title: s1_KO_fin_0dpa.rep1

status: Public on Dec 22 2023

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7, with cutadapt v 3.5) and mapped with STAR (v 2.7.10, with parameters --twopassMode Basic and supplying the Ensembl danRer11 annotation) to zebrafish genome (danRer11).
The mapped reads were counted using R/Bioconductor GenomicAlignments package(v 1.30.0).
Assembly: danRer11
Supplementary files format and content: tab-delimited text files include normalized counts  for each Sample by library size

organism: Danio rerio

source_name: caudal fin

growth_protocol: Zebrafish of the outbred Ekkwill (EK) strain at about 4-8 months of age and regeneration-associated silencer (s1) knockout derived from the EK were used for collecting fin tissues. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily, and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.

extract_protocol:
Fins were amputated at 50% of their original length using scalpel (Sterile Scalpel Blades #22, Feather). Biological triplicate pools of caudal fin clips from regeneration-associated silencer (s1) knockout fish and their WT siblings were collected at 0 dpa (freshly amputated), 1 dpa, or 4 dpa time points via scalpel (Sterile Scalpel Blades #22, Feather) from 10 fish per pool. Fin tissues were homogenized in Tri-reagent (Sigma) and RNA was isolated by ethanol precipitation followed by purification with an RNA Clean & Concentrator Kit-5 (Zymo).
cDNA was synthesized from 20 ng of total RNA with a Maxima H-minus RT reverse transcription kit. PCR was performed using Kapa HiFi HotStart Master Mix and adaptor primers. The amplified cDNA was purified using 0.6x SPRI beads. cDNAs were tagged using Tn5 transposase and amplified by Q5 polymerase. Size selection was performed with gel-cutting and extraction, and 300 - 800 bp DNA fragments were collected for sequencing. Libraries were sequenced using a DNBSEQ-MGI2000, 100 bp PE, by BGI Americas.

treatment_protocol: Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water.

value: caudal fin

value: s1 silencer homozygous knockout

tag: time


title: WT_fin_4dpa.rep1

type: SRA

city: Madison

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

country: USA

institute: Morgridge Institute For Research

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

value: Ekkwill


title: s1_KO_fin_4dpa.rep2


title: D2 Foxp1CTL + ControlAAV #3

status: Public on Feb 20 2024

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

library_source: transcriptomic single cell

data_processing:
cellranger mkfastq
cellranger count
cellbender
doubletfinder
harmony
seurat
Assembly: mm10 (GRCm38p6)
Supplementary files format and content: matrix.mtx.gz' has raw counts for all samples
Supplementary files format and content: barcodes.tsv' has list of barcodes for all samples matching with raw counts
Supplementary files format and content: features.tsv' has list of genes matching to raw counts
Supplementary files format and content: meta.tsv' has all meta information including assigned celltypes

molecule: polyA RNA

organism: Mus musculus

source_name: Dorsal Striatum

extract_protocol:
We sacrificed P18 mice by rapid decapitation and quickly dissected the brain and transferred it into ice-cold nACSF that contained (mM): 125 NaCl, 25 NaHCO3, 10 Dextrose, 3 KCl, 1.25 NaH2PO4, 2 CaCl2.2H2O, 2 MgCl2 with 7.3-7.4 pH and 300-305 mOsm osmolality. We placed the brain onto an ice-cold 1.0 mm stainless steel brain matrix (Stoelting, Cat#51386) and obtained three 1.0 mm thick striatal sections which were then transferred into a petri-dish containing cold nACSF. Using forceps and under a dissection microscope, striatum was dissected out from these slices, flash frozen in liquid N2, and stored at -80°C. The striatal tissue was collected from P18 mice of required genotypes at different time points and stored. Protocol for isolating nuclei was adapted and modified from our previously published work6. Briefly, tissue was homogenized 20 times with pestle A, followed by 20 times with pestle B, in a glass Dounce tissue grinder (Sigma, Cat#D8938) in 2 ml ice-cold EZ Nuclei Lysis Buffer (Sigma, Cat #NUC-101). Homogenized samples were transferred into 15 ml tube with an additional 2 ml ice-cold EZ Nuclei Lysis Buffer, incubated on ice for 3 min and centrifuged at 500 X g for 5 min at 4°C. The supernatant was discarded, and nuclei pellet was resuspended in 3 ml ice-cold Nuclei Suspension Buffer (NSB; 1X PBS, 0.01% Ultrapure BSA, and 0.1% RNase inhibitor) and again centrifuged at 500 X g for 5 min at 4°C. The supernatant was then discarded, and nuclei pellet was resuspended in 300-400 µl NSB, and filtered through 40 µm size Flowmi cell strainer (Bel-Art Products, Cat# H13680-0040). An aliquot of the filtered nuclei suspension was mixed with Trypan Blue and transferred into a disposable cell counting chamber nuclei to visualize and count the healthy nuclei under a light microscope to determine desired nuclei concentration (targeting 700-1,200 nuclei/µl).
Libraries from a total of 9 mice (3 mice/genotype) were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10X Genomics, Cat#1000121) targeting 10,000 nuclei per sample as per the manufacturer’s instructions. All mice were injected either with ControlAAV or Foxp1AAV in their striatum at P1 age where only a fraction of neurons was infected that were identified based on the presence of AAV transcripts. However, the proportion of AAV transcripts is exceptionally small in the pool of total transcripts that are captured by snRNA-seq experiment and therefore we used a modified approach 12 where we amplified the viral transcript specific sequences and prepared separate libraries. Briefly, we used 5% of the total cleaned up cDNA (amplified from the GEMs that were generated from each sample for the targeted 10,000 nuclei) and amplified the viral transcripts with reverse primer 10X_Enrich_R – 5’CTACACGACGCTCTTCCG3’ and forward primers 10X_WPRE_F1 – 5’ACGAGTCGGATCTCCCTTT3’ (for ControlAAV infected mice) and 10X_mCherry_F1 – 5’GCATGGACGAGCTGTACA3’ (for Foxp1AAV infected mice) for 25 cycles using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB, Cat# M0531S). We used different forward primers for ControlAAV and Foxp1AAV infected mice since ControlAAV vector has a WPRE sequence at the 3’end whereas we had to remove WPRE sequence from the AAVFoxp1 vector to accommodate Foxp1 and mCherry into the vector and thus have the mCherry sequence at 3’end of Foxp1AAV vector. The amplified PCR product was run on an agarose gel, where a ~250 bp product was excised from the gel and eluted using QIAquick Gel Extraction Kit (Qiagen, Cat#28706) in 20 µl elution buffer (NEB). 5% of this first round amplified product was used to perform a second round of amplification using the reverse primer, i. e. 10X_WPRE_F1 and forward primers 10X_WPRE_F2 – 5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACGAGTCGGATCTCCCTTT3’ (for AAVControl infected mice) and 10X_mCherry_F2 –5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTACAAGTAGACCCAGCTT3’ (for AAVFoxp1 infected mice) for 20 cycles using the same Phusion polymerase. Once again, this amplified PCR product was loaded on an agarose gel where similar size product (~250 bp) was excised and eluted in 30 µl elution buffer. The eluted PCR products were once again cleaned up using SPRIselect Reagent and subjected to sample-index PCR amplification according to the manufacturer’s instructions (10X Genomics) to generate cDNA libraries. Finally, both (total and AAV_transcript) libraries were subjected to quality control using 4200 TapeStation System (Agilent, Cat# G2991BA) and quantified using Qubit 2.0 Fluorometer (Invitrogen). For each sample, 5 nM of the total libraries and 0.5 nM of the AAV transcript libraries (10% of the total library) were pooled and sequenced on a NovaSeq 6000 (Illumina) platform on S4 flow cell.

value: Dorsal Striatum

value: D2 Foxp1CTL


title: D2 Foxp1CTL + ControlAAV #1


title: s1_KO_fin_1dpa.rep3


title: D2 Foxp1cKO + ControlAAV #2

value: D2 Foxp1cKO


title: D2 Foxp1CTL + ControlAAV #2


title: D2 Foxp1cKO + ControlAAV #3


title: s1_KO_fin_0dpa.rep2


title: s1_KO_fin_1dpa.rep2


title: s1_KO_fin_4dpa.rep1


title: WT_fin_4dpa.rep2


title: WT_fin_4dpa.rep3


title: WT_fin_1dpa.rep2


title: WT_fin_1dpa.rep1


title: s1_KO_fin_0dpa.rep3


title: s1_KO_fin_1dpa.rep1


title: WT_fin_1dpa.rep3


title: WT_fin_0dpa.rep3


title: s1_KO_fin_4dpa.rep3


title: WT_fin_0dpa.rep1


title: 4_dpa_rep3

library_source: genomic

data_processing:
library strategy: HiCAR (Hi-C on accessible regulatory DNA)
The data were analyzed by https://github.com/jianhong/nf-core-hicar pipeline. Reads were aligned to danRer11 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MAPS is used to call the significant chromatin interaction fro HiCAR library.
Assembly: danRer11
Supplementary files format and content: Chromatin interactions  identified by MAPS, provided in BEDPE formate.

molecule: genomic DNA

source_name: fish fin

growth_protocol: Zebrafish of the outbred Ekkwill (EK) strain at about 6-8 months of age were used for collecting fin nuclei. Fish were housed at approximately 4 fish per liter in Pentair aquarium racks and fed three times daily, and the water temperature was maintained at 27.5 °C and fish were kept on a 14/10 light/dark cycle.

extract_protocol:
Fins were amputated at 50% of their original length using scalpel (Sterile Scalpel Blades #22, Feather). Biological triplicate pools of WT caudal fin clips were collected at 0 dpa (freshly amputated), 1 dpa, or 4 dpa time points via scalpel (Sterile Scalpel Blades #22, Feather) from 10 fish per pool. Fin tissues were frozen in liquid nitrogen and grinded using a motar and a pestle on dry ice for 5 min.
Nuclei collected by pulverizing frozen zebrafish fin tissues (0, 1 and 4 dpa) were cross-linked and treated with Tn5 transposase that were assembled with an engineered DNA adaptor. The Tn5 adaptor contains a Mosaic End (ME) sequence for Tn5 recognition and a single-stranded flanking sequence that can be ligated to the CviQI-digested DNA fragment with a splint oligo. The nuclei were treated with the 4-base cutter CviQI and then T4-ligase for connecting the Tn5 adaptor to the spatially proximal genomic DNA. The cross-links were reversed, and the purified DNA was digested by another 4-base cutter NlaIII, followed by circularization and PCR amplification to generate HiCAR DNA libraries for Next-Generation-Sequencing (NGS).

