title: S. maltophilia K279a, dual species infection, rep4


title: Sample_10006600427208

status: Public on Nov 04 2022

type: SRA

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

library_source: transcriptomic

data_processing:
Sequence reads were demultiplexed and converted from BCL to fastq file format using bcl2fastq2 conversion software V2.20.0422 (Illumina, Inc. San Diego, CA, USA).
Adapters from the 3’end of the raw sequences were trimmed using cutadapt-1.2.1.
Trimmed sequence were collapsed into single unique reads along with their total read count using the fastx collapser tool (http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the human (hg38) genome and the known calibrator sequences using bowtie2, allowing for up to 10 alignments per read to account for reads from duplicated miRNA loci.
Reads overlapping with mature miRNA loci were identified using htseq-count from the HTseq python package. These reads were further filtered to identify those with perfect alignment to the genome, and the total read counts for mature miRNAs were then computed by summing the total read count per sequence (isomiR) overlapping each miRNA locus. Mature miRNAs were annotated using miRBase (Release 22).
The calibrator counts were used to compute normalization factors per sample (calcNormFactors from edgeR). MicroRNA read counts were then normalized by using the calibrator RNA normalization factors (norm.factors in DGEList from edgeR), followed by reads per million (RPM) normalization and log2 transformation (voom from limma). MicroRNAs with average RPM < 1 were excluded from further analyses.
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: Serum

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. Serum were collected and stored at -80°C.    The miRNeasy Serum/Plasma Kit (Cat No./ID: 217184, Qiagen, Hilden, Germany) in combination with an automated Qiacube system, was used to purify total RNA, including miRNA, from 100 µl serum.
For assessment of extracted RNA quality and relative size, selected samples were measured using the Agilent Eukaryote Total RNA Pico assay and an Agilent 2100 Bioanalyzer (Waldbronn, Germany). The sequencing libraries were prepared using extracted RNA samples eluted in 14 µl water, a pool of 10 synthetic calibrator RNAs, and the NEXTflex small RNA-seq kit v3 (Bioo Scientific, Austin, TX, USA). Double-stranded cDNA was prepared by PCR amplification (22 cycles) and fragments/libraries were run on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) or LabChip GX DNA High Sensitivity (Perkin Elmer, Waltham, MA, US) for quality control and quantitation. Individual libraries were normalized to 10 nM and pooled. The library pool was purified with the QIAquick PCR Purification Kit (Qiagen AB, Sweden) according to instructions. Automated size selection was performed using the Blue Pippin (Sage Science, Beverly, MA, USA), with a range of 135 to 175 bp to select the ~152 bp fragments. Following size selection, the pool was evaluated on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the High Sensitivity DNA kit. The pool of libraries was quantified with the KAPA Library Quantification Kit (Roche, Pleasanton, CA, USA). Quantitated libraries were further diluted and normalized to 2.4 nM before clustering on the cBot (Illumina, Inc., San Diego, CA, USA). Single read sequencing was performed for 51 cycles on a HiSeq4000 flowcell, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA). One in-house pooled reference sample consisting of plasma from ten random healthy individuals was included in each sample preparation batch.

tag: lane

tag: Sex

value: Female

value: FalsePos

tag: histology

tag: agescaled

tag: smokingstatus

value: Current

tag: survival


title: Breast Cancer BC0712

type: RNA

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: female

tag: age

tag: er (allread)

tag: pgr (allread)

tag: response

value: SD


title: Breast Cancer BC0693

value: PR


title: Sample_10006600427083

value: Late

value: SCLC

value: Former


title: S. maltophilia K279a, dual species infection, rep1

city: Birmingham

first: Melissa

middle: Skye

last: McDaniel

state: AL

address: 845 19th St S BBRB 744

department: Microbiology

country: USA

institute: University of Alabama at Birmingham

data_processing:
Raw reads were trimmed using Trim Galore! (v. 0.4.4) and Cutadapt (v. 1.9.1) and were evaluated for quality with FastQC
Reads were aligned to the published genome of S. maltophilia K279a or the Mus musculus genome build GRCm39/mm39 using the STAR aligner (v. 2.7.3a)
Read counts were obtained via Subread FeatureCounts
Differential expression analysis was performed with DESeq2
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include gene counts from FeatureCounts and differential expression values as calculated using DESeq2

organism: Stenotrophomonas maltophilia

source_name: Lung

extract_protocol:
For RNA isolation from the lung, BALB/cJ mice (8-10 weeks old) were obtained from Jackson laboratories (Bar Harbor, ME).  Mice were anesthetized with isoflurane and intratracheally infected with either S. maltophilia, P. aeruginosa, or both (~107 CFU each in 100 µL PBS). Mice were euthanized 24 hours post-infection, and lungs were inflated with RNA-later to preserve RNA integrity. Whole lungs were homogenized, and cells were lysed by bead beating (0.1 mm silica) in Trizol reagent (Invitrogen), and a full lung RNA extraction was performing using a standard protocol (50). Extracted RNA samples were sent to GENEWIZ (South Plainfield, NJ) for DNase treatment, host and bacterial rRNA depletion (Ribo-Zero Gold rRNA Removal Kit (Epidemiology), Illumina), and library preparation using standard protocols. For bacterial RNA-seq, single-end directional samples were DNase treated (DNase I, NEB) using a standard protocol, before being run through a second Trizol extraction to purify the sample of enzyme.
Sequencing libraries were constructed using the directional RNA Library Prep Kit (NEB) and tagged for multiplexing via the NE Next Multiplex Oligos for Illumina (NEB).
For in vivo bacterial samples, a pathogen-specific probe list for S. maltophilia was generated using previously published methods (28). Briefly, 100 bp probes were generated to cover annotated coding sequences of S. maltophilia, with 15 bp spacer sequences added on either end to allow for amplification of the probe library.   5’ SPACER : ATCGCACCAGCGTGT  3’ SPACER: CACTGCGGCTCCTCA  Probes completely covered the sense strand of each gene and were also generated to tile every other 100 bp of the antisense strand for a total of 68,704 probe sequences Figure S1). Probes with significant homology to the mouse genome or to bacterial non-coding RNAs (P <0.05 with BLAST analysis) were manually removed from the list. The resulting oligo pool was synthesized by Genscript (Piscataway, NJ). Before hybridization, DNA oligos were amplified and then transcribed (MEGAshortscript T7 Transcription Kit, Ambion), with added biotin-16-UTP (Roche) to generate biotinylated RNA probes.   Prepared cDNA libraries were hybridized to the generated pathogen-specific RNA probes using previously described methods (28) with a few modifications. Briefly, the synthesized probes and the prepared cDNA library were incubated in hybridization buffer for 24 hours at 68°C. Blocking primers were modified for compatibility with NEB multiplexing primers and a 3’ ddc’ modification was added to maintain barcoding.   Hybridization primer FWD:   AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT/3ddC/  Hybridization primer REV:  CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT/3ddC/  Hybridized cDNA was isolated via streptavidin beads and then eluted. Enriched samples were amplified using universal primers that maintained sample barcoding before sequencing.

tag: tissue

value: Lung

tag: genotype

value: WT

tag: treatment

value: Dual-species murine pulmonary infection with P. aeruginosa


title: HD_VglutCb_tot_R4

city: Linköping

first: Susanne

last: Bauer

address: BKV, Cellbiologi Pl 10

department: BKV

country: Sweden

institute: Linköpings universitet

data_processing:
RNAseq data was analyzed with nf-core/rnaseq 3.0 pipeline, using default parameters. STAR/Salmon were used for alignment and quantification
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: raw transcript counts obtained from salmon are provided in raw_count.csv.

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
Flash frozen brain hemispheres were homogenized and total RNA ("Input") was isolated from tissue homogenate using Trizol and purified using the Qiagen Rneasy Mini kit. For "RiboTag IP" samples, 12CA5 monoclonal anti-HA antibody (Roche) was coupled to protein G-coated dynabeads (Invitrogen) and incubated with tissue homogenate for 90 min to immunoprecipitate HA-tagged ribosomes and their attached mRNAs. Ribosome-bound mRNAs were isolated using Qiazol and purified using the Qiagen miRNeasy kit.
Libraries were prepared according to protovol using the Illumina TruSeq stranded mRNA kit

tag: source

value: mRNA from flash frozen brain tissue

value: HD

tag: celltype

tag: preparation

value: Input

value: Cerebellum


title: S. maltophilia K279a, single species infection, rep4

value: Single-species murine pulmonary infection


title: HD_VglutCb_tot_R3


title: E14.5 cochlear ducts, Sox2-Tbx2LOF vs control, rep 1

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 3000ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml.  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

source_name: control 1

label_protocol: 1000ng of total RNA were used as input. Synthesis of Cy3- or Cy5-labeled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations, except for a twofold downscaling of all reaction volumes.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: To induce recombination, 4 mg of tamoxifen were orally applied to timed pregnant dams in a single pulse at E12.5. Cochlear ducts were then mechanically dissected from E14.5 embryos.

tag: strain

value: NMRI

tag: developmental stage

value: cochlear duct

source_name: Sox2-Tbx2LOF, 1


title: Sample_10006600426869

tag: lane

tag: Sex

value: Male

value: Middle

value: SQ

value: Current


title: Breast Cancer BC0645

value: female

value: PR


title: 330155 control_normal gland

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

data_processing:
18 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina Stranded mRNA Prep and paired-end sequencing. The sequencing quality of the reads was assessed per sample using FastQC (version 0.11.5), Preseq (version 2.0.3), Picard tools (version 1.119) and RSeQC (version 2.6.4). Sequencing reads were trimmed of low-quality bases and adapter sequences were removed using Cutadapt (version 1.18). The trimmed reads were aligned using the GRCh38 (GENCODE hg38, version 30). Gene expression levels are quantified using RSEM (version 1.3.0 DEseq2 (version 1.28.1). Raw read counts (expected counts from RSEM) were imported into the NIH Integrated Data Analysis Platform for downstream analysis (https://nidap.nih.gov/).
Assembly: Mouse_mm10
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: normal mammary glalnd

growth_protocol: mouse mammary tumors developed in vivo

extract_protocol: total RNA extracted with RNAeasy tissue Qiagen kit

value: normal mammary glalnd

value: wild type


title: burn_MRSA_DJK5_22

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

data_processing:
Quality of RNA-Seq data was assessed with FastQC v0.11.8 and MultiQC v1.8
RNA-Seq reads were aligned to the reference genome using STAR v2.7.3a
Aligned reads were counted using HTSeq’s count function v0.11.2
Assembly: Ensembl GRCh38 v98
Supplementary files format and content: Count/text files generated by HTSeq, describing the number of aligned reads to each gene, one gene per line

molecule: polyA RNA

source_name: Skin organoid model

growth_protocol: N/TERT cells were cultured in Keratinocyte-SFM medium, and skin models were established by seeding cells onto a ThinCert filter insert in a 12-well plate. The cells were submerged in the DermaLife K Keratinocyte Complete Medium until reaching confluency (in 3-4 days), at which time the culture medium was switched to a differentiation medium. The apical side of the skin was air-exposed the next day to induce stratification. After 2-3 days, the concentration of linoleic acid in the differentiation medium was increased. N/TERT skin was ready for experiments after culturing at air-liquid interface at 37°C and 7.3% CO2 for 10 days.

