title: Sprague Dawley_SON non-targeting shRNA_rep4L

value: Brain

value: Supraoptic nucleus


title: eNOS WT White matter 2

status: Public on Jul 12 2022

type: SRA

city: Charlestown

first: Mahesh Chandra

last: Kodali

state: MA

department: Neurology

country: USA

institute: Massachusetts General Hospital / Harvard Medical School

library_source: transcriptomic

data_processing:
Libraries are loaded onto Novaseq6000 sequencing platform according to activity and expected data volume. A paired-end 150 bp sequencing strategy was used and all samples were sequenced to 20M PE Reads.
Transcript abundance from RNA-seq reads was quantified using Salmon, and gene-level counts were obtained using tximport, against the C57BL/6J mouse genome annotation Genome Reference Consortium Mouse Build 39  (GRCm39), obtained from the National Center for Biotechnology Information. Subsequently, raw counts were processed with DESeq2 to determine differentially expressed genes.
Assembly: Genome Reference Consortium Mouse Build 39 (GRCm39)

molecule: total RNA

organism: Mus musculus

source_name: Brain - White Matter

extract_protocol:
RNA was extracted from mouse cerebral vessels after trizol homogenization, and then using QIAGEN miRNeasy micro Kit. Samples were later DNAse treated and cleaned up using RNEasy minelute clean up kit, finally eluted in RNAse free water from Qiagen.
Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Library construction is performed based on manufacturer’s recommendation for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio USA Inc., California, USA) followed by Nextera® XT DNA Library Prep Kit (Illumina, California, USA). Final library quantity was measured by KAPA SYBR® FAST qPCR and library quality evaluated by TapeStation D1000 ScreenTape (Agilent Technologies, CA, USA). Final library size was about 430bp with an insert size of about 200bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 20M PE reads per sample (10M in each direction).

tag: tissue

value: Brain - White Matter

tag: strain

tag: Sex

value: Male

tag: genotype

value: eNOS+/+


title: TS3-2

type: RNA

city: Kawasaki

first: Takao

last: Inoue

state: Kanagawa

address: 3-25-26, Tonomachi

department: Division of Molecular Target and Gene Therapy Products

country: Japan

institute: National Institute of Health Sciences

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 Array using the GeneChip Hybridization Oven. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The scanned data were processed for signal values using Microarray Suite 5.0 software  .

label: biotin

source_name: The NMuLi cells transfected with TS3 at 10 nM using Lipofectamine 2000 for 24hr.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: The NMuLi cells were maintained at 37 °C and 5% CO2 in Dulbecco’s Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The NMuLi cells transfected with the gapmer ASOs using Lipofectamine 2000 (Invitrogen, Gaithersburg, MD, USA) according to the manufacturer’s protocol. The cells treated with transfection reagent in the absence of ASO were used as a control.

tag: treatment

tag: cell line

value: NMuLi

value: Liver


title: Sprague Dawley_SON non-targeting shRNA_rep3L

city: Bristol

first: Michael

middle: Paul

last: Greenwood

address: Whitson Street

department: Bristol Medical School / Translational Health Sciences

country: United Kingdom

institute: University of Bristol

data_processing:
RNA-seq reads were processed using RTA and CASAVA from Illumina’s suite of sequencing software.
All raw reads were merged per library, and pre-processed for quality assessment, adaptor removal, quality trimming and size selection using the FastQC toolkit to generate quality plots for all read libraries.
We adopted a phred30 quality cutoff (99.9% base call accuracy).
Paired end (2 x 75 bp) raw input data is initially aligned with STAR to the sixth iteration of the Rattus norvegicus reference genome (Rn6).
FeatureCounts is used to generate read counts for each gene present in the Rn6 genome annotation.
DEseq2 (v1.28.1) package in R was used to call differentially expressed genes.
Assembly: Rn6
Supplementary files format and content: FeatureCount output - ALL_Final_only_counts.gene.txt
Supplementary files format and content: Deseq2 differential gene expression analysis - SON_Creb3l1_RNAseq_processed_data.xls

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Brain

growth_protocol: Male Sprague Dawley rats weighing 250-274 grams were purchased from commercial supplier Envigo. Rats were housed under a 12:12 light/dark cycle at a temperature of 21-22°C and a relative humidity of 40-50% with food and water ad libitum.

extract_protocol:
A 1 mm punch was used for tissue collection from frozen cryostat cut sections. QIAzol Lysis Reagent (Qiagen) followed by Direct-zol RNA miniprep extraction kit (Zymo research). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were constructed using TruSeq® Stranded mRNA library preparation kit (20020594, Illumina)

treatment_protocol: Animal were able to serve as their own controls with control virus (non-tergeting shRNA) sterotaxically injected into one SON and experimental virus (Creb3l1 knockdown) into the other.

tag: brain region

value: Sprague-Dawley

tag: time

value: 3 weeks

value: control

tag: shRNA construct

value: AAV control shRNA


title: eNOS WT White matter 3


title: PAM-1 KO rep1 H3K27ac ChIP-seq

city: Sha Tin

first: Yile

last: Huang

state: Hong Kong

address: Room 503, Li Ka Shing Health and Science Buiding, Prince of Wales Hospital, Sha Tin

department: Chemical Pathology

country: China

institute: The Chinese University of HongKong

library_source: genomic

data_processing:
The raw data were first preprocessed by initial quality assessment, adaptors trimming, and low-quality filtering
The remaining reads were aligned to the mouse reference genome (mm9) by Bowtie2
Peak regions were called by software MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: C2C12 myoblast

growth_protocol: Mouse C2C12 myoblast cell (CRL-1772) was obtained from American Type Culture Collection (ATCC) and cultured in DMEM medium with 10% fetal bovine serum, 1% penicillin/ streptomycin at 37°C in 5% CO2.

extract_protocol:
C2C12 cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.125M glycine for 10 minutes. Chromatin was fragmented using S220 sonicator (Covaris), followed by incubation with 5ug of antibodies and 50uL Dynabeads Protein G magnetic beads (Life Technologies) at 4°C on rotator for overnight. Anti Ddx5 (ab21696, Abcam) was used in ChIP assay. Beads were washed with 1mL RIPA buffer for 5 times, followed by decrosslink at 65°C for 16 hours and DNA extraction with phenol/chloroform. Immunoprecipitated DNA was resuspended in 50uL of water.
NEBNext Ultra II DNA Library Preparation kit for Illumina (NEB)

treatment_protocol: To delete PAM-1 exon1, target-specific guide RNAs (gRNAs) were designed using CRISPR design tool (http://crispr.mit.edu), followed by cloning into BbsI digested px330 plasmid (Addgene, 42230). To perform genomic deletion, a pair of gRNAs containing plasmids were co-transfected into C2C12 cells with screening plasmid pSIREN-RetroQ (Clontech) using Lipotectamine 2000. Cells were selected with 2.5ug of puromycin for 3 days at 48 hours post-trasnsfection. Cells were diluted to 1 cell per well in 96 well plate. Individual colonies were PCR validated.

tag: cell type

value: C2C12 myoblast

tag: antibody

value: H3K27ac (ab4729, Abcam)


title: TS2-C1-10-3

source_name: The NMuLi cells transfected with TS2-C1 at 10 nM using Lipofectamine 2000 for 24hr.


title: eNOS WT White matter 1


title: siPAM-1 rep2 H3K27ac ChIP-seq

extract_protocol:
C2C12 cells were crosslinked with 1% formaldehyde at room temperature for 10 minutes, followed by quenching with 0.125M glycine for 10 minutes. Chromatin was fragmented using S220 sonicator (Covaris), followed by incubation with 5ug of antibodies and 50uL Dynabeads Protein G magnetic beads (Life Technologies) at 4°C on rotator for overnight. Anti-histone H3-K27 acetylation (Abcam, ab4729) was used in ChIP assay. Beads were washed with 1mL RIPA buffer for 5 times, followed by decrosslink at 65°C for 16 hours and DNA extraction with phenol/chloroform. Immunoprecipitated DNA was resuspended in 50uL of water.
NEBNext Ultra II DNA Library Preparation kit for Illumina (NEB)

treatment_protocol: Oligonucleoties of siRNA against mouse PAM-1 and scrambled control were obtained from Ribobio Technologies (Guangzhou, China). siRNAs were transfected at 100nM into C2C12 using Lipofectamine 2000 (Life Technologies). To delete PAM-1 exon1, target-specific guide RNAs (gRNAs) were designed using CRISPR design tool (http://crispr.mit.edu), followed by cloning into BbsI digested px330 plasmid (Addgene, 42230). To perform genomic deletion, a pair of gRNAs containing plasmids were co-transfected into C2C12 cells with screening plasmid pSIREN-RetroQ (Clontech) using Lipotectamine 2000. Cells were selected with 2.5ug of puromycin for 3 days at 48 hours post-trasnsfection. Cells were diluted to 1 cell per well in 96 well plate. Individual colonies were PCR validated.


title: eNOS HET Grey matter 3

source_name: Brain - Grey Matter

value: Brain - Grey Matter

value: eNOS+/-


title: siPAM-1 rep1 H3K27ac ChIP-seq


title: siNC H3K27ac ChIP-seq


title: eNOS HET Grey matter 2


title: eNOS HET Grey matter 1


title: TS2-C1-10-4

value: transfected with TS2-C1 at 10 nM using Lipofectamine 2000 for 24hr.


title: Sprague Dawley_SON non-targeting shRNA_rep2L


title: Sprague Dawley_SON non-targeting shRNA_rep1L


title: daf-16(mgDf50);pmk-1(miy7) Replicate 1 [d16DE_1]

city: Dallas

first: Benjamin

last: Weaver

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using STAR (v2.5.3a)
Duplicate alignments were removed using picard-tools(v2.10)
Read counts were generated using featureCounts (subread) for coding genes from igenomes (Refseq)
Normalized read counts generated using edgeR
Genome_build: ce10
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

organism: Caenorhabditis elegans

source_name: pmk-1 caspase resistent (D327E) with daf-16 deletion mutation_whole worm

growth_protocol: C elegans strains were cultured on solid agar plates with OP50 bacteria lawn.

extract_protocol:
Trizol extraction
Illumina NextSeq 500 Kits

treatment_protocol: Synchronized young adult worms were bleached and then the eggs were incubated in M9 for 24 hours to obtain synchronized L1s. L1s were plated on OP50 for 48hrs at 20°C until >95% of wild type worms reached late L4 stage

tag: Stage

value: late L4

value: whole worm


title: TS3-C1-7-4

source_name: The NMuLi cells transfected with TS3-C1-7 at 10 nM using Lipofectamine 2000 for 24hr.


title: Lignin-treated S. aureus, 2 hours post-treatment, replicate 3 [L-2-3_S118]

city: Gainesville

first: Kelly

last: Rice

address: 1355 Museum Drive

institute: University of Florida

description: MOPS-2 hr vs. Lignin-2 hr.txt

data_processing:
Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® Novaseq with a read length configuration of 150 paired end (PE) for 13.5M PE reads per sample (6.75M in each direction).
Raw data files (.fastq) were imported into CLC Genomics Workbench 21 (QIAGEN, Hilden, Germany). All subsequent data processing was performed using CLC genomics workbench, unless otherwise specified.
Trim-read function was run using default parameters to remove adapter sequences.
sequences were subjected to an in silico rRNA depletion by mapping them to a sequence file containing all of S. aureus rRNA genes.
The unmapped reads (those that did not align to rRNA genes) were then mapped to a gene track generated from a MRSA252 genome (NCBI accession# NC_002952) sequence file that contains small RNA (sRNA) annotations, RPKM values calculated, and subjected to quantile normalization
Supplementary files format and content: tab-delimited text files include normalized RPKM values for each sample

organism: Staphylococcus aureus

source_name: S. aureus UAMS-1

growth_protocol: Overnight cultures were diluted to OD600=0.025 in TSB (3% w/v) with a flask: volume ratio of 10:1 and grown for two hours at 37°C and 250 rpm prior to treatment.

