title: MWCNT_D07_1.0mg/kg MWCNT

description: Rat lung, Day07, 1.0mg/kg MWCNT, replicate 4

source_name: 7 day post-instillation in 1.0mg/kg MWCNT-exposed rat lung


title: MWCNT_D03_Control for MWCNT

status: Public on Jul 09 2020

type: RNA

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

description: Rat lung, Day03, Control for MWCNT, replicate 4

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Rat Genome Microarray (G4131F; Agilent Technologies) at 65 °C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent, G2505C) at 5 μm resolution.

data_processing: The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.

molecule: total RNA

organism: Rattus norvegicus

source_name: 3 day post-instillation in rat lung as cotrol for MWCNT

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: Seven-week-old male Sprague-Dawley (Crl:CD[SD]) rats were purchased from Charles River Laboratories Japan (Yokohama, Japan). Rats were housed in metal cages with in a room with 35%– 70% humidity and a controlled temperature of 20°C–26°C and fed a chow diet ad libitum. All procedures and animal handling were approved by the Institutional Animal Care and Use Committee of the National Institute of Advanced Industrial Science (Tsukuba, Japan) and Technology and the BioSafety Research Center Inc. (Iwata, Japan)..

extract_protocol: Blood-perfused rat right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: 0.5, 1.0 and 2.0 mg/mL of CNF (CNF1, CNF2, and CNF3) and MWCNT suspensions were prepared with distilled water with preservatives as each vehicle control. Each rat received a single intratracheal instillation dose (1 mg/kg) of the CNFs, MWCNT, and vehicles. Rats were dissected at 1, 3, 7, 30, and 90 days post-instillation. Lungs were perfused with physiological saline, excised, and used for whole genome microarray analysis.

tag: strain

value: Sprague-Dawley (Crl:CD[SD])

tag: Sex

value: male

tag: treatment

value: Control for MWCNT

tag: time

tag: tissue

value: lung


title: CNF3_D90_1.0mg/kg CNF3

description: Rat lung, Day90, 1.0mg/kg CNF3, replicate 4

source_name: 90 day post-instillation in 1.0mg/kg CNF3-exposed rat lung

value: 1.0mg/kg CNF3


title: CNF3_D30_2.0mg/kg CNF3

description: Rat lung, Day30, 2.0mg/kg CNF3, replicate 4

source_name: 30 day post-instillation in 2.0mg/kg CNF3-exposed rat lung

value: 2.0mg/kg CNF3


title: MWCNT_D01_0.5mg/kg MWCNT

description: Rat lung, Day01, 0.5mg/kg MWCNT, replicate 4

source_name: 1 day post-instillation in 0.5mg/kg MWCNT-exposed rat lung

value: 0.5mg/kg MWCNT


title: MWCNT_D03_2.0mg/kg MWCNT

description: Rat lung, Day03, 2.0mg/kg MWCNT, replicate 4

source_name: 3 day post-instillation in 2.0mg/kg MWCNT-exposed rat lung

value: 2.0mg/kg MWCNT


title: s504m

type: SRA

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstr. 74

country: Germany

institute: Institut für Klinische Chemie und Laboratoriumsmedizin

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling
kallisto" was used to quantify TPM of genes using the following command line parameters "quant --single -l 75 -s 5 -i transcriptome.idx  -b 100
Genome_build: mm10
Supplementary_files_format_and_content: Per Sample Zipped Folders containing text, h5 and json files for the read quantification from kallisto

organism: Mus musculus

source_name: Adrenal Glands

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Male

value: Adrenal Glands

tag: age

value: 8-16 weeks

tag: genotype


title: s525f

value: Female


title: CNF3_D30_Control for CNF3

description: Rat lung, Day30, Control for CNF3, replicate 4

source_name: 30 day post-instillation in rat lung as cotrol for CNF3

value: Control for CNF3


title: s186m


title: CNF3_D07_1.0mg/kg CNF3

description: Rat lung, Day07, 1.0mg/kg CNF3, replicate 4

source_name: 7 day post-instillation in 1.0mg/kg CNF3-exposed rat lung


title: CNF3_D07_0.5mg/kg CNF3

description: Rat lung, Day07, 0.5mg/kg CNF3, replicate 4

source_name: 7 day post-instillation in 0.5mg/kg CNF3-exposed rat lung

value: 0.5mg/kg CNF3


title: CNF3_D07_2.0mg/kg CNF3

description: Rat lung, Day07, 2.0mg/kg CNF3, replicate 4

source_name: 7 day post-instillation in 2.0mg/kg CNF3-exposed rat lung


title: CNF3_D07_Control for CNF3

description: Rat lung, Day07, Control for CNF3, replicate 4

source_name: 7 day post-instillation in rat lung as cotrol for CNF3


title: P21 motoneurons, biological rep 3

city: Istanbul

first: Bilal

middle: Ersen

last: Kerman

state: Beykoz

address: Kavacik Mah. Ekinciler Cad. No:19

country: Turkey

institute: Istanbul Medipol University

description: Post-myelination gene expression data from spinal motoneurons

hyb_protocol: Biotinylated aRNA (15 µg) was fragmented and hybridized to Affymetrix Rat Genome RAE230A/B arrays according to the manufacturer’s protocol.

scan_protocol: Standard Affymetrix protocol

data_processing: Analysis and normalization were performed using two methods: dChip 1.3 (Li and Wong, 2001) and Drop Method (Aimone and Gage, 2004) software packages.

label: biotin

molecule: polyA RNA

source_name: Laser captured spinal motoneurons after completion myelination

label_protocol: Around 50 ng RNA was obtained per pool of 4 rats. RNA (50 ng) was amplified in 2 rounds using the MessageAmp aRNA Kit (Ambion Inc, Austin, TX). This method utilizes reverse transcription with T7-oligo(dT) primers followed by in vitro transcription with T7 RNA Polymerase.

extract_protocol: Total RNA was purified using the Absolutely RNA Nanoprep Kit (Stratagene, La Jolla, CA), and yield was assessed using the RiboGreen RNA Quantitation Reagent (Molecular Probes, Inc, Eugene, OR).

treatment_protocol: 12-micron thin cryostat sections were stained with cresyl violet, rapidly dehydrated through xylenes and stored until use in a vacuum dessicator. An Arcturus PixCell II machine (Arcturus, Mountain View, CA) was used to laser capture between 1,500 and 2,000 MNs per gene chip at the lumbar level of the spinal cord.

value: Wistar albino


title: CNF3_D03_2.0mg/kg CNF3

description: Rat lung, Day03, 2.0mg/kg CNF3, replicate 3

source_name: 3 day post-instillation in 2.0mg/kg CNF3-exposed rat lung


title: CNF3_D03_Control for CNF3

description: Rat lung, Day03, Control for CNF3, replicate 4

source_name: 3 day post-instillation in rat lung as cotrol for CNF3


title: CNF3_D03_1.0mg/kg CNF3

description: Rat lung, Day03, 1.0mg/kg CNF3, replicate 4

source_name: 3 day post-instillation in 1.0mg/kg CNF3-exposed rat lung


title: CNF3_D03_0.5mg/kg CNF3

description: Rat lung, Day03, 0.5mg/kg CNF3, replicate 4

source_name: 3 day post-instillation in 0.5mg/kg CNF3-exposed rat lung


title: CNF3_D01_0.5mg/kg CNF3

description: Rat lung, Day01, 0.5mg/kg CNF3, replicate 4

source_name: 1 day post-instillation in 0.5mg/kg CNF3-exposed rat lung


title: P21 motoneurons, biological rep 4


title: CNF2_D90_1.0mg/kg CNF2

description: Rat lung, Day90, 1.0mg/kg CNF2, replicate 4

source_name: 90 day post-instillation in 1.0mg/kg CNF2-exposed rat lung

value: 1.0mg/kg CNF2


title: CNF3_D01_Control for CNF3

description: Rat lung, Day01, Control for CNF3, replicate 4

source_name: 1 day post-instillation in rat lung as cotrol for CNF3


title: P1 motoneurons, biological rep 3

description: During myelination gene expression data from spinal motoneurons

source_name: Laser captured spinal motoneurons during active myelination


title: P1 motoneurons, biological rep 4


title: CNF3_D01_1.0mg/kg CNF3

description: Rat lung, Day01, 1.0mg/kg CNF3, replicate 4

source_name: 1 day post-instillation in 1.0mg/kg CNF3-exposed rat lung


title: P21 motoneurons, biological rep 1


title: P1 motoneurons, biological rep 2


title: CNF2_D90_2.0mg/kg CNF2

description: Rat lung, Day90, 2.0mg/kg CNF2, replicate 4

source_name: 90 day post-instillation in 2.0mg/kg CNF2-exposed rat lung

value: 2.0mg/kg CNF2


title: P21 motoneurons, biological rep 2


title: CNF2_D90_0.5mg/kg CNF2

description: Rat lung, Day90, 0.5mg/kg CNF2, replicate 3

source_name: 90 day post-instillation in 0.5mg/kg CNF2-exposed rat lung

value: Sprague-Dawley (Crl:CD[SD])

value: 0.5mg/kg CNF2


title: P1 motoneurons, biological rep1


title: CNF3_D01_2.0mg/kg CNF3

description: Rat lung, Day01, 2.0mg/kg CNF3, replicate 4

source_name: 1 day post-instillation in 2.0mg/kg CNF3-exposed rat lung

value: male


title: GCB

city: Nanjing

first: Tang

last: Chao

address: 305 East Zhongshan Road, Nanjing,  China

country: China

institute: Jinling Hospital, School of Medicine, Nanjing University

description: GH3 cell with CAB and BRC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Gene Ontology using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: GH3 cell with CAB and BRC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rat pituitary tumor cell lines GH3 and MMQ were obtained from the Chinese Academy of Medical Science (Beijing, China). GH3 and MMQ cells were cultured in Ham’s F10 medium and F12 medium respectively containing 15% horse serum, 2.5% fetal calf serum, 1% penicillin and streptomycin and maintained at 37℃ in a 5% CO2 atmosphere

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: CAB and BRC were obtained from Abcam (Cambridge, MA, USA). The drugs were dissolved in DMSO and diluted to 50μmol/l using serum-free medium (DMSO with final concentration 0.2%).

tag: cell line

tag: cell type

value: pituitary adenoma cells


title: CNF2_D90_Control for CNF2

description: Rat lung, Day90, Control for CNF2, replicate 4

source_name: 90 day post-instillation in rat lung as cotrol for CNF2

value: Control for CNF2

value: lung


title: CNF2_D30_2.0mg/kg CNF2

description: Rat lung, Day30, 2.0mg/kg CNF2, replicate 4

source_name: 30 day post-instillation in 2.0mg/kg CNF2-exposed rat lung


title: MC

description: MMQ cell with CAB

source_name: MMQ cell with CAB

value: MMQ


title: GB

description: GH3 cell with BRC

source_name: GH3 cell with BRC


title: MCB

description: MMQ cell with CAB and BRC

source_name: MMQ cell with CAB and BRC


title: GH3

description: control

source_name: control


title: CNF2_D30_1.0mg/kg CNF2

description: Rat lung, Day30, 1.0mg/kg CNF2, replicate 4

source_name: 30 day post-instillation in 1.0mg/kg CNF2-exposed rat lung


title: GC

description: GH3 cell with CAB

source_name: GH3 cell with CAB


title: WT RNA-Seq rep3

city: Beijing

first: Yaqi

last: Wang

address: Changchun Street No.45

institute: Xuanwu Hospital,Capital Medical University

data_processing:
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent ofbases with qualities of <20. The clean reads were then aligned to mm10 genome using the star program.
Htseq-count was used to calculate gene expression
The RNA-seq differential gene expression analysis was performed using DESeq2 algorithm
Genome_build: mm10
Supplementary_files_format_and_content: include RPKM values for each Sample .

