title: iPSC rep1

city: Yushima, Bunkyo-ku, Tokyo

first: Ryota

last: Kurimoto

state: Tokyo

department: Systems BioMedicine

institute: Tokyo Medical and Dental University

data_processing:
Raw datas were cut adaptors and check quality by Trim Galore.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR
TPM and other parameters were counted by iDEP.94
Supplementary_files_format_and_content: csv

source_name: iPSC

growth_protocol: Induction of differentiation of induced pluripotent stem cells (iPSCs) into iPSC-mesenchymal stem cells (MSCs) was performed according to a previous report15 with some modifications. The iPSC line 253G1 was maintained on a 10 cm dish coated with Geltrex (Life Technologies, CA, United States) in Essential 8 (E8) medium (Life Technologies, CA, United States). iPSCs were plated onto Geltrex-coated dishes in E8 medium with 10 μM Y-27632 (BioVision, CA, United States) and cultured for 2 additional days in a differentiation medium comprising 10 ng/mL basic fibroblast growth factor (FGF; R&D Systems, MN, USA), 4 μM SB431542 (Stemgent, MA, United States), and 4 μM WNT agonist CHIR99021 (CHIR) (Stemgent) in Essential 6 (E6) medium (Life Technologies). Differentiation medium was daily changed for 5 days. On day 6, differentiated neural crest cells (NCCs) were plated on a Geltrex-coated dish in mesenchymal stem cell (MSC) culture media (MEMα + 10% fetal bovine serum [FBS] + 1% penicillin-streptomycin + 1 [v/v%] 100× non-essential amino acid solution [NEAA; Gibco], 1 [v/v%] 100× GlutaMAX [Gibco]). After three passages, the surface coating was switched from Geltrex to 1% gelatin (Wako, Osaka, Japan) to support iPSC-MSC adhesion and growth.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Grand Island, NY, USA).
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (NEBNext Ultra II RNA Library Prep Kit for Illumina, E7770S) and NEBNext rRNA Depletion Kit (Human, E6310S).  Libraries were sequenced on the Illumina NEXT-Seq 500 following the manufacturer's protocols.

treatment_protocol: no treatment

value: iPSC


title: krrA 205-1

status: Public on Jan 10 2022

type: SRA

city: Nashville

first: Hualiang

last: Pi

state: TN

address: 1161 21st Avenue South

country: USA

institute: VUMC

description:
krrA 205
5425-HP-49

library_source: transcriptomic

data_processing:
Raw data files (.fastq) were imported into the CLC Genomics Workbench software (Version 20.0.1) platform for analysis. The Illumina paired reads option was chosen for import.
Imported reads were trimmed to remove adapters using CLC Genomics Workbench
To remove rRNA reads, all paired reads were aligned to a sequence list containing all rRNA sequences for each corresponding bacterial strain. Unmapped (non-rRNA) reads were collected and used for subsequent analysis. Steps were performed using CLC Genomics Workbench. Refrence genomes NC_009089 and  NC_013315 were used for CD630 and CD196, respectively.
Expression values (as RPKM) for Gene Tracks were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench. For cross-comparison between strain a 'consensus genome' was generated by BLASTing every CD630 gene agains each CD196 gene and generating a gene track of the resulting consensus sequences.
Comparison of samples was performed using the "Differential Expression in Two Groups" function in CLC Genomics Workbench
Output was exported to MS Excel and manually curated if neccesary

molecule: total RNA

organism: Bacillus anthracis

source_name: Bacterial cells, pelleted

growth_protocol: Bacteria were grown in BHIS medium at 37°C anaerobically or with 1.5% oxygen

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit. DNA was removed by treatment with Invitrogen  TURBO Dna-free kit and rRNA was depleted using the Invitrogen RiboMinus Transcriptome Isolation kit (bacteria) and the RiboMinus Concentration Module
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina

treatment_protocol: Samples were stored at -80°C prior to RNA extraction

tag: strain

value: Sterne

tag: genotype

value: {delta}krrA

tag: growth media

value: LB

tag: atomosphere

value: aerobic

tag: growth temperature


title: MSC rep2

country: Japan

organism: Homo sapiens

source_name: MSC derived from iPSC

tag: cell type

value: MSC


title: iPSC rep2


title: MSC rep1


title: Donor2 PD146a L2

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description:
Activated T cells
Total RNA

data_processing:
Quality control with Fastqc
Trimming overrepresented sequences with cutadapt
Mapping to human genome assembly GRCh37 - hg19
Counts generation by feature counts
DE analysis DESeq2
Genome_build: GRCh37 - hg19

source_name: CD4+ human total memory

extract_protocol: Extraction was performed using TRI reagent RT by MRC directly on agarose-streptavidin beads, followed by RNA column purification with Zymo spin kit from Zymo research.

tag: experimental

value: miR-146a pulldown

tag: activation state

value: day 5 post-activation

value: Primary T cells


title: AEC-ON 3D

city: Los Angeles

first: Evelyn

last: Tran

state: CA

address: 1441 Eastlake Ave

department: Biochemistry/Surgery

institute: University of Southern California

data_processing:
Raw data from each sample (2D and 3D) were processed using the CellRanger function cellranger count (10x Genomics, v3.1.0, default settings) to align to the human genome (hg19, 10x Genomics, v1.2.0).
Data from each sample were then aggregated using the CellRanger pipeline (10x Genomics, v3.1.0, cellranger aggr function, default settings).
Pre-processed outputs (barcodes.tsv, features.tsv, matrix.mtx) were analyzed in R using the Seurat package (R, v3.6.0). Cells with less than 500 transcripts profiled and more than 18% of their transcriptome of mitochondrial origin were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file (.tsv) of detected cellular barcodes for 2D and 3D aggregated data
Supplementary_files_format_and_content: Tab-delimited file (.tsv) of gene names for 2D and 3D aggregated data
Supplementary_files_format_and_content: Matrix of UMIs associated with features (genes) and barcodes

source_name: Lung

growth_protocol: For the 2D sample, AEC-ON cells were grown in media containing Y-27632 on standard tissue culture dishes. For the 3D sample, AEC-ON cells were grown in Transwell organotypic culture with mouse MLg lung fibroblasts for 2 months in basal media containing SB-431542. Full details on growth conditions can be found in Materials and Methods.

extract_protocol:
AEC-ON cells grown in 2D and 3D were processed in parallel. Cells grown to about 80% confluence in 2D were detached with Accutase at room temperature, collected in growth media, centrifuged, resuspended, and counted manually using a hemacytometer. In parallel, AEC-ON organoids were released from Matrigel in three rounds of Dispase treatment at 37°C followed by centrifugation. The initial release of organoids and subsequent disaggregation into a single-cell suspension was monitored by visual inspection. The final single-cell suspension was then counted manually with a hemacytometer. Both 2D and 3D cell suspensions were FACS sorted for GFP+ SV40 LgT-transduced epithelial cells. Samples were then prepared as recommended by the 10x Genomics user manual.
Libraries were constructed according to recommended user guidelines for the 10x Genomics Chromium Single Cell 3' GEM, Library, & Bead kit v3 (PN-1000092).

treatment_protocol: No treatment

value: AEC line

tag: tissue donor

value: Donor Lung-ON

tag: culture type

value: 3D organoids


title: WT 205-3

description:
WT 205
5425-HP-48

value: Wild-type


title: DM RPTECs_mRNA

city: Kaohsiung

first: Yi-Chun

last: Tsai

address: No.100 , Tzyou 1st Road

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
For small RNA sequencing:
Sequencing data was processed with the Illumina software
Initially, the sequences generated went through a filtering process to obtain qualified reads. Trimmomatic was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using miRDeep2 to clip the 3' adapter sequence and discarding reads shorter than 17 nucleotides
Only reads that mapped perfectly to the human genome five or less times were used for miRNA detection
Supplementary_files_format_and_content: excel files include miRNA, raw read counts and normalized values for samples 1 and 2.

source_name: renal proximal tubular epithelial cells

growth_protocol: RPTECs were grown under normoxia and hypoxia conditions and maintained in 37 °C incubator containing 5% CO2 until confluence.

extract_protocol:
total RNAs from RPTECs were extracted by Trizol Reagent according to the manufacturer’s instructions.
Small RNA/mRNA library construction and deep sequencing was carried out using Illumina sample preparation kit, according to the TruSeq Small RNA Sample Preparation Guide.

tag: tissue

value: Kidney

value: renal proximal tubular epithelial cells


title: Donor3 PDCTRL

description:
Activated T cells
Total RNA

value: control pulldown


title: Donor2 PD146a L1

description:
Activated T cells
Total RNA


title: Donor1 PD146a L2

description:
Activated T cells
Total RNA


title: WT 205-2

description:
WT 205
5425-HP-47


title: normal individual RPTECs_miRNA


title: Donor1 PD146a L1

description:
Activated T cells
Total RNA


title: Donor1 PDCTRL L2

description:
Activated T cells
Total RNA

value: control


title: Donor2 Input CTRL

description:
Activated T cells
Total RNA

value: control input


title: LnCaP_Scr_Control Sample_Replicate1

city: Helsinki

first: Harri

last: Itkonen

address: Room B125b / B129b

department: Department of Biochemistry and Developmental Biology

country: Finland

institute: University of Helsinki

description: LnCaP_Scr_Control Sample_Replicate1

data_processing:
Two biological replicates of each condition were used for the assay
Samples were multiplexed and paired-end sequenced with 150bp read length
Sequencing reads were aligned to Hg19 (GRCh37) using STAR
Raw counts of reads were mapped to genes using HTSeq counts
Normalised counts were generated using DESeq2
Genome_build: Genome_build: Hg19 (GRCh37)
Supplementary_files_format_and_content: normalied counts for each condition (title).  Txt tab-limited format.  Ensembl gene ids.
Supplementary_files_format_and_content: raw counts for each condition (title).  Txt tab-limited format.  Ensembl gene ids.

source_name: LnCaP

extract_protocol:
RNA was isolated with Illustra RNAspin Minikit (GE healthcare, cat num. 25-0500-72)
Libraries for sequencing were prepared by the Norwegian High Throughput Sequencing Centre using Strand-specific TruSeq RNA-seq library prep kit

treatment_protocol: Knockdown of OGT for 48 hours and treated with either DMSO or CDK inhibitor (0.5μM AT7519) for 4 hours prior to harvesting

tag: cell line

value: LnCaP

tag: sirna

value: Scr

tag: agent

value: DMSO


title: WT vehicle3

description:
WT vehicle
5425-HP-39

value: Sterne

value: LB

value: aerobic


title: Donor3 Input 150

description:
Activated T cells
Total RNA

value: miR-150 input

value: day 5 post-activation


title: High Fat High Sugar Diet 3

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to the Mesocricetus auratus genome assembly version 1.0 using Hisat2 (Kim et al., 2015)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2  (Love et al., 2014)
Genome_build: Mesocricetus auratus genome assembly version 1.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mesocricetus auratus

source_name: liver

extract_protocol:
RNA was collected from each sample and passed through Qiashredder column (Qiagen) at 21,000 x g for 2 min to homogenize any remaining genomic DNA in the aqueous phase. Aqueous phase was combined with 600 µL of RLT lysis buffer (Qiagen, Valencia, CA) with 1% beta mercaptoethanol (MilliporeSigma) and RNA was extracted using Qiagen AllPrep DNA/RNA 96-well system.
One hundred nanograms of RNA was used as input for rRNA depletion and NGS library preparation following the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus workflow (Illumina)

treatment_protocol: Four to six-week-old male Syrian Golden hamsters (ENVIGO) were randomly assigned to either regular rodent chow (Teklad Global 16% Protein Rodent Diet, Envigo) or a HFHS diet for 16 weeks (Purina Chow #5001 with 11.5% Corn Oil, 11.5% Coconut Oil, 0.5% Cholesterol, 0.25% Deoxycholic Acid, and 10% Fructose: Dyets Inc., Dyet#615088)

tag: age


title: SKOV3_PDE10Ako_5H5_UnTx

city: Mobile

first: Lucian

last: Madeira da Silva

state: AL

address: 1660 Springhill Ave

department: Mitchell Cancer Institute

institute: University of South Alabama

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence files were aligned with STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.11.3 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization of transcript abundances and fold change calculations were calculated using DESeq2 version 1.26.0 following their vignette (default settings)
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: SKOV3 PDE10A knockout clone 5H5 (KO 5H5) cells

growth_protocol: SKOV3 cells were routinely grown in McCoy's growth medium supplemented with 10% fetal bovine serum and penicillin/streptomycin

extract_protocol:
RNA extracted with TRIzol and treated with TURBO DNA-free kit as per manufacturer's instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.  RNA with a RNA Integrity Number (RIN) of ≥7.0 was used for sequencing library preparation.
RNA passing quality control was converted to a sequencing ready library using the NEBNext Ultra II Directional RNA library kit as per the manufacturer’s instructions (NEB, Ipswich, MA). The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturers recommendations for onboard clustering (Illumina, San Diego, CA).  We generated between 30-35 million paired end 75bp sequencing reads per sample for transcript level abundance.