extract_protocol:
Cells were washed with nuclease-free Tris-EDTA buffer, then pelleted and stored at -80°C for less than 30 days prior to RNA extraction. Cells were lysed with a FastPrep-24 (MP Biomedicals, Solon, OH) and total RNA was extracted with QIAGEN RNeasy prep kits (QIAGEN, Germantown, MD), and genomic DNA was degraded with the Ambion Turbo DNA-free kit (Austin, TX). RNA samples were submitted to the University of Florida ICBR Gene Expression core to obtain RNA integrity number (RIN) values using an Agilent Bioanalyzer 2100 (Agilent Technologies, Inc, Santa Clara, CA).
Extracted RNA was submitted for sequencing to Novogene (Sacramento, CA), where RNA sample quality was also assessed by BioAnalyzer High Sensitivity RNA Assay (Agilent Technologies Inc., Santa Clara, CA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Waltham, MA). Ribosomal RNA depletion was performed with Ribo-Zero Plus rRNA Removal Kit (Illumina Inc., San Diego, CA). Samples were randomly primed and fragmented based on the manufacturer’s recommendation. The first cDNA strand was synthesized with the Protoscript II Reverse Transcriptase with an extension period of approximately 40 minutes at 42⁰C. All remaining steps for library construction were executed according to the NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Ipswich, MA). Final library quantities were assessed by Qubit 2.0 (ThermoFisher, Waltham, MA) and quality was assessed by TapeStation D1000 ScreenTape (Agilent Technologies Inc., Santa Clara, CA). Average final library size was about 375 bp with an insert size of about 200 bp. Illumina® 8-nt dual-indices were used.

treatment_protocol: At the time of treatment, selected cultures were treated with 1 M MOPS or 5 mg ASL/ml; the final concentration of MOPS in all cultures was 50 mM. To determine the effects of treatments at different times post-treatment, cell pellets were harvested at 20 min. and 2 hours post-treatment.

value: 5 mg/ml alkaline sorghum lignin in 50 mM MOPS pH 7.2 (final concentration); treatment

tag: time point

value: 2 hours post-treatment


title: daf-16(mgDf50);pmk-1(miy7) Replicate 2 [d16DE_2]


title: Lignin-treated S. aureus, 2 hours post-treatment, replicate 2 [L-2-2_S117]

description: MOPS-2 hr vs. Lignin-2 hr.txt


title: Lignin-treated S. aureus, 2 hours post-treatment, replicate 1 [L-2-1_S116]

description: MOPS-2 hr vs. Lignin-2 hr.txt


title: daf-16(mgDf50);pmk-1(km25) Replicate 1 [d16P1_2]

source_name: pmk-1 null with daf-16 deletion mutation_whole worm


title: daf-16(mgDf50);pmk-1(km25) Replicate 1 [d16P1_1]


title: MOPS-treated S. aureus, 2 hours post-treatment, replicate 3 [M-2-3_S106]

description: MOPS-2 hr vs. Lignin-2 hr.txt

value: 50 mM MOPS pH 7.2 (final concentration); control


title: eNOS WT Grey matter 2

value: Male

value: eNOS+/+


title: TS2-C1-10-2

value: NMuLi

value: Liver


title: MOPS-treated S. aureus, 2 hours post-treatment, replicate 2 [M-2-2_S105]

description: MOPS-2 hr vs. Lignin-2 hr.txt


title: eNOS WT Grey matter 1


title: TS2-C1-10-1


title: TS2-3

source_name: The NMuLi cells transfected with TS2 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS2-2

value: transfected with TS2 at 10 nM using Lipofectamine 2000 for 24hr.


title: daf-16(mgDf50) mRNA Replicate 2 [d16_2]

source_name: daf-16 deletion mutation_whole worm


title: TS2-4


title: eNOS KO + Sodium Nitrate White matter2

value: Brain - White Matter

value: eNOS-/-

value: Sodium Nitrate


title: daf-16(mgDf50) mRNA Replicate 1 [d16_1]


title: eNOS KO + Sodium Nitrate White matter1


title: TS2-1


title: TS1-G1-6-3

source_name: The NMuLi cells transfected with TS1-G1-6 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS1-T1-5-4

source_name: The NMuLi cells transfected with TS1-T1-5 at 10 nM using Lipofectamine 2000 for 24hr.


title: daf-16(m26);pmk-1(miy7) Replicate 2 [DRDE_2]

source_name: pmk-1 caspase resistent (D327E) with daf-16 splice site mutation_whole worm


title: Lignin-treated S. aureus, 20 minutes post-treatment, replicate 3 [L-20-3_S115]

description: MOPS-20 min vs. Lignin-20 min.txt

value: 20 minutes post-treatment


title: eNOS KO White matter1


title: eNOS WT Grey matter 3

value: Brain - Grey Matter


title: TS1-G1-6-2

value: transfected with TS1-G1-6 at 10 nM using Lipofectamine 2000 for 24hr.


title: daf-16(m26);pmk-1(miy7) Replicate 1 [DRDE_1]


title: Lignin-treated S. aureus, 20 minutes post-treatment, replicate 2 [L-20-2_S114]

description: MOPS-20 min vs. Lignin-20 min.txt


title: eNOS KO White matter2


title: eNOS WT White matter2


title: daf-16(m26);pmk-1(km25) Replicate 1 [DRP1_1]

source_name: pmk-1 null with daf-16 splice site mutation_whole worm


title: daf-16(m26);pmk-1(km25) Replicate 2 [DRP1_2]


title: Lignin-treated S. aureus, 20 minutes post-treatment, replicate 1 [L-20-1_S113]

description: MOPS-20 min vs. Lignin-20 min.txt


title: MOPS-treated S. aureus, 20 minutes post-treatment, replicate 2 [M-20-2_S102]

description: MOPS-20 min vs. Lignin-20 min.txt


title: MOPS-treated S. aureus, 20 minutes post-treatment, replicate 3 [M-20-3_S103]

description: MOPS-20 min vs. Lignin-20 min.txt


title: MOPS-treated S. aureus, 2 hours post-treatment, replicate 1 [M-2-1_S104]

description: MOPS-2 hr vs. Lignin-2 hr.txt


title: eNOS WT White matter1


title: daf-16(m26) mRNA Replicate 2 [DR_2]

source_name: daf-16 splice site mutation_whole worm


title: TS1-G1-6-1


title: TS1-G1-6-4


title: daf-16(m26) mRNA Replicate 1 [DR_1]


title: MOPS-treated S. aureus, 20 minutes post-treatment, replicate 1 [M-20-1_S101]

description: MOPS-20 min vs. Lignin-20 min.txt


title: Bend3, rBMP4, +inhibitor, 8 hr

city: MEMPHIS

first: Zhengjun

last: Wang

state: TN

address: 71 S Manassas Street

institute: University of Tennessee Health Science Center

description: bldn

data_processing:
Transcript abundance from RNA-seq reads were quantified using Salmon
gene-level counts were obtained using tximport against the C57BL/6 J mouse genome annotation Genome Reference Consortium Mouse Build 39 (GRCm39),
RAW counts were processed with DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: endothelial cells

extract_protocol:
Total RNA was extracted from micro punched samples using the RNeasy Mini kit. 800ng of total RNA was used for the construction of sequencing libraries.
After the QC procedures, mRNA from eukaryotic organisms is enriched from total RNA using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/ul before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).

value: endothelial cells


title: Bend3 conrol

description: bwt


title: MCN_water deprived_72 hours_Input

data_processing:
Data proceesing was performed by the EpiQuest service by Zymo Research.
ChIP-seq reads were aligned to rat Rn6 genome using Bowtie.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: Rn6
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Supplementary files format and content: ChIP-seq output - Creb3l1 ChIP-seq processed data.xls

source_name: Hypothalamus

growth_protocol: Male Sprague Dawley rats weighing 250-274 grams were purchased from commercial supplier Envigo. Rats were housed in groups of 3 under a 12:12 light/dark cycle at a temperature of 21-22°C and a relative humidity of 40-50%.

extract_protocol:
ChIP was performed using SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, 38191). Samples were disrupted for 15 seconds with a Biomasher homogeniser (Takara Bio). To crosslink proteins to the DNA, formaldehyde (Sigma-Aldrich, F8775) was added to each sample to a final concentration of 1.6% followed by end over end mixing (Tube Rotor, VWR, 444-0502) for 20 minutes at room temperature (RT). Crosslinking was stopped by adding 50 µl of 10x glycine solution per 500 µl sample followed by end over end mixing for 5 minutes at RT.
ChIP-seq DNA libraries were prepared from 1 ng of ChIP DNA and 1 ng of Input DNA using a proprietary library protocol from the EpiQuest service by Zymo Research.

treatment_protocol: Animals were water deprived for 72 hours.

value: Hypothalamus

value: Magnocellular neurone enriched

value: 72 hours water deprivation

tag: chip antibody


title: wild type mRNA Replicate 2 [BPW158_2]

source_name: wild type_whole worm

value: late L4

value: wild type

value: whole worm


title: wild type mRNA Replicate 3 [BPW158_3]


title: wild type mRNA Replicate 1 [BPW158_1]


title: MCN_water deprived_72 hours_Creb3l1

value: Male

value: Creb3l1, Sigma-Aldrich, HPA024069


title: Bend3, rBMP4,8 hr

description: bbmp

value: rBMP4 25ng/ml, 8hr


title: pmk-1(miy7) mRNA Replicate 3 [BPW157_3]

source_name: pmk-1 caspase resistent (D327E)_whole worm


title: pmk-1(miy7) mRNA Replicate 2 [BPW157_2]


title: TS1-T1-5-1

value: transfected with TS1-T1-5 at 10 nM using Lipofectamine 2000 for 24hr.

value: NMuLi

value: Liver


title: Visium melanoma_2

city: leuven

first: Panagiotis

middle: Cristophe

last: Karras

state: belgium

address: Herestraat 49

country: Belgium

institute: VIB Center for Cancer Biology

description: spatial transcriptomics in primary mouse melanoma tumors

data_processing:
library strategy: spatial transcriptomics
scRNAseq: CellRanger v.3.1.0
bulk RNAseq: RSEM
SpaceRanger output  analyzed using the Seurat spatial vignett
Assembly: mm10 for mouse and hg19 for human
Supplementary files format and content: h5; csv

organism: Mus

source_name: NRASQ61K/°;Ink4a-/- primary lesion

extract_protocol: Libraries for scRNA-seq were created using the 10X Genomics Chromium platform according to the manufacturer’s instructions. Library construction was performed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (n = 16; 10x Genomics, catalog number 1000092) or the Chromium Single Cell A Chip Kit and 5′ Library & Gel Bead Kit (10x Genomics, catalog number 1000014). We opted for high target recovery (median 5000, range 5000-10000), keeping within the range of optimal input concentration per target recovery, as recommended by the manufacturer. In brief, cells were partitioned into gel bead-in-emulsions (GEMs) at limiting dilutions, where lysis and reverse transcription occurred, yielding uniquely barcoded full-length cDNA from polyadenylated mRNA. GEMs were subsequently broken, and the pooled fraction was amplified and subjected to fragmentation, end repair and adaptor ligation of size-selected fractions.For bulk RNAseq about 500 pg of RNA per sample was reverse-transcribed and amplified using a modified SMARTseq2 protocol (Rambow et al. 2018). Prior to generating sequencing libraries using the NexteraXT kit (Illumina, cat. no. FC-131-10), cDNA profiles were monitored using the Bioanalyzer. Sequencing was performed on a Nextseq500 platform (Illumina, SE75bp). Differential analyses between siPRRX1 and siCtrl samples were executed using the DeSeq2 pipeline. Visium libraries were sequenced on the Illumina Novaseq 6000 instrument (parameters: SP flowcell 100 cycles single reads, lane 1 = 220pM + 1% PhiX / lane 2 = 215pM + 1% PhiX).

