title: M00017913_15M_Liver_iPCRtag66

value: C57BL/6 J


title: M00017578_24M_Cortex_iPCRtag64

status: Public on Jun 03 2024

type: SRA

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

library_source: genomic

data_processing:
RRBS and WGBS datasets were processed as described previously (RRBS: Stubbs et al., 2017; WGBS: von Meyenn, 2022), aligning reads to the bisulfite converted GRCm38 mouse genome using Bismark v0.22.3 (Krueger and Andrews, 2011).
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

molecule: genomic DNA

organism: Mus musculus

source_name: Cortex

extract_protocol:
Genomic DNA was isolated from ~10 mg frozen tissue using the DNeasy Blood & Tissue Kit (Qiagen)
RRBS libraries were prepared from isolated DNA following published protocols (Stubbs et al 2017). Briefly, RRBS libraries were prepared by MspI digestion of 100–500 ng genomic DNA, followed by end-repair and T-tailing using Klenow Exo- (Fermentas). Adapter ligation was performed overnight (in-house adapters) using T4 DNA Ligase (NEB), followed by a clean-up step using AMPure XP beads (Agencourt, 0.9×). Subsequently, libraries were bisulfite-treated according to the manufacturer’s instructions (Sigma Imprint Kit; 2 step protocol) and purified using an automated liquid handling robotic system (Agilent Bravo). The libraries were amplified using KAPA HiFi Uracil HotStart DNA Polymerase (KAPA Biosystems), indexing the samples with individual primers. All amplified libraries were purified (AMPure XP beads, 0.8×) and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer.

tag: tissue

value: Cortex

tag: strain

tag: age

tag: genotype

value: wildtype


title: Sfp1-AA_Ifh1-AA_Rapamycin_H3K9ac

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3 and 972-h pombe genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800". The data were filtered to retain only the mapped reads with at most 5 hits in the reference, reads that mapped to both sacCer3 and 972-h genomes were discarded. The reads mapped uniquely to the sacCer3 genome were used for further analysis.
Assembly: sacCer3
Supplementary files format and content: bigwig files were obtained using Galaxy server (Afgan et al., 2018).

organism: Saccharomyces cerevisiae

growth_protocol:
Cells were grown at 30 degrees in YPED to mid-log phase before treatment
Yeast cells were grown at 30 degrees in YPED to mid-log phase before treatment.

extract_protocol:
ChIP protocol was performed as previously described (Zencir et al., 2020, Ribaud et al., 2012). The cells were crosslinked with 1% formaldehyde for 10 min and quenched by adding 125 mM glycine for 5 min at room temperature. Briefly, crosslinked cells were lysed by bead beating, chromatin was sonicated, and the soluble fraction was incubated with the appropriate antibodies for 1 hr at 4°C. Magnetic beads coupled to IgG against rabbit or mouse (Invitrogen, Dynabeads™ M-280 Sheep Anti-Rabbit or Anti-Mouse IgG) were added into the samples and incubated for additional 3 h at 4°C. A defined amount (5% of total chromatin) of crosslinked and sonicated chromatin from S. pombe was added to S. cerevisiae chromatin prior to the immunoprecipitation step. ChIP was performed using the following antibodies: anti-histone H3 ChIP, (Abcam ab1791); anti-H3K9ac (Millipore 07-352); anti-RNAPII (Abcam ab5131); fanti-Flag (Sigma F3165); anti-Myc (a homemade antibody, clone 9E10). The DNAs were purified using the MinElute PCR Purification Kit (Qiagen) before library preparation.
TruSeq ChIP library preparation kit (Illumina)

treatment_protocol: For stress experiments; cells were incubated in YEPD medium until log phase at 30°C, then the samples were treated with rapamycin at a final concentration of 200 nM for 20 min to inhibit the growth regulator TORC1. The cells were collected following rapamycin treatment at the indicated time points before crosslinking. For conditional depletion of target proteins 'Anchor-away system' was used; log-phase growing cells (OD600 = 0.3–0.4) were treated with 1 μg/mL rapamycin before collection of the cells. For TBP anchor-away, cells were treated with rapamycin for 30 min. For Sfp1 and Ifh1 single and double anchor-way, cells were treated with rapamycin for 60 min.

value: HHY168 background;  SFP1-FRB::KANMX IFH1-FRB::HIS MATalpha

tag: treatment

value: 60 min rapamycin


title: Sfp1-AA_Ifh1-AA_Vehicle_H3K9ac

tag: chip antibody

value: Anti-H3 Lys9 acetylation (Millipore, 07-352)

value: No rapamycin


title: M00017562_24M_Cortex_iPCRtag60


title: M00017579_24M_Heart_iPCRtag39

source_name: Heart

value: Heart


title: M00017589_24M_Lung_iPCRtag46

source_name: Lung

value: Lung


title: deltastb3deltatod6deltadot6_Vehicle_H3K9ac

value: W303 background, deltatod6::KanMX deltastb3::NatMX deltadot6::HIS3, MATa


title: M00017589_24M_Heart_iPCRtag47


title: TBP-AA_Rapamycin_Ifh1

value: HHY154 background, tor1-1 fpr1::NATMX RPL13A-FK::TRP TBP-FRB::KANMX, MATalpha

value: 30 min rapamycin


title: TBP-AA_Rapamycin_RNAPII


title: TBP-AA_Vehicle_Ifh1

value: Anti-Ifh1 (Pocono Farm, generated from Ifh1-6p)


title: TBP-AA_Vehicle_RNAPII

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (Abcam, ab5131)


title: M00018000_15M_Cortex_iPCRtag92


title: M00018011_15M_Cortex_iPCRtag72


title: TBP-AA_Vehicle_H3

value: Anti-H3 (Abcam, ab1791)


title: M01-20523_3M_Lung_iPCRtag11


title: M00017560_24M_Liver_iPCRtag34

source_name: Liver

value: Liver


title: M00018003_15M_Heart_iPCRtag87


title: M00018002_15M_Cortex_iPCRtag94


title: M02-20525_3M_Liver_iPCRtag1


title: CRF1_Rapamycin_RNAPII

value: YDS2 background; rpa43::hyg rrn3::hyg +pGEN with Rpa43-rrn3 fusion  MATalpha (CARA strain)

value: 20 min rapamycin


title: M00018004_15M_Liver_iPCRtag72

value: C57BL/6 J


title: M02-20523_3M_Liver_iPCRtag8

value: wildtype


title: M00018011_15M_Heart_iPCRtag71


title: TBP-AA_Rapamycin_H3K9ac


title: deltastb3deltatod6deltadot6_Rapamycin_H3K9ac


title: M00017912_15M_Liver_iPCRtag65


title: CRF1_Vehicle_RNAPII


title: CRF1_Rapamycin_H3K9ac


title: M02-20523_3M_Heart_iPCRtag24


title: M00017560_24M_Cortex_iPCRtag58

value: Cortex


title: TBP-AA_Vehicle_H3K9ac


title: WT_Rapamycin_RNAPII

value: W303 background; leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100 MATa


title: M02-20522_3M_Heart_iPCRtag23


title: WT_Vehicle_RNAPII


title: TBP-AA_Rapamycin_H3


title: M00017579_24M_Lung_iPCRtag38


title: WT_Rapamycin_H3


title: M03-NB_NewBorn_Liver_iPCRtag21

value: NewBorn


title: M00017576_24M_Lung_iPCRtag46


title: WT_Rapamycin_H3K9ac_rep2


title: M00017589_24M_Liver_iPCRtag45


title: WT_Vehicle_H3K9ac_rep2

value: No rapamycin


title: WT_Rapamycin_H3K9ac_rep1


title: M00017563_24M_Lung_iPCRtag45


title: WT_Vehicle_H3K9ac_rep1

extract_protocol:
H3, H3K9ac, and RNAPII ChIP-seq was performed as described previously (Ribaud et al., 2012; PMID: 21952045) with the following modification. A defined amount (5% of total chromatin) of previously cross-linked chromatin from S.pombe was added to S.cerevisiae chromatin prior to immunoprecipitation step.
ChIP protocol was performed as previously described (Zencir et al., 2020, Ribaud et al., 2012). The cells were crosslinked with 1% formaldehyde for 10 min and quenched by adding 125 mM glycine for 5 min at room temperature. Briefly, crosslinked cells were lysed by bead beating, chromatin was sonicated, and the soluble fraction was incubated with the appropriate antibodies for 1 hr at 4°C. Magnetic beads coupled to IgG against rabbit or mouse (Invitrogen, Dynabeads™ M-280 Sheep Anti-Rabbit or Anti-Mouse IgG) were added into the samples and incubated for additional 3 h at 4°C. A defined amount (5% of total chromatin) of crosslinked and sonicated chromatin from S. pombe was added to S. cerevisiae chromatin prior to the immunoprecipitation step. ChIP was performed using the following antibodies: anti-histone H3 ChIP, (Abcam ab1791); anti-H3K9ac (Millipore 07-352); anti-RNAPII (Abcam ab5131); fanti-Flag (Sigma F3165); anti-Myc (a homemade antibody, clone 9E10). The DNAs were purified using the MinElute PCR Purification Kit (Qiagen) before library preparation.
TruSeq ChIP library preparation kit (Illumina)

value: Anti-H3 Lys9 acetylation (Millipore, 07-352)


title: M00018003_15M_Lung_iPCRtag79

value: Lung


title: M04-20527_3M_Cortex_iPCRtag20


title: M00018011_15M_Liver_iPCRtag69


title: M00017897_15M_Lung_iPCRtag75


title: CRF1_Vehicle_H3K9ac


title: M00017579_24M_Liver_iPCRtag37


title: M00017913_15M_Cortex_iPCRtag44


title: section1_control_12h

city: Stockholm

first: Franziska

last: Hildebrandt

address: Svante Arrhenius Väg 20C, Stockholm

country: Sweden

institute: Stockholm University

library_source: transcriptomic single cell

data_processing:
Raw sequencing data (.fastq) were processes using the stpipeline to generate count matrices
H&E and CY3 images were aligned using the spotdetector tool
Assembly: mm10 (GRCm38.101), PlasmoDB-48_PbergheiANKA
Supplementary files format and content: stdata.tsv.gz: gene expression count-data
Supplementary files format and content: spotfiles_0.1.tsv.gz, spot-coordinate data
Supplementary files format and content: .jpg, images from spatial transcrptomics analysis (Fluoercence or Hematoxylin&Eosin)

molecule: polyA RNA

organism:
Plasmodium berghei ANKA
Mus musculus

source_name: liver

extract_protocol:
Livers were dissected at the respective timepoints, divided into approxmately 6x6mm large pieces and frozen in Methylbutane at -30°C for 5-10 seconds and embedded in OCT before sectioning them in 10µm thick sections.
Libraries were constructed as previously described in Hildebrandt et al. (2021), https://doi-org.ezp.sub.su.se/10.1038/s41467-021-27354-w
Spatial Transcriptomics

value: liver

tag: timepoint

value: control

tag: sample id


title: M00017563_24M_Cortex_iPCRtag61


title: section1_control_38h


title: section2_infected_38h

value: infected


title: section1_control_24h


title: section2_control_38h


title: section7_control_12h


title: section1_infected_38h


title: M00017549_24M_Heart_iPCRtag49

value: Heart


title: M04-20525_3M_Cortex_iPCRtag4


title: M00017560_24M_Lung_iPCRtag42


title: WT_Vehicle_H3


title: section8_infected_24


title: section3_infected_24


title: M00017912_15M_Cortex_iPCRtag36


title: section2_infected_12h


title: section1_infected_12h


title: M00017576_24M_Liver_iPCRtag38


title: M02-20523_3M_Lung_iPCRtag16


title: Standard3

city: Attlanta

first: Analia

middle: J

last: Vazquez Cegla

state: GA

address: 2015 Uppergate Dr.

