title: H3K4me2_ChIPSeq_input_genomic_control [MM2.GC]

city: Berkeley

first: Shelby

last: Wilson

address: 16 Barker Hall # 3204

institute: University of California, Berkeley

data_processing:
quality assessment of sequencing results with FastQC (Babraham Bioinfomatics)
Libraries were aligned to both the 110 Rattus norvegicus 4 (rn4) and Rattus norvegicus 6 (rn6) genome assemblies using bowtie 1.1.2
Remove unaligned reads
core diffReps analysis was conducted using default parameters
peak files generated and analyzed using HOMER v4.9. First, two tag directories containing pooled, within-group (four merged immunoprecipitated or four merged genomic control) libraries were assembled. Next, the findPeaks command was utilized to call peaks of variable length by specifying a minimum size of 1000bp, limiting clonal tag filtering to account for MNase digestion, and disabling local filtering to help identify discrete histone peaks within broader regions of enrichment. The resulting peak files were then annotated using the annotatePeaks.pl command and rn6 assembly. Peak files produced from within treatment group pooled tag directories were then used as input for HOMER known and de novo motif finding analysis (findMotifsGenome.pl) with default parameters.
Genome_build: rn4 for peak calling in diffReps, rn6 for HOMER peaks and motif analysis
Supplementary_files_format_and_content: .bed files resulting from default diffReps analysis, with "GC" as control and "IP" as signal files

organism: Rattus norvegicus

growth_protocol: Four adult male Fischer 344 rats were caged in groups of two for three months and fed rat chow ad libitum.

extract_protocol:
epididymides and vas deferens were excised; the vas deferens was immediately placed in a 37°C phosphate buffered saline (PBS) with 1% bovine serum albumin (BSA) and incubated at 37°C for five minutes to facilitate spermatozoa swim-out. Approximately 2.5mL of sperm cell suspension was collected from epididymides 60 and vas deferens pooled for each rat. The total sperm concentration was determined using a hemocytometer.
Following sperm collection, each sample was split with 4 million sperm for a genomic control library and 10 million sperm for immunoprecipitation. Genomic control samples were subjected to a modified QIAamp DNA Micro Kit extraction protocol. The immunoprecipitated sample was made using a modified nChIP-seq protocol by doubling the time for MNase digestion (to a total of 10 minutes), using 30 U enzyme per two million sperm, and using 5 ug of ChIP-seq validated H3K4me2 antibody. Libraries were prepared from four paired genomic control and immunoprecipitated samples using NuGen’s Ovation® Ultralow Library System V2
average size and raw concentration of each library was determined using 2 Fragment Analyzer (AATI) with a High Sensitivity NGS Fragment Analysis kit (cat# DNF 486-0500). Subsequently, each library was diluted into three different concentrations and quantified by qPCR in 85 triplicates using the KAPA quantification Kit. Samples were then multiplexed across two lanes. Genewiz (www.genewiz.com) performed sequencing using 50bp single end reads on an Illumina HiSeq2500 platform.

treatment_protocol: The rats were vehicle controls exposed to 3% tween20 (Sigma-Aldrich) in corn oil by oral gavage five days per week. These controls showed no adverse effects of their vehicle exposure, and were chosen because future studies looking for toxicant-induced changes would involve control rats exposed to a similar vehicle, making this population the most appropriate group of background controls.

value: Fischer 344

value: 4 million mature sperm

tag: collection method

value: Epididymal and vas deferens swim up

tag: chip antibody

value: none (input)


title: H3K4me2_ChIPSeq_immunoprecipitated [MM2.IP]

status: Public on Feb 01 2018

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

tag: strain

tag: tissue

value: 10 million mature sperm


title: H3K4me2_ChIPSeq_input_genomic_control [MM1.GC]


title: H3K4me2_ChIPSeq_immunoprecipitated [MM1.IP]


title: H3K4me2_ChIPSeq_immunoprecipitated [AA2.IP]


title: H3K4me2_ChIPSeq_input_genomic_control [AA2.GC]


title: H3K4me2_ChIPSeq_input_genomic_control [AA1.GC]


title: SAMPLE 5_H510 T-3775440 500 nmol/L 72h

type: RNA

city: Fujisawa

first: SHINJI

last: TAKAGI

address: 26-1 Muraoka Higashi 2-chome

department: Oncology Drug Discovery Unit

country: Japan

institute: Takeda Pharmaceutical Company

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

molecule: total RNA

organism: Homo sapiens

label_protocol: labelled cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit with DNase I treatment with  in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Treatment with test article or DMSO for 72 hours

tag: cell line

tag: cell type

value: small cell lung cancer (SCLC) cell line

tag: treated with


title: before_molt

city: Hefei

first: Xing young

last: Chen

address: 130, Changjiang Xi Road

country: China

institute: Anhui Agricultural University

description: gene expression before molt

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Anser sp.

source_name: skin sample from ventral

label_protocol: The microarrays were performed following Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) protocol and RNA Spike-In-One Color. We used about 400 ng total RNA as the starting material for amplification and labelling. Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

growth_protocol: The geese were reared on a floor system in open-sided houses. At 10 wk of age the birds were transferred to pens (3×3 m2) in groups of 25 per pen. Each pen contained on one side a 3×3 m2 outside ground area with a water bath. When half geese were going to molting, six randomly selected geese were reared on a separated pen with same conditions. The experimental geese were fed a commercial maize-soybean-based diet containing 155 g CP/kg feed with a metabolic energy content of 10.87 MJ/kg and sufficient forage. The birds had free access to feed and water.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: time

value: before molt

value: skin

tag: gender

value: female


title: HN15-Chronic SIV

city: San Antonio

first: Mahesh

last: Mohan

state: Texas

address: 8715 West Military Road

department: Host Pathogen Interaction Program

institute: Southwest National Primate Research Center

description: Gene expression in Colonic epithelium during chronic SIV infection

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Rhesus Macaque Genome Oligo Microarray (4 x 44K, Agilent Technologies) in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 12 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples.

organism: Macaca mulatta

source_name: chronically SIV-infected

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: Total RNA was extracted using the miRNeasy mini kit from Qiagen Inc.

treatment_protocol: Four animals were infected Intravenously with 100TCID50 dose of SIVmac251. The other 4 served as uninfected control animals.

value: Colonic Epithelium

value: Colon

tag: age

value: 4.25  years


title: HV48-Chronic SIV

value: 5.87  years


title: Ovarian tumor from patient 4

type: genomic

city: LYON

first: Daniel

last: PISSALOUX

address: 28 rue Laënnec

department: Biopathology

country: France

institute: Centre Léon Bérard

description: FFPE sample

hyb_protocol: Co-hybridization was performed on 4x180K Agilent SurePrint G3 Human whole-genome oligonucleotide arrays (Agilent #G4449A) at 65°C for 24 hours, in a rotating oven at 20rpm. Slides were then washed with Oligo aCGH Wash Buffer 1 at room temperature for 5 min followed by 1 min wash with Oligo aCGH Wash Buffer 2 at 37°C. Finally, slides were dried.

scan_protocol: Slides were scanned using Agilent Surescan scanner G2600D with 3 μm resolution.

data_processing:
Scan images were processed using Agilent Feature Extraction Software V11.0 and the analysis was carried out using the Agilent Genomic Workbench software V7.0. The identification of aberrant copy number segments was based on ADM-2 segmentation algorithm with a threshold of 7.
Basically, chromosomal loci were considered as amplified if log2ratio were ≥ 1.6, and were considered as homozygously deleted if log2ratio were ≤ −1. However, these thresholds were manually adapted according to the percentage of tumor cells.

source_name: Ovarian tumor from yo-PCD patient 4

label_protocol: Fragmentation and labeling were done according to the manufacturer’s recommendation for the CGH arrays (Agilent Technologies, Santa Clara, CA) with some modifications. In brief, reference and tumor DNA were heat-denatured and fragmented during 10min at 95°C. Then, tumor DNA was chemically labeled with Universal Linkage System (ULS™, Agilent #5190-0450) Cy5-dye, whereas reference DNA was labeled with Cy3-dye. The labeled samples were then purified using Agilent KREApure columns (Agilent #5190-0418).

growth_protocol: FFPE archived samples of ovarian tumors

extract_protocol: DNA extraction was performed using the QIAamp DNA Micro kit (Qiagen #56304, Sussex, UK) according to the manufacturer’s instructions, and DNA was eluted in 25 μl of water.

