title: T111

description: 10x Genomics

source_name: scRNA-seq on MCC tumor resected from skin of pembrolizumab treated male patient

value: Resected tumor from skin

value: MCPyV negative


title: T104

status: Public on May 22 2023

type: SRA

city: Long Beach

first: Ling

last: Gao

email: ling.gao@va.gov, lingg3@hs.uci.edu

state: California

address: 5901 E.7th Street

country: USA

institute: Department of Veterans Affairs

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics  Cloud  Analysis platform (https://www.10xgenomics.com/products/cloud-analysis). FASTQ files were aligned to GRCh38 human reference genome using Cell Ranger Count v6.1.2. The number of average mapped reads per cell across the libraries were thereafter normalized using Cell Ranger Aggr function. Output files from Cell Ranger were imported to R and analyzed further using Seurat.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: scRNA-seq on MCC tumor resected from parotid gland of a treatment naïve female patient

extract_protocol:
Resected patient tumors were dissociated followed by red blood cell lysis, washed, and passed through 22µm sterile filters to obtain single-cell suspensions. Dead cells were excluded by SYTOX staining and live cells were collected by the FACSAria Fusion flow cytometer (BD Biosciences) and BD FACSDiva (v8.0.1). Sorted cells were washed with PBS containing 0.04% BSA and resuspended at a final density of ~1000 cells/µL.
Libraries were created targeting ~10,000 cells/sample for capture using Chromium Single Cell 3’ Reagent Kits following the CG00052 Rev B. user guide. Each library was subsequently sequenced on the Illumina NovaSeq 6000 platform to targeting an average of ~50,000 reads/cell.

tag: cell type

value: Merkel cell carcinoma tumor

tag: tissue

value: Resected tumor from parotid gland

tag: mcpyv status


title: T101

description: 10x Genomics

source_name: scRNA-seq on MCC tumor resected from skin of a treatment naïve male patient

value: MCPyV positive


title: 13C_M_77

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 13C_M_79


title: T102

description: 10x Genomics

source_name: scRNA-seq on MCC tumor resected from lymph node of a treatment naïve male patient

value: Resected tumor from lymph node


title: 13C_M_75


title: 13C_M_76


title: 13C_M_91


title: 13C_M_74


title: T98B

description: 10x Genomics

source_name: scRNA-seq on paired MCC tumor resected from the lymph node of a treatment naïve male patient


title: T99

description: 10x Genomics


title: 13C_M_72


title: T96

description: 10x Genomics

source_name: scRNA-seq on MCC tumor resected from lymph node of pembrolizumab treated female patient


title: 13C_M_73


title: 13C_M_71


title: T98A

description: 10x Genomics


title: T112A

description: 10x Genomics

source_name: scRNA-seq on MCC tumor resected from skin of a treatment naïve female patient


title: EWS-502 shSIX1 KD5 Biological Replicate 2

city: Aurora

first: Heide

last: Ford

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

library_source: transcriptomic

data_processing:
Pre-alignment QC was performed using FastQC; samples with uniformly poor quality were discarded.
Illumina adapters were removed using BBDuk and reads <50bp after trimming were discarded
Reads were aligned and quantified using STAR (2.6.0a) to the Ensembl human transcriptome (GRCh38.p12, release 96)
Lowly abundant genes were removed as those <1 mean raw count or <1 mean count per million (CPM) across the dataset
Assembly: GRCh38
Supplementary files format and content: Text file containing STAR gene count values

growth_protocol: EWS-502 cells were maintained in DMEM High Glucose supplemented with 10% FBS, 1% Sodium Pyruvate, 1% NEAAs, and 1% HEPES in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the RNeasy Mini Plus RNA extraction kit (Qiagen)
RNA libraries for RNA-seq were prepared using the NuGEN Universal Plus mRNA-Seq with NuQuant for bulk RNA-seq following the manufacturer's protocols

treatment_protocol: Cells were maintained in 1ug/ml Puromycin after shRNA transduction

tag: cell line

value: Ewing sarcoma cells

tag: treatment

value: shSIX1 KD5


title: 13C_M_68


title: 13C_M_70


title: 13C_M_69


title: EWS-502 shSIX1 KD5 Biological Replicate 3


title: EWS-502 shSIX1 KD5 Biological Replicate 1


title: 13C_M_87


title: 13C_M_67


title: EWS-502 shSIX1 KD4 Biological Replicate 3

value: shSIX1 KD4


title: EWS-502 shSIX1 KD4 Biological Replicate 2


title: T100

description: 10x Genomics


title: 13C_M_66


title: 13C_M_65


title: EWS-502 SCR Biological Replicate 3

value: shScramble


title: EWS-502 shSIX1 KD4 Biological Replicate 1


title: 13C_M_64


title: 13C_M_63


title: EWS-502 SCR Biological Replicate 1


title: EWS-502 SCR Biological Replicate 2


title: A673 shSIX1 KD6 Biological Replicate 3

growth_protocol: A673 cells were maintained in DMEM High Glucose supplemented with 10% FBS, 1% Sodium Pyruvate, 1% NEAAs, and 1% HEPES in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Cells were maintained in 5ug/ml Puromycin after shRNA transduction

value: shSIX1 KD6


title: 13C_M_62


title: 13C_M_61


title: A673 shSIX1 KD6 Biological Replicate 2


title: A673 shSIX1 KD4 Biological Replicate 3


title: 13C_M_59


title: A673 shSIX1 KD4 Biological Replicate 2


title: 13C_M_60


title: 13C_M_58


title: 13C_M_56


title: A673 SCR Biological Replicate 2


title: 13C_M_55


title: A673 SCR Biological Replicate 1


title: A673 SCR Biological Replicate 3


title: 13C_M_57


title: 13C_M_54


title: 13C_M_53


title: A673 shSIX1 KD6, SIX1 (Atlas)

data_processing:
CUT&RUN reads were quality assessed by FastQC, MultiQC and filtered with BBDuk.
ChIPseq reads were aligned to the hg38 human genome assembly using Bowtie2 (v2.3.4.3).
Samtools (v.1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool.
The normalization ratio for each sample was calculated by dividing the number of uniquely mapped human reads of the sample with the lowest number of reads by the number of uniquely mapped human reads of each sample. These normalization ratios were used to randomly sub-sample reads to obtain the same number of reads for each sample using using samtools view -s.
Bedtools genomecov was used to create bedgraph files from the bam files.
Bigwig files were created using deepTools bamCoverage and visualized using IGV.
Peaks were called using MACS2 (v2.1.2).
IDR was used to identify the reproducible peaks between the replicates.
Further processing of the peak data was performed in R, using in particular the following tools: valR, and DiffBind.
Average profiles and heatmaps were generated using ngs.plot.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&RUN

extract_protocol:
Cells were adsorbed onto activated Concavalin A beads and then incubated with antibodies O/N at 4°C. pAG-MNase was added to each sample to produce chromatin fragments under targets.
Fragmentation was terminated with the addition of STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 ug/mL RNaseA, 50 μg/mL Glycogen) and 0.5 ng/ul E.coli spike-in DNA. DNA was purified using a column purification kit and used for library assembly.
CUT&RUN libraries were assembled using the NEBNext II Ultra Library Prep kit and dual-index primers following manufacturer protocols

value: Ewing sarcoma

tag: cut and_run_antibody

value: Rb SIX1 (Atlas Antibodies HPA0011893)


title: A673 SCR, FLI1 (Abcam)

value: Rb FLI1 (Abcam ab15289)


title: 13C_M_51


title: 13C_M_50


title: A673 shSIX1 KD4, SIX1 (Atlas)


title: A673 shSIX1 KD6, IgG (CST)

value: Rb IgG (CST #2729S)


title: 13C_M_49


title: 13C_M_48


title: A673 SCR, IgG (CST)


title: 13C_M_47


title: A673 shSIX1 KD6 Biological Replicate 1


title: 13C_M_52


title: A673 shSIX1 KD4, IgG (CST)


title: A673 shSIX1 KD4 Biological Replicate 1


title: 13C_M_45


title: 13C_M_44


title: 23.3 sel 3

city: San Francisco

first: Harish

last: Vasudevan

address: 1450 3rd street

institute: UCSF

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
hg19

extract_protocol:
Single nuclear isolation of frozen tumors
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Mouse MPNST xenograft

tag: genotype


title: 23.3 sel 1

description: 10x Genomics


title: 23.3 sel 2

description: 10x Genomics


title: 23.3 vehicle 2

description: 10x Genomics


title: 13C_M_43


title: rpa49△ yeast, replicate 1

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

description:
A49-1
WT vs A49 sumnorm.csv

data_processing:
library strategy: NET-seq
Base-calling was performed using bcl2fastq software (version 2.20.00).
Using the UMI sequence (included in the linker), reads were deduplicated with fqtrim (version 0.9.7) with the "-C" option.
Reads containing the 5' sequence and UMI 5'-AGNNNNNNNNTG-3' were isolated, and this sequence was removed using cutadapt (version 3.4) with "-g -no-indels" parameters.
The 5'-CTGTAGGCACCAT-3' sequence was removed from the 3' end of reads with cutadapt (version 3.4) and the parameters "-a -no-indels".
STAR (version 2.7.1a) was used to align the reads to the Saccharomyces cerevisiae genome. The STAR alignIntronMax parameter was set to 1.
BAM files were sorted and indexed using SAMtools (version 1.6).
Sorted BAM files were converted to BED files using BEDTools (version 2.28.0).
Genome coverage files were generated using BEDTools (version 2.28.0) with the genomecov function and parameters "-strand" and "+strand".
Data processing and visualization was performed using R (version 4.0.2) and RStudio (1.3.959).
Assembly: S. cerevisiae R64-1-1
Supplementary files format and content: Processed data are included in a .csv file format. The header/column names specify which strain and replicate that the values in the table are representing.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast cultures were grown at 30ºC with nutation.

extract_protocol:
Extraction methods were based on previously published methods from our lab (data available at GSE142457, GSE166983, and GSE175553). In brief, cells were harvested via filtration and flash frozen. Cells were lysed under cryogenic conditions. Finally, an immunoprecipitation was performed for Pol I and a acidic phenol/chloroform extraction was used to isolate the total RNA from the cells.
DNA libraries were constructed exactly as previously published (Jacobs and Huffines et al., "The small-molecule BMH-21 directly inhibits transcription elongation and DNA occupancy of RNA polymerase I in vivo and in vitro", JBC, 2021). Briefly, a DNA linker containing a UMI sequence was ligated onto the 3' end of RNA reads. Samples were precipitated, reads were reverse transcribed, and DNA was circularized. Circular DNAs were amplified, libraries were purified with PCRClean DX beads, and sequencing was performed.

