title: Intestinal Organoids, Syngeneic, rep3

city: Houston

first: Tyler

last: Leach

state: Texas

address: One Baylor Plaza

department: Duncan Cancer Center

institute: Baylor College of Medicine

data_processing:
The alignment, deduplication, QC checks, DMR calling, segmentation and annotation were done through the end-to-end pipeline wg-blimp v0.10.0 (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3470-5#Sec1)
Assembly: mm39
Supplementary files format and content: Text files and bed files

source_name: Intestinal

growth_protocol: Isolated crypts were counted and embedded in Matrigel and culture media (1:1) at 2-5 crypts per µl. Crypt culture media consists of Advanced DMEM that was supplemented with EGF 40 ng/ml, Noggin 200 ng/ml, R-spondin 500 ng/ml, N2 (1X), B27 (1X), 10uM γ-27632, 100 U/ml penicillin, and 100µg/ml streptomycin. Intestinal crypts in10-50µl droplets of Matrigel and culture media were plated onto the bottom of  24-well plate and allowed to solidify for 15-30 minutes in a 37°C incubator. five hundred microliters of crypt culture medium per well were then overlaid onto the Matrigel. Crypt culture medium were changed every three days and maintained at 37°C in fully humidified chambers containing 5% CO2.

extract_protocol:
Intestinal organoids were harvested and washed with PBS. The genomic DNAwas extracted with the Quick-DNA Miniprep Kit. The Genomic and RNA Profiling Core first conducted Sample Quality checks using the NanoDrop spectrophotometer and Agilent Tapestation.  Prior to library preparation, we sheared the genomic DNA targeting an average fragment size of ~350 bp. We then used Zymo’s EZ DNA Methylation Gold kit (Cat # 11-335) for bisulfite conversion followed by library prep with the IDT xGen™ Methyl-seq kit (0000810647) and sequencing on our Illumina NovaSeq 6000.
Samples were denatured, end-repaired and 3’adapted before extension of the complementary strand. The resulting double-stranded DNA was then 5’adapted and PCR amplified. The resulting libraries were quantitated by Picogreen and fragment size assessed with the Agilent 2100 Bioanalyzer. All samples were pooled equimolarly and the pool was re-quantitated by Picogreen and also re-assessed on the Bioanalyzer. 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.

treatment_protocol: BMTs were performed as previously described (Zhao et al., 2018, PMID: 30106382). Syngeneic (B6→B6) and allogeneic (BALB/c→B6) BMT recipients received lethal irradiation. Crypts isolated from small intestine of syngeneic or allogeneic recipients 7 days after BMT were cultured with matigel and change culture medium every 2 or 3 days.

value: Intestinal

value: Intestinal Organoids

tag: group

value: Syngeneic


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_60

status: Public on Sep 11 2024

type: SRA

city: Ithaca

first: Conor

last: Loy

state: NY

address: 237 Tower Rd, Room 314

country: USA

institute: Cornell University

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_60

library_source: transcriptomic

data_processing:
Sequencing data was processed using a custom bioinformatics pipeline. Since pools sequenced on the Illumina NextSeq 2000 were optimized to produce paired-end, 61 bp reads, matched sequencing data from the Illumina NextSeq 500 were trimmed using Seqtk (v1.2).
Samples were then quality filtered and trimmed using BBDuk (v38.90), aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR (v2.7.0f, default parameters).
Prior to feature quantification using featureCounts (v2.0.0), samples were deduplicated using Picard MarkDuplicates (v2.19.2). Mitochondrial, ribosomal, X, and Y chromosome genes were bioinformatically removed prior to analysis.
Samples were filtered on the basis of DNA contamination, rRNA contamination, total counts, and RNA degradation. DNA contamination was estimated by calculating the ratio of reads mapping to introns and exons. rRNA contamination was measured using SAMtools (v1.14). Total counts were calculated using featureCounts (v2.0.0). Degradation was estimated by calculating the 5’-3’ bias using Qualimap (v2.2.1).
Samples were removed from analysis if either the intron to exon ratio was greater than 4, if a sample had less than 90,000 total feature counts, or if the rRNA contamination, total counts, or 5’-3’ bias was greater than 4 standard deviations from the mean.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: comma-delimited .csf file includes the gene counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasma, extracted cell-free RNA

extract_protocol:
Plasma samples were received on dry ice and stored at -80°C until processed. Prior to cfRNA extraction, plasma samples were thawed at room temperature and centrifuged at 1300 x g for 10 minutes at 4°C. cfRNA was extracted from plasma using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000). Extracted RNA was DNase treated with 14 µl of 10 µl DNase Turbo Buffer (Invitrogen, AM2238), 3 µl DNase Turbo (Invitrogen, AM2238), and 1 µl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37°C, then concentrated into 12 µl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer® RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit™ 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using both the Illumina NextSeq 500/550 platform (paired-end, 150 bp) and the Illumina NextSeq 2000 platform (paired-end, 100 bp).

tag: tissue

value: Plasma, extracted cell-free RNA

tag: diagnosis

value: KD

tag: site

value: UCSD


title: NKT_MAIT_GD_Blood_F

city: Aurora

first: Tonya

last: Brunetti

state: CO

address: 12800 East 19th Avenue

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation  were made by the BD Rhapsody WTA Analysis Pipeline software (revision 4)
Assembly: GRCh38
Supplementary files format and content: comma-separated raw count matrix
Supplementary files format and content: comma-separated VDJ

molecule: polyA RNA

source_name: Blood

extract_protocol:
To extract thymocytes for both single-cell RNA sequencing (scRNAseq) and flow cytometry, the thymus tissue was placed in complete RPMI 1640 media (Gibco, #22400-071) (10% heat-inactivated fetal bovine serum (FBS, Sigma-Aldrich), 1% non-essential amino acids (Sigma-Aldrich), 1% Sodium Pyruvate (Sigma-Aldrich), 1X GlutaMAX (Gibco), 1% Penicillin/Streptomycin (Gibco), and 1X 2-mercaptoethanol (BME, Sigma-Aldrich)), cut into small pieces, and gently pressed with the back of a 10 ml syringe to release thymocytes. The resulting suspension was passed through a 70 µm filter. Thymocytes and PBMCs were isolated using a Ficoll-Paque density gradient provided by Cytiva. PBMCs were cryopreserved in FBS with 10% DMSO from Sigma-Aldrich and stored in liquid nitrogen. Tetramer staining for MAIT and iNKT cells was performed on freshly isolated thymocytes. For tetramer staining of MAIT and iNKT cells, freshly isolated thymocytes were used. To enrich for thymic MAIT and thymic/blood iNKT cells, up to 2x109 cells were incubated with MR1-5-OP-RU-PE-Tet or CD1d-PBS57-PE respectively in MACS buffer (0.5% BSA, 2mM ETDA, PBS), for 25 mins at room temperature. Cells were washed twice and incubated with anti-PE microbeads (Miltenyi), followed by separation using an autoMACS Pro Separator (Miltenyi) according to manufacturer’s instructions. Enriched MAIT and iNKT from thymus, enriched iNKT from PBMC, unenriched gd T ,CD4+ and CD8+ from thymus, and unenriched MAIT, gd T , CD4+ and CD8+ T cells from PBMC were stained with the following cell surface markers in MACS buffer at room temperature for 20 mins: CD3-AF488 (clone OKT3, Biolegend), CD14-eFluor450 (clone 61D3, ThermoFisher), CD19-eFluor450 (clone H1B19, ThermoFisher), Va7.2-BV785 (clone 3C10, Biolegend), Va24-PerCP-Cy5.5 (clone C15, Biolegend), CD4-AF710 (clone OKT4, Tonbo), CD8a-PE-Cy7 (clone SK1, Tonbo), TCR-BV650 (clone 11F2, BD Biosciences), FcgR block (Miltenyi). Cells were washed twice and resuspended in MACS buffer prior to cell sorting on the Aria 3 (BD Biosciences).
Single cell whole transcriptomes and TCR sequencing libraries were prepared using the BD Rhapsody Single-Cell Analysis System (BD Biosciences) according to the manufacturer's specifications. Prior to cell sorting on the Aria 3 (BD Biosciences) and during cell surface antibody staining, up to 2 x106 enriched or unenriched cells were labeled with an oligonucleotide-tagged antibody sample tag (BD Biosciences). From infant thymus and PBMC donors up to 5 populations were sorted after doublet, viability, B cell (CD19+CD3-) and monocyte (CD14+CD3-) discrimination: 1. MAIT cells (MR1-5-OP-RU-Tet+Va7.2+CD3+), 2. iNKT cells (CD1d-PBS57-Tet+Va24+CD3+), 3. gd T cells (CD3+TCRgd+), 4. CD4+ T cells (CD4+CD8-CD3+) and CD8+ T cells (CD8+CD4-CD3+). Prior to cDNA library preparation for the WTA and VDJ libraries, all cell subsets from the different donors were pooled, with up to 12 unique sample tags combined per library. Libraries were quantified and pooled according to equivalent molar concentrations and sequenced on the NovaSeq sequencing platform at the University of Colorado Genomics Core with the following read lengths: read 1 – 150 cycles; read 2 – 150 cycles; and i7 index - 8 cycles.

value: Blood

tag: Sex

value: F/M

tag: age

value: 41/68 years


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_134

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_134


title: CD4_CD8_NKT_MAIT_GD_Blood_E

description: BD Rhapsody

value: F

value: 24 years


title: Retina C89, Myrf fl/fl

city: Portland

first: Gregory

middle: J

last: Duncan

state: Oregon

address: 3181 SW Sam Jackson Park Road, BRB 453

institute: OHSU

data_processing:
Raw reads were sorted based on barcodes and FASTQC files were produced
Reads were aligned to Mus musculus (GRCm38/Mm10)
Expression counts were performed using STAR.
DeSeq2 was run using Basepair software to determine differentially expressed genes between whole retina and the ganglion cell layer
DeSeq2 was run using Basepair software to determine differentially expressed genes between the ganglion cell layer of Myrf fl/fl and Myrf fl/fl Sox10 CreERT
Assembly: mm10
Supplementary files format and content: .csv containing STAR expression counts
Supplementary files format and content: .csv containing DeSeq2 comparisons

organism: Mus musculus

source_name: Retina

extract_protocol:
Eyes were dissected and snap frozen in OCT, then sectioned on a cryostat at 20 µm thickness and mounted onto Poly-L-Lysine (P1524, Sigma) coated membrane slides (414190-9041-000, Zeiss). Sections were fixed in 70% ethanol for two minutes before staining in Harris Modified Hematoxylin (HHS32, Sigma) with 0.2% glacial acetic acid for 30s. Sections were then immersed in 70% ethanol twice and 100% ethanol twice for 30s each and stored at -80°C in a sealed container until LCM was performed. A Zeiss Palm Microbeam microscope was used to conduct LCM with cut segments extracted onto the lid of adhesive cap tubes (415190-9181-000, Zeiss). The ganglion cell layer was identified and sectioned—at least 20 sections per animal. For sampling of the whole retina, laser incisions were made through each retinal layer. Samples were treated with RLT lysis buffer and RNA isolated using the MicroRNAeasy kit (74004, Qiagen) as per the manufacturer’s instructions.
RNA quantity and quality were evaluated on an Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico. cDNA libraries were produced by loading 15ng of RNA for use with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and sequenced with a NovaSeq 6000 at 50 million reads per sample.

