title: ST13, VDJ

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

description: 10x Genomics 3’

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome using the CellRanger Pipeline v8
Unfiltered RNA UMI counts were loaded into Seurat v4.0.1 (Stuart et al., 2019) for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fewer than 500 features or a mitochondrial content higher than 20%.
Data from each sample were SCT normalisedand scaled, before batch correction using Seurat’s FindIntegratedAnchors.
To evaluate the expression of the 11 surface protein, the antibody-derived tags (ADT) counts for the cells retained after filtering were loaded in the integrated seurat object and normalised using the CLR normalisation method.
BCR reads were aligned to the GRCh38 reference genome (vdj_GRCh38_alts_ensembl-5.0.0) and consensus BCR annotation was performed using the cellranger vdj program (v8.0.0)
Assembly: GRCh38-2020-A and vdj_GRCh38_alts_ensembl-5.0.0
Supplementary files format and content: h5 files contain the raw count matrix for each sample
Supplementary files format and content: the rds file contains the Seurat object of all integrated samples
Library strategy: VDJ-Seq

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated blood from five PAPS patients and two HD. Total B cells were isolated with the EasySep™ Human B-cell Isolation Kit (Stemcell Technologies). B cells were resuspended at 10x106/mL and incubated with Human TruStain FcX Fc Blocking reagent for 10min at 4°C. Cells were then incubated with the 10 following antibodies conjugated to an antibody-derived tag for 30 min at 4°C : CD19 (HIB19,TotalSeq, BioLegend) CD27 (0323), CD24 (ML5), CD38 (HIT2), CD5 (UCHT2), HLA-DR (L243), CD86 (IT2.2), IgM (MHM-88), IgD (IA6-2), CD21 (Bu32).
The scRNA-seq libraries were generated using Chromium Next GEM Single Cell 5’ V(D)J Reagent Kit v.1.1 with Feature Barcoding (10X Genomics) according to the manufacturer’s protocol. Gene expression (mRNA), ADT and VDJ BCR libraries were constructed. Briefly, cells were counted and up to 10 000 cells were loaded in the 10X Genomics Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq S2 flowcell (Illumina).

value: Peripheral blood

value: Primary cells

value: B cells

tag: group

value: control


title: WT, BAY 24HR, Rep1

status: Public on Oct 08 2024

type: SRA

city: Oslo

first: Jason

last: Matthews

address: Sognsvannsveien 9

department: Nutrition

country: Norway

institute: University of Oslo

library_source: transcriptomic

data_processing:
The raw RNA seq paired end fastq files were quantified using the Salmon tool (v1.10.1) with “libtype” flag as automatic and mm10 version of the Salmon index file. The index was generated using the salmon “index” flag with the mm10 transcripts fasta file supplied.
The “tximport” import function from the tximport package was used to import the Salmon quantification data for further processing including differential expression analysis using DeSeq2.
Assembly: mm10
Supplementary files format and content: There are three files including txi_length_data.txt, txi_abundance_data.txt and txi_counts_data.txt. These are generated by tximport function of R package tximport (v1.26.1)

molecule: total RNA

organism: Mus musculus

source_name: PyMT

growth_protocol: The PyMT cell line was isolated from a spontaneous mammary tumour that developed in mouse mammary tumour virus-Polyoma virus middle T-antigen (MMTV-PyMT) female mice on a C57BL/6 background. PyMT cells were cultured in Dulbecco’s Modified Eagle Media (Sigma-Aldrich), supplemented with 10% v/v fetal bovine serum (FBS; Sigma-Aldrich), 1% v/v penicillin-streptomycin (Sigma-Aldrich), and 1% v/v L-glutamine (Sigma-Aldrich). Cells were incubated at 37℃ and 5% CO2, in a 100% humidified environment and sub-cultured when they reached 80% confluency.

extract_protocol:
PyMT WT, AhrKO and LT-BAY cells were plated in a 12-well plate at a density of 1×105 cells/well in quadruplicates. Total RNA was isolated with the Aurum™ Total RNA isolation kit (BioRad), following manufacturer’s protocol.
Total RNA was isolated with the Aurum™ Total RNA isolation kit (BioRad), following manufacturer’s protocol.

treatment_protocol: PyMT AhrKO cells were generated using CRISPR/Cas9. Briefly, the guide oligos forward 5´‑CCTACGCCAGTCGCAAGCGG-3´ and reverse 5´‑CCGCTTGCGACTGGCGTAGG-3´ were annealed and ligated into the pSpCas9(BB)-2A-Puro (PX459) plasmid (Addgene, Watertown, MA, USA; plasmid #62988). PyMT cells were transfected with 4 µg of PX459 containing AHR gRNA. Forty-eight hours after transfection, cells were selected with 4 µg/ml puromycin for 5 days. PyMT PX459 cells which represent a pooled cell population were expanded. For the PyMT cells transfected with PX459 AHR gRNA we did single cell dilution cloning and isolated independent clones as previously described {Rasmussen, 2023 #3456}. After screening the clones for AHR activity, DNA was isolated, and the region surrounding the target site of the Ahr gene was amplified using forward: 5´- TGTTTCGTCGGTAGAGCAGT-3´ and reverse 5´-AGTCCTAGCCCCAATCAGTCT-3´. The presence of indels resulting in frame shift mutations was confirmed by DNA sequencing. PyMT cells transfected with PX459 vector with no gRNA and exposed to puromycin as described for AhrKO cells, were used as control cells in further experiments and will be referred to as WT cells. In addition, we generated long-term-BAY2416964 (LT-BAY) cells by supplementing the media of WT cells with 1 µM of BAY2416964 when the cells were sub-cultured for at least 6 weeks.

tag: cell line

value: PyMT

tag: cell type

value: breast cancer cell

tag: genotype

value: WT

tag: treatment

tag: time


title: LT-BAY, DMSO, Rep4

value: 6 weeks


title: CRC P1 TIL ADT

city: Portland

first: Wesley

last: Rosales

state: OR

address: 4805 NE Glisan St

country: USA

institute: Earle A. Chiles Research Institute

library_source: other

data_processing:
CellRanger v7.0.1 (v6.1.2 for CRC P1-P4 samples) count  with "include_introns=false" parameter and vdj
Assembly: GRCh38-2020-A
Supplementary files format and content: CRC_CD8TIL_SeuratObject.rds.gz, HNSCC_CD8TILSeuratObject.rds.gz: Seurat objects containing normalized count data, dimension reductions, clustering, and TCR information
Supplementary files format and content: CRC_CD8TIL_metadata.csv, HNSCC_CD8TIL_metadata.csv: Metadata for each cell present in seurat object including cluster, patient ID, etc.
Supplementary files format and content: CRC_CD8TIL_AData.h5ad.gz, HNSCC_CD8TIL_AData.h5ad.gz: Anndata object containing spliced and unspliced gene counts of CD8 T cells.
Supplementary files format and content: CRC_CD8TIL_RNACounts.rds.gz, HNSCC_CD8TIL_RNACounts.rds.gz: Raw mRNA count data of CD8 T cells
Supplementary files format and content: CRC_CD8TIL_ADTCounts.rds.gz, HNSCC_CD8TIL_ADTCounts.rds.gz: Raw ADT count data of CD8 T cells
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: Colorectal Cancer Tissue

extract_protocol:
Tumor digests from patients with CRC or HNSCC were stained for CD45 and CD3, and live (PI-) CD45+CD3+ T cells were FACS sorted into a 1.5 ml eppendorf containing 100 ul of MACS buffer.
Library was performed according to manufacturer's instructions (Chromium Next GEM Single Cell 5’ kit protocol, 10X genomics)

tag: tissue

value: Colorectal Cancer Tissue

tag: library type

value: ADT

tag: adt

value: TotalSeq-C antibodies (CD4, cat #344651 401 clone SK3; CD8, cat #344753 clone SK1; CD39, cat #328237 clone A1; CD103, cat #350233 402 clone Ber-ACT8; CD127, cat#351356 clone A019D5; CD25, cat#302649 clone BC96; PD-1, 403 cat#329963, clone EH12.2H7; ICOS, cat#313553 clone C398.4A)


title: LT-BAY, DMSO, Rep3


title: Y15, VDJ

description: 10x Genomics 3’


title: SI19, VDJ

description: 10x Genomics 3’

value: patient


title: LT-BAY, DMSO, Rep1


title: WT, DMSO, Rep4

value: DMSO


title: WT, DMSO, Rep3


title: LO17, VDJ

description: 10x Genomics 3’


title: ER16, VDJ

description: 10x Genomics 3’


title: SE12, VDJ

description: 10x Genomics 3’


title: WT, DMSO, Rep2


title: BL18, VDJ

description: 10x Genomics 3’


title: AHRKO, DMSO, Rep4

value: AHRKO


title: TI11, GEX

description: 10x Genomics 3’

data_processing:
Sequencing reads were demultiplexed and aligned to the human reference genome using the CellRanger Pipeline v8
Unfiltered RNA UMI counts were loaded into Seurat v4.0.1 (Stuart et al., 2019) for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fewer than 500 features or a mitochondrial content higher than 20%.
Data from each sample were SCT normalisedand scaled, before batch correction using Seurat’s FindIntegratedAnchors.
To evaluate the expression of the 11 surface protein, the antibody-derived tags (ADT) counts for the cells retained after filtering were loaded in the integrated seurat object and normalised using the CLR normalisation method.
BCR reads were aligned to the GRCh38 reference genome (vdj_GRCh38_alts_ensembl-5.0.0) and consensus BCR annotation was performed using the cellranger vdj program (v8.0.0)
Assembly: GRCh38-2020-A and vdj_GRCh38_alts_ensembl-5.0.0
Supplementary files format and content: h5 files contain the raw count matrix for each sample
Supplementary files format and content: the rds file contains the Seurat object of all integrated samples
Library strategy: CITE-Seq


title: WT, DMSO, Rep1


title: AHRKO, DMSO, Rep3


title: CRC P1 TIL GEX

molecule: polyA RNA

value: mRNA


title: Y15, GEX

description: 10x Genomics 3’


title: SI19, GEX

description: 10x Genomics 3’


title: TI11, VDJ

description: 10x Genomics 3’


title: ST13, GEX

description: 10x Genomics 3’


title: AHRKO, DMSO, Rep2


title: AHRKO, DMSO, Rep1


title: RFP 3

city: San Francisco

first: Bikem

last: Soygur

state: California

address: 35 Medical Center Way, Parnassus, RMB, PodB, 913D

department: Obstetrics, Gynecology & Reproductive Sciences

institute: UCSF

description:
RFP3
GFP_HighvsRFP_deg.csv
GFP_LowvsRFP_deg.csv

data_processing:
Raw fastq reads were processed using the program fastp to remove adapter sequences, poly-N reads, and low quality reads (based on Q20, Q30, and %GC scores).
Resulting cleaned reads were mapped to the mm10 reference genome (indexed using Hisat2) using the splice aware aligner Hisat2 (v2.0.5). The number of reads mapping to each gene was calculated using featureCounts v.1.5.0-p3. FPKM values were calculated for each gene, normalizing for gene length and sequencing depth.
Differential expression analysis was performed using DESeq2 (v.1.20.0), and adjusted p-values were calculated using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted p-value ≤ 0.05 were classified as differentially expressed.
Assembly: mm10
Supplementary files format and content: CSV files containing DESeq2 differential expression results for each pair wise comparison, prior to filtering for significant genes. Files also contain raw counts and FPKM normalized counts per sample.

