title: ChIP-seq, Ctcf, Gemcitabine-resistant cells, replicate2


title: Thapsigargin, ChIP-seq

status: Public on Nov 30 2024

type: SRA

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt.
Trimmed reads mapped to reference genome by bowtie2 or STAR.
Peaks calling by HOMER.
Gene counts were quantified by featurecounts.
DEGs were identified by DESeq.
Assembly: hg19 for ChIP-seq, and hg38 for RNA-seq.
Supplementary files format and content: bigWig files
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts values for each Sample.

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Chromatin immunoprecipitation (ChIP) assay primarily according to the instructions of the ChIP assay kit (Cell Signaling Technology, 9003). 2х10^7 LX-2 cells for each IP.
ChIP-Seq library construction using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645L).

tag: cell line

tag: treatment

value: Thapsigargin

tag: antibody


title: WT_virion_rep2

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

library_source: transcriptomic

data_processing:
BBduk from BBTools was used to processed CLIP-seq reads before mapping.
Reads were then aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2–best–strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
SAMTools was used to generate various file types of mapped reads for further analysis.
Assembly: hg19 and NL4-3
Supplementary files format and content: tab-delimited files showing summarization of reads (i.e. chromosomal locations and counts).
Library strategy: CLIP-seq

molecule: total RNA

source_name: cell line

growth_protocol: 293T cells grown in 10cm dishes were transfected with 10 μg of the indicated PR- NL4-3-derived proviral plasmids using polyethylenimine (PolySciences).

extract_protocol:
UV-crosslinked cells and virions were lysed with RIPA buffer. Gag-RNA complexes were immunoprecipitated from lysates and RNA was subsequently extracted for CLIP-seq library construction.
Libraries were constructed using sequential ligations of 3' barcoded adapter followed by 5' adapter. CLIP-seq libraries were PCR amplified using primers containing Illumina adapter sequences.

treatment_protocol: For PAR-CLIP, one day following transfection and 14-16 hours before cells and virions are harvested, 100 μM 4-thiouridine (4SU) or 6-thioguanosine (6SG) was added to the cell culture medium. Afterwards, Gag and RNAs are crosslinked via UV irradiation.

tag: tissue

value: cell line

tag: cell type

value: 293T cells transfected

tag: genotype

value: WT


title: Gag-SRSF5_cell_rep1

data_processing:
BBduk from BBTools was used to processed CLIP-seq reads before mapping.
Reads were then aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
In the case of reads that mapped to the human genome, locations were only reported for those with the minimum number of observed mismatches for each read (Bowtie criteria: -m 10 -v 2–best–strata for mapping to hg19, and - m 1 -v 2 for mapping to the viral genomes).
SAMTools and BEDTools were used to generate various file types of mapped reads for further analysis.
Assembly: hg19 and NL4-3
Supplementary files format and content: tab-delimited files showing summarization of reads (i.e. chromosomal locations and counts).
Library strategy: CLIP-seq


title: Wt-3.IP_R1

city: Guangzhou

first: Ning

address: 600 Tianhe road

country: China

institute: Sun Yat-sen University

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software.
Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes,.
Assembly: hg38
Supplementary files format and content: Excel formats including Acetylated sites, Acetylated RNA, enrichment information, Annotations

extract_protocol:
RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions.Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

value: Human renal tubular epithelial cell

value: Wild-type control

tag: condition

value: IP


title: ChIP-seq, Ctcf, Parental cells, replicate2

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

data_processing:
RNA-seq data sets were trimmed and aligned to mouse genome build mm10 using STAR. All ATAC-seq and ChIP-seq data sets were trimmed and aligned to mouse genome build mm10 using Bowtie2.
Duplicate reads of all RNA-seq, ATAC-seq and ChIP-seq data were removed with SAMtools.
MACS2 was used to identify regions of ATAC-seq and ChIP-seq peaks.
The ATAC-seq and ChIP-seq peaks were used for known motif enrichment analysis of each sample, which were performed using HOMER (v4.10).
Assembly: mm10
Supplementary files format and content: The processed BigWig (.bw) coverage files were generated using deeptools bamCoverage (Version 3.3.1)

organism: Mus musculus

source_name: Pancrease

extract_protocol:
1,000,000 fresh cells were collected for each RNA-seq sample. Total RNA was extracted using the TRIzol reagent (Invitrogen, USA). 50,000 fresh cells were collected for each ATAC-seq and ChIP-seq sample. 3,000,000 fresh cells were collected for each ChIP-seq sample.
Total RNA was purified using RNeasy Mini Kit (QIAGEN, Germany) and run on an Agilent Bioanalyzer 2100 to assess RNA integrity. The RNA‐seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina, USA) according to the manufacturer's instructions. For ATAC-seq fresh cells were lysed in lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630 [Sigma-Aldrich]) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500 x g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome (DIATRE Biotech, China) and tagmentation buffer at 37 °C for 30 min. After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library for 13 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 98 °C for 15 s, 60 °C for 30 s, and 72 °C for 3 min; following by 72 °C 5 min. After the PCR reaction, libraries were purified with Agencourt Ampure XP beads (Beckman, USA) to remove contaminating primer dimmers and quantitated using Qubit 2.0 Fluorimeter (Invitrogen, USA). For ChIP-seq, the following antibodies were used for ChIP experiments: FOXA1 (ab23738, Abcam, USA), H3K27ac (ab4729, Abcam, USA), H3K27me3 (9733S, CST, USA), SMC3 (ab9263, Abcam, USA), CTCF (Millipore, 07-729). For each condition, approximately 10 million fixed cells were lysed to prepare nuclear extracts. After chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein A Dynabeads (Invitrogen, USA) coupled with 3-5 μg of antibody. After immunoprecipitation, the beads were recovered using a magnet and then washed. DNA was eluted and cross‐links reverted at 55°C for 4 hours then purified with QIAquick PCR Purification Kit (QIAGEN, USA). DNA was quantitated using the Qubit dsDNA HS assay and a Qubit 2.0 Fluorimeter (Invitrogen). For each ChIP-seq, 5-10 ng of purified ChIP-DNA was used to generate the sequencing library using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech, China).

value: Pancrease

value: primary tumor

value: Pancreatic cancer cell

value: DMSO


title: Control, ChIP-seq


title: Gag-SRSF4_cell_6SG_rep1


title: ChIP-seq, Ctcf, Parental cells, replicate1


title: T3M4M16_3

city: omaha

first: Prakash

last: Radhakrishnan

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

data_processing:
Raw data (raw reads) of FASTQ format were first processed through fastp.
Sequence reads were trimmed for adaptor sequence/low-quality sequences.
Trimmed sequence reads were mapped to GRCh38/Hg38 using HISAT2.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
Final data processing for differential gene expression analysis was done using DESeq.
Processed files are provided as normalized abundance measurements (differential gene expression, file name: KOvsWT_deg).
Assembly: GRCh38/hg38
Supplementary files format and content: KOvsWT_deg.txt, KOvsWT_gene_count.txt

source_name: PDAC

growth_protocol: Cell lines were grown in DMEM media (10% FBS, 1% antibiotic) until they reached 80-90% confluency

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit

value: PDAC

value: Pancreatic Cancer

value: MUC16 knockout


title: T3M4M16_2


title: mCherry-PRS_Pum2-ELP-GFP_condensateRNA_sample3

city: Durham

first: Daniel

middle: Mark

last: Shapiro

state: NC

address: 101 Science Dr

institute: PhD Candidate at Chilkoti Lab at Duke University

description: RNA from purified condensates from Pum2-ELP-GFP + mCherry-PRS sample 3

library_source: other

data_processing:
Rockhopper Bacterial RNA-seq software.
Pum2-ELP-sfGFP on pET25b+ plasmid and mCherry(-PRS) on pBAD33.1 plasmids added as secondary replicon to E. coli BL21 genome.
Allowed mismatches: 0.15. Minimum seed length: 0.33. Minimum expression of UTRs and ncRNAs: 0.5. Minimum reads mapping to a transcript: 20. Minimum transcript length: 50. Minimum count to seed a transcript: 50. Minimum count to extend a transcript: 5.
Raw counts were converted to TPM with transcript length output from Rockhopper software.
Assembly: E. coli BL21 (DE3) + plasmid genbank files
Supplementary files format and content: .csv files contain raw counts for each gene
Supplementary files format and content: .csv files contain the calculated length of each genetic transcript

molecule: other

organism: Escherichia coli

source_name: Escherichia Coli BL21

growth_protocol: Cells were grown in 2xYT + 1% glucose + 40mg/mL Kanamycin + 25mg/mL Chloramphenicol. Inoculated at OD600 0.1, .2% arabinose added at OD 0.3, media switched to 0.02mM IPTG at OD 0.8. Cells lysed 4.5 hours after IPTG induction.

extract_protocol:
35mL of cells sonicated 2min 10 on 40 off 85% amplitude. Condensates extracted with OptiPrep density gradient ultracentrifugation at 100k x g overnight at 37C. RNA extracted with TRIzol LS reagent.
KAPA RNA Hyperprep kit with manufacturer's instructions (Roche). 6min fragmentation step, 10 library amplification cycles.

treatment_protocol: Cells expressed etiher mCherry or mCherry with 5x UGUACAUA (mCherry-PRS) in the 3' UTR from the pBAD33.1 plasmid.

