title: MED1 ChIP, BT549 cells, Dex, BioRep2

value: Bethyl Laboratories, A300-793A

tag: treatment


title: GR ChIP, BT549 cells, Dex, BioRep1

status: Public on Nov 29 2023

type: SRA

city: Odense

first: Simon

middle: Toftholm

last: Jakobsen

state: Syddanmark

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

library_source: genomic

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove PCR duplicates and low quality reads, before MACS2 was used to call peaks using defult settings.
Homer was used to generate files for plotting the data of the regions of interest.
Assembly: hg38
Supplementary files format and content: RPKM normalized bigwig files the ChIP-seq data or MACS2 called peaks in narrowPeak format

molecule: genomic DNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: BT549 cells were maintained in RPMI supplemented with 10% FBS and antibiotics and culutred at 37oC and 5% CO2

extract_protocol:
In brief, for each chromatin immunoprecipitation cells of two 15cm plates were crosslinked at RT using 2mM disuccinimidyl glutarate (DSG) for 20min followed by 1% formaldehyde for 10min, which was quenched in 0.1M glycine for 10min. Cells were washed twice in cold PBS and scraped off the plates in cold PBS containing protease inhibitors (Roche, Complete 11836170001 and Halt, Thermo Scientific, 78438). Crosslinked material was resuspended in lysis buffer 1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100) for 10min followed by 5min in lysis buffer 2 (10mM Tris-HCL pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA) before resuspending in lysis buffer 3 (10mM Tris-HCL pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0,5% N-lauroylsarcosine). Samples were sonicated using Covaris Ultrasonicator ME220 until DNA fragments had a size between 150-500bp. Chromatin was immunoprecipitated overnight using protein A coated dynabeads (Dynabeads, 10002D) with specific antibodies. After washing the beads, chromatin was eluted and decrosslinked by incubating at 65oC over-night in elution buffer (50mM Tris-HCL, 10mM EDTA, 1% SDS). Samples were treated with RNase A (20ng/mL) for 1h followed by proteinase K (200ng/mL) for 2h before DNA was purified by standard phenol-chloroform purification.
Purified DNA was submitted to library preparation using NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E765). The samples were sequenced on a NovaSeq 6000 (Illumi-na) to reach approximately 25M paired-end reads per sample.

treatment_protocol: 40μM KJ-PYR-9 (dissolved in DMSO) for 3hr, SMARTpool siRNA targeting MYC or GCN5 was used to KD MYC for 72h, 0,5μM DEX treatment for 2hr

tag: tissue

value: Cell line

tag: cell line

tag: cell type

value: TNBC

tag: antibody

value: Cell Signaling, D6H2L

value: Veh


title: MED1 ChIP, BT549 cells, Veh, BioRep1


title: Sample_91

city: Tromsø

first: Ilona

last: Urbarova

address: Hansine Hansens veg 18

department: Department of Community Medicine

country: Norway

institute: UiT The Arctic University of Norway

library_source: transcriptomic

data_processing:
FASTQ files were created using bcl2fastq 2.17 (Illumina, Inc., San Diego, CA, USA).
The sequencing reads in the individual FASTQ files from NLCB cohort were trimmed and quality filtered using cutadapt-1.2.1.
Trimmed reads were mapped to the human genome (hg38) using STAR aligner and counted using featureCounts.
mRNA read counts were normalized using reads per million (RPM) normalization and log2 transformation (voom from limma).
The count matrix was filtered based on Reads Per Million (RPM) values using following filtering criteria: rowSums(rpm(matrix)) > ncol(matrix) * 2 and annotated using AnnotationDbi R package v1.52.0 (org.Hs.eg.db human database).
Genome_build: GRCh38

molecule: total RNA

source_name: Whole blood

extract_protocol:
Inclusion criteria were: (i) patients with suspected LC that will during routine examination have a biopsy or blood samples taken, (ii) patients with relapse of LC, (iii) patients aged 18 years or more, (iv) written informed consent, (v) sampling does not imply significant delay of treatment, and (vi) sampling does not imply a significantly increased risk compared to routine diagnostic sampling. The recruited participants included individuals that were symptomatic of lung cancer, but not all were diagnosed with a confirmed lung cancer diagnosis and for those that were confirmed, the study sample comprised patients of any histological subtype and stage. Symptomatic persons with a CT scan which indicated LC but who during diagnostic follow-up were not diagnosed with lung cancer are hereafter referred to as FalsePos (“false positives”). During diagnostic workup of patients with suspected LC, blood samples were collected together with phenotype data. None of the patients had started cancer treatment at the time of sampling. Phenotype data were collected from questionnaires and electronic health records from the hospital. PAXgene tubes were collected and stored at -80°C.  Total RNA was extracted from PAX tubes using the Qiagen PAXgene Blood miRNA Kit (Qiagen, MD, USA) in combination with an automated Qiacube system according to manufacturer’s instructions.
RNA quantity, quality and purity were evaluated using Qubit (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent, CA, USA) and NanoDrop (Thermo Fisher Scientific, MA, USA). 400 ng of total RNA was then incubated with magnetic beads coated with oligo-dT, then all other RNAs except mRNA were removed by washing. RNA sequencing libraries for samples from NLCB cohort were generated using the Lexogen SENSE mRNA-Seq library prep kit according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria). In brief, library preparation was initiated by random hybridization of starter/stopper heterodimers to the poly(A) RNA still bound to the magnetic beads. These starter/stopper heterodimers contain Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction extends the starter to the next hybridized heterodimer, where the newly-synthesized cDNA insert was ligated to the stopper. Second-strand synthesis was performed to release the library from the beads. The resulting double-stranded library was purified and amplified (12 PCR cycles) after adding the adaptors and indexes. Finally, libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA). The size range of the DNA fragments were measured to be in the range of 200-600 bp with average library size 300 bp.   Prior to sequencing, the libraries were quantified (KAPA Library Quantification Kit (Illumina/ABI Prism), normalized and pooled. Quantitated libraries were further diluted to 2.3 pM and subject to clustering by a cBot Cluster Generation System prior to sequencing on one HiSeq4000 flowcell (Illumina Inc. San Diego, CA, USA), according to manufacturer’s instructions. Finally, single-end read sequencing was performed for 50 cycles on an Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA, USA).

value: Whole blood

tag: Sex

value: male

value: FalsePos

tag: histology

tag: agescaled

tag: smokingstatus

value: Ever

tag: survival


title: Sample_83

value: Never


title: Sample_84

value: female

value: Middle

value: SQ


title: MED1 ChIP, BT549 cells, Dex, BioRep1

value: Dex


title: MED1 ChIP, BT549 cells, Veh, BioRep3


title: BRD4, BT549 cells, siCtl, BioRep3

value: Bethyl Laboratories, A301-985A

value: siCtl


title: Sample_87

value: Advanced

value: AD


title: Sample_85


title: Sample_86


title: Sample_89

value: Other


title: MED1 ChIP, BT549 cells, Dex, BioRep3

value: Cell line

value: TNBC

value: Bethyl Laboratories, A300-793A


title: MED1 ChIP, BT549 cells, Veh, BioRep2

value: Veh


title: MYC ChIP, BT549 cells, Dex, BioRep3

value: Cell Signaling, 13987


title: Sample_82

value: Whole blood

value: male


title: Sample_81

value: Early

value: Ever


title: MYC ChIP, BT549 cells, Veh, BioRep2


title: Sample_8

value: Middle

value: SCLC


title: MYC ChIP, BT549 cells, Veh, BioRep3


title: MYC ChIP, BT549 cells, Veh, BioRep1


title: Sample_90

value: SQ


title: Sample_79

value: female

value: FalsePos


title: Sample_80


title: Sample_78

value: Advanced

value: Never


title: MYC ChIP, BT549 cells, Dex, BioRep1

value: Dex


title: MYC ChIP, BT549 cells, Dex, BioRep2

value: Cell line


title: MED1 ChIP, MCF7 cells, KJPYR9, BioRep2

value: TNBC


title: sow + Myodin [N10-Lf]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Fastq files were analysed with docker4seq package. In brief, fastq files quality was evaluated with fastqc. Fastq were trimmed with Skewer and mapped with STAR 2.5 against Sus scrofa genome retrieved from EMBL repository. Differential expression analysis was performed with DEseq2.
Assembly: Sscrofa11.1
Supplementary files format and content: raw counts, tab delimited

molecule: polyA RNA

organism: Sus scrofa

source_name: sow + Myodin

extract_protocol:
RNeasy Plus Universal Mini Kit (Qiagen)
TruSeq stranded mRNA library preparation kit (Illumina)

treatment_protocol: i.m. injections of 4 mg/kg b.w. of Sustanon (250 mg/ml) (T) or undergo i.m. injections of 5 mg/kg b.w. of Myodin (25 mg/ml) (N).

value: Liver

value: Myodin


title: MED1 ChIP, MCF7 cells, KJPYR9, BioRep1

value: Bethyl Laboratories, A300-793A


title: Sample_76

value: Whole blood

value: Other


title: MED1 ChIP, MCF7 cells, Veh, BioRep2

value: Veh


title: Sample_72

value: male

value: Ever


title: Input, Veh, MCF7 cells


title: MED1 ChIP, MCF7 cells, Veh, BioRep1


title: Input, KJPYR9, BT549 cells


title: MED1 ChIP, MCF7 cells, Veh, BioRep3


title: Sample_70


title: Input, KJPYR9, MCF7 cells


title: Sample_67

value: Middle


title: Sample_69


title: Sample_7


title: MED1 ChIP, MCF7 cells, KJPYR9, BioRep3


title: Sample_75

value: Early

value: SQ


title: MED1 ChIP, BT549 cells, KJPYR9, BioRep3


title: MED1 ChIP, BT549 cells, KJPYR9, BioRep2


title: Sample_73

value: female

value: FalsePos


title: MED1 ChIP, BT549 cells, Veh, BioRep3_9937


title: Sample_68


title: MED1 ChIP, BT549 cells, Veh, BioRep2_9936


title: Sample_65

value: Never


title: MED1 ChIP, BT549 cells, KJPYR9, BioRep1


title: Sample_66

value: Advanced

value: SCLC


title: MED1 ChIP, BT549 cells, Veh, BioRep1_9935

value: Cell line

value: TNBC


title: Sample_63

value: AD


title: Sample_64


title: Sample_62


title: Input, Veh, BT549 cells_A006


title: Sample_61


title: Sample_6


title: MYC ChIP, BT549 cells, KJPYR9, BioRep3

value: Cell Signaling, 13987


title: Input, KJPYR9, BT549 cells_A007


title: MYC ChIP, BT549 cells, KJPYR9, BioRep2


title: Sample_59

value: Whole blood


title: Input, Veh, BT549 cells


title: BT549 cells, DEX treatment, BioRep1

data_processing:
Sequencing data was demulitplexed using bcl2fastq before aligned to the human genome version GRCh38.
Samtools was used to remove low quality read.
FeatureCounts were used to quantify raw read coverage before further analysis was performed using DESeq2.
Assembly: hg38

extract_protocol:
Total RNA was harvested from cells with Tri-reagent (Sigma-Aldrich, 93289) and purified with chloroform on EconoSpin Columns (EconoSpin, 1910). Ribosomal RNA was depleted using the NEBNext rRNA depletion kit (Biolabs, E6310) before the library was prepared with the NEBNext RNA Library Prep kit (Biolabs, E7540).
Samples were sequenced on a NovaSeq 6000 (Illumina) to reach approximately 25M paired-end reads per sample.

