title: 3744-MS-102: SD Rat Kidney, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-57: SD Rat Kidney, 8 h, High (100 mg/kg thioacetamide)

status: Public on Sep 20 2018

type: SRA

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

country: USA

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Treatment

library_source: transcriptomic

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.2) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Rattus norvegicus transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Rattus norvegicus transcriptome (Rnor_6.0)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

molecule: total RNA

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Frozen whole kidney and heart samples were powdered in liquid nitrogen, since these organs are histologically heterogeneous. Total RNA was isolated from liver, powdered kidney, and powdered heart, using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (Roche, Indianapolis, IN). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (Roche). Pooled libraries were subjected to 75-bp paired-end sequencing according to the manufacturer’s protocol (Illumina HiSeq3000, San Diego, CA). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

tag: strain

value: Sprague-Dawley

tag: tissue

value: Kidney

tag: duration

value: 8 h

tag: dose

value: High (100 mg/kg thioacetamide)


title: 3744-MS-31: SD Rat Kidney, 24 h, Vehicle (3 ml/kg saline)

description: Control

value: Vehicle (3 ml/kg saline)


title: 3744-MS-108: SD Rat Kidney, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment

value: Low (25 mg/kg thioacetamide)


title: 3744-MS-48: SD Rat Kidney, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-98: SD Rat Kidney, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-38: SD Rat Kidney, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-45: SD Rat Kidney, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-59: SD Rat Kidney, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-39: SD Rat Kidney, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-58: SD Rat Kidney, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-100: SD Rat Kidney, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-91: SD Rat Liver, 24 h, High (100 mg/kg thioacetamide)

description: Treatment

source_name: Liver

value: Liver


title: 3744-MS-24: SD Rat Liver, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-6: SD Rat Liver, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-26: SD Rat Liver, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-3: SD Rat Liver, 24 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-22: SD Rat Liver, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-40: SD Rat Kidney, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-5: SD Rat Liver, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-7: SD Rat Liver, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-2: SD Rat Liver, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-20: SD Rat Liver, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-21: SD Rat Liver, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-19: SD Rat Liver, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-42: SD Rat Kidney, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-101: SD Rat Kidney, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-17: SD Rat Liver, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-14: SD Rat Liver, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-27: SD Rat Liver, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-1: SD Rat Liver, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-94: SD Rat Liver, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-46: SD Rat Kidney, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-8: SD Rat Liver, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-18: SD Rat Liver, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-23: SD Rat Liver, 24 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-15: SD Rat Liver, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-12: SD Rat Liver, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-28: SD Rat Liver, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-9: SD Rat Liver, 8 h, Low (25 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-4: SD Rat Liver, 24 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-13: SD Rat Liver, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-11: SD Rat Liver, 8 h, High (100 mg/kg thioacetamide)

description: Treatment


title: 3744-MS-10: SD Rat Liver, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 3744-MS-29: SD Rat Liver, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: 59B_tumor vs reference

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
raw data file: US22502676_252252210599_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210599_S01_CGH_105_Dec08_1_4.txt

hyb_protocol: samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following manufacturer's instructions

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1) according to the specifications of the used platforms: 4x44k, 4x105k, 4x180k. All data was processed with HG18.

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction. Sample processed data reflects normalized log2 ratio representing test/reference (ch1/ch2) according to sample information.

molecule: genomic DNA

organism: Homo sapiens

source_name: tumor

label_protocol: ENZO labeling for Cy3 and Cy5 following manufacturer's instructions

extract_protocol: 10x10mu FFPE sections were cut for DNA isolation according to protocol by HF van Essen et al.  (2012)

tag: histology

value: squalors cell carcinoma

source_name: reference

value: normal


title: 59A_tumor vs reference

description:
raw data file: US22502676_252252210599_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210599_S01_CGH_105_Dec08_1_3.txt


title: 29B_tumor vs reference

description:
raw data file: US22502676_252252210595_S01_Cropped_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210595_S01_Cropped_CGH_105_Dec08_1_1.txt

value: adenocarcinoma

value: WT


title: 88B_tumor vs reference

description:
raw data file: US22502676_252252210582_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210582_S01_CGH_105_Dec08_1_2.txt


title: 89A_tumor vs reference

description:
raw data file: US22502676_252252210602_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210602_S01_CGH_105_Dec08_1_2.txt


title: 89C_tumor vs reference


title: RAS1

type: RNA

city: San Francisco

first: Andrei

last: Goga

state: CA

address: 513 Parnassus Ave

department: Cell & Tissue Biology

institute: UCSF

hyb_protocol: Hybridization samples were randomized on the 4 x 44K format to correct any batch bias. Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent). The Agilent Stock Mouse 4X44K (014868) platform was used.

scan_protocol: Standard Agilent protocol.

data_processing:
Data are normalized using quantile normalization method that is proposed by Bolstad et al (2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.  A small number of probes (245) have replicate spots, and these were summarized by taking the median intensity.
Values represent log2 based intensity of the same probe, an indication of gene expression level.

organism: Mus musculus

source_name: primary tumor

label_protocol: RNA was amplified and labeled with Cy3-CTP (experimental samples) using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3  were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent).

growth_protocol: Mice at >3 weeks were removed from doxycycline diet to induce oncogene expression in the liver.

extract_protocol: Total RNA was isolated from LAP-tTA FVB controls (n=4), LAP-tTA-Tet-o-H-RASV12 tumor tissue (n=4) or LAP-tTA-Tet-o-MYC tumor tissue (n=4). RNA isolation was performed using a combination of organic extraction and solid-phase extraction according to the manufacture’s instructions  (mirVana mirna isolation kit, Ambion). RNA quality was assessed with the Nanodrop ND-8000 (Nanodrop Technologies) and a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies) and run on Agilent mouse whole genome 4x44K (014868) Ink-jet arrays.

treatment_protocol: Tumor bearing mice were sacrificed and tissue was flash frozen.

value: FVB/N

tag: genotype

value: LAP-tTA x TRE-HRAS (RAS)

tag: disease state

value: RAS Tumor

value: primary liver tumor


title: 3744-MS-16: SD Rat Liver, 8 h, Vehicle (3 ml/kg saline)

description: Control


title: Control3

source_name: non-tumor liver

value: LAP-tTA (LT2) control

value: Non-tumor Control

value: non-tumor liver


title: 29A_tumor vs reference

description:
raw data file: US22502676_252252210595_S01_Cropped_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210595_S01_Cropped_CGH_105_Dec08_1_2.txt


title: 88A_tumor vs reference

description:
raw data file: US22502676_252252210582_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210582_S01_CGH_105_Dec08_1_1.txt


title: MYC2

value: LAP-tTA x TRE-MYC (MYC)

value: MYC Tumor


title: 58B_tumor vs reference

description:
raw data file: US22502676_252252210581_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210581_S01_CGH_105_Dec08_1_3.txt


title: Control4


title: RAS4


title: RAS2


title: RAS3


title: MYC3


title: 28B_tumor vs reference

description:
raw data file: US22502676_252252210588_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210588_S01_CGH_105_Dec08_1_4.txt


title: Control2


title: 58A_tumor vs reference

description:
raw data file: US22502676_252252210581_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210581_S01_CGH_105_Dec08_1_4.txt


title: MYC4


title: MYC1


title: Apheresis Platelet stored for 8 days _case_rep2

city: Guangzhou

first: Zhaohu

last: Yuan

address: Panfu road 1, Yuexiu District, Guangzhou

country: China

institute: Guangzhou First People’s Hospital

description: Gene expression of human platelets stored for 8 days

hyb_protocol: 1.5 ug of Cy3-labelled miRNA (specific activity >10.0 pmol Cy3/ug miRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanning is performed with the Agilent Scanner G2505C (Agilent Technologies) and Feature Extraction (version10.7.1.1, Agilent Technologies) is used to read the raw intensity of the image.

data_processing: The scanned images were analyzed with Feature Extraction software (version10.7.1.1, Agilent Technologies) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Day 8

label_protocol: Cyanine-3-CTP(Cy3)) labeled miRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and miRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Healthy,male type O Apheresis Platelet were stored in blood bank refrigerator at 22°with oscillation.

extract_protocol: Total RNA was extracted by TRIzol® Reagent (Invitrogen life technologies) and RNasey Mini Kit (Qiagen p/n 74104) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 (Thermo Scientific). RNA integrity was assessed by Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Healthy,male type O Apheresis Platelet were stored for 2, 5 and 8 days.

tag: cell type

value: Apheresis Platelet

tag: gender

value: male

tag: blood type

value: O blood types


title: Apheresis Platelet stored for 8 days_case_rep1


title: Apheresis Platelet stored for 8 days _case_rep3


title: Apheresis Platelet stored for 5 days_case_rep3

description: Gene expression of human platelets stored for 5 days

source_name: Day 5


title: Apheresis Platelet stored for 5 days_case_rep2


title: Control1


title: 28A_tumor vs reference

description:
raw data file: US22502676_252252210588_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210588_S01_CGH_105_Dec08_1_4.txt


title: 87A_tumor vs reference

description:
raw data file: US22502676_252252210586_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210586_S01_CGH_105_Dec08_1_1.txt


title: 87B_tumor vs reference

description:
raw data file: US22502676_252252210586_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210586_S01_CGH_105_Dec08_1_1.txt


title: LHD510_100nM_3

city: Cambridge

first: Ajamete

last: Kaykas

address: 22 Windsor St

institute: Novartis

description: LHD510 100nM

data_processing:
Aligned raw data using Star with reference genome GRCh38.
Ran HTSeq-count and RSEM to generate gene counts and tpm expression values.
Performed differential expression using DESeq2.
Genome_build: Ensembl human GRch38
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files include gene counts from RSEM.

