title: Patient plasma 73

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL315L3

value: FEMALE

value: PRIMARY RIGHT KNEE REPLACEMENT


title: Patient plasma 74

status: Public on Dec 29 2024

type: SRA

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL317L3

library_source: transcriptomic

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files was performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
UMI tags were extracted from raw files using UMI-tools software.
The first round of alignment using Bowtie1 was performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
Reads were collapsed according to associated UMI to remove PCR amplification bias.
UMI-based counts for each miRNA in a sample were generated from both alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference was performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Assembly: GRCh38
Supplementary files format and content: 1 combined tab-delimited text file includes raw count values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: plasma

growth_protocol: No growth

extract_protocol:
RNA was extracted from 200 µL of human plasma or synovial fluid using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204) or 250 µL to 1 mL human urine using Norgen Biotek's Urine Cell-Free Circulating RNA Purification Mini Kit following manufacturer instructions (Cat #56900).
miRNA libraries for miRNA-seq were prepared using Qiagen's QIAseq miRNA Library Kit optimized for biofluid samples (Cat # 331505). Individual libraries were quantified using a fluorometric high-sensitivity dsDNA assay and assessed using Bioanalyzer high sensitivity assay.

treatment_protocol: No treatment

tag: age

tag: Sex

value: MALE

tag: bmi

tag: procedure

tag: tissue

value: plasma

tag: leap id


title: Patient plasma 72

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL312L3

value: PRIMARY LEFT KNEE REPLACEMENT


title: esg-Gal4_ISCs-EBs_Pe_polyA_rep2

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description: polyA selected RNA sequencing from Pe-fed control sorted ISCs/EBs replicate 2

data_processing:
We used both R1 and R2 reads from the 150bp HiSeq paired-end sequencing runs.  Reads were trimmed of the adapters 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' and 'AGATCGGAAGAGCGTCGTGTAGGGAAAGA' at the 3' ends of R1 and R2 reads, respectively, using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting. Trimmed reads were mapped against the dm6 r6.31 transcriptome combined by a collection of D.melanogaster transposon consensus sequences (Senti et al., 2015 EMBO J, PMID: 26302790) using salmon/1.10.0 using options of --validateMappings --incompatPrior 0.0 --seqBias --gcBias. The output files of salmon (quant.sf) were used for the differential expression analysis of transposon mRNAs. The processed quant.sf files also contain the counts of r6.31 transcriptome.
Assembly: dm6/release 6.31
Supplementary files format and content: *_quant.sf: mRNA counts produced after the mapping by salmon; <transcript Name> <transcript Length> <Effective Length of the transcript> <transcript counts per one million transcripts (TPM)> <Number of mapped Reads>

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: adult midgut-ISCs_EBs

growth_protocol: Flies were kept at standard conditions at room temperature.

extract_protocol:
Midguts were dissected from 7 - 14 days old females (250 ~ 500 per replicates) in cold PBS after one week of heat-inactivation of Gal80, thus activation of escargot-gal4. After breaking down the tissues by elastase, Intestinal stem cells (ISCs) and Enteroblasts (EBs) were collected by Fluorescence-activated single cell sorting using Red stinger whose expression was driven by escargot-gal4. About 250000 to 750000 cells were collected per replicate.  Total RNA was extracted from collected ISCs/EBs using TRIZOL (Invitrogen) and a residual genomic DNA was removed by DNase I (Thermo Fisher). Oligo-dT magnetic beads (NEB) was used to purify polyA+ RNA.
The RNA-seq library was made from polyA+ RNA using NEB Ultra II Directional RNA library prep kit (NEB). We used the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers to amplify the libraries.

value: adult midgut-ISCs_EBs

value: female

tag: strain

value: Oregon R

tag: genotype

value: esg-Gal4 x UAS-GFP

value: 7 - 14 days old

tag: condition

value: standard food + Pseudomonas entomophila (Pe)


title: esg-Gal4_aub-RNAi_ISCs-EBs_Sucrose_polyA_rep1

description: polyA selected RNA sequencing from Sucrose-fed aub-RNAi sorted ISCs/EBs replicate 1

value: esg-Gal4 x UAS-GFP; UAS-aub[RNAi]

value: standard food + Sucrose


title: Patient plasma 71

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL308L3


title: Patient plasma 69

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL302L3


title: Patient plasma 70

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL304L3


title: esg-Gal4_ISCs-EBs_Sucrose_polyA_rep2

description: polyA selected RNA sequencing from Sucrose-fed control sorted ISCs/EBs replicate 2


title: esg-Gal4_ISCs-EBs_Sucrose_polyA_rep1

description: polyA selected RNA sequencing from Sucrose-fed control sorted ISCs/EBs replicate 1


title: Patient plasma 68

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL301L3


title: Patient plasma 67

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL300L3


title: esg-Gal4_ISCs-EBs_Pe_polyA_rep1

description: polyA selected RNA sequencing from Pe-fed control sorted ISCs/EBs replicate 1


title: Patient plasma 66

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL298L3


title: esg-Gal4_aub-RNAi_ovaries_sRNA

description: small RNA sequencing from ovaries (aub RNAi in the gut)

data_processing:
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting. The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses. Trimmed reads were mapped with bowtie v1.2.3 to the Drosophila melanogaster dm6 genome (allowing up to one mismatch) or to the transposon reference sequences (allowing up to three mismatches). The sam file was further processed to the bam file, then to the bed file using samtools/1.10 and bedtools/2.28.0.
Assembly: dm6/release 6.31
Supplementary files format and content: *_TE_3MM_mappers.bed: bed file of small RNA reads that are mapping to the transposon consensus sequences (allowing up to three mismatches, --all --best --strata option in bowtie)
Supplementary files format and content: *.tile-coverage.txt: counts of piRNA (>22nt & <41nt) reads that uniquely mapped to the genomic 0.5kb tiles (allowing up to one mismatch), normalised to one million genome unique mappers; <tile coordinate> <counts per one million genome unique mappers> <library name>

source_name: ovaries

extract_protocol:
Small RNA sequencing was performed on whole guts, ovaries and sorted Red stinger positive cells (ISCs + EBs). For the whole guts, flies were dissected in cold PBS 16 hours after being fed with Pe or 5% sucrose. The crop, the Malpighian tubules and the hindgut were carefully removed. 40 midguts have been dissected per replicate for each condition. Collected tissues were transferred in an Eppendorf tube containing 400 µL of PBS and kept on ice. Once all the tissues were dissected, 10 µL of elastase (Sigma-Aldrich, 10 µg/ µL) was added in each Eppendorf. Samples were kept at 27°C in a heat block for at least 1 hour until the tissues were totally degraded. Tissues were disrupted by pipetting up and down every 5 minutes. Samples were then centrifuged at 300 rcf for 20 minutes at 4°C and the supernatant was removed to obtain cell pellets. The same protocol has been applied for the ovaries. About 10 pairs of ovaries have been dissected per genotype. The Red stinger positive cells (ISCs + EBs) were collected from 250 ~ 500 midguts that were treated with elastase as above. Cells have been sorted using the fluorescence-activated single cell sorting. About 250000 to 750000 cells were collected per replicate.              Total RNA was extracted by TRIZOL (Invitrogen) and the genomic DNA was removed by DNase I (Thermo Fisher).
Small RNAs were first size-selected from the total RNA by 12% w/v UREA-PAGE using radio-labelled 19mer (5′-CGUACGCGGGUUUAAACGA) and 35mer (5'-CUCAUCUUGGUCGUACGCGGAAUAGUUUAAACUGU) spikes, and oxidised using sodium periodate. The oxidised small RNAs were further size-selected by PAGE. The size-selected oxidised small RNAs were ligated to the 3' adapter 5rApp/NNNNAGATCGGAAGAGCACACGTCT/3ddC, and then to the 5' adapter ACACUCUUUCCCUACACGACGCUCUUCCGAUCUNNNN where Ns are randomised. The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the RT primer GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT. The library was amplified using KAPA LongRange DNA polymerase (Sigma) with a universal TruSeq forward primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and a barcode-containing TruSeq reverse primer (e.g. CAAGCAGAAGACGGCATACGAGATxxxxxxGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where xxxxxx were the barcode).

value: ovaries

value: esg-Gal4 x UAS-GFP; UAS-aub[RNAi] VRDC #106999

tag: treatment

value: oxidised

value: standard food


title: Patient plasma 64

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL294L3

value: FEMALE


title: Patient plasma 61

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL287L3


title: esg-Gal4_aub-RNAi_ISCs-EBs_Pe_sRNA_rep1

description: small RNA sequencing from Pe-fed aub-RNAi sorted ISCs/EBs replicate 1


title: Patient plasma 60

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL284L3


title: esg-Gal4_ISCs-EBs_Pe_sRNA_rep2

description: small RNA sequencing from Pe-fed control sorted ISCs/EBs replicate 2


title: esg-Gal4_aub-RNAi_ISCs-EBs_Pe_sRNA_rep3

description: small RNA sequencing from Pe-fed aub-RNAi sorted ISCs/EBs replicate 3


title: esg-Gal4_ISCs-EBs_Pe_sRNA_rep3

description: small RNA sequencing from Pe-fed control sorted ISCs/EBs replicate 3


title: Patient plasma 56

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL260L3

value: PRIMARY BILATERAL KNEE REPLACEMENT


title: esg-Gal4_aub-RNAi_ISCs-EBs_Sucrose_sRNA_rep3

description: small RNA sequencing from Sucrose-fed aub-RNAi sorted ISCs/EBs replicate 3


title: esg-Gal4_aub-RNAi_ISCs-EBs_Sucrose_sRNA_rep2

description: small RNA sequencing from Sucrose-fed aub-RNAi sorted ISCs/EBs replicate 2


title: Patient plasma 63

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL290L3


title: Patient plasma 65

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL296L3

value: MALE

value: PRIMARY RIGHT KNEE REPLACEMENT


title: Patient plasma 55

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL255L3

value: plasma


title: Patient plasma 62

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL288L3


title: esg-Gal4_aub-RNAi_ISCs-EBs_Pe_sRNA_rep2

description: small RNA sequencing from Pe-fed aub-RNAi sorted ISCs/EBs replicate 2

value: adult midgut-ISCs_EBs


title: Patient plasma 57

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL263L3

value: PRIMARY LEFT KNEE REPLACEMENT


title: esg-Gal4_ISCs-EBs_Sucrose_sRNA_rep3

description: small RNA sequencing from Sucrose-fed control sorted ISCs/EBs replicate 3

value: female

value: Oregon R


title: aub-HN2-QC42_midgut_Pe_sRNA_rep3

description: small RNA sequencing from Pe-fed aub mutant midguts replicate 3

source_name: adult midguts

value: adult midguts

value: aub[HN2] x aub[QC42]

value: 5 - 8 days old


title: esg-Gal4_ISCs-EBs_Sucrose_sRNA_rep2

description: small RNA sequencing from Sucrose-fed control sorted ISCs/EBs replicate 2

value: esg-Gal4 x UAS-GFP

value: 7 - 14 days old

value: standard food + Sucrose


title: esg-Gal4_ISCs-EBs_Pe_sRNA_rep1

description: small RNA sequencing from Pe-fed control sorted ISCs/EBs replicate 1

value: oxidised

value: standard food + Pseudomonas entomophila (Pe)