source_name: Hippocampus

extract_protocol:
RNA was isolated using Trizol reagent.  3 ug  total RNA was used to prepare  sequencing libraries by NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: 8 month

value: wild type


title: APP/PS1 RNA-Seq rep2

value: APPswe/PS1dE9 double transgenic mice


title: APP/PS1 RNA-Seq rep3


title: WT RNA-Seq rep2


title: WT RNA-Seq rep1


title: CNF2_D30_Control for CNF2

description: Rat lung, Day30, Control for CNF2, replicate 4

source_name: 30 day post-instillation in rat lung as cotrol for CNF2


title: CNF2_D03_1.0mg/kg CNF2

description: Rat lung, Day03, 1.0mg/kg CNF2, replicate 4

source_name: 3 day post-instillation in 1.0mg/kg CNF2-exposed rat lung


title: CNF2_D07_Control for CNF2

description: Rat lung, Day07, Control for CNF2, replicate 4

source_name: 7 day post-instillation in rat lung as cotrol for CNF2


title: APP/PS1 ATAC-Seq rep3

library_source: genomic

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Trimmomatic.
Quality filtered reads were then mapped to mm10 reference genome using BWA(0.7.10), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools and used for peak calling. MACS2(2.1.1)was used to call peaks and an initial threshold q-value of 0.05 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MACS2

molecule: genomic DNA

extract_protocol:
Selected 50 average size islets were lysed in lysis buffer.Nuclei were then incubated with the Tn5 transposome and tagmentation.
Libaray was prepared according to protocols of TruePrep DNA Library Prep Kit V2 for illumina(Vazyme Biotech, Nanjing, China) .The libraries were sequenced on HiSeq platform and using PE150 sequencing strategy


title: CNF2_D03_2.0mg/kg CNF2

description: Rat lung, Day03, 2.0mg/kg CNF2, replicate 4

source_name: 3 day post-instillation in 2.0mg/kg CNF2-exposed rat lung


title: CNF2_D07_1.0mg/kg CNF2

description: Rat lung, Day07, 1.0mg/kg CNF2, replicate 4

source_name: 7 day post-instillation in 1.0mg/kg CNF2-exposed rat lung


title: CNF2_D07_0.5mg/kg CNF2

description: Rat lung, Day07, 0.5mg/kg CNF2, replicate 4

source_name: 7 day post-instillation in 0.5mg/kg CNF2-exposed rat lung


title: MMQ

description: control


title: CNF2_D30_0.5mg/kg CNF2

description: Rat lung, Day30, 0.5mg/kg CNF2, replicate 4

source_name: 30 day post-instillation in 0.5mg/kg CNF2-exposed rat lung


title: APP/PS1 ATAC-Seq rep1


title: MB

description: MMQ cell with BRC

source_name: MMQ cell with BRC


title: CNF2_D03_0.5mg/kg CNF2

description: Rat lung, Day03, 0.5mg/kg CNF2, replicate 3

source_name: 3 day post-instillation in 0.5mg/kg CNF2-exposed rat lung


title: CNF2_D07_2.0mg/kg CNF2

description: Rat lung, Day07, 2.0mg/kg CNF2, replicate 4

source_name: 7 day post-instillation in 2.0mg/kg CNF2-exposed rat lung


title: WT ATAC-Seq rep3


title: WT ATAC-Seq rep2


title: APP/PS1 RNA-Seq rep1


title: CNF2_D03_Control for CNF2

description: Rat lung, Day03, Control for CNF2, replicate 4

source_name: 3 day post-instillation in rat lung as cotrol for CNF2


title: WT ATAC-Seq rep1


title: WTsp1

first: Wenyan

address: Tsinghua University

department: School of Medicine

institute: Institute for Immunology

data_processing:
Illumina Hiseq platform for PE150 sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2
FPKM were calculated using RSEM tool
Genome_build: GRCm38
Supplementary_files_format_and_content: excel, all genes fpkm

source_name: spleen

extract_protocol:
60 LTi-like cells were sorted by FACS by 7AAD-Lin-CD45+CD90+CD127+CD4+Rorc+ into cell lysis with ribonuclease inhibitor. Then we carried out the amplification by the Smart-Seq2 method.
The cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation.

tag: tisse

value: spleen


title: CNF2_D01_2.0mg/kg CNF2

description: Rat lung, Day01, 2.0mg/kg CNF2, replicate 4

source_name: 1 day post-instillation in 2.0mg/kg CNF2-exposed rat lung


title: WTsp2


title: CNF2_D01_1.0mg/kg CNF2

description: Rat lung, Day01, 1.0mg/kg CNF2, replicate 3

source_name: 1 day post-instillation in 1.0mg/kg CNF2-exposed rat lung


title: CNF2_D01_0.5mg/kg CNF2

description: Rat lung, Day01, 0.5mg/kg CNF2, replicate 4

source_name: 1 day post-instillation in 0.5mg/kg CNF2-exposed rat lung


title: KOmLN2

source_name: mLN

value: mLN


title: KOmLN1


title: KOgut2

source_name: gut

value: gut


title: CNF1_D90_1.0mg/kg CNF1

description: Rat lung, Day90, 1.0mg/kg CNF1, replicate 4

source_name: 90 day post-instillation in 1.0mg/kg CNF1-exposed rat lung

value: 1.0mg/kg CNF1


title: WTmLN1


title: CNF1_D90_2.0mg/kg CNF1

description: Rat lung, Day90, 2.0mg/kg CNF1, replicate 4

source_name: 90 day post-instillation in 2.0mg/kg CNF1-exposed rat lung

value: 2.0mg/kg CNF1


title: WTgut1


title: CNF1_D90_0.5mg/kg CNF1

description: Rat lung, Day90, 0.5mg/kg CNF1, replicate 4

source_name: 90 day post-instillation in 0.5mg/kg CNF1-exposed rat lung

value: 0.5mg/kg CNF1


title: WTgut2


title: CNF2_D01_Control for CNF2

description: Rat lung, Day01, Control for CNF2, replicate 4

source_name: 1 day post-instillation in rat lung as cotrol for CNF2

value: Sprague-Dawley (Crl:CD[SD])


title: WTmLN2


title: KOgut1


title: s354m

source_name: Adrenal Glands

value: Male

value: Adrenal Glands

value: 8-16 weeks


title: CNF1_D30_1.0mg/kg CNF1

description: Rat lung, Day30, 1.0mg/kg CNF1, replicate 4

source_name: 30 day post-instillation in 1.0mg/kg CNF1-exposed rat lung

value: male


title: CNF1_D30_2.0mg/kg CNF1

description: Rat lung, Day30, 2.0mg/kg CNF1, replicate 4

source_name: 30 day post-instillation in 2.0mg/kg CNF1-exposed rat lung

value: lung


title: CNF1_D07_2.0mg/kg CNF1

description: Rat lung, Day07, 2.0mg/kg CNF1, replicate 3

source_name: 7 day post-instillation in 2.0mg/kg CNF1-exposed rat lung


title: CNF1_D07_1.0mg/kg CNF1

description: Rat lung, Day07, 1.0mg/kg CNF1, replicate 4

source_name: 7 day post-instillation in 1.0mg/kg CNF1-exposed rat lung


title: CNF1_D30_Control for CNF1

description: Rat lung, Day30, Control for CNF1, replicate 4

source_name: 30 day post-instillation in rat lung as cotrol for CNF1

value: Control for CNF1


title: CNF1_D07_0.5mg/kg CNF1

description: Rat lung, Day07, 0.5mg/kg CNF1, replicate 4

source_name: 7 day post-instillation in 0.5mg/kg CNF1-exposed rat lung


title: 14M2

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

hyb_protocol: The hybridization, washing, and scanning were performed according to the manufacturer’s instructions.

scan_protocol: The BeadChips were scanned using a HiScanSQ System (Illumina, San Diego, CA). The microarray images were registered and extracted automatically during the scan using the manufacturer’s default settings.

data_processing: Data are cyclic loess normalized with LIMMA .

organism: Homo sapiens

source_name: BxPC-3 cell lines

label_protocol: 495ng total RNA was labeled using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion, Austin, TX). Briefly, the protocol features a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides to generate biotinylated cRNA. The purified cRNA is then quantified and the fragment size was determined using an Agilent 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA). Then, 750ng of labeled biotinylated cRNA probe was hybridized overnight to the Illumina HumanHT-12 v4 Expression BeadChip.

growth_protocol: For gene expression analysis, BxPC-3 cells were cultured in DMEM with 2% FBS and seeded at a density of 10^5 cells per well in 12-well plates after starving (DMEM with 0.2% FBS). Time zero in the expression arrays occurs 24 hours after cell starvation.

extract_protocol: Total RNA was isolated from cells pellets and extracted using the RNeasy plus Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions

treatment_protocol: Samples labeled cetuximab treatment are treated with 10µg/ml cetuximab starting at time 0 (24 hours after starvation).

value: negative control

value: 7 days

tag: replicate


title: CNF1_D03_1.0mg/kg CNF1

description: Rat lung, Day03, 1.0mg/kg CNF1, replicate 4

source_name: 3 day post-instillation in 1.0mg/kg CNF1-exposed rat lung


title: 12C2

value: cetuximab treatment

value: 5 days


title: CNF1_D03_2.0mg/kg CNF1

description: Rat lung, Day03, 2.0mg/kg CNF1, replicate 4

source_name: 3 day post-instillation in 2.0mg/kg CNF1-exposed rat lung


title: CNF1_D03_0.5mg/kg CNF1

description: Rat lung, Day03, 0.5mg/kg CNF1, replicate 4

source_name: 3 day post-instillation in 0.5mg/kg CNF1-exposed rat lung


title: CNF1_D90_Control for CNF1

description: Rat lung, Day90, Control for CNF1, replicate 3

source_name: 90 day post-instillation in rat lung as cotrol for CNF1


title: CNF1_D30_0.5mg/kg CNF1

description: Rat lung, Day30, 0.5mg/kg CNF1, replicate 4

source_name: 30 day post-instillation in 0.5mg/kg CNF1-exposed rat lung


title: 13C2

value: 6 days


title: D5-2-5nM-PLB_2

city: Tianjin

first: Yapu

last: Li

state: China

address: 288 Nanjing Road

institute: PUMC

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p10 genome using STAR-2.5.3a with default parameters for strand specific library
Fragements Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a cufflinks-2.2.1 with default parameters
Genome_build: GRCh38.p10.genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: human embryonic stem cell derived cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: D2 FACS sorting APLNR+ cells(the same sample as APLRN+ _1/2), plated in each well of a growth factors reduced (GFR) matrigel-coated 24-well plate for 12h cultured with customer mTESR1 medium  with 50 ng/ml of bFGF (cat# 100-18B-100, Peprotech) and 40 ng/ml ,of VEGF (cat# 100-20-100, Peprotech),then added 2.5nM pladienolide B (PLB) to the culture medium ,then cultured with 2.5nM pladienolide B (PLB)for another 60h, change the medium daily,collecting all the cell at day5 for RNA-seq

value: 2.5 nM pladienolide B (PLB)

value: human embryonic stem cell derived cells


title: CNF1_D07_Control for CNF1

description: Rat lung, Day07, Control for CNF1, replicate 4

source_name: 7 day post-instillation in rat lung as cotrol for CNF1


title: 14C2


title: D5-1-25nM-PLB_1

treatment_protocol: D2 FACS sorting APLNR+ cells(the same sample as APLRN+ _1/2), plated in each well of a growth factors reduced (GFR) matrigel-coated 24-well plate for 12h cultured with customer mTESR1 medium  with 50 ng/ml of bFGF (cat# 100-18B-100, Peprotech) and 40 ng/ml ,of VEGF (cat# 100-20-100, Peprotech),then added 1.25nM pladienolide B (PLB) to the culture medium ,then cultured with 1.25nM pladienolide B (PLB)for another 60h, change the medium daily,collecting all the cell at day5 for RNA-seq

value: 1.25 nM pladienolide B (PLB)


title: D5-2-5nM-PLB_1


title: 14C1


title: 13M2


title: CNF1_D03_Control for CNF1

description: Rat lung, Day03, Control for CNF1, replicate 4

source_name: 3 day post-instillation in rat lung as cotrol for CNF1


title: 13M1


title: 14M1


title: 12C1


title: D5-DMSO_1

treatment_protocol: D2 FACS sorting APLNR+ cells(the same sample as APLRN+ _1/2), plated in each well of a growth factors reduced (GFR) matrigel-coated 24-well plate for 12h cultured with customer mTESR1 medium  with 50 ng/ml of bFGF (cat# 100-18B-100, Peprotech) and 40 ng/ml ,of VEGF (cat# 100-20-100, Peprotech),then added 1:1000 DMSO to the culture medium ,then cultured with DMSO foranother 60h, Change the medium daily,collecting all the cell at day5 for RNA-seq

