title: NJA02202.F21


title: NJA02202.G04

status: Public on May 30 2021

type: SRA

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: Small intestine and colon were removed from C57BL/J wild-type mice and kept on ice in phosphate buffered saline (PBS). Lumina of colon and small intestine were washed three times with PBS and adipose tissue connected to the exterior of the small intestine or colon was removed. Colon and small intestine were opened longitudinally, and any remaining mucous on covering the epithelial layer was gently rubbed off. Tissues were washed once in PBS before being cut into 0.5 - 1 mm long fragments. Colon fragments were immersed in 10mM EDTA-PBS and incubated for 105 minutes on ice, with shaking every 15 minutes. Small intestinal fragments were similarly immersed in 10mM EDTA-PBS on ice and shaken. After 15 minutes, small intestinal fragments were allowed to settle at the bottom and the supernatant was discarded and replaced with new 10mM EDTA-PBS and shaken vigorously. This procedure was repeated 1-2 times, with supernatant fractions investigated through light microscopy before discarding, in order to enrich for crypts. Small intestinal fragments were then incubated on ice for 45-60 minutes for a total of 105 minutes. Following EDTA-PBS treatment fractions were triturated 10-15 times. Colon fractions were strained through a 100 um filter while small intestinal fractions were strained through a 70 um filter. Fractions were centrifuged at 300g for 5 minutes and dissociated using TrypLE Express (Invitrogen) at 37°C for 15-20 minutes. Enzymatic dissociation was supervised using light microscopy during regular intervals to obtain an appropriate amount of single cells and multiplets. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's protocol before staining for FACS sorting was performed.

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

tag: strain

tag: tissue

value: spleen

tag: facs cellnumber

value: Singlet

tag: age (days)


title: NJA02202.F15


title: NJA02202.G05


title: NJA02202.F22

value: Multiplet


title: NJA02202.G03


title: NJA02202.F17


title: NJA02202.G02


title: NJA02202.F20


title: NJA02202.G09


title: NJA02202.F18


title: NJA02202.G08


title: NJA02202.F19


title: NJA02202.G06


title: NJA02202.F16


title: NJA02202.F23


title: NJA02202.G10


title: NJA02202.F13


title: NJA02202.F11


title: NJA02202.F12


title: NJA02202.F09


title: NJA02202.F07


title: NJA02202.F08


title: NJA02202.F10


title: NJA02202.F04


title: NJA02202.F05


title: NJA02202.E24


title: NJA02202.F02


title: NJA02202.G07


title: NJA02202.H12


title: NJA02202.E15


title: NJA02202.F01


title: NJA02202.E14


title: NJA02202.E13


title: NJA02202.E20


title: NJA02202.E23


title: NJA02202.E19


title: NJA02202.E18


title: NJA02202.E12


title: NJA02202.E10


title: NJA02202.E09


title: NJA02202.E22


title: NJA02202.E11


title: NJA02202.E16


title: NJA02202.E08


title: NJA02202.F14


title: NJA02202.E17


title: NJA02202.F06


title: NJA02202.E07


title: NJA02202.E06


title: NJA02202.E21


title: NJA02202.F03


title: NJA02202.E03


title: NJA02202.E02


title: NJA02202.E04


title: NJA02202.D22


title: NJA02202.D23


title: NJA02202.D21


title: NJA02202.D19


title: NJA02202.D17


title: NJA02202.D20


title: NJA02202.D15


title: NJA02202.D18


title: NJA02202.D10


title: NJA02202.D12


title: NJA02202.D09


title: NJA02202.D08


title: NJA02202.D07


title: NJA02202.G14


title: NJA02202.D06


title: NJA02202.E05


title: NJA02202.D24


title: NJA02202.D05


title: NJA02202.D04


title: NJA02202.D02


title: NJA02202.E01


title: NJA02202.D13


title: NJA02202.D11


title: NJA02202.D14


title: NJA02202.C24


title: NJA02202.D16


title: NJA02202.C23


title: NJA02202.C13


title: NJA02202.C17


title: NJA02202.C16


title: NJA02202.C14


title: NJA02202.C21


title: NJA02202.C15


title: NJA02202.C22


title: NJA02202.C20


title: NJA02202.C10


title: NJA02202.C18


title: NJA02202.C11


title: NJA02202.C09


title: NJA02202.C08


title: NJA02202.D03


title: NJA02202.C07


title: NJA02202.C19


title: NJA02202.C06


title: NJA02202.D01


title: NJA02202.C04


title: NJA02202.C02


title: NJA02202.C03


title: NJA02202.B24


title: NJA02202.C01


title: NJA02202.B23


title: NJA02202.B22


title: NJA02202.B21


title: NJA02202.C05


title: NJA02202.B20


title: NJA02202.B19


title: NJA02202.B18


title: NJA02202.B17


title: NJA02202.B08


title: NJA02202.B16


title: NJA02202.B15


title: NJA02202.B07


title: NJA02202.B10


title: NJA02202.B06


title: NJA02202.B14


title: NJA02202.B02


title: NJA02202.B05


title: NJA02202.B03


title: NJA02202.B04


title: NJA02202.A24


title: NJA02202.B01


title: NJA02202.A23


title: NJA02202.A22


title: NJA02202.A21


title: NJA02202.A20


title: NJA02202.A19


title: NJA02202.A18


title: NJA02202.B13


title: NJA02202.C12


title: NJA02202.B12


title: NJA02202.A17


title: NJA02202.A15


title: NJA02202.A14


title: NJA02202.B09


title: NJA02202.A10


title: NJA02202.A08


title: NJA02202.A03


title: NJA02202.A02


title: NJA02202.A09


title: NJA02202.A11


title: NJA02202.A13


title: NJA02201.P24


title: NJA02202.A07


title: NJA02202.A05


title: NJA02202.A06


title: NJA02201.P23


title: NJA02201.P22


title: NJA02201.P21


title: NJA02201.P20


title: NJA02201.P18


title: NJA02201.P17


title: NJA02201.P16


title: NJA02201.P15


title: NJA02201.P14


title: NJA02202.A12


title: NJA02201.P13


title: NJA02201.P12


title: NJA02201.P11


title: NJA02201.P10


title: NJA02202.A01


title: NJA02202.A04


title: NJA02201.P09


title: NJA02201.P08


title: NJA02201.P05


title: NJA02201.O24


title: NJA02201.O22


title: NJA02201.P19


title: NJA02201.P01


title: NJA02201.O19


title: NJA02201.O20


title: NJA02201.O21


title: NJA02201.O18


title: NJA02201.O16


title: NJA02201.O17


title: NJA02201.O15


title: NJA02201.O14


title: NJA02201.O13


title: NJA02201.P07


title: NJA02201.P03


title: NJA02201.O23


title: NJA02201.O10


title: NJA02201.P06


title: NJA02201.P02


title: NJA02202.A16


title: NJA02201.O08


title: NJA02201.O11


title: NJA02201.O12


title: NJA02201.O07


title: NJA02201.O09


title: NJA02201.O06


title: NJA02201.O04


title: NJA02201.O05


title: HEK_CAP-4_cytoRP

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

description:
HEK_CAP4h_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_CAP4h_cytoRP_R2_S4

data_processing:
Reads were trimmed to remove ligated 3’ linker (CTGTAGGCACCATCAAT) with Cutadapt
Reads without linker were discarded and the unique molecular identifier (UMI) was then extracted from remaining reads using a custom script. UMIs consisted of either 6 or 10 random nucleotides at the 3’ end ligated as part of the 3’ linker, and either 0 or 4 random nucleotides at the 5’ end
Trimmed reads were filtered after alignment using bowtie1 to human rRNA (allowing 1 internal and 1 5’ mismatch) and human tRNA (allowing 1 internal, 1 5’, and 3 3’ mismatches). Remaining reads were aligned to the GRCh38 human reference genome from GENCODE using STAR 2.7.3. For mitoRP samples with mouse spike-ins, the M17 mouse reference genome from GENCODE was merged with the human genome. STAR mismatch parameters for mitoRP and cytoRP: --outFilterMismatchNoverReadLmax 0.07 and --outFilterMismatchNmax 3. STAR parameters for RNA-seq: default
PCR duplicates were identified by their UMI and removed using a custom script
Read counts were summed across genes using Rsubread featureCounts. Parameters for mitoRP: readShiftType  = "upstream", readShiftSize = 14, read2pos = 3, allowMultiOverlap = TRUE, useMetaFeatures = TRUE, countMultiMappingReads = TRUE, strandSpecific = 1, GTF.featureType='CDS'. The GTF annotation file was modified to exclude the first 6 codons of all genes (which are variable depending on whether there is a 5’ UTR) and all overlapping regions. Paramters for cytoRP: readShiftType  = "downstream", readShiftSize = 17, read2pos = 5, allowMultiOverlap = TRUE, useMetaFeatures = TRUE, countMultiMappingReads = TRUE, strandSpecific = 1, GTF.featureType='CDS'. Parameters for RNA-seq: allowMultiOverlap = TRUE, minOverlap=22, countMultiMappingReads = TRUE, GTF.featureType='CDS'. The GTF annotation file was modified to exclude overlapping regions in mitochondrial genes.
Read counts were normalized to feature size and library size (transcripts per 10000 for mito-encoded genes, RPKM for nuc-encoded genes) using a custom script
Read coverage for mitochondrial mRNA mapping mitoRP reads was transformed to A-site density using a custom script. Offsets from the 3’ end of 30:[-13], 31:[-14], 32:[-15], 33:[-15], 34:[-15 or -16] were typically used.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files were made using a custom script for A-site transformation and bedtools genomeCoverageBed. Only read lengths given in the file name are included.
Supplementary_files_format_and_content: xlsx files give relative synthesis values for OXPHOS subunits across samples: mitoribosome profiling, cytoribosome profiling, and RNAseq

organism: Homo sapiens

growth_protocol: Dermal human fibroblasts, HeLa S3 and HEK293 were grown in DMEM (Thermo), supplemented with 10% FBS (Thermo). Human myoblasts and myocytes were grown in Human Skeletal Muscle Basal Media Kit (Cell Applications) in the absence of antibiotics to 75-80% confluency.

