title: cortex,rep3

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: Couch Biomedical Research Bldg 06316

department: Genetics

institute: Washington University of St. Louis

data_processing:
nf-callingcards
Reads are prepared by extracting barcodes (UMItools) and trimming adapters (Trimmomatic)
If not already done, genome is prepared (Samtools faidx and aligner indicies)
Reads were aligned (bwa)
Alignment QC metrics were extracted (samtools) and reads were mapped to identify Calling Cards insertions (custom scripts).
Peak calling and significance statistics were determined (pycallingcards)
Assembly: mm10
Supplementary files format and content: Analyzed Calling Cards data is outputted as qBED (formerly CCF) files. Each row is a discrete SRT insertion and has six columns: CHROM,START,END,VALUE,STRAND,ANNOTATION. The VALUE represents the number of sequencing reads associated with that insertion. The ANNOTATION column stores sample-specific information such as i5/i7/SRT barcode.
Library strategy: Calling Cards

source_name: brain tissue

extract_protocol:
Tissue was homogenized in Trizol and total RNA was isolated using the Zymo RNA Clean & Concentrator-5 (Zymo R1014) kit. For detailed protocol, see Nat Prot (link).
First strand cDNA synthesis was performed by reverse transcribing polyA mRNAs using an oligo(dT) primer that also adds on a common primer sequence. RNA/DNA duplexes were removed by RNase H treatment. TdTomato self-reporting transcripts (SRTs) were amplified by PCR. PCR products were tagmented and indexed using the Illumina Nextera XT library preparation kit. For detailed protocol, see Nat Prot (link).

value: brain tissue

tag: brain region

value: cortex

value: CD-1 IGS


title: midbrain,rep3

status: Public on Feb 01 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

value: midbrain

tag: genotype

value: WT

tag: strain


title: midbrain,rep2


title: hindbrain,rep3

value: hindbrain


title: F4/80+ cells isolated from medium-content tumor, Day11 [Y22_M_TAM_3]

city: ShenZhen

first: Huan

last: Ren

address: 1088 Xueyuan Avenue

country: China

institute: Southern university of science and technology

data_processing:
CASAVA base recognition.
Clean data were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data through in-house perl scripts.
Paired-end clean reads were aligned to the reference genome(GRCm38/mm10) using Hisat2 (v2.0.5)
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads as a matrix table for each sample.

source_name: liver

extract_protocol:
RNA was harvested using TRIzol Reagent (Life Technologies), total amounts and integrity of RNA were assessed using the Agilent 5400.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols, the effective concentration of the library is higher than that of 2nM.

value: liver

tag: cell type

value: F4/80+ cells

tag: treatment

tag: time

value: Day 11


title: PZEV_IME1_KAR4_1-5H

type: RNA

city: DC

first: Zachory

last: Park

state: Washington DC

address: 37th and O Streets NW

department: Biology

institute: Georgetown University

description: PzevIME1 pRIM4

hyb_protocol: Labeled cRNA was allowed to hybridze for 17 hours at 65 degrees C and 20 RPM. After hybridization, slides were washed sequentially with wash buffer 1 for 1 minute, 2 for 1 minute, and then acetonitrile for 30 seconds.

scan_protocol: Scanned on an Agilent G2505C

data_processing: Agilent Feature Extractor was used.

organism: Saccharomyces cerevisiae

source_name: WT

label_protocol: Brauer et al. 2008

growth_protocol: Cells were grown in YPD and then back diluted to YPA at an OD of 0.1 and allowed to grow for 16-18 hours before being transferred to Spo media (1% Kac) at an OD of 0.5. 1 uM of estradiol was added to overexpression strains.

extract_protocol: Cells were lysed with bead beating. Phenol saturated with 0.1 M citrate was added. Lysates were incubated at 65 degrees C for 30 minutes vortexing every 5 minutes. Lysates were chilled on ice for 30 minutes. The aqueous phase was transferred and chlorofom was added. Samples were mixed lightly and centrifuged before being moved to a new tube containing sodium acetate. Samples were washed with 100% ethanol and left to incubate at -20 degrees C for 30 minutes to 16 hours. Samples were then spun at full speed for 5 minutes to pellet the RNA. Pellets were washed with 70% ethanol and pulse-spun. Remaining alcohol was aspirated and RNA was resuspending in 100 uL of water. Samples were further cleaned using the Qiagen Rneasy kit.


title: hindbrain,rep2


title: PZEV_IME1_26JUN2014_KAR4_9H

description: PzevIME1 pRIM4


title: PZEV_IME1_26JUN2014_KAR4_7H

description: PzevIME1 pRIM4


title: cortex,rep2


title: midbrain,rep1


title: PZEV_IME1_26JUN2014_KAR4_8H

description: PzevIME1 pRIM4


title: gfp.cds.1.IP.combined: HeLa CDS MPm6A m6A-IP rep 1

city: Chicago

first: Philip

middle: Cody

last: He

state: IL

address: 929 E 57th Street

institute: University of Chicago

description:
MPm6A m6A-IP
mpm6a_oligo_ratios_gfp.cds.txt

data_processing:
Library strategy: MPm6A
For m6A-seq and RNA-seq: HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome (hg38) with options -k 1 and --known-splicesite-infile generated by the hisat2_extract_splice_sites.py script with the UCSC hg38 GTF. samtools (version 1.7) was used to generate, sort and index bam files.
For MPm6A: Reads were mapped back to a reference genome containing the designed sequences with HISAT27 (version 2.1.0),  with option -k 1. Counts for each sequence were calculated with samtools (version 1.7) idxstats and sequences with at least 10 counts for all barcoded experimental and mutant sequences were retained.
For m6A-seq: The callPeakBinomial function and reportJointPeak from the MeRIPtools R package (version 0.1.0) was used to call m6A peaks with options min_counts = 15, peak_cutoff_fdr = 0.05, peak_cutoff_oddRatio = 1.5, and joint_threshold = 2.  RADAR R/Bioconductor package (version 0.2.1)8 was used to perform differential methylation analysis with options fragmentLength = 150, binSize =5 0, minCountsCutOff = 10, FDR cutoff = .1, log2FC cutoff = 1. Significantly differentially methylated regions were annotated to the RefSeq database (hg38). Bedgraph files for the forward and reverse strand were created using deeptools (version 3.1.3) bamCoverage with options --binSize 10, --normalizeUsing CPM, --exactScaling, --filterRNAstrand forward/reverse.
For RNA-seq: DESeq2 (version 1.18.1 ) was used to detect differentially expressed genes using a significance threshold of adjusted p-value <.05.12 To identify genes that have a significant change in response to EJC KD in WT vs. METTL3mut cells, the design formula ~ genotype + treatment + genotype:treatment was used.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

organism: Homo sapiens

source_name: HeLa

growth_protocol: DMEM, high glucose, pyruvate (Gibco 11995040), 9.1% FBS, Penicillin Streptomycin (100 U/mL), 47C 5% CO2

extract_protocol:
Trizol extraction of RNA
For m6A-seq and RNA-seq: Illumina Stranded Truseq. MPm6A: Custom library construction as described in methods.

tag: cell line

value: HeLa

value: CDS GFP MPm6A library

tag: input or ip


title: hindbrain,rep1


title: cortex,rep1


title: gfp.3.4.IP.combined: HeLa 3'UTR MPm6A m6A-IP rep 4

description:
MPm6A m6A-IP
mpm6a_oligo_ratios_gfp.3.txt

value: 3'UTR GFP MPm6A library


title: gfp.3.3.IP.combined: HeLa 3'UTR MPm6A m6A-IP rep 3


title: Geniculate Ganglion from Egr4-/- knockout adult 1

city: Indianapolis

first: Brian

last: Pierchala

state: IN

department: Anatomy, Cell Biology & Physiology

institute: Indiana University School of Medicine

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.5) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) were assessed using bamutils (from NGSUtils v.0.5.9). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.1.5.1) with the following parameters: “-s 2 -Q 10”.
The data was normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.12.1) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2FPKM and raw counts values for each Sample

source_name: Geniculate Ganglion

extract_protocol:
Total RNA was extracted from isolated Geniculate Ganglia from four Egr4+/+ and four Egr4-/- mice each using the RNeasy plus micro kit (Qiagen, catalog no. 74034) according to the manufacturer instructions. Purified total RNA was first evaluated for its quantity and quality using an Agilent Bioanalyzer 2100 (Agilent genomics). A RIN (RNA Integrity Number) value of seven or higher was required to pass quality control. Only RNA samples with RIN>8 were only used for sequencing.
One nanogram of total RNA was used for library preparation using the Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc.) and the Illumina Nextera XT DNA Library Kit (lllumina). The resulting uniquely indexed libraries were quantified and quality accessed by Qubit and Agilent Bioanalyzer. The multiple libraries were then pooled in equal molarity. The pooled libraries were sequenced with 2×150bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using the v1.5 reagent kit.

value: Geniculate Ganglion

value: All cells in Geniculate Ganglia


title: Geniculate Ganglion from Egr4-/- knockout adult 2


title: Geniculate Ganglion from Egr4-/- knockout adult 4


title: Geniculate Ganglion from Egr4+/+ wild type adult 4


title: Geniculate Ganglion from Egr4-/- knockout adult 3


title: Geniculate Ganglion from Egr4+/+ wild type adult 2


title: Geniculate Ganglion from Egr4+/+ wild type adult 1


title: gfp.5.4.IN.combined: HeLa 5'UTR MPm6A input rep 4

description:
MPm6A input
mpm6a_oligo_ratios_gfp.5.txt

value: 5'UTR GFP MPm6A library

value: input


title: Geniculate Ganglion from Egr4+/+ wild type adult 3


title: gfp.cds.2.IP.combined: HeLa CDS MPm6A m6A-IP rep 2


title: gfp.3.1.IP.combined: HeLa 3'UTR MPm6A m6A-IP rep 1


title: PZEV_IME1_26JUN2014_KAR4_1H

description: PzevIME1 pRIM4


title: gfp.5.2.IN.combined: HeLa 5'UTR MPm6A input rep 2


title: gfp.5.3.IN.combined: HeLa 5'UTR MPm6A input rep 3


title: gfp.5.1.IN.combined: HeLa 5'UTR MPm6A input rep 1


title: PZEV_IME1_26JUN2014_KAR4_11H

description: PzevIME1 pRIM4


title: gfp.cds.4.IN.combined: HeLa CDS MPm6A input rep 4

description:
MPm6A input
mpm6a_oligo_ratios_gfp.cds.txt


title: PZEV_IME1_26JUN2014_KAR4_4H

description: PzevIME1 pRIM4


title: gfp.3.2.IP.combined: HeLa 3'UTR MPm6A m6A-IP rep 2


title: PZEV_IME1_KAR4_2-5H

description: PzevIME1 pRIM4


title: PZEV_IME1_26JUN2014_KAR4_10H

description: PzevIME1 pRIM4


title: 23AUG2014_PZEV_IME1_KAR4_0H

description: PzevIME1 pRIM4


title: 23AUG2014_PZEV_IME1_KAR4_0H_26AUG2014

description: PzevIME1 pRIM4


title: WT_P_IME1_kar4d_8H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_9H_26AUG2014

description: pIME1 pRIM4


title: gfp.cds.2.IN.combined: HeLa CDS MPm6A input rep 2


title: WT_P_IME1_kar4d_8H

description: pIME1 pRIM4


title: POD_liver_nuclei_120h

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description: 10x Genomics single nuclei 3' gene expression v3

data_processing:
Demultiplexing, alignment (to a modified version of the mm10 reference counting intronic reads in addition to those aligned to exons), and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Quality control, normalisation, data integration, and downstream analysis using Seurat 4.1.1
Assembly: mm10 (Ensembl 93)
Supplementary files format and content: fastq: fastq files of individual samples; mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample
Library strategy: snRNA-seq (10x)