value: yeast


title: rpa49△ yeast, replicate 3

description:
A49-3
WT vs A49 sumnorm.csv


title: rpa34△ yeast, replicate 2

description:
A34-2
WT vs A34 sumnorm.csv


title: rpa49△ yeast, replicate 2

description:
A49-2
WT vs A49 sumnorm.csv


title: 13C_M_42


title: A673 SCR, SIX1 (Atlas)


title: rpa34△ yeast, replicate 3

description:
A34-3
WT vs A34 sumnorm.csv


title: 23.3 vehicle 1

description: 10x Genomics


title: rpa34△ yeast, replicate 1

description:
A34-1
WT vs A34 sumnorm.csv


title: Lacrimal Gland, Female, replicate 1

first: Helen

last: Makarenkova

address: 10550 N Torrey Pines Rd, MB-218

department: Molecular Medicine

institute: The Scripps Research Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lacrimal Gland

extract_protocol:
One female and two male samples were prepared for scRNAseq analysis. For each sample, six dissected LGs of three animals aged of 2 months were combined and processed as follows. First, LGs were quickly minced on ice in a dish pre-filled with cold DPBS, rinsed, and transferred to a 12-well plate placed in a shaking water bath (37°C, 80 rpm) containing 2 mL of digestion medium of following composition: DMEM/F12 , 0.5% BSA , 15 mM HEPES, 3 mM CaCl2 , 125 U/mL collagenase IV , 1 U/mL dispase II  and 20 U/mL DNase-I. After 30 min, samples were gently triturated by pipetting up and down 15 times with a wide-bored 1 mL tip. At 60 and 90 min, samples were gently triturated 10 to 15 times with a regular 1 mL pipet tip. At the end of the digestion (90 min in total), cells were pelleted (300 x g, 5 min, 4 °C), washed with cold HBSS buffer supplemented with 10 mM HEPES and 1 mM EDTA and gently re-suspended in 1 mL of accutase solution. After 5 min at 37°C, cell suspension was pipetted up and down 5 times and left at RT for 2 min. Then, accutase was inactivated by the addition of 1 mL of DMEM/F12 supplemented with 10% FBS and 15 mM HEPES. Cells were pelleted (300 x g, 5 min, 4 °C) and incubated for 10 min at RT with HBSS supplemented with 10 mM HEPES, 2 mM MgCl2, 2 mM CaCl2 and 200 U/mL DNase-I. Cell suspension was sequentially passed 2 times through a 3 mL syringe with needles: 18G, 22G and 25G. Dissociated cells were filtered through a pre-wet 70-µm mesh cell strainer and pelleted (300 x g, 5 min, 4 °C) before incubation for 5 min at RT with 5 mL of RBC lysis buffer 1X  to deplete erythrocytes. After centrifugation (300 x g, 5 min, 4 °C) and re-suspension into cold HBSS supplemented with 0.5% BSA and 10 mM HEPES, cells were passed through a pre-wet 30-µm mesh cell strainer. After centrifugation (400 x g, 5 min, 4 °C), dead cells and debris were depleted using the MS columns and the dead cell removal kit . The cell suspension was washed 3 times with cold scRNA-seq buffer composed of DPBS supplemented with 0.04% BSA, and pelleted at 400 x g, 5 min, 4 °C. The number of cells and the viability rate (78-79%) were evaluated using trypan blue staining analyzed with the Countess 3. Cell suspension volumes were then adjusted with cold scRNA-seq buffer to obtain between 700 and 1200 cells per µL and cells were counted again to obtain the final cell density. Cells were kept on ice at all times.
Cells were processed for scRNA-seq using the Chromium Single Cell 3' kit (v3.1 Chemistry) from 10X Genomics (Pleasanton, CA) according to the manufacturer’s protocols. cDNA was amplified by 11 cycles. Analysis of cDNA and libraries was done using Bioanalyzer or TapeStation (Agilent).

value: Lacrimal Gland

value: 2 months old

tag: Sex

value: Female


title: WT yeast, replicate 3

description:
WT-3
WT vs A34 sumnorm.csv
WT vs A49 sumnorm.csv

value: wild-type


title: NF95.6 parental

description: Bulk RNA-seq

data_processing:
Libraries were demultiplexed, quality assessed via FASTQC, and then aligned to the human genome using HISAT2
hg19
See manuscript for TPM matrices as supplementary info

extract_protocol:
RNA extraction from bulk tissues or cell lines
Library was performed according to the manufacter’s instructions for Illumina Tru Seq RNA kit.

value: Human pNF cell line


title: 13C_M_46


title: WT yeast, replicate 1

description:
WT-1
WT vs A34 sumnorm.csv
WT vs A49 sumnorm.csv


title: NF95.11b parental

description: Bulk RNA-seq


title: 13C_M_39


title: 13C_M_40


title: Src CD library at 32 hours, rep2

city: Seattle

first: Douglas

last: Fowler

state: Washington

department: Genome Sciences

institute: University of Washington

library_source: other

data_processing:
Samples were sequenced on the nextSeq 500 (Illumina)
All reads were processed using  bcl2fastq v.2.16 and ea-utils v.1.1.2-537.
Functional scores were calculated using Enrich2 v1.2 software and Src_Barcode_Map.txt.
Assembly: NA
Supplementary files format and content: Src_Barcode_Map.txt provides the linkage between the barcode sequence (first column) and the full length variant sequence of Src's catalytic domain (second column). This document was generated through the following steps: 1)Custom subassembly scripts to link barcode sequence with full length catalytic domain sequence. 2) Custom subassembly filtering script for high quality reads. 3) Filtering out  WT barcodes with aberrant activity score using 2x Std. Dev. of WT barcode mean activity score. 4) Spike in of 6 barcode sequences of control Src variants (3 each for K298M and T341I).

molecule: other

source_name: Synthetic sequence

growth_protocol: Green Monster BY4741 S. cerevisiae were grown in C-Leu medium supplemented with 2% galactose.

extract_protocol:
Plasmid extraction from culture samples using Yeast Plasmid Prep I (Zymogen) according to manufacturer's protocol
Extracted barcodes were amplifed and sample indices appended using 2x KAPA2G Robust HotStart ReadyMix with Thermocycler conditions of: Initial denaturation at 95ºC for 3 min, followed by 17 cycles of 95ºC for 15s, 60ºC for 15s, and 72ºC for 15s. Amplicons were quantified using KAPA Library Quantification Kit.

treatment_protocol: S. cerevisiae was grown in presence of 800nM Hsp90 inhibitor radicicol

value: Green Monster BY4741

tag: molecule

value: plasmid DNA

value: 800 nM radicicol


title: Src CD library at 32 hours, rep1


title: Src CD library at 25 hours, rep2


title: 13C_M_38


title: Src CD library at 25 hours, rep1


title: Src CD library at 19 hours, rep2


title: SNF94.3

description: Bulk RNA-seq

value: Human MPNST cell line


title: SNF02.2

description: Bulk RNA-seq


title: 13C_M_37


title: Input Src CD library at time 0, rep1


title: 13C_M_41


title: 13C_M_36


title: Src CD library at 19 hours, rep1


title: Input Src CD library at time 0, rep2


title: 13C_M_35


title: WT yeast, replicate 2

description:
WT-2
WT vs A34 sumnorm.csv
WT vs A49 sumnorm.csv


title: NF9511b NF2 CRISPRi sg2 Rep2

description: Bulk RNA-seq


title: YQ0157

city: Beijing

first: Song

last: Liu

address: No. 5, Dong Dan San Tiao

country: China

institute: Peking Union Medical College Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCh38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: endometrium

extract_protocol:
Total RNA was extracted from epithelial cells using the TRIzol method according to standard protocols (Life Technologies, Inc., Gaithersburg, MD, USA).
The purified products were evaluated using the Agilent 2200 TapeStation and diluted to 10 pM for cluster generation in situ on the HiSeq2500single-end flow cell followed by sequencing (1 × 50 bp) on the HiSeq 2500. rRNAs were removed from total RNA using an EpicentreRibo-Zero rRNA Removal Kit (Illumina, USA). Then, the PCR products were size-selected by polyacrylamide gel electrophoresis according to the instructions of the NEBNext® Multiplex mRNA/LncRNA Library Prep Set for Illumina® and Chain specific library sequencing was performed using the UNG enzymatic method (New England Biolabs, Inc., Ipswich, MA, USA).

treatment_protocol: The eutopic endometrial sample was collected from the uterine cavity using a SAP-1 device (Saipujiuzhou, Beijing, China) under sterile conditions. Samples for histologic dating that were processed for histological evaluation (haematoxylin-eosin) and immunohistochemistry were fixed in 4% formalin and processed to wax under standardized conditions in the same laboratory. Samples for RNA detection were stored in liquid nitrogen.

value: endometrium

tag: disease state

value: control

tag: menstrual phase

value: Secretory phase

tag: days in_menstrual_cycle


title: YQ0237

value: endometriosis


title: YQ0147


title: YQ0207


title: YQ0187


title: YQ0167


title: NF9511b NF2 CRISPRi sg2 Rep1

description: Bulk RNA-seq


title: 13C_M_33


title: YQ0137


title: 13C_M_34


title: NF9511b NF2 CRISPRi sg1 Rep2

description: Bulk RNA-seq


title: SNF96.2

description: Bulk RNA-seq


title: 13C_M_32


title: YQ0107


title: 13C_M_31


title: Cattle_yak_testis

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Yak, LU_Bosgru_v3.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Bos grunniens x Bos taurus

source_name: Testicular tissue of cattle_yak after sexual maturity for single-cell RNA sequencing

extract_protocol:
The frozen testicular tissue was removed and immediately placed in a 37 ℃ water bath for 2 min. After the tissue was melted, take it out with tweezers, place it in the resuscitation solution (DMEM/F12 medium+0.5mol/L sucrose+20% FBS), place it in a 37 ℃ water bath for 2min, preheat the DPBS to wash the tissue block for 2-3 times, place the tissue block in DMEM/F12 medium (Gibco, Waltham, MA, USA), and cut the tissue with ophthalmic scissors. Transfer the testicular tissue of cutted to a 15mL centrifuge tube, and add a solution with 0.2% collagenase IV (2 mg/mL) (Sigma, City of Saint Louis, USA) and hyaluronidase (2 mg/mL) solution (Sigma, City of Saint Louis, USA) (1:1) of 8~10 times the total amount of tissue. The centrifuge tube was placed in a 37℃ constant temperature shaker at 120 rpm (30 min, after 15min, 200μL tissue digestive fluid was taken every 3min to observe the digestive condition under the microscope until the free tubules with no mass tissue could be clearly observed), centrifuge at 1000 r/min for 5 min and drain the supernatant. 0.25% trypsin solution (2.5 mg/mL) (Gibco, Waltham, MA, USA), 8-10 times the total amount of tissue blocks, was added again. Finally, the tissue digestible solution was placed in a constant temperature shaker at 37℃ at 120 rpm (40 min, after 15min, 200μL tissue digestible solution was taken every 3min to observe the digestion condition under the microscope until the single cell suspension could be clearly observed). Fetal bovine serum was added to terminate digestion. The mixed cell suspension was blown evenly and filtered through 70μm and 40μm screens successively. The filtrate was collected and centrifuged at 300×g 4℃ for 5 min, the supernatant was abandoned, and the cells were re-suspended in DMEM/F12 complete medium containing 10% FBS, and cultured at 37 ℃ with 5% CO2. Part of the cell suspension was stained with Trypan blue and counted by automatic counter to calculate the number of cells and viability. The concentration was ~1000 cells/uL and cell viability>90% were used for scRNA seq.
The Cell suspension was loaded onto the Chromium Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) and the bead and cells with Cell Barcode were wrapped in the droplet. The droplet containing cells was collected, and then the cells were lysed in the droplet, so that the mRNA in the cells combined with the bead Cell Barcode to form a Single Cell GEMs, and the reverse transcription reaction was performed in the droplet to construct the cDNA library. GEM-RT-PCR was performed with a 96-hole reaction module (Bio-Rad; CT022510) in the C1000 Touch thermal cycler to generate barcode cDNA using the following procedures: 53°C for 45 min; 85°C for 5 minutes; Maintain at 4°C. The sample index on the library sequence is used to distinguish the source of the target sequence.

