title: 18_3414.sample

city: Milan

first: Giulia

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference mouse genome GRCm38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode v. M13 for the striatum tissue; Gencode v. M16 for the SVZ tissue)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: NestinTK-  PBS

extract_protocol:
SVZ and striatum were removed, flash frozen on dry ice, and RNA was harvested using Rnase Mini Kit (Qiagen Cat No./ID: 74106)
For SVZ tissue libraries were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA) performing 10 cycles of amplification, according to the manufacturer’s instructions, while for the striatum tissue libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

value: neural precursor cells from SVZ

value: brain

tag: genotyping

value: wild type

value: PBS


title: Day3_SNC_rep2

status: Public on Dec 08 2022

type: SRA

city: Ann Arbor

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

country: USA

institute: University of Michigan

description:
Reprocess of GSM4653877
post_injury_day_3.RDS

library_source: transcriptomic

data_processing:
NovaSeq control software 1.6.0, RTA v3.4.4
Cellranger version 3.1.0 used with mm10 genome to align and count reads and generate filtered_feature_bc_matrix with default settings
filtered_feature_bc_matrix imported with R 4.1.2 and Seurat 4.0.5; cells with more than 7500 features, fewer than 500 features, more than 15% mitochondrial removed
Seurat SCTransform + CCA used to normalize and integrate datasets
PCA dimension reduction
UMAP visualization
Assembly: mm10
Supplementary files format and content: Seurat Objects in R data format. Read into R using the command readRDS()

molecule: total RNA

organism: Mus musculus

source_name: sciatic nerve trunk

extract_protocol:
mice were perfused with ice-cold saline solution, sciatic nerve trunks harvested and kept on ice. On ice, nerves were minced and subsequentily digested in collagenase at 37°C for 45-60 min. To block gene transcription, actinomycin D was added to the digestion step.  Cell suspensions were loaded on a Percoll gradient, cells collected, and myelin depleted using a myelin depletion column. To enrich for immune cells, some samples were run over an anti-CD45 or anti-CD11b column (Miltenyi, 130-052-301).
The Chromium Next GEM Single Cell 3’ Reagent kit v3.1 (Dual Index) was used. Barcoding and library preparation was performed following the manufacturer’s protocols. Briefly, to generate single-cell gel-bead-in-emulsion (GEMs) solution, approximately 15,000 cells, in a final volume of 43 µl, were loaded on a Next GEM Chip G (10x Genomics) and processed with the 10x Genomics Chromium Controller

treatment_protocol: mid-thigh sciatic nerve crush

tag: strain

tag: condition


title: 17_3422.sample

middle: Maria

tag: cell type

tag: tissue

tag: treatment


title: Tasmanian_devil_HiC

city: Cerdanyola del Valles

first: Lucía

last: Alvarez-Gonzalez

state: Barcelona

address: Campus de la UAB, Bellaterra

department: Dept. Biologia Cel.lular, Fisiologia i Immunologia

country: Spain

institute: Universitat Autonoma de Barcelona

library_source: genomic

data_processing:
HiC: BBDuk (version 09/2019) was used for quality check and trimming of the raw fastq sequences. HiC data processing was conducted using TADbit
ChIP-seq: Reads were trimmed using Trimmomatic (version 0.39).  Trimmed fastq files were then aligned to the reference genome using bwa-mem (version 0.7.17). Alignments with a MAPQ > 30 were extracted and used as input for MACS2 (version 2.2.7.1).
RNA-seq: BBDuk (version 09/2019) was used for quality check and trimming of the raw. Then, reads were mapped with STAR (version 2.7.10a ) using the end-to-end alignment mode and gene expression quantification was performed with featureCounts.
Assembly: Elephant (this paper); Aardvark (OryAfe1.0_HiC); Tasmanian devil (mSarHar1.11); Tammar wallaby (me-1k)
Supplementary files format and content: HiC: Mapped reads files; ChIP-seq: BedGraph coverage files;RNA-seq: tab-delimited text files include raw counts

molecule: genomic DNA

organism: Sarcophilus harrisii

source_name: Fibroblasts

growth_protocol: Fibroblasts cell cultures were incubated at 37°C in 10% CO2. A cell fraction of each cell line was kept for immunofluorescence analysis and quality controls (see below) and the rest were fixated with 1% formaldehyde for 10’ at RT for Hi-C and ChIP-seq

extract_protocol:
For HiC:  Fibroblasts were processed following the in situ Hi-C protocol described by Vara et. Al 2019; For CTCF ChIP-seq: Lysates were clarified from Mnase I digested nuclei and CTCF-DNA complexes were isolated with CTCF antibody (Millipore, #07-729); For H3K4me ChIP-seq: Lysates were clarified from Mnase I digested nuclei and H3K4me3-DNA complexes were isolated with H3K4me3 antibody (Abcam, #ab8580); For RNA-seq: RNA was TRIzol (Invitrogen) extracted from Tasmanian devil cultured fibroblasts according to manufactures instructions.
Libraries were prepared for sequencing using standard Illumina protocols
Hi-C
ChIP-seq
RNA-seq

value: Fibroblasts


title: 2D13_rep2

city: Warszawa

first: Anna

last: Stroynowska-Czerwińska

address: Trojdena 4

department: Laboratory of Structural Biology

country: Poland

institute: International Institute of Molecular and Cell Biology

data_processing:
library strategy: CUT&RUN
Trimming was perfromed using TrimGalore! And FastQ Trimmer on Galaxy server.
CUT&RUN reads were aligned to hg38 genome using Bowtie2 with default parameters on Galaxy server.
Aligned reads were filtered out from blacklist reads, reads <20MAPQ and deduplicated
For peak calling MACS2 on Galaxy server was used.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated on filtered aligned reads
Supplementary_files_format_and_content: bed files were generated with MACS2

organism: Homo sapiens

source_name: Cervix cancer cells

growth_protocol: HeLa S3 cells and HeLa S3-derived stable cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Biowest) supplemented with 10% fetal bovine serum (FBS, Biowest) and penicillin-streptomycin solution (Biowest) at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
DNA was extracted from chromatin-DNA complexes released to supernatant by Mnase activity in HeLa S3 cells
Libraries were prepared using NEBNext Ultra II DNA Library Prep kit (NEB #E7103), according to protocol of Nan Liu, published on protocols.io dx.doi.org/10.17504/protocols.io.bagaibse. The libraries were paired-end sequenced on Illumina NovaSeq 6000.

value: stable HeLa S3 cell line expressing NLS-EYFP-2D13

tag: experiment

value: greenCUT&RUN

tag: c&r antibody

value: anti-GFP-Mnase (Marc Timmers)

tag: control sample


title: Day3_SNC_rep1

description:
Reprocess of GSM4653876
post_injury_day_3.RDS


title: 2D46_rep1

value: stable HeLa S3 cell line expressing NLS-EYFP-2D46


title: Elephant_HiC

organism: Loxodonta africana


title: 8_4013.sample

source_name: NestinTK-  GCV

value: Ganciclovir


title: control1_after

city: 上海

first: Zhu

last: YouWei

state: Shanghai

address: 130 Dong'an Road

department: Institutes of Biomedical Sciences

country: China

institute: Fudan university

data_processing:
Raw data statistics: Perform statistical analysis on subreads to obtain information such as the number, average length and GC content of subreads sequence.
CCS analysis:Perform Circular Consensus Calling on subreads to obtain high-quality CCS reads by using pbccs software (version 3.3.0), and perform statistical analysis on CCS sequences.
barcode split: Split CCS reads according to barcode by using lima software (version 1.9.0), and statistics the split results.
Statistics of target sequences abundance:If the target area is specified, the target sequence is captured according to the 10nt of upstream and downstream of the target sequence, otherwise, the target sequence refs to the full-length sequences.
Statistics of base distribution: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is extracted and mutation abundance information is counted.
Assembly: HIV-1, complete genome (GenBank: AF033819.3)
Supplementary files format and content: The target sequence is captured according to the 10nt of upstream and downstream of the HIV protease/ reverse transcriptase (PR/RT) region sequences (headers represent the date of sequencing and the sequencing number of the ccs reads)
Supplementary files format and content: The CCS reads are aligned to the reference sequence by using BWA software, and the section on the alignment is preserved to bam files

organism: Human immunodeficiency virus 1

source_name: peripheral blood

extract_protocol:
PacBio Sequel instrument (Pacific Biosciences of California, Inc., California, USA)
For each sample, >2ug purified PCR fragments (1kb~10kb) was used for library preparation. Fragmented DNAs were treated with End Prep Enzyme Mix for end repairing, 5’Phosphorylation and 3’dA-tailing in one reaction, followed by a T-A ligation to add universal hairpin adapters to both ends. Then the SMRTbell libraries were validated by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 3.0 Fluorometer. The final SMRTbell libraries were loaded on PacBio Sequel instrument according to manufacturer’s instructions (Pacific Biosciences of California, Inc., California, USA).

value: peripheral blood

tag: cell line

value: Primary cell

value: PBMC

tag: genotype

value: HAART only

tag: age

value: 23 years old

tag: gender

value: male


title: Day1_SNC_rep5


title: 6_4051.sample


title: Day1_SNC_rep4


title: 2C57_rep2

value: stable HeLa S3 cell line expressing NLS-EYFP-2C57


title: At ChIP-Seq GLK2 AT5G44190 replicate 2

city: Hong Kong

first: Sibo

last: REN

address: Sha tin CUHK

institute: The Chinese University of Hong Kong

data_processing:
ChIP-seq reads 100 bp from 3’ end were trimmed with the bowtie2 parameter -3 100.
ChIP-seq reads were aligned to plant reference genomes (Arabidopsis thaliana TAIR10, Nicotiana benthamiana version 2.5.1, Solanum lycopersicum SL4.0, Oryza sativa MSU7.0 and Zea mays RefGen_v4) using Bowtie 2 (version 2.3.2).
The ENCODE2 ChIP-seq pipline with MACS2 (version 2.2.1) and IDR (version 2.0.4.2) were used for peak calling. Peak summit positions were retrieved by using the “--call-summits” function in MACS2. The regions +/- 75bp from the summit position with signal fold-change in NarrowPeak format were then supplied to IDR, and the regions passed the IDR 0.01 and summit signal foldchange cut-off were kept and resized back to 150bp.
BigWig files were generated using the samtools view with binsize 1bp.
Supplementary files format and content: bigWig, narrowPeak

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
The nuclei were then isolated by filtration and centrifugation, and the chromatin was sonicated to sub-kb fragments using Bioruptor.
ChIP-seq libraries were prepared using the HiSeq X Ten.

value: Leaf

tag: replicate

value: replicate 2

tag: chip antibody

value: Rabbit polyclonal anti-GFP, Invitrogen, Cat# A-11122


title: 5_3403.sample

value: neural precursor cells from SVZ

value: brain

value: wild type


title: 19_3430.sample

value: PBS


title: Day1_SNC_rep3


title: 20_4041.sample

source_name: NestinTK+ PBS

value: NestinTK


title: At ChIP-Seq GLK1 AT2G20570 replicate 2


title: 2C57_rep1

value: greenCUT&RUN

value: anti-GFP-Mnase (Marc Timmers)


title: At ChIP-Seq GLK2 AT5G44190 replicate 1

value: replicate 1


title: 2C14_rep2

value: stable HeLa S3 cell line expressing NLS-EYFP-2C14


title: Day1_SNC_rep1


title: 16_3434.sample


title: Day1_SNC_rep2


title: Day0_Naive_rep2


title: 15_4054.sample


title: 13_4045.sample


title: RNA of geraniol3

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

description: Transcriptome of geraniol-treated P. aeruginosa PAO1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Assembly: Pseudomonas aeruginosa PAO1

organism: Pseudomonas aeruginosa PAO1

source_name: exponential growth phase culture

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAO1 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 1.0E8 CFU/mL. Geraniol was then added at a concentration of either 0 (control) or 1.25 μl/mL, respectively, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h.

