title: human primary epithelial tubular_48h CTRL3

description:
US-1583932
Epithelial_FPKM.txt

value: Kidney 48h CTRL


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C9_AD012

status: Public on Nov 24 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:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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 P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: ACA

tag: gender

value: female


title: AM255

city: Kuopio

first: Mikael

last: Marttinen

address: Yliopistonranta 1E

department: Biomedicine

country: Finland

institute: University of Eastern Finland

library_source: transcriptomic

data_processing:
FastQC version 0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to examine the quality of the RNA sequencing reads. Illumina sequencing adapter sequences were removed, and reads were quality trimmed using the Trimmomatic version 0.38 (Bolger et al., 2014). The obtained trimmed reads were then mapped against the ribosomal and mitochondrial reference sequences (build mm10) using the Bowtie 2 version 2.2.3 (Langmead et al., 2012). Successfully mapped reads were abandoned. The rest of the reads were subjected to pseudo alignment to mouse reference transcriptome (build mm10) and transcript abundance analysis using kallisto version 0.44.0 (Bray et al, 2016).
Transcript abundance estimates were collapsed to gene-level counts using R package tximport version 1.10.1 (Soneson, 2016). Gene-level counts were pre-filtered (mean of gene count > 10) and variance stabilized using R package DESeq2 version 1.22.2 (Love et al., 2014). Observed batch effect was corrected using removeBatchEffect function from limma version 3.38.3 (Ritchie et al., 2015).
Genome_build: Mm10
Supplementary_files_format_and_content: .csv file containing variance stabilised data filtered for low count genes and batch corrected. Rows are features (genes), columns are cases (mice).

molecule: polyA RNA

source_name: STD A-wt Tau-wt

growth_protocol: The mice were kept in a controlled environment (constant temperature, 22 ± 1 °C, humidity 50 – 60 %, lights on 07:00-19:00), with food and water available ad libitum.

extract_protocol:
The hippocampus tissue samples of all female mice were collected into microcentrifuge tubes and weighed. Samples were homogenized in 250 µl of phosphate-buffered saline (DPBS, Lonza, Walkersville, MD, USA) using a stirrer. Fractions of homogenates were taken to RNA isolation (50 µl of homogenate and 500 µl Tri Reagent (Sigma-Aldrich, St. Louis, MO, USA)
Library preparation and sequencing was conducted in Finnish Functional Genomics Centre (FFGC), Turku Centre for Biotechnology, University of Turku and Åbo Akademi University. The quality of the total RNA samples as well as prepared libraries was ensured with Advanced Analytical Fragment Analyzer. Sample and library concentration was measured with Qubit® Fluorometric Quantitation, Life Technologies. Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047). The 45 libraries with good quality were pooled in one pool and run in 2 lanes. The samples sequenced using Illumina HiSeq 3000 instrument. Single-read sequencing with 1 x 50 bp read length was used, followed by 8 + 8 bp dual index run.

treatment_protocol: The dietary intervention started at the age of 7 months, so that half of the mice / group received a chow mimicking typical western diet (TWD; Adjusted Calories diet, TD 88137, Harlan Tecklad, Madison, WI, USA, with 21% w/w fat, 0.15 % cholesterol and 35% sucrose) while the other half continued with standard rodent chow (STD) (5% w/w fat and 0% cholesterol) until sacrificed at the age of 13 months.

value: Hippocampus

tag: genotype

value: wild type

tag: diet

value: standard diet

tag: batch


title: human primary epithelial tubular_48h TGFb1

city: Boston

first: Thomas

last: Gan

state: MA

address: 33 Ave Lous Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

description:
US-1583936
Epithelial_FPKM.txt

data_processing:
Alignment and differential gene expression analysis was performed in Omicsoft Array Studio version 9.0.8.92.
Cleaned reads were aligned to the mouse and human B38 genome references, for the UUO kidney and primary cells respectively, and the rat B6.0 genome reference for the BDL model, using the Omicsoft Aligner with a maximum of 2 allowed mismatches.
Gene level counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R82 gene models.
Genome_build: Human.B38, Mouse.B38, Rat.B6.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode).

molecule: total RNA

organism: Homo sapiens

source_name: epithelial tubular cells

extract_protocol:
Total RNA was extracted from tissue or cultured cells following the instruction of RNeasy Mini QIAcube Kit (Qiagen, #74116).
Sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Illumina, #RS-122-2201) according to the manufacturer’s instructions.  The resulting cDNA libraries were sequenced on an Illumina HiSeqTM 4000 using a 50 base paired-end run.

tag: replicate group

value: Kidney 48h TGFB

value: Kidney

tag: cell type

value: epithelial tubular cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D10_AD001

value: SSp

value: male


title: human primary epithelial tubular_48h CTRL2

description:
US-1583929
Epithelial_FPKM.txt


title: AM253

source_name: STD A-tg Tau-wt

value: APP/PS1 transgenic (A+Tw)


title: PM247

source_name: TWD A-wt Tau-wt

value: typical western diet


title: DSS2

city: Beijing

first: shimeng

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District

department: College of Animal Science and Technology

country: China

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM NA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The diet with CMFG (100 mg/kg body weight (BW)/day) were pre-fed to the experimental mice for 3 weeks to investigate its prophylactic effects on alleviating DSS induced colitis (2.5% (w/v) DSS in drinking water ad libitum for 7 days). Mice in the DSS group underwent oral gavage of PBS. Colonic tissues were immediately snap-frozen in liquid nitrogen and homogenized. Total RNA recovered from two separate group include DSS and CMFGDSS.

value: colon

tag: treatment

value: DSS

value: 8 weeks-old


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C9_AD007

value: brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D10_AD002

value: PTLp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C9_AD010

value: ACA


title: Atoh7-zsGreen/lacZ E17.5 scRNA-seq

city: Buffalo

first: Xiuqian

last: Mu

state: NY

address: 701 Ellicott Street

department: Ophthalmology

institute: University at Buffalo

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 2.1.1 mkoutput with Bcl2Fastq 2.19.1
Cellranger 2.1.1 Count against mm10 genome to produce count matrix
Seurat 3.0 used for marker gene analysis and visualization
Genome_build: mm10

source_name: Retina

extract_protocol:
Chromimum Single Cell 3' v2 (10x Genomics)
TruSeq Stranded RNA (illumina)

value: Neural retina

tag: developmental stage

tag: phenotype

value: Retinal ganglion cell deficiency


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C9_AD008


title: AM246

value: Hippocampus

value: female

value: wild type


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C9_AD006


title: Pou4f2-tdTomato/+ E17.5 scRNA-seq


title: Atoh7-zsGreen/+ E17.5 scRNA-seq


title: Atoh7-zsGreen/+ E14.5 scRNA-seq

value: Norma retinal development


title: RNA-Seq CDK6-Knockout, replicate 3

city: Vienna

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

country: Austria

institute: University of Veterinary Medicine

data_processing:
Alignment to genome version GRCm38 using BWA  (ATAC-Seq) or STAR (RNA-Seq)
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig,raw count file (tab delimited)

source_name: BCR-ABL+ cell lines

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
QIAGEN RNeasy extraction kit
Phenol-Chloroform extraction
RNA-seq: SENSE mRNA-Seq Library Prep kit, 50 bp single-end; ATAC-seq: Libraries were amplified using custom Nextera primers.

value: Pre/Pro-B-cells


title: human primary epithelial tubular_48h CTRL1

description:
US-1583889
Epithelial_FPKM.txt

value: Kidney 48h CTRL

value: Kidney

value: epithelial tubular cells


title: AM256

source_name: STD A-wt Tau-tg

value: tau P301L transgenic (AwT+)

value: standard diet


title: AM245

source_name: TWD A-tg Tau-tg

value: transgenic for both APP/PS1 and tau P301L (A+T+)

value: typical western diet


title: AM244

source_name: TWD A-tg Tau-wt

value: APP/PS1 transgenic (A+Tw)


title: RNA-Seq CDK6-Knockout, replicate 2


title: human primary epithelial tubular_24h TGFb2

description:
US-1583924
Epithelial_FPKM.txt

value: Kidney 24h TGFB


title: human primary epithelial tubular_24h TGFb1

description:
US-1583886
Epithelial_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C8_AD012

value: brain

value: PTLp

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C8_AD010


title: RNA-Seq CDK6-Knockout, replicate 1


title: PM242

source_name: TWD A-wt Tau-tg

value: Hippocampus


title: human primary epithelial tubular_24h TGFb3

description:
US-1583906
Epithelial_FPKM.txt


title: Atoh7-zsGreen/lacZ E14.5 scRNA-seq

value: Neural retina


title: PM241

value: female


title: PM239


title: human primary epithelial tubular_24h CTRL 2

description:
US-1583919
Epithelial_FPKM.txt

value: Kidney 24h CTRL


title: human primary epithelial tubular_24h CTRL 1

description:
US-1583937
Epithelial_FPKM.txt


title: RNA-Seq CDK6-Wildtype, replicate 1

value: Pre/Pro-B-cells


title: RNA-Seq CDK6-Wildtype, replicate 3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C8_AD006

value: SSp


title: RNA-Seq CDK6-Wildtype, replicate 2


title: cardiac 6h TGFb1 3

description:
US-1508678
Fibroblasts_FPKM.txt

source_name: Fibroblast

value: cardiac 6h TGFb1

value: heart

value: Fibroblast


title: Normal_rIL-33_d21_RNA4

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
PE-101
DACE111_IGO_10855_23_S116

data_processing:
Trimmomatic (v0.36) was used to remove adaptor sequences. RNAseq reads were aligned to (GRCm38 - mm10) with STAR (v2.5.3a)
Genome wide transcript counting was performed by featureCounts (v1.6.3) to generate raw count table
Differential expression analysis was performed with DESeq2 (v1.20.0) package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: sorted primary pancreatic epithelial cells

growth_protocol: 5-6 weeks-old KC (p48-Cre;RIK;LSLKrasG12D) mice were injected intraperitoneally once daily doses with 1 ug of murine recombinant IL-33 (#580504, R&D Systems) or vehicle (PBS) for 5 consecutive days, and cells were harvested at the indicated time-points.