source_name: Liver

extract_protocol:
Tris-Salt-Tween based nuclei isolation
10x Genomics single nuclei 3’ gene expression v3

value: Liver

tag: disease

value: POD

tag: timepoint


title: POD_liver_nuclei_336h


title: POD_liver_nuclei_168h


title: PZEV_IME1_26JUN2014_KAR4_5H

description: PzevIME1 pRIM4


title: gfp.cds.1.IN.combined: HeLa CDS MPm6A input rep 1


title: WT_P_IME1_kar4d_9H

description: pIME1 pRIM4


title: POD_liver_nuclei_048h


title: POD_liver_nuclei_042h


title: POD_liver_nuclei_072h


title: gfp.3.4.IN.combined: HeLa 3'UTR MPm6A input rep 4

description:
MPm6A input
mpm6a_oligo_ratios_gfp.3.txt


title: WT_P_IME1_kar4d_7H_26AUG2014

description: pIME1 pRIM4


title: POD_liver_nuclei_036h


title: POD_liver_nuclei_030h


title: POD_liver_nuclei_024h


title: POD_liver_nuclei_018h


title: WT_P_IME1_kar4d_7H

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_6H_26AUG2014

description: pIME1 pRIM4


title: gfp.cds.3.IN.combined: HeLa CDS MPm6A input rep 3


title: gfp.3.2.IN.combined: HeLa 3'UTR MPm6A input rep 2


title: WT_P_IME1_kar4d_5H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_6H

description: pIME1 pRIM4


title: 2020.8.9.m6A: HeLa siRNPS1-1 (4) m6A-IP rep 3

description:
m6A-IP from m6A-seq
HeLa_siRNPS1_differential_methylation.bed

data_processing:
Library strategy: m6A-seq
For m6A-seq and RNA-seq: HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome (hg38) with options -k 1 and --known-splicesite-infile generated by the hisat2_extract_splice_sites.py script with the UCSC hg38 GTF. samtools (version 1.7) was used to generate, sort and index bam files.
For MPm6A: Reads were mapped back to a reference genome containing the designed sequences with HISAT27 (version 2.1.0),  with option -k 1. Counts for each sequence were calculated with samtools (version 1.7) idxstats and sequences with at least 10 counts for all barcoded experimental and mutant sequences were retained.
For m6A-seq: The callPeakBinomial function and reportJointPeak from the MeRIPtools R package (version 0.1.0) was used to call m6A peaks with options min_counts = 15, peak_cutoff_fdr = 0.05, peak_cutoff_oddRatio = 1.5, and joint_threshold = 2.  RADAR R/Bioconductor package (version 0.2.1)8 was used to perform differential methylation analysis with options fragmentLength = 150, binSize =5 0, minCountsCutOff = 10, FDR cutoff = .1, log2FC cutoff = 1. Significantly differentially methylated regions were annotated to the RefSeq database (hg38). Bedgraph files for the forward and reverse strand were created using deeptools (version 3.1.3) bamCoverage with options --binSize 10, --normalizeUsing CPM, --exactScaling, --filterRNAstrand forward/reverse.
For RNA-seq: DESeq2 (version 1.18.1 ) was used to detect differentially expressed genes using a significance threshold of adjusted p-value <.05.12 To identify genes that have a significant change in response to EJC KD in WT vs. METTL3mut cells, the design formula ~ genotype + treatment + genotype:treatment was used.
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

value: siRNPS1 KD


title: POD_liver_nuclei_012h


title: gfp.3.1.IN.combined: HeLa 3'UTR MPm6A input rep 1


title: POD_liver_nuclei_006h


title: Healthy_liver_nuclei_002

value: Uninjured


title: Healthy_liver_nuclei_001


title: 2020.8.8.m6A: HeLa siRNPS1-1 (4) m6A-IP rep 2


title: 2020.8.7.m6A: HeLa siRNPS1-1 (4) m6A-IP rep 1


title: POD_liver_nuclei_003h


title: CO_7M_BRep2

city: Athens

first: Corinne

last: Nielsen

address: Irvine Hall

department: Biological Sciences

institute: Ohio University

description: P7 Cdh5(PAC)-CreERT2; Rbpjflox/flox (mutant)

data_processing:
Cutadapt (version 1.10) and Perl scripts (LC Sciences, Houston) were used to remove reads that contained adaptor contamination, and low-quality bases.
Sequence quality was verified using FastQC (version 0.10.1). HISAT (version 2) was used to map reads to the Mus musculus (GRCm39 Ensembl release 96) genome.
Mapped reads were assembled using StringTie (version 1.3.4). StringTie and edgeR was used to estimate expression levels of all transcripts, by calculating FPKM values from a merged and compiled transcriptome.
Differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by edgeR.
Assembly: Mus musculus GRCm39 Ensembl release 96
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: Primary (freshly isolated CD31+)

growth_protocol: Brain tissue from P7 experimental mice was harvested immediately after euthanasia by rapid decapitation (to avoid possible anesthesia induced changes in gene expression). Tissue was collected and minced in ice-cold digestion buffer (DMEM, supplemented with 5% heat inactivated Fetal Bovine Serum, and 1% Penicillin-Streptomycin) containing 700 U/ml. Collagenase II, 2.4 U/ml. Neutral, and 140U/ml. DNase I. Minced brain tissue was digested for not more than 45 minutes at 37 °C. Digested tissue homogenate was filtered through a 40μm nylon cell strainer and cell pellet collected by centrifugation at 300g for 10 minutes at 4 °C. Cell pellet was resuspended in isotonic Percoll solution and layered over a  70% Percoll gradient. An upper myelin and pellet of lysed RBCs and debris were removed, and an interphase consisting mainly of cells of the myeloid lineage, including endothelial cells was collected by density gradient centrifugation of 70% Percoll gradient tubes at 500g for 30 minutes without application of centrifuge brakes. The collected interphase containing endothelial cells was washed with PBS and resuspended either in FACS or MACS buffer for subsequent isolation and enrichment of brain endothelial cell population.

extract_protocol:
RNA from freshly isolated pool of brain endothelial cells from >20 biological replicates, for both cohorts (control and mutant) was isolated using RNeasy Plus Micro Kit (Qiagen). Pooled RNA was concentrated using spin columns (Zymo). Sequencing was carried out in triplicates, for control and mutant experimental cohorts. RNA integrity was checked using Agilent Technologies 2100 Bioanalyzer. 1 ug of total RNA was used for the construction of sequencing libraries.
Poly(A) RNA sequencing library was prepared following TruSeq-stranded-mRNA sample preparation protocol (Illumina). RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

treatment_protocol:
Experimental mice received intragastric administration of 100 μg Tamoxifen (Sigma) in 50 μl of peanut oil (Planters) at postnatal day (P) P1 and P2. Male and female mice were used indiscriminately in all experiments. Care and experimental procedures performed on animals were approved by Ohio University Institutional Animal Care and Use Committee (IACUC) Animal Protocol #16-H-024.
PBS washed cell pellets from the Percoll density gradient centrifugation were resuspended in PBS containing 0.5% BSA and 2 mM EDTA (MACS buffer), and CD31 coated magnetic microbeads at 9:1 dilution, for positive selection of brain endothelial cells, and incubated at 4 °C for 20 minutes. When placed within a magnetic field in a MACS column CD31- cells were washed away with MACS buffer, and magnetically retained CD31+ brain endothelial cells were eluted as the positively selected cell fraction in MACS buffer, and pelleted for resuspension in buffer of choice, based on subsequent experiment.

value: brain endothelial cell

value: P7, Mixed background (FVB/N and C57BL/6)

tag: age

value: tamoxifen induction of Cre-recombination


title: 2020.8.6.m6A: HeLa siUPF1-1 (4) m6A-IP rep 3

description:
m6A-IP from m6A-seq
HeLa_siUPF1_differential_methylation.bed

value: siUPF1 KD

value: WT


title: gfp.3.3.IN.combined: HeLa 3'UTR MPm6A input rep 3


title: CO_7M_CRep3


title: 2% input gDNA isolated from P7 FVB/NJ mice

library_source: genomic

data_processing:
Raw FASTQ files were cleaned using Trimmomatic and aligned using Burrows Wheeler Aligner.
ChIP-seq reads were aligned to Mus musculus- ref: mm10.
Peak detection was achieved using MACS2 (Zhang et al., 2008) and visualized via IGV (V2.13.2).
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Pooled isolated brain ECs from more than three biological replicates were crosslinked in a final concentration of 1% formaldehyde for 10 min at RT, and crosslinking reaction quenched with glycine solution, for 5 min at RT. Nuclei from lysed cell were isolated and chromatin was digested around nucleosomal boundaries using Micrococcal nuclease (Cell Signaling). Additionally, MNase digested DNA was sonicated with a probe sonicator (20 kHz, Fisherbrand) for three sets of 10 sec pulses, at 20% amplitude.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. 2 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRIselect beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Experimental mice received intragastric administration of 100 μg Tamoxifen (Sigma) in 50 μl of peanut oil (Planters) at postnatal day (P) P1 and P2. Male and female mice were used indiscriminately in all experiments. Care and experimental procedures performed on animals were approved by Ohio University Institutional Animal Care and Use Committee (IACUC) Animal Protocol #16-H-024.

value: brain endothelial

tag: chip antibody


title: Rb1_B_ P-DNA isolated from P7 FVB/NJ mice

description: IP-DNA isolated from P7 FVB/NJ mice

value: Rbpj (Cell Signaling 1:50, #5313)


title: WT_P_IME1_kar4d_4H_26AUG2014

description: pIME1 pRIM4


title: CO_7M_ARep1


title: WT_P_IME1_kar4d_5H

description: pIME1 pRIM4


title: CO_7C_CRep3

description: P7 Cdh5(PAC)-CreERT2; Rbpjflox/WT (control)


title: WT_P_IME1_kar4d_4H

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_3H

description: pIME1 pRIM4


title: 2020.8.5.m6A: HeLa siUPF1-1 (4) m6A-IP rep 2

value: HeLa


title: CO_7C_BRep2


title: CO_7C_ARep1


title: WT_P_IME1_kar4d_3-5H_26AUG2014

description: pIME1 pRIM4


title: C. rodentium, inulin diet, rep 6

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus musclaris genome (Grcm38) using HISAT
DEG assessed using DeSeq2
Assembly: GRCm38
Supplementary files format and content: excel file with count data and Ensembl gene ID for each sample

source_name: Colon

growth_protocol: mice were fed the respective diets for either 35 days (T muris) or 8 days (C rodentium)