value: skin

tag: tumor

value: melanoma

tag: tumor stage


title: TS1-T1-5-3


title: pmk-1(miy7) mRNA Replicate 1 [BPW157_1]


title: TS1-T1-5-2


title: Visium melanoma_4


title: Visium melanoma_3


title: TS1-4

source_name: The NMuLi cells transfected with TS1 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS1-C1-7-4

source_name: The NMuLi cells transfected with TS1-C1-7 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS1-2

value: transfected with TS1 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS1-C1-7-1

value: transfected with TS1-C1-7 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS1-C1-7-3


title: pmk-1(km25) mRNA Replicate 2 [BPW156_2]

source_name: pmk-1 null_whole worm


title: E15.5_StomachIntestine_SpatialRNASeq

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
For 10X Chromium single cell RNA-seq data, reads alignment, filtering, barcode counting, and UMI counting were performed using cellranger 4.0 with default parameters
For 10X Visium Spatial RNA-seq data, reads alignment, filtering, barcode counting, and UMI counting were performed using Spaceranger v1.2 with default parameters
Sample integration, normalization and scaled gene expression data were calculated by Seurat3.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw UMIcounts and scaled data for each cell

source_name: E15.5 mouse embyro stomach and intestine cells

extract_protocol:
Single cells were captured in the 10X Genomics Chromium Single Cell 3’ Solution, and RNA-seq libraries were generated following the manufacturer’s instruction (10X Genomics) and subjected to high-throughput sequencing on an Illumina Novaseq PE150 platform.
single cells were captured using the 10X Genomics Chromium Single Cell 3' Solution according to the manufacturers protocol. (10XGenomics, Pleasanton)
high-throughput sequencing were on Illumina Novaseq PE150 platform.

tag: age

value: stomach and intestine cells

tag: sequencing

value: SpatialRNASeq


title: Needles, H6

city: Helsinki

first: Fred

last: Asiegbu

address: Latokartanonkaari 7

country: Finland

institute: University of Helsinki

description: Pinus sylvestris L.

data_processing:
All samples need to pass through the following three steps before library construction
mRNA  is enriched using oligo(dT) beads. The mRNA  is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase.
The original raw data from Illumina are transformed to Sequenced Reads by base calling
Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.
Perform de novo alignments with trinity
Assembly: no reference
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Pinus sylvestris

source_name: Scots pine needles

extract_protocol:
Needles were flash frozen in liquid nitrogen, and RNA was harvested using CTAB reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Scots pine needles

tag: family

value: 1 year

tag: phenotype

value: susceptible


title: E13.5_StomachIntestine_SpatialRNASeq

source_name: E13.5 mouse embyro stomach and intestine cells


title: E15.5_LargeIntestine_scRNASeq

source_name: E15.5 mouse embyro large intestine cells

value: large intestine cells

value: scRNASeq


title: E15.5_DistalSmallIntestine_scRNASeq

source_name: E15.5 mouse embyro distal small intestine cells

value: distal small intestine cells


title: Needles, H4

description: Pinus sylvestris L.

value: resistant


title: Needles, H5

description: Pinus sylvestris L.


title: TS9-4

source_name: The NMuLi cells transfected with TS9 at 10 nM using Lipofectamine 2000 for 24hr.

tag: treatment


title: E15.5_ProximalSmallIntestine_scRNASeq

source_name: E15.5 mouse embyro proximal small intestine cells

value: proximal small intestine cells


title: TS1-3

tag: cell line


title: Needles, H7

description: Pinus sylvestris L.


title: TS9-2

value: transfected with TS9 at 10 nM using Lipofectamine 2000 for 24hr.


title: TS1-1

value: NMuLi


title: TS9-3

value: Liver


title: pmk-1(km25) mRNA Replicate 3 [BPW156_3]

value: late L4

tag: strain

tag: genotype

value: whole worm


title: Needles, H3

description: Pinus sylvestris L.


title: Needles, H2

description: Pinus sylvestris L.


title: pmk-1(km25) mRNA Replicate 1 [BPW156_1]


title: Needles, H1

description: Pinus sylvestris L.


title: E13.5_LargeIntestine_scRNASeq

source_name: E13.5 mouse embyro large intestine cells


title: HEK293T RHBDD2-CKO bio rep 2

city: Bunkyo-ku

first: Morito

last: Kurata

state: Tokyo

address: １－５－４５ Yushima Bunkyo-ku

department: Comprehensive Pathology

institute: Tokyo Medical and Dental University

data_processing:
Mapping: Hisat2 v2.0.5.
Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%). Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Reference genome version:Homo_sapiens_Ensemble_94
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
DEseq2 for differential analysis
Supplementary files format and content: b37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

growth_protocol: HEK293T cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, FUJIFILM Wako Pure Chemical Co., Osaka, Japan).

extract_protocol:
Total RNA was extracted  by RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol including DNase I treatment.
NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: Targeted genes, C9orf89, MAGI2, MLPH, and RHBDD2 were knockout by CRISPRv2 vectors

value: Human embryonic kidney


title: E13.5_DistalSmallIntestine_scRNASeq

source_name: E13.5 mouse embyro distal small intestine cells


title: HEK293T RHBDD2-CKO bio rep 3


title: Needles, H8

description: Pinus sylvestris L.


title: E13.5_ProximalSmallIntestine_scRNASeq

source_name: E13.5 mouse embyro proximal small intestine cells


title: Needles, F8

description: Pinus sylvestris L.


title: Needles, F7

description: Pinus sylvestris L.


title: HEK293T MLPH-CKO bio rep 3

value: MLPH-KO


title: HEK293T RHBDD2-CKO bio rep 1


title: E13.5_Stomach_scRNASeq

source_name: E13.5 mouse embyro stomach cells

value: stomach cells


title: E15.5_Stomach_scRNASeq

source_name: E15.5 mouse embyro stomach cells


title: Needles, F6

description: Pinus sylvestris L.


title: HEK293T MLPH-CKO bio rep 2


title: Needles, F5

description: Pinus sylvestris L.


title: TS9-1


title: TS8-1

source_name: The NMuLi cells transfected with TS8 at 10 nM using Lipofectamine 2000 for 24hr.


title: Control-4

source_name: The NMuLi cells treated with transfection reagent in the absence of ASO.


title: TS8-4

value: transfected with TS8 at 10 nM using Lipofectamine 2000 for 24hr.


title: E11.5_LargeIntestine_scRNASeq

source_name: E11.5 mouse embyro large intestine cells


title: HEK293T MLPH-CKO bio rep 1


title: Control-3

value: treated with transfection reagent in the absence of ASO.


title: TS8-2


title: Control-2


title: TS8-3


title: Needles, F3

description: Pinus sylvestris L.

value: Scots pine needles

value: 1 year


title: HEK293T MAGI2-CKO bio rep 3


title: E11.5_Stomach_scRNASeq

source_name: E11.5 mouse embyro stomach cells


title: Needles, F4

description: Pinus sylvestris L.


title: HEK293T MAGI2-CKO bio rep 2


title: E10.5_Stomach_scRNASeq

source_name: E10.5 mouse embyro stomach cells


title: Needles, F2

description: Pinus sylvestris L.


title: HEK293T MAGI2-CKO bio rep 1


title: E11.5_SmallIntestine_scRNASeq

source_name: E11.5 mouse embyro small intestine cells

value: small intestine cells


title: Control-1


title: E10.5_Intestine_scRNASeq

source_name: E10.5 mouse embyro intestine cells

value: intestine cells

value: scRNASeq


title: Needles, F1

description: Pinus sylvestris L.

source_name: Scots pine needles

value: resistant


title: E9.5_GutTube_scRNASeq

source_name: E9.5 mouse embyro guttube cells

value: guttube cells


title: HEK293T C9orf89-CKO bio rep 3


title: Needles, C7

description: Pinus sylvestris L.

value: susceptible


title: Needles, C5

description: Pinus sylvestris L.


title: Needles, C6

description: Pinus sylvestris L.


title: Needles, C8

description: Pinus sylvestris L.


title: HEK293T C9orf89-CKO bio rep 2


title: WGBS_RELA6_NonRecur

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Raw RRBS FASTQ files were mapped to NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP RRBS mode (Xi and Li, 2009). DNA methylation ratio and differential methylated cytosine (DMCs/DMRs) were analyzed by using MOABS (Sun et al., 2014). CpG sites with five or more reads covered were used for downstream analysis. Bisulfite conversion rates were estimated on the basis of lambda phage genome spike-ins. The bedGraph files including single base pair DNA methylation ratios were transformed to bigwig file format which can be visualized using the UCSC genome browser. DNA methylation heatmaps were plotted using R package https://www.rdocumentation.org/packages/heatmap3/versions/1.1.6/topics/heatmap3 heatmap3 by taking the shared CpGs among all the samples as input. DNA methylation phylogenetics analysis was performed by using R package ape
To compare multiple groups’ DMCs, we merge all the DMCs in all two-group comparisons (union DMC sets). The UpSetR (Conway et al., 2017) package was used to visualize the union of DMC sets among multiple two-group comparisons. To analyze dynamic changes of DMCs among tumor recurrent, we first separate DMCs to three categories (Hyper; Hypo; NoChange) based on adjacent two recurrent stages. Then, by considering four adjacent recurrent stages (P vs. cerebellum; R1 vs. cerebellum; R2 vs. cerebellum and R3 vs. cerebellum), we filtered out those DMCs with hyper/hypo and hypo/hyper switch between any two adjacent stages due to the small numbers. We finally separated DMCs into seven categories: consistent Hyper; consistent Hypo; Gain Hyper; Gain Hypo; Loss Hyper; Loss Hypo and switch (between hyper/hypo and NoChange). R alluvial package (https://www.rdocumentation.org/packages/alluvial/versions/0.1-2/topics/alluvial) was used to visualize the dynamic changes of DMCs along tumor recurrence. Colored density scatterplot of DNA methylation ratios was performed by using R package smoothScatter (https://www.rdocumentation.org/packages/graphics/versions/3.6.1/topics/smoothScatter). GREAT (McLean et al., 2010) was used to predict DMRs’ functions.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to do quality checks for raw fastq files. Raw FASTQ files were aligned to NCBI Human Reference Genome Build GRCh37 (hg19) using HISAT2 (Kim et al., 2019) with default settings. The uniquely mapped reads were used for downstream analysis. HTSeq (Anders et al., 2015) was used to count the reads count mapped in exon regions for each gene. Read counts matrix (row as genes; column as samples) were inputted to DESeq2 (Love et al., 2014) to identify differentially expressed genes (DEGs). We consider genes with FDR<=0.05 and fold change >= 2 folds as DEGs. Principal component analysis of DEGs was performed using R package DESeq2. DEGs’ function enrichment was using GSEA (Subramanian et al., 2005).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: GEO.merge.normalized2.txt: normalized counts for RNA-seq samples

