110_CD3posP1_H12_R1

tag: tissue

tag: treatment


title: GL26110_CD3posP1_G06_R1

tag: cell type


title: Sertraline control bio rep 7 [Ser_P2_G01_S21]

description:
96 well plate
Ser_P2_G01_S21_L004
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: age

tag: concentration

tag: time point


title: Sertraline dose level 10 bio rep 6 [Ser_P2_F11_S131]

description:
96 well plate
Ser_P2_F11_S131_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: 308 [202775280026_R07C01]

description: DNA methylation

tag: year

tag: whr

tag: ldl

tag: fibrinogen

tag: insulin

tag: glucose

tag: creatinin


title: GL26110_CD3posP1_F05_R1


title: 299 [202772890073_R06C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: sbp

tag: dbp

tag: crp

tag: uric acid

tag: calcium


title: GL26110_CD3posP1_E12_R1

tag: tissue

tag: cell type

tag: treatment


title: Sertraline dose level 9 bio rep 6 [Ser_P2_F10_S129]

description:
96 well plate
Ser_P2_F10_S129_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: age

tag: concentration

tag: time point


title: Sertraline dose level 8 bio rep 6 [Ser_P2_F09_S130]

description:
96 well plate
Ser_P2_F09_S130_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: 299 [202772890073_R05C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: insulin


title: 285 [202193490076_R06C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: sbp

tag: dbp

tag: crp

tag: glucose

tag: creatinin


title: 285 [202193490076_R05C01]

description: DNA methylation

tag: age

tag: uric acid

tag: calcium


title: Sertraline dose level 7 bio rep 6 [Ser_P2_F08_S134]

description:
96 well plate
Ser_P2_F08_S134_L008
Ser.raw.counts.txt
na

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 284 [202128330024_R06C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen


title: GL26110_CD3posP1_B05_R1

tag: cell type


title: 284 [202128330024_R05C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: sbp

tag: dbp

tag: insulin

tag: glucose


title: 252 [202775280060_R01C01]

description: DNA methylation

tag: age

tag: uric acid

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_F09_R1

tag: tissue

tag: treatment


title: Sertraline dose level 6 bio rep 6 [Ser_P2_F07_S135]

description:
96 well plate
Ser_P2_F07_S135_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: concentration

tag: time point


title: 252 [202775280060_R02C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp


title: 217 [202772890073_R07C01]

description: DNA methylation

tag: Sex

tag: bmi

tag: sbp

tag: dbp

tag: insulin

tag: glucose


title: 217 [202772890073_R08C01]

description: DNA methylation

tag: age

tag: uric acid

tag: creatinin

tag: calcium


title: Sertraline dose level 5 bio rep 6 [Ser_P2_F06_S132]

description:
96 well plate
Ser_P2_F06_S132_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: GL26110_CD3posP1_A03_R1

tag: cell type


title: 205 [202123800036_R08C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: ldl

tag: fibrinogen

tag: crp


title: GL26110_CD3posP1_H06_R1


title: 205 [202123800036_R07C01]

description: DNA methylation

tag: age

tag: Sex

tag: bmi

tag: sbp

tag: dbp

tag: insulin

tag: glucose


title: Sertraline dose level 3 bio rep 6 [Ser_P2_F04_S138]

description:
96 well plate
Ser_P2_F04_S138_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration


title: GL26110_CD3posP1_D04_R1

tag: cell type


title: Sertraline dose level 4 bio rep 6 [Ser_P2_F05_S133]

description:
96 well plate
Ser_P2_F05_S133_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: time point


title: GL26110_CD3posP1_C08_R1


title: Sertraline dose level 2 bio rep 6 [Ser_P2_F03_S139]

description:
96 well plate
Ser_P2_F03_S139_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_E11_R1


title: 191 [202193490102_R03C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: uric acid

tag: creatinin

tag: calcium


title: 193 [202123800036_R05C01]