value: Retina

tag: strain

tag: genotype

value: Myrf fl/fl

tag: time

value: 18 weeks old

value: Male

tag: cell type

value: Neurons


title: Col-0_inflorescence_low RI_AGO1-RIP-TRM-sRNA-seq

city: Shanghai

first: Susu

last: Chen

address: 1200 Cailun Road, Pudong New District, Shanghai, China

country: China

institute: Shanghai University of Traditional Chinese Medicine

description:
AGO1 RIP low quality PBA+OX
immunoprecipitated RNA

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (version 0.6.6).
Trimmed sequence reads were mapped to TAIR10 using ShortStack (version- 3.8.5 parameters- --align_only –nohp --mmap u --bowtie_m 1000 --ranmax 50 --mismatches 0).
Reads count extraction was performed using featureCounts (version- v2.0.1 parameters- -O --largestOverlap -fraction).
Reads count normalization was performed using DESeq2 and custom R scripts.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include sequence counts for each Sample.

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: The seeds were grown in soil. After cultivated in 4 ℃ for three days, the seeds were transferred to 16/8 h (light/dark) greenhouse.

extract_protocol:
Total RNAs were extracted from inflorescence tissues using TRIzol reagent (Invitrogen, USA) following standard protocols. For "conventional sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "NaIO4 treatment" library, total RNA was separated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For "PBA-PAGE" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaCl solution. For "TRM-sRNA-seq" library, total RNA was separated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For AGO1-RIP samples, protein was extracted from Col-0 inflorescence. After immunoprecipitation, AGO1-bound RNAs were isolated by phenol-chloroform extraction and ethanol precipitation.
All types of small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer's instructions and purified using Monarch PCR & DNA kit (NEB, USA).

value: inflorescence

tag: ecotype

tag: library type

value: TRM-RIP-sRNA-seq


title: Intestinal Organoids, Syngeneic, rep2

library_source: genomic

molecule: genomic DNA

value: Intestinal

value: Intestinal Organoids


title: Col-0_T15_ inflorescence_sRNA-seq_Rep2

description: T15 CK R2

value: conventional sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_118

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_118

value: Plasma, extracted cell-free RNA

value: KD


title: Intestinal Organoids, Syngeneic, rep1

value: Syngeneic


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_122

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_122

value: UCSD


title: CD4_CD8_NKT_MAIT_GD_Thymus_D

description: BD Rhapsody

source_name: Thymus

value: Thymus

value: M

value: 10 weeks


title: Col-0_ T15_inflorescence_sRNA-seq_Rep1

description: T15 CK R1


title: CD4_CD8_NKT_MAIT_GD_Thymus_C

description: BD Rhapsody

value: F

value: 16 weeks


title: Col-0_T10_ inflorescence_sRNA-seq_Rep2

description: T10 CK R2


title: Intestinal Organoids, Allogeneic, rep2

value: Allogeneic


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_132

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_132


title: Intestinal Organoids, Allogeneic, rep3


title: Col-0_ T10_inflorescence_sRNA-seq_Rep1

description: T10 CK R1


title: Intestinal Organoids, Allogeneic, rep1


title: Col-0_ T0_inflorescence_TRM-sRNA-seq_Rep1

description: T0 PBA+OX R1

value: TRM-sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_59

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_59


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_58

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_58


title: VDJ AntiDBI_03

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description: 10x Genomics Single Cell 5' and V(D)J amplification protocols

data_processing:
barcode/feature matrices and clonotype data generated using multi and aggregate function from cellranger v7.0.0 with default parameter. For barcode/feature matrices, DecontX was applied.
Assembly: Mus Musculus 20201 reference (mm10, Ensembl 98)
Supplementary files format and content: filtered_contig_annotation.csv: clonotype data with annotation from all samples
Supplementary files format and content: metadata.csv: metadata from Seurat analysis with cluster information
Supplementary files format and content: matrix.mtx/genes.tsv/barcodes.tsv: 10x format for count data

source_name: tumor

extract_protocol:
MCA205 tumors were collected, enzymatically dissociated and T cells were sorted, counted and resuspended in PBS + 0.5% human albumin  in a 1:1 CD4+:CD8+ ratio. A total of 10000 cells were loaded to the 10x Chip K for emulsion and barcoding.
Libraries were constructed according to the manufacturer's protocol (Next GEM Single Cell 5' Reagent Kits v2 + mouse TCR Amplification Kit, Dual Index)
scRNA-seq + TCRseq

tag: disease

value: MCA205 fibrosarcoma

value: tumor

value: T cells

tag: treatment

value: Anti-DBI + chemoimmunotherapy


title: RCCBRM59-B

city: Los Angeles

first: Daria

last: Kessler

state: California

address: 9139 Hargis St.

institute: Saint John's Health Center

data_processing:
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
Initial analysis included alignment with TopHat2.
Gene expression counts were obtained using cufflinks.
FastQC was used for quality control.
Assembly: hg38 was used for alignment
Supplementary files format and content: tab-delimited .xlsx file includes raw counts for each Sample

source_name: Sample from patient number 54 of the study.

extract_protocol:
Total RNA was isolated from selected tumor areas with the High Pure RNA Paraffin Kit (Roche Diagnostics). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase Kit (Roche) following manufacturer's protocols.

value: Sample derived from renal cancer-derived brain metastasis FFPE tissue.

value: Patient 54 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: RCCBRM58-B

source_name: Sample from patient number 53 of the study.

value: Patient 53 did not receive any kind of IO treatment.


title: Col-0_ T0_inflorescence_sRNA-seq_Rep1

description: T0 CK R1

value: inflorescence

value: conventional sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_117

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_117

value: Plasma, extracted cell-free RNA

value: KD

value: UCSD


title: RCCBRM57-B

source_name: Sample from patient number 52 of the study.

value: Patient 52 did not receive any kind of IO treatment.


title: VDJ AntiDBI_02


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_213_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_213_trimmed


title: Col-0_ seedling_TRM-sRNA-seq_Rep3

description:
Col-0 seedling PBA+OX R3
LMW RNA

source_name: seedling

value: seedling


title: VDJ AntiDBI_01


title: Col-0_T0_ inflorescence_sRNA-seq_Rep2

description: T0 CK R2


title: RCCBRM55-B

source_name: Sample from patient number 50 of the study.

value: Patient 50 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_193_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_193_trimmed


title: VDJ Istoype_03

value: IgG2a + chemoimmunotherapy


title: RCCBRM56-B

source_name: Sample from patient number 51 of the study.

value: Patient 51 did not receive any kind of IO treatment.


title: Col-0_ seedling_TRM-sRNA-seq_Rep2

description:
Col-0 seedling PBA+OX R2
LMW RNA

value: TRM-sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_229_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_229_trimmed


title: CD4_CD8_Thymus_A

description: BD Rhapsody

value: Thymus

value: M

value: 20 weeks


title: Col-0_ seedling_TRM-sRNA-seq_Rep1

description:
Col-0 seedling PBA+OX R1
LMW RNA


title: VDJ Istoype_01

value: MCA205 fibrosarcoma

value: tumor

value: T cells


title: Col-0_ inflorescence_TRM-sRNA-seq_Rep2

description: Col-0 PBA+OX R2

value: inflorescence


title: VDJ Istoype_02


title: LUNBRM44-B

source_name: Sample from patient number 34 of the study.

value: Sample derived from lung cancer-derived brain metastasis FFPE tissue.

value: Patient 34 received different kind of IO treatments before and after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: LUNBRM43-B

source_name: Sample from patient number 49 of the study.

value: Patient 49 did not receive any kind of IO treatment.


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_131

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_131

value: Plasma, extracted cell-free RNA

value: KD

value: UCSD


title: Col-0_ inflorescence_TRM-sRNA-seq_Rep1

description: Col-0 PBA+OX R1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_235_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_235_trimmed


title: AntiDBI_03

value: Anti-DBI + chemoimmunotherapy


title: LUNBRM42-B

source_name: Sample from patient number 48 of the study.

value: Patient 48 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: Col-0_ inflorescence_sRNA-seq_Rep2

description: Col-0 CK R2

value: conventional sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_208_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_208_trimmed


title: AntiDBI_02


title: Col-0_ inflorescence_sRNA-seq_Rep1

description: Col-0 CK R1


title: AntiDBI_01


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_57

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_57


title: hen1-2_ inflorescence_sRNA-seq(PBA+OX)_Rep2

description: hen1-2 PBA+OX R2

value: TRM-sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_203_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_203_trimmed


title: LUNBRM40-B

source_name: Sample from patient number 46 of the study.

value: Patient 46 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: Istoype_03

value: IgG2a + chemoimmunotherapy


title: LUNBRM39-B

source_name: Sample from patient number 45 of the study.

value: Patient 45 did not receive any kind of IO treatment.


title: hen1-2_ inflorescence_sRNA-seq(PBA+OX)_Rep1

description: hen1-2 PBA+OX R1


title: Istoype_02

value: MCA205 fibrosarcoma


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_56

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_56

source_name: Plasma, extracted cell-free RNA


title: CD4_CD8_NKT_MAIT_Thymus_B

description: BD Rhapsody

value: Thymus

value: M

value: 20 weeks


title: LUNBRM38-B

source_name: Sample from patient number 44 of the study.

value: Sample derived from lung cancer-derived brain metastasis FFPE tissue.

value: Patient 44 did not receive any kind of IO treatment.


