title: GNE-274 Rep 3

data_processing:
Paired-end reads were aligned to the human reference genome (NCBI Build 38) using GSNAP (PMID: 20147302) version ‘2013-10-10’, allowing a maximum of two mismatches per read sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’)
Reads aligning to locations in the human genome containing substantial sequence homology to the MT chromosome or to blacklisted regions identified by the ENCODE consortium were omitted from downstream analyses, and so were duplicate reads.
Remaining aligned reads were used to quantify chromatin accessibility according to the ENCODE pipeline standards with minor modifications as follows
Accessible peak locations were identified as described; briefly, we called peaks significance (cutoff of p=1e-7) on a condition-level pooled sample containing all pseudo-fragments observed in all replicates within each condition. Peaks in the pooled sample that were independently identified as significant (cutoff of p=1e-7) in two or more of the constituent biological replicates were retained for downstream analysis, using the union of all condition-level reproducible peaks to form the atlas
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of peaks with genomic corrdinates, annotations, significance in each condition and counts in each replicate

extract_protocol:
Cells were detached using Accutase® Cell Detachment Solution (Cat#, Corning, City), counted and resuspended in growth media containing 5% DMSO. Cells were aliquoted into cryovials, frozen
Active Motif (Carlsbad, CA) performed transposase reactions, library preparations and sequencing (Illumina)


title: SAM24360839

status: Public on Jul 25 2019

type: SRA

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

country: USA

institute: Genentech

library_source: transcriptomic

data_processing:
RNA sequencing (RNAseq) data were analyzed with HTSeqGenie [Pau and Reeder, R package, 2012] in BioConductor [Huber et al, Nat Methods 2015] as follows: reads were trimmed to 75 bp, filtered for quality and rRNA/adapter contamination, and aligned to the reference genome GRCh38
Gene expression was quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample x gene length x size factor).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of read counts for all genes and replicates

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: MDA-MB-134 VI, MDA-MB-330, EFM-19, T-47D, and BT-474 cells were grown in hormone deprivation media for at least 3 days prior to treatment

extract_protocol:
Total RNA was extracted from duplicates using Qiagen RNeasy kit as per manufacturer’s protocol and quality control of RNA samples was done to determine their quantity and quality.
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina)
The libraries were multiplexed and then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads

treatment_protocol: Cells were treated with either 1 nM E2, or 1 M 4-OH tamoxifen, GDC-0810, fulvestrant, GNE-274 or GDC-0927 for 24 hours

tag: cell line

tag: ligand

value: DMSO

tag: concentration

tag: time


title: GNE-274 Rep 2

library_source: genomic

molecule: genomic DNA

growth_protocol: MCF7 cells were cultured in hormone deprivation media for 5 days

treatment_protocol: After 5 days, 1 nM E2 or 100 nM test compound was added for 45 minutes


title: SAM24360840


title: SAM24360838


title: GDC-0927 Rep 2


title: SAM24360837


title: SAM24360836


title: GDC-0927-45m_ERa

data_processing:
Fastq sequencing files for all ChIP-seq samples were first filtered for read quality (Phred scores 23+). Reads were then aligned to the human reference genome (NCBI Build 38) and the drosophila reference genome using GSNAP (PMID: 20147302) version ‘2013-10-10’, allowing a maximum of two mismatches per read sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’), followed by removal of duplicate reads.
Reads that aligned to the human genome were used to quantify ER chromatin binding. Peaks of 200 bp width were identified in each sample individually relative to the respective input samples using MACS 2.1.0 (PMID: 18798982) using a cutoff of p=1e-7 and 3-fold increase over input control
An atlas of peaks was generated, encompassing all significant peaks observed in any of the samples and joining overlapping ones.
We quantified the level of chromatin binding within each peak as the number of pseudo-fragments overlapping the peak in question based on the spike-in adjusted BigWig files. Read counts for each sample were normalized based on the number of reads outside of the atlas for each sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tables of peaks with genomic corrdinates, annotations, significance, and pseudo-counts in each condition

extract_protocol:
Cells were fixed by incubation in 11% formaldehyde solution for 15 minutes at room temperature. Fixation was stopped by the addition of a 2.5 M glycine solution. Cells were washed in a 0.5% Igepal-PBS solution prior to snap-freezing.
Active Motif (Carlsbad, CA) performed chromatin isolation, immunoprecipitation reactions, library generation and sequencing. ER ChIP reactions were conducted using 30 μg MCF7 breast cancer cell line chromatin and 4 μg of ER alpha antibody (sc-543, Santa Cruz Biotechnology, Dallas, TX). The ChIP reactions also contained a drosophila chromatin spike in for the normalization of the sequencing data.  Libraries were prepared from each ER ChIP reaction, as well as an input/control DNA sample, and single-end sequencing data were generated on the Illumina platform


title: GDC-0927 Rep 3


title: SAM24360834


title: 4-OH tamoxifen Rep 2

value: 4-OH tamoxifen


title: SAM24360833


title: SAM24360835


title: Fulv-45m_ERa

value: Fulvestrant


title: 4-OH tamoxifen Rep 1


title: Fulvestrant Rep 3


title: SAM24331041

growth_protocol: MCF7, HCC1500, Cama-1, MDA-MB-330, BT-474, EFM-19 and T47D cells were grown in hormone deprivation media for at least 3 days prior to treatment

extract_protocol:
Total RNA was extracted from duplicates using Qiagen RNeasy kit as per manufacturer’s protocol and quality control of RNA samples was done to determine their quantity and quality.
Approximately 500 ng of total RNA was used as an input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). In addition, RNA input of 100 ng was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina); The libraries were multiplexed and then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads


title: Fulvestrant Rep 1


title: SAM24331043


title: Fulvestrant Rep 2


title: SAM24331042


title: 4-OH tamoxifen Rep 3


title: E2 Rep 1


title: SAM24331040


title: SAM24360832


title: E2 Rep 2


title: GDC-0927 Rep 1


title: SAM24331036


title: SAM24331037


title: Vehicle Rep 3

value: Vehicle


title: Vehicle Rep 1


title: SAM24331035


title: SAM24331033


title: GNE-274 Rep 1


title: SAM24331031


title: SAM24331032


title: SAM24331030


title: SAM24331029


title: IgG_SLC6ips_17786

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: IgG, replica #2, condition #1

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: hg19
Supplementary_files_format_and_content: IgG_SLC9ips_17784.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ips_17785.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: IgG_SLC6ips_17786.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC6ips_17787.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC6ebs_17788.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ebs_17789.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ips_17785.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC6ips_17787.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC6ebs_17788.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC9ebs_17789.bed (BED, signal enriched regions)

source_name: Human Induced Pluripotent Stem Cells (hiPSCs)

growth_protocol: hiPSC lines were differentiated via embryoid body (EB) in serum-free condition cultures with the successive addition of BMP4 50 ng/ml (d0-d3), CHIR99021 3µM (d2-d3) and hematopoietic cytokines (d3-d15; SCF 300ng/ml, Flt3 300ng/ml, IL6 and IL3 10ng/ml) and maintained at 37 ºC in 5% CO2

extract_protocol:
Chromatin immunoprecipitation assays were performed using ChIP-IT High Sensitive kit (Active Motif) following the manufacturer's instructions
Libraries were prepared according to Illumina instructions.

treatment_protocol: Doxycycline (Doxi) was added at a final concentration of 1 µg/ml to induce the expression of GATA2 transgene from days 2 to 7 of differentiation

value: iGATA2-hiPSC CL6

tag: chip antibody

value: Ab172730, Abcam


title: E2 Rep 3


title: SAM24331028


title: SAM24322065


title: SAM24322064


title: SAM24331034


title: SAM24322063


title: SAM24322062


title: JH0064.Day 63

type: protein

city: Irvine

first: Arlo

middle: Zan

last: Randall

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

description: ALS samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

hyb_protocol: ALS samples were diluted 1:2 in a 3 mg mL-1 E. coli lysate solution in protein arraying buffer (Maine Manufacturing, Sanford, ME, USA) and incubated at room temperature for 30 min. Chips were rehydrated in blocking buffer for 30 min. Blocking buffer was removed, and chips were probed with pre-incubated serum samples using sealed, fitted slide chambers to ensure no cross-contamination of sample between pads. Chips were incubated overnight at 4°C with agitation. Chips were washed five times with TBS-0.05% Tween 20, followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA, USA) diluted 1:200 in blocking buffer at room temperature. Chips were washed three times with TBS-0.05% Tween 20, followed by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Frederick, MD, USA) at room temperature protected from light. Chips were washed three times with TBS-0.05% Tween 20, three times with TBS, and once with water. Chips were air dried by centrifugation at 1,000 x g for 4 min and dried overnight in dessicator before scanning.

scan_protocol: Probed microarrays (slides) were scanned using a GenePix 4300A High-Resolution Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) an image file (.tif) was saved for each array using GenePix Pro 7 software. The scanned image files were quantified using the Mapix software (Innopsys) auto gridding feature. For this process two input files are required: (1) a .gal file that defines the array and sub-array layout and (2) the tiff image file for an array. Once the auto-gridding is complete the overlay of the mapped array, subarray, and individual spot locations are shown in the graphical user interface (GUI). If the automatic gridding fails to map to the correct positions the mapping can be manually adjusted using the GUI. Once the gridding is confirmed to be correct the array spots are quantified and saved to an output .gpr file. For each spot on the slide the gpr file contains the foreground intensity (median of pixels inside of circle defining spot) and local background intensity (median of pixels just outside of circle defining spot).