title: Patient plasma 54

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL252L3

value: FEMALE


title: esg-Gal4_ISCs-EBs_Sucrose_sRNA_rep1

description: small RNA sequencing from Sucrose-fed control sorted ISCs/EBs replicate 1


title: aub-HN2-QC42_midgut_Pe_sRNA_rep2

description: small RNA sequencing from Pe-fed aub mutant midguts replicate 2


title: Patient plasma 52

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL240L3


title: esg-Gal4_ovaries_sRNA

description: small RNA sequencing from ovaries (control RNAi in the gut)

value: ovaries

value: standard food


title: Patient plasma 53

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL241L3

value: MALE


title: Patient plasma 51

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL234L3

value: plasma


title: esg-Gal4_aub-RNAi_ISCs-EBs_Sucrose_sRNA_rep1

description: small RNA sequencing from Sucrose-fed aub-RNAi sorted ISCs/EBs replicate 1

value: adult midgut-ISCs_EBs

value: esg-Gal4 x UAS-GFP; UAS-aub[RNAi] VRDC #106999


title: Patient plasma 59

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL282L3

value: PRIMARY BILATERAL KNEE REPLACEMENT


title: Patient plasma 58

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL278L3

value: PRIMARY LEFT KNEE REPLACEMENT


title: aub-HN2-QC42_midgut_Pe_sRNA_rep1

description: small RNA sequencing from Pe-fed aub mutant midguts replicate 1

value: adult midguts

value: female

value: Oregon R


title: aub-HN2-QC42_midgut_Sucrose_sRNA_rep3

description: small RNA sequencing from Sucrose-fed aub mutant midguts replicate 3

value: aub[HN2] x aub[QC42]

value: 5 - 8 days old


title: Patient plasma 49

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL230L3

value: PRIMARY RIGHT KNEE REPLACEMENT


title: Patient plasma 50

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL233L3


title: Patient plasma 48

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL229L3


title: Patient plasma 47

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL228L3


title: aub-HN2-QC42_midgut_Sucrose_sRNA_rep2

description: small RNA sequencing from Sucrose-fed aub mutant midguts replicate 2

value: oxidised

value: standard food + Sucrose


title: w1118_midgut_Pe_sRNA_rep1

description: small RNA sequencing from Pe-fed w1118 midguts replicate 1

value: standard food + Pseudomonas entomophila (Pe)


title: Patient plasma 45

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL223L3

value: FEMALE


title: aub-HN2-QC42_midgut_Sucrose_sRNA_rep1

description: small RNA sequencing from Sucrose-fed aub mutant midguts replicate 1


title: Patient plasma 46

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL227L3


title: w1118_midgut_Sucrose_sRNA_rep2

description: small RNA sequencing from Sucrose-fed w1118 midguts replicate 2


title: Patient plasma 40

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL203L3


title: Patient plasma 41

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL206L3


title: w1118_midgut_Sucrose_sRNA_rep3

description: small RNA sequencing from Sucrose-fed w1118 midguts replicate 3


title: Patient plasma 44

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL222L3


title: Patient plasma 39

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL201L3


title: Patient plasma 42

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL209L3


title: w1118_midgut_Sucrose_sRNA_rep1

description: small RNA sequencing from Sucrose-fed w1118 midguts replicate 1


title: Multiplexed Hilar Lymph Nodes 2, T-cells, TCR

city: Pittsburgh

first: Kaveh

last: Moghbeli

state: PA

address: 3459 Fifth Avenue

country: USA

institute: University of Pittsburgh

description:
Library name: hln_2_tcr
20221115_TCR_LN_filtered_contig_annotations.csv
20221115_TCR_LN_all_contig_annotations.csv

data_processing:
Libraries were sequenced using the Illumina platform. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using 10x Genomics CellRanger v5 and CellRanger VDJ pipelines.
Assembly: 10x GRCh38-2020-A human reference genome
Supplementary files format and content: 10x H5 files for Gene expression/HTO multiplexed data and CSV files for TCR annotations
Library strategy: TCR-Seq

source_name: hilar lymph node

extract_protocol:
Explanted lungs and HLN from study participants undergoing re-transplantation were obtained after receiving approval from our Institutional Review Board. Explanted lungs from research-consented organ donors whose lungs were rejected for clinical transplantation were obtained following approval from our institutional Committee for Oversight of Research and Clinical Training Involving Decedents. Following transplant, lung and HLN tissues were cross sectioned, placed into a tissue cartridge in zinc formalin fixation solution for 48 to 72 hours. Sections were then placed in 70% ethanol prior to paraffin embedding. Samples were embedded within 1 week of transplant. The tissue was then manually cut into fine pieces and transferred to a GentleMACS Dissociator (Miltenyi Biotec) for 30 minutes at 37°C. Following dissociation, tissue was filtered in the following order: first through a stainless-steel mesh filter, then through a 100-micron filter, then through a 70-micron filter. The suspension was then centrifuged at 1500 rpm for 5 minutes. Cells were then counted and frozen back at -80°C for future analyses.
Sorted cells were captured for single-cell RNA and T cell receptor (TCR) sequencing using the 10x Genomics 5’ assay per manufacturer instructions. Libraries were sequenced using the Illumina platform.

value: hilar lymph node

tag: cell type

value: T-cell

tag: library type

value: TCR

value: IPF

tag: batch


title: Multiplexed Hilar Lymph Nodes 2, T-cells, HTO

description:
Library name: hln_2_hto
20221115_HTO_LN_filtered_feature_bc_matrix.h5
20221115_HTO_LN_raw_feature_bc_matrix.h5

library_source: other

data_processing:
Libraries were sequenced using the Illumina platform. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using 10x Genomics CellRanger v5 and CellRanger VDJ pipelines.
Assembly: 10x GRCh38-2020-A human reference genome
Supplementary files format and content: 10x H5 files for Gene expression/HTO multiplexed data and CSV files for TCR annotations
Library strategy: CITE-seq

molecule: protein

value: HTO

tag: hto

value: HTO-4-TotalC (IPF_1), HTO-5-TotalC (IPF_2), HTO-6-TotalC (IPF_3)


title: Multiplexed Hilar Lymph Nodes 2, T-cells, GEX

description:
Library name: hln_2_mRNA
20221115_HTO_LN_filtered_feature_bc_matrix.h5
20221115_HTO_LN_raw_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced using the Illumina platform. Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using 10x Genomics CellRanger v5 and CellRanger VDJ pipelines.
Assembly: 10x GRCh38-2020-A human reference genome
Supplementary files format and content: 10x H5 files for Gene expression/HTO multiplexed data and CSV files for TCR annotations

value: mRNA


title: Multiplexed Lungs 2, T-cells, GEX

description:
Library name: lung_2_mRNA
20221115_HTO_Lung_filtered_feature_bc_matrix.h5
20221115_HTO_Lung_raw_feature_bc_matrix.h5

source_name: lung

value: lung


title: Patient plasma 37

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL197L3

value: MALE

value: PRIMARY LEFT KNEE REPLACEMENT

value: plasma


title: Patient plasma 36

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL184L3


title: w1118_midgut_Pe_sRNA_rep2

description: small RNA sequencing from Pe-fed w1118 midguts replicate 2

value: adult midguts

value: female

value: Oregon R

value: 5 - 8 days old


title: w1118_midgut_Pe_sRNA_rep3

description: small RNA sequencing from Pe-fed w1118 midguts replicate 3

value: oxidised

value: standard food + Pseudomonas entomophila (Pe)


title: Patient plasma 43

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL211L3


title: Multiplexed Lungs 2, T-cells, HTO

description:
Library name: lung_2_hto
20221115_HTO_Lung_filtered_feature_bc_matrix.h5
20221115_HTO_Lung_raw_feature_bc_matrix.h5


title: Patient plasma 35

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL180L3

value: PRIMARY RIGHT KNEE REPLACEMENT


title: Patient plasma 33

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL177L3


title: Patient plasma 34

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL179L3


title: Multiplexed Lungs and Hilar Lymph Nodes 1, T-cells, GEX

description:
Library name: lung_and_hln_1_mRNA
20220813_HTO2_filtered_feature_bc_matrix.h5
20220813_HTO2_raw_feature_bc_matrix.h5

source_name: lung and hilar lymph node

value: lung and hilar lymph node

value: T-cell

value: mixed sample (control, CLAD)


title: Patient plasma 32

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL175L3

value: FEMALE


title: Multiplexed Hilar Lymph Nodes 1, T-cells, TCR

description:
Library name: hln_1_tcr
20220813_TCR1_filtered_contig_annotations.csv
20220813_TCR1_all_contig_annotations.csv

value: hilar lymph node

value: TCR


title: Patient plasma 31

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL173L3


title: Multiplexed Hilar Lymph Nodes 1, T-cells, HTO

description:
Library name: hln_1_hto
20220813_HTO1_filtered_feature_bc_matrix.h5
20220813_HTO1_raw_feature_bc_matrix.h5

value: HTO

value: HTO-1-TotalC (CLAD_2),  HTO-2-TotalC (CLAD_1), HTO-3-TotalC (Control_1), HTO-4-TotalC (Control_2)


title: Patient plasma 29

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL163L3

value: PRIMARY LEFT KNEE REPLACEMENT


title: Patient plasma 30

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL165L3

value: MALE

value: PRIMARY BILATERAL KNEE REPLACEMENT

value: plasma


title: Patient plasma 38

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL199L3


title: Patient plasma 28

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL154L3


title: Patient plasma 27

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL143L3


title: Multiplexed Lungs 1, T-cells, GEX

description:
Library name: lung_1_mRNA
20211111_HTO_filtered_feature_bc_matrix.h5
20211111_HTO_raw_feature_bc_matrix.h5

value: lung

value: mRNA


title: Multiplexed Lungs 1, T-cells, TCR

description:
Library name: lung_1_tcr
20211111_TCR_filtered_contig_annotations.csv
20211111_TCR_all_contig_annotations.csv


title: Multiplexed Lungs 1, T-cells, HTO

description:
Library name: lung_1_hto
20211111_HTO_filtered_feature_bc_matrix.h5
20211111_HTO_raw_feature_bc_matrix.h5

value: HTO-1-TotalC (Control_1), HTO-2-TotalC (Control_2), HTO-3-TotalC (CLAD_1), HTO-4-TotalC (CLAD_2)


title: Multiplexed Lungs 2, T-cells, TCR

description:
Library name: lung_2_tcr
20221115_TCR_Lung_filtered_contig_annotations.csv
20221115_TCR_Lung_all_contig_annotations.csv

value: IPF


title: Patient plasma 26

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL140L3


title: Patient plasma 25

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL133L3

value: PRIMARY RIGHT KNEE REPLACEMENT


title: Patient plasma 24

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL117L3


title: Patient plasma 23

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL114L3


title: Patient plasma 22

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL110L3


title: Multiplexed Lungs and Hilar Lymph Nodes 1, T-cells, TCR

description:
Library name: lung_and_hln_1_tcr
20220813_TCR2_filtered_contig_annotations.csv
20220813_TCR2_all_contig_annotations.csv

value: lung and hilar lymph node


title: Multiplexed Lungs and Hilar Lymph Nodes 1, T-cells, HTO

description:
Library name: lung_and_hln_1_hto
20220813_HTO2_filtered_feature_bc_matrix.h5
20220813_HTO2_raw_feature_bc_matrix.h5

value: T-cell

value: HTO-1-TotalC (CLAD_3, Lung), HTO-2-TotalC (CLAD_3, HLN), HTO-3-TotalC (Control_3, Lung), HTO-4-TotalC (Control_3, HLN)


title: Canonical ADLD Duplication Example

type: genomic

first: Quasar

last: Padiath

address: 130 DeSoto St., Dept. of Human Genetics

department: Human Genetics

hyb_protocol: Samples and hybridization buffer (Agilent Oligo aCHG/ChIP-on-chip Hybridization Kit) were combined and applied to microarrays (Design# 035726_20110728) enclosed in Agilent SureHyb chambers. Hybridization was carried out for 24 hours at 65°C.