treatment_protocol: Small amounts of tumor tissues were collected by scrapping 20 unstained slides containing 8 μm FFPE sections. Paraffin was removed using the Deparaffinization Solution (Qiagen #19093)

tag: tumor type

value: High grade serous carcinoma

tag: age at tumor diagnosis

tag: staging at tumor diagnosis

value: III

tag: percentage of tumor cells

source_name: Male reference DNA, commercial

tag: reference

value: Promega #G1471


title: SAMPLE 3_H510 DMSO 72h

source_name: H510 DMSO 72h

value: DMSO for 72hrs


title: SAMPLE 2_H510 DMSO 72h


title: H3K4me2_ChIPSeq_immunoprecipitated [AA1.IP]

value: Fischer 344


title: SAMPLE 4_H510 T-3775440 500 nmol/L 72h


title: HR42-PREINF

source_name: pre-infection

value: 5.5  years


title: 1.5day_after_molt

description: gene expression 1.5 day after molt

value: 1.5 days after molt


title: HB31-Chronic SIV

value: 6.82  years


title: U2OS_10Gy_4h

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: Irradiated with 10Gy (1Gy/min) & 4h of recovery

data_processing:
Quality control of reads was performed with FastQC software
Reads were mapped to the human genome (hg19) with Bowtie2.0.4
Peak detection was carried with the MACS program (detected peaks are given in bed files)
p65 target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Peak intersections and their genomic coordinates were found using Bedtools software
The significance of differences between control untreated cells and cells subjected to TNFα and IR was estimated using MACS software; the FDR=0.05 level was selected as the significance threshold.
Genome_build: hg19
Supplementary_files_format_and_content: fastq - raw data from Illumina sequencer; bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: U2OS cells

growth_protocol: The wild-type U2-OS cells were purchased from ATCC (HTB-96) and used as a primary model. Cells were grown in McCoy’s 5A medium supplemented with 10% heat-inactivated fetal bovine serum (HyClone) and gentamicin (40 mg/mL; Krka) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
2x10^6 cells were inoculated on 10 cm2 dish 2 days before experiments. At the appointed experimental points a two-step cross-linking procedure was applied for an efficient fixation of NF-κB dimers with DNA [27]. Cells were washed twice with PBS, a solution of DSG (disuccinimidyl glutarate) in PBS was added to the final concentration of 2 mM, and then cells were incubated for 45 minutes at RT with rotation. Next, cells were washed twice with PBS and the second fixation was performed using 1% formaldehyde for 10 min at RT. Formaldehyde fixation was quenched by glycine (125 mM final concentration) and then nuclei were isolated using buffers and protocol from iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Chromatin of nuclei re-suspended in 200 µl was sheared using Bioruptor® PLUS combined with the Bioruptor® Water cooler & Single Cycle Valve (at HIGH power setting) with 15 cycles of 30 sec shearing followed by 30 sec of standby; chromatin fragments with approximate length 100-600 bp were obtained. Chromatin immunoprecipitation was carried out using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode) with 3µl/sample of anti-RelA(p65) polyclonal antibody (C15310256, Diagenode) or without antibody (mock-IP), according to the manufacturer protocol.
Immunoprecipitated DNA fragments and input DNA were sequenced using the HiSeq 1500 system with TruSeq workflow (Illumina)

treatment_protocol: Any treatment started 48 h after inoculation of cells; all steps, with the exception of irradiation, were carried out at 37 °C and 5% CO2. For ChIP-Seq analysis wild-type cells were harvested after 0.5 and 4 hours of stimulation with TNFα (30ng/ml). Alternatively, cells were irradiated with 10 Gy IR dose at a 1Gy/min dose rate using 6 MeV photons (generated by linear accelerator Clinac 600, Varian), the medium was replaced with a fresh one, and cells were analyzed 2 or 4 hours after irradiation.

value: U2OS cells

value: osteosarcoma

tag: Sex

value: 15 years

tag: tissue/cells

value: bone

value: NFKB p65 polyclonal Ab (Diagenode, C15310256)


title: FT11-Chronic SIV

value: Colonic Epithelium

value: 3.2  years


title: HD08-PREINF

value: Colon

value: 6.25 years


title: SAMPLE 1_H510 DMSO 72h

value: small cell lung cancer (SCLC) cell line


title: HH07-PREINF

value: 6.35  years


title: HF54-PREINF

value: 6.42  years


title: U2OS_10Gy_2h

description: Irradiated with 10Gy (1Gy/min) & 2h of recovery

value: female


title: U2OS_TNFalpha_4h

description: TNFalpha treated for 4h (30ng/ml)


title: U2OS_TNFalpha_30min

description: TNFalpha treated for 30min (30ng/ml)


title: B16-BL6 tumor_ALA+30 Gy Xray_4

city: Tsukuba

first: Junko

last: Takahashi

state: Ibaraki

address: 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology　(AIST)

description: gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated after ALA treatment C57BL6J mouse.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC 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- G4122F Whole Mouse Genome Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. The quantile normalization method was used in our microarray analysis.

organism: Mus musculus

source_name: B16-BL6 mouse melanoma

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 RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the RNeasy mini kit from B16-BL6 melanoma preserved in RNAlater (Qiagen). Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: RNAlater conservation at -80ºC

value: melanoma tumor

value: male

tag: treatment

value: ALA+30 Gy Xray

tag: background strain


title: B16-BL6 tumor_ALA+30 Gy Xray_3


title: U2OS_control

description: untreated control

tag: chip antibody


title: B16-BL6 tumor_ALA+30 Gy Xray_1

tag: tissue


title: B16-BL6 tumor_30 Gy Xray_4

value: 30 Gy Xray


title: B16-BL6 tumor_ALA+30 Gy Xray_2


title: Rhesus macaque_13-R377_Dorsal Prefrontal_Cortex

city: West Point

first: Keith

last: Tanis

address: 770 Sumnetown Pike

institute: Merck & Co, Inc

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493700

library_source: transcriptomic

data_processing:
Genome alignment and gene quantitation was performed using Omicsoft Array Studio version 7.2.2.29
Cleaned reads were aligned to the human B37.3 genome reference using the Omicsoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RSEM algorithm as implemented in Omicsoft Array Studio and using Ensembl release 75 gene models
Genome_build: human B37.3
Supplementary_files_format_and_content: xlsx files include read count values for each sample
Supplementary_files_format_and_content: xlsx files include RPKM values for each sample

source_name: Dorsal Prefrontal_Cortex

extract_protocol:
MagMax 96-well isolation Kit (Ambion #AM1839)
Illumina TruSeq Stranded Total RNA sample preparation kit (Illumina Catalog #: RS-122-2203)

tag: age(weeks)

tag: batch

tag: animal id

value: F


title: Rhesus macaque_10-0280_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493691

source_name: Visual _Cortex

value: M


title: Rhesus macaque_09-R964_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493695


title: Rhesus macaque_13-0372_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493698


title: Rhesus macaque_04-R437_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493693


title: Rhesus macaque_07-R704_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493696


title: Rhesus macaque_05-0041_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493699


title: Rhesus macaque_09-R967_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493697


title: Rhesus macaque_12-0197_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493694


title: Rhesus macaque_04-0427_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493690


title: B16-BL6 tumor_30 Gy Xray_3


title: Rhesus macaque_13-0460_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493689


title: Rhesus macaque_09-0085_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493688


title: Rhesus macaque_14-R403_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493685


title: B16-BL6 tumor_ALA+20Gy Xray_4

value: ALA+20 Gy Xray


title: Rhesus macaque_01-R016_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493687


title: B16-BL6 tumor_20 Gy Xray_4

description: gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated C57BL6J mouse.

value: 20 Gy Xray


title: B16-BL6 tumor_ALA+20Gy Xray_1


title: B16-BL6 tumor_control_1

description: gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks control C57BL6J mouse.

value: control


title: B16-BL6 tumor_ALA control_1

value: ALA


title: Rhesus macaque_04-R495_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493682


title: B16-BL6 tumor_30 Gy Xray_1

description: gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks Xray irradiated after ALA treatment C57BL6J mouse.


title: B16-BL6 tumor_20 Gy Xray_1

description: gene expression analysis performed on a B16-BL6 tumor preparation from a male 8 weeks ALA treatment C57BL6J mouse.


title: B16-BL6 tumor_20 Gy Xray_2


title: B16-BL6 tumor_ALA+20Gy Xray_2


title: B16-BL6 tumor_ALA control_2


title: Rhesus macaque_13-0193_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493681


title: B16-BL6 tumor_control_2


title: B16-BL6 tumor_20 Gy Xray_3


title: Rhesus macaque_10-0091_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493680


title: B. fragilis 638R, anaerobic, biological rep2

city: Rio de Janeiro

first: Felipe

middle: Lopes

last: Teixeira

state: Rio de Janeiro

address: Av. Carlos Chagas Filho 373

department: Microbiologia Médica

country: Brazil

institute: Universidade Federal do Rio de Janeiro

description: Gene expression data from wild-type B. fragilis during anaerobiosis

hyb_protocol: Hybridization of fragmented cDNA was carried out at 45 ºC for 16 hours on custom B. fragilis arrays in the 81/100 format. Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G plus with autoloader.