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_130

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_130


title: Istoype_01

value: tumor

value: T cells


title: hen1-2_ inflorescence_sRNA-seq(PBA)_Rep1

description: hen1-2 PBA R1

value: inflorescence

value: PBA-PAGE


title: hen1-2_ inflorescence_sRNA-seq(PBA)_Rep2

description: hen1-2 PBA R2


title: LUNBRM37-B

source_name: Sample from patient number 43 of the study.

value: Patient 43 received different kind of IO treatments before and after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: LUNBRM36-B

source_name: Sample from patient number 37 of the study.

value: Patient 37 received different kind of IO treatments before and after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: Primary mouse SHH MB tumor cells replicate 4

city: Toronto

first: Kinjal

last: Desai

state: ON

address: 686 Bay Street, PGCRL 16-14

department: Developmental and Stem Cell

country: Canada

institute: The Hospital for Sick Children

description: 10x Genomics

data_processing:
The four libraries were aggregated using CellRanger aggr from 10X Genomics using default parameters.
Quality check, filtering and downstream processing of the aggregated sample was done by adapting the pipeline from Seurat, which is briefly outlined as follows. In order to avoid low quality cells and doublets from further analysis, cells with less than 200 expressed genes, greater than 7500 genes, greater than 60,000 transcripts or mitochondrial gene expression greater than 10% of the total gene expression of the cell were excluded.
After filtering we obtained 6,739 cells. The gene expression values were further log normalized and corrected for biases from cell cycle states, transcript distribution and mitochondrial gene distribution.
Top 4000 variable genes were identified using variance stabilizing transformation method incorporated in Seurat followed by principal component analysis and graph-based clustering. The clusters were then visualised using Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP).
Top marker genes of each cluster were identified using “FindAllMarkers” function in Seurat and the genes were then used to annotate the clusters through literature search. In order to identify differentially expressed genes between Sox2+ and Sox2- cells, we did differential expression analysis using Wilcoxon rank sum test implemented in “FindMarkers” function of Seurat.
Assembly: mm10
Supplementary files format and content: log normalized gene expression values

source_name: Brain tumor cells

extract_protocol:
Viably-frozen single-cell suspensions (-80°C) from primary Ptc end-point MB were thawed in DMEM supplemented with DNAseI. Cells were pelleted at 200 RCF and resuspended in 0.1% BSA/PBS, supplemented with DNAseI, and filtered through a 35uM nylon filter. Cells were stained with propidium iodide or DAPI before live-cell sorting.
Live cells were collected into 0.1% BSA/PBS before proceeding with scRNA-seq using the 10x Genomics platform, as per the manufacturer’s guidelines.
Samples were sequenced with an Illumina HiSeq 2500 machine as paired-end reads (read 1: 26 bases; read 2: 98 bases; index 1: 8 bases)

value: Brain tumor

tag: cell line

value: SHH MB


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_55

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_55

value: Plasma, extracted cell-free RNA

value: KD

value: UCSD


title: LUNBRM35-B

source_name: Sample from patient number 42 of the study.

value: Patient 42 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: Primary mouse SHH MB tumor cells replicate 3

description: 10x Genomics


title: LUNBRM41-B

source_name: Sample from patient number 47 of the study.

value: Patient 47 did not receive any kind of IO treatment.


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_222_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_222_trimmed


title: Primary mouse SHH MB tumor cells replicate 2

description: 10x Genomics


title: hen1-2_ inflorescence_sRNA-seq(OX)_Rep2

description: hen1-2 OX R2

source_name: inflorescence

value: NaIO4 treatment


title: LUNBRM34-B

source_name: Sample from patient number 41 of the study.

value: Patient 41 did not receive any kind of IO treatment.


title: Primary mouse SHH MB tumor cells replicate 1

description: 10x Genomics


title: hen1-2_ inflorescence_sRNA-seq(CK)_Rep2

description: hen1-2 CK R2

value: conventional sRNA-seq


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_129

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_129


title: LUNBRM33-B

source_name: Sample from patient number 40 of the study.

value: Sample derived from lung cancer-derived brain metastasis FFPE tissue.

value: Patient 40 did not receive any kind of IO treatment.


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_218_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_218_trimmed


title: Whole brains; vehicle; 12 days treatment (P15), CT179_Rep3

data_processing:
Adaptors are trimmed using Trim Galore v. 0.5.0.
The raw trimmed reads were aligned to the reference genome using the STAR aligner, v.2.6.0c.
The STAR alignments were processed to extract raw read counts for genes using htseq-count v.0.6.1p2 (HTSeq).
Assigning reads to genes by htseq-count was done in the mode “intersection_nonempty”, and only uniquely mapping reads are counted.
To identify the set of differentially expressed genes between vehicle and CT-179 treatment conditions, two-condition differential expression was done with the edgeR R package v.3.28.1, using R v.3.6.
Assembly: mm10
Supplementary files format and content: AllGenes_FPKM_edgeR.tsv

source_name: whole brain

extract_protocol:
RNA was harvested using RNeasy Mini Plus Kit (Qiagen). 1-2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Sequencing was done as paired end reads with a read length of 100 bases

treatment_protocol: In vitro: Cells were treated for the time specified prior to wash and RNA extraction. In vivo: P3 Ptc mice were treated with vehicle or CT179 from P3-P15 and sacrificed on P15; whole brains were harvested for homogenisation and RNA extraction.

value: Whole mouse brain tissue

value: Ptch1+/-; IR

value: OLIG2 inhibition

value: 15 days


title: hen1-2_ inflorescence_sRNA-seq(CK)_Rep1

description: hen1-2 CK R1

value: inflorescence


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_212_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_212_trimmed


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_207_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_207_trimmed


title: Whole brains; vehicle; 12 days treatment (P15), CT179_Rep2


title: LUNBRM27-B

source_name: Sample from patient number 38 of the study.

value: Patient 38 did not receive any kind of IO treatment.


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_47

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_47


title: Whole brains; vehicle; 12 days treatment (P15), CT179_Rep1


title: LUNBRM31-B

source_name: Sample from patient number 39 of the study.

value: Patient 39 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: LUNBRM18-B

value: Patient 37 received different kind of IO treatments before and after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: L.er_ inflorescence_sRNA-seq(PBA+OX)_Rep1

description: L.er PBA+OX R1

value: TRM-sRNA-seq


title: Whole brains; vehicle; 12 days treatment (P15), Vehicle_Rep3

value: Vehicle


title: L.er_ inflorescence_sRNA-seq(PBA)_Rep2

description: L.er PBA R2

value: PBA-PAGE


title: LUNBRM17-B

source_name: Sample from patient number 36 of the study.

value: Patient 36 did not receive any kind of IO treatment.


title: hen1-2_ inflorescence_sRNA-seq(OX)_Rep1

description: hen1-2 OX R1

value: NaIO4 treatment


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_128

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_128

value: Plasma, extracted cell-free RNA

value: KD

value: UCSD


title: Whole brains; vehicle; 12 days treatment (P15), Vehicle_Rep2


title: LUNBRM15-B

source_name: Sample from patient number 35 of the study.

value: Sample derived from lung cancer-derived brain metastasis FFPE tissue.

value: Patient 35 did not receive any kind of IO treatment.


title: Whole brains; vehicle; 12 days treatment (P15), Vehicle_Rep1

value: Whole mouse brain tissue

value: Ptch1+/-; IR


title: LUNBRM14-B

source_name: Sample from patient number 34 of the study.

value: Patient 34 received different kind of IO treatments before and after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: L.er_ inflorescence_sRNA-seq(OX)_Rep2

description: L.er OX R2

value: inflorescence


title: L.er_ inflorescence_sRNA-seq(PBA+OX)_Rep2

description: L.er PBA+OX R2


title: L.er_ inflorescence_sRNA-seq(OX)_Rep1

description: L.er OX R1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_202_trimmed

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_202_trimmed


title: BREBRM54-B

source_name: Sample from patient number 33 of the study.

value: Sample derived from breast cancer-derived brain metastasis FFPE tissue.

value: Patient 33 did not receive any kind of IO treatment.


title: Primary mouse SHH MB SOX2+/MKI67+ tumor cells replicate 2

data_processing:
Reads were mapped to mm10 using the Bowtie 2 aligner. Duplicate reads, unmapped or poor quality (Q <30) reads, mitochondrial reads, chrY reads, and regions documented to show artificially high signal (blacklisted regions) were filtered out.
Following alignment, open chromatin regions/peaks were called using Macs2.0. Default parameters were used except for the following: --keep-dup all -B --nomodel --SPMR -q 0.05 --slocal 6250 --llocal 6250. The Macs2.0 bdgcmp function was used to calculate the signal intensity as the fold enrichment of the signal per million reads in a sample over a modelled local background.
A composite of unique peaks for GFP+ and GFP-, and RFP+ and RFP- subpopulations were generated. The signal intensity was calculated as the fold enrichment of the signal per million reads in a sample over a modelled local background using the bdgcmp function in MACS2.
To identify genes associated with the GFP+ and GFP-  and the RFP+ and RFP– subpopulations, the unique open chromatin regions or peaks associated with each group were overlapped with a 3kb window around a Gencode v19 transcription start site (2.5kb upstream, 0.5 kb downstream).
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
After sorting, live cells were collected into 0.1%BSA/PBS. 35,000 – 50,000 cells were collected, depending on sample viability. Equal numbers of GFP+ and GFP-  or RFP+ and RFP- cells were used for downstream ATAC protocol.
Each sample was washed in PBS and centrifuged at 600g for 10 minutes. Cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630, 0.1% tween) was used to lyse cells and the nuclei were immediately spun down at 600g for 10 minutes at 4°C. Following nuclei prep, the pellets were resuspended in a transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water) for 30 minutes at 37°C. Following transposition, the samples were purified using Qiagen MinElute Kit. Next, library fragments were amplified using the NEBNext High Fidelity 2X PCR Master MixEndFragment (NEB) and the libraries were purified using a Qiagen MinElute Kit. Following purification, the libraries were selected for 100-600bp size range using Pippin Prep (Sage Science). The resulting libraries were controlled for quality by qPCR.
ATAC-seq libraries passing QC were sequenced on an Illumina HiSeq 2500 platform, using a Rapid Run mode flow cell to generate 50 bp single-end reads.

value: Brain tumor cells

value: SHH MB

tag: sorted cells


title: BREBRM53-B

source_name: Sample from patient number 32 of the study.

value: Patient 32 did not receive any kind of IO treatment.


