title: Human Thyroid Organoid c-AMP day23_rep2


title: Projet_Gen3G-Plasma-V1-PubM2159

status: Public on Oct 24 2022

type: SRA

city: Chicoutimi

first: Luigi

last: Bouchard

state: Quebec

address: 305 rue Saint-Vallier, Pavillon des Augustines

department: Biochimie et génomique fonctionnelle

country: Canada

institute: Université de Sherbrooke

library_source: transcriptomic

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with FASTX-Toolkit. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using STAR. As rRNA contamination was almost inexistant in our samples (average of 1.04±0.90% of total mapped reads based on metrics from STAR), the mapping step to the rRNA was removed to speed tup the process.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple sample (PMID : 30956140).
Samples with < 500k miRNAs reads and samples with >25M miRNAs reads were considered outliers and removed from the downstream analysis (differential analysis using DESeq2 package).
DESeq2 function collapseReplicates was used to combined technical replicates in the analysis for data that were extracted and sequenced twice. Technical replicate have the same ID and fastq files contains either "pilote" or "projet". Technical replicate are identified in the technical replicates column (N = 12 originally, 9 gave consent for genetic data sharing)
Assembly: GRCh37
Supplementary files format and content: tab-seperated value files include raw read counts (non-normalized) for each Sample
Supplementary files format and content: Gen3G_Plasma_miRNA_v1_geo_rawcounts.txt

molecule: total RNA

organism: Homo sapiens

source_name: plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from either 500μl of plasma kept at −80 °C until extraction. Seventy-five μl of nuclease-free water was used to eluate total RNA which was then precipitated following the method described by Burgos et al. (PMID: 23525801). Briefly, 35 μl of cold (4°C) 7 M ammonium acetate solution (ThermoFisher Scientific, catalogue # 02002268) were added to 70μl of total RNA. This was followed by the addition of 420μl of chilled (−20°C) absolute ethanol (Commercial Alcohols, ON, Canada; catalogue # P006EAAN) and overnight precipitation at −20°C. The mix was then centrifuged at 16 000g at 4°C for 30 min. RNA pellets were then washed twice with 200 μl of cold 80% ethanol followed by centrifugation at 16 000g at 4°C for 5min. It was then dried for 30min at room temperature and 5μl of nuclease-free water was added. The total volume was used for library preparation.
Samples were randomized before library preparation. An adapted version of the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) protocol from Burgos et al. (PMID: 23525801) was used to manage low concentrated miRNA samples. In this protocol, half of the standard volumes were used for ligation (3′ and 5′ ends) of RNA sample (5μl), reverse transcription, barcoding (index 1-20: one index per sample) and PCR amplification (15 cycles) to preserve the ratio between RNA amount (which is lower in plasma samples) and the reagents. Purification and size-selection (145-160bp) of the libraries were done by migration on a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, catalogue # EC6265BOX) followed by elution in 300 μl of nuclease-free water and overnight incubation at 500 RPM at room temperature on an incubating microplate shaker (VWR, ON, Canada, catalogue #12620-930). The libraries were then precipitated according to the manufacturer's instructions (including incubation of the precipitation mix at −80°C for 30min) and were resus- pended in 25 μl of 10 mM Tris-HCI pH 8.5 buffer. The Agilent 2100 Bioanalyzer and Agilent High Sensitivity DNA Kit (Agilent, Mississauga, ON, Can- ada; catalog # 5067-4626) or the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and a LabChip GX (PerkinElmer, catalog# CLS760672) instrument were used to assess the quality of each library (i.e., concentration, library length and primer dimers absence). Library sequencing, including quality control and sample pooling, was performed at the McGill University and Génome Québec Innovation Centre (Québec, Canada). Librairies were quantified by qPCR and pooled equimolarly (HiSeq 2500: 7pM final molarity; 12 libraries with different indexes per lane; HiSeq 4000: 10pM final molarity; 20 libraries with dif- ferent indexes per lane), before being denatured and clustered on single-read Illumina flow cells (catalog # GD-401-3001 and catalog GD-410-1001) according to the manufacturer’s standard protocol. The libraries were then sequenced on Illumina HiSeq 2500 or HiSeq 4000 sequencing platforms for 50 cycles, with 7 cycles indexing read. Twelve samples were extracted twice and sequenced on both platforms to confirm standardization and platform comparability.

tag: tissue

value: plasma

tag: Sex

value: female

tag: pregnancy status_1

value: Normal


title: Projet_Gen3G-Plasma-V1-PubM2155


title: D28

city: Dublin

first: Eoin

last: Brennan

address: Belfield, Dublin 4

country: Ireland

institute: University College Dublin

description:
Doyle_et_al.Normalized_read_counts.xlsx
D28

data_processing:
Raw transcript reads were aligned to the human genome using Partek Flow Software
Reads were quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files of normalized read counts for each sample.

source_name: Kidney

extract_protocol:
Kidney biopsy tissue was frozen at -80C in RNALater until processing. RNA extracted using E.Z.N.A.® Total RNA Kit I
BGI standard protocol

value: Kidney

tag: source

value: Percutaneous kidney biopsy

tag: age

tag: egfr

value: Female

tag: progressive ckd


title: Projet_Gen3G-Plasma-V1-PubM2161


title: D19

description:
Doyle_et_al.Normalized_read_counts.xlsx
D19

value: Male


title: Projet_Gen3G-Plasma-V1-PubM2154

value: Other pregnancy complications


title: D51

description:
Doyle_et_al.Normalized_read_counts.xlsx
D51


title: Human Thyroid Organoid c-AMP day16_rep1

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Removal of low-quality bases and Illumina adapter sequences were performed using Trimmomatic software (Bolger et al. 2014) and sequence reads were aligned against the human reference genome using HiSat2 software (Kim, 2015). Raw reads were determined with HTSeq software (Anders et al 2015) using the Ensembl genome annotation GRCh38.p13.
Genome_build: GRCh38
Supplementary_files_format_and_content: File containing raw counts per sample.

source_name: hESC-derived differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of NKX2-1/GFP+ alive cells
Ovarion Solo RNA-seq Systems (NuGen)

tag: cell line

tag: time point


title: Human Thyroid Organoid c-AMP day16_rep2


title: Projet_Gen3G-Plasma-V1-PubM2149


title: Projet_Gen3G-Plasma-V1-PubM2145


title: D11

description:
Doyle_et_al.Normalized_read_counts.xlsx
D11


title: Projet_Gen3G-Plasma-V1-PubM2142


title: dnmt3aa, 2dpf, rep3

type: RNA

city: Obu

first: Nobuyoshi

last: Shimoda

state: Aichi

address: Morioka 7-430

department: Research Core Facility

country: Japan

institute: National Institute for Geriatrics and Gerontology

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions.  On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to D. rerio (Zebrafish) Oligo Microarray V3 (Design ID: Agilent-026437) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor.  Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Danio rerio

source_name: dnmt3aa, 2 dpf, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: To extract total RNA from zebrafish embryos, pools of 20 live embryos were homogenized in 800 ul TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) using a homogenizer (IKA T10 basic, IKA-Werke GmbH & Co.KG, Staufen, Germany).  Extracted RNA was then purified by a RNeasy Mini kit (QIAGEN, Hilden, Germany).  The quantity and quality of total RNA were measured by an Agilent RNA 6000 Nano Kit (Agilent).  RIN values for all RNA samples were higher than 9.0.

tag: developmental stage

value: 2 days postfertilization (dpf)

tag: genotype


title: D9

description:
Doyle_et_al.Normalized_read_counts.xlsx
D9


title: Projet_Gen3G-Plasma-V1-PubM2141

value: Gestational diabetes mellitus

tag: pregnancy status_2


title: dnmt3aa, 2dpf, rep1

source_name: dnmt3aa, 2 dpf, replicate 1


title: dnmt3aa, 2dpf, rep2

source_name: dnmt3aa, 2 dpf, replicate 2


title: D23

description:
Doyle_et_al.Normalized_read_counts.xlsx
D23


title: Human Thyroid Organoid c-AMP day23_rep1


title: dnmt3bb.2, 2dpf, rep2

source_name: dnmt3bb.2, 2 dpf, replicate 2


title: dnmt3bb.2, 2dpf, rep3

source_name: dnmt3bb.2, 2 dpf, replicate 3


title: rad6E49K-3V5 input  repeat 2

city: Salt Lake City

first: Mahesh

middle: B

last: Chandrasekharan

state: UT

address: 2000 Circle of Hope Room 4343

department: Radiation Oncology

country: USA

institute: University of Utah SOM

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6E49K-3V5, TRP CEN
E49K-Bre1_control.lambda_control.bw

library_source: genomic

data_processing:
Fastq files were aligned sequentially to two separate genome indices using Novocraft Novoalign (version 3.08.02), allowing for one random alignment for multimapping reads. Adapter sequences were given to Novoalign for trimming during alignment. The first index is to Saccharomyces cerevisiae genome. The second index is to Candida glabrata.
Non-orthologous best alignments to each genome were identifed using cross_species_alignment_picker (https://github.com/tjparnell/HCI-Scripts/blob/master/BamFile/cross_species_alignment_picker.pl)
Alignments were processed together with MultiRepMacsChIPSeq wrapper package (https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq, version 11.1). Alignments to high copy regions, including mtDNA, telomeres, rRNA and tRNA genes, were excluded. Alignments were extended by 150 bp to represent fragment size. Fragment coverage was scaled by the fraction of Candida alignments per million. Coordinate duplicate alignments were removed, allowing a maximum of one. Replicates were depth-normalized to Reads Per Million before taking the mean. Macs2 parameters for lambda control normalization used 500 bp for Small lambda and 5000 bp for Large lambda. Fold enrichment of ChIP fragment pileup over lambda control were generated as log2 bigWig files.
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig files representing depth-normalized (Reads Per Million), replicate-mean fragment pileup coverage (ChIP) or calculated lambda control reference coverage (Input).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Sonicated soluble chromatin

growth_protocol: Yeast were grown in synthetic omission medium without tryptophan at 30°C with constant shaking at 225 rpm to an OD A600  of 0.8-1.0.

extract_protocol:
S. cerevisiae strain YZS375 transformed with pMC6-based constructs to express either Rad6-3V5 or the mutants (rad6-P43L-3V5, rad6-E49K-3V5 or rad6-P47T-3V5) or strain YZS413 (bre1Δ) transformed with vector pRS314 were grown in –TRP medium to mid-log phase, and cross-linked with 1% formaldehyde (Sigma) for 20 min at room temperature. Crosslinking of cells was stopped by adding glycine (0.125M) and washed once with PBS. Multiple aliquots of 100 x 107 cross-linked cells were harvested. For the reference or spike-in genome, C. glabrata transformed with pMC8 was grown in YPAD medium supplemented with cloNAT (100 µg/ml), subjected to formaldehyde crosslinking as described above and aliquots of 20 x 107 cells were harvested. Cross-linked S. cerevisiae (100 x 107) and C. glabrata (20 x 107) cells were combined prior to spheroplasting, followed by nuclei isolation and chromatin preparation as previously described. Briefly, nuclei were resuspended in FA140 buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 140 mM NaCl) and sonicated in Diagenode Bioruptor® Pico for 30 min (60 cycles of 30 sec ON and 30 sec OFF). After centrifugation (13,200 rpm, 15 min at 4°C), an aliquot of the dialysate (25 μl) was set aside for isolating input DNA. Prior to immunoprecipitation, chromatin was precleared with 50μl Protein A or Protein G Dynabeads (Invitrogen) blocked with bovine serum albumin and fish skin gelatin. Pre-cleared chromatin was then combined with anti-V5 antibody (15 μl; Bio-Rad, Catalog No. MCA1360) or custom anti-Bre1 antibody (15 μl), incubated overnight at 4°C with end-over-end rotation. The immune-complex was captured by adding 50 μl Protein A or Protein G Dynabeads and incubating for an additional 2.5 h. Bead-bound complexes were then washed sequentially for 5 min each with end-over-end rotation at 4°C with FA buffer+140 mM NaCl (3 washes), FA buffer+1000 mM NaCl (2 washes), FA buffer+500 mM NaCl (2 washes), and one wash each with LiCl/NP40 buffer (10 mM Tris.Cl, pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% sodium deoxycholate) and TE (10 mM Tris.Cl, pH 8.0, 1 mM EDTA). Elution, reverse crosslinking of ChIP and input DNA, and enzymatic digestion to remove RNA or protein were performed as described. Library construction was performed using NEBNext Multiplex Oligos (Index Primers Set 1 or Set2) and NEBNext ChIP-seq Library Prep Reagent Set for Illumina prior to 50 bp single-end sequencing using Illumina Hiseq2500
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina
NEB's Index Primer Set1 and Primer Set 2

tag: strain

value: YZS375 rad6E49K-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6E49K-3V5, TRP CEN


title: rad6p47T-3V5 input  repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMXrad6P47T-3V5, TRP CEN
P47T-Bre1_control.lambda_control.bw

