title: Psoriatic Skin Tissue Rep24

city: Kolkata

first: Raghunath

last: Chatterjee

state: WB

address: 203 BT Road, HGU, Indian Statistical Institute

department: Human Genetics Unit

country: India

institute: Indian Statistical institute

data_processing:
Illumina HiSeq 4000 software was used for basecalling to generate single-end reads of 50 bases
Sequenced reads were trimmed for adaptor sequences using CutAdapt, quality trimmed at the 3′ ends, then mapped to the human genome (hg19/GRCh37) using novoalign v3.09.01 with parameters -l 16 -m -h90 -rA
The mapped reads were converted to BAM format and sorted based on chromosomal locations using samtools sort
Raw read counts of known miRNAs (as present in miRBase) were generated using HTSeq counts v0.11.1 with parameters -f bam -s no -t miRNA -i Name -a 1 -r pos --nonunique=all
Differential expression analysis was carried out using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for all known miRNAs for each sample.

source_name: Lesional Psoriatic skin tissue

extract_protocol:
Skin biopsy tissues were snap frozen in liquid nitrogen and grinded using mortar and pestle. RNA extraction was performed using mirVana™ miRNA Isolation Kit (Thermo Fisher) following manufacturer’s protocol.
MicroRNA libraries were prepared using NEBNext small RNA Prep kit for Illumina Sequencing

tag: sample name

value: Lesional Psoriatic skin

tag: age of onset

tag: pasi score


title: Adjacent Normal Skin Tissue Rep24

status: Public on Sep 02 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Adjacent normal skin tissue

tag: tissue

value: Adjacent normal skin


title: resHif1aKO, control 2, day 3 MI, snRNAseq

city: St Louis

first: Farid

middle: Faridovich

last: Kadyrov

state: MO

address: Clinical Sciences Research Building, Rm. 9900  4939 Children's Place, Campus Box 8086

department: IM-Cardiology

country: USA

institute: Washington University in St Louis

data_processing:
For monocytes, macrophages, and dendritic cells from macHif1a KO and control mice: Sequencing reads were aligned to the GRcm38 transcriptome using CellRanger (v3.1.0) from 10X Genomics. For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Arg1ZsGr mice 2 and 30 days after myocardial infarction: Sequencing reads were aligned to the mm10-2020-A transcriptome using CellRanger (v7.1.0). For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Control>ZsGr and Hif1a>ZsGr mice 5 days after syngeneic heart transplant: Sequencing reads were aligned to the mm10-2020-A transcriptome using CellRanger (v7.1.0). For monocytes, macrophages, and dendritic cells from Arg1DTR mice 3 days after myocardial infarction: Sequencing reads were aligned to the mm10-2020-A transcriptome using CellRanger (v8.0.0). For nuclei from control and resHif1aKO mice 3 days after myocardial infarction: Sequencing reads were aligned to the mm10-2020-A transcriptome using CellRanger (v8.0.0).
Assembly: mm10
Supplementary files format and content: tab severated values files an matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Hearts were perfused with PBS, weighed, minced, and digested for 45 minutes at 37⁰C in DMEM (Gibco 11965-084) containing 4500 U/ml Collagenase IV (Millipore Sigma C5138), 2400 U/ml Hyaluronidase I (Millipore Sigma H3506), and 6000 U/ml DNAse I (Millipore Sigma D4527). Enzymes were deactivated with HBSS containing 2% FBS and 0.2% BSA and filtered through 40-micron strainers. Cells were incubated with ACK lysis buffer (Gibco A10492-01) for 5 minutes at room temperature. Cells were washed with DMEM and resuspended in 100 µl of FACS buffer (PBS containing 2% FBS and 2mM EDTA). Cells were incubated in a 1:200 dilution of fluorescence conjugated monoclonal antibodies for 30 minutes at 4⁰C. Samples were washed in FACS buffer and resuspended in a final volume of 250 µl FACS buffer. Flow cytometry and sorting was performed using a BD FACS melody. For sorting of monocytes, macrophages, and dendritic cells in macHif1aKO mice for single cell RNA sequencing, antibodies used were: CD45 PerCP/Cy5.5 (BioLegend 103132), Ly6g FITC (BioLegend 127606), Ly6c APC (BioLegend 128016), DAPI (BD Pharmingen 564907), and CD64 PE/Cy7 (BioLegend 139313). For sorting of monocytes, macrophages, and dendrtic cells in Arg1ZsGr, antibodies used were: CD45 PerCP/Cy5.5(BioLegend 103132), CD11b BV421 (BioLegend 101235), Ly6g APC/Cy7 (BioLegend 127623), Ly6c BV510 (BioLegend 128033), CD64 PE/Cy7 (BioLegend 139313). Endogenous ZsGreen signal was used to sort ZsGr- and ZsGr+ cells. For sorting of monocytes and macrophages in Arg1tdT-CreERT2 Csf1rlsl-DTR-mCherry mice 3 days after I/R, antibodies used were: CD45 PerCP/Cy5.5 (BioLegend 103132), CD11b BV785 (BioLegend 101243), Ly6g APC/Cy7 (BioLegend 127623), Ly6c BV510 (BioLegend 128033), CD64 PE/Cy7 (BioLegend 139313). For single nucleus RNA sequencing of control and resHif1aKO, hearts from 6 Control and 6 resHif1aKO mice were perfused with PBS and minced, and nuclei were isolated using the 10X Genomics Nuclei Isolation Kit with RNase Inhibitor (PN-1000494). The resulting single nuclei preparations were pooled based on experimental condition and were stained with a 1:200 dilution of DRAQ5 (ThermoFisher Scientific 65-0880-96). DRAQ5+ nuclei were sorted into 300 µl of Wash Buffer with RNase Inhibitor.
For monocytes, macrophages, and dendritic cells from macHif1a KO and control mice: Single cell RNA sequencing libraries were generated using the 10X Genomics 5’v1 platform. For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Arg1ZsGr mice 2 and 30 days after myocardial infarction: Single cell RNA sequencing libraries were generated using the 10X Genomics 5’v1 platform. For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Control>ZsGr and Hif1a>ZsGr mice 5 days after syngeneic heart transplant: Libraries were generated using the 10x 3’v3.1 platform. For monocytes and macrophages from control and Arg1DTR mice sorted 3 days after myocardial infarction: libraries were generated using the 10x 3’v3.1 platform. For nuclei isolated from control and resHif1aKO mice 3 days after myocardial infarction: 2 libraries were generated using the 10X Genomics 5'v2 platform.

value: heart

tag: cell type

value: nuclei


title: resHif1aKO, control 1, day 3 MI, snRNAseq


title: SAC, P11P6, OFF, rep147

city: Baltimore

first: Rebecca

last: James

state: MD

address: 725 N. Wolfe Street

department: Neuroscience

institute: Johns Hopkins University

description:
P11b_72
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 v2.1.0. SAM files were converted to BAM files using SAMtools v1.3.1. Transcript abundance estimation and normalization were performed using the Cuffquant and Cuffnorm tools, respectively, in Cufflinks v2.2.1. Downstream analyses were performed using Monocle2 in RStudio.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell Supplementary files format and content: Cuffnorm matrix containing annotations for each gene Supplementary files format and content: Cuffnorm matrix containing annotations for each sample
Supplementary files format and content: Some processed data files without data - they are empty files because the supplied reference annotation GTF file we used in Cufflinks to assemble the transcriptomes did not contain TSS/ CDS gene attributes. I

molecule: polyA RNA

source_name: starburst amacrine cell

extract_protocol:
Retinas from ChatCre/+; ROSA-LSL-TD-Tomato mice were isolated at P1, P4, P8, P11 and P16 in ice cold HBSS, and the retinal pigmented epithelium and inner limiting membranes were removed. Retinas were digested with papain, triturated slowly 15-20 time with a P1000 pipet tip, strained into a 50 mL conical tube, and pelleted for 3 minutes at 1.3k rpm. The pellet was gently resuspended and cells were washed three times in ice cold Hibernate A media lacking Ca2+, Mg2+, and phenol red, with pelleting between the washes. Care was taken to tap the tube gently to dislodge the pellet before adding media and resuspending the pellet, to prevent cell lysis and subsequent accumulation of DNA and cellular debris, which forms as a sticky gel-like substance in the supernatant. Washed and resuspended cells in ice cold Hibernate A were subjected to FACS to isolate single cells in cell lysis buffer before proceeding with Smart-seq2 mRNA sequencing as in Chevee et al., 2018.
A modified Smart-seq2 mRNA sequencing protocol was used to construct libraries, described in Chevee et al., 2018.

tag: tissue type

value: retina

tag: cell line

value: starburst amacrine cell

tag: genotype/strain

tag: age

value: Postnatal day 11


title: T-AQP4_02 [L49914_Track-90525]

