title: Islets, Lepr KO, scRNA-seq

city: Houston

first: Aaron

middle: R

last: Cox

state: TX

address: 1825 Pressler St

department: Institute of Molecular Medicine

institute: University of Texas Health Science Center at Houston

description: sample pooled from 4 mice

data_processing:
Cell Ranger software v3.1 (10x Genomics) with default settings was used for alignment, barcode assignment, and UMI counting of the raw sequencing data.
Cells with detected genes was <600, total features >6500, or mitochondrial DNA percent > 10% were removed.
Control (wild-type) and Lepr KO datasets were merged and integrated using the functions FindIntegrationAnchors and IntegrateData
Assembly: mm9
Supplementary files format and content: Tab-separated value files
Supplementary files format and content: Matrix files

source_name: Pancreatic islets

extract_protocol:
Islets were freshly harvest from the pancreas by collagenase type V digestion (in HBSS; 5-6 min, 37C shaking water bath). Digestion was stopped by adding 45 ml of cold RPMI + 10% FBS. Samples were centrifuged at 339xg at 4C for 2 min using swing buckets. Supernatant was removed, the pellet was resuspended in 10 ml of cold RPMI + 10% FBS and transferred to a 10 cm non-tissue culture dish. Islets were hand picked into 1.5 ml tubes. To ensure a clean and pure islet prep, islets were handpicked 2 more times and then transferred to 5 ml polystyrene tubes for generation of single cell suspension. Two ml RPMI + 10% FBS was added and then centrifuged at 339xg at 4C for 2 min using swing buckets. Supernatant was removed and pellets were resuspended in 1 ml of pre-warmed TrypLE Express and incubated for 10 min at 37C with pipetting up and down every 2 min to facilitate dispersion. To stop, 2 ml of cold RPMI + 10% FBS was added and the suspension was strained through a 40 µm filter. Supernatant was removed and pellets resuspend in 250 µL of cold RPMI + 10% FBS for viability and cell counting.
Single-cell capture and cDNA libraries were prepared by the Baylor College of Medicine Single Cell Genomics Core according to manufacturer's protocols (10x Genomics). Single-cell suspensions (~1000 cells/μl in PBS) were loaded into a microfluidic chip and placed in the 10x Genomics Chromium Controller to generate single-cell gel beads in emulsion with a targeted cell recovery of 10,000 cells. cDNA libraries were prepared with chromium single-cell 3’ reagent kit v3.1 (10x Genomics).

value: Pancreatic islets

tag: age

value: 8-10 weeks

value: 0.1mg/g BW tamoxifen


title: DND1-KO,hPGCLC,day4,rep2

status: Public on Feb 01 2025

type: SRA

city: Haining

first: zhaoyu

last: Gu

state: Zhejiang

address: 718 East Haizhou Road

department: ZJE

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Step 1: Data preprocessing using Cutadapt. - Software: Cutadapt - Version: 4.1 - Parameters: -j 20 -u 20 -U 20
Step 2: Quality control and trimming using Trim Galore. - Software: Trim Galore - Version: 0.6.7 - Parameters: -q 25 --phred33 -e 0.1 --stringency 4 --gzip --trim-n
Step 3: Read alignment using STAR. - Software: STAR - Version: 2.7.10a - Parameters: --runThreadN 15 --runMode alignReads --readFilesCommand zcat --twopassMode Basic --outSAMtype BAM SortedByCoordinate --genomeDir /home/data/genome/STAR_RNA_UCSCfa_GENCODEgtf_hg38_index --readFilesIn ${i}/02_trimmed/${i}_1_cut_val_1.fq.gz ${i}/02_trimmed/${i}_2_cut_val_2.fq.gz --outFileNamePrefix ${i}/03_mapped/
Step 4: Sorting using Samtools. - Software: Samtools - Version: 1.6 - Parameters: sort -@ 20
Step 5: Counting using FeatureCounts. - Software: FeatureCounts - Version: 2.0.1 - Parameters: -T 10 -a /home/data/genome/GENCODE/gencode_v41_gtf/gencode.v41.annotation.gtf -p -C -t exon -g gene_name
Assembly: hg38
Supplementary files format and content: The "Geneid" column contains the gene identifiers, while the "Chr", "Start", "End", "Strand", and "Length" columns provide genomic information about each gene.  The remaining columns contain the read counts for each sample, indicating the number of reads mapped to each gene in the specified sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: The H1 hESCs (46, XY) were cultured in the Nuwacell® ncTarget hPSC medium (Nuwacell, RP01020) supplemented with 50ng/ml Primocin (InvivoGen, ant-pm-2) on Matrigel (Corning, 354234)-coated plates. The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.  For the induction of iMeLC and hPGCLCs, hESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) in basic DMEM/F-12 (1:1) medium (GIBCO, C11330500BT) supplemented with 20% KnockOut Serum (GIBCO, 10828028), 1% non-essential amino acids (GIBCO, 11140-050), 0.1 nM β-mercaptoethanol (GIBCO, 21985023), 1× Penicillin-Streptomycin-Glutamine (Invitrogen, 10378016) and 10 ng/ml FGF2 (Peprotech, 100-18B). The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.

extract_protocol:
The cells were pelleted down and snap frozen until use. RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For hPGCLCs, to enrich mRNA from extracted total RNA, VAHTS mRNA Capture Beads (Vazyme, N401) was applied. After enrichment, VAHTS universal V8 RNA-seq library Prep Kit for Illumina (Vazyme, NR605) was utilized to prepare libraries for sequencing, which briefly contains fragmentation, cDNA synthesis, adapter ligation, PCR amplification and purification. For hESCs and three different germ lyers,after the RNA sample passes the test, magnetic beads with Oligo(dT) are used to enrich eukaryotic mRNA. Then fragmentation buffer is added to break the mRNA into short fragments. Using the mRNA as a template, six-base random primers (random hexamers) are used to synthesize one-strand cDNA. Then buffer, dNTPs, and DNA polymerase I and RNase H are added to synthesize two-strand cDNA. Double-stranded cDNA was then purified using AMPure XP beads. The purified double-stranded cDNA is first subjected to end repair, A-tailing and ligation of sequencing adapters, and then AMPure XP beads are used for fragment size selection. Finally, PCR amplification was performed, and the PCR product was purified with AMPure XP beads to obtain the final sequencing library.

tag: cell line

tag: cell type

value: hPGCLCs

tag: genotype


title: HM_25_ZT2_M1_MCC3804A212_S108

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

country: USA

institute: University of Pittsburgh

description: Library name: HM_25_ZT2_M1_MCC3804A212_S108

data_processing:
FASTQC
HTSeq
DESeq2 normalization (median of ratios)
Cosinor modeling
Assembly: Mus musculus Ensembl GRCm38
Supplementary files format and content: .Rdata

organism: Mus musculus

source_name: Brain

extract_protocol:
Qiagen Rneasy Plus Micro Kit( (Qiagen)
SMART Stranded Total RNA kit (Takara)

tag: tissue

value: Brain

value: Homogenate tissue

value: Wildtype C57BL/6J mice


title: Islets, wild-type, scRNA-seq

description: sample pooled from 4 mice

library_source: transcriptomic single cell

tag: strain

value: Lepr-lp/lp

tag: treatment


title: NANOS3-KO,hPGCLC,day4,rep1

treatment_protocol: For the induction of iMeLC and hPGCLCs, hESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) in basic DMEM/F-12 (1:1) medium (GIBCO, C11330500BT) supplemented with 20% KnockOut Serum (GIBCO, 10828028), 1% non-essential amino acids (GIBCO, 11140-050), 0.1 nM β-mercaptoethanol (GIBCO, 21985023), 1× Penicillin-Streptomycin-Glutamine (Invitrogen, 10378016) and 10 ng/ml FGF2 (Peprotech, 100-18B). The cells were maintained at 37℃ with 5% CO2. The medium was changed every other day. The cells were passaged with Dispase (STEMCELL, 07923) when they were approximately 80% confluent.


title: dKO_Veh2__scRNA

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
scRNA.NSCLC.with.dKO.rds
scRNA.NSCLC.all.rds
scRNA.onlyT.with.dKO.rds

data_processing:
we add the exogenous sequence of plasmids into mm10 genome reference. The cellranger (v5.0.1) was used to generate the index of genome reference and to align the raw data with the mm10 genome reference, removing duplicated reads by adjusting unique molecules identities (UMIs), estimating single-cell by splitting barcodes, quantify the gene counts on single-cell levels and summarize the sequencing reads information, mapping ratio, and cells and genes’ detection.
The FindVariableFeatures was implemented to identify 4,000 high-variable genes with vst model for data scaling and subsequent clustering and dimension reducing. The 25 principal component analysis factors were used to embedding calculation and the 20 principal component analysis factors were used to neighbors’ estimation. The openTSNE, t-SNE, UMAP and force atlas2 (fa2) were used to reduce the dimension following previously reported methods. The major population and subpopulation were identified by classical signatures, and top markers were calculated by FindAllMarkers with wilcox.test.
Assembly: mm10
Supplementary files format and content: MTX
Supplementary files format and content: RDS

source_name: NSCLC

extract_protocol:
The lung cancers tissues were collected from sensitive (n=2), sensitive+anti-PD1(n=2), resistant (n=2) and resistant+anti-PD1 (n=2), resistant dKO (n=2), resistant + ant-PD1+veh (n=1), resistant + ant-PD1+warfarin (n=1) groups and washed with PBS supplemented with 2% fetal bovine serum (FBS). The lung tumors were digested by Collagenase I and IV into single cells and filtered through a 100um filter to obtain a single-cell suspension. Cell numbers were counted and the concentration of single-cell suspension was about 1000 cells/μl. The cell activity of single-cell suspension was more than 85%.
Machine and cDNA libraries were amplified according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (1000268). The constructed library was sequenced using the Illumina Nova 6000 platform in PE150 sequencing platform.
10X 3' scRNA

value: NSCLC

tag: group

value: immunotherapy-resistant dKO+veh


title: HM_3_ZT6_M2_MCC3804A242_S96

description: Library name: HM_3_ZT6_M2_MCC3804A242_S96


title: liver_ATAC_383_l2_s1

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
383_peaks.narrowPeak.gz
383_scaled.bw

library_source: genomic

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.

