title: miRNA-seq_76.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: WJL3307_RLF_N029_JoinT

status: Public on Dec 31 2023

type: SRA

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Library strategy: LAM-HTGTS (linear amplification mediated high-throughput genomic translocations sequencing)
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

molecule: genomic DNA

organism: Mus musculus

source_name: vAbl-ProB

growth_protocol: vAbl ProB cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h. Indicated inhibitors were added to some of the samples the same day as STI-571.

tag: cell line

value: vAbl-ProB

tag: cell type

value: pro-B cells

tag: genotype

value: WT

tag: treatment

value: Polαi #1

tag: total reads


title: WJL3299_RLF_N029_JoinT


title: WJL3297_RLF_N029_JoinT


title: WT 50

city: Bethesda

first: David

middle: A

last: Talmage

state: MD

address: 35 Convent Dr, Room 3B-101

department: NINDS

institute: National Institutes of Health

description:
Sequencing batch 1
VV50

library_source: transcriptomic

data_processing:
QC inspection using FastQC, MultiQC, and Fastx_Screen
Adaptor sequences clipped, low quality and/or nucleotide biased positions in sequences were trimmed using Trimmomatic and QC was repeated
Alignment to ref. genome using HISAT2 and QC of alignment using RSeqC
Transcript assembly using StringTie, QC using gffcompare
Gene and isoform level enumeration using IsoformSwitchAnalyzeR
within sample normalization (cpm), cross-sample normalization CyclicLowess, PCA for outlier detection
Sequence batch correction using Limma, filter and floor values to 2.25
ANCOVA for differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: Gene level enumeration text file, ANCOVA adjusted expression text file

molecule: polyA RNA

source_name: Dentate Gyrus

extract_protocol:
Rneasy Micro Kit (Qiagen)
NEBNext Library Prep Kit

tag: strain

tag: tissue

value: Dentate Gyrus

tag: Sex

value: Male

tag: age

value: postnatal day 70


title: miRNA-seq_75.P

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 (Andrews 2010) and multiQC v1.10 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v3.3 (Martin 2011) and filtered for a minimum length of 17nt.
Mapping steps were performed with bowtie v1.3.0 (Langmead et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012), whereas reads were mapped first against the genomic reference GRCm38.p6 provided by Ensembl (Zerbino et al. 2018) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004), filtered for miRNAs of mmu only, allowing for one mismatch.
Assembly: GRCm39 Assembly GCA_000001635.9; miRBase v22.1
Supplementary files format and content: XLS file containing read counts of miRDeep2 mapped miRNAs

molecule: total RNA

source_name: Peritubular capillaries, biol rep 3

extract_protocol: Realseq Libaray preperation kit according to manufacturer's specification

value: Kidney

value: male

tag: laser microdissected

value: Yes

tag: microvascular compartment

tag: disease state

value: Sham-operated

tag: time


title: WJL3296_RLF_N029_JoinT


title: RNA-seq FL bud E10-E10.25 Hand2_WT replicate 2

city: Basel

first: Aimee

last: Zuniga

address: Mattenstrasse, 28 4058

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Total RNA extracted from forelimb buds of wild-type mouse (Prrx1-Cre;Hand2+/+) at E10-10.25 stage

data_processing:
Raw single-end sequencing reads of 85bp read length from Tbx3 and Hand2 samples of mouse forelimb buds were subjected to quality check using FastQC v0.11.4 (FastQC: a quality control tool for high throughput sequence data)
High-quality sequencing reads were aligned on reference genome and transcriptome (ensembl release-91) of mouse (mm10) using a fast accurate aligner STAR v2.5.2 (Dobin A et al., 2012).
Subsequently, rsem-calculate-expression utility of RSEM v1.3.0 (Li, Bo, and Colin N. Dewey, 2011) was used to quantify expression levels of genes and transcripts across all the samples.
Genome_build: mm10
Supplementary_files_format_and_content: .txt, rsem quantifications

source_name: forelimb buds

extract_protocol:
Samples were defrosted and total RNA extracted using QIAGEN RNeasy kit according to manufactures instructions. The RNA quality was evaluated using the Fragment Analyzer in combination with the High Sensitivity RNA Analysis kit (Advanced Analytical). Only samples with a RIN ≥8.0 were used for library construction.
RNA-seq libraries were constructed using the using the Clontech SMARTer kit and 85bp single end reads were sequenced on the Illumina NextSeq 500.

treatment_protocol: For both Hand2 and Tbx3 samples, three replicates were analyzed per genotype. One replicate consists of one pair of forelimb buds, which were flash frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: Swiss albino

value: forelimb buds

tag: developmental stage


title: RNA-seq FL bud E10-E10.25 Hand2_WT replicate 3


title: WJL3298_RLF_N029_JoinT


title: WJL3295_RLF_N029_JoinT


title: WJL3293_RLF_N029_JoinT


title: RNA-seq FL bud E10-E10.25 Hand2_WT replicate 1

description: Total RNA extracted from forelimb buds of wild-type mouse (Prrx1-Cre;Hand2+/+)  at E10-10.25 stage


title: miRNA-seq_19.P

source_name: Peritubular capillaries, biol rep 2


title: WJL3304_RLF_N029_JoinT


title: WJL3294_RLF_N029_JoinT


title: miRNA-seq_17.P

source_name: Peritubular capillaries, biol rep 1


title: WJL3291_RLF_N029_JoinT


title: miRNA-seq_76.G

source_name: Glomeruli, biol rep 4

value: Glomeruli


title: WJL3292_RLF_N029_JoinT


title: miRNA-seq_17.V

source_name: Post-capillary venules, biol rep 1

value: Post-capillary venules


title: WJL3289_RLF_N029_JoinT


title: RNA-seq FL bud E9.75-E10 Tbx3_del replicate 2

description: Total RNA extracted from forelimb buds of Tbx3-deficient mouse (Tbx3ΔVenus/ΔVenus) at E9.75-10.0 stage. In the Tbx3ΔVenus allele (PMID:25343378, mice provided by V.M. Christoffels and A.M. Pieterson), a Venus reporter gene, transcription termination and polyadenylation sequence were inserted at the start codon, which drives Venus expression in all Tbx3-expressing cells and disrupts endogenous Tbx3 expression.


title: miRNA-seq_75.G

source_name: Glomeruli, biol rep 3


title: WJL3287_RLF_N029_JoinT

value: ATMi


title: RNA-seq FL bud E9.75-E10 Tbx3_del replicate 1


title: WJL3286_RLF_N029_JoinT


title: RNA-seq FL bud E9.75-E10 Tbx3_WT replicate 3

description: Total RNA extracted from forelimb buds of wild-type mouse at E9.75-10.0 stage


title: WJL3285_RLF_N029_JoinT


title: miRNA-seq_17.G

source_name: Glomeruli, biol rep 1


title: WJL3284_RLF_N029_JoinT

value: CTR


title: WJL3283_RLF_N029_JoinT

value: vAbl-ProB


title: miRNA-seq_19.G

source_name: Glomeruli, biol rep 2


title: RNA-seq FL bud E10-E10.25 Hand2_del replicate 2

description: Total RNA extracted from forelimb buds of Hand2-deficient mouse (Prrx1-Cre;Hand2Δ/Δc) at E10-10.25 stage.


title: WJL3282_RLF_N029_JoinT

value: pro-B cells


title: RNA-seq FL bud E9.75-E10 Tbx3_WT replicate 1

value: WT


title: WJL3281_RLF_N029_JoinT


title: WJL3280_RLF_N029_JoinT


title: Input Tbx3 FL bud E9.75-E10.25 replicate 2

description: Input for Tbx3 ChIP-seq at E9.75-E10.25 (28-32 somites)

data_processing:
High quality reads for Tbx3 samples were aligned on mm10 reference using Bowtie v2.2.9.
Mapped reads were filtered for duplicates using Picard (BroadInstitute 2015). Filtered bam files were subsequently sorted and indexed using Samtools (Li et al., 2009).
Peaks were called using Masc2 (Zhang et al. 2008) with settings  -g mm -p 1e-3 --nomodel --extsize --call-summits -B --SPMR.
Evidences from these replicates were combined using MSPC (PMID: 25957351) with -r biological -s 1E-5 -W 1E-2 settings.
Normalized profiles were generated in wig/bigWig format to visualize on UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files to visualize signal; bigBed files with called peak regions.

extract_protocol:
The protein/DNA complexes were eluted using an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 65oC overnight. Samples were treated for 15 min RT with RNase A and then with Proteinase K for one hour at 56oC. Finally, the DNA was purified using MicroChip Diapure columns (Diagenode).
Libraries were prepared using MicroPlex Library preparation kit V2 (Diagenode) according to the manufactures instructions and 80 bp paired-end reads were sequenced using the Illumina Nextseq 500.

treatment_protocol: Chromatin immunoprecipitation was performed as previously described (PMID: 27974206): Two replicates were generated and analysed: Per replicate 70 Tbx33XF/3XF forelimb buds were cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain DNA fragments with an average size ranging between 100-600 bp. Protein A and G Dynabeads (Invitrogen 10001D, 10003D) were incubated overnight at 4oC with 5µg with 5 µg of anti-flagM2 antibody. Subsequently, the sonicated chromatin complexes were incubated with the M2 anti-FLAG antibodies coupled to beads overnight at 4oC. The immuno-complexes were then sequentially washed to remove non-specific complexes.

tag: chip antibody


title: RNA-seq FL bud E9.75-E10 Tbx3_del replicate 3


title: WJL3279_RLF_N029_JoinT


title: miRNA-seq_19.A

source_name: Arterioles, biol rep 2

value: Arterioles


title: ChIP Tbx3 FL bud E9.75-E10.25 replicate 2

description: For Tbx3 ChIP-seq, a 3XFlag epitope tag was inserted into the carboxy-terminal end of the endogenous Tbx3 coding region.

