title: 401_4_0614_CD3

description:
X3_GS0614_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 400_1_0612_PBMCs

status: Public on Jun 16 2021

type: SRA

city: San Diego

first: Hao

last: Wang

state: CA

address: 9452 Medical Center Dr

country: USA

institute: University of California, San Diego

description:
X2_GS0612_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human GRCh38 reference using STAR(v 2.6.1c )
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using featureCounts program (v1.6.5) and features with 0 counts across all samples were removed
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

molecule: polyA RNA

organism: Homo sapiens

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
PBMCs were stained with anti-human CD3, CD4, CD8, CD14, CD19, CD56, and live/dead viability antibodies (see Supplemental Table S2 for antibody details). Subsequently, live CD4+ single positive (SP) (CD14-CD19-CD56-CD3+CD4+CD8-), CD8+ SP (CD14-CD19-CD56-CD3+CD4-CD8+), and CD4+CD8+ DP (CD14-CD19-CD56-CD3+CD4+CD8+) cells were sorted into TRIzol LS Reagent (Invitrogen, Carlsbad, CA) using a BD FACSAria cell sorter (BD Biosciences, San Jose, CA). Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (5 ng) was amplified following the Smart-seq2 protocol. cDNA was purified using AMPure XP beads (1:1 ratio; Beckman Coulter, Carlsbad, CA). From this step, 1 ng cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA library preparation kit and index kit (set B and C, respectively), Illumina, San Diego, CA).

treatment_protocol: No specific treatment involved

tag: tissue

value: Cryopreserved PBMC

tag: disease group

value: dengue patient without warning signs of plasma leakage

tag: cell subtype

value: PBMC


title: 3_GS0372_CD3_Deng1

description:
X3_GS0372_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: VCPFF-2: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing, Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3' gene counting, Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

organism: Mus musculus

extract_protocol:
Mice were aged to 1 or 2 months of age. Upon tissue harvest, mice were euthanized and perfused with 1U/ml heparin in PBS. Left hemisphere of the brains were dissected out and flash frozen on dry ice. Flash frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice 15 minutes. The suspension was filtered through a 30 um filter to remove debris and pelleted at 500 x g 5 min at 4o C. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U/uL RNasin (Promega)). Nuclei pellets were resuspended in 500 uL Nuclei Wash and 900 uL 1.8 M Sucrose. This 1400 uL mixture was carefully layered on top of 500 uL 1.8 M sucrose and centrifuged at 13,000 x g 45 min 4oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in Nuclei wash at 1200 nuclei/uL and filtered through a 40 um FlowMi Cell Strainer.
Isolated single nuclei were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 5’ Reagent Kits as per manufacturer’s instructions (10x Genomics) The generated scRNAseq libraries were sequenced using an Illumina sequencer.

tag: mouse genotype

value: VCPfl/fl

tag: strain

value: nuclei of brain

tag: age

value: 2 months


title: 3_GS0284_CD3_Deng1

description:
X3_GS0284_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 398_1_0612_CD4CD8

description:
X2_GS0612_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0365_CD3_Deng1

description:
X3_GS0365_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 397_1_0612_CD4

description:
X2_GS0612_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0324_CD3_Deng1

description:
X3_GS0324_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E6732 - ALS Cre Control

city: New York

first: Paul

middle: Francis

last: Gugger

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone Health

data_processing:
Trimmed low quality bases and removed adapter contamination with Trimmomatic 0.36 with parameters ILLUMINACLIP:adapters.fa:2:30:10:1:true TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:35
Aligned reads to the mouse mm10 genome build using STAR 2.7.3a including parameters  --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD XS --outSAMmapqUnique 60 --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outStd BAM_Unsorted
Sorted BAM files with samtools sort 1.9
Counted reads per gene using featureCounts function in subread 1.6.3 with parameter -p for paired-end
Normalized read counts by library size as log2(counts per million) using edgeR 3.26.8
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with raw read pair counts and log2(CPM) normalized read pair counts per gene (rows) per sample (columns)

source_name: Lumbar Spinal Cord

growth_protocol: All experiments were performed on male C57BL/6J mice intercrossed with the following strains: B6.129P2(Cg)-CX3CR1tm2.1(cre/ERT2)Litt/WganJ (JAX Stock No: 021160), Ager floxed mice in wildtype or B6.Cg-Tg(SOD1G93A)1Gur/J (JAX Stock No:004435) backgrounds. All mice were maintained under pathogen-free conditions and all experiments were performed under protocols approved by the New York University School of Medicine Institute Animal Care Committee (IACUC) in accordance with international and NIH guidelines. All mice were housed in a temperature- (19–23 °C) and humidity-regulated (30–70% relative humidity) environment with a 12/12 h light/dark cycle and received standard chow food (Lab Diets, Cat: 5053) pellets and water ad libitum.

extract_protocol:
Mice were anesthetized with Ketamine and Xylazine. The spinal column was rapidly removed, and the lumbar spinal cord was retrieved. Lumbar spinal cords were flash frozen and stored at -80˚C until processed. Frozen tissue was kept on dry ice until homogenized in Qiazol reagent (Qiagen Inc, Cat: 79306). Crude homogenate was mixed with chloroform (70µL per 350µL homogenate) to facilitate removal of lipids, and allowed to equilibrate at room temperature for 2 min. Spun at 13,000 x g for 15 min at 4˚C. The aqueous phase containing the RNA was transferred to a new tube. Then the following steps were completed as detailed by the manufacturer’s instructions using an RNeasy Mini Kit (Qiagen, Cat: 74104) with on-column DNAse digestion (Qiagen, Cat:79254). RNA concentration was determined via a NanoDrop spectrophotometer (ThermoFisher, Model: ND-1000) and RNA integrity (RIN) was measured using RNA 6000 Pico Kit in a 2100 Bioanalyzer (Agilent).
High quality lumbar spinal cord RNA samples, as confirmed by Bioanalyzer, (RINs: 7.9-8.7) free of DNase and RNase were prepared for sequencing using the TruSeqStranded mRNA library prep kit (Illumina, Cat: 20020594) and the NovaSeq 6000 SP Reagent Kit v1.5 (Illumina, Cat: 20028401). High-throughput RNA sequencing (RNA-seq) was completed using an Illumina NovaSeq 6000 sequencer performed by the NYU Grossman School of Medicine Genome Technology Core.

treatment_protocol: Tamoxifen was used to delete Ager at 3 months of age. All animals were administered 0.2 μg of tamoxifen (TAM, Sigma, Cat: T5648), once daily every  day for a total of five intraperitoneal injections at 3 months (12 weeks) of age. These mice were sacrificed at the age of 4 months. All animals were then deeply anaesthetized using Ketamine and Xylazine and humanely sacrificed and utilized for post-mortem molecular analyses.

value: Lumbar Spinal Cord

tag: cell type

value: Bulk

value: 120 days

tag: genotype

value: SOD1G93A Ager+/+ Cx3cr1Cre/+


title: 396_1_0612_CD3

description:
X2_GS0612_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0386_CD3_Deng1

description:
X3_GS0386_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 390_1_0296_CD8

description:
X1_GS0296_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 389_1_0296_CD4CD8

description:
X1_GS0296_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0603_CD3_Deng1

description:
X2_GS0603_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0489_CD3_Deng1

description:
X2_GS0489_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0297_CD3_Deng1

description:
X3_GS0297_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E5248 - ALS microglia Ager deleted

value: SOD1G93A Agerfl/fl Cx3cr1Cre/+


title: E5231 - ALS microglia Ager deleted


title: E5568 - ALS microglia Ager deleted


title: 3_GS0502_CD3_Deng1

description:
X3_GS0502_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E5642 - ALS Cre Control


title: 387_1_0296_PBMCs

description:
X1_GS0296_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 386_1_0296_CD3

description:
X1_GS0296_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 399_1_0612_CD8

description:
X2_GS0612_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 388_1_0296_CD4

description:
X1_GS0296_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0478_CD3_Deng1

description:
X2_GS0478_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: VCPFF-1: Isolated single nuclei from cortex of 2 month old VCPfl/fl mice


title: 385_1_0291_PBMCs

description:
X1_GS0291_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0330_CD3_Deng1

description:
X2_GS0330_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E1776 - ALS microglia Ager deleted


title: E6578 - ALS Cre Control


title: 2weeks_run

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

description: 10x raw data contains cell barcode and UMI, cell barcode and UMI, cDNA reads

data_processing:
Chromium data was demultiplexed with cellranger mkfastq v2.0.2.
Gene-cell count matrix was generated by cellranger count v2.0.2 against Ensembl GRCm38.p5 reference genome.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Filtered count matrix from cellranger count is stored in three files: barcodes.tsv, genes.tsv and matrix.mtx.

molecule: total RNA

source_name: muscle endothelial cells

extract_protocol:
Mashed muscle was enzymatically digested in digestion buffer containing 2 mg/ml Dispase II, 2 mg/ml Collagenase IV, 2 mM CaCl2 and 2% BSA in PBS at 37°C for 10 min, with gentle shaking every 3 min. Viable endothelial cells (CD31+, CD45-, SYTOX blue-) were sorted by a FACS Aria III (BD Bioscience) sorter, and ECs were directly sorted into ice cold collecting medium (EGM2). The collected ECs were placed on ice (no more than 30 min) until loading into 10x genomics chromium.
Library construction was performed according to the 10x Chromium Single Cell 3' Reagent Kit v2.

treatment_protocol: Mice were individually housed in open cages equipped with an upright running wheel device for the duration of the intervention. Non-running control (sedentary) mice were also single caged in cages of equal dimensions but without running wheels. Continuous recording of wheel movements was performed out of which total distance (km), speed (m.s−1), and number of running bouts was calculated.