description: DNA methylation

tag: age

tag: Sex

tag: bmi

tag: sbp

tag: ldl

tag: fibrinogen


title: Sertraline dose level 1 bio rep 6 [Ser_P2_F02_S136]

description:
96 well plate
Ser_P2_F02_S136_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment


title: 179 [202060330182_R06C01]

description: DNA methylation

tag: dbp

tag: crp

tag: insulin

tag: glucose


title: GL26110_CD3posP1_A04_R1

tag: cell type


title: 179 [202060330182_R05C01]

description: DNA methylation

tag: year

tag: whr

tag: triglyceride

tag: hdl

tag: uric acid


title: Sertraline control bio rep 6 [Ser_P2_F01_S137]

description:
96 well plate
Ser_P2_F01_S137_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: age

tag: Sex

tag: concentration

tag: time point


title: GL26110_CD3posP1_D11_R1

tag: tissue


title: Sertraline dose level 10 bio rep 5 [Ser_P2_E11_S142]

description:
96 well plate
Ser_P2_E11_S142_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage


title: 156 [202163550169_R05C01]

description: DNA methylation

tag: bmi

tag: sbp

tag: ldl

tag: fibrinogen

tag: creatinin

tag: calcium


title: GL26110_CD3posP1_A01_R1

tag: cell type

tag: treatment


title: Sertraline dose level 9 bio rep 5 [Ser_P2_E10_S143]

description:
96 well plate
Ser_P2_E10_S143_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: 152 [202060330182_R03C01]

description: DNA methylation

tag: year

tag: whr

tag: dbp

tag: triglyceride

tag: insulin

tag: glucose


title: 151 [202123800146_R08C01]

description: DNA methylation

tag: age

tag: Sex

tag: hdl

tag: crp

tag: uric acid


title: GL26110_CD3posP1_G08_R1

tag: tissue


title: 152 [202060330182_R04C01]

description: DNA methylation

tag: bmi

tag: sbp

tag: ldl

tag: fibrinogen


title: 204 [202193490101_R04C01]

description: DNA methylation

tag: creatinin

tag: calcium


title: 151 [202123800146_R07C01]

description: DNA methylation

tag: year

tag: whr


title: Sertraline dose level 8 bio rep 5 [Ser_P2_E09_S140]

description:
96 well plate
Ser_P2_E09_S140_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 204 [202193490101_R03C01]

description: DNA methylation

tag: age

tag: Sex

tag: dbp

tag: triglyceride

tag: insulin

tag: glucose


title: 193 [202123800036_R06C01]

description: DNA methylation

tag: bmi

tag: sbp

tag: hdl

tag: crp

tag: uric acid


title: 147 [202128330024_R08C01]

description: DNA methylation

tag: year

tag: ldl

tag: fibrinogen

tag: creatinin

tag: calcium


title: Sertraline dose level 7 bio rep 5 [Ser_P2_E08_S141]

description:
96 well plate
Ser_P2_E08_S141_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 147 [202128330024_R07C01]

description: DNA methylation

tag: age

tag: Sex

tag: whr

tag: dbp

tag: triglyceride

tag: insulin


title: 191 [202193490102_R04C01]

description: DNA methylation

tag: bmi

tag: sbp

tag: hdl

tag: crp

tag: glucose

tag: uric acid


title: GL26110_CD3posP1_D05_R1

tag: tissue

tag: cell type


title: GL26110_CD3posP1_F04_R1

tag: treatment


title: 145 [202193490037_R06C01]

description: DNA methylation

tag: year

tag: ldl

tag: fibrinogen

tag: creatinin

tag: calcium


title: Sertraline dose level 6 bio rep 5 [Ser_P2_E07_S145]

description:
96 well plate
Ser_P2_E07_S145_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: age

tag: Sex

tag: concentration

tag: time point


title: 144 [202163550035_R08C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: hdl