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
RawExpressionCountTable.csv
TCR_data.csv

data_processing:
library strategy: Plate base Single cell RNA seq (SMARTseq2)
Fragments were aligned to the human reference genome hg38 with support of Ensembl 98 splice sites using the aligner gsnap (v2019-06-10).
Counts per gene and cell were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1)
T-cell receptor sequences were assembled per cell using TraCeR (v0.5)
Assembly: hg38
Supplementary files format and content: Counts per gene per cell, CSV
Supplementary files format and content: T-cell receptor sequences, CSV

source_name: Blood

growth_protocol: 2.5-5x10^7 PBMCs were plated in 2 ml RPMI-1640 medium (GIBCO), supplemented with 5% (v/v) human AB-serum (Sigma Aldrich, Schnelldorf, Germany) in 6-well cell culture plates.

extract_protocol:
CD154+ memory cells were isolated by MACS and further purified by FACS sorting on a FACS Aria Fusion (BD Bioscience, San Jose, CA, USA) based on dual expression of CD154 and CD69 and expression of CD45RO. Cells were directly sorted into skirted 96-well PCR plates which were equipped with 2 µl lysis buffer (nuclease-free water with 0.2% Triton-X 100 solution (Roche Diagnostics GmbH, Mannheim, Germany) with 4 U/µL RNase Inhibitor (New England Biolabs)) in advance. After FACS sorting plates were shortly centrifuged (30 sec, 200xg) and immediately frozen at -80°C until shipment.
Library preparation and sequencing was performed at the DRESDEN-concept Genome Center (DcGC, TU Dresden, Germany). The workflow was based on the previously described SMARTseq2 protocol 81. After thawing the samples, 2 ul of a primer mix was added (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription was performed at 42°C for 90 min after filling up to 10 ul with RT buffer mix for a final concentration of 1X superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using 2X Kapa HiFi HotStart Readymix (Roche) at a final 1X concentration and 0.1 uM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6X volume of hydrophobic Sera-Mag Beads (Cytvia: GE24152105050250,) and DNA was eluted in 12 ul nuclease free water. The cDNA quality and concentration of a few representative samples was determined with the Fragment Analyzer (Agilent). For library preparation, 2 µl amplified cDNA was tagmented in 1X Tagmentation Buffer using 0.8 µl bead-linked transposome (Illumina DNA Prep, (M) Tagmentation, Illumina) at 55°C for 15 min in a total volume of 4 µL. The reaction was stopped by adding 1 µl of 0.1 % SDS (37°C, 15 min). Magnetic beads were bound to a magnet, the supernatant was removed, beads were resuspended in 4 µl indexing PCR Mix containing 1x KAPA Hifi HotStart Ready Mix (Roche). After adding 700 nM unique dual indexing primers (i5 and i7) using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter), the reaction mixture was subjected to a PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min). After PCR, libraries are quantified with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium) and equimolarly pooled using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter GmbH). The pooled libraries were then purified with 0.9x volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6x and 0.9x volume of beads. Re-double size selection with 0.6x and 0.9x volume of beads was performed if needed.

treatment_protocol: PBMC were stimulated for 7 h in presence of 1 µg/ml CD40 pure antibody (Miltenyi Biotec, Bergisch Gladbach, Germany) with AQP4, Influenza A H1N1 (HA) and C.albicans MP65 peptide pools or PMA/Ionomycin

value: Blood

value: CD4 T cell

value: T cell

tag: treatment

value: AQP4 peptide pool


title: Psoriatic Skin Tissue Rep23


title: SAC, P11P5, OFF, rep146

description:
P11b_71
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Adjacent Normal Skin Tissue Rep23


title: resHif1aKO, hif1aKO 2, day 3 MI, snRNAseq


title: resHif1aKO, hif1aKO 1, day 3 MI, snRNAseq


title: T-AQP4_02 [L49915_Track-90439]


title: T-AQP4_02 [L49913_Track-90401]


title: SAC, P11P4, OFF, rep145

description:
P11b_70
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep22


title: Arg1DTR, DTR, day 3 MI, scRNAseq

value: monocyte, macrophage, DC


title: Arg1DTR, control, day 3 MI, scRNAseq


title: SAC, P11P3, ON, rep144

description:
P11b_69
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49911_Track-90491]


title: SAC, P11O9, ON, rep143

description:
P11b_68
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49912_Track-90529]


title: Psoriatic Skin Tissue Rep21


title: SAC, P11P7, OFF, rep148

description:
P11b_73
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: TYW2 timecourse Lane 4 MULTI

city: Palo Alto

first: Christopher

last: McGinnis

state: CA

address: Biomedical Innovations Building 4600, 240 Pasteur Drive

department: Pathology

institute: Stanford University

data_processing:
scRNA-seq library FASTQs were pre-processed using Cell Ranger version 6.0.0 (10x Genomics) and aligned to the mm-10-3.0.0 reference transcriptome.
MULTI-seq FASTQs were processed using deMULTIplex2 (Zhu, Conrad, and Gartner, Genome Biology, 2024)
Assembly: mm10
Supplementary files format and content: Cellranger output files: mRNA barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: deMULTIplex2 output files: MULTI-seq count table csv

source_name: Tumor

extract_protocol:
Primary tumors were surgically removed, dissociated, and cryopreserved with CELLBANNKER2. Cryopreserved samples were then thawed, 3-4 tumors from each background/timepoint were pooled, and pooled tumor cells were barcoded with  MULTI-seq lipid-modified oligonucleotides. Barcoded samples from each background/timepoint were then pooled into BSA-containing PBS prior to FACS isolation of CD45+ tumor immune cells.
Libraries were prepared according to manufacturers instructions (10x Genomics V3.1) with a separate MULTI-seq library prep workflow performed following cDNA amplification, as described previously (McGinnis, Patterson, et al., Nature Methods, 2019)

value: Tumor

tag: strain

tag: genotype

value: TYW2 KO and WT melanoma tumors

tag: tumor stage

value: Day 18 and 21


title: T-AQP4_02 [L49910_Track-90450]


title: SAC, P11O8, OFF, rep142

description:
P11b_67
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49909_Track-90388]


title: Adjacent Normal Skin Tissue Rep21


title: SAC, P11O7, OFF, rep141

description:
P11b_66
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: TYW2 timecourse Lane 2 MULTI


title: Psoriatic Skin Tissue Rep20


title: T-AQP4_02 [L49908_Track-90412]


title: TYW2 timecourse Lane 1 MULTI


title: Adjacent Normal Skin Tissue Rep20


title: SAC, P11O4, OFF, rep139

description:
P11b_64
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep19


title: TYW2 timecourse Lane 4


title: T-AQP4_02 [L49907_Track-90413]


title: T-AQP4_02 [L49906_Track-90452]


title: Adjacent Normal Skin Tissue Rep22


title: Adjacent Normal Skin Tissue Rep19


title: TYW2 timecourse Lane 3


title: T-AQP4_02 [L49903_Track-90393]


title: Psoriatic Skin Tissue Rep18


title: T-AQP4_02 [L49904_Track-90528]


title: TYW2 timecourse Lane 2


title: TYW2 timecourse Lane 1


title: SAC, P11O11, ON, rep136

description:
P11b_61
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: TYW2 timecourse Lane 3 MULTI


title: Adjacent Normal Skin Tissue Rep18


title: Wfdc15a_P25RST_KO3

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

country: Japan

institute: Yokohama City University

data_processing:
For gene expression analysis from fastq files, RNA-seq reads were quality-checked with FastQC (version 0.11.8, Babraham Bioinformatics), trimmed using Trim Galore! (version 0.6.6, Babraham Bioinformatics) and mapped with Hisat2 (version 2.1.0) on the mm10 mouse genome using default parameters. Read count was performed by using SeqMonk (version 1.48.1, Babraham Bioinformatics).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes log2-transformed rpm values for each sample.

source_name: Testis

extract_protocol:
Whole testes were collected from P25 mice. Tunica albuginea was removed and the whole testicular tissues were homogenized to isolate total RNA using Isogen (Nippon Gene) according to the manufacturer’s instructions. Round spermatids from P25 mice were isolated by FACS with Vybrant DyeCycle Green (ThermoScientific) and lysed in RLT plus buffer (Qiagen) for RNA-seq library preparation.
About 2 ng of the purified total RNA from whole testis or 100-200 round spermatid samples were used for RNA-seq library preparation using the Smart-seq2 protocol.