country: USA

institute: Emory University

library_source: transcriptomic

data_processing:
Processed by Novogene. Performed alignments with HISAT2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values and raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: 16HBE14o- (WT CFTR)

growth_protocol: Cells plated on Transwells (Corning 3470) at a density of 250,000 cells per well.

extract_protocol:
Cells were scraped and pooled into 1 mL conical tubes (2 Transwells per sample) and centrifuged at 500g for 10 min at 4°C. RNA was isolated using a Quick-RNA Miniprep Kit (#R1054, Zymo Research).
RNA was sequenced and analyzed in bulk by Novogene. Briefly, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: Cells treated with low glucose (5.5 mM) or high glucose (17.5 mM) media for 7 days with daily media changes

tag: disease state

value: WT

tag: cell line

tag: cell type

value: Airway epithelial cells

value: WT CFTR

value: Normal glucose (not polarized cells)


title: Standard2


title: M00017897_15M_Cortex_iPCRtag52


title: M00017560_24M_Heart_iPCRtag50


title: Standard1


title: M00017897_15M_Liver_iPCRtag67

value: Liver


title: NG16HBEWT6

value: Normal glucose


title: M05-20522_3M_Cortex_iPCRtag28

value: C57BL/6 J

value: wildtype


title: NG16HBEWT5


title: NG16HBEWT3


title: M00017621_24M_Cortex_iPCRtag76

value: Cortex


title: M00018004_15M_Lung_iPCRtag80


title: M00018004_15M_Cortex_iPCRtag96


title: NG16HBEWT2


title: M04-20526_3M_Cortex_iPCRtag12


title: NG16HBEWT4


title: M01-20526_3M_Liver_iPCRtag5


title: NG16HBECF5

source_name: 16HBEge (DeltaF508 CFTR)

value: CF

value: DeltaF508 CFTR


title: M04-20525_3M_Heart_iPCRtag3


title: NG16HBECF6


title: NG16HBEWT1


title: NG16HBECF3


title: M00017912_15M_Heart_iPCRtag81


title: NG16HBECF4


title: M00017912_15M_Heart_iPCRtag35


title: NG16HBECF2


title: M00017562_24M_Lung_iPCRtag44


title: HG16HBEWT5

value: High glucose


title: M00017897_15M_Heart_iPCRtag51


title: M04-20527_3M_Heart_iPCRtag19


title: HG16HBEWT4


title: NG16HBECF1


title: M00017562_24M_Heart_iPCRtag52


title: HG16HBEWT2


title: M00017913_15M_Heart_iPCRtag43


title: M00017561_24M_Lung_iPCRtag43

value: Lung


title: HG16HBEWT1


title: HG16HBECF6


title: HG16HBECF4


title: M05-20522_3M_Heart_iPCRtag27


title: HG16HBECF2


title: M00017561_24M_Cortex_iPCRtag59


title: HG16HBECF5


title: M00018003_15M_Liver_iPCRtag71


title: M01-20523_3M_Cortex_iPCRtag27


title: M01-20523_3M_Liver_iPCRtag3


title: M00017563_24M_Liver_iPCRtag37


title: M00017912_15M_Cortex_iPCRtag89


title: Daoy cells, TTBK2 knockout, rep1

city: Taipei

first: Won-Jing

last: Wang

address: 155, Sec.2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
The original data obtained by high-throughput sequencing were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format.
The obtained raw paired-end reads were filtered by Trimmomatic to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software.
For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 with biological duplicate.
Differentially expressed genes (DEGs) analysis of two conditions was performed in R using DEGseq (without biological replicate) and DESeq2 (with biological replicate), which based on negative binomial distribution and Poisson distribution model, respectively.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Brain; Cerebellum

growth_protocol: Daoy cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using the Quick-RNA™ Miniprep Kit.RNA Purity and quantification were checked using SimpliNanoTM - Biochrom Spectrophotometers (Biochrom, MA, USA). RNA degradation and integrity were monitored by Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). A total amount of 1 μg total RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Brain; Cerebellum

value: Daoy

value: SHH-type medulloblastoma cell

value: TTBK2 knockout


title: HG16HBECF1


title: M04-20526_3M_Heart_iPCRtag11

value: Heart


title: Daoy cells, TTBK2 knockout, rep2

value: TTBK3 knockout


title: M00017913_15M_Lung_iPCRtag74


title: Daoy cells, WT, rep1

value: WT


title: M00017897_15M_Cortex_iPCRtag91


title: M00017621_24M_Heart_iPCRtag75


title: HG16HBEWT3

value: Airway epithelial cells

value: WT CFTR


title: pDMG Sample-3

city: Lyon

first: Marie

last: Castets

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were preprocessed using spaceranger mkfastq (v 2.0.0) to generate fastq files
Expression levels of 17 943 genes were quantified using spaceranger count (v 2.0.0)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz : List of spatial barcodes
Supplementary files format and content: features.tsv.gz : List of gene Ids
Supplementary files format and content: matrix.mtx.gz : Gene expression data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg : Aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg : Image of tissue and spots
Supplementary files format and content: scalefactors_json.json : Scalefactors in json format
Supplementary files format and content: tissue_hires_image.png : Hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png : Low-res image of tissue
Supplementary files format and content: tissue_positions.csv : List of spatial barcodes and coordinates specifying spots
Library strategy: Spatial trancriptomics

source_name: Midline

extract_protocol:
FFPE tissue sections were placed on Visium slides and prepared according to 10X Genomics protocols.
Probes hybridised on mRNA were captured on Visium slides and a gene expression library prepared following 10X genomics dedicated protocol.

value: Midline

tag: disease

value: Diffusion Midline Glioma (DMG)


title: M04-20527_3M_Lung_iPCRtag18

value: C57BL/6 J

value: wildtype


title: pDMG Sample-1

description: FFPE Spatial transcriptome sequencing


title: M02-20523_3M_Cortex_iPCRtag32

value: Cortex


title: HG16HBECF3

value: CF

value: DeltaF508 CFTR


title: M05-20522_3M_Lung_iPCRtag26

value: Lung


title: Res259 cells, WT, 24h BMP7, rep 3

data_processing:
Reads were pseudo-aligned using Kallisto (v 0.46.2) with the Ensembl v96 reference
Assembly: GRCh38
Supplementary files format and content: abundance.tsv : Tab delimited text file including Kallisto estimated counts and TPM

growth_protocol: Res259 cells were grown as a monolayer in DMEM medium with GlutaMAX-I, 4,5 g/L D-Glucose and 110 mg/L pyruvate (Gibco, 31966) supplemented with 10% foetal bovine serum (FBS), 1X MEM non-essential amino acid solution (Gibco, 11140050) and 1X Penicillin-Streptomycin (Gibco, 15140122). Cells were incubated in a humid atmosphere at 37 °C with 5% CO2.

extract_protocol:
1000 ng of total RNAs were isolated using the Nucleospin RNA kit
Libraries were prepared with Illumina Stranded mRNA Prep following recommendations

treatment_protocol: Cells were treated with 50 ng of human recombinant BMP7

value: Astrocytoma, grade II

value: Wild-Type

tag: time (hours)

value: BMP7 (50ng/mL)


title: Res259 cells, WT, 24h BMP7, rep 2


title: pDMG Sample-2

description: FFPE Spatial transcriptome sequencing


title: M00017913_15M_Lung_iPCRtag42


title: Res259 cells, K27M, 24h BMP7, rep 2


title: Daoy cells, WT, rep2

value: Brain; Cerebellum

value: Daoy

value: SHH-type medulloblastoma cell


title: M00017897_15M_Lung_iPCRtag50


title: Res259 cells, K27M, 24h BMP7, rep 3


title: M04-20526_3M_Lung_iPCRtag10


title: Res259 cells, K27M, 24h BMP7, rep 1


title: M00017563_24M_Heart_iPCRtag53

value: Heart


title: M00017577_24M_Cortex_iPCRtag63


title: M00017577_24M_Heart_iPCRtag55


title: M00017912_15M_Lung_iPCRtag34


title: M02-20522_3M_Lung_iPCRtag15


title: Res259 cells, WT, 3h BMP7, rep 1


title: Res259 cells, WT, 3h BMP7, rep 2


title: Res259 cells, WT, 3h BMP7, rep 3


title: M00018000_15M_Heart_iPCRtag84


title: M00018000_15M_Lung_iPCRtag76


title: Res259 cells, K27M, 3h BMP7, rep 3


title: Res259 cells, K27M, 3h BMP7, rep 1


title: Res259 cells, K27M, 3h BMP7, rep 2


title: M00018001_15M_Liver_iPCRtag69

value: Liver


title: Res259 cells, WT, no treatment, rep 3


title: M00017621_24M_Lung_iPCRtag74


title: M00018004_15M_Heart_iPCRtag88


title: Res259 cells, WT, no treatment, rep 2


title: Res259 cells, WT, 24h BMP7, rep 1


title: M04-20525_3M_Lung_iPCRtag2


title: Res259 cells, WT, no treatment, rep 1


title: M01-20526_3M_Cortex_iPCRtag29


title: Res259 cells, K27M, no treatment, rep 3


title: Res259 cells, K27M, no treatment, rep 2


title: M00017576_24M_Heart_iPCRtag54


title: M00017897_15M_Liver_iPCRtag49


title: BEAS-2B cells, SgO24UT 3

city: Columbus

first: Benjamin

middle: Stuart

last: Johnson

address: 473 W 12th Ave rm524

department: Department of Internal Medicine

institute: The Ohio State University

data_processing:
ROSALIND
Cutadapt  used to trim reads
Quality scores obtained by FastQC
reads aligned to Homo sapiens genome build GRCh38 by STAR
quantificaton of individual sample reads with Htseq
data normalized with Relatice Log Expression from DEseq2 r pacage. The RSeQC software quality control process was used to generate read distribution percentages, violin plots, identity heatmaps, and sample MDS plots
Assembly: GRCh38
Supplementary files format and content: FBXO24_normalizedCounts

growth_protocol: BEAS-2B cells were grown in HITES media (DMEM/F12 supplemented with 10% FBS, insulin, transferrin, hydrocortisone, β-estradiol, HEPES, L-glutamine and penicillin/streptomycin) at 37C with 5% CO2

extract_protocol:
RNeasy Plus mini kit according to manufacture protocol
RNA Library was construted by Novogene according to the following work flow "Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification."

treatment_protocol: Cells were infected with PA103, MOI 1, for 24 hours

value: Broncheal Epithelial Cells

value: FBXO24 Knockout

value: Untreated


title: BEAS-2B cells, SgO24UT 2


title: BEAS-2B cells, SgO24UT 1


title: M00018000_15M_Liver_iPCRtag68

value: C57BL/6 J


title: BEAS-2B cells, SgO24PA 3

value: PA103 Infection


title: M04-20527_3M_Liver_iPCRtag17

value: wildtype


title: M05-20522_3M_Liver_iPCRtag25


title: M00017912_15M_Liver_iPCRtag33


title: M00017577_24M_Liver_iPCRtag39


title: BEAS-2B cells, SgConUT 2

value: WT


title: M02-20522_3M_Cortex_iPCRtag31

value: Cortex


title: M00018002_15M_Heart_iPCRtag86


title: M00017577_24M_Lung_iPCRtag47

value: Lung


title: M00017561_24M_Heart_iPCRtag51


title: M02-20522_3M_Liver_iPCRtag7


title: BEAS-2B cells, SgConPA 2


title: M00017913_15M_Cortex_iPCRtag90


title: BEAS-2B cells, SgConUT 1


title: BEAS-2B cells, SgConPA 3


title: BEAS-2B cells, SgConPA 1


title: Res259 cells, K27M, no treatment, rep 1

value: Astrocytoma, grade II


title: Ambient Air Sample #2

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

description: Sample 3 (AA_sample_4)

data_processing:
CellRanger 7.0.1 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger wereused for further analysis.
Assembly: hg38
Supplementary files format and content: filtered gene-barcode matrices in HDF5 format

source_name: breast

growth_protocol: Primary breast epithelial cells were derived from breast tissues collected from two healthy female donors in ambient air and physioxia. The derived single cells were cultured at 5% O2 and ambient air respectively, in primary cell culture media containing low glucose DMEM and F-12 culture medium (1:3). The culture medium was supplemented with 5% fetal bovine serum, 5 µg/ml bovine insulin, 0.4 μg/ml hydrocortisone and 20 ng/ml EGF and penicillin-streptomycin. The cells were plated on 804G conditioned media – coated plates with primary cell culture medium and further supplemented with 4 μL/mL of adenine, 5 μmol/L of ROCK inhibitor Y-27632, 1 μmol/L of BMP inhibitor, DMH-1 and 1 μmol/L of TGFβ inhibitor A-83-01.