value: Escherichia Coli BL21

value: Bacterial

value: IPTG induction of Pum2-ELP-GFP_arabinose induction of mCherry-PRS


title: T3M4M16_1


title: mCherry-PRS_Pum2-ELP-GFP_lysate_totalRNA_sample3

description: RNA from cell lysates from Pum2-ELP-GFP + mCherry-PRS sample 3


title: ChIP-seq, Ctcf, Gemcitabine-resistant cells, replicate1

value: Gemcitabine resistant

value: Gemcitabine (in DMSO)


title: Gag-SRSF4_cell_rep1

value: cell line

value: 293T cells transfected


title: Gag-SRSF1_cell_6SG_rep1

value: WT


title: T3M4WT_3

value: MUC16 expressing


title: Gag-SRSF1_cell_rep1


title: ChIP-seq, H3K27me3, Gemcitabine-resistant cells, replicate3


title: Control, ATF4 ChIP-seq

value: anti-ATF4 (Cell Signaling Technology, 11815)


title: Control, H3K27ac ChIP-seq

value: anti-histone H3 (acetyl K27) (Abcam, 4729)


title: ChIP-seq, H3K27me3, Parental cells, replicate3

value: Pancrease

value: primary tumor


title: mCherry-PRS_Pum2-ELP-GFP_condensateRNA_sample2

description: RNA from purified condensates from Pum2-ELP-GFP + mCherry-PRS sample 2


title: WT-1.Input_R1

value: Human renal tubular epithelial cell

value: Wild-type control

value: input


title: T3M4WT_2

value: PDAC

value: Pancreatic Cancer


title: Gag-NCx3_cell_rep3


title: mCherry-PRS_Pum2-ELP-GFP_lysate_totalRNA_sample1

description: RNA from cell lysates from Pum2-ELP-GFP + mCherry-PRS sample 1

value: Escherichia Coli BL21

value: Bacterial


title: ChIP-seq, H3K27me3, Gemcitabine-resistant cells, replicate2

value: Pancreatic cancer cell

value: Gemcitabine resistant


title: T3M4WT_1


title: mCherry-PRS_Pum2-ELP-GFP_condensateRNA_sample1

description: RNA from purified condensates from Pum2-ELP-GFP + mCherry-PRS sample 1

value: IPTG induction of Pum2-ELP-GFP_arabinose induction of mCherry-PRS


title: Gag-NCx3_cell_rep1

value: cell line

value: 293T cells transfected


title: ChIP-seq, H3K27me3, Gemcitabine-resistant cells, replicate1

value: Gemcitabine (in DMSO)


title: GS-9 (biol rep3)

city: Tübingen

first: Ghazaleh

last: Tabatabai

address: Otfried-Müller-Straße 2

country: Germany

institute: Hertie-Institut für klinische Hirnforschung

data_processing:
nf-core/rnaseq pipeline v1.4
qbic-pipelines/rnadeseq v.1.42
Trim Galore v.0.6.4
STAR v2.6.1d
Assembly: GRCh37
Supplementary files format and content: raw_gene_counts.tsv read counts not normalized

extract_protocol:
RNA was isolated using the QIAGEN Rneasy mini kit and 200 ng were used for library preparation
libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit according to the manufacturer's instructions

value: glioma


title: mCherry_Pum2-ELP-GFP_lysate_totalRNA_sample3

description: RNA from cell lysates from Pum2-ELP-GFP + mCherry sample 3

value: IPTG induction of Pum2-ELP-GFP_arabinose induction of mCherry


title: mCherry-PRS_Pum2-ELP-GFP_lysate_totalRNA_sample2

description: RNA from cell lysates from Pum2-ELP-GFP + mCherry-PRS sample 2


title: mCherry_Pum2-ELP-GFP_condensateRNA_sample3

description: RNA from purified condensates from Pum2-ELP-GFP + mCherry sample 3


title: ChIP-seq, H3K27me3, Parental cells, replicate1

value: Pancrease

value: WT

value: DMSO


title: Gag-NCx2_cell_rep2


title: mCherry_Pum2-ELP-GFP_lysate_totalRNA_sample2

description: RNA from cell lysates from Pum2-ELP-GFP + mCherry sample 2


title: GS-2 (biol rep3)


title: mCherry_Pum2-ELP-GFP_condensateRNA_sample2

description: RNA from purified condensates from Pum2-ELP-GFP + mCherry sample 2


title: ChIP-seq, H3K27ac, Gemcitabine-resistant cells, replicate3

value: primary tumor


title: Gag-NCx2_cell_rep1


title: GS-2 (biol rep2)


title: Gag-hnRNPK_cell_rep3


title: Gag-NCx3_cell_rep2


title: ChIP-seq, H3K27ac, Parental cells, replicate3


title: GS-2 (biol rep1)


title: mCherry_Pum2-ELP-GFP_condensateRNA_sample1

description: RNA from purified condensates from Pum2-ELP-GFP + mCherry sample 1


title: ChIP-seq, H3K27ac, Gemcitabine-resistant cells, replicate2


title: Gag-hnRNPK_cell_rep2


title: T98G (biol rep3)


title: mCherry_Pum2-ELP-GFP_lysate_totalRNA_sample1

description: RNA from cell lysates from Pum2-ELP-GFP + mCherry sample 1


title: Mouse Embryoid body (day 2) from Epiblast stem cells

city: Westmead

first: V. Pragathi

last: Masamsetti

state: NSW

address: 214 Hawkesbury rd

department: Embryology Unit

country: Australia

institute: Children's Medical Research Institute

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
We performed bioinformatics analysis of single-cell RNA sequencing (scRNA-Seq) data with hashtag oligonucleotides (HTOs). Data was demultiplexed using Cell Ranger (Zheng, Terry et al. 2017), followed by normalization (SCTranform), clustering, and differential expression analysis with Seurat package (Butler, Hoffman et al. 2018). HTO-based demultiplexing identified cell populations and their transcriptomic profiles, enabling downstream comparative analysis. The counts were filtered for a minimum of 200 genes/features, minimum of 1000 reads per cell and maximum of 20% MT gene expression.  The samples were aggregated using Seurat package followed by calculation of PCA, T-SNE and UMAP. The cells were annotated using clustifyr package using Pijuan Atlas dataset.
Assembly: Delmix mouse epiblast stem cells
Supplementary files format and content: cellranger_PM4_HTO_outs_multi_count_raw_feature_bc_matrix_barcodes.tsv.gz
Supplementary files format and content: cellranger_PM4_HTO_outs_multi_count_raw_feature_bc_matrix_features.tsv.gz
Supplementary files format and content: cellranger_PM4_HTO_outs_multi_count_raw_feature_bc_matrix_matrix.mtx.gz
Supplementary files format and content: cellranger_PM4_HTO_outs_multi_multiplexing_analysis_assignment_confidence_table

source_name: Mouse embryoid body  from epiblast cell line

extract_protocol:
Mouse epiblast cells and embryoid bodies were collected at the specified stages and single cells were dissociated using Trypsin treatment and counted to load 10,000 cells into on channel of a 10X Chromium chip.  One channel per sample was used. After cell separation and reverse transcription reactions occurred, library preparation followed in accordance with the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) protocol.  Libraries were sent to Novogene for sequencing. Single cell suspensions were passed through 40μm cell strainer (Corning) and concentration was adjusted to 1000 cells/μL. Suspensions were loaded in single-cell-G Chip (10X Genomics) for target output of 10,000 cells per sample. Single-cell droplet capture was performed on the Chromium Controller (10X Genomics).
cDNA library preparation was performed in accordance with the Single-Cell 3’ v 3.0 or v3.1 protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent). Samples were sequenced using paired-ended, dual indexing, using cycles 28, 10, 10, 90 (R1, i7, i5, R2), for an output of 200 million reads per sample.

treatment_protocol: Mouse epiblast stem cells and embryoid bodies - Day 2

value: Delmix

value: Mouse Epiblast cell line

value: Embryoid body Day 2


title: ChIP-seq, H3K27ac, Gemcitabine-resistant cells, replicate1


title: GS-9 (biol rep2)


title: Mouse Epiblast stem cells

description: 10X Genomics

source_name: Mouse cell line

value: Mouse cell line

value: No treatment


title: T98G (biol rep2)


title: GS-9 (biol rep1)


title: ChIP-seq, H3K27ac, Parental cells, replicate2

value: Pancreatic cancer cell


title: Gag-hnRNPK_cell_rep1


title: ChIP-seq, H3K27me3, Parental cells, replicate2


title: ChIP-seq, H3K27ac, Parental cells, replicate1


title: Gag-hnRNPF_cell_rep2


title: LNZ308 (biol rep3)


title: Gag-hnRNPF_cell_rep3


title: T98G (biol rep1)


title: Ctr_2D_nconf_4

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version Version 0.11.9) then quality trimmed using Trimgalore (version 0.6.7)
Trimmed reads were mapped to dog genome using STAR aligner (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1)
Raw counts were normalized using DESeq2 (version 1.36.0,
Normalized counts were batch corrected for replicates for the 2D samples
Assembly: ENSMBL Canis_lupus_familiaris release 108
Supplementary files format and content: txt matrix with log2 normalized and batch corrected values per sample.

molecule: polyA RNA

organism: Canis lupus familiaris

source_name: MDCKII

growth_protocol: MDCKII cell lines were grown in modified Eagle’s medium (MEM, Lonza) containing 5% fetal calf serum (FCS) and 1% 100x Penicillin/Streptomycin/L-Glutamine (P/S/G). The cells were cultivated at 37°C and 5% CO2. MDCKII cells were seeded on coverslips, for non-confluent and confluent conditions, or in a matrix hydrogel (basement membrane extract, BME, from R&D Systems) in 3D to form cysts. Cells were grown on coverslips up to a confluency of 100%, in BME for 5-7 days before using them for further analyses.

extract_protocol:
PolyA+RNA was purified  from 100 ng total RNA using Poly(A) mRNA Magnetic Isolation module Kit (NEB E7490L, New England Biolabs).
RNA Sequencing library was prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).
Directional RNA Library Prep, single reads run 72 bp with an average of 26.9 M reads per sample

treatment_protocol: To generate a PALS1 knockout in MDCKII cells (#ECACC 00062107) frameshift mutations were introduced via CRISPR/Cas9. CRISPOR was used to design the following guide RNA/DNA-sequences CACCGATCATTAGTCGGATAGTAAA, AAACTTTACTATCCGACTAATGATC. The gRNAs/gDNAs (100µM, 8µl each) were phosphorylated and annealed via adding 2µl 10x PNK buffer, 1 µl ATP (5mM) and 1 µl Polynucleotide Kinase and incubation for 1 h at 37°C followed by incubation at 95°C for 5 min to stop the reaction. Resulting oligonucleotides were inserted into the px459 plasmid via digestion using BbsI and ligation by T4 Ligase. MDCKII cells with a confluency of 60% were transfected using Lipofectamine™ 2000 following the manufacturer’s protocol. Selection was done using puromycin (4µg/ml) for 48 h. Potential knockout cells were separated to analyze single cell clones. Potential clones were sequenced and only clones with frameshift mutations were kept. Genotype labels WT refer to wild type, not mutated cells; KO to knock-out cells; Ctr to cells treated by  the KO protocol but not targeted.