scan_protocol: After hybridization, slides were sequentially washed. Sample were then scanned in an G2565CA Agilent microarray scanner at 5 µm resolution.

data_processing: aCGH data was extracted using Agilent’s Feature Extraction program and assessed for quality based on background noise, signal intensity, signal-to-noise ratio, reproducibility, and derivative log ratio standard deviation. Following extraction, the raw data were normalized to the control (Cy3) and analyzed using Agilent Cytogenetics version 4.0.3.12. Human genome assembly GRCh38/hg38 was used for all genome coordinates.

molecule: genomic DNA

source_name: Blood

label_protocol: DNA test and reference samples (0.2 µg each) were digested with Alu I and Rsa I for 2 hours at 37°C, followed by heat inactivation for 20 minutes at 65°C. After digestion and inactivation, the DNA was labeled using Cy5-dUTP for the test samples and Cy3-dUTP for the reference samples, and then purified using the Agilent SureTag DNA Labeling Kit.

extract_protocol: Genomic DNA from whole blood was isolated using the Gentra Puregene kit (Qiagen) according to the manufacturer’s instructions.

value: Female

tag: clinical phenotype

value: ADLD

value: Blood

tag: clincal phenotype

value: No ADLD

tag: sample type

value: Control


title: Canonical ADLD Deletion Example


title: Patient plasma 21

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL103L3

tag: age


title: Patient plasma 20

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL97L3

tag: Sex

value: FEMALE

value: PRIMARY LEFT KNEE REPLACEMENT


title: s16 Lung tissue from SHAM rats

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

data_processing:
bcl2fastq2-2.18.12 (demultiplex)
Cutadapt 1.15 (adapter trimming)
FastQC v0.11.5 (quality control)
Rsubread v2.8.1 align
Rsubread v2.8.1 featureCounts
edgeR v3.36.0 TMM (normalization)
limma 3.50.0 (linearization)
Assembly: mRatBN7.2
Supplementary files format and content: tsv CPM TMM quantile normalized CPM (Count per Million)

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
RNAeasy Mini Kit (QIAGEN)
TruSeq Stranded Total RNA library prep kit (Illumina)

treatment_protocol: Lung biopsies from common bile duct ligation (CBDL) rats or SHAM-operated rats

value: Lung

value: SHAM


title: Multiplexed Hilar Lymph Nodes 1, T-cells, GEX

description:
Library name: hln_1_mRNA
20220813_HTO1_filtered_feature_bc_matrix.h5
20220813_HTO1_raw_feature_bc_matrix.h5

value: hilar lymph node

value: mixed sample (control, CLAD)


title: Patient plasma 18

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL95L3

tag: bmi

value: plasma


title: Family 3 Genomic DNA


title: s15 Lung tissue from SHAM rats


title: Patient plasma 19

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL96L3

value: MALE

tag: procedure


title: Patient plasma 15

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL78L3

tag: tissue


title: Patient plasma 17

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL88L3

value: PRIMARY BILATERAL KNEE REPLACEMENT

tag: leap id


title: Patient plasma 14

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL76L3


title: s11 Lung tissue from SHAM rats


title: s10 Lung tissue from SHAM rats


title: Patient plasma 16

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL80L3


title: s9 Lung tissue from SHAM rats


title: s12 Lung tissue from SHAM rats


title: Patient plasma 13

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL74L3


title: Trem2 Wildtype, replicate 3, infarction core

city: Shenzhen

first: Kunyu

last: Li

state: Guangdong

address: No. 1068 Xueyuan Avenue, Shenzhen University Town, Xili, Nanshan District

country: China

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

data_processing:
Sequences data were filtered for adaptor/low-quality sequence using SOAPnuke v1.5.2. software (Parameters -l 15 -q 0.2 -n 0.05).
Filtered sequence reads were mapped to GRCm39/mm39 using HISAT2 v2.0.4. software (Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8)
Align clean reads to the reference genes by using Bowtie2 and quantify the gene expression based on the alignment results with R package Subread.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: mouse brain tissue

extract_protocol:
RNA was extracted using Trizol-like total RNA extraction reagent (Phygene, PH1420), 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using MGIEasy stLFR Library Prep Kit following manufacturers' protocols

value: mouse brain tissue

tag: tissue location

value: infarction core

tag: strain background

value: Trem2 wildtype

value: photothrombotic model of ischemic stroke


title: Family 2 Genomic DNA

value: Male

value: Female


title: Patient plasma 12

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL62L3


title: s14 Lung tissue from SHAM rats


title: Family 1 Genomic DNA

value: No ADLD

value: Blood


title: Trem2 Wildtype, replicate 2, infarction core

tag: genotype


title: s13 Lung tissue from SHAM rats

tag: treatment


title: Trem2 Wildtype, replicate 1, infarction core


title: Patient plasma 11

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL59L3

value: PRIMARY RIGHT KNEE REPLACEMENT


title: s8 Lung tissue from CBDL rats

value: CBDL


title: Trem2 knockout, replicate 2, infarction core

value: Trem2 knockout


title: s7 Lung tissue from CBDL rats

value: Lung


title: Trem2 knockout, replicate 1, infarction core


title: Patient plasma 10

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL57L3

value: PRIMARY LEFT KNEE REPLACEMENT


title: Patient plasma 9

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL56L3

value: FEMALE


title: s5 Lung tissue from SHAM rats

value: SHAM


title: Trem2 knockout, replicate 3, infarction core


title: Trem2 Wildtype, replicate 2, peri-infarction zone

value: peri-infarction zone


title: Trem2 Wildtype, replicate 3, peri-infarction zone


title: Trem2 Wildtype, replicate 1, peri-infarction zone


title: Patient plasma 8

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL55L3

value: plasma


title: s4 Lung tissue from SHAM rats


title: Trem2 knockout, replicate 1, peri-infarction zone

value: mouse brain tissue


title: Trem2 Wildtype, replicate 3, contralateral site

value: contralateral site


title: Trem2 knockout, replicate 3, peri-infarction zone


title: Patient plasma 6

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL36L3

value: MALE


title: Patient plasma 7

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL39L3


title: s3 Lung tissue from CBDL rats


title: s1 Lung tissue from CBDL rats


title: Trem2 Wildtype, replicate 2, contralateral site

value: Trem2 wildtype

value: photothrombotic model of ischemic stroke


title: Patient plasma 5

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL35L3

value: PRIMARY BILATERAL KNEE REPLACEMENT


title: s2 Lung tissue from CBDL rats


title: Trem2 Wildtype, replicate 1, contralateral site


title: Trem2 knockout, replicate 1, contralateral site


title: Trem2 knockout, replicate 3, contralateral site


title: Igri_stage III_biol rep 4

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

data_processing:
Illumina RTA3 was used for basecalling and .cbcl files were converted to .fastq using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence and low-quality sequence and then mapped to Morex v2 whole genome using hisat2 v2.0.5 with default parameters. Hisat2 output was converted and sorted by samtools view and samtools sort, respectively.
The number of reads falling in the exons of transcripts were counted using subread v1.5.2 with parameters -p -t exon -g Parent.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated in Excel using standard formula. In short number of reads falling in the exons were normalized by the size of transcript and by the size of the library.
Assembly: Morex V2 by Masher et al. 2019
Supplementary files format and content: Tab-delimited text file including RAW counts for each Sample
Supplementary files format and content: Excel table including RAW counts for each Sample, calculated MEAN, SD and FPKM values

organism: Hordeum vulgare

source_name: microspores

extract_protocol:
Total RNA was isolated using Nucleo Spin RNA Plant Kit ((740949.50, MACHEREY-NAGEL, Düren, Germany) according to manufacturer's protocol.
RNA libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina for Illumina sequencing.

value: microspores

tag: developmental stage

value: stage III

value: bi- and multi-cellular structures

value: Igri

value: pre-treatment of anthers in 0.4M mannitol for 48h at 21C, followed by 48 h incubation of isolated microspores in KBP nutrient medium in the dark at 21C


title: Trem2 knockout, replicate 2, contralateral site

value: Trem2 knockout


title: Patient plasma 4

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL33L3

value: PRIMARY RIGHT KNEE REPLACEMENT


title: s6 Lung tissue from CBDL rats

value: Lung

value: CBDL


title: ccRCC_replica13

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description: Library name: ccRCC_rep13

data_processing:
RNA sequencing data were analyzed using Ion Torrent Software Suite version 5.4. The alignment was carried out using the Torrent Mapping Alignment Program (TMAP) against the reference sequence derived from the hg19 (GRCh37) assembly.
Assembly: GRCh37 (hg19)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Kidney

extract_protocol:
RNA was extracted from FFPE tissue following the protocol of RecoverAll™ Total Nucleic Acid Isolation Kit (Invitrogen, Thermo Fisher Scientific). After nucleic acid extraction, TURBO DNA-free™ kit (Invitrogen, Thermo Fisher Scientific) was used to ensure genomic DNA removal from RNA samples.
Whole transcriptome sequencing was done using the AmpliSeq Whole Transcriptome on the S5 System (Thermo (Fisher) Scientific, MA, USA). The targeted RNA-seq library was prepared using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo (Fisher) Scientific, MA, USA). After that, the library was purified using Agencourt AMPure XP Beads (Beckman Coulter, Indianapolis, IN, USA) and quantified using an Ion Library TaqMan™ Quantitation Kit (Applied Biosystems, Waltham, MA, USA). After diluting the libraries to 100pM, they were pooled equally. The resulting template libraries were then sequenced on the Ion S5 XL Semiconductor sequencer using the Ion 540 Chip (Life Technologies Corporation, Carlsbad, CA) prepared on a fully automated Ion Chef System (Thermo (Fisher) Scientific, MA, USA).