extract_protocol:
Trizol RNA extraction protocol
Poly-A RNA-Seq / Paired-end 50

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1mg/mL) & Dispase (2U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, GFP-positive; CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected directly into Trizol-LS.

tag: experimental condition

tag: model

value: C;RIK GEMM

tag: oncotype

value: KrasWT

tag: time point

value: Day 21

value: pancreas

tag: sorting strategy

tag: age (upon sample collection)

value: 8 weeks old

tag: Sex

value: Male


title: cardiac 6h TGFb1 2

description:
US-1508649
Fibroblasts_FPKM.txt

tag: tissue


title: Flag Leaves_Control_2

city: Hefei

first: Meng

last: Wang

address: School of Life Sciences, West Campus of University of Science and Technology of China, No. 443 Huangshan Road, Shushan District, Hefei, Anhui, China

institute: USTC

data_processing:
RNA sequencing reads were quality-checked with fastqc. The reads were trimmed with Trimmomatic-0.36 by cutting Illumina TruSeq adapters from the reads, and read length below 36 bp was dropped.
Reads were aligned to high confidence (HC) genes of IWGSC wheat genome assembly RefSeq v1.0 with STAR (2.7.3a) allowing maximum 5 bp mismatches.
Differential expression analysis was performed using DEseq2 (1.26.0) with 0.05 nominal FDR control level IHW (1.14.0) p-value adjustment.
The genes which passed the threshold of FDR < 0.05 and a fold change of ≥ 2 were considered as differentially expressed genes (DEGs).
Genome_build: IWGSC wheat genome assembly RefSeq v1.0
Supplementary_files_format_and_content: raw counts

organism: Triticum aestivum

source_name: Flag Leaves

growth_protocol: Wheat plants (Triticum aestivum cv. Bobwhite S26 ) were grown in hydroponic systems in the greenhouse conditions (22˚C/18˚C with 16-hour-light/8-hour-dark cycle, 60% relative humidity).

extract_protocol:
Isolation of total RNA from the roots and flag leaves was carried out using the Isol-RNA Lysis Reagent (5 PRIME, USA). The total RNA was digested with RNase-Free DNase (Qiagen, Germany) to remove the genomic DNA followed by RNA cleaning with RNeasy Plant Mini Kit (Qiagen, Germany). The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, USA) and a Bioanalyzer 2100 (Agilent, Germany).
Strand-specific cDNA libraries (dUTP method) were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina, USA). Total RNA samples (1 μg) were poly-A enriched and then reverse-transcribed into double-stranded cDNA with Actinomycin added during first-strand synthesis. The cDNA samples were fragmented, and end-repaired before ligation of TruSeq adapters containing the index for multiplexing fragments. After ligation, these TruSeq adapters were selectively enriched by PCR amplification on both ends. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, USA). The product is a smear with an average fragment size of approximately 250 bp. The libraries were normalized to 10 nM in 10 mM Tris-Cl, pH8.5 with 0.1% Tween 20. TruSeq PE Cluster Kit v3-cBot-HS (Illumina, USA) was used for cluster generation using 8 pM of pooled normalized libraries on the cBOT.
Sequencing was performed on the Illumina HiSeq 2000 paired end at 2 × 101 bp (Illumina, USA).

treatment_protocol: All the seedlings were first maintained in iron-sufficient hydroponic solution for 7 days and then half of the plants were transferred to iron-deficient hydroponic solutions. Solutions for the hydroponic system were prepared as previously described with different Fe(III)-EDTA concentrations (iron-sufficient condition: 100.0 μM Fe; iron-deficient condition: 10.0 μM Fe) (Wang et al. 2019). After around 90 days growth on hydroponic solution, plants reached the anthesis stage. Roots and flag leaves were collected at 8-10 days post anthesis (DPA), i.e., around the commencement of grain filling.

tag: cultivar

value: Bobwhite S26

value: Flag Leaves

tag: day

value: 8-10 days post anthesis (DPA)


title: cardiac 6h TGFb1 1

description:
US-1508638
Fibroblasts_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C8_AD008

tag: strain

tag: age

value: brain

tag: source

value: PTLp

tag: target

value: ACA

tag: gender

value: male


title: Flag Leaves_Control_3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C8_AD002

value: SSp


title: human primary epithelial tubular_24h CTRL 3

description:
US-1583882
Epithelial_FPKM.txt

tag: replicate group

value: Kidney 24h CTRL

value: Kidney

tag: cell type

value: epithelial tubular cells


title: cardiac 6h CTRL 3

description:
US-1508644
Fibroblasts_FPKM.txt

value: cardiac 6h CTRL

value: heart

value: Fibroblast


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C7_AD008


title: Normal_rIL-33_d21_RNA3

description:
PE-101
DACE097_IGO_10855_25_S118

tag: experimental condition

value: C;RIK GEMM

tag: genotype

value: KrasWT

tag: treatment

value: Day 21

value: pancreas

value: Female


title: Flag Leaves_Control_1

value: Bobwhite S26

value: Flag Leaves

value: 8-10 days post anthesis (DPA)


title: cardiac 6h CTRL 2

description:
US-1508659
Fibroblasts_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C7_AD010

value: brain

value: PTLp

value: ACA

value: female


title: Normal_PBS_d21_RNA5

description:
PE-101
DACE110_IGO_10855_26_S119

value: C + Vehicle d21

tag: model

tag: oncotype

value: PBS

tag: time point

value: 8 weeks old

value: Male


title: Flag Leaves_Low Fe_1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C8_AD001

value: SSp

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C7_AD006


title: Flag Leaves_Low Fe_3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C7_AD002


title: Normal_rIL-33_d21_RNA2

description:
PE-101
DACE068_IGO_10855_24_S117

value: C;RIK GEMM

value: KrasWT

tag: sorting strategy

tag: age (upon sample collection)

value: 9 weeks old

tag: Sex


title: Normal_PBS_d21_RNA4

description:
PE-101
DACE109_IGO_10855_22_S115

value: Day 21

tag: tissue

value: pancreas

value: Female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C7_AD007

tag: strain


title: Roots_Control_2

source_name: Roots

tag: cultivar

value: Bobwhite S26

value: Roots

tag: day

value: 8-10 days post anthesis (DPA)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C7_AD001

tag: age

value: brain

tag: source

value: PTLp

tag: target


title: Normal_PBS_d21_RNA3

description:
PE-101
DACE069_IGO_10855_21_S114

value: C + Vehicle d21


title: Normal_PBS_d21_RNA2

description:
PE-101
DACD926_IGO_10855_7_S100

value: PBS


title: Roots_Control_3


title: cardiac 48h TGFb1 2

description:
US-1508640
Fibroblasts_FPKM.txt

tag: replicate group

value: cardiac 48h TGFb1

value: heart

tag: cell type

value: Fibroblast


title: Roots_Low Fe_3


title: Flag Leaves_Low Fe_2

value: Flag Leaves


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD008

value: ACA

tag: gender

value: male


title: Roots_Low Fe_2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD012

value: female


title: Normal_rIL-33_d21_RNA1

description:
PE-101
DACD925_IGO_10855_6_S99

tag: experimental condition

value: C;RIK GEMM

tag: genotype

value: KrasWT

tag: treatment

value: Day 21

value: 8 weeks old


title: cardiac 48h CTRL 3

description:
US-1508625
Fibroblasts_FPKM.txt

value: cardiac 48h CTRL


title: Kras*_rIL-33_d21_RNA3

description:
PE-101
DACE107_IGO_10855_20_S113

value: KC + rIL-33 d21

tag: model

value: KC;RIK GEMM

tag: oncotype

tag: time point

value: pancreas

value: Female


title: cardiac 48h CTRL 1

description:
US-1508657
Fibroblasts_FPKM.txt


title: cardiac 48h TGFb1 3

description:
US-1508670
Fibroblasts_FPKM.txt


title: cardiac 48h CTRL 2

description:
US-1508676
Fibroblasts_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD007

value: brain

value: PTLp


title: cardiac 24h TGFb1 3

description:
US-1508675
Fibroblasts_FPKM.txt

value: cardiac 24h TGFb1

value: heart


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD006

value: SSp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD004


title: Kras*_rIL-33_d21_RNA1

description:
PE-101
DACD917_IGO_10855_3_S96

tag: sorting strategy

tag: age (upon sample collection)

tag: Sex

value: Male


title: Normal_PBS_d21_RNA1

description:
PE-101
DACD921_IGO_10855_1_S94

value: C + Vehicle d21

value: PBS

tag: tissue


title: Roots_Control_1

tag: cultivar

value: Bobwhite S26

value: Roots

tag: day

value: 8-10 days post anthesis (DPA)


title: H3K27Ac Low Replicate 1

city: Saint Louis

first: Daniel

last: Hawiger

state: Missouri

address: 1100 South  Grand Boulevard

department: Molecular Microbiology and Immunology

institute: Saint Louis University

data_processing:
Basecalling was performed by Torrent Suite version 4 and 5 software using default settings
Aligmentment to the Mouse mm10 genome sequence was performed using the TMAP map4 algorithm without soft clipping. Reads flagged as PCR duplicates were removed using Samtools.
Genome coverage at each base pair for Input and each ChIP sample was calcluted using BEDtools.
Enrichment in ChIP sample coverage relative to Input coverage in sliding 250 bp windows with 50 bp steps was calculated using custom R scripts.
ChIP enrichment was averaged for all replicates to generate final processed data files. Averaged ChIP enrichment files were quantile normalized to each other for all downstream analysis.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Text graph file (sgr) of enrichment normalized to Input

source_name: CD4 postive T cells

growth_protocol: Mice were housed under specific pathogen free conditions in the Saint Louis University animal facility

extract_protocol:
Chromatin IP DNA was recovered using Qiagen MinElute columns.
Ion Torrent IonXpress barcoded sequencing libraries were constructed using the Ion Xpress Plus Fragment Library Kit (Life Technologies) according to the manufacturer's directions except that size selection was performed using Beckman Agencourt magnetic beads.