treatment_protocol: two biological replicates RNA collected from untreated cells (two distinct tissue culture passages)

value: ovarian cancer cells

tag: pde10a status

value: PDE10A knockout cells


title: SKOV3_PDE10Ako_2F4

source_name: SKOV3 PDE10A knockout clone 2F4 (2F4) cells


title: krrA vehicle2

description:
krrA vehicle
5425-HP-41

value: {delta}krrA


title: High Fat High Sugar Diet 1

value: Four to six-week-old male Syrian Golden hamster


title: 3-JQ1 [3_J]

city: Hamburg

first: Nicola

last: Wanner

address: Martinistr

country: Germany

institute: UKE Hamburg-Eppendorf

description: bulk RNA-seq

data_processing:
Quality control was done with FastQC (Barbraham Bioinformatics). Raw reads were trimmed using TrimGalore! (Barbraham Bioinformatics) and mapped with RNA Star to mm9 using Galaxy Freiburg.
Read counts extracted with htseq-count.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene from every sample

organism: Mus musculus

source_name: kidney

growth_protocol: E12.5 embryonic kidneys were grown in DMEM medium with 10% fetal bovine serum, 100 µg/ml of penicillin, 100µg/ml of streptomycin.

extract_protocol:
Total RNA of kidney cultures was isolated using the Qiagen RNeasy Micro Kit
All steps were performed according to standard protocol of Ilumina/BGI library preparation.
RNA sequencing was performed by GATC, Germany (single-end) or BGI, Hongkong (paired-end)

treatment_protocol: Cultures were treated for 24 h with either DMSO or JQ1.

value: kidney cultures

tag: time point

tag: treatment

tag: strain background


title: AEC-TN

data_processing:
Raw fastq files were imported to Partek Flow using the USC High Performance Computing Commons (HPCC) through the USC Norris Medical Library Bioinformatics Core. Partek Flow was used to process RNA-seq data to obtain raw gene counts.
Unaligned reads were imported to Partek Flow. Pre-alignment QA/QC was performed. Bases were trimmed from both ends using the "Trim bases" option, remaining settings were default.
Trimmed reads were then aligned to the human genome using STAR aligner (v2.6.1d): Homo sapiens - hg 38, GENCODE Genes - release 29.
Aligned reads were assessed for quality using the "Post-alignment QA/QC" option. Aligned reads were quantified to the transcriptome using the annotation model "Partek E/M" and genome version hg38 - GENCODE Genes - release 29  on default settings.
Raw gene counts were saved and imported to R (v3.6.0 "Planting of a Tree") for normalization (default settings) and differential gene expression analyses (LFC shrinkage type 'Normal') using DESeq2.
Genome_build: Homo sapiens, GENCODE Genes, hg38, version 29
Supplementary_files_format_and_content: Matrix table of raw gene counts generated by Partek Flow which were then converted to whole integers to use in DESeq2
Supplementary_files_format_and_content: csv file of FPKM values normalized by Partek Flow

growth_protocol: AEC lines were maintained on standard tissue culture dishes in media containing ROCK inhibitor Y-27632. Cells were passaged and re-plated up to Passage 10 when, at subconfluence, cell lines were collected for total RNA extraction. The fibroblast line HLF-133 was briefly cultured on plastic in DMEM plus 10% FBS medium before harvesting. Primary AT2 cells purified from donor lung tissue were collected for RNA extraction immediately after purification. Primary AT2:AT1 intermediate and AT1-like cells resulting from transdifferentiation of purified AT2 cells on Transwell filters were collected after 2, 4, and 6 days in culture.

extract_protocol:
Total RNA was extracted and purified using the Illustra TriplePrep kit (GE Healthcare 28-9425-44)
Purified total RNA was submitted to the USC Molecular Genomics Core facility for library preparation and sequencing. RNA quality was assessed on the Bioanalyzer (Agilent) then rRNA-depleted using Ribo-Zero rRNA Removal kit for human samples (Illumina MRZH11124) before proceeding with library preparation (TruSeq mRNA Stranded Library preparation kit, Illumina 20020594).

treatment_protocol: No treatments.

value: alveolar epithelial cell (AEC) line

tag: source tissue/donor

value: Donor Lung-TN


title: Donor2 PD150

description:
Activated T cells
Total RNA

value: miR-150 pulldown

value: Primary T cells


title: AEC-ON 2D

value: AEC line

value: Donor Lung-ON

value: 2D monolayer


title: Donor3 PD150

description:
Activated T cells
Total RNA


title: Regular Diet 4


title: krrA vehicle1

description:
krrA vehicle
5425-HP-40

tag: strain

value: Sterne

tag: genotype

tag: growth media

tag: atomosphere


title: 2-JQ1 [2_J]

description: bulk RNA-seq


title: SKOV3_PDE10Ako_2F4_UnTx

tag: cell type


title: High Fat High Sugar Diet 4


title: AEC-ON


title: Donor2 PDCTRL

description:
Activated T cells
Total RNA

tag: experimental

value: control pulldown

tag: activation state


title: Donor2 Input 150

description:
Activated T cells
Total RNA


title: WT vehicle1

description:
WT vehicle
5425-HP-37

value: Wild-type

value: LB

value: aerobic

tag: growth temperature


title: 2-DMSO [2_D]

description: bulk RNA-seq

tag: tissue

value: DMSO


title: WT vehicle2

description:
WT vehicle
5425-HP-38


title: SKOV3_EV1B9

source_name: SKOV3 empty vector clone 1B9 (EV 1B9) cells

value: ovarian cancer cells

value: empty vector control cells

tag: cell line


title: Donor1 Input 150

description:
Activated T cells
Total RNA

value: miR-150 input

value: day 5 post-activation


title: Donor1 PDCTRL

description:
Activated T cells
Total RNA


title: 3-DMSO [3_D]

description: bulk RNA-seq

value: kidney cultures


title: Donor1 Input CTRL

description:
Activated T cells
Total RNA

value: control input


title: Regular Diet 5

value: Four to six-week-old male Syrian Golden hamster


title: Donor1 PD150

description:
Activated T cells
Total RNA

value: miR-150 pulldown

value: Primary T cells


title: SKOV3_EV1B9_UnTx


title: Regular Diet 1


title: SKOV3_PDE10Ako_5H5

value: PDE10A knockout cells


title: SKOV3_P_UnTx

source_name: SKOV3 cells

value: parental cells


title: 1-JQ1 [1_J]

description: bulk RNA-seq


title: 1-DMSO [1_D]

description: bulk RNA-seq


title: SKOV3_P


title: High Fat High Sugar Diet 2


title: Hypothalamus309935

status: Public on Jan 09 2022

city: Hangzhou

first: Xin

last: Shao

state: Zhejiang

address: #866 Yuhangtang Rd.

country: China

institute: Zhejiang University

data_processing:
The raw sequencing data from Illumina® Xten were aligned and quantified using the FastQC (version 0.11.5) and Drop-seq Alignment Cookbook (version 2.0.0). The mouse genome mm10 was used as the reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: Brain

extract_protocol:
Hypothalamus region of the mouse brain was isolated by laser capture microdissection (LCM) and collected in 96-well plate containing barcoded magnetic beads. The tissue was lysed in the well, allowing mRNA to be captured by oligonucleotides on the surface of the magnetic beads. In detail, each well was loaded with 50 μL 2X lysis buffer (Tris-HCl(pH7.5) 120 μL, LiCl 80 μL, 10% SDS 120 μL, EDTA 16 μL, 500 mM DTT 12 μL, DNase and RNase-free water 852 μL). The tissue was lysed on ice for 12 minutes. The beads were washed with 6X SSC (Invitrogen, Cat#AM9770) and then the suspension was transfered to 1.5 mL centrifugal tube. The supernatant was removed. The beads were re-suspended with 500 μL 6X SSC, and the supernatant was removed after centrifugation. The beads were re-suspended with 300 μL 50 mM Tris(pH8.0, Beyotime Biotec., Cat#ST780) and then remove the supernatant. The beads were re-suspended with 20 μL RT Mix(DNase and RNase-free water 16.16 μL， 5X Superscript II first-strand buffer 8 μL, betaine (Sigma, Cat#B0300) 8 μL, 10 mM dNTPs 4 μL, DTT (Beyotime Biotec., Cat#ST041) 0.2 μL, MgCl2 (Invitrogen, Cat#AM9530G) 0.24 μL, 50 μM TSO primer 0.4 μL, PrimeScript II Reverse Transcriptase (Takara, Cat#2690A) 2 μL, and RNase Inhibitor 1 μL). The captured mRNA underwent reverse transcription (RT) at 42 ℃ for 90 min. Remove supernatant after centrifugation. The beads were washed with 200 μL TE-SDS (10% SDS and TE(pH8.0, Invitrogen, Cat#AM9849)), 200 μL TE-TW (10% Tween-20 (Sigma, Cat#P7949) and TE(PH8.0)), and 200 μL 10 mM Tris (pH8.0) in turn and remove the supernatant. The beads were re-suspended with 200 μL exonuclease mix (DNase and RNase-free water 170 μL, 10X Exol Buffer 20 μL, and Exol (Annoron, Cat#M0293L) 10 μL) and then incubated at 37 ℃ for 60 min. The beads were washed with 200 μL TE-SDS, 200 μL TE-TW and 200 μL 10 mM Tris (pH8.0) in turn and remove the supernatant.
Beads were distributed to 4 tubes. To every tube, 12.5 μL of PCR mix was added, which included 2X HiFi HotStart Readymix (Kapa Biosystems) and 0.5 μL 10 μM TSO-PCR primer. The PCR program was as follows: 98 ℃ for 3 min; 6 cycles of 98 ℃ 20 s, 65 ℃ 45 s, and 72 ℃ 6 min; 72 ℃  10 min and 4 ℃ hold. After pooling all PCR products, AMPure XP beads (Beckman Coulter) were used to purify the cDNA library. cDNA library was prepared following the guidance of Illumina Nextera XT DNA Library Preparation Kits.

tag: direction

value: Sagittal

tag: region

value: Hypothalamus

tag: organ

value: Brain


title: Regular Diet 2

tag: age


title: Regular Diet 3


title: lung biopsy [lung935]