value: gastrocnemius muscle

tag: treatment

value: single house voluntary running 14 days

value: endothelial cells (EC)


title: 384_1_0291_CD8

description:
X1_GS0291_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: Sedentary

value: single house sedentary


title: 2_GS0510_CD3_Deng1

description:
X2_GS0510_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 383_1_0291_CD4CD8

description:
X1_GS0291_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0445_CD3_Deng1

description:
X2_GS0445_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E5386 - ALS Cre Control


title: 382_1_0291_CD4

description:
X1_GS0291_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0382_CD3_Deng1

description:
X2_GS0382_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 381_1_0291_CD3

description:
X1_GS0291_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0366_CD3_Deng1

description:
X2_GS0366_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0497_CD3_Deng1

description:
X2_GS0497_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 380_1_0288_PBMCs

description:
X1_GS0288_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 378_1_0288_CD4CD8

description:
X1_GS0288_CD4_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 379_1_0288_CD8

description:
X1_GS0288_CD8
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 377_1_0288_CD4

description:
X1_GS0288_CD4
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0475_CD3_Deng1

description:
X1_GS0475_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0351_CD3_Deng1

description:
X1_GS0351_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 376_1_0288_CD3

description:
X1_GS0288_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0388_CD3_Deng1

description:
X2_GS0388_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: MT-D705

city: QingDao

first: Qilai

last: Huang

address: Binhai road 72#

country: China

institute: Shandong University

description:
Processed data files:
SNP DiR-seq T-47D-rep1.txt
SNP DiR-seq T-47D-rep2.txt
SNP DiR-seq T-47D-rep3.txt
SNP DiR-seq SK-BR-3-rep1.txt
SNP DiR-seq SK-BR-3-rep2.txt
SNP DiR-seq SK-BR-3-rep3.txt

data_processing:
The next-generation sequencing Data quality statistical software Cutadapt (version 1.9.1) was used to remove the adapters and low-quality sequences from the original sequencing Data (Pass Filter Data) to obtain Clean Data for subsequent information analysis.
The overlap area between read1 and read2 of Clean Reads was combined using Pandaseq (version 2.7) to produce complete sequences.
According to the Barcode sequence of read1 of each sample, the spliced Tag starting position is split into the corresponding sample with perfect matching, and the result is saved in FASTQ file.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every barcode and every sample (bundled into a tar archive)
Supplementary_files_format_and_content: SNP_barcode_id.txt
Supplementary_files_format_and_content: Samples to library relationships information.txt

extract_protocol:
Twenty-four hours post-transfection, cells were washed twice and harvested in 1 × PBS, and Total RNA was extracted from all surviving cells using RNeasy Plus Mini Kit (74136, QIAGEN). We treated the mRNA with RapidOut DNA Removal Kit (K2981, Thermo Scientific) to remove the trace amount of genomic DNA residue according to the product manual. The purified RNA was then subjected to reverse transcription with High-Capacity cDNA Reverse Transcription Kits (4374967, Applied Biosystems). Briefly, 1.5μg RNA was added into 10μl of 2× RT Master Mix and made up to the final 20μl with nuclease-free water. The reactions were incubated at 25°C for 10 min, followed by 120 min at 37°C, then were inactivated Reverse Transcriptase by heating to 85°C for 5 min. The cDNA products were stored at -20°C or -80°C and ready for qPCR analysis and preparing the NGS sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
We combined the 35 libraries into seven i7 indexes for Illumina sequencing.
To help the user demultiplex the raw data, we provided all the necessary information in "Sample to library relationship information.txt".

tag: cell line

value: breast cancer cell lines T-47D, SK-BR-3

tag: sample type

value: multiplexed

tag: molecule

value: total RNA


title: 1_GS0337_CD3_Deng1

description:
X1_GS0337_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC


title: 1_GS0336_CD3_Deng1

description:
X1_GS0336_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient with warning signs of plasma leakage


title: hTERT-RPE1-Cas9 rep 4

city: Frankfurt am Main

first: Manuel

last: Kaulich

state: Select...

address: Theodor-Stern-Kai 7, Bldg 75, Rm 0.222

department: Institute of Biochemistry II

country: Germany

institute: Goethe University Frankfurt

description: Sample 4

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary Table S7_RPE1_RNAseq_readcounts.xlsx

source_name: ATCC®

growth_protocol: Monoclonal RPE1(Cas9) cells were cultured asynchronously and harvested at 90% confluency.

extract_protocol:
RNA was purified using the QIAGEN RNeasy Plus Mini Kit (Cat No.: 74134), according to the manufacturer's protocol. RNA was stored at -80°C and analyzed by RNA-Seq in quadruplicates.
3'DGE mRNA-seq (research*/clinical**/diagnostic***) grade sequencing service (Next Generation Diagnostics srl)

treatment_protocol: untreated

value: Retina


title: 1_GS0326_CD3_Deng1

description:
X1_GS0326_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: hTERT-RPE1-Cas9 rep 3

description: Sample 3


title: 1_GS0530_CD3_Deng1

description:
X1_GS0530_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0406_CD3_Deng1

description:
X1_GS0406_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: hTERT-RPE1-Cas9 rep 2

description: Sample 2


title: hTERT-RPE1-Cas9 rep 1

description: Sample 1


title: 1_GS0393_CD3_Deng1

description:
X1_GS0393_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0392_CD3_Deng1

description:
X1_GS0392_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0373_CD3_Deng1

description:
X1_GS0373_CD3
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E428K-GC 2

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

description:
Genomic Edit A
atrial IPS-CMs with gene correction of SCN5A-E428K
HON021020_007

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text tables

growth_protocol: human recombinant vitronectin coated plates in Essential 8 Flex medium

extract_protocol:
Maxwell 16 LEV simplyRNA Tissue kit (Promega)
Universal Plus mRNASeq kit (Tecan)
NovaSeq6000 SP flowcell, 2x50 nt reads

treatment_protocol: 1 µM retinoic acid (RA) for 5 days

value: gene correction of SCN5A-E428K

value: Atrial iPSC-Derived Cardiomyocytes


title: Control 2

description:
Control A
atrial IPS-CMs from healthy people
HON021020_004

source_name: atrial IPS-CMs from healthy people

value: wild type


title: E428K-GC 1

description:
Genomic Edit A
atrial IPS-CMs with gene correction of SCN5A-E428K
HON021020_006


title: 3_GS0390_PBMC_Deng1

description:
X3_GS0390_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: PBMC


title: Control 1

description:
Control A
atrial IPS-CMs from healthy people
HON021020_003


title: 3_GS0297_PBMC_Deng1

description:
X3_GS0297_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E428K 2

description:
Mutant A
atrial IPS-CMs carrying SCN5A-E428K mutation
HON021020_002

value: SCN5A-E428K mutation


title: 3_GS0300_PBMC_Deng1

description:
X3_GS0300_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0287_PBMC_Deng1

description:
X3_GS0287_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0372_PBMC_Deng1

description:
X3_GS0372_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: E428K 1

description:
Mutant A
atrial IPS-CMs carrying SCN5A-E428K mutation
HON021020_001


title: 3_GS0284_PBMC_Deng1

description:
X3_GS0284_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P138_RNAseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
RNA-Seq data data were trimmed with Trim Galore (v0.4.1, default parameters) and mapped to the Polistes canadensis genome assembly using TopHat v2.0.12 as previously described in Patalano et al. PNAS, 2015 . Strand specific quantification was performed using RNA-seq pipeline in Seqmonk software Version 1.39.0 (www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Gene expression levels were normalized in terms of reads per million (reads per kilobase per million, RPKM). To normalize across nests a scaling factor was calculated using the DEseq2 package in R (Allnest_normSizeFactor.txt) log transform with only orientated samples (ALLRNAseqlogand features).
Genome_build: Polistes canadensis GCF_001313835.1
RNA-seq reports: This file tab-delimited is the strand specific quantification performed using RNA-seq pipeline in Seqmonk version 1.39.0 (www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Gene expression levels were normalized in terms of reads per million (reads per kilobase per million, RPKM). To normalize across nests a scaling factor was calculated using the DEseq2 package in R (Allnests_normSizeFactor.txt) and log transformed for samples P188 to P212 (All_RNAseq_log_and features.txt). Lines indicated individual wasp, column indicated genes.

organism: Polistes canadensis

source_name: Brain

extract_protocol:
Heads were cut off and immediately placed in RNA later solution (Ambion) and kept at -20°C until brain dissection.
Total RNAwas extracted from single brains using theQIAGENAll PrepDNA/RNAMini Kit according to the manufacturer’s instructions.
50 to 200 ng of total RNA was enriched for mRNA using Dynabeads Oligo(dT)25 from Invitrogen in two subsequent steps of purification with fresh beads. Fragmentation was done by incubation of mRNAs for 5 min at 94 °C in the First-Strand Buffer (Invitrogen), and directly followed by cDNA synthesis using a SuperScript III Kit (Invitrogen) according to the manu- facturer’s instructions. dUTPs were incorporated for second-strand synthesis for library orientation except for samples P188 to P212. cDNA was end-repaired, A-tailed, and ligated with a methylated Adaptor Oligo Kit (Illumina) using the NEB Next Kit (New England Biolabs) according to the manufacturer’s instructions. dUTP excision was done before amplification using USER mix (New England Biolabs). Libraries were amplified with 16 cycles using 2× Phusion HF buffer (New England Biolabs). Size selection and cleaning between steps were performed with the AMPure XP system (Agencourt) to select DNA fragments between 250 bp and 500 bp. Paired-end libraries were sequenced on Illumina HiSeq system.