value: DMSO


title: D5-1-25nM-PLB_2


title: CNF1_D01_2.0mg/kg CNF1

description: Rat lung, Day01, 2.0mg/kg CNF1, replicate 4

source_name: 1 day post-instillation in 2.0mg/kg CNF1-exposed rat lung

value: 2.0mg/kg CNF1


title: APLRN+ _1

treatment_protocol: Before inducing differentiation, hESCs (H1) colonies were pretreated with 1 mg/ml accutase (cat# A1110501, Invitrogen) to yield a single cell suspension. From this suspension, 3.5 × 104 cells were plated in each well of a growth factors reduced (GFR) matrigel-coated 12-well plate (cat# 354230, Corning) and cultured in mTESR1 media (cat# 85852, Stem cell) containing 10 uM of Y27632 (cat# 688000, Calbiochem) for 24 hours. mTESR1 medium was then changed to customer mTESR1 medium (cat# 05892, Stem cell) with a supplement of 50 ng/ml of Activin A (cat# 120-14-1000, Peprotech) and 40 ng/ml of BMP4 (cat# 120-05ET-1000, Peprotech) and kept for two days ,Then FACS sorting APLNR+ cells for RNA-


title: 13C1


title: 12M1


title: 11C3

value: 4 days


title: 12M2


title: CNF1_D01_0.5mg/kg CNF1

description: Rat lung, Day01, 0.5mg/kg CNF1, replicate 4

source_name: 1 day post-instillation in 0.5mg/kg CNF1-exposed rat lung

value: Sprague-Dawley (Crl:CD[SD])

value: 0.5mg/kg CNF1


title: CNF1_D01_Control for CNF1

description: Rat lung, Day01, Control for CNF1, replicate 4

source_name: 1 day post-instillation in rat lung as cotrol for CNF1


title: APLRN+ _2


title: CNF1_D01_1.0mg/kg CNF1

description: Rat lung, Day01, 1.0mg/kg CNF1, replicate 4

source_name: 1 day post-instillation in 1.0mg/kg CNF1-exposed rat lung

value: 1.0mg/kg CNF1


title: MCF7_TET2WT_WGBS

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality bases and adapter-containing reads were trimmed from WGBS-seq raw data by trim_galore with default parameters.
Bsmap v2.74 was used to align reads to the reference genome (hg19) under the parameters: –w 100 –v 0.1. The coverage depth and methylation level of each cytosine were extracted by methratio.py from bam files.
Only CpG dinucleotides were analysed, information from both strands were combined, and a coverage of at least five reads was required, which were filtered from methratio.py output by awk.
For hyper-DM and hypo-DM CpG sites, we used the cutoff of 30% methylation difference. Distribution analysis of DNA methylation on enhancers and EREs were performed using transformed DNA methylation datas, which came from our home-made smooth algorithm.
hg19
txt, CpG DNA methylation value.

source_name: MCF7 cells

growth_protocol: MCF-7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco) and 100 U/ml penicillin/streptomycin (Invitrogen).For estrogen stimulation, MCF-7 cells were cultured in phenol red-free RPMI 1640 medium (HyClone) plus 10% charcoal-depleted FBS (Biological Industries) for 5 days and followed by EtOH or E2 (1nM) treatment for 24 hours.

extract_protocol:
DNA (1 mg) with 0.5% non-methylated DNA spike-in was sheared by Covaris M220 instrument to an average size of 350 bp in length.
DNA was then end-repaired, dA-tailed, and ligated with methylated adaptors. Bisulfite conversion was carried out using an EpiTect fast bisulfite conversion kit (Qiagen) according to the manufacturer’s instructions. Twenty minutes were used in both conversion steps. Bisulfite-converted DNA was then amplified with five PCR cycles to obtain the final library.

value: wild type


title: D5-DMSO_2


title: MCF7_TET2KO_WGBS

value: TET2 knockout


title: MCF7_TET2KO_RNA-seq.rep1

description: Total RNA after depletion of rRNA

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality bases and adapter-containing reads were trimmed from RNA-seq raw data by trim-galore with default parameters.
Remaining trimmed sequence were mapped against the reference genome (hg19) with hisat2, which allowed mapping across splicing junctions by read segmentation. All programs were performed with default settings unless otherwise specified.
The expression level of each gene was quantified with normalized FPKM with FPKM_count.pl in RSeQC software.
Differentially expressed genes were identified using DESeq2 package, Log2(Fold change) >=1 and adjusted pvalue<=0.05 are used to define up-regulated genes; Log2(Fold change) <=-1 and adjusted pvalue<=0.05 are used to define down-regulated genes.
hg19
xls, gene expression.

extract_protocol:
RNA samples were prepared by RNeasy minikit (Qiagen). Depletion of rRNA was carried out using ribo-zero kit (Epicentre).
Barcoded RNA-seq libraries were constructed using NEBNext ultra directional RNA library prep kit for Illumina according to the manufacturer’s instructions (New England Biolabs).


title: 11M3


title: APP/PS1 ATAC-Seq rep2

source_name: Hippocampus

value: Hippocampus

value: 8 month

value: APPswe/PS1dE9 double transgenic mice


title: 10C3

value: cetuximab treatment

value: 3 days


title: 9M3

value: negative control

value: 2 days


title: 9C3


title: MCF7_TET2WT_RNA-seq.rep2

description: Total RNA after depletion of rRNA


title: 8C3

value: 1 day


title: 10M3


title: 8M3


title: 7C3

value: 8 hrs


title: MCF7_TET2KO-EtOH_RNA-Seq

description: Total RNA after depletion of rRNA


title: MCF7_TET2KO_RNA-seq.rep2

description: Total RNA after depletion of rRNA


title: 6C3

value: 4 hrs


title: MCF7_TET2KO-E2_RNA-Seq

description: Total RNA after depletion of rRNA


title: 7M3


title: MCF7_TET2WT-EtOH_RNA-Seq

description: Total RNA after depletion of rRNA


title: MCF7_TET2KO_Input.rep1

data_processing:
Basecalls performed using CASAVA version 1.4
Low-quality bases and adapter-containing reads were trimmed from ChIP-seq raw data using trim-galore package under default parameters.
Trimmed reads were mapped to reference genome(hg19) using bowtie2(v2.3.3.1) under default parameters.
Duplicate reads were removed with samtools rmdup(v1.9) to get the unique mapped reads, then the mapped unique and monoclonal reads were extended to 150bp to match the average length of insert DNA fragments of our ChIP-seq libraries.
Extended mapped unique and monoclonal reads were transformed to bedGraph files and bigWig files, which were used to calculate tag density under 50-bp resolution.
hg19
bigWig, ChIP-seq signal density file.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Library preparation and sequencing procedures were carried out as described previously according to Illumina protocols with minor modifications (Illumina, San Diego).

tag: chip antibody


title: MCF7_TET2KO_H3K4me1_ChIP-seq.rep2

value: anti-H3K4me1, Active Motif, 39297


title: MCF7_TET2WT_RNA-seq.rep1

description: Total RNA after depletion of rRNA


title: MCF7_TET2WT-E2_RNA-Seq

description: Total RNA after depletion of rRNA


title: 6M3


title: MCF7_TET2KO_H3K4me1_ChIP-seq.rep1


title: MCF7_TET2KO_H3K27ac_ChIP-seq.rep2

value: anti-H3K27Ac, Active Motif, 39133


title: MCF7_TET2KO_H3K27ac_ChIP-seq.rep1


title: 13C3

value: 6 days


title: 14C3

value: 7  days


title: 12C3

value: 5 days


title: 13M3


title: 12M3


title: 14M3

value: 7 days


title: MCF7_TET2WT_H3K4me1_ChIP-seq.rep1

value: wild type


title: MCF7_TET2WT_Input.rep1


title: MCF7_TET2WT_H3K4me1_ChIP-seq.rep2


title: MCF7_TET2WT_H3K27ac_ChIP-seq.rep1


title: 11C1

value: 4 days


title: MCF7_TET2KO-EtOH_H3K27ac_ChIP-seq

value: TET2 knockout


title: MCF7_TET2KO-E2_H3K4me1_ChIP-seq


title: MCF7_TET2KO-E2_H3K27ac_ChIP-seq


title: 11M1


title: 10M1


title: MCF7_TET2WT-EtOH_H3K4me1_ChIP-seq


title: 9M1


title: 10C1


title: MCF7_TET2WT_H3K27ac_ChIP-seq.rep2


title: 9C1


title: 8M1


title: 7M1


title: 6C1


title: 7C1


title: 5C4

value: 2 hrs


title: 8C1

value: cetuximab treatment


title: 6M4


title: MCF7_TET2WT-E2_Input


title: MCF7_TET2KO-E2_Input


title: MCF7_TET2WT-EtOH_H3K27ac_ChIP-seq


title: MCF7_TET2KO-E2_ER_ChIP-seq_Input


title: MCF7_TET2KO-EtOH_ER_ChIP-seq

value: anti-ERα, Cell Signaling Technology, 8644S


title: 4M1

value: negative control

value: 1 hr


title: 5M1


title: 4C1


title: MCF7_TET2WT-E2_H3K27ac_ChIP-seq


title: 3C1

value: 30 min


title: 3M1


title: MCF7_TET2WT-E2_ER_ChIP-seq_Input


title: 2C1

value: 10 min


title: MCF7_TET2WT-EtOH_ER_ChIP-seq


title: MCF7_TET2WT-E2_H3K4me1_ChIP-seq


title: MCF7_TET2WT-E2_ER_ChIP-seq


title: 1C1

value: 5 min


title: 2M1


title: 1M1


title: 84332: In vitro activated B cells, DT40 cells Igh(Pax5/+) Prdm1(GFP/+)

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: ChIP-Seq In vitro activated B cells, DT40 cells Igh(+/+) Prdm1(GFP/+)

data_processing:
Plasmablasts for ChIP-sequencing were isolated by magnetic enrichment with CD138 MicroBeads, which is most likely the source of the observed human genomic contamination.
ChIP-Seq: All reads passed a basic quality control (chastity) filter. Adapter were removed with cutadapt and the reads were filtered against the rDNA with bowtie2. The remaining reads were aligned with bowtie 1.0, first to the mouse genome (mm9), and remaining unaligned reads to the chicken genome (gal5). Peaks were called with macs 2.1 using a Pro-B cell Rag2(-/-) input (GSM1145867,GSM1296537) for mouse, and no input for chicken. Chicken reads were counted over union chicken peaks using featureCount (from subread 1.5.0) and normalization factors for scaling the mouse tracks based on the chicken spike-in reads were calculated using the estimateSizeFactors function of DESeq2 With R version 3.4.1. This resulted in the ollowing factors: 0.83 (84330), 2.18 (84331), 0.78 (84332), and 0.78 (84333). Aligned mouse reads were converted to read coverage tracks using a pipeline that involves  samtools version 1.9, bedtools version 2.7.21 and ucsc kent utilities, considering the appropriate normalization factors. Aligned chicken reads were deduplicated using   rmdup command (samtools version 1.9) before coverage conversion. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM).
RNA-Seq: Mouse reads that passed basic quality control (chastity) at their first pure bases were preprocessed: Read 1 was trimmed 5’ by 6 cycles, adapter were removed with cutadapt and the reads were filtered against the rDNA with bowtie2. The remaining reads were aligned with tophat (1.4.1) to the transcriptome and the genome of Mus musculus mm9. Reads were counted over mm9 merged gene models using featureCount (from subread 1.5.0). Differential expression between knock in and wildtype samples was analyzed in DESeq2, for each cell type. In brief, the model design "~ group" and Negative Binomial GLM fitting and Wald statistisc (DESeq function) was used, whereby   group specifies the combinations of the conditions (plasma_cell, plasma_blast, wt, ki). Transcripts per million (TPMs) were calculated as described previously.
Genome_build: mm9 (RNA-Seq, ChIP-Seq); gal5 (ChIP-Seq)
Supplementary_files_format_and_content: bed = MACS peak coordinates in BED format; bigwig = read coverage (reads per million) in bigWIG format; txt = normalized count values, such as TPMs, in ASCII text format tab delimited.