growth_protocol: Cells were plated down to 50-80% density 24-well plates DMEM + 10% FBS + 2mM L-Glutamine + 100 units/ml penicillin + 100 micro-g/ml streptomycin for at least 6 hours before compound treatment.

extract_protocol:
RNA extraction was carried out using the Qiagen RNeasy 96 Kit.
TruSeq Stranded mRNA Library Prep kit with Poly A selection.

treatment_protocol: U2OS cells were treated with 100nM, 1000nM and 10000nM of DMSO, AML108, AMN107, BGW675, JAA804, LEE837 and LHD510 for 12 hrs.

tag: cell line

value: osteosarcoma cell line

tag: treatment


title: LHD510_100nM_1

description: LHD510 100nM


title: 57A_tumor vs reference

description:
raw data file: US22502676_252252210578_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210578_S01_CGH_105_Dec08_1_1.txt

value: Carcinoid


title: 57B_tumor vs reference

description:
raw data file: US22502676_252252210578_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210578_S01_CGH_105_Dec08_1_1.txt

value: normal


title: 86B_tumor vs reference

description:
raw data file: US22502676_252252210573_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210573_S01_CGH_105_Dec08_1_4.txt

value: Papillary renal cell carcinoma


title: LHD510_100nM_2

description: LHD510 100nM


title: 86C_tumor vs reference

description:
raw data file: US22502676_252252210573_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210573_S01_CGH_105_Dec08_1_4.txt


title: 86A_tumor vs reference


title: 56A_tumor vs reference

description:
raw data file: US22502676_252252210572_S01_Cropped_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210572_S01_Cropped_CGH_105_Dec08_1_1.txt

value: adenocarcinoma


title: LHD510_1000nM_1

description: LHD510 1000nM


title: LHD510_1000nM_3

description: LHD510 1000nM


title: LHD510_10000nM_3

description: LHD510 10000nM


title: 26A_tumor vs reference

description:
raw data file: US22502676_252252210569_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210569_S01_CGH_105_Dec08_1_2.txt


title: Apheresis Platelet stored for 2 days_case_rep2

description: Gene expression of human platelets stored for 2 days

source_name: Day 2


title: Apheresis Platelet stored for 2 days_case_rep3


title: Apheresis Platelet stored for 5 days_case_rep1


title: 85B_tumor vs reference

description:
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_4.txt

value: squalors cell carcinoma


title: LHD510_10000nM_2

description: LHD510 10000nM


title: LHD510_10000nM_1

description: LHD510 10000nM


title: 26B_tumor vs reference

description:
raw data file: US22502676_252252210569_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210569_S01_CGH_105_Dec08_1_2.txt


title: LEE837_100nM_3

description: LEE837 100nM

value: Homoharringtonine


title: 55B_tumor vs reference

description:
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_1.txt


title: 85A_tumor vs reference

description:
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_3.txt

value: large cell carcinoma


title: LEE837_100nM_2

description: LEE837 100nM


title: LHD510_1000nM_2

description: LHD510 1000nM


title: 56B_tumor vs reference

description:
raw data file: US22502676_252252210572_S01_Cropped_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210572_S01_Cropped_CGH_105_Dec08_1_1.txt


title: Apheresis Platelet stored for 2 days_case_rep1


title: LEE837_1000nM_3

description: LEE837 1000nM


title: 55C_tumor vs reference

description:
raw data file: US22502676_252252210433_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210433_S01_CGH_105_Dec08_1_3.txt


title: LEE837_100nM_1

description: LEE837 100nM


title: 25A_tumor vs reference

description:
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_1.txt


title: 55A_tumor vs reference

description:
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_1.txt


title: LEE837_1000nM_2

description: LEE837 1000nM


title: LEE837_1000nM_1

description: LEE837 1000nM


title: 84B_tumor vs reference

description:
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_4.txt


title: 54A_tumor vs reference

description:
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_1.txt


title: LEE837_10000nM_3

description: LEE837 10000nM


title: LEE837_10000nM_1

description: LEE837 10000nM


title: JAA804_100nM_2

description: JAA804 100nM

value: Triptolide


title: 25B_tumor vs reference

description:
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210568_S01_CGH_105_Dec08_1_1.txt


title: JAA804_100nM_1

description: JAA804 100nM


title: JAA804_1000nM_2

description: JAA804 1000nM


title: 24C_tumor vs reference

description:
raw data file: US22502676_252252210563_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210563_S01_CGH_105_Dec08_1_2.txt


title: JAA804_100nM_3

description: JAA804 100nM


title: 83C_tumor vs reference

description:
raw data file: US22502676_252252210553_S01_Cropped_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210553_S01_Cropped_CGH_105_Dec08_1_1.txt


title: 83A_tumor vs reference

description:
raw data file: US22502676_252252210553_S01_Cropped_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210553_S01_Cropped_CGH_105_Dec08_1_1.txt


title: 54B_tumor vs reference

description:
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_1.txt


title: JAA804_1000nM_1

description: JAA804 1000nM


title: JAA804_1000nM_3

description: JAA804 1000nM


title: JAA804_10000nM_3

description: JAA804 10000nM


title: 83B_tumor vs reference


title: JAA804_10000nM_2

description: JAA804 10000nM


title: 53A_tumor vs reference

description:
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_1.txt


title: LEE837_10000nM_2

description: LEE837 10000nM


title: DMSO_0nM_8

description: DMSO 0nM

value: DMSO


title: JAA804_10000nM_1

description: JAA804 10000nM


title: 23B_tumor vs reference

description:
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_2.txt

value: Ossificating fibromyxoid tumor


title: 23A_tumor vs reference

description:
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_2.txt


title: DMSO_0nM_7

description: DMSO 0nM


title: 53B_tumor vs reference

description:
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210551_S01_CGH_105_Dec08_1_1.txt


title: 24B_tumor vs reference

description:
raw data file: US22502676_252252210563_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210563_S01_CGH_105_Dec08_1_2.txt

value: Thymoma


title: DMSO_0nM_5

description: DMSO 0nM


title: 82A_tumor vs reference

description:
raw data file: US22502676_252252210546_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210546_S01_CGH_105_Dec08_1_3.txt


title: DMSO_0nM_6

description: DMSO 0nM


title: 52A_tumor vs reference

description:
raw data file: US22502676_252252210545_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210545_S01_CGH_105_Dec08_1_2.txt


title: 24A_tumor vs reference


title: 52B_tumor vs reference

description:
raw data file: US22502676_252252210545_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210545_S01_CGH_105_Dec08_1_2.txt


title: DMSO_0nM_4

description: DMSO 0nM


title: DMSO_0nM_2

description: DMSO 0nM


title: DMSO_0nM_3

description: DMSO 0nM


title: DMSO_0nM_18

description: DMSO 0nM


title: 22B_tumor vs reference

description:
raw data file: US22502676_252252210577_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210577_S01_CGH_105_Dec08_1_4.txt


title: 81A_tumor vs reference

description:
raw data file: US22502676_252252210539_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210539_S01_CGH_105_Dec08_1_3.txt


title: DMSO_0nM_1

description: DMSO 0nM


title: 81B_tumor vs reference

description:
raw data file: US22502676_252252210539_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210539_S01_CGH_105_Dec08_1_4.txt


title: 51A_tumor vs reference

description:
raw data file: US22502676_252252210538_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210538_S01_CGH_105_Dec08_1_3.txt


title: DMSO_0nM_16

description: DMSO 0nM


title: DMSO_0nM_17

description: DMSO 0nM


title: 51B_tumor vs reference

description:
raw data file: US22502676_252252210538_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210538_S01_CGH_105_Dec08_1_1.txt


title: 82B_tumor vs reference

description:
raw data file: US22502676_252252210546_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210546_S01_CGH_105_Dec08_1_3.txt


title: DMSO_0nM_9

description: DMSO 0nM


title: DMSO_0nM_15

description: DMSO 0nM


title: 21A_tumor vs reference

description:
raw data file: US22502676_252252210536_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210536_S01_CGH_105_Dec08_1_1.txt


title: 21B_tumor vs reference

description:
raw data file: US22502676_252252210536_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210536_S01_CGH_105_Dec08_1_1.txt


title: 84A_tumor vs reference

description:
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210567_S01_CGH_105_Dec08_1_3.txt


title: DMSO_0nM_14

description: DMSO 0nM


title: DMSO_0nM_13

description: DMSO 0nM


title: 80A_tumor vs reference

description:
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_4.txt


title: DMSO_0nM_12

description: DMSO 0nM


title: 50A_tumor vs reference

description:
raw data file: US22502676_252252210535_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210535_S01_CGH_105_Dec08_1_1.txt


title: 22A_tumor vs reference

description:
raw data file: US22502676_252252210577_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210577_S01_CGH_105_Dec08_1_4.txt


title: DMSO_0nM_11

description: DMSO 0nM


title: DMSO_0nM_10

description: DMSO 0nM


title: 50B_tumor vs reference

description:
raw data file: US22502676_252252210535_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210535_S01_CGH_105_Dec08_1_1.txt