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard Illumina

treatment_protocol: mcie were infected with 20 T. muris eggs 3 times, or 10^9 CFU C. rodentium

value: Colon

tag: diet

value: inulin


title: C. rodentium, inulin diet, rep 5


title: WT_P_IME1_kar4d_3-5H

description: pIME1 pRIM4


title: Rb2_C_IP-DNA isolated from P7 FVB/NJ mice

description: IP-DNA isolated from P7 FVB/NJ mice


title: 2020.8.3.m6A: HeLa siControl (4) m6A-IP rep 3

description: m6A-IP from m6A-seq

value: siControl KD


title: 2020.8.2.m6A: HeLa siControl (4) m6A-IP rep 2

description: m6A-IP from m6A-seq


title: WT_P_IME1_kar4d_3H_26AUG2014

description: pIME1 pRIM4


title: C. rodentium, inulin diet, rep 2


title: C. rodentium, inulin diet, rep 4


title: C. rodentium, inulin diet, rep 1


title: 2020.8.1.m6A: HeLa siControl (4) m6A-IP rep 1

description:
m6A-IP from m6A-seq
HEK293T_siEIF4A3_6_differential_methylation.bed


title: C. rodentium, control diet, rep 6

value: control


title: WT_P_IME1_kar4d_2H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_2H

description: pIME1 pRIM4


title: C. rodentium, control diet, rep 5


title: 2019.12.20.9.m6A: HEK293T siEIF4A3-2 (3) m6A-IP rep 3

value: siEIF4A3-2 KD


title: C. rodentium, control diet, rep 4


title: C. rodentium, control diet, rep 3


title: 2019.12.20.8.m6A: HEK293T siEIF4A3-2 (3) m6A-IP rep 2


title: WT_P_IME1_kar4d_2-5H_26AUG2014

description: pIME1 pRIM4


title: C. rodentium, control diet, rep 2


title: T. muris, inulin diet, rep 4

source_name: Caecum

value: Caecum


title: WT_P_IME1_kar4d_2-5H

description: pIME1 pRIM4


title: 2019.12.20.7.m6A: HEK293T siEIF4A3-2 (3) m6A-IP rep 1


title: WT_P_IME1_kar4d_1H_26AUG2014

description: pIME1 pRIM4


title: C. rodentium, control diet, rep 1


title: T. muris, inulin diet, rep 3


title: WT_P_IME1_kar4d_1H

description: pIME1 pRIM4


title: T. muris, inulin diet, rep 2


title: C. rodentium, inulin diet, rep 3


title: 2019.12.20.6.m6A: HEK293T siControl (3) m6A-IP rep 3

description: m6A-IP from m6A-seq


title: T. muris, inulin diet, rep 1


title: 2020.8.4.m6A: HeLa siUPF1-1 (4) m6A-IP rep 1


title: T. muris, control diet, rep 2


title: WT_P_IME1_kar4d_16H_26AUG2014

description: pIME1 pRIM4


title: 2019.12.20.5.m6A:  HEK293T siControl (3) m6A-IP rep 2

description: m6A-IP from m6A-seq


title: 2019.12.20.4.m6A: HEK293T siControl (3) m6A-IP rep 1

description: m6A-IP from m6A-seq


title: WT_P_IME1_kar4d_16H

description: pIME1 pRIM4


title: T. muris, control diet, rep 1


title: T. muris, control diet, rep 3


title: 2019.12.20.2.m6A: HEK293T siEIF4A3-1 (3) m6A-IP rep 2

description:
m6A-IP from m6A-seq
HEK293T_siEIF4A3_5_differential_methylation.bed

value: siEIF4A3-1 KD


title: TA0527

city: Hangzhou

first: Hong

last: Wu

address: 79 Qingchun Road

department: Department of Cardiology

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data were processed following standard protocols using Cell Ranger version 6.0.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: thoracic aorta

extract_protocol:
Mice were euthanized and perfused with PBS and aortas were harvested and placed in a petri dish containing DMEM with 10% fetal bovine serum (FBS) on ice. Perivascular adipose tissues and connective tissues were carefully removed. After collecting all grafts, to obtain single cell suspensions, arteries were washed with PBS for three times, cut into fine pieces and incubated with 1 mg/ml papain digesting solution [1 mg/ml papain (Sigma, P4762), 0.5 mg/ml 1,4-Dithioerythritol (Sigma, D8255), 0.156 mg/ml Taurine (Sigma, T8691), 0.25 mg/ml bovine serum albumin in PBS]. The digestion was performed at 37 ℃ water bath with reciprocal shaking. Detached cells in the supernatant were collected and suspended in DMEM with 10% FBS. Vascular allografts were then incubated with fresh digestion solutions every 10 min. After 3-4 digestions, the remaining tissues were incubated with 1 mg/ml papain digesting solution and 2 mg/ml collagenase I (Gibco, 17018029) and 1 mg/ml dispase II (Sigma, D4693) in Hank’s balanced salt solution containing calcium and magnesium. Detached cells were collected and fresh digestion solutions were added until the tissues dissolved completely. All digested cells from one sample were pooled together at the end of the digestion process. After sufficient digestion, cells were filtered through a 40-μm cell strainer, and the collected cells were centrifuged 8 min at 500 g speed at 4 ℃. Subsequently, cell pellet was suspended in PBS and stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit, Hoechst 33342  for 30 mins on ice. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+ & Dead Cell Stain- ) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Samples were subjected to scRNA-seq. A ChromiumTM Single Cell 3' Reagent Kit v2 or V3 chemistry (10x Genomics) was used and a standard protocol was followed. The library was generated and sequenced on a Novaseq6000 PE150 platform (Illumina) with paired-end 150 bp sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: thoracic aorta

value: nucleated living cells

value: ApoE-deficient

value: 12-16 weeks old

value: 4 wks Angiotensin Ⅱ-induction


title: Ang_T

description: 10x Genomics


title: Ang_A

description: 10x Genomics

source_name: abdominal aorta

value: abdominal aorta


title: Sham_T

description: 10x Genomics


title: 2019.12.20.3.m6A: HEK293T siEIF4A3-1 (3) m6A-IP rep 3

value: WT


title: 2019.12.20.1.m6A: HEK293T siEIF4A3-1 (3) m6A-IP rep 1


title: 2019.11.20.6.m6A: HeLa siEIF4A3-2 (2) m6A-IP rep 3

description:
m6A-IP from m6A-seq
HeLa_siEIF4A3_6_differential_methylation.bed


title: WT_P_IME1_kar4d_15H_26AUG2014

description: pIME1 pRIM4


title: kidney CKD treated with iron dextran (122320_ad_IPFe)

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: kidney

extract_protocol:
Total RNA was extracted from whole kidney tissues using RNeasy micro kit (catalog number 74004; Qiagen) according to the manufacturer’s instructions. Following RNA isolation, total RNA integrity was checked using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA concentration was measured using the NanoDrop system (Thermo Fisher Scientific, Inc., Waltham, MA).
RNA libraries were prepared for sequencing using  Illumina TruSeq stranded mRNA library preparation kit

value: kidney

tag: disease state

value: CKD

value: iron dextran 0.5 g/kg IP weekly


title: kidney CKD treated with iron dextran (111710_ad_IPFe)


title: WT_P_IME1_kar4d_15H

description: pIME1 pRIM4


title: AA0527

description: 10x Genomics


title: 2019.11.20.5.m6A: HeLa siEIF4A3-2 (2) m6A-IP rep 2

value: HeLa


title: WT_P_IME1_kar4d_14H

description: pIME1 pRIM4


title: kidney CKD treated with iron dextran (042702_ad_IPFe)


title: WT_P_IME1_kar4d_13H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_14H_26AUG2014

description: pIME1 pRIM4


title: kidney CKD untreated (120102_adenine)


title: WT_P_IME1_kar4d_13H

description: pIME1 pRIM4


title: Sham_A

description: 10x Genomics


title: 2019.11.20.4.m6A: HeLa siEIF4A3-2 (2) m6A-IP rep 1


title: 2019.11.20.3.m6A: HeLa siControl (2) m6A-IP rep 3

description: m6A-IP from m6A-seq


title: kidney CKD untreated (110310_adenine)


title: 2019.11.20.2.m6A: HeLa siControl (2) m6A-IP rep 2

description: m6A-IP from m6A-seq


title: kidney CKD untreated (022301_adenine)


title: Bisulfite-Seq Idh2R172K/+; Tet2-/- #2

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

data_processing:
Alignments were done with bwa-meth to mm10
Methylation calls were done with MethylDackel
Supplementary files format and content: Methylation bedgraph

source_name: CD4+ CXCR5+ PD-1+ (Tfh)  cells

extract_protocol:
At sacrifice, single cell suspensions were prepared from the hematopoietic organs (spleen and LNs). The tissues were crushed with a 1 mL syringe plunger through a 40 µm nylon mesh in cold buffer (phosphate-buffered saline (PBS 1X) without MgCl2 and CaCl2, supplemented with 0.5% bovine serum albumin, 2mM EDTA pH8.0). After centrifugation, cells are resuspended in red blood cell lysis buffer for 8 minutes at room temperature. After wash, cells were counted on a ViCell Counter and resuspended at the appropriate dilution for further experiment. CD3 T cell were isolated using spleen and LN isolated by negative selection using biotin coupled antibodies: anti-CD19 (Biolegend #115504) anti-B220 (Biolegend #103204), anti-Ter119 (Biolegend #116204), anti-NK1.1 (BioLegend #108704), anti-CD49b (Biolegend #108904), anti- Ly-6G/Ly-6C (Biolegend #108404), anti-CD11b (Biolegend #101204), anti-CD11c (BioLegend #117304), followed by Streptavidin Particles Plus - DM (BD, #557812) incubation according to manufacturer’s instructions. Then, Tfh cells (viable CD4+ CXCR5+ PD-1+) were sorted using a FACSAria II or FACSAria Fusion fluorescence-activated cell sorter (BD Biosciences, purity check>98%). 250.000 Tfh were collected and extracted using the AllPrep DNA/RNA Micro Kit (Qiagen #80284), following the manufacturer’s instructions.
Oxidative bisulfite sequencing (OxBS)

value: Spleen and lymph node


title: Bisulfite-Seq Idh2R172K/+; Tet2-/- #4


title: Bisulfite-Seq Idh2R172K/+; Tet2-/- #1


title: Bisulfite-Seq Idh2R172K/+; Tet2-/- #3


title: WT_P_IME1_kar4d_12H_26AUG2014

description: pIME1 pRIM4


title: 2019.11.20.1.m6A: HeLa siControl (2) m6A-IP rep 1

description: m6A-IP from m6A-seq

value: siControl KD


title: WT_P_IME1_kar4d_12H

description: pIME1 pRIM4


title: kidney CKD untreated (021320_adenine)


title: kidney CKD treated with iron dextran (062910_ad_IPFe)


title: WT_P_IME1_kar4d_11H

description: pIME1 pRIM4


title: 2019.9.17.9.m6A: HeLa siRBM8A-1 (1) m6A-IP rep 3

description:
m6A-IP from m6A-seq
HeLa_siRBM8A_differential_methylation.bed

value: siRBM8A-1 KD


title: WT_P_IME1_kar4d_11H_26AUG2014

description: pIME1 pRIM4


title: kidney control (042301_control)

value: control


title: 2019.9.17.8.m6A: HeLa siRBM8A-1 (1) m6A-IP rep 2


title: Bisulfite-Seq Tet2-/- #4


title: Bisulfite-Seq Tet2-/- #2


title: 2019.9.17.7.m6A: HeLa siRBM8A-1 (1) m6A-IP rep 1


title: WT_P_IME1_kar4d_10H_26AUG2014

description: pIME1 pRIM4


title: kidney control (012822_control)


title: Bisulfite-Seq Tet2-/- #1


title: WT_P_IME1_kar4d_10H

description: pIME1 pRIM4


title: Bisulfite-Seq Tet2-/- #3


title: kidney control (012811_control)


title: Bisulfite-Seq Idh2R172K/+ #4


title: Bisulfite-Seq Idh2R172K/+ #3


title: WT_P_IME1_kar4d_1-5H

description: pIME1 pRIM4


title: WT_P_IME1_kar4d_1-5H_26AUG2014

description: pIME1 pRIM4


title: Naïve N3

city: Hsinchu

first: Ling-ya

last: Huang

state: Taiwan

address: 1001 University Road

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
GATK v.4.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using GATK (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using GATK
Read count extraction and normalization were performed using GATK
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen

growth_protocol: Female C57BL/6J mice (4–6 weeks of age) were obtained from the National Laboratory Animal Center (Taipei, Taiwan), and all animal studies were approved and performed in accordance with the standard procedures established by the Institutional Animal Care and Use Committee.