data_processing: Foreground spot intensities were adjusted by local background by subtraction, and negative values were converted to 1. Next, all foreground values were transformed using the base 2 logarithm. The dataset was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT controls for each sample. Since the IVTT control spots carry the chip, sample and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding to the non-specific antibody binding to the IVTT controls (a.k.a. background). With the normalized data, a value of 0.0 means that the intensity is no different than the background, and a value of 1.0 indicates a doubling with respect to background

label: biotin

molecule: protein

source_name: Subject: JH0064; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

label_protocol: not provided

growth_protocol: Each of the three live-attenuated strains that comprise ACE527 vaccine were grown as Master (MCB) and Working Cell Banks (WCB) and were produced under Good Manufacturing Practice at the Walter Reed Army Institute of Research (WRAIR) Pilot BioProduction Facility (PBF), Silver Spring, MD, USA. Vials from the WCBs were expanded into shake flasks to prepare a starter culture which was subsequently transferred into a 30L working volume bioreactor and grown for 5–7 h. At the desired cell density, the cells were harvested by continuous flow centrifugation. The resulting pellet was washed by centrifugation and resuspended in stabilizer solution (100 mM mannitol, 50 mM sucrose), 1.2 mL volumes were aliquoted and lyophilized in 5 mL vials which were stored at −20 °C ± 5 °C. Each strain met pre-set physical, microbiological, biochemical and antigenic criteria before being released for use in the clinical trial.

extract_protocol: not provided

treatment_protocol: Vaccine doses were prepared in a research pharmacy by reconstituting individual vials of each strain and mixing to provide 3 × 10^9 cfu of each in 10 mL of PBS per subject. ≤ two hours before dosing, the mixture was added to 190 mL of CeraVacx® buffer (Cera Products Columbia, MD). For volunteers allocated to receive dmLT, individual vials were reconstituted and diluted to a concentration of 50 µg/mL, from which 0.5 mL was added to the reconstituted vaccine ≤ five minutes before dosing. Placebo preparations consisted of 10 mL of PBS mixed with 190 mL of CeraVacx®. The CeraVacx® buffer used as the placebo and to deliver the three vaccine strains in this study has been used for the same purposes in prior Phase 1 and 2b trials of ACE527 [9], [10].

tag: tissue

value: antibody lymphocyte supernatants (ALS)

tag: subject identifier

tag: treatment group

value: Ace 527 + dmLT

tag: protected

value: yes

tag: molecule

value: anti-IgA antibody


title: Vehicle Rep 2


title: SAM24322049


title: JH0064.Day 7

source_name: Subject: JH0064; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: SAM24322046


title: SAM24322048


title: JH0065.Day 7

source_name: Subject: JH0065; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: Placebo

value: no


title: JH0064.Day 0

source_name: Subject: JH0064; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0065.Day 63

source_name: Subject: JH0065; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0064.Day 35

source_name: Subject: JH0064; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: JH0064.Day 56

source_name: Subject: JH0064; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24322047


title: SAM24321903


title: JH0064.Day 7.Post

source_name: Subject: JH0064; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0064.Day 28

source_name: Subject: JH0064; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0065.Day 56

source_name: Subject: JH0065; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24321901


title: JH0065.Day 28

source_name: Subject: JH0065; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0065.Day 35

source_name: Subject: JH0065; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24321898


title: SAM24321899


title: ULG1-7

type: RNA

city: Utrecht

first: Sharon

last: Berendsen

state: Utrecht

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Affymetrix Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalization in R (package affy)

source_name: human glioblastoma tumor tissue

label_protocol: Genechip 3' IVT Express kit (Affymetrix)

extract_protocol: Nucleospin® TriPrep (Macherey-Nagel, Düren, Germany) and the QIASymphony RNA (Qiagen, Venlo, The Netherlands) kits

treatment_protocol: Glioblastoma tumor tissue was snap-frozen in nitrogen.

tag: tumor contact with subventricular zone yes/no


title: JH0061.Day 7

source_name: Subject: JH0061; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0061.Day 35

source_name: Subject: JH0061; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24321897

source_name: cell line


title: SAM24321896


title: JH0061.Day 63

source_name: Subject: JH0061; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: SAM24321900


title: SAM24321902


title: JH0065.Day 0

source_name: Subject: JH0065; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0065.Day 7.Post

source_name: Subject: JH0065; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: SAM24318757


title: JH0061.Day 56

source_name: Subject: JH0061; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24318758


title: SAM24321894


title: SAM24321895


title: SAM24318761


title: JH0061.Day 7.Post

source_name: Subject: JH0061; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0016.Day 0

source_name: Subject: JH0016; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0061.Day 28

source_name: Subject: JH0061; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0061.Day 0

source_name: Subject: JH0061; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0016.Day 28

source_name: Subject: JH0016; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: SAM24318756


title: JH0016.Day 7.Post

source_name: Subject: JH0016; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: SAM24318760


title: SAM24318755


title: SAM24318759


title: JH0016.Day 63

source_name: Subject: JH0016; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0016.Day 35

source_name: Subject: JH0016; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24318754


title: SAM24318753


title: SAM24318752


title: SAM24318747


title: SAM24318749


title: SAM24318748


title: SAM24318745


title: SAM24318744


title: JH0012.Day 28

source_name: Subject: JH0012; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: Ace 527


title: JH0012.Day 63

source_name: Subject: JH0012; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0012.Day 7.Post

source_name: Subject: JH0012; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: SAM24318742


title: JH0012.Day 56

source_name: Subject: JH0012; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: JH0012.Day 7

source_name: Subject: JH0012; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0016.Day 7

source_name: Subject: JH0016; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0071.Day 63

source_name: Subject: JH0071; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0012.Day 0

source_name: Subject: JH0012; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0071.Day 7

source_name: Subject: JH0071; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0071.Day 28

source_name: Subject: JH0071; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0071.Day 56

source_name: Subject: JH0071; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: JH0016.Day 56

source_name: Subject: JH0016; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24318746

source_name: cell line


title: JH0012.Day 35

source_name: Subject: JH0012; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: JH0071.Day 35

source_name: Subject: JH0071; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24318741


title: SAM24314569


title: SAM24318743


title: SAM24314568


title: SAM24314570


title: JH0049.Day 28

source_name: Subject: JH0049; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0049.Day 7.Post

source_name: Subject: JH0049; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0071.Day 0

source_name: Subject: JH0071; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0049.Day 56

source_name: Subject: JH0049; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24314566


title: SAM24314565


title: JH0071.Day 7.Post

source_name: Subject: JH0071; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: SAM24314567


title: SAM24318740


title: SAM24314564


title: SAM24314563


title: JH0049.Day 35

source_name: Subject: JH0049; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24314558


title: SAM24314561


title: JH0049.Day 63

source_name: Subject: JH0049; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0049.Day 7

source_name: Subject: JH0049; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0049.Day 0

source_name: Subject: JH0049; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0066.Day 7.Post

source_name: Subject: JH0066; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: SAM24314557


title: SAM24314556


title: SAM24314562


title: SAM24314555


title: JH0066.Day 56

source_name: Subject: JH0066; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: JH0066.Day 28

source_name: Subject: JH0066; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: SAM24314553


title: SAM24314554


title: SAM24314552


title: JH0066.Day 0

source_name: Subject: JH0066; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0066.Day 7

source_name: Subject: JH0066; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: SAM24314551

source_name: cell line


title: JH0017.Day 28

source_name: Subject: JH0017; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: SAM24314549


title: JH0017.Day 35

source_name: Subject: JH0017; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24314545


title: JH0017.Day 56

source_name: Subject: JH0017; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24314550


title: JH0017.Day 7.Post

source_name: Subject: JH0017; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0017.Day 7

source_name: Subject: JH0017; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0017.Day 0

source_name: Subject: JH0017; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0017.Day 63

source_name: Subject: JH0017; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: SAM24314546


title: SAM24314544


title: SAM24314543


title: SAM24314542


title: JH0066.Day 35

source_name: Subject: JH0066; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: SAM24314541


title: JH0015.Day 0

source_name: Subject: JH0015; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: SAM24314539


title: SAM24314540


title: SAM24314538


title: JH0015.Day 7.Post

source_name: Subject: JH0015; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0015.Day 63

source_name: Subject: JH0015; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0015.Day 56

source_name: Subject: JH0015; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: SAM24314537


title: GCM-treated_rat_microglia_DNaseI-seq_rep1

city: Warsaw

first: Michał

last: Dąbrowski

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
for each sample, all component fastq files were merged into one fastq file. Example: cat EXP1/MG_2GCM_S5_L007_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L008_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L005_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L004_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L006_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L001_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L003_R1_001.fastq.gz,EXP1/MG_2GCM_S5_L002_R1_001.fastq.gz > 2GCM_All_Lanes_All_Samples.fastq (upon gzip decompression)
raw sequence reads of 26 bp length were filtered by minimum threshold quality 30 in minimum 90% of the bases with fastq_quality_filter from FASTX-Toolkit version 0.0.14. Configuration: `fastq_quality_filter -q 30 -p 90`
Adapter removal was done with cutadapt version 1.8.3
The reads were then trimmed to length 20 by fastx_trimmer. After preprocessing, any reads of length less than 20 were discarded. Configuration: `fastx_trimmer -l 20 -m 20`
reads were mapped to rat genome rn5 with bowtie version 1.1.2  with parameters: `-v 2 -m 1 --all --best --strata -S`
Genome_build: rn5
Converting sam files into bam files with `samtools view -b`. samtools version 1.1.2
Sorting bam files with `samtools sort`
indexing bam files with `samtools index`
reads were de-duplicated with Picard (Picard Tools version 1.95) using default settings. As a result of the modified sequencing protocol, the DNaseI cut site was placed at the 3' end of the read. Since most software works on 5' end, reads were reversed by swapping the 0 and 16 flags in .sam files. This action has changed the strandedness of the reads, but it's irrelevant as long as further analyses disregard the strandedness.
DNase-I hotspots identified with hotspot algorithm on each bam file (hotspot: https://github.com/rthurman/hotspot)
Supplementary_files_format_and_content: *.fdr0.01.hot.bed (FDR thresholded hotspots, bed files for all samples)
Defining open chromatin regions in rat microglia across treatment conditions: intersection of hotspots from both replicates of a condition were defined as condition-specific, reproducible regions. Overlapping condition-specific regions from two or more conditions were then merged (union). At this stage, total number of defined open chromatin regions is 129,499.
We calculated the number of cuts (5’ ends of reads) in each region (using countDNaseCuts.py, url link below). Second, raw counts were converted into Counts per Milion (CPM) per Base. Third, only regions with CPMs per base greater than 0.001 in at least two samples were used for further steps. Total number of regions after this step is 126,640. Fourth, differential analysis was performed with DiffBind and edgeR package. (pipeline: https://bitbucket.org/seventm/dnase)
Supplementary_files_format_and_content: 1. Tab-delimited text file with coordinates of all defined regions, and counts of raw DNase-I cuts in all replicates. 2. csv files containing quantitative and statistical details of differential analysis for GCMvsUntreated and LPSvsUntreated.

