title: FRG control condition, biological rep1

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology and Dermato-Cosmetology

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

description: Gene expression data from liver tissue of FRG mice under NTBC treatment

hyb_protocol: 12.5 μg fragmented aRNA was hybridized to Affymetrix Mouse 430 2.0 arrays along with a hybridization cocktail solution and then placed in a Genechip Hybridization Oven-645 (Affymetrix) rotating at 60 rpm at 45 ºC for 16 h. After incubation, arrays were washed on a Genechip Fluidics Station-450 (Affymetrix) and stained with the Affymetrix HWS kit as indicated by the manufacturer’s protocols.

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G and the quality control matrices were confirmed with the Affymetrix GCOS software following the manufacturer’s guidelines.

data_processing: Background correction, quantile normalization and summarization were done with Robust Multi-array Analysis algorithm using Transcriptome Analysis Console (TAC) 4.0.2 (Applied Biosystems)

source_name: FRG liver under continuous NTBC therapy

label_protocol: Total RNA (100 ng) was used for amplification and in vitro transcription using the Genechip 3’ IVT Express Kit following the manufacturer’s instructions (Affymetrix). The amplified RNA was purified with magnetic beads and 15 μg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Unless specified otherwise, all mice received continuous NTBC treatment (16 mg/l) through their drinking water, supplemented with 3 % (w/v) dextrose for taste. Mice were fed with irradiated LabDiet® 5LJ5 chow ad libitum, which is a low-tyrosine and low-phenylalanine diet that acts as a surrogate for the protein-restricted diet of HT1 patients. All mouse caring, breeding and experimental procedures were performed in accordance with the ethical standards of the Vrije Universiteit Brussel and National Rules on Animal Experimentation. Mice were group-housed in individual ventilated cages (IVC) in a temperature (19 – 23 °C) and humidity (30 – 70% relative humidity) regulated environment with a 14/10-hour light/dark cycle under continuous NTBC treatment (16 mg/l) administered through their drinking water. Cage environment was enriched with cardboard shelters, nesting material and wooden sticks.

extract_protocol: Total RNA was extracted from all samples using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions. The isolated RNA was quantified at 260 nm using a Nanodrop spectrophotometer (Thermo Scientific). Total RNA was reverse transcribed into cDNA using iScriptTM cDNA Synthesis Kit (Bio-Rad) followed by cDNA purification with the Genelute PCR clean up kit (Sigma-Aldrich).

treatment_protocol: At the age of 11 weeks, NTBC therapy was discontinued for seven consecutive days for the FRG 7 days withdrawal group whereas it was administered continuously for the FRG control group.

tag: gender

value: male

tag: tissue

value: liver

value: 12 weeks

value: continuous NTBC therapy


title: Daedalus_WT2_MPP

status: Public on Dec 23 2020

type: SRA

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

country: USA

institute: Yale University

description:
Sorted from mice in the steady state, with no immunological challenge or disease.
In order to better assess the transcriptomic changes resulting from ablation of the Daedalus locus we performed an RNA-seq analysis on progenitors from Daedalus KO and WT mice.
Daedalus_RNASeq_Gene_Expression.txt

library_source: transcriptomic

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment and junction mapping to mouse genome GRCm38/mm10 performed using Tophat2 and Bowtie2 (Trapnell et. Al. Genome Biology, 2013)
Transcript quantitation, normalization and differential expression testing performed using Cufflinks ((Trapnell et. al. 2012 Nature Protocols)
Data analysis and visualization performed in R, using packages cummeRbund (http://compbio.mit.edu/cummeRbund/) and pheatmap (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of normalized FPKM between samples

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow derived haematopoietic progenitors (MPPs: cKit+, Sca1+, Flt3lo) from Daedalus (Linc7) wildtype mice

growth_protocol: Mice deficient in the Daedalus locus were generated by injection of Cas9 RNA and chimeric guideRNAs flanking the locus (SuppTable1) into C57/B6N embryos as previously reported. The offspring of one of these mice were interbred to create a line of Daedalus deficient mice. All mice were housed and maintained under pathogen-free conditions in Yale University animal facilities. Female and male littermates from heterozygous crossings between 4 and 12 weeks old were used for this experiment.

extract_protocol:
Purified populations of haematopoietic progenitors were spun down in FACS medium, washed and RNA was extracted. Purified RNA was obtained using QIAGEN RNeasy Micro kit or Zymo-research Direct-zol RNA Microprep kit.
mRNA for RNAseq analysis was purified using PolyA+ selection and processed by the Yale Center for Genome Analysis using standard methodology using Illumina TruSeq mRNA-Seq Sample Prep Kits, library quality and concentration assayed using a Bioanalyzer, RNA was sequenced on a HiSeq2500 with 75bp pair-ended reads.

treatment_protocol: Purified populations of haematopoietic progenitors were sorted from WT and KO littermate mice as described in the methods section. The progenitor populations sorted were gated on lineage negative cells (Lineage cocktail: B220, CD4, CD8, CD11b, CD11c, CD19, Gr1, NK1.1, TCRgd, Ter119). Three subpopulations were separated based on expression of three markers - cKit, Sca1 and Flt3/CD135, these populations are as follows Haematopoietic stem cells (HSCs: cKit+, Sca1+, Flt3-ve); multipotent progenitors (MPPs: cKit+, Sca1+ Flt3lo); lymphoid-primed multipotent progenitors (MPPs: cKit+, Sca1+ Flt3hi).

tag: cell type/tissue

value: Bone marrow derived haematopoietic progenitors.

tag: strain

tag: genotype/variation

value: wild type


title: Daedalus_WT2_HSC

source_name: Bone marrow derived haematopoietic progenitors (HSCs: cKit+, Sca1+, Flt3-ve) from Daedalus (Linc7) wildtype mice


title: Daedalus_WT1_HSC


title: Daedalus_WT1_MPP


title: GEM-PNST_4

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Paired-end fastq files were aligned to mm10 (mouse) genomes using Tophat (Neurofibroma, single-end) and HISAT2 (paraspinal tumors and GEM-PNST, paired-end).
Raw counts were calculated using featureCounts.

molecule: total RNA

source_name: GEM-PNST tumor

growth_protocol: Mice raised in animal facility under standard conditions until a specific timepoint or tumor size limit reached.

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) following manufacturer's protocol
RNA libraries were prepared according to the Illumina protocol (Nextera 817 XT DNA Sample Preparation Kit).

treatment_protocol: No drugs were administered to mice during these experiments.

tag: tumor stage

value: GEM-PNST tumor

value: Ink4a/Arf+/-; Nf1fl/fl; DhhCre GEM-PNST


title: HBD2

type: RNA

city: Zhengzhou

first: Yue

last: Du

address: No.1 Jianshe East Road

country: China

institute: The First Affiliated Hospital of Zhengzhou University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: The chip probe signals were collected by the Agilent Feature Extraction software, and the raw data was standardized by GeneSpring GX v12.1 software (Agilent Technologies).

organism: Homo sapiens

source_name: MIA PaCa-2 cells, HBD2

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the cells and quality was evaluated using NanoDrop ND-1000. RNA integrity was assessed by standard denaturing gel electrophoresis.

value: Pancreatic cancer cell line

tag: treatment

value: HBD2 treatment

tag: cell line

value: MIA PaCa-2


title: FRG seven days withdrawal condition, biological rep2

description: Gene expression data from liver tissue of FRG mice after seven days NTBC therapy discontinuation

label: biotin

source_name: FRG liver after seven days NTBC therapy withdrawal

tag: age


title: GEM-PNST_3


title: Paraspinal_tumor_subgroup_1_2

source_name: Paraspinal tumor

value: Paraspinal tumor

value: Ink4a/Arf+/-; Nf1fl/fl; DhhCre Paraspinal tumor, sub-cluster #1


title: FRG control condition, biological rep3


title: Paraspinal_tumor_subgroup_1_1


title: FRG seven days withdrawal condition, biological rep3

value: after seven days NTBC therapy withdrawal


title: ADDC

source_name: MIA PaCa-2 cells, ADDC

value: ADDC treatment


title: GEM-PNST_2


title: Neurofibroma_12

source_name: Neurofibroma tumor

value: Neurofibroma tumor

value: Nf1fl/fl; DhhCre Neurofibroma


title: FRG seven days withdrawal condition, biological rep1

value: male


title: Paraspinal_tumor_subgroup_2_2

value: Ink4a/Arf+/-; Nf1fl/fl; DhhCre Paraspinal tumor, sub-cluster #2


title: GEM-PNST_1


title: Paraspinal_tumor_subgroup_2_1


title: Control

source_name: MIA PaCa-2 cells, control

value: untreated


title: FRG control condition, biological rep2

value: liver

value: 12 weeks

value: continuous NTBC therapy


title: Neurofibroma_8


title: Neurofibroma_9


title: Neurofibroma_11


title: Neurofibroma_7


title: Neurofibroma_6


title: NB-TU 63: Neuroblastoma primary tumor at diagnosis 63

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

description: Collected during surgery of male and female patients

data_processing:
RNA-seq reads were mapped with GSNAP v2014-12- 28 [20147302] (“-- maxsearch=100 -- npaths=1 -- max-mismatches=1 --novelsplicing=0 “) to human reference genome build GRCh37. Known SNPs and splice sites were extracted from dbSNP build 138 and Ensembl GRCh37 build 75, respectively.
DESeq2-normalized fragments per million (FPM), log2 scale
Genome_build: hg19
Supplementary_files_format_and_content: DESeq expression matrix (log2): cpm and rpkm

source_name: Tumor at diagnosis. Patient p63

growth_protocol: Samples were fresh frozen. Not grown.