extract_protocol:
Skin samples were excised and placed into RNAlater (ThermoFisher Scientific), and total RNA was extracted using the Rneasy Micro Kit (Qiagen). Quality of RNA was assessed using the Agilent 2100 Bioanalyzer, Eukaryotic Total RNA Nano Chip (Agilent Technologies, Santa Clara, CA).
DNA libraries were constructed from polyA-enriched RNA using the Kapa Stranded RNA-Seq kit (Kapa Biosystems, Wilmington MA)

treatment_protocol: Thermal damage was created by applying a digital soldering iron to N/TERT skin at 100°C for 4 seconds. MRSA biofilm was established by seeding 5 μl of 4 x 10^8 CFU/ml on top of the thermally damaged skin and cultured at 37°C and 5% CO2 for 24 hours. DJK-5 peptide (30 μl of 0.4%) was administered on top of the pre-formed biofilm. Skin samples were collected 24 hours post-peptide treatment for RNA-isolation.

value: Skin organoid model

tag: cell line

value: N/TERT keratinocytes

value: Wild type

value: Burn + MRSA infection + DJK5 treatment


title: Sample_10006600356666

value: Female

value: Early

tag: histology

value: Other

tag: agescaled

tag: smokingstatus

value: Former


title: Breast Cancer BC0350

tag: age

tag: er (allread)


title: Mouse lung, infected, Dual species, rep4

value: Lung

value: WT

value: S. maltophilia K279a, P. aeruginosa mPA08-31


title: HD_VglutCb_tot_R2

value: mRNA from flash frozen brain tissue

value: HD

value: Input

value: Cerebellum


title: HD_VglutCer_R1

source_name: Cerebrum

value: RiboTag IP

value: Cerebrum


title: S. maltophilia K279a, single species infection, rep2

value: Single-species murine pulmonary infection


title: burn_MRSA_DJK5_19

value: Skin organoid model

value: N/TERT keratinocytes


title: HD_VglutCb_R6


title: HD_VglutCb_tot_R1


title: burn_MRSA_DJK5_18

value: Wild type

value: Burn + MRSA infection + DJK5 treatment


title: Sample_10006600356330

value: Male

value: Late

value: SCLC

value: Current

tag: survival


title: S. maltophilia K279a, single species infection, rep1

tag: tissue

value: Lung

value: WT


title: Sample_10006600356218

value: SQ


title: burn_MRSA_15

tag: genotype

value: Burn + MRSA infection


title: HemSC3 [CD133C]

city: Shanghai

first: Jialin

last: Chen

address: 639 Zhizaoju Road, Huangpu District

country: China

institute: Shanghai Ninth People's Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. 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.
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
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 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: primary hemangioma stem cells

growth_protocol: HemMCs were cultured in StemPro™ MSC serum-free medium (Thermo Fisher Scientific), and HemSCs were cultured in EGM-2 supplemented with Growth Medium 2 Supplement Mix (PromoCell) and 10% fetal bovine serum with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated from HemMCs and HemSCs using TRIzol and the RNA Nano 6000 Assay Kit with the Bioanalyzer 2100 system, 1 ug of total RNA was used for the construction of sequencing libraries.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: For transcriptional analysis, HemMCs were transferred to complete EGM2 for 3 days

tag: cell type

value: primary hemangioma stem cells

tag: treatment

value: culture in EGM2

tag: time

value: 3 days


title: burn_MRSA_17


title: burn_MRSA_DJK5_20


title: E14.5 cochlear ducts, Sox2-Tbx2LOF vs control, rep 3

source_name: control 3

value: NMRI

value: male

value: cochlear duct

source_name: Sox2-Tbx2LOF, 3


title: Breast Cancer BC2211

value: female

tag: pgr (allread)

tag: response

value: PR


title: E14.5 cochlear ducts, Sox2-Tbx2LOF vs control, rep 2

source_name: control 2

tag: strain

tag: developmental stage

source_name: Sox2-Tbx2LOF, 2


title: S. maltophilia K279a, single species infection, rep3

value: Single-species murine pulmonary infection


title: burn_MRSA_14

value: Skin organoid model

value: N/TERT keratinocytes

value: Wild type


title: Sample_10006600355879

tag: lane

tag: Sex

value: Male

value: Late

value: AD

value: Former


title: HemSC2 [CD133B]

value: WT


title: HemMC3 [CD146C]

source_name: primary hemangioma mural cells

value: primary hemangioma mural cells


title: HD_VglutCb_R3

tag: source

value: mRNA from flash frozen brain tissue

value: HD

tag: celltype

tag: preparation

value: RiboTag IP

value: Cerebellum


title: HemSC1 [CD133A]

value: primary hemangioma stem cells

value: culture in EGM2

value: 3 days


title: burn_12

tag: cell line

value: burn


title: Sample_10006600355431

value: Female

value: FalsePos

tag: histology

tag: agescaled

tag: smokingstatus

value: Never


title: Sample_10006600355655

value: Male

value: Other

value: Current

tag: survival


title: HemMC2 [CD146B]

tag: cell type

tag: genotype


title: HD_VglutCb_R1

tag: tissue


title: HD_VglutCb_R2


title: Sample_10006600354980

value: Late

value: Former


title: Sample_10006600356093


title: burn_MRSA_13

value: Skin organoid model

value: N/TERT keratinocytes

value: Wild type

tag: treatment

value: Burn + MRSA infection


title: HD_SST_tot_R3

value: mRNA from flash frozen brain tissue

value: HD

value: SST

value: Input

value: Cerebrum


title: HD_VglutCb_R5

value: RiboTag IP

value: Cerebellum


title: HemMC1 [CD146A]

value: primary hemangioma mural cells

value: WT

value: culture in EGM2

tag: time

value: 3 days


title: Sample_10006600354644

value: Female

value: Early

value: Other


title: HD_VglutCb_R4


title: Sample_10006600354868

value: Male

value: Late

value: Former


title: burn_11

value: Skin organoid model

value: N/TERT keratinocytes

value: Wild type

value: burn


title: burn_10


title: RNA-Seq hTERT RPE-1, Top1, pre-dose, rep 3

city: Solna

first: Jan

middle: Eric

last: Grosser

address: Solnavägen 9

institute: Karolinska institutet

description: Diff_exp_counts.tsv, column 17, sample.pre_3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR  and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: hg38, Ensembl assembly 101
Supplementary files format and content: bam (aligned reads), tsv (differential expression analysis table with log2 read counts per million)

source_name: hTERT RPE-1

growth_protocol: Retinal Pigmented Epithelial cells immortalized with hTERT RPE-1 were grown in DMEM F12 (Gibco) and supplemented with 10% FBS, 100U/mL penicillin, and 100 mg/ml streptomycin, at 37 °C, 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the TRIzol reagent (15596026, Thermo Fisher).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 5 to 10 µg of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies).
mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Htert RPE-1 cells were treated or not with a “pre-dose” of CPT (25 nM) for 1 hour. Next, the drug was removed, allowinged the cells to adapt for 24 hours, before harvest. This resulted in two  different conditions: untreated or pre-dose treated cells.

value: hTERT RPE-1

value: htert-immortalized retinal pigment epithelial cells

value: pre-dose, 25 nM camptothecin (CPT), 1 h, harvest 24 h later


title: HD_SST_tot_R1

value: mRNA from flash frozen brain tissue

value: HD

value: SST

value: Input

value: Cerebrum


title: burn_9


title: HD_SST_tot_R2


title: RNA-Seq hTERT RPE-1, Top1, pre-dose, rep 2

description: Diff_exp_counts.tsv, column 18, sample.pre_2


title: Sample_10006600354308

value: Middle


title: untreated_4

value: untreated


title: untreated_3


title: RNA-Seq hTERT RPE-1, Top1, pre-dose, rep 1

description: Diff_exp_counts.tsv, column 21, sample.pre


title: Sample_10006600353857

value: Male

value: Early

value: SQ


title: Sample_10006600353396

value: Late

value: AD

value: Current


title: Sample_10006600353633

value: FalsePos

value: Former


title: HD_SST_R3

value: RiboTag IP


title: untreated_2

value: Skin organoid model

value: N/TERT keratinocytes

value: Wild type


title: RNA-Seq hTERT RPE-1, Top1, untreated, rep 2

description: Diff_exp_counts.tsv, column 20, sample.ut_2

value: hTERT RPE-1

value: htert-immortalized retinal pigment epithelial cells


title: HD_SST_R4

value: mRNA from flash frozen brain tissue

value: HD

value: SST

value: Cerebrum


title: HD_SST_R1


title: RNA-Seq hTERT RPE-1, Top1, untreated, rep 1

description: Diff_exp_counts.tsv, column 22, sample.ut

value: untreated


title: Sample_10006600352958

value: Female

value: Other

value: Never


title: RNA-Seq hTERT RPE-1, Top1, untreated, rep 3

description: Diff_exp_counts.tsv, column 19, sample.ut_3


title: HD_SST_R2


title: ChIP-Seq hTERT RPE-1, Top1, pre-dose + challenging dose, rep 3

library_source: genomic

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software v2.19.
The .fastq files were quality controlled with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (Ewels et al., 2016) and trimmed with cutadapt v2.10 (Martin 2011).
The samples were then aligned to hg38 reference genome with bowtie2 (Langmead and Salzberg 2012).
Subsequently, the bam files were sorted and indexed using Samtools (Li, Handsaker et al. 2009) and deduplicated using the MarkDuplicates command of the Picard set of command line tools (http://broadinstitute.github.io/picard).
Counts per million (CPM) normalized BigWig files were generated using bamCoverage and bamCompare of the deeptools suite (Ramírez, Ryan et al. 2016) and visualized using IGV (Robinson, Thorvaldsdóttir et al. 2011).
Assembly: hg38
Supplementary files format and content: bam (aligned and deduplicated reads), bw (bigWig, read coverage, averaged per condition)