molecule: genomic DNA

source_name: liver tissue

extract_protocol:
We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher), homogenized the tissue powder in ice-cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol [pH 7.5]) using a 1-mL dounce for 40 strokes, and rotated for 5 min at 4°C. We filtered the solution through a Miracloth (Calbiochem), centrifuged at 1,100 × g for 10 min at 4°C, washed the pellet with 250 μL NIB containing 0.5% Triton-X, centrifuged at 500 × g for 5 min at 4°C, and resuspended the pellet in 250 μL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 [pH 7.4]). After counting isolated nuclei, we pelleted 50,000 nuclei at 500 × g for 5 min at 4°C
We prepared ATAC-seq libraries using the omni-ATAC protocol with 5 ul Tn5 transposase per reaction, cleaned the transposase reaction and final libraries with Zymo DNA Clean and Concentrator (D4029), visualized and quantified the libraries using a TapeStation, and sequenced 150-bp paired-end reads on either an Illumina HiSeq 4000 or HiSeq X ten.

value: liver tissue


title: dKO_Veh1_scRNA


title: liver_ATAC_382_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
382_peaks.narrowPeak.gz
382_scaled.bw


title: Resis_ICI2_scRNA

description: scRNA.NSCLC.all.rds


title: liver_ATAC_378_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
378_peaks.narrowPeak.gz
378_scaled.bw


title: CE-DND1-rAPOBEC1+NANOS3-ADAR,hESC,rep2

value: hESCs

value: DND1-rAPOBEC1, NANOS3-ADAR


title: liver_ATAC_382_l3_s2


title: liver_ATAC_378_l2_s1


title: HM_22_ZT18_F1_MCC3804A249_S89

description: Library name: HM_22_ZT18_F1_MCC3804A249_S89


title: CE-DND1-rAPOBEC1+NANOS3-ADAR,hESC,rep1


title: Resis_ICI1_scRNA

description: scRNA.NSCLC.all.rds


title: HM_24_ZT22_F2_MCC3804A250_S97

description: Library name: HM_24_ZT22_F2_MCC3804A250_S97


title: HM_23_ZT22_M4_MCC3804A234_S95

description: Library name: HM_23_ZT22_M4_MCC3804A234_S95


title: liver_ATAC_378_l1_s1


title: liver_ATAC_374_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
374_peaks.narrowPeak.gz
374_scaled.bw


title: Resis_Ctrl1_scRNA

description: scRNA.NSCLC.all.rds

value: immunotherapy-resistant+veh


title: HM_21_ZT18_M2_MCC3804A248_S140

description: Library name: HM_21_ZT18_M2_MCC3804A248_S140


title: HM_20_ZT14_F1_MCC3804A236_S111

description: Library name: HM_20_ZT14_F1_MCC3804A236_S111


title: Control H1,hPGCLC,day4,rep1

value: WT control


title: Control H1,hPGCLC,day4,rep2


title: liver_ATAC_382_l2_s1


title: Resp_ICI2_scRNA

description: scRNA.NSCLC.all.rds


title: NANOS3-ADAR,hESC,rep2


title: liver_ATAC_374_l1_s1


title: HM_2_ZT2_F1_MCC3804A209_S84

description: Library name: HM_2_ZT2_F1_MCC3804A209_S84


title: NANOS3-ADAR,hESC,rep1


title: DND1-KO,hPGCLC,day4,rep1


title: HM_19_ZT14_M2_MCC3804A201_S83

description: Library name: HM_19_ZT14_M2_MCC3804A201_S83


title: BaseLine2_scRNA

description: scRNA.NSCLC.all.rds

value: immunotherapy-sensitive+veh


title: liver_ATAC_372_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
372_peaks.narrowPeak.gz
372_scaled.bw


title: NANOS3-KO,hESC,rep2


title: liver_ATAC_372_l1_s1


title: Resis_Ctrl2_scRNA

description: scRNA.NSCLC.all.rds


title: HM_18_ZT10_F2_MCC3804A241_S88

description: Library name: HM_18_ZT10_F2_MCC3804A241_S88


title: NANOS3-KO,hESC,rep1


title: BaseLine1_scRNA

description: scRNA.NSCLC.all.rds


title: HM_17__ZT10_M2_MCC3804A206_S121

description: Library name: HM_17__ZT10_M2_MCC3804A206_S121


title: Res9_RNA

description: Comparison of Gene Counts and Differential Parameters in Resistant vs. Sensitive.xlsx

data_processing:
The RNA-seq reads were aligned to the mouse reference genome (mm10) using STAR (v2.6.0a).Transcript abundance was quantified and normalized as transcripts per kilobase million (TPM).
To identify differentially expressed genes, DESeq2 (v.1.26.0, RRID:SCR_000154) was employed. Genes with an absolute fold change greater than 0.5 and a p value of less than 0.05 were considered as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: EXCEL contains the raw data with sample names and normalized data processed with DESeq2, prefixed with "DESeq2_". Other columns present the differential parameters.

extract_protocol:
RNA-seq libraries were generated using an Illumina stranded mRNA sample preparation kit (NEB, E7770) following the manufacturer's protocol.
The libraries were subsequently sequenced on an Illumina NovaSeq 6000 sequencing machine, producing paired end reads with a length of 150 base pairs (bp).

value: immunotherapy-resistant


title: DND1-ADAR,hESC,rep2


title: Res8_RNA


title: HM_16_ZT6_F2_MCC3804A232_S138

description: Library name: HM_16_ZT6_F2_MCC3804A232_S138


title: liver_ATAC_369_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
369_peaks.narrowPeak.gz
369_scaled.bw


title: DND1-ADAR,hESC,rep1


title: liver_ATAC_369_l2_s1


title: HM_15_ZT6_M3_MCC3804A215_S129

description: Library name: HM_15_ZT6_M3_MCC3804A215_S129


title: HM_14_ZT2_F3_MCC3804A240_S139

description: Library name: HM_14_ZT2_F3_MCC3804A240_S139


title: Resp_ICI1_scRNA

description: scRNA.NSCLC.all.rds


title: DND1-KO,hESC,rep2


title: liver_ATAC_372_l3_s1


title: Res6_RNA


title: Res7_RNA


title: liver_ATAC_369_l1_s1


title: HM_13_ZT2_M3_MCC3804A238_S125

description: Library name: HM_13_ZT2_M3_MCC3804A238_S125


title: Res5_RNA


title: liver_ATAC_368_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
368_peaks.narrowPeak.gz
368_scaled.bw


title: Control H1,hESC,rep2


title: HM_12_ZT22_F1_MCC3804A235_S103

description: Library name: HM_12_ZT22_F1_MCC3804A235_S103


title: liver_ATAC_368_l2_s2


title: Res3_RNA


title: HM_11_ZT22_M2_MCC3804A233_S87

description: Library name: HM_11_ZT22_M2_MCC3804A233_S87


title: Control H1,hESC,rep1


title: liver_ATAC_368_l2_s1


title: CD3+CD8+CD69- cells (P5) - 3

city: Aarhus

first: Juan Luis

last: Garcia-Rodriguez

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
Trim Galore phred > 20
STAR alignement
Subread used for Feature counts calling
Assembly: hg19/GRCh37
Supplementary files format and content: Raw counts generated using Subread

source_name: Blood

extract_protocol:
Rneasy Micro Kit (Qiagen)
Library preparation was performed using Illumina Stranded Total RNA-seq with Ribo-Zero Plus rRNA depletion kit

value: Blood

value: CD8+ T cells isolated from PBMCs

value: CD8+ T cells

value: No treatment


title: HM_10_ZT_18_F1_MCC3804A224_S137

description: Library name: HM_10_ZT_18_F1_MCC3804A224_S137

value: Brain


title: liver_ATAC_368_l1_s1


title: CD3+CD8+CD69+ cells after co-culturing with moDC+LPS+antigen (P4) - 3

value: co-culturing with moDC+LPS+antigen


title: HM_1_ZT2_M1_MCC3804A225_S86

description: Library name: HM_1_ZT2_M1_MCC3804A225_S86

value: Homogenate tissue

value: Wildtype C57BL/6J mice


title: Res2_RNA

value: NSCLC


title: liver_ATAC_366_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
366_peaks.narrowPeak.gz
366_scaled.bw


title: liver_ATAC_368_l3_s2


title: Res1_RNA


title: StressFB_Day5_Flask13_Fed-Batch-5-13

city: Newark

first: Mark

last: Blenner

state: Delaware

department: Department of Chemical and Biomolecular Engineering

institute: University of Delaware

description:
Replicate 2
Day5_CountTable.xlsx

data_processing:
All RNA-Seq processing achieved using internal University of Delaware Biomix HPC cluster and analysis completed using R
RNA-Seq processing completed using Trimmomatic (0.39) for adapter removal
FastQC (0.11.9) for quality control analysis and visualization of raw reads
STAR (2.7.3a) for alignment of the trimmed paired reads to the CHO CriGri-PICR reference genome assembly (GCF_003668045.1_CriGri-PICR). Original fasta file adapted to include the IgG light and heavy chain sequence on separate scaffold for alignment
SAMtools (0.1.19) for file format conversion
HTSeq (0.10.0) for generation of the read count tables
Characterization of heritability performed in R and adapted from Shaffer, S. M. et al. Cell. (2020). For MemorySeq samples and noise control samples, the transcripts per million (TPM) were calcualted and genes were filtered out such that only protein-coding genes and TPM ≥2.5 were included in the dataset. Metrics of variation, including average, standard deviation, coefficient of variation, skewness, and kurtosis were all calculated for each gene in each dataset. Using the relationship between log2(TPM) and coefficient of variation, a Poisson regression model was generated and heritable gene expression states were defined as genes with TPM ≥2.5 and in the 98th percentile for residuals from the Poisson regression fit. Using Pearson correlation coefficients, a k-clique percolation algorithm was employed to define networks of co-fluctating genes
Gene ontology (GO) enrichment analysis was completed on the clusters identified above and also for the differentiall expressed genes present from the stress-induced flask using the topGO (2.46.0) R package with a minimum node size of 10. The statistical test of significance was conducted using Fisher’s exact test with the classic, weighted, and elimination methods to ensure physically significant enrichment was captured with an adjusted p value < 0.05. A catalog of GO terms for each gene ID was identified using the ENSEMBL MART for cgpicr_gene_ensembl
Differential gene expression analysis (DGEA) was conducted using the DESeq2 (1.34.0) package. A log2 fold change (L2FC) threshold of 0.58 or a 1.5-fold change and an adjusted p-value of 0.05 defined genes with significant differential expression.
Assembly: CHO CriGri-PICR reference genome assembly (GCF_003668045.1_CriGri-PICR)
Supplementary files format and content: XLSX files containing combined count tables for each annotated gene

molecule: polyA RNA

organism: Cricetulus griseus

source_name: Ovary

growth_protocol: Cell cultures were maintained according to the CHOZN® Platform Technical Bulletin (Sigma-Aldrich) with some modifications.These cells were grown in EX-CELL CD CHO (Sigma-Aldrich, St. Louis, MO), deficient in glutamine and seeded and passaged in 125-mL Erlenmeyer flasks (Corning, Corning, NY) with a working volume of 25 mL. The cells were cultured in a Minitron incubator (INFORS HT, Bottmingen, Switzerland) at 37 °C, 5% CO2, 80% relative humidity, and shaking at 100 rpm with passages every 3 days at a cell density of 500,000 cells/mL. Each cell line was passaged at least three times post-thaw to ensure similarly aged, healthy cultures for single-cell cloning and transcriptomic analysis.