extract_protocol:
miRNeasy Micro Kit
RNA-Seq, New England Biolab kit with polyA enrichment

value: Tumor cells from the primary tumor


title: imb_koenig_2017_10_JKRS33_SRSF6_rep4

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

country: Germany

institute: University Würzburg

description:
SRSF6 iCLIP replicate 4
in vivo iCLIP

data_processing:
Basic sequencing quality checks were applied to all reads using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Remaining adapter sequences were trimmed from the right end of the reads using Flexbar (version 3.0.0) allowing up to one mismatch in 10 nt, requiring a minimal overlap of 1 nt of read and adapter. After trimming off the adapter, the barcode is trimmed off of the left end of the reads (first 9 nt) and added to the header of the read, such that the information is kept available for downstream analysis. Reads shorter than 15 nt were removed from further analysis. Trimmed and filtered reads were mapped to the human genome (assembly version GRCh38) and its annotation based on GENCODE release 25 (Harrow et al., 2012) using STAR (version 2.5.2b) (Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited on the 5’ end of reads and only uniquely mapping reads were kept for further analysis. Duplicate reads were marked using the dedup function of the bamUtils tool suit (version 1.0.13, https://github.com/statgen/bamUtil). Marked duplicates with identical random barcodes were removed as they are considered technical duplicates, while biological duplicates showing distinct random barcodes were kept for further analysis. bedgraph files of the positions upstream of the 5' end of the reads were produced separated by strand. They were transform to bigwig files using bedGraphToBigWig of the kentUtils tool suit (version v302).
https://github.com/ENCODE-DCC/kentUtils
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig

source_name: Human pancreatic beta cell line EndoC-βH1

growth_protocol: The EndoC-βH1 cells were plated in a 10cm petri dish at a density of 8x10^6 cells, and cultured as described by Brozzi, F. Diabetologia, 58, 2307-2316, 2015.

extract_protocol:
EndoC-βH1 cells were lysed in 1ml lysis buffer followed by immunoprecipitation as described on previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016)
iCLIP libraries were prepared from EndoC-βH1 cells in wild-type conditions according to the previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016). For immunoprecipitation, we used 7.5 µg polyclonal anti-SRSF6 antibody produced in rabbit ((aa250-300) LS-C290327, LifeSpan Bioscience), per sample. The libraries were sequenced as single-end reads on HiSeq 2500 sequencing system.

tag: cell type

value: pancreatic beta cell line

tag: passage

tag: antibody

value: Anti-SRSF6/SRP55 (aa250-300) LS-C290327, LifeSpan Bioscience.

tag: barcode

value: CGAG


title: cardiomyocytes, neg control rep 1

city: New York

first: Kelly

middle: Madigan

last: Banks

state: NY

address: 1300 York Ave, LC711

department: Surgery

institute: Weill Cornell Medicine

data_processing:
Tophat and Cufflinks
DESeq2 Differential Analysis in R
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts file

source_name: 30 day old cardiomyocytes

growth_protocol: Basal media RPMI+B27+Ascorbic Acid+ Glutamax+ MTG, Days 1-3 +BMP4, Activin A; Days 3-6+ XAV, VEGF; Day 8-10+VEGF

extract_protocol:
Rneasy kit
TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: 10 days treament with indicated hormones started at day 20 in culture

value: Negative Control

value: 30 day old cardiomyocytes


title: cardiomyocytes, MPTD rep 3

source_name: 30 day old cardiomyocytes, 10 days with treatment MPTD

value: MPTD


title: cardiomyocytes, neg control rep 2


title: cardiomyocytes, DexT3 rep 3

source_name: 30 day old cardiomyocytes, 10 days with treatment Dex/T3

value: Dexamethosone/ T3


title: cardiomyocytes, DexT3 rep 1


title: cardiomyocytes, MPTD rep 1


title: cardiomyocytes, DexT3 rep 2


title: cardiomyocytes, MPTD rep 2


title: Neurofibroma_10


title: imb_koenig_2017_10_JKRS33_SRSF6_rep3

description:
SRSF6 iCLIP replicate 3
in vivo iCLIP

value: ATAC


title: cardiomyocytes, neg control rep 3


title: Neurofibroma_5

value: Neurofibroma tumor


title: Inflammatory monocytes, WT_2

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig (coverage for mapped reads)

source_name: inflammatory monocytes

growth_protocol: Mouse KP cells were transfected with pLKO.1-Tet on-shNpm1-3(N3), pLKO.1-Tet on-shNpm1-4(N4) or pLKO.1-Tet on-shNpm1-5 (N5) and then selected by using 2ug/ml puromycin, to get the 3 stable cell lines. These 3 stable cell lines (N3, N4 or N5) were treated with or without 100ng/ml Doxycline .

extract_protocol:
Extract total RNA by using Rneasy Plus Mini Kit (Qiagen)
The quantity and quality of total RNA was assessed on a 2100 BioAnalyzer instrument (Agilent Technologies, Inc.). 1 ng of total RNA was used to prepare libraries using Trio RNA-Seq library prep kit (Tecan Genomics, Inc., part number 0506-96, mammalian rRNA Deplete) following the manufacturerâs instructions (https://www.nugen.com/sites/default/files/M01440v2_User_Guide%3A_Trio_RNA-Seq_4270.pdf). Briefly, the library prep consists of the following steps: DNase treatment to remove genomic DNA, first strand and second stand cDNA synthesis from the input RNA, single primer isothermal amplification (SPIA) of the resultant cDNAs, enzymatic fragmentation and construction of unique barcoded libraries, PCR library amplification (for these samples, 4 cycles were used) and a final step to remove rRNA transcripts. The Agencourt AMPure XP bead (Beckman Coulter) purified libraries were quantified using by qPCR and the size distribution was checked using Agilent TapeStation 2200. The libraries were subjected to paired-end 50 bp sequencing on HiSeq 2500 sequencing system (Illumina, v4 chemistry).$

treatment_protocol: Control group includes KP-N3, KP-N4 and KP-N5 stable cell lines (Npm1 is normally expressed); Knockdown group includes KP-N3, KP-N4 and KP-N5 stall cell lines treated with Doxycycline ( Npm1 is Knockdown).

value: inflammatory monocytes

tag: genotype

value: WT


title: Inflammatory monocytes, CD69_KO_2


title: Inflammatory monocytes, CD69_KO_B


title: Inflammatory monocytes, CD69_KO_1


title: Inflammatory monocytes, WT_B


title: Inflammatory monocytes, WT_1


title: imb_koenig_2017_10_JKRS33_SRSF6_rep1

description:
SRSF6 iCLIP replicate 1
in vivo iCLIP

value: CGCC


title: imb_koenig_2017_10_JKRS33_SRSF6_rep2

description:
SRSF6 iCLIP replicate 2
in vivo iCLIP

value: TACG


title: Neurofibroma_4

value: Nf1fl/fl; DhhCre Neurofibroma


title: Neurofibroma_3


title: Neurofibroma_1


title: Neurofibroma_2


title: NB-TU 62: Neuroblastoma primary tumor at diagnosis 62

source_name: Tumor at diagnosis. Patient p62


title: NB-TU 57: Neuroblastoma primary tumor at diagnosis 57

source_name: Tumor at diagnosis. Patient p57


title: NB-TU 48: Neuroblastoma primary tumor at diagnosis 48

source_name: Tumor at diagnosis. Patient p48


title: NB-TU 05: Neuroblastoma primary tumor at diagnosis 5

source_name: Tumor at diagnosis. Patient p05


title: STA-NB-15: Neuroblastoma cell line STA-NB-15

description: Low passage cell line established from dissemianted neuroblastoma cells

source_name: Primary neuroblastoma cell line established at the Children's Cancer Research Institute

growth_protocol: In RPMI medium

value: Primary neuroblastoma cell line


title: NB-TU 53: Neuroblastoma primary tumor at diagnosis 53

source_name: Tumor at diagnosis. Patient p53


title: NB-TU 54: Neuroblastoma primary tumor at diagnosis 54

source_name: Tumor at diagnosis. Patient p54


title: NB-TU 02: Neuroblastoma primary tumor at diagnosis 2

source_name: Tumor at diagnosis. Patient p02


title: NB-TU 47: Neuroblastoma primary tumor at diagnosis 47

source_name: Tumor at diagnosis. Patient p47


title: NB-TU 49: Neuroblastoma primary tumor at diagnosis 49

source_name: Tumor at diagnosis. Patient p49


title: NB-TU 50: Neuroblastoma primary tumor at diagnosis 50

source_name: Tumor at diagnosis. Patient p50


title: NB-TU 44: Neuroblastoma primary tumor at diagnosis 44

source_name: Tumor at diagnosis. Patient p44


title: NB-TU 55: Neuroblastoma primary tumor at diagnosis 55

source_name: Tumor at diagnosis. Patient p55


title: NB-TU 06: Neuroblastoma primary tumor at diagnosis 6

source_name: Tumor at diagnosis. Patient p06


title: NB-TU 52: Neuroblastoma primary tumor at diagnosis 52

source_name: Tumor at diagnosis. Patient p52


title: Primitive tumor [DNA11182-040]

city: Milan

first: Marco

last: Silvestri

state: ITALY

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

description: Gene expression data from Primitive Breast Cancer Tumor

hyb_protocol: 18 hrs in hybridization cocktail ( according to manufacturer's instructions) in rotating oven

scan_protocol: GeneChipScanner 3000 Affymetrix

data_processing: Data were processed using frma function from frma R package (McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics,    11(2):242-253.) with default parameter.

label: Biotin

source_name: Primitve Breast Cancer Tumor

label_protocol: NUGEN Encore Biotin Module kit using 5 ug of cDNA

extract_protocol: RNA extraction miRNeasy FFPE  kit (Qiagen) , RNA amplification with WTOvation FFPE RNA Amplification system v2 (NUGEN)

tag: type

value: Primitive

value: FFPE

tag: grade


title: Primitive tumor [DNA11182-049]


title: STA-NB-6: Neuroblastoma cell line STA-NB-6

description: Low passage cell line established from a neuroblastoma tumor


title: STA-NB-7: Neuroblastoma cell line STA-NB-7


title: Primitive tumor [DNA11182-046]


title: Primitive tumor [DNA11182-044]


title: HSA

source_name: MIA PaCa-2 cells, HSA

value: Pancreatic cancer cell line

value: HSA treatment

value: MIA PaCa-2


title: Primitive tumor [DNA11182-034]


title: Primitive tumor [DNA11182-047]


title: Primitive tumor [DNA11182-030]


title: SC-GN_6: Ganglioneuroma 6

source_name: Ganglioneuroma

value: Ganglioneuroma


title: Primitive tumor [DNA11182-033]


title: Primitive tumor [DNA11182-037]


title: Primitive tumor [DNA11182-050]


title: SC-GN_3: Ganglioneuroma 3


title: SC-GN_1: Ganglioneuroma 1


title: SC-GN_4: Ganglioneuroma 4


title: SC-GN_5: Ganglioneuroma 5


title: SC-GN_2: Ganglioneuroma 2


title: Primitive tumor [DNA11182-029]


title: Primitive tumor [DNA11182-025]


title: MCF7_4

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling
Adaptor sequences and low-quality score bases (Phred score < 30) were first trimmed using Trimmomatic
The resulting reads were aligned to the GRCh38 human reference genome assembly, using STAR
Read counts for each sample are obtained using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: For in vivo studies, MCF7 wildtype or FLCN KO cells were injected into the fourth mammary fat pads of NSG female mice. 48h before tumor inoculation, mice were injected subcutaneously with 1 μg of 17 β-estradiol (E8875, Sigma) dissolved in corn oil and 17 β-estradiol injections were repeated once per week until experimental endpoint. Mammary tumors were monitored by palpation every few days and tumor volumes were calculated from weekly caliper measurements.