value: WT


title: 80B_tumor vs reference

description:
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_4.txt


title: 79A_tumor vs reference

description:
raw data file: US22502676_252252210529_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210529_S01_CGH_105_Dec08_1_3.txt


title: BGW675_100nM_3

description: BGW675 100nM

value: Miglitol


title: 79B_tumor vs reference

description:
raw data file: US22502676_252252210529_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210529_S01_CGH_105_Dec08_1_3.txt


title: BGW675_100nM_1

description: BGW675 100nM


title: BGW675_1000nM_3

description: BGW675 1000nM


title: 49B_tumor vs reference

description:
raw data file: US22502676_252252210530_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210530_S01_CGH_105_Dec08_1_2.txt


title: 49A_tumor vs reference

description:
raw data file: US22502676_252252210530_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210530_S01_CGH_105_Dec08_1_2.txt


title: 19A_tumor vs reference

description:
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_2.txt


title: BGW675_1000nM_2

description: BGW675 1000nM


title: BGW675_1000nM_1

description: BGW675 1000nM


title: BGW675_10000nM_3

description: BGW675 10000nM


title: 19B_tumor vs reference

description:
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210531_S01_CGH_105_Dec08_1_2.txt


title: 78A_tumor vs reference

description:
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_3.txt


title: BGW675_10000nM_2

description: BGW675 10000nM


title: 48A_tumor vs reference

description:
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_2.txt


title: 78B_tumor vs reference

description:
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_3.txt


title: BGW675_10000nM_1

description: BGW675 10000nM


title: 48B_tumor vs reference

description:
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210497_S01_CGH_105_Dec08_1_2.txt


title: AMN107_100nM_3

description: AMN107 100nM

value: Nilotinib


title: AMN107_100nM_2

description: AMN107 100nM


title: AMN107_100nM_1

description: AMN107 100nM


title: BGW675_100nM_2

description: BGW675 100nM


title: 18B_tumor vs reference

description:
raw data file: US22502676_252252210539_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210539_S01_CGH_105_Dec08_1_1.txt


title: 18C_tumor vs reference

description:
raw data file: US22502676_252252210522_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210522_S01_CGH_105_Dec08_1_1.txt


title: 18A_tumor vs reference

description:
raw data file: US22502676_252252210522_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210522_S01_CGH_105_Dec08_1_1.txt


title: AMN107_1000nM_3

description: AMN107 1000nM


title: AMN107_1000nM_1

description: AMN107 1000nM


title: 77A_tumor vs reference

description:
raw data file: US22502676_252252210504_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210504_S01_CGH_105_Dec08_1_3.txt


title: 77B_tumor vs reference

description:
raw data file: US22502676_252252210504_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210504_S01_CGH_105_Dec08_1_3.txt


title: AMN107_10000nM_2

description: AMN107 10000nM


title: AMN107_10000nM_1

description: AMN107 10000nM


title: 47B_tumor vs reference

description:
raw data file: US22502676_252252210519_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210519_S01_CGH_105_Dec08_1_1.txt


title: AML108_100nM_2

description: AML108 100nM

value: Pyrazolanthrone


title: 47A_tumor vs reference

description:
raw data file: US22502676_252252210519_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210519_S01_CGH_105_Dec08_1_1.txt


title: AML108_100nM_3

description: AML108 100nM


title: 17A_tumor vs reference

description:
raw data file: US22502676_252252210527_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210527_S01_CGH_105_Dec08_1_2.txt


title: AMN107_10000nM_3

description: AMN107 10000nM


title: 17B_tumor vs reference


title: AML108_100nM_1

description: AML108 100nM


title: 76B_tumor vs reference

description:
raw data file: US22502676_252252210511_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210511_S01_CGH_105_Dec08_1_1.txt

value: small cell (lung) carcinoma


title: 76A_tumor vs reference

description:
raw data file: US22502676_252252210511_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210511_S01_CGH_105_Dec08_1_1.txt


title: 46B_tumor vs reference

description:
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_2.txt

value: Transitional cell carcinoma


title: AML108_1000nM_3

description: AML108 1000nM

value: osteosarcoma cell line


title: AML108_1000nM_1

description: AML108 1000nM


title: 16B_tumor vs reference

description:
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_3.txt

value: positive

value: normal


title: AML108_10000nM_3

description: AML108 10000nM


title: 16A_tumor vs reference

description:
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_4.txt

value: adenocarcinoma


title: AML108_1000nM_2

description: AML108 1000nM


title: 46A_tumor vs reference

description:
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210524_S01_CGH_105_Dec08_1_2.txt

value: squalors cell carcinoma


title: AML108_10000nM_2

description: AML108 10000nM


title: 75A_tumor vs reference

description:
raw data file: US22502676_252252210485_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210493_S01_CGH_105_Dec08_1_1.txt


title: 45B_tumor vs reference

description:
raw data file: US22502676_252252210485_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210485_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_H9_AD001_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Sequencing reads mapping, quality filtering and the summary of DNA methylation level for each cytosine was performed as previously described in Luo et al., 2017 with minor modifications. Non-clonal mapped reads were filtered for MAPQ > 10 using samtools view -bq10 option.
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

source_name: Human frontal cortex (BA10)

growth_protocol: Male C57Bl/6J mice were purchased from Jackson laboratories at 8 weeks of age and maintained in our facility for 48h before dissection. Animals were maintained in the Salk animal barrier facility on 12h dark-light cycles with food ad-libitum. Human brain specimens were obtained from University of Miami Brain Endowment Bank. snmC-seq with Shrimp Alkaline Phosphatase treatment (snmC-seq + SAP) was applied to frontal cortex (Brodmann Area 10, BA10) tissue of a deceased 58-year-old Caucasian male with PMI = 23.4. snmC-seq2 was applied to BA10 tissue of a deceased 25-year-old Caucasian male with PMI = 20.8.

extract_protocol: Bisulfite-converted samples were denatured at 95°C for 3 minutes, then placed on ice for 2 minutes. 5µL Random Priming master mix [1µL 10x Blue Buffer (Enzymatics B0110), 0.25µL Klenow Exo- (50U/µL, Enzymatics, P7010-HC-L), 0.5µL dNTP (10mM each, NEB N0447L), 3.25µL water] was added and incubated at 4°C for 5 min, 25°C for 5 min, and 37°C for 60 min followed by 4°C. 1.5µL enzyme mix containing Exonuclease 1 (20U/µL, Enzymatics X8010L) and rSAP (1U/µL, NEB M0371L) was added, then incubated at 37°C for 30 min followed by 4°C. 0.8x SPRI beads were added, mixed and incubated for 5 minutes at room temperature to allow DNA to bind. The beads were washed 3 times with 80% ethanol and eluted in 10µL EB buffer (Qiagen 19086). The plates were denatured again at 95°C for 3 minutes, and 10.5µL Adaptase master mix [2µL G1, 2µL G2, 1.25µL G3, 0.5µL G4 and 0.5µL G5 (Swift Biosciences 33096)] was added and incubated at 37°C for 30 minutes, then 95°C for 2 minutes. 25µL 2x KAPA HiFi HotStart ReadyMix (Kapa, KK2602) and 5µL custom indexing primer mix (6µM P5, 10µM P7) were added. The PCR was programmed as follows: 1) 95°C 2 min, 2) 98°C 30 sec, 3) 98°C 15 sec, 4) 64°C for 30 sec, 5) 72°C for 2 min, 6) 72°C 5 min, 7) 4°C hold. Repeat steps 3-5 for 15 total cycles. PCR reactions were cleaned with 0.8X SPRI beads for three rounds. Library concentration was determined with Qubit™ dsDNA BR Assay Kit (ThermoFisher Q32853). Libraries were sequenced using Illumina Novaseq instrument.

tag: Sex

value: Male

tag: age

value: 25 yr

tag: genome build

tag: library strategy


title: AMN107_1000nM_2

description: AMN107 1000nM


title: AML108_10000nM_1

description: AML108 10000nM


title: 171130_MB_EB_Hs_25yr_BA10_H8_AD012_indexed


title: 171130_MB_EB_Hs_25yr_BA10_H7_AD010_indexed


title: 45A_tumor vs reference

description:
raw data file: US22502676_252252210485_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210485_S01_CGH_105_Dec08_1_3.txt

value: large cell carcinoma


title: 171130_MB_EB_Hs_25yr_BA10_H6_AD002_indexed


title: 15B_tumor vs reference

description:
raw data file: US22502676_252252210429_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210429_S01_CGH_105_Dec08_1_2.txt


title: 74B_tumor vs reference

description:
raw data file: US22502676_252252210409_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210409_S01_CGH_105_Dec08_1_4.txt

value: Spindle cell


title: 171130_MB_EB_Hs_25yr_BA10_H3_AD012_indexed


title: 171130_MB_EB_Hs_25yr_BA10_H2_AD010_indexed


title: 70B_tumor vs reference

description:
raw data file: US22502676_252252210015_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210015_S01_CGH_105_Dec08_1_2.txt


title: 74A_tumor vs reference

description:
raw data file: US22502676_252252210409_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210409_S01_CGH_105_Dec08_1_4.txt