organism: Rattus norvegicus

growth_protocol: Microglial cultures were prepared from 1-day-old Wistar rat pups as previously described (Aleksandra Ellert-Miklaszewska et al. 2013; A. Ellert-Miklaszewska et al. 2016). Cerebral cortices were dissociated mechanically and by trypsinisation, and cells were plated at a density of 3 x 10^5 cells/cm2 on poly-L-lysine-coated flasks in Dulbecco’s modified Eagle medium, DMEM (with Glutamax, 4.5 g/L glucose, 10% heat-inactivated fetal bovine serum (FBS), 100 U/mL penicillin, and 0.1 mg/mL streptomycin). Cells were maintained at 37ºC in a humidified atmosphere of 5% CO2/95% (Heraeus, Hanau, Germany).  Culture medium was changed after 3 days and then twice a week. After 2 weeks, microglial cells were recovered from confluent cultures by mild shaking and centrifugation (300 x g for 5 min). Cell viability was determined by trypan blue exclusion. Cells were suspended in a culture medium and plated at a density of 2-3 x 10^5 cells/cm2 onto culture dishes for cells growing in suspension (Sarstaed) and incubated for 48 h prior to experiments.

extract_protocol:
Briefly, 10^6 – 5 x 10^6 microglial cells (the same number of cells for each condition) were stimulated for 6 h with 100 ng/ml LPS, GCM or left untreated. Then, cells were lysed, nuclei were collected  and digested 10 min at room temperature with a series of DNaseI dilutions (0.2-3.2 U/reaction, Roche Diagnostics). Digested DNA was enclosed in low melting point (LMP) agarose blocks. DNAse-I activity at different concentrations was determined using pulsed field gel electrophoresis (PFGE) and the CHEF-DRII apparatus (Biorad),  and DNAseI activity at three optimal concentrations was selected  for further processing.
DNA fragment ends were repaired and a “linker 1” (HPLC-purified,  annealed oligonucleotides: AGTTCCTTGGCACCCGAGAATTCCATCCGAC and GTCGGATGGAATTCTCGGGTGCCAAGG) using T4 DNA ligase (1 U/μL) and ligation buffer (10X) (Roche Diagnostics).  DNA with a ligated “linker 1” was isolated from agarose blocks and digested with MmeI enzyme (2 U/μL; New England Biolabs). Fragments containing “linker1” were purified using streptavidin beads (Dynal M-280; Invitrogen). Subsequently, a “linker 2” (HPLC-purified,  annealed oligonucleotides: GATCGTCGGACTGTAGAACTCTGAAC and GTTCAGAGTTCTACAGTCCGACGATCNN) was ligated to DNA on beads and the beads were treated with 0.15 M NaOH to denature DNA. The obtained DNA fragments attached to the streptavidin beads were used as a template for PCR reaction performed with primers containing the standard Ilumina library preparation sequences and indexes. PCR products were resolved in 3% agarose gels and purified from gel using DEAE-cellulose chromatography papers, and sequenced on Illumina Hi-seq 1500.

treatment_protocol: Microglia were stimulated with 100 ng/mL LPS from Salmonella enteritidis (Sigma-Aldrich, Saint Louis, MO, USA) or conditioned media from rat C6 glioma cultures (GCM). C6 glioma cells (ATTC) were grown in DMEM medium with 10% FBS (Gibco), and antibiotics (100 U/mL penicillin, and 0.1 mg/mL streptomycin). The medium was changed every 3-4 days. After seeding 1 x 10^6 C6 cells onto 100-mm dishes, standard culture media were exchanged for 8 ml of 10% FBS high-glucose DMEM with Glutamax and conditioned media were harvested after 24 h from 85-90% confluent cultures and centrifuged at 300 x g for 10 min to remove cell debris.

tag: strain

value: Wistar

tag: age

value: neonate; 1-day-old

tag: cell type

value: microglia

tag: condition

value: cell culture

tag: treatment


title: GCM-treated_rat_microglia_DNaseI-seq_rep2

value: conditioned media from rat C6 glioma cultures (GCM


title: JH0003.Day 7.Post

source_name: Subject: JH0003; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: LPS-treated_rat_microglia_DNaseI-seq_rep1

value: 100 ng/mL LPS


title: JH0015.Day 35

source_name: Subject: JH0015; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: LPS-treated_rat_microglia_DNaseI-seq_rep2


title: JH0015.Day 28

source_name: Subject: JH0015; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0003.Day 7

source_name: Subject: JH0003; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: si-CEBPa - Untreated - T47D T0 si-CEBPa short arrest rep2

first: Miguel

last: Beato

state: Barcelona

address: Dr. Aiguader, 88

department: Gene expression, stem cells and cancer

institute: CRG

description: Cell culture and hormone treatments: T47D breast cancer cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100μg/ml streptomycin. For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal treated FBS (DCC/FBS) and 48 h later medium was replaced by fresh medium without serum. After 24h in serum-free conditions, cells were incubated with R5020 (10nM) for different times at 37ºC. For the experiments with a short arrest, cells were incubated for 4 hours with 10% charcolized-serum before hormone treatment.

data_processing:
Trim sequencing adapters and low quality ends with trimmomatic using recommended parameters in Bolger et al. 2014
Align trimmed reads with BWA against hg38 human assembly for ChIP-seq samples
Convert SAM to BAM with samtools
Peak calling with MACS2 for ChIP-seq samples
Align trimmed reads with STAR against hg38 human assembly for RNA-seq samples, using GENCODE v24 annotation
Genome_build: hg38

extract_protocol:
ChIP protocol: Chromatin Immunoprecipitation (ChIP) in cultured cells: ChIP assays were performed as described (Strutt and Paro, 1999) using anti-PR (Santa Cruz, H190); anti-C/EBPα (Cell Signaling, 8178S); anti-BRG1 [EPNCIR111A] (Abcam, ab110641), anti-LSD1 (Abcam, ab17721); anti-Topo2α (Santa Cruz, sc-3659), anti-P300 (Santa Cruz, sc-584x and sc-585x), anti SRC3 (Santa Cruz, sc-9119x). Quantification of chromatin immunoprecipitation was performed by real time PCR using Roche Lightcycler (Roche). The fold enrichment of target sequence in the immunoprecipitated (IP) compared to input (Ref) fractions was calculated using the comparative Ct (the number of cycles required to reach a threshold concentration) method with the equation 2Ct(IP)-Ct(Ref). Each of these values were corrected by the human β-globin gene and referred as relative abundance over time zero. Primers sequences are available on request.
RNA extraction(RNA-seq): RNA extraction and RT-PCR  Total RNA was prepared and cDNA generated as previously described (Vicent et al., 2006). Quantification of LUC and GAPDH gene products was performed by real time PCR. Each value calculated using the standard curve method was corrected by the human GAPDH and expressed as relative RNA abundance over time zero. Primer sequences for DUSP1, C/EBPα, PGR are available on request.
RNA-seq libraries were constructed following the Illumina Truseq Stranded mRNA Sample Prep Kit (RS-122-2101). ChIP-seq libraries were constructed following the NEBNext DNA samples prep kit (Ref.: NEB # E6000S) and PE adaptors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
RNA-seq and ChIP-seq. We use the NEBNext Ultra DNA Library Prep Kit for Illumina kit (Ref.:#7370), with amplification by real-timePCR (light cycler) to determine the number of cycles to amplify the library

tag: passages


title: JH0003.Day 56

source_name: Subject: JH0003; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: si-CEBPa - Progesterone - T47D T360 s-iCEBPa short arrest rep2

tag: cell line


title: JH0003.Day 0

source_name: Subject: JH0003; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: Progesterone - T47D T360 si-control short arrest rep2


title: JH0003.Day 28

source_name: Subject: JH0003; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: si-CEBPa - Progesterone - T47D T360 si-CEBPa short arrest rep1


title: JH0003.Day 35

source_name: Subject: JH0003; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: JH0029.Day 56

source_name: Subject: JH0029; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: Untreated_rat_microglia_DNaseI-seq_rep2

value: untreated


title: Progesterone - T47D T360 si-control short arrest rep1


title: JH0029.Day 35

source_name: Subject: JH0029; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: JH0015.Day 7

source_name: Subject: JH0015; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: Untreated_rat_microglia_DNaseI-seq_rep1


title: Untreated - T47D T0 si-control short arrest rep1


title: Progesterone - ICRF rep2

source_name: Progesterone - ICRF


title: Untreated - T47D T0 si-control short arrest rep2


title: JH0003.Day 63

source_name: Subject: JH0003; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: Progesterone - ICRF rep1


title: JH0029.Day 0

source_name: Subject: JH0029; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: si-CEBPa - Untreated - T47D T0 si-CEBPa short arrest rep1


title: Untreated - ICRF rep2

source_name: Untreated - ICRF


title: JH0029.Day 28

source_name: Subject: JH0029; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: Untreated - ICRF rep1


title: ChIP-Topo2a - Progesterone – siCEBPa

source_name: ChIP-Topo2a - Progesterone – siCEBPa

value: anti-Topo2alpha (Santa Cruz, sc-3659)


title: ChIP-Topo2a - Untreated – siCEBPa

source_name: ChIP-Topo2a - Untreated – siCEBPa


title: ChIP-Topo2a - Progesterone – siControl

source_name: ChIP-Topo2a - Progesterone – siControl


title: ChIP-Topo2a - Untreated – siControl

source_name: ChIP-Topo2a - Untreated – siControl


title: ChIP-RAD21 - Progesterone – siCEBPa

source_name: ChIP-RAD21 - Progesterone – siCEBPa

value: Anti-Rad21 antibody - ChIP Grade (ab992


title: ChIP-RAD21 - Untreated – siCEBPa

source_name: ChIP-RAD21 - Untreated – siCEBPa


title: ChIP-RAD21 - Untreated – siControl

source_name: ChIP-RAD21 - Untreated – siControl


title: ChIP-PR - Progesterone – siCEBPa

source_name: ChIP-PR - Progesterone – siCEBPa

value: H190 Santa Cruz


title: JH0018.Day 0

source_name: Subject: JH0018; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: ChIP-PR - Untreated – siCEBPa