data_processing: Data analysis was carried out using Affymetrix Expression Console software version 3.0 (TAC 3.0) using default settings.

label: biotin

organism: Bacteroides fragilis

source_name: parental strain grown in anaerobiosis

label_protocol: Biotinylated cDNA was prepared according to standard Affymetrix protocols (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Overnight cultures of B. fragilis638R were diluted 1:50 into BHI broth and grown under anaerobic conditions untile they reached OD550 of 0.3-0.4. The culture was then split in two parts prior to RNA extraction. On was used as anaerobic control and the other was exposed to atmospheric oxygen at 37 ºC for another 1 hour.

extract_protocol: Total RNA was isolated by the hot phenol method and treated as described by Sund et al, 2008, Mol. Microbiol.67:129-142.

tag: strain

tag: genotype

value: Wild-type

tag: condition

value: anaerobiosis


title: Rhesus macaque_09-R964_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493679


title: Rhesus macaque_99-R013_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493676


title: B. fragilis bmoR mutant, O2 exposed, biological rep2

description: Gene expression data from B. fragilis bmoR mutant strain during oxidative stresse conditions

source_name: mutant strain exposed to atmospheric oxygen

value: bmoR mutant

value: oxidative stress


title: B16-BL6 tumor_30 Gy Xray_2

tag: gender


title: Rhesus macaque_14-R403_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493675


title: B. fragilis bmoR mutant, anaerobic, biological rep1

description: Gene expression data from B. fragilis bmoR mutant strain  during anaerobiosis

source_name: mutant strain grown in anaerobiosis


title: Slow4 15 repl1

city: Planegg-Martinsried

first: Annabella

last: Königer

address: Großhaderner Straße 2

department: Biology II

country: Germany

institute: LMU Munich

data_processing:
Read quality was checked for each sample using FastQC (version 0.11.5)
High quality raw reads were mapped to the D. ananassae transcriptome (including non-coding RNAs) using the annotation of FlyBase release 1.05 . Mapping was done with NextGenMap (version 0.4.12) using default parameters.
We used python to count the number of hits per trancript and to combine hits per transcript for each gene to get gene counts for each sample.
A .tsv file (gene_counts.tsv) containing all gene counts of all samples was used for subsequent analysis in DESeq2 (version 1.16.1)

organism: Drosophila ananassae

source_name: whole male flies pooled

growth_protocol: All flies were kept at low density and raised in 50 ml vials containing standard cornmeal molasses medium, at a constant room temperature (22  ±  1 °C) and at a 14:10 hours light:dark cycle

extract_protocol:
Samples were immediately shock-frosted in liquid nitrogen and RNA was extracted using the MasterPure RNA Purification Kit (Epicentre) and following the standard protocol without DNaseI digestion
poly(A) enrichment, fragmentation by sonication, 3’-cDNA synthesis

treatment_protocol: At the age of 4–6 days, flies were subjected to a  cold shock. The vials were placed in an ice water bath (0 ± 0.5 °C) for exactly 3 hours.  For the recovery phase, they were placed back at room temperature (22  ±  1 °C). Flies for RNA-extraction were sampled at three different timepoints: before the cold shock (without any treatment), after 15 min. recovery  time and after  90 min. recovery time.

value: whole body

tag: fly strain

value: 15 min. after cold shock


title: B. fragilis bmoR mutant, O2 exposed, biological rep1


title: Slow4 90 repl1

value: 90 min. after cold shock


title: Slow4 RT repl2

value: without treatment


title: B. fragilis bmoR mutant, anaerobic, biological rep2


title: Slow4 15 repl2


title: B16-BL6 tumor_ALA control_3

value: melanoma tumor

value: male


title: B16-BL6 tumor_ALA+20Gy Xray_3


title: Slow4 RT repl1


title: Rhesus macaque_13-0193_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493673


title: Rhesus macaque_04-R437_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493671


title: B. fragilis 638R, O2 exposed, biological rep2

description: Gene expression data from wild-type B. fragilis during oxidative stresse conditions

source_name: parental strain exposed to atmospheric oxygen


title: B16-BL6 tumor_control_3


title: Slow3 90 repl2


title: Slow4 90 repl2


title: Rhesus macaque_10-0280_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493674


title: 143

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

institute: MGH

description: extra cellular RNA

hyb_protocol: none provided by the submitter

scan_protocol: The samples were then scanned on an EMD Millipore Guava 6HT flow cytometer. Flow cytometry quantification data was analyzed with the Firefly™ Analysis Workbench software.

data_processing: To determine if a particular miRNA signal is detected, assay background is subtracted from the measured miRNA signal and the result is compared to a target-specific detection threshold. This detection threshold is based on comparison of fluorescence intensity of sample wells to negative (water only) wells. Samples with below-detection threshold fluorescence intensity were counted as missing for the analysis (to avoid bias). The data was used after subtracting the background from the raw data.

label: Fireplex

source_name: Plasma

label_protocol: none provided by the submitter

extract_protocol: In brief, plasma (40 μL) was mixed with 36 μL Digest Buffer and 4 μL Protease Mix and incubated at 60°C for 45 minutes with shaking. For each sample run, Firefly Particles (35 μL) were added to a well of a 96-well filter plate and filtered. Next, 25 μL of Hybe Buffer was added to each well followed by 25 μL of sample (or water in the case of no-sample controls). The plate was incubated at 37°C for 60 minutes with shaking.  After rinsing twice with 1X Rinse B and once with 1X Rinse A, 75 μL of 1X Labeling Buffer was added to each well. The plate was incubated at room temperature for 60 minutes with shaking. After two rinses with Rinse B followed by one rinse with 1X Rinse A, a catch plate was added to the vacuum manifold and the filter plate put under constant vacuum. 65 μL of 95°C RNAse-free water was added twice to each well to elute the ligated sample. 30 μL of this melt-off was added to a clean PCR plate and mixed with 20 μL PCR master mix. The mixture underwent 27 cycles of PCR amplification followed by 6 cycles of asymmetric amplification.  Next 60 μL of Hybe Buffer was added back to each well of the original particles followed by 20 μL of the PCR product, and the plate was incubated at 37°C for 30 minutes with shaking. After rinsing twice with 1X Rinse A, 75 μL of 1X Reporting Buffer was added to each well and the plate incubated at room temperature for 15 minutes with shaking.  After rinsing twice with 1X Rinse A, 175 μL of Run Buffer was added to each well.

tag: age

tag: bmi

tag: race

value: Caucasian


title: 141

description: extra cellular RNA

value: non-Caucasian


title: Rhesus macaque_13-R372_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493670

tag: Sex

value: F


title: 135

description: extra cellular RNA


title: 148

description: extra cellular RNA


title: 151

description: extra cellular RNA


title: B. fragilis 638R, anaerobic, biological rep1


title: B. fragilis 638R, O2 exposed, biological rep1


title: Slow3 90 repl1


title: Rhesus macaque_8741-5_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493669


title: Rhesus macaque_04-0427_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493667


title: Rhesus macaque_05-R504_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493665


title: Rhesus macaque_04-R495_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493666


title: Slow3 RT repl1


title: Slow3 15 repl1


title: Rhesus macaque_13-R377_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493664


title: Slow3 RT repl2


title: 129

description: extra cellular RNA


title: 125

description: extra cellular RNA


title: Slow3 15 repl2


title: 133

description: extra cellular RNA


title: 134

description: extra cellular RNA


title: 128

description: extra cellular RNA


title: Slow2 15 repl2


title: Slow2 90 repl1


title: Rhesus macaque_05-R552_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493663

value: M


title: Slow2 RT repl2


title: Slow2 15 repl1


title: Rhesus macaque_13-0460_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493657


title: 123

description: extra cellular RNA


title: 124

description: extra cellular RNA


title: Slow2 90 repl2


title: Rhesus macaque_13-0446_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493655


title: Rhesus macaque_08-R887_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493656


title: 122

description: extra cellular RNA


title: Rhesus macaque_8741-5_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493654


title: Slow1 90 repl2


title: Slow2 RT repl1


title: Rhesus macaque_05-R552_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493692


title: Rhesus macaque_08-R887_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493653


title: 110

description: extra cellular RNA


title: Slow1 90 repl1


title: Slow1 15 repl2


title: 109

description: extra cellular RNA


title: 130

description: extra cellular RNA


title: Rhesus macaque_05-R504_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493652