treatment_protocol: 40μM KJ-PYR-9 (dissolved in DMSO) for 3hr or SMARTpool siRNA targeting MYC was used to KD MYC for 72h

tag: genotype

value: WT

value: DEX


title: Sample_58

value: Other


title: Sample_55

value: Ever


title: MYC ChIP, BT549 cells, KJPYR9, BioRep1


title: MYC ChIP, BT549 cells, Veh, BioRep2_A021

value: Veh


title: MYC ChIP, BT549 cells, Veh, BioRep1_A020


title: Sample_54

value: male


title: Sample_57

value: Middle


title: Sample_52

value: female


title: MED1 ChIP, T47D cells, BioRep3

value: ER+ breast cancer

value: Bethyl Laboratories, A300-793A

value: Non


title: Input, T47D cells


title: Sample_51

value: FalsePos


title: MED1 ChIP, T47D cells, BioRep2

value: Cell line


title: Sample_5

value: Advanced

value: SCLC


title: Sample_53

value: SQ


title: Sample_46

value: Whole blood

value: AD


title: MYC ChIP, T47D cells, BioRep2

value: Cell Signaling, 13987


title: MYC ChIP, T47D cells, BioRep1


title: MYC ChIP, T47D cells, BioRep3


title: Input, MCF7 cells


title: Sample_45


title: Sample_49

value: Early


title: MYC ChIP, BT549 cells, Veh, BioRep3_A022

value: TNBC


title: MED1 ChIP, MCF7 cells, BioRep2


title: Sample_43

value: Ever


title: Sample_44

value: male


title: MED1 ChIP, MCF7 cells, BioRep1


title: MED1 ChIP, MCF7 cells, BioRep3


title: MYC ChIP, MCF7 cells, BioRep3


title: MYC ChIP, MCF7 cells, BioRep2


title: Sample_50

value: Never


title: MYC ChIP, MCF7 cells, BioRep1


title: Sample_38


title: Input, MDA-MB-231 cells


title: MED1 ChIP, MDA-MB-231 cells, BioRep3


title: MED1 ChIP, T47D cells, BioRep1


title: Sample_41


title: Sample_35

value: female


title: MED1 ChIP, MDA-MB-231 cells, BioRep2


title: Sample_34


title: Sample_36


title: MED1 ChIP, MDA-MB-231 cells, BioRep1


title: Sample_33


title: Sample_32

value: Middle


title: MYC ChIP, MDA-MB-231 cells, BioRep2


title: Sample_31


title: MYC ChIP, MDA-MB-231 cells, BioRep1


title: Sample_30


title: Sample_42

value: Other


title: MED1 ChIP, BT549 cells, BioRep3

value: Bethyl Laboratories, A300-793A

value: Non


title: Sample_3


title: Sample_29


title: MED1 ChIP, BT549 cells, BioRep1

value: Cell line


title: MYC ChIP, BT549 cells, BioRep3


title: Sample_28

value: FalsePos


title: MED1 ChIP, BT549 cells, BioRep2


title: Sample_27


title: Sample_26


title: Sample_25

value: Advanced


title: Sample_37


title: Sample_23

value: SCLC


title: SYO1_sgELOA3_SPT6_ChIP

city: Chicago

first: Marc

last: Morgan

state: IL

address: 303 East Superior St, SQI 7-511

country: USA

institute: Northwestern University

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg38 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg38 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: SYO1, G402 and DLD1 cells were grown in DMEM supplemented with 15% fetal bovine serum.

extract_protocol:
RNA was prepared usng a Qiagen Rneasy Miniprep kit. ChIP DNA was purified using a Zymo ChIP clean and concentrator kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were subjected to treatment wih Doxycycline at 2ug/ml and JQ1 and 1uM for 24 or 48 hours.

value: Synovial Sarcoma

value: ELOA3 mutant

tag: chip antibody


title: SYO1_sgELOA3_Rpb1_ChIP

value: POLR2A (Rpb1)


title: SYO1_sgELOA3_PAF1_ChIP


title: SYO1_sgELOA3_NELFE_ChIP

value: NELF-E


title: Sample_214

value: Whole blood


title: Sample_215

value: Ever


title: RNAPII S5p, BT549 cells, siGCN5, BioRep3

value: TNBC

value: Cell Signaling, 13523


title: Sample_211

value: male

value: AD


title: Sample_212

value: female


title: Input, BT549 cells


title: SYO1_sgELOA3_NELFA_ChIP

value: NELF-A


title: SYO1_sgELOA3_NELFB_ChIP

value: NELF-B


title: Sample_4


title: Sample_210

value: Early

value: SQ


title: Sample_21

value: Other


title: MYC ChIP, MDA-MB-231 cells, BioRep3

value: Cell line

value: Cell Signaling, 13987

value: Non


title: SYO1_sgELOA3_Input

value: Synovial Sarcoma

value: ELOA3 mutant

value: Input


title: Sample_209

value: Whole blood

value: FalsePos

value: Ever


title: SYO1_sgELOA3_NELFCD_ChIP

value: NELF-CD


title: Sample_22

value: male


title: MYC ChIP, BT549 cells, BioRep1

value: TNBC


title: SYO1_sgELOA3_1uM_JQ1_Rpb1_ChIP

value: POLR2A (Rpb1)


title: SYO1_sgELOA3_1uM_JQ1_SPT6_ChIP


title: Sample_208

value: female

value: Middle


title: Sample_207


title: SYO1_sgELOA3_1uM_JQ1_PAF1_ChIP


title: Sample_204


title: Sample_205

value: AD


title: SYO1_sgELOA3_1uM_JQ1_NELFE_ChIP

value: NELF-E


title: SYO1_sgELOA3_1uM_JQ1_NELFB_ChIP

value: NELF-B


title: Sample_203

value: SQ


title: SYO1_sgELOA3_1uM_JQ1_NELFA_ChIP

value: NELF-A


title: Sample_201


title: Sample_200


title: SYO1_sgELOA3_ELOA3_ChIP

value: Synovial Sarcoma


title: SYO1_sgELOA3_1uM_JQ1_ELOA3_ChIP

value: ELOA3 mutant


title: SYO1_sgControl_SPT6_ChIP

value: wild-type


title: SYO1_sgControl_Rpb1_ChIP


title: SYO1_sgELOA3_1uM_JQ1_Input

value: Input


title: Sample_2

value: Whole blood

value: Advanced

value: SCLC


title: SYO1_sgControl_PAF1_ChIP


title: Sample_198

value: FalsePos

value: Ever


title: Sample_197

value: male

value: Early


title: SYO1_sgControl_NELFE_ChIP


title: Sample_195


title: SYO1_sgControl_NELFCD_ChIP

value: NELF-CD


title: SYO1_sgControl_NELFB_ChIP


title: Sample_194

value: Other


title: Sample_206


title: SYO1_sgELOA3_1uM_JQ1_NELFCD_ChIP


title: SYO1_sgControl_Input


title: castrated boar + Sustanon [T1-Lmc]

source_name: castrated boar + Sustanon

value: Liver

value: Sustanon


title: Sample_192

value: Middle


title: SYO1_sgControl_ELOA3_ChIP


title: Sample_191

value: AD


title: Sample_190

value: female


title: Sample_196

value: SQ


title: Sample_187


title: SYO1_sgControl_1uM_JQ1_NELFE_ChIP

value: Synovial Sarcoma

value: wild-type

value: NELF-E


title: Sample_186

value: Whole blood

value: Advanced


title: SYO1_sgControl_1uM_JQ1_PAF1_ChIP


title: Sample_193

value: SCLC


title: Sample_188

value: Ever


title: SYO1_sgControl_1uM_JQ1_NELFCD_ChIP


title: SYO1_sgControl_1uM_JQ1_Input

value: Input


title: Sample_183

value: male

value: FalsePos


title: SYO1_sgControl_1uM_JQ1_NELFB_ChIP

value: NELF-B


title: SYO1_sgControl_1uM_JQ1_NELFA_ChIP

value: NELF-A


title: Sample_185

value: Early


title: SYO1_sgControl_1uM_JQ1_Rpb1_ChIP

value: POLR2A (Rpb1)


title: Sample_182

value: AD


title: SYO1_sgControl_NELFA_ChIP


title: SYO1_sgControl_1uM_JQ1_ELOA3_ChIP


title: SYO1_Tet_ELOA_Rpb1_ChIP


title: Sample_199

value: female


title: MYC ChIP, BT549 cells, BioRep2

value: Cell line

value: TNBC

value: Cell Signaling, 13987

value: Non


title: Sample_19

value: Whole blood

value: Never


title: Sample_184

value: Other


title: Sample_181

value: Advanced

value: Ever


title: Sample_180


title: SYO1_Tet_ELOA_HA_ChIP

value: Synovial Sarcoma

value: wild-type

value: Hemagglutinin tag


title: SYO1_Tet_ELOA_JQ1_Rpb1_ChIP


title: Sample_71

value: male

value: Middle

value: SQ


title: Sample_179

value: FalsePos


title: Sample_178

value: AD


title: Sample_177


title: Sample_18

value: female


title: SYO1_Tet_ELOA3_JQ1_Rpb1_ChIP

value: POLR2A (Rpb1)


title: SYO1_sgControl_1uM_JQ1_SPT6_ChIP


title: SYO1_TetGFP_Rpb1_ChIP


title: SYO1_Tet_ELOA3_HA_ChIP


title: Sample_173


title: Sample_171


title: Sample_172

value: Early


title: Sample_175


title: SYO1_Tet_ELOA_JQ1_HA_ChIP


title: Sample_17

value: SCLC


title: SYO1_TetGFP_JQ1_Rpb1_ChIP


title: Sample_170

value: Whole blood


title: Sample_169


title: SYO1_TetGFP_JQ1_HA_ChIP


title: SYO1_TetGFP_HA_ChIP


title: Sample_168

value: Never


title: SKOV3 cells siPAI1 plus platelets biological rep3

city: Dublin

first: Tanya

middle: E

last: Kelly

email: kellyt9@tcd.ie, kellyt14@tcd.ie

address: James' Street

department: Histopathology and Morbid Anatomy

country: Ireland

institute: Trinity College Dublin School of Medicine

data_processing:
Sequence reads were concatenated and then mapped to GrCh38 using HiSat2 which employs soft-trimming.
Reads were aggregated with featureCounts using Ensemble v 101  annotation file with parameters -s 2 (for reversed strandedness) and -pBP to only include fragments with properly paired mates.
TPM values were calculated, and genes with a maximum TPM < than 1 across all samples were removed.
Read count extraction and normalization were performed using CombatSeq
Assembly: GrCh38-hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: SK-OV-3 cells were maintained in McCoy's 5A supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, and pen/strep in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA extraction was performed using Rneasy mini spin kit (Qiagen). 500ng of total RNA were used for library construction, employing the poly-A tail method for mRNA enrichment.
First Strand cDNA synthesis was performed using Illumina’s First Strand Act D Mix and SuperScript II Reverse Transcriptase (Invitrogen). Library construction was performed using the Illumina TruSeq Stranded mRNA Library Prep Kit.
Poly-A selection for RNA-seq

treatment_protocol:
Treatments with PAI-1 siRNA, negative control, or no treatment  (two sets of each) were performed in antibiotic-free medium and incubated for 24 hours in 5% CO2 at 37°C.  This was performed for n = 3 using 3 separate cell passages and 3 separate donor platelet isolations.
Healthy donor platelets were isolated from whole blood in a modified Tyrode's buffer, activated with CaCl2, and added to one well of each untreated, PAI-1 siRNA, and negative control siCONTROL at 1000:1 and incubated for 24h in 5% CO2 at 37°C.