value: Brain

tag: experiment

value: Queen removal (early commitment)


title: P113_RNAseq

value: Control


title: P112_RNAseq


title: 3_GS0324_PBMC_Deng1

description:
X3_GS0324_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 3_GS0386_PBMC_Deng1

description:
X3_GS0386_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P111_RNAseq


title: P110_RNAseq


title: 3_GS0502_PBMC_Deng1

description:
X3_GS0502_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P108_RNAseq


title: 2_GS0603_PBMC_Deng1

description:
X2_GS0603_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P109_RNAseq


title: 3_GS0365_PBMC_Deng1

description:
X3_GS0365_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HER2 -positive breast cancer (microdissected, stroma) 07

type: genomic

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center Research Institute

description: clinical specimen, breast tissues

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing: Genome Studio software (V2011.1 Methylation module 1.9.0) was used.  Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Specimen was obtained from each patient by core needle biopsy of a primary tumor before starting neoadjuvant therapy, and fixed using the PAXgene Tissue System (Qiagen, Hilden, Germany) and embedded in low-melting paraffin. Cancer cells or stroma cells were purified by the Leica LMD7000 system (Leica, Wetzlar, Germany) using 10 slices of 10-μm sections of block. This was conducted by an experienced pathologist (S. F.).  Genomic DNA was extracted by a PAXgene DNA kit (Qiagen).

tag: gender

value: Female

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIB

tag: histology

value: Invasive ductal carsinoma

tag: er

value: Negative

tag: pgr

tag: chemotherapy effect


title: HER2 -positive breast cancer (microdissected, stroma) 09

description: clinical specimen, breast tissues

value: IIIB


title: HER2 -positive breast cancer (microdissected, stroma) 06

description: clinical specimen, breast tissues

value: IIA


title: HER2 -positive breast cancer (microdissected, stroma) 08

description: clinical specimen, breast tissues

value: IIIA

value: Positive

value: Grade3 (rDCIS)


title: P107_RNAseq

tag: tissue


title: 2_GS0489_PBMC_Deng1

description:
X2_GS0489_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: Cryopreserved PBMC

tag: disease group

value: dengue patient with warning signs of plasma leakage

tag: cell subtype


title: HER2 -positive breast cancer (microdissected, stroma) 05

description: clinical specimen, breast tissues

tag: age


title: HER2 -positive breast cancer (microdissected, stroma) 04

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 31

description: clinical specimen, breast tissues


title: 2_GS0388_PBMC_Deng1

description:
X2_GS0388_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P106_RNAseq


title: 2_GS0330_PBMC_Deng1

description:
X2_GS0330_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 2_GS0478_PBMC_Deng1

description:
X2_GS0478_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HER2 -positive breast cancer (microdissected, stroma) 03

description: clinical specimen, breast tissues

value: IIIC


title: HER2 -positive breast cancer (microdissected, stroma) 01

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 29

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 34

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 32

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 23

description: clinical specimen, breast tissues


title: P105_RNAseq


title: 2_GS0510_PBMC_Deng1

description:
X2_GS0510_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: PBMC


title: HER2 -positive breast cancer (microdissected, cancer cell) 26

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 33

description: clinical specimen, breast tissues


title: P103_RNAseq


title: HER2 -positive breast cancer (microdissected, stroma) 02

description: clinical specimen, breast tissues


title: P102_RNAseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 27

description: clinical specimen, breast tissues


title: 2_GS0382_PBMC_Deng1

description:
X2_GS0382_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HER2 -positive breast cancer (microdissected, cancer cell) 22

description: clinical specimen, breast tissues


title: HER2 -positive breast cancer (microdissected, cancer cell) 28

description: clinical specimen, breast tissues


title: P101_RNAseq


title: 2_GS0366_PBMC_Deng1

description:
X2_GS0366_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HER2 -positive breast cancer (microdissected, cancer cell) 24

description: clinical specimen, breast tissues


title: P104_RNAseq


title: P147_BSseq

library_source: genomic

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence were  trimmed to remove both poor quality calls and adapters using Trim Galore (version 0.3.5 with default parameters, www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were then aligned to genome assembly (EVM/PASA; Patalano et al. PNAS, 2015) using Bismark (version 0.12.2, with the parameters: --bowtie2 --score_min L,0,−0.4).
Genome_build: Polistes canadensis GCF_001313835.1
Bisulfite-Seq
Quantification was done in SeqMonk over probes which contain 50 CpGs each with a minimum read count of 4. Only 10bb to 3kbp probes overlapping genes were kept.

extract_protocol:
Heads were cut off and immediately placed in RNA later solution (Ambion) and kept at -20°C until brain dissection.
Genomic DNA was extracted from single brains using the QIAGEN All Prep DNA/RNA Mini Kit according to the man- ufacturer’s instructions.
Between 200 ng and 500 ng of input genomic DNA was used per library and spiked with unmethylated lambda DNA  to provide an esti- mation of BS conversion efficiency. DNA was end-repaired, A-tailed, and ligated with a methylation Adaptor Oligo Kit (Illumina) using the NEB Next kit according to the manufacturer’s instructions. The adaptor-ligated DNA was treated with sodium-BS using an Imprint DNA Modification Kit from Sigma–Aldrich according to the manufacturer’s instructions for the two-step protocol. BS-treated DNA was amplified using KAPA HiFi Uracil + DNA Polymerase (KAPA Biosystems) with 15 cycles. Size selection and cleaning between steps were performed with an AMPure XP system (Agencourt) to select DNA fragments between 250 bp and 500 bp.

value: Queen removal


title: 1_GS0475_PBMC_Deng1

description:
X1_GS0475_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq

value: dengue patient without warning signs of plasma leakage


title: 2_GS0497_PBMC_Deng1

description:
X2_GS0497_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P100_RNAseq

value: Brain


title: P146_BSseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 30

description: clinical specimen, breast tissues


title: 1_GS0351_PBMC_Deng1

description:
X1_GS0351_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P145_BSseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 20

description: clinical specimen, breast tissues


title: P144_BSseq


title: 1_GS0336_PBMC_Deng1

description:
X1_GS0336_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0337_PBMC_Deng1

description:
X1_GS0337_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P143_BSseq


title: P142_BSseq


title: 1_GS0326_PBMC_Deng1

description:
X1_GS0326_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0530_PBMC_Deng1

description:
X1_GS0530_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P141_BSseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 21

description: clinical specimen, breast tissues


title: 1_GS0406_PBMC_Deng1

description:
X1_GS0406_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: HER2 -positive breast cancer (microdissected, cancer cell) 18

description: clinical specimen, breast tissues


title: P134_BSseq

value: Control


title: 2_GS0445_PBMC_Deng1

description:
X2_GS0445_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P133_BSseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 19

description: clinical specimen, breast tissues

value: Female


title: 1_GS0392_PBMC_Deng1

description:
X1_GS0392_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0393_PBMC_Deng1

description:
X1_GS0393_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: 1_GS0373_PBMC_Deng1

description:
X1_GS0373_PBMC
Microscaled (SmartSeq2) cDNA amplification - RNA seq


title: P132_BSseq


title: Case 1-cDNA set9-B

first: Panos

last: Roussos

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: single nuclear RNAseq

data_processing:
Paired-end sequencing reads were processed using cell ranger v3.1.0. We aligned sequencing reads to a pre-mRNA reference genome to capture unspliced pre-mRNA as recommended by 10x genomics. Samples were demultiplexed using a customized method.
HTO tags were quantatified using kallisto indexing and tag extraction (KITE)
Genome_build: GRCh38.premrna

extract_protocol:
frozen tissues were homogenized in lysis buffer and nuclei purified by sucrose gradient ultracentrifugation
Nuclei were hash tagged and partitioned using 10x Genomics B chips. Libraries were generated according to 10x Genomics recommendations via Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (PN-1000075)

tag: diagnosis

tag: tissue type

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

tag: cell type

value: nuclei

tag: library type

value: cDNA


title: P131_BSseq

tag: experiment


title: PBMC_LEI_1

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: PBMCs

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450/HumanMethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing:
Data was processed with the minfi package in R
Normalization was performed with the Illumina method (minfi)

label: Cy3, Cy5

source_name: peripheral blood

extract_protocol: Genomic DNA was extracted and purified from PBMCs using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

tag: Sex

value: F

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

value: Negative

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

value: UA

tag: diagnosis at year = 1

value: RAr


title: PBMC_LEI_45

description: PBMCs

tag: age

value: SpA


title: P130_BSseq

tag: tissue


title: PBMC_LEI_60

description: PBMCs

value: M


title: Case 1-HTO set9-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

value: HTO


title: PBMC_LEI_31

description: PBMCs


title: P129_BSseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 14

description: clinical specimen, breast tissues

tag: gender

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIA

tag: histology

value: Invasive ductal carsinoma

tag: er

tag: pgr

tag: chemotherapy effect


title: P138_BSseq

tag: experiment

value: Queen removal


title: HER2 -positive breast cancer (microdissected, cancer cell) 17

description: clinical specimen, breast tissues

value: IIIA

value: Positive

value: Grade3 (rDCIS)


title: PBMC_LEI_19

description: PBMCs

tag: Sex

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity

value: PsA


title: HER2 -positive breast cancer (microdissected, cancer cell) 15

description: clinical specimen, breast tissues

tag: gender

value: Female

tag: age


title: P128_BSseq

tag: tissue

value: Brain

value: Control


title: Case 3-cDNA set8-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

tag: cell type

value: nuclei

tag: library type

value: cDNA


title: PBMC_LEI_37

description: PBMCs

value: Negative

tag: wellbeing

tag: diagnosis at bl

value: UA

tag: diagnosis at year = 1


title: PBMC_LEI_22

description: PBMCs

tag: Sex

value: F

tag: tender joints

value: OA


title: Case 3-HTO set8-B

description: single nuclear RNAseq

value: HTO


title: HER2 -positive breast cancer (microdissected, cancer cell) 16

description: clinical specimen, breast tissues

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIIB

tag: histology

value: Others

tag: er

tag: pgr

tag: chemotherapy effect


title: PBMC_LEI_53

description: PBMCs

tag: age

value: M

tag: swollen joints

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity


title: P99_RNAseq

tag: tissue

tag: experiment


title: Case 3-cDNA set8-A

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type

tag: library type


title: PBMC_LEI_58

description: PBMCs

tag: Sex

tag: tender joints

tag: wellbeing

value: discovery

tag: diagnosis at bl

tag: diagnosis at year = 1


title: P98_RNAseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 13

description: clinical specimen, breast tissues

tag: gender

tag: age

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIA

tag: histology

value: Invasive ductal carsinoma

tag: er

tag: pgr

tag: chemotherapy effect


title: PBMC_LEI_47

description: PBMCs

tag: swollen joints

tag: esr

tag: crp

tag: rf

value: Positive

tag: pain

tag: disease activity


title: Case 5-cDNA set7-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type

