title: Ctlab-16wk-Tdtneg2

description: 10x Genomics

value: ApoE-/-, Myh11-Cre, Rosa-TdTomato

value: 16 wks High Fat Diet, Antibodies


title: PDGFD-KO-16wk-Tdt1

status: Public on Feb 03 2023

type: SRA

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

country: USA

institute: Stanford University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Fastq files from each experimental group and mouse genotype were aligned to the reference genome (mm10) individually using CellRanger Software. Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization. The aggregated dataset was then analyzed using the R package Seurat v4.1.1.
Assembly: Mouse genotype were aligned to the reference genome (mm10) individually using CellRanger Software (10x Genomics). Individual datasets were aggregated using the CellRanger aggr command without subsampling normalization.
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: total RNA

organism: Mus musculus

source_name: Aorta

extract_protocol:
The aortic root and ascending aorta were excised and washed three times in PBS. Collected tissues were placed into an enzymatic dissociation cocktail in Hank’s Balanced Salt Solution (HBSS)) and minced. After incubation at 37 °C for 1 h, the cell suspension was strained, pelleted by centrifugation.
Cells were loaded into a 10X Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10X Genomics Chromium controller according to the manufacturer’s instructions. Single-cell libraries were then constructed according to the manufacturer’s instructions.
Libraries from individual samples were multiplexed into one lane prior to sequencing on an Illumina platform with targeted depth of 50,000 reads per cell.

tag: tissue

value: Aorta

tag: cell type

value: smooth muscle cells

tag: genotype

value: Pdgfd lacZ/lacZ, ApoE-/-, Myh11-Cre, Rosa-TdTomato

tag: treatment

value: 16 wks High Fat Diet


title: Ctlab-16wk-Tdt2

description: 10x Genomics


title: F121A, male #1

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: transcriptomic

data_processing:
Sequencing data was trimmed, aligned and normalized (reads per million mapped reads) using default settings via Partek bioinformatics software.
Supplementary files format and content: Xlsx file includes RPKM values for each Sample

source_name: Colon

growth_protocol: Mouse grown under SPF conditions

extract_protocol:
RNA from frozen colonic tissues was extracted using Qiagen RNeasy Universal kit. Integrity of the isolated RNA was analysed using the Agilent TS HS RNA Kit and TapeStation 4200
1000ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L). RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L). Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: No treatment

value: Colon

value: Whole tissue

value: Naive


title: HFHS_IntraEpi_1

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
4samples_barcodes.tsv.gz
4samples_features.tsv.gz
4samples_matrix.mtx.gz

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix files

source_name: small intestine

extract_protocol:
Mice were euthanized using isoflurane (VETONE) and secondary cervical dislocation. The intestines were maintained in a moistened state, and the Peyer’s patches and the remaining mesentery/fat were excised. The small intestine from ileum to jejunum was collected and gently flushed with a syringe with ice cold 1 × Hanks' Balanced Salt Solution (HBSS) media (without Ca2+ and Mg2+) (SIGMA, Cat# H4641) to remove the feces. The intestine was cut open and dissected into 1 cm segments, which were then transferred into a 50 mL tube and gently shaken to let the tissue stretch. They were then washed twice with ice cold 1 × HBSS and the extra HBSS removed using a pipet. 20 ml pre-digestion solution (1 × HBSS with 5% FBS, 5 mM EDTA and 1 mM DTT) was added and incubated for 20 min at 37 °C with 250 rpm rotation in an incubator. The 1 × HBSS containing the epithelial cell layer was collected on ice after vortex and passed through a 100 μm cell strainer. For intraepithelial immune cell isolation, the 1 × HBSS containing the epithelial cell layer was centrifuged at 2000 rpm for 5 mins. The cell pellet was resuspended in 20 ml 40% percoll (Sigma-Aldrich, Cat# P4937) and 20 ml 70% percoll added to the bottom of each tube, spun at 2000 rpm for 20 mins (accelerate at 6 and brake at 2) at room temperature. The middle layer of cells was collected, washed, spun down with 1 × PBS, and resuspended in RPMI 1640 culture media (Corning Cellgro, Cat# 10-040-CV) (supplemented with 10% FBS (Corning, Cat# MT35015CV), 1% Penicillin-Streptomycin-Glutamine (Gibco, Cat# 10378016), 1% MEM Non-Essential Amino Acids Solution (Gibco, Cat# 11140050), 1% HEPES (Gibco, Cat# 15630056), and 1% Sodium Pyruvate (Gibco, Cat# 11360070)) for further FACS or flow cytometry analysis. For intraepithelial immune cell scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live hematopoietic cells (gated as DAPI-CD45.2+ cells). For IEC isolation, the epithelial cell layer in the 1 × HBSS was spun at 2000 rpm for 5 mins. The cell pellet was resuspended in RPMI 1640 culture media for further FACS. For epithelial structural cell scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live non- hematopoietic cells (gated as DAPI-CD45.2- cells). For lamina propria immune cell isolation, the epithelial cell layer was removed and the remaining intestine tissues washed twice with RPMI 1640 culture media. The extra media was removed and 10 ml RPMI 1640 culture media with 1mg/ml Collagenase type I (Thermo Fisher Scientific, Cat# 17100017) was added. The sample was incubated for 20 min at 37 °C with 250 rpm rotation and vigorously vortexed to allow the tissue to fully dissolve before passing through 100 μm cell strainer. Media containing the lamina propria cells was centrifuged at 2000 rpm for 5 mins and the cell pellet resuspended in 20 ml 40% percoll. 20 ml 70% percoll was added to the bottom of each tube and spun at 2000 rpm for 20 mins (accelerate at 6 and brake at 2) at room temperature. The middle layer of cells was collected, washed, spun down with 1 × PBS, and resuspended in RPMI 1640 culture media for further FACS or flow cytometry analysis. For lamina propria immune cell scRNA-seq, single cell suspensions were sorted using a FACSAria III flow cytometer to purify live hematopoietic cells (gated as DAPI-CD45.2+ cells).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Intraepithelial immune cells

value: small intestine

tag: strain

tag: age

value: 16 weeks


title: CEA, Sample 8

city: Ashburn

first: Yuhan

last: Wang

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
The libraries were pooled and sequenced on an Illumina NextSeq 550 with 26 bases for read 1 and 50 bases for read 2. Samples were demultiplexed using bcl2fastq v2.20 software from Illumina with default settings.
Sequencing adapters were trimmed from the reads with Cutadapt v2.1.0 (Martin, 2011) prior to alignment with STAR v2.7.5c (Dobin et al., 2013) to the Mus musculus GRCm38.90 genome assembly from Ensembl (ensembl.org).
STAR alignment was performed with the following additional parameters: "--alignSJoverhangMin 8 --alignSJDBoverhangMin 8 --alignIntronMin 20 --alignIntronMax 150000 --outSAMmultNmax 20 --outSAMattributes NH HI NM MD CR CY UR UY --quantMode TranscriptomeSAM GeneCounts"
Gene counts were generated with the STARsolo v2.7.5c algorithm (github.com/alexdobin/STAR/) using the following additional parameters: “--soloType CB_UMI_Simple --soloCBwhitelist smartscrb_whitelist.txt --soloCBstart 2 --soloCBlen 8 --soloUMIstart 10 --soloUMIlen 10 -soloBarcodeReadLength 0 --soloCBmatchWLtype 1MM_multi_pseudocounts --soloStrand Forward --soloFeatures Gene --soloUMIdedup 1MM_Directional --soloUMIfiltering MultiGeneUMI --soloCellFilter None”.
Assembly: GRCm38.90

source_name: brain

growth_protocol: All methods for animal care and use were conducted according to National Institutes of Health guidelines for animal research and approved by the Institutional Animal Care and Use Committee (IACUC) at Janelia Research Campus.

extract_protocol:
Cells were hand-picked into PCR strip tubes containing 3 μl lysis buffer (0.2% TritonX-100 (Sigma) and 0.1 U/μl RNase inhibitor (Lucigen)) and cDNA libraries were prepared using the Smart-SCRB chemistry as described previously (Cembrowski et al., 2018; Xu et al., 2020).
600 pg cDNA from each pooled sample was used in a modified Nextera XT library preparation (Illumina) (Soumillon et al., 2014) using the P5NEXTPT5 primer and extending the tagmentation time to 15 min. The resulting libraries were purified according to the Nextera XT protocol (0.6x beads ratio) and quantified by qPCR using Kapa Library Quantification (Kapa Biosystems).

treatment_protocol: The manual single-cell sorting procedure to isolate non-fluorescent cell bodies from micro-dissected brain slices was similar to a previously described protocol (Hempel et al., 2007). Briefly, mice were deeply anesthetized with isoflurane and decapitated to collect 300 µm coronal brain slices. The CEA was manually dissected with spring scissors using the GFP signal as guidance. Two to three tissue sections from each animal were taken to cover the entire CEA and subjected to protease digestion, after which cells were dissociated. Intact neurons were manually selected into individual wells. Neurons collected from seven animals were pooled for sequencing.

value: neurons

value: 6 to 8 weeks

value: central amygdala (CEA)

tag: plate


title: CEA, Sample 7


title: CEA, Sample 6


title: CtlCT-16wk-Tdt2

description: 10x Genomics


title: CEA, Sample 18


title: CtlCT-16wk-Tdtneg1

description: 10x Genomics


title: CtlCT-16wk-Tdtneg2

description: 10x Genomics


title: CtlCT-16wk-Tdt1

description: 10x Genomics


title: Ctlab-8wk-Tdtneg2

description: 10x Genomics

value: 8 wks High Fat Diet, Antibodies


title: PDGFD-KO-16wk-Tdtneg3

description: 10x Genomics


title: CEA, Sample 5


title: CEA, Sample 4


title: Ctlab-8wk-Tdtneg1

description: 10x Genomics


title: Ctlab-8wk-Tdt2

description: 10x Genomics


title: CEA, Sample 2


title: rsc18

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
Trim input file and remove adapters.
Tag reads with cell barcode and UMI
Align reads to PhiX, then to mouse.
Aggregate reads and de-duplicate UMIs.
Post-processing in R with custom scripts and Seurat.
Assembly: NCBIM37
Supplementary files format and content: Tab delimited file containing count values.