source_name: brain

extract_protocol:
Freshly resected ependymoma tumor specimens from 10 patients undergoing serial surgical resections of primary and recurrent tumors (total 33, 3.67±1.76) over a period of 13 years (5.8 ±3.8) at Texas Children’s Hospital were obtained for this study.
Genomic DNA was extracted with Allprep DNA/RNA mini kit (Qiagen).  and concentrations measured using the Qubit® dsDNA BR Assay Kit (Thermo Fisher Scientific), followed by DNA quality assessment with the Fragment AnalyzerTM and either the DNF-487 Standard Sensitivity or the DNF-488 High sensitivity genomic DNA Analysis Kit (Advanced Analytical). RRBS libraries were prepared using the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode Cat# C02030033), according to the manufacturer's protocol. 100ng of genomic DNA were used to start library preparation for each sample. Following library preparation, samples were pooled together either by 8 (mouse contamination up to 10%), 7 (mouse contamination up to 25%), 5 (mouse contamination up to 40%) or 4 (mouse contamination up to 55%). In total, 16 pools were prepared. PCR clean-up after the final library amplification was performed using a 1.5x beads:sample ratio of Agencourt® AMPure® XP (Beckman Coulter). RRBS library pools quality control was performed by measuring DNA concentration of the pools using the Qubit® dsDNA HS Assay Kit (Thermo Fisher Scientific), and the profile of the pools was checked using the High Sensitivity DNA chip for 2100 Bioanalyzer (Agilent). Each RRBS library pool was deep sequenced on one lane HiSeq3000 (Illumina) using 50 bp single-read sequencing (SR50).
RNAseq libraries for transcriptome analysis were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system per manufacturers’ instructions. Sample prep began with 1 µg of total RNA from each sample. Poly-A RNA was purified from the sample with oligo dT magnetic beads, and the poly(A) RNA was fragmented with divalent cations. Fragmented poly-A RNA was converted into cDNA through reverse transcription and were repaired using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. 3’ A-tailing with exo-minus Klenow polymerase was followed by ligation of Illumina paired-end oligo adapters to the cDNA fragment. Ligated DNA was PCR amplified for 15 cycles and purified using AMPure XP beads. After purification of the PCR products with AMPure XP beads, the quality and quantity of the resulting

value: brain

tag: diagnosis

value: pediatric Ependymoma


title: Needles, C3

description: Pinus sylvestris L.


title: HEK293T C9orf89-CKO bio rep 1

tag: cell type


title: HEK293T Nontarget bio rep 3

value: WT


title: Needles, C2

description: Pinus sylvestris L.


title: control 1 Marginal zone hyperplasia

status: Public on Jul 11 2022

type: genomic

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description: Cytoscan HD

hyb_protocol: Samples were hybridized onto Cytoscan HD arrays Cytoscan HD and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Nexus biodiscovery 7.5 edition Software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: Laterocervical LN

label_protocol: CytoScan™ Reagent Kit / 901808,t/GPL16131

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

tag: type of sample

value: Marginal zone hyperplasia

tag: gender

value: male

value: frozen tissue


title: WGBS_PFA6_NonRecur_R1


title: Needles, C1

description: Pinus sylvestris L.


title: n55-2 Pediatric Nodal Marginal Zone Lymphoma

description: Cytoscan HD

source_name: Axilar LN

value: Pediatric nodal marginal zone lymphoma


title: control 3 Marginal zone hyperplasia

description: Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software 9.0
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

source_name: Cervical LN

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

value: FFPE


title: n21 Pediatric Nodal Marginal Zone Lymphoma

description: Cytoscan HD


title: Ishikawa

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: cultured in DMEM

data_processing:
Remove sequences that have low quality base N.
Filter out artificial sequences using tagdust with default parameter. tagdust version is 1.13.
Remove sequences that match to rRNA references up to [error] errors. rRNAdust version is 1.00.
RNAs were aligned to the human genome and were used to search for miRNA sequences in the miRBase 21.0 database. We selected sequences with a single match.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file of tag number matched to miRNAs

source_name: Endometrial cancer cell line

growth_protocol: Cells were cultured in DMEM.

extract_protocol:
Total RNA was purified using ISOGEN reagent according to the manufacturer's instructions (NipponGene, Toyama, Japan).
Short RNA libraries were prepared for sequencing using 'TruSeq Small RNA Sample Prep Kit'.

value: Uterus

tag: disease

value: adenocarcinoma

value: Ishikawa


title: HEC-1A

description: cultured in DMEM


title: Wildtype2

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw data Fastqc
Raw Data was processed with fastp
Hisat2/Tophat  for blasting
Stringtie for assemble
featureCounts for gene analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Total RNA was extracted by using Trizol reagent. Total 2ug RNA for the construction of sequencing libraries
mRNA were enriched by Oligo(dT) bread and then fragmented by fragmentation buffer. cDNA was synthesized by reverse transcription using 6bp random primers and purified by QIAQuick PCR kit. After adapter ligation, DNA was PCR amplified sequences and band isolated from an agarose gel.


title: Wildtype1


title: Pd1_CKO1


title: Pd1_CKO2


title: Needles, C4

description: Pinus sylvestris L.

value: Scots pine needles

value: 1 year


title: 8_Jak2_NbTz_6061

city: Cambridge

first: David

last: Mooney

address: 58 Oxford Street

institute: Harvard University

data_processing:
Sequenced mRNA from Jak2 V617F Vav-iCre and WT-Jak2 Vav-iCre mice were aligned and quantified using salmon, and were mapped unto an Ensembl GRCm38 reference transcriptome index.
Transcripts were then converted to gene IDs using the AnnotationDbi, RMaria and tximport packages in R
Differentially expressed genes, defined as genes with an adjusted p-value ≤ 0.1, were then determined using DEseq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Artificial fibrotic matrix

growth_protocol: Monocytes were isolated using a negative selection isolation kit (Stem Cell Technologies) and encapsulated in hydrogels in culture in minimal essential media alpha (aMEM) with glutamax and no nucleosides (Gibco), supplemented with 10% heat-inactivated fetal bovine serum (Catalog 10082-147, Gibco), 1% penicillin-streptomycin (Thermo), recombinant mouse animal-free GM-CSF (100 ng/mL, PeproTech), recombinant mouse animal-free IL4 (200 ng/mL, PeproTech), and 100 ng/mL PGE2 (Sigma).

extract_protocol:
Hydrogels were digested with 100-150 uL of 300 U/mL collagenase IV (Worthington) and 34 U/mL of alginate lyase (Sigma-Aldrich) in DBPS + Ca/Mg, 0.5% BSA at 37° C for 15 minutes, followed by addition of another 100-150 uL of 300 U/mL collagenase IV and incubation at 37° C for 15 minutes. Next, 0.5 mL wash buffer (DPBS without Ca/Mg, 2 mM EDTA, 0.5% BSA) was added, and the samples were transferred to a deep-bottom 1.2 mL 96-well plate. The plate was centrifuged at 400g for 5 minutes at 4° C and the supernatant discarded. A final set of washes was performed with cold 0.2 mL wash buffer on ice, followed by centrifugation at 400g for 5 minutes at 4° C to obtain a clean cell pellet. and cells were lysed for RNA isolation (Purelink RNA Microscale Kit, Thermo). RNA was quantified and quality checks were performed by TapeStation, nanoDrop, and RiboGreen.
cDNA libraries were prepared for RNA-sequencing by Kapa mRNA Hyperprep and normalized by qPCR.

treatment_protocol: Cells were encapsulated in either viscous or elastic matrix hydrogels

value: monocytes

value: Jak2 V617F Vav-iCre

tag: viscoelasticity

value: elastic

tag: time point

value: day 3


title: 6_Jak2_VLVG_6065

value: viscous


title: HEK293T Nontarget bio rep 2

value: Human embryonic kidney


title: HEK293T Nontarget bio rep 1

value: WT


title: 7_Jak2_NbTz_6065


title: 4_WT_NbTz_6060

value: Vav-iCre


title: 3_WT_NbTz_6064


title: 1_WT_VLVG_6064


title: 5_Jak2_VLVG_6061


title: 2_WT_VLVG_6060


title: Pediatric Nodal marginal zone lymphoma 58

source_name: right neck mass, lymph  nodes

label_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602

value: Pediatric Nodal marginal zone lymphoma

value: female


title: VLVG-30_1

hyb_protocol: A volume of 1.5 uL of lysates were used in the nanoString hybridization reaction and the remaining were stored at -80°C. nCounter Elements (nanoString) hybridization was performed according to manufacturer’s instructions. Aliquots of master stocks of probe A and B (IDT) were thawed and diluted to 0.6 nM and 3 nM working pools, respectively. Hybridization buffer (nanoSTring) was mixed sequentially with Probe A and B working pools, followed by the addition of 1.5 uL of RNA lysate. The total reaction volume was adjusted with RNA-ase-free water to 15 uL. Subsequently, hybridization was performed for 20 hours at 67°C on a thermocycler, followed by ramping to 4°C.

scan_protocol: Hybridized samples were loaded on nanoString cartridges for analysis.

data_processing: Data were analyzed using nSolver and nCounter Advanced Analysis.

label: not provided

source_name: primary human monocytes

label_protocol: not provided

growth_protocol: Primary human monocytes were isolated from fresh human bone marrow donors less than 35 years old from Lonza (1M-125) by a density gradient with Lymphoprep and SepMate-15 tubes (StemCell Technologies) and negative isolation (EasySep Human Monocyte Isolation Kit, StemCell Technologies). Prior to hydrogel encapsulation on Day 0, monocytes were cultured overnight on ultra-low attachment 100 mm dishes (Corning) at 5 e5 cells/mL in minimal essential media alpha (aMEM) with glutamax and no nucleosides (Gibco), supplemented with 10% heat-inactivated fetal bovine serum (Catalog 10082-147, Gibco), 1% penicillin-streptomycin (Thermo), recombinant human GM-CSF (100 ng/mL, Peprotech), recombinant human IL-4 (200 ng/mL Peprotech), and PGE2 (100 ng/mL, Sigma).

extract_protocol: Cells (~100,000) from each sample were suspended in 0.05 mL RNA-later (ThermoFisher) at 4C until analysis. The RNA-later was diluted with 4-fold volume of cold PBS (without Ca or Mg). Samples were centrifuged at 800 x g for 10 minutes at 4°C and lysed and homogenized at 10,000 cells/uL with RLT buffer (Qiagen) + 1% 2-mercaptoethanol (Sigma).

treatment_protocol: Cells were encapsulated in soft vs stiff and viscous vs elastic hydrogels for 3 days, and then recoverd for RNA lysis and nanoString analysis. Soft ~ 0.75 kPa, Stiff ~ 7.5 kPa elastic moduli.