value: fish fin

tag: time point

value: 4 dpa


title: 0_dpa_rep3

value: 0 dpa (freshly amputated)


title: brain, RNAi control 3

status: Public on Oct 24 2023

city: Philadelphia

first: Dong

last: Li

state: PA

address: 3615 Civic Center BLVD

institute: Children's Hospital of Philadelphia

data_processing:
aligned onto the BDGP6 fly reference genome
features were counted by featureCounts
DESeq2 was then used to detected differentially expressed genes
Assembly: BDGP6 fly reference genome
Supplementary files format and content: tabl-delimited text file includes raw coutns for each sample

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen)
RNA libararies were prepared using Illumina TruSeq Library Prep Kit folloiwing manufacturer's protocols

value: brain

value: wild type


title: Tula8_Day7

status: Public on Sep 26 2023

city: Canyon

first: Matthew

last: Scott

state: TX

address: 3201 Russell Long Blvd

institute: Texas A&M University

description:
Tula8.Day7_S57_L002
MM_252_raw_gene_count.txt

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina TruSeq adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.36.0 and glmmSeq v0.2.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated via PAXgene Blood miRNA Kits, per product instruction, with automated processing through QIAcube instrumentation.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: All samples were collected into PAXgene Blood RNA tubes (Qiagen) and stored per product recommendation the same day of collection.

value: Whole blood

value: Day 7

tag: treatment

value: Tulathromycin

tag: sequencing lane

tag: individual id


title: 1_dpa_rep1

value: 1 dpa


title: 4_dpa_rep2


title: Tfap2a_CUT&RUN_24hpf_n2

status: Public on Dec 18 2023

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

description: CUT&RUN

data_processing:
Reads trimmed using TrimGalore
Reads mapped using Biotie2
Peak called using MACS2
Peaks visualized using UCSC on bigWig-generated files.
DanRer10 called peaks lifted to danRer11 using UCSC
Assembly: DanRer10
Supplementary files format and content: Peak bed file
Library strategy: CUT&RUN

source_name: Whole embryo

growth_protocol: Wild-type zebrafish were crossed, and embryos were collected and maintained at 28 degrees celsius for 24 hours post-fertilization (hpf)

extract_protocol:
Ten zebrafish embryos at 24hpf were dissociated in calcium-free wash buffer, washed three times with PBS, and filtered through a 40μm gauze. Approximately 250k cells were attached to CoA beads per sample, incubated with a 1:100 ratio of anti-Tfap2a or IgG antibody, and cleaved with pAG-MNase for 30 minutes. The cut fragments were purified, and library preparation was conducted using KAPA kits. Sequencing was performed with 150PE reads at 20 million reads per sample
Library construction was performed using the KAPA Biosciences kit following the manufacturer's protocol.

treatment_protocol: Embryos were not subject to treatment

value: Whole embryo


title: 0_dpa_rep1


title: Tula8_Day56

description:
Tula8.Day56_S60_L002
MM_252_raw_gene_count.txt

value: Day 56


title: 4_dpa_rep1


title: brain, RNAi control 1


title: 0_dpa_rep2


title: Tula8_Day0

description:
Tula8.Day0_S55_L002
MM_252_raw_gene_count.txt

value: Day 0


title: Tula8_Day14

description:
Tula8.Day14_S58_L002
MM_252_raw_gene_count.txt

value: Day 14


title: Tfap2a_CUT&RUN_24hpf_n1

description: CUT&RUN


title: WT_fin_0dpa.rep2

value: caudal fin

value: Ekkwill


title: brain, RNAi control 2


title: Tula7_Day7

description:
Tula7.Day7_S51_L002
MM_252_raw_gene_count.txt


title: Tula8_Day21

description:
Tula8.Day21_S59_L002
MM_252_raw_gene_count.txt

value: Day 21


title: 1_dpa_rep2


title: 1_dpa_rep3


title: Tula8_Day3

description:
Tula8.Day3_S56_L002
MM_252_raw_gene_count.txt

value: Day 3


title: Tula7_Day56

description:
Tula7.Day56_S54_L002
MM_252_raw_gene_count.txt


title: Tula6_Day7

description:
Tula6.Day7_S45_L002
MM_252_raw_gene_count.txt


title: Tula7_Day21

description:
Tula7.Day21_S53_L002
MM_252_raw_gene_count.txt


title: Tula6_Day56

description:
Tula6.Day56_S48_L002
MM_252_raw_gene_count.txt


title: Tula7_Day14

description:
Tula7.Day14_S52_L002
MM_252_raw_gene_count.txt


title: Tula6_Day3

description:
Tula6.Day3_S44_L002
MM_252_raw_gene_count.txt


title: Tula6_Day0

description:
Tula6.Day0_S43_L002
MM_252_raw_gene_count.txt


title: Tula5_Day7

description:
Tula5.Day7_S39_L002
MM_252_raw_gene_count.txt


title: Tula5_Day3

description:
Tula5.Day3_S38_L002
MM_252_raw_gene_count.txt


title: Tula7_Day0

description:
Tula7.Day0_S49_L002
MM_252_raw_gene_count.txt


title: Tula5_Day56

description:
Tula5.Day56_S42_L002
MM_252_raw_gene_count.txt


title: Tula5_Day14

description:
Tula5.Day14_S40_L002
MM_252_raw_gene_count.txt


title: Tula5_Day0

description:
Tula5.Day0_S37_L002
MM_252_raw_gene_count.txt


title: Tula4_Day56

description:
Tula4.Day56_S36_L002
MM_252_raw_gene_count.txt


title: Tula4_Day21

description:
Tula4.Day21_S35_L002
MM_252_raw_gene_count.txt


title: Tula6_Day14

description:
Tula6.Day14_S46_L002
MM_252_raw_gene_count.txt


title: Tula5_Day21

description:
Tula5.Day21_S41_L002
MM_252_raw_gene_count.txt


title: Tula4_Day3

description:
Tula4.Day3_S32_L002
MM_252_raw_gene_count.txt


title: Tula6_Day21

description:
Tula6.Day21_S47_L002
MM_252_raw_gene_count.txt


title: Tula4_Day7

description:
Tula4.Day7_S33_L002
MM_252_raw_gene_count.txt


title: Tula4_Day14

description:
Tula4.Day14_S34_L002
MM_252_raw_gene_count.txt


title: Tula4_Day0

description:
Tula4.Day0_S31_L002
MM_252_raw_gene_count.txt


title: Tula7_Day3

description:
Tula7.Day3_S50_L002
MM_252_raw_gene_count.txt


title: Tula3_Day7

description:
Tula3.Day7_S27_L002
MM_252_raw_gene_count.txt


title: 36-114-2017-3-29-2017_S36

status: Public on Sep 18 2024

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 36 bases, and leading and trailing basepairs below a quality score of 3
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 14 --dta -x GCF_002263795.1_ARS-UCD1.2
Read assembly and quantification was performed with StringTie v2.1.7 with parameters -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE.py with parameters python prepDE.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.32.1.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: comma-delimited text file of gene counts for each sample

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: brd severity

tag: year

tag: sample day

tag: Sex

value: Male

tag: animal id

tag: developmental stage

value: Bull


title: Tild8_Day21

description:
Tild8.Day21_S5_L003
MM_252_raw_gene_count.txt

value: Tildipirosin


title: Tula3_Day56

description:
Tula3.Day56_S30_L002
MM_252_raw_gene_count.txt


title: Tula3_Day3

description:
Tula3.Day3_S26_L002
MM_252_raw_gene_count.txt


title: Tild7_Day3

description:
Tild7.Day3_S80_L002
MM_252_raw_gene_count.txt


title: Tild8_Day0

description:
Tild8.Day0_S1_L003
MM_252_raw_gene_count.txt


title: Tula3_Day0

description:
Tula3.Day0_S25_L002
MM_252_raw_gene_count.txt


title: Tild8_Day56

description:
Tild8.Day56_S6_L003
MM_252_raw_gene_count.txt


title: Tula3_Day14

description:
Tula3.Day14_S28_L002
MM_252_raw_gene_count.txt


title: Tild7_Day14

description:
Tild7.Day14_S82_L002
MM_252_raw_gene_count.txt


title: Tild8_Day3

description:
Tild8.Day3_S2_L003
MM_252_raw_gene_count.txt


title: Tild7_Day0

description:
Tild7.Day0_S79_L002
MM_252_raw_gene_count.txt


title: Tild5_Day7

description:
Tild5.Day7_S75_L002
MM_252_raw_gene_count.txt


title: Tild8_Day14

description:
Tild8.Day14_S4_L003
MM_252_raw_gene_count.txt


title: Tild7_Day7

description:
Tild7.Day7_S81_L002
MM_252_raw_gene_count.txt


title: Tula3_Day21

description:
Tula3.Day21_S29_L002
MM_252_raw_gene_count.txt


title: Tild7_Day56

description:
Tild7.Day56_S84_L002
MM_252_raw_gene_count.txt


title: Tild7_Day21

description:
Tild7.Day21_S83_L002
MM_252_raw_gene_count.txt


title: Tild5_Day56

description:
Tild5.Day56_S78_L002
MM_252_raw_gene_count.txt


title: Tild8_Day7

description:
Tild8.Day7_S3_L003
MM_252_raw_gene_count.txt


title: Tild5_Day3

description:
Tild5.Day3_S74_L002
MM_252_raw_gene_count.txt


title: Tild5_Day21

description:
Tild5.Day21_S77_L002
MM_252_raw_gene_count.txt


title: hc6052_ATAC

status: Public on Dec 05 2024

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

description: 10x Genomics snATAC-seq

library_source: genomic single cell

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene for hg38 GRCh38 human genome assembly and Gencode v32 gene annotations.
We performed unsupervised clustering with RNA UMI counts using Seurat v5 integrative analysis pipeline. First, cell barcodes were filtered for low quality nuclei by requiring ≥ 500 ATAC fragments, > 5 TSS enrichment (GRCh38 GENCODE v46) using SnapATAC2, ≥ 200 genes detected per nuclei.
Assembly: hg38 GRCh38
Supplementary files format and content: The raw_feature_bc_matrix.h5 is a Cell Ranger output that includes feature-barcode matrices containing cellular, non-cellular, and background barcodes.
The atac_fragments.tsv.gz is a Cell Ranger output that contains one line per unique fragment. And the atac_fragments.tsv.gz.tbi is the Tabix index for the fragment file.
hippocampus_RNA_seurat_object_filtered_cells.h5: Seurat object after quality control
hippocampus_RNA_seurat_object_filtered_cells_metadata.tsv: cell metadata for the Seurat object
Bigwig files were generated using deepTools bamCoverage with default settings and --normalizeUsing RPKM. Reads were combined across donors for indicated cell type or cell type by age group.