source_name: Oocyte

extract_protocol:
Messenger RNA was purified from oocyte total RNA using poly-dT magnetic beads, and mRNA was fragmented.
First strand cDNA synthesis was carried out using random hexamer priming, followed by second strand cDNA synthesis. Fragment ends were repaired, A-tailed, and ligated with sequencing adapters, followed by size selection, amplification via PCR, and purification. Final libraries were quantified using Qubit, and run on an Agilent Bioanalyzer system to check for proper size distribution. Post QC, libraries were pooled and sequenced on an Illumina sequencing platform. Clustering of the index-coded samples was performed as per the manufacturer’s instructions, and libraries were subsequently sequenced to generate paired-end reads

treatment_protocol: MII oocytes were collected from 4-week-old Sycp3CreERT2/+; Rosa26nTnG/+ females  that were superovulated by injection of 5 IU of pregnant mare serum gonadotropin (PMSG) followed 48 hours later by 5 IU of human chorionic gonadotropin (hCG). 13 hours after hCG injection, females were euthanized, cumulus-oocyte complexes (COCs) were isolated from the oviduct in M2 media containing 4mg/ml BSA, then COCs were incubated in M2 media containing 0.3 mg/ml Hyaluronidase for 1 min to remove cumulus cells. Denuded oocytes were washed in M2 media containing BSA and transferred to glass-bottom petri dishes containing a drop of media. GFP and RFP expression were checked under an Olympus IX71 microscope with an attached Lumencor Sola Light Engine. Oocytes were hand-picked based on their GFP expression.

value: RFP

tag: Sex

value: female

tag: age

value: Oocyte

value: Sycp3CreERT2/+; Rosa26nT-nG/+

tag: background

value: Mixed genetic background


title: LT-BAY, DMSO, Rep2


title: LO17, GEX

description: 10x Genomics 3’

value: Peripheral blood

value: Primary cells

value: B cells


title: RFP 1

description:
RFP1
GFP_HighvsRFP_deg.csv
GFP_LowvsRFP_deg.csv


title: S14, VDJ

description: 10x Genomics 3’

value: control


title: ER16, GEX

description: 10x Genomics 3’


title: GFP High 3

description:
GFPH3
GFP_HighvsGFP_Low_deg.csv
GFP_HighvsRFP_deg.csv

value: GFP High


title: GFP Low 2

description:
GFPL2
GFP_HighvsGFP_Low_deg.csv
GFP_LowvsRFP_deg.csv

value: GFP Low


title: GFP Low 1

description:
GFPL1
GFP_HighvsGFP_Low_deg.csv
GFP_LowvsRFP_deg.csv


title: S14, GEX

description: 10x Genomics 3’


title: SE12, GEX

description: 10x Genomics 3’


title: pDC_3

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: ileum

extract_protocol:
Total RNA was extracted from cells with TRIzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: ileum

value: plasmacytoid dendritic cells

value: Female


title: BL18, GEX

description: 10x Genomics 3’

value: patient


title: GFP Low 3

description:
GFPL3
GFP_HighvsGFP_Low_deg.csv
GFP_LowvsRFP_deg.csv


title: cDC1_3

value: type1 conventional dendritic cells


title: cDC2_3

value: type2 conventional dendritic cells


title: GFP High 2

description:
GFPH2
GFP_HighvsGFP_Low_deg.csv
GFP_HighvsRFP_deg.csv


title: Mac_3

value: macrophages


title: pDC_2

value: Male


title: GFP High 1

description:
GFPH1
GFP_HighvsGFP_Low_deg.csv
GFP_HighvsRFP_deg.csv

value: female

value: Oocyte


title: cDC1_2


title: cDC2_2


title: Neuro2a, Serum free

city: Salt Lake City

first: Justin

last: English

state: UT

address: 15 N Medical Drive East, Rm 4100

department: Biochemistry

institute: University of Utah

data_processing:
Barcodes were obtained by collecting the first 24 nucleotides of each read from demultiplexed fastq files.
Paired-end reads were trimmed using TrimGalore and joined using FastQ-Join.
Barcodes were clustered within each sample via Starcode using a Levenshtein distance of one.
Assembly: Custom barcode dictionary.
Supplementary files format and content: finalBarcodeMap.csv contains the barcode sequences and associated candidate transcriptional response elements
Supplementary files format and content: rpms.csv contains the barcode reads per million for each treatment and plasmid library

source_name: Brain

growth_protocol: Cell lines were maintained in maintenance media (typically DMEM supplemented with 10% FBS and antibiotics) in a 37C humidified incubator with 5% carbon dioxide.

extract_protocol:
RNA was isolated from cell pellets using the AllPrep DNA/RNA Mini Kit (Qiagen) with QIAshredder columns (Qiagen).
RNA libraries were prepared using the Superscript IV One-Step RT-PCR System (Invitrogen) with custom primers. DNA libraries from plasmid inputs were prepared using the Platinum SuperFI II Green PCR Master Mix (Invitrogen) with custom primers.

treatment_protocol: Cells on 10 cm dishes were transfected with 10 micrograms of the TRE-MPRA plasmid library when subconfluent.Six hours after transfection, the maintenance media was replaced with serum-free media. The following day, cells were treated for six hours. Cells were then trypsinied and pellets were frozen at -80 C until processing.

value: Brain

value: Epithelial

value: adult


title: Neuro2a, Fetal bovine serum

value: 10% fetal bovine serum


title: RFP 2

description:
RFP2
GFP_HighvsRFP_deg.csv
GFP_LowvsRFP_deg.csv

value: RFP

value: Sycp3CreERT2/+; Rosa26nT-nG/+

value: Mixed genetic background


title: Control group rep2 TCR

city: Tianjin

first: Yihan

last: Mei

address: Nanjing road

country: China

institute: Peking union medical school

description:
10X genomics
Con_2_TCR

data_processing:
The gene count matrix was created using the Cell Ranger toolkit (version 6.1.2, https://www.10xgenomics.com/support/software/cell-ranger/latest ).
Assembly: GRCm38
Supplementary files format and content: barcode.tsv.gz: llist of cell varcodes; features.tsv.gz: list of gene IDs; matrix.mtx.gz: gene expression

molecule: other

source_name: Bone marrow

extract_protocol:
To harvest bone marrow, place the euthanized mouse in a supine position and sterilize the skin using ethanol. The Ilium\femur\fibula bones were cut off, ground in cold complete buffer (PBS with 2% fetal bovine serum (FBS) and 10mmol/L EDTA), and filtered through a 40 mm strainer. Then, gradient centrifugation (400G, 5min) was carried out and resuspended. EasySep™ Mouse T Cell Isolation Kit (STEMCELL, Cat # 19851) was applied to T cell negative enrichment. The enriched T cells were stained with the antibody against mouse CD3 and DAPI. DAPI- mCherry- CD3+ cells were sorted in both groups by flow cytometry with a BD FACSAria™ III sorter (BD Biosciences) for the scRNA-seq library.
Single-cell RNA-seq libraries were prepared using the 10 Chromium Single-cell 5’ and VDJ library construction (10 Genomics), following the manufacturer’s instructions. Purified libraries were subject to NovaSeq 6000 sequencer (Illumina) for 150-bp paired-end sequencing.

value: Bone marrow

tag: strain

value: WT

value: TCR


title: Control group rep1 TCR

description:
10X genomics
Con_1_TCR


title: pDC_1

value: ileum

value: plasmacytoid dendritic cells

value: Female


title: Mac_2

value: macrophages


title: RUNX1::RUNX1T1 group rep1 TCR

description:
10X genomics
AEKI_1_TCR


title: RUNX1::RUNX1T1 group rep2 TCR

description:
10X genomics
AEKI_2_TCR


title: cDC2_1

value: type2 conventional dendritic cells


title: Control group rep2

description:
10X genomics
Con_2

library_source: transcriptomic single cell

value: mRNA


title: cDC1_1

value: type1 conventional dendritic cells


title: Mac_1


title: RUNX1::RUNX1T1 group rep2

description:
10X genomics
AEKI_2


title: Control group rep1

description:
10X genomics
Con_1


title: KRAS pancreatic organoids overexpressing SPIB, replicate 2, RNA-seq

city: New York

first: Giovanni

last: Valenti

address: 1130 St Nicholas Ave

institute: Columbia University

data_processing:
We use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes values files includes EST counts each sample
Supplementary files format and content: Tab-delimited text file includes TPM for each sample

source_name: Pancreas

growth_protocol: Organoids were grown from single cells suspension from murine pancreas and maintained in culture medium in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA for RNA-seq was harvested from organiod with Rneasy mini plus kit (Qiagen)
Library was performed according to the manufacter's instructions (Illumina TruSeq Stranded mRNA kit)

value: Pancreas

value: Organoids

tag: genetic modification

value: KRAS/SPIB

value: Day 7


title: H69AR cells, siCtrl, rep 3

city: Philadelphia

first: Israel

last: Canadas

state: PA

address: 333 Cottman Ave.

department: Nuclear Dynamics and Cancer Program

institute: Fox Chase Cancer Center

data_processing:
Paired-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R.
Assembly: hg19
Supplementary files format and content: Expression data in excel format

extract_protocol:
Total RNAs were extracted and purified using the Rneasy MiniKit (QIAGEN) from the cells at day 3 post-transfection. Using a 2100 Bioanalyzer RNA 6000 Nano assay (Agilent), quality of RNA was assessed. RNA concentration was measured using a Qubit 2.0 Fluorometer (Life Technologies).
Illumina sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: Cells were transfected with siCtrl or siTREX1.

value: Small Cell Lung Cancer

value: siCtrl


title: KRAS pancreatic organoids overexpressing SPIB, replicate 1, RNA-seq


title: H69AR cells, siTREX1, rep 3


title: H69AR cells, siTREX1, rep 2


title: KRAS pancreatic organoids, replicate 2, RNA-seq

value: KRAS


title: H69AR cells, siTREX1, rep 1


title: H69AR cells, siCtrl, rep 1


title: RUNX1::RUNX1T1 group rep1

description:
10X genomics
AEKI_1

value: Bone marrow


title: Dclk1-ZSGreen+/TdTomato+ cells from pancreas at 2 wks after KRAS activation, scRNAseq

description: 10x Genomics

data_processing:
Singe-cell RNA sequencing data were analyzed using the 10X CellRanger software (10x Genomics). Samples were combined using the Cell Ranger aggregate function. Gene-cell matrix was filtered to remove cells with less than 1000 transcripts and/or a high fraction of mitochondrial counts (>20%). The gene-cell matrix was then normalized to count per million of reads (cpm).
Assembly: mm10
Supplementary files format and content: Tab-separated values files

extract_protocol:
Pancreas from Dclk1-DTR-ZSGreen, Mist1-Kras-TdTomato-Dclk1-DTR-ZSGreen mice at 2 weeks after KRAS activation and Mist1-Kras-TdTomato-Dclk1-DTR-ZSGreen mice16 weeks after KRAS activation were collected in ice-cold HBSS. Pancreas were dissociated with a scalpel and incubated in digestion medium (DMEM high glucose GlutaMAX, 1 mg/ml Collagenase P, 10 mM HEPES, Antibiotic-Antimycotic) at 37°C for 20 minutes with shacking. Isolated cells were then incubated in Accutase at 37°C for 5 minutes and filtered with 40 µm filters. Red blood cells were lysed by incubating cells in ACK lysing buffer on ice for 5 minutes. Cells were washed and resuspended in ice-cold PBS/0.5% BSA. DAPI was added for vital staining. Vital Dclk1 cells were sorted using FACS Aria II (Becton Dickinson) according to the presence of ZGreen and TdTomato signals using a C57BL/6-J mouse as negative control. Sorted cells were collected and immediately delivered for sequencing.
Library was performed according to the manufacter's instructions (10x Genomics)

value: Dclk1 cells

value: 10 weeks old


title: cropseq_hek293T_library1_grna

city: Durham

first: Charles

last: Gersbach

state: NC

address: 2127 Campus Drive

institute: Duke University

description:
293T_LRB100_NTlib1_barcodes.tsv.gz
293T_LRB100_NTlib1_features.tsv.gz
293T_LRB100_NTlib1_matrix.mtx.gz

data_processing:
Each lane of cells was processed using cellranger (version 6.0.1) count using default parameters and mapping to the GRCh38-and-mm10-2020 reference genome from 10x Genomics
Assembly: GRCh38-and-mm10-2020
Supplementary files format and content: Sparse matrices in Market Exchange (MEX) format for UMI counts for each barcode/gene or barcode/gRNA pair. Files are barcodes.tsv: This file contains the barcodes represented in the mtx file. genes.tsv: This file contains all annotated genes and gRNAs. matrix.mtx:  contained the "gene id" index, "cell id" index, and the total UMI count per cell and gene/gRNA combination.
Supplementary files format and content: R1/R2/I1/I2 .fastq files for lane 1 and 2 of the sequencing run. Read 1 contains UMI and cell barcode information. Read 2 contains the RNA transcript sequence.