treatment_protocol: Antigen-targeting chimeric antibodies specific to dendritic cells were injected i.p. five days prior to cell collection

value: lymph nodes and spleen

tag: strain

tag: antibody

value: H3K27Ac Cell Signaling Rabbit mAb8173


title: Kras*_rIL-33_d21_RNA2

description:
PE-101
DACE101_IGO_10855_17_S110

value: KC + rIL-33 d21

value: Day 21

value: 8 weeks old


title: cardiac 24h TGFb1 2

description:
US-1508673
Fibroblasts_FPKM.txt

tag: replicate group

value: Fibroblast


title: H3K27Ac Low Replicate 2


title: Kras*_PBS_d21_RNA4

description:
PE-101
DACE120_IGO_10855_18_S111

value: KC + Vehicle d21

value: KC;RIK GEMM

value: pancreas

value: Female


title: cardiac 24h TGFb1 1

description:
US-1508702
Fibroblasts_FPKM.txt

value: cardiac 24h TGFb1

value: heart

tag: cell type


title: cardiac 48h TGFb1 1

description:
US-1508663
Fibroblasts_FPKM.txt

value: cardiac 48h TGFb1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD001

tag: age

value: brain

tag: source

value: PTLp

tag: target

value: SSp

tag: gender

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C6_AD002


title: H3K27Ac Naïve Replicate 2

value: lymph nodes and spleen


title: Kras*_PBS_d21_RNA3

description:
PE-101
DACE103_IGO_10855_19_S112

tag: experimental condition

tag: model

tag: genotype

tag: treatment

value: PBS

value: Male


title: H3K27Ac High Replicate 2

value: H3K27Ac Cell Signaling Rabbit mAb8173


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD012

value: ACA

value: female


title: H3K27Ac High Replicate 1


title: cardiac 24h CTRL 3

description:
US-1508674
Fibroblasts_FPKM.txt

value: cardiac 24h CTRL

value: Fibroblast


title: Roots_Low Fe_1

value: Bobwhite S26

value: Roots

value: 8-10 days post anthesis (DPA)


title: Kras*_rIL-33_d21_RNA4

description:
PE-101
DACD912_IGO_10855_5_S98

value: KC + rIL-33 d21

value: KC;RIK GEMM

tag: oncotype

tag: time point

value: Day 21

value: pancreas

tag: sorting strategy

tag: age (upon sample collection)

value: 8 weeks old

value: Female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD010

tag: tissue

value: brain

value: PTLp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD008

tag: strain

value: male


title: Kras*_PBS_d21_RNA2

description:
PE-101
DACD928_IGO_10855_4_S97

value: KC + Vehicle d21

value: PBS

tag: Sex

value: Male


title: cardiac 24h CTRL 2

description:
US-1508686
Fibroblasts_FPKM.txt

tag: replicate group

value: cardiac 24h CTRL

value: heart


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD004

value: SSp

value: female


title: Kras*_rIL-33_d0_RNA3

description:
PE-101
DACE117_IGO_10855_8_S101

value: KC + rIL-33 d0

value: Day 0 (last treatment day)

value: 5 weeks old


title: cardiac 24h CTRL 1

description:
US-1508660
Fibroblasts_FPKM.txt

tag: cell type

value: Fibroblast


title: Kras*_PBS_d21_RNA1

description:
PE-101
DACD923_IGO_10855_2_S95

value: KC;RIK GEMM

value: Day 21

value: pancreas


title: H3K27Ac Naïve Replicate 1

value: lymph nodes and spleen

tag: antibody

value: H3K27Ac Cell Signaling Rabbit mAb8173


title: H3K4me3 High Replicate 3

value: H3K4me3 Cell Signaling Rabbit mAb9752


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD006

tag: age

value: brain

tag: source

value: PTLp


title: Kras*_rIL-33_d0_RNA4

description:
PE-101
DACE118_IGO_10855_9_S102

value: Male


title: D. simulans, late stage 5, replicate 3

city: Davis

first: Susan

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

description:
sim_st5_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: sim_sec_crosses_allele_specific_counts.txt

data_processing:
Adapter sequences trimmed using Cutadapt (v. 1.7.1).
Reads aligned to genomes using Tophat2 (v. 2.0.13).
Variants to identify allele-specific reads called using GATK haplotype caller.
Allele-specific reads counted using custom Python and R scripts (available with publication).
Counts normalized to upper quantile for total number of counts mapped per individual to a genome.
Genome_build: D. simulans (version r2.02); D. sechellia (version r1.3); D. mauritiana M17 assembly (Nolte et al., 2013; see Methods in publication).
Supplementary_files_format_and_content: *.txt: Allele-specific counts, mapping each hybrid individual to both parental genomes.

organism: Drosophila simulans

source_name: late stage 5 embryo

growth_protocol: Cornmeal media, 25 degrees, population-controlled, eggs collected from mothers 4-14 days old.

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Standard Illumina mRNA-Seq library prep protocols, using Illumina TruSeq kits.

treatment_protocol: Crosses between species as specified, to produce hybrid maternal transcriptomes for stage 2 embryos and hybrid zygotic transcriptomes for late stage 5 embryos.

value: embryo

tag: generation

value: Parental

tag: embryonic stage

value: late stage 5

tag: embryo sex

value: unknown

tag: replicate number


title: H3K4me3 Low Replicate 3

value: H3K4me3 Cell Signaling Rabbit mAb9755


title: D. simulans, late stage 5, replicate 2,

description:
sim_st5_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: sim_sec_crosses_allele_specific_counts.txt


title: H3K4me3 Low Replicate 2

value: H3K4me3 Cell Signaling Rabbit mAb9754


title: H3K4me3 High Replicate 1

value: H3K4me3 Cell Signaling Rabbit mAb9751


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD002

source_name: C57BL/6J P56 Mouse Brain

tag: target

value: SSp

tag: gender

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD012

value: ACA

value: female


title: H3K4me3 Low Replicate 1

value: lymph nodes and spleen

value: H3K4me3 Cell Signaling Rabbit mAb9753


title: D. simulans, stage 2, replicate 1

description:
sim_st2_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: sim_sec_crosses_allele_specific_counts.txt

source_name: stage 2 embryo

value: stage 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C5_AD001

value: brain


title: Kras*_rIL-33_d0_RNA2

description:
PE-101
DACE116_IGO_10855_11_S104

tag: experimental condition

value: KC + rIL-33 d0

tag: model

value: KC;RIK GEMM

tag: genotype

tag: oncotype

tag: treatment

tag: time point

value: Day 0 (last treatment day)

value: pancreas

value: 5 weeks old


title: H3K4me3 Naïve Replicate 1

tag: tissue

tag: strain


title: D. simulans, stage 2, replicate 3

description:
sim_st2_3
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: sim_sec_crosses_allele_specific_counts.txt

value: embryo

value: Parental

value: unknown


title: Hopx High replicate 3

description: Hopx hi3

data_processing:
Basecalling was performed by Torrent Suite version 5 software using the default settings for total RNA and an 8 nt read length cutoff for the small RNA libraries
Alignment to Mus musculus genome sequence (mm10) was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
For total RNA total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of annotated genes

extract_protocol:
RNA was purified using Trizol and the  mirVana RNA isolation kit (Invitrogen) according to the manufacturer's directions
Ion Xpress IonXpressRNA barcoded sequencing libraries were constructed using the Eukaryotic Ribominus and Ion Total RNA v2 kits (Life Technologies) according to the manufacturer's directions for total RNA and small RNA libraries

treatment_protocol: Antigen-targeting chimeric antibodies specific to dendritic cells were injected i.p. five days prior to cell sorting . T cell were restimulated by APCs in vitro for 12h and resorted. RNA was extracted from resorted T cells


title: Kras*_PBS_d0_RNA3

description:
PE-101
DACE115_IGO_10855_10_S103

value: KC + Vehicle d0

value: PBS

tag: sorting strategy

tag: age (upon sample collection)

tag: Sex

value: Male


title: Atoh7 heterozygous

description: Norma retinal development

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 2.1.1 mkoutput with Bcl2Fastq 2.19.1
Cellranger 2.1.1 Count against mm10 genome to produce count matrix
Seurat 3.0 used for marker gene analysis and visualization
Genome_build: mm10
Supplementary_files_format_and_content: CSV File containing UMI corrected read counts