organism: Homo sapiens

source_name: hippocampus

extract_protocol:
Frozen brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS). 120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading.
Libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression). 10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.
snATAC-seq
snRNA-seq

value: hippocampus

tag: donor id


title: Tild5_Day14

description:
Tild5.Day14_S76_L002
MM_252_raw_gene_count.txt


title: Tild3_Day56

description:
Tild3.Day56_S72_L002
MM_252_raw_gene_count.txt


title: Tild3_Day14

description:
Tild3.Day14_S70_L002
MM_252_raw_gene_count.txt


title: Tild5_Day0

description:
Tild5.Day0_S73_L002
MM_252_raw_gene_count.txt


title: Tild3_Day7

description:
Tild3.Day7_S69_L002
MM_252_raw_gene_count.txt


title: Tild3_Day3

description:
Tild3.Day3_S68_L002
MM_252_raw_gene_count.txt


title: Tild10_Day7

description:
Tild10.Day7_S9_L003
MM_252_raw_gene_count.txt


title: Tild2_Day7

description:
Tild2.Day7_S63_L002
MM_252_raw_gene_count.txt


title: Tild3_Day21

description:
Tild3.Day21_S71_L002
MM_252_raw_gene_count.txt


title: Tild2_Day21

description:
Tild2.Day21_S65_L002
MM_252_raw_gene_count.txt


title: Tild2_Day0

description:
Tild2.Day0_S61_L002
MM_252_raw_gene_count.txt


title: Tild10_Day3

description:
Tild10.Day3_S8_L003
MM_252_raw_gene_count.txt


title: Tild2_Day56

description:
Tild2.Day56_S66_L002
MM_252_raw_gene_count.txt


title: Tild2_Day14

description:
Tild2.Day14_S64_L002
MM_252_raw_gene_count.txt


title: Tild2_Day3

description:
Tild2.Day3_S62_L002
MM_252_raw_gene_count.txt


title: Tild3_Day0

description:
Tild3.Day0_S67_L002
MM_252_raw_gene_count.txt


title: Oxyt9_Day56

description:
Oxyt9.Day56_S84_L003
MM_252_raw_gene_count.txt

value: Oxytetracycline


title: Tild10_Day0

description:
Tild10.Day0_S7_L003
MM_252_raw_gene_count.txt

value: Whole blood


title: Tild10_Day21

description:
Tild10.Day21_S11_L003
MM_252_raw_gene_count.txt


title: Tild10_Day56

description:
Tild10.Day56_S12_L003
MM_252_raw_gene_count.txt


title: Tild10_Day14

description:
Tild10.Day14_S10_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day7

description:
Oxyt9.Day7_S81_L003
MM_252_raw_gene_count.txt

value: Day 7


title: 45-156-2017-3-29-2017_S45


title: Oxyt9_Day3

description:
Oxyt9.Day3_S80_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day14

description:
Oxyt9.Day14_S82_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day21

description:
Oxyt9.Day21_S83_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day56

description:
Oxyt6.Day56_S78_L003
MM_252_raw_gene_count.txt


title: Oxyt9_Day0

description:
Oxyt9.Day0_S79_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day7

description:
Oxyt6.Day7_S75_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day3

description:
Oxyt6.Day3_S74_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day14

description:
Oxyt6.Day14_S76_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day21

description:
Oxyt6.Day21_S77_L003
MM_252_raw_gene_count.txt


title: Oxyt6_Day0

description:
Oxyt6.Day0_S73_L003
MM_252_raw_gene_count.txt


title: Oxyt5_Day0

description:
Oxyt5.Day0_S67_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day0

description:
Oxyt4.Day0_S61_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day56

description:
Oxyt4.Day56_S66_L003
MM_252_raw_gene_count.txt


title: Oxyt5_Day7

description:
Oxyt5.Day7_S69_L003
MM_252_raw_gene_count.txt


title: Oxyt5_Day14

description:
Oxyt5.Day14_S70_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day7

description:
Oxyt2.Day7_S57_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day3

description:
Oxyt4.Day3_S62_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day21

description:
Oxyt2.Day21_S59_L003
MM_252_raw_gene_count.txt


title: Oxyt5_Day21

description:
Oxyt5.Day21_S71_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day14

description:
Oxyt4.Day14_S64_L003
MM_252_raw_gene_count.txt


title: Oxyt5_Day3

description:
Oxyt5.Day3_S68_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day3

description:
Oxyt2.Day3_S56_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day56

description:
Oxyt2.Day56_S60_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day14

description:
Oxyt2.Day14_S58_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day21