growth_protocol: All cells were grown at 37°C. HEK293T/17 cells were cultured in DMEM + 10% FBS and NIH3T3 cells were cultured in DMEM + 10% CBS.

extract_protocol:
cells were washed three times, trypsinized, and strained through a 40 µm cell strainer
Approximately 10,000 cells were captured per lane of a 10x Chromium chip (Next GEM Chip G) using Chromium Next GEM Single Cell 3ʹ HT Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening (10x Genomics, Inc, Document number CG000418, Rev D). CROP-seq protospacer sequences were amplified from barcoded cDNA.


title: Dclk1-ZSGreen+ cells from pancreas at 2 wks after KRAS activation, scRNAseq

description: 10x Genomics


title: direct_capture_hek293T_library1_grna

description:
293T_MCH2_NTlib1_barcodes.tsv.gz
293T_MCH2_NTlib1_features.tsv.gz
293T_MCH2_NTlib1_matrix.mtx.gz


title: cropseq_hek293T_library1_gene_exp


title: direct_capture_hek293T_library1_gene_exp


title: KRAS pancreatic organoids, replicate 1, RNA-seq


title: Dclk1-ZSGreen+/TdTomato+ cells from pancreas at 16 wks after KRAS activation, scRNAseq

description: 10x Genomics

value: 24 weeks old


title: H69AR cells, siCtrl, rep 2


title: Dclk1-ZSGreen+ cells from normal pancreas, scRNAseq

description: 10x Genomics

value: 8 weeks old


title: ips, DupExon8-9, edited [dup8-9cl12-3]

city: EVRY-COURCOURONNES

first: Tao

last: WANG

state: France

address: 1 bis, rue de l’Internationale

department: R & D

institute: genethon

data_processing:
paired-end reads were aligned to the reference transcriptome using STAR version  2.7.11b using default settings and Gene expression was measured by featureCounts version 2.0.6
Read count extraction was performed using R 4.3.0 and the tximport package (v1.28.0)
Differential gene expression was performed using R and the package DESeq2 (v1.40.1) and using arguments lfcThreshold = 0, pAdjustMethod = "fdr", independentFiltering = T
Assembly: GRCh38.p13 / transcriptome gencode.v43
Supplementary files format and content: tab-delimited file containing counts per gene (row) and sample (columns) from tximport function

source_name: IPS

extract_protocol:
Total RNA extraction was performed from myotubes (at day 8 of differentiation) lysates using the RNeasy Plus kit (Qiagen). Total RNA concentration was quantified using a Nanodrop spectrophotometer (ND8000 Labtech, Wilmington Delaware). The RNA quality was evaluated using an Agilent RNA 6000 Pico Kit on a 2100 Bioanalyzer instrument (Agilent Technologies) and Illumina RNA seq was performed on three replicates of each selected clone.
The sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced according to the Illumina NovaSeq™ 6000 protocol.
sequencing performed by Azenta using NovaSeq 2x150

value: IPS

value: edited


title: ips, DupExon2-9, edited [dup2-9cl14-3]


title: BB-p53n EZH2i 3

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
reads were trimmed with trimmomatic
alignment done with subjunc (subread package) against the mm39 genome
genes counted with featureCounts (subread package) using the Ensembl annotation (Mus_musculus.GRCm39.108)
Assembly: mm39
Supplementary files format and content: tab delimited text format of read counts assigned to Ensembl annotated features

source_name: OPC

growth_protocol: mutant primary OPC lines were maintained in SATO media supplemented with 10ng/mL PDGF-AA (Dulbecco's modified Eagle's medium (DMEM), 10 mg/ml bovine serum albumin (BSA), 10 mg/ml apotransferrin, 1.6 mg/ml putrescine, 6 ng/ml progesterone, 4 μg/ml selenium, 5 mg/ml insulin, 1 mM sodium pyruvate, 2 mM l-glutamine, 100 U/ml penicillin, 100 g/ml streptomycin, 5 mg/ml N-acetyl-cysteine, Trace Element B, 10 μg/ml biotin, 50 mM forskolin)

extract_protocol:
total RNA was extracted with Trizol (invitrogen) and then purified with Qiagen RNeasy minElute cleanup kit
For RNA-sequencing, approximately 500ng of total RNA per sample was used for library construction with the Kapa mRNA HyperPrep Kit (Roche) and sequenced using the Illumina NovaSeq 6000 instrument according to the manufacturer’s instructions for 150 bp paired-end read runs.

treatment_protocol: BB-p53n OPCs were treated with 5uM Tazemetostat (from Selleck EZH2i) for 48 hours in normal SATO media supplemented with PDGF-AA. 1/10,000 dilution of DMSO added to BB-p53n OPCs for vehicle controls.

value: OPC

value: primary cells

value: 5uM Tazemetostat


title: BB-p53n EZH2i 2


title: ips, DupExon2-9, untreated [dup2-9-3]

value: untreated


title: BB-p53n EZH2i 1


title: ips, DupExon2, edited, [dup2cl7-3]


title: BB-p53n DMSO 2

value: DMSO vehicle


title: BB-p53n DMSO 3


title: ips, WT [C25-3]

value: WT


title: BB-p53n DMSO 1


title: Dclk1-ZSGreen+ cells from pancreas at 16 wks after KRAS activation, scRNAseq

description: 10x Genomics

value: Pancreas


title: ips, DupExon8-9, edited [dup8-9cl12-2]


title: ips, DupExon2-9, edited [dup2-9cl14-2]


title: p53n OPC 1

value: control


title: p53n OPC 3


title: ips, DupExon2, untreated [dup2-2]


title: gut, FCDSS3r1, RNAseq

city: Shanghai

first: Yue

last: Yin

address: NO.650 Xin Songjiang Road, Shanghai, P.R.China

institute: Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
TopHat software (version 2.0.0)
The library was then subjected to sequencing on the Illumina HiSeq xten/NovaSeq 6000 platform, with a read length of 2 × 150 base pairs.
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Differential expression genes (DEGs) were identified by calculating the expression of each transcript based on the fragments per kilobase of exon per million mapped reads (FPKM) method.
Assembly: mm10
Supplementary files format and content: tab-delimited tex fle includes raw counts for each Sample

source_name: FcεRIα knockout (FC)

extract_protocol:
TRIzol® Reagent (Invitrogen) was used under the manufacturer's directions, followed by the removal of genomic DNA using DNase I (TaK).
The preparation of the RNA-seq transcriptome library was achieved with the TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA).

value: intestine

value: balb/c

value: FC


title: ips, DupExon8-9, untreated [dup8-9-2]


title: ips, WT [C25-2]


title: gut, FCDSS1r1, RNAseq


title: ips, DupExon8-9, edited [dup8-9cl12-1]


title: gut, WTDSS3r1, RNAseq

source_name: wild type


title: gut, WTDSS1r1, RNAseq


title: ips, DupExon8-9, untreated [dup8-9-1]


title: gut, WTDSS2r1, RNAseq


title: ips, DupExon2, untreated [dup2-3]


title: ips, DupExon2-9, edited [dup2-9cl14-1]


title: sperm HCD PANDORA-seq rep 3

city: Riverside

first: Changcheng

last: Zhou

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

description: RNAs were treated with T4PNK, then AlkB before cDNA library construction.

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with ploy A.; and 7) the reads shorter than 15 nt and longer than 45 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: sperm

growth_protocol: 3 week old LDLR-/- male mice were fed a low cholesterol or high cholesterol diet for 9 weeks

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol: small RNA-seq processed with PANDORA-seq were treated wih AlkB and PNK4

value: sperm

value: LDLRKO

value: high cholesterol diet

value: 9 weeks


title: ips, DupExon2-9, untreated [dup2-9]

value: IPS


title: ips, DupExon2-9, untreated [dup2-9-2]


title: sperm HCD PANDORA-seq rep 2


title: ips, DupExon2, edited, [dup2cl7-1]

value: edited


title: ips, DupExon2, edited, [dup2cl7-2]


title: p53n OPC 2

value: OPC


title: sperm HCD PANDORA-seq rep 1


title: HEK293, DRD2 and dopamine

source_name: Kidney

value: Kidney

value: Epithelial

value: fetal

value: Female

value: 30 uM dopamine


title: gut, FCDSS2r1, RNAseq


title: HEK293, DRD2


title: sperm LCD PANDORA-seq rep 3

value: low cholesterol diet


title: sperm HCD traditional rep 3

description: RNAs were sequenced with standard protocols.


title: ips, WT [C25-1]

value: WT

value: untreated


title: ips, DupExon2, untreated [dup2-1]


title: sperm HCD traditional rep 2


title: sperm LCD PANDORA-seq rep 1


title: HEK293, DRD1


title: sperm LCD traditional rep 3


title: sperm LCD traditional rep 2


title: sperm LCD PANDORA-seq rep 2


title: ips, DupExon8-9, untreated [dup8-9-3]


title: HeLa, Fetal bovine serum

source_name: Cervical carcinoma

value: Cervical carcinoma

value: HeLa

value: adult

value: 10% fetal bovine serum


title: HEK293, OPRM1 and morphine

value: 100 nM morphine


title: sperm LCD traditional rep 1

value: sperm

value: LDLRKO

value: 9 weeks


title: HeLa, Serum free


title: sperm HCD traditional rep 1

value: high cholesterol diet


title: intima HCD female rep 5 [F1HCD11]

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample ...