value: Neural retina

tag: developmental stage

value: Atoh7 heterozygous

tag: phenotype

value: Normal retinal development


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD008

tag: age

tag: source

value: PTLp

value: ACA

value: male


title: Kras*_PBS_d0_RNA2

description:
PE-101
DACE114_IGO_10855_12_S105


title: D. simulans, stage 2, replicate 2,

description:
sim_st2_2
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: sim_sec_crosses_allele_specific_counts.txt

tag: generation

tag: embryonic stage

value: stage 2

tag: embryo sex

tag: replicate number


title: H3K4me3 High Replicate 2

value: lymph nodes and spleen

tag: antibody

value: H3K4me3 Cell Signaling Rabbit mAb9751


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD007

value: brain

tag: target

tag: gender


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD006

value: SSp

value: female


title: Hopx High replicate 1

description: Hopx hi1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD004


title: Atoh7 null

description: Retinal ganglion cell deficiency

tag: genotype

value: Atoh7 null

value: Retinal ganglion cell deficiency


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD010

tag: tissue


title: Kras*_PBS_d0_RNA1

description:
PE-101
DACE060_IGO_10855_14_S107

tag: experimental condition

value: KC + Vehicle d0

tag: model

value: KC;RIK GEMM

tag: oncotype

tag: treatment

tag: time point

value: Day 0 (last treatment day)

value: pancreas

value: 6 weeks old


title: Hopx Low replicate 3

description: Hopx lo3

tag: strain


title: D. simulans, late stage 5, replicate 1

description:
sim_st5_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: sim_sec_crosses_allele_specific_counts.txt

value: embryo

value: Parental

value: late stage 5

value: unknown


title: Hopx Low replicate 2

description: Hopx lo2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD001

tag: age

value: PTLp

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C4_AD002

tag: source


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD010

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD012

value: brain


title: Hopx Low replicate 1

description: Hopx lo1

value: lymph nodes and spleen


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD008


title: Naive replicate 3


title: Naive replicate 2


title: Naive replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD006

value: SSp

value: female


title: Hopx High replicate 2

description: Hopx hi2


title: Input Replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD007


title: micro Hopx hi2

description: Hopx High replicate 2

data_processing:
Basecalling was performed by Torrent Suite version 5 software using the default settings for total RNA and an 8 nt read length cutoff for the small RNA libraries
Alignment to Mus musculus genome sequence (mm10) was performed using TMAP map4 algorithm with 5' and 3' softclipping and a minimum seed length of 20 nt
For total RNA total sequencing base pair coverage in all exons was summed for all annotated genes in each sample and normalized to total coverage using bedtools and custom R scripts as described in Wu et al. 2015 PLoS Genetics 11:e1005655.
For small RNA, the sequencing base pair coverage as summed for annotated microRNAs and normalized to total microRNA coverage
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Microsoft Excel File with normalized sequencing coverage of annotated genes

treatment_protocol: Antigen-targeting chimeric antibodies specific to dendritic cells were injected i.p. five days prior to cell collection and RNA extraction

tag: cell type

value: CD4 postive T cells

tag: molecule subtype

value: micro RNA


title: micro Hopx hi3

description: Hopx High replicate 3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD004


title: micro Hopx lo2

description: Hopx Low replicate 2


title: Kras*+Injury_KCshBrd4.552_RNA1

description:
PE-50
2_C266_RH_552_IGO_06389_B_2_S3_L001

growth_protocol: When indicated, 5 weeks-old mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) for 2 consecutive days; and FACS-sorted cells were analyzed 2 days thereafter. 6 days prior to the caerulein treatment, mice were placed on doxycycline diet to induce the expression of GFP-linked shRNA targeting Brd4 or Ren (control).

value: KC-GEMM-ESC  derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh552)

value: Doxycycline diet (6 days) + caerulein

value: Day 2 post-caerulein

tag: sorting strategy

value: 5 weeks old


title: Kras*+Injury_KCshBrd4.552_RNA2

description:
PE-50
5_C267_LH_552_IGO_06389_B_5_S8_L001

value: pancreas


title: Kras*+Injury_KCshBrd4.1448_RNA3

description:
PE-50
9_C261_2RH_1448_IGO_06389_B_9_S6_L001

value: KC-GEMM-ESC  derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh1448)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD010


title: Kras*_rIL-33_d0_RNA1

description:
PE-101
DACE059_IGO_10855_13_S106

value: KC + rIL-33 d0

value: KC;RIK GEMM

value: Day 0 (last treatment day)

tag: age (upon sample collection)

value: 6 weeks old

tag: Sex

value: Male


title: micro Hopx lo1

description: Hopx Low replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD001

value: brain

value: PTLp

tag: target

value: male


title: Kras*+Injury_KCshBrd4.1448_RNA2

description:
PE-50
6_C260_LH_1448_IGO_06389_B_6_S7_L001

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh1448)


title: Kras*+Injury_KCshBrd4.1448_RNA1

description:
PE-50
3_C261_LH_1448_IGO_06389_B_3_S5_L001


title: Kras*+Injury_KCshRen.713_RNA3

description:
PE-50
7_C264_RH_REN_IGO_06389_B_7_S2_L001

value: Kras*+Injury-shRen

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Renilla (sh713)


title: micro naive3

description: Naive replicate 3

value: lymph nodes and spleen

value: CD4 postive T cells

value: micro RNA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD007

value: ACA

tag: gender


title: Kras*+Injury_KCshBrd4.552_RNA3

description:
PE-50
8_C270_NH_552_IGO_06389_B_8_S1_L001

value: KC-GEMM-ESC  derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh552)

tag: genotype

value: Doxycycline diet (6 days) + caerulein

value: Day 2 post-caerulein

value: pancreas

value: 5 weeks old


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD006

tag: tissue

value: SSp

value: female


title: Kras*+Injury_KCshRen.713_RNA2

description:
PE-50
4_C272_2LH_REN_IGO_06389_B_4_S9_L001

tag: experimental condition


title: micro naive1

description: Naive replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C3_AD002

value: brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD004

value: PTLp


title: micro Hopx hi1

description: Hopx High replicate 1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD002

value: male


title: micro naive2

description: Naive replicate 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD001


title: micro Hopx lo3

description: Hopx Low replicate 3


title: Kras*+Injury_KCshRen.713_RNA1

description:
PE-50
1_C264_2RH_REN_IGO_06389_B_1_S4_L001

tag: model


title: Injury_CshBrd4.1448_RNA3

description:
PE-50
DAC_B396_IGO_06389_C_15_S2

value: C-shRNA GEMM

tag: oncotype

value: KrasWT


title: Hopx hi2

description: Hopx High replicate 2


title: Hopx hi1

description: Hopx High replicate 1


title: Hopx hi3

description: Hopx High replicate 3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C1_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C1_AD010


title: Injury_CshBrd4.1448_RNA2

description:
PE-50
DAC_B094_IGO_06389_C_14_S17

tag: treatment


title: Injury_CshBrd4.1448_RNA1

description:
PE-50
DAC_A940_IGO_06389_C_16_S11

tag: time point


title: Hopx lo3

description: Hopx Low replicate 3

tag: strain


title: Injury_CshRen.713_RNA3

description:
PE-50
DAC_B092_IGO_06389_C_5_S14

value: Injury-shRen

tag: age


title: naive3

description: Naive replicate 3

value: lymph nodes and spleen


title: naive2

description: Naive replicate 2

value: CD4 postive T cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C1_AD006

tag: source


title: naive1

description: Naive replicate 1

tag: cell type


title: Normal_CshRen.713_RNA2

description:
PE-50
DACA604_IGO_06389_D_9_S8

value: Normal-shRen

value: Doxycycline diet (6 days)

value: Day 6 post-doxycycline


title: Hopx lo2

description: Hopx Low replicate 2


title: Hopx lo1

description: Hopx Low replicate 1


title: D. sechellia, late stage 5, replicate 3

description:
sec_st5_3
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

organism: Drosophila sechellia

value: embryo

tag: generation

value: Parental

tag: embryonic stage

value: late stage 5

tag: embryo sex

value: unknown

tag: replicate number


title: Injury_CshRen.713_RNA1

description:
PE-50
DAC_A166_IGO_06389_C_9_S7

value: Doxycycline diet (6 days) + caerulein

value: Day 2 post-caerulein

value: pancreas

tag: sorting strategy

value: 5 weeks old


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C1_AD004

value: brain

value: PTLp

tag: target

value: SSp

tag: gender

value: female


title: Normal_CshRen.713_RNA3

description:
PE-50
DACA607_IGO_06389_D_10_S15

value: C-shRNA GEMM

tag: genotype

value: KrasWT

tag: tissue


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD007

value: ACA

value: male


title: D. sechellia, late stage 5, replicate 1

description:
sec_st5_1
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C1_AD002


title: D. sechellia, stage 2, replicate 3

description:
sec_st2_3
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: stage 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C1_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD004


title: PDAC_RNA1

description:
PE-50
C5_6_PDAC_1215_C5_1_IGO_06389_C_40_S33

source_name: sorted PDAC cells

growth_protocol: For caerulein or PBS (control) treatments, 5 weeks-old KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) littermate male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) or PBS for 2 consecutive days.