source_name: ChIP-PR - Untreated – siCEBPa


title: JH0029.Day 7

source_name: Subject: JH0029; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: Ace 527 + dmLT


title: JH0029.Day 63

source_name: Subject: JH0029; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: yes


title: JH0029.Day 7.Post

source_name: Subject: JH0029; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: anti-IgA antibody


title: ChIP-PR - Progesterone – siControl

source_name: ChIP-PR - Progesterone – siControl


title: JH0018.Day 7.Post

source_name: Subject: JH0018; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0018.Day 56

source_name: Subject: JH0018; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: ChIP-PR - Untreated – siControl

source_name: ChIP-PR - Untreated – siControl


title: ChIP-CEBPa - Untreated – siCEBPa

source_name: ChIP-CEBPa - Untreated – siCEBPa

value: anti-C/EBPalpha (Cell Signaling, 8178S)


title: ChIP-CEBPa - Untreated – siControl

source_name: ChIP-CEBPa - Untreated – siControl


title: JH0018.Day 35

source_name: Subject: JH0018; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: no


title: ChIP-PR – Untreated

source_name: ChIP-PR – Untreated


title: ChIP-RAD21 - Progesterone – siControl

source_name: ChIP-RAD21 - Progesterone – siControl


title: F2 Placenta_control in utero F1_rep5

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

description: pure air filtered exposure

hyb_protocol: Hybridization was performed at the CRB GADIE (INRA Jouy-en-Josas, France, http://crb-gadie.inra.fr/). Equal amounts of Cy3-labeled samples (600 ng, Specific Activity > 6.0 pmol Cy3/μg of cRNA) were mixed with blocking agent and fragmentation buffer, and then 24 μl of the mixture was hybridized into the Rabbit Custom Gene Expression Microarrays (GEO accession GPL18913, Agilent-042421 Rabbit BDR version 2, Agilent Technologies) for transcriptomic analysis (12775 genes) . After 17 h at 65 °C, hybridized slides were washed twice for 1 min at room temperature in GE Wash Buffer 1 and 1 min at 37°C with the GE Wash Buffer 2 (Agilent Technologies) and air-dried and scanned immediately.

scan_protocol: After hybridization, the scanned images were analyzed using Feature Extraction Software (v10.7.3.1; Agilent Technologies). Data were normalized using intra-array median subtraction and log2 transformation. The raw data intensity files were read into R (www.r-project.org). Identification of differentially expressed genes from EC and CC F2 placentas was achieved using Limma package (Ritchie et al 2015). P values obtained by this analysis were adjusted for multiple testing using the Benjamini-Hochberg procedure. Probes with adjusted P value <0.05 were considered significant.

data_processing: A median normalization was operated for each micro-array using Limma R package. Duplicated probes signal has been averaged.

organism: Oryctolagus cuniculus

source_name: pure air filtered exposure

label_protocol: Eight samples of each group were used as biological replicates for the microarray analysis: 200 ng total RNA from fetal placenta tissue were amplified and labeled with cyanine 3 (Cy3) dye using the One color Microarray-based Gene Expression Analysis low input Quick Amp labeling kit (Agilent Technologies). Excess dye was removed with RNeasy mini kit (Qiagen), and dye incorporation and concentration were determined using the microarray setting on the Nanodrop 2000 (Thermo Scientific, Madrid, Spain) and Bioanalyzer 2100 (Agilent Technologies).

extract_protocol: RNAs were extracted twice in 3M sodium acetate pH 4-5, aquaphenol and chloroform/isoamylic ethanol (24:1), then precipitated in isopropanol at -80°C overnight. A purification procedure using DNAse I (Qiagen) treatment at 25°C for 15 min was performed prior to elution. The RNA pellet was washed with ethanol, dried and solubilized in RNase-free water (10µl of H2O for 100mg of tissue). RNAs were purified with the RNeasy mini kit (Quiagen). RNAs were quantified by Nanodrop and their quality was verified on a Bioanalyser.

treatment_protocol: Total RNAs were extracted from pieces of labyrinthine area randomly collected from each of the litters of the control (n=8 CC) and the exposed (n=8 EC, eight replicates per condition)  and frozen in liquid nitrogen. These samples were ground in a solution D+ (namely: thiocyanate guanidine 4M, sodium citrate 25mM pH 7, N-lauryl-sarcosine 0.5%, β-mercaptoethanol 0.1M).

tag: developmental stage

value: 28dpc (late gestation)

value: placental labyrinthine area

tag: gender

value: male


title: F2 Placenta_control in utero F1_rep6

description: pure air filtered exposure

value: female


title: F2 Placenta_control in utero F1_rep7

description: pure air filtered exposure


title: F2 Placenta_control in utero F1_rep3

description: pure air filtered exposure


title: ChIP-CEBPa – Progesterone

source_name: ChIP-CEBPa – Progesterone


title: F2 Placenta_control in utero F1_rep4

description: pure air filtered exposure


title: F2 Placenta_control in utero F1_rep8

description: pure air filtered exposure


title: F2 Placenta_control in utero F1_rep2

description: pure air filtered exposure


title: ChIP-CEBPa – Untreated

source_name: ChIP-CEBPa – Untreated


title: JH0018.Day 63

source_name: Subject: JH0018; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0018.Day 7

source_name: Subject: JH0018; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0073.Day 35

source_name: Subject: JH0073; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: Bulk RNA sequencing MPP4 Mettl3KO 1

city: New York

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Fastq files were aligned using bowtie
For single cell RNA sequencing samples, data was demultiplexed and post-processed using custom pipelines (Cell Ranger 2.2) provided by 10x Genomics. For bulk RNA sequencing, data were aligned using the tophat  software to the GRCh37-lite human reference genome. Fragments Per Kilobase of transcript per Million mapped reads were calculated using the cufflink software. Differentially expressed genes were identified as those with FPKM greater than 1 for Mettl3 f/f or Mettl3 cKO showing differential expression greater than twofold (up or down) with a Benjamini–Hochberg corrected P value less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: csv; Single-cell expression matrices were generated using cellular barcodes and unique molecular identifiers (UMIs). UMItabs contain the UMI count for each specified gene (rows) for each cell (columns).
Supplementary_files_format_and_content: FPKM for bulk RNA-Seq

molecule: polyA RNA

organism: Mus musculus

source_name: Sorted bone marrow MPP4

extract_protocol:
3 replicates (from 3 different mice) of LK, HSC, MPP1, MPP2 and MPP4 cells were sorted from Mettl3 f/f and Mettl3 cKO mice base on cell surface marker.
For bulk sequencing, RNA was extracted from cells using the SMARTer RNA extraction method for minimal cells RNA extraction. After amplification, cDNA was subjected to automated Illumina paired-end library construction. Libraries were sequenced on Illumina HiSeq2000 instruments with paired reads of 50 bp in length per sample.

tag: weeks after pipc treatment

tag: sorting strategy

tag: genotype / variation

value: Mx1-Cre; Mettl3 fl/fl


title: Bulk RNA sequencing MPP4 Mettl3KO 2


title: Bulk RNA sequencing MPP4 WT 3

value: Mettl3 fl/fl


title: Bulk RNA sequencing MPP4 Mettl3KO 3


title: Bulk RNA sequencing MPP2 Mettl3KO 3

source_name: Sorted bone marrow MPP2


title: ChIP-PR – Progesterone

source_name: ChIP-PR – Progesterone

tag: chip antibody


title: Bulk RNA sequencing MPP2 Mettl3KO 2


title: Bulk RNA sequencing MPP2 WT 3


title: Bulk RNA sequencing MPP2 Mettl3KO 1


title: JH0073.Day 56

source_name: Subject: JH0073; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

tag: tissue

tag: subject identifier

tag: treatment group


title: Bulk RNA sequencing MPP2 WT 2


title: Bulk RNA sequencing MPP4 WT 2


title: JH0018.Day 28

source_name: Subject: JH0018; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: protected

tag: molecule


title: JH0073.Day 63

source_name: Subject: JH0073; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: F2 Placenta_ exposed in utero F1 _rep7

description: diesel exhaust exposure

source_name: diesel exhaust exposure


title: F2 Placenta_ exposed in utero F1 _rep8

description: diesel exhaust exposure


title: F2 Placenta_control in utero F1_rep1

description: pure air filtered exposure


title: F2 Placenta_ exposed in utero F1 _rep5

description: diesel exhaust exposure


title: JH0073.Day 0

source_name: Subject: JH0073; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: Bulk RNA sequencing MPP4 WT 1


title: F2 Placenta_ exposed in utero F1 _rep4

description: diesel exhaust exposure


title: F2 Placenta_ exposed in utero F1 _rep3

description: diesel exhaust exposure


title: F2 Placenta_ exposed in utero F1 _rep6

description: diesel exhaust exposure


title: Bulk RNA sequencing MPP2 WT 1


title: F2 Placenta_ exposed in utero F1 _rep2

description: diesel exhaust exposure


title: Bulk RNA sequencing MPP1 Mettl3KO 3

source_name: Sorted bone marrow MPP1


title: n3_10A.PM_2LLT

city: Toronto

first: Corey

last: Lourenco

state: ON

department: Medical Biophysics

country: Canada

institute: University of Toronto

data_processing:
Fastq files were filtered using Xenome in order to filter out mouse contamination
RNA-seq reads were mapped and quantified using the STAR aligner (v2.5.2a) against hg19 with Gencode Annotations v24 lifted to hg19.
Expressed genes were defined as requiring at least 10 reads in at least 2 samples. Read counts were upper quantile normalized. Finally, EBSeq was used to test for differential expression between experimental conditions.
Genome_build: hg19
Supplementary_files_format_and_content: csv, ReadsPerGene

source_name: xenograft tissue_PIK3CA^H1047R + MYC

growth_protocol: 1E6 cells (10A.PE or 10APM) were injected sub-cutaneously in female NOD-SCID mice. Tumours were harvested at them same time point and flash frozen.

