title: Dorsal striatum, Nicotine withdrawal 2

status: Public on Oct 31 2024

type: SRA

city: Seoul

first: BAEKSUN

last: KIM

state: Seoul

address: 75-10, Ohyeon-ro 6-gil, Gangbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology

library_source: transcriptomic

data_processing:
DESeq2
Raw data in FASTQ format was obtained and preprocessed for read count normalization with DESeq2 method according to the previous study (MI Love, et al., 2014. https://doi.org/10.1186/s13059-014-0550-8)
Assembly: mm9
Supplementary files format and content: processed data (DESeq2).xlsx

molecule: total RNA

organism: Mus musculus

source_name: nicotine withdrawal group

extract_protocol:
Trizol extraction
TruSeq Small RNA Library Prep

tag: tissue

value: Dorsal striatum

tag: treatment

value: Nicotine


title: Dorsal striatum, Nicotine withdrawal 3


title: Dorsal striatum, Control 3

source_name: control group

value: Saline


title: Dorsal striatum, Nicotine withdrawal 1


title: Dorsal striatum, Control 1


title: Dorsal striatum, Control 2


title: Dlx5CE_Col1GFP_21-49

city: Houston

first: Shion

last: Orikasa

state: TX

address: 7500 Cambridge St

country: USA

institute: University of Texas Health Science Center at Houston School of Dentistry

library_source: transcriptomic single cell

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and tdTomato_WPRE to the mouse genome (mm10).
Further downstream analysis steps were performed using the Seurat R package.
We filtered out cells with less than 1000 genes per cell and with more than 15% mitochondrial read content.
The downstream analysis steps include normalization, identification of highly variable genes across the single cells, scaling based on number of UMI, dimensionality reduction (PCA, and UMAP), unsupervised clustering, and the discovery of differentially expressed cell-type specific markers.
Assembly: mm10_trans_nono
Supplementary files format and content: raw_feature_bc_matrix/barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz

source_name: Femur bone marrow

extract_protocol:
Femurs were dissected, distal epiphyseal growth plates were removed and proximal ends were cut off. Remaining bones were cut roughly, and cells were enzymatically dissociated. GFP+ and tdTomato+ cells were FACS-isolated. ~73,000 cells were loaded onto 10X Genomic Chromium Single Cell Solution v2
10X Genomics Chromium Single Cell 3' v2 Libraries

value: Femur bone marrow

tag: developmental stage

value: Postnatal day 49

tag: genotype

value: Col1-GFP; Dlx5CE; R26R-tdTomato


title: C-SZ-4wk-A

city: Rochester

first: Kuntol

last: Rakshit

state: MN

address: 200 1st St. SW

department: Physiology & Biomedical Engineering

institute: Mayo Clinic

data_processing:
RNA-seq libraries were aligned to the mouse genome mm10 using TopHat64 and assembled using StringTie65. Gene expression was normalized to counts per million (CPM) and genes that were expressed 1 CPM in at least 2 replicates were filtered prior to differential analysis.
Assembly: mm10
Supplementary files format and content: Excel Sheet containing normalized CPM count matrix for each sample in different columns

source_name: Pancreas

extract_protocol:
Total islet mRNA was extracted using RNeasy Kit (Qiagen, Germantown, MD)
RNA quality was initially assessed using Qubit fluorometry (ThermoFisher Scientific, Waltham, MA) and the Agilent Fragment Analyzer (Santa Clara, CA). cDNA libraries were prepared using 150 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). The concentration and size distribution of completed libraries were determined using an Agilent Bioanalyzer DNA 1000 chip and Qubit fluorometry. Libraries were sequenced at six samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 x 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina Real Time Analysis version 2.7.7.

value: Pancreas

tag: cell line

value: Islets of Langerhans

tag: cell type

value: predominantly Beta-cells

value: Control (Bmal1fl/fl)

value: Streptozotocin (STZ)

tag: time

value: 4 weeks


title: K-SZ-24h-B

value: Beta-cell specific Bmal1 KO (Bmal1fl/flRIPCreERT/+)


title: C-CB-24h-B

value: Citrate Buffer (VEH)


title: K-SZ-4wk-A


title: K-CB-24h-B


title: K-CB-24h-A


title: C-SZ-4wk-B


title: K-SZ-24h-A


title: C-CB-24h-A


title: C-SZ-24h-B


title: K-SZ-4wk-B


title: Plate2_H06 M

city: Palo Alto

first: Rebeca

last: Arroyo Hornero

state: California

address: Campus Drive

institute: Stanford

data_processing:
Data was processed with STAR
Assembly: mm10
Supplementary files format and content: counts.csv

source_name: epidermis

extract_protocol:
Cells isolated from epidermis were stained and single cell sorted on a FACS Aria Fusion (BD Biosciences) into Takara Smart-Seq Single Cell kit lysis buffer and frozen at -80C.
The Illumina Nextera XT DNA Library Prep and Unique Dual Index Kits (Illumina) were used for library preparation according to manufacturer's instructions.

value: epidermis

value: LC

tag: sorted cell_type

value: M


title: Plate2_H05 E

value: E


title: Plate2_H04 M


title: Plate2_H03 M


title: Plate2_H02 M


title: Plate2_H01 M


title: C-SZ-24h-A


title: Plate2_G11 E


title: Plate2_G09 M


title: Plate2_G10 M


title: Plate2_G05 E


title: Plate2_G06 M


title: Plate2_G04 M


title: Plate2_G08 M


title: Plate2_G02 M


title: Plate2_F05 E


title: Plate2_G03 E


title: Plate2_F07 E


title: Plate2_F12 E


title: Plate2_F11 M


title: Plate2_F08 E


title: Plate2_G01 E


title: Plate2_E12 E


title: Plate2_F04 E


title: Plate2_F03 E


title: Plate2_F09 E


title: Plate2_E11 E


title: Plate2_F01 E


title: Plate2_E10 E


title: Plate2_G07 M


title: Plate2_E09 E


title: Plate2_E07 E


title: Plate2_E08 E


title: Plate2_F10 E


title: Plate2_E05 E


title: Plate2_F06 E


title: Plate2_G12 M


title: Plate2_E06 E


title: Plate2_E03 E


title: Plate2_F02 E


title: Plate2_D12 E


title: Plate2_E01 E


title: Plate2_E02 E


title: Plate2_D09 E


title: Plate2_D06 E


title: Plate2_D07 E


title: Plate2_D04 E


title: Plate2_D05 E


title: Plate2_D01 E


title: Plate2_D02 E


title: Plate2_C12 M


title: Plate2_D03 E


title: Plate2_C11 M


title: Plate2_E04 E


title: Plate2_C10 M


title: Plate2_C09 M


title: Plate2_D10 E


title: sg-control-2

city: Nashville

first: Jin

last: Chen

state: Tennessee

address: T-3207E Medical Center North, 1161 21st Avenue South

institute: Vanderbilt University Medical Center

data_processing:
Raw sequencing data was filtered for low quality reads, high levels of unknown bases, and connector contamination, performed by BGI Americas.
Clean reads were aligned to the reference genome using HISAT, performed by BGI Americas
Clean reads were then aligned to reference genes using Bowtie2, performed by BGI Americas.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, and read counts for each sample
Supplementary files format and content: tab-delimited text file includes differential expression statistical analyses for each gene

organism: Homo sapiens

source_name: lung squamous cell carcinoma

growth_protocol: HCC2814 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 0.1% penicillin-streptomycin.

extract_protocol:
RNA was extracted using RNAqueous Micro Total RNA Isolation Kit (Invitrogen), per manufacturer's instructions.
The library was constructed by polyA selection by BGI Americas.

treatment_protocol: HCC2814 were treated with non-targeting sgRNA control (sgCtrl, WT) or sgRNA targeting mLST8 (sgmL8, mLST8 KO) for 48-72 hours followed by antibiotic selection.

value: lung squamous cell carcinoma

value: epithelial cell

value: WT


title: Plate2_D08 E


title: sg-control-3


title: sg-control-1


title: Plate2_C06 M


title: Plate2_C08 M


title: sg-mLST8 KO-3

value: mLST8 KO


title: Plate2_C05 M


title: sg-mLST8 KO-1


title: Plate2_C04 M


title: sg-mLST8 KO-2


title: Plate2_C02 E


title: Rod-like3 [degradome sequencing]

city: Wuhan

first: li

last: chen

address: Huazhong Agricultural University

country: China

institute: National Key Laboratory of Crop Genetic Improvement

data_processing:
For the degradome-sequencing data, the clean reads were matched against GenBank and Rfam databases. Degradation sequences with a single base over 0.7% in the clean reads as poly-N filtered either. The filtered reads were mapped to the B. napus genome/cDNA to identify fragments of degraded mRNAs. Identification and classification categories of the spliced miRNA targets were processed according to the CleaveLand 3.0 pipeline.
The height of the degradome peak at each occupied transcript position is placed into one of five possible categories, described below. Category 0: >1 raw reads at the position, abundance at position is equal to the maximum on the transcript, and there is only one maximum on the transcript; Category 1: >1 raw reads at the position, abundance at position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; Category 2: >1 raw reads at the position, abundance at position is less than maximum but higher than the median for the transcript; Category 3: >1 raw reads at the position, abundance at position is equal to or less than the median for the transcript; Category 4: Only 1 raw read at the position. Then the representative miRNAs and corresponding targets were analyzed in all five categories, in which a red circle indicates the cleavage site of each transcript.
Genome_build: Brassica napus genome
Supplementary_files_format_and_content: abundance: length abundance sequence

organism: Brassica napus

source_name: shoot apex

growth_protocol: normal and rod-like B.napus were grown in the same experimental field at Huazhong Agriculture University (Wuhan, Hubei Province, China). Shoot apexes from the early bolting stage (3 months old) of B. napus were sampled

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. The quantity and purity were assayed with an Agilent 2100 Bioanalyzer (AgilentTechnologies, Palo Alto, CA) to ensure sample reliability. Each RNA sample was generated from the shoot apexes of 6 different plants.
For degradome sequencing, approximately 200 µg of total RNA were used for the purification of poly adenylated RNA molecules using the Oligotex mRMA kit (Qiagen). Then, using T4 RNA ligase (Ambion), the single-stranded 5′ RNA adaptor was ligated to the cleaved products that had a 5′-monophosphate end. The ligated products were purified and subjected to 5 PCR cycles for reverse transcription reactions, digested with MmeI, and ligated to a 3′ double-stranded DNA adaptor. Finally, the samples were subjected to another 20 cycles of PCR amplification, and gel-purified PCR products were subjected to sequencing

value: shoot apical meristem

tag: development stage

value: early bolting stage


title: rod-like2

data_processing:
Sequenced reads were trimmed for adaptor sequence, abandon seqences small than 18 nt, and masked for low-complexity or low-quality sequence, then mapped to ref2 database using soap -v 0 -r 2 -s 7 -p 7 -a clean.fa -d ref_genome.fa -o match_genome.soap
The secondary hairpin structures were predicted using Mireap with the following parameters: a hairpin structure with a free energy less than –18 kcal mol–1, the spacebetween miRNA and miRNA* is less than 300 nt, the candidates have more than 16 matched nucleotides and fewer than 4 nucleotide bulges between miRNA and miRNA*, and the minimal folding free energy index (MFEI) values are more than 0.85
Genome_build: Brassica napus genome
Supplementary_files_format_and_content: Supplementary_files_format_and_content: abundance

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s instructions. The quantity and purity were assayed with an Agilent 2100 Bioanalyzer (AgilentTechnologies, Palo Alto, CA) to ensure sample reliability. Each RNA sample was generated from the shoot apexes of 6 different plants.
sRNA library construction and deep sequencing were performed as described previously. Briefly, small RNAs with 18–30-nt long small RNAs were purified from 10 µg of total RNA in a 15% polyacrylamide gel by electrophoresis and ligated to 5′and 3′ RNA adaptors. The purified RNAs were transcribed into cDNA, followed by PCR amplification to generate the DNA pool. Finally, 4 libraries were sequenced on an Illumina Genome Analyzer at the Beijing Genomics Institute (BGI, Shenzhen, China).