title: 108

description: extra cellular RNA


title: Rhesus macaque_12-0233_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493650


title: Slow1 15 repl1


title: 107

description: extra cellular RNA


title: Slow1 RT repl1


title: Rhesus macaque_13-0372_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493659


title: Slow1 RT repl2


title: Fast4 90 repl2


title: 120

description: extra cellular RNA


title: 102

description: extra cellular RNA


title: Fast4 90 repl1


title: Fast4 15 repl2


title: 104

description: extra cellular RNA


title: Rhesus macaque_10-0091_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493649


title: 100

description: extra cellular RNA


title: Fast4 15 repl1


title: Rhesus macaque_09-R967_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493645


title: Rhesus macaque_12-0197_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493647


title: Rhesus macaque_09-0085_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493644


title: Rhesus macaque_12-0233_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493651


title: Rhesus macaque_07-R704_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493643


title: 93

description: extra cellular RNA


title: Fast3 90 repl2


title: Fast4 RT repl1


title: Rhesus macaque_13-0446_Dorsal Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493642


title: Fast3 90 repl1


title: Rhesus macaque_01-R016_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493641


title: 101

description: extra cellular RNA


title: Fast3 15 repl2


title: Rhesus macaque_13-R372_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493648


title: 98

description: extra cellular RNA


title: Fast3 15 repl1


title: Fast4 RT repl2


title: CUP9_del_mut_Rep1

city: Würzburg

first: Tobias

last: Ludwig

address: Josef-Schneider-Straße 2

institute: Institute for Molecular Infection Biology

description:
total RNA with poly(A)+ selection
NG-7548_TF61y_tha_v1_lib81421_3900_3_1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. albicans Build 21 transcriptome using STAR v2.5.3a with parameters --runThreadN 3 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif
Raw read counts per reference feature were calculated using HTSeq v0.7.2
Raw read counts were normalized and analysed for differentially expressed genes using DESeq2 v1.14.1
Genome_build: Candida albicans Build 21
Supplementary_files_format_and_content: tab-delimeted text files include raw read counts for each sample, tab-delimited text file contains the mean of normalized counts, log2 fold change, log2 fold change standard error, wald statistics, p-value and adjusted p-value for each replicate pair after differential gene expression analysis sample

organism: Candida albicans

source_name: cup9_del_yeast cell

growth_protocol: C. albicans reference strain and deletion mutant were grown on Todd-Hewitt agar at 37°C for 24 h.

extract_protocol:
Total RNA was extracted using RiboPure(TM) RNA purification kit for yeast (Ambion, Life Technologies)
Library construction was carried out by GATC Biotech (Konstanz, Germany). Briefly, the protocol included poly(A)+ RNA selection, mRNA  fragmentation, random primer cDNA synthesis, adaptor ligation and Illumina(HiSeq2500) sequencing

tag: genotype/variation

value: CUP9 deletion mutant


title: Fast3 RT repl2

tag: treatment


title: WT_Rep2

description:
total RNA with poly(A)+ selection
NG-7548_401_tha_v2_lib81424_3900_3_1

source_name: WT_yeast cell

value: wildtype


title: 91

description: extra cellular RNA


title: CUP9_del_mut_Rep2

description:
total RNA with poly(A)+ selection
NG-7548_TF61y_tha_v2_lib81425_3900_3_1


title: 94

description: extra cellular RNA


title: 78

description: extra cellular RNA


title: WT_Rep1

description:
total RNA with poly(A)+ selection
NG-7548_401_tha_v1_lib81420_3900_3_1


title: 75

description: extra cellular RNA


title: Rhesus macaque_99-R013_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493639


title: 92

description: extra cellular RNA


title: Fast2 90 repl2


title: 80

description: extra cellular RNA


title: 73

description: extra cellular RNA


title: hEGFR-T_ Day5_Mouse#27_Spleen [37 6 27S]

city: Minneapolis

first: Christopher

middle: A

last: Pennell

state: Minnesota

address: 420 Delaware St SE

department: Laboratory Medicine & Pathology

institute: University of Minnesota

description:
37 6 27S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

scan_protocol: CodeSets were scanned by University of Minnesota Genomic Center personnel according to the manufacturer's protocol.

data_processing: The data were normalized using the nanoString nSolver software platform.

organism: Mus musculus domesticus

source_name: hEGFR-T_ Day5_Mouse#27_Spleen

extract_protocol: Total RNA was isolated from spleens and colons using the RNAeasy MidiKit per manufacturer's protocol.

tag: strain background

tag: mouse id

tag: treated with

value: control hEGFRT-cells

value: Spleen

tag: time point


title: hEGFR-T_ Day5_Mouse#30_Spleen [40 6 30S]

description:
40 6 30S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#30_Spleen

tag: tissue


title: hEGFR-T_ Day5_Mouse#28_Spleen [38 6 28S]

description:
38 6 28S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#28_Spleen


title: hEGFR-T_ Day5_Mouse#29_Spleen [39 6 29S]

description:
39 6 29S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#29_Spleen


title: 72

description: extra cellular RNA


title: hEGFR-T_ Day5_Mouse#26_Spleen [36 6 26S]

description:
36 6 26S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#26_Spleen


title: Fast3 RT repl1


title: 74

description: extra cellular RNA


title: 1331-35-post

city: Birmingham

first: Rebecca

last: Arend

state: Alabama

address: 619 19th Street South 176F Rm 10250

institute: University of Alabama at Birmingham

description:
35-post
Patient 35 data were removed from the analysis because it was not a high grade PSC case.

hyb_protocol: nCounter Gene Expression Protocol MAN-C0003-03 (20131213) using 100ng total RNA

scan_protocol: Data Collection is carried out in the nCounter® Digital Analyzer. At the high data resolution, 280 images per sample or fields of view (FOV) are collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV) format

data_processing:
nCounter® Expression Data Analysis Guide-MAN-C0019-04, using nSolver Analysis Software v2.5.
Data were normalized with the nSolver Analysis software to various housekeeping genes, fold change comparison between pre and post treatment samples

source_name: Ovarian Tumor Tissue

extract_protocol: Total RNA extracted from frozen tissues in RNAlater with Invitrogen PureLink RNA Mini Kit (cat#12183018A)

value: ovarian tumor

tag: pre/post neoadjuvant chemotherapy (nact)

value: post


title: Fast2 15 repl2


title: 69

description: extra cellular RNA


title: CART-19_ Day5_Mouse#24_Spleen [34 5 24S]

description:
34 5 24S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#24_Spleen

value: human CD19-specific CAR T-cells


title: 68

description: extra cellular RNA


title: 1331-32-post


title: Fast2 90 repl1

value: whole body


title: 1331-36-post


title: 64

description: extra cellular RNA


title: Fast2 RT repl2


title: Fast2 RT repl1


title: CART-19_ Day5_Mouse#25_Spleen [35 5 25S]

description:
35 5 25S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#25_Spleen


title: 1331-28-post


title: CART-19_ Day5_Mouse#23_Spleen [33 5 23S]

description:
33 5 23S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#23_Spleen


title: CART-19_ Day5_Mouse#22_Spleen [32 5 22S]

description:
32 5 22S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#22_Spleen


title: hEGFR-T_ Day5_Mouse#30_Colon [30 6 30C]

description:
30 6 30C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#30_Colon

value: Colon


title: 1331-27-post


title: Fast1 90 repl2

value: 90 min. after cold shock


title: 57

description: extra cellular RNA


title: hEGFR-T_ Day5_Mouse#29_Colon [29 6 29C]

description:
29 6 29C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#29_Colon


title: 60

description: extra cellular RNA


title: Fast2 15 repl1

source_name: whole male flies pooled

value: 15 min. after cold shock


title: 59

description: extra cellular RNA


title: 1331-24-post


title: 1331-22-post


title: 54

description: extra cellular RNA


title: CART-19_ Day5_Mouse#21_Spleen [31 5 21S]

description:
31 5 21S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#21_Spleen


title: 58

description: extra cellular RNA

source_name: Plasma


title: Rhesus macaque_05-0041_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493660

source_name: Visual _Cortex

tag: age(weeks)

tag: batch

tag: animal id


title: Fast1 90 repl1


title: 1331-23-post


title: hEGFR-T_ Day5_Mouse#28_Colon [28 6 28C]

description:
28 6 28C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#28_Colon


title: Fast1 15 repl2


title: hEGFR-T_ Day5_Mouse#27_Colon [27 6 27C]

description:
27 6 27C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#27_Colon


title: 1331-21-post


title: 1331-20-post


title: Fast1 15 repl1


title: hEGFR-T_ Day5_Mouse#26_Colon [26 6 26C]