tag: library type


title: P211_RNAseq

tag: tissue

value: Brain

tag: experiment

value: Queen removal (late commitment)


title: PBMC_LEI_76

description: PBMCs

tag: age

tag: Sex

tag: tender joints

tag: wellbeing

tag: diagnosis at bl

tag: diagnosis at year = 1


title: HER2 -positive breast cancer (microdissected, cancer cell) 10

description: clinical specimen, breast tissues

tag: gender

value: Female

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIIC

tag: histology

tag: er

tag: pgr

tag: chemotherapy effect


title: Case 3-HTO set8-A

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

tag: cell type

value: nuclei

tag: library type


title: HER2 -positive breast cancer (microdissected, cancer cell) 12

description: clinical specimen, breast tissues

tag: age

value: IIIA

value: Negative


title: P210_RNAseq

tag: tissue

tag: experiment


title: PBMC_LEI_68

description: PBMCs

tag: Sex

value: F

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

value: UA


title: HER2 -positive breast cancer (microdissected, cancer cell) 11

description: clinical specimen, breast tissues

tag: gender

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIB

tag: histology

tag: er

tag: pgr

tag: chemotherapy effect


title: Case 5-HTO set7-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type

tag: library type

value: HTO


title: P209_RNAseq

tag: tissue

tag: experiment


title: HER2 -positive breast cancer (microdissected, cancer cell) 07

description: clinical specimen, breast tissues

tag: age


title: Case 5-HTO set7-A

description: single nuclear RNAseq


title: P208_RNAseq


title: PBMC_LEI_65

description: PBMCs

tag: Sex

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at year = 1


title: Case 4-cDNA set6-B

description: single nuclear RNAseq

tag: diagnosis

value: cDNA


title: CTL_BR2_TCR_MAPKi

city: Dundee

first: Laura

last: Spinelli

address: Dow Street

department: Cell Signalling and Immunology

institute: University of Dundee

description:
BR2: + TCR 4hr+MEKi
BR2_TCR_MAPKi_S8_L001

data_processing:
raw reads aligned against the Mus musculus mm10 reference genome using the STAR aligner (version 2.4.2a)
number of reads associated with each gene counted using subreads package (version 1.5.0)
noise from low count genes reduced using the filterByExpr function.
resulting count matrix  normalised by the Trimmed Mean of M-values (TMM) method using the edgeR package
EdgeR RPKM function used on TMM-normalised counts to calculate FPKM values, with total exon length calculated using GenomicRanges (Lawrence, 2013) as the sum of the non-overlapping exonic regions for a gene.
Genome_build: Mus Musculus mm10
Supplementary_files_format_and_content: text file includes  FPKM values for each Sample/replicate

source_name: CTL_+ TCR 4hr+MEKi

growth_protocol: Cytotoxic T lymphocytes (CTL) were generated from P14 transgenic mice. Cells were activated for 48hr, then washed out and cultured for further five days in complete RPMI media supplemented with 20 ng/mL IL-2. On day seven cells were plated at a cell density of 1x106 live cells/mL in complete RPMI media supplemented with 20 ng/mL IL-2 and left to rest at 37ºC with 5% CO2 for 1hr prior stimulation with 100 ng/mL gp33-41 peptide for 4hr in the presence or absence of IC87114 inhibitor (10 µM), or MEK inhibitor PD184252 (2 µM).

extract_protocol:
Total RNA was extracted from cell pellets using Qiagen RNAeasy mini kit (Qiagen) as per manufacturer’s instructions.
Libraries preparation was started from 300 ng of total RNA using the Illumina TruSeq Stranded mRNA sample preparation kit (15031047) as per manufacturer’s instructions.

treatment_protocol: Some samples were treated with 10 µM PI3Kp110δ IC87114 inhibitor or 2 µM MEK PD184252 inhibitor

tag: strain

value: LCMV-P14 TCR transgenic

value: cytotoxic T lymphocytes (CTL)

tag: treatment

value: + TCR 4hr+MEKi


title: HER2 -positive breast cancer (microdissected, cancer cell) 02

description: clinical specimen, breast tissues

tag: gender

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIA

tag: histology

value: Invasive ductal carsinoma

tag: er

tag: pgr

tag: chemotherapy effect


title: PBMC_LEI_61

description: PBMCs

tag: age

tag: Sex

value: M

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

value: discovery

tag: diagnosis at bl


title: Case 4-HTO set6-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type

tag: library type


title: HER2 -positive breast cancer (microdissected, cancer cell) 09

description: clinical specimen, breast tissues

tag: gender

value: Female

tag: clinical tumor stage

tag: clinical nodal stage

value: Positive


title: P206_RNAseq

tag: tissue

value: Brain

tag: experiment

value: Queen removal (late commitment)


title: HER2 -positive breast cancer (microdissected, cancer cell) 06

description: clinical specimen, breast tissues

tag: clinical stage

value: IIIA

tag: histology

tag: er

tag: pgr

tag: chemotherapy effect


title: Case 4-cDNA set6-A

description: single nuclear RNAseq

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

value: nuclei


title: HER2 -positive breast cancer (microdissected, cancer cell) 25

description: clinical specimen, breast tissues

tag: age


title: HER2 -positive breast cancer (microdissected, cancer cell) 03

description: clinical specimen, breast tissues

value: IIIC

value: Negative


title: CTL_BR1_TCR_MAPKi

description:
BR1: + TCR 4hr+MEKi
BR1_TCR_MAPKi_S4_L001

tag: strain

tag: treatment


title: P204_RNAseq


title: P205_RNAseq


title: HER2 -positive breast cancer (microdissected, cancer cell) 01

description: clinical specimen, breast tissues


title: PBMC_LEI_29

description: PBMCs

tag: Sex

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

value: UA

tag: diagnosis at year = 1


title: CTL_BR3_TCR_PI3Ki

description:
BR3: + TCR 4hr+PI3Kdi
BR3_TCR_PI3Ki_S11_L001

source_name: CTL_+ TCR 4hr+PI3Kdi

value: LCMV-P14 TCR transgenic

tag: cell type

value: + TCR 4hr+PI3Kdi


title: PBMC_LEI_30

description: PBMCs


title: Case 1-cDNA set9-A

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: library type

value: cDNA


title: Case 4-HTO set6-A

description: single nuclear RNAseq

value: HTO


title: Case 1-HTO set9-A

description: single nuclear RNAseq


title: P203_RNAseq

tag: tissue

tag: experiment


title: CTL_BR2_TCR_PI3Ki

description:
BR2: + TCR 4hr+PI3Kdi
BR2_TCR_PI3Ki_S7_L001

tag: strain

value: cytotoxic T lymphocytes (CTL)

tag: treatment


title: Case 2-cDNA set5-B

description: single nuclear RNAseq


title: Case 2-HTO set5-B

description: single nuclear RNAseq


title: P201_RNAseq


title: P202_RNAseq


title: P198_RNAseq


title: CTL_BR1_TCR_PI3Ki

description:
BR1: + TCR 4hr+PI3Kdi
BR1_TCR_PI3Ki_S3_L001


title: CTL_BR2_TCR

description:
BR2: + TCR 4hr
BR2_TCR_S6_L001

source_name: CTL_+ TCR 4hr

value: + TCR 4hr


title: PBMC_LEI_17

description: PBMCs

tag: age

tag: Sex

value: M

tag: tender joints

tag: swollen joints

value: discovery


title: HER2 -positive breast cancer (microdissected, cancer cell) 08

description: clinical specimen, breast tissues

tag: gender

value: Female

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIB

tag: histology

value: Invasive ductal carsinoma

tag: er

tag: pgr

tag: chemotherapy effect


title: PBMC_LEI_64

description: PBMCs

value: F

tag: esr

tag: crp

tag: rf

value: Positive

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

tag: diagnosis at year = 1


title: PBMC_LEI_15

description: PBMCs

tag: age

tag: Sex

tag: tender joints

tag: swollen joints


title: CTL_BR3_TCR

description:
BR3: + TCR 4hr
BR3_TCR_S10_L001

tag: strain

tag: cell type

tag: treatment


title: Case 2-cDNA set5-A

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

value: nuclei

tag: library type


title: P127_BSseq

tag: tissue

value: Brain

tag: experiment

value: Control


title: P197_RNAseq

value: Queen removal (late commitment)


title: CTL_BR1_TCR

description:
BR1: + TCR 4hr
BR1_TCR_S2_L001

value: LCMV-P14 TCR transgenic


title: Case 2-HTO set5-A

description: single nuclear RNAseq


title: P212_RNAseq


title: Control 3-cDNA set4-B

description: single nuclear RNAseq

value: control

value: cDNA


title: HER2 -positive breast cancer (microdissected, cancer cell) 04

description: clinical specimen, breast tissues

tag: gender

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

tag: histology

tag: er

value: Negative

tag: pgr

tag: chemotherapy effect


title: P196_RNAseq


title: PBMC_LEI_24

description: PBMCs

tag: age

tag: Sex

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

value: UA

tag: diagnosis at year = 1


title: PBMC_LEI_39

description: PBMCs


title: HER2 -positive breast cancer (microdissected, cancer cell) 05

description: clinical specimen, breast tissues

tag: gender

tag: clinical tumor stage

tag: clinical nodal stage

tag: clinical stage

value: IIA


title: Control 3-HTO set4-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type

tag: library type

value: HTO


title: P193_RNAseq

tag: tissue

tag: experiment


title: PBMC_LEI_55

description: PBMCs

tag: age

tag: Sex

value: M

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

value: discovery


title: PBMC_LEI_26

description: PBMCs

tag: rf

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

tag: diagnosis at year = 1


title: CTL_BR2_IL2

description:
BR2: Unstimulated
BR2_IL2_S5_L001

tag: strain

value: cytotoxic T lymphocytes (CTL)

tag: treatment

value: Unstimulated


title: Control 3-cDNA set4-A

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type

tag: library type


title: PBMC_LEI_8

description: PBMCs

tag: age

tag: Sex

value: F


title: RNASeq_MII_Mutant rep5

city: Nanjing City

first: Haifeng

last: Sun

state: JiangSu province

address: Tianyuan East Road 818

institute: Nanjing Medical University

data_processing:
The read quality was controlled using fastqc and trim_galore
Clean reads were aligned to the mouse genome mm10 using HISAT2 with default parameters
The read counts were quantified using featureCounts.
Differential expression testing was performed using the R package DESeq2.
FPKM was calculated by RSEM with default parameters.
Genes with adjusted P-value < 0.05 and a fold change > 2 were marked as differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: MII Oocyte

extract_protocol:
Oocytes and embryos were collected at the time point as described in Supplementary Table 1.
The RNA-seq libraries for the harvested samples were generated based on Smart-seq2. Sequence libraries were constructed using the KAPA HyperPlus Prep Kit (KK8514) according to the manufacturer’s instructions.