value: Mouse monoclonal M2 anti-FLAG antibodies (Sigma, F1804)


title: WJL3278_RLF_N029_JoinT


title: WJL3290_RLF_N029_JoinT


title: WJL3277_RLF_N029_JoinT


title: miRNA-seq_17.A

source_name: Arterioles, biol rep 1


title: WJL3288_RLF_N029_JoinT


title: Input Tbx3 FL bud E9.75-E10.25 replicate 1


title: miRNA-seq_62.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Cecal ligation & puncture (CLP) sepsis

value: 4 h


title: RNA-seq FL bud E9.75-E10 Tbx3_WT replicate 2


title: WJL3274_RLF_N029_JoinT


title: miRNA-seq_76.A

source_name: Arterioles, biol rep 4

value: Kidney

value: male

value: Yes


title: WJL3273_RLF_N029_JoinT


title: miRNA-seq_59.W

source_name: Whole kidney, biol rep 3


title: ChIP Tbx3 FL bud E9.75-E10.25 replicate 1

value: Swiss albino

value: forelimb buds


title: miRNA-seq_7.W

source_name: Whole kidney, biol rep 2


title: WJL3272_RLF_N029_JoinT

source_name: vAbl-ProB


title: miRNA-seq_75.A

source_name: Arterioles, biol rep 3

value: Sham-operated


title: WJL3269_RLF_N029_JoinT

value: ATMi


title: miRNA-seq_6.W

source_name: Whole kidney, biol rep 1


title: WJL3268_RLF_N029_JoinT


title: MC_DTA

first: Samer

last: Hattar

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

data_processing:
Samples were demultiplexed and .fastq files were generated using the 10X Genomics Longranger software (ver. 2.2.2) 'mkfastq' function
Demultiplexed samples were aligned to the mouse genome (mm10) and digital gene expression matrices were generated using the 10X Genomics Cellranger software (ver. 3.0.2) 'count' function
Gene expression matrices were loaded into the Seurat package in R using the 'Read10X' function, and Seurat objects were created with the 'CreateSeuratObject' function using the following parameters: min.cells = 3, min.features = 300
High quality cells were selected using the Seurat 'subset' function with the following criteria: percent.mt < 10 & nFeature_RNA > 500
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of raw UMI counts for each gene/cell separated by sample (.csv format)

source_name: Motor cortex

extract_protocol:
For each sample, the brain was extracted after rapid anesthesia induction with 5% isoflurane. The vmPFC was manually excised and the cells dissociated according to a published protocol (Saxena et al., 2012, Biotechniques). Cell viability was measured with Trypan blue and resuspended in ice-cold PBS to desired concentrations for 10X Genomics single cell capture.
Sequencing libraries were prepared using the 10X Genomics 3' single cell gene expression V2 kit following the manufacturer's protocol

treatment_protocol: Mice were housed in a 12 h light:12 h dark (T24) cycle at a temperature of 22--25°C with food and water ad libitum

value: Opn4-Cre/+; Brn3b-zDTA/+


title: miRNA-seq_62.V

source_name: Post-capillary venules, biol rep 4

value: Post-capillary venules


title: WJL3267_RLF_N029_JoinT

value: vAbl-ProB

value: pro-B cells


title: WJL3266_RLF_N029_JoinT

value: CTR


title: WJL3265_RLF_N029_JoinT


title: WJL3276_RLF_N029_JoinT


title: PFC_DTA_rep3

source_name: Ventromedial prefrontal cortex


title: WJL3263_RLF_N029_JoinT


title: WJL3264_RLF_N029_JoinT


title: WJL3275_RLF_N029_JoinT


title: WJL3262_RLF_N029_JoinT


title: miRNA-seq_7.V

source_name: Post-capillary venules, biol rep 2

value: WT


title: WJL3271_RLF_N029_JoinT


title: miRNA-seq_6.V

source_name: Post-capillary venules, biol rep 1


title: WJL3261_RLF_N029_JoinT


title: WJL3270_RLF_N029_JoinT


title: WJL3260_RLF_N029_JoinT


title: PFC_DTA_rep2


title: PFC_DTA_rep1


title: miRNA-seq_62.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: miRNA-seq_59.P

source_name: Peritubular capillaries, biol rep 3


title: WJL3258_RLF_N029_JoinT


title: WJL3257_RLF_N029_JoinT


title: PFC_CTRL_rep2

value: Opn4-Cre/+; Brn3b-+/+


title: miRNA-seq_7.P

source_name: Peritubular capillaries, biol rep 2

value: Cecal ligation & puncture (CLP) sepsis


title: MC_CTRL


title: PFC_CTRL_rep1


title: WJL3254_RLF_N029_JoinT


title: miRNA-seq_59.V

source_name: Post-capillary venules, biol rep 3

value: 4 h


title: miRNA-seq_6.P

source_name: Peritubular capillaries, biol rep 1

value: Kidney


title: WJL3253_RLF_N029_JoinT


title: WJL3252_RLF_N029_JoinT


title: L-KOLPS-2

city: Zürich

first: Jain

last: Nikhil

address: Vladimir-Prelog-Weg 1/5-10

department: Health Science and Technology

institute: ETH Zürich

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (42 nt reads, paired end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters). Only reads mapping as matched pairs were used in the analysis, and the 8 samples were normalized to the same number of unique alignments (by downsampling)
Aligns were extended in silico at their 3’-ends to a length of 200 bp, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1e-7, without control file, and with the -nomodel option.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
Supplementary_files_format_and_content: BED = MACS2 peaks in BED6+4 format

growth_protocol: Isolated BM cells were seeded in 60 mm non-treated plastic dishes for 7 days at 37 oC and 5% CO2 conditions.

extract_protocol:
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were thawed in a 37oC water bath, pelleted, washed with cold PBS. Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina)
Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter)

treatment_protocol: Cells were activated with LPS for 6 h.

value: Bone-marrow-derived macrophage

value: activated with LPS

value: Lamin-A KO


title: WJL3103_RLF_N027_JoinT


title: miRNA-seq_62.G

source_name: Glomeruli, biol rep 4

value: male

value: Yes

value: Glomeruli


title: WJL3102_RLF_N027_JoinT


title: WJL3101_RLF_N027_JoinT


title: L-KOLPS-1


title: L-KO-2


title: miRNA-seq_7.G

source_name: Glomeruli, biol rep 2


title: WJL3100_RLF_N027_JoinT


title: WJL3259_RLF_N029_JoinT


title: WJL3256_RLF_N029_JoinT

value: ATMi


title: WJL3099_RLF_N027_JoinT


title: miRNA-seq_59.G

source_name: Glomeruli, biol rep 3


title: WJL3255_RLF_N029_JoinT


title: L-KO-1


title: WJL3090_RLF_N027_JoinT


title: Control-LPS-2

value: wild type


title: miRNA-seq_6.G

source_name: Glomeruli, biol rep 1


title: WJL3088_RLF_N027_JoinT

source_name: vAbl-ProB

value: vAbl-ProB


title: Control-2


title: miRNA-seq_62.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: WJL3089_RLF_N027_JoinT

value: pro-B cells


title: Control-LPS-1


title: miRNA-seq_59.A

source_name: Arterioles, biol rep 3

value: WT


title: WJL3087_RLF_N027_JoinT

value: CTR


title: WJL3085_RLF_N027_JoinT


title: miRNA-seq_7.A

source_name: Arterioles, biol rep 2


title: Control-1


title: WJL3086_RLF_N027_JoinT


title: WJL3084_RLF_N027_JoinT


title: WJL3083_RLF_N027_JoinT


title: wt-pcontrol, input

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Reads were aligned to the S. pombe v2.20 genome plus corresponding plasmid using Bowtie2
Reads with mapping quality greater than 30 were kept for further analyses using SAMtools and BEDTools
Genome-wide enrichments were calculated by normalizing IP reads to corresponding input data using deepTools and visualized using IGV.
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: bigwig files were generated using bedtools and deepTools

organism: Schizosaccharomyces pombe

source_name: wt-pcontrol, input

growth_protocol: Cells were grown in liquid yeast extract plus supplements (YES) media at 32C to a concentration of 5x10^6-1x10^7 cells/mL

extract_protocol:
Cells were lysed by bead beating and chromatin was sheared by sonication. Lysates were incubated with antibody and Protein-G Dynabeads overnight. Immunoprecipitated genomic DNA was recovered using PCR purification columns.
Libraries were prepared for Illumina sequencing with 1-5 ng of ChIP or 10 ng of input DNA using NEXTflex adaptors and Ampure XP beads. Barcoded libraries were pooled and sequenced following an Illumina MiniSeq workflow.

treatment_protocol: Cells were fixed with 1% formaldehyde for 15 min at room temperature

value: wt-pcontrol


title: WJL3082_RLF_N027_JoinT


title: miRNA-seq_6.A

source_name: Arterioles, biol rep 1

value: Cecal ligation & puncture (CLP) sepsis


title: WJL3091_RLF_N027_JoinT


title: wt-phet, input

source_name: wt-phet, input

value: wt-phet


title: WJL3064_RLF_N027_JoinT


title: WJL3081_RLF_N027_JoinT


title: WJL3098_RLF_N027_JoinT


title: wt-pcontrol, H3K9me2 ChIP-seq

source_name: wt-pcontrol, IP

value: anti-H3K9me2 ChIP antibody


title: WJL3080_RLF_N027_JoinT


title: miRNA-seq_57.W

source_name: Whole kidney, biol rep 3

value: Kidney

value: No

value: Whole kidney

value: Sham-operated

value: 4 h


title: WJL3063_RLF_N027_JoinT


title: miRNA-seq_61.W

source_name: Whole kidney, biol rep 4

value: male


title: wt-phet, H3K9me2 ChIP-seq

source_name: wt-phet, IP


title: miRNA-seq_33.W

source_name: Whole kidney, biol rep 2


title: WJL3062_RLF_N027_JoinT


title: WJL3061_RLF_N027_JoinT


title: miRNA-seq_61.V

source_name: Post-capillary venules, biol rep 4

value: Yes

value: Post-capillary venules


title: miRNA-seq_3.W

source_name: Whole kidney, biol rep 1


title: female high protein low carbohydrate(HPLC) diet rep5

city: Shenzhen

first: li

last: anqi

address: No. 66, Gongchang Road, Guangming District

country: China

institute: School of Pharmaceutical Sciences (Shenzhen)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dmel-all-r6.39 whole genome using hisat2 with parameters -p 6 -q -x genome_tran -1.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: dmel-all-r6.39
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wild-type (W1118)

value: brain

value: female

value: HPLC diet (P:C=1:1,90g/L)


title: female high protein low carbohydrate(HPLC) diet rep4


title: WJL3059_RLF_N027_JoinT

value: vAbl-ProB

value: pro-B cells


title: WJL3056_RLF_N027_JoinT


title: female high protein low carbohydrate(HPLC) diet rep3


title: female high protein low carbohydrate(HPLC) diet rep2


title: WJL3057_RLF_N027_JoinT


title: WJL3053_RLF_N027_JoinT


title: female high protein low carbohydrate(HPLC) diet rep1


title: WJL3058_RLF_N027_JoinT


title: miRNA-seq_61.P

source_name: Peritubular capillaries, biol rep 4

value: WT

value: Peritubular capillaries


title: miRNA-seq_3.V

source_name: Post-capillary venules, biol rep 1


title: female low protein high carbohydrate(LPHC) diet rep5

value: LPHC diet (P:C=1:2,360g/L)


title: WJL3060_RLF_N027_JoinT

source_name: vAbl-ProB


title: WJL3046_RLF_N027_JoinT


title: WJL3044_RLF_N027_JoinT


title: WJL3047_RLF_N027_JoinT


title: WJL3045_RLF_N027_JoinT


title: WJL3043_RLF_N027_JoinT


title: miRNA-seq_57.V

source_name: Post-capillary venules, biol rep 3

value: Kidney


title: WJL3055_RLF_N027_JoinT


title: miRNA-seq_33.P

source_name: Peritubular capillaries, biol rep 2


title: female low protein high carbohydrate(LPHC) diet rep3


title: miRNA-seq_3.P

source_name: Peritubular capillaries, biol rep 1


title: WJL3039_RLF_N027_JoinT


title: miRNA-seq_61.G

source_name: Glomeruli, biol rep 4

value: Glomeruli


title: WJL3042_RLF_N027_JoinT


title: WJL3037_RLF_N027_JoinT


title: WJL3038_RLF_N027_JoinT


title: WJL3035_RLF_N027_JoinT


title: male high protein low carbohydrate(HPLC) diet rep5

value: HPLC diet (P:C=1:1,180g/L)