title: 171130_MB_EB_Hs_25yr_BA10_G8_AD012_indexed


title: 171130_MB_EB_Hs_25yr_BA10_G8_AD002_indexed


title: 15A_tumor vs reference

description:
raw data file: US22502676_252252210429_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210429_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_G7_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_G5_AD012_indexed


title: 70C_tumor vs reference

description:
raw data file: US22502676_252252210015_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210015_S01_CGH_105_Dec08_1_2.txt


title: 70A_tumor vs reference

description:
raw data file: US22502676_252252210015_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210015_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_G5_AD001_indexed


title: 75C_tumor vs reference

description:
raw data file: US22502676_252252210485_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210493_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_G5_AD010_indexed


title: 171130_MB_EB_Hs_25yr_BA10_G4_AD012_indexed


title: 75B_tumor vs reference

description:
raw data file: US22502676_252252210493_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210493_S01_CGH_105_Dec08_1_1.txt


title: 40A_tumor vs reference

description:
raw data file: US22502676_252252210016_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210016_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_G3_AD012_indexed


title: 171130_MB_EB_Hs_25yr_BA10_G2_AD012_indexed


title: 10C_tumor vs reference

description:
raw data file: US22502676_252252210179_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210179_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_G3_AD010_indexed


title: 10A_tumor vs reference

description:
raw data file: US22502676_252252210179_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210179_S01_CGH_105_Dec08_1_1.txt


title: 10B_tumor vs reference

description:
raw data file: US22502676_252252210179_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210179_S01_CGH_105_Dec08_1_1.txt


title: 39B_tumor vs reference

description:
raw data file: US22502676_252252210268_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210268_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_G10_AD001_indexed


title: 9A_tumor vs reference

description:
raw data file: US22502676_252252210269_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210269_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_G10_AD010_indexed


title: 39A_tumor vs reference

description:
raw data file: US22502676_252252210268_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210268_S01_CGH_105_Dec08_1_1.txt


title: 9B_tumor vs reference

description:
raw data file: US22502676_252252210269_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210269_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_F9_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F7_AD001_indexed


title: 38B_tumor vs reference

description:
raw data file: US22502676_252252210270_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210270_S01_CGH_105_Dec08_1_3.txt


title: 40B_tumor vs reference

description:
raw data file: US22502676_252252210016_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210016_S01_CGH_105_Dec08_1_2.txt


title: 38C_tumor vs reference

description:
raw data file: US22502676_252252210270_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210270_S01_CGH_105_Dec08_1_3.txt


title: 38A_tumor vs reference

description:
raw data file: US22502676_252252210270_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210270_S01_CGH_105_Dec08_1_3.txt


title: 37C_tumor vs reference

description:
raw data file: US22502676_252252210310_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210310_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_F5_AD001_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F6_AD002_indexed


title: 37A_tumor vs reference

description:
raw data file: US22502676_252252210310_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210310_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_F4_AD001_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F3_AD010_indexed


title: 37B_tumor vs reference

description:
raw data file: US22502676_252252210310_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210310_S01_CGH_105_Dec08_1_3.txt


title: 7B_tumor vs reference

description:
raw data file: US22502676_252252210312_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210312_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_F2_AD012_indexed


title: 40C_tumor vs reference

description:
raw data file: US22502676_252252210016_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210016_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_G1_AD002_indexed


title: 66B_tumor vs reference

description:
raw data file: US22502676_252252210313_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210313_S01_CGH_105_Dec08_1_2.txt


title: 66A_tumor vs reference

description:
raw data file: US22502676_252252210313_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210313_S01_CGH_105_Dec08_1_2.txt


title: 7A_tumor vs reference

description:
raw data file: US22502676_252252210312_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210312_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_F1_AD001_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F11_AD010_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F12_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F9_AD001_indexed


title: 171130_MB_EB_Hs_25yr_BA10_F1_AD010_indexed


title: 36B_tumor vs reference

description:
raw data file: US22502676_252252210330_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210330_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_E7_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_E6_AD010_indexed


title: 35B_tumor vs reference

description:
raw data file: US22502676_252252210325_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210325_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_E5_AD002_indexed


title: 35A_tumor vs reference

description:
raw data file: US22502676_252252210325_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210325_S01_CGH_105_Dec08_1_3.txt


title: 5A_tumor vs reference

description:
raw data file: US22502676_252252210372_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210372_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_E4_AD012_indexed


title: 5B_tumor vs reference

description:
raw data file: US22502676_252252210372_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210372_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_E4_AD002_indexed


title: 36A_tumor vs reference

description:
raw data file: US22502676_252252210330_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210330_S01_CGH_105_Dec08_1_3.txt


title: 171130_MB_EB_Hs_25yr_BA10_E3_AD010_indexed


title: 64A_tumor vs reference

description:
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_3.txt


title: 64B_tumor vs reference

description:
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210265_S01_CGH_105_Dec08_1_3.txt


title: 34A_tumor vs reference

description:
raw data file: US22502676_252252210395_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210395_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_E3_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_E4_AD010_indexed


title: 34B_tumor vs reference

description:
raw data file: US22502676_252252210395_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210395_S01_CGH_105_Dec08_1_2.txt


title: 4B_tumor vs reference

description:
raw data file: US22502676_252252210417_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210417_S01_CGH_105_Dec08_1_1.txt


title: 1759HA Ast_injury_IP_RNAseq

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina CASAVA 1.8.2
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using mm10 RefSeq as reference
Remove outliers (1645HA, 1729HA and 1683HA)
Normalization (TMM), quantitation and differential expression analysis using EdgeR. For IP vs IP IP and Flow vs Flow, IP and flow samples were separately analyzed.
Genome_build: mm10

source_name: spinal cord

extract_protocol:
HA and FT samples underwent on-column DNA digestion using the RNase-Free Dnase Set (Qiagen) and RNA purified with the RNeasy Micro kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent) using the RNA Pico chip. RNA concentration determined by RiboGreen RNA Assay kit (Life Technologies).
cDNA was generated from 5ng of IP or FT RNA using the Nugen Ovation® 2 RNA-Seq Sytstem V2 kit (Nugen). 1 ug of cDNA was fragmented using the Covaris M220. Paired-end libraries for multiplex sequencing were generated from 300 ng of fragmented cDNA using the Apollo 324 automated library preparation system (Wafergen Biosystems), enriched over 10 cycles of PCR cycles and purified with Agencourt AMPure XP beads (Beckman Coulter).

value: Wild type

tag: rna sample type

value: HA IP

tag: condition

value: SCI + hydro gel CT


title: 1762HA Ast_injury_IP_RNAseq


title: 1724HA Ast_injury_IP_RNAseq


title: 36C_tumor vs reference

description:
raw data file: US22502676_252252210330_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210330_S01_CGH_105_Dec08_1_3.txt

value: WT


title: 171130_MB_EB_Hs_25yr_BA10_E2_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_E1_AD010_indexed


title: 63A_tumor vs reference

description:
raw data file: US22502676_252252210418_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210418_S01_CGH_105_Dec08_1_1.txt

value: Carcinoid


title: 171130_MB_EB_Hs_25yr_BA10_E11_AD012_indexed


title: 1732HA Ast_injury_IP_RNAseq

value: SCI + hydrogel +growth factors


title: 33B_tumor vs reference

description:
raw data file: US22502676_252252210419_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210419_S01_CGH_105_Dec08_1_2.txt


title: 33A_tumor vs reference

description:
raw data file: US22502676_252252210419_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210419_S01_CGH_105_Dec08_1_1.txt


title: 171130_MB_EB_Hs_25yr_BA10_E11_AD010_indexed


title: 3A_tumor vs reference

description:
raw data file: US22502676_252252210422_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210422_S01_CGH_105_Dec08_1_3.txt


title: 63B_tumor vs reference

description:
raw data file: US22502676_252252210418_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210418_S01_CGH_105_Dec08_1_1.txt


title: 1687HA Ast_injury_IP_RNAseq


title: 3B_tumor vs reference

description:
raw data file: US22502676_252252210422_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210422_S01_CGH_105_Dec08_1_3.txt


title: 1685HA Ast_injury_IP_RNAseq


title: 62B_tumor vs reference

description:
raw data file: US22502676_252252210405_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210405_S01_CGH_105_Dec08_1_1.txt


title: 62A_tumor vs reference

description:
raw data file: US22502676_252252210405_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210405_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_D8_AD002_indexed


title: 9935HA Ast_injury_IP_RNAseq

value: SCI only


title: 171130_MB_EB_Hs_25yr_BA10_D6_AD012_indexed


title: 4A_tumor vs reference

description:
raw data file: US22502676_252252210417_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210417_S01_CGH_105_Dec08_1_1.txt


title: 9874HA Ast_injury_IP_RNAseq


title: 32A_tumor vs reference

description:
raw data file: US22502676_252252210406_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210406_S01_CGH_105_Dec08_1_2.txt


title: 32B_tumor vs reference

description:
raw data file: US22502676_252252210406_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210406_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_D5_AD012_indexed


title: 9843HA Ast_injury_IP_RNAseq


title: 61B_tumor vs reference

description:
raw data file: US22502676_252252210436_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210436_S01_CGH_105_Dec08_1_4.txt


title: 61A_tumor vs reference

description:
raw data file: US22502676_252252210436_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210436_S01_CGH_105_Dec08_1_3.txt


title: 31A_tumor vs reference

description:
raw data file: US22502676_252252210433_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210433_S01_CGH_105_Dec08_1_1.txt