title: PTCP53 304 cells; CT-179-treated; day 6_Rep2

value: OLIG2 inhibition

value: 144 hours


title: Primary mouse SHH MB SOX2+/MKI67+ tumor cells replicate 1


title: Plasma cell-free RNA, RNA seq gene counts for sample: cfrna_kd_121

description:
cell-free RNA was isolated from pediatric patients with KD, MIS-C, bacterial infection, viral infections, as well as other hospitalizede pediatric patients and healthy controls.  We conducted RNA sequencing of the extracted cell-free RNA, and quantified the gene transcripts.
cfrna_kd_121

source_name: Plasma, extracted cell-free RNA


title: L.er_ inflorescence_sRNA-seq(CK)_Rep1

description: L.er CK R1

value: conventional sRNA-seq


title: PTCP53 304 cells; vehicle; day 6_Rep3

value: Vehicle


title: Primary mouse SHH MB SOX2+/MKI67- tumor cells replicate 2


title: PTCP53 304 cells; CT-179-treated; day 6_Rep1


title: Primary mouse SHH MB SOX2+/MKI67- tumor cells replicate 1


title: L.er_ inflorescence_sRNA-seq(CK)_Rep2

description: L.er CK R2


title: BREBRM52-B

source_name: Sample from patient number 31 of the study.

value: Patient 31 did not receive any kind of IO treatment.


title: BREBRM51-B

source_name: Sample from patient number 30 of the study.

value: Patient 30 did not receive any kind of IO treatment.


title: PTCP53 304 cells; vehicle; day 6_Rep2


title: BREBRM49-B

source_name: Sample from patient number 28 of the study.

value: Patient 28 did not receive any kind of IO treatment.


title: Primary mouse SHH MB SOX2+ tumor cells replicate 4

source_name: Brain tumor cells


title: Primary mouse SHH MB SOX2+ tumor cells replicate 3


title: PTCP53 304 cells; vehicle; day 6_Rep1


title: L.er_ inflorescence_sRNA-seq(PBA)_Rep1

description: L.er PBA R1

value: PBA-PAGE


title: PTCP53 304 cells; CT-179-treated; day 6_Rep3


title: Mitochondria, RNase+ProK, 9wk biol rep5

city: Parkville

first: Adam

middle: James

last: Trewin

state: Victoria

address: Royal Pde

department: Anatomy and Physiology

country: Australia

institute: University of Melbourne

data_processing:
Sequencing and base-calling was performed on the NovaSeq 6000 platform.
Reads underwent initial quality check with FastQC v0.74, then quality filtering and adapter trimming was conducted with Cutadapt v4.6.
Filtered reads were aligned using STAR v2.7.11a in 2-pass mode.
Gene expression was quantified at the gene level using HTseq-counts v2.0.5 and collated into a counts matrix
Assembly: Ensembl mRatBN7.2 v106
Supplementary files format and content: tab-delimited counts matrix text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Mitochondria, immunoprecipitation isolation from gastrocnemius skeletal muscle

growth_protocol: Wistar Kyoto 4-5 week old male rats were obtained from the Animal Resource Centre, Perth, Western Australia. Rats were housed in pairs and maintained for a 1-week familiarisation period with a 12-hour light/dark cycle, constant temperature of 21 ± 2°C, and humidity levels between 40 and 70%. Rats had ad libitum access to standard chow diet and tap water until 9 weeks of age.

extract_protocol:
Whole skeletal muscle tissue (SM) was mechanically disrupted with 2 cycles at 4m/s for 10 s (MP Biomedical FastPrep) in a cryotube with with a 5 mm stainless steel bead, and homogenised in TRI-reagent. SM total RNA was extracted using spin-columns with on-column DNase-I digest as per the manufacturer’s instructions (Zymo DirectZol RNA Miniprep kit #R2050, Zymo Research). Purified isolated mitochondria (MT) samples were homogenised in 5 volumes of TRI-reagent, then RNA was extracted using spin-columns with on-column DNase-I digest as per the manufacturer’s instructions (Zymo Direct-Zol Micro Prep kit #R2060, Zymo Research).
Skeletal muscle tissue total RNA (50 ng) and isolated mitochondria total RNA (10 ng) was converted to cDNA libraries (Zymo-SeqRiboFreeTotal RNA kit #R300, Zymo Research). Left ventricle tissue total RNA (100 ng) was converted to cDNA libraries (Illumina TruSeq Stranded Total RNA Ribo-Zero H/M/R)

treatment_protocol: At 9-weeks of age, animals were heavily anaesthetised with 5% isoflurane gas then humanely killed via exsanguination following removal of the heart. The inner red portion of the gastrocnemius skeletal muscle was dissected and one portion was snap frozen for subsequent whole tissue RNA extraction, and another portion of fresh tissue was used for mitochondrial isolation via immunoprecipitation (#130-096-946, Miltenyi Biotek, Australia) followed by RNase-A and proteinase-K purification steps.

value: Wistar Kyoto

value: male

tag: age (weeks)

value: wild-type

value: RNaseA + ProteinaseK


title: Mitochondria, RNase+ProK, 9wk biol rep4

value: Mitochondria, immunoprecipitation isolation from gastrocnemius skeletal muscle


title: Mitochondria, RNase+ProK, 9wk biol rep3


title: BREBRM48-B

source_name: Sample from patient number 27 of the study.

value: Sample derived from breast cancer-derived brain metastasis FFPE tissue.

value: Patient 27 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: Primary mouse SHH MB SOX2+ tumor cells replicate 2

value: Brain tumor cells

value: SHH MB


title: PTCP53 304 cells; CT-179-treated; day 1_Rep2

value: OLIG2 inhibition

value: 24 hours


title: BREBRM46-B

source_name: Sample from patient number 26 of the study.

value: Patient 26 did not receive any kind of IO treatment.


title: Mitochondria, RNase+ProK, 9wk biol rep6


title: Primary mouse SHH MB SOX2- tumor cells replicate 3


title: BREBRM45-B


title: Whole muscle, 9wk, biol rep6

source_name: Gastrocnemius skeletal muscle

value: Gastrocnemius skeletal muscle


title: BREBRM47-B


title: PTCP53 304 cells; vehicle; day 1_Rep2

value: Vehicle


title: Primary mouse SHH MB SOX2+ tumor cells replicate 1


title: BREBRM32-B

source_name: Sample from patient number 25 of the study.

value: Patient 25 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: PTCP53 304 cells; vehicle; day 1_Rep1


title: Whole muscle, 9wk, biol rep4


title: Mitochondria, RNase+ProK, 9wk biol rep2


title: Primary mouse SHH MB SOX2- tumor cells replicate 2


title: BREBRM28-B

source_name: Sample from patient number 23 of the study.

value: Patient 23 did not receive any kind of IO treatment.


title: BREBRM25-B

source_name: Sample from patient number 21 of the study.

value: Patient 21 did not receive any kind of IO treatment.


title: Whole muscle, 9wk, biol rep2

value: Wistar Kyoto


title: Mitochondria, RNase+ProK, 9wk biol rep1

value: male


title: Primary mouse SHH MB SOX2- tumor cells replicate 1


title: Whole muscle, 9wk, biol rep3

value: wild-type


title: BREBRM24-B

source_name: Sample from patient number 20 of the study.

value: Patient 20 did not receive any kind of IO treatment.


title: PTCP53 304 cells; CT-179-treated; day 1_Rep1


title: Whole muscle, 9wk, biol rep1


title: Lgr5+ intestinal stem cells, Allo recipient, replicate 4

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

description: gvhd, replicate 4

data_processing:
The fastq files are processed by trim_galore to eliminate any adapter sequence, trim by quality, and filter for length (< 20bp), and trimmed fastq files were aligned by bowtie2
Peaks (narrowPeak) are called using macs2 (https://github.com/macs3-project/MACS). After all sample-wise peaks are determined, a merged peak file is created using bedops
Supplementary files format and content: mm10
Supplementary files format and content: narrowPeak

source_name: intestine

growth_protocol: Female mice aged 8 to 12 weeks old were used for experiments. All mice were kept under specific pathogen-free conditions and cared for according to regulations reviewed and approved by the University of Michigan or Baylor College of Medicine Committee on the Use and Care of Animals, which are based on the University of Michigan or Baylor College of Medicine Laboratory Animal Medicine guidelines.

extract_protocol:
We FACS sorted 50000 Lgr5+ISCs each independently biology samples, which were pooled 3-4 mice together from Lgr5-GFP allogeneic or syngeneic recipients seven days following BMT.
To generate the ATAC-Seq library, we used the Omni-ATAC-Seq protocol  We used the Omni-ATAC-Seq protocol (Corces et al., 2017). The final libraries were cleaned using Qiagen MinElute columns and AMPure XP beads before quantitation with the Qubit HS dsDNA kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and quantitated by qPCR using KAPA’s Illumina Library quantitation kit before PE-150 sequencing on a NovaSeq6000 S4 shared flow cell at the Advanced Genomics Core.

treatment_protocol: BMTs were performed as previously described (Zhao et al., 2018, PMID: 30106382). Syngeneic (B6-GFP-Lgr5) and allogeneic (BALB/c→B6-GFP-Lgr5) BMT recipients received lethal irradiation.

tag: recipient

value: Allo

value: Lgr5+ intestinal stem cells

value: intestine

value: 8-12 weeks old


title: B_CS_PC_22

city: Bengaluru

first: Prathibha

last: Ranganathan

state: Karnataka

address: Electronic City Phase I

country: India

institute: Centre for Human Genetics

data_processing:
paired end sequencing data was checked for quality before and after trimming using FastQC v0.11.9. low quality reads were trimmed based on base-quality scores and read length using TrimGalore v0.6.4.
Genes and transcripts were quantified acorss the three groups. The reads were mapped against the human reference transcriptome and genome (hg38) using TopHat version 2.1.0. quantification was performed using Cufflinks version 2.2.1
for differential expression in pairwise comparisons, log2 fold of 1 and q value <0.05 were considered significant
Supplementary files format and content: hg38
Supplementary files format and content: .csv file of FPKM values for all samples  (GeneExp_matrix_groups)

source_name: Prostate (benign)

extract_protocol:
Total RNA was isolated using Rneasy mini kit (Qiagen). 1 microgram of total RNA was used for making the libraries.
Library prepared for RNA seq using NEBNext Ultra II RNA Prep Kit and validated using Ribogreen mRNA kit

tag: tissue

value: Prostate (benign)


title: Crude mitochondria, RNase, rep3

source_name: Mitochondria, immunoprecipitation isolation from skeletal muscle

growth_protocol: A 14 week old male Wistar Kyoto rat was obtained from the Animal Resource Centre, Perth, Western Australia and humanely killed following dissection of the heart under heavy anaesthesia using 5% isoflurane gas.