extract_protocol:
Cultured cells were harvested via trypsinization, followed by determination of cell viability. Avoidance of cell doublets was ensured with phase contrast microscopy.
cDNA libraries were prepared according to manufacturer's instructions for the Chromium Single Cell 3' Reagent Kit v3. cDNA quantitation was done with HSDNA Chips on  Agilent Technologies' Bioanalyzer system (G2943CA) and amplified with the Chromium TM Single cell Library kit V3.

value: breast

value: epithelial cells

tag: passages

value: 1 to 2

tag: condition

value: Ambient Air


title: Physioxia Sample #2

description: Sample 4 (physioxia_sample_4)

value: Physioxia


title: M00017621_24M_Liver_iPCRtag73


title: M04-20526_3M_Liver_iPCRtag9


title: M00017913_15M_Heart_iPCRtag82

value: Heart


title: BEAS-2B cells, SgO24PA 2


title: M00017913_15M_Liver_iPCRtag41

value: Liver


title: BEAS-2B cells, SgConUT 3

value: Broncheal Epithelial Cells


title: Ambient Air Sample #1

description: Sample 1 (Normaxia-1)


title: M04-20525_3M_Liver_iPCRtag1


title: CTRL4

city: Barcelona

first: Jaïr

middle: Dilmé

last: Capó

state: Barcelona

address: C/ Sardenya 416

country: Spain

institute: Sequentia Biotech

description:
raw_counts.txt
normalized_counts_TMM.txt

data_processing:
A trimming step was performed in order to remove adapters and low quality bases from the reads. The following parameters were used: minimum length was set to 15 bp and the quality score to 25. The software BBDuk was used for this scope.
The high quality reads from human samples were aligned against the Homo sapiens genome (GRCh38 from Ensembl) with STAR aligner (version 2.7.1a)
The identification and expression quantification of miRNAs, snoRNAs, snRNAs and piRNAs was performed with the COMPSRA pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text file includes TMM-normalized values for each sample.

source_name: peripheral blood

growth_protocol: A peripheral blood sample (9 mL) from each FRDA patient and healthy individual was obtained.

extract_protocol:
Total RNA, including miRNAs fraction, was extracted from these cell pellets according to manufacturer’s instructions (Trizol®, Ambion, Waltham, MA, USA).
NEB small RNA library preparation kit

treatment_protocol: PBMCs from a peripheral blood sample of each FRDA patients and CTRL subjects were isolated using density-gradient medium. About 4 ml of fresh blood was gently layered on equal volume of Ficoll-Paque Plus® (GE Healthcare, Little Chalfont, UK) and then centrifuged at 400xg for 40 minutes at RT without brake. The mononuclear cell layer was transferred in a new tube and washed two times with Phosphate Buffered Saline (PBS). The cell pellet was resuspended in 1 ml of Trizol® (Ambion, Waltham, MA, USA) and stored at -80°C.

value: peripheral blood

value: PBMCs

value: wild type sequence of FXN gene

value: Healthy individual (control)

tag: group

value: control


title: WT-rep3 [ncRNA-seq]

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were trimmed for adaptor sequences and low quality bases using trimmomatic (0.38)
The trimmed reads length less than 17 bp were removed. Clean reads for each sample were aligned by bowtie2 (2.3.4.1) with parameter “--very-sensitive-local” to the artificial small ncRNA reference which include ENSEMBL annotated small ncRNAs (miRNA, misc_RNA, Mt_rRNA, Mt_tRNA, snoRNA, snRNA, tRNA) and 45S pre-rRNA (NR_046233.2).
Read counts per ncRNA were calculated by a perl script.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma separated text files with raw gene counts for every gene and every sample

source_name: bone marrow cells

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen).
1~3 μg total RNA per sample was used for library construction, which was generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB) following manufacturer’s instructions. After synthesis of first strand cDNA, PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 170~370 bp (the length of snoRNA plus adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. After clustering of the index-coded samples, the library preparations were sequenced on an Illumina NovaSeq platform.

tag: tag

value: bone marrow

value: wildtype


title: WT-rep2 [ncRNA-seq]


title: BEAS-2B cells, SgO24PA 1

value: FBXO24 Knockout

value: PA103 Infection


title: Physioxia Sample #1

description: Sample 2 (Hypoxia-1)

tag: tissue

value: breast


title: CTRL3


title: WT-rep1 [ncRNA-seq]


title: CTRL1


title: CTRL2


title: KO-rep3 [RiboMeth-seq]

data_processing:
Library strategy: RiboMeth-seq
Illumina Casava1.8 software used for basecalling.
Sequenced data were trimmed with trimmomatic and keep reads which length more than 16bp.
Clean data were mapped to rRNA reference (NR_003278.3 18S rRNA, NR_003280.2 5.8S rRNA, NR_003279.1 28S rRNA) using bowtie2 with parameter “--end-to-end -k 1”.
The sam files obtained from the alignment were converted to the bed files.
5’ and 3’ ends counting was done by bedtools (2.29.0) and combined to calculate RiboMeth score. The scores were normalized to average values for -6 and +6 nucleotides.
Genome_build: GRCm38
Supplementary_files_format_and_content: BedGraph files with each sample RiboMeth score.

extract_protocol:
Briefly, 1μg total RNA was subjected to alkaline hydrolysis, which was performed in 50 mM bicarbonate buffer pH 9.2 for 12 min at 95℃. The reaction was stopped by ethanol precipitation using 3M NaOAc (Sigma), pH 5.2 and Glycoblue (Invitrogen) as a carrier in liquid nitrogen. The size of generated RNA fragments was assessed by electrophoresis (1% agarose gel, 80V, 50 min) and were ranging from 50 to 200 nt.   RNA fragments were directly 3’-end dephosphorylated using 5 U Antarctic Phosphatase (NEB) for 30 min at 37℃, and then phosphorylated at the 5’-end using T4 PNK and 1mM ATP for 1h at 37℃.Resulting RNA fragments were then purified using Rneasy MinElute Cleanup kit (QIAGEN) according to the manufacturer instructions with minor modification. Finally, 10 μL of nuclease-free water was used to elute RNA fragments.
Construction of RNA fragments library was performed by LC Sciences (China) using TruSeq Small RNA Sample Prep Kits (Illumina) following manufacturer instruction. After PCR amplification, products were purified on a 6% poly-acrylamide Tris-borate-EDTA gel. DNA fragments corresponding to 140~270 bp (the length of fragments plus adaptors) were recovered, and were sequenced on Illumina Hiseq2500 platform and single-end 50 bp reads were generated.

value: Mat KO


title: PAT12 (LOG)

value: homozygous expansion of GAA repeat sequence in FXN gene

value: Friedreich Ataxia patients sample

value: LOG


title: KO-rep2 [ncRNA-seq]


title: KO-rep1 [ncRNA-seq]


title: KO-rep2 [RiboMeth-seq]


title: PAT9 (LOG)


title: PAT11 (LOG)


title: WT-rep3 [RiboMeth-seq]


title: PAT10 (LOG)


title: Sample 5, Lab A, Bulk

city: Oslo

first: Karl-Johan

last: Malmberg

address: Ullernchausseen 70

country: Norway

institute: Oslo University Hospital

description:
3' mRNA library: count matrices of gene expression
Sample A5

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x Genomics Cell Ranger pipeline with default settings (v3.0.2) and aligning to the hg19 genome build and Ensembl 93 annotations.
Assembly: hg19
Supplementary files format and content: Cellranger output files, count matrices: barcode.tsv, genes.tsv, matrix.mtx

source_name: Peripheral blood

extract_protocol:
Cells were harvested and surface stained with the following antibodies: CD57-FITC (HNK-1) from BioLegend; KIR3DL1S1-APC (Z27.3.7), CD56-ECD (N901), CD158b1/b2,j-PE-Cy5.5 (GL183), from Beckman Coulter; KIR2DL1-APC-Cy7 (REA284), NKG2C-PE (REA205), NKG2A-PE Vio770 (REA110) from Miltenyi Biotec. 12,000 cells were directly sorted into Eppendorf tubes at 4°C for each sample using a FACSAriaII (Beckton Dickinson).
Standard 10X Genomics library preparation

value: Peripheral blood

value: NK cells


title: WT-rep1 [RiboMeth-seq]


title: WT-rep2 [RiboMeth-seq]


title: PAT7 (IOG)

value: IOG


title: PAT5 (IOG)

value: peripheral blood


title: PAT6 (IOG)

value: PBMCs


title: PAT8 (IOG)


title: PAT4 (EOG)

value: EOG


title: PAT1 (EOG)


title: PAT3 (EOG)


title: KO-rep3 [ncRNA-seq]


title: Sample 1, Lab A, Bulk

description:
3' mRNA library: count matrices of gene expression
Sample A1


title: Sample 4, Lab A, Bulk

description:
3' mRNA library: count matrices of gene expression
Sample A4


title: AC093-8/26/2002-33 Cerebrospinal fluid

city: Seattle

first: Kai

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Cerebrospinal fluid

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

value: Healthy Subject

tag: anatomical location

value: Entire brain and spinal cord

tag: rna source

value: total cell-free biofluid RNA


title: B41_510_NS01_BX_S43

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Align the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
QC methods used samtools sort 1.10, Picard 2.22.4, and FastQC 0.11.9
Assembly: hg38
Supplementary files format and content: Salmon gene expression file (tab-delimited)

source_name: Breast

extract_protocol:
RNA was extracted from paraffin-embedded baseline tumor samples
ribo-zero RNAseq libraries were made using an Illumina TruSeq Stranded Total RNA kit

value: Breast

tag: Sex

value: Female

tag: race

value: White

value: Untreated


title: Sample 2, Lab A, Bulk

description:
3' mRNA library: count matrices of gene expression
Sample A2


title: BQ339 Cerebrospinal fluid


title: KO-rep1 [RiboMeth-seq]

value: bone marrow

tag: genotype

value: Mat KO


title: PAT2 (EOG)