extract_protocol:
Melanoma tumor were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female C57BL/6J mice (n=10) were subcutaneously implanted with 1×104 B16F10 cells in 100 μl of PBS. Three days after implantation, the mice bearing B16F10 tumors were treated with LPPC-DOX (containing 0.5 mg/kg DOX), LPPC-CpG (containing 0.05 mg/kg CpG), LPPC-DOX-CpG (containing 0.5 mg/kg DOX and 0.05 mg/kg CpG) or vehicle by skin application every day. Tumor size was measured with a caliper, and tumor volume was calculated as L × H × W. The mice were sacrificed when the tumor size exceeded 2000 mm3

value: Spleen

tag: Sex

value: Female

value: spleenocyte

value: Naive


title: Naïve N2


title: 2019.9.17.4.m6A: HeLa siEIF4A3-1 (1) m6A-IP rep 1

description:
m6A-IP from m6A-seq
HeLa_siEIF4A3_5_differential_methylation.bed

value: siEIF4A3-1 KD


title: kidney control (042310_control)


title: WT_P_IME1_kar4d_0H_26AUG2014

description: pIME1 pRIM4


title: Naïve N1


title: WT_P_IME1_kar4d_0H

description: pIME1 pRIM4


title: 2019.9.17.2.m6A: HeLa siControl (1) m6A-IP rep 2

description: m6A-IP from m6A-seq


title: Bisulfite-Seq Idh2R172K/+ #2


title: 2019.9.17.3.m6A: HeLa siControl (1) m6A-IP rep 3

description: m6A-IP from m6A-seq


title: 2019.9.17.1.m6A: HeLa siControl (1) m6A-IP rep 1

description: m6A-IP from m6A-seq


title: WT_P_IME1_kar4d_0-5H_26AUG2014

description: pIME1 pRIM4


title: Bisulfite-Seq Idh2R172K/+ #1


title: Bisulfite-Seq WT #3


title: 2019.9.17.5.m6A: HeLa siEIF4A3-1 (1) m6A-IP rep 2


title: LPPC/mp LM1

value: LPPC/mp


title: 2019.9.17.6.m6A: HeLa siEIF4A3-1 (1) m6A-IP rep 3


title: Bisulfite-Seq WT #2


title: LPPC/mp LM2


title: LPPC/mp/CD28_6


title: WT_P_IME1_kar4d_0-5H

description: pIME1 pRIM4


title: Bisulfite-Seq WT #4


title: 2020.8.8.IN: HeLa siRNPS1-1 (4) input rep 2

description:
input for m6A-seq
HeLa_siRNPS1_differential_methylation.bed

value: siRNPS1 KD

value: input


title: Bisulfite-Seq WT #1


title: LPPC/mp/CD28_5


title: 2020.8.7.IN: HeLa siRNPS1-1 (4) input rep 1

value: WT


title: starvation 4

description: pIME1 pRIM4


title: 2020.8.6.IN: HeLa siUPF1-1 (4) input rep 3

description:
input for m6A-seq
HeLa_siUPF1_differential_methylation.bed

value: siUPF1 KD


title: ATAC-Seq Idh2R172K/+; Tet2-/- #4

data_processing:
Trimming by TrimGalore, alignment by BWA, filtering by Picard + Samtools
Peak calling by MACS2 (shift reads by 75bp, extend by 150bp)
Counts by FeatureCounts
Please see nfcore atacseq pipeline for more details
Supplementary files format and content: Peak annotations
Supplementary files format and content: Peak counts

extract_protocol: At sacrifice, single cell suspensions were prepared from the hematopoietic organs (spleen and LNs). The tissues were crushed with a 1 mL syringe plunger through a 40 µm nylon mesh in cold buffer (phosphate-buffered saline (PBS 1X) without MgCl2 and CaCl2, supplemented with 0.5% bovine serum albumin, 2mM EDTA pH8.0). After centrifugation, cells are resuspended in red blood cell lysis buffer for 8 minutes at room temperature. After wash, cells were counted on a ViCell Counter and resuspended at the appropriate dilution for further experiment. CD3 T cell were isolated using spleen and LN isolated by negative selection using biotin coupled antibodies: anti-CD19 (Biolegend #115504) anti-B220 (Biolegend #103204), anti-Ter119 (Biolegend #116204), anti-NK1.1 (BioLegend #108704), anti-CD49b (Biolegend #108904), anti- Ly-6G/Ly-6C (Biolegend #108404), anti-CD11b (Biolegend #101204), anti-CD11c (BioLegend #117304), followed by Streptavidin Particles Plus - DM (BD, #557812) incubation according to manufacturer’s instructions. Then, Tfh cells (viable CD4+ CXCR5+ PD-1+) were sorted using a FACSAria II or FACSAria Fusion fluorescence-activated cell sorter (BD Biosciences, purity check>98%). OMNI-ATAC method was used. 50.000 Tfh cells were collected, washed in PBS and resuspend in RSB buffer (containing 0.1% NP40, 0.1% Tween- 20, and 0.01% Digitonin). After wash in RSB buffer (containing 0.1% Tween-20), the pellet was incubated at 37C for 30 mintutes in transposition reaction mix using the Nextera DNA LibraryPrep Kit (#FC-121-1030, Illumina). Clean-up of transposed fragments was done using MinElute Reaction Cleanup (#28004, Qiagen) according to the manufactor protocole and stored at -20C until further processing.


title: ATAC-Seq Idh2R172K/+; Tet2-/- #3


title: LPPC/mp/CD28_4


title: LPPC/mp/CD28_3


title: 2020.8.5.IN: HeLa siUPF1-1 (4) input rep 2


title: starvation 6

description: pIME1 pRIM4


title: ATAC-Seq Idh2R172K/+; Tet2-/- #1


title: ATAC-Seq Idh2R172K/+; Tet2-/- #2


title: 2020.8.3.IN: HeLa siControl (4) input rep 3

description: input for m6A-seq


title: LPPC/mp/CD28_2


title: LPPC/mp/CD28_1


title: WT_P_IME1_KAR4_7H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_8H_26AUG2014

description: pIME1 pRIM4


title: LPPC/mp/CD152_5


title: 2020.8.2.IN: HeLa siControl (4) input rep 2

description: input for m6A-seq


title: WT_P_IME1_KAR4_8H

description: pIME1 pRIM4


title: starvation 5

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_7H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_9H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_9H_26AUG2014

description: pIME1 pRIM4


title: LPPC/mp/CD152_6


title: 2020.8.1.IN: HeLa siControl (4) input rep 1

description: input for m6A-seq


title: ATAC-Seq Tet2-/- #3


title: ATAC-Seq Tet2-/- #4


title: WT_P_IME1_KAR4_6H

description: pIME1 pRIM4


title: ATAC-Seq Tet2-/- #2


title: LPPC/mp/CD152_2


title: LPPC/mp/CD152_4


title: 2019.12.20.9.IN: HEK293T siEIF4A3-2 (3) input rep 3

description:
input for m6A-seq
HEK293T_siEIF4A3_6_differential_methylation.bed

value: siEIF4A3-2 KD


title: 2019.12.20.8.IN: HEK293T siEIF4A3-2 (3) input rep 2


title: LPPC/mp/CD152_3


title: ATAC-Seq Idh2R172K/+ #1


title: 2019.12.20.5.IN: HEK293T siControl (3) input rep 2

description: input for m6A-seq


title: ATAC-Seq Tet2-/- #1


title: WT_P_IME1_KAR4_4H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_5H_26AUG2014

description: pIME1 pRIM4


title: 2019.12.20.7.IN: HEK293T siEIF4A3-2 (3) input rep 1


title: ATAC-Seq WT #4


title: ATAC-Seq WT #3


title: WT_P_IME1_KAR4_3H

description: pIME1 pRIM4


title: ATAC-Seq Idh2R172K/+ #3


title: 2019.12.20.6.IN: HEK293T siControl (3) input rep 3

description: input for m6A-seq


title: WT_P_IME1_KAR4_5H

description: pIME1 pRIM4


title: LPPC/mp/CD152_1


title: ATAC-Seq Idh2R172K/+ #2


title: ATAC-Seq WT #2


title: WT_P_IME1_KAR4_6H_26AUG2014

description: pIME1 pRIM4


title: 2019.12.20.1.IN: HEK293T siEIF4A3-1 (3) input rep 1

description:
input for m6A-seq
HEK293T_siEIF4A3_5_differential_methylation.bed


title: 2019.12.20.4.IN: HEK293T siControl (3) input rep 1

description: input for m6A-seq


title: ATAC-Seq Idh2R172K/+ #4


title: 2019.11.20.6.IN: HeLa siEIF4A3-2 (2) input rep 3

description:
input for m6A-seq
HeLa_siEIF4A3_6_differential_methylation.bed


title: WT_P_IME1_KAR4_3-5H

description: pIME1 pRIM4


title: TFH_Idh2R172K/+; Tet2-/- #4

data_processing:
Alignments were done with STAR to mm10
Counts were obtained by featureCounts on Gencode mouse transcriptome reference
Please see nfcore rnaseq pipeline for more details
Supplementary files format and content: gene counts

extract_protocol: At sacrifice, single cell suspensions were prepared from the hematopoietic organs (spleen and LNs). The tissues were crushed with a 1 mL syringe plunger through a 40 µm nylon mesh in cold buffer (phosphate-buffered saline (PBS 1X) without MgCl2 and CaCl2, supplemented with 0.5% bovine serum albumin, 2mM EDTA pH8.0). After centrifugation, cells are resuspended in red blood cell lysis buffer for 8 minutes at room temperature. After wash, cells were counted on a ViCell Counter and resuspended at the appropriate dilution for further experiment. CD3 T cell were isolated using spleen and LN isolated by negative selection using biotin coupled antibodies: anti-CD19 (Biolegend #115504) anti-B220 (Biolegend #103204), anti-Ter119 (Biolegend #116204), anti-NK1.1 (BioLegend #108704), anti-CD49b (Biolegend #108904), anti- Ly-6G/Ly-6C (Biolegend #108404), anti-CD11b (Biolegend #101204), anti-CD11c (BioLegend #117304), followed by Streptavidin Particles Plus - DM (BD, #557812) incubation according to manufacturer’s instructions. Then, Tfh cells (viable CD4+ CXCR5+ PD-1+) were sorted using a FACSAria II or FACSAria Fusion fluorescence-activated cell sorter (BD Biosciences, purity check>98%). 250.000 Tfh were collected and extracted using the AllPrep DNA/RNA Micro Kit (Qiagen #80284), following the manufacturer’s instructions.