extract_protocol:
80,000 to 120,000 cells were collected for extraction and for fed-batch flasks, 1 to 5 million cells were used for extraction. RNA was extracted using the miRNeasy Mini Kit (Qiagen, Germantown, MD) following manufacturer’s protocol. All RNA samples were run on the Agilent5200 Fragment Analyzer (Agilent, Santa Clara, CA) to verify RNA quality prior to submission for sequencing. Samples with an RNA integrity number of  6.0 or greater and at least 100 ng of high quality RNA were sent for sequencing, as quantified by measuring absorbance at 260 and 280 nm using the DS-11 nanospectrophotometer (DeNovix, Wilmington, DE). Samples were stored at -80°C prior to shipment
RNA library preparation, sequencing and analysis was conducted at Azenta Life Sciences (South  Plainfield, NJ, USA) as follows:  The RNA samples received were 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 libraries were 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 libraries were 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).  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 2.20 software. One mis-  match was allowed for index sequence identification.

treatment_protocol: 3 types of samples were collected for RNA-seq. The first were samples collected from limited dilution cloning cell pools. For these, sufficient cell culture volume was collected and serially diluted to obtain a final concentration of 2.5 cells/mL in an 80%/20% mix of EX-CELL Cloning Media (Sigma-Aldrich, St. Louis, MO) and conditioned media. Six non-treated 96-well plates (CELLTREAT, Pepperell, MA) were seeded with 200 μL of the mix for an average of 0.5 cells/well. Plates incubated under static conditions at 37 °C, 5% CO2, and 80% relative humidity. They were expanded until they reached roughly 100,000 cells in the well prior to RNA extraction. The next series of samples were those extracted from a standard passage flask, conditions identical to those described in the growth protocol. The last samples were collected on Day 0 or Day 5 of stress-induced fed-batch production. Standard fed-batch protocol was meant the flasks were seeded at a cell density of 500,000 cells/mL in 30 mL of EX-CELL® AdvancedTM CHO Fed-batch Medium (Sigma-Aldrich, St. Louis, MO). Starting day 3, EX-CELL® AdvancedTM Feed 1 (Sigma-Aldrich, St. Louis, MO) was fed at 5% of the total volume every other day and D-(+)-glucose solution was fed to maintain a concentration of 4 g/L of glucose starting day 4. The flasks were then either stressed with ammonia (10 uM), lactate (15 uM), or heigtened osmolarity (up to 440 mOsm/kg). Cell pellets were collected and stored for RNA extraction by washing with PBS and resuspension of 1 to 5 million cells in RNAlater stabilization solution (ThermoFisher Scientific, Waltham, MA)

value: Ovary

value: CHOZN GS -/- ZFN Clone 23

value: Chinese Hamster Ovary (CHO)

value: Expressing a mAb and glutamine synthetase gene

value: Harvested from an ammonia/lactate/osmolality stressed fed-batch flask on Day 5


title: CD3+CD8+CD69+ cells after co-culturing with cHSPC-pDC+R837+antigen (P2) - 3


title: Sen3_RNA

value: immunotherapy-sensitive


title: liver_ATAC_366_l2_s1

value: liver tissue


title: liver_ATAC_366_l1_s2


title: StressFB_Day5_Flask12_Fed-Batch-5-12

description:
Replicate 1
Day5_CountTable.xlsx


title: DND1-KO,hESC,rep1

value: hESCs


title: CD3+CD8+CD69+ cells after co-culturing with cHSPC-pDC+R837 (P1) - 3

value: Blood

value: co-culturing with cHSPC-pDC+R837


title: Sen2_RNA


title: Res4_RNA

value: immunotherapy-resistant


title: StressFB_Day5_Flask11_Fed-Batch-5-11

description:
Replicate 3
Day5_CountTable.xlsx

value: Harvested from an osmolality stressed fed-batch flask on Day 5


title: CD3+CD8+CD69- cells (P5) - 2

value: CD8+ T cells isolated from PBMCs

value: CD8+ T cells

value: No treatment


title: liver_ATAC_366_l1_s1


title: Sen1_RNA


title: StressFB_Day5_Flask10_Fed-Batch-5-10

description:
Replicate 2
Day5_CountTable.xlsx


title: NSCLC4_RNA

description: Comprehensive Gene Counts and Differential Parameters in NSCLC vs. Normal.xlsx


title: liver_ATAC_365_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
365_peaks.narrowPeak.gz
365_scaled.bw


title: NSCLC3_RNA


title: CD3+CD8+CD69+ cells after co-culturing with moDC+LPS+antigen (P4) - 2

value: co-culturing with moDC+LPS+antigen


title: liver_ATAC_365_l2_s1


title: StressFB_Day5_Flask9_Fed-Batch-5-9

description:
Replicate 1
Day5_CountTable.xlsx


title: CD3+CD8+CD69+ cells after co-culturing with moDC+LPS (P3) - 2

value: co-culturing with moDC+LPS


title: StressFB_Day5_Flask8_Fed-Batch-5-8

description:
Replicate 3
Day5_CountTable.xlsx

value: Ovary

value: Harvested from an lactate stressed fed-batch flask on Day 5


title: NSCLC2_RNA

value: NSCLC


title: CD3+CD8+CD69+ cells after co-culturing with cHSPC-pDC+R837+antigen (P2) - 2


title: liver_ATAC_365_l1_s1


title: CD3+CD8+CD69+ cells after co-culturing with moDC+LPS (P3) - 3


title: StressFB_Day5_Flask7_Fed-Batch-5-7

description:
Replicate 2
Day5_CountTable.xlsx

value: CHOZN GS -/- ZFN Clone 23

value: Chinese Hamster Ovary (CHO)

value: Expressing a mAb and glutamine synthetase gene


title: NSCLC1_RNA


title: Normal3_RNA

source_name: Normal lung

value: Normal lung

value: Normal


title: CD3+CD8+CD69+ cells after co-culturing with cHSPC-pDC+R837 (P1) - 2

value: Blood


title: liver_ATAC_363_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
363_peaks.narrowPeak.gz
363_scaled.bw

value: liver tissue


title: StressFB_Day5_Flask5_Fed-Batch-5-5

description:
Replicate 3
Day5_CountTable.xlsx

value: Harvested from an ammonia stressed fed-batch flask on Day 5


title: Normal2_RNA


title: StressFB_Day5_Flask6_Fed-Batch-5-6

description:
Replicate 1
Day5_CountTable.xlsx


title: liver_ATAC_363_l1_s1


title: liver_ATAC_363_l2_s2


title: Normal1_RNA


title: CD3+CD8+CD69+ cells after co-culturing with moDC+LPS+antigen (P4) - 1


title: StressFB_Day5_Flask3_Fed-Batch-5-3

description:
Replicate 1
Day5_CountTable.xlsx


title: liver_ATAC_360_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
360_peaks.narrowPeak.gz
360_scaled.bw


title: liver_ATAC_360_l2_s2


title: StressFB_Day5_Flask4_Fed-Batch-5-4

description:
Replicate 2
Day5_CountTable.xlsx


title: CD3+CD8+CD69+ cells after co-culturing with moDC+LPS (P3) - 1


title: StressFB_Day5_Flask2_Fed-Batch-5-2

description:
Replicate 2
Day5_CountTable.xlsx

value: Harvested from a standard fed-batch flask on Day 5


title: 21-mo seminal vesicle rep2

city: Guangzhou

first: Yun

last: Xie

state: China

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

institute: sun yat-sen university

data_processing:
Reads were aligned to the mouse Ensemble genome GRCm38 using Hisat2 aligner.
The reads mapped the genome were calculated using featureCounts.
Assembly: mm10
Supplementary files format and content: read counts table

source_name: seminal vesicle

extract_protocol:
Total RNA wasextracted using TRIzol™ Reagent.
lncRNA-seq

value: seminal vesicle


title: liver_ATAC_360_l2_s1


title: 21-mo seminal vesicle rep1


title: liver_ATAC_360_l1_s1


title: CD3+CD8+CD69+ cells after co-culturing with cHSPC-pDC+R837 (P1) - 1

value: CD8+ T cells isolated from PBMCs

value: CD8+ T cells

value: co-culturing with cHSPC-pDC+R837


title: StressFB_Day5_Flask1_Fed-Batch-5-1

description:
Replicate 1
Day5_CountTable.xlsx


title: CD3+CD8+CD69+ cells after co-culturing with cHSPC-pDC+R837+antigen (P2) - 1


title: Human, colorectal cancer, scRNAseq, T5

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

institute: The Affiliated Hospital of Nanchang University

data_processing:
The raw reads were processed to gene expression matrices using Cell Ranger (10×genomics). The Seurat software package was used for further quality control. To remove low quality cells and likely multiple captures, the following quality control steps: the cells with gene numbers less than 200, UMI less than 1000 and log10Genes Per UMI less than 0.7 were filtered out. Furthermore, the cells where ＞20% of the counts belonged to mitochondrial genes and 5% of the counts belonged to hemoglobin genes were removed. Additionally, the DoubletFinder package (version 2.0.2) was used to identify potential doublet. Finally, 124528 cells (Median: 5319 cells/patient) were obtained for the downstream analysis. We obtained 1717 genes and 5763 UMIs per cell on average
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz files
In barcodes.tsv.gz, the one-to-one correspondence between the barcode and the sample is as follows:
barcode-1 = sample N1
barcode-2 = sample N2
barcode-3 = sample N3
barcode-4 = sample P1
barcode-6 = sample P12
barcode-7 = sample P3
barcode-8 = sample P4
barcode-10 = sample T2
barcode-11 = sample T3
barcode-12 = sample T5