value: Testis

value: Round spermatid

value: KO


title: Psoriatic Skin Tissue Rep17

value: Lesional Psoriatic skin


title: T-AQP4_02 [L49902_Track-90501]


title: SAC, P11O10, OFF, rep135

description:
P11b_60
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49901_Track-90427]


title: SAC, P11N8, ON, rep134

description:
P11b_59
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49900_Track-90443]


title: SAC, P11O6, ON, rep140

description:
P11b_65
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Adjacent Normal Skin Tissue Rep17

value: Adjacent normal skin


title: Wfdc15a_P25RST_KO2


title: SAC, P11N7, ON, rep133

description:
P11b_58
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Wfdc15a_P25RST_KO1


title: SAC, P11O3, OFF, rep138

description:
P11b_63
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49899_Track-90386]


title: Wfdc15a_P25RST_Het2

value: Hetero


title: SAC, P11N6, OFF, rep132

description:
P11b_57
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: T-AQP4_02 [L49898_Track-90395]


title: Psoriatic Skin Tissue Rep15


title: SAC, P11N4, ON, rep130

description:
P11b_55
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell


title: Wfdc15a_P25RST_WT2

value: WT


title: T-AQP4_02 [L49896_Track-90530]

description:
RawExpressionCountTable.csv
TCR_data.csv

value: Blood


title: Adjacent Normal Skin Tissue Rep15


title: SAC, P11N3, OFF, rep129

description:
P11b_54
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: Postnatal day 11


title: Wfdc15a_P25RST_WT1


title: SAC, P11N2, ON, rep128

description:
P11b_53
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep14


title: T-AQP4_02 [L49895_Track-90444]

value: CD4 T cell

value: T cell


title: Adjacent Normal Skin Tissue Rep14


title: Wfdc15a_P25testis_KO3


title: T-AQP4_02 [L49894_Track-90411]

value: AQP4 peptide pool


title: Wfdc15a_P25testis_KO2


title: SAC, P11N11, OFF, rep127

description:
P11b_52
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep16


title: Psoriatic Skin Tissue Rep13


title: T-AQP4_02 [L49892_Track-90391]


title: SAC, P11N10, ON, rep126

description:
P11b_51
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Adjacent Normal Skin Tissue Rep13


title: T-AQP4_02 [L49891_Track-90423]


title: Wfdc15a_P25testis_KO1


title: Adjacent Normal Skin Tissue Rep16


title: Wfdc15a_P25testis_Het1


title: SAC, P11N5, OFF, rep131

description:
P11b_56
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11M9, OFF, rep125

description:
P11b_50
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep12


title: T-AQP4_02 [L49897_Track-90365]


title: Wfdc15a_P25RST_Het1


title: Wfdc15a_P25testis_WT2


title: Adjacent Normal Skin Tissue Rep12


title: T-AQP4_02 [L49889_Track-90430]


title: SAC, P11M8, OFF, rep124

description:
P11b_49
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep11


title: T-AQP4_02 [L49888_Track-90480]


title: Wfdc15a_P25testis_WT1


title: Adjacent Normal Skin Tissue Rep11


title: Wfdc15a testis, KO2, rep06

data_processing:
For gene expression analysis from fastq files, RNA-seq reads were quality-checked with FastQC (version 0.11.8, Babraham Bioinformatics), trimmed using Trim Galore! (version 0.6.6, Babraham Bioinformatics) and mapped with Hisat2114 (version 2.1.0) on the mm10 mouse genome using default parameters. Read count was performed by using SeqMonk (version 1.48.1, Babraham Bioinformatics).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes log2-transformed rpm values for each sample.

source_name: Adult whole testis

extract_protocol:
Whole testes from adult mice were collected at 15 weeks of age. Tunica albuginea was removed and the whole testicular tissues were homogenized to isolate total RNA using Isogen (Nippon Gene) according to the manufacturer’s instructions.
About 2 ng of the purified total RNA was used for RNA-seq library preparation using the Smart-seq2 protocol with 11 cycles of PCR.

value: Adult whole testis


title: Wfdc15a testis, KO2, rep05


title: SAC, P11M7, OFF, rep123

description:
P11b_48
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11M5, OFF, rep121

description:
P11b_46
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49887_Track-90410]


title: T-AQP4_02 [L49886_Track-90415]


title: Psoriatic Skin Tissue Rep10


title: Adjacent Normal Skin Tissue Rep10


title: Wfdc15a testis, KO1, rep03


title: SAC, P11M4, OFF, rep120

description:
P11b_45
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49884_Track-90406]


title: SAC, P11M3, OFF, rep119

description:
P11b_44
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49890_Track-90455]


title: Adjacent Normal Skin Tissue Rep9


title: T-AQP4_02 [L49885_Track-90392]


title: Psoriatic Skin Tissue Rep9


title: T-AQP4_02 [L49883_Track-90373]


title: SAC, P11M1, OFF, rep117

description:
P11b_42
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Wfdc15a testis, KO1, rep02


title: SAC, P11O2, OFF, rep137

description:
P11b_62
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Wfdc15a testis, KO1, rep01


title: SAC, P11M6, ON, rep122

description:
P11b_47
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep8


title: T-AQP4_02 [L49882_Track-90460]


title: SAC, P11M12, OFF, rep116

description:
P11b_41
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Wfdc15a testis, Het2, rep04


title: Adjacent Normal Skin Tissue Rep8


title: Wfdc15a testis, Het2, rep03


title: SAC, P11M11, OFF, rep115

description:
P11b_40
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep7


title: T-AQP4_02 [L49880_Track-90433]

description:
RawExpressionCountTable.csv
TCR_data.csv


title: Wfdc15a testis, Het2, rep02


title: T-AQP4_02 [L49879_Track-90493]


title: SAC, P11M2, ON, rep118

description:
P11b_43
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11M10, ON, rep114

description:
P11b_39
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Adjacent Normal Skin Tissue Rep7


title: Wfdc15a testis, KO2, rep04


title: T-AQP4_02 [L49878_Track-90361]


title: SAC, P11L8, OFF, rep112

description:
P11b_37
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Wfdc15a testis, WT2, rep03


title: Adjacent Normal Skin Tissue Rep6


title: Psoriatic Skin Tissue Rep6


title: SAC, P11L7, OFF, rep111

description:
P11b_36
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Wfdc15a testis, Het1, rep01


title: Wfdc15a testis, WT2, rep02


title: Wfdc15a testis, WT2, rep01


title: SAC, P11L6, OFF, rep110

description:
P11b_35
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49876_Track-90490]


title: SAC, P11L5, ON, rep109

description:
P11b_34
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11L9, OFF, rep113

description:
P11b_38
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep4


title: SAC, P11L4, OFF, rep108

description:
P11b_33
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep5


title: Adjacent Normal Skin Tissue Rep4


title: Arg1ZsGr, Control, ZsGr+, day5 HTX, scRNAseq

description: 10X Genomics

data_processing:
For monocytes, macrophages, and dendritic cells from macHif1a KO and control mice: Sequencing reads were aligned to the GRcm38 transcriptome using CellRanger (v3.1.0) from 10X Genomics. For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Arg1ZsGr mice 2 and 30 days after myocardial infarction: Sequencing reads were aligned to the mm10-2020-A transcriptome using CellRanger (v7.1.0) For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Control>ZsGr and Hif1a>ZsGr mice 5 days after syngeneic heart transplant: Sequencing reads were aligned to the mm10-2020-A transcriptome using CellRanger (v7.1.0).
Assembly: mm10
Supplementary files format and content: tab seperated values files and matrix files

source_name: Heart

extract_protocol:
Hearts were perfused with PBS, weighed, minced, and digested for 45 minutes at 37⁰C in DMEM (Gibco 11965-084) containing 4500 U/ml Collagenase IV (Millipore Sigma C5138), 2400 U/ml Hyaluronidase I (Millipore Sigma H3506), and 6000 U/ml DNAse I (Millipore Sigma D4527). Enzymes were deactivated with HBSS containing 2% FBS and 0.2% BSA and filtered through 40-micron strainers. Cells were incubated with ACK lysis buffer (Gibco A10492-01) for 5 minutes at room temperature. Cells were washed with DMEM and resuspended in 100 µl of FACS buffer (PBS containing 2% FBS and 2mM EDTA). Cells were incubated in a 1:200 dilution of fluorescence conjugated monoclonal antibodies for 30 minutes at 4⁰C. Samples were washed in FACS buffer and resuspended in a final volume of 250 µl FACS buffer. Flow cytometry and sorting was performed using a BD FACS melody. For sorting of monocytes, macrophages, and dendritic cells in macHif1aKO mice for single cell RNA sequencing, antibodies used were: CD45 PerCP/Cy5.5 (BioLegend 103132), Ly6g FITC (BioLegend 127606), Ly6c APC (BioLegend 128016), DAPI (BD Pharmingen 564907), and CD64 PE/Cy7 (BioLegend 139313). For sorting of monocytes, macrophages, and dendrtic cells in Arg1ZsGr, antibodies used were: CD45 PerCP/Cy5.5(BioLegend 103132), CD11b BV421 (BioLegend 101235), Ly6g APC/Cy7 (BioLegend 127623), Ly6c BV510 (BioLegend 128033), CD64 PE/Cy7 (BioLegend 139313). Endogenous ZsGreen signal was used to sort ZsGr- and ZsGr+ cells.
For monocytes, macrophages, and dendritic cells from macHif1a KO and control mice: Single cell RNA sequencing libraries were generated using the 10X Genomics 5’v1 platform.  For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Arg1ZsGr mice 2 and 30 days after myocardial infarction: Single cell RNA sequencing libraries were generated using the 10X Genomics 5’v1 platform. For ZsGr- and ZsGr+ monocytes, macrophages, and dendritic cells from Control>ZsGr and Hif1a>ZsGr mice 5 days after syngeneic heart transplant: Libraries were generated using the 10x 3’v3.1 platform.