source_name: Intima

growth_protocol: 3 week old LDLR-/- male mice were fed a low cholesterol or high cholesterol diet for 8 weeks before mating with LDLR-/- females. F1 generation were fed a low cholesterol diet from 3-19 weeks old

extract_protocol:
Total RNA was isolated from the intima by flushed the aorta with TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intima

value: female

value: Paternal HCD


title: intima HCD female rep 4 [F1HCD10]


title: intima HCD female rep 3 [F1HCD9]


title: MDA-MB-231, Serum free

source_name: Mammory gland

value: Mammory gland

value: Epithelial

value: Female


title: intima HCD female rep 2 [F1HCD8]


title: HEK293, Thapsigargin

value: Kidney

value: fetal

value: 2 uM thapsigargin


title: A375, Fetal bovine serum

source_name: Melanoma

value: Melanoma


title: MDA-MB-231, Fetal bovine serum

value: adult


title: A375, Serum free


title: intima HCD female rep 1 [F1HCD7]


title: intima HCD male rep 4 [F1HCD5]

value: male


title: intima HCD male rep 3 [F1HCD4]


title: HEK293, DRD1 and dopamine

value: 30 uM dopamine


title: HEK293, MRGPRX2 and (R)-zn3573


title: HEK293, MRGPRX2


title: intima HCD male rep 5 [F1HCD6]


title: HEK293, ADRB2


title: HEK293, ADRB2 and epinephrine

value: 1 uM epinephrine


title: intima HCD male rep 2 [F1HCD2]

value: LDLRKO


title: intima LCD female rep 6 [F1LCD11]

value: Paternal LCD


title: HEK293, OPRM1


title: intima LCD female rep 5 [F1LCD10]


title: intima LCD female rep 7 [F1LCD12]


title: HEK293, PAR1 and thrombin

value: 10 nM thrombin


title: intima HCD male rep 1 [F1HCD1]

value: Intima


title: intima LCD female rep 4 [F1LCD9]

value: female


title: HEK293, eGFP, rep 1


title: HEK293, eGFP, rep 2


title: HEK293, HTR2A


title: intima LCD female rep 3 [F1LCD8]


title: HEK293, Desferoxamine

value: 100 uM desferoxamine mesylate


title: HEK293, PAR1


title: HEK293, Lithium chloride

value: 40 mM lithium chloride


title: intima LCD female rep 2 [F1LCD7]


title: intima LCD male rep 2 [F1LCD3]


title: HEK293, Dexamethasone

value: Epithelial

value: 100 nM dexamethasone


title: intima LCD female rep 1 [F1LCD6]


title: HEK293, Cadmium chloride

value: Kidney

value: Female

value: 30 uM cadmium chloride


title: HEK293, Zinc sulfate

value: fetal

value: 200 uM zinc sulfate


title: HEK293, eGFP and epinephrine


title: HEK293, HTR2A and 5-HT

value: 100 nM serotonin


title: intima LCD male rep 4 [F1LCD5]

value: male


title: intima LCD male rep 1 [F1LCD2]


title: HEK293, GPR91 and CES, rep 3

value: 30 uM cis-epoxy-succinate


title: Cultured MuSCs, MyoD High, rep3

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

institute: University of Tsukuba

description: 10x Genomics

data_processing:
feature-barcode matrices were generated by aligning the reads to the mouse genome (mm10 Ensemble: version 92) with CellRanger v3.1.0.
Assembly: GRCm39
Supplementary files format and content: tsv file and mtx file

source_name: skeletal muscle

growth_protocol: Mouse muscle stem cells were cultured in growth medium containing 39% DMEM, 39% Ham's F12, 20% fetal bovine serum (FBS), 1% Ultraser G with antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Approximately 10,000 cells were processed using the Chromium Next GEN Single Cell 3’Reagent Kits v3.1
RNA libraries for scRNA-seq were prepared using a chromium controller from10X Genomics, according to the manufacturer’s instructions.

treatment_protocol: Muscel stem cells from MyoD-KI mice were cultured for 5 days, then MyoD-tdTomato low and high populations were sored by a flowcytometer.

value: skeletal muscle

value: muscle stem cells

value: MyoD-tdTomato high

value: MyoD-KI

value: Culture for 5 days


title: intima LCD male rep 3 [F1LCD4]

value: Intima

value: LDLRKO

value: Paternal LCD


title: Cultured MuSCs, MyoD High, rep2

description: 10x Genomics


title: HEK293, AICAR

value: Epithelial

value: 100 uM 5-Aminoimidazole-4-carboxamide ribonucleotide


title: Cultured MuSCs, MyoD High, rep4

description: 10x Genomics


title: HEK293, GPR91 and CES, rep 2

value: Kidney

value: Female


title: Cultured MuSCs, MyoD High, rep1

description: 10x Genomics


title: HEK293, GPR91 and CES, rep 1

value: fetal


title: 60min Torin1 treatment biological replicate 2

city: Boston

first: Ryan

middle: Jared

last: Marina

state: MA

address: 45 Shattuck Street

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
Dataset1
TTseq_Torin1-60_F._normD1.07.bw
TTseq_Torin1-60_R._normD1.07.bw

data_processing:
TT-seq reads were filtered (mean quality score ≥20) and mapped to the Drosophila (dm6) genome using STAR (version 2.7.3a)
Reads not mapping to spike-in sequences were aligned to the mm10 genome and deduplicated using STAR
Gene counts were generated using the featureCounts function of the Rsubread package (version 2.0.1).
Differentially expressed genes and per-gene normalized counts values were then quantified using DESeq2 (version 1.26.0). Given comparable spike-recovery values between samples, normalization was performed using DESeq2 generated size factors. These normalization factors were also used to generate combined bedGraphs using bigWigMerge (UCSC).
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: bigWigs representing replicate-merged, spike-normalized read coverage.
Library strategy: TT-seq (4sU RNA-seq)

source_name: CY 2.4 Albino ES cells

extract_protocol:
RNA samples were harvested using TRIzol reagent (invitrogen) from cells metabolically labeled with 500 mM 4sU exactly at 10min to the end of the given length of treatments. RNA samples then were treated to remove residual DNA by using RNeasy Micro Kit (Qiagen, 74004) combined with Amplification Grade DNase I (18068015, Invitrogen) and Superase-In RNase inhibitor (AM2694, Thermo Fisher Scientific). RNA samples next were chemically fragmented by cold 5 × fragmentation solution at 94°C for 3.0 minutes and biotinylated as described in Duffy et al. (2015). After removing of the excess biotin, biotinylated RNA was heated at 65°C for 5min, placed on ice for 2 min, and mixed with 50 µl of Dynabeads MyOne Streptavidin C1 (Invitrogen, 65001). The Dynabeads engaged biotinylated RNA was eventually eluted and purified using Norgen RNA clean-up and concentration MicroElute kit (Norgen #61000) and for library construction.
Nascent RNA libraries for TT-seq were prepared using TruSeq RNA Library Preparation Kit v2, Set A and B following manufacturer's protocol.

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

value: Torin1 treatment


title: 60min Torin1 treatment biological replicate 3


title: HEK293, GPR91, rep 2


title: 60min Torin1 treatment biological replicate 1


title: HEK293, GPR91, rep 1


title: HEK293, ATP/GTP sample 3

value: 50 uM ATP/GTP


title: 30min Torin1 treatment biological replicate 2

description:
Dataset1
TTseq_Torin1-30_F._normD1.16.bw
TTseq_Torin1-30_R._normD1.16.bw


title: 30min Torin1 treatment biological replicate 1


title: 30min Torin1 treatment biological replicate 3


title: HEK293, ATP/GTP sample 2


title: 15min Torin1 treatment biological replicate 2

description:
Dataset1
TTseq_Torin1-15_F._normD1.09.bw
TTseq_Torin1-15_R._normD1.09.bw


title: HEK293, Forskolin, rep 1

value: 20 uM forskolin


title: HEK293, Fetal bovine serum, rep 3

value: 10% fetal bovine serum


title: HEK293, Forskolin, rep 3


title: HEK293, ATP/GTP sample 1


title: HEK293, GPR91, rep 3


title: Control for 60min Torin1 treatment biological replicate 3

description:
Dataset1
TTseq_Control-60_F._normD1.09.bw
TTseq_Control-60_R._normD1.09.bw

value: WT control for Torin1 treatment

value: DMSO


title: Control for 60min Torin1 treatment biological replicate 2


title: 15min Torin1 treatment biological replicate 1


title: HEK293, Forskolin, rep 2


title: HEK293, Fetal bovine serum, rep 1


title: Control for 30min Torin1 treatment biological replicate 3

description:
Dataset1
TTseq_Control-30_F._normD1.08.bw
TTseq_Control-30_R._normD1.08.bw


title: HEK293, Serum free, rep 8


title: Control for 15min Torin1 treatment biological replicate 3

description:
Dataset1
TTseq_Control-15_F._normD1.00.bw
TTseq_Control-15_R._normD1.00.bw


title: HEK293, Serum free, rep 7


title: HEK293, Serum free, rep 6


title: Control for 30min Torin1 treatment biological replicate 2


title: Control for 30min Torin1 treatment biological replicate 1


title: 15min Torin1 treatment biological replicate 3


title: Control for 15min Torin1 treatment biological replicate 1


title: Control for 60min Torin1 treatment biological replicate 1


title: HEK293, Serum free, rep 3


title: HEK293, Serum free, rep 4


title: HEK293, Fetal bovine serum, rep 2


title: HEK293, Serum free, rep 1


title: HEK293, Serum free, rep 2


title: Control 60min DMSO  biological replicate 3

description:
dataset1
mm10_mESC_PROseq_CONT_60m_5pr_F.bedGraph.bz2
mm10_mESC_PROseq_CONT_60m_5pr_R.bedGraph.bz2
mm10_mESC_PROseq_CONT_60m_3pr_F.bedGraph.bz2
mm10_mESC_PROseq_CONT_60m_3pr_R.bedGraph.bz2

data_processing:
Unique molecular identifiers (UMIs) were extracted using UMI tools (version 1.1.2)
Read pairs were adapter trimmed using cutadapt (version 1.14)
UMI length (6) was trimmed off ends of both reads and an additional nucleotide (7) was removed from read 1 (R1) using seqtk trimfq.
Data was mapped to a combined dm6 (spike) and mm10 (reference) genome using bowtie (version 1.2.2)
Reads mapping to mm10 were deduplicated using UMI sequences, sorted using samtools (version 1.3.1)
Reference reads were separated into 5’ and 3’ end reads and subsequently converted to strand-specific bedGraph format using a custom script (bowtie2stdBedGraph.pl). For R1 (3’ end), “+” and “-“ strand orientations were swapped to generate accurate 3’ end positions.
Data was normalized to spike-in read number to adjust for sample-specific variability in nascent transcription and sequencing depth
Assembly: mm10
Supplementary files format and content: bedGraph
Supplementary files format and content: bedGraphs representing normalized 5’ and 3' ends of RNA combined from all replicates
Library strategy: PRO-seq

extract_protocol:
For nascent RNA, cells were permeabilized as described in Mimoso and Adelman, 2023.
Nuclear run-on with biotinylated NTPs and RNA purification was performed. Extracted RNAs were then ligated with sequencing adapters and amplified by PCR.

value: WT control


title: Control 60min DMSO  biological replicate 2


title: GBM cell line LN827 sensitive cells received TTFields for 24 hours batch 2 replicate 3

city: Los Angeles

first: David

last: Tran

state: CA

address: 1441 Eastlake Ave

department: Department of Neurological Surgery

institute: University of Southern California

description:
GBM cell line LN827 sensitive cells received TTFields for 24 hours
LN827T24_2_3

data_processing:
Paired-end reads were trimmed with trimmomatic v/0.36, and alignment and gene counts generated against the GRCh38.p12 genome assembly using the annotation GeneCode release 28 by STAR v2.6.0b with default options and quantmode=GeneCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited csv file includes raw counts for each Sample
Supplementary files format and content: tab-delimited csv file include TPM values for each Sample
Supplementary files format and content: tab-delimited csv file include CPM values for each Sample
Supplementary files format and content: tab-delimited csv file include RPKM values for each Sample

growth_protocol: GBM cell lines were grown in DMEM supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
RNA was extracted utilizing QIAGEN RNeasy Midi Kit (Cat#75144) according to the manufacturer’s instructions.
Illumina TruSeq Stranded mRNA Library Prep Kit was used by NOVOGENE.
End repair, A-tailing, adaptor ligation

treatment_protocol: GBM cells were treated with TTFields at the clinically approved frequency of 200 kHz

value: GBM cell line

tag: code

tag: batch

tag: replicate

value: TTFields

tag: time point

value: 24 hours


title: Control 60min DMSO  biological replicate 1

tag: cell line


title: GBM cell line LN827 sensitive cells received TTFields for 24 hours batch 2 replicate 1

description:
GBM cell line LN827 sensitive cells received TTFields for 24 hours
LN827T24_2_1

tag: cell type


title: GBM cell line LN827 sensitive cells received TTFields for 24 hours batch 2 replicate 2

description:
GBM cell line LN827 sensitive cells received TTFields for 24 hours
LN827T24_2_2