tag: insulin


title: 144 [202163550035_R07C01]

description: DNA methylation

tag: year

tag: glucose

tag: uric acid


title: 156 [202163550169_R06C01]

description: DNA methylation

tag: ldl

tag: fibrinogen

tag: crp

tag: creatinin


title: Sertraline dose level 5 bio rep 5 [Ser_P2_E06_S144]

description:
96 well plate
Ser_P2_E06_S144_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: Sex

tag: treatment


title: GL26110_CD3posP1_D01_R1

tag: cell type


title: 131 [202193490107_R02C01]

description: DNA methylation

tag: calcium


title: 131 [202193490107_R01C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride


title: 111 [202060330182_R02C01]

description: DNA methylation

tag: year

tag: hdl

tag: insulin

tag: glucose

tag: uric acid


title: GL26110_CD3posP1_B03_R1

tag: tissue


title: 100 [202163550169_R02C01]

description: DNA methylation

tag: ldl

tag: fibrinogen

tag: crp

tag: creatinin


title: 111 [202060330182_R01C01]

description: DNA methylation

tag: age

tag: Sex


title: Sertraline dose level 3 bio rep 5 [Ser_P2_E04_S146]

description:
96 well plate
Ser_P2_E04_S146_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: 100 [202163550169_R01C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: calcium


title: 82 [202123800036_R04C01]

description: DNA methylation

tag: year

tag: hdl

tag: insulin

tag: glucose

tag: uric acid


title: Sertraline dose level 2 bio rep 5 [Ser_P2_E03_S149]

description:
96 well plate
Ser_P2_E03_S149_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: age


title: GL26110_CD3posP1_B04_R1

tag: cell type


title: Sertraline dose level 1 bio rep 5 [Ser_P2_E02_S148]

description:
96 well plate
Ser_P2_E02_S148_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: Sex

tag: treatment


title: 80 [202163550104_R06C01]

description: DNA methylation

tag: bmi

tag: ldl

tag: fibrinogen

tag: crp

tag: creatinin


title: 80 [202163550104_R05C01]

description: DNA methylation

tag: whr

tag: sbp

tag: dbp

tag: triglyceride

tag: calcium


title: 75 [202193490101_R02C01]

description: DNA methylation

tag: year

tag: hdl

tag: insulin

tag: glucose

tag: uric acid


title: 145 [202193490037_R05C01]

description: DNA methylation

tag: age

tag: Sex


title: 82 [202123800036_R03C01]

description: DNA methylation

tag: bmi


title: Sertraline control bio rep 5 [Ser_P2_E01_S150]

description:
96 well plate
Ser_P2_E01_S150_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: treatment

tag: concentration

tag: time point


title: GL26110_CD3posP1_H02_R1

tag: cell type


title: Sertraline dose level 10 bio rep 4 [Ser_P2_D11_S108]

description:
96 well plate
Ser_P2_D11_S108_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_E09_R1


title: GL26110_CD3posP1_E10_R1


title: 75 [202193490101_R01C01]

description: DNA methylation

tag: whr

tag: sbp

tag: dbp

tag: ldl

tag: fibrinogen

tag: creatinin


title: Sertraline dose level 9 bio rep 4 [Ser_P2_D10_S110]

description:
96 well plate
Ser_P2_D10_S110_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: 63 [202193490107_R08C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: hdl

tag: crp

tag: insulin

tag: glucose

tag: calcium


title: Sertraline dose level 4 bio rep 5 [Ser_P2_E05_S147]

description:
96 well plate
Ser_P2_E05_S147_L008
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: Sex

tag: treatment


title: GL26110_CD3posP1_F12_R1

tag: cell type


title: 71 [202193490123_R03C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: uric acid


title: 71 [202193490123_R04C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: ldl

tag: fibrinogen

tag: creatinin


title: 63 [202193490107_R07C01]