value: Heart

value: monocyte, macrophage, DC


title: Adjacent Normal Skin Tissue Rep5


title: T-AQP4_02 [L49872_Track-90466]


title: SAC, P11L3, OFF, rep107

description:
P11b_32
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Psoriatic Skin Tissue Rep3


title: SAC, P11L2, OFF, rep106

description:
P11b_31
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49871_Track-90375]


title: Arg1ZsGr, Hif1aKO, ZsGr+, day5 HTX, scRNAseq

description: 10X Genomics


title: T-AQP4_02 [L49877_Track-90477]


title: Arg1ZsGr, Hif1aKO, ZsGr-, day5 HTX, scRNAseq

description: 10X Genomics


title: Adjacent Normal Skin Tissue Rep3


title: T-AQP4_02 [L49870_Track-90508]


title: SAC, P11L1, OFF, rep105

description:
P11b_30
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49875_Track-90486]


title: Arg1ZsGr, ZsGr-, day30 MI, scRNAseq

description: 10X Genomics


title: T-AQP4_02 [L49868_Track-90518]


title: Psoriatic Skin Tissue Rep2


title: T-AQP4_02 [L49874_Track-90498]


title: Adjacent Normal Skin Tissue Rep2


title: Arg1ZsGr, Control, ZsGr-, day5 HTX, scRNAseq

description: 10X Genomics


title: T-AQP4_02 [L49867_Track-90499]


title: Arg1ZsGr, ZsGr-, day2 MI, scRNAseq

description: 10X Genomics


title: Arg1ZsGr, ZsGr+, day30 MI, scRNAseq

description: 10X Genomics


title: SAC, P11L11, OFF, rep103

description:
P11b_28
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49873_Track-90372]


title: Psoriatic Skin Tissue Rep1


title: SAC, P11L12, OFF, rep104

description:
P11b_29
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49866_Track-90544]


title: SAC, P11L10, OFF, rep102

description:
P11b_27
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Arg1ZsGr, ZsGr+, day2 MI, scRNAseq

description: 10X Genomics


title: T-AQP4_02 [L49865_Track-90479]


title: SAC, P11K9, OFF, rep101

description:
P11b_26
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49864_Track-90404]


title: Adjacent Normal Skin Tissue Rep1


title: macHif1aKO, hif1aKO, day5 MI, scRNAseq

description: 10X Genomics


title: Sample 14_Input7, WT

city: San Francisco

first: Gabriel

last: McKinsey

address: 1550 4th St. Room 545E

department: Pediatrics

institute: University of California San Francisco

library_source: genomic

data_processing:
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were aligned to mm10 mouse genome using bowtie2, subsequently filtered using sambamba and indexed using samtools.
Significant peaks were determined using MACS2. Master peakfile was created using bedtools and counts per significant peak were extracted from sorted bam files.
Extracted counts were analysed using DESeq2.
Assembly: mm10
Supplementary files format and content: Bigwig file format, which was created from sorted BAM files and normalization against mouse genome length using deeptools.

molecule: genomic DNA

source_name: Microglia cells

extract_protocol:
Anti H3K9ac ChIP-seq were performed using using the iDeal ChIP-seq kit for Histones (Diagenode, Cat.#C01010059) and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, Cat.#E7103S). Briefly, microglia were sorted from Itgb8fl/fl;Emx1Cre mouse brain cortex and were pooled from different individuals with same genotype to achieve > 200 k cells per replicates. The microglia were fixed with 1% formaldehyde at 20℃ for 8 min then quenched with 0.125 M Glycine. The nuclei were isolated and sonicated using a Diagenode disruptor for 20 cycles (30 seconds “ON”, 30 seconds “OFF”, high power). The chromatin fragments were enriched using 2 ul of anti-H3K9ac antibody (Millipore, 07-352) per reaction.
The ChIPed DNA was purified and processed for library preparation. The ChIP DNA libraries were size selected using SPRIselect beads (Beckman Coulter, Cat.#B23317) and quantified using Agilent 2100 Bioanalyzer and Qubit (Invitrogen, Cat.#Q33238). The pooled libraries were then sent to Azenta Life Sciences for paired-end sequencing (2x150 bp) on Illumina HiSeq platform.

value: Microglia cells


title: Sample 13_Input6, WT


title: SAC, P11K8, ON, rep100

description:
P11b_25
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49863_Track-90504]

description:
RawExpressionCountTable.csv
TCR_data.csv


title: SAC, P11K7, OFF, rep99

description:
P11b_24
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 12_Input5, ITGB8KO


title: macHif1aKO, control, day5 MI, scRNAseq

description: 10X Genomics


title: NC

city: Nanning

first: jinglin

last: mi

address: shuangyong road

country: China

institute: the first affiliated hospital of guangxi medical university

data_processing:
First，a tRNA library was adapted from the tRNAScan-SE library by appending CCA to tRNAs from the genomic tRNA database (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/). Isodecoders with identical scores were consolidated for ease of identity assignment, decreasing the number of reference genes and pseudogenes. Then, raw reads were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3). Then, trimmed reads from all samples were aligned using bowtie2 software to the aforementioned tRNA library with sensitive options. Mapped reads on each tRNA were counted using samtools. Normalized IP and Input raw expression data by TPM method, then calculate IP/Input as tRNA methylation level base on normalized results. t-test was used to detect statistical differences in methylation level of tRNA.
Assembly: mm10
Supplementary files format and content: Methylated_tRNAs.xlsx
Library strategy: m7G-tRNA MeRIP-Seq

source_name: TC-1 Cell

extract_protocol:
Cell supernatants were centrifuged at 10,000 ×g for 45 min at 4 °C to remove the larger vesicles. The supernatants were extracted and filtered through a 0.45 µm filter. Then, the samples were centrifuged again at 10,000 ×g and at 4 °C for 70 min and resuspended in PBS.
The m7G-tRNA MeRIP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Briefly, total RNA was purified for small RNA fraction ( <200nt) with the MirVana Isolation Kit (ThermoFisher). The anti-m7G MeRIP was performed on the small RNA with GenSeq® m7G MeRIP Kit (GenSeq, Inc.) by following the manufacturer’s instructions except omit the fragmentation procedure. Then, the MeRIP/Input small RNAs were demethylated with AlkB enzyme mix for 100 min at 37°C. The demethylated small RNA was used for library construction with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. All libraries were size-selected for tRNA fraction before sequencing and then sequenced in a NovaSeq platform (Illumina, Inc., San Diego, CA, USA).

value: TC-1 Cell

value: mouse lung epithelial cells


title: IR


title: SAC, P11K6, ON, rep98

description:
P11b_23
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 11_Input4, ITGB8KO


title: T-AQP4_02 [L49862_Track-90360]


title: T-AQP4_02 [L49861_Track-90380]


title: SAC, P11K5, OFF, rep97

description:
P11b_22
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49860_Track-90516]


title: NC [Ribo-seq]

library_source: other

data_processing:
Raw data were obtained after sequencing on an Illumina NovaSeq 6000 sequencer. Raw data quality control was first performed using Q30 values. Using cutadapt software (v1.9.3) to remove splices, remove low-quality reads and obtain high-quality clean reads, use bowtie to match the spliced data to rRNA sequences, and obtain clean reads that are not matched to rRNA. use Tophat2 software to match clean reads to the reference genome. The clean reads were then aligned to the reference genome using Tophat2 software. Then, HTSeq software (v0.9.1) was used to obtain the raw count numbers, and edgeR or DESeq2 was used to normalize and calculate the fold change and p-value between the two groups of samples to screen for differentially expressed genes, and edgeR was used by default for differential analysis. GO functional analysis and KEGG pathway analysis were performed using differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Gene Expression Profiling.xlsx
Library strategy: Ribo-seq

molecule: other

source_name: mouse lung fibroblasts

extract_protocol: Ribosome profilng service was provided by CloudSeq Inc.(Shanghai, China) by following the manual for the GenSeq® Ribo Profile Kit (GenSeq,Inc.). Briefly, the cycloheximide-treated cells were lysed with lysis buffer and digested with nuclease. Digested samples were purified with size exclusion chromatography to obtain ribosome footprints. Ribosome protected fragments were size-selected with polyacrylamide gel electrophoresis (PAGE), and subjected to rRNA removal. Then, purified RNA fragments were end-repaired, ligated with 3’ adapters and reverse-transcribed to cDNA. The cDNA was PAGE gel purified, circularized, and amplified by PCR. The resulting libraries were purifed and sequenced in a NovaSeq platform (Illumina).