value: MDCKII

value: Ctr

value: non-confluentluent


title: Gag-NCx2_cell_rep3

value: cell line

value: 293T cells transfected


title: ChIP-seq, Foxa1, Gemcitabine-resistant cells, replicate3

value: Gemcitabine resistant

value: Gemcitabine (in DMSO)


title: ChIP-seq, Foxa1, Parental cells, replicate3

value: Pancrease


title: LNZ308 (biol rep2)

value: glioma


title: Gag-hnRNPA_cell_rep3

value: WT


title: Gag-hnRNPA_cell_rep2


title: KO1_2D_nconf_1

value: KO


title: Ctr_2D_nconf_3


title: LNZ308 (biol rep1)


title: Ctr_2D_nconf_2


title: ChIP-seq, Foxa1, Parental cells, replicate2

value: primary tumor

value: DMSO


title: ChIP-seq, Foxa1, Gemcitabine-resistant cells, replicate2


title: Gag-hnRNPA1_cell_rep1


title: Ctr_2D_nconf_1


title: ChIP-seq, Foxa1, Gemcitabine-resistant cells, replicate1


title: Gag-dNC-NC_cell__6SG_rep1


title: ChIP-seq, Foxa1, Parental cells, replicate1


title: LN229 (biol rep1)


title: Gag-hnRNPF_cell_rep1


title: KO1_3D_7d_3


title: LN229 (biol rep2)


title: ATAC-seq, Gemcitabine-resistant cells, replicate3


title: KO1_3D_7d_2


title: LN18 (biol rep2)


title: Gag-dNC-NC_cell_rep1


title: WT_2D_nconf_4


title: Gag-dNC-NC_cell_rep3


title: ATAC-seq, Gemcitabine-resistant cells, replicate2


title: ATAC-seq, Parental cells, replicate3


title: Gag-CNBP7_cell_rep3


title: ATAC-seq, Parental cells, replicate2


title: Gag-CNBP7_cell_rep2


title: Ctr_3D_7d_2


title: Gag-dNC-NC_cell_rep2


title: Gag-CNBP7_cell_rep1


title: LN229 (biol rep3)


title: CA2_Hyperthermia_scRNAseq

city: Shenyang

first: Xueli

last: Niu

address: No.77 Puhe Road, Shenyang North New Area

institute: China Medical University

data_processing:
The demutilplex,barcode processing,gene counting and aggregation were made using the cell Ranger software  v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov)
Assembly: mm10
Supplementary files format and content: Tab-separted value files and matrix files

source_name: Condyloma acuminatum

extract_protocol:
The tissues were washed in ice-cold DMEM, dissociated, and homogenized using a tissue dissociation kit (MiltenyiBiotec, Köln, Germany) according to the manufacturer's instructions. Erythrocyte lysis solutions (MiltenyiBiotec) were used to remove erythrocytes, and cell counts and viability were estimated with a fluorescent cell analyser (Rigel S2, Countstar, China) and AO/PI reagent. Finally, fresh cells were washed twice in DMEM and resuspended at 1 × 10^6 cells/ml in phosphate buffered solution (PBS) and 0.04% bovine serum albumin for single-cell sequencing.
To generate single-cell gel bead emulsions, single-cell suspensions of CA tissues were immediately injected into Chromium controllers (10×Genomics) with a target of 9,000 cells. Based on the principles of microwell technology, the Microwell & Magnetic Beads kit (SeekOne) was used to capture single cells and for transcriptome library construction. Nucleic acid-modified beads were used to molecularly label mRNAs of different cellular origins, resulting in the construction of a high-throughput single-cell transcriptome library compatible with the sequencer (Illumina)

treatment_protocol: Fresh CA tissues were divided into two parts and placed separately in culture dishes containing dulbecco's modified eagle medium (DMEM) in a circulating water bath at 44°C and 37°C for 30 min. After processing, the dishes with the tissues were placed in a 37°C incubator and incubated for 4h before tissue dissociation and cell purification.

value: Condyloma acuminatum

value: T cells

value: 44 degreeC water bath,30min


title: ATAC-seq, Gemcitabine-resistant cells, replicate1

value: Pancreatic cancer cell


title: LN18 (biol rep1)


title: Ctr_3D_7d_3

value: MDCKII


title: CA2_Control_scRNAseq

value: 37 degreeC water bath,30min


title: Ctr_3D_7d_1

value: Ctr


title: ATAC-seq, Parental cells, replicate1


title: Gag-CNBP6_cell_rep3

value: cell line


title: WT_3D_7d_4


title: LN18 (biol rep3)


title: CA1_Hyperthermia_scRNAseq


title: KO1_3D_7d_1


title: RNA-seq, Gemcitabine-resistant cells, replicate3


title: WT_3D_7d_3


title: Gag-CNBP6_cell_rep2

value: 293T cells transfected


title: CA1_Control_scRNAseq


title: Gag-CNBP6_cell_rep1


title: Gag-CNBP5_cell_rep3


title: RNA-seq, Gemcitabine-resistant cells, replicate2

value: Gemcitabine resistant


title: NPC_TB_EV_3

city: Columbia

first: Pallav

last: Singh

state: Missouri

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

data_processing:
Trimgalore 0.6.7 was used for removing Illumina adapters, ambiguous nucleotides (N’s), any sequence reads with total read length < 20 bp and the quality Phred score < 20
Hisat2 version 2.2.1 was used for alinging the sequences with the assembely
Cufflinks version 2.2.1 was used for obtaining the FPKM values as well as cuffdiff method within the package was used for finding out the differentially expressed genes
Assembly: GRCh38.108
Supplementary files format and content: annotated output with FPKM values in csv file format

source_name: Brain

growth_protocol: iPS cells were grown for 6 days and maintained in an undifferentiated state; TB cells were grown for days, and differentiated from IPS cells to Day 6 TB cells following the BAP model; NPC stocks were maintained and experimetnal NPC cells were passaged out 24 hours prior to treatment with EVs

extract_protocol: EVs were isolated from the culture medium of the iPS and TB cells using a System Biosciences ExoQuick-TC Ultra EV Isolation Kit for Cell Culture Medium; RNA was extracted from neural progenitor cells using a Qiagen Allprep DNA/RNA/miRNA Universal kit

treatment_protocol: NPC cells were treated with EVs isolated from iPS or TB cells grown to Day 6 and were incubated with EVs for 24 hours

value: Brain

value: Neural Progenitor Cell

value: Cells had EVs from TB cells applied into medium


title: NPC_TB_EV_4


title: RNA-seq, Parental cells, replicate2

value: Pancrease

value: WT


title: WT_3D_7d_1


title: RNA-seq, Parental cells, replicate3

value: primary tumor


title: Gag-CNBP5_cell_rep1


title: RNA-seq, Gemcitabine-resistant cells, replicate1

value: Gemcitabine (in DMSO)


title: KO1_2D_nconf_4

value: KO

value: non-confluentluent


title: Gag-CNBP5_cell_rep2


title: WT_2D_nconf_2


title: NPC_iPS_EV_4

value: Cells had EVs from iPS cells applied into medium


title: NPC_TB_EV_1


title: NPC_TB_EV_2


title: Gag-CNBP4_cell_rep3


title: KO1_2D_nconf_3


title: Gag-CNBP4_cell_rep2


title: Gag-CNBP4_cell_rep1


title: tomato seedlings, K23 & salt, rep2

city: Bengaluru

first: Nataraja

last: Karaba

state: Karnataka

address: GKVK

department: Plant Physiology

country: India

institute: University of Agricultural Sciences, GKVK,

description:
uplog- S_vs_K23S
downlog- S_vs_K23S
uplog- K23C_vs_K23S
downlog- K23C_vs_K23S

data_processing:
The quality check was conducted using FastQC, and low-quality reads were subsequently removed using the Trimmomatic program with a quality threshold set at 20.
Alignment of the reads was performed using STAR against the Solanum lycopersicum  genome (SL3.1) obtained from NCBI.
Read counting was carried out using BEDTools. Differential expression analysis was conducted using DESeq2 with a log2 fold change cutoff set to 2.
Gene annotation was performed using OmicsBox for gene ontology analysis.
Assembly: SL3.1
Supplementary files format and content: excel files with calculated log2 fold changes

organism: Solanum lycopersicum

source_name: whole seedling (root & shoot)

growth_protocol: Five-day-old colony cultures with actively growing mycelial discs measuring around 0.9 cm in diameter were transferred into conical flasks containing 100 mL PDB. One-day-old germinated seeds of tomato (Solanum lycopersicum L, cv. Arka Saurabh) were incubated in 100 mL of culture for 3 h, and washed thoroughly with sterile water.

extract_protocol:
The RNA from the plant material  was extracted  with 1 ml of TrizolTM  and material was incubated on a shaker at room temperature for 15 min. After the addition of 250ml. l chloroform and a second incubation phase, the sample was centrifuged (30 min, 4°C). The supernatant was mixed with isopropanol and incubated on ice, followed by centrifugation. The pellet was washed twice with 80% ethanol, dried and resuspended in RNAse-free water.  The quality and concentration of the extracted RNA were tested spectrophotometrically. Then the RNA integrity was evaluated using a bioanalyzer (Bioanalyzer 2100, Agilent)
Library construction was done by Novogene Genomics, UK

treatment_protocol: For the control set, germinated seeds were incubated in water without EF. After treatment with EF, the pre-germinated seeds were placed between two layers of moist germination paper. Salt stress treatment was imposed by saturating the germination paper with 130 mM NaCl, as described by Pallavi and Nataraja (2022). Seven days after these treatments, the shoots and roots were collected for transcriptome analyses.

value: whole seedling (root & shoot)

value: Arka Saurabh

value: K23 colonised with salt


title: KO1_2D_nconf_2

value: MDCKII


title: NPC_iPS_EV_2


title: NPC_iPS_EV_3


title: RNA-seq, Parental cells, replicate1

value: Pancreatic cancer cell

value: DMSO


title: WT_3D_7d_2

value: cell line


title: WT_2D_nconf_3


title: tomato seedlings, K23 & salt, rep1


title: Gag-CNBP3_cell_rep3

value: 293T cells transfected


title: tomato seedling, Control & salt, rep3

description:
uplog- S_vs_K23S
downlog- S_vs_K23S
uplog- C_vs_S
downlog- C_vs_S

value: Control with salt


title: WT_2D_nconf_1


title: NPC_Control_4

value: Brain

value: Neural Progenitor Cell

value: Cells did not receive any EVs, as a negative control


title: Gag-CNBP3_cell_rep2

value: WT


title: NPC_iPS_EV_1


title: tomato seedling, Control & salt, rep2


title: Gag-CNBP3_cell_rep1


title: NPC_Control_3


title: L_2

city: Qiqihar

first: Ming

last: Jiang

address: No.333, Bukui Street, Jianhua Distric

institute: Qiqihar Medical University

description: Saposhnikovia divaricata (Turcz.) Schischk

data_processing:
Illumina Casava2.19 software used for basecalling.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include readcount values for each Sample...

