title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_D10_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C9_AD001_indexed

status: Public on Aug 26 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: AI

tag: Sex

value: male

tag: age

tag: strain


title: lymphocytic choriomeningitis virus infected conventional effector memory T cells replicate 1

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
LCMV.ConvMem.1
bulk mRNA
experiment_1_bulk_rnaseq_norm_counts.txt
experiment_1_bulk_rnaseq_raw_counts.txt

library_source: transcriptomic

data_processing:
Illumina bcl2fastq (bulk RNAseq) or 10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Read mapping was performed via Hisat2 (Bulk RNAseq) or Cell Ranger count (scRNAseq) using the mouse reference genome (mm10).
Gene level quantification was completed using Subread featureCounts (bulk RNASeq) or Cell Ranger count software.
Raw counts data was imported into R for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample

molecule: total RNA

source_name: CD8-positive T cell precursors

growth_protocol: Mice were infected with LCMV-Arm intraperitoneally and enrichment of antigen-specific CD8 T cell precursors or LCMV-specific CD8 T cells at memory time points was performed.

extract_protocol:
RNA was isolated using Qiagen RNeasy plus mini kit (Bulk RNAseq) or cells were processed by FACS and supplied as input to the 10 Genomics single cell protocol (scRNAseq).
Sequencing libraries were created using TruSeq Stranded mRNA Library Prep Kit (Bulk RNA-seq) or the Chromium Single Cell 3’ Gene Expression Kit v2 (scRNA-seq) and were prepared for sequencing using standard Illumina protocols.
Bulk RNAseq and (single cell) scRNAseq

tag: tissue

value: spleen

tag: timepoint

value: 90 days post infection

tag: cell type (subset)

value: conventional effector memory T cells


title: lymphocytic choriomeningitis virus infected central memory T cells replicate 2

description:
LCMV.CM.2
bulk mRNA
experiment_1_bulk_rnaseq_norm_counts.txt
experiment_1_bulk_rnaseq_raw_counts.txt

value: central memory T cells


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C9_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C8_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C8_AD006_indexed


title: lymphocytic choriomeningitis virus infected central memory T cells replicate 3

description:
LCMV.CM.3
bulk mRNA
experiment_1_bulk_rnaseq_norm_counts.txt
experiment_1_bulk_rnaseq_raw_counts.txt


title: CS2

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: RPE of mice exposed to cigarette smoke

data_processing:
Fastq files were generated from reads passing chastity filter and used for further analysis. Illumina adapter, polyA, and polyT sequence trimming was performed with Trimmomatic v0.36.
Transcript level quantitation was performed using Kallisto v0.45.0 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl ftp site. Gene level quantification was generated by summarization of the transcript level quantitation using tximport v1.8.0 with the option “countFromAbundance=lengthScaledTPM”. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR.
Gene-level differential expression analysis was performed between control (Air) and cigarette smoking (CS) treatment using the exact test from the edgeR v3.26.6 package.
Genome_build: GRCm38.p6 with Ensembl v98
Supplementary_files_format_and_content: counts, normalized cpm

molecule: polyA RNA

source_name: RPE/choroid

extract_protocol:
Total RNA from mouse RPE/choroid using triplicate biological replicates for air or smoking were isolated using RNeasy Mini Kit (Qiagen, Valencia, CA), with on-column DNA digestion by RNase-free DNase, following the manufacturer's instructions. RNA integrity was verified using Agilent 4200 TapeStation (Agilent, Santa Clara, CA).
Stranded RNA-seq library construction was carried out using 100 ng of RNA with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA). Libraries were paired-end sequenced to 126 bases using a HiSeq 2500 Sequencing System (Illumina, San Diego, CA).

treatment_protocol: An equal number of 2-month female and male C57BL/6J mice (RD8 negative) were placed in a smoking chamber for 2.5 hours per day, 5 days per week for 6 months, as described previously(28), or raised in a filtered air environment for 6 months.

tag: exposure

value: cigarette smoking

value: 8 month


title: Air2

description: RPE of mice exposed to filtered air

value: filtered air


title: lymphocytic choriomeningitis virus infected central memory T cells replicate 1

description:
LCMV.CM.1
bulk mRNA
experiment_1_bulk_rnaseq_norm_counts.txt
experiment_1_bulk_rnaseq_raw_counts.txt


title: CS3

description: RPE of mice exposed to cigarette smoke


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C6_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C8_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C9_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C7_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C7_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C8_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C7_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C7_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C8_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C6_AD010_indexed


title: Lung, 9527+oil, 118M-1-17

city: New Orleans

first: Yao-Zhong

last: Liu

state: LA

address: 1440 Canal Street, Suite 1610

department: Biostatistics and Data Science

institute: Tulane University School of Public Health and Tropical Medicine

data_processing:
The transcript quantification analysis of fastq data was performed using Salmon (Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Specifically, an index file was first built using the reference transcriptome for mouse (Mus_musculus.GRCm38.cdna.all.fa). Then fastq data of each sample was aligned to the index file for transcript quantification using “salmon quant” command, which resulted in a quant.sf file containing count information for each transcript.
The resultant files, quant.sf files, for all the samples were then grouped and analyzed together using R and Bioconductor’s tximport package (Soneson C, Love MI, Robinson MD (2015). “Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences.” F1000Research, 4. doi: 10.12688/f1000research.7563.1.), which generated a count matrix, with rows as transcript IDs and columns as specific samples.
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: csv files include transcript count for each sample

source_name: lung

extract_protocol:
Total RNA from mouse lung was extracted using Qiagen RNAesy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 18 WT (wild type) female mice (3 per treatment group)  and 18 WT male mice (3 per treatment group) treated with saline, oil, Corexit 9500, Corexit 9527, 9500+oil, 9527+oil on day 0, 7 and 13 (@ concentration of 0.1 WAF) before euthanasia on day 14.