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMXrad6P47T-3V5, TRP CEN


title: wt, 2dpf, rep3

source_name: wt, 2 dpf, replicate 3

value: wild-type


title: Projet_Gen3G-Plasma-V1-PubM2135


title: wt, 2dpf, rep2

source_name: wt, 2 dpf, replicate 2


title: D35

description:
Doyle_et_al.Normalized_read_counts.xlsx
D35


title: Rad6-3V5 input  repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX Rad6-3V5, TRP CEN
RAD6WT-Bre1_control.lambda_control.bw

value: YZS375 RAD6-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX Rad6-3V5, TRP CEN


title: rad6P43L-3V5 input  repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P43L-3V5, TRP CEN
P43L-Bre1_control.lambda_control.bw

value: YZS375 rad6P43L-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN


title: BC51

city: Nanning

first: Zhenxing

last: Wang

state: Guangxi

address: Zhongshan Street

department: Center for Genomic and Personalized Medicine

country: China

institute: Guangxi Medicla University

data_processing:
RNA-seq analysis was carried out by Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).
The quality control of the raw sequencing data, including the purity and quantity of RNA and RNA integrity number (RIN) values, was appraised by adopting FastQC software.
After pretreatment using Fastp software, the filtered data were compared with the human reference genome (HG19) using HISAT2 (Pertea et al., 2016) and StringTie software (Pertea et al., 2015) with the default mapping parameters before merged the data by Cufflinks software (Ghosh and Chan, 2016).
The genes complyed with P < 0.05 and |fold change|> 2 were considered to be the differential genes (DEGs)
The differentially expressed genes were annotated based on the Gene Ontology (GO) database and the outcome was described by GOplot.
Assembly: hg19
Supplementary files format and content: The excel file includes the RPKM value for each Sample

source_name: bladder cancer

extract_protocol:
Total RNA  was extracted with Trizol reagent (Life Technologies Corporation, Carlsbad, CA, USA).
RNA-seq library was constructed in line with the instruction of the Illumina TruSeq RNA Sample Preparation Kit (Illumina)

value: bladder cancer

tag: tp53 signture_score

tag: tp53 signture_group

value: High

tag: tp53 mutation

tag: overall survival(month)

tag: survival state

tag: gender

value: Old

tag: tumor size

value: Large

tag: grade

value: HG

tag: tobacco smoking_history

value: No

tag: lymph node_metastasis


title: wt, 2dpf, rep1

source_name: wt, 2 dpf, replicate 1

value: 2 days postfertilization (dpf)


title: bre1Δ input repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ bre1Δ::KanMX pRS314 TRP CEN
bre1d-Bre1_control.lambda_control.bw

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN


title: BC52

tag: tissue

value: Low

value: Male

tag: age

value: Small

value: Yes


title: Projet_Gen3G-Plasma-V1-PubM2131

value: plasma

tag: Sex

value: female

tag: pregnancy status_1

value: Normal


title: dnmt3bb.2, 2dpf, rep1

source_name: dnmt3bb.2, 2 dpf, replicate 1

tag: developmental stage

tag: genotype


title: Projet_Gen3G-Plasma-V1-PubM2127


title: BC48

value: unknown

value: LG


title: Projet_Gen3G-Plasma-V1-PubM2165


title: rad6p47T-3V5 V5 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMXrad6P47T-3V5, TRP CEN
P47T-v5.fragment.bw

tag: strain

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMXrad6P47T-3V5, TRP CEN

tag: chip antibody

value: anti-V5 MCA1360


title: dnmt3aa, 1dpf, rep3

source_name: dnmt3aa, 1 dpf, replicate 3

value: 1 day postfertilization (dpf)


title: dnmt3aa, 1dpf, rep2

source_name: dnmt3aa, 1 dpf, replicate 2


title: BC50

value: bladder cancer

tag: tp53 signture_score

tag: tp53 signture_group

value: Old

value: Large

value: HG


title: BC47

value: Low

tag: tp53 mutation

tag: overall survival(month)


title: Projet_Gen3G-Plasma-V1-PubM2117


title: dnmt3aa, 1dpf, rep1

source_name: dnmt3aa, 1 dpf, replicate 1


title: Projet_Gen3G-Plasma-V1-PubM2121

source_name: plasma


title: Rad6-3V5 V5 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX Rad6-3V5, TRP CEN
RAD6WT-v5.fragment.bw

value: YZS375 RAD6-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX Rad6-3V5, TRP CEN


title: BC46

tag: survival state

tag: gender

value: Male

value: Young

value: Small

value: Yes

value: No


title: bre1Δ V5 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ bre1Δ::KanMX pRS314 TRP CEN
bre1d-v5.fragment.bw

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN


title: BC49

value: High

tag: tumor size

tag: grade


title: Projet_Gen3G-Plasma-V1-PubM2120

value: plasma

value: female

value: Normal


title: BC45

value: bladder cancer

tag: tobacco smoking_history

tag: lymph node_metastasis


title: rad6P43L-3V5 V5 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P43L-3V5, TRP CEN
P43L-v5.fragment.bw

value: YZS375 rad6P43L-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN

value: anti-V5 MCA1360


title: dnmt3bb.2, 1dpf, rep1

source_name: dnmt3bb.2, 1 dpf, replicate 1

value: 1 day postfertilization (dpf)


title: wt, 1dpf, rep3

source_name: wt, 1 dpf, replicate 3

value: wild-type


title: rad6p47T-3V5 Bre1 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMXrad6P47T-3V5, TRP CEN
P47T-Bre1.fragment.bw

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMXrad6P47T-3V5, TRP CEN


title: dnmt3bb.2, 1dpf, rep3

source_name: dnmt3bb.2, 1 dpf, replicate 3


title: rad6E49K-3V5 Bre1 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6E49K-3V5, TRP CEN
E49K-Bre1.fragment.bw

value: YZS375 rad6E49K-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6E49K-3V5, TRP CEN


title: Projet_Gen3G-Plasma-V1-PubM2108

tag: tissue


title: wt, 1dpf, rep1

source_name: wt, 1 dpf, replicate 1


title: rad6E49K-3V5 V5 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6E49K-3V5, TRP CEN
E49K-v5.fragment.bw


title: Projet_Gen3G-Plasma-V1-PubM2115

tag: Sex


title: Projet_Gen3G-Plasma-V1-PubM2101

tag: pregnancy status_1


title: Projet_Gen3G-Plasma-V1-PubM2112


title: BC39

value: Low

value: Female

tag: age

value: Old

value: Small

value: HG


title: dnmt3aa, 5-somite, rep1

source_name: dnmt3aa, 5 somite, replicate 1

tag: developmental stage

value: 5 somite

tag: genotype


title: rad6P43L-3V5 input  repeat 1

tag: strain


title: wt, 1dpf, rep2

source_name: wt, 1 dpf, replicate 2


title: rad6E49K-3V5 input  repeat 1


title: bre1Δ Bre1 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ bre1Δ::KanMX pRS314 TRP CEN
bre1d-Bre1.fragment.bw

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN

tag: chip antibody


title: BC44

value: bladder cancer

tag: tp53 signture_score

tag: tp53 signture_group

value: High

value: Male

value: Large

value: Yes

value: No


title: rad6P43L-3V5 Bre1 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P43L-3V5, TRP CEN
P43L-Bre1.fragment.bw

value: YZS375 rad6P43L-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN


title: dnmt3bb.2, 5-somite, rep3

source_name: dnmt3bb.2, 5 somite, replicate 3


title: dnmt3bb.2, 1dpf, rep2

source_name: dnmt3bb.2, 1 dpf, replicate 2

value: 1 day postfertilization (dpf)


title: BC38

tag: tp53 mutation

tag: overall survival(month)

value: unknown


title: dnmt3aa, 5-somite, rep3

source_name: dnmt3aa, 5 somite, replicate 3


title: Projet_Gen3G-Plasma-V1-PubM2118

value: plasma

value: female

value: Normal


title: BC43

value: Low

tag: survival state

tag: gender

value: Old

value: Small


title: Projet_Gen3G-Plasma-V1-PubM2107

value: Gestational diabetes mellitus


title: Rad6-3V5 Bre1 ChIP repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX Rad6-3V5, TRP CEN
RAD6WT-Bre1.fragment.bw

source_name: Sonicated soluble chromatin

value: YZS375 RAD6-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX Rad6-3V5, TRP CEN


title: Projet_Gen3G-Plasma-V1-PubM2098

value: Other pregnancy complications


title: BC37

source_name: bladder cancer

value: bladder cancer

value: High

value: Male

value: Young

tag: tumor size

value: Large

tag: grade

value: LG


title: BC42

value: HG

tag: tobacco smoking_history

value: No

tag: lymph node_metastasis


title: Projet_Gen3G-Plasma-V1-PubM2105

tag: tissue

value: plasma

tag: Sex

value: female


title: dnmt3aa, 5-somite, rep2

source_name: dnmt3aa, 5 somite, replicate 2

value: 5 somite


title: rad6p47T-3V5 input  repeat 1

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMXrad6P47T-3V5, TRP CEN


title: Projet_Gen3G-Plasma-V1-PubM2102

tag: pregnancy status_1

value: Normal


title: BC41

tag: age

value: Old

value: unknown


title: BC40

value: Female


title: Projet_Gen3G-Plasma-V1-PubM2092


title: BC36

value: bladder cancer

value: Yes


title: bre1Δ input repeat 1

tag: genotype

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN


title: BC34

value: High

value: Male

value: Small


title: Projet_Gen3G-Plasma-V1-PubM2100


title: Projet_Gen3G-Plasma-V1-PubM2088


title: BC33

value: LG


title: dnmt3bb.2, 5-somite, rep2

source_name: dnmt3bb.2, 5 somite, replicate 2

tag: developmental stage


title: Rad6-3V5 input  repeat 1

tag: strain

value: YZS375 RAD6-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX Rad6-3V5, TRP CEN