extract_protocol:
Total RNA Mini Kit (Geneaid, cat# RT100)
KAPA mRNAseq Hyperprep Kit

treatment_protocol: Mice were housed in the McGill Animal Care Facility in standard cages with food and water ad libidum. Mice were maintained at 22-24°C on a 12-hr light/ 12-hr dark cycle. All studies were approved by the Animal Resource Centre at McGill University and comply with guidelines set by the Canadian Council of Animal Care. Tumors were resected and harvested when tumor volumes reached between 150 and 300 mm3.

value: FLCN KO


title: MCF7_1


title: MCF7_3


title: MCF7_16


title: MCF7_5


title: MCF7_2


title: Primitive tumor [DNA11182-015]


title: Primitive tumor [DNA11182-009]


title: Primitive tumor [DNA11182-020]


title: U-12-3-A4-SOMA_1

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

data_processing:
Adequate sequencing quality was confirmed using FastQC version 0.11.8 (Andrews, 2010).
To remove the “QuantSEQ FWD” adaptor sequence, the reads were trimmed using cutadapt version 1.18.
The trimmed reads were mapped to the combined human and mouse reference genome using the STAR aligning software v 2.6.0c.
The RSEM software, version v1.3.1, was used to generate count tables.
Genome_build: Homo sapiens GRCh38.89, and Mus musculus GRCm38.91
Supplementary_files_format_and_content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

source_name: hESC

growth_protocol: Prior to differentiation, hESCs were cultured for 6 passages on mitomycin-C-inactivated MEFs in medium containing Dulbecco’s Modified Eagle Medium (KO-DMEM) (Gibco), 20% knockout-serum replacement (KOSR) (Gibco), 1% Penicillin/Streptomycin (P/S) (Gibco), 1% non-essential amino acids (NEAA) (Gibco), 0.4mM L-Glutamine (Gibco), 0.1mM β-mercaptoethanol (Gibco) and 4ng/ml FGF2 (Peprotech) supplemented with or without Activin A 20ng/ml (R&D Biosystems). The U-12-3-A3-4i samples were cultured on mitomycin-C-inactivated feeders for an additional 6 passages in media containing KO-DMEM, 20% KOSR, 1% P/S, 1% NEAA, 20ng/ml recombinant hLIF (Peprotech), 8ng/ml hFGF2, 1ng/ml recombinant hTGFβ1 (Peprotech), 3μM CHIR99021 (Axon Medchem), 1μM PD0325901 (Cayman), 5μM SB203580 (Bio-Techne), 5μM SP600125 (TOCRIS) and 10μM ROCKi (Enzo Life Sciences)] . The U-12-3-A3-PGCLC, U-12-3-A3-SOMA, U-12-3-A4-PGCLC, and U-12-3-A4-SOMA samples were obtained from differentiating U-12-3-A3-4i samples for a period of 4 days as Embryoid Bodies in medium containing human Leukaemia Inhibitory Factor (hLIF), Bone Morphogenetic Protein (BMP4), Epidermal Growth Factor (EGF), Stem Cell Factor (SCF), ROCKi  supplemented with (U-12-3-A3-PGCLC and U-12-3-A3-SOMA) or without (U-12-3-A4-PGCLC and U-12-3-A4-SOMA) 20ng/ml of Activin A.

extract_protocol:
Manufacturers protocol from Qiagen RNEasy Plus Mini Kit (the Primed and 4i samples) and Qiagen RNEasy Plus Micro Kit (the PGCLC and SOMA samples)
Illumina mRNA sequencing libraries were made from 2 ng total RNA of each sample using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Vienna, Austria) according to manufacturer's protocol. Nineteen PCR cycles were used during the enrichment PCR. The size distribution, purity (absence of free adaptors) and quantity of the resulting libraries were measured using a High Sensitivity DNA chip (Agilent Technologies, Santa Clara, CA, US). The libraries were equimolarly pooled and sequenced in an Illumina Nextseq 500 high throughput flow cell, generating single-end 75bp reads.

treatment_protocol: The U-12-3-A3-PGCLC, U-12-3-A3-SOMA, U-12-3-A4-PGCLC, and U-12-3-A4-SOMA samples are live sorted (negative for 7AAD) TNAP+PDPN+ (the PGCLC samples), and TNAP-PDPN- (the SOMA samples) cells obtained from dissocition of D4 Embryoid bodies sorted using a BD Biosciences FACS Fusion Cell Sorter

value: hESC


title: U-12-3-A4-SOMA_3


title: U-12-3-A4-PGCLC_3


title: Primitive tumor [DNA11182-016]


title: Primitive tumor [DNA11182-007]


title: Primitive tumor [DNA11182-006]


title: Primitive tumor [DNA11182-005]


title: Primitive tumor [DNA11182-013]


title: U-12-3-A4-SOMA_4


title: U-12-3-A3-SOMA_3


title: U-12-3-A4-PGCLC_2


title: U-12-3-A4-PGCLC_1


title: U-12-3-A4-SOMA_2


title: U-12-3-A3-SOMA_1


title: Primitive tumor [DNA11182-003]


title: Primitive tumor [DNA11153-059]


title: U-12-3-A3-SOMA_2


title: Primitive tumor [DNA11182-004]


title: Primitive tumor [DNA11153-063]


title: Primitive tumor [DNA11182-002]


title: U-12-3-A3-PGCLC_3


title: Primitive tumor [DNA11153-060]


title: U-12-3-A3-PGCLC_2


title: Primitive tumor [DNA11153-052]


title: Primitive tumor [DNA11153-049]


title: U-12-3-A3-PGCLC_1


title: Primitive tumor [DNA11153-062]


title: Primitive tumor [DNA11153-047]


title: Primitive tumor [DNA11153-045]


title: Primitive tumor [DNA11153-048]


title: Primitive tumor [DNA11153-053]


title: Primitive tumor [DNA11153-051]


title: U-12-3-A4-PGCLC_4


title: U-12-3-A3-4i_1


title: U-19-1-OA2-Primed_3


title: U-12-3-A3-4i_2


title: U-19-1-OA2-Primed_2


title: U-19-1-Primed_2


title: U-12-3-A3-Primed_3


title: U-19-1-OA2-Primed_1


title: U-12-3-A3-Primed_2


title: U-19-1-Primed_3


title: Primitive tumor [DNA11153-061]


title: Primitive tumor [DNA11153-041]


title: Primitive tumor [DNA11153-030]


title: Primitive tumor [DNA11153-025]


title: Primitive tumor [DNA11153-040]


title: Primitive tumor [DNA11153-027]


title: Primitive tumor [DNA11153-029]


title: Primitive tumor [DNA11153-044]


title: U-19-1-Primed_1


title: Primitive tumor [DNA11153-015]


title: Primitive tumor [DNA11153-026]


title: U-12-3-A3-Primed_1


title: Primitive tumor [DNA11153-009]


title: Primitive tumor [DNA11153-021]


title: Primitive tumor [DNA11153-006]


title: Primitive tumor [DNA11153-011]


title: U-12-3-A2-Primed_2


title: U-12-3-A2-Primed_1


title: Primitive tumor [DNA11153-008]


title: U-12-3-A2-Primed_3


title: Donor 6 B Cell Subset 4  (P4) T16

city: Scottsdale

first: Sangkon

last: Oh

state: AZ

address: 13400 east Shea street

department: immunology

institute: Mayo Clinic

data_processing:
Final pooled libraries were sequenced on an Illumina NextSeq 500 with paired-end 75 base read lengths. Quality control of raw reads was performed with the FASTQC software (S 2010). Reads were aligned to the human reference genome (GRCh38) using hisat2 after quality and adapter trimming by cutadapt (Martin , Kim, Langmead et al. 2015). Alignment BAM files were processed by samtools, and HTSeq-count was used to quantify total number of counts for each gene (Li, Handsaker et al. 2009, Anders, Pyl et al. 2015). Genes with sequencing counts per million (CPM) less than 1 were filtered from further analysis. DESeq2 was used to perform differential gene expression analysis comparing different cell populations at 0 and 16 h’s (Love, Huber et al. 2014). UCSC genome browser was used to visualize the coverage for various genes of interest across cell populations and time points (Kent, Sugnet et al. 2002).
Overall 17278 common genes in each sample were used for downstream analysis  where log normalization with a scaling factor of 10000 was done using Seurat. After this, each gene was scaled. Highly variable genes across the samples were then calculated  using Seurat (Stuart, Butler, et al., 2019 and Butler et al., 2018). These genes were then used to do dimension reduction - principal component analysis and canonical correlation analysis which are used for the visualization and clustering  step below.
To determine the optimal number of components to be used for the clustering step, we performed  both jacktraw analysis and elbow plot analysis where an optimal of 10 principal components was determined and used for the clustering and visualization  steps below.To determine how different populations named above clustered, we used the function RUNTSNE() with the selected 10 dimensions above and an optimal perplexity of 4, at time 0 and at time 16.
The achieved clusters above were visualized using the function TSNEplot() from Seurat. Finally, differential expression analysis was achieved using the function Linnorm.limma () (Yip et al. 2017) from Linnorm package in R where different experimental designs were compared. A volcano plot visualization of DEGs was then plotted using ggplot function from the R package ggplot2
In our further analysis, we repeated the analysis above but with fewer genes in three different experimental settings. Specifically, analysis was done using surface markers genes, transcription factor genes and cytokine genes respectfully
Supplementary_files_format_and_content: Differentally Expressed genes spreadsheet for different experimental designs in .csv formart.

source_name: PBMCs

growth_protocol: FACS sorted B cell subsets were incubated  in the complete RPMI 1640 (Invitrogen) (cRPMI) supplemented with 25 mM HEPES (Invitrogen), 1% non-essential amino acids, 2 mM L-glutamate (Invitrogen), 50 mg/mL penicillin, and 50 mg/mL streptomycin (Life Technologies), and 10% fetal bovine serum (FBS) (Gibco).