description:
Oxyt4.Day21_S65_L003
MM_252_raw_gene_count.txt


title: Oxyt1_Day7

description:
Oxyt1.Day7_S51_L003
MM_252_raw_gene_count.txt


title: Oxyt2_Day0

description:
Oxyt2.Day0_S55_L003
MM_252_raw_gene_count.txt


title: Oxyt4_Day7

description:
Oxyt4.Day7_S63_L003
MM_252_raw_gene_count.txt


title: Oxyt1_Day56

description:
Oxyt1.Day56_S54_L003
MM_252_raw_gene_count.txt


title: 33-104-2017-3-29-2017_S33

value: Healthy


title: Oxyt1_Day21

description:
Oxyt1.Day21_S53_L003
MM_252_raw_gene_count.txt


title: Oxyt1_Day3

description:
Oxyt1.Day3_S50_L003
MM_252_raw_gene_count.txt


title: NC7_Day56

description:
NC7.Day56_S18_L001
MM_252_raw_gene_count.txt

value: Negative Control


title: NC7_Day7

description:
NC7.Day7_S15_L001
MM_252_raw_gene_count.txt


title: NC15_Day21

description:
NC15.Day21_S35_L001
MM_252_raw_gene_count.txt


title: NC7_Day3

description:
NC7.Day3_S14_L001
MM_252_raw_gene_count.txt


title: NC7_Day21

description:
NC7.Day21_S17_L001
MM_252_raw_gene_count.txt


title: NC5_Day7

description:
NC5.Day7_S9_L001
MM_252_raw_gene_count.txt


title: NC5_Day21

description:
NC5.Day21_S11_L001
MM_252_raw_gene_count.txt


title: NC7_Day14

description:
NC7.Day14_S16_L001
MM_252_raw_gene_count.txt


title: NC5_Day14

description:
NC5.Day14_S10_L001
MM_252_raw_gene_count.txt


title: Oxyt1_Day14

description:
Oxyt1.Day14_S52_L003
MM_252_raw_gene_count.txt


title: Oxyt1_Day0

description:
Oxyt1.Day0_S49_L003
MM_252_raw_gene_count.txt


title: NC7_Day0

description:
NC7.Day0_S13_L001
MM_252_raw_gene_count.txt


title: NC15_Day3

description:
NC15.Day3_S32_L001
MM_252_raw_gene_count.txt


title: NC5_Day0

description:
NC5.Day0_S7_L001
MM_252_raw_gene_count.txt


title: NC15_Day14

description:
NC15.Day14_S34_L001
MM_252_raw_gene_count.txt


title: NC15_Day7

description:
NC15.Day7_S33_L001
MM_252_raw_gene_count.txt


title: NC5_Day56

description:
NC5.Day56_S12_L001
MM_252_raw_gene_count.txt


title: NC13_Day56

description:
NC13.Day56_S30_L001
MM_252_raw_gene_count.txt


title: NC15_Day56

description:
NC15.Day56_S36_L001
MM_252_raw_gene_count.txt


title: NC13_Day3

description:
NC13.Day3_S26_L001
MM_252_raw_gene_count.txt


title: NC13_Day21

description:
NC13.Day21_S29_L001
MM_252_raw_gene_count.txt


title: NC15_Day0

description:
NC15.Day0_S31_L001
MM_252_raw_gene_count.txt


title: NC13_Day0

description:
NC13.Day0_S25_L001
MM_252_raw_gene_count.txt


title: NC5_Day3

description:
NC5.Day3_S8_L001
MM_252_raw_gene_count.txt


title: NC13_Day7

description:
NC13.Day7_S27_L001
MM_252_raw_gene_count.txt


title: NC13_Day14

description:
NC13.Day14_S28_L001
MM_252_raw_gene_count.txt


title: NC12_Day56

description:
NC12.Day56_S24_L001
MM_252_raw_gene_count.txt


title: NC1_Day7

description:
NC1.Day7_S3_L001
MM_252_raw_gene_count.txt


title: NC12_Day7

description:
NC12.Day7_S21_L001
MM_252_raw_gene_count.txt


title: NC1_Day56

description:
NC1.Day56_S6_L001
MM_252_raw_gene_count.txt


title: Flor8_Day0

description:
Flor8.Day0_S13_L002
MM_252_raw_gene_count.txt

value: Florfenicol


title: Flor7_Day3

description:
Flor7.Day3_S8_L002
MM_252_raw_gene_count.txt


title: NC12_Day14

description:
NC12.Day14_S22_L001
MM_252_raw_gene_count.txt


title: NC12_Day3

description:
NC12.Day3_S20_L001
MM_252_raw_gene_count.txt


title: Flor8_Day21

description:
Flor8.Day21_S17_L002
MM_252_raw_gene_count.txt


title: NC12_Day21

description:
NC12.Day21_S23_L001
MM_252_raw_gene_count.txt


title: Flor8_Day14

description:
Flor8.Day14_S16_L002
MM_252_raw_gene_count.txt


title: NC12_Day0

description:
NC12.Day0_S19_L001
MM_252_raw_gene_count.txt


title: NC1_Day3

description:
NC1.Day3_S2_L001
MM_252_raw_gene_count.txt


title: NC1_Day21

description:
NC1.Day21_S5_L001
MM_252_raw_gene_count.txt


title: Flor8_Day3

description:
Flor8.Day3_S14_L002
MM_252_raw_gene_count.txt


title: NC1_Day14

description:
NC1.Day14_S4_L001
MM_252_raw_gene_count.txt


title: Flor8_Day7

description:
Flor8.Day7_S15_L002
MM_252_raw_gene_count.txt


title: Flor8_Day56

description:
Flor8.Day56_S18_L002
MM_252_raw_gene_count.txt

value: Day 56


title: Flor7_Day21

description:
Flor7.Day21_S11_L002
MM_252_raw_gene_count.txt


title: NC1_Day0

description:
NC1.Day0_S1_L001
MM_252_raw_gene_count.txt

value: Day 0


title: Flor7_Day7

description:
Flor7.Day7_S9_L002
MM_252_raw_gene_count.txt


title: 51-168-2017-3-29-2017_S51

value: Steer


title: Flor6_Day7

description:
Flor6.Day7_S3_L002
MM_252_raw_gene_count.txt


title: Flor6_Day56

description:
Flor6.Day56_S6_L002
MM_252_raw_gene_count.txt


title: Flor6_Day21

description:
Flor6.Day21_S5_L002
MM_252_raw_gene_count.txt


title: Flor4_Day7

description:
Flor4.Day7_S81_L001
MM_252_raw_gene_count.txt


title: Flor4_Day56

description:
Flor4.Day56_S84_L001
MM_252_raw_gene_count.txt


title: Flor6_Day0

description:
Flor6.Day0_S1_L002
MM_252_raw_gene_count.txt


title: Flor4_Day21

description:
Flor4.Day21_S83_L001
MM_252_raw_gene_count.txt


title: Flor7_Day14

description:
Flor7.Day14_S10_L002
MM_252_raw_gene_count.txt

value: Day 14


title: Flor7_Day56

description:
Flor7.Day56_S12_L002
MM_252_raw_gene_count.txt


title: Flor6_Day3

description:
Flor6.Day3_S2_L002
MM_252_raw_gene_count.txt


title: Flor4_Day0

description:
Flor4.Day0_S79_L001
MM_252_raw_gene_count.txt


title: Flor6_Day14

description:
Flor6.Day14_S4_L002
MM_252_raw_gene_count.txt


title: Flor3_Day7

description:
Flor3.Day7_S75_L001
MM_252_raw_gene_count.txt


title: Flor4_Day3

description:
Flor4.Day3_S80_L001
MM_252_raw_gene_count.txt


title: Flor3_Day56

description:
Flor3.Day56_S78_L001
MM_252_raw_gene_count.txt


title: Flor7_Day0

description:
Flor7.Day0_S7_L002
MM_252_raw_gene_count.txt


title: Flor4_Day14

description:
Flor4.Day14_S82_L001
MM_252_raw_gene_count.txt


title: Flor10_Day7

description:
Flor10.Day7_S21_L002
MM_252_raw_gene_count.txt


title: Flor10_Day3

description:
Flor10.Day3_S20_L002
MM_252_raw_gene_count.txt


title: Flor3_Day21

description:
Flor3.Day21_S77_L001
MM_252_raw_gene_count.txt


title: Flor3_Day14

description:
Flor3.Day14_S76_L001
MM_252_raw_gene_count.txt


title: Flor10_Day21

description:
Flor10.Day21_S23_L002
MM_252_raw_gene_count.txt


title: Flor10_Day56

description:
Flor10.Day56_S24_L002
MM_252_raw_gene_count.txt


title: Flor3_Day0

description:
Flor3.Day0_S73_L001
MM_252_raw_gene_count.txt


title: Flor3_Day3

description:
Flor3.Day3_S74_L001
MM_252_raw_gene_count.txt


title: Flor10_Day14

description:
Flor10.Day14_S22_L002
MM_252_raw_gene_count.txt


title: Flor10_Day0

description:
Flor10.Day0_S19_L002
MM_252_raw_gene_count.txt


title: Enro9_Day7

description:
Enro9.Day7_S63_L001
MM_252_raw_gene_count.txt

value: Enrofloxacin


title: Enro9_Day3

description:
Enro9.Day3_S62_L001
MM_252_raw_gene_count.txt


title: Enro9_Day14

description:
Enro9.Day14_S64_L001
MM_252_raw_gene_count.txt


title: Enro6_Day56

description:
Enro6.Day56_S54_L001
MM_252_raw_gene_count.txt


title: Enro8_Day3

description:
Enro8.Day3_S56_L001
MM_252_raw_gene_count.txt


title: Enro8_Day7

description:
Enro8.Day7_S57_L001
MM_252_raw_gene_count.txt


title: Enro6_Day7

description:
Enro6.Day7_S51_L001
MM_252_raw_gene_count.txt


title: Enro5_Day14

description:
Enro5.Day14_S46_L001
MM_252_raw_gene_count.txt


title: Enro2_Day7

description:
Enro2.Day7_S39_L001
MM_252_raw_gene_count.txt


title: Enro5_Day3

description:
Enro5.Day3_S44_L001
MM_252_raw_gene_count.txt


title: Enro9_Day56

description:
Enro9.Day56_S66_L001
MM_252_raw_gene_count.txt


title: Enro9_Day0

description:
Enro9.Day0_S61_L001
MM_252_raw_gene_count.txt


title: Enro8_Day0

description:
Enro8.Day0_S55_L001
MM_252_raw_gene_count.txt


title: Enro5_Day21

description:
Enro5.Day21_S47_L001
MM_252_raw_gene_count.txt

value: Day 21


title: Enro6_Day21

description:
Enro6.Day21_S53_L001
MM_252_raw_gene_count.txt


title: Enro5_Day56

description:
Enro5.Day56_S48_L001
MM_252_raw_gene_count.txt


title: Enro9_Day21

description:
Enro9.Day21_S65_L001
MM_252_raw_gene_count.txt


title: Enro8_Day56

description:
Enro8.Day56_S60_L001
MM_252_raw_gene_count.txt


title: Enro8_Day21

description:
Enro8.Day21_S59_L001
MM_252_raw_gene_count.txt


title: Enro5_Day0

description:
Enro5.Day0_S43_L001
MM_252_raw_gene_count.txt


title: Enro6_Day14

description:
Enro6.Day14_S52_L001
MM_252_raw_gene_count.txt


title: Enro8_Day14

description:
Enro8.Day14_S58_L001
MM_252_raw_gene_count.txt


title: Enro6_Day0

description:
Enro6.Day0_S49_L001
MM_252_raw_gene_count.txt


title: Enro6_Day3

description:
Enro6.Day3_S50_L001
MM_252_raw_gene_count.txt

value: Day 3


title: Enro2_Day3

description:
Enro2.Day3_S38_L001
MM_252_raw_gene_count.txt


title: Enro5_Day7

description:
Enro5.Day7_S45_L001
MM_252_raw_gene_count.txt


title: Enro2_Day56

description:
Enro2.Day56_S42_L001
MM_252_raw_gene_count.txt


title: Enro2_Day21

description:
Enro2.Day21_S41_L001
MM_252_raw_gene_count.txt


title: Enro10_Day56

description:
Enro10.Day56_S72_L001
MM_252_raw_gene_count.txt


title: Enro10_Day3

description:
Enro10.Day3_S68_L001
MM_252_raw_gene_count.txt


title: Enro10_Day21

description:
Enro10.Day21_S71_L001
MM_252_raw_gene_count.txt


title: Enro10_Day0

description:
Enro10.Day0_S67_L001
MM_252_raw_gene_count.txt


title: Enro2_Day14

description:
Enro2.Day14_S40_L001
MM_252_raw_gene_count.txt


title: Ceft8_Day7

description:
Ceft8.Day7_S39_L003
MM_252_raw_gene_count.txt

value: Ceftiofur


title: Ceft8_Day0

description:
Ceft8.Day0_S37_L003
MM_252_raw_gene_count.txt


title: Ceft8_Day21

description:
Ceft8.Day21_S41_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day14

description:
Ceft6.Day14_S34_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day0

description:
Ceft6.Day0_S31_L003
MM_252_raw_gene_count.txt


title: Enro2_Day0

description:
Enro2.Day0_S37_L001
MM_252_raw_gene_count.txt


title: Ceft6_Day3

description:
Ceft6.Day3_S32_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day56

description:
Ceft6.Day56_S36_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day7

description:
Ceft6.Day7_S33_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day56

description:
Ceft5.Day56_S30_L003
MM_252_raw_gene_count.txt


title: Ceft8_Day56

description:
Ceft8.Day56_S42_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day3

description:
Ceft5.Day3_S26_L003
MM_252_raw_gene_count.txt


title: Enro10_Day7

description:
Enro10.Day7_S69_L001
MM_252_raw_gene_count.txt


title: Ceft5_Day21

description:
Ceft5.Day21_S29_L003
MM_252_raw_gene_count.txt


title: Enro10_Day14

description:
Enro10.Day14_S70_L001
MM_252_raw_gene_count.txt


title: Ceft8_Day3

description:
Ceft8.Day3_S38_L003
MM_252_raw_gene_count.txt


title: Ceft8_Day14

description:
Ceft8.Day14_S40_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day14

description:
Ceft5.Day14_S28_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day0

description:
Ceft5.Day0_S25_L003
MM_252_raw_gene_count.txt


title: Ceft6_Day21

description:
Ceft6.Day21_S35_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day7

description:
Ceft4.Day7_S21_L003
MM_252_raw_gene_count.txt


title: Ceft5_Day7

description:
Ceft5.Day7_S27_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day0

description:
Ceft4.Day0_S19_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day56

description:
Ceft4.Day56_S24_L003
MM_252_raw_gene_count.txt


title: Ceft3_Day3

description:
Ceft3.Day3_S14_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day14

description:
Ceft4.Day14_S22_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day3

description:
Ceft4.Day3_S20_L003
MM_252_raw_gene_count.txt


title: Ceft3_Day0

description:
Ceft3.Day0_S13_L003
MM_252_raw_gene_count.txt


title: Ceft3_Day21

description:
Ceft3.Day21_S17_L003
MM_252_raw_gene_count.txt


title: Ceft3_Day7

description:
Ceft3.Day7_S15_L003
MM_252_raw_gene_count.txt


title: Ceft10_Day7

description:
Ceft10.Day7_S45_L003
MM_252_raw_gene_count.txt


title: Ceft4_Day21

description:
Ceft4.Day21_S23_L003
MM_252_raw_gene_count.txt


title: Ceft10_Day14

description:
Ceft10.Day14_S46_L003
MM_252_raw_gene_count.txt


title: Ceft10_Day0

description:
Ceft10.Day0_S43_L003
MM_252_raw_gene_count.txt


title: WT_d6_3

status: Public on Sep 22 2023

city: Würzburg

first: Hao

last: Wu

address: versbacherstr 7-9

country: Germany

institute: institute for systemsimmunology, wurzburg university

description: DESeq2_comparison_mPiC_d6_vs_WT_d6_table

data_processing:
Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina). To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt [1] version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a CTGTCTCTTATACACATCT). Processed reads were subsequently mapped to the mouse genome (GRCm38.p6 primary assembly and mitochondrion) using STAR v2.7.2b with default parameters based on RefSeq annotation version 108.20200622 for GRCm38.p6
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package. Multi-mapping and multi-overlapping reads were counted non-strand-specific with a fractional count for each alignment and overlapping feature (command line parameters: -s 0 -t exon -M -O --fraction). The count output was utilized to identify differentially expressed genes using DESeq2 version 1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”. Differences in gene expression were considered significant if padj < 0.05.
Assembly: GRCm38.p6 primary assembly and mitochondrion
Supplementary files format and content: DESeq2_comparison

extract_protocol:
1x10^6 T cells were harvested in RNAprotect Cell Reagent and stored at -80°C o/n before total RNA was extracted using the RNeasy Plus Micro Kit (both Quiagen)
RNA quality and quantity were checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies) and RNA Pico kit depending on the sample concentration. The RIN for all samples was >7. cDNA libraries suitable for sequencing were prepared from 5 ng of total RNA with SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s instructions (1/4 volume). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of each library was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended reagent volumes. Libraries were quantified again by QubitTM 3.0 Fluometer (Thermo Fisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent) before pooling. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 19-36 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5.
Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at ~20 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5. Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina).