organism: Saposhnikovia divaricata

source_name: leaves

extract_protocol:
Retinas were removed, flash frozen in dry ice, and RNA was harvested using Trizol reagent. Illumina TreSeq RNA Sample Prep Kit (Cat # FC-122-10）
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaves


title: Gag-CNBP2_cell_rep3


title: L_1


title: tomato seedling, K23 rep3

description:
uplog- C_vs_K23
downlog- C_vs_K23
uplog- K23C_vs_K23S
downlog- K23C_vs_K23S

value: K23 colonised


title: tomato seedling, Control & salt, rep1


title: NPC_Control_1


title: NPC_Control_2


title: Gag-CNBP2_cell_rep2


title: tomato seedling, K23, rep2


title: M_3


title: M_2


title: B stimulated EphA2 CAR transduced T cell co-cultured with U373

city: Beijing

first: yi

last: hu

address: No.10 Yangfangdian Road

institute: Beijing Shijitan Hospital

description:
TU373B
TU373B_TU373.anno.txt

data_processing:
Raw data were first processed through custom Perl a scripts. Clean data (clean reads) were read by removing reads containing poly-N with 5′-adapter contaminants, without 3′ adapter or the insert tag, or containing poly-A or -T or -G or -C from raw data, as well as low-quality reads.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
DEGseq was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs). DESeq2 was designed for differential gene expression analysis between two samples with biological replicates under the theoretical basis obeys the hypothesis of negative binomial distribution for the value of count. Differing from DESeq, DESeq2 estimates the depth parameters of samples and gene-specific, as well as uses "linear regression" for dispersion to "shrink", which was mainly considering genes of the same expression level may share the similarity deviations or own their the expression characteristics. DESeq2 estimates the expression level of each gene in per sample by the linear regression, then calculates the p-value with Wald test. Finally the p-value was corrected by the BH method. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
Assembly: ensemble release-80
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: T cell

growth_protocol: Human peripheral blood mononuclear cells(PBMCs) were seperated from healthy donors by gradient centrifugation

extract_protocol:
Total RNA was extracted from cell using Trizol Reagent (Invitrogen) following the manufacturer’s instructions. The quantity and purity of RNA were measured on a Nanodrop Technologies ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc.). Only samples with the appropriate absorbance measurements (A260/A280 of ~2.0, and A260/A230 of 1.9-2.2) were considered for inclusion in the present study
A total amount of 2 µg total RNA per sample was used as input material for generating the sequencing libraries using NEBNext®Ultra™ RNA Library Prep Kit (#E7530L, NEB, USA) following the manufacturer’s. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: T cells in PBMCs were isolated and stimulated with anti-CD3 and anti-CD28 beads, and then transduced with retrovirus. On day 5, the transduced T cells were subjected to CAR expression detection and then expanded in X-VIVOTM15 serum-free medium which containing 10% GemCellTM Human Serum AB(Gemini Bio) and IL-2. One day 7, the cells were subjected to cytotoxicity assay and in vivo tumor treatment.

value: T cell

value: B stimulated EphA2 CAR transduced,  co-cultured with U373


title: tomato seedling, K23, rep1

value: whole seedling (root & shoot)


title: Gag-CNBP2_cell_rep1


title: EphA2 CAR transduced T cell co-cultured with U373

description:
TU373
TU373B_TU373.anno.txt

value: EphA2 CAR transduced,  co-cultured with U373


title: M_1


title: WT_cell_6SG_rep1


title: L_3


title: WT_cell_rep3


title: B stimulated EphA2 CAR transduced T cell co-cultured with U251

description:
TU251B
TU251B_TU251.anno.txt

value: B stimulated EphA2 CAR transduced,  co-cultured with U251


title: tomato seedling, Control, rep2

description:
uplog- C_vs_K23
downlog- C_vs_K23
uplog- C_vs_S
downlog- C_vs_S

value: Arka Saurabh

value: Control


title: EphA2 CAR transduced T cell co-cultured with U251

description:
TU251
TU251B_TU251.anno.txt

value: EphA2 CAR transduced,  co-cultured with U251


title: C_2


title: WT_cell_rep2

value: cell line


title: tomato seedling, Control, rep1


title: WT_cell_rep1

value: 293T cells transfected


title: C_1


title: tomato seedlings, K23 & salt, rep3

value: K23 colonised with salt


title: tomato seedling, Control, rep3


title: C_3


title: H287_control_1

status: Public on Nov 29 2024

type: RNA

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

country: Japan

institute: Hokkaido University

description: Gene expression in no-treatment rice anthers

hyb_protocol: For microarray hybridization, 600ng of cyanine 3-labeled cRNA were fragmented and hybridized with the 8 x 60K microarray at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2600D DNA microarray scanner using one-color scan setting for 8 x 60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green : 20 bit).

data_processing: Signal data for all the samples obtained were log2-logged using R (4.1.0) and normalized by the Quantile Normalization method using limma (3.48.3) (Ritchie et al., 2015).

organism: Oryza sativa

source_name: H287, control

label_protocol: The microarray analysis was performed on a One-Color Spike-Mix containing cyanine-3 (Cy3)-CTP (Agilent) added to the RNA samples and labeled using the Quick Amp Labeling Kit (Agilent).

growth_protocol: Materials were grown with 20 individuals sown in one Wagener pot (1/5000 100 m2) and grown in a greenhouse at 25/19℃ (day/night cycle) with only the main stem maintained by cutting off the offshoots.

extract_protocol: Total RNA was extracted using TRIzol® Plus RNA Purification kit (Invitrogen). The extracted RNA was quantified using NanoDrop ND-2000 UV-VIS spectrophotometer (Thermo Scientific) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The low-temperature treatment was applied for 4 days during the booting stage, which can be estimated by AD. The plants at AD = ± 1 cm, corresponding to the early microspore stage (late tetrad to uninucleate pollen), were exposed to the low temperature of 12℃ for 4 days.

value: no-treated

tag: strain


title: R75_control_1

source_name: R75, control


title: H287_low-temperature_1

description: Gene expression in cold-treatment rice anthers

source_name: H287, cold-treated

value: cold-treated


title: R75_low-temperature_1

source_name: R75, cold-treated


title: Kirara_low-temperature_2

source_name: Kirara, cold-treated

value: Kirara


title: H287_control_2


title: R45_control_2

source_name: R45, control


title: Kasalath_control_2

source_name: Kasalath, control

value: Kasalath


title: R85_low-temperature_1

source_name: R85, cold-treated


title: Lambayeque1_control_2

source_name: Lambayeque1, control


title: R85_control_1

source_name: R85, control


title: R75_low-temperature_2


title: R85_low-temperature_2


title: R45_control_1


title: Kasalath_control_1


title: R45_low-temperature_1

source_name: R45, cold-treated


title: R85_control_2


title: R45_low-temperature_2


title: H287_low-temperature_2


title: Kirara_low-temperature_1


title: R75_control_2


title: Kirara_control_1

source_name: Kirara, control


title: PL9_low-temperature_2

source_name: PL9, cold-treated


title: Kasalath_low-temperature_1

source_name: Kasalath, cold-treated


title: Lambayeque1_low-temperature_1

source_name: Lambayeque1, cold-treated


title: Kasalath_low-temperature_2


title: PL9_low-temperature_1


title: Kirara_control_2


title: Lambayeque1_control_1


title: PL9_control_2

source_name: PL9, control


title: A58_low-temperature_2

source_name: A58, cold-treated


title: PL9_control_1


title: Koshihikari_control_2

source_name: Koshihikari, control

value: Koshihikari


title: Sasanishiki_low-temperature_2

source_name: Sasanishiki, cold-treated

value: Sasanishiki


title: A58_control_2

source_name: A58, control


title: Fukoku_control_1

source_name: Fukoku, control

value: Fukoku


title: Koshihikari_control_1


title: Fukoku_control_2


title: Koshihikari_low-temperature_1

source_name: Koshihikari, cold-treated


title: A58_control_1


title: A58_low-temperature_1


title: Fukoku_low-temperature_1

source_name: Fukoku, cold-treated


title: G2019S_uninfected_1 wpi

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

description: Library name: G2019S_uninfected_1wpi

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.1
Seurat standard pipeline for the downstream analysis
Assembly: mm10
Supplementary files format and content: One seurat file which is saved with .rds extension. This file contains the information of four sampls integrated using seurat package.

source_name: Colon

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Colon

value: Primary cells

value: Colonic lamina propria cells

value: KI

value: uninfected at 1week

tag: batch

value: Same batch


title: Lambayeque1_low-temperature_2


title: WT_infected_1 wpi

description: Library name: WT_infected_1wpi

value: WT

value: infected at 1week


title: Koshihikari_low-temperature_2


title: G2019S_infected_1 wpi

description: Library name: G2019S_infected_1wpi


title: Fukoku_low-temperature_2


title: Sasanishiki_control_2

source_name: Sasanishiki, control


title: Sasanishiki_low-temperature_1


title: Nipponbare_low-temperature_2

source_name: Nipponbare, cold-treated

value: Nipponbare


title: LG9-36

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissues and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: hemi brain section

extract_protocol:
Fresh frozen tissues were embedded in OCT and sectioned at 10 um on cryostat.
Spatial transcriptome sequencing libraries were prepared with 10X genomics Visium Spatial Gene Expression kit according to manufacturer's instructions.