description: DNA methylation

tag: hdl

tag: insulin

tag: glucose

tag: calcium


title: Sertraline dose level 8 bio rep 4 [Ser_P2_D09_S109]

description:
96 well plate
Ser_P2_D09_S109_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: Sex

tag: concentration

tag: time point


title: 42 [202775280062_R06C01]

description: DNA methylation

tag: crp


title: 50 [202193490076_R04C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: uric acid


title: 42 [202775280062_R05C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: ldl

tag: fibrinogen

tag: creatinin


title: Sertraline dose level 7 bio rep 4 [Ser_P2_D08_S112]

description:
96 well plate
Ser_P2_D08_S112_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: treatment


title: Sertraline dose level 6 bio rep 4 [Ser_P2_D07_S111]

description:
96 well plate
Ser_P2_D07_S111_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: developmental stage

tag: age


title: GL26110_CD3posP1_G07_R1

tag: cell type


title: GL26110_CD3posP1_F11_R1


title: GL26110_CD3posP1_B08_R1


title: 40 [202163550035_R05C01]

description: DNA methylation

tag: Sex

tag: hdl

tag: insulin

tag: glucose

tag: calcium


title: 37 [202163550169_R08C01]

description: DNA methylation

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: crp


title: 40 [202163550035_R06C01]

description: DNA methylation

tag: year

tag: triglyceride

tag: ldl

tag: fibrinogen

tag: uric acid


title: Sertraline dose level 4 bio rep 4 [Ser_P2_D05_S113]

description:
96 well plate
Ser_P2_D05_S113_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age

tag: treatment

tag: concentration

tag: time point


title: 37 [202163550169_R07C01]

description: DNA methylation

tag: Sex

tag: hdl

tag: insulin

tag: glucose

tag: creatinin

tag: calcium


title: Sertraline dose level 5 bio rep 4 [Ser_P2_D06_S114]

description:
96 well plate
Ser_P2_D06_S114_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_H05_R1

tag: cell type


title: GL26110_CD3posP1_D03_R1


title: GL26110_CD3posP1_D12_R1


title: GL26110_CD3posP1_G05_R1


title: Sertraline dose level 2 bio rep 4 [Ser_P2_D03_S115]

description:
96 well plate
Ser_P2_D03_S115_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: Sertraline dose level 1 bio rep 4 [Ser_P2_D02_S117]

description:
96 well plate
Ser_P2_D02_S117_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_G11_R1


title: GL26110_CD3posP1_G10_R1


title: 50 [202193490076_R03C01]

description: DNA methylation

tag: year

tag: bmi

tag: whr

tag: sbp

tag: dbp

tag: triglyceride


title: Sertraline control bio rep 4 [Ser_P2_D01_S118]

description:
96 well plate
Ser_P2_D01_S118_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: tissue

tag: developmental stage

tag: age


title: Sertraline dose level 9 bio rep 3 [Ser_P2_C10_S119]

description:
96 well plate
Ser_P2_C10_S119_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: treatment

tag: concentration

tag: time point


title: Sertraline dose level 8 bio rep 3 [Ser_P2_C09_S120]

description:
96 well plate
Ser_P2_C09_S120_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

tag: Sex


title: Sertraline dose level 3 bio rep 4 [Ser_P2_D04_S116]

description:
96 well plate
Ser_P2_D04_S116_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_F08_R1


title: GL26110_CD3posP1_C05_R1


title: GL26110_CD3posP1_A06_R1


title: GL26110_CD3posP1_F03_R1


title: GL26110_CD3posP1_D06_R1


title: GL26110_CD3posP1_C01_R1


title: Sertraline dose level 6 bio rep 3 [Ser_P2_C07_S122]

description:
96 well plate
Ser_P2_C07_S122_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: Sertraline dose level 5 bio rep 3 [Ser_P2_C06_S123]

description:
96 well plate
Ser_P2_C06_S123_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400030_R08C01]