treatment_protocol: Day0 samples were directly purified from spleen and lymph node. Day2 samples were purified from naïve mice and stimulated with anti-CD3/CD28. Day6 samples  were acitivated as day2 samples followed with a 4 days treatment of IL-2.

tag: cell line

tag: cell type

value: CD8 T cells

value: wild type

value: Day 6


title: Ceft10_Day56

description:
Ceft10.Day56_S48_L003
MM_252_raw_gene_count.txt


title: WT

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: spleen

extract_protocol:
C57BL/6 mice were infected with 2x10^6 IU LCMV clone13 after 2 times CD4 T cell depletion (d-2 and d0) with 300µg GK1.5 anti-CD4 antibody. At the chronic infection phase (> d21), splenocytes were isolated and CD8+, CD44+, PD-1high cells were sorted using a FACS AriaIII cell sorter and directly subjected to scRNA-sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD8+, CD44+,PD-1high T cell

value: spleen

tag: strain

value: untreated


title: CD8, HTO-derived cDNA

description:
Hashtag-derived oligonucleotide (HTO)
HTO

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Lymph nodes

extract_protocol:
C57BL/6 host mice were infected with 4x10^6 IU LCMV clone13 and and CD4 T cell were depleted with 200µg GK1.5 anti-CD4 antibody (d-1 and d1). At day 23 post infection, lymph nodes were used to isolate CD8+ tdTomato+ (HIF-1a-deficient) and tdTomato+GFP+ (WT) P14 donor cells by FACS sorting. Each sample was labelled with one specific hashtag (1:400 dilution) and various CITE-seq antibodies (1:800 dilution).
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Lymph nodes

tag: library type

value: HTO

tag: antibodies/tags

value: Anti-mouse Hashtag1/TotalSeq-A0301; Anti-mouse Hashtag2/TotalSeq-A302;


title: CD8, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

tag: tissue

value: ADT

value: Anti-mouse IL-33Ra/TotalSeq-A0837 ; Anti-mouse/human KLRG1/TotalSeq-A0250 ; Anti-mouse CD185/TotalSeq-A0846 ; Anti-mouse CD278/TotalSeq-A0847; Anti-mouse CD103/TotalSeq-A0201; Anti-mouse CD49b/TotalSeq- A0421; Anti-mouse CD5/TotalSeq-A0111; Anti-mouse/rat/human CD27/TotalSeq-A0191; Anti-mouse CD127/TotalSeq-A0198; Anti-mouse CD200R/TotalSeq-A0807


title: Ceft10_Day3

description:
Ceft10.Day3_S44_L003
MM_252_raw_gene_count.txt

value: Whole blood

tag: time


title: WT_d6_2

tag: genotype


title: WT_d6_1


title: CD8, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: WT_d2_3

value: Day 2


title: Ceft3_Day56

description:
Ceft3.Day56_S18_L003
MM_252_raw_gene_count.txt

value: Day 56

tag: treatment

tag: sequencing lane


title: Ceft3_Day14

description:
Ceft3.Day14_S16_L003
MM_252_raw_gene_count.txt

value: Day 14

tag: individual id


title: Ceft10_Day21

description:
Ceft10.Day21_S47_L003
MM_252_raw_gene_count.txt

value: Day 21

value: Ceftiofur


title: WT_d0_2

description: DESeq2_comparison_mPiC_d2_vs_WT_d2_table

value: CD8 T cells

value: wild type

value: Day 0


title: WT_d2_2


title: mPiC_d6_2

value: Slc25a3-fl/fl Cd4-cre

value: Day 6


title: WT_d0_1


title: mPiC_d0_3

description: DESeq2_comparison_mPiC_d0_vs_WT_d0_table


title: mPiC_d0_2


title: mPiC_d6_1


title: mPiC_d6_3


title: WT_d0_3


title: mPiC_d2_1


title: mPiC_d2_2


title: WT_d2_1


title: mPiC_d2_3


title: Lactation_MG

status: Public on Sep 16 2023

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

country: China

institute: Zhejiang University

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: Bos_taurus ensemblV99
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

source_name: Mammary gland

extract_protocol:
Animals were euthanized by cervical dislocation using a sharp knife in previously numbed individuals within a surgery room to obtain a ~10 g MG sample. Samples then were rinsed in DBPS and quickly transferred into MACS Tissue Storage Solution (NO. 130-100-008, Miltenyi Biotec, Germany) which was stored in a 37°C vacuum container and was quickly taken to the lab. The dissociation of MG was done according to published studies with some modifications described here. In brief, the MG tissue samples were placed in a sterile RNA-free cell culture dish with 1 × PBS (with 5% FBS) and were cut into 5mm pieces. The tissues were then washed using 1 × PBS (with 5% FBS) after removing non-targeted tissues such as white adipose tissue. Subsequently, samples were gently placed in 20mM EDTA (with 5% FBS) which had been incubated at 37°C at 100rpm for 20min. After that, samples were digested with 25U/ml hyaluronidase, 0.5mg/mL CollagenaseⅡ, 0.5 mg/mL Collagenase IV, 25 U/ml DNAse I and 5% FBS in HBSS for 30 min at 37 °C. The mixture was strained through a 70-30 μm cell strainer and transferred into a new EP tube, centrifuged at around 25°C, 300 × g for 5 mins. After removing the supernatant, the cells were washed with 3 mL HBSS (with 5% FBS) and centrifuged at around 25°C at 300 g for 5 mins. The Countess II Automated Cell Counter (AMQAX1000, ThermoFisher, USA) was applied to measure cell number and viability. The requirement for cell viability is greater than 90%. If the viability for isolated cells was lower than the threshold, we used MACS Dead Cell Remove Kit (NO. 130-090-101, Miltenyi biotec, Germany) to remove dead cells by following the manufacturer’s recommendations.
Single-cell RNA-Seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3' Gel Bead and Library V3 Kit."
Single-Cell RNA-Seq

tag: breed

value: Holstein dairy cow

value: mammary gland

value: adult


title: SpontaneousEarly2

status: Public on Sep 06 2023

city: Houston

first: Ailiang

last: Zeng

address: 12515 stoney creek dr

department: Cancer Biology

institute: MD Anderson Cancer Center

description: 10x Genomics

data_processing:
FastQ preparation: mkfastq (cellranger):https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq
Count Matrix Generation: count (cellranger):https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
Data Normalization: scTransform (Satija):https://satijalab.org/seurat/v3.1/sctransform_vignette.html
https://satijalab.org/seurat/articles/integration_large_datasets.html
Assembly: mm10-3.0.0 (mouse), GRCh38-3.0.0 (human)
Supplementary files format and content: tsv.gz/barcodes
Supplementary files format and content: tsv.gz/genes
Supplementary files format and content: mtx.gz/counts

source_name: glioblatoma

extract_protocol:
Tumor samples were mechanically minced before enzymatic digestion, cells were then spun down at 800g with the brake off in a 0.9M sucrose solution to remove myelin. Cell pellets were then frozen. Upon bringing samples back up CD45+ FACs selection was performed before entering the 10x protocol
https://assets.ctfassets.net/an68im79xiti/4tjk4KvXzTWgTs8f3tvUjq/2259891d68c53693e753e1b45e42de2d/CG000183_ChromiumSingleCell3__v3_UG_Rev_C.pdf

value: glioblatoma

value: immune cells

value: QPP

value: Tamoxifen


title: SpontaneousEarly1

description: 10x Genomics


title: SpontaneousCtrl2

description: 10x Genomics

source_name: Control

value: Control

value: Vehicle


title: endothelial_ATACseq_uninjured_rep3

status: Public on Jul 24 2023

data_processing:
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (danRer10).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and Bigwig files were generated by kentUtils.
Supplementary files format and content: danRer10
Supplementary files format and content: bigwig file coverted from coverage output by macs2

source_name: Heart

extract_protocol:
Heart ventricular resections are performed on adult Tg(fli1:EGFP) zebrafish. Hearts were collected at 1 dpa and 3dpa. Uninjured zebrafish hearts were used as control.
Hearts are dissociated dissociated using Liberase DH (Roche) and EGFP+  cells were isolated by FACS. 100,000 cells/nuclei were used for library preparation.
ATAC library preparation was performed as described in (Buenrostro et al., 2013).

treatment_protocol: Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult fish between 4~12 month old were used in this study.