source_name: Retrosplenial cortex

extract_protocol:
Microdissect, dissociate, and pool cells across acute brain slices in B6 mice.
As in (Erwin*, Bristow*, … , Cembrowski; eLife 2021)

value: Retrosplenial cortex

value: WT mouse

value: neuron


title: CEA, Sample 3


title: Ctlab-8wk-Tdt1

description: 10x Genomics

value: Aorta

value: ApoE-/-, Myh11-Cre, Rosa-TdTomato


title: CEA, Sample 1


title: PDGFab-8wk-Tdtneg2

description: 10x Genomics

value: smooth muscle cells


title: PDGFab-8wk-Tdt2

description: 10x Genomics


title: PDGFab-8wk-Tdt1

description: 10x Genomics


title: PDGFab-8wk-Tdtneg1

description: 10x Genomics


title: rsc16


title: CEA, Sample 9


title: rsc15


title: Ctlab-16wk-Tdtneg1

description: 10x Genomics

value: 16 wks High Fat Diet, Antibodies


title: Ctlab-16wk-Tdt1

description: 10x Genomics


title: rsc13


title: PDGFab-16wk-Tdtneg2

description: 10x Genomics


title: PDGFab-16wk-Tdt2

description: 10x Genomics


title: PDGFab-16wk-Tdtneg1

description: 10x Genomics


title: rsc12


title: PDGFab-16wk-Tdt1

description: 10x Genomics


title: rsc2


title: N2 + vha-6 RNAi + elt-2 RNAi, rep 3 [exp2]

city: Lausanne

first: Terytty Yang

last: Li

address: EPFL SV IBI-SV LISP AI 1145

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa --sjdbGTFfile Caenorhabditis_elegans.WBcel235.89.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

organism: Caenorhabditis elegans

source_name: N2 + vha-6 RNAi + elt-2 RNAi, rep 3

growth_protocol: Synchronized worm eggs were obtained by alkaline hypochlorite treatment of gravid worms grown on E. coli OP50-seeded plates, which were transferred onto RNAi plates and cultured at for 2.5 days at 20°C to allow developing to L4/young adult phase.

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment

treatment_protocol: RNAi treatment was started from L1 and worms were collected after reaching L4/young adult stage in 2.5 days

value: WT

tag: RNAi treatment

value: vha-6 RNAi 25percent + elt-2 RNAi 40percent + control RNAi 35percent


title: rsc17


title: N2 + elt-2 RNAi, rep 3 [exp2]

source_name: N2 + elt-2 RNAi, rep 3

value: elt-2 RNAi 40percent + control RNAi 60percent


title: Cisplatin with NR 1

city: philadelphia

first: tomohito

last: doke

state: Pennsylvania

address: smilow, 3400 Civic Center Blvd STRC 12-188

department: Medicine

institute: University of Pennsylvania

data_processing:
Adaptor and low-quality reads were trimmed using Trim-galore
Reads were aligned to the mouse (GRCm38) reference genome using STAR (v2.4.1d)
The aligned reads were mapped to the genes using HTSeq-0.6.1
Differentially expressed genes between experimental groups were identified using DESeq2 version 1.10.1.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: whole kidney

extract_protocol:
Total RNA was isolated from the kidneys of mice and human using the RNeasy mini kit
Sequencing libraries were constructed using the Illumina TruSeq RNA Preparation Kit.

treatment_protocol: NAD precursors (NMN and NR) were injected before cisplatin injection. Kidneys were collected 3 days after cisplatin injection.

value: whole kidney

value: Cisplatin with NR


title: Cisplatin with NR 4


title: Cisplatin with NR 3


title: N2 + elt-2 RNAi, rep 2 [exp2]

source_name: N2 + elt-2 RNAi, rep 2


title: N2 + elt-2 RNAi, rep 1 [exp2]

source_name: N2 + elt-2 RNAi, rep 1


title: Cisplatin with NMN 1

value: Cisplatin with NMN


title: Cisplatin4

value: Cisplatin


title: rsc11


title: Cisplatin with NMN 4


title: rsc14


title: N2 + vha-6 RNAi, rep 2 [exp2]

source_name: N2 + vha-6 RNAi, rep 2

value: vha-6 RNAi 25percent + control RNAi 75percent


title: Cisplatin with NMN 3


title: N2 + vha-6 RNAi, rep 3 [exp2]

source_name: N2 + vha-6 RNAi, rep 3


title: Cisplatin3


title: Cisplatin with NMN 2


title: rsc3


title: Cisplatin1


title: N2 + control RNAi, rep 2 [exp2]

source_name: N2 + control RNAi, rep 2

value: Control RNAi


title: rsc1


title: N2 + control RNAi, rep 3 [exp2]

source_name: N2 + control RNAi, rep 3


title: Cisplatin2


title: N2 + vha-6 RNAi, rep 1 [exp2]

source_name: N2 + vha-6 RNAi, rep 1


title: N2 + vha-6 RNAi + elt-2 RNAi, rep 2 [exp2]

source_name: N2 + vha-6 RNAi + elt-2 RNAi, rep 2


title: PBS4

value: PBS


title: N2 + vha-19 RNAi, rep 3

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa --sjdbGTFfile Caenorhabditis_elegans.WBcel235.89.gtf --sjdbOverhang 49
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

value: vha-19 RNAi 25percent + control RNAi 75percent


title: PBS3


title: PBS2


title: PBS1


title: N2 + vha-19 RNAi, rep 1


title: N2 + vha-16 RNAi, rep 2

value: vha-16 RNAi 25percent + control RNAi 75percent


title: N2 + vha-16 RNAi, rep 3


title: N2 + vha-19 RNAi, rep 2


title: N2 + vha-16 RNAi, rep 1


title: N2 + vha-6 RNAi, rep 3


title: N2 + vha-6 RNAi, rep 2


title: N2 + vha-6 RNAi, rep 1


title: Epidermal cells - nonexpanded_ batch2

city: baltimore

first: Yingchao

last: Xue

state: MD

address: 1500 orleans st, room 216

institute: johns hopkins university

data_processing:
The Cell Ranger software pipeline (v4.0.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the mouse reference genome (refdata-gex-mm10-2020-A) customized to include the transgene used in the experiment (command cellranger count).  As the output, we obtained the feature-barcode matrix that contains gene expression counts for each cell barcode.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Epidermis

extract_protocol:
Skin samples were incubated in 0.4% Dispase II solution in 4 °C overnight. Epidermal sheetswere separated from the dermis manually on the next day and digested in 0.25% trypsin/EDTA toobtain single cells(51). Isolated cells were then stained with PI/DCV for flow cytometry sortingfor single live cells in the flow cytometry core at the Johns Hopkins School of Public Health. PI-/DCV+ single live cells were selected and submitted to JHMI Deep Sequencing & MicroarrayCore for single-cell sequencing.
scRNA libraries were prepared for sequencing using standard Illumina protocols
scRNA seq

value: epidermis

value: 8 weeks

value: Lgr6-EGFP-Ires-CreERT2 crossed with R26-tdTomato reporter mice

value: expanded


title: N2 + control RNAi, rep 3


title: Epidermal cells - nonexpanded_ batch1


title: Epidermal cells - expanded_ batch2


title: N2 + control RNAi, rep 2


title: N2 + control RNAi, rep 1


title: N2 + control RNAi, rep 1 [exp2]

source_name: N2 + control RNAi, rep 1


title: pAC-dsRed rep2

city: Waltham

first: Katharine

last: Abruzzi

state: MA

address: 415 South St.

department: Biology

institute: HHMI; Brandeis University

description:
CR_SEQ_27
control sample used as background to call editing sites

data_processing:
Trim reads:cutadapt -q 20 --trim-n --minimum-length=10 -o $file1 -p $file2 $infile1 $infile2
Align via STAR : STAR  --runThreadN 8 --outFilterMismatchNoverLmax 0.06 --outFileNamePrefix $prefix"_" --outFilterMatchNmin 15 --outFilterMultimapNmax 1  --genomeDir $star_indices --outSJfilterReads Unique --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --alignMatesGapMax 25000 --readFilesIn $file1 $file2
remove PCR duplicates:java -Xmx4g -jar $PICARD_JAR MarkDuplicates --INPUT $input_for_picard --OUTPUT $dupremove_bam --METRICS_FILE dup.txt --VALIDATION_STRINGENCY LENIENT --REMOVE_DUPLICATES true --TMP_DIR tmp --ASSUME_SORTED true
generate raw read counts:python -m HTSeq.scripts.count -q -r pos -f bam $sort_out --stranded=no --minaqual=10 $gtf_file > $prefix"_unique_raw.txt"
generate transcript counts:stringtie -A $prefix"_gene_abundance.txt" -o $assembled_transcript -p 6 -e -G $gtf_file $sort_out
Assembly: dm6
Supplementary files format and content: Bedgraph file listing all potential editing sites

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

extract_protocol:
400 GFP-positive cells were isolated by FACS sorting and lysed in 100µl of Lysis buffer
Libaries were constructed using Smart-seq2 protocol

tag: cell line

value: Drosophila S2 cells

value: pAC-dsRed


title: pMT-Hrp48-ADAR rep1


title: pMT-Hrp48-ADAR rep2


title: pAC_dsRed rep1

description:
CR_SEQ_26
control sample used as background to call editing sites


title: TE glucose and insulin 3

city: Jouy-en-josas

first: Sophie

last: Calderari

address: Allée de Vilvert

country: France

institute: INRAE UMR1198 BREED

data_processing:
raw data were obtain from an Illumina NextSeq NB552053 after demultiplexing performed with bcl2fastq2 v2.2.18.12 and adaptor trimming with Cutadapt 1.15
after deleting poor quality base (under 30) at the end of the sequence, reads longer than 35 bp were kept
reads were mapped using the splice junction mapper TopHat (v2.1.1) with parameters -N 2 --read-edit-dist 2 --b2-sensitive --no-coverage-search
the gene count table was performed with featureCounts (v1.6.0) with parameters -p -B -C
Data normalization and single-gene level analysis of the differential expression were performed using the DESeq2 package
Assembly: Ensembl 98 Oryctolagus cuniculus 2.0
Supplementary files format and content: tab-delimited text files include normalized expression values for each Sample

organism: Oryctolagus cuniculus

source_name: trophectoderm

growth_protocol: In vitro development in Global medium supplemented with 10% of human sera albumin and supplemented with Insulin:1.7 μM and/or Glucose 15mM in humidified atmosphere with 5% O2 and CO2 at 38°C.