value: Viscous

tag: stiffness

value: stiff (E~7.5 kPa)

tag: donor


title: VLVG-30_2


title: VLVG-10_2

value: soft (E~0.75 kPa)


title: VLVG_30_1


title: VLVG-10_1


title: VLVG_10_3


title: VLVG_30_2


title: VLVG_10_2


title: VLVG_30_3


title: VLVG_10_1


title: NbTz-30_2

value: Elastic


title: NbTz-10_2


title: NbTz-10_1


title: NbTz_30_1


title: NbTz_10_3


title: NbTz_10_1


title: NbTz_10_2


title: NbTz-30_1


title: NbTz-10_3


title: NbTz_30_2


title: blood, Day 0, UGA4, 428

city: Bethesda

first: Megan

last: Hockman

state: MD

address: 50 South Drive

department: NIAID

institute: National Institutes of Health

data_processing:
Trim Galore! v0.6.6
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!
STAR v2.6.1d
Trimmed sequence reads were mapped to GRCh38.p10 using STAR (parameters- quantMode: TranscriptomeSAM twopassMode: Basic runRNGseed: 0 outFilterMultimapNmax: 20 alignSJDBoverhangMin: 1 outSAMattributes: NH HI AS NM MD quantTranscriptomeBan: Singleend)
Salmon v1.4.0
Aligned reads were used to perform transcript quantification using salmon quant in alignment-based mode (parameters - libType: IU)
Assembly: hg38
Supplementary files format and content: comma-separated value tables contain transcripts-per-million for each sample

source_name: Whole Blood

extract_protocol:
Total RNA was isolated from each blood sample in randomized batches using the PAXgene Blood miRNA Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s recommendations and stored at -80°C in a LoBind twin.tec 96-well PCR plate (Eppendorf, Hamburg, Germany). All samples were quantified with the Qubit BR RNA Assay on a Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and their fragment size distribution was measured with an RNA Screentape on a 4200 TapeStation System (Agilent, Santa Clara, CA)
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the manufacturer’s protocols using either 1ug of input RNA or, in the case of several low-yield samples, the maximum possible input mass. AMPure XP Beads (Beckman Coulter, Brea, CA) were used in place of the supplied NEBNext Sample Purification Beads. Libraries were prepared in 3 batches with two negative library prep controls in each batch to monitor for reagent or sample-to-sample contamination. Each library was barcoded with NEBNext Multiplex Oligos for Illumina (NEB, Ipswich, MA) in a rotating scheme, which ensured that each pool had a unique set of barcodes. Each library was quantified with the Qubit dsDNA HS Assay on a Qubit 2.0 Fluorometer and fragment size was measured with an HSD1000 Screentape (Agilent, Santa Clara, CA) on a 4200 TapeStation System. All libraries made from experimental samples were of sufficient molarity for pooling and sequencing.
A single sequencing library was prepared from a single biological sample. Libraries were then pooled with equimolar input at either 2nM or 3nM into sets of 96 libraries for RNA sequencing on a NovaSeq 6000 with the S1 2x150 - 300 Cycle configuration (Illumina, San Diego, CA) at the Genomics Core Facility (Center for Genomics and Systems Biology, New York University).

value: Whole Blood

tag: time

value: Day 0


title: blood, Day 0, UGA4, 427

tag: tissue


title: blood, Day 0, UGA4, 458


title: blood, Day 0, UGA4, 452


title: blood, Day 0, UGA4, 443


title: blood, Day 0, UGA4, 442


title: blood, Day 0, UGA4, 426


title: blood, Day 0, UGA4, 54


title: blood, Day 0, UGA4, 459


title: blood, Day 0, UGA4, 46


title: blood, Day 0, UGA4, 437


title: blood, Day 0, UGA4, 455


title: blood, Day 0, UGA4, 50


title: blood, Day 0, UGA4, 449


title: blood, Day 0, UGA4, 451


title: blood, Day 0, UGA4, 99


title: blood, Day 0, UGA4, 431


title: blood, Day 0, UGA4, 446


title: blood, Day 0, UGA4, 436


title: TS1-C1-7-2

data_processing: The scanned data were processed for signal values using Microarray Suite 5.0 software  .

source_name: The NMuLi cells transfected with TS1-C1-7 at 10 nM using Lipofectamine 2000 for 24hr.

extract_protocol: Total RNA was isolated using a Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

value: NMuLi

value: Liver


title: blood, Day 0, UGA4, 423


title: blood, Day 0, UGA4, 416


title: blood, Day 0, UGA4, 418


title: blood, Day 0, UGA4, 410


title: blood, Day 0, UGA4, 414


title: blood, Day 0, UGA4, 434


title: blood, Day 0, UGA4, 409


title: blood, Day 0, UGA4, 408


title: blood, Day 0, UGA4, 391


title: blood, Day 0, UGA4, 388


title: blood, Day 0, UGA4, 404


title: blood, Day 0, UGA4, 407


title: blood, Day 0, UGA4, 380


title: blood, Day 0, UGA4, 403


title: blood, Day 0, UGA4, 38


title: blood, Day 0, UGA4, 378


title: blood, Day 0, UGA4, 377


title: blood, Day 0, UGA4, 379


title: blood, Day 0, UGA4, 373


title: blood, Day 0, UGA4, 387


title: blood, Day 0, UGA4, 369


title: blood, Day 0, UGA4, 372


title: blood, Day 0, UGA4, 419


title: blood, Day 0, UGA4, 375


title: blood, Day 0, UGA4, 370


title: blood, Day 0, UGA4, 389


title: blood, Day 0, UGA4, 371


title: blood, Day 0, UGA4, 368


title: blood, Day 0, UGA4, 366


title: blood, Day 0, UGA4, 390


title: blood, Day 0, UGA4, 354


title: blood, Day 0, UGA4, 334


title: blood, Day 0, UGA4, 329


title: blood, Day 0, UGA4, 355


title: blood, Day 0, UGA4, 400


title: blood, Day 0, UGA4, 336


title: blood, Day 0, UGA4, 351


title: blood, Day 0, UGA4, 295


title: blood, Day 0, UGA4, 383


title: blood, Day 0, UGA4, 360


title: blood, Day 0, UGA4, 282


title: blood, Day 0, UGA4, 327


title: blood, Day 0, UGA4, 300


title: blood, Day 0, UGA4, 252


title: blood, Day 0, UGA4, 325


title: blood, Day 0, UGA4, 29


title: blood, Day 0, UGA4, 406


title: blood, Day 0, UGA4, 288


title: blood, Day 0, UGA4, 34


title: blood, Day 0, UGA4, 294


title: blood, Day 0, UGA4, 222


title: blood, Day 0, UGA4, 219


title: blood, Day 0, UGA4, 232


title: blood, Day 0, UGA4, 243


title: blood, Day 0, UGA4, 249


title: blood, Day 0, UGA4, 337


title: blood, Day 0, UGA4, 251


title: blood, Day 0, UGA4, 238


title: blood, Day 0, UGA4, 207


title: blood, Day 0, UGA4, 504


title: blood, Day 0, UGA4, 65


title: blood, Day 0, UGA4, 8


title: blood, Day 0, UGA4, 151


title: blood, Day 0, UGA4, 66


title: blood, Day 0, UGA4, 175


title: blood, Day 0, UGA4, 83


title: blood, Day 0, UGA4, 510


title: blood, Day 0, UGA4, 136


title: blood, Day 0, UGA4, 495


title: blood, Day 0, UGA4, 501


title: blood, Day 0, UGA4, 487


title: blood, Day 0, UGA4, 497


title: blood, Day 0, UGA4, 217


title: blood, Day 0, UGA4, 498


title: blood, Day 0, UGA4, 488


title: blood, Day 0, UGA4, 481


title: blood, Day 0, UGA4, 211


title: blood, Day 0, UGA4, 140


title: blood, Day 0, UGA4, 469


title: blood, Day 0, UGA4, 473


title: blood, Day 0, UGA4, 477


title: blood, Day 0, UGA4, 460


title: blood, Day 0, UGA4, 467


title: blood, Day 0, UGA4, 454


title: blood, Day 0, UGA4, 482


title: blood, Day 0, UGA4, 453


title: blood, Day 0, UGA4, 440


title: blood, Day 0, UGA4, 439


title: blood, Day 0, UGA4, 420


title: blood, Day 0, UGA4, 421


title: blood, Day 0, UGA4, 401


title: blood, Day 0, UGA4, 445


title: blood, Day 0, UGA4, 430


title: blood, Day 0, UGA4, 376


title: blood, Day 0, UGA4, 357


title: blood, Day 0, UGA4, 364


title: blood, Day 0, UGA4, 362


title: blood, Day 0, UGA4, 359


title: blood, Day 0, UGA4, 350


title: blood, Day 0, UGA4, 353


title: blood, Day 0, UGA4, 345


title: blood, Day 0, UGA4, 349


title: blood, Day 0, UGA4, 340


title: blood, Day 0, UGA4, 343


title: blood, Day 0, UGA4, 342


title: blood, Day 0, UGA4, 341


title: blood, Day 0, UGA4, 344


title: blood, Day 0, UGA4, 348


title: blood, Day 0, UGA4, 338


title: blood, Day 0, UGA4, 397


title: blood, Day 0, UGA4, 333


title: blood, Day 0, UGA4, 363


title: blood, Day 0, UGA4, 316


title: blood, Day 0, UGA4, 320


title: blood, Day 0, UGA4, 315


title: blood, Day 0, UGA4, 323


title: blood, Day 0, UGA4, 358


title: blood, Day 0, UGA4, 328


title: blood, Day 0, UGA4, 322


title: blood, Day 0, UGA4, 309


title: blood, Day 0, UGA4, 307


title: blood, Day 0, UGA4, 310


title: blood, Day 0, UGA4, 312


title: blood, Day 0, UGA4, 308


title: blood, Day 0, UGA4, 330


title: blood, Day 0, UGA4, 382


title: blood, Day 0, UGA4, 356


title: blood, Day 0, UGA4, 347


title: blood, Day 0, UGA4, 30


title: blood, Day 0, UGA4, 293


title: blood, Day 0, UGA4, 303


title: blood, Day 0, UGA4, 299


title: blood, Day 0, UGA4, 305


title: blood, Day 0, UGA4, 292


title: blood, Day 0, UGA4, 271


title: blood, Day 0, UGA4, 283


title: blood, Day 0, UGA4, 284


title: blood, Day 0, UGA4, 272


title: blood, Day 0, UGA4, 289


title: blood, Day 0, UGA4, 306


title: blood, Day 0, UGA4, 291


title: blood, Day 0, UGA4, 263


title: blood, Day 0, UGA4, 248


title: blood, Day 0, UGA4, 203


title: blood, Day 0, UGA4, 267


title: blood, Day 0, UGA4, 236


title: blood, Day 0, UGA4, 244


title: blood, Day 0, UGA4, 141


title: blood, Day 0, UGA4, 196


title: blood, Day 0, UGA4, 171


title: blood, Day 0, UGA4, 129


title: blood, Day 0, UGA4, 224


title: blood, Day 0, UGA4, 16


title: blood, Day 0, UGA4, 134


title: blood, Day 0, UGA4, 161


title: blood, Day 0, UGA4, 166


title: blood, Day 0, UGA4, 184


title: blood, Day 0, UGA4, 194


title: blood, Day 0, UGA4, 425


title: blood, Day 0, UGA4, 128


title: blood, Day 0, UGA4, 432


title: blood, Day 0, UGA4, 415


title: blood, Day 0, UGA4, 381


title: blood, Day 0, UGA4, 399


title: blood, Day 0, UGA4, 352


title: blood, Day 0, UGA4, 450


title: blood, Day 0, UGA4, 346


title: blood, Day 0, UGA4, 367


title: blood, Day 0, UGA4, 335


title: blood, Day 0, UGA4, 227


title: blood, Day 0, UGA4, 324


title: blood, Day 0, UGA4, 281


title: blood, Day 0, UGA4, 297


title: blood, Day 0, UGA4, 286


title: blood, Day 0, UGA4, 155


title: blood, Day 0, UGA4, 302


title: 3m-GliaKO1

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

institute: UCL Institute Of Ophthalmology

data_processing:
RNA sequencing files were analyzed using Galaxy Tools (usegalaxy.org)67.
Paired-end FASTQ files were aligned to the GRCm38 mouse genome using HISAT2 (v2.1.0)68, and BAM files were created.
Aligned reads were then counted using featureCounts (v1.6.4) to create gene count tables, which were analyzed by DESeq2 (v1.22.1) to identify differentially expressed genes.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files from FeatureCounts contain raw counted reads, per gene, per row, for each sample
Supplementary files format and content: tab-delimited text file from DESeq2 contain log2 fold change of each read between pooled control and treated samples per gene with p and q-values