description:
26 6 26C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#26_Colon


title: Fast1 RT repl2

value: without treatment


title: CART-19_ Day5_Mouse#25_Colon [25 5 25C]

description:
25 5 25C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#25_Colon


title: 53

description: extra cellular RNA


title: CART-19_ Day5_Mouse#24_Colon [24 5 24C]

description:
24 5 24C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#24_Colon


title: 51

description: extra cellular RNA


title: Fast1 RT repl1


title: CART-19_ Day5_Mouse#22_Colon [22 5 22C]

description:
22 5 22C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#22_Colon


title: 1331-13-post

source_name: Ovarian Tumor Tissue


title: 1331-18-post


title: 50

description: extra cellular RNA


title: 1331-14-post


title: 39

description: extra cellular RNA


title: 43

description: extra cellular RNA


title: CART-19_ Day5_Mouse#21_Colon [21 5 21C]

description:
21 5 21C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#21_Colon


title: 1331-9-post


title: 36

description: extra cellular RNA


title: CART-19_ Day5_Mouse#23_Colon [23 5 23C]

description:
23 5 23C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#23_Colon


title: 106 DAS_NO_Leaf 8 6n8_R2

city: Berlin

first: Reinhard

last: Kunze

state: Berlin

address: Albrecht-Thaer-Weg 6

department: Institute of Biology

institute: Freie Universität Berlin

description: 150 kg N/ha

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented in 1x Agilent fragmentation buffer (Agilent Technologies catalog number 5188-5242)  and 2x Agilent blocking agent (Agilent Technologies catalog number 5188-5242) following the manufacturers instructions. Hybridization was performed in a Agilent hybridization oven (Agilent Technologies catalog number G2545-90002) at standard conditions as recommended by the manufacturer. Subsequently, microarrays were washed 1 minute with GE Wash Buffer 1 at ambient temperature and 1 minute with GE Wash buffer 2 (Agilent Technologies catalog number 5188-5327) at 37°C.

scan_protocol: Microarrays were scanned immediately after washing with an Agilent High-Resolution Scanner (G2505C) using default settings.

data_processing: The images were processed with the Agilent Feature Extraction software 10.1 using default settings  (protocol GE1_105_Dec08 (Read Only) and GridName US91803681_252963410002_S01_grid (from grid_file)). The resulting processed signals of all individual hybridizations were quantile-normalized using the ranked median quantiles according to Bolstad et al. (2003). Bioinformatics 19, 185-193).

organism: Brassica napus

source_name: B. napus Mozart - NO - leaf 8 - rep2

label_protocol: Cy3-labeled cRNA was synthesized with the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies catalog number 5190-2305) according to the manufacturer's instructions.

growth_protocol: Plants were grown in seasonal climate simulating growth chambers as described in Franzaring et al., Environmental and Experimental Botany 72 (2011) 284-296. Leaf discs from leaf #4 at 78, 85, 92 and 99 day after sowing (DAS) and leaf #8 at 92 and 106 DAS were collected from plants grown under optimum N supply (150 kg N/ha) or mild N deficiency (75 kg N/ha).

extract_protocol: Total RNA was extracted from 500 mg frozen and ground tissue by a hot phenol method (Shirzadegan et al. (1991) Nucleic Acids Res. 19, 6055) and purified with the RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA was photometrically quantified with a NanoPhotometer (Implen, München, Germany) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Leaf senescence was monitored in plants treated with low amounts of N fertilizer (75 kg N/ha) or optimal amounts of N fertilizer (150 kg N/ha).

tag: cultivar

value: Mozart

value: leaf number 8

tag: time (das

value: Days After Sowing):106 DAS

value: optimum N


title: 49

description: extra cellular RNA

tag: age

value: Caucasian


title: 106 DAS_NO_Leaf 8 6n8_R3

description: 150 kg N/ha

source_name: B. napus Mozart - NO - leaf 8 - rep3


title: hEGFR-T_Day2_Mouse#13_Spleen [18 3 15S]

description:
18 3 15S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: 35

description: extra cellular RNA

tag: bmi


title: 1331-12-post


title: hEGFR-T_Day2_Mouse#15_Spleen [20 3 15S]

description:
20 3 15S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: 1331-11-post


title: 34

description: extra cellular RNA

tag: race


title: 30

description: extra cellular RNA


title: 1331-2-post


title: 38

description: extra cellular RNA


title: 99 DAS_NO_Leaf 4 5n4_R3

description: 150 kg N/ha

source_name: B. napus Mozart - NO - leaf 4 - rep3

value: leaf number 4

value: Days After Sowing):99 DAS


title: hEGFR-T_Day2_Mouse#11_Spleen [16 3 11S_rep2]

description:
16 3 11S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

value: control hEGFRT-cells


title: hEGFR-T_Day2_Mouse#12_Spleen [17 3 12S_rep1]

description:
17 3 12S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

value: Spleen


title: 106 DAS_NL_Leaf 8 6_8_R3

description: 75 kg N/ha

source_name: B. napus Mozart - NL - leaf 8 - rep3

value: N deficiency


title: 29

description: extra cellular RNA


title: 106 DAS_NO_Leaf 8 6n8_R1

description: 150 kg N/ha

source_name: B. napus Mozart - NO - leaf 8 - rep1


title: hEGFR-T_Day2_Mouse#14_Spleen [19 3 14S]

description:
19 3 14S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: 99 DAS_NO_Leaf 4 5n4_R2

description: 150 kg N/ha

source_name: B. napus Mozart - NO - leaf 4 - rep2


title: 106 DAS_NL_Leaf 8 6_8_R2

description: 75 kg N/ha

source_name: B. napus Mozart - NL - leaf 8 - rep2


title: 1331-8-post

value: ovarian tumor

value: post


title: 1331-36-pre

value: pre


title: 106 DAS_NL_Leaf 8 6_8_R1

description: 75 kg N/ha

source_name: B. napus Mozart - NL - leaf 8 - rep1


title: 23

description: extra cellular RNA

source_name: Plasma

value: non-Caucasian


title: CART-19_Day2_Mouse#10_Spleen [15 2 10S]

description:
15 2 10S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

value: human CD19-specific CAR T-cells


title: 1331-3-post


title: 99 DAS_NL_Leaf 4 5_4_R3

description: 75 kg N/ha

source_name: B. napus Mozart - NL - leaf 4 - rep3


title: hEGFR-T_Day2_Mouse#12_Spleen [17 3 12S_rep2]

description:
17 3 12S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 99 DAS_NL_Leaf 4 5_4_R2

description: 75 kg N/ha

source_name: B. napus Mozart - NL - leaf 4 - rep2


title: 18

description: extra cellular RNA


title: 17

description: extra cellular RNA


title: 1331-28-pre


title: 1331-1-post


title: CART-19_Day2_Mouse#7_Spleen [12 2 7S_rep2]

description:
12 2 7S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 99 DAS_NO_Leaf 4 5n4_R1

description: 150 kg N/ha

source_name: B. napus Mozart - NO - leaf 4 - rep1


title: CART-19_Day2_Mouse#7_Spleen [12 2 7S_rep1]

description:
12 2 7S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: hEGFR-T_Day2_Mouse#11_Spleen [16 3 11S_rep1]

description:
16 3 11S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 92 DAS_NO_Leaf 8 4n8_R2

description: 150 kg N/ha

value: Days After Sowing):92 DAS


title: CART-19_Day2_Mouse#6_Spleen [11 2 6S_rep2]

description:
11 2 6S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 1331-35-pre

description:
35-pre
Patient 35 data were removed from the analysis because it was not a high grade PSC case.


title: 92 DAS_NO_Leaf 4 4n4_R3

description: 150 kg N/ha


title: 12

description: extra cellular RNA


title: 92 DAS_NO_Leaf 8 4n8_R1

description: 150 kg N/ha


title: 1331-32-pre


title: CART-19_Day2_Mouse#6_Spleen [11 2 6S_rep1]

description:
11 2 6S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 11

description: extra cellular RNA


title: 1331-21-pre


title: hEGFR-T_Day2_Mouse#15_Colon [10 3 15C]

description:
10 3 15C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..