tag: developmental stage

value: MII Oocyte

tag: genotype

value: Rnf114 Mutant


title: P191_RNAseq

tag: tissue

value: Brain

tag: experiment


title: P190_RNAseq


title: CTL_BR3_IL2

description:
BR3: Unstimulated
BR3_IL2_S9_L001


title: P192_RNAseq


title: CTL_BR1_IL2

description:
BR1: Unstimulated
BR1_IL2_S1_L001


title: P189_RNAseq


title: PBMC_LEI_70

description: PBMCs

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf

value: Positive

tag: pain


title: RNASeq_MII_Mutant rep3

tag: strain


title: Control 2-HTO set3-B

description: single nuclear RNAseq

tag: diagnosis

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

value: nuclei


title: Control 3-HTO set4-A

description: single nuclear RNAseq

value: control

tag: tissue type


title: Control 2-cDNA set3-B

description: single nuclear RNAseq

tag: cell type

value: cDNA


title: RNASeq_MII_Mutant rep4


title: PBMC_LEI_75

description: PBMCs

value: Negative

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

tag: diagnosis at year = 1


title: Control 2-cDNA set3-A

description: single nuclear RNAseq

tag: library type


title: PBMC_LEI_69

description: PBMCs

tag: age

tag: Sex

value: UA


title: P187_RNAseq

tag: tissue

tag: experiment

value: Queen removal (late commitment)


title: RNASeq_MII_Mutant rep1

tag: developmental stage

tag: genotype


title: Control 2-HTO set3-A

description: single nuclear RNAseq

value: HTO


title: PBMC_LEI_62

description: PBMCs

value: M

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf


title: Control 1-cDNA set2-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type


title: PBMC_LEI_6

description: PBMCs

tag: pain

tag: disease activity

tag: wellbeing

value: discovery

tag: diagnosis at bl


title: P186_RNAseq


title: CTL_BR3_TCR_MAPKi

description:
BR3: + TCR 4hr+MEKi
BR3_TCR_MAPKi_S12_L001

tag: strain

value: LCMV-P14 TCR transgenic

value: cytotoxic T lymphocytes (CTL)

tag: treatment

value: + TCR 4hr+MEKi


title: PBMC_LEI_49

description: PBMCs

tag: age

tag: Sex

tag: diagnosis at year = 1


title: Case 5-cDNA set7-A

description: single nuclear RNAseq

tag: library type


title: RNASeq_MII_Control rep5

tag: developmental stage

value: MII Oocyte

tag: genotype

value: wildtype


title: P185_RNAseq

tag: tissue

value: Brain

tag: experiment


title: P188_RNAseq


title: PBMC_LEI_52

description: PBMCs

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf


title: Control 1-HTO set2-B

description: single nuclear RNAseq

tag: diagnosis

tag: tissue type

tag: cell type


title: PBMC_LEI_59

description: PBMCs

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl


title: RNASeq_MII_Control rep4

tag: strain


title: PBMC_LEI_40

description: PBMCs

tag: age

tag: Sex

value: F

tag: diagnosis at year = 1


title: P184_RNAseq

tag: tissue

tag: experiment


title: Control 1-cDNA set2-A

description: single nuclear RNAseq

value: frozen brain/Prefrontal cortex/Medulla/Choroid plexus

tag: library type


title: RNASeq_MII_Mutant rep2

tag: developmental stage

tag: genotype

value: Rnf114 Mutant


title: PBMC_LEI_50

description: PBMCs

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf


title: Control 4-HTO set1-B

description: single nuclear RNAseq

tag: diagnosis

value: control

tag: tissue type

tag: cell type

value: nuclei


title: Control 4-cDNA set1-A

description: single nuclear RNAseq

value: cDNA


title: P180_RNAseq


title: PBMC_LEI_38

description: PBMCs

value: Negative

tag: pain

tag: disease activity

tag: wellbeing

tag: diagnosis at bl

value: UA


title: P183_RNAseq

tag: tissue

value: Queen removal (late commitment)


title: RNASeq_2CELL_Mutant rep4

source_name: 2-cell embyro

tag: strain

value: 2-cell embyro


title: Control 1-HTO set2-A

description: single nuclear RNAseq

tag: library type

value: HTO


title: PBMC_LEI_10

description: PBMCs

tag: age

tag: Sex

value: Positive

value: discovery

tag: diagnosis at year = 1


title: RNASeq_MII_Control rep1

tag: developmental stage

tag: genotype


title: P182_RNAseq

tag: experiment


title: Control 4-cDNA set1-B

description: single nuclear RNAseq


title: Control 4-HTO set1-A

description: single nuclear RNAseq


title: RNASeq_2CELL_Mutant rep2


title: RNASeq_MII_Control rep2


title: P181_RNAseq


title: PBMC_LEI_16

description: PBMCs

tag: tender joints

tag: swollen joints

tag: esr

tag: crp

tag: rf


title: PBMC_LEI_72

description: PBMCs

tag: pain

tag: disease activity

value: RA


title: RNASeq_2CELL_Mutant rep1


title: RNASeq_MII_Control rep3

value: MII Oocyte


title: primary human RPE cells with siVEGFR2 rep3

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

data_processing:
Seqtk was used to remove rRNA reads, adaptors and poor quality reads (length < 25 or Q20>0.01).
Clean reads were mapped to hg38 genome by Hisat2 v2.0.4 (Pertea M et al., 2016) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of gene expression was calculated by Stringtie v1.3.0 (Pertea M et al., 2016).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include FPKM value of gene expressionS for each sample .

source_name: primary RPE cells

growth_protocol: the primary cells were cultured in 10% FBS DMEM medium with 1% penecilin/streptomyosin and high glucose (4.5 mg/l)

extract_protocol:
RNA was extracted using Trizol reagent from the RPE cells. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The RPE cells were transfected with either siControl or siVEGFR2 via RNAiMAX. Twenty-four hours after transfection, the high glucose media were changed into glucose free media and the cells were kept under glucose depletion condition for 18 hours.

tag: primary or cell line

value: primary

value: retina

tag: treatment

tag: conditioned medium

value: glucose depletion


title: RNASeq_2CELL_Mutant rep3

tag: strain


title: primary human RPE cells with siVEGFR2 rep1

tag: tissue


title: P179_RNAseq

value: Brain


title: PBMC_LEI_67

description: PBMCs

tag: age

tag: Sex

value: M

tag: wellbeing

tag: diagnosis at bl


title: primary human RPE cells with siVEGFR2 rep2


title: P178_RNAseq

tag: experiment


title: P176_RNAseq


title: P175_RNAseq


title: PBMC_LEI_9

description: PBMCs

tag: tender joints

tag: diagnosis at year = 1


title: RNASeq_2CELL_Control rep4

tag: developmental stage

tag: genotype

value: wildtype


title: PBMC_LEI_66

description: PBMCs

value: F

tag: swollen joints

tag: esr

tag: crp

tag: rf


title: P177_RNAseq


title: RNASeq_2CELL_Control rep5


title: PBMC_LEI_14

description: PBMCs

tag: pain

tag: disease activity


title: PBMC_LEI_73

description: PBMCs


title: PBMC_LEI_7

description: PBMCs


title: P173_RNAseq


title: RNASeq_1CELL_Mutant rep5

source_name: 1-cell embyro

tag: strain

value: 1-cell embyro

value: Rnf114 Mutant


title: P174_RNAseq

tag: tissue


title: primary human RPE cells with siControl rep3

tag: primary or cell line

tag: treatment

value: siControl

tag: conditioned medium


title: P167_RNAseq

value: Queen removal (early commitment)


title: PBMC_LEI_56

description: PBMCs

tag: age

tag: Sex

tag: wellbeing

tag: diagnosis at bl

value: UA


title: RNASeq_2CELL_Control rep2

tag: developmental stage

value: 2-cell embyro


title: primary human RPE cells with siControl rep2


title: P166_RNAseq

tag: experiment


title: PBMC_LEI_57

description: PBMCs

tag: tender joints

tag: swollen joints

value: Positive

tag: diagnosis at year = 1


title: P172_RNAseq

value: Queen removal (late commitment)


title: primary human RPE cells with siControl rep1


title: HEK293E torin input rep3

first: Brian

middle: Frederick

last: Pickering

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: Input.gene.counts.txt

data_processing:
miCLIP:Low-quality bases, reads with more than two ambiguous base calls, and adapter sequence were removed using FLEXBAR tool (--max-uncalled 2 --min-read-length 15 --pre-trim-phred 30, 3’ adapter: AGATCGGAAGAGCGGTTCAG). Then, PCR-duplicated reads of identical sequences were removed using the pyDuplicateRemover.py script of the pyCRAC tool suite (version 1.2.2.3). Unique reads were mapped with Burrows-Wheeler Aligner (bwa-0.7.1) using hg38 as reference genome. Further analysis including the identification of CIMS was performed as using the CTK package (v1.1.3). A custom perl script was then used to filter the identified putative m6A residues from the CIMS file. This script filters C to T transitions based on the number of transitions.  Additionally, we filtered for called sites that have a DRACH sequence.
RNA-seq  Adapters were trimmed using FLEXBAR tool (--min-read-length 15, --pre-trim-phred 32, 3’ adaptor: AGATCGGAAGAGCACACGTCT).  Gene count tables were generated using STAR aligned to hg38 transcriptome and normalized using DESeq2 (v1.22.2).
Genome_build: hg38
Supplementary_files_format_and_content: bed files contain pooled miCLIP unique m6A sites from biological triplicates.  Sample replicate is indicated for each site in the fourth column.  Gene counts were normalized using DESeq and provided in the file “Input.gene.counts.txt”.