tag: gender

tag: treatment

value: lung


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C6_AD006_indexed


title: CS1

description: RPE of mice exposed to cigarette smoke


title: Lung, 9500+oil, 118M-1-15


title: Lung, 9500+oil, 118M-1-14


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C6_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C5_AD008_indexed


title: Lung, 9527, 118M-1-11


title: Lung, 9500+oil, 118M-1-13


title: Lung, 9527, 118M-1-12


title: Air1

description: RPE of mice exposed to filtered air


title: Lung, 9527, 118M-1-10


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C6_AD004_indexed


title: Lung, 9527+oil, 118M-1-16


title: Lung, 9527+oil, 118M-1-18


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C5_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C5_AD006_indexed


title: Lung, 9500, 118M-1-9


title: Lung, oil, 118M-1-6

value: oil


title: Lung, 9500, 118M-1-8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD002_indexed


title: Lung, oil, 118M-1-5


title: Lung, saline, 118M-1-3

value: saline


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C5_AD001_indexed


title: Lung, oil, 118M-1-4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD008_indexed


title: Lung, saline, 118M-1-2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD004_indexed


title: Lung, 9527+oil, 118-1-17

value: female


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD001_indexed


title: Lung, 9500+oil, 118-1-13


title: Lung, saline, 118M-1-1


title: Lung, 9527+oil, 118-1-16


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C4_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C3_AD012_indexed


title: Lung, 9500+oil, 118-1-14


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C3_AD008_indexed


title: Lung, 9500+oil, 118-1-15


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C3_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C3_AD010_indexed


title: Lung, 9500, 118M-1-7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C3_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD012_indexed


title: Lung, 9527, 118-1-12


title: Lung, 9527, 118-1-11


title: Lung, 9500, 118-1-9


title: Lung, 9527, 118-1-10


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C5_AD002_indexed


title: Lung, 9500, 118-1-8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD006_indexed


title: Lung, oil, 118-1-6


title: Lung, 9500, 118-1-7


title: Lung, 9527+oil, 118-1-18


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD006_indexed


title: Lung, oil, 118-1-5


title: Lung, saline, 118-1-2


title: Lung, saline, 118-1-3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C1_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C1_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C1_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C1_AD010_indexed


title: Lung, saline, 118-1-1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD008_indexed


title: whole blood from patient with neutropenic fever_46

city: Solna

first: Anna

last: Berggren

address: Avdelning för Infektion, Broliden/Färnert gruppVisionsgatan 4J7:20

department: Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
A standard alignment using STAR (v2.6.1).
SeqMonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) software was used to perform datanalysis.
All BAM files were loaded to SeqMonk. Samples were grouped and RNA-Seq quantitation pipeline was used.
DESeq analysis pipeline was used to list differencially expressed genes.
Supplementary_files_format_and_content: Annotated probe reports from SeqMonk were saved as .txt files. These text files list the number of differencially expressed genes at FDR cutoff value <=0.05 and 1.5 fold change.

organism: Homo sapiens

source_name: patient with bacteria_blood

growth_protocol: No growth performed

extract_protocol:
Blood was collected into PAXgene tubes and stored in -18°C. The tubes were thawed at room temperature over night and then centrifuged for 10 minutes at 3000 x g using a swing-out rotor. Supernatant was removed. 4 ml H2O was added to the pellet, the tube was then vortexed until the pellet was visibly dissolved. Tubes were centrifuged for 10 minutes at 3000 x g using a swing-out rotor, supernatant was discarded. 350 µl resuspension buffer (BR1) was added followed by vortex until the pellet was visibly dissolved. Samples were then loaded into the QIAcube shaker and the protocol “PAXgene Blood RNA Part A” was run followed by the protocol “PAXgene Blood RNA Part B”. (PAXgene® Blood RNA Kit Handbook, PreAnalytiX, Qiagen). The concentration (OD260) and purity (OD260/280 ratio) of extracted total RNA was measured using NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, MA, USA).  Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA, USA) was used to assess the RNA integrity using the RNA ScreenTape assay according to the manufacturer’s instructions.
Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions. To construct libraries suitable for Illumina sequencing the Illumina TruSeq Stranded mRNA sample preparation protocol which includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries was used. The yield and quality of the amplified libraries was analysed using Qubit by Thermo Fisher and the Agilent Tapestation. The indexed cDNA libraries were normalised and combined and the pools were sequenced on the NextSeq 550 for a 75-cycle v2 sequencing run generating 75 bp single-end reads. Basecalling and demultiplexing was performed using CASAVA software with default settings generating Fastq files for further downstream mapping and analysis."

treatment_protocol: No treatment performed

tag: type of infection

value: Patient with bacteria

value: blood


title: whole blood from patient with neutropenic fever_66

source_name: patient with bactera_blood

value: Patient with bactera


title: whole blood from patient with neutropenic fever_233

source_name: patient with co-infection_blood

value: Patient with co-infection


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD008_indexed

value: AI


title: whole blood from patient with neutropenic fever_59


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C3_AD002_indexed

value: male


title: whole blood from patient with neutropenic fever_25


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C1_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD007_indexed


title: whole blood from patient with neutropenic fever_240

source_name: patient with unknown etiology_blood

value: Patient with unknown etiology


title: whole blood from patient with neutropenic fever_238


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD002_indexed


title: Lung, oil, 118-1-4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD001_indexed


title: whole blood from patient with neutropenic fever_237


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C2_AD004_indexed


title: whole blood from patient with neutropenic fever_213


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD006_indexed


title: whole blood from patient with neutropenic fever_234


title: whole blood from patient with neutropenic fever_236


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C12_AD012_indexed


title: whole blood from patient with neutropenic fever_208


title: whole blood from patient with neutropenic fever_206


title: whole blood from patient with neutropenic fever_205


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD012_indexed


title: whole blood from patient with neutropenic fever_204


title: whole blood from patient with neutropenic fever_84


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD001_indexed


title: whole blood from patient with neutropenic fever_239


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C11_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD010_indexed


title: whole blood from patient with neutropenic fever_76


title: whole blood from patient with neutropenic fever_69


title: whole blood from patient with neutropenic fever_30


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD008_indexed


title: whole blood from patient with neutropenic fever_12


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD008_indexed


title: whole blood from patient with neutropenic fever_23


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C10_AD001_indexed


title: whole blood from patient with neutropenic fever_20


title: whole blood from patient with neutropenic fever_3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD012_indexed


title: whole blood from patient with neutropenic fever_13


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD010_indexed


title: whole blood from patient with neutropenic fever_78


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD004_indexed


title: whole blood from patient with neutropenic fever_248

source_name: patient with respiratory virus _blood

value: Patient with respiratory virus


title: whole blood from patient with neutropenic fever_243

source_name: patient with respiratory virus_blood


title: whole blood from patient with neutropenic fever_224


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B8_AD004_indexed


title: whole blood from patient with neutropenic fever_225


title: whole blood from patient with neutropenic fever_74


title: whole blood from patient with neutropenic fever_227


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD006_indexed


title: whole blood from patient with neutropenic fever_223


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD002_indexed


title: whole blood from patient with neutropenic fever_28


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B9_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B8_AD007_indexed


title: whole blood from patient with neutropenic fever_209


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B8_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B8_AD001_indexed


title: whole blood from patient with neutropenic fever_56


title: whole blood from patient with neutropenic fever_50


title: whole blood from patient with neutropenic fever_5


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B7_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B7_AD007_indexed