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: in n=635? (yes, no)

value: yes

tag: clad status (clad, no clad, na)

value: CLAD


title: lung biopsy [lung947]


title: lung biopsy [lung949]

value: No CLAD


title: lung biopsy [lung946]


title: lung biopsy [lung939]


title: lung biopsy [lung937]


title: lung biopsy [lung928]


title: lung biopsy [lung940]


title: lung biopsy [lung924]


title: lung biopsy [lung948]


title: lung biopsy [lung933]


title: lung biopsy [lung938]


title: lung biopsy [lung944]


title: lung biopsy [lung932]


title: lung biopsy [lung945]


title: lung biopsy [lung930]


title: lung biopsy [lung934]


title: lung biopsy [lung936]


title: lung biopsy [lung942]


title: lung biopsy [lung927]


title: lung biopsy [lung926]


title: lung biopsy [lung925]


title: lung biopsy [lung929]


title: lung biopsy [lung941]


title: lung biopsy [lung923]


title: lung biopsy [lung931]


title: lung biopsy [lung943]


title: lung biopsy [lung921]


title: lung biopsy [lung920]


title: lung biopsy [lung916]


title: lung biopsy [lung918]


title: lung biopsy [lung906]


title: lung biopsy [lung917]


title: lung biopsy [lung914]


title: lung biopsy [lung922]


title: lung biopsy [lung907]


title: lung biopsy [lung913]


title: lung biopsy [lung904]


title: lung biopsy [lung903]


title: lung biopsy [lung911]


title: lung biopsy [lung910]


title: lung biopsy [lung900]


title: lung biopsy [lung908]


title: lung biopsy [lung909]


title: lung biopsy [lung897]


title: lung biopsy [lung898]


title: lung biopsy [lung896]


title: lung biopsy [lung915]


title: lung biopsy [lung894]


title: lung biopsy [lung901]


title: lung biopsy [lung912]


title: lung biopsy [lung895]


title: lung biopsy [lung919]


title: lung biopsy [lung881]


title: lung biopsy [lung885]


title: lung biopsy [lung905]


title: lung biopsy [lung887]


title: lung biopsy [lung883]


title: lung biopsy [lung878]


title: lung biopsy [lung873]


title: lung biopsy [lung902]


title: lung biopsy [lung899]


title: lung biopsy [lung882]


title: lung biopsy [lung891]


title: lung biopsy [lung888]


title: lung biopsy [lung892]


title: lung biopsy [lung886]


title: lung biopsy [lung884]


title: lung biopsy [lung890]


title: lung biopsy [lung889]


title: lung biopsy [lung893]


title: lung biopsy [lung879]


title: lung biopsy [lung880]


title: lung biopsy [lung876]


title: lung biopsy [lung871]


title: lung biopsy [lung875]


title: lung biopsy [lung877]


title: lung biopsy [lung868]


title: lung biopsy [lung872]


title: lung biopsy [lung867]


title: lung biopsy [lung865]


title: lung biopsy [lung870]


title: lung biopsy [lung874]


title: lung biopsy [lung864]


title: lung biopsy [lung860]


title: lung biopsy [lung854]


title: lung biopsy [lung858]


title: lung biopsy [lung861]


title: lung biopsy [lung866]


title: lung biopsy [lung863]


title: lung biopsy [lung862]


title: lung biopsy [lung857]


title: lung biopsy [lung859]


title: lung biopsy [lung849]


title: lung biopsy [lung855]


title: lung biopsy [lung856]


title: lung biopsy [lung850]


title: lung biopsy [lung851]


title: lung biopsy [lung852]


title: lung biopsy [lung853]


title: lung biopsy [lung847]


title: lung biopsy [lung848]


title: lung biopsy [lung846]


title: lung biopsy [lung844]


title: lung biopsy [lung842]


title: lung biopsy [lung843]


title: lung biopsy [lung840]


title: lung biopsy [lung841]


title: lung biopsy [lung837]


title: lung biopsy [lung845]


title: lung biopsy [lung839]


title: lung biopsy [lung838]


title: lung biopsy [lung836]


title: lung biopsy [lung834]


title: lung biopsy [lung826]


title: lung biopsy [lung835]


title: lung biopsy [lung821]


title: lung biopsy [lung828]


title: lung biopsy [lung818]


title: lung biopsy [lung830]


title: lung biopsy [lung831]


title: lung biopsy [lung820]


title: lung biopsy [lung832]


title: lung biopsy [lung823]


title: lung biopsy [lung827]


title: lung biopsy [lung825]


title: lung biopsy [lung833]


title: lung biopsy [lung822]


title: lung biopsy [lung824]


title: lung biopsy [lung817]


title: lung biopsy [lung829]


title: lung biopsy [lung819]


title: lung biopsy [lung809]


title: lung biopsy [lung808]


title: lung biopsy [lung812]


title: lung biopsy [lung815]


title: lung biopsy [lung816]


title: lung biopsy [lung806]


title: lung biopsy [lung805]


title: lung biopsy [lung813]


title: lung biopsy [lung814]


title: lung biopsy [lung811]


title: lung biopsy [lung810]


title: lung biopsy [lung802]


title: lung biopsy [lung804]


title: lung biopsy [lung801]


title: lung biopsy [lung869]


title: lung biopsy [lung798]


title: lung biopsy [lung795]


title: lung biopsy [lung796]


title: lung biopsy [lung791]


title: lung biopsy [lung789]


title: lung biopsy [lung793]


title: lung biopsy [lung790]


title: lung biopsy [lung788]


title: lung biopsy [lung800]


title: lung biopsy [lung797]


title: lung biopsy [lung807]


title: lung biopsy [lung792]


title: lung biopsy [lung803]


title: lung biopsy [lung787]


title: lung biopsy [lung786]


title: lung biopsy [lung799]


title: lung biopsy [lung784]


title: lung biopsy [lung783]


title: lung biopsy [lung776]


title: lung biopsy [lung777]


title: lung biopsy [lung779]


title: lung biopsy [lung773]


title: lung biopsy [lung772]


title: lung biopsy [lung774]


title: lung biopsy [lung778]


title: lung biopsy [lung775]


title: lung biopsy [lung780]


title: lung biopsy [lung768]

tag: type (3bmb, highsft, lowsft)

value: no


title: lung biopsy [lung766]


title: lung biopsy [lung771]


title: lung biopsy [lung762]


title: lung biopsy [lung767]


title: lung biopsy [lung754]


title: lung biopsy [lung781]


title: lung biopsy [lung761]


title: lung biopsy [lung753]


title: lung biopsy [lung750]


title: lung biopsy [lung769]


title: lung biopsy [lung752]


title: lung biopsy [lung759]


title: lung biopsy [lung746]


title: lung biopsy [lung785]


title: lung biopsy [lung749]


title: lung biopsy [lung782]


title: lung biopsy [lung730]


title: lung biopsy [lung735]


title: lung biopsy [lung729]


title: lung biopsy [lung724]


title: lung biopsy [lung721]


title: lung biopsy [lung725]


title: lung biopsy [lung718]


title: lung biopsy [lung703]


title: lung biopsy [lung717]


title: lung biopsy [lung715]


title: lung biopsy [lung706]


title: lung biopsy [lung691]


title: lung biopsy [lung704]


title: lung biopsy [lung697]


title: lung biopsy [lung732]


title: lung biopsy [lung722]


title: lung biopsy [lung720]


title: lung biopsy [lung693]


title: lung biopsy [lung690]


title: lung biopsy [lung716]


title: lung biopsy [lung689]


title: lung biopsy [lung679]


title: lung biopsy [lung688]


title: lung biopsy [lung707]


title: lung biopsy [lung687]


title: lung biopsy [lung676]


title: lung biopsy [lung681]


title: lung biopsy [lung670]


title: lung biopsy [lung667]


title: lung biopsy [lung678]


title: lung biopsy [lung760]


title: lung biopsy [lung666]


title: lung biopsy [lung668]


title: lung biopsy [lung662]


title: lung biopsy [lung664]


title: lung biopsy [lung655]


title: lung biopsy [lung651]


title: lung biopsy [lung658]


title: lung biopsy [lung645]


title: lung biopsy [lung656]


title: lung biopsy [lung650]


title: lung biopsy [lung640]


title: lung biopsy [lung634]


title: lung biopsy [lung639]


title: lung biopsy [lung632]


title: lung biopsy [lung631]


title: lung biopsy [lung630]


title: lung biopsy [lung794]


title: lung biopsy [lung627]


title: lung biopsy [lung621]


title: lung biopsy [lung617]


title: lung biopsy [lung619]


title: lung biopsy [lung613]


title: lung biopsy [lung614]


title: lung biopsy [lung610]


title: lung biopsy [lung612]


title: lung biopsy [lung599]


title: lung biopsy [lung611]


title: lung biopsy [lung602]


title: lung biopsy [lung597]


title: lung biopsy [lung586]


title: lung biopsy [lung584]


title: lung biopsy [lung594]


title: lung biopsy [lung580]


title: lung biopsy [lung590]


title: lung biopsy [lung582]


title: lung biopsy [lung561]


title: lung biopsy [lung570]


title: lung biopsy [lung564]


title: lung biopsy [lung560]


title: lung biopsy [lung552]


title: lung biopsy [lung555]


title: lung biopsy [lung609]


title: lung biopsy [lung579]


title: lung biopsy [lung577]


title: lung biopsy [lung569]


title: lung biopsy [lung551]


title: lung biopsy [lung740]


title: lung biopsy [lung536]


title: lung biopsy [lung534]


title: lung biopsy [lung574]


title: lung biopsy [lung529]


title: lung biopsy [lung533]


title: lung biopsy [lung528]


title: lung biopsy [lung527]


title: lung biopsy [lung506]


title: lung biopsy [lung517]


title: lung biopsy [lung516]


title: lung biopsy [lung508]


title: lung biopsy [lung514]


title: lung biopsy [lung522]


title: lung biopsy [lung515]


title: lung biopsy [lung503]


title: lung biopsy [lung476]


title: lung biopsy [lung468]


title: lung biopsy [lung494]


title: lung biopsy [lung491]


title: lung biopsy [lung513]


title: lung biopsy [lung500]


title: lung biopsy [lung496]


title: lung biopsy [lung469]


title: lung biopsy [lung487]


title: lung biopsy [lung460]


title: lung biopsy [lung459]


title: lung biopsy [lung461]


title: lung biopsy [lung484]


title: lung biopsy [lung475]


title: lung biopsy [lung458]


title: lung biopsy [lung490]


title: lung biopsy [lung451]


title: lung biopsy [lung478]


title: lung biopsy [lung450]


title: lung biopsy [lung454]


title: lung biopsy [lung447]


title: lung biopsy [lung444]


title: lung biopsy [lung439]


title: lung biopsy [lung437]


title: lung biopsy [lung443]


title: lung biopsy [lung446]


title: lung biopsy [lung445]


title: lung biopsy [lung448]


title: lung biopsy [lung421]


title: lung biopsy [lung426]


title: lung biopsy [lung395]


title: lung biopsy [lung403]


title: lung biopsy [lung424]


title: lung biopsy [lung388]


title: lung biopsy [lung427]


title: lung biopsy [lung401]


title: lung biopsy [lung436]


title: lung biopsy [lung431]


title: lung biopsy [lung416]


title: lung biopsy [lung415]


title: lung biopsy [lung429]


title: lung biopsy [lung417]


title: lung biopsy [lung423]


title: lung biopsy [lung433]


title: lung biopsy [lung409]


title: lung biopsy [lung385]


title: lung biopsy [lung391]


title: lung biopsy [lung368]


title: lung biopsy [lung361]


title: lung biopsy [lung382]


title: lung biopsy [lung381]


title: lung biopsy [lung379]


title: lung biopsy [lung376]


title: lung biopsy [lung357]


title: lung biopsy [lung418]


title: lung biopsy [lung372]


title: lung biopsy [lung364]


title: lung biopsy [lung365]


title: lung biopsy [lung348]


title: lung biopsy [lung345]


title: lung biopsy [lung347]


title: lung biopsy [lung344]


title: lung biopsy [lung369]


title: lung biopsy [lung356]


title: lung biopsy [lung329]


title: lung biopsy [lung321]


title: lung biopsy [lung323]


title: lung biopsy [lung326]


title: lung biopsy [lung302]


title: lung biopsy [lung297]


title: lung biopsy [lung295]


title: lung biopsy [lung309]


title: lung biopsy [lung330]


title: lung biopsy [lung340]


title: lung biopsy [lung327]


title: lung biopsy [lung296]


title: lung biopsy [lung293]


title: lung biopsy [lung279]


title: lung biopsy [lung331]


title: lung biopsy [lung290]


title: lung biopsy [lung281]


title: lung biopsy [lung271]


title: lung biopsy [lung273]


title: lung biopsy [lung276]


title: lung biopsy [lung284]


title: lung biopsy [lung287]


title: lung biopsy [lung267]


title: lung biopsy [lung268]


title: lung biopsy [lung262]


title: lung biopsy [lung254]


title: lung biopsy [lung257]


title: lung biopsy [lung250]


title: lung biopsy [lung253]


title: lung biopsy [lung266]


title: lung biopsy [lung245]


title: lung biopsy [lung260]


title: lung biopsy [lung270]


title: lung biopsy [lung241]


title: lung biopsy [lung237]


title: lung biopsy [lung282]


title: lung biopsy [lung235]


title: lung biopsy [lung242]


title: lung biopsy [lung236]


title: lung biopsy [lung255]


title: lung biopsy [lung223]


title: lung biopsy [lung232]


title: lung biopsy [lung228]


title: lung biopsy [lung227]


title: lung biopsy [lung231]


title: lung biopsy [lung224]


title: lung biopsy [lung222]


title: lung biopsy [lung205]


title: lung biopsy [lung214]


title: lung biopsy [lung234]


title: lung biopsy [lung215]


title: lung biopsy [lung206]


title: lung biopsy [lung212]


title: lung biopsy [lung233]


title: lung biopsy [lung197]


title: lung biopsy [lung198]


title: lung biopsy [lung213]


title: lung biopsy [lung193]


title: lung biopsy [lung183]


title: lung biopsy [lung192]