title: WT_P_IME1_KAR4_3H_26AUG2014

description: pIME1 pRIM4


title: ATAC-Seq WT #1


title: 2019.12.20.2.IN: HEK293T siEIF4A3-1 (3) input rep 2


title: 2019.11.20.5.IN: HeLa siEIF4A3-2 (2) input rep 2


title: TFH_Idh2R172K/+; Tet2-/- #3


title: WT_P_IME1_KAR4_2H

description: pIME1 pRIM4


title: 2019.12.20.3.IN: HEK293T siEIF4A3-1 (3) input rep 3


title: WT_P_IME1_KAR4_2H_26AUG2014

description: pIME1 pRIM4


title: 2019.11.20.4.IN: HeLa siEIF4A3-2 (2) input rep 1


title: 2019.11.20.3.IN: HeLa siControl (2) input rep 3

description: input for m6A-seq


title: TFH_Idh2R172K/+; Tet2-/- #1


title: TFH_Tet2-/- #4


title: WT_P_IME1_KAR4_3-5H_26AUG2014

description: pIME1 pRIM4


title: TFH_Idh2R172K/+; Tet2-/- #2


title: WT_P_IME1_KAR4_2-5H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_4H

description: pIME1 pRIM4


title: TFH_Tet2-/- #3


title: 2019.11.20.1.IN: HeLa siControl (2) input rep 1

description: input for m6A-seq


title: WT_P_IME1_KAR4_1H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_2-5H

description: pIME1 pRIM4


title: 2020.8.9.IN: HeLa siRNPS1-1 (4) input rep 3


title: 2019.9.17.9.IN: HeLa siRBM8A-1 (1) input rep 3

description:
input for m6A-seq
HeLa_siRBM8A_differential_methylation.bed


title: 2019.9.17.8.IN: HeLa siRBM8A-1 (1) input rep 2


title: TFH_Tet2-/- #1


title: TFH_Idh2R172K/+ #4


title: 2019.9.17.6.IN: HeLa siEIF4A3-1 (1) input rep 3

description:
input for m6A-seq
HeLa_siEIF4A3_5_differential_methylation.bed


title: 2019.11.20.2.IN: HeLa siControl (2) input rep 2

description: input for m6A-seq


title: 2019.9.17.5.IN: HeLa siEIF4A3-1 (1) input rep 2


title: TFH_Idh2R172K/+ #2


title: WT_P_IME1_KAR4_15H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_15H

description: pIME1 pRIM4


title: 2019.9.17.4.IN: HeLa siEIF4A3-1 (1) input rep 1


title: TFH_Tet2-/- #2


title: WT_P_IME1_KAR4_16H

description: pIME1 pRIM4


title: TFH_Idh2R172K/+ #1


title: scATAC_B6_Cast_F1_Treg_Tconv

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v1.2).
For B6/Cast F1 allele-specific read alignment, we adapted the diploid pseudogenome alignment strategy implemented in the lapels/suspenders pipeline (Huang et al, Database, 2014) and used in recent studies (van der Veeken et al, Immunity, 2019; van der Veeken et al, Immunity, 2020; Zhong et al, Nature Immunology, 2021; Yang et al, eLife, 2022;) for allele-specific mapping. We obtained B6 and Cast pseudogenomes, MOD files, and variant vcf files from the UNC collaborative cross project (http://csbio.unc.edu/CCstatus/index.py?run=Pseudo) and Mouse Genome Project (Keane et al, Nature, 2011). Reads were aligned to both B6 and Cast pseudogenomes, shifted to a common set of B6-based reference coordinates, and assigned to an allele of origin based on which allele has stronger mapping. Non-specific reads with equally strong mapping to both alleles were randomly split in half into B6 and Cast groups to obtain the final reads used for allele-specific analyses. Allele-specific BAMs were converted to fragments files using Sinto for input into downstream scATAC analysis.
Hashtag processing followed the original recommendations of the ASAP-seq paper (Mimitou et al, Nature Biotech, 2021), using asap_to_kite (https://github.com/caleblareau/asap_to_kite) to process FASTQs files for downstream quantification by the bustools and kite workflows {Melsted et al, Nature Biotech 2021; Booeshagi et al, bioRxiv, 2022}. We used the HTODemux() (Stoeckius et al, Genome Biology, 2018)  function in the Seurat package (v4.0.2) (Hao et al, Cell, 2021) to remove doublets and call hashtag identities.
To enable comparisons across conditions and datasets, we used a common set of open chromatin regions throughout the study. After initially processing data mapped to a set of pan-immune cell OCRs defined by the Immgen consortium (Yoshida et al, Cell, 2019), we used iterative sub-clustering at increasing resolution in the spleen Treg/Tconv dataset, guided by the silhouette score, to group cells into “metacells” with median size of 350 cells each. We used Archr v1.0.1 (Granja et al, Nature Genetics, 2021) and MACS2 v2.2.7.1 (Zhang et al, Genome Biology, 2008) to call fixed-width peaks of 250bp within each of these subgroups of cells, merged into a final set of high-resolution peaks. We compared de novo peak calls with peaks from the Immgen cis-regulatory atlas, keeping only those Immgen peaks that overlapped at least one peak in the de novo merged peak set. In cases where new Treg-specific peaks overlapped with an existing Immgen peak, we retained the Immgen version for cross-reference compatibility. In cases where a Treg peak did not match an Immgen peak, it was added to the reference peak set. In total, our final Immgen+Treg reference OCR set consisted of 216419 peaks. Unless otherwise stated, this OCR set was used for all datasets throughout the study, with two exceptions. In the spleen and colon Treg comparisons, we re-called peaks in colon Tregs and added any missing regions to the reference peak set for that analysis. In the B6/Cast F1 analysis, to avoid missing Cast-specific peaks, we called peaks on Cast allele-specific reads and added any new regions to the peak set for F1 analyses.
Data analysis was performed using Signac v1.4 (Stuart et al, Nature Methods, 2021). For quality control, only cells with at least 1-4x103 fragments per cell (depending on sequencing depth of experiment), greater than 50 percent reads in peaks (relaxed to 30 in colon samples due to presence of colon-specific peaks), TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05 were retained for further analysis. Putative doublets identified by ArchR v1.0.1 (Granja et al, Nature Genetics, 2021) and non-Treg, non-Tconv contaminant cells were also removed. We used the latent semantic indexing approach as previously described (Cusanovich et al, Cell, 2018; Stuart et al, Cell, 2019). Binarized count matrices were normalized using the term frequency-inverse document frequency (TF-IDF) transformation and reduced in dimensionality by singular value decomposition (SVD). As the first component was highly correlated with sequencing depth, SVD components 2-30 were used to generate a shared nearest neighbor (SNN) graph for clustering and as input into UMAP (McInnes et al, ArXiv, 2018) with cosine distance metric for visualization. For visualization of B6/Cast F1 datasets, we created 2 features per OCR, one corresponding to B6-assigned reads and one corresponding to Cast-specific reads, using both versions as independent features for visualization and clustering.
Assembly: mm10
Supplementary files format and content: .mtx ATAC counts matrices, peaks.tsv files have OCR locations, barcodes.tsv files have cell barcodes
Supplementary files format and content: fragments.tsv.gz files have raw ATAC fragments, fragments.tsv.gz.tbi files are index of fragments files; Note there are 2 separate files for B6/Cast F1 experiment, each corresponding to reads assigned to either B6- or Cast- specific alleles (allele specific + 1/2 non-specific)
Supplementary files format and content: Metadata.txt files have relevant metadata, including cell population assignment, UMAP coordinates
Supplementary files format and content: Hashtag_Counts.txt files contain raw counts of ASAPseq hashtags by cell barcode for cells included in ATAC counts matrices

extract_protocol:
Treg or Tconv were sorted from mice of the appropriate genotype and desired organ, as detailed in experimental design, into DMEM + 5% FCS in DNA Lo-Bind tubes for input in to scATAC-seq/ASAP-seq as detailed in the next step.
For non-hashtagged experiments, nuclei isolation, transposition, GEM generation, and library construction targeting capture of 10000 cells were carried out as detailed in the Chromium Next GEM Single Cell ATAC manual (10x Genomics). Libraries were pooled and sequenced on an Illumina NovaSeq to a final median depth of approximately 20-30,000 paired-end reads per cell.     For experiments with multiple conditions per scATAC run, we hashtagged cells using a modification of the ASAP-seq strategy (Mimitou et al, Nature Biotech, 2021) for low cell input primary cell samples. Before sorting, cells were hashtagged with TotalSeqA DNA-barcoded hashtag antibodies at the same time as staining with fluorophore-conjugated antibodies (BioLegend). Cells were sorted into DMEM + 5% FCS in DNA Lo-Bind tubes (Eppendorf, cat # 022431021). After spinning down for 5 min at 500g in a refrigerated centrifuge at 4C, cells were resuspended in 100 μl chilled 0.1x Omni Lysis buffer (1x Omni Lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 substitute/IGEPAL, 0.01% Digitonin, 1% BSA in nuclease free water) diluted 1:10 in Wash/Lysis Dilution Buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 1% BSA in nuclease free water)), gently mixed by pipetting and incubated on ice for 6.5 min. Following lysis, 100 μl chilled wash buffer was added and gently mixed by pipetting. Cells were spun down for 5min at 500g at 4C, all but 5 μl of supernatant was removed, and 45 μl of chilled 1x nuclei buffer (10x Genomics) was added without mixing. After one more centrifugation step at 500g, 4C for 5 min, supernatant was removed, and samples were resuspended in 7ul 1x nuclei buffer for cell counting and input into transposition, barcoding, and library preparation according to the Chromium Next GEM Single Cell ATAC manual (10x Genomics).     Modifications to the original 10X protocol were made as described in the original ASAP-seq publication and as detailed at https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf. Briefly, 0.5 μl of 1uM BOA bridge oligo was spiked into the barcoding reaction. During GEM incubation, an additional 5 min incubation at 40C was added to the beginning of the protocol. 43.5 instead of 40.5 μl of Elution Solution I was added during silane bead elution to recover 43 μl. 40 μl was used for SPRI clean up as indicated in the protocol, while 3 μl was set aside. During SPRI cleanup, the supernatant was saved. The bead bound fraction was processed as in the protocol, while for the supernatant fraction, 32 μl SPRI was added for 5 min. Beads were collected on a magnet, washed twice with 80% ethanol, and eluted in 42 μl EB. This 42 μl was combined with the 3 μl set aside from the previous step as input into the HTO indexing reaction. HTO Indexing PCR was run with partial P5 and indexed Rpxx primers as: 95C 3 min, 12-14 cycles of (95C 20 sec, 60C 30 sec, 72C 20 sec), 72C 5 min. The PCR product was cleaned up with 1.6X SPRI purification for quantification and sequencing alongside ATAC libraries.

value: Treg, Tconv

value: wt

value: B6/Cast F1 Hybrid

tag: molecule subtype

value: nuclear DNA


title: scATAC_Gata3_WT_KO_Treg

value: Treg


title: WT_P_IME1_KAR4_1H

description: pIME1 pRIM4


title: 2019.9.17.3.IN: HeLa siControl (1) input rep 3

description: input for m6A-seq

value: HeLa

value: siControl KD


title: 2019.9.17.2.IN: HeLa siControl (1) input rep 2

description: input for m6A-seq


title: 2019.9.17.7.IN: HeLa siRBM8A-1 (1) input rep 1

value: siRBM8A-1 KD


title: scATAC_Spleen_Colon_Treg

source_name: Spleen, Colon

value: Spleen, Colon


title: TFH_WT #4

value: Spleen and lymph node


title: TFH_Idh2R172K/+ #3


title: TFH_WT #3


title: 2019.9.17.1.IN: HeLa siControl (1) input rep 1

description: input for m6A-seq


title: WT_P_IME1_KAR4_13H

description: pIME1 pRIM4


title: scATAC_FoxP3_WT_KO_Treg_Tconv

value: Spleen


title: WT_P_IME1_KAR4_13H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_14H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_14H_26AUG2014

description: pIME1 pRIM4


title: 3M Cre+

city: Rochester

first: Antonion

last: Korcari

state: NY

address: 142 Westminster Rd, Appartment number 914 9th floor

institute: University of Rochester Medical Center

description: 3M Cre+

data_processing:
Following library preparation and quality control (QC), libraries were sequenced using the S2 NovaSeq flow cell system (Illumina, San Diego, CA), generating an average of 65,000 reads per cell for all groups.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

source_name: FDL tendon

extract_protocol:
A total of 16 FDL tendons per group per age were pooled together into low glucose Dulmecco’s Modified Eagle Medium (DMEM) and subsequently digested in Collagenase Type I (5mg/ml) (Worthington Biochemical, Lakewood, NJ, LS004196) and Collagenase Type IV (1mg/ml) (Worthington Biochemical, Lakewood, NJ, LS004188). Young WT tendons were completely digested after two hours, while young DTR and aged C57BL/6J WT tendons after ninety minutes. After digestion, the single-cell suspension was filtered for any potential debris via a 70 μm and a 50 μm cell strainer and resuspended in Dulbecco’s Phosphate Buffer Solution (dPBS). Next, the single cell suspension was centrifuged for 10min at 500xg while being at 4°C. After removal of supernatant, the single cell suspension was resuspended in 0.5% Bovine Serum Albumin (BSA)
Libraries were prepared using a Chromium Single Cell 3 Reagent Kit (version 3, 10X Genomics, Pleasanton, CA) following the directions of the manufacturer. Cells were loaded into the kit and processed using a chromium controller (10X Genomics).