title: whole blood from patient with neutropenic fever_21


title: whole blood from patient with neutropenic fever_18


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B7_AD004_indexed


title: whole blood from patient with neutropenic fever_16


title: seq006431

city: San Diego

first: Samuel

last: Levy

state: California

address: 10578 Science Center Drive, Suite 210

institute: Bluestar Genomics

data_processing:
Basecalls were converted using bcl2fastq2.
Sequencing reads were aligned to the hg19 reference genome using BWA-MEM with default parameters. BAM files containing the locations of aligned reads were filtered for poorly mapped (MAPQ < 30) and not properly paired reads. Chromatin states were determined with ChromHMM using all ChIPseq files as input.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (gene counts per gene for 5hmC) and bed files (chromatin state coordinates) : Format for gene counts file (chrID, begin, end, gene symbol, length, strand, number reads) and format for chromatin state coordinates (chrID, begin, end, state)

extract_protocol:
Chromatin was extracted from primary PDAC tissues that were formaldehyde fixed by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Immunoprecapitated chromatin was subjected to RNase and proteinase K treatment, followed by reverse-crosslinking and DNA isolation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs using the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

tag: cohort

value: Tissue

tag: chip antibody


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B7_AD012_indexed


title: seq006430


title: seq006429


title: whole blood from patient with neutropenic fever_86


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B6_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B7_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B6_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD012_indexed


title: seq006428


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B8_AD010_indexed


title: seq006427


title: seq006426


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD006_indexed


title: whole blood from patient with neutropenic fever_6


title: seq006424


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B6_AD004_indexed


title: seq006425


title: seq006423


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B6_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_C6_AD002_indexed


title: seq006421


title: seq006422


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD001_indexed


title: seq006419


title: seq006420


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B5_AD008_indexed


title: seq000395

data_processing:
Library strategy: 5hmC
Basecalls were converted using bcl2fastq2.
Sequencing reads were aligned to the hg19 reference genome using BWA-MEM with default parameters
Gene-based counting of 5hmC reads were determine by defining genes bodies from transcription start to transcription stop, coordinates obtained from the genome annotation version XXXX
Prior to identifying chromatin states, BAM files containing the locations of aligned reads were filtered for poorly mapped (MAPQ < 30) and not properly paired reads. Chromatin states were determined using ChromHMM.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (gene counts per gene for 5hmC) and bed files (chromatin state coordinates) : Format for gene counts file (chrID, begin, end, gene symbol, length, strand, number reads) and format for chromatin state coordinates (chrID, begin, end, state)

extract_protocol:
Peripheral blood was collected in Streck Blood Collection Tubes and processed within 24 hours of collection. This involve two centriguations to isolated the plasma. Cell free DNA was extracted from plasma using the Qiasymphony cell free DNA extraction automation.
10 ng of cell free DNA was used as input to a click chemistry enrichment protocol to identify DNA fragments bearing a 5-hydromethylcytosine (5hmC) residue. The biotinylation of DNA fragments contain 5hmC residue was enriched using strepavidin coated magnetic beads.


title: seq000396


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B2_AD006_indexed


title: seq000402


title: seq006418


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B4_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B3_AD007_indexed


title: seq000408


title: seq000409


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B3_AD006_indexed


title: seq000586


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B4_AD007_indexed


title: seq000588


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B4_AD006_indexed


title: seq000587


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B4_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B3_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B2_AD008_indexed


title: seq000601


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B3_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B2_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B4_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B4_AD002_indexed


title: seq000603


title: seq000635


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B2_AD007_indexed


title: seq000634


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B2_AD012_indexed


title: seq000697


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B1_AD012_indexed


title: seq000700


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B1_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B1_AD007_indexed


title: seq-wph4am

source_name: Non-cancer

value: Validation


title: seq-pwk9n8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B1_AD010_indexed


title: seq-jht3md


title: seq-eka36c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD004_indexed


title: seq-jakrc4


title: seq000211


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD007_indexed


title: seq-c69mn8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B2_AD010_indexed


title: seq000215


title: seq000643


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD008_indexed


title: seq000636


title: seq000698


title: seq000209


title: seq000203


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B11_AD007_indexed


title: seq000201


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B12_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B11_AD004_indexed


title: seq000198


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B11_AD012_indexed


title: seq000195


title: seq-69yt8b


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B11_AD006_indexed


title: seq-t8vc4b


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B10_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B1_AD002_indexed


title: seq-8p34r6


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B11_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B10_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B10_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B10_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B11_AD008_indexed


title: seq-c4dw3k


title: seq-8ht7yb


title: seq-eubvh4


title: seq-6dutec


title: seq-ta6mc7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B10_AD008_indexed


title: seq-b98dmh


title: seq-6upmja


title: seq-vct8jk


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A9_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A9_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B10_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A9_AD002_indexed


title: seq-89pka4


title: seq-jk8r63


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A9_AD001_indexed


title: seq-ucakp3


title: seq-7rxekh


title: seq-rmcpt3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A8_AD004_indexed


title: seq-7hxea4


title: seq-p4fb9n


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A9_AD008_indexed


title: seq-y3b8xc


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A9_AD004_indexed


title: seq-ft49nk


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A8_AD008_indexed


title: seq-bfepj8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A7_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A8_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A8_AD007_indexed


title: seq-mh8jad


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A8_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A7_AD002_indexed


title: seq-dcavnf


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A6_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A7_AD007_indexed


title: seq-7pvt3b


title: seq-93nfwh


title: seq-brt9pj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A7_AD012_indexed


title: seq-kpauej


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A6_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A7_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A6_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A8_AD010_indexed


title: seq-7jwp6b


title: seq-7bumr3


title: seq-xtk7u3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A5_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A6_AD001_indexed


title: seq-4yum9c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A6_AD006_indexed


title: seq-86xj9d


title: seq-vnyc7j


title: seq-hfared


title: seq-javm36


title: seq-ha7b4n


title: seq-v43nrf


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A5_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A5_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A5_AD004_indexed


title: seq-am7c3k


title: seq-ukr68h


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A4_AD006_indexed


title: seq-6apdt4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A5_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A4_AD012_indexed


title: seq-bxpm63


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A4_AD001_indexed


title: seq-awnb4f


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A4_AD002_indexed


title: seq-enmdch


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A4_AD004_indexed


title: seq-8tw6nj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A5_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A3_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A3_AD010_indexed


title: seq-jxdb34


title: seq-fj8ekp


title: seq-atc4h7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A3_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A3_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_B1_AD006_indexed


title: seq-9akbx4


title: seq-rdfeaj


title: seq-vwap9c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD008_indexed