source_name: colorectal specimens

extract_protocol:
The tissue samples were removed from patients and quickly immersed in Dulbecco’s modified eagle medium (DMEM; Cat#11995065, Gibco) containing 10% fetal bovine serum (FBS; Cat#10091148, Gibco). Samples were minced into about 0.5 mm3 pieces and enzymatically digested in digestion medium DMEM supplemented with trypsin (Cat#15090046, Gibco), collagenase I (Cat# 17018029, Gibco), collagenase II (Cat# 17101015, Gibco) and collagenase IV (Cat# 17104019, Gibco). The samples were incubated and digested at 37℃ for approximately 60 min and then filtered using a 100μm strainer (Corning). Following centrifugation (300g) at 4℃ for 5 min, the cells were resuspended with medium containing red cell lysate (Cat#130094183, MACS). After standing 10min at 4℃, the single-cell suspension was centrifuged at 300g for 5min and resuspended in 100μl medium. Cell concentration and viability were detected under Luna Cell Counter.
The suspensions were then converted to separate barcoded scRNA-seq libraries using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Cat#1000268, 10×genomics) according to the manufacturer’s instruction. Libraries were sequenced on an Illumina Nova 6000 PE150

value: colorectal specimens

tag: disease state

value: colorectal cancer

value: epithelial cells, endothelial cells, fibroblasts, smooth muscle cells, T cells, B cells, myeloid cells, plasma cells, mast cells, neural cells


title: StressFB_Day0_Flask3_Fed-Batch-0-3

description:
Replicate 3
Day0_CountTable.xlsx

value: Ovary

value: Harvested from a standard fed-batch flask on Day 0


title: CD3+CD8+CD69- cells (P5) - 1

value: No treatment


title: Human, colorectal cancer, scRNAseq, T3


title: 13-mo seminal vesicle rep3


title: StressFB_Day0_Flask2_Fed-Batch-0-2

description:
Replicate 2
Day0_CountTable.xlsx

value: CHOZN GS -/- ZFN Clone 23

value: Chinese Hamster Ovary (CHO)

value: Expressing a mAb and glutamine synthetase gene


title: liver_ATAC_358_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
358_peaks.narrowPeak.gz
358_scaled.bw


title: 13-mo seminal vesicle rep2


title: StressFB_Day0_Flask1_Fed-Batch-0-1

description:
Replicate 1
Day0_CountTable.xlsx


title: liver_ATAC_358_l2_s2


title: liver_ATAC_358_l2_s1


title: 13-mo seminal vesicle rep1


title: Human, colorectal cancer, scRNAseq, T2


title: 21-mo seminal vesicle rep3


title: Human, colorectal tissue with adenomatous polyps, scRNAseq, P4


title: NoiseControl_Sample40_Bulk-Population-40

description:
Replicate 40
Noise_Control_FinalTable.xlsx

value: Harvested from a passage flask


title: 3-mo seminal vesicle rep3


title: NoiseControl_Sample39_Bulk-Population-39

description:
Replicate 39
Noise_Control_FinalTable.xlsx


title: liver_ATAC_358_l1_s1

value: liver tissue


title: Human, colorectal tissue with adenomatous polyps, scRNAseq, P3


title: Human, colorectal tissue with inflammatory polyps, scRNAseq, P12


title: NoiseControl_Sample38_Bulk-Population-38

description:
Replicate 38
Noise_Control_FinalTable.xlsx


title: liver_ATAC_357_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
357_peaks.narrowPeak.gz
357_scaled.bw


title: 3-mo seminal vesicle rep1


title: Human, colorectal tissue with inflammatory polyps, scRNAseq, P1


title: 3-mo seminal vesicle rep2


title: VtA4

city: Daegu

first: Bo-Yoon

last: Park

address: 170 Hyeonchung-ro

country: South Korea

institute: Yeungnam University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10_NCBI_108
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Hindlimb

extract_protocol:
Mouse hindlimb issue was flash frozen on dry ice and RNA was harvested using Trizol reagent. The TruSeq Stranded mRNA Library Prep Kit was used with 1 ug of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hindlimb

tag: condition

value: lymph node transfer with ABTAA treatment


title: liver_ATAC_357_l3_s1


title: liver_ATAC_357_l1_s1


title: NoiseControl_Sample37_Bulk-Population-37

description:
Replicate 37
Noise_Control_FinalTable.xlsx


title: liver_ATAC_356_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
356_peaks.narrowPeak.gz
356_scaled.bw


title: VtA3


title: NoiseControl_Sample35_Bulk-Population-35

description:
Replicate 35
Noise_Control_FinalTable.xlsx


title: Human, normal colorectal mucosa sample, scRNAseq, N3

value: normal colorectal mucosa


title: Human, normal colorectal mucosa sample, scRNAseq, N2


title: NoiseControl_Sample34_Bulk-Population-34

description:
Replicate 34
Noise_Control_FinalTable.xlsx


title: Human, normal colorectal mucosa sample, scRNAseq, N1


title: VtA2


title: liver_ATAC_356_l1_s1


title: NoiseControl_Sample33_Bulk-Population-33

description:
Replicate 33
Noise_Control_FinalTable.xlsx


title: WGBS-HG03516-Rep2

city: Saint Louis

first: Ting

last: Wang

state: Missouri

address: 4515 McKinley Avenue

institute: WUSTL

data_processing:
Adapter trimming by Trim Galore
Deduplicatin by FastUniq
Bismark
methylGrapher
Assembly: hg38 and human pangenome v1
Supplementary files format and content: Tab-delimited text file generated by Bismark, indicating the methylation count for each cytosine in CpG context.
Supplementary files format and content: Tab-delimited text file generated by methylGrapher, displaying the methylation count for each cytosine across all contexts.

extract_protocol:
Qiagen AllPrep DNA/RNA kit
200ng of gDNA, including 0.2% Unmethylated Lambda DNA (Promega, Cat# D1521) were fragmented in a final volume of 50uL using the Covaris LE220 targeting ~350bp inserts. A 1.5x AMPure clean-up was performed post fragmentation on the EpMotion 5075 (Eppendorf) resulting in a final volume of 20uL. The fragmented gDNA was bisulfite converted with the EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research, Cat # D5043) according to the manufacturer’s recommendations on the EpMotion 5075. The bisulfite converted DNA (bsDNA) was quantitated on the Qubit Flex using the Qubit ssDNA Assay Kit (Thermo Fisher Scientific, Cat #Q10212). Automated whole genome bisulfite (WGBS) libraries were constructed with ~100ng of bsDNA using the Accel-NGS Methyl-Seq DNA Library Kit (Swift BioSciences, Cat # 30096) and unique dual indexes (UDI) (Swift, X9096) on the EpMotion 5075. Eight PCR cycles will be performed during the indexing PCR step, followed by a final 0.85x AMPure cleanup.

value: 1000 Genomes LCL


title: liver_ATAC_356_l2_s1


title: VLNT4

value: lymph node transfer


title: liver_ATAC_352_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
352_peaks.narrowPeak.gz
352_scaled.bw


title: VLNT3


title: WGBS-HG03516-Rep1


title: liver_ATAC_352_l2_s1


title: WGBS-HG01978-Rep2


title: NoiseControl_Sample32_Bulk-Population-32

description:
Replicate 32
Noise_Control_FinalTable.xlsx


title: NoiseControl_Sample31_Bulk-Population-31

description:
Replicate 31
Noise_Control_FinalTable.xlsx


title: liver_ATAC_352_l1_s1


title: WGBS-HG01978-Rep1


title: NoiseControl_Sample36_Bulk-Population-36

description:
Replicate 36
Noise_Control_FinalTable.xlsx


title: VLNT2


title: liver_ATAC_351_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
351_peaks.narrowPeak.gz
351_scaled.bw


title: NoiseControl_Sample30_Bulk-Population-30

description:
Replicate 30
Noise_Control_FinalTable.xlsx


title: WGBS-HG01952-Rep2


title: VtA1


title: NoiseControl_Sample29_Bulk-Population-29

description:
Replicate 29
Noise_Control_FinalTable.xlsx


title: LE4

value: lymphedema


title: NoiseControl_Sample28_Bulk-Population-28

description:
Replicate 28
Noise_Control_FinalTable.xlsx


title: liver_ATAC_351_l2_s2


title: LE3


title: liver_ATAC_351_l2_s1


title: WGBS-HG01952-Rep1


title: NoiseControl_Sample27_Bulk-Population-27

description:
Replicate 27
Noise_Control_FinalTable.xlsx


title: WGBS-HG00741-Rep2


title: liver_ATAC_351_l1_s1


title: liver_ATAC_351_l1_s2


title: LE1


title: liver_ATAC_350_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
350_peaks.narrowPeak.gz
350_scaled.bw


title: LC, WISP2 (SP deletion) overexpression, rep2

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

data_processing:
Standard workflow for bulk-rna sequencing
Assembly: GRh38-1.2.0
Supplementary files format and content: matrix files with fpkm and count

source_name: testis

extract_protocol:
Total RNA was extracted from 106 cells using TRIzol Reagent (Thermo Fisher Scientific). 3 mg per sample were constructed into libraries through NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) following manufacturer’s manuals.
Sequencing data were generated on Illumina NovaSeq 6000 platform with 150-bp paired-end read length by Novogene.

value: testis

value: Leydig cell

value: WISP3mut OE


title: WGBS of P60 M+N+ (eGFP+) sorted beta-cells from male mice - Rep 4

city: Nashville

first: Guoqiang

state: TN

address: 2213 Garland Avenue

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Trimming: All sequencing library reads were trimmed of adapters and assessed for quality using Trim Galore (version 0.6.6), which is a wrapper tool for Cutadapt (1.16) and FastQC.
Mapping: Trimmed, bisulfute-converted reads were mapped to the mouse genome assembly (mm39) using abismal and output as SAM files.
Formatting: Paired-end mates are merged into single-end entries using the format_reads function within the methylation analysis tool, MethPipe (version 5.0.1), sorted using the SAMtools package (version 1.5), and then de-duplicated (i.e., reads mapping to identical genomic locations were removed) using the duplicate-remover function within MethPipe.
Methylation Analysis: Various utilities within the MethPipe software package (version 5.0.1) were used to output data for mapped reads, CpG methylation estimates, and most relevant for this project: hypomethylared regions (HMRs) and differentially methylated regions (DMRs).
Assembly: mm39
Supplementary files format and content: Meth files (.CpG.meth) are tab-delimited text files of CpG methylation levels for symmetrically methylated CpG sites. HMR files (.hmr) are BED-formatted, tab-delimited files of hypomethylated regions (HMRs) called considering just methylation levels at CpG sites. Methdiff (.methdiff) tab-delimited text files list the differential methlyation score of each CpG site when comparing methylomes. DMR (.dmr) tab-delimited text files list differentially methylated regions (DMRs) called between methylomes; we then took the DMR files and filtered regions based on their genomic size (>= 50 bp) and number of differentially methylated CpGs (in our case at least 2) - these tab-delimited text files have the string 'at_least_50bp_and_2_CpGsites_significantly_diff_methylated.txt' in their filename.