title: dnmt3bb.2, 5-somite, rep1

source_name: dnmt3bb.2, 5 somite, replicate 1


title: Projet_Gen3G-Plasma-V1-PubM2083

value: plasma

value: female


title: Projet_Gen3G-Plasma-V1-PubM2091


title: wt, 5-somite, rep3

source_name: wt, 5 somite, replicate 3

value: 5 somite

value: wild-type


title: rad6p47T-3V5 V5 ChIP repeat 1

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMXrad6P47T-3V5, TRP CEN

tag: chip antibody

value: anti-V5 MCA1360


title: Projet_Gen3G-Plasma-V1-PubM2089

value: Other pregnancy complications


title: Rad6-3V5 V5 ChIP repeat 1


title: BC35

value: bladder cancer

tag: tp53 signture_score

tag: tp53 signture_group

value: Young

value: HG

value: No


title: Projet_Gen3G-Plasma-V1-PubM2081

value: Normal


title: BC30

value: High

tag: tp53 mutation

tag: overall survival(month)

value: Male

value: unknown


title: rad6E49K-3V5 V5 ChIP repeat 1

value: YZS375 rad6E49K-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6E49K-3V5, TRP CEN


title: bre1Δ V5 ChIP repeat 1

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN


title: rad6P43L-3V5 V5 ChIP repeat 1

value: YZS375 rad6P43L-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN


title: dnmt3bb.2, shield, rep3

source_name: dnmt3bb.2, shield, replicate 3

value: shield


title: Projet_Gen3G-Plasma-V1-PubM2084

source_name: plasma

value: plasma

value: female


title: BC32

value: Low

tag: survival state

tag: gender

value: Old

value: Small

value: Yes


title: BC28

value: bladder cancer

tag: tumor size

tag: grade

value: HG


title: BC31

value: High

value: Large

tag: tobacco smoking_history

value: No

tag: lymph node_metastasis


title: dnmt3aa, shield, rep3

source_name: dnmt3aa, shield, replicate 3


title: dnmt3bb.2, shield, rep2

source_name: dnmt3bb.2, shield, replicate 2


title: dnmt3bb.2, shield, rep1

source_name: dnmt3bb.2, shield, replicate 1


title: dnmt3aa, shield, rep2

source_name: dnmt3aa, shield, replicate 2


title: Rad6-3V5 Bre1 ChIP repeat 1

value: YZS375 RAD6-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX Rad6-3V5, TRP CEN


title: wt, 5-somite, rep2

source_name: wt, 5 somite, replicate 2

value: 5 somite

value: wild-type


title: dnmt3aa, shield, rep1

source_name: dnmt3aa, shield, replicate 1


title: rad6P43L-3V5 Bre1 ChIP repeat 1

value: YZS375 rad6P43L-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN


title: Projet_Gen3G-Plasma-V1-PubM2073

tag: tissue

value: plasma

tag: Sex

value: Normal


title: Projet_Gen3G-Plasma-V1-PubM2078

value: female

tag: pregnancy status_1


title: BC29

value: Male

tag: age

value: Young

value: LG


title: Projet_Gen3G-Plasma-V1-PubM2077


title: rad6E49K-3V5 Bre1 ChIP repeat 1

value: YZS375 rad6E49K-3V5

tag: genotype

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6E49K-3V5, TRP CEN


title: BC26

value: bladder cancer

value: Low

value: unknown

value: HG


title: Projet_Gen3G-Plasma-V1-PubM2074


title: BC27

value: Old

value: Large

value: No

value: Yes


title: wt, shield, rep2

source_name: wt, shield, replicate 2

tag: developmental stage

value: shield

value: wild-type


title: rad6E49K-3V5 repeat 3

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6E49K-3V5, TRP CEN
15050X18

data_processing:
Fastq files were trimmed of adapter sequences using Cutadapt (v. 1.16) with options -O 6 and -m 20.
Fastq files were aligned to the genome with STAR (version 2.6.1b) in basic two pass mode, with options --alignIntronMax 1100 and --alignMatesGapMax 2000.
Alignments were counted to genes with Subread featureCounts (version 1.6.3) with options -p -s 2 --largestOverlap using a SacCer3 R64-1-1 annotation file with UTRs added.
Gene with counts less than 5 alignments were removed prior to analysis with DESeq2 (version 1.20) using genotype as the condition model.
Genome_build: SacCer3 R64
Supplementary_files_format_and_content: Excel file containing the featureCount raw counts and DESeq2 regularized log2 count data for genes.

molecule: polyA RNA

source_name: Total RNA

extract_protocol:
Total RNA was isolated using the acid-phenol method. Yeast cells were grown to OD600nm 0.7 and harvested (10.5 X 107), washed with RNase-free water and stored at -80°C. Frozen cells were resuspended in 0.3 ml TES buffer (10 mM Tris.Cl pH 7.5, 10 mM EDTA, 0.5% SDS), combined with equal volume of Phenol pH 4.3 (Thermo Scientific) and incubated at 65°C for 1h with agitation (140 rpm) in a Thermomixer (Eppendorf). The lysate was cooled on ice for 10 min and centrifuged (13200 rpm, 10 min at 4°C). Supernatant (0.25 ml) was combined with equal volume of 25:24:1 Phenol-choloroform-isoamyl alcohol pH 4.3 (Thermo Scientific), mixed well by vortexing and end-over-end rotation for 10 min at 4°C, and centrifuged (13200 rpm, 10 min at 4°C). Supernatant (0.2 ml) was overlaid onto 0.8 ml 5.7M CsCl (Sigma) and centrifuged in a Beckman Optima Tabletop Ultracentrifuge with MLA-130 rotor (30000 rpm, 18h at 4°C). The pellet was dissolved in 0.2 ml RNase-free TE pH 7.0 (Ambion) by incubating for 1h at 4°C, before precipitation using ethanol and sodium acetate pH 4.3 (Ambion) and centrifuged (13200 rpm, 20 min at 4°C). The pellet was washed with 70% ethanol, dried and dissolved in 0.1X TE. Equal amount of RNA (50 μg) was further purified using Qiagen RNeasy Mini Kit by following the manufacturer’s recommendations. Purified RNA was used in library preparation with Illumina TruSeq HT Stranded mRNA Library Preparation Kit with PolyA Selection. For RNA isolated from strains DHY217 and YMC203, Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold rRNA Removal Kit Yeast was used. The libraries were subjected to 50 bp single-read sequencing in HiSeq 2500. Three independent RNA isolates from each yeast strain were sequenced.
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries with dual index adapters were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2103).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.
RNA-seq: llumina TruSeq HT stranded mRNA library preparation with Poly A selection to facilitate the use of dual index. Illumina TruSeq Stranded total RNA with Ribo-Zero Yeast protocol was followed for library preparation

tag: strain


title: wt, shield, rep1

source_name: wt, shield, replicate 1


title: wt, shield, rep3

source_name: wt, shield, replicate 3


title: Projet_Gen3G-Plasma-V1-PubM2069

value: plasma

value: Normal


title: BC23

source_name: bladder cancer

tag: tp53 signture_score

value: Male


title: rad6E49K-3V5 repeat 1

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6E49K-3V5, TRP CEN
15050X16


title: dnmt3aa, 1~2-cell, rep2

source_name: dnmt3aa, 1~2-cell, replicate 2

value: 1-cell to 2-cell


title: Projet_Gen3G-Plasma-V1-PubM2064

value: female


title: bre1Δ Bre1 ChIP repeat 1

source_name: Sonicated soluble chromatin

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN

tag: chip antibody


title: rad6P47T-3V5 repeat 3

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P47T-3V5, TRP CEN
15050X15

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P47T-3V5, TRP CEN


title: BC24

value: bladder cancer

tag: tp53 signture_group

value: Low

tag: tp53 mutation


title: rad6P47T-3V5 repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P47T-3V5, TRP CEN
15050X14


title: dnmt3aa, 1~2-cell, rep3

source_name: dnmt3aa, 1~2-cell, replicate 3


title: Projet_Gen3G-Plasma-V1-PubM2065


title: Projet_Gen3G-Plasma-V1-PubM2071


title: BC25

tag: overall survival(month)

tag: survival state

value: HG


title: Projet_Gen3G-Plasma-V1-PubM2063


title: rad6E49K-3V5 repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6E49K-3V5, TRP CEN
15050X17

value: YZS375 rad6E49K-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6E49K-3V5, TRP CEN


title: Projet_Gen3G-Plasma-V1-PubM2062


title: BC21

value: High

tag: gender

value: Female

value: Old

tag: tumor size

value: unknown

value: No


title: dnmt3bb.2, 1~2-cell, rep3

source_name: dnmt3bb.2, 1~2-cell, replicate 3


title: BC20

value: Large

tag: grade

tag: tobacco smoking_history

value: Yes


title: rad6P47T-3V5 repeat 1

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P47T-3V5, TRP CEN
15050X13


title: dnmt3bb.2, 1~2-cell, rep2

source_name: dnmt3bb.2, 1~2-cell, replicate 2

value: 1-cell to 2-cell


title: wt, 5-somite, rep1

source_name: wt, 5 somite, replicate 1

value: 5 somite

value: wild-type


title: Projet_Gen3G-Plasma-V1-PubM2053

source_name: plasma

tag: tissue

value: plasma

value: female

value: Normal


title: rad6P43L-3V5 repeat 2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P43L-3V5, TRP CEN
15050X11

value: YZS375 rad6P43L-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN


title: wt, 1~2-cell, rep3

source_name: wt, 1~2-cell, replicate 3


title: Projet_Gen3G-Plasma-V1-PubM2056

tag: Sex


title: BC19

value: bladder cancer

value: Male

tag: lymph node_metastasis


title: BC16

value: High

tag: age

value: Small

value: HG


title: Projet_Gen3G-Plasma-V1-PubM2052

tag: pregnancy status_1


title: dnmt3bb.2, 1~2-cell, rep1

source_name: dnmt3bb.2, 1~2-cell, replicate 1

tag: developmental stage

tag: genotype


title: BC22

tag: tp53 signture_score

value: Low

value: Old

value: unknown


title: BC18

value: Young

value: Large

value: Yes


title: bre1Δ repeat2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ bre1Δ::KanMX pRS314 TRP CEN
15050X8

tag: strain

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN


title: wt, 1~2-cell, rep2

source_name: wt, 1~2-cell, replicate 2

value: 1-cell to 2-cell

value: wild-type


title: BC17

tag: tp53 signture_group

value: No


title: rad6P43L-3V5 repeat 1

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P43L-3V5, TRP CEN
15050X10

value: YZS375 rad6P43L-3V5


title: bre1Δ repeat3

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ bre1Δ::KanMX pRS314 TRP CEN
15050X9


title: wt, 1~2-cell, rep1

source_name: wt, 1~2-cell, replicate 1


title: rad6p47T-3V5 Bre1 ChIP repeat 1

value: YZS375 rad6P47T-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMXrad6P47T-3V5, TRP CEN

tag: chip antibody


title: dnmt3aa, 1~2-cell, rep1

source_name: dnmt3aa, 1~2-cell, replicate 1


title: rad6P43L-3V5 repeat 3

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX rad6P43L-3V5, TRP CEN
15050X12

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX rad6P43L-3V5, TRP CEN


title: LysM-Cre;Rosa26-Runx1tg3_Day5_MCSF

city: Atlanta

first: Mohd

middle: Nazir

last: Khan

state: GA

address: 21 Ortho Lane

department: Orthopaedics

institute: Emory University

description: Osteoclast differentiation

data_processing:
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Clean reads were mapped to mouse reference genome (GRCm39) using STAR alignment.
Read count extraction and normalization were performed using DESeq2 method.
Pairwise gene expression levels were calculated using fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) value
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Mus musculus

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow was isolated from long bones by flushing in α-MEM (10% fetal bovine serum [FBS], 1× penicillin-streptomycin) and erythrocytes were lysed using RBC lysis buffer. Cells were plated on a petri dish to expand bone marrow macrophages which were used for osteoclast differentiation.