value: Kidney

value: ccRCC


title: Patient plasma 3

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL32L3

value: FEMALE

value: PRIMARY LEFT KNEE REPLACEMENT

value: plasma


title: Trem2 knockout, replicate 2, peri-infarction zone

value: mouse brain tissue

value: peri-infarction zone


title: ccRCC_replica12

description: Library name: ccRCC_rep12


title: Patient plasma 1

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL16L3


title: ccRCC_replica10

description: Library name: ccRCC_rep10


title: Patient plasma 2

description:
2023_Match414_3biofluids_miRNA_counts.tsv
PL23L3

value: MALE


title: ccRCC_replica9

description: Library name: ccRCC_rep9


title: Igri_stage III_biol rep 2

value: microspores


title: Igri_stage III_biol rep 3

value: stage III


title: Igri_stage III_biol rep 1

value: bi- and multi-cellular structures


title: ccRCC_replica8

description: Library name: ccRCC_rep8


title: ccRCC_replica7

description: Library name: ccRCC_rep7


title: Igri_stage II_biol rep 4

value: stage II

value: bi-cellular pollen grains

value: Igri

value: pre-treatment of anthers in 0.4M mannitol for 48h at 21C, followed by 24 h incubation of isolated microspores in KBP nutrient medium in the dark at 21C


title: ccRCC_replica6

description: Library name: ccRCC_rep6


title: ccRCC_replica5

description: Library name: ccRCC_rep5


title: ccRCC_replica11

description: Library name: ccRCC_rep11


title: ccRCC_replica4

description: Library name: ccRCC_rep4


title: NEB Ctcf cKO6

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

institute: OHRI

description: Cut&run-seq Ctcf

library_source: genomic

data_processing:
FastQ Groomer: Fastq file reformatting
Trimmomatic: Read trimming
Bowtie2 (mapping to the mm9 genome)
Macs2 (peak calling)
Deeptools (scaling)
Assembly: mm9
Supplementary files format and content: bigwig (data mapped to the mm9 genome), bedgraph (data mapped to the mm9 genome and scaled), bed (called peaks)

source_name: dorsal telencephalon

extract_protocol:
mechanical trituration - E13.5 microdissected murine neocortex
NEBNext® UltraTM II Library Prep Kit (New England Biolabs)
cut&run-seq

value: dorsal telencephalon

value: Adnp cKO


title: NEB Ctcf cKO4

description: Cut&run-seq Ctcf


title: NEB Ctcf Ctl2

description: Cut&run-seq Ctcf

value: control


title: Igri_stage II_biol rep 3


title: ccRCC_replica3

description: Library name: ccRCC_rep3

value: Kidney

value: ccRCC


title: NEB Ctcf Ctl1

description: Cut&run-seq Ctcf


title: Igri_stage II_biol rep 2


title: control_replica10

description: Library name: Ctrl_rep10


title: ccRCC_replica2

description: Library name: ccRCC_rep2


title: control_replica9

description: Library name: Ctrl_rep9


title: Igri_stage II_biol rep 1


title: control_replica8

description: Library name: Ctrl_rep8


title: Abcam Chd4 CKO6

description: Cut&run-seq Chd4


title: Igri_stage I_biol rep 4

value: stage I

value: uni-cellular  microspores

value: pre-treatment of anthers in 0.4M mannitol for 48 h at 21C


title: Abcam Chd4 Ctl2

description: Cut&run-seq Chd4


title: control_replica6

description: Library name: Ctrl_rep6


title: control_replica5

description: Library name: Ctrl_rep5


title: Igri_stage I_biol rep 3


title: Abcam Chd4 Ctl1

description: Cut&run-seq Chd4


title: control_replica3

description: Library name: Ctrl_rep3


title: Igri_stage I_biol rep 1


title: control_replica2

description: Library name: Ctrl_rep2


title: control_replica1

description: Library name: Ctrl_rep1


title: Igri_stage 0_biol rep 4

value: stage 0

value: no pre-treatment of anthers


title: IgG Ctl2

description: Cut&run-seq negative control


title: 27 RIC-CD8-3-28 3 StP219

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: Rictor-/- stimulated CD8+ T cells

data_processing:
Sequenced reads were mapped to GRCm38 (Ensembl version 92) using STAR 2.6.0a with default parameters
STAR 2.6.0a was used to obtain read counts per gene based on ENSEMBL annotation Mus_musculus.GRCm38.92.gtf.
Assembly: Genome_build:  GRCm38 version 92
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include STAR gene-based read counts for each sample

source_name: Sorted T cells

growth_protocol: CD4+ and CD8+ pooled lymph node and spleen cells from B6 wt, B6-CD4-cre-Rptorfl/fl or B6-CD4-cre;Rictorfl/fl mice were negatively sorted with magnetic microbeads and cultured in RPMI-10 with 5 ng/ml IL-7 (control cultures) or plate bound 10 µg/ml anti-CD3 (145-2C.11) and anti-CD28 (37.51) mAbs for 48 hours.

extract_protocol:
Cells were washed and resuspended in 250 µl PBS and 750 µl Trizol-LS added. Total RNA was isolated and purified using RNeasy columns (Qiagen), including DNase treatment. The total RNA preparations were examined by capillary electrophoresis using a Shimadzu MultiNA microchip electrophoresis system and a Qubit device to assess RNA integrity determine 18/28S RNA and total RNA amounts, respectively.
RNA samples were fragmented using ultrasound (4 pulses of 30 s each at 4°C). Oligonucleotide adaptors were ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer.
The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adaptor was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified with 12-14 cell cycles to about 10-20 ng/μL using a high fidelity DNA polymerase.
The TruSeq barcode sequences, which are part of the 5' and 3' TruSeq sequencing adapters, are included. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.

treatment_protocol: The cells were stained with MFG-E8-EGFP fusion protein (Kranich et al., 2020, PMID: 32944180) and 7-AAD and sorted on a FACSAria III as negative for both markers to rigorously remove dead cells from the analysis. 0.2-1.1x106 MFG-E8- 7-AAD- cells were sorted.

tag: cell type

value: Magnetically sorted lymph node and spleen CD8+ T cells

value: Cultures stimulated with plate bound 10 ug/ml anti-CD3 (145-2C.11) and anti-CD28 (37.51) mAbs (48 h)


title: Igri_stage 0_biol rep 3

value: microspores


title: 26 RIC-CD8-3-28 2 StP219

description: Rictor-/- stimulated CD8+ T cells


title: 25 RIC-CD8-3-28 1 StP219

description: Rictor-/- stimulated CD8+ T cells


title: Igri_stage 0_biol rep 2


title: control_replica7

description: Library name: Ctrl_rep7


title: APP/PS1, KYL, replicate 1, snRNASeq

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

description:
Library name: ADKYL1
Novogene

data_processing:
Alignment is done by cellranger (version 3.0.1) to GRCm38 pre-mRNA reference. Downstream differential analysis and subcluster analysis is done by Seurat. Genome_build: GRCm38
Assembly: GRCm38
Supplementary files format and content: filtered count matrix from Seurat

source_name: Hippocampi

extract_protocol:
Mice were anesthetized with isoflurane, and their brains were dissected. Hippocampi were dissected from brain, immediately frozen in liquid nitogen and stored at −80°C
The frozen hippocampal tissues were homogenized with prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, the homogenate was mixed 1:1 with OptiPrep, and the solution was centrifuged at 10,000 × g for 20 min at 4°C. The pellet of separated nuclei was washed to remove the OptiPrep and resuspended in DMEM/F12 supplemented with 10% fetal bovine serum. The nuclei were counted with a hemocytometer and then diluted to 400 nuclei per microliter. All buffers and gradient solutions for nuclear extraction contained 60 U/mL RNasin (Promega). the snRNA-seq libraries were generated using a Chromium Single Cell 3′ Library Kit v3 (10x Genomics, 1000078) according to the manufacturer’s instructions. The concentrations of the final libraries were measured by Qubit (Thermo Fisher Scientific), and fragment lengths were determined using Fragment Analyzer (Advanced Analytical Technologies). The libraries were subjected to paired-end sequencing.

value: Hippocampi

value: Tg

value: KYL


title: APP/PS1, aCSF, replicate 3, snRNASeq

institute: Hong Kong University of Science and Technology

description:
Library name: AD3
Novogene

value: aCSF


title: APP/PS1, aCSF, replicate 1, snRNASeq

description:
Library name: AD1
Novogene


title: APP/PS1, aCSF, replicate 2, snRNASeq

description:
Library name: AD2
Novogene


title: APP/PS1, KYL, replicate 2, snRNASeq

description:
Library name: ADKYL2
Novogene


title: APP/PS1, KYL, replicate 3, snRNASeq

description:
Library name: ADKYL3
Novogene


title: control_replica4

description: Library name: Ctrl_rep4


title: Igri_stage I_biol rep 2

value: Igri


title: 24 RAP-CD8-3-28 3 StP219

description: Raptor-/- stimulated CD8+ T cells


title: Igri_stage 0_biol rep 1


title: WT, aCSF, replicate 3, snRNASeq

description:
Library name: WT3
Novogene

value: WT


title: WT, aCSF, replicate 2, snRNASeq

description:
Library name: WT2
Novogene


title: 23 RAP-CD8-3-28 2 StP213

description: Raptor-/- stimulated CD8+ T cells


title: 22 RAP-CD8-3-28 1 StP212

description: Raptor-/- stimulated CD8+ T cells


title: WT, aCSF, replicate 1, snRNASeq

description:
Library name: WT1
Novogene


title: Golden Promise_stage III_biol rep 4

value: stage III

value: bi- and multi-cellular structures

value: Golden Promise

value: pre-treatment of anthers in 0.4M mannitol for 48h at 21C, followed by 48 h incubation of isolated microspores in KBP nutrient medium in the dark at 21C


title: Golden Promise_stage III_biol rep 3


title: HS, Input, Rep2

city: Boston

first: Uri

last: WEISSBEIN

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
library strategy: CHART-seq
CHART reads were trimmed with Trim-galore
Reads were aligned to mouse mm10 and drosophila genome reference genome with Bowtie2
Removal of reads that aligned to more than one position in the genome,  duplicated reads or reads with low mapping quality score
Heatmaps and BigWig files were created with Deeptools
Tracks were normalized according to the number of reads aligned to the drosophila genome
Assembly: mm10
Supplementary files format and content: Bigwig coverage  generated by using bamCoverage from Deeptools

molecule: other

growth_protocol: NIH3T3 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum, 1% Penicilin- Streptomycin-Neomycin (PSN) antibiotic mixture and 1% non-essential amino acids from GibcoTM. HCT8 cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 1% Penicilin- Streptomycin-Neomycin (PSN) antibiotic mixture from and 1% non-essential amino-acids from GibcoTM.

extract_protocol:
cells were resuspended in 1XPBS and crosslinked with 1% formaldehyde for 10 min at room temperature. The formaldehyde was quenched with addition of 0.125M glycine, washed three times with PBS-0.05% tween-20, and cell pellets were snap freeze in liquid nitrogen for CHART experiment as previously published with biotenylated 7SL sense or antisense probes
After CHART, libraries were constFor each sample 2pg of drosophila S2 cells sonicated DNA was spike-in. sequencing libraries were than prepared with NEBNext® Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: NIH3T3 cells were resuspended in 2ml of DMEM pre-warmed to 37 ˚C and incubated for 15min at 37 ˚C (control) or 45 ˚C (heat-shock). Cells were collected and CHART-Seq was preformed with antisense or sense probes

tag: cell line

value: fibroblast

value: wt

value: HS


title: HS, Sense, Rep2


title: 20 RAP-CD8-7 2 StP213

description: Raptor-/- unstimulated CD8+ T cells

value: Control cultures with 5 ng/ml IL-7 (48 hours)


title: Golden Promise_stage III_biol rep 1


title: Control, Sense, Rep2

value: No HS


title: Control, Input, Rep2


title: 19 RAP-CD8-7 1 StP212

description: Raptor-/- unstimulated CD8+ T cells

value: Magnetically sorted lymph node and spleen CD8+ T cells


title: Golden Promise_stage II_biol rep 3

value: microspores

value: stage II

value: bi-cellular pollen grains

value: pre-treatment of anthers in 0.4M mannitol for 48h at 21C, followed by 24 h incubation of isolated microspores in KBP nutrient medium in the dark at 21C