value: FDL tendon

value: Scx-Cre+; DTR F/+

value: 5 daily injections of DT


title: TFH_WT #2


title: 3M Cre-

description: 3M Cre-

value: Scx-Cre-; DTR F/+


title: WT_P_IME1_KAR4_12H_26AUG2014

description: pIME1 pRIM4


title: Short-term control non-loaded bone 3 [Q13+Q14 Left]

first: Matt

last: Prideaux

state: Indiana

address: MS5055P, 635 Barnhill Dr

department: ICMH

institute: Indiana University

description: ILMN_613_mRNAseq_STAR_featureCounts_edgeR_20191126_GEO.xlsx

data_processing:
The sequence data were mapped to the mouse reference genome mm10 using STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed with edgeR
Assembly: mouse reference genome mm10
Supplementary files format and content: excel table including raw counts, log2 fold change, p-values and FDR

source_name: Osteocyte-enriched cortical bone

extract_protocol:
RNA was harvested using ZymoResearch Direct-zol RNA MicroPrep kit. 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep kit (KK8581). Dual Index.

treatment_protocol: Mice given regular drinking water were subjected to a single bout of tibial loading at 8.25N. 24 hours after the loading bout, RNA was harvested from osteocyte-enriched cortical bone from the contralateral non-loaded (left) tibia. RNA from the left tibiae from two mice were combined to provide sufficient RNA for analysis

value: Osteocyte-enriched cortical bone

value: WT

value: Non-loaded

value: 5 days


title: Idh2R172K/+; Tet2-/- #4

source_name: Llymph node tissue

extract_protocol: Total RNA was extracted from lymph node tissue (healthy or tumoral) using Nucleospin RNAPlus kit (#740984.250, Macherey Nagel) from 7/9 months old mice.

value: Lymph node


title: Idh2R172K/+; Tet2-/- #3


title: Short-term control loaded bone 2 [Q13+Q14 Right]

treatment_protocol: Mice given regular drinking water were subjected to a single bout of tibial loading at 8.25N. 24 hours after the loading bout, RNA was harvested from osteocyte-enriched cortical bone from the loaded (right) tibia. RNA from the right tibiae from two mice were combined to provide sufficient RNA for analysis

value: 8.25 N loading


title: 21M WT

description: 21M WT


title: Short-term control loaded bone 3 [Q15+Q16 Right]


title: Short-term control non-loaded bone 2 [Q11+Q12 Left]


title: WT_P_IME1_KAR4_12H

description: pIME1 pRIM4

data_processing: Agilent Feature Extractor was used.

extract_protocol: Cells were lysed with bead beating. Phenol saturated with 0.1 M citrate was added. Lysates were incubated at 65 degrees C for 30 minutes vortexing every 5 minutes. Lysates were chilled on ice for 30 minutes. The aqueous phase was transferred and chlorofom was added. Samples were mixed lightly and centrifuged before being moved to a new tube containing sodium acetate. Samples were washed with 100% ethanol and left to incubate at -20 degrees C for 30 minutes to 16 hours. Samples were then spun at full speed for 5 minutes to pellet the RNA. Pellets were washed with 70% ethanol and pulse-spun. Remaining alcohol was aspirated and RNA was resuspending in 100 uL of water. Samples were further cleaned using the Qiagen Rneasy kit.


title: Idh2R172K/+; Tet2-/- #2


title: Short-term control loaded bone 1 [Q11+Q12  Right]


title: WT_P_IME1_KAR4_16H_26AUG2014

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_11H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_11H_26AUG2014

description: pIME1 pRIM4


title: Idh2R172K/+; Tet2-/- #1


title: Tet2-/- #4


title: TFH_WT #1


title: WT_P_IME1_KAR4_10H_26AUG2014

description: pIME1 pRIM4


title: Short-term control non-loaded bone 1 [Q9+Q10  Left]


title: Tet2-/- #3


title: WT_P_IME1_KAR4_10H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_1-5H_26AUG2014

description: pIME1 pRIM4


title: Long-term L-BAIBA non-loaded bone 3 [R15+R11 Left]

description: ILMN_429_mRNAseq_STAR_featurecounts_edgeR_20190207_GEO.xlsx

treatment_protocol: Mice given 100mg/kg L-BAIBA in their drinking water were subjected to three bouts of tibial loading at 8.25N per week for two weeks. 24 hours after the final loading bout, RNA was harvested from osteocyte-enriched cortical bone from the contralateral non-loaded (left) tibia. RNA from the left tibiae from two mice were combined to provide sufficient RNA for analysis

value: L-BAIBA non-loaded

value: 2 wks


title: Long-term L-BAIBA non-loaded bone 2 [R13+R14 Left]


title: Short-term L-BAIBA non-loaded bone 2 [Q7+Q8 Left]

treatment_protocol: Mice given 100mg/kg L-BAIBA in their drinking water for 5 days were subjected to a single bout of tibial loading at 8.25N. 24 hours after the loading bout, RNA was harvested from osteocyte-enriched cortical bone from the contralateral non-loaded (left) tibia. RNA from the left tibiae from two mice were combined to provide sufficient RNA for analysis


title: 2020.8.4.IN: HeLa siUPF1-1 (4) input rep 1

extract_protocol:
Trizol extraction of RNA
For m6A-seq and RNA-seq: Illumina Stranded Truseq. MPm6A: Custom library construction as described in methods.

value: HeLa

value: siUPF1 KD

value: input


title: WT_P_IME1_KAR4_1-5H

description: pIME1 pRIM4


title: Tet2-/- #1


title: Tet2-/- #2


title: Short-term L-BAIBA loaded bone 3 [Q7+Q8 Right]

treatment_protocol: Mice given 100mg/kg L-BAIBA in their drinking water for 5 days were subjected to a single bout of tibial loading at 8.25N. 24 hours after the loading bout, RNA was harvested from osteocyte-enriched cortical bone from the loaded (right) tibia. RNA from the right tibiae from two mice were combined to provide sufficient RNA for analysis

value: L-BAIBA & 8.25 N loading


title: Long-term L-BAIBA non-loaded bone 1 [R4+R5 Left]


title: Short-term L-BAIBA non-loaded bone 1 [Q5+Q6 Left]


title: WT_P_IME1_KAR4_0H_26AUG2014

description: pIME1 pRIM4


title: LPPC/mp LM3

value: Spleen

value: Female

value: spleenocyte

value: LPPC/mp


title: Long-term L-BAIBA loaded bone 3 [R15+R11 Right]

treatment_protocol: Mice given 100mg/kg L-BAIBA in their drinking water were subjected to three bouts of tibial loading at 8.25N per week for two weeks. 24 hours after the final loading bout, RNA was harvested from osteocyte-enriched cortical bone from the loaded (right) tibia. RNA from the right tibiae from two mice were combined to provide sufficient RNA for analysis


title: Idh2R172K/+ #4


title: Long-term L-BAIBA loaded bone 2 [R13+R14 Right]


title: Short-term L-BAIBA loaded bone 1 [Q1+Q2 Right]


title: Short-term L-BAIBA loaded bone 2 [Q5+Q6 Right]


title: Idh2R172K/+ #3


title: Long-term L-BAIBA loaded bone 1 [R4+R5 Right]


title: WT_P_IME1_KAR4_0H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_0-5H

description: pIME1 pRIM4


title: WT_P_IME1_KAR4_0-5H_26AUG2014

description: pIME1 pRIM4


title: Idh2R172K/+ #2


title: Long-term control non-loaded bone 3 [R12+R16 Left]

treatment_protocol: Mice given regular drinking water were subjected to three bouts of tibial loading at 8.25N per week for two weeks. 24 hours after the final loading bout, RNA was harvested from osteocyte-enriched cortical bone from the contralateral non-loaded (left) tibia. RNA from the left tibiae from two mice were combined to provide sufficient RNA for analysis


title: Idh2R172K/+ #1


title: Long-term control non-loaded bone 2 [R9+R10 Left]


title: starvation 2

description: pIME1 pRIM4


title: WT #4


title: WT, aorta, control

city: Houston

first: Yanming

last: Li

state: TX

address: One Baylor Plaza

department: Michael E. DeBakey Department of Surgery

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The raw fastq data for each sample were submitted to Cell Ranger ATAC for read filtering and alignment, barcode counting, identification of transposase cut sites, detection of accessible chromatin peaks, and cell calling by using “cellranger-atac count.”
Assembly: mm10
Supplementary files format and content: hd5 file with peak matrics
Supplementary files format and content: tsv.gz file with fragments

source_name: ascending aorta

extract_protocol:
Single-nuclei suspensions were prepared according to the manufacturer’s instructions (10x Genomics). Nuclei were loaded with a capture target of 10,000 nuclei per sample.
ScATAC-seq libraries were prepared for sequencing according to the 10x Genomics scATAC-seq solution protocol. ScATAC-seq libraries were sequenced by using PE150 sequencing on an Illumina NovaSeq with a target depth of 25,000 reads per nucleus.

treatment_protocol: Four-week-old male WT mice were fed with a high fat diet (HFD) for 8 weeks and AngII infusion during the last 4 weeks through an osmotic minipump were used to challenge the mice inducing aortic aneurysm and dissection. Mice fed a standard rodent laboratory diet for 8 weeks and infused with saline during the last 4 weeks were used as controls. We collected ascending aortic tissues after 7 days of AngII infusion for sc-ATACseq to capture the early response to aortic stress.

value: ascending aorta

value: aortic cells

value: control


title: WT, aorta, challenged

description: 10x Genomics

value: WT

value: HFD and AngII infusion


title: starvation 3

description: pIME1 pRIM4

source_name: WT


title: KELLY_SOX11

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description: SOX11 viewpoint

data_processing:
Sequencing reads from the 4C library were demultiplexed using the demultiplex.py script (https://gist.github.com/meren/7632184) and aligned using bowtie2 (v.2.3.1). For the cis chromosome, mapped read counts were summarized per DpnII restriction fragment.
4C coverage profiles were obtained by normalizing the per fragment coverage to reads per million (RPM) on the cis chromosome and smoothing the normalized coverage using the rollmean function from the R ‘zoo’ package with a window size of 21 fragments. For visualization purposes, the viewpoint was removed (chr2:58210000-4835000) and the plot was generated using R package Sushi (v1.32.0) with normalized bedgraph files. Interaction peaks were called on the raw fragment count data using the peakC R package33. Settings and parameters were: “single analysis”, window=2e6, vp.pos= 5834393 (SOX11), minDist=15e3, wSize=21, qWd=2, qWr=2.
Assembly: hg19
Supplementary files format and content: Normalized bedgraph files
Library strategy: 4C-Sequencing

source_name: bone marrow

growth_protocol: Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2mM L-Glutamine and 100 IU/ml penicillin/streptaviding at 37°C in a 5% CO2 humid atmosphere.