value: hemi brain section

value: SRY:+; YMT:+

value: 5wk cuprizone

tag: Sex

value: Male


title: Laboratory Small intestine, mRNA-derived cDNA

city: Philadelphia

first: Ken

last: Cadwell

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description:
Library name: Lab_SI_LPL_20190822
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x genomics Cell Ranger pipeline and aligning to the mm10 genome build and Ensembl 93 annotations. Rewilded files are labeled 'wild' and laboratory mice are labeled 'lab' in the files.
Further processing was done with Seurat v5.0.3 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis). Ambient RNA contamination was removed using SoupX.
BCR sequences were generated from single-cell RNA-seq data using TRUST4 v1.14. The germline V(D)J gene was first annotated using IgBLAST v.1.20, in tandem with the IMGT/GENE-DB release 202113-2. Further analysis of mutations and clonaity was preformed using the Immcantation portal.
Assembly: mm10/Ensembl 93
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

source_name: Small intestine lamina propria

extract_protocol:
Small intestine lamina propria samples were collected from four lab mice and four rewilded mice. The tissues were incubated in HBSS supplemented with 2% HEPES, 1% sodium pyruvate, 5 mM EDTA, and 1 mM DL-dithiothreitol, then minced. The small intestine was enzymatically digested with collagenase and resuspended in a 40% and 80% Percoll gradient to isolate lymphocytes. Immune cells were sorted using CD45+ antibodies and counted with a Bio-Rad TC20 automated cell counter. Cells from the four mice in each condition were pooled equally and loaded into a Chromium Controller (10X Genomics).
scRNA-seq libraries were constructed using Chromium Single Cell 3′ v3.3 Reagent Kit (PN-1000268) according to the manufacturer’s protocol. aAmplified cDNA was evaluated on an Agilent BioAnalyzer 2100 withg a High Sensitivity DNA Kit (Agilent Technologies) and final libraries on an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).
Individual libraries were diluted to 2nM and pooled for sequencing. Pools were sequenced with 100 cycle run kits (28bp Read1, 8bp Index1 and 91bp Read2) on the NovaSeq 6000 Sequencing System (Illumina).

treatment_protocol: Laboratory and Rewilded

value: Small intestine lamina propria

value: Immune cells


title: Rewilded Small intestine, mRNA-derived cDNA

description:
Library name: Wild_SI_LPL_20190829
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: LG9-39


title: Sasanishiki_control_1

value: no-treated

value: Sasanishiki


title: Nipponbare_control_2

source_name: Nipponbare, control


title: WT_uninfected_1 wpi

description: Library name: WT_uninfected_1wpi

value: Colon


title: Nipponbare_low-temperature_1

value: cold-treated


title: LG9-NY-215

value: Control


title: LG9-NY-206


title: LG9-NY-195


title: LG9-NY-196


title: LG9-NY-189

value: SRY:-; YMT:-

value: Female


title: LG70-NY-41

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with a unique gene count over 5000 or less than 300, cells with UMI counts over 15000, and cells with a high fraction of mitochondrial reads (>1%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4.0.0 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

source_name: Hippocamus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: Hippocamus


title: FCG-NY-210


title: LG70-NY-37


title: Nipponbare_control_1


title: LG70-NY-36


title: LG9-NY-193


title: LG70-NY-39


title: LG70-NY-40


title: LG9-NY-190


title: LG70-NY-26

value: 3wk cuprizone


title: LG70-NY-33


title: LG70-NY-38


title: LG70-NY-34


title: LG93E4-NY-28

value: SRY:+; YMT:+; P301S tau:+; Human ApoE4:E4/E4


title: LG93E4-NY-92

value: SRY:+; YMT:+; P301S tau:-; Human ApoE4:E4/E4


title: LG70-NY-25


title: LG93E4-NY-29


title: LG93E4-NY-48

value: SRY:+; YMT:-; P301S tau:+; Human ApoE4:E4/E4


title: LG70-NY-24


title: LG93E4-NY-79


title: LG93E4-NY-45


title: LG93E4-NY-18


title: LG93E4-NY-47

value: SRY:+; YMT:-; P301S tau:-; Human ApoE4:E4/E4


title: LG93E4-NY-30


title: LG180-NY-542

value: hemi brain section


title: LG93E4-NY-31

value: Male


title: LG93E4-NY-39

value: SRY:-; YMT:+; P301S tau:+; Human ApoE4:E4/E4


title: LG93E4-NY-41

value: SRY:-; YMT:+; P301S tau:-; Human ApoE4:E4/E4


title: LG70-NY-23


title: LG93E4-NY-24

value: SRY:-; YMT:-; P301S tau:+; Human ApoE4:E4/E4


title: LG93E4-NY-3


title: LG93E4-NY-37

value: SRY:-; YMT:-; P301S tau:-; Human ApoE4:E4/E4


title: LG93E4-NY-22


title: LG93E4-NY-32


title: LG93E4-NY-81


title: LG93E4-NY-36


title: LG93E4-NY-80


title: LG93E4-NY-38


title: LG9-NY-173

value: SRY:+; YMT:+

value: 5wk cuprizone


title: LG93E4-NY-23


title: LG9-NY-204

value: Control


title: LG9-NY-172


title: LG93E4-NY-84


title: LG9-NY-175

value: SRY:+; YMT:-


title: LG9-NY-181


title: LG9-NY-202


title: LG9-NY-171


title: LG9-NY-167


title: LG9-NY-168


title: LG9-NY-165


title: LG9-NY-183

value: SRY:-; YMT:+

value: Female


title: LG9-NY-178

value: Hippocamus


title: LG9-NY-203


title: LG9-NY-177


title: LG9-NY-162


title: LG93E4-NY-42


title: LG9-NY-199

value: SRY:-; YMT:-


title: LG9-NY-185


title: SRY-NY-854


title: LG9-NY-180


title: SRY-NY-863


title: LG9-NY-197


title: SRY-NY-901

value: 3wk cuprizone


title: SRY-NY-900


title: LG9-NY-198


title: SRY-NY-869


title: SRY-NY-895


title: SRY-NY-845


title: SRY-NY-891


title: SRY-NY-899


title: SRY-NY-859


title: SRY-NY-839


title: FCG-NY1-14


title: SRY-NY-832


title: SRY-NY-846


title: SRY-NY-866


title: LG9-NY-179


title: SRY-NY-896


title: LG9-NY-176


title: SRY-NY-881


title: SRY-NY-787


title: SRY-NY-882


title: SRY-NY-815


title: SRY-NY-878


title: SRY-NY-803


title: SRY-NY-902


title: Jax_37

value: WT


title: Jax_31


title: Jax_38


title: Jax_32


title: Jax_36


title: Jax_16


title: Jax_15


title: Jax_30


title: Jax_3


title: Jax_1


title: Early, Ctrl, replicate4, scATACseq

city: Solna

first: Bastien

last: Hervé

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description: 10X Genomics

library_source: genomic single cell

data_processing:
A total of 6 +1 batches were collected from the sequencing facility. Fastq files from 19 +9 samples were processed throughout the 10X genomics standard pipeline. Gene expression and chromatin accessibility libraries were input into cellranger-arc ‘count’ v2.0.2 with default settings to align the biological readouts on the associated mm10 reference genome v2020-A-2.0.0. Sample aggregation of both transcriptomic and genomics metrics was done using the ‘aggr’ of the same cellranger executable file, without normalization. The aggregated count matrix and fragments file were loaded into R v4.3.2. The former was lodged into a Seurat v5.0.3 assay while the latter accommodate into a Signac v1.13.0 chromatin assay associated to an Ensembl base annotation v79 for mouse where UCSC nomenclature was applied to provide gene names readability. If not specifically mentioned, the following depictions of the analysis pipeline belong to either Seurat or Signac packages. Cell free mRNA contamination was removed from each droplet using Cellbender v0.3.0. Genes called in all sample by Cellbender were included into the feature list. Potential cells called in both Cellranger and Cellbender were included into the cell list. A total of 181,674 cells were retrieved. Most of the genes affected by the ambient RNA removal were canonical genes and ribosomal genes. After assessing that each cell could be uniquely identified, quality metrics for both gene expression and peak accessibility were calculated. Among others, the mitochondrial ratio, the cell cycle score, the nucleosome signal, and the Transcription Start Site (TSS) enrichment were generated to support the following quality control cutoffs. Depending of the quality of each sample, for each cell, a maximum of 30,000/150,000 and a minimum of 1,000 ATAC counts, a maximum of 10,000/50,000 and a minimum of 600 RNA counts, a minimum of 600 detected genes, a maximum of 0.8/1.5 nucleosomal signal, a TSS minimum enrichment of 2 and a maximum percentage of mitochondrial information of 15/50 were prerequisite to consider a given cell for the downstream analysis. These thresholds shrinked by around 12.6% the overall number of cells, from 179,078 down to 156,205. While these thresholds are on purpose not too strained, they did not lead to any clustering perturbation downstream.
Assembly: mm10
Supplementary files format and content: EAE_multiomics.rds : Aggregation of cells from all samples in a Seurat object with associated metadata
Supplementary files format and content: EAE_multiomics_annotation.csv : Metadata annotation of the aggregation of cells from all samples in a Seurat object
Supplementary files format and content: EAE_multiomics_fragments.tsv.gz : Aggregation of fragments from all samples
Supplementary files format and content: EAE_multiomics_fragments.tsv.gz.tbi : Index of aggregation of fragments from all samples
Supplementary files format and content: EAE_multiomics_peak_annotation.tsv : Annotation of peaks called by Macs2, following 10Xgenomics cellranger-arc peaks annotation guidelines
Supplementary files format and content: EAE_multiomics.bedpe : Association of peaks to genes (LinkPeaks), peaks to genes (Cicero) and peaks annotation to generate a bedpe file similar to cellranger-arc output
Supplementary files format and content: EAE_multiomics_peaks2genes.rds : Peaks to genes links using LinkPeaks function from Signac package with 500,000bp maximum distance from TSS and minimum 10 cells to validate the link
Supplementary files format and content: EAE_multiomics_peaks2peaks.rds : Cicero connections calculation on all celltypes downsampled to 1000 cells per timepoint, and generation of connection graphs via generate_ccans and ConnectionsToLinks functions
Supplementary files format and content: EAE_multiomics_OLG_peaks2genes : Peaks to genes links on OLGs populations, using LinkPeaks function from Signac package with 50,000bp maximum distance from TSS and minimum 10 cells to validate the link
Supplementary files format and content: EAE_multiomics_OLG_DORCs_peaks2genes : Peaks to genes links on OLGs populations for potential DORC genes, using LinkPeaks function from Signac package with 500,000bp maximum distance from TSS and minimum 10 cells to validate the link
Supplementary files format and content: Astro_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Astrocytes population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Astro_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Astrocytes population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Astro_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Astrocytes population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Astro_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Astrocytes population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: OPC_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of OPC population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: OPC_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of OPC population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: OPC_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of OPC population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: OPC_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of OPC population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: COP_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of COP population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: COP_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of COP population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: COP_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of COP population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: COP_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of COP population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Micro_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Microglia population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Micro_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Microglia population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Micro_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Microglia population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: Micro_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of Microglia population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL1_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL1 population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL1_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL1 population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL1_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL1 population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL1_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL1 population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL2_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL2 population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL2_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL2 population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL2_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL2 population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL2_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL2 population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL56_Ctrl-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL56 population at Ctrl time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL56_Early-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL56 population at Early time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL56_Peak-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL56 population at Peak time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file
Supplementary files format and content: MOL56_Late-TileSize-100-normMethod-rc.bw : Bigwig file of fragments coverage in 100bp window size of MOL56 population at Late time point normalized by relative count (rc) as a scaling factor of 10,000 divided by the total number of fragments involved in this file