title: seq000485


title: seq000466


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A3_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD012_indexed


title: seq-krh69c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD007_indexed


title: seq-fetavj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD004_indexed


title: seq-xy6a9k


title: seq-8krnea


title: seq-8rpcfb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A1_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD002_indexed


title: seq-hdtark


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A3_AD006_indexed


title: seq-dmrpv6


title: seq000747


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A1_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD010_indexed


title: seq-a4pme7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD006_indexed


title: seq000573


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A11_AD008_indexed


title: seq-43ewt9


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A2_AD004_indexed


title: seq-7tfym6


title: seq-cnrhkb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A11_AD010_indexed


title: seq-ytuxc4


title: seq-6fjcy8


title: seq-xvmfra


title: seq-hk9yvj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H9_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A12_AD001_indexed


title: seq-t9xrab


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H8_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A11_AD002_indexed


title: seq-86jd43


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A11_AD004_indexed


title: seq-3jb6ra


title: seq-udr37j


title: seq-ejaxt9


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A10_AD006_indexed


title: seq000227


title: seq000231


title: seq000226


title: seq000224


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H9_AD001_indexed


title: seq-y9mfuh


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A10_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H7_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H7_AD004_indexed


title: seq-mevxkj


title: seq-xyrt96


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A10_AD008_indexed


title: seq-v9m7a8


title: seq-ruebn7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A10_AD004_indexed


title: seq-ycrbk7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H6_AD002_indexed


title: seq-9fnyu7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H9_AD002_indexed


title: seq-6wyamh


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A10_AD012_indexed


title: seq-um6wcd


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H5_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H6_AD001_indexed


title: seq-7r6ueb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H5_AD002_indexed


title: seq-cday6m


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H6_AD006_indexed


title: seq-yjvdr8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H5_AD012_indexed


title: seq-cef46d


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H4_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H3_AD004_indexed


title: seq-7nft8k


title: seq-abftxk


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H3_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H3_AD001_indexed


title: seq-vfar3j


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H4_AD002_indexed


title: seq-6j89uk


title: seq-tcfyd7


title: seq-3pm8f6


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H1_AD006_indexed


title: seq-jm7a6p


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H4_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_9_CEMBA180412_3D_10_A10_AD002_indexed


title: seq-9muyad


title: seq-kxe7m3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H2_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H2_AD004_indexed


title: seq-4p9ncm


title: seq-ked69a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H5_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H2_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H11_AD004_indexed


title: seq-78vjpe


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H1_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H1_AD004_indexed


title: seq-46fhcj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H4_AD001_indexed


title: seq-wh7a63


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H11_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H11_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H11_AD001_indexed


title: seq-hya7wj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H12_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H10_AD002_indexed


title: seq-ewhanj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G6_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G9_AD001_indexed


title: seq-pdaecf


title: seq-wc9xrf


title: 1021. Over Weight.Fat

type: RNA

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

label: biotin

source_name: Subject: 1021.Condition: Over Weight.Fat

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: subject id

tag: pair

tag: condition

value: Over Weight

value: Fat


title: 1017. Over Weight.Fat

source_name: Subject: 1017.Condition: Over Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H1_AD002_indexed


title: 1020. Over Weight.Fat

source_name: Subject: 1020.Condition: Over Weight.Fat


title: 1010. Over Weight.Fat

source_name: Subject: 1010.Condition: Over Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G7_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G8_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H12_AD002_indexed


title: seq-tdb76c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H12_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H10_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_H10_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G8_AD001_indexed


title: seq-uptjah


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G7_AD006_indexed


title: seq-4rhac8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G7_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G9_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G9_AD006_indexed


title: seq-wbehrd


title: 1004. Over Weight.Fat

source_name: Subject: 1004.Condition: Over Weight.Fat


title: 2024. Normal Weight.Fat

source_name: Subject: 2024.Condition: Normal Weight.Fat

value: Normal Weight


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G7_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 1018. Over Weight.Fat

source_name: Subject: 1018.Condition: Over Weight.Fat


title: 2017. Normal Weight.Fat

source_name: Subject: 2017.Condition: Normal Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G9_AD004_indexed


title: 1006. Over Weight.Fat

source_name: Subject: 1006.Condition: Over Weight.Fat


title: 2019. Normal Weight.Fat

source_name: Subject: 2019.Condition: Normal Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G6_AD006_indexed


title: seq-mh4kjf


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD002_indexed


title: seq-9ycwtb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G6_AD001_indexed


title: seq-v4k3mj


title: seq-v7rwxa


title: seq-ncwkab


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G6_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G6_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD008_indexed


title: seq-rvpau4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G4_AD006_indexed


title: seq-he4u3j


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G6_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G5_AD006_indexed


title: 2016. Normal Weight.Fat

source_name: Subject: 2016.Condition: Normal Weight.Fat


title: 1003. Over Weight.Fat

source_name: Subject: 1003.Condition: Over Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G4_AD012_indexed


title: seq-f6rxv8


title: seq-7kt9ad


title: 2011. Normal Weight.Fat

source_name: Subject: 2011.Condition: Normal Weight.Fat


title: 2013. Normal Weight.Fat

source_name: Subject: 2013.Condition: Normal Weight.Fat


title: 2005. Normal Weight.Fat

source_name: Subject: 2005.Condition: Normal Weight.Fat


title: 2007. Normal Weight.Fat

source_name: Subject: 2007.Condition: Normal Weight.Fat


title: 2008. Normal Weight.Fat

source_name: Subject: 2008.Condition: Normal Weight.Fat


title: 2002. Normal Weight.Fat

source_name: Subject: 2002.Condition: Normal Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G3_AD004_indexed


title: seq-p84bma

source_name: Non-cancer


title: 1024. Over Weight.Fat

source_name: Subject: 1024.Condition: Over Weight.Fat


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G3_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G1_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G4_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G2_AD002_indexed


title: seq-rkfx7a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G3_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G4_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G2_AD010_indexed


title: seq-7mu6t8


title: 1002. Over Weight.Fat

source_name: Subject: 1002.Condition: Over Weight.Fat


title: 1018. Over Weight.Skin

source_name: Subject: 1018.Condition: Over Weight.Skin

value: Skin


title: 1020. Over Weight.Skin

source_name: Subject: 1020.Condition: Over Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G1_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: seq-879fem