extract_protocol:
107 separated single cells that were cross-linked with 2% formaldehyde for 10 min at room temperature, cells were lysed. Cross-linked DNA was digested was digested using 200U of NlaIII (NEB #R0125S) as primary restriction enzyme. This was followed by proximity ligation using 50U of T4 DNA ligase (Roche #10799009001) and ligated DNA circles were de-cross-links overnight using proteinase K and purified with NucleoMag P-Beads (Macherey-Nagel, Düren, Germany) to obtain an intermediate 3C template. To generate the 4C template, DNA was redigested using 50U DpnII (NEB #0543S) as secondary antibody followed again by proximity ligation. Digestion and ligation efficiency were evaluated via agarose gel electrophoresis.
Adaptor-containing reading and non-reading primers, specific to the viewpoints of interest, were designed to amplify all captured, interacting DNA fragments (SOX11 viewpoint reading = CCACCAAAATTTTCATCATG and non-reading = TCTTCTATGCATCCGATTCT; without adapter sequence). 4C-sequencing fragments were amplified using the Expand Long Template PCR System (Roche, 11681834001) and using High Pure PCR Product Purification kit (Roche #11732676001) and QIAquick PCR Purification kit (Qiagen #28106). Sequencing was performed on the NextSeq 500 platform (single-end, 75 nt, loading concentration 1.6 pM).

treatment_protocol: Cells were not treated.

value: bone marrow

value: KELLY

value: neuroblast

value: wild type


title: SMC-Yap1KO, aorta, AngII

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Samples of ascending aorta were harvested from  mice (n=3) and were pooled in Hanks’ Balanced Salt Solution (HBSS, #14175095, Thermo Fisher Scientific, Waltham, MA) with 10% fetal bovine serum. Extra-aortic tissues, such as periaortic fat, were removed, and the aortic tissues were cut into small pieces and incubated with enzyme cocktail in HBSS containing Ca2+/Mg2+ (#14025092, Thermo Fisher) for 60 minutes at 37 °C. The cell suspension was filtered through a 40-μm cell strainer (CLS431750-50EA, Sigma-Aldrich), centrifuged at 350 g for 5 minutes, and resuspended by using cold HBSS (#14175095) with fetal bovine serum (5% vol/vol). Cells were stained with 4′, 6-diamidino-2-phenylindole (DAPI) and were sorted to select viable cells (≥95% viability) by using flow cytometry (FACS Aria III, BD Biosciences, Franklin Lakes, NJ).
Single-cell suspensions were dispensed separately onto the Chromium Controller (10x Genomics, Pleasanton, CA) with a target of 10,000 cells/sample. The scRNA-seq library was constructed by using the Chromium Single-Cell 3′ v3 Reagent Kit (10x Genomics). Cells were mixed with barcoded primer-linked gel beads. Each cell was barcoded with a unique index, and every transcript within a single cell was barcoded with a unique molecular identifier (UMI). cDNAs were pooled, truncated, and amplified to generate cDNA libraries that were sequenced using a Next Generation sequencer NovaSeq 6000 (Illumina, Inc., San Diego, CA) in a pair-end fashion to obtain more than 80,000 reads per cell.

treatment_protocol: To study mice with the SMC-specific deletion of Yap, we used four-week-old male Yap1f/f; Myh11-CreERT2+ mice in which the Cre allele was inserted into the Y chromosome (X/YCre+). When the mice were 6 weeks old, they were given 2 mg/day intraperitoneal injections of tamoxifen (Sigma T-5648) for 5 consecutive days to induce the SMC-specific deletion of Yap (SMC-Yap-/-). Littermates of Yap1f/f; Myh11-CreERT2+ mice injected with corn oil (vehicle) were used as a control (SMC-Yap+/+). After the last injection, the mice were rested for 7 days for Cre recombination. Eight-week-old male SMC-Yap-/- or SMC-Yap+/+ mice were infused with either saline or a low-rate of AngII infusion (1000 ng/kg/min) for 4 weeks and fed with either a standard rodent laboratory diet or HFD. We collected aortic tissues after 7 days of AngII infusion for sc-RNAseq to capture the early response to aortic stress

value: SMC-specific Yap1-KO

value: AngII infusion


title: Long-term control non-loaded bone 1 [R1+R2 Left]

value: Osteocyte-enriched cortical bone

value: Non-loaded

value: 2 wks


title: WT #3

value: Lymph node


title: Long-term control loaded bone 3 [R9+R10 Right]

treatment_protocol: Mice given regular drinking water were subjected to three bouts of tibial loading at 8.25N per week for two weeks. 24 hours after the final loading bout, RNA was harvested from osteocyte-enriched cortical bone from the loaded (right) tibia. RNA from the right tibiae from two mice were combined to provide sufficient RNA for analysis

value: 8.25 N loading


title: CLBGA_SOX11

description: SOX11 viewpoint

source_name: brain

value: brain

value: CLB-GA


title: WT #2


title: SHEP_SOX11

description: SOX11 viewpoint

value: SH-EP


title: Long-term control loaded bone 2 [R3+R7 Right]


title: WT, aorta, AngII

description: 10x Genomics

value: ascending aorta

value: aortic cells


title: WT, aorta, Saline

description: 10x Genomics

value: WT

value: Saline infusion


title: Long-term control loaded bone 1 [R1+R2 Right]


title: SKNAS_SOX11

description: SOX11 viewpoint

value: bone marrow

value: SK-N-AS


title: WT #1


title: Heart, Dexmedetomidine preconditioning, rep 3 (DIR3)

city: Guangzhou

first: Zhaorong

last: Chen

address: Zhongshan Er Road

institute: Sun yat-sen University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore.py on Python.
Trimmed sequence reads were mapped to mm9 using star2.pl on Perl.
Read count extraction and normalization were performed using htseq-count.pl on Perl.
RPKM values were generated using counts2rpkm.pl on Perl.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: heart

extract_protocol:
A total amount of 1 µg RNA per sample was obtained. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol:
Mice were subjected to myocardial ischemia/reperfusion (I/R, 30 min/120 min).
IR group: vehicle of Yohimbine and vehicle of Dexmedetomidine was administrated separately before IR surgery.
DIR group: vehicle of Yohimbine was injected 30 min before 10 µg/kg Dexmedetomidine administration and IR surgery was performed 20 min after Dexmedetomidine administration.
All drugs were slowly infused via caudal vein within 10 min.
Apical tissues were harvested for mRNA sequencing. Each group contained 3 samples.

value: heart

value: Dexmedetomidine preconditioning


title: IgG_CLBGA

data_processing:
Prior to mapping to the human reference genome (GRCh37/hg19) with bowtie2, quality of the raw sequencing data of CUT&RUN-seq was evaluated using FastQC. Quality of aligned reads were filtered using min MAPQ 30 and reads with known low sequencing confidence were removed using Encode Blacklist regions
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize 10 and normalizeUsing RPKM. Peak calling was performed using MACS2 taking a q value of 0.05 as threshold.
Library strategy: CUT&RUN

extract_protocol:
0.5M cells were harvested for CUT&RUN. CUT&RUN was performed using Cutana pA/G-MNase (Epicypher, 15-1016) according to the manufacturer’s protocol. Retrieved genomic DNA was purified with the MinElute PCR purification kit and eluted in 10 mL of buffer EB.
Sequencing libraries were prepared with the automated Swift 2S system. CUTandRun libraries were sequenced on NextSeq 500 High Output Kit V2.5, 75 cycli.

value: neuroblast

value: wild type


title: T05 (single)

city: Yinchuan

first: Meng

last: Zhu

address: 1160 Shengli Street

institute: Ningxia Medical University

data_processing:
Illumina Casava 1.7 software used for base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome reference build GRCh38 with Bowtie v0.12.2 software.
Framents Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Stingtie v1.2.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Gastric cancer

extract_protocol:
Total RNA was extracted from fresh frozen tissues using TRIzol reagent (Invitrogen, Waltham, MA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Clinical specimens (1×1cm2) were resected within ten minutes after isolation of the stomach and rapidly put into liquid nitrogen after washing with saline to remove blood traces.

value: Gastric cancer

value: RNA extraction


title: CTCF_CLBGA

value: CTCF Merck 07-729


title: Heart, Dexmedetomidine preconditioning, rep 2 (DIR2)


title: SHEP

data_processing:
Prior to mapping to the human reference genome (GRCh37/hg19) with bowtie2, quality of the raw sequencing data of ATAC-seq was evaluated using FastQC and adapter trimming was done using TrimGalore. Quality of aligned reads were filtered using min MAPQ 30 and reads with known low sequencing confidence were removed using Encode Blacklist regions.
Assembly: hg19
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize 10 and normalizeUsing RPKM.

growth_protocol: Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37°C in a 5% CO2 humid atmosphere, supplemented with 10% tetracyclin-free FBS to avoid leakage.

extract_protocol:
50,000 cells were harvested and spin down for 5 min at 800g. ATAC-seq was performed as previously described with minor changes (Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Nextera DNA Library Prep Kit, cat#FC-121-1030)). Samples were purified using the DNA clean & concentrator kit from Zymo (cat#D4013).
The transposased DNA fragments were amplified using the KAPA HiFi HotStart Readymix (cat#07 958 927 001) and purified using Agencourt AMPure XP beads (Beckmamn Coulter, cat#A63881). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat#KK4854). ATAC-seq libraries were sequenced on the NextSeq 500 platform (Illumina) using the Nextseq 500 High Output kit V2 75 or 150 cycles (Illumina).


title: Heart, Dexmedetomidine preconditioning, rep 1 (DIR1)


title: N04 (single)

source_name: Adjacent tissue

value: Adjacent tissue


title: CLBGA

value: brain


title: T04 (single)


title: IMR32


title: Heart, vehicle preconditioning, rep 3 (IR3)

value: vehicle preconditioning


title: SMC-Yap1KO, aorta, Saline

description: 10x Genomics

value: SMC-specific Yap1-KO


title: Heart, vehicle preconditioning, rep 2 (IR2)


title: N03 (single)


title: quiescent 6h GDF11 R2 2020

city: Stuttgart

first: Stefan

last: Legewie

address: Allmandring 30E

department: Institute of Biomedical Genetics, Systems Biology

country: Germany

institute: University of Stuttgart

description:
DEseq_quiescent_6h_GDF11_vs_quiescent_ctrl.csv
rpkm_quiescent_GDF11.csv

data_processing:
Samples were demultiplexed (bcl2fastq v.2.19.1.403, Illumina) and FastQ files were generated.
Raw sequence reads were assessed with FastQC (v.0.11.5, Babraham Bioinformatics) and aligned to the human reference genome GRCh38.p7 (GTF annotation file from Gencode human release 25) using STAR aligner v.2.5.2b (3).
Mapped data were summarized on the gene level using the featureCounts software (v.1.6.2, Subread) (4). Further data evaluation, normalization and pairwise differential expression analyses were carried out in R (v.3.5.0) using the Bioconductor package DESeq2 (v.1.20.0) following the recommended analysis workflow (5).
To calculate the robust reads per kilobase of transcript per million mapped reads (RPKMs) for each gene, the Bioconductor
packages GenomicRanges (v.1.32.1) and (v.1.40.6) with the above mentioned GTF annotation file and robust fragments per million (FPM) data computed by DESeq2 were used (6, 7).
To calculate fold changes, this package uses a maximum likelihood model with the assumption of a negative binomial distribution of reads fitted to the read counts of all samples available for a given combination of conditions.
Additionally, based on those models, p-values were calculated for each fold change that refer to the differential expression compared to a reference condition
Assembly: human reference genome GRCh38.p7 (GTF annotation file from Gencode human release 25)
Supplementary files format and content: csv files include RPKM values for each Sample or fold-changes and BH adjusted p-Values

growth_protocol: MCF10A cell lines were cultured in DMEM/F12 growth-medium.  When required, the medium was supplemented with selective antibiotics to maintain transgene expression (400 μg/ml geneticin disulphate (G418, ROTH), 50 μg/ml hygromycin B (Thermo Fisher Scientific) or 5 μg/ml blasticidin S hydrochloride (ROTH))

extract_protocol:
Total RNA was isolated from the cells using the High Pure RNA Isolation Kit by Roche according to the manufacturer‘s instruction.
TruSeq stranded mRNA LT Sample Prep Kit (Illumina) was used according to the manufacturer’s instructions. Libraries were prepared with a starting amount of 500 ng RNA, amplified in 11 PCR cycles, and profiled using a DNA 1000 kit and a 2100 Bioanalyzer (both Agilent)
Afterwards, the libraries were quantified in a Qubit 2.0 Fluorometer using the dsDNA HS Assay Kit (both Thermo Fisher). All libraries were pooled in equimolar ratios and sequenced on the NextSeq 500 sequencing system (Illumina)

value: epithelial cell

value: 10 nM GDF11

tag: cell state

value: quiescent


title: quiescent 6h GDF11 R1 2020


title: N02 (single)

tag: tissue

value: WT


title: proliferating 6h TGFB R3 2018

description:
DEseq_proliferating_6h_TGFB_vs_proliferating_ctrl.csv
rpkm_proliferating_TGFB.csv

value: 100 pM TGFb

value: proliferating


title: Heart, vehicle preconditioning, rep 1 (IR1)

tag: genotype

value: heart


title: T02 (single)


title: N01 (single)


title: N05 (single)


title: control mouse testis (wild type) [957J]