title: DRG neurons, MSMP depletion, replicate1

city: London

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Samples were de-multiplexed using Bcl2Fastq and then aligned to the mouse GRCm39 genome reference. Sample de-multiplexing, sequence alignment, barcode processing and single cell 3’ unique molecular identifier (UMI) counting were performed by using Cell Ranger Software Suite (v7.1.0).
Assembly: mouse GRCm39 genome
Supplementary files format and content: comma-separated values and matrix files

source_name: DRG

extract_protocol:
Muscle spindle macrophages (MSMP) were FACS-sorted from Pv:ChR2 mice after optogenetically activating proprioceptive neurons. L4-6 DRGs were freshly dissected from MSMP depletion mice and homogenised with homogenisation buffer. Neuronal nuclei from homogenised DRG were sorted by FACS.
Sorted MSMP or DRG neuronal nuclei were collected in cold PBS and processed for 10x single-cell RNA sequencing according to 10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) protocol. The library of MSMP or DRG was sequenced by Illumina NovaSeq 6000 platform. read length 150bp

value: DRG

value: Neuronal nuclei

tag: genotype

value: WT

tag: condition

value: MSMP depletion


title: HEK293, Serum free, rep 5

value: Kidney

value: Epithelial

value: fetal

value: Female


title: DRG neurons, MSMP depletion, replicate3


title: DRG neurons, control, replicate3

value: control


title: Control for 15min Torin1 treatment biological replicate 2

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

tag: treatment


title: GBM cell line LN827 sensitive cells received TTFields for 6 hours batch 2 replicate 3

description:
GBM cell line LN827 sensitive cells received TTFields for 6 hours
LN827T6_2_3

value: 6 hours


title: GBM cell line LN827 sensitive cells received TTFields for 6 hours batch 2 replicate 2

description:
GBM cell line LN827 sensitive cells received TTFields for 6 hours
LN827T6_2_2


title: GBM cell line LN827 sensitive cells received TTFields for 6 hours batch 2 replicate 1

description:
GBM cell line LN827 sensitive cells received TTFields for 6 hours
LN827T6_2_1


title: GBM cell line LN827 Control cells without any treatment batch 2 replicate 2

description:
GBM cell line LN827 Control cells without any treatment
LN827C_2_2

value: C

value: NT

value: 0 days


title: Muscle spindle macrophages, optogenetic activation of proprioceptive neurons, replicate3

source_name: Muscle

tag: tissue

value: Muscle

value: Macrophages

value: optogenetic activation activation of proprioceptive neurons


title: GBM cell line LN428 sensitive cells received TTFields for 24 hours batch 2 replicate 3

description:
GBM cell line LN428 sensitive cells received TTFields for 24 hours
LN428T24_2_3

value: GBM cell line

value: TTFields

value: 24 hours


title: DRG neurons, control, replicate1

value: DRG

value: Neuronal nuclei

value: WT


title: GBM cell line LN428 sensitive cells received TTFields for 24 hours batch 2 replicate 1

description:
GBM cell line LN428 sensitive cells received TTFields for 24 hours
LN428T24_2_1


title: Muscle spindle macrophages, optogenetic activation of proprioceptive neurons, replicate1


title: Muscle spindle macrophages, control, replicate3


title: Muscle spindle macrophages, control, replicate2


title: DRG neurons, MSMP depletion, replicate2

value: MSMP depletion


title: GBM cell line LN428 sensitive cells received TTFields for 6 hours batch 2 replicate 3

description:
GBM cell line LN428 sensitive cells received TTFields for 6 hours
LN428T6_2_3


title: Muscle spindle macrophages, optogenetic activation of proprioceptive neurons, replicate2


title: Mouse muscle spindle macrophages, replicate4

data_processing:
Sequences were demultiplexed and adapters trimmed with bcl2fastq-v2.20 (Illumina).
Read quality controls were carried out using FastQC-v0.11.9, trimming reads less than Phred33 quality score 20 and removing remaining adapters with Trim-Galore (v0.6.6).
RNA-seq analysis was run using the COMBINE lab’s Salmon-DESeq2 pipeline. Salmon-v1.6.0 was used in mapping-based mode to quantify read sets.
Reads were mapped to the M25 GENCODE reference mouse genome.
Differential gene expression analysis was carried out using DESeq2-v1.34.0 in R-v4.1.2.
Assembly: M25

source_name: Muscle spindle macrophages

extract_protocol:
Laser capture micro-dissected muscle tissues or macrophages sorted from muscles, hearts and lungs were processed for RNA extraction. RNA was extracted by using RNeasy micro-kit and DNase on-column digestion (Qiagen) following the manufacturer’s guidelines.
RNA with a RIN factor above 8 was used for library preparation. cDNA libraries for each sample were generated at Source Bioscience Laboratory (Cambridge, UK) by using NEBNext Single Cell/Low Input Library Prep Kit (Ilumina).
read length 150 bp

value: Muscle spindle macrophages


title: GBM cell line LN827 Control cells without any treatment batch 2 replicate 1

description:
GBM cell line LN827 Control cells without any treatment
LN827C_2_1


title: Mouse muscle spindle macrophages, replicate3


title: GBM cell line LN428 Control cells without any treatment batch 2 replicate 1

description:
GBM cell line LN428 Control cells without any treatment
LN428C_2_1


title: GBM cell line LN428 Control cells without any treatment batch 2 replicate 2

description:
GBM cell line LN428 Control cells without any treatment
LN428C_2_2


title: Mouse muscle spindle macrophages, replicate2


title: GBM cell line U87 sensitive cells received TTFields for 24 hours batch 2 replicate 3

description:
GBM cell line U87 sensitive cells received TTFields for 24 hours
U87T24_2_3


title: Mouse muscle spindle macrophages, replicate1


title: GBM cell line LN428 sensitive cells received TTFields for 24 hours batch 2 replicate 2

description:
GBM cell line LN428 sensitive cells received TTFields for 24 hours
LN428T24_2_2


title: DRG neurons, control, replicate2

value: control


title: Muscle spindle macrophages, control, replicate1


title: Mouse lung macrophages, replicate3

source_name: Lung macrophages

value: Lung macrophages


title: GBM cell line LN428 sensitive cells received TTFields for 6 hours batch 2 replicate 1

description:
GBM cell line LN428 sensitive cells received TTFields for 6 hours
LN428T6_2_1

value: 6 hours


title: Mouse lung macrophages, replicate4


title: GBM cell line U87 sensitive cells received TTFields for 6 hours batch 2 replicate 3

description:
GBM cell line U87 sensitive cells received TTFields for 6 hours
U87T6_2_3


title: GBM cell line LN428 sensitive cells received TTFields for 6 hours batch 2 replicate 2

description:
GBM cell line LN428 sensitive cells received TTFields for 6 hours
LN428T6_2_2


title: GBM cell line U87 sensitive cells received TTFields for 24 hours batch 2 replicate 1

description:
GBM cell line U87 sensitive cells received TTFields for 24 hours
U87T24_2_1


title: GBM cell line U87 sensitive cells received TTFields for 6 hours batch 2 replicate 2

description:
GBM cell line U87 sensitive cells received TTFields for 6 hours
U87T6_2_2


title: Mouse lung macrophages, replicate1


title: Mouse heart macrophages, replicate4

source_name: Heart macrophages

value: Heart macrophages


title: GBM cell line U87 Control cells without any treatment batch 2 replicate 2

description:
GBM cell line U87 Control cells without any treatment
U87C_2_2

value: C

value: NT


title: Mouse heart macrophages, replicate3


title: GBM cell line U87 sensitive cells received TTFields for 6 hours batch 2 replicate 1

description:
GBM cell line U87 sensitive cells received TTFields for 6 hours
U87T6_2_1


title: GBM cell line U87 Control cells without any treatment batch 2 replicate 1

description:
GBM cell line U87 Control cells without any treatment
U87C_2_1

value: 0 days


title: Mouse heart macrophages, replicate1


title: GBM cell line LN827 resistant cells received TTFields more than 4 weeks batch 1 replicate 2

description:
GBM cell line LN827 resistant cells received TTFields more than 4 weeks
LN827W5_1_2

value: 5 weeks


title: Mouse heart macrophages, replicate2


title: GBM cell line U87 sensitive cells received TTFields for 24 hours batch 2 replicate 2

description:
GBM cell line U87 sensitive cells received TTFields for 24 hours
U87T24_2_2


title: Mouse non-muscle spindle areas, replicate3

source_name: Non-muscle spindle areas

value: Non-muscle spindle areas


title: GBM cell line LN827 resistant cells received TTFields more than 4 weeks batch 1 replicate 1

description:
GBM cell line LN827 resistant cells received TTFields more than 4 weeks
LN827W5_1_1

value: GBM cell line

value: 4 weeks


title: Mouse non-muscle spindle areas, replicate4


title: Mouse non-muscle spindle areas, replicate2


title: GBM cell line LN827 resistant cells received TTFields more than 4 weeks batch 1 replicate 3

description:
GBM cell line LN827 resistant cells received TTFields more than 4 weeks
LN827W5_1_3

value: TTFields


title: Mouse lung macrophages, replicate2


title: GBM cell line LN428 resistant cells received TTFields more than 4 weeks batch 1 replicate 3

description:
GBM cell line LN428 resistant cells received TTFields more than 4 weeks
LN428W5_1_3


title: Mouse muscle spindle areas, replicate4

source_name: Muscle spindle areas

value: Muscle spindle areas


title: GBM cell line U87 resistant cells received TTFields more than 4 weeks batch 1 replicate 3

description:
GBM cell line U87 resistant cells received TTFields more than 4 weeks
U87W5_1_3


title: Mouse muscle spindle areas, replicate2


title: GBM cell line LN428 resistant cells received TTFields more than 4 weeks batch 1 replicate 2

description:
GBM cell line LN428 resistant cells received TTFields more than 4 weeks
LN428W5_1_2


title: Mouse muscle spindle areas, replicate1


title: Mouse non-muscle spindle areas, replicate1


title: GBM cell line U87 resistant cells received TTFields more than 4 weeks batch 1 replicate 1

description:
GBM cell line U87 resistant cells received TTFields more than 4 weeks
U87W5_1_1


title: GBM cell line LN827 sensitive cells received TTFields less than 1 week batch 1 replicate 3

description:
GBM cell line LN827 sensitive cells received TTFields less than 1 week
LN827W1_1_3

value: 5 days


title: Mouse muscle spindle areas, replicate3

value: WT


title: ganyu2 HT22 cells

city: 珠海

first: HOU

last: YU

address: 拱北街道海安园

institute: 澳门科技大学

description:
raw_counts.txt
diff_expressions.txt

data_processing:
The bcl2fastq (v2.19.1.403) software is used to convert Illumina BCL files to FASTQ format with specific tile selection.
Fastp (v0.23.0) performs quality control and adapter trimming on the FASTQ files.  hisat2 (v2.1.0) aligns the processed reads to the Mus_musculus.GRCm38 reference genome in paired-end mode.
The htseq-count (v0.10.0) is employed to count reads mapped to features using the provided Mus_musculus.GRCm38 annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes differentially expressed genes between the intervention group and the control group. Genes were filtered based on the criteria of p.adjust < 0.01 and |logFC| ≥ 2

source_name: cell

growth_protocol: HT22 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
0.1-1 μg of total RNA per sample was prepared for library preparation. The NEBNext®Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II mRNA Library Prep Kit for Illumina® were used for mRNA isolation and library construction following the manufacturers’ protocols.
RNA libraries for RNA-seq were prepared using mRNA-Seq library prep kit following manufacturer's protocols

treatment_protocol: Hb group: HT22 treated with oxyhemoglobin; ganyu group:HT22 treated with oxyhemoglobin and NTR1; Control group: HT22 cells treated with no intervention.