value: geraniol-treated sample


title: 2C14_rep1


title: 2A13_rep2

value: stable HeLa S3 cell line expressing NLS-EYFP-2A13


title: 2A13_rep1


title: RNA of geraniol2


title: RNA of geraniol1


title: 2D13_rep1

value: stable HeLa S3 cell line expressing NLS-EYFP-2D13


title: NLS-EYFP_rep2

value: stable HeLa S3 cell line expressing NLS-EYFP


title: neurons, N/D replicate #2

city: New York

first: Edmund

last: Au

address: 630 West 168th Street, room P&S14-401

institute: Columbia University Irving Medical Center

data_processing:
RTA (Illumina for base calling.
bdcl2fastq2 (version 2.20) for converting BCL to fastq format coupled for adaptor trimming.
We performed a pseudoalignment to a kallisto index created from mouse transcriptome GRCm38 using kallisto (0.44.0).
We tested for differentially expressed genes under various conditions using Sleuth.
Genome_build: GRCm38
Supplementary_files_format_and_content: .csv Kallisto TPM counts for each gene for each sample

source_name: ES-derived neurons

growth_protocol: Transgenic ES cell lines were cultured and differentiated for 12 days to allow for expression of various gain of function constructs integral to the experiment before extraction. Cells are cultured in a modified GMEM (Gibco) media that contains small molecules (XAV-939 and SAG (Tocris)) in free floating culture into embryoid bodies (EBs). Conditional tdTomato reporter labels differentiated, post-mitotic neurons in these cultures.

extract_protocol:
Day 12 EBs were collected into a 15mL conical tube and spun down at 200xg for 5 minutes. EBs were then suspended in 500uL of 1x AccuMax (Gibco) enzyme solution with 10 Units DNAaseI (Thermo) and incubated at 370C for lysing. Lysate was quenched with 5mL of HEPES buffered saline and triturated into a single cell suspension and filtered with a 70um cell strainer. tdTomato+ differentiated neurons were sorted by flow cytometry (BD Influx System) directly into Trizol. mRNA was purified using an RNA miniprep kit (Zymo) and measured with a Bioanalyzer (Agilent) to ensure an RIN score of 7 or greater.
mRNA was enriched using a standard poly-A-pull-down prior to library construction with Illumina TruSeq chemistry.
The library is sequenced using Illumina NovaSeq 6000.

treatment_protocol: Two distinct ES cell lines are genetically designed to model neuron development with the addition of key factors that produce specific neuron classes

value: ES-derived neurons

tag: parental line

value: Dlx6-Cre; Ai9

tag: transcriptional specifiers

value: Nkx2-1, Dlx2

tag: time

value: differentiated for 12 days


title: 3_4052.sample

source_name: NestinTK+ GCV

value: neural precursor cells from SVZ

tag: strain

tag: genotyping

value: Ganciclovir


title: RNA of control3

description: Transcriptome of control of P. aeruginosa PAO1

value: native sample


title: 4_4001.sample

tag: cell type

value: brain


title: NLS-EYFP_rep1


title: neurons, N/D replicate #1


title: neurons, N/D/S replicate #2

value: Nkx2-1, Dlx2, St18


title: RNA of control2


title: HeLa_rep2

value: HeLa S3 cell line

value: greenCUT&RUN


title: 2_4055.sample

tag: tissue

value: NestinTK


title: RNA of control1

tag: treatment


title: At ChIP-Seq GLK1 AT2G20570 replicate 1

value: Leaf

value: replicate 1

value: Rabbit polyclonal anti-GFP, Invitrogen, Cat# A-11122


title: HeLa_rep1

tag: experiment

value: anti-GFP-Mnase (Marc Timmers)


title: 1_4003.sample


title: Day0_Naive_rep1

tag: condition


title: 9_4035.sample


title: Aged RVLM, set1, biological replicate 2

status: Public on Dec 07 2022

type: RNA

city: El Paso

first: Sivasai

last: Balivada

state: Texas

address: 4th floor, Bioscience research building

institute: University of Texas at El Paso

description:
Aged RVLM
Aged 1503053

data_processing:
Matrix non-normalized: To calculate threshold cycle (Ct) values, the background fluorescence of each well was identified by setting the start of baseline at cycle 3 and the end of baseline at cycle 15 for each array plate. The threshold value for Ct was manually selected, and the same threshold value (1.52) was used for all the arrays. After threshold selection, the Ct values of each array plate were exported as an Excel file. StepOnePlus software (Applied Biosystems) was used for Ct values extraction.
Matrix normalized: The Ct values for three of the five housekeeping genes (B2m, Hprt1, and Rplp1) were identified to be consistent between arrays and were therefore used as reference genes for normalizing RNA expression. The geometric mean of the B2m, Hprt1, and Rplp1 Ct values for each experimental RVLM sample/array was used for the ΔCt value calculation of each gene. Normalization process was performed in Microsoft Excel. Genes that showed <30 Ct value in more than 50% of the arrays were used in the final analysis. Seventy-nine of the 84 GABA and glutamate neurotransmission-related genes met these criteria. In contrast, Avp, Gabra6, Gabrr1, Grm6, and Slc1a7 genes did not meet these criteria and were removed from the final analysis.  Target gene signal normalized to geometric mean of B2m, Hprt1, and Rplp1 reference genes signal;  2–ΔCt, where –ΔCt = –(Ct_Target –geometric mean of B2m, Hprt1, and Rplp1 reference genes Ct values).  See Data table below.
Fold Change: Aged vs. young, aged vs. middle-aged, and middle-aged vs. young rats RVLM gene expression differences are represented as fold change values calculated using the 2–ΔΔCt method (Livak and Schmittgen, 2001). Fold change calculations were performed in Microsoft Excel.

label: SYBR Green

organism: Rattus norvegicus

source_name: Rostral ventrolateral medulla, Aged

label_protocol: Fifty ng of RNA from each sample was reverse transcribed and preamplified using an RT2 preamp cDNA synthesis kit (Qiagen, Inc.) with PBR-152Z RT2 preamp pathway primer mix (Qiagen, Inc.). Quantitative polymerase chain reactions were performed on these preamplified samples on StepOnePlus master cycler (Applied Biosystems™, Thermo Fisher Scientific) using Rat GABA & Glutamate RT2 Profiler PCR arrays (Qiagen, Inc., GeneGlobe ID PARN-152Z) with SYBR Green ROX qPCR master mix (Qiagen, Inc.,).

extract_protocol: Total RNA was extracted with Rneasy Lipid tissue Mini Kit followed by DNase I treatment.

value: Fischer 344

value: Male

tag: weight

tag: developmental stage

value: Aged

value: RVLM


title: Aged RVLM, set1, biological replicate 4

description:
Aged RVLM
Aged 15030515


title: Aged RVLM, set1, biological replicate 5

description:
Aged RVLM
Aged 1503051


title: Aged RVLM, set2, biological replicate 6

description:
Aged RVLM
Aged 17M2247


title: Aged RVLM, set2, biological replicate 9

description:
Aged RVLM
Aged 17M2254


title: Aged RVLM, set2, biological replicate 10

description:
Aged RVLM
Aged 17M225


title: Aged RVLM, set1, biological replicate 1

description:
Aged RVLM
Aged 1503052


title: Aged RVLM, set2, biological replicate 7

description:
Aged RVLM
Aged 17M2249


title: neurons, N/D/S replicate #1

value: ES-derived neurons

value: Dlx6-Cre; Ai9

value: differentiated for 12 days


title: Middle-aged RVLM, set2, biological replicate 7

description:
Middle-aged RVLM
Middle-aged 17M258

source_name: Rostral ventrolateral medulla, Middle-aged

value: Middle-aged


title: Aged RVLM, set1, biological replicate 3

description:
Aged RVLM
Aged 1503054


title: Middle-aged RVLM, set2, biological replicate 8

description:
Middle-aged RVLM
Middle-aged 17M252


title: Middle-aged RVLM, set1, biological replicate 3

description:
Middle-aged RVLM
Middle-aged 1504067


title: Middle-aged RVLM, set1, biological replicate 4

description:
Middle-aged RVLM
Middle-aged 1504061


title: Middle-aged RVLM, set1, biological replicate 2

description:
Middle-aged RVLM
Middle-aged 1504065


title: Middle-aged RVLM, set1, biological replicate 5

description:
Middle-aged RVLM
Middle-aged 1504068


title: Young RVLM, set2, biological replicate 8

description:
Young RVLM
Young 17M2236

source_name: Rostral ventrolateral medulla, Young

value: Young


title: Aged RVLM, set2, biological replicate 8

description:
Aged RVLM
Aged 17M2252


title: Young RVLM, set1, biological replicate 2

description:
Young RVLM
Young 1503059


title: Middle-aged RVLM, set2, biological replicate 6

description:
Middle-aged RVLM
Middle-aged 17M251


title: Young RVLM, set1, biological replicate 3

description:
Young RVLM
Young 15030510


title: Young RVLM, set2, biological replicate 7

description:
Young RVLM
Young 17M2242


title: Young RVLM, set2, biological replicate 6

description:
Young RVLM
Young 17M2237


title: Young RVLM, set1, biological replicate 4

description:
Young RVLM
Young 1503057


title: Young RVLM, set1, biological replicate 5

description:
Young RVLM
Young 1503056


title: Young RVLM, set1, biological replicate 1

description:
Young RVLM
Young 1503058


title: CCI, replicate 2

type: genomic

city: Zhuhai

first: Ying

last: Wang

state: Guangdong

address: 52 Meihua East Road

institute: The Fifth Affiliated Hospital, Sun Yat-sen University

description: DNA methylation of promoters in lumbar spinal cord of CCI2 rat on Day 14 after surgery

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, USA). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, USA)

scan_protocol: From the normalized log2-ratio data, a sliding-window (1500bp) peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) is applied to analysis the MeDIP-chip data. A one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether the probes are drawn from a significantly more positive distribution of intensity log2-ratios than those in the rest of the array. Each probe receives a -log10 p-value score from the windowed KS test around that probe (*_pvalues.gff). If several adjacent probes rise significantly above a set threshold, the region is assigned to an enrichment peak (EP). The peak data files (*_peaks.gff) are generated from the p-value data files (*_pvalues.gff). NimbleScan detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged.

data_processing: When comparing two groups’ differentially enriched regions we average the log2-ratio values for each group (Experiment and Control) and calculate M’ value (defined by the following equation) for each probe. Then we rerun the NimbleScan sliding-window peak-finding algorithm on these data to find the differential enrichment peaks (DEP). M’ = Average(log2 MeDIPE/InputE) - Average(log2 MeDIPC/InputC). The differential enrichment peaks (DEP) called by the NimbleScan algorithm are filtered according to the following criteria: i) At least one of the two groups has a median(log2 MeDIP/Input) >=0.3 and median(M')>0  ii) At least half of probes in a peak may have coefficient of variability (CV) <= 0.8 in both two groups

source_name: lumbar spinal cord, CCI, replicate 2 (IP sample)

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Genomic DNA (gDNA) was extracted from lumbar spinal cords using a DNeasy Blood & Tissue Kit (Qiagen, Germany) following the manufacturer's recommendations. The purified gDNA was then quantified and quality assessed by nanodrop ND-1000.