source_name: HEK293E torin input rep3

growth_protocol: Cells were grown as per ATCC guidelines.

extract_protocol:
Total RNA was extracted with Trizol (n=3 biological replicates).  Poly(A) mRNA was then isolated using two rounds of selection with oligo(dT) magnetic beads (New England Biolabs).  30 ug of poly(A) RNA was used for each replicate in this study.
miCLIP libraries were prepared as previously described (PMID: 28349454).

tag: cell line

tag: cell type

value: embryonic kidney

tag: antibody name

tag: replicate number


title: HEK293E insulin input rep3

description: Input.gene.counts.txt

source_name: HEK293E insulin input rep3


title: HEK293E torin input rep1

description: Input.gene.counts.txt

source_name: HEK293E torin input rep1


title: P165_RNAseq

tag: tissue


title: RNASeq_1CELL_Mutant rep4

tag: strain

tag: genotype


title: RNASeq_2CELL_Control rep3


title: HEK293E torin input rep2

description: Input.gene.counts.txt

source_name: HEK293E torin input rep2


title: RNASeq_2CELL_Control rep1


title: PBMC_LEI_5

description: PBMCs

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity

value: discovery

value: RA


title: PBMC_LEI_54

description: PBMCs

tag: age

tag: Sex

tag: wellbeing

tag: diagnosis at bl


title: P164_RNAseq

tag: experiment


title: PBMC_LEI_48

description: PBMCs

tag: tender joints

tag: swollen joints

value: Negative

tag: diagnosis at year = 1


title: RNASeq_1CELL_Control rep5

tag: developmental stage


title: RNASeq_1CELL_Mutant rep1


title: HEK293E insulin input rep2

description: Input.gene.counts.txt

source_name: HEK293E insulin input rep2

tag: cell line

tag: cell type

tag: antibody name

tag: replicate number


title: P162_RNAseq

tag: tissue


title: RNASeq_1CELL_Mutant rep3

tag: strain

tag: genotype


title: PBMC_LEI_43

description: PBMCs

tag: esr

tag: crp

tag: rf

tag: pain

tag: disease activity


title: PBMC_LEI_42

description: PBMCs

tag: age

tag: Sex

tag: wellbeing

tag: diagnosis at bl


title: RNASeq_1CELL_Control rep4

tag: developmental stage


title: P161_RNAseq

tag: experiment


title: RNASeq_1CELL_Mutant rep2


title: HEK293E torin miclip rep1

source_name: HEK293E torin miclip rep1

tag: cell line

tag: cell type

value: Rabbit polyclonal anti-N6-methyladenosine (m6A) (Abcam #ab151230)


title: PBMC_LEI_36

description: PBMCs

tag: tender joints

tag: swollen joints

tag: diagnosis at year = 1


title: P160_RNAseq

tag: tissue

value: Brain


title: P163_RNAseq


title: PBMC_LEI_35

description: PBMCs

tag: esr


title: RNASeq_1CELL_Control rep2

tag: strain

tag: genotype


title: HEK293E insulin miclip rep3

source_name: HEK293E insulin miclip rep3

tag: antibody name

tag: replicate number


title: HEK293E insulin miclip rep2

source_name: HEK293E insulin miclip rep2


title: RNASeq_1CELL_Control rep1


title: PBMC_LEI_34

description: PBMCs

tag: age

value: M

tag: crp

tag: rf

tag: pain

tag: disease activity


title: P154_RNAseq

source_name: Brain

tag: experiment


title: P157_RNAseq


title: HEK293E insulin input rep1

description: Input.gene.counts.txt

source_name: HEK293E insulin input rep1

tag: cell line


title: HEK293E torin miclip rep3

source_name: HEK293E torin miclip rep3

tag: cell type


title: PBMC_LEI_33

description: PBMCs

source_name: peripheral blood

tag: Sex

tag: tender joints

tag: wellbeing

tag: diagnosis at bl


title: HEK293E insulin miclip rep1

source_name: HEK293E insulin miclip rep1


title: PBMC_LEI_32

description: PBMCs

tag: swollen joints

tag: esr

tag: diagnosis at year = 1


title: HEK293E torin miclip rep2

source_name: HEK293E torin miclip rep2

tag: antibody name


title: P152_RNAseq

tag: tissue


title: BRCA1_MUT3

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

institute: Centre hospitalier universitaire vaudois

data_processing:
Reads were first trimmed to remove polyA and Illumina TruSeq adapter sequences using cutadapt, and aligned to the human reference GRCh37 (hg19) genome using the STAR aligner.
The number of counts was summarized at the gene level using featureCounts. Reads that uniquely mapped to the reference genome averaged 93.6% ± 0.2% (s.d.). The rate of these reads mapping to ribosomal RNA averaged 0.03% ± 0.002% (s.d.) while 97.8% ± 0.2% (s.d.) mapped to exonic protein-coding sequences.
Read counts were normalized into reads per kilobase per million (RPKM) and log2 transformed after addition of a pseudocount value of 1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 of (RPKM +1) values for each sample

source_name: UWB1.289 with mutation in BRCA1 - replicate 3

extract_protocol:
RNA from UWB1.289 (BRCA1 2594delC mutant; n = 3) and UWB1.289 BRCA1+ (BRCA1 WT; n = 3) cell lines was extracted using the RNA easy kit (Qiagen, Hilden, Germany). RNA quality was assessed using the Fragment Analyzer (Advances Analytical Technologies Inc., Ankeny, USA).
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA reagents (Catalog number RS-122-2201; Illumina; San Diego, USA) according to the protocol supplied by the manufacturer and using 1ug of total RNA.

value: MUT

value: BRCA1 2594delC


title: PBMC_LEI_21

description: PBMCs

tag: age

value: F


title: RNASeq_1CELL_Control rep3

tag: strain

tag: developmental stage

value: 1-cell embyro

tag: genotype

value: wildtype


title: CML_LTHSC-2

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1824 6th Avenue South

department: Hematology/Oncology

institute: University of Alabama at Birmingham

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N724-Nextera_DualIndex_N516_SL238834

data_processing:
Illumina Converter was used to convert bcl files to obtain raw fastq files
Raw fastq files were trimmed with Trim Galore! version 0.4.4 with parameters --fastq_args "--nogroup --noextract"
Trimmed reads were aligned using STAR version 2.5.3a with parameters --genomeDir --readFilesIn --outFileNamePrefix --outReadsUnmapped Fastx --runThreadN --outSAMtype BAM SortedByCoordinate --outSAMattributes ALL --readFilesCommand gunzip -c --outSAMattrRGline
HTSeq-count version 0.9.1 created the raw count files from the STAR aligned files with paramters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
DESeq2 version 1.18.1 was used for differential expression
Genome_build: Gencode GRCm38 p4 Release 11
Supplementary_files_format_and_content: tab delimited text file containing raw counts from HTSeq-count

growth_protocol: All the resepctive mesenchymal progenitors and long-term hematopoietic stem cells were FACS sorted from either normal or CML primary mice using conventional cell surface markers.

extract_protocol:
Sequencing libraries were prepared with the SMARTer Ultra Low Input RNA Kit for Sequencing (v4, TaKaRa Clontech, catalog no. 634891) and Nextera XT DNA Library Preparation Kit (96 samples, Illumina, cat no. FC-131-1096).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor stage

value: CML

value: Bone marrow

value: Leukemic stem cells


title: CML_LTHSC-3

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N724-Nextera_DualIndex_N517_SL238835


title: BRCA1_MUT2

source_name: UWB1.289 with mutation in BRCA1 - replicate 2


title: CML_LTHSC-1

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N724-Nextera_DualIndex_N515_SL238833


title: PBMC_LEI_2

description: PBMCs

tag: crp

tag: rf

value: Positive

tag: pain

tag: disease activity

value: UA


title: P151_RNAseq

tag: experiment

value: Queen removal (early commitment)


title: BRCA1_MUT1

source_name: UWB1.289 with mutation in BRCA1 - replicate 1


title: PBMC_LEI_18

description: PBMCs

tag: Sex

tag: tender joints

tag: wellbeing

value: discovery


title: P150_RNAseq


title: Normal_LTHSC-4

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N723-Nextera_DualIndex_N518_SL238832

value: Normal

tag: cell type

value: Hematopoietic stem cells


title: PBMC_LEI_13

description: PBMCs

tag: swollen joints

tag: esr

tag: diagnosis at bl

tag: diagnosis at year = 1

value: RA


title: Normal_LTHSC-3

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N723-Nextera_DualIndex_N517_SL238831

tag: strain

tag: tissue


title: BRCA1_WT3

source_name: UWB1.289 with forced expression of wild-type BRCA1 - replicate 3

value: WT


title: Normal_LTHSC-2

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N723-Nextera_DualIndex_N516_SL238830


title: P148_RNAseq

value: Brain


title: CML_LTHSC-4

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N724-Nextera_DualIndex_N518_SL238836