value: testis

value: Germ cell

tag: developmental stage

value: Postsexual maturity


title: NF9511b NF2 CRISPRi sg1 Rep1

description: Bulk RNA-seq


title: YQ0097


title: NF9511b 48h Sel Rep2

description: Bulk RNA-seq

value: 1 uM Selumetinib


title: NF9511b 48h Sel Rep1

description: Bulk RNA-seq


title: YQ0057


title: NF9511b 24h Sel Rep2

description: Bulk RNA-seq


title: YQ0077


title: 13C_M_27


title: 13C_M_28


title: YQ0047


title: YQ0027


title: 13C_M_23


title: NF9511b 1h Sel Rep1

description: Bulk RNA-seq


title: 13C_M_24


title: NF9511b 1h Sel Rep2

description: Bulk RNA-seq


title: ImmunoSEQ_Replicate2_bis

city: Epalinges

first: Raphael

last: Genolet

address: Biopole 3, Chemin des Boveresses 155

department: Departement d'oncologie UNIL-CHUV

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois (CHUV)

data_processing:
Ad hoc perl script
MiXCR software from MiLaboratories
Assembly: TCR alignment was performed using the IMGT database
Supplementary files format and content: Text file with the list of TCRs
Library strategy: Targeted amplification

source_name: peripheral blood mononuclear cell (PBMC) donnoe 2

growth_protocol: PBMC were obtained from leukapheresis of healthy donor.

extract_protocol:
mRNA were extracted using the Dynabeads mRNA DIRECT purification kit
Custum protocol for TCR sequencing describe in the manuscript.
ImmunoSEQ commercially available kit for TCR amplification
SMARTer (Takara) commercially available kit for TCR amplification

value: PBMC

tag: repertoire

value: beta TCR repertoire


title: ImmunoSEQ_Replicate1_bis

source_name: peripheral blood mononuclear cell (PBMC) donnor 2

tag: cell type


title: NF9511b 24h Sel Rep1

description: Bulk RNA-seq

tag: tissue


title: 13C_M_25


title: 13C_M_22


title: ImmunoSEQ_Replicate2

source_name: peripheral blood mononuclear cell (PBMC) donnor 1


title: 13C_M_21


title: 13C_M_30


title: NF9511b 10d Sel Rep2

description: Bulk RNA-seq


title: ImmunoSEQ_Replicate3


title: 13C_M_20


title: NF9511b 10d Sel Rep1

description: Bulk RNA-seq


title: ImmunoSEQ_Replicate1


title: VS7

description: Bulk RNA-seq

source_name: Human schwannoma

value: Human schwannoma


title: 13C_M_19


title: VS9

description: Bulk RNA-seq


title: YQ0037


title: 13C_M_18


title: VS6

description: Bulk RNA-seq


title: 13C_M_17


title: VS4

description: Bulk RNA-seq


title: VS33

description: Bulk RNA-seq


title: MKL-1

data_processing:
Rsubread for alignment
Sequence reads were mapped to GRCh38 reference human genome
Read count extraction was carried out using featureCounts() function
Differential analysis on raw data and sample distance calculations on normalized data performed using DESeq2
Assembly: hg38
Supplementary files format and content: consolidated tab-delimited text file represents raw counts for each sample

growth_protocol: Suspension cultures were maintained in RPMI-1640 media supplemented with 10% Fetal bovine serum, penicillin-streptomycin (100 U/ml) and L-glutamine (4mM), at 37C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). >1.0 ug of total RNA was evaluated for quality using Agilent Bioanalyzer Nano RNA chip prior to library construction
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA following manufacturer's protocols.

value: Merkel cell carcinoma cell line

value: MCPyV positive

tag: time

value: Day 0


title: 13C_M_26

tag: brain region


title: MCC-21


title: 13C_M_16

tag: age


title: VS32

description: Bulk RNA-seq


title: 13C_M_15

tag: strain


title: 13C_M_14


title: MCC-9

tag: cell line

value: MCPyV negative


title: MCC-16

tag: treatment


title: VS29

description: Bulk RNA-seq


title: VS30

description: Bulk RNA-seq


title: hepA rep3

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

country: Japan

institute: Kagoshima University

data_processing:
Quality check of obtained raw reads by FastQC (version 0.11.9)
Obtained reads were trimmed and quality-filtered using the Trim Galore! (version 0.6.7), Trimmomatic (version 0.39), and cutadapt (version 3.7).
Trimmed reads were mapped to the Aspergillus luchuensis mut. kawachii IFO 4308 genome using STAR (version 2.7.9a).
Reads on annotated genes were counted and FPKM values were calculated using featureCounts (version 2.0.1) and RSEM (version 1.3.1).
Assembly: GCF_016861625.1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Aspergillus luchuensis

source_name: mut. kawachii

extract_protocol:
Total RNA was extracted using RNAiso Plus reagent (Takara Bio) and SV total RNA isolation system (Promega).
After the enrichment of mRNA by by NEBNext Poly(A) mRNA Magnetic Isolation Module New England BioLabs), cDNA library was prepared by SMARTer Stranded RNA-Seq Kit (Clontech) and MGIEasy Universal Library Conversion Kit (App-A) (MGI Tech) according to the manufacturer’s instruction.

value: mut. kawachii

value: hepA


title: MCC-5


title: VS28

description: Bulk RNA-seq


title: laeA rep2

value: laeA


title: hepA rep2


title: 13C_M_13


title: MCC-8


title: laeA rep1


title: laeA rep3


title: MCC-3


title: VS26

description: Bulk RNA-seq


title: hepA rep1


title: 13C_M_11


title: VS25

description: Bulk RNA-seq


title: MCC-2


title: 13C_M_10


title: control rep3

value: control


title: VS24

description: Bulk RNA-seq


title: control rep2


title: 13C_M_9


title: Patient7 (P7)

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

data_processing:
1. Alignment. Sequence reads were mapped using 10x Genomics CellRanger multi pipeline (version cellranger-6.0.0) with the 10x human reference transcriptome (version 2020-A).
2. Background noise removal. The CellBender ‘remove-background’ tool was applied to the raw CellRanger count matrices to eliminate technical artifacts (including ambient RNA).
Supplementary files format and content: raw.h5ad: anndata object with gene expression (GEX) counts from CellBender (filtered output) in the ".X" slot .

source_name: Carotid plaque

extract_protocol:
Carotid tissue was extensively washed in RPMI, finely minced and tissue fragments were incubated in collagenase type I, elastase type III , and DNase, with trypsin inhibitor, polymixin B , andCaCl2, in RPMI medium 1640 with 5% FBS in a shaker at 37°C for 45 min. Cell suspension was filtered through an 80-μm Nylon mesh and washed in media. Collected cells were incubated with live/dead stain at 1:1,000 in PBS for 10 min at 4 °C.
Cells were then washed with FACS buffer (PBS with 2% FBS), stained for CD45 antibody for 30 min at RT then washed twice with FACS buffer, resuspended in a final FACS buffer volume of 500 μl, filtered through an Easy Strain 100-μm cell strainer and sorted for live CD45+ cells using FACS ARIAIII in FBS.

treatment_protocol: Carotid plaques were extracted from patients undergoing carotid endarterectomy (CEA).Patients were defined as symptomatic if they experienced symptoms (stroke, transitory ischemic attack, or amaurosis fugax) with a carotid plaque with a degree of stenosis greater than 70%. Asymptomatic carotid plaques were associated with no documented clinical symptoms but had indication for CEA due to a high degree of stenosis, according to NASCET (North American Symptomatic Carotid Endarterectomy Trial) or ESCT (European Carotid Surgery Trial) criteria

value: Carotid plaque

tag: sorting strategy

value: Live CD45+ cells

tag: subject status


title: Patient6 (P6)

value: patients undergoing carotid endarterectomy


title: VS23

description: Bulk RNA-seq

tag: genotype


title: control rep1


title: VS21

description: Bulk RNA-seq


title: Patient3 (P3)


title: 13C_M_12


title: VS20

description: Bulk RNA-seq


title: Patient2 (P2)


title: FA-300

first: Yan

address: No. 10, Xitoutiao, You An Men, Fengtai District

department: Department of Biochemistry and Molecular Biology

institute: Capital Medical University

data_processing:
Typically, base call quality diminishes toward the end of a read. This is characteristic to first- and second-generation sequencing technologies (Sanger, Illumina, SOLiD, 454)
SOAPnuke, a filtering software independently developed by BGI, is used for filtering.
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts or in FPKM (fragments per thousand nucleotides per million mapped reads).
Genome_build: B73 reference genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: MC3T3-E1 cells were purchased from the ATCC (Manassas, VA, USA). Cells were cultured in a humidified atmosphere of 5% CO2 and 95% air at 37℃ in an alpha modification of Eagle’s medium (Invitrogen Life Technologies, Carlsbad, CA, USA) supplemented with 10% FBS, 100 U/mL penicillin, and 0.1 mg/mL streptomycin.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC3T3-E1 cells were cultured in a 10-cm culture dish at 5 × 105 cells/mL at 37°C in 5% CO2 in medium supplemented with formaldehyde at different concentrations.

tag: agent

value: FA 300 microM


title: Patient1 (P1)


title: Patient5 (P5)


title: 13C_M_7


title: FA-100

value: FA 100 microM


title: 13C_M_4


title: VS19

description: Bulk RNA-seq


title: 13C_M_5


title: VS18

description: Bulk RNA-seq


title: 13C_M_3


title: VS17

description: Bulk RNA-seq


title: Tumor conditioned media (TCM)-conditioned mesenchymal stromal cells 1

city: Galway

first: Aideen

last: Ryan

address: University Road

country: Ireland

institute: National University of Ireland, Galway

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) was used for base-calling
Trimmed reads (trimmed 5’, 3’-adaptor   bases using cutadapt) were aligned to reference genome using Hisat2 software
The transcript abundances   for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were   calculated with R package Ballgown
The differentially expressed genes and transcripts were filtered using   R package Ballgown
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample ...