value: homozygous expansion of GAA repeat sequence in FXN gene

value: Friedreich Ataxia patients sample


title: B41_503_1A2_BX_S42

value: Black

tag: treatment


title: B41_506_1_BX_S83

value: Unknown


title: B41_502_A1_BX_S41


title: B41_494_A1_BX_S35


title: ACBQ0279 Cerebrospinal fluid


title: BQ6144 Cerebrospinal fluid


title: B41_496_1_BX_S36


title: #2BQ0268 Cerebrospinal fluid


title: AC634 Cerebrospinal fluid


title: BQ11019 Cerebrospinal fluid


title: B41_493_A1_BX_S81


title: AC192 Cerebrospinal fluid


title: Sample 3, Lab A, Bulk

description:
3' mRNA library: count matrices of gene expression
Sample A3

value: Peripheral blood

value: NK cells


title: B41_500_B1_BX_S40


title: B41_497_B01_BX_S37


title: AC840 Cerebrospinal fluid


title: B41_489_A1_BX_S33


title: AC-067 Cerebrospinal fluid


title: B41_499_A01_BX_S39


title: B41_491_NS01_BX_S34


title: AC224 Cerebrospinal fluid


title: B41_492_3_BX_S80


title: AC532 Cerebrospinal fluid


title: B41_498_A01_BX_S38


title: AC169 Cerebrospinal fluid


title: AC061-2/19/2002-33 Cerebrospinal fluid


title: B41_473_NS01_BX_S30


title: BQ/AC0486 Cerebrospinal fluid


title: AC-054 Cerebrospinal fluid


title: B41_475_NS01_BX_S79


title: B41_465_A_BX_S27


title: AC089 Cerebrospinal fluid


title: B41_474_NS01_BX_S31

value: Asian


title: BQ0474 Cerebrospinal fluid


title: B41_460_NS01_BX_S25


title: B41_468_A1_BX_S29


title: BQ9123 Cerebrospinal fluid


title: 2BQ0453-8/11/2008-33 Cerebrospinal fluid


title: ACBQ0439 Cerebrospinal fluid


title: B41_455_A01_BX_S71


title: AC078 Cerebrospinal fluid


title: B41_486_NS01_BX_S32


title: AC/BQ259 Cerebrospinal fluid


title: B41_466_1_BX_S28


title: B41_458_1A_BX_S84


title: BQ11014 Cerebrospinal fluid


title: AC\BQ0280 Cerebrospinal fluid


title: AC086 Cerebrospinal fluid


title: B41_450_NS01_BX_S78


title: B41_464_A1_BX_S26


title: 2BQ0243 Cerebrospinal fluid


title: AC098 Cerebrospinal fluid


title: AC075 Plasma

source_name: Plasma

value: Entire cardiovascular system


title: B41_446_NS01_BX_S67


title: B41_448_A_BX_S69


title: B41_440_B_BX_S65


title: BQ11014 Plasma

value: Healthy Subject


title: AC087-6/25/2002-33 Plasma


title: B41_451_1_BX_S70


title: AC-050 Plasma


title: B41_431_A1_BX_S62


title: BQ11013 Plasma


title: AC142 Plasma


title: B41_435_BBX_BX_S63


title: B41_459_A1_BX_S72


title: B41_447_A2_BX_S68


title: B41_430_1_BX_S61


title: B41_444_A_BX_S66


title: AC/BQ353 Plasma


title: AC758 Plasma


title: AC-054 Plasma


title: B41_428_A2_BX_S60


title: AC064 Plasma


title: AC-059 Plasma


title: BQ6115 Plasma


title: B41_427_1A_BX_S59


title: B41_417_A1_BX_S58


title: B41_416_1A_BX_S88


title: AC009 Plasma


title: AC759 Plasma


title: B41_438_B1_BX_S64


title: B41_412_A2_BX_S57


title: AC218 Plasma


title: B41_408_A_BX_S56


title: B41_424A_A2_BX_S16


title: AC061-2/19/2002-33 Plasma


title: B41_398_NS01_BX_S54


title: B41_420A_A4_BX_S77


title: B41_401_A1_BX_S74


title: B41_400_A_BX_S55


title: BQ6129 Plasma


title: BQ9116 Plasma


title: AC-071 Plasma


title: B41_425A_B1_BX_S45


title: B41_399_A_BX_S73


title: B41_394_A1_BX_S52


title: AC084 Plasma


title: B41_390_A2_BX_S51


title: B41_381_NS01_BX_S50


title: 2BQ0243 Plasma


title: LP285 Plasma


title: AC/BQ248 Plasma


title: B41_374_A_BX_S24


title: AC634 Plasma


title: AC060 Plasma


title: B41_367_A1_BX_S23


title: AC839 Plasma


title: AC/BQ259 Plasma


title: BQ6167 Plasma


title: B41_362_1_BX_S44


title: B41_512_NS01_BX_S86


title: B41_363_1A_BX_S46


title: #2AC/BQ134 Plasma


title: AC080-6/13/2002-33 Plasma


title: AC\BQ0280 Plasma


title: B41_359_B1_BX_S21


title: B41_356_2_BX_S38


title: B41_364_A_BX_S22


title: B41_395_2_BX_S53


title: B41_380_B1_BX_S49


title: BQ0435 Plasma


title: B41_351_A1_BX_S44


title: BQ0006 Plasma


title: BQ0499 Plasma


title: B41_355_2_BX_S20


title: AC148 Plasma


title: AC195 Plasma


title: B41_354_A_BX_S47


title: AC/BQ278 Plasma


title: B41_348_NS01_BX_S42


title: B41_345_A2_BX_S82


title: AC104 Plasma


title: BQ6144 Plasma


title: B41_353_NS01_BX_S37


title: B41_343_1A_BX_S19


title: AC112 Plasma


title: BQ0436 Plasma


title: B41_341_A2_BX_S18


title: B41_331_B_BX_S15


title: BQ11019 Plasma


title: AC224 Plasma


title: B41_330_A1_BX_S14


title: B41_335_NS01_BX_S17


title: AC-067 Plasma


title: AC840 Plasma


title: AC170 Cerebrospinal fluid

value: Entire brain and spinal cord


title: B41_322_NS01_BX_S11


title: B41_329_A1_BX_S34


title: B41_321_I_BX_S33


title: AC644 Cerebrospinal fluid

value: total cell-free biofluid RNA


title: B41_328_NS01_BX_S13

value: Breast


title: AC184 Cerebrospinal fluid


title: BQ11004 Plasma


title: B41_306_A1_BX_S8

value: Female


title: 2BQ0292 Cerebrospinal fluid


title: AC-066 Cerebrospinal fluid


title: B41_314_A1_BX_S10

value: White


title: B41_313_NS01_BX_S31

value: Untreated


title: BQ6119 Cerebrospinal fluid


title: AC088-7/08/2002-33 Cerebrospinal fluid


title: B41_305_NS01_BX_S26


title: B41_312_1A_BX_S29


title: AC069 Cerebrospinal fluid


title: AC068-3/26/2002-33 Cerebrospinal fluid


title: B41_333_A1_BX_S16


title: BQ/AC0397 Cerebrospinal fluid


title: BQ356 Cerebrospinal fluid


title: B41_311_A01_BX_S28


title: B41_292_A1_BX_S4


title: BQ0277 Cerebrospinal fluid


title: B41_324_NS01_BX_S12


title: B41_304_A1_BX_S7


title: BQ6140 Plasma


title: AC-063 Cerebrospinal fluid


title: 2BQ325 Cerebrospinal fluid


title: B41_297_NS01_BX_S6


title: AC081 Cerebrospinal fluid


title: B41_346_1_BX_S36


title: B41_290_1_BX_S3


title: B41_286_A_BX_S76


title: B41_293_A1_BX_S5


title: B41_288_A1_BX_S96


title: AC036-2/28/2002-43 Cerebrospinal fluid


title: BQ/AC0442 Cerebrospinal fluid


title: #2BQ8117 Cerebrospinal fluid


title: AC-062 Cerebrospinal fluid


title: B41_287_A1_BX_S2


title: 2BQ0342 Cerebrospinal fluid


title: B41_278_1A_BX_S24


title: BQ210 Cerebrospinal fluid


title: AC157 Cerebrospinal fluid


title: B41_285_A1_BX_S95


title: BQ9121 Cerebrospinal fluid


title: BQ6104 Cerebrospinal fluid


title: B41_275_A01_BX_S94


title: BQ6136 Cerebrospinal fluid


title: B41_269_NS01_BX_S22


title: AC-048 Cerebrospinal fluid


title: B41_280_A1_BX_S1


title: B41_267_NS01_BX_S21


title: #2AC/BQ137 Cerebrospinal fluid


title: AC/BQ260 Cerebrospinal fluid


title: B41_264_A_BX_S20


title: B41_254_1A_BX_S16


title: BQ/AC0472 Cerebrospinal fluid


title: B41_260_A1_BX_S18


title: AC110 Cerebrospinal fluid


title: B41_259_NS01_BX_S92


title: B41_253_A1_BX_S15


title: AC108 Cerebrospinal fluid


title: B41_258_A1_BX_S17


title: #2AC/BQ134 Cerebrospinal fluid


title: BQ8113 Cerebrospinal fluid


title: B41_261_A1_BX_S19


title: BQ9116 Cerebrospinal fluid


title: BQ6127 Cerebrospinal fluid


title: B41_310_NS01_BX_S9


title: B41_250_1A_BX_S14


title: B41_274_B01_BX_S23


title: B41_251_A001_BX_S46


title: B41_273_A1_BX_S93


title: AC/BQ248 Cerebrospinal fluid


title: B41_245_A1_BX_S10


title: B41_244_2_BX_S9


title: AC060 Cerebrospinal fluid


title: AC/BQ353 Cerebrospinal fluid


title: AC/ST217-5/05/2004-33 Cerebrospinal fluid


title: BQ0435 Cerebrospinal fluid


title: AC194 Cerebrospinal fluid


title: B41_237_NS01_BX_S5


title: B41_248_NS01_BX_S12


title: B41_236_A1_BX_S91


title: B41_247_1A_BX_S11


title: B41_235_B_BX_S4


title: BQ0006 Cerebrospinal fluid


title: AC/BQ278 Cerebrospinal fluid


title: AC104 Cerebrospinal fluid


title: B41_241_A1_BX_S7


title: BQ6129 Cerebrospinal fluid


title: BQ6167 Cerebrospinal fluid


title: B41_232_NS01_BX_S3


title: B41_240_2B_BX_S6


title: AC064 Cerebrospinal fluid


title: B41_242_B_BX_S8


title: AC112 Cerebrospinal fluid


title: B41_224_B2_BX_S30


title: AC-050 Cerebrospinal fluid


title: BQ6140 Cerebrospinal fluid


title: BQ0499 Cerebrospinal fluid


title: AC148 Cerebrospinal fluid


title: AC839 Cerebrospinal fluid


title: AC759 Cerebrospinal fluid


title: B41_230_A1_BX_S2


title: B41_226_A1_BX_S35


title: B41_249_A1_BX_S13


title: BQ11004 Cerebrospinal fluid


title: AC218 Cerebrospinal fluid


title: B41_214_NS01_BX_S33


title: BQ11013 Cerebrospinal fluid


title: B41_228_NS01_BX_S1


title: B41_210_1_BX_S23


title: AC075 Cerebrospinal fluid


title: CTRL-treated cells, scRNA-Seq

city: Ann Arbor

first: Carlos

last: Aguilar

state: MI

address: 2800 Plymouth Rd

department: Biomedical Engineering

institute: University of Michigan

description: 10x Genomics

data_processing:
Fastq files were checked for quality using FastQC
Fastq files were aligned to the GRCm38/mm10 reference transcriptome using Kallisto version 0.46.2 with the following parameters:  -b 100 --single -l 76 -s 20 -t 8
Assembly: mm10
Supplementary files format and content: mtx

source_name: Hindlimb muscle

extract_protocol:
RNA was isolated using the Trizol lysis reagent, followed by the Qiagen Rneasy micro kit.
Takara Bio SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing was used for cDNA synthesis. Illumina library prep was performed with theNexteraXT DNA Library Preparation Kit andNexteraXT Index Kit, using an input of 500pgof full-length cDNA amplicons per sample

value: Hindlimb muscle

tag: strain

value: DMSO Vehicle

value: female


title: AC-059 Cerebrospinal fluid


title: B41_211_1A_BX_S24


title: B41_220_1A_BX_S27


title: B41_231_NS01_BX_S41


title: AC142 Cerebrospinal fluid


title: B41_223_B2_BX_S29


title: paneth cells, IFNAR1 KO, TNF, rep 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were quality checked with fastqc and quality filtered with trimmomatic (v0.39; parameters:SLIDINGWINDOW:4:30 MINLEN:50)
Reads were aligned to the mm39 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples

source_name: small intestine

extract_protocol:
RNA was obtained with the Aurum Total RNA Mini kit (Bio-Rad) according to the manufacturer’s protocol
RNA was used to generate a sequencing libary for the Element AVITI accoring to the manufacturers instructions from the AVITI 150 cycles Cloudbreak sequencing kit single-end reads