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G3_AD007_indexed


title: seq-fpcx79


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G2_AD008_indexed


title: 1017. Over Weight.Skin

source_name: Subject: 1017.Condition: Over Weight.Skin


title: seq-hxm736


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G4_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G3_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G1_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G1_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G1_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G4_AD008_indexed


title: seq-7atckb


title: 1021. Over Weight.Skin

source_name: Subject: 1021.Condition: Over Weight.Skin


title: 1010. Over Weight.Skin

source_name: Subject: 1010.Condition: Over Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD008_indexed


title: 1006. Over Weight.Skin

source_name: Subject: 1006.Condition: Over Weight.Skin


title: 1004. Over Weight.Skin

source_name: Subject: 1004.Condition: Over Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD007_indexed


title: seq-nbh3a6


title: 1003. Over Weight.Skin

source_name: Subject: 1003.Condition: Over Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G2_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G2_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD012_indexed


title: seq-xdfw3h


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G11_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G11_AD012_indexed


title: seq-ec3rjd


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD002_indexed


title: 2019. Normal Weight.Skin

source_name: Subject: 2019.Condition: Normal Weight.Skin


title: seq-pvxba7


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G11_AD004_indexed


title: seq-v7cx49


title: 2024. Normal Weight.Skin

source_name: Subject: 2024.Condition: Normal Weight.Skin


title: seq-tprh94


title: seq-bydhmc


title: seq-3a9reh


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G12_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G11_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G11_AD007_indexed


title: 2016. Normal Weight.Skin

source_name: Subject: 2016.Condition: Normal Weight.Skin


title: seq-6jfvt8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD012_indexed


title: seq-bmdk48


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD007_indexed


title: 2017. Normal Weight.Skin

source_name: Subject: 2017.Condition: Normal Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F9_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F9_AD001_indexed


title: seq-my9tc8


title: 2013. Normal Weight.Skin

source_name: Subject: 2013.Condition: Normal Weight.Skin


title: seq000860

source_name: Non-cancer


title: 2008. Normal Weight.Skin

source_name: Subject: 2008.Condition: Normal Weight.Skin


title: seq000849


title: seq-wrvj4f


title: seq-emnjcp


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F9_AD007_indexed


title: 2007. Normal Weight.Skin

source_name: Subject: 2007.Condition: Normal Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F9_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD012_indexed


title: 2005. Normal Weight.Skin

source_name: Subject: 2005.Condition: Normal Weight.Skin


title: 2002. Normal Weight.Skin

source_name: Subject: 2002.Condition: Normal Weight.Skin


title: 1002. Over Weight.Skin

source_name: Subject: 1002.Condition: Over Weight.Skin


title: 2011. Normal Weight.Skin

source_name: Subject: 2011.Condition: Normal Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD004_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F9_AD002_indexed


title: 1024. Over Weight.Skin

source_name: Subject: 1024.Condition: Over Weight.Skin


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD006_indexed


title: seq-36hrpc


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F7_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G10_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F7_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD002_indexed


title: seq-xe4jch


title: seq-thvwpc


title: seq-fbvr7c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F9_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F7_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F6_AD007_indexed


title: seq-4bean8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F8_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F6_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F6_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F5_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F6_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F7_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F7_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F5_AD001_indexed


title: RH3B

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

data_processing:
Base-calling using illumina basespace
Split files by RNA-tag using initial 8nt Tagseq barcode using SplitRNATagSeqFastQ.py https://github.com/ewallace/pyRNATagSeq.
Concatenate files with same tag/index combination from distinct lanes.
Further processing with CutDedupTrimQuant.py from 5' adapter trimming with flexbar, then deduplication of 3' 5nt UMIs with DedupEndFastQ.py, then trimming of the UMI and quality filtering with flexbar
kallisto to quantify reads (counts/TPMs) per gene
Genome_build: CNA3
Supplementary_files_format_and_content: Collated TPMs across all samples and genes (single transcript, no isoforms.

organism: Cryptococcus neoformans H99

source_name: yeast cells

growth_protocol:
- Grow a 10mL culture of C. neoformans in YPD for 5 days.
- In duplicate, pre-warm 2x 100mL each of YPD at 25C, YPD at 37C, RPMI + serum at 25C, RPMI + serum at 37C, in incubators shaking at 60rpm.
- Fix and freeze 3mL of stationary-phase culture:
- Place 4 x 3mL of one stationary-phase culture in separate falcon tubes.
- Resuspend each cell pellet in a different pre-warmed medium condition (YPD at 25C, YPD at 37C, RPMI + serum at 25C, RPMI + serum at 37C), and start stopwatch. Transfer to 100mL total in shaking flasks in appropriate incubator as soon as possible.
- At 10, 30, 60 and 120 minutes after inoculation, fix and freeze 10mL from each condition, as above.

extract_protocol:
- Fix and freeze yeast culture:
- Pre-chill a 50mL tube with 6mL 100% Methanol  on dry ice (tightly capped so CO2 does not dissolve in MetOH).
- Add 10mL of culture to the chilled MetOH, cap tube, shake to mix, place on dry ice for up to 5 min.
- Spin 2 min at ~2500g, pour off supernatant.
- Resuspend cell pellet in 1mL ice-cold H2O and transfer to 2mL screw-cap tube.
- Spin 1min at 5000g, remove supernatant carefully, and freeze pellet in sealed tube at -80C.
- Freeze-dry the pellet in a lyophilizer until dry.
- Extract RNA using the RNAeasy plant and fungi kit (Qiagen)
RNAtagseq essentially as described in Shishkin et al., Nat. Methods 2015, "Simultaneous generation of many RNA-seq libraries in a single reaction", doi: 10.1038/nmeth.3313. Edits to protocol at https://github.com/ewallace/protocols/blob/master/RNAtagseq.md

value: yeast cells

tag: medium

value: RPMI+

tag: temperature

tag: growth time mins.

tag: biological replicate

value: B

tag: tagid

tag: tagseq

value: CGACTTGGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F5_AD007_indexed

tag: brain region

tag: Sex

tag: age

tag: strain


title: RC4B

tag: tissue

value: CATCTGTAT


title: RH1B

value: GCCCTCCGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F4_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F5_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F4_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F4_AD002_indexed


title: RC2B

value: ATGTTGTAT


title: RC3B

value: GTGGCTGCT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F6_AD012_indexed

value: AI

value: male


title: RC1B

value: CTTGGGCCT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F4_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F4_AD008_indexed


title: YH4B

value: YPD

value: CAACACTTT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F3_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F4_AD006_indexed


title: RH4B

value: CACGATGAT


title: RH2B

value: GGTACCGGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F3_AD002_indexed


title: YH3B

value: AAGACGGGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F3_AD001_indexed


title: YC4B

value: ACAATCTCT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F2_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F3_AD007_indexed


title: YC3B

value: yeast cells

value: CTGTAGGGT


title: YC2B

value: B

value: ATAATTCTT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F3_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F2_AD001_indexed