source_name: Bone marrow-derived

growth_protocol: After generating single cell suspensions from the bone marrow of Balb/c mice, MSCs were centrifuged at 400 x g for 5 minutes, re-suspended in 25ml culture medium and plated at a density of 9x105 per cm2 in a T175 flask. MSCs were incubated at 37°C, 21% O2, 5% CO2 (Normoxia) or 37°C, 5% O2, 5% CO2 (Hypoxia) and non-adherent cells were removed 24 hours later. Medium was changed every 3-4 days and cells were passaged at 85% confluency.

extract_protocol:
MSCs were collected and lysed using lysis buffer from the Bioline Isolate II RNA mini kits (Qiagen) according to manufacturer’s protocols. RNA was extracted according to manufacturer’s instructions. 1-2µg of total RNA was enriched by oligo(dT) magnetic beads (rRNA removal) and sequencing libraries were prepared.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Balb/c MSCs were seeded at a density of 50,000 cells/ml of MSC medium in a T175 flask. For MSC conditioning, cells were seeded at a density of 0.03x106 per well of a 6-well plate in 2ml of appropriate MSC culture medium. 24 hours after seeding, MSC medium was removed and replaced with 40% fresh MSC medium + 60% TCM from CT26 cancer cells.

value: Bone marrow-derived

value: Primary MSC

value: WT

value: TCM-conditioned

value: 72h conditioning


title: Tumor conditioned media (TCM)-conditioned mesenchymal stromal cells 2


title: Tumor conditioned media (TCM)-conditioned mesenchymal stromal cells 3


title: 13C_M_2

source_name: C57BL/6J Male P56 Mouse Brain


title: Pancreatic cancer 21

city: Meldola

first: Tania

last: Rossi

state: FC

address: Via Piero Maroncelli 40

department: Biosciences Laboratory

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

data_processing:
CLC Genomics Workbench 22.0.1
FASTQ files were loaded in the CLC Genomics Workbench, Biomedical analysis plugin.
The tool "QIAseq miRNA quantification" was run using default options.
Assembly: QIAseq Small RNA mirBase v22
Supplementary files format and content: tab-delimited text files include expression values (exact mature) for each sample

source_name: Plasma-derived extracellular vesicles

extract_protocol:
Pasma/Serum RNA purification Mini kit, Norgen
QIAseq miRNA Library Kit

value: Plasma-derived extracellular vesicles

value: Gemcitabine + Nab-paclitaxel

tag: disease state

value: Metastatic


title: 13C_M_8

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: VS14

description: Bulk RNA-seq

value: Human schwannoma


title: VS1

description: Bulk RNA-seq


title: Pancreatic cancer 20


title: Mesenchymal stromal cells 3


title: 13C_M_6


title: 13C_M_0


title: VS12

description: Bulk RNA-seq


title: Mesenchymal stromal cells 2


title: Mesenchymal stromal cells 1


title: CD45, anti-PD1

city: Los Angeles

first: Linh

middle: My

last: Tran

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description:
10X Genomics Chromium™ Single Cell 3’
PD1

data_processing:
The demultiplexing were made using the Cell Ranger software v4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Murine tumors were harvested and minced into smaller pieces using a sharp blade before incubation with 1mg/mL Collagenase IV (Roche) for 30 minutes at 37C with frequent agitation. After incubation, 10mL of fresh culture media was added before filtration through a 70μm filter. Following centrifugation, cell pellets were resuspended in 3mL of red blood cell lysis solution (BioLegend) on ice for 5 min followed by the addition of 10mL complete media. Single cell suspensions were then washed with PBS, and stained with Zombie-NIR LIVE/DEAD stain and CD45 antibody for 30 min at 4oC. Live/CD45+ leukocytes were sorted by BD Biosciences Aria II cell sorter with 100-mm nozzle.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: tumor

value: FVB/NCrl

value: 7-9 weeks old


title: CD45, CXCL910-DC and anti-PD1

description:
10X Genomics Chromium™ Single Cell 3’
Combo

value: CXCL9/10-DC and anti-PD1


title: M40

description: Bulk RNA-seq

source_name: Human MPNST

value: Human MPNST


title: CD45, control

description:
10X Genomics Chromium™ Single Cell 3’
Control


title: VS10

description: Bulk RNA-seq


title: VS15

description: Bulk RNA-seq


title: 13C_M_1


title: Pancreatic cancer 16


title: M7370

description: Bulk RNA-seq


title: Pancreatic cancer 19

value: Locally Advanced


title: Pancreatic cancer 15


title: CD45, CXCL910-DC

description:
10X Genomics Chromium™ Single Cell 3’
CXCL910


title: Tspan12 KO treated with F4L5.13, replicate 1, scRNAseq

city: Minneapolis

first: Harald

last: Junge

state: MN

address: 2001 6th St SE

department: Department of Opthalmology

institute: University of Minnesota

description: 10x Genomics

data_processing:
Single-cell RNA-Seq data was processed and analyzed using Partek Flow software Version 9.0.
Assembly: mm10
Supplementary files format and content: Count matrix file, features on rows (.txt)

source_name: Retina

extract_protocol:
Retinas were dissected and then digested in papain solution (20 units/ml papain, 0.005% DNase I  and 200 units/ml Collagenase type 4 in Ames’ solution) at 37°C for 15 min with constant agitation. After digestion, the tissue was triturated with a p1000 pipet tip 10-20 strokes to break up larger tissue fragments. Cells were pelleted at 300 g for 5 min at 4°C, the supernatant discarded, and the cell pellet immediately resuspended in 1 ml upper gradient solution (1 mg/ml albumin, 1 mg/ml ovomucoid inhibitor and 0.005% DNase I in Ames’ solution, equilibrated with 95% O2, 5% CO2 gas). The cell suspension was passed through a 50 µm cell strainer. To remove debris, the 1 ml cell suspension was carefully placed over 5 ml of lower gradient solution (i.e., 10 mg/ml albumin, 10 mg/ml ovomucoid inhibitor in Ames’ solution) and centrifuged at 100 g for 6 minutes at 4°C (whole cells were pelleted, while membrane fragments remained at the interface). The supernatant was discarded, and the pelleted cells were resuspended in 1 ml upper gradient solution. To remove photoreceptors and dead cells, the cell suspension was incubated with magnetic beads coupled with anti-CD73 and Annexin V  at 4 °C for 20 min with end-to-end mixing. After removing the magnetic beads with a magnetic stand, the supernatant was pelleted at 300 g for 5 min at 4 °C. The pelleted cells were resuspended in upper gradient solution and counted using a LOGOS cell counter. Cell preparations with 60-80% viability were used for further library construction and sequencing.
Single cell reverse transcription and cDNA synthesis was performed using a Chromium platform (10x Genomics) and Chromium Single Cell 3′ library & Gel Bead kit v3 (10x Genomics) following the manufacturer’s instructions. Samples were indexed using Single Index Kit T Set A (10x Genomics). An appropriate sequencing library size range and the cDNA concentration were determined using an Agilent 2100 Bioanalyzer. The libraries were sequenced at Novogene using Illumina HiSeq system, with 150 bp paired end read length at a 50,000 reads/cell sequencing depth.

treatment_protocol: F4L5.13 were administrated intraperitoneally to Tspan12 KO mice (10 mg/kg at P6, P9, P12, thereafter 4 mg/kg every three days)

value: Retinal cells

value: Retina


title: WT, replicate 1, scRNAseq

description: 10x Genomics


title: VS11

description: Bulk RNA-seq


title: Pancreatic cancer 18


title: M6174

description: Bulk RNA-seq


title: Pancreatic cancer 14


title: Old_VM_pos_CD3_CD28_Stimulation 3

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

data_processing:
Raw fastq files were aligned to mouse genome using HISAT2
alignment was done using HISAT2; RNA-seq QC and metrics were collected using Picard tools and   gene counts were extracted using featureCounts
Assembly: Mouse genome build GRCm38
Supplementary files format and content: Data matrix of raw counts

source_name: spleen

extract_protocol:
Single Cell RNA Purification Kit (Cat. 51800) [Norgene Biotek Corp.]
SMARTer low input RNA kit (Takara)

treatment_protocol:
cells stimulated for 48h with Gibco™ Dynabeads™ Mouse T-Activator CD3/CD28
cells are either untreated or stimulated for 48h with Gibco™ Dynabeads™ Mouse T-Activator CD3/CD28 (see above)

value: old

value: CD8+ T cell

tag: subpopulation

value: virtual memory AsGM1+ stimulated


title: Old_VM_pos_CD3_CD28_Stimulation 2


title: M4375

description: Bulk RNA-seq


title: Pancreatic cancer 13


title: SYNOVIUM_WT_biol rep 2

city: Ghent

first: Carolien

last: Vlieghe

address: Corneel Heymanslaan 10

department: Department of Internal Medicine and Pediatrics (Rheumatology Unit)

country: Belgium

institute: VIB Inflammation Research Center-University of Ghent

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Assembly: Mus musculus.Ensembl.GRCm38.82
Supplementary files format and content: D_rawCounts.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: D_fpkmCounts.txt: Matrix table with FPKM values for all biologically meaningfully expressed genes for each sample.

source_name: Synovium (from ankle)

extract_protocol:
RNA was isolated by means of the RNeasy Micro kit following manufacturer’s instructions (Qiagen).
Per sample, an amount of 1µg of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version:# 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were equimolarly pooled and sequenced on Illumina NovaSeq 6000 (S1 flow cell, 100 cycles, single read, lane 1+2) at the VIB Nucleomics Core (www.nucleomics.be).