title: 17 RAP-CD4-3-28 2 StP213

description: Raptor-/- stimulated CD4+ T cells

value: Magnetically sorted lymph node and spleen CD4+ T cells

value: Cultures stimulated with plate bound 10 ug/ml anti-CD3 (145-2C.11) and anti-CD28 (37.51) mAbs (48 h)


title: HS, Antisense, Rep1


title: 18 RAP-CD4-3-28 3 StP219

description: Raptor-/- stimulated CD4+ T cells


title: Golden Promise_stage II_biol rep 4


title: HS, Sense, Rep1


title: Control, Sense, Rep1


title: Control, Input, Rep1


title: 16 RAP-CD4-3-28 1 StP212

description: Raptor-/- stimulated CD4+ T cells


title: HS, Input, Rep1


title: AR24Q_6w_spinal cord

city: Nagoya city

first: Madoka

last: Iida

address: Tsurumai 65

country: Japan

institute: Nagoya University

description:
Library name: 24-6
10xGenomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: spinal cord

extract_protocol:
Mice were deeply anesthetized, and the entire spinal cord were dissected and snap-frozen in powdered CO2 in liquid nitrogen. Spinal cords from 4 mice for each condition were pooled for homogenization and nuclear isolation. Fresh frozen murine spinal cord was placed in a Dounce homogenizer (Kimble Chase 2 ml Tissue Grinder) containing ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal and 0.2 U/μl RNase inhibitor). After homogenizing, the lysate was diluted with 1.4 mL of lysis buffer and incubated for 5 minutes. The homogenate was passed over a 70 μm strainer (Fisher Scientific). The filtered lysate was centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the pellet was resuspended in 1.5 ml lysis buffer and incubated for 3 minutes on ice. Then, the pellet was centrifuged at 500 × g for 5 minutes and resuspended in 1500 µl of wash buffer (1× PBS with 1% BSA and RNase Inhibitor). The nuclei were washed and centrifuged at 500 × g for 5 minutes three times and filtered through a 40 µm cell strainer. The cell suspensions were processed according to the debris removal solution (Milteni Biotec) protocol. Cells were resuspended in cold PBS with 0.04% BSA and stained with DAPI. The nuclei were sorted with a FACS Aria instrument (Becton Dickson) with a 100 nm nozzle and 405 nm excitation laser. These nuclei were centrifuged, inspected for appearance, and concentrated for the next step.
The nuclei per sample were run on the 10 × Chromium Single cell 3’ gene expression v3.1 platform. Sequencing libraries were constructed according to the manufacturer’s instructions, and cDNA samples were run on an Agilent Bioanalyzer using the High Sensitivity DNA Chip as quality control and determination of cDNA concentrations. The samples were run on an Illumina NovaSeq 6000 at Read 1 = 28 bp and Read 2 = 90 bp, with a minimum depth of 20,000 reads per nucleus. For alignment, introns and exons were included in the reference genome (mm10) using the CellRanger v5.0.1 pipeline (10X Genomics). Sequencing data were analyzed using the R package Seurat Version 4.1.3. The gene barcode matrices for each sample were imported into R using the Read10X function.

treatment_protocol: The spinal cord samples were obtained from AR-97Q and AR-24Q mice at 6 weeks.

value: spinal cord

value: Pre-onset

value: 6 weeks


title: AR97Q_6w_spinal cord

description:
Library name: 97-6
10xGenomics


title: Golden Promise_stage II_biol rep 1

value: Golden Promise


title: Control, Antiense, Rep1


title: Golden Promise_stage II_biol rep 2


title: 21 RAP-CD8-7 3 StP219

description: Raptor-/- unstimulated CD8+ T cells


title: 15 RAP-CD4-7 3 StP219

description: Raptor-/- unstimulated CD4+ T cells


title: 9-S-OX-4

type: RNA

city: Beer-Sheva

first: Isana

last: Veksler-Lublinsky

address: P.O.B. 653 Beer-Sheva

country: Israel

institute: Ben-Gurion university of the Negev

description:
microRNA
OX-S-8

data_processing: Use Transcriptome Analysis Console (TAC, version 4.0.3) for normalization, filtering, and analysis of miRNA and mRNA raw CEL files. Identify DEGs and DEmiRNAs using the eBayes method in TAC and export normalized signals, fold change, and p-values. Calculate distances between samples using Rtsne package (version 0.17) and visualize data using ggplot2 (version 3.4.4). Define DEGs and DEmiRNAs by Fold change ≥ 2 (up) or ≤ -2 (down) and p-value < 0.05. Generate volcano plots using ggplot2. Perform GO enrichment analysis using ClusterProfiler (version 4.10.1) and use simplifyEnrichment (version 1.12.0) for clustering analysis and heatmap visualization of GO terms. Collect target genes of DEmiRNAs from TarBase-v9.0 and processed CLASH datasets. Visualize network between DEGs, DEmiRNAs, and GO terms using networkD3 (version 0.4).

label: biotin

source_name: NPCE cell line (ODM2)

label_protocol: For exosomal miRNA profiling, use GeneChip® miRNA 4.0 Array and Flashtag™ Bundle–ThermoFisher (Cat: 902445). For primary HTM transcriptome profiling, use Clariom™ S Assay, human. ThermoFisher (Cat: 902926).

growth_protocol: Culture immortalized NPCE cells in DMEM supplemented with 10% FBS EVs-depleted serum, 2mM L-glutamine and 1IU/ml penicillin/streptomycine. Incubate the cells at 37°C in 5% CO2 and use them at 80% confluence for up to 20 passages. For primary HTM cells, isolate them from healthy donor corneal rims and culture according to established protocols.

extract_protocol: For EVs isolation, use a series of ultracentrifugation steps on conditioned media: 300× g for 10 minutes to remove cells, 2000× g for 10 minutes to eliminate dead cells, 10,000× g for 30 minutes to clear cell debris, and 100,000× g for 70 minutes, followed by adittional PBS washing step in  100,000× g for 70 minutes. For miRNA extraction from EVs, use the Total Exosomal RNA Purification Kit (Norgen Biotek Corp.), following the manufacturer's guidelines and eluting in 50 µL. For mRNA extraction from TM cells, use Norgen Biotek Corp catalog no. 17200, following the manufacturer's guidelines.

treatment_protocol: expose NPCE cells to 1.5 mM AAPH for 24 hours (L), or 15mM AAPH for 1 hours(S)

value: Non-pigmented ciliary epithelium

tag: condition

value: Short Oxidative stress


title: HS, Antisense, Rep2

value: fibroblast

value: wt


title: Golden Promise_stage III_biol rep 2

value: stage III

value: bi- and multi-cellular structures

value: pre-treatment of anthers in 0.4M mannitol for 48h at 21C, followed by 48 h incubation of isolated microspores in KBP nutrient medium in the dark at 21C


title: 8-S-OX-3

description:
microRNA
OX-S-7


title: Golden Promise_stage I_biol rep 4

value: microspores

value: stage I

value: uni-cellular  microspores

value: pre-treatment of anthers in 0.4M mannitol for 48 h at 21C


title: 14 RAP-CD4-7 2 StP213

description: Raptor-/- unstimulated CD4+ T cells

value: Magnetically sorted lymph node and spleen CD4+ T cells

value: Control cultures with 5 ng/ml IL-7 (48 hours)


title: 6-S-OX-1_

description:
microRNA
OX-S-5


title: 10_a-S-OX

description:
microRNA
OX-S-4


title: Golden Promise_stage I_biol rep 3


title: Control, Antiense, Rep2

value: No HS


title: 9_a-S-OX

description:
microRNA
OX-S-3


title: 13 RAP-CD4-7 1 StP212

description: Raptor-/- unstimulated CD4+ T cells


title: 8_a-S-OX

description:
microRNA
OX-S-2


title: Golden Promise_stage I_biol rep 2


title: Golden Promise_stage 0_biol rep 4

value: stage 0

value: no pre-treatment of anthers


title: 6_a-CTL

description:
microRNA
CTL-6

value: Control


title: 10-Control

description:
microRNA
CTL-7

value: Non-pigmented ciliary epithelium

value: Oxidative stress


title: 12 WT-CD8-3-28 3 StP219

description: Wt stimulated CD8+ T cells

value: Magnetically sorted lymph node and spleen CD8+ T cells

value: Cultures stimulated with plate bound 10 ug/ml anti-CD3 (145-2C.11) and anti-CD28 (37.51) mAbs (48 h)


title: 11 WT-CD8-3-28 2 StP213

description: Wt stimulated CD8+ T cells


title: Golden Promise_stage 0_biol rep 3

value: Golden Promise


title: 9 WT-CD8-7 3 StP219

description: Wt unstimulated CD8+ T cells


title: 7_a-S-OX

description:
microRNA
OX-S-1

value: Short Oxidative stress


title: 7-S-OX-2

description:
microRNA
OX-S-6


title: 5-L-OX-5

description:
microRNA
OX-5


title: 10 WT-CD8-3-28 1 StP212

description: Wt stimulated CD8+ T cells


title: 5_a-CTL

description:
microRNA
CTL-5


title: Golden Promise_stage 0_biol rep 2


title: Golden Promise_stage 0_biol rep 1


title: 4-M-S-ox

description:
mRNA
OX-S-3

source_name: primary trabecular meshwork cells

value: primary trabecular meshwork cells


title: P24

city: Jining

first: Chunyu

last: bai

address: NO133，Hehua Road

institute: Jining Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: placenta

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: PIH

value: placenta


title: 8 WT-CD8-7 2 StP213

description: Wt unstimulated CD8+ T cells


title: P18


title: 5-N-S-ox-exo

description:
mRNA
OX-S-2


title: 7 WT-CD8-7 1 StP212

description: Wt unstimulated CD8+ T cells


title: P11


title: 6-H-S-ox-exo

description:
mRNA
OX-S-1


title: 3-L-OX-3

description:
microRNA
OX-3


title: 6 WT-CD4-3-28 3 StP219

description: Wt stimulated CD4+ T cells


title: 5 WT-CD4-3-28 2 StP213

description: Wt stimulated CD4+ T cells


title: G20

value: GDM


title: 9-I-L-ox-exo

description:
mRNA
OX-3


title: 3_a-CTL

description:
microRNA
CTL-3


title: 4 WT-CD4-3-28 1 StP212

description: Wt stimulated CD4+ T cells


title: 4-L-OX-4

description:
microRNA
OX-4


title: 2_a-CTL

description:
microRNA
CTL-2


title: G3


title: 2-L-OX-2

description:
microRNA
OX-2


title: 3 WT-CD4-7 3 StP219

description: Wt unstimulated CD4+ T cells


title: 8-F-L-ox-exo

description:
mRNA
OX-2


title: 7-E-L-ox-exo

description:
mRNA
OX-1


title: G15


title: N3

value: Normal


title: 4_a-CTL

description:
microRNA
CTL-4


title: 1-L-OX-1

description:
microRNA
OX-1


title: N2


title: 1 WT-CD4-7 1 StP212

description: Wt unstimulated CD4+ T cells

value: Magnetically sorted lymph node and spleen CD4+ T cells

value: Control cultures with 5 ng/ml IL-7 (48 hours).


title: 2-L-cont-exo

description:
mRNA
CTL-2


title: 1_a-CTL

description:
microRNA
CTL-1


title: 1-K-cont-exo

description:
mRNA
CTL-1


title: N1


city: Changsha

first: Xudong

last: Xiang

address: NO.139 Middle Renmin Road

institute: Central South University

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: After washing, the chip was scanned with an Agilent seanner g2505c scanner.

data_processing:
The R/biconductor package was used for centralization, standardization and smoothing, and the Nimblegen sliding window method was used to detect the enrichment peak.
Nimblescan v25 (Roche - nimblegen) was used for peak finding, and the m’ method was used for differential enrichment peak (DEP) analysis.