molecule: genomic DNA

extract_protocol:
Top1 ChIP was performed on RPE-1 cells as described previously (Cameron et al. 2021) with minor modifications. Briefly, after treating with the challenging dose or 24 h after treatment with pre-dose, cells were treated for 5 minutes with 1 μM CPT to increase the probability to trap Top1 on the DNA. Cells were crosslinked with 1% formaldehyde (Thermo Fisher, 28906) for 5 min. Cross-linking was stopped by the addition of 125 mM glycine (Sigma, 50046) and cells were washed twice with cold PBS.
After harvesting cells, the pellet was washed once with PBS plus 0.5% BSA and resuspended in TE-SDS 0.1% (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, SDS 0.1%) with complete protease inhibitor tablet (Roche) to a final concentration of 1x10000000 cells/ml. Samples were sonicated with a Bandelin probe sonicator (30% amplitude, 4 times 30’’ ON/ 30’’ OFF) and then with Covaris ME220 sonicator for 10 min using the 1 ml High Cell protocol (Peak power: 75, Duty % factor: 15, Cycles/Burst: 1000, Average power: 11.25) to produce chromatin fragments of 200-500 bp on average.
After centrifugation, sonicated extracts were adjusted to the conditions of RIPA buffer (10mM Tris pH 8.0, 1mM EDTA pH 8.0, 1% Triton X100, 0.1% SDS, 200 mM NaCl, Na Deoxycholate 0.1%). 2 μg of anti-Top1 (ab109374) were mixed with 30 μl of Protein A/G magnetic beads (Pierce, 88803) and incubated at 4°C for 6 h with rotation. Chromatin from 10×1000000 cells was added to the Protein A/G-antibody complexes and incubated overnight at 4°C with rotation. Immunoprecipitates were washed twice with RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 1% TritonX100, 0.1% Na-Deoxycholate, 0.1% SDS, 200 mM NaCl); twice with RIPA buffer plus 300 mM NaCl; twice with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-Deoxycholate); and twice with TE. The beads were then resuspended in 125 μl TE plus 0.5% SDS supplemented with proteinase K (500 μg/ml, Thermo Fisher 25530049) and incubated overnight at 65ºC. The DNA was recovered from the eluate using the QiaQuick PCR purification kit and finally dissolved in Tris-HCl ph 8.5. All ChIP-seq experiments were performed in duplicates.
DNA from ChIP was quantified with the Qubit dsDNA HS Assay Kit. Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara, R400676). Size selection was performed in the range of 200 – 700 bp with AMPure XP beads (Beckman, A63880) and confirmed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906). The sequencing run was Single End and Dual Index with 75 bp reads.

treatment_protocol: htert RPE-1 cells were treated or not with a “pre-dose” of 25 nM of CPT (S1288, Selleckchem)  for 1 hour. Next, the drug was removed, allowinged the cells to adapt for 24 hours, before challenging them or not with a higher concentration dose of 100 nM of CPT for 1 hour before harvest. This resulted in four different treatment conditions: untreated, challenging dose treated, pre-dose treated and pre-dose+challenging dose treated cells.

tag: chip antibody


title: Sample_10006600352846

value: Late

value: SCLC

value: Current


title: SF-150102-00008, CMML38

city: Gainesville

first: Meghan

last: Ferrall-Fairbanks

state: FL

address: 1275 Center Drive

department: Biomedical Engineering

institute: University of Florida

description:
10x Genomics
FT-SA73059

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BM-MNCs

extract_protocol:
60 million cryopreserved BM-MNCs per sample were obtained. Samples were thawed, washed with 20% FBS in PBS and treated with DNAse I for 15min to reduce cell clumping. First, dead cell removal was performed according to manufacturer instructions (Miltenyi Biotech, Catalog number: 130-090-101) followed by CD34 enrichment, also according to manufacturer protocol (Miltenyi Biotec, Catalog number: 130-046-703).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics v3) was used to encapsulate and barcode for cDNA preparation of enriched CD34+ BM-MNCs in 40 samples across 29 unique patients. The targeted cell population sizes were 5,000 cells for each sample (Supplementary Table S7). The libraries were constructed according to the manufacturer’s protocol, sequenced on an Illumina NovaSeq, and mapped to the human genome (GRCh38) using CellRanger (10X Genomics).

value: BM-MNCs

value: HSCs

tag: disease state

value: CMML

value: ruxolitinib


title: Sample_10006600352497

tag: lane

value: AD


title: ChIP-Seq hTERT RPE-1, Top1, pre-dose + challenging dose, rep 1

value: hTERT RPE-1

value: htert-immortalized retinal pigment epithelial cells

value: Top1 (Abcam, ab109374)

value: pre-dose, 25 nM camptothecin (CPT), 1 h, 24 h later, challenging dose, 100 nM CPT, 1 h, harvest


title: ChIP-Seq hTERT RPE-1, Top1, pre-dose + challenging dose, rep 2


title: SF-140613-0036, CMML36

description:
10x Genomics
FT-SA73057

value: chemotherapy


title: HD_PV_tot_R1

value: mRNA from flash frozen brain tissue

value: HD

value: PV

value: Input

value: Cerebrum


title: Sample_10006600352161

tag: Sex

value: Female

value: FalsePos


title: HD_PV_R2

tag: source

value: RiboTag IP


title: ChIP-Seq hTERT RPE-1, Top1, pre-dose, rep 2

value: pre-dose, 25 nM camptothecin (CPT), 1 h, harvest 24 h later


title: Sample_10006600352385

value: Male

value: Late

value: Former


title: SF-140925-00135, CMML35

description:
10x Genomics
FT-SA73056

value: BM-MNCs

value: HSCs

value: CMML

value: HMA


title: untreated_1

value: Skin organoid model

value: N/TERT keratinocytes

value: Wild type

value: untreated


title: Sample_10006600351947

value: Middle

value: Other


title: ChIP-Seq hTERT RPE-1, Top1, challenging dose, rep 2

value: hTERT RPE-1

value: htert-immortalized retinal pigment epithelial cells

value: Top1 (Abcam, ab109374)

value: challenging dose, 100 nM camptothecin (CPT), 1 h, harvest


title: SF-141114-00033, CMML34

description:
10x Genomics
FT-SA73055

value: ruxolitinib


title: HD_PV_R5

value: mRNA from flash frozen brain tissue

value: HD

tag: celltype

value: PV

value: RiboTag IP

value: Cerebrum


title: HD_PV_tot_R3

tag: preparation

value: Input


title: HD_PV_re_R2


title: Sample_10006600351598

value: Female

value: FalsePos

value: Current


title: HD_PV_R3


title: SF-141104-00108, CMML33

description:
10x Genomics
FT-SA73054

value: BM-MNCs

value: HSCs

value: CMML

value: HMA


title: Sample_10006600351835

value: Male

value: Late

value: SQ

value: Former


title: ChIP-Seq hTERT RPE-1, Top1, challenging dose, rep 1

tag: cell line

value: hTERT RPE-1

value: htert-immortalized retinal pigment epithelial cells

value: Top1 (Abcam, ab109374)

value: challenging dose, 100 nM camptothecin (CPT), 1 h, harvest


title: ChIP-Seq hTERT RPE-1, Top1, untreated, rep 2

value: untreated


title: Sample_10006600351150

tag: histology


title: SF-140804-00065, CMML37

description:
10x Genomics
FT-SA73058


title: SF-130328-00016, CMML32

description:
10x Genomics
FT-SA73052


title: HD_GadCer_tot_R3

value: mRNA from flash frozen brain tissue

value: HD

value: Input

value: Cerebrum


title: SF-160722-00003, CMML30

description:
10x Genomics
FT-SA46670

value: BM-MNCs


title: SF-161123-00029, CMML31

description:
10x Genomics
FT-SA46671

value: HSCs


title: HD_PV_R1

value: PV

value: RiboTag IP


title: ChIP-Seq hTERT RPE-1, Top1, pre-dose, rep 1

value: pre-dose, 25 nM camptothecin (CPT), 1 h, harvest 24 h later


title: ChIP-Seq hTERT RPE-1, Top1, untreated, rep 1


title: SF-160628-00045, CMML29

description:
10x Genomics
FT-SA46669

value: CMML


title: Sample_10006600350587

value: Male

value: FalsePos

tag: agescaled

value: Never


title: SF-130709-00171, CMML39

description:
10x Genomics
FT-SA73053

value: HMA


title: Sample_10006600349129

tag: smokingstatus


title: HD_GadCer_tot_R2


title: HD_GadCer_R2


title: Sample_10006600348454

value: Middle

value: SQ

value: Former

tag: survival


title: HD_GadCer_R6

value: mRNA from flash frozen brain tissue


title: HD_PV_tot_R2

value: HD


title: SF-140318-00065, CMML27

description:
10x Genomics
FT-SA46667

tag: cell type


title: SF-140507-00419, CMML28

description:
10x Genomics
FT-SA46668


title: C2-D5-i : Plants at day 5 not treated and inoculated with Z. tritici _ repetition 2

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

description:
raw data block: Lame 3_Bloc3Ctr2J3i
Gene expression after 5 days of treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Wheat Gene Expression Microarrays GE 4x44 (Agilent, Santa Clara, CA, USA) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: Wheat plants at day 5 not treated and inoculated (i) with Z. tritici _ repetition 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds of the cultivar (cv.) Alixan (Limagrain, France), susceptible to STB, were pregerminated in square Petri dishes (12 × 12 cm) on moist filter paper as described by Siah et al. (2010), and germinated grains were delicately transferred into three-liter pots filled with universal loam (Gamm Vert, France). The prepared pots were then placed in the greenhouse at 21 ± 2°C with a 16/8 h day-night cycle. For each condition and each sampling modality, three pots harboring 12 wheat plants each (n=36), were used.