source_name: In vitro activated B cells, DT40 cells

extract_protocol: Not provided

value: In vitro activated B cells, DT40 cells

value: Igh(Pax5/+) Prdm1(GFP/+)

tag: cell preparation

value: 4d LPS in vitro stimulation, MACS depleted

value: anti-Pax5 A1


title: 84333: In vitro plasmablasts, DT40 cells Igh(Pax5/+) Prdm1(GFP/+)

description: ChIP-Seq In vitro plasmablasts, DT40 cells Igh(Pax5/+) Prdm1(GFP/+)

source_name: In vitro plasmablasts, DT40 cells

value: In vitro plasmablasts, DT40 cells

value: 4d LPS in vitro stimulation, MACS enriched


title: 0C1

source_name: BxPC-3 cell lines


title: 4M3


title: 84331: In vitro plasmablasts, DT40 cells Igh(+/+) Prdm1(GFP/+)

value: Igh(+/+) Prdm1(GFP/+)


title: 58410: Plasma cells Igh(+/+) Prdm1(GFP/+)

description: mRNA-Seq Plasma cells Igh(+/+) Prdm1(GFP/+)

source_name: Plasma cells

value: Plasma cells

value: Ex vivo MACS enriched and FACS sorted from bone marrow


title: 58411: Plasma cells Igh(Pax5/+) Prdm1(GFP/+)

description: mRNA-Seq Plasma cells Igh(Pax5/+) Prdm1(GFP/+)


title: 0C3


title: 54808: Plasma cells Igh(Pax5/+) Prdm1(GFP/+)


title: 1M3


title: 5M3

value: 2 hrs


title: 3C3

value: cetuximab treatment


title: 54807: Plasma cells Igh(Pax5/+) Prdm1(GFP/+)


title: 4C3


title: 5C2


title: 2M3


title: 3M3


title: 1C3


title: 5C3


title: 0M3


title: 0M1


title: 4C2


title: 2C3


title: 5M2


title: 51806: In vitro plasmablasts Igh(+/+) Prdm1(GFP/+)

description: mRNA-Seq In vitro plasmablasts Igh(+/+) Prdm1(GFP/+)

source_name: In vitro plasmablasts

value: In vitro plasmablasts

value: 4d LPS in vitro stimulation, FACS sorted


title: 54806: Plasma cells Igh(+/+) Prdm1(GFP/+)


title: 51805: In vitro plasmablasts Igh(Pax5/+) Prdm1(GFP/+)

description: mRNA-Seq In vitro plasmablasts Igh(Pax5/+) Prdm1(GFP/+)


title: 84330: In vitro activated B cells, DT40 cells Igh(+/+) Prdm1(GFP/+)


title: 51803: In vitro plasmablasts Igh(Pax5/+) Prdm1(GFP/+)


title: 4M2

value: negative control

value: 1 hr


title: 51801: In vitro plasmablasts Igh(+/+) Prdm1(GFP/+)


title: 51802: In vitro plasmablasts Igh(Pax5/+) Prdm1(GFP/+)


title: 3M2

value: 30 min


title: 51804: In vitro plasmablasts Igh(+/+) Prdm1(GFP/+)


title: 3C2


title: 1C2

value: 5 min


title: E3823_E4.Trem2ko.M.mRNA-seq

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
FASTQ TO BAM
FEATURECOUNTS
EDGER
Genome_build: mm10
Supplementary_files_format_and_content: raw expresison counts from featurecounts

source_name: brain

growth_protocol: All animal experiments were approved by the University of Pittsburgh Institutional Animal Care and Use Committee. All procedures were carried out in accordance with the approved guidelines. APP23 transgenic mice (C57Bl6 background) expressing human APP751 familial Swedish AD mutation (APPK670N, M671L) were crossed to wild-type C57BL/6 mice to generate APP23 hemizygous mice

extract_protocol:
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with cold 0.1 M PBS, pH 7.4: left hemisphere fixed in 4% paraformaldehyde for histology. The cortex was dissected from the other and snap frozen on dry ice for RNA and protein isolation
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.

treatment_protocol: We crossed 6.5 month olf male and female Trem2ko mice with APP/PSEN1dE9 mice expressing human APOE3 or APOE4 isoforms and assessed amyloid pathology, glial response, and whole-brain transcriptome.

value: Male

value: brain

tag: apoe

value: WT


title: E3742_E4.Trem2ko.M.mRNA-seq


title: 1M2


title: E3740_E4.Trem2ko.M.mRNA-seq


title: E3446_E4.Trem2ko.F.mRNA-seq

value: Female


title: E3741_E4.Trem2ko.M.mRNA-seq


title: MCF7_TET2KO-EtOH_H3K4me1_ChIP-seq

value: TET2 knockout

value: anti-H3K4me1, Active Motif, 39297


title: E3266_E4.Trem2ko.F.mRNA-seq


title: E3679_E4.M.mRNA-seq


title: E3261_E4.Trem2ko.F.mRNA-seq


title: E3855_E4.M.mRNA-seq


title: E3445_E4.Trem2ko.F.mRNA-seq


title: E3473_E4.F.mRNA-seq


title: 10M2

value: 3 days


title: 11C2

value: 4 days


title: 11M2


title: old-ERR_23

city: haifa

first: Moshe

last: Levi

state: Washington, DC

address: 37th and O Streets NW

department: Department of Biochemistry and Molecular & Cellular Biology at Georgetown University Medical Center

institute: Georgetown University

data_processing:
Normalized read counts per million were generated using the RNA-seq Analysis plugin (Ion Torrent Community, Thermo Fisher Scientific). Gene expression table was converted to LN scale and quantile normalized. Genes with expression levels less than 4 across all samples were filtered out.
Genome_build: mm10 transcriptome
Supplementary_files_format_and_content: Expression table in tab-delimited format

source_name: kidney

growth_protocol: Mice: Studies were performed in 4-month-old and 21-month-old male C57BL/6 male mice obtained from the NIA aging rodent colony.

extract_protocol: Approximately 300-500 ng of kidneys RNA were used to generate barcoded RNA libraries using Ion AmpliSeq Transcriptome Mouse Gene Expression Panel, Chef-Ready Kit. Library quantification was performed using the Ion Library Quantitation Kit (Thermo Fisher Scientific). Sequencing was done on an Ion Proton with signal processing and base calling using Ion Torrent Suite (Thermo Fisher Scientific). Raw reads were mapped to Ampliseq supported mm10 transcriptome.

treatment_protocol:
Mice received pan-ERR agonist SLU-PP-332 at a dose of 25 mg/kg body weight/day, administered intraperitoneally. Mice were dosed for 8 weeks, following which they underwent euthanasia and the kidneys were harvested.
Mice received 3% DMSO vehicle or the pan-ERR agonist SLU-PP-332 (Dr. Thomas Burris, Washington University) at a dose of 25 mg/kg body weight/day, administered intraperitoneally. Mice were dosed for 8 weeks, following which they underwent euthanasia and the kidneys were harvested.

value: kidney


title: 10C2


title: 0M2


title: old-ERR_22

value: 21-month-old male C57BL/6 male mice obtained from the NIA aging rodent colony.


title: old-ERR_21


title: 0C2

value: cetuximab treatment


title: 9C2

value: 2 days


title: 9M2


title: 8C2

value: 1 day


title: 8M2

value: negative control


title: 6C2

value: 4 hrs


title: 7M2

value: 8 hrs


title: E3357_E4.F.mRNA-seq


title: 7C2


title: D3971_E3.Trem2ko.M.mRNA-seq


title: E3471_E4.F.mRNA-seq


title: D3940_E3.Trem2ko.M.mRNA-seq


title: E3459_E4.F.mRNA-seq


title: D3941_E3.Trem2ko.M.mRNA-seq


title: D3942_E3.Trem2ko.M.mRNA-seq


title: old_19

treatment_protocol:
Mice received vehicle at a dose of 25 mg/kg body weight/day, administered intraperitoneally. Mice were dosed for 8 weeks, following which they underwent euthanasia and the kidneys were harvested.
Mice received 3% DMSO vehicle or the pan-ERR agonist SLU-PP-332 (Dr. Thomas Burris, Washington University) at a dose of 25 mg/kg body weight/day, administered intraperitoneally. Mice were dosed for 8 weeks, following which they underwent euthanasia and the kidneys were harvested.


title: MCF7_TET2KO-E2_ER_ChIP-seq

value: anti-ERα, Cell Signaling Technology, 8644S


title: old_17


title: old_15


title: D3893_E3.Trem2ko.F.mRNA-seq


title: D3887_E3.Trem2ko.F.mRNA-seq


title: D3834_E3.Trem2ko.F.mRNA-seq


title: old-ERR_20


title: old_14


title: D3833_E3.Trem2ko.F.mRNA-seq


title: old_18


title: young-ERR_13

value: 4-month-old male C57BL/6 male mice obtained from the NIA aging rodent colony


title: D3936_E3.M.mRNA-seq

value: Male

value: brain


title: young-ERR_12


title: young-ERR_11


title: D3866_E3.M.mRNA-seq

value: WT


title: D3811_E3.M.mRNA-seq


title: young-ERR_9


title: D3810_E3.M.mRNA-seq


title: X0158_E3.F.mRNA-seq

value: Female


title: old_16


title: D3722_E3.F.mRNA-seq


title: D3514_E3.F.mRNA-seq


title: young-ERR_7


title: young_6


title: young_5


title: E4127_APP.E4.Trem2ko.M .mRNA-seq

value: APP


title: D3502_E3.F.mRNA-seq


title: 2C2

value: 10 min


title: young_3


title: young_4


title: young_2


title: E3616_APP.E4.Trem2ko.M.mRNA-seq


title: young_1


title: E3467_APP.E4.Trem2ko.M.mRNA-seq


title: E3705_APP.E4.Trem2ko.M.mRNA-seq


title: young-ERR_10


title: E3451_APP.E4.Trem2ko.M.mRNA-seq


title: G12_tumor

type: genomic

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

description:
FFPE
202184900129_R07C01

hyb_protocol: supplier protocol (Illumina)

scan_protocol: supplier protocol (Illumina)

data_processing: supplier software (GenomeStudio)

label: Cy5 and Cy3

source_name: neuroendocrine tumor

label_protocol: supplier protocol (Illumina)

growth_protocol: fixed tissue (FFPE)

extract_protocol: as previously described: https://www.ncbi.nlm.nih.gov/pubmed/25540324