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours.

extract_protocol: Genomic DNA (gDNA) was extracted from samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA).

treatment_protocol: 100ug house dust mite, 100ug ovalbumin and 15ug lipopolysaccharide were used to establish the Th17-mediated neutrophil-predominant asthma model, the control  group received saline instead.

value: lung

tag: genotype/variation

tag: fraction

value: IP

source_name: lung of Th17-mediated neutrophil-predominant asthma mice_input

value: input


title: lung of control mice

source_name: lung of control mice

value: control

source_name: lung of control mice_input


title: 2 WT-CD4-7 2 StP213

description: Wt unstimulated CD4+ T cells

value: Control cultures with 5 ng/ml IL-7 (48 hours)


title: 5 ATF6 transgenic, HA-Tag  antibody, Replicate 2

status: Public on Dec 28 2024

city: München

first: Robert

middle: Stefan

last: Piecyk

state: Bayern

address: Marchioninistr. 15

department: Klinik und Poliklinik für Strahlentherapie und Radioonkologie

institute: LMU Klinikum

description: Library name: TG_HA_R2

data_processing:
CUT&RUN data were analysed using the nf-core/cutandrun pipeline v3.2.2 with Nextflow version 24.04.2, using default parameters and following software dependencies: bedtools (v2.30.0), bowtie (v2.4.4), deeptools (v3.5.1), fastqc (v0.12.1), picard (v3.1.0), python (v3.9.12), samtools (v1.17), Genrich (v0.6.1), TrimGalore (v0.6.6), ucsc (v377).
Reads were aligned to mm10 reference genome.
Consensus peaks were defined by running Genrich (v0.6.1) with the following parameters: -m 30 -e chrM -r -l 5 -q 0.2 -a 500 -g 15 -l 15 -d 50.
Direct target genes identified from CUT&RUN analysis were determined by using HOMER’s annotatePeaks.pl tool on the final peak set and selecting genes with a peak located within ±1 kb of their transcription start site (TSS).
Assembly: mm10
Supplementary files format and content: bigWig files for each sample
Library strategy: CUT&Run

source_name: liver

extract_protocol:
Livers from mice were harvested and directly processed for nuclei isolation using liver swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2) with the help of a douncer. Homogenized tissue was passed through a 70 µm strainer and centrifuged (400g, 5 min, 4°C). Tissue pellets were resuspended in liver lysis buffer (10 mM Tris pH 7.5, 1% NP-40, 2 mM MgCl2, 10% Glycerol, 3 mM CaCl2) and centrifuged again. Pellets containing the nuclei were washed twice in PBS and counted. 500K nuclei were used.
CUT&RUN was performed as described in Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017) and libraries were prepared using NEBNext DNA Library Prep Kit for Illumina (NEB E7645).

value: liver

value: liver tissue

value: Hepatocyte

value: 5 ATF6 transgenic

value: No treatment

tag: cut&run antibody

value: HA-Tag


title: 5 ATF6 transgenic, ATF6  antibody, Replicate 4

description: Library name: TG_ATF6_R4


title: 5 ATF6 transgenic, IgG antibody, Replicate 5

description: Library name: TG_IgG_R5

value: IgG


title: 5 ATF6 transgenic, HA-Tag  antibody, Replicate 3

description: Library name: TG_HA_R3


title: 5 ATF6 transgenic, ATF6  antibody, Replicate 1

description: Library name: TG_ATF6_R1


title: 5 ATF6 transgenic, HA-Tag  antibody, Replicate 4

description: Library name: TG_HA_R4


title: 5 ATF6 transgenic, ATF6  antibody, Replicate 5

description: Library name: TG_ATF6_R5


title: 5 ATF6 transgenic, HA-Tag  antibody, Replicate 5

description: Library name: TG_HA_R5


title: 5 ATF6 transgenic, ATF6  antibody, Replicate 2

description: Library name: TG_ATF6_R2


title: Wildtype, ATF6 antibody, Replicate 5

description: Library name: WT_ATF6_R5

value: Wildtype


title: 5 ATF6 transgenic, IgG antibody, Replicate 2

description: Library name: TG_IgG_R2


title: 5 ATF6 transgenic, IgG antibody, Replicate 1

description: Library name: TG_IgG_R1


title: 5 ATF6 transgenic, ATF6  antibody, Replicate 3

description: Library name: TG_ATF6_R3


title: 5 ATF6 transgenic, IgG antibody, Replicate 4

description: Library name: TG_IgG_R4


title: 5 ATF6 transgenic, HA-Tag  antibody, Replicate 1

description: Library name: TG_HA_R1


title: 5 ATF6 transgenic, IgG antibody, Replicate 3

description: Library name: TG_IgG_R3


title: Wildtype, ATF6 antibody, Replicate 1

description: Library name: WT_ATF6_R1


title: Wildtype, ATF6 antibody, Replicate 4

description: Library name: WT_ATF6_R4


title: Wildtype, ATF6 antibody, Replicate 2

description: Library name: WT_ATF6_R2


title: Wildtype, ATF6 antibody, Replicate 3

description: Library name: WT_ATF6_R3


title: Wildtype, IgG antibody, Replicate 3

description: Library name: WT_IgG_R3


title: Wildtype, IgG antibody, Replicate 2

description: Library name: WT_IgG_R2


title: ccRCC_replica1

description: Library name: ccRCC_rep1

value: Kidney

value: ccRCC


title: Wildtype, IgG antibody, Replicate 1

description: Library name: WT_IgG_R1


title: Wildtype, IgG antibody, Replicate 4

description: Library name: WT_IgG_R4


title: Wildtype, IgG antibody, Replicate 5

description: Library name: WT_IgG_R5


title: 5 ATF6 transgenic, Replicate 5

description: Library name: TG_R5

data_processing:
ATAC-Seq data was analysed using the nf-core/atacseq pipeline v2.1.2 with Nextflow version 24.0.2, using default paramters.
Reads were aligned to mm10 reference genome.
Consensus peaks were defined by running Genrich (v0.6.1) with the following parameters: -j -m 30 -e chrM -r -l 15 -q 0.01 -a 500 -g 15 -l 15 -d 50.
Direct target genes identified from ATAC-Seq analysis were determined by using HOMER’s annotatePeaks.pl tool on the final peak set and selecting genes with a peak located within ±1 kb of their transcription start site (TSS).
Assembly: mm10
Supplementary files format and content: bigWig files for the merged replicates for wildtype and 5 ATF6 transgenic

extract_protocol:
Livers from mice were harvested and directly processed for nuclei isolation using liver swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2) with the help of a douncer. Homogenized tissue was passed through a 70 µm strainer and centrifuged (400g, 5 min, 4°C). Tissue pellets were resuspended in liver lysis buffer (10 mM Tris pH 7.5, 1% NP-40, 2 mM MgCl2, 10% Glycerol, 3 mM CaCl2) and centrifuged again. Pellets containing the nuclei were washed twice in PBS and counted. 50K nuclei were used.
50K nuclei were resuspended in 50 μL of ice-cold cell lysis buffer containing 0.1% NP-40 and 0.01% digitonin in wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA in ddH2O) for 3-5 min. 1 mL of ice-cold wash buffer was then added to stop cell lysis, and nuclei were centrifuged (500g, 10 min, 4°C). 4.5 μL of each of the tagmentation oligos, Tn5_ME and Tn5-R1N, were annealed in oligo annealing buffer (10 mM Tris-HCl pH 7.5, 50 mM NaCl, and 10 mM EDTA final concentration in ddH2O) by heating at 95°C (3 min) followed by a ramp down by 1°C to 25°C. The same procedure was performed for Tn5_ME and Tn5-R2N. Tn5 was assembled with annealed oligos by combining 50 μL Tn5 (1 mg/mL stock) with 25 μL annealed Tn5_ME and Tn5-R1N and 25 μL Tn5_ME and Tn5-R2N. Nuclei were resuspended in 40 μL tagmentation buffer (38.8 mM Tris-acetate, 77.6 mM K-acetate, 11.8 Mg-acetate, 18.8% dimethylformamide, and 0.12% NP-40 in ddH2O), to which 5 μL ice-cold PBS + 1% BSA and 5 μL pre-assembled Tn5 was added. Samples were incubated on a Thermomixer (37°C, 30 min, 500 rpm) before being subjected to MinElute (Qiagen) cleanup to extract tagmented DNA. Eluted DNA was pre-amplified with P5 and P7 primers using the NEBNext HF 2x PCR Master Mix (New England Biolabs) in a thermocycler set to 72°C (5 min), 98°C (30 sec), and 5 cycles of 98°C (10 sec), 63°C (30 sec), and 72°C (1 min). A qPCR side reaction was performed with the resulting pre-amplified libraries to determine the necessary additional cycles (5 cycles fewer than the number of cycles corresponding to ⅓ of max fluorescence) for complete amplification. After finishing amplification, 50 μL of each library was subjected to 2-sided size selection by addition of 27.5 μL (0.55x) AMPure XP beads, incubation (5 min), transfer of supernatant to new tubes, addition of 42.5 μL (1.4x) AMPure XP beads to the supernatant, incubation (5 min), three washes with 80% ethanol, and elution of DNA. Resulting libraries were then sequenced on the NextSeq 2000 platform (Illumina).


title: 5 ATF6 transgenic, Replicate 4

description: Library name: TG_R4


title: 5 ATF6 transgenic, Replicate 3

description: Library name: TG_R3


title: 5 ATF6 transgenic, Replicate 2

description: Library name: TG_R2


title: Wildtype, Replicate 1

description: Library name: WT_R1


title: Wildtype, Replicate 2

description: Library name: WT_R2


title: Alt-2a

city: Houston

first: Cynthia

last: Reinhart-King

state: TX

address: 6100 Main Street

department: Biomedical Engineering

institute: Rice University

description: Library name: Sample 13

data_processing:
Demultiplexed FASTQ files obtained from the VANTAGE core were aligned to the Mus musculus transcriptome using Kallisto. To build the kallisto transcriptome index, we utilized the Mus_musculus.GRCm38.cdna.all.fa.gz file found at ‘https://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/cdna/’ and the Mus_musculus.GRCm38.9.gtf.gz file found at ‘https://ftp.ensembl.org/pub/release-96/gtf/mus_musculus/’. Differential expression analysis was carried out in R using DEseq2.
Assembly: GRCm38
Supplementary files format and content: comma separated values files contain raw counts