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen). 250 ng of total RNA was used for the generation of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Osteoclast differentiation was done in 48-well plate at aseeding density of BMMs (15 000 cells/well) and trated with osteoclast media. Media was every 2 days.
Osteoclast media consist of α-MEM supplemented with 10% FBS, 1× penicillin-streptomycin, 30 ng/mL M-CSF and 50 ng/mL RANKL (R&D Systems)

tag: cell line

value: Bone marrow derived macrophage

tag: cell type

value: Osteoclasts

value: Runx1 over expression

tag: time

value: Day 5

tag: treatment

value: MCSF


title: Projet_Gen3G-Plasma-V1-PubM2048

value: plasma

value: female

value: Normal


title: LysM-Cre;Rosa26-Runx1tg3_Day5_MCSF_RANKL

description: Osteoclast differentiation


title: LysM-Cre;Rosa26-Runx1tg3_Day3_MCSF_RANKL

description: Osteoclast differentiation

value: Day 3


title: LysM-Cre;Rosa26-Runx1tg2_Day5_MCSF_RANKL

description: Osteoclast differentiation


title: Projet_Gen3G-Plasma-V1-PubM2038


title: BC15

value: bladder cancer

value: Low

tag: tp53 mutation

tag: overall survival(month)

tag: survival state

tag: gender

value: Male

value: Old

tag: tumor size

value: Large

tag: grade

value: HG

value: Yes


title: rad6Δ repeat2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX pRS314 TRP CEN
15050X5

source_name: Total RNA

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX pRS314 TRP CEN


title: bre1Δ repeat1

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ bre1Δ::KanMX pRS314 TRP CEN
15050X7

value: Mat a ura3-52 leu2-3,112 his3 trp1delta bre1delta::KanMX pRS314 TRP CEN


title: Projet_Gen3G-Plasma-V1-PubM2046

tag: tissue

tag: Sex

tag: pregnancy status_1


title: LysM-Cre;Rosa26-Runx1tg3_Day3_MCSF

description: Osteoclast differentiation

value: Bone marrow derived macrophage

value: Osteoclasts

tag: genotype


title: BC14

tag: tp53 signture_score

value: Female

tag: age

tag: tobacco smoking_history

value: No

tag: lymph node_metastasis


title: BC11

tag: tp53 signture_group

value: High


title: LysM-Cre;Rosa26-Runx1tg2_Day5_MCSF

description: Osteoclast differentiation

tag: cell line

tag: cell type

value: Runx1 over expression

tag: time

value: Day 5

value: MCSF


title: BC13

value: bladder cancer

tag: tp53 mutation

tag: overall survival(month)


title: Projet_Gen3G-Plasma-V1-PubM2040

value: plasma

value: female

value: Normal


title: rad6Δ repeat1

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX pRS314 TRP CEN
15050X4

tag: strain


title: Projet_Gen3G-Plasma-V1-PubM2033


title: rad6Δ repeat3

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX pRS314 TRP CEN
15050X6


title: Projet_Gen3G-Plasma-V1-PubM2034


title: LysM-Cre;Rosa26-Runx1tg2_Day3_MCSF_RANKL

description: Osteoclast differentiation

value: Day 3

tag: treatment


title: BC12

tag: survival state

tag: gender

value: Male

value: Old

tag: tumor size

value: unknown

tag: grade

value: HG


title: LysM-Cre;Rosa26-Runx1tg2_Day3_MCSF

description: Osteoclast differentiation

value: Bone marrow derived macrophage

tag: genotype


title: Rad6-3V5 repeat2

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX Rad6-3V5, TRP CEN
15050X2

value: YZS375 RAD6-3V5

value: Mat a ura3-52 leu2-3,112 his3 trp1delta rad6delta::KanMX Rad6-3V5, TRP CEN


title: Rad6-3V5 repeat3

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX Rad6-3V5, TRP CEN
15050X3


title: Projet_Gen3G-Plasma-V1-PubM2032

tag: tissue

tag: Sex

tag: pregnancy status_1


title: BC9

tag: tp53 signture_score

value: Low

tag: age

value: Large

tag: tobacco smoking_history

value: No

tag: lymph node_metastasis

value: Yes


title: BC10

tag: tp53 signture_group

value: High


title: Projet_Gen3G-Plasma-V1-PubM2030


title: LysM-Cre;Rosa26-Runx1tg1_Day5_MCSF

description: Osteoclast differentiation

tag: cell line

tag: cell type

value: Osteoclasts

value: Runx1 over expression

tag: time

value: Day 5

value: MCSF


title: Projet_Gen3G-Plasma-V1-PubM2029

value: plasma

value: female

value: Normal


title: Rad6-3V5 repeat1

description:
Mat a ura3-52 leu2-3,112 his3 trp1Δ rad6Δ::KanMX Rad6-3V5, TRP CEN
15050X1

tag: strain


title: LysM-Cre;Rosa26-Runx1tg1_Day3_MCSF_RANKL

description: Osteoclast differentiation

value: Day 3

tag: treatment


title: BC8

value: bladder cancer

tag: tp53 mutation

tag: overall survival(month)

tag: survival state

tag: gender

value: Female

value: Old

value: unknown


title: BC7

tag: tissue

value: Male

tag: tumor size

tag: grade

value: HG


title: Projet_Gen3G-Plasma-V1-PubM2022

tag: Sex

tag: pregnancy status_1


title: Projet_Gen3G-Plasma-V1-PubM2021


title: Rosa26-Runx1tg3_Day5_MCSF

description: Osteoclast differentiation

value: Bone marrow derived macrophage

tag: genotype

value: Wild type control


title: LysM-Cre;Rosa26-Runx1tg1_Day3_MCSF

description: Osteoclast differentiation


title: BC6

tag: tp53 signture_score

value: High

tag: age

value: LG

tag: tobacco smoking_history

value: Yes

tag: lymph node_metastasis

value: No


title: Rosa26-Runx1tg3_Day5_MCSF_RANKL

description: Osteoclast differentiation

tag: cell line

tag: cell type

value: Osteoclasts

tag: time

value: Day 5


title: BC4

tag: tp53 signture_group

value: Low

tag: tp53 mutation


title: BC5

tag: overall survival(month)

tag: survival state

value: Young

value: Large


title: Projet_Gen3G-Plasma-V1-PubM2018

tag: tissue

value: plasma

value: female

value: Normal


title: Projet_Gen3G-Plasma-V1-PubM2019

value: Other pregnancy complications


title: Projet_Gen3G-Plasma-V1-PubM2016

value: Gestational diabetes mellitus


title: LysM-Cre;Rosa26-Runx1tg1_Day5_MCSF_RANKL

description: Osteoclast differentiation

value: Runx1 over expression

tag: treatment


title: Rosa26-Runx1tg3_Day3_MCSF_RANKL

description: Osteoclast differentiation

value: Bone marrow derived macrophage

value: Day 3


title: Projet_Gen3G-Plasma-V1-PubM2012

tag: replicate

value: technical replicate


title: Rosa26-Runx1tg3_Day3_MCSF

description: Osteoclast differentiation

value: Wild type control

value: MCSF


title: BC3

value: bladder cancer

tag: gender

value: Female

value: Old

tag: tumor size

value: Small

tag: grade

value: HG

value: No


title: BC2

tag: tp53 signture_score

value: High

value: Male

value: Young

value: Yes


title: Rosa26-Runx1tg2_Day5_MCSF_RANKL

description: Osteoclast differentiation

value: Osteoclasts

tag: genotype

value: Day 5


title: Projet_Gen3G-Plasma-V1-PubM2008

value: plasma

tag: Sex

value: female

tag: pregnancy status_1

value: Gestational diabetes mellitus


title: BC1

value: Low

tag: age

value: unknown

tag: tobacco smoking_history

tag: lymph node_metastasis


title: Rosa26-Runx1tg2_Day3_MCSF_RANKL

description: Osteoclast differentiation

tag: cell line

value: Bone marrow derived macrophage

tag: cell type

value: Wild type control

tag: time

value: Day 3


title: Projet_Gen3G-Plasma-V1-PubM2006

value: Normal


title: MDMs HP 8 h biol rep 3

city: Marburg

first: Ho Ryun

last: Chung

address: Hans-Meerwein-Straße 6

department: Institute for Medical Bioinformatics and Biostatistics

country: Germany

institute: Philipps University of Marburg

data_processing:
Reads were mapped using salmon 1.3.0 in the quant mode with the options i ,l, SF, validateMappings and noLengthCorrection. A custom index was used to discriminate between human, Drosophila, and ERCC reads.
BAM files were sorted and indices were generated with samtools.
Differential gene expression was determined in R with the tximeta, SummarizedExperiment, and DESeq2 packages. The R script is available for download in this dataset.
Assembly: hg38, BDGP6.28
Supplementary files format and content: SF: salmon quantification file
Supplementary files format and content: TSV: tab-separated file

source_name: blood

extract_protocol:
3-5*10^5 MDMs were washed once with PBS. Trifast reagent (Peqlab) was added to the cells together with an amount of 10% of Drosophila Schneider S2 cells relative to MDMs; total TRIfast volume was 500 µl. The pellet was fully resuspended and incubated for 5 min at RT in an 1.5 ml Eppendorf tube. 100 µl of chloroform were added, and the tube was shaken by hand for 15 s. After 3 min of incubation at RT, the tube was centrifuged at 12.000g at 4 degrees centigrade. The upper phase was transferred to a fresh tube, and 2 µl of Glycoblue (Thermo Fisher Scientific) were added followed by 250 µl of isopropanol. After mixing by shaking, the sample was incubated for 10 min at RT followed by centrifugation at 12.000g at 4 degrees centigrade. The supernatant was discarded, and the pellet was washed with 500 µl of 70% (v/v) ethanol. The supernatant was discarded, the pellet was air-dried and subsequently dissolved in 40 µl of water supplemented with 20 U of SUPERase-In RNase inhibitor (Thermo Fisher Scientific). A synthetic ERCC RNA spike-in mix (Thermo Fisher Scientific) was added to the sample according to the manufactur
The QuantSeq FWD Kit (Lexogen) was used according to the manufacturer’s instructions.