title: normal2


title: Plate2_B10 M


title: normal1


title: Plate2_C07 M


title: Plate2_B09 M


title: RMUGS_R replicate 3

city: Boston

first: Huy

last: Nguyen

state: MA

address: 450 Brookline Ave

department: Radiation Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Kallisto (version 0.48.0) was used to map the raw RNA-seq reads against the GENCODE human reference gene annotation (Release 44) and generate raw transcript abundance estimates.
The tximport Bioconductor R package was used to summarize the transcript abundance estimates to produce gene-level estimated counts.
Assembly: hg38
Supplementary files format and content: tab-delimited file with matrix table of raw gene counts for every gene and every sample

source_name: ovary

growth_protocol: RMUGS and RMUGS-R cell lines were grown in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin (100U/mL).  RMUGS-R cells were grown for 2 weeks without the drug and sent for RNA seq

extract_protocol:
Total RNA was prepared using a Qiagen kit according to the manufacturer’s instructions
rRNA depletion was performed from [100ng] of purified RNA using QIAseq FastSelect rRNA HMR reagents according to manufacturer’s protocol. Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation reagents on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: ovary

value: IFO50320 RMUG-S (JCRB cell bank)

value: mucinous cystadenocarcinoma

value: PARGi resistant cells (After being treated with PARG inhibitor for 4 months, they were subsequently cultured in the absence of the drug. )


title: Plate2_B07 E


title: RMUGS_R replicate 2


title: Plate2_C03 M


title: RMUGS replicate 3

value: untreated


title: RMUGS_R replicate 1


title: RMUGS replicate 2


title: Plate2_B12 M


title: Plate2_B08 M


title: Plate2_B04 E


title: Normal [degradome sequencing]


title: rod-like1


title: Plate2_C01 E


title: Plate2_B06 M


title: Plate2_B11 E


title: BAH 8 left adrenal vein sample

city: Budapest

first: Bálint

last: Vékony

address: Korányi Sándor utca 2/a

department: Department of Internal Medicine and Oncology

country: Hungary

institute: Semmelweis University

data_processing:
FASTQ files were uploaded to GeneGlobe (QIAGEN) for analysis, which performed adopter trimming, discarded low-quality reads, and aligned the results to GRCh38 using bowtie. Readcounts for miRNA were achived by mapping the results to miRBase v21.
Normalization, DeSeq2 and the neural network algorithm were then ran locally, using R.
Assembly: GRCh38, MirBase v21, piRNABank
Supplementary files format and content: Excel file containing the raw readcounts derived from the analysis performed by the GeneGlobe software.

source_name: EDTA coagulated plasma

extract_protocol:
RNA was isolated using the miRNEasy Serum/Plasma kit by QIAGEN.
The libraries were constructed using the QiaSeq miRNA Library Kit by QIAGEN.
5 µl-s of isolate were used for each library. After library preparation, a Qubit 4 spectrophotometer was used, to measure library concentrations, and to achieve equimolar pooling, then the NebNext Library Quant Kit (New England Biolabs) was utilised to measure the final pooled concentration before sequencing

value: EDTA coagulated plasma

tag: disease state

value: BAH


title: BAH 7 left adrenal vein sample


title: Plate2_A12 M

value: epidermis


title: BAH 7 right adrenal vein sample


title: Plate2_A11 M

value: LC


title: BAH 6 left adrenal vein sample


title: Plate2_A10 E


title: Plate2_B05 E


title: RMUGS replicate 1


title: Plate2_A09 M

value: M


title: BAH 5 left adrenal vein sample


title: Plate2_A08 E

value: E


title: Plate2_B02 M


title: BAH 6 right adrenal vein sample


title: Plate2_B03 M


title: BAH 4 left adrenal vein sample


title: BAH 4 right adrenal vein sample


title: Plate2_A06 M


title: BAH 3 left adrenal vein sample


title: BAH 3 right adrenal vein sample


title: Plate2_A03 M


title: Plate2_A07 E


title: Plate2_A05 E


title: Plate2_A04 M


title: Plate2_B01 E


title: BAH 8 right adrenal vein sample


title: BAH 2 left adrenal vein sample


title: Plate2_A02 M


title: BAH 2 right adrenal vein sample


title: Plate2_A01 M


title: BAH 1 left adrenal vein sample


title: BAH 1 right adrenal vein sample


title: Plate1_H12 M


title: BAH 5 right adrenal vein sample


title: UPA 10 left adrenal vein sample

value: UPA


title: Plate1_H11 E


title: UPA 9 left adrenal vein sample


title: Plate1_H09 M


title: Plate1_H10 E


title: UPA 10 right adrenal vein sample


title: UPA 9 right adrenal vein sample


title: Plate1_H08 M


title: Plate1_H06 M


title: UPA 8 left adrenal vein sample


title: UPA 8 right adrenal vein sample


title: Plate1_H05 M


title: Plate1_H04 M


title: Plate1_H02 M


title: Plate1_H07 E


title: Plate1_H03 E


title: UPA 7 left adrenal vein sample


title: UPA 6 right adrenal vein sample


title: UPA 7 right adrenal vein sample


title: Plate1_H01 E


title: UPA 5 left adrenal vein sample


title: UPA 6 left adrenal vein sample


title: Plate1_G12 E


title: UPA 5 right adrenal vein sample


title: UPA 4 left adrenal vein sample


title: UPA 4 right adrenal vein sample


title: Plate1_G11 M


title: Plate1_G10 M


title: UPA 3 left adrenal vein sample


title: Plate1_G08 M


title: UPA 3 right adrenal vein sample


title: UPA 2 right adrenal vein sample


title: Plate1_G05 M


title: Plate1_G09 M


title: UPA 2 left adrenal vein sample


title: Plate1_G06 E


title: Plate1_G07 M


title: UPA 1 right adrenal vein sample


title: Pcif1-KO HEK293T no siDis3 control 2

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1.
Bedgraphs (in RPM) of the reverse complement of the first nucleotide of read 1 were constructed using custom Python scripts.
For each gene/ENSG, a single PCT 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq reads per million mapped reads (RPM) count both within the first intron and within 10kb from the TSS of the TSL1 ENST transcript, and without overlapping with the 3'UTR of any transcript. For each gene/ENSG, a single full-length RNA 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq RPM read count within the 3'UTR of the TSL1 ENST transcript. PCT read counts and full-length RNA read counts are denoted as the RPM respectively at the identified PCT 3’end and full-length RNA 3’end. Only PCTs that passed the following cutoff filters were used in differential PCT analysis: Minimum PCT RPM of 1.0, minimum full-length RNA RPM of 5.0, mean WT_siScram PCT RPM > mean WT_no-siDis3 PCT RPM, and mean Pcif1-KO_siScram PCT RPM > mean Pcif1-KO_no-siDis3 PCT RPM.
For each gene/ENSG, a single PCT 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq reads per million mapped reads (RPM) count both within the first intron and within 10kb from the TSS of the TSL1 ENST transcript, and without overlapping with the 3'UTR of any transcript. For each gene/ENSG, a single full-length RNA 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq RPM read count within the 3'UTR of the TSL1 ENST transcript. PCT RPM and full-length RPM are denoted as the RPM respectively at the identified PCT 3’end and full-length RNA 3’end. Only PCTs that passed the following cutoff filters were used in differential PCT analysis: Minimum PCT RPM of 1.0, minimum full-length RNA RPM of 5.0, mean WT_siScram PCT RPM > mean WT_no-siDis3 PCT RPM, and mean Pcif1-KO_siScram PCT RPM > mean Pcif1-KO_no-siDis3 PCT RPM.
Assembly: hg38
Supplementary files format and content: bedgraph

molecule: nuclear RNA

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37°C, and in DMEM supplemented with 10% FBS. Cells within passage 3–25 were used for experiments. HEK293T cells were regularly subjected to MycoAlert Plus Mycoplasma kit (Lonza LT07) to verify that they were mycoplasma-free.

extract_protocol:
48hr later, cells were harvested by scraping and nuclei was enriched using Nuclei EZ (Sigma NUC-101). Nuclei were homogenized in Trizol-LS and nuclear RNA was isolated using Phase-Lock (HEAVY) tubes according to manufacturer’s protocol. Residual genomic DNA was removed using RQ1 RNase-free DNAse (Promega M6101) before RNA was purified with RNA concentrator (Zymo R1015).
RNA-seq library was prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit-REV (Lexogen 016).
3’ mRNA-Seq

treatment_protocol: Cells were seeded in 12-well plates 24hr prior to transfection. Cells were then transfected with 5pmol siRNA against Dis3 (Silencer Select S229660), against scrambled control (Silencer Select 4390843) and/or against PCF11 (Silencer Select S28362); using Lipofectamine RNAimax (Invitrogen 13778030) according to manufacturer’s instructions.

value: Human embryonic kidney


title: Plate1_G03 E


title: UPA 1 left adrenal vein sample


title: Plate1_F11 M


title: Plate1_G01 E


title: Plate1_G02 M


title: Pcif1-KO HEK293T no siDis3 control 1


title: Plate1_G04 M


title: Pcif1-KO HEK293T no siDis3 control 3


title: Plate1_F12 M


title: WT HEK293T no siDis3 control 2

value: WT


title: WT HEK293T no siDis3 control 3


title: Plate1_F07 E


title: Plate1_F10 M


title: Plate1_F06 M


title: WT HEK293T no siDis3 control 1


title: Plate1_F09 M


title: Infection-8hrs-3

city: New Delhi

first: Sujatha

last: Sunil

state: Delhi

address: Aruna Asaf Ali Road

department: Vector Borne Disease Group

country: India

institute: International Centre for genetic engineering and Biotechnology

data_processing:
Quality checks were performed using FastQC
Sequenced reads were trimmed for adaptor sequence using cutadapt  then mapped to GRCh38.p13 human genome assembly using STAR v2.7.3a.
Feautecount tool has been used to count read per gene
Differential expression analysis has been done using edgeR.
Assembly: GRCh38.p13

source_name: human monocytic cell line derived from an acute monocytic leukemia patient

growth_protocol: THP1, human monocytic cell line were routinely generated by re-plating in non-adherent T175 flask using RPMI media supplemented with  10% Fetal Bovine Serum (FBS), 0.05mM of 2-mercaptoethanol.

extract_protocol:
Total RNA was isolated using TRIZOL method
Libraries were prepared according to illumina's instructions using Truseq Stranded mRNA kit

treatment_protocol: THP1 monocytes activated into adherant macrophages using 100ng/ml of Phorbol 12-myristate 13-acetate (PMA)

value: PMA induced activated macrophages

value: 8 hours post Chikungunya infected macrophages


title: Infection-8hrs-2


title: Infection-8hrs-1


title: Plate1_F03 M


title: Infection-42hrs-1

data_processing:
Quality checks were performed using FastQC
Sequenced reads were trimmed for adaptor sequence using cutadapt  then mapped to GRCh38.p13 human genome assembly using STAR v2.7.3a.
Feautecount tool has been used to count read per gene
Differential expression analysis has been done using edgeR.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: read count per gene

source_name: 42 hours post Chikungunya infected macrophages

tag: source cell type

value: human monocytic cell line derived from an acute monocytic leukemia patient

value: 42 hours post Chikungunya infected


title: Plate1_F04 M


title: Infection-36hrs-3

source_name: 36 hours post Chikungunya infected macrophages

value: 36 hours post Chikungunya infected


title: Plate1_F02 M


title: Infection-36hrs-1


title: Plate1_E12 M


title: Infection-42hrs-3


title: Plate1_F08 M


title: Infection-24hrs-2

source_name: 24 hours post Chikungunya infected macrophages

value: 24 hours post Chikungunya infected


title: Plate1_E10 M


title: Plate1_E11 M


title: Infection-24hrs-3


title: Plate1_F01 M


title: Infection-24hrs-1


title: Infection-36hrs-2


title: Infection-42hrs-2


title: Plate1_F05 E


title: Plate1_E08 M


title: Control-2

source_name: Untreated macrophages

value: Untreated


title: Control-3


title: Plate1_E06 E


title: AntigomiR-3

value: AntagomiR-122b-5p transfected


title: Control-1


title: AntigomiR-2


title: Plate1_E05 E


title: Plate1_E03 E


title: Plate1_E04 M


title: AntigomiR-1


title: RXRɑ_Proliferating_ChIP-Seq

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

library_source: genomic

data_processing:
Sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end and converted to bedgraph files using the bedtools2 package.
Assembly: mm9
Supplementary files format and content: Bedgraph files were generated with the bedtools2 package and represent coverage depth of sequencing over the genome.