treatment_protocol: mice were injected with PBS or TNF. The small intestine was isolaed after 15h and PC were purified using a cell sorter for RNA isolation

value: purified paneth cells

value: IFNAR1 KO

value: TNF

tag: time

value: small intestine


title: AC084 Cerebrospinal fluid


title: AC087-6/25/2002-33 Cerebrospinal fluid


title: AC009 Cerebrospinal fluid


title: B41_218_A1_BX_S26


title: BQ0436 Cerebrospinal fluid


title: B41_213_A1_BX_S25


title: AC080-6/13/2002-33 Cerebrospinal fluid


title: B41_221_1_BX_S28


title: paneth cells, IFNAR1 KO, TNF, rep 1


title: AC195 Cerebrospinal fluid


title: paneth cells, IFNAR1 KO, TNF, rep 2


title: paneth cells, IFNAR1 KO, PBS, rep 3

value: PBS


title: AC-071 Cerebrospinal fluid


title: LP285 Cerebrospinal fluid


title: AC758 Cerebrospinal fluid


title: BQ6115 Cerebrospinal fluid


title: B41_203_B2_BX_S19


title: B41_204_A1_BX_S20


title: 2BQ0342 Plasma


title: ATRA+Agonist-treated cells, scRNA-Seq

description: 10x Genomics


title: AC036-2/28/2002-43 Plasma


title: paneth cells, IFNAR1 KO, PBS, rep 2


title: B41_206_A_BX_S22


title: B41_205_2_BX_S21


title: BQ356 Plasma


title: paneth cells, IFNAR1 KO, PBS, rep 1


title: AC110 Plasma


title: AC068-3/26/2002-33 Plasma


title: B41_200_A1_BX_S18

value: Black


title: AC089 Plasma

value: Entire cardiovascular system


title: BQ/AC0472 Plasma

value: Healthy Subject


title: paneth cells, TNF, rep 4

data_processing:
Reads were quality checked with fastqc and quality filtered with trimmomatic (v0.39; parameters:SLIDINGWINDOW:4:30 MINLEN:50)
Reads were aligned to the mm10 reference genome with the STAR aligner (v2.7.10a) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples

source_name: purified paneth cells


title: AC/BQ260 Plasma


title: paneth cells, TNF, rep 2


title: B41_190_A4_BX_S13


title: BQ9121 Plasma


title: B41_188_1_BX_S12


title: paneth cells, TNF, rep 1


title: AC-062 Plasma


title: B41_199_A1_BX_S17


title: B41_196_A1_BX_S15


title: ACBQ0439 Plasma


title: #2BQ8117 Plasma


title: AC086 Plasma


title: AC184 Plasma


title: BQ210 Plasma


title: paneth cells, PBS, rep 2


title: paneth cells, PBS, rep 3


title: AC108 Plasma


title: BQ/AC0442 Plasma


title: B41_187_A2_BX_S48


title: B41_186_4_BX_S11


title: AC644 Plasma


title: paneth cells, TNF, rep 3


title: 2BQ0453-8/11/2008-33 Plasma


title: AC/ST217-5/05/2004-33 Plasma


title: paneth cells, PBS, rep 1


title: B41_195_1A_BX_S14


title: BQ6104 Plasma


title: B41_180_B_BX_S9


title: B41_178_A1_BX_S7


title: AC-048 Plasma


title: #2AC/BQ137 Plasma


title: Gypsy Moth Strain CT, Day 5, Replicate 2

city: Quebec City

first: Christopher

middle: Ian

last: Keeling

state: QC

address: 1055 rue du PEPS

department: Canadian Forest Service

country: Canada

institute: Natural Resources Canada

data_processing:
Sequencing reads were assessed for quality with FastQC (v0.11.5) (Andrews, 2019).
Sequences were trimmed for adapters, quality, and minimum length with Trimmomatic (v0.36) (Bolger et al., 2014).
The existing annotations from the draft genome were augmented by merging them with the read mapping information from all samples using StringTie prior to counting reads at each locus with featureCounts (v2.0.0, counting gene_id meta-features) (Liao et al., 2014).
Statistical analyses were conducted with the DESeq2 package (v1.28.1) (Love et al., 2014) in R (v4.0.2) (R Core Team, 2020), using the apeglm package (v1.10.0) (Zhu et al., 2019) for shrinkage estimation.
Data in this GEO submission report the normalized counts after variance stabilizing transformation with vst(fitType='local') within DESeq2.
Genome_build: lda.genome.v0.3.fasta available here: https://doi.org/10.17605/OSF.IO/UNZ2V
Supplementary_files_format_and_content: PROJECT_Cusson_pupae_flight_vst_counts.txt: Normalized count data after variance-stabilizing transformation.
Supplementary_files_format_and_content: The 'PROJECT_Cusson_pupae_flight_representative_transcripts.fa' contains a representative transcript sequence for each locus in the genome for which gene-level expression levels are reported. The best representative at each locus was chosen based upon the highest expression of the various splice variants from StringTie, counting transcript_id meta-features.

organism: Lymantria dispar dispar

source_name: Gypsy Moth Strain CT_Day 5

growth_protocol: Eggs from laboratory colonies were held at 5±1°C and ~100% RH with L:D of 16:8 for 144 days to ensure that diapause requirements were met. All eggs produced by 100 individual females from each geographic population (CT 32nd lab generation and RM 34th lab generation) were mixed together, as is the normal process for maintaining these colonies. From the pool of mixed eggs, packets of about 500 eggs were made. Eggs were incubated at 25±1°C and 60% RH with L:D of 16:8 to initiate hatch.

extract_protocol:
Samples were homogenized individually in Trizol reagent (Ambion, Life Technologies; 4 to 7 mL depending on the size of the pupa) using 15 mL disposable tissue grinders (VWR, Cat.47732-446). For each sample, 500 µL of the homogenate was transferred to a 1.5 mL microfuge tube, to which another 500 µL of Trizol was added. The tubes were then centrifuged for 4 min at 17,000 x g to pellet debris. 400 µL of the supernatant was subsequently used for RNA extraction using the Direct-zol RNA miniprep kit (Zymo Research). RNAs were eluted using 50 µL of water, quantified using a NanoDrop ND1000 spectrophotometer (Thermo Fisher Scientific Inc.) and assessed for quality using a 2100 Bioanalyzer system (Agilent).
RNASeq libraries and Ion Proton sequencing were performed at the Genomic Analysis Platform of the Institute of Integrative and Systems Biology (Laval University, Quebec, QC, Canada) using the NEBNext Ultra II directional RNA library prep kit (New England BioLabs) with the NEBNext Poly (A) mRNA magnetic isolation module. Ion Proton sequencing was performed on an Ion Chef with a P1 chip according to manufacturer's instructions.

treatment_protocol: Larvae were reared in cohorts of 6 at 25±1°C and 60% RH with L:D of 16:8, using methods previously described (Keena 1996). The high wheat germ artificial diet (Bell et al. 1091) was optimized for the individual populations using Wesson salt mix without iron and by adding 0.21 g (RM population) or 0.13 g (CT population) amorphous FePO4/L of diet. Pupae were harvested daily and separated according to sex.

value: CT

tag: sampling timepoint (day)


title: BQ6119 Plasma

value: total cell-free biofluid RNA


title: BQ339 Plasma


title: Gypsy Moth Strain CT, Day 11, Replicate 3

source_name: Gypsy Moth Strain CT_Day 11


title: AC-066 Plasma


title: Gypsy Moth Strain CT, Day 5, Replicate 1


title: BQ6127 Plasma


title: Gypsy Moth Strain CT, Day 11, Replicate 1


title: AC081 Plasma


title: B41_184_1_BX_S10

value: Breast


title: AC170 Plasma


title: B41_172_1_BX_S5

value: Female


title: Gypsy Moth Strain CT, Day 11, Replicate 2


title: Gypsy Moth Strain CT, Day 3, Replicate 3

source_name: Gypsy Moth Strain CT_Day 3


title: #2BQ0268 Plasma


title: AC093-8/26/2002-33 Plasma


title: AC157 Plasma


title: B41_170_2A_BX_S4

value: White


title: BQ6136 Plasma


title: AC169 Plasma


title: Gypsy Moth Strain CT, Day 8, Replicate 3

source_name: Gypsy Moth Strain CT_Day 8


title: Gypsy Moth Strain CT, Day 3, Replicate 1


title: B41_168_A1_BX_S3

value: Asian

value: Untreated


title: B41_164_NS01_BX_S46


title: 2BQ0292 Plasma


title: B41_177_1_BX_S47


title: Gypsy Moth Strain CT, Day 8, Replicate 2


title: AC078 Plasma


title: wild-type mutant seedlings

city: Belgarde

first: Ivana

last: Nikolic

address: Vojvode Stepe 444a

country: Serbia

institute: Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade

description: A comparison of transcriptome changes under oxidative stress

data_processing:
The initial step involved processing the raw reads in fastq format, followed by the calculation of Q20, Q30, and GC content for the clean reads. The raw reads were subjected to filtering, excluding any reads with adapter contamination, reads containing more than 10% of uncertain nucleotides, and low-quality reads (with a Qscore < 5 for more than 50% of the bases) using the fastp tool. All the downstream analyses were based on clean, high-quality data.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
featureCounts was used to count the number of reads mapped to each gene.
The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to analyzing differential gene expression, the read counts for each sequenced library were adjusted using the edgeR program package by applying a scaling normalization factor. Differential expression analysis of two groups was performed using the edgeR (without biological replicates) R package. The p-values were adjusted using the Benjamini–Hochberg method to control the false discovery rate. Genes with corrected p-value (padj) < 0.05 and an absolute fold change of 2 (|log2(Fold Change)| ≥ 1) identified by edgeR were classified as differentially expressed.
Enrichment analysis was done using the clusterProfiler R package. R package (with correction of gene length bias and threshold of corrected p-value < 0.05) was considered to test the statistical enrichment of differentially expressed genes in GO terms and KEGG pathways.
Assembly: Arabidopsis thaliana reference genome (ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1)
Supplementary files format and content: Excel files including FPKM values for each sample in three comparisons: 1) Differential gene expression analysis between knockout mutant dss1(I) and wild-type seedlings under H2O2 (KO_DSS1_IvsWT_deg_all.xls.gz), 2) Differential gene expression analysis between knockout mutant dss1(I) and dss1(V) seedlings under H2O2 (KO_DSS1_IvsKO_DSS1_V_deg_all.xlsx.gz) and 3) Differential gene expression analysis between knockout mutant dss1(V) and wild-type seedlings under H2O2 (KO_DSS1_VvsWT_deg_all.xlsx.gz).