value: cell

value: Mouse hippocampal neuronal


title: GBM cell line U87 resistant cells received TTFields more than 4 weeks batch 1 replicate 2

description:
GBM cell line U87 resistant cells received TTFields more than 4 weeks
U87W5_1_2


title: GBM cell line LN827 sensitive cells received TTFields less than 1 week batch 1 replicate 2

description:
GBM cell line LN827 sensitive cells received TTFields less than 1 week
LN827W1_1_2


title: ganyu1 HT22 cells

description:
raw_counts.txt
diff_expressions.txt


title: Hb3 HT22 cells


title: GBM cell line LN428 sensitive cells received TTFields less than 1 week batch 1 replicate 3 technical replicate 2

description:
GBM cell line LN428 sensitive cells received TTFields less than 1 week
LN428W1_1_3_2


title: GBM cell line LN827 sensitive cells received TTFields less than 1 week batch 1 replicate 1

description:
GBM cell line LN827 sensitive cells received TTFields less than 1 week
LN827W1_1_1


title: Hb1 HT22 cells


title: Hb2 HT22 cells


title: GBM cell line LN428 sensitive cells received TTFields less than 1 week batch 1 replicate 2

description:
GBM cell line LN428 sensitive cells received TTFields less than 1 week
LN428W1_1_2

value: 7 days


title: GBM cell line LN428 sensitive cells received TTFields less than 1 week batch 1 replicate 3 technical replicate 1

description:
GBM cell line LN428 sensitive cells received TTFields less than 1 week
LN428W1_1_3_1


title: Control3 HT22 cells

description:
raw_counts.txt
diff_expressions.txt


title: GBM cell line LN428 resistant cells received TTFields more than 4 weeks batch 1 replicate 1

description:
GBM cell line LN428 resistant cells received TTFields more than 4 weeks
LN428W5_1_1


title: Control2 HT22 cells

description:
raw_counts.txt
diff_expressions.txt


title: GBM cell line U87 sensitive cells received TTFields less than 1 week batch 1 replicate 3

description:
GBM cell line U87 sensitive cells received TTFields less than 1 week
U87W1_1_3


title: GBM cell line U87 sensitive cells received TTFields less than 1 week batch 1 replicate 2

description:
GBM cell line U87 sensitive cells received TTFields less than 1 week
U87W1_1_2


title: GBM cell line LN827 Control cells without any treatment batch 1 replicate 3

description:
GBM cell line LN827 Control cells without any treatment
LN827C_1_3


title: Control1 HT22 cells

description:
raw_counts.txt
diff_expressions.txt


title: QSC

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

description: 10x Genomics

data_processing:
We used Cell Ranger version 7.1.0 (10x Genomics) to process raw sequencing data and Seurat suite version 4.1.0 for downstream analysis.
The Seurat R package was used for graph-based clustering and visualizations; all functions were enabled using this package or the standard R version 4.1.2 package and used with default parameters unless otherwise noted.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tibialis anterior (TA) muscle

extract_protocol:
QSCs and ASCs from the TA muscles of Pax7-CreERT2;Rosa26-mTmG mice were fluorescently sorted as previously described (Li et al., 2019). Briefly, mononuclear muscle-derived cells were isolated from the hind-limb muscles of adult (2-month-old) mice by digesting the muscle chops with 2 U/ml dispase and 0.2% collagenase for 45 min. The cells were filtered through 70-µm and 40-µm cell strainers, suspended at 103 –107 cells/ml, and directly sorted with a BD Aria II Cell Sorting System. QSCs and ASCs were washed and resuspended in PBS supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Cell suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell gel bead-in emulsions (GEMs). GEM-reverse transcription (GEM-RT) was performed in a Veriti 96-well thermal cycler. After RT, GEMs were harvested and the cDNAs were amplified and cleaned with an SPRIselect Reagent Kit (Beckman Coulter). Indexed sequencing libraries were constructed using a Chromium Single-Cell 3’ Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. The libraries were sequenced with an Illumina NovaSeq 6000.

value: Muscle stem cells

value: tibialis anterior (TA) muscle

value: Pax7 CreERT2/+ ;Rosa26 mTmG/+

value: 8 weeks old


title: GBM cell line U87 sensitive cells received TTFields less than 1 week batch 1 replicate 1

description:
GBM cell line U87 sensitive cells received TTFields less than 1 week
U87W1_1_1

value: 3 days


title: GBM cell line LN827 Control cells without any treatment batch 1 replicate 2

description:
GBM cell line LN827 Control cells without any treatment
LN827C_1_2

value: C

value: NT

value: 0 days


title: ASC

description: 10x Genomics


title: ganyu3 HT22 cells

description:
raw_counts.txt
diff_expressions.txt


title: RNA-Seq K2_1, K2_2, replicate2

description: K2_1, K2_2, replicate2

data_processing:
Index codes were added to attribute sequences to each sample
Raw-  sequencing data were mapped to the mouse genome mm10 assembly using HISAT with default parameters.
DEGSeq2 was used to calculate the read coverage for each gene. Differentially expressed genes were filtered using a change greater than 2-fold and p-value < 0.05 as a criterion for differential expression.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: muscle cell

growth_protocol: Primary myoblast cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using TRIzol (Ambion, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
The library construction was performed by Novagene. Sequencing libraries were generated using an NEBNext Ultra TM RNA Library Prep Kit for Illumina (#E7530L, NEB, USA) following the manufacturer’s recommendations..

treatment_protocol: primary myoblast were cultured with 10ug/ml FGF.

value: muscle cell

value: Primary myoblast

value: eIF5A knockout

value: primary myoblast proliferation

tag: time

value: Day 2


title: RNA-Seq K3_1, K3_2, replicate3

description: K3_1, K3_2, replicate3


title: GBM cell line LN827 Control cells without any treatment batch 1 replicate 1

description:
GBM cell line LN827 Control cells without any treatment
LN827C_1_1

value: GBM cell line


title: RNA-Seq WT3_1, WT3_2, replicate3

description: WT3_1, WT3_2, replicate3

value: WT


title: GBM cell line LN428 Control cells without any treatment batch 1 replicate 3

description:
GBM cell line LN428 Control cells without any treatment
LN428C_1_3


title: GBM cell line LN428 Control cells without any treatment batch 1 replicate 2

description:
GBM cell line LN428 Control cells without any treatment
LN428C_1_2


title: RNA-Seq WT2_1, WT2_2, replicate2

description: WT2_1, WT2_2, replicate2


title: RNA-Seq K1_1, K1_2, replicate1

description: K1_1, K1_2, replicate1


title: RNA-Seq WT1_1, WT1_2, replicate1

description: WT1_1, WT1_2, replicate1


title: Ribo-Seq KO2, replicate2

description: KO2, replicate2

data_processing:
The original sequencing data, contained in a Fastq file, were processed by removal of low-quality reads (for which bases with mass value sQ ≤ 5 accounted for > 50% of the entire read), reads with more than 10% bases for which information could not be determined (designated as ‘N’), reads with 5’ joint contamination, reads lacking an inserted fragment and 3’ joint sequence, the 3’ joint sequence itself (which was required but then trimmed), rRNA reads, and tRNA reads.
The Tophat2 software package (http://ccb.jhu.edu/software/tophat/index.shtml) was used to clean data from the mouse genome database (Ensembl Mus_musculus_Ensembl_97.gtf) for transcriptome comparison, and quantitative analysis of gene levels was performed using HTSeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Cell lysates were centrifuged at 18,000 x g at 4 ℃ for 15 min and the supernatant was digested with RNase Ⅰ.
Ribosome-protected RNA fragments (RPF) were obtained using MicroSpin S-400 column resin; the was column enriched for ribosome-mRNA complexes and the targeted RNA fragments were purified by PAGE. The purified RNA fragments were end-repaired and A-tailed, and 5’ and 3’ joints were directly added to the ends. RNA reverse transcriptase was used to synthesize cDNA, and additional steps of PCR enrichment and PAGE-based screening of target fragments were used to obtain a library containing target fragments. The library was verified by quality control screening and sequencing.
Ribosome-seq

treatment_protocol: primary myoblast were cultured with 10ug/ml FGF.Cells were treated with cycloheximide (CHX; 100 μg/ml) for 10 minutes

value: primary myoblast


title: GBM cell line LN428 sensitive cells received TTFields less than 1 week batch 1 replicate 1

description:
GBM cell line LN428 sensitive cells received TTFields less than 1 week
LN428W1_1_1

value: TTFields


title: Ribo-Seq WT1, replicate1

description: WT1, replicate1


title: GBM cell line U87 Control cells without any treatment batch 1 replicate 1

description:
GBM cell line U87 Control cells without any treatment
U87C_1_1


title: Ribo-Seq WT2, replicate2

description: WT2, replicate2


title: Polysome-Seq KO2, replicate2

description: KO2, replicate2


title: NoCa_3

first: Matthew

middle: Ryan

last: Sullivan

address: 140 Fenway

department: Pharmaceutical Sciences

institute: Northeastern University

description:
Second dataset gene_count.xls
Calcium negative r3

data_processing:
Unknown, performed by Novogene
Assembly: hg18
Supplementary files format and content: raw gene counts of all samples in excel format, along with basic gene information

source_name: Blood

growth_protocol: NK cells were purchased form Stemcell technologies and thawed 24hrs prior to experiment, allowing for overnight rest

extract_protocol:
RNA was extracted and prepared using QIAGEN Rneasy kit
Novogene ultra-low input

treatment_protocol: NK cells were combined with anti-KRLG1 antibody treated CHO-K1 cells transfected to express KLRG1, and incubated together for 30 minutes prior to sorting based on fluorscent signal produced by ratiometric calcium dye.

value: Blood

value: Primary cells

value: Rodent and immune cells combined

tag: cell population

value: Calcium negative


title: NoCa_2

description:
First dataset gene_count.xlsx
Calcium negative r2


title: NoCa

description:
First dataset gene_count.xlsx
Calcium negative r1


title: Polysome-Seq KO1, replicate1

description: KO1, replicate1


title: Ca_2

description:
Second dataset gene_count.xls
Calcium positive r2

value: Calcium positive


title: Ca

description:
First dataset gene_count.xlsx
Calcium positive r1


title: S032, IDS, Ascites

city: Helsinki

first: Matías

last: M. Falco

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

description: 10x Genomics, v3.1 chemistry

data_processing:
The Cell Ranger v.6.0.1 pipeline (10x Genomics) was used for demultiplexing, alignment, barcode processing, and unique molecular identifier (UMI) quantification.
Assembly: GRCh38.d1.vd1
Supplementary files format and content: Txt file with data frame with raw counts and additional txt file with metadata information for each cell

source_name: Ascites

extract_protocol:
Tumor specimens were incubated overnight in a mixture of collagenase and hyaluronidase (Department of Pathology, University of Turku) to obtain single-cell suspensions.
Library construction was performed according to the manufacturer's (10x Genomics) protocols for indicated assay chemistries (v2, v3, and v3.1).

value: Ascites

value: NACT


title: Polysome-Seq WT1, replicate1

description: WT1, replicate1


title: CHO

description:
CHO gene counts.xlsx
CHO

value: CHO


title: M3_U1

city: Baltimore

first: Lisa

middle: Nicole

last: Learman

state: MD

address: 725 N. Wolfe St., PCTB 917

institute: Johns Hopkins University School of Medicine

data_processing:
Trimmomatic 0.39 (http://www.usadellab.org/cms/?page=trimmomatic) was used to trim adapters and low-quality reads from the raw paired-end fastq files, using default parameters.
FastQC analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to determine the quality of each file.
Reads were aligned to mouse reference genome mm10 using the HISAT2 (2.2.0) (https://daehwankimlab.github.io/hisat2/) splice-mapping algorithm with default parameters.
Read coverage tables for each gene were created using StringTie (2.1.3) (https://ccb.jhu.edu/software/stringtie/).
Read coverage tables for each transcript were created using Salmon (1.4) (https://salmon.readthedocs.io/en/latest/salmon.html).
APAlyzer (https://bioconductor.org/packages/release/bioc/html/APAlyzer.html) was used to discern differential expression of intronic polyadenylation isoforms.
DESeq2 was used (1.12.3) (https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3) to determine normalized gene counts and differential gene or transcript expression.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for each each Ensembl ID, 1 file per sample

source_name: MECS Cortical/Hippocampal Tissue

growth_protocol: Adult, 3–5-month-old, C57BL6JL male mice were used in all studies. They were housed in groups of three to five littermates in standard individually ventilated cages with ad libitum access to standard chow and water. Mice were kept on a 12 h light/12 h dark cycle with lights on at 7:00 AM.