extract_protocol:
Total RNA was isolated from cell lysates using a modified protocol for the RNAqueous™ Micro Total RNA Isolation Kit (Thermo Fisher Scientific), including on-column DNase digestion
NGS library construction was performed using the SMART-Seq v4 Ultra Low Input RNA kit (Clontech) with 5 ng of input total RNA according to manufacturer’s protocol to generate cDNAs. Prior to final library preparation, 15 ng of cDNA was sheared using the Covaris AFA system.  The Low Input Library Prep Kit V2 (Clontech) with 2 ng of sheared cDNA was used for final library construction
Bulk RNA-seq

treatment_protocol: During incubation, cells were stimulated with class B CpG oligodeoxynucleotide (ODN 2006, CpG-B) (InvivoGen) at 2.5 µg/mL for 16 hours.

tag: individual

value: Donor 6

value: Human B Cells

tag: surface molecules

value: CpG-B

tag: time


title: Donor 6 B Cell Subset 3  (P3) T16


title: Donor 6 B Cell Subset 1  (P1) T16


title: Donor 6 B Cell Subset 2  (P2) T16


title: Primitive tumor [DNA11153-003]


title: Donor 6 B Cell Subset 3  (P3) T0

value: control


title: Donor 6 B Cell Subset 4  (P4) T0


title: Primitive tumor [DNA11153-022]


title: Primitive tumor [DNA11153-001]


title: Donor 6 B Cell Subset 1  (P1) T0


title: Donor 5 B Cell Subset 6  (P6) T16

value: Donor 5


title: Primitive tumor [DNA11063-062]


title: Donor 5 B Cell Subset 4  (P4) T16


title: Primitive tumor [DNA11063-050]


title: Primitive tumor [DNA11063-055]


title: U-12-3-A3-4i_3


title: Donor 5 B Cell Subset 3  (P3) T16


title: Primitive tumor [DNA11063-063]


title: Donor 5 B Cell Subset 2  (P2) T16


title: Donor 5 B Cell Subset 1  (P1) T16


title: Donor 5 B Cell Subset 5  (P5) T0


title: Primitive tumor [DNA11063-046]


title: Primitive tumor [DNA11063-042]


title: Donor 5 B Cell Subset 5  (P5) T16


title: Primitive tumor [DNA11063-032]


title: Primitive tumor [DNA11063-038]


title: Primitive tumor [DNA11063-043]


title: Primitive tumor [DNA11063-039]


title: Primitive tumor [DNA11063-021]


title: Primitive tumor [DNA11063-052]


title: Primitive tumor [DNA11063-018]


title: Donor 5 B Cell Subset 6  (P6) T0


title: Donor 5 B Cell Subset 4  (P4) T0


title: Primitive tumor [DNA11063-033]


title: Primitive tumor [DNA11063-020]


title: Donor 5 B Cell Subset 1  (P1) T0


title: Donor 4 B Cell Subset 6  (P6) T16

value: Donor 4


title: Primitive tumor [DNA11063-028]


title: Donor 5 B Cell Subset 3  (P3) T0


title: Donor 4 B Cell Subset 5  (P5) T16


title: treatment_day3 rep23

city: London

first: Benjamin

middle: Aaron

last: Taylor

state: London

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
Base calling performed with Illumina HiSeq 2000
Ribsosomal sequences filtered using SortMeRNA v2.1b
Quality trimming performed with Trimmomatic v0.36 to first remove leading and trailing bases with phred scores <3 and then to further remove low-quality sequences using the MAXINFO option with target length 36 and strictness 0.7.
Reads mapped to the P. dominula genome assembly using STAR v2.7 with default options
Transcript assembly performed using StringTie2 v1.3.5 and converted to raw counts using the prepDE function
Genome_build: GenBank accession GCA_001465965.1
Supplementary_files_format_and_content: Comma-delimited text file with raw gene counts for every gene (rows) and every sample (columns)

organism: Polistes dominula

source_name: Brain tissue

growth_protocol: Nests were maintained in the lab with ad libitum access to water, nesting materials (cardboard) and dipteran larvae.

extract_protocol:
Brain tissue was extracted and flash frozen on steel beads cooled in dry ice. Tissue was suspended in QIAzol reagent and homogenized in a Qiagen TissueLyser LT. RNA was then extracted using a Qiagen RNeasy Mini Kit according to manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols

tag: tissue

value: brain

tag: age (days)

tag: condition

value: treatment day 3


title: treatment_day3 rep24


title: Donor 4 B Cell Subset 4  (P4) T16


title: Donor 4 B Cell Subset 2  (P2) T16


title: treatment_day3 rep21


title: treatment_day3 rep20


title: treatment_day3 rep22


title: treatment_day3 rep19


title: Donor 4 B Cell Subset 1  (P1) T16


title: Primitive tumor [DNA11063-009]


title: treatment_day3 rep17


title: treatment_day3 rep18


title: Donor 4 B Cell Subset 6  (P6) T0


title: Primitive tumor [DNA11063-015]


title: Primitive tumor [DNA11063-011]


title: treatment_day3 rep16


title: Primitive tumor [DNA11063-012]


title: Primitive tumor [DNA11063-016]


title: Primitive tumor [DNA11063-010]


title: treatment_day3 rep15


title: Donor 4 B Cell Subset 3  (P3) T16


title: Primitive tumor [DNA11063-007]


title: Donor 4 B Cell Subset 5  (P5) T0


title: Primitive tumor [DNA11063-049]


title: treatment_day3 rep14


title: treatment_day3 rep12


title: Donor 4 B Cell Subset 4  (P4) T0


title: treatment_day3 rep11


title: Donor 4 B Cell Subset 3  (P3) T0


title: Primitive tumor [DNA11063-006]


title: Primitive tumor [DNA11063-005]


title: treatment_day3 rep13


title: treatment_day3 rep09


title: treatment_day3 rep08


title: treatment_day3 rep10


title: treatment_day3 rep05


title: treatment_day3 rep07


title: Primitive tumor [DNA10381-044]


title: Donor 4 B Cell Subset 1  (P1) T0


title: Donor 4 B Cell Subset 2  (P2) T0


title: Primitive tumor [DNA10381-039]


title: Primitive tumor [DNA11063-003]


title: Primitive tumor [DNA10381-045]


title: Primitive tumor [DNA10381-042]


title: treatment_day3 rep03


title: treatment_day3 rep04


title: Donor 3 B Cell Subset 6  (P6) T16

value: Donor 3


title: treatment_day3 rep06


title: treatment_day3 rep01


title: Donor 3 B Cell Subset 4  (P4) T16


title: treatment_day12 rep34

value: treatment day 12


title: Donor 6 B Cell Subset 2  (P2) T0


title: Donor 3 B Cell Subset 3  (P3) T16


title: treatment_day12 rep33


title: treatment_day3 rep02


title: treatment_day12 rep31


title: treatment_day12 rep32


title: Primitive tumor [DNA10381-031]

value: Primitive

value: FFPE


title: Primitive tumor [DNA10381-021]


title: Primitive tumor [DNA10381-036]


title: Primitive tumor [DNA10381-029]


title: Donor 3 B Cell Subset 2  (P2) T16


title: Donor 3 B Cell Subset 1  (P1) T16


title: treatment_day12 rep29


title: treatment_day12 rep28


title: Donor 3 B Cell Subset 6  (P6) T0


title: Donor 3 B Cell Subset 5  (P5) T16


title: treatment_day12 rep25


title: treatment_day12 rep26


title: treatment_day12 rep24


title: Primitive tumor [DNA10381-012]


title: Primitive tumor [DNA10381-020]


title: Donor 3 B Cell Subset 4  (P4) T0


title: treatment_day12 rep30


title: Primitive tumor [DNA10381-003]


title: treatment_day12 rep21


title: Primitive tumor [DNA10339-042]


title: treatment_day12 rep20


title: Primitive tumor [DNA10339-048]


title: Primitive tumor [DNA10339-041]


title: treatment_day12 rep19


title: Primitive tumor [DNA10339-040]


title: treatment_day12 rep18


title: Primitive tumor [DNA10339-039]


title: Donor 3 B Cell Subset 5  (P5) T0


title: Donor 3 B Cell Subset 2  (P2) T0


title: Donor 3 B Cell Subset 3  (P3) T0


title: treatment_day12 rep16


title: Donor 3 B Cell Subset 1  (P1) T0


title: treatment_day12 rep23


title: treatment_day12 rep22


title: treatment_day12 rep15


title: treatment_day12 rep12


title: treatment_day12 rep13


title: Donor 2 B Cell Subset 6  (P6) T16

value: Donor 2


title: Donor 2 B Cell Subset 5  (P5) T16


title: treatment_day12 rep14


title: Donor 5 B Cell Subset 2  (P2) T0


title: treatment_day12 rep11


title: Primitive tumor [DNA10339-034]


title: treatment_day12 rep17


title: Primitive tumor [DNA10339-020]


title: treatment_day12 rep10


title: Primitive tumor [DNA10339-028]


title: Donor 2 B Cell Subset 4  (P4) T16


title: treatment_day12 rep09


title: Donor 2 B Cell Subset 3  (P3) T16


title: Primitive tumor [DNA10339-018]


title: Primitive tumor [DNA10339-015]


title: c_4

city: Planegg-Martinsried

first: Johanna

last: Geuder

address: Großhadernerstr. 2

institute: LMU

description:
GATCAGCTTACA
UMI_counts_urinary.txt

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCh38.84)
Genome_build: Human: hg38, Ensembl 84
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

growth_protocol: urinary cells were cultured in RE/MC medium.