molecule: genomic DNA

source_name: C2C12 Myoblast

growth_protocol: Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium, Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% fetal bovine serum, at 37ºC with 5% CO2. The cells were maintained below 80% confluence in this growth medium.

extract_protocol:
Cells were crosslinked and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent to the McGill University Genome Quebec Innovation Centre for sequencing using Illumina HiSeq 2000 platform.
RNA and genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.

tag: strain

tag: chip antibody

value: RXRɑ (Santa Cruz_sc-553)

value: C2C12 Myoblast


title: Plate1_E02 M

value: epidermis


title: LIV_12

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

description: Liver C57BL/6J.AGO134-/-

data_processing:
Reads were aligned to the GRCm38 reference genome using GSNAP (version 2013-11-01)
Aligned reads within exons defined by GENCODE (v27) were counted using the countFeatures method from HTSeqGenie (v 4.2.1)

source_name: Liver

extract_protocol:
on column total RNA isolation using kit
TruSeq Illumina Paired Ends

value: Liver


title: Plate1_E01 E

value: LC


title: Plate1_E09 E

value: E


title: LIV_10

description: Liver C57BL/6J.AGO134-/-


title: Plate1_D12 M

value: M


title: LIV_11

description: Liver C57BL/6J.AGO134-/-


title: LIV_08

description: Liver C57BL/6J.AGO134-/-


title: Plate1_D11 M


title: LIV_07

description: Liver C57BL/6J.AGO134-/-


title: Plate1_D08 E


title: LIV_06

description: Liver C57BL/6J.AGO134-/-


title: Plate1_D09 E


title: Plate1_D07 M


title: Plate1_D10 M


title: LIV_05

description: Liver C57BL/6J.WT


title: Plate1_E07 M


title: LIV_04

description: Liver C57BL/6J.WT


title: Plate1_D05 M


title: LIV_02

description: Liver C57BL/6J.WT


title: LIV_03

description: Liver C57BL/6J.WT


title: LIV_01

description: Liver C57BL/6J.WT


title: Plate1_D06 M


title: Plate1_D03 M


title: KID_11

description: Kidney C57BL/6J.AGO134-/-

source_name: Kidney

value: Kidney


title: Plate1_D04 M


title: Plate1_D01 M


title: KID_10

description: Kidney C57BL/6J.AGO134-/-


title: KID_08

description: Kidney C57BL/6J.AGO134-/-


title: Plate1_C11 M


title: Plate1_C10 M


title: KID_05

description: Kidney C57BL/6J.WT


title: KID_12

description: Kidney C57BL/6J.AGO134-/-


title: KID_04

description: Kidney C57BL/6J.WT


title: Plate1_D02 M


title: Plate1_C09 M


title: Plate1_C08 M


title: KID_07

description: Kidney C57BL/6J.AGO134-/-


title: KID_02

description: Kidney C57BL/6J.WT


title: Plate1_C06 M


title: Plate1_C07 M


title: KID_03

description: Kidney C57BL/6J.WT


title: Plate1_C12 M


title: Plate1_C05 M


title: KID_01

description: Kidney C57BL/6J.WT


title: Plate1_C04 M


title: Plate1_C03 M


title: BM_05

description: Bone Marrow NA

source_name: Bone Marrow

value: Bone Marrow


title: Plate1_C02 M


title: Plate1_C01 M


title: SKIN_11

description: Skin C57BL/6J.AGO134-/-

source_name: Skin

value: Skin


title: SKIN_12

description: Skin C57BL/6J.AGO134-/-


title: SKIN_10

description: Skin C57BL/6J.AGO134-/-


title: Plate1_B12 E


title: Plate1_B11 E


title: SKIN_08

description: Skin C57BL/6J.AGO134-/-


title: KID_06

description: Kidney C57BL/6J.AGO134-/-


title: Plate1_B10 E


title: SKIN_07

description: Skin C57BL/6J.AGO134-/-


title: SKIN_06

description: Skin C57BL/6J.AGO134-/-


title: SKIN_04

description: Skin C57BL/6J.WT


title: Plate1_B07 M


title: Plate1_B09 E


title: SKIN_03

description: Skin C57BL/6J.WT


title: SKIN_05

description: Skin C57BL/6J.WT


title: Plate1_B05 E


title: SKIN_02

description: Skin C57BL/6J.WT


title: Plate1_B03 M


title: Plate1_B08 M


title: EYE_12

description: Eye C57BL/6J.AGO134-/-

source_name: Eye

value: Eye


title: Plate1_B04 E


title: Plate1_B06 M


title: EYE_11

description: Eye C57BL/6J.AGO134-/-


title: SKIN_01

description: Skin C57BL/6J.WT


title: Plate1_B02 E


title: EYE_10

description: Eye C57BL/6J.AGO134-/-


title: Plate1_A12 M


title: EYE_08

description: Eye C57BL/6J.AGO134-/-


title: EYE_06

description: Eye C57BL/6J.AGO134-/-


title: Plate1_B01 E


title: EYE_07

description: Eye C57BL/6J.AGO134-/-


title: Plate1_A10 M


title: EYE_05

description: Eye C57BL/6J.WT


title: Plate1_A09 M


title: Plate1_A08 E


title: Plate1_A07 E


title: EYE_03

description: Eye C57BL/6J.WT


title: EYE_02

description: Eye C57BL/6J.WT


title: Plate1_A06 M


title: EYE_01

description: Eye C57BL/6J.WT


title: Plate1_A04 M


title: LUN_11

description: Lung C57BL/6J.AGO134-/-

source_name: Lung

value: Lung


title: Plate1_A05 E

source_name: epidermis


title: Plate1_A03 M


title: LUN_10

description: Lung C57BL/6J.AGO134-/-


title: Plate1_A02 M


title: Plate1_A01 M


title: LUN_12

description: Lung C57BL/6J.AGO134-/-


title: LUN_07

description: Lung C57BL/6J.AGO134-/-


title: LUN_08

description: Lung C57BL/6J.AGO134-/-


title: LUN_06

description: Lung C57BL/6J.AGO134-/-


title: Plate1_A11 M


title: Ago134 TH2 14d 003

data_processing:
HTSeqGenie 4.2.1
Reads were aligned to the GRCm38 reference genome using GSNAP (version 2013-11-01)
Aligned reads within exons defined by GENCODE (v27) were counted using the countFeatures method from HTSeqGenie
Assembly: GRCm38
Supplementary files format and content: counts

source_name: FACS-sorted CD4+ TCRb+ T cells from mouse splenocytes

extract_protocol:
on colum total RNA isolation using kit
TrueSeq Immumina Paired Ends

value: primary CD4+ Tcells

value: Th2 14d


title: Ago134 TH2 14d 002

value: FACS-sorted CD4+ TCRb+ T cells from mouse splenocytes


title: LUN_05

description: Lung C57BL/6J.WT


title: WT TH2 14d 003

value: WT


title: LUN_04

description: Lung C57BL/6J.WT


title: EYE_04

description: Eye C57BL/6J.WT


title: LUN_03

description: Lung C57BL/6J.WT


title: Ago134 TH2 14d 001


title: LUN_02

description: Lung C57BL/6J.WT


title: WT TH2 14d 002


title: WT TH2 14d 001


title: Ago134 TH2 7d 004

value: Th2 7d


title: Ago134 TH2 7d 003


title: Ago134 TH2 7d 002


title: ILE_11

description: Ileum C57BL/6J.AGO134-/-

source_name: Ileum

value: Ileum


title: ILE_10

description: Ileum C57BL/6J.AGO134-/-


title: ILE_08

description: Ileum C57BL/6J.AGO134-/-


title: Ago134 TH2 7d 001


title: ILE_07

description: Ileum C57BL/6J.AGO134-/-


title: WT TH2 7d 002


title: WT TH2 7d 004


title: ILE_05

description: Ileum C57BL/6J.WT


title: WT TH2 7d 001


title: ILE_03

description: Ileum C57BL/6J.WT


title: ILE_04

description: Ileum C57BL/6J.WT


title: ILE_02

description: Ileum C57BL/6J.WT


title: DRG, ash1l, 2

city: Shanghai

first: Wan-Jie

last: Du

address: 131 Dong'an Road

department: State Key Laboratory of Medical Neurobiology and MOE Frontier Center for Brain Science, Institutes of Brain Science

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were trimmed by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes Count values for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: dorsal root ganglion

extract_protocol:
Dorsal root ganglions were removed, quickly frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: dorsal root ganglion


title: LUN_01

description: Lung C57BL/6J.WT


title: DRG, ash1l, 1


title: ILE_01

description: Ileum C57BL/6J.WT


title: DRG, wt, 3


title: COL_12

description: Colon C57BL/6J.AGO134-/-

source_name: Colon

value: Colon


title: DRG, wt, 1


title: DRG, wt, 2


title: COL_10

description: Colon C57BL/6J.AGO134-/-


title: Y541S, EP, SERD

first: Jackson

last: Liang

department: Discovery Oncology

institute: Genentech

data_processing:
CellRanger pipeline
Assembly: GRCm38
Supplementary files format and content: Matrix, barcodes, features

source_name: Mammary mature luminal cells

growth_protocol: Animals were raised under standard husbandry methods until 6 months of age.

extract_protocol:
Mammary glands were dissected from treated animals; EpCAM+ cells were isolated from tissues by FACS. Sorted cells with viability >85% were sequenced.
Libraries were prepared using the 10X Genomics single cell gene expression kit v3.1
Single cell RNA-seq 3' Expression

treatment_protocol: Animals were implanted with hormone pellets (E2 & P4), then dosed daily with vehicle (MCT) or giredestrant (30 mg/kg, p.o.) for four days

tag: er mutation

value: E2/P4 + giredestrant

value: Mammary gland

value: Mammary epithelial cell


title: ILE_12

description: Ileum C57BL/6J.AGO134-/-


title: COL_08

description: Colon C57BL/6J.AGO134-/-


title: Y541S, EP, vehicle

value: E2/P4 + vehicle


title: WT TH2 7d 003


title: ILE_06

description: Ileum C57BL/6J.AGO134-/-


title: COL_07

description: Colon C57BL/6J.AGO134-/-


title: WT, EP, SERD


title: COL_04

description: Colon C57BL/6J.WT


title: COL_03

description: Colon C57BL/6J.WT


title: DRG, ash1l, 3


title: COL_05

description: Colon C57BL/6J.WT


title: CTRL9

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

data_processing:
Raw paired-end reads were aligned to human reference genome version GRCh38 (gencode v40). Read alignment and transcript quantification of RNA-seq data was performed with the nf-core RNA-seq (v3.12.0) STAR-Salmon pipeline using Nextflow (v23.04.2) and its default settings (STAR v2.7.10a, Salmon v1.10.1, Trimgalore v0.6.7). Output files of Salmon (i.e., quant.genes.sf) were imported for downstream analysis, which include relative abundance (=TPM, Transcripts Per Million) estimated counts and effective length.
Assembly: GRCh38 (gencode v40)
Supplementary files format and content: quant.genes.sf files (star salmon output files with relative abundance (=TPM, Transcripts Per Million) estimated counts and effective length)

source_name: liver

extract_protocol:
Total RNA isolation of FFPE liver biopsies and library preparation were performed as described previously (Montanari NR et al. Multi-parametric analysis of human livers reveals variation in intrahepatic inflammation across phases of chronic hepatitis B infection. J Hepatol. 2022 Aug;77(2):332-343. PMID: 35218813). Core needle liver biopsies were sectioned, deparaffinized, and total RNA was isolated using the RNeasy FFPE Kit (Qiagen, Germany) following the manufacturer’s instructions. Prior to sequencing, rRNA was depleted.
Library preparation and sequencing were performed by EA Genomics (Q2 solutions, USA) on the Illumina HiSeq platform (100 bp paired-end reads, 50 million reads per sample) and by GenomeScan (Leiden, The Netherlands) on the Illumina NovaSeq 6000 (150 bp paired-end reads, 30 million reads/sample) using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina sequencing. All samples passed the library preparation QC.
Library preparation and sequencing were performed by EA Genomics (Q2 solutions, USA) and by GenomeScan (Leiden, The Netherlands).