extract_protocol:
RNA from xenograft tissue was harvested using the RNeasy Plus Universal Kit (Cat# 73404, Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared using standard Illumina protocol

tag: host strain

value: NOD-SCID

tag: cell line source

value: MCF10A parental cell line

value: breast cancer cell line

tag: ectopic alleles expressed

value: PIK3CA^H1047R + MYC

value: Xenograft tissue (derived from MCF10A parental cell line)


title: Bulk RNA sequencing MPP1 WT 1


title: n3_10A.PE_4LT

source_name: xenograft tissue_PIK3CA^H1047R + EV control

tag: cell type

value: PIK3CA^H1047R + EV control


title: n2_10A.PM_6LT

description: 10A_xeno_HR-MYC_Cage_6-LT_RNA_AGCGATAG_S12


title: n1_10A.PM_4RT

description: 10A_xeno_HR-MYC_Cage_4-RT_RNA_TCTCGCGC_S11


title: JH0020.Day 0

source_name: Subject: JH0020; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: Placebo


title: Bulk RNA sequencing MPP1 WT 3


title: JH0073.Day 7.Post

source_name: Subject: JH0073; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: Ace 527 + dmLT

value: yes

value: anti-IgA antibody


title: Bulk RNA sequencing MPP1 WT 2


title: Bulk RNA sequencing HSC Mettl3KO 2

source_name: Sorted bone marrow HSCs


title: JH0073.Day 7

source_name: Subject: JH0073; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0073.Day 28

source_name: Subject: JH0073; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: Bulk RNA sequencing HSC Mettl3KO 3


title: Bulk RNA sequencing MPP1 Mettl3KO 2


title: Bulk RNA sequencing MPP1 Mettl3KO 1


title: JH0020.Day 28

source_name: Subject: JH0020; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: no


title: JH0020.Day 63

source_name: Subject: JH0020; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: n2_10A.PE_3NT

description: 10A_xeno_HR-EV_Cage_3-NT_RNA_TCCGCGAA_S10


title: n1_10A.PE_1NT

description: 10A_xeno_HR-EV_Cage_1-NT_RNA_CGGCTATG_S9


title: F2 Placenta_ exposed in utero F1 _rep1

description: diesel exhaust exposure

value: 28dpc (late gestation)

value: placental labyrinthine area


title: JH0020.Day 56

source_name: Subject: JH0020; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: Bulk RNA sequencing HSC Mettl3KO 1


title: Bulk RNA sequencing HSC WT 3


title: Bulk RNA sequencing HSC WT 2


title: Bulk RNA sequencing HSC WT 1


title: Chromium10X_Mettl3KO_3

source_name: Bone marrow

value: Lin-; c-Kit+


title: HF-06 [Bisulfite-Seq]

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

description:
Table S1_DMCsv2.xlsx
14362X10

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003).
To evaluate sequencing quality, FastQC (0.11.7) was used both before and after adapter trimming via TrimGalore (0.4.4).
The bisulfite-reduced and sequenced reads were then aligned to the CT- and GA-converted human hg38 (GRCh38.p12) genome assembly via Bismark (v0.20.0) to quantify relative alignment of methylated and unmethylated CpGs, respectively.
We then quantified differential DNA methylation on a CpG site-specific (DMC) basis to exploit the base-pair resolution afforded by WGBS using the R package methylKit (1.8.0). Alignments were first filtered for those with <99.9% methylated CpGs and sequencing depth > 10X to remove PCR-biased and low-coverage CpG sites, respectively.
Genome_build: hg38 (GRCh38.p12.genome.fa)
Supplementary_files_format_and_content: Differential DNA methylation was generated and exported as .xlsx

source_name: Left Ventricle Endocardium

extract_protocol:
Endocardial samples were removed, flash frozen on dry ice, and DNA was isolated DNA from cardiac whole-tissue using DNeasy® Mini Kit (Qiagen Inc., Valencia, CA). DNA quality was assessed using Qubit dsDNA HS Assay to ensure uniform concentrations of dsDNA were used. Extracted DNA was then bisulfite-reduced using the Agilent SureSelect XT Human Methyl-Seq Enrichment System. Sequencing of bisulfite-reduced samples was then performed using HiSeq 125 Cycle Paired-End Sequencing analysis.
Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq PE Cluster Kit v4-cBot (PE-401-4001).

treatment_protocol: Human heart biopsies taken from left ventricle of patients with end-stage heart failure during Ventricular Assist Device (LVAD) implantation.

tag: diagnosis

value: HF

tag: age

tag: Sex

value: M

tag: race

value: CAU


title: Chromium10X_Mettl3KO_2

tag: weeks after pipc treatment

value: Mx1-Cre; Mettl3 fl/fl


title: HF-05 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14362X9


title: Chromium10X_WT_3

tag: sorting strategy

value: Mettl3 fl/fl


title: Chromium10X_Mettl3KO_1

tag: genotype / variation


title: Chromium10X_WT_1


title: JH0020.Day 7

source_name: Subject: JH0020; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0020.Day 7.Post

source_name: Subject: JH0020; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: HF-03 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14362X6


title: Chromium10X_WT_2


title: HF-02 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14362X4


title: JH0047.Day 7

source_name: Subject: JH0047; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0047.Day 63

source_name: Subject: JH0047; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: HF-01 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14362X1


title: JH0047.Day 0

source_name: Subject: JH0047; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0020.Day 35

source_name: Subject: JH0020; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: NF-03 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14907X3

value: CON


title: NF-01 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14907X1

value: F


title: HF-04 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14362X2


title: JH0044.Day 7.Post

source_name: Subject: JH0044; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: Ace 527


title: HEPS_E+Dox_Rep3

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
Single cell RNA-seq
processed data file: HTSeq_counts.txt

data_processing:
RNA-seq reads were aligned to hg19 using STAR (version 2.4.2a) with parameters (--outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HTSeq_counts.txt: HT-Seq counts / gene counts.

source_name: Human Induced Pluripotent Stem Cells

extract_protocol:
HEPs (CD31+CD34+CD45-) and CD45+ cells were FACS-purified from three independent biological replicates.
Pools of 50 cells were sorted directly into 2.3 μl of lysis buffer (0.2 % (v/v) Triton X-100 and 2 U/μl RNase inhibitor (Clontech)) in 96 well plates and stored at −80 °C.
RNA-seq was carried out using the Smart-seq2 protocol according to Picelli S et al. (2014).
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit.
Pooled libraries were run on the Illumina Hi-Seq 2500.

value: Hemogenic progenitors (CD31+CD34+CD45-)

tag: treatment

value: Dox+

tag: day


title: HEPS_E+Dox_Rep2


title: HEPS_E+Dox_Rep1


title: NF-02 [Bisulfite-Seq]

description:
Table S1_DMCsv2.xlsx
14907X2


title: JH0047.Day 28

source_name: Subject: JH0047; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: tissue

value: antibody lymphocyte supernatants (ALS)

tag: subject identifier

value: Placebo


title: JH0047.Day 56

source_name: Subject: JH0047; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

tag: treatment group

tag: protected

value: yes

value: anti-IgA antibody


title: Z2D8Q

city: La Jolla

first: Vahid

middle: H

last: Gazestani

state: California

address: 8110 La Jolla Shores Drive, Suite 201

institute: UCSD

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Outlier samples are removed. Expression data are log2 transformed and quantile normalized for probes with detection p-value <0.05 (standard settings).

source_name: leukocyte transcriptome

label_protocol: Standard Illumina labeling protocol

extract_protocol: four to six milliliters of blood were collected into ethylenediaminetetraacetic-coated tubes from all subjects. Total RNA was extracted following standard procedures and manufacturer’s instructions (Ambion)

value: leukocyte

tag: gender

tag: age (months)

value: TD


title: A6P6J

value: LD


title: JH0047.Day 35

source_name: Subject: JH0047; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

tag: molecule


title: M5K7D

tag: cell type


title: Y7B8X

tag: diagnosis


title: W3V3W


title: W2S8C_repB


title: Q4T9E


title: HEPS_E-Dox_Rep3

value: Dox-


title: JH0044.Day 35

source_name: Subject: JH0044; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: R8B4U_repB

value: M


title: JH0044.Day 0

source_name: Subject: JH0044; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0047.Day 7.Post

source_name: Subject: JH0047; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: G7M9T_repB


title: R8B4U_repA


title: N6V4Z


title: T7W6Y

value: PreemieNoDelay


title: K8L4C


title: Z2F3D


title: G7M9T_repA


title: R5Z6M


title: P8C4J


title: D7Z5U


title: HEPS_B+Dox_Rep2


title: JH0044.Day 28

source_name: Subject: JH0044; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: XRN1-null replicate 1 for Ribo-seq

city: Tuebingen

first: Eugene

last: Valkov

state: Baden-Wuerttemberg

address: Max-Planck-Ring 5

department: Biochemistry

country: Germany

institute: Max Planck Institute for Developmental Biology

description:
small RNA
XRN1_1_Riboseq

data_processing:
Library strategy: Ribo-seq
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translational efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimtied file for translational efficiency analysis

growth_protocol: 6.4x10^6 cells of HEK293T WT or XRN1-null cells were plated on 15 cm dishes 24 hrs before harvesting.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). For Ribo-Seq, the original procedure of Ingolia et al (2012) Nature Protocols was followed with modifications from Calviello et al (2016) Nature Methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: genotype


title: JH0044.Day 63

source_name: Subject: JH0044; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: HEPS_B+Dox_Rep1


title: Wild-type replicate 2 for Ribo-seq

description:
small RNA
WT_2_Riboseq

value: Wild-type


title: HEPS_B-Dox_Rep2


title: JH0028.Day 56

source_name: Subject: JH0028; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