title: WJL3036_RLF_N027_JoinT


title: female low protein high carbohydrate(LPHC) diet rep4


title: WJL3034_RLF_N027_JoinT


title: WJL3041_RLF_N027_JoinT


title: miRNA-seq_33.G

source_name: Glomeruli, biol rep 2

value: Sham-operated


title: WJL3033_RLF_N027_JoinT


title: miRNA-seq_57.G

source_name: Glomeruli, biol rep 3

value: 4 h


title: miRNA-seq_57.P

source_name: Peritubular capillaries, biol rep 3

value: male


title: WJL3054_RLF_N027_JoinT


title: WJL3027_RLF_N027_JoinT

value: ATMi


title: miRNA-seq_3.G

source_name: Glomeruli, biol rep 1

value: Yes


title: miRNA-seq_33.V

source_name: Post-capillary venules, biol rep 2

value: Post-capillary venules


title: male high protein low carbohydrate(HPLC) diet rep2

value: Wild-type (W1118)

value: brain


title: female low protein high carbohydrate(LPHC) diet rep1

value: female


title: WJL3026_RLF_N027_JoinT

value: vAbl-ProB


title: WJL3024_RLF_N027_JoinT

value: pro-B cells

value: CTR


title: WJL3025_RLF_N027_JoinT


title: male high protein low carbohydrate(HPLC) diet rep4


title: male high protein low carbohydrate(HPLC) diet rep3


title: miRNA-seq_61.A

source_name: Arterioles, biol rep 4

value: WT

value: Arterioles


title: male high protein low carbohydrate(HPLC) diet rep1


title: WJL3040_RLF_N027_JoinT


title: miRNA-seq_57.A

source_name: Arterioles, biol rep 3

value: Kidney


title: WJL3021_RLF_N027_JoinT


title: WJL3022_RLF_N027_JoinT


title: male low protein high carbohydrate(LPHC) diet rep5

value: LPHC diet (P:C=0:1,180g/L)


title: WJL3020_RLF_N027_JoinT


title: male low protein high carbohydrate(LPHC) diet rep4


title: miRNA-seq_3.A

source_name: Arterioles, biol rep 1


title: male low protein high carbohydrate(LPHC) diet rep3


title: WJL3016_RLF_N027_JoinT


title: WJL3018_RLF_N027_JoinT


title: WJL2938_RLF_N026_JoinT


title: miRNA-seq_100.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Healthy control

value: 0 h


title: male low protein high carbohydrate(LPHC) diet rep2

source_name: Brain

value: male


title: WJL2937_RLF_N026_JoinT


title: WJL3019_RLF_N027_JoinT

value: ATMi


title: miRNA-seq_98.W

source_name: Whole kidney, biol rep 3


title: WJL2935_RLF_N026_JoinT


title: male low protein high carbohydrate(LPHC) diet rep1


title: WJL3023_RLF_N027_JoinT


title: miRNA-seq_96.W

source_name: Whole kidney, biol rep 2


title: miRNA-seq_93.W

source_name: Whole kidney, biol rep 1


title: WJL2936_RLF_N026_JoinT

source_name: vAbl-ProB


title: WJL2926_RLF_N026_JoinT


title: miRNA-seq_100.V

source_name: Post-capillary venules, biol rep 4

value: Yes

value: Post-capillary venules


title: miRNA-seq_98.V

source_name: Post-capillary venules, biol rep 3


title: female low protein high carbohydrate(LPHC) diet rep2

value: Wild-type (W1118)

value: brain

value: LPHC diet (P:C=1:2,360g/L)


title: WJL2925_RLF_N026_JoinT

value: vAbl-ProB

value: pro-B cells


title: WJL2934_RLF_N026_JoinT


title: WJL2924_RLF_N026_JoinT


title: WJL2923_RLF_N026_JoinT


title: WJL2922_RLF_N026_JoinT


title: miRNA-seq_96.V

value: WT


title: WJL3017_RLF_N027_JoinT

value: CTR


title: WJL2920_RLF_N026_JoinT


title: WJL2921_RLF_N026_JoinT


title: WJL2919_RLF_N026_JoinT


title: miRNA-seq_93.V

source_name: Post-capillary venules, biol rep 1

value: Kidney


title: WJL2918_RLF_N026_JoinT


title: miRNA-seq_100.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: WJL2915_RLF_N026_JoinT


title: WJL2916_RLF_N026_JoinT


title: miRNA-seq_98.P


title: WJL2899_RLF_N026_JoinT


title: miRNA-seq_96.P

source_name: Peritubular capillaries, biol rep 2


title: WJL2898_RLF_N026_JoinT


title: WJL2895_RLF_N026_JoinT


title: miRNA-seq_93.P

source_name: Peritubular capillaries, biol rep 1


title: WJL2933_RLF_N026_JoinT


title: WJL2897_RLF_N026_JoinT


title: NT-2

city: Bangalore

first: Nehanjali

last: Dwivedi

state: Karnataka

address: MSCTR, 8th floor A block

country: India

institute: MSCTR

data_processing:
Sequence reads were filtered for quality using Trimmomatic and filtered reads were separated based on mapping to human (GRCh38) and mouse (GRCm39) reference assembly using FastQ Screen. Separated reads were aligned to respective genome using STAR pipeline.
Assembly: Genome Reference Consortium Human Build 38 (GRCh38) and mouse (GRCm39)

organism: Homo sapiens

source_name: Xenograft tumor

growth_protocol: HeLa cells were cultured in DMEM medium, pH 7.2, supplemented with 10% FBS and 1X penicillin-streptomycin solution at 37°C.

extract_protocol:
RNA was harvested using TRIzol method as per the manufacturer's instructions
Library for RNAseq was prepared using illumina TruSeq library preparation kit.

treatment_protocol: Once tumors grew to about 100mm3 in diameter, tumors were injected with α-LCN2 antibody every alternate day (100µg) directly into the tumor with PBS as the vehicle control in no treatment group. Animals were sacrificed when the tumor grew ~2000mm3, after 2 weeks of treatment.

value: Xenograft tumor

value: HeLa

value: Epithelial Cells

value: No Treatment


title: TR-2

value: Anti-LCN2 Monoclonal Antibody


title: WJL2896_RLF_N026_JoinT


title: WJL2892_RLF_N026_JoinT


title: WJL2891_RLF_N026_JoinT


title: WJL2894_RLF_N026_JoinT


title: TR-1


title: miRNA-seq_98.G

source_name: Glomeruli, biol rep 3

value: male

value: Glomeruli

value: Healthy control

value: 0 h


title: WJL2890_RLF_N026_JoinT


title: miRNA-seq_100.G

source_name: Glomeruli, biol rep 4

value: Yes


title: NT-1


title: WJL2888_RLF_N026_JoinT


title: WJL2893_RLF_N026_JoinT


title: miRNA-seq_96.G

source_name: Glomeruli, biol rep 2


title: WJL2882_RLF_N026_JoinT


title: miRNA-seq_100.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: miRNA-seq_93.G

source_name: Glomeruli, biol rep 1


title: WJL2880_RLF_N026_JoinT

value: vAbl-ProB


title: BRD4-ChIP-seq-JQ1 MDA-MB-231

city: Xia Men

first: Xiao

last: Lu

address: Xiang'an south road

institute: Xiamen university

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v2.3.4.1) and generated SAM files were converted to BAM files using Samtools (v.1.9)  using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters which were converted to BigWig files using Deeptools. BigWig files were visualized using the Integrative Genomics Viewer (Broad Institute).
HOMER suit of tools was used. Aligned bam files were subjected to peak calling using findPeaks tools with the -style factor.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using deeptools and were visualized using the Integrative Genomics Viewer (Broad Institute).

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Cells were washed once with cold PBS prior to cross-linking with 2 mM DSG for 45 minutes followed by 1% formaldehyde (28908, Thermo) for 15 min at room temperature, To quench the cross-linking reaction, 2.5 M glycine dissolved in PBS was added and cells were incubated at room temperature for a further 5 minutes. Cells were washed twice with ice-cold PBS and lysed using cell lysis buffer (50 mM Tris pH 8.0, 0.5% NP40, 50 mM NaCl) to remove the cytoplasmic proteins. The pellet was resuspended in nuclear lysis buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 400 mM NaCl, 20 mM Tris pH 8.0, 0.1% SDS). Chromatin DNA was sheared to 300–500 bp average in size through sonication using a Bioruptor instrument (Diagenode). Fragmented chromatin was diluted 1:1 with dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100) and immunoprecipitated with IgG or indicated specific antibodies overnight at 4°C, followed by incubation with protein A/G magnetic Dynabeads for 4 h. Dynabeads were washed once each with ChIP wash buffer 1 (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and ChIP wash buffer 2 (20 mM Tris pH 8.0, 400 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and washed twice with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA pH 8.0). After washing and elution, the protein–DNA complex was reversed by heating overnight at 65°C. Immunoprecipitated DNA was purified by QIAquick spin columns. Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing.
Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing. Briefly, Chip DNA was end-blunted and added with an ‘A’ base. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Cells were treated with indicated drugs.

value: breast cancer


title: BRD4-ChIP-seq-control MDA-MB-231

value: control


title: WJL2881_RLF_N026_JoinT

value: pro-B cells


title: miRNA-seq_98.A

source_name: Arterioles, biol rep 3

value: Kidney

value: WT


title: miRNA-seq_33.A

source_name: Arterioles, biol rep 2

value: Sham-operated

value: 4 h


title: WJL2879_RLF_N026_JoinT


title: MDA-MB-231 BET-151-1

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0)
Cufflinks (v2.2.1) was used to calculate the expression of RefSeq annotated genes
Assembly: hg38
Supplementary files format and content: txt files include FPKM values for each Sample

extract_protocol:
Cells were lyzed by trizol.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd  Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of NEBNext rRNA Depletion Kit (NEB E6310). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (NEB, E7760), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq X-Ten at Amogene (Xiamen, China) Biotech Co., Ltd following the vendor's recommended protocol.

treatment_protocol: Cells were infected with indicated lentivirus and/or treated with indicated drugs.

value: 3 days


title: WJL2877_RLF_N026_JoinT


title: WJL2875_RLF_N026_JoinT


title: WJL2878_RLF_N026_JoinT


title: WJL2876_RLF_N026_JoinT


title: miRNA-seq_93.A

source_name: Arterioles, biol rep 1


title: miRNA-seq_96.A


title: WJL2874_RLF_N026_JoinT


title: WJL2872_RLF_N026_JoinT


title: WJL2873_RLF_N026_JoinT


title: MDA-MB-231 Molib-1

value: 0.5uM MOLIB


title: WJL2889_RLF_N026_JoinT


title: RNA-seq_88.W

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.8 (Andrews 2010) and multiQC v1.7 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using bbduk from the bbmap package v38.69 (Bushnell 2015) and filtered for a minimum length of 17nt and phred quality of 30.
Alignment steps were performed with STAR v2.7 (Dobin et al. 2013) using samtools v1.9 (Li et al. 2009) for indexing, whereas reads were mapped against the genomic reference GRCm38.p6 provided by Ensembl (Zerbino et al. 2018).
Assignment of features to the mapped reads was done with htseq-count v0.13 (Anders, Pyl, and Huber 2015).
Assembly: GRCm39 Assembly GCA_000001635.9
Supplementary files format and content: CSV file containing gene read counts from featureCount