value: Synovium (from ankle)

value: WT


title: SYNOVIUM_WT_biol rep 3


title: Pancreatic cancer 17

value: Plasma-derived extracellular vesicles


title: M2663

description: Bulk RNA-seq


title: Old_VM_pos_CD3_CD28_Stimulation 1


title: Tspan12 KO, replicate 1, scRNAseq

description: 10x Genomics


title: Pancreatic cancer 12

value: Gemcitabine + Nab-paclitaxel


title: Old_TM_pos_CD3_CD28_Stimulation 4

value: true memory AsGM1+ stimulated


title: Pancreatic cancer 11


title: Old_TM_pos_CD3_CD28_Stimulation 3


title: SYNOVIUM_ARE_biol rep 3

value: TNFdARE


title: M1538

description: Bulk RNA-seq


title: M1495

description: Bulk RNA-seq


title: Pancreatic cancer 10

value: Metastatic


title: M10481

description: Bulk RNA-seq


title: Old_TM_pos_CD3_CD28_Stimulation 2


title: Pancreatic cancer 9


title: ILEUM_WT_biol rep 3

source_name: Gut (Ileum)

value: Gut (Ileum)


title: MPNST 46

description: Bulk RNA-seq


title: ILEUM_WT_biol rep 2


title: Old_TM_pos_CD3_CD28_Stimulation 1


title: Old_VM_pos 4

treatment_protocol:
untreated
cells are either untreated or stimulated for 48h with Gibco™ Dynabeads™ Mouse T-Activator CD3/CD28 (see above)

value: virtual memory AsGM1+


title: N22

description: Bulk RNA-seq

source_name: Human pNF

value: Human pNF


title: Old_VM_pos 3


title: Pancreatic cancer 7


title: SYNOVIUM_WT_biol rep 1


title: N20

description: Bulk RNA-seq


title: ILEUM_ARE_biol rep 3


title: N16

description: Bulk RNA-seq


title: Old_VM_pos 2


title: Pancreatic cancer 5


title: ILEUM_ARE_biol rep 2


title: SYNOVIUM_ARE_biol rep 2


title: Old_VM_pos 1


title: N15

description: Bulk RNA-seq


title: Pancreatic cancer 4


title: Old_TM_pos 3

value: true memory AsGM1+


title: ILEUM_ARE_biol rep 1


title: SYNOVIUM_ARE_biol rep 1


title: N13

description: Bulk RNA-seq


title: Pancreatic cancer 8


title: Pancreatic cancer 3

value: Locally Advanced


title: Old_TM_pos 2


title: ILEUM_WT_biol rep 1


title: Old_TM_pos 1


title: N7

description: Bulk RNA-seq


title: Pancreatic cancer 2


title: Old_Naive_pos 4

value: naive AsGM1+


title: N3

description: Bulk RNA-seq


title: TREG_C_6

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Assembly: Mus musculus.Ensembl.GRCm38.82
Supplementary files format and content: ABC_rawCounts.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: ABC_fpkmCounts.txt: Matrix table with FPKM values for all biologically meaningfully expressed genes for each sample.

source_name: mLN

extract_protocol:
RNA was isolated by means of the RNeasy Micro kit following manufacturer’s instructions (Qiagen).
Per sample, an amount of 100pg or 2ng of total RNA was used as input for the SMART-Seq v4 PLUS protocol to generate full-length cDNA (version “011821”) from Takara Bio USA, Inc. Subsequently, 3ng of purified double-stranded cDNA is enzymatically fragmented and stem-loop adapters ligated. Libraries are then amplified and indexed, generating Illumina-compatible libraries with unique dual indexes (UDIs) according to the manufacturer’s protocol. Sequence-libraries of each sample were finally equimolarly pooled and sequenced on NovaSeq6000 using the Xp workflow, v1.5 kits, single read (100-8-8-0) at the VIB Nucleomics Core (www.nucleomics.be).

value: mLN

value: TREG


title: TREG_C_5

source_name: Ileum

value: Ileum


title: Macrophages, MAGL fl/fl (WT), S5

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

source_name: Macrophages

extract_protocol:
Non parenchymal cells were isolated from mouse liver 24 hours after Ccl4 injectio . F480+ Cd11b+ macrophages were sorted by Flow cytometry cell sorter (BD FACS ARIAIII in RLT lysis buffer.RNAs were isolatetd using RNEasy microkit Qiagen 74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Sex

value: male

value: liver

value: F480+ Cd11b+ macrophages sorted from liver

value: MAGL fl/fl (WT)

value: 11 weeks old

value: 1 intraperitoneal  injection CCl4


title: TREG_C_4

source_name: iLN+pLN

value: iLN+pLN

value: TNFdARE


title: Pancreatic cancer 6

value: Plasma-derived extracellular vesicles

value: Gemcitabine + Nab-paclitaxel

value: Metastatic


title: Old_Naive_pos 3

value: old

value: CD8+ T cell


title: N1

first: Harish

institute: UCSF

description: Bulk RNA-seq

data_processing:
Libraries were demultiplexed, quality assessed via FASTQC, and then aligned to the human genome using HISAT2
hg19
See manuscript for TPM matrices as supplementary info

extract_protocol:
RNA extraction from bulk tissues or cell lines
Library was performed according to the manufacter’s instructions for Illumina Tru Seq RNA kit.

value: Human pNF


title: Macrophages, MAGL fl/fl (WT), S4


title: Human Group 1 Tumor MPNST 3

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
hg19

source_name: peripheral nerve tumor

extract_protocol:
Single nuclear isolation of frozen tumors
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: peripheral nerve tumor


title: TREG_C_3

source_name: Synovium ankle

value: Synovium ankle

value: TREG


title: Macrophages, MAGL fl/fl (WT), S1

value: male


title: TREG_C_2

value: mLN


title: Old_Naive_pos 1

value: naive AsGM1+


title: TREG_C_8

value: WT


title: Human Group 1 Tumor MPNST 2

description: 10x Genomics


title: N12

description: Bulk RNA-seq


title: Young_Naive_pos 4

value: young


title: TREG_C_1

value: Ileum


title: Macrophages, MAGL fl/fl (WT), S3

value: liver

value: F480+ Cd11b+ macrophages sorted from liver

value: MAGL fl/fl (WT)

value: 11 weeks old

value: 1 intraperitoneal  injection CCl4


title: Macrophages, MAGL Mye-/-, S12

value: MAGL Mye-/-


title: TCONV_C_8

value: iLN+pLN

value: TCONV


title: Human Group 2 Tumor pNF 3

description: 10x Genomics

value: peripheral nerve tumor


title: Human Group 1 Tumor MPNST 1

description: 10x Genomics


title: Young_Naive_pos 3

value: CD8+ T cell


title: TCONV_C_6


title: Macrophages, MAGL Mye-/-, S11

value: 10 weeks old


title: Macrophages, MAGL Mye-/-, S8

value: male


title: TCONV_C_5


title: Young_Naive_pos 1


title: Human Group 2 Tumor pNF 2

description: 10x Genomics


title: Old_Naive_pos 2

value: old


title: Human Group 2 Tumor pNF 1

description: 10x Genomics


title: Old_Naive_neg 4

value: naive AsGM1-


title: TCONV_C_4

value: TNFdARE


title: Macrophages, MAGL Mye-/-, S10


title: Macrophages, MAGL Mye-/-, S9


title: Old_Naive_neg 3


title: TCONV_C_2

value: mLN


title: SCRAMBLE capture (rep3)

type: RNA

city: Trento

first: Michela

middle: A.

last: Denti

address: Via Sommarive 9

department: Department of Cellular, Computational and Integrative Biology

institute: University of Trento

data_processing:
Analysed with Genex software. N/A values (not expressed miRNA) substituted with a Ct=40. miRNAs were considered if they were detetcted in at least 2 of the 3 replicate samples.
2^-ΔCt in Matrix normalized Table. Normalization performed by the global mean of all miRNAs’ Cts. 2^-ΔΔCt in Fold Change Table, where -ΔΔCt = -[averageΔCttest -averageΔCtcontrol]

label: SYBR Green

source_name: Kelly cells

label_protocol: RT-qPCR assays were performed using the Exiqon miRCURY LNA™ Universal RT microRNA PCR, microRNA Ready-to-Use PCR, Human panel I and II, version 4, following manufacturer's instructions

growth_protocol: Human neuroblastoma Kelly cell line was grown in RPMI-1640 medium (Gibco®, Life Technologies) supplemented with 2 mM L-Glutamine, Penicillin/Streptomycin and 10% Fetal Bovine Serum (FBS). Cell cultures were maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: Not necessary: the eluted material was directly retrotranscribed.

treatment_protocol: Cells were crosslinked with 2% paraformaldehyde. After several washes with ice-cold DPBS (Dulbecco’s Phosphate Buffered Saline), cells were lysed and homogenized with glass beads. In parallel, biotinylated capture or scramble oligonucleotides were immobilised on MyOne streptavidin magnetic beads (Dynabeads Magnetic Separation Technology – Thermo Fisher Scientific). Cell lysates were incubated with these beads. After several washes, the beads were incubated at 60°C for 5 minutes to reverse the interaction between the biotin-labelled DNA: mRNA:miRNA complexes and the magnetic beads. Cross-linked nucleic acids and proteins were incubated for 45 minutes at 70°C to reverse the cross-linkages.

tag: tumour

value: neuroblastoma


title: SCRAMBLE capture (rep2)


title: Old_Naive_neg 2


title: TCONV_C_1

value: Ileum


title: Tx-iPSC-RPE_1

city: Singapore

first: Paul

last: Blakeley

address: 61 Biopolis Dr, Proteos, Singapore 138673

country: Singapore

institute: Institute of Molecular and Cell Biology, A*STAR

data_processing:
The alignment of reads to the reference geneome, gene counting and aggregation were made using Cell Ranger v4.0.0
Assembly: GRCh38 and OryCun2.0
Supplementary files format and content: comma seperated values containing read counts per gene

source_name: Induced Pluripotent Stem Cell

growth_protocol: The ESCs and iPSCs were seeded in a 6-well culture dish coated with Matrigel® and grown to 90% confluency before starting the directed differentiation using a modified published protocol (PMID: 35589753). At the end of the differentiation, at day 16, the medium was switched to RPE maintenance media (termed RPE medium) PMID: 30040247) containing Dulbecco’s Modified Eagle Medium:Nutrient Mix F-12 (DMEM/F12, Gibco), supplemented with 2% heat-inactivated fetal bovine serum (FBS, Gibco), 1X GlutaMAX (Gibco), 1X MEM Non-Essential Amino Acids solution (Gibco), 1X Sodium Pyruvate (100 mM, Gibco), 1X Penicillin-Streptomycin (10,000 U/mL, Gibco) and 10 mM Nicotinamide (Sigma-Aldrich) and cells were grown to day 30 before manually purifying and re-plating them onto transwell inserts (0.4 µm, Corning) pre-coated with 10 µg/mL Synthemax-II (Corning) in RPE medium. The RPE cells were further grown for 60 days before proceeding with RPE characterization on day 90 ESC- and iPSC-RPE cells. The culture was maintained at 37 °C under 5% CO2 and medium was changed every 2 to 3 days.