city: Alhambra

first: Yi-Tsung

last: Lu

state: CA

address: 516 SAN PASQUAL DR

institute: University of Southern California

description: on-treatment

hyb_protocol: cfDNA was prepared using Infinium HD FFPE Assay, and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
data was processed using Sesame package in R
processed data matrix: beta value was calculated based on default parameters of Sesame package

label: cy3, cy5

source_name: cfDNA methylation

extract_protocol: cfDNA extracted by QIAamp Circulating Nucleic Acid kit

tag: response

value: STA/INC

tag: disease

value: muscle invasive bladder cancer


title: GL26110_CD3posP1_D07_R1


title: Sertraline dose level 7 bio rep 3 [Ser_P2_C08_S121]

description:
96 well plate
Ser_P2_C08_S121_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400017_R07C01]

description: on-treatment


title: Sertraline dose level 4 bio rep 3 [Ser_P2_C05_S124]

description:
96 well plate
Ser_P2_C05_S124_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400038_R07C01]

description: on-treatment

value: DWNSTG


title: cfDNA from on-treatment patients [204367400004_R07C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400038_R08C01]

description: on-treatment


title: Sertraline dose level 3 bio rep 3 [Ser_P2_C04_S125]

description:
96 well plate
Ser_P2_C04_S125_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_E05_R1


title: cfDNA from on-treatment patients [204367400030_R07C01]

description: on-treatment


title: GL26110_CD3posP1_D08_R1


title: cfDNA from on-treatment patients [204367400038_R06C01]

description: on-treatment


title: Sertraline dose level 2 bio rep 3 [Ser_P2_C03_S126]

description:
96 well plate
Ser_P2_C03_S126_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400032_R08C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400073_R08C01]

description: on-treatment


title: Sertraline dose level 1 bio rep 3 [Ser_P2_C02_S127]

description:
96 well plate
Ser_P2_C02_S127_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_E02_R1


title: cfDNA from on-treatment patients [204367400032_R07C01]

description: on-treatment


title: GL26110_CD3posP1_G09_R1


title: cfDNA from on-treatment patients [204367400042_R08C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400017_R06C01]

description: on-treatment


title: Sertraline dose level 10 bio rep 2 [Ser_P2_B11_S86]

description:
96 well plate
Ser_P2_B11_S86_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400004_R06C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400042_R07C01]

description: on-treatment


title: GL26110_CD3posP1_G02_R1


title: Sertraline control bio rep 3 [Ser_P2_C01_S128]

description:
96 well plate
Ser_P2_C01_S128_L007
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_E04_R1


title: cfDNA from on-treatment patients [204367400004_R05C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400042_R06C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400017_R05C01]

description: on-treatment


title: GL26110_CD3posP1_E06_R1


title: GL26110_CD3posP1_C11_R1


title: cfDNA from on-treatment patients [204367400042_R04C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400034_R08C01]

description: on-treatment


title: Sertraline dose level 7 bio rep 2 [Ser_P2_B08_S100]

description:
96 well plate
Ser_P2_B08_S100_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400042_R05C01]

description: on-treatment


title: Sertraline dose level 6 bio rep 2 [Ser_P2_B07_S101]

description:
96 well plate
Ser_P2_B07_S101_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: genomic DNA from gastric cardia tissue 6

city: Shantou

first: Shuhui

last: Liu

address: No. 22, Xinling Road, Shantou, P.R. China

department: Department of Pathology

country: China

institute: Shantou University Medical College

description: gastric cardia cancer

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC 850k Human DNA Methylation Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: gastric cardia tissue 6

extract_protocol: genomic DNA was extracted from gastric cardia tissue samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