value: neuroendocrine tumor

tag: tumor type

value: PNET

tag: hereditary

value: Sporadic


title: E3450_APP.E4.Trem2ko.M.mRNA-seq


title: F12_tumor

description:
FFPE
202184900129_R06C01

value: SINET


title: E3325_APP.E4.Trem2ko.M.mRNA-seq


title: E3322_APP.E4.Trem2ko.M.mRNA-seq


title: E12_tumor

description:
FFPE
202184900129_R05C01

value: DNET


title: D12_tumor

description:
FFPE
202184900129_R04C01

value: VHL


title: E4132_APP.E4.Trem2ko.F .mRNA-seq


title: X0152_APP.E4.Trem2ko.F.mRNA-seq


title: B12_tumor

description:
FFPE
202184900129_R02C01


title: E3738_APP.E4.Trem2ko.F.mRNA-seq


title: A12_tumor

description:
FFPE
202184900129_R01C01


title: E3820_APP.E4.Trem2ko.F.mRNA-seq


title: G11_tumor

description:
FFPE
202184900109_R07C01


title: H11_tumor

description:
FFPE
202184900109_R08C01


title: E11_tumor

description:
FFPE
202184900109_R05C01


title: E3408_APP.E4.Trem2ko.F.mRNA-seq


title: F11_tumor

description:
FFPE
202184900109_R06C01


title: H12_tumor

description:
FFPE
202184900129_R08C01


title: E3319_APP.E4.Trem2ko.F.mRNA-seq


title: D11_tumor

description:
FFPE
202184900109_R04C01


title: C11_tumor

description:
FFPE
202184900109_R03C01


title: E3702_APP.E4.Trem2ko.F.mRNA-seq


title: E3830_APP.E4.M.mRNA-seq


title: E3475_APP.E4.M.mRNA-seq


title: E3474_APP.E4.M.mRNA-seq


title: E3333_APP.E4.M.mRNA-seq


title: A11_tumor

description:
FFPE
202184900109_R01C01


title: H10_tumor

description:
FFPE
202184900085_R08C01


title: C12_tumor

description:
FFPE
202184900129_R03C01


title: G10_tumor

description:
FFPE
202184900085_R07C01


title: B11_tumor

description:
FFPE
202184900109_R02C01


title: E3310_APP.E4.M.mRNA-seq


title: F10_tumor

description:
FFPE
202184900085_R06C01


title: E3777_APP.E4.F.mRNA-seq


title: E3356_APP.E4.F.mRNA-seq


title: E3179_APP.E4.M.mRNA-seq


title: E3703_APP.E4.Trem2ko.F.mRNA-seq


title: D10_tumor

description:
FFPE
202184900085_R04C01


title: C10_tumor

description:
FFPE
202184900085_R03C01


title: E10_tumor

description:
FFPE
202184900085_R05C01


title: E3327_APP.E4.F.mRNA-seq


title: A10_tumor

description:
FFPE
202184900085_R01C01


title: E3204_APP.E4.F.mRNA-seq


title: G09_tumor

description:
FFPE
202184900081_R07C01


title: 2M2

value: negative control


title: H09_tumor

description:
FFPE
202184900081_R08C01


title: F09_tumor

description:
FFPE
202184900081_R06C01

value: Unknown primary


title: E3203_APP.E4.F.mRNA-seq


title: E3200_APP.E4.F.mRNA-seq


title: E09_tumor

description:
FFPE
202184900081_R05C01

value: GNET


title: C09_tumor

description:
FFPE
202184900081_R03C01


title: D3891_APP.E3.Trem2ko.M.mRNA-seq


title: E3177_APP.E4.F.mRNA-seq


title: B09_tumor

description:
FFPE
202184900081_R02C01


title: D09_tumor

description:
FFPE
202184900081_R04C01


title: D3707_APP.E3.Trem2ko.M.mRNA-seq


title: D3890_APP.E3.Trem2ko.M.mRNA-seq


title: D3700_APP.E3.Trem2ko.M.mRNA-seq


title: A09_tumor

description:
FFPE
202184900081_R01C01


title: 6M2

value: 4 hrs


title: D3663_APP.E3.Trem2ko.M.mRNA-seq


title: D3601_APP.E3.Trem2ko.M.mRNA-seq


title: G08_tumor

description:
FFPE
202163550167_R07C01


title: B10_tumor

description:
FFPE
202184900085_R02C01


title: F08_tumor

description:
FFPE
202163550167_R06C01


title: D3939_APP.E3.Trem2ko.F.mRNA-seq


title: D3965_APP.E3.Trem2ko.F.mRNA-seq


title: D08_tumor

description:
FFPE
202163550167_R04C01


title: D3938_APP.E3.Trem2ko.F.mRNA-seq


title: C08_tumor

description:
FFPE
202163550167_R03C01


title: D3706_APP.E3.Trem2ko.M.mRNA-seq


title: D3885_APP.E3.Trem2ko.F.mRNA-seq


title: D3627_APP.E3.Trem2ko.F.mRNA-seq


title: G07_tumor

description:
FFPE
202163550152_R07C01


title: D3884_APP.E3.Trem2ko.F.mRNA-seq


title: B08_tumor

description:
FFPE
202163550167_R02C01


title: A08_tumor

description:
FFPE
202163550167_R01C01


title: D3755_APP.E3.M.mRNA-seq


title: D3599_APP.E3.Trem2ko.F.mRNA-seq


title: H07_tumor

description:
FFPE
202163550152_R08C01


title: D3643_APP.E3.M.mRNA-seq


title: H08_tumor

description:
FFPE
202163550167_R08C01


title: D3562_APP.E3.M.mRNA-seq


title: B07_tumor

description:
FFPE
202163550152_R02C01


title: C07_tumor

description:
FFPE
202163550152_R03C01


title: D3563_APP.E3.M.mRNA-seq


title: D3723_APP.E3.M.mRNA-seq


title: D3569_APP.E3.M.mRNA-seq


title: H06_tumor

description:
FFPE
202163550130_R08C01


title: A07_tumor

description:
FFPE
202163550152_R01C01


title: D3742_APP.E3.F.mRNA-seq


title: D3930_APP.E3.F.mRNA-seq


title: E08_tumor

description:
FFPE
202163550167_R05C01


title: D3721_APP.E3.F.mRNA-seq


title: G06_tumor

description:
FFPE
202163550130_R07C01


title: E07_tumor

description:
FFPE
202163550152_R05C01


title: F06_tumor

description:
FFPE
202163550130_R06C01


title: D3720_APP.E3.F.mRNA-seq


title: D3645_APP.E3.F.mRNA-seq


title: F07_tumor

description:
FFPE
202163550152_R06C01


title: D3641_APP.E3.M.mRNA-seq


title: E06_tumor

description:
FFPE
202163550130_R05C01


title: B06_tumor

description:
FFPE
202163550130_R02C01


title: C06_tumor

description:
FFPE
202163550130_R03C01


title: D3638_APP.E3.F.mRNA-seq


title: IP_shRai1_Veh

city: Ann Arbor

first: Patricia

last: Garay

state: MI

address: 1137 Catherine St 5815 Med Sci II

institute: University of Michigan

data_processing:
Full length reads were mapped to mm9 using Bowtie1. Only uniquely mapping reads were analyzed further.
BAM Files were converted to Bigwig files in a strand specific manner. Bigwigs were normalized to dm6 reads *10 million non-rRNA and non-mitochondrial reads.
DESeq2 was used to call differential gene expression between TTX-treated, BIC-treated, and vehicle-treated samples, and between shCtrl and shRai1 treated samples (model built incorporating biological replicate effect; beta prior=true; alpha=0.05).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files represent genome coverage by the reads in a strand specific manner after normalizing to dm6 10 million non-rRNA non-mtRNA reads.

source_name: mouse forebrain cultures

growth_protocol: Mouse forebrain tissue was dissected from E18 embryos, cells were dissociated and plated on poly-D-lysine coated coverslips in Neurobasal medium with 2.5% FBS, 1X B27 supplement, 25 uM beta-mercaptoethanol, and 0.5 mM Glutamax. Half-volume feeds of medium without FBS were performed every 3-4 days.

extract_protocol: Library preparation was derived from an adaptation of the NEBNext protocol.

treatment_protocol: On day in vitro (DIV) 14, cells were infected with lentivirus containing control or Rai1-targeted shRNA. On DIV 17, neurons were treated for 4 hours with tetrodotoxin-citrate (TTX, Tocris, 1 uM final concentration) or bicuculline-methiodide (BIC, Abcam, 20 uM final concentration) or vehicle (water).

tag: strain

tag: day in vitro harvested

tag: embryonic day

tag: antibody

tag: lentivirus

value: Veh


title: A06_tumor

description:
FFPE
202163550130_R01C01

tag: tissue


title: H05_tumor

description:
FFPE
202163550114_R08C01


title: G05_tumor

description:
FFPE
202163550114_R07C01


title: IP_shRai1_BIC

tag: treatment

value: BIC


title: IP_shRai1_TTX

value: TTX


title: IP_shCtrl_Veh

value: shCtrl


title: IP_shCtrl_TTX


title: F05_tumor

description:
FFPE
202163550114_R06C01


title: D06_tumor

description:
FFPE
202163550130_R04C01


title: E05_tumor

description:
FFPE
202163550114_R05C01


title: Input_shRai1_Veh


title: D3639_APP.E3.F.mRNA-seq

tag: Sex

value: Female

value: brain


title: ND+EV, biological rep3

city: Providence

first: Guangbin

last: Shi

state: RI

address: 1 Hoppin street

department: Surgery

institute: Rhode Island Hospital

description: Gene expression data from left ventricle after left circumflex coronary artery underwent an ameroid constrictor.

hyb_protocol: Following fragmentation, 3.75 ug ss-cDNA were hybridized for 16 hr at 45°C at 60 rpm rotation on GeneChip Porcine Gene 1.0 ST Array. Fluidics Protocol FS450_0002 was used for the wash and stain reaction.

scan_protocol: GeneChips were scanned using the 3000 7G Affymetrix scanner.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) software with default settings

organism: Sus scrofa

source_name: Swine with ND+EV3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50ng total RNA (GeneChip WT PIUS Reagent kit, Catalog number 902280, ThermoFisher).

growth_protocol: Male Yorkshire swine fed either Normal diet (ND) or High fat diet (HFD) for 12 weeks.

treatment_protocol: Intact male Yorkshire swine fed either Normal diet (ND) or High fat diet (HFD) underwent placement of an ameroid constrictor on their left circumflex coronary artery. Subsequently ND and HFD animals received either intra-myocardial injection of vehicle-daline as controls or EVs into the ischemic territory. Five weeks later, myocardial tissue were harvest for RNA isolation and gene array.

tag: breed

value: Yorkshire

tag: gender

value: male

value: ND+EV

value: heart

tag: tissue region

value: Left ventricle ischemic zone


title: Input_shRai1_TTX

tag: cell type


title: D05_tumor

description:
FFPE
202163550114_R04C01

value: neuroendocrine tumor

value: DNET


title: ND+EV, biological rep2

source_name: Swine with ND+EV2


title: Input_shCtrl_TTX


title: Input_shRai1_BIC


title: Input_shCtrl_Veh


title: C05_tumor

description:
FFPE
202163550114_R03C01

value: PNET

value: VHL


title: Input_shCtrl_BIC


title: D07_tumor

description:
FFPE
202163550152_R04C01


title: B05_tumor

description:
FFPE
202163550114_R02C01


title: E3234_APP.E4.M.mRNA-seq

value: Male

value: APP


title: IP_shCtrl_BIC


title: A05_tumor

description:
FFPE
202163550114_R01C01

value: SINET

value: Sporadic


title: ND+EV, biological rep1

source_name: Swine with ND+EV1


title: CXCL12-treated uterus-day8-1

city: SEONGNAM-SI

first: YOUN JUNG

last: KANG

address: 335 PANGYO-RO

department: MEDICINE

country: South Korea

institute: CHA University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: uterus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.


title: CXCL12-treated uterus-day3-2


title: CXCL12-treated uterus-day8-2


title: ND, biological rep2

source_name: Swine with ND2

value: ND


title: ND, biological rep3

source_name: Swine with ND3


title: CXCL12-treated uterus-day8-3


title: CXCL12-treated uterus-day3-1


title: Saline-treated uterus-2 (CXCL12 control)

value: saline


title: Saline-treated uterus-1 (CXCL12 control)


title: G04_tumor

description:
FFPE
202163530167_R07C01


title: C2C12 Undifferentiated rep3 [RNA-seq]

city: Durham

first: Kathleen

last: McCann

state: NC

address: 111 TW Alexander Dr

institute: National Institute of Environmental Health Sciences

description:
RNA-seq_raw_counts.txt
RNA-seq_normalized_counts.txt

data_processing:
Base calling and generation of FASTQ files performed using bcl2fastq2
small RNA-seq: Reads were assigned to a custom index of mouse H/ACA snoRNA sequences using salmon 0.12.0 with default parameters; total RNA-seq: Reads were filtered to remove pairs where one or both mates' mean base quality was below 20 and aligned to mm10 using STAR 2.5.1b
small RNA-seq: Counts were imported into R using tximport and combined into snoRNA families based on identifiers in snoRNAs_tx2gene.txt; total RNA-seq: Counts per gene were determined using featureCounts 1.5.1 based on GENCODE M24 annotations
Normalized counts were generated using DESeq2 1.18.1
Genome_build: small RNA-seq: Custom set of H/ACA snoRNA transcripts, sequence extracted from Ensembl release 95 (supplemental file snoRNAs.fa); total RNA-seq: mm10
Supplementary_files_format_and_content: raw and normalized count matrices, tab-delimited text

source_name: C2C12 mouse myoblasts

growth_protocol: All cells were cultured at 37°C in 5% CO2.

extract_protocol:
For small RNA sequencing, total RNA was isolated using TRIzol Reagent, DNase-treated, and further purified using RNeasy mini spin columns (Qiagen). Small RNAs (>17 nt, < 200 nt) were purified using the mirVana miRNA isolation kit (Invitrogen). The 5.8S and 5S ribosomal RNAs were removed using the RiboMinus Eukaryote System v2 (Invitrogen). The purified small RNAs were treated with T4 Polynucleotide Kinase (NEB), purified using the Directzol microprep kit (Zymo) and their concentrations were determined using a Qubit 3 Fluorometer. For total RNA sequencing, Total RNA was isolated from C2C12 myoblasts before and after differentiation into myotubes using TRIzol Reagent, DNase-treated, and further purified using RNeasy mini spin columns (Qiagen). RNA concentration and quality were analyzed on a Qubit 3 Fluorometer and an Agilent Bioanalyzer.
TGIRT template-switching reverse transcription reactions and adapter ligations were performed as described previously (Qin et al., 2016; Shurtleff et al., 2017) using 50 ng of RNA. The ligated cDNA products were purified using a MinElute column (Qiagen) and PCR amplified using Phusion High-Fidelity DNA polymerase (Thermo Fisher Scientific) and 200 nM of both Illumina multiplex primer and Illumina barcode primer (Table S6). PCR was performed for 17 cycles, as described previously (Shurtleff et al., 2017), and PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter). Libraries for RNA-seq analysis were prepared using the TruSeq Stranded Total RNA Gold Library Prep Kit (Illumina) following manufacturer?s instructions.hing reverse transcription reactions and adapter ligations were performed as described previously (Qin et al., 2016; Shurtleff et al., 2017) using 50 ng of RNA. The ligated cDNA products were purified using a MinElute column (Qiagen) and PCR amplified using Phusion High-Fidelity DNA polymerase (Thermo Fisher Scientific) and 200 nM of both Illumina multiplex primer and Illumina barcode primer (Table S6). PCR was performed for 17 cycles, as described previously (Shurtleff et al., 2017), and PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter).