extract_protocol:
For in vitro RPE cultures, day 90 ESC-RPEs (n=1) and iPSC-RPEs (n=1) grown on Transwell inserts were dissociated into single cells with TrypLE Express for 30 min, at 37°C, 5% CO2 and resuspended to 1,000 cells/μL in 0.04% BSA in PBS prior to scRNA-seq. Six animals (Tx-ESC-RPE: n=3; Tx-iPSC-RPE: n=3) were sacrificed in deep anesthesia at 4-weeks post-surgery. After enucleation, the entire globes were washed thoroughly with PBS. The anterior segments were removed, and posterior poles (approximately 5 x 5 mm) were cut from the globes. The neuroretina was carefully removed, and the implant was taken out, and transferred into an Eppendorf tube with 500 μL PBS, using intraocular forceps (Alcon). The cells on implant were dissociated with 0.25% Trypsin-EDTA (Gibco) for 20 to 30 min at 37 °C, 5% CO2 with gentle resuspending every 5 min. Tx-RPE cells were filtered using a 30 µm strainer and resuspended in 0.04% BSA in PBS. RPE cell counting was performed. Due to the low number of cells retrieved, we spiked-in A549 (CCL-185, ATCC) immortalized cells to avoid library preparation failure due to insufficient cell count. The concentration was adjusted to 1,000 cells/μL in 0.04% BSA in PBS prior to scRNA-Seq.
Single cell suspensions from in vitro ESC- and iPSC-RPE and from transplanted Tx-ESC- and Tx-iPSC-RPE were maintained at 4 °C for less than 30 min before being transported to 10x Genomics Chromium instrument for  scRNA-seq. Using the 10x Genomics Single Cell 3’ Reagent Dual Index Kit V3, we performed droplet based single cell encapsulation, followed by bar-coded reverse transcription to generate the bar-coded complementary DNA (cDNA) library.

treatment_protocol: For transplanted RPE, day 60 ESC-RPE (n=3) and day 60 iPSC-RPE (n=3) were subretinally transplanted as a monolayer into immunocompetent rabbit eyes for 30 more days before harvesting single cells for single-cell RNA-sequencing.

value: Retinal pigment epithelial cell

value: Subretinally transplanted


title: Old_Naive_neg 1


title: Pancreatic cancer 1

value: Plasma-derived extracellular vesicles

value: Gemcitabine + Nab-paclitaxel

value: Metastatic


title: iPSC-RPE

value: In vitro culture


title: TREG_B_8

value: iLN+pLN

value: TREG

value: WT


title: Young_Naive_pos 2

value: young

value: CD8+ T cell

value: naive AsGM1+


title: SCRAMBLE capture (rep1)


title: Young_Naive_neg 4

value: naive AsGM1-


title: MAPT capture (rep3)


title: Tx-ESC-RPE_3

source_name: Embryonic Stem Cell


title: TREG_B_7

value: Synovium ankle


title: TREG_B_6

value: mLN


title: Tx-iPSC-RPE_3


title: Young_Naive_neg 3


title: Tx-ESC-RPE_2


title: TREG_B_5


title: Tx-iPSC-RPE_2


title: Tx-ESC-RPE_1


title: Young_Naive_neg 2


title: Young_Naive_neg 1


title: ESC-RPE


title: TREG_B_4

value: TNFdARE


title: MAPT capture (rep1)

value: neuroblastoma


title: MAPT capture (rep2)


title: Old_Dimer_pos 4

treatment_protocol:
mice vaccinated with pCI/stCtat DNA-vaccine
cells are either untreated or stimulated for 48h with Gibco™ Dynabeads™ Mouse T-Activator CD3/CD28 (see above)

value: old

value: dimer+


title: RACE_vs_SEQTR_Replicate3_bis

data_processing:
Ad hoc perl script
MiXCR software from MiLaboratories
Assembly: TCR alignment was performed using the IMGT database
Supplementary files format and content: Text file with the list of TCRs
Library strategy: Targeted amplification

source_name: peripheral blood mononuclear cell (PBMC) donnoe 4

extract_protocol:
mRNA were extracted using the Dynabeads mRNA DIRECT purification kit
Custum protocol for TCR sequencing describe in the manuscript.
ImmunoSEQ commercially available kit for TCR amplification
SMARTer (Takara) commercially available kit for TCR amplification

value: PBMC

tag: repertoire

value: beta TCR repertoire


title: TREG_B_3

tag: cell type


title: TREG_B_2

tag: tissue


title: Old_Dimer_pos 3


title: TREG_B_1

value: Ileum


title: Old_Dimer_pos 2


title: RACE_vs_SEQTR_Replicate1_bis


title: TCONV_B_8

value: TCONV


title: MEF-siHsf1+GCN5_rep3

city: Frederick

first: Chengkai

last: Dai

state: Maryland

address: Building 560, Room 32-31B, Center for Cancer Research, Mouse Cancer Genetics Program

department: CCR

institute: National Cancer Institute

data_processing:
For CUT&RUN-seq, the sequencing data were analyzed using the EpiCypher Cut&Run pipeline (Basepair Inc.). Briefly, following trimming, the raw sequencing reads were aligned to the mouse (GRCm38/mm10) and E. coli (strain K-12 MG1655) reference genomes respectively using Bowtie2. Subsequently, CUT&RUN peaks were called using SEACR with the stringent and spike-in normalization settings.
For RNA-seq, filtered raw data were mapped to the reference genome using HISAT2. RUVseq package was used to normalize the data. DESeq2 was used to analyze the DEG of samples (padj<=0.05 |log2FoldChange|>=0.0 are set as threshold).
Assembly: mm10 and K-12 MG1655
Supplementary files format and content: *.bed: Peak BED files
Supplementary files format and content: *.bigwig: bigWig files.
Supplementary files format and content: Gene_Count.txt: Tab-delimited text file includes raw RNA-seq read counts.
Supplementary files format and content: Gene_FPKM.txt: Tab-delimited text file includes normalized RNA-seq read counts.

source_name: Immortalized mouse embryonic fibroblasts

growth_protocol: MEFs were maintained in high glucose DMEM supplemented with 10% HyClone bovine growth serum and 1% penicillin–streptomycin.

extract_protocol:
Cut&Run experiments were performed using a CUTANA™ ChIC/CUT&RUN kit (Cat# 14-1048, EpiCypher) according to the manufacturer’s instructions. Briefly, proliferating MEFs were crosslinked with 1% formaldehyde in PBS for 1 min on culture plates. After quenching with glycine, cells were scraped off the plates and counted. 5x10^5 crosslinked cells were used for each sample. For the IgG control, both Hsf1WT and Hsf1CKO MEFs were mixed at a 1:1 ratio and incubated with rabbit IgG negative control antibodies. For the experimental groups, either Hsf1WT or Hsf1CKO MEFs (two biological replicates each group) were incubated with rabbit anti-c-MYC (D3N8F) monoclonal Abs (Cat#13987, Cell Signaling Technology). Of note, wash, cell permeabilization, and antibody buffers were all supplemented with 1% Triton X-100 and 0.05% SDS. Reversing cross-links was achieved by adding 0.8 μl of 10% SDS and 1 μl of 20 μg/μl Proteinase K to each sample and incubated at 550C overnight. Following purification, 0.5 ng E. coli spike-in DNAs were added to each eluted DNA sample.
Total RNAs were extracted from 5x10^5 MEFs, triplicates each experimental group, using Direct-zol RNA miniprep plus kit (Cat#R2073, Zymo Research). 1.5 μl of ERCC ExFold RNA spike-in mix 1 (1:10 dilution, Cat#4456739, ThermoFisher Scientific Inc.) was added to each siControl RNA sample and 1.5 μl of mix 2 (1:10 dilution) was added to each siHsf1 RNA sample.
For CUT&RUN-seq, total 10 ng DNAs each sample were used to generate sequencing libraries using a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (Cat#E7645, New England Biolabs Inc.). The clustering of indexed samples was performed using a TruSeq PE Cluster kit v3-cBot-HS (Cat#PE-401-3001, Illumina, Inc.).

treatment_protocol: To delete Hsf1, these MEFs were pre-treated with ethanol or 1 mM (Z)-4-Hydroxytamoxifen (4-OHT) for 7 days. To knock down Hsf1, MEFs stably expressing LacZ or V5-GCN5 were transfected with 10 nM control or Hsf1-targeting siRNAs for 2 days.

value: MEFs

value: Hsf1 KD

value: siHsf1 for 2 days + stable GCN5 expression


title: RACE_vs_SEQTR_Replicate3

source_name: peripheral blood mononuclear cell (PBMC) donnoe 3


title: Old_Dimer_pos 1


title: TCONV_B_6

value: WT


title: Young_Dimer_pos 4

value: young

value: CD8+ T cell


title: RACE_vs_SEQTR_Replicate2


title: Young_Dimer_pos 3


title: MEF-siControl_rep1

data_processing:
For RNA-seq, filtered raw data were mapped to the reference genome using HISAT2. RUVseq package was used to normalize the data. DESeq2 was used to analyze the DEG of samples (padj<=0.05 |log2FoldChange|>=0.0 are set as threshold).
Assembly: mm10
Supplementary files format and content: xls files for raw and normalized gene counts

source_name: cell line

extract_protocol:
Total RNAs were extracted from 5x105 MEFs, triplicates each experimental group, using Direct-zol RNA miniprep plus kit (Cat#R2073, Zymo Research). 1.5 μl of ERCC ExFold RNA spike-in mix 1 (1: 10 dilution, Cat#4456739, ThermoFisher Scientific Inc.) was added to each siControl RNA sample and 1.5 μl of mix 2 (1:10 dilution) was added to each siHsf1 RNA sample.
Sequencing libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit.

treatment_protocol: To knock down c-Myc, 100 nM control and c-Myc-targeting siRNAs were transfected into MEFs for 2 days.

value: cell line

value: Immortalized mouse embryonic fibroblasts

value: Myc WT

value: siControl for 2 days


title: MEF-siControl_rep2


title: MEF-siMyc_rep2

value: Myc KD

value: sic-Mcy for 2 days


title: RACE_vs_SEQTR_Replicate1


title: TCONV_B_4

value: iLN+pLN

value: TNFdARE


title: SEQTR_vs_RACE_Replicate3

value: PBMC

value: beta TCR repertoire


title: MEF-siMyc_rep1


title: TCONV_B_3

value: Synovium ankle

value: TCONV


title: RACE_vs_SEQTR_Replicate2_bis


title: Young_Dimer_pos 2

source_name: spleen

value: dimer+


title: MEF-siHsf1+GCN5_rep2

value: MEFs

value: Hsf1 KD

value: siHsf1 for 2 days + stable GCN5 expression


title: MEF-siHsf1+LacZ_rep3

value: siHsf1 for 2 days + stable LacZ expression


title: MEF-siHsf1l+GCN5_rep1


title: Young_Dimer_pos 1

value: young

value: CD8+ T cell


title: TCONV_B_2

value: mLN


title: SEQTR_vs_RACE_Replicate1


title: SEQTR_vs_RACE_Replicate2


title: sdLN preDC ADT

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
Hashtag1_TotalA0301: day 3
Hashtag2_TotalA0302: day 5
Hashtag3_TotalA0303: day 7
hashtag4_TotalA0304: ctrl

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where  HTO sequences were concatenated and treated as Custom library with default settings (v5.0.1) and aligning to the mm10 genome build.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: sdLN

extract_protocol:
sdLN were harvest from the mice. Single cell suspension were generated by digesting the tissue with Collagenase D and DNase I. The single cell suspension was stained with the antibody mix and sorted for the population of interest.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics) according to manufacturer’s instructions.