extract_protocol: Total RNA was extracted from wheat leaves using RNeasy Plant Mini Kit (Qiagen, Courtaboeuf, France). RNA quality was determined with Nanodrop by analyzing their absorbance ratios A260/280 and A260/230, which were found to range between 2.0 and 2.2. Moreover, RNA quality was also examined with Bioanalyzer 2100 (Agilent, France) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples

treatment_protocol: At day 0 (DO), corresponding to three weeks after sowing, plants were hand-sprayed with 30 mL of either a solution of 100 mg.L-1 mycosubtilin from Bacillus subtilis mock (control) treatment. At two days after treatment (D2), half of the plants treated with mycosubtilin, as well as control plants, were inoculated by hand-spraying 30 mL of Z. tritici spore suspension (106 spores.mL-1), mixed with 0.05 % of Tween 20, on the plants of each pot. Leaf samples were harvested at two (D2), five (D5) and fifteen (D15) days after treatment for transcriptomic analyses.  For each condition, i.e. plants treated with mycosubtilin (M) or not (control, C), and inoculated with Z. tritici (i) or not (Ni), nine third leaves sampled from three different pots (three leaves per pot), were randomly harvested, bulked per pot, immediately frozen in liquid nitrogen and stored at -80°C for further analyses. Thereafter, 100 mg of frozen pooled leaves were ground in a mortar with liquid nitrogen for RNA extraction.

tag: cultivar

value: Alixan

value: leaves

tag: age

value: three weeks after sowing at D0


title: Sample_10006600348678

source_name: Serum

value: Current


title: HD_GadCer_tot_R1

tag: genotype

value: Input

tag: tissue

value: Cerebrum


title: SF-120926-00014, CMML26

description:
10x Genomics
FT-SA46666

value: BM-MNCs

value: HSCs

tag: treatment


title: HD_GadCer_R5

value: RiboTag IP


title: Sample_10006600348342

value: Male

value: AD


title: 6-AD-001 rep2, CMML25

description:
10x Genomics
FT-SA46665

tag: disease state

value: CMML


title: Sample_10006600348230

tag: lane

value: FalsePos


title: Sample_10006600349017

tag: Sex

value: Late

value: SCLC


title: HD_GadCer_R1

tag: source

value: mRNA from flash frozen brain tissue


title: SF-100109-101914, CMML23

description:
10x Genomics
FT-SA40031


title: Sample_10006600347904

value: Female

value: Never


title: C3-D5-i : Plants at day 5 not treated and inoculated with Z. tritici _ repetition 3

description:
raw data block: Lame 5_Bloc2Ctr3J3I
Gene expression after 5 days of treatment

source_name: Wheat plants at day 5 not treated and inoculated (i) with Z. tritici _ repetition 3

value: Alixan

value: leaves


title: C1-D5-i : Plants at day 5 not treated and inoculated with Z. tritici _ repetition 1

description:
raw data block: Lame 2_Bloc2Ctr1J3i
Gene expression after 5 days of treatment

source_name: Wheat plants at day 5 not treated and inoculated (i) with Z. tritici _ repetition 1

value: three weeks after sowing at D0


title: Sample_10006600348118

value: Middle

value: SQ

value: Former


title: SF-120425-00035, CMML24

description:
10x Genomics
FT-SA46664

value: BM-MNCs

value: HSCs


title: HD_GadCer_R4

value: HD

tag: celltype

value: RiboTag IP

value: Cerebrum


title: HD_GadCer_R3

tag: preparation


title: HD_GadCb_tot_R3

source_name: Cerebellum

value: Input

value: Cerebellum


title: M3-D5-i : Plants treated 5 days with mycosubtilin and inoculated with Z. tritici _ repetition 3

description:
raw data block: Lame 5_Bloc1M3J3i
Gene expression after 5 days of treatment

source_name: Wheat plants treated 5 days (D5) with mycosubtilin (M) and inoculated (i) with Z. tritici _ repetition 3


title: M1-D5-i : Plants treated 5 days with mycosubtilin and inoculated with Z. tritici _ repetition 1

description:
raw data block: Lame 2_Bloc1M1J3i
Gene expression after 5 days of treatment

source_name: Wheat plants treated 5 days (D5) with mycosubtilin (M) and inoculated (i) with Z. tritici _ repetition 1


title: M2-D5-i : Plants treated 5 days with mycosubtilin and inoculated with Z. tritici _ repetition 2

description:
raw data block: Lame 3_BlockM2J3i
Gene expression after 5 days of treatment

source_name: Wheat plants treated 5 days (D5) with mycosubtilin (M) and inoculated (i) with Z. tritici _ repetition 2


title: Sample_10006600347891

value: Male

value: Late

value: SCLC

value: Current


title: 6-AD-001, CMML25

description:
10x Genomics
FT-SA40030

value: CMML


title: HD_GadCb_tot_R2

value: mRNA from flash frozen brain tissue


title: 6-AC-001, CMML22

description:
10x Genomics
FT-SA40029


title: C2-D5-Ni : Plants at day 5 not treated and not inoculated _ repetition 2

description:
raw data block: Lame 4_Block1Ctr2J3NI
Gene expression after 5 days of treatment

source_name: Wheat plants at day 5 not treated and not inoculated (Ni) with Z. tritici _ repetition 2

value: Alixan

value: leaves

value: three weeks after sowing at D0


title: C1-D5-Ni : Plants at day 5 not treated and not inoculated _ repetition 1

description:
raw data block: Lame 1_Block1C1J3NI
Gene expression after 5 days of treatment

source_name: Wheat plants at day 5 not treated and not inoculated (Ni) with Z. tritici _ repetition 1


title: M3-D5-Ni : Plants treated 5 days with mycosubtilin and not inoculated with Z. tritici _ repetition 3

description:
raw data block: Lame 7_Bloc2M3J3NI
Gene expression after 5 days of treatment

source_name: Wheat plants treated 5 days (D5) with mycosubtilin (M) and not inoculated (Ni) with Z. tritici _ repetition 3


title: 6-AE-001, CMML21

description:
10x Genomics
FT-SA40028


title: HD_GadCb_R2


title: M1-D5-Ni : Plants treated 5 days with mycosubtilin and not inoculated with Z. tritici _ repetition 1

description:
raw data block: Lame 2_Bloc4M1J3NI
Gene expression after 5 days of treatment

source_name: Wheat plants treated 5 days (D5) with mycosubtilin (M) and not inoculated (Ni) with Z. tritici _ repetition 1


title: M2-D5-Ni : Plants treated 5 days with mycosubtilin and not inoculated with Z. tritici _ repetition 2

description:
raw data block: Lame 5_Bloc4M2J3NI
Gene expression after 5 days of treatment

source_name: Wheat plants treated 5 days (D5) with mycosubtilin (M) and not inoculated (Ni) with Z. tritici _ repetition 2


title: Sample_10006600347443

value: FalsePos

value: Former


title: SF-161129-00158, CMML20

description:
10x Genomics
FT-SA40027

value: BM-MNCs

value: HSCs


title: Sample_10006600347779

value: Female


title: SF-141010-00049, CMML19

description:
10x Genomics
FT-SA40026


title: C3-D5-Ni : Plants at day 5 not treated and not inoculated _ repetition 3

description:
raw data block: Lame 7_Bloc3Ctr3J3NI
Gene expression after 5 days of treatment

source_name: Wheat plants at day 5 not treated and not inoculated (Ni) with Z. tritici _ repetition 3


title: Sample_10006600347219

value: Early

value: Other


title: HD_GadCb_R1

value: HD

value: RiboTag IP

value: Cerebellum


title: HD_GadCb_R5


title: 4-S-001, CMML17

description:
10x Genomics
FT-SA40024

value: HMA


title: Sample_10006600347331

value: Current


title: HD_GadCb_tot_R1

value: Input


title: Sample_10006600347667

value: Male

value: Late

value: AD


title: C3-D2-Ni : Plants at day 2 not treated and not inoculated _ repetition 3

description:
raw data block: Lame 6_Bloc3Ctr3J0NI
Gene expression after 2 days of treatment

source_name: Wheat plants at day 2 not treated and not inoculated (Ni) with Z. tritici _ repetition 3

value: Alixan

value: leaves

value: three weeks after sowing at D0


title: HD_GadCb_R4

value: mRNA from flash frozen brain tissue


title: SF-140602-00025, CMML13

description:
10x Genomics
FT-SA38820

value: BM-MNCs

value: HSCs

value: CMML


title: C2-D2-Ni : Plants at day 2 not treated and not inoculated _ repetition 2

description:
raw data block: Lame 4_Bloc4Ctr2J0NI
Gene expression after 2 days of treatment

source_name: Wheat plants at day 2 not treated and not inoculated (Ni) with Z. tritici _ repetition 2


title: HD_GadCb_re_R1


title: Sample_10006600347094

value: Female

value: Middle

value: Other

value: Former


title: M3-D2-Ni : Plants treated 2 days with mycosubtilin and not inoculated with Z. tritici _ repetition 3

description:
raw data block: Lame 6_Bloc2M3J0NI
Gene expression after 2 days of treatment

source_name: Wheat plants treated 2 days (D2) with mycosubtilin (M) and not inoculated (Ni) with Z. tritici _ repetition 3


title: Sample_10006600347107

value: FalsePos


title: HD_GadCb_R3

value: HD

value: RiboTag IP

value: Cerebellum


title: Sample_10006600347555

value: Current


title: 2-V-001, CMML18

description:
10x Genomics
FT-SA40025

source_name: BM-MNCs


title: SF-140722-00012, CMML15

description:
10x Genomics
FT-SA38821


title: Sample_10006600346880

source_name: Serum


title: C_VglutCer_tot_R3

source_name: Cerebrum

value: Control

value: Input

value: Cerebrum


title: CEBPA_double_mutant_CHIC

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Promoter Capture Hi-C data were processed with the HiCUP pipeline (PMID: 26835000)
The paired-end sequencing reads, called di-tag, were separately mapped to the hg38 genome, repaired and filtered for experimental artifact (i.e., self-ligation and re-ligation products) and PCR duplicates. Mapped di-tags were then analysed with GOTHiC (PMID: 28379994)
The HOMER software package was used to determine statistically significant interactions, taking into account the p-value and false discovery rate (FDR) relative to a background model.
Assembly: hg38
Supplementary files format and content: BED file of HiC fragments with significant interactions and their target gene

source_name: CD34+ AML patient cells

growth_protocol: Patient cells were cultured at the concentration of 1x106 cell/mL in StemSpanTM Serum-Free Expansion Medium II (SFEM II) (STEMCELL Technologies) supplemented with 10% StemSpanTM CD34+ Expansion Supplement and 175nM UM171 (STEMCELL Technologies).