extract_protocol:
For mitoribosome profiling, growth medium was aspirated and cells were quickly rinsed once with ice-cold 1X PBS ph:7.4. Lysis was performed on ice in a glass homogenizer with a loose setting. We used 50 ml of lysis buffer for 106 cells. We used lauryl maltoside at 0.25% in combination with 50 mM NH4Cl, 20 mM MgCl2, 0.5 mM DTT, 10 mM Tris pH: 7.5 and 1X EDTA-free Protease inhibitor cocktail (Roche). For Cytoribosome profiling, cell cultures growth and lysis were performed as for mitoribosome profiling. We used lysis and buffer conditions described in Shalgi et al, 2013, for polysome profiling. For RNA-seq, some of the lysates prepared for mitoribosome profiling were reserved and  further treated with 90 ug/mL of Proteinase K and 0.5 % SDS at 42 0C for 20 minutes.
Mitoribosome profiling, Cytoribosome profiling and RNA-seq: All libraries were prepared as described in Ingolia et al, 2012, with a few modifications. For mito-and cytoribosome profiling we did not rRNA deplete. For RNA-seq we included gel purified RNA sizes of 30-70 nucleotides. For all libraries we introduced randomized nucleotides to serve as a unique molecular identifier (UMI) to the linker ligation at 3’ (/5rApp/NNNNNNNNNNCTGTAGGCACCATCAAT/3ddC/) and the reverse transcription step at 5’(/5Phos/NNNNGATCGTCGGACTGTAGAACTCTGAACCTGTC/iSp18/CACTCA/iSp18/CAAGCAGAAGACGGCATACGAGATATTGATGGTGCCTACAG). Length of UMI differs across samples.

tag: cell line/type

tag: genotype

value: WT

tag: treatment

value: 4 hours with 100 ug/mL of chloramphenicol (Sigma, CAT C3175)

tag: mouse spike-in%

tag: umi

tag: molecule subtype

value: cytoribosome protected fragments


title: HEK_CAP-3_cytoRP

description:
HEK_CAP4h_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_CAP4h_cytoRP_R1_S5


title: spleen_normal Se_GD_rep2

type: RNA

city: Xi'an

first: YuFeng

last: Liu

state: ShanXi

address: The First Affiliated Hospital of Xi'an Jiao Tong University

country: China

institute: mouse

hyb_protocol: Array hybridizations were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images.

data_processing:
Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies).
Differentially expressed genes between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. Gene ontology and pathway analyses were performed in the standard enrichment computation method.

label: biotin

source_name: spleen_normal Se_GD

label_protocol: Sample labeling  according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

extract_protocol: RNA was isolated from spleen and then quantified by NanoDrop ND-1000 (NanoDrop Technologies Inc., USA). RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Whole Mouse Genome Oligo Microarrays (Agilent Technologies) were used for gene expression analyses and offer a broad view on all known genes and transcripts in the mouse genome.

value: balb/c

tag: Sex

value: female

tag: mouse condition

value: Graves’ disease (GD)

tag: dietary se supply

value: normal


title: NJA02201.O03


title: spleen_normal Se_GD_rep3


title: spleen_normal Se_GD_rep1


title: spleen_low Se_GD_rep1

source_name: spleen_low Se_GD

value: low


title: NJA02201.O02


title: spleen_low Se_nonGD_rep3

source_name: spleen_low Se_nonGD

value: non-GD (Graves’ disease)


title: HEK_KOplWT-2_cytoRP

description:
HEK_KOplWT2_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_KOplusWT2_cytoRP_R1_S5

value: LRPPRC KO + LRPPRC

value: untreated


title: HEK_KOplWT-3_cytoRP

description:
HEK_KOplWT2_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_KOplusWT_cytoRP_R2_S6


title: NJA02201.O01


title: spleen_low Se_GD_rep3


title: spleen_low Se_GD_rep2


title: spleen_low Se_nonGD_rep1


title: NJA02201.N24


title: spleen_low Se_nonGD_rep2


title: LPS Stimulated Colon Carcinoma Cell Line

city: Yufu

first: Sotaro

last: Ozaka

state: Oita

address: 1-1 Idaigaoka, Hasama

country: Japan

institute: Oita University

hyb_protocol: Samples were applied to microarrays enclosed in SurePrint G3 Mouse GE 8x60K Microarray v1 <G4852A>.

scan_protocol: Scanned using an Agilent High-Resolution Microarray Scanner.

data_processing: GeneSpring GX <version 13.0.0> was used for data analysis.

source_name: CMT93 LPS stimulated colon carcinoma cells

label_protocol: The cDNA was produced using a poly dT primer with a T7 promoter and reverse transcriptase in 100 mg of RNA ( 37°C, 2h). RNA was synthesized from the prepared cDNA and T7 RNA polymerase in the presence of Cy die (Cy3).

growth_protocol: CMT93 cells were cultured in Dulbecco's modified Eagle medium (DMEM).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: CMT93 cells were stimulated for 24 hours with 3 μg/mL of LPS.

tag: cell line

tag: age

value: 19 month

value: rectum


title: Control Colon Carcinoma Cell Line

source_name: CMT93 colon carcinoma cells


title: NJA02201.N23


title: NJA02201.N22


title: HEK_KO-2_cytoRP

description:
HEK_KO2_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_KO2_cytoRP_R1_S3

value: LRPPRC KO


title: HEK_KO-3_cytoRP

description:
HEK_KO2_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_KO2_cytoRP_R2_S4


title: NJA02201.N21

value: spleen


title: NJA02201.N20


title: HEK_KOplWT-3_RNAseq

description:
HEK_KOplWT2_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx, DESeq_output_KOvsWTaddback.xlsx
HEK_KOplusWT2_RNA_seq_R2_S6

value: rRNA-depleted total RNA


title: HEK_KOplWT-2_RNAseq

description:
HEK_KOplWT2_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx, DESeq_output_KOvsWTaddback.xlsx
HEK_KOplusWT2_RNA_seq_R1_S5


title: NJA02201.N18

value: Multiplet


title: NJA02201.N19


title: HEK_KO-2_RNAseq

description:
HEK_KO2_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx, DESeq_output_KOvsWTaddback.xlsx
HEK_KO2_RNA_seq_R1_S3


title: HEK_KOplWT-3_mitoRP

description:
HEK_KOplWT2_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
KOplusWT2-R2_S6

value: mitoribosome protected fragments


title: NJA02201.N17


title: NJA02201.N16

value: Singlet


title: HEK_KOplWT-2_mitoRP

description:
HEK_KOplWT2_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
KOplusWT2-R1_S5


title: HEK_KO-3_RNAseq

description:
HEK_KO2_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx, DESeq_output_KOvsWTaddback.xlsx
HEK_KO2_RNA_seq_R2_S4


title: HEK_KO-3_mitoRP

description:
HEK_KO2_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
KO2-R2_S4


title: HEK_KOplWT-1_mitoRP

description:
HEK_KOplWT1_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
KOplusWT1-2_S5


title: NJA02201.N15


title: NJA02201.N14


title: NJA02201.N11


title: NJA02201.N12


title: HEK_KO-2_mitoRP

description:
HEK_KO2_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
KO2-R1_S3


title: NJA02201.N10


title: Fibroblast_ANX2h-2_mitoRP

description:
Fibro_ANX_2h_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HF_ANS_2h_2_S7

source_name: Dermal fibroblasts, anonymous donor

value: Dermal fibroblasts, anonymous donor

value: WT

value: 2 hours with 100 ug/mL anisomycin dissolevd in DMSO (Sigma, CAT A9789)


title: HEK_KO-1_mitoRP

description:
HEK_KO1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
KO1_S3


title: Fibroblast_ANX2h-1_mitoRP

description:
Fibro_ANX_2h_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HF_ANS_2hr_1_S3

value: 2 hours with 100 ug/mL anisomycin dissolved in DMSO (Sigma, CAT A9789)


title: NJA02201.N09


title: Fibroblast_NT-1_mitoRP

description:
Fibro_NT_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HF_NoANS_1_S1


title: NJA02201.N08


title: Fibroblast_NT-2_mitoRP

description:
Fibro_NT_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HF_NoANS_2_S4


title: Fibroblast_CHX30m-2_mitoRP

description:
Fibro_CHX_30m_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Plus-CHX-30min-R2_S10

value: 30 minutes with 100 ug/mL of cycloheximide dissolved in DMSO (Sigma, CAT C7698)


title: Fibroblast_CHX30m_1_mitoRP

description:
Fibro_CHX_30m_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Plus-CHX-30min-R1_S5