title: 1F_tumor vs reference

description:
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_1.txt


title: 9596HA Ast_injury_IP_RNAseq


title: 171130_MB_EB_Hs_25yr_BA10_D4_AD001_indexed


title: 171130_MB_EB_Hs_25yr_BA10_D3_AD012_indexed


title: 9596HAflow Ast_injury_IP_RNAseq

value: flow through


title: 1E_tumor vs reference

description:
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_4.txt


title: 1D_tumor vs reference

description:
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_3.txt


title: 9843HA_flow Ast_injury_IP_RNAseq


title: 1A_tumor vs reference

description:
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_2.txt


title: 171130_MB_EB_Hs_25yr_BA10_D1_AD010_indexed


title: 171130_MB_EB_Hs_25yr_BA10_D12_AD012_indexed


title: 90A_tumor vs reference

description:
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_4.txt
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_4.txt

value: phyllodes tumor


title: 9935FLOW_S7 Ast_injury_IP_RNAseq


title: 90B_tumor vs reference

description:
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210488_S01_CGH_105_Dec08_1_3.txt


title: 60B_tumor vs reference

description:
raw data file: US22502676_252252210490_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210490_S01_CGH_105_Dec08_1_2.txt

value: positive


title: 171130_MB_EB_Hs_25yr_BA10_D12_AD002_indexed


title: 60A_tumor vs reference

description:
raw data file: US22502676_252252210490_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210490_S01_CGH_105_Dec08_1_2.txt

value: normal


title: 1732FLOW_FT Ast_injury_IP_RNAseq


title: 1729FLOW_FT Ast_injury_IP_RNAseq


title: 30B_tumor vs reference

description:
raw data file: US22502676_252252210491_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210491_S01_CGH_105_Dec08_1_1.txt


title: 30A_tumor vs reference

description:
raw data file: US22502676_252252210491_S01_CGH_105_Dec08_1_3.txt
raw data file: US22502676_252252210491_S01_CGH_105_Dec08_1_1.txt

value: adenocarcinoma


title: 171130_MB_EB_Hs_25yr_BA10_C8_AD012_indexed


title: 31B_tumor vs reference

description:
raw data file: US22502676_252252210433_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210433_S01_CGH_105_Dec08_1_2.txt

value: squalors cell carcinoma


title: 1685FLOW_FT Ast_injury_IP_RNAseq


title: 171130_MB_EB_Hs_25yr_BA10_C7_AD010_indexed

value: Male


title: 1C_tumor vs reference

description:
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_2.txt
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_2.txt


title: 1687FLOW_FT Ast_injury_IP_RNAseq


title: 171130_MB_EB_Hs_25yr_BA10_D2_AD001_indexed

value: 25 yr


title: 1B_tumor vs reference

description:
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210483_S01_CGH_105_Dec08_1_1.txt


title: 9874HAflow Ast_injury_IP_RNAseq


title: 171130_MB_EB_Hs_25yr_BA10_C7_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_C1_AD012_indexed


title: 30C_tumor vs reference

description:
raw data file: US22502676_252252210491_S01_CGH_105_Dec08_1_1.txt
raw data file: US22502676_252252210491_S01_CGH_105_Dec08_1_1.txt


title: 1759FLOW_FT Ast_injury_IP_RNAseq


title: 171130_MB_EB_Hs_25yr_BA10_D12_AD001_indexed


title: 1762FLOW_FT Ast_injury_IP_RNAseq


title: 171130_MB_EB_Hs_25yr_BA10_C12_AD002_indexed


title: Low oleic acid line 2

city: Changsha

first: Gang

last: Xiao

address: nongda raod 1#

institute: Hunan agricultural university

description: Gene expression in low oleic acid line.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalization for data was performed using GeneSpring GX Software (Agilent) with default parameters.

organism: Brassica napus

source_name: Low oleic acid line2 seeds

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The transgenic plants were cultivated in a net shed.

extract_protocol: Total RNAs were isolated with an RNeasy Plant Mini Kit (Qiagen, Germany). The RNAs were treated with DNase I (Takara, Japan).

treatment_protocol: Each plant was bagged for self-fertilization, developing seeds were selected for RNA extraction.

tag: tissue

value: seed

tag: oleic acid

value: low


title: High oleic acid line 1

description: Gene expression in high oleic acid line.

source_name: High oleic acid line 1 seeds

value: high


title: Rectum tissue isolated from Rhesus Macaque at Day 6 in Animal ID D2

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: RNA isolated from Rectum from Rhesus Macaque

data_processing:
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.2)
Ensembl build Mmul_1 using illumina's igenomes resource
We mapped reads to the genome Macaca mulatta genome (build Mmul_1) with STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq (version 0.6.1). HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed.
Genome_build: Macaca mulatta Ensembl (build Mmul_1) from illumina's igenomes resource: https://support.illumina.com/sequencing/sequencing_software/igenome.html
Genome_build: Chlorocebus_sabeus 1.0 from https://www.ncbi.nlm.nih.gov/assembly/GCA_000409795.1/
Supplementary_files_format_and_content: A raw gene count matrix of files generated with ht-seq is attached

organism: Macaca mulatta

growth_protocol: please refer to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097788/

extract_protocol:
mRNA was isolated using the QIAGEN miRNeasy Kit.
Whole transcriptome libraries were constructed using the TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA) according to the manufacturer’s guide.
Libraries were quality controlled and quantitated using the BioAnalzyer 2100 system and qPCR (Kapa Biosystems, Woburn, MA).

value: Rectum

tag: timepoint

value: Day 6


title: Rectum tissue isolated from Rhesus Macaque at Day 6 in Animal ID D3

treatment_protocol: please refer to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097788/


title: Rectum tissue isolated from Rhesus Macaque at Day 84 in Animal ID F4

value: Day 84


title: Rectum tissue isolated from Rhesus Macaque at Day 6 in Animal ID D1


title: Rectum tissue isolated from Rhesus Macaque at Day 84 in Animal ID F3


title: High oleic acid line 2

source_name: High oleic acid line 2 seeds


title: Rectum tissue isolated from Rhesus Macaque at Day 84 in Animal ID F2


title: Rectum tissue isolated from Rhesus Macaque at Day 84 in Animal ID F1


title: Low oleic acid line 1

description: Gene expression in low oleic acid line.

source_name: Low oleic acid line 1 seeds


title: 1645FLOW_TF Ast_injury_IP_RNAseq

value: Wild type


title: 171130_MB_EB_Hs_25yr_BA10_B9_AD001_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 6 in Animal ID D4


title: 1683FLOW_FT Ast_injury_IP_RNAseq

value: SCI + hydro gel CT


title: 171130_MB_EB_Hs_25yr_BA10_B7_AD002_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 3 in Animal ID C2

value: Day 3


title: Rectum tissue isolated from Rhesus Macaque at Day 3 in Animal ID C3


title: Rectum tissue isolated from Rhesus Macaque at Day 3 in Animal ID C4


title: 171130_MB_EB_Hs_25yr_BA10_C4_AD002_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 3 in Animal ID C1


title: 1724FLOW_FT Ast_injury_IP_RNAseq

value: flow through


title: 171130_MB_EB_Hs_25yr_BA10_B7_AD001_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 2 in Animal ID B2

value: Day 2


title: 171130_MB_EB_Hs_25yr_BA10_B3_AD010_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 2 in Animal ID B4


title: 171130_MB_EB_Hs_25yr_BA10_B9_AD010_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 2 in Animal ID B3


title: Rectum tissue isolated from Rhesus Macaque at Day 2 in Animal ID B1


title: 171130_MB_EB_Hs_25yr_BA10_B2_AD002_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 1 in Animal ID A4

value: Day 1


title: Rectum tissue isolated from Rhesus Macaque at Day 1 in Animal ID A2


title: 171130_MB_EB_Hs_25yr_BA10_B1_AD010_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 12 in Animal ID E1

value: Day 12


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID E4

value: Baseline


title: Rectum tissue isolated from Rhesus Macaque at Day 12 in Animal ID E3


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID E3


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID E2


title: 171130_MB_EB_Hs_25yr_BA10_B1_AD012_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 12 in Animal ID E2


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID C2


title: 171130_MB_EB_Hs_25yr_BA10_B1_AD001_indexed


title: Rectum tissue isolated from Rhesus Macaque at Day 12 in Animal ID E4


title: 171130_MB_EB_Hs_25yr_BA10_B12_AD002_indexed


title: 171130_MB_EB_Hs_25yr_BA10_A7_AD001_indexed


title: MIN6-H3K27ac-Chipseq

city: Boston

first: Chen

last: Weng

state: OH

address: 415 Main St, Cambridge

department: Genetics

institute: Broad Institute and Whitehead Institute

description: A Chipseq for H3K27ac binding sites

data_processing:
All ChIPmentation reads were mapped to mm9 of the human genome using Bowtie (version 1.1.2). The first 36 bases of each reads were applied for alignment with up to 3 mismatches allowed. To remove duplication, only the uniquely mapped reads were kept for further analysis. Peak calling was performed using Macs (Version 1.4).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Pancreatic beta cell line

growth_protocol: MIN6 cells are cultured in high glucose DMEM containing GlutaMax (Invitrogen), 1 mM Sodium pyruvate (Invitrogen), and 50 uM beta-mercaptoethanol. MIN6 cells are changed to fresh medium every two days.