extract_protocol:
RNA was harvested using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). 750pg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-seq V4 ultra low input RNA kit

value: trophectoderm

value: Glucose and inuslin


title: TE glucose and insulin 1


title: TE insulin 3

value: Insulin


title: Epidermal cells - expanded_ batch1


title: TE glucose and insulin 2


title: TE insulin 2


title: pMT-Hrp48-APOBEC rep2


title: TE insulin 1


title: TE glucose 3

value: Glucose


title: pMT-Hrp48-APOBEC rep1


title: pMT-ADAR rep2

value: pMT-ADAR


title: pMT-Thor-ADAR rep2

value: pMT-Thor-ADAR


title: TE glucose 2


title: TE glucose 1


title: pMT-ADAR rep1


title: pMT-Thor-ADAR rep1


title: TE control 3

value: Control


title: pMT-APOBEC rep2

value: pMT-APOBEC


title: pMT-APOBEC rep1


title: ICM glucose and insulin 3

source_name: Inner cell mass

value: Inner cell mass


title: pMT-Thor-APOBEC rep1

value: pMT-Thor-APOBEC


title: pMT-Thor-APOBEC rep2


title: TE control 2


title: TE control 1


title: ICM insulin 3


title: CHB 3_(miRNA-4_0)

type: RNA

city: Chengdu

first: Chengxia

last: Xie

address: Wangjiang Campus, Sichuan University, Wuhou District

country: China

institute: Sichuan University

description: PBMCs at 3, CHB group

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The raw data for the microarray was uploaded to Gminix-Cloud Biotechnology Information (GCBI; http://www.gcbi.com.cn/gclib/html/index) for further study, and then analyzed the data using Robust Multichip Analysis algorithm.

label: biotin

organism: Homo sapiens

source_name: PBMCs from the CHB patient

label_protocol: Affymetrix Human Transcriptome Array 2.0 was used for differentially expressed lncRNAs and mRNAs detection, while Affymetrix miRNA 4.0 was used for miRNAs detection.

growth_protocol: The peripheral blood mononuclear cells (PBMCs) were obtained from three patients with SC HBV and three patients with CHB.

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: The peripheral blood mononuclear cells (PBMCs) were separated from patients blood, and collected for further total RNA extraction.

value: PBMCs

tag: disease state

value: CHB


title: SC HBV 2_(miRNA-4_0)

description: PBMCs at 2, SC HBV group

source_name: PBMCs from the SC HBV patient

value: SC HBV


title: ICM insulin 2


title: SC HBV 3_(miRNA-4_0)

description: PBMCs at 3, SC HBV group


title: ICM insulin 1


title: ICM glucose and insulin 1


title: SC HBV 1_(miRNA-4_0)

description: PBMCs at 1, SC HBV group


title: ICM glucose 3


title: CHB 1_(miRNA-4_0)

description: PBMCs at 1, CHB group


title: ICM glucose 2


title: ICM control 3


title: ICM glucose 1


title: HiC Teff rep2

city: washington dc

first: Shaoqi

last: Zhu

state: WASHINGTON

address: 725 21st st nw

institute: the george washington university

library_source: genomic

data_processing:
Hi-C libraries were mapped to mouse genome using distiller-nf (https://github.com/open2c/distiller-nf). UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Default parameters in distiller-nf was used to get paired reads on the same chromosome with mapq>=10. Cool files with 10kb rosolution were generated.
Cool files were converted into text files using cooler (https://github.com/open2c/cooler) and then to hic files using Juicer (https://github.com/aidenlab/juicer) pre function.
Assembly: mm9

molecule: genomic DNA

source_name: P14 effector CD8 T cells

extract_protocol:
Naive P14 TCR transgenic CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 8 post infection, KLRG1+IL-7Ra- P14 cells were sort purified as effector CD8 T cells, which were then crosslinked, digested with MboI restriction enzyme and underwent proximity ligation.
The biotinylated DNA segments were captured, and ligated to the Illumina Paired End Adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-4000 platform.

value: wild type

value: splenocytes

tag: cell phenotype

value: TCRbeta+ CD8+ CD45.2+ KLRG1+ IL-7Ra–


title: IgG Cut&Run, CTCFKO Day4

data_processing:
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Trim Galore (v0.6.7) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low quality sequences and remove adapters.
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Samtools (Li et al., 2009) was used to transfer sam files to bam files and sort bam files. Picard MarkDuplicates (v2.21.6) (https://github.com/broadinstitute/picard) was used to remove duplicate reads in the bam files.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling. We used the criteria of a q value of < 0.05, 2 fold change at peak summit as identified binding sites.
Assembly: mm9
Library strategy: Cut&Run

source_name: P14 early effector CD8 T cells

extract_protocol:
Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Ctcf wild-type or floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 post infection, P14 cells were sort purified and used for Tcf1 CUT&RUN analysis in formaldehyde-fixed cells along with naive CD8T cells as positive control.
The DNA segments from Tcf1 Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: CTCF KO

value: GFP+ TCRbeta+ CD8+ CD45.2+


title: Tcf1 Cut&Run, WT naive, rep2

source_name: naïve CD8 T cells

value: GFP+ TCRbeta+ CD62Lhi CD44lo-med CD8+


title: mouse feces_16S

data_processing:
Purified products were sequenced using the Illumina MiSeq platform . FASTQ data was processed and analyzed using Quantitative Insights into Microbial Ecology 2 (QIIME2) version 2019.4 32. Single-end sequences were demultiplexed, and reads were denoised and clustered using Divisive Amplicon Denoising Algorithm (DADA2) 31. Primers were trimmed off and single end reads were truncated to ≥150 base pairs. A phylogenetic tree was constructed and features were assigned taxonomy using Greengenes reference database with 99% confidence 31.
Analysis was performed on a rarefied feature table of 7340 reads per sample after filtration of mitochondria and chloroplast sequences.
Supplementary files format and content: Xlsx file includes OTUs, taxonomy and reads per sample.
Library strategy: 16S DNA-seq

organism: mouse gut metagenome

source_name: Feces

extract_protocol:
DNA was extracted from fecal samples using the Invitrogen Purelink™ Microbiome DNA Purification Kit according to the manufacturer’s instructions, following two minutes of bead beating (Bio Spec). Following DNA extraction, the V4 variable region of the bacterial 16S rRNA gene was amplified by polymerase chain reaction (PCR) using the 515F and 806R primers, and each sample received a unique 515F barcoded primer. Primer sequences used were: 515F- (barcode) 5′-AATGATACGGCGACCACCGAGATCTACACGCTAGCCTTCGTCGCTATGGTAATTGTG TGYCAGCMGCCGCGGTAA-3′ and 806 R 5′- CAAGCAGAAGACGGCATACGAGATAGTCAGTCAGCCGGACTACHVGGGTWTCTAAT -3′ 31.
PCR reactions were carried out with the Primestar taq polymerase (Takara) for 30 cycles of denaturation (95 °C), annealing (55 °C) and extension (72 °C), and a final elongation at 72 °C. Amplicons were purified using AMPure magnetic beads (Beckman Coulter), and subsequently quantified using Picogreen dsDNA quantitation kit (Invitrogen). Samples were pooled at equal concentrations (50 ng/µl), loaded on 2% E-Gel (Thermo Fisher), and purified using NucleoSpin Gel and PCR Clean-up (Macherey-Nagel).

value: Feces

value: multiplexed sample:F121A and WT


title: Spatial Transcriptomics Sample 2

data_processing:
scRNA-seq1: Trim input file and remove adapters
scRNA-seq2: Tag reads with cell(scRNA-seq)
scRNA-seq3: Align reads to PhiX, then to mouse
scRNA-seq4: Aggregate reads and de-duplicate UMIs
scRNA-seq5: Post-processing in R with custom scripts and Seurat
ST1: spaceranger mkfastq pipeline demultiplexes base call files and produces fastq files
ST2: spaceranger counts pipeline spatially aligns fastq files
ST3: Post-processing in R with custom scripts and Seurat
Assembly: scRNA-seq: NCBIM37; spatial transcriptomics: mm10
Supplementary files format and content: Tab delimited file containing count values.
Library strategy: spatial transcriptomics

source_name: Brain

extract_protocol:
scRNA-seq: Microdissect, dissociate, and pool cells across acute brain slices in B6 mice; spatial transcriptomics (ST): flash frozen brains, cryosectioning 10um and place on 10xgenomics visium slides, tissue staining for NeuN and DAPI, permeabilization and library construction following manufacturer's protocol
scRNA-seq: As in (Erwin*, Bristow*, … , Cembrowski; eLife 2021); ST: as described by 10x genomics for Visium workflow

value: WT


title: TKO_3

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: cvs with raw counts

source_name: Aortic lesion

extract_protocol:
Trizol (Invitrogen) was used for RNA isolation
PolyA selection

treatment_protocol: 8 weeks old CD4-specific KLF10 knockout mice (TKO) and WT male mice were intraperitoneally injected once with the AAV-PCSK9D377Y gain-of-function transgene and placed on high cholesterol diet for 12 weeks ad libitum to develop advanced atherosclerotic plaques. Aortic tissue was harvested and RNA-Seq analysis was performed using Illumina HiSeq2500 V4 2x150 bp  (Genewiz, South Plainfield, NJ).

value: CD4-specific KLF10 knockout mice

value: 8 weeks old

tag: Sex

value: male

tag: diet

value: high cholesterol diet


title: CHB 2_(miRNA-4_0)

description: PBMCs at 2, CHB group


title: P1 TSA RNA-seq rep3

city: Nanjing

first: Zhang

last: Jing

address: Nanjing University

institute: Nanjing University

data_processing:
RNA-seq: The adaptors-trimmed and quality-filtered reads were mapped to mm10 or rn6 using HISAT2 version 2.1.0 with default parameters. Transcript assembly was performed using StringTie version 1.3.5. Expression levels measured as fragments per kilobase of exon model per million mapped fragments (FPKM).
ATAC-seq: Raw reads were trimmed for adaptor with cutadapt and aligned to mm10 using Bowtie2. The duplications in aligned reads were excluded by Picard Mark Duplicates. The unduplicated reads were used to call peaks with MACS2. ENCODE blacklist regions were removed. For visualization, bigwig files were generated using bedGraphToBigWig.
HiChIP: Raw reads were trimmed for adaptor with cutadapt. The reads passed quality control were aligned to mm10  using the HiC-Pro pipeline.  Default settings were used to  assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices.
Genome_build: RNA-seq: mm10 (mouse) and rn6 (rat), ATAC-seq: mm10, HiChIP: mm10.