value: sdLN

value: CD135+ preDC from sdLN

value: wild type + Prtn3-Ert2Cre.lsl-tdTomato

value: multiplexed sample:untreated + Tamoxifen

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI :D3-tamoxifen/TotalSeq-A0301 ; D5-tamoxifen--/TotalSeq-A0302 ; D7-tamoxifen--/TotalSeq-A0303 ; WT--untreated/TotalSeq-A0304


title: sdLN preDC mRNA

value: mRNA


title: TCONV_B_1

value: Ileum

value: TNFdARE


title: TREG_A_8

value: iLN+pLN

value: TREG

value: WT


title: Mouse3_replciate2_beta

source_name: Splenocytes

value: Splenocyte

tag: mice strain

value: beta TCR repertoire


title: TCONV_B_5

value: TCONV


title: Mouse3_replicate1_beta


title: MEF-siControl+GCN5_rep3

value: MEFs

value: Hsf1 WT

value: siControl for 2 days + stable GCN5 expression


title: MEF-siHsf1l+LacZ_rep1

value: Hsf1 KD

value: siHsf1 for 2 days + stable LacZ expression


title: MEF-siHsf1+LacZ_rep2


title: TREG_A_7

value: Synovium ankle


title: SI Crypts_sc_KO2

city: Heidelberg

first: Llorenç

last: Solé Boldo

address: Im Neuenheimer Feld, 580

institute: DKFZ

description: single cell RNA

data_processing:
Alignment of the raw fastq-data with CellRanger v.2.1.0 to reference genome.
QC and data filtereing with CellRanger v.2.1.0.
Sample combination with CellRanger v.2.1.0.
QC and sample integration with Seurat v.3.1.1.
Clustering and visualization with Seurat v.3.1.1.
Assembly: mm9
Supplementary files format and content: Seurat object containing the resulting count matrix for all samples as resulted from CellRanger analysis and before QC with Seurat.

source_name: Small Intestine

extract_protocol:
Small intestine crypts were isolated from three WTwt and three Tet2/3 dkoKO mice as previously described (Sato and Clevers, 2013). Single-cell suspensions from intestinal crypts were obtained by enzymatic digestion, incubating crypts in MEM medium supplemented with 2 mg/ml Trypsin and 2000 U/ml DNAse I for 30 minutes at 37ºC in a water bath, as previously described (Grun et al., 2015). Apoptotic and dead cells were removed from suspension using the Dead Cell Removal Kit (Miltenyi Biotec).
Approximately 20,000 cells per sample were loaded into the Chromium Controller system, and libraries were subsequently prepared using the Chromium Single Cell 3’ Reagent Kit v.2 (10X Genomics), following the manufacturer’s instructions. Libraries were sequenced on a HiSeq 4000 device (Illumina) using paired-end (26+74bp) settings for 100 cycles.

tag: strain

value: Small intestine crypts

tag: age

value: 11 weeks


title: Mouse3_replicate2_alpha

first: Raphael

institute: Centre Hospitalier Universitaire Vaudois (CHUV)

value: alpha TCR repertoire


title: Mouse3_replicate1_alpha


title: TREG_A_6

source_name: mLN

value: mLN


title: TREG_A_5

source_name: Ileum

value: Ileum


title: TREG_A_4

value: iLN+pLN

value: TNFdARE


title: SI Crypts_sc_KO1

description: single cell RNA


title: SI Crypts_sc_WT3

description: single cell RNA

value: wild type


title: SI Crypts_sc_WT2

description: single cell RNA


title: Mouse2_replciate2_beta

value: Splenocyte


title: MEF-siControl+GCN5_rep2

tag: treatment


title: MEF-siControl+LacZ_rep2

value: siControl for 2 days + stable LacZ expression


title: MEF-siControl+LacZ_rep1


title: Mouse2_replicate1_beta

value: beta TCR repertoire


title: MEF-siControl+LacZ_rep3

value: MEFs


title: SI Crypts_sc_WT1

description: single cell RNA


title: Hsf1WTCKO MEF-IgG

description: IgG

data_processing:
Library strategy: CUT&RUN-seq
For CUT&RUN-seq, the sequencing data were analyzed using the EpiCypher Cut&Run pipeline (Basepair Inc.). Briefly, following trimming, the raw sequencing reads were aligned to the mouse (GRCm38/mm10) and E. coli (strain K-12 MG1655) reference genomes respectively using Bowtie2. Subsequently, CUT&RUN peaks were called using SEACR with the stringent and spike-in normalization settings.
For RNA-seq, filtered raw data were mapped to the reference genome using HISAT2. RUVseq package was used to normalize the data. DESeq2 was used to analyze the DEG of samples (padj<=0.05 |log2FoldChange|>=0.0 are set as threshold).
Assembly: mm10 and K-12 MG1655
Supplementary files format and content: *.bed: Peak BED files
Supplementary files format and content: *.bigwig: bigWig files.
Supplementary files format and content: Gene_Count.txt: Tab-delimited text file includes raw RNA-seq read counts.
Supplementary files format and content: Gene_FPKM.txt: Tab-delimited text file includes normalized RNA-seq read counts.

value: Hsf1 WT + CKO (1:1)

value: Ethanol + 4-OHT for 7 days

tag: antibody

value: Normal rabbit IgG (EpiCypher, 13-0042k)


title: Mouse2_replicate2_alpha


title: SI Crypts_sc_KO3

description: single cell RNA


title: TREG_A_3

value: TREG


title: TREG_A_1


title: Mouse2_replicate1_alpha


title: Hsf1CKO MEF-MYC_rep2

value: Hsf1 CKO

value: 4-OHT for 7 days

value: c-Myc/N-Myc (Cell Signaling Technology, 13987, lot 5)


title: TCONV_A_8

value: TCONV

value: WT


title: MEF-siControl+GCN5_rep1

value: Hsf1 WT

value: siControl for 2 days + stable GCN5 expression


title: SI Crypts_KO2 [RNA-seq]

data_processing:
Basecalling: bcl2fastq 2.20.0.422
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Transcriptome mapping: Tophat 2.0.6.
Computation of count data: htseq-py.
Downstream analyses were performed with DESeq 1.10.1 and Cuffdiff 2.0.
Assembly: mm9
Supplementary files format and content: count table containing the count values for all genes in all samples.

extract_protocol:
We followed a previously published protocol to isolate intestinal crypts [PMID: 23097115]. Briefly, the small intestine (Jejunum) was flushed with ice-cold PBS then cut open longitudinally. The Jejunum was minced into small pieces in cold PBS (2-5 mm) and then incubated for 30 min at 4 °C in PBS containing 2 mM EDTA. Intestinal fragments were then transferred into cold PBS and the villi fraction was mechanically isolated by shaking. Then the intestinal fragments were transferred into fresh cold PBS and the crypts fraction was mechanically isolated by vigorously shaking. This step was repeated further two times to recover the crypts. Crypts fractions were then combined and passed through a 70 µm cell strainer. The combined fractions of crypts were then washed in PBS, centrifuged at 300g for 3 min, and stored at -80°C for RNA extraction.  Total mRNA was extracted using TRIzol.
Libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina), according to manufacturer´s instructions.

value: Small intestine

value: 11 weeks


title: Mouse1_replciate2_beta

value: Splenocyte


title: Hsf1CKO MEF-MYC_rep1


title: TCONV_A_7

value: Synovium ankle


title: SI Crypts_KO1 [RNA-seq]


title: Mouse1_replicate1_beta

value: beta TCR repertoire


title: TCONV_A_6

value: mLN


title: Hsf1WT MEF-MYC_rep2

value: MEFs

value: Ethanol for 7 days


title: SI Crypts_WT3 [RNA-seq]

value: wild type


title: TCONV_A_5

value: Ileum


title: SI Crypts_WT2 [RNA-seq]


title: Hsf1WT MEF-MYC_rep1


title: SI Crypts_WT1 [RNA-seq]


title: TCONV_A_3

value: TNFdARE


title: Mouse1_replicate1_alpha

value: alpha TCR repertoire


title: SEQTR_Replicate2_bis

source_name: peripheral blood mononuclear cell (PBMC) donnor 2

value: PBMC


title: SI Crypts_KO3 [RNA-seq]


title: SEQTR_Replicate1_bis


title: TCONV_A_1

value: TCONV


title: SEQTR_Replicate2

source_name: peripheral blood mononuclear cell (PBMC) donnor 1


title: SEQTR_Replicate3


title: liquid pooled library, replicate 2

first: Julia

last: Willett

state: Minnesota

address: 689 23rd Avenue SE, 4-149 Micro Research Facility

data_processing:
Reads were trimmed to remove Illumina adapter sequences using Trimmomatic and were mapped to the OG1RF reference genome (GenBank CP002621.1, NCBI RefSeq NC_017316.1) using Bowtie.
SMarT TnSeq analysis was performed using custom scripts and the Mesabi supercomputer at the Minnesota Supercomputing Institute.  The technical quality of the sequencing results was evaluated using theFastQCpackage produced by Babraham Bioinformatics (63).  We placed particular emphasis on thequality of the read tails as well as the presence of adapter contamination.  Thecutadaptpackage was used to remove residual adapters and the primed transposon region from the sequenced forward reads (64).
The trimmed reads were then aligned to theE. faecalisOG1RF reference genome using bwa-mem (65).  Mapped reads not beginning or ending at a TA site wereremoved due to the potential for integrations independent of transposon activity.  Bedtoolsgenomecovwas used to quantify the number of integrations on a per position basis (66).
R and the package “sqldf,” which provides an SQL interface for Rdataframes (67), were used to summarize the integration data at each TA site in the OG1RF genome.  These were filtered for the strains present in the SMarT TnSeq library using the 2D barcodes assigned to each transposon mutant stock tube.
Integration sites, matched between sample sets, were evaluated for a significant change in the proportion of integrations received using a Chi-squared test and a Monte Carlo-based method that models the effect of experimental replicates and determines whether the mean proportionparameteris significantly different for each gene between experimental conditions.  The Chi-squared results were filtered for significance (adjusted p < 0.05), and results with a significant p value that did not meet the highest confidence level from the Monte Carlo simulations (value = 1.19) were removed.
Assembly: NC_017316
Supplementary files format and content: tab-delimited file showing reads mapped to a specific nucleotide in the OG1RF genome (site of Tn insertion) plus metadata about the specific gene/intergenic region where the insertion is located.  The file also contains statistical comparison to a previously generated version of the library and the log2 fold change between this library and the previously generated version.
Library strategy: Tn-Seq

organism: Enterococcus faecalis

growth_protocol: Cells were grown overnight in BHI growth medium in deep-well 96-well plates.  200 uL from each well was combined in a Falcon tube.  Cells were pelleted and stored at -20 oC until DNA extraction.