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected directly into Trizol-LS.

tag: experimental condition

value: PDAC

tag: model

value: KPflC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

tag: sample collection time point

value: PDAC lesion

tag: age / stage (upon sample collection)


title: Kras*+Injury_RNA4

description:
PE-50
DACC040_IGO_06389_E_9_S22

value: Kras*+Injury

value: KC;RIK GEMM

tag: treatment

value: Caerulein

value: 5 - 6 weeks old


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD002

tag: strain

tag: age

tag: source


title: cardiac 6h CTRL 1

description:
US-1508671
Fibroblasts_FPKM.txt

tag: replicate group

value: cardiac 6h CTRL

value: heart

tag: cell type

value: Fibroblast


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD012

value: brain

value: PTLp


title: D. sechellia, stage 2, replicate 2,

description:
sec_st2_2
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: embryo

tag: generation

value: Parental

tag: embryonic stage

tag: embryo sex

value: unknown

tag: replicate number


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD010

tag: tissue

tag: target

value: ACA

tag: gender

value: female


title: PDAC_RNA3

description:
PE-50
C5_RenOff_2_PDAC_IGO_06389_C_39_S4

tag: experimental condition

value: PDAC

tag: model

tag: alleles (gemm)

value: pancreas

tag: sorting strategy


title: PDAC_RNA2

description:
PE-50
C5_RenOff_1_PDAC_IGO_06389_C_38_S3

value: KPflC;RIK GEMM

tag: oncotype (sorted cells)

tag: treatment

tag: sample collection time point

value: PDAC lesion

tag: age / stage (upon sample collection)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD001

tag: strain

tag: age

tag: source

value: SSp

value: male


title: Normal_CshRen.713_RNA1

description:
PE-50
DACA603_IGO_06389_D_8_S16

value: Normal-shRen

value: C-shRNA GEMM

tag: genotype

tag: oncotype

value: KrasWT

value: Doxycycline diet (6 days)

tag: time point

value: Day 6 post-doxycycline

value: 5 weeks old


title: D. sechellia, late stage 5, replicate 2,

description:
sec_st5_2
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

tag: tissue

value: embryo

tag: generation

tag: embryonic stage

value: late stage 5

tag: embryo sex

tag: replicate number


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C12_AD006

value: brain

value: PTLp

tag: target

tag: gender


title: Injury_CshRen.713_RNA2

description:
PE-50
DAC_A682_IGO_06389_C_8_S6

tag: experimental condition

value: Injury-shRen

tag: model

value: Doxycycline diet (6 days) + caerulein

value: Day 2 post-caerulein

tag: sorting strategy


title: Hif1a_Hif2a_ko_Hyp_Rep1

city: Chongqing

first: liao

last: bin

address: 118 Xingguang Avenue

institute: Chongqing General Hospital, Chongqing University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome using HISAT2
Transcript abundance was calculated using STRINGTIE
Differential expression analysis was performed using DESeq2
Genome_build: human miRBase build 22
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample

source_name: glioblastoma

growth_protocol: U87-MG cells were incubated in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, 100U/ml penicillin and 100μg/ml streptomycin. HIF1α knock-out, HIF2α knock-out and HIF1α/HIF2α knock-out simultaneously cells was made through CRISPR/Cas9 system.

extract_protocol:
RNA was extracted from cell samples using Trizol reagent combined with Qiagen miRNeasy Mini Kit.
Performed by Genminix Informatics Co., Ltd. (Shanghai, China) in accordance with standard Illumina protocols.

treatment_protocol: The cells were cultured under normoxia condition(21% O2) and hypoxia condition (1% O2) in Hypoxia Incubator Chamber (STEMCELL) for 24h and then the cells were collected.

tag: cell line

value: Hif1a Hif2a knock-out

tag: treatment

value: hypoxia


title: Hif2a_ko_Hyp_Rep2

value: Hif2a knock-out


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C11_AD006

tag: strain

tag: age

value: SSp

value: female


title: Hif1a_Hif2a_ko_Hyp_Rep3

tag: genotype


title: Kras*+Injury_RNA3

description:
PE-50
DAC_B612_IGO_06389_C_45_S6

value: Kras*+Injury

value: KC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: Caerulein

tag: sample collection time point

value: pancreas

tag: age / stage (upon sample collection)

value: 5 - 6 weeks old


title: Hif1a_Hif2a_ko_Hyp_Rep2


title: Hif2a_ko_Hyp_Rep1


title: Kras*+Injury_RNA2

description:
PE-50
DAC_A954_IGO_06389_C_29_S18

tag: tissue


title: D. sechellia, stage 2, replicate 1

description:
sec_st2_1
mRNA
processed data file: sim_sec_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: embryo

tag: generation

value: Parental

tag: embryonic stage

value: stage 2

tag: embryo sex

value: unknown


title: Kras*_RNA2

description:
PE-50
DAC_B098_IGO_06389_C_47_S8

value: Kras*

value: PBS

value: Day 2 post-PBS


title: Kras*+Injury_RNA1

description:
PE-50
DAC_A226_IGO_06389_C_34_S20

value: Day 2 post-caerulein


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C11_AD007

value: brain

tag: source

value: PTLp

tag: target

value: ACA

tag: gender

value: male


title: Kras*_RNA3

description:
PE-50
DAC_B837_IGO_06389_C_32_S1

tag: experimental condition

tag: model

tag: sorting strategy


title: Hif2a_ko_Hyp_Rep3

tag: cell line

value: Hif2a knock-out

tag: treatment

value: hypoxia


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C11_AD001

tag: strain

tag: age

value: SSp


title: Hif1a_ko_Hyp_Rep1

tag: genotype

value: Hif1a knock-out


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD012

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C11_AD002


title: Kras*_RNA1

description:
PE-50
DAC_A897_IGO_06389_C_44_S5

value: KC;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

tag: sample collection time point

value: pancreas

value: 5 - 6 weeks old


title: Australian AD S80

type: RNA

first: Eric

last: Vornholt

address: 800 E. Leigh St. Box 980126

institute: Icahn School of Medicine

hyb_protocol: Ten µg of fragmented cRNA were hybridized on the Affymetrix GeneChip Human Genome U133A 2.0 (HG-U133A 2.0).

scan_protocol: Each array was scanned on the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) and raw probe intensities stored in .CEL files by the GeneChip Operating Software (GCOS v1.4).

data_processing: Array quality was assessed by monitoring the ratios of GAPDH and by the percentage of Present genes (%P) and array exhibiting GAPDH 3 and %P > 40% were considered of good quality. Expression values were calculated following the pre-processing procedure: 1) GCRMA background correction, 2) log2 transformation, 3) quantile normalization and 4) median-polish probeset summarization using Partek Genomics Suite (PGS) v6.23 (PGS; Partek Inc., St. Louis, MO). The batch effect removal option in PGS was used to control for batch effect. mRNA and miRNA microarray quality was further assessed using a principal components analysis (PCA) which was conducted on the expression values for both array types in which samples were plotted along the first three principle components (PCs) to identify potential microarray outliers.

label: biotin

source_name: prefrontal cortex

label_protocol: Starting from 300ng of total RNA, cDNA synthesis and cRNA labelling were performed using the GeneChip 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA containing the small RNA fraction was isolated from 100mg fresh frozen tissue from the prefrontal cortex (PFC) using the mirVana-PARIS kit (Life Technologies, Carlsbad, CA) following manufacturer's protocols. RNA concentration was measured using the Quant-iT Broad Range RNA Assay kit (Life Technologies) and the RNA Integrity Number (RIN) was measured on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

tag: tissue

value: prefrontal cortex

tag: diagnosis

value: Control

tag: Sex

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: Injury_RNA5

description:
PE-50
DAC_A999_IGO_06389_C_43_S35

tag: experimental condition

value: Injury

tag: model

value: C;RIK GEMM

value: KrasWT

tag: treatment

value: Caerulein

tag: sorting strategy

tag: age / stage (upon sample collection)


title: Hif1a_ko_Hyp_Rep2

tag: cell line

tag: genotype


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD008

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: ACA

tag: gender


title: Australian AD S76

tag: diagnosis

value: Alcohol

tag: Sex

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology


title: Australian AD S73

tag: hepatology

tag: toxicology

tag: smoking


title: Hif1a_ko_Hyp_Rep3

tag: cell line

tag: genotype

tag: treatment

value: hypoxia


title: Australian AD S82

tag: tissue

tag: age


title: Australian AD S77


title: WT_Hyp_Rep3

value: WT


title: Australian AD S69


title: Normal_RNA4

description:
PE-50
DAC_B873_IGO_06389_C_30_S32

tag: experimental condition

value: Normal

tag: model

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: PBS

tag: sample collection time point

value: Day 2 post-PBS

tag: sorting strategy

tag: age / stage (upon sample collection)


title: Australian AD S74

tag: diagnosis

tag: Sex

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere


title: Injury_RNA3

description:
PE-50
DAC_A950_IGO_06389_C_26_S31

tag: treatment

value: Day 2 post-caerulein

value: pancreas

value: 5 - 6 weeks old


title: Injury_RNA2

description:
PE-50
DAC_A756_IGO_06389_C_61_S12

tag: tissue


title: WT_Nor_Rep3

tag: cell line

tag: genotype

value: normoxia


title: Injury_RNA1

description:
PE-50
DAC_A224_IGO_06389_C_46_S7

tag: experimental condition

value: Injury

tag: model


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD007

tag: strain

tag: age

tag: source

tag: target

tag: gender

value: male


title: WT_Hyp_Rep2


title: Normal_RNA3

description:
PE-50
DAC_B097_IGO_06389_C_33_S19

value: C;RIK GEMM

tag: alleles (gemm)