organism: Rattus norvegicus

source_name: Cardiomyocyte

extract_protocol:
Genomic DNA was extracted with DNA Clean & Concentrator kit(ZYMO).
Libraries were constructed according to the Illumina instruction.

treatment_protocol: Cardiomyocytes from embryonic day 18.5 and postnatal days 1/3/7 of mouse and postnatal days 1 of rats were isolated from left ventricles. Rat cardiomyocytes were treated with the 100 nM TSA one day after plating  and DMSO was used as negative control. 1 million cells were harvested in TRIzol RNA Isolation Reagents (Thermo, 15596018) for  RNAseq. 50000 cells were harvested and transposed with Tn5 transposase for ATAC-seq. 3 million cells were were harvested and fixed with 1% formaldehyde for HiChIP. MboI restriction enzyme was used to digest chromatin in HiChIP.

tag: time point


title: Tcf1 Cut&Run, WT naive, rep1


title: TKO_2


title: P1 TSA RNA-seq rep2


title: Spatial Transcriptomics Sample 1


title: Kras mutant, 5

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the zebrafish genome by Rsubread version 2.10.5
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function
Genes were identified using Ensembl annotation to the GRCz11 genome, version 101
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

organism: Danio rerio

source_name: Liver

growth_protocol: E3 medium comprising 5mM NaCl, 0.17mM KCl, 0.33mM CaCl2, 0.33mM MgSO4

extract_protocol:
Total RNA was extracted from individual micro-dissected zebrafish livers using the RNeasy Micro Kit (QIAGEN, #74004).
RNA (100 ng per sample) was used for RNA-sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo-Zero depletion (Illumina). Indexed libraries were sequenced on a NextSeq 500 instrument (Illumina) to generate 80 bp paired end reads and yielding at least 20 million reads per sample.

treatment_protocol: Treatment group received oxycycline (20mg/L) from 2-7 days post-fertilisation (dpf)

value: Liver

value: hepatocytes

value: kras mutant

value: Doxycycline (20mg/L) from 2-7 days post-fertilisation (dpf)


title: Tcf1 Cut&Run, CTCFKO Day4, rep1


title: P1 TSA RNA-seq rep1


title: Kras mutant, 4


title: TKO_1


title: HiC Teff rep1

value: wild type


title: WT_4

value: CD4-Cre transgenic mice


title: ICM control 2

value: Inner cell mass

value: Control


title: Kras mutant, 3


title: TKO_4


title: CTCF Cut&Run, CTCF KO WT naive, rep2

data_processing:
The sequencing quality of Cut&Run libraries were assessed by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Trim Galore (v0.6.7) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low quality sequences and remove adapters.
Bowtie2 (v2.3.4.1, Langmead et al., Nature Methods) was used to align the sequencing reads to the mouse genome. UCSC genes for mouse mm9 from iGenome (http://support.illumina.com/sequencing/sequencing_software/igenome.html) were used for gene annotation.
Samtools (Li et al., 2009) was used to transfer sam files to bam files and sort bam files. Picard MarkDuplicates (v2.21.6) (https://github.com/broadinstitute/picard) was used to remove duplicate reads in the bam files.
For Cut&Run libraries, MACS2 (v2.1.1, Zhang et al., Genome Biol) was used for peaks calling using IgG as control. We used the criteria of a q value of < 0.05, 4 fold change at peak summit as identified binding sites.
Assembly: mm9
Library strategy: Cut&Run

extract_protocol:
Naive P14 TCR transgenic, hCD2-Cre, Rosa26-lsl-GFP, Tbet/Runx3 wild-type or double floxed CD8+ T cells were adoptively transferred into CD45 disparate recipients followed by infection with LCMV Armstrong. On day 4 post infection, P14 cells were sort purified and used for CTCF CUT&RUN analysis in live cells.
The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-2000 platform.

value: CTCF-deficient

value: splenocytes

value: GFP+ TCRbeta+ CD8+ CD62Lhi CD44lo-med


title: Tcf1 Cut&Run, WT Day4, rep1

value: GFP+ TCRbeta+ CD8+ CD45.2+


title: Kras mutant, 2


title: WT_2


title: Tcf1 Cut&Run, CTCFKO Day4, rep2

value: CTCF KO


title: WT_1


title: Kras mutant, 1


title: Tcf1 Cut&Run, WT Day4, rep2


title: P1 control RNA-seq rep1


title: K562 cells, KSHV VIRF4, dox, IFN-beta, rep2

first: Connor

middle: Hayakawa

last: Ludwig

address: 443 Via Ortega

department: Bioengineering

description:
K562_CL195_IFN_dox_BR2
CL195_IFN-dox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

data_processing:
Demultiplexing with bcl2fastq (v2.19.0.316)
Construction of a custom transcriptome from a FASTA containing viral transgenes appended to the end of the GRCh38 human reference genome using hisat2-build
Alignment of sequencing reads to custom transcriptome using hisat2 (2.2.1)
DESeq2 (1.32.0) in R (4.1.3) according to this Bioconductor tutorial: http://bioconductor.org/help/course-materials/2016/CSAMA/lab-3-1386 rnaseq/rnaseq_gene_CSAMA2016.pdf
Assembly: GRCh38 appended with viral transgenes
Supplementary files format and content: comma-separated values files (outputs of DESeq2) containing log2 fold changes, adjusted p-values, gene symbols, and additional fields

growth_protocol: K562 cells were cultured in RPMI + Glutamine (Gibco #11-875-119) supplemented with 10% fetal bovine serum (Omega Scientific #FB-15) and penicillin-streptomycin-glutamine (Gibco #10378-016) in a humidified incubator with 5% CO2 at 37C

extract_protocol:
RNA was harvested from 1e6 cells using the RNeasy Mini Kit (Qiagen #74104), lysed with 600uL RLT buffer, and homogenized with QIAshredder columns (Qiagen #79654). A total of 500ng of total RNA (prior to polyA enrichment) was used as input for NGS library preparation.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB #E7770S), which first involved enrichment of polyadenylated mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB 1372 #E7490). All steps were performed in accordance with the NEB protocol.

treatment_protocol: Lentivirally integrated genes encoding full-length viral proteins (or mCitrine) under the control of the TetON system were inducibly expressed upon the addition of 1000ng/uL doxycycline for 48 hours. Interferon beta was added at 10ng/mL 24 hours after initial dox addition for 24 hours to a subset of samples as indicated.

value: erythroleukemia

value: KSHV VIRF4

value: dox, IFN-beta


title: CTCF Cut&Run, WT Day4, rep2


title: Wild type, 3

value: Wild type

value: No treatment


title: CTCF Cut&Run, CTCF KO WT naive, rep1


title: Adipose Mettl3 cko cold ribo rep2

city: Hangzhou

first: Renxiang

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
library strategy: Ribo-seq
Illumina CASAVA1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 mRNA index using HISAT2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for every Sample.

growth_protocol: Mice were maintained in specific pathogen-free conditions.

extract_protocol:
Adipose tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. m6A-antibody was used for capturing m6A-modified mRNA. Altracentrifugation was used for collecting ribosome-protected mRNA fragments.
1 ug of total RNA was used for the construction of sequencing libraries accroding to TruSeq Small RNA Sample Preparation Kit (Illumina).

treatment_protocol: For cold exposure, mice were individually housed in plastic cages at 4 ℃ for 7 days.

value: adipose tissue

value: eight weeks

value: METTL3 flox/flox Adipoq-Cre +/-

value: cold


title: K562 cells, KSHV VIRF4, dox, IFN-beta, rep1

description:
K562_CL195_IFN_dox_BR1
CL195_IFN-dox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv


title: Adipose Mettl3 cko cold ribo rep1


title: P1 control RNA-seq rep3


title: CTCF Cut&Run, WT Day4, rep1

value: wild type


title: K562 cells, KSHV VIRF4, dox, no IFN-beta, rep2

description:
K562_CL195_noIFN_dox_BR2
CL195_noIFN-dox_CL048_noIFN-dox_varPlasmid.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: dox, no IFN-beta


title: Wild type, 2

value: Liver

value: hepatocytes


title: CTCF Cut&Run, Tbx21&Runx3 KO Day4, rep2

value: Tbet/Runx3 deficient

value: splenocytes


title: WT_3

value: CD4-Cre transgenic mice

value: 8 weeks old

value: male

value: high cholesterol diet


title: Wild type, 1


title: P1 control RNA-seq rep2


title: Adipose WT cold ribo rep2

value: METTL3 flox/flox


title: CTCF Cut&Run, Tbx21&Runx3 KO Day4, rep1

value: GFP+ TCRbeta+ CD8+ CD45.2+


title: K562 cells, KSHV VIRF4, dox, no IFN-beta, rep1

description:
K562_CL195_noIFN_dox_BR1
CL195_noIFN-dox_CL048_noIFN-dox_varPlasmid.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: erythroleukemia

value: KSHV VIRF4


title: siMEF2A RNA-seq rep3

data_processing:
The adaptors-trimmed and quality-filtered reads were mapped to hg38 using HISAT2 version 2.1.0 with default parameters. Transcript assembly was performed using StringTie version 1.3.5. Expression levels measured as fragments per kilobase of exon model per million mapped fragments (FPKM).
Genome_build: hg38

source_name: iPSC-CM

growth_protocol: Human induced pluripotent stem cell (hiPSC) line ZSSY001 (RC01001-A) was plated on 6-well plates coated with Matrigel  and maintained with Essential 8 TM Medium. At ~80% confluence, medium was replaced with inducing medium to begin the process of differentiation.