extract_protocol:
For RNA extraction, frozen samples were thawed and then pipette mixed thoroughly to disrupt the pellets and then centrifuged at 13,000 x g for 10 min. RNA extraction was then performed with on-column DNase I treatment (Zymo Research DirectZol RNA Microprep #2060) and eluted in 12 µL nuclease free water.
Total RNA extracted from mitochondria from differential centrifugation (6.3 ng), mitochondria and mitoplasts isolated from magnetic-bead IP (40 ng) methods were converted to cDNA libraries (Zymo-Seq RiboFree Total RNA #R300, Zymo Research)

treatment_protocol: The hindlimb muscles were rapidly excised and cut into 200 mg pieces. Each piece was immediately placed in 1 mL ice-cold lysis buffer containing 5ul/ml protease inhibitors (Sigma #P8340), minced using fine scissors and incubated on ice for 30 min. Samples were then mechanically homogenised with an ice-cold Teflon-tipped glass dounce homogeniser (10 passes with rotation at 350 rpm) and the homogenate was pooled. To compare different isolation methods, intact mitochondria were then isolated from separate aliquots of the same homogenate using either the magnetic-bead immunoprecipitation method described above, or a differential centrifugation method.

value: RNaseA


title: PTCP53 304 cells; vehicle; day 1_Rep3

value: SHH MB

value: 24 hours


title: Lgr5+ intestinal stem cells, Allo recipient, replicate 2

description: gvhd, replicate 2


title: B_CS_PC_20


title: Lgr5+ intestinal stem cells, Allo recipient, replicate 1

description: gvhd, replicate 1


title: BREBRM23-B

source_name: Sample from patient number 19 of the study.

value: Sample derived from breast cancer-derived brain metastasis FFPE tissue.

value: Patient 19 did not receive any kind of IO treatment.


title: BREBRM30-B

source_name: Sample from patient number 24 of the study.

value: Patient 24 did not receive any kind of IO treatment.


title: B_CS_PC_21


title: BREBRM21-B

source_name: Sample from patient number 18 of the study.

value: Patient 18 did not receive any kind of IO treatment.


title: Crude mitochondria, RNase, rep1

value: Mitochondria, immunoprecipitation isolation from skeletal muscle


title: B_CS_PC_19


title: B_CS_PC_17


title: Crude mitochondria, RNase, rep2

value: Wistar Kyoto


title: B_CS_PC_18


title: BREBRM20-B

source_name: Sample from patient number 17 of the study.

value: Patient 17 did not receive any kind of IO treatment.


title: Lgr5+ intestinal stem cells, Syn recipient, replicate 2

description: control, replicate 2

value: Syn


title: Lgr5+ intestinal stem cells, Allo recipient, replicate 3

description: gvhd, replicate 3


title: B_CS_PC_16


title: Lgr5+ intestinal stem cells, Syn recipient, replicate 1

description: control, replicate 1


title: Mitoplast, RNase, rep3

value: male

value: wild-type


title: MELBRM13-B

source_name: Sample from patient number 13 of the study.

value: Sample derived from melanoma-derived brain metastasis FFPE tissue.

value: Patient 13 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: BREBRM19-B

source_name: Sample from patient number 16 of the study.

value: Patient 16 did not receive any kind of IO treatment.


title: B_CS_PC_15

value: Prostate (benign)


title: Lgr5+ intestinal stem cells, Syn recipient, replicate 3

description: control, replicate 3

value: Lgr5+ intestinal stem cells

value: intestine

value: 8-12 weeks old


title: KO-7A, mice with graft-versus-host-disease, allogeneic (Allo) (BALB/c→ C57BL/6) transplant 7 days after BMT

description: 10x Genomics

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

extract_protocol:
Intestinal crypt cells which were approximately 8000-10000 cells each independently biology samples which were pooled 3-4 mice together. The viability of cells was between 85-90%, as confirmed with 0.2% Trypan Blue staining. The samples were performed on the 10x Genomics Chromium platform following the user guide manual CG00053 Rev C and Single Cell 3’ Reagent Kit.
The samples were performed on the 10x Genomics Chromium platform following the user guide manual CG00053 Rev C and Single Cell 3’ Reagent Kit. The resulting libraries were sequenced on Illumina’s NovaSeq.

treatment_protocol:
BMTs were performed as previously described (Zhao et al., 2018, PMID: 30106382). Syngeneic (B6→B6) and allogeneic (BALB/c→B6) BMT recipients received lethal irradiation.
Small intestines were collected and flushed with ice-cold PBS, cut longitudinally into roughly 2-mm-long pieces, incubated in 10 mM EDTA at 4°C for 40 minutes, shaken in ice-cold PBS for 3 minutes, filtered with the 70-μm cell strainer to get the enriched crypts. The isolated crypts were incubated in TrypLE express supplemented with DNase I (800U/ml) at 37°C for 20 minutes, then filtered with the 40-μm-mesh cell strainer to get the crypts single cells.

value: intestinal crypt epithelial cells


title: PTCP53 304 cells; CT-179-treated; day 1_Rep3

value: SHH MB

value: OLIG2 inhibition

value: 24 hours


title: Mitoplast, RNase, rep2

value: Mitochondria, immunoprecipitation isolation from skeletal muscle

value: RNaseA


title: B_CS_PC_14


title: Mitochondria, RNase+ProK, rep3

value: Wistar Kyoto

value: RNaseA + ProteinaseK


title: Mitoplast, RNase, rep1

value: male


title: KO-5, mice with graft-versus-host-disease, allogeneic (Allo) (BALB/c→ C57BL/6) transplant 7 days after BMT

description: 10x Genomics


title: Whole muscle, 9wk, biol rep5

value: Gastrocnemius skeletal muscle

value: wild-type


title: MELBRM12-B

source_name: Sample from patient number 12 of the study.

value: Sample derived from melanoma-derived brain metastasis FFPE tissue.

value: Patient 12 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: KO-4, control mice, syngeneic (C57BL/6→C57BL/6) transplant 7 days after BMT

description: 10x Genomics


title: B_CS_PC_13

value: Prostate (benign)


title: MELBRM10-B

source_name: Sample from patient number 10 of the study.

value: Patient 10 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: B_CS_PC_12


title: Mitochondria, RNase+ProK, rep2


title: MELBRM9-B

source_name: Sample from patient number 9 of the study.

value: Patient 9 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: KO-3, control mice, syngeneic (C57BL/6→C57BL/6) transplant 7 days after BMT

description: 10x Genomics

value: intestine

value: 8-12 weeks old


title: YO780_F13_d5_out_YSEQ171

city: Seattle

first: Gareth

last: Cromie

address: 720 Broadway Avenue

institute: PNRI

data_processing:
Alignment was carried out using Bowtie2 (version 2.1.0) with the parameters [-N 1 -I 50 -X 450 -p 6 --reorder -x -S] and allowing 1 mismatch per read. Read alignments were then converted to gene counts using featureCounts (version 1.4.0) in the Subread package, with the parameters [-a -o -t gene –g ID –s 2 -T 1 -p -P -d 50 -D 450].
Assembly: S288c reference (R64-1-1), extended to include ncRNAs and genes present in F45, a strain produced by the same cross that generated F13, but absent in S288c
Supplementary files format and content: tab-delimited text file includes raw and normalized (Trimmed Mean of M-values) counts for each sample

organism: Saccharomyces cerevisiae

extract_protocol:
Hot acid phenol
For each sample, 5 µg of total RNAwas processed using the Tru-Seq stranded mRNA kit (Illumina) following manufacturer instructions

value: day5 out


title: Mitochondria, RNase, rep3


title: B_CS_PC_11


title: MELBRM8-B

source_name: Sample from patient number 8 of the study.

value: Patient 8 did not receive any kind of IO treatment.


title: B_CS_PC_10


title: YO780_F13_d5_out_YSEQ170


title: Mitochondria, RNase, rep2


title: MELBRM11-B

source_name: Sample from patient number 11 of the study.

value: Patient 11 did not receive any kind of IO treatment.


title: B_CS_PC_9


title: YO780_F13_d5_in_YSEQ171

value: day5 in


title: MELBRM7-B

source_name: Sample from patient number 7 of the study.

value: Patient 7 received different kind of IO treatments before FFPE tissue collection  from which RNA was extracted and subjected to whole gene expression  profiling.


title: MELBRM6-B

source_name: Sample from patient number 6 of the study.

value: Patient 6 received different kind of IO treatments before FFPE tissue collection  from which RNA was extracted and subjected to whole gene expression  profiling.


title: Mitochondria, RNase, rep1

value: Mitochondria, immunoprecipitation isolation from skeletal muscle

value: Wistar Kyoto

value: RNaseA


title: MELBRM5-B

source_name: Sample from patient number 5 of the study.

value: Patient 5 received different kind of IO treatments before FFPE tissue collection  from which RNA was extracted and subjected to whole gene expression  profiling.


title: Mitochondria, RNase+ProK, rep1

value: male

value: wild-type

value: RNaseA + ProteinaseK


title: WNTi+FGF8 (batch B)

city: Nice

first: Michele

last: Bertacchi

state: Provence Alpes Côte d Azur

address: 28, avenue Valrose

institute: iBV - Institut de Biologie Valrose

data_processing:
FastQ files of each sample were processed with Cell Ranger count pipeline (10X Genomics) version 6.1.1, that performs alignment, filtering, barcode counting, and UMI counting, using the pre-processed Homo sapiens reference GRCh38-2020-A (GENCODE v32/Ensembl 98) from 10X Genomics.
See Materials and Merthods in original paper for further details
Assembly: Homo sapiens reference GRCh38-2020-A (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab separated values files and matrix files

source_name: Brain organoid

extract_protocol:
Organoids were freshly collected at day 69 and dissociated with Papain; See Materials and Merthods in original paper
scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v.2 (10x Genomics, PN-120237). Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (High Sensitivity DNA Assay; Agilent Technologies).