value: blood

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: HP 8 h


title: Projet_Gen3G-Plasma-V1-PubM2003


title: MDMs HP+AA 8 h biol rep 3

value: HP+AA 8 h


title: Rosa26-Runx1tg2_Day3_MCSF

description: Osteoclast differentiation

value: MCSF


title: Projet_Gen3G-Plasma-V1-PubM2005


title: Rosa26-Runx1tg1_Day5_MCSF_RANKL

description: Osteoclast differentiation

value: Osteoclasts


title: Rosa26-Runx1tg1_Day5_MCSF

description: Osteoclast differentiation

value: Day 5


title: MDMs HP+AA 6 h biol rep 3

value: HP+AA 6 h


title: MDMs HP 6 h biol rep 3

value: HP 6 h


title: MDMs control 6 h biol rep 3

value: vehicle 6 h


title: Rosa26-Runx1tg1 _Day3_MCSF_RANKL

description: Osteoclast differentiation


title: MDA-MB-231 cells, shYAP1-3

city: ZHEJIANG

first: MISHA

last: MAO

state: Hangzhou

address: 3 Qingchun East road

institute: zhejiang university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epithelial, triple-negative breast cancer cell

value: YAP1 knockdown

value: No


title: Rosa26-Runx1tg1_Day3_MCSF

description: Osteoclast differentiation

value: Bone marrow derived macrophage

value: Wild type control


title: MDA-MB-231 cells, shYAP1-2

value: Day 3


title: MDMs HP+AA 4 h biol rep 3

value: blood

value: HP+AA 4 h


title: MDA-MB-231 cells, shYAP1-1


title: MDMs HP 4 h biol rep 3

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: HP 4 h


title: Rosa26-Runx1tg2_Day5_MCSF

description: Osteoclast differentiation

value: MCSF


title: MDA-MB-231 cells, shNC-3

value: WT


title: DRG, CCI-7d, Male

city: Baltimore

first: Chi

last: Zhang

state: MD

address: 720 Rutland Avenue

institute: Johns Hopkins University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
We used cell-by-gene count matrix produced by 10X's Cell Ranger for all downstream analysis. We first applied Scrublet (Wolock et al., 2019) with default parameters to remove doublets from the raw count matrix for 4 individual datasets (i.e., male-sham, male-CCI, female-sham, female-CCI). After doublet removal, we filtered out cells with fewer than 1,500 genes expressed and cells with more than 10% mitochondrial genes expressed. For clustering analysis, we utilized Seurat’s integration workflow (Stuart et al., 2019). Before the integration, four datasets were transformed into four individual Seurat objects with standard steps including “CreateSeuratObject,” “NormalizeData,” and “FindVariableFeatures.” Subsequently, we used “FindIntegrationAnchors” with the top 3,000 variable genes to find anchors among the four datasets. Next, “IntegrateData” was used to merge the four individual datasets. After the integration, default clustering steps embedded in Seurat were performed with 20 principal components and 3,000 variable genes. We annotated cell types for each cluster based on well-known markers in dorsal root ganglion cells.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: *mtx: raw_matrix
Supplementary files format and content: *feaures.tsv: gene_annotation
Supplementary files format and content: *barcodes.tsv: cell_annotation

source_name: dorsal root ganglion (DRG)

extract_protocol:
Bilateral L4-5 DRGs were collected from mice at day 7 after bilateral sciatic CCI or sham surgery. Male and female mice from the same litter were subjected to the same surgery (sham or CCI). Bilateral L4-5 DRGs were collected from each mouse and DRGs from five mice of the same group (20 DRGs in total) were pooled as one sample for sequencing. The four groups included Female-Sham, Male-Sham, Female-CCI, and Male-CCI. DRGs were dissected out, digested with 1 mg/mL type I collagenase (Thermo Fisher Scientific) and 5 mg/mL dispase II (Thermo Fisher Scientific) at 37°C for 70 min (10 DRGs/tube), and disassociated into single cells in Neurobasal medium containing 1% bovine serum albumin (BSA). Cells were filtered through a 40 µm cell strainer and centrifuged at 500×g for 5 min. The pellet was resuspended in 500 μL of Triple Express (Thermo Fisher Scientific) and digested at 37°C for 2 min. The reaction was stopped with 1 mL of fetal bovine serum. The cell suspension was laid onto 5 mL of Neurobasal medium containing 20% Percoll and centrifuged at 1,400 RPM for 8 min. The upper layer was removed first and then the lower layer. The pellet was washed with 2 mL of Neurobasal medium containing 1% BSA and centrifuged at 500×g for 5 min. The pellet was resuspended with 500 μL of Neurobasal medium containing 1% BSA. The GFP+ cells were sorted into 500 μL of Neurobasal medium containing 1% BSA and centrifuged at 500×g for 5 min to remove most supernatant. The pellet was resuspended with the remaining supernatant to a concentration of ~1000 cells/μL.
The single cell suspensions were further processed with Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3 (PN-1000094) according to the manufacturer’s instructions to construct the scRNA-seq library.

value: neuron

value: dorsal root ganglion (DRG)

tag: strain

value: PirtEGFPf mouse strain (C57BL/6 background)

value: 7-8 weeks old

value: male

value: CCI


title: DRG, CCI-7d, Female

description: 10x Genomics

tag: tissue

value: female


title: MDMs HP+AA 2 h biol rep 3

tag: treatment

value: HP+AA 2 h


title: MDMs control 8 h biol rep 3

value: vehicle 8 h


title: DRG, Sham, Female

description: 10x Genomics

value: sham


title: MDA-MB-231 cells, shNC-2

value: epithelial, triple-negative breast cancer cell

value: No

value: Day 3


title: HC PBMC

city: Shanghai

first: Qing

last: Min

address: DongAn Road

institute: Fudan University

description: 10x Genomics

data_processing:
Single-cell RNA-sequencing reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38), normalized for batch effects, and filtered for cell events using the Cell Ranger software (v6.0.1).  Fast QC (v0.11.2) was used for quality control. The Seurat package (v4.0.0) was used for normalization based on the expression matrix according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
PBMC were isolated with the use of Ficoll density gradient centrifugation
PBMC suspensions (300-600/μl) were mixed with 10x Barcoded Gel Beads and formed Gel Bead-In-EMulsions (GEMs) in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, enzymatic fragmentation, 50 adaptor, and sample index attachment. The libraries were constructed using Chromium Single Cell 30 Reagent Kits (v2): Single Cell 30 Library & Gel Bead Kit v2 (PN-120237), Single Cell 30 Chip Kit v2 (PN-120236), and i7 Multiplex Kit (PN-120262) (10x Genomics).

value: peripheral blood

value: PBMC


title: P PBMC

description: 10x Genomics


title: DRG, Sham, Male

description: 10x Genomics


title: MDMs HP 2 h biol rep 3

value: blood

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: HP 2 h


title: MDA-MB-231 cells, shNC-1

value: WT


title: MDMs control 2 h biol rep 3

value: vehicle 2 h


title: TR233_RNAseq

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

description: processed data file: human_normalized_RNAsig_gene_expression.txt

data_processing:
Base calling was performed with Torrent suite.
Alignment was performed with STAR.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using FeaturesCounts function from Subread software.
The data were filtered, normalized and the differential gene expression was computed using the packages limma (https://bioconductor.org/packages/release/bioc/html/limma.html) and edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) on R.
Alignment for variant call was performed with STAR.
The variant calling was performed with samtools 1.6, the file were also called for single nucleotide variation and indel with bcftools.
The SNV impact was calculated with snpEff 4.3.
Genome_build: GCRh38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample; variant calling format for each cell line sample and human sample.

source_name: Tumour tissue from Human lung adenocarcinoma

growth_protocol: Cells were cultured in minimum supplemented medium (DMEM+10% FBS + 1% PEN/STREP) for over 12 months or over 60 passages. Mouse wild type primary epithelial cells (PLE) and mesothelial cells (PMC) were not cultured.

extract_protocol:
Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit.
Libraries were prepared according to ThermoScientific Ion Torrent specifications for carcinogen cell lines and with Illumina TruSeq for human samples.

value: Tumour tissue from patient affected from lung adenocarcinoma

tag: passages

tag: diagnosis

value: Lung adenocarcinoma


title: pRetroX-Klf4, rep2

city: Seoul

first: Jinwoo

last: Nah

address: 1, Gwanak-ro, Gwanak-gu, Seoul

department: Life science

country: South Korea

institute: Seoul National University

data_processing:
Raw ATAC-seq FASTQ files were trimmed with cutadapt
Samples were aligned to the GRCm38/mm10 reference genome using Bowtie2
Unmapped, unpaired, and mitochondrial reads were removed using BAMTools filter
PCR duplicates were removed using Picard MarkDuplicates
Peak calling was performed using MACS2
Bigwig files were generated from Bam files using bamCoverage with BPM normalization
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Spleen

growth_protocol: OT-I CD8 T-cells were maintained in RPMI suppplemented with 10% FBS, antibiotics, and 2-mercaptoethanol with 5% CO2 at 37°C

extract_protocol:
50,000 cells of naïve, effector, and GFP+ cells from exhausted (pRetroX-GFP) and reinvigorated (pRetroX-Klf4) cells, were isolated using flow cytometry.
DNA libraries of each group were prepared using ATAC-Seq kit (The Cell BiologicsTM) according to the manufacturer’s instructions.

treatment_protocol: Naïve OT-I CD8 T-cells were treated with OVA peptide (10ng/ml), anti-CD28 (2μg/ml), and mIL-2(100U/ml) for 2days to generate Effector OT-I CD8 T-cells. For generation of gene induced exhausted CD8 T cells, OT-I CD8 T-cells transduced with pRetroX-GFP/pRetroX-Klf4 were repeatedly stimulated with OVA peptide in vitro. After that, cells were cultured with OVA peptide (10ng/ml), anti-CD28 (2μg/ml), mIL-2 (100U/ml) and doxycycline (500ng/ml) for 2days

value: Spleen

value: CD8 T-cells

value: OT-I, pRetroX-Klf4 transduced

value: in vitro exhaustion + OVA (with Dox)


title: TR214_RNAseq


title: TR218_RNAseq


title: pRetroX-GFP, rep3

value: OT-I, pRetroX-GFP transduced


title: pRetroX-Klf4, rep1


title: pRetroX-GFP, rep2


title: MDMs control 8 h biol rep 2

value: vehicle 8 h


title: TR213_RNAseq


title: MDMs HP+AA 6 h biol rep 2

value: HP+AA 6 h


title: pRetroX-GFP, rep1


title: TR212_RNAseq


title: Effector, rep3

value: OT-I

value: OVA


title: TR160_RNAseq


title: Spring Norstar [S001CC4]

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

institute: National Research Council, Canada

description:
S001CC4
Wheat
RawCountData.xlsx

data_processing:
Read mapping and de novo assembly - We trimmed adaptor sequence, discarded low-quality reads (Phred Score <=20 (http://www.phrap.com/phred)) and eliminated short reads (length <= 20 bps) using a software package from Stanford (De Wit et al., 2012). STAR (v2.4.2a, Dobin et al., 2013) was used for mapping reads, and generating raw count/gene/sample.
The unmapped reads from the above mapping against IWGSC reference genome were submitted to Trinity (v2.1.1, Haas et al, 2013) for de novo assembly. The de novo assembled reference was annotated using BlastX against Arabidopsis thaliana (TAIR10) protein database. The de novo assembled reference was used for collecting read-counts for additional 58,180 genes.
DESeq2 (Love et al., 2014) was applied for data normalization across all 24 samples and subsequent DEG identification for each treatment-control pair and winter cultivars as compared with their spring counterparts. After calling for DEGs, the normalized data along with fold changes, p-values and other statistics are saved for downstream analysis.
Genome_build: IWGSC Version 2.2 survey genome assembly was used as reference [IWGSC reference genome 2.2 (2014). ftp://ftpmips.helmholtz-muenchen.de/plants/wheat/IWGSC/genome_assembly/genome_arm_assemblies_CLEANED_REPMASKED/].
Supplementary_files_format_and_content: RawCountData.xlsx: In Excel file format, including raw read counts data against wheat genome and de novo assembly.

organism: Triticum aestivum

growth_protocol: Plants for LT50 were grown hydroponically as described in detail previously (Limin and Fowler, 2002). The procedure outlined by Fowler (2008) was used to determine the LT50 of each genotype at the end of each cold acclimation period. Field wheat lines were seeded on August 29th in 2013 and 2014 in two replicates for each year. First leaf samples were collected on 30th of September in 2013 and 2014. Leaf samples were further collected after four weeks at 29th of October in 2013 and five weeks at 7th of November in 2014. The 2014 samples were left for five weeks of cold treatments due to high temperatures existing during the cold acclimation period. All leaf samples were frozen with liquid N2 immediately after harvesting and store at -80°C.

extract_protocol:
Total RNA was extracted from leaf tissues using the Plant Mini kit (Qiagen) according to manufacturer's instructions and its quantity and quality were measured with the NanoDrop 2000. One μg of total RNA was used for cDNA synthesis using the QuantiTect Reverse Transcription kit (Qiagen).
RNA-seq libraries were prepared according to Illumina's instructions, using the TruSeq RNA Sample Preparation Kit v2 (Illumina) and pair-end sequencing (126 cycles) was conducted on Illumina HiSeq 2500 following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

treatment_protocol: For cold treatment, the selected wheat varieties grow in chambers with 16-h-light (~120 μmol m-2s-1) and 8-h-dark at 23°C up to the stage of 4 leaves (3-4 weeks) and then transferred at 4°C for cold treatment for six weeks. The 3rd fully opened leaf from not treated and cold treated plants was collected and immediately frozen in liquid N2. Samples were store at -80°C until lipid analysis.