title: NJA02201.N06


title: NJA02201.N05


title: Fibroblast_DMSO30m-1_mitoRP

description:
Fibro_DMSO_30m_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
No-CHX-30min-R1_S4

value: 30 min with DMSO (Sigma, CAT 276855)


title: HEK-3_cytoRP

description:
HEK_NT_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_NT_cytoRP_R1_S3

value: cytoribosome protected fragments


title: HEK-4_cytoRP

description:
HEK_NT_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_NT_cytoRP_R2_S4


title: NJA02201.N04


title: Fibroblast_DMSO30m-2_mitoRP

description:
Fibro_DMSO_30m_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
No-CHX-30min-R2_S9


title: NJA02201.N13


title: HEK-1_cytoRP

description:
HEK_WT2_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_WT2_cytoRP_R1_S1


title: HEK-2_cytoRP

description:
HEK_WT2_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_WT2_cytoRP_R2_S2


title: Myocyte-6_cytoRP

description:
Myo_Diff2d2_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Differentiated_2D2_cytoRP_R2_S6

source_name: Myocytes (Myoblasts, 2 days post-differentiation induction)

value: treated with  0.4 ug/mL dexamethasone (Sigma, CAT D4902)


title: Myocyte-5_cytoRP

description:
Myo_Diff2d2_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Differentiated_2D2_cytoRP_R1_S5

value: Myocytes (Myoblasts, 2 days post-differentiation induction)


title: NJA02201.N01


title: NJA02201.M23


title: Myoblast-5_cytoRP

description:
Myo_NonDiff2_1_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated2_cytoRP_R1_S1

source_name: Myoblasts, anonymous donor

value: Myoblasts, anonymous donor

value: untreated


title: NJA02201.N07


title: NJA02201.N03


title: NJA02201.M21


title: NJA02201.M22


title: NJA02201.M24


title: NJA02201.M19


title: HEK-1_RNAseq

description:
HEK_WT2_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_WT2_RNAseq_R1_S1


title: HEK-2_RNAseq

description:
HEK_WT2_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_WT2_RNAseq_R2_S2


title: HEK-3_RNAseq

description:
HEK_NT_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_NT_RNA_seq_R1_S3


title: NJA02201.M17


title: HEK-4_RNAseq

description:
HEK_NT_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
HEK_NT_RNA_seq_R2_S4


title: NJA02201.M16


title: Myoblast-3_RNAseq

description:
Myo_NonDiff1_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated_RNA_R1_S1


title: NJA02201.M15


title: NJA02201.M14


title: Myoblast-4_RNAseq

description:
Myo_NonDiff1_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated_RNA_R2_S2


title: Myocyte-4_RNAseq

description:
Myo_Diff2d1_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
Differentiated_2D_RNA_R2_S6


title: NJA02201.N02


title: NJA02201.M13


title: Myocyte-3_RNAseq

description:
Myo_Diff2d1_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
Differentiated_2D_RNA_R1_S5


title: NJA02201.M12


title: Myoblast-6_cytoRP

description:
Myo_NonDiff2_2_cytoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated2_cytoRP_R2_S2


title: NJA02201.M11


title: NJA02201.M20


title: Fibroblast-3_RNAseq

description:
Fibro_NT4_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
Exp4_NT_RNA.fastq.gz


title: NJA02201.M10


title: NJA02201.M09


title: HEK-3_mitoRP

description:
HEK_WT2_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
WT2-R2_S2


title: HEK-2_mitoRP

description:
HEK_WT2_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
WT2-R1_S1


title: HEK-1_mitoRP

description:
HEK_WT1_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
WT1-2_S2


title: NJA02201.M08


title: HelaIP-2_mitoRP

description:
Hela_IP_8U_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HL-8U-R2_S4

source_name: HeLa S3

value: HeLa S3


title: NJA02201.M06

value: spleen


title: NJA02201.M07


title: NJA02201.M04


title: Hela-4_mitoRP

description:
Hela_F6_HM_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HM-2-6_S8


title: Hela-3_mitoRP

description:
Hela_F6_HM_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HM-1-6_S6


title: NJA02201.M05


title: Hela-2_mitoRP

description:
Hela_F6_H_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
H-2-6_S4


title: Hela-1_mitoRP

description:
Hela_F6_H_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
H-1-6_S2


title: NJA02201.M03


title: NJA02201.L24


title: NJA02201.M01


title: Myocyte-2_mitoRP

description:
Myo_Diff2d1_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Differentiated_2D_R2_S6


title: Myoblast-8_mitoRP

description:
Myo_NonDiff5_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated5_R2_S2


title: Myocyte-1_mitoRP

description:
Myo_Diff2d1_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Differentiated_2D_R1_S5


title: NJA02201.M02


title: NJA02201.L23


title: NJA02201.L22


title: NJA02201.L21


title: NJA02201.L20


title: Myoblast-1_mitoRP

description:
Myo_NonDiff1_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated_R1_S1


title: Myoblast-2_mitoRP

description:
Myo_NonDiff1_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated_R2_S2


title: NJA02201.L19


title: Fibroblast-3_mitoRP

description:
Fibro_NT4_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Exp4_NT_S1


title: Fibroblast-2_mitoRP

description:
Fibro_Glu_2_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Glucose-R2_S6


title: Fibroblast-1_mitoRP

description:
Fibro_Glu_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Glucose-R1_S1


title: NJA02201.L18


title: NJA02201.L15


title: NJA02201.L17


title: NJA02201.L13


title: NJA02201.L12


title: 4_con

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: untreated

data_processing:
Partek Flow (build 8.0.19.0610).
Trim bases based on quality score, min Phred score 20.
STAR - 2.6.1d aligned to hg38.
Quantify to annotation model (Partek E/M). Gene level qualntifiaction, RPKM normalization.
Genome_build: hg38

source_name: human MDA-MB-231 cells

growth_protocol: cells were grown in RPMI 1640 (2,000 mg/liter glucose) media, supplemented with 10% fetal bovine serum (FBS), 2% L-glutamine and 1% penicillin-streptomycin solution

extract_protocol:
total RNA was isolated using miRNeasy Mini Kit (Cat# 217004; QIAGEN, Hilden, Germany) according to manufacturer’s protocols
Libraries were prepared at the INCPM from the RNAs using in-house protocol.

treatment_protocol: TNBC cells were stimulated by 10ng/ml recombinant human (rh) TNFα (#300-01A, PeproTech, NJ, USA) and 0.4ng/ml rhIL-1β (#200-01B, PeproTech) for 6 weeks in the presence of the two cytokines together (replaced twice a week)

value: control


title: 2_con

description: untreated


title: 3_treat

description: treatment with 10ng/ml recombinant human (rh) TNFα (#300-01A, PeproTech, NJ, USA) and 0.4ng/ml rhIL-1β

value: treatment


title: 5_treat


title: Myoblast-7_mitoRP

description:
Myo_NonDiff5_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Non_Differentiated5_R1_S1

value: mitoribosome protected fragments


title: NJA02201.L11

value: Singlet


title: NJA02201.L08


title: NJA02201.L10


title: NJA02201.L07


title: Treat3_S24

source_name: Human TNBC BT-549 cells

growth_protocol: cells were grown in DMEM (4,500 mg/liter glucose) media, supplemented with 10% fetal bovine serum (FBS), 2% L-glutamine and 1% penicillin-streptomycin solution


title: NJA02201.L06


title: Con2_S21

description: untreated


title: Treat1_S20


title: 6_con

description: untreated


title: NJA02201.L04


title: Con1_S19

description: untreated


title: Molm13_PRMT5i_input

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

library_source: genomic

data_processing:
Base calling using Illumina RTA 2.4.11
Fastq files were trimmed and filtered using cutadapt v.1.15  -n-nextseq-trim=20 -m 18
Aligned to merged GRCh38_no_alt_analysis_set_GCA_000001405.15_clean and BDGP6 without chrM using bowtie2 v2.3.3.1
Aligned bam files were deduplicated using umi_tools dedup v0.5.5
bedgraph files were generated by from deduplicated bams using deeptools v3.1.1 bamCoverage -binSize 100 --normalizeUsing CPM -of bedgraph
normalized bw files were generated from bedgraph files using lowess normalization driven by bdpg6 genomic bins. (https://github.com/diderote/lowSpike/blob/master/prepackage_implementation/lowSpike.ipynb)
average normalized bigwigs were generated using deeptools bigwigCompare --operation mean --binsize 20
Genome_build: GRCh38_no_alt_analysis_set_GCA_000001405.15_bdgp6_noM
Supplementary_files_format_and_content: bw: condition averaged lowess normalized hg38 bigwig files.

molecule: genomic DNA

source_name: Molm13 Cells

growth_protocol: Molm13 cells were cultured in RPMI1640 supplemented with 10% FBS.