value: lumbar spinal cord

value: male

tag: sample type

value: IP-DNA

source_name: lumbar spinal cord, CCI, replicate 2 (Input sample)

value: Input-DNA


title: Middle-aged RVLM, set1, biological replicate 1

description:
Middle-aged RVLM
Middle-aged 1504062


title: CCI, replicate 1

description: DNA methylation of promoters in lumbar spinal cord of CCI1 rat on Day 14 after surgery

source_name: lumbar spinal cord,CCI, replicate 1 (IP sample)

source_name: lumbar spinal cord,CCI, replicate 1 (Input sample)


title: Sham, replicate 3

description: DNA methylation of promoters in lumbar spinal cord of Sham3 rat on Day 14 after surgery

source_name: lumbar spinal cord, Sham, replicate 3 (IP sample)

source_name: lumbar spinal cord, Sham, replicate 3 (Input sample)


title: Sham, replicate 2

description: DNA methylation of promoters in lumbar spinal cord of Sham2 rat on Day 14 after surgery

source_name: lumbar spinal cord, Sham, replicate 2 (IP sample)

source_name: lumbar spinal cord, Sham, replicate 2 (Input sample)


title: CHOW [15600]

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

label: cy3, cy5

organism: Canis lupus familiaris

source_name: Saliva

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood was purified using Proteinase K and phenol/chloroform with standard protocols. Genomic DNA extracted from saliva was extracted using the PerformaGene ND-100 Kit protocol.

tag: breed

value: Chow Chow


title: CHOW [29628]


title: CHOW [29619]


title: CHOW [29625]


title: MPOO [29574]

value: Medium Poodle - FCI


title: GLEN [4252]

source_name: Whole blood

value: Glen of Imaal Terrier


title: BMD- [29675]

value: Bernese Mountain Dog


title: CHOW [29624]


title: CCI, replicate 3

description: DNA methylation of promoters in lumbar spinal cord of CCI3 rat on Day 14 after surgery

source_name: lumbar spinal cord, CCI, replicate 3 (IP sample)

tag: gender

source_name: lumbar spinal cord, CCI, replicate 3 (Input sample)


title: CHOW [29623]


title: CHOW [29621]


title: MPOO [28470]


title: CHOW [29626]


title: SALU [27931]

value: Saluki


title: MPOO [28471]


title: CHOW [27589]


title: MPOO [28540]


title: PEMB [6635]

value: Pembroke Welsh Corgi


title: SALU [27919]


title: PEMB [6634]


title: BORZ [27925]

value: Borzoi


title: BULD [1197]

value: Bulldog


title: DOBP [6044]

value: Doberman Pinscher


title: Sham, replicate 1

description: DNA methylation of promoters in lumbar spinal cord of Sham1 rat on Day 14 after surgery

source_name: lumbar spinal cord, Sham, replicate 1 (IP sample)

source_name: lumbar spinal cord, Sham, replicate 1 (Input sample)


title: BLDH [28397]

value: Bloodhound


title: BORZ [27926]


title: HUSK [28488]

value: Siberian Husky


title: ITGY [28927]

value: Italian Greyhound


title: TPOO [27569]

value: Toy Poodle


title: CHOW [28881]


title: AUCD [27920]

value: Australian Cattle Dog


title: IWOF [24220]

value: Irish Wolfhound


title: BMD- [28877]


title: BLDH [1224]


title: SALU [27935]


title: CHIH [29576]

value: Chihuahua


title: SALU [27307]


title: BOX- [27199]

value: Boxer


title: SALU [27324]


title: DOBP [550]

source_name: Lymphocytes


title: SALU [27304]


title: CHIH [27323]


title: CHIH [27322]


title: SALU [27320]


title: BOX- [27189]


title: MPOO [27221]


title: SALU [27300]


title: COLL [27114]

value: Collie


title: BOST [27202]

value: Boston Terrier


title: MBLT [27125]

value: Miniature Bull Terrier


title: ESET [27021]

value: English Setter


title: AKIT [27032]

value: Akita


title: SALU [27315]

value: Saluki


title: WEIM [27436]

value: Weimaraner


title: SALU [27313]


title: PNTR [27059]

value: Pointer


title: SALU [27309]


title: SAMO [27123]

value: Samoyed


title: DOBP [27112]

value: Doberman Pinscher


title: COLL [27134]


title: BMAL [27146]

value: Belgian Malinois


title: BMD- [8434]

value: Bernese Mountain Dog


title: BMD- [2675]


title: BSJI [27185]

value: Basenji


title: BMD- [22420]


title: BMD- [951]


title: PUG [27052]

value: Pug


title: BMD- [22394]


title: BMD- [22408]


title: ECKR [27280]

value: English Cocker Spaniel


title: STBD [26691]

source_name: Muscle

value: Saint Bernard


title: BMD- [20640]


title: HUSK [26687]

value: Siberian Husky


title: AHRT [1119]

value: American Hairless Terrier


title: CAAN [26699]

value: Canaan Dog


title: STBD [26688]


title: MPOO [26698]

value: Medium Poodle - FCI


title: STBD [26690]


title: ENTL [26697]

value: Entlebucher Mountain Dog


title: STBD [26689]


title: SALU [27310]


title: BRIA [26696]

value: Briard


title: BMD- [26695]


title: GMSP [26684]

value: German Spaniel - FCI


title: HOVA [26685]

value: Hovawart


title: CHIH [26683]

value: Chihuahua


title: AMAL [26677]

value: Alaskan Malamute


title: WSSD [26680]

value: White Swiss Shepherd Dog


title: AIRT [26676]

value: Airedale Terrier


title: BORZ [26675]

value: Borzoi


title: AMAL [26679]


title: CHIH [26672]


title: STBD [26673]


title: CHIH [26671]


title: IWOF [26678]

value: Irish Wolfhound


title: LEON [21536]

value: Leonberger


title: STBD [26670]


title: STBD [26669]


title: EURA [26299]

value: Eurasier


title: GORD [26298]

value: Gordon Setter


title: STBD [26666]

value: Saint Bernard


title: ALES [26296]

value: Alano Espanol


title: WSSD [26667]


title: PEKE [1139]

value: Pekingese


title: AFFN [1138]

value: Unknown


title: CAAN [26229]

value: Canaan Dog


title: HOVA [26217]


title: SKYE [26228]

value: Skye Terrier


title: BRIA [26214]

value: Briard


title: PUG [26209]

value: Pug


title: XOLO [26248]

value: Xoloitzcuintli


title: FXTE [20236]

value: Fox Terrier


title: CHIN [24653]

value: Japanese Chin


title: WELT [966]

value: Welsh Terrier


title: GSNZ [26674]

value: Giant Schnauzer


title: PRES [1127]

value: Presa Canario


title: AMST [24028]

value: American Staffordshire Terrier


title: FCR- [24385]

value: Flat-Coated Retriever


title: SALU [1233]

value: Saluki


title: FOXH [23106]

value: Foxhound


title: KEES [23583]

value: Keeshond


title: KEES [13721]

source_name: Unknown Source


title: KEES [15642]


title: KEES [22824]


title: LAKE [26238]

value: Lakeland Terrier


title: KEES [14413]


title: FOXH [23116]


title: FOXH [23123]


title: FOXH [23114]


title: FOXH [23095]


title: FOXH [23058]


title: FOXH [23125]


title: FOXH [23085]


title: FOXH [23121]


title: FOXH [23112]


title: AIRT [9247]

value: Airedale Terrier


title: FOXH [23117]


title: FOXH [23081]


title: FOXH [23120]


title: FOXH [23068]


title: FOXH [23097]


title: UNKN [13435]

value: Unknown


title: UNKN [13436]


title: UNKN [24396]


title: UNKN [13433]


title: UNKN [13438]


title: UNKN [13445]


title: UNKN [13446]


title: FOXH [23104]


title: FOXH [23086]


title: UNKN [13437]


title: FOXH [23079]


title: UNKN [13444]


title: UNKN [13441]


title: UNKN [13442]


title: FOXH [23108]


title: UNKN [24395]


title: FOXH [23103]


title: UNKN [24394]


title: UNKN [13443]


title: UNKN [13432]


title: FOXH [23124]


title: FOXH [23071]


title: UNKN [24399]


title: UNKN [13440]


title: UNKN [24393]


title: UNKN [13439]


title: UNKN [13434]


title: UNKN [24398]


title: UNKN [24391]


title: UNKN [24397]


title: UNKN [24369]


title: UNKN [24380]


title: UNKN [24373]


title: UNKN [24389]


title: UNKN [24381]


title: UNKN [24386]


title: UNKN [24384]


title: UNKN [24376]


title: UNKN [24387]


title: UNKN [24390]


title: UNKN [24367]


title: UNKN [24388]


title: UNKN [24378]


title: UNKN [24365]


title: UNKN [24371]


title: UNKN [24372]


title: UNKN [24370]


title: UNKN [24366]


title: UNKN [24375]


title: UNKN [24364]


title: UNKN [24348]


title: UNKN [24360]


title: UNKN [24358]


title: UNKN [24357]


title: UNKN [24368]


title: UNKN [24379]


title: UNKN [24374]


title: UNKN [24356]


title: UNKN [24343]


title: UNKN [24345]


title: UNKN [13501]


title: UNKN [13500]


title: UNKN [13498]


title: UNKN [13487]


title: UNKN [13493]


title: UNKN [13491]


title: UNKN [13486]


title: UNKN [13485]


title: UNKN [13499]


title: UNKN [13481]


title: UNKN [13483]


title: UNKN [13475]


title: UNKN [13490]


title: UNKN [13473]


title: UNKN [13489]


title: UNKN [13472]


title: UNKN [13478]


title: UNKN [13480]


title: UNKN [13477]


title: UNKN [13464]


title: UNKN [13469]


title: UNKN [13471]


title: UNKN [13463]


title: UNKN [13462]


title: UNKN [13468]


title: UNKN [13484]


title: UNKN [13497]


title: UNKN [13461]


title: UNKN [13467]


title: UNKN [13466]


title: UNKN [13465]


title: UNKN [13538]


title: UNKN [24339]


title: UNKN [13536]


title: UNKN [24333]


title: UNKN [24332]


title: UNKN [13451]


title: UNKN [13452]


title: UNKN [13457]


title: UNKN [13458]


title: UNKN [13531]


title: UNKN [13456]


title: UNKN [13529]


title: UNKN [13533]


title: UNKN [13455]


title: UNKN [13449]


title: UNKN [13450]


title: UNKN [13448]


title: UNKN [13454]


title: UNKN [13453]


title: UNKN [13447]


title: UNKN [13527]


title: UNKN [13525]


title: UNKN [13518]


title: UNKN [13460]


title: UNKN [13516]


title: UNKN [13523]


title: UNKN [13517]


title: UNKN [13459]


title: UNKN [13522]


title: UNKN [13521]


title: UNKN [13514]


title: UNKN [13520]


title: UNKN [13506]


title: UNKN [13504]


title: UNKN [13503]


title: ARPD [36089]

value: Argentine Pila Dog


title: UNKN [13509]


title: ARPD [36091]


title: UNKN [13505]


title: MUTT [37718]

value: Mixed Breed


title: ARPD [36094]


title: BEAG [14188]

value: Beagle


title: MPIN [22887]

value: Miniature Pinscher


title: ARPD [36093]


title: AZWK [37000]

value: Azawakh


title: AZWK [37003]


title: UNKN [13502]


title: BEAG [13178]


title: AZWK [37002]


title: AZWK [37001]


title: ARPD [36086]


title: AZWK [36999]


title: ARPD [36079]


title: ARPD [36077]


title: ARPD [36075]


title: ARPD [36084]