source_name: Whole kidney, biol rep 3

extract_protocol: Lexogen Quantseq according to manufacturer's protocol

value: No

value: Whole kidney

value: Cecal ligation & puncture (CLP) sepsis


title: WJL2870_RLF_N026_JoinT

source_name: vAbl-ProB


title: WJL2871_RLF_N026_JoinT


title: WJL2868_RLF_N026_JoinT


title: RNA-seq_92.W

source_name: Whole kidney, biol rep 4

value: male


title: WJL2869_RLF_N026_JoinT


title: WJL2862_RLF_N026_JoinT


title: MDA-MB-231 Molib-2


title: RNA-seq_92.V

source_name: Post-capillary venules, biol rep 4

value: Post-capillary venules


title: WJL2860_RLF_N026_JoinT


title: RNA-seq_32.W

source_name: Whole kidney, biol rep 1


title: RNA-seq_50.W

source_name: Whole kidney, biol rep 2


title: MDA-MB-231 JQ1.1

value: 0.5uM JQ1


title: WJL2861_RLF_N026_JoinT


title: WJL2856_RLF_N026_JoinT


title: MDA-MB-231 DMSO-2

value: DMSO


title: RNA-seq_88.V

source_name: Post-capillary venules, biol rep 3

value: Yes


title: MDA-MB-231 MW-JQ1-2

value: breast cancer


title: MDA-MB-231 DMSO-1


title: MDA-MB-231 MW-JQ1-1


title: WJL2855_RLF_N026_JoinT

value: vAbl-ProB


title: RNA-seq_32.V

source_name: Post-capillary venules, biol rep 1


title: MDA-MB-231 JQ1.2


title: RNA-seq_92.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: MDA-MB-231 JQ1-1


title: RNA-seq_50.V

source_name: Post-capillary venules, biol rep 2

value: Kidney


title: WJL2854_RLF_N026_JoinT

value: pro-B cells


title: WJL2853_RLF_N026_JoinT


title: MDA-MB-231 JQ1-2

value: WT


title: WJL2852_RLF_N026_JoinT


title: WJL2859_RLF_N026_JoinT


title: RNA-seq_50.P

source_name: Peritubular capillaries, biol rep 2


title: WJL2804_RLF_N025_JoinT

value: ATMi


title: MDA-MB-231 con-2

value: CTRL

value: 3 days


title: WJL2851_RLF_N026_JoinT


title: RNA-seq_32.P

source_name: Peritubular capillaries, biol rep 1


title: RNA-seq_88.P

source_name: Peritubular capillaries, biol rep 3


title: WJL2857_RLF_N026_JoinT


title: WJL2858_RLF_N026_JoinT


title: WJL2800_RLF_N025_JoinT

value: CTR


title: WJL2803_RLF_N025_JoinT


title: MDA-MB-231 shM3-CD-2

value: shM3 add back METTL3-CD

value: 2-3 months


title: WJL2799_RLF_N025_JoinT


title: WJL2801_RLF_N025_JoinT


title: MDA-MB-231 con-1

description: control


title: WJL2798_RLF_N025_JoinT


title: WJL2917_RLF_N026_JoinT


title: MDA-MB-231 BET-151-2


title: WJL2797_RLF_N025_JoinT


title: MDA-MB-231 shM3-CD-1


title: RNA-seq_88.G

source_name: Glomeruli, biol rep 3

value: male

value: Glomeruli

value: Cecal ligation & puncture (CLP) sepsis


title: RNA-seq_50.G

source_name: Glomeruli, biol rep 2


title: WJL2794_RLF_N025_JoinT


title: WJL2796_RLF_N025_JoinT


title: WJL2795_RLF_N025_JoinT


title: MDA-MB-231 shM3-2 [V7-2]


title: WJL2791_RLF_N025_JoinT


title: WJL2790_RLF_N025_JoinT


title: WJL2789_RLF_N025_JoinT


title: MDA-MB-231 shM3-1 [V7-1]


title: RNA-seq_88.A

source_name: Arterioles, biol rep 3

value: Arterioles


title: MDA-MB-231 shM3-WT-1

value: shM3 add back METTL3-WT


title: WJL2802_RLF_N025_JoinT


title: WJL2788_RLF_N025_JoinT


title: RNA-seq_32.G

source_name: Glomeruli, biol rep 1

value: Yes


title: WJL2792_RLF_N025_JoinT

value: vAbl-ProB


title: RNA-seq_92.A

source_name: Arterioles, biol rep 4


title: MDA-MB-231 B5-2 [V5-2]

value: breast cancer


title: WJL2786_RLF_N025_JoinT

source_name: vAbl-ProB


title: RNA-seq_92.G

source_name: Glomeruli, biol rep 4

value: Kidney


title: WJL2783_RLF_N025_JoinT

value: pro-B cells


title: WJL2787_RLF_N025_JoinT


title: MDA-MB-231 B5-1 [V5-1]

value: WT


title: WJL2784_RLF_N025_JoinT


title: WJL2782_RLF_N025_JoinT


title: RNA-seq_50.A

source_name: Arterioles, biol rep 2


title: MDA-MB-231 shM3-WT-2


title: WJL2781_RLF_N025_JoinT

value: ATMi


title: RNA-seq_32.A

source_name: Arterioles, biol rep 1


title: RNA-seq_46.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Sham-operated


title: BLU9931 +Palbociclib_3

city: shanghai

first: Yanshuang

last: Zhang

state: China

address: 1954 Huashan Road, Shanghai Jiao Tong University, Shanghai 200030, PR China

institute: Shanghai Jiao Tong University

data_processing:
Illumina San Diego, CA software used for basecalling.
Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: H520 cell line

extract_protocol:
RNA was harvested using RNAiso reagent. The Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LUSC


title: RNA-seq_28.W

source_name: Whole kidney, biol rep 3


title: RNA-seq_26.W

source_name: Whole kidney, biol rep 1


title: WJL2779_RLF_N025_JoinT


title: WJL2778_RLF_N025_JoinT

value: CTR


title: RNA-seq_27.W

source_name: Whole kidney, biol rep 2

value: male


title: Palbociclib_3


title: WJL2776_RLF_N025_JoinT


title: WJL2785_RLF_N025_JoinT


title: RNA-seq_46.V

source_name: Post-capillary venules, biol rep 4

value: Post-capillary venules


title: WJL2777_RLF_N025_JoinT


title: WJL2773_RLF_N025_JoinT


title: Palbociclib_2


title: Palbociclib_1


title: WJL2780_RLF_N025_JoinT


title: WJL2768_RLF_N025_JoinT

value: ATRi


title: WJL2771_RLF_N025_JoinT


title: RNA-seq_26.V

source_name: Post-capillary venules, biol rep 1


title: BLU9931 +Palbociclib_1


title: WJL2772_RLF_N025_JoinT


title: BLU9931_3


title: RNA-seq_27.V

source_name: Post-capillary venules, biol rep 2


title: WJL2805_RLF_N025_JoinT


title: BLU9931 +Palbociclib_2


title: BLU9931_2


title: BLU9931_1


title: WJL2775_RLF_N025_JoinT


title: WJL2766_RLF_N025_JoinT


title: RNA-seq_46.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: WJL2765_RLF_N025_JoinT


title: Control_3


title: RNA-seq_28.V

source_name: Post-capillary venules, biol rep 3


title: RNA-seq_28.P

source_name: Peritubular capillaries, biol rep 3


title: WJL2763_RLF_N025_JoinT

value: Polθi #1


title: WJL2770_RLF_N025_JoinT


title: Control_1


title: WJL2769_RLF_N025_JoinT


title: Control_2


title: WJL2774_RLF_N025_JoinT


title: WJL2761_RLF_N025_JoinT


title: WJL2760_RLF_N025_JoinT

value: Parp1i #2


title: RNA-seq_27.P

source_name: Peritubular capillaries, biol rep 2

value: Yes


title: WJL2767_RLF_N025_JoinT

value: vAbl-ProB


title: WJL2762_RLF_N025_JoinT


title: WJL2758_RLF_N025_JoinT


title: WJL2757_RLF_N025_JoinT

value: Parp1i #1


title: RNA-seq_46.G

value: Kidney

value: Glomeruli


title: RNA-seq_28.G

source_name: Glomeruli, biol rep 3

value: WT


title: TF-1, H3K26me2 WT

city: Durham

first: Yiran

last: Guo

state: North Carolina

address: 3 Genome Ct

institute: Duke University

data_processing:
CUT&Tag reads were aligned to human genome build GRCh38/hg38 using Bowtie2 alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR-caused duplicates using the Picard and Samtools.
Profiles of CUT&Tag read densities were displayed with the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters (macs2 callpeak -f BAMPE --keep-dup 1)
To calibrate CUT&Tag signals in TF-1 cells (human sample), the spike-in control genome (mm10) was used to quantitatively compare the genomic profiles.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

growth_protocol: The TF-1 human erythroleukemic cell line was obtained from ATCC and cultivated in the RPMI 1640 base medium supplemented with 10% of FBS and 2 ng/ml of recombinant human GM-CSF.

extract_protocol:
Cells were trypsinized with 0.05% trypsin and cell pellets were collected for CUT&Tag.
CUT&Tag was performed with the anti-Myc tag antibody (CST #2276s) according to manufacturer’s instructions (CUTANA™ pAG-Tn5 for CUT&Tag, EpiCypher, Cat# 15-1017). Multiplexed CUT&Tag libraries were pooled and subjected to paired-end (PE) sequencing.

treatment_protocol: TF-1 cell lines with stable expression of WT or mutant DNMT3A were established with MSCV-based retrovirus followed by drug selection.

value: Human embryonic kidney

value: H3K36me2 (Active Motif#AB_2793207)


title: TF-1, myc-DNMT3A R882C/M674T/R676K batch2

value: Myc-Tag (CST#2276)


title: WJL2756_RLF_N025_JoinT

source_name: vAbl-ProB

value: pro-B cells


title: WJL2754_RLF_N025_JoinT


title: TF-1, myc-DNMT3A R882C/R676K batch2


title: WJL2755_RLF_N025_JoinT


title: WJL2752_RLF_N025_JoinT


title: WJL2753_RLF_N025_JoinT


title: TF-1, myc-DNMT3A R882C batch2


title: WJL2764_RLF_N025_JoinT

value: ATMi


title: RNA-seq_26.G

source_name: Glomeruli, biol rep 1

value: male

value: Sham-operated


title: RNA-seq_27.G

source_name: Glomeruli, biol rep 2


title: TF-1, myc-DNMT3A R882H/M674T/R676K batch2


title: RNA-seq_46.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: WJL2759_RLF_N025_JoinT


title: RNA-seq_26.P

source_name: Peritubular capillaries, biol rep 1

value: Peritubular capillaries


title: WJL2749_RLF_N025_JoinT

value: Mre11(en)i #2


title: WJL2750_RLF_N025_JoinT


title: RNA-seq_28.A

source_name: Arterioles, biol rep 3


title: TF-1, myc-DNMT3A R882H/R676K batch2


title: WJL2751_RLF_N025_JoinT


title: TF-1, myc-DNMT3A R882H batch2


title: RNA-seq_27.A

source_name: Arterioles, biol rep 2


title: WJL2745_RLF_N025_JoinT

value: CTR


title: WJL2744_RLF_N025_JoinT


title: TF-1, myc-DNMT3A R676K batch2


title: WJL2747_RLF_N025_JoinT

value: Mre11(en)i #1


title: WJL2746_RLF_N025_JoinT

value: vAbl-ProB


title: RNA-seq_26.A

source_name: Arterioles, biol rep 1

value: Yes


title: TF-1, myc-DNMT3A WT batch2


title: WJL2742_RLF_N025_JoinT

value: ATRi


title: RNA-seq_82.W

source_name: Whole kidney, biol rep 4

value: Kidney

value: No

value: Whole kidney

value: Cecal ligation & puncture (CLP) sepsis


title: WJL2741_RLF_N025_JoinT

value: WT


title: WJL2740_RLF_N025_JoinT

value: pro-B cells


title: RNA-seq_56.W

source_name: Whole kidney, biol rep 3


title: WJL2739_RLF_N025_JoinT

value: ATMi


title: WJL2738_RLF_N025_JoinT


title: WJL2748_RLF_N025_JoinT


title: RNA-seq_55.W

source_name: Whole kidney, biol rep 2

value: male


title: WJL2737_RLF_N025_JoinT


title: RNA-seq_22.W

source_name: Whole kidney, biol rep 1


title: WJL2735_RLF_N025_JoinT

value: Polθi #1


title: WJL2734_RLF_N025_JoinT


title: WJL2736_RLF_N025_JoinT


title: 4B-27

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

data_processing:
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg38  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted into gene body regions of RefSeq genes using featureCounts.
Assembly: hg38
Supplementary files format and content: txt file for all sample with raw reads count summarised to gene body regions of Refseq genes.