title: YC0B

value: GCGAGTTGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F11_AD006_indexed


title: YC1B

value: GTCCATATT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F12_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F2_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD010_indexed


title: YH2B

value: CAAGTGATT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F12_AD012_indexed


title: YM9B

value: CCGCGGGAT


title: RH4A

value: RPMI+

value: A

value: CGATCCAGT


title: YH1B

value: YPD

value: GTCTCCCAT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F12_AD001_indexed

value: AI

value: male


title: RH3A

value: GTGGCTGCT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F2_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F1_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F12_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F11_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F12_AD007_indexed


title: RH2A

value: GTTAGAAAT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F12_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F11_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F11_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E9_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E9_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E9_AD008_indexed


title: RH1A

value: yeast cells

value: CTTGGGCCT


title: RC4A

value: ATGTTGTAT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD012_indexed


title: RC2A

value: ACAATCTCT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F11_AD001_indexed


title: YH4A

value: AAGTGCCGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E9_AD010_indexed


title: RC3A

value: CGACTTGGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E9_AD006_indexed


title: RC1A

value: AGAGGACCT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E8_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E7_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E8_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E7_AD001_indexed


title: YH1A

value: GTCCATATT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD004_indexed


title: YC4A

value: GCGAGTTGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E8_AD007_indexed


title: YC3A

value: A

value: AGTTAGAGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E8_AD008_indexed


title: YC2A

value: YPD

value: GGTACCGGT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E8_AD010_indexed

value: AI


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E6_AD012_indexed

value: male


title: YH3A

value: CGCCAGACT


title: YC1A

value: CTGGTTCAT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E6_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E8_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E7_AD008_indexed


title: YC0A

value: yeast cells

value: CATCTGTAT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E6_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E6_AD004_indexed


title: seq-yh8fpe

value: Validation


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E7_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD006_indexed


title: YM9A

value: CAACACTTT


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E9_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E6_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD008_indexed


title: seq-r9nfk8


title: seq-ur38ph


title: seq-ea6k73


title: HepG2_H_rep4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 48hr high glucose (40 mg/dL) DMEM treated HepG2 cells

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

source_name: HepG2, high glucose, replicate4

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced per manufacturer’s protocol.

growth_protocol: Human liver hepatocellular carcinoma HepG2 cells were cultured in DMEM (high glucose) medium supplemented with 10% heat-inactivated fetal bovine serum, 1% Streptomycin and Penicillin.

extract_protocol: The mRNA samples were extracted from HepG2 cells by using RNeay Mini Kit. All samples were treated by DNase in the columns. The RNA quality of these samples was checked by Nanodrop spectrophotometer.

treatment_protocol: DMEM glucose-free media supplemented with low concentration (40 mg/dL) or high concentration (450 mg/dL) of glucose were used for cell treatments.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: treatment

value: high glucose


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E6_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD002_indexed


title: HepG2_H_rep3

source_name: HepG2, high glucose, replicate3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E4_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_F10_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E4_AD012_indexed


title: seq-3m4pvk

tag: cohort


title: YH2A

value: CGTGGTAAT


title: HepG2_H_rep2

source_name: HepG2, high glucose, replicate2


title: seq-rty7nb


title: HepG2_H_rep1

source_name: HepG2, high glucose, replicate1


title: HepG2_L_rep4

description: Gene expression after 48hr low glucose (40 mg/dL) DMEM treated HepG2 cells

source_name: HepG2, low glucose, replicate4

value: low glucose


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E4_AD008_indexed


title: HepG2_L_rep3

source_name: HepG2, low glucose, replicate3


title: P746 96HAI infestation rep3

city: Shanghai

first: Yao

last: Luming

address: DongChun Rd

department: Plant science

country: China

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
The paired-end reads were aligned to the transcript sequences with Bowtie using the following parameters: -v2 -a -m10 -best -strata.
 The number of reads mapped to each transcript was counted and divided  by the length of the transcript. The total number of aligned reads to calculate the normalized gene expression value (Transcripts Per Million reads, TPM).
Genome_build: Glycine max v2.1, Ensembl Plants
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each transcript

organism: Glycine max

source_name: leaf

growth_protocol: Seedlings were grown in a chamber at 26 ℃ with a 16 h photoperiod and 70% relative humidity.

extract_protocol:
Total RNA was isolated using an RNAprep Pure Kit (For Plant) with DNase digestion (Tiangen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Each leafle tof the trifoliolate was infested with six aphids，and  aphids were caged on leaves. The caged areas of leaf samples from both aphid-infested and mock-treated seedlings were harvested at 24 hai, 48 hai, and 96 hai for subsequent analysis.

tag: genotype

tag: Stage

value: 96 hours after infestation

value: infestation


title: HepG2_L_rep2

source_name: HepG2, low glucose, replicate2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E4_AD001_indexed


title: HepG2_L_rep1

source_name: HepG2, low glucose, replicate1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD002_indexed


title: P746 96HAI infestation rep2


title: seq000493

source_name: Non-cancer


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E4_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD012_indexed


title: seq-uhf3jc


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_G11_AD001_indexed


title: P746 96HAI infestation rep1


title: seq-utf9j4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD008_indexed


title: P746 96HAI mock rep3

value: mock


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD004_indexed


title: P746 96HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD008_indexed


title: seq-69ud4h


title: P746 96HAI mock rep1


title: seq-8rnf4a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD007_indexed


title: P746 48HAI infestation rep2

value: 48 hours after infestation


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E5_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD006_indexed


title: P746 48HAI infestation rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD006_indexed


title: seq-jvxwhc


title: P746 48HAI mock rep3


title: seq-b3jnxa


title: seq-y6bfad


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD004_indexed


title: seq-ej7rdb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD010_indexed


title: P746 48HAI infestation rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E3_AD010_indexed


title: seq-vpdj49


title: seq-7vxybe


title: P746 48HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD001_indexed


title: P746 24HAI infestation rep3

value: 24 hours after infestation


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E1_AD007_indexed


title: P746 24HAI infestation rep2


title: seq000568


title: seq-4hwmdk


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E2_AD007_indexed


title: seq-cyk4e3


title: P746 48HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD004_indexed


title: P746 24HAI mock rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD007_indexed


title: seq-6v4krm


title: seq-97ye8m


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD001_indexed


title: P746 24HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD002_indexed


title: P746 24HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD006_indexed


title: seq-4hnwkd


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD008_indexed


title: P203 96HAI infestation rep3


title: seq-y8khn9


title: P203 96HAI infestation rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD006_indexed


title: seq-4dc3nh


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD001_indexed


title: P203 96HAI infestation rep1


title: P746 24HAI infestation rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD007_indexed