title: UNKN [13507]


title: ARPD [36080]


title: ARPD [36067]


title: UNKN [13511]


title: ARPD [36066]


title: ARPD [36065]


title: ARPD [36064]


title: ARPD [36069]


title: ARPD [36063]


title: MPIN [33445]


title: NORF [34291]

value: Norfolk Terrier


title: BEAG [33038]


title: FXTE [33439]

value: Fox Terrier


title: BMAL [31966]

value: Belgian Malinois


title: NORF [31784]


title: AIRT [31965]


title: SPOO [31963]

value: Standard Poodle


title: LAKE [33291]


title: NORF [31783]


title: MNTY [33513]

value: Manchester Terrier (Toy)


title: NORF [31781]


title: ARPD [36074]


title: DDMT [33274]

value: Dandie Dinmont Terrier


title: BEAG [30743]


title: BEDT [31736]

value: Bedlington Terrier


title: SCWT [31233]

value: Soft Coated Wheaten Terrier


title: NORF [31762]


title: ARPD [36072]


title: BEAG [31606]


title: BEAG [31242]


title: BORT [28918]

value: Border Terrier


title: BORT [28917]


title: BOX- [33041]

value: Boxer


title: MNTY [33539]


title: WIFX [24274]

value: Wire Fox Terrier


title: VILL [35097]

value: Village Dog


title: JACK [6159]

value: Jack Russell Terrier


title: JACK [6165]


title: JACK [6167]


title: JACK [6173]


title: JACK [6166]


title: SKYE [28514]

value: Skye Terrier


title: SKYE [8390]


title: VILL [35094]


title: NORF [4673]


title: SKYE [8389]


title: VILL [35099]


title: VILL [35093]


title: VILL [35091]


title: VILL [35095]


title: PARS [2137]

source_name: Buccal cells

value: Parson Russell Terrier


title: MUTT [31605]

value: Mixed Breed


title: VILL [35086]


title: JACK [6161]


title: GSHP [10652]

value: German Shorthaired Pointer


title: VILL [35101]


title: BEAG [10654]

value: Beagle


title: VILL [35098]


title: VILL [35080]


title: VILL [35087]


title: GSHP [9003]


title: CHBR [14539]

value: Chesapeake Bay Retriever


title: NORF [4672]

value: Norfolk Terrier


title: VILL [35092]


title: MPIN [13106]

value: Miniature Pinscher


title: SHIH [10713]

value: Shih Tzu


title: SPDI [37815]

value: Spino Degli Iblei


title: SAMO [7779]

value: Samoyed


title: SPDI [37812]


title: SPDI [37818]


title: SPDI [37820]


title: SPDI [37816]


title: SPDI [37817]


title: SPDI [37813]


title: SPDI [37811]


title: SPDI [37805]


title: SPDI [37807]


title: SPDI [37810]


title: SPDI [37808]


title: SPDI [37801]


title: SPDI [37802]


title: SLOU [35530]

value: Sloughi


title: SLOU [35528]


title: SLOU [35518]


title: SPDI [37814]


title: LDSR [35474]

value: Landseer


title: SLOU [35515]


title: SPDI [37809]


title: LDSR [35473]


title: SPDI [37804]


title: SPDI [37803]


title: SPDI [37806]


title: LDSR [35498]


title: LDSR [35472]


title: LDSR [35470]


title: SLOU [35509]


title: LDSR [35469]


title: PQRB [34869]

value: Phuquoc Ridgeback


title: SLOU [34824]


title: LDSR [35468]


title: PQRB [34874]


title: SLOU [34825]


title: LDSR [35495]


title: PQRB [34773]


title: SLOU [34646]


title: PQRB [34763]


title: SLOU [34644]


title: PQRB [34766]


title: SLOU [34645]


title: KMUN [34614]

value: Kleine Munsterlander


title: SLOU [34662]


title: CHBR [34615]


title: SVAL [34555]

value: Swedish Vallhund


title: SVAL [34554]


title: SVAL [34552]


title: SVAL [34553]


title: BKHW [34540]

value: Bakharwal


title: PYRS [34488]

value: Pyrenean Shepherd


title: SLAP [34544]

value: Swedish Lapphund


title: AMST [34493]

value: American Staffordshire Terrier


title: PYRS [34486]


title: SLAP [34543]


title: RSTR [34485]

value: Russell Terrier


title: CCRT [34413]

value: Curly-Coated Retriever


title: POPO [34478]

value: Portuguese Podengo Pequeno


title: POPO [34479]


title: POPO [34477]


title: ANAT [34438]

value: Anatolian Shepherd Dog


title: POPO [34431]


title: SLOU [34642]


title: RSTR [34463]


title: SMFX [33812]

value: Smooth Fox Terrier


title: THRB [34146]

value: Thai Ridgeback


title: AFOX [34455]

value: American Foxhound


title: BTCO [34476]

value: Blue Tick Coonhound


title: SHIB [34127]

value: Shiba Inu


title: PGRT [33610]

value: Prague Ratter


title: LOWC [33687]

value: Lowchen


title: MNTY [33537]

value: Manchester Terrier (Toy)


title: SMFX [33811]


title: MANT [33536]

value: Manchester Terrier (Standard)


title: MNTY [33533]


title: MANT [33538]


title: MANT [33534]


title: MNTY [33527]


title: SMFX [33810]


title: MNTY [33531]


title: MANT [33526]


title: MANT [33524]


title: MNTY [33530]


title: MNTY [33529]


title: AMST [33493]


title: MANT [33528]


title: DDMT [33270]

value: Dandie Dinmont Terrier


title: MNTY [33522]


title: WELT [33494]

value: Welsh Terrier


title: MNTY [33523]


title: MALT [33733]

value: Maltese


title: BGPC [33253]

value: Berger Picard


title: ARPD [36054]

value: Argentine Pila Dog


title: ARPD [36055]


title: ARPD [36058]


title: CCDH [36592]

value: Chinese Chuandong Hound


title: CCDH [36591]


title: VILL [36495]

value: Village Dog


title: FCR- [36583]

value: Flat-Coated Retriever


title: VILL [36496]


title: VILL [36493]


title: FCR- [36049]


title: VILL [36494]


title: VILL [36459]


title: VILL [36456]


title: VILL [36339]


title: VILL [36338]


title: VILL [36343]


title: MCUR [33297]

value: Mountain Cur


title: VILL [36335]


title: ARPD [36060]


title: VILL [36341]


title: VILL [36320]


title: VILL [36321]


title: ARPD [36053]


title: VILL [36319]


title: VILL [36318]


title: VILL [36231]


title: VILL [36312]


title: ARPD [36059]


title: VILL [36229]


title: VILL [36311]


title: VILL [36228]


title: VILL [36308]


title: BRKI [33571]

value: Brog Khyi


title: VILL [36227]


title: KIAO [33569]

value: Khyi Apso


title: BRKI [33570]


title: MUTT [33572]

value: Mixed Breed


title: KIAO [33568]


title: VILL [36225]


title: VILL [36226]


title: VILL [36206]


title: VILL [36342]


title: VILL [36310]


title: VILL [36334]


title: VILL [36205]


title: VILL [36216]


title: VILL [36337]


title: BBDT [33559]

value: Barbado Da Terceira


title: VILL [36203]


title: VILL [36214]


title: VILL [36204]


title: VILL [36202]


title: CFOU [36003]

value: Cesky Fousek


title: PUDL [36050]

value: Pudelpointer


title: VILL [36188]


title: VILL [36187]


title: VILL [36213]


title: VILL [36186]


title: CFOU [36001]


title: VILL [36185]


title: APBT [35776]

value: American Pit Bull Terrier


title: BRBT [36002]

value: Barbet


title: SHIB [35753]

value: Shiba Inu


title: VILL [36184]


title: APBT [35770]


title: APBT [35769]


title: AMBD [35740]

value: American Bulldog


title: SKWH [35738]

value: Silken Windhound


title: APBT [35768]


title: SKWH [35734]


title: SLOU [35595]

value: Sloughi


title: VILL [36215]


title: SLOU [35583]


title: SLOU [35578]


title: DNGO [35313]

organism: Canis lupus dingo

value: Dingo


title: DNGO [35312]


title: DNGO [35310]


title: DNGO [35301]

source_name: Unknown Tissue


title: DNGO [35297]


title: DNGO [35294]


title: DNGO [35295]


title: MUTT [34709]


title: MUTT [34710]


title: MUTT [34708]


title: PARS [35741]

value: Parson Russell Terrier


title: MUTT [34704]


title: MUTT [34511]


title: MUTT [33597]


title: MUTT [33076]


title: PNTR [35745]

value: Pointer


title: MUTT [31593]


title: KEES [34510]

value: Keeshond


title: KELP [34855]

value: Australian Kelpie


title: MUTT [31699]


title: MUTT [31592]


title: KELP [34856]


title: MUTT [31073]


title: MUTT [30515]


title: MUTT [30312]


title: MUTT [30747]


title: DNGO [35298]


title: MUTT [30307]


title: MUTT [30735]


title: DNGO [35296]


title: MUTT [30269]


title: MUTT [29802]


title: SCOT [29646]

value: Scottish Terrier


title: MUTT [30518]


title: MUTT [25087]


title: MUTT [25085]


title: MUTT [28402]


title: MUTT [29803]


title: MUTT [25018]


title: MUTT [28350]


title: MUTT [24214]


title: KELP [34857]


title: BORD [23513]

value: Border Collie


title: MUTT [24793]

value: Mixed Breed


title: COLL [27343]

value: Collie


title: MUTT [24887]


title: MUTT [22886]


title: MUTT [24476]


title: MUTT [24475]


title: MUTT [24313]


title: MUTT [21928]


title: MUTT [21927]


title: AUSS [24275]

value: Australian Shepherd


title: AUSS [21481]


title: BORD [16121]


title: MUTT [14498]


title: MUTT [11118]


title: MUTT [10674]


title: BORD [14482]


title: MUTT [9002]


title: MUTT [8378]


title: MUTT [13225]


title: MUTT [13846]


title: COLL [7964]

value: Unknown


title: MUTT [7674]


title: MUTT [8115]


title: MUTT [7752]


title: MUTT [13562]


title: MUTT [24795]


title: MUTT [7809]


title: COLL [7966]


title: MUTT [7728]


title: BORD [7676]


title: GSD- [35057]

value: German Shepherd Dog


title: SHWD [33857]

value: Spanish Water Dog


title: PQRB [34143]

value: Phuquoc Ridgeback


title: SHWD [33853]


title: SHWD [33858]


title: BLPS [35829]

value: Blue Picardy Spaniel


title: SHIK [35736]

value: Shikoku


title: SHWD [33854]


title: PQRB [34148]


title: SHIK [35735]


title: SHIK [35756]


title: XOLO [35818]

value: Xoloitzcuintli


title: PQRB [34147]


title: SHWD [33852]


title: BLPS [35258]


title: GSD- [35061]


title: SHIK [35751]


title: SHIK [35752]


title: GSPZ [34561]

value: German Spitz


title: GWHP [33144]

value: German Wirehaired Pointer


title: BCHD [31949]

value: Bluetick Coonhound


title: PHAR [31951]

value: Pharaoh Hound


title: WELT [31782]

value: Welsh Terrier


title: WSSP [31698]

value: Welsh Springer Spaniel


title: SHWD [33856]


title: WSSD [33064]

value: White Swiss Shepherd Dog


title: WELT [31737]


title: MUTT [33599]

value: Mixed Breed


title: WELT [33071]


title: MUTT [34590]


title: MUTT [33594]


title: MUTT [34294]


title: MUTT [33595]