extract_protocol:
Cells were fixed in 1% formaldehyde for 5 min at RT, and then lyzed with sonication buffer (16.7mM Tris pH 8, 167mM NaCl, 0.1% SDS, 1% Triton, 1mM EDTA) supplemented with proteasome inhibitor cocktail (Millipore, #535140). Chromatin was sonicated with Bioruptor Pico (Diagenode) for 14 cycles with 30s on and off. Immunoprecipitation was performed with 4ug of cell lysate and 2ug of antibody against H3K27me3 (Cell Signaling, C36B11) overnight at 4oC, and the antibody-chromatin complex was then pulled down with 20ul of magnetic Protein A beads (NEB S1425s) 20 ng of drosophila chromatin (Active Motif, 53083) was included for normalization. The beads were washed twice with each of the following buffers: high salt buffer (20 mM Tris pH 8, 500 mM NaCl, 0.1% SDS, 1 % TritonX-100 and 2 mM EDTA); Li buffer (10 mM Tris pH 8, 0.25 M LiCl, 1% NP40, 1% sodium deoxycholate and 1 mM EDTA,); TE buffer (pH 8). The beads were then suspended in 30ul buffer (100 mM Tris pH 8, 250 mM NaCl, 1mM EDTA and 0.1% SDS,) with 1ul of Proteinase K (Invitrogen, AM2546) and incubated at 65oC for 4 h. The DNA in the supernatant was purified with Agencourt AMPure beads (Beckman Coulter A63880).
DNA library was constructed using NEB E7645 as per protocol.

treatment_protocol: Cells were treated with DMSO (0.05%), EZH2 inhibitor (GSK343) 1 uM or PRMT5 inhibitor (GSK3186000A) 1 uM for 4 days.

tag: cell type

value: Acute Myeloid Leukemia

tag: antibody


title: NJA02201.L05

tag: strain


title: NJA02201.L14

tag: tissue


title: NJA02201.L03

tag: facs cellnumber


title: NJA02201.L02

tag: age (days)


title: Molm13_EZH2i_input


title: NJA02201.L01


title: Molm13_DMSO_input


title: 1_treat


title: HelaIP-1_mitoRP

description:
Hela_IP_8U_1_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HL-8U-R1_S3

tag: cell line/type

value: WT


title: NJA02201.K23

value: Multiplet


title: NJA02201.K24


title: Molm13_H3K27me3_PRMT5i_1

value: Cell Signaling, C36B11


title: Molm13_H3K27me3_EZH2i_1


title: NJA02201.K19


title: NJA02201.K20


title: Con3_S23

description: untreated


title: NJA02201.K18


title: Molm13_H3K27me3_EZH2i_2


title: NJA02201.K21


title: Molm13_PE_rep2

description:
Molm13_PE_2
Paired End RNAseq
processed data file: RSEM.count.matrix.txt

data_processing:
Base calling using Illumina RTA 2.4.11.
Sequenced reads were hard clipped 1 bp at the 5' and 3 bps at the 3' read ends. Using Skewer v0.2.2, reads were then trimmed of adaptor sequences and low 3' base quality (q20), while read pairs with reads 18 or smaller were filtered out.
Reads mapped to GRCh38.p7 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Counts were estimated using RSEM gene.results.
Genome_build: Ensembl 87: GRCh38.p7
Supplementary_files_format_and_content: RSEM.count.matrix.txt: Tab-delimited text file contains aggregated RSEM gene.results output for all samples.

extract_protocol:
RNA were purified with RNeasy plus Mini Kit from Qiagen.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with DMSO (0.005%), EZH2 inhibitor (1uM), PRMT5 inhibitor (1uM) or combination of both inhibitors for 4 days.

tag: condition

value: PRMT5 and EZH2 Inhibition


title: Molm13_PE_rep1

description:
Molm13_PE_1
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: NJA02201.K16


title: Molm13_PE_rep4

description:
Molm13_PE_4
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: NJA02201.K17


title: Molm13_PE_rep3

description:
Molm13_PE_3
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: Molm13_P5i_1uM_rep4

description:
Molm13_P5i_1uM4
Paired End RNAseq
processed data file: RSEM.count.matrix.txt

value: PRMT5 Inhibition


title: Molm13_P5i_1uM_rep3

description:
Molm13_P5i_1uM3
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: NJA02201.K13


title: NJA02201.K15


title: NJA02201.K12


title: NJA02201.K14


title: Treat2_S22

tag: treatment


title: Molm13_P5i_1uM_rep2

description:
Molm13_P5i_1uM2
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: Molm13_P5i_1uM_rep1

description:
Molm13_P5i_1uM1
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: Molm13_H3K27me3_DMSO_2


title: NJA02201.K10


title: Molm13_EZH2i_rep4

description:
Molm13_EZH2i4
Paired End RNAseq
processed data file: RSEM.count.matrix.txt

value: EZH2 Inhibition


title: Molm13_H3K27me3_DMSO_1


title: Molm13_EZH2i_rep3

description:
Molm13_EZH2i3
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: Molm13_EZH2i_rep2

description:
Molm13_EZH2i2
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: NJA02201.K08


title: Molm13_EZH2i_rep1

description:
Molm13_EZH2i1
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: NJA02201.K06


title: NJA02201.K05


title: Molm13_DMSO_rep4

description:
Molm13_DMSO4
Paired End RNAseq
processed data file: RSEM.count.matrix.txt

value: DMSO Control


title: Molm13_DMSO_rep3

description:
Molm13_DMSO3
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: Molm13_DMSO_rep1

description:
Molm13_DMSO1
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: SEQ7219

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

description: cfDNA

data_processing:
Raw sequencing reads were trimmed and filtered for low-quality bases using fastx_toolkit (v 0.0.14), followed by alignment to the human genome reference (hg19) using Bowtie2 (v 2.2.6) with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Aligned read pairs were then sorted, indexed and deduplicated using Picard (v 2.6.0). Alignments with Mapping Quality Score ≥ 10 were counted for gene bodies, according to the gene start and gene end annotations by the GENCODE Project (release 19)24, using featureCounts from R package Rsubread (v 1.30.9) without strand information25.
The 5hmC-Seal libraries were sequenced to produce a median number of ~20 million reads in each sample, and a median number of ~7 million unique reads were mapped to the ~20,000 gene body regions
Genome_build: hg19

source_name: Plasma

extract_protocol:
For each study subject, approximately 2-3 mL of frozen plasma was processed by centrifuging twice at 1,350 × g for 12 min, and then centrifuging at 13,500 × g for 12 min, followed by cfDNA extraction using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Germany)
Each cfDNA sample was first repaired and ligated with adaptors. Next, the T4 bacteriophage enzyme β-glucosyltransferase (β-GT) was used to transfer an engineered glucose moiety containing an azide-group to 5hmC in duplex DNA. A biotin tag was then installed onto the azide group using Huisgen cycloaddition (“click”) chemistry, followed by capturing of 5hmC-containing DNA fragments using avidin beads. The 5hmC-Seal library for each cfDNA sample was then constructed through PCR amplification, followed by paired-end sequencing (PE38) on the Illumina NextSeq500 platform at Shanghai Epican Genetech Co. Ltd. (Shanghai, China), according to the manufacturer’s protocol. We randomized cfDNA samples when constructing the 5hmC-Seal libraries and sequencing. The 5hmC-Seal was shown to be technically robust and stable in our previous studies using duplicate samples and spike-in controls
5hmC-Seal

tag: population

value: Chinese


title: SEQ7151

description: cfDNA


title: NJA02201.J24


title: NJA02201.K02


title: NJA02201.K04


title: NJA02201.K03


title: NJA02201.J22


title: SEQ7312

description: cfDNA


title: NJA02201.J21


title: NJA02201.K07


title: SEQ7108

description: cfDNA


title: SEQ7107

description: cfDNA


title: NJA02201.J20


title: SEQ7084

description: cfDNA


title: NJA02201.J18


title: NJA02201.J19


title: NJA02201.J16


title: NJA02201.K11


title: NJA02201.J17


title: Molm13_DMSO_rep2

description:
Molm13_DMSO2
Paired End RNAseq
processed data file: RSEM.count.matrix.txt