title: P203 96HAI mock rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E10_AD006_indexed


title: seq-8neybf


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E10_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E12_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD002_indexed


title: seq-uek6r9


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E10_AD007_indexed


title: seq-hyvcfj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E11_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D9_AD006_indexed


title: seq-uc6jfb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D9_AD008_indexed


title: P203 48HAI infestation rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E10_AD012_indexed


title: seq-pw7byh


title: P203 48HAI infestation rep2


title: seq-k9fhwn


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D9_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD010_indexed


title: P203 48HAI infestation rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD008_indexed


title: seq-69pt4c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D9_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_E10_AD001_indexed


title: P203 48HAI mock rep3


title: seq-c9jfd7


title: P203 96HAI mock rep2


title: P203 96HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD006_indexed


title: seq-cfnbha


title: P203 48HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D9_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD012_indexed


title: seq-9yavk4


title: P203 48HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD012_indexed


title: seq-hf3tmj


title: P203 24HAI infestation rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD002_indexed


title: seq-hnftpk


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD006_indexed


title: seq-andx67


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D6_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D8_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D5_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D7_AD002_indexed


title: seq-bhc4fn


title: seq-vpkjeb


title: P203 24HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D6_AD010_indexed


title: P203 24HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D5_AD007_indexed


title: seq-ebfjun


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D5_AD004_indexed


title: P203 24HAI infestation rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D6_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD010_indexed


title: seq-ch8d9e


title: Dongnong47 96HAI infestation rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D5_AD010_indexed


title: seq-ywkjam


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD012_indexed


title: P203 24HAI infestation rep1


title: Dongnong47 96HAI infestation rep1


title: seq005889


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD008_indexed


title: Dongnong47 96HAI mock rep3


title: P203 24HAI mock rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D6_AD007_indexed


title: seq005342


title: Dongnong47 96HAI infestation rep3


title: Dongnong47 96HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D6_AD004_indexed


title: seq005207


title: seq005839


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D3_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D6_AD006_indexed


title: Dongnong47 96HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D3_AD006_indexed


title: Dongnong47 48HAI infestation rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D5_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D3_AD004_indexed


title: Dongnong47 48HAI infestation rep2


title: seq005952


title: seq005315


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D3_AD002_indexed


title: seq005834


title: Dongnong47 48HAI infestation rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD004_indexed


title: Dongnong47 48HAI mock rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD008_indexed


title: seq005935


title: seq005901


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD004_indexed


title: Dongnong47 48HAI mock rep1


title: Dongnong47 24HAI infestation rep3


title: seq001966


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D3_AD007_indexed


title: seq001682


title: seq001927


title: Dongnong47 24HAI infestation rep1


title: Dongnong47 24HAI infestation rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D3_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D4_AD007_indexed


title: Dongnong47 48HAI mock rep3


title: seq001961


title: Dongnong47 24HAI mock rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D12_AD007_indexed


title: Dongnong47 24HAI mock rep2


title: seq002131


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D2_AD010_indexed


title: seq001979


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD007_indexed


title: Dongnong47 24HAI mock rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D12_AD012_indexed


title: seq001669


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D12_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D11_AD002_indexed


title: seq001991


title: seq001768


title: seq001978


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D11_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D10_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D10_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D11_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C9_AD010_indexed


title: seq001671


title: seq001960


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D10_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D10_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D10_AD010_indexed


title: seq-tmvbdj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C9_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C9_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C9_AD012_indexed


title: seq-4pvkcb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D1_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C9_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_D12_AD010_indexed


title: seq000214

value: Discovery


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD010_indexed

value: AI


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD004_indexed

value: male


title: seq-9yt4dm


title: NB4.shPR.Rep2

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The salmon program was used for quantification of transcript expression.
The reference transcriptome was built with the Ensembl gene annotation file and the hg38 genome (GRCh38.98).
|log2(fold change)| >=1 and the FDR < 0.01 were used for determining differentially expressed genes.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file containing the FPKM value and DEseq2 statistics per gene

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA). Ribosomal RNAs were depleted according to the manufacturer's protocol (Vazyme, China, N406-01).
RNA-seq libraries were preapared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, E7530S) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were treated with arsenic trioxide for 6 hours.

value: sh-PML/RARa


title: NB4.shPR.Rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD008_indexed


title: seq-yr34mb


title: NB4.Vec.Rep2

value: vector


title: seq-ybr4f7


title: NB4.Vec.Rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD001_indexed


title: seq-yrfdhb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD001_indexed


title: seq-ujbcm9


title: IEC Cl13 IFNAR rep1

first: Nicola

last: Allen

address: 10010 N Torrey Pines Rd

department: Molecular Neurobiology

institute: Salk Institute for Biological Studies

description: samples obtained at day 9 post infection

data_processing:
Raw sequencing files were processed with CASAVA 1.8.2 (Illumina) to generate .fastq files.
Fastq files were uploaded onto the Galaxy project portal (https://usegalaxy.org/). We first obtained read quality reports by running the ‘Fastqc’ module (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), which gave us overall high-quality scores. Next, we used Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013) to align RNA-seq reads to the mouse genome with the following parameters: mm10, GRCm38, 75bp length of the genomic sequence around annotated junctions and STAR Galaxy version 2.7.2b default parameters for seed, alignment, limits and chimeric alignment.
To assemble RNA- seq alignments into potential transcripts and to obtain gene abundance estimation files, we used StringTie (Pertea et al., 2015) with mouse .gtf file (https://www.gencodegenes.org/mouse/) as reference to guide assembly. Default parameters were used with Minimum isoform fraction: 0.15, Minimum anchor length for junctions:10, Minimum junction coverage: 1, Minimum bundle reads per bp coverage to consider for assembly: 2, Gap between read mappings triggering a new bundle: 50, Fraction of bundle allowed to be covered by multi-hit reads: 0.95, trimming of predicted transcripts based on coverage: disabled, multi-mapping correction: disabled.
Next, differentially expressed features were determined by DESeq2 (Love et al., 2014). We defined differentially expressed genes (DEG) by false discovery rate (FDR)-adjusted p.value<0.05 and fold-change ≥2 throughout the manuscript.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files contain DESeq2 normalized gene counts for each gene and for each sample

source_name: small intestine

extract_protocol:
intestinal epithelial cells (IEC) from 3 mice per group were pooled, stained and FACS-purified based on a CD45-EpCAM+ gate from small intestine cellular preparations at day 9 post-infection. Sorted cells were placed in 350 μl RLT (Qiagen) + beta-mercaptoethanol (10 μl/ml, Life Technologies) and stored at -80 C. The following day, RNA was extracted with RNAeasy Micro Kit (Qiagen) by following the manufacturer’s protocol and re-suspended in molecular grade distilled H2O and stored at -80 C until library preparation.
mRNA stranded libraries were constructed by using TruSeq RNA Library Prep Kit v2 (Illumina) followed by single-end sequencing of 75 base-pair fragments with a HiSeq 4000 (Illumina). Raw sequencing files were processed with CASAVA 1.8.2 (Illumina) to generate .fastq files.