value: liver

tag: name of_sample

tag: material

value: FFPE

tag: sample id

tag: group

value: CTRL


title: WT, EP, vehicle

tag: treatment

tag: tissue


title: CTRL8


title: COL_11

description: Colon C57BL/6J.AGO134-/-

tag: genotype


title: CTRL6


title: COL_02

description: Colon C57BL/6J.WT


title: CTRL4


title: TH2 Cre;A2 G

description: Th2 Ago2KO

data_processing:
To generate the counts table, we trimmed the UMI off the read sequence, then aligned the reads to the mouse genome. The number of UMIs from reads aligning to each microRNA (defined by miRBase v22) was then counted. Control RNA sequences were included in each library in standard concentrations, and the number of UMIs derived from each standard are also included in the count table.
Assembly: GRCm38
Supplementary files format and content: To generate the counts table, we trimmed the UMI off the read sequence, then aligned the reads to the mouse genome. The number of UMIs from reads aligning to each microRNA (defined by miRBase v22) was then counted. Control RNA sequences were included in each library in standard concentrations, and the number of UMIs derived from each standard are also included in the count table.

source_name: FACS-sorted CD4+ TCRb+ T cells from mouse spleenocytes

extract_protocol:
on column total RNA isolation using kit
TrueSeq Illumina single-end

value: 5 days of Th2 differentiation culture


title: COL_01

description: Colon C57BL/6J.WT


title: TH2 Cre;A2 E

description: Th2 Ago2KO

value: FACS-sorted CD4+ TCRb+ T cells from mouse spleenocytes


title: CTRL3


title: CTRL1


title: CTRL2


title: TH2 Cre;A2 D

description: Th2 Ago2KO

value: primary CD4+ Tcells


title: ENEG6

value: ENEG


title: TH2 Cre B

description: Th2 WT Cre


title: ENEG7


title: TH2 Cre A

description: Th2 WT Cre


title: COL_06

description: Colon C57BL/6J.AGO134-/-


title: ENEG5


title: CTRL7


title: nT Cre;A2 G

description: nT Ago2KO

value: nT


title: nT Cre;A2 E

description: nT Ago2KO


title: nT Cre;A2 F

description: nT Ago2KO


title: CTRL5


title: nT Cre;A2 D

description: nT Ago2KO


title: TH2 Cre;A2 F

description: Th2 Ago2KO


title: ENEG3


title: nT Cre C

description: nT WT Cre


title: ENEG12


title: ENEG16


title: TH2 Cre C

description: Th2 WT Cre


title: ENEG11


title: nT Cre A

description: nT WT Cre


title: ENEG1


title: ENEG10


title: TH2-14d_A134_002

description: Th2 Ago134KO d14


title: TH2-14d_A134_003

description: Th2 Ago134KO d14


title: TH2-14d_WT_003

description: Th2 WT d14

value: WT


title: ENEG2


title: hESC_ExoEasyMaxi_Eluate_2

city: La Jolla

first: Louise

middle: C

last: Laurent

address: SCRM, 2880 Torrey Pines Scenic Drive

department: Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: embryonic stem cell

extract_protocol:
RNA Isolation method was "500uL of biofluid was incubated with 100uL warmed Slurry and 900uL warmed Lysis Buffer A (containing 2-Mercaptoethanol) for 10 min at 60C. To this 1.5 mL of 100% ethanol was added and centrifuged for 2min at 1000rpm. To the pellet 300uL Lysis Buffer A was added and incubated for 10 min at 60C. 300uL 100% Ethanol was added, loaded onto the filter column and centrifuged for 30sec at 1000xg followed by 1 min at 16000xg. The column was washed thrice with 400uL Wash Solution for 1 min at 16000 xg and then centrifuged once again for 3 min to dry the membrane. RNA was eluted in 14uL water with a slow spin for 2 mins at 300 xg followed by a spin for 3 min at 16000 xg.". RNA Isolation kit was Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: disease

value: Healthy Subject

tag: anatomical location

value: Entire embryo

tag: rna source

value: other


title: hESC_qEV_F05_3


title: TH2-14d_WT_001

description: Th2 WT d14

tag: cell type


title: TH2-7d_A134_004

description: Th2 Ago134KO d7


title: ENEG4


title: hESC_DGUC_F8_2


title: hESC_DGUC_F8_1


title: TH2-7d_A134_002

description: Th2 Ago134KO d7


title: TH2-7d_A134_003

description: Th2 Ago134KO d7


title: nT Cre B

description: nT WT Cre


title: TH2-7d_A134_001

description: Th2 Ago134KO d7


title: TH2-14d_A134_004

description: Th2 Ago134KO d14


title: hESC_DGUC_F11_3


title: hESC_Total_Input_1

value: total cell-free biofluid RNA


title: TH2-7d_WT_003

description: Th2 WT d7


title: TH2-7d_WT_002

description: Th2 WT d7


title: hESC_DGUC_F01_3


title: hESC_DGUC_F02_3


title: TH2-7d_WT_001

description: Th2 WT d7


title: TH2-14d_WT_002

description: Th2 WT d14


title: hESC_qEV_F15_1


title: nT_A134_sorted_003

description: nT Ago134KO


title: Female_plasma_pool_LDL

source_name: Plasma

value: Entire cardiovascular system


title: hESC_DGUC_F11_2


title: hESC_qEV_F11_1


title: nT_A134_sorted_002

description: nT Ago134KO


title: hESC_qEV_F14_3


title: hESC_Cells_1


title: nT_WT_sorted_004

description: nT WT


title: nT_A134_sorted_001

description: nT Ago134KO


title: hESC_DGUC_F05_3


title: nT_WT_sorted_003

description: nT WT


title: Female_plasma_pool_LFF


title: hESC_DGUC_F05_2


title: TH2-7d_WT_004

description: Th2 WT d7


title: hESC_qEV_F08_1


title: hESC_qEV_F10_3


title: nT_WT_sorted_002

description: nT WT


title: hESC_qEV_F08_2


title: hESC_qEV_F04_2


title: nT_A134_sorted_004

description: nT Ago134KO


title: nT_WT_sorted_001

description: nT WT


title: hESC_DGUC_F10_1


title: P042.1_GEX

city: New Delhi,

first: Asgar

last: Ansari

address: Aruna Asaf Ali Marg, Jawaharlal Nehru University,

institute: National Institute of Immunology,

description:
Gene Expression
DemuxHTO3_RNA

data_processing:
Single-cell RNA sequencing (FASTQ) data from the 5’ RNA expression, VDJ-TCR and CSP libraries were simultaneously processed using the cellranger multipipeline of Cell Ranger software v7.0.1 (10x Genomics). Unique molecular identifier (UMI) counts were assigned to the cell barcodes and mapped to reference genomes: GRCh38-2020-A for RNA, GRCh38-alts-ensembl-7.0.0 for VDJ-TCR, and TotalSeq-C (BioLegend) feature barcodes for CSP to generate a filtered RNA/CSP count matrix and filtered VDJ-TCR contig annotations. To demultiplex the cells from all three patients, raw reads from the 5’ RNA expression and multiplexing capture (CSP) libraries were again processed with a cellranger multipipeline to generate a sample-filtered RNA count matrix for each sample. Cell barcodes from all three patients were assigned to their respective patient IDs, and unassigned or doublets were discarded during demultiplexing. Next, the demultiplexed filtered count data from all patients were merged and analyzed via the R platform-based Seurat v4.3.0 package.
Assembly: GRCh38
Supplementary files format and content: cellranger multi output matrix files: Combined_filtered_barcodes.tsv.gz, Combined_filtered_features.tsv.gz, Combined_filtered_matrix.mtx.gz
Supplementary files format and content: cellranger multi output vdj-t files: Combined_filtered_contig_annotations.csv
Supplementary files format and content: cellranger multi output matrix files: DemuxHTO2_filtered_barcodes.tsv.gz, DemuxHTO2_filtered_features.tsv.gz, DemuxHTO2_filtered_matrix.mtx.gz
Supplementary files format and content: cellranger multi output matrix files: DemuxHTO3_filtered_barcodes.tsv.gz, DemuxHTO3_filtered_features.tsv.gz, DemuxHTO3_filtered_matrix.mtx.gz
Supplementary files format and content: cellranger multi output matrix files: DemuxHTO4_filtered_barcodes.tsv.gz, DemuxHTO4_filtered_features.tsv.gz, DemuxHTO4_filtered_matrix.mtx.gz

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs from three acute dengue patients (P022.1, P042.1, P032.1) were thawed and and revived in 10 mL of prewarmed RPMI 1640 at 37°C. The revived PBMCs were treated with DNase I (StemCell Technologies) at 100 µg/mL to prevent the cellular clumps. Revived PBMCs used for downstream analysis were >80% viable, as assessed by acridine orange (AO) and propidium iodide (PI) staining. The cells were washed with 20 mL of PBS-2 mM EDTA buffer. A total of 3x106 PBMCs were blocked with 10% heat-inactivated human plasma by incubating for 10 minutes at 4°C. The cells were surface stained with fluorochrome-tagged and TotalSeq-C (BioLegend) anti-human antibodies for 1 hour at 4°C according to the manufacturer’s instructions. PBMCs from each patient were also stained with anti-human Hashtag antibodies (BioLegend) before pooling. The three PBMCs were stained with following Hashtag antibodies, HTO2, HTO3, and HTO4, respectively. For FACS sorting of activated CD4+ T cells, ICOS+CD38+ cells were gated on CD4+ T cells after excluding dead cells, CD14, CD16 monocytes, CD20 B cells and CD8 T cells. FACS-sorted ICOS+CD38+ CD4+ T cells from three patients were pooled together in equal numbers and resuspended at a density of 1100 cells/µL with >90% viability.
FACS-sorted ICOS+CD38+ CD4+ T cells were processed for gel bead-in-emulsion (GEM) generation, barcoding and cDNA preparation (10x Genomics) according to the manufacturer’s recommendation. Single-cell RNA sequencing library preparation was performed using Chromium Next GEM Single-Cell 5’ Reagent Kit v2.0 (Dual Index) with immune profiling (VDJ) and cell surface protein feature barcode technology (10x Genomics). The initial cDNA amplification was performed with 13 amplification cycles. After amplification, the cDNA pellet was used to amplify the VDJ T-cell receptor (TCR), after which the VDJ library was prepared via 8 cycles of amplification; preparation of the 5’ gene expression library was performed via 14 cycles of amplification. A cell surface protein (CSP) library was generated from the amplified cDNA supernatant after 8 amplification cycles. The quality and concentration of the cDNA libraries were assessed using the 5200 Fragment Analyzer system (Agilent) with an Agilent DNF-474 HS NGS Fragment Kit and a Qubit 4.0 fluorometer (Thermo-Fisher) with a dsDNA HS assay kit according to the manufacturer’s recommendations. In addition, the insert size of the library was determined using a TapeStation 4150 (Agilent) and an Agilent high-sensitivity D1000 ScreenTape assay.  The three libraries were pooled in molar concentrations according to a sequencing depth of ~30,000 reads/cell for 5’ gene expression and ~5,000 reads/cell for the VDJ and CSP libraries and sequenced on an Illumina NovaSeq 6000 platform (150 bp, paired-end) with the following parameters: read1 - 26 cycles; read2 - 90 cycles; and i7 and i5 indexes - 10 cycles.
scRNA-seq with VDJ immune profiling and cell surface protein (CSP) expression