tag: oncotype (sorted cells)

value: KrasWT

tag: sample collection time point

tag: sorting strategy

tag: age / stage (upon sample collection)


title: Injury_RNA4

description:
PE-50
DAC_A955_IGO_06389_C_27_S17

value: Caerulein


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD006

value: brain

value: PTLp

value: SSp

value: female


title: WT_Hyp_Rep1

value: WT

value: hypoxia


title: Normal_RNA2

description:
PE-50
DAC_A962_IGO_06389_C_48_S9

value: Normal

value: PBS


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD004


title: Normal_RNA1

description:
PE-50
DAC_A946_IGO_06389_C_25_S16

value: Day 2 post-PBS


title: Australian AD S68

value: prefrontal cortex

tag: diagnosis

value: Control

tag: Sex

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: WT_Nor_Rep1

tag: cell line

tag: genotype

tag: treatment

value: normoxia


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD001

tag: strain

tag: age

tag: tissue

tag: source

tag: target

tag: gender

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C10_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD012

value: ACA


title: BDL wk5 liver 5

description:
RS-720744
BDL_FPKM.txt

organism: Rattus norvegicus

source_name: Liver

tag: replicate group

value: Liver


title: Australian AD S65

tag: diagnosis

tag: Sex

tag: rin

tag: brain weight

tag: ph


title: BDL wk5 liver 4

description:
RS-720743
BDL_FPKM.txt


title: 0246_c56d_ITGA6+_RNA-seq

city: Amsterdam

first: Robin

last: Struijk

address: Meibergdreef 9

department: Center for Reproductive Medicine

country: Netherlands

institute: Amsterdam UMC location AMC

data_processing:
Base-calling and demultiplexing was performed using Illumina CASAVA 1.8.2
Paired-end reads of 2×100bp were trimmed using Trimmomatic v0.32. Reads ≥ 15 nucleotides passed the filter.
Alignment of trimmed reads to the hg19 human reference genome was performed using TopHat/Bowtie2 v2.1.0
Count data was obtained using HTSeq v0.5.4p3.
Counts were normalized using edgeR, employing a published trimmed mean of M-values method (Robinson et al. , 2010, Robinson and Oshlack, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include processed log2 counts-per-million (log2CPM) values for every gene, per sample

source_name: mixed testicular cells

growth_protocol: Testicular biopsies were subjected to a two-step enzyme digestion (1mg/mL type I collagenase (4196, Worthington), 1mg/mL type II hyaluronidase (H2126, Sigma) and 1mg/mL trypsin TRL3 (3707, Worthington), followed by 1mg/mL type I collagenase and 1mg/mL type II hyaluronidase) and the resulting single-cell suspension was plated overnight in 1× MEM containing 20% FCS. The next day, floating cells (containing the germ cell fraction) were separated from the attached cell fraction via gentle pipetting and transferred to a new culture flask. The medium used for PTC culture contained StemPro-34 SFM medium (10639–011, Life Technologies) supplemented with several key growth factors promoting spermatogonial stem cells self-renewal (GDNF, EGF, PDGF, LIF).

extract_protocol:
Total RNA was extracted from ITGA6+ sorted primary testicular cells using a MagNA Pure LC instrument (Life Technologies). RNA was amplified using the Ovation RNA-Seq System V2 kit (NuGEN Technologies, lot no. 1307479-B) according to manufacturer’s protocol.
A total of 1 µg amplified cDNA was barcoded with a unique set of standard Illumina TruSeq indexed adapters by ligation and sequenced on an Illumina HiSeq 2000 high-throughput sequencer according to manufacturer's protocol.

treatment_protocol: Mixed primary testicular cell fractions were either directly subjected to magnetic-activated cell sorting for ITGA6+ cells (day 0; d0-PTC) to enrich for spermatogonia or first brought into culture and then sorted.

value: testis

tag: donor age

tag: sorting

tag: culture duration

value: 56 days


title: Australian AD S66

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD010

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD008

tag: gender


title: Australian AD S62

tag: diagnosis

value: Alcohol

tag: Sex

tag: rin

tag: brain weight


title: Australian AD S60

tag: ph


title: 0246_c3d_ITGA6+_RNA-seq

tag: donor age

tag: sorting

tag: culture duration

value: 3 days


title: Australian AD S64

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: Australian AD S61

tag: age

tag: toxicology

tag: smoking


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD007

tag: strain

tag: tissue

tag: source

tag: target


title: BDL wk5 liver 2

description:
RS-720741
BDL_FPKM.txt

tag: replicate group


title: Australian AD S57

tag: diagnosis

tag: Sex

tag: rin

tag: brain weight


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD006

value: SSp

tag: gender

value: female


title: 0246_c1d_ITGA6+_RNA-seq

tag: donor age

tag: sorting

tag: culture duration

value: 1 day


title: BDL wk5 liver 1

description:
RS-720740
BDL_FPKM.txt


title: BDL wk5 sham liver 5

description:
RS-720738
BDL_FPKM.txt


title: BDL wk5 sham liver 6

description:
RS-720739
BDL_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD004


title: 0246_c13d_ITGA6+_RNA-seq

value: 13 days


title: 0179_c56d_ITGA6+_RNA-seq


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD002


title: Australian AD S56

value: prefrontal cortex

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: BDL wk5 liver 3

description:
RS-720742
BDL_FPKM.txt

tag: tissue


title: 0246_f0_ITGA6+_RNA-seq

value: 0 hours


title: 0179_c13d_ITGA6+_RNA-seq


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B8_AD012

tag: strain

tag: age

tag: source


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B9_AD001

tag: target


title: 0246_c4h_ITGA6+_RNA-seq

value: 4 hours


title: Australian AD S51

tag: diagnosis

value: Control

tag: Sex

value: Male

tag: toxicology

tag: smoking


title: Australian AD S54

tag: rin

tag: brain weight


title: BDL wk5 sham liver 4

description:
RS-720737
BDL_FPKM.txt

tag: replicate group


title: Australian AD S48

tag: ph


title: BDL wk5 sham liver 2

description:
RS-720735
BDL_FPKM.txt


title: 0179_c3d_ITGA6+_RNA-seq

tag: donor age

tag: sorting

tag: culture duration


title: 0179_c1d_ITGA6+_RNA-seq


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B8_AD008

value: ACA

tag: gender

value: male


title: Australian AD S45

tag: tissue

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: BDL wk3 liver 5

description:
RS-720723
BDL_FPKM.txt

value: Liver


title: BDL wk5 sham liver 1

description:
RS-720734
BDL_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_C11_AD010

tag: strain

tag: age

tag: source

tag: target


title: BDL wk5 sham liver 3

description:
RS-720736
BDL_FPKM.txt


title: 0179_c4h_ITGA6+_RNA-seq

value: testis


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B8_AD004

value: brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B8_AD007

value: PTLp


title: Australian AD S46

tag: diagnosis

value: Alcohol

tag: Sex

tag: rin

tag: toxicology

tag: smoking


title: BDL wk3 liver 4

description:
RS-720722
BDL_FPKM.txt

tag: replicate group


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B8_AD002


title: Australian AD S43

tag: brain weight

tag: ph


title: 0179_f0_ITGA6+_RNA-seq

tag: tissue

tag: donor age

tag: sorting

tag: culture duration


title: 0077_c53d_ITGA6+_RNA-seq

value: 53 days


title: BDL wk3 liver 2

description:
RS-720720
BDL_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B8_AD001

value: SSp

tag: gender


title: 0077_c13d_ITGA6+_RNA-seq


title: Australian AD S40

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: BDL wk3 liver 1

description:
RS-720719
BDL_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD012

tag: strain

tag: age

tag: source

tag: target

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD010


title: BDL wk3 sham liver 5

description:
RS-720718
BDL_FPKM.txt


title: 0077_c3d_ITGA6+_RNA-seq

value: 3 days


title: Australian AD S33

tag: diagnosis

tag: Sex

tag: rin

tag: toxicology

tag: smoking


title: Australian AD S42

tag: tissue

tag: brain weight

tag: ph


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD008

tag: gender


title: BDL wk3 sham liver 4

description:
RS-720717
BDL_FPKM.txt

tag: replicate group


title: Australian AD S30

tag: pmi

tag: hemisphere


title: 0077_c1d_ITGA6+_RNA-seq

tag: donor age

tag: sorting

tag: culture duration

value: 1 day


title: 0077_c4h_ITGA6+_RNA-seq


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD006

tag: strain

tag: age

tag: source


title: BDL wk3 sham liver 3

description:
RS-720716
BDL_FPKM.txt


title: 0077_f0_ITGA6+_RNA-seq


title: Australian AD S27

value: prefrontal cortex

tag: diagnosis

tag: Sex

tag: neuropathology

tag: hepatology


title: BDL wk3 sham liver 2

description:
RS-720715
BDL_FPKM.txt

tag: tissue


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD004

tag: target


title: Australian AD S35

tag: rin

tag: brain weight

tag: ph

tag: toxicology

tag: smoking


title: Australian AD S26

tag: pmi

tag: hemisphere


title: Australian AD S25


title: BDL wk3 sham liver 1

description:
RS-720714
BDL_FPKM.txt

tag: replicate group


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD002

tag: strain

tag: gender


title: Australian AD S24

tag: age


title: 0034_c13d_ITGA6+_RNA-seq

tag: donor age

tag: sorting

tag: culture duration

value: 13 days


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B7_AD001

tag: source


title: 0034_c1d_ITGA6+_RNA-seq

tag: tissue


title: 0034_c3d_ITGA6+_RNA-seq


title: abr1_hrcC_rep3

city: Albany

first: Jennifer

last: Lewis

address: 800 Buchanan St

institute: University of California, Berkeley

data_processing:
Base-calling was performed using CASAVA software.
Read quality was assessed with FastQC, and the first 12 nucleotides of each read were removed with Trimmomatic.
Reads were aligned to the Arabidopsis TAIR10 genome with either STAR or HISAT2 and read counts determined by the program featureCounts.
Normalized abundance measurements were generated by the edgeR and limma-voom algorithms, from which a consensus list of differentially expressed genes was derived.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Plants were grown in a controlled environment room with a 9-h photoperiod (130 mE∙m-2s-1) at constant 22°C and 60% RH