tag: cultivar

value: Spring Norstar

value: Leaf tissues

value: Cold treatment 6 weeks


title: MDMs HP 6 h biol rep 2

value: blood

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: HP 6 h


title: MDMs control 6 h biol rep 2

value: vehicle 6 h


title: Effector, rep2

value: Spleen


title: MDMs HP+AA 4 h biol rep 2

value: HP+AA 4 h


title: TR138_RNAseq

value: Tumour tissue from patient affected from lung adenocarcinoma

value: Lung adenocarcinoma


title: Effector, rep1

value: CD8 T-cells


title: Spring Norstar [S001CC1]

description:
S001CC1
Wheat
RawCountData.xlsx


title: Naive, rep3


title: TR107_RNAseq


title: MDMs control 4 h biol rep 3

value: control 4 h


title: MDMs control 4 h biol rep 2

value: vehicle 4 h


title: TR097_RNAseq


title: Naive, rep2

value: OT-I


title: Naive, rep1


title: MDMs HP+AA 2 h biol rep 2

value: HP+AA 2 h


title: Spring Norstar [S001CC2]

description:
S001CC2
Wheat
RawCountData.xlsx

value: Spring Norstar

value: Control


title: TR081_RNAseq


title: MDMs HP 2 h biol rep 2

value: HP 2 h


title: Klf4, rep3

data_processing:
The ends of the reads less than Phred quality score 20 and the adapter sequences were trimmed
the reads shorter than 50 bp were removed by using cutadapt (v.2.8)
Aligner STAR (v.2.7.1.a) was used to map filtered reads to the reference genome and RSEM(v.1.3.1) was used to estimate gene expression
The TCC R package (v.1.26.0) was used to normalize and compare the tag count data
Normalization factors were calculated using the iterative DEseq2 method
Assembly: mm10
Supplementary files format and content: tab-delimited text files including TPM values for each sample

source_name: spleen

growth_protocol: OT-I CD8 T-cells were maintained in RPMI suppplemented with 10% FBS, antibiotics, 2-mercaptoethanol, mIL-7 (5ng/ml), mIL-15 (5ng/ml), and OVA peptide (257-264) (10ng/ml) with 5% CO2 at 37°C

extract_protocol:
0.5~1x10^6 GFP+ cells were isolated from CD8 T-cells transduced with MigRI/Klf4 using flow cytometry
Total RNA was extracted using TRI Reagent according to the manufacturer’s instructions (Molecular Research Center, Inc.)
cDNA libraries were prepared using the TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA) according to the manufacturer's instructions.

treatment_protocol: OT-I CD8 T-cells transduced with MigRI/Klf4 were daily stimulated with OVA peptide in vitro and then harvested on day5

value: spleen

value: OT-I, Klf4 transduced

value: in vitro exhaustion


title: TR152_RNAseq


title: Norstar [S001CBC]

description:
S001CBC
Wheat
RawCountData.xlsx

value: Norstar

value: Leaf tissues

value: Cold treatment 6 weeks


title: MDMs control 2 h biol rep 2

value: blood

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: vehicle 2 h


title: MDMs HP+AA 8 h biol rep 2

value: HP+AA 8 h


title: TR074_RNAseq

value: Tumour tissue from patient affected from lung adenocarcinoma

value: Lung adenocarcinoma


title: Projet_Gen3G-Plasma-V1-PubM2054

value: plasma

value: female

value: Gestational diabetes mellitus


title: Klf4, rep2

value: CD8 T-cells


title: MDMs HP+AA 8 h biol rep 1


title: Klf4, rep1

value: spleen


title: TR064_RNAseq


title: MDMs HP 4 h biol rep 2

value: HP 4 h


title: Norstar [S001CC0]

description:
S001CC0
Wheat
RawCountData.xlsx


title: Spring Norstar [S001CC5]

description:
S001CC5
Wheat
RawCountData.xlsx

value: Spring Norstar

value: Control


title: Norstar [S001CBB]

description:
S001CBB
Wheat
RawCountData.xlsx

value: Norstar

value: Leaf tissues


title: MDMs HP 8 h biol rep 1

value: blood

value: HP 8 h


title: TR058_RNAseq


title: Norstar [S001CBF]

description:
S001CBF
Wheat
RawCountData.xlsx


title: MigRI, rep3

value: OT-I, MigRI transduced

value: in vitro exhaustion


title: MDMs control 8 h biol rep 1

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: vehicle 8 h


title: TR075_RNAseq

value: Tumour tissue from patient affected from lung adenocarcinoma

value: Lung adenocarcinoma


title: TR057_RNAseq


title: MigRI, rep2


title: MDMs HP+AA 6 h biol rep 1

value: HP+AA 6 h


title: Norstar [S001CBD]

description:
S001CBD
Wheat
RawCountData.xlsx


title: MigRI, rep1

value: CD8 T-cells


title: Norstar [S001CBE]

description:
S001CBE
Wheat
RawCountData.xlsx


title: Klf4 cKO

data_processing:
Low quality reads were filtered out and adaptor sequences were trimmed by Trimmomatic.
HISAT2 was used to map filtered reads to the reference genome and StringTie was used to estimate gene expression.
Size factor for read count data was calculated using edgeR (calcNormFactors), and counts were TMM (Trimmed mean of M-values) normalized.
DEG analysis was performed using edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files including TPM values for each sample

source_name: tumor

extract_protocol:
3x10^5 MC38-gp100 cells were inoculated into Rag2 KO mice (day0), and PmelI CD8 T-cells transduced with MigRI/Klf4 were adoptively transferred by IV injection on day7. Then, 1~2x10^4 GFP+ tumor-infiltrating CD8 T-cells were isolated on day15.
3x10^5 MC38 cells were inoculated into control (WT) and Klf4 cKO mice (day0), and 1~2x10^4 PD1+ CD8+ TILs were isolated on day 14.
Total RNA was extracted using TRI Reagent according to the manufacturer’s instructions (Molecular Research Center, Inc.)
cDNA libraries were prepared using SMART-seq v4 Ultra Low Input RNA Kit for Illumina, according to the manufacturer's instructions.

value: tumor

value: Klf4 cKO


title: MDMs HP 6 h biol rep 1

value: HP 6 h


title: NR179_RNAseq

source_name: Normal tissue from Human lung adenocarcinoma

value: Healthy tissue from patient affected from lung adenocarcinoma


title: Winter Manitou [S001CB6]

description:
S001CB6
Wheat
RawCountData.xlsx

value: Winter Manitou

value: Cold treatment 6 weeks


title: NR218_RNAseq


title: Control (WT)

value: Control (WT)


title: NR144_RNAseq


title: MDMs control 6 h biol rep 1

value: blood

value: vehicle 6 h


title: MDMs HP+AA 4 h biol rep 1

value: HP+AA 4 h


title: NR124_RNAseq


title: Winter Manitou [S001CB5]

description:
S001CB5
Wheat
RawCountData.xlsx

value: Leaf tissues


title: Klf4

value: PmelI, Klf4 transduced


title: Winter Manitou [S001CB8]

description:
S001CB8
Wheat
RawCountData.xlsx


title: MigRI

value: PmelI, MigRI transduced


title: MDMs HP 4 h biol rep 1

value: monocyte-derived macrophages (MDMs)

value: diploid female

value: HP 4 h


title: NR107_RNAseq

value: Lung adenocarcinoma


title: Winter Manitou [S001CB9]

description:
S001CB9
Wheat
RawCountData.xlsx

value: Control


title: Winter Manitou [S001CBA]

description:
S001CBA
Wheat
RawCountData.xlsx


title: MDMs HP+AA 2 h biol rep 1

value: HP+AA 2 h


title: MDMs HP 2 h biol rep 1

value: HP 2 h


title: PND4_CKO10_LRH

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

data_processing:
Reads with a quality score less than 20 were removed and alignment was performed using the STAR open source alignment tool
To evaluate RNA abundance at the gene level, reads mapped to each gene were quantified using featureCounts.
Normalization and analysis of differential abundance were performed using the package DEseq2 in R
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw reads in the file d4ckovsctrlRAWREADS.txt
Supplementary files format and content: Results from DEseq2 analysis in pnd4lrhconvsckopairwise.xlsx

source_name: Whole ovary

extract_protocol:
RNA was extracted from postnatal day 4 (PND4) ovaries with PureLink RNA Mini-Extraction kit according to the manufacturer's instructions (Invitrogen, Waltham, MA).  Quality of RNA was assessed using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) and only samples of high quality were used.
The library preparation was performed with a New England Biolabs mRNA stranded library preparation kit (Rowley, MA) and library QC followed.

value: Whole ovary

value: mixed, from whole ovary

value: CKO


title: MDMs control 2 h biol rep 1

value: vehicle 2 h


title: PND4_CKO4_LRH


title: mESC_polyA_Ctrl_FTO+_rep1

city: Chicago

first: Shun

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

data_processing:
Adapters of all raw eTAM-seq data sets were removed by Cutadapt v1.18. The six-nt-long random barcodes in the 5’ end of R2 reads were extracted by the subcommand extract from UMI-tools v1.1.1. R2 reads longer than 39 nt were used for further analysis. For HeLa cells, reads were first mapped to the human rRNA sequences using HISAT-3N v2.2.1. Then unmapped reads were mapped to the human genome (hg38) and the GENCODE v27 gene annotation. For mESCs, reads were first mapped to the mouse rRNA sequences using HISAT-3N. Then unmapped reads were mapped to the mouse genome (mm10) and the GENCODE vM25 gene annotation. Only uniquely mapped reads were remained and then subjected to deduplication by the subcommand dedup from UMI-tools. Reads with > 50% unconverted A were eliminated. Finally, custom scripts were used to count converted and unconverted As for each genomic positions.Site-specific quantification was estimated by the model developed in this study.
Assembly: hg38, mm10
Supplementary files format and content: m6A sites with accessibility and methylation levels in the plain txt format

growth_protocol: Human HeLa cell line and wild-type (WT) mouse embryonic stem cells (mESC) were purchased from ATCC. HeLa cell line was grown in DMEM (Gibco, 11965092) media supplemented with 10% FBS (Gibco) and 1% 100× Pen/Strep (Gibco). mESCs were maintained in DMEM (Invitrogen) supplemented with 15% FBS (Gibco), 1% nucleosides (100×) (Millipore), 1 mM L-glutamine (Gibco), 1% nonessential amino acids (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 1,000 U/ml LIF (Millipore), 3 μM CHIR99021 (Stemcell), and 1 μM PD0325901 (Stemcell). All cells were cultured at 37°C under 5.0% CO2. Mettl3 cKO mES cell lines were generated following previously reported methods (PMID: 31949099). Briefly, mESCs derived from Mettl3flox/flox mouse blastocyst were transfected with 200 ng PB-CAG-Puromycin-P2A-CreERT2 and 100 ng PBase by electroporation. After 24 h, electroporated cells were treated with 1 μg/ml Puromycin to generate stable Mettl3flox/flox; CreERT2 mES clones. To induce deletion, Mettl3flox/flox; CreERT2 ESC cells were treated with 1 μg/ml 4-hydroxytamoxifen (Sigma). These Mettl3 KO cells were cultured for 48 h before harvesting. Untreated Mettl3flox/flox; CreERT2 ESC cells were used as ctrl mESCs.