source_name: Spinal Cord

extract_protocol:
At early, peak, and late stage, mice were perfused with PBS, and spinal cords were collected. Spinal cord tissues were then dissociated into a single cell suspension according to the manufacturer’s protocol of Adult Brain Dissociation Kit, mouse and rat (Miltenyi Biotec, 130-107-677, we did not perform the red blood cells removal step since majority of the red blood cells had been removed with PBS perfusion). For the debris removal step, majority of the samples were processed with 38% percoll except 1 Naïve sample, 3 CFA-Ctrl samples, 3 EAE early stage samples, 2 + 1 EAE peak stage samples, and 2 + 1 EAE late stage samples were processed debris removal solution (Miltenyi Biotec, 130-107-677) according to the manufacturer’s protocol to enrich more OPCs. Spinal cord single EGFP+ cells were enriched with the BD FACSAria III Cell Sorter (BD Biosciences). The cells were then lysed and washed according to the demonstrated protocol, Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (10x Genomics, CG000365), with modifications: the cells were centrifuged for 10 min at 300 g and 4°C, resuspended in lysis buffer (containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% IGEPAL (CA-630), 0.001% Digitonin, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor) and incubated on ice for 3 min. After the incubation, wash buffer (containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/ul RNase inhibitor) was added on top without mixing. The nuclei were centrifuged for 5 min at 500 g and 4°C. Nuclei were washed once in wash buffer followed by another wash with diluted 1x Nuclei buffer (10x Genomics, PN-1000283) containing 1% BSA, 1 mM DTT and 1 U/ul RNase inhibitor.
Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-24-49 read setup for ATAC (minimum 25,000 read pairs per cell) and a 28-10-10-90 read setup for RNA (minimum 20,000 read pairs per cell).
The Chromium Next GEM Single Cell Multiome ATAC + Gene Expression chemistry (10x Genomics, PN-1000283) was applied to create single cells ATAC and RNA libraries. 26 +10 EAE mice (8 +6 mice from early stage, 8 +2 mice from peak stage and 10 +2 mice from late stage), 12 +6 CFA-Ctrl mice (4 +6 mice from early stage, 4 mice from peak stage and 4 mice from late stage) were used for independent replicates.

treatment_protocol: For the EAE induction, animals were injected subcutaneously with an emulsion of MOG35–55 in complete Freund's adjuvant (CFA) (Hooke Laboratories, EK-2110, containing 1 mg MOG35-55/mL emulsion and 2-5 mg killed mycobacterium tuberculosis H37Ra/mL emulsion, Hooke Laboratories adjusted concentrations by lot) followed by the intraperitoneal injection of pertussis toxin in PBS on day 0 and day 1 (200-225 ng per animal, adjusted by lot according to Hooke manufacturer’s instructions). Scores of EAE were graded according to the following criteria: 0, asymptomatic; 1, limp tail or titubation; 2, limp tail and weakness of hindlimbs; 3, limp tail and complete paralysis of hindlimbs; 4, limp tail, complete paralysis of two hindlimbs with forelimb involvement; 5, moribund or dead; 0.5 for intermediate symptoms. CFA-control mice were injected subcutaneously with the control emulsion containing CFA but without MOG35–55 (Hooke Laboratories, CK-2110), and followed by the administration of pertussis toxin in PBS on day 0 and day 1 (200-225 ng per animal, adjusted by lot according to Hooke manufacturer’s instructions). Spinal cords from EAE and CFA-Ctrl were collected at early (day 8-9), peak (day 14-15), and late stage (day 38-40)

tag: timepoint

value: Early

tag: sequencing id

value: Spinal Cord

value: Sox10:Cre-RCE:LoxP (EGFP)

tag: replicate

tag: debris removal

value: debris

value: male

tag: data tissue_collection

tag: number of_mice

value: CFA-Ctrl

tag: eae scores


title: Early, Ctrl, replicate5, scATACseq

description: 10X Genomics

tag: cell line

value: female


title: Early, Ctrl, replicate5, scRNAseq

description: 10X Genomics

tag: treatment


title: Early, Ctrl, replicate4, scRNAseq

description: 10X Genomics


title: Naive, Ctrl, replicate1, scATACseq

description: 10X Genomics

value: Peak

value: pooled male and female


title: Late, EAE, replicate6, scATACseq

description: 10X Genomics

value: Late

value: EAE


title: SRY-NY-837


title: Early, Ctrl, replicate3, scRNAseq

description: 10X Genomics


title: Peak, EAE, replicate5, scRNAseq

description: 10X Genomics


title: Early, EAE, replicate7 scATACseq

description: 10X Genomics


title: Early, EAE, replicate7, scRNAseq

description: 10X Genomics


title: Early, EAE, replicate6, scRNAseq

description: 10X Genomics


title: LG311_43

description:
PSUK aged mice treated with control or TLR7 inhibitor
counts_genes_sorted_PSUK.csv

data_processing:
RNA-seq reads were mapped using the BlueBee genomics platform and the GENCODE GRCm38 mouse genome (Lexogen QuantSeq 2.2.3) as reference genome.
Counts were normalized using the median of ratios method.
Differential gene expression was analyzed with the DESeq2 1.38.3 package
To control for multiple testing, we used the Benjamini–Hochberg approach to constrain the FDR
Assembly: mm10 genome
Supplementary files format and content: csv: read counts

molecule: nuclear RNA

source_name: brain hippocampus

extract_protocol:
RNA was isolated from microglia using the Quick-RNA MicroPrep Kit (Zymo Research, R1051)
cDNA library generation was done using the QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) for Illumina (K01596, Lexogen) following manufacturer’s instructions.

value: brain hippocampus

value: Male

tag: age

value: PSUK+

value: Inhibitor


title: LG311_51

tag: tissue


title: LG311_63


title: Jax_2

value: Hippocamus

value: Control


title: Early, EAE, replicate5, scATACseq

description: 10X Genomics

value: Early


title: Jax_14

value: WT

value: 3wk cuprizone


title: LG311_40

value: Female


title: Early, Ctrl, replicate3, scATACseq

description: 10X Genomics

value: Spinal Cord

value: Sox10:Cre-RCE:LoxP (EGFP)

value: debris


title: Early, EAE, replicate6, scATACseq

description: 10X Genomics

value: male


title: Naive, Ctrl, replicate1, scRNAseq

description: 10X Genomics

value: Peak

value: pooled male and female


title: Peak, EAE, replicate5, scATACseq

description: 10X Genomics

value: EAE


title: Late, EAE, replicate6, scRNAseq

description: 10X Genomics

value: Late


title: LG311_56

value: brain hippocampus


title: LG311_37

value: PSUK+


title: LG311_44

value: Inhibitor


title: LG311_55


title: LG311_47

value: Male

value: Ctrl


title: LG311_45


title: LG311_46


title: LG311_35


title: LG311_42


title: LG311_41


title: Early, EAE, replicate5, scRNAseq

description: 10X Genomics

value: Early


title: LG311_59


title: F_KO_Mye_T_3

description:
primary microglia from either WT or TLR7KO mice treated with DMSO or myelin
TLR7KOPrimaryMG_gene_count.csv

source_name: primary microglia

value: primary microglia

value: postnatal d1-3

value: myelin


title: F_KO_Mye_T_2

value: Female


title: lumbosacral spinal cord tissue of E19 ETU-induced ARMs6 (miRNA)

first: Zhonghua

last: Yang

address: No.36 street, Heping district

institute: Shengjing hospital of China medical university

data_processing:
Basecalls performed using CASAVA version 1.8.
We used Tophat v2.0.9  to map the cleaned reads to the mouse mm10 reference genome with two mismatches.
After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using Cuffdiff.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
The fold-changes were also estimated according to the FPKM in each sample.The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Genome_build: mm10
Supplementary_files_format_and_content: E19lncRNA_expression.xls
Supplementary_files_format_and_content: E19miRNA_expression.xls

organism: Rattus norvegicus

source_name: lumbosacral spinal cord tissue of ETU-induced ARMs

extract_protocol:
Total RNA was extracted using mir VanaTM miRNA Isolation kit (Cat# AM1561, Ambion)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: ETU-induced ARMs

value: lumbosacral spinal cord

tag: development stage

value: embryonic day 19

value: Wistar


title: LG311_57

tag: genotype


title: lumbosacral spinal cord tissue of E19 ETU-induced ARMs5 (miRNA)

tag: strain


title: Female_KO_2

value: DMSO


title: lumbosacral spinal cord tissue of E19 ETU-induced ARMs4  (miRNA)


title: Female_KO_3


title: lumbosacral spinal cord tissue of E19 normal fetal rats6 (miRNA)

source_name: lumbosacral spinal cord tissue of normal fetal rats

value: normal


title: Female_KO_1


title: lumbosacral spinal cord tissue of E19 normal fetal rats5 (miRNA)


title: F_WT_Mye_T_3

value: WT


title: LG311_58

value: brain hippocampus


title: lumbosacral spinal cord tissue of E19 normal fetal rats4  (miRNA)


title: lumbosacral spinal cord tissue of E19 ETU-induced ARMs3 (lncRNA)


title: F_WT_Mye_T_2


title: F_WT_Mye_T_1


title: F_WT_3


title: F_WT_2


title: lumbosacral spinal cord tissue of E19 normal fetal rats2 (lncRNA)