extract_protocol:
ChIP-seq was done following a ChIPmentation protocol (PMID 26280331). Min6 cells were crosslinked with 1% formaldehyde at room temperature followed by glycine quenching. To isolate nuclei, the cells were lysed with Lysis buffer I (50 mM HEPES; pH 7.5, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Nonidet‐40, 0.25% Triton X-100 and protease inhibitor cocktail) for 10 minutes at 4°C. The collected nuclei were then washed with a lysis buffer II (200mM NaCl, 1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris-Cl pH8.0 and protease inhibitor cocktail) for 20 minutes at room temperature. The nuclei pellets were resuspended in lysis buffer III (10mM Tris-Cl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine and protease inhibitor cocktail) for sonication. The chromatin was sheared for 10 cycles (15 seconds on and 45 seconds off at constant power 3) on Branson 450 sonifier.  250ug of chromatin was used for each pulldown (NIPBL, Bethyl Laboratories, A301-778A). First, 50ul of Dynabeads M-280 (Life Technologies, Sheep Anti-Rabbit IgG, Cat# 11204D) was washed three times with 0.5mg/ml of BSA/PBS on ice and then incubated with designed antibody for at least 2 hours at 4°C. The beads/antibody complexes were then washed with BSA/PBS. The pulldown was down in binding buffer (1% Trixon-X 100, 0.1% Sodium Deoxycholate and protease inhibitor cocktail in 1X TE) by mixing the beads/antibody complexes and chromatin. After pulling down for overnight, the beads/antibody/chromatin complexes were washed with RIPA buffer (50mM HEPES pH8.0, 1% NP-40, 0.7% Sodium Deoxycholate, 0.5M LiCl, 1mM EDTA and protease inhibitor cocktail). The beads complexes were then subjected to ChIPmentation by incubating with homemade Tn5 transposase in tagmentation reaction buffer (10mM Tris-Cl pH8.0 and 5mM MgCl2) for 10 minutes at 37°C. To remove free DNA, beads were washed twice with 1x TE  on ice. The pulldown DNA was recovered by reversing crosslink for overnight followed by PCRClean DX beads purification.
To generate ChIP-seq libraries, PCR was applied to amplify the pulldown DNA with illumina nextera primers. Size selection was then done with PCRClean DX beads to choose the fragments ranging from 100bp to 1000bp. All ChIP-seq libraries were sequenced on illumine HiSeq2500 platform (1x50bp).

value: Pancreatic beta cell line


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID E1


title: MIN6-MAU2-Chipseq

description: A Chipseq for MAU2 binding sites


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID B4


title: 171130_MB_EB_Hs_25yr_BA10_A6_AD012_indexed

value: Male


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID C1


title: MIN6-H3K4me3-Chipseq

description: A Chipseq for H3K4me3 binding sites


title: Min6-NIPBL-Chipseq

description: A Chipseq for NIPBL binding sites


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID C4


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID B3


title: Rectum tissue isolated from Rhesus Macaque at Day 1 in Animal ID A3


title: 171130_MB_EB_Hs_25yr_BA10_A5_AD012_indexed

value: 25 yr


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID B2


title: Rectum tissue isolated from Rhesus Macaque at Day 1 in Animal ID A1


title: 171130_MB_EB_Hs_25yr_BA10_B1_AD002_indexed


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID B1


title: 171130_MB_EB_Hs_25yr_BA10_A5_AD001_indexed


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID A4


title: 171130_MB_EB_Hs_25yr_BA10_A3_AD012_indexed


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID A3


title: E2_destGFP_neg_5

city: MINNEAPOLIS

first: Ryan

last: Langlois

state: MN

description:
Sample12-1_S40
destGFP experiment (#2) ; destabilized GFP negative FACS-sorted cells from lung of mouse infected with destabilized GFP IAV

data_processing:
Raw sequence reads were mapped to mouse genome and influenza (H1N1) transcripts  separately using the Bowtie2 aligner (v2.2.4) with local mode, -L22 and -N 1 parameters.
Mapped read were sorted and filtered by removing PCR duplicates with Samtools (v1.16)
Expression was quantified using featureCounts from the Subread package (v1.5) with ENSEMBL gene models (GRCm38.87) for mouse expression and a custom annotation file (file provided with manuscript) for influenza expression.
Differentially expressed genes were determined using edgeR from the bioconductor package.
Genome_build: mm10 and influenza (H1N1) PR8mRNA-var
Supplementary_files_format_and_content: raw expression counts

molecule: polyA RNA

growth_protocol: Lungs from infefected C57BL/6 were taken at 24 hours post infection. Live CD45-CD31- cells were FACS sorted directly into cell lysis buffer for RNA extraction.

extract_protocol:
RNA was isolated from FACS-sorted cells using RNeasy Micro or Micro Plus kit (Qiagen)
cDNA libraries were prepared using the SMARTer Universal Low Input RNA Kit (Takara Bio)

treatment_protocol: Mice were infected with 10^5 pfu of the indicated virus.

tag: strain

tag: mcherry-iav infection status

value: uninfected

tag: gfp-iav infection status

value: destGFP-IAV infected

value: FACS-sorted cells from lung

tag: gfp/dest fluorescence

value: negative

tag: mcherry fluorescence level


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID A2

value: Rectum


title: E2_destGFP_pos_5

description:
Sample12-2_S41
destGFP experiment (#2) ; destabilized GFP positive FACS-sorted cells from lung of mouse infected with destabilized GFP IAV

tag: cell type

value: positive


title: E2_destGFP_pos_4

description:
Sample11-2_S39
destGFP experiment (#2) ; destabilized GFP positive FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: 171130_MB_EB_Hs_25yr_BA10_A1_AD001_indexed


title: E2_destGFP_neg_4

description:
Sample11-1_S38
destGFP experiment (#2) ; destabilized GFP negative FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: E2_destGFP_pos_3

description:
Sample10-2_S37
destGFP experiment (#2) ; destabilized GFP positive FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: 171130_MB_EB_Hs_25yr_BA10_A12_AD010_indexed


title: Pool_2447_AD006_indexed

value: 58 yr

value: snmC-seq + SAP


title: Pool_2446_AD008_indexed


title: E7_ST2neg-transfer_Nb_lung_eo_rep2

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: eosinophils in lungs

growth_protocol: Prior to the infection, we transferred ST2- memory Th2 cells from mice 40 days after infection of 500 organisms of Larvae of Nippostrongylus brasiliensis (Nb). One month later, the mice were infected with 500 organisms of the Larvae. We sorted eosinophils  from the lungs of the mice 4 days after the infection.

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

value: lung

value: eosinophils

value: BALB/c


title: E8_ST2pos-transfer_Nb_lung_eo_rep1

growth_protocol: Prior to the infection, we transferred ST2+ memory Th2 cells from mice 40 days after infection of 500 organisms of Larvae of Nippostrongylus brasiliensis (Nb). One month later, the mice were infected with 500 organisms of the Larvae. We sorted eosinophils  from the lungs of the mice 4 days after the infection.


title: E9_ST2pos-transfer_Nb_lung_eo_rep2


title: N17_Nb_ST2lo_rep2

source_name: CD4+CD25-CD44hiST2- lung cells

growth_protocol: T cells were sorted from lungs of BALB/c mice 40 days after infection of 500 organisms of Nippostrongylus brasiliensis (L3) by flow cytometry

value: T cell


title: E4_nCD4-transfer_Nb_lung_eo_rep1

growth_protocol: Prior to the infection, we transferred naïve CD4+T cells from mice 40 days after infection of 500 organisms of Larvae of Nippostrongylus brasiliensis (Nb). One month later, the mice were infected with 500 organisms of the Larvae. We sorted eosinophils  from the lungs of the mice 4 days after the infection.


title: E5_nCD4-transfer_Nb_lung_eo_rep2


title: N16_Nb_ST2hi_rep2

source_name: CD4+CD25-CD44hiST2+ lung cells


title: E2_destGFP_pos_1

description:
Sample8-2_S34
destGFP experiment (#2) ; destabilized GFP positive FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: E2_destGFP_neg_2

description:
Sample9-1_S35
destGFP experiment (#2) ; destabilized GFP negative FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: N5_Nb_Naive_CD4_rep1

source_name: CD4+CD44low lung cells


title: Pool_2441_AD002_indexed


title: Pool_2435_AD002_indexed


title: Rectum tissue isolated from Rhesus Macaque at Baseline in Animal ID A1


title: N2_Nb_ST2lo_rep1


title: Pool_2440_AD002_indexed


title: N1_Nb_ST2hi_rep1


title: E2_destGFP_neg_1

description:
Sample8-1_S33
destGFP experiment (#2) ; destabilized GFP negative FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: Testis H3K4me3 ChIP-Seq followed by bisulfite sequencing