extract_protocol:
Cells were cultured to 70-80% confluency, rinsed with 1× PBS (Gibco), and lysed by the direct addition of TRIzol reagent (Invitrogen). Total RNA was then collected following the manufacturer’s protocol. Poly A+ RNA was extracted from purified total RNA using Dynabeads mRNA DIRECT Purification Kits (Invitrogen). Modification-free control RNAs were prepared from HeLa or mESC total RNA according to a previously published protocol (PMID: 34594034, 32518404).
RNA was annealed to 2 pmol of RT primer (AGACGTGTGCTCTTCCGATCT) at 70ºC for 2 min, then reverse transcribed in 1× RT buffer (Thermo Scientific, EP0753, containing 50 mM Tris-HCl, pH 8.3; 75 mM KCl, 3 mM MgCl2, 10 mM DTT) with 5 mM of RNaseOUT (Invitrogen, 10777019) and 200 U of Maxima H- Reverse Transcriptase (Thermo Scientific, EP0753) at 50ºC for 1h. The cDNA was released by boiling the beads in 0.5% (v/v) SDS for 10 min. The eluate was purified by DNA Clean & Concentrator (Zymo) kits. Purified cDNA was ligated to cDNA Adapter (/5Phos/NNNNNN AGATCGGAAGAGCACACGTCTG/3SpC3/) using 30 U of T4 RNA ligase (NEB) at 25ºC overnight, following a previously published protocol (PMID: 35288668). The reaction was purified again by DNA Clean & Concentrator (Zymo) kits and then PCR amplified with NEBNext Ultra II Q5 Master Mix (NEB, M0544X) and NEBNext Unique Dual Index Primer for Illumina (NEB, E6440S) following the manufacturer’s directions. Typically, 10-11 cycles of PCR were carried out to generate enough DNA. The resulting library was purified by AMPure XP beads (Beckman Coulter, A63882) following the manufacturer’s directions and submitted for next-generation sequencing.

treatment_protocol: FTO-, FTO+ and IVT RNA samples were deaminated on beads with 200 pmol of TadA8.20 in the deamination buffer (50 mM Tris, 25 mM KCl, 2.5 mM MgCl2, 2 mM dithiothreitol, and 10 % (v/v) glycerol; pH 7.5) supplemented with 10% (v/v) of SUPERase•In RNase Inhibitor (Invitrogen, AM2696) at 53ºC for 1 h. This reaction was repeated twice at 44ºC, 1h each by draining the supernatant on a magnetic rack and resuspending the beads in fresh reaction mixtures, lasting 3 h in total. The beads were washed sequentially by resuspension in 0.1% PBST (v/v), 1× Binding/Wash buffer, and twice in 10 mM Tris HCl (pH 7.5).

value: mESC

value: TadA8.20 + FTO

value: Mettl3 cko ctrl

tag: library type

value: in vivo transcribed RNA


title: Winter Manitou [S001CB7]

description:
S001CB7
Wheat
RawCountData.xlsx

value: Winter Manitou

value: Leaf tissues


title: PND4_CKO1_LRH


title: Manitou [S001CAC]

description:
S001CAC
Wheat
RawCountData.xlsx

value: Manitou

value: Cold treatment 6 weeks


title: Manitou [S001CAB]

description:
S001CAB
Wheat
RawCountData.xlsx


title: MSODB_day21_rep3

city: Lund

first: Yuan

last: Li

address: Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
The acquired RNA-seq data were first demultiplexed with Illumina Experiment Manager, then had quality checked using MultiQC and next mapped to the human reference genome (GRCh38) by the STAR aligner v2.5.0
The generated bam files first went through quality control with MultiQC, then were sorted (according to coordinates), indexed using Samtools v1.12 and finally counted (at gene level) by featureCounts v2.0.1, only fragments that were uniquely mapped to gene exons were considered, fragments mapped to multiple genome locations, overlapping genes, or introns were ignored.
Assembly: GRCh38
Supplementary files format and content: csv file, raw fragment count matrix

source_name: Bone marrow

extract_protocol:
For Day 0, 0.5 million cells were washed twice with PBS and lysed with 350 µL RLT buffer with 1% ß-mercaptoethanol (ME) (Sigma-Aldrich #M6250). For Day 21, collected cartilage scaffolds were snap-freezed and stored at -70°C. The scaffolds were homogenized and lysed with the TissueRuptor II (Quiagen #9002755) in 300 µL of RLT buffer with 1% ß-ME. RNA from cells and scaffolds was extracted using the RNeasy Mini Kit (Qiagen # 74104) and RNeasy Fibrous Tissue Mini Kit (Quiagen #74704) respectively, according to manufacturer’s protocols.
rRNA depletion and RNA-seq library construction were performed with the SMARTer Stranded Total RNA Sample Prep Kit - HI  Mammalian (TakaraBio) and the constructed libraries then had quality checked using Bioanalyzer (high-sensitivity DNAassay) and Qubit (dsDNA HS assay kit)

treatment_protocol: Tissues were cultured for 3 weeks in chondrogenic medium (DMEM supplemented with 1% penicillin-streptomycin-glutamine (Gibco), 1% HEPES (1M) (Gibco), 1% sodium pyruvate (100mM) (Gibco), 1% ITS (100x) (Insulin, Transferrin, Selenium) (Gibco), 0,47mg/ml linoleic acid (Sigma), 0.12% bovine serum albumin (BSA) (Sigma), 0.1mM ascorbic acid (Sigma), 10-7M dexamethasone (Sigma) and 10ng/ml TGF-β3 (Novartis))

value: MSODB

tag: chondrogenic stage


title: mESC_polyA_WT_IVT_rep2

tag: genotype

value: wild type

value: in vitro transcribed RNA


title: PND4_CON9_LRH

value: CON


title: mESC_polyA_Ctrl_FTO-_rep1


title: MSODB_day21_rep2


title: Manitou [S001CA9]

description:
S001CA9
Wheat
RawCountData.xlsx


title: Manitou [S001CAA]

description:
S001CAA
Wheat
RawCountData.xlsx

value: Control


title: MSODB_day21_rep1


title: PND4_CON8_LRH

value: Whole ovary


title: mESC_polyA_M3cko_FTO+_rep1

value: Mettl3 cko


title: PND4_CKO11_LRH

value: mixed, from whole ovary

value: CKO


title: MSODB_day0_rep3


title: mESC_polyA_M3cko_FTO-_rep1

value: mESC


title: mESC_polyA_WT_FTO+_rep2

value: TadA8.20 + FTO


title: PND4_CON7_LRH


title: Manitou [S001CAE]

description:
S001CAE
Wheat
RawCountData.xlsx


title: Manitou [S001CAD]

description:
S001CAD
Wheat
RawCountData.xlsx


title: mESC_polyA_WT_FTO+_rep1


title: MSODB_day0_rep1


title: mESC_polyA_WT_FTO-_rep2


title: mESC_polyA_WT_IVT_rep1


title: mESC_polyA_WT_FTO-_rep1


title: 16h_3

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E. Young Drive South, MRL 6619

department: Pathology and Laboratory Medicine

institute: UCLA

data_processing:
Adapter and quality trimming of raw FASTQ files was performed using Trimmomatic.
FastQC was used to analyze FASTQ files before and after trimming.
Trimmed FASTQ files were aligned to GRCm38/mm10 using STAR.
HTSeq-count was used to extract gene counts.
Differential gene expression analysis was performed using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Gene counts

source_name: Liver

extract_protocol:
Total RNA was extracted using TRIzol and the RNeasy Mini Kit with on-column DNase I digestion (Qiagen).
Library preparation and sequencing was done at GENEWIZ.

value: Liver

value: WT

value: 16 hour fast


title: 4h_3

value: 4 hour fast


title: CON 32394

city: Beaverton

first: Lyndsey

middle: Elizabeth

last: Shorey-Kendrick

state: Oregon

address: 505 NW 185th Ave

institute: Oregon Health and Science University

data_processing:
The procedure of raw reads filtering is as follows:  (1) Remove reads containing adapters;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.  2 Directory tree  QC/  |--
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. We use HISAT2 to  accomplish the mapping
The raw data was filtered and mapped to the rhesus macaque genome.
Gene expression levels were quantified using FPKM values to screen for differentially expressed genes (DEGs).
Supplementary files format and content: matrix processed file including counts per gene/sample, DEG results, annotation, and fpkm

organism: Macaca mulatta

source_name: placenta

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
A Poly-A enrichment step was used to select for mRNA molecules followed by fragmentation, reverse transcription, and Illumina-compatible adaptor ligation

value: placenta

value: trophoblast cells


title: CON 27343


title: CON 33957


title: CON 28385


title: 4h_1


title: 145790 Late MF

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
Cellranger (10x Genomics, version 3.0.1) was used for transcript alignment, counting, and inter-library normalization of single cell samples. Seurat(version 4.0.0) was used for cluster analysis.
Supplementary files format and content: GRCh38

source_name: Peripheral blood

extract_protocol:
Cryopreserved BMMCs/PBMCs
Non-lymphoid CD34 cells were identified by the following immunostaining panel: CD34, CD38, CD3, CD7, CD19, and 7AAD. 7AAD- CD3-CD7- CD19- CD34+ cells were sorted and subsequently labeled with a panel of oligonucleotide conjugated antibodies according to TotalSeqA protocol from 10X Genomics (Pleasanton, CA). Oligonucleotide labeled cells were subjected to droplet bead capture, followed by cell lysis, reverse transcription, and amplification following protocol.

value: Peripheral blood

tag: disease state

value: Late MF


title: 145790 Early MF

description: 10x Genomics

value: Early MF


title: 4h_2


title: P B-cell

description: 10x Genomics

data_processing:
Single-cell RNA-sequencing reads were aligned to the Genome Reference Consortium Human Build 38 (GRCh38), normalized for batch effects, and filtered for cell events using the Cell Ranger software (v3.0.0). Cells expressing fewer than 200 genes and cells with a mitochondrial UMI rate higher than 20% were excluded. Mitochondrial genes were removed from the expression matrix but used for cell expression regression to avoid the cell status effect for clustering analysis and marker analysis of each cluster. The Seurat package (version: 2.3.4) was used for normalization based on the expression matrix according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
CD19+ B cells were sorted from fresh isolated PBMC using MoFlo XDP (Beckman) and resuspended with PBS supplied with 2%BSA
CD19+ B cells were processed using the 10x Genomic Chromium Single Cell Platform at a concentration of 700-1,000 cells per microliter, as described in the manufacturer’s protocol. Approximately 8,000-10,000 cells were loaded onto 30 library chips following the Single Cell 30 Reagent Kits (v2) User Guide. The cells were then partitioned into GelBeads in Emulsion in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, enzymatic fragmentation, 50 adaptor, and sample index attachment. The libraries were constructed using Chromium Single Cell 30 Reagent Kits (v2): Single Cell 30 Library & Gel Bead Kit v2 (PN-120237), Single Cell 30 Chip Kit v2 (PN-120236), and i7 Multiplex Kit (PN-120262) (10x Genomics).