title: lumbosacral spinal cord tissue of E19 ETU-induced ARMs1  (lncRNA)


title: F_WT_1


title: lumbosacral spinal cord tissue of E19 normal fetal rats3 (lncRNA)


title: M_KO_Mye_T_3


title: lumbosacral spinal cord tissue of E19 normal fetal rats1  (lncRNA)


title: lumbosacral spinal cord tissue of E17 ETU-induced ARMs5 (miRNA-Seq)

data_processing:
Basecalls performed using CASAVA version 1.8.
We used Tophat v2.0.9  to map the cleaned reads to the mouse mm10 reference genome with two mismatches.
After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using Cuffdiff.
The p-value significance threshold in multiple tests was set by the false discovery rate (FDR).
The fold-changes were also estimated according to the FPKM in each sample.The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Genome_build: mm10
Supplementary_files_format_and_content: E17lncRNA_expression.xlsx
Supplementary_files_format_and_content: E17miRNA_expression.txt

value: embryonic day 17


title: lumbosacral spinal cord tissue of E17 ETU-induced ARMs6 (miRNA-Seq)


title: M_KO_3


title: F_KO_Mye_T_1


title: M_KO_Mye_T_1


title: lumbosacral spinal cord tissue of E17 ETU-induced ARMs4  (miRNA-Seq)


title: lumbosacral spinal cord tissue of E17 normal fetal rats6 (miRNA-Seq)


title: M_WT_Mye_T_3


title: M_KO_Mye_T_2


title: lumbosacral spinal cord tissue of E17 normal fetal rats5 (miRNA-Seq)


title: M_WT_Mye_T_2


title: lumbosacral spinal cord tissue of E17 ETU-induced ARMs3 (ncRNA-Seq)


title: M_KO_1


title: M_WT_Mye_T_1


title: lumbosacral spinal cord tissue of E19 ETU-induced ARMs2 (lncRNA)


title: M_WT_3


title: lumbosacral spinal cord tissue of E17 ETU-induced ARMs2 (ncRNA-Seq)


title: M_WT_2


title: lumbosacral spinal cord tissue of E17 normal fetal rats3 (ncRNA-Seq)


title: M_WT_1


title: lumbosacral spinal cord tissue of E17 ETU-induced ARMs1  (ncRNA-Seq)


title: NIA_180

description:
WT aged mice treated with TLR7 agonist or saline
gene_count_TLR7Agonist.csv

value: 9.60 months

value: Gardiquimod


title: lumbosacral spinal cord tissue of E17 normal fetal rats2 (ncRNA-Seq)


title: lumbosacral spinal cord tissue of E17 normal fetal rats1  (ncRNA-Seq)


title: NIA_178


title: NIA_179


title: M_KO_2

value: Male


title: NIA_177


title: ICA-2

city: Guangzhou

first: Yan

last: Lin

state: Alabama

address: 63th Duobao Road

institute: Nanfang College Guangzhou

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: Rattus_norvegicus
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney

extract_protocol:
Kidneys were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CIAKI protocol was established as followed: furosemide was administrated intragastrically at 200 mg/kg and dehydration for 6h before the contrast medium was injected at 15mL/kg by tail vein. To investigate the effect of icariin, before establishment of CIAKI protocol, rats in CIAKI+ICA group received icariin (100 mg/kg) intragastrically once daily for three consecutive days.

value: kidney

tag: weight

value: intragastric icariin (100mg/kg) for three days, intragastic furosemide (200mg/kg), then iopromide (370 mg I/mL, 15mL/kg)


title: lumbosacral spinal cord tissue of E17 normal fetal rats4  (miRNA-Seq)


title: ICA-3


title: ICA-1


title: NIA_176

tag: Sex


title: CIAKI-2

value: intragastic furosemide (200mg/kg), then intravenous iopromide (370 mg I/mL, 15mL/kg)


title: NIA_175


title: CIAKI-3


title: CIAKI-1


title: NIA_169

value: Saline


title: CON-2


title: NIA_174

value: Female


title: NIA_170


title: CON-3


title: NIA_167


title: CON-1


title: NIA_168


title: NIA_166


title: NIA_165


title: NIA_164


title: NIA_160

value: 12.12 months


title: NIA_159


title: NIA_158


title: NIA_157


title: NIA_156


title: NIA_155


title: NIA_154


title: Wildtype_20DAP_Biologicalrep3

city: Denton

first: Amira

last: Rasoul

address: 1504 W Mulberry St

department: Biology

institute: University of North Texas

description:
Library name: Sample 9
wt20.txt
S20-3

data_processing:
The software SOAPnuke (version v1.5.2) was used to filter the reads according to the following criteria: 1) removal of reads containing adaptor sequences, 2) removal of reads with more than 0.1% unknown bases (N), and 3) removal of low-quality reads, defined as those in which the percentage of bases with a quality score lower than 20 exceeds 40%. After filtering, the remaining reads, referred to as "CleanReads," were stored in FASTQ format. The SOAPnuke software was run with the parameters -n 0.001, -l 20, -q 0.4, and -A0.25, and further information can be found on the software's GitHub page: https://github.com/BGI-flexlab/SOAPnuke.
An average of 33.2 million reads per sample were obtained after confirming quality with FastQC. All paired-end reads were mapped to the T. arvense genome (GenBank Acc.: GCA_911865555.2, (Nunn et al., 2022) using HISAT2 v. 2.2.1 (Kim et al., 2019) and sorted with Samtools (Li et al., 2009). Transcripts were assembled using StringTie v. 2.2.1 (Pertea et al., 2016) using GenBank Acc.: GCA_911865555.2 as the reference annotation to guide assembly. The resulting assembly was converted into FASTA format with gffread (Pertea and Pertea, 2020).  A transcript-to-gene matrix was generated with AGAT (Dainat et al., 2023), with genes defined as locations on the genome from which transcript isoforms are transcribed. Filtering of duplicates was carried out using both the tr2aacds script from EviGene (Gilbert, 2023) and CD-HIT-EST (Li et al., 2001) with a cutoff of 0.95. Finally, chimeras were detected and removed using the method described in (Yang and Smith, 2013). The filtered transcript assembly contained 30,757 total sequences with a mean length of 1,404 bp. Analysis of the filtered transcript assembly with BUSCO (Manni et al., 2021) indicated that 93.9% of genes in the ‘brassicales_odb10’ database were represented. BLAST (Altschul et al., 1990) was used to assign homologs from the A. thaliana database (UPID: UP000006548) from UniProt (The UniProt Consortium, 2019). The quasi-mapping mode of Salmon (Patro et al., 2017) was then used to obtain raw counts used for transcript quantitation.
Assembly: GCA_911865555.2
Supplementary files format and content: File format: Text file (.txt), The files are organized by group (WT or fae1-3 mutant), with separate files for each time point (14, 17, and 20 DAP). Within each file, there is a column for the gene ID, followed by columns for each of the three biological replicates within the respective group. The TPMs (Transcripts Per Million) for each replicate are provided in the corresponding columns.

organism: Thlaspi arvense

source_name: Embryo

extract_protocol:
RNA was extracted using the CTAB method
The mRNA was enriched and purified using oligo dT beads to select for poly(A)-tailed mRNA. RNA fragmentation was followed by first-strand cDNA synthesis using random N6 primers, and second-strand cDNA synthesis was subsequently performed. The synthesized cDNA was subjected to end-repair, followed by 3' adenylation, and adaptors were ligated to the 3' adenylated cDNA fragments. Multiple rounds of PCR amplification were then carried out to enrich the cDNA template using appropriate primers. The PCR products were denatured by heat, and cyclization was achieved through splint oligos and DNA ligase. DNA nanoballs were synthesized from the cyclized products, and sequencing was performed on the DNBSEQ platform (DNBSEQ Technology).

value: Embryo

value: Wildtype


title: fae1-3_14DAP_Biologicalrep3

description:
Library name: Sample 12
fae14.txt
F14-3


title: fae1-3_17DAP_Biologicalrep3

description:
Library name: Sample 15
fae17.txt
F17-3


title: fae1-3_20DAP_Biologicalrep3

description:
Library name: Sample 18
fae20.txt
F20-3


title: fae1-3_20DAP_Biologicalrep2

description:
Library name: Sample 17
fae20.txt
F20-2


title: fae1-3_17DAP_Biologicalrep2

description:
Library name: Sample 14
fae17.txt
F17-2


title: fae1-3_14DAP_Biologicalrep2

description:
Library name: Sample 11
fae14.txt
F14-2


title: Wildtype_20DAP_Biologicalrep2

description:
Library name: Sample 8
wt20.txt
S20-2


title: fae1-3_17DAP_Biologicalrep1

description:
Library name: Sample 13
fae17.txt
F17-1


title: fae1-3_20DAP_Biologicalrep1

description:
Library name: Sample 16
fae20.txt
F20-1


title: NIA_150


title: Wildtype_20DAP_Biologicalrep1

description:
Library name: Sample 7
wt20.txt
S20-1


title: NIA_149


title: LG9-NY-170

value: Hippocamus

value: SRY:-; YMT:+

value: Control


title: Wildtype_17DAP_Biologicalrep3

description:
Library name: Sample 6
wt17.txt
S17-3


title: NIA_148

value: WT


title: NIA_147

value: brain hippocampus


title: Wildtype_17DAP_Biologicalrep2

description:
Library name: Sample 5
wt17.txt
S17-2


title: NIA_146


title: Wildtype_17DAP_Biologicalrep1

description:
Library name: Sample 4
wt17.txt
S17-1


title: NIA_145


title: Wildtype_14DAP_Biologicalrep2

description:
Library name: Sample 2
wt14.txt
S14-2


title: Wildtype_14DAP_Biologicalrep1

description:
Library name: Sample 1
wt14.txt
S14-1


title: NIA_144


title: fae1-3_14DAP_Biologicalrep1

description:
Library name: Sample 10
fae14.txt
F14-1


title: XY Z-Del 14.5 dpc repilcate 5

city: Oxford

first: Michelle

last: Simon

state: Oxfordshire

address: Harwell

department: Bioinformatics

country: United Kingdom

institute: MRC

data_processing:
CellRanger 4 – Alignment and counting
Scrublet - Doublet Identification
Seurat – Cell level QC
Monocle3 – Clustering and downstream analysis
Assembly: mm10/
Supplementary files format and content: Matrix Market (mtx) format and tab-separated values.