value: ovarian adenocarcinoma epithelial morphology

value: human, female, ovarian, adenocarcinoma, ascites, hypodiploid

value: PAI-1 siRNA with healthy donor platelets

tag: time


title: SKOV3 cells siPAI1 plus platelets biological rep2


title: SKOV3 cells siPAI1 plus platelets biological rep1


title: SKOV3 cells siCONTROL plus platelets biological rep2

value: siCONTROL with healthy donor platelets


title: SKOV3 cells siCONTROL plus platelets biological rep3


title: Sample_166

value: Advanced

value: Ever


title: SKOV3 cells siCONTROL plus platelets biological rep1


title: Sample_165

value: male


title: SKOV3 cells no si with platelets biological rep3

value: healthy donor platelets


title: SYO1_Tet_ELOA3_Rpb1_ChIP

value: Synovial Sarcoma

value: wild-type


title: Sample_163

value: Middle

value: AD


title: SKOV3 cells no si with platelets biological rep2


title: Sample_162

value: Other


title: SKOV3 cells no si with platelets biological rep1


title: Sample_161

value: Early

value: SQ


title: Sample_160

value: Whole blood


title: SKOV3 cells siPAI1 biological rep2

value: PAI-1 siRNA


title: SKOV3 cells siPAI1 biological rep1

value: ovarian adenocarcinoma epithelial morphology


title: Sample_159

value: female


title: Sample_16


title: Sample_167


title: Sample_158

value: FalsePos


title: SKOV3 cells siCONTROL biological rep3

value: human, female, ovarian, adenocarcinoma, ascites, hypodiploid

value: siCONTROL


title: SKOV3 cells siCONTROL biological rep1


title: SKOV3 cells siCONTROL biological rep2


title: Sample_156

value: Ever


title: SKOV3 cells untreated biological rep3


title: Sample_157

value: male


title: RNA3-809-B 22

city: Umeå

first: Elizabeth

last: Sands

state: Västerbotten

address: Stipendiegränd 4B 0302

department: EMG

country: Sweden

institute: Umea University

data_processing:
Tuxedo Suite in the Cyverse Discovery Environment
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic_0.36.0 Parameters: window size: 20, Phred quality score: PHRED+33, Read crop length: 0, Palindrome clip threshold: 30, Simple clip threshold: 10, Leading quality: 3,Trailing quality: 3, Read head crop length: 0, Window size: 4, Seed mismatches: 2, Minimum read length: 50
Trimmed sequence reads were mapped using HTProcess-prepare-directories-and-runFastqc0.2 Paired end spacing: 500, Standard deviation for paired end spacing estimated: 75
TopHat_2_PE was then used to prepare bam files for CuffDiff analysis. Parameters: FastQ quality scale: PHRED33, Anchor length: 8, Maximum intron length: 500, Maximum number of mismatches that can appear in the anchor region of spliced alignment: 0, Minimum intron length: 10, Minimum isoform fraction: 0.15, Maximum number of alignments to be allowed: 20, Minimum intron length that may be found during split segment (default) search: 10, Maximum intron length that may be found during split segment (default) search: 500, Number of mismatched allowed in each segment alignment for reads mapped independently: 2, Minimum number of read segments: 20, Mate pair inner distance: 50, Bowtie 2 speed and sensitivity: Sensitive (slower)
Read count extraction and normalization were performed using CuffDiff_2.2.1a. Parameters: Minimum per-locus counts for significance testing: 10, Library size estimation for normalization: Normalize by hits to known transcripts
Assembly: Genome and annotation files accessed from ORCAE Online Resource for Community Annotation of Eukaryotes (ORCAE) database (http://bioinformatics.psb.ugent.be/orcae/).. Fasta ostreococcus_RCC809_genome.tfa annotation file V2.0 2009. Ost809_gff3_LATEST-2.tar Annotation was later improved using a BLAST2GO and ORCAE ost809__cds.tfa
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Ostreococcus sp. RCC809

source_name: Single celled organism

growth_protocol: Ostreococcus RCC809 cultures were maintained in ASW supplemented with Keller medium and antibiotics at 21C

extract_protocol:
RNA was harvested using Spectrum Plant Total RNA Kit (Sigma-Aldrich). 3.1 to 16 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina Tru-Seq RNA library preparation kit following manufacturer's protocols.

treatment_protocol: When cultures reached log phase (20-30 million cells per ml), they were transferred to red, green, and blue lights at 4umol photons m-2 s-1

value: Single celled organism

value: WT

value: Day 3


title: SKOV3 cells untreated biological rep2


title: SYO1_Tet_ELOA3_JQ1_HA_ChIP

value: Synovial Sarcoma

value: wild-type

value: Hemagglutinin tag


title: RNA3-809-G 21


title: Sample_155

value: Middle


title: Sample_164


title: RNA3-809-R 20


title: SKOV3 cells siPAI1 biological rep3


title: Sample_152


title: Sample_154

value: Other


title: Huh7 cells, shNAT_3

city: Xi'an

first: Yamei

last: Dang

state: Shaanxi

address: No.169 Changle West Road, Xincheng District,

country: China

institute: Fourth Military Medical University

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence ,then mapped to mm8 whole genome using v0.12.2
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM
Data fitering steps prior to assembly,the low quality reads(1,reads containing sequencing adaptors;2, reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed, Cutadapt software(version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination
After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome. The mapped reads of each sample were assembled using StringTie with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Assembly: mm8
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

growth_protocol: Huh7 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Control and NAT10 knock-down cells were infected with SINV for 6 hours

tag: shRNA

value: shNAT

value: Liver

value: Huh7 cells

value: Hepatocellular carcinoma cells


title: Huh7 cells, shNAT_V_2, SINV infection 6 hours

tag: agent

value: SINV infection 6 hours


title: RNA3-809-B 3


title: RNA3-809-G 1


title: Huh7 cells, shNAT_2


title: Huh7 cells, shNAT_V_1, SINV infection 6 hours


title: Huh7 cells, shNAT_V_3, SINV infection 6 hours


title: Sample_150

value: Whole blood

value: FalsePos


title: Huh7 cells, shNAT_1


title: RNA3-809-R 19


title: SKOV3 cells untreated biological rep1

value: ovarian adenocarcinoma epithelial morphology

value: human, female, ovarian, adenocarcinoma, ascites, hypodiploid


title: RNA1-809-R 15

value: Single celled organism


title: Huh7 cells, shCon_1

value: shCon


title: Huh7 cells, shCon_V_1, SINV infection 6 hours


title: Huh7 cells, shCon_2


title: SpOvary

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description: single cell mRNA

library_source: transcriptomic single cell

data_processing:
Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3′ Reagent kit v3.1 Chemistry. Libraries were sequenced by Genewiz/Azenta on the Illumina NovaSeq. Single-cell unique molecular identifier (Fujii et al., 2009) counting (counting of unique barcodes given to individual transcript molecules) was performed using Cell Ranger from 10x Genomics. The reference files were generated for each species using CellRanger mkref (Spur-4.2, Lvar3, and Pm v3 assembly available on echinobase). Cellranger gene expression matrices were further analyzed using the R package Seurat (Stuart et al., 2019). Individual datasets were normalized by scaling gene expression in each cell by total gene expression. tSNE analysis was performed with the following parameters: dimension 15 and resolution 0.5. Cell cluster marker genes for single cell RNA sequencing datasets were extracted using the FindMarkers function in Seurat (using R) and were then sorted based on the pct1/pct2 ratio.
Assembly: Spur-4.2, Lvar3, Pm v3 assembly available on echinobase
Supplementary files format and content: tab-delimited text files include matrices that contain UMI-corrected counts for each cell and integrated seurat object

organism: Strongylocentrotus purpuratus

source_name: Ovary

extract_protocol: Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3’ Reagent kit v3 Chemistry. Libraries were sequenced by Genewiz on the Illumina Hiseq (2x150 bp paired-end runs).

value: ovary


title: Sample_149

value: female

value: Advanced

value: AD

value: Ever


title: Huh7 cells, shCon_V_2, SINV infection 6 hours


title: Brca1d11/d11, 53bp1-/- ENDseq

city: St Louis

first: John

last: Krais

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University School of Medicine

library_source: other

data_processing:
trimmomatic-0.36.jar PE -phred33
bwa mem -t 12 -M -k 32
picard.jar MarkDuplicates REMOVE_DUPLICATES=true
bedtools genomecov -bg -scale $rpm
Assembly: mm10
Supplementary files format and content: bw, bigwig file of ENDseq reads
Library strategy: ENDseq

molecule: other

organism: Mus musculus

growth_protocol: MEFs were maintained in DMEM+10%FBS

extract_protocol:
See PMID 32840769 for detailed protocol and processing
See PMID 32840769 for detailed library construction methods

treatment_protocol: 1uM doxocyclin (DOX) for 24 hours with tamoxifen for the last 5h

value: 1uM doxocyclin (DOX) for 24 hours with tamoxifen added the last 5h


title: Sample_148


title: Sample_147

value: male


title: R22035327LR02-116-plus A-12_R1.fastq

city: shanghai

first: Yongfeng

last: Liu

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

description: R22035327LR02-116-plus A-12_R1.fastq.gz

data_processing:
Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
FPKM  method is used in calculated expression level
Assembly: hg19

extract_protocol: mRNA was extracted from total RNA using magnetic beads with oligo-dT then were fragmented randomly. The first strand of cDNA and the second strand are then synthesized using reverse transcriptase. The reverse transcription product is subjected to terminal repair, followed by addition of an A base at the 3' end. Subsequently, the fragments were ligated with a Illumina universal adapter. After PCR amplified, the ligation products were purified in order to remove the incompletely ligated fragment and the self-ligated adapter. Library sizes were detected using an Agilent 2100 Bioanalyzer and library concentrations were detected using Qubit 2.0. The DNA sequencing was performed according to Illumina's standard protocol.