title: MANN [33441]

value: Mannara


title: KLBD [34550]

value: Karelian Bear Dog


title: KLBD [34549]


title: AUSS [30323]

value: Australian Shepherd


title: REDB [34484]

value: Redbone Coonhound


title: MUTT [33729]


title: GSPZ [34559]


title: REDB [34472]


title: KLBD [34547]


title: GSPZ [33869]


title: MUTT [31104]


title: KLBD [34546]


title: COLL [29644]

value: Collie


title: MUTT [34597]


title: PRKS [31634]

value: Prazsky Krysavik


title: MUTT [31952]


title: MUTT [29637]


title: MUTT [29639]


title: MUTT [31950]


title: MUTT [29635]


title: KLBD [34548]


title: MUTT [31701]


title: MUTT [29388]


title: MUTT [28404]


title: MUTT [28352]


title: MUTT [29383]


title: MUTT [28869]


title: COLL [28863]


title: MUTT [29377]


title: MUTT [33732]


title: COLL [29386]


title: MUTT [27619]


title: MUTT [29634]


title: SHWD [33851]

value: Spanish Water Dog


title: MUTT [28864]


title: MUTT [27606]


title: GSPZ [33562]


title: KLBD [34545]


title: PYMF [33850]

value: Unknown


title: MUTT [31967]


title: SEAL [33458]

value: Sealyham Terrier


title: ALHK [33565]

value: Alaskan Husky


title: ALHK [33574]


title: ALHK [33564]


title: DNSZ [33348]

value: Danish Spitz


title: DNSZ [33357]


title: SEAL [33337]


title: DNSZ [33327]


title: ALHK [33840]


title: MUTT [27903]


title: DNSZ [33326]


title: DNSZ [33328]


title: SEAL [33335]


title: CHIN [30660]

value: Japanese Chin


title: SEAL [33234]


title: CAIR [26283]

value: Cairn Terrier


title: Drah [31615]

value: Drahthaar


title: CASD [31263]

value: Central Asian Shepherd Dog


title: Tree [31105]

value: Treeing Walker Coonhound


title: Tree [30322]


title: DDMT [26279]

value: Dandie Dinmont Terrier


title: LHSA [30316]

value: Lhasa Apso


title: DDMT [26280]


title: AMST [29581]

value: American Staffordshire Terrier


title: AESK [25081]

value: American Eskimo Dog


title: BRUS [14951]

value: Brussels Griffon


title: APPZ [21835]

value: Appenzeller Mountain Dog


title: SEAL [33233]


title: LAB- [31943]

value: Labrador Retriever


title: PARS [33225]

value: Parson Russell Terrier


title: BEAU [31830]

value: Beauceron


title: AESK [10812]


title: BULD [29585]

value: Bulldog


title: SEAL [33232]

value: Sealyham Terrier


title: SEAL [33231]


title: GALG [27758]

value: Galgo Espanol


title: SEAL [33282]


title: GALG [27759]


title: PHAR [12800]

value: Pharaoh Hound


title: GALG [27772]


title: GALG [27771]


title: GALG [27756]


title: GALG [27755]


title: GALG [27770]


title: PARS [33224]


title: MUTT [26984]

value: Mixed Breed


title: GALG [27761]


title: GALG [27754]


title: MUTT [24885]


title: AUSS [26350]

value: Australian Shepherd


title: MUTT [30308]


title: MUTT [26906]


title: AUSS [25967]


title: MUTT [25017]


title: MUTT [24505]


title: BEAU [24461]


title: BEAU [24234]


title: BEAU [24753]


title: MUTT [25287]


title: BEAU [24202]


title: MUTT [10744]


title: MUTT [20355]


title: MUTT [20133]


title: MUTT [10609]


title: MUTT [8116]


title: MUTT [14484]


title: MUTT [26645]


title: COLL [8492]

value: Collie


title: MUTT [30313]


title: MUTT [20132]


title: MUTT [7981]


title: MUTT [7648]


title: BRUS [6036]


title: MUTT [25180]


title: MUTT [7649]


title: SUSX [5904]

value: Sussex Spaniel


title: AESK [7781]


title: LANC [5377]

value: Lancashire Heeler


title: DARG [7553]

value: Dogo Argentino


title: MALT [7307]

value: Maltese


title: BORD [24311]

value: Border Collie


title: Mouse_control_epithelial

city: Edinburgh

first: Philippa

middle: TK

last: Saunders

address: 47 Little France Crescent

department: College of Medicine and Veterinary Medicine

country: United Kingdom

institute: The University of Edinburgh

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Assembly: mm10 (Ensemble 84)
Supplementary files format and content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: Uterus

extract_protocol:
Enzymatic digestion and FACS
Uteri were removed and mesenchymal and epithelial cells isolated using FACS
10X Genomics Single cell 3' gene expression V3

value: Pdgfrb-BAC-eGFP

value: Control uterus

tag: population

value: Epithelial cells

tag: Sex

value: F


title: BEAU [25094]

value: Beauceron


title: Mouse_24hrs_mesenchyme

description: 10X Genomics Single cell 3' gene expression V3

value: Repairing uterus

value: Mesenchymal cells


title: DDMT [4362]

value: Dandie Dinmont Terrier


title: LANC [4356]


title: Mouse_48hrs_epithelial

value: Remodelled uterus


title: M1190 ATAC-seq

city: Columbus

first: Janek

middle: S

last: Walker

state: Ohio

address: 410 W 12th Ave

department: Division of Hematology, Department of Internal Medicine

institute: The Ohio State University

description: Eµ-PRMT5/TCL1 6 mo 3

data_processing:
150 bp paired-end reads were trimmed for adaptors and low-quality bases with Cutadapt (Martin et al., 2011) and mapped to the mouse reference genome GRCm38 using the Bowtie2 algorithm (Langmead et al., 2012) with maximum fragment length of 1000 and no-mixed, no-discordant and very-sensitive options.
After removal of duplicate reads, deepTools2 were used to generate normalized genome coverage files (Ramírez et al., 2016).
After removal of duplicate reads, DNase2hotspots (Baek et al., 2012) software package (https://sourceforge.net/projects/dnase2hotspots) was used to identify hotspots (enriched regions) from ATAC-seq.
ATAC-seq peak locations were determined using the MACS2 algorithm (v2.1.1.)(Feng et al., 2012) with a cutoff p-value of 1E-5 with “--broad --nomodel --shift -100 --extsize 200” options.
Consensus peak regions from all samples were generated as the union of the overlapping peaks using R GenomicRanges package (Lawrence et al., 2013), then annotated using R ChIPpeakAnno package (Zhu et al., 2010).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: BigWig file with genome wide normalized read coverage score (counts per million) using deepTools2

source_name: Spleenic B cells

extract_protocol:
10e5 cells were washed once in 50 μl PBS, resuspended in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifuged for 10 minutes at 4 °C. On centrifugation, the pellet was washed briefly in 50 μl MgCl2 buffer (10 mM Tris pH 8.0 and 5 mM MgCl2) before incubating in the transposase reaction mix (12.5 μl 2 × TD buffer, 2 μl transposase (Illumina) and 10.5 μl nuclease-free water) for 30 min at 37 °C. After DNA purification with the MinElute kit, 1 μl of the eluted DNA was used in a qPCR reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies).
Library amplification was performed using custom Nextera primers. The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 25-bp paired-end configuration.

tag: transgene

value: Spleen


title: LANC [4357]


title: smMUNS [34613]

value: Small Munsterlander


title: Mouse_48hrs_mesenchyme


title: PRES [1093]

value: Presa Canario


title: DDMT [4360]


title: DCAN [1201]

value: Dogo Canario


title: M1196 ATAC-seq

description: Eµ-PRMT5/TCL1 6 mo 1


title: M1243 ATAC-seq

description: Eµ-PRMT5/TCL1 3 mo 4


title: DCAN [1200]


title: M1237 ATAC-seq

description: Eµ-PRMT5/TCL1 3 mo 3


title: DCAN [1169]


title: PRES [1082]


title: SUSX [955]

value: Sussex Spaniel


title: M1194 ATAC-seq

description: Eµ-TCL1 6 mo 2


title: M1193 ATAC-seq

description: Eµ-TCL1 6 mo 1


title: M1238 ATAC-seq

description: Eµ-PRMT5/TCL1 3 mo 1


title: PRES [1096]


title: M1265 ATAC-seq

description: Eµ-TCL1 3 mo 3


title: EFOX [942]

value: English Foxhound


title: M1262 ATAC-seq

description: Eµ-TCL1 3 mo 1


title: M1264 ATAC-seq

description: Eµ-TCL1 3 mo 2


title: DNSZ [33320]

value: Danish Spitz


title: DNSZ [33319]


title: AFFN [33498]

value: Affenpinscher


title: M1197 3_vs_6_mo_RNA-seq

description: Eµ-PRMT5/TCL1 6 mo 2

data_processing:
150 bp paired-end reads were trimmed for adaptors and low-quality bases with Cutadapt (Martin et al., 2011) and mapped to the mouse reference genome GRCm38 with STAR aligner (v2.6.0c)(Dobin et al., 2013)
featureCount function (Liao et al., 2014) from the subread package was used to generate gene counts based on Ensebml gene annotation release 95 (Zerbino et al., 2018).
Pairwise comparisons were performed to identify differentially expressed genes using voom method from R limma package (Ritchie et al., 2015, Law et al., 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV matrix counts table generated using Subread FeatureCounts

extract_protocol:
B cells were isolated using EasySepTM mouse pan B cell isolation kit (STEMCELL Technologies; Cat #19844). Cell pellets were captured and washed in PBS on ice prior to resuspension in TRIzol reagent and stored at -80°. Total RNA was isolated from TRIzol suspensions using a chloroform/ethanol extraction method and quantified via Qubit RNA HS Assay kit (Invitrogen).
Sequencing libraries were prepared using Illumina TruSeq stranded mRNA library preparation kit and sequenced on HiSeq 4000 instrument targeting approximately 60-80x106 read pairs per sample.


title: M1197 ATAC-seq

description: Eµ-PRMT5/TCL1 6 mo 2


title: TERV [34298]

value: Belgian Tervuren


title: M1243 3_vs_6_mo_RNA-seq

description: Eµ-PRMT5/TCL1 3 mo 3


title: M1196 3_vs_6_mo_RNA-seq

description: Eµ-PRMT5/TCL1 6 mo 1


title: TERV [34296]


title: M1238 3_vs_6_mo_RNA-seq

description: Eµ-PRMT5/TCL1 3 mo 1


title: M1242 3_vs_6_mo_RNA-seq

description: Eµ-PRMT5/TCL1 3 mo 2


title: DCAN [1168]


title: BMAL [34286]

value: Belgian Malinois


title: M1242 ATAC-seq

description: Eµ-PRMT5/TCL1 3 mo 2


title: M1193 3_vs_6_mo_RNA-seq

description: Eµ-TCL1 6 mo 1


title: PYMF [33834]

value: Pyrenean Mastiff


title: M1264 3_vs_6_mo_RNA-seq

description: Eµ-TCL1 3 mo 2


title: PYMF [33826]


title: PYMF [33842]


title: PYMF [33837]


title: PARS [33226]

value: Parson Russell Terrier


title: M0980 (L30) bulk RNA-seq

description: Eµ-PRMT5/TCL1 3

data_processing:
Data processing was performed according to the CLEAR workflow
BCR reads were binned by specific heavy (H) and light-chain V genes. MiXCR (v3.0.5)(Bolotin et al., 2015) was used with default parameters to identify preprocessed reads containing CDR3 regions from B-cell heavy, kappa, and lambda chains, generating a list of unique CDR3 sequences associated with their relative abundances and specific V(D)J gene usage.
Global DEG analysis was performed using DESeq2 (v1.20.0)(Love et al., 2014)
Differentially expressed genes were annotated with Metascape (Zhou et al., 2019)
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV matrix counts table generated using Subread FeatureCounts, Unfiltered; MiXCR clonal output


title: PYMF [33821]


title: LAEK [34576]

value: Belgian Laekenois


title: AMWS [2454]

value: American Water Spaniel


title: M0701 (L32) bulk RNA-seq

description: Eµ-PRMT5 4


title: AMWS [2163]


title: M0317 (L31) bulk RNA-seq

description: Eµ-PRMT5 3


title: TERV [34295]


title: M0799 (L22) bulk RNA-seq

description: Eµ-PRMT5 1


title: E4474 (L25) bulk RNA-seq

description: Eµ-PRMT5 2


title: AMWS [2168]


title: M1194 3_vs_6_mo_RNA-seq

description: Eµ-TCL1 6 mo 2


title: LABD [34178]

value: Labradoodle


title: CLR-69, CAC PDX, APC Mut

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version [UNKNOWN], which is used to both normalize the full dataset and analyze differential expression between sample groups.
Supplementary files format and content: hg19
Supplementary files format and content: tab-delimited file containing normalized counts

source_name: Colitis Associated Cancer patient-derived xenograft (PDX)

growth_protocol: The PDX samples were grown as xenograft and, when the mice were sacrificed, the tumors were flash frozen and also submitted for RNA extraction and sequencing.