title: lung biopsy [lung199]


title: lung biopsy [lung190]


title: lung biopsy [lung189]


title: lung biopsy [lung354]


title: lung biopsy [lung180]


title: lung biopsy [lung156]


title: lung biopsy [lung178]


title: lung biopsy [lung172]


title: lung biopsy [lung179]


title: lung biopsy [lung169]


title: lung biopsy [lung175]


title: lung biopsy [lung140]


title: lung biopsy [lung144]


title: lung biopsy [lung141]


title: lung biopsy [lung154]


title: lung biopsy [lung133]


title: lung biopsy [lung171]


title: lung biopsy [lung134]


title: lung biopsy [lung176]


title: lung biopsy [lung136]


title: lung biopsy [lung170]


title: lung biopsy [lung126]


title: lung biopsy [lung129]


title: lung biopsy [lung121]


title: lung biopsy [lung120]


title: lung biopsy [lung122]


title: lung biopsy [lung118]


title: lung biopsy [lung316]


title: lung biopsy [lung137]


title: lung biopsy [lung165]


title: lung biopsy [lung116]


title: lung biopsy [lung117]


title: lung biopsy [lung131]


title: lung biopsy [lung135]


title: lung biopsy [lung108]


title: lung biopsy [lung86]


title: lung biopsy [lung109]


title: lung biopsy [lung103]


title: lung biopsy [lung97]


title: lung biopsy [lung91]


title: lung biopsy [lung114]


title: lung biopsy [lung92]


title: lung biopsy [lung104]


title: lung biopsy [lung95]


title: lung biopsy [lung107]


title: lung biopsy [lung79]


title: lung biopsy [lung84]


title: lung biopsy [lung82]


title: lung biopsy [lung83]


title: lung biopsy [lung75]


title: lung biopsy [lung65]


title: lung biopsy [lung62]


title: lung biopsy [lung66]


title: lung biopsy [lung99]


title: lung biopsy [lung81]


title: lung biopsy [lung53]


title: lung biopsy [lung98]


title: lung biopsy [lung52]


title: lung biopsy [lung63]


title: lung biopsy [lung58]


title: lung biopsy [lung71]


title: lung biopsy [lung188]


title: lung biopsy [lung40]


title: lung biopsy [lung47]


title: lung biopsy [lung59]


title: lung biopsy [lung41]


title: lung biopsy [lung36]


title: lung biopsy [lung27]


title: lung biopsy [lung30]


title: lung biopsy [lung25]


title: lung biopsy [lung18]


title: lung biopsy [lung17]


title: lung biopsy [lung22]


title: lung biopsy [lung48]


title: lung biopsy [lung19]


title: lung biopsy [lung669]

value: highSFT


title: lung biopsy [lung11]


title: lung biopsy [lung1]


title: lung biopsy [lung68]

value: lowSFT


title: lung biopsy [lung35]


title: lung biopsy [lung14]


title: lung biopsy [lung625]


title: lung biopsy [lung159]


title: lung biopsy [lung745]


title: lung biopsy [lung455]


title: lung biopsy [lung3]


title: lung biopsy [lung31]


title: lung biopsy [lung187]


title: lung biopsy [lung61]


title: lung biopsy [lung677]


title: lung biopsy [lung203]


title: lung biopsy [lung161]


title: lung biopsy [lung23]


title: lung biopsy [lung588]


title: lung biopsy [lung6]


title: lung biopsy [lung20]


title: lung biopsy [lung425]


title: lung biopsy [lung633]


title: lung biopsy [lung102]


title: lung biopsy [lung692]


title: lung biopsy [lung57]


title: lung biopsy [lung64]


title: lung biopsy [lung581]


title: lung biopsy [lung93]


title: lung biopsy [lung219]


title: lung biopsy [lung218]


title: lung biopsy [lung541]


title: lung biopsy [lung605]


title: lung biopsy [lung339]


title: lung biopsy [lung432]


title: lung biopsy [lung181]


title: lung biopsy [lung393]


title: lung biopsy [lung288]


title: lung biopsy [lung519]


title: lung biopsy [lung38]


title: lung biopsy [lung463]


title: lung biopsy [lung143]


title: lung biopsy [lung338]


title: lung biopsy [lung550]


title: lung biopsy [lung367]


title: lung biopsy [lung457]


title: lung biopsy [lung34]


title: lung biopsy [lung510]


title: lung biopsy [lung558]


title: lung biopsy [lung644]


title: lung biopsy [lung322]


title: lung biopsy [lung147]


title: lung biopsy [lung39]


title: lung biopsy [lung200]


title: lung biopsy [lung452]


title: lung biopsy [lung653]


title: lung biopsy [lung483]


title: lung biopsy [lung757]


title: lung biopsy [lung764]


title: lung biopsy [lung643]


title: lung biopsy [lung149]


title: lung biopsy [lung111]


title: lung biopsy [lung464]


title: lung biopsy [lung701]


title: lung biopsy [lung67]


title: lung biopsy [lung489]


title: lung biopsy [lung333]


title: lung biopsy [lung719]


title: lung biopsy [lung589]


title: lung biopsy [lung392]


title: lung biopsy [lung646]


title: lung biopsy [lung414]


title: lung biopsy [lung130]


title: lung biopsy [lung435]


title: lung biopsy [lung350]


title: lung biopsy [lung485]


title: lung biopsy [lung438]


title: lung biopsy [lung332]


title: lung biopsy [lung230]


title: lung biopsy [lung248]


title: lung biopsy [lung758]


title: lung biopsy [lung694]


title: lung biopsy [lung313]


title: lung biopsy [lung616]


title: lung biopsy [lung537]


title: lung biopsy [lung741]


title: lung biopsy [lung380]


title: lung biopsy [lung56]


title: lung biopsy [lung636]


title: lung biopsy [lung441]


title: lung biopsy [lung683]


title: lung biopsy [lung737]


title: lung biopsy [lung371]


title: lung biopsy [lung105]


title: lung biopsy [lung60]


title: lung biopsy [lung221]


title: lung biopsy [lung578]


title: lung biopsy [lung572]


title: lung biopsy [lung486]


title: lung biopsy [lung412]


title: lung biopsy [lung479]


title: lung biopsy [lung360]


title: lung biopsy [lung474]


title: lung biopsy [lung398]


title: lung biopsy [lung168]


title: lung biopsy [lung320]


title: lung biopsy [lung556]


title: lung biopsy [lung261]


title: lung biopsy [lung269]


title: lung biopsy [lung726]


title: lung biopsy [lung127]


title: lung biopsy [lung70]


title: lung biopsy [lung709]


title: lung biopsy [lung148]


title: lung biopsy [lung265]


title: lung biopsy [lung319]


title: lung biopsy [lung49]


title: lung biopsy [lung46]


title: lung biopsy [lung289]


title: lung biopsy [lung324]


title: lung biopsy [lung160]


title: lung biopsy [lung635]


title: lung biopsy [lung705]


title: lung biopsy [lung731]


title: lung biopsy [lung132]


title: lung biopsy [lung283]


title: lung biopsy [lung744]


title: lung biopsy [lung411]


title: lung biopsy [lung509]


title: lung biopsy [lung263]


title: lung biopsy [lung101]


title: lung biopsy [lung249]


title: lung biopsy [lung652]


title: lung biopsy [lung396]


title: lung biopsy [lung355]


title: lung biopsy [lung654]


title: lung biopsy [lung337]


title: lung biopsy [lung521]


title: lung biopsy [lung13]


title: lung biopsy [lung698]


title: lung biopsy [lung539]


title: lung biopsy [lung85]


title: lung biopsy [lung374]


title: lung biopsy [lung592]


title: lung biopsy [lung549]


title: lung biopsy [lung73]


title: lung biopsy [lung343]


title: lung biopsy [lung80]


title: lung biopsy [lung428]


title: lung biopsy [lung256]


title: lung biopsy [lung119]


title: lung biopsy [lung739]


title: lung biopsy [lung713]


title: lung biopsy [lung736]


title: lung biopsy [lung624]


title: lung biopsy [lung466]


title: lung biopsy [lung504]


title: lung biopsy [lung708]


title: lung biopsy [lung89]


title: lung biopsy [lung264]


title: lung biopsy [lung373]


title: lung biopsy [lung157]


title: lung biopsy [lung294]


title: lung biopsy [lung700]


title: lung biopsy [lung113]


title: lung biopsy [lung649]


title: lung biopsy [lung638]


title: lung biopsy [lung5]


title: lung biopsy [lung473]


title: lung biopsy [lung246]


title: lung biopsy [lung69]


title: lung biopsy [lung377]


title: lung biopsy [lung742]


title: lung biopsy [lung112]


title: lung biopsy [lung42]


title: lung biopsy [lung587]


title: lung biopsy [lung512]


title: lung biopsy [lung648]


title: lung biopsy [lung4]


title: lung biopsy [lung453]


title: lung biopsy [lung647]


title: lung biopsy [lung598]


title: lung biopsy [lung45]


title: lung biopsy [lung315]


title: lung biopsy [lung226]


title: lung biopsy [lung151]


title: lung biopsy [lung50]


title: lung biopsy [lung155]


title: lung biopsy [lung363]


title: lung biopsy [lung604]


title: lung biopsy [lung728]


title: lung biopsy [lung477]


title: lung biopsy [lung680]


title: lung biopsy [lung554]


title: lung biopsy [lung349]


title: lung biopsy [lung568]


title: lung biopsy [lung29]


title: lung biopsy [lung208]


title: lung biopsy [lung481]


title: lung biopsy [lung32]


title: lung biopsy [lung77]


title: lung biopsy [lung278]


title: lung biopsy [lung511]


title: lung biopsy [lung449]


title: lung biopsy [lung467]


title: lung biopsy [lung275]


title: lung biopsy [lung684]


title: lung biopsy [lung532]


title: lung biopsy [lung618]


title: lung biopsy [lung72]


title: lung biopsy [lung488]


title: lung biopsy [lung472]


title: lung biopsy [lung659]


title: lung biopsy [lung607]


title: lung biopsy [lung600]


title: lung biopsy [lung573]


title: lung biopsy [lung765]


title: lung biopsy [lung370]


title: lung biopsy [lung299]


title: lung biopsy [lung493]


title: lung biopsy [lung177]


title: lung biopsy [lung359]


title: lung biopsy [lung158]


title: lung biopsy [lung525]


title: lung biopsy [lung620]


title: lung biopsy [lung378]


title: lung biopsy [lung204]


title: lung biopsy [lung576]


title: lung biopsy [lung723]


title: lung biopsy [lung142]


title: lung biopsy [lung346]


title: lung biopsy [lung44]


title: lung biopsy [lung259]


title: lung biopsy [lung7]


title: lung biopsy [lung562]


title: lung biopsy [lung755]


title: lung biopsy [lung240]


title: lung biopsy [lung78]


title: lung biopsy [lung115]


title: lung biopsy [lung456]


title: lung biopsy [lung163]


title: lung biopsy [lung128]


title: lung biopsy [lung43]


title: lung biopsy [lung675]


title: lung biopsy [lung763]


title: lung biopsy [lung252]


title: lung biopsy [lung272]


title: lung biopsy [lung542]


title: lung biopsy [lung747]


title: lung biopsy [lung399]


title: lung biopsy [lung220]


title: lung biopsy [lung734]


title: lung biopsy [lung559]


title: lung biopsy [lung505]


title: lung biopsy [lung756]


title: lung biopsy [lung543]


title: lung biopsy [lung661]


title: lung biopsy [lung406]


title: lung biopsy [lung387]


title: lung biopsy [lung733]


title: lung biopsy [lung196]


title: lung biopsy [lung16]


title: lung biopsy [lung518]


title: lung biopsy [lung186]


title: lung biopsy [lung738]


title: lung biopsy [lung682]


title: lung biopsy [lung686]


title: lung biopsy [lung545]


title: lung biopsy [lung629]


title: lung biopsy [lung150]


title: lung biopsy [lung229]


title: lung biopsy [lung546]


title: lung biopsy [lung314]


title: lung biopsy [lung366]


title: lung biopsy [lung162]


title: lung biopsy [lung585]


title: lung biopsy [lung247]


title: lung biopsy [lung501]


title: lung biopsy [lung495]


title: lung biopsy [lung699]


title: lung biopsy [lung125]


title: lung biopsy [lung665]


title: lung biopsy [lung583]


title: lung biopsy [lung334]


title: lung biopsy [lung714]


title: lung biopsy [lung563]