title: BRCA1_WT1

source_name: UWB1.289 with forced expression of wild-type BRCA1 - replicate 1


title: BRCA1_WT2

source_name: UWB1.289 with forced expression of wild-type BRCA1 - replicate 2


title: P153_RNAseq


title: PBMC_LEI_12

description: PBMCs

tag: age


title: P147_RNAseq


title: Normal_LTHSC-1

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N723-Nextera_DualIndex_N515_SL238829

tag: tumor stage


title: PBMC_LEI_77

description: PBMCs

tag: crp

value: Negative


title: P146_RNAseq


title: CML_6C3-4

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N722-Nextera_DualIndex_N518_SL238828

value: 6C3+ stromal progenitors


title: RNA-sequencing STING-KO Unstimulated 3_S1_L001

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

data_processing:
the resulted data were demultiplexed using CASAVA version 1.4
Tophat2 alignment of raw paoired reads to mm10 genome
Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: genes.fpkm_tracking

source_name: heart endothelial cells

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
RNA was prepared according to manufacture's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: genotype

value: STING-KO

tag: passages

value: Unstimulated


title: PBMC_LEI_74

description: PBMCs

value: M

tag: rf

tag: pain

tag: disease activity


title: RNA-sequencing C57BL6 TNF, 10 ng/ml, 4 hours 2_S1_L001

value: wildtype

value: TNF, 10 ng/ml, 4 hours


title: P145_RNAseq

tag: experiment


title: PBMC_LEI_71

description: PBMCs

tag: Sex

value: F

tag: tender joints

tag: wellbeing


title: P144_RNAseq


title: PBMC_LEI_51

description: PBMCs

tag: swollen joints

tag: esr


title: P149_RNAseq


title: RNA-sequencing C57BL6 Unstimulated 1_S1_L001


title: P143_RNAseq


title: PBMC_LEI_41

description: PBMCs

tag: diagnosis at bl

tag: diagnosis at year = 1


title: CML_6C3-1

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N722-Nextera_DualIndex_N515_SL238825

tag: strain

value: CML

tag: tissue

value: Bone marrow

tag: cell type


title: Normal_6C3-4

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N721-Nextera_DualIndex_N518_SL238824

tag: tumor stage


title: P142_RNAseq

value: Queen removal (early commitment)


title: CML_6C3-2

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N722-Nextera_DualIndex_N516_SL238826


title: Normal_6C3-3

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N721-Nextera_DualIndex_N517_SL238823


title: PBMC_LEI_28

description: PBMCs

tag: age

tag: crp

value: discovery

value: UA


title: P141_RNAseq


title: Normal_6C3-2

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N721-Nextera_DualIndex_N516_SL238822

value: Normal


title: PBMC_LEI_27

description: PBMCs

tag: rf

value: RA


title: Normal_6C3-1

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N721-Nextera_DualIndex_N515_SL238821


title: CML_Thy-4

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N720-Nextera_DualIndex_N518_SL238820

value: Bone forming Thy+ progenitors


title: PBMC_LEI_20

description: PBMCs

tag: pain


title: CML_6C3-3

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N722-Nextera_DualIndex_N517_SL238827


title: CML_Thy-3

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N720-Nextera_DualIndex_N517_SL238819


title: PBMC_LEI_63

description: PBMCs

value: Positive

tag: disease activity


title: PBMC_LEI_4

description: PBMCs

value: Negative


title: KOPN57bi-NoTreatment-3

type: RNA

city: Setagaya-ku

first: NOBUTAKA

last: KIYOKAWA

department: Pediatric Hematology & Oncology Research

institute: National Research Institute for Child Health & Development

description: Gene expression data from Ph-positive BCP-ALL cells without treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome-U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: KOPN-57bi cells without treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Not adapted

extract_protocol: Trizol (Invitrogen, CA. USA) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: KOPN57bi cells were cultured for 24 h in the absence or presence of lenalidomide (5 uM) or imatinib (0.5 uM) alone or both, and harvested.

value: BCP-ALL cells

tag: genotype

value: Philadelphia chromosome-positive

tag: treatment


title: KOPN57bi-NoTreatment-2


title: 31: PHAGF_Control_rep3

city: Quanzhou

first: Yiming

last: Zeng

state: Fujian

address: Zhongshan North Road No.34, Licheng District

department: Department of Pulmonary and Critical Care Medicine, Respiratory Medicine Center of Fujian Province

institute: The Second Affiliated Hospital of Fujian Medical University

description: Gene expression without β-elemene treatment

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: primary human airway granulation fibroblasts, replicate 3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Cells were cultured in DMEM (HyClone, Cat# SH30243.01) supplemented with 20% FBS (HyClone, Cat# SH30070.03), at 37°C, 5% CO2. Cells were passaged every 3 days and passages 3-7 used in experiments.

extract_protocol: Total RNAs of cells were isolated using TRIzol reagent (TaKaRa, Cat# 9109) and measured using a NanoDrop 2000 (Thermo Fisher Scientific, Waltham, Massachusetts, U.S.).

treatment_protocol: Three human airway granulation fibroblast samples were cultured on 6-well plates and treated with or without 160ug/ml β-elemene (Sigma-Aldrich, Cat# SJ05001280278, CAS# 515-13-9) for 48 hours.

tag: primary cell source

value: human airway hyperplastic granulation tissue

tag: β-elemene intervention

value: no


title: KOPN57bi-NoTreatment-1


title: KOPN57bi-Lenalidomide-Imatinib-2

description: Gene expression data from Ph-positive BCP-ALL cells treated with  Imatinib and Lenalidomide

source_name: KOPN-57bi cells treated with Imatinib and Lenalidomide

value: Imatinib and Lenalidomide


title: KOPN57bi-Lenalidomide-Imatinib-3


title: PBMC_LEI_93

description: PBMCs

tag: Sex

value: M

tag: tender joints

tag: swollen joints

tag: wellbeing

value: HD


title: CML_Thy-2

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N720-Nextera_DualIndex_N516_SL238818

tag: strain

value: CML


title: 32: PHAGF_elemene-treated_rep3

description: Gene expression after β-elemene treatment for 48h.

source_name: primary human airway granulation fibroblasts, 160ug/ml β-elemene, 48h, replicate 3

value: yes


title: CML_Thy-1

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N720-Nextera_DualIndex_N515_SL238817

tag: tissue

value: Bone marrow


title: PBMC_LEI_92

description: PBMCs

tag: esr

tag: diagnosis at bl

tag: diagnosis at year = 1


title: PBMC_LEI_25

description: PBMCs

tag: age

tag: crp

value: discovery


title: 21: PHAGF_Control_rep2

source_name: primary human airway granulation fibroblasts, replicate 2

tag: cell type


title: PBMC_LEI_91

description: PBMCs

value: F

tag: rf

tag: pain

tag: disease activity


title: Normal_Thy-4

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N719-Nextera_DualIndex_N518_SL238816

tag: tumor stage

value: Normal


title: Normal_Thy-3

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N719-Nextera_DualIndex_N517_SL238815


title: KOPN57bi-Lenalidomide-2

description: Gene expression data from Ph-positive BCP-ALL cells treated with Lenalidomide

source_name: KOPN-57bi cells treated with Lenalidomide

tag: genotype

tag: treatment

value: Lenalidomide


title: 12: PHAGF_elemene-treated_rep1

source_name: primary human airway granulation fibroblasts, 160ug/ml β-elemene, 48h, replicate 1

tag: primary cell source

tag: β-elemene intervention


title: 11: PHAGF_Control_rep1

source_name: primary human airway granulation fibroblasts, replicate 1


title: KOPN57bi-Lenalidomide-Imatinib-1


title: KOPN57bi-Lenalidomide-1


title: KOPN57bi-Imatinib-3

description: Gene expression data from Ph-positive BCP-ALL cells treated with Imatinib

source_name: KOPN-57bi cells treated with Imatinib

value: Imatinib


title: PBMC_LEI_90

description: PBMCs

source_name: peripheral blood

tag: Sex

tag: tender joints

tag: swollen joints

tag: wellbeing


title: PBMC_LEI_89

description: PBMCs

tag: esr

tag: diagnosis at bl


title: PBMC_LEI_87

description: PBMCs

tag: age

tag: diagnosis at year = 1


title: pnet2_abc_2

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include raw counts and TPM values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling plants

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 7-day-old seedlings using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: tissue

value: whole seedlings

value: pnet2_abc mutant

tag: ecotype


title: PBMC_LEI_86

description: PBMCs

tag: crp

tag: rf

tag: pain


title: PBMC_LEI_85

description: PBMCs

tag: disease activity


title: PBMC_LEI_84

description: PBMCs


title: 22: PHAGF_elemene-treated_rep2

source_name: primary human airway granulation fibroblasts, 160ug/ml β-elemene, 48h, replicate 2

tag: cell type


title: pnet2_bc_3

tag: genotype

value: pnet2_bc mutant


title: pnet2_abc_3


title: PBMC_LEI_83

description: PBMCs


title: pnet2_bc_2


title: pnet2_bc_1


title: Normal_mSSC-4

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N716-Nextera_DualIndex_N518_SL238808

tag: strain

tag: tumor stage

value: Murine skeletal stem cells


title: Normal_Thy-2

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N719-Nextera_DualIndex_N516_SL238814

value: Bone forming Thy+ progenitors


title: CML_mSSC-2

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N718-Nextera_DualIndex_N516_SL238810


title: CML_mSSC-1

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N718-Nextera_DualIndex_N515_SL238809


title: Normal_Thy-1

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N719-Nextera_DualIndex_N515_SL238813


title: CML_mSSC-4

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N718-Nextera_DualIndex_N518_SL238812


title: CML_mSSC-3

description:
Cells from CML Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N718-Nextera_DualIndex_N517_SL238811


title: Normal_mSSC-3

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N716-Nextera_DualIndex_N517_SL238807