source_name: endocrine islets, postnatal day-60, male mice

extract_protocol:
Mice were euthanized either two days (P2) or 2-months after birth. Their islets were isolated, dissociated into single cells, and used for FACS cell sorting based on the expression of eYFP and Apple fluorescent proteins. Dead cells were excluded using DAPI staining. Collected cells ere immediately processed for genomic DNA isolation using Zymo kit D4011.
Tagmentation-based WGBS (T-WGBS) libraries were prepared very similarly to previously reported methods (Adey and Shendure 2012, Barnentt et al. 2020, Wang et al., 2013). Genomic DNA from purified beta-cell subtypes were extracted using a kit from Zymo. For each stage/sex, at least three batches of cells from FACS (4-7 mice for each batch, at least 30,000 cells) were combined, yielding 100-150 ng DNA. Library concentrations and size distributions were evaluated using an Agilent 2200 TapeStation with a D5000 screentape. T-WGBS DNA libraries were sequenced at Vanderbilt University’s genomics research core, VANTAGE, using 2×150bp paired-end reads on the Illumina NovSeq 6000, obtaining approximately 300-500 million reads per library.

value: all islet cells

value: Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple


title: NoiseControl_Sample26_Bulk-Population-26

description:
Replicate 26
Noise_Control_FinalTable.xlsx

value: Ovary


title: NoiseControl_Sample25_Bulk-Population-25

description:
Replicate 25
Noise_Control_FinalTable.xlsx

value: CHOZN GS -/- ZFN Clone 23


title: WGBS-HG00741-Rep1


title: VLNT1


title: WGBS of P60 M+N+ (eGFP+) sorted beta-cells from female mice - Rep 3

source_name: endocrine islets, postnatal day-60, female mice


title: liver_ATAC_348_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
348_peaks.narrowPeak.gz
348_scaled.bw


title: WGBS of P60 M+N+ (eGFP+) sorted beta-cells from male mice - Rep 2

value: endocrine islets, postnatal day-60, male mice


title: NoiseControl_Sample24_Bulk-Population-24

description:
Replicate 24
Noise_Control_FinalTable.xlsx

value: Chinese Hamster Ovary (CHO)

value: Expressing a mAb and glutamine synthetase gene


title: liver_ATAC_350_l3_s1

value: liver tissue


title: WGBS-HG00621-Rep2


title: WGBS of P60 M+N+ (eGFP+) sorted beta-cells from female mice - Rep 1

value: endocrine islets, postnatal day-60, female mice


title: liver_ATAC_350_l1_s1


title: LC, Recombinant WISP2 treatment, rep2


title: NoiseControl_Sample21_Bulk-Population-21

description:
Replicate 21
Noise_Control_FinalTable.xlsx

value: Harvested from a passage flask


title: liver_ATAC_348_l2_s1


title: NoiseControl_Sample20_Bulk-Population-20

description:
Replicate 20
Noise_Control_FinalTable.xlsx


title: WGBS of P60 M-N+ (eGFP-) sorted beta-cells from male mice - Rep 4


title: LC, Recombinant WISP2 treatment, rep1


title: WGBS of P60 M-N+ (eGFP-) sorted beta-cells from female mice - Rep 3


title: NoiseControl_Sample22_Bulk-Population-22

description:
Replicate 22
Noise_Control_FinalTable.xlsx


title: LE2

value: Hindlimb


title: WGBS-HG00621-Rep1

value: 1000 Genomes LCL


title: NoiseControl_Sample23_Bulk-Population-23

description:
Replicate 23
Noise_Control_FinalTable.xlsx


title: LC, WISP2 (SP deletion) overexpression, rep1

value: WISP2mut OE


title: liver_ATAC_348_l1_s1


title: LC, normal control, rep2

value: no


title: liver_ATAC_347_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
347_peaks.narrowPeak.gz
347_scaled.bw


title: NoiseControl_Sample18_Bulk-Population-18

description:
Replicate 18
Noise_Control_FinalTable.xlsx


title: LC, normal control, rep1

value: testis


title: WGBS of P60 M-N+ (eGFP-) sorted beta-cells from female mice - Rep 1


title: RNA-SeqofOCI-AML3:Untreated,Repeat4

city: Jena

first: Faezeh

last: Ghazvini Zadegan

address: Hans-Knoll-Strase 2

department: Department of Hematology/Oncology, Clinic of Internal Medicine II

country: Germany

institute: Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB)

data_processing:
usegalaxy.eu
Initial Assessment with FastQC tool to control the quality of raw sequencing data.
Cutadapt tool was used for trimming adapter sequences, removing low-quality bases, and filtering out sequences of inadequate length.
Aligning sequencing reads to a reference genome is accomplished using STAR (Spliced Transcripts Alignment to a Reference) tool.
Quantifying gene expression levels is performed using the featureCounts tool, while the identification of differentially expressed features is carried out using the DESeq2 tool.
manipulation of de Bruijn graphs, via the removal of errors and the simplification of repeated regions
Assembly: not provided
Supplementary files format and content: A tabular file containing normalized abundance measurements generated by the DESeq2 tool

source_name: Peripheralblood

value: Peripheralblood

value: AML

value: Untreated


title: NoiseControl_Sample17_Bulk-Population-17

description:
Replicate 17
Noise_Control_FinalTable.xlsx


title: WGBS of P2 M+N+ (eGFP+) sorted beta-cells from male mice - Rep 2

source_name: endocrine islets, postnatal day-2, male mice

value: all islet cells

value: Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple


title: liver_ATAC_347_l1_s1


title: RNA-SeqofOCI-AML3:Untreated,Repeat3


title: liver_ATAC_347_l2_s1


title: RNA-SeqofOCI-AML3:Untreated,Repeat2


title: WGBS of P2 M-N+ (eGFP-) sorted beta-cells from male mice - Rep 2

value: endocrine islets, postnatal day-2, male mice


title: WGBS of P2 M+N+ (eGFP+) sorted beta-cells from female mice - Rep 1

source_name: endocrine islets, postnatal day-2, female mice


title: NoiseControl_Sample14_Bulk-Population-14

description:
Replicate 14
Noise_Control_FinalTable.xlsx

value: Ovary

value: CHOZN GS -/- ZFN Clone 23


title: WGBS of P2 M-N+ (eGFP-) sorted beta-cells from female mice - Rep 1

value: endocrine islets, postnatal day-2, female mice


title: liver_ATAC_346_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
346_peaks.narrowPeak.gz
346_scaled.bw

value: liver tissue


title: liver_ATAC_346_l3_s1


title: NoiseControl_Sample13_Bulk-Population-13

description:
Replicate 13
Noise_Control_FinalTable.xlsx

value: Chinese Hamster Ovary (CHO)

value: Expressing a mAb and glutamine synthetase gene


title: NoiseControl_Sample16_Bulk-Population-16

description:
Replicate 16
Noise_Control_FinalTable.xlsx

value: Harvested from a passage flask


title: liver_ATAC_346_l1_s1


title: RNA-SeqofOCI-AML3:ATRA_GSK-LSD1_MB3,Repeat3


title: P14_Casz1 -/- IHC-73

city: Beijing

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.2.1) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v2.2.1) with default parameters.
Raw counts were calculated by featureCounts (v2.0.1) software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for smartseq.

source_name: Cochlea

extract_protocol:
Cochlear samples were incubated in choline chloride solution containing 20 U/mL papain (Cat# LK003178, Worthington) and 100 U/mL DNase I (Cat# LK003172, Worthington) for 20 min at 37°C, and this was followed by digestion with a protease (Cat# P5147, Sigma; 1 mg/mL) and dispase (Cat# LS02104, Worthington; 1 mg/mL) for 20 min at 25°C. The components of the choline chloride solution contained 92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4.7H2O, 0.5 mM CaCl2.2H2O, and 12 mM N-acetyl-L-cysteine. Next, the post-digested cochlear samples were gently triturated using fire-polished glass Pasteur pipettes (13-678-20b; Fisher) with 4 different pore sizes (largest size the first, and smallest one the last). The picked endogenous IHCs and iOHCs were immediately subjected to reverse-transcription and cDNA amplification using a Smart-Seq HT kit (Cat# 634437, Takara).
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).
Single cell full length cDNA RNA-Seq

value: Cochlea


title: liver_ATAC_345_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
345_peaks.narrowPeak.gz
345_scaled.bw


title: NoiseControl_Sample19_Bulk-Population-19

description:
Replicate 19
Noise_Control_FinalTable.xlsx


title: RNA-SeqofOCI-AML3:ATRA_GSK-LSD1_MB3,Repeat2


title: WGBS of P60 M-N+ (eGFP-) sorted beta-cells from male mice - Rep 2

value: endocrine islets, postnatal day-60, male mice


title: NoiseControl_Sample12_Bulk-Population-12

description:
Replicate 12
Noise_Control_FinalTable.xlsx


title: P14_Casz1 -/- IHC-72


title: liver_ATAC_345_l2_s1


title: NoiseControl_Sample11_Bulk-Population-11

description:
Replicate 11
Noise_Control_FinalTable.xlsx


title: NoiseControl_Sample15_Bulk-Population-15

description:
Replicate 15
Noise_Control_FinalTable.xlsx


title: RNA-SeqofOCI-AML3:ATRA,Repeat3

value: ATRA


title: RNA-SeqofOCI-AML3:Untreated,Repeat1


title: P14_Casz1 -/- IHC-71


title: RNA-SeqofOCI-AML3:ATRA_GSK-LSD1_MB3,Repeat1


title: NoiseControl_Sample10_Bulk-Population-10

description:
Replicate 10
Noise_Control_FinalTable.xlsx


title: liver_ATAC_345_l1_s1


title: NoiseControl_Sample8_Bulk-Population-8

description:
Replicate 8
Noise_Control_FinalTable.xlsx


title: P14_Casz1 -/- IHC-70


title: RNA-SeqofOCI-AML3:ATRA,Repeat2


title: liver_ATAC_344_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
344_peaks.narrowPeak.gz
344_scaled.bw