extract_protocol:
One colony was picked with a pipet and directly transferred into RLT+
Library was constructed using the prime-seq protocol

value: c

tag: Sex

value: female

tag: cluster

value: b


title: e_2

description:
TCTTATCCTCGA
UMI_counts_urinary.txt

value: e


title: treatment_day12 rep06


title: treatment_day12 rep07


title: treatment_day12 rep08


title: d_4

description:
GGATTCACCGAA
UMI_counts_urinary.txt

value: d

value: male

value: a


title: Donor 2 B Cell Subset 2  (P2) T16

value: Human B Cells

tag: treatment

value: CpG-B


title: Donor 2 B Cell Subset 1  (P1) T16


title: Donor 2 B Cell Subset 5  (P5) T0

value: control


title: treatment_day12 rep05

value: brain


title: Donor 2 B Cell Subset 6  (P6) T0


title: d_3

description:
GGCATTGTTCTG
UMI_counts_urinary.txt


title: treatment_day12 rep04


title: Donor 2 B Cell Subset 4  (P4) T0


title: Primitive tumor [DNA10339-014]


title: Primitive tumor [DNA10339-008]


title: Primitive tumor [DNA10339-004]


title: Primitive tumor [DNA10339-005]


title: f_2

description:
AGTAGTTAGCCG
UMI_counts_urinary.txt

value: f


title: c_3

description:
AACAGCGCCATG
UMI_counts_urinary.txt


title: Donor 2 B Cell Subset 3  (P3) T0


title: Primitive tumor [DNA10339-001]


title: treatment_day12 rep02


title: Donor 2 B Cell Subset 2  (P2) T0


title: treatment_day12 rep01


title: Donor 2 B Cell Subset 1  (P1) T0


title: Donor 1 B Cell Subset 6  (P6) T16

value: Donor 1


title: e_1

description:
TACCTAGGTGTA
UMI_counts_urinary.txt


title: control_worker rep12

value: worker


title: Primitive tumor [DNA10299-026]

value: Primitive


title: d_2

description:
CCAAGATCCGTA
UMI_counts_urinary.txt


title: f_3

description:
TGTGCCAAGGTG
UMI_counts_urinary.txt


title: treatment_day12 rep03

value: treatment day 12


title: control_worker rep10


title: control_worker rep11


title: c_2

description:
AGCTAAGACCTT
UMI_counts_urinary.txt


title: f_1

description:
AAGTGGTTGCGG
UMI_counts_urinary.txt


title: Donor 1 B Cell Subset 4  (P4) T16


title: Primitive tumor [DNA10299-023]

value: FFPE


title: Donor 1 B Cell Subset 3  (P3) T16


title: control_worker rep09


title: Primitive tumor [DNA10299-019]


title: Primitive tumor [DNA10299-033]


title: Primitive tumor [DNA10299-025]


title: Primitive tumor [DNA10299-022]


title: Primitive tumor [DNA10299-016]


title: control_worker rep08


title: a_4

description:
GTATGCTTCCTA
UMI_counts_urinary.txt


title: d_1

description:
CAGCACTTCACA
UMI_counts_urinary.txt


title: b_2

description:
TCGAGTCTGGCA
UMI_counts_urinary.txt


title: control_worker rep07


title: Donor 1 B Cell Subset 2  (P2) T16


title: Donor 1 B Cell Subset 1  (P1) T16


title: b_1

description:
AGCCATAGTAGA
UMI_counts_urinary.txt


title: Donor 1 B Cell Subset 6  (P6) T0


title: Primitive tumor [DNA10299-007]


title: control_worker rep05


title: c_1

description:
ACATAAGTCAGG
UMI_counts_urinary.txt

value: c


title: Donor 1 B Cell Subset 5  (P5) T0


title: a_3

description:
GTTGTGCTCCAA
UMI_counts_urinary.txt


title: control_worker rep04


title: Donor 1 B Cell Subset 4  (P4) T0


title: Primitive tumor [DNA10082-010]


title: a_1

description:
CTGGACTAACAA
UMI_counts_urinary.txt


title: Primitive tumor [DNA10299-006]


title: control_worker rep03


title: Donor 1 B Cell Subset 3  (P3) T0


title: control_worker rep06


title: a_2

description:
TCGGCTGTCCAA
UMI_counts_urinary.txt


title: control_worker rep02


title: Donor 1 B Cell Subset 1  (P1) T0


title: queen rep26

value: queen


title: control_worker rep01


title: Donor 1 B Cell Subset 5  (P5) T16


title: Primitive tumor [DNA10140-006]


title: Primitive tumor [DNA10082-006]


title: Primitive tumor [DNA10082-005]


title: run14

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

institute: The Research Institute of Molecular Pathology (IMP)

description: All saliva samples were left-over material obtained from anonymous, routine SARS-CoV-2 testing pipelines (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details). Different samples measured to be positive, were later used as positive controls for various experiments. Hundreds of negative samples were also used as negative controls or as diluents to generate titration curves of synthetic viral RNA in various experiments.

data_processing:
Library strategy: SARSeq
Demultiplexing of reads to plates by i5 and i7 indices according to SARSeq pipeline
Demultiplexing of reads to wells by well indices according to SARSeq pipeline
Assignment of reads to predefined amplicons within each well according to SARSeq pipeline
Genome_build: -
Supplementary_files_format_and_content: Read count per amplicon and well in table or plate layout:
run2.xlsx - read counts for specific SARS-CoV2 and RNAseP (human control) amplicons, as well as non-specific amplicons generated by the same primers. Samples are a dilution of synthetic SARS-CoV2 RNA in gargle (saliva + HBSS buffer) from a negative individual. This experiment tested specificity of the RT-PCR setup.
run4.xlsx - read counts for two different SARS-CoV2 amplicons (N1 and N3) and a human control (ribosome) obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA as indicated. This experiment tested 30 well-specific indices.
run5.xlsx - read counts for two different SARS-CoV2 amplicons (N1 and N3) and a human control (ribosome) obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA as indicated. This experiment tested 96 well-specific indices.
run7b.xlsx - read counts for two different SARS-CoV2 (N1 and N3), two influenza A, influenza B, human rhinovirus, and a human control amplicon (ribosome) obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA or other viral RNAs as indicated. This experiment tested the capacity to multiplex different viral amplicons in the same reaction.
run8.xlsx - read counts for two different SARS-CoV2 (N1 and N3) and a human control amplicon (ribosome) obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA as indicated. This experiment tested the sensitivity of the assay.
run9.xlsx - read counts for two different SARS-CoV2 (N1 and N3) and a sample quality control (counts for ribosome amplicon/counts for reverse transcription synthetic control) obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA as indicated. This run also includes swab samples collected in viral transport medium (VTM) from patients at the Clinical Center of the University of Sarajevo, Bosnia. Samples with i5/i7 indices 233-256 were analyzed in three different manners taking into account one or both well-specific indices (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details).
run10.xlsx - read counts for two different SARS-CoV2 (N1 and N3) and a human control amplicon (ribosome), as well as additional spike-in controls (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details), obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA as indicated. This experiment tested the sensitivity of the assay.
run11.xlsx - read counts for two different SARS-CoV2 (N1 and N3) and a human control amplicon (ribosome), as well as additional spike-in controls (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details), obtained from gargle (saliva + HBSS buffer) and swab-samples previously tested by the Austrian Agency for Health and Food Safety (AGES) in a diagnostic pipeline. Several replicates are shown.
run14.xlsx - read counts for 12 different SARS-CoV2 (N1 through Orf1b) and three human control amplicons (rRNA, GAPDH and RNaseP) as well as the read counts for non-specific amplicons generated by the same primers. Also, this run contains an experiment in which different RT-PCR conditions were tested on gargle (saliva + HBSS buffer) from a positive individual or from a negative individual but with different amounts of synthetic SARS-CoV2 RNA, as indicated. For this experiment, we provide read counts for two different SARS-CoV2 (N1 and N3) and a human control amplicon (ribosome), as well as additional spike-in controls (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details). Read counts for amplicons from other viruses (influenza, HRV) are shown to be zero in these samples that did not contain those viruses.
run15.xlsx - read counts for two different SARS-CoV2 (N1 and N3) and a human control amplicon (ribosome), as well as additional spike-in controls (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details) obtained from gargle (saliva + HBSS buffer) with different amounts of synthetic SARS-CoV2 RNA as indicated. This experiment contained different amounts of added spike-in control RNAs and PCR was conducted for different numbers of cycles, as indicated.

source_name: saliva sample

extract_protocol:
Samples were extracted with DNA QuickExtractsolution (1:1 ratio mix), except where indicated in the accompanying Excel files (specifically, some samples in runs 11, 14 and 15 were extracted in TCEP/EDTA)
libraries were constructed as part of the newly developed SARSeq protocol

tag: infection

value: saliva

tag: source

value: multiple anonymous donors


title: Primitive tumor [DNA10064-017]


title: run10


title: run11

description: All saliva samples were left-over material obtained from anonymous, routine SARS-CoV-2 testing pipelines (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details). Different samples measured to be positive, were later used as positive controls for various experiments. Hundreds of negative samples were also used as negative controls or as diluents to generate titration curves of synthetic viral RNA in various experiments. Saliva samples were obtained by the Austrian Agency for Health and Food Safety (AGES) in a diagnostic pipeline and provided to us fully anonymized. These are part of preliminary investigations and results of a clinical performance study approved by the local Ethic Committee of Vienna (#EK 20-208-0920).


title: queen rep25


title: H5P5KDMD8

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: hg18
Supplementary_files_format_and_content: raw counts

source_name: 5k PIC 2 DM

extract_protocol:
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

tag: culture

value: PIC 5k

tag: tag

value: DM

value: liver organoid


title: Primitive tumor [DNA10082-012]


title: H5P5KEMD14

source_name: 5k PIC 2 EM

value: EM


title: H5P3P5KEM

source_name: 5k PIC 2 EM fig2


title: Primitive tumor [DNA10064-015]


title: queen rep23


title: Primitive tumor [DNA10064-012]


title: run2


title: H5P3P1KEM

source_name: 1k PIC 2 EM fig2

value: PIC 1k


title: Donor 1 B Cell Subset 2  (P2) T0

tag: cell type

value: Human B Cells

value: control


title: Primitive tumor [DNA10064-010]


title: treatment_day12 rep27

value: brain


title: H5P3MGEM

source_name: MG 2 EM fig2

value: Matrigel


title: H5P1KEMD14

source_name: 1k PIC 2 EM


title: H5P1KDMD8

source_name: 1k PIC 2 DM


title: CYGB+ cell duplicate 2 of 2, biological replicate 3 of 3

city: Birmingham

first: Garret

last: Rochford

state: West Midlands

address: School of Biosciences

department: School of Biosciences

institute: University of Birmingham

hyb_protocol: cRNA was quantified on the Nanodrop and quality control checked with the 2100 Agilent Bioanalyser. 300ng cRNA hybridised to agilent SurePrint G3 Human Gene Expression 8x 60K v1 microarray according to the manufactureres instructions.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C

data_processing:
Data processing using GeneSpring GX Human Agilent 60K genes software (ver. 7.3.1) was used for background subtraction and LOWESS normalization. Differential gene expression was determined using parametric testing and Benjamini Hochberg corrections for multiple testing corrections with a p value of 0.05. Gene Ontology analysis was performed using PANTHER (ver.10.0) with Statistical Over-Representational Test and Functional Classification Test. This analysis uses binomial statistics to identify under and over represented gene groups with alpha threshold of 0.05.
Single colour quantile normalization. Changes determined using parametric testing with Benjamini Hochberg corrections for multiple testing corrections with p value of 0.05

source_name: transgenic cell line

label_protocol: Fifty nanograms of total RNA was used to generate cyanine-labelled cRNA according to the Agilent Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling) protocol. Samples were cyanine3 labelled.