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Libraries were constructed according to the Illumina instruction.

treatment_protocol: Cells were transfected with 50 nM scramble siRNA (Sangon Biotech) or si-MEF2A (Sangon Biotech) using Lipofectamine® 2000 Reagent (Invitrogen, 11668).

value: iPSC-CM


title: Adipose WT cold ribo rep1

value: adipose tissue

value: eight weeks


title: K562 cells, KSHV VIRF3, dox, IFN-beta, rep2

description:
K562_CL194_IFN_dox_BR2
CL194_IFN-dox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: KSHV VIRF3

value: dox, IFN-beta


title: Adipose Mettl3 cko cold m6A rep2

data_processing:
library strategy: m6A-Seq
Illumina CASAVA1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 mRNA index using HISAT2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for every Sample.

value: METTL3 flox/flox Adipoq-Cre +/-

value: cold

tag: antibody

value: anti-m6A (Synaptic Systems, 202003)


title: ONC24hC57RPECD45RPE_S4_L002

city: Cambridge

first: Aviv

last: Regev

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
3'-end
eyecup.mtx, eyecup_gene.tsv, eyecup_cell.tsv, eyecut_celltype.tsv

data_processing:
For 10x 3' v2 data, the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
For 10x 3' v3 data, the 10x Genomics Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing and single cell UMI counting
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Assembly: GRCm38
Supplementary files format and content: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary files format and content: celltype.tsv, a tab-delimited file with annotated cell type information for each cell
Supplementary files format and content: gene.tsv, gene names (row names of the sparse count matrix)

source_name: Mouse eyecup

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Eyecups were dissected in HBSS+HEPES and digested in trypsin/EDTA, after which RPE sheets were released by manual shaking into 20% FBS in HBSS+HEPES, and dissociated into single cell suspensions using manual trituration. Single cell suspensions were incubated with anti-CD90, CD45, CD140a and GLAST antibodies (conjugated to various fluorophores) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded. Collected cells were loaded into 10X Chromium Single Cell Chips at ~1,000 cells/ul.
Single cell libraries were made with Chromium 3’ V2 or V3 platforms (10X Genomics, Pleasanton, CA) following the manufacturer’s protocols. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina NextSeq 500 or HiSeq X.

treatment_protocol: C57BL/6J and Vglut2:cre;Stp15 mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. Eyecups were trypsinized and gently shaken to release RPE cells.

value: Male

value: 8 weeks

tag: version


title: control RNA-seq rep3

value: scramble siRNA


title: ONC48hC57RPECD45RPE2_S6_L003


title: Adipose Mettl3 cko cold m6A rep1


title: ONC48hC57RPECD45RPE1_S5_L003


title: Adipose WT cold m6A rep2


title: ONC12hC57RPECD45RPE2_S2_L001


title: ONC12hC57RPECD45RPE1_S1_L001


title: Adipose WT cold m6A rep1


title: Adipose WT RT m6A rep2

value: untreated


title: control RNA-seq rep1


title: K562 cells, KSHV VIRF3, dox, no IFN-beta, rep1

city: Stanford

institute: Stanford University

description:
K562_CL194_noIFN_dox_BR1
CL194_noIFN-dox_CL048_noIFN-dox_varPlasmid.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: dox, no IFN-beta


title: K562 cells, KSHV VIRF2, dox, IFN-beta, rep2

description:
K562_CL290_IFN_dox_BR2
CL290_IFN-dox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: KSHV VIRF2


title: K562 cells, KSHV VIRF2, dox, IFN-beta, rep1

description:
K562_CL290_IFN_dox_BR1
CL290_IFN-dox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv


title: Adipose WT RT m6A rep1

value: METTL3 flox/flox


title: K562 cells, KSHV VIRF2, dox, no IFN-beta, rep2

description:
K562_CL290_noIFN_dox_BR2
CL290_noIFN-dox_CL048_noIFN-dox_varPlasmid.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: erythroleukemia


title: brSIRT6-KO rep 4

city: Beersheba

first: Dmitrii

middle: Nikolaevich

last: Smirnov

address: David Ben Gurion Blvd 1

department: Department of Life Sciences

institute: Ben-Gurion University of the Negev

data_processing:
nf-core/rnaseq pipeline (v3.0)
Filtering and trimming of the raw reads were done using fastp tool.
nf-core/rnaseq pipeline was used to map trimmed reads to the mouse GRCm39 reference genome (STAR) and to quantify gene expression using the Salmon tool.
DESeq2 R package was used to normalize gene expression profiles, following by differential expression analysis.
Gene Ontology analysis was conducted via ClusterProfiler R package.
Assembly: mm39
Supplementary files format and content: comma-delimited text file include row expression counts for each sample

source_name: brain

extract_protocol:
RNA was extracted from mice's left brain hemispheres, using the NucleoSpin RNA Plus kit (MACHEREY-NAGEL GmbH & Co. K.G., catalog number 740984.50), following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using in-house INCPM mRNA-seq kit (G-INCPM, Weizmann Institute of Science), for full-length RNA-seq with polyA-based capturing

value: Female

value: brain

value: brain-specific SIRT6 knockout


title: V3ONCMC21d7VglutCD45_S2_L004

description:
3'-end
ONC-retina-MC21.mtx, ONC-retina-MC21_gene.tsv, ONC-retina-MC21_cell.tsv, ONC-retina-MC21_celltype.tsv

source_name: Mouse retina

value: 7-12 weeks

value: Vglut2-Cre x STP15


title: brSIRT6-KO rep 3


title: siMEF2A RNA-seq rep2

value: iPSC-CM


title: K562 cells, KSHV VIRF3, dox, IFN-beta, rep1

description:
K562_CL194_IFN_dox_BR1
CL194_IFN-dox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: KSHV VIRF3

value: dox, IFN-beta


title: K562 cells, KSHV VIRF3, dox, no IFN-beta, rep2

description:
K562_CL194_noIFN_dox_BR2
CL194_noIFN-dox_CL048_noIFN-dox_varPlasmid.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv


title: siMEF2A RNA-seq rep1


title: Adipose Mettl3 cko cold input rep2

data_processing:
Illumina CASAVA1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 mRNA index using HISAT2. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for every Sample.

value: adipose tissue

value: eight weeks

value: METTL3 flox/flox Adipoq-Cre +/-

value: cold


title: control RNA-seq rep2

value: scramble siRNA


title: K562 cells, KSHV VIRF2, dox, no IFN-beta, rep1

description:
K562_CL290_noIFN_dox_BR1
CL290_noIFN-dox_CL048_noIFN-dox_varPlasmid.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: dox, no IFN-beta


title: V3ONCd7VglutCD45_S2_L003

value: Male

value: 6 weeks


title: Adipose Mettl3 cko cold input rep1


title: brSIRT6-KO rep 2


title: brSIRT6-KO rep 1


title: K562 cells, KSHV VIRF2, no dox, IFN-beta, rep2

description:
K562_CL290_IFN_nodox_BR2
CL290_IFN-nodox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv

value: erythroleukemia

value: KSHV VIRF2

value: no dox, IFN-beta


title: Adipose WT cold input rep2

value: METTL3 flox/flox


title: K562 cells, KSHV VIRF2, no dox, IFN-beta, rep1

description:
K562_CL290_IFN_nodox_BR1
CL290_IFN-nodox_CL048_noIFN-dox_varIFN.csv
Ludwig_VIRF-IFN_RNA-seq_se_counts.csv


title: N2 + vha-6 RNAi + elt-2 RNAi, rep 1 [exp2]

data_processing:
After sequencing on the BGIseq-500 platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa --sjdbGTFfile Caenorhabditis_elegans.WBcel235.89.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

source_name: N2 + vha-6 RNAi + elt-2 RNAi, rep 1

extract_protocol:
On the day of the extraction, 1 ml of TriPure Isolation Reagent (Cat. 11667165001, Roche) was added to each tube. RNA was then extracted by using a column-based kit from Macherey-Nagel (Cat. 740955.250).
RNA libraries were prepared for sequencing using standard BGISeq500 protocols with polyA enrichment

value: WT

value: vha-6 RNAi 25percent + elt-2 RNAi 40percent + control RNAi 35percent


title: Cisplatin with NR 2

data_processing:
Adaptor and low-quality reads were trimmed using Trim-galore
Reads were aligned to the mouse (GRCm38) reference genome using STAR (v2.4.1d)
The aligned reads were mapped to the genes using HTSeq-0.6.1
Differentially expressed genes between experimental groups were identified using DESeq2 version 1.10.1.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: whole kidney

extract_protocol:
Total RNA was isolated from the kidneys of mice and human using the RNeasy mini kit
Sequencing libraries were constructed using the Illumina TruSeq RNA Preparation Kit.

value: whole kidney

value: Cisplatin with NR


title: WT rep 4

value: Female

value: brain


title: Adipose WT cold input rep1

value: adipose tissue

value: eight weeks


title: WT rep 3


title: APP 6month, scRNAseq

city: Seoul

first: BYOUNGGOOK

last: CHO

address: 30 Pildong-ro 1-gil, Jung-gu

country: South Korea

institute: Dongguk university

description:
10x Genomics
A_6m

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Brain samples from male wild-type and App-KI transgenic mice were prepared in the same single-cell isolation batch to minimize potential batch effects. Hippocampus tissues from 1-, 3-, and 6-month-old wild-type and App-KI mice were then dissected
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, filtered cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: neuronal cell

value: Hippocampus

value: APP-NLGF

value: 6 month


title: Adipose WT RT input rep2

value: untreated


title: APP 3month, scRNAseq

description:
10x Genomics
A_3m

value: 3 month


title: Adipose WT RT input rep1


title: WT rep 2


title: APP 1month, scRNAseq

description:
10x Genomics
A_1m

value: 1 month


title: WT rep 1


title: Vglut48h5050rgcscd45_S12_L007

description:
3'-end
ONC-retina.mtx, ONC-retina_gene.tsv, ONC-retina_cell.tsv, ONC-retina_celltype.tsv

value: Mixed

value: 6-8 weeks

value: Vglut2-Cre x STP15


title: Control 6month, scRNAseq

description:
10x Genomics
C_6m


title: Control 3month, scRNAseq

description:
10x Genomics
C_3m


title: ICM control 1

data_processing:
raw data were obtain from an Illumina NextSeq NB552053 after demultiplexing performed with bcl2fastq2 v2.2.18.12 and adaptor trimming with Cutadapt 1.15
after deleting poor quality base (under 30) at the end of the sequence, reads longer than 35 bp were kept
reads were mapped using the splice junction mapper TopHat (v2.1.1) with parameters -N 2 --read-edit-dist 2 --b2-sensitive --no-coverage-search
the gene count table was performed with featureCounts (v1.6.0) with parameters -p -B -C
Data normalization and single-gene level analysis of the differential expression were performed using the DESeq2 package
Assembly: Ensembl 98 Oryctolagus cuniculus 2.0
Supplementary files format and content: tab-delimited text files include normalized expression values for each Sample

source_name: Inner cell mass

extract_protocol:
RNA was harvested using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems). 750pg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-seq V4 ultra low input RNA kit

value: Inner cell mass

value: Control


title: primary T cells, Th17_DMSO_rep2

city: New York

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

description:
TMP269_counts.txt
WT_Rep2

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
For RNA-Seq: Tophat (v2.1.0) alignment was performed using the mm9 reference genome. HT-seq was used to find read counts across genes. DESeq2 was used to find differentially expressed genes with FDR < 0.1 and Fold-change > 1.5.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html.  For RNA-Seq: Tab-delimited text file of normalized counts for all samples.