source_name: Retinal Tissue

extract_protocol:
Isolated retinae from Astro-KO mice were lysed, and total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen). The sample was assessed using the RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA) and 2100 Bioanalyzer (Agilent). Total RNA samples > 200 ng with an RNA integrity number > 8.0 were sequenced.
The sequencing library was prepared using the TruSeq® Stranded mRNA library prep kit (Illumina, San Diego, CA, USA). Poly-A RNA was purified using poly-T oligo-attached magnetic beads. The eluted mRNA was then fragmented by incubation with the first-strand buffer at 94 °C for 8 min. First-strand cDNA was synthesized by mixing the cleaved RNA fragments, Superscript II reverse transcriptase, and random primers and incubating in a thermal cycler (25 °C for 10 min; 42 °C for 15 min; 70 °C for 15 min; hold at 4 °C). The cDNA was labelled using a cDNA plate barcode label reagent. The sample was then mixed with DNA polymerase I, RNase H, and the barcode label reagents and incubated at 16 °C for 10 min to synthesize second-strand cDNA and digest the template RNA. The cDNA was purified with AMPure XP beads, the 3’ ends were adenylated using an A-tailing mix, and the mixture was incubated in a thermal cycler (37 °C for 30 min; 70 °C for 5 min; hold at 4 °C). The adapters were ligated to the cDNA using a ligation mix, and the mixture was incubated at 20 °C for 15 min. After several rounds of PCR amplification, the enriched DNA fragments were purified by AMPure XP beads. The quality and quantity of the library were then validated with the Agilent 2100 Bioanalyzer. Bulk RNA sequencing was performed with an Illumina NovaSeq 6000 following the manufacturer’s procedures.

value: Retinal Tissue


title: 3m-Control3

value: Control


title: 3m-Control2


title: 12m-Control1


title: 12m-Control2


title: blood, Day 0, UGA4, 278


title: 3m-GliaKO3


title: 12m-Control3


title: blood, Day 0, UGA4, 393


title: 12m-GliaKO2


title: 12m-GliaKO1


title: 12m-GliaKO3


title: 3m-GliaKO2


title: 3m-Control1


title: blood, Day 0, UGA4, 85


title: scRNA-seq NPCTKO #1

city: Wuhan

first: Xuan

last: Liu

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: Wuhan university

data_processing:
Raw sequencing data were first processed using the CellRanger V4.0.0 pipeline.
We used DoubletFinder to remove doublet.
We used seurat to generate the sparse count matrix and downstream analysis.
We used infercnv(V1.2.0) to calculate copy number variant. And params were cutoff=0.1,HMM=TRUE, others are default.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every cell.
Supplementary_files_format_and_content: tsv files include cell barcode files and gene files.

source_name: GBM cells

extract_protocol:
Tumor tissues were dissected and enzymatically digested into single cells, then they were suspended in cold PBS.
Libraries were constructed using the Single Cell 3′ Library Kit V2 (10× Genomics).

value: GBM

tag: age

value: 3 months

tag: model

value: NPCTKO


title: blood, Day 0, UGA4, 77


title: scRNA-seq NPCTKO #2


title: blood, Day 0, UGA4, 47


title: bulk RNA NSCHRas-shp53 #3

data_processing:
Cutadapt (version 1.16, http://cutadapt.readthedocs.io/en/stable/guide.html) was used for adaptor sequence remove with the parameters -u 0 -u -30 -U 0 -U -30 -m 30
Cleaned reads were mapped to the mouse reference genome (UCSC mm10) using TopHat (version 2.1.1, http://ccb.jhu.edu/software/tophat/index.shtml) with default settings.
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: RNA-seq_Model1_NPCTKO_and_Model2_NSCHRas_shP53_raw_count.txt: Tab-delimited text file includes raw counts for each Sample.
Supplementary_files_format_and_content: RNA-seq_Model1_NPCTKO_and_Model2_NSCHRas_shp53_FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

extract_protocol:
RNA isolation was performed using the TRIZOL reagent (Invitrogen) according to manufacturer’s instructions. Tissue or cells were homogenized using a glass-Teflon in 1 ml or 500 µl TRIZOL reagent on ice and phase separation was achieved with 200 µl or 100 µl chloroform. After centrifugation at 12,000× g for 15 min at 4°C, RNA was precipitated by mixing aqueous phase with equal volumes of isopropyl alcohol and 0.5 µl 20 mg/ml glycogen. Precipitation were dissolved in DNase/RNase-free water (not diethylpyrocarbonate treated, Ambion).
Total RNA was extracted as described above. The concentration and quality of RNA was measured with Nanodrop 2000c (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). Briefly, mRNA was extracted by poly-A selected with magnetic beads with poly-T and transformed into cDNA by first and second strand synthesis. Newly synthesized cDNA was purified by AMPure XP beads (1:1) and eluted in 50 μl nucleotide-free water. RNA-seq libraries were sequenced by Illumina NovaSeq 6000 platform with pair-end reads of 150 bp. The sequencing depth was 60 million reads per library.


title: blood, Day 0, UGA4, 62


title: bulk RNA NSCHRas-shp53 #2


title: sid2_mat

city: Bern

first: Michael

last: Raissig

address: Altenbergrain 12

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

data_processing:
Read quality was assessed with FastQC
mapped against the Bd21-3v1.0 genome using bowtie2
Mapped reads were counted using summarised overlap and differentially expressed genes were analysed using DeSeq2 in R
Assembly: Bd21-3v1.0
Supplementary files format and content: DeSEQ2 analysis file comparing WT and bdmute containing all output statistics
Supplementary files format and content: Raw count files of the three replicates per 2 individuals

organism: Brachypodium distachyon

source_name: mature leaf tissue

growth_protocol: grown on ½ MS plates at 20ºC with ~100 µmol photons m-2 s-1 light for 7 days

extract_protocol:
Total RNA was isolated using Qiagen’s RNeasy Plant Mini kit with on-column DNAse digestion according to the manufacturer's instructions
Kapa mRNA HyperPrep (Roche)

value: mature leaf tissue


title: sid5_mat


title: blood, Day 0, UGA4, 70


title: bulk RNA NSCHRas-shp53 #1


title: bulk RNA NPCTKO #3


title: blood, Day 0, UGA4, 424


title: sid1_mat


title: WT5_mat

value: Bd21-3 (wild type)


title: blood, Day 0, UGA4, 386


title: blood, Day 0, UGA4, 275


title: bulk RNA NPCTKO #2


title: DA_57

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

institute: University of Navarra

description:
57da_S24_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2

data_processing:
library strategy: RT-PCR-based amplicon sequencing
Using an in-house computational pipeline based on Kernel written in ultra-fast C++ and a GUI written in Java (see https://gitlab.com/maccarthyslab/SHMPrep), Illumina pair-reads were assembled and collapsed according to their unique molecular identifier (UMI) to reconstruct unique overlap VH186.2DJ regions in FASTA format.
These sequences in FASTA format were then submitted to IMGT/HighV-QUEST (Aouinti et al. PLoS One 2015, PMID: 26540440) for VH186.2-D-J usage and CDR3 clonality identification.
Then, customized Python and R scripts were used for mutational analyses (see https://gitlab.com/maccarthyslab/SHMServer) after randomly resampling during 1000 iterations one single sequence per CDR3 clone, allowing us to increase our sensitivity for unique mutations, which are expected to derive from independent mutational events, and avoid overestimating mutation frequencies by repeated counting of non-unique mutations inherited within the clonal CDR3 lineage. For each group of Exo1+/+, Exo1-/-, and Exo1DA/DA  iterations, frequencies of mutation were normalized to the potential maximum number of the corresponding mutation subtype as we have previously described (MacCarthy et al., DNA Repair 2009, PMID:18952008), which corrects for sequence composition and size of CDR3 repertoire.
Genome_build: IMGT/V-QUEST mouse reference directory sets
Supplementary_files_format_and_content: Tab-delimited text files for each mouse genotype (wild type or WT, Exo1-/- or KO,  Exo1DA/DA or DA), where each row in every file corresponds to a mutation observed during the random 1000 iterations that were run within each group of mice. Additional descriptions (in columns) for each of these mutations (in rows) include:
sequence_id: the sequence belonging to the "dataset_id" sample
dataset_id: the individual mouse that was sampled
nt_position: site of the mutation
mutation_from: the nucleotide base of the consensus sequence in the IMGT/V-QUEST reference
mutation_to: the nucleotide base of the mutated sequence
hotspot_type: either one of an AID overlapping WGCW, WRC, or GYW motif; or Polh WA and TW motif. NA is recorded if none of the previous motifs were identified.
iteration: number between 1-1000

source_name: spleen

extract_protocol:
Age-matched mice (Exo1+/+, Exo1-/-, and Exo1DA/DA) were immunized intraperitoneally with 200 µg NP(33)-CGG (BioSearch Technologies) on alum. For primary response analysis, animals were sacrificed, and spleens were removed 10 days after a single immunization, followed by cellular disggregation and lysis of erythrocytes. Total RNA was extracted from splenocytes using Purelink RNA Mini Kit (ThermoFisher) and cDNA was generated using AccuScript High Fidelity 1st Strand cDNA Synthesis Kit (Stratagene). The Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2, was amplified using a nested PCR as previously described (Roa et al., PNAS 2008, PMID:18854411), and PCR products were gel purified and stored in 50 μL buffer containing 10mM Tris (pH 8.0) until library preparation.
Gel-purified PCR amplicons of VH186.2 region were submited to TruSeq® DNA library preparation (Illumina) following manufacturer’s instructions. After quality control by Bioanalyzer (Bio-Rad), libraries were paired-end sequenced on a MiSeq Sequencer (Illumina) at Einstein Epigenetics Facility.