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Wild-type plants (Columbia-0), dss1(I), and dss1(V) mutants of Arabidopsis thaliana were cultured in sterile Murashige and Skoog (MS) agar medium containing 1% sucrose (Suc) . The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were obtained using CRISPR/Cas9 technology. After 5 days of dormancy at +4°C, seedlings were grown on the plates for 14 days. Plants were grown in a growth chamber under standard conditions as follows: a long-day regime (16 h day), light intensity of 150 µmol m^-2s^-1, relative humidity of 70%, day/night temperatures of 21°C/19°C.

extract_protocol:
Plant tissue was frozen in liquid nitrogen and ground using a mortar and pestle. RNA was isolated from 30 mg of powdered sample by the GeneJET RNA Purification kit (Thermo Fisher Scientific,Waltham, MA, USA) according to the manufacturer’s protocol. 3.7-5.6 ug of total RNA was used for construction of sequncing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV 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 activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: To analyze the stress response, fourteen-day-old Arabidopsis was grown on new agar plates containing 10 mM H2O2. Seedlings were collected and immediately frozen in liquid nitrogen 3 days after the start of treatment. All samples were stored at -80°C prior to use.

value: seedlings

tag: cell type

value: plant

value: wild-type

value: hydrogen preroxide


title: B41_163_NS01_BX_S95


title: Gypsy Moth Strain CT, Day 1, Replicate 3

source_name: Gypsy Moth Strain CT_Day 1

value: female


title: Gypsy Moth Strain CT, Day 3, Replicate 2


title: dss1(V) mutant seedlings

value: dss1(V) knockdown


title: B41_165_A1_BX_S1


title: BQ9123 Plasma


title: BQ9114 Plasma


title: After_CRISPRi_Rep_6

city: Los Angeles

first: Frank

last: Attenello

address: 1501 San Pablo St

institute: University of Southern California

description: After_Rep_5,After_Rep_6,Before_Rep_5,Before_Rep_6

data_processing:
Sequencing reads were aligned to the expected CRiNCL library sequences, counted and quantified, statistics calculated, and graphs plotted, all utilizing the ScreenProcessing package pipeline (https://github.com/mhorlbeck/ScreenProcessing)
Assembly: human CRISPRi non-coding library (CRinCL)
Supplementary files format and content: Count table of sequenced reads aligned to to the CRinCL reference, generated by the ScreenProcessing package mentioned in data processing step above.

source_name: glioblastoma

growth_protocol: U87 cells (ATCC, HTB-14; RRID:CVCL_0022), HEK293T cells (ATCC, CRL-3216; RRID:CVCL_0063), and U251 cells (Sigma-Aldrich, 09063001-1VL; RRID:CVCL_0021) were maintained in D10 medium, which contained high glucose Dulbecco’s modified Eagle’s medium (DMEM) (Gibco, 11995-081) supplemented with 10% fetal bovine serum (FBS) (Seradigm, 97068-085) and 1X antibiotic-antimycotic (Gibco, 15240-062). USC02 cells, a primary glioma stem cell (GSC) line, were a gift from Thomas C. Chen and maintained in cancer stem cell (CSC) medium containing DMEM/F-12 (Gibco, 11320-033) supplemented with 1% B-27 (Life Technologies, 12587-010), 1X antibiotic-antimycotic, and 20 ng/mL epidermal growth factor (EGF) (Peprotech, AF-100-15) and basic fibroblast growth factor (bFGF) (Peprotech, 100-18B) (Attenello et al. J Neurosci Res. 2021). All cells were kept in a humidified incubator at 37 °C with 5% CO2 and confirmed to be mycoplasma free with the LookOut Mycoplasma PCR Detection Kit (Sigma-Aldrich, MP0035) immediately prior to a large-scale screen and at least once every two months.

extract_protocol:
For deep sequencing following screen, cells were collected from the top chamber by trypsinization. After harvesting and purifying genomic DNA, PCR was utilized to amplify sgRNA encoding regions. Then, using custom primers, sgRNA enconding regions were sequenced on Illumina HiSeq 4000 at high coverage, as previously described (Liu et al. Science 2017, Gilbert et al. Cell 2014).
The U87-specific CRISPR inhibition (CRISPRi) library, derived from the human CRISPRi non-coding library (CRinCL) (Addgene #86542, a gift from Jonathan Weissman) by selecting sub-libraries that targeted all expressed lncRNAs in U87 (Liu et al. Science 2017), was used to generate the sgRNA pool used for screening.
U87 cells expressing dCas9-KRAB-BFP were generated by lentiviral infection. pHR-SFFV-dCas9-BFP-KRAB was a gift from Stanley Qi & Jonathan Weissman (Addgene plasmid #46911; http://n2t.net/addgene:46911; RRID:Addgene_46911) (Gilbert et al. Cell 2013). Fluorescence associated cell sorting (FACS) was used 48 hours post-transduction to isolate cells stably expressing BFP (U87+dCas9-KRAB). The U87-specific CRISPR inhibition (CRISPRi) library, derived from the human CRISPRi non-coding library (CRinCL) (Addgene #86542, a gift from Jonathan Weissman) by selecting sub-libraries that targeted all expressed lncRNAs in U87, was used to generate the sgRNA pool used for screening (Liu Science 2017). TransIT-Lenti (Mirus, 6600) was used to package the plasmids for transfection in HEK293Ts and viral production was allowed to occur for 48 hours before harvesting. Filtered viral supernatant was then added to U87+dCas9-KRAB cells with polybrene (Sigma-Aldrich, TR-1003-G) at a final concentration of 4 µg/mL at an MOI < 0.3. Two days after infection, cells were treated with 0.75 µg/mL puromycin (Gibco, A1113803) for 3 days, allowed to recover for one day without puromycin, and used for assays the next day (T0), with cells being maintained at a coverage of 1000X. Two independent screen replicates were conducted, with cells collected at T0 and at the endpoint, and processed for sequencing on Illumina HiSeq 4000 and analyzed as previously described (Liu et al. Science 2017). A scatterplot of invasion phenotype of sgRNA of two independent replicates was generated, with the x and y-axes representing different screen replicates. Analysis output denoted p-value and effect sizes  for lncRNAs targeted in the screen. A specific screen score, incorporating these values, was calculated via x -log10 p value relative to negative internal control sgRNA targets as previously described(Liu et al. Science 2017, Gilbert et al. Cell 2014). These were plotted via volcano plot for selection of highest screen scores.

treatment_protocol: Boyden chambers comprised of polyethylene terephthalate with 8 µm pore size and coated in a layer of Matrigel (Corning, 354481) were used to test invasion of cells. U87 screen cells, prepared as described above, were seeded at a density of 5 x 105 cells. For individual knockdown validation, U87 cells (5 x 105), U251 cells (1.25 x 105), or USC02 cells (2 x 105) were seeded in the top chamber with serum-free medium while the lower chamber contained D10 medium as the chemoattractant. Chambers were then incubated for 24 hours in a humidified incubator at 37 °C with 5% CO2.

value: glioblastoma

tag: cell line


title: AC532 Plasma


title: B41_161_A1_BX_S45

value: Black


title: Gypsy Moth Strain CT, Day 1, Replicate 2


title: AC192 Plasma

value: Entire cardiovascular system


title: dss1(I) mutant seedlings

value: dss1(I) knockdown


title: Gypsy Moth Strain CT, Day 5, Replicate 3

value: CT


title: B41_159_NS01_BX_S94


title: 2BQ325 Plasma

value: Healthy Subject

value: total cell-free biofluid RNA


title: After_CRISPRi_Rep_5


title: AC-063 Plasma


title: BQ/AC0486 Plasma


title: Gypsy Moth Strain CT, Day 1, Replicate 1


title: Before_CRISPRi_Rep_6


title: B41_166_2_BX_S2

value: Breast

value: Female


title: B41_154_A1_BX_S91

value: White


title: Before_CRISPRi_Rep_5


title: BQ0277 Plasma


title: B41_158_A1_BX_S93

value: Untreated


title: Gypsy Moth Strain CT, Day 8, Replicate 1


title: B41_153_1_BX_S90


title: B41_152_4_BX_S89


title: BQ/AC0397 Plasma


title: Survival Bone marrow Delta beta3

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
FastQC was used for quality control of the raw sequence reads
PRINSEQ-lite was used for quality based read filtering and trimming
STAR was used for alignment against the mouse reference genome (GRCm38)
featureCounts was used to obtain read counts
DESeq2 was used for normalization and differential gene expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each sample

source_name: Bone marrow

extract_protocol:
Leukemic blasts were isolated from bone marrow and spleen of diseased animals by sorting Venus+ cells using a BD FACSymphonyTM S6 Cell Sorter (BD Bioscience). RNA was isolated using RNeasy Mini Kit (Qiagen).
RNA libraries were generated using poly-A enrichment

value: Bone marrow

value: AML blast


title: AC088-7/08/2002-33 Plasma


title: B41_150_1_BX_S86


title: Survival Bone marrow Delta beta1


title: B41_148_A2_BX_S85


title: Survival Bone marrow Delta beta2


title: AC-1055 Plasma


title: B41_147_1_BX_S44


title: Survival Bone marrow WT3


title: AC098 Plasma


title: Survival Bone marrow WT1


title: BQ11045 Plasma


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-kainate, rep2

city: Madison

first: Olivia

middle: Rose

last: Hoffman

email: ohoffman@wisc.edu, asroopra@wisc.edu

state: WI

address: 1111 Highland Avenue

department: Department of Neuroscience

institute: University of Wisconsin-Madison

description:
4 days post-SE
030222_15
Hom_KA3

data_processing:
Reads were mapped to the mm39 build mouse genome (yielding WT_Hom_reads.TSV) and subjected to Likelihood Ratio Tests using Deseq2 (yielding WT_Hom_deseq_annot.TSV).
Transcripts per million were calculated, and genes were classified as expressed if they had at least 3 TPM in all samples of any one of the 4 conditions (saline:WT, kainate:WT, saline:EZH2nHom, kainate:EZH2nHom).
Deseq2 output was then filtered for only expressed genes, and adjusted p-values were recalculated for the reduced number of genes.
Of the 10556 expressed genes, 6241 were found to be differentially expressed by 1.2-fold at an adjusted p<10-2 (yielding WT_Hom_deseq_3TPM_filtered_0pt05.gcts).
Assembly: mm39
Supplementary files format and content: WT_Hom_deseq_annot.TSV is the annotated, Deseq2-processed counts file containing every gene with count >0 in any one sample.
Supplementary files format and content: WT_Hom_deseq_3TPM_filtered_0pt05.tsv containing normalized expression values for 6241 differentially expressed genes across the four conditions. Genes were classified as expressed if they had at least 3 TPM in all samples of any one of the 4 conditions. Parameters for differential expression were a fold change of >1.2 and adjusted p-value<0.05.

source_name: R. Hippocampus

growth_protocol: Homozygous neuronal deletion of EZH2 was accomplished by mating Synapsin1-Cre driver mice with mice bearing EZH2 floxed alleles on a C57BL6 background. WT controls were Cre-positive.

extract_protocol:
On day 4 post-SE, hippocampi were extracted, flash frozen in liquid nitrogen, and stored at -80 degrees Celsius until all samples were accrued. RNA was harvested with Trizol, and clean-up was carried out with the RNeasy Mini Kit (Qiagen).
Purified samples were submitted to the Gene Expression core at the University of Wisconsin-Madison Biotechnology Center for library preparation, quality control analysis, and Illumina sequencing (https://biotech.wisc.edu).
RNA libraries were prepared via H/M/R (Gold) cytoplasmic and mitochondiral rRNA depletion.

treatment_protocol: WT and EZH2nHom mice were injected (i.p.) with saline or SE was induced via the repeated low dose kainate model.

value: R. Hippocampus

value: Hom

value: Kainate

value: EZH2(-/-);Syn1Cre(+/-) (Cre-positive, homozygous EZH2 neuronal knockout)


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-saline, rep4

description:
4 days post-saline
022622_11
Hom_Sal4

value: Saline


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-kainate, rep4

description:
4 days post-SE
033022_2
Hom_KA5


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-saline, rep5

description:
4 days post-saline
040922_1
Hom_Sal5


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-saline, rep2

description:
4 days post-saline
021422_5
Hom_Sal2


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-saline, rep3

description:
4 days post-saline
022222_2
Hom_Sal3


title: B41_126_LV_BX_S71


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-kainate, rep1

description:
4 days post-SE
030922_2
Hom_KA2


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-kainate, rep3

description:
4 days post-SE
033022_3
Hom_KA4


title: B41_128_1_BX_S73


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 homozygous neuronal knockout, 4 days post-saline, rep1

description:
4 days post-saline
021422_8
Hom_Sal1


title: Survival Spleen Delta beta2

source_name: Spleen

value: Spleen


title: Survival Bone marrow WT2


title: AC250 Plasma

value: Entire cardiovascular system


title: Survival Spleen Delta beta1


title: Survival Spleen Delta beta3


title: AC069 Plasma


title: B41_112_A1_BX_S92


title: AC618 Plasma


title: BQ211 Plasma


title: BQ6109 Plasma


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-kainate, rep5

description:
4 days post-SE
110121_2
WT_KA5

value: WT


title: B41_141_1_BX_S83


title: Survival Spleen WT2


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-kainate, rep4

description:
4 days post-SE
081321_2
WT_KA4


title: B41_124_A1_BX_S69


title: B41_118_D_BX_S65


title: Survival Spleen WT3


title: B41_138_1_BX_S81


title: WT CD34+.Mouse.RNA.Seq.Sample.3

city: Cardiff

first: Girish

middle: K

last: Patel

address: Maindy Road

institute: Cardiff University

data_processing:
Trimmed and quality-checked reads were aligned to the GRCm38 mouse reference genome using STAR
normalised reads were generated using featureCounts (v1.5.0)
differentially expressed genes were then generated using the standard DESeq2 pipeline
Assembly: GRCm38/mm10
Supplementary files format and content: .txt data file normalised reads for each sample.