value: PBMC

value: ICOS+CD38+ CD4+ T cells

value: Untreated, direct ex vivo


title: hESC_DGUC_F7_3


title: P032.1_GEX

description:
Gene Expression
DemuxHTO4_RNA


title: Combined_TCR

description:
VDJ-T
Combined_VDJT


title: hESC_qEV_F04_1


title: P022.1_GEX

description:
Gene Expression
DemuxHTO2_RNA


title: hESC_ExoEasyMaxi_FT_3


title: hESC_DGUC_F01_2


title: Combined_GEX

description:
Gene Expression
Combined_RNA


title: hESC_qEV_F01_2


title: hESC_qEV_F13_2


title: RNA-seq for CD8-TCR-noStimulation Experiment-Replicate 2

city: Beijing

first: Xin

last: Lin

state: Beijng

address: chengfu road, Haidian

institute: Tsinghua University

data_processing:
ATAC-seq: Raw fastq reads were trimmed to remove the Nextera sequencing adaptors using trim_galore. The trimmed reads were mapped to the mouse reference (hg38) genome using BWA. Reads with a mapping quality of <30 and duplications were removed using SAMtools. Motif enrichment scores were analyzed by chromVAR (Schep et al., 2017). RNA-seq: The adaptors of paired-end reads were trimmed and quality control checks were carried out using trim-galore. Reads were aligned to human genome reference from GENCODE using HISAT2. Aligned reads stored in SAM format were manipulated to generate bam files using SAMtools with parameter is ‘samtools view –b –h –F 4 –f 3’. featureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from GENCODE. Differential gene expression analysis was conducted, which used raw counts as input using R package DESeq2
Assembly: Hg38
Supplementary files format and content: bw and counts files

source_name: CD8 T cells

extract_protocol:
ATAC-seq: Nuclei of 50,000 T cells were isolated according to the Omni-ATAC protocol (Corces et al., 2017). The cell pellet was lysed with 0.1 ml Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin (G9441; Promega), 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl (pH 7.4) for 3 min on ice. Then, 1 ml wash buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 1% bovine serum albumin (130-091-376; Miltenyi Biotec) and 0.1% Tween-20) was added to the lysed cells. Nuclei were spun down for 5 min at 500g and 4 °C and resuspended in 50 μL wash buffer.  RNA-seq: RNA-seq library preparation was performed using Smart-seq2 (Picelli et al., 2014) as described with modification allowing higher quality library generation. Briefly, 1,000 sorted T cells were directly sorted into 8 μl RLT lysis buffer and 1% (vol/vol) 2-mercaptoethanol.
ATAC-seq: .The isolated nuclei were combined with 5 µl 10 mM MgCl2, 10 µl 5× TTBL, 5 µl Tn5 transposome (TD501; Vazyme) and 20 µl H2O to form a transposition mix, which was then incubated for 60 min at 37 °C with gentle shaking at 500 r.p.m.  The reactions were cleaned up with the DNA Clean & Concentrator kit (D4014; Zymo Research) and eluted in 21 µl H2O. For PCR reactions, each well was mixed with 2.5 μl 10 μM N5 index primer (AATGATACGGCGACCACCGAGATCTACAC (8-bp barcode) TCGTCGGCAGCGTC), 2.5 µl 10 μM N7 index primer (CAAGCAGAAGACGGCATACGAGAT (8-bp barcode) GTCTCGTGGGCTCGG) and 25 µl NEBNext High-Fidelity 2X PCR Master Mix (M0541L; New England Biolabs). Amplification was carried out using the following thermocycling program: 72 °C for 5 min; 98 °C for 30 s; nine cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; and a final 72 °C for 5 min. Afterwards, the amplified libraries were purified using 1.2× SPRIselect Beads (A63881; Beckman Coulter) and quantified by Qubit 3.0 Fluorometer (Q33216; Thermo Fisher Scientific). The size ranges of the PCR products were assessed using an Agilent 4200 Bioanalyzer. All libraries were sequenced with paired-end 150-bp reads on the illumina Novaseq platform. RNA-seq: RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2×) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.