title: lung biopsy [lung185]


title: lung biopsy [lung10]


title: lung biopsy [lung520]


title: lung biopsy [lung87]


title: lung biopsy [lung603]


title: lung biopsy [lung548]


title: lung biopsy [lung751]


title: lung biopsy [lung462]


title: lung biopsy [lung311]


title: lung biopsy [lung21]


title: lung biopsy [lung277]


title: lung biopsy [lung465]


title: lung biopsy [lung191]


title: lung biopsy [lung312]


title: lung biopsy [lung244]


title: lung biopsy [lung615]


title: lung biopsy [lung202]


title: lung biopsy [lung413]


title: lung biopsy [lung318]


title: lung biopsy [lung567]


title: lung biopsy [lung310]


title: lung biopsy [lung394]


title: lung biopsy [lung225]


title: lung biopsy [lung384]


title: lung biopsy [lung110]


title: lung biopsy [lung497]


title: lung biopsy [lung166]


title: lung biopsy [lung353]


title: lung biopsy [lung601]


title: lung biopsy [lung593]


title: lung biopsy [lung430]


title: lung biopsy [lung362]


title: lung biopsy [lung400]


title: lung biopsy [lung51]


title: lung biopsy [lung402]


title: lung biopsy [lung167]


title: lung biopsy [lung544]


title: lung biopsy [lung291]


title: lung biopsy [lung471]


title: lung biopsy [lung608]


title: lung biopsy [lung15]


title: lung biopsy [lung375]


title: lung biopsy [lung397]


title: lung biopsy [lung243]


title: lung biopsy [lung553]


title: lung biopsy [lung201]


title: lung biopsy [lung54]


title: lung biopsy [lung300]


title: lung biopsy [lung710]


title: lung biopsy [lung352]


title: lung biopsy [lung207]


title: lung biopsy [lung482]


title: lung biopsy [lung672]


title: lung biopsy [lung502]


title: lung biopsy [lung526]


title: lung biopsy [lung106]


title: lung biopsy [lung298]


title: lung biopsy [lung90]


title: lung biopsy [lung727]


title: lung biopsy [lung408]


title: lung biopsy [lung139]


title: lung biopsy [lung499]


title: lung biopsy [lung88]


title: lung biopsy [lung557]


title: lung biopsy [lung251]


title: lung biopsy [lung258]


title: lung biopsy [lung182]


title: lung biopsy [lung591]


title: lung biopsy [lung628]


title: lung biopsy [lung74]


title: lung biopsy [lung24]


title: lung biopsy [lung301]


title: lung biopsy [lung303]


title: lung biopsy [lung405]


title: lung biopsy [lung410]


title: lung biopsy [lung28]


title: lung biopsy [lung442]


title: lung biopsy [lung8]


title: lung biopsy [lung305]


title: lung biopsy [lung571]


title: lung biopsy [lung492]


title: lung biopsy [lung328]


title: lung biopsy [lung626]


title: lung biopsy [lung702]


title: lung biopsy [lung342]


title: lung biopsy [lung210]


title: lung biopsy [lung623]


title: lung biopsy [lung507]


title: lung biopsy [lung153]


title: lung biopsy [lung743]


title: lung biopsy [lung673]


title: lung biopsy [lung696]


title: lung biopsy [lung422]


title: lung biopsy [lung209]


title: lung biopsy [lung239]


title: lung biopsy [lung685]


title: lung biopsy [lung351]


title: lung biopsy [lung174]


title: lung biopsy [lung547]


title: lung biopsy [lung336]


title: lung biopsy [lung146]


title: lung biopsy [lung606]


title: lung biopsy [lung530]


title: lung biopsy [lung575]


title: lung biopsy [lung100]


title: lung biopsy [lung152]


title: lung biopsy [lung217]


title: lung biopsy [lung404]


title: lung biopsy [lung383]


title: lung biopsy [lung524]


title: lung biopsy [lung440]


title: lung biopsy [lung194]


title: lung biopsy [lung595]


title: lung biopsy [lung138]


title: lung biopsy [lung306]


title: lung biopsy [lung642]


title: lung biopsy [lung164]


title: lung biopsy [lung657]


title: lung biopsy [lung195]


title: lung biopsy [lung770]


title: lung biopsy [lung96]


title: lung biopsy [lung94]


title: lung biopsy [lung76]


title: lung biopsy [lung711]


title: lung biopsy [lung540]


title: lung biopsy [lung285]


title: lung biopsy [lung748]


title: lung biopsy [lung637]


title: lung biopsy [lung325]


title: lung biopsy [lung358]


title: lung biopsy [lung2]


title: lung biopsy [lung292]


title: lung biopsy [lung420]


title: lung biopsy [lung238]


title: lung biopsy [lung286]


title: lung biopsy [lung280]


title: lung biopsy [lung124]


title: lung biopsy [lung55]


title: lung biopsy [lung434]


title: lung biopsy [lung211]


title: lung biopsy [lung26]


title: lung biopsy [lung173]


title: lung biopsy [lung674]


title: lung biopsy [lung566]


title: lung biopsy [lung145]


title: lung biopsy [lung37]


title: lung biopsy [lung9]


title: lung biopsy [lung565]


title: lung biopsy [lung335]


title: lung biopsy [lung695]


title: lung biopsy [lung538]


title: lung biopsy [lung308]


title: lung biopsy [lung390]


title: lung biopsy [lung407]


title: lung biopsy [lung596]


title: lung biopsy [lung123]


title: lung biopsy [lung216]


title: lung biopsy [lung274]


title: lung biopsy [lung523]


title: lung biopsy [lung389]


title: lung biopsy [lung386]


title: lung biopsy [lung12]


title: lung biopsy [lung663]


title: lung biopsy [lung304]


title: lung biopsy [lung419]


title: lung biopsy [lung660]


title: lung biopsy [lung498]


title: lung biopsy [lung622]


title: lung biopsy [lung641]


title: lung biopsy [lung317]


title: lung biopsy [lung535]


title: lung biopsy [lung712]


title: lung biopsy [lung480]


title: lung biopsy [lung307]


title: lung biopsy [lung33]


title: lung biopsy [lung341]


title: lung biopsy [lung671]


title: lung biopsy [lung184]


title: lung biopsy [lung470]


title: panH3_HU-_ChIP-seq 2

city: Charlottesville

first: Stephen

middle: Aurelien

last: Hoang

state: Virginia

address: 501 Locust Ave, Suite 301

institute: HemoShear Therapeutics

library_source: genomic

data_processing:
Images generated by the Illumina sequencer were initially processed using the the Illumina pipeline
Read alignment was done using BWA 0.5.9-r16 using the UCSC SacCer1 reference genome. Only unique alignments with no mismatches were kept.
Tags were shifted 100bp in the 3' direction and binned into 150bp windows.
The H3T45p and panH3 smples were normalized using the DESeq normalization procedure [PMID: 20979621], and differential enrichments were calculated.
Windows with significant H3T45p enrichment over panH3 were called as peaks (FDR adj p-value < 0.1)
Genome_build: SacCer1
Supplementary_files_format_and_content: Bedgraph files contain binned tag counts or normalized differential (H3T45p-panH3) tag counts. Bed files contain coordinates of significantly enriched windows (H3T45p over panH3).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: BY4741 strain yeast cells were grown in YPD media to mid-log phase (OD600<1.0)

extract_protocol:
Mid-log phase cells are utilized in chromatin immunoprecipitation (ChIP) experiments as described before (Kuo,M.H. 1999) with the following minor modifications. Sonication is performed for 6x10 cycles with Diagenode Bioruptor. ChIP washes are performed at 4oC. ChIP elution buffer contains 1.0% SDS, 10 mM Tris, 1 mM EDTA, pH 8.0. Crosslinking is reversed overnight at 65oC. The eluted DNA is purified with Invitrogen PureLink PCR Purification Kit.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit. (Part# 11257047)

treatment_protocol: HU group cells are treated with 200mM hydroxurea (Sigma) for 2 hours

tag: strain

tag: antibody

value: Histone H3, C-terminal antibody(pAB)

tag: vendor/catalog#

value: Active Motif 39163

tag: treatment


title: panH3_HU+_ChIP-seq 1

value: Hydroxyurea


title: H3T45p_HU+_ChIP-seq 1

value: Histone H3 phospho Thr45 antibody(pAB)

value: Active Motif 39737


title: H3T45p_HU-_ChIP-seq 2


title: MOUSE-WT-E375-cell-A6

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

data_processing:
STAR alignment
Htseq-count
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: single cell

growth_protocol: Mice used were intercrosses of PDGFRa::H2B-GFP/+, in which a cassette containing human H2B fused to enhanced green protein (H2B-GFP) was targeted to the Pdgfra locus, and first filial generation (F1) hybrids (C57BL/6JxCBA/J) (Charles River). All embryos used in this study were obtained from natural mating.

extract_protocol:
Dissociated single cells were transferred immediately into Smart-Seq2 single-cell lysis buffer and immediately frozen on dry ice.
Smart-Seq2 library was prepared as described in Picelli S et al. 2014.

treatment_protocol: Embryos were flushed at E3.75 from uterine horns using flushing using M2. The zona pellucida was removed using acid Tyrode’s solution. Embryos were subjected to immunosurgery. Single-cell dissociation of ICMs was performed in a 1:1 mixture of Accutase and 0.025% trypsin plus 1% chick serum.

tag: developmental stage


title: MOUSE-WT-E375-cell-C8


title: MOUSE-WT-E375-cell-A5


title: MOUSE-WT-E375-cell-C2


title: MOUSE-WT-E375-cell-B4


title: liver biopsy [liver118]

source_name: liver biopsy

treatment_protocol:
All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: Y

tag: steatohepatitis (y, n, na)

value: N

tag: fibrosis (y, n, na)


title: liver biopsy [liver161]


title: liver biopsy [Liv236]


title: liver biopsy [liver67]


title: liver biopsy [liver50]


title: liver biopsy [liver47]


title: liver biopsy [liver163]


title: liver biopsy [liver136]


title: lung biopsy [lung531]


title: liver biopsy [liver169]


title: MOUSE-WT-E375-cell-C7


title: MOUSE-WT-E375-cell-A4


title: MOUSE-WT-E375-cell-C1


title: MOUSE-WT-E375-cell-B3


title: MOUSE-WT-E375-cell-B8


title: MOUSE-WT-E375-cell-B2


title: MOUSE-WT-E375-cell-C6


title: MOUSE-WT-E375-cell-A3


title: liver biopsy [liver83]


title: liver biopsy [liver140]


title: MOUSE-WT-E375-cell-C5


title: MOUSE-WT-E375-cell-A2


title: MOUSE-WT-E375-cell-B1


title: MOUSE-WT-E375-cell-B7


title: MOUSE-WT-E375-cell-C4


title: MOUSE-WT-E375-cell-A8


title: MOUSE-WT-E375-cell-A1


title: MOUSE-WT-E375-cell-C3


title: MOUSE-WT-E375-cell-B5


title: Z_Oligomers

city: Amsterdam

first: Vanessa

last: Donega

address: Boelelaan 1108

department: Anatomy and Neuroscience

country: Netherlands

institute: Amsterdam UMC

description:
Z_Oligomers
UMC-TS-B010

data_processing:
Libraries were de-multiplexed and raw reads were aligned to the hg19 human RefSeq transcriptome with Burrows-Wheeler Aligner (BWA)
The quality control, normalization, and identification of differentially expressed genes were done with DESeq2, an R (version 3.6.3) based package
Read counts were normalized by using the median of ratios method from the DESeq2 pipeline
The gene expression was corrected for the covariate sex.
Genes were considered differentially expressed with an adjusted (adj.) p-value of less than 0.05 and a Log2 fold change of at least 2 for the comparison LPS and PBS and a Log2 fold change of at least 0.5 for Ab1-42 oligomers and vehicle stimulation.
Genome_build: hg19 human
Supplementary_files_format_and_content: tsv file with gene counts for every gene and every sample following alignment and trimming

source_name: MDMi cells

growth_protocol: The protocol for generating MDMi cells is based on established protocols (Leone et al., 2006; Ohgidani et al., 2015; Ryan et al., 2017), with minor adaptations to optimize the expression of TREM2, TYROBP and PROS1 (Ormel et al., 2020). To generate MDMi cells, monocytes were thawed on ice-cold RPMI medium and plated at a density of 600.000 cells/well or 200.000 cells/well in a 48- or 96-well plate for transcriptome and phagocytosis assays, respectively. The wells were coated with poly-L lysine (PLL, Sigma Aldrich) at 37 °C in 5% CO2 for 30 minutes. Cells were left to adhere to the wells under standard humified culture conditions at 37 °C in 5% CO2 for at least 1 hr, then cells were washed with PBS (Invitrogen) and the medium was replaced by 25% ACM (Astrocyte conditioned medium SCC1811, Sanbio) in RPMI medium. To induce the differentiation towards MDMi cells, the 25% ACM/RPMI medium was replaced on day four and day eight with RPMI containing 25% ACM, 10 ng/ml human M-CSF (130-096-491, Miltenyi Biotec), 10 ng/mL GM-CSF (130-093-862, Miltenyi Biotec), 1 ng/ml TGFb (130-095-067, Miltenyi Biotec), 12.5 ng/ml IFN-g (130-096-872, Miltenyi Biotec), and 100 ng/mL IL-34 (130-108-997, Miltenyi Biotec).