source_name: skin tissue

extract_protocol:
total RNA was extracted using Rneasy micro kit (QIAGEN).
libraries were generated using Illumina TruSeq RNA Library Prep Kit (v2) and were subsequently sequenced on a Illumina HiSeq 4000

value: skin tissue


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-saline, rep5

description:
4 days post-saline
082821_1
WT_Sal5


title: AC194 Plasma

value: Healthy Subject


title: AC085 Plasma

value: total cell-free biofluid RNA


title: Survival Spleen WT1


title: B41_125_A_BX_S70

value: Breast


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-kainate, rep3

description:
4 days post-SE
081321_5
WT_KA3


title: B41_130_NS01_BX_S42

value: Female


title: #2BQ8119 Plasma


title: BQ0474 Plasma


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-kainate, rep2

description:
4 days post-SE
081321_10
WT_KA2


title: HPV8 CD34+.Mouse.RNA.Seq.Sample.3


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-kainate, rep1

description:
4 days post-SE
070721_8
WT_KA1


title: BQ0497 Plasma


title: BQ6120 Plasma


title: WT CD34+.Mouse.RNA.Seq.Sample.2


title: B41_117_B01_BX_S95

value: White


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-saline, rep1

description:
4 days post-saline
062921_2
WT_Sal1


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-saline, rep4

description:
4 days post-saline
070721_4
WT_Sal4


title: AC/BQ265 Plasma


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-saline, rep3

description:
4 days post-saline
071421_8
WT_Sal3


title: B41_119_1_BX_S66

value: Untreated


title: B41_136_1_BX_S79

value: Black


title: BQ11002 Plasma


title: B41_135_A001_BX_S77


title: HPV8 CD34+.Mouse.RNA.Seq.Sample.2


title: R. Hippocampus, C57BL6 mouse, Cre-positive EZH2 wildtype, 4 days post-saline, rep2

description:
4 days post-saline
081321_7
WT_Sal2


title: #2BQ6114 Plasma


title: B41_115_1_BX_S93


title: WT CD34+.Mouse.RNA.Seq.Sample.1


title: AC249 Plasma


title: WT Lrig1+.Mouse.RNA.Seq.Sample.3


title: AC094 Plasma


title: WT Lrig1+.Mouse.RNA.Seq.Sample.2


title: CX3CR2creER Trem2flox/flox Ldlr-/- 4

city: Minneapolis

first: Jesse

middle: W

last: Williams

state: MN

address: 2101 6th St. SE

department: Dept. Integrative Biology & Physiology

institute: University of Minnesota

data_processing:
Alignment, mapping and counting were performed using the CHURP pipeline
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing read count

source_name: adrenal gland

extract_protocol:
Whole murine adrenal gland from Trem2 deficient or Trem2 WT atherogenic mice fed on HFD for 16 weeks. Tissue was lysed using Trizol.
Library was constructed by the University of Minnesota Genomic Core using the TruSeq RNA Library Prep Kit.

value: adrenal gland

value: CX3CR2creER Trem2flox/flox Ldlr-/-


title: WT Lrig1+.Mouse.RNA.Seq.Sample.1


title: HPV8 CD34+.Mouse.RNA.Seq.Sample.1


title: CX3CR2creER Trem2WT Ldlr-/- 4

value: CX3CR2creER Trem2WT Ldlr-/-


title: B41_121_NS01_BX_S67

source_name: Breast


title: B41_127_A2_BX_S72


title: CX3CR2creER Trem2flox/flox Ldlr-/- 3


title: 2BQ0293 Plasma

last: Wang

source_name: Plasma


title: B41_95_A1_BX_S85


title: B41_122_NS01_BX_S68

value: Unknown


title: CX3CR2creER Trem2WT Ldlr-/- 5


title: HPV8 Lrig1+.Mouse.RNA.Seq.Sample.1


title: HPV8 Lrig1+.Mouse.RNA.Seq.Sample.2


title: B41_101_2_BX_S86


title: HPV8 Lrig1+.Mouse.RNA.Seq.Sample.3


title: CX3CR2creER Trem2WT Ldlr-/- 2


title: B41_93_I_BX_S64


title: CX3CR2creER Trem2WT Ldlr-/- 1


title: B41_107_1A_BX_S90


title: CX3CR2creER Trem2flox/flox Ldlr-/- 2


title: B41_105_2_BX_S88


title: B41_91_NS01_BX_S84


title: whole blood, scBS-5, scBS-seq

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

institute: The Babraham Institute

description:
Sample 5502
sample5498-5505_processed_cov.tar.gz

data_processing:
scM&T-seq data was processed as described previously (Angermueller et al. 2016). scBS-seq data was processed as described previously; briefly, reads had 6bp removed on their 5’-ends to remove the random primed portion of the reads, and were also adapter- and quality-trimmed using Trim Galore (v0.6.7; options --clip_r1 6). Trimmed reads were  aligned to the bisulfite converted GRCm38 mouse genome using Bismark v0.22.3 in single-end mode (Krueger and Andrews, 2011; options: --non_directional). Methylation calls were extracted after duplicate reads had been removed (deduplicate_bismark).
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

source_name: whole blood

extract_protocol:
scM&T-seq (Angermueller et al 2016, https://doi.org/10.1038/nmeth.3728)
scBS-seq (Clark et al 2017, https://doi.org/10.1038/nprot.2016.187)
scBS-seq

value: whole blood

value: wild type

value: whole blood depleted of red blood cells

value: wildtype


title: AC0024 Plasma

value: Entire cardiovascular system


title: B41_116_A1_BX_S94


title: whole blood, scBS-8, scBS-seq

description:
Sample 5505
sample5498-5505_processed_cov.tar.gz


title: BQ9115 Plasma


title: BQ9120 Plasma


title: Atherosclerotic stress, Ldlr-/-, 8 week HFD, CD45+ sorted GEX

description: GEX

data_processing:
10x formated output files for GEX were generated using cellranger
10x formated output files for HTO and ADT were generated using CITE-seq-Count
Further analysis was performed using Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Single-cell dissociated tissue was CD45-sorted to only include immune cells. Male mice were labeled using Hashtag9 and female labeled using Hashtag10.
Library was generated according to Chromium Single Cell 3ʹ v3 protocol (10x Genomics).


title: Atherosclerotic stress, Ldlr-/-, 8 week HFD, CD45+ sorted HTO

description: HTO

library_source: other

molecule: protein

tag: antibodies/tags

value: Anti-mouse Hashtag9/TotalSeq-A0309 (male), Anti-mouse Hashtag10/TotalSeq-A0310 (female)


title: AC103 Plasma

value: Healthy Subject


title: Cold stress, C57bl/6 WT, 12 hour cold, CD45+ sorted GEX

description: GEX


title: CX3CR2creER Trem2WT Ldlr-/- 3


title: AC/BQ294 Plasma

value: total cell-free biofluid RNA


title: whole blood, scBS-4, scBS-seq

description:
Sample 5501
sample5498-5505_processed_cov.tar.gz


title: whole blood, scRNA-seq 2

data_processing:
data was processed as described previously (Linker et al., 2019). Briefly, the RNA-seq reads were adapter and quality-trimmed using Trim Galore (v0.6.7), and aligned to the GRCm38 mouse genome build using STAR
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file include raw counts values for each cell. Rows are genes, columns are cells.

extract_protocol:
scM&T-seq (Angermueller et al 2016, https://doi.org/10.1038/nmeth.3728)
scBS-seq (Clark et al 2017, https://doi.org/10.1038/nprot.2016.187)

value: C57BL/6 J


title: AC049 Plasma


title: whole blood, scBS-3, scBS-seq

description:
Sample 5500
sample5498-5505_processed_cov.tar.gz


title: whole blood, scBS-2, scBS-seq

description:
Sample 5499
sample5498-5505_processed_cov.tar.gz


title: BQ11028 Plasma


title: B41_108_2_BX_S91

value: Breast

value: Female


title: whole blood, scRNA-seq 1


title: CX3CR2creER Trem2flox/flox Ldlr-/- 1


title: ACBQ0279 Plasma


title: whole blood, scBS-7, scBS-seq

description:
Sample 5504
sample5498-5505_processed_cov.tar.gz


title: BQ/AC0463 Plasma


title: whole blood, EpiAge VII, scBS-seq

description: Sample 5129


title: B41_84_NS01_BX_S62

value: White

value: Untreated


title: Cold stress, C57bl/6 WT, 12 hour cold, CD45+ sorted HTO

description: HTO

value: adrenal gland


title: 2BQ0201 Plasma


title: whole blood, scBS-6, scBS-seq

description:
Sample 5503
sample5498-5505_processed_cov.tar.gz


title: BQ258 Plasma


title: 2BQ0457 Plasma


title: whole blood, EpiAge VI, scBS-seq

description: Sample 5128


title: B41_80_NS01_BX_S80


title: 2BQ0381 Plasma


title: B41_129_1_BX_S74


title: B41_83_NS01_BX_S81


title: AC167 Plasma


title: B41_74_A1_BX_S76


title: Salivary gland control murine liver, 38h post injection, snRNAseq

city: Stockholm

first: Miren

last: Urrutia Iturritza

address: Svante Arrhenius väg 20C

department: The Department of Molecular Biosciences, The Wenner-Gren Institute (MBW)

institute: Stockholm University

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation steps were carried out using the Cell Ranger software v3.1.0
Assembly: custom reference genome combining Mus musculus (GRCm38.101) and Plasmodium berghei (PlasmoDB-48_PbergheiANKA)
Supplementary files format and content: Matrix files

source_name: Liver

extract_protocol:
The livers were collected, and lobes were separated. Each lobe was segmented and  frozen in -30°C 2-Methylbutane.  Frozen liver tissues were homogenized using the Kimble Dounce grinder in homogenization buffer with RNAse inhibitors.  Nuclei were isolated from snap frozen liver tissue with a sucrose gradient.  Homogenized tissue was then subjected to density gradient (29% cushion – Optiprep) ultracentrifugation. Nuclei were resuspended and 2 biological replicates of each condition were pooled before nuclei were stained using DAPI. Intact nuclei were FACS-purified from remaining debris and sorted into BSA coated tubes. The sorted nuclei were pelleted by centrifugation and then resuspended in PBS with 0.04% BSA.
Nuclei suspensions were loaded on a GemCode Single-Cell Instrument (10x Genomics) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3ʹGel Bead and Library Kit (10x Genomics, V2 and V3 technology) according to the manufacturer’s instructions. Briefly, GEM-RT was performed in a 96-Deep Well Reaction Module. After RT, GEMs were broken down and the cDNA was cleaned up with DynaBeads MyOne Silane Beads and SPRIselect Reagent Kit. cDNA was amplified with 96-Deep Well Reaction Module. Amplified cDNA product was cleaned up with SPRIselect Reagent Kit prior to enzymatic fragmentation. Indexed sequencing libraries were generated using the reagents in the GemCode Single-Cell 3ʹ Library Kit with the following intermediates: (1) end repair; (2) A-tailing; (3) adapter ligation; (4) post-ligation SPRIselect cleanup and (5) sample index PCR. Pre-fragmentation and post-sample index PCR samples were analyzed using the Agilent 2100 Bioanalyzer. snRNA-seq libraries were pooled in equal ratios and loaded on a S4 lane Illumina NovaSeq 6000, resulting in 2500 - 3000 million read-pairs.
single-nuclei RNA sequencing