extract_protocol: CHi-C in primary AML cells was performed as described in Assi et al. (PMID: 30420649)

value: CD34+ AML cells

value: CEBPA double mutant

tag: disease

value: Acute Myeloid Leukemia


title: SF-100109-110236, CMML11

description:
10x Genomics
FT-SA33818

value: BM-MNCs

value: HSCs


title: C_VglutCer_tot_R2

value: mRNA from flash frozen brain tissue


title: Sample_10006600346992

value: Male

value: Late

tag: histology

value: SCLC


title: C_VglutCer_tot_R1


title: SF-140401-00158, CMML12

description:
10x Genomics
FT-SA33819

value: CMML


title: SF-120628-00475, CMML14

description:
10x Genomics
FT-SA33816


title: Sample_10006600346656

value: Female

value: FalsePos

tag: agescaled

value: Former


title: M2-D2-Ni : Plants treated 2 days with mycosubtilin and not inoculated with Z. tritici _ repetition 2

description:
raw data block: Lame 4_Bloc3M2J0NI
Gene expression after 2 days of treatment

source_name: Wheat plants treated 2 days (D2) with mycosubtilin (M) and not inoculated (Ni) with Z. tritici _ repetition 2

value: Alixan

value: leaves

value: three weeks after sowing at D0


title: C_VglutCer_R6

value: Control

value: RiboTag IP

value: Cerebrum


title: Sample_10006600346768

value: Early

value: AD

tag: smokingstatus

value: Current


title: SF-130612-00056, CMML16

description:
10x Genomics
FT-SA33817

value: BM-MNCs

value: HSCs


title: C1-D2-Ni : Plants at day 2 not treated and not inoculated _ repetition 1

description:
raw data block: Lame 1_Block4_C1J0NI
Gene expression after 2 days of treatment

source_name: Wheat plants at day 2 not treated and not inoculated (Ni) with Z. tritici _ repetition 1


title: Sample_10006600346432

value: Middle

tag: survival


title: C_VglutCer_R4

value: mRNA from flash frozen brain tissue


title: C_VglutCer_R5


title: SF-100109-106293, CMML9

description:
10x Genomics
FT-SA33814

tag: cell type

value: CMML


title: A549-Input (MeRIP-Seq)

city: Fuzhou

first: Jiahui

last: Chu

state: Fujian

address: 156 west erhuan north road

institute: PLA 900th Hospital

data_processing:
Agilent 2100 Bioanalyzer was used to detect library quality
The library concentration was diluted to 8 pM and the hiseq300/4000 PE Cluster Kit (# pe-410-1001, Illumina) was used to generate clusters in Illumina cBot
HISAT2

Genome_build: hg19
Supplementary_files_format_and_content: The Excel file contains the all sample peaks

source_name: lung adenocarcinoma cell

growth_protocol: The lung adenocarcinoma cell line A549 and A549/DDP were cultured routinely in DMEM (Gibco-Invitrogen, Carlsbad, CA, USA), with 10% Fetal Bovine Serum (FBS), with Penicillin Streptomycin (Gibco) at 37℃ in an atmosphere of 5% CO2 in air.

extract_protocol:
Enrichment of RNA fragments containing m6A methylation sites by immunoprecipitation with anti-n6-methyadenosine (m 6A) antibodies
The sequencing libraries of post-m6a mRNA and input mRNA were constructed respectively with KAPA Stranded mrna-seq Kit

tag: cell line

value: lung adenocarcinoma cell

tag: phenotype

value: cisplatin-sensitive cells

tag: rip antibody


title: M1-D2-Ni : Plants treated 2 days with mycosubtilin and not inoculated with Z. tritici _ repetition 1

description:
raw data block: Lame 1_Block3M1J0NI
Gene expression after 2 days of treatment

source_name: Wheat plants treated 2 days (D2) with mycosubtilin (M) and not inoculated (Ni) with Z. tritici _ repetition 1

tag: cultivar

tag: tissue

tag: age


title: A549-IP (MeRIP-Seq)

value: anti-m6A antibody


title: 5-E-001, CMML7

description:
10x Genomics
FT-SA27355

tag: disease state

tag: treatment

value: HMA


title: DDP-IP (MeRIP-Seq)

value: cisplatin-resistant cells


title: M1647_MUT_14mo_F

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

source_name: Muscle_RAP1 MUT_14MF

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: The Rap1 I312R knockin mouse was generated using Crispr/Cas9 technology53. Briefly, a sgRNA (GAACTGCCATTAAGGTGATC) and a single-strand donor oligonucleotides was generated by IDT (https://www.idtdna.com/pages), which contains the desired mutation (CAGCCAGACGAGGAGGAAGAAGAACCAAAAGTTTCTACGCAAGAAGTGGGAACTGCCATTAAGGTGCGGCGCCAGCTAATGGAGAAGTTCAACTTGGATCTATCAACAGTTACACAGGCC; the four bold and underlined nucleotides were changed from the wildtype sequence for introducing the true and silent mutations).  The Rap1 I312R knock-in mouse was back-crossed with C57BL6 mice four times. All animal experiments were carried out according to the ‘‘Guide for the Care and Use of Laboratory Animals’’ (National Academy Press, USA, 1996), and were approved by the Institutional Animal Care and Use Committee of National Institute on Aging.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kits (#74104) for brain and liver tissues and RNeasy fibrous tissue mini kit (#74704) for heart and muscle tissues. Brain and liver tissues were homogenized using a Precellys 24 Tissue homogenizer (Bertin Instruments, Rockville, MD) at 5500-6000rpm for 30 seconds, using 1 mL cold RLT buffer containing 10% β-mercaptoethanol (BME) together with glass beads, while heart and muscle tissues were similarly homogenized  in 1 mL cold RLT buffer with 10% BME using zirconia beads. Homogenates were centrifuged at 12,000 rpm for 4 mins at 4°C to pellet any unhomogenized  tissue and beads, and RNA  isolated according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

value: Muscle

tag: Sex

value: F

tag: age (months)

tag: rap1 genotype

value: RAP1 MUT


title: DDP-Input (MeRIP-Seq)


title: C_VglutCer_R1

tag: source

tag: genotype

value: Control

tag: celltype

tag: preparation

value: RiboTag IP

value: Cerebrum


title: 5-H-001, CMML8

description:
10x Genomics
FT-SA27354

value: other


title: M1610_WT_15mo_F

source_name: Muscle_RAP1 WT_15MF

value: RAP1 WT


title: 4-Q-001, CMML6

description:
10x Genomics
FT-SA27351

value: BM-MNCs

value: HSCs


title: X_6

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software (HCS) HD 3.4.0 and Real-Time Analysis (RTA) v2.7.7 software. The bcl2fastq conversion software was used for sample demultiplexing and FASTQ conversion.
RNA-seq data was analyzed using a STAR-StringTie-Cufflinks pipeline. De-multiplexed raw sequence reads (FASTQ format) were mapped to the reference human genome assembly (GRCh37/hg19) using STAR (Spliced Transcripts Alignment to a Reference) software with a 2-pass alignment approach that uses initial alignment to detect novel junctions and insert them into the genome index, followed by a second pass to re-align reads using both annotated (GENCODE, Release 29, GRCh37) and novel (detected in the first pass) junctions. Mapped reads were then passed onto StringTie for transcript assembly and quantitation of gene- and transcript isoform expression as FPKM (fragments per kilobase of transcript per million mapped fragments). Subsequently, FPKM expression values were normalized with Cufflinks tools (e.g., Cuffquant, Cuffnorm).
Processed data are Cufflinks-Cufffnorm output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: Dec. 2013, GRCh38/hg38
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol (Ensembl ID), FPKM values, and FPKM status for each transcript and were prepared from the StringTie-Cuffnorm gene-level output files.

source_name: HBMSC 3.4 (clone 6) xenograft tumor (subcutaneous)

growth_protocol: HBMSC 3.4 (Sample A) and it's subline (clone 6; Sample B) were cultured in RPMI 1640 medium supplemented with 10% FBS, and at 37°C in a humidified atmosphere containing 5% CO2 (v/v). Once the cell cultures reached ~75% confluency, the cells were harvested for isolation of total cellular RNA. HMSC3.5 (clone 6) cells were injected into the mammary fat pad (Sample C) or subcutaneously (Sample D) into the flanks of 4–5-week-old NOD scid gamma (NSG) mice. When tumor volumes reached ~500 mm^3, the mice were eutanized, and tumors were harvested for isolation of total cellular RNA.

extract_protocol:
Total cellular RNA was isolated from HBMSC cell cultures and xenograft tumor samples using the TRIzol Reagent (Invitrogen) and a modified protocol that incorporates an additional extraction with phenol/chloroform/isoamyl alcohol (25:24:1, pH 4.3) followed by an additional clean-up step with an RNeasy spin column (Qiagen).
Indexed RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA), according to the manufacturer’s standard protocol. Briefly, poly-adenylated mRNA was purified from total RNA (100 ng) and rRNA removed by binding to magnetic oligo(dT)25 beads, which was followed by RNA fragmentation. Double-stranded cDNA was then generated by random-primed first-strand synthesis and subsequent second strand synthesis in the presence of dUTP for strand marking. The double-stranded cDNA was then end repaired, 3’-dA tailed, and an Illumina-compatible NEBNext adaptor was ligated. Uridine excision was performed with the USER (Uracil-Specific Excision Reagent) enzyme, and the libraries were then indexed and enriched by high-fidelity PCR amplification (15 cycles) with Q5 High-Fidelity DNA Polymerase and NEBNext multiplex primers.

treatment_protocol: All cell cultures and xenograft tumors were untreated.