source_name: Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).
nano-hmC-Seal

tag: diagnosis

value: Acute myeloid leukemia

tag: gender (1 = male, 2 = female)


title: WJL2733_RLF_N025_JoinT

tag: cell line

value: Parp1i #2


title: 4B-43


title: WJL2731_RLF_N025_JoinT

tag: cell type


title: RNA-seq_56.V

source_name: Post-capillary venules, biol rep 3

tag: genotype

value: Post-capillary venules


title: WJL2743_RLF_N025_JoinT

tag: treatment

value: CTR


title: 4B-26


title: RNA-seq_55.V

source_name: Post-capillary venules, biol rep 2


title: 4B-45


title: WJL2730_RLF_N025_JoinT

value: Parp1i #1

tag: total reads


title: WJL2729_RLF_N025_JoinT

value: vAbl-ProB


title: 4B-53


title: WJL2728_RLF_N025_JoinT


title: 4B-19


title: RNA-seq_22.V

source_name: Post-capillary venules, biol rep 1

tag: strain

value: Yes


title: 4B-47


title: RNA-seq_82.P

source_name: Peritubular capillaries, biol rep 4

tag: tissue

value: Peritubular capillaries


title: RNA-seq_82.V

source_name: Post-capillary venules, biol rep 4

value: Kidney

tag: Sex


title: 4B-4

tag: age


title: 4B-28


title: WJL2725_RLF_N025_JoinT

source_name: vAbl-ProB


title: WJL2724_RLF_N025_JoinT

value: Mre11(en)i #2


title: 4B-20


title: RNA-seq_56.P

source_name: Peritubular capillaries, biol rep 3

tag: laser microdissected


title: WJL2732_RLF_N025_JoinT


title: WJL2722_RLF_N025_JoinT


title: WJL2723_RLF_N025_JoinT


title: RNA-seq_55.P

source_name: Peritubular capillaries, biol rep 2

tag: microvascular compartment


title: WJL2721_RLF_N025_JoinT

value: Mre11(en)i #1


title: WJL2720_RLF_N025_JoinT


title: WJL2718_RLF_N025_JoinT


title: 4B-52


title: RNA-seq_22.P

source_name: Peritubular capillaries, biol rep 1

tag: disease state

value: Cecal ligation & puncture (CLP) sepsis


title: 4B-5


title: WJL2719_RLF_N025_JoinT

value: WT


title: 4B-18


title: RNA-seq_82.G

source_name: Glomeruli, biol rep 4

value: Glomeruli

tag: time


title: WJL2717_RLF_N025_JoinT

value: pro-B cells


title: WJL2727_RLF_N025_JoinT


title: WJL2716_RLF_N025_JoinT


title: RNA-seq_56.G

source_name: Glomeruli, biol rep 3

value: male


title: WJL2709_RLF_N025_JoinT

value: ATMi


title: 4B-6

value: Acute myeloid leukemia


title: WJL2726_RLF_N025_JoinT


title: WJL2708_RLF_N025_JoinT


title: RNA-seq_55.G

source_name: Glomeruli, biol rep 2


title: WJL2706_RLF_N025_JoinT


title: 4B-1


title: RNA-seq_22.G

source_name: Glomeruli, biol rep 1


title: RNA-seq_82.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: WJL2705_RLF_N025_JoinT


title: 4B-50


title: WJL2703_RLF_N025_JoinT


title: 4B-51


title: WJL2702_RLF_N025_JoinT


title: WJL2704_RLF_N025_JoinT


title: 4B-49


title: RNA-seq_56.A

source_name: Arterioles, biol rep 3


title: RNA-seq_55.A

source_name: Arterioles, biol rep 2


title: WJL2701_RLF_N025_JoinT


title: WJL2698_RLF_N025_JoinT


title: 4B-46

source_name: Plasma


title: WJL2699_RLF_N025_JoinT


title: 4B-48


title: RNA-seq_22.A

source_name: Arterioles, biol rep 1


title: WJL2695_RLF_N025_JoinT


title: 4B-42


title: WJL2696_RLF_N025_JoinT


title: WJL2700_RLF_N025_JoinT


title: RNA-seq_76.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Sham-operated


title: RNA-seq_75.W

source_name: Whole kidney, biol rep 3


title: WJL2693_RLF_N025_JoinT

value: vAbl-ProB

value: CTR


title: WJL2707_RLF_N025_JoinT


title: 4B-41


title: WJL2692_RLF_N025_JoinT


title: WJL2691_RLF_N025_JoinT


title: RNA-seq_19.W

source_name: Whole kidney, biol rep 2


title: 4B-40


title: WJL2688_RLF_N025_JoinT


title: 4B-37


title: WJL2689_RLF_N025_JoinT


title: WJL2690_RLF_N025_JoinT


title: WJL2687_RLF_N025_JoinT


title: WJL2686_RLF_N025_JoinT


title: 4B-36


title: 4B-34


title: WJL2684_RLF_N025_JoinT


title: WJL2685_RLF_N025_JoinT


title: 4B-33


title: RNA-seq_75.V

source_name: Post-capillary venules, biol rep 3

value: Yes

value: Post-capillary venules


title: WJL2694_RLF_N025_JoinT

source_name: vAbl-ProB


title: WJL2682_RLF_N025_JoinT


title: RNA-seq_19.V

source_name: Post-capillary venules, biol rep 2

value: Kidney


title: RNA-seq_17.V

source_name: Post-capillary venules, biol rep 1


title: RNA-seq_76.V

source_name: Post-capillary venules, biol rep 4


title: RNA-seq_17.W

source_name: Whole kidney, biol rep 1


title: RNA-seq_76.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: 4B-32


title: WJL2678_RLF_N025_JoinT


title: WJL2680_RLF_N025_JoinT


title: 4B-31


title: WJL2677_RLF_N025_JoinT


title: WJL2679_RLF_N025_JoinT


title: WJL2676_RLF_N025_JoinT


title: RNA-seq_75.P

source_name: Peritubular capillaries, biol rep 3


title: 4B-25


title: WJL2673_RLF_N025_JoinT

value: ATRi


title: 4B-24


title: WJL2675_RLF_N025_JoinT


title: WJL2674_RLF_N025_JoinT


title: WJL2683_RLF_N025_JoinT


title: RNA-seq_19.P

source_name: Peritubular capillaries, biol rep 2

value: WT


title: WJL2681_RLF_N025_JoinT


title: 4B-22


title: WJL2672_RLF_N025_JoinT


title: WJL2670_RLF_N025_JoinT


title: RNA-seq_17.P

source_name: Peritubular capillaries, biol rep 1


title: 4B-16


title: RNA-seq_75.G

source_name: Glomeruli, biol rep 3

value: Glomeruli


title: WJL2668_RLF_N025_JoinT

value: pro-B cells


title: WJL2671_RLF_N025_JoinT


title: RNA-seq_19.G

source_name: Glomeruli, biol rep 2

value: male


title: WJL2669_RLF_N025_JoinT

value: ATMi


title: 4B-8

source_name: Plasma

value: Acute myeloid leukemia


title: RNA-seq_76.G

source_name: Glomeruli, biol rep 4


title: WJL2667_RLF_N025_JoinT

value: Polθi #1


title: WJL2666_RLF_N025_JoinT


title: WJL2664_RLF_N025_JoinT

value: Parp1i #2


title: 4B-7


title: 4B-2


title: WJL2665_RLF_N025_JoinT


title: WJL2663_RLF_N025_JoinT


title: RNA-seq_76.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: WJL2662_RLF_N025_JoinT


title: TF-1, myc-DNMT3A R882C/R676K, CST

data_processing:
CUT&Tag reads were aligned to human genome build GRCh38/hg38 using Bowtie2 alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of CUT&Tag read densities were displayed with the Integrative Genomics Viewer (IGV, Broad Institute).
The MACS2 software was used for peak identification with default parameters (macs2 callpeak -f BAMPE --keep-dup 1)
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Cells were trypsinized with 0.05% trypsin and pellets were collected for CUT&Tag. CUT&Tag was performed according to manufacturer’s instructions (CUTANA™ pAG-Tn5 for CUT&Tag, EpiCypher, Cat# 15-1017) with the antibodies against FLAG (Sigma cat#F1804). WT-BAHD1-expressing cells labeled as WT#1_SE were processed in parallel with samples labeled as EV (which is a negative control with empty vector) and mut#1_W667G_SE (which expressed a BAHD1 W677G mutant), followed by the single-end (SE) sequencing; the rest of libraries for WT and the two BAH mutants of BAHD1 (WT#2_PE, mut#1_W667G_PE and mut#2_Y669A_PE) were processed in a separate experiment and subjected to paired-end (PE) sequencing later on.
CUT&Tag library was performed according to manufacturer’s instructions (CUTANA™ pAG-Tn5 for CUT&Tag, EpiCypher, Cat# 15-1017)

value: Human embryonic kidney

value: Myc-Tag (CST #2276)


title: WJL2661_RLF_N025_JoinT

data_processing:
Library strategy: LAM-HTGTS (linear amplification mediated high-throughput genomic translocations sequencing)
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203) and Liang et al., 2021 PNAS (PMC8166026).
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (https://expressionanalysis.github.io/ea-utils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2.
Assembly: The cross library contamination in the co-tagged PCR was filtered by the inner barcodes from I7-nested primers.
Supplementary files format and content: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovoSeq  sequencing

value: vAbl-ProB

value: Parp1i #1


title: TF-1, myc-DNMT3A R882H/M674T/R676K, CST


title: WJL2660_RLF_N025_JoinT


title: RNA-seq_19.A

source_name: Arterioles, biol rep 2

value: Yes

value: Sham-operated


title: RNA-seq_75.A

source_name: Arterioles, biol rep 3

value: Kidney


title: WJL2658_RLF_N025_JoinT


title: WJL2657_RLF_N025_JoinT


title: RNA-seq_17.A

source_name: Arterioles, biol rep 1


title: RNA-seq_17.G

source_name: Glomeruli, biol rep 1


title: WJL2656_RLF_N025_JoinT

source_name: vAbl-ProB


title: TF-1, myc-DNMT3A R676K, CST


title: WJL2655_RLF_N025_JoinT

value: Mre11(en)i #2


title: WJL2653_RLF_N025_JoinT


title: WJL2659_RLF_N025_JoinT


title: WJL2651_RLF_N025_JoinT

value: Mre11(en)i #1


title: TF-1, myc-DNMT3A R882H, CST


title: RNA-seq_62.W

source_name: Whole kidney, biol rep 4

value: WT

value: No

value: Whole kidney

value: Cecal ligation & puncture (CLP) sepsis

value: 4 h


title: WJL2652_RLF_N025_JoinT

value: pro-B cells


title: WJL2654_RLF_N025_JoinT


title: TF-1, myc-DNMT3A WT, CST


title: 2040 plasma;VTE

data_processing:
Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.9 (Andrews 2010) and multiQC v1.10 (Ewels et al. 2016).
Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v3.3 (Martin 2011) and filtered for a minimum length of 17nt.
Mapping steps were performed with bowtie v1.3.0 (Langmead et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012), whereas reads were mapped first against the genomic reference GRCh38.p12 provided by Ensembl (Zerbino et al. 2018) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004), filtered for miRNAs of mmu only, allowing for one mismatch.
Assembly: GRCh38.p12; miRBase v22.1
Supplementary files format and content: CSV file containing read counts of miRDeep2 mapped miRNAs
Supplementary files format and content: CSV file containing rpm normalized read counts of miRDeep2 mapped miRNAs