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the mm10 genome assembly. H3K4me3 ChIP-Seq reads were mapped to the reference genome using bwa aln (0.7.12).The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome.
Reads from Testis_H3K4me3_BSSeq were aligned to the mm10 reference using bismark 0.19.0.
Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000. DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously(17).
Uniquely mapping reads with a mapping quality score ≥ 30 were used for peak calling. NCIS was used to estimate the background fraction relative to an input DNA library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000. Peak strength was subsequently calculated by subtracting the NCIS normalized input read count from the ChIP-Seq read count.
Genome_build: mm10
For each SSDS experiment, the associated BAM file contains all paired end ssDNA reads identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection:
it : ITR length
uh : microhomology length
os : microhomology offset
mm : # mismatches
For each SSDS experiment, a BED file of ssDNA fragments is also provided. Colum 4 gives the alignment phred score for each read (underscore separated). Column 5 gives the ITR-associated detail listed above (it_uh_os). DSB hotspots are provided in bedgraph format for each DMC1 SSDS sample. Background corrected hotspot strength is listed in the fourth column. DSB hotspots in blacklisted regions were not used for analyses.
For the Testis_H3K4me3_BSSeq sample, the processed data file is the bedgraph generated by bismark. This gives the percent methyated reads for each locus.

source_name: Testis

extract_protocol:
For H3K4me3 CHiP-Seq and DMC1 SSDS protocols from testis, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Testis sample preparation was performed as described previously (Brick et al., 2012).
DMC1 and H3K4Me3 ChIP were performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-H3K4Me3 samples were prepared according to manufacturer's protocol (Illumina) and anti-DMC1 libraries were prepared following the method described in (Khil et al., 2012).
For H3K4me3 CHiP-Seq and DMC1 SSDS protocols from testis, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Testis sample preparation was performed as described previously (Brick et al., 2012).
DMC1 and H3K4Me3 ChIP were performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-H3K4Me3 samples were prepared according to manufacturer's protocol (Illumina) and anti-DMC1 libraries were prepared following the method described in (Khil et al., 2012).

value: Adult

tag: genotype

value: wild-type

tag: antibody

value: Anti-H3K4me3 (Abcam 8580)

tag: sequencing technique

tag: protocols

value: H3K4me3 ChIP-Seq was performed from whole testis as described, however the library preparation protocol was modified to perform bisulfite sequencing. Immediately following sequencing adapter ligation, we performed bisulfite conversion using the Qiagen EpiTect Bisulfite Kit (Cat # 59104). Subsequent library amplification was performed using KAPA HiFi Uracil+ Kit, which is designed to tolerate uracil residues in bisulfite-treated DNA.


title: E6_ST2neg-transfer_Nb_lung_eo_rep1


title: E2_destGFP_neg_3

description:
Sample10-1_S36
destGFP experiment (#2) ; destabilized GFP negative FACS-sorted cells from lung of mouse infected with destabilized GFP IAV


title: E2_GFP_pos_3

description:
Sample6-2_S32
destGFP experiment (#2) ; GFP postive FACS-sorted cells from lung of mouse infected with GFP IAV

value: GFP-IAV infected


title: E2_GFP_neg_3

description:
Sample6-1_S31
destGFP experiment (#2) ; GFP negative FACS-sorted cells from lung of mouse infected with GFP IAV

value: uninfected


title: Pool_2421_AD006_indexed

tag: Sex

value: Male

tag: age

tag: genome build


title: N15_Nb_Naive_CD4_rep2


title: E2_GFP_pos_2

description:
Sample5-2_S30
destGFP experiment (#2) ; GFP postive FACS-sorted cells from lung of mouse infected with GFP IAV

value: FACS-sorted cells from lung


title: E2_GFP_neg_2

description:
Sample5-1_S29
destGFP experiment (#2) ; GFP negative FACS-sorted cells from lung of mouse infected with GFP IAV

value: negative


title: Pool_2371_AD002_indexed

tag: library strategy


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A1_AD006_indexed

source_name: Mouse primary motor cortex


title: Pool_2372_AD008_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A1_AD004_indexed


title: Bordetella pertussis ΔbvgAΔs2013 mutant versus Bordetella pertussis ΔbvgA mutant replicat 3

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

description: The transcriptomic analysis aims at determining the effect of the absence of s2013 RNA in a delta-bvga mutant context (avirulent mutant)

hyb_protocol: Hybridization was performed in 40% formamide, 5x Denhardt’s solution, 0.1% SDS, 1 mM Sodium pyrophosphate and 5x SSC during 14-16h at 52°C under agitation in rotating oven. Slides were then washed sequentially in 2× SSC/0.2% SDS during 5 min, 0.5× SSC during 10 min, 0.05x SSC during 5 min and 0.01x SSC during 1 min at room temperature before drying.

scan_protocol: Scanned on an Innoscan 700 scanner (Innopsys), images were segmented using Mapix Software (version 3.2.1).

data_processing: For normalization and differential expression analyses the LIMMA package (Linear Models for Microarray Data), running under the statistical language R v3,2,1, was used. Statistically significant regulation was identified using moderated t-statistic with empirical Bayes shrinkage of the standard errors. Because of multiple testing, obtained P-values were corrected using Benjamini & Hochberg method to control false discovery rates.

organism: Bordetella pertussis

source_name: pellet of bacteria

label_protocol: 15 µg of total RNA was reverse transcribed with 400 units of SuperScript III (Invitrogen) in presence of 100µM Cy3-dCTP or Cy5-dCTP (GE) and 300 mM of hexanucleotide random (Roche) during 2 hours à 42°C. The labelled cDNA was then NaOH treated to degrade RNA and purified on Qiaquick PCR purification kit (Qiagen) according to the manufacturer’s instructions.

growth_protocol: The Bordetella pertussis Tohama I deletion mutants were grown on Bordet-Gengou agar plates supplemented with 15% sheep blood for 3 to 4 days at 37°C. Bacteria were then grown in Stainer-Scholte (SS) medium supplemented with 0.1% cyclodextrin and 0.5% casamino acids (Difco) at 37°C.

extract_protocol: Total RNA was extracted from pellets using Tri Reagent (Sigma) as recommended by the manufacturer and further treated with DNase I (Sigma) to remove any contaminating genomic DNA.

value: ΔbvgAΔs2013 mutant

value: ΔbvgA mutant


title: Pool_2368_AD008_indexed

value: 58 yr


title: E2_GFP_pos_1

description:
Sample4-2_S28
destGFP experiment (#2) ; GFP postive FACS-sorted cells from lung of mouse infected with GFP IAV

value: positive


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A1_AD007_indexed


title: Pool_2433_AD002_indexed

value: snmC-seq + SAP


title: Pool_2245_AD010_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A1_AD002_indexed


title: Bordetella pertussis ΔbvgA mutant versus Bordetella pertussis ΔbvgAΔs2013 mutant replicat 2


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A12_AD010_indexed


title: Bordetella pertussis ΔbvgAΔs2013 mutant versus Bordetella pertussis ΔbvgA mutant replicat 2


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A1_AD001_indexed


title: Pool_2244_AD002_indexed


title: E2_GFP_neg_1

description:
Sample4-1_S27
destGFP experiment (#2) ; GFP negative FACS-sorted cells from lung of mouse infected with GFP IAV


title: Bordetella pertussis ΔbvgA mutant versus Bordetella pertussis ΔbvgAΔs2013 mutant replicat 3


title: E2_naïve_3

description:
Sample3-1_S26
destGFP experiment (#2) ; FACS-sorted cells from lung of naïve (not infected with IAV) mouse


title: Bordetella pertussis ΔbvgAΔs2013 mutant versus Bordetella pertussis ΔbvgA mutant replicat 1


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A12_AD007_indexed


title: Pool_2241_AD002_indexed


title: E2_naïve_2

description:
Sample2-1_S25
destGFP experiment (#2) ; FACS-sorted cells from lung of naïve (not infected with IAV) mouse


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A12_AD006_indexed


title: Bordetella pertussis ΔbvgA mutant versus Bordetella pertussis ΔbvgAΔs2013 mutant replicat 1


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD012_indexed


title: E2_naïve_1

description:
Sample1-1_S24
destGFP experiment (#2) ; FACS-sorted cells from lung of naïve (not infected with IAV) mouse


title: Pool_2240_AD002_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD010_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD008_indexed


title: Pool_2231_AD010_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD004_indexed


title: E1_GFP_neg_mCherry_low_3

description:
Sample10-2_S22
mCherry experiment (#1) ; GFP negative, mCherry low FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV

value: mCherry-IAV infected

value: low


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD007_indexed


title: E1_GFP_neg_mCherry_neg_3

description:
Sample10-1_S21
mCherry experiment (#1) ; GFP negative, mCherry negative FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: E1_GFP_neg_mCherry_high_3

description:
Sample10-3_S23
mCherry experiment (#1) ; GFP negative, mCherry high FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV

value: high


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD006_indexed


title: Pool_2228_AD010_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD012_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A11_AD001_indexed


title: E1_GFP_neg_mCherry_high_2

description:
Sample9-3_S19
mCherry experiment (#1) ; GFP negative, mCherry high FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD006_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD007_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD008_indexed


title: Pool_2220_AD002_indexed


title: Pool_2219_AD006_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD002_indexed


title: Pool_2214_AD002_indexed


title: E1_GFP_neg_mCherry_low_2

description:
Sample9-2_S18
mCherry experiment (#1) ; GFP negative, mCherry low FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD001_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD004_indexed


title: E1_GFP_neg_mCherry_neg_2

description:
Sample9-1_S17
mCherry experiment (#1) ; GFP negative, mCherry negative FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: E1_GFP_neg_mCherry_high_1

description:
Sample8-3_S15
mCherry experiment (#1) ; GFP negative, mCherry high FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A12_AD008_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A2_AD007_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A2_AD006_indexed


title: Pool_2211_AD002_indexed


title: E1_GFP_neg_mCherry_low_1

description:
Sample8-2_S14
mCherry experiment (#1) ; GFP negative, mCherry low FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: Pool_2199_AD010_indexed


title: Pool_2224_AD006_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A2_AD004_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A2_AD002_indexed


title: E1_GFP_neg_mCherry_neg_1

description:
Sample8-1_S13
mCherry experiment (#1) ; GFP negative, mCherry negative FACS-sorted cells from lung of mouse infected with mCherry and GFP IAV