value: Heart

value: endothelial cells

value: uninjured


title: endothelial_ATACseq_uninjured_rep2


title: C0_replicat1

status: Public on Aug 23 2023

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data (2×150 bp PE reads) were quality controlled using Trim-Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining high quality Illumina reads were aligned to our previously published N. oceanica IMET1 genome (Gong, Kang, Kim, Wang, Wei, Xin, Shen, Wang, You, Lim, Jeong, Park, Oh, Pan, Poliner, Yang, Li-Beisson, Li, Hu, Poetsch, Farre, Chang, Jeong, Jeong, Xu, 2020) with STAR (Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras, 2013) with duplication marked using Picard (https://broadinstitute.github.io/picard/).
The abundance of expression was quantified using featureCounts (Liao, Smyth, Shi, 2014) and StringTie (Kovaka, Zimin, Pertea, Razaghi, Salzberg, Pertea, 2019). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by featureCounts (Liao, Smyth, Shi, 2014) and normalized to CPM, FPKM (fragments per kilobase of exon model per million mapped fragments) and TPM values. Besides, raw counts from featureCounts (Liao, Smyth, Shi, 2014) were used for the differential gene expression analysis with edgeR (R package)
Assembly: Nannochloropsis oceanica IMET1
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Nannochloropsis oceanica

source_name: Cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
Total microalgal RNA was extracted using Trizol reagents (Invitrogen, USA). The concentration and purity of the RNA were determined spectrophotometrically (NanoDrop-1000, Thermo Scientific, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm). The seed cultures were bubbled with air-level CO2. At the logarithmic phase (OD750=2.5), cells were harvested by centrifugation, one was sampled for RNA extraction as control (C0) with three replicates and the other was washed with fresh medium (nitrogen-free) for three times before being used for the following experiments. Cell pellets were inoculated into Nitrogen-free (for sampling of mRNA-seq, ChIP-seq and HiC-seq) and Nitrogen-repletion f/2 medium (for physiological measurement). Cultures started with the same initial cell concentration of OD750 = 2.5 and were exposed to continuous illumination of 50±5 μmol m−2 s−1. Cell aliquots were collected  for sampling of mRNA-seq, ChIP-seq and HiC-seq after being transferred to the designated conditions for one and two days  as nitrogen-deprivation samples (N1 and N2) with three replicates

value: Nitrogen-repletion


title: C0_replicat2


title: endothelial_ATACseq_3dpa_rep2

value: 3 day post vetricular apex amputation


title: 2 weeks post transection 1

status: Public on Jul 18 2023

data_processing:
Sequences were aligned to the zebrafish genome (danRer10) using Bowtie2 (v 2.2.5)
The mapped reads were filtered by samtools (v 1.3.1, with parameter -q 30) and duplicates were removed by picard (v 1.91)
Peak calls were determined using MACS2 (v 2.1.0, with parameter -f BAM -g 1.5e9 -q 0.05 --nomodel --shift 37 --extsize 73), and csaw(v 1.20.0, cutoff P value <0.05).
DiffBind(v 2.14.0) was used to call differential accessible sites.
Supplementary_files_format_and_content: bigwig files were generated by deeptools::bamCoverage (v 2.1.0) and normalized to 1x sequencing depth by ignore chrX for extaned reads

source_name: spinal cord

extract_protocol:
Sham injured and injured (2 mm rostral and caudal to the lesion site) spinal cords were dissected into a single cell suspension using 0.25% trypsin-EDTA; dissociated cells were processed for FACS sorting using an Astrios sorter, to collect live and single cells. 50.000 cells were processed for ATAC-seq.
Library preparation as described in Buenrostro et al., 2015
Libraries were sequenced on the Illumina HiSeq 4000 platform, with over 40 million 150 bp paired-end reads obtained for each library.


title: sham 3

value: sham


title: 2 weeks post transection 3


title: endothelial_ATACseq_uninjued_rep1


title: mPiC_d0_1

value: CD8 T cells

value: Slc25a3-fl/fl Cd4-cre

value: Day 0


title: endothelial_ATACseq_3dpa_rep1


title: endothelial_ATACseq_1dpa_rep3

value: 1 day post vetricular apex amputation


title: endothelial_ATACseq_1dpa_rep1


title: endothelial_ATACseq_3dpa_rep3


title: Oxyt5_Day56

description:
Oxyt5.Day56_S72_L003
MM_252_raw_gene_count.txt

value: Whole blood

value: Day 56

value: Oxytetracycline


title: sham 1


title: endothelial_ATACseq_1dpa_rep2


title: sham 2


title: spinal cord, 1 week post transection 3 (RNA-seq)

data_processing:
Reads were trimed by trim_galore and them aligned to the zebrafish genome (danRer10) using Tophat2 (v 2.2.1)
Mapped reads were filtered by samtools (v 1.3.1)and counted by htseq-count (v 0.6.0)
Differential analyses were performed by Bioconductor package DESeq2 (v 1.26.0)
Supplementary_files_format_and_content: text file contain raw counts for genes exported by htseq-counts (v 0.6.0)

source_name: spinal cord, 1 week post transection

extract_protocol:
Sham injured and injured (2 mm rostral and caudal to the lesion site) spinal cords were dissected and RNA was harvested using Trizol reagent. Genomic DNA was removed using RNA Clean and Concentrator Kit (Zymo Research).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Hiseq4000 (50bp, SR, 1 lane)

value: injured

value: spinal cord


title: spinal cord, 1 week post transection 2 (RNA-seq)


title: spinal cord, sham 3 (RNA-seq)

source_name: spinal cord, sham


title: spinal cord, 1 week post transection 1 (RNA-seq)


title: spinal cord, sham 1 (RNA-seq)


title: spinal cord, sham 2 (RNA-seq)


title: 2 weeks post transection 2


title: spinal cord, sham 3 (ATAC-seq)

data_processing:
Sequences were aligned to the zebrafish genome (danRer10) using Bowtie2 (v 2.2.5)
The mapped reads were filtered by samtools (v 1.3.1, with parameter -q 30) and duplicates were removed by picard (v 1.91)
Peak calls were determined using MACS2 (v 2.1.0, with parameter -f BAM -g 1.5e9 -q 0.05 --nomodel --shift 37 --extsize 73), and csaw(v 1.20.0, cutoff P value <0.05).
DiffBind(v 2.14.0) was used to call differential accessible sites.
Supplementary_files_format_and_content: bigwig files were generated using deeptools (v 3.1.3) Scores represent count per million reads


title: spinal cord, 1 week post transection 2 (ATAC-seq)


title: cdHFD_female_ZT20_rep_3

status: Public on Jun 16 2023

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Reference genome (GRCm38/mm10) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
All the downstream analyses were based on the clean data with high quality. FeatureCounts was used to count the reads numbers mapped to each gene. Normalized DESEq2 data in log values were used for all subsequent analyzes
Assembly: mm10
Supplementary files format and content: Raw counts values for each sample are shown

source_name: liver

extract_protocol:
Total RNA was extracted from livers using Trizol reagent (Thermofisher, Germany) and columns (Zymo Research, USA) according to the manufactory’s instructions. Trueseq RNAseq comprising 40 million reads per sample (12GB) was performed at Novogene (Germany).
Samples underwent quality control and only those with RNA integrity number (RIN) higher than 6.5 were used. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: liver

value: wild type (WT)


title: danRer11_WT_7dpi

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: danRer11
Supplementary files format and content: h5 files for count table

extract_protocol: Samples were processed following the 10X Chromium platform following the manufacturer’s guidelines, using 10X Single Cell 3’ v3 chemistry (10X Genomics, Pleasanton, USA).

value: WT

value: Ekkwill (EK)

tag: age

value: 6 months


title: danRer11_WT_sham


title: spinal cord, sham 2 (ATAC-seq)

value: uninjured


title: spinal cord, sham 1 (ATAC-seq)


title: spinal cord, 1 week post transection 3 (ATAC-seq)


title: spinal cord, 1 week post transection 1 (ATAC-seq)


title: danRer11_hbegfaKO_7dpi

value: hbegfaKO


title: danRer11_hbegfaKO_sham

value: sham


title: cdHFD_male_ZT20_rep_2


title: cdHFD_male_ZT20_rep_1


title: cdHFD_male_ZT14_rep_1


title: cdHFD_female_ZT14_rep_4


title: cdHFD_female_ZT8_rep_3


title: cdHFD_male_ZT14_rep_3


title: cdHFD_male_ZT14_rep_2


title: cdHFD_female_ZT8_rep_4


title: cdHFD_male_ZT8_rep_1


title: cdHFD_male_ZT8_rep_2


title: cdHFD_female_ZT2_rep_3


title: chow_female_ZT14_rep_4


title: cdHFD_female_ZT20_rep_4


title: cdHFD_male_ZT2_rep_1


title: chow_female_ZT20_rep_3


title: chow_male_ZT20_rep_2


title: chow_female_ZT20_rep_4


title: chow_male_ZT14_rep_2


title: chow_male_ZT14_ep_1


title: chow_female_ZT8_rep_3


title: cdHFD_male_ZT2_rep_2


title: chow_male_ZT8_rep_2


title: cdHFD_female_ZT2_rep_4


title: chow_female_ZT8_rep_4


title: chow_female_ZT14_rep_3


title: chow_male_ZT8_rep_1


title: chow_female_ZT2_rep_4


title: chow_male_ZT2_rep_1


title: Sample 23 - LPS, 18h, rep3

status: Public on Mar 31 2023

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

description: Matrix Column Q

data_processing:
Using cutadapt version 1.18 (https://cutadapt.readthedocs.io/en/stable/), the reads of the sequencing run were scanned for adapter contaminations, continuous polyA sequences and continuous polyG sequences at the 3’ end and had the contaminations removed if they were found. The reads of the samples prior to adapter trimming and after adapter trimming were analyzed with FastQC version v0.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the spike-in complemented Ensembl release 101 of the Mus musculus high coverage assembly GRCm38 from the Genome Reference Consortium. The alignment was performed with the splice-aware aligner STAR version 2.6.1a (https://github.com/alexdobin/STAR)1. The alignments were quantified based on the annotations of Ensembl GRCm38.101 and the spike-in specific annotations of Lexogen with the featureCounts software program version 1.6.4 of the subread analysis package (http://subread.sourceforge.net/).
A differential gene expression analysis was conducted using DESeq2 (version v1.18.1; https://bioconductor.org/packages/release/bioc/html/DESeq2.html ). The analysis used the counts of unique alignments. Significance was determined at adj P<0.1.
Assembly: GRCm38
Supplementary files format and content: tab-separated values (tsv) file including library names, gene IDs and individual normalized counts
Supplementary files format and content: tab-separated values (tsv) file including gene annotation and raw counts

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages (BMDMs) were generated by culturing bone marrow cells in DMEM supplemented with 10 % FCS, 1 % Penicillin/Streptomycin and 15 % L929 cell-conditioned medium (LCM). On day 6 of differentiation, BMDMs were collected and plated for experiments. Experiments were performed in DMEM supplemented with 10 % FCS and 1 % Penicillin/Streptomycin, unless stated otherwise.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit together with the RNase-free DNase Set for DNA digestion (both Qiagen) according to manufacturer instructions
Libraries were prepared manually according to the manufacturer’s instructions using QuantSeq 3' mRNA-Seq FWD Library Prep Kit. Briefly, 150 ng total RNA was used as input for reverse transcription with oligo(dT) primer containing an Illumina-compatible sequence at its 5’ end. After RNA removal, the second strand of the cDNA was synthesized by a random primer containing an Illumina-compatible linker sequence at its 5’ end. Finally, individual sample barcodes (dual indexing) for multiplexing were introduced via 15 cycles of PCR (determined by qPCR). All libraries were analyzed for adapter dimers, size distribution and concentration on a Fragment Analyzer (Agilent). After pooling the libraries in an equimolar ratio, the concentration and the size distribution of the lane mix was analyzed by Qubit (Thermo Fisher Scientific) and by Fragment Analyzer (Agilent), respectively. A 2 nM dilution of the lane mix was denatured and diluted for sequencing on a NextSeq 2000 instrument

treatment_protocol: For RNA Sequencing, 1 Million BMDMs per condition were left untreated (control), stimulated with 30 µM S14 or 100 ng/mL LPS for 3 h or 18 h before harvesting cells for RNA isolation.