value: no


title: HEPS_E-Dox_Rep2


title: JH0044.Day 56

source_name: Subject: JH0044; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: HEPS_B-Dox_Rep3


title: JH0044.Day 7

source_name: Subject: JH0044; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0028.Day 0

source_name: Subject: JH0028; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: XRN1-null replicate 2 for Ribo-seq

description:
small RNA
XRN1_2_Riboseq


title: JH0028.Day 7.Post

source_name: Subject: JH0028; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: S2N9L


title: K8T4M


title: E7C2S


title: B6E9M


title: G8K4F


title: V5R5J


title: S8M8Z


title: B3E8L


title: G9Q5B


title: G5T3V_repB


title: G5T3V_repA


title: Wild-type replicate 1 for Ribo-seq

description:
small RNA
WT_1_Riboseq


title: HEPS_B-Dox_Rep1


title: JH0028.Day 28

source_name: Subject: JH0028; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: HEPS_A+Dox_Rep3


title: XRN1-null replicate 1 for RNA-seq

description:
messenger RNA
XRN1_1_RNAseq

data_processing:
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translational efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimtied file for translational efficiency analysis


title: XRN1-null replicate 2 for RNA-seq

description:
messenger RNA
XRN1_2_RNAseq


title: HEPS_A+Dox_Rep1


title: Wild-type replicate 1 for RNA-seq

description:
messenger RNA
WT_1_RNAseq


title: HEPS_A-Dox_Rep3


title: JH0028.Day 63

source_name: Subject: JH0028; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0019.Day 35

source_name: Subject: JH0019; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: Ace 527 + dmLT


title: JH0028.Day 35

source_name: Subject: JH0028; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: control_4T1

city: Wuhan

first: zhang

last: qiulei

state: hubei

address: No. 1277, Jiefang Road,

department: union hospital

institute: Huazhong university of science and technology

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, then mapped to Mus musculus whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.2.31 was used to quantify gene abundances
Differential gene expression analysis was done using R package DEGeq v1.30.0
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited txt file include TPM values for each Sample

source_name: murine breast cancer cells

growth_protocol: All cells were maintained at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted from the 4T1 cells using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: M2 macrophages and 4T1 cells were plated into upper and lower chambers of transwell co-culture systems respectively for 3 days. we performed RNA-sequencing analysis of control 4T1 cells and M2 macrophages co-cultured 4T1 cells.

value: murine breast cancer cells

value: control 4T1


title: HEPS_A-Dox_Rep1

source_name: Human Induced Pluripotent Stem Cells

value: Hemogenic progenitors (CD31+CD34+CD45-)


title: M2_4T2

value: M2 macrophages co-cultured 4T1


title: JH0019.Day 7.Post

source_name: Subject: JH0019; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: JH0019.Day 0

source_name: Subject: JH0019; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: HEPS_A+Dox_Rep2

value: Dox+


title: Wild-type replicate 2 for RNA-seq

description:
messenger RNA
WT_2_RNAseq


title: Species_mixing_CC4_1W

city: Biberach

first: Christian

middle: Thaddaeus

last: Wohnhaas

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

description: Human HEK293 and murine 3T3 cell lines were mixed

data_processing:
Reads: Read 1: 20 bp (cell barcode and UMI), Read 2: 50 (sequence read)
Raw base BCL files were demultiplexed using bcl2fastq v2.17.1.14 with the parameters “--minimum-trimmed-read-length 20” and “--mask-short-adapter-read 1”. The 50 bp read 2 containing the cDNA sequence was aligned using STAR aligner 2.3.0 against a merged reference of both human hg19 and murine mm10 for the species mixing experiment whereas the reads of MDMs were aligned to the GRCh38 reference genome and annotated according to Ensembl release 86. The STAR genome indices were generated using the parameters “--sjdbOverhang 49” and “--genomeSAsparseD 2”. Drop-seq tools software version 1.12 was then applied to generate a digital expression matrix for each sample.
Genome_build: merged hg19 and mm10 (species mixing), GRCh38 (monocyte-derived macrophages)
Supplementary_files_format_and_content: tab-delimited text files include counts per gene for each cell barcode

organism:
Homo sapiens
Mus musculus

source_name: HEK293/3T3 cell lines

growth_protocol: HEK293 and NIH 3T3 cells were grown in DMEM supplemented with 10 % FCS at 37 °C and 5 % CO2 to approximately 70 % – 80 % confluence. Monocyte-derived macrophages were generated from monocytes isolated from PBMCs. PBMCs were separated with LeucosepTM tubes (Greiner Bio-One, Kremsmünster, Austria) filled withFicoll® Paque Plus (GE Healthcare, Chicago, IL) according to the manufacturer’s instructions. Monoytes were purified from PBMCs by the EasySepTM Human Monocyte Isolation Kit (Stemcell Technologies, Vancouver, BC, Canada) following the manufacturer’s instructions. Monocytes were cultivated in X-VIVOTM 10 Medium (Lonza, Basel, Switzerland) supplemented with 100 ng/ml of GM-CSF (rhGM-CSF, R&D Systems, Minneapolis, MN). On day 6 of the differentiation protocol 50 – 75 % of fresh medium was added per well. Monocyte-derived macrophages were harvested on day 11.

extract_protocol:
Droplet-based single-cell partitioning using Dolomite Bio´s Drop-seq system
Single-cell RNA-Seq libraries were generated using the Drop-seq protocol and Nextera XT DNA sample preparation kit

value: HEK293/3T3 cell lines

tag: time point

value: week 1

tag: preservation protocol

value: CellCover 4C

tag: experiment

value: species mixing


title: HEPS_E-Dox_Rep1


title: HEPS_A-Dox_Rep2


title: Species_mixing_CC20_15W

value: week 15

value: CellCover -20C


title: Species_mixing_CC20_1W


title: CON_6m_F_3

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description:
PolyA RNA
processed data file: Interventions_assigned_reads.txt

data_processing:
HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing Illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Interventions_assigned_reads.txt: Tab-delimited text file includes gene counts for each sample.

source_name: Liver

extract_protocol:
After sacrifice, liver was removed and frozen on dry ice. RNA was extracted from liver tissues with PureLink RNA Mini Kit.
Sequencing libraries were prepared for sequencing using Illumina TruSeq RNA Sample Preparation v2 protocol.

treatment_protocol: Mice were kept on control diet (Purina 5LG6 for UM-HET3, GHRKO and Snell dwarf mice; 14% kcal protein, 76% kcal carbohydrate, and 10% kcal fat diet from Research Diets for C57BL/6J mice) or the same diet supplied with the certain compounds (acarbose, rapamycin, 17aE2, Protandim). In case of CR, Purina 5LG6 diet was restricted by 40%. In case of C57Bl/6J mice, controls were fed diet containing 0.86% w/w methionine whereas MR mice were fed the same diet but with 0.12% w/w methionine.

tag: strain

tag: Sex

value: Female

tag: age

value: 6 months

value: Liver

tag: intervention

value: Control

tag: dose

tag: intervention duration


title: CON_6m_M_2

value: Male

tag: tissue


title: CON_6m_M_3


title: CON_6m_M_1


title: CON_6m_F_2


title: Species_mixing_MeOH_15W

value: methano preservationl fixation


title: Species_mixing_MeOH_1W


title: J2U5N

source_name: leukocyte transcriptome

value: leukocyte

tag: gender

value: M

value: LD


title: JH0019.Day 63

source_name: Subject: JH0019; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

tag: subject identifier

tag: treatment group

value: Ace 527 + dmLT

tag: protected

value: yes

value: anti-IgA antibody


title: C3K7G_repB

tag: cell type

tag: age (months)

tag: diagnosis


title: C8Z9D

value: TD


title: JH0019.Day 7

source_name: Subject: JH0019; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

tag: molecule


title: B4Z9C


title: X4K7S


title: CON_6m_F_1


title: JH0010.Day 0

source_name: Subject: JH0010; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

value: no


title: JH0019.Day 28

source_name: Subject: JH0019; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: C3K7G_repA


title: U7P8G


title: N4X8D


title: Species_mixing_DMSO_15W

tag: cell line

value: HEK293/3T3 cell lines

tag: time point

value: week 15

tag: preservation protocol

value: DMSO cryopreservation

value: species mixing


title: MR_14m_M_3

tag: strain

tag: Sex

value: 14 months

value: Liver

value: Methionine Restriction

value: 12 months


title: Species_mixing_DMSO_1W

value: week 1

tag: experiment


title: JH0010.Day 28

source_name: Subject: JH0010; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0019.Day 56

source_name: Subject: JH0019; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: Species_mixing_fresh

value: fresh

value: no preservation


title: JH0010.Day 56

source_name: Subject: JH0010; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: JH0010.Day 7

source_name: Subject: JH0010; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: Ace 527 + dmLT


title: MR_14m_M_1

value: Male

tag: age

tag: intervention

tag: dose


title: MR_14m_M_2

tag: tissue

tag: intervention duration


title: M9M7V

value: leukocyte

tag: gender

value: M


title: G9A6Q

value: TD


title: M6U9X


title: JH0010.Day 63

source_name: Subject: JH0010; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group

tag: protected

value: no

value: anti-IgA antibody


title: MRCON_14m_M_3

value: MR Control


title: W9M6F

tag: cell type

tag: age (months)

tag: diagnosis


title: MRCON_14m_M_2


title: Egr1KO_TET1_91171_rep1

city: NY

first: zhixiong

last: sun

address: 3908 pardes building, NYSPI

department: Psychiatry

institute: Columbia University

data_processing:
Sequencing adapters in raw sequencing reads were removed by Trim_Galore (v.0.5.0) amd Cutadapt (v.1.17). Moreover, the reads whose length is less than 30 were filtered. After trimming, reads were mapped to mm10 by Bowtie2 (v2.3.4.1). Subsequently, Picard (v.2.18.3) was used to move PCR duplicates. MACS2 (v2.1.1) was used to call broad peaks on two replicates. Significant and reproducible peaks on two replicates were reported.  In Bedtools (v2.26.0), the subroutine "genomeCov" was used to generate visualized signals (BEDGRAPH format), which were normalized to 1 million (Reads per million, RPM).
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH

extract_protocol:
Tissue pellets were homogenized in lysis buffer. After clarifying the lysate from sonicated nuclei, the genomic DNA fragments were obtained from anti-TET1 immunoprecipitated chromatin
Libraries were prepared according to the protocol developed by Blecher-Gonen et al. (PMID: 23429716)

treatment_protocol: C57BL/6 male mice were anesthetized with avertin and decapitated. Brains were chilled in ice-cold phosphate buffer saline and sliced using a Vibratome (Ted Pella) into 300 mm slices. Prefrontal cortices were micro-dissected, minced into small pieces (~1 mm3) and immediately cross-linked in 1% formaldehyde for 20 min at room temperature (RT), and quenched by adding 125 mM glycine for 5 min at RT. The tissue was then rinsed twice in cold phosphate-buffered saline (PBS) containing halt protease inhibitor cocktail (Pierce Biotechnology, Inc.) and centrifuged at 850 g for 10 min at 4 °C

tag: strain background

tag: genotype/variation

value: 6-week old

value: male

tag: tissue/cell type

value: frontal cortex

tag: chip antibody

value: TET1 (Active Motif, 91171)


title: Egr1KO_TET1_91171_rep2

tag: Sex


title: JH0010.Day 7.Post

source_name: Subject: JH0010; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

tag: molecule


title: G9P3X

value: LD


title: M4B9S


title: B5Z4P


title: Z7B6Y


title: JH0036.Day 35

source_name: Subject: JH0036; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: Placebo


title: Egr1KO_TET1_5D6_rep2

tag: age

value: TET1 (Active Motif, 61741)


title: MRCON_14m_M_1

tag: strain

value: 14 months

value: Liver

tag: intervention

tag: dose


title: JH0010.Day 35

source_name: Subject: JH0010; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

tag: tissue

value: antibody lymphocyte supernatants (ALS)

value: Ace 527 + dmLT


title: JH0036.Day 7.Post

source_name: Subject: JH0036; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

tag: subject identifier


title: Egr1KO_TET1_input DNA

description: Egr1KO_TET1_input DNA

source_name: Egr1KO_TET1_input DNA


title: JH0036.Day 28

source_name: Subject: JH0036; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: treatment group


title: J2Y7X

value: leukocyte

tag: gender


title: Egr1KO_TET1_5D6_rep1


title: EST_6m_M_3

source_name: Liver

value: Male

value: 6 months

tag: intervention duration

value: 2 months


title: EST_6m_M_2


title: WT_TET1_input DNA

description: WT_TET1_input DNA

source_name: WT_TET1_input DNA

value: wild type


title: N9D8X

source_name: leukocyte transcriptome

tag: cell type

value: M

tag: age (months)

value: TD


title: EST_6m_F_3

value: Female


title: N8T4C

tag: diagnosis

value: PreemieNoDelay


title: EST_6m_M_1


title: WT_TET1_91171_rep2

tag: strain background

tag: genotype/variation

value: 6-week old

value: male

value: frontal cortex

value: TET1 (Active Motif, 91171)


title: WT_TET1_91171_rep1

tag: tissue/cell type

tag: chip antibody


title: U3V4P

value: ASD


title: JH0036.Day 63

source_name: Subject: JH0036; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: Placebo

tag: protected

value: no

tag: molecule

value: anti-IgA antibody


title: JH0036.Day 7

source_name: Subject: JH0036; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: R5N7K

value: leukocyte


title: E9M4P


title: WT_TET1_5D6_rep2

tag: age

tag: Sex

value: TET1 (Active Motif, 61741)


title: EST_6m_F_2

tag: strain

value: 6 months

value: Liver

tag: intervention

tag: dose

value: 2 months


title: JH0036.Day 0

source_name: Subject: JH0036; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

tag: tissue

tag: subject identifier

tag: treatment group


title: H8B5H_repB

tag: cell type

tag: gender

value: M


title: PROT_6m_M_2

value: Male

value: Protandim

tag: intervention duration


title: EST_6m_F_1

value: Female


title: WT_TET1_5D6_rep1

tag: strain background

value: wild type

value: 6-week old

value: male


title: D2

first: Maria

last: Plataki

state: New York

address: 1300 York Ave | Box 96

department: Joan and Sanford I. Weill Department of Medicine

institute: Weill Cornell Medicine

description: RNASeq_expression.genes_RPKM_Maria_Plataki.xls

data_processing:
Illumina bcl2fastq v2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using tophat-2.0.11
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Excel include RPKM values for each Sample ...

source_name: Lung

extract_protocol:
Lungs were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) was used for extraction of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: diet

value: 10% Fat

tag: exposure

value: Room air


title: D3


title: H8B5H_repA

tag: age (months)

tag: diagnosis

value: ASD


title: PROT_6m_M_3


title: C3

value: 60% Fat


title: PROT_6m_F_3


title: JH0036.Day 56

data_processing: Foreground spot intensities were adjusted by local background by subtraction, and negative values were converted to 1. Next, all foreground values were transformed using the base 2 logarithm. The dataset was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT controls for each sample. Since the IVTT control spots carry the chip, sample and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding to the non-specific antibody binding to the IVTT controls (a.k.a. background). With the normalized data, a value of 0.0 means that the intensity is no different than the background, and a value of 1.0 indicates a doubling with respect to background

source_name: Subject: JH0036; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: Placebo

tag: protected

value: no

tag: molecule

value: anti-IgA antibody


title: D1


title: PROT_6m_M_1

tag: Sex

tag: age

value: 6 months

value: Liver

value: 2 months


title: JH0069.Day 63

source_name: Subject: JH0069; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: Ace 527

value: yes


title: PROT_6m_F_2

tag: strain

value: Female

tag: intervention

value: Protandim


title: HEPS_B+Dox_Rep3

source_name: Human Induced Pluripotent Stem Cells

value: Hemogenic progenitors (CD31+CD34+CD45-)

tag: treatment

value: Dox+

tag: day


title: C2

tag: tissue

value: Lung


title: JH0069.Day 28

source_name: Subject: JH0069; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group


title: PROT_6m_F_1

tag: dose

tag: intervention duration


title: JH0069.Day 35

source_name: Subject: JH0069; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: JH0069.Day 7.Post

source_name: Subject: JH0069; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0069.Day 56

source_name: Subject: JH0069; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: JH0069.Day 7

source_name: Subject: JH0069; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0069.Day 0

source_name: Subject: JH0069; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: C1

tag: diet

value: Room air


title: RAP_6m_M_3

value: Male

value: Rapamycin

value: 42 ppm


title: B3

value: 10% Fat

tag: exposure

value: >95% oxygen


title: L5S3Z

tag: cell type

value: leukocyte

tag: gender

value: M

tag: age (months)

value: ASD


title: B2


title: RAP_6m_M_2

value: 6 months

value: Liver

value: 2 months


title: RAP_6m_M_1


title: JH0042.Day 63

source_name: Subject: JH0042; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: Ace 527 + dmLT

tag: protected

value: yes

tag: molecule

value: anti-IgA antibody


title: B1

value: Lung


title: R6W8B

tag: diagnosis

value: TD


title: JH0042.Day 7.Post

source_name: Subject: JH0042; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: F7X5A


title: RAP_6m_F_3

source_name: Liver

tag: strain

tag: Sex

value: Female

tag: age


title: J7S7Z

source_name: leukocyte transcriptome


title: Z6A9K

value: AutFeat


title: A3

value: 60% Fat


title: U6Q8M


title: RAP_6m_F_2

tag: intervention

value: Rapamycin

value: 42 ppm


title: JH0042.Day 0

source_name: Subject: JH0042; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

tag: tissue


title: A2

value: >95% oxygen


title: JH0042.Day 35

source_name: Subject: JH0042; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

tag: subject identifier


title: RAP_6m_F_1


title: M2V5W

value: leukocyte

value: M


title: A1


title: W7R4W


title: L7M7K


title: Pparg ablated urothelial basal cells under homeostasis, replicate 3

first: Chang

last: Liu

address: 1130 St Nicholas Ave, Room 311

data_processing:
Sequencing data were processed by RTA (Illumina) for base calling
bcl2fastq2 (version 2.17) for converting BCL to fastq format, coupled with adaptor trimming.
The reads were mapped to Mouse: UCSC/mm10 as reference genome using STAR(2.5.2b) and featureCounts(v1.5.0-p3).
Differentially expressed genes were identified using DEseq, an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: UCSC/mm10
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: Urothelium

extract_protocol:
Bladder was isolated, treated with EDTA, then whole urothelium was scrapped off and GFP+ cells were collected by FACS for RNA extraction
Only samples having a total amount more than 100ng and a RIN>8 were used for RNAseq.  mRNA were enriched using poly-A pull-down before proceed for library preparation using  Illumina TruSeq RNA prep kit.

treatment_protocol: Adult animal was induced by tamoxifen 5 days in a row, and the animal was sacrificed 2 weeks after the last induction

value: Basal cells

tag: genotype

value: K5CreER; Pparg; mTmG (+/-, fl/fl, fl/fl)


title: Pparg ablated urothelial basal cells under homeostasis, replicate 2


title: CR_6m_M_2

value: Male

value: 6 months

value: Liver

value: CR

tag: dose

value: 2 months


title: JH0042.Day 28

first: Arlo

last: Randall

source_name: Subject: JH0042; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

extract_protocol: not provided

value: antibody lymphocyte supernatants (ALS)

tag: treatment group

value: Ace 527 + dmLT

value: yes

value: anti-IgA antibody


title: Q9T2N

value: TD


title: JH0042.Day 7

source_name: Subject: JH0042; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: CR_6m_M_1

tag: intervention duration


title: JH0042.Day 56

source_name: Subject: JH0042; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: N2V6E


title: T5X2N

value: ASD


title: JH0013.Day 28

source_name: Subject: JH0013; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: Placebo

value: no


title: B4J4L

value: leukocyte


title: Y4T5L

value: M


title: D4M4M


title: JH0013.Day 63

source_name: Subject: JH0013; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: A5G5M


title: WT urothelial basal cells under homeostasis, replicate 3

value: Basal cells

value: K5CreER; Pparg; mTmG (+/-, fl/+, fl/fl)


title: JH0013.Day 7

source_name: Subject: JH0013; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: CR_6m_F_3

value: Female


title: CR_6m_F_2

value: 6 months


title: JH0013.Day 7.Post

source_name: Subject: JH0013; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: U6T4R

value: LD


title: U7U3C

value: PDDNOS


title: WT urothelial basal cells under homeostasis, replicate 2


title: CR_6m_M_3

value: Male

value: Liver

value: CR

value: 2 months


title: JH0013.Day 0

source_name: Subject: JH0013; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: anti-IgA antibody


title: CR_6m_F_1


title: WT urothelial basal cells under homeostasis, replicate 1


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 7

extract_protocol:
Bladder was isolated, treated with EDTA, then whole urothelium was scrapped off and collected for RNA extraction
Only samples having a total amount more than 100ng and a RIN>8 were used for RNAseq.  mRNA were enriched using poly-A pull-down before proceed for library preparation using  Illumina TruSeq RNA prep kit.