source_name: plasma

extract_protocol:
Total RNA extraction from 200 µl plasma using miRNeasy Mini Kit (Cat 217004)
RealSeq single-adapter ligation protocol for small RNA-sequening of biofluids

value: plasma

tag: main group

value: VTE


title: WJL2650_RLF_N025_JoinT


title: TF-1, myc-DNMT3A R882C, CST

value: Human embryonic kidney

tag: chip antibody


title: RNA-seq_6.W

source_name: Whole kidney, biol rep 1

value: male


title: WJL2648_RLF_N025_JoinT

value: vAbl-ProB

value: CTR


title: 2022 plasma;Control

value: Control


title: RNA-seq_62.V

source_name: Post-capillary venules, biol rep 4

value: Yes

value: Post-capillary venules


title: RNA-seq_59.W

source_name: Whole kidney, biol rep 3

value: Kidney


title: RNA-seq_59.V

source_name: Post-capillary venules, biol rep 3


title: WJL2646_RLF_N025_JoinT

value: ATRi


title: WJL2647_RLF_N025_JoinT


title: WJL2644_RLF_N025_JoinT

value: WT


title: RNA-seq_7.V

source_name: Post-capillary venules, biol rep 2


title: 1821 plasma;VTE


title: 1838 plasma;Control


title: WJL2643_RLF_N025_JoinT

value: ATMi


title: WJL2642_RLF_N025_JoinT


title: RNA-seq_6.V

source_name: Post-capillary venules, biol rep 1


title: WJL2641_RLF_N025_JoinT


title: RNA-seq_62.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: RNA-seq_7.W

source_name: Whole kidney, biol rep 2

value: No

value: Whole kidney

value: Cecal ligation & puncture (CLP) sepsis


title: WJL2639_RLF_N025_JoinT

value: pro-B cells

value: Polθi #1


title: WJL2640_RLF_N025_JoinT


title: RNA-seq_59.P

source_name: Peritubular capillaries, biol rep 3

value: 4 h


title: 1801 plasma;Control

value: plasma


title: 1782 plasma;VTE

value: VTE


title: 1755 plasma;VTE


title: WJL2637_RLF_N025_JoinT

value: vAbl-ProB

value: Parp1i #2


title: WJL2636_RLF_N025_JoinT


title: WJL2635_RLF_N025_JoinT


title: RNA-seq_7.P

source_name: Peritubular capillaries, biol rep 2

value: male

value: Yes


title: WJL2649_RLF_N025_JoinT

value: CTR


title: WJL2645_RLF_N025_JoinT

value: ATRi


title: 1720 plasma;VTE


title: WJL2634_RLF_N025_JoinT

value: WT

value: Parp1i #1


title: WJL2633_RLF_N025_JoinT


title: 1719 plasma;VTE


title: 1802 plasma;Control

value: Control


title: RNA-seq_6.P

source_name: Peritubular capillaries, biol rep 1

value: Kidney

value: Peritubular capillaries


title: WJL2631_RLF_N025_JoinT


title: RNA-seq_62.G

source_name: Glomeruli, biol rep 4

value: Glomeruli

value: Cecal ligation & puncture (CLP) sepsis


title: WJL2630_RLF_N025_JoinT

value: pro-B cells


title: WJL2629_RLF_N025_JoinT


title: WJL2632_RLF_N025_JoinT


title: WJL2628_RLF_N025_JoinT

value: Mre11(en)i #2


title: 1683 plasma;Control

value: plasma


title: RNA-seq_7.G

source_name: Glomeruli, biol rep 2

value: 4 h


title: WJL2626_RLF_N025_JoinT

value: vAbl-ProB


title: 1632 plasma;Control


title: WJL2624_RLF_N025_JoinT

value: Mre11(en)i #1


title: WJL2625_RLF_N025_JoinT


title: RNA-seq_6.G

source_name: Glomeruli, biol rep 1

value: male


title: WJL2627_RLF_N025_JoinT

source_name: vAbl-ProB


title: RNA-seq_62.A

source_name: Arterioles, biol rep 4

value: Yes

value: Arterioles


title: 1606 plasma;Control

source_name: plasma


title: WJL2623_RLF_N025_JoinT


title: WJL2622_RLF_N025_JoinT

value: CTR


title: 1561 plasma;VTE

value: VTE


title: WJL2621_RLF_N025_JoinT

value: WT


title: RNA-seq_59.A

source_name: Arterioles, biol rep 3


title: 1455 plasma;VTE


title: WJL2620_RLF_N025_JoinT


title: BcellsfromCKOmicereplicate3

city: Shanghai

first: dai

last: dai

state: Shanghai

address: 上海市黄浦区山东中路仁济医院西院区

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Clean reads were aligned to mm10 reference genome with Hisat2 (v2.1.0) using default parameters. Gene expression levels were counted with HT-seq (v0.11.2) or featureCounts using default ‘union’ mode. Differential expressions of genes were conducted by DESeq2 (v1.24.0) package.
Assembly: mm10
Supplementary files format and content: comma-separated values, containing the raw counts of genes for all processed samples or the differentially expressed genes analysis results.

source_name: spleen

extract_protocol:
Splenic B cells from C57BL/6J mice were retrovirally transduced with pMYs-IRES-GFP or pMYs-Zeb2-IRES-GFP plasmids. Splenic B cells from Cas9-EGFP mice were retrovirally transduced with sg-NC, sg-Zeb2, sg-T-bet plasmids. The infected cells were further cultured in the presence of mouse ABC-skewing cocktail as described above for 3 days. Cells were stained with anti-mouse CD19 and CD19+EGFP+ (for overexpression) or CD19+EGFP+BV421+ cells were FACS sorted. The harvested cells were washed twice in PBS by centrifugation at 400 g for 5 min. RNA was extracted with RNeasy Micro kit for Zeb2 overexpressed B cells or TRIzol reagent.
RNA was assessed with an Agilent 2100 Bioanalyzer (RNA integrity number > 7 for all samples) and used as input for TruSeq RNAseq library kit or SMART-Seq v4 Ultra Low Input RNA kit for Sequencing. After quality assessment, cDNA libraries were pooled and processed by an Illumina NovaSeq 6000 sequencer for 150 bp paired-end sequencing.

value: spleen


title: RNA-seq_59.G

source_name: Glomeruli, biol rep 3

value: Kidney


title: 1409 plasma;VTE


title: BcellsfromCKOmicereplicate2

address: 上海市黄浦区山东中路仁济医院西院区


title: BcellsfromCKOmicereplicate1

address: 上海市黄浦区山东中路仁济医院西院区


title: BcellsfromWTmicereplicate3

address: 上海市黄浦区山东中路仁济医院西院区


title: 1399 plasma;VTE


title: RNA-seq_6.A

source_name: Arterioles, biol rep 1


title: RNA-seq_61.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Sham-operated


title: 1652 plasma;Control

value: Control


title: BcellsfromWTmicereplicate1

address: 上海市黄浦区山东中路仁济医院西院区


title: 1332 plasma;VTE


title: BcellsfromWTmicereplicate2

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_57.W

source_name: Whole kidney, biol rep 3


title: Tbx21_B_replicate3 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_33.W


title: Zeb2_B_replicate2 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: Tbx21_B_replicate1 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: 1148 plasma;Control


title: WJL2638_RLF_N025_JoinT

value: pro-B cells

value: Polθi #1


title: 1075 plasma;VTE

value: plasma


title: RNA-seq_3.W

source_name: Whole kidney, biol rep 1

value: 4 h


title: Zeb2_B_replicate1 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_61.V

source_name: Post-capillary venules, biol rep 4

value: Post-capillary venules


title: RNA-seq_7.A

source_name: Arterioles, biol rep 2

value: male

value: Cecal ligation & puncture (CLP) sepsis


title: NC_B_replicate3 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: NC_B_replicate2 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: 1066 plasma;Control


title: NC_B_replicate1 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: ABC_replicate3 (in vitro induction)

address: 上海市黄浦区山东中路仁济医院西院区


title: ABC_replicate2 (in vitro induction)

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_33.V

source_name: Post-capillary venules, biol rep 2

value: Yes


title: Tbx21_B_replicate2 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: 941 plasma;VTE


title: RNA-seq_3.V

source_name: Post-capillary venules, biol rep 1


title: ABC_replicate1 (in vitro induction)

address: 上海市黄浦区山东中路仁济医院西院区


title: NC_B_replicate3 (in vitro induction)

address: 上海市黄浦区山东中路仁济医院西院区


title: Zeb2_B_replicate3 (sg edited)

address: 上海市黄浦区山东中路仁济医院西院区


title: 1046 plasma;Control


title: NC_B_replicate2 (in vitro induction)

address: 上海市黄浦区山东中路仁济医院西院区


title: Tofa-treated_replicate3

address: 上海市黄浦区山东中路仁济医院西院区


title: NC_B_replicate1 (in vitro induction)

address: 上海市黄浦区山东中路仁济医院西院区


title: 712 plasma;VTE


title: 1227 plasma;Control


title: Tofa-treated_replicate2

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_57.P

source_name: Peritubular capillaries, biol rep 3

value: Peritubular capillaries


title: Tofa-treated_replicate1

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_33.P

source_name: Peritubular capillaries, biol rep 2


title: 707 plasma;VTE

value: VTE


title: Tofa-mock_replicate3

address: 上海市黄浦区山东中路仁济医院西院区


title: Tofa-mock_replicate2

address: 上海市黄浦区山东中路仁济医院西院区


title: 697 plasma;Control


title: RNA-seq_57.V

source_name: Post-capillary venules, biol rep 3

value: WT


title: Tofa-mock_replicate1

address: 上海市黄浦区山东中路仁济医院西院区

value: spleen


title: 611 plasma;VTE


title: 940 plasma;Control


title: Zeb2_B_replicate2 (Zeb2 overexpression)

address: 上海市黄浦区山东中路仁济医院西院区


title: Zeb2_B_replicate1 (Zeb2 overexpression)

address: 上海市黄浦区山东中路仁济医院西院区


title: NC_B_replicate3 (Zeb2 overexpression)

address: 上海市黄浦区山东中路仁济医院西院区


title: 573 plasma;Control


title: NC_B_replicate2 (Zeb2 overexpression)

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_57.G

value: Kidney

value: Glomeruli


title: 560 plasma;Control


title: NC_B_replicate1 (Zeb2 overexpression)