title: SEQ7057

description: cfDNA


title: SEQ7039

description: cfDNA


title: SEQ7032

description: cfDNA


title: SEQ7365

description: cfDNA


title: NJA02201.J14


title: NJA02201.J23


title: SEQ6997

description: cfDNA


title: Molm13_H3K27me3_PRMT5i_2


title: NJA02201.J15


title: SEQ6502

description: cfDNA


title: NJA02201.J13


title: SEQ6969

description: cfDNA


title: SEQ6521

description: cfDNA


title: NJA02201.J12


title: SEQ6476

description: cfDNA


title: NJA02201.J10


title: NJA02201.J11


title: SEQ6475

description: cfDNA


title: NJA02201.J08


title: NJA02201.J09


title: SEQ6473

description: cfDNA


title: NJA02201.J06


title: SEQ6427

description: cfDNA


title: NJA02201.J05


title: NJA02201.J04


title: SEQ6419

description: cfDNA


title: SEQ6410

description: cfDNA


title: SEQ6420

description: cfDNA


title: SEQ6361

description: cfDNA


title: NJA02201.J03


title: NJA02201.I23


title: NJA02201.J01


title: SEQ6351

description: cfDNA


title: NJA02201.I24


title: NJA02201.I22


title: NJA02201.I20


title: NJA02201.I21


title: SEQ6326

description: cfDNA


title: SEQ6321

description: cfDNA


title: SEQ6329

description: cfDNA


title: SEQ6470

description: cfDNA


title: NJA02201.I19


title: SEQ6316

description: cfDNA


title: NJA02201.I16


title: NJA02201.I17


title: SEQ6306

description: cfDNA


title: NJA02201.J02


title: SEQ6307

description: cfDNA


title: NJA02201.I15


title: SEQ6303

description: cfDNA


title: SEQ6292

description: cfDNA


title: SEQ6242

description: cfDNA


title: NJA02201.I13


title: NJA02201.I11


title: SEQ6347

description: cfDNA


title: SEQ6285

description: cfDNA


title: SEQ6180

description: cfDNA


title: SEQ6220

description: cfDNA


title: SEQ6184

description: cfDNA


title: NJA02201.I09


title: NJA02201.I10


title: NJA02201.K22


title: NJA02201.I08


title: SEQ6099

description: cfDNA


title: NJA02201.I06


title: SEQ6069

description: cfDNA


title: NJA02201.I05


title: NJA02201.I14


title: NJA02201.I02


title: SEQ6057

description: cfDNA


title: NJA02201.I01


title: SEQ6160

description: cfDNA


title: NJA02201.H24


title: NJA02201.I07


title: NJA02201.H23


title: NJA02201.I03


title: SEQ5936

description: cfDNA


title: SEQ5941

description: cfDNA


title: SEQ6078

description: cfDNA


title: SEQ5978

description: cfDNA


title: SEQ6034

description: cfDNA


title: NJA02201.H22


title: SEQ5935

description: cfDNA


title: NJA02201.H17


title: NJA02201.H20


title: NJA02201.H18


title: SEQ5933

description: cfDNA


title: NJA02201.H15


title: SEQ6068

description: cfDNA


title: SEQ6059

description: cfDNA


title: SEQ5911

description: cfDNA


title: NJA02201.H14


title: SEQ5906

description: cfDNA


title: SEQ5886

description: cfDNA


title: NJA02201.I04


title: NJA02201.H13


title: SEQ6054

description: cfDNA


title: NJA02201.H12


title: SEQ5883

description: cfDNA


title: NJA02201.H21


title: SEQ5983

description: cfDNA


title: SEQ5830

description: cfDNA


title: SEQ5829

description: cfDNA


title: NJA02201.H10


title: NJA02201.H09


title: SEQ5556

description: cfDNA


title: SEQ5567

description: cfDNA


title: SEQ5544

description: cfDNA


title: SEQ5542

description: cfDNA


title: SEQ5529

description: cfDNA


title: NJA02201.H06


title: NJA02201.H05


title: NJA02201.H04


title: NJA02201.H08


title: SEQ5515

description: cfDNA


title: SEQ5512

description: cfDNA


title: NJA02201.H02


title: NJA02201.H01


title: NJA02201.H11


title: NJA02201.G23


title: SEQ5396

description: cfDNA


title: NJA02201.G22


title: SEQ5475

description: cfDNA


title: NJA02201.G24


title: SEQ5500

description: cfDNA


title: NJA02201.G20


title: SEQ5366

description: cfDNA


title: NJA02201.G21


title: SEQ5365

description: cfDNA


title: SEQ5328

description: cfDNA


title: NJA02201.G18


title: NJA02201.G17


title: NJA02201.G14


title: NJA02201.G16


title: SEQ5233

description: cfDNA


title: SEQ5518

description: cfDNA


title: SEQ5198

description: cfDNA


title: SEQ5369

description: cfDNA


title: SEQ5046

description: cfDNA


title: NJA02201.G12


title: SEQ5232

description: cfDNA


title: NJA02201.G13


title: SEQ5045

description: cfDNA


title: NJA02201.G08


title: SEQ5041

description: cfDNA


title: NJA02201.G07


title: NJA02201.G09


title: NJA02201.G06


title: SEQ5040

description: cfDNA


title: SEQ5003

description: cfDNA


title: NJA02201.G05


title: SEQ5022

description: cfDNA


title: SEQ4753

description: cfDNA


title: SEQ4994

description: cfDNA


title: SEQ4991

description: cfDNA


title: NJA02201.G04


title: NJA02201.G03


title: SEQ4677

description: cfDNA


title: NJA02201.G02


title: NJA02201.G01


title: NJA02201.F24


title: NJA02201.F23


title: NJA02201.F20


title: SEQ3325

description: cfDNA


title: NJA02201.F21


title: SEQ3830

description: cfDNA


title: NJA02201.G19


title: SEQ3651

description: cfDNA


title: NJA02201.G11


title: SEQ3318

description: cfDNA


title: NJA02201.F18


title: NJA02201.F19


title: SEQ3246

description: cfDNA


title: NJA02201.F17


title: SEQ3212

description: cfDNA


title: SEQ1961

description: cfDNA


title: SEQ4357

description: cfDNA


title: NJA02201.F14


title: SEQ3833

description: cfDNA


title: NJA02201.F15


title: NJA02201.F13


title: SEQ1771

description: cfDNA


title: SEQ1768

description: cfDNA


title: NJA02201.F12


title: SEQ1752

description: cfDNA


title: SEQ1763

description: cfDNA


title: NJA02201.F11


title: NJA02201.F10


title: SEQ1737

description: cfDNA


title: NJA02201.F09


title: SEQ1743

description: cfDNA


title: NJA02201.F08


title: SEQ1733

description: cfDNA


title: SEQ1736

description: cfDNA


title: NJA02201.F05


title: NJA02201.F07


title: SEQ1773

description: cfDNA


title: SEQ1729

description: cfDNA


title: SEQ1679

description: cfDNA


title: NJA02201.F16


title: SEQ1664

description: cfDNA


title: NJA02201.F02


title: NJA02201.F04


title: NJA02201.F01


title: NJA02201.E24


title: SEQ1661

description: cfDNA


title: NJA02201.E23


title: SEQ1663

description: cfDNA


title: SEQ13655

description: cfDNA


title: SEQ13552

description: cfDNA


title: NJA02201.E22


title: NJA02201.E21


title: SEQ13551

description: cfDNA


title: SEQ12604

description: cfDNA


title: NJA02201.E19


title: NJA02201.E20


title: SEQ12625

description: cfDNA


title: SEQ11751

description: cfDNA


title: NJA02201.E17


title: SEQ11750

description: cfDNA


title: SEQ10716

description: cfDNA


title: SEQ10226

description: cfDNA


title: NJA02201.E16


title: SEQ9875

description: cfDNA


title: NJA02201.E14


title: SEQ9948

description: cfDNA


title: SEQ9871

description: cfDNA


title: NJA02201.E11


title: NJA02201.E10


title: NJA02201.E15


title: NJA02201.E09


title: SEQ9785

description: cfDNA


title: SEQ9781

description: cfDNA


title: NJA02201.E08


title: NJA02201.E07


title: SEQ9776

description: cfDNA


title: NJA02201.E06


title: NJA02201.E05


title: SEQ9763

description: cfDNA


title: NJA02201.E18


title: SEQ9656

description: cfDNA


title: NJA02201.E03


title: NJA02201.E02


title: SEQ9654

description: cfDNA


title: NJA02201.E01


title: SEQ9602

description: cfDNA


title: NJA02201.D24


title: SEQ9601

description: cfDNA


title: NJA02201.D23


title: SEQ9600

description: cfDNA


title: SEQ9598

description: cfDNA


title: NJA02201.D21


title: SEQ9577

description: cfDNA


title: NJA02201.D22


title: NJA02201.D18


title: NJA02201.D19


title: SEQ9505

description: cfDNA


title: SEQ9569

description: cfDNA


title: SEQ9774

description: cfDNA


title: NJA02201.D17


title: NJA02201.D15


title: NJA02201.D14


title: SEQ9559

description: cfDNA


title: NJA02201.D13


title: SEQ9556

description: cfDNA


title: SEQ9638

description: cfDNA


title: NJA02201.D12


title: SEQ9554

description: cfDNA


title: NJA02201.D09


title: NJA02201.D08


title: SEQ9576

description: cfDNA


title: NJA02201.D07


title: NJA02201.D06


title: SEQ9575

description: cfDNA


title: SEQ9521

description: cfDNA


title: SEQ9574

description: cfDNA


title: NJA02201.H03


title: SEQ9493

description: cfDNA


title: NJA02201.D04


title: SEQ8955

description: cfDNA


title: SEQ8956

description: cfDNA


title: NJA02201.D05


title: SEQ8945

description: cfDNA


title: NJA02201.D01


title: NJA02201.D11


title: NJA02201.C24


title: NJA02201.D03


title: SEQ5326

description: cfDNA


title: SEQ9282

description: cfDNA


title: SEQ9520

description: cfDNA


title: NJA02201.D02


title: SEQ9558

description: cfDNA


title: SEQ9483

description: cfDNA


title: SEQ9617

description: cfDNA


title: SEQ8940

description: cfDNA


title: NJA02201.C20


title: SEQ9158

description: cfDNA


title: NJA02201.C19


title: NJA02201.C18


title: SEQ9283

description: cfDNA


title: NJA02201.C21


title: SEQ9157

description: cfDNA


title: NJA02201.C17


title: NJA02201.C23


title: NJA02201.C22


title: NJA02201.C16


title: SEQ8938

description: cfDNA


title: NJA02201.C15


title: SEQ9160

description: cfDNA


title: SEQ8986

description: cfDNA


title: SEQ9079

description: cfDNA


title: 7d_1_F5

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
Trypanosome isolated from skin at 7 days post-infection, #18
single_trypanosomes_normalized_reads.csv