treatment_protocol: Mouse embryonic stem cells were differentiated with retinoic acid for six days. C2C12 myoblasts were differentiated into myotubes for 7 days.

tag: cell line

value: Undifferentiated control


title: C2C12 Myotubes rep2 [RNA-seq]

value: Differentiated into myotubes


title: C2C12 Myotubes rep1 [RNA-seq]


title: C2C12 Undifferentiated rep2 [RNA-seq]


title: C2C12 Myotubes rep3 [RNA-seq]


title: HFD, biological rep1

source_name: Swine with HFD1

value: Yorkshire

value: HFD


title: HFD, biological rep2

source_name: Swine with HFD2

value: male


title: ND, biological rep1

source_name: Swine with ND1

value: heart


title: C2C12 Undifferentiated rep1 [RNA-seq]


title: HFD+EV, biological rep3

source_name: Swine with HFD+EV3

value: HFD+EV

value: Left ventricle ischemic zone


title: sml1rad53_E_20h_rep2

city: Milan

first: Christopher

last: Bruhn

address: Via Adamello 16

country: Italy

institute: Fondazione Istituto FIRC di Oncologia Molecolare (IFOM)

data_processing:
BAM files were converted to FASTQ using BEDTools (Galaxy server, bedtools v2.24.0)
Reads were annealed to the SacCer_Apr2011/sacCer3 transcriptome using Sailfish (Galaxy server, Sailfish v0.7.6, k-mer size: 21, bias correction)
The R package DESeq2 (version 1.16.1) was used to identify differentially expressed ORFs by pairwise comparison (fitType = "local", pAdjustMethod = “BH”)
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited matrix text file: First column contains yeast ORF (YORF) as feature identifier, following columns contain bias-corrected reads per ORF (Sailfish output) for all samples

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown at 28°C in a shaking flask in synthetic complete medium with the indicated carbon source and harvested at a density of 1x10^7 cells / mL.

extract_protocol:
Total mRNAs were extracted from 2x10^7 cells using the RNeasy mini kit (QIAGEN) according to the manufacturer's instructions.
Libraries for RNA sequencing were prepared following the manufacturer protocols for transcriptome sequencing with the Ion Proton sequencer (Thermo Fisher Scientific/Life Technologies). Briefly, 1 µg of total RNA was poly-A selected using the Dynabeads mRNA Direct Micro Purification kit (Thermo Fisher Scientific, Cat# 61021) according to manufacturer’s protocol. 50 ng of poly-A RNA were used to prepare strand-specific barcoded RNA libraries with the Ion Total RNA-Seq kit v2.0 (Thermo Fisher Scientific, Cat# 4475936). Poly-A RNA was fragmented with RNAse III, and purified with Nucleic Acid Binding Beads. RNA fragments were hybridized and ligated with Ion Adaptor and subsequently reverse transcribed into cDNA. The cDNA was amplified with the Ion Torrent barcode primer and purified with Nucleic Acid Binding Beads. Final libraries were quantified on the Qubit fluorometer with HS DNA (Thermo Fisher Scientific/Life Technologies) and checked for size on an Agilent Bioanalyzer with HS DNA kit (Agilent, Santa Clara, CA). Ten barcoded libraries were pooled together on an equimolar basis at a final concentration of 11 pM and clonally amplified using the Ion Proton™ Hi Q™Template Kit (Thermo Fisher Scientific/Life Technologies) with IonOneTouch 2 instrument (Thermo Fisher Scientific/Life Technologies). After emulsion PCR, DNA positive ISPs were recovered and enriched according to standard protocols with the IonOneTouch ES Instrument (Thermo Fisher Scientific/Life Technologies). A sequencing primer was annealed to DNA positive ISPs and the sequencing polymerase bound, prior to loading of ISPs into Ion P1 sequencing chips. Sequencing of the samples was conducted according to the Ion Proton™ Hi-Q Sequencing Kit Protocol on Ion Proton instrument.

treatment_protocol: For the carbon source switch, cells were washed once with synthetic complete medium with 3% ethanol and then resuspended in synthetic complete medium with 3% ethanol. For the harvest, cells were pelleted and the pellet was snap-frozen in liquid nitrogen without washing.

tag: genotype/variation


title: H04_tumor

description:
FFPE
202163530167_R08C01

value: neuroendocrine tumor


title: C04_tumor

description:
FFPE
202163530167_R03C01

value: PNET


title: B04_tumor

description:
FFPE
202163530167_R02C01


title: mESCs untreated T=0 rep2 (small RNA-seq)

description: size selected total RNA

source_name: E14TG2a, mouse embryonic stem cells

value: mouse embryonic stem cells (mESCs)

value: control


title: F04_tumor

description:
FFPE
202163530167_R06C01


title: HFD+EV, biological rep1

source_name: Swine with HFD+EV1

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: mESCs +RA T=6 rep2 (small RNA-seq)

description: size selected total RNA

value: RA


title: HFD+EV, biological rep2

source_name: Swine with HFD+EV2


title: mESCs +RA T=6 rep3 (small RNA-seq)

description: size selected total RNA


title: sml1rad53hht2_E_1h_rep2


title: D04_tumor

description:
FFPE
202163530167_R04C01

value: DNET


title: mESCs untreated T=0 rep3 (small RNA-seq)

description: size selected total RNA


title: mESCs untreated T=0 rep1 (small RNA-seq)

description: size selected total RNA


title: mESCs +RA T=6 rep1 (small RNA-seq)

description: size selected total RNA


title: E04_tumor

description:
FFPE
202163530167_R05C01


title: sml1hht2_E_1h_rep2


title: A04_tumor

description:
FFPE
202163530167_R01C01

value: SINET

value: Sporadic


title: sml1_E_20h_rep2


title: ILC3 cells at 23 hours replicate 2

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the human genome by Rsubread version 1.22.2
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Intestine

extract_protocol:
RNA was harvested using RNeasy Micro Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 6 mice per timepoint were sacrified (ZT4,ZT10,ZT16 and ZT23). Small intestine were digested and single cell suspension from 6 mice were pooled and stained with appropriate antibodies. Cells were FACS-sorted

value: Intestine

tag: time (hours)

tag: batch

value: female


title: H03_tumor

description:
FFPE
202163530149_R08C01

source_name: neuroendocrine tumor

tag: tumor type

tag: hereditary


title: ILC3 cells at 23 hours replicate 1


title: G03_tumor

description:
FFPE
202163530149_R07C01


title: sml1rad53_E_1h_rep2

tag: strain


title: ILC3 cells at 16 hours replicate 1


title: ILC3 cells at 10 hours replicate 2


title: sml1_E_1h_rep2


title: ILC3 cells at 10 hours replicate 1


title: F03_tumor

description:
FFPE
202163530149_R06C01


title: ILC3 cells at 4 hours replicate 2


title: sml1rad53hht2_D_rep2


title: ILC2 cells at 10 hours replicate 2


title: D03_tumor

description:
FFPE
202163530149_R04C01


title: C03_tumor

description:
FFPE
202163530149_R03C01


title: sml1rad53_D_rep2


title: B03_tumor

description:
FFPE
202163530149_R02C01


title: ILC2 cells at 10 hours replicate 1


title: ILC2 cells at 16 hours


title: sml1hht2_D_rep2


title: sml1_D_rep2


title: sml1rad53_E_20h_rep1


title: WT-input

city: Philadelphia

first: Matthew

middle: Darrell

last: Weitzman

address: 4050 CTRB, 3501 Civic Center Blvd

department: Pathology & Laboratory Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Preprocessing involved adapter cutting adapters using cutadapt (v. 1.18) and extracting the UMIs using umi_tools (v 1.0.0).
Alignment was achieved using GSNAP version 2019-09-12. Reads were aligned to the human and adenovirus 5 genome simultaneously.
After the alignment we used umi_tools to deduplicate reads based on the UMIs, which was followed by removing all non-unique reads.
We then used clipper (v 0.1.4) to find significant enriched eclip peaks following instructions from https://github.com/YeoLab/clipper/wiki/CLIPper-Home.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files show the coverage for both the reads mapping to the forward and reverse strand.

source_name: HeLa_Ad5_size matched input

growth_protocol: HeLa cells were obtained from the American Type Culture Collection (ATCC) and cultured at 37°C and 5% CO2 (Cat#: ATCC CCL-2), and were grown in DMEM supplemented with 10% v/v fetal bovine serum (FBS) and 1% v/v Pen/Strep of streptomycin.

extract_protocol:
The CLIP protocol was adapted from existing protocols (PMID: 28766298). In short, approximately 2x107 HeLa cells were crosslinked on ice with 0.8 J/cm2 UV 254 nm in a UV Stratalinker 2400 (Stratagene), washed in PBS with 2 mM EDTA and 0.2 mM PMSF, flash frozen in liquid nitrogen and stored at -80°C. 100 μl of Protein G Dynabeads per sample were washed 3x in iCLIP lysis buffer A (50 mM Tris-HCl ph 7.4, 10 mM NaCl, 0.2% v/v NP-40, 0.1% w/v SDS, 0.5% w/v Sodium deoxycholate, 1x cOmplete Protease Inhibitor Cocktail), resuspended in 100 μl iCLIP lysis buffer A and incubated with 10 μg of α-hnRNP-C antibody rotating 1 h at RT. Cell pellets were resuspended in 1 ml of iCLIP lysis buffer B (same as buffer A but with 1% v/v NP-40) and incubated on ice for 15 min. Samples were sonicated with a Diagenode Biorupter on low setting for 30 s on and 30 s off for five rounds at 4°C. 2 μl of TURBO DNase (Thermo Fisher) and 10 μl of 1:10  diluted RNase I (Thermo Fisher) were added and samples incubated in Thermomixer at 1200 rpm at 37°C for 5 min, samples placed on ice and 22 μl SUPERase·In RNase Inhibitor was added. 500 μl of cleared lysate were added to washed beads and incubated rotating at 4°C for 2 h. Beads were washed 2x in High Salt buffer , 2x in Wash buffer and 2x FastAP buffer. 100 μl of FastAP master mix and 8 μl FastAP enzyme was added and samples were incubated with a Thermomixer at 1200 rpm at 37°C for 15 min. 300 PNK master mix  and 7 μl T4 PNK enzyme was added and samples were incubated with a Thermomixer at 1200 rpm at 37°C for 20 min. Beads were washed and resuspended in Ligase buffer with 2.5 μl RNA Ligase high conc., 2.5 μl of RNA adapters (3SR_RNA ), and incubated at RT for 75 min. Beads were washed and a fraction saved for immunoblotting. For the remaining fraction, beads were resuspended in lysis buffer with DTT,  eluted by incubation in Thermomixer, 1200 rpm, 70°C, run on SDS-PAGE and transferred onto Nitrocellulose o/n, 30V. Lanes for the RBP band (plus 75 kDa) and size-matched input were cut from the membranes RNA was eluted with 20 μl of Proteinase K (Thermo Fisher) in a Thermomixer at 1200 rpm at 50 °C for 1 h. RNA was extracted with acid phenol/chloroform/isoamyl alcohol (pH 4.5), and concentrated using RNA Clean and Concentrator (Zymo).Size-matched inputs were ligated to 3SR_RNA. All RNA samples were reverse transcribed with 0.9 μl AffinityScript Enzyme at 55 °C for 45 min with RT primer SR_RTv2 . RNA and excess primers were removed with 3.5 μl ExoSAP-IT 1 M NaOH. cDNA was purified using 10 μl MyONE Silane beads and ligated to 5’ linker SR_DNA  o/n at RT. After clean up, cDNA was quantified by qPCR using NEBNext universal and index primers (NEB E7335S). Libraries were indexed using NEBNext High-Fidelity PCR Master Mix (NEB M0541S) for 11 cycles (size-matched input) or 15 cycles (hnRNP-C IP). Libraries were size selected by 1.0x AmpureXP beads (Beckman Coulter A63880), quantified by QuBit HS DNA and Bioanalyzer High Sensitivity DNA assay, and pooled for sequencing.
seCLIP (See above); Stranded 75bp single end

treatment_protocol: Cells were mock-infected or infected with either wildtype Ad5 or delta E1B-55K (dl110) Ad5 for two hours in low-serum media. Growth media was replaced with full serum media and infection continued for 24 hours.