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD012_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A2_AD001_indexed


title: E1_mCherry_high_3

description:
Sample7-3_S12
mCherry experiment (#1) ; mCherry high FACS-sorted cells from lung of mouse infected with mCherry IAV


title: Pool_2196_AD008_indexed


title: 180118_CEMBA_mm_P56_P63_4B_CEMBA180104_4B_1_CEMBA180104_4B_2_A10_AD010_indexed


title: Pool_2186_AD010_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD008_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD010_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD007_indexed


title: Pool_2186_AD002_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD006_indexed


title: E1_mCherry_neg_3

description:
Sample7-1_S10
mCherry experiment (#1) ; mCherry negative FACS-sorted cells from lung of mouse infected with mCherry IAV


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD002_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD004_indexed


title: Pool_2183_AD002_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A1_AD001_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A12_AD008_indexed


title: E1_mCherry_low_2

description:
Sample6-2_S8
mCherry experiment (#1) ; mCherry low FACS-sorted cells from lung of mouse infected with mCherry IAV


title: Pool_2126_AD006_indexed


title: E1_mCherry_high_2

description:
Sample6-3_S9
mCherry experiment (#1) ; mCherry high FACS-sorted cells from lung of mouse infected with mCherry IAV


title: Pool_2126_AD002_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A12_AD007_indexed


title: E1_mCherry_neg_2

description:
Sample6-1_S7
mCherry experiment (#1) ; mCherry negative FACS-sorted cells from lung of mouse infected with mCherry IAV


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A12_AD004_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A12_AD002_indexed


title: Pool_2125_AD006_indexed


title: E1_mCherry_high_1

description:
Sample5-3_S6
mCherry experiment (#1) ; mCherry high FACS-sorted cells from lung of mouse infected with mCherry IAV


title: E1_mCherry_low_3

description:
Sample7-2_S11
mCherry experiment (#1) ; mCherry low FACS-sorted cells from lung of mouse infected with mCherry IAV


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A10_AD012_indexed


title: E1_mCherry_low_1

description:
Sample5-2_S5
mCherry experiment (#1) ; mCherry low FACS-sorted cells from lung of mouse infected with mCherry IAV


title: Pool_2114_AD010_indexed


title: Pool_2106_AD008_indexed


title: E1_mCherry_neg_1

description:
Sample5-1_S4
mCherry experiment (#1) ; mCherry negative FACS-sorted cells from lung of mouse infected with mCherry IAV


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A10_AD007_indexed


title: Pool_2106_AD002_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A10_AD006_indexed


title: E1_24h_control_1

description:
Sample3-1_S3
mCherry experiment (#1) ; FACS-sorted cells from lung of 24 hour control (not infected with IAV) mouse


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A10_AD004_indexed


title: Pool_2099_AD010_indexed


title: E1_48h_control_1

description:
Sample2-1_S2
mCherry experiment (#1) ; FACS-sorted cells from lung of 48 hour control (not infected with IAV) mouse


title: Pool_2089_AD002_indexed


title: E1_naïve_1

description:
Sample1-1_S1
mCherry experiment (#1) ; FACS-sorted cells from lung of naïve (not infected with IAV) mouse


title: cortex_systemic_rep2

city: Irapuato

first: Ruairidh

middle: J H

last: Sawers

address: Km9.6 Car. N. Irapuato-Leon

country: Mexico

institute: LANGEBIO-CINVESTAV

description: Gene expression data from arbusculated and systemtic cells in mycorrhizal rice roots

hyb_protocol: The labeled cRNA samples were mixed with 0.1 mg•ml–1 sonicated herring sperm DNA in a hybridization buffer containing 100 mM 2-N-morpholinoethanesulfonic acid (Mes), 1 M NaCl, 20 mM EDTA, and 0.01% Tween 20, denatured at 99°C for 5 min, and equilibrated at 45°C for 5 min before hybridization. The hybridization mix was then transferred to the rice GeneChip microarray cartridge and hybridized at 45°C for 16 h on a rotisserie at 60 rpm. The hybridized arrays were then rinsed and stained in a fluidics station (Affymetrix). The arrays were first rinsed with wash buffer A [6× SSPE (0.9 M NaC/0.06 M NaH2PO4/0.006 M EDTA)/0.01% Tween 20/0.005% antifoam] at 25°C for 10 min, incubated with wash buffer B (100 mM Mes/0.1 M NaCl/0.01% Tween 20) at 50°C for 20 min, stained with streptavidin-phycoerythrin (SAPE) (100 mM Mes/1 M NaCl/0.05% Tween 20 containing 10 mg/ml SAPE and 2 mg/ml BSA) at 25°C for 10 min, washed with wash buffer A at 25°C for 20 min, and stained with biotinylated anti-streptavidin antibody at 25°C for 10 min. After staining, arrays were stained with SAPE at 25°C for 10 min and washed with wash buffer A at 30°C for 30 min.

scan_protocol: The probe arrays were scanned twice, and the intensities were averaged with a GeneArray Scanner (Agilent Technologies, Palo Alto, CA) by using MAS 5.0 (Affymetrix).

data_processing: RMA using R/Bioconductor AFFY::rma (normalize  =  TRUE; background  = TRUE)

label: biotin

organism: Oryza sativa Japonica Group

source_name: systemic cells, mycorrhizal rice root

label_protocol: Total RNA (5 m g) from each sample was reverse-transcribed at 42°C for 1 h by using 100 pmol of an oligo(dT)24 primer containing a 5' T7 RNA polymerase promoter sequence [5'-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG(dT)24-3'], 50 mM Tris•HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.5 mM dNTPs, and 200 units of SuperScript II reverse transcriptase (Invitrogen). The second strand of cDNA was synthesized by using 40 units of Escherichia coli DNA polymerase I, 10 units of E. coli DNA ligase, and 2 units of RNase H in a reaction containing 25 mM Tris•HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 10 mM (NH4)2SO4, 0.15 mM b -NAD+, 1 mM dNTPs, and 1.2 mM DTT. The reaction proceeded at 16°C for 2 h and was terminated by using EDTA. Double-stranded cDNA products were purified by phenol/chloroform extraction and ethanol precipitation. Biotinylated complementary RNAs (cRNAs) were transcribed in vitro from synthesized cDNA by T7 RNA Polymerase (ENZO BioArray High Yield RNA transcript-labeling kit, Enzo Biochem). cRNAs were purified by using affinity resin (Qiagen RNEasy spin columns) and randomly fragmented by incubating at 94°C for 35 min in a buffer containing 40 mM Tris•acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate to produce molecules of » 35–200 bases.

growth_protocol: Rice seeds were surface-sterilized, pre-germinated and grown in a growth chamber with a 12h/12h day/night cycle at 28°C/22°C and 60% humidity. Plants were fertilized every second day with half Hoagland solution, adjusted to 25mM KH2PO4. Plants were harvested at 7 weeks.

extract_protocol: Fresh roots of mycorrhizal and non-mycorrhizal rice plants were collected at 7 wpi, cut into 3-5 mm pieces and immediately fixed, embedded and processed as previously described (Gutjahr et al., 2012). Root sections were arranged in parallel on UV-treated poly-L-lysine slides. A laser microbeam system (P.A.L.M. Microlaser Technologies, http://www.zeiss.de/ micro-dissection) was utilized for microdissection of cortical root cells. For cutting, the following parameters were selected using P.A.L.M. Robosoftware 2003 (http://www.zeiss.de/microdissection): auto- LPC focus 50, with energy of 95 and a speed of 100. Approximately 2000 cortical cells were isolated as combined cell units. Isolated specimens were catapulted onto the adhesive surface on the inside of the lid of a 0.5ml reaction tube (Carl Zeiss, http://www.zeiss.com/), collected by centrifugation (11 000g for 30 sec) and immediately subjected to 350μl RLT buffer (Qiagen, http:// www.qiagen.com/), 40 units),1μl RNaseOUT (Invitrogen, http:// www.invitrogen.com/) and 3.5 μl β-mercaptoethanol (Sigma-Aldrich, http://www.sigmaaldrich.com/). The sample was vigorously mixed and incubated at 56°C for 5 min to facilitate cell-wall disruption. At this stage, the lysate was either stored at 80°C or further processed for RNA isolation. Total RNA of each cell population was extracted using an RNeasy micro kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Plants in the treatment group were inoculated at planting with 250 spores of Rhizophagus irregularis.

tag: cultivar

value: Nipponbare

tag: inoculation

value: Rhizophagus irregularis

value: systemic root cortical cell


title: Pool_2084_AD002_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A10_AD001_indexed


title: 171219_CEMBA_mm_P56_P63_4B_CEMBA171213_4B_1_CEMBA171213_4B_2_A10_AD002_indexed