title: UM2_TCRbulk_betachain

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files are TCR tables with CDR3 sequences and V,D and J gene annotation

source_name: Uveal Melanoma

extract_protocol:
Reverse transcription of tumor RNA was performed using random hexamers and SuperScript IV according to manufacturer instruction (ThermoFisher). cDNAs were cleaned using Agencourt RNA clean XP kit (Beckman Coulter). Specific Valpha and Vbeta primers slightly modified were used in 2 semi-nested PCR steps followed by a barcoding step.
bulk TCR-seq

value: PBMC


title: Brain tissue of rats in sham operation group Replicate 3

status: Public on Mar 31 2021

type: RNA

city: Nantong

first: Jinglei

last: Wang

state: Jiangsu

address: 20 Xisi Road

country: China

institute: Affiliated Hospital of Nantong University

description: Biological replicate 3 of 3. Sham group.

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

molecule: total RNA

organism: Rattus norvegicus

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: All rats were raised in a temperature-controlled room (22 ± 1 ˚C) with a 12-h light/dark cycle and food and water were available ad libitum.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: tissue

value: brain

tag: age

value: day 1

tag: group

value: control


title: Arabidopsis_wild_air_150min_rep1

city: Kinokawa

first: Katsura

last: Izui

state: Wakayama

address: 930 Nishimitani

department: School of Biology-oriented Science and Technology

country: Japan

institute: Kinki University

description: Gene expression data from rosette leaves of 7-week old Arabidopsis thaliana that was exposed to clean air (concentration of formaldehyde was less than 0.04 ppm) for 150 minutes.

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: The data were analyzed with R/Bioconductor using GC-RMA by gcrma package as normalization method.

label: Biotin

organism: Arabidopsis thaliana

source_name: Rosette leaves of Arabidopsis thaliana which was exposed to clean air (less than 0.04 ppm) for 150 minutes.

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Arabidopsis thaliana wild type plants were grown on modified MS-agar medium (half strength inorganic compounds for MS medium, 1.5 mg/L thiamine-HCl, 2.5 mg/L pyridoxine-HCl, 0.25 mg/L nicotinic acid, 15 g/L sucrose, 8 g/L agar and adjusted to pH 5.8 with KOH) for 3 weeks. The 3-week old plants were transferred and grown in inorganic soil (ratio of vermiculite to perlite was 2 to 1) that absorbed 1 ml/L HYPONeX (HYPONeX Japan, Osaka, Japan) for 4 weeks at 22oC under 10 hours light (70-100 µmol/m2/sec.) in an incubator. For the acclimation before exposure, the 7-week old plants were kept under constant light (approx. 70 µmol/m2/sec.) at 24oC for 72 hours from 0:30 p.m. The plants were exposed to formaldehyde after 72 hours of acclimation. The environmental formaldehyde concentration was kept at less than 0.08 ppm until plants’ growth and experiments.

extract_protocol: Approximately 100 mg of  rosette leaves were applied to total RNA extruction using Plant RNA isolation mini kit (Agilent) under its protocol.

treatment_protocol: After the acclimation of plants, formaldehyde exposure experiments were started at 0:30 p.m. and finished at 3:00 p.m. For the exposure, 3 plants were placed into the chamber (volume: 10 L) each exposure condition and these plants were treated as replications. During exposure, the chamber was ventilated by gas that was adjusted to each exposure concentration at flow rate of 200 ml/min, and kept humidity of 50-60% at 24oC under the light (approx. 70 µmol/m2/sec.). The exposure condition was non-treatment (acclimation condition, outside of the exposure chamber, less than 0.08 ppm), air-control (less than 0.04 ppm), low-concentration (1-2 ppm) and high-concentration (14-16 ppm). The rosette leaves of the exposed plants (approx. 100 mg/each sample) were placed into vials and were frozen by liquid nitrogen immediately.

tag: ecotype

value: Columbia

tag: genotype

value: wild type

value: 7-week old

value: Rosette leaf


title: Arabidopsis_wild_non_150min_rep3

description: Gene expression data from rosette leaves of 7-week old Arabidopsis thaliana that was non-treatment.

source_name: Rosette leaves of Arabidopsis thaliana which was non-treatment.


title: S6_23

type: SRA

city: Montpellier

first: Gabriel

last: Jimenez-Dominguez

state: Occitanie

address: 208 Avenue des apothicaires

department: Hérault

country: France

institute: Institut de Recherche en Cancérologie de Montpellier (IRCM)

description: er-rar-count.txt

library_source: transcriptomic

data_processing:
Basecalling was performed using the two-channel SBS sequencing technology
TopHat (v2.1.0) splice junction mapper was used for RNA-Seq reads
RNA-Seq reads were aligned to the hg38 reference genome using the ultra high-throughput short read aligner Bowtie version: 2.2.6.0
Extraction of reads per gene was performed by the HTSeq-Count software
The read count matrix was normalized with edgeR (McCarthy et al., 2012) TMM algorithm
Sequencing Analysis Viewer 1,8,37 (Illumina) software was used for senquencing quality control. compressed .BCL files were generated by the NetSeq500 and demultiplexed by the bcl2fastq 2.0 (Illumina) software. Quality control on these files was performed by the FastQC v0,11,3 software.
Genome_build: hg38

organism: Homo sapiens

source_name: MELN Invasive ductal carcinoma cell line

growth_protocol: MELN cells were cultured in phenol red-free Dulbecco’s modified Eagle medium (Gibco) containing 5% dextran-charcoal treated FCS (Invitrogen) and antibiotics (Gibco).

extract_protocol:
RNA was isolated using the Zymo Research kit (Zymo research)
Illumina TruSeq kit and submitted to NextSeq500

treatment_protocol: siRNAs were transfected using Interferrin (Polyplus). When indicated, cells were treated with 100nM Estradiol (E2) or/and  10μM of all-trans retinoic acid (RAR) and then harvested 18 hours later.

tag: cell line

value: MCF-7 ERE-beta-globin Luciferase Neo

value: Breast

tag: treatment

value: 100nM E2 and 10μM RA, No siRNA


title: UM2_TCRbulk_alphachain

institute: Institut Curie

tag: cell type


title: Brain tissue of rats in sham operation group Replicate 2

description: Biological replicate 2 of 3. Sham group.


title: Arabidopsis_wild_non_150min_rep2


title: Muscle_PRE_Inter1_GS33_Rep1

type: genomic

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

hyb_protocol: The amplification products were then fragmented, precipitated, resuspended, and then hybridised onto the BeadChips.

scan_protocol: The chips were washed and then stained prior to application on an HMEPIC array according to the manufacturer’s protocol. The HMEPIC arrays were then visualised and analysed using the Illumina HiScan instrument and GeneStudio software (Illumina).

data_processing:
Any sample with > 10% of probes with detection p-value > 0.01 was removed (default parameter of the champ.load function). All probes with missing β-values, with a detection p-value > 0.01, probes with a bead count < 3 in at least 5% of samples, non-CG probes and probes aligning to multiple locations in Pidsley et al. 2016 were removed, and probes located on the sex chromosomes were removed. SNP-related probes (“EUR” population probes in Zhou et al. 28) were also removed. β-values were obtained, and defined as  β-value =(intensity of the Methylated allele)/(intensity of the Unmethylated allele + intensity of the Methylated allele + 100)   Then, β-mixture quantile normalization (BMIQ) method was applied to adjust for the Type I and Type II probe designs for methylation profiles generated from the HM450 and HMEPIC arrays. To identify technical and biological sources of variation in each individual dataset, Singular Value Decomposition (SVD) was performed. In all pre-processed datasets, both the plate and the position on the plate were identified as significant technical effects. Thus, all β-values were converted to M-values and the ComBat function from the sva package used to adjust directly for these technical artefacts.
The Matrix signal intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Vastus lateralis, at baseline during first intervention, from individual GS33, Rep1

label_protocol: For bisulphite conversion of gDNA for subsequent methylation arrays, 500 ng total gDNA was bisulfite converted using the EZ DNA methylation kit (ZYMO research) as per the manufacturer’s instructions. Bisulfite converted DNA (bDNA) was then used for the methylation array protocol. riefly, bDNA was used for amplification of the regions of interest for binding to the Infinium BeadChip arrays.

extract_protocol: Total gDNA was extracted from 15 mg muscle tissue using the Allprep DNA/RNA/miRNA universal kit (Qiagen). The manufacturer’s protocol was modified to include the use of a Bullet Blender Gold Homogeniser (NextAdvance) in combination with dry ice for complete tissue digestion to ensure no enzymatic digestion of the DNA. Following isolation, DNA quantity and quality was measured using the dsDNA Broad Range Qubit kit (ThermoFisher scientific) on a Qubit Flourometer V2.0.

tag: subject id

tag: Sex

value: F

tag: treatment/timepoint

value: at baseline during first intervention

value: Vastus lateralis


title: S6_30

description: er-rar-count.txt

value: 10μM RA, LCoR siRNA


title: Muscle_4WP_Inter2_GS66_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS66, Rep1

value: M


title: Muscle_CON_Inter1_GS45_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS45, Rep1


title: Brain tissue of rats in sham operation group Replicate 1

description: Biological replicate 1 of 3. Sham group.


title: S6_20

description: er-rar-count.txt

value: 100nM E2 , No siRNA


title: UM1_TCRbulk_alphachain

value: PBMC


title: S6_21

description: er-rar-count.txt

value: 10μM RA, No siRNA


title: S6_19

description: er-rar-count.txt


title: Muscle_12WP_Inter2_GS6_Rep1

description: Same individual as in GSM4577424, GSM4577446, GSM4577465

source_name: Vastus lateralis, after 12 weeks of HIIT during second intervention, from individual GS6, Rep1


title: UM1_TCRbulk_betachain


title: mRNA_gcn4∆+SM_replicate_2

city: Bethesda

first: Swati

last: Gaikwad

state: MD

address: Building 6, Room 233

department: Section on Nutrient Control Of Gene Expression

country: USA

institute: National Institutes of Health

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv

data_processing:
For ribo-seq samples of experiment 1, experiment 2 and experiment 3, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq samples of experiment 1 and experiment 3, the same protocol mentioned above for ribo-seq analysis was followed. RNA-seq samples of experiment 2 and ribo-seq samples of experiment 4, were processed identically as described above, except that PCR duplicates were removed from trimmed sequencing reads and these sequences were aligned to the yeast genome (sacCer3) with tophat (version 2.1.1). For RNA-seq samples of experiment 4, adapter sequences were removed with cutadat (version 3.0) followed by removing rRNA reads with Bowtie2. The rRNA free Fastq records were mapped to genome with hisat2 (https://github.com/DaehwanKimLab/hisat2) and bam files were filtered to keep perfect matched reads only. Finally reads were counted with R RiboProR package (https://github.com/hzhanghenry/RiboProR).
Translational efficiency change analysis was performed with R DESeq2 package.
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed data (csv) files contain five sections of DESeq2 analysis, each with 5 columns of data, providing:  Fold changes in mutant (treated cells) versus WT (untreated cells) in translational efficiency (TE Change) (section 1), TE in WT (or untreated cells) (section 2); TE in mutant (or treated cells) (section 3) ribosome occupancy  (Ribo Change) (section 4), or mRNA abundance (mRNA Change) (section 5) all presented as ratios of mutant to WT values (or treated to untreated cells values). In each section, there are five columns providing: systemmatic gene name (Gene_ID), log2 values of the indicated parameter, pvalue, padj (FDR or adjusted p value), and common gene name.