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_61.P

source_name: Peritubular capillaries, biol rep 4


title: RNA-seq_33.G

source_name: Glomeruli, biol rep 2


title: CUTRUN-Zeb2

address: 上海市黄浦区山东中路仁济医院西院区

data_processing:
ATAC-Seq analysis: Clean reads were aligned to GRCm38 reference genome using Bowtie2 (v2.3.5) with the default setting followed by removing PCR duplicates using Sambamba. Peaks were called using Genrich with parameter -FDR 0.01. For track display, alignments were converted to bigwig file using bedtools.
CUT&RUN analysis:  The adaptor sequences were discarded by Trimmomatic before alignment. To visualize CUT&RUN datasets with UCSC genome browser, the CUT&RUN reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 (v2.3.5) software. Duplicated reads were removed using ‘make tag directory’ in HOMER(v4.11) with the parameter -tbp 1. The makeUCSCfile in Homer was used for visualization in UCSC genome browser.
CUT&Tag analysis: After trimming the adapters of reads and removing low-quality bases by TrimGalore software in paired-end mode, clean reads were mapped to mm10 reference genome with Bowtie2 (v2.3.5) followed by removing PCR duplicates using Picard (v2.19.0). The genome browser tracks in bigwig format were produced from merged replicates using deepTools (v2.0) and peaks were called using MACS2 (v2.1.2) using parameters -f BAMPE –SPMR -nomodel. Enriched transcription factor binding motifs were searched by HOMER (v4.11). A set of sequences were searched for individual matches to each of the motif using FIMO. All analysis data were visualized using the UCSC genome browser.
Assembly: mm10
Supplementary files format and content: BigWigfile for display of dense, continuous data in a genome browser track
Supplementary files format and content: BedGraph file that allows display of continuous-valued data in a track in UCSC.
Supplementary files format and content: narrowpeak file containing peaks from merged sample.

extract_protocol:
ATAC-Seq: CD11c+T-bet+ and CD11c-T-bet- B cells were sorted by flow cytometry from bm12-induced T-bet reporter mice. Splenic B cells from B-Zeb2KO and CD19-cre mice were cultured in the presence of mouse ABC-skewing cocktail as described above for 3 days and were purified using Dead Cell Removal Microbeads. The harvested cells were resuspended in lysis buffer (10 mM Tris-Cl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Igepal CA-630) and incubated on ice for 10 min following centrifugation  at 500g for 5 min. CUT&RUN: CD19hiCD11c+CD21- cells were sorted from IMQ-induced lupus mice and incubated with Concanavalin A Magnetic Beads. Cells were permeabilized and then incubated with primary antibodies against Zeb2 for 2 hours followed with Goat Anti-Rabbit IgG secondary antibody for 1 hour. This mixture of beads and cells was resuspended in pAG-MNase Enzyme and incubated for 1 hour followed with activation of enzyme by adding Calcium Chloride at 4°C for 30 min. Then, DNA was extracted using phenol–chloroform–isoamyl alcohol as the input.  CUT&Tag: Splenic B cells from C57BL/6J mice were cultured in the presence of mouse ABC-skewing cocktail as described above for 3 days and were purified using Dead Cell Removal Microbeads. The harvested cells were incubated with Concanavalin A Magnetic Beads. Cells were permeabilized and then incubated with primary antibodies against Zeb2 for 2 hours followed with Goat Anti-Rabbit IgG secondary antibody for 1 hour in Dig-Wash Buffer at room temperature. The 0.04 uM pG-Tn5 transposon were added for tagmentation at room temperature for 1 hour. Then, DNA was extracted using phenol–chloroform–isoamyl alcohol.
ATAC-Seq: DNA library for ATAC-seq was generated by PCR using TruePrep Index Kit v2 for Illumina for 11 cycles. PCR cleanup of libraries was performed using VAHTS DNA Clean Beads at a 1:1.2 ratio. CUT&RUN: The libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's instruction. Libraries with different indexes from NEBNext Multiplex Oligos for Illumina were pooled and sequenced with an Illumina Hiseq PE150. CUT&Tag: CUT&Tag libraries were prepared and cleaned up using Ampure XP beads (Beckman Coulter, Cat#A63880) and pooled together for paired-end sequencing..
ATAC-Seq, CUT&RUN,CUT&Tag


title: RNA-seq_3.G

source_name: Glomeruli, biol rep 1


title: CUTTAG-NC

address: 上海市黄浦区山东中路仁济医院西院区


title: CUTTAG-ZEB2

address: 上海市黄浦区山东中路仁济医院西院区


title: 544 plasma;VTE

source_name: plasma


title: 558 plasma;VTE


title: 520 plasma;Control


title: CKOBcells, rep2

address: 上海市黄浦区山东中路仁济医院西院区

source_name: spleen


title: WTBcells, rep1

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_3.P

source_name: Peritubular capillaries, biol rep 1


title: Zeb2_B_replicate3 (Zeb2 overexpression)

address: 上海市黄浦区山东中路仁济医院西院区


title: CKOBcells, rep1

address: 上海市黄浦区山东中路仁济医院西院区


title: 408 plasma;Control


title: RNA-seq_61.G

source_name: Glomeruli, biol rep 4


title: RNA-seq_33.A

value: Arterioles


title: 334 plasma;VTE


title: CD11c-T-bet-Bcells, rep2

address: 上海市黄浦区山东中路仁济医院西院区


title: CD11c-T-bet-Bcells, rep3

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_3.A

source_name: Arterioles, biol rep 1

value: Sham-operated


title: CD11c-T-bet-Bcells, rep1

address: 上海市黄浦区山东中路仁济医院西院区


title: CD11c+T-bet+Bcells, rep2

address: 上海市黄浦区山东中路仁济医院西院区


title: CD11c+T-bet+Bcells, rep3

address: 上海市黄浦区山东中路仁济医院西院区


title: RNA-seq_100.W

source_name: Whole kidney, biol rep 4

value: No

value: Whole kidney

value: Healthy control

value: 0 h


title: 275 plasma;Control

value: plasma

value: Control


title: WTBcells, rep2

address: 上海市黄浦区山东中路仁济医院西院区


title: CD11c+T-bet+Bcells, rep1

address: 上海市黄浦区山东中路仁济医院西院区


title: 115 plasma;Control


title: RNA-seq_61.A

source_name: Arterioles, biol rep 4

value: male

value: 4 h


title: RNA-seq_98.W

source_name: Whole kidney, biol rep 3


title: blood monocytes, LDLR-/- ApoB100/100, 3 months high-fat diet

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1

country: Finland

institute: university of eastern finland

description: 10x Genomics 3' scRNA-Seq

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing (cell calling) and gene counting were carried out using the Cell Ranger pipeline (version 3.0.2; 10x Genomics) and the 10x Genomics mm10 reference transcriptome package (version 3.0.0). Additionally, a custom quantification was performed including miRNA genes and this raw count matrix is provided as additional file for each sample.
Assembly: mm10
Supplementary files format and content: Tab-separated files and matrix files from the raw_feature_bc_matrix folder of Cell Ranger count pipeline output. Custom gtf file was used that contains microRNA genes.
Supplementary files format and content: Metadata files include a matching cell barcode in last column and indicate cell-containing droplets that were used in demultiplexing (R package DSB) and clustering (Python Scanpy workflow).

source_name: blood monocytes

extract_protocol:
Mice were sacrificed and tissue collections performed as described below. WAT: 200 mg of eWAT was minced and added to 2.5 ul of Miltenyi Adipose Tissue Dissociation solution (supplemented with BSA and HEPES) and incubated 45 min at 37C. During dissociation, the tissue was triturated 3 times (at 25, 35 and 45 min) to reduce cell multiplets. Tissue samples were passed through a 30 um cell strainer and washed with 3 ml of RPMI. Cells were centrifuged at 400 g for 8 min at 4C. The resulting cell pellet was resuspended in 300 ul of FACSs buffer. Samples were lysed using 1X RBC Lysis Buffer, Multi-species (eBioscience #00-4300-54) followed by TotalSeq staining (BioLegend) according to the manufacturer recommendations. Specifically, cells were gently mixed with 9x ice cold 1X RBC lysis buffer and incubated for 3 min on ice. Next, we added PBS to normalize the buffer and collected the cells by centrifugation at 400 g for 8 min at 4C). Cell pellets were resuspended with TotalSeq Mouse Hashtag Ab-DNA conjugate in FACS buffer (PBS-BSA). The solution was incubated in ice for 15-20 min to allow for hashtag Ab binding. Afterwards, cells were washed two times with PBS-BSA to removed unbound hashtag Ab. Dead cells were removed with Miltenyi Dead Cell Removal (Miltenyi Biotec #130-090-101). Blood: 150 ul of EDTA blood were gently mixed with 9x ice-cold 1x red blood cell lysis buffer and incubated for 3 min. Subsequently, cells were centrifuged at 500 g for 5 min at 4C. Cell pellets were resuspended with TotalSeq Mouse Hashtag Ab-DNA conjugate in FACS buffer (PBS-BSA). Next, cells were passed through a 30 um cell strainer and enriched for monocytes by anti-mouse Cd115 magnetic selection with Miltenyi mouse Cd115 MicroBead kit (# 130-096-354) as described by the manufacturer. First, we use 90 ul of cells resuspended in PBS with 0.5% BSAA and 2mM EDTA and mix it with 10 ul of Cd115-Biotin conjugates. After mixing and incubating for 10 min at 4C, cells were washed by adding 1-2 ml of buffer and centrifuged at 300g for 5-10 min at 4C. Cell pellets were resuspended in 80 ul of buffer. 20 ul of Anti-Biotin MicroBeads were added to the solution, mixed and incubated for 15 min at 4C. Cells were washed with 1-2 ml of buffer and centrifuged at 300g for 5-10 min at 4C. Cells were resuspended in 500 ul of buffer. MS columns were place in the magnet and cells were passed through a 30 um cell strainer before adding it to the MS column. All the steps were done at 4C afterwards. The columns were washed three times with 500 ul of buffer. After removing the column from the magnet, we added 1 ml of elution buffer and centrifuged the cells at at 300g for 5-10 min at 4C. From both tissues, cell pellets were resuspended in PBS containing 0.04 % BSA and counted by hemocytometry with trypan blue staining. Cell viability was between 74 % and 85 %. We aimed for a cell concentration of 3000 cells per sample and loaded the cell suspension into the Chromium Controller microfluidics chip (10x Genomics). In each experiment group, cell isolation was carried out separately from 3 male mice and subsequently the cells were pooled in equal proportions into one lane of the Chromium Controller microfluidics chip (10x Genomics).
The Chromium Single Cell 3’ Kit (v2 Chemistry; 10x Genomics) was used to prepare scRNA-Seq libraries.