source_name: primary T cells, Th17_DMSO

growth_protocol: CD4+ T cells were purified from spleen. Naïve T cells were activated with plate bound anti-CD3 and anti-CD28 plus IL6(20ng/mL), TGFb(2.5ng/mL) . The cells were cultured for 48-72h and treated with TMP269 before harvesting for further analysis.

extract_protocol:
For ChIP-Seq: Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies. For RNA-Seq: Compound treated cells were collected and RNA was extracted using a Nucleospin RNA kit (Clontech).
ChIP-Seq: ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size. RNA-Seq: Extracted RNA was subjected to polyA selection and standard Illumina RNA-seq library prep procedures.

value: primary T cells

value: control


title: Dermal cells, D3, scRNAseq

city: Beijing

first: Yaqi

last: Wang

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

description: 10x Genomics

data_processing:
Single cell RNA-seq data were aligned to mm10 genome reference and counted the expression of genes of each barcode using cellranger (V3.0.2)
We loaded filtered feature matrixes into R by package DropletUtils
Barcodes with less than median-3*median absolute deviation total UMI counts or barcodes with less than median-3*median absolute deviation total features or barcodes with higher than median+2*median absolute deviation proportion of total mitochondrial counts were defined as low quality cells which were removed for downstream analysis using R package scater.
Then we normalized UMI count matrixs by R package scran and imported into the Seurat (V3.2.3) R toolkit for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, comma-separated values and matrix files

source_name: neonatal mouse derma

extract_protocol:
The single-cell suspension was then subjected to a BD Influx cell sorter to exclude debris and doublets. Cells were pelleted and washed with 3 times PBS with 0.04% BSA twice to remove ambient RNA as well as minimize cell aggregation. Cells were filtered using a 70-mm cell strainer to remove any remaining cell debris and large clumps.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: A single-cell suspension from neonatal dermal was prepared by mechanical and enzymatic dissociation as previously described (Hou et al., 2013). In brief, the limbs and tail were removed from the euthanized new-born mice (1–3 d) before gently pulling away the skin from the body. The skin was digested with 0.35% collagenase II in a 37 °C water bath for 1hr.

value: neonatal mouse derma

tag: time

value: 3 days of transdifferentiation


title: primary T cells, Th17_TMP269_rep2

description:
TMP269_counts.txt
TMP269_Rep2

source_name: primary T cells, Th17_TMP269


title: primary T cells, Th17_TMP269_rep1

description:
TMP269_counts.txt
TMP269_Rep1


title: Vglut48h5050rgcscd45_S12_L006


title: Dermal cells, D2, scRNAseq

description: 10x Genomics

tag: tissue

value: 2 days of transdifferentiation


title: Dermal cells, D4, scRNAseq

description: 10x Genomics

value: 4 days of transdifferentiation


title: primary T cells, Th17_DMSO_rep1

description:
TMP269_counts.txt
WT_Rep1

tag: cell type


title: Vglut48h5050rgcscd45_S12_L005


title: d106S-IL12 reanalysis

city: Boston

first: Stephanie

last: Dougan

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

data_processing:
The 10x Cellranger pipeline (v6.1.0) was used to align fastq.gz reads to the Mm10 reference genome and generate a single-cell feature count matrix for each library using default parameters.
The count matrices were imported for downstream analysis into R using the Seurat (v4.0.2) package. Cells were called from barcodes using the Seurat R package
Count normalization, clustering, and differential expression analysis was done in Seurat
Assembly: Mm10
Supplementary files format and content: For each sample, a MEX sparse matrix (compressed) containing raw gene-level counts for all sequenced barcodes

source_name: Tumor

extract_protocol:
Tumors were excised, digested with Miltenyi tumor digest kit, washed and FACS sorted for CD45+, live (Zombie -) cells. Samples were loaded onto a 10x controller to generate single cell GEMs
Library preparation was performed with the Chromium Single Cell 5’ Library and Gel Bead Kit

treatment_protocol: PBS, d106S, or d106S-IL12 intratumoral treatment

value: Tumor

value: Melanoma

tag: genotype

value: Wild-type


title: Vglut48h5050rgcscd45_S12_L004


title: primary T cells, Input_HDAC7

source_name: primary T cells, Input_HDAC7


title: d106S reanalysis

tag: treatment


title: Dermal cells, D0, scRNAseq

description: 10x Genomics

value: 0 days of transdifferentiation


title: primary T cells, Input_HDAC4

source_name: primary T cells, Input_HDAC4

tag: strain


title: Vglut48h5050rgcscd45_S12_L003

tag: age


title: primary T cells, HDAC7_rep2

source_name: primary T cells, HDAC7

tag: chip antibody

value: HDAC7 (Epigentek, A-4007)


title: Vglut48h5050rgcscd45_S12_L002


title: PBS reanalysis

value: PBS


title: 53_Nab6-HF

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description: CRAC

data_processing:
Alignment. Command: STAR --readFilesIn file1.fastq file2.fastq --genomeDir index_file
samtools view -bS file.sam
samtools sort file.bam
samtools index -b file.bam
Coverage map (+strand). Command: bamCoverage -b file.bam --binSize 1 --filterRNAstrand forward --normalizeUsing CPM
Coverage map (-strand). Command: bamCoverage -b file.bam --binSize 1 --filterRNAstrand reverse --normalizeUsing CPM
Read counting. Command: featureCounts file.bam -a annotation.gtf --largestOverlap --extraAttributes gene_name -s 2 -T 50 -p -B
Assembly: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping. The genome and associated annotation file are included as part of this submission.
Supplementary files format and content: The .txt files (generated using featureCounts) contain information on the number of reads mapping to each transcript. The bigwig files provide coverage maps across the yeast genome.
Demultiplexing. Command: pyBarcodeFilter.py -f raw_file.fastq -b barcodes_file.txt
Adapter stripping and quality control. Command: flexbar -r file.fastq -a adapters.txt -ao 4 -m 14 -at RIGHT -u 2 -q TAIL -qf i1.8
Collapsing. Command: pyFastqDuplicateRemover.py -f file.fastq
Removal of low-complexity reads. Command: bbduk.sh in=file.fasta entropy=0.65 entropywindow=10 entropyk=6
Alignment. Command: novoalign -f file.fasta -r Random -d genome.novoindex
Further collapsing of reads aligning to the same location and with identical random barcodes.
Coverage maps. Command: pyGTF2bedGraph.py --gtf annotation_file.gtf -c chromosome_lengths.txt -t reads
Read counting. Command: pyReadCounters.py -f file.bam --file_type=novo --sense --gtf=annotation_file.gtf
Assembly: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping
Supplementary files format and content: The .txt files (generated using pyReadCounters.py) contain information on the number of reads mapping to each transcript. The bedGraph files provide coverage maps across the yeast genome.

organism: Saccharomyces cerevisiae

source_name: haploid cells

growth_protocol: For RNAseq experiments (1-50), cells were cultured to 0.125 OD600 and either harvested directly or treated with Congo Red and harvested 1, 2, or 4 hours later.  Approximately 5 OD600 units were collected by centrifugation and frozen at -80°C.  For CRAC experiments (51-54), cells were cultured to 0.4 OD600 in 700 mL SD -TRP medium containing 2% glucose. Cells were then subjected to 100 mJ of 254nm UV-crosslinking (4-6 seconds), collected by filtration, resuspended in 50 mL of ice cold PBS, centrifuged to pellet, and frozen at -80°C.

extract_protocol:
For RNAseq experiments (1-50), cells were lysed with zirconia beads and vortexing, and RNA was extracted using hot phenol-chloroform. The CRAC (samples 51-54) protocol is based on Tuck and Tollervey, 2013. Modifications are described in Bresson et al., 2020.
RNAseq libraries were prepared from 500ng of each total-RNA sample using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the manufacturer's protocol. The CRAC (samples 51-54) protocol is based on Tuck and Tollervey, 2013. Modifications are described in Bresson et al., 2020.


title: 54_Nab6-HF

description: CRAC


title: primary T cells, HDAC7_rep1


title: primary T cells, HDAC4_rep2

source_name: primary T cells, HDAC4

value: HDAC4 (Bethyl, 303-467A)


title: 52_Mrn1-HF

description: CRAC


title: Vglut24h8020rgccd45_S11_L005

value: Male

value: 6-8 weeks


title: Vglut24h8020rgccd45_S11_L006

value: Vglut2-Cre x STP15


title: Control 1month, scRNAseq

description:
10x Genomics
C_1m

value: neuronal cell

value: Hippocampus

value: 1 month


title: 51_Mrn1-HF

description: CRAC


title: Vglut24h8020rgccd45_S11_L004


title: 50_dMRN1_dNAB6_60CR_120min

description: RNAseq

value: delta-mrn1 delta-nab6

tag: congo red

value: 60 ug/uL

tag: timepoint

value: 2 hr


title: Dermal cells, D1, scRNAseq

description: 10x Genomics

value: neonatal mouse derma

value: 1 days of transdifferentiation


title: K562 cells, KSHV VIRF4 W671A, dox, rep1

description:
K562_CL459_dox_BR1
CL459-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

tag: cell line

value: erythroleukemia

value: KSHV VIRF4 W671A

value: dox


title: DEA-1237-3

city: Huntsville

first: Marie-Claire

last: Boutrin

address: 7000 Adventist Blvd NW

institute: Oakwood University

hyb_protocol: Labeled cDNA(2ug) derived from each RNAsample was hybridized with each array for over 16 to 18 h. The slides and arrays were washed and spun dry.

scan_protocol: The slides were scanned with a Roche MS200 microarray scanner with a resolution of 2 um.

data_processing:
The normalization was done with the NimbleScan 2.6.0.0 built-in normalization function. Microarray data analysis was performed with a Partek Genomics suite (v6.5)
Differentially expressed genes were determined using fold-change (≥1.25) plus p (≤ 0.05) with FDR = 0.05.

organism: Porphyromonas gingivalis W83

source_name: Porphyromonas gingivalis W83 PG1237-deficient mutant

label_protocol: cDNA (0.5 to 1 ug) was used to start the amplification and labeling reaction using a NimbleGen one-color labeling kit, in which Cy3 was randomly incorporated into the newly synthesized DNA by the Klenow fragment.

growth_protocol: Fresh cultures of P. gingivalis strains (mutants and wild type) were grown from overnight cell cultures under anaerobic conditions at 37ºC in BHI broth. P. gingivalis strains were grown to early exponential phase (OD600:~0.3) in BHI broth under anaerobic conditions at 37ºC.