value: mouse lung fibroblasts


title: Sample 10_Input3, ITGB8KO


title: SAC, P11K4, ON, rep96

description:
P11b_21
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49859_Track-90462]


title: Sample 9_Input2, WT


title: SAC, P11K3, ON, rep95

description:
P11b_20
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 8_Input1, WT


title: IR [Ribo-Seq]


title: NC-3

data_processing:
The first step is to construct a database of tRNAs. tRNA data was downloaded from the GtRNAdb website. The tRNA data were downloaded from the GtRNAdb website, and representative tRNAs were selected from these tRNAs based on anticodon and score. three bases of CCA were added to the 3' end of their sequences. After sequencing by Illumina sequencer, image analysis, and base identification, the raw reads were harvested after QC. Q30 was first used for QC. The original reads were de-joined using cutadapt software (v1.9.3), and low quality reads were removed, and reads with length >=15 nt were retained to obtain the trimmed reads. The trimmed reads of each sample were then compared to a pre-prepared tRNA database using bowtie2 software (v2.2.4). The number of reads matched to each tRNA was counted as the raw expression of the tRNA using samtools (v1.3.1), and the data were normalized and screened for differential expression using edgeR software.
Assembly: mm10
Supplementary files format and content: tRNA Expression Profiling.xlsx
Library strategy: tRNA-seq

extract_protocol:
Cell supernatants were centrifuged at 10,000 ×g for 45 min at 4 °C to remove the larger vesicles. The supernatants were extracted and filtered through a 0.45 µm filter. Then, the samples were centrifuged again at 10,000 ×g and at 4 °C for 70 min and resuspended in PBS.
tRNA sequencing service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was size-selected for small RNA fraction (<200nt) with the MirVana Isolation Kit (ThermoFisher). The enriched small RNAs were demethylated with AlkB enzyme mix for 100 min at 37°C. The demethylated small RNA was used for library construction with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. All libraries were size-selected for tRNA fraction before sequencing and then sequenced in a NovaSeq platform (Illumina, Inc., San Diego, CA, USA).


title: NC-2


title: T-AQP4_02 [L49858_Track-90467]


title: Sample 7_H3K9ac7, WT


title: T-AQP4_02 [L49856_Track-90533]


title: SAC, P11K1, OFF, rep93

description:
P11b_18
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 6_H3K9ac6, WT


title: SAC, P11K2, OFF, rep94

description:
P11b_19
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49855_Track-90422]


title: SAC, P11K12, OFF, rep92

description:
P11b_17
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: IR-3


title: Sample 5_H3K9ac5, ITGB8KO


title: T-AQP4_02 [L49854_Track-90484]


title: SAC, P11K11, OFF, rep91

description:
P11b_16
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 4_H3K9ac4, ITGB8KO


title: T-AQP4_02 [L49853_Track-90509]


title: IR-2


title: SAC, P11J9, ON, rep90

description:
P11b_15
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: IR-1


title: SAC, P11J8, OFF, rep89

description:
P11b_14
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 3_H3K9ac3, ITGB8KO


title: T-AQP4_02 [L49852_Track-90459]


title: Sample 2_H3K9ac2, WT


title: T-AQP4_02 [L49851_Track-90426]


title: SAC, P11J7, ON, rep88

description:
P11b_13
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 1_H3K9ac1, WT


title: unknown, P11J6, filtered out, rep87

description:
P11b_12
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_02 [L49850_Track-90369]


title: NC-1


title: Sample 14_ATA14, ITGB8KO

extract_protocol:
ATAC-seq were carried out following the Omni-ATAC-seq protocol (Corces et al., 2017). Briefly, 50 k cortical microglia (CD11b+Fcrls+ Ly-6C–) from Itgb8fl/fl;Emx1Cre mouse brains cells were sorted into Eppendorf tubes by a BD FACSAriaTM II (BD Bioscience). After being washed with cold dPBS, microglia were permeabilized with ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and washed with ATAC-RSB buffer with 0.1% Tween-20.
The isolated microglial nuclei were then incubated in transposition mixture at 37℃ for 60 min. The DNA were purified using a Zymo DNA clean and concentrator-5 kit (Zymo research, Cat.#D4014) and amplified using NEBNext® High-Fidelity 2x PCR Master Mix (NEB, Cat. #M0541s) for 9 cycles. The ATAC libraries were size selected using SPRIselect beads (Beckman Coulter, Cat.#B23317) and quantified using Agilent 2100 Bioanalyzer and Qubit (Invitrogen, Cat.#Q33238). The pooled libraries were then sent to Azenta Life Sciences for paired-end sequencing (2x150 bp) on Illumina HiSeq platform.


title: T-AQP4_02 [L49849_Track-90437]


title: unknown, P11J5, filtered out, rep86

description:
P11b_11
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: RNA-seq of activated murine CD8+ T cells:treated with blebbistatin 2

city: China

first: 达瀚

last: 温

address: Dongdan Santiao No. 5

institute: Medicine Basic sciences, Peking Union Medical College

data_processing:
RNA sequencing data was processed using HISAT2 v2.1.0 and StringTie v1.3.4.
Remove adapter-contaminated reads, low-quality reads, and reads containing more than 5% N
Contrast ratio analysis using HISAT2
Differentially expressed genes was calculated using DESeq2 v1.22.2 with a threshold of log2|foldchange| >= 2 & padj < 0.05.
Functional enrichment analysis was conducted by the function ‘enrichGO’ from clusterProfiler v3.18.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Spleen

extract_protocol:
Total RNA was isolated from murine T cells treated with Veh., Ble (2 µM) for 24 hr by using TRIzol-chloroform method.
Libraries for RNA sequencing were constructed using the Illumina TruSeq RNA Sample Prep kit v2 and sequenced on an Illumina NovaSeq 6000 platform

value: Spleen

tag: agent

value: blebbistatin


title: Sample 13_ATA13, ITGB8KO


title: SAC, P11J4, OFF, rep85

description:
P11b_10
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: Sample 12_ATA12, WT


title: RNA-seq of activated murine CD8+ T cells:treated with blebbistatin 1


title: T-AQP4_02 [L49847_Track-90366]


title: RNA-seq of activated murine CD8+ T cells:treated with Vehicle 3

value: Vehicle


title: T-AQP4_02 [L49848_Track-90539]


title: SAC, P11J2, OFF, rep83

description:
P11b_8
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell


title: RNA-seq of activated murine CD8+ T cells:treated with Vehicle 2


title: Sample 10_ATA10, WT

value: WT


title: T-AQP4_02 [L49846_Track-90488]

description:
RawExpressionCountTable.csv
TCR_data.csv

value: Blood


title: Sample 11_ATA11, ITGB8KO


title: SAC, P11J3, OFF, rep84

description:
P11b_9
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: Postnatal day 11


title: T-AQP4_01 [L49844_Track-90424]

value: CD4 T cell

value: T cell


title: NC-4

data_processing:
Raw data were obtained after sequencing on an Illumina NovaSeq 6000 sequencer. The raw data were first QC'd using Q30 values. The cutadapt software (v1.9.3) was used to remove splices and low quality reads to obtain high quality clean reads. hisat2 was used to compare the clean reads to the reference genome, and then HTSeq (v0.9.1) was used to obtain the raw counts, which were normalized by edgeR and the p-value and the fold change between the two groups were calculated to screen for differentially expressed genes. Then, HTSeq software (v0.9.1) was used to obtain the raw counts, and edgeR was used to normalize and calculate the fold change and p-value between the two groups of samples to screen for differentially expressed genes. GO functional analysis and KEGG pathway analysis were performed using differentially expressed mRNA.
Assembly: mm10
Supplementary files format and content: mRNA Gene Expression Profiling.xlsx

extract_protocol:
Cell supernatants were centrifuged at 10,000 ×g for 45 min at 4 °C to remove the larger vesicles. The supernatants were extracted and filtered through a 0.45 µm filter. Then, the samples were centrifuged again at 10,000 ×g and at 4 °C for 70 min and resuspended in PBS.
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.