value: CD8 T cells

value: TCR-noStimulation


title: RNA-seq for CD8-TCR-noStimulation Experiment-Replicate 3


title: hESC_ExoEasyMaxi_FT_2


title: RNA-seq for CD8-TCR-1uM Experiment-Replicate 3


title: hESC_qEV_F09_2


title: Combined_ADT_HTO

description:
Antibody Capture
Combined_CSP

library_source: other

molecule: protein


title: RNA-seq for CD8-TCR-noStimulation Experiment-Replicate 1


title: hESC_qEV_F13_1


title: RNA-seq for CD8-TCR-1uM Experiment-Replicate 1


title: Female_plasma_pool_total


title: RNA-seq for CD8-TCR-1uM Experiment-Replicate 2


title: hESC_qEV_F06_3


title: RNA-seq for CD8-TCR-10nM Experiment-Replicate 3


title: hESC_qEV_F10_2


title: RNA-seq for CD8-TCR-10nM Experiment-Replicate 2


title: RNA-seq for CD8-TCR-10nM Experiment-Replicate 1


title: hESC_DGUC_F12_2


title: hESC_DGUC_F12_3


title: RNA-seq for CD8-TCR-100nM Experiment-Replicate 2


title: RNA-seq for CD8-TCR-100nM Experiment-Replicate 3


title: hESC_DGUC_F06_3


title: hESC_qEV_F02_3


title: RNA-seq for CD8-TCR-100nM Experiment-Replicate 1


title: hESC_DGUC_F04_1


title: RNA-seq for CD8-STAR-noStimulation Experiment-Replicate 3

value: STAR-noStimulation


title: RNA-seq for CD8-STAR-noStimulation Experiment-Replicate 2


title: RNA-seq for CD8-STAR-noStimulation Experiment-Replicate 1


title: hESC_qEV_F06_2


title: hESC_ME_VN96_Supernatant_1


title: RNA-seq for CD8-STAR-1uM Experiment-Replicate 3


title: RNA-seq for CD8-STAR-1uM Experiment-Replicate 2


title: hESC_DGUC_F03_3


title: hESC_DGUC_F06_2


title: hESC_qEV_F15_3


title: RNA-seq for CD8-STAR-1uM Experiment-Replicate 1


title: RNA-seq for CD8-STAR-10nM Experiment-Replicate 3


title: hESC_qEV_F05_2


title: RNA-seq for CD8-STAR-10nM Experiment-Replicate 2


title: Female_plasma_pool_Chylo


title: hESC_ME_VN96_Eluate_3


title: RNA-seq for CD8-STAR-100nM Experiment-Replicate 2


title: RNA-seq for CD8-STAR-10nM Experiment-Replicate 1


title: RNA-seq for CD8-STAR-100nM Experiment-Replicate 1


title: RNA-seq for CD8-STAR-100nM Experiment-Replicate 3


title: hESC_qEV_F09_1


title: hESC_ExoEasyMaxi_FT_1


title: RNA-seq for CD8-28zCAR-noStimulation Experiment-Replicate 3


title: hESC_qEV_F12_1


title: hESC_qEV_F12_3


title: RNA-seq for CD8-28zCAR-noStimulation Experiment-Replicate 2


title: RNA-seq for CD8-28zCAR-noStimulation Experiment-Replicate 1


title: hESC_qEV_F01_1


title: hESC_DGUC_F11_1


title: RNA-seq for CD8-28zCAR-1uM Experiment-Replicate 3


title: hESC_qEV_F03_3


title: hESC_DGUC_F8_3


title: RNA-seq for CD8-28zCAR-1uM Experiment-Replicate 2


title: hESC_DGUC_F05_1


title: RNA-seq for CD8-28zCAR-1uM Experiment-Replicate 1


title: hESC_DGUC_F06_1


title: RNA-seq for CD8-28zCAR-10nM Experiment-Replicate 3


title: hESC_DGUC_F02_2


title: RNA-seq for CD8-28zCAR-10nM Experiment-Replicate 1


title: hESC_DGUC_F02_1


title: RNA-seq for CD8-28zCAR-100nM Experiment-Replicate 3


title: RNA-seq for CD8-28zCAR-100nM Experiment-Replicate 2


title: hESC_qEV_F08_3


title: hESC_qEV_F14_2


title: Female_plasma_pool_HDL


title: RNA-seq for CD4-TCR-noStimulation Experiment-Replicate 2

source_name: CD4 T cells

value: CD4 T cells


title: RNA-seq for CD8-28zCAR-10nM Experiment-Replicate 2


title: RNA-seq for CD8-28zCAR-100nM Experiment-Replicate 1


title: RNA-seq for CD4-TCR-noStimulation Experiment-Replicate 1


title: RNA-seq for CD4-TCR-1uM Experiment-Replicate 3


title: hESC_ME_VN96_Eluate_2


title: hESC_qEV_F11_2


title: hESC_qEV_F05_1


title: RNA-seq for CD4-TCR-1uM Experiment-Replicate 2


title: hESC_qEV_F07_3


title: hESC_Cells_3


title: hESC_qEV_F15_2


title: RNA-seq for CD4-TCR-10nM Experiment-Replicate 1


title: RNA-seq for CD4-TCR-10nM Experiment-Replicate 2


title: RNA-seq for CD4-TCR-10nM Experiment-Replicate 3


title: RNA-seq for CD4-TCR-noStimulation Experiment-Replicate 3


title: hESC_DGUC_F7_2


title: hESC_DGUC_F10_3


title: RNA-seq for CD4-TCR-100nM Experiment-Replicate 3


title: RNA-seq for CD4-TCR-100nM Experiment-Replicate 2


title: hESC_qEV_F04_3


title: hESC_DGUC_F01_1


title: RNA-seq for CD4-TCR-100nM Experiment-Replicate 1


title: hESC_qEV_F07_2


title: RNA-seq for CD4-STAR-noStimulation Experiment-Replicate 1


title: RNA-seq for CD4-STAR-noStimulation Experiment-Replicate 2


title: RNA-seq for CD4-STAR-noStimulation Experiment-Replicate 3


title: hESC_DGUC_F10_2


title: hESC_DGUC_F09_3


title: RNA-seq for CD4-STAR-1uM Experiment-Replicate 3


title: hESC_qEV_F11_3


title: RNA-seq for CD4-TCR-1uM Experiment-Replicate 1


title: hESC_DGUC_F04_3


title: hESC_Total_Input_3


title: RNA-seq for CD4-STAR-1uM Experiment-Replicate 1


title: RNA-seq for CD4-STAR-1uM Experiment-Replicate 2


title: hESC_ME_CTRL_Supernatant_1


title: hESC_Cells_2


title: RNA-seq for CD4-STAR-10nM Experiment-Replicate 3


title: hESC_qEV_F01_3


title: RNA-seq for CD4-STAR-10nM Experiment-Replicate 1


title: RNA-seq for CD4-STAR-10nM Experiment-Replicate 2


title: hESC_qEV_F02_1


title: hESC_qEV_F14_1


title: hESC_qEV_F10_1


title: RNA-seq for CD4-STAR-100nM Experiment-Replicate 3


title: RNA-seq for CD4-STAR-100nM Experiment-Replicate 2


title: hESC_qEV_F13_3


title: hESC_DGUC_F12_1


title: RNA-seq for CD4-STAR-100nM Experiment-Replicate 1


title: hESC_Total_Input_2


title: RNA-seq for CD4-28zCAR-noStimulation Experiment-Replicate 2


title: RNA-seq for CD4-28zCAR-noStimulation Experiment-Replicate 1


title: hESC_qEV_F09_3


title: RNA-seq for CD4-28zCAR-noStimulation Experiment-Replicate 3


title: RNA-seq for CD4-28zCAR-1uM Experiment-Replicate 3


title: hESC_qEV_F03_2


title: hESC_qEV_F06_1


title: RNA-seq for CD4-28zCAR-1uM Experiment-Replicate 1


title: RNA-seq for CD4-28zCAR-10nM Experiment-Replicate 3


title: RNA-seq for CD4-28zCAR-1uM Experiment-Replicate 2


title: hESC_DGUC_F7_1


title: hESC_DGUC_F09_1


title: hESC_qEV_F07_1


title: hESC_DGUC_F03_2


title: hESC_DGUC_F04_2


title: RNA-seq for CD4-28zCAR-10nM Experiment-Replicate 2


title: hESC_ME_VN96_Supernatant_3


title: hESC_qEV_F12_2


title: RNA-seq for CD4-28zCAR-100nM Experiment-Replicate 3


title: hESC_DGUC_F09_2


title: hESC_DGUC_F03_1


title: RNA-seq for CD4-28zCAR-100nM Experiment-Replicate 2


title: RNA-seq for CD4-28zCAR-100nM Experiment-Replicate 1


title: hESC_qEV_F03_1


title: hESC_ExoEasyMaxi_Eluate_3


title: hESC_ME_VN96_Supernatant_2


title: 293T_CD9_B1_1

source_name: cell culture

value: Entire fetal kidney


title: 293T_CD9_FT2_1


title: 293T_CD63_B2_3_2


title: 293T_CD81_B1_8


title: 293T_CD81_FT2_9


title: 293T_CD81_FT2_2


title: 293T_CD9_B2_6


title: 293T_Total_Input_1


title: 293T_CD81_B1_7


title: 293T_CD81_FT2_1


title: 293T_CD63_B1_1


title: 293T_ON_CD81_B1_2


title: 293T_CD63_B1_2


title: 293T_CD63_B2_6


title: RNA-seq for CD4-28zCAR-10nM Experiment-Replicate 1


title: 293T_ON_CD81_B1_1


title: 293T_CD63_B2_3


title: 293T_CD81_FT2_5


title: 293T_Total_Input_4


title: 293T_CD63_FT2_5


title: 293T_CD9_B2_2


title: 293T_ON_CD81_FT2_3


title: 293T_CD81_B1_6


title: 293T_CD81_FT2_8


title: 293T_ON_CD81_FT2_2


title: 293T_CD81_B2_6


title: 293T_CD81_B1_3


title: 293T_CD63_B1_5


title: 293T_CD9_FT2_2


title: 293T_CD63_B1_4


title: 293T_CD9_FT2_3


title: 293T_ON_CD81_B2_2


title: 293T_CD9_B2_5


title: 293T_CD81_FT2_3


title: 293T_CD81_B1_1


title: 293T_CD63_FT2_4


title: 293T_CD63_FT2_3


title: 293T_ON_CD81_B2_1


title: 293T_CD81_FT2_4


title: 293T_CD63_B2_4


title: 293T_Total_Input_3


title: 293T_CD63_B2_2


title: 293T_CD81_B1_2


title: 293T_CD63_FT2_6


title: 293T_CD81_B2_5


title: 293T_CD9_B1_3


title: 293T_CD9_B1_2


title: 293T_CD81_B2_9


title: 293T_CD63_B2_1


title: 293T_ON_CD81_FT2_1


title: 293T_CD81_B2_8


title: 293T_CD9_FT2_4


title: 293T_CD9_B2_1


title: 293T_CD63_B2_5


title: 293T_CD63_B1_6


title: 293T_CD9_FT2_6


title: 293T_Total_Input_2


title: 293T_CD81_B2_1


title: 293T_CD81_B2_7


title: 293T_CD9_B1_6


title: 293T_CD63_B1_3


title: 293T_CD9_B2_3


title: sn-ATAC-seq, GBM38, tumor

city: Atlanta

first: Steven

last: Sloan

state: Georgia

address: 615 Michael Street, Room 375

institute: Emory University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger ARC (cellranger-arc-2.0.0).
Assembly: hg38
Supplementary files format and content: tab-delimited text files, matrix files, alignment files, ATAC-seq fragment files
Library strategy: single cell multiome

source_name: human glioblastoma

extract_protocol:
GBM nuclei extraction: ~20 mg of tissue was dissociated with a 2-ml Dounce homogenizer in homogenization buffer (0.26 M sucrose, 0.03 M KCl, 0.01 M MgCl2, 0.02 M Tricine-KOH pH 7.8, 0.001 M DTT, 0.5 mM Spermidine, 0.15 mM Spermine, 0.3% NP40, and cOmplete Protease inhibitor). This was followed by filtering through a 40um Flowmi cell strainer, then a 20um bucket-style cell strainer, and centrifugation for 10 min at 600 r.c.f. After the majority of the supernatant was carefully removed, the pellet was resuspended in homogenization buffer and mixed with an equal volume of 50% iodixanol solution to make a final concentration of 25% iodixanol. Next, a 30% iodixanol solution, followed by a 40% iodixanol solution, was layered under the 25% mixture and centrifuged for 20 min at 3000 r.c.f without the centrifuge brake. Post-centrifugation, a thin white nuclei band was carefully collected from the interface of the 30% and 40% iodixanol solutions. Nuclei underwent 1-2 wash steps to remove any additional debris by gently mixing nuclei in ATAC- RSB-Tween buffer (0.01 M Tris-HCl pH 7.5, 0.01 M NaCl, 0.003 M MgCl2, 0.1% Tween-20) and centrifuging for 10 min at 600 r.c.f.
Libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression kit following the manufacturer’s instructions. Per sample, 16,100 nuclei were resuspended in 1x diluted nuclei buffer (10x Genomics) with 2% BSA (Sigma) with a capture target of 10,000 nuclei

value: human glioblastoma

tag: Sex

value: male

value: IDHwt


title: sn-RNA-seq, GBM25, tumor

description: 10x Genomics Chromium Single Cell Multiome

value: female


title: 293T_CD9_B1_4

value: Healthy Subject


title: sn-ATAC-seq, GBM25, tumor


title: sn-RNA-seq, GBM25, margin


title: 293T_CD81_FT2_6


title: 293T_CD81_B2_4


title: 293T_CD81_B1_4


title: 293T_CD81_B1_9


title: sn-ATAC-seq, GBM20, tumor


title: 293T_CD9_B1_5


title: 293T_ON_CD81_B2_3


title: Kuramochi_CD9_FT1_2

value: Ovarian Serous Adenocarcinoma

value: Ovarian structure


title: male_mdd_9_input

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

data_processing:
All sequencing data was extracted from FASTQ files.
Adapters were trimmed using TrimGalore.
The trimmed reads were aligned to human genome using STAR.
rRNA contamination was removed on the basis rRNA co-ordinates bed file of the GRCh38 genome using SortMeRNA.
m6A peaks were identified using TRESS with threshold of false discovery rate (FDR) < 0.05 and fold change > 1.5.
Differential methylation was conducted using TRESS.
Assembly: GRch38
Supplementary files format and content: Counts.txt, PeakCounts.txt

source_name: Brain

extract_protocol:
Total RNA was extracted from postmortem brain tissues using RNeasy Lipid Tissue Mini Kit (QIAGEN, #74804) following the manufacturer's instructions. RNA was treated with DNase during this process. Total RNA was then fragmented to ~200nt using focused-ultrasonicator (Covaris, #S220). 20ug of total RNA was subjected into immunoprecipitation with m6A-specific antibody (Synaptic Systems #202003). The RNA was eluted with 100uL of RLT buffer and purified using RNA Clean and Concentrator (Zymo Research, #R1015).
Recovered immunoprecipitation fragments per sample or corresponding input total RNA were subjected into SMARTer Starnded Total RNA-seq Kit v2 (Takara, #634412)

value: Brain

tag: gender

value: Major Depressive Disorder (MDD)


title: sn-RNA-seq, GBM38, tumor


title: Kuramochi_CD63_FT2_3

value: other


title: male_mdd_7_input


title: 293T_ON_CD81_B1_3


title: 293T_CD9_FT2_5


title: 293T_CD63_FT2_1


title: 293T_CD81_B2_2


title: 293T_CD81_B1_5


title: Kuramochi_CD81_FT1_3


title: 293T_Total_Input_6

value: total cell-free biofluid RNA


title: 293T_CD63_FT2_2


title: sn-RNA-seq, GBM20, tumor


title: Kuramochi_DGUC_F07


title: Kuramochi_CD81_FT1_2


title: 293T_Total_Input_5


title: Kuramochi_CD81_B2_3


title: sn-RNA-seq, GBM20, margin


title: Kuramochi_CD9_B2_3


title: sn-ATAC-seq, GBM20, margin


title: Kuramochi_CD9_B2_1


title: Kuramochi_CD63_FT2_1


title: male_mdd_8_input


title: Kuramochi_CD63_FT1_2


title: sn-ATAC-seq, GBM25, margin


title: Kuramochi_DGUC_F7_qEV_F04


title: male_mdd_5_input


title: male_mdd_6_input


title: male_ctrl_8_input

value: Control


title: Kuramochi_CD9_FT1_1


title: male_mdd_4_input


title: male_mdd_3_input


title: male_ctrl_6_input


title: male_ctrl_5_input


title: male_ctrl_4_input


title: male_mdd_2_input


title: male_ctrl_9_input


title: Kuramochi_Total_Input_2


title: Kuramochi_CD63_B2_3


title: male_ctrl_1_input


title: female_mdd_9_input


title: Kuramochi_CD81_B1_3


title: male_ctrl_7_input


title: Kuramochi_CD81_FT1_1


title: Kuramochi_DGUC_F06


title: Kuramochi_CD9_B2_2


title: Kuramochi_DGUC_F02


title: Kuramochi_CD63_B2_2


title: Kuramochi_CD63_FT1_1


title: Kuramochi_CD63_FT1_3


title: female_mdd_6_input


title: Kuramochi_DGUC_F03


title: Kuramochi_DGUC_F01


title: male_ctrl_3_input


title: Kuramochi_DGUC_F7_qEV_F05


title: male_mdd_10_input


title: male_ctrl_10_input

description: The male_ctr_10 was not included in the PeakCounts.txt because it was excluded as an outlier from the analysis.