value: Bone marrow-derived macrophages

value: wild-type

value: LPS


title: chow_male_ZT20_rep_1


title: chow_male_ZT2_rep_2


title: chow_female_ZT2_rep_3


title: Sample 24 - LPS, 18h, rep4

description: Matrix Column R


title: Sample 18 - S14, 18h, rep2

description: Matrix Column K


title: Sample 22 - LPS, 18h, rep2

description: Matrix Column P


title: Sample 21 - LPS, 18h, rep1

description: Matrix Column O


title: Sample 20 - S14, 18h, rep4

description: Matrix Column N


title: Sample 14 - UT, 18h, rep2

description: Matrix Column G

value: untreated


title: Sample 17 - S14, 18h, rep1

description: Matrix Column J


title: Sample 11 - LPS, 3h, rep3

description: Matrix Column D


title: Sample 16 - UT, 18h, rep4

description: Matrix Column I


title: Sample 15 - UT, 18h, rep3

description: Matrix Column H


title: Sample 9 - LPS, 3h, rep1

description: Matrix Column Y


title: Sample 8 - S14, 3h, rep4

description: Matrix Column X


title: Sample 10 - LPS, 3h, rep2

description: Matrix Column C


title: Sample 7 - S14, 3h, rep3

description: Matrix Column W


title: Sample 19 - S14, 18h, rep3

description: Matrix Column L


title: Sample 5 - S14, 3h, rep1

description: Matrix Column U


title: Sample 4 - UT, 3h, rep4

description: Matrix Column T


title: Sample 12 - LPS, 3h, rep4

description: Matrix Column E


title: Sample 13 - UT, 18h, rep1

description: Matrix Column F


title: J130_S92

status: Public on Mar 09 2023

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, and leading and trailing basepairs below a quality score of 3
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 14 --dta -x GCF_002263795.1_ARS-UCD1.2
Read assembly and quantification was performed with StringTie v2.1.7 with parameters -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.1_ARS-UCD1.2_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.32.1.
Assembly: GCF_002263795.1
Supplementary files format and content: comma-delimited text file of gene counts for each sample

extract_protocol:
Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit per product instruction.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library preparation kits, using standard Illumina protocols.

tag: disease

value: Y

tag: saletype

value: Direct

tag: vaccinated

tag: pen number

tag: arrival weight (lbs)


title: Sample 6 - S14, 3h, rep2

description: Matrix Column V

tag: cell type


title: Sample 3 - UT, 3h, rep3

description: Matrix Column S


title: J122_S89

tag: animal id


title: J124_S91

value: N


title: J113_S87

value: Auction


title: J123_S90


title: J103_S82


title: Sample 1 - UT, 3h, rep1

description: Matrix Column B


title: J109_S84


title: J111_S85


title: J121_S88


title: J052_S70


title: J062_S74


title: J097_S81


title: J108_S83


title: J031_S61


title: Sample 2 - UT, 3h, rep2

description: Matrix Column M


title: J041_S66


title: J092_S80


title: J078_S77


title: J038_S64


title: J040_S65


title: J086_S78


title: J071_S75


title: J059_S73


title: J112_S86


title: J024_S58


title: J091_S79


title: J050_S69


title: J026_S59


title: J047_S68


title: J013_S51


title: J055_S72


title: J076_S76


title: J011_S50


title: J015_S53


title: J053_S71


title: J019_S55


title: J023_S57


title: J043_S67


title: J027_S60


title: LG252_biolrep_2

status: Public on Dec 24 2022

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v2.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GCA_028583425.1 (MPM_Emac_v1.0)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Eublepharis macularius

source_name: tissues enclosing oral mucosa, dental lamina and dental mesenchyme

extract_protocol:
Soft tissues from adult gecko jaws that included unerupted teeth and dental lamina were dissected and place in cold 1X HANKS solution without Calcium and Magnesium with 10% fetal bovine serum (FBS). The tissues were chopped into small segments. Animal LG252 pieces were placed in the dissection media with collagenase D (SIGMA, COLLD-RO; 1.5 U/ml)/ Dispase II (SIGMA, D4693; 2.4 U/ml) for 37°C for 4-5 hours in an orbital shaker. LG255 pieces were placed into Bacillus Licheniforms protease (SIGMA, 85380; 10 mg/ml) in dissection media on a shaker at 4 degrees for 6 hours.  Once the cells were mechanically dissociated, cells were spun down and counted. They were transferred into FACS buffer (2 ml EDTA, 2% FBS, 1X PBS) and resuspended in 2 ml final volume. Cells were passed through a 40 µm cell filter to remove clumps. Live versus dead cells were distinguished with propidium iodide exclusion (1:5000 in FACS buffer). Cells were fluorescence activated cell sorted in DMEM + 5% FBS media. Then, we collected cells at a final concentration of 50,000 cell/ml.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).


title: J033_S63


title: LG255_biolrep_2

description: 10x Genomics

value: tissues enclosing oral mucosa, dental lamina and dental mesenchyme


title: LG255_biolrep_1

description: 10x Genomics


title: J032_S62


title: J017_S54


title: D28 post-injury FDL, biol rep 1

status: Public on Oct 25 2022

city: Rocheser

first: Jessica

last: Ackerman

state: NY

address: 665 Elmwood Ave

institute: University of Rochester

data_processing:
Demultiplexing: spaceranger-1.3.1/spaceranger mkfastq --run=. --samplesheet=spaceRanger.csv --output-dir ./spaceRanger --nopreflight --jobmode=slurm --localcores=24 --localmem=120
Counting: spaceranger-1.3.1/spaceranger count --fastqs=./fastq_path --jobmode=slurm --maxjobs=100 --nopreflight --transcriptome=${REF} --project=${PROJECT} --id=Sample_${SAMPLEPREFIX} --sample=${SAMPLEPREFIX} --slide=${SLIDE} --area=${AREA} --image=${IMAGE}
Assembly: combined cellranger provided “refdata-gex-mm10 2020-A” and user provided tdTomato sequence
Supplementary files format and content: feature barcode matrix data (.tsv, .mtx)
Supplementary files format and content: aligned fiducials, detected tissue image, scale factors, hi-res tissue image, lo-res tissue image, and tissue positions. These can be used to visualize the transcriptomic information on the original tissue sample.

source_name: murine hindpaw

extract_protocol:
Whole hindpaws from experimental mice were collected and fresh frozen prior to sectioning onto gene expression slides (10X Visium)
RNA extraction, cDNA amplification, and library construction were carried out according to the 10X Genomics Visium user guide, rev F

treatment_protocol: Experimental mice were given tamoxifen D-7 to -4 prior to complete transection and repair of the FDL tendon in the hindpaw to label resident Scx-lin+ cells and visualize their contribution

value: murine hindpaw

value: 10-12 weeks

tag: strain

value: Scx-CreER; Ai9 F/+

value: Day 28


title: NSD2_2

status: Public on Oct 19 2022

data_processing:
Barcode correction, alignment are performed using umitools and STAR aligner
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Cells were annotated using known cell type markers
Assembly: Human: GRCh38, Mouse: GRCm38
Supplementary files format and content: processed expression matrix: RDS files that contain seurat objects with or without CellBender step
Supplementary files format and content: Intronic read ratios per cell type: Text file, one row per cell barcode
Supplementary files format and content: processed expression matrix of only OPC: RDS files that contain seurat objects (with CellBender) that contain OPC clustering information

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol:
Nuclei for snRNA-seq were isolated from human BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3? v3.1 (1000121, 10x Genomics) according to the manufacturer?s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.^SAMPLE = GSM6428210
Nuclei for snRNA-seq were isolated from human BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3? v3.1 (1000121, 10x Genomics) according to the manufacturer?s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.^SAMPLE = GSM6428210

tag: Sex

value: M


title: NSD2_4

extract_protocol:
Nuclei for snRNA-seq were isolated from human BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3? v3.1 (1000121, 10x Genomics) according to the manufacturer?s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.^SAMPLE = GSM6428210

value: F


title: LG252_biolrep_1

description: 10x Genomics

tag: tissue


title: J014_S52

source_name: Whole blood


title: D28 post-injury FDL, biol rep 2

tag: time


title: J022_S56


title: D21 post-injury FDL, biol rep 2

value: Day 21


title: P56_WT_YL12

description: transcriptome

data_processing:
10X Genomics CellRanger v3.0.2
Seurat v3 and v4
Supplementary files format and content: raw counts matrix for filtered cells/nuclei in H5AD format

source_name: frontal cortex

extract_protocol:
Nuclei isolation protocol was modified from our previous work (Ayhan et al., 2021). Since homogenization of mouse cortex generated much fewer debris, we just did twice fltering through 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art) without doing sucrose-gradient centrifugation
The single-nuclei RNA-seq libraries were prepared using Chromium Single Cell 3ʹ Reagent Kits v3 (CG000185 Rev B) from 10x Genomics
Single nuclei RNA-seq was performed on Illumina NovaSeq 6000

tag: genotype

value: WT

tag: gender

value: female

tag: rna preparation batch

tag: library preparation batch

tag: sequencing batch


title: NSD2_3

tag: age


title: D14 post-injury FDL, biol rep 2

value: Day 14


title: D21 post-injury FDL, biol rep 1


title: P56_WT_YL10

description: transcriptome


title: NSD2_1

extract_protocol: RNA-seq


title: Uninjured FDL control, D0 biol rep 2

value: Day 0


title: D14 post-injury FDL, biol rep 1


title: BM2 [VDJ]

status: Public on Oct 05 2022

city: Atlanta

first: Eliver

last: Ghosn

state: GA

address: 1760 Haygood Dr NE

department: Lowance Center for Human Immunology

institute: Emory University School of Medicine

data_processing:
Gene expression libraries were sequenced together on a NovaSeq 6000 platform (Illumina, San Diego, CA). ADT and V(D)J libraries were sequenced separately on a Next-seq platform (Illumina, San Diego, CA).
Cell Ranger Software (v.3.1.0) was used to perform barcode processing and single-cell 5′ unique molecular identifier (UMI) counting. Reads from GEX and ADT libraries were processed simultaneously using “cellranger count” with "--r2-length=98 --expect-cells=5000", while reads from V(D)J libraries were aligned by running “cellranger vdj”.
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx files are the sparse matrices of the gene expression and surface-protein expression data.