tag: strain background

tag: immunization

value: 10 days post 200 mg NP(33)-CGG on alum (primary response)

value: spleen


title: bulk RNA NPCTKO #4

tag: strain


title: DA_21

description:
21da_S21_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2

tag: genotype


title: blood, Day 0, UGA4, 412


title: blood, Day 0, UGA4, 365


title: DA_56

description:
56da_S23_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: bulk RNA NPCTKO #1


title: DA_50

description:
50da_S22_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: blood, Day 0, UGA4, 221


title: DA_75

description:
75da_S18_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: DA_74

description:
74da_S17_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: D283_C217_C238_mut_L004

city: Lund

first: Markus

last: Ringner

address: Sölvegatan 35

country: Sweden

institute: Lund University

description:
sex: 2F + 1M
snRNA-seq
mRNA

data_processing:
Reads were demultiplexed and aligned to Transcriptome mm10-3.0.0_premrna, using Cell Ranger Pipeline Version 3.1.0 (default settings).
The gene Malat1 was filtered out. Genes detected in fewer than 3 single nuclei were removed. After the filtering, 23481 genes remained.
Single nuclei with less than 500 genes, more than 10,000 genes (doublets), or with a fraction of transcripts that map to mitochondrial genes > 0.9 were filtered out. After the filtering steps, data for 1772 control (WT) and 3968 mutant (KO) single nuclei remained.
Genome_build: mm10-3.0.0_premrna
Supplementary_files_format_and_content: umicountsAllcells.csv: Comma-separated text file containing UMI counts of mapped reads per gene (a total of 23481 genes) for each single nuclei (a total of 1772 wt and 3968 mut single nuclei).

source_name: Adult mouse midbrain

extract_protocol:
Single nuclei isolation and FACS.
Single nucleus libraries were made using Single Cell 3' v3 on Chromium platform (10X Genomics & SciLifeLab, Stockholm) in accordance with the manufacturer’s protocols.

value: Adult mouse midbrain

value: mDA

value: DatCreEed

value: PRC2 mutant

tag: timepoint

value: 8 months

tag: flowcell lane

tag: Sex

value: pooled male and female


title: KO_48

description:
48ko_S9_L001
processed data file: KO_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: blood, Day 0, UGA4, 5

value: Whole Blood

value: Day 0


title: WT1_mat


title: blood, Day 0, UGA4, 139


title: DA_80

description:
80da_S20_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: D283_C217_C238_mut_L003

description:
sex: 2F + 1M
snRNA-seq
mRNA

tag: cell type


title: WT2_mat


title: KO_49

description:
49ko_S10_L001
processed data file: KO_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: DA_79

description:
79da_S19_L001
processed data file: DA_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: blood, Day 0, UGA4, 108


title: D283_C217_C238_mut_L001

description:
sex: 2F + 1M
snRNA-seq
mRNA


title: D283_C217_C238_mut_L002

description:
sex: 2F + 1M
snRNA-seq
mRNA


title: KO_59

description:
59ko_S11_L001
processed data file: KO_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: WT_25

description:
25wt_S5_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2

value: wild type


title: WT_20

description:
20wt_S13_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: WT_48

description:
48wt_S14_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: WT_59

description:
59wt_S16_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: WT_55

description:
55wt_S15_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: C221_C224_C228_wt_L003

description:
sex: 2F + 1M
snRNA-seq
mRNA

value: wt


title: C221_C224_C228_wt_L002

description:
sex: 2F + 1M
snRNA-seq
mRNA


title: WT_67

description:
67wt_S6_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: C221_C224_C228_wt_L004

description:
sex: 2F + 1M
snRNA-seq
mRNA


title: Wt ,drought,  time point ZT16 rep1

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

department: Biosciences

country: Italy

institute: University of Milan

data_processing:
Reads were mapped on the reference Arabidopsis thaliana genome (TAIR, version 10) using the bowtie2 program
Estimation of gene expression levels was performed using RSEM
Identification of differentially expressed genes was performed by the quasi-likelihood F-test as implemented by edgeR.  False Discovery Rate (FDR) cut-off value of 0.05 was applied for the identification of significantly differentially expressed genes.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delineated file with  48 rows and 26986 columns reporting the number of reads assigned to each gene

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: In this study we used wild–type Arabidopsis plants, ecotype Columbia (Col–0) and mutant lines aba1-6 (Niyogi et al., 1998),  gi-2 (Fowler et al., 1999).  Seeds were germinated and plants grown in a controlled environment at a temperature of 21–23 °C, 65% relative humidity, either under long day (16 h light / 8 h dark) or short day (8 h light / 16 h dark) photocycles. Light was cool white fluorescent tubes (Osram, Sylvania) at a fluency of 120–150 μmol m-2 s-1 (Photosynthetically active radiation). Samples used for RNAseq analysis derived from an experiment previously described (Riboni et al., 2013). 3 week-old plants grown under short day conditions were moved to LD at Zeitgaber time (ZT) 8 (that is, at the end of the subjective day). Samples were harvested at ZT1, ZT8 (in the last short day) and ZT12 and ZT16 (the photo extension period). For each time point / treatment / genotype combination, we analyzed two biological replicates, each one consisting of approximately 50 seedlings pooled from three different Arabasket pots. To avoid soil carryover, we harvested only the aerial part of plants (i.e., above the hypocotyl).

extract_protocol:
RNA was extracted using the Trizol reagent (Invitrogen). For RNA sequencing, RNA Quality Control was performed with an electrophoretic run on a Bioanalyzer instrument using the RNA 6000 Nano Kit (Agilent). RNA Integrity Number was determined, and all the samples were considered suitable for processing (RIN > 8). RNA concentration was estimated through a spectrophotometric measurement using a Nanoquant Infinite M200 instrument (Tecan).
Sequencing libraries were prepared using the TruSeq™ RNA Sample Preparation Kit (Illumina)

treatment_protocol: Water deficit conditions were imposed as previously detailed (Riboni et al., 2013), so that under normal irrigation conditions plants grew under a Relative Soil Water Content (RSWC) of 80 – 90%, and 30% RSWC under water deficit conditions. RSWC was kept constant by daily weighing of pots and applications of water to maintain the desired value. Note that water defict was imposed soon after germination (i.e. in the short day) for each genotype and mantained throughout the experiment.

tag: ecotype

value: Columbia

tag: protocol

value: drought,  time point ZT16


title: Wt ,drought,  time point ZT16 rep2


title: blood, Day 0, UGA4, 69


title: blood, Day 0, UGA4, 75


title: C221_C224_C228_wt_L001

description:
sex: 2F + 1M
snRNA-seq
mRNA


title: Wt, normal watering,  time point ZT16 rep1

value: normal watering,  time point ZT16


title: WT_68

description:
68wt_S7_L001
processed data file: WT_combined_clonal_sampling_data.tab
Pair-end sequencing of RT-PCR-based amplification of Mus musculus IGHV1-72*01 allele (IMGT accession number J00530:206-499), referred here as VH186.2


title: Wt, normal watering,  time point ZT16 rep2


title: S429_mut

description: mRNA

data_processing:
Reads were mapped to the mm10 mouse genome using STAR v2.7.0a with default settings.
Reads per gene was computed using rpkmforgenes.py with default settings and NCBI RefSeq annotation with addition of the mCherry cDNA sequence.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: data.counts_geo.csv: Comma-separated text file containing number of mapped reads per gene for all samples.

extract_protocol:
FACS
Smart-seq2

value: SertCreEed

tag: sequencing batch

value: 4 months

tag: biological replicate

value: Female


title: S427_mut

description: mRNA


title: blood, Day 0, UGA4, 326


title: Wt ,drought,  time point ZT12 rep2

value: drought,  time point ZT12


title: Wt, normal watering,  time point ZT8 rep1

value: normal watering,  time point ZT8


title: Wt, normal watering,  time point ZT12 rep2

value: normal watering,  time point ZT12


title: Wt, normal watering,  time point ZT8 rep2


title: Wt ,drought,  time point ZT12 rep1


title: blood, Day 0, UGA4, 11


title: blood, Day 0, UGA4, 319


title: S374_wt

description: mRNA

value: Adult mouse midbrain


title: blood, Day 0, UGA4, 313


title: S426_mut

description: mRNA

value: PRC2 mutant

value: Male


title: blood, Day 0, UGA4, 39


title: Wt ,drought,  time point ZT8 rep2

value: drought,  time point ZT8


title: Wt ,drought,  time point ZT1 rep1

value: drought,  time point ZT1


title: Wt ,drought,  time point ZT1 rep2


title: blood, Day 0, UGA4, 270

value: Whole Blood

value: Day 0


title: blood, Day 0, UGA4, 264


title: blood, Day 0, UGA4, 280


title: blood, Day 0, UGA4, 162


title: S425_mut

description: mRNA


title: Wt, normal watering,  time point ZT1 rep2

value: wt

value: normal watering,  time point ZT1


title: Gi ,drought,  time point ZT16 rep2

value: Columbia

value: drought,  time point ZT16


title: Gi ,drought,  time point ZT16 rep1


title: Wt, normal watering,  time point ZT12 rep1


title: Wt, normal watering,  time point ZT1 rep1


title: blood, Day 0, UGA4, 126


title: S447_mut

description: mRNA

value: SertCreEed

value: 8 months


title: Wt ,drought,  time point ZT 8 rep1

value: drought,  time point ZT 8


title: S369_wt

description: mRNA

value: 4 months


title: Gi, normal watering,  time point ZT12 rep2


title: Gi, normal watering,  time point ZT16 rep2

value: normal watering,  time point ZT16


title: S373_wt

description: mRNA

value: Female


title: S446_mut

description: mRNA

value: Adult mouse midbrain


title: Gi, normal watering,  time point ZT12 rep1

value: normal watering,  time point ZT12


title: blood, Day 0, UGA4, 100


title: Gi, normal watering,  time point ZT16 rep1


title: Gi ,drought,  time point ZT12 rep1

value: drought,  time point ZT12


title: blood, Day 0, UGA4, 246


title: S443_mut

description: mRNA

value: PRC2 mutant

value: Male


title: blood, Day 0, UGA4, 220

value: Whole Blood


title: Gi, normal watering,  time point ZT8 rep2

value: normal watering,  time point ZT8


title: S385_wt

description: mRNA

value: wt


title: Gi ,drought,  time point ZT1 rep2

value: drought,  time point ZT1


title: Gi ,drought,  time point ZT8 rep2

value: Columbia

value: drought,  time point ZT8


title: S442_mut

description: mRNA

value: SertCreEed


title: Gi ,drought,  time point ZT8 rep1


title: blood, Day 0, UGA4, 411

value: Day 0


title: S367_wt

description: mRNA


title: blood, Day 0, UGA4, 213


title: blood, Day 0, UGA4, 215


title: S383_wt

description: mRNA

value: 8 months


title: Gi ,drought,  time point ZT1 rep1


title: blood, Day 0, UGA4, 396


title: Gi ,drought,  time point ZT12 rep2


title: Gi, normal watering,  time point ZT1 rep2

value: normal watering,  time point ZT1


title: Aba1-6 ,drought,  time point ZT16 rep2

value: Aba1-6 ,drought,  time point ZT16


title: Gi, normal watering,  time point ZT8 rep1


title: Gi, normal watering,  time point ZT1 rep1


title: S382_wt

description: mRNA

value: Female


title: C270_mut

description: mRNA

value: Adult mouse midbrain

value: mDA

value: DatCreEed

value: 4 months


title: S381_wt

description: mRNA


title: Aba1-6 ,drought,  time point ZT16 rep1


title: blood, Day 0, UGA4, 225


title: blood, Day 0, UGA4, 1


title: C269_mut

description: mRNA

value: PRC2 mutant

value: Male


title: D943_wt

description: mRNA


title: Aba1-6, normal watering,  time point ZT12 rep2

value: normal watering,  time point ZT12


title: Aba1-6 ,drought,  time point  ZT12 rep2

value: Aba1-6 ,drought,  time point  ZT12


title: Aba1-6 ,drought,  time point ZT12  rep1

value: Aba1-6 ,drought,  time point ZT12


title: Aba1-6, normal watering,  time point ZT16 rep1

value: Columbia

value: normal watering,  time point ZT16


title: Aba1-6 ,drought,  time point ZT8 rep2

value: Aba1-6 ,drought,  time point ZT8


title: Aba1-6, normal watering,  time point ZT12 rep1


title: blood, Day 0, UGA4, 51

value: Whole Blood

value: Day 0


title: blood, Day 0, UGA4, 384


title: blood, Day 0, UGA4, 405


title: D942_wt

description: mRNA

value: wt


title: Aba1-6, normal watering,  time point ZT8 rep2

value: normal watering,  time point ZT8


title: blood, Day 0, UGA4, 392


title: Aba1-6, normal watering,  time point ZT1

value: normal watering,  time point ZT1


title: Aba1-6, normal watering,  time point ZT16 rep2


title: Aba1-6, normal watering,  time point ZT8 rep1


title: Aba1-6 ,drought,  time point ZT1 rep2

value: Aba1-6 ,drought,  time point ZT1


title: D237_mut

description: mRNA

value: Adult mouse midbrain

value: mDA

value: Female


title: blood, Day 0, UGA4, 64


title: D878_wt

description: mRNA

value: DatCreEed

value: 4 months


title: C213_b_mut

description: mRNA

value: PRC2 mutant

value: Male


title: blood, Day 0, UGA4, 438


title: Aba1-6 ,drought,  time point ZT1 rep1


title: blood, Day 0, UGA4, 86


title: C214_b_mut

description: mRNA


title: Aba1-6, normal watering,  time point ZT1 rep2


title: HUVEC cells, P3, siSREBF2 16hr TNF, Biol Rep 3

city: New Haven

first: Joseph Wayne

middle: Montano

last: Fowler

state: CT

address: 10 Amistad St.