extract_protocol:
TRIzol reagent (Thermo Fisher Scientific, Inc., Waltham, MA) was used to extract RNA from Arabidopsis leaves, according to the manufacturer’s instructions.  Samples were treated with DNase and further purified using RNA Clean and Concentrator kits (Zymo Research Corp.) and RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Using a needleless 1 mL syringe, the leaves of wild-type and abr1 mutants infiltrated with either 10 mM MgCl2 (Control), 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000, or 1 x 108 cfu/mL P. syringae pv. tomato DC3000 ΔhrcC.  Tissues were harvested at 12 h post-infiltration.

tag: ecotype

tag: genotype

value: leaves

tag: plant age

value: six weeks old

tag: treatment

value: 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000 ΔhrcC

tag: treatment duration


title: WT_Nor_Rep2

tag: cell line

value: WT

value: normoxia


title: 0034_c66d_ITGA6+_RNA-seq

value: 66 days


title: abr1_Mg_rep3

value: 10 mM MgCl2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD012

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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

value: brain

tag: target

value: ACA


title: 0034_c4h_ITGA6+_RNA-seq

value: testis

value: 4 hours


title: Australian AD S18

tag: diagnosis

value: Control

tag: Sex

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: 0034_f0_ITGA6+_RNA-seq

tag: tissue

tag: donor age

tag: sorting

tag: culture duration

value: 0 hours


title: abr1_DC_rep3

tag: ecotype

tag: genotype

tag: plant age

tag: treatment

value: 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000

tag: treatment duration


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD008

tag: strain

tag: age

tag: source

value: PTLp

tag: target

tag: gender

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B6_AD002

value: SSp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B6_AD001


title: WT_hrcC_rep3

value: leaves

value: six weeks old


title: Synovial fluid neutrophil patient 54

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description: SF.Gene.Rep.Matrix.csv

data_processing:
Fastq files were aligned to the human genome using Tophat v2.0.4 including the --max-multihits 1 option. RPKM were calculated using Cufflinks v2.0.2 and statistical analysis was carried out using cuffdiff with FDR < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: gene_exp.diff file contains statistical analysis of replicate data (Blood PMN vs SF PMN)
Supplementary_files_format_and_content: SF.Gene.Rep.Matrix.csv contains a matrix of gene expression values (RPKM) for each biological sample

source_name: Neutrophil (PMN)

extract_protocol:
Neutrophils were isolated from peripheral blood using Polymorphprep. Neutrophils were isolated from synovial fluid using Ficoll-Paque.  RNA was extracted from 10^7 neutrophils using Trizol. RNA was cleaned using Qiagen RNeasy kit including on-column DNase digestion step, eluted in water and frozen at -80oC. RNA was poly-A selected prior to library construnction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: F

value: Knee synovial fluid


title: Blood neutrophil patient 54

description: SF.Gene.Rep.Matrix.csv

value: Peripheral blood


title: abr1_DC_rep2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD006

value: female


title: Australian AD S20

value: prefrontal cortex

tag: diagnosis

tag: Sex

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: WT_DC_rep3

tag: ecotype

tag: genotype

value: WT

tag: tissue

tag: plant age


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD004

tag: strain

tag: age

value: brain


title: Australian AD S13

value: Alcohol

tag: toxicology

tag: smoking


title: WT_Mg_rep3

tag: treatment

value: 10 mM MgCl2

tag: treatment duration


title: Synovial fluid neutrophil patient 42

description: SF.Gene.Rep.Matrix.csv

tag: gender


title: abr1_hrcC_rep2

value: 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000 ΔhrcC


title: Synovial fluid neutrophil patient 10

description: SF.Gene.Rep.Matrix.csv

value: M


title: WT_DC_rep2

value: 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD001

tag: source

value: PTLp

tag: target


title: TAMR-ATF2 si2 repl5

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All data analyses were performed on R using Bioconductor packages. Raw intensity data from the array scanner was processed using the BASH and HULK algorithms as implemented in the bead array package.

source_name: TAMR cells

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

growth_protocol: MCF7 cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% foetal bovine serum (FBS), 5mM L-glutamine and 1% penicillin/streptomycin. TAMR cells were maintained in DMEM phenol red-free supplemented with 5% charcoal/dextran-stripped FBS (CSS), 1% P/S and 100nM 4-hydroxytamoxifen (4-OH-Tam).

extract_protocol: Total RNA was extracted from the cells using the Qiagen RNeasy kit (Crawley, UK) following manufacturer's protocol.

treatment_protocol: 2.5x10^5 cells/well in 6-well plate were transfected with 100nM of each of the ATF2-siRNA duplexes including the siControl (si-NT) using RNAiMAX, according to manufacturer’s instructions (Thermofisher Scientific, Paisley, UK) and incubated in DMEM phenol red-free medium with 5% CSS. Following overnight incubation, the transfected cells were changed to their standard growth medium for 48 hours.

tag: cell line

value: TAMR cells

tag: sirna

value: ATF2 si2

tag: group

value: Estrogen receptor positive


title: TAMR-ATF2 si2 repl3


title: abr1_Mg_rep2

value: leaves

value: six weeks old


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B5_AD002

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: SSp

value: male


title: Australian AD S70

tag: diagnosis

tag: Sex

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: TAMR-ATF2 si2 repl4


title: TAMR-ATF2 si2 repl1


title: Blood neutrophil patient 10

description: SF.Gene.Rep.Matrix.csv

tag: age

tag: tissue

value: Peripheral blood


title: WT_hrcC_rep2

tag: ecotype

tag: genotype

value: WT

tag: plant age

tag: treatment

tag: treatment duration


title: WT_Mg_rep2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B4_AD007

tag: strain

value: brain

tag: source

tag: target

value: ACA

tag: gender


title: TAMR-ATF2 si2 repl2

tag: cell line

tag: sirna

tag: group


title: abr1_hrcC_rep1


title: TAMR-ATF2 si1 repl5

value: ATF2 si1


title: abr1_DC_rep1


title: TAMR-ATF2 si1 repl4


title: abr1_Mg_rep1

value: 10 mM MgCl2


title: H889_R

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to hg19 genome using tophat v2.0.13
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq/miRNAseq reads count were calculated using HTSeq 0.6.1p1

growth_protocol: Cells were harvested at >80% viability

extract_protocol:
Tumors were collected and RNA extracted using Trizol reagent and purified with a Qiagen RNeasy kit
Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.

value: untreated


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B4_AD001

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: NJH29_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B4_AD002


title: H865_R


title: TAMR-ATF2 si1 repl2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B4_AD004

value: female


title: H847_R


title: WT_DC_rep1

value: 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000


title: SHP77_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B4_AD006

value: PTLp


title: WT_hrcC_rep1

value: 1 x 108 cfu/mL Pseudmonas syringae pv. tomato DC3000 ΔhrcC


title: H841_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B3_AD012


title: H82_R


title: TAMR siNT repl5

value: TAMR cells

value: siNT

value: Estrogen receptor positive


title: TAMR siNT repl3


title: TAMR siNT repl2


title: H774_R


title: TAMR-ATF2 si1 repl3


title: TAMR siNT repl1


title: WT_Mg_rep1

value: leaves

value: six weeks old


title: Blood neutrophil patient 42

description: SF.Gene.Rep.Matrix.csv

value: F


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B3_AD007

value: male


title: TAMR-ATF2 si1 repl1


title: MCF7-ATF2 si2 repl5

source_name: MCF7 cells

value: MCF7 cells

value: ATF2 si2


title: MCF7-ATF2 si2 repl3


title: H735_R


title: H740_R


title: RNA isolated from 1µM CAG treated sample

city: ISTANBUL

first: Wissem

last: Mhiri

address: DAVUTPASA MAH. DAVUTPASA CADDESI ESENLER

department: chemistry

country: Turkey

institute: Yildiz technial university

description: Sample 1B

data_processing:
Solexa/Illumina FASTQ variants for base-calling
Reads were filtered using the software SOAPnuke (v1.5.2, https://github.com/BGI-flexlab/SOAPnuke) in order to obtain clean reads, which were then stored in FASTQ format. Clean reads were mapped using HISAT (v2.0.4, http://www.ccb.jhu.edu/software/hisat) and transcriptome assembly was set using StringTie software (v1.0.4, http://ccb.jhu.edu/software/stringtie)
The clean data were mapped to the unigene library using Bowtie2 (v2.2.5, http://bowtie-bio.sourceforge.net/Bowtie2/index.shtml), then the expression level for each gene from our data was measured using REM (v1.2.12, http://deweylab.biostat.wisc.edu/REM). FPKM for each unigene was calculated to determine the unigene expression profiles
The clean data were mapped to the unigene library using Bowtie2 (v2.2.5, http://bowtie-bio.sourceforge.net/Bowtie2/index.shtml), then the expression level for each gene from our data was measured using REM (v1.2.12, http://deweylab.biostat.wisc.edu/REM). FPKM for each unigene was calculated to determine the unigene expression profiles. Genes with differential expression (DEG) between the two samples were identified via PossionDis, followed by their hierarchical clustering and their Gene Ontology analysis using pheatmap and phyper R functions, respectively.
The selected DEGs were compared to KEGG pathway database and Gene Ontology for pathway mapping and GO-term enrichment, respectively. The DEGs were also analyzed for a more general overview of changes in gene expression in the involved pathways.
Supplementary_files_format_and_content: excel

source_name: roots

growth_protocol: Calli were developed using root explants which were cut and placed into fresh MS medium containing 0.5 mL of 2,4-dichlorophenoxyacetic acid (2,4-D). The obtained callus cultures were continuously sub-cultured for 9 months.