value: peripheral blood

value: B cell


title: MSODB_day0_rep2

value: MSODB


title: HC B-Cell

description: 10x Genomics


title: 145790 AML

description: 10x Genomics

value: AML


title: CON 27702


title: WAT ZT21 RNA 3 [CLH_RNA_36]

first: Nathan

last: Waldeck

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

description: processed data file: All_RNA_Counts.txt

data_processing:
ATAC-sequencing reads were trimmed and aligned to the mouse reference genome (mm10) using the ENCODE ATAC-sequencing pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline).
HOMER was used to identify and annotate peaks and motifs in ATAC-Seq data
RNA-seq reads aligned to mm10 using STAR 2.7.5
RSEM 1.3.0 was used to assign transcript counts to gene features (Ensembl 98)
Differential Gene epression (DESeq2), data visulaization (pheatmap, gplots, ggplot2), KEGG pathway analysis (limma), rhythmic analyses (JTK-Cycle) were performed in R (4.1.0)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Table with rhythmic genomic features obtained from JTK_Cycle

source_name: WAT ZT21 RNA

extract_protocol:
NuTRAP nuclei and ribosomal RNA were isolated according to established methods (PMID 28122230). Brown adipose and inguinal white adipose depots were snap frozen in liquid nitrogen, minced, dounce homogenized, spun down and FACS sorted to isolate for ATAC-Seq. Tissues were minced, homogenized, ribosomal RNA was affinity purified using anti-GFP antibodies and protein G Dynabeads and extracted using the Qiagen Micro RNeasy kit.
ATAC-seq libraries were constructed according to the Omni-ATAC protocol (PMID 28846090). RNA-Seq libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit

tag: time point

value: white adipocytes

tag: molecule subtype

value: ribosomal mRNA


title: PND4_CON6_LRH

value: Whole ovary

value: mixed, from whole ovary

value: CON


title: 16h_2

value: Liver

value: WT


title: THC 28755

value: THC


title: T-cells, IL1A-, R6

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

data_processing:
Quality of raw read data was checked using FastQC (v0.11.8).
Reads were quality- and adapter-trimmed using Trimmomatic (v0.39)
Reads were rRNA-filtered using SortMeRNA (v2.1b) with a single rRNA database concatenated from all rRNA databases shipped with SortMeRNA.
Reads were mapped against the human reference genome and corresponding annotation GRCh38.103 (obtained from www.ensembl.org) using HiSAT2 (v2.1.0).
Reads were counted using Rsubread (v1.34.0) subsequently generating a read counts matrix.
Assembly: GRCh38.103
Supplementary files format and content: raw_counts.tsv = Raw counts of sequencing reads (matrix table)
Supplementary files format and content: mrn_counts.tsv = MRN (Median Ratio Normalization) counts of sequencing reads (matrix table)

source_name: Peripheral blood mononuclear cells (PBMCs)

extract_protocol:
A total amount of 1 µg of RNA per sample was used as the input material for the RNA sample preparations. Sequencing libraries were generated using an NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations and index codes were added to attribute sequences to each sample. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out by using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5x) or by using sonication with a Diagenode Bioruptor Pico for fragmentation of RNA strands. First-strand cDNA was synthesized using random hexamer primers and M-MuL V Reverse Transcriptase (RNase H-). Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activity. After adenylation of the 3' ends of the DNA fragments, NEBNext adaptors with a hairpin loop structure were ligated to prepare the fragments for hybridization.
To preferentially select cDNA fragments 150-200 bp in length, the library fragments were purified with an AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 µI of USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA Polymerase, Universal PCR primers and Index (X) Primer. Finally, the PCR products were purified (AMPure XP system), and library quality was assessed on an Agilent Bioanalyzer 2100 system. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a PE Cluster Kit cBot-HS (Illumina) according to the manufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina platform, and paired-end reads were generated (Novogene).

value: CD4+ T-cell

tag: t-cell clone


title: WAT ZT21 RNA 2 [CLH_RNA_35]

description: processed data file: All_RNA_Counts.txt


title: T-cells, IL1A-, R7


title: 16h_1

value: 16 hour fast


title: THC 28226

value: placenta

value: trophoblast cells


title: T-cells, IL1A-, R5


title: WAT ZT21 RNA 1 [CLH_RNA_34]

description: processed data file: All_RNA_Counts.txt


title: THC 31215


title: WAT ZT17 RNA 3 [CLH_RNA_33]

description: processed data file: All_RNA_Counts.txt

source_name: WAT ZT17 RNA


title: T-cells, IL1A+, R4


title: THC 27521


title: THC 32864


title: WAT ZT17 RNA 1 [CLH_RNA_31]

description: processed data file: All_RNA_Counts.txt


title: WAT ZT13 RNA 2 [CLH_RNA_29]

description: processed data file: All_RNA_Counts.txt

source_name: WAT ZT13 RNA


title: Chick Brachial spinal cord - RNA-seq 3 [sample_6]

first: DongAhn

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

description: Brachial spinal cord 3

data_processing:
Quality of RNA-seq raw reads were checked with FastQC (v. 0.11.9). Next, the raw data was trimmed for low quality and illumina truseq adapter sequences using trimmomatic-0.39 with the following options: “ILLUMINACLIP:[AdapterFile]:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50”. The resulting clean reads were aligned to GRCg6a for chick with STAR (v. 2.7.5a) and were quantified using featureCounts.
To account for different gene length in multiple species, RPKM normalization implemented in python bioinfokit was used.
Assembly: GRCg6a for chick
Supplementary files format and content: Tab-separated file with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Brachial spinal cord

extract_protocol:
For chick MN RNA sequencing, HH stage 12-13 chick embryos were electroporated with a plasmid that drives nuclear YPF expression under the control of Hb9 promoter. After 3day incubation, brachial level spinal cords were isolated and dissociated. 5000-23000 YFP+ MNs and the rest of YFP- cells were collected using a FACS sorter (BD, FACSAria III) and PicoPure RNA Isolation Kit (Arcturus, KIT0202) was used to extract total RNAs. cDNA was synthesized and amplified using Ovation RNA amplification system v2 (Nugen, 3100-12).
The sequencing library was prepared using the TruSeq RNA sample prep Kit (Illumina, CA).

value: Brachial spinal cord

tag: developmental stage


title: Chick Brachial spinal cord - RNA-seq 2 [sample_4]

description: Brachial spinal cord 2


title: Chick Brachial spinal cord - RNA-seq 4 [sample_8]

description: Brachial spinal cord 4


title: WAT ZT13 RNA 1 [CLH_RNA_28]

description: processed data file: All_RNA_Counts.txt


title: T-cells, IL1A+, R2


title: Th17 scRNAseq

city: München

first: Laurens

last: Lehner

address: Arcisstraße 21

institute: Technical University of Munich

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 applying the count function with 4000 expected cells and chemistry set to auto (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol: Libary was constructed according to manufacter's instructions (Chromium Next GEM Single Cell 5' Reagents v2 (Dual Index), 10x Genomics, Inc.)

value: Th17 cells

value: blood


title: T-cells, IL1A+, R3


title: T-cells, IL1A+, R1


title: Chick Brachial spinal cord - RNA-seq 1 [sample_2]

description: Brachial spinal cord 1


title: Chick brachial motor neurons - RNA-seq 4 [sample_7]

description:
Chicken_CountDf.txt
sample_7

data_processing:
Quality of RNA-seq raw reads were checked with FastQC (v. 0.11.9). Next, the raw data was trimmed for low quality and illumina truseq adapter sequences using trimmomatic-0.39 with the following options: “ILLUMINACLIP:[AdapterFile]:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50”. The resulting clean reads were aligned to GRCm38 for mouse and GRCg6a for chick with STAR (v. 2.7.5a) and were quantified using featureCounts.
To account for different gene length in multiple species, RPKM normalization implemented in python bioinfokit was used.
Genome_build: GRCm38 for mouse and GRCg6a for chick
Supplementary_files_format_and_content: Tab-separated file with raw gene counts for every gene and every sample

source_name: Brachial motor neurons

extract_protocol:
For mouse, spinal cords of Hb9-GFP (Jackson laboratory) were dissociated and GFP+ MNs were manually collected. The regions for forelimb MNs were visualized under a fluorescence dissection scope and separated from other neurons using a sharp scalpel. The spinal cords were digested with pronase for 30min at RT.    For chick MN RNA sequencing, HH stage 12-13 chick embryos were electroporated with a plasmid that drives nuclear YPF expression under the control of Hb9 promoter. After 3day incubation, limb level spinal cords were isolated and dissociated. 5000-23000 YFP+ MNs were collected using a FACS sorter (BD, FACSAria III) and PicoPure RNA Isolation Kit (Arcturus, KIT0202) was used to extract total RNAs. cDNA was synthesized and amplified using Ovation RNA amplification system v2 (Nugen, 3100-12).
The sequencing library was prepared using the TruSeq RNA sample prep Kit (Illumina, CA).

value: Brachial motor neurons


title: WAT ZT9 RNA 1 [CLH_RNA_25]

description: processed data file: All_RNA_Counts.txt

source_name: WAT ZT9 RNA


title: memory T-cells, control 3

city: Graz

first: Silvia

last: Fibi-Smetana

state: Styria

address: Stremayrgasse 16

department: Biomedical Informatics

country: Austria

institute: Graz University of Technology

data_processing:
Quality control with FastQC (v 0.11.9)
Mapping and counting with STAR (v 2.7.5a)
Differential expression with protein-coding genes (retrieved from BioMart Ensembl Genes release 104) with the DESeq2 (version 1.28.1) R package.
Functional analysis with DAVID (v 2021)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, tab separated text file

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads
Sequencing libraries were generated using an NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations

treatment_protocol: Resting T-cell clones categorized as IL-1alpha+ (> 30% IL-1alpha expression) and IL-1alpha– (0% IL-alpha expression) were restimulated with phorbol-12-myristat-13-acetat (PMA) and ionomycin (both from Sigma–Aldrich) for 3 h. A total amount of 1 µg of RNA per sample was used as the input material for the RNA sample preparations.

value: memory T-cells

value: Control


title: memory T-cells, control 2


title: Chick brachial motor neurons - RNA-seq 3 [sample_5]

description:
Chicken_CountDf.txt
sample_5


title: WAT ZT13 RNA 3 [CLH_RNA_30]

description: processed data file: All_RNA_Counts.txt

value: white adipocytes

value: ribosomal mRNA


title: WAT ZT5 RNA 3 [CLH_RNA_24]

description: processed data file: All_RNA_Counts.txt

source_name: WAT ZT5 RNA


title: memory T-cells, knock-out 3

value: Knock-out

value: GSDME knock-out


title: memory T-cells, knock-out 2


title: WAT ZT17 RNA 2 [CLH_RNA_32]

description: processed data file: All_RNA_Counts.txt


title: Chick brachial motor neurons - RNA-seq 2 [sample_3]

description:
Chicken_CountDf.txt
sample_3


title: Chick brachial motor neurons - RNA-seq 1 [sample_1]

description:
Chicken_CountDf.txt
sample_1


title: WAT ZT5 RNA 2 [CLH_RNA_23]

description: processed data file: All_RNA_Counts.txt


title: memory T-cells, knock-out 1


title: WAT ZT1 RNA 2 [CLH_RNA_20]

description: processed data file: All_RNA_Counts.txt

source_name: WAT ZT1 RNA


title: HeLa_polyA_WT_IVT_rep3

value: HeLa

value: wild type

value: in vitro transcribed RNA


title: HeLa_polyA_WT_IVT_rep1


title: WAT ZT1 RNA 3 [CLH_RNA_21]

description: processed data file: All_RNA_Counts.txt


title: WAT ZT9 RNA 3 [CLH_RNA_27]

description: processed data file: All_RNA_Counts.txt


title: Spring Norstar [S001CC3]

description:
S001CC3
Wheat
RawCountData.xlsx

value: Spring Norstar

value: Leaf tissues

value: Cold treatment 6 weeks


title: WAT ZT9 RNA 2 [CLH_RNA_26]

description: processed data file: All_RNA_Counts.txt


title: WAT ZT1 RNA 1 [CLH_RNA_19]

description: processed data file: All_RNA_Counts.txt


title: HeLa_polyA_WT_FTO+_rep3

value: TadA8.20 + FTO

value: in vivo transcribed RNA


title: memory T-cells, control 1


title: HeLa_polyA_WT_FTO+_rep2