extract_protocol:
10 mL of ice-cold PBS with proteinase inhibitors and RNase inhibitors was added per 500 mg of tissue, which was homogenized with 25 strokes in a Dounce homogenizer. The suspension was placed in a 150 mm dish and irradiated at 400 mJ/cm2 in a Stratalinker on ice. Cells were pelleted via centrifugation and frozen at -80 C until use. Cells were lysed and input (bulk) RNA samples removed and stored. After pre-clearing with Protein G Dynabeads, the rest of the lysate incubated with the following antibodies:  Anti-SNRP70/U1-70K antibody (ab83306, Abcam) or Anti-Sam 68 antibody (07-415-I, Millipore Sigma). Following immunoprecipitation, washes, and elution, RNA from the input and immunoprecipitation samples was purified by RNeasy mini kit (Qiagen), and then subjected to RNA sequencing.
RIPseq libraries were prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina). Library quality was validated by high sensitivity DNA analysis kit using the Advanced Analytical Fragment Analyzer CE. Sequencing of RNA-Seq libraries was performed on a NovaSeq instrument (Illumina) with 100 bp single-end reads according to manufacturer’s instructions. The depth of RNA-seq was 50 million reads per sample.

treatment_protocol: For maximal electroconvulsive stimulation (MECS) studies, following attachment of saline-soaked earclips, a 1s, 100 Hz, 85 mA stimulus of 0.5-ms square-wave pulses was administered using the Ugo Basile ECT unit (Model 57800). At these settings, all animals had generalized tonic-clonic convulsions with hindlimb extension. 90 minutes after MECS, animals were sacrificed and tissue dissected for use in subsequent assays. Control animals were handled in parallel with MECS-stimulated animals.

value: mixed cortex/hippocampus (brain)

value: Maximal electroconvulsive stimulation (MECS)

tag: antibody

value: U1 snRNP antibody


title: GBM cell line LN428 Control cells without any treatment batch 1 replicate 1

description:
GBM cell line LN428 Control cells without any treatment
LN428C_1_1

value: C

value: NT

value: 0 days


title: M2_U1


title: S032, chemo-naive, Ascites

description: 10x Genomics, v3.1 chemistry

value: Chemo-naive


title: C3_U1

source_name: Naïve Cortical/Hippocampal Tissue

value: Naïve


title: S030, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry

source_name: Peritoneum

value: Peritoneum


title: S031, chemo-naive, Peritoneum

description: 10x Genomics, v3 chemistry


title: C2_U1


title: GBM cell line U87 Control cells without any treatment batch 1 replicate 2

description:
GBM cell line U87 Control cells without any treatment
U87C_1_2

value: GBM cell line


title: M1_U1


title: S030, IDS, Omentum

description: 10x Genomics, v2 chemistry

source_name: Omentum

value: Omentum


title: Ribo-Seq KO1, replicate1

description: KO1, replicate1

value: muscle cell

value: primary myoblast

value: eIF5A knockout

value: primary myoblast proliferation

value: Day 2


title: C1_U1


title: GBM cell line U87 Control cells without any treatment batch 1 replicate 3

description:
GBM cell line U87 Control cells without any treatment
U87C_1_3


title: S031, IDS, Omentum

description: 10x Genomics, v3 chemistry

value: NACT


title: M3_In

value: mixed cortex/hippocampus (brain)


title: S029, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry


title: S029, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: D18WT2

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
RNA-seq reads were first mapped to human genome hg38 with published General Transfer Format (gtf) files, including all types of RNAs using Tophat 2 version 2.1.0.34,35 RNA-seq reads from ZNHIT3 ∆251-254 were also mapped to the human genome hg38 using STAR to confirm the expression of exogenous ZNHIT3.36 Differential expression (DE) analysis was performed by cufflinks version 2.2.1, and genes with adjusted p value less than 0.05 were considered significant DE genes.37 Exon skipping events were detected and quantified using rMATS version 4.0.2. Significant exon skipping events were defined by adjusted p value less than 0.05 and |inclusion level difference| more than 20%. Gene Ontology analysis was performed using PANTHER release 8.0 and visualized by ggplot2.38
Assembly: hg38
Supplementary files format and content: genes.fpkm is gene expression for each total RNA-seq library.

growth_protocol: SH-SY5Y neuroblastoma cells were obtained from ATCC and confirmed negative for mycoplasma using the Southern Biotech Mycoplasma Detection Kit. Cells were maintained in 15% fetal bovine serum (Gibco) in Eagle’s Minimum Essential Medium (MEM, Corning) with 1% penicillin/ streptomycin (Thermo Fisher Scientific). Cells were cultured at 37 °C with 5% CO2 and passaged at around 80% confluency. SH-SY5Y cells were differentiated into neurons as previously described with a few modifications as follows 32. A day after plating, the cells were infected with the virus. 48 hours post-infection, the cells were induced with fresh differentiation medium containing serum-free neurobasal/B27 plus culture medium (Thermo Fisher Scientific), Glutamax (Thermo Fisher Scientific), penicillin/ streptomycin, 50 ng/ml BDNF (Alomone Labs), 20 mM KCl, 2 mM dibutyryl cyclic AMP (db-cAMP), and 10 μM all-trans retinoic acid for 18 days.

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen) and treated with DNase I (NEB) according to the manufacturer’s instructions.
The rRNA-depleted RNA-seq libraries were prepared according to previously described protocols.33 Briefly, the Ribo-Zero rRNA Removal Kit was used to deplete rRNAs, and the NEBNext UltraTM RNA Library Prep Kit was used to prepare libraries.


title: M2_In

value: Maximal electroconvulsive stimulation (MECS)


title: S028, chemo-naive, Mesentery

description: 10x Genomics, v2 chemistry

source_name: Mesentery

value: Mesentery


title: Polysome-Seq WT2, replicate2

description: WT2, replicate2

value: WT


title: D18WT3


title: M1_In


title: D18WT1


title: D18Depleted2


title: D18Depleted1


title: D18Depleted3


title: C3_In


title: D18C14R3


title: S027, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry


title: D18C14R1


title: C1_In


title: D18C14R2


title: D0WT3


title: D0WT2


title: S027, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: S025, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry


title: S028, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: D0WT1


title: D0Depleted2


title: skin, SMIR, 32 days, rep 4

first: xiaoyan

last: Meng

address: Changhai road 225. Shanghai, China

institute: eastern hepatobililary surgical hospital

data_processing:
sequencing was carried out using the Illumina Novaseq 6000 instrument.
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2.
Clean reads were aligned to the Human genome hg38 using STAR. StringTie.
The expression of the transcript was calculated by FPKM using Perl.
Assembly: rn6
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample.

organism: Rattus

source_name: skin

extract_protocol:
Rats were deeply anesthetized with isoflurane, transcardially perfused with nuclease-free saline (pH 7.4). The incised skin and muscle tissue were rapidly dissected, the C3-C6 DRGs of LPI and C2-C5 DRGs of SMIR were then extracted. All samples were immediately transferred to ice-cold RNAlater solution and refrigerated at 4°C for 48 hours. Then samples were removed from RNAlater solution, placed into fresh 1.5 mL conical tubes and stored at -80℃. Total RNA was isolated, then Gel electrophoresis and Qubit were used to exam the RNA quality and RNA integrity number (RIN). For RNA sequencing, RNA samples from seven to nine biological replicates at each time point were separated into three independent pools. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit, and sequencing was carried out using the Illumina Novaseq 6000 instrument.
Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (RS-122-2001, Illumina, San Diego, CA, USA)

value: skin

value: SMIR

value: 32 days

tag: replicated animal_number

value: replicated 4


title: muscle, SMIR, 32 days, rep 4

source_name: muscle

value: muscle


title: DRG, SMIR, 32 days, rep 4

source_name: DRG

value: DRG


title: D0Depleted3


title: C2_In

value: Naïve


title: S022, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry

value: Omentum

value: Chemo-naive


title: D0C14R2


title: skin, SMIR, 32 days, rep 3

value: replicated 3


title: D0Depleted1


title: D0C14R1


title: D0C14R3


title: S022, IDS, Mesentery

description: 10x Genomics, v2 chemistry


title: muscle, SMIR, 32 days, rep 3


title: DRG, SMIR, 32 days, rep 3


title: Microglia_ZBTB18_SF_02

city: Freiburg

first: Maria

middle: Stella

last: Carro

state: Deutschland

address: Breisacherstrasse 64

country: Germany

institute: Uniklinik Freiburg

data_processing:
Basecalling was performed by Albacore implemented in the nanopore software.
Postprocessing was performed using the NanoPoreSeq pipeline, available at github (https://github.com/heilandd/NanoPoreSeq)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Immortalized Human Microglia - SV40

growth_protocol: Immortalized Human Microglia - SV40 was grown in DMEM 10%FBS

extract_protocol:
RNA was extracted with Trizol reagent. We then performed mRNA purification from total RNA samples using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, Carlsbad, USA).
Library was prepared using the Low Input by PCR Barcoding Kit and the cDNA-PCR Sequencing Kit (Oxford Nanopore Technologies, Oxford, United Kingdom) as recommended by the manufacturer.

treatment_protocol: Immortalized Human Microglia - SV40 was conditioned with medium from BTSC233 (GBM cells) transduced with empty vector (EV), ZBTB18 fumm lenght (FL) or ZBTB18 Nte-Short form (SF)

value: Immortalized Human Microglia - SV40

value: microglia

value: Conditioned with BTSC233 (GBM cells) transduced with ZBTB18 Nte short form (Nte-SF)


title: S021, IDS, Omentum

description: 10x Genomics, v2 chemistry

value: NACT


title: S021, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry


title: S025, IDS, Peritoneum

description: 10x Genomics, v2 chemistry

value: Peritoneum


title: Microglia_ZBTB18_SF_03


title: skin, SMIR, 32 days, rep 2

value: replicated 2


title: Microglia_EV_03

value: Conditioned with BTSC233 (GBM cells) transduced with control empty vector (EV)


title: Microglia_ZBTB18_SF_01


title: muscle, SMIR, 32 days, rep 2


title: S020, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: Microglia_EV_02


title: S020, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry


title: Microglia_ZBTB18_FL_02

value: Conditioned with BTSC233 (GBM cells) transduced with ZBTB18 Fill lenght (FL)


title: DRG, SMIR, 32 days, rep 2

value: SMIR


title: S019, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry


title: Microglia_ZBTB18_FL_01


title: Microglia_Ctrl_03

value: No treatment


title: Microglia_Ctrl_02


title: Microglia_EV_01


title: skin, SMIR, 32 days, rep 1

value: skin

value: 32 days

value: replicated 1


title: S019, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: Microglia_Ctrl_01


title: muscle, SMIR,  32 days, rep 1

value: muscle


title: S018, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry

value: Omentum


title: DRG, SMIR, 32 days, rep 1

value: DRG


title: ChIPseq_Torin_2week_Input_S2_R1_001.fastq.gz

library_source: genomic

data_processing:
Raw reads were filtered (mean quality score ≥20) and adapter sequences were removed using cutadapt (version 1.14)
Reads were mapped to the mm10 reference genome using bowtie (version 1.2.2)
Fragment midpoints were approximated by shifting mapped coordinates downstream by 75bp (approximating 150nt insert) and were converted to bedGraphs with both single bp bins or bin sizes of 50bp using the script (bowtie2stdBedGraph.pl)
Binned bedGraphs were then normalized by relative sequencing depth and converted to bigwig format
Assembly: mm10
Supplementary files format and content: BigWig
Supplementary files format and content: bigWigs representing depth-normalized read coverage

molecule: genomic DNA

source_name: CY 2.4 Albino ES cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10min at room temperature. After quenching and cell lysis, chromatin was sonicated by using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared with size selection step using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7103S, NEB) complemented with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (E7335S, NEB). 500ng DNA was used as starting material for input samples and 1.934-30.45ng DNA was used as starting material for ChIP samples. Libraries were amplified using 7-9 cycles for input samples and 12-14 cycles for ChIP samples on the thermocycler according to the protocol. Post amplification samples were beads purified and validated using Agilent High sensitivity DNA kit.