extract_protocol:
DNA was extracted using a Qiagen Dneasy kit with an additional lysozyme treatment prior to lysis.
Libraries were prepared using a NEBNext Ultra II FS DNA Library Prep Kit for Illumina and a Nextera® XT Index Kit v2 Set A.  Libraries were sequenced on a NextSeq P1 flow cell (150 PE) with ~2.1 million reads per sample (~300 reads/mutant).

value: liquid pooling


title: liquid pooled library, replicate 1


title: liquid pooled library, replicate 3


title: Yak_testis

first: Xingdong

last: Wang

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Yak, LU_Bosgru_v3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos grunniens

source_name: Testicular tissue of yak after sexual maturity for single-cell RNA sequencing

extract_protocol:
The frozen testicular tissue was removed and immediately placed in a 37 ℃ water bath for 2 min. After the tissue was melted, take it out with tweezers, place it in the resuscitation solution (DMEM/F12 medium+0.5mol/L sucrose+20% FBS), place it in a 37 ℃ water bath for 2min, preheat the DPBS to wash the tissue block for 2-3 times, place the tissue block in DMEM/F12 medium (Gibco, Waltham, MA, USA), and cut the tissue with ophthalmic scissors. Transfer the testicular tissue of cutted to a 15mL centrifuge tube, and add a solution with 0.2% collagenase IV (2 mg/mL) (Sigma, City of Saint Louis, USA) and hyaluronidase (2 mg/mL) solution (Sigma, City of Saint Louis, USA) (1:1) of 8~10 times the total amount of tissue. The centrifuge tube was placed in a 37℃ constant temperature shaker at 120 rpm (30 min, after 15min, 200μL tissue digestive fluid was taken every 3min to observe the digestive condition under the microscope until the free tubules with no mass tissue could be clearly observed), centrifuge at 1000 r/min for 5 min and drain the supernatant. 0.25% trypsin solution (2.5 mg/mL) (Gibco, Waltham, MA, USA), 8-10 times the total amount of tissue blocks, was added again. Finally, the tissue digestible solution was placed in a constant temperature shaker at 37℃ at 120 rpm (40 min, after 15min, 200μL tissue digestible solution was taken every 3min to observe the digestion condition under the microscope until the single cell suspension could be clearly observed). Fetal bovine serum was added to terminate digestion. The mixed cell suspension was blown evenly and filtered through 70μm and 40μm screens successively. The filtrate was collected and centrifuged at 300×g 4℃ for 5 min, the supernatant was abandoned, and the cells were re-suspended in DMEM/F12 complete medium containing 10% FBS, and cultured at 37 ℃ with 5% CO2. Part of the cell suspension was stained with Trypan blue and counted by automatic counter to calculate the number of cells and viability. The concentration was ~1000 cells/uL and cell viability>90% were used for scRNA seq.
The Cell suspension was loaded onto the Chromium Single Cell Controller instrument (10x Genomics, Pleasanton, CA, USA) and the bead and cells with Cell Barcode were wrapped in the droplet. The droplet containing cells was collected, and then the cells were lysed in the droplet, so that the mRNA in the cells combined with the bead Cell Barcode to form a Single Cell GEMs, and the reverse transcription reaction was performed in the droplet to construct the cDNA library. GEM-RT-PCR was performed with a 96-hole reaction module (Bio-Rad; CT022510) in the C1000 Touch thermal cycler to generate barcode cDNA using the following procedures: 53°C for 45 min; 85°C for 5 minutes; Maintain at 4°C. The sample index on the library sequence is used to distinguish the source of the target sequence.

value: testis

tag: cell line

value: Germ cell

tag: developmental stage

value: Postsexual maturity


title: SEQTR_Replicate1

last: Genolet

address: Biopole 3, Chemin des Boveresses 155


title: Marc-145 cells, siSRCAP, 24 h [SiSRCAP_RNA_2]

status: Public on May 21 2023

city: Taian

first: Guofei

last: Ding

address: Daizong Street, Taishan District, Tai'an City, Shandong Province

institute: shandong agricultural university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. （Default Parameter developed by Wuhan Seqhealth Co., Ltd.）
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Chlorocebus sabaeus

source_name: Marc-145 cells

growth_protocol: Marc-145 cells were grown in DMEM medium containing 10% FBS, and supplemented with supplemented with penicillin (100 units/ml) and streptomycin (100 mg/ml).

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol:
Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence. For SRCAP siRNA, cells were transfected using Lipofectamine RNAiMAX reagent (Invitrogen, USA).
The transfected cells were infected with PRRSV TA-12 and total RNA was extracted 24 hours after infection.

value: Marc-145 cells

value: Renal epithelial cells

tag: genotype

value: SRCAP knockdown

tag: time


title: Marc-145 cells, siControl, 24 h [SiN_C_RNA_2]

value: N.C. knockdown


title: Marc-145 cells, siSRCAP, 24 h [SiSRCAP_RNA_1]


title: Lacrimal Gland, Male, replicate 1

city: La Jolla

first: Helen

last: Makarenkova

address: 10550 N Torrey Pines Rd, MB-218

institute: The Scripps Research Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lacrimal Gland

extract_protocol:
One female and two male samples were prepared for scRNAseq analysis. For each sample, six dissected LGs of three animals aged of 2 months were combined and processed as follows. First, LGs were quickly minced on ice in a dish pre-filled with cold DPBS, rinsed, and transferred to a 12-well plate placed in a shaking water bath (37°C, 80 rpm) containing 2 mL of digestion medium of following composition: DMEM/F12 , 0.5% BSA , 15 mM HEPES, 3 mM CaCl2 , 125 U/mL collagenase IV , 1 U/mL dispase II  and 20 U/mL DNase-I. After 30 min, samples were gently triturated by pipetting up and down 15 times with a wide-bored 1 mL tip. At 60 and 90 min, samples were gently triturated 10 to 15 times with a regular 1 mL pipet tip. At the end of the digestion (90 min in total), cells were pelleted (300 x g, 5 min, 4 °C), washed with cold HBSS buffer supplemented with 10 mM HEPES and 1 mM EDTA and gently re-suspended in 1 mL of accutase solution. After 5 min at 37°C, cell suspension was pipetted up and down 5 times and left at RT for 2 min. Then, accutase was inactivated by the addition of 1 mL of DMEM/F12 supplemented with 10% FBS and 15 mM HEPES. Cells were pelleted (300 x g, 5 min, 4 °C) and incubated for 10 min at RT with HBSS supplemented with 10 mM HEPES, 2 mM MgCl2, 2 mM CaCl2 and 200 U/mL DNase-I. Cell suspension was sequentially passed 2 times through a 3 mL syringe with needles: 18G, 22G and 25G. Dissociated cells were filtered through a pre-wet 70-µm mesh cell strainer and pelleted (300 x g, 5 min, 4 °C) before incubation for 5 min at RT with 5 mL of RBC lysis buffer 1X  to deplete erythrocytes. After centrifugation (300 x g, 5 min, 4 °C) and re-suspension into cold HBSS supplemented with 0.5% BSA and 10 mM HEPES, cells were passed through a pre-wet 30-µm mesh cell strainer. After centrifugation (400 x g, 5 min, 4 °C), dead cells and debris were depleted using the MS columns and the dead cell removal kit . The cell suspension was washed 3 times with cold scRNA-seq buffer composed of DPBS supplemented with 0.04% BSA, and pelleted at 400 x g, 5 min, 4 °C. The number of cells and the viability rate (78-79%) were evaluated using trypan blue staining analyzed with the Countess 3. Cell suspension volumes were then adjusted with cold scRNA-seq buffer to obtain between 700 and 1200 cells per µL and cells were counted again to obtain the final cell density. Cells were kept on ice at all times.
Cells were processed for scRNA-seq using the Chromium Single Cell 3' kit (v3.1 Chemistry) from 10X Genomics (Pleasanton, CA) according to the manufacturer’s protocols. cDNA was amplified by 11 cycles. Analysis of cDNA and libraries was done using Bioanalyzer or TapeStation (Agilent).

value: Lacrimal Gland

value: 2 months old

value: Male


title: Marc-145 cells, siControl, 24 h [SiN_C_RNA_1]


title: TCONV_A_4

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Assembly: Mus musculus.Ensembl.GRCm38.82
Supplementary files format and content: ABC_rawCounts.txt: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: ABC_fpkmCounts.txt: Matrix table with FPKM values for all biologically meaningfully expressed genes for each sample.

source_name: iLN+pLN

value: iLN+pLN


title: Mouse1_replicate2_alpha

city: Epalinges

value: Splenocyte


title: 13B_M_3061

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 13B_M_3065


title: 13B_M_3056


title: 13B_M_3055


title: 13B_M_3062


title: 13B_M_3060


title: 13B_M_3063


title: 13B_M_3067


title: 13B_M_3057


title: 13B_M_3064


title: 13B_M_3066


title: 13B_M_3058


title: Lacrimal Gland, Male, replicate 2

description: 10x Genomics

tag: Sex


title: 13B_M_3054


title: 13B_M_3053


title: 13B_M_3052


title: 13B_M_3051


title: 13B_M_3050


title: 13B_M_3049


title: 13B_M_3047


title: 13B_M_3048


title: 13B_M_3046


title: 13B_M_3045


title: 13B_M_3043


title: 13B_M_3044


title: 13B_M_3042


title: 13B_M_3041


title: 13B_M_3040


title: 13B_M_3059


title: 13B_M_3039


title: 13B_M_3035


title: 13B_M_3037


title: 13B_M_3033


title: 13B_M_3034


title: 13B_M_3029


title: 13B_M_3031


title: 13B_M_3036


title: 13B_M_3027


title: 13B_M_3038


title: 13B_M_3025


title: 13B_M_3030


title: 13B_M_3032


title: 13B_M_3021


title: 13B_M_3022


title: 13B_M_3026


title: 13B_M_3019


title: 13B_M_3020


title: 13B_M_3016


title: 13B_M_3017


title: 13B_M_3014


title: 13B_M_3018


title: 13B_M_3015


title: 13B_M_3011


title: 13B_M_3010


title: 13B_M_3013


title: 13B_M_3012


title: 13B_M_3023


title: 13B_M_3009


title: 13B_M_3008


title: 13B_M_3006


title: 13B_M_3005


title: 13B_M_3004


title: 13B_M_2938


title: 13B_M_2936


title: 13B_M_2932


title: 13B_M_2933


title: 13B_M_2928


title: 13B_M_2929


title: 13B_M_2925


title: 13B_M_2931


title: 13B_M_2923


title: 13B_M_2930


title: 13B_M_2926


title: 13B_M_2920


title: 13B_M_2921


title: 13B_M_2924


title: 13B_M_2919


title: 13B_M_2922


title: 13B_M_2917


title: 13B_M_2937


title: 13B_M_2939


title: 13B_M_2916


title: 13B_M_2935


title: 13B_M_2918


title: 13B_M_2927


title: 13B_M_2915


title: 13B_M_3007


title: 13B_M_2913


title: 13B_M_2914