extract_protocol: Total RNA was extracted from fresh cultures using a total RNA isolation kit (Promega, WI). Additional DNase treatment was carried out using DNase kit (Ambion, Austin, TX). Samples from untreated cultures of P. gingivalis W83 were processed similarly and used as controls. RNA quality was checked using Agilent Bioanalyzer and Agilent RNA 6000 Nano.

treatment_protocol: At OD600~0.3 time point, the bacteria cultures were stressed with Diethylamine (DEA) NONOate (15µl, 24mM stock concentration) for the NO stress studies. Untreated wild type and mutant strains cell cultures grown under the same conditions were used as controls. Samples were taken after 15 mins of NO stress treatment and controls were taken from untreated cultures at the same time.

value: PG1237-deficient mutant

tag: treatment/time point

value: Fresh culture, Abs ~0.3, 15 min post NO stress


title: Vglut24h8020rgccd45_S11_L003

tag: Sex


title: 48_dNAB6_60CR_120min

description: RNAseq


title: K562 cells, KSHV VIRF4 wt, dox, rep2

description:
K562_CL195_dox_BR2
CL195-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: KSHV VIRF4 wt


title: 49_dMRN1_dNAB6_0min

description: RNAseq

value: 0 hr


title: Vglut24h8020rgccd45_S11_L002

value: Male

value: 6-8 weeks


title: primary T cells, HDAC4_rep1

value: primary T cells

value: HDAC4 (Bethyl, 303-467A)


title: ONCRGCimmune48h_S2_L008


title: CTR-1237-2

value: Fresh culture, Abs ~0.3


title: DEA-1237-2


title: DEA-1237-1


title: K562 cells, KSHV VIRF2 del321-325, dox, rep2

description:
K562_CL458_dox_BR2
CL458-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: KSHV VIRF2 del321-325


title: 46_wt_60CR_120min

description: RNAseq

value: wild type

value: 60 ug/uL


title: ONCRGCimmune48h_S2_L004


title: K562 cells, KSHV VIRF4 W671A, dox, rep2

description:
K562_CL459_dox_BR2
CL459-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: K562 cells, KSHV VIRF2 del321-325, dox, rep1

description:
K562_CL458_dox_BR1
CL458-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: CTR-1237-1


title: CTR-1237-3


title: K562 cells, KSHV VIRF4 wt, dox, rep1

description:
K562_CL195_dox_BR1
CL195-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: Vglut24h8020rgccd45_S11_L007

value: Vglut2-Cre x STP15


title: ONCRGCimmune48h_S2_L003


title: K562 cells, KSHV VIRF2 wt, dox, rep2

description:
K562_CL290_dox_BR2
CL290-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: KSHV VIRF2 wt


title: ONCRGCimmune48h_S2_L002


title: DEA-W83-3

source_name: Porphyromonas gingivalis W83

value: Fresh culture, Abs ~0.3, 15min post NO stress


title: K562 cells, KSHV VIRF2 wt, dox, rep1

description:
K562_CL290_dox_BR1
CL290-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: erythroleukemia


title: DEA-W83-2


title: 45_dNAB6_dSLT2_2CR_240min

description: RNAseq

value: delta-nab6 delta-slt2

value: 2 ug/uL

value: 4 hr


title: 43_dNAB6_dSLT2_2CR_60min

description: RNAseq

value: 1 hr


title: K562 cells, EBV A876 EBNA2 effector domains + B95-8 EBNA2 CBF1-binding domain, dox, rep2

description:
K562_CL406_dox_BR2
CL406-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: dox


title: 44_dNAB6_dSLT2_2CR_120min

description: RNAseq

value: 2 hr


title: DEA-W83-1


title: K562 cells, EBV A876 EBNA2 effector domains + B95-8 EBNA2 CBF1-binding domain, dox, rep1

description:
K562_CL406_dox_BR1
CL406-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: 42_dNAB6_dSLT2

description: RNAseq

value: 0 hr


title: CTR-W83-2


title: 41_dSLT2_2CR_240min

description: RNAseq


title: ONCRGCimmune24h_S6_L004

value: Male

value: 6-8 weeks


title: K562 cells, EBV B95-8 EBNA2 effector domains + A876 EBNA2 CBF1-binding domain, dox, rep2

description:
K562_CL405_dox_BR2
CL405-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: ONCRGCimmune24h_S6_L003


title: K562 cells, EBV B95-8 EBNA2 effector domains + A876 EBNA2 CBF1-binding domain, dox, rep1

description:
K562_CL405_dox_BR1
CL405-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: CTR-W83-1

value: Fresh culture, Abs ~0.3


title: ONCRGCimmune24h_S6_L002


title: 40_dSLT2_2CR_120min

description: RNAseq


title: K562 cells, EBV A876 EBNA2 wt, dox, rep2

description:
K562_CL404_dox_BR2
CL404-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: EBV A876 EBNA2 wt


title: erythroid, edit, 7b

city: Oxford

first: James

middle: Oliver Joshua

last: Davies

state: Oxon

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Molecular Haematology Unit

institute: Weatherall Institute of Molecular Medicine, Oxford University

data_processing:
ATAC-seq data were aligned using Bowtie2 and peak called with MACS2. Comparison of peaks was performed with DESeq2
Assembly: Hg19
Supplementary files format and content: bw

source_name: Blood cells

growth_protocol: CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x105 cells were resuspended on day 0 in Phase I media at 2x105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x105 cells ml-1. Cells were counted on day 9 and diluted to 2x105 cells ml-1 Phase II media. HUDEP-2 cells were cultured in expansion phase as previously described Canver, M. C. et al.,2015.

extract_protocol: Assay for transposase-accessible chromatin (ATAC)–sequencing. The protocol was adapted for small cell numbers from Buenrostro et al. Cells were harvested into 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spin down at 4°C for 10 minutes at 500 g. Nuclei were then resuspended in 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 and 22.5 μl water). Post incubation for 30 min at 37°C, Transposed fragments were purified using a Qiagen MinElute Kit into 23 μl elution buffer. Purified fragments were then amplified by PCR as previously described.

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: HbE gRNA


title: 38_dSLT2_0min

description: RNAseq


title: ONCRGCimmune24h_S6_L001

source_name: Mouse retina


title: ICM glucose and insulin 2

city: Jouy-en-josas

first: Sophie

address: Allée de Vilvert

institute: INRAE UMR1198 BREED

value: Inner cell mass

value: Glucose and inuslin


title: K562 cells, EBV A876 EBNA2 wt, dox, rep1

description:
K562_CL404_dox_BR1
CL404-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

data_processing:
Demultiplexing with bcl2fastq (v2.19.0.316)
Construction of a custom transcriptome from a FASTA containing viral transgenes appended to the end of the GRCh38 human reference genome using hisat2-build
Alignment of sequencing reads to custom transcriptome using hisat2 (2.2.1)
DESeq2 (1.32.0) in R (4.1.3) according to this Bioconductor tutorial: http://bioconductor.org/help/course-materials/2016/CSAMA/lab-3-1386 rnaseq/rnaseq_gene_CSAMA2016.pdf
Assembly: GRCh38 appended with viral transgenes
Supplementary files format and content: comma-separated values files (outputs of DESeq2) containing log2 fold changes, adjusted p-values, gene symbols, and additional fields

value: erythroleukemia


title: ONCRGCimmune48h_S2_L001


title: erythroid, edit, 7a


title: K562 cells, EBV B95-8 EBNA2 wt, dox, rep2

description:
K562_CL403_dox_BR2
CL403-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: EBV B95-8 EBNA2 wt


title: erythroid, edit, 4b


title: CTR-W83-3

value: wild type


title: 37_dNAB6_2CR_240min

description: RNAseq

value: 2 ug/uL

value: 4 hr


title: ONCRGCimmune24h_S6_L008


title: K562 cells, EBV B95-8 EBNA2 wt, dox, rep1

description:
K562_CL403_dox_BR1
CL403-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: dox


title: 47_dMRN1_60CR_120min

description: RNAseq

value: 60 ug/uL

value: 2 hr


title: 36_dNAB6_2CR_120min

description: RNAseq


title: 35_dNAB6_2CR_60min

description: RNAseq

value: 1 hr


title: erythroid, edit, 4a


title: 39_dSLT2_2CR_60min

description: RNAseq


title: K562 cells, HHV7 U8, dox, rep2

description:
K562_CL456_dox_BR2
CL456-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: HHV7 U8


title: K562 cells, HCMV RL5A, dox, rep2

description:
K562_CL418_dox_BR2
CL418-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: HCMV RL5A


title: erythroid, edit, 1b

value: Blood cells


title: erythroid, edit, 1a

value: Differentiated erythroid cells


title: K562 cells, HHV7 U8, dox, rep1

description:
K562_CL456_dox_BR1
CL456-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: K562 cells, HCMV RL5A, dox, rep1

description:
K562_CL418_dox_BR1
CL418-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: 33_dMRN1_2CR_240min

description: RNAseq


title: 32_dMRN1_2CR_120min

description: RNAseq


title: 34_dNAB6_0min

description: RNAseq

value: 0 hr


title: K562 cells, HHV7 U84, dox, rep2

description:
K562_CL457_dox_BR2
CL457-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: HHV7 U84


title: erythroid, control, c2

value: HbE/beta thalassaemia

value: Control


title: erythroid, edit, a2

value: HbE gRNA


title: 31_dMRN1_2CR_60min

description: RNAseq


title: erythroid, control, c1


title: 30_dMRN1_0min

description: RNAseq


title: K562 cells, HHV7 U84, dox, rep1

description:
K562_CL457_dox_BR1
CL457-CL048_dox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: erythroleukemia


title: K562 cells, mCitrine, dox, rep1

description:
K562_CL048_dox_BR1
CL048_dox-nodox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: mCitrine


title: 29_wt_2CR_240min

description: RNAseq

value: wild type

value: 2 ug/uL


title: ONCd7VglutImmuneAstro2_S4_L002

description:
3'-end
ONC-retina.mtx, ONC-retina_gene.tsv, ONC-retina_cell.tsv, ONC-retina_celltype.tsv

value: Mixed

value: 6-8 weeks

value: Vglut2-Cre x STP15


title: iPSC-derived cardiomyocyte from ViPSC, sample 3

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

data_processing:
Reads were mapped to human GRCh38 reference genome using STAR pipeline at Novogene - Advancing Genomics company
Then, for each gene, the count of transcripts for each sample was recorded via HtSeq.
Assembly: human GRCh38
Supplementary files format and content: Excel files, each file has the following columns: transcript ID (gene_ID), transcript count, gene name, chromosome number, the starting point of the transcript on the chromosome,  the starting end of the transcript on the chromosome, transcript length,
Supplementary files format and content: See file Read_count_All.xlsx for all sample processed data.