value: HeLa

tag: infection

tag: hpi

tag: ip

value: size matched input


title: ILC3 cells at 16 hours replicate 2

tag: tissue


title: A03_tumor

description:
FFPE
202163530149_R01C01


title: ILC2 cells at 4 hours replicate 2


title: sml1_E_20h_rep1


title: sml1rad53hht2_E_1h_rep1


title: WT-2

value: hnRNP-C


title: mock-input

source_name: HeLa_Mock_size matched input

value: Mock


title: H02_tumor

description:
FFPE
202163530106_R08C01


title: mock-2


title: G02_tumor

description:
FFPE
202163530106_R07C01


title: WT-1


title: mock-1


title: dl110-input

source_name: HeLa_dl110_size matched input


title: ILC2 cells at 23 hours replicate 2


title: ILC2 cells at 4 hours replicate 1


title: sml1hht2_E_1h_rep1


title: F02_tumor

description:
FFPE
202163530106_R06C01


title: dl110-2


title: E02_tumor

description:
FFPE
202163530106_R05C01


title: sml1rad53_E_1h_rep1


title: cc011-16_p0_CD66P

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
align with STAR 2.6.0b-1  using galaxy
raw count generated by featrueCounts  1.6.0.3  using galaxy
counts normalization and differential expression using DESeq2  2.11.40.2 using galaxy
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: normailzed count file generated by DESeq2

source_name: Trachea organoid

extract_protocol: qiagen mirneasy micro kit

value: Trachea

tag: cd66 status

tag: culture type

value: Organoid Culture


title: cc011-16_p0_CD66N


title: dl110-1


title: D02_tumor

description:
FFPE
202163530106_R04C01


title: sml1_E_1h_rep1


title: cc03-17_p0_cd66P


title: cc011-16_CD66P

source_name: Trachea

value: Primary


title: C02_tumor

description:
FFPE
202163530106_R03C01

value: neuroendocrine tumor


title: cc011-16_CD66N


title: cc03-17_p0_cd66N


title: sml1rad53hht2_D_rep1


title: sml1hht2_D_rep1


title: sml1rad53_D_rep1


title: ILC3 cells at 4 hours replicate 1


title: cc03-17_cd66P


title: cc02-17_p0_CD66P


title: cc02-17_p0_CD66N


title: H01_tumor

description:
FFPE
202163530086_R08C01

value: PNET


title: cc02-17_CD66P


title: sml1_D_rep1


title: KAM5M: cKO Male Anti-mesometrial Decidua

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description: gestation day 8.5

data_processing:
The raw sequence files were first chekced for quality by FASTQC.
The base quality trimming was performed using fqtrim (v 0.9.4) for phred 30 and minimum read length of 20.
Reference mapping was performed using hisat2 (v 2.0.3).
Counted mapped reads to genes with featureCounts and Ensembl  annotation
edgeR-robust DE analysis with genes filtered at rowSum >1
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text file with raw read counts for each gene

source_name: Decidua

growth_protocol: Gestation day 8.5

extract_protocol:
Freshly collected gestation day 8.5 mesometrial and anti-mesometrial decudua from littermate  control and Foxa2 conditional knockout uterus were snap frozen in liquid nitrogen. Total RNA was isolated from frozen speciment using a standard TRIzol-based protocol (Catalog 15596026, Thermo Fisher). To eliminate genomic DNA contamination, extracted RNA was treated with DNase I and purified using a RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of RNA were determined using a Fragment Analyzer (Advanced Analytical Technologies).
Libraries were prepared by Novogene using an Illumina TruSeq mRNA kit (Illumina Inc.) and sequenced (paired-end 150; 30 million read pairs) using an Illumina NovaSeq 6000.

treatment_protocol: FOXA2 was conditionally deleted in the utterus. Floxed Foxa2 mice were crossed with or LtfiCre  mice to generate conditional knockout animals. Floxed Foxa2f/f mice (stock no. 022620) and LtfiCre mice (stock no. 026030) were obtained from The Jackson Laboratory. Gestational time points were obtained by the mating of 8- to 10-wk old Control (Foxa2f/f) and FOXA2 cKO (LtfiCr/+Foxa2f/f) females to wild-type CD-1 male mice with the day that a vaginal plug was observed was considered day 0.5 of gestation. For FOXA2 cKO dams, mice received i.p. injections of recombinant mouse LIF (10 μg in saline; catalog #554008, BioLegend) at 1000 h and 1800 h on GD 3.5

tag: Sex

value: Male

tag: genotype

value: Ltf c/+ Foxa2 f/f

value: Anti-mesometrial Decidua


title: cc02-17_CD66N


title: F01_tumor

description:
FFPE
202163530086_R06C01

value: DNET


title: E01_tumor

description:
FFPE
202163530086_R05C01

value: VHL


title: D01_tumor

description:
FFPE
202163530086_R04C01


title: KAM4M: cKO Male Anti-mesometrial Decidua

description: gestation day 8.5


title: KAM3M: cKO Male Anti-mesometrial Decidua

description: gestation day 8.5


title: KAM2M: cKO Male Anti-mesometrial Decidua

description: gestation day 8.5


title: KAM1M: cKO Male Anti-mesometrial Decidua

description: gestation day 8.5


title: B02_tumor

description:
FFPE
202163530106_R02C01


title: cc03-17_cd66N


title: B01_tumor

description:
FFPE
202163530086_R02C01


title: A01_tumor

description:
FFPE
202163530086_R01C01

value: SINET

value: Sporadic


title: A02_tumor

description:
FFPE
202163530106_R01C01


title: KAM4F: cKO Female Anti-mesometrial Decidua

description: gestation day 8.5

value: Female

value: Foxa2 f/f


title: C01_tumor

description:
FFPE
202163530086_R03C01


title: E03_tumor

description:
FFPE
202163530149_R05C01


title: KAM3F: cKO Female Anti-mesometrial Decidua

description: gestation day 8.5


title: KAM2F: cKO Female Anti-mesometrial Decidua

description: gestation day 8.5


title: KAM1F: cKO Female Anti-mesometrial Decidua

description: gestation day 8.5


title: ILC2 cells at 23 hours replicate 1

value: Intestine

tag: gender

value: female


title: G01_tumor

description:
FFPE
202163530086_R07C01


title: CAM5M: Control Male Anti-mesometrial Decidua

description: gestation day 8.5


title: KAM5F: cKO Female Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM4M: Control Male Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM3M: Control Male Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM1M: Control Male Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM2M: Control Male Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM5F: Control Female Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM4F: Control Female Anti-mesometrial Decidua

description: gestation day 8.5


title: RMG Anaer Stationary RNA-seq rep1

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

institute: University of Wisconsin

data_processing:
RNA-seq: Reads were filtered for low quality and adapter readthrough using trimmomatic version 0.30 using the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:22:10 SLIDINGWINDOW:4:28 MINLEN:75. Gene read counts were obtained using the revised protein-coding annotations from this study, using RSEM v1.2.3 and Bowtie v1.0.0 using the following parameters:  --paired-end --calc-ci --estimate-rspd --forward-prob 0 --phred33-quals.
RSEM expected counts were used for downstream differential expression analysis. Pearson correlation between of gene counts between biological replicates was used to detect outlier libraries. All the retained libraries had inter-replicate Pearson correlation of at least 0.95. Features representing rRNA and tRNA, and genes with count sums less 5000 across all remaining samples were removed from the matrix. Gene count normalization and differential expression testing was performed using DESeq2 v1.14.1 run on R 3.3.0.
Genome_build: Genbank sequences CP023715.1, CP023716.1, CP023717.1, CP023718.1, and CP023719.1
Supplementary_files_format_and_content: 5p.complete.bedgraph files contain plus and minus strand, genome-wide read coverage for the corresponding sample where only the first base in the read is counted towards read coverage; coverage values are not normalized, negative values correspond reads mapped to the minus strand and positive coverage values correspond to reads mapped to plus strand. complete.bedgraph files contain plus and minus strand, genome-wide read coverage for the corresponding sample where every base in the read is counted towards read coverage; coverage values are not normalized, negative values correspond reads mapped to the minus strand and positive coverage values correspond to reads mapped to plus strand. compiledDESeq2.results.txt is a tab-delimited text file that contains the log2 fold change and adjusted p-value (aka q-value or FDR) for pair-wise differential expression analysis of RNA-seq gene counts. RNAseq.RSEM.expectedCounts.txt is a tab-delimited text file that contains the expected reads counts per gene as determined by rsem (used as described in corresponding data processing step description) compiled from all 19 RNA-seq data sets.

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

source_name: cell culture

growth_protocol: Zymomonas mobilis subsp. mobilis ZM4 ATCC31821 grown in rich medium with glucose (RMG) containing per L 10 g yeast extract, 2.6 g KH2PO4, 5 g K2HPO4, and 20 g glucose or minimal media with glucose (MMG) containing per L 20 g glucose, 2.6 g KH2PO4, 5 g K2HPO4, 0.5 g NaCl, 1 g (NH4)2SO4, 0.2 g MgSO4·7H2O, 25 mg Na2MoO4·2H2O, 10 mg CaCl2·2H2O, 1 mg calcium pantothenate, 25 mg FeSO4·7H2O, and 20 g glucose, and was adjusted to pH 6.4 with HCl. Cell growth was monitored in real-time by light scattering (termed OD) at 600 nM and extracellular glucose concentration was measurement by YSI 2700 Select. Overnight starter cultures of ZM4 were grown in RMG in an anaerobic chamber and used to inoculate 3L cultures of media in bioreactors (Applikon Biotechnology). Anaerobic cultures were sparged with N2/CO2 gas mix at a rate of 150mL/min and cells were agitated at 300 rpm. Aerobic cultures were sparged with atmospheric air at a rate of 700mL/min and agitated at 500 rpm. All multiomics samples were collected at 50% glucose depletion from the media (mid-glucose phase time point) and 1-hour post glucose depletion (stationary phase time point).

extract_protocol: Ten mL of culture was added to 1.25mL of ice-cold ethanol/phenol stop solution, and RNA was extracted using hot phenol method as described in PMID:21601083; total RNA was DNase I treated prior to all library construction.

tag: time point

value: stationary

tag: rna-pretreatment

tag: molecule subtype

value: rRNA-depleted RNA


title: RMG Aero mid-Glucose RNA-seq rep3

value: mid-glucose


title: MMG Anaer Stationary RNA-seq rep3


title: RMG Anaer Stationary RNA-seq rep2


title: RMG Aero Stationary RNA-seq rep2


title: RMG Aero mid-Glucose RNA-seq rep2


title: RMG Aero mid-Glucose RNA-seq rep1


title: RMG Anaer mid-Glucose RNA-seq rep1


title: RMG Anaer Stationary RNA-seq rep3


title: RMG Aero Stationary RNA-seq rep4


title: RMG Aero Stationary RNA-seq rep1


title: RMG Anaer mid-Glucose RNA-seq rep3


title: RMG Aero Stationary RNA-seq rep3


title: RMG Anaer mid-Glucose RNA-seq rep2


title: KM5M: cKO Male Mesometrial Decidua

description: gestation day 8.5

value: Mesometrial Decidua


title: CAM3F: Control Female Anti-mesometrial Decidua

description: gestation day 8.5


title: CAM2F: Control Female Anti-mesometrial Decidua

description: gestation day 8.5


title: MMG Anaer mid-Glucose RNA-seq rep2


title: MMG Anaer Stationary RNA-seq rep1


title: RMG Anaer Stationary term-seq rep3

data_processing:
Library strategy: term-seq
term-seq: In-line barcodes were removed from the 5’ end of reads and sequencing adapter readthrough was removed using trimmomatic v0.30 with the following parameters: HEADCROP:7 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10  MINLEN:25. Reads were aligned to Z. mobilis ZM4 chromosome and plasmid sequences using Bowtie v1.0.0 with the following parameters -S -m 1 --phred33-quals -v 2. Read 5'-only coverage was calculated for each position in the genome for both plus and minus strands using BEDTools v2-2.20.1 genomeCoverageBed with the following parameters: -5 -d. Because term-seq libraries result in read sequences in the reverse complement to the starting RNA sequence, the strandedness of the read coverage data was reversed at the step of genomeCoverageBed, such that the parameter “-strand -“ was used to tabulate plus strand read coverage and vice versa. Positions with zero read coverage were removed and plus and minus strand data were concatenated to generate 5p.complete.bedgraph files where negative covearge values correspond to minus strand values.
Genome_build: Genbank sequences CP023715.1, CP023716.1, CP023717.1, CP023718.1, and CP023719.1
Supplementary_files_format_and_content: 5p.complete.bedgraph files contain plus and minus strand, genome-wide read coverage for the corresponding sample where only the first base in the read is counted towards read coverage; coverage values are not normalized, negative values correspond reads mapped to the minus strand and positive coverage values correspond to reads mapped to plus strand. complete.bedgraph files contain plus and minus strand, genome-wide read coverage for the corresponding sample where every base in the read is counted towards read coverage; coverage values are not normalized, negative values correspond reads mapped to the minus strand and positive coverage values correspond to reads mapped to plus strand. compiledDESeq2.results.txt is a tab-delimited text file that contains the log2 fold change and adjusted p-value (aka q-value or FDR) for pair-wise differential expression analysis of RNA-seq gene counts. RNAseq.RSEM.expectedCounts.txt is a tab-delimited text file that contains the expected reads counts per gene as determined by rsem (used as described in corresponding data processing step description) compiled from all 19 RNA-seq data sets.