title: liver_ATAC_344_l3_s1


title: RNA-SeqofOCI-AML3:ATRA,Repeat1


title: NoiseControl_Sample9_Bulk-Population-9

description:
Replicate 9
Noise_Control_FinalTable.xlsx


title: P14_Casz1 -/- IHC-69


title: P14_Casz1 -/- IHC-68


title: RNA-SeqofOCI-AML3:AM80_GSK-LSD1_MB3,Repeat3


title: P14_Casz1 -/- IHC-67


title: liver_ATAC_343_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
343_peaks.narrowPeak.gz
343_scaled.bw


title: liver_ATAC_344_l1_s1


title: P14_Casz1 -/- IHC-66


title: liver_ATAC_342_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
342_peaks.narrowPeak.gz
342_scaled.bw


title: NoiseControl_Sample6_Bulk-Population-6

description:
Replicate 6
Noise_Control_FinalTable.xlsx


title: P14_Casz1 -/- IHC-65


title: RNA-SeqofOCI-AML3:AM80_GSK-LSD1_MB3,Repeat1


title: NoiseControl_Sample5_Bulk-Population-5

description:
Replicate 5
Noise_Control_FinalTable.xlsx


title: liver_ATAC_342_l2_s1


title: NoiseControl_Sample4_Bulk-Population-4

description:
Replicate 4
Noise_Control_FinalTable.xlsx


title: RNA-SeqofOCI-AML3:AM80,Repeat3


title: liver_ATAC_342_l1_s1


title: NoiseControl_Sample3_Bulk-Population-3

description:
Replicate 3
Noise_Control_FinalTable.xlsx


title: liver_ATAC_340_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
340_peaks.narrowPeak.gz
340_scaled.bw


title: P14_Casz1 -/- IHC-63


title: RNA-SeqofOCI-AML3:AM80,Repeat2


title: NoiseControl_Sample2_Bulk-Population-2

description:
Replicate 2
Noise_Control_FinalTable.xlsx


title: P14_Casz1 -/- IHC-61


title: NoiseControl_Sample7_Bulk-Population-7

description:
Replicate 7
Noise_Control_FinalTable.xlsx


title: liver_ATAC_337_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
337_peaks.narrowPeak.gz
337_scaled.bw


title: P14_Casz1 -/- IHC-60


title: P14_Casz1 -/- IHC-62


title: NoiseControl_Sample1_Bulk-Population-1

description:
Replicate 1
Noise_Control_FinalTable.xlsx


title: moDC cell type, 96PA1, replicate 2

city: Los Angeles

first: Giorgia

last: Del Vecchio

address: 610 Charles E Young Dr S, Room 5146

institute: University of California Los Angeles

data_processing:
Raw reads were quality checked using FastQC v.0.11.9.
Sequence reads were trimmed for adaptors sequence and low quality reads using trimmomatic
Trimmed sequence reads were mapped to the human genome version GRCh38/hg38 using STAR v.2.7.9a keeping unique alignments and those with up to 4 mismatches
Counts were generated using the quantMode GeneCounts option in STAR that counts the number of reads per gene while mapping
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited txt file with Ensembl gene ID and raw counts for each sample

source_name: Monocyte Derived Dendritic Cells

extract_protocol:
RNA from stimulated mDC, moDC, and LCDC was isolated using Quick-RNA Microprep kit.
RNA concentration and quality were determined using TapeStation  and sequencing libraries were prepared using the KAPA mRNA HyperPrep kit following manufacturer's protocol.

value: Monocyte Derived Dendritic Cells

value: stimulated with C. acne strain 96PA1


title: RNA-SeqofOCI-AML3:AM80,Repeat1

value: Peripheralblood

value: AML


title: moDC cell type, 96PA1, replicate 3


title: liver_ATAC_340_l2_s1


title: moDC cell type, 96PA1


title: liver_ATAC_340_l1_s1


title: MemorySeq_Sample40_Single-Cell-40

description:
Replicate 40
Memory_Seq_Samples_FinalTable.xlsx

value: Derived from a single-cell clone


title: P14_Casz1 -/- IHC-59


title: liver_ATAC_337_l2_s1


title: MemorySeq_Sample38_Single-Cell-38

description:
Replicate 38
Memory_Seq_Samples_FinalTable.xlsx


title: moDC cell type, 5PA1, replicate 3

value: stimulated with C. acne strain 5PA1


title: MemorySeq_Sample39_Single-Cell-39

description:
Replicate 39
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-64


title: liver_ATAC_337_l1_s1


title: P14_Casz1 -/- IHC-57


title: MemorySeq_Sample36_Single-Cell-36

description:
Replicate 36
Memory_Seq_Samples_FinalTable.xlsx


title: moDC cell type, 5PA1, replicate 2


title: moDC cell type, 5PA1


title: liver_ATAC_336_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
336_peaks.narrowPeak.gz
336_scaled.bw


title: MemorySeq_Sample35_Single-Cell-35

description:
Replicate 35
Memory_Seq_Samples_FinalTable.xlsx


title: RNA-SeqofOCI-AML3:AM80_GSK-LSD1_MB3,Repeat2


title: moDC cell type, 43PA1, replicate 3

value: stimulated with C. acne strain 43PA1


title: liver_ATAC_336_l1_s1


title: P14_Casz1 -/- IHC-54


title: moDC cell type, 43PA1, replicate 2


title: MemorySeq_Sample33_Single-Cell-33

description:
Replicate 33
Memory_Seq_Samples_FinalTable.xlsx

value: Ovary


title: P14_Casz1 -/- IHC-55


title: P14_Casz1 -/- IHC-58


title: MemorySeq_Sample34_Single-Cell-34

description:
Replicate 34
Memory_Seq_Samples_FinalTable.xlsx

value: CHOZN GS -/- ZFN Clone 23


title: moDC cell type, 43PA1


title: P14_Casz1 -/- IHC-52


title: MemorySeq_Sample31_Single-Cell-31

description:
Replicate 31
Memory_Seq_Samples_FinalTable.xlsx


title: moDC cell type, 42PA3, replicate 2

value: stimulated with C. acne strain 42PA3


title: liver_ATAC_335_l1_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
335_peaks.narrowPeak.gz
335_scaled.bw

value: liver tissue


title: MemorySeq_Sample32_Single-Cell-32

description:
Replicate 32
Memory_Seq_Samples_FinalTable.xlsx

value: Chinese Hamster Ovary (CHO)


title: moDC cell type, 42PA3, replicate 3


title: liver_ATAC_334_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
334_peaks.narrowPeak.gz
334_scaled.bw


title: liver_ATAC_336_l3_s1


title: MemorySeq_Sample37_Single-Cell-37

description:
Replicate 37
Memory_Seq_Samples_FinalTable.xlsx

value: Expressing a mAb and glutamine synthetase gene


title: P14_Casz1 -/- IHC-56


title: P14_Casz1 -/- IHC-51


title: moDC cell type, 42PA3


title: liver_ATAC_334_l2_s1


title: liver_ATAC_335_l3_s1


title: P14_Casz1 -/- IHC-50


title: P14_Casz1 -/- IHC-49


title: liver_ATAC_335_l2_s1


title: P14_Casz1 -/- IHC-53


title: liver_ATAC_334_l1_s1


title: MemorySeq_Sample30_Single-Cell-30

description:
Replicate 30
Memory_Seq_Samples_FinalTable.xlsx


title: MemorySeq_Sample29_Single-Cell-29

description:
Replicate 29
Memory_Seq_Samples_FinalTable.xlsx


title: moDC cell type, 110PA4, replicate 2

value: stimulated with C. acne strain 110 PA4


title: MemorySeq_Sample27_Single-Cell-27

description:
Replicate 27
Memory_Seq_Samples_FinalTable.xlsx


title: moDC cell type, 110PA4


title: P14_Casz1 -/- IHC-47

value: Cochlea


title: P14_Casz1 -/- IHC-48


title: liver_ATAC_333_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
333_peaks.narrowPeak.gz
333_scaled.bw


title: moDC cell type, 110PA3, replicate 3

value: stimulated with C. acne strain 110 PA3


title: P14_Casz1 -/- IHC-46


title: liver_ATAC_333_l1_s1


title: MemorySeq_Sample26_Single-Cell-26

description:
Replicate 26
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-45


title: liver_ATAC_332_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
332_peaks.narrowPeak.gz
332_scaled.bw


title: MemorySeq_Sample23_Single-Cell-23

description:
Replicate 23
Memory_Seq_Samples_FinalTable.xlsx


title: moDC cell type, 110PA3, replicate 2


title: MemorySeq_Sample25_Single-Cell-25

description:
Replicate 25
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-44


title: moDC cell type, 110PA3


title: liver_ATAC_332_l2_s1


title: moDC cell type, 110PA4, replicate 3


title: moDC cell type, cells alone, replicate 5

value: cells alone


title: MemorySeq_Sample22_Single-Cell-22

description:
Replicate 22
Memory_Seq_Samples_FinalTable.xlsx


title: MemorySeq_Sample21_Single-Cell-21

description:
Replicate 21
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-43


title: moDC cell type, cells alone, replicate 4

value: Monocyte Derived Dendritic Cells


title: liver_ATAC_332_l1_s1


title: MemorySeq_Sample28_Single-Cell-28

description:
Replicate 28
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-42


title: moDC cell type, cells alone, replicate 3


title: liver_ATAC_333_l2_s1


title: liver_ATAC_331_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
331_peaks.narrowPeak.gz
331_scaled.bw


title: P14_Casz1 -/- IHC-41


title: moDC cell type, cells alone, replicate 2


title: P14_Casz1 -/- IHC-40


title: liver_ATAC_331_l1_s1


title: MemorySeq_Sample18_Single-Cell-18

description:
Replicate 18
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-39


title: moDC cell type, cells alone


title: P14_Casz1 -/- IHC-38


title: liver_ATAC_325_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
325_peaks.narrowPeak.gz
325_scaled.bw