source_name: Cardiac

growth_protocol: iPSC reprogramming was performed with a CytoTune™-iPS 2.0 Sendai Reprogramming Kit as directed by the manufacturer’s instructions. Briefly, cells were transduced with CytoTune™-iPS 2.0 Sendai reprogramming vectors and then transferred to feeder cells in fibroblast medium (DMEM supplemented with 10% FBS, 1% MEM Non-Essential Amino Acids Solution, and 0.1% 2-mercaptoethanol). Putative hiPSC colonies were identified via Tra1-60 live staining, transferred into Matrigel-coated wells containing mTeSR medium, and expanded without feeder cells.

extract_protocol:
iPSC-CMs were trypsinized into single cells, fixed with fixation and permeabilization solution (51-2090KZ) for 30 minutes at 4 °C, and blocked in Human BD Fc Block (564219) at room temperature for 10 minutes. Cells were then incubated with primary antibodies and isotype control antibodies at room temperature for 40 minutes, incubated with corresponding fluorescently conjugated secondary antibodies for 30 minutes, and resuspended in wash buffer (554723). Flow cytometry was performed with an LSR Fortessa instrument (BD Biosciences, USA).
AiPSC, ViPSC, AiPSC-CM, and ViPSC-CM RNA sequencing was performed by Novogene - Advancing Genomics using Illumina NovaSeq 6000 platforms
RNA quality control was achieved by removing reads containing adapters, having more than 10% of undetermined bases, and low-quality reads. Less than 2% of these reads were removed in all samples.

value: Cardiac

value: human-induced pluripotent stem cell-derived cardiomyocyte

value: iPS-CM

value: WT


title: K562 cells, mCitrine, dox, rep2

description:
K562_CL048_dox_BR2
CL048_dox-nodox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: dox


title: 28_wt_2CR_120min

description: RNAseq

value: 2 hr


title: ONCd7VglutImmuneAstro1_S2_L001


title: iPSC-derived cardiomyocyte from ViPSC, sample 2


title: K562 cells, mCitrine, no dox, rep1

description:
K562_CL048_nodox_BR1
CL048_dox-nodox.csv
Ludwig_HHV_RNA-seq_se_counts.csv

value: no dox


title: K562 cells, mCitrine, no dox, rep2

description:
K562_CL048_nodox_BR2
CL048_dox-nodox.csv
Ludwig_HHV_RNA-seq_se_counts.csv


title: iPSC-derived cardiomyocyte from ViPSC, sample 1


title: iPSC-derived cardiomyocyte from AiPSC, sample 3


title: 27_wt_2CR_60min

description: RNAseq

value: 1 hr


title: iPSC-derived cardiomyocyte from AiPSC, sample 2


title: 25_dMRN1_dNAB6_60CR_120min

description: RNAseq

value: delta-mrn1 delta-nab6

value: 60 ug/uL


title: erythroid, edit, a1

value: Blood cells

value: Differentiated erythroid cells

value: HbE/beta thalassaemia

value: HbE gRNA


title: ONCd7C57RGCImmuneAstro1_S13_L007

value: Male


title: iPSC-derived cardiomyocyte from AiPSC, sample 1


title: 23_dNAB6_60CR_120min

description: RNAseq


title: 24_dMRN1_dNAB6_0min

description: RNAseq

value: 0 hr


title: iPSC reprogrammed from human ventricular cardiac fibroblast, sample 3

value: human-induced pluripotent stem cell

value: iPS


title: ONCd7C57GLAST_S12_L005

value: 6-8 weeks


title: 26_wt_0min

description: RNAseq

value: wild type


title: ONCd4Vglut2CD45CD140a_S12_L006

value: Mixed

value: Vglut2-Cre x STP15


title: iPSC reprogrammed from human ventricular cardiac fibroblast, sample 2

value: Cardiac

value: WT


title: Retinoblastoma,rep3

city: shanghai

first: xiaomeng

last: cheng

state: Shanghai

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with default settings
Trimmed sequence reads were mapped to hg38 using STAR with default settings
Read count extraction were performed using featurecounts with default settings
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Retinoblastoma

extract_protocol:
Total RNA samples were isolated using TRIzol reagent (Life Technologies, NY, USA).
The PA-seq libraries were constructed by following the protocol published before by Ni et al. (BMC Genomics,2013).The concentration of the RNA-seq libraries was measured by Qubit fluorometry (Life Technologies, NY, USA) before loading onto the Illumina HiSeq2000 platform.

value: Retinoblastoma

value: cell differentiation


title: Retinoblastoma,rep2


title: Retinoblastoma,rep4


title: Retinoblastoma,rep1


title: iPSC reprogrammed from human ventricular cardiac fibroblast, sample 1


title: 21_wt_60CR_120min

description: RNAseq

value: 60 ug/uL

value: 2 hr


title: 22_dMRN1_60CR_120min

description: RNAseq


title: Normal_retina,rep5


title: ONCd4C57CD45CD140a_S16_L008


title: Retinoblastoma,rep5


title: ONCd7C57RGCImmuneAstro2_S14_L007


title: ONCd4C57GLAST_S14_L007


title: 19_dNAB6_dSLT2_2CR_120min

description: RNAseq

value: delta-nab6 delta-slt2

value: 2 ug/uL


title: iPSC reprogrammed from human atrial cardiac fibroblast, sample 3


title: iPSC reprogrammed from human atrial cardiac fibroblast, sample 2


title: ONCd7C57GLAST_S12_L006


title: ONC48hC57ImmuneAstro_S9_L006


title: Normal_retina,rep4


title: Normal_retina,rep3


title: 18_dNAB6_dSLT2_2CR_60min

description: RNAseq

value: 1 hr


title: iPSC reprogrammed from human atrial cardiac fibroblast, sample 1


title: HeLa_L42A-CMT2D_biol rep3

first: Ge

last: Bai

state: Zhejiang Province

institute: Zhejiang university

data_processing:
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads
Genomic alignment (version from Ensembl genome browser) was using STAR(version:  2.7.10a) to get uniquely mapping reads
The reads count value of each gene was calculated by FeatureCounts (version:2.0.1)
Assembly: hg38
Supplementary files format and content: Tab-separated reads count value file

source_name: HeLa

extract_protocol:
CLIP was performed as previously described with slight modifications (Liu et al., 2016). HeLa cells were seeded in 10 cm dish and then transfected with plasmids expressing V5-tagged GlyRSWT, GlyRSP234KY or GlyRSP234KY-L42A. After 24 hours, cells were treated with 250 μM AS for 1 hour, then the medium was aspirated and the cells were washed twice with 5 mL ice-cold PBS. Subsequently, 4 ml of ice-cold PBS was added to the culture dish and the cells were irradiated once with 400 mJ/cm2 at 254 nm in UV-linker (UVP-CL-1000) on ice. After irradiation, the cells were scraped, collected, and lysed on ice with 1 mL lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Nonidet P-40, 1×Protease Inhibitor Cocktail and 2.5 U/μL RNase inhibitor). After 30 min of incubation, the cell lysates were centrifuged at 12, 000 rpm, at 4℃ for 15 min, and then the supernatant was carefully collected and added 6 μg G3BP1 antibody (Santa cruz), then the mixture was incubated at 4˚C with gentle rotation overnight. The next day, the mixture was subsequently added 80 μL of protein A/G beads (Invitrogen), and continued to incubate at 4˚C with gentle rotation. After 4 hours, the supernatant was discarded and the beads were washed 3 times with 1 mL of high-salt buffer (5 × PBS supplemented with 0.1% SDS and 1% Nonidet P-40) and another 3 times with 1 mL of wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2 and 0.2% Tween-20). Subsequently, the beads were treated with 2 mg/mL proteinase K at 50˚C for 1 h, then magnetically separated, discarded, and the supernatant was added 1 mL Trizol reagent. Finally, protein-bind RNA were extracted using Trizol reagent and were precipitated by ethanol.
The CLIP RNA was assessed by Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit(Thermo Fisher Scientifc,USA). Briefly, CLIP RNA were fragmented to approximately 200bp. Then, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®(Life Technologies, USA) and then sequenced on Illumina （Illumina,USA）platformat with pair-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: HeLa

value: epithelial


title: Normal_retina,rep2


title: 17_dNAB6_dSLT2

description: RNAseq

value: 0 hr


title: 16_dSLT2_2CR_240min

description: RNAseq

value: 4 hr


title: 15_dSLT2_2CR_120min

description: RNAseq


title: 20_dNAB6_dSLT2_2CR_240min

description: RNAseq


title: HeLa_L42A-CMT2D_biol rep2


title: HeLa_L42A-CMT2D_biol rep1


title: 13_dSLT2_0min

description: RNAseq


title: HeLa_CMT2D_biol rep2


title: 14_dSLT2_2CR_60min

description: RNAseq


title: HeLa_CMT2D_biol rep3


title: HeLa_CMT2D_biol rep1


title: 12_dNAB6_2CR_240min

description: RNAseq


title: ONC48hC57ImmuneAstro_S9_L005

data_processing:
For 10x 3' v2 data, the 10x Genomics Cell Ranger Single Cell Software Suite 2.0.1 was used to perform sample demultiplexing and single cell UMI counting
For 10x 3' v3 data, the 10x Genomics Cell Ranger Single Cell Software Suite 3.1.0 was used to perform sample demultiplexing and single cell UMI counting
Sample alignment to mouse genome GRCm38 with a costumized transcriptome reference using the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Assembly: GRCm38
Supplementary files format and content: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary files format and content: celltype.tsv, a tab-delimited file with annotated cell type information for each cell
Supplementary files format and content: gene.tsv, gene names (row names of the sparse count matrix)

value: Male

value: 6-8 weeks


title: ONC12hC57CD45CD140aRGC_S6_L003


title: ONC12hC57GLAST_S5_L003


title: 11_dNAB6_2CR_120min

description: RNAseq


title: ONC12hC57CD45CD140a2_S8_L004


title: 10_dNAB6_2CR_60min

description: RNAseq


title: HeLa_WT_biol rep3