value: Liver

value: Salivary gland control injected

value: 38h post injection


title: whole blood, scBS-1, scBS-seq

description:
Sample 5498
sample5498-5505_processed_cov.tar.gz

value: whole blood


title: Salivary gland control murine liver, 12h post injection, snRNAseq

description: 10x Genomics

value: 12h post injection


title: B41_90_B_BX_S83

value: Other


title: Trmt6 KO2

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v2.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim-tRNAseq computational pipeline using the common parameters --species Mmus --cluster-id 0.97 --threads 15 --min-cov 0.0005 --max-mismatches 0.075 --local-modomics --max-multi 4 --remap --remap-mismatches 0.05
Assembly: mm10
Supplementary files format and content: tab-separated read count per anicodon or isodecoder

extract_protocol:
RNA from Drosophila BG3-c2, HEK293T, and human iPS cells was isolated with Trizol (Sigma Aldrich) according to the manufacturer’s instructions. For total RNA isolation from yeast, frozen cells were resuspended in 100 mM sodium acetate pH=4.5, 10 mM EDTA pH=8.0, 1% SDS (1 ml per 50 OD600 units). An equal volume of hot acid phenol (pH=4.3) was added, and the cell suspension was vortexed vigorously followed by incubation at 65℃ for 5 min with intermittent mixing. After addition of 1/10 volume 1-Bromo-3-chloropropane (BCP, Sigma Aldrich), samples were centrifuged at 10,000 x g for 5 min and the aqueous phase was transferred to a new tube. Following an additional round of hot acid phenol/BCP and a round of BCP only extraction, RNA was precipitated from the aqueous phase by the addition of 3 volumes of ethanol. For RNA isolation from yeast under conditions that preserve tRNA charging, frozen cells were resuspended in ice-cold 100 mM sodium acetate pH=4.5, 10 mM EDTA pH=8.0. One volume of cold acid phenol (pH=4.3) was added and cells were lysed with glass beads. One-tenth volume of BCP was then added and the samples were centrifuged at 10,000 x g/4℃ for 5 min, followed by a second round of cold phenol-BCP and one round of BCP-only extraction. RNA was ethanol-precipitated from the aqueous phase and pellets were washed in 80% ethanol containing 50 mM sodium acetate, pH=4.5, briefly air-dried, and resuspended in 50 mM sodium acetate pH=4.5, 1 mM EDTA pH=8.0. Two synthetic standards corresponding to E.coli tRNALys(UUU) with intact 3’-CCA (5’-GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA-3’) or a 3’-CC (5’- GGGTCGTTAGCTCAGTTGGTAG AGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACC-3’) were added to 5 - 10 µg of total RNA in a 3:1 molar ratio at 0.06 pmol/µg, followed by incubation at 37oC in 50 mM Tris-HCl pH=9.0 to deacylate tRNAs. Deacylation was omitted for samples subjected to oxidation and β-elimination. Total RNA was subsequently dephosphorylated and purified by ethanol precipitation in 0.3M sodium acetate pH=4.5 with 25 µg glycogen (Ambion) as a carrier. RNA was resolved on a denaturing 10% polyacrylamide/7M urea/1xTBE gel and species migrating at the size range of mature tRNAs (60 – 90 nt) were excised and gel slices were crushed with disposable pestles. Following addition of 400 µl gel elution buffer (0.3M sodium acetate pH=4.5, 0.25% SDS, 1mM EDTA pH=8.0), the gel slurry was incubated at 65℃ for 10 min, snap-frozen on dry ice, and thawed at 65℃ for 5 min. RNA was eluted overnight at room temperature with continuous mixing. Gel pieces were removed with Costar Spin-X centrifuge tube filters and RNA was recovered from the flow-through by ethanol precipitation in the presence of 25 µg of glycogen.
50 to 200 ng of gel-purified tRNA was ligated to one of four adapters with distinct barcodes.Ligation was performed for 3 hours at 25°C in a 20-µl reaction volume containing pre-adenylated adapter and RNA substrate in a 4:1 molar ratio, 1x T4 RNA Ligase Reaction Buffer, 200 U of T4 RNA ligase 2 (truncated KQ; NEB), 25% PEG 8000, and 10 U SUPERase In (Ambion). Ligation products were separated from excess adapter on denaturing 10% polyacrylamide/7M urea/1xTBE gels. Bands migrating at 95-125 nt were excised and ligation products were recovered from crushed gel slices. Reverse transcription reactions contained 125 nM adapter-ligated tRNA pool, 125 nM primer(5’pRNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC-3’) and 500 nM TGIRT (InGex) in a final volume of 20 µl. Reactions were performed in 50 mM Tris-HCl pH=8.3, 75 mM KCl, 3 mM MgCl2, 5 mM DTT (from a freshly made 100 mM stock), and 10 U SUPERase In. After TGIRT addition, reactions were pre-incubated at 42℃ for 10 min, initiated by addition of dNTPs to a final concentration of 1.25 mM, and incubated at 42℃ for 16 hours in a Themrocycler. For Superscript III RT, template and primer were denatured at 75℃ for 5 min and chilled on ice, and reverse transcription was performed in the presence of 1X First-Strand Buffer, 5 mM DTT, 0.5 mM dNTPs, 10 U SUPERase In, and 200 U Superscript III (Invitrogen) at 57℃ for 60 min. Template RNA was hydrolyzed by the addition of 1 µl 5M NaOH and incubation at 95℃ for 3 min. cDNA between 60 and 150 nt was excised and cDNA was eluted from crushed gel slices in 400 µl 10 mM Tris-HCl pH=8.0, 1 mM EDTA at 70℃/2000 rpm for 1 hour in a Thermoblock, followed by ethanol precipitation. Purified cDNA was circularized with CircLigase ssDNA ligase (Lucigen) in 1x reaction buffer supplemented with 1 mM ATP, 50 mM MgCl2, and 1M betaine for 3 hours at 60℃, followed by enzyme inactivation for 10 min at 80℃. One-fifth of circularized cDNA was directly used for library construction PCR. Amplification was performed with KAPA HiFi Polymerase in 1x GC buffer with initial denaturation at 95℃ for 3 min, followed by five to six cycles of 98℃ for 20 sec, 62℃ for 30 sec, 72℃ for 30 sec. PCR products were purified with DNA Clean&Concentrator (Zymo Research) and resolved on 8% polyacrylamide/1xTBE gels alongside pBR322 DNA-MspI Digest (NEB). The 130-220 bp region of each lane was excised and DNA was eluted from crushed gel slices in 400 µl water with continuous mixing at room temperature overnight. After ethanol precipitation in 0.3M sodium acetate pH=5.5 and 25 µg glycogen, libraries were dissolved in 10 µl 10 mM Tris-HCl pH=8.0, quantified with Qubit, and sequenced for 150 cycles on an Illumina Novaseq platform.

value: Bone marrow

value: HSPCs

value: Trmt6fl/fl, MX1-cre


title: BQ/2AC0245 Plasma

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

value: Healthy Subject

value: Entire cardiovascular system


title: Palbociclib treated subcutaneous FL8 allograft tumor #5

first: Julia

last: Arand

address: Schwarzspanierstr. 16

institute: Medical University of Vienna

data_processing:
Raw sequencing reads were also demultiplexed by the vendor to generate approximately 20 million paired-end reads per sample.  Fastq files were trimmed using CutAdapt (v2.10) (Martin et al., 2011 using TruSeq sequencing adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), and a minimum read length of at least 25. Reads were then aligned to the ENSEMBL mm10 genome using HiSat2 (Kim et al., 2019) using reverse strandedness and discarding unaligned reads. Counts were assigned to genes using featureCounts (Liao et al., 2014) at ENSEMBL gene annotation (v93). Differential expression analysis was conducted using DESeq2 (Love et al., 2014) on R v4.1.2 (https://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: The processed csv file represents countspermillion (post featurecounts is a conversion to CPM)

source_name: Tumor allograft

growth_protocol: FL8 cells were suspended at concentration of 106 cells/100 µL in 10% w/v methacrylated gelatin (Sigma 276685) and 0.067% w/v LAP (Sigma 900889) suspended in RPMI (Sigma R0883). 200 µL aliquots in 96-well plates were photocrosslinked into solid capsules at 405 nm light (Amazon 0191673174324) for 3 min at room temperature. Capsules were implanted in the subcutaneous flanks of NSG mice.

extract_protocol:
Tumors were frozen down and stored at -80 C before being sent to Novogene for tissue processing and RNA extraction.
Library construction was carried out by Novogene.
PairedEnd150

treatment_protocol: When average tumor size reached 75 mm3 mice were randomized into treatment groups. Mice either received vehicle (0.5% methocel Sigma 94378) or palbociclib (LC Laboratories P-7788) at a dose of 75 mg/kg via oral gavage for 3 consecutive days and given 4 days with no treatment.

value: Tumor allograft

value: Palbociclib


title: whole blood, EpiAge VIII, scBS-seq

description: Sample 5130

value: wild type

value: whole blood depleted of red blood cells

value: wildtype


title: B41_86_A1_BX_S82

data_processing:
Align the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
QC methods used samtools sort 1.10, Picard 2.22.4, and FastQC 0.11.9
Assembly: hg38
Supplementary files format and content: Salmon gene expression file (tab-delimited)

value: Breast

value: Female

value: White

value: Untreated


title: B41_106_1A_BX_S89


title: BQ8113 Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

value: total cell-free biofluid RNA


title: B41_92_2C_BX_S40

extract_protocol:
RNA was extracted from paraffin-embedded baseline tumor samples
ribo-zero RNAseq libraries were made using an Illumina TruSeq Stranded Total RNA kit


title: Trmt6 KO1


title: Salivary gland control murine liver, 24h post injection, snRNAseq

description: 10x Genomics

value: Liver

value: Salivary gland control injected

value: 24h post injection


title: Palbociclib treated subcutaneous FL8 allograft tumor #1


title: B41_77_1_BX_S79

value: Black


title: WT-rep2 [scRNA-Seq]

first: Jiang

last: Penglei

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2.
The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded.
Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes.
Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with raw gene umi.

source_name: mouse HSC

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

treatment_protocol: FACS-sorted HSC were kept on ice until lysed and reverse transcribed.

value: bone marrow


title: Trmt6 WT2

value: Bone marrow

value: HSPCs


title: Trmt6 WT1


title: BQ0422 Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: KO-rep2 [scRNA-Seq]

value: Mat KO


title: whole blood, EpiAge V, scBS-seq

description: Sample 5127

value: whole blood

value: wild type

value: whole blood depleted of red blood cells


title: BQ8104 Plasma


title: B41_79_B2_BX_S61

value: Breast

value: Female


title: whole blood, EpiAge IV, scBS-seq

description: Sample 5126

value: wildtype


title: Palbociclib treated subcutaneous FL8 allograft tumor #2

value: Tumor allograft

value: Palbociclib


title: AC/BQ0392 Plasma

value: total cell-free biofluid RNA


title: Palbociclib treated subcutaneous FL8 allograft tumor #4


title: AC\BQ0264 Plasma


title: BQ6133 Cerebrospinal fluid

source_name: Cerebrospinal fluid

value: Entire brain and spinal cord


title: whole blood, EpiAge III, scBS-seq

description: Sample 5125


title: 2BQ0381 Cerebrospinal fluid


title: BQ8123 Plasma


title: whole blood, EpiAge II, scBS-seq

description: Sample 5124


title: B41_72_1_BX_S75

value: White

value: Untreated


title: Palbociclib treated subcutaneous FL8 allograft tumor #3


title: BQ6109 Cerebrospinal fluid