value: Colon


title: 1331-20-pre


title: 92 DAS_NO_Leaf 4 4n4_R1

description: 150 kg N/ha

value: Mozart


title: hEGFR-T_Day2_Mouse#14_Colon [9 3 14C]

description:
9 3 14C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: CART-19_Day2_Mouse#9_Spleen [14 2 9S]

description:
14 2 9S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: hEGFR-T_Day2_Mouse#13_Colon [8 3 13C]

description:
8 3 13C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: 92 DAS_NO_Leaf 8 4n8_R3

description: 150 kg N/ha

value: leaf number 8


title: CART-19_Day2_Mouse#8_Spleen [13 2 8S]

description:
13 2 8S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 1331-12-pre


title: 1331-13-pre


title: 1331-27-pre


title: 92 DAS_NL_Leaf 8 4_8_R2

description: 75 kg N/ha


title: 14

description: extra cellular RNA


title: 99 DAS_NL_Leaf 4 5_4_R1

description: 75 kg N/ha

source_name: B. napus Mozart - NL - leaf 4 - rep1


title: 1331-24-pre


title: 1331-11-pre


title: 13

description: extra cellular RNA


title: 1331-23-pre


title: 15

description: extra cellular RNA


title: 1331-22-pre


title: 1331-3-pre


title: 1331-2-pre


title: 1331-8-pre


title: 9

description: extra cellular RNA


title: 1331-1 pre


title: hEGFR-T_Day2_Mouse#12_Colon [7 3 12C_rep1]

description:
7 3 12C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#7_Colon [2 2 7C_rep2]

description:
2 2 7C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#7_Colon [2 2 7C_rep1]

description:
2 2 7C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#9_Colon [4 2 9C]

description:
4 2 9C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#10_Colon [5 2 10C]

description:
5 2 10C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 92 DAS_NO_Leaf 4 4n4_R2

description: 150 kg N/ha


title: 92 DAS_NL_Leaf 4 4_4_R1

description: 75 kg N/ha


title: 8

description: extra cellular RNA


title: CART-19_Day2_Mouse#6_Colon [1 2 6C_rep1]

description:
1 2 6C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: 1331-18-pre


title: axolotl_resection_48_3

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

institute: University of Pittsburgh

description:
axolotl_surgery_48_3
A48_r4

data_processing:
Tophat 2 was used to align paired-end sequence reads to the GRCm30 genome for mouse and GRCz10 genome for zebrafish29
For mouse and zebrafish samples, Cufflinks was used to estimate gene expression levels in aligned reads and the resulting data was processed with Cuffdiff to identify differentially expressed genes between resected and sham groups at each time point and species
Trinity was used to produce a de novo transcriptome for Axolotl.
RSEM was used to analyzed Axolotl data.
Genome_build: GRCm30 (mouse), GRCz10 (zebrafish); FASTA for Axolotl transcripts is available on the series record.
Supplementary_files_format_and_content: text files with expression values (TPM, FPKM)

organism: Ambystoma mexicanum

source_name: Heart ventricles

extract_protocol:
Total RNA from the lower half of the ventricle of resected and sham hearts was isolated using Trizol at three different time points: 12, 24, and 48 hours post-surgery. Three biological replicates were used for each time point and condition in each species. For neonatal mice and axolotls, each replicate represents myocardium from a single animal. Due to the smaller size of the zebrafish, each biological replicate represents three pooled tissue samples. Poly-adenylated mRNA was isolated using the Wafergen #400047 protocol.
RNA-sequencing libraries were prepared with the IntegenX Directional PrepX mRNA kit. Paired-end (50 base pairs) sequencing was performed using an Illumina HiSeq 2500.

treatment_protocol: neonatal CD1 mice, adult axoltol and zebrafish are subjected to apical resection to remove ~15% of the ventricular mass. Sham surgeries are performed as control.

value: Heart ventricles

tag: strain

value: wild-type, black

tag: timepoint

value: 48 hours post resection

tag: surgical treatment

value: apical resection


title: 1331-14-pre

source_name: Ovarian Tumor Tissue


title: 85 DAS_NO_Leaf 4 3n4_R3

description: 150 kg N/ha

value: leaf number 4

value: Days After Sowing):85 DAS

tag: treatment

value: optimum N


title: B4-1

first: Huachun

last: Cui

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) used for basecaling.
The trimmed reads were aligned to the mm10 genome using Hisat2 software.
The transcript abundances for each sample was estimated with StringTie.
Fragments per kilobase of transcript per million mapped reads (FPKM) value for gene and transcript level were calculated with R package Ballgown.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file including FPKM values for each Sample.

source_name: Alveolar epithelial cells (AECs)

growth_protocol: C57BL/6 mice (8-10 week old) were intratracheally instilled with bleomycin (1.5U/kg body weight) for 2 and 4 weeks, or LPS (2mg/kg body weight) for 1 day. Mouse lungs tissues were collected and digested with tissue digestion buffer. After red blood cell lysis, cells were incubated with biotin-conjugated anti-CD16/32, CD45, CD31, CD90, Ter119 and PDGFRα antibodies followed by depletion with streptavidin-conjugated magnetic beads. After that, primary AECs were isolated using biotin-conjugated anti-EpCAM antibody and streptavidin-conjugated magnetic beads.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Purified AECs were lyzed and stored in Trizol reagent.

value: lung

tag: cell type

value: Alveolar epithelial cells (AECs)

value: Bleomycin for 4 weeks


title: 92 DAS_NL_Leaf 8 4_8_R3

description: 75 kg N/ha

value: N deficiency


title: B2-2

value: Bleomycin for 2 weeks


title: axolotl_resection_48_1

description:
axolotl_surgery_48_1
A48_r1


title: hEGFR-T_Day2_Mouse#12_Colon [7 3 12C_rep2]

description:
7 3 12C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

tag: strain background

tag: genotype/variation

tag: mouse id

tag: treated with

value: control hEGFRT-cells


title: 85 DAS_NL_Leaf 4 3_4_R3

description: 75 kg N/ha

tag: tissue


title: LPS-3

value: LPS for 1 day


title: axolotl_sham_48_3

description:
axolotl_sham_48_3
A48_s3

value: sham surgery


title: 78 DAS_NO_Leaf 4 2n4_R3

description: 150 kg N/ha

value: Mozart

value: Days After Sowing):78 DAS


title: 85 DAS_NL_Leaf 4 3_4_R1

description: 75 kg N/ha


title: 85 DAS_NO_Leaf 4 3n4_R1

description: 150 kg N/ha


title: hEGFR-T_Day2_Mouse#11_Colon [6 3 11C_rep2]

description:
6 3 11C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

value: Colon

tag: time point


title: 92 DAS_NL_Leaf 8 4_8_R1

description: 75 kg N/ha

value: leaf number 8

value: Days After Sowing):92 DAS


title: hEGFR-T_Day2_Mouse#11_Colon [6 3 11C_rep1]

description:
6 3 11C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: axolotl_sham_48_1

description:
axolotl_sham_48_1
A48_s1

value: Heart ventricles

value: wild-type, black

value: 48 hours post resection


title: 78 DAS_NL_Leaf 4 2_4_R3

description: 75 kg N/ha

value: leaf number 4


title: 78 DAS_NL_Leaf 4 2_4_R2

description: 75 kg N/ha


title: 92 DAS_NL_Leaf 4 4_4_R3

description: 75 kg N/ha


title: 1331-9-pre

value: ovarian tumor

tag: pre/post neoadjuvant chemotherapy (nact)

value: pre


title: axolotl_resection_24_3

description:
axolotl_surgery_24_3
A24_r3

value: 24 hours post resection

value: apical resection


title: 92 DAS_NL_Leaf 4 4_4_R2

description: 75 kg N/ha

tag: cultivar

value: N deficiency


title: 78 DAS_NL_Leaf 4 2_4_R1

description: 75 kg N/ha

tag: time (das


title: CART-19_Day2_Mouse#8_Colon [3 2 8C]

description:
3 2 8C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

value: human CD19-specific CAR T-cells


title: B4-4

value: lung

value: Alveolar epithelial cells (AECs)

value: Bleomycin for 4 weeks


title: Con2

value: Control


title: B4-2


title: 85 DAS_NO_Leaf 4 3n4_R2

description: 150 kg N/ha

value: Mozart

value: Days After Sowing):85 DAS

value: optimum N


title: CART-19_Day2_Mouse#6_Colon [1 2 6C_rep2]

description:
1 2 6C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

value: Colon


title: Con1


title: axolotl_sham_24_3

description:
axolotl_sham_24_3
A24_s3

value: Heart ventricles

value: wild-type, black

value: sham surgery


title: hEGFR-T_ Day5_Mouse#27_Spleen [37 6 27S; inflammation]

description:
37 6 27S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#27_Spleen

value: control hEGFRT-cells

value: Spleen


title: 85 DAS_NL_Leaf 4 3_4_R2

description: 75 kg N/ha

value: leaf number 4


title: hEGFR-T_ Day5_Mouse#26_Spleen [36 6 26S; inflammation]

description:
36 6 26S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#26_Spleen