extract_protocol:
RNA isolation was performed using the miRNeasy Mini kit (217004, Qiagen) according to the manufacturer’s protocol including the DNase treatment. The RNA concentration was determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Waltham).
cDNA libraries were prepared according to the CelSeq2 protocol (Hashimshony et al., 2012; Simmini et al., 2014) by Single Cell Discoveries, Utrecht (Muraro et al., 2016). Briefly, for each sample a custom-made primer was added to the RNA, denatured at 70 °C for 2 min, and immediately cooled down. mRNA was reverse transcribed into cDNA using clean-up beads (ThermoFisher Scientific, Ambion, Waltham, USA). The purified cDNA was transcribed in vitro to obtain amplified RNA using the MegaScript kit, which was followed by purification with Agencourt RNAclean XP (RNAse free) beads (Beckman Coulter). Amplified RNA was fragmented with fragmentation buffer and purified using the RNA cleanXP beads. Quality of the amplified RNA was determined with the RNA 6000 Pico chips (Agilent) on an Agilent 2100 bioanalyzer. Next, the amplified RNA was reverse transcribed and amplified by PCR. Libraries were labelled with a 4 bp unique molecular identifier (UMI) that was added to the primer. Samples from the different stimulation and control conditions were pooled in libraries for each donor (see Supplementary Table 1). The quality of the libraries was determined with the DNA High Sensitivity chips on an Agilent 2100 bioanalyzer (Agilent). Libraries were sequenced on the Illumina NextSeq 500 platform using paired-end sequencing (75 bp) with a depth of 10M reads per sample.
Cel-seq2

treatment_protocol: At day 10 in culture, MDMi cells were treated with 500 nM stable human Ab1-42 oligomers (180222EMH, gift from Crossbeta) or 100 ng/mL lipopolysaccharide in PBS (LPS, L4391-1MG, E. coli 0111:B4, Sigma-Aldrich). As a control for the oligomer and LPS condition, the same volume of vehicle (20 mM HEPES, 150 mM NaCl and 200 mM sucrose, pH 7.2) or PBS was added, respectively. After 24 hrs of stimulation, MDMi cells were washed with PBS and collected for RNA isolation (48-well plates) in Trizol (Ambion, Life Technologies, Carlsbad, CA, USA)

tag: gender

value: Male

tag: cell type

value: monocyte-derived microglia-like cells (MDMi)

value: Oligomers


title: Z_Vehicle

description:
Z_Vehicle
UMC-TS-B010

value: Vehicle


title: MOUSE-WT-E375-cell-D6


title: MOUSE-WT-E375-cell-A7


title: Z_LPS

description:
Z_LPS
UMC-TS-B010

value: LPS


title: MOUSE-WT-E375-cell-F2


title: MOUSE-WT-E375-cell-D5


title: AB_Vehicle

description:
AB_Vehicle
UMC-TS-B009

value: Female


title: MOUSE-WT-E375-cell-B6


title: AB_Oligomers

description:
AB_Oligomers
UMC-TS-B009


title: AB_LPS

description:
AB_LPS
UMC-TS-B009


title: MOUSE-WT-E375-cell-F8


title: Z_PBS

description:
Z_PBS
UMC-TS-B010

value: PBS


title: AB_PBS

description:
AB_PBS
UMC-TS-B009


title: MOUSE-WT-E375-cell-F7


title: MOUSE-WT-E375-cell-E4


title: AJ_LPS

description:
AJ_LPS
UMC-TS-B008


title: AJ_Oligomers

description:
AJ_Oligomers
UMC-TS-B008


title: AJ_Vehicle

description:
AJ_Vehicle
UMC-TS-B008


title: AJ_PBS

description:
AJ_PBS
UMC-TS-B008


title: AA_Oligomers

description:
AA_Oligomers
UMC-TS-B007


title: AA_Vehicle

description:
AA_Vehicle
UMC-TS-B007


title: MOUSE-WT-E375-cell-E3


title: AK_LPS

description:
AK_LPS
UMC-TS-B006


title: AK_Oligomers

description:
AK_Oligomers
UMC-TS-B006


title: AA_PBS

description:
AA_PBS
UMC-TS-B007


title: MOUSE-WT-E375-cell-F6


title: MOUSE-WT-E375-cell-D4


title: AG_Oligomers

description:
AG_Oligomers
UMC-TS-B005


title: AG_LPS

description:
AG_LPS
UMC-TS-B005


title: MOUSE-WT-E375-cell-E8


title: MOUSE-WT-E375-cell-F1


title: MOUSE-WT-E375-cell-E2


title: C_Oligomers

description:
C_Oligomers
UMC-TS-B004


title: AK_PBS

description:
AK_PBS
UMC-TS-B006


title: AA_LPS

description:
AA_LPS
UMC-TS-B007


title: MOUSE-WT-E375-cell-E7


title: AG_PBS

description:
AG_PBS
UMC-TS-B005


title: AG_Vehicle

description:
AG_Vehicle
UMC-TS-B005


title: AK_Vehicle

description:
AK_Vehicle
UMC-TS-B006


title: B_LPS

description:
B_LPS
UMC-TS-B003


title: C_LPS

description:
C_LPS
UMC-TS-B004


title: MOUSE-WT-E375-cell-F5


title: B_Oligomers

description:
B_Oligomers
UMC-TS-B003


title: C_PBS

description:
C_PBS
UMC-TS-B004


title: C_Vehicle

description:
C_Vehicle
UMC-TS-B004


title: MOUSE-WT-E375-cell-D3


title: MOUSE-WT-E375-cell-D2


title: MOUSE-WT-E375-cell-F4


title: A_Oligomers

description:
A_Oligomers
UMC-TS-B002


title: B_PBS

description:
B_PBS
UMC-TS-B003


title: A_LPS

description:
A_LPS
UMC-TS-B002


title: A_PBS

description:
A_PBS
UMC-TS-B002


title: M_Oligomers

description:
M_Oligomers
UMC-TS-B001


title: M_Vehicle

description:
M_Vehicle
UMC-TS-B001


title: A_Vehicle

description:
A_Vehicle
UMC-TS-B002


title: M_LPS

description:
M_LPS
UMC-TS-B001


title: MOUSE-WT-E375-cell-E6


title: B_Vehicle

description:
B_Vehicle
UMC-TS-B003


title: MOUSE-WT-E375-cell-E1


title: MOUSE-WT-E375-cell-D8


title: MOUSE-WT-E375-cell-D1


title: TEST+TREATED-2

city: Hyderabad

first: Kishore

last: Parsa

state: TELANGANA

address: University of Hyderabad Campus, Gachibowli

department: CIMPS

country: India

institute: Dr. Reddy's Institute of Life Sciences

description: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); puromycin selection; Treated with 100µg/ml of OxLDL for 24 hours - Sample 11

data_processing:
Quality check and pre-processing of raw data was done by FASTQC and Trimmomatic softwares.
Preprocessed reads were aligned to reference genome GRCm38 using Stat-Aligner.
Quantification of aligned reads performed using HTSeq-Count.
Normalization and differential expression analysis of raw counts performed by DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Readcounts.xlsx: Read counts of individual samples.
Supplementary_files_format_and_content: CTRL_TREATED_vs_CTRL.xlsx: Differential gene regulation in: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); Treated with 100µg/ml of OxLDL for 24 hours vs. Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL).
Supplementary_files_format_and_content: TEST_vs_CTRL.xlsx: Differential gene regulation in: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST) vs. Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL).
Supplementary_files_format_and_content: TEST_TREATED_vs_CTRL_TREATED.xlsx: Differential gene regulation in: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); Treated with 100µg/ml of OxLDL for 24 hours vs. Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); Treated with 100µg/ml of OxLDL for 24 hours.

source_name: RAW 264.7 macrophage cell line

growth_protocol: RAW 264.7 cells (ATCC catalog# TIB-71) were cultured at 37˚C with 5% CO2 in DMEM media supplemented with 10% heat inactivated Fetal Bovine Serum (FBS), 1mM Sodium pyruvate, 100units/ml penicillin and 100µg/ml streptomycin.

extract_protocol:
The cells were pelleted by centrifugation and flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit. 150 ng total RNA was used for preparing libraries for RNA sequencing.
The RNA was fragmented and then converted to cDNA according to the kit protocol (NEB #E7770S). The cDNA was end repaired and further purified using AMPure XP beads (A63880 AMPure XP). The cleaned cDNA was adapter ligated, purified and subjected to 12 PCR cycles of amplification using primers provided in the kit (NEB #E7770S). The PCR products were purified using AMPure XP beads. The quantification and size distribution of the prepared library was accomplished using Qubit fluorimeter and Agilent Tape station D1000 Kit (Agilent Technologies) following manufacturer’s instructions.

treatment_protocol: The cells were treated with 100µg/ml OxLDL for 24 hours.

tag: cell line

value: Macrophage cell line

tag: shRNA

value: sh-PHLPP1 (TEST)

tag: passages

value: Passage 10

value: BALB/c

value: 100ug/ml OxLDL for 24 hours


title: TEST+TREATED-1

description: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); puromycin selection; Treated with 100µg/ml of OxLDL for 24 hours - Sample 10

value: Passage 9


title: TEST+TREATED-3

description: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); puromycin selection; Treated with 100µg/ml of OxLDL for 24 hours - Sample 12

value: Passage 11


title: TEST-3

description: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); puromycin selection - Sample 9


title: MOUSE-WT-E375-cell-E5


title: TEST-1

description: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); puromycin selection - Sample 7


title: PBMC 24HR LSF 15µM RNA P3

city: Melbourne

first: Assam

last: El-Osta

address: 75 Commercial Road

country: Australia

institute: Baker Heart and Diabetes Institute

data_processing:
Basecalls using Illumina pipeline v. 1.6 for Illumina GAIIx.
Fastq files aligned and quantified to GRCh38 cDNA (Ensembl) with Kallisto quant v0.45.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_abundance.tsv: Files are formatted as tab-separated values and include TPMs.

source_name: peripheral blood mononuclear cell

growth_protocol: Isolation of peripheral blood mononuclear cells by ficoll centrifugation of blood from healthy volunteers.

extract_protocol:
Trizol extraction with column purification and assessed for quality by Multi-NA.
Poly A enrichment combined with NEBNext Ultra directional RNA library prep kit.
Barcoded libraries pooled and sequenced on Illumina GAIIx.

treatment_protocol: Ex vivo treatment of peripheral blood mononuclear cells with 15 µM L-sulforaphane for 24 hours.

value: Peripheral blood mononuclear cell

value: 15uM L-sulforaphane for 24 hours

tag: subject

tag: diagnosis

value: Healthy


title: CTRL+TREATED-3

description: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); puromycin selection; Treated with 100µg/ml of OxLDL for 24 hours - Sample 6

value: sh-Luc (CTRL)


title: CTRL+TREATED-1

description: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); puromycin selection; Treated with 100µg/ml of OxLDL for 24 hours - Sample 4


title: CTRL+TREATED-2

description: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); puromycin selection; Treated with 100µg/ml of OxLDL for 24 hours - Sample 5


title: TEST-2

description: Stable RAW 264.7 cells nucleofected with sh-PHLPP1 (TEST); puromycin selection - Sample 8


title: CTRL-2

description: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); puromycin selection - Sample 2


title: PBMC 24HR UNTREATED RNA P4

value: Untreated control


title: PBMC 24HR UNTREATED RNA P3


title: M_PBS

description:
M_PBS
UMC-TS-B001

value: monocyte-derived microglia-like cells (MDMi)


title: PBMC 24HR LSF 15µM RNA P4


title: CTRL-3

description: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); puromycin selection - Sample 3


title: MOUSE-WT-E375-cell-D7


title: MOUSE-WT-E375-cell-F3


title: PBMC 24HR UNTREATED RNA P2


title: PBMC 24HR LSF 15µM RNA P2


title: KF7 at 0 g/L succinic acid

city: Chengdu

first: Ranran

last: Su

address: Chuanda Road

institute: SiChuan University

description: Gene expression data from Saccharomyces cerevisiae KF7 and fermented with 0 g/L succinic acid .