data_processing:
After demultiplexing, data quality was examined using FastQC (version 0.11.7). Illumina adaptors were removed using cutadapt (version 3.2). Trimmed reads were mapped to the TREU927 (version 48) genome with the ERCC spike-in sequences included, using RNASTAR (version 2.6.1b). Read counts for each gene were determined using featureCounts (version 2.0.1) and genes with ≥ 5 aligned reads were considered detected. Only those scRNAseq datasets with > 200 and < 1000 detected genes and a library size between 2 x 105 and 2 x 106 reads were considered for analysis. Principal component analysis (PCA) was performed selecting the 1000 genes with the highest variance. The following libraries were excluded from the analysis due to BARP gene expression: "0h_1_B5_1", "0h_1_G2", "0h_1_C5_1". Differential gene expression analysis was conducted with DESeq2 (version 1.30.0) and SCDE  (version 2.18.0; only used in early vs. late analysis). Features with an absolute log2 fold change > 2 and adjusted P value < 0.01 (DEseq2) or a z-score > 1.96 (SCDE) were considered as differentially expressed, respectively.
Genome_build: Tbrucei TEU927 version 48 and human GRCh38
Supplementary_files_format_and_content: csv; count table

organism: Trypanosoma brucei

source_name: skin

extract_protocol:
After natural infection, skin equivalents were cultured for another 4 h, 12 h, 24 h, and 7 d, respectively. In addition, freshly collected MCFs obtained from tsetse flies were used. Skin equivalents were dissociated and single viable parasites were sorted based on their tdTomato and Calcein AM signal with a FACSAria III cytometer (BD Biosciences) into 48-well plates containing 2.6 µl of 1x lysis buffer (Takara) supplemented with 0.01 µl of RNase inhibitor (40 U/µl; Takara). Immediately after sorting, cells were placed on ice for 5 min and stored at -80 °C.
Library preparation and sequencing was carried out as described previously (Muller et al., 2018). Briefly, 0.2 µl of a 1:20 x 106 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher Scientific) were added to the lysates of single parasites and libraries were prepared using SMART-Seq v.4 Ultra Low Input RNA Kit (Takara) using a quarter of the reagent volumes recommended by the manufacturer. 27 cycles were used for PCR amplification and cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter) using 15 μl of elution buffer (Takara). Library quantification was performed with a Qubit 3 Fluorometer with dsDNA Hs Assay kit (Life Technologies) and the quality of the libraries was assessed using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended volumes, 10 min for tagmentation at 55 °C and 1 min extension time during PCR amplification. Libraries were pooled and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina’s NextSeq 500.

tag: timepoint


title: 7d_1_G3

description:
Trypanosome isolated from skin at 7 days post-infection, #20
single_trypanosomes_normalized_reads.csv


title: 7d_1_G4

description:
Trypanosome isolated from skin at 7 days post-infection, #21
single_trypanosomes_normalized_reads.csv


title: 7d_1_F4

description:
Trypanosome isolated from skin at 7 days post-infection, #17
single_trypanosomes_normalized_reads.csv


title: 7d_1_H3

description:
Trypanosome isolated from skin at 7 days post-infection, #24
single_trypanosomes_normalized_reads.csv


title: 7d_1_H2

description:
Trypanosome isolated from skin at 7 days post-infection, #23
single_trypanosomes_normalized_reads.csv


title: 7d_1_H4

description:
Trypanosome isolated from skin at 7 days post-infection, #25
single_trypanosomes_normalized_reads.csv


title: SEQ9169

description: cfDNA


title: 7d_1_F3

description:
Trypanosome isolated from skin at 7 days post-infection, #16
single_trypanosomes_normalized_reads.csv


title: 7d_1_G2

description:
Trypanosome isolated from skin at 7 days post-infection, #19
single_trypanosomes_normalized_reads.csv


title: 7d_1_F2

description:
Trypanosome isolated from skin at 7 days post-infection, #15
single_trypanosomes_normalized_reads.csv


title: NJA02201.C14


title: SEQ8985

description: cfDNA


title: 7d_1_E5

description:
Trypanosome isolated from skin at 7 days post-infection, #14
single_trypanosomes_normalized_reads.csv


title: NJA02201.C13


title: 7d_1_E4

description:
Trypanosome isolated from skin at 7 days post-infection, #13
single_trypanosomes_normalized_reads.csv


title: NJA02201.C12


title: SEQ8983

description: cfDNA


title: 7d_1_G5

description:
Trypanosome isolated from skin at 7 days post-infection, #22
single_trypanosomes_normalized_reads.csv


title: 7d_1_D5

description:
Trypanosome isolated from skin at 7 days post-infection, #11
single_trypanosomes_normalized_reads.csv


title: 7d_1_E3

description:
Trypanosome isolated from skin at 7 days post-infection, #12
single_trypanosomes_normalized_reads.csv


title: NJA02201.C11


title: 7d_1_D4

description:
Trypanosome isolated from skin at 7 days post-infection, #10
single_trypanosomes_normalized_reads.csv


title: SEQ8982

description: cfDNA


title: NJA02201.C09


title: 7d_1_C5

description:
Trypanosome isolated from skin at 7 days post-infection, #8
single_trypanosomes_normalized_reads.csv


title: SEQ8981

description: cfDNA


title: NJA02201.C07


title: 7d_1_D3

description:
Trypanosome isolated from skin at 7 days post-infection, #9
single_trypanosomes_normalized_reads.csv


title: 7d_1_C4

description:
Trypanosome isolated from skin at 7 days post-infection, #7
single_trypanosomes_normalized_reads.csv


title: 7d_1_C3

description:
Trypanosome isolated from skin at 7 days post-infection, #6
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: NJA02201.C08


title: 7d_1_A4

description:
Trypanosome isolated from skin at 7 days post-infection, #2
single_trypanosomes_normalized_reads.csv


title: 7d_1_B3

description:
Trypanosome isolated from skin at 7 days post-infection, #3
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 7d_1_B4

description:
Trypanosome isolated from skin at 7 days post-infection, #4
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 7d_1_B5

description:
Trypanosome isolated from skin at 7 days post-infection, #5
single_trypanosomes_normalized_reads.csv


title: 7d_1_A3

description:
Trypanosome isolated from skin at 7 days post-infection, #1
single_trypanosomes_normalized_reads.csv


title: NJA02201.C05


title: 24h_1_H5

description:
Trypanosome isolated from skin at 24 hours post-infection, #26
single_trypanosomes_normalized_reads.csv


title: NJA02201.C06


title: SEQ8980

description: cfDNA


title: 24h_1_H4

description:
Trypanosome isolated from skin at 24 hours post-infection, #25
single_trypanosomes_normalized_reads.csv


title: SEQ8896

description: cfDNA


title: SEQ8895

description: cfDNA


title: 24h_1_H2

description:
Trypanosome isolated from skin at 24 hours post-infection, #23
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: NJA02201.C03


title: 24h_1_H3

description:
Trypanosome isolated from skin at 24 hours post-infection, #24
single_trypanosomes_normalized_reads.csv


title: 24h_1_G5

description:
Trypanosome isolated from skin at 24 hours post-infection, #22
single_trypanosomes_normalized_reads.csv


title: NJA02201.C04


title: SEQ8891

description: cfDNA


title: 24h_1_G4

description:
Trypanosome isolated from skin at 24 hours post-infection, #21
single_trypanosomes_normalized_reads.csv


title: NJA02201.C02


title: SEQ8903

description: cfDNA


title: 24h_1_G2

description:
Trypanosome isolated from skin at 24 hours post-infection, #19
single_trypanosomes_normalized_reads.csv


title: SEQ8902

description: cfDNA


title: 24h_1_F5

description:
Trypanosome isolated from skin at 24 hours post-infection, #18
single_trypanosomes_normalized_reads.csv


title: SEQ8818

description: cfDNA


title: 24h_1_F3

description:
Trypanosome isolated from skin at 24 hours post-infection, #16
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: SEQ8804

description: cfDNA


title: NJA02201.C01


title: NJA02201.B23


title: SEQ8881

description: cfDNA


title: NJA02201.B24


title: 24h_1_E5

description:
Trypanosome isolated from skin at 24 hours post-infection, #14
single_trypanosomes_normalized_reads.csv


title: 24h_1_D5

description:
Trypanosome isolated from skin at 24 hours post-infection, #12
single_trypanosomes_normalized_reads.csv


title: SEQ8880

description: cfDNA


title: 24h_1_E3

description:
Trypanosome isolated from skin at 24 hours post-infection, #13
single_trypanosomes_normalized_reads.csv


title: NJA02201.B22


title: NJA02201.B20


title: 24h_1_G3

description:
Trypanosome isolated from skin at 24 hours post-infection, #20
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 24h_1_D3

description:
Trypanosome isolated from skin at 24 hours post-infection, #10
single_trypanosomes_normalized_reads.csv


title: 24h_1_F4

description:
Trypanosome isolated from skin at 24 hours post-infection, #17
single_trypanosomes_normalized_reads.csv


title: 24h_1_C5

description:
Trypanosome isolated from skin at 24 hours post-infection, #9
single_trypanosomes_normalized_reads.csv


title: 24h_1_C3

description:
Trypanosome isolated from skin at 24 hours post-infection, #7
single_trypanosomes_normalized_reads.csv


title: 24h_1_C4

description:
Trypanosome isolated from skin at 24 hours post-infection, #8
single_trypanosomes_normalized_reads.csv


title: 24h_1_F2

description:
Trypanosome isolated from skin at 24 hours post-infection, #15
single_trypanosomes_normalized_reads.csv