value: colorectal cancer

value: wild type

value: with 4 mM adenosine supplementation for 6 hours


title: Sample_146

value: Early

value: Never


title: Brca1CC/CC, 53bp1-/- ENDseq

value: Brca1CC/CC, 53bp1-/-


title: R20063881LR01-116-shY3-g-6h

data_processing:
Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5).
Use Bowtie2 to map clean reads to reference gene and use BWA to reference genome.
FPKM method is used in calculated expression level
Assembly: hg19
Supplementary files format and content: FPKMs

source_name: glucose deprivation 6 h on shYAP3 cells

value: colorectal cancer cell

value: YAP knockdown

value: glucose deprivation


title: Sample_15

value: Whole blood

value: Middle

value: Other


title: Brca1+/+, 53bp1-/- ENDseq


title: Huh7 cells, shCon_V_3, SINV infection 6 hours

value: shCon

value: SINV infection 6 hours

value: Liver

value: Huh7 cells

value: Hepatocellular carcinoma cells


title: Sample_144

value: male

value: SQ

value: Ever


title: R20063880LR01-116-shY1-g-6h

source_name: glucose deprivation 6 h on shYAP1 cells


title: Sample_145

value: female

value: FalsePos


title: R20063877LR01-116-shYAP1-ctrl

source_name: interfere YAP expression

value: control


title: Huh7 cells, shCon_3


title: R20063879LR01-116-NC-g-6h

source_name: glucose deprivation 6 h on NC cells

value: colorectal cancer cell

value: wild type


title: R20063878LR01-116-shYAP3-ctrl

value: YAP knockdown


title: Sample_143

value: Whole blood

value: Advanced

value: SCLC


title: Brca1CC/CC, 53bp1+/+ ENDseq

value: Brca1CC/CC, 53bp1+/+

value: 1uM doxocyclin (DOX) for 24 hours with tamoxifen added the last 5h


title: Sample_142


title: R20063876LR01-116-NC-ctrl

source_name: no treatment


title: Brca1+/+, 53bp1+/+ ENDseq


title: Sample_141

value: Never


title: SYO1_Tet_ELOA3_JQ1_and_Doxycycline_ChIP_Input

value: Synovial Sarcoma

value: wild-type


title: SYO1_Tet_GFP_JQ1_and_Doxycycline_ChIP_Input


title: Sample_14

value: male

value: Early

value: Other


title: Leo1_01_12

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

institute: Karolinska Institute

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.10a) was used to index the human reference genome (GRCh38) obtained from Ensembl and ERCC-92 spike ins and then map the fastq files.
featureCounts (v1.5.1) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Homo_sapiens.GRCh38.101.gtf) as well as the ERCC-92 spike ins.
Assembly: GRCh38
Supplementary files format and content: counts.txt is a tab delimited text file with ensembl gene ids and counts for all the samples
Supplementary files format and content: counts_ercc.txt is a tab delimited text file with the ERCC-92 gene ids and counts for all the samples

growth_protocol: Cells were cultured in RPMI medium 1640 (Thermo Scientific). The RPMI was supplemented with 10% FBS (Thermo Scientific) and and 1% penicillin/streptomycin (10,000 U/mL) (Thermo Scientific). Cells were routinely passaged when the confluency reached 0.7-1x106 cells/ml. Quiescent cells were obtained in cultures in RPMI medium 1640 supplemented with 0.1% FBS after ten days incubation.

extract_protocol:
Total RNA was subjected to quality control with Agilent Tapestation according to the manufacturer’s instructions
To construct libraries suitable for Illumina sequencing, the Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA.
The protocol includes mRNA isolation, cDNA synthesis, ligation of adapters and amplification of indexed libraries. The yield and quality of the amplified libraries was analyzed using Qubit by Thermo Fisher and quality was checked by using Agilent Tapestation.


title: Leo1_01_11


title: SYO1_Tet_GFP_Doxycycline_ChIP_Input


title: Sample_138

value: female

value: Middle

value: Ever


title: WT_01_8

value: WT


title: Sample_136

value: FalsePos


title: WT_01_9


title: Sample_135

value: AD


title: SYO1_Tet_ELOA3_JQ1_and_Doxycycline_ChIP_ELOA3


title: Sample_139

value: Whole blood


title: WT_01_7


title: Leo1_10_5


title: Sample_134


title: SYO1_Tet_ELOA3_JQ1_and_Doxycycline_ChIP_POLR2A

value: POLR2A (Rpb1)


title: SYO1_Tet_ELOA3_JQ1_and_Doxycycline_ChIP_HA

value: Hemagglutinin tag


title: Sample_133

value: Advanced


title: Brca1d11/d11, 53bp1+/+ ENDseq

value: 1uM doxocyclin (DOX) for 24 hours with tamoxifen added the last 5h


title: SYO1_Tet_GFP_JQ1_and_Doxycycline_ChIP_ELOA3


title: Leo1_10_4


title: SYO1_Tet_GFP_JQ1_and_Doxycycline_ChIP_HA


title: Leo1_01_10


title: Sample_132


title: SYO1_Tet_ELOA3_Doxycycline_ChIP_Input


title: SYO1_Tet_GFP_JQ1_and_Doxycycline_ChIP_Ser2P_POLR2A

value: Serine-2-Phosphorylated POLR2A


title: WT_10_2


title: HDLECs_Zmiz1siRNA_2

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

data_processing:
Raw files were processed using basepairtech ATAC seq pipelines. (https://www.basepairtech.com/analysis/atac-seq/)
Sequenced reads were aligned to the human (hg19) reference genome using basepairtech Bowtie2 alignment pipeline.
Peaks were called using basepairtech ATAC Peak MACS2 tool.
Assembly:  hg19
Supplementary files format and content: bigwig, csv for peaks/foldEnrichment

source_name: HDLECs

growth_protocol: Human Dermal Lymphatic Endothelial Cells (HDLECs) (Promocell, C-12216) were cultured in endothelial cell growth medium MV2 (EGM-MV2) (Promocell, C-22022) supplemented with Growth Medium MV 2 SupplementMix (Promocell, C-39226) at 37 °C and 5% CO2.

extract_protocol: ATAC sequencing library was prepared using Active motif ATAC seq kit as per manufacturer instruction (Active Motif, 53150). Briefly, intact nuclei were isolated from control and Zmiz1 siRNA transfected HDLECs. Samples were treated with a hyperactive Tn5 transposase which tag the target DNA with sequencing adapters and fragment the DNA simultaneously.

treatment_protocol: HDLECs were transfected with a pool of control non-targeting siRNA (Horizon, D-001810-10-05) and Zmiz1 siRNA (Horizon, L-007034-00-0005) using Lipofectamine 3000 (Thermo Fisher, L3000015) following manufacturer instructions. The final concentration of siRNA solution was 200 nM.

value: HDLECs

value: Endothelial Cells

value: Zmiz1 siRNA

value: 48 hours


title: Leo1_10_6


title: SYO1_Tet_ELOA3_JQ1_and_Doxycycline_ChIP_Ser2P_POLR2A

value: Synovial Sarcoma

value: wild-type


title: HDLECs_Zmiz1siRNA_1


title: Sample_131

value: male

value: SCLC


title: Sample_130

value: Middle

value: SQ

value: Ever


title: SYO1_Tet_GFP_JQ1_and_Doxycycline_ChIP_POLR2A


title: SYO1_Tet_ELOA3_Doxycycline_ChIP_ELOA3


title: HDLECs_CtrlsiRNA_3

value: Control siRNA


title: Sample_140

value: Whole blood

value: female

value: Other


title: HDLECs_CtrlsiRNA_2


title: AZA_SPA-2

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 26 (based on Ensembl 88)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

source_name: cell line

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: cell line

value: acute myeloid leukemia


title: AZA_SPA-3


title: Sample_129

value: FalsePos


title: PmOvary

description: single cell mRNA

organism: Patiria miniata

value: ovary


title: WT_10_1

value: WT


title: Sample_13

value: Advanced


title: SYO1_Tet_ELOA3_Doxycycline_ChIP_HA

value: Synovial Sarcoma

value: Hemagglutinin tag


title: HDLECs_Zmiz1siRNA_3

value: HDLECs

value: Endothelial Cells

value: Zmiz1 siRNA

value: 48 hours


title: HDLECs_CtrlsiRNA_1


title: WT_10_3


title: SYO1_Tet_ELOA3_Doxycycline_ChIP_Ser2P_POLR2A

value: wild-type

value: Serine-2-Phosphorylated POLR2A


title: SYO1_Tet_ELOA3_Doxycycline_ChIP_POLR2A

value: POLR2A (Rpb1)


title: Sample_127

value: Whole blood

value: male

value: Ever


title: AZA-3.

value: cell line

value: acute myeloid leukemia

value: AZA


title: Sample_126

value: Early

value: SQ


title: Luciferase-expressing HepG2 cells, sedanolide, replicate 3

city: Takamatsu

first: Yosuke

last: Tabei

state: Kagawa

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

data_processing:
The quality of the sequence data was evaluated using FastQC.
Trimmomatic was used to trim adaptor sequences and remove low-quality reads.
The sequences were aligned to the GRCh38 human reference genome using the alignment tool STAR.
Reads in transcripts per million (TPM) formats were computed using RNA-seq by Expectation-Maximization (RSEM).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

growth_protocol: Luciferases-expressing HepG2 cells were cultured in DMEM supplemented with 10% FBS, 1% MEM NEAA, and 1 mM sodium pyruvate at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit according to the manufacturer’s instructions.
A cDNA library was prepared using an MGIEasy RNA Directional Library Prep Set.

treatment_protocol: Luciferases-expressing HepG2 cells were seeded in 6-well plates at 9 × 105 cells/well. After incubation for one day, the cells were treated with 100 μM sedanolide for 24 h.

value: hepatoblastoma

value: Sedanolide


title: Sample_125

value: Advanced

value: AD


title: AZA-2.


title: Luciferase-expressing HepG2 cells, sedanolide, replicate 2


title: SYO1_Tet_GFP_Doxycycline_ChIP_ELOA3

value: Synovial Sarcoma


title: AZA-1.


title: SYO1_Tet_GFP_Doxycycline_ChIP_HA

value: Hemagglutinin tag


title: Sample_122

value: Middle

value: Other


title: Sample_124

value: FalsePos


title: Sample_123

value: Whole blood


title: Luciferase-expressing HepG2 cells, control, replicate 2

value: Control


title: Luciferase-expressing HepG2 cells, sedanolide, replicate 1


title: DAC-3

value: Decitabine


title: SYO1_Tet_GFP_Doxycycline_ChIP_Ser2P_POLR2A

value: wild-type

value: Serine-2-Phosphorylated POLR2A


title: Luciferase-expressing HepG2 cells, control, replicate 3


title: Sample_120

value: female

value: Ever


title: SYO1_Tet_GFP_Doxycycline_ChIP_POLR2A

value: POLR2A (Rpb1)


title: CT-2.

value: cell line

value: acute myeloid leukemia

value: Untreated


title: CT-3.


title: G402_Tet_GFP_JQ1_and_Doxycycline_Rep2

value: Malignant Rhabdoid Tumor


title: Sample_121


title: G402_Tet_ELOA3_JQ1_and_Doxycycline_Rep1


title: Sample_12

value: male


title: YXL4TgLIF_2.fq.gz

city: New Brunswick

first: Xue

last: Yang

state: New Jersey

address: 195 Little Albany St

institute: Rutgers cancer institute of new jersey

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.