treatment_protocol: FGF8 100ng/ML in culture medium; See Materials and Merthods in original paper

value: Brain organoid

value: Neural progenitors and neurons


title: B_CS_PC_7

source_name: Prostate (benign)

value: Prostate (benign)


title: B_CS_PC_8


title: WNTi+FGF8 (batch A)

growth_protocol: See Materials and Merthods in original paper


title: B_CS_PC_6


title: MELBRM3-B

source_name: Sample from patient number 3 of the study.

value: Sample derived from melanoma-derived brain metastasis FFPE tissue.

value: Patient 3 received different kind of IO treatments before FFPE tissue collection  from which RNA was extracted and subjected to whole gene expression  profiling.


title: YO780_F13_d5_out_YSEQ169

value: day5 out


title: WNTi (batch B)

value: control


title: MELBRM4-B

source_name: Sample from patient number 4 of the study.

value: Patient 4 received different kind of IO treatments after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: B_CS_PC_5


title: MELBRM2-B

source_name: Sample from patient number 2 of the study.

value: Patient 2 received different kind of IO treatments before and after FFPE tissue collection from which RNA was extracted and subjected to whole gene expression profiling.


title: B_CS_PC_4


title: YO780_F13_d2_YSEQ170


title: WNTi (batch A)


title: YO780_F13_d5_in_YSEQ170

value: day5 in


title: YO780_F13_d2_YSEQ169


title: 9311_TRM-sRNA-seq_Rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore(version 0.6.6)
Trimmed sequence reads were mapped to TAIR10 using ShortStack (version- 3.8.5 parameters- --align_only –nohp --mmap u --bowtie_m 1000 --ranmax 50 --mismatches 0)
Reads count extraction  was performed using featureCounts(version- v2.0.1 parameters- -O --largestOverlap -fraction)
Reads count normalization  was performed using DESeq2 and custom R scripts
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include sequence counts for each Sample

organism: Oryza sativa

source_name: inflorescences, leaves, roots

growth_protocol: The seeds were grown in soil, After cultivated in 4 ℃ for three days, the seeds were transferred to 16/8 h (light/dark) greenhouse.

extract_protocol:
Total RNAs were extracted from inflorescence tissues using TRIzol reagent (Invitrogen, USA) following standard protocols.For "conventional sRNA-seq" library, total RNA was seperated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaCl solution; For "NaIO4 treatment" library, total RNA was seperated in 16% denaturing PAGE gel to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution; For "PBA-PAGE" library, total RNA was seperated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaCl solution; For"TRM-sRNA-seq"library, total RNA was seperated in 16% denaturing PAGE gel supplemented with 2% PBA to excise 18-30 nt, and gel purified RNA was treated by NaIO4 solution. For AGO1-RIP samples，protein was extracted from Col-0 inflorescence. After  immunoprecipitation, AGO1-bound RNAs were isolated by phenol-chloroform extraction and ethanol precipitation.
All types of small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer's instructions and purified using Monarch PCR & DNA kit (NEB, USA).

value: inflorescences, leaves, roots

value: WT

value: TRM-sRNA-seq


title: MELBRM1-B

source_name: Sample from patient number 1 of the study.

value: Patient 1 did not receive any kind of IO treatment.


title: PBMC, CAP Patient 14, 6 months post-enrollment

city: New York

first: Justin

last: Frere

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

data_processing:
Samples were uplaoded to Illumina Basespace and aligned to either the Mesocricetus Auratus MesAur1.0 genome or Homo Sapiens GRCH38 as appropriate using the RNA Sequence Alignment application. The alignment was conducted using the Salmon alignment tool. The resulting quantifications of alignment were either utilized directly for analysis or were further processed using DESeq2.
Assembly: MesAur1.0; GRCH38
Supplementary files format and content: Salmon Files

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMCs were isolated from whole blood using Ficoll gradient and frozen in -80C. Frozen PBMC aliquots were thawed dropwise using 37C T-cell media. After thawing, PBMC were then incubated at 37C and 5% CO2 for 24 hours in tissue-culture treated 96 well plates in 250 uL of T-cell media. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit per protocol (Life Technologies)
Libraries were poly-A enriched and constructed using TruSeq PolyA kits

value: Peripheral Blood Mononuclear Cells

tag: condition

value: COVID-associated pernio (CAP)

tag: timepoint

value: 6 months post-enrollment


title: B_CS_PC_3


title: 9311_TRM-sRNA-seq_Rep1


title: YO780_F13_d5_in_YSEQ169


title: S2_noHia5

city: Boston

first: Thomas

last: Tullius

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Predict m6A positions using HiFi kinetics (fibertools predict-m6a)
Align reads using pbmm2
Extract fiberseq data and generate bed file (fibertools ft extract)
Footprints identified using an HMM (custom scripts available at hhtps://github.com/churchmanlab)
Assembly: dm6
Supplementary files format and content: bed formatted mapped molecule locations with ZMW ID in column 4 and methylation locations in column 12
Supplementary files format and content: bed formatted mapped molecule locations with ZMW ID in column 4 and footprint starts and lengths in column 12 and 13
Library strategy: Fiber-seq

organism: Drosophila melanogaster

growth_protocol: HeLa S3 cells were maintained in DMEM + 10% Fetal Bovine Serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. Extracted DNA was treated with RNase A and XmaI. This was followed by a Phenol:Chloroform:Isoamyl Alcohol extraction, a chloroform:isoamyl alcohol extraction, and a second ethanol precipitation.
PacBio SMRTbell libraries were prepared from DNA (102-182-700)

tag: mtase conditions


title: YO1914_Sfl1_d5_out_YSEQ171

value: Sfl1 deletion


title: B_CS_PC_2


title: YO1914_Sfl1_d5_out_YSEQ170


title: B_CS_PC_1


title: S2_Hia5_200U_nakedDNA

value: 200 U Hia5 for 2hr at 37C


title: PBMC, CAP Patient 7, 6 months post-enrollment


title: PBMC, CAP Patient 12, 6 months post-enrollment


title: PBMC, CAP Patient 13, 6 months post-enrollment


title: PBMC, CAP Patient 11, 6 months post-enrollment


title: YO1914_Sfl1_d5_out_YSEQ169


title: S2_Hia5_200U_Trp_10uM_3

tag: cell treatment

value: 10uM triptolide, 30 minutes

value: 200 U Hia5 for 10 min at 25C


title: A_CR_PC_3

value: Prostate (benign)


title: B_CS_PC_0


title: YO780_F13_d2_YSEQ171


title: S2_Hia5_200U_Trp_10uM_2


title: A_CR_PC_2


title: PBMC, CAP Patient 10, 4 weeks post-enrollment

value: 4 weeks post-enrollment


title: YO1914_Sfl1_d5_in_YSEQ169


title: A_CR_PC_1


title: S2_Hia5_200U_Trp_10uM_1


title: PBMC, CAP Patient 5, 4 weeks post-enrollment


title: S2_Hia5_200U_7


title: YO1914_Sfl1_d5_in_YSEQ171


title: PBMC, CAP Patient 9, 4 weeks post-enrollment


title: YO1914_Sfl1_d2_YSEQ171


title: S2_Hia5_200U_6


title: PBMC, CAP Patient 8, 4 weeks post-enrollment


title: YO1914_Sfl1_d2_YSEQ170


title: C_Control_BPH_30


title: YO1914_Sfl1_d5_in_YSEQ170


title: PBMC, CAP Patient 7, 4 weeks post-enrollment


title: S2_Hia5_200U_5


title: C_Control_BPH_28


title: PBMC, CAP Patient 6, 4 weeks post-enrollment


title: C_Control_BPH_29


title: YO1779_Tec1_d5_out_YSEQ170

value: Tec1 deletion

value: day5 out


title: S2_Hia5_200U_4


title: PBMC, CAP Patient 3, 4 weeks post-enrollment


title: S2_Hia5_200U_3


title: YO1779_Tec1_d5_out_YSEQ171


title: C_Control_BPH_26


title: A_CR_PC_0


title: YO1779_Tec1_d5_out_YSEQ169


title: Primary mouse SHH MB SOX2- tumor cells replicate 4

source_name: Brain tumor cells

value: Brain tumor cells

value: SHH MB


title: YO1779_Tec1_d5_in_YSEQ171

value: day5 in


title: C_Control_BPH_25


title: PBMC, CAP Patient 5, Enrollment

value: Enrollment


title: S2_Hia5_200U_1


title: C_Control_BPH_27


title: YO1779_Tec1_d5_in_YSEQ170


title: C_Control_BPH_24


title: PBMC, CAP Patient 3, Enrollment


title: YO1779_Tec1_d5_in_YSEQ169


title: S2_Hia5_200U_2


title: PBMC, CAP Patient 4, Enrollment


title: C_Control_BPH_23


title: PBMC, CAP Patient 2, Enrollment


title: NSUN2-1

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: The cells were collected after transfecting the plasmids for 48h

data_processing:
Raw reads were subjected to base calling using Guppy basecaller (version 6.3.8+d9e0f64) from fast5 raw files. The base calling process included setting a minimum quality score threshold of 7, utilizing the rna_r9.4.1_70bps_hac.cfg configuration file, and employing the --fast5_out parameter.
The "pass" reads were further aligned to a reference genome sequence (mm39) using Minimap2 (version 2.17-r941) with the following parameters: "-ax splice -uf -k14."
Samtools was utilized for bam file conversion and sorting.
Fast5 files were aligned to their corresponding fastq files using "Nanopolish index". The "Nanopolish eventalign" command was then applied to partition the signal values from fast5 files onto individual 5-mer sequences.
Using the m6Anet, m5Cnet and Nanopsu to detect and quantify the modified sites. Using NanoCount to quantify transcripts.
Assembly: mm39, hg38
Supplementary files format and content: tsv

extract_protocol:
Total RNA was extracted using Trizol reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) and the mRNA was purified using the Dynabeads® mRNA Purification Kit Dynabeads Oligo(dT)25 (#61002, Invitrogen). mRNA was treated by DNaseⅠ buffer (AM8170G, Thermo Fisher Scientific) and Turbo DNase (Thermo Fisher Scientific, AM2238) at 37 ℃ for 10 min and purified by ethanol precipitation to remove genomic DNA.
Nanopore direct RNA sequencing libraries were prepared using about 1000ng mRNA following the SQK-RNA002 kit protocol (version: DRS_9080_v2_revK_14Aug2019). DRS library was added to the flow cell for sequencing on the Mk1C and GridION platform.