value: gastric cardia tissue

tag: disease state

value: tumor


title: GL26110_CD3posP1_H07_R1

tag: cell type


title: genomic DNA from gastric cardia tissue 15

description: normal gastric cardia sample

source_name: gastric cardia tissue 15

value: normal


title: genomic DNA from gastric cardia tissue 16

description: gastric cardia cancer

source_name: gastric cardia tissue 16


title: genomic DNA from gastric cardia tissue 11

description: normal gastric cardia sample

source_name: gastric cardia tissue 11

value: Female


title: cfDNA from on-treatment patients [204367400030_R06C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400032_R06C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400032_R05C01]

description: on-treatment


title: genomic DNA from gastric cardia tissue 14

description: gastric cardia cancer

source_name: gastric cardia tissue 14


title: genomic DNA from gastric cardia tissue 8

description: gastric cardia cancer

source_name: gastric cardia tissue 8


title: genomic DNA from gastric cardia tissue 2

description: gastric cardia cancer

source_name: gastric cardia tissue 2


title: cfDNA from on-treatment patients [204367400075_R05C01]

description: on-treatment


title: genomic DNA from gastric cardia tissue 4

description: gastric cardia cancer

source_name: gastric cardia tissue 4


title: genomic DNA from gastric cardia tissue 3

description: normal gastric cardia sample

source_name: gastric cardia tissue 3


title: Sertraline dose level 5 bio rep 2 [Ser_P2_B06_S102]

description:
96 well plate
Ser_P2_B06_S102_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

source_name: whole body

value: whole body

value: larva

value: 5 dpf/24 hr post hatch

value: 24 hr


title: Sertraline dose level 8 bio rep 2 [Ser_P2_B09_S88]

description:
96 well plate
Ser_P2_B09_S88_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: Sertraline dose level 4 bio rep 2 [Ser_P2_B05_S103]

description:
96 well plate
Ser_P2_B05_S103_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: genomic DNA from gastric cardia tissue 10

description: gastric cardia cancer

source_name: gastric cardia tissue 10


title: cfDNA from on-treatment patients [204367400004_R03C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400038_R05C01]

description: on-treatment


title: GL26110_CD3posP1_A08_R1


title: GL26110_CD3posP1_C07_R1


title: cfDNA from on-treatment patients [204367400042_R03C01]

description: on-treatment


title: genomic DNA from gastric cardia tissue 13

description: normal gastric cardia sample

source_name: gastric cardia tissue 13


title: Sertraline dose level 3 bio rep 2 [Ser_P2_B04_S104]

description:
96 well plate
Ser_P2_B04_S104_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400017_R04C01]

description: on-treatment


title: genomic DNA from gastric cardia tissue 9

description: normal gastric cardia sample

source_name: gastric cardia tissue 9


title: Sertraline dose level 2 bio rep 2 [Ser_P2_B03_S105]

description:
96 well plate
Ser_P2_B03_S105_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: genomic DNA from gastric cardia tissue 1

description: normal gastric cardia sample

source_name: gastric cardia tissue 1


title: genomic DNA from gastric cardia tissue 12

description: gastric cardia cancer

source_name: gastric cardia tissue 12


title: cfDNA from on-treatment patients [204367400034_R07C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400030_R05C01]

description: on-treatment


title: GL26110_CD3posP1_B01_R1

source_name: brain


title: Sertraline dose level 1 bio rep 2 [Ser_P2_B02_S106]

description:
96 well plate
Ser_P2_B02_S106_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400017_R03C01]

description: on-treatment

source_name: cfDNA methylation


title: cfDNA from on-treatment patients [204367400004_R02C01]

description: on-treatment


title: genomic DNA from gastric cardia tissue 5

description: normal gastric cardia sample

source_name: gastric cardia tissue 5


title: cfDNA from on-treatment patients [204367400034_R06C01]

description: on-treatment


title: Sertraline control bio rep 2 [Ser_P2_B01_S107]

description:
96 well plate
Ser_P2_B01_S107_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_F02_R1


title: cfDNA from on-treatment patients [204367400030_R04C01]