value: CY 2.4 Albino ES cells

value: Mouse embryonic stem cell

tag: chip antibody


title: ChIPseq_Torin_2week_CIC_1_S4_R1_001.fastq.gz

value: PA1-46018, Thermo Fisher Scientific


title: Microglia_ZBTB18_FL_03

value: Immortalized Human Microglia - SV40

value: microglia


title: ChIPseq_Ctrl_2week_Input_S1_R1_001.fastq.gz

value: DMSO


title: ChIPseq_Ctrl_2week_CIC_2_S5_R1_001.fastq.gz


title: S018, IDS, Omentum

description: 10x Genomics, v2 chemistry

value: NACT


title: ChIPseq_Torin_60min_CIC_1_S4_R1_001.fastq.gz


title: ChIPseq_Ctrl_2week_CIC_1_S3_R1_001.fastq.gz


title: S017, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry

value: Peritoneum

value: Chemo-naive


title: ChIPseq_Ctrl_60min_Input_S1_R1_001.fastq.gz


title: muscle, SMIR, 10 days, rep 4

value: SMIR

value: 10 day

value: replicated 4


title: S017, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: ChIPseq_Ctrl_60min_CIC_2_S5_R1_001.fastq.gz


title: S015, IDS, Omentum

description: 10x Genomics, v2 chemistry


title: ChIPseq_Torin_60min_CIC_2_S6_R1_001.fastq.gz


title: S015, chemo-naive, Omentum

description: 10x Genomics, v2 chemistry


title: ChIPseq_Ctrl_60min_CIC_1_S3_R1_001.fastq.gz


title: skin, SMIR, 10 days, rep 3

value: skin

value: replicated 3


title: S014, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry


title: Epidermis Replicate 5

city: New Haven

first: Luke

last: Ziolkowski

state: CT

address: 333 Cedar Street SHM B146

department: Cellular & Molecular Physiology

institute: Yale University School of Medicine

data_processing:
Primary analysis performed using Illumina's CASAVA 1.8.2 software suite.
Raw reads were filtered and trimmed using Trimmomatic v0.39 with default parameters
Filtered high-quality reads were aligned to the duck reference genome using the STAR aligner v2.7.9a with default parameters
Aligned reads were counted by the featureCounts program within the Subread package v2.0.1 with default parameters
FPKM values were calculated from read counts using the edgeR v3.34.1 package (Bioconductor v3.13) in R v4.1. Statistical analysis of differential expression of genes between groups was evaluated using the Fisher’s Exact Test with the Benjamini-Hochberg method for false discovery in edgeR.
Assembly: The duck reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.fna.gz) and gene annotation (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/355/885/GCF_000355885.1_BGI_duck_1.0/GCF_000355885.1_BGI_duck_1.0_genomic.gff.gz) were obtained from the National Center for Biotechnology Information (accessed on May 27, 2021).
Supplementary files format and content: Excel format (.xlsx) with columns for Gene symbols, fold change, FDR-adjusted p-values, raw counts and FPKM for mean and individual samples of Pacinian inner cores (7) and epidermis (6)

organism: Anas platyrhynchos

source_name: Bill epidermis

growth_protocol: Single inner cores of Pacinian corpuscles were manually isolated and collected from bill-skin of E25-E26 duck embryos in RNase-free conditions for eventual transcriptomic analysis. The inner core was first separated from the outer core. Aspiration pipettes with tip diameters of ~50–100 µm filled with 3 µl of RNA Lysis Buffer (Zymo) were then used to aspirate the inner core by applying light negative pressure.  The lysis buffer with the inner core from the pipette was then deposited into a 1.5 ml microcentrifuge tube using positive pressure and 10 µl of extra RNA Lysis Buffer was added to each tube. Samples were then stored at −80°C until RNA isolation.

extract_protocol:
RNA was isolated using the Quick-RNA Microprep Kit (Zymo) per the manufacturer’s instructions. RNA concentrations of 113–782  pg/µl and RIN values in the range of 7.1–9.5 were acquired from inner cores, assessed via a 2100 Bioanalyzer (Agilent). RNA from a total of 6-7 inner cores was collected from 5 independent embryos. RNA was also isolated from the epidermis of 6 separate bill-skin preparations as a control.
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs)

value: Bill epidermis


title: Epidermis Replicate 6


title: Epidermis Replicate 3


title: Epidermis Replicate 2


title: ChIPseq_Torin_60min_Input_S2_R1_001.fastq.gz


title: DRG, SMIR, 10 days, rep 3


title: Epidermis Replicate 4


title: skin, SMIR, 10 days, rep 4


title: skin, SMIR, 10 days, rep 2

value: replicated 2


title: S016, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry


title: ChIPseq_Torin_2week_CIC_2_S6_R1_001.fastq.gz


title: DRG, SMIR, 10 days, rep 4

value: DRG


title: Pacinian inner core Replicate 6

source_name: Pacinian corpuscle inner core

value: Pacinian corpuscle inner core


title: S014, IDS, Tumor

description: 10x Genomics, v2 chemistry

source_name: Tumor

value: Tumor


title: DRG, SMIR, 10 days, rep 2


title: S013, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry


title: muscle, SMIR, 10 days, rep 2

value: muscle


title: Pacinian inner core Replicate 5


title: Pacinian inner core Replicate 4


title: S012, IDS, Omentum

description: 10x Genomics, v2 chemistry

value: Omentum


title: Pacinian inner core Replicate 3


title: S011, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry


title: muscle, SMIR,  10 days, rep 1

value: replicated 1


title: Pacinian inner core Replicate 2


title: skin, SMIR, 2 days, rep 4

value: 2 days


title: Pacinian inner core Replicate 1


title: S011, IDS, Omentum

description: 10x Genomics, v2 chemistry

value: NACT


title: Epidermis Replicate 1


title: DRG, SMIR, 10 days, rep 1


title: MH-seq data of seedling

city: Nanjing

first: dongyang

last: Zheng

state: Jiang su

address: NJAU Wei gang No.1

department: college of agriculture

institute: Nanjing Agricultural University

data_processing:
fasp to remove the adapter. only reads length greater than 50 bp were retained
All clean reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0) using bowtie2 (Langmead and Salzberg 2012) with parameter -N 1
Duplicated reads were removed using Sambamba (Tarasov et al. 2015). Reads with mapping quality equal to or greater than 20 were retained for further analyses.
The MACS2 (Zhang et al. 2008)(version 2.0) program with parameters “--SPMR –g 14e9 -q 0.01 --nomodel” was used for calling MHS peaks.
Genome_build: International Wheat Genome Sequencing Consortium (IWGSC) reference sequence (version 1.0)
Supplementary_files_format_and_content: bigwig files, were generated using " bamCoverage --binSize 20  --normalizeUsing RPKM "
Supplementary_files_format_and_content: peak txt file

organism: Triticum aestivum

source_name: bread wheat

growth_protocol: Common wheat (Tritium aestivum cultivar ‘Chinese Spring’) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C. The germinated seeds with residual endosperm were transferred to soil (1:1:3 mixture of vermiculite: perlite: peat soil) or Hoagland solution and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.

extract_protocol:
2-3 g of ten-day-old whole seedlings or spikelet from Chinese spring (CS) were collected for a 10 min cross-link in 1% of formaldehyde fixation buffer (27.4 g sucrose + 2 ml 1M Tris-HCl pH8.0 + 400 μl 500 mM EDTA + 5.6 ml 36% Formaldehyde) under vacuum at 23-25℃. After adding 125 mM of Glycine to quench the excessive formaldehyde, the cross-linked leaves were washed three time with excessive autoclave ddH2O. The air-dry cross-linked leaves or spikelet were ground into a fine powder in liquid nitrogen and used for nuclei preparation
the purified nuclei pellet was digested in MNase digestion buffer (20 mM Tris-HCl, 4 mM MgCl2, 1mM CaCl2, 60 mM KCl, pH 7.5) with the amount of MNase (M0247, 2,000 gels units/μl, NEB) as 0 unit (U), 90 U, 100 U, 700 U and 900 U, respectively. Each enzymatic reaction was stopped by adding 16 μl 0.5 M EDTA (pH 8.0). Each digested nuclei were reversely cross-linked at 65℃ overnight for reverse cross-linking. MNased DNA was recovered by sequentially extracting using 1 volume of phenol, phenol:chloroform mixture and chloroform, then followed by ethanol precipitation. 40-100 bp small-sized DNA fragments were recovered from running 2% of agarose gel in 1xTBE buffer and used for MH-seq library preparation. MH-seq library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S). The MH-seq library was finally sequenced using Illumina NovaSeq platform.
Mnase-seq small sizes

tag: cultivar

value: Chinese Spring (CS)

value: seedling

tag: developmental stage

value: 10 days

value: WT


title: MH-seq data of spikelet

value: spikelet

value: booting stage


title: Pacinian inner core Replicate 7


title: S012, chemo-naive, Peritoneum

description: 10x Genomics, v2 chemistry

value: Peritoneum

value: Chemo-naive


title: direct_capture_hek293T_library1_nih3t3_library2_0hr_grna

first: Charles

last: Gersbach

address: 2127 Campus Drive

institute: Duke University

description:
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_0hr_mix_barcodes.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_0hr_mix_features.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_0hr_mix_matrix.mtx.gz

data_processing:
Each lane of cells was processed using cellranger (version 6.0.1) count using default parameters and mapping to the GRCh38-and-mm10-2020 reference genome from 10x Genomics
Assembly: GRCh38-and-mm10-2020
Supplementary files format and content: Sparse matrices in Market Exchange (MEX) format for UMI counts for each barcode/gene or barcode/gRNA pair. Files are barcodes.tsv: This file contains the barcodes represented in the mtx file. genes.tsv: This file contains all annotated genes and gRNAs. matrix.mtx:  contained the "gene id" index, "cell id" index, and the total UMI count per cell and gene/gRNA combination.
Supplementary files format and content: R1/R2/I1/I2 .fastq files for lane 1 and 2 of the sequencing run. Read 1 contains UMI and cell barcode information. Read 2 contains the RNA transcript sequence.

organism:
Homo sapiens
Mus musculus

extract_protocol:
cells were washed three times, trypsinized, and strained through a 40 µm cell strainer
Approximately 10,000 cells were captured per lane of a 10x Chromium chip (Next GEM Chip G) using Chromium Next GEM Single Cell 3ʹ HT Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening (10x Genomics, Inc, Document number CG000418, Rev D). CROP-seq protospacer sequences were amplified from barcoded cDNA.


title: direct_capture_hek293T_library1_nih3t3_library2_72hr_grna

description:
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_72hr_mix_barcodes.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_72hr_mix_features.tsv.gz
293T_MCH2_NTlib1-NIH3T3_MCH2_NTlib2_72hr_mix_matrix.mtx.gz