title: MemorySeq_Sample16_Single-Cell-16

description:
Replicate 16
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 96PA1, replicate 3

source_name: Myeloid Dencritic Cell

value: Myeloid Dencritic Cell

value: stimulated with C. acne strain 96PA1


title: mDC cell type, 96PA1, replicate 2


title: P14_Casz1 -/- IHC-37


title: MemorySeq_Sample17_Single-Cell-17

description:
Replicate 17
Memory_Seq_Samples_FinalTable.xlsx


title: liver_ATAC_331_l3_s1


title: mDC cell type, 96PA1


title: liver_ATAC_325_l2_s1


title: P14_Casz1 -/- IHC-36


title: mDC cell type, 5PA1, replicate 3


title: MemorySeq_Sample14_Single-Cell-14

description:
Replicate 14
Memory_Seq_Samples_FinalTable.xlsx


title: liver_ATAC_323_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
323_peaks.narrowPeak.gz
323_scaled.bw


title: P14_Casz1 -/- IHC-35


title: liver_ATAC_325_l1_s1


title: MemorySeq_Sample15_Single-Cell-15

description:
Replicate 15
Memory_Seq_Samples_FinalTable.xlsx


title: MemorySeq_Sample13_Single-Cell-13

description:
Replicate 13
Memory_Seq_Samples_FinalTable.xlsx


title: MemorySeq_Sample20_Single-Cell-20

description:
Replicate 20
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 5PA1, replicate 2


title: P14_Casz1 -/- IHC-34


title: liver_ATAC_323_l1_s1


title: MemorySeq_Sample19_Single-Cell-19

description:
Replicate 19
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-33


title: MemorySeq_Sample12_Single-Cell-12

description:
Replicate 12
Memory_Seq_Samples_FinalTable.xlsx


title: liver_ATAC_253_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
253_peaks.narrowPeak.gz
253_scaled.bw


title: mDC cell type, 43PA1, replicate 3


title: liver_ATAC_253_l2_s1


title: P14_Casz1 -/- IHC-32


title: MemorySeq_Sample11_Single-Cell-11

description:
Replicate 11
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 43PA1, replicate 2


title: P14_Casz1 -/- IHC-31


title: MemorySeq_Sample10_Single-Cell-10

description:
Replicate 10
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 43PA1


title: MemorySeq_Sample9_Single-Cell-9

description:
Replicate 9
Memory_Seq_Samples_FinalTable.xlsx


title: liver_ATAC_238_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
238_peaks.narrowPeak.gz
238_scaled.bw


title: P14_Casz1 -/- IHC-30


title: liver_ATAC_253_l1_s1


title: liver_ATAC_323_l2_s1


title: MemorySeq_Sample8_Single-Cell-8

description:
Replicate 8
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 42PA3, replicate 3


title: P14_Casz1 -/- IHC-29


title: liver_ATAC_238_l2_s1


title: MemorySeq_Sample6_Single-Cell-6

description:
Replicate 6
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-28


title: mDC cell type, 5PA1


title: MemorySeq_Sample7_Single-Cell-7

description:
Replicate 7
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 42PA3, replicate 2


title: MemorySeq_Sample5_Single-Cell-5

description:
Replicate 5
Memory_Seq_Samples_FinalTable.xlsx


title: liver_ATAC_238_l1_s1


title: mDC cell type, 42PA3


title: P14_Casz1 -/- IHC-27


title: liver_ATAC_223_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
223_peaks.narrowPeak.gz
223_scaled.bw


title: mDC cell type, 110PA4, replicate 3


title: liver_ATAC_223_l2_s1


title: mDC cell type, 110PA4, replicate 2


title: MemorySeq_Sample4_Single-Cell-4

description:
Replicate 4
Memory_Seq_Samples_FinalTable.xlsx


title: MemorySeq_Sample2_Single-Cell-2

description:
Replicate 2
Memory_Seq_Samples_FinalTable.xlsx


title: mDC cell type, 110PA3, replicate 3


title: P14_Casz1 -/- IHC-24


title: MemorySeq_Sample3_Single-Cell-3

description:
Replicate 3
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-23


title: P14_Casz1 -/- IHC-25


title: mDC cell type, 110PA3, replicate 2


title: mDC cell type, 110PA4


title: liver_ATAC_221_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
221_peaks.narrowPeak.gz
221_scaled.bw


title: liver_ATAC_221_l3_s1


title: MemorySeq_Sample1_Single-Cell-1

description:
Replicate 1
Memory_Seq_Samples_FinalTable.xlsx


title: P14_Casz1 -/- IHC-26


title: P14_Casz1 -/- IHC-22


title: P14_Casz1 -/- IHC-20


title: liver_ATAC_217_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
217_peaks.narrowPeak.gz
217_scaled.bw


title: P14_Casz1 -/- IHC-21


title: mDC cell type, cells alone, replicate 3


title: CD8+CD127+PD-1- biol rep 2

city: Melbourne

first: Maliha

last: Alikhan

state: VIC

address: Level 5, Block E, Monash Medical Centre, 246 Clayton Road, Clayton

department: Department of Medicine

country: Australia

institute: Monash University

data_processing:
Raw fastq files were analysed using the RNAsik pipeline v1.5.3 using STAR aligner with the Mus musculus GRCm38 reference.
Reads were quantified using featureCounts producing raw genes count matrix and various quality control metrics. Raw counts were then analysed with Degust, a web tool that performs normalisation using trimmed mean of M values (TMM) for RNA composition.
Assembly: Mus musculus GRCm38
Supplementary files format and content: processed data.tsv
Supplementary files format and content: tab-separated values files including raw counts for each Sample

source_name: Kidney

extract_protocol:
Total RNA was isolated from each population using the Agencourt RNAdvance Cell Kit (Beckman Coulter). Samples were processed starting with 2ng total RNA.
cDNA libraries were generated using the Single Primer Isothermal Amplification (SPIA) RNA-Seq protocol. Libraries were quantitated by Qubit and qPCR and one equimolar pool was made based upon qPCR results. Following denaturation 2.0pM of library pool was clustered on a high output NextSeq run (75bp SR sequencing using Illumina NextSeq550 Hihg Output mode).

treatment_protocol: Mice were immunised with recombinant mouse MPO and then low-dose sheep anti-mouse basement membrane (BM) globulin was administered to trigger glomerulonephritis. Twenty-one days later, kidneys were isolated and the following cells were flow sorted: CD4+CD127+PD-1-, CD4+CD127-PD-1+, CD8+CD127+PD-1- and CD8+CD127-PD-1+.

value: Kidney

value: WT


title: CD8+CD127+PD-1- biol rep 3


title: liver_ATAC_217_l2_s1

source_name: liver tissue


title: mDC cell type, 110PA3


title: CD8+CD127+PD-1- biol rep 1


title: liver_ATAC_223_l1_s1


title: liver_ATAC_217_l1_s1


title: mDC cell type, cells alone, replicate 2


title: CD8+CD127-PD-1+ biol rep 3


title: liver_ATAC_204_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
204_peaks.narrowPeak.gz
204_scaled.bw


title: mDC cell type, cells alone


title: P14_Casz1 -/- IHC-17


title: CD8+CD127-PD-1+ biol rep 2


title: P14_Casz1 -/- IHC-16


title: liver_ATAC_204_l1_s2


title: LCDC cell type, 96PA1, replicate 2

source_name: Langerhans cell-derived Dendritic Cell

value: Langerhans cell-derived Dendritic Cell


title: LCDC cell type, 96PA1, replicate 3


title: liver_ATAC_204_l2_s1


title: CD8+CD127-PD-1+ biol rep 1


title: CD4+CD127+PD-1- biol rep 3


title: mDC cell type, cells alone, replicate 4


title: liver_ATAC_204_l1_s1


title: LCDC cell type, 96PA1


title: P14_Casz1 -/- IHC-15


title: liver_ATAC_221_l1_s1


title: CD4+CD127+PD-1- biol rep 2


title: P14_Casz1 -/- IHC-14


title: liver_ATAC_201_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
201_peaks.narrowPeak.gz
201_scaled.bw


title: CD4+CD127+PD-1- biol rep 1


title: liver_ATAC_201_l3_s1


title: P14_Casz1 -/- IHC-13


title: P14_Casz1 -/- IHC-18


title: LCDC cell type, 5PA1, replicate 3

value: stimulated with C. acne strain 5PA1


title: P14_Casz1 -/- IHC-12


title: CD4+CD127-PD-1+ biol rep 2


title: liver_ATAC_201_l2_s1


title: CD4+CD127-PD-1+ biol rep 1


title: LCDC cell type, 5PA1


title: P14_Casz1 -/- IHC-11


title: liver_ATAC_201_l1_s1


title: liver_ATAC_200_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
200_peaks.narrowPeak.gz
200_scaled.bw


title: RR, vNSP15 mutant

city: Galveston

first: Shailendra

last: Chauhan

state: Texas

address: UTMB Health - Galveston Campus 301 University Boulevard

department: Pathology

institute: UTMB

data_processing:
STAR v. 2.7.10a
basecalling illumina RTA 2.11.3.0
Sequence reads were trimmed for adpator sequences/low quality sequence using cutadapt v.1.15
Trimmed sequence reads were mapped to GRCm39 reference genome and counted reads using STAR 2.7.10a with parameter --outFilterType BySJout --outfilterMultimapNmax 20 --alignIntronMax 1000000 --alignMateGapMax 1000000 --alignSJoverhangmin 8 --alignSJDBoverhangmin 1 --quantMode GeneCounts
DESeq2 1.42.0
Assembly: GRCm39
Supplementary files format and content: microsoft excel file for log2 normalized counts for each sample

source_name: Lung

extract_protocol:
Trizol
RNA libraries were prepared using SMART-3Seq protocol

value: Lung

tag: infection

value: vNSP15 mutant


title: P14_Casz1 -/- IHC-10


title: LCDC cell type, 43PA1, replicate 2

value: stimulated with C. acne strain 43PA1


title: P14_Casz1 -/- IHC-9


title: liver_ATAC_200_l2_s1

value: liver tissue


title: LCDC cell type, 43PA1, replicate 3


title: R, vNSP15 mutant


title: LCDC cell type, 43PA1,


title: LCDC cell type, 5PA1, replicate 2


title: L, vNSP15 mutant


title: LCDC cell type, 42PA3, replicate 3

value: stimulated with C. acne strain 42PA3


title: liver_ATAC_200_l1_s2


title: P14_Casz1 -/- IHC-19


title: P14_Casz1 -/- IHC-7


title: liver_ATAC_200_l1_s1


title: LCDC cell type, 42PA3, replicate 2


title: RR, vNSP1 mutant

value: vNSP1 mutant


title: liver_ATAC_177_l2_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
177_peaks.narrowPeak.gz
177_scaled.bw