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Saccharomyces cerevisiae Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450/250.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.

data_processing:
The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
q-value ≤ 5% and Fold Change ≥2 or≤0.5

source_name: Saccharomyces cerevisiae KF7 in the YPD medium and 0 g/L succinic acid was supplemented

label_protocol: Biotinylated cRNA were prepared according to the Ambion #1792 cRNA扩增标记试剂盒

growth_protocol: at 35℃, 200 rpm growth for 6 hours, with different succinic acid supplement (0-60 g/L).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Saccharomyces cerevisiae KF7

tag: agent

value: 0 g/L succinic acid


title: PBMC 24HR LSF 15µM RNA P1


title: spleen RPRC infected LCMV Clone 13 day 30 Sample 42

first: Luke

middle: C

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

institute: WEHI

description:
spleen RPRC infected LCMV Clone 13 day 30
biological replicate

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread 1.26.1
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: spleen

extract_protocol:
RNA was isolated from freshly sorted cells with the miRNeasy kit (Qiagen).
Total RNA from the equivalent of 500 cells was used to generate libraries from each sample for whole-transcriptome analysis following the Clontech v4 low-input RNA protocol following the manufacturer’s instructions.

tag: strain background

tag: transcgenic strain

value: Ccl19-cre x R26R-EYFP

value: RPRC

tag: condition

value: infected

value: LCMV Clone 13

tag: timepoint

value: day 30


title: NBRC2018 at 20 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae NBRC2018 and fermented with 20 g/L succinic acid .

source_name: Saccharomyces cerevisiae NBRC2018 in the YPD medium and 20 g/L succinic acid was supplemented

tag: strain

value: Saccharomyces cerevisiae NBRC2018

value: 20 g/L succinic acid


title: CTRL-1

description: Stable RAW 264.7 cells nucleofected with sh-Luc (CTRL); puromycin selection - Sample 1

value: Macrophage cell line

value: Passage 9

value: BALB/c

tag: treatment


title: spleen RPRC infected LCMV Clone 13 day 30 Sample 38


title: spleen RPRC infected LCMV Clone 13 day 30 Sample 46


title: spleen RPRC infected LCMV Clone 13 day 8 Sample 70

description:
spleen RPRC infected LCMV Clone 13 day 8
biological replicate

value: day 8


title: KF7 at 60 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae KF7 and fermented with 60 g/L succinic acid .

source_name: Saccharomyces cerevisiae KF7 in the YPD medium and 60 g/L succinic acid was supplemented

value: 60 g/L succinic acid


title: KF7 at 20 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae KF7 and fermented with 20 g/L succinic acid .

source_name: Saccharomyces cerevisiae KF7 in the YPD medium and 20 g/L succinic acid was supplemented


title: PBMC 24HR UNTREATED RNA P1

value: Peripheral blood mononuclear cell

value: Healthy


title: NBRC2018 at 0 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae NBRC2018 and fermented with 0 g/L succinic acid .

source_name: Saccharomyces cerevisiae NBRC2018 in the YPD medium and 0 g/L succinic acid was supplemented


title: spleen MRC infected LCMV Clone 13 day 30 Sample 41

description:
spleen MRC infected LCMV Clone 13 day 30
biological replicate

value: MRC


title: spleen MRC infected LCMV Clone 13 day 30 Sample 45


title: spleen RPRC infected LCMV Clone 13 day 8 Sample 62


title: spleen MRC infected LCMV Clone 13 day 8 Sample 69

description:
spleen MRC infected LCMV Clone 13 day 8
biological replicate


title: NBRC1958 at 0 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae NBRC1958 and fermented with 0 g/L succinic acid .

source_name: Saccharomyces cerevisiae NBRC1958 in the YPD medium and 0 g/L succinic acid was supplemented

value: Saccharomyces cerevisiae NBRC1958


title: NBRC1958 at 20 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae NBRC1958 and fermented with 20 g/L succinic acid .

source_name: Saccharomyces cerevisiae NBRC1958 in the YPD medium and 20 g/L succinic acid was supplemented


title: NBRC2018 at 60 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae NBRC2018 and fermented with 60 g/L succinic acid .

source_name: Saccharomyces cerevisiae NBRC2018 in the YPD medium and 60 g/L succinic acid was supplemented


title: NBRC1958 at 60 g/L succinic acid

description: Gene expression data from Saccharomyces cerevisiae NBRC1958 and fermented with 60 g/L succinic acid .

source_name: Saccharomyces cerevisiae NBRC1958 in the YPD medium and 60 g/L succinic acid was supplemented


title: spleen MRC infected LCMV Clone 13 day 8 Sample 65


title: spleen MRC infected LCMV Clone 13 day 8 Sample 61


title: spleen EYFP- infected LCMV Clone 13 day 30 Sample 44

description:
spleen EYFP- infected LCMV Clone 13 day 30
biological replicate

value: EYFP-


title: spleen EYFP- infected LCMV Clone 13 day 30 Sample 40

value: Ccl19-cre x R26R-EYFP


title: Human dermal fibroblasts_2D_irradiated_rep3 (miRNA)

city: Saint-Viance

first: Pauline

last: Rouaud-Tinguely

address: ZI de la Nau

department: R&D

country: France

institute: SILAB

description:
S7
miRNA expression after 4 days to irradiation

hyb_protocol: Dries RNA was resuspended to 10x Agilent blocking agent following the manufacturers instructions, 2x Agilent hybridization buffer was added and hybridized to Human miRNA V19 microarrays for 20 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for AgilentG3 miRNA array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11_5_1_1 (Agilent) using default parameters (protocol miRNA_1105_Oct12 and Grid: 046064_D_F_20121223) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Human dermal fibroblasts, 4 days of irradiation, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng RNA using Complete Labeling and Hyb kit for miRNA Microarray System (Agilent Technologies; Santa Clara, CA, USA), according to the manufacturer's instructions.

growth_protocol: Normal human fibroblasts (NHF) were isolated from human breast skin, collected from healthy female (aged 20-28 years) undergoing plastic surgery. The skin was collected after written informed consent from the donors, institutional approval, and handled according to the Declaration of Helsinki Principles. Fibroblasts were cultured in monolayer at 37°C under 5% CO2 in Minimal Essential Medium (MEM; Gibco; Inchinnan Business Park, UK) supplemented with 10% fetal bovine serum (FBS; Sigma), 1% penicillin/streptomycin (Gibco; Inchinnan Business Park, UK), 0.1% fungizone (Gibco; Inchinnan Business Park, UK). Cells were used at passage 5 and 6, grown to 80% confluency before treatment.

extract_protocol: Total RNA was extracted using the miRNeasy Micro Kit (Qiagen). Quantification and quality assessment of the isolated RNA samples were performed and verified using a NanoDrop 2000c spectrophotometer (ThermoFisher) and an Agilent Bioanalyzer2100 (Agilent Technologies) according to the manufacturer's instructions.

treatment_protocol: Prior to irradiation, the growth medium was removed and the cell monolayer was rinsed with PBS. Cells were then covered with PBS and irradiated at 25°C every day during 4 consecutive days with a dose of 26J/cm² during 15 minutes, with a solar simulator « CPS+» (Atlas; Linsengericht, Germany). Between each treatment, cells were cultivated with MEM supplemented with 2% FBS at 37°C. One day after the last irradiation, stress-induced senescence (SIS) fibroblasts were used for following experiments. Control cells were held on 25 °C under similar conditions without irradiation.

tag: stress

value: irradiation

value: dermal fibroblasts


title: Human dermal fibroblasts_2D_irradiated_rep1 (miRNA)

description:
S5
miRNA expression after 4 days to irradiation

source_name: Human dermal fibroblasts, 4 days of irradiation, replicate 1


title: spleen EYFP- infected LCMV Clone 13 day 30 Sample 36

value: infected

value: LCMV Clone 13


title: Human dermal fibroblasts_2D_irradiated_rep2 (miRNA)

description:
S6
miRNA expression after 4 days to irradiation

source_name: Human dermal fibroblasts, 4 days of irradiation, replicate 2


title: Human dermal fibroblasts_2D_irradiated_rep4 (miRNA)

description:
S8
miRNA expression after 4 days to irradiation

source_name: Human dermal fibroblasts, 4 days of irradiation, replicate 4


title: spleen EYFP- infected LCMV Clone 13 day 8 Sample 68

description:
spleen EYFP- infected LCMV Clone 13 day 8
biological replicate


title: spleen EYFP- infected LCMV Clone 13 day 8 Sample 64


title: spleen RPRC infected LCMV Clone 13 day 8 Sample 66

value: RPRC


title: Human dermal fibroblasts_2D_normal medium_rep4 (miRNA)

description:
S4
miRNA expression without irradiation

source_name: Human dermal fibroblasts, 4 days with normal medium, replicate 4

value: control


title: spleen MRC infected LCMV Clone 13 day 30 Sample 37

value: day 30


title: spleen TRC infected LCMV Clone 13 day 30 Sample 43

description:
spleen TRC infected LCMV Clone 13 day 30
biological replicate

value: TRC


title: Human dermal fibroblasts_2D_normal medium_rep3 (miRNA)

description:
S3
miRNA expression without irradiation

source_name: Human dermal fibroblasts, 4 days with normal medium, replicate 3


title: spleen TRC infected LCMV Clone 13 day 30 Sample 39


title: spleen TRC infected LCMV Clone 13 day 30 Sample 35


title: protoplasted rep3

city: 杭州市

first: Yao

last: Jie

state: 浙江

address: 浙江大学紫金港校区农学院A

institute: ZheJiang University

data_processing:
The raw data were converted into fastq files by using fastq-dump (version 2.9.6). After demultiplexed, raw reads were mapped to the reference genome (K326) using the 10X Genomics CellRanger (version 4.0.0) pipeline with the default parameters.
The reference genome of the tobacco BY2 cell line is current unavailable, we thus choose the K326 genome of Nicotiana tabacum to align the bulk RNA-seq reads) with STAR (Dobin et al., 2013). The K326 genome was downloaded from the SOL genomics database (https://solgenomics.net/) (Sierro et al., 2014). The read alignment rates of the six samples were 90.54% - 91.84%, indicating that the K326 reference genome can be used for BY2 transcriptome data quantification. Gene expression values were calculated based on the uniquely mapped reads using featureCounts (version 2.0.2; Liao et al., 2014), and DEseq2 (version 1.28.1; Love et al., 2014) was used to identify differentially expressed genes.
Genome_build: K326_2014
Supplementary_files_format_and_content: *_datamatrix.csv: Comma-delimited text files include UMI counts values in each cell.

molecule: polyA RNA

organism: Nicotiana tabacum

source_name: Tobacco BY-2 cell line

growth_protocol: Tobacco (Nicotiana tabacum) BY-2 (Bright Yellow-2) cells were obtained from Miu’s laboratory (School of Biological Engineering in Huainan Normal University, Anhui, China) and cultured in Murashige and Skoog medium (sigma, M5524, USA), pH 5.8, with the following supplements: 0.2 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D), 30 g/L sucrose, 200 mg/L KH2PO4, 100 mg/L myo-inositol and 1 mg/L thiamin (VB1). BY2 cells were grown in 40 ml culture medium in 200 ml Erlenmeyer flasks on a rotary shaker that is maintained in the dark at 150 rpm and 26°C. BY-2 cells were sub-cultured weekly from a 7 d-old liquid culture by transferring 5 mL BY-2 cells to 40 mL fresh BY-2 culture medium.

extract_protocol: The obtained BY2 protoplasts were divided into two parts and cryopreserved, one for bulk RNA paired-end sequencing (with three replicates) and another for single-cell RNA sequencing (with two replicates). Illumina libraries were constructed with Gene Expression v3 kits (10X Genomics).