extract_protocol:
20-30mg frozen tissue was homogenized in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018), phase separation was induced with 200 µL chloroform, and RNA was extracted from the aqueous phase using the miRNeasy Micro Kit (Qiagen catalog # 217084) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 350 µL input. Samples were eluted in 15 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA with RIN values of 9.2-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 44 million paired reads was generated per sample. Ribosomal reads represented 1.4-3.0% of the total reads generated and the percent of mRNA bases averaged 67%.

tag: msk impact_id

tag: genotype

value: wntMUT


title: CLR-48a, CAC PDX, APC Mut

value: Colitis Associated Cancer patient-derived xenograft (PDX)


title: LABD [34177]


title: LABD [34176]


title: CLR-47, CAC PDX, APC Mut


title: LABD [34171]


title: CLR-4t6, CAC PDX, APC WT

value: wntWT


title: M1262 3_vs_6_mo_RNA-seq

description: Eµ-TCL1 3 mo 1

tag: strain

value: Spleen


title: PYMF [33822]


title: M0322 (L24) bulk RNA-seq

description: Eµ-TCL1 1


title: LABD [34170]


title: CLR-41a, CAC PDX, APC WT


title: M1040 (L27) bulk RNA-seq

description: Eµ-PRMT5/TCL1 2


title: CLR-39, CAC PDX, APC WT


title: PYMF [33836]


title: M0942 (L26) bulk RNA-seq

description: Eµ-PRMT5/TCL1 1


title: MAUS [31935]

value: Miniature Australian Shepherd


title: CLR-38, CAC PDX, APC WT


title: LABD [34169]


title: CLR-112a, CAC PDX, APC WT


title: N2_3

city: Montreal

first: Robyn

last: Branicky

state: Quebec

address: 1205 Docteur Penfield Ave,, Stewart Bldg, W5/26

department: Biology

country: Canada

institute: McGill University

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities using Trimmomatic 0.35 and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on annotations from Ensembl version 88
Expression values were also computed using RSEM version 1.2.28 based on Ensembl version 88 transcript annotations
Assembly: WBcel235
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: N2_Control_replicate 6

growth_protocol: C. elegans were grown on Nematode Growth Media (NGM) plates at 20°C and fed on the E. coli strain OP50.

extract_protocol:
Total RNA was isolated using the QIAzol Lysis Reagent (Qiagen 79306) and RNeasy Mini Spin columns and wash buffers RW1 and RPE from the RNeasy Mini Kit (Qiagen 74106).
cDNA libraries were prepared from polyA-enriched mRNA using the KAPA Stranded mRNA-Seq Kit or KAPA HyperPrep mRNA-Seq Kit and were further amplified for sequencing.

tag: genotype/var

value: young adult

value: transferred bacteria

tag: library preparation kit

value: KAPA RNA HyperPrep

tag: strand orientation

value: forward


title: CLR-109, CAC PDX, APC Mut

tag: tissue


title: MAUS [31937]


title: P-0057984-T01-IM6

source_name: Colitis Associated Cancer Sample

value: Colitis Associated Cancer Sample

tag: tumor location

value: Colon


title: N2_2

source_name: N2_Control_replicate 5

tag: treatment


title: P-0058164-T01-IM6

source_name: Sporadic Colorectal Cancer Sample

value: Sporadic Colorectal Cancer Sample


title: N2_1

source_name: N2_Control_replicate 4


title: LABD [34168]

source_name: Saliva


title: P-0020135-T01-IM6

value: Rectum


title: P-0058766-T01-IM7


title: P-0028913-T01-IM6


title: C118D_PQ_3

source_name: C118D_0.1mM PQ_replicate 3

value: 0.1 mM Paraquat + transferred bacteria


title: MAUS [31933]

source_name: Whole blood


title: P-0043364-T04-IM7


title: C118D_PQ_1

source_name: C118D_0.1mM PQ_replicate 1


title: P-0059615-T01-IM7

value: Bowel


title: C118D_PQ_2

source_name: C118D_0.1mM PQ_replicate 2


title: P-0058972-T01-IM7


title: C118D_3

source_name: C118D_Control_replicate 3


title: C118D_2

source_name: C118D_Control_replicate 2


title: 3180, CAC PDX treated with LGK-974, APC WT, Replicate 2


title: LABD [34166]


title: 3180, CAC PDX treated with LGK-974, APC WT, Replicate 1


title: 3180, CAC PDX treated with G007-LK, APC WT, Replicate 2


title: 3180, CAC PDX treated with G007-LK, APC WT, Replicate 1


title: MAUS [31934]


title: C118D_1

source_name: C118D_Control_replicate 1


title: young_3

source_name: N2_young adults_replicate 3

value: KAPA RNA Stranded


title: P-0014021-T01-IM5


title: 3172, CAC PDX treated with LGK-974, APC Mut, Replicate 2


title: P-0059360-T01-IM7


title: young_2

source_name: N2_young adults_replicate 2


title: 3180, CAC PDX treated with Vehicle, APC WT, Replicate 2

value: Vehicle


title: MAUS [31931]


title: LABD [34167]

value: Labradoodle


title: MAUS [31936]


title: 3180, CAC PDX treated with Vehicle, APC WT, Replicate 1

value: Colitis Associated Cancer patient-derived xenograft (PDX)


title: 3172, CAC PDX treated with G007-LK, APC Mut, Replicate 2


title: LABD [34164]


title: MAUS [31932]


title: young_1

source_name: N2_young adults_replicate 1


title: P-0058976-T01-IM7


title: 3172, CAC PDX treated with Vehicle, APC Mut, Replicate 2

source_name: Colitis Associated Cancer patient-derived xenograft (PDX)


title: L4_3

source_name: N2_L4 larvae_replicate 3

value: L4 larvae


title: 3172, CAC PDX treated with G007-LK, APC Mut, Replicate 1


title: MAUS [31927]


title: MAUS [31926]


title: 3172, CAC PDX treated with Vehicle, APC Mut, Replicate 1


title: MAUS [31925]


title: L4_2

source_name: N2_L4 larvae_replicate 2


title: 3085, CAC PDX treated with LGK-974, APC WT, Replicate 2


title: 3085, CAC PDX treated with LGK-974, APC WT, Replicate 1


title: 3085, CAC PDX treated with G007-LK, APC WT, Replicate 2


title: 3172, CAC PDX treated with LGK-974, APC Mut, Replicate 1


title: HUSK [2439]

source_name: Buccal cells

value: Siberian Husky


title: L4_1

source_name: N2_L4 larvae_replicate 1


title: 3085, CAC PDX treated with G007-LK, APC WT, Replicate 1


title: MUTT [33479]

value: Mixed Breed


title: 3085, CAC PDX treated with Vehicle, APC WT, Replicate 1


title: WHIM2 Erlotinib Resistant 106305

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC v.0.11.8 to identify any quality concerns with the raw data.
Alignment (phase 1): Fastq files were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v6 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal: An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam".  The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq".  These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Dead Cell Removal: An in-house R script using the Seurat v4 R package was used to identify and remove barcodes associated with dead or poor quality cells.  The 10X "subset_bam" and "bamtofastq" scripte were once again used to filter the bam files for each sample to generate fastq files containing only the reads from good quality human cells.
Alignment (phase 2): Each sample was re-aligned to the human GRCh38 genome provided by 10X using the CellRanger "count" algorithm with the Force Cells option set to the exact number of good quality cells identified in the previous step.
Merging: All samples were then merged into one file using the CellRanger "aggr" algorithm and default settings. Output includes the features, barcodes, and matrix files provided with this submission, along with a Loupe CellBrowser file.
Genome_build: GRCh38
Supplementary_files_format_and_content: The process data files are the merged data from all samples, and include the 10X formatted features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz files that can be imported directly into R using the Seurat package. Also a .cloupe file that can be viewed in the Loupe Cell Browser v4 and above.

source_name: Mammary Gland Tumor

growth_protocol: Mice were injected with 500,000 WHIM2 cells in the MG region and allowed to grow until 100mm2

extract_protocol: 10X Genomics 3' library kit v3.0

treatment_protocol: Mice were placed on Erlotinib infused chow (367 ppm) when tumors were ~10mm2 and harvested when tumors started to emerge resistant and continue tumor growth

tag: cell type

value: erlotinib-resistant

value: WHIM2 PDX mammary tumor

value: Erlotinib treated


title: MUTT [33487]

source_name: Saliva


title: WHIM2 Erlotinib Resistant 107679

data_processing:
Base Calling: The sequencing libraries were multiplexed and clustered onto a flowcell. After clustering, the flowcell was loaded onto the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1).  Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Genome_build: GRCh38 and GRCm38 M12
Supplementary_files_format_and_content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.

extract_protocol:
Tumor tissue was flash frozen and then a Qiagen RNeasy mini kit used to extract total RNA
The RNA sample received was quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).