description: on-treatment


title: Sertraline dose level 9 bio rep 2 [Ser_P2_B10_S87]

description:
96 well plate
Ser_P2_B10_S87_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26110_CD3posP1_F01_R1


title: Sertraline dose level 9 bio rep 1 [Ser_P2_A10_S93]

description:
96 well plate
Ser_P2_A10_S93_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400030_R03C01]

description: on-treatment


title: Sertraline dose level 10 bio rep 1 [Ser_P2_A11_S92]

description:
96 well plate
Ser_P2_A11_S92_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400017_R02C01]

description: on-treatment


title: GL26150_CD3posP1_E09_R1


title: cfDNA from on-treatment patients [204367400075_R04C01]

description: on-treatment


title: GL26110_CD3posP1_A07_R1


title: Sertraline dose level 8 bio rep 1 [Ser_P2_A09_S94]

description:
96 well plate
Ser_P2_A09_S94_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400032_R02C01]

description: on-treatment


title: GL26150_CD3posP1_D12_R1


title: genomic DNA from gastric cardia tissue 7

description: normal gastric cardia sample

source_name: gastric cardia tissue 7


title: GL26110_CD3posP1_F10_R1


title: cfDNA from on-treatment patients [204367400034_R04C01]

description: on-treatment


title: Sertraline dose level 7 bio rep 1 [Ser_P2_A08_S95]

description:
96 well plate
Ser_P2_A08_S95_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400073_R04C01]

description: on-treatment


title: GL26150_CD3posP1_C03_R1


title: cfDNA from on-treatment patients [204367400004_R08C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400034_R03C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400032_R01C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400073_R05C01]

description: on-treatment


title: GL26150_CD3posP1_E08_R1


title: Sertraline dose level 6 bio rep 1 [Ser_P2_A07_S96]

description:
96 well plate
Ser_P2_A07_S96_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400042_R02C01]

description: on-treatment


title: Sertraline dose level 4 bio rep 1 [Ser_P2_A05_S98]

description:
96 well plate
Ser_P2_A05_S98_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: Sertraline dose level 5 bio rep 1 [Ser_P2_A06_S97]

description:
96 well plate
Ser_P2_A06_S97_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400075_R03C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400073_R02C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400034_R02C01]

description: on-treatment


title: GL26150_CD3posP1_B09_R1


title: cfDNA from on-treatment patients [204367400017_R01C01]

description: on-treatment


title: GL26150_CD3posP1_G12_R1


title: Sertraline dose level 3 bio rep 1 [Ser_P2_A04_S99]

description:
96 well plate
Ser_P2_A04_S99_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400004_R01C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400075_R06C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400030_R02C01]

description: on-treatment


title: Sertraline dose level 2 bio rep 1 [Ser_P2_A03_S90]

description:
96 well plate
Ser_P2_A03_S90_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: cfDNA from on-treatment patients [204367400042_R01C01]

description: on-treatment


title: GL26110_CD3posP1_B06_R1


title: Sertraline dose level 1 bio rep 1 [Ser_P2_A02_S89]

description:
96 well plate
Ser_P2_A02_S89_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt


title: GL26150_CD3posP1_G10_R1

value: Myeloid


title: cfDNA from on-treatment patients [204367400038_R01C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400030_R01C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400038_R02C01]

description: on-treatment


title: cfDNA from on-treatment patients [204367400073_R01C01]

description: on-treatment


title: GL26150_CD3posP1_F11_R1


title: cfDNA from pre-treatment patients [203490650016_R08C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650023_R08C01]

description: pre-treatment


title: GL26150_CD3posP1_D09_R1


title: GL26150_CD3posP1_G02_R1


title: cfDNA from pre-treatment patients [203490650044_R08C01]

description: pre-treatment


title: Paroxetine dose level 8 bio rep 8 [Par_P3_H09_S4]

description:
96 well plate
Par_P3_H09_S4_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt

value: Paroxetine


title: GL26150_CD3posP1_D05_R1

value: brain

value: Microglia


title: cfDNA from pre-treatment patients [203490650023_R07C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650014_R08C01]

description: pre-treatment


title: GL26150_CD3posP1_D04_R1

value: Tcell


title: cfDNA from pre-treatment patients [203490650042_R07C01]

description: pre-treatment

value: STA/INC


title: cfDNA from pre-treatment patients [203490650045_R08C01]

description: pre-treatment

value: muscle invasive bladder cancer


title: cfDNA from pre-treatment patients [203490650042_R08C01]

description: pre-treatment


title: GL26150_CD3posP1_G04_R1


title: cfDNA from pre-treatment patients [203490650016_R07C01]

description: pre-treatment


title: Paroxetine dose level 7 bio rep 8 [Par_P3_H08_S1]

description:
96 well plate
Par_P3_H08_S1_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_B10_R1


title: Paroxetine dose level 6 bio rep 8 [Par_P3_H07_S2]

description:
96 well plate
Par_P3_H07_S2_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Paroxetine dose level 5 bio rep 8 [Par_P3_H06_S21]

description:
96 well plate
Par_P3_H06_S21_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: Sertraline control bio rep 1 [Ser_P2_A01_S91]

description:
96 well plate
Ser_P2_A01_S91_L006
Ser.raw.counts.txt
Ser.sansF8.filtered.normFinal.txt

value: Sertraline


title: Paroxetine dose level 10 bio rep 8 [Par_P3_H11_S5]

description:
96 well plate
Par_P3_H11_S5_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_D11_R1


title: GL26150_CD3posP1_C04_R1


title: cfDNA from pre-treatment patients [203490650014_R07C01]

description: pre-treatment

value: DWNSTG


title: Paroxetine dose level 4 bio rep 8 [Par_P3_H05_S20]

description:
96 well plate
Par_P3_H05_S20_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650063_R06C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650049_R08C01]

description: pre-treatment


title: Paroxetine dose level 9 bio rep 8 [Par_P3_H10_S3]

description:
96 well plate
Par_P3_H10_S3_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_B05_R1


title: Paroxetine dose level 3 bio rep 8 [Par_P3_H04_S19]

description:
96 well plate
Par_P3_H04_S19_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_E12_R1


title: cfDNA from pre-treatment patients [203490650023_R06C01]

description: pre-treatment


title: Paroxetine dose level 2 bio rep 8 [Par_P3_H03_S18]

description:
96 well plate
Par_P3_H03_S18_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650042_R06C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650014_R05C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650028_R08C01]

description: pre-treatment


title: GL26150_CD3posP1_C08_R1


title: Paroxetine dose level 1 bio rep 8 [Par_P3_H02_S17]

description:
96 well plate
Par_P3_H02_S17_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650016_R06C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650016_R05C01]

description: pre-treatment


title: GL26150_CD3posP1_H03_R1


title: cfDNA from pre-treatment patients [203490650044_R07C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650020_R07C01]

description: pre-treatment


title: Paroxetine dose level 10 bio rep 7 [Par_P3_G11_S15]

description:
96 well plate
Par_P3_G11_S15_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: GL26150_CD3posP1_G05_R1


title: cfDNA from pre-treatment patients [203490650045_R07C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650020_R08C01]

description: pre-treatment


title: cfDNA from pre-treatment patients [203490650044_R06C01]

description: pre-treatment


title: GL26150_CD3posP1_G08_R1


title: cfDNA from pre-treatment patients [203490650044_R05C01]

description: pre-treatment


title: Paroxetine dose level 9 bio rep 7 [Par_P3_G10_S14]

description:
96 well plate
Par_P3_G10_S14_L006
Par.raw.counts.txt
Par.sansG07.filtered.normFinal.txt


title: cfDNA from pre-treatment patients [203490650042_R05C01]

description: pre-treatment