value: Overexpression NSUN2 plasmids


title: C_Control_BPH_22


title: YO1779_Tec1_d2_YSEQ171


title: YO1779_Tec1_d2_YSEQ170


title: pcDNA3-1

value: Empty pcDNA3 plasmids


title: PBMC, CAP Patient 1, Enrollment

value: Peripheral Blood Mononuclear Cells


title: pancreatic cancer shNC1

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the mouse reference genome mm10 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v7.1.0 (10x Genomics).
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.
Assembly: mm10
Supplementary files format and content: ATG.integrated.rds: Seurat object that holds processed values and stores raw counts data in its $RNA@counts slot and barcodes in orig. ident slot.
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 5' Reagent Kits v2 (Dual index). The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 5’ gene library.
The libraries were sequenced on DNBSEQ-G400 (MGI Tech).

value: orthotopic syngeneic PDAC tumors (transplanted KPC shNC)

tag: Sex

value: Female

tag: strain


title: PBMC, Control Patient 6

value: Control


title: pancreatic cancer shATG1

source_name: shATG

value: orthotopic syngeneic PDAC tumors (transplanted KPC shATG7)


title: C_Control_BPH_20


title: C_Control_BPH_21


title: Infected 4 days, Replicate 5

city: Denton

first: Mauricio

middle: S.

last: Antunes

address: 1155 Union Cir

department: Department of Biological Sciences

institute: University of North Texas

data_processing:
FastQC was used to assess the quality of small RNA-seq data.
Trimmomatic was used to remove adapter sequences in addition to removing low quality reads. Furthermore, reads of 16–30 nt in length were kept for further analysis.
Bowtie2 was used to map the trimmed reads to the Arabidopsis thaliana mature miRNA reference transcriptome obtained from mirBase.
Samtools and miRNA annotation file obtained from miRbase were used to process the alignment file to compute read counts for mature miRNAs.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file include read counts for each sample.

source_name: Leaf

extract_protocol:
Two infiltrated leaves from each plant (mock or infected) were harvested into a 1.5 ml microcentrifuge tube as a single biological replicate, totaling five replicates per treatment. Samples were flash frozen in liquid N2, followed by grinding with a sterile pestle. Total RNA was extracted with TRIzol (ThermoFischer Scientific), following standard protocol.
For small RNA library preparation, RNA was quantified with QuBit (ThermoFisher Scientific) Broad Range kit and RNA quality was checked the High Sensitivity RNA ScreenTape Analysis (Agilent). Libraries were generated with the QIAseq miRNA Library Kit (Qiagen) and sequenced using a NextSeq 550 High Output kit at the University of North Texas Health Science Center Genomics Core.

value: Leaf

tag: age

value: 5 weeks


title: PBMC, Control Patient 5


title: C_Control_BPH_19

value: Prostate (benign)


title: YO1737_Dig1_d5_out_YSEQ171

tag: genotype

value: Dig1 deletion


title: PBMC, Control Patient 4


title: YO1737_Dig1_d5_out_YSEQ170


title: Infected 4 days, Replicate 3


title: YO1914_Sfl1_d2_YSEQ169

value: Sfl1 deletion


title: Infected 4 days, Replicate 2


title: PBMC, Control Patient 3


title: YO1737_Dig1_d5_out_YSEQ169

value: day5 out


title: Infected 3 days, Replicate 5


title: C_Control_BPH_16


title: YO1737_Dig1_d5_in_YSEQ170


title: PBMC, Control Patient 2


title: Infected 3 days, Replicate 4


title: YO1737_Dig1_d5_in_YSEQ169


title: C_Control_BPH_14


title: C_Control_BPH_18


title: C_Control_BPH_17


title: Infected 3 days, Replicate 3


title: THP1_untreated_rep3

city: Chapel Hill

first: Austin

last: Hepperla

state: NC

address: 7018B Mary Ellen Jones Building

institute: University of North Carolina at Chapel Hill

data_processing:
Reads were then filtered for adaptor contamination using cutadapt and filtered such that at least 90% of bases of each read had a quality score > 30.
Reads were aligned to the reference genome (hg19) using STAR version 2.5.2b retaining only primary alignments.
Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using Salmon, and differentially expressed genes were detected using DESeq2 with the criteria of adjusted p-values (adjP) < 0.05.
The ClusterProfiler R package (v3.14.3) was employed to analyze the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional pathway annotation. Enrichment analysis for GO terms and KEGG pathways utilizes enrichGO and enrichKEGG functions and visualizes the result with bubble plots.
Assembly: hg19
Supplementary files format and content: Results txt file is the direct DESeq2 output

growth_protocol: Cells cultured under monocyte conditions (not differentiated into macrophages).

extract_protocol:
Samples were extracted using the Qiagene RNeasy mini kit.
Library preparation and sequencing were performed by Novogene as paired-end 150-bp reads.

treatment_protocol: Samples were either treated with 5ug/mL 2'3'-cGAMP or untreated (water alone).

value: WT

value: untreated


title: THP1_untreated_rep2


title: Infected 4 days, Replicate 4


title: YO1737_Dig1_d2_YSEQ171


title: YO1779_Tec1_d2_YSEQ169

value: Tec1 deletion


title: THP1_untreated_rep1


title: YO1737_Dig1_d2_YSEQ170


title: Infected 3 days, Replicate 2


title: C_Control_BPH_13


title: THP1_cGAMP_treated_rep3

value: 5ug/mL cGAMP


title: C_Control_BPH_12


title: Infected 3 days, Replicate 1


title: YO1737_Dig1_d2_YSEQ169


title: Infected 4 days, Replicate 1


title: C_Control_BPH_11


title: THP1_cGAMP_treated_rep2


title: YO1737_Dig1_d5_in_YSEQ171

value: day5 in


title: Mock 4 days, Replicate 5


title: C_Control_BPH_15


title: Mock 4 days, Replicate 4


title: THP1_cGAMP_treated_rep1


title: C_Control_BPH_9


title: L6mito_input120ng_0.5x

data_processing:
A 1.3 pM loading pool was prepared with 20% Phi-X spike-in and was sequenced on a single-408 end 75 bp run. Sequenced reads underwent quality checks with FastQC before the adapter and reads 409 <20nt were trimmed. Following sequencing, read1 was trimmed using fastp (fastp 0.20.0) and then mapped using blast (2.9.0+) with switch -task blastn and word length set to 19nt to miRbase mouse mature miRNAs (mature.fa download march 12 2018, miRbase v22.1). Raw read counts for each mature miRNA  generated using short perl script.
Assembly: miRbase v22.1
Supplementary files format and content: .csv file includes raw read counts for each miRNA for each sample

extract_protocol:
Mitochondria were isolated from approximately 5x10^6 L6 myoblast cells with the MACS Mitochondria Isolation Kit (mouse) (cat# 130-094-532, Miltenyi Biotec). Following isolation, the mitochondrial fraction was resuspended in 50 μL ice-cold Storage Buffer (cat# 130-094-532, Miltenyi Biotec) and incubated with 312 μg RNase-A (cat# 19101, Qiagen) for 1 h at 37°C. Following incubation, RNase-A was degraded by the addition of 5 μL proteinase-K (stock concentration 600 mAU/mL) (cat# 19131, Qiagen) and inverting the tube briefly. The solution was centrifuged at 8,000g for 10-minutes at 4C. The supernatant was aspirated, and the mitochondria pellet was washed twice with 100 μL ice-cold Storage Buffer (cat#130-096-946, Miltenyi Biotec), and centrifuged at 13,000g for 2-minutes at 4C between washes. The mitochondria pellet was resuspended in 100 μL storage buffer (cat# 130-094-532, Miltenyi Boitec) and stored at -80°C until further analyses.  For RNA extraction from isolated mitochondria, frozen samples were suspended in 5x volumes of TriReagent (cat# R2061, Integrated Sciences), thawed on ice and then centrifuged at 16,000xg for 2 min at 4°C to pellet the mitochondria. The mitochondria pellet was first sheared 20x through a fine pipette tip. Total RNA was extracted from isolated mitochondrua using Zymo Direct-Zol Micro Prep kit (#R2061, Integrated Sciences) with on-column DNase-I digest (#E1010, Integrated Sciences) as per the manufacturer's protocol. RNA was eluted in 12ul NFW.
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (cat# #E7560S, New England Biolabs.) with modifications Briefly, the 3’ and 5’ adapters and reverse transcription primer were diluted 0.5x, 0.3x, or 0.1x and 20 end-point PCR cycles were conducted. Following PCR amplification, the cDNA library was cleaned using the Monarch PCR & DNA Cleanup Kit (5 μg) (cat# T1030L, New England Biolabs.) using the 7:1 ratio of binding buffer:sample as per the manufacturer’s instructions. Uniquely indexed libraries were placed into an equimolar pool and were run in separate lands of a 6% Novex TBE-polyacrylamide gel (cat# EC6265BOX, Thermo Fisher Scientific), with 5 μL Quick-Load pBR322 DNA-MspI Molecular Marker (cat#E7560S, New England Biolabs.) run in a separate lane. Bands corresponding to the 143 and 190bp molecular markers were manually excised and extracted from the gel as per the manufacturer's protocol (cat#E7560S, New England Biolabs.).