value: blood monocytes

tag: diet

value: 3 months high-fat diet


title: blood monocytes, LDLR-/- ApoB100/100, 1 month high-fat diet, LPS injection

description: 10x Genomics 3' scRNA-Seq

value: 1 month high-fat diet

value: LPS injection (100ng, one time, intraperitoneal, 2 weeks before sacrifice)


title: RNA-seq_57.A

source_name: Arterioles, biol rep 3

value: WT

value: Yes


title: 38 plasma;VTE

value: VTE


title: 89 plasma;Control


title: blood monocytes, LDLR-/- ApoB100/100, 1 month high-fat diet

description: 10x Genomics 3' scRNA-Seq


title: blood monocytes, wild type, chow diet

description: 10x Genomics 3' scRNA-Seq

value: wild type

value: chow


title: white adipose tissue, LDLR-/- ApoB100/100, 3 months high-fat diet

description: 10x Genomics 3' scRNA-Seq

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue


title: white adipose tissue, LDLR-/- ApoB100/100, 1 month high-fat diet, LPS injection

description: 10x Genomics 3' scRNA-Seq


title: RNA-seq_100.V

source_name: Post-capillary venules, biol rep 4

value: Kidney

value: Post-capillary venules


title: white adipose tissue, LDLR-/- ApoB100/100, 1 month high-fat diet

description: 10x Genomics 3' scRNA-Seq


title: 10 plasma;VTE


title: RNA-seq_98.V

value: Healthy control

value: 0 h


title: Treated_11

city: Guangzhou

first: Rui

last: Xiang

state: Guangdong

address: the 26th Yuancun Erheng Road

institute: the sixth affiliated hospital of Sun Yat-sen University

description: from patients with endometriosis who received surgery

data_processing:
FastQC (v0.11.7, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was employed to process raw sequencing data.
Trim_galore was used to remove reads containing adapters, more than 10 % unknown nucleotides (N), and more than 50% of low quality (Q-value no more than 20) bases.
HISAT2 was used to map the processed paired-end reads to the human genome GRCh38 from Gencode v26.
FeatureCount was used to generate the count value of gene expression in the form of a matrix.
TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value matrix was caculated.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts and TPM for every gene and every sample

source_name: secretory eutopic endometrium

extract_protocol:
Total RNA from each sample was extracted by RNeasy Micro Kit (74004；Qiagen). Then it was quantified with Quabit HS RNA Kit (Q32855; Thermo Fisher Scientific). RIN was measured by Agilent Bioanalyzer 2100 (Agilent) and only those with RIN > 7 were considered as qualified.
MALBAC® KT110700796 (Xukang Medical·Yikon Genomics, Suzhou, Chian) was used for RNA reverse transcription and amplification. 1 uL of cDNA was diluted 10-fold and detected with Agilent Bioanalyzer 2100 (Agilent). cDNA size is 1000-10000bp.

value: endometriosis with surgical treatment

value: eutopic endometrium

value: endometrial cells


title: kidney, PND28, PAX8-cre Glis3 WT, rep4

city: Research Triangle Park

first: Hong Soon

last: Kang

state: NC

address: 111 T.W. Alexander Dr.

department: IIDL

institute: NIH/NIEHS

data_processing:
Read pairs were filtered to retain only those with mean base quality scores at least 20, then aligned via STAR v2.5 with parameters "--outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
Counts per gene were determined via featureCounts (Subread v1.5.0-p1) with parameters "-s0 -Sfr -p" for the unstranded PAX8-cre dataset and "-s2 -Sfr -p" for the reverse-stranded mCherry dataset.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand {Unstranded,Stranded} --outWigNorm RPM", followed by conversion to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: counts-per-gene matrix per dataset (tab-delimited text)
Supplementary files format and content: normalized depth tracks (bigWig)

source_name: kidney

extract_protocol:
Purelink RNA mini kit was used for RNA extraction
RNA libraries were prepared using TruSeq RNA library preparation kit from Illumina following manufacturer’s protocol.

value: kidney

value: PAX8-cre Glis3 WT


title: white adipose tissue, wild type, chow diet

description: 10x Genomics 3' scRNA-Seq

value: male


title: Treated_10


title: RNA-seq_96.W

source_name: Whole kidney, biol rep 2

value: No

value: Whole kidney


title: RNA-seq_93.V

source_name: Post-capillary venules, biol rep 1

value: WT

value: Yes


title: blood monocytes, LDLR-/- ApoB100/100, chow diet

description: 10x Genomics 3' scRNA-Seq

value: blood monocytes


title: kidney, PND28, PAX8-cre Glis3 WT, rep1


title: kidney, PND28, PAX8-cre Glis3 KO, rep5

value: PAX8-cre Glis3 KO


title: kidney, PND28, PAX8-cre Glis3 KO, rep4


title: RNA-seq_93.W

source_name: Whole kidney, biol rep 1


title: RNA-seq_100.P

source_name: Peritubular capillaries, biol rep 4

value: Peritubular capillaries


title: white adipose tissue, LDLR-/- ApoB100/100, chow diet

description: 10x Genomics 3' scRNA-Seq

value: epididymal white adipose tissue

value: chow


title: Treated_12


title: Treated_9


title: kidney, PND28, PAX8-cre Glis3 WT, rep3


title: RNA-seq_98.P

source_name: Peritubular capillaries, biol rep 3

value: Kidney

value: Healthy control


title: Treated_7

value: endometriosis with surgical treatment


title: kidney, PND28, PAX8-cre Glis3 KO, rep3


title: kidney, PND28, PAX8-cre Glis3 KO, rep2


title: RNA-seq_96.P

source_name: Peritubular capillaries, biol rep 2

value: 0 h


title: kidney, PND28, PAX8-cre Glis3 WT, rep5


title: kidney, PND14, PAX8-cre Glis3 WT, rep4


title: kidney, PND14, PAX8-cre Glis3 WT, rep5


title: RNA-seq_96.V

source_name: Post-capillary venules, biol rep 2

value: Post-capillary venules


title: kidney, PND14, PAX8-cre Glis3 WT, rep3

value: kidney


title: Treated_6

value: eutopic endometrium

value: endometrial cells


title: RNA-seq_93.P

source_name: Peritubular capillaries, biol rep 1

value: male


title: kidney, PND14, PAX8-cre Glis3 WT, rep2

value: PAX8-cre Glis3 WT


title: Treated_5


title: Treated_8


title: RNA-seq_100.G

source_name: Glomeruli, biol rep 4

value: WT

value: Glomeruli


title: RNA-seq_98.G

source_name: Glomeruli, biol rep 3

value: Yes


title: kidney, PND14, PAX8-cre Glis3 KO, rep5

value: PAX8-cre Glis3 KO


title: kidney, PND14, PAX8-cre Glis3 WT, rep1


title: Treated_3


title: Treated_4


title: Treated_2


title: kidney, PND14, PAX8-cre Glis3 KO, rep1


title: RNA-seq_96.G

source_name: Glomeruli, biol rep 2


title: kidney, PND28, PAX8-cre Glis3 KO, rep1


title: kidney, PND14, PAX8-cre Glis3 KO, rep3


title: kidney, PND14, PAX8-cre Glis3 KO, rep2


title: RNA-seq_93.G

source_name: Glomeruli, biol rep 1


title: kidney, PND14, PAX8-cre Glis3 KO, rep4


title: kidney, PND7, PAX8-cre Glis3 WT, rep5


title: kidney, PND7, PAX8-cre Glis3 WT, rep3


title: Treated_1


title: RNA-seq_100.A

source_name: Arterioles, biol rep 4

value: Arterioles


title: kidney, PND7, PAX8-cre Glis3 WT, rep4


title: kidney, PND7, PAX8-cre Glis3 WT, rep1


title: Untreated_6

description: from patients with endometriosis who didn't receive surgery

value: endometriosis without surgical treatment


title: Untreated_5


title: kidney, PND7, PAX8-cre Glis3 WT, rep2


title: RNA-seq_98.A

source_name: Arterioles, biol rep 3


title: RNA-seq_96.A

source_name: Arterioles, biol rep 2


title: kidney, PND7, PAX8-cre Glis3 KO, rep4


title: Untreated_4

source_name: secretory eutopic endometrium


title: kidney, PND7, PAX8-cre Glis3 KO, rep5

source_name: kidney


title: RNA-seq_93.A

source_name: Arterioles, biol rep 1


title: kidney, PND7, PAX8-cre Glis3 KO, rep2


title: Untreated_3


title: Untreated_2


title: kidney, PND28, mCherry Glis3 WT, rep5

value: mCherry Glis3 WT


title: test_re_rep3

city: Chongqing

first: Xuemei

address: No. 1, Medical College Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

source_name: peritoneal cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: peritoneal cells

value: rPepO training with S.a restimulation


title: kidney, PND7, PAX8-cre Glis3 KO, rep1


title: kidney, PND28, mCherry Glis3 WT, rep4


title: test_re_rep2


title: Untreated_1


title: kidney, PND28, mCherry Glis3 WT, rep2


title: test_re_rep1


title: kidney, PND28, mCherry Glis3 WT, rep1


title: kidney, PND28, mCherry Glis3 WT, rep3


title: test_rep3

value: rPepO training


title: kidney, PND28, mCherry Glis3 KO, rep5

value: mCherry Glis3 KO


title: HyDs3_2

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

institute: Jawaharlal Nehru University

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning thea reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Phytozome v3.3.2
Supplementary_files_format_and_content: FPKM values in excel format

organism: Sorghum bicolor

source_name: Stem Internode

growth_protocol: Hybrid Sweet Sorghum CSH22SS plants were raised in an open field

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions

value: Middle internode

tag: developmental stage

value: Booting (Ds3)

tag: cultivar


title: HyDs3_1


title: kidney, PND28, mCherry Glis3 KO, rep3

value: kidney


title: test_rep2

tag: cell type


title: HyDs2_2

value: Booting (Ds2)


title: kidney, PND28, mCherry Glis3 KO, rep2

tag: genotype


title: kidney, PND28, mCherry Glis3 KO, rep1


title: kidney, PND7, PAX8-cre Glis3 KO, rep3


title: test_rep1

tag: treatment


title: HyDs2_1


title: kidney, PND14, mCherry Glis3 WT, rep4


title: kidney, PND14, mCherry Glis3 WT, rep5


title: control_re_rep3

value: negative control with S.a restimulation


title: kidney, PND14, mCherry Glis3 WT, rep3


title: HyDs1_2

value: Booting (Ds1)


title: kidney, PND14, mCherry Glis3 WT, rep2


title: kidney, PND14, mCherry Glis3 KO, rep5


title: HyDs1_1


title: control_re_rep1

value: WT


title: control_re_rep2


title: kidney, PND14, mCherry Glis3 WT, rep1


title: kidney, PND14, mCherry Glis3 KO, rep4; outlier removed from analysis


title: HyP_2

value: Physiological Maturity


title: kidney, PND14, mCherry Glis3 KO, rep2


title: control_rep3

value: negative control


title: kidney, PND28, mCherry Glis3 KO, rep4


title: HyP_1


title: control_rep2


title: kidney, PND7, mCherry Glis3 WT, rep5


title: kidney, PND7, mCherry Glis3 WT, rep4


title: control_rep1


title: HyM_2

value: Milky stage


title: HyM_1


title: kidney, PND7, mCherry Glis3 WT, rep2


title: GF5_MC903

city: seoul

first: Jimin

last: Cha

address: 50-1, Yonsei-ro

country: South Korea

institute: Yonsei university

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 1.3.4d, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read count values for each sample

source_name: Skin

growth_protocol: Not applicable

extract_protocol:
Skin fresh tissue was achieved, total skin RNA were prepared using RNeasy® Fibrous Tissue Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were generated using TruSeq RNA Sample Prep Kit v2(Illumina), and the samples were sequenced on HiSeq4000.

treatment_protocol: The mice were treated with ethanol or MC903 for 5 times daily.

value: Skin

tag: group

value: germ-free


title: kidney, PND7, mCherry Glis3 WT, rep3

value: mCherry Glis3 WT


title: HyB_2

value: Booting


title: kidney, PND7, mCherry Glis3 WT, rep1


title: kidney, PND7, mCherry Glis3 KO, rep5


title: HyB_1


title: kidney, PND7, mCherry Glis3 KO, rep4


title: kidney, PND7, mCherry Glis3 KO, rep3


title: GF5_Ctrl

tag: strain

value: Ethanol


title: kidney, PND7, mCherry Glis3 KO, rep2

tag: tissue