treatment_protocol: 6 to 10 week old C57BL/6 female mice were left uninfected or infected with 2x10^6 pfu LCMV ARM or LCMV Cl13 intravenously. Different groups of mice were infected with 2x10^6 pfu LCMV Cl13 and intraperitoneally injected with IFNAR neutralizing antibody (MAR1-5A3; BioXCell) or mouse IgG1 isotype control (MOPC-21; BioXcell) on days -1 and 0 p.i.  (500 µg/mouse) as well as on days 2, 4 and 6 p.i. (250 µg/mouse) with Cl13.

value: female

value: small intestinal epithelial cells

tag: infection

value: LCMV Cl13

value: anti-IFNAR1 antibody (MAR1-5A3; BioXCell)


title: IEC Cl13 IFNAR rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD012_indexed


title: seq-kdmxac


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD002_indexed


title: IEC Cl13 Isotype rep1

value: IgG1 isotype control (MOPC-21; BioXcell)


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C8_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD004_indexed


title: seq-8mucnf


title: IEC Cl13 rep3

value: not applicable


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C5_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD001_indexed


title: IEC Cl13 rep2


title: seq-jnxp3a


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C5_AD007_indexed


title: IEC Cl13 Isotype rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD007_indexed


title: IEC ARM rep3

value: LCMV Armstrong


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD002_indexed


title: IEC Cl13 rep1


title: IEC ARM rep2


title: seq-8d3caj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C5_AD002_indexed


title: seq-mej84n


title: seq-cp4rx3


title: seq-u8kr4e


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD010_indexed


title: seq000580


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD007_indexed


title: seq-urjwbc


title: IEC ARM rep1


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C7_AD006_indexed


title: IEC Uninfected rep3

description: not applicable

value: uninfected


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C5_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C5_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C6_AD008_indexed


title: IEC Uninfected rep2

description: not applicable


title: seq-ynkw4b


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD010_indexed


title: IEC Uninfected rep1

description: not applicable


title: seq000235


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD008_indexed


title: seq-unxce4


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C2_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD001_indexed


title: seq-y86wae


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C2_AD008_indexed


title: seq-txcfrj


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C1_AD012_indexed


title: sapx tapx pgr5 rep1

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

country: Japan

institute: Shimane University

data_processing:
Mapping reads, data processing, and statistical analysis were performed using the CLC Genomic Workbench (Ver.9.5.2).
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files  include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: fully expanded rosette leaves

growth_protocol: Plants were grown under low light conditions (40-60 µmol photons/m2/s) for 18 days.

extract_protocol:
Total RNA extracted as describe above was purified using NucleoSpin RNA plus (Takara).
Total RNA was fragmented and converted to double-stranded DNA using TruSeq RNA Sample Preparation Kit v2 (Illumina). Quality and quantity of the resulting library were assessed by using a Bioanalyzer and a KAPA library quantification kit (KAPA Biosystems), respectively.

treatment_protocol: Plants were  exposed to high light (1,500 µmol photons /2/s) for 90 min

tag: genotype/variation

value: sapx tapx pgr5

value: Exposed to high light (1,500 µmol photons/m2/s) for 90 min


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD002_indexed


title: pgr5 rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C4_AD002_indexed


title: seq000238


title: sapx tapx pgr5 rep2


title: pgr5 rep2


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C2_AD002_indexed


title: sapx tapx pgr5 rep3


title: seq-k46y9c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C2_AD004_indexed


title: pgr5 rep1


title: seq000508


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C2_AD012_indexed


title: sapx tapx rep3

value: sapx tapx


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C1_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C1_AD002_indexed


title: sapx tapx rep2


title: seq-xhuktb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C3_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C1_AD006_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C1_AD007_indexed


title: seq-9p8f3k


title: seq-jw9evd


title: seq-me4vdc


title: seq-nhyrdk


title: seq000490


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C12_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C12_AD010_indexed


title: wild type rep2

value: wild type


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD004_indexed


title: wild type rep1


title: wild type rep3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C12_AD002_indexed


title: MG71D

city: Grugliasco

first: Eugenio

last: Martignani

state: TO

address: Largo Braccini 2

department: Veterinary Science

country: Italy

institute: University of Torino

data_processing:
Basecalling was performed with software bcl2fastq v1.8
Sequenced reads were mapped to bosTau8 whole genome using STAR v2.5
Aligned reads were counted at the gene level with Rsubread's featureCounts (with options useMetaFeatures = T,  GTF.featureType = 'exon', countMultiMappingReads = F, countChimericFragments=F, allowMultiOverlap = F, strandSpecific = 0, isPairedEnd = Y) using ENSEMBL annotation v85.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were obtained using R package edgeR's rpkm function.
Genome_build: bosTau8 UMD3.1, genome-build-accession NCBI:GCA_000003055.3
Supplementary_files_format_and_content: RPKM normalized counts

organism: Bos taurus

growth_protocol: Cell were isolated from bovine udders

extract_protocol:
Cells were sorted in tubes containing 0,1% volume of FBS, centrifuged and lised with Trizol. RNA was then extracted and quantified.
Truseq mRNA non stranded (Illumina)

treatment_protocol: Cells were directly sorted with a FACSAria III

tag: breed

value: Piedmontese

tag: animal id

tag: cell type

value: Primary mammary epithelial cells

tag: cell fraction


title: seq-vufpeh

value: Discovery


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C2_AD001_indexed

value: AI

value: male


title: seq-cfyrx3


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD012_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C1_AD001_indexed


title: sapx tapx rep1


title: MG71C


title: MG71B


title: seq-8utnhb


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C12_AD001_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD002_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD007_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C12_AD006_indexed


title: seq-84mtcn


title: MG71A


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C12_AD004_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD008_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD001_indexed


title: seq-7hveu8


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD010_indexed


title: MG70D


title: MG70C


title: seq-xe38wa


title: seq-xbr67h


title: MG70A


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B8_AD010_indexed


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C10_AD010_indexed


title: seq-bn6493


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_C11_AD006_indexed


title: seq-abnf4c


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180412_3D_7_CEMBA180412_3D_8_B9_AD008_indexed


title: MG52C