growth_protocol: PE/CA-PJ41 immortalised human oral squamous carcinoma cells were cultured RPMI1640 cell culture media supplemented with 10% (v/v) foetal bovine serum, 2mM L-glutamine, 100 U/mL penicillin and 100 ug/mL stereptomycin.

extract_protocol: RNA was extracted on three separate ocassions using the Qiagen RNA mini prep kit.

treatment_protocol: PE/CA-PJ41 cell lines were transfected with the pCMV6-Neo plasmid containing the human cytoglobin cDNA sequence using Turbofectin 8.0 (Origene). Stable clones were selected using the cloning ring method in G418 sulfate (Roche). Genomic integration of the vector was confirmed by PCR using a Phusion High-Fidelity Kit (NEB). Cells were incubated for 24 hours in supplemented cell culture media prior to RNA extraction.

tag: original disease

value: Human oral squamous cell carcinoma

tag: transfection vector

value: CYGB transfection vector


title: Primitive tumor [DNA10064-008]

tag: type

value: Primitive

tag: grade


title: CYGB+ cell duplicate 2 of 2, biological replicate 2 of 3


title: queen rep20


title: CYGB+ cell duplicate 2 of 2, biological replicate 1 of 3


title: queen rep24


title: Primitive tumor [DNA10051-018]

value: FFPE


title: queen rep21


title: Primitive tumor [DNA10051-017]


title: queen rep19


title: H5MGEMD14

source_name: MG 2 EM


title: queen rep22


title: H5MGDMD8

source_name: MG 2 DM


title: queen rep18


title: H2P5KEMD14

source_name: 5k PIC 1 EM


title: queen rep17


title: Primitive tumor [DNA10051-014]

source_name: Primitve Breast Cancer Tumor


title: queen rep16


title: CYGB+ cell duplicate 1 of 2, biological replicate 3 of 3


title: CYGB+ cell duplicate 1 of 2, biological replicate 1 of 3


title: Primitive tumor [DNA10051-008]


title: PAO1 ∆pilY1 ∆mvaU ∆mvaT rpoD-vsvG RNA-Seq (AML127.1) 3

city: Boston

first: Andrew

middle: M

last: Lippa

state: MA

address: 300 Longwood Ave

department: Pediatrics, Division of Infectious Diseases

institute: Boston Children's Hospital

description:
Sample 15
AML127.1.3
RNAtag-Seq
RpoD-V_RNA-seq_PAO1_all_counts.txt

data_processing:
Sequencing reads from each pooled sample were demultiplexed based on their associated barcode sequence using custom scripts; allowing up to 1 mismatch in the barcode, provided this did not make assignment of the read to a different barcode possible. Barcode sequences were subsequently trimmed from the first read as were terminal G's from the second read that may have been added by SMARTScirbe during template switching.
Reads were aligned to the PAO1 reference genome (NCBI RefSeq NC_002516.2) using BWA.
Read counts were assigned to the genes and other genomic features using custom scripts.
Differential expression analysis was conducted with DESeq2 and/or EdgeR.
For visualization of RNASeq data, the bam alignment files were sorted using samtools (version 1.10), split by strand and converted to the bedgraph file format using bedtools (version 2.92.2).
The read depth in the bedgraphs files were normalized to the sample with the fewest number of mapped reads using custom R scripts.
The normalized bedgraph files were subsequently converted to the bigwig file format using the bedgraphToBigWig executable (downloaded from the UCSC database) for visualization in a genome browser.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: bigWig files were generated using the bedgraphtobigwig script package from UCSC; Scores represent normalized RNASeq read density.
Supplementary_files_format_and_content: 5primeRNAseq_PAO1_counts.tsv: Read counts.

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial cells grown to OD 0.35

growth_protocol: Bacterial cultures were started from single colonies, grown overnight to saturation, and back-diluted in LB media to OD600 ~0.01 and grown with aeration at 250 rpm at 37°C to a final OD600 ~0.35.

extract_protocol:
Total RNA was extracted using Trireagent and ethanol precipitation using the method of Goldman, et al. (Mol Cell, 2011. 42(6): p. 817-25.). Note that samples 1-9 were grown together on a single day and sequenced together; samples 10-15 were grown together and sequenced together at a later date.
Illumina cDNA libraries were generated using a modified version of the RNAtag-Seq protocol. 500 ng - 1 µg total RNA was fragments, depleted of genomic DNA, dephosphorylated and ligated to DNA adapters carrying 5'-AN8-3' barcodes of known sequence with a 5' phosphate and a 3' blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (EpiCentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a  primer designed to the constant region of the barcode adaptor with addition of an adapter to the 3' end of the cDNA by template switching using SMARTScribe (Clonetech); (ii) PCR amplification using primers whose 5' ends target the constant region of the 3' or 5' adaptors and whose 3' ends contain the full Illumina P5 or P7 sequences.

tag: genotype

value: PAO1 with deletion of pilY1, mvaU, and mvaT genes and epitope-tagged rpoD-vsvG

tag: growth phase

value: mid-logarithmic phase culture


title: CYGB+ cell duplicate 1 of 2, biological replicate 2 of 3


title: NCE cell replicate 3 of 3, biological replicate 1 of 3

value: empty transfection vector


title: Primitive tumor [DNA10051-006]


title: Primitive tumor [DNA10051-001]


title: Primitive tumor [DNA10051-004]


title: PAO1 ∆pilY1 ∆mvaU ∆mvaT rpoD-vsvG RNA-Seq (AML127.1) 2

description:
Sample 14
AML127.1.2
RNAtag-Seq
RpoD-V_RNA-seq_PAO1_all_counts.txt
normalized_AML127.1.2_PAO1_pe_plus.bw
normalized_AML127.1.2_PAO1_pe_minus.bw


title: queen rep15

tag: tissue

value: queen


title: H2P2P5KEM

source_name: 5k PIC 1 EM fig2

value: PIC 5k


title: PAO1 ∆pilY1 ∆mvaU ∆mvaT rpoD-vsvG RNA-Seq (AML127.1) 1

description:
Sample 13
AML127.1.1
RNAtag-Seq
RpoD-V_RNA-seq_PAO1_all_counts.txt


title: H2P2P1KEM

source_name: 1k PIC 1 EM fig2


title: PAO1 ∆pilY1 rpoD-vsvG RNA-Seq (AML121) 3

description:
Sample 12
AML121.3
RNAtag-Seq
RpoD-V_RNA-seq_PAO1_all_counts.txt
normalized_AML121.3_PAO1_pe_plus.bw
normalized_AML121.3_PAO1_pe_minus.bw

value: PAO1 with deletion of pilY1 gene and epitope-tagged rpoD-vsvG


title: queen rep13

source_name: Brain tissue

tag: age (days)


title: queen rep14

tag: condition


title: H2P2MGEM

source_name: MG 1 EM fig2

value: liver organoid


title: queen rep12


title: NCE cell replicate 3 of 3, biological replicate 3 of 3


title: H2P1KEMD14

source_name: 1k PIC 1 EM

value: EM


title: PAO1 ∆pilY1 rpoD-vsvG RNA-Seq (AML121) 1

description:
Sample 10
AML121.1
RNAtag-Seq
RpoD-V_RNA-seq_PAO1_all_counts.txt


title: PAO1 ∆pilY1 rpoD-vsvG RNA-Seq (AML121) 2

description:
Sample 11
AML121.2
RNAtag-Seq
RpoD-V_RNA-seq_PAO1_all_counts.txt


title: queen rep11


title: H2P1KDMD8

source_name: 1k PIC 1 DM

value: PIC 1k

value: DM


title: queen rep10


title: PAO1 ∆pilY1 ∆mvaU ∆mvaT RNA-Seq (AML85.1.1) 3

description:
Sample 9
dmvaUdmvaTdpilY1.3
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt

value: PAO1 with deletion of pilY1, mvaU, and mvaT genes


title: NCE cell replicate 2 of 3, biological replicate 3 of 3


title: H2P5KDMD8

source_name: 5k PIC 1 DM


title: NCE cell replicate 3 of 3, biological replicate 2 of 3


title: NCE cell replicate 2 of 3, biological replicate 1 of 3


title: PAO1 ∆pilY1 ∆mvaU ∆mvaT RNA-Seq (AML85.1.1) 2

description:
Sample 8
dmvaUdmvaTdpilY1.2
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt


title: H2MGEMD14

source_name: MG 1 EM


title: NCE cell replicate 1 of 3, biological replicate 3 of 3


title: NCE cell replicate 2 of 3, biological replicate 2 of 3


title: H2MGDMD8

source_name: MG 1 DM


title: queen rep09

value: brain


title: queen rep08


title: NCE cell replicate 1 of 3, biological replicate 2 of 3


title: queen rep07


title: PAO1 ∆pilY1 ∆mvaU ∆mvaT RNA-Seq (AML85.1.1) 1

description:
Sample 7
dmvaUdmvaTdpilY1.1
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt
normalized_dmvaUdmvaTdpilY1.1_PAO1_pe_plus.bw
normalized_dmvaUdmvaTdpilY1.1_PAO1_pe_minus.bw


title: PAO1 ∆pilY1 ∆mvaU RNA-Seq (AML77) 2

description:
Sample 5
dmvaUdpilY1.2
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt

value: PAO1 with deletion of pilY1 and mvaU genes


title: PW032-710

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
12-nt cell barcodes (CBs) and 9-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cells in our microwell system using the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the molecular counts of each individual cell. The first two columns contain the gene ID and gene symbol for each gene and all subsequent columns correspond to profiles of individual cells. There is a header contain the cell-identifying barcode sequence for each cell.

source_name: glioma surgical specimen

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: glioma surgical specimen

tag: Sex

value: male

tag: idh1 status

value: IDH1 wildtype

tag: diagnosis

value: WHO Grade IV Glioblastoma

tag: primary/recurrent

value: primary


title: queen rep06


title: PW032-706

value: female

value: recurrent


title: PAO1 ∆pilY1 ∆mvaU RNA-Seq (AML77) 1

description:
Sample 4
dmvaUdpilY1.1
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt

value: mid-logarithmic phase culture


title: queen rep05

value: queen


title: NCE cell replicate 1 of 3, biological replicate 1 of 3

value: Human oral squamous cell carcinoma

value: empty transfection vector


title: PW017-703


title: PAO1 ∆pilY1 ∆mvaU RNA-Seq (AML77) 3

description:
Sample 6
dmvaUdpilY1.3
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt


title: Th17 Polarized CD4 T-Cells

first: Christian

last: Harman

address: 300 Cedar Street, The Anlyan Center

institute: Yale University

description:
In order to uncover novel non-coding loci with the potential to regulate lymphoid cell biology, an RNA-sequencing analysis was performed on murine naïve and effector CD4 T-cells to identify differentially expressed RNAs that might mark such loci.
CD4_Gene_Expression_09-22-2015.txt