title: RNA-seq of activated murine CD8+ T cells:treated with Vehicle 1


title: SAC, P11J1, OFF, rep82

description:
P11b_7
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 9_ATA9, ITGB8KO


title: T-AQP4_01 [L49843_Track-90371]

value: AQP4 peptide pool


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse midbrain, biological replicate 1

city: Cleveland

first: Ming

last: Hu

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

data_processing:
To facilitate comparison across different samples, only R1 reads was used and was trimed to 50bp for downstream analysis.
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeaks (except for input samples)

source_name: midbrain

extract_protocol:
~30 mg fixed tissues were thawed on ice and the nuclei preparation was performed using truChIP® Chromatin Shearing Kit (Covaris) following the manufacturer’s instruction. The lysed nuclei were sheared using Covaris M220 with following setting: Setting: power, 75 W; duty factor, 8%; cycle per burst, 200; time, 12 min; temp, 7 °C. The sheared chromatins were cleared by centrifugation at 15,000×g for 12 min. The supernatant was collected and incubated with M-280 sheep anti-rabbit magnetic beads (Thermo Fisher, 11203D) for 3 hours at 4°C with slow rotation for preclearing. ~5% of precleared cell lysate was saved as input control after the incubation was done. The rest of precleared lysate was mixed M-280 sheep anti-rabbit magnetic beads that coupled with 0.9 μg of CTCF antibody (3418, Cell Signaling) and rotate at 4°C for 16 hours. On the next day, the beads were collected using magnetic stand and the supernatant was discarded. The beads are then washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. Washed beads were treated with 10 μg Rnase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 hours at 37°C, followed by reverse crosslinking in the presence of proteinase K (20 μg) overnight at 65°C. After reverse crosslinking the DNA was purified and quantified. The input control DNA was reverse crosslinked and purified in the same way as ChIPed DNA as described above.
Library preparation was performed using QIAseq Ultralow Input Library Kit (Qiagen) starting from 10–100 ng ChIPed DNA or input DNA. After PCR the amplified libraries were purified with SPRI Beads to extract fragments between 200-600bp for sequencing.

value: midbrain

tag: developmental stage

value: embryonic 12.5 day

tag: chip antibody


title: SAC, P11J12, OFF, rep81

description:
P11b_6
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: RNA-seq of activated murine CD8+ T cells:treated with blebbistatin 3


title: SAC, P11J11, ON, rep80

description:
P11b_5
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 7_ATA7, ITGB8KO

value: Microglia cells


title: KO LPS4_H3_121

city: Singapore

first: Anna

last: Barron

address: Clinical Science Building,11 Mandalay Road

country: Singapore

institute: Lee Kong Chian Sch. Of Medicine

data_processing:
Sequence reads were QC checked using MultiQC 1.13 before pseudoaligning to Salmon 1.9.0 using the Mus musculus genome Ensembl release 99 reference
Transcript were then annotated using TxiMeta 1.16.0 before importing into DESEQ2 for differential expression analysis
Read count extraction and normalization were performed using DESEQ 2 version 1.36.0 on R 4.2 environment
Assembly: Mus musculus genome Ensembl release 99
Supplementary files format and content: comma-delimited (.csv) files include raw count values for each sample

source_name: hippocampus

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra library preparation kit by Novogene AIT

value: hippocampus

value: TSPOKO

value: injected with LPS

tag: time

value: 3 month old


title: T-AQP4_01 [L49841_Track-90435]


title: KO LPS3_C6_246


title: SAC, P11J10, OFF, rep79

description:
P11b_4
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 6_ATA6, WT


title: T-AQP4_01 [L49840_Track-90524]


title: SAC, P11I9, ON, rep78

description:
P11b_3
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: KO LPS1_B1_1


title: T-AQP4_01 [L49838_Track-90507]


title: Sample 4_ATA4, ITGB8KO


title: SAC, P11I6, OFF, rep76

description:
P11b_1
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 3_ATA3, WT


title: KO PBS4_B9_4_9

value: injected with PBS


title: Sample 5_ATA5, ITGB8KO


title: T-AQP4_01 [L49837_Track-90514]


title: unknown, P11I2, filtered out, rep75

description:
P11b_0
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: Sample 2_ATA2, WT


title: Sample 8_ATA8, WT


title: T-AQP4_01 [L49835_Track-90419]


title: SAC, P11H7, OFF, rep74

description:
P11a_73
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49842_Track-90502]


title: KO PBS2_F3 28_8


title: T-AQP4_01 [L49834_Track-90481]


title: SAC, P11H6, ON, rep73

description:
P11a_72
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Sample 1_ATA1, WT


title: T-AQP4_01 [L49832_Track-90531]


title: H3K4me3 PLAC-seq on postnatal 0 day mouse forebrain, biological replicate 2

data_processing:
The PLAC-seq data was processed using MAPS pipeline (https://github.com/ijuric/MAPS). In brief, the raw sequencing reads were mapped using BWA-MEM to mm10 reference genome in single-end mode for each of the two ends separately. The independently mapped ends were then paired-up and the read pairs were kept if they satisfy certain criteria. Then “samtools rmdup” is used to remove PCR duplicates.     We then partitioned the genome into 10Kb bins, and counted the number of paired-end reads in each 10Kb bin pair. Next, we defined the “AND”, “XOR” and “NOT” sets as 10Kb bin pairs where both two ends, only one end, and neither end contain replicated H3K4me3 ChIP-seq peaks from the corresponding tissue, respectively. We only kept the bin pairs in “AND” and “XOR” sets with >=1 counts for the downstream analysis of interaction calling. We assumed that the counts in the “AND” and “XOR” sets follow the positive Poisson distribution, and fitted a positive Poisson regression to adjust for systematic biases from effective fragment size, GC content, mappability, ChIP enrichment level (measured by the number of short-range [<1Kb] reads within each 10Kb bin), and 1D genomic distance. Next, we defined the normalized contact frequency as the ratio between the observed contact frequency and the expected contact frequency obtained from the positive Poisson regression. Finally, we identified long-range significant chromatin interactions at 10Kb resolution in autosomal chromosomes between 1D genomic distance range of 20Kb ~ 1Mb, such that these 10Kb bin pairs satisfied: (1) FDR<1% and (2) normalized contact frequency >=2. The significant interactions in the “AND” set are referred as “Promoter-to-Promoter” interactions and the ones in the “XOR” set are referred as “Promoter-to-Non-promoter” interactions.    The PLAC-seq data from the two biological replicates were combined by summing up the read counts in 10Kb bin pairs in the “AND” and “XOR” sets. To account for the variable sequencing depths, we further down-sampled above combined data. Specifically, for each of 19 autosomal chromosomes, we counted the total number of paired-end reads in the “AND” and “XOR” sets across 12 tissues. We identified the tissue with the minimal number of reads, and randomly down-sampled the paired-end reads in the “AND” and “XOR” sets in the remaining 11 tissues to match that minimal number. After such down-sampling procedure, we ensured that for each chromosome, the total number of paired-end reads in the “AND” and “XOR” sets are the same across 12 tissues. MAPS was applied to the combined, down-sampled data of each tissue as described above to identify long-range interactions.    For visualization, the deduped, valid read pairs were used to generate the raw contact matrix (without normalization) in the .hic format using Juicer.
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.     Peaks were called using MACS2 with regular peak calling at P threshold of 0.01. Such relaxed peak sets were generated for each biological/technical replicate, and also for the pooled replicates. Peaks from the pooled replicate set were defined as the replicated peak set if they overlapped (at least 1 bp) the peaks from both biological/technical replicates.
“combined_downsampled.hic” files were generated via Juicebox after combining the two biological replicates from the same tissue and further down-sampled to make all 12 tissues have the same number of usable reads.   “combined_downsampled_MAPS_call.bedpe” files were the long-range interactions called using combined, down-sampled datasets of each tissue.  “rep1/2_MAPS_call.bedpe” files were the long-range interactions called from each biological replicate.  A detailed description for each column in “MAPS_call.bedpe” files can be found at https://github.com/ijuric/MAPS.
Assembly: mm10
Library strategy: PLAC-Seq

source_name: forebrain

extract_protocol:
In brief, 30-50mg tissues were dissociated, lysed and then digested 2 hours at 37oC using 100 U of MboI followed by biotin fill-in and proximity ligation at room temperature for 4 hours. Then the nuclei were further sonicated and immunoprecipitated against the antibodies. After immunoprecipitation, reverse crosslink was performed overnight at 65 oC after adding proteinase K to extract DNA.
DNA fragments containing ligation junctions were enriched with streptavidin beads followed by on-beads end repair, A-tail adding, adapter ligation and PCR amplification.