source_name: Mammary Tumor

extract_protocol:
Upon sacrifice, tumors were surgically removed from the mice, and small pieces of the tumors were cut and snap-frozen in liquid nitrogen. RNA was isolated from snap-frozen tumor sections using a combination of TRIZOL (#15596026, Thermo Fisher Scientific) and RNeasy micro kits (#74004, Qiagen, Hilden, Germany). In brief, tumor sections were combined with 5 mm stainless steel beads (69989, Qiagen) in 1 mL of ice-cold TRIZOL into 2 mL microcentrifuge tubes. The samples were then homogenized by placing the tubes in a TissueLyser II device (#85300, Qiagen) set to shake at 30 Hz for 2 minutes. After ensuring samples were completely homogenized, the lysate was transferred to a new 1.5 mL tube without the stainless steel beads. Samples were allowed to incubate at room temperature in TRIZOL for 5 minutes. 0.2 mL of chloroform was added to each sample, shaken vigorously, and allowed to incubate at room temperature for 2-3 minutes. The samples were centrifuged at 4 for 30 minutes at 12,000 xg. The aqueous top layer was carefully removed and added to a new tube containing 0.5 mL 70% ethanol and mixed carefully by pipetting up and down several times. The RNA and ethanol mix was applied to the RNeasy spin columns via centrifugation at 10,000 xg for 30 seconds. RNA and ethanol mix was applied to the columns in 0.5 mL aliquots until all samples had been applied to the column. The samples were washed with 0.7 mL RW1 buffer and centrifuged at 10,000 xg for 30 seconds. The flow-through was discarded, and samples were washed with 0.5 mL RPE buffer and centrifuged at 10,000 xg for 30 seconds. The flow-through was discarded, and samples were washed with 0.5 mL RPE buffer and centrifuged at 10,000 xg for 2 minutes. The flow through was discarded, and the columns were placed into fresh collection tubes and centrifuged at 10,000 xg for an additional 1 minute. Then RNA was eluted in 35 µLof RNase-free water and centrifuged at max speed (14,000 xg) for 1 minute in fresh 1.5 mL microcentrifuge tubes. RNA concentration and purity were measured via nanodrop. Samples were stored at -80 until further use.
RNA samples were submitted to the Vanderbilt Technologies for Advanced Genomics (VANTAGE) core facility for bulk RNA sequencing. Samples underwent quality control via RNA ScreenTape to ensure all samples had a RINe greater than 7. All of our samples had RINe numbers greater than 8.1, and most were greater than 9.0. The VANTAGE core performed mRNA enrichment and cDNA library preparation via the stranded mRNA Library Prep kit (New England Biolabs, Ipswich, MA, USA). Paired-End 150 bp sequencing was performed on the Illumina NovaSeq 6000 targeting an average of 50M reads per sample.

value: Mammary Tumor

value: MMTV-PYMT positive

value: STZ + AL711


title: Alt-2b

description: Library name: Sample 14


title: Alt-1a

description: Library name: Sample 11


title: liver, gradual reoxygen_3h,2

city: Haikou

first: tian

last: jiang

address: 58 of Ren min Road

institute: Hainan University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
Assembly: genome of Trachinotus blochii (unpublished)

organism: Trachinotus blochii

extract_protocol:
The total RNA was extracted from the liver by the Trizol Reagent (Invitrogen). RNA degradation and contamination were monitored on 1% agarose gel. The RNA purity was assessed using a NanoPhotometer® spectrophotometer (IMPLEN, München, Germany). The RNA concentration was measured using the Qubit® RNA Assay Kit in the Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). All RNA OD ratios of 260/280 and 260/230 were greater than 1.8, and the RNA integrity number (RIN) was greater than 8.0.We used Qubit 2.0 for preliminary quantification, diluted the library to 1 ng/uL, and used the highly sensitive Agilent 2100 to detect the insert size of the library.
The different libraries were pooled according to the requirements of the effective concentration and target data volume, and the Illumina SE 50 was used for sequencing.

value: gradual reoxygen_3h


title: Alt-1b

description: Library name: Sample 12


title: Wildtype, Replicate 3

description: Library name: WT_R3


title: liver, gradual reoxygen_12h,3

value: gradual reoxygen_12h


title: Wildtype, Replicate 4

description: Library name: WT_R4


title: STZ-2b

description: Library name: Sample 10

value: STZ


title: liver, gradual reoxygen_3h,3


title: STZ-2a

description: Library name: Sample 9


title: liver, rapid reoxygen_12h,2

value: rapid reoxygen_12h


title: STZ-1b

description: Library name: Sample 8


title: liver, gradual reoxygen_12h,2

value: liver


title: liver, rapid reoxygen_12h,1


title: liver, rapid reoxygen_3h,3

value: rapid reoxygen_3h


title: STZ-1a

description: Library name: Sample 7


title: liver, gradual reoxygen_3h,1


title: BSA_rep1, PE250

city: hangzhou

first: bo

last: zhong

state: zhejiang

address: No. 928, 2nd Street, Xiasha Higher Education Park, Qiantang District, Hangzhou City, Zhejiang Province

institute: Zhejiang Sci-Tech University

description: Library name: BSA_rep1

data_processing:
the raw reads were analyzed using fastqc to assess the sequencing quality. Adapters were then removed using trim-galore in paired mode.The resulting read pairs were merged using bbmerge with default parameters. If necessary, primers could be removed using cutadpt with paramater --revcomp.
To generate the same VNAR sequences, the modified primer needed to be removed from the merged sequences.
DNA sequences were counted using the R package dplyr and then translated into amino acid sequences using Biostrings in six different frames. Only the longest amino acid sequences were kept for each DNA sequence.
Differential expression of VNARs was identified using DESeq2 with the following cutoff values: q ≤ 0.05 and abs(log2(foldChange)) ≥ 1.
Assembly: Chiloscyllium_plagiosum_GCF_004010195.1_ASM401019v2
Supplementary files format and content: txt

organism: Chiloscyllium plagiosum

source_name: spleen and PBMC

growth_protocol: The sharks were maintained in a controlled environment with a water temperature of 25 °C and a salt concentration ranging between 1.020 and 1.025.

extract_protocol:
Two weeks after the final vaccination, the sharks were sacrificed using humanitarian execution methods and the spleen was then carefully isolated and stored at -80 °C for future study.Total RNA from the spleen was isolated using TRIzol (Thermo Fisher Scientific) according to the manual. cDNA synthesis was carried out using the SuperScript III First-Strand Synthesis System (Thermo Fisher Scientific).
VNAR libraries for next-generation sequencing were prepared, utilizing the primers provided.The PCR products ranging from 300 to 500 bp were recovered. In our assay, the PCR cycles ranged between 25 and 30 cycles. Sequencing libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, USA) as the manufacturer's recommendations. Indexes were added to attribute sequences to each sample.

treatment_protocol: For vaccination, the antigen was diluted to a concentration of 2 μg/μl using 1x PBS and thoroughly mixed with Freund’s Adjuvant (Sigma) in an equal volume. Each shark received a subcutaneous injection of 100 μg of antigen every two weeks, with a total of 6 consecutive vaccinations.

value: spleen and PBMC

value: immune BSA as control


title: BSA_rep2, PE250

description: Library name: BSA_rep2


title: Control-3b

description: Library name: Sample 6

value: Control


title: liver, rapid reoxygen_3h,2


title: 5 ATF6 transgenic, Replicate 1

description: Library name: TG_R1

value: liver tissue

value: Hepatocyte

value: 5 ATF6 transgenic


title: Control-3a

description: Library name: Sample 5


title: liver, rapid reoxygen_3h,1


title: liver, gradual reoxygen_12h,1


title: Cre, PE250

description: Library name: Cre

value: immune Cre antigen


title: Control-2b

description: Library name: Sample 4


title: liver, hypoxia_12h,3


title: Cre_NT, PE250

description: Library name: Cre_NT

value: immune Cre_NT antigen


title: liver, hypoxia_12h,2


title: Control-2a

description: Library name: Sample 3

value: Mammary Tumor


title: liver, hypoxia_12h,1


title: Contol-1b

description: Library name: Sample 2

value: MMTV-PYMT positive


title: Control-1a

description: Library name: Sample 1


title: liver, hypoxia_0h,1


title: liver, normoxia_12h,2


title: liver, hypoxia_0h,3


title: liver, normoxia_12h,3


title: Sample 6, Anti-PD1

description: Library name: Sample6

data_processing:
Raw base calls have been processed by CellRanger 2.1.1. to demultiplex reads and generate count matrices.
Assembly: GRCm38
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample; an H5 file is included for each sample

growth_protocol: Mouse liver tissue were immediately digested and single cells harvested and stored.

extract_protocol:
Animals were sacrificed and livers perfused with 0.9% NaCl buffer. Liver tumors were collected, minced, digested with Collagenase and DNase, and subsequently passed through a 100μm filter. Lymphocytes were then purified by a 2-step Percoll gradient. MACS were employed for sorting live CD45+ cells. Single-cell 3’ RNA (gene expression) libraries were generated according to the ‘Chromium Single Cell 3’ Reagents Kits User Guide (v3.1 Chemistry)’ (#CG000204, 10x Genomics).
Library construction was performed with Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics) following the manufacturer’s protocol.
150bp paired-end

treatment_protocol: Mice were injected oncogenic plasmids to the liver by HDTVi,

value: liver tumor

value: Immune cells (CD45+)

value: ATF6 transgenic

value: AAV8-Cre, Anti-PD1


title: Sample 3, Anti-IgG

description: Library name: Sample3

value: AAV8-Cre Anti-IgG


title: liver, normoxia_0h,2

value: liver


title: Sample 1, Anti-IgG

description: Library name: Sample1


title: BALB/c mice, Vehicle, biol rep 6

city: Shanghai

first: Haiyu

last: Wang

address: Pudongxinqu

institute: Mobio

description:
Library name: C2_4
10x Genomics

data_processing:
Cell Ranger 8.0.1 software was used to map reads to a reference genome and quantify gene expression levels. Data analysis and clustering were performed using the “seurat” R package of R software (version 4.3.3). Cell-to-cell communication analysis was performed using the R software package “CellChat”.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

growth_protocol: Four- to six-week-old male BALB/c mice weighing 20.0 ± 2 g were purchased from BEJING HFK BIOSCIENCE Co., Ltd. (Beijing, China). Mice were housed in a specific pathogen-free environment. Each mouse was subcutaneously injected with 5×10^5 H22 cells into the right flank. Tumor volumes were measured daily using a caliper and calculated with the following formula: volume = (length × width2)/2. The mice were euthanized when the tumor volume exceeded 1500 mm^3 or if the maximum tumor diameter exceeded 15 mm.

extract_protocol:
Collected tumor tissue were stored in the tissue storage solution immediately after resection and transferred on ice. Samples were washed three times and cut into approximately 1–2 mm3 pieces before being collected in the D-PBS buffer (Gibco), and projected to enzymatical digestion with Tumor Dissociation Kit (for mouse, Miltenyi Biotec) for 15 min on a rotor (140rpm/min) at 37℃ according to the manufacturer’s protocol. The dissociated cells then passed through a 30μm SmartStrainer (Miltenyi Biotec) in the DMEM medium (Gibico) with 10% FBS and at 4℃ centrifuged at 500 g for 5 min. After the removal of the supernatant, the pelleted cells were re-suspended in 1 mL of red blood cell lysis buffer (Miltenyi Biotec) and incubated on ice for 2 min for red blood cell lysis before terminating the reaction with DMEM medium (Gibico, with 10% FBS). After being centrifuged at 400 g for another 5 min, the cell pellets would be re-suspended in sorting buffer (D-PBS supplemented with 1% FBS).
After quality inspection, a single-cell suspension with a cell viability of more than 80%, a clumping rate of less than 10%, a background debris of less than 50%, and a moderate cell concentration was obtained. Subsequently, cell barcode-labeled beads and cells were passed through the 10X Genomics platform, and the cells and enzymes were encapsulated with oil droplets to form gel bead inemulsion. Cells are lysed within each independent oil droplet, and the ploy-A of the intracellular mRNA is labeled with a cell barcode on the bead. The reverse transcription is performed to form cDNA. Finally, the oil phase was removed and the next-generation sequencing library was constructed.