title: B2-3

value: Bleomycin for 2 weeks


title: axolotl_resection_48_2

description:
axolotl_surgery_48_2
A48_r2

value: 48 hours post resection

value: apical resection


title: B2-1

value: lung


title: axolotl_resection_12_3

description:
axolotl_surgery_12_3
A12_r3

value: 12 hours post resection


title: axolotl_resection_12_2

description:
axolotl_surgery_12_2
A12_r2


title: 78 DAS_NO_Leaf 4 2n4_R2

description: 150 kg N/ha

value: Days After Sowing):78 DAS


title: Health_rep6

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Health

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

extract_protocol: Phenol/Chloroform precipitation

tag: cell-type

value: peripheral blood mononuclear cells


title: hEGFR-T_ Day5_Mouse#30_Spleen [40 6 30S; inflammation]

description:
40 6 30S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#30_Spleen


title: CART-19_ Day5_Mouse#22_Spleen [32 5 22S; inflammation]

description:
32 5 22S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#22_Spleen

value: human CD19-specific CAR T-cells


title: LPS-1

value: Alveolar epithelial cells (AECs)

value: LPS for 1 day


title: CART-19_ Day5_Mouse#21_Spleen [31 5 21S; inflammation]

description:
31 5 21S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#21_Spleen


title: 78 DAS_NO_Leaf 4 2n4_R1

description: 150 kg N/ha

value: Mozart

value: optimum N


title: LPS-2


title: Con3

value: Control


title: axolotl_sham_12_3

description:
axolotl_sham_12_3
A12_s3

value: Heart ventricles

value: wild-type, black

value: sham surgery


title: axolotl_sham_48_2

description:
axolotl_sham_48_2
A48_s2


title: hEGFR-T_ Day5_Mouse#28_Spleen [38 6 28S; inflammation]

description:
38 6 28S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#28_Spleen

value: control hEGFRT-cells

value: Spleen


title: hEGFR-T_ Day5_Mouse#29_Spleen [39 6 29S; inflammation]

description:
39 6 29S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#29_Spleen


title: axolotl_sham_12_2

description:
axolotl_sham_12_2
A12_s2


title: axolotl_resection_24_2

description:
axolotl_surgery_24_2
A24_r2

value: 24 hours post resection


title: Health_rep5


title: axolotl_sham_12_1

description:
axolotl_sham_12_1
A12_s1


title: Malaria_rep6

source_name: Malaria


title: Malaria_rep5


title: hEGFR-T_ Day5_Mouse#26_Colon [26 6 26C; inflammation]

description:
26 6 26C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#26_Colon

value: Colon


title: hEGFR-T_ Day5_Mouse#27_Colon [27 6 27C; inflammation]

description:
27 6 27C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#27_Colon


title: axolotl_sham_24_2

description:
axolotl_sham_24_2
A24_s2


title: axolotl_resection_24_1

description:
axolotl_surgery_24_1
A24_r1

value: apical resection


title: CART-19_ Day5_Mouse#25_Spleen [35 5 25S; inflammation]

description:
35 5 25S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#25_Spleen


title: Malaria_rep4


title: axolotl_sham_24_1

description:
axolotl_sham_24_1
A24_s1


title: COPD_rep6

source_name: COPD


title: African Green Monkey_10015_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493634

organism: Chlorocebus aethiops

source_name: Visual _Cortex

tag: age(weeks)

tag: batch

tag: animal id

tag: Sex

value: M


title: hEGFR-T_ Day5_Mouse#30_Colon [30 6 30C; inflammation]

description:
30 6 30C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#30_Colon


title: CART-19_ Day5_Mouse#23_Spleen [33 5 23S; inflammation]

description:
33 5 23S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#23_Spleen


title: African Green Monkey_10019_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493638

value: F


title: CART-19_ Day5_Mouse#23_Colon [23 5 23C; inflammation]

description:
23 5 23C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#23_Colon


title: CART-19_ Day5_Mouse#24_Colon [24 5 24C; inflammation]

description:
24 5 24C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#24_Colon


title: hEGFR-T_ Day5_Mouse#29_Colon [29 6 29C; inflammation]

description:
29 6 29C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#29_Colon


title: hEGFR-T_ Day5_Mouse#28_Colon [28 6 28C; inflammation]

description:
28 6 28C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 control hEGFR-T-cells..

source_name: hEGFR-T_ Day5_Mouse#28_Colon


title: CART-19_ Day5_Mouse#24_Spleen [34 5 24S; inflammation]

description:
34 5 24S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#24_Spleen


title: African Green Monkey_10018_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493637


title: axolotl_resection_12_1

description:
axolotl_surgery_12_1
A12_r1

source_name: Heart ventricles

tag: strain

tag: timepoint

value: 12 hours post resection

tag: surgical treatment


title: CART-19_ Day5_Mouse#25_Colon [25 5 25C; inflammation]

description:
25 5 25C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#25_Colon

tag: strain background

value: human CD19-specific CAR T-cells


title: African Green Monkey_10016_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493635


title: Pneumonia_rep6

source_name: Pneumonia

value: peripheral blood mononuclear cells


title: African Green Monkey_10017_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493636


title: African Green Monkey_10014_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493633


title: African Green Monkey_10013_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493632


title: CART-19_ Day5_Mouse#21_Colon [21 5 21C; inflammation]

description:
21 5 21C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#21_Colon

tag: genotype/variation


title: CART-19_ Day5_Mouse#22_Colon [22 5 22C; inflammation]

description:
22 5 22C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient five days after adoptive transfer of 3E+06 CART-19 T-cells.

source_name: CART-19_ Day5_Mouse#22_Colon

tag: mouse id


title: Pneumonia_rep5


title: African Green Monkey_10012_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493631


title: hEGFR-T_Day2_Mouse#15_Spleen [20 3 15S; inflammation]

description:
20 3 15S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..

tag: treated with


title: COPD_rep4


title: African Green Monkey_10011_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493630


title: Health_rep4

source_name: Health


title: Pneumonia_rep4


title: African Green Monkey_10010_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493629


title: Malaria_rep3

source_name: Malaria


title: Health_rep3


title: COPD_rep5


title: African Green Monkey_10009_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493628


title: African Green Monkey_10008_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493627


title: hEGFR-T_Day2_Mouse#14_Spleen [19 3 14S; inflammation]

description:
19 3 14S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..

tag: tissue


title: hEGFR-T_Day2_Mouse#12_Spleen [17 3 12S_rep2; inflammation]

description:
17 3 12S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

tag: time point


title: COPD_rep3


title: African Green Monkey_10007_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493626


title: hEGFR-T_Day2_Mouse#13_Spleen [18 3 15S; inflammation]

description:
18 3 15S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: hEGFR-T_Day2_Mouse#11_Spleen [16 3 11S_rep1; inflammation]

description:
16 3 11S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10004_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493623


title: CART-19_Day2_Mouse#9_Spleen [14 2 9S; inflammation]

description:
14 2 9S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10002_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493621


title: hEGFR-T_Day2_Mouse#11_Spleen [16 3 11S_rep2; inflammation]

description:
16 3 11S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: Pneumonia_rep2


title: Health_rep1


title: COPD_rep2


title: Pneumonia_rep1


title: COPD_rep1


title: Health_rep2


title: Malaria_rep2


title: African Green Monkey_10019_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493619

source_name: Dorsolateral Prefrontal_Cortex


title: Malaria_rep1


title: CART-19_Day2_Mouse#7_Spleen [12 2 7S_rep1; inflammation]

description:
12 2 7S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#7_Spleen [12 2 7S_rep2; inflammation]

description:
12 2 7S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#6_Spleen [11 2 6S_rep2; inflammation]

description:
11 2 6S_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10005_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493624


title: African Green Monkey_10001_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493620


title: CART-19_Day2_Mouse#10_Spleen [15 2 10S; inflammation]

description:
15 2 10S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: CART-19_Day2_Mouse#8_Spleen [13 2 8S; inflammation]

description:
13 2 8S
One of five biological replicates. Total RNA extracted from spleen of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10003_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493622


title: hEGFR-T_Day2_Mouse#12_Spleen [17 3 12S_rep1; inflammation]

description:
17 3 12S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10018_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493618


title: African Green Monkey_10006_Visual_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493625


title: African Green Monkey_10017_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493617


title: hEGFR-T_Day2_Mouse#15_Colon [10 3 15C; inflammation]

description:
10 3 15C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: CART-19_Day2_Mouse#6_Spleen [11 2 6S_rep1; inflammation]

description:
11 2 6S_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10014_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493614


title: hEGFR-T_Day2_Mouse#14_Colon [9 3 14C; inflammation]

description:
9 3 14C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: hEGFR-T_Day2_Mouse#13_Colon [8 3 13C; inflammation]

description:
8 3 13C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 control hEGFR-T-cells..