tag: cell type

value: myoblast

value: male

tag: input

tag: ratios of_adapters


title: L6mito_input60ng_0.1x


title: C_Control_BPH_10


title: NPC_ST19

city: GuangZhou

first: Dong-Mei

last: Chi

address: 651 Dongfeng Road East

institute: SYSUCC

data_processing:
BCR reads were aligned to human reference VDJ dataset (http://cf.10Xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0.tar.gz) using CellRanger (“vdj” option; version 3.0.1; 10x Genomics).
Sequencing data in FASTQ files and manually aligned histological images were analysed with Space Ranger (version 1.3.0) and the probe set for alignment provided by 10X Genomics (Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A).
Assembly: hg38
Supplementary files format and content: BCR information were respectively represented by comma-separated text files including 20 samples.
Supplementary files format and content: 10X Genomics standard output format of spatial transcriptomics

source_name: Nasopharynx

extract_protocol:
Viable single cells were prepared from the PBMC and tumor of 10 nasopharyngeal carcinoma patients; formalin-fixed paraffin-embedded (FFPE) biopsy sections were prepared from 12 nasopharyngeal carcinoma patients
10X Genomics protocol CG000086 and CG000407

value: Nasopharynx

tag: disease state

value: Nasopharyngeal carcinoma


title: L6mito_input60ng_0.3x

tag: cell line


title: Mock 4 days, Replicate 3


title: C_Control_BPH_7


title: NPC_ST17


title: Mock 4 days, Replicate 2


title: NPC_ST18


title: C_Control_BPH_8


title: Mock 4 days, Replicate 1


title: L6mito_input30ng_0.1x


title: C_Control_BPH_5


title: Mock 3 days, Replicate 5


title: NPC_ST12


title: NPC_ST16


title: L6mito_input15ng_0.1x


title: C_Control_BPH_4


title: Mock 3 days, Replicate 4


title: C_Control_BPH_6


title: L6mito_input15ng_0.3x


title: Mock 3 days, Replicate 3


title: AC_TRM-sRNA-seq

organism: Solanum lycopersicum

source_name: flowers, leaves, roots, fruits

value: flowers, leaves, roots, fruits

value: AC

tag: ecotype

tag: library type

value: TRM-sRNA-seq


title: NPC_ST11


title: C_Control_BPH_3


title: L6mito_input7ng_0.3x


title: Mock 3 days, Replicate 2

value: Leaf

value: 5 weeks


title: NPC_ST10


title: NPC_ST9


title: L6mito_input30ng_0.3x


title: L6mito_input3.5ng_0.1x


title: Mock 3 days, Replicate 1


title: NPC_ST8


title: C_Control_BPH_1

value: Prostate (benign)


title: NPC_ST7


title: L6mito_input3.5ng_0.3x


title: zero_4

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: smallRNA

data_processing:
FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers.
We used Bowtie 1.0.1 to align the reads against the human genome (GRCh38), with a mismatch 0, to avoid false positives employing Partek Flow application, software version 7.0. Only the miRNAs with 10 or more reads were considered for differential expression analysis.
Mapped reads were quantified to mirbase v22 using Partek E/M method, so the processed data file contains counts values normalized by Partek E/M method
Genome_build: GRCh38
Supplementary_files_format_and_content: read count table

organism: other sequences

source_name: negative control without biological material

extract_protocol:
Total RNA from extracellular vesicles and platelets from surplus platelet concentrates obtained from Finnish Red Cross Blood Services was extracted using RNA Qiagen miRNeasy micro kit
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).
Small RNA-Seq

treatment_protocol: Platelets were isolated from surplus platelet concentrates by size exclusion chromatography (platelet sample), and diluted to 250 x 10E6 per mL concentration. Platelets were then activated through 1) CLEC-2, 2) GPVI receptor, or 3) thrombin and collagen co-activation. Non-activated platelets were used as control. After 30 minute incubation platelets were removed by centrifugation, and platelet-derived EVs (PEVs) were isolated from the platelet-free supernatant by cushioned-density ultracentrifugation.

tag: sample type

value: PBS

tag: platelet activation

value: no activation


title: zero_3

description: smallRNA


title: L6mito_input1.8ng_0.1x


title: C_Control_BPH_0

tag: tissue


title: L6mito_input1.8ng_0.3x


title: NPC_ST6


title: PC-3 cells-E2F1

city: Chongqing

first: Li

middle: qiu

last: Liu

address: No. 10, Changjiang Road, Daping, Yuzhong District, Chongqing

institute: Chongqing Daping Hospital

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length: <35 base pairs), and low-quality reads using Cutadapt (v1.9.1) and Trimmomatic (v0.35).FastQC is used to ensure high-quality reads.
The clean reads were mapped to the human genome (assembly human genome GRCh38) using the Burrows-Wheeler Aligner software
Peak detection was performed using the MACS (v2.1.1) peak finding algorithm
Annotation of peak sites to gene features was performed using the ChIPseeker R package
Peak calling and motif generation were performed by Homer.
Assembly: hg38
Supplementary files format and content: The bigwig results of PHF8 were provided with a format of bw
Supplementary files format and content: The bigwig results of E2F1 were provided with a format of bw
Library strategy: CUT&Tag

growth_protocol: 1640 medium with 10% FBS

extract_protocol:
CUT&Tag assay was performed according to its manufacturer’s instructions (Hyperactive® Universal CUT&Tag Assay Kit for Illumina, Vazyme, Cat# TD903). Cells were trypsinized and centrifuged at 1000 r.p.m for 5 minutes. Then cells and beads were suspended with wash buffer and binding buffer respectively. Cells were incubated with beads for 20 minutes at room temperature. Then, 3 μg of primary antibody [PHF8 (Cell Signaling Technology Cat# 93801, RRID: AB_2800215) and E2F1 (Abcam Cat# ab179445)] was added and incubated overnight at 4 °C with slow rotation. After removing primary antibodies, secondary antibodies were added and incubated for 1 hour at room temperature. Dig-wash buffer, pA/G-Tnp, Dig-300 buffer and 5XTTBL were successively used for fragmenting DNA. Then DNA fragments were purified and extracted with Proteinase K, 100 μl Buffer L/B和20 μl DNA Extract Beads.
DNA library was constructed with proper primers and amplified for 20 cycles (TruePrep® Index Kit V2 for Illumina, Vazyme, Cat# TD202).

value: human PCa cells

value: WT


title: zero_2

description: smallRNA


title: PC-3 cells-PHF8


title: KO blastocysts EM-seq_r1

status: Public on Sep 10 2024

city: Shanghai

first: Xinyu

address: Siping Road 1239

institute: Tongji University

description: KO E4.5 blastocysts EM-seq replicate1

library_source: other

data_processing:
For raw paired-end transcriptome sequencing data, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. STAR v2.6.1c was used to align the clean sequence data to the mouse reference genome (mm10), and RSEM v1.3.1 was used to quantify gene expression from the aligned sequences for each gene. The gene annotation file was obtained from the mouse GENCODE release (GRCm38.99). The R package DESeq2 v1.42.1 was used to identify differentially expressed genes between distinct Isca2 groups in mice. GSEA analysis was performed using the R package clusterProfiler v4.10.1, providing normalized enrichment scores and nominal p-values. KEGG functional annotation was conducted using the KOBAS online tool (http://bioinfo.org/kobas).
Assembly: mm10
Supplementary files format and content: aligned sequence file(bam) and gene expression quantification file(genes.results)

molecule: other

source_name: E4.5 blastocysts

growth_protocol: Animal welfare and the experimental procedures adhered to the ethical provisions on the Care and Use of Experimental Animals of Wenzhou Medical University and were approved and authorized by the Animal Experimental Committee of the University (No. xmsq2021-0068). Animals were maintained under a 12 h light/dark cycle and provided with food and water ad libitum in individually ventilated units.

extract_protocol:
To collected pre-implantation embryos, Isca2+/- female mouse intraperitoneal with 6.5 international unit of pregnant mares’ serum gonadotropin and, 45 to 47 h later, with 5 IU of human chorionic gonadotropin and crossed to Isca2+/- males. Embryos were isolated in M2 medium (Sigma: M7167) and cultured in potassium-supplemented optimised medium (Merck: MR-121-D) at 37℃ in 5% CO2.
The RNA-seq procedure was performed as previously described. Briefly, E4.5 blastocysts were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the single cell full length mRNA-amplification kit (N712, Vazyme). Library preparation was performed using the TruePrep DNA Library Prep Kit (TD501, Vazyme) according to the manufacturer’s instructions. All libraries were sequenced using the NovaSeq X Plus (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: E4.5 blastocysts

value: Isca2 -/-


title: KO blastocysts EM-seq_r2

description: KO E4.5 blastocysts EM-seq replicate2


title: G77 blastocysts EM-seq_r2

description: G77 E4.5 blastocysts EM-seq replicate2

value: Isca2 G77S/G77S


title: zero_1

description: smallRNA


title: NPC_ST5


title: WT blastocysts EM-seq_r3

description: WT E4.5 blastocysts EM-seq replicate3

value: wild type


title: G77 blastocysts EM-seq_r1

description: G77 E4.5 blastocysts EM-seq replicate1


title: WT blastocysts EM-seq_r2

description: WT E4.5 blastocysts EM-seq replicate2


title: C_Control_BPH_2

extract_protocol:
Total RNA was isolated using Rneasy mini kit (Qiagen). 1 microgram of total RNA was used for making the libraries.
Library prepared for RNA seq using NEBNext Ultra II RNA Prep Kit and validated using Ribogreen mRNA kit


title: RNA_seq_2TX-3a-R832_3 HSC

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

institute: Washington University in St. Louis

description: NovaSeq X Plus (300 cycles)

data_processing:
For RNA- seq, reads were sequenced using NovaSeq X Plus platform and aligned to mm10 using STAR and geen counts identified using subread:feature count. For WGBS, reads were sequenced using NovaSeq platform. Reads were aligned to mm10,  deduplicated and CpG methylation extracted using Bismark.
Assembly: mm10

source_name: HSC

growth_protocol: 250 CD45.2 HSCs of the indicated genotypes were competitively transplanted with competetive 250,000 CD45.1 whole bone marrow cells in lethally irradiated primary recipient mice.  Serial transplant was performed by repeating this process.

extract_protocol:
For RNA sequencing, 4000 HSC cells were sorted using Aurora cell sorter. And RNA was extracted using NucleoSpin RNA plus XS (Takara: 740990.50) . For WGBS, genomic DNA (gDNA) was prepared from the cells using PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific #K1820-02).
RNA librariers for RNA seq was preapred using Takara Clontech SMARTer mRNA library kit following manufactures protocol. For WGBS, using 200 ng of gDNA and 0.2% lambda DNA was bisulfite treated using EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research #D5042) and processed with xGen™ Methyl-Seq Library Prep (IDT, 10009824) to generate Illumina-compatible WGBS libraries.

tag: Stage

value: Secondary

value: HSC

tag: treatment

value: Vav-Cre


title: RNA_seq_2TX-3a-E752_1 HSC

description: NovaSeq X Plus (300 cycles)


title: WT blastocysts EM-seq_r1

description: WT E4.5 blastocysts EM-seq replicate1


title: RNA_seq_2TX-3a-KO_4 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-E752_4 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-E752_3 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-KO_1 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-KO_2 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-KO_3 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-Het_3 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-Het_4 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-E752_2 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-R832_1 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-R832_2 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-Control_4 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-Control_2 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-Control_3 HSC

description: NovaSeq X Plus (300 cycles)


title: RNA_seq_2TX-3a-Control_1 HSC

description: NovaSeq X Plus (300 cycles)


title: G77 blastocysts EM-seq_r3

description: G77 E4.5 blastocysts EM-seq replicate3