value: forebrain

value: postnatal 0 day

value: H3K4me3 (Millipore, 04-745)


title: SAC, P11H5, ON, rep72

description:
P11a_71
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell


title: KO LPS2_B1_2_0


title: T-AQP4_01 [L49839_Track-90357]

value: Blood


title: IR-4

value: mouse lung fibroblasts


title: WT LPS4_B9_3

value: WT


title: H3K4me3 PLAC-seq on postnatal 0 day mouse forebrain, biological replicate 1


title: T-AQP4_01 [L49831_Track-90431]

value: CD4 T cell

value: T cell

value: AQP4 peptide pool


title: SAC, P11I7, OFF, rep77

description:
P11b_2
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: Postnatal day 11


title: H3K4me3 PLAC-seq on embryonic 16.5 day mouse forebrain, biological replicate 2

value: embryonic 16.5 day


title: WT LPS3_B9_2

value: hippocampus


title: KO PBS3_F9_PBSKO

value: TSPOKO


title: WT LPS2_B9_1

value: injected with LPS

value: 3 month old


title: SAC, P11H4, OFF, rep71

description:
P11a_70
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: H3K4me3 PLAC-seq on embryonic 16.5 day mouse forebrain, biological replicate 1

value: forebrain


title: SAC, P11H10, OFF, rep69

description:
P11a_68
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49830_Track-90382]


title: WT LPS1_A9_LPS_1


title: T-AQP4_01 [L49829_Track-90377]


title: SAC, P11H11, OFF, rep70

description:
P11a_69
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: H3K4me3 PLAC-seq on embryonic 14.5 day mouse forebrain, biological replicate 2

value: embryonic 14.5 day


title: SAC, P11G9, OFF, rep68

description:
P11a_67
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: KO PBS1_E8_2PBSY

value: injected with PBS


title: H3K4me3 PLAC-seq on embryonic 14.5 day mouse forebrain, biological replicate 1

value: H3K4me3 (Millipore, 04-745)


title: WT PBS4_A9_1


title: T-AQP4_01 [L49827_Track-90363]

description:
RawExpressionCountTable.csv
TCR_data.csv

value: Blood


title: SAC, P11G8, OFF, rep67

description:
P11a_66
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell


title: WT PBS3_A10_5

value: WT


title: H3K4me3 PLAC-seq on embryonic 13.5 day mouse forebrain, biological replicate 2

value: embryonic 13.5 day


title: SAC, P11G7, OFF, rep66

description:
P11a_65
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49826_Track-90378]

value: CD4 T cell

value: T cell


title: WT PBS2_A10_2


title: H3K4me3 PLAC-seq on embryonic 13.5 day mouse forebrain, biological replicate 1


title: T-AQP4_01 [L49825_Track-90449]

value: AQP4 peptide pool


title: SAC, P11G6, OFF, rep65

description:
P11a_64
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: Postnatal day 11


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse forebrain, biological replicate 1

value: embryonic 12.5 day


title: SAC, P11G5, OFF, rep64

description:
P11a_63
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse neural tube, biological replicate 2

source_name: neural tube

value: neural tube


title: T-AQP4_01 [L49824_Track-90418]


title: WT PBS1_A10_1

value: hippocampus


title: mouse mOSNs, 8w_rep2, scRNAseq

city: Guangzhou

first: Jin

last: Xu

state: Guangdong

address: No. 135 Xingang Xi Road

institute: Sun Yat-sen University

description: 10x Genomics v3

data_processing:
For each scRNA-seq dataset, raw reads were aligned to the Mus musculus reference genome mm10 (Ensembl 98) and converted into gene-barcode matrices using CellRanger version 4.0.0. Count data were further processed using the R package Seurat version 4.1.0. High-quality cells that expressed 400-5,000 genes and had mitochondrial content <10% were retained for downstream analysis. Single-cell RNA-seq datasets across different replicates and time points were integrated using the standard integration workflow (https://satijalab.org/seurat/articles/integration_introduction.html).  Cell identity is annotated using canonical marker genes.  High-quality mature OSN expressing a single OR (detected in at least 4 UMIs) were kept for subclustering analysis.
Assembly: mm10
Supplementary files format and content: *.barcodes.tsv.gz, *.features.tsv.gz, *.matrix.mtx.gz : filtered raw counts output by CellRanger count
Supplementary files format and content: combined_mouse_OE_scRNA_umi_counts.csv.gz : Merged raw counts table for high-quality cells in all scRNA-seq datasets
Supplementary files format and content: combined_mouse_OE_scRNA_metadata.csv.gz : Metadata for high-quality cells in all scRNA-seq datasets

source_name: FACS-enriched mature OSNs

growth_protocol: All mice were housed in barrier facilities in a 12 h light/dark cycle with free access to standard mouse diet and water.

extract_protocol:
Mice were deeply anesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). Mice were then rapidly decapitated, and turbinate tissues were washed and immersed in ice-cold PBS. Tissues were minced into small pieces and disaggregated in 0.25% Trypsin-EDTA (1x) (GIBCO) with gentle agitation at 37 °C for 20 min. After adequate disaggregation, adding equal volume DMEM containing 10% Fetal Bovine Serum (FBS, GIBCO) to stop the disaggregation reaction then the disaggregated cells were washed with ice-cold PBS and filtered through a 40 μm strainer. 7-AAD (Invitrogen) was added to exclude dead cells. For fluorescent reporter-expressing mouse lines (PWK/PhJ*129P2/OlaHsd (OMP-ChR2-YFP), fluorescence-positive cells (mOSNs) were sorted. Cells were sorted into DMEM containing 10% FBS and centrifuged for 5 minutes at 300 g and resuspended with PBS.
Single-cell sequencing libraries were prepared using the Chromium Single Cell 3′ Reagent Kit V3 (10x Genomics) according to the manufacturer’s guidelines. Sequencing library fragments were examined using the Agilent High Sensitivity DNA kit (Agilent) and quantified via qPCR by the KAPA library quantification kit (Roche).

value: FACS-enriched mature OSNs

value: F1 of PWK/PhJ and OMP-ChR2-YFP (OCY58)

value: 8 weeks


title: T-AQP4_01 [L49823_Track-90475]


title: SAC, P11G4, OFF, rep63

description:
P11a_62
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

extract_protocol:
Retinas from ChatCre/+; ROSA-LSL-TD-Tomato mice were isolated at P1, P4, P8, P11 and P16 in ice cold HBSS, and the retinal pigmented epithelium and inner limiting membranes were removed. Retinas were digested with papain, triturated slowly 15-20 time with a P1000 pipet tip, strained into a 50 mL conical tube, and pelleted for 3 minutes at 1.3k rpm. The pellet was gently resuspended and cells were washed three times in ice cold Hibernate A media lacking Ca2+, Mg2+, and phenol red, with pelleting between the washes. Care was taken to tap the tube gently to dislodge the pellet before adding media and resuspending the pellet, to prevent cell lysis and subsequent accumulation of DNA and cellular debris, which forms as a sticky gel-like substance in the supernatant. Washed and resuspended cells in ice cold Hibernate A were subjected to FACS to isolate single cells in cell lysis buffer before proceeding with Smart-seq2 mRNA sequencing as in Chevee et al., 2018.
A modified Smart-seq2 mRNA sequencing protocol was used to construct libraries, described in Chevee et al., 2018.

value: retina


title: T-AQP4_01 [L49822_Track-90394]

extract_protocol:
CD154+ memory cells were isolated by MACS and further purified by FACS sorting on a FACS Aria Fusion (BD Bioscience, San Jose, CA, USA) based on dual expression of CD154 and CD69 and expression of CD45RO. Cells were directly sorted into skirted 96-well PCR plates which were equipped with 2 µl lysis buffer (nuclease-free water with 0.2% Triton-X 100 solution (Roche Diagnostics GmbH, Mannheim, Germany) with 4 U/µL RNase Inhibitor (New England Biolabs)) in advance. After FACS sorting plates were shortly centrifuged (30 sec, 200xg) and immediately frozen at -80°C until shipment.
Library preparation and sequencing was performed at the DRESDEN-concept Genome Center (DcGC, TU Dresden, Germany). The workflow was based on the previously described SMARTseq2 protocol 81. After thawing the samples, 2 ul of a primer mix was added (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription was performed at 42°C for 90 min after filling up to 10 ul with RT buffer mix for a final concentration of 1X superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using 2X Kapa HiFi HotStart Readymix (Roche) at a final 1X concentration and 0.1 uM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6X volume of hydrophobic Sera-Mag Beads (Cytvia: GE24152105050250,) and DNA was eluted in 12 ul nuclease free water. The cDNA quality and concentration of a few representative samples was determined with the Fragment Analyzer (Agilent). For library preparation, 2 µl amplified cDNA was tagmented in 1X Tagmentation Buffer using 0.8 µl bead-linked transposome (Illumina DNA Prep, (M) Tagmentation, Illumina) at 55°C for 15 min in a total volume of 4 µL. The reaction was stopped by adding 1 µl of 0.1 % SDS (37°C, 15 min). Magnetic beads were bound to a magnet, the supernatant was removed, beads were resuspended in 4 µl indexing PCR Mix containing 1x KAPA Hifi HotStart Ready Mix (Roche). After adding 700 nM unique dual indexing primers (i5 and i7) using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter), the reaction mixture was subjected to a PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min). After PCR, libraries are quantified with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium) and equimolarly pooled using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter GmbH). The pooled libraries were then purified with 0.9x volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6x and 0.9x volume of beads. Re-double size selection with 0.6x and 0.9x volume of beads was performed if needed.