extract_protocol:
Ten mL of culture was added to 1.25mL of ice-cold ethanol/phenol stop solution, and RNA was extracted using hot phenol method as described in PMID:21601083; total RNA was DNase I treated prior to all library construction.
Termination sequencing libraries were prepared as described in PMID:27120414 using 2.5ug DNase-treated total RNA as input and used 3' sequencing adapters with a 5mer in-line barcode. After 3' adapter ligation, six samples were pooled prior to rRNA-depletion with the Illumina RiboZero Bacteria Kit.


title: RMG Anaer mid-Glucose term-seq rep3


title: MMG Anaer mid-Glucose RNA-seq rep1


title: RMG Anaer Stationary term-seq rep1


title: MMG Anaer Stationary RNA-seq rep2


title: RMG Anaer mid-Glucose term-seq rep1


title: CAM1F: Control Female Anti-mesometrial Decidua

description: gestation day 8.5


title: RMG Anaer mid-Glucose term-seq rep2


title: RMG Anaer Stationary term-seq rep2


title: MMG Anaer mid-Glucose RNA-seq rep3


title: KM4M: cKO Male Mesometrial Decidua

description: gestation day 8.5


title: RMG Aero Stationary term-seq rep3


title: KM3M: cKO Male Mesometrial Decidua

description: gestation day 8.5


title: KM2M: cKO Male Mesometrial Decidua

description: gestation day 8.5


title: KM1M: cKO Male Mesometrial Decidua

description: gestation day 8.5


title: RMG Aero Stationary term-seq rep1


title: RMG Aero Stationary term-seq rep2


title: RMG Aero mid-Glucose term-seq rep3


title: MMG Anaer Stationary term-seq rep3


title: RMG Aero mid-Glucose term-seq rep2


title: RMG Aero mid-Glucose term-seq rep1


title: KM5F: cKO Female Mesometrial Decidua

description: gestation day 8.5


title: RMG Aero Stationary term-seq rep4


title: MMG Anaer Stationary term-seq rep2


title: MMG Anaer Stationary term-seq rep1


title: KM4F: cKO Female Mesometrial Decidua

description: gestation day 8.5


title: Tumor9

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: Crta Can Ruti; cami de les escoles, S/N

country: Spain

institute: Germans Trias i Pujol Health Research Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using a HiScan and standard recommended Illumina scanner setting

data_processing: There was preprocessing using the normalization method Funnorm, recommended for tumor samples as implemented in the minfi Bioconductor Package (v 1.24). CpGs were annotated with the closer gene. Probes containing single nucleotide polymorphisms were discarded from analyses to avoid confounding.

source_name: Tumor

label_protocol: Standard Illumina's Infinium HD Methylation Protocol

extract_protocol: MagMAX™ DNA Multi-Sample kit was used using following manufacturer’s instructions (Thermo Fisher Scientific)

tag: individual

value: patient 9

value: M

tag: disease state

value: Hepatoblastoma

value: Tumor


title: MMG Anaer mid-Glucose term-seq rep1


title: MMG Anaer mid-Glucose term-seq rep2


title: MMG Anaer mid-Glucose term-seq rep3


title: KM2F: cKO Female Mesometrial Decidua

description: gestation day 8.5


title: RMG Anaer Stationary RppH- TSS-seq rep2

data_processing:
Library strategy: TSS-seq
TSS-seq: In-line barcodes were removed from the 5’ end of reads and sequencing adapter readthrough was removed using trimmomatic v0.30 with the following parameters: HEADCROP:6 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10  MINLEN:25. Reads were aligned to Z. mobilis ZM4 chromosome and plasmid sequences using Bowtie v1.0.0 with the following parameters -S -m 1 --phred33-quals -v 2. Read 5'-only coverage was calculated for each position in the genome for both plus and minus strands using BEDTools v2-2.20.1 genomeCoverageBed with the following parameters: -5 -d. Positions with zero read coverage were removed and plus and minus strand data were concatenated to generate 5p.complete.bedgraph files where negative coverage values correspond to minus strand values.
Genome_build: Genbank sequences CP023715.1, CP023716.1, CP023717.1, CP023718.1, and CP023719.1
Supplementary_files_format_and_content: 5p.complete.bedgraph files contain plus and minus strand, genome-wide read coverage for the corresponding sample where only the first base in the read is counted towards read coverage; coverage values are not normalized, negative values correspond reads mapped to the minus strand and positive coverage values correspond to reads mapped to plus strand. complete.bedgraph files contain plus and minus strand, genome-wide read coverage for the corresponding sample where every base in the read is counted towards read coverage; coverage values are not normalized, negative values correspond reads mapped to the minus strand and positive coverage values correspond to reads mapped to plus strand. compiledDESeq2.results.txt is a tab-delimited text file that contains the log2 fold change and adjusted p-value (aka q-value or FDR) for pair-wise differential expression analysis of RNA-seq gene counts. RNAseq.RSEM.expectedCounts.txt is a tab-delimited text file that contains the expected reads counts per gene as determined by rsem (used as described in corresponding data processing step description) compiled from all 19 RNA-seq data sets.

extract_protocol:
Ten mL of culture was added to 1.25mL of ice-cold ethanol/phenol stop solution, and RNA was extracted using hot phenol method as described in PMID:21601083; total RNA was DNase I treated prior to all library construction.
TSS-seq libraries were constructed following methods from PMID:22617957 and PMID:27120414. RNA 5’ pyrophosphohydrolase (RppH) (New England BioLabs M0356S) was used in place of tobacco acid pyrophosphatase for pre-treatment of total RNA. For RppH-treated libraries, 2.5ug total RNA was incubated with 20U RppH and 2uL 10x Reaction Buffer in a final volume of 20uL at 37°C for 2hrs. RppH-untreated samples used 4uL H2O in place of RppH. TSS-seq 5' adapters contained 4mer in-line barcodes; after 5' adapter ligation three RppH-treated and three RppH-untreated samples were pooled prior to rRNA-depletion with the Illumina RiboZero Bacteria Kit.

value: RppH-untreated


title: KM3F: cKO Female Mesometrial Decidua

description: gestation day 8.5


title: KM1F: cKO Female Mesometrial Decidua

description: gestation day 8.5


title: RMG Anaer Stationary RppH- TSS-seq rep1


title: RMG Anaer mid-Glucose RppH- TSS-seq rep3


title: CM5M: Control Male Mesometrial Decidua

description: gestation day 8.5

value: Male

value: Ltf c/+ Foxa2 f/f


title: RMG Anaer mid-Glucose RppH- TSS-seq rep1


title: Tumor6

value: patient 6

value: F


title: Tumor23

value: patient 23


title: Tumor5

value: patient 5


title: RMG Aero Stationary RppH- TSS-seq rep4


title: Tumor8

value: patient 8


title: Tumor33

value: patient 33


title: RMG Anaer Stationary RppH- TSS-seq rep3

value: stationary


title: Tumor7

value: patient 7


title: RMG Aero Stationary RppH- TSS-seq rep3

value: rRNA-depleted RNA


title: Tumor30

value: patient 30


title: RMG Aero Stationary RppH- TSS-seq rep2


title: RMG Aero Stationary RppH- TSS-seq rep1


title: CM3M: Control Male Mesometrial Decidua

description: gestation day 8.5

value: Mesometrial Decidua


title: Tumor28

value: patient 28

value: M


title: Tumor26

value: patient 26

value: Hepatoblastoma

value: Tumor


title: RMG Anaer mid-Glucose RppH- TSS-seq rep2

value: mid-glucose

value: RppH-untreated


title: CM2M: Control Male Mesometrial Decidua

description: gestation day 8.5

value: Male

value: Ltf c/+ Foxa2 f/f


title: RMG Aero mid-Glucose RppH- TSS-seq rep3


title: RMG Aero mid-Glucose RppH- TSS-seq rep2


title: Tumor25

value: patient 25


title: Tumor32

value: patient 32


title: RMG Aero mid-Glucose RppH- TSS-seq rep1


title: CM1M: Control Male Mesometrial Decidua

description: gestation day 8.5


title: CM4M: Control Male Mesometrial Decidua

description: gestation day 8.5


title: Tumor20

value: patient 20


title: CM5F: Control Female Mesometrial Decidua

description: gestation day 8.5

value: Female

value: Foxa2 f/f


title: Tumor31

value: patient 31

value: F


title: MMG Anaer Stationary RppH- TSS-seq rep2

value: stationary

value: rRNA-depleted RNA


title: MMG Anaer Stationary RppH- TSS-seq rep1


title: Tumor4

value: patient 4

value: M


title: MMG Anaer Stationary RppH- TSS-seq rep3


title: MMG Anaer mid-Glucose RppH- TSS-seq rep3


title: CM4F: Control Female Mesometrial Decidua

description: gestation day 8.5

value: Mesometrial Decidua


title: Tumor2

value: patient 2

value: Hepatoblastoma

value: Tumor


title: MMG Anaer mid-Glucose RppH- TSS-seq rep1

value: mid-glucose

value: RppH-untreated


title: Tumor18

value: patient 18


title: CM3F: Control Female Mesometrial Decidua

description: gestation day 8.5


title: Tumor22

value: patient 22


title: Tumor21

value: patient 21


title: RMG Anaer Stationary RppH+ TSS-seq rep3

value: RppH-treated


title: CM2F: Control Female Mesometrial Decidua

description: gestation day 8.5

value: Female

value: Foxa2 f/f


title: RMG Anaer Stationary RppH+ TSS-seq rep2


title: RMG Anaer Stationary RppH+ TSS-seq rep1


title: Tumor17

value: patient 17


title: CM1F: Control Female Mesometrial Decidua

description: gestation day 8.5


title: Tumor16

value: patient 16


title: WT-C-TP-1 Lib2

city: Seongnam-si

first: Joohyun

last: Jee

state: Gyeonggi-Do

address: 712 CHA Bio Complex, 335 Pangyo-Ro, Sampyeong-Dong, Bundang-Gu

department: Department of Microbiology

data_processing:
Single cell RNA-Seq data were processed by align reads, generate feature-barcode matrices and perform clustering and gene expression analysis using the Cell Ranger (v.3.1.0) with default options.
Subsequently, data QC, filtering, and visualization were used for the Seurat (v.2.3) R package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include average gene expression values by clusters.

source_name: colon

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: Colon epithelium

value: colon

tag: treatment

value: irradiation exposed after 2 weeks

value: wild type


title: RMG Anaer mid-Glucose RppH+ TSS-seq rep2

tag: strain

value: rRNA-depleted RNA


title: Tumor13

value: patient 13

value: M

value: Hepatoblastoma


title: Lung_Het_03

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from mm10 UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: Lung

extract_protocol:
RNA was column-extracted using RNeasy Mini kit (Qiagen)
RNA-seq libraries were prepared from about 200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Asynchronously growing early passage MEFs were harvest at ~90% confluence. Whole Lungs were collected from 10 day old animals.

value: Lung

tag: genotype/variation

value: Het


title: RMG Anaer mid-Glucose RppH+ TSS-seq rep1

value: mid-glucose


title: Lung_Het_02