source_name: liver

extract_protocol:
Total RNA from the liver tissue of TgL and TgLC mouse with Tamoxifen injection was extracted using RNeasy kits (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: 32 µg/g of body weight for female mice and 64 µg/g of body weight for male mice; i.p., once

value: liver

value: TgLC

value: Tamoxifen


title: G402_Tet_GFP_JQ1_and_Doxycycline_Rep1


title: 8266-liver


title: DAC-2


title: HAEC, Altered Paclitacel, rep1

city: Cambridge

first: Antonio Gabino

last: Salazar Martin

state: Massachusetts

address: 400 Main Street, Building E25-449

institute: Massachusetts Institute of Technology

description: Processed data in barcode, feature and matrix files

data_processing:
Illumina’s bcl2fastq software was used to demultiplex samples according to sample-specific indices introduced in the post-tagmentation PCR. Demultiplexed FASTQs were aligned with human reference genome hg19 using an implementation of the Drop-seq Pipeline maintained by the Broad Institute. Mapped reads filtered for quality were used to generate digital gene expression matrices (DGEs) for each sample. UMI-collapsed data were used to generate the final counts table used for analysis; DGEs were combined from separate array samples by retaining the genes detected in all samples to generate counts tables for further analysis.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human aorta

extract_protocol:
Following unimodal (flow) or bimodal (flow and chemical treatment) stimulation, HAEC were washed with PBS and 0.05% Trypsin-EDTA was injected. Cells were incubated for 5 min and collected in a microcentrifuge tube with complete medium. Cells were centrifugated (300g for 5 minutes) and resuspended for analysis.
After whole-transcriptions-amplification, samples libraries were prepared for sequencing using the Nextera XT DNA tagmentation/amplification. Libraries were purified with SPRI ratios of 0.6x and 0.8x applied to the amplified and tagmented product, respectively. Final libraries had an average fragment size distribution between 400 and 600 bp. Libraries were loaded onto a NextSeq 500 at a final loading concentration of 2.2 pM with a read structure as follows: (read 1) 20 cycles covering the 12-bp cell barcode and 8-bp unique molecular identifiers (UMIs); (read 2): 50 cycles on the mRNA strand; (index 1) 8 cycles covering sample-specific barcode sequences. Each sample was allotted 200 million reads for a target sequencing depth of 10-15k reads per cell.

value: Human aorta

value: Primary human aortic endothelial cells

value: Altered flow (2.5 dynes/cm2), Paclitaxel


title: YXL3TgLIF_2.fq.gz


title: Luciferase-expressing HepG2 cells, control, replicate 1

value: hepatoblastoma

value: Control


title: Sample_117

data_processing:
FASTQ files were created using bcl2fastq 2.17 (Illumina, Inc., San Diego, CA, USA).
The sequencing reads in the individual FASTQ files from NLCB cohort were trimmed and quality filtered using cutadapt-1.2.1.
Trimmed reads were mapped to the human genome (hg38) using STAR aligner and counted using featureCounts.
mRNA read counts were normalized using reads per million (RPM) normalization and log2 transformation (voom from limma).
The count matrix was filtered based on Reads Per Million (RPM) values using following filtering criteria: rowSums(rpm(matrix)) > ncol(matrix) * 2 and annotated using AnnotationDbi R package v1.52.0 (org.Hs.eg.db human database).
Genome_build: GRCh38

value: Whole blood

value: Middle

value: SQ


title: DAC-1

value: Decitabine


title: Sample_119

value: female

value: FalsePos

value: Ever


title: AZA_SPA-1

value: cell line

value: acute myeloid leukemia


title: Sample_113

value: male


title: 8530-liver

value: liver

value: TgL


title: 8264-liver

value: TgLC

value: Tamoxifen


title: G402_Tet_ELOA3_JQ1_Rep1

value: Malignant Rhabdoid Tumor

value: wild-type


title: HAEC, Altered Rapamycin, rep1

description: Processed data in a unique matrix file

value: Human aorta

value: Primary human aortic endothelial cells

value: Altered flow (2.5 dynes/cm2), Rapamycin


title: Sample_115

value: Whole blood

value: Advanced

value: AD


title: G402_Tet_ELOA3_Doxycycline_Rep2


title: G402_Tet_GFP_JQ1_Rep2


title: HAEC, Physio Paclitaxel, rep1

value: Physiologic flow (30 dynes/cm2), Paclitaxel


title: HAEC, Physio Rapamycin, rep1

description: Processed data in a unique matrix file

value: Physiologic flow (30 dynes/cm2), Rapamycin


title: Sample_114

value: female

value: SCLC

value: Ever


title: 8270-liver

value: liver


title: 8267-liver

value: TgL


title: G402_Tet_GFP_JQ1_Rep1


title: CT-1.

value: cell line

value: acute myeloid leukemia

value: Untreated


title: HAEC, Altered Control, rep2

value: Altered flow (2.5 dynes/cm2), Control (no drug)


title: G402_Tet_ELOA3_JQ1_Rep2

value: Malignant Rhabdoid Tumor

value: wild-type


title: Sample_110


title: G402_Tet_ELOA3_Doxycycline_Rep1


title: HAEC, Altered Control, rep1

description: Processed data in a unique matrix file

value: Human aorta

value: Primary human aortic endothelial cells


title: Sample_111

value: Whole blood

value: FalsePos


title: HSPCs, mRNA-derived cDNA

city: Lund

first: Anna

last: Konturek-Ciesla

address: Box 188

department: Department of Molecular Hematology

institute: Lund University

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Post-sequencing libraries were processed using Cell Ranger 7.0.0. The FASTQ files were aligned to the mouse reference genome (mm10) to create unique molecular identifier (UMI) count tables of gene expression. The HTO demultiplexing was performed with cellhashr, available at [https://github.com/BimberLab/cellhashR]. The following HTO tags were used: ice_noTP/TotalSeq-A0301; 37ºC_noTP/TotalSeq-A0302; ice_TP/TotalSeq-A0303; 37ºC_TP/TotalSeq-A0304.
Further data processing was done with Seurat v4.1.1 (cell and gene filtering, dimensionality reduction, analysis of IER signature).
All code, software versions (conda/mamba environment specifications) etc needed to reproduce the CITE-seq analysis is hosted at [https://github.com/razofz/DB_AKC_citeseq]
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Hdf5 file with filtered count matrix
Supplementary files format and content: Seurat (R package) object, in .rds (Rdata) format
Supplementary files format and content: Comma-separated files for Seurat-processed metadata and UMAP embeddings per cell
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Bone Marrow

extract_protocol:
Lineage-Sca1+cKit+ cells were FACS-purified, counted and checked for viability using hematocytometer. Cell suspension was adjusted to a concentration of 1,250 cells/µL and 54,000 cells were loaded onto Chromium Controller (10x Genomics).
Libraries were generated using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics). mRNA and hashing oligos (HTO) were reverse transcribed, barcoded and purified using a Dynabeads bead cleanup mix. The cDNA was amplified by PCR according to the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 protocol with additional primer amplifying the HTO-derived tags (5’-GTGACTGGAGTTCAGACGTGTGCTC-3’). SPRI size selection was performed to separate fragments containing mRNA-derived (>300 bp) and HTO-derived (<180 bp) cDNA. mRNA-derived cDNA sequencing library was next generated according to manufacturer’s instructions (10x Genomics). HTO-derived sequencing library was prepared according to CITE-seq_and_Hashing_protocol_190213 (https://cite-seq.com/protocols). HTO-derived fragments we purified with 2X SPRI beads (Beckman Coulter) and amplified using the KAPA HiFI HotStart Library Amplification Kit (Roche) with SI-PCR primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’) as i5 primer (Illumina), TruSeq D708_s primer 5’-CAAGCAGAAGACGGCATACGAGATGCGCATTAGTGACTGGAGTTCAGACGTGTGC-3’ as i7 primer (Illumina) and the following cycling conditions: 95°C for 3 min followed by 12 cycles 95°C for 20 sec; 64°C for 30 sec; 72°C for 20 sec and final elongation 72°C for 5 min. Final cDNA- and HTO-derived libraries were pooled and sequenced on Illumina NovaSeq 6000 instrument using S2 Reagent Kit v1.5 (100 cycles). Preparation of libraries and sequencing were done at the Center for Translational Genomics, Lund University.

treatment_protocol: Bone marrow cells were isolated and cKit-enriched in ice-cold staining buffer (PBS/2%FBS) with or without 5 uM triptolide (TP). Aliquots of cells were next incubated on ice or at 37ºC in culture media (DMEM/10mM HEPES/2%FBS) with or without 5 uM TP for 90 min. Following incubation, the cells were stained with fluorochrome- and oligo-conjugated antibodies and subjected to cell sorting.

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells

value: Different cell isolation protocols

value: wild type

tag: library type

value: mRNA

tag: antibodies/tags


title: G402_Tet_GFP_Doxycycline_Rep2


title: HSPCs, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

molecule: protein

tag: treatment

value: HTO

value: Anti-CD45 and Anti-MHC class I antibodies:ice_noTP/TotalSeq-A0301; 37ºC_noTP/TotalSeq-A0302; ice_TP/TotalSeq-A0303; 37ºC_TP/TotalSeq-A0304


title: SBM2: LN:Q11-Batf3KO

first: Anita

last: Chong

address: 5841 South Maryland Avenue

institute: The University of Chicago

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Base-calling was performed by Novogene Inc. with CASAVA 1.8 software.
Reads with adaptor contamination,  or N>10%, or low quality were removed.
Clean reads were mapped to the mm10 genome assembly using STAR v2.5.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for each sample.

source_name: Mediastinal lymph node

extract_protocol:
OT-1 cells were gated and sorted into 96-well plates (100 cells per well).
Sequencing libraries were generated using Nextera XT DNA Library Prep Kit and Nextera XT Index Kit (Illumina) according to the SmartSeq2 protocol.