treatment_protocol: When the tumors reached approximately 100 mm^3, the mice were randomly divided into three groups to receive oral treatment: the azvudine group (1 mg/kg, QD), and the control group (solvent). The solvent was prepared by sequentially adding the following reagents: 5% DMSO, 40% PEG300, 5% Tween-80, and 50% saline

value: tumor

tag: strain

value: Balb/c

value: Liver cancer cells

tag: Sex

value: Male

tag: age

value: 4-6 weeks old

value: Vehicle treament

tag: batch


title: VR23_WRi-3

city: Verona

first: Davide

last: Pasini

state: VR

address: Piazzale Ludovico Antonio Scuro 10

country: Italy

institute: University of Verona

data_processing:
Barcodes from genomic DNA sequencing were quantified using BWA(0.7.18) and FeatureCounts from Rsubread(2.18.0)
A FASTA reference file was first generated from the barcode pool provided by Cellecta.
The sequencing reads were then aligned to the reference using the BWA-MEM algorithm.
The resulting BAM files were subsequently used to quantify barcode abundances through the FeatureCounts functionality, as implemented in the R package Rsubread
Assembly: For the purpose of the work, a fake genome has been created as a reference. Each unique barcode is treated as a chromosome and is joined with spacers provided directly by the Cellecta kit, which generate reads.
Supplementary files format and content: Result is stored in a tabular file .tsv where every barcode has a count number referred to the number of occurences in each sample after the alignment with the fake genome

source_name: Cancer cells

extract_protocol:
DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen).
We amplified the barcodes from the CloneTracker XP™ library and added the Illumina adaptors as well as unique sample index sequences for multiplex sequencing using the NGS Prep Kit for Barcode libraries in pScribe (LNGS-300). After quantification by Fragment Analyzer High Sensitivity NGS kit (Agilent Technologies, Santa Clara, CA, USA) we first combined PCR products from each sample at the same amount, then we purified and concentrated the pool using QIAGEN QIAquick PCR Purification Kit (QIAGEN) following the manufacturer's protocol. We quantified the libraries pool using NanoDrop spectrophotometer

tag: parental pdo

value: Cancer cells

value: WRi


title: BALB/c mice, Vehicle, biol rep 4

description:
Library name: C1_5
10x Genomics

tag: tissue


title: BALB/c mice, Vehicle, biol rep 2

description:
Library name: C1_4
10x Genomics


title: VR23_WRi-1


title: liver, normoxia_12h,1


title: Sample 5, Anti-PD1

description: Library name: Sample5


title: BALB/c mice, Vehicle, biol rep 3

description:
Library name: C2_1
10x Genomics


title: VR23_+WR-2

value: +WR


title: Sample 4, Anti-PD1

description: Library name: Sample4


title: BALB/c mice, Vehicle, biol rep 1

description:
Library name: C1_3
10x Genomics


title: VR23_+WR-1


title: VR23_P0


title: Sample 2, Anti-IgG

description: Library name: Sample2


title: liver, normoxia_0h,1


title: BALB/c mice, Azvudine treatment, biol rep 6

description:
Library name: F1_4
10x Genomics

value: Azvudine treatment


title: BALB/c mice, Azvudine treatment, biol rep 5

description:
Library name: F2_2
10x Genomics


title: BALB/c mice, Azvudine treatment, biol rep 4

description:
Library name: F2_3
10x Genomics


title: BALB/c mice, Azvudine treatment, biol rep 3

description:
Library name: F1_2
10x Genomics


title: VR06_WRi-1


title: BALB/c mice, Vehicle, biol rep 5

description:
Library name: C1_2
10x Genomics


title: Sample 44157, Positive, Replicate 5

description:
Library name: 44157
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44157

data_processing:
RNA-Seq data was analysed using the nf-core/rnaseq pipeline v3.14.0 with Nextflow version 23.10.1, using default parameters.
Sequence reads were trimmed for adapter/low-quality sequence using Trim Galore (v0.6.7).
Reads were aligned to mm10 reference genome using STAR (v2.6.1) approach.
Extraction of the read count matrices was performed using Salmon (v1.10.1) approach.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes bias-corrected counts without an offset (TPM)

growth_protocol: Mouse liver tissue were immediately harvested and frozen in liquid nitrogen.

extract_protocol:
Animals were sacrificed and Livers were collected, snap frozed in liquid nitrogen.Total RNA isolation from snap-frozen liver tissue or cultured cells was performed with RNeasy Mini Kit (Qiagen, 74106). The on-column DNA digestion was carried out using an RNase-free DNase kit (Qiagen) or RNA samples were treated with TURBO DNase (ThermoFisher Scientific, AM1907) according to the manufacturer’s protocol to completely remove genomic DNA.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols ( TruSeq Stranded).

treatment_protocol: Mouse were feeding CD-HFD for 12 months.

value: liver tissue

value: Hepatocyte, immune cells

value: 12m CD-HFD feeding


title: BALB/c mice, Azvudine treatment, biol rep 1

description:
Library name: F1_1
10x Genomics


title: VR23_WRi-2


title: VR06_+WR-3


title: Sample 44806, Positive, Replicate 4

description:
Library name: 44806
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44806


title: VR06_P0


title: VR06_+WR-1


title: VR01_+WR-3


title: Let7 activity low

city: Kyoto

first: Koji

last: Eto

address: 54, Kawaharacho, Shogoin

department: CiRA

institute: Kyoto University

data_processing:
The sequenced reads were mapped to the human reference genome (hg19) using Tophat v2.1.0 after trimming the adaptor sequences and low-quality bases with cutadapt-1.9.1, and uniquely mapped reads (MAPQ>=20) were used for further analysis.
The expression level of each gene was calculated as RPM (reads per million mapped reads) using cufflinks-2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: The tab-delimited text file including RPM values for each gene in each sample.

source_name: imMKCLs

growth_protocol: imMKCLs were cultured on 10cm dishes in basal medium (IMDM, Sigma-Aldrich #I3390, St. Louis, MO) supplemented with L-glutamine (25030-081; Thermo Fisher Scientific, Waltham, MA), insulin-transferrin-selenium (41400-045; Thermo Fisher Scientific), 50 μg/mL ascorbic acid (A4544; Sigma-Aldrich), and 450 μM 1-thioglycerol (M6145; Sigma-Aldrich) with 50ng/ml SCF, TPO and doxycyclin

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen)
1 ng of total RNA was used for the cDNA synthesis and library construction using the SC3-seq method (Nakamura et al.,  Nuceic Acids Res. (2015)). The obtained libraries were sequenced with a MiSeq Reagent Kit v3 (Illumina, San Diego, CA).

treatment_protocol: imMKCLSs were transfected with artificial let7-responsive mRNAs and sorted with FACS Aria II.

value: blood cells

value: immortalized megakaryocyte cell line

tag: passage

tag: status

value: Let7 activity low


title: Sample 44993, Negative, Replicate 4

description:
Library name: 44993
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44993

value: liver

tag: genotype

value: wildtype

tag: treatment


title: VR06_WRi-2

tag: cell type


title: VR01_+WR-1


title: VR01_WRi-1


title: BALB/c mice, Azvudine treatment, biol rep 2

description:
Library name: F2_1
10x Genomics

value: tumor

value: Balb/c

tag: cell line


title: distal paracancerous region

city: Anhui

first: 午洋

last: 张

state: State

address: No.17 Lujiang Road, Hefei City, Anhui Province, China

institute: The First Affiliated Hospital of USTC

description: Library name: sameple 3

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Assembly: mm10;hsa
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: pancreas

growth_protocol: Tissues were processed with DPBS on ice, minced, and digested with trypsin and DNase I in PBS containing 5% FBS for 40 minutes at 37°C. Cells were extracted and filtered every twenty minutes, and red blood cells were lysed.

extract_protocol:
The study was approved by the Ethics Committee of USTC (Ethics Approval No.: 2024-RE-359). All pancreatic cancer patients who participated in this study at the No. 1 Affliated Hospital of USTC provided consent forms. None of the patients received any neoadjuvant therapy before tissue collection. Fresh tumor specimens and adjacent mucosal specimens were resected intraoperatively and there were no cancer cells remaining at the end of the resected samples as confirmed by the histopathologist. Representative hemoglobin/eosin (H&E)-stained sections of the excised specimens used for scRNA-seq were delineated with the help of a pathologist to delineate the three adjacent subregions (tumor core, tumor margin, and distal paracancerous region), after which each of the three regions was digested into single-cell suspensions and analyzed using droplet-based scRNA-seq.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: WT or KO mice were injected with 3 × 106 MFC cells/per mouse to induce tumor formation for 3d or 10d.

value: pancreas

value: CAFs

value: MFAP5+ fibroblasts

value: untreated


title: peripheral tumor region

description: Library name: sameple 2


title: VR06_+WR-2

value: Cancer cells


title: VR01_WRi-2

value: WRi


title: VR06_WRi-3


title: VR01_+WR-2

value: +WR


title: Sample 44437, Negative, Replicate 5

description:
Library name: 44437
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44437

value: liver tissue


title: Let7 activity high

value: Let7 activity high


title: VR01_P0


title: Sample 44438, Negative, Replicate 6

description:
Library name: 44438
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44438

value: Hepatocyte, immune cells

value: 12m CD-HFD feeding


title: VR06_WR24h_b

data_processing:
Reads were aligned to the GRCh38 genome using STAR v2.7 and expression quantification were performed with RSEM
Assembly: GRCh38
Supplementary files format and content: comma-delimited file containing raw counts for each sample at baseline
Supplementary files format and content: comma-delimited file containing raw counts for each sample in the adaptation experiment

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
RNA from organoids were isolated using the TRIzol® Reagent (Life Technologies), followed by the column based PureLink RNA Mini Kit (Thermo Fisher Scientific). Purified RNA quality was evaluated using RNA 6000 Nano kit on a Bioanalyzer 2100 (Agilent) and only RNA with an RNA Integrity Number (RIN) greater than 9 were used.
RNA-seq library were obtained using poly(A) enrichment with TrueSeq Stranded mRNA Library Prep kit (Illumina).

tag: individual

tag: disease state

value: pancreatic cancer

value: pancreatic ductal adenocarcinoma

tag: replicate

value: b

tag: condition

value: baseline PDO grown without WNT3A and RSPO1 for 24h


title: Sample 44989, Negative, Replicate 3

description:
Library name: 44989
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44989

value: liver

value: wildtype


title: VR23_WR24h_a

value: a


title: VR06_WR24h_a


title: Sample 44803, Positive, Replicate 3

description:
Library name: 44803
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44803


title: Sample 44439, Negative, Replicate 2

description:
Library name: 44439
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44439


title: VR23_WR_b

value: adapted to the removal of WNT3a and RSPO1 from the normal PDO media


title: VR06_WR_c

value: c


title: Sample 44582, Positive, Replicate 2

description:
Library name: 44582
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44582


title: core tumor region

description: Library name: sameple 1

value: pancreas

value: CAFs

value: MFAP5+ fibroblasts

value: untreated


title: Sample 44154, Negative, Replicate 1

description:
Library name: 44154
Column name in RNA_CDHFD_gene_counts_length_scaled.tsv: 44154

value: liver tissue