title: 24h_1_D4

description:
Trypanosome isolated from skin at 24 hours post-infection, #11
single_trypanosomes_normalized_reads.csv


title: 24h_1_B5

description:
Trypanosome isolated from skin at 24 hours post-infection, #6
single_trypanosomes_normalized_reads.csv


title: SEQ8717

description: cfDNA


title: NJA02201.B19


title: 24h_1_B3

description:
Trypanosome isolated from skin at 24 hours post-infection, #4
single_trypanosomes_normalized_reads.csv


title: NJA02201.B18


title: SEQ8971

description: cfDNA


title: NJA02201.B21


title: 24h_1_B4

description:
Trypanosome isolated from skin at 24 hours post-infection, #5
single_trypanosomes_normalized_reads.csv


title: 24h_1_A5

description:
Trypanosome isolated from skin at 24 hours post-infection, #3
single_trypanosomes_normalized_reads.csv


title: SEQ8710

description: cfDNA


title: NJA02201.B16


title: 24h_1_A3

description:
Trypanosome isolated from skin at 24 hours post-infection, #1
single_trypanosomes_normalized_reads.csv


title: SEQ8790

description: cfDNA


title: SEQ8718

description: cfDNA


title: NJA02201.B17


title: SEQ8782

description: cfDNA


title: 12h_1_H3

description:
Trypanosome isolated from skin at 12 hours post-infection, #25
single_trypanosomes_normalized_reads.csv


title: 12h_1_H4

description:
Trypanosome isolated from skin at 12 hours post-infection, #26
single_trypanosomes_normalized_reads.csv


title: 12h_1_G5

description:
Trypanosome isolated from skin at 12 hours post-infection, #23
single_trypanosomes_normalized_reads.csv


title: NJA02201.B15


title: NJA02201.B14


title: SEQ8857

description: cfDNA


title: NJA02201.B13


title: 12h_1_H2

description:
Trypanosome isolated from skin at 12 hours post-infection, #24
single_trypanosomes_normalized_reads.csv


title: 12h_1_G3

description:
Trypanosome isolated from skin at 12 hours post-infection, #21
single_trypanosomes_normalized_reads.csv


title: SEQ8856

description: cfDNA


title: NJA02201.B12


title: 12h_1_G2

description:
Trypanosome isolated from skin at 12 hours post-infection, #20
single_trypanosomes_normalized_reads.csv


title: SEQ8709

description: cfDNA


title: SEQ8908

description: cfDNA


title: 12h_1_H5

description:
Trypanosome isolated from skin at 12 hours post-infection, #27
single_trypanosomes_normalized_reads.csv


title: 12h_1_F4

description:
Trypanosome isolated from skin at 12 hours post-infection, #18
single_trypanosomes_normalized_reads.csv


title: SEQ8703

description: cfDNA


title: NJA02201.B11


title: 24h_1_A4

description:
Trypanosome isolated from skin at 24 hours post-infection, #2
single_trypanosomes_normalized_reads.csv


title: SEQ8783

description: cfDNA


title: NJA02201.B10


title: 12h_1_E5

description:
Trypanosome isolated from skin at 12 hours post-infection, #15
single_trypanosomes_normalized_reads.csv


title: 12h_1_F3

description:
Trypanosome isolated from skin at 12 hours post-infection, #17
single_trypanosomes_normalized_reads.csv


title: SEQ8886

description: cfDNA


title: 12h_1_F2

description:
Trypanosome isolated from skin at 12 hours post-infection, #16
single_trypanosomes_normalized_reads.csv


title: NJA02201.B09


title: 12h_1_E4

description:
Trypanosome isolated from skin at 12 hours post-infection, #14
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 12h_1_D5

description:
Trypanosome isolated from skin at 12 hours post-infection, #12
single_trypanosomes_normalized_reads.csv


title: 12h_1_G4

description:
Trypanosome isolated from skin at 12 hours post-infection, #22
single_trypanosomes_normalized_reads.csv


title: 12h_1_D4

description:
Trypanosome isolated from skin at 12 hours post-infection, #11
single_trypanosomes_normalized_reads.csv


title: NJA02201.B08


title: 12h_1_D3

description:
Trypanosome isolated from skin at 12 hours post-infection, #10
single_trypanosomes_normalized_reads.csv


title: SEQ8849

description: cfDNA


title: NJA02201.B07


title: 12h_1_E3

description:
Trypanosome isolated from skin at 12 hours post-infection, #13
single_trypanosomes_normalized_reads.csv


title: SEQ8745

description: cfDNA


title: 12h_1_C4

description:
Trypanosome isolated from skin at 12 hours post-infection, #8
single_trypanosomes_normalized_reads.csv


title: 12h_1_C3

description:
Trypanosome isolated from skin at 12 hours post-infection, #7
single_trypanosomes_normalized_reads.csv


title: 12h_1_C5

description:
Trypanosome isolated from skin at 12 hours post-infection, #9
single_trypanosomes_normalized_reads.csv


title: NJA02201.B06


title: SEQ8673

description: cfDNA


title: 12h_1_B4

description:
Trypanosome isolated from skin at 12 hours post-infection, #5
single_trypanosomes_normalized_reads.csv


title: NJA02201.B05


title: 12h_1_A5

description:
Trypanosome isolated from skin at 12 hours post-infection, #3
single_trypanosomes_normalized_reads.csv


title: 12h_1_B3

description:
Trypanosome isolated from skin at 12 hours post-infection, #4
single_trypanosomes_normalized_reads.csv


title: 12h_1_F5

description:
Trypanosome isolated from skin at 12 hours post-infection, #19
single_trypanosomes_normalized_reads.csv


title: SEQ8672

description: cfDNA


title: NJA02201.B04


title: SEQ8330

description: cfDNA


title: SEQ8885

description: cfDNA


title: 12h_1_A4

description:
Trypanosome isolated from skin at 12 hours post-infection, #2
single_trypanosomes_normalized_reads.csv


title: SEQ8328

description: cfDNA


title: NJA02201.B01


title: 4h_1_H5

description:
Trypanosome isolated from skin at 4 hours post-infection, #27
single_trypanosomes_normalized_reads.csv


title: SEQ8324

description: cfDNA


title: 12h_1_B5

description:
Trypanosome isolated from skin at 12 hours post-infection, #6
single_trypanosomes_normalized_reads.csv


title: 4h_1_H3

description:
Trypanosome isolated from skin at 4 hours post-infection, #25
single_trypanosomes_normalized_reads.csv


title: SEQ8320

description: cfDNA


title: NJA02201.A23


title: 4h_1_G5

description:
Trypanosome isolated from skin at 4 hours post-infection, #23
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 4h_1_G3

description:
Trypanosome isolated from skin at 4 hours post-infection, #21
single_trypanosomes_normalized_reads.csv


title: NJA02201.A21


title: SEQ8243

description: cfDNA


title: 4h_1_H2

description:
Trypanosome isolated from skin at 4 hours post-infection, #24
single_trypanosomes_normalized_reads.csv


title: NJA02201.A22


title: 4h_1_G4

description:
Trypanosome isolated from skin at 4 hours post-infection, #22
single_trypanosomes_normalized_reads.csv


title: NJA02201.A20


title: NJA02201.A24


title: 4h_1_G2

description:
Trypanosome isolated from skin at 4 hours post-infection, #20
single_trypanosomes_normalized_reads.csv


title: SEQ8737

description: cfDNA


title: 12h_1_A3

description:
Trypanosome isolated from skin at 12 hours post-infection, #1
single_trypanosomes_normalized_reads.csv


title: 4h_1_F3

description:
Trypanosome isolated from skin at 4 hours post-infection, #17
single_trypanosomes_normalized_reads.csv


title: SEQ8671

description: cfDNA


title: 4h_1_F4

description:
Trypanosome isolated from skin at 4 hours post-infection, #18
single_trypanosomes_normalized_reads.csv


title: 4h_1_F5

description:
Trypanosome isolated from skin at 4 hours post-infection, #19
single_trypanosomes_normalized_reads.csv


title: SEQ8734

description: cfDNA


title: 4h_1_F2

description:
Trypanosome isolated from skin at 4 hours post-infection, #16
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 4h_1_E5

description:
Trypanosome isolated from skin at 4 hours post-infection, #15
single_trypanosomes_normalized_reads.csv


title: 4h_1_E3

description:
Trypanosome isolated from skin at 4 hours post-infection, #13
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: 4h_1_H4

description:
Trypanosome isolated from skin at 4 hours post-infection, #26
single_trypanosomes_normalized_reads.csv


title: 4h_1_E4

description:
Trypanosome isolated from skin at 4 hours post-infection, #14
single_trypanosomes_normalized_reads.csv


title: SEQ8733

description: cfDNA


title: NJA02201.A17


title: 4h_1_D5

description:
Trypanosome isolated from skin at 4 hours post-infection, #12
single_trypanosomes_normalized_reads.csv


title: 4h_1_D3

description:
Trypanosome isolated from skin at 4 hours post-infection, #10
single_trypanosomes_normalized_reads.csv


title: NJA02201.A16


title: SEQ4462

description: cfDNA


title: 4h_1_C5

description:
Trypanosome isolated from skin at 4 hours post-infection, #9
single_trypanosomes_normalized_reads.csv