title: hEGFR-T_Day2_Mouse#12_Colon [7 3 12C_rep2; inflammation]

description:
7 3 12C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: HR-27-V1

city: Haifa

first: Shai

middle: S

last: Shen-Orr

address: 1st Efron Street

department: Immunology

country: Israel

institute: Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion

description: PBMC from CD patient at baseline, Responder at week 14

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain  Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre- mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls  (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Fragmented and labeled sscDNA were diluted in hybridization buffer at a concentration of 23 ng/ul for a 2.3 ug total and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Human Clariom S was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain  Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files, which were used for subsequent analysis.

data_processing: Preprocessing was perfomed in R using the oligo package. Raw CEL files were summarized and normalized using RMA and quantile normalization (oligo::rma), using the probe definition and annotation packages pd.clariom.s.human and clariomshumantranscriptcluster.db

source_name: peripheral blood mononuclear cells

label_protocol: The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT Plus Kit (Affymetrix, Santa Clara, CA). With the same kit was synthesized the sense strand cDNA before to be fragmented and labeled. All steps of the labeling protocol were performed as suggested by Affymetrix, starting from 5.5 ug of ssDNA. Each eukaryotic GeneChip® probe array contains probe sets for several B. subtilis genes that are absent in the samples analyzed (lys, phe, thr, and dap). This Poly-A RNA Control Kit contains in vitro synthesized, polyadenylated transcripts for these B. subtilis genes that are pre-mixed at staggered concentrations to allow GeneChip® probe array users to assess the overall success of the assay. Poly-A RNA Controls final concentration in each target are lys 1:100,000, phe 1:50,000, thr 1:25,000 and dap 1:6,667.

extract_protocol: Total RNA was extracted from Paxgene-cryopreserved whole blood using PreAnalytiX standard protocol. Quality was verified using Agilent Bioanalyzer TapeStation

tag: disease state

tag: treatment

tag: patient

tag: time

tag: status

value: Responder

tag: crp

tag: hbi

tag: bmi


title: HR-40-V1


title: HR-28-V1


title: HR-24-V1


title: HR-26-V1

description: PBMC from CD patient at baseline, Non-responder at week 14

value: Non-responder


title: hEGFR-T_Day2_Mouse#12_Colon [7 3 12C_rep1; inflammation]

description:
7 3 12C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10013_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493613

tag: age(weeks)

tag: batch

tag: animal id

tag: Sex


title: African Green Monkey_10012_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493612


title: hEGFR-T_Day2_Mouse#11_Colon [6 3 11C_rep2; inflammation]

description:
6 3 11C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

tag: strain background

tag: genotype/variation


title: African Green Monkey_10011_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493611


title: hEGFR-T_Day2_Mouse#11_Colon [6 3 11C_rep1; inflammation]

description:
6 3 11C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

tag: treated with

tag: mouse id


title: African Green Monkey_10010_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493610


title: HR-23-V1


title: African Green Monkey_10015_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493615


title: African Green Monkey_10016_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493616


title: CART-19_Day2_Mouse#10_Colon [5 2 10C; inflammation]

description:
5 2 10C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.

tag: tissue

tag: time point


title: African Green Monkey_10009_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493609


title: CART-19_Day2_Mouse#9_Colon [4 2 9C; inflammation]

description:
4 2 9C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: HR-39-V1

tag: disease state

tag: treatment


title: African Green Monkey_10008_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493608


title: HR-20-V1

tag: patient

tag: time


title: African Green Monkey_10007_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493607


title: CART-19_Day2_Mouse#7_Colon [2 2 7C_rep2; inflammation]

description:
2 2 7C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10006_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493606


title: African Green Monkey_10005_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493605


title: African Green Monkey_10004_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493604


title: HR-37-V1

description: PBMC from CD patient at baseline, Responder at week 14

tag: status

tag: crp


title: CART-19_Day2_Mouse#6_Colon [1 2 6C_rep2; inflammation]

description:
1 2 6C_rep2
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10003_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493603


title: HR-35-V1

tag: hbi

tag: bmi


title: CART-19_Day2_Mouse#6_Colon [1 2 6C_rep1; inflammation]

description:
1 2 6C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10002_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493602

tag: age(weeks)

tag: batch


title: CART-19_Day2_Mouse#8_Colon [3 2 8C; inflammation]

description:
3 2 8C
One of five biological replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: HR-22-V1


title: CART-19_Day2_Mouse#7_Colon [2 2 7C_rep1; inflammation]

description:
2 2 7C_rep1
One of five biological replicates and one of two technical replicates. Total RNA extracted from colon of human CD19 transgenic hemizygous recipient two days after adoptive transfer of 3E+06 CART-19 T-cells.


title: African Green Monkey_10001_Dorsolateral Prefrontal_Cortex

description:
Illumina TruSeq Stranded Total RNA Ribo-Zero
US-1493601

tag: animal id

tag: Sex


title: HR-30-V1

description: PBMC from CD patient at baseline, Non-responder at week 14


title: HR-33-V1


title: HR-31-V1


title: HR-29-V1


title: Pneumonia_rep3

tag: cell-type


title: HR-42-V1


title: HR-36-V1


title: HR-48-V1


title: HR-46-V1


title: HCC5_3DPDX_WES

status: Public on Jan 31 2018

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

description: liver

data_processing:
Library strategy: Whole exome sequencing
After checking the read quality by FastQC, the low-quality base below Q20 were trimmed using Cutadapt.
High quality reads were then aligned to the human reference genome hg19 using Burrows Wheeler Aligner (BWA) with minimum seed length of 45.
Duplicated reads were further removed using MarkDuplicates.jar in PicardTools.
For the read alignment, the suspicious intervals were examined for the more accurate realignment using RealignerTargetCreator tool in GenomeAnalysisTK and Mills-and-1000G-gold.standard-INDELs.hg19 was referred as the known indel set.
Base quality score recalibration (BQSR) process was done to adjust the quality score using BaseRecalibrator Tool in GATK. For the realigned and recalibrated reads, variants were called using UnifiedGenotyper tool in GATK.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: vcf files containing genetic variants are being submitted to an NCBI Variation database.

source_name: Patient-derived HCC

extract_protocol: The quality and quantity of purified DNA were assessed by fluorometry (Qubit, Invitrogen) and gel electrophoresis. Briefly, 500ng of genomic DNA from each samples were fragmented by acoustic shearing on a Covaris S2 instrument. Fragments of 150–300 bp were ligated to Illumina's adapters and PCR-amplified. The samples were concentrated to 300 ng in 3.4 μl DW using a Speedvac machine (Thermo Scientific) and hybridized with RNA probes, SureSelect XT Human All Exon V5 Capture library for 16-24 h at 65°C. After hybridization, the captured targets were pulled down by biotinylated probe/target hybrids using streptavidin-coated magnetic beads (Dynabeads My One Streptavidine T1; Life Technologies Ltd.) and buffers. The selected regions were then PCR-amplified using Illumina PCR primers. Libraries were quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies) and KAPA Library Quantification Kit (KK4824, Kapa Biosystems). The resulting purified libraries were applied to an Illumina flow cell for cluster generation and sequenced using 100 bp paired-end reads on an Illumina Hiseq2500 sequencer by following the manufacturer's protocols. Image analysis were performed using the HiSeq control Software version 1.8.4.

treatment_protocol: No treatment.

tag: tissue origin

value: hepatocellular carcinoma (HCC)

tag: sample type

tag: line


title: HCC11_3DPDX_WES

description: liver


title: HCC6_3DPDX_WES

description: liver


title: HCC8_3DPDX_WES

description: liver


title: HCC4_3DPDX_WES

description: liver


title: HCC13_3DPDX_WES

description: liver


title: HCC7_3DPDX_WES

description: liver


title: HCC14_3DPDX_WES

description: liver


title: HR-32-V1


title: HCC14_PDX_WES

description: liver


title: HCC2_3DPDX_WES

description: liver


title: HR-44-V1


title: HR-47-V1


title: HCC1_3DPDX_WES

description: liver


title: HCC6_PDX_WES

description: liver


title: HCC4_PDX_WES

description: liver


title: HCC13_PDX_WES

description: liver


title: HCC8_PDX_WES

description: liver


title: HCC7_PDX_WES

description: liver


title: HCC11_PDX_WES

description: liver


title: HCC3_3DPDX_WES

description: liver


title: HCC1_PDX_WES

description: liver


title: HCC5_PDX_WES

description: liver


title: HCC3_PDX_WES

description: liver


title: HCC2_PDX_WES

description: liver