treatment_protocol: Female mice aged 8-14 weeks old were inoculated with UTI89, infection was confirmed by urine culture and histology. Antibiotics was given at 30h post infection and kept till the day of sacrifice. The animal was sacrificed 4 weeks post infection

value: Whole urothelium, mixed cell type

value: ShhCre;Pparg (+/-, fl/fl)


title: Pparg ablated urothelial basal cells under homeostasis, replicate 1

value: K5CreER; Pparg; mTmG (+/-, fl/fl, fl/fl)


title: H8M9E

value: leukocyte


title: ACA_6m_M_2

value: Acarbose


title: ACA_6m_M_3


title: ACA_6m_M_1


title: ACA_6m_F_3


title: JH0013.Day 35

source_name: Subject: JH0013; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: Placebo

value: no


title: ACA_6m_F_2

value: Female


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 4


title: N5V9N

value: M


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 5


title: JH0002.Day 63

source_name: Subject: JH0002; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: SNELLCON_5m_M_3

value: 5 months

value: Snell Dwarf Mice Control


title: JH0002.Day 0

source_name: Subject: JH0002; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0002.Day 7.Post

source_name: Subject: JH0002; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 2


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 1


title: JH0002.Day 7

source_name: Subject: JH0002; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 6


title: JH0013.Day 56

source_name: Subject: JH0013; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: ACA_6m_F_1

source_name: Liver

value: 6 months


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium 4 weeks after UTI, replicate 3


title: H4D6C

source_name: leukocyte transcriptome

value: ASD


title: SNELLCON_5m_M_2

value: Male

value: Liver


title: B4L7F

value: LD


title: F8F3V

value: PreemieNoDelay


title: SNELL_5m_M_3

value: Snell Dwarf Mice


title: A3W6D


title: G2R8S


title: N8T8F

value: PDDNOS


title: H7P2H


title: WT whole urothelium 4 weeks after UTI, replicate 4

source_name: Urothelium

value: Whole urothelium, mixed cell type

value: wild type


title: WT whole urothelium 4 weeks after UTI, replicate 3


title: SNELL_5m_M_1


title: JH0002.Day 56

source_name: Subject: JH0002; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: anti-IgA antibody


title: WT whole urothelium 4 weeks after UTI, replicate 1


title: WT whole urothelium 4 weeks after UTI, replicate 2


title: RAP_12m_M_3

value: 12 months

value: Rapamycin

value: 14 ppm

value: 8 months


title: WT whole urothelium 4 weeks after UTI, replicate 5


title: JH0050.Day 28

source_name: Subject: JH0050; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: Ace 527

value: yes


title: JH0002.Day 35

source_name: Subject: JH0002; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: no


title: SNELLCON_5m_M_1

value: Male

value: 5 months

value: Snell Dwarf Mice Control


title: JH0002.Day 28

source_name: Subject: JH0002; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0050.Day 7.Post

source_name: Subject: JH0050; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0050.Day 0

source_name: Subject: JH0050; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium under homeostasis, replicate 4

extract_protocol: Only samples having a total amount more than 100ng and a RIN>8 were used for RNAseq.  mRNA were enriched using poly-A pull-down before proceed for library preparation using  Illumina TruSeq RNA prep kit.

value: ShhCre;Pparg (+/-, fl/fl)


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium under homeostasis, replicate 2


title: U5C5L_repB

value: leukocyte

value: M

value: TD


title: RAP_12m_M_2

value: Liver


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium under homeostasis, replicate 3

value: Whole urothelium, mixed cell type


title: ShhCre;Pparg (+/-, fl/fl) whole urothelium under homeostasis, replicate 1


title: RAP_12m_F_3

value: Female


title: JH0050.Day 63

source_name: Subject: JH0050; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: anti-IgA antibody


title: R7A6H

value: ASD


title: D2K7P


title: S6G4L

value: PreemieNoDelay


title: WT whole urothelium under homeostasis, replicate 4

value: wild type


title: JH0050.Day 35

source_name: Subject: JH0050; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: Ace 527

value: yes


title: SNELL_5m_M_2

value: Male

value: Snell Dwarf Mice


title: RAP_12m_F_2

value: 12 months

value: Rapamycin

value: 14 ppm

value: 8 months


title: WT whole urothelium under homeostasis, replicate 3


title: JH0050.Day 56

source_name: Subject: JH0050; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: N9X2K

value: leukocyte

value: M


title: RAP_12m_F_1

value: Liver


title: M2C4J


title: JH0026.Day 28

source_name: Subject: JH0026; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: no


title: RAP_12m_M_1


title: JH0026.Day 35

source_name: Subject: JH0026; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: WT whole urothelium under homeostasis, replicate 2

value: Whole urothelium, mixed cell type


title: Z8C9B_repB

value: TD


title: JH0050.Day 7

source_name: Subject: JH0050; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: anti-IgA antibody


title: V2P7Y

value: ASD


title: Z8C9B_repA


title: S4X9Y_repB


title: Y7Y4Z


title: GHRKO_5m_M_3

value: 5 months

value: GHRKO


title: GHRCON_5m_M_2

value: Male

value: GHRKO Control


title: GHRCON_5m_M_3


title: WT whole urothelium under homeostasis, replicate 1

value: wild type


title: GHRKO_5m_M_2


title: GHRKO_5m_M_1


title: RRBS_mm_fc_Egr1ko_rep1

data_processing:
Adapter in raw sequencing reads were removed by Cutadapt (v.11.2) and low quality sequences were trimmed off by a customized Perl script. Reads trimmed were mapped to mm10 by Bismark (v0.16.3) with Bowtie2 (v2.2.9). PCR duplicates in RRBS-seq were removed by another customized Perl script.
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH

source_name: Frontal cortex from 6 week old Egr1-/- mouse brain

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Genomic DNA was extracted from mouse frontal cortex tissues using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions. Five microgram genomic DNA per sample was used for library construction using a customized Reduced Representation Bisulfite Sequencing (RRBS) method.
Five microgram mouse genomic DNA was spiked with 0.02% unmethylated cl857 Sam7 Lambda DNA (Promega) and sonicated to 200-bp fragments with Covaris M2 (AB). After end repair, dA tailing, the DNA fragments were ligated with cytosine-methylated Illumina TruSeq DNA adapters using T4 DNA ligase (NEB) overnight. Adapter-ligated DNA was digested with MseI and MluCI (NEB) to enrich DNA fragments containing CpG sites. After purification, DNA fragments were subject to bisulfite conversion using the EpiTect Bisulfite Kit (Qiagen). After bisulfite conversion, the single-stranded uracil-containing DNA was subjected to 12 cycles of PCR reaction with Illumina TruSeq PCR primers and 2.5 U Pfu TurboCx Hotstart DNA polymerase (Agilent) to recover enough DNA for sequencing. The recovered libraries were sequenced on Hiseq 4000 platform with 75bp paired end mode (Illumina).

tag: developmental stage

tag: tissue/cell type

value: brain (frontal cortex)

value: male


title: JH0026.Day 63

source_name: Subject: JH0026; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: JH0026.Day 7

source_name: Subject: JH0026; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: JH0026.Day 0

source_name: Subject: JH0026; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: RRBS_mm_fc_Egr1ko_rep2

tag: gender


title: CON_12m_M_3

source_name: Liver

value: 12 months

value: Control


title: GHRCON_5m_M_1


title: RNA-Seq_mm_fc_Tet1ko_rep1

data_processing:
Sequencing adapters in raw sequencing reads were removed by Cutadapt (v.11.2). Moreover, the bad quality of bases in either ends of reads were trimmed by a customized Perl script. After trimming, reads were mapped to mm10 by RSEM (v1.3.0) with Bowtie2 (v2.2.9). Subsequently, DESeq2 (v 1.14.1) was employed to identify differentially expressed genes (DEGs), which were defined as (1) |log2FC|>log2(1.5); (2) p-value adjusted < 0.05.
6wk_rep1, 6wk_rep2 and 6wk_rep3 processed RNA-seq data based on raw data from from existing GSM Samples, these are used as control for our RNA-seq analysis. The GSM for 6wk_rep1: GSM1173821, GSM1173822; for 6wk_rep2: GSM1173823; for 6wk_rep3: GSM1173824
Genome_build: mm10
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH

source_name: Frontal cortex from 8 week old Tet1-/- mouse brain

extract_protocol:
Total RNA was extracted from mouse frontal cortex tissues using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions. mRNA-Seq libraries were generated from 500ng total RNA with polyA+ selection of mRNA using the TruSeq Stranded mRNA Library Preparation Kit (Cat# RS-122-2101, Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA-Seq_mm_fc_Tet1ko_rep2


title: RRBS_mm_fc_Tet1ko_rep1


title: RRBS_mm_fc_Tet1ko_rep2


title: JH0007.Day 7.Post

source_name: Subject: JH0007; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: Ace 527 + dmLT

value: yes


title: RNA-Seq_mm_fc_Egr1ko_rep2


title: JH0026.Day 7.Post

source_name: Subject: JH0026; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: no