tag: tissue

value: Mediastinal lymph node

value: OT-1 T cells

value: T cells

value: I.N. SIIN-Q11


title: Sample_11

first: Ilona

last: Urbarova

institute: UiT The Arctic University of Norway

source_name: Whole blood

extract_protocol:
Inclusion criteria were: (i) patients with suspected LC that will during routine examination have a biopsy or blood samples taken, (ii) patients with relapse of LC, (iii) patients aged 18 years or more, (iv) written informed consent, (v) sampling does not imply significant delay of treatment, and (vi) sampling does not imply a significantly increased risk compared to routine diagnostic sampling. The recruited participants included individuals that were symptomatic of lung cancer, but not all were diagnosed with a confirmed lung cancer diagnosis and for those that were confirmed, the study sample comprised patients of any histological subtype and stage. Symptomatic persons with a CT scan which indicated LC but who during diagnostic follow-up were not diagnosed with lung cancer are hereafter referred to as FalsePos (“false positives”). During diagnostic workup of patients with suspected LC, blood samples were collected together with phenotype data. None of the patients had started cancer treatment at the time of sampling. Phenotype data were collected from questionnaires and electronic health records from the hospital. PAXgene tubes were collected and stored at -80°C.  Total RNA was extracted from PAX tubes using the Qiagen PAXgene Blood miRNA Kit (Qiagen, MD, USA) in combination with an automated Qiacube system according to manufacturer’s instructions.
RNA quantity, quality and purity were evaluated using Qubit (Thermo Fisher Scientific, MA, USA), Bioanalyzer (Agilent, CA, USA) and NanoDrop (Thermo Fisher Scientific, MA, USA). 400 ng of total RNA was then incubated with magnetic beads coated with oligo-dT, then all other RNAs except mRNA were removed by washing. RNA sequencing libraries for samples from NLCB cohort were generated using the Lexogen SENSE mRNA-Seq library prep kit according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria). In brief, library preparation was initiated by random hybridization of starter/stopper heterodimers to the poly(A) RNA still bound to the magnetic beads. These starter/stopper heterodimers contain Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction extends the starter to the next hybridized heterodimer, where the newly-synthesized cDNA insert was ligated to the stopper. Second-strand synthesis was performed to release the library from the beads. The resulting double-stranded library was purified and amplified (12 PCR cycles) after adding the adaptors and indexes. Finally, libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA). The size range of the DNA fragments were measured to be in the range of 200-600 bp with average library size 300 bp.   Prior to sequencing, the libraries were quantified (KAPA Library Quantification Kit (Illumina/ABI Prism), normalized and pooled. Quantitated libraries were further diluted to 2.3 pM and subject to clustering by a cBot Cluster Generation System prior to sequencing on one HiSeq4000 flowcell (Illumina Inc. San Diego, CA, USA), according to manufacturer’s instructions. Finally, single-end read sequencing was performed for 50 cycles on an Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions (Illumina, Inc., San Diego, CA, USA).

value: male

value: Middle

value: SCLC

value: Ever


title: HAEC, Physio Control, rep2

value: Human aorta

value: Primary human aortic endothelial cells

value: Physiologic flow (30 dynes/cm2), Control (no drug)


title: Sample_107

value: Whole blood

value: Early

value: SQ


title: G402_Tet_GFP_DMSO_Rep2

data_processing:
Basecalls were performed using bcl2fastq v2.17
ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg38 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg38 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

value: Malignant Rhabdoid Tumor

value: wild-type


title: G402_Tet_ELOA3_DMSO_Rep1


title: SBM1: LN:Q11-Batf3KO

tag: cell line


title: Sample_106


title: HAEC, Physio Control, rep1

description: Processed data in a unique matrix file

tag: cell type


title: M48Nb2: CD11b+, Naïve

source_name: mediastinal lymph nodes

extract_protocol:
Target subset DCs were gated and sorted into 96-well plates (100 cells per well).
Sequencing libraries were generated using Nextera XT DNA Library Prep Kit and Nextera XT Index Kit (Illumina) according to the SmartSeq2 protocol.

value: mediastinal lymph nodes

value: CD11b+ DCs

value: Naive


title: Sample_109

value: AD


title: G402_Tet_GFP_Doxycycline_Rep1

extract_protocol:
RNA was prepared usng a Qiagen Rneasy Miniprep kit. ChIP DNA was purified using a Zymo ChIP clean and concentrator kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit


title: M48Nb1: CD11b+, Naïve


title: SWM1: LN:Q11-WT

value: Mediastinal lymph node

value: OT-1 T cells

value: T cells

value: WT

value: I.N. SIIN-Q11


title: G402_Tet_GFP_DMSO_Rep1


title: G402_Tet_ELOA3_DMSO_Rep2


title: M48Sb1: CD11b+, S-Q11


title: M48S3N2: CD103+, S-Q11, SIINFEKL non-presenting DCs

value: CD103+ DCs


title: SWL2: Lung:Q11-WT

source_name: Lung

value: Lung


title: Sample_105

value: male

value: FalsePos

value: Ever


title: Sample_104

value: Whole blood

value: female

value: Never


title: M48Sb2: CD11b+, S-Q11

value: mediastinal lymph nodes


title: SBL2: Lung:Q11-Batf3KO


title: M48S3N1: CD103+, S-Q11, SIINFEKL non-presenting DCs


title: SWM2: LN:Q11-WT


title: SYO1_sgp53_2_JQ1_Rep1

value: Synovial Sarcoma

value: p53 sgRNA


title: SWL1: Lung:Q11-WT


title: Sample_102

value: Advanced

value: AD


title: Sample_103

value: SCLC


title: SBL1: Lung:Q11-Batf3KO

value: OT-1 T cells

value: T cells


title: Sample_101

value: Middle

value: Other


title: SYO1_sgp53_1_JQ1_Rep2


title: N4: Naïve

source_name: spleen and lymph nodes

value: spleen and lymph nodes

value: OT-1 TCR-Tg

value: Naive


title: M48S3P1: CD103+, S-Q11, SIINFEKL-presenting DCs

value: CD103+ DCs

value: I.N. SIIN-Q11


title: Sample_100

value: Whole blood

value: female

value: Early

value: Ever


title: SYO1_sgp53_2_JQ1_Rep2

value: Synovial Sarcoma

value: p53 sgRNA


title: M48S3P2: CD103+, S-Q11, SIINFEKL-presenting DCs

value: mediastinal lymph nodes


title: M48N3_2: CD103+, Naïve


title: Sample_10

value: male

value: FalsePos


title: N1: Naïve

value: OT-1 T cells

value: T cells


title: M48N3_1: CD103+, Naïve


title: R22035326LR02-116-CTRL-12_R1.fastq

value: colorectal cancer

value: wild type

value: no treatment


title: N2: Naïve

value: spleen and lymph nodes

value: OT-1 TCR-Tg

value: Naive


title: SYO1_sgp53_2_DMSO_Rep2


title: SYO1_sgp53_1_JQ1_Rep1


title: SYO1_sgCtrl_JQ1_Rep1

value: wild-type


title: SYO1_sgCtrl_JQ1_Rep2


title: Sample_1

value: Whole blood


title: SYO1_sgp53_2_DMSO_Rep1


title: S13: CD11b+, S-Q11

value: Lung

value: CD11b+ DCs

value: I.N. SIIN-Q11


title: 5C_FixMC38_NonDraining

first: Michelle

last: Piquet

state: MA

address: 250 Massachusetts Ave,

institute: Novartis Institutes for BioMedical Research

description:
10x Genomics
NA-40-YZ09

data_processing:
The demultiplexing of the raw base calls, alignment, filtering, barcode counting, and UMI counting were made using the Cell Ranger software v3.0.1
Assembly: mm10
Supplementary files format and content: Tab separated values for genes and resulting barcodes for each library.
Supplementary files format and content: Count matrix files (dgCMatrix format)

source_name: Lymph node

extract_protocol:
Single-cell suspensions of LNs were prepared for analysis by flow cytometry or single cell RNAseq. LNs were dissected and incubated at 37 °C in RPMI containing 0.1 mg ml−1 DNase I (Invitrogen), 0.2 mg ml−1 collagenase P (Roche) and 0.8 mg ml−1 dispase (Roche) for 50–60 min, as previously described. Liberated cells in suspension were collected into cold medium containing 2% fetal bovine serum and 5 mM EDTA every 15–20 min and replaced with fresh digestion medium. Following complete digestion of the LN, cells were passed through a 70-μm cell strainer, washed and resuspended in cold PBS. Single cells obtained form LN digestion were resuspended in mouse FC block (Miltenyi #130-092-575). Biotinylated PDPN (8.1.1, 1:100) antibody was used for positive selection, using the EasySep Selection Kit (Stemcell Technologies #18559). Cells were then washed in cold PBS, counted, and resuspended at 106 cells/mL for sequencing.
The 10x Genomics Chromium Single Cell 3’ Reagents v3 kit (10x Genomics, Pleasanton, CA) was used with standard conditions and volumes to process cell suspensions for 3’ transcriptional profiling. The cell suspension volumes were calculated for a target cell recovery of 6000 cells for all disassociated samples and loaded on the Chromium according to manufacturer’s guidelines.

value: Lymph node


title: Escherichia coli C227-11 - 4 weeks after inoculation, rep1

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

data_processing:
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness)
featureCounts -s 2 -t transcript -g locus_tag
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Assembly: ASM20383v1
Supplementary files format and content: combined_counts.txt: A tab separated matrix with samples as columns and genes as rows

organism: Escherichia coli

source_name: bacterial cell

extract_protocol:
RNAprotect Bacteria (Qiagen), following the manufacturer´s instruction. RNeasy mini kit (Qiagen), 700 µl of lysate with 470 µl of absolute ethanol. Followed by RNAase-free DNase set (Qiagen)+centrifugation steps to prevent DNA and ethanol contamination.
A total of 1 µg of total RNA was subjected to rRNA depletion using Ribo-Zero rRNA Removal Kit Bacteria (Illumina). The cDNA libraries were constructed using the resulting tRNA and the NEBNext Ultra II Directional RNA Library Prep Kit (NEB). Libraries were sequenced as single-read (75 bp read length) on an Illumina NextSeq500 platform at a depth of 8–10 million reads

tag: strain

value: bacterial cell

value: 4 weeks after inoculation


title: Escherichia coli C227-11 - 4 weeks after inoculation, rep2


title: N3: Naïve


title: S10: CD11b+, Naïve


title: 5B_FixMC38_NonDraining

description:
10x Genomics
VA-40-YR09


title: S14: CD11b+, S-Q11


title: 5A_FixMC38_NonDraining

description:
10x Genomics
DA-40-YK09


title: Escherichia coli C227-11 - 1 week after inoculation, rep4

value: 1 week after inoculation


title: Escherichia coli C227-11 - 1 week after inoculation, rep3


title: 4C_FixMC38_Draining

description:
10x Genomics
LB-48-NY06


title: S22: CD103+, S-Q11

value: CD103+ DCs


title: Escherichia coli C227-11 - 1 week after inoculation, rep2


title: SYO1_sgCtrl_DMSO_Rep2

first: Marc

last: Morgan

institute: Northwestern University

value: Synovial Sarcoma


title: SYO1_sgCtrl_DMSO_Rep1


title: Escherichia coli C227-11 - 1 week after inoculation, rep1


title: S21: CD103+, S-Q11


title: G402_Tet_ELOA3_del_DD2_JQ1_and_Doxycycline_Rep2

value: Malignant Rhabdoid Tumor


title: Escherichia coli C227-11 - 0 weeks after inoculation, rep3

value: 0 weeks after inoculation


title: 4B_FixMC38_Draining

description:
10x Genomics
RA-40-YV09


title: 4A_FixMC38_Draining

description:
10x Genomics
ZA-40-YN09


title: 3C_LiveMC38_NonDraining

description:
10x Genomics
FB-40-ND07


title: S18: CD103+, Naïve


title: S17: CD103+, Naïve


title: Escherichia coli C227-11 - 0 weeks after inoculation, rep2


title: G402_Tet_ELOA3_del_DD2_JQ1_and_Doxycycline_Rep1


title: SYO1_sgp53_1_DMSO_Rep2

value: p53 sgRNA


title: Escherichia coli C227-11 - 0 weeks after inoculation, rep1


title: SYO1_sgp53_1_DMSO_Rep1


title: S9: CD11b+, Naïve


title: G402_Tet_ELOA3_del_ELOA_JQ1_and_Doxycycline_Rep2


title: 3A_LiveMC38_NonDraining

description:
10x Genomics
RB-49-NR06


title: G402_Tet_ELOA3_del_ELOA_JQ1_and_Doxycycline_Rep1


title: G402_Tet_ELOA3_del_DD1_JQ1_and_Doxycycline_Rep2


title: G402_Tet_ELOA3_del_DD1_JQ1_and_Doxycycline_Rep1


title: 2B_LiveMC38_Draining

description:
10x Genomics
NB-49-NV06


title: 2C_LiveMC38_Draining

description:
10x Genomics
BB-40-NH07


title: 2A_LiveMC38_Draining

description:
10x Genomics
VB-49-NN06


title: G402_Tet_ELOA3_del_TFIIS_JQ1_and_Doxycycline_Rep1


title: V2

city: Durham

first: Shane

middle: Mitchell

last: O'Neil

state: NC

address: 701 W Main St

department: Neuroscience

institute: Duke University

data_processing:
MiXCR v3.0.13
MiXCR align, assemble, export
Assembly: MiXCR -s mmu
Supplementary files format and content: MiXCR exportClones -c TRA
Supplementary files format and content: MiXCR exportClones -c TRB