title: PBMC_LEI_81

description: PBMCs

tag: Sex

tag: tender joints


title: pnet2_ac_3

value: pnet2_ac mutant


title: MT-D703

first: Qilai

last: Huang

institute: Shandong University

description:
Processed data files:
SNP DiR-seq BT-474-rep1.txt
SNP DiR-seq BT-474-rep2.txt
SNP DiR-seq BT-474-rep3.txt
SNP DiR-seq plasmid1-rep1.txt
SNP DiR-seq plasmid1-rep2.txt
SNP DiR-seq plasmid1-rep3.txt

data_processing:
The next-generation sequencing Data quality statistical software Cutadapt (version 1.9.1) was used to remove the adapters and low-quality sequences from the original sequencing Data (Pass Filter Data) to obtain Clean Data for subsequent information analysis.
The overlap area between read1 and read2 of Clean Reads was combined using Pandaseq (version 2.7) to produce complete sequences.
According to the Barcode sequence of read1 of each sample, the spliced Tag starting position is split into the corresponding sample with perfect matching, and the result is saved in FASTQ file.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every barcode and every sample (bundled into a tar archive)
Supplementary_files_format_and_content: SNP_barcode_id.txt
Supplementary_files_format_and_content: Samples to library relationships information.txt

molecule: other

organism:
Homo sapiens
synthetic construct

source_name: BT-474, plasmid library

extract_protocol:
Twenty-four hours post-transfection, cells were washed twice and harvested in 1 × PBS, and Total RNA was extracted from all surviving cells using RNeasy Plus Mini Kit (74136, QIAGEN). We treated the mRNA with RapidOut DNA Removal Kit (K2981, Thermo Scientific) to remove the trace amount of genomic DNA residue according to the product manual. The purified RNA was then subjected to reverse transcription with High-Capacity cDNA Reverse Transcription Kits (4374967, Applied Biosystems). Briefly, 1.5μg RNA was added into 10μl of 2× RT Master Mix and made up to the final 20μl with nuclease-free water. The reactions were incubated at 25°C for 10 min, followed by 120 min at 37°C, then were inactivated Reverse Transcriptase by heating to 85°C for 5 min. The cDNA products were stored at -20°C or -80°C and ready for qPCR analysis and preparing the NGS sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols
We combined the 35 libraries into seven i7 indexes for Illumina sequencing.
To help the user demultiplex the raw data, we provided all the necessary information in "Sample to library relationship information.txt".

tag: cell line

value: breast cancer cell line BT-474, plasmid library 1

tag: sample type

value: multiplexed

tag: molecule

value: total RNA and plasmid mixture


title: KOPN57bi-Lenalidomide-3

value: BCP-ALL cells

value: Philadelphia chromosome-positive

tag: treatment


title: PBMC_LEI_79

description: PBMCs

tag: age

tag: swollen joints

tag: esr

tag: wellbeing

tag: diagnosis at bl

value: HD

tag: diagnosis at year = 1


title: Normal_mSSC-2

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N716-Nextera_DualIndex_N516_SL238806

tag: tissue

value: Bone marrow


title: PBMC_LEI_82

description: PBMCs

value: M

tag: crp

tag: rf

tag: pain

tag: disease activity


title: KOPN57bi-Imatinib-2

tag: genotype


title: pnet2_ac_2

tag: ecotype


title: pnet2_ac_1


title: sh118_shPontin_RA_GROseq

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

description: GRO-seq Experiment 2: Teton-shPontin#2 stable line was under 24hrs treatment with 5uM retinoic acid, +2ug/ml Dox for 5 days for Pontin KD

data_processing:
Library strategy: GRO-seq
Basecalls performed using Illuminal CASAVA software.
GRO-seq reads were aligned to human genome (hg19) using bowtie with “--best --strata –m 1 –v 2” parameters. Duplicated reads were eliminated for subsequent analysis.
To balance the clonal amplification bias and total useful reads, only at most three reads was allowed for each unique genomic position.
edgeR 3.16.5 was used to call the differential eRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: NTera2 cell line was obtained from ATCC were cultured in Minimum Essential Media (MEM) media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Cells were subjected to nuclear run-on for 5minutes at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE I, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: Before GRO-seq sample collection, the NTera2 cells were maintained in the growing medium to get the appropriate conflency, followed by treatemnt of cells with either 5μM all-trans Retinoic Acid (RA), or Dimethyl sulfoxide (DMSO) as vehcile control for 24 hour. To perform inducible knockdown experiments for Pontin, we used two Tet-On inducibe stable lines for Pontin shRNAs (Tet-on shPontin#1 and Tet-on shPontin#2 and both have very good knockdown efficiency). To induce Pontin expression knockdown, 2μg/ml doxycycline was added into culture media for about 5 days before the GRO-seq sample collection (the RA/DMSO treatment was performed on Day 4).

tag: cell line

value: NTera2 Tet-On shRNA stable line #2

value: Full media +5uM retinoic acid for 24 hours, +2ug/ml Dox for 5 days


title: Normal_mSSC-1

description:
Cells from Normal Mice
CB4A5ANXX_s*_0_Nextera_DualIndex_N716-Nextera_DualIndex_N515_SL238805

tag: strain

tag: tumor stage

value: Normal

tag: cell type


title: sh118_shCtrl_Veh_GROseq

description: GRO-seq Experiment 2: Teton-shPontin#2 stable line was under 24hrs treatment with DMSO vehicle control, no dox treatment

tag: treatment

value: Full media +DMSO vehicle control for 24 hours, no Dox


title: KOPN57bi-Imatinib-1

value: Imatinib


title: Col-0_wild type_3

value: whole seedlings

tag: age

value: wild type


title: Col-0_wild type_2


title: Full_shPontin_GROseq

description: GRO-seq Experiment 1: Teton-shPontin#1 stable line was under 24hrs treatment with 5uM retinoic acid, +2ug/ml Dox for 5 days for Pontin KD

value: NTera2 Tet-On shRNA stable line #1


title: sh118_shCtrl_RA_GROseq

description: GRO-seq Experiment 2: Teton-shPontin#2 stable line was under 24hrs treatment with 5uM retinoic acid, no dox treatment

value: Full media +5uM retinoic acid for 24 hours, no Dox


title: Col-0_wild type_1


title: Full_shCtrl_GROseq

description: GRO-seq Experiment 1: Teton-shPontin#1 stable line was under 24hrs treatment with 5uM retinoic acid, no dox treatment


title: DMSO_replicate 1

city: Gainesville

first: Daiqing

last: Liao

state: Florida

address: 2033 Mowry Road

department: Anatomy and Cell Biology

institute: University of Florida

hyb_protocol: Samples were hybridized with Affymetrix GeneChip Human Transcriptome Array 2.0 and scanned at the University of Florida Interdisciplinary Center for Biotechnology Research.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: For data analysis, we performed differential expression (DE) analysis using R package limma to compare the DMSO group and the A-485 group. Limma utilizes linear model approach to identify differentially expressed genes and employs empirical Bayesian methods to stabilize the variance estimation. Differentially expressed genes with p-value < 0.05 and fold change (FC) ≥ 1.25 or ≤ -1.25 were identified

label_protocol: All microarray sample preparation reactions used the  Ambion® WT Expression Kit, combined with the GeneChip WT Terminal Labeling and  Controls Kit (Affymetrix)

growth_protocol: MCF-7 cells were grown at 37 °ºC with 5% CO2 in a humidified atmosphere. MCF-7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM with 4.5 g/L glucose, L-glutamine and sodium pyruvate, Corning) supplemented with 10% bovine calf serum (HyClone, GE Healthcare Bio-Sciences), penicillin (10 units/ml), and streptomycin (10 µg/ml) (designated as complete media).

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer instructions.

treatment_protocol: MCF-7 cells were treated with A-485 at 3 µM or DMSO control for 24 hours in complete media.

tag: drug treatment

value: DMSO

tag: cancer type

value: ER+ breast cancer


title: A485_replicate 1


title: LK0923 cell line grown with CAF in 2D

status: Public on Jun 15 2021

city: Linköping

first: Emilia

last: Wiechec

address: Sandbäcksgatan 7

department: Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

description: Gene expression data; RMA expression value derived from TAC software

hyb_protocol: Hybridization was done according to the GeneChip® WT Hy-bridization User Manual for use with the Ambion® WT Expression Kit (Affymetrix). A total of 5.5 µg of sscDNA was fragmented and hybridized on a Human Exon 1.0 ST Array.

scan_protocol: Hybridized arrays were scanned with an Affymetrix GeneChip® 3000 fluorescent scanner.

data_processing: Raw intensity CEL files generated by the GeneChip Command Console were imported into Transcriptome Analysis Console (TAC) and CHP files were generated for gene level analysis using the RMA summarization method.

source_name: cell co-culture with CAF

label_protocol: Labeling was done according to the GeneChip® WT Terminal La-beling  User Manual for use with the Ambion® WT Expression Kit (Affymetrix). The starting amount of total RNA was 100 ng. 15 µg of cRNA was used for single-stranded cDNA-synthesis (sscDNA).

growth_protocol: Tumor cells and CAFs were co-cultured in 2D in cell culture flasks. Tumor cell and CAF numbers were adjusted to that an approximate ratio of 3:1 was achieved by the end of co-culture

extract_protocol: Total RNA extraction was performed using the RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol:
Tumor cells were separated from CAFs by magnetic activated cell sorting (MACS).
Gene expression data from HNSCC cell lines grown with or without CAFs in 2D

value: HNSCC cell line (larynx)


title: LK0949 cell line grown with CAF in 2D

value: HNSCC cell line (tongue)


title: LK0949 cell line grown without CAF in 2D

source_name: cell culture without CAF


title: DMSO_replicate 2


title: LK0858 cell line grown with CAF in 2D


title: LK0942 cell line grown without CAF in 2D


title: pnet2_abc_1

value: pnet2_abc mutant


title: LK0923 cell line grown without CAF in 2D


title: LK0824 cell line grown with CAF in 2D


title: LK0858 cell line grown without CAF in 2D