title: mouse mOSNs, 8w_rep1, scRNAseq

description: 10x Genomics v3


title: T-AQP4_01 [L49828_Track-90463]


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse neural tube, biological replicate 1


title: SAC, P11G3, OFF, rep62

description:
P11a_61
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse midbrain, biological replicate 2

value: midbrain


title: mouse OE, 19d_rep2, scRNAseq

description: 10x Genomics v3

source_name: Whole olfactory epithelium

value: Whole olfactory epithelium

value: 19 days


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse midbrain, biological replicate 1

value: H3K4me3 (Millipore, 04-745)


title: T-AQP4_01 [L49820_Track-90417]

value: Blood


title: T-AQP4_01 [L49819_Track-90538]


title: SAC, P11G11, ON, rep60

description:
P11a_59
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell


title: mouse mOSNs, 8w, scATACseq

description: 10x Genomics V1.1

library_source: genomic single cell

data_processing:
For each scATAC-seq dataset, raw reads were preprocessed using CellRanger ATAC version 2.0.0, including read filtering, alignment to Mus musculus reference genome mm10 provided by 10X Genomics, peak calling, cell calling, and peak-barcode count matrices. Count data and fragment files were loaded into R (Version 4.1.3) and further processed using the R package Siganc. For each scATAC-seq data, we calculated the nucleosome signal (the ratio of mononucleosomal to nucleosome-free fragments), TSS enrichment score, and the percentage of reads in peaks for each cell. High-quality cells with 5000-40000 fragments, TSS enrichment score >= 4, nucleosome signal <2, and the percentage of reads in peaks >= 40 were retained for downstream analysis. Next, scATAC-seq datasets across two different time points were integrated using the integration workflow (https://stuartlab.org/signac/articles/integrate_atac.html). Cell identity is annotated by gene activity scores of canonical marker genes and cross-modality label transfer.  Cells in the olfactory neuronal lineage (HBCs, GBCs, INPs, Immature OSNs and mature OSNs) and mature OSNs were extracted  for further subclustering analysis.
Assembly: mm10
Supplementary files format and content: *.filtered_peak_bc_matrix.h5, *.fragments.tsv.gz, *.singlecell.csv, *.peaks.bed: cell-by-peak count matrix, fragments in each cell, cellular quality control information and called peaks output by CellRanger
Supplementary files format and content: combined_mouse_OE_scATAC_metadata.csv.gz: Metadata for high-quality cells in all scATAC-seq datasets

extract_protocol:
Mice were deeply anesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). Mice were then rapidly decapitated, and turbinate tissues were washed and immersed in ice-cold PBS. Tissues were minced into small pieces and disaggregated in 0.25% Trypsin-EDTA (1x) (GIBCO) with gentle agitation at 37 °C for 20 min. After adequate disaggregation, adding equal volume DMEM containing 10% Fetal Bovine Serum (FBS, GIBCO) to stop the disaggregation reaction then the disaggregated cells were washed with ice-cold PBS and filtered through a 40 μm strainer. 7-AAD (Invitrogen) was added to exclude dead cells. For fluorescent reporter-expressing mouse lines (PWK/PhJ*129P2/OlaHsd (OMP-ChR2-YFP), fluorescence-positive cells (mOSNs) were sorted. Cells were sorted into DMEM containing 10% FBS and centrifuged for 5 minutes at 300 g and resuspended with PBS.
Single-cell sequencing libraries were prepared using the Chromium Single Cell ATAC Reagent Kit V1.1 (10x Genomics) according to the manufacturer’s guidelines. Sequencing library fragments were examined using the Agilent High Sensitivity DNA kit (Agilent) and quantified via qPCR by the KAPA library quantification kit (Roche).


title: mouse mOSNs, 19d_rep1, scRNAseq

description: 10x Genomics v3


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse liver, biological replicate 2

source_name: liver

value: liver


title: T-AQP4_01 [L49818_Track-90370]

value: CD4 T cell

value: T cell


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse limb, biological replicate 2

source_name: limb

value: limb


title: T-AQP4_01 [L49817_Track-90451]

source_name: Blood

value: AQP4 peptide pool


title: KPC46 TAK981-treated 2

city: New York

first: Hyojae

middle: James

last: Lee

state: NY

address: 101 6th Ave

institute: New York Genome Center

description: 10x Genomics

data_processing:
The FASTQ files for the control samples were then processed further using seqtk to randomly subsample 55,000,000 read pairs, which resulted in similar number of cells across all samples for the downstream analysis. The FASTQ files then went through unique molecular identifier (UMI) quantification for which 10x CellRanger v6.1.2 was run on an Amazon Web Service (AWS) EC2 instance (r6i.16xlarge with 64 vCPU, 512 GiB memory). The reads were aligned to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PDAC tumor

extract_protocol:
KPC tumors were isolated from 4 mice, two treated with TAK-981 and two control mice. Tumors were dissociated using the mouse Tumor Dissociation Kit (Miltenyi) and the gentleMACS Octo Dissociator (Miltenyi), followed by 70 µm cell strainer filtering with 10 ml of cell wash buffer (1x PBS + 0.04% BSA) and centrifugation at 300 relative centrifugal force (rcf) for 5 min at room temperature. The pellets were treated with 1 ml ACK lysing buffer (Gibco) for 1 min, diluted with 10 ml wash buffer, centrifuged at 300 rcf for 5 min at 4°C, and resuspended with 10-15 ml wash buffer (aiming for 1,500 cells/µl). Cells were counted using Thermo Fisher Countess 3 Cell Counter and 10,000-20,000 total live cells were prepared for each sample. For cells with less than 70% viability, dead cell removal was performed with aim for >80% viability for all samples using Dead Cell Removal Kit (Miltenyi).
Library was performed according to the manufacter’s instructions (Single Cell 3’ v3.1 Chemistry Dual index, 10x Genomics).

value: PDAC tumor

value: KPC46 organoid

value: PDAC

value: TAK-981 (Subasumstat)


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse liver, biological replicate 1

value: embryonic 12.5 day


title: T-AQP4_01 [L49816_Track-90362]

data_processing:
library strategy: Plate base Single cell RNA seq (SMARTseq2)
Fragments were aligned to the human reference genome hg38 with support of Ensembl 98 splice sites using the aligner gsnap (v2019-06-10).
Counts per gene and cell were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1)
T-cell receptor sequences were assembled per cell using TraCeR (v0.5)
Assembly: hg38
Supplementary files format and content: Counts per gene per cell, CSV
Supplementary files format and content: T-cell receptor sequences, CSV


title: SAC, P11F8, OFF, rep57

description:
P11a_56
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

data_processing:
Single-cell RNA sequencing FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 v2.1.0. SAM files were converted to BAM files using SAMtools v1.3.1. Transcript abundance estimation and normalization were performed using the Cuffquant and Cuffnorm tools, respectively, in Cufflinks v2.2.1. Downstream analyses were performed using Monocle2 in RStudio.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell Supplementary files format and content: Cuffnorm matrix containing annotations for each gene Supplementary files format and content: Cuffnorm matrix containing annotations for each sample
Supplementary files format and content: Some processed data files without data - they are empty files because the supplied reference annotation GTF file we used in Cufflinks to assemble the transcriptomes did not contain TSS/ CDS gene attributes. I

source_name: starburst amacrine cell

value: retina

value: Postnatal day 11


title: SAC, P11G2, ON, rep61

description:
P11a_60
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: KPC46 vehicle control 2

description: 10x Genomics

value: Vehicle (Cremophor)


title: KPC46 TAK981-treated 1

description: 10x Genomics


title: SAC, P11F6, ON, rep55

description:
P11a_54
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: H3K4me3 PLAC-seq on embryonic 12.5 day mouse limb, biological replicate 1


title: KPC46 vehicle control 1

description: 10x Genomics


title: Control ChIP-seq (input DNA) on postnatal 0 day mouse forebrain

description: The library was sequenced twice on different machines.

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Assembly: mm10

value: forebrain

value: postnatal 0 day


title: SAC, P11F5, OFF, rep54

description:
P11a_53
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49815_Track-90416]

value: Blood


title: T-AQP4_01 [L49814_Track-90522]