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment and junction mapping to mouse genome GRCm38/mm10 performed using Tophat2 and Bowtie2 (Trapnell et. Al. Genome Biology, 2013)
Transcript quantitation, normalization and differential expression testing performed using Cufflinks ((Trapnell et. al. 2012 Nature Protocols)
Data analysis and visualization performed in R, using packages cummeRbund (http://compbio.mit.edu/cummeRbund/) and pheatmap (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of normalized FPKM between samples

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes, incubated under Th17 conditions in vitro

growth_protocol: Groups of littermate mice of the genotypes specified above were sacrificed, lymph nodes were extracted (not mesenteric) and reduced to a single cell suspension through the use of a strainer. Naive and memory CD4 T-Cells cells purified by FACS sorting for the markers described above as outlined in the methods section of this paper. Naive (CD44- CD62Lhi) and Memory cells were harvested for RNA, and Naive CD4 T-Cells of the reporter genotypes were plated for polarization into defined CD4 effector subsets (Th1,Th2, Th9, Th17) as well as under neutralizing (Th0) and regulatory T-cell (Treg) conditions.

extract_protocol:
Purified populations of Naïve, Memory and effector CD4 T-cells were spun down in FACS medium, washed and RNA was extracted. Purified RNA was obtained using QIAGEN RNeasy Micro kit or Zymo-research Direct-zol RNA Microprep kit.
mRNA for RNAseq analysis was purified using PolyA+ selection and processed by the Yale Center for Genome Analysis using standard methodology using Illumina TruSeq mRNA-Seq Sample Prep Kits, library quality and concentration assayed using a Bioanalyzer, RNA was sequenced on a HiSeq2500 with 75bp pair-ended reads.

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and polarized under “Th17” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th17” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and the cytokines Il6, Il23 and TGF-B are added to stimulate Th17 cell differentiation and proliferation.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.

tag: cell type/tissue

value: CD4 T-Cells

tag: strain

value: C57/BL6 Il17 GFP reporter


title: Treg Polarized CD4 T-Cells

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes, incubated under Treg conditions in vitro

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and polarized under neutral “Treg” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Treg” culture conditions, antibodies blocking IL-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and the cytokines TGF-B and IL-2 are added to stimulate Treg-cell differentiation and proliferation.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.

value: C57/BL6 FoxP3 RFP reporter


title: Th2 Polarized CD4 T-Cells

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes, incubated under Th2 conditions in vitro

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and polarized under neutral “Th2” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th2” culture conditions, antibodies blocking interferon gamma (IFNγ) are also added to block Th1 differentiation, and cytokines IL-2 and IL-4 are added to stimulate Th2-cell differentiation and proliferation.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.

value: C57/BL6 IL4-GFP reporter


title: Th9 Polarized CD4 T-Cells

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes, incubated under Th9 conditions in vitro

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and polarized under neutral “Th9” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th9” culture conditions, antibodies blocking interferon gamma (IFNγ) are also added to block Th1 differentiation, and the cytokines IL-4 and TGFB are added to stimulate Th9-cell differentiation and proliferation.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.

value: C57/BL6 Il9 GFP reporter


title: queen rep04

value: brain


title: PJ053

value: glioma surgical specimen


title: PAO1 ∆pilY1 RNA-Seq (AML91) 3

description:
Sample 3
dpilY1.3
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt

value: PAO1 with deletion of pilY1 gene


title: Th0 CD4 T-Cells

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes, incubated under neutralizing conditions in vitro

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking IL-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and IL-2 is added to stimulate T-cell differentiation and proliferation.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.


title: queen rep03


title: PAO1 ∆pilY1 RNA-Seq (AML91) 2

description:
Sample 2
dpilY1.2
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt
normalized_dpilY1.2_PAO1_pe_plus.bw
normalized_dpilY1.2_PAO1_pe_minus.bw


title: Memory CD4 T-Cells

source_name: CD44hi CD62L- CD4 T-Cells sorted from lymph nodes

treatment_protocol:
"Memory-like" CD44hi CD62L- CD4 T-cells from wild-type C57/BL6 mice were sorted and sequenced.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.


title: PAO1 ∆pilY1 RNA-Seq (AML91) 1

description:
Sample 1
dpilY1.1
RNAtag-Seq
5primeRNAseq_PAO1_counts.txt

source_name: Bacterial cells grown to OD 0.35


title: queen rep02


title: Naïve CD4 T-Cells

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and sequenced.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.


title: queen rep01


title: run9

description: All saliva samples were left-over material obtained from anonymous, routine SARS-CoV-2 testing pipelines (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details). Different samples measured to be positive, were later used as positive controls for various experiments. Hundreds of negative samples were also used as negative controls or as diluents to generate titration curves of synthetic viral RNA in various experiments. Anonymized saliva samples in VTM were provided by the Clinical Center of the University of Sarajevo. Approval (#06-04-9-33163 from 21/07/2020) was obtained from the Ethics Committee of the Clinical Center of the University of Sarajevo.

source_name: saliva sample

tag: infection

value: saliva

tag: source

value: multiple anonymous donors


title: PW016-703

value: male

value: IDH1 wildtype

value: WHO Grade IV Glioblastoma

value: primary


title: S1-Nut +Sel

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description:
Replicate1 nutlin + Selinexor treated
NUT_Sel_FPKM.txt.gz

data_processing:
Sequenced reads were mapped to hg38 whole genome using hisat2 with default parameters
The reads are quantified using featureCounts from Subread package
Picard tools is used to determine the average insert size and standard deviation
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample analyzed (Genesymbol,GeneID,SET1-CSH-NUT10,SET2-CSH-NUT10,SET1-NBAT1SH3-NUT10,SET2-NBAT1SH3-NUT10)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample analyzed (Genesymbol,Geneid,S1.NT,S2.NT,S1.Nut,S2.Nut,S1.Nut.sel,S2.Nut.sel,S1.Sel,S2.Sel)

extract_protocol: Total RNA after drug treatment was extracted using SV total RNA isolation system from Promega.

treatment_protocol: Nut and Sel  treatment

tag: cell line

tag: treatment

value: nutlin + Selinexor


title: DMS-MaPseq analysis of SARS-CoV-2, replicate #1

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

description: In vitro refolded SARS-CoV-2 genome, DMS treated

data_processing:
All the relevant analysis steps, from reads alignment to data normalization and structure modeling, were performed using RNA Framework. All tools referenced in the following paragraphs are distributed as part of the RNA Framework suite (https://github.com/dincarnato/RNAFramework). Specific analysis parameters are detailed in the respective paragraphs. For structure predictions, optimal slope (2.4) and intercept (-0.2) values were identified by jackknifing, using a DMS-MaPseq dataset for ex vivo deproteinized E. coli rRNAs we previously published (accession: SRR8172706) and the rf-jackknife tool (parameters: -rp '-md 600 -nlp' -x). After clipping adapter sequences using Cutadapt v2.11 (parameters: -a AGATCGGAAGAGCACAC -A AGATCGGAAGAGCGT -O 1 -m 100:100), paired-end reads were merged using PEAR v0.9.11 and then mapped to the SARS-CoV-2 reference using the rf-map tool and the Bowtie2 algorithm, with soft-clipping enabled, (parameters: -b2 -cq5 20 -ctn -cmn 0 -cl 150 -mp '--very-sensitive-local'). An MM file was then generated from the resulting BAM alignment using the rf-count tool, by only keeping reads covering at least 150 bases. Insertions and deletions were ignored (as they account for less than 6% of DMS-induced mutations when using TGIRT-III), considering only mutations having Phred qualities > 20. Furthermore, mutations were only considered when the two surrounding bases had Phred qualities > 20 as well. Mutations falling within 3 bases from each other were excluded, as well as reads with more than 10% mutated bases (parameters: -m -ds 150 -es -nd -ni -mm -me 0.1). DRACO was invoked with default parameters. Following DRACO analysis, windows in which the median coverage (calculated on reads passing DRACO’s filtering) was above 5,000X were selected. To select windows coherently folding into multiple conformations in both replicates, we retained windows predicted to have the same number of conformations in two replicates, overlapping by at least 75% of their length, and considered only their intersection. Deconvoluted reactivity profiles for matching conformations from the two replicates were then averaged and used for secondary structure modeling.
Genome_build: MT415321.1
Supplementary_files_format_and_content: Additional data files are available at: http://www.incarnatolab.com/datasets/DRACO_Morandi_2020.php