value: xenograft tumor

value: HBMSC 3.4 (clone 6) xenograft tumor grown subcutaneously


title: 4-K-001, CMML5

description:
10x Genomics
FT-SA27352

value: AML


title: C_VglutCb_tot_R3

source_name: Cerebellum

value: mRNA from flash frozen brain tissue

value: Input

value: Cerebellum


title: M1609_MUT_15mo_F

source_name: Muscle_RAP1 MUT_15MF


title: T_6

source_name: HBMSC 3.4 (clone 6) xenograft tumor (mammary fat pad)

value: HBMSC 3.4 (clone 6) xenograft tumor grown in mammary fat pad


title: C_VglutCb_tot_R4


title: M1602_WT_15mo_F

value: Muscle


title: C_VglutCb_tot_R2


title: 4-J-003, CMML4

description:
10x Genomics
FT-SA27353

value: CMML

value: post BMT


title: H1647_MUT_14mo_F

source_name: Heart_RAP1 MUT_14MF

value: Heart

value: F

value: RAP1 MUT


title: SF-100109-111451, CMML10

description:
10x Genomics
FT-SA33815


title: LTB4121, CMML2

description:
10x Genomics
FT-SA27349


title: C_VglutCer_R3

value: Control

value: RiboTag IP

value: Cerebrum


title: C_VglutCer_R2


title: M1600_MUT_15mo_F


title: BMDM, Txn1 KO, 3

city: New York

first: Daniel

middle: Parker

last: Ball

state: New York

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

description:
C57 wt-vs-Txn1 KO_Differential_expression_analysis_table.csv
GO_analysis.csv

data_processing:
Sequencing libraries were multiplexed and clustered onto a flowcell and loaded onto the Illumina HiSeq 4000 instrument according to manufacturer’s instructions and sequenced using a 2x150 bp Paired End configuration. Image analysis and base calling were conducted by the Illumina Control Software. Raw sequencing data (.bcl files) were converted to fastq and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed using Trimmomatic v.0.36 and mapped to the Mus musculus GRCm38  reference genomes (ENSEMBL) using the STAR aligner v.2.5.2b. Unique gene hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads within exon regions were counted.
Gene hit count tables were used for downstream differential expression analysis. DESeq2 was used for comparative gene expression analysis between sample groups.
The Wald test was used to generate p-values and log2FC. Genes with an adjusted p-value < 0.05 and absolute log2FC > 1 were defined as differentially expressed genes for each comparison. Gene ontology analysis was performed on the statistically significant set of genes using GeneSCF v.1.1-p2 software.
Assembly: GRCm38 - mm10
Supplementary files format and content: Log2FC, p-value, p-adjusted, and RPKM values for the differential expression measured for the indicated gene.

source_name: bone marrow

extract_protocol:
Total RNA content was collected and purified using the Rneasy kit (Qiagen) following the manufacturer's directions
Library preparation, polyA selection, and sequencing were performed as follows. Briefly, RNA samples were quantified using a Qubit 2.0 fluorometer (ThermoFisher Scientific) and RNA integrity assessed with a 4200 TapeStation (agilent Technologies). Samples were then normalized using the ERCC RNA Spike-In Mix kit (ThermoFisher Scientific) following the manufacturer’s recommendations. The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s recommendations.

value: bone marrow

value: Primary

value: Macrophages

tag: strain background

value: pooled male and female


title: H1646_WT_14mo_F

source_name: Heart_RAP1 WT_14MF

value: RAP1 WT


title: H1609_MUT_15mo_F

source_name: Heart_RAP1 MUT_15MF


title: H1610_WT_15mo_F

source_name: Heart_RAP1 WT_15MF


title: C_VglutCb_R4

value: mRNA from flash frozen brain tissue


title: C_VglutCb_R3

value: Cerebellum


title: C_VglutCb_tot_R1

value: Input


title: JOE_1

city: Kalyani

first: Kartiki

middle: V.

last: Desai

state: West Bengal

address: N.S.S kalyani

country: India

institute: National Institute of Biomedical Genomics

data_processing:
NovaSeq software was used for base calling and FASTQC was used for quality check.
Sequence reads were trimmed for adaptor sequence using CutAdapt, and masked for low-complexity or low-quality sequence, then mapped with the human genome (GrCh38.1) by Hisat2.0 with parameters  -q -x -1 -2 -S
Aligned sequences were processed by Featurecounts package to get transcript specific counts with parameters -p s 2 -t -g -a -o
FeatureCounts data was processed using TMM normalization of edger package at usegalaxy.org
Assembly: GrCh38.1
Supplementary files format and content: Tab-delimited text files include normalized counts from Edge R for each Sample Vec_1 Vec_2 JOE_1 JOE_2.

growth_protocol: Vec and JOE cells were cultured in DMEM media with 5 % FBS and 1X PenStrep.

extract_protocol:
RNA was extracted by RNAeasy Qiagen mini kit (Qiagen, Germany)
1µg of RNA was used to construct RNA-seq library using TruSeq® Stranded Total RNA Library Prep. 2X100 bp paired end sequencing (50milllion reads each) was carried out using illumina NovaSeq 6000 platform

tag: transfected with

value: V5 tagged JMJD6


title: HBMSC34

source_name: HBMSC 3.4 human bone marrow stem cells

value: cell culture

tag: cell type

value: HBMSC 3.4 human bone marrow stem cells


title: LTB3966, CMML1

description:
10x Genomics
FT-SA27348

source_name: BM-MNCs

value: BM-MNCs

value: HSCs

value: CMML


title: BMDM, Txn1 KO, 2

tag: cell line


title: JOE_2


title: M1646_WT_14mo_F

source_name: Muscle_RAP1 WT_14MF

value: Muscle

value: F


title: BMDM, control, 3

value: Wild-type


title: B1646_WT_14mo_F

source_name: Brain_RAP1 WT_14MF

value: Brain


title: C_VglutCb_R2

value: Control

value: RiboTag IP


title: C_VglutCb_R5


title: B1647_MUT_14mo_F

source_name: Brain_RAP1 MUT_14MF

value: RAP1 MUT


title: Vec_ 2

value: vector


title: BMDM, control, 2

value: bone marrow

value: Primary

value: Macrophages

value: pooled male and female


title: BMDM, control, 1


title: Vec_1


title: H1600_MUT_15mo_F

value: Heart


title: Total9

city: Toronto

first: Caitriona

middle: M

last: McEvoy

address: 200 Elizabeth St

institute: University Health Network

description: 10x Genomics

data_processing:
Mapping and quantification were performed using the 10X Genomics CellRanger pipeline version 3.1.0.
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney core biopsy

extract_protocol:
All living donor samples used for sequencing were processed within one hour of organ retrieval. Biopsies were collected in RPMI 1640 on ice, and mechanically dissociated with a blade before enzymatic digestion at 37ºC with 0.1 mg/ml DNase I, 3300 CDA units/ml Collagenase MA  and 1430 NP units/ml BP neutral protease  for 20 minutes at 37ºC with intermittent agitation. Cell suspensions were filtered through 35µm cell strainer snap-cap FACS tubes and a plunger from a 1ml syringe was used to gently mash remaining tissue in the strainer before rinsing strainer lid with 1:1 volume of FBS on ice. A low frequency (<1%) of immune cells in the single cell suspension from a kidney biopsy core necessitated immune enrichment in 10 samples (5 males, 5 females) using magnetic EasySep Human CD45 depletion kit II as per the manufacturer’s modified instructions for positive selection of CD45-expressing cells.
Samples were prepared according to 10X Genomics Single Cell 3’ v3 Reagent kit user guide. Samples were washed twice in PBS plus 0.04% BSA, and viability was determined by a hemocytometer via Trypan Blue staining. Following counting, the appropriate volume for each sample was calculated for a target capture of 9,000 cells. For CD45-enriched samples, all cells were sequenced. Samples that were too low in cell concentration as defined by the user guide were washed, re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x single cell B chip. After droplet generation, samples were transferred onto a pre-chilled 96 well plate, heat sealed and incubated overnight in a Veriti 96-well thermos cycler. The next day, sample cDNA was recovered using Recovery Agent provided by 10x and subsequently cleaned up using a Silane DynaBead mix as outlined by the user guide. Purified cDNA was amplified for 11 cycles before being cleaned up using SPRIselect beads. Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3’ Reagent Kits v3 user guide with modifications to the PCR cycles based on the calculated cDNA concentration. The molarity of each library was calculated based on library size as measured bioanalyzer and qPCR amplification data. Samples were pooled and normalized to 1.5 nM. Library pool was denatured using 0.2N NaOH  for 8 minutes at room temperature, neutralized with 400mM Tris-HCL. Library pool at a final concentration of 300pM were loaded to sequence on Novaseq 6000 (Illumina). Samples were sequenced with the following run parameters: Read 1-28 cycles, Read 2- 90, index 1-10 cycles, index 2-10 cycles. Across samples, cells were sequenced to a target depth of 40,000 reads per cell.

tag: group

value: Total homogenate

value: Kidney core biopsy

value: Male


title: BMDM, Txn1 KO, 1


title: C_SST_tot_R4

source_name: Cerebrum

value: mRNA from flash frozen brain tissue

value: SST

value: Input

value: Cerebrum


title: H1602_WT_15mo_F

value: F

value: RAP1 WT


title: Total7

description: 10x Genomics


title: Total8

description: 10x Genomics

value: Female


title: C_SST_tot_R2

value: Control


title: B1609_MUT_15mo_F

source_name: Brain_RAP1 MUT_15MF

value: Brain

value: RAP1 MUT


title: B1610_WT_15mo_F

source_name: Brain_RAP1 WT_15MF


title: Cold_CD81+_C

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: CD81+ APCs in Cold

data_processing:
Fastq files were pseudoaligned against the mouse transcriptome by Kallisto (version 0.46.1) (Bray et al., 2016) with default parameters.
Transcript-level raw counts from Kallisto were imported into R using the Bioconductor package tximport (version 1.12.3), and the expression levels of each gene were estimated.
Differential expression analysis between the two groups was performed using the DESeq2 (1.24.0), which generated log2(‒fold change) and adjusted P-value.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: adipocyte progenitor cell

growth_protocol: Total RNA was isolated from sorted CD81+ and CD81- cells from wild-type C57BL/6J mice at 10-weeks-old.

extract_protocol:
RNA was harvested using RNeasy Micro Kit (QIAGEN).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions

treatment_protocol: Thermoneutral or Cold 3days following Thermoneutral 2 weeks

value: adipocyte progenitor cell

value: WT

value: Cold


title: B1602_WT_15mo_F


title: Cold_CD81-_C

description: CD81- APCs in Cold


title: CD45_10

description: 10x Genomics

value: CD45 enriched


title: B1600_MUT_15mo_F


title: Total6

description: 10x Genomics

value: Total homogenate


title: Cold_CD81+_B

description: CD81+ APCs in Cold


title: L1646_WT_14mo_F

source_name: Liver_RAP1 WT_14MF

value: Liver


title: C_VglutCb_R1

data_processing:
RNAseq data was analyzed with nf-core/rnaseq 3.0 pipeline, using default parameters. STAR/Salmon were used for alignment and quantification
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: raw transcript counts obtained from salmon are provided in raw_count.csv.