source_name: Bone marrow

extract_protocol:
PBMCs were isolated from whole blood using EasySep™ Direct Human PBMC Isolation Kit (Catalog #19654 Stem Cell Technologies). B cells were enriched from fresh whole bone marrow using EasySep™ B Cell Enrichment: Complete Processing Kit for Whole Blood (Catalog # 19954 Stem Cell Technologies)
Libraries were prepared according to Chromium Single Cell V(D)J Reagent Kit (v1 Chemistry) with Feature Barcoding technology for Cell Surface Protein User Guide.

value: Bone marrow

value: B-cell enriched

tag: disease status

value: Healthy donor


title: BM1 [VDJ]


title: P56_WT_YL01

description: transcriptome

value: male


title: Uninjured FDL control, D0 biol rep 1


title: P56_WT_YL08

description: transcriptome


title: BM2 [GEX]

description: 20A0000285-Ssq_5GEX_BM-BCell_630-2551_31yoF_C2_L004


title: S.046.J109_S46

status: Public on Aug 29 2022

data_processing:
FastQC v0.11.9 was used for read quality assessment.
Trimmomatic v0.39 was used for read pair trimming and adaptor removal (parameters- SLIDINGWINDOW:4:20 MINLEN:28 LEADING:3 TRAILING:3 ILLUMINACLIP:adaptor.fa:2:30:20:2:TRUE).
Trimmed reads were mapped to the ARS-UCD1.2 bovine genome assembly with HISAT2 v2.2.1 (parameters- -hSbo).
Gene-level transcriptome assembly was performed with StringTie v2.1.7 (parameters-e -G ARSUCD1.2.gff)
Raw gene counts were generated by the Python3 program prepDE.py, provided by the authors of StringTie (parameters- -l 150).
Assembly: ARS-UCD1.2
Supplementary files format and content: Comma-delimited text file of annotated raw gene counts of all samples.

extract_protocol:
Total RNA was isolated from Tempus RNA blood tubes with Tempus Spin RNA Isolation Kit (Applied Biosystems), based on manufacturer’s instruction.
Sequencing libraries were constructed with the TruSeq Stranded mRNA Library Prep Kit (Illumina), following manufacturer’s instruction.

value: Whole blood

tag: timepoint

tag: pasture location

tag: age at_sampling

tag: vaccination

value: Y


title: S.038.J015_S38


title: S.039.J022_S39


title: S.043.J038_S43

value: N


title: S.041.J027_S41


title: S.036.J124_S36


title: S.037.J009_S37


title: BM1 [ADT]

tag: cell type


title: S.045.J053_S45


title: BM2 [ADT]


title: S.047.J113_S47


title: BM1 [GEX]

description: 20A0000285-Ssq_5GEX_BM-BCell_3031489_20yoM_B2_L004


title: S.034.J109_S34


title: S.044.J040_S44


title: S.032.J040_S32


title: S.040.J023_S40


title: S.031.J038_S31


title: S.042.J032_S42


title: S.030.J032_S30


title: S.035.J113_S35


title: S.029.J027_S29


title: S.026.J015_S26


title: S.022.J109_S22


title: S.027.J022_S27


title: S.025.J009_S25


title: S.012.J124_S12


title: S.014.J015_S14


title: S.016.J023_S16


title: S.024.J124_S24


title: S.023.J113_S23


title: S.015.J022_S15


title: S.033.J053_S33


title: S.019.J038_S19


title: S.018.J032_S18


title: S.020.J040_S20


title: S.010.J109_S10


title: S.017.J027_S17


title: S.021.J053_S21


title: S.008.J040_S8


title: S.011.J113_S11


title: S.009.J053_S9


title: S.013.J009_S13


title: S.005.J027_S5


title: S.006.J032_S6


title: S.007.J038_S7


title: S.004.J023_S4


title: S.003.J022_S3


title: Tdt Control IgG [H3K4me3 CUT&Tag]

status: Public on Aug 04 2022

first: Jeffrey

last: Dilworth

email: jdilworth@ohri.ca, fdilworth@wisc.edu

state: WI

address: 1111 Highland Ave - WIMR II 4518

department: Cell and Regenerative Biology

institute: University of Wisconsin - Madison

data_processing:
Library strategy: CUT&Tag
Nextera adapters were trimmed from sequenced reads with Cutadapt 2.6 (Python 3.7.4).
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.3.4.1 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Trimmed sequences were aligned to spike-in DNA (Amp - pBluescript II SK(+)) using Bowtie2 version 2.3.4.1 with the following parameters: --very-sensitive .
Duplicates, non-uniquely aligned reads were filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads.
Spike-in normalized genome coverage was calculated using bamCoverage v3.3.2 (Deeptools v3.3.2).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Spike-in normalized bigwigs.

source_name: Satellite Stem cells

extract_protocol:
Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were then sorted by fluorescence activated cell sorting. FACS sorted cells were collected in microfuge tubes. Cells were permeabilized with digitonin and the genomic DNA was cleaved and tagged by pA-Tn5 after incubation with histone H3 lysine 4 trimethyl primary antibody.
Library was prepared using i5 and i7 universal primers and NEBNext High-fidelity 2x PCR Master mix. Before following the thermal cycling conditions recommended by the manufacturer, the samples were incubated at 72°C for gap filling.

treatment_protocol: Cardiotoxin Injections into the tibialis anterior and gastrocnemius muscle of hind limb.

value: Tdt Control

tag: treatment

value: Cardiotoxin injury

value: Tibialis Anterior and Gastrocnemius muscles

value: Satellite Stem cells

tag: development stage

value: Adult

tag: antibody

value: IgG-His


title: Tdt Control - IgG [H3K27me3 CUT&Tag]

extract_protocol:
Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were then sorted by fluorescence activated cell sorting. FACS sorted cells were collected in microfuge tubes. Cells were permeabilized with digitonin and the genomic DNA was cleaved and tagged by pA-Tn5 after incubation with histone H3 lysine 27 trimethyl primary antibody.
Library was prepared using i5 and i7 universal primers and NEBNext High-fidelity 2x PCR Master mix. Before following the thermal cycling conditions recommended by the manufacturer, the samples were incubated at 72°C for gap filling.

tag: strain

tag: tissue


title: S.001.J009_S1


title: S.002.J015_S2


title: Jmjd3 - KO [H3K27me3 CUT&Tag]

tag: genotype

value: Jmjd3 KO


title: Tdt Control [H3K27me3 CUT&Tag]


title: Utx - KO [H3K27me3 CUT&Tag]

value: Utx KO


title: Tdt Control [H3K4me3 CUT&Tag]


title: Utx Ko rep-1 [RNA-seq]

data_processing:
Sequencing adapters were trimmed using Cutadapt v2.6.
Transcript quantification with Salmon v1.1.0.
Differential expression with DEseq2 v1.28.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Table containing differentially expressed genes.
Supplementary_files_format_and_content: Quantified transcripts for all samples.

extract_protocol: Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were further collected in microfuge tubes by fluorescence activated cell sorting.


title: J-lab [CUT&Tag]

extract_protocol:
Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were then sorted by fluorescence activated cell sorting. FACS sorted cells were collected in microfuge tubes. Cells were permeabilized with digitonin and the genomic DNA was cleaved and tagged by pA-Tn5 after incubation with UTX and JMJD3 lab generated and commercial primary antibodies.
Library was prepared using i5 and i7 universal primers and NEBNext High-fidelity 2x PCR Master mix. Before following the thermal cycling conditions recommended by the manufacturer, the samples were incubated at 72°C for gap filling.

value: Tdt.Ctrl/ Pax7 gCre/gCre TdT Fl/Fl

value: JMJD3 (lab generated)


title: Jmjd3 - KO [H3K4me3 CUT&Tag]


title: U-lab [CUT&Tag]

value: UTX (lab generated)


title: Utx Ko rep-2 [RNA-seq]


title: IgG-TF [CUT&Tag]

value: IgG-TF


title: Utx - KO [H3K4me3 CUT&Tag]


title: Tdt Control rep-1 [RNA-seq]


title: Jmjd3 Ko rep-1 [RNA-seq]


title: Jmjd3 Ko rep-2 [RNA-seq]


title: Tdt.Control [scRNA-seq]

description: Single-cell RNA-Seq

data_processing:
Performed on 10X Cell Ranger pipeline.
cellranger mkfastq  v2.1.1
cellranger count v2.1.1
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar archives include barcodes.tsv, features.tsv, and matrix.mtx files; single-cell gene expression matrix.


title: Jmjd3-Ko [scRNA-seq]

description: Single-cell RNA-Seq


title: Utx-Ko [scRNA-seq]

description: Single-cell RNA-Seq


title: Allogeneic islet graft

status: Public on May 25 2022

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: Room 604, Building 1, Yinxingzhijie 1 Qi Guanlan, Longhua District

institute: Shenzhen Second People's Hospital

data_processing:
Sequences obtained from sequencing using the 10x Genomics single-cell RNA sequencing platform were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10x Genomics). Cells were removed if they were expressing fewer than 200 unique genes, more than 4,500 unique genes, or greater than 15% mitochondrial reads. Genes not detected in at least 3 cells were removed from subsequent analysis.
To analyze the single-cell RNA-seq data, we performed Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) using the Seurat R Package (version 3.1.5) with the first 75 principal components, after performing principal component analysis (PCA) on the 2000 most variable genes. Identification of significant clusters was performed using the FindClusters() algorithm in the Seurat package with the resolution set as 0.6. Marker genes for each significant clusters were found using the Seurat function FindAllMarkers(). Cell types were determined using a combination of marker genes identified from the literature and the CellMarker web tool (http://biocc.hrbmu.edu.cn/CellMarker/).
All single-cell sequencing data statistical analysis was performed in R (version 4.0.5) using Seurat (3.1.5). Wilcoxon Rank Sum test was applied for comparisons in two groups. Statistical significance was accepted for p < 0.05.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files.

source_name: islet graft

extract_protocol:
After dissociation, the concentration of single-cell suspension was adjusted to 700–1,200 cells/μl. Cell viability was determined by trypan blue staining with TC20 automated cell counter (Bio-rad, Hercules, CA). The ratio of viable cells was required to be more than 85%. The input cells were then loaded onto the channel of Single Cell B Chip (v3 chemistry, PN-1000153) and loaded onto a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in emulsion).
Reverse transcription and library preparation was performed using the Chromium Single Cell 3’ Reagent Kits following the 10x Genomics protocol.
Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell on an Illumina NovaSeq 6000 by Novogene Bioinformatics Technology Co., Ltd (Tianjing, China).

value: Balb/c

value: pancreatic islet

tag: condition

value: Balb/c islets to C57bl/6 recipients