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Vero E6

extract_protocol:
Approximately 5x106 of the harvested infected cells were resuspended in 1 mL of TriPure Isolation Reagent (Sigma Aldrich, cat. 11667157001) and 200 μl of chloroform were added. The sample was vigorously vortexed for 15 sec and then incubated for 2 min at room temperature, after which it was centrifuged for 15 min at 12,500 x g (4°C). The upper aqueous phase was collected in a clean 2 mL tube, supplemented with 1 mL (~2 volumes) of 100% ethanol, and then loaded on an RNA Clean & Concentrator-25 column (Zymo Research, cat. R1017). In vitro folding was carried out as previously described5,10. Briefly, ~5 μg of total RNA from infected Vero E6 cells was first depleted of ribosomal RNAs using the RiboMinus™ Eukaryote System v2 (ThermoFisher Scientific, cat. A15026), following manufacturer instructions. Ribo- RNA in a volume of 39 μl was denatured at 95°C for 2 min, then transferred immediately to ice and incubated for 1 min. 10 μl of ice-cold 5X RNA Folding Buffer [500 mM HEPES pH 7.9; 500 mM NaCl] supplemented with 20 U of SUPERase•In™ RNase Inhibitor (ThermoFisher Scientific, cat. AM2696) were added. RNA was then incubated for 10 min at 37°C to allow secondary structure formation. Subsequently, 1 μl of 500 mM MgCl2 (pre-warmed at 37°C) was added and RNA was further incubated for 20 min at 37°C to allow tertiary structure formation. For probing of RNA, DMS was pre-diluted 1:6 in 100% ethanol and added to a final concentration of 150 mM. Samples were then incubated at 37°C for 2 min. Reactions were then quenched by the addition of 1 volume DTT 1.4 M and then purified on an RNA Clean & Concentrator-5 column (Zymo Research, cat. R1013).
DMS-MaPseq of SARS-CoV-2 was conducted a previously described, with minor changes. First, probed RNA was fragmented to a median size of 150 nt by incubation at 94°C for 8 min in RNA Fragmentation Buffer [65 mM Tris-HCl pH 8.0; 95 mM KCl; 4 mM MgCl2], then purified with NucleoMag NGS Clean-up and Size Select beads (Macherey Nagel, cat. 744970), supplemented with 10 U SUPERase•In™ RNase Inhibitor, and eluted in 8 μl NF H2O. Eluted RNA was supplemented with 1 μl 50 μM random hexamers and 2 μl dNTPs (10 mM each), then incubated at 70°C for 5 min and immediately transferred to ice for 1 min. Reverse transcription reactions were conducted in a final volume of 20 μl. Reactions were supplemented with 4 μl 5X RT Buffer [250 mM Tris-HCl pH 8.3; 375 mM KCl; 15 mM MgCl2], 1 μl DTT 0.1 M, 20 U SUPERase•In™ RNase Inhibitor and 200 U TGIRT™-III Enzyme (InGex, cat. TGIRT50). Reactions were incubated at 25°C for 10 min to allow partial primer extension, followed by 2 h at 57°C. TGIRT-III was degraded by addition of 2 μg Proteinase K, followed by incubation at 37°C for 20 min. Proteinase K was inactivated by addition of Protease Inhibitor Cocktail (Sigma Aldrich, cat. P8340). Reverse transcription reactions were then used as input for the NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module (New England Biolabs, cat. E6111L). Second strand synthesis was performed by incubating 1 h at 16°C, as per manufacturer instructions. DsDNA was purified using NucleoMag NGS Clean-up and Size Select beads, and used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina, following manufacturer instructions.

treatment_protocol: Vero E6 cells were cultured in T-175 flasks in Dulbecco’s modified Eagle’s medium (DMEM; Lonza, cat. 12-604F), supplemented with 8% fetal calf serum (FCS; Bodinco), 2 mM L-glutamine, 100 U/mL of penicillin and 100 µg/mL of streptomycin (Sigma Aldrich, cat. P4333-20ML) at 37°C in an atmosphere of 5% CO2 and 95%–99% humidity. Cells were infected at a MOI of 1.5 with SARS-CoV-2/Leiden-0002 (GenBank accession: MT510999), a clinical isolate obtained from a nasopharyngeal sample at LUMC, which was passaged twice in Vero E6 cells before use. Infections were performed in Eagle’s minimal essential medium (EMEM; Lonza, cat. 12-611F) supplemented with 25 mM HEPES, 2% FCS, 2 mM L-glutamine, and antibiotics. At 16 h post-infection, infected cells were harvested by trypsinization, followed by resuspension in EMEM supplemented with 2% FCS, and then washed with 50 mL 1X PBS. All experiments with infectious SARS-CoV-2 were performed in a biosafety level 3 facility at the LUMC.

value: Vero E6


title: DMS-MaPseq analysis of SARS-CoV-2, replicate #2


title: S2_Sel

description:
Replicate2 Selinexor  treated
NUT_Sel_FPKM.txt.gz

value: Selinexor


title: run8

description: All saliva samples were left-over material obtained from anonymous, routine SARS-CoV-2 testing pipelines (see https://www.medrxiv.org/content/10.1101/2020.10.28.20217778v1 for details). Different samples measured to be positive, were later used as positive controls for various experiments. Hundreds of negative samples were also used as negative controls or as diluents to generate titration curves of synthetic viral RNA in various experiments.


title: S1_Sel

description:
Replicate1 Selinexor  treated
NUT_Sel_FPKM.txt.gz


title: S2-Nut +Sel

description:
Replicate2 nutlin + Selinexor treated
NUT_Sel_FPKM.txt.gz


title: Th1 Polarized CD4 T-Cells

city: New Haven

source_name: CD44- CD62Lhi CD4 T-Cells sorted from lymph nodes, incubated under Th1 conditions in vitro

treatment_protocol:
"Naïve" CD44- CD62Lhi CD4 T-cells from wild-type C57/BL6 mice were sorted and polarized under neutral “Th1” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th1” culture conditions, antibodies blocking IL-4 are also added to block Th2 differentiation, and IL-12 and IL-2 are added to stimulate Th1-cell differentiation and proliferation.
Naïve T-cells from wild-type mice were sorted and polarized under neutral “Th0” conditions, with stimulation from anti-CD28 and anti-CD3 antibodies, which bind the TCR and CD28 costimulatory receptor, stimulating antigen binding. In the “Th0” culture conditions, antibodies blocking Il-4 and interferon gamma (IFNγ) are also added to block Th1 and Th2 differentiation, and Il2 is added to stimulate T-cell differentiation and proliferation. In addition, purified populations of “naïve” CD4 T-cells were sorted from several reporter mouse lines were isolated, polarized into effector subsets in culture and sorted using reporter expression to generate highly purified effector populations. Naïve CD4 T-cells from IFNγ, Il-4, Il-9, Il-17 and FoxP3 reporter mice were sorted and polarized under Th1, Th2, Th9, Th17 and Treg conditions respectively (see above for specific culture conditions). Purified populations were obtained by fluorescence-activated cell sorting of cells expressing the respective reporter genes to generate CD4 effector T-cell populations with a very high purity.

value: CD4 T-Cells

value: C57/BL6 IFNg-Thy1.1 reporter


title: J21856_TCR

city: Kiel

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

institute: University Hospital Schleswig-Holstein

data_processing:
Bcl2fastq2/2.20.0.422
Cellranger-3.1.0 (count, VDJ)
Seurat v3.2.0
Genome_build: GRCh38 v3.0.0 (scRNA),  GRCh38 v2.0.0 (TCR)
Supplementary_files_format_and_content: tab-delimited text files with expression data
raw matrix files (Cellranger)
filtered matrix files (Cellranger)
TCR clonotypes
tab-delimited text file with Seurat metadata

source_name: blood

extract_protocol:
CD154+ cells were isolated by MACS and further purified by FACS sorting on a MACSQuant Tyto (Miltenyi Biotec) based on dual expression of CD154 and CD69. Sorted CD154+ T cells were removed from the sorting chamber into pre-coated low-bind collection tubes, 1ml RPMI-1640 medium supplemented with 5% AB Serum was added, and cells were centrifuged for 5 min at 400 x g, 4°C. The supernatant was carefully removed leaving 10-30μl to reach a maximum concentration of 1000 cells /μl.
Single-cell suspensions were loaded on a ChromiumChip G (10x Genomics) according to the manufacturer’s instructions for processing with the Chromium Next GEM Single Cell 5′ Library and  Gel  Bead  Kit  v1.1. TCR  single-cell  libraries  were subsequently prepared from the same cells with the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell.
Chromium Next GEM Single Cell 5′ Library

treatment_protocol: PBMCs were stimulated for 7h with peptide pools of SARS-CoV-2 and reactive CD154+CD4+ T cells were isolated

tag: individual

value: control

tag: who class

value: healthy

tag: severity

value: blood

tag: cell type

value: CD154+ T cells


title: PJ052

tag: tissue

value: glioma surgical specimen

value: IDH1 mutant


title: run4

city: Vienna

value: saliva


title: unlesioned-4

city: Erlangen

first: Daniel

last: Wehner

address: Staudtsraße 2

department: Division Biological Optomechanics

institute: Max Planck Institut for the Science of Light

data_processing:
bcl2fastq 2.19.1
alignment with GSNAP (2018-07-04) aligner and Ensembl 92 zebrafish annotation to zebrafish (GRCz11) reference
featureCounts (1.6.2) to detect reads and used the Ensembl 92 zebrafish annotation
Genome_build: GRCz11
Supplementary_files_format_and_content: tab separated file from featureCounts; the first columns describing the gene (ID, Start, End, Strand, Length) followed by the 8 sequenced samples

organism: Danio rerio

source_name: pdgfrb+ cells

growth_protocol: Zebrafish embryos were raised in E3 medium at 28.5°C

extract_protocol:
Total RNA Purification Plus Micro Kit (Norgen Biotek)
Library construction followed the instruction from the SMARTSeq 2 manual

treatment_protocol: mechanical lesion to the spinal cord; enzymatic tisue dissociation using Trypsin, FACS

tag: transgenic line

value: GFP+ cells ( mysopetal and perivascular cells)

tag: protocol

value: unlesioned

tag: age

value: 4 day post-fertilzation


title: S2-Nut

description:
Replicate2 nutlin treated
NUT_Sel_FPKM.txt.gz

value: nutlin


title: J21855_TCR


title: Primitive tumor [JB26]

description: Gene expression data from Primitive Breast Cancer Tumor

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were processed using RMA algorithm implemented in oligo Bioconductor package (McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics,    11(2):242-253.)

source_name: Primitve Breast Cancer Tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: type

value: Primitive

value: FFPE

tag: grade


title: run15

value: multiple anonymous donors


title: Primitive tumor [JB18]


title: Primitive tumor [JB24]


title: Primitive tumor [JB16]


title: lesioned-4

value: 1 day post-lesion


title: run7b


title: HL60 EIF2S3, DOX(+)

city: Guangzhou

first: Lihua

last: Xu

address: 151 Yanjiang West Road, Yuexiu, Guangzhou, Guangdong, China

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTP
mRNA-seq reads were aligned to the GRCh38 genome assembly using Hisat2 version 2.1.0 with default parameters
Gene abundance measurements were generationed and normalized  using stringtie version 1.3.4b Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR function package in R program version 3.4.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: HL60 cells

growth_protocol: All cells were incubated at 37°C in 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent.RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system.
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: acute myeloid leukemia cells

value: treated with DOX


title: Primitive tumor [JB28]

first: Marco

last: Silvestri

address: Via Amadeo 42

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano


title: run5


title: J21854_TCR

value: COVID-19 patient

value: WHO 7

value: severe


title: HL60 EIF2S3, DOX(-)

value: untreated


title: S2-NT

description:
Control Replicate2 nontreated
NUT_Sel_FPKM.txt.gz

value: nontreated


title: Primitive tumor [JB10]


title: unlesioned-3


title: J15893_TCR

value: WHO 5

value: mild-moderate

value: blood

value: CD154+ T cells


title: S1-NT

description:
Control Replicate1 nontreated
NUT_Sel_FPKM.txt.gz