extract_protocol:
Total RNA was isolated from the frozen calli of A. thaliana using TRIzol reagent
Libraries were constructed following the High-Throughput illumina sequencing library protocol. After being checked for integrity, 40µg of total RNA was used to purify the poly-A-containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: Calli were then divided into two groups based on the supplemented CAG concentration: control group and 1 µM CAG. Three biological repetitions were set for each concentration. Calli were developed in a plant growth cabin at 25°C ±1°C under 16h light/8h dark light conditions for 21 days

value: 1uM Cycloastragenol

value: callus


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B3_AD006

city: La Jolla

value: brain

value: SSp


title: RNA isolated from non-treated sample

description: Sample 1A

value: non-treated


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B2_AD012

value: ACA

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B3_AD004

value: PTLp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B3_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B3_AD002


title: H719_R

value: untreated


title: H69_R


title: H69CPR_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B2_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B2_AD004


title: MCF7-ATF2 si2 repl2


title: MCF7-ATF2 si1 repl5

value: ATF2 si1


title: GK81

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description:
34_N
Gene expression data from papillary thyroid carcinoma

hyb_protocol: Hybridization was performed according to manufacturer’s standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner

data_processing: Raw CEL files were imported in R and pre-processed using the robust multi-array average method implemented in the oligo Bioconductor package

label: Biotin

source_name: non-neoplastic thyroid

label_protocol: RNA was labeled and processed according to manufacturer’s recommended protocols.

extract_protocol: RNA was extracted from snap-frozen tissues using Qiagen miRNeasy Mini Kit and quantified by Qubit 2.0 Fluorometer (Thermo Fisher).

treatment_protocol: Patients received RAI treatment following tumor surgical resection (thyroidectomy)

tag: histological variant

value: non-neoplastic thyroid

tag: tissue type

tag: collection before/after rai

value: Before

tag: patient id

tag: patient rai responce

value: Refractory

tag: rai uptake at the metastatic site

value: No

tag: disease

value: Persistence

tag: lesion by ptc-ma

tag: lesion class

tag: patients with available multiple tumor specimens

tag: tumor purity class by cibersort

value: high purity

tag: mir expression profiles

value: Not Available


title: MCF7-ATF2 si2 repl1

value: MCF7 cells

value: ATF2 si2

value: Estrogen receptor positive


title: MCF7-ATF2 si2 repl4


title: H526_R

tag: treatment


title: GK75

description:
30_N
Gene expression data from papillary thyroid carcinoma

value: Available


title: MCF7-ATF2 si1 repl4


title: MCF7-ATF2 si1 repl2


title: GK69

description:
27_N
Gene expression data from papillary thyroid carcinoma


title: MCF7-ATF2 si1 repl3


title: GK73

description:
29_N
Gene expression data from papillary thyroid carcinoma

value: low purity


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B2_AD010

tag: strain

tag: age

tag: tissue

value: brain

tag: source

tag: target

value: ACA

tag: gender


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B2_AD001

value: PTLp

value: SSp

value: male


title: H524_R

tag: cell line

value: untreated


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B2_AD002


title: GK71

description:
28_N
Gene expression data from papillary thyroid carcinoma

tag: histological variant

value: non-neoplastic thyroid

tag: tissue type

tag: collection before/after rai

value: Before

tag: patient id


title: GK66

description:
26_N
Gene expression data from papillary thyroid carcinoma

tag: patient rai responce

value: Refractory

tag: rai uptake at the metastatic site

value: No

tag: disease

tag: lesion by ptc-ma


title: H660_R


title: H510A_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD012

value: female


title: GK56

description:
19_N
Gene expression data from papillary thyroid carcinoma

value: Yes

value: Persistence

tag: lesion class

tag: patients with available multiple tumor specimens

tag: tumor purity class by cibersort

value: high purity

tag: mir expression profiles

value: Not Available


title: GK64

description:
25_N
Gene expression data from papillary thyroid carcinoma

value: Available


title: MCF7-ATF2 si1 repl1

value: MCF7 cells

tag: sirna

value: ATF2 si1

tag: group

value: Estrogen receptor positive


title: H446_R

tag: treatment


title: MCF7 siNT repl4

value: siNT


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD010

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: ACA

tag: gender


title: GK46

description:
13_N
Gene expression data from papillary thyroid carcinoma

tag: histological variant

value: non-neoplastic thyroid

tag: tissue type

tag: collection before/after rai

tag: patient id

tag: patient rai responce


title: MCF7 siNT repl5

tag: cell line


title: H345_R

value: untreated


title: H378_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD008

value: male


title: H250_R


title: H2330_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD006

value: SSp


title: H748_R


title: H2227_R


title: GK42

description:
11_N
Gene expression data from papillary thyroid carcinoma

value: Before

value: Refractory

tag: rai uptake at the metastatic site

tag: disease

tag: lesion by ptc-ma

tag: lesion class

tag: patients with available multiple tumor specimens

value: No

tag: tumor purity class by cibersort


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD004

tag: strain

tag: age

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD002

tag: tissue

tag: source


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD001

tag: target

tag: gender


title: H2198_R

tag: treatment


title: MCF7 siNT repl2

tag: sirna

tag: group


title: GK24

description:
2_N
Gene expression data from papillary thyroid carcinoma

tag: histological variant

tag: tissue type

tag: collection before/after rai

tag: patient id

tag: patient rai responce

value: Avid

value: Yes

value: Remission

value: low purity

tag: mir expression profiles


title: GK32

description:
7_N
Gene expression data from papillary thyroid carcinoma

tag: rai uptake at the metastatic site

tag: disease

value: Persistence

tag: lesion by ptc-ma

tag: lesion class

tag: patients with available multiple tumor specimens

value: Available


title: H2195_R

tag: cell line


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD010

tag: strain

tag: age

tag: tissue

value: brain

tag: source

tag: target


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD008

value: PTLp

tag: gender


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B1_AD007

value: ACA


title: GK99

description:
46_L
Gene expression data from papillary thyroid carcinoma

source_name: papillary thyroid carcinoma

tag: histological variant

value: Classical

tag: tissue type

value: lymph node metastasis post RAI

value: After

value: WT

tag: tumor purity class by cibersort


title: GK22

description:
1_N
Gene expression data from papillary thyroid carcinoma

value: non-neoplastic thyroid

tag: collection before/after rai

value: Before

tag: patient id

tag: patient rai responce

value: high purity


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD007

value: male


title: GL00

description:
47_L
Gene expression data from papillary thyroid carcinoma

value: Refractory

tag: rai uptake at the metastatic site

value: No

tag: disease

tag: mir expression profiles


title: H2141_R

tag: treatment

value: untreated


title: H2171_R

tag: cell line


title: H211_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD006

tag: strain

value: SSp

value: female


title: H2196_R


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD004

tag: age


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD002

tag: tissue


title: MCF7 siNT repl3

value: MCF7 cells

tag: sirna

value: siNT

tag: group

value: Estrogen receptor positive


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_B12_AD001

value: brain

tag: source

value: PTLp

tag: target

tag: gender


title: GK97

description:
44_L
Gene expression data from papillary thyroid carcinoma

tag: histological variant

value: Follicular

tag: tissue type

value: lymph node metastasis post RAI

value: Yes

value: Persistence

tag: lesion by ptc-ma

tag: lesion class

tag: patients with available multiple tumor specimens

tag: tumor purity class by cibersort

value: Available


title: H2108_R


title: GK93

description:
42_L2
Gene expression data from papillary thyroid carcinoma

value: Classical

value: lymph node metastasis_2 post RAI

tag: collection before/after rai

value: After

tag: patient id

tag: patient rai responce

tag: rai uptake at the metastatic site

tag: disease

value: high purity

tag: mir expression profiles


title: GK98

description:
45_L
Gene expression data from papillary thyroid carcinoma

value: Refractory

value: No


title: GK90

description:
41_L1
Gene expression data from papillary thyroid carcinoma

value: lymph node metastasis_1 post RAI


title: GK92

description:
42_L1
Gene expression data from papillary thyroid carcinoma

value: low purity


title: H209_R

tag: cell line

tag: treatment

value: untreated


title: GK88

description:
40_L1
Gene expression data from papillary thyroid carcinoma

value: pTERT


title: GK91

description:
41_L2
Gene expression data from papillary thyroid carcinoma

value: Not Available


title: GK89

description:
40_L2
Gene expression data from papillary thyroid carcinoma


title: H2081_R


title: H2029_R