title: LCDC cell type, 42PA3


title: P14_Casz1 -/- IHC-6


title: R, vNSP1 mutant


title: N, vNSP1 mutant


title: N, vNSP15 mutant


title: liver_ATAC_177_l2_s1


title: P14_Casz1 -/- IHC-4


title: P14_Casz1 -/- IHC-5


title: liver_ATAC_177_l1_s2


title: LCDC cell type, 110PA4, replicate 2

value: stimulated with C. acne strain 110 PA4


title: L, vNSP1 mutant


title: P14_Casz1 -/- IHC-2

value: Cochlea


title: LCDC cell type, 110PA4


title: P14_Casz1 -/- IHC-8


title: P14_Casz1 -/- IHC-3


title: LCDC cell type, 110PA3, replicate 3

value: stimulated with C. acne strain 110 PA3


title: liver_ATAC_175_l2_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
175_peaks.narrowPeak.gz
175_scaled.bw


title: N, wt SARS-CoV-2

value: WT SARS-CoV-2


title: R, wt SARS-CoV-2


title: liver_ATAC_175_l1_s1


title: LCDC cell type, 110PA3, replicate 2


title: N6W 10x Single Cell 3' v3.1

city: Providence

first: Alexander

last: Fleischmann

state: RI

address: 185 meeting street

department: Neuroscience

institute: Brown University

description: 10x Single Cell 3' v3.1

data_processing:
The generated FASTQ files were processed with Cell Ranger ARC (v2.0.0) for Multiome ATAC + Gene expression experiments and with Cell Ranger (v6.0.0) for Single Cell 3' v3.1 experiments (10x Genomics).
Assembly: Reads were aligned to the mouse (Mus musculus) pre-mRNA reference genome (cellranger-arc-mm10-2020-A-2.0.0)
Supplementary files format and content: Matrix files

source_name: SSp - wild-derived mice

extract_protocol:
Each biological replicate was minced separately and placed into a tube containing cold Nuclei PURE Lysis Buffer and 10% Triton X-100 (Sigma, NUC201-1KT). The minced tissue was transferred into a 7 ml ice-cold tissue grinder (Sigma, D9063), homogenized up and down 20-25 times, and filtered on ice through cell strainers of 100μm, 70μm and 40 μm (Pluriselect, 43-10040). RNasin Plus diluted 1/200 (Promega, N2611) was added in all solutions.
Single -nuclei isolation for multiome sequencing experiments: After centrifuging at 500 rpm for 5 min at 4°C, the supernatant was aspirated and gently resuspended in 100 μl of a cold lysis solution containing Nuclei PURE Lysis Buffer, 10% Triton X-100, 0.01% of digitonin (ThermoFisher, BN2006), and 1% nuclease-free UltraPure™ BSA (ThermoFisher, AM2616). After 1 minute of incubation, 200 μl of cold 1X Nuclei Buffer (10x Genomics, 2000153/2000207) was added, the suspension was filtered again with a 40 μm cell strainer, centrifuged at 500 rpm for 5 min at 4°C, and gently resuspended into a final volume of 50 μl of cold 1X Nuclei Buffer.
Single -nuclei isolation for RNA sequencing experiments: After centrifuging at 500 rpm for 5 min at 4°C, the supernatant was aspirated and gently resuspended in 400 μl of a cold wash solution containing 1X Hanks’ Balanced Salt Solution HBSS and 1% nuclease-free UltraPure™ BSA. This step was repeated for a total of two times, and nuclei were resuspended into a final volume of 50 μl of cold wash solution.
Single-nuclei libraries were generated using the Single Cell Multiome ATAC + Gene Expression kit (10x Genomics, PN-1000283). Manufacturer’s instructions were followed for Tn5-based transposition, cell capture, barcoding, reverse transcription, cDNA amplification, and ATAC and RNA libraries construction. For wild-derived mice, 4 of 6 biological replicates for aPir, 1 of 4 for pPir, and 1 of 2 for SSp were processed using the Single Cell 3' Reagent Kits v3.1 dual index (10x Genomics, PN-1000268). Final libraries (40 libraries from gene expression and 32 libraries from ATAC experiments) were evaluated for quality and quantified using the Qubit fluorometer. The fragment size distribution was evaluated by Agilent TapeStation 2200 (Agilent Technologies). Libraries were further evaluated for proper incorporation of the Illumina adaptors on the Roche LightCycler 480 using the Roche Kapa library quant assay according to manufacturer’s protocol.

value: primary somatosensory cortex

value: wild-derived mice


title: liver_ATAC_174_l3_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
174_peaks.narrowPeak.gz
174_scaled.bw


title: L, wt SARS-CoV-2


title: liver_ATAC_174_l3_s1


title: LCDC cell type, 110PA3


title: P14_Casz1 -/- IHC-1


title: LCDC cell type, 110PA4, replicate 3


title: N2W 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 1, mock

value: Mock


title: N2W 10x Multiome - GEX

description: 10x Multiome - GEX


title: 3, mock


title: liver_ATAC_174_l2_s2


title: N7 10x Multiome - ATAC

description: 10x Multiome - ATAC

source_name: SSp - C57Bl/6 mice (lab mice)

value: C57Bl/6 mice (lab mice)


title: LCDC cell type, cells alone, replicate 5

value: cells alone


title: liver_ATAC_177_l1_s1


title: LCDC cell type, cells alone, replicate 3

value: Langerhans cell-derived Dendritic Cell


title: liver_ATAC_174_l2_s1


title: L, mock


title: N7 10x Multiome - GEX

description: 10x Multiome - GEX


title: LCDC cell type, cells alone, replicate 2


title: N6 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: liver_ATAC_172_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
172_peaks.narrowPeak.gz
172_scaled.bw


title: liver_ATAC_172_l2_s1


title: alveolarbone1

first: Jiayi

state: Beijing

address: No.22 Zhongguancun south Rd., Haidian district, Beijing, China

institute: Peking university school and hospital of stomatology

description: Library name: Sample1

data_processing:
Raw reads were processed to generate a gene expression matrix. Low-quality reads were removed using FastQC (v.0.11.9) and Fastp (v1).
The cell barcodes and unique molecular identifiers (UMIs) were extracted after trimming poly-A tails and adaptor sequences.
Reads were then mapped to the reference genome GRCh38, while gene and UMI counts were acquired. The number of UMIs per gene per cell was calculated by grouping the genes and UMIs based on the cell barcode. Expression matrix files was generated and used for further analysis.
The above procedure was integrated into CeleScope (https://github.com/singleron-RD/CeleScope, v2.1.0), which was utilized for analysis.
Assembly: mm10
Supplementary files format and content: tsv.gz, mtx.gz, barcodes, featues and matrix of sequencing data.

source_name: Alveolar bone

extract_protocol:
Alveolar bone within 1mm of the extraction socket was immediately collected and cleansed with ice-cold PBS containing 1% FBS. Alveolar bone was pooled from 6 mice per group. Tissue was minced into 1–2 mm size and digested with 2 ml GEXSCOPE® Bone Tissue Dissociation Solution for 60min at 37℃. Samples were then filtered and centrifuged. Single-cell suspensions were obtained after removal of red cells with 2 mL GEXSCOPE® red blood cell lysis buﬀer  at 25°C for 10 min and later analyzed using scRNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Healthy C57BL/6J mice (6-8 weeks old) weighing 20-25g were used. A nickel-titanium coil spring was attached to the maxillary right first molar and maxillary incisors via a 0.020-inch stainless steel ligature in order to provide mesial orthodontic force on the first molar. The constant force was maintained at 25g. For the control group, no force was applied after spring attachment.

value: Alveolar bone


title: N6 10x Multiome - GEX

description: 10x Multiome - GEX


title: liver_ATAC_174_l1_s1

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.


title: N4 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 10^9 cells per gram of soil 12 weeks E

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

description: 10^9 Samples Processed Data File

data_processing:
Raw reads were aligned to the genomes of the eight members of MSC-2 using the Burrows Wheeler Aligner
Resulting SAM files were used with GTF files of the eight members of MSC-2 to obtian counts using HTSeq
Raw count files were normalized using DESeq2
Assembly: https://data.pnnl.gov/group/nodes/dataset/33234
Supplementary files format and content: Processed data files are text .csv files with raw counts for each gene for each sample. One processed data file contains all data for samples inoculated with 10^8 cells per gram of soil (10_8_Samples_Processed_Data_File). The other contains all data for samples inoculated with 10^9 cells per gram of soil (10_9_Samples_Processed_Data_File)

organism:
Sinorhizobium meliloti
Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Ensifer adhaerens
Sphingopyxis sp.
Dyadobacter sp.
Neorhizobium tomejilense
Variovorax beijingensis

source_name: MSC-2 Species (Streptomyces sp001905665, Neorhizobium tomejilense, a Dyadobacter sp., a Sphingopyxis sp., Ensifer adhaerens, Variovorax beijingensis, Sinorhizobium meliloti and Rhodococcus sp003130705)

growth_protocol: MSC-2 community members were grown in R2A media prior to inoculation into soil. Soil was incubated at 20C at Kennedy Space Center before tubes from each timepoint were frozen at -80C

extract_protocol:
RNA was extracted from 2 g portions of soil using the Quick-RNA Fecal/Soil Microbe Microprep kit (ZYMO REsearch, Irvine, CA).
NEBNext®Ultra™II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Time was the only treatment here.  MSC-2 community members were incubated in soil with chitin as a major carbon source

tag: dilution

value: 10^9 cells per gram of soil

tag: time

value: 12 weeks

tag: replicate

value: E


title: 2, mock

value: Lung


title: Lymphedema5

source_name: Subcutaneous fat

extract_protocol:
Fat issue was flash frozen on dry ice and RNA was harvested using Trizol reagent. The TruSeq Stranded mRNA Library Prep Kit was used with 1 ug of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Subcutaneous fat


title: Lymphedema4


title: 10^9 cells per gram of soil 12 weeks D

description: 10^9 Samples Processed Data File

value: D