institute: Yale University

data_processing:
Reads aligned to hg19 build of human genome with STAR
Quantified to hg19 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: hg19
Supplementary files format and content: tab-delimited text file include cpm values for each Sample

source_name: HUVEC

growth_protocol: HUVECs were obtained from the Yale School of Medicine, Vascular Biology and Therapeutics Core facility. Cells were cultured in EGM-2 media (Lonza) with 10% fetal bovine serum (FBS), penicillin/streptomycin and glutamine (2.8 mM) in a 37°C incubator with 5% CO2 supply

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

treatment_protocol: HUVEC were treated with 20nM of indicated siRNA for 10 hours and refed with fresh media. 48hrs later, HUVEC were treated with 10ng/mL TNF for indicated time.

tag: cell line

value: HUVEC

value: Primary Endothlelial Cell

value: SREBF2 Knockdown

tag: treatment

value: 10ng/mL TNF, 16hr


title: HUVEC cells, P3, siSREBF2 0hr TNF, Biol Rep 2

value: Vehicle


title: HUVEC cells, P3, siSREBF2 0hr TNF, Biol Rep 3


title: HUVEC cells, P3, siSREBF2 0hr TNF, Biol Rep 1


title: blood, Day 0, UGA4, 385

tag: tissue

value: Whole Blood

tag: time

value: Day 0


title: Aba1-6 ,drought,  time point ZT8 rep1

value: Columbia

value: Aba1-6 ,drought,  time point ZT8


title: blood, Day 0, UGA4, 318


title: D238_mut

description: mRNA


title: HUVEC cells, P3, siSREBF2 16hr TNF, Biol Rep 1


title: HUVEC cells, P3, siSREBF2 16hr TNF, Biol Rep 2


title: HUVEC cells, P3, siPDHA1 16hr TNF, Biol Rep 3

value: PDHA1 Knockdown


title: blood, Day 0, UGA4, 58


title: HUVEC cells, P3, siPDHA1 16hr TNF, Biol Rep 1


title: blood, Day 0, UGA4, 37


title: C241_wt

description: mRNA

value: Adult mouse midbrain

value: wt


title: HUVEC cells, P3, siPDHA1 16hr TNF, Biol Rep 2


title: HUVEC cells, P3, siPDHA1 0hr TNF, Biol Rep 3


title: C240_wt

description: mRNA

value: mDA

value: Female


title: HUVEC cells, P3, siPDHA1 0hr TNF, Biol Rep 2


title: C248_wt

description: mRNA

value: DatCreEed

value: 4 months


title: D226_mut

description: mRNA

value: PRC2 mutant


title: HUVEC cells, P3, siPDHA1 0hr TNF, Biol Rep 1

value: HUVEC


title: HUVEC cells, P3, siControl 16hr TNF, Biol Rep 3

value: Primary Endothlelial Cell

value: CTRL


title: D192_mut

description: mRNA


title: HUVEC cells, P3, siControl 0hr TNF, Biol Rep 3


title: HUVEC cells, P3, siControl 16hr TNF, Biol Rep 2

value: 10ng/mL TNF, 16hr


title: HUVEC cells, P3, siControl 0hr TNF, Biol Rep 2

value: Vehicle


title: HUVEC cells, P3, siControl 16hr TNF, Biol Rep 1


title: D187_mut

description: mRNA


title: HUVEC cells, P3, siControl 0hr TNF, Biol Rep 1


title: D186_mut

description: mRNA


title: PD LRRK2_SP06_ASTROS_2

city: L'Hospitalet de Llobregat

first: Meritxell

last: Pons

state: Barcelona

address: Avinguda de la Gran Via, 199-203

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

data_processing:
The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4.
Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of FASTQ sequence files by CASAVA.
Illumina adapters were removed with Trimmomatic (v0.36), considering default parameters but requiring a minimum average quality of 20.
Trimmed paired-end reads were aligned to the human reference genome (GRCh38_primary) using STAR v2.7.1a with ENCODE parameters for long RNA.
Annotated genes (gencode v30) were quantified using the featureCounts function from the Bioconductor package Rsubread (v1.34.7).
Based on the read counts per gene matrix, the differential expression analysis was conducted using with DESeq2 package v1.24.0 (37). A generalized linear model was fitted to estimate the log2 Fold Change between groups and a Wald test was used to test the differential gene expression between groups.
Genes passing an adjusted p-value (Benjamini and Hochberg FDR) lower than 0.05 and an absolute value of log2 Fold Change higher than 1 were considered to be differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Processed data is a  tab-delimited TXT file referring to the matrix of raw counts for each gene in every sample analyzed.

source_name: Induced pluripotent stem cells

growth_protocol: Human iPSC were routinely cultured in mTESR medium on matrigel coated plates. Astrocytes were obtained according to Serio et al., 2013 and cultured with CNTF.

extract_protocol:
Total RNA was extracted using Quiazol lysis reagent (Qiagen) and RNAeasy extraction kit (Qiagen) according to manufacturer's instructions.
The RNASeq libraries were prepared from total RNA using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013).
The mRNA was fragmented in the presence of divalent metal cations and at high temperature (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.

value: Induced pluripotent stem cells

value: Astrocytes

tag: disease

value: Parkinson's disease LRRK2 G2019S

value: astrocyte differentiation


title: PD LRRK2_SP13_ASTROS_2


title: PD LRRK2_SP06_ASTROS_1


title: blood, Day 0, UGA4, 287

value: Whole Blood

value: Day 0


title: blood, Day 0, UGA4, 22


title: PD LRRK2_SP13_ASTROS_1


title: blood, Day 0, UGA4, 279


title: blood, Day 0, UGA4, 298


title: CTL_SP17_ASTROS_2

value: Control


title: blood, Day 0, UGA4, 55


title: D295_wt

description: mRNA

value: Adult mouse midbrain

value: mDA

value: wt

value: Male


title: blood, Day 0, UGA4, 332


title: PD LRRK2_SP12_ASTROS_2


title: PD LRRK2_SP12_ASTROS_1


title: blood, Day 0, UGA4, 331


title: CTL_SP17_ASTROS_1


title: CTL_SP09_ASTROS_2


title: C250_wt

description: mRNA

value: DatCreEed

value: 8 months

value: Female


title: blood, Day 0, UGA4, 296


title: blood, Day 0, UGA4, 321


title: D833_wt

description: mRNA


title: blood, Day 0, UGA4, 317


title: D296_wt

description: mRNA

value: 4 months


title: D176_mut

description: mRNA

value: PRC2 mutant


title: MCF10A_48h_2

city: Farmington

first: Olga

last: Anczukow

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Read filtering and cropping of reads to same length using Trimmomatic (v0.39)
mapping of reads to Gencode GRCh38 v.32 reference transcript annotation using STAR in 2-pass mode (v2.7.3a)
Transcript assembly and quantification with Stringtie (v2.1.3b)
Differential splicing using rMATS (v4.1.0)
Genome_build: GRCh38 v .32
Supplementary_files_format_and_content: gene_count_matrix

source_name: human mammary epithelial cells

growth_protocol: For 3D culture assays, MCF-10A and MCF-10A MYC-ER cells were seeded at a density of 10,000 cells per well in triplicate on a 4-well glass chamber slide coated with Matrigel Growth Factor Reduced (BD Biosciences) as described (Debnath et al., 2003; Liberzon et al., 2015). Media was replaced at 72h.

extract_protocol:
Cells were washed with PBS (1X) and the Matrigel was dissolved by incubating slides at 4°C in Cell Recovery Solution (BD Biosciences). Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions.
Barcoded RNA libraries were prepared starting with 1ug for MCF-10A of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent).
Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina HiSeq, equal amounts of 3 libraries were pooled per lane.

treatment_protocol: Starting on day 3, cells were treated with 1μM 4-hydroxy tamoxifen (4-OHT) (Sigma) for 48h, 24h, 8h, or 0h, prior to collection. All samples were collected at the same time on day 5.

value: wild-type

value: 4OHT 48h


title: blood, Day 0, UGA4, 314


title: MCF10A_48h_1


title: D175_mut

description: mRNA


title: D170_mut

description: mRNA


title: MCF10A_24h_1

value: 4OHT 24h


title: blood, Day 0, UGA4, 170


title: MCF10A_24h_2


title: MCF10A_8h_2

value: 4OHT 8h


title: MCF10A_8h_1


title: MCF10A_24h_3


title: MCF10A_8h_3


title: D161_mut

description: mRNA


title: MCF10A_0h_3

value: 4OHT 0h


title: D294_wt

description: mRNA


title: blood, Day 0, UGA4, 402

value: Whole Blood


title: CTL_SP09_ASTROS_1

value: Induced pluripotent stem cells

value: Astrocytes

value: astrocyte differentiation


title: MCF10A_0h_2


title: D147_wt

description: mRNA

value: Adult mouse midbrain

value: mDA


title: blood, Day 0, UGA4, 262

value: Day 0


title: MCF10A_48h_3


title: D107_wt

description: mRNA

value: DatCreEed

value: wt

value: Male


title: MYCER_48h_3


title: C42_mut

description: mRNA

value: 8 months


title: blood, Day 0, UGA4, 422


title: MYCER_48h_2


title: blood, Day 0, UGA4, 177


title: MYCER_48h_1


title: blood, Day 0, UGA4, 169


title: D282_mut

description: mRNA

value: PRC2 mutant

value: Female


title: MYCER_24h_3


title: MYCER_24h_2


title: D276_mut

description: mRNA


title: D265_mut

description: mRNA


title: MYCER_8h_1


title: MYCER_8h_3


title: C51_wt

description: mRNA


title: MCF10A_0h_1

value: wild-type


title: MYCER_8h_2


title: MYCER_0h_3


title: MYCER_0h_1


title: MYCER_0h_2