title: WHIM2 Erlotinib Resistant 107677


title: WHIM2 Parental 106361

value: parental

value: vehicle treated


title: gravid_1

source_name: N2_gravid adults_replicate 1

tag: developmental stage

value: gravid adult

value: forward


title: gravid_2

source_name: N2_gravid adults_replicate 2


title: 3085, CAC PDX treated with Vehicle, APC WT, Replicate 2


title: gravid_3

source_name: N2_gravid adults_replicate 3


title: MUTT [33485]


title: Wild_Type_Control_3

source_name: N2_Control_replicate 3

value: young adult

value: transferred bacteria

value: reverse


title: WHIM2 Parental 107668


title: WHIM2 Parental 107647b


title: Wild_Type_Control_2

source_name: N2_Control_replicate 2

value: KAPA RNA Stranded


title: WHIM2 Parental 107672


title: MUTT [33473]


title: WHIM2 Erlotinib Resistant 107676


title: MUTT [33472]


title: MUTT [33484]


title: Wild_Type_Control_1

source_name: N2_Control_replicate 1


title: atxr5/atxr6/polq rep1 (DNA seq)

city: New Haven

first: Yannick

last: Jacob

state: Connecticut

address: YSB 416 260 Whitney Avenue

department: Department of Molecular, Cellular  & Developmental Biology

institute: Yale university

description: sorted 16C nuclei

data_processing:
Library strategy: DNA-seq
DNA-seq:Paired-end reads were filtered and trimmed using fastp. Reads with quality inferior to 20 were removed from the data sets. Sequencing datasets were aligned against the A. thaliana genome (TAIR10) using bowtie2 with default parameters. Duplicate reads were removed using Picard toolkit (MarkDuplicates with REMOVE_DUPLICATES=true). The mapped reads were then filtered based on mapping quality using samtools (-q 30). For generating the chromosomal representations, the program featureCounts (version 1.6.4,) was used to count the paired-end fragments present in each 200kb regions of the A. thaliana genome. The log2 ratio was centered on the average ratio of any two compared libraries on the first 5 Mbp of chromosome 1 for normalization.
RNA-seq: Paired-end reads were filtered and trimmed using fastp. Reads with quality inferior to 20 were removed from the data sets. Biological replicates were analyzed for consistency with deepTools2. Data sets were aligned against the Arabidopis genome (TAIR10) using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Transposable elements (TE) were defined according Panda et al 2016. FeatureCounts (version 1.6.4)was used to count the paired-end fragments overlapping with TEs. TPM (transcripts per million) values were calculated for TEs. They were considered to be upregulated in mutant lines if they showed 2-fold up-regulation as compared to Col in both biological replicates and had a value of TPM >= 5.
Genome_build: RNA-seq: TAIR10;  DNA-seq: TAIR10
Supplementary_files_format_and_content: bedgraph: 200kb windows, normalized against the wild type (see DNA seq processing)
Supplementary_files_format_and_content: bigwig: RPKM of RNA seq over the genome using deeptools.

source_name: 16C nuclei

growth_protocol: Arabidopsis plants were grown under cool‐white fluorescent lights (~100 μmol m−2 s−1) in long‐day conditions (16 h light/8 h dark).

extract_protocol:
Genomic DNA was extracted from sorted 16C nuclei using the ArcturusTM PicoPureTM DNA Extraction Kit (ThermoFisher Scientific, Waltham, MA). Samples were incubated at 65C overnight and at 95C for 10 minutes. The DNA samples were then purified using a genomic DNA Clean and Concentrator kit (Zymo Research, Irvine, CA).
Sequencing libraries were generated at the Yale Center for Genome Analysis (YCGA) using the xGen Prism DNA library prep kit for NGS (Integrated DNA Technologies, Coralville, IA).

tag: ecotype

value: leaves

tag: age

value: 4 weeks

value: atxr5/atxr6/polq mutant


title: atxr5/atxr6/Polq rep2 (DNA seq)

description: sorted 16C nuclei


title: polq rep2 (DNA seq)

description: sorted 16C nuclei

value: polq mutant


title: Wild_Type-_0_1mM_PQ_3

source_name: N2_0.1mM PQ_replicate 3

value: 0.1 mM Paraquat + transferred bacteria


title: MUTT [33464]

source_name: Whole blood

tag: breed

value: Mixed Breed


title: Wild_Type-_0_1mM_PQ_2

source_name: N2_0.1mM PQ_replicate 2


title: polq rep1 (DNA seq)

description: sorted 16C nuclei


title: atxr5/atxr6/gcn5 rep2 (RNA-seq)

data_processing:
DNA-seq:Paired-end reads were filtered and trimmed using fastp. Reads with quality inferior to 20 were removed from the data sets. Sequencing datasets were aligned against the A. thaliana genome (TAIR10) using bowtie2 with default parameters. Duplicate reads were removed using Picard toolkit (MarkDuplicates with REMOVE_DUPLICATES=true). The mapped reads were then filtered based on mapping quality using samtools (-q 30). For generating the chromosomal representations, the program featureCounts (version 1.6.4,) was used to count the paired-end fragments present in each 200kb regions of the A. thaliana genome. The log2 ratio was centered on the average ratio of any two compared libraries on the first 5 Mbp of chromosome 1 for normalization.
RNA-seq: Paired-end reads were filtered and trimmed using fastp. Reads with quality inferior to 20 were removed from the data sets. Biological replicates were analyzed for consistency with deepTools2. Data sets were aligned against the Arabidopis genome (TAIR10) using STAR (version 2.7.2a) allowing 2 mismatches (--outFilterMismatchNmax 2). Transposable elements (TE) were defined according Panda et al 2016. FeatureCounts (version 1.6.4)was used to count the paired-end fragments overlapping with TEs. TPM (transcripts per million) values were calculated for TEs. They were considered to be upregulated in mutant lines if they showed 2-fold up-regulation as compared to Col in both biological replicates and had a value of TPM >= 5.
Genome_build: RNA-seq: TAIR10;  DNA-seq: TAIR10
Supplementary_files_format_and_content: bedgraph: 200kb windows, normalized against the wild type (see DNA seq processing)
Supplementary_files_format_and_content: bigwig: RPKM of RNA seq over the genome using deeptools.

source_name: 3-week-old leaves

extract_protocol: For each biological replicate, one leaf from three individual plant growing in the same flat were pooled. RNA was extracted from three-week old leaf tissue using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). RNA quality was verified using the Agilent 2100 Bioanalyzer Nano RNA Assay. Libraries were prepared at the YCGA with 1 ug of total RNA using Illumina’s TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, San Diego, CA).

value: 3 weeks

value: atxr5/atxr6/tsk mutant


title: MUTT [33462]


title: atxr5/atxr6/tsk rep2 (DNA seq)

description: sorted 16C nuclei


title: MUTT [33480]


title: atxr5/atxr6/tsk rep1 (DNA seq)

description: sorted 16C nuclei


title: Wild_Type-_0_1mM_PQ_1

source_name: N2_0.1mM PQ_replicate 1


title: C118S_Control_3

source_name: C118S_Control_replicate 3


title: WHIM2 Parental 107647

value: WHIM2 PDX mammary tumor


title: C118S_Control_2

source_name: C118S_Control_replicate 2


title: MUTT [31162]


title: tsk rep1 (RNA-seq)

value: tsk mutant


title: MUTT [31159]


title: C118S-_0_1mM_PQ_3

source_name: C118S_0.1mM PQ_replicate 3


title: tsk rep2 (RNA-seq)


title: C118S_Control_1

source_name: C118S_Control_replicate 1


title: tsk rep1 (DNA seq)

description: sorted 16C nuclei


title: atxr5/atxr6 rep2 (DNA seq)

description: sorted 16C nuclei

value: atxr5/atxr6 mutant


title: atxr5/atxr6 rep1 (RNA-seq)


title: tsk rep2 (DNA seq)

description: sorted 16C nuclei


title: MUTT [330]


title: atxr5/atxr6 rep2 (RNA-seq)


title: atxr5/atxr6 rep1 (DNA seq)

description: sorted 16C nuclei


title: C118S-_0_1mM_PQ_2

source_name: C118S_0.1mM PQ_replicate 2


title: Col0 rep2 (RNA-seq)

value: wild type


title: C118S-_0_1mM_PQ_1

source_name: C118S_0.1mM PQ_replicate 1


title: yellow skin color, 4 months old, biol rep 2

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

description: no

data_processing:
The original data was filtered by removing N-containing, jointed and low-quality reads, and the GC content
HISAT2 was used to align paired-end clean reads to the reference genome.
The mapped readings of each skin sample were put together using StringTie
new transcripts were annotated by Pfam, GO, KEGGand other databases
Using the Feature-Counts program, the readings mapped to each gene were calculated
Assembly: GCA_003368295.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Carassius auratus

source_name: celestial goldfish

extract_protocol:
According to the instructions, skin tissue samples in three groups were taken, and the total RNA of each sample was extracted by RNA extraction kit (Invitrogen, Carlsbad, CA, USA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: skin

tag: skin color

value: yellow


title: yellow skin color, 4 months old, biol rep 3

description: no


title: atxr5/atxr6/gcn5 rep1 (RNA-seq)


title: MUTT [31607]


title: MUTT [329]


title: Col0 rep1 (RNA-seq)


title: MUTT [574]


title: Col0 rep2 (DNA seq)

description: sorted 16C nuclei


title: beta-catenin dTF Dermo1

city: Cambridge

first: Wei

last: Hsu

state: MA

address: 245 First St

department: Mineralized TIssue Biology

institute: Forsyth Institute

data_processing:
Base call data generation, run quality assessment, aligment to a reference genome were done by Ion PGM Torrent Sever (Torrent_Suite v4.6)
Assembly: mm10
Supplementary files format and content: tab-delimited text files

source_name: Skeletal mesenchyme at E15.5

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using ion Total RNA-Seq Kit v2 (ThermoFisher) following manufacturer's protocols.

value: Skeletal mesenchyme at E15.5

value: Primary cells

value: beta-catenin fx/dm; Dermo1-Cre


title: beta-catenin Dermo1

value: beta-catenin fx/fx; Dermo1-Cre


title: MUTT [576]


title: white skin color, 4 months old, biol rep 3

description: no

value: white


title: MUTT [575]


title: white skin color, 4 months old, biol rep 2

description: no


title: Col0 rep1 (DNA seq)

description: sorted 16C nuclei

value: leaves

value: 4 weeks


title: CWFD [32895]

value: Czechoslovakian Wolfdog


title: Control

value: beta-catenin fx/fx


title: white skin color, 4 months old, biol rep 1

description: no


title: CWFD [32883]


title: brown skin color, 4 months old, biol rep 3

description: no

value: brown


title: MUTT [31157]

source_name: Saliva

value: Mixed Breed


title: brown skin color, 4 months old, biol rep 2

description: no


title: HepG2 STAT3sh2

city: Wuhan

first: zhang

last: Cheng

address: Huangjiahu

institute: Wuhan University of Science and Technology

data_processing:
not provided
Assembly: not provided
Supplementary files format and content: ALLSample_Count.txt

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol: not provided

treatment_protocol: Control and STAT3 knockdown HepG2 cell lines were constructed by shRNA.

tag: cell line

value: STAT3 shRNA


title: HepG2 Ctrlsh3

value: Ctrl shRNA


title: IRSE [32919]

value: Irish Setter


title: MUTT [10815]


title: HepG2 Ctrlsh1


title: IRSE [32907]


title: brown skin color, 4 months old, biol rep 1

description: no


title: IRSE [32918]


title: yellow skin color, 4 months old, biol rep 1

description: no


title: HepG2 STAT3sh3


title: Lmna p.H222P PBS, rep1

city: Paris

first: Antoine

last: MUCHIR

address: 105 bld de l'Hopital

country: France

institute: INSERM

description: Gene expression data from heart

hyb_protocol: According to the standard Affymetrix protocol

scan_protocol: GeneChip software

data_processing: Image files were obtained with Affymetrix GeneChip software and subjected to robust multichip analysis using Affymetrix microarray “.cel” image files and GeneTraffic 3.0 software (Stratagene).

label: biotin

source_name: Lmna p.H222P PBS

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

growth_protocol: cardiac tissue (ventricles)