treatment_protocol: Protoplasts were prepared from 3 d-old tobacco BY-2 suspension cells. The 40-ml cell culture was filtered using a 40-μm nylon mesh (BD Falcon, USA) was to collect BY2 cells, which were washed twice with protoplast wash solution (0.5 M mannitol, 4 mM 2-(N-morpholino) ethanesulfonic acid (pH 5.7)). The cells were then divided into three parts. One part was immediately cryopreserved in liquid nitrogen for bulk RNA paired-end sequencing (with three replicates), the other two parts were resuspended in 10 mL of enzyme solution (pH 5.7), containing 1.5% cellulase "Onozuka RS" (Yakult Pharmaceutical Ind. Co. Ltd., Tokyo, Japan), 0.5% macerase (Yakult Pharmaceutical Ind. Co. Ltd., Tokyo, Japan), 0.5 M mannitol, and 4 mM 2-(N-morpholino) ethanesulfonic acid , in a 20-ml Petri dish and incubated for 2 h at 26°C on a rotary shaker that is maintained in the dark at 60 rpm. Protoplasts were recovered by filtration through a 40-μm nylon mesh and washed twice with protoplast wash solution at 150 g for 3 min.

tag: age

value: three day-old BY-2 suspension cells

value: protoplasted


title: protoplasted rep2

address: 浙江大学紫金港校区农学院A


title: Human dermal fibroblasts_2D_normal medium_rep1 (miRNA)

description:
S1
miRNA expression without irradiation

source_name: Human dermal fibroblasts, 4 days with normal medium, replicate 1


title: protoplasted rep1

address: 浙江大学紫金港校区农学院A


title: unprotoplasted rep3

address: 浙江大学紫金港校区农学院A

value: upprotoplasted


title: spleen RPRC infected LCMV Armstrong day 30 Sample 30

description:
spleen RPRC infected LCMV Armstrong day 30
biological replicate

source_name: spleen

value: LCMV Armstrong


title: spleen TRC infected LCMV Clone 13 day 8 Sample 63

description:
spleen TRC infected LCMV Clone 13 day 8
biological replicate

value: day 8


title: spleen RPRC infected LCMV Armstrong day 8 Sample 58

description:
spleen RPRC infected LCMV Armstrong day 8
biological replicate


title: spleen RPRC infected LCMV Armstrong day 30 Sample 34


title: spleen RPRC infected LCMV Armstrong day 8 Sample 54


title: spleen TRC infected LCMV Clone 13 day 8 Sample 59


title: spleen RPRC infected LCMV Armstrong day 30 Sample 26


title: spleen RPRC infected LCMV Armstrong day 8 Sample 50


title: spleen MRC infected LCMV Armstrong day 30 Sample 33

description:
spleen MRC infected LCMV Armstrong day 30
biological replicate

value: MRC


title: unprotoplasted rep2

address: 浙江大学紫金港校区农学院A


title: BY-2 cells_scRNA-seq_rep_2

address: 浙江大学紫金港校区农学院A


title: unprotoplasted rep1

address: 浙江大学紫金港校区农学院A


title: spleen EYFP- infected LCMV Clone 13 day 8 Sample 60


title: spleen MRC infected LCMV Armstrong day 8 Sample 53

description:
spleen MRC infected LCMV Armstrong day 8
biological replicate


title: spleen MRC infected LCMV Armstrong day 8 Sample 57


title: spleen MRC infected LCMV Armstrong day 8 Sample 49


title: spleen MRC infected LCMV Armstrong day 30 Sample 25


title: spleen TRC infected LCMV Clone 13 day 8 Sample 67


title: spleen EYFP- infected LCMV Armstrong day 30 Sample 24

description:
spleen EYFP- infected LCMV Armstrong day 30
biological replicate


title: spleen EYFP- infected LCMV Armstrong day 30 Sample 28


title: Human dermal fibroblasts_2D_normal medium_rep2 (miRNA)

description:
S2
miRNA expression without irradiation

source_name: Human dermal fibroblasts, 4 days with normal medium, replicate 2


title: spleen EYFP- infected LCMV Armstrong day 30 Sample 32


title: spleen EYFP- infected LCMV Armstrong day 8 Sample 56

description:
spleen EYFP- infected LCMV Armstrong day 8
biological replicate


title: spleen EYFP- infected LCMV Armstrong day 8 Sample 48


title: Cal27-RIP-seq-HNRNPC-input

city: Nanjing

first: Weiwen

last: Zhu

state: Jiangsu

address: Hanzhong Road 140#

department: Stomatology

institute: Nanjing Medical University

description: Raw_gene_counts_matrix_HNRNPC-RIP-seq.xls

data_processing:
TMM (trimmed mean of M-values) was used to normalize the gene expression
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with gene reads count for every gene and every sample

source_name: Oral cancer cell line

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1-3 ug of total RNA for the construction of sequencing libraries.
RNA-seq library was prepared with approximately 1μg of total RNA using RibomovalTM rRNA Depletion Kit (Human/Mouse/Rat) (Geneseed, Guangzhou, China). Briefly, ribosomal RNA was removed from the total RNA. Next, the ribominus RNAs were fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. The library quality and concentration was assessed by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer.

treatment_protocol: Cal27 cells were harvested by RIP lysis buffer, then the lysates were immunoprecipitated by 5μg anti-HNRNPC antibody. The purified input and HNRNPC-IP RNA samples were then subjected to RNA-seq analysis.

value: Oral cancer cell

tag: rip antibody


title: Cal27-RIP-seq-HNRNPC-IP

value: Anti-HNRNPC


title: BY-2 cells_scRNA-seq_rep_1

address: 浙江大学紫金港校区农学院A


title: spleen TRC infected LCMV Armstrong day 30 Sample 31

description:
spleen TRC infected LCMV Armstrong day 30
biological replicate

value: Ccl19-cre x R26R-EYFP


title: Cal27-HNRNPC-KD-2

extract_protocol:
Cells were washed with 1 X PBS for 3 times, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1-3 ug of total RNA for the construction of sequencing libraries.
mRNA was captured from approximately 1μg of total RNA using VAHTSTM mRNA Capture Beads. Next, mRNA-seq library was prepared with RNA-seq Library Prep Kit for Illumina  (Geneseed, Guangzhou, China). Briefly, the mRNA was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. The library quality and concentration was assessed by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer.

treatment_protocol: For RNA-seq analysis, Cal27 cells were transfected by lentivirus to knockdown CYTOR or HNRNPC expression level

tag: lentivirus transfection

value: HNRNPC-knockdown


title: spleen TRC infected LCMV Armstrong day 30 tech rep 1 Sample 23a

description:
spleen TRC infected LCMV Armstrong day 30 tech rep 1
technical replicate

tag: cell type


title: spleen TRC infected LCMV Armstrong day 30 tech rep 2 Sample 23b

description:
spleen TRC infected LCMV Armstrong day 30 tech rep 2
technical replicate


title: Cal27-HNRNPC-KD-3


title: spleen TRC infected LCMV Armstrong day 30 tec rep 2 Sample 27

description:
spleen TRC infected LCMV Armstrong day 30 tec rep 2
biological replicate


title: Cal27-HNRNPC-KD-1


title: spleen MRC infected LCMV Armstrong day 30 Sample 29


title: spleen TRC infected LCMV Armstrong day 8 Sample 51

description:
spleen TRC infected LCMV Armstrong day 8
biological replicate


title: spleen TRC infected LCMV Armstrong day 8 Sample 55


title: Cal27-HNRNPC-NC-3

value: NC, scrambled insert


title: spleen TRC infected LCMV Armstrong day 8 Sample 47

value: infected


title: spleen RPRC naive none day 0 Sample 22

description:
spleen RPRC naive none day 0
biological replicate

value: naive

value: day 0


title: spleen RPRC naive none day 0 Sample 20

value: RPRC


title: spleen RPRC naive none day 0 Sample 19


title: spleen MRC naive none day 0 Sample 21

description:
spleen MRC naive none day 0
biological replicate


title: Cal27-HNRNPC-NC-1


title: Cal27-CYTOR-KD-3

value: CYTOR-knockdown


title: spleen EYFP- infected LCMV Armstrong day 8 Sample 52

value: EYFP-


title: spleen MRC naive none day 0 Sample 5


title: Cal27-CYTOR-KD-2


title: spleen MRC naive none day 0 Sample 9


title: spleen CD140a- naive none day 0 tech rep 1 Sample 8a

description:
spleen CD140a- naive none day 0 tech rep 1
technical replicate


title: Cal27-CYTOR-KD-1


title: spleen EYFP- naive none day 0 Sample 18

description:
spleen EYFP- naive none day 0
biological replicate


title: Cal27-CYTOR-NC-3


title: spleen CD140a- naive none day 0 Sample 4

description:
spleen CD140a- naive none day 0
biological replicate


title: spleen TRC naive none day 0 Sample 13

description:
spleen TRC naive none day 0
biological replicate

value: TRC


title: spleen EYFP- naive none day 0 Sample 16


title: spleen TRC naive none day 0 Sample 17


title: spleen TRC naive none day 0 Sample 15


title: spleen TRC naive none day 0 Sample 3


title: lymph node MRC naive none day 0 Sample 12

description:
lymph node MRC naive none day 0
biological replicate

source_name: lymph node


title: Cal27-HNRNPC-NC-2


title: lymph node MRC naive none day 0 Sample 7


title: Cal27-CYTOR-NC-1


title: Neuroepithelial stem cells - CTRL11 (P10052_137)

city: Stockholm

first: Jakob

last: Schuy

address: Akademiska stråket 1

country: Sweden

institute: Karolinska Institutet

description:
Sample 6
P10052_137
This cell line served as reference

data_processing:
Transcript abundance: Salmon V1.1.0
Gene expression changes: DeSeq2 package in R (Love et al., 2014)
Tx2Gene list: GRCh38.p13/hg38, release 36
Gene annotations: BioMart - Ensembl for gene annotation
Genome_build: GRCh38.p13/hg38
Supplementary_files_format_and_content: Excel files contain the DeSeq2 output for Samples 1-3 compared to the merged control lines (e.g. Sample1 compared to Sample4-6) including gene annotation and statistics

source_name: Neuroepithelial stem cells

growth_protocol: The iPSC colonies were neurally induced to capture neuroepithelial stem cells (NESCs) (Falk et al., 2012). Briefly, neural induction was achieved by culturing the iPSCs in 0.5 ng/mL hNoggin and 3.3 µM CHIR99021 until day 10. The medium was supplemented with 10 µM SB431542 until day 4. The cells were replated at 40,000 cells/cm2 onto 0.1 mg poly-l-ornithine 1 μg/ml laminin L2020–coated plates in medium containing Dulbecco modified eagle medium/F-12 GlutaMAX, 1% N2, 0.1% B27, 10 ng/mL FGF2, 10 ng/mL EGF, and 1% Pen/Strep.

extract_protocol:
Illumina TrueSeq Stranded mRNA kit
Nova-Seq 6000 platform

value: Neuroepithelial stem cells

tag: cell source

value: iPSC-derived

tag: disease state

value: Control cell line


title: lymph node TRC naive none day 0 Sample 11

description:
lymph node TRC naive none day 0
biological replicate


title: lymph node MRC naive none day 0 Sample 2


title: Neuroepithelial stem cells - CTRL11 (P10052_113)

description:
Sample 6
P10052_113
This cell line served as reference


title: spleen CD140a- naive none day 0 Sample 71


title: lymph node TRC naive none day 0 Sample 6


title: lymph node TRC naive none day 0 Sample 10


title: Neuroepithelial stem cells - CTRL9 (P10052_138)

description:
Sample 5
P10052_138
This cell line served as reference


title: spleen CD140a- naive none day 0 techl rep 2 Sample 8b

description:
spleen CD140a- naive none day 0 techl rep 2
technical replicate


title: Neuroepithelial stem cells - CTRL9 (P10052_125)

description:
Sample 5
P10052_125
This cell line served as reference


title: Neuroepithelial stem cells - CTRL7 (P10052_139)

description:
Sample 4
P10052_139
This cell line served as reference


title: Neuroepithelial stem cells - CTRL7 (P10052_124)

description:
Sample 4
P10052_124
This cell line served as reference


title: lymph node TRC naive none day 0 Sample 1


title: Neuroepithelial stem cells - CTRL9 (P10052_112)

description:
Sample 5
P10052_112
This cell line served as reference


title: Neuroepithelial stem cells - DSB3 (P10052_136)

description:
Sample 3
P10052_136
DESeq2_output_DSB3_comparedToAllCTRL.xlsx

value: Trisomy 21


title: Cal27-CYTOR-NC-2


title: spleen EYFP- naive none day 0 Sample 14