title: female_mdd_3_input


title: Kuramochi_DGUC_F04


title: female_mdd_8_input


title: male_mdd_1_input


title: female_mdd_10_input


title: female_mdd_1_input


title: female_mdd_7_input


title: Kuramochi_DGUC_F05


title: Kuramochi_CD81_B2_2


title: Kuramochi_DGUC_F7_qEV_F03


title: female_ctrl_8_input


title: Kuramochi_DGUC_F7_qEV_F01


title: male_ctrl_2_input


title: female_ctrl_4_input


title: Kuramochi_DGUC_F7_qEV_F12


title: female_mdd_2_input


title: Kuramochi_CD9_B1_1


title: Kuramochi_DGUC_F11


title: Kuramochi_CD9_B1_3


title: female_ctrl_2_input


title: female_mdd_5_input


title: Kuramochi_CD81_B2_1


title: female_ctrl_9_input


title: Kuramochi_CD9_FT2_2


title: Kuramochi_CD63_B1_3


title: female_ctrl_5_input


title: female_ctrl_6_input


title: Kuramochi_DGUC_F7_qEV_F09


title: female_mdd_4_input


title: Kuramochi_DGUC_F12


title: male_mdd_4_m6A


title: Kuramochi_CD9_FT2_3


title: Kuramochi_CD9_B1_2


title: Kuramochi_CD63_B2_1


title: Kuramochi_DGUC_F7_qEV_F02


title: male_mdd_3_m6A


title: male_mdd_2_m6A


title: male_mdd_8_m6A


title: Kuramochi_DGUC_F7_qEV_F13


title: female_ctrl_1_input


title: Kuramochi_DGUC_F7_qEV_F11


title: Kuramochi_DGUC_F08


title: female_ctrl_3_input


title: male_mdd_1_m6A


title: male_mdd_9_m6A


title: male_mdd_7_m6A


title: Kuramochi_DGUC_F09


title: Kuramochi_CD81_B1_2


title: male_mdd_6_m6A


title: female_ctrl_7_input


title: Kuramochi_DGUC_F10


title: male_ctrl_7_m6A


title: male_ctrl_6_m6A


title: male_mdd_5_m6A


title: Kuramochi_CD63_B1_1


title: Kuramochi_CD81_B1_1


title: male_ctrl_5_m6A


title: Kuramochi_CD81_FT2_2


title: Kuramochi_CD81_FT2_1


title: male_mdd_10_m6A


title: Kuramochi_CD81_FT2_3


title: Kuramochi_DGUC_F7_qEV_F06


title: Kuramochi_DGUC_F7_qEV_F08


title: male_ctrl_8_m6A


title: Kuramochi_CD9_FT2_1


title: Kuramochi_DGUC_F7_qEV_F10


title: male_ctrl_3_m6A


title: male_ctrl_1_m6A


title: male_ctrl_10_m6A


title: male_ctrl_9_m6A


title: female_mdd_8_m6A


title: male_ctrl_4_m6A


title: Kuramochi_CD9_FT1_3


title: Kuramochi_CD63_FT2_2


title: male_ctrl_2_m6A


title: female_mdd_6_m6A


title: Kuramochi_CD63_B1_2


title: Kuramochi_IgG_B1_1


title: female_mdd_5_m6A


title: female_mdd_9_m6A


title: Kuramochi_DGUC_F7_qEV_F07


title: Kuramochi_Total_Input_3


title: Kuramochi_IgG_FT2_1


title: female_mdd_3_m6A


title: Kuramochi_IgG_B2_1


title: female_mdd_2_m6A


title: female_mdd_10_m6A


title: female_mdd_1_m6A


title: Kuramochi_IgG_FT2_2


title: female_mdd_7_m6A


title: Kuramochi_IgG_B2_3


title: Kuramochi_IgG_FT1_2


title: female_mdd_4_m6A


title: Kuramochi_IgG_B1_2


title: Kuramochi_IgG_FT2_3


title: female_ctrl_8_m6A


title: Kuramochi_IgG_FT1_3


title: female_ctrl_6_m6A


title: female_ctrl_9_m6A


title: female_ctrl_5_m6A


title: Kuramochi_IgG_B1_3


title: female_ctrl_3_m6A


title: Kuramochi_IgG_FT1_1


title: female_ctrl_7_m6A


title: BeWo_CD81_FT2_2

source_name: immobilized cell

value: Choriocarcinoma

value: Placental structure


title: BeWo_CD63_B2_1


title: Kuramochi_IgG_B2_2


title: BeWo_CD63_FT2_2


title: female_ctrl_2_m6A


title: BeWo_CD81_B2_3


title: female_ctrl_1_m6A


title: si-PCIF1_catabolicSLAM_6hPost-s4U

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 --q -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
SLAM-PILE v1.0, a T > C alignment software package based on STAR and Rsamtools to recover T > C conversions from SLAM-Seq datasets. Briefly, trimmed reads were first mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1. The counts of each of the four nucleotides in every genomic location were analyzed using Rsamtools Pileup (version 2.6.0). T > C conversions in each gene were calculated by comparing the counts of each of the four nucleotide to the sequence in hg38, and the mRNA half-life for each gene was calculated by fitting the T > C conversion rates at time 0, 3, 6 and 12h (post removal of s4U) to the equation of exponential decay with power 2.
Assembly: hg38
Supplementary files format and content: half-lives.xlsx: This file includes the half-lives of mRNA of each gene derived from fitting T > C conversion rate at different timepoint to a function of exponential decay with base 2, the r-squared of the fitting included. The HEK293T cells were either Pcif1-KO or WT. The m6Am status of each gene were also included, 'n' for non-m6Am gene and 'm' for m6Am gene. The T > C conversion rates of each gene were generated either using SLAM-PILE or SLAM-DUNK, as shown in the names of each sub-sheets.

extract_protocol:
At T=0, 3, 6, and 12hr post addition of U-containing media, the medium was removed, the cells were washed twice with cold PBS, and the cells were directly lysed with 350ul TRIzol®-LS. Cells were harvested with Trizol-LS. RNA was isolated and IAA-treatment was performed according to SLAM-seq catabolics module protocol (Lexogen 062.24). Residual genomic DNA was removed using RQ1 RNase-free DNAse (Promega M6101), purified with RNA concentrator (Zymo R1015)
RNA-seq library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina 20020596).

treatment_protocol:
Cells were seeded in 6-well plates and after 12hr, when the cells reached approximately 50% confluence, the medium was carefully removed and replaced with fresh medium containing 50uM 4SU. The cells were then incubated further in the dark at 37 degrees for 24hr, with the fresh medium containing 50uM 4SU being replaced every 3hr.
Next, the medium was carefully removed and the cells were washed twice with 1x PBS. Fresh medium containing 5M uridine (U) was then added and the cells were further incubated at 37 degrees in the dark.

tag: cell line

value: Human embryonic kidney

value: WT

value: si-PCIF1 + 24h s4U + 6h U


title: si-PCIF1_catabolicSLAM_0hPost-s4U

value: si-PCIF1 + 24h s4U + 0h U


title: BeWo_CD9_B2_2


title: BeWo_PLAP_B2_3


title: BeWo_CD9_FT2_1


title: si-PCIF1_catabolicSLAM_12hPost-s4U

value: si-PCIF1 + 24h s4U + 12h U


title: BeWo_CD9_FT2_3


title: si-PCIF1_catabolicSLAM_3hPost-s4U

value: si-PCIF1 + 24h s4U + 3h U


title: BeWo_Total_Input_1


title: BeWo_PLAP_B1_4


title: si-SCR_catabolicSLAM_12hPost-s4U

value: si-SCR + 24h s4U + 12h U


title: si-SCR_catabolicSLAM_6hPost-s4U

value: si-SCR + 24h s4U + 6h U


title: BeWo_CD81_B2_1


title: si-SCR_catabolicSLAM_3hPost-s4U

value: si-SCR + 24h s4U + 3h U


title: BeWo_PLAP_FT1_6


title: female_ctrl_4_m6A

value: female


title: si-SCR_catabolicSLAM_0hPost-s4U

value: si-SCR + 24h s4U + 0h U


title: siPcif1-ATRA BE(2)-C m6ACE-input 3

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first filtered for a quality score of 20, then trimmed of 5′ and 3′ adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC.
The 8-mer UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed.
Reads were mapped to the methylated spike-in using Bowtie2, or to the hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR. Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates.
Read-start coordinates in hg38-mapped reads that began with an adenosine nucleotide, and had a minimum mean read count of 1 across the triplicate samples were collated. m6A or m6Am sites were identified as read starts that were at least 2-fold enriched in m6ACE libraries than in the corresponding input libraries. This enrichment was calculated using DESeq2 performed on A-only sites across triplicate pairs of m6ACE and corresponding input libraries (FDR < 0.1, padj < 0.05). Identified sites that were 1–4 nucleotides upstream of another identified significant Rm6AC site or sites found within clustered read-starts were filtered out.
To calculate the relative methylation level (RML) of each site in each sample: The read-start counts at positions –4 to 0 of each site in the m6ACE library were summed and divided by the read-start counts at positions –51 to 0 of the same site in the input library to give ‘X’. Similarly, the read-start counts at positions -4 to 0 of the spike-in m6A site in the m6ACE library were summed and divided by the read-start counts at positions –21 to 0 of the same spike-in m6A site in the input library to give ‘Y’. X was normalized to Y to give RML. RML values of each site was averaged across triplicates for each sample condition.
Assembly: hg38
Supplementary files format and content: bedgraph

growth_protocol: ATCC BE(2)-C CRL-2268 cells were cultivated in a sterile 5% CO2 incubator at 37°C, and in DMEM supplemented with 10% FBS. Cells within passage 3–20 were used for experiments. Cells were regularly subjected to MycoAlert Plus Mycoplasma kit (Lonza LT07) to verify that they were mycoplasma-free.

extract_protocol:
Cells were washed twice with cold PBS and RNA extracted using Trizol LS (Ambion 10296) according to manufacturer’s protocol with an additional ethanol precipitation step.
Library was prepared using m6ACE

treatment_protocol: BE(2)-C cells were seeded into T75 flasks and transfected with siRNA against Pcif1 (Silencer Select S34301) or against scrambled control (Silencer Select 4390843) for 24hr using Lipofectamine RNAimax (Invitrogen 13778030) as per manufacturer's protocol. For differentiation by ATRA treatment, BE(2)-C cells were subsequently treated with 10µM ATRA for 4day with ATRA-containing media replaced freshly every 24hr.

value: Human neuroblastoma cell line

value: siPcif1 - ATRA


title: BeWo_CD81_B1_3

value: other


title: BeWo_CD63_B1_1


title: BeWo_CD81_B2_2


title: siPcif1-ATRA BE(2)-C m6ACE-input 1


title: siScram-ATRA BE(2)-C m6ACE-input 3

value: siScram - ATRA


title: siPcif1-ATRA BE(2)-C m6ACE-input 2


title: BeWo_PLAP_B1_1

value: Choriocarcinoma


title: BeWo_PLAP_B1_3

value: Placental structure


title: siScram-ATRA BE(2)-C m6ACE-input 2


title: BeWo_CD9_B2_3


title: siPcif1-ATRA BE(2)-C m6ACE 3


title: BeWo_CD63_FT2_3


title: siScram-ATRA BE(2)-C m6ACE-input 1


title: siPcif1-ATRA BE(2)-C m6ACE 1


title: siPcif1-ATRA BE(2)-C m6ACE 2


title: BeWo_CD9_B2_1


title: siScram-ATRA BE(2)-C m6ACE 2


title: BeWo_CD63_B1_2


title: BeWo_CD81_B1_2


title: BeWo_PLAP_B1_5


title: siScram-ATRA BE(2)-C m6ACE 1


title: BeWo_IgG_B2_3


title: BeWo_PLAP_B1_2


title: BeWo_CD9_B1_3


title: NASH11

value: liver

value: FFPE

value: NASH


title: BeWo_CD9_B1_1


title: NASH10


title: NASH9


title: BeWo_PLAP_FT1_5


title: BeWo_PLAP_B2_6


title: NASH8


title: BeWo_PLAP_FT2_4


title: NASH7


title: BeWo_Total_Input_4

value: total cell-free biofluid RNA


title: NASH4


title: NASH6


title: BeWo_Total_Input_6


title: siScram-ATRA BE(2)-C m6ACE 3

value: WT


title: NASH1


title: BeWo_PLAP_FT2_5


title: BeWo_CD81_B1_1


title: ENEG_NASH9


title: BeWo_PLAP_FT1_4


title: NASH3


title: BeWo_CD63_B2_3


title: NASH2


title: ENEG_NASH7


title: ENEG_NASH6


title: BeWo_CD9_B1_2


title: ENEG_NASH8


title: BeWo_PLAP_B1_6


title: BeWo_CD81_FT2_1


title: ENEG_NASH4


title: BeWo_CD81_FT2_3


title: ENEG_NASH5


title: ENEG_NASH3


title: BeWo_PLAP_B2_5


title: BeWo_PLAP_B2_2


title: ENEG_NASH1


title: ENEG_NASH2


title: Tumor cells,palbocilib treatment group,rep3

first: chenyu

last: liu

address: No.10, West Toujiao, Right Anmenwai, Fengtai District

institute: Capital Medical University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: LNCaP

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: LNCaP

value: palbocilib treatment


title: BeWo_IgG_B1_1


title: Tumor cells,palbocilib treatment group,rep1


title: BeWo_Total_Input_3


title: Tumor cells,palbocilib treatment group,rep2


title: BeWo_CD9_FT2_2


title: BeWo_Total_Input_5


title: BeWo_CD63_B1_3


title: BeWo_CD63_B2_2


title: Tumor cells,control group,rep2

value: control


title: Tumor cells,control group,rep3


title: BeWo_Total_Input_2


title: Tumor cells,control group,rep1


title: BeWo_CD63_FT2_1


title: BeWo_PLAP_FT2_6


title: BeWo_PLAP_B2_4


title: BeWo_IgG_B2_4


title: BeWo_IgG_FT1_2


title: P3HR1-ZHT_HT_24h_rep2

city: Ann Arbor

first: Elliott

middle: Daniel

last: SoRelle

state: MI

address: 1137 Catherine St.