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

data_processing:
Reads of murine mRNA were aligned to GRCh38.p10 Gencode release using HISAT2 2.0.5.
Aligned reads present within adequate GENCODE gene annotation regions were counted using featureCounts.
Count data were analyzed obtained using featureCounts.
Data were normalized using DESeq2 in R programming environment.
Assembly: mm10
Supplementary files format and content: One processed data txt file with read counts (Counts_genocode_vM13_MOlszewska_220622.txt) and one with normalized signals (Normalized_RNA_220622.txt) for all samples.

source_name: testis

extract_protocol:
RNA was extracted using RNeasy AllPrep kit (Qiagen, Hilden, Germany).
Sequencing libraries of testis tissues were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) and sequenced on an Illumina NovaSeq6000 platform.
Paired end 100bp RNA sequencing.

value: testis

value: male


title: proliferating 6h TGFB R2 2018


title: proliferating 6h TGFB R1 2018


title: starvation 1

city: DC

first: Zachory

last: Park

address: 37th and O Streets NW

institute: Georgetown University

description: pIME1 pRIM4

tag: strain


title: T01 (single)


title: heterozygous mouse testis (Tcte1+/-) [1190J]


title: control mouse testis (wild type) [956J]

value: wild type


title: N05 (paired-end)


title: quiescent 3h GDF11 R2 2020

description:
DEseq_quiescent_3h_GDF11_vs_quiescent_ctrl.csv
rpkm_quiescent_GDF11.csv

tag: cell type


title: heterozygous mouse testis (Tcte1+/-) [950J]


title: quiescent 3h GDF11 R1 2020

tag: treatment


title: heterozygous mouse testis (Tcte1+/-) [927J]


title: T05 (paired-end)

value: Gastric cancer


title: N04 (paired-end)

value: RNA extraction


title: proliferating 6h TGFB low R3 2018

description:
DEseq_proliferating_6h_TGFB_low_vs_proliferating_ctrl.csv
rpkm_proliferating_TGFB.csv

value: 2.5 pM TGFb

tag: time


title: T03 (single)


title: proliferating 6h TGFB low R2 2018

tag: cell line


title: heterozygous mouse testis (Tcte1+/-) [925J]


title: T04 (paired-end)


title: 9-mo AD-CD11c- rep2

city: Chongqing

first: Yiguo

last: Qiu

state: Chongqing

address: 13 Tianchi Road, Banan Distri

institute: Chongqing International Institute for Immunology

data_processing:
After reviewing the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome (ENSEMBL) using STAR aligner v.2.5.2b, a splice aligner that detects and incorporates splice junctions to align the entire read sequences.
BAM files were generated, and unique gene hit counts were calculated using Counts (Subread package v.1.5.2).
Only unique reads that fell within exon regions were counted. Differential expression was considered significant with an FDR-adjusted p value < 0.05.
Genome_build: Mus musculus reference genome (ENSEMBL)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: microglia

extract_protocol:
Total RNA was extracted from FACS-sorted cell pellets using RNeasy Plus Universal Mini Kit, according to manufacturer’s instructions (QIAGEN).
Microglial samples of 9-mo old 5XFAD and OPN-KO.5XFAD mice were processed with SMART-Seq v4 Ultra Low Input Kit for Sequencing for full-length cDNA synthesis and amplification (Clontech, Mountain View, CA), and Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add index to the cDNA fragments. The final library was assessed with Agilent TapeStation.

tag: strain/genotype


title: 9-mo AD-CD11c- rep1


title: control mouse testis (wild type) [959J]


title: N03 (paired-end)

value: Adjacent tissue


title: 9-mo OPNKOAD-CD11c+ rep2

value: brain


title: proliferating 6h TGFB low R1 2018


title: homozygous mouse testis (Tcte1-/-) [1328J]


title: T03 (paired-end)


title: 9-mo OPNKOAD-CD11c+ rep1


title: homozygous mouse testis (Tcte1-/-) [1006J]


title: quiescent 3h TGFB R2 2020

description:
DEseq_quiescent_3h_TGFB_vs_quiescent_ctrl.csv
rpkm_quiescent_TGFB.csv


title: N02 (paired-end)


title: 9-mo AD-CD11c+ rep2


title: quiescent 3h TGFB R1 2020


title: homozygous mouse testis (Tcte1-/-) [1003J]


title: proliferating 3h TGFB low R3 2018

description:
DEseq_proliferating_3h_TGFB_low_vs_proliferating_ctrl.csv
rpkm_proliferating_TGFB.csv


title: T02 (paired-end)


title: proliferating 3h TGFB low R2 2018


title: N01 (paired-end)


title: DH1- Vismodegib treated tumor sample rep2

city: Birmingham

first: Dongquan

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

description:
DH1- Vismodegib treated tumor sample
Tumor_results-gene_reads.txt
Tumor_results-gene_reads_rpkm.txt

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software, (.bcl files) generated from Illumina HiSeq was converted into FASTQ FASTQ files were de-multiplexed using Illumina's bcl2fastq 2.17 software
Sequence reads in fastq format were trimmed at each end of reads using read quality score vendor sequencing adaptors removed, and reads aligned against mouse mm10 genome  using STAR algorithm
Adaptor sequences were removed using Cutadapt tool before alignment HISAT2 algorithm.  Reads Per Kilobase of transcript per million mapped reads (RPKM) methods were  applied for normalization after PCR replicates were removed using SAMtools.  Gene level quantification and statistics were performed using Partek Genomic Suite (PGS, St Louis, MO).
Genome_build: mm10

source_name: mammary tumors (Balb/c 4T1 model)

growth_protocol: 4T1 Cells were maintained in culture in DMEM F12 supplemented with 10% FBS

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA was then sent to GENEWIZ for sample anaylsis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 500,000 4T1 cells were injected into the inguinal mammary fat pat of Balb/c mice. After tumor establishment, mice were treated with either DMSO (Vehicle control) or Vismodegib (2mg per mouse) 3 times weekly for 3 weeks

value: Balb/c

value: Mammary Tumor

value: 10 week old mice

value: Vismodegib (2mg)


title: DH1- Vismodegib treated tumor sample rep1


title: proliferating 3h TGFB low R1 2018

value: epithelial cell


title: quiescent ctrl R2 2020

description:
DEseq_quiescent_6h_GDF11_vs_quiescent_ctrl.csv
rpkm_quiescent_ctrl.csv

value: quiescent


title: Placenta, Atp11a, WT, 7d

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 to obtain ~33M reads per sample.
Library quality was assessed with FASTQC and visualized in Seqmonk.
Reads were then aligned with STAR using the GrCM38/mm10 build.
Count tables were assembled with htseq-count using the reverse strand and intersection-nonempty settings
Assembly: mm10
Supplementary files format and content: Tab delimited raw counts are provided for all samples

source_name: Placenta

growth_protocol: Whole placentas were dissected at E14.5, frozen in liquid nitrogen and stored at -80 until sample processing.

extract_protocol:
Total RNA was isolated from E14.5 frozen placentas with the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol.
Libraries were constructed with the NEB Ultra II Directional RNA Library Prep, using poly-A capture for mRNA enrichment.

treatment_protocol: 6-11 placentas per genotype (WT,HET,KO)  in each mutant mouse line were selected for RNAseq analysis

value: Placenta

tag: mouse line

value: WT

tag: litter


title: Placenta, Atp11a, WT, 4g

tag: age


title: DH2- DMSO treated tumor sample rep2

description:
DH2- DMSO treated tumor sample
Tumor_results-gene_reads.txt
Tumor_results-gene_reads_rpkm.txt

value: DMSO


title: Placenta, Atp11a, WT, 6h


title: Placenta, Atp11a, WT, 3e


title: homozygous mouse testis (Tcte1-/-) [1270J]

value: testis


title: DH2- DMSO treated tumor sample rep1


title: Placenta, Atp11a, WT, 1h


title: quiescent 6h TGFB R2 2020

description:
DEseq_quiescent_6h_TGFB_vs_quiescent_ctrl.csv
rpkm_quiescent_TGFB.csv

value: 100 pM TGFb


title: quiescent ctrl R1 2020


title: 9-mo AD-CD11c+ rep1


title: quiescent 6h TGFB R1 2020


title: proliferating ctrl R3 2018

description:
DEseq_proliferating_6h_TGFB_vs_proliferating_ctrl.csv
rpkm_proliferating_ctrl.csv

value: proliferating


title: Placenta, Atp11a, WT, 1f


title: Damage-seq of BPDE-dG: 2 uM BPDE exposed genomic DNA from BEAS-2B cells rep 2

city: Zürich

first: Shana

last: Sturla

state: No

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zürich

description:
NGS9665
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

data_processing:
Filteration of common adaptor contaminations and non-specific reads using BBMap v38.9.
The paired-end reads were mapped to the reference human genome hg38 using Burrows-Wheeler Aligner v0.7.17.
Deduplication using Picard tools v2.25.3.
Identify damage sites using customized scripts.
Normalization of damage level using size factor calculated by DESeq2 (Bioconductor 3.1.2).
Assembly: hg38
Supplementary files format and content: bigwig, normalized damage level along genome.
Supplementary files format and content: bigwig, mean of normalized damage level along genome calculated from biological triplicates.
Library strategy: Damage-seq

growth_protocol: BEAS-2B cells were cultured in BEGM Bronchial Epithelial Cell Growth Medium Bullet Kit (Lonza, Basel, Switzerland) at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Genomic DNA extracted from BEAS-2B cells was fragmented and ligated with customized adapter 1 using NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched using an anti-BPDE antibody and the damage site was marked by polymerase stalling using NEBNext Ultra II Q5 polymerase. Non-specific DNA fragments were removed using subtractive hybridization and the resulting DNA product was subjected to adapter 2 ligation. The ligation product were indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

treatment_protocol: BEAS-2B cells grown in 10 cm dishes were exposed to (+)-anti-BPDE (0.25–2 μM) for 24 h. Negative control cells were exposed to 0.1% solvent (anhydrous tetrahydrofuran/5% triethylamine).

value: lung cell line

value: wild type

value: exposed to 2 uM BPDE


title: Damage-seq of BPDE-dG: 2 uM BPDE exposed BEAS-2B cells rep 2

description:
NGS10100
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: Damage-seq of BPDE-dG: 2 uM BPDE exposed genomic DNA from BEAS-2B cells rep 1

description:
NGS9664
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: Damage-seq of BPDE-dG: 2 uM BPDE exposed BEAS-2B cells rep 3

description:
NGS10101
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: T01 (paired-end)

value: Gastric cancer

value: RNA extraction


title: Placenta, Atp11a, HOM, 4a

value: KO