source_name: T cell

extract_protocol:
NucleoSpin RNA purification kit
SMARTer® Mouse TCR a/b Profiling Kit (Takara)

value: T cell

value: Vehicle


title: V3


title: 3B_LiveMC38_NonDraining

description:
10x Genomics
JB-49-NZ06


title: I2


title: I1


title: 1D_Naive

description:
10x Genomics
ZB-49-NJ06


title: G402_Tet_ELOA3_del_TFIIS_JQ1_and_Doxycycline_Rep2

address: 303 East Superior St, SQI 7-511


title: I3


title: Mt03_Sauton_rep4

city: Hyderabad

first: Nitesh

middle: Kumar

last: Singh

state: Telangana

address: Habsiguda

department: Bioinformatics

country: India

institute: Center for Cellular and Molecular Biology

data_processing:
Illumina adapters and low-quality reads were removed from raw sequencing reads using cutadapt. Reads with quality scores less than 20 and smaller than 36 bp were discarded.
The processed reads were then mapped to the Mycobacterium tuberculosis H37RV, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, using hisat2 with default parameters.
Uniquely aligned reads were counted using featureCounts of Subread package. There were 4008 genes in the gtf file, downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/reference/GCF_000195955.2_ASM19595v2/, for which we had count information. Genes with total read count 10 across all the samples were removed resulting in 3987 genes for SigA knockdown experiment and 3999 genes for SigB knockout experiment, which were used for further analysis.
Differential gene expression analysis was performed using DESeq2. Genes with adjusted p-value < 0.05 and absolute log2 Fold change > 0.5 were considered differentially expressed.
For PCA plot and heat map, the raw read counts were rlog normalized, available with the DESeq2 package.
Assembly: Mycobacterium tuberculosis H37RV GCF_000195955.2_ASM19595v2
Supplementary files format and content: Count file in csv format that has uniquely aligned reads mapped to each gene, counted using featureCounts.

organism: Mycobacterium tuberculosis

growth_protocol: hbhA mutant strains was grown in 7H9 + ADC and Sauton's media till 0.8 OD. Mycobacterial strains was cultured in Middlebrook 7H9 medium (BD Biosciences) supplemented with 10% albumin, dextrose, NaCl, catalase (ADC) along with 0.2% glycerol (Sigma) and 0.05% Tween-80 (Sigma).

extract_protocol:
RNA was isolated from exponentially growing cultures equivalent to 10 O.D.600units. The collected cells were resuspended in TRIzol reagent (Invitrogen), lysed using a bead beater (MP FastPrep system, MP Biomedicals) as per manufacturer's instructions, and the TRIzol-lysed cell mix was extracted with chloroform, followed by precipitation of RNA using isopropanol. The RNA pellet was dissolved in RNase-free water (30µl with 2µl of RiboLock (Thermo Scientific). DNA contamination was removed by DNase I (Invitrogen) treatment, and the RNA was further purified using RNeasy mini columns (Qiagen).
Total RNA was quantified using Qubit RNA BR kit and quality was assessed using Agilent 4200 Tapestation. Libraries were generated using Illumina stranded total RNA ribozero plus.
Final library was quantified using Qubit ds DNA HS kit and sequenced on Illumina NovaSeq 6000 on SP flow cell.

treatment_protocol: Mto3∆hbhA was inoculated at 0.05 OD, in 7H9 and Sauton's media. At 0.8  OD total RNA was islolated and RNA seq was performed.

value: control

value: Sauton


title: 1C_Naive

description:
10x Genomics
DB-49-NG06


title: DGRP_Mix_Sleep_Wakefulness_Run1, replicate 1, scRNA-seq

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description: 10x Genomics 3'

data_processing:
The 10x data was mapped to the Drosophila Melanogaster (BDGP6 assembly) genome using CellRanger v.3.1.0. SNP data for the DGRP lines was downloaded from http://dgrp2.gnets.ncsu.edu/ and liftOver was used to convert these to dm6 coordinates, SNPs were then filtered to include only those present uniquely in one of the lines used (88, 287, 303, 313, 359, 379, 441, 646, 892 and 908). This vcf file was used to run demuxlet from the popscle package [https://github.com/statgen/popscle] with default parameters, tools from https://github.com/aertslab/popscle_helper_tools were utilized to speed up computation.
Scanpy (v1.4.4) was used to process the 10x libraries, samples were first loaded and cells were annotated with genotypes determined by demuxlet. Demuxlet determined doublets and ambiguous cells were removed, any cells assigned to a genotype not present in that experiment were also removed. Finally, scrublet was used to remove remaining doublets using an expected doublet rate determined by the following formula based on the known doublet rate of the 10x chromium device and the number of doublets expected to be remaining after demuxlet (within-genotype doublets):  (0.008 * (n_cells / 1000)) * (num_lines / (num_lines ^ 2)). Following doublet removal, cells with less than 200 genes were removed, as well as cells with more than 20-30% UMIs assigned to mitochondrial genes. All remaining cells were combined into a single sample for further processing. Cells were normalized to a total of 10000 counts per cell and log transformed, highly variable genes were identified using default parameters and number of counts and percentage mitochondrial reads were regressed out, finally, counts were scaled to unit variance with a zero mean with a max value of 10. A principal component analysis was performed on the data and the pcacv workflow from vsn-pipelines (v0.25.0) [https://doi.org/10.5281/zenodo.3703108] was used to determine the number of principal components (PCs)(58 PCs)  to continue with for further dimensionality reduction and clustering. Both UMAP and tSNE dimensionality reductions were computed and clusters were determined using the louvain algorithm at various resolutions. Final anndata objects were converted to loom files for visualization in SCope (https://scope.aertslab.org).
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Brains were dissected in ice-cold Schneider’s Medium with 30 mM of the transcription inhibitor Actinomycin D (Sigma-Aldrich 1410). Within 45 min after starting dissections, the brains were dissociated with an enzyme mixture of dispase (3mg/mL), collagenase (100mg/mL) and trypsin-EDTA (0.05%) in a Thermoshaker at 25C for 15 min. The dissociation was reinforced by pipetting the solution at least four times during the incubation. After washing with DPBS 15 mM Actinomycin D, resuspending the cell pellet in 100-200 ml DPBS 0.04% BSA and filtering the cell pellet with a 10mM pluriStrainer (ImTec Diagnostics_435001050).
Library preparations for the single cell RNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3.1 NextGEM chemistry (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were assessed using LUNA dual florescence cell counter (Logos Biosystems). For each sample a targeted cell recovery of 10000 cells was aimed for. The dissociated cells from a fly brain are typically quite small (averaging between 1-4 um) and we have seen that this affects the counting accuracy. In order to get consistent counting accuracy, the average of cell counts from three independent measurements were consider for loading the fly cells to the 10X controller. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3.1 user guide; CG000204 Rev D), and at the different check points the library quality was accessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). For a targeted sequencing saturation of 50-60%, sequencing was performed at a depth of 30,000 - 60,000 reads per cell and single cell libraries were sequenced either on Illumina’s NovaSeq 6000 platform or HiSeq 2500 platform using paired-end sequencing workflow and with recommended 10X; v3.1 read parameters (28-8-0-91 cycles).
Single-cell RNA-seq (10X Genomics)

treatment_protocol: After entraining flies for three days, four to eight days-old single flies were loaded during the active period between ZT 0-2 and sleep was recorded in 12:12 LD condition in a constant environment of 55-65% humidity and 22℃. Locomotion was tracked in a high-resolution video-based Raspberry Pi-enabled device (ethoscope) (Geissmann et al., 2017). Targeted mechanical sleep deprivation was delivered in a feed-back loop triggered by 10 seconds of quiescence of a fly by the rotation of the respective tube. Flies at different points of their sleep-wake cycle and ZT time were collected and their brains dissected.

value: Brain

value: Mixed

value: Various


title: C2

value: Naive


title: DGRP_Mix_Sleep_Wakefulness_Run3, replicate 1, scRNA-seq

description: 10x Genomics 3'


title: Mt03_Sauton_rep3


title: 1B_Naive

description:
10x Genomics
HB-49-NC06

value: Lymph node


title: C1


title: G402_Tet_ELOA3_JQ1_and_Doxycycline_Rep2

city: Chicago

value: wild-type


title: DGRP_Mix_Sleep_Wakefulness_Run4, replicate 1, scRNA-seq

description: 10x Genomics 3'


title: G402_Tet_ELOA3_GFP_JQ1_and_Doxycycline_Rep1


title: DGRP_Mix_Sleep_Wakefulness_Run2, replicate 1, scRNA-seq

description: 10x Genomics 3'


title: G402_Tet_ELOA3_WT_JQ1_and_Doxycycline_Rep2


title: Mt03_Sauton_rep2


title: Leo1_B_0.1_in

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.10a) was used to index a combined human (hg38) and drosophila melanogaster (dm6) reference genome obtained from UCSC and then map the fastq files.
HOMER was used to call peaks and perform annotation and counting
Assembly: hg38, dm6
Supplementary files format and content: counts_histone_peaks.txt is a tab delimited text file with annotated called peaks and counts by Homer
Supplementary files format and content: counts_TSS_2kb.txt is a tab delimited text file with the counts found in a 2kb window around TSS of genes (Ensembl)

extract_protocol:
BJ-5ta fibroblasts were fixed in 1% paraformaldehyde for 8 min. Formaldehyde fixation was quenched by adding glycine (final concentration, 0.125 M) and ChIP was performed using the iDeal ChIP-seq kit (Diagenode, Liege, Belgium) according to the manufacturer’s instructions. Chromatin extracts from one million cells were sonicated to yield 100 to 500 bp fragments using a Bioruptor Pico sonication device (Diagenode) set on high power for one round of 10 cycles with 30 seconds on and 30 seconds off at 4 °C.
Fragmentation was verified after library preparation with agarose gel electrophoresis using an Agilent Tapestation 2200 machine and software (Agilent, Sundbyberg, Sweden) to carry out a high sensitivity D1000 analysis (Supplementary Figure 3).
Spike-in Chromatin (Active Motif), was added in an amount of 10ng to each sample