source_name: Cerebellum

extract_protocol:
Flash frozen brain hemispheres were homogenized and total RNA ("Input") was isolated from tissue homogenate using Trizol and purified using the Qiagen Rneasy Mini kit. For "RiboTag IP" samples, 12CA5 monoclonal anti-HA antibody (Roche) was coupled to protein G-coated dynabeads (Invitrogen) and incubated with tissue homogenate for 90 min to immunoprecipitate HA-tagged ribosomes and their attached mRNAs. Ribosome-bound mRNAs were isolated using Qiazol and purified using the Qiagen miRNeasy kit.
Libraries were prepared according to protovol using the Illumina TruSeq stranded mRNA kit

value: RiboTag IP

value: Cerebellum


title: C_6

source_name: HBMSC 3.4 (clone 6)

value: cell culture

value: Immortalized subline of HBMSC 3.4 (clone 6)


title: L1647_MUT_14mo_F

source_name: Liver_RAP1 MUT_14MF


title: L1610_WT_15mo_F

source_name: Liver_RAP1 WT_15MF


title: CD45_8

description: 10x Genomics

value: Kidney core biopsy


title: L1609_MUT_15mo_F

source_name: Liver_RAP1 MUT_15MF

value: F


title: Cold_CD81+_A

description: CD81+ APCs in Cold


title: C_SST_R6

value: mRNA from flash frozen brain tissue

value: SST

value: Cerebrum


title: C_SST_R4

value: Control


title: C_SST_tot_R3

value: Input


title: Cold_CD81-_A

description: CD81- APCs in Cold

value: adipocyte progenitor cell


title: Cold_CD81-_B

description: CD81- APCs in Cold

value: WT


title: C_SST_tot_R1


title: C_SST_R3


title: L1602_WT_15mo_F

value: RAP1 WT


title: TN_CD81+_D

description: CD81+ APCs in TN

value: Thermoneutral


title: TN_CD81-_D

description: CD81- APCs in TN


title: CD45_9

description: 10x Genomics

value: CD45 enriched

value: Male


title: C_SST_R1

value: RiboTag IP


title: CD45_5

description: 10x Genomics


title: C_PV_tot_R1

value: PV


title: CD45_7

description: 10x Genomics

value: Female


title: C_SST_R2


title: CD45_4

description: 10x Genomics


title: TN_CD81-_C

description: CD81- APCs in TN


title: CD45_6

description: 10x Genomics


title: C_PV_tot_R3


title: Total4

description: 10x Genomics

value: Total homogenate


title: TN_CD81+_C

description: CD81+ APCs in TN


title: C_PV_tot_R2


title: TN_CD81-_B

description: CD81- APCs in TN


title: Total5

description: 10x Genomics

value: Kidney core biopsy


title: C_PV_R2


title: TN_CD81+_B

description: CD81+ APCs in TN


title: L1600_MUT_15mo_F

value: Liver

value: F

value: RAP1 MUT


title: Total3

description: 10x Genomics


title: TN_CD81-_A

description: CD81- APCs in TN


title: M1347_WT_2mo_M

source_name: Muscle_RAP1 WT_2MM

value: Muscle

value: M


title: TN_CD81+_A

description: CD81+ APCs in TN


title: M1327_WT_2mo_M


title: Total2

description: 10x Genomics


title: C_PV_R5

value: mRNA from flash frozen brain tissue

value: Control

value: Cerebrum


title: C_PV_R1


title: Total1

description: 10x Genomics


title: Il6r.ko_CD8_anti-PDL1_4

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

state: California

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

data_processing:
RNA-sequencing data were analyzed using HTSeqGenie in BioConductor. Reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed
Filtered reads were aligned to the reference genome GRCm38 using GSNAP
Gene expression levels were quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM)
Assembly: GRCm38
Supplementary files format and content: RPKM_matrix

source_name: subcutaneous MC38 tumor

growth_protocol: MC38 tumors were digested using the Miltenyi mouse tumor dissociation kit. Single-cell suspensions were stained with appropriate flow cytometry antibodies, and CD8 T cells (>10,000 per sample) were FACS-sorted directly in Qiagen Rneasy lysis buffer (CD8 T cells identified as CD45+ Thy1+ B220- CD4- CD8+).

extract_protocol:
Total RNA was extracted using the RNEasy Mini kit (Qiagen)
0.1 μg of total RNA was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Libraries were multiplexed and sequenced on Illumina HiSeq4000 (Illumina, San Diego, CA) to generate 30 million single-end 50 basepair reads.

value: CD8 T cell


title: Il6r.ko_CD8_anti-PDL1_5


title: C_PV_R4

first: Susanne

last: Bauer

institute: Linköpings universitet


title: Il6r.ko_CD8_anti-PDL1_3


title: CD45_1

description: 10x Genomics


title: Il6r.ko_CD8_anti-PDL1_2


title: C_PV_R6


title: M1348_MUT_2mo_M

source_name: Muscle_RAP1 MUT_2MM


title: C_PV_R3


title: M1340_MUT_2mo_M


title: C_GadCer_tot_R3

value: Input


title: C_GadCer_tot_R2


title: Il6r.ko_CD8_anti-PDL1_1


title: R58-HS3

city: Guangzhou

first: Siqi

last: Xu

state: Guangdong

address: Zhongshan 2nd Road

institute: Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software,version 1.8 ) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Cutadapt software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Pertea M et al.,Nature methods,2008
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

source_name: rheumatoid fibroblast-like synoviocytes

extract_protocol:
The RNA of  rheumatoid fibroblast-like synoviocytes was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit(Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: individual

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: HS3 (siHuR)


title: M1227_WT_5mo_M

source_name: Muscle_RAP1 WT_5MM

tag: tissue

value: RAP1 WT


title: Il6r.ko_CD8_isotype_5


title: H1327_WT_2mo_M

source_name: Heart_RAP1 WT_2MM

value: Heart


title: CD45_3

description: 10x Genomics

source_name: Kidney core biopsy

value: CD45 enriched

value: Female

tag: age


title: M1228_MUT_5mo_M

source_name: Muscle_RAP1 MUT_5MM


title: H1340_MUT_2mo_M

source_name: Heart_RAP1 MUT_2MM


title: LTB5109, CMML3

description:
10x Genomics
FT-SA27350

source_name: BM-MNCs

value: BM-MNCs

value: HSCs

tag: disease state

value: CMML


title: H1347_WT_2mo_M


title: C_GadCer_tot_R1

city: Linköping

address: BKV, Cellbiologi Pl 10

source_name: Cerebrum


title: CD45_2

description: 10x Genomics

value: Kidney core biopsy


title: H1348_MUT_2mo_M

value: M

value: RAP1 MUT


title: H1228_MUT_5mo_M

source_name: Heart_RAP1 MUT_5MM


title: H1227_WT_5mo_M

source_name: Heart_RAP1 WT_5MM


title: Il6r.ko_CD8_isotype_4

tag: treatment


title: R58-NC

value: NC


title: C_GadCer_R2

value: mRNA from flash frozen brain tissue

value: Control

value: RiboTag IP

value: Cerebrum


title: Il6r.ko_CD8_isotype_3

value: CD8 T cell


title: R50-9S3

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: 9S3 (siHASML)


title: Il6r.ko_CD8_isotype_2


title: C_GadCer_R6


title: R50-HS3

value: HS3 (siHuR)


title: C_GadCer_R1


title: R58-9S3


title: R50-NC


title: Il6r.ko_CD8_isotype_1


title: R6-HS3


title: C_GadCer_R5


title: C_GadCer_R4


title: WT_CD8_anti-PDL1_4

value: WT

value: isotype


title: WT_CD8_anti-PDL1_5


title: B1348_MUT_2mo_M

source_name: Brain_RAP1 MUT_2MM

value: Brain

tag: Sex


title: B1340_MUT_2mo_M

tag: age (months)


title: WT_CD8_anti-PDL1_3


title: R6-9S3


title: C_GadCb_tot_R3

source_name: Cerebellum

value: Input

value: Cerebellum


title: R6-NC


title: B1327_WT_2mo_M

source_name: Brain_RAP1 WT_2MM

value: M

tag: rap1 genotype

value: RAP1 WT


title: C_GadCer_R3

tag: source


title: WT_CD8_anti-PDL1_2

tag: genotype


title: B1347_WT_2mo_M


title: AML3948 (scTCR-seq)

first: Bettina

last: Nadorp

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

description: Chromium Single Cell Immune Profiling Kits (scTCR-Seq, 10x Genomics)

data_processing:
Library strategy: scTCR-Seq
Indexed BAM files containing position-sorted reads aligned to the genome.
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment to GRCh38 (version 5.0.1) was performed with 10x Genomics Cell Ranger Single Cell Gene Expression Software (version 2020-A).
HTOs each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
3' libraries were filtered for incorrectly assigned hash tags using Souporcell, doublet filtered using scDblFinder, and ambient RNA contamination was removed using SoupX.  Please see publication for detailed processing steps.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files for Single Cell RNAseq, CITEseq, TCR-seq:
feature reference
metadata
processed ADT counts
processed RNA counts
filtered barcodes
filtered features
filtered gene-barcode matrix
clonotypes
feature reference file 5 prime
filtered contig annotations
filtered count matrix

source_name: bone marrow

extract_protocol:
Cryopreserved bone marrow aspirates were obtained from Ohio State University’s sample bank (adult AML samples), from St. Jude Children’s Research Hospital AML16 clinical trial (pediatric AML samples) or from the Children’s Oncology Group AML cell bank (pediatric AML sample). All subjects provided written consent for banking and research use of these specimens, in accordance with the regulations of the institutional review boards of all participating institutes. Cryopreserved primary human bone marrow mononuclear cells were obtained from STEMCELL Technologies or from StemExpress. Frozen human bone marrow samples were thawed and transferred into 50mL conical tubes containing PBS + 2% fetal bovine serum (FBS). Cell suspensions were centrifuged at 350 x g for 5 minutes at 4C, and the supernatant was discarded. Samples were then subjected to dead cell depletion, using a dead cell removal kit (Miltenyi Biotec, 130-090-101), or stained with DAPI (0.5mg/mL) and sorted for live cells (DAPIlow), using a FACSAria IIu SORP cell sorter (BD Biosciences). For cell sorting, all samples were gated based on forward and side scatter, followed by doublet exclusion, and then gated on DAPIlow for viable cells. Samples were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. For CITE-seq, enriched live cells were first tagged with cell-hashing oligo-tagged antibodies (Biolegend) according to the manufacturer’s instructions. Samples were than counted, and a maximum of 10e5 cells for each sample was pooled together and stained with a CITE-Seq antibody cocktail (Biolegend) according to the manufacturer’s instructions. For scTCR-Seq, T cells were enriched using a pan T cell isolation kit (Miltenyi Biotec, 130-096-535) or sorted for live CD45+ CD3+ cells. For cell sorting, samples were stained with PerCP-conjugated anti-human CD45 (1:400, Biolegend, 304025), FITC-conjugated anti-human CD3 (1:100, Biolegend,  300452). And DAPI (0.5mg/mL). Sorted samples were gated based on forward and side scatter, followed by doublet exclusion and then gated on DAPIlow for viable cells. CD45+ CD3+ cells were sorted into 5mL poly-propylene tubes containing 300mL ice-cold PBS + 2% FBS. Following cell sorting, samples were centrifuged at 350 x g for 5 minutes at 4C. Libraries were prepared using the Chromium Single Cell 3’ Reagent Kits (v3 and v3.1, CITE-Seq) or the Chromium Single Cell Immune Profiling Kits (v1.1 and v2, scTCR-Seq, 10x Genomics).  Hashtag and antibody-derived tag (ADT) libraries were prepared according to the New York Genome Center CITE-Seq and hashing protocol (https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf). Libraries were run on an Illumina NovaSeq 6000.
Chromium Single Cell 3’ Reagent Kits (v3 )