source_name: Gonadal

extract_protocol:
Noon on the day that the copulatory plug was detected was counted as 0.5 dpc. Mice were killed by dislocation of the neck, which was confirmed by palpation, and then embryos were decapitated in ice-cold, phosphate - buffered saline solution. Embryos collected at 11.5 and 12.5 dpc were staged accurately based on the number of tail somites (ts), here 18-19 ts (11.5 dpc) and 25-32 ts (12.5 dpc). Gonads at all three stages were carefully dissected away from the mesonephros. Dissected gonads were dissociated in trypsin for 10 to 15 min, at 37°C, depending on stage. The reaction was quenched with fetal bovine serum and, following centrifugation, cells were resuspended in phosphate-buffered saline/0.4% bovine serum albumin. Cell viability was assessed with Trypan Blue and haemocytometer analysis. Most gonads were then immediately fixed with 100% ice-cold methanol to allow sample preservation before cell capture. The fixation had no adverse effects on the samples. Fixed and unfixed 12.5 dpc gonads were used in subsequent analyses. All 11.5 and 14.5 dpc gonads were fixed. Samples were genotyped for sex chromosomes and presence of Znrf3 mutation before being brought to the Wellcome Centre for Human Genetics(Oxford,UK) for rehydation in saline-sodium citrate buffer and library construction.
Samples were transported to the Oxford Genomics Centre, Wellcome Centre for Human Genetics (Oxford, UK), for cell capture on the 10x Chromium System. scRNA-seq libraries were generated using the Chromium Single Cell 3′ v.2 assay (10x Genomics). Libraries were sequenced using the X platform (Illumina) to a depth of ∼50,000 reads per cell.

value: Gonadal

value: XY Z-Del


title: XY WT 12.5 dpc repilcate 3

value: XY WT


title: XY WT 14.5 dpc repilcate 2


title: XY Z-Del 14.5 dpc repilcate 3


title: Wildtype_14DAP_Biologicalrep3

description:
Library name: Sample 3
wt14.txt
S14-3


title: XY Z-Del 12.5 dpc repilcate 4


title: XY WT 14.5 dpc repilcate 1


title: XY WT 12.5 dpc repilcate 5


title: XY Z-Del 14.5 dpc repilcate 4


title: XY Z-Del 12.5 dpc repilcate 5


title: XY Z-Del 14.5 dpc repilcate 1


title: XY Z-Del 14.5 dpc repilcate 2


title: XX WT 12.5 dpc repilcate 4

value: XX WT


title: XY Z-Del 12.5 dpc repilcate 8


title: XX WT 14.5 dpc repilcate 2


title: XY Z-Del 12.5 dpc repilcate 6


title: XX WT 12.5 dpc repilcate 3


title: XX WT 12.5 dpc repilcate 1


title: XY WT 12.5 dpc repilcate 6


title: XY Z-Del 12.5 dpc repilcate 3


title: XY WT 12.5 dpc repilcate 4


title: XX WT 12.5 dpc repilcate 2


title: XY WT 12.5 dpc repilcate 1


title: INV_p12

city: Utrecht

first: Gijs

middle: Jacob Fransiscus

last: van Son

address: Heidelberglaan 25

country: Netherlands

institute: Prinses maxima centrum

data_processing:
Cellranger count v6.1.1
Assembly: hg38
Supplementary files format and content: 10X filtered read count matrices

source_name: small intestine

growth_protocol: Ileum N39 triple reporter line (Goblet cells; MUC2-GFP, enteroendocrine (EEC) cells; CHGA-iRFP and Paneth cells: DEFA5-dsRED) obtained from44 were passaged on the integrin-binding domain of Invasin (5 µg/ml) in transwell system with 3 µm pore size (Greiner Bio-one, 662630) using expansion medium. Differentiation was induced using a 2-step differentiation protocol. The first step is to add 500 µl of patterning medium to the lower compartment of the transwell system for 7 days (refresh medium every 2 days with patterning medium), the upper compartment is just air. The second step is to induce Paneth cells,  500 µl maturation medium (as described in44) was added to the lower compartment of the transwell system, with just air in the upper compartment. This culture condition was maintained for 7 days with refreshing maturation medium in the lower compartment every day.

extract_protocol:
10X RNA sequencing
GEX 3'

treatment_protocol: Inv497 coat or BME coat

value: small intestine

tag: cell type

value: various

value: MUC2-GFP CHGA-iRFP  DEFA5-dsRED


title: XX WT 14.5 dpc repilcate 1


title: XY Z-Del 12.5 dpc repilcate 2


title: INV_p0


title: XY Z-Del 12.5 dpc repilcate 1


title: XY Z-Del 11.5 dpc repilcate 4


title: XY Z-Del 12.5 dpc repilcate 7


title: human tumor cells from mice 106, tested group, ISRIB treament

city: Rennes

first: Simon

last: Leonard

address: 2 avenue du Prof Léon Bernard

country: France

institute: Université Rennes

data_processing:
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed reads are mapped to GRCh38  with HISAT2, splice-aware aligner.
Transcript is assembled by StringTie with aligned reads.
Known genes and transcripts are assembled with StringTie based on reference genome model. After assembly, the abundance of gene/transcript is calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample.
Assembly: hg38
Supplementary files format and content: Text files including counts for each sample

growth_protocol: After mice sacrifice and human tumor cells sorted, cells were immediately pelleted and frozen.

extract_protocol:
RNA was harvested using NucleoSpin RNA isolation Kit (Macherey Nagel), by remplaced B-mercaptoethanol with DTT. Minimal of 1.0ug of total RNA was used for construction of sequencing librairies, except for samples m968-T for which only 0.658ug was used. The sequencing was performed by Macrogen, Inc. using the Novaseq 6000
RNA librairies for RNAseq were prepared using Truseq stranded mRNA kit following manufacturer's protocol.

treatment_protocol:
XG7 cells were injected directly in NSG femelle mice femur. Two week after engraftment, mice were randomized into 2 groups. One group of mice was pretreated with high dose (charge dose) of ISRIB for 3 days, and futher maintened at lower dose (maintenance) of ISRIB every two day. All mice receiving the combinaison of two inhibitors AZD1208 and AZD5991.
AZD1208 (from MedChem dissolved in 10% DMSO, 45% PEG300, 5% Tween80, and 40% NaCl 0.9) : 30 mg/kg, daily by oral gavage; AZD5991 (from AstraZeneca dissolved in 10% DMSO and 90% vehicle (20% HPBCD)) : 10 mg/kg, once a week by IV; ISRIB (from Sigma; dissolved in 5% DMSO, 2% Tween20, 20% PEG400, and 73% Dextrose5%) (maintenance dose) : 2mg/kg, every two day by IP ; ISRIB (charge dose) : 3x maintenance dose three succesive day by IP.

value: myeloma

value: AZD1208 + AZD5991 + ISRIB


title: XY Z-Del 11.5 dpc repilcate 1


title: XY WT 11.5 dpc repilcate 2


title: human tumor cells from mice 987, tested group, ISRIB treament


title: XY WT 11.5 dpc repilcate 1


title: XX WT 11.5 dpc repilcate 1


title: BME

value: BME


title: human tumor cells from mice 104, tested group, ISRIB treament


title: human tumor cells from mice 985, control group


title: human tumor cells from mice 973, tested group, ISRIB treament


title: human tumor cells from mice 988, control group


title: brain,rAAV2-retro injection,rep2

city: Wuhan

first: Hu

last: Zheng

state: Hubei

address: shizishan street No.1

department: College of Veterinary Medicine

institute: Huazhong Agricultural University

data_processing:
Raw data were processed using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) pipeline (v1.11)
Assembly: mm10
Supplementary files format and content: Comma-separated values cell-gene matrix files

source_name: brain

extract_protocol:
Single-cell suspensions were collected from prefrontal cortex of 12-week c57bl/6 mouse brains. The tissues were digested with 3mg protease XXIII and 30U/ml papin, and single cells were suspended with 0.5% BSA.
Single-cell mRNA library was performed by the BD Rhapsody Single-Cell Analysis System (BD Biosciences, USA). Firstly，single-cell suspension in BSA was loaded into a BD Rhapsody cartridge with >200,000 microwells. Secondly, single-cell mRNA was captured by magnetic beads with barcoded capture oligos.Then, magnetic beads were collected for cDNA synthesis and library construction following the BD Rhapsody single cell 3’ whole transcriptome amplification (WTA) workflow. Finally, the libraries were sequenced on Illumina NovaSeq 6000 (Illumina, USA) with 300-bp reads (150-bp paired-end reads).

value: brain


title: human tumor cells from mice 990, control group


title: primary TREM-2-/- macrophages, TGF-β1，24h

city: Whhu

first: Xiao

last: Zihao

state: Anhui

address: 92# West Zhe Shan Road

department: Nephrology

institute: Yi Ji Shan hospital affiliated to Wan Nan Medical college

description: FPKM-KO

data_processing:
The mixed sequencing libraries of different samples are denatured into single-stranded DNA using 0.1M NaOH, diluted to a concentration of 8 pM, and then subjected to in situ amplification on the Nova.Seq 6000 S4 Reagent Kit (300 cycles). The amplified fragments are then sequenced using sequencing instruments such as the Illumina NovaSeq 6000 for 150 cycles.
Assembly: mm10
Supplementary files format and content: xlsx file includes FPKM value for each Sample.

source_name: abdominal cavity

extract_protocol:
RNA was  isolated and preserved in Trizol
RNA sequencing libraries are prepared using kits, which include fragmenting the RNA, reverse transcribing it into the first strand of cDNA with random primers, synthesizing the second strand cDNA with dUTP, repairing the ends of the double-stranded cDNA and adding an A, then ligating with Lumina compatible adapters, and finally amplifying the libraries through PCR to obtain the final product; the prepared libraries are quality-checked using an Agilent 2100 and quantified by qPCR methods, and sequencing is performed using the Illumina NovaSeq 6000 sequencer.

value: abdominal cavity

value: primary cell

value: myeloid cell

value: TREM-2 knockdown


title: XY WT 12.5 dpc repilcate 2


title: primary WT macrophages, TGF-β1，24h

value: WT


title: human tumor cells from mice 978, tested group, ISRIB treament


title: human tumor cells from mice 967, control group


title: human tumor cells from mice 969, control group


title: brain,rAAV2-retro injection,rep3