tag: antibody

value: input


title: 1A_Naive

description:
10x Genomics
HA-40-YG09


title: LUNG scRNASEQ pre-cDCs

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: 10x Genomics

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the mm10 transcriptome + eGFP sequence using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.3.6.1  using the Seurat (v3) package
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

extract_protocol:
Spleens, and lungs  were cut into small pieces and digested with collagenase VIII (1 mg/ml; Sigma-Aldrich) and deoxyribonuclease I (0.4 mg/ml; Roche) in RPMI 1640 for 15 min (spleen) or 25 min (lung) at 37°C. Digested tissues were passed through a 70-μm cell strainer (BD Biosciences) and washed with FACS buffer (3% FCS and 5 mM EDTA in PBS). For lung, leukocytes were enriched by Percoll gradient centrifugation (GE Healthcare). For BM, the femur, tibia and hip extremities were cut and spun for 30 s at 10,000 rpm. Cells were resuspended in FACS buffer after centrifugation. Single cell suspensions from the bone marrow, spleen and lung were enriched for pre-cDCs by staining lineage-restricted markers with FITC-conjugated antibodies (CD3, Ly6G, SiglecF, B220, CD19, Ly6D, NK1.1, and Ter119) and depleting T, B, plasmacytoid, and red blood cells, neutrophils, eosinophils, and their precursors using the EasySep Mouse FITC Positive Selection Kit II (Stemcell technologies). Cells were stained and FACS sorted on an Aria Fusion (BD) with a 100um nozzle.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: pre-cDC

value: Lung

tag: age

value: 6-8 weeks old


title: V1


title: SPLEEN pre-cDCs

description: 10x Genomics

source_name: Spleen

value: Spleen


title: Mt03_Sauton_rep1


title: BONEMARROW pre-cDCs

description: 10x Genomics

value: Bone Marrow


title: Leo1_A_0.1_in


title: WT_B_0.1_in

value: WT


title: Mt03_WT_rep3


title: G402_Tet_ELOA3_GFP_JQ1_and_Doxycycline_Rep2

value: Malignant Rhabdoid Tumor


title: Mt03_WT_rep4


title: G402_Tet_GFP_JQ1_and_Doxycycline_Rep4


title: WT_A_0.1_in


title: G402_Tet_GFP_JQ1_and_Doxycycline_Rep3


title: Mt03_WT_rep2


title: Mt03_WT_rep1


title: Leo1_B_10_in


title: G402_Tet_ELOA3_del_DD2_Doxycycline_Rep1


title: DsodB MSB treated 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

description: Count and RPKM data

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A nidulans FGSC A4 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: genome:  https://fungidb.org/common/downloads/Current_Release/AnidulansFGSCA4/fasta/data/FungiDB-56_AnidulansFGSCA4_Genome.fasta; gff3:  https://fungidb.org/common/downloads/Current_Release/AnidulansFGSCA4/gff/data/FungiDB-56_AnidulansFGSCA4.gff
Supplementary files format and content: Excel file includes count and RPKM values for each Sample

organism: Aspergillus nidulans

source_name: mycelium

growth_protocol: Submerged cultivation: 500 ml Erlenmeyer flasks containing 100 ml of Barratt’s minimal nitrate broth were inoculated with 5×107 conidia and incubated at 37° C and at 3.7 Hz shaking frequency for 16 h

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.
RNA-seq (single read, 75 bp)

treatment_protocol: 0.16 mM menadione sodium bisulfite (MSB) treated and untreated

value: mycelium

value: DsodB mutant

value: MSB treated


title: G402_Tet_ELOA3_del_DD2_Doxycycline_Rep2


title: Leo1_A_10_in

first: Anastasios

last: Damdimopoulos

institute: Karolinska Institute


title: DsodB MSB treated 2

description: Count and RPKM data


title: DsodB MSB treated 1

description: Count and RPKM data


title: G402_Tet_ELOA3_del_ELOA_Doxycycline_Rep2


title: WT_B_10_in


title: HbhA_KO_Sauton_rep3

value: HbhA KO

value: Sauton


title: HbhA_KO_Sauton_rep4


title: DsodB untreated 3

description: Count and RPKM data

value: untreated


title: G402_Tet_ELOA3_WT_JQ1_and_Doxycycline_Rep1


title: G402_Tet_ELOA3_del_ELOA_Doxycycline_Rep1


title: DsodB untreated 2

description: Count and RPKM data


title: WT_A_10_in


title: HbhA_KO_Sauton_rep2


title: G402_Tet_ELOA3_del_DD1_Doxycycline_Rep2


title: Leo1_B_0.1_H3


title: HbhA_KO_Sauton_rep1


title: G402_Tet_ELOA3_del_DD1_Doxycycline_Rep1


title: Leo1_A_0.1_H3


title: HbhA_KO_rep4


title: THS30.3 MSB treated 3

description: Count and RPKM data

value: reference strain


title: WT_B_0.1_H3


title: G402_Tet_ELOA3_del_TFIIS_Doxycycline_Rep1


title: THS30.3 MSB treated 2

description: Count and RPKM data


title: THS30.3 MSB treated 1

description: Count and RPKM data


title: THS30.3 untreated 3

description: Count and RPKM data


title: HbhA_KO_rep1


title: Leo1_A_10_H3


title: G402_Tet_ELOA3_GFP_Doxycycline_Rep2


title: Leo1_B_10_H3


title: HbhA_KO_rep2


title: WT_A_0.1_H3


title: G402_Tet_ELOA3_GFP_Doxycycline_Rep1


title: THS30.3 untreated 2

description: Count and RPKM data


title: G402_Tet_ELOA3_WT_Doxycycline_Rep2


title: THS30.3 untreated 1

description: Count and RPKM data


title: G402_Tet_ELOA3_WT_Doxycycline_Rep1


title: DsodB untreated 1

description: Count and RPKM data


title: WT_A_10_H3


title: Glycera alba body wall replicate 3 [GaBW3]

city: Caparica

first: Pedro

middle: M.

last: Costa

address: Campus de Caparica

department: Department of Life Sciences

country: Portugal

institute: NOVA School of Science and Technology, NOVA University of Lisbon

data_processing:
Data quality was assessed with the FastQC quality-control tool v0.11.9 for high throughput sequence data. Reads with low-quality and the Illumina adapter were trimmed by using TrimGalore v0.6.6.
Reads were combined and assembled with Trinity v2.6.6.
Coding regions within the assembled transcriptome were predicted using TransDecoder v5.5.0.
Reads were mapped against the respective assembled transcriptome with Kallisto v0.43.0.
The tximport v1.18.0 package was used to import the data into R, while edgeR v3.34.0 and limma v3.48.1 packages were used for identifing the differentially-expressed transcripts between organs for both species.
Supplementary_files_format_and_content: xlsx: Data frame with the predicted coding regions that were differentially-expressed between organs (log2 fold change, average log2 counts per million, likelihooh ratio statistics and FDR adjusted p-value, sequences and their length).
Supplementary_files_format_and_content: fasta: Nucleotidic sequences of the predicted coding regions that were differentially-expressed between the organs.

organism: Glycera alba

source_name: Body wall

extract_protocol:
RNA was isolated from whole-tissue preserved in RNAlater using the RNeasy Mini Kit (Qiagen) combined with on-column DNA digestion with the RNase-Free DNase set (Qiagen).
Library preparation was done using Stranded mRNA Library Preparation Kit and the generated RNA fragments were sequenced in an Illumina Novaseq platform, using 150bp paired-end sequencing reads: 100M for samples HdG2 and HdPR2, 40M for the remaining.

value: Body wall


title: G402_Tet_ELOA3_del_TFIIS_Doxycycline_Rep2

value: wild-type


title: HbhA_KO_rep3


title: G402_Tet_GFP_Doxycycline_Rep4


title: HDLECs_Zmiz1siRNA_3

first: Rajan

last: K C

institute: Tulane University

description: Raw counts

data_processing:
Sequenced reads were aligned to the human (hg19) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Assembly:  hg19
Supplementary files format and content: Comma separated spreadsheet file with raw counts for every gene for every sample.

source_name: HDLECs

extract_protocol: RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 1 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).

treatment_protocol:
HDLECs were transfected with a pool of control non-targeting siRNA (Horizon, D-001810-10-05) and Zmiz1 siRNA (Horizon, L-007034-00-0005) using Lipofectamine 3000 (Thermo Fisher, L3000015) following manufacturer instructions. The final concentration of siRNA solution was 200 nM.
Total RNA was extracted from control and Zmiz1 siRNA transfected HDLECs using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732).

value: HDLECs

value: Human Dermal Lymphatic Endothelial Cells (HDLECs)

value: Zmiz1 siRNA

value: 48 hours


title: Glycera alba body wall replicate 2 [GaBW2]


title: Glycera alba body wall replicate 1 [GaBW1]


title: DLD1_Tet_ELOA3_JQ1_and_Doxycycline_Rep2

value: Colorectal Carcinoma


title: HDLECs_Zmiz1siRNA_1

description: Raw counts


title: HDLECs_Zmiz1siRNA_2

description: Raw counts


title: Glycera alba proboscis replicate 2 [GaPR2]

source_name: Proboscis

value: Proboscis


title: WT_B_10_H3

value: WT


title: DLD1_Tet_ELOA3_JQ1_and_Doxycycline_Rep1


title: Glycera alba proboscis replicate 3 [GaPR3]


title: HDLECs_CtrlsiRNA_3

description: Raw counts

value: Control siRNA


title: HDLECs_CtrlsiRNA_2

description: Raw counts


title: DLD1_Tet_ELOA3_Doxycycline_Rep2


title: leaf, 72 hpi, susceptible, rep1

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression after 72 hpi in susceptible NIL  rep 1

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method .

organism: Triticum aestivum

source_name: leaf, susceptible, 72 hpi, rep-1

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Wheat seed were sown in small pots in equal mix of autoclaved soil and soil rite. The pots were kept in climate controlled growth chamber with 16h light and 8 h dark cycle with 80-90 % humidity. Temprature was maintained at 25ºC during light phase and 20ºC during dark phase.

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations.

treatment_protocol: 25 days old seedlings were injected with stem rust spore suspension ( ~ 6X10¬5 spores/ml in water and 1 ppm tween 20 detergent) using a hypodermal syringe, plants were then initially kept undisturbed for 24 hours in dark and 90% humidity, and then to normal growth (16h light, 8 h dark) conditions. Leaf tissue was collected at 0, 10 & 72 hpi time points.

value: Leaf

value: 25 day

tag: phenotype

value: susceptible NIL

tag: infection

value: stem rust race

value: 72 hpi


title: Glycera alba proboscis replicate 1 [GaPR1]


title: leaf, 72 hpi, resistant, rep2

description: Gene expression after 72 hpi in resistant NIL rep 2

source_name: leaf, resistant, 72 hpi, rep-2

value: resistant NIL


title: DLD1_Tet_ELOA3_Doxycycline_Rep1