value: Acute Myeloid Leukemia

value: Bone Marrow

value: mononuclear cells

tag: assay

value: Chromium Single Cell Immune Profiling


title: WT_CD8_anti-PDL1_1


title: B1228_MUT_5mo_M

source_name: Brain_RAP1 MUT_5MM

value: RAP1 MUT


title: C_GadCb_tot_R2

value: mRNA from flash frozen brain tissue

value: Control

tag: celltype

tag: preparation


title: AML2975 (scTCR-seq)


title: AML2910 (scTCR-seq)


title: C_GadCb_R2

value: RiboTag IP


title: L1347_WT_2mo_M

source_name: Liver_RAP1 WT_2MM

value: Liver


title: WT_CD8_isotype_5

source_name: subcutaneous MC38 tumor

value: CD8 T cell


title: C_GadCb_R1


title: WT_CD8_isotype_4

value: WT


title: C_GadCb_R6


title: AML1133 (scTCR-seq)


title: L1340_MUT_2mo_M

source_name: Liver_RAP1 MUT_2MM


title: B1227_WT_5mo_M

source_name: Brain_RAP1 WT_5MM


title: AML0693 (scTCR-seq)


title: L1348_MUT_2mo_M


title: L1228_MUT_5mo_M

source_name: Liver_RAP1 MUT_5MM


title: L1327_WT_2mo_M


title: WT_CD8_isotype_2

value: isotype


title: C_GadCb_R5


title: AML0102 (scTCR-seq)


title: C_GadCb_tot_R1


title: AML0134 (scTCR-seq)


title: WT_CD8_isotype_1


title: C_GadCb_R4


title: anti-CD3/28+ IL2+IL6_replicate 3 [SAM24371036]

source_name: spleen

growth_protocol: Spleens from 8 week-old female C57BL/6J mice were mashed through sterile 70um filters and naïve CD8+ T cells were isolated by FACS (Thy1+ CD8A+ CD62L+ CD44-).

treatment_protocol: T cells were plated in RPMI + 10% FCS and either IL-6 (10ng/ml), plate-bound anti-CD3/CD28 antibodies + IL-2 (10 ng/ml), or plate-bound anti-CD3/CD28 antibodies + IL-2 + IL-6. Cells were spun for 1 minute at 500g to synchronize contact with plate-bound antibodies, incubated at 37° C, and harvested after 4 hours for RNA extraction.

value: naive CD8 T cell

tag: agent

value: anti-CD3/CD28 + IL-2

tag: strain


title: Control0005_AML009 (scTCR-seq)

value: Acute Myeloid Leukemia and Healthy Control

tag: cell type


title: C_GadCb_R3

value: Cerebellum


title: INFRF02_Bortezomib

city: Palo Alto

first: Tanja

middle: A

last: Gruber

address: 1000 Welch Road Suite 300

department: Pediatrics

institute: Stanford University

data_processing:
Nextflow (nf-core v 2.3, nextflow v22.02.1-edge) was used to perform QC, align FASTQ files to reference genome using "star_rsem" aligner and generate counts.
Assembly: hg38
Supplementary files format and content: tab-delimited gene counts include RPKM values for each Sample

source_name: Bone Marrow

extract_protocol:
Trizol extraction
RNA sequencing was performed according to the manufacturer's instructions using the Illumina TrueSeq total stranded RNA kit.

treatment_protocol: Cells were exposed to bortezomib or DMSO for 20 hours

value: Leukemia

value: Bortezomib


title: INFRF02_DMSO

value: Bone Marrow

value: DMSO (control)


title: AML051 (scTCR-seq)

value: Acute Myeloid Leukemia

value: mononuclear cells

value: Chromium Single Cell Immune Profiling


title: INF006D_Bortezomib


title: WT_CD8_isotype_3


title: anti-CD3/28+ IL2+IL6_replicate 2 [SAM24371035]


title: zsGreen cells control(SG)

city: Boston

first: Ming

last: Zhai

state: Massachusetts

address: Avenue Louis Pasteur

department: Cardiovascular Division, Department of Medicine

institute: Brigham and Women's Hospital

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells. We processed the unique molecular identifier (UMI) count matrix using the R package Seurat[1] (version 3.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: None SMC linage cells

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volum BSA. Cells were isolated from the plaque-rich parts of the aorta
RNA libraries were prepared with Chromium single cell 3” Reagent v3 Kits according to the manufeaturer's protocol.

value: Other cells except SMC

tag: strain background

value: untreated


title: L1227_WT_5mo_M

source_name: Liver_RAP1 WT_5MM

value: Liver

value: M

value: RAP1 WT


title: INF006D_DMSO


title: Control4003b (scTCR-seq)

value: Healthy Control


title: BMDM_GW4064_24h_rep1

city: Tokushima

first: Hideki

last: Arimochi

address: 3-18-15 Kuramoto

institute: Tokushima University

description: Gene expression after 24hr in DMSO treated BMDM

hyb_protocol: 1650 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel was set to Green and Green PMT was set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended processed signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Male C57BL6/J mice were used to bone marrow derived macrophages (BMDMs). Bone marrow cells were collected from femurs and tibias by flushing these bones with 10 mL of culture medium.  After lysis of the red blood cells, the cells were cultivated for 7 days in 10 mL of culture medium containing recombinant mouse M-CSF at a concentration of 10 ng/mL.

extract_protocol: Total RNA was extracted from BMDMs treated for 24 hr with 10 micro M GW4064 or DMSO under M2 conditions using the ReliaPrep RNA Cell Miniprep system. RNA integrity was detected using an Agilent 2100 Bioanalyzer, while microarray analysis was performed using a 44K Whole Genome mRNA microarray system

treatment_protocol: M2 macrophages were generated by cultivation of BMDMs with 10 ng/mL of recombinant mouse IL-4 for 24 hr. GW4064 dissolved in DMSO were diluted with the culture medium and then added into the culture medium during M2 induction.

value: BMDM


title: zsGreen cells of knockout group(PG)


title: tdTomato cells control(SR)

source_name: SMC linage cells

value: SMC


title: anti-CD3/28+ IL2_replicate 2 [SAM24371032]

value: naive CD8 T cell

value: anti-CD3/CD28 + IL-2


title: Control0182b (scTCR-seq)


title: anti-CD3/28+ IL2_replicate 3 [SAM24371033]


title: Control4003a (scTCR-seq)


title: INF016D_Bortezomib

value: Leukemia


title: tdTomato cells knock out PADI4(PR)


title: anti-CD3/28+ IL2+IL6_replicate 1 [SAM24371034]


title: BMDM_DMSO_24h_rep1

value: DMSO


title: anti-CD3/28+ IL2_replicate 1 [SAM24371031]


title: Control0082 (scTCR-seq)

value: Bone Marrow


title: INF001R_Bortezomib

value: Bortezomib


title: Quadriceps amiR Rep5

city: Trento

first: Alessandro

last: Romanel

state: TN

address: Via Sommarive 9

country: Italy

institute: University of Trento

data_processing:
Data was processed by ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt
Reads were aligned to the Mus musculus genome (mm10) using STAR
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Quadriceps

extract_protocol:
Quadriceps were isolated, flash frozen in liquid nitrogen. RNA was extracted using Trizol, following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols. (TruSeq Stranded mRNA)

value: Quadriceps

value: amiR LSD1 + PRMT6

tag: library prep

value: polyA-enriched


title: IL6_replicate 3 [SAM24371018]


title: AML052 (scTCR-seq)

value: Acute Myeloid Leukemia

tag: tissue

value: mononuclear cells

value: Chromium Single Cell Immune Profiling


title: IL6_replicate 2 [SAM24371017]


title: Quadriceps amiR Rep3


title: INF001D_DMSO

value: DMSO (control)


title: Control0182a (scTCR-seq)


title: IL6_replicate 1 [SAM24371016]


title: INF001D_Bortezomib


title: Quadriceps amiR Rep2


title: Control0004 (scTCR-seq)


title: Quadriceps amiR Rep4


title: AML3948 (scRNA-seq)

description: Chromium Single Cell 5’ polyA RNA

data_processing:
Indexed BAM files containing position-sorted reads aligned to the genome.
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment to GRCh38 (version 5.0.1) was performed with 10x Genomics Cell Ranger Single Cell Gene Expression Software (version 2020-A).
HTOs each cell were normalized using a centered log ratio (CLR) transformation across cells.
Samples were demultiplexed based on HTOs using the HTODemux function in Seurat.
3' libraries were filtered for incorrectly assigned hash tags using Souporcell, doublet filtered using scDblFinder, and ambient RNA contamination was removed using SoupX.  Please see publication for detailed processing steps.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files for Single Cell RNAseq, CITEseq, TCR-seq:
feature reference
metadata
processed ADT counts
processed RNA counts
filtered barcodes
filtered features
filtered gene-barcode matrix
clonotypes
feature reference file 5 prime
filtered contig annotations
filtered count matrix

value: Chromium Single Cell 5’ polyA RNA


title: INF016D_DMSO


title: untreated_replicate_3 [SAM24371015]


title: Quadriceps amiR Rep1


title: INF001R_DMSO