department: Microbiology & Immunology

institute: The University of Michigan

description: 10x Genomics; Site: UCLA

data_processing:
Read assembly, demultiplexing, barcode processing, and counting were performed using the cellranger pipeline (v3) from 10x Genomics
Assembly: hg38 + NC007605 (EBV Type 1) or hg38 + NC009338 (EBV type 2), depending on viral strain. P3HR1 line is infected with a Type 2 EBV strain. Akata and B958 lines are infected with Type 1 EBV strains
Supplementary files format and content: Tab-separated values (tsv) and matrix (.mtx) files

growth_protocol: All cell lines grown in R10 (RPMI + 10% heat inactivated FBS)

extract_protocol:
Cells were harvested from culture at specified times after specified treatments and enriched to >90% viability by Ficoll gradient prior to single-cell library preparation
Library preparation was performed according to manufacturer's protocol -- 10x Genomics v2 3' Gene Expression Kit

treatment_protocol: Treatments in culture as described above

value: B cell

value: 25 nM 4-hydroxytamoxifen, 24h


title: P3HR1-ZHT_MeOH_24h

description: 10x Genomics; Site: UCLA

value: Methanol, 24h


title: Akata_Unstim

description: 10x Genomics; Site: Duke

source_name: Akata BL

value: Akata BL

value: Untreated


title: Akata_Ig_24h

description: 10x Genomics; Site: Duke

value: 10 ug/mL anti-human IgG, 24h


title: UW228-3 cells cultured in Neural stem cell media, replicate 3

city: Stockholm

first: Niek

last: van Bree

address: Solnavägen 9

department: Microbiology, Tumor and Cell biology (MTC)

country: Sweden

institute: Karolinska Institutet

data_processing:
Original image data file from Illumina NovaSeq 6000 is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads are filtered to obtain clean reads by removing reads containing adaptors, more than 10% uncertain nucleotides, or when low quality nucleotides (Base Quality less than 5) constitute more than 50% of the read.
RNA sequence reads were mapped against the human reference genome GRCh38/hg38 using Hisat2 v2.0.5 (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each sample
Supplementary files format and content: xls file includes RPKM values for each sample

source_name: Tumor

growth_protocol: Standard culture media was used for UW228-3 (RPMI + 10% FBS + 1% Pen/Strep) and D425 Med (DMEM/F12 + 10% FBS + 1% Pen/Strep).

extract_protocol:
Total RNA was extracted using TRIzol Reagent (ThermoFisher, 15596018) and Direct-zol RNA extraction kit (Zymo Research, R2052) according to manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers according to Novogene's workflow.

treatment_protocol: UW228-3 and D425 Med cells were gradually conditioned towards complete neural stem cell medium by increasing the concentration of this medium from 25% to 100% over a course of four passages. Neural stem cell medium for UW228-3 cells was supplemented with 1% FBS to prevent cell death. Neural stem cell medium consists of DMEM/F12 + 1% N2 supplement + 0.1% B27 supplement, 1% Pen/Strep, 10 ng/ml FGF2, 10 ng/ml EGF.

value: Tumor

value: SHH medulloblastoma

value: Neural Stem Cell Media


title: BeWo_IgG_B1_6

value: Choriocarcinoma

value: Placental structure

value: other


title: P3HR1-ZHT_HT_72h

description: 10x Genomics; Site: Duke

value: 25 nM 4-hydroxytamoxifen, 72h


title: BeWo_IgG_B1_4


title: P3HR1-ZHT_HT_48h

description: 10x Genomics; Site: Duke

value: 25 nM 4-hydroxytamoxifen, 48h


title: BeWo_IgG_B2_5


title: P3HR1-ZHT_HT_24h

description: 10x Genomics; Site: Duke


title: BeWo_IgG_B1_5


title: BeWo_IgG_B2_6


title: BeWo_IgG_FT2_4


title: P3HR1-ZHT_Unstim

description: 10x Genomics; Site: Duke


title: BeWo_IgG_FT2_6


title: BeWo_IgG_FT1_1


title: UW228-3 cells cultured in normal media, replicate 3

value: WT

value: Normal Culture Media (RPMI + 10% FBS + 1% Pen/Strep)


title: BeWo_IgG_FT1_3


title: UW228-3 cells cultured in normal media, replicate 1


title: UW228-3 cells cultured in normal media, replicate 2


title: BeWo_IgG_FT2_5


title: DiFi_CD63_FT2_1

value: Colorectal Carcinoma

value: Colon structure


title: D425 cells cultured in Neural stem cell media, replicate 3

value: Grp 3 Medulloblastoma


title: DiFi_DGUC_F11


title: D425 cells cultured in Neural stem cell media, replicate 2


title: D425 cells cultured in Neural stem cell media, replicate 1


title: D425 cells cultured in normal media, replicate 3

value: Normal Culture Media (DMEM/F12 + 10% FBS + 1% Pen/Strep)


title: D425 cells cultured in normal media, replicate 2


title: PBMCs, P7prog

city: Cleveland

first: Lily

last: Wang

state: OH

address: 9500 Euclid Ave

institute: Cleveland Clinic

description: 10x Genomics

data_processing:
Cellranger Version 5.0.0 was used for alignment and gene counting
Assembly: GRCh38-2020-A
Supplementary files format and content: Seurat Object containing all samples post filtering with metadata

extract_protocol:
10X genomics
10X 5 prime

value: PBMC

tag: disease state

value: metastatic Triple negative breast cancer

value: Immune

tag: patient number

value: anti-PD-1/PD-L1 therapy and chemotherapy

value: prog


title: PBMCs, P7base

description: 10x Genomics

value: base


title: D425 cells cultured in normal media, replicate 1

value: Tumor


title: UW228-3 cells cultured in Neural stem cell media, replicate 1

value: SHH medulloblastoma

value: Neural Stem Cell Media


title: UW228-3 cells cultured in Neural stem cell media, replicate 2


title: DiFi_DGUC_F08

value: other


title: DiFi_CD9_FT1_1


title: PBMCs, P5prog

description: 10x Genomics


title: DiFi_DGUC_F7_qEV_F09


title: DiFi_DGUC_F10


title: PBMCs, P5base

description: 10x Genomics


title: DiFi_DGUC_F12


title: DiFi_CD9_B1_2


title: DiFi_CD81_B1_3


title: PBMCs, P22base

description: 10x Genomics


title: DiFi_CD9_FT1_2


title: DiFi_DGUC_F7_qEV_F06


title: DiFi_DGUC_F7_qEV_F08


title: PBMCs, P22res

description: 10x Genomics

value: res


title: PBMCs, P14res

description: 10x Genomics


title: PBMCs, P1base

description: 10x Genomics


title: PBMCs, P1prog

description: 10x Genomics


title: DiFi_Total_Input_5

value: total cell-free biofluid RNA


title: PBMCs, P14base

description: 10x Genomics


title: DiFi_CD81_B1_2


title: DiFi_CD81_FT1_3


title: DiFi_CD63_FT2_2


title: DiFi_CD9_FT2_2


title: DiFi_CD63_B1_1


title: DiFi_CD63_B1_3


title: DiFi_CD63_FT1_2


title: PBMCs, P0base

description: 10x Genomics


title: SKOV3_KO_1

city: Busan

first: EUNJI

last: KO

address: Busan

institute: Kosin University College of Medicine

description: HERV-K119 KO cells

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to GRCh38 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: ovary

growth_protocol: Cultured in RPMI 1640 (Thermo Fisher Scientific, Rockford, IL, USA) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA), 1% penicillin, and L-glutamine (Thermo Fisher Scientific). These cell lines were maintained at 37°C in a humidified environment containing 5% CO2 with 90% humidity.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Approximately 18 h after transfection, the cells were treated with 100 μg/mL hygromycin for 2 days.

value: ovary

value: epithelial

value: HERV-K119 KO

value: Hygromycin


title: OVCAR3_KO_1

description: HERV-K119 KO cells


title: OVCAR3_MOCK_1

description: Control

value: Control


title: DiFi_Total_Input_4

value: Colorectal Carcinoma

value: Colon structure


title: DiFi_CD81_FT1_1


title: SKOV3_MOCK_1

description: Control


title: DiFi_CD63_FT1_1


title: SMARCB1_DMSO_rep2_RNA

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

address: 269 Campus Drive

institute: Stanford University

data_processing:
Aligned to hg38 genome with STAR aligner
Reads counted with HTseq
Assembly: hg38
Supplementary files format and content: tab-delimitated text file that contains raw counts for each file

growth_protocol: G401 rhabdoid kidney tumor cells were cultured in McCoy5a's medium (Sigma-Aldrich cat# 8403) supplemented with 10% FBS serum (Biowest S162TA) + 1% Pen/Strep + 1% glutamax (thermo scientific 35050061)

extract_protocol:
RNA was harvested using Ribolace kit (Immagina). 1.5ug of RNA was used to construct library
Library was prepared using Laceseq kit (Immagina) following manufactor's protocol

treatment_protocol: After 24hrs of seeding and reached 80% confluency, G401 SMARCB1-inducible or GFP-inducible cells were treated with 0.1ug/mL doxycycline or equivalent DMSO for 12hrs. Treated cells were harvested for experiment.


title: DiFi_CD63_FT1_3


title: GFP_Dox_rep2_RNA


title: SMARCB1_Dox_rep2_RNA


title: GFP_DMSO_rep1_RNA


title: DiFi_Total_Input_3


title: SMARCB1_DMSO_rep1_RNA


title: GFP_Dox_rep1_RNA


title: PBMCs, P0res

description: 10x Genomics

value: PBMC

value: metastatic Triple negative breast cancer

value: Immune


title: DiFi_DGUC_F09


title: DiFi_DGUC_F05


title: DiFi_CD9_B2_1


title: SMARCB1_Dox_rep2_Ribo

description: RNA associated with active ribosome


title: DiFi_CD63_FT2_3


title: SMARCB1_DMSO_rep2_Ribo

description: RNA associated with active ribosome


title: DiFi_CD9_B1_1


title: GFP_DMSO_rep2_RNA


title: DiFi_DGUC_F7_qEV_F05


title: GFP_DMSO_rep2_Ribo

description: RNA associated with active ribosome


title: DiFi_DGUC_F7_qEV_F03


title: DiFi_DGUC_F07


title: SMARCB1_DMSO_rep1_Ribo

description: RNA associated with active ribosome


title: DiFi_DGUC_F7_qEV_F07


title: DiFi_CD9_B2_2


title: DiFi_CD81_B1_1


title: GFP_DMSO_rep1_Ribo

description: RNA associated with active ribosome


title: GFP_Dox_rep1_Ribo

description: RNA associated with active ribosome


title: DiFi_CD9_FT2_1


title: SMARCB1_Dox_rep1_RNA


title: IB region of MuV-infected A549 cells

city: Bunkyo-ku

first: Hiroshi

last: Katoh

state: Tokyo

country: Japan

institute: The University of Tokyo

data_processing:
The barcodes and unique-molecular-identifiers in the reads were extracted using UMI-tools (version 1.0.0) with the command: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were mapped by the aligning software HISAT2 (version 2.1.0) to the reference genome (GRCm38).
Read counts per gene was performed with featureCounts (version 1.6.4) and UMI-tools with the command: umi_tools count --method=directional --per-gene --per-cell --gene-tag=XT.
The duplicates in unique molecular identifiers were discarded.
Using the resulting counts, differentially expressed genes (those with adjusted p-values < 0.1) were extracted by the R library DESeq2 (version 1.20.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: cytoplasmic RNA

extract_protocol:
Lysis solution(0.1% Tween and 400 ug/ml of ProteinaseK in PBS) were loaded onto the specimens and incubated for 30 min at 55℃. cDNA;mRNA hybrids were purified with a Qiagen MinElute PCR Purification kit.
Library was constructed according to the CEL-seq2 method as follows: polyA RNAs were converted in situ to cDNAs using a polyT primer with a 5'-tail containing T7 promoter, 5' Illumina sequence adaptor, UMI and cell barcode sequences. The cDNAs were extracted and second strand DNAs were synthesized by nick translation method. The cDNAs were linearly amplified as RNAs (aRNAs) by IVT reaction, followed by reverse transcription using random primer with a 5'-tail containing 3' Illumina sequence adaptor.
Spatial transcriptome analysis using PIC (photo isolation chemistry).  PIC is a bulk RNA-seq technique to prepare cDNA libraries from specific regions (not cells) in tissue sections.

value: Human cell line derived from lung cancer

value: MuV infection


title: DiFi_CD63_B1_2


title: DiFi_Total_Input_1


title: DiFi_CD9_B2_3