title: 4h_1_D4

description:
Trypanosome isolated from skin at 4 hours post-infection, #11
single_trypanosomes_normalized_reads.csv


title: NJA02201.A15


title: NJA02201.A14


title: 4h_1_B5

description:
Trypanosome isolated from skin at 4 hours post-infection, #6
single_trypanosomes_normalized_reads.csv


title: SEQ8735

description: cfDNA


title: 4h_1_C4

description:
Trypanosome isolated from skin at 4 hours post-infection, #8
single_trypanosomes_normalized_reads.csv


title: 4h_1_C3

description:
Trypanosome isolated from skin at 4 hours post-infection, #7
single_trypanosomes_normalized_reads.csv


title: 4h_1_B4

description:
Trypanosome isolated from skin at 4 hours post-infection, #5
single_trypanosomes_normalized_reads.csv


title: NJA02201.A18


title: NJA02201.A13


title: SEQ4458

description: cfDNA


title: 4h_1_B3

description:
Trypanosome isolated from skin at 4 hours post-infection, #4
single_trypanosomes_normalized_reads.csv


title: 4h_1_A4

description:
Trypanosome isolated from skin at 4 hours post-infection, #2
single_trypanosomes_normalized_reads.csv


title: SEQ4825

description: cfDNA


title: NJA02201.A19


title: SEQ4460

description: cfDNA


title: NJA02201.A12


title: NJA02201.A11


title: SEQ4461

description: cfDNA


title: SEQ4457

description: cfDNA


title: 4h_1_A3

description:
Trypanosome isolated from skin at 4 hours post-infection, #1
single_trypanosomes_normalized_reads.csv


title: 0h_1_H5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #48
single_trypanosomes_normalized_reads.csv

source_name: salivary gland-positive tsetse flies


title: NJA02201.A10


title: 0h_1_H4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #47
single_trypanosomes_normalized_reads.csv


title: SEQ4456

description: cfDNA


title: NJA02201.A09


title: 0h_1_H3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #46
single_trypanosomes_normalized_reads.csv


title: 0h_1_H2_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #45
single_trypanosomes_normalized_reads.csv


title: SEQ4455

description: cfDNA


title: 4h_1_A5

description:
Trypanosome isolated from skin at 4 hours post-infection, #3
single_trypanosomes_normalized_reads.csv


title: NJA02201.A08


title: 0h_1_H2

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #44
single_trypanosomes_normalized_reads.csv


title: 0h_1_G5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #43
single_trypanosomes_normalized_reads.csv


title: 0h_1_G4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #41
single_trypanosomes_normalized_reads.csv


title: 0h_1_G5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #42
single_trypanosomes_normalized_reads.csv


title: SEQ4444

description: cfDNA


title: NJA02201.A07


title: 0h_1_G3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #39
single_trypanosomes_normalized_reads.csv


title: 0h_1_F5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #35
single_trypanosomes_normalized_reads.csv


title: SEQ4443

description: cfDNA


title: SEQ4454

description: cfDNA


title: 0h_1_G3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #40
single_trypanosomes_normalized_reads.csv


title: 0h_1_F4_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #34
single_trypanosomes_normalized_reads.csv


title: 0h_1_F4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #33
single_trypanosomes_normalized_reads.csv


title: NJA02201.A05


title: SEQ4413

description: cfDNA


title: NJA02201.A06


title: SEQ4412

description: cfDNA


title: 0h_1_G2_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #38
single_trypanosomes_normalized_reads.csv


title: 0h_1_G2

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #37
single_trypanosomes_normalized_reads.csv


title: SEQ3194

description: cfDNA


title: NJA02201.A04


title: 0h_1_F5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #36
single_trypanosomes_normalized_reads.csv


title: SEQ3187

description: cfDNA


title: NJA02201.A01


title: W_2

city: beijing

first: Tongtong

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

description: processed data file: WT-DSS-Mont.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WT-DSS-Mont.txt: Tab-delimited text file of normalized gene counts for each sample.

source_name: Colon

extract_protocol:
Colon were removed, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were treated with 2% DSS (group D), water (group W), or 2% DSS plus Montmorillonite powder (DS) for 7 days.

tag: genotype

value: wild type

value: 7 weeks

value: Male

value: Colon

value: Water


title: 0h_1_E5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #27
single_trypanosomes_normalized_reads.csv


title: SEQ4754

description: cfDNA


title: 0h_1_E4_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #26
single_trypanosomes_normalized_reads.csv


title: NJA02201.A02

source_name: spleen

value: spleen


title: W_1

description: processed data file: WT-DSS-Mont.txt

tag: Sex


title: 0h_1_F2

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #29
single_trypanosomes_normalized_reads.csv


title: 0h_1_F3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #31
single_trypanosomes_normalized_reads.csv


title: 0h_1_F3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #32
single_trypanosomes_normalized_reads.csv


title: 0h_1_E5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #28
single_trypanosomes_normalized_reads.csv


title: 0h_1_F2_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #30
single_trypanosomes_normalized_reads.csv


title: SEQ3097

description: cfDNA


title: 0h_1_E4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #25
single_trypanosomes_normalized_reads.csv


title: 0h_1_E3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #24
single_trypanosomes_normalized_reads.csv


title: 0h_1_E3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #23
single_trypanosomes_normalized_reads.csv


title: DS_1

description: processed data file: WT-DSS-Mont.txt

value: Dextran sulfate plus Montmorillonite powder


title: 0h_1_D5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #21
single_trypanosomes_normalized_reads.csv


title: DS_2

description: processed data file: WT-DSS-Mont.txt


title: D_2

description: processed data file: WT-DSS-Mont.txt

value: Dextran sulfate


title: 0h_1_D5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #22
single_trypanosomes_normalized_reads.csv


title: P9__Cancer__Tissue__stage__1

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

data_processing:
Remove index and adaptor sequences using TagCleaner (version 0.16)
Trim reads to 28 nucleotides using FASTX-Toolkit (version 0.0.14)
miRNAs were identified using the miRDeep2 program (version 2.0.0.7), using the deafult parameters with the exception of allowing for 1 mismatch and discarding read less than 16 nucleotides in length.
Raw miRNA counts were normalised and statistically anlaysed using the DESeq2 package (version 1.18.1) in R (version 3.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited file containing raw miRNA counts

source_name: Colon tissue

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit and TRIzol LS Reagent (for exosomes) or QIAzol (for tissues) following the manufacturer's instructions.
Libraries were constructed using the TruSeq® SmallRNA Library Prep Kit, following the manufacturer’s instructions. A total of 1 µg RNA or 100 to 300 ng of exosomal RNA was used as input for library construction.

tag: patient diagnosis

value: colorectal cancer

tag: patient colorectal cancer stage

value: Stage 1


title: P8__Exo__Exosome__stage__4

source_name: Exosome

value: Stage 4

value: exosome


title: D_1

description: processed data file: WT-DSS-Mont.txt


title: P6__Exo__Exosome__stage__3

value: Stage 3


title: 0h_1_D3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #18
single_trypanosomes_normalized_reads.csv


title: 0h_1_D4_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #20
single_trypanosomes_normalized_reads.csv


title: 0h_1_D4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #19
single_trypanosomes_normalized_reads.csv


title: 0h_1_D3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #17
single_trypanosomes_normalized_reads.csv


title: P5__Exo__Exosome__stage__3


title: 0h_1_C5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #16
single_trypanosomes_normalized_reads.csv


title: 0h_1_C5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #15
single_trypanosomes_normalized_reads.csv


title: P4__Exo__Exosome__stage__2

value: Stage 2


title: 0h_1_C4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #14
single_trypanosomes_normalized_reads.csv


title: 0h_1_C3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #13
single_trypanosomes_normalized_reads.csv


title: 0h_1_C3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #12
single_trypanosomes_normalized_reads.csv


title: 0h_1_B5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #10
single_trypanosomes_normalized_reads.csv


title: HDAC2KD_RNAseq rep2

city: Nanjing

first: liming

last: chen

state: Jiangsu

address: Qixiaqu wenyuanlu 1hao

department: college of life science

institute: Nanjing Normal University

data_processing:
Basecalls performed using CASAVA 1.8
All reads were trimmed of adapters and sequencing quality lower than 20
The RNAseq reads were aligned to hg38 with tophat2
Assemble transcripts with cufflinks and find differentially expressed genes with cuffdiff
Supplementary_files_format_and_content: tab-deliminated txt file for the abundance measureament of RNAseq

source_name: breast

growth_protocol: MCF7cell were cultured in Roswell Park Memorial Institute medium-1640 (RPMI-1640) (Life Technologies) supplemented with 10% FBS and 1% penicillin-streptomycin solution (Life Technologies), with 10 cm dish (typically 1-2 × 107cells) .

extract_protocol: For the RNA –seq:  Followed by library preparation and next-generation sequencing.

treatment_protocol: siRNAs against TRPS1, HDAC2 and control siRNA(GenePharma) were transfected into MCF7 cells for 72h using Lipofectamine RNAiMAX reagent(Invitrogen) .

tag: cell line

value: HDAC2 knock down


title: HDAC2KD_RNAseq rep1


title: TRPS1KD_RNAseq rep2

value: TRPS1 knock down


title: P3__Exo__Exosome__stage__2


title: P20__Normal__Colon__Tissue__stage__4

value: adjacent normal colon


title: P7__Exo__Exosome__stage__4


title: 0h