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

value: heart

value: Lmna p.H222P

tag: transduction

value: PBS


title: CWFD [32894]


title: Lmna p.H222P PBS, rep2

description: Gene expression data from heart


title: Lmna p.H222P PBS, rep3

description: Gene expression data from heart


title: IRSE [32917]


title: HepG2 STAT3sh1


title: CWFD [32882]


title: Lmna WT cofilin-1, rep3

description: Gene expression data from heart

source_name: Lmna WT cofilin-1

value: Lmna WT


title: CWFD [32893]


title: 7ATP4

first: Chun Ming

middle: Stanley

last: Wu

address: 21 Sassoon Road, Pokfulam, Hong Kong SAR, China

country: Hong Kong

institute: University of Hong Kong

description: Geneid

data_processing:
Base-calling was perform during the sequencing run by RTA version 2.11.3 running under NextSeq Control Software version 4.0.1.41.
RNA-Seq reads were trimmed to remove Illumina adapter, poly(A) and low-quality bases using cutadapt (version 2.8).
The trimmed reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2) with trimming disabled and with STAR selected to align the reads to the hg19 human genome.
Read counts in transcripts were determined according to Ensembl GRCh38/hg38 release 87 gene annotations for protein coding, lincRNA and antisense gene biotypes
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Adipose tissue

growth_protocol: All MSCs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Kit following manufacturer's protocols.

treatment_protocol: No treatment

value: Adipose tissue

value: Mesenchymal stem cells (MSCs)

value: Primary

tag: passage

value: Passage 4


title: 5UBP4

description: Geneid

source_name: Umbilical cord

value: Umbilical cord


title: 6ATP4

description: Geneid


title: 7UBP4

description: Geneid


title: Lmna WT cofilin-1, rep1

description: Gene expression data from heart

tag: genotype


title: 5ATP4

description: Geneid


title: HepG2 Ctrlsh2


title: CWFD [32881]

source_name: Whole blood


title: Lmna WT cofilin-1 (T25A), rep3

description: Gene expression data from heart

source_name: Lmna WT cofilin-1 (T25A)

value: cofilin-1 (T25A)


title: Lmna WT cofilin-1, rep2

description: Gene expression data from heart


title: CWFD [32892]

value: Czechoslovakian Wolfdog


title: M8P4

description: Geneid

source_name: Bone marrow

value: Bone marrow


title: CWFD [32880]


title: Lmna WT cofilin-1 (T25A), rep2

description: Gene expression data from heart


title: IRSE [32906]


title: M6P4

description: Geneid


title: M3P4

description: Geneid


title: 6UBP4

description: Geneid


title: Lmna WT PBS, rep3

description: Gene expression data from heart

source_name: Lmna WT PBS


title: Lmna WT cofilin-1 (T25A), rep1

description: Gene expression data from heart


title: LUGI [32958]

value: Cane Lupino del Gigante


title: AWOLF [32925]

description: Canis lupus italicus

organism: Canis lupus

value: Appenine Wolf


title: LUGI [32954]


title: IRSE [32916]


title: Lmna WT PBS, rep2

description: Gene expression data from heart


title: L38_CLL_PBMC_VDJ

data_processing:
Sequencing was carried out on an Illumina Novaseq to achieve 75 bp reads.
Read counts were normalized to library size, scaled by 10,000, log-transformed, and based on the following criteria: cells with less than 250 genes detected or with a proportion of unique molecular identifiers mapped to mitochondrial genes over 0.15 were excluded from analysis; genes detected in less than 5 cells were also excluded.
Cell-to-cell variation in gene expression driven by the number of detected molecules and mitochondrial gene expression was regressed out using linear regression.
Following the Single Cell 5′ Kits (v2) user guide (manual part no. CG00052 Rev A.), data was processed by the Cell Ranger pipeline (v2.0.1; 10x Genomics) & . Count matrices were analyzed using the Seurat package (v2.2.1) in R.
Read counts were normalized to library size, scaled by 10,000, log-transformed, and filtered. Dimensionality reduction was performed with principal component analysis followed by UMAP projection and graph-based clustering using the first 10 principal components.
Assembly: h38
Supplementary files format and content: 10X barcode TSV tables, 10X feature TSV tables, expression matrices, and Loupe visualization files generated by 10X software
Library strategy: scVDJ-seq

source_name: PBMC

extract_protocol:
Cells were washed and partitioned into nanoliter-scale Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics Barcode but uses a pool of ~750,000 barcodes to separately index each cell’s transcriptome. The silane magnetic beads and Solid Phase Reversible Immobilization beads were used to clean up the GEM reaction mixture and the barcoded cDNA was then amplified in a PCR step.
Libraries were prepared using the Chromium Next GEM Single Cell 5' Kit (v2) (PN-1000263): Library Construction kit (PN-1000190), Chromium Next GEM Chip K Single Cell Kit (PN-1000286), Chromium Single Cell Human BCR Amplification Kit (PN-1000253), and Dual Index Kit TT Set A (PN-1000215) (10x Genomics). Optimal cDNA amplicon size was achieved using Covaris machine prior to library construction. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adapter ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

tag: disease

value: Chronic Lymphocytic Leukemia

value: PBMC

tag: barcode


title: L35_CLL_PBMC_VDJ


title: L34_Richter's_PBMC_VDJ

value: Richter's Transformation


title: L37_Richter's_PBMC_VDJ


title: IRSE [32914]

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

value: Irish Setter


title: L36_Richter's_Lymph_Node_VDJ

source_name: Lymph Node

value: Lymph Node


title: L33_Richter's_Lymph_Node_VDJ


title: Lmna WT PBS, rep1

description: Gene expression data from heart

value: heart

value: PBS


title: CWFD [32891]


title: CWFD [32879]


title: CTC-21-A6

city: Bangkok-noi

first: Chandhanarat

last: Chandhanayingyong

state: Bangkok

address: 2 Wanglang road

department: Orthopaedic Surgery

country: Thailand

institute: Mahidol University

hyb_protocol: The hybridization reactions were prepared using the standard chemistry reagents provided in PanCancer progression panel kit (Nanostring) according to the manufacturers’ instructions.

scan_protocol: Scanning was performed using the NanoString nCounter Digital Analyzer.

data_processing: Following the manufacturer's guidelines and using the NanoString nSolver analysis software, counts were firstly corrected to background noise using the geometric mean of 8 negative and 6 positive control spike-ins in each lane. Housekeeping genes with raw count >50 and selected by the geNorm algorithm were retained for normalisation. The original raw data from Nanostring nCounter platform is recorded in a RCC file.

label: NanoString

source_name: Colorectal adenocarcinoma

extract_protocol: Total RNA was extracted from FFPE tissue using a high-purity FFPE RNA isolation kit (Roche) according to the manufacturer’s instructions.

tag: tussue

value: primary colorectal cancer


title: CTC-21-A5


title: L38_CLL_PBMC_GEX

library_source: transcriptomic single cell

data_processing:
Sequencing was carried out on an Illumina Novaseq to achieve 75 bp reads.
Read counts were normalized to library size, scaled by 10,000, log-transformed, and based on the following criteria: cells with less than 250 genes detected or with a proportion of unique molecular identifiers mapped to mitochondrial genes over 0.15 were excluded from analysis; genes detected in less than 5 cells were also excluded.
Cell-to-cell variation in gene expression driven by the number of detected molecules and mitochondrial gene expression was regressed out using linear regression.
Following the Single Cell 5′ Kits (v2) user guide (manual part no. CG00052 Rev A.), data was processed by the Cell Ranger pipeline (v2.0.1; 10x Genomics) & . Count matrices were analyzed using the Seurat package (v2.2.1) in R.
Read counts were normalized to library size, scaled by 10,000, log-transformed, and filtered. Dimensionality reduction was performed with principal component analysis followed by UMAP projection and graph-based clustering using the first 10 principal components.
Assembly: h38
Supplementary files format and content: 10X barcode TSV tables, 10X feature TSV tables, expression matrices, and Loupe visualization files generated by 10X software


title: L37_Richter's_PBMC_GEX


title: CTC-17-A8


title: CTC-17-A7


title: CTC-21-A3


title: L36_Richter's_Lymph_Node_GEX


title: CWFD [32890]

extract_protocol: Genomic DNA was extracted from whole blood was purified using Proteinase K and phenol/chloroform with standard protocols. Genomic DNA extracted from saliva was extracted using the PerformaGene ND-100 Kit protocol.


title: SWFD [32902]

value: Saarlos Wolfdog


title: CTC-17-A1


title: CTC-16-A8


title: L35_CLL_PBMC_GEX


title: CTC-16-A7


title: IRSE [32915]


title: CWFD [32878]


title: CTC-16-A1


title: CWFD [32889]


title: L34_Richter's_PBMC_GEX


title: LUGI [32943]


title: CTC-15-A5


title: CWFD [32877]


title: IRSE [32913]


title: L33_Richter's_Lymph_Node_GEX


title: CTC-15-A4


title: SWFD [32901]


title: MUTT [24141]

value: Mixed Breed


title: WT_1 [CUT&RUN]

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
library strategy: CUT&RUN
The sequencing reads were processed using the CUT&RUNTools package with default settings.
Coverage tracks in bigwig format were generated using deepTools package v3.5.1.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN Kit (Epicypher) according to the user manual.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit

value: Cardiomyocytes

value: WT


title: IgG Control [CUT&RUN]


title: CM_CIART-/-_2 [ATAC-seq]

data_processing:
The Sequencing reads were trimmed to remove adapter sequences and low-quality bases using Cutadapt v3.4.
The trimmed reads were aligned to the human GRCh37 reference genome using bowtie2 v2.4.4 with parameters '-X 2000 --very-sensitive -k 5'.
Duplicate reads were discarded using picard v2.26.2.
Peaks were identified for each replicate sample using Genrich v0.6.1 with parameters '-j -q 0.05 -a 200.0' and '-e' to remove mitochondrial genome and regions not assembled into chromosomes, and '-E' to exclude 'N' homopolymers or high mappability regions in the genome.
Coverage tracks in bigwig format were generated using the deepTools package v3.5.1.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol: Cells were collected and respended in ATAC-seq buffer, and proceeded with transposase reaction. Tagmented DNA was purified by Zymo columns.

value: CIART Konckout


title: CM_CIART-/-_3 [ATAC-seq]


title: NEWF [24272]

value: Newfoundland


title: IRSE [32912]


title: CTC-14-A9


title: WT_2 [CUT&RUN]


title: CM_WT_3 [ATAC-seq]


title: SWFD [32900]


title: CTC-14-A8


title: CTC-12-A9


title: CWFD [32888]

value: Czechoslovakian Wolfdog


title: CM_WT_2 [ATAC-seq]


title: CTC-12-A7


title: CTC-11-A6


title: CTC-03-A11


title: CM_WT_1 [ATAC-seq]


title: IRSE [32911]


title: CTC-03-A9


title: CWFD [32876]


title: SWFD [32899]


title: CM_CIART-/-_1 [ATAC-seq]


title: WT_SARS-CoV-2 [scRNA-seq]

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v5.0.0)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus SARS-CoV-2 viral genome (NC_045512.2) and to extract gene expression UMI counts matrix.
Assembly: hg19
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

extract_protocol:
At 24 hpi, hPSC-AWOs were dissociated into a single cell suspension using Accutase cell detachment solution (Innovative Cell Technologies) and incubated at 37 oC for ~5 min followed by gentle pipetting to break apart groups of cells. Cells were then washed twice in 1x PBS and filtered using a 40 μm Flowmi cell strainer (Bel-Art Scienceware). Cell count and cell viability were then determined using trypan blue staining and a Countess II automated cell counter (ThermoFisher Scientific).
Target cell inputs of 10,000 cells for each condition were then loaded into a Chromium Controller using Chromium Next GEM (Gel Bead-In Emulsion) single Cell 5’ Library & Gel Bead Kit v1.1 (10× Genomics) according to manufacturer’s instructions. After generation of GEMs, cDNA synthesis and library preparation of all samples was completed using the Chromium Single Cell 5’ Library Kit v1.1 (10× Genomics) according to manufacturer’s instructions.

value: Airway Organoids

value: SARS-CoV-2 Infection


title: CTC-03-A5


title: CTC-02-A10