organism: Saccharomyces cerevisiae

source_name: Whole cells

growth_protocol: Yeast cells were generally grown to an OD600 of 0.5-0.6 in synthetic complete medium lacking isoleucine and valine (SC-Ilv) at 30°C.

extract_protocol:
For RNA sequencing libraries, total RNA extraction was carried out using a miRNeasy Mini Kit (Qiagen; 217004) and library construction was carried by the NHLBI core sequencing facility using the TruSeq Stranded mRNA Library Prep Kit (Illumina).
Ribosome profiling and RNA-seq

treatment_protocol: Cells were treated with the antimetabolite Sulfometuron methyl (SM) at 1 µg/mL for 25 before harvesting.

tag: strain

value: 249 (MATa gcn4::kanMX4 his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)


title: Muscle_CON_Inter1_GS37_Rep1

source_name: Vastus lateralis, at start of control period during first intervention, from individual GS37, Rep1


title: S6_18

description: er-rar-count.txt

value: Ethanol, No siRNA


title: mRNA_gcn4∆+SM_replicate_1

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv


title: S6_17

description: er-rar-count.txt


title: Ribo_gcn4∆+SM_replicate_2

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv

data_processing:
Library strategy: Ribo-seq
For ribo-seq samples of experiment 1, experiment 2 and experiment 3, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq samples of experiment 1 and experiment 3, the same protocol mentioned above for ribo-seq analysis was followed. RNA-seq samples of experiment 2 and ribo-seq samples of experiment 4, were processed identically as described above, except that PCR duplicates were removed from trimmed sequencing reads and these sequences were aligned to the yeast genome (sacCer3) with tophat (version 2.1.1). For RNA-seq samples of experiment 4, adapter sequences were removed with cutadat (version 3.0) followed by removing rRNA reads with Bowtie2. The rRNA free Fastq records were mapped to genome with hisat2 (https://github.com/DaehwanKimLab/hisat2) and bam files were filtered to keep perfect matched reads only. Finally reads were counted with R RiboProR package (https://github.com/hzhanghenry/RiboProR).
Translational efficiency change analysis was performed with R DESeq2 package.
Genome_build: sacCer3
Supplementary_files_format_and_content: Processed data (csv) files contain five sections of DESeq2 analysis, each with 5 columns of data, providing:  Fold changes in mutant (treated cells) versus WT (untreated cells) in translational efficiency (TE Change) (section 1), TE in WT (or untreated cells) (section 2); TE in mutant (or treated cells) (section 3) ribosome occupancy  (Ribo Change) (section 4), or mRNA abundance (mRNA Change) (section 5) all presented as ratios of mutant to WT values (or treated to untreated cells values). In each section, there are five columns providing: systemmatic gene name (Gene_ID), log2 values of the indicated parameter, pvalue, padj (FDR or adjusted p value), and common gene name.

extract_protocol:
For Ribosome profiling library preparation a modified protocol was used, as previously described (McGlincy and Ingolia 2017).
Ribosome profiling and RNA-seq


title: Muscle_4WP_Inter1_GS60_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS60, Rep1


title: Ribo_gcn4∆+SM_replicate_1

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv


title: CD34+, Basal Media Day14_Rep1

city: Baton Rouge

first: shahensha

last: shaik

state: LA

address: 3261 Patrick F Taylor Hall

department: Department of Mechanical Engineering

institute: Louisiana State University

data_processing:
Quality of the run, read lengths and coverage were performed using the torrent suite software.
STAR program was used to generate output alignments translated into transcript coordinates which are later used as input for RSEM
Alignment to HG38 performed using RSEM
Bedtools program was used to extract the miRNA data by interspersing the bam files with mature human miRNA sequences from miRbase.org
Differential expression perfromed by edgeR
Genome_build: HG38
Supplementary_files_format_and_content: Results Txt and CSV

source_name: Adipose Tissue

growth_protocol: The CD34+ ASCs were sorted using Magnetic sorting and then plated in 6 well plates at a density of 8000 cells per cm2 and cultured till 80-90% confluence was obtained in basal media which is composed of 10% fetal bovine serum, 1% antibiotics in DMEM/F12 media.

extract_protocol:
miRNAs on the respective days from ASCs were isolated using Purelink miRNA isolation kit (Thermofisher Scientific, K157001). The quality and purity of miRNAs was analyzed using fragment analyzer
cDNA libraries were constructed using the Ion Total RNA-Seq Kit v2 (Catalog number: 4475936), protocol for the small RNA libraries. Templates for RNASeq were prepared with the Ion PI™ Hi-Q OT2 200 template Kit (A26434) using the Ion OneTouch™ 2 System for Ion Proton™ System semiconductor sequencing.

treatment_protocol: CD34+ cells were treated with endothelial medium containing 50 ng/ml of VEGF, 2% FBS, and 1% antibiotic in DMEM/F12 media. The CD34+ cells and CD34 depleted ASCs treated with basal medium served as controls. The media was replaced every 3 days for up to 14 days

value: CD34+ Adipose Stem Cells


title: Muscle_4WP_Inter1_GS41_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS41, Rep1


title: CD34+, Endothelial Media Day14_Rep2


title: mRNA_gcn4∆_replicate_1

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv

growth_protocol: Yeast cells were generally grown to an OD600 of 0.5-0.6  in synthetic complete medium at 30°C.

treatment_protocol: No additional treatment


title: Ribo_gcn4∆_replicate_2

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv


title: mRNA_gcn4∆_replicate_2

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv


title: CD34+, Basal Media Day9_Rep2


title: Ribo_gcn4∆_replicate_1

description:
Experiment 4
DESeq2_gcn4+SM_vs_gcn4.csv


title: CD34+, Endothelial Media Day14_Rep1


title: CD34+, Endothelial Media Day9_Rep2


title: CD34+, Basal Media Day9_Rep1


title: CD34+, Basal Media Day14_Rep2


title: mRNA_rps26∆∆_replicate_1

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.11

extract_protocol:
For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using hot phenol-chloroform extraction. Five µg of total RNA was randomly fragmented by mixing with 2× alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ≈ 9.3). After incubation for 20 min at 95ºC, fragmentation reactions were mixed with ice-cold stop solution (300 mM NaOAc pH 5.5, 30 µg GlycoBlue (Invitrogen; AM9516)). RNA was precipitated by adding one part of isopropanol followed by the standard protocol of precipitation. Fragment size selection, library generation, and sequencing were carried out using the same protocol described above for RPF library preparation, except the Ribo-Zero Gold rRNA Removal Kit (Illumina; MRZ11124C), was employed to remove rRNA after linker-ligation.
Ribosome profiling and RNA-seq

value: JVY09 (MATa ura3-52 leu2-3 leu2-112 trp1-[delta]63 his4-303(AUU) kanMX6::PGAL1-RPS26A rps26b[delta]::hphMX6)


title: mRNA_rp26∆∆_replicate_2

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.12


title: S6_25

description: er-rar-count.txt

value: Ethanol, LCoR siRNA


title: CD34+, Endothelial Media Day9_Rep1


title: Muscle_PRE_Inter2_GS22_Rep1

description: Same individual as in GSM4577432, GSM4577448, GSM4577492

source_name: Vastus lateralis, at baseline during second intervention, from individual GS22, Rep1

value: at baseline during second intervention


title: mRNA_WT3_replicate_2

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.10


title: Arabidopsis_wild_non_150min_rep1

value: Columbia

value: wild type

value: 7-week old

value: Rosette leaf


title: Muscle_PRE_Inter1_GS34_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS34, Rep1

value: F

value: at baseline during first intervention


title: CD34+, Basal Media Day3_Rep2


title: mRNA_WT3_replicate_1

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.9


title: Muscle_8WP_Inter2_GS8_Rep1

description: Same individual as in GSM4577420, GSM4577441, GSM4577486

source_name: Vastus lateralis, after 8 weeks of HIIT during second intervention, from individual GS8, Rep1

value: Vastus lateralis


title: Muscle_PRE_Inter1_GS48_Rep1

source_name: Vastus lateralis, at baseline during first intervention, from individual GS48, Rep1

value: M


title: CD34+, Basal Media Day3_Rep1


title: Ribo_rp26∆∆_replicate_2

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.8

extract_protocol:
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast" Martin Marcos et al. (2017) eLife 6:e31250
Ribosome profiling and RNA-seq


title: Ribo_rps26∆∆_replicate_1

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.7


title: CD34+, Endothelial Media Day3_Rep2


title: Muscle_4WP_Inter2_GS2_Rep1

description: Same individual as in GSM4577415, GSM4577435, GSM4577476

source_name: Vastus lateralis, after 4 weeks of HIIT during second intervention, from individual GS2, Rep1


title: Ribo_WT3_replicate_2

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.6


title: CD34+, Endothelial Media Day3_Rep1


title: Ribo_WT3_replicate_1

description:
Experiment 3
DESeq2_rps26_vs_WT3.csv

growth_protocol: Yeast cells were generally grown cultured at 30°C to O.D. 600 of 0.8 O.D. in SC+Gal/Raf medium containing 2% galactose and 2% raffinose in place of glucose. Cells were pelleted and shifted to glucose-containing SC medium for 3h before harvesting at O.D. 600 = 0.4-0.5


title: mRNA_WT2_replicate_2

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv

extract_protocol:
For RNA sequencing library preparation a modified protocol was used, as previously described (McGlincy and Ingolia 2017).
Ribosome profiling and RNA-seq

value: BY4741 (MATa his3-[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)


title: mRNA_WT2_replicate_1

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv


title: mRNA_tma64∆_replicate_2

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv

value: 4051 (MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0 tma64[delta]::kanMX4)


title: Gli1-Null control diet-2

city: New York

first: James

last: Salzer

state: NY

address: 435 East 30th street

department: Neuroscience

institute: New York University

description:
1 male and 1 female
15

data_processing:
the raw sequencing data files were processed using FASTQC v.0.11.5 for quality control.
Fastq files were aligned to the mm10 mouse reference genome utilizing TopHat v2.1.1.
The aligned bam files were quantified for gene expression values utilizing HTSeq-count 0.11.1.
DESeq2 v1.12 was used for analysis of the quantified count matrix.
Genome_build: mm10 mouse reference genome
Supplementary_files_format_and_content: Excel sheet with RNA reads and DEseq2 abundance measurements of all samples

organism: Mus musculus

source_name: subventricular zones pooled from 2 brains

growth_protocol: The Gli1CreERT2/+ mice (Jax # 007913) which have CreERT2 knocked into the Gli1 locus were bred with the reporter Rosa-CAG-EGFP-LoxP (RCE) (Jax# 032037) mice to generate Gli1Het (Gli1CreERT2/+;RCE) with intact Gli1 expression and Gli1Null (Gli1CreERT2/CreERT2;RCE) mice with global knockout of Gli1. To permanently label the GLI1 pool of NSCs with GFP, we administered 5 mg tamoxifen (Sigma) in corn oil on alternate days for a total of four intraperitoneal injections to 10 week old mice. A week after the last dose of tamoxifen/corn oil, the demyelinated group was fed 0.2% cuprizone in the chow for 3 weeks while the healthy control group remained on regular chow. All mice had access to food and water ad libitum and were housed in a room with 12 hour dark/light cycle. Brain tissues were harvested from 6 (3 Males and 3 Females) mice per genotype (Gli1Het and Gli1Null) per diet (cuprizone and control) after euthanizing them with CO2. Coronal sections of 1mm thickness were made and the SVZ was carefully dissected under a microscope from each section. For each RNA sample, the SVZ from one female and one male mice was pooled together. Overall, we had 3 RNA samples/genotype from control diet group and 3 RNA samples/genotype from cuprizone diet group. The SVZ were then dissociated into single cell suspension following the manufacturer’s protocol in the papain dissociation kit (Worthington Biochemicals # LK003150). The cell suspension was passed through a 50µm celltrix filter (Sysmex-Partec # 04-0042-2317) immediately before FACsorting the GFP+ NSCs using a MoFlo XDP cell sorter (Beckman Coulter) in the NYU Cytometry core facility.

extract_protocol:
Total RNA was isolated using Arcturus PicoPure RNA isolation kit (Applied Biosystems # 12204-01). mRNA was purified and cDNA was synthesized using SMART-Seq V4 RNA kit (Clontech # 634889). 3ng of cDNA were then amplified by 6 cycles of PCR.
The sequencing libraries were generated using Nextera XT DNA Library Preparation Kit (Illumina #FC-131-1024). The generated libraries were then mixed for multiplexing on 3 lanes and sequenced on Illumina HiSeq 2500 platform with 150bp paired end module

treatment_protocol: 5 mg tamoxifen in corn oil on alternate days for a total of four intraperitoneal injections

value: neural stem cells

tag: diet

value: normal chow

value: 10 weeks


title: S6_22

description: er-rar-count.txt

value: MCF-7 ERE-beta-globin Luciferase Neo

value: Breast

value: 10μM RA, No siRNA


title: Gli1-Null cuprizone diet-1

description:
1 male and 1 female
17

treatment_protocol: 5 mg tamoxifen in corn oil on alternate days for a total of four intraperitoneal injections one week before starting cuprizone diet

value: 0.2% cuprizone for 3 weeks

value: subventricular zones pooled from 2 brains


title: Ribo_tma64∆_replicate_1

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv


title: Gli1-Null control diet-1

description:
1 male and 1 female
13


title: Gli1-Null cuprizone diet-2

description:
1 male and 1 female
19


title: Gli1-Null cuprizone diet-3

description:
1 male and 1 female
21


title: mRNA_tma64∆_replicate_1

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv


title: Ribo_WT2_replicate_2

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv


title: Gli1-Het cuprizone diet-3

description:
1 male and 1 female
4


title: Gli1-Het cuprizone diet-2

description:
1 male and 1 female
2


title: Gli1-Null control diet-3

description:
1 male and 1 female
25


title: Ribo_WT2_replicate_1

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv


title: Gli1-Het cuprizone diet-1

description:
1 male and 1 female
23


title: S6_26

description: er-rar-count.txt

value: Ethanol, LCoR siRNA


title: mRNA_WT1+SM_replicate_2

description:
Experiment 1
DESeq2_WT+SM_vs_WT1.csv


title: Gli1-Het control diet-3

description:
1 male and 1 female
9


title: mRNA_WT1+SM_replicate_1

description:
Experiment 1
DESeq2_WT+SM_vs_WT1.csv


title: Gli1-Het control diet-2

description:
1 male and 1 female
7


title: mRNA_tma∆∆_replicate_2

description:
Experiment 1
DESeq2_tma_vs_WT1.csv

value: H4520 (MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0 tma64[delta]::hygMX4 tma20[delta]::kanMX4)


title: Gli1-Het control diet-1

description:
1 male and 1 female
27


title: Muscle_4WP_Inter1_GS39_Rep1

source_name: Vastus lateralis, after 4 weeks of HIIT during first intervention, from individual GS39, Rep1


title: mRNA_tma∆∆_replicate_1

description:
Experiment 1
DESeq2_tma_vs_WT1.csv


title: Ribo_tma64∆_replicate_2

description:
Experiment 2
DESeq2_tma64_vs_WT2.csv


title: mRNA_WT1_replicate_2

description:
Experiment 1
DESeq2_tma_vs_WT1.csv
DESeq2_WT+SM_vs_WT1.csv


title: IR 3

city: Tucson

first: Megha

last: Padi

state: Arizona

address: 1515 N Campbell

institute: University of Arizona

data_processing:
Illumina BCL2Fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2.
Gene level raw reads annoation was carried with HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: raw count

source_name: Parotid salivary gland tissue

extract_protocol:
Parotid salivary glands were extracted and the tissue snap frozen. RNA was isolated with TRIzol reagent then treated with RNAse-free DNAse. cDNA libraries were prepared with the Illumina TruSeq™ Stranded Total RNA Library Prep Kit and Illumina RNA single indexing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with one 5 Gy radiation dose.

value: Parotid salivary gland

value: treated

value: FVB

value: 28 days


title: IR 2


title: UT 3

value: untreated


title: UT 2


title: Ribo_WT1+SM_replicate_1

description:
Experiment 1
DESeq2_WT+SM_vs_WT1.csv

value: BY4741 (MATa his3-[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)


title: mRNA_WT1_replicate_1


title: Ribo_tma∆∆_replicate_2

description:
Experiment 1
DESeq2_tma_vs_WT1.csv


title: Ribo_WT1+SM_replicate_2

description:
Experiment 1
DESeq2_WT+SM_vs_WT1.csv


title: Ribo_tma∆∆_replicate_1

description:
Experiment 1
DESeq2_tma_vs_WT1.csv


title: Ribo_WT1_replicate_1


title: UT 1


title: Ribo_WT1_replicate_2


title: WT_120 h_rep4

city: Yokohama

first: kiyokazu

last: kakugawa

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: IMS

institute: Riken

description: WT rep4

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were alingned to the mm10 genome assembly using Hisat2 with default option
data were processed with Cufflinks ver2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: text file with fpkm values summarized across the replicates

source_name: WT_120h  treated with anti-CD3e antibody (1 micro g/mL), anti-CD28 antibody (1 micro g/mL),TGFb(5 ng /mL), Retinoic Acid (250nM) and IL-27(25ng/mL)

growth_protocol: Naive CD4 T cells (1 x 10^5) cells were seeded onto 96-well plates pre-coated with anti-CD3 (1 or 2 ug/mL) and cultured under the CD4 CTL condition (anti-CD28, IL-27, TGFb, and retinoic acid).

extract_protocol:
RNA was harvested using Trizol reagent.Total RNA was purified using a miRNeasy micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wildtype

tag: background strain

value: spleen

value: CD4 T cells


title: E8IKO_120 h_rep4

description: E8IKO rep4

source_name: E8IKO_120 h treated with anti-CD3e antibody (1 micro g/mL), anti-CD28 antibody (1 micro g/mL),TGFb(5 ng /mL), Retinoic Acid (250nM) and IL-27(25ng/mL)


title: E8IKO_naïve_rep4

description: E8IKO rep4

source_name: E8IKO_Naive CD4 T cells (CD4+CD62L+CD44-) cells from spleen cells

value: naive


title: WT_7d CD4pCd8ap_rep4

description: WT rep4

source_name: WT_CD4 positive CD8 alpha positive after 7 days in culture

value: 7d CD4pCd8ap


title: E8IKO_7d CD4pCd8an_rep4

description: E8IKO rep4

source_name: E8IKO_CD4 positive CD8 alpha negative after 7 days in culture

value: 7d CD4pCd8an


title: WT_7d CD4pCd8an_rep4

description: WT rep4

source_name: WT_CD4 positive CD8 alpha negative after 7 days in culture


title: E8IKO_7d CD4pCd8an_rep3

description: E8IKO rep3


title: E8IKO_120 h_rep3

description: E8IKO rep3


title: E8IKO_48 h_rep3

description: E8IKO rep3

source_name: E8IKO_48 h treated with anti-CD3e antibody (1 micro g/mL), anti-CD28 antibody (1 micro g/mL),TGFb(5 ng /mL), Retinoic Acid (250nM) and IL-27(25ng/mL)


title: IR 1


title: E8IKO_48 h_rep4

description: E8IKO rep4


title: WT_7d CD4pCd8ap_rep3

description: WT rep3


title: WT_48 h_rep3

description: WT rep3

source_name: WT_48hr treated with anti-CD3e antibody (1 micro g/mL), anti-CD28 antibody (1 micro g/mL),TGFb(5 ng /mL), Retinoic Acid (250nM) and IL-27(25ng/mL)


title: WT_120 h_rep3

description: WT rep3


title: E8IKO_naïve_rep3

description: E8IKO rep3


title: WT_naïve_rep4

description: WT rep4

source_name: WT_Naive CD4 T cells (CD4+CD62L+CD44-) cells from spleen cells


title: WT_48 h_rep4

description: WT rep4


title: WT_naïve_rep3

description: WT rep3


title: E8IKO_48 h_rep2

description: E8IKO rep2


title: E8IKO_120 h_rep2

description: E8IKO rep2


title: WT_7d CD4pCd8ap_rep2

description: WT rep2


title: WT_7d CD4pCd8an_rep2

description: WT rep2


title: WT_120 h_rep2

description: WT rep2


title: E8IKO_naïve_rep2

description: E8IKO rep2


title: WT_48 h_rep2

description: WT rep2


title: WT_7d CD4pCd8an_rep3

description: WT rep3


title: WT_naïve_rep2

description: WT rep2


title: E8IKO_7d CD4pCd8an_rep1

description: E8IKO rep1


title: E8IKO_120 h_rep1

description: E8IKO rep1


title: E8IKO_48 h_rep1

description: E8IKO rep1


title: E8IKO_naïve_rep1

description: E8IKO rep1


title: WT_7d CD4pCd8ap_rep1

description: WT rep1


title: WT_7d CD4pCd8an_rep1

description: WT rep1


title: FFPE Breast cancer 34296, HER2, FBC+

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer IBMCC-CIC

description: Sample name: 34296

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: OncoScan console (v1.3) from Affymetrix was used to assess genome wide copy number

label: biotin

source_name: FFPE breast cancer tissue

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

growth_protocol: Not applicable

extract_protocol: Genomic DNAs were extracted according to manufacturer's protocols.

treatment_protocol: Not applicable

tag: ki67 ihq

tag: p53 ihq

tag: histologic grade

tag: hormone receptor (hr)

tag: her2 ihq

tag: subtype

tag: brca status

value: FBC+

value: FFPE breast cancer tissue


title: FFPE Breast cancer 34647, luminal A, FBC-

description: Sample name: 34647

value: luminal A

value: FBC-

tag: tissue


title: FFPE Breast cancer 34262, luminal A, FBC+

description: Sample name: 34262


title: FFPE Breast cancer 34643, luminal A, FBC-

description: Sample name: 34643


title: WT_120 h_rep1

description: WT rep1

tag: genotype


title: FFPE Breast cancer 34648, luminal A, FBC-

description: Sample name: 34648


title: WT_naïve_rep1

description: WT rep1

tag: treatment


title: FFPE Breast cancer 34644, luminal A, FBC-

description: Sample name: 34644


title: FFPE Breast cancer 34646, luminal B, FBC-

description: Sample name: 34646

value: luminal B


title: FFPE Breast cancer 34256, luminal A, FBC+

description: Sample name: 34256


title: FFPE Breast cancer 34261, luminal A, BRCA+

description: Sample name: 34261

value: BRCA+


title: FFPE Breast cancer 34642, luminal A, FBC-

description: Sample name: 34642


title: FFPE Breast cancer 34260, luminal A, FBC+

description: Sample name: 34260


title: FFPE Breast cancer 34641, luminal A, FBC-

description: Sample name: 34641

value: nd


title: FFPE Breast cancer 34252, luminal A, FBC+

description: Sample name: 34252


title: FFPE Breast cancer 34299, luminal A, FBC+

description: Sample name: 34299


title: FFPE Breast cancer 34254, luminal A, FBC+

description: Sample name: 34254


title: FFPE Breast cancer 34020, HER2, FBC+

description: Sample name: 34020


title: FFPE Breast cancer 34255, HER2, FBC+

description: Sample name: 34255


title: FFPE Breast cancer 34017, luminal B, FBC+

description: Sample name: 34017


title: Brain_Old_BW_P35529

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
S24
RNASeqCounts_BW.txt

data_processing:
Indexed sequences were checked by FastQC | version: 0.11.5.
Trimmed adapter by TrimGalore-0.4.5.
Reads were mapped to the P. maniculatus and P. leucopus reference genome using STAR | version 2.7.2b with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes Peromyscus_maniculatus_bairdii.HU_Pman_2.1.101.gtf and GCF_004664715.1_Pero_0.1_genomic.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10.
Genome_build: Peromyscus_maniculatus_bairdii.HU_Pman_2.1 and GCF_004664715.1_Pero_0.1_genomic
Supplementary_files_format_and_content: RNASeqCounts_*.txt: Tab-delimited text files include gene counts for each sample.

organism: Peromyscus maniculatus

source_name: Brain

growth_protocol: Deer mice, P. maniculatus were obtained from the Peromyscus Genetic Stock Center (PGSC), University of South Carolina (USC), Columbia, SC (RRID:SCR_002769). P. maniculatus bairdii (BW Stock), was closed colony bred in captivity since 1948 and descended from 40 ancestors wild-caught near Ann Arbor, Michigan. P. leucopus (LL Stock) was derived from 38 wild ancestors captured between 1982 and 1985.

extract_protocol:
Total RNA was extracted from brain using the RNeasy Mini Kit (Qiagen).
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB#E7490/NEB#E7760).

treatment_protocol: Brain tissues of 7-months-old and 2- to 3-years-old outbred deer mice P. maniculatus and P. leucopus were collected at sacrifice.

tag: stock

value: BW

value: Brain

tag: age of animal at termination

value: 25 months


title: FFPE Breast cancer 34259, FBC+

description: Sample name: 34259


title: Brain_Old_BW_P35505

description:
S23
RNASeqCounts_BW.txt

value: 26 months


title: FFPE Breast cancer 31946, luminal B, FBC-

description: Sample name: 31946


title: FFPE Breast cancer 34019, luminal A, FBC+

description: Sample name: 34019


title: FFPE Breast cancer 34253, TNC, FBC+

description: Sample name: 34253

value: TNC


title: Primary Induction Response case 07, array 01

city: Catania

first: Daniele

middle: F

last: Condorelli

state: Italy

address: Via S. Sofia 64

department: Biomedical and Biotechnological Sciences

country: Italy

institute: University of Catania

hyb_protocol: Fragmented and labeled target (Sense Strand-cDNA  5.2-5.5 µg) was used for hybridization to the “GeneChip Human Transcriptome Array 2.0” according to the protocol supplied by the manufacturer was used for  hybridization step. The hybridization has been performed in an hybridization oven at 45°C for 16 hours with rotation at 60 rpm.

scan_protocol: Scanning was performed using the  Affymetrix Scanner GCS3000 7G.

data_processing: Data analysis was performed using Affymetrix® Expression Console™ software (v.1.4). Expression level analysis was obtained using the normalization method based on the processing algorithm Robust Multi-array Average (RMA).

source_name: frozen sample

label_protocol: Biotinylated fragmented sense strand cDNA were prepared according to the protocol supplied by the Affymetrix for Human Transcriptome Array 2.0 (HTA).

extract_protocol: Total RNA (100 ng) was extracted from frozen bone marrow using RNeasy Mini Kit (Qiagen, Milan - Italy) according to the manufacturer’s instructions. The concentration and the quality of  RNA were determined using a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific, USA).

value: bone marrow

tag: disease state

value: pediatric acute myeloid leukemia; primary induction response case

tag: gender

value: female

tag: patient age

tag: tumor stage


title: Primary Induction Response case 06, array 01


title: Brain_Old_BW_P35274

description:
S20
RNASeqCounts_BW.txt

value: 28 months


title: FFPE Breast cancer 31841, TNC, FBC-

description: Sample name: 31841


title: Brain_Old_BW_P35279

description:
S19
RNASeqCounts_BW.txt


title: Primary Induction Response case 08, array 01

value: male


title: WT_48 h_rep1

description: WT rep1

value: wildtype

tag: background strain

value: spleen

tag: cell type

value: CD4 T cells


title: Brain_Young_BW_P36175

description:
S18
RNASeqCounts_BW.txt

value: 7 months


title: Brain_Young_BW_P36183

description:
S17
RNASeqCounts_BW.txt


title: Brain_Old_BW_P35261

description:
S21
RNASeqCounts_BW.txt

value: 29 months


title: Primary Induction Response case 05, array 01


title: Brain_Young_BW_P36023

description:
S15
RNASeqCounts_BW.txt


title: Brain_Young_BW_P35997

description:
S16
RNASeqCounts_BW.txt


title: FFPE Breast cancer 32103, luminal A, FBC-

description: Sample name: 32103

tag: ki67 ihq

tag: p53 ihq

value: luminal A

value: FBC-

value: FFPE breast cancer tissue


title: Brain_Young_BW_P36017

description:
S14
RNASeqCounts_BW.txt

value: BW

value: Brain


title: FFPE Breast cancer 31844, luminal A, FBC-

description: Sample name: 31844

tag: histologic grade

tag: hormone receptor (hr)


title: FFPE Breast cancer 31929, luminal A, FBC-

description: Sample name: 31929

tag: her2 ihq

tag: subtype


title: FFPE Breast cancer 32106, luminal A, FBC-

description: Sample name: 32106

value: nd

tag: brca status

tag: tissue


title: Primary Induction Response case 04, array 01


title: Primary Induction Failure Patient 02, array 01

value: pediatric acute myeloid leukemia; primary induction failure patient


title: Primary Induction Response case 01, array 01

value: bone marrow


title: Primary Induction Failure Patient 04, array 01


title: Primary Induction Response case 03, array 01

value: pediatric acute myeloid leukemia; primary induction response case


title: Brain_Young_BW_P35992

description:
S13
RNASeqCounts_BW.txt


title: AtHB25-B

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

institute: Universitat Politècnica de València

library_source: genomic

data_processing:
Sequences were cleaned of adaptor with cutadapt (Martin, 2012)
Sequences were mapped with BWA (Li and Durbin , 2009) to the Arabidopsis thaliana reference genome (TAIR10).
Sequences sorted with samtools sort (Li et al., 2009; Li, 2011).
Unique mapped sequences were filtered with samtools view (Li et al., 2009; Li, 2011). Parameters: -q 3.
Duplicated sequences were marked with Picard MarkDuplicates (Picard Toolkit, 2019). Parameters: VALIDATION_STRINGENCY=LENIENT.
MACS2 (Zhang et al., 2008) was used to call peaks. Threeshold was set up with a q-value/FDR of 0.05. Parameters: --gsize 1.118e8 --keep-dup auto --bdg --SPMR
Graphical visualition of each 175 chormosomic peaks was done to ensure their reliability evalutationg the peak area, normal distribution of lectures and forward and reverse lecture distribution with the CLC genomics program. Peak list was reduced to 146 peaks with an average length of 141 base pairs.
PAVIS (Huang et al., 2013) was used for distances to TTS peak analysis.
TAIR10 was used to find genes within 3000 bp fom peaks.
GO enrichment analysis was performed with genes from previous step. The online tool agriGO was used for this analysis (Tian et al., 2017).
Gene annotation was made with The Arabidopsis Genome Integrative Explorer (PlantGenIE.org) (Sundell et al., 2015)
Motif analysis was performed with HOMER findMotifsGenome.pl and TAIR10 in 200 bp arround the peak center (Heinz et al., 2010). Parameters: -dumpFasta.
Fasta sequencesobtained  from HOMER motif analysis were used to find the number of AtHB25 (DAP-seq) binding motifs for each peak, using HOMER findMotifsGenome.pl. Paremeters: -find (AtHB25 motif file)
Genome_build: TAIR10
Supplementary_files_format_and_content: MACS2 result with peak infomation (genomic location and statistical significance)

source_name: Developing seeds at maturation stage (DAP7-DAP14)

growth_protocol: proUBQ10-AtHB25-3xHA transgenic double mutant hb22 hb25 background (Col-0) plants were grown in under greenhouse conditions (16h light / 8h dark, at 16-23 ºC and 70-75% RH).

extract_protocol:
Transgenic proUBQ10-AtHB25-3xHA siliques in maturation stage (ranging from 7 days-after pollination (DAP) to 14 DAP) were collected and gently ground. They were filtered using liquid nitrogen to obtain high seed enrichment (5 grams approximately). The ChIP protocol was performed as described by Gendrel et al. (2005). Mouse monoclonal antibody HA.11 (clone 16B12) COVANCE and Dynabeads® Protein G were used for the immunoprecipitation. An equivalent sample with no antibody was used as a negative control. The presence of HB25:HA after the immunoprecipitation with antiHA:HPR antibody was confirmed by immunodetection. Two ChIP replicas and the sample without antibody were sequenced with the 1x50 bp HiSeq2500 by the Genomic Unit of CRG (Barcelona, Spain).
NEBNext® Ultra™ DNA Library Prep Kit for Illumina®

treatment_protocol: non treated plants

tag: transgenic line

value: transgenic proUBI-AtHB25-3xHAplants

tag: genotype

value: backgroud double mutant athb22 athb25

tag: ecotype

tag: chip antibody


title: No antibody


title: Primary Induction Response case 02, array 01

tag: disease state

tag: gender

value: male


title: AtHB25-A


title: polII-Bab_GAL4-n1

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

institute: Menzies Institute for Medical Research

data_processing:
Library strategy: DamID-seq
FASTQ files were processed using damidseq_pipeline, default options.
Genome_build: DmBDGP6
Supplementary_files_format_and_content: gatc.bedgraph files were generated using the damidseq_pipeline software, at GATC fragment resolution.  Score represents the normalised log2(Dam-fusion/Dam) enrichment, averaged over replicates and scaled.

organism: Drosophila melanogaster

source_name: dissected adult ovary

extract_protocol:
Adult ovaries were dissected in PBS, and processed for DamID-seq as previously described (Marshall et al., 2016; Marshall and Brand, 2017) with the following modifications. Briefly, DNA was extracted using a Quick-DNA Miniprep plus kit (Zymo), digested with DpnI (NEB) overnight and cleaned-up with a PCR purification kit (Machery-Nagel), DamID adaptors were ligated, digested with DpnII (NEB) for 2 hours, and amplified via PCR using Advantage cDNA polymerase (Clontech).
2 µg DNA was sonicated in a Bioruptor Plus (Diagenode). DamID adaptors were removed by AlwI digestion, and 500 ng of the resulting fragments end-repaired with a mix of enzymes (T4 DNA ligase (NEB) + Klenow Fragment (NEB) + T4 polynucleotide kinase (NEB)), A-tailed with Klenow 3’ to 5’ exo- (NEB), ligated to Illumina Truseq LT adaptors using Quick Ligase enzyme (NEB) and amplified via PCR with NEBNext Hi-fidelity enzyme (NEB).

value: ovary

tag: developmental stage

value: Adult

tag: genotype/variation


title: polII-en_GAL4-n1


title: Dam-tj_GAL4-n1


title: polII-tj_GAL4-n2


title: Dam-Bab-n1


title: polII-tj_GAL4-n1


title: Dam-en-n1


title: Primary Induction Failure Patient 01, array 01

value: female

tag: patient age

tag: tumor stage


title: AGS_YY1_siRNA_2, Biological Replicate 2

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

description: Gene expression data of AGS gastric cancer cell line with YY1 knock down - Replicate 2

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with GeneChip® Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip® Scanner 3000.

data_processing: Gene level normalized expression signal intensity data of the HTA 2.0 arrays were calculated from CEL files using Gene Level-SST-RMA method which performs GCCN and SST prior to RMA in Affymetrix Expression Console (v1.4.1.46) .

source_name: YY1 knock down AGS gastric cancer cells

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: AGS gastric cancer cells  were seeded in 6 well culture dishes and maintained in media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: The total RNA was isolated from the cells using RNeasy mini kit (Qiagen) following manufacturer's standard protocol.

treatment_protocol: Upon reaching 60-70% confluency, the cells were transfected with 100 nmol of control NTC (non targeting control) siRNA and YY1 siRNA using oligofectamine (Invitrogen), following the standard protocol.

tag: cell line

value: gastric adenocarcinoma cell line AGS

value: YY1 knockdown


title: AGS_NTC_siRNA_1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line treated with siNTC - Replicate 1

source_name: Non targeted control AGS gastric cancer cells

value: control


title: Non-cancer control N98

city: Nagoya

first: Atsushi

last: Natume

address: 65 Tsurumai-cho

institute: Nagoya University

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

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

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: urine

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from urine using the SeraMir Exosome RNA Purification Kit (System Biosciences Inc.).

tag: disease

value: Non-cancer control

value: Female

tag: age


title: Non-cancer control N99


title: Non-cancer control N100

value: Male


title: Non-cancer control N94


title: Non-cancer control N97


title: S2001IJ: M7035_3KO_ADN43

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

data_processing:
Alignment was performed using Ion Torrent tmap with default parameters to Ampliseq mouse transcriptome v1
Genome_build: Amplisq mouse transcriptome v1
Supplementary_files_format_and_content: tab-delimited file expression counts

source_name: Lung tumor tissue at 7 months post-NNK

extract_protocol:
RNA was isolated using the miRNeasy kit from Qiagen according to the manufacturer's protocol. Purified RNA samples were then cleaned and resuspended in nuclease-free water using the RNeasy MinElute Cleanup kit from Qiagen according to the manufacturer’s protocol. RNA quantity was measured using the Nanodrop 1000. Quality of RNA samples was quantitatively assessed by computation of RNA integrity numbers (RINs) using the Agilent RNA 6000 Pico kit (Agilent) following the manufacturer’s protocol.
Barcoded libraries were constructed using the Ion AmpliSeq Transcriptome Mouse Gene expression assay (Ion Torrent/ThermoFisher Scientific) according to the manufacturer's protocol.  10 ng of total RNA was used as input for library generation.
Eight libraries were multiplexed together on one Ion Proton chip and sequenced using the Ion Proton platform (Ion Torrent)

value: Lung tumor tissue

value: 44 weeks old

tag: nnk

value: NNK exposed

tag: time point

value: 7 month post-NNK


title: S20016A: M7007_2KO_NRM01

source_name: Normal lung tissue at end of 3 months post-NNK

value: Normal lung tissue

value: 28 weeks old

value: 3 month post-NNK


title: S20015B: M7008_2KO_ADN01

source_name: Lung tumor tissue at 3 months post-NNK


title: Non-cancer control N91


title: Dam-tj_GAL4-n2


title: Non-cancer control N92


title: Non-cancer control N93


title: FFPE Breast cancer 31808, luminal A, FBC-

description: Sample name: 31808

tag: ki67 ihq

tag: p53 ihq

tag: histologic grade

tag: hormone receptor (hr)

tag: her2 ihq

tag: subtype

value: luminal A

tag: brca status

value: FBC-

value: FFPE breast cancer tissue


title: AGS_YY1_siRNA_1, Biological Replicate 1

description: Gene expression data of AGS gastric cancer cell line with YY1 knock down - Replicate 1

tag: genotype


title: S20015A: M7008_2KO_NRM01

tag: tissue


title: iBMDM-Reg1WT-0h-rep1

city: Beijing

first: Meiling

last: Piao

address: Shuangqing Road 30

department: Life Science

institute: Tsinghua University

data_processing:
Calculate smartSHAPE score from smartSHAPE sequencing data:
1) The 3’ adaptor is removed with Cutadapt
2) Duplicated reads were collapsed with custom script;
3) The first 10nt were removed using trimmomatic
4) Clean reads were mapped to human rRNA with Bowtie2
5) Un-mapped reads were mapped to the human (hg38) or mouse (mm10) genome using STAR
6) Sam files were convert into .tab files using icSHAPE-pipe sam2tab;
7) The smartSHAPE score was calculated using icSHAPE-pipe calcSHAPENoCont
For uvCLAP data:
Raw reads were trimmed by Cutadapt and collapsed to remove duplicated reads. The clean reads were mapped to mouse rRNA by Bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. Peaks were called out by Piranha with Reg1 group as response sample and GFP group as covariate sample. The bin size was set to 50 with -z 50.
For RNA-Seq data:
Raw reads were trimmed by Cutadapt. The trimmed reads were mapped to mouse rRNA by bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. We set parameter --quantMode TranscriptomeSAM GeneCounts to generate the read count file. The RNA-Seq differentail expression analysis is carried by DESeq2.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: .shape format: tab-seperated file, each row represent a transcript. The meaning of each column: transcript_id, length, a star symbol, reactivity score for each base

molecule: polyA RNA

source_name: iBMDM cell line

growth_protocol: HEK293T cells, iBMDM and Raw264.7 cells were cultured were maintained in DMEM (Gibco) medium with high glucose, supplemented with 10% FBS and 1% Penicillin-Streptomycin at 37°C with 5% CO2.

extract_protocol:
For smartSHAPE and RNA-Seq, RNAs were isolated with Trizol reagents.
For smartSHAPE, cells were treated with NAI-N3 or DMSO and RNAs were isolated with Trizol followed by rRNA removal. RNAs were reverse transcribed with random primers, and RNase I digestion was performed at 37 °C for 30 min. Enrichment was performed using MyOne C1 beads. After elution, cDNAs were ligated with biotinylated 3’ adaptor using CircLigase and immobilized with MyOne C1 beads. Second strand synthesis and 5’ligation was performed on the beads. smartSHAPE libraries were generated by amplification of ligation products. RNA seq libraries of Reg1 KO and WT iBMDMs were generated with KAPA RNA Hyper Prep kit. uvCLAP libraries were generated as published protocol (PMID: 29559621).

treatment_protocol: For structure probing, cells were treated with NAI-N3 or DMSO at 37°C for 5min and quenched by adding 500 µl Trizol. For RNA seq, cells were treated with 100 ng/ml LPS for 0 h or 3 h before RNA isolation. For uvCLAP, cells were maintained in media supplied with 50 µM biotin overnight and treated with 100 ng/mL LPS for 3 h.

value: iBMDM

value: WT


title: Non-cancer control N96

tag: gender


title: S20014B: M2026_1KO_ADN01

source_name: Lung tumor tissue at end of NNK exposure

tag: genotype/variation

value: 16 weeks old

value: end of NNK exposure


title: iBMDM-Reg1WT-0h-rep3


title: S20014A: M2026_1KO_NRM01

source_name: Normal lung tissue at end of NNK exposure


title: Non-cancer control N95

value: Non-cancer control


title: iBMDM-Reg1KO-0h-rep3


title: iBMDM-Reg1KO-0h-rep2


title: S20013A: M2027_1KO_NRM01


title: S20013B: M2027_1KO_ADN01


title: Non-cancer control N89

value: Female


title: Non-cancer control N88


title: S20012A: M2258_0KO_NRM01

source_name: Normal lung tissue at baseline

value: 8 weeks old

value: No exposure

value: Baseline


title: iBMDM-Reg1KO-0h-rep1


title: Non-cancer control N87

value: Male


title: iBMDM-Reg1WT-3h-rep3


title: Non-cancer control N86


title: iBMDM-Reg1WT-0h-rep2


title: Non-cancer control N90


title: iBMDM-Reg1WT-3h-rep2


title: FFPE Breast cancer 31813, luminal B, FBC-

description: Sample name: 31813

value: luminal B


title: S20011A: M2257_0KO_NRM01

value: Normal lung tissue


title: S2000ZG: M7037_3KO_ADN04

value: Lung tumor tissue

value: 44 weeks old

value: NNK exposed

value: 7 month post-NNK


title: iBMDM-Reg1WT-3h-rep1


title: iBMDM-Reg1KO-3h-rep3


title: Non-cancer control N84


title: S2000ZB: M7037_3KO_ADC01


title: iBMDM-Reg1KO-3h-rep2


title: S2000ZA: M7037_3KO_NRM01

source_name: Normal lung tissue at end of 7 months post-NNK


title: AGS_NTC_siRNA_2, Biological Replicate 2

description: Gene expression data of AGS gastric cancer cell line treated with siNTC - Replicate 2

value: gastric adenocarcinoma cell line AGS

value: control


title: Non-cancer control N83


title: Non-cancer control N81


title: Non-cancer control N82


title: Non-cancer control N85


title: Non-cancer control N80


title: iBMDM-Reg1KO-3h-rep1

value: iBMDM


title: S2000YP: M7046_3KO_ADN14


title: Ly6Chi-NAIN3-rep2

data_processing:
Library strategy: smartSHAPE
Calculate smartSHAPE score from smartSHAPE sequencing data:
1) The 3’ adaptor is removed with Cutadapt
2) Duplicated reads were collapsed with custom script;
3) The first 10nt were removed using trimmomatic
4) Clean reads were mapped to human rRNA with Bowtie2
5) Un-mapped reads were mapped to the human (hg38) or mouse (mm10) genome using STAR
6) Sam files were convert into .tab files using icSHAPE-pipe sam2tab;
7) The smartSHAPE score was calculated using icSHAPE-pipe calcSHAPENoCont
For uvCLAP data:
Raw reads were trimmed by Cutadapt and collapsed to remove duplicated reads. The clean reads were mapped to mouse rRNA by Bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. Peaks were called out by Piranha with Reg1 group as response sample and GFP group as covariate sample. The bin size was set to 50 with -z 50.
For RNA-Seq data:
Raw reads were trimmed by Cutadapt. The trimmed reads were mapped to mouse rRNA by bowtie2, and the remaining un-mapped reads were re-mapped to mouse genome (mm10) by STAR. We set parameter --quantMode TranscriptomeSAM GeneCounts to generate the read count file. The RNA-Seq differentail expression analysis is carried by DESeq2.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: .shape format: tab-seperated file, each row represent a transcript. The meaning of each column: transcript_id, length, a star symbol, reactivity score for each base

source_name: Ly6Chi mouse colonic macrophage

tag: strain


title: S2000YI: M7046_3KO_ADN08


title: Ly6Clo-NAIN3-rep2

source_name: Ly6Clo mouse colonic macrophage


title: Ly6Chi-NAIN3-rep1


title: S2000YA: M7046_3KO_NRM01


title: Non-cancer control N78


title: Non-cancer control N79


title: S2000XY: M7035_3KO_ADN22


title: Primary Induction Failure Patient 03, array 01

value: bone marrow

tag: disease state

value: pediatric acute myeloid leukemia; primary induction failure patient

value: female

tag: patient age

tag: tumor stage


title: Ly6Clo-NAIN3-rep1


title: S2000XK: M7035_3KO_ADN09

tag: age

tag: nnk


title: Non-cancer control N77

tag: disease

value: Non-cancer control


title: Non-cancer control N76


title: S2000ZJ: M7037_3KO_ADN07

tag: time point


title: S2000XD: M7035_3KO_ADN02


title: S2000XB: M7035_3KO_ADC01


title: Lane1_1D_H3K27ace_scram

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Reads were aligned to the hg19 build of the human genome using Burrows-Wheeler Aligner (BWA)
Peaks for K27me3 samples were called using SICER software to detect broad enrichment patterns.
Peaks for K27ace samples were called using MACS2 software to detect narrow enrichment patterns.
Genome_build: hg19
Supplementary_files_format_and_content: TDF Files (for visualization), MACS2 Peak BED Files (K27ace samples) and SICER Peak BED Files (K27me3 samples)

source_name: Cell line

growth_protocol: Jurkat T cells (Clone E6-1; ATCC, TIB-152) were maintained in medium A (RPMI 1640 supplemented with 10% FCS, 10 mmol/L HEPES, pH 7.4, and 2 mmol/L L-glutamine) at less than 106 cells/mL.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP DNA library preparation was performed using 10 ng per reaction, and input DNA using the Ovation Ultralow DR Multiplex System (NuGen #0330).

treatment_protocol: Jurkat T cells were transiently transfected with indicated siRNA by electroporation at 315 mV for 10 ms and harvested 36 to 48 hours later. 2 x 106 Jurkat cells were transfected with 120 nM of ON-TARGETplus Human BMI1 siRNA (648) (Dharmacon cat# L-005230-01-0005) or 100 nM of ON-TARGETplus Human EZH2 siRNA (2146) (Dharmacon, cat# L-004218-00-0005).

tag: cell type

value: Jurkat E6

tag: chip antibody

value: H3K27ac (Abcam, Cat# ab4729)


title: Lane1_3D_H3K27ace_EZH2


title: S2000XA: M7035_3KO_NRM01


title: Lane1_3B_H3K27me3_EZH2

value: H3K27me3 (Cell Signaling Technology, Cat# 9733S)


title: Lane1_2B_H3K27me3_BMI1


title: S2000X0: M7035_3KO_ADN24


title: Non-cancer control N73

value: Male


title: Non-cancer control N75

value: Female


title: Non-cancer control N74


title: Brain_Old_BW_P35266

description:
S22
RNASeqCounts_BW.txt

source_name: Brain

tag: stock

value: BW

value: Brain

tag: age of animal at termination

value: 29 months


title: Non-cancer control N70


title: S2000WA: M7034_3KO_NRM01

value: Normal lung tissue

value: 44 weeks old

value: NNK exposed


title: S2000VA: M7052_2KO_NRM01

value: 28 weeks old

value: 3 month post-NNK


title: Non-cancer control N71


title: Lane1_1B_H3K27me3_scram


title: Non-cancer control N72


title: Lane1_2D_H3K27ace_BMI1


title: Lane1_5_pct_IN_EZH2


title: Lane1_5_pct_IN_BMI1


title: Lane1_5_pct_IN_scrambled


title: S2000UA: M7050_2KO_NRM01


title: S2000TA: M2022_1KO_NRM01

value: 16 weeks old

value: end of NNK exposure


title: Day 7 Treg 6_BF-ATAC-6

description: Day 7 Treg

data_processing:
Sequencing Reads were aligned to GRCh37 (hg19) build of the human genome using Burrows-Wheeler Alignment (BWA)
Peaks were called using MACS2 software.
TDF files for visualization were generated using in-house scripts
Genome_build: hg19
Supplementary_files_format_and_content: TDF Files (visualization) and BED Files (Peak calls)

source_name: PBMCs

growth_protocol: Following bead isolation, naïve T cells were cultured in a 24-well tissue culture plate for 7 days in cRPMI media (RPMI, 10% FCS, 10mM HEPES, 1mM Sodium Pyruvate, 1% Non-essential Amino Acids, 2mM L-Glutamine, Penicillin/Streptomycin, culture-grade 50uM 2-mercaptoethanol) with T regulatory inducing cytokines: anti-CD28 (2µg/ml, BD BioSciences cat# 555725), plate-bound anti-CD3 (2µg/ml, BD BioSciences cat# 555329), IL-2 (10ng/ml, Peprotech Cat# 200-02), and TGFβ (5ng/ml, Peprotech cat# 100-21C). During the 7 day incubation, additional media with cytokines was added on day 3. On day 5, cells were harvested and washed once with DPBS. Cells were resuspended in fresh cRPMI media with only CD28 and replated on freshly coated anti-CD3 plates until day 7 harvest for ATAC-seq analysis.

extract_protocol:
ATAC-seq was performed from 50,000 Treg cells per a previously published protocol (Buenrostro, Nature Methods, 2013). Briefly, nuclei were prepared by washing cells with PBS, followed by lysis using cold lysis buffer. Nuclei were spun and the pellet was then resuspended in the transposase reaction mix for 30 min at 37 °C. The samples were then purified using a Qiagen Minelute kit.
Amplified libraries were purified, and the sizes of library DNA were determined by the Fragment Analyzer (Advanced Analytical Technologies, IA) using the High Sensitivity NGS Fragment Analysis Kit (Cat # DNF-486). The enrichment of accessible region was determined by the fold difference between positive and negative genomic loci using real-time PCR. The libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 4000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.

treatment_protocol: No other treatments performed.

value: Day 7


title: Non-cancer control N68

value: Non-cancer control


title: S2000SA: M2025_1KO_NRM01


title: Non-cancer control N69


title: Non-cancer control N67


title: S2000RA: M2230_0KO_NRM01

value: 8 weeks old

value: No exposure

value: Baseline


title: S2000QA: M2229_0KO_NRM01


title: S2000PN: M7033_3KO_ADN13

value: Lung tumor tissue

value: 7 month post-NNK


title: 198_2887_3_TimePoint3

city: La Jolla

first: Ferran

last: soldevila

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Sequencing Run Id: 003580

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm9 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh37.p13.gencode.r19
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

source_name: peripheral blood mononuclear cells

extract_protocol:
2x10^6 PBMC from each sample were transferred directly to Quiazol regent (QIAGEN), resuspended and immediately aliquoted and stored at -80ºC. RNA was extracted using the Qiagen miRNeasy Mini kit with on-column DNase treatment
500 ng of total RNA was used as input for library preparation using the Illumina TruSeq Stranded mRNA Library Prep Kit.
Libraries were sequenced on the HiSeq3000

tag: treatment

value: pertussis antigenic challenge

tag: primed

value: aP

tag: time

value: 3 days

value: PBMC


title: 197_2887_2_TimePoint2

description: Sequencing Run Id: 003580

value: 1 days


title: 196_2887_1_TimePoint1

description: Sequencing Run Id: 003580

value: 0 days


title: S2000PK: M7033_3KO_ADN10

tag: tissue

value: 44 weeks old

value: NNK exposed


title: 194_2923_4_TimePoint4

description: Sequencing Run Id: 003580

value: 7 days


title: 195_2923_5_TimePoint5

description: Sequencing Run Id: 003580

value: 14 days


title: S2000PA: M7033_3KO_NRM01

value: Normal lung tissue

tag: genotype/variation


title: S2000NB: F1765_3KO_ADN01


title: Non-cancer control N66

value: Non-cancer control

tag: gender

value: Female


title: S2000NA: F1765_3KO_NRM01


title: Non-cancer control N65

value: Male


title: 193_2923_3_TimePoint3

description: Sequencing Run Id: 003580


title: Non-cancer control N64


title: Non-cancer control N62


title: Non-cancer control N61


title: Non-cancer control N63


title: Day 0 1_BF-ATAC-1

description: Day 0

value: Day 0


title: S2000LA: F7044_2KO_NRM01

value: 28 weeks old

value: 3 month post-NNK


title: 192_2923_2_TimePoint2

description: Sequencing Run Id: 003580

value: pertussis antigenic challenge


title: 191_2923_1_TimePoint1

description: Sequencing Run Id: 003580

value: aP


title: Non-cancer control N58


title: Non-cancer control N59


title: S2000KA: M2021_1KO_NRM01

value: 16 weeks old

value: end of NNK exposure


title: 190_2903_5_TimePoint5

description: Sequencing Run Id: 003580

value: PBMC


title: Non-cancer control N60


title: S2000JA: F2058_1KO_NRM01


title: Non-cancer control N57


title: Non-cancer control N56


title: 189_2903_4_TimePoint4

description: Sequencing Run Id: 003580


title: Non-cancer control N55


title: S2000IA: M2228_0KO_NRM01

value: 8 weeks old

value: No exposure

value: Baseline


title: 188_2903_3_TimePoint3

description: Sequencing Run Id: 003580

value: 3 days


title: Non-cancer control N54


title: S2000HA: F2225_0KO_NRM01


title: 187_2903_2_TimePoint2

description: Sequencing Run Id: 003580

value: 1 days


title: Non-cancer control N53


title: S2000GD: F1768_3KO_ADN02

value: Lung tumor tissue

value: 44 weeks old

value: NNK exposed

value: 7 month post-NNK


title: 186_2903_1_TimePoint1

description: Sequencing Run Id: 003580

value: 0 days


title: S2000GC: F1768_3KO_ADN01


title: S2000FC: F1767_3KO_ADN01


title: Non-cancer control N52

value: Non-cancer control

value: Female


title: S2000FA: F1767_3KO_NRM01

value: Normal lung tissue


title: 183_2904_3_TimePoint3

description: Sequencing Run Id: 003580

value: pertussis antigenic challenge

value: aP


title: S2000EA: F7017_2KO_NRM01

value: 28 weeks old

value: 3 month post-NNK


title: Non-cancer control N49


title: 99_2726_4_TimePoint4

description: Sequencing Run Id: 003560

value: wP

value: 7 days

value: PBMC


title: Non-cancer control N51

value: Male


title: 182_2904_2_TimePoint2

description: Sequencing Run Id: 003580

value: 1 days


title: 181_2904_1_TimePoint1

description: Sequencing Run Id: 003580


title: S2000DG: F7016_2KO_ADN04

value: Lung tumor tissue


title: S2000DF: F7016_2KO_ADN03


title: 98_2726_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: 97_2726_2_TimePoint2

description: Sequencing Run Id: 003560


title: S2000DA: F7016_2KO_NRM01

value: NNK exposed


title: Non-cancer control N48


title: Non-cancer control N46


title: Non-cancer control N45


title: 184_2904_4_TimePoint4

description: Sequencing Run Id: 003580


title: S2000GA: F1768_3KO_NRM01

value: 44 weeks old

value: 7 month post-NNK


title: S2000CA: F2057_1KO_NRM01

value: 16 weeks old

value: end of NNK exposure


title: Non-cancer control N43

value: Non-cancer control


title: S2000BA: F2017_1KO_NRM01

value: Normal lung tissue


title: 95_2699_5_TimePoint5

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 14 days


title: Non-cancer control N50


title: Non-cancer control N42

value: Female


title: S2000AA: F2224_0KO_NRM01

value: 8 weeks old

value: No exposure

value: Baseline


title: 94_2699_4_TimePoint4

description: Sequencing Run Id: 003560

value: wP

value: 7 days

value: PBMC


title: S20009A: F2223_0KO_NRM01


title: Non-cancer control N41

value: Male


title: S20008D: F2016_1KO_ADN03

value: Lung tumor tissue

value: NNK exposed


title: 93_2699_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: Non-cancer control N47


title: S20008C: F2016_1KO_ADN02

value: 16 weeks old


title: 92_2699_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: 90_2706_5_TimePoint5

description: Sequencing Run Id: 003560


title: Non-cancer control N44

value: Non-cancer control


title: S20008A: F2016_1KO_NRM01

value: Normal lung tissue

value: end of NNK exposure


title: 96_2726_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 0 days


title: Non-cancer control N39


title: Non-cancer control N40


title: S20007D: F7021_3KO_ADN02

value: 44 weeks old

value: 7 month post-NNK


title: Non-cancer control N38


title: 9_2689_4_TimePoint4

description: Sequencing Run Id: 003560

value: aP


title: S20007C: F7021_3KO_ADN01


title: S20007A: F7021_3KO_NRM01


title: Non-cancer control N36


title: Non-cancer control N35


title: S20006E: F7020_3KO_ADN03


title: 88_2706_3_TimePoint3

description: Sequencing Run Id: 003560

value: wP


title: 87_2706_2_TimePoint2

description: Sequencing Run Id: 003560


title: S20006D: F7020_3KO_ADN02


title: Non-cancer control N33

value: Female


title: 85_2707_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days

value: PBMC


title: Non-cancer control N37


title: S20006C: F7020_3KO_ADN01

value: Lung tumor tissue


title: 91_2699_1_TimePoint1

description: Sequencing Run Id: 003560


title: S20005E: F7018_2KO_ADN02

value: 28 weeks old

value: NNK exposed

value: 3 month post-NNK


title: Non-cancer control N34


title: 83_2707_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: 86_2706_1_TimePoint1

description: Sequencing Run Id: 003560


title: Non-cancer control N32

value: Non-cancer control


title: 185_2904_5_TimePoint5

description: Sequencing Run Id: 003580


title: 84_2707_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: 89_2706_4_TimePoint4

description: Sequencing Run Id: 003560


title: S2000XP: M7035_3KO_ADN13


title: S20005A: F7018_2KO_NRM01

value: Normal lung tissue


title: Non-cancer control N28


title: Non-cancer control N29


title: 80_1655_5_TimePoint5

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: S20004B: F7015_2KO_ADN01


title: Non-cancer control N27


title: S20004A: F7015_2KO_NRM01


title: Non-cancer control N30

value: Male


title: Non-cancer control N26


title: S20002A: F2015_1KO_NRM01

value: 16 weeks old

value: end of NNK exposure


title: S20005B: F7018_2KO_ADN01


title: 78_1655_3_TimePoint3

description: Sequencing Run Id: 003560


title: 79_1655_4_TimePoint4

description: Sequencing Run Id: 003560


title: S20006A: F7020_3KO_NRM01

value: 44 weeks old

value: 7 month post-NNK


title: Non-cancer control N25


title: 77_1655_2_TimePoint2

description: Sequencing Run Id: 003560

value: wP

value: 1 days


title: FFPE Breast Cancer 32105, luminal B, FBC+

description: Sample name: 32105

data_processing:
ChAS console from Affymetrix was used to assess genome wide copy number
Weighted Log2 Ratios

source_name: FFPE breast cancer tissue

tag: ki67 ihq

tag: p53 ihq

tag: histologic grade

tag: hormone receptor (hr)

tag: her2 ihq

tag: subtype

value: luminal B

tag: brca status

value: FBC+

value: FFPE breast cancer tissue


title: Non-cancer control N31

tag: disease

tag: age


title: 76_1655_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days

tag: cell type

value: PBMC


title: 82_2707_2_TimePoint2

description: Sequencing Run Id: 003560


title: FFPE Breast Cancer 32102, luminal A, FBC+

description: Sample name: 32102

value: nd

value: luminal A


title: 75_2719_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: 81_2707_1_TimePoint1

description: Sequencing Run Id: 003560


title: Non-cancer control N23

value: Non-cancer control


title: Non-cancer control N24

value: Female


title: 8_2689_3_TimePoint3

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: aP

value: 3 days


title: 74_2719_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: Non-cancer control N20


title: FFPE Breast Cancer 31950, luminal B, FBC-

description: Sample name: 31950

value: FBC-


title: Non-cancer control N21


title: 73_2719_3_TimePoint3

description: Sequencing Run Id: 003560

value: wP


title: S20003A: F2222_0KO_NRM01

value: Normal lung tissue

value: 8 weeks old

tag: nnk

value: No exposure

tag: time point

value: Baseline


title: FFPE Breast Cancer 31948, luminal B, FBC-

description: Sample name: 31948

value: luminal B

value: FFPE breast cancer tissue


title: S20001A: F2221_0KO_NRM01


title: Non-cancer control N18


title: 72_2719_2_TimePoint2

description: Sequencing Run Id: 003560

tag: treatment

tag: primed

value: 1 days

value: PBMC


title: FFPE Breast Cancer 31947, FBC-

description: Sample name: 31947

tag: tissue


title: Non-cancer control N17


title: FFPE Breast Cancer 31933, luminal B, FBC-

description: Sample name: 31933

value: nd


title: Non-cancer control N22

value: Non-cancer control

value: Male


title: FFPE Breast Cancer 31930, TNC, FBC-

description: Sample name: 31930

value: TNC


title: FFPE Breast Cancer 32104, luminal B, FBC+

description: Sample name: 32104

value: FBC+


title: Non-cancer control N14


title: 71_2719_1_TimePoint1

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

tag: time

value: 0 days


title: 7_2689_2_TimePoint2

description: Sequencing Run Id: 003560

value: aP


title: 70_2696_5_TimePoint5

description: Sequencing Run Id: 003560

value: wP

value: 14 days


title: FFPE Breast Cancer 31928, luminal A, FBC-

description: Sample name: 31928

value: luminal A

value: FBC-


title: 69_2696_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: Non-cancer control N19

tag: gender

value: Female


title: FFPE Breast Cancer 31846, luminal B, FBC-

description: Sample name: 31846

tag: ki67 ihq

value: luminal B

value: FFPE breast cancer tissue


title: Non-cancer control N13


title: 68_2696_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days

value: PBMC


title: FFPE Breast Cancer 31845, luminal B, FBC-

description: Sample name: 31845

tag: p53 ihq


title: Non-cancer control N16

value: Non-cancer control


title: 67_2696_2_TimePoint2

description: Sequencing Run Id: 003560

value: 1 days


title: Non-cancer control N12


title: FFPE Breast Cancer 31842, TNC, FBC-

description: Sample name: 31842

tag: histologic grade

value: TNC


title: 66_2696_1_TimePoint1

description: Sequencing Run Id: 003560


title: FFPE Breast Cancer 31812, HER2, FBC-

description: Sample name: 31812

tag: hormone receptor (hr)


title: 65_2687_5_TimePoint5

description: Sequencing Run Id: 003560


title: Non-cancer control N10

value: Male


title: FFPE Breast Cancer 31811, luminal A, FBC-

description: Sample name: 31811

tag: her2 ihq


title: 64_2687_4_TimePoint4

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge


title: Non-cancer control N11


title: Non-cancer control N9


title: FFPE Breast Cancer 31810, luminal B, FBC-

description: Sample name: 31810

value: nd

tag: subtype


title: FFPE Breast Cancer 31775, luminal A, BRCA+

description: Sample name: 31775

tag: brca status

value: BRCA+


title: Non-cancer control N8

tag: disease


title: Non-cancer control N15

tag: age


title: Non-cancer control N7


title: 62_2687_2_TimePoint2

description: Sequencing Run Id: 003560

value: wP

tag: cell type


title: Non-cancer control N6


title: 61_2687_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days


title: 60_1829_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: FFPE Breast Cancer 31757, BRCA+

description: Sample name: 31757


title: FFPE Breast Cancer 31772, luminal B, BRCA+

description: Sample name: 31772


title: 63_2687_3_TimePoint3

description: Sequencing Run Id: 003560


title: FFPE Breast Cancer 31756, TNC, BRCA+

description: Sample name: 31756


title: 6_2689_1_TimePoint1

description: Sequencing Run Id: 003560

value: aP


title: Non-cancer control N4


title: Non-cancer control N5


title: 59_1829_4_TimePoint4

description: Sequencing Run Id: 003560

value: 7 days


title: FFPE Breast Cancer 31707, luminal A, BRCA+

description: Sample name: 31707

value: luminal A


title: Non-cancer control N3


title: 58_1829_3_TimePoint3

description: Sequencing Run Id: 003560


title: FFPE Breast Cancer 31705, TNC, BRCA+

description: Sample name: 31705


title: FFPE Breast Cancer 31704, TNC, BRCA+

description: Sample name: 31704


title: Non-cancer control N1


title: FFPE Breast Cancer 31692, TNC, BRCA+

description: Sample name: 31692


title: 57_1829_2_TimePoint2

description: Sequencing Run Id: 003560


title: 56_1829_1_TimePoint1

description: Sequencing Run Id: 003560


title: 55_1832_5_TimePoint5

description: Sequencing Run Id: 003560


title: FFPE Breast Cancer 31770, TNC, BRCA+

description: Sample name: 31770


title: FFPE Breast Cancer 31691, TNC, BRCA+

description: Sample name: 31691


title: 54_1832_4_TimePoint4

description: Sequencing Run Id: 003560


title: FFPE Breast Cancer 31690, TNC, BRCA+

description: Sample name: 31690


title: 53_1832_3_TimePoint3

description: Sequencing Run Id: 003560


title: Other brain tumor Ot24

value: Other brain tumor


title: Other brain tumor Ot25

value: Female


title: Non-cancer control N2


title: 51_1832_1_TimePoint1

description: Sequencing Run Id: 003560


title: Other brain tumor Ot26


title: 52_1832_2_TimePoint2

description: Sequencing Run Id: 003560


title: 50_2704_5_TimePoint5

description: Sequencing Run Id: 003560


title: Other brain tumor Ot27


title: Other brain tumor Ot22


title: Other brain tumor Ot21


title: Other brain tumor Ot23


title: 49_2704_4_TimePoint4

description: Sequencing Run Id: 003560


title: 48_2704_3_TimePoint3

description: Sequencing Run Id: 003560

value: 3 days


title: Other brain tumor Ot18


title: Other brain tumor Ot19


title: Other brain tumor Ot17


title: VSMC_Hypoxia+E2

city: Seoul

first: Youngjoo

last: Lee

address: 209, Neungdong-ro, Gwangjin-gu

department: Bioscience and Biotechnology

country: South Korea

institute: Sejong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to rn6 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: vascular smooth muscle cells

growth_protocol: VSMCs were routinerly cultured on coated plastic in DMEM/F12 medium.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTer® Stranded RNA-Seq Kit standard protocols.

treatment_protocol: VSMCs were pretreated with In-Cl (0.1 μM), DPN (0.1 μM), E2 (10 nM) before treatment under hypoxic conditions for 24 h

value: vascular smooth muscle cells


title: VSMC_CON


title: VSMC_Hypoxia+DPN


title: VSMC_Hypoxia


title: VSMC_Hypoxia+In-Cl


title: 47_2704_2_TimePoint2

description: Sequencing Run Id: 003560

value: PBMC


title: 46_2704_1_TimePoint1

description: Sequencing Run Id: 003560


title: Other brain tumor Ot16

source_name: urine


title: 45_2703_5_TimePoint5

description: Sequencing Run Id: 003560


title: 5_2685_5_TimePoint5

description: Sequencing Run Id: 003560


title: K6: atbbd1 knock-out seedlings treated with 20% PEG for 6 hours

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

institute: Korea University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and differentially expressed genes were identified using TopHat2-Cufflinks pipeline
Genome_build: TAIR 10
Supplementary_files_format_and_content: FPKM values for each sample, in excel file

source_name: Leaves

growth_protocol: Plant were growed at 23°C long day condition on soil.

extract_protocol:
Total RNA was extracted using trizol reagent
mRNA libraries were prepared  1 μg of total RNA using TruSeq standard mRNA kit (Illumina), according to the manufacturer's instruction.

treatment_protocol: Plants were watered with 20% PEG to induce drought condition.

value: Leaves

value: Stress with 20% PEG for 6 hours


title: 44_2703_4_TimePoint4

description: Sequencing Run Id: 003560


title: O6: p35S:AtBBD1 seedlings treated with 20% PEG for 6 hours


title: 43_2703_3_TimePoint3

description: Sequencing Run Id: 003560


title: Other brain tumor Ot20

value: Male


title: Other brain tumor Ot15


title: Other brain tumor Ot14


title: 42_2703_2_TimePoint2

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 1 days


title: C8161.9 control shRNA 2

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

hyb_protocol: Fragmented aRNA was hybridized at 42°c overnight using the HybBag mixing system with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Devicess™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.

data_processing: 2 replicate samples were averaged. The F532 channel data in each raw data file should be ignored. Only Cy5 dye was used for the experiment. The data from all microarrays in each experimental set was then passed to Rosetta resolver (v.7.2.2.0.0) for analysis. Testing was performed by combining technical replicates and performing statistical analyses using Rosetta Resolver’s proprietary modeling techniques. Normalization algorithm -> Median scaling.

source_name: Melanoma cell line

label_protocol: High-quality RNA (RIN=10) was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The product ws conjugated with Cy5 NHS ester.

growth_protocol: DMEM-F12 with 5% FBS + 1xPenstrep

extract_protocol: Five million cells were pellted and RNA was isolated with Qiagen Rneasy kit

treatment_protocol: Lentiviral infection of shRNA plasmids

value: Melanoma cell line

tag: cell line

tag: genotype/variation

value: Stably Transfected w Luc-shRNA plasmid


title: C8161.9 NCOA3 shRNA 1

value: Stably Transfected w NCOA3-shRNA plasmid


title: C8161.9 control shRNA 1


title: Other brain tumor Ot11


title: Other brain tumor Ot10


title: C8161.9 NCOA3 shRNA 2


title: 41_2703_1_TimePoint1

description: Sequencing Run Id: 003560

tag: treatment

value: wP

value: 0 days


title: 40_2702_5_TimePoint5

description: Sequencing Run Id: 003560

tag: primed

value: 14 days


title: Other brain tumor Ot9


title: 4_2685_4_TimePoint4

description: Sequencing Run Id: 003560

value: aP

value: 7 days


title: 39_2702_4_TimePoint4

description: Sequencing Run Id: 003560


title: Other brain tumor Ot8

value: Other brain tumor

value: Female


title: VTA_Male_1_snRNA-seq

city: Birmingham

first: Jeremy

middle: Jason

last: Day

state: AL

address: 1825 University Blvd

department: Neurobiology

institute: UAB

data_processing:
Cell demultiplexing and genome alignment in Cell Ranger using Emsemble pre-mRNA (v95) reference assembly GTF file. Raw count data obtained in Cell Ranger.
Genome_build: rn6
Supplementary_files_format_and_content: Cell Ranger output matrices for barcodes, features, and gene expression counts are provided for each sample.

source_name: Ventral tegmental area

growth_protocol: Male and female Sprague-Dawley rats (200-250g) were purchased from Charles River Laboratories and individually housed for 1 week prior to tissue collection. Rats were maintained on a 12 h light/dark cycle with ad libitum access to food and water, and were briefly handled for 3 days prior to tissue collection (1-2min/day) to acclimate them to the experimenters. All experimental procedures were approved by the University of Alabama at Birmingham Institutional Animal Care and Use Committee, and were conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Rats were euthanized by decapitation, and brains were rapidly removed and chilled in ice cold Hibernate A media without Ca2+ or Mg2+ (BrainBits, HACAMG500) for 30-60 sec. Chilled brains were then blocked into 1-mm-thick coronal sections on wet ice. Sections containing the VTA (ranging from -4.92 to -6.46mm AP relative to bregma) were transferred to glass petri dishes on dry ice, and the VTA was microdissected from neighboring brain regions (n = 6 rats per sex).  VTA tissue was then transferred to ice-cold centrifuge tubes, and stored at −80°C until the day of nuclei isolation and harvesting. To harvest nuclei, frozen VTA tissue was briefly thawed on wet ice before being chopped by scalpel 100 times in two orthogonal directions. Tissue from three rats per sex was combined and transferred to 5 ml of ice cold lysis buffer (10 mM tris-HCl, 10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal in nuclease-free water (Sigma-Aldrich, 18896-50ML) for 15 min, mixing the tissue by inversion every 2 min. Lysis was quenched after 15 min with 5 ml of complete Hibernate A (Thermo Fisher Scientific, A1247501) supplemented with B27, GlutaMAX (Life Technologies, 35050-061), and NxGen RNase Inhibitor (0.2 U/μl; Lucigen, 30281-2). Tissue was then triturated by fire-polished Pasteur pipette (three pipettes of decreasing diameter; 8 to 10 passes per pipette) for 35 min and passed through a 40-μm prewet filter. The samples were then pelleted at 500 rcf for 10 min at 4°C followed by a wash in 10 ml of nuclei wash and resuspension buffer [1× phosphate-buffered saline (PBS), 1% bovine serum albumin (BSA), and NxGen RNase Inhibitor]. Supernatant was then removed, and the pellet was gently resuspended in 800 μl of wash buffer before 7-aminoactinomycin D (Thermo Fisher Scientific, 00-6993-50) staining and fluorescence-activated cell sorting (FACS) to further purify the nuclei for sequencing (BD FACS Aria, 70-μm nozzle, BD Biosciences). Immediately after FACS, nuclei were washed a final time at 250 rcf in 10 ml of supplemented Hibernate A containing 1% BSA for 10 min at 4°C to remove any remaining fine debris and nascent RNA. Nuclei were then brought to a concentration of 1400 nuclei/μl. A total of 11,367 nuclei pooled from three rats per sex and treatment group were loaded into a single well of the Chromium Single Cell B Chip using four of the eight available wells.
FACS-sorted nuclei were subject to 10X GEM generation and barcoding, GEM-RT cleanup and cDNA amplication, and library construction using a Chromium Single Cell 3ʹ Reagent Kit (v3 chemistry). Libraries were quantified and underwent sequencing (~500M total 75bp paired-end reads) on an Illumina sequencing platform (NextSeq 500).

treatment_protocol: Rats were experimentally naïve at the time of VTA sample collection.

tag: strain

value: Sprague-Dawley

tag: Sex

tag: tissue

value: Ventral tegmental area


title: W6: Wild-type seedlings treated with 20% PEG for 6 hours

value: Leaves


title: VTA_Male_2_snRNA-seq


title: 38_2702_3_TimePoint3

description: Sequencing Run Id: 003560

tag: time

value: 3 days

value: PBMC


title: VTA_Female_1_snRNA-seq


title: Other brain tumor Ot7

tag: gender

value: Male


title: Other brain tumor Ot6


title: Other brain tumor Ot5


title: 37_2702_2_TimePoint2

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 1 days


title: Other brain tumor Ot12


title: 36_2702_1_TimePoint1

description: Sequencing Run Id: 003560


title: Other brain tumor Ot4


title: 35_2691_5_TimePoint5

description: Sequencing Run Id: 003560


title: Other brain tumor Ot3


title: 34_2691_4_TimePoint4

description: Sequencing Run Id: 003560


title: 33_2691_3_TimePoint3

description: Sequencing Run Id: 003560


title: VTA_Female_2_snRNA-seq


title: Experiment2 Restraint+Propranolol Rep_3

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

description:
101036360019_B.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

hyb_protocol: Standard Illumina hybridization protocol (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

source_name: Sorted Femoral Bone Marrow Cells (Leukemia Negative)

label_protocol: Biotinylated cDNA was prepared with the NuGEN Encore Biotin Module following amplifcation with NuGEN Ovation PicoSL WTA System V2 (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from sorted femoral bone marrow cell samples (leukemia cells gated out) lysed in RLT buffer following the protocol from a QIAGEN RNeasy mini kit on a QIACube instrument and included DNase I treatment.

value: SCID mice (CB17/Icr-Prkdcscid )

value: male

value: femoral bone marrow leukocytes

value: 6-8 weeks

tag: experiment #

tag: experiment condition

value: restraint stress+propranolol

tag: replicate #


title: W0: Wild-type seedlings (control)

value: before stressed with PEG


title: 32_2691_2_TimePoint2

description: Sequencing Run Id: 003560

value: wP


title: Other brain tumor Ot2

value: Other brain tumor


title: Other brain tumor Ot1

value: Female


title: Meningioma M28

value: Meningioma


title: 30_2686_5_TimePoint5

description: Sequencing Run Id: 003560

value: 14 days


title: Experiment2 Restraint+Propranolol Rep_2

description:
101036360019_A.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: Experiment2 Restraint Rep_5

description:
101036350051_G.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: restraint stress


title: 3_2685_3_TimePoint3

description: Sequencing Run Id: 003560

value: aP

value: 3 days


title: 31_2691_1_TimePoint1

description: Sequencing Run Id: 003560

value: 0 days

value: PBMC


title: Experiment2 Restraint Rep_4

description:
101036350051_F.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip


title: 29_2686_4_TimePoint4

description: Sequencing Run Id: 003560

value: pertussis antigenic challenge

value: 7 days


title: Meningioma M27

value: Male


title: 28_2686_3_TimePoint3

description: Sequencing Run Id: 003560


title: Meningioma M26


title: Meningioma M25


title: Meningioma M23


title: Meningioma M24


title: Meningioma M22


title: Experiment2 Restraint+Propranolol Rep_1

description:
101036350051_H.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: SCID mice (CB17/Icr-Prkdcscid )

value: male

value: femoral bone marrow leukocytes


title: Experiment2 Restraint Rep_3

description:
101036350051_E.AVG_Signal
Illumina MouseRef-8 v2.0 expression beadchip

value: 6-8 weeks


title: 26_2686_1_TimePoint1

description: Sequencing Run Id: 003560

value: wP


title: Meningioma M21