title: BY001+PD1-2

city: shanghai

first: lu

last: weiqiang

state: shanghai

address: 500 dongchuan

institute: East China Normal University

description: gene expression data from CT26 tumor with BY001 plus anti-PD-1 antibody treatment for two weeks.

hyb_protocol: Fragmentation and hybridization were performed using Agilent gene expression Hybridization Kit following the manufacturer's recommendations. 0.6 μg Cy3-labeled linearly amplified cRNA (specific activity > 9.0 pmol Cy3/μg cRNA) was fragmented at 60 °C for 30 min in reaction volume of 25 μL containing 2x Blocking Agent and 1x Fragmentation Buffer and stopped by 25 μL 2x Gene Expression Hybridization Buffer HI-RPM. 40 μL hybridization samples were hybridized to Agilent SurePrint G3 Mouse GE V2.0 microarrays in a rotating Agilent hybridization oven at 65 °C for 17 hours. After hybridization, microarray slides were washed with Gene Expression wash Buffer1 and Gene Expression wash Buffer2 37 °C following the manufacturer's recommendations. Then slowly minimized droplets on the microarray slides.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8*60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent Technologies) to extracting raw data. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data was analyzed and quantile normalized using Genespring 13.1 (Agilent Technologies).

label_protocol: Cyanine-3-CTP (Cy3)-labeled cRNA was prepared from 0.2 μg RNA using Agilent One-Color RNA Spike-In Kit (Agilent Technologies) and then purified by Qiagen’s RNeasy mini spin columns following the manufacturer's recommendations. cRNA was quantitated using NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific).

growth_protocol: The murine colorectal cancer cell lines CT26 were maintained in DMEM medium supplemented with 10% FBS (Gibco, Waltham, MA, USA) and 1% penicillin/streptomycin solution (Gibco) at 37 °C under a humidified atmosphere (5% CO2). 500,000 CT26 tumor cells were suspended in 100 μL PBS and implanted s.c. into the flank of mice. Mice were randomized into four different treatment groups when tumor volumes reached 100-200 mm3 (V = 0.52 × the longest diameter × (the shortest diameter)2).

extract_protocol: RNA was prepared using mirVanaTM miRNA Isolation Kit (ThermoFisher Scientific, Waltham, MA) according to the manufacturer's instructions. RNA was clean-up by RNasey Mini Kit (QIAGEN, Valencia, CA), and quantified by the NanoDrop ND-2000 (Thermo Fisher Scientific). RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: CT26 tumor-bearing mouse were treated with vehicle, BY001 ( (75 mg/kg, p.o., daily),  anti-PD-1 antibody (50 μg/mouse, i.p., twice a week) or combination of BY001 and anti-PD1 antibody for two weeks. Then total fresh tumor tissues were collected for microarray.

value: CT26 tumor

tag: cancer type

value: colorectal cancer

tag: agent

value: BY001 plus anti-PD-1 antibody


title: PD1-1

status: Public on Oct 19 2020

type: RNA

country: China

description: gene expression data from CT26 tumor with anti-PD-1 antibody treatment for two weeks.

molecule: total RNA

organism: Mus musculus

tag: tissue

value: anti-PD-1 antibody


title: colon_DSS_vehicle_4

city: Mechelen

first: Maté

last: Ongenaert

address: Generaal De Wittelaan L11A3

country: Belgium

institute: Galapagos

description: Gene expression of control animals (4% DSS in drinking water)

hyb_protocol: 600 ng of Cyanine 3-labeled amplified cRNA are hybridized at 65°C for 17 hours.

scan_protocol: Scanning is performed with Agilent Technologies’ scanner using default parameters for 8x60k format (61*21.6 mm; 3 micrometer scan resolution; 20 bit TIFF; green channel)

data_processing: Data are extracted with Feature Extraction 11.5.1.1 software (Agilent Technologies). This software reads and processes microarray image files to prepare them for analysis. Feature Extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. It determines feature intensities, rejects outliers and calculates statistical confidences. Quality was assessed using the arrayQualityMetrics R/BioConductor package. A filter was set to remove probes that are not expressed above background (cut-off defined such that a probe must have a valid and above background signal in at least 40% of the samples). Background correction (using the “normexp” method with an offset of 16) and quantile normalization were applied to obtain log2 transformed and normalized expression data. Within-array replicate probes are summarized with the mean. Differential expression analysis was performed using empirical Bayes methods and generalized linear models (limma R/BioConductor package). All data is MIAME compliant

source_name: colon mucosa, 4% DSS (3 cycli) in drinking water

label_protocol: Before labeling reaction, samples are diluted to 100 ng/ml. Then, Agilent Technologies’ Low Input Quick Amp Labeling Kit generates fluorescent cRNA with 100 ng of total RNA. The method first uses reverse transcriptase to synthesize the first and second strands of cDNA and then T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP. Before proceeding to the sample hybridization, labeled cRNA and dye concentrations are quantified with NanoDrop ND-1000 spectrophotometer (Thermo Scientific): - cRNA concentration (ng/μl), - Cyanine 3 concentration (pmol/μl). After labeling step, cRNA sample size ranges from 50 to 3000 nucleotides. Thus, fragmentation is required to take away secondary structures. Fragmentation step is achieved with specific buffer (Agilent Technologies) and allows obtaining cRNA length between 50 to 200 nucleotides and then optimal hybridization with Agilent 60-mer oligonucleotide microarrays. This step is incubation at 60°C for 30 minutes.

growth_protocol: Standard animal housing conditions

extract_protocol: For RNA preparation from mouse colon, mucosal samples were obtained by cutting lengthwise thirty millimeters of the most distal part of descending colon and scraping mucosa from the connective tissue. Mucosa was sampled into homogenization tubes containing 1.4 mm ceramic beads and was immediately snap frozen in liquid nitrogen. Mucosa samples were homogenized using the Precellys 24 homogenizer (Bertin Technologies™, France). Total RNA were isolated and further purified with NucleoSpin 96 RNA Tissue Core Kit (Macherey-Nagel™) according to the manufacturer’s instructions. RNA yield were determined by spectrophotometry at 260/280 nm.

treatment_protocol: Chronic colitis was induced in eight weeks old mice by cyclical administration of 4% DSS via drinking water, involving 3 cycles of DSS for 4 days interrupted by washout periods of 3 days under regular drinking water. The mice (n=5 per group) were assigned in 3 groups:  1/ Drinking water,  2/ DSS in water and filgotinib vehicle 3/ DSS in water and filgotinib. Filgotinib was given at 30 mg/kg, once a day by oral gavage.

tag: strain

value: Balb/cJ

tag: gender

value: female

value: colon mucosa

value: 4% DSS

tag: compound

value: vehicle control


title: PD1-2


title: BY001-1

description: gene expression data from CT26 tumor with BY001 treatment for two weeks.


title: colon_DSS_filgotinib_1

description: Gene expression of control animals (4% DSS in drinking water and 30 mg/kg filgotinib)

source_name: colon mucosa, 4% DSS (3 cycli) in drinking water + 30 mg/kg filgotinib (once daily by oral gavage)

value: 30 mg/kg filgotinib


title: colon_DSS_filgotinib_4


title: colon_DSS_vehicle_5


title: colon_water_2

description: Gene expression of control animals (drinking water)

source_name: colon mucosa, drinking water

value: water


title: Control-2

description: gene expression data from CT26 tumor with vehicle treatment for two weeks.

value: vehicle


title: colon_DSS_vehicle_1


title: colon_DSS_filgotinib_2


title: colon_water_1


title: colon_DSS_vehicle_3


title: Control-1


title: colon_water_5


title: colon_DSS_filgotinib_5


title: colon_water_4


title: BY001+PD1-1

description: gene expression data from CT26 tumor with BY001 plus anti-PD-1 antibodytreatment for two weeks.


title: tyroFahPM_cleaved_EM3146

type: SRA

city: Worcester

first: Athma

middle: A

last: Pai

state: MA

address: 368 Plantation Street, ASC5-2057

department: RNA Therapeutics Institute

country: USA

institute: University of Massachusetts Medical School

library_source: transcriptomic

data_processing:
Mus Musculus mm10 genome adapted with Nme2Cas9 mRNA sequence was used for all analyses
Reads mapped using STAR/2.7.5a
Reads were counted with HTSeq v.0.10.0
Differential expression analysis was performed using DESeq2
Genome_build: GRCm38.p6 (GCA_000001635.8)
Supplementary_files_format_and_content: htseq and kallistocount files

source_name: liver tissue

extract_protocol:
Total RNA was isolated from liver tissues using TRIzol reagent, and separated by Chloroform
libraries were prepared according to Illumina's protocol for TruSeq stranded mRNA (Illumina, 20020594)
RNA-seq library preparation was performed with 1ug of total RNA per sample using the TruSeq Stranded mRNA Library prep kit (Illumina, 20020595) following the manufacturer protocol. Libraries were sequenced on an Illumina NextSeq 500 with single end 75 nucleotide reads and an average of 19.88million reads

treatment_protocol: each sample treated with respective vector

value: liver

tag: mouse id

tag: disease state

value: Tyrosinemia FAH mice with G to A point mutation

tag: gene target

value: FAH

tag: vector

value: AAV HDR cleaved


title: tyroFahPM_cleaved_EM3145


title: tyroFahPM_cleaved_EM2929


title: tyroFahPM_cleaved_EM2928


title: tyroFahPM_cleaved_EM2930


title: BY001-2


title: tyroFahPM_cleaved_EM2996


title: tyroFahPM_cleaved_EM2927


title: tyroFahPM_uncleaved_EM3144

value: AAV HDR uncleaved


title: tyroFahPM_cleaved_EM2994


title: tyroFahPM_cleaved_EM2993


title: tyroFahPM_uncleaved_EM2999


title: tyroFahPM_uncleaved_EM3000


title: tyroFahPM_uncleaved_EM2998


title: Dclk1+ cells of PDAC 01

status: Public on Oct 20 2020

city: Kyoto

first: Takahisa

last: Maruno

state: Kyoto

address: 54 Syogoin-Kawahara-cho, Sakyo-ku

department: Gastroenterology and hepatology

country: Japan

institute: Kyoto university

description: mPDAC01 Dclk1+

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to 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 to obtain background subtracted and spatially detrended Processed Signal intensities. Data were normalized   on GeneSpring GX 14.5 (Agilent). Features flagged in Feature Extraction as not positive and significant or not above background were excluded.

source_name: Dclk1-positive PDACs cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 20ng Total RNA using the Pico WTA System(Ovation) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Dclk1CreERT2-IRES-EGFP/+; Pdx1-Flp; KrasFSF-G12D/+; Trp53frt/frt mice

tag: cell type

value: FACS-sorted Dclk1+ PDAC


title: colon_water_3


title: tyroFahPM_uncleaved_EM2991


title: tyroFahPM_uncleaved_EM2992


title: tyroFahPM_uncleaved_EM2990


title: tyroFahPM_donorSCRAM_EM3149

value: AAV.Nme2Ca9.gRNA targeting Fah.scramble donor DNA


title: tyroFahPM_uncleaved_EM2989


title: tyroFahPM_donorSCRAM_EM3148


title: tyroFahPM_guideSCRAM_EM3142

value: vector:AAV.Nme2Ca9.scramble gRNA.Fah donor DNA


title: tyroFahPM_donorSCRAM_EM3147


title: tyroFahPM_PBS_EM2988

value: vector:PBS (negative control)


title: tyroFahPM_PBS_EM2926


title: tyroFahPM_PBS_EM2987


title: tyroFahPM_guideSCRAM_EM3141


title: healthy_Nme2_WX7059

value: Healthy C57Bl/6 mice

value: AAV Nme2Cas9


title: healthy_Nme2_WX7058


title: tyroFahPM_guideSCRAM_EM3140


title: tyroFahPM_uncleaved_EM2997


title: healthy_Nme2_WX7057


title: tyroFahNEO_dualgRNA5_EM2964

value: Tyrosinemia mice with neomycin casette

value: HPD

value: dual gRNA design 1


title: healthy_dualgRNA5_EM2978


title: healthy_dualgRNA5_EM2970


title: healthy_dualgRNA5_EM2969


title: tyroFahPM_uncleaved_EM3143


title: tyroFahNEO_dualgRNA5_EM2963


title: tyroFahNEO_dualgRNA5_EM2962


title: tyroFahNEO_dualgRNA5_EM2960


title: healthy_dualgRNA4_EM2971

value: dual gRNA design 4


title: tyroFahNEO_dualgRNA5_EM2959


title: tyroFahNEO_dualgRNA5_EM2920


title: healthy_dualgRNA4_EM2968


title: healthy_dualgRNA4_EM2976


title: tyroFahNEO_dualgRNA5_EM2921


title: tyroFahNEO_dualgRNA4_WX5386


title: healthy_dualgRNA4_EM2967


title: tyroFahNEO_dualgRNA4_EM2918


title: tyroFahNEO_dualgRNA4_EM2919


title: healthy_dualgRNA5_EM2977


title: tyroFahNEO_dualgRNA4_WX5383


title: tyroFahNEO_dualgRNA4_WX5384


title: tyroFahNEO_dualgRNA4_EM2917


title: tyroFahNEO_PBS_EM2966

value: PBS


title: tyroFahNEO_PBS_WX5387

value: liver


title: tyroFahNEO_PBS_EM2965


title: batch2_RiboSeq_ko

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

data_processing:
Library strategy: Ribo-seq
Adapters were removed with cutadapt v2.1
Ribo-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20 --trimmed-only
RNA-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20
Trimmed sequences were mapped to the mm10 genome assembly with GENCODE M22 genome annotation using STAR v2.7.1a with default parameters.
Read counts were extracted from STAR output.
Genome_build: mm10
Supplementary_files_format_and_content: tsv (tab-separated txt), gene-level read counts from STAR output

molecule: polyA RNA

source_name: Embryonic fibroblast

growth_protocol: Wild-type and eIF4G2(-/-) knock-out cells were grown in 150 mm plates (SPL Life Sciences) at 30-60% density in DMEM (PanEco, Moscow, Russia) supplemented with 10% FBS (HyClone). Cells were re-plated once in 3 days to obtain 12 plates per experiment.

extract_protocol:
Cells were put on ice, washed with ice-cold PBS supplemented with 100 ug/ml cycloheximide, lyzed in (20 mM Tris-HCl, pH 7.5 250 mM NaCl 1,5 mM MgCl2, 1mM DTT, 0,5% Triton X-100, 100 μg/ml cycloheximide and 20 U/ml TURBO DNAse). For total poly(A)-plus RNA sequencing, the lysates were deproteinized using Trizol-LS (Invitrogen) extraction, RNA was precipitated, purified via Oligotex resin (QIAGEN), and fragmented via mild alkaline hydrolysis. For ribosome footprints sequencing, the lysates were treated with RNase I (Ambion), the 80S monosomes were purified via 10-60% sucrose density gradient centrifugation, and deproteinized using acid phenol extraction. Both RNA_seq and ribo_seq RNA fragments were further purified via 15% PAGE and the RNA from 28 to 34 nt long was excised and extracted from gel slices.
RNA was dephosphorylated using T4 PNK, then preadenylated Universal miRNA cloning linker (NEB) was ligated to RNA fragments using truncated T4 RNA ligase 2 (NEB), excised from 15% PAG, and reverse transcribed with SuperScript III revertase (Invitrogen). The DNA was excised from 7.5% PAG and circularized using CircLigase II (Illumina). The resulting libraries were depleted of rRNA-derived products, amplified with NEB TrueSeq adapters and sequenced.

tag: cell line

value: NIH 3T3

tag: genotype

tag: rna population

value: cytoplasmic RNA


title: tyroFahNEO_dualgRNA5_WX8321


title: tyroFahNEO_dualgRNA4_WX5389


title: batch2_RNASeq_ko

data_processing:
Adapters were removed with cutadapt v2.1
Ribo-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20 --trimmed-only
RNA-Seq: cutadapt -a AGATCGGAAGAG -j 4 --minimum-length 20 -q 20
Trimmed sequences were mapped to the mm10 genome assembly with GENCODE M22 genome annotation using STAR v2.7.1a with default parameters.
Read counts were extracted from STAR output.
Genome_build: mm10
Supplementary_files_format_and_content: tsv (tab-separated txt), gene-level read counts from STAR output

value: polyA RNA


title: Input for the EBF1-ChIP in dHet-proB-Rep2

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

library_source: genomic

data_processing:
Basecalling and fastq files generation was performed by using Illumina bcl2fastq 2.17.1.14 (pipeline version 0.2.1)
ChIPSeq: The reads were aligned to the mm9 genome assembly using bowtie2 with default configurations
ChIPSeq: Duplicated reads were filtered and blacklisted regions were removed using samtools and Picard.
ChIPSeq: Peaks were identified using MACS2 (v2.1.0.20150731) with q-value cutoff 0.01 and filtered for p-value cut-off 10e-10 (EBF1) or 10e-7 (Pax5). The peaks were further filtered with the fold change cut-off 4.
ATACSeq: The paried-end sequencing reads were trimmed using trim galore (0.4.0), which is a wrapper for the Cutadapt (1.8.1) tools. The trimmed reads were mapped to the mouse genome (mm9) using bowtie2 (2.2.8) with the default settings.
ATACSeq: The duplicated reads were removed using Picard tools (1.136). The reads mapping to blacklisted regions, mitochondrial genome and the reads with mapping quality below 30 were removed. The properly mapped reads were used for identifying peaks by MACS2 (2.1.1) with the BAMPE mode and q-value cut off 0.01. The differentially induced peaks were identified by comapring between the samples and further filtered for a p-value cutoff 10-10 and fold change 4.
The reads were normalized to 10 million mapped reads using Homer tools (v 4.1) in bedGraph format for visualization.
Genome_build: mm9
Supplementary_files_format_and_content: The reads normalized to 10 million in the bedGraph format were generated using Homer tools

molecule: genomic DNA

source_name: Ebf1+/- Pax5+/- dHet fetal liver proB cells,Replicate2

growth_protocol: The normal pro-B cell lines were established by culturing c-Kit+ fetal liver cells of Ebf1+/+ or Ebf1+/-Pax5+/- cells with OP9 feeder cells in OptiMEM medium supplemented with 4%FCS, 50μM 2-ME, 1% Penicillin-Streptmycin-Glutamine, 10ng/ml Stem cell factor (SCF), 10ng/ml Flt3-L, and 5ng/ml IL-7. Leukemic Ebf1+/-Pax5+/- cell lines were established similarly using bone marrow CD19+AA4.1hi cells.

extract_protocol:
Cells were crosslinked  with formaldehyde, lysed and DNA was fragmented into pieces of average 300bp by sonication. Chromatin was precipitated with a specific antibody and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.
Library preparation for ChIP analysis was performed with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog #E7370) according to the manufacturer’s protocol. No size selection was used and amplification was performed using 10 PCR cycles. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.

value: Ebf1+/- Pax5+/- proB fetal liver cells

tag: chip antibody


title: tyroFahNEO_dualgRNA4_WX5385


title: Input for the EBF1-ChIP in dHet-proB-Rep1

source_name: Ebf1+/- Pax5+/- dHet fetal liver proB cells,Replicate1


title: EBF1-ChIP in dHet-proB-Rep1

source_name: Ebf1+/- Pax5+/- Rag2-/- dHet fetal liver proB cells,Replicate1

value: Ebf1+/- Pax5+/-  proB fetal liver cells


title: batch2_RiboSeq_wt

value: wild-type


title: EBF1-ChIP in dHet-proB-Rep2

source_name: Ebf1+/- Pax5+/- Rag2-/- dHet fetal liver proB cells,Replicate2


title: old Mito-Q treated rep#2

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Reads trimmed using Trim Galore
Alignment: STAR v 2.7
QC and geneCounts: QoRTs
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file containing IDs and read counts

source_name: Hematopoietic Stem Cell

growth_protocol: Mice were housed in plastic cages in a controlled environment with 12-hour light-dark cycles and chow and water were provided ad libitum.

extract_protocol:
Mice were euthanised by spinal dislocation followed by the dissection of the spinal bones and both femurs, tibias and iliacs. Bones were crushed using a pestle and mortar and cells were collected in  ice-cold PBS+2%FBS, filtered and washed. Bone marrow cells were c-kit enriched and live SLAM-HSCs (Lin- Ckit+ Sca1+ CD48- CD150+) were FACS sorted into trizol for RNA isolation.
Sequencing libraries were produced using Nextera XT DNA Preparation Kit (Illumina) following a modified version of the manufacturer’s protocol with 20-fold volume reduction

treatment_protocol: Mito-Q treated mice received 5 daily consecutive i.p. injections with 2mg/kg MitoQ; CCCP-treated mice received a single i.p. injection of 0.3 mg/kg.

value: C57BL/6 Jrj

tag: mouse age

value: >18 months

tag: treatment

value: Mito-Q


title: old Mito-Q treated rep#3


title: batch2_RNASeq_wt


title: old Mito-Q treated rep#4


title: old Mito-Q treated rep#5


title: old Mito-Q treated rep#1


title: old control rep#3

value: control


title: young CCCP treated rep#5

value: 8- 12 weeks

value: CCCP


title: old control rep#1


title: colon_DSS_filgotinib_3

value: Balb/cJ

value: female

value: colon mucosa

value: 4% DSS

value: 30 mg/kg filgotinib


title: young CCCP treated rep#3


title: old control rep#2


title: young CCCP treated rep#2


title: young control rep #4


title: young CCCP treated rep#1


title: young control rep #2


title: young control rep #3


title: young control rep #1


title: Old MMP high rep #2

treatment_protocol: Mice were untreated


title: Young MMP high rep #3


title: Old MMP high rep #1


title: Old MMP high rep #3


title: Young MMP high rep #1


title: Old MMP low rep #3


title: Young MMP high rep #4


title: Young MMP low rep #2


title: Old MMP low rep #1


title: Young MMP low rep #3


title: Old MMP low rep #2


title: sciatic nerve macrophages (WThSOD1 BM grafted at onset into G93A) (MP isolated at end stage)_rep2

city: Paris

first: Severine

last: Boillee

address: Pitie-Salpetriere Hospital, 47 bd de l'Hopital, Batiment ICM

department: Institut du Cerveau - ICM

country: France

institute: Paris Brain Institute, Inserm U1127, CNRS, Sorbonne University

description: Nr-137-MP WT->G93A EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)

data_processing:
RNA-Seq data analysis was performed by GenoSplice (www.genosplice.com).
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc. All the samples presented and used for the analyses passed all the quality controls.
Reads were mapped using STARv2.4.0 (Dobin et al., 2013; PMID: 23104886) on the mm10 Mouse genome assembly.
Gene expression regulation study was performed as already described (Noli et al., 2015; PMID: 26584541). Briefly, for each gene present in the mouse FAST DB v2018_1 annotations, reads aligning on constitutive regions (that are not prone to alternative splicing) were counted. Based on these read counts, normalization and differential gene expression were performed using DESeq2 (Love et al., 2014; PMID: 25516281) on R (v.3.2.5). Only genes expressed in at least one of the compared experimental conditions were further analyzed. Genes were considered as expressed if their rpkm value was greater than 96% of the background rpkm value based on intergenic regions. Results were considered statistically significant for p-values ≤ 0.05 and fold-changes ≥ 1.5.
Additional analyses were performed using R software and Ingenuity Pathway Analysis (IPA, Qiagen).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with fpkm values for every gene and every of the 51 NON_GRAFTED samples (PART 1 of Study, see "Overall Design") (CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)
Supplementary_files_format_and_content: Matrix table with fpkm values for every gene and every of the 23 GRAFTED samples (PART 2 of study, see "Overall Design") (CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)

extract_protocol:
Mice were all females and were deeply anesthetized using Xylazine (Rompun 0.2%) and Ketamine (Imalgene 500) and transcardially perfused with ice-cold 0.1M PBS.     For sciatic nerve peripheral macrophages (MP), two whole left and right sciatic nerves (from the gastrocnemius muscles to the spine vertebrae) were collected and pooled, except for the macrophages at the pre-symptomatic stage where four sciatic nerves coming from two mice of the same age were needed to recover enough cells, and for spinal cord microglial cells (MG), whole spinal cords were flushed using 0.1M PBS. Tissues were chopped in DMEM-F10 (1:1, Life Technologies) culture medium supplemented with 10% Fetal Calf Serum (FCS, low endiotoxins, Life technologies). Tissues were passed through a 100μm nylon filter (Falcon). Myelin was removed using a percoll gradient (30-37-70% percoll, GE healthacare) in 0.1M PBS. The whole procedure was performed at 4°C and did not use enzymatic digestion/ incubation at 37°C to avoid ex-vivo activation of the cells. Briefly, 1.6 ml of 70% Percoll solution were laid at the bottom of 5ml polypropylene tubes (Falcon), gently covered by 1.6 ml of 37% Percoll. Cells were homogenized in 30% Percoll solution and carefully laid on top and centrifuged (without break) for 40 minutes at 800g at 4°C. The 30% percoll layer containing myelin was removed and cells were recovered at the interface between the 37% and the 70% Percoll layers. Cells were resuspended in 0.1M PBS, 0.5% BSA (Sigma Aldrich), 2mM EDTA (Life Technologies).    Microglial cells (MG) or peripheral macrophages (MP) were isolated using an anti-CD11b magnetic microbead-coupled antibody and MS columns (Miltenyi Biotec) according to manufacturer’s instructions. Between 1.0x10^5 and 1.8x10^5 microglial cells were recovered from spinal cords (one spinal cord from one animal per sample, see Publication for more details) and between 3x10^4 and 5x10^4 macrophages were recovered from sciatic nerves (two sciatic nerves from one animal per sample except for the pre-symptomatic stage where 4 sciatic nerves from two mice were pooled, see Publication for more details) depending on the genotype and disease stage of the mice. For RNA isolation, cells were centrifuged at 300g at 4°C and kept at -80C until further use.    RNA was extracted from spinal cord microglial cells and from sciatic nerve macrophages using the Nucleospin RNA XS kit (Macherey Nagel) with a final RNA elution in 10μl.
Microglial cell RNA concentration was determined with a RNA 6000 pico kit (Agilent Technologies) on an Agilent Bioanalyzer. Although the number of microglial cells and macrophages and therefore the total quantity of RNA obtained from the two cell populations, were different, to compare microglial cells and macrophages, we used the same protocol and the same kits and we therefore used only a fraction of the microglial RNA obtained. One ng of microglial cell RNA (from total RNA of 1.50-7ng/microglial sample) and whole total eluted RNA of sciatic nerve macrophages (RNA quantities for macrophage were too low to be measured, but estimated from the number of cells, in comparison to microglia) were used to perform cDNA synthesis using the Smart-Seq v4 Ultra Low Input RNA kit for sequencing (Clontech laboratories) with linear pre-amplification.
Library preparation was made with 150 pg of amplified cDNA for every sample (microglia and macrophages) using the Nextera XT DNA Library Preparation Kit (Illumina). Eight samples were run with a 400 million cartridge to reach an average coverage of 50 million reads per sample (75bp, paired-ends). Sequencing was performed using the NextSeq 500 high Output Kit V2 on a Illumina NextSeq 500. Library preparations and sequencing were performed by the ICM iGenSeq core facility.

value: mutant hSOD1-G93A (C57BL/6J)

tag: bone-marrow grafting status

value: bone-marrow (BM) grafted animal

tag: bone-marrow grafting type

value: wildtype hSOD1 BM grafted at onset into mutant hSOD1-G93A animal

value: end stage

value: sciatic nerve

value: peripheral macrophages (MP)


title: sciatic nerve macrophages (G93A BM grafted at onset into G93A) (MP isolated at end stage)_rep2

description: Nr-134-MP G93A->G93A EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)

value: mutant hSOD1-G93A BM grafted at onset into mutant hSOD1-G93A animal

tag: tissue


title: sciatic nerve macrophages (WThSOD1 BM grafted at onset into G93A) (MP isolated at end stage)_rep3

description: Nr-138-MP WT->G93A EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)

tag: strain


title: sciatic nerve macrophages (WThSOD1 BM grafted at onset into G93A) (MP isolated at end stage)_rep1

description: Nr-136-MP WT->G93A EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages (G93A BM grafted at onset into G93A) (MP isolated at end stage)_rep1

description: Nr-133-MP G93A->G93A EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: young CCCP treated rep#4

value: C57BL/6 Jrj


title: sciatic nerve macrophages (G93A BM grafted at onset into G93A) (MP isolated at early symptomatic)_rep3

description: Nr-129-MP G93A->G93A EarlySympt-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)

value: early symptomatic


title: sciatic nerve macrophages (G93A BM grafted at onset into G93A) (MP isolated at early symptomatic)_rep2

description: Nr-128-MP G93A->G93A EarlySympt-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages (WThSOD1 BM grafted at onset into G93A) (MP isolated at early symptomatic)_rep2

description: Nr-132-MP WT->G93A EarlySympt-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages (WThSOD1 BM grafted at onset into G93A) (MP isolated at early symptomatic)_rep1

description: Nr-131-MP WT->G93A EarlySympt-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: Young MMP high rep #2


title: spinal cord microglia (WThSOD1 BM grafted at onset into G93A) (MG isolated at end stage)_rep2

description: Nr-125-MG WT->G93A EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)

value: spinal cord

value: microglial cells (MG)


title: spinal cord microglia (WThSOD1 BM grafted at onset into G93A) (MG isolated at end stage)_rep3

description: Nr-126-MG WT->G93A EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages (G93A BM grafted at onset into G93A) (MP isolated at early symptomatic)_rep1

description: Nr-127-MP G93A->G93A EarlySympt-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (G93A BM grafted at onset into G93A) (MG isolated at end stage)_rep2

description: Nr-122-MG G93A->G93A EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (G93A BM grafted at onset into G93A) (MG isolated at end stage)_rep1

description: Nr-121-MG G93A->G93A EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (WThSOD1 BM grafted at onset into G93A) (MG isolated at end stage)_rep1

description: Nr-124-MG WT->G93A EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: Young MMP low rep #1

value: 8- 12 weeks


title: spinal cord microglia (WThSOD1 BM grafted at onset into G93A) (MG isolated at early symptomatic)_rep2

description: Nr-119-MG WT->G93A EarlySympt-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (WThSOD1 BM grafted at onset into G93A) (MG isolated at early symptomatic)_rep3

description: Nr-120-MG WT->G93A EarlySympt-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (G93A BM grafted at onset into G93A) (MG isolated at end stage)_rep3

description: Nr-123-MG G93A->G93A EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages (G93A BM grafted at onset into G93A) (MP isolated at end stage)_rep3

description: Nr-135-MP G93A->G93A EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (WThSOD1 BM grafted at onset into G93A) (MG isolated at early symptomatic)_rep1

description: Nr-118-MG WT->G93A EarlySympt-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (G93A BM grafted at onset into G93A) (MG isolated at early symptomatic)_rep2

description: Nr-116-MG G93A->G93A EarlySympt-2 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia (G93A BM grafted at onset into G93A) (MG isolated at early symptomatic)_rep3

description: Nr-117-MG G93A->G93A EarlySympt-3 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: colon_DSS_vehicle_2

description: Gene expression of control animals (4% DSS in drinking water)

value: Balb/cJ

tag: gender

value: vehicle control


title: sciatic nerve macrophages G93A (at age corresponding to end stage)_rep3

description: Nr-113-MP-WT-EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: non-grafted animal

value: age corresponding to end stage


title: spinal cord microglia (G93A BM grafted at onset into G93A) (MG isolated at early symptomatic)_rep1

description: Nr-115-MG G93A->G93A EarlySympt-1 (in Matrix Table: CHIOT_fpkm_values_all_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (at age corresponding to end stage)_rep2

description: Nr-100-MP-WT-EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (end stage)_rep4

description: Nr-53-MP-G93A-EndStage-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: end stage (mean age:169.4 days)


title: sciatic nerve macrophages G93A (end stage)_rep3

description: Nr-52-MP-G93A-EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: mutant hSOD1-G93A (C57BL/6J)


title: sciatic nerve macrophages G93A (early symptomatic)_rep4

description: Nr-49-MP-G93A-EarlySympt-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: early symptomatic (10% weight loss) (mean age:152.6 days)


title: sciatic nerve macrophages G93A (end stage)_rep1

description: Nr-50-MP-G93A-EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (end stage)_rep2

description: Nr-51-MP-G93A-EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (early symptomatic)_rep3

description: Nr-48-MP-G93A-EarlySympt-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (early symptomatic)_rep2

description: Nr-46-MP-G93A-EarlySympt-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (early symptomatic)_rep1

description: Nr-45-MP-G93A-EarlySympt-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (onset)_rep3

description: Nr-112-MP-G93A-Onset-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

source_name: sciatic nerve macrophages G93A (onset)

value: onset (weight peak) (mean age:105 days)


title: sciatic nerve macrophages G93A (onset)_rep1

description: Nr-40-MP-G93A-Onset-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (onset)_rep2

description: Nr-44-MP-G93A-Onset-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: sciatic nerve macrophages G93A (pre-symptomatic)_rep2

description: Nr-110-MP-G93A-PreSympt-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: pre-symptomatic (mean age:50.8 days)


title: sciatic nerve macrophages G93A (at age corresponding to end stage)_rep4

description: Nr-114-MP-WT-EndStage-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: sciatic nerve


title: sciatic nerve macrophages G93A (pre-symptomatic)_rep3

description: Nr-111-MP-G93A-PreSympt-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: peripheral macrophages (MP)


title: spinal cord microglia Control WT (at age corresponding to end stage)_rep4

description: Nr-39-MG-WT-EndStage-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: wildtype hSOD1 (C57BL/6J)

value: age corresponding to end stage (mean age:165.4 days)


title: sciatic nerve macrophages G93A (pre-symptomatic)_rep1

description: Nr-107-MP-G93A-PreSympt-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control WT (at age corresponding to end stage)_rep2

description: Nr-37-MG-WT-EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control WT (at age corresponding to end stage)_rep1

description: Nr-35-MG-WT-EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control WT (at age corresponding to onset)_rep3

description: Nr-18-MG-WT-Onset-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: age corresponding to onset (mean age:107.3 days)


title: spinal cord microglia Control WT (at age corresponding to onset)_rep4

description: Nr-19-MG-WT-Onset-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: spinal cord


title: spinal cord microglia Control WT (at age corresponding to end stage)_rep3

description: Nr-38-MG-WT-EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: microglial cells (MG)


title: spinal cord microglia Control WT (at age corresponding to onset)_rep1

description: Nr-16-MG-WT-Onset-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to end stage)_rep4

description: Nr-34-MG-B6-EndStage-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: age corresponding to end stage (mean age:165.6 days)


title: sciatic nerve macrophages G93A (at age corresponding to end stage)_rep1

description: Nr-55-MP-WT-EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to end stage)_rep2

description: Nr-31-MG-B6-EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to end stage)_rep1

description: Nr-30-MG-B6-EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to end stage)_rep3

description: Nr-32-MG-B6-EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to onset)_rep3

description: Nr-14-MG-B6-Onset-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: age corresponding to onset (mean age:109.8 days)


title: spinal cord microglia G93A (end stage)_rep4

description: Nr-28-MG-G93A-EndStage-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

source_name: spinal cord microglia G93A (end stage)


title: spinal cord microglia Control B6 (at age corresponding to onset)_rep4

description: Nr-15-MG-B6-Onset-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (end stage)_rep3

description: Nr-27-MG-G93A-EndStage-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to onset)_rep2

description: Nr-13-MG-B6-Onset-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (end stage)_rep1

description: Nr-25-MG-G93A-EndStage-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control B6 (at age corresponding to onset)_rep1

description: Nr-12-MG-B6-Onset-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (early symptomatic)_rep4

description: Nr-24-MG-G93A-EarlySympt-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia Control WT (at age corresponding to onset)_rep2

description: Nr-17-MG-WT-Onset-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (early symptomatic)_rep3

description: Nr-23-MG-G93A-EarlySympt-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (early symptomatic)_rep2

description: Nr-22-MG-G93A-EarlySympt-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (early symptomatic)_rep1

description: Nr-20-MG-G93A-EarlySympt-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (onset)_rep4

description: Nr-10-MG-G93A-Onset-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

source_name: spinal cord microglia G93A (onset)


title: spinal cord microglia G93A (onset)_rep2

description: Nr-7-MG-G93A-Onset-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (onset)_rep3

description: Nr-8-MG-G93A-Onset-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (pre-symptomatic)_rep4

description: Nr-4-MG-G93A-PreSympt-4 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (pre-symptomatic)_rep3

description: Nr-3-MG-G93A-PreSympt-3 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: spinal cord microglia G93A (onset)_rep5

description: Nr-103-MG-G93A-Onset-5 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: ChIRP-seq: NDL-input rep2

city: Dunedin

first: Sarah

middle: D

last: Diermeier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Library strategy: ChIRP-seq
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using Bowtie2.
Peaks were called across different replicates and against background controls using HOMER (getDifferentialPeaksReplicates.pl)
Peaks => 50-fold enrichment were annotated with HOMER (annotatePeaks.pl) to GENCODE vM16.
Motifs were identified using HOMER (findMotifsGenome.pl) +/- 500 bp around the peaks.
Genome_build: mm10
Supplementary_files_format_and_content: txt, annotated peak files incorporating all replicates, in comparison to input and background controls, >50-fold enrichment

source_name: primary NDL cells

growth_protocol: Cell lines were grown in DMEM + 10%FBS + 1% P/S

extract_protocol:
DNA was enriched and extracted according to a previously described protocol (Chu et al., 2011). Briefly, 20 million cells were harvested and fixed in 1% glutaraldehyde solution for each reaction. ChIRP was performed using biotinylated oligo probes designed against mouse MaTAR25 or Cyclophilin B. Independent even and odd probe pools were used to ensure lncRNA-specific retrieval.
Illumina TruSeq ChIP Library Preparation Kit

value: FVB

value: MMTV-PyMT

value: Mammary tumor

tag: pulldown


title: spinal cord microglia G93A (pre-symptomatic)_rep2

description: Nr-2-MG-G93A-PreSympt-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: non-grafted animal


title: spinal cord microglia G93A (onset)_rep1

description: Nr-6-MG-G93A-Onset-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: mutant hSOD1-G93A (C57BL/6J)


title: spinal cord microglia G93A (pre-symptomatic)_rep1

description: Nr-1-MG-G93A-PreSympt-1 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)


title: ChIRP-seq: NDL-cycloB rep1

value: Cyclophilin B oligo pool


title: ChIRP-seq: NDL-total rep2

value: MaTAR25 oligos 1-14


title: ChIRP-seq: NDL-total rep1


title: ChIRP-seq: 4T1-even rep3

value: BALB/c

value: wild type

value: MaTAR25 even oligo pool


title: ChIRP-seq: 4T1-cycloB rep1


title: spinal cord microglia G93A (end stage)_rep2

description: Nr-26-MG-G93A-EndStage-2 (in Matrix Table: CHIOT_fpkm_values_all_NON_GRAFTED_samples_Matrix.txt)

value: end stage (mean age:169.4 days)


title: tyroFahPM_cleaved_EM2995

value: liver

tag: mouse id

value: Tyrosinemia FAH mice with G to A point mutation

value: FAH

value: AAV HDR cleaved


title: RNA-seq: KO2 rep2

data_processing:
Illumina Casava software used for basecalling.
The quality of the raw data was evaluated using FastQC.
The reads were mapped to mm10 using STAR.
The GENCODE mV5 annotation set was used as a reference and the reads per gene record were counted using the HTSeq package.
Differential gene expression was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads (generated with HTSeq-count) for each Sample.

extract_protocol:
Total RNA was extracted using TRIzol
Libraries for polyA+ RNA-Sequencing were prepared from 1 μg RNA per sample using TruSeq chemistry (Illumina)

value: mammary tumor


title: RNA-seq: KO2 rep4


title: ChIRP-seq: NDL-input rep1


title: RNA-seq: KO2 rep3


title: ChIRP-seq: 4T1-odd rep1

value: MaTAR25 odd oligo pool


title: ChIRP-seq: 4T1-even rep1


title: ChIRP-seq: 4T1-total rep2


title: ChIRP-seq: 4T1-even rep2


title: ChIRP-seq: 4T1-odd rep2


title: ChIRP-seq: 4T1-total rep1


title: ChIRP-seq: 4T1-input rep1


title: ChIRP-seq: 4T1-input rep4


title: ChIRP-seq: 4T1-input rep3


title: ChIRP-seq: 4T1-input rep2


title: RNA-seq: KO1 rep3


title: RNA-seq: KO1 rep1


title: Subject 27 without EEC enrichment technical replicate 6

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 6

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
The analyses were performed using the Eoulsan pipeline (17), including read filtering, mapping, alignment filtering, read quantification, normalization and differential analysis. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the human genome from Ensembl version 88 using STAR (version 2.5.2b). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, human GTF genome annotation version 88 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3.
Genome_build: Hg19 (Ensembl 88)
Supplementary_files_format_and_content: tab-delimited text files include gene counting for each Sample

organism: Homo sapiens

source_name: Subject 27

extract_protocol:
Total RNA was extracted using the RNAeasy Mini Plus Kit (Qiagen)
10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards an average of 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina)

treatment_protocol: For cells sorting experiments, epithelial cells were rinsed in FACS buffer (PBS, 3% FCS, 2 mM EDTA), blocked with Human Fc Receptor Binding Inhibitor Antibody (eBioscience) and stained (30 min, 4°C) with the following antibodies: CD45-BV421 (Bio Legend) and CD24-PeCy7 (Bio Legend). Dead cells were excluded with propidium iodure (eBiosciences). During sorting experiments, cells were placed in FACS buffer with RNAse inhibitor (Life Technologies). CD24 marker was used to select differentiated cells, and CD45 was used to get rid of B lymphocytes that also expressed CD24. Enriched EEC were CD45-negative, CD24-positive sorted by FACS. Cells were isolated on a MoFlo Astrios EQ (Beckam Coulter). Data were analyzed with software FlowJo. V10.0.7 (Tree Star).

tag: individual

value: Patient 28

value: female

tag: phenotype

value: Diabetic Obese

value: No EEC enrichment

value: EEC


title: Subject 27 without EEC enrichment technical replicate 7

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 7


title: Subject 27 without EEC enrichment technical replicate 8

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 8


title: RNA-seq: KO1 rep2


title: Subject 27 without EEC enrichment technical replicate 5

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 5


title: Subject 27 without EEC enrichment technical replicate 4

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 4


title: Subject 27 technical replicate 7

description: Patient 27, Diabetic Obese, technical replicate 7

value: Patient 27

value: EEC enrichment


title: Subject 27 technical replicate 8

description: Patient 27, Diabetic Obese, technical replicate 8


title: Subject 27 without EEC enrichment technical replicate 1

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 1


title: RNA-seq: KO2 rep1

value: BALB/c


title: Subject 27 without EEC enrichment technical replicate 2

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 2


title: Subject 27 technical replicate 6

description: Patient 27, Diabetic Obese, technical replicate 6


title: Subject 27 technical replicate 4

description: Patient 27, Diabetic Obese, technical replicate 4


title: RNA-seq: Control rep2

value: wild type


title: Subject 26 technical replicate 7

description: Patient 26, Diabetic Obese, technical replicate 7

source_name: Subject 26

value: Patient 26

value: male


title: Subject 27 technical replicate 2

description: Patient 27, Diabetic Obese, technical replicate 2


title: Subject 26 technical replicate 6

description: Patient 26, Diabetic Obese, technical replicate 6


title: Subject 26 technical replicate 8

description: Patient 26, Diabetic Obese, technical replicate 8


title: Subject 26 technical replicate 5

description: Patient 26, Diabetic Obese, technical replicate 5


title: RNA-seq: Control rep1


title: Subject 26 technical replicate 4

description: Patient 26, Diabetic Obese, technical replicate 4


title: Subject 27 without EEC enrichment technical replicate 3

description: Patient 27, without EEC enrichment, Diabetic Obese, technical replicate 3


title: Subject 25 technical replicate 8

description: Patient 25, Diabetic Obese, technical replicate 8

source_name: Subject 25

value: Patient 25


title: Subject 26 technical replicate 3

description: Patient 26, Diabetic Obese, technical replicate 3


title: Subject 26 technical replicate 1

description: Patient 26, Diabetic Obese, technical replicate 1


title: Subject 25 technical replicate 7

description: Patient 25, Diabetic Obese, technical replicate 7


title: Subject 25 technical replicate 4

description: Patient 25, Diabetic Obese, technical replicate 4


title: Subject 25 technical replicate 6

description: Patient 25, Diabetic Obese, technical replicate 6


title: Subject 25 technical replicate 3

description: Patient 25, Diabetic Obese, technical replicate 3


title: Subject 24 technical replicate 4

description: Patient 24, Diabetic Obese, technical replicate 4

source_name: Subject 24

value: Patient 24


title: Subject 24 technical replicate 7

description: Patient 24, Diabetic Obese, technical replicate 7


title: Subject 24 technical replicate 5

description: Patient 24, Diabetic Obese, technical replicate 5


title: Subject 25 technical replicate 1

description: Patient 25, Diabetic Obese, technical replicate 1


title: Subject 25 technical replicate 2

description: Patient 25, Diabetic Obese, technical replicate 2


title: Subject 24 technical replicate 6

description: Patient 24, Diabetic Obese, technical replicate 6


title: Subject 24 technical replicate 8

description: Patient 24, Diabetic Obese, technical replicate 8


title: Subject 27 technical replicate 3

description: Patient 27, Diabetic Obese, technical replicate 3


title: Subject 27 technical replicate 5

description: Patient 27, Diabetic Obese, technical replicate 5


title: Subject 24 technical replicate 2

description: Patient 24, Diabetic Obese, technical replicate 2


title: Subject 24 technical replicate 3

description: Patient 24, Diabetic Obese, technical replicate 3


title: Subject 23 technical replicate 6

description: Patient 23, Diabetic Obese, technical replicate 6

source_name: Subject 23

value: Patient 23


title: Subject 23 technical replicate 4

description: Patient 23, Diabetic Obese, technical replicate 4


title: Subject 23 technical replicate 8

description: Patient 23, Diabetic Obese, technical replicate 8


title: Subject 26 technical replicate 2

description: Patient 26, Diabetic Obese, technical replicate 2


title: Subject 23 technical replicate 3

description: Patient 23, Diabetic Obese, technical replicate 3


title: Subject 23 technical replicate 7

description: Patient 23, Diabetic Obese, technical replicate 7


title: Subject 24 technical replicate 1

description: Patient 24, Diabetic Obese, technical replicate 1


title: Subject 25 technical replicate 5

description: Patient 25, Diabetic Obese, technical replicate 5


title: Subject 23 technical replicate 5

description: Patient 23, Diabetic Obese, technical replicate 5


title: Subject 22 technical replicate 7

description: Patient 22, Diabetic Obese, technical replicate 7

source_name: Subject 22

value: Patient 22


title: Subject 23 technical replicate 1

description: Patient 23, Diabetic Obese, technical replicate 1


title: Subject 22 technical replicate 8

description: Patient 22, Diabetic Obese, technical replicate 8


title: Subject 22 technical replicate 6

description: Patient 22, Diabetic Obese, technical replicate 6


title: Subject 22 technical replicate 4

description: Patient 22, Diabetic Obese, technical replicate 4


title: Subject 22 technical replicate 5

description: Patient 22, Diabetic Obese, technical replicate 5


title: Subject 22 technical replicate 2

description: Patient 22, Diabetic Obese, technical replicate 2


title: Subject 22 technical replicate 1

description: Patient 22, Diabetic Obese, technical replicate 1


title: Subject 21 technical replicate 6

description: Patient 21, Diabetic Obese, technical replicate 6

source_name: Subject 21

value: Patient 21


title: Subject 21 technical replicate 7

description: Patient 21, Diabetic Obese, technical replicate 7


title: Subject 21 technical replicate 8

description: Patient 21, Diabetic Obese, technical replicate 8


title: Subject 21 technical replicate 5

description: Patient 21, Diabetic Obese, technical replicate 5


title: Subject 21 technical replicate 2

description: Patient 21, Diabetic Obese, technical replicate 2


title: Subject 21 technical replicate 3

description: Patient 21, Diabetic Obese, technical replicate 3


title: Subject 21 technical replicate 4

description: Patient 21, Diabetic Obese, technical replicate 4


title: Subject 21 technical replicate 1

description: Patient 21, Diabetic Obese, technical replicate 1


title: Subject 20 technical replicate 8

description: Patient 20, Diabetic Obese, technical replicate 8

source_name: Subject 20

value: Patient 20


title: Subject 20 technical replicate 7

description: Patient 20, Diabetic Obese, technical replicate 7


title: Subject 20 technical replicate 2

description: Patient 20, Diabetic Obese, technical replicate 2


title: Subject 20 technical replicate 4

description: Patient 20, Diabetic Obese, technical replicate 4


title: Subject 20 technical replicate 1

description: Patient 20, Diabetic Obese, technical replicate 1


title: Subject 19 technical replicate 8

description: Patient 19, Diabetic Obese, technical replicate 8

source_name: Subject 19

value: Patient 19


title: Subject 20 technical replicate 5

description: Patient 20, Diabetic Obese, technical replicate 5

value: female


title: Subject 20 technical replicate 3

description: Patient 20, Diabetic Obese, technical replicate 3

value: Diabetic Obese


title: Subject 23 technical replicate 2

description: Patient 23, Diabetic Obese, technical replicate 2


title: Subject 22 technical replicate 3

description: Patient 22, Diabetic Obese, technical replicate 3


title: Subject 19 technical replicate 6

description: Patient 19, Diabetic Obese, technical replicate 6


title: Subject 19 technical replicate 7

description: Patient 19, Diabetic Obese, technical replicate 7


title: Subject 19 technical replicate 4

description: Patient 19, Diabetic Obese, technical replicate 4


title: Subject 19 technical replicate 2

description: Patient 19, Diabetic Obese, technical replicate 2


title: Subject 19 technical replicate 5

description: Patient 19, Diabetic Obese, technical replicate 5


title: Subject 18 technical replicate 8

description: Patient 18, Diabetic Obese, technical replicate 8

source_name: Subject 18

value: Patient 18


title: Subject 19 technical replicate 1

description: Patient 19, Diabetic Obese, technical replicate 1

value: EEC


title: Subject 18 technical replicate 5

description: Patient 18, Diabetic Obese, technical replicate 5


title: Subject 18 technical replicate 7

description: Patient 18, Diabetic Obese, technical replicate 7


title: Subject 18 technical replicate 6

description: Patient 18, Diabetic Obese, technical replicate 6


title: Subject 18 technical replicate 4

description: Patient 18, Diabetic Obese, technical replicate 4


title: Subject 18 technical replicate 3

description: Patient 18, Diabetic Obese, technical replicate 3


title: Subject 18 technical replicate 1

description: Patient 18, Diabetic Obese, technical replicate 1


title: Subject 17 technical replicate 8

description: Patient 17, Diabetic Obese, technical replicate 8

source_name: Subject 17

value: Patient 17


title: Subject 17 technical replicate 6

description: Patient 17, Diabetic Obese, technical replicate 6

value: EEC enrichment


title: Subject 20 technical replicate 6

description: Patient 20, Diabetic Obese, technical replicate 6


title: Subject 17 technical replicate 5

description: Patient 17, Diabetic Obese, technical replicate 5


title: Subject 17 technical replicate 4

description: Patient 17, Diabetic Obese, technical replicate 4


title: Subject 17 technical replicate 3

description: Patient 17, Diabetic Obese, technical replicate 3


title: Subject 17 technical replicate 2

description: Patient 17, Diabetic Obese, technical replicate 2


title: Subject 17 technical replicate 1

description: Patient 17, Diabetic Obese, technical replicate 1


title: Subject 27 technical replicate 1

description: Patient 27, Diabetic Obese, technical replicate 1

value: Patient 27


title: Subject 16 technical replicate 8

description: Patient 16, Diabetic Obese, technical replicate 8

source_name: Subject 16

value: Patient 16


title: Subject 19 technical replicate 3

description: Patient 19, Diabetic Obese, technical replicate 3


title: Subject 16 technical replicate 3

description: Patient 16, Diabetic Obese, technical replicate 3


title: Subject 16 technical replicate 7

description: Patient 16, Diabetic Obese, technical replicate 7


title: Subject 16 technical replicate 6

description: Patient 16, Diabetic Obese, technical replicate 6


title: Subject 16 technical replicate 5

description: Patient 16, Diabetic Obese, technical replicate 5


title: Subject 15 technical replicate 8

description: Patient 15, Non diabetic Obese, technical replicate 8

source_name: Subject 15

value: Patient 15

value: Non diabetic Obese


title: Subject 16 technical replicate 2

description: Patient 16, Diabetic Obese, technical replicate 2


title: Subject 18 technical replicate 2

description: Patient 18, Diabetic Obese, technical replicate 2

value: male


title: Subject 16 technical replicate 4

description: Patient 16, Diabetic Obese, technical replicate 4


title: Subject 17 technical replicate 7

description: Patient 17, Diabetic Obese, technical replicate 7


title: Subject 15 technical replicate 6

description: Patient 15, Non diabetic Obese, technical replicate 6


title: Subject 15 technical replicate 7

description: Patient 15, Non diabetic Obese, technical replicate 7


title: Subject 15 technical replicate 5

description: Patient 15, Non diabetic Obese, technical replicate 5


title: PBS4

city: Lisbon

first: Bruno

last: Costa-Silva

address: Av Brasilia

country: Portugal

institute: Champalimaud Foundation

description:
RNQ201709000053_Ex_vs_PBS.xlsx
RNQ201709000053_Ex_vs_PBS_Differentially_Expressed.xlsx

data_processing:
lllumina HiSeq 4000 platform.
Differential Expression for RNA-Seq tool which is a multi-factorial statistical analysis tool based on a negative binomial model. It uses a generalized linear model approach influenced by the multi-factorial EdgeR metho.
The expression levels of all samples were assessed through the mapping of the high-quality reads of each sample, where 88.9% to 94.38% of the total fragments were mapped against the Mus musculus (GRCm38) genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: RNQ201709000053_Ex_vs_PBS.xlsx: Differential expression analysis among samples from each group. Max group mean: For each group in the statistical comparison, the average RPKM is calculated; this value is the maximum of the average RPKMs.
Supplementary_files_format_and_content: RNQ201709000053_Ex_vs_PBS_Differentially_Expressed.xlsx: Differentially expressed genes.

source_name: Bone Marrow cd11b+ cells

extract_protocol:
The femurs and tibiae of C57Bl/6 female mice were flushed. The single cell preparation was centrifuged (500 g, 10 min, 4 °C) and the resulting pellet resuspended in ACK buffer. After 2 minutes at room temperature, the lysis was stopped by adding more buffer and the sample was centrifuged (500 g, 10 min, 4 °C). Cells underwent MACS bead isolation using CD11b Microbeads (Miltenyi Biotec,130-049-601, Germany), which enabled the isolation of CD11b+ cells from the preparation. Total RNA was isolated using RNeasy Mini kit (74104, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Animals were educated 3 weeks, every other day with PC-Evs or PBS.

tag: Sex

value: Female

value: Bone marrow cd11b+ cells

value: Untreated


title: PBS2

tag: cell type


title: PBS3


title: Subject 15 technical replicate 4

description: Patient 15, Non diabetic Obese, technical replicate 4


title: PBS1


title: Exo4

value: Pancreatic cancer extracellular vesicles (PC Evs)


title: Subject 15 technical replicate 3

description: Patient 15, Non diabetic Obese, technical replicate 3


title: wound_scRNAseq

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: scRNA-Seq generated using 10x genomics Single Cell 3’ Reagent Kits. Data were aggregated using Cell Ranger software.

data_processing:
The 10X Genomics Cell Ranger version 3.0.1 software pipeline with default parameters was used to perform sample demultiplexing, barcode processing, alignment to the mm10 reference genome, and single-cell gene counting. Data were further filtered, processed and analyzed using the Seurat R toolkit version 3(Butler et al, 2018 PMID: 29608179, Stuart et al, 2019 PMID: 31178118). Filtering of initial data involved selecting cells with > 200 and < 4000 features and < 7.5% mitochondrial genes. Data were normalized using the NormalizeData() function with parameters normalization.method = ‘LogNormalize’ and scale.factor = 10000. Variable genes were identified with the FindVariableFeatures() function with parameters with selection.method = 'vst' and nfeatures = 2000. Data were scaled with the ScaleData() function with parameters vars.to.regress = "percent.mt" and "nUMI". Principal components were calculated from these variable genes using the function RunPCA(). Selection of significant PCs to include in further analyses was determined using the JackStraw() method with the num.replicate parameter set to 100, along with visualization of each PC using the DimHeatmap() function. Significant PCs (1:13, 15, 16 and 18) were then selected, and clusters were identified using the FindNeighbors() function using the significant PCs then the FindClusters() function with the parameter resolution = 0.5. Nonlinear dimensionality reduction and visualization was performed with tSNE using the RunTSNE(), and UMAP(Becht et al, 2019 PMID: 30531897) using the RunUMAP() function. Marker genes for clusters and between samples were determined using the FindAllMarkers() function with parameters min.pct = 0.25 and thresh.use = 0.25. Gene ontology analysis was performed on marker genes using the ‘clusterProfiler’ R package with default parameters(Yu et al, 2012 PMID: 22455463). Cell lineage and pseudotime inference on mouse colon fibroblasts was performed using the Slingshot R package (Street et al, 2018 PMID: 29914354). The Seurat object was transformed into a SingleCellExperiment object and Slingshot trajectory analysis was performed in an unsupervised manner using Seurat clustering information and UMAP dimensionality reduction.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing gene expression for each cell. Column names indicate sample_barcode for single cell

source_name: PDGFRA+ mouse colon fibroblasts

extract_protocol:
Tissue samples were minced with a razor blade into 1 cm fragments, suspended in enzymatic digestion buffer collagenase and DNase I, incubated with frequent agitation at 37°C for 30 min, and triturated briefly with a 5 ml pipet. Cells in a single-cell suspension were then passed through a 100micron mesh filter, centrifuged, stained with a live/dead stain and anti-CD45 antibodies for FACS sorting of leukocytes, and anti-PDGFRa for cells of fibroblast lineage.
Single cell suspensions were loaded onto the 10X Genomics Chromium Controller instrument to generate single cell GEMs. GEM-RT and library construction were performed following the 10X Genomics Protocol. Library fragment size distributions was determined using an Agilent Bioanalyzer High Sensitivity chip, and library DNA concentrations were determined using a Qubit 2.0 Fluorometer (Invitrogen). Libraries were sequencedusing an Illumina HiSeq4000.

value: skin wound


title: Ex03


title: Ex02


title: control_scRNAseq

value: control


title: Subject 16 technical replicate 1

description: Patient 16, Diabetic Obese, technical replicate 1

value: female


title: Subject 15 technical replicate 2

description: Patient 15, Non diabetic Obese, technical replicate 2


title: Subject 14 technical replicate 7

description: Patient 14, Non diabetic Obese, technical replicate 7

source_name: Subject 14

value: Patient 14


title: Subject 14 technical replicate 8

description: Patient 14, Non diabetic Obese, technical replicate 8


title: Total-Pol-II-Control

city: Madrid

first: Cian

last: Lynch

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Mouse ES cells in serum/LIF.  ChIP for Total RNA Pol II (pool of 3 replicates, of 20million reads each)

data_processing:
ChIP-seq processing:
ChIP-seq analysis was performed with the RUbioSeq pipeline (v3.8), using the following tools: FastQC v0.11.5, BWA v0.7.10, SAMtools v0.1.19, Picard tools v1.107, Bedtools v2.16.2 and MACS2 v2.1.1.20160309.
seqMINER 1.3.3 was used to build the peak profiles of the different samples
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: BED files containing aligned reads for each sample, with duplicates removed and with a balanced number of reads, used as input for MACS2.

source_name: mESCs_serum/LIF_ChIP for Total RNA Pol II (pool of 3 replicates)

growth_protocol: Culture of mouse ES cells in standard serum/LIF media on 0.1% gelatin

extract_protocol:
ChIP-Seq METHODS: ChIP-seq for RNA Pol II was performed as described by Young and colleagues (Rahl PB et al., 2010, Cell).  Briefly, cells were fixed using 1% formaldehyde, scrape-harvested, resuspended in ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and sonicated using Covaris water bath sonicator to generate fragments of 150 to 500 bp. Soluble chromatin was diluted 10 fold in ChIP Dilution buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 150 mM NaCl) precleared with Agarose Protein A/G beads (Santa Cruz), and then incubated with antibody specific for total RNA Pol II (N-20, sc-899x, Santa Cruz) or specific for the RNA Pol II Ser5P-phoshorylated form (Abcam #ab5131).  After incubation, immunocomplexes were collected with Agarose Protein A/G beads (Santa Cruz). Next, the immunocomplexes were washed sequentially with Low Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), High Salt Wash Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl Wash Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate-Na, 1mM EDTA, 10mM Tris-HCl, pH 8.1) and washed twice with TE (10 mM Tris-HCl pH7.5, 1mM EDTA).  Immunocomplexes were eluted in ChIP elution buffer (1%SDS, 0.1M NaHCO3) and the crosslinking was reverted by incubation at 65 ºC for 8 hrs with 200 mM NaCl. Samples were treated with Proteinase K and RNase A, and DNA was extracted using Phenol-Chloroform.  DNA precipitation was in 100% ethanol with 0.1 M NaAcetate ph5.2 and 2 uLs glycogen (Roche).  The DNA pellet was washed with 70% ethanol, and resuspended in ddH2O. Purified chromatin was used for library construction.  For ChIP-seq the amount of DNA used was ~5 ng from each sample (as quantitated by fluorometry). Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Q5 High-Fidelity DNA Polymerase (NEB) and Illumina PE primers (15 cycles), and further purified with a double-sided SPRI size selection to obtain a size distribution in the range of 230-500bp. Libraries were applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols, to 20-25 million reads per replicate, to a total of >60 million reads per condition.
For ChIP-seq the amount of DNA used was ~5 ng from each sample (as quantitated by fluorometry). Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Q5 High-Fidelity DNA Polymerase (NEB) and Illumina PE primers (15 cycles), and further purified with a double-sided SPRI size selection to obtain a size distribution in the range of 230-500bp. Libraries were applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols, to 20-25 million reads per replicate, to a total of >60 million reads per condition.

treatment_protocol: Cells were cultured in three media variations: serum/LIF or serum/LIF+2i or serum/LIF+CDK8/19i

tag: strain background

value: BL6/129 mixed

tag: developemental stage

value: ES cells

tag: culture condition

value: serum/LIF

value: Rabbit anti-RPB1 Santa Cruz #sc-899x


title: Ex01


title: Subject 14 technical replicate 6

description: Patient 14, Non diabetic Obese, technical replicate 6

value: EEC enrichment

value: EEC


title: Total-Pol-II-8i

description: Mouse ES cells in serum/LIF+CDK8/19i.  ChIP for Total RNA Pol II (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF +CDK8/19i_ChIP for Total RNA Pol II (pool of 3 replicates)

value: serum/LIF +CDK8/19i

tag: chip antibody


title: Subject 14 technical replicate 3

description: Patient 14, Non diabetic Obese, technical replicate 3

value: Non diabetic Obese


title: Subject 14 technical replicate 4

description: Patient 14, Non diabetic Obese, technical replicate 4


title: Subject 14 technical replicate 5

description: Patient 14, Non diabetic Obese, technical replicate 5


title: Ser5P-Control

description: Mouse ES cells in serum/LIF.  ChIP for RNA Pol II-Ser5-Phospho (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF_ChIP for RNA Pol II-Ser5-Phospho (pool of 3 replicates)

value: Rabbit anti-RPB1-Serine5-phosphorylated Abcam #ab5131


title: Ser5P-8i

description: Mouse ES cells in serum/LIF+CDK8/19i.  ChIP for RNA Pol II-Ser5-Phospho (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF +CDK8/19i_ChIP for RNA Pol II-Ser5-Phospho (pool of 3 replicates)


title: Ser2P-Control

description: Mouse ES cells in serum/LIF.  ChIP for RNA Pol II-Ser2-Phospho (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF_ChIP for RNA Pol II-Ser2-Phospho (pool of 3 replicates)

value: Rabbit anti-RPB1-Serine2-phosphorylated Abcam #ab5095


title: Subject 14 technical replicate 2

description: Patient 14, Non diabetic Obese, technical replicate 2


title: Ser2P-8i

description: Mouse ES cells in serum/LIF+CDK8/19i.  ChIP for RNA Pol II-Ser2-Phospho (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF +CDK8/19i_ChIP for RNA Pol II-Ser2-Phospho (pool of 3 replicates)


title: Subject 13 technical replicate 8

description: Patient 13, Non diabetic Obese, technical replicate 8

source_name: Subject 13

value: Patient 13


title: Total-Pol-II-2i

description: Mouse ES cells in serum/LIF+2i.  ChIP for Total RNA Pol II (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF +2i_ChIP for Total RNA Pol II (pool of 3 replicates)

value: serum/LIF +2i


title: Subject 13 technical replicate 6

description: Patient 13, Non diabetic Obese, technical replicate 6


title: Subject 13 technical replicate 5

description: Patient 13, Non diabetic Obese, technical replicate 5


title: Ser5P-2i

description: Mouse ES cells in serum/LIF+2i.  ChIP for RNA Pol II-Ser5-Phospho (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF +2i_ChIP for RNA Pol II-Ser5-Phospho (pool of 3 replicates)


title: Subject 15 technical replicate 1

description: Patient 15, Non diabetic Obese, technical replicate 1

value: Patient 15


title: Normalhuman epidermal melanocytes (N)

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
10X Genomics cellranger v3.1.0
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: feature-barcode matrix files

source_name: xenograft melanoma cells

growth_protocol: Normal cell culture conditions in DMEM with 10% FBS

extract_protocol:
10x Genomics Single Cell Protocol for the Cell Preparation Guide
Libraries were prepared following the Chromium Single Cell 3’ v3 library kit (10X Genomics) protocol. Briefly, cell suspension and gel mix were added to a chromium single cell B chip. The chip is loaded into the chromium controller where individual cells are captured in uniquely labeled GEMs. GEMs udergo reverse transcription, GEM dissolution and DNA cleanup. The result is  a pool of cDNA with uniquely barcoded molecules.

tag: sample type

value: PDX

value: Melanocyte


title: Subject 14 technical replicate 1

description: Patient 14, Non diabetic Obese, technical replicate 1

value: female

tag: treatment


title: PDX M27

value: Melanoma


title: Input

description: Mouse ES cells negative control Input

source_name: Input pooled from Input of the three culture conditions. mESCs_serum/LIF, Serum/LIF+2i, serum/LIF+CDK8/19i (pool of 3 replicates)

value: BL6/129 mixed

value: background control

value: No antibody Input control


title: PDX M15


title: Subject 13 technical replicate 3

description: Patient 13, Non diabetic Obese, technical replicate 3


title: Subject 13 technical replicate 4

description: Patient 13, Non diabetic Obese, technical replicate 4


title: Subject 13 technical replicate 2

description: Patient 13, Non diabetic Obese, technical replicate 2


title: PDX M12


title: Subject 13 technical replicate 1

description: Patient 13, Non diabetic Obese, technical replicate 1


title: Subject 12 technical replicate 8

description: Patient 12, Non diabetic Obese, technical replicate 8

source_name: Subject 12

value: Patient 12


title: Subject 13 technical replicate 7

description: Patient 13, Non diabetic Obese, technical replicate 7

value: EEC enrichment


title: Subject 12 technical replicate 7

description: Patient 12, Non diabetic Obese, technical replicate 7

value: EEC


title: Subject 12 technical replicate 5

description: Patient 12, Non diabetic Obese, technical replicate 5


title: Ser2P-2i

description: Mouse ES cells in serum/LIF+2i.  ChIP for RNA Pol II-Ser2-Phospho (pool of 3 replicates, of 20million reads each)

source_name: mESCs_serum/LIF +2i_ChIP for RNA Pol II-Ser2-Phospho (pool of 3 replicates)

value: ES cells


title: Subject 12 technical replicate 4

description: Patient 12, Non diabetic Obese, technical replicate 4

value: Non diabetic Obese


title: Non pregnant Patient 2 (RNA-seq)

city: Los Angeles

first: Giorgia

last: Del Vecchio

address: 610 Charles E Young Dr S, Room 5146

institute: University of California Los Angeles

data_processing:
We first used the FastQC (version v0.11.8) program to assess the quality of our sequenced reads. All the samples passed this step of quality control before proceeding further into analysis.
The RNA-seq reads were aligned to the human reference genome (hg19) using the STAR (v 2.5.2b) software with the following configurations:  --quantMode GeneCounts --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 1 --clip5pNbases 5. We used the --quantMode GeneCounts option in STAR that counts the number reads per gene while mapping.
Starting with the RNA-Seq read counts matrix, we then used the DESeq2 (version v1.20.0) package in R to perform data normalization (rlog function) and DEG analysis. We set a cutoff for adjusted P value ≤ 0.05 and a fold change ≥ 1 or ≤  -1.
Genome_build: hg19
Supplementary_files_format_and_content: gene Counts text file

source_name: Plasma

extract_protocol:
Peripheral venous blood was collected into EDTA-coated tubes. Blood was then centrifuged at 2000 X g for 7 minutes at 4°C, in order to collect only the plasma fraction. Plasma was centrifuged at 16000 X g for 10 min at 4°C to remove all the residual cells, aliquoted and stored at −80°C. Cell-free RNA was extracted from 200 μL of plasma using the miRNeasy serum/plasma kit (Qiagen). Total RNA was quantified using the Qubit RNA HS Assay kit  (Thermofisher Scientific). RNA integrity was verified using the Agilent High sensitivity RNA Screen Tape System (Agilent) on a 2200 TapeStation System (Agilent,).
The RNA-sequencing (RNA-seq) library construction was performed using the ultra-low input specific kit, NuGen Ovation SoLo RNA-Seq kit with Human rRNA AnyDeplete kit (NuGen), according to the manufacturer's instructions. Libraries were sequenced using 100 bp single-end reads on the Hiseq4000 System (Illumina)

tag: complication during pregnancy

value: Non pregnant


title: Non pregnant Patient 4 (RNA-seq)


title: Non pregnant Patient 1 (RNA-seq)


title: Non pregnant Patient 5 (RNA-seq)


title: Non pregnant Patient 7 (RNA-seq)


title: Non pregnant Patient 6 (RNA-seq)


title: Subject 12 technical replicate 6

description: Patient 12, Non diabetic Obese, technical replicate 6


title: Chronic  hypertension Patient 2, cord blood (RNA-seq)

value: Chronic  hypertension


title: Subject 12 technical replicate 2

description: Patient 12, Non diabetic Obese, technical replicate 2


title: Chronic  hypertension Patient 2, delivery (RNA-seq)


title: Chronic  hypertension Patient 2, 2nd Trimester (RNA-seq)


title: Subject 11 technical replicate 7

description: Patient 11, Non diabetic Obese, technical replicate 7

source_name: Subject 11

value: Patient 11


title: Chronic  hypertension Patient 2, 1st Trimester (RNA-seq)


title: Chronic  hypertension Patient 2, 3rd Trimester (RNA-seq)


title: Subject 12 technical replicate 3

description: Patient 12, Non diabetic Obese, technical replicate 3


title: Subject 11 technical replicate 8

description: Patient 11, Non diabetic Obese, technical replicate 8


title: Subject 11 technical replicate 6

description: Patient 11, Non diabetic Obese, technical replicate 6


title: Chronic  hypertension Patient 1, cord blood (RNA-seq)


title: Chronic  hypertension Patient 1, delivery (RNA-seq)


title: Subject 11 technical replicate 5

description: Patient 11, Non diabetic Obese, technical replicate 5


title: Subject 12 technical replicate 1

description: Patient 12, Non diabetic Obese, technical replicate 1


title: Chronic  hypertension Patient 1, 3rd Trimester (RNA-seq)


title: Subject 11 technical replicate 3

description: Patient 11, Non diabetic Obese, technical replicate 3


title: Subject 11 technical replicate 4

description: Patient 11, Non diabetic Obese, technical replicate 4


title: Non pregnant Patient 3 (RNA-seq)


title: Chronic  hypertension Patient 1, 2nd Trimester (RNA-seq)


title: Subject 11 technical replicate 2

description: Patient 11, Non diabetic Obese, technical replicate 2


title: Subject 11 technical replicate 1

description: Patient 11, Non diabetic Obese, technical replicate 1


title: Preeclampsia/gestational hypertension Patient 8, cord blood (RNA-seq)

value: Preeclampsia/gestational hypertension


title: Chronic  hypertension Patient 1, 1st Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 8, 3rd Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 8, delivery (RNA-seq)


title: Subject 10 technical replicate 8

description: Patient 10, Non diabetic Obese, technical replicate 8

source_name: Subject 10

value: Patient 10

value: male


title: Subject 10 technical replicate 6

description: Patient 10, Non diabetic Obese, technical replicate 6


title: Subject 10 technical replicate 5

description: Patient 10, Non diabetic Obese, technical replicate 5


title: Preeclampsia/gestational hypertension Patient 8, 1st Trimester (RNA-seq)


title: Subject 10 technical replicate 7

description: Patient 10, Non diabetic Obese, technical replicate 7


title: Subject 10 technical replicate 4

description: Patient 10, Non diabetic Obese, technical replicate 4


title: Preeclampsia/gestational hypertension Patient 7, cord blood (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 7, 3rd Trimester (RNA-seq)


title: Subject 10 technical replicate 2

description: Patient 10, Non diabetic Obese, technical replicate 2


title: Preeclampsia/gestational hypertension Patient 7, 2nd Trimester (RNA-seq)


title: Subject 10 technical replicate 3

description: Patient 10, Non diabetic Obese, technical replicate 3


title: Preeclampsia/gestational hypertension Patient 7, 1st Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 7, delivery (RNA-seq)


title: Subject 9 technical replicate 8

description: Patient 9, Non diabetic Obese, technical replicate 8

source_name: Subject 9

value: Patient 9


title: Subject 9 technical replicate 6

description: Patient 9, Non diabetic Obese, technical replicate 6

value: female


title: Preeclampsia/gestational hypertension Patient 6, cord blood (RNA-seq)


title: Subject 9 technical replicate 4

description: Patient 9, Non diabetic Obese, technical replicate 4


title: Preeclampsia/gestational hypertension Patient 6, 3rd Trimester (RNA-seq)


title: Subject 9 technical replicate 3

description: Patient 9, Non diabetic Obese, technical replicate 3


title: Preeclampsia/gestational hypertension Patient 8, 2nd Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 6, 1st Trimester (RNA-seq)


title: Subject 10 technical replicate 1

description: Patient 10, Non diabetic Obese, technical replicate 1


title: Preeclampsia/gestational hypertension Patient 5, cord blood (RNA-seq)


title: Subject 9 technical replicate 7

description: Patient 9, Non diabetic Obese, technical replicate 7


title: Preeclampsia/gestational hypertension Patient 5, delivery (RNA-seq)


title: Subject 9 technical replicate 1

description: Patient 9, Non diabetic Obese, technical replicate 1


title: Subject 8 technical replicate 7

description: Patient 8, Non diabetic Obese, technical replicate 7

source_name: Subject 8

value: Patient 8


title: Preeclampsia/gestational hypertension Patient 5, 3rd Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 5, 1st Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 5, 2nd Trimester (RNA-seq)


title: Subject 8 technical replicate 8

description: Patient 8, Non diabetic Obese, technical replicate 8


title: Preeclampsia/gestational hypertension Patient 4, cord blood (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 4, delivery (RNA-seq)


title: Subject 8 technical replicate 2

description: Patient 8, Non diabetic Obese, technical replicate 2


title: Subject 8 technical replicate 4

description: Patient 8, Non diabetic Obese, technical replicate 4


title: Subject 8 technical replicate 5

description: Patient 8, Non diabetic Obese, technical replicate 5


title: Preeclampsia/gestational hypertension Patient 4, 2nd Trimester (RNA-seq)


title: Subject 9 technical replicate 5

description: Patient 9, Non diabetic Obese, technical replicate 5


title: Preeclampsia/gestational hypertension Patient 4, 3rd Trimester (RNA-seq)


title: Subject 8 technical replicate 1

description: Patient 8, Non diabetic Obese, technical replicate 1


title: Subject 7 technical replicate 8

description: Patient 7, Non diabetic Obese, technical replicate 8

source_name: Subject 7

value: Patient 7


title: Subject 9 technical replicate 2

description: Patient 9, Non diabetic Obese, technical replicate 2


title: Subject 7 technical replicate 7

description: Patient 7, Non diabetic Obese, technical replicate 7


title: Subject 8 technical replicate 3

description: Patient 8, Non diabetic Obese, technical replicate 3


title: Preeclampsia/gestational hypertension Patient 3, delivery (RNA-seq)


title: Subject 7 technical replicate 5

description: Patient 7, Non diabetic Obese, technical replicate 5


title: Preeclampsia/gestational hypertension Patient 3, 3rd Trimester (RNA-seq)


title: Subject 8 technical replicate 6

description: Patient 8, Non diabetic Obese, technical replicate 6


title: Preeclampsia/gestational hypertension Patient 3, 2nd Trimester (RNA-seq)


title: Subject 7 technical replicate 4

description: Patient 7, Non diabetic Obese, technical replicate 4


title: Preeclampsia/gestational hypertension Patient 3, 1st Trimester (RNA-seq)


title: Subject 7 technical replicate 3

description: Patient 7, Non diabetic Obese, technical replicate 3


title: Preeclampsia/gestational hypertension Patient 2, cord blood (RNA-seq)


title: Subject 7 technical replicate 6

description: Patient 7, Non diabetic Obese, technical replicate 6


title: Subject 7 technical replicate 2

description: Patient 7, Non diabetic Obese, technical replicate 2


title: Preeclampsia/gestational hypertension Patient 2, 3rd Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 4, 1st Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 2, 2nd Trimester (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 2, 1st Trimester (RNA-seq)


title: Subject 6 technical replicate 7

description: Patient 6, Non diabetic Obese, technical replicate 7

source_name: Subject 6

value: Patient 6


title: Preeclampsia/gestational hypertension Patient 2, delivery (RNA-seq)


title: Subject 6 technical replicate 8

description: Patient 6, Non diabetic Obese, technical replicate 8


title: Preeclampsia/gestational hypertension Patient 3, cord blood (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 1, cord blood (RNA-seq)


title: Subject 6 technical replicate 6

description: Patient 6, Non diabetic Obese, technical replicate 6


title: Preeclampsia/gestational hypertension Patient 1, delivery (RNA-seq)


title: Preeclampsia/gestational hypertension Patient 1, 3rd Trimester (RNA-seq)


title: Subject 6 technical replicate 5

description: Patient 6, Non diabetic Obese, technical replicate 5


title: Subject 6 technical replicate 4

description: Patient 6, Non diabetic Obese, technical replicate 4


title: Subject 6 technical replicate 3

description: Patient 6, Non diabetic Obese, technical replicate 3


title: Preeclampsia/gestational hypertension Patient 1, 2nd Trimester (RNA-seq)


title: Subject 6 technical replicate 2

description: Patient 6, Non diabetic Obese, technical replicate 2


title: Subject 6 technical replicate 1

description: Patient 6, Non diabetic Obese, technical replicate 1


title: Preeclampsia/gestational hypertension Patient 1, 1st Trimester (RNA-seq)


title: Gestational diabetes Patient 7, cord blood (RNA-seq)

value: Gestational Diabetes


title: Gestational diabetes Patient 7, delivery (RNA-seq)


title: Subject 5 technical replicate 8

description: Patient 5, Non diabetic Obese, technical replicate 8

source_name: Subject 5

value: Patient 5


title: Subject 7 technical replicate 1

description: Patient 7, Non diabetic Obese, technical replicate 1

value: EEC enrichment


title: Gestational diabetes Patient 7, 3rd Trimester (RNA-seq)


title: Gestational diabetes Patient 7, 2nd Trimester (RNA-seq)


title: Subject 5 technical replicate 5

description: Patient 5, Non diabetic Obese, technical replicate 5

value: EEC


title: Subject 5 technical replicate 3

description: Patient 5, Non diabetic Obese, technical replicate 3


title: Gestational diabetes Patient 7, 1st Trimester (RNA-seq)


title: Subject 5 technical replicate 4

description: Patient 5, Non diabetic Obese, technical replicate 4


title: Subject 5 technical replicate 2

description: Patient 5, Non diabetic Obese, technical replicate 2


title: Gestational diabetes Patient 6, delivery (RNA-seq)


title: Gestational diabetes Patient 6, 2nd Trimester (RNA-seq)


title: Subject 5 technical replicate 1

description: Patient 5, Non diabetic Obese, technical replicate 1


title: Gestational diabetes Patient 6, 3rd Trimester (RNA-seq)


title: Subject 4 technical replicate 8

description: Patient 4, Non diabetic Obese, technical replicate 8

source_name: Subject 4

value: Patient 4


title: Gestational diabetes Patient 6, 1st Trimester (RNA-seq)


title: Subject 4 technical replicate 7

description: Patient 4, Non diabetic Obese, technical replicate 7

value: Non diabetic Obese


title: Subject 4 technical replicate 6

description: Patient 4, Non diabetic Obese, technical replicate 6


title: Gestational diabetes Patient 5, cord blood (RNA-seq)


title: Gestational diabetes Patient 5, delivery (RNA-seq)


title: Subject 4 technical replicate 4

description: Patient 4, Non diabetic Obese, technical replicate 4


title: Gestational diabetes Patient 5, 3rd Trimester (RNA-seq)


title: Subject 5 technical replicate 6

description: Patient 5, Non diabetic Obese, technical replicate 6


title: Gestational diabetes Patient 5, 2nd Trimester (RNA-seq)


title: Subject 4 technical replicate 3

description: Patient 4, Non diabetic Obese, technical replicate 3


title: Subject 5 technical replicate 7

description: Patient 5, Non diabetic Obese, technical replicate 7


title: Subject 4 technical replicate 2

description: Patient 4, Non diabetic Obese, technical replicate 2


title: Gestational diabetes Patient 5, 1st Trimester (RNA-seq)


title: Gestational diabetes Patient 4, delivery (RNA-seq)


title: Gestational diabetes Patient 6, cord blood (RNA-seq)


title: Gestational diabetes Patient 4, 3rd Trimester (RNA-seq)


title: Subject 3 technical replicate 8

description: Patient 3, Non diabetic Obese, technical replicate 8

source_name: Subject 3

value: Patient 3


title: Subject 4 technical replicate 1

description: Patient 4, Non diabetic Obese, technical replicate 1


title: Gestational diabetes Patient 4, 2nd Trimester (RNA-seq)


title: Gestational diabetes Patient 4, 1st Trimester (RNA-seq)


title: Subject 3 technical replicate 7

description: Patient 3, Non diabetic Obese, technical replicate 7


title: Subject 3 technical replicate 6

description: Patient 3, Non diabetic Obese, technical replicate 6


title: Gestational diabetes Patient 3, cord blood (RNA-seq)


title: Subject 3 technical replicate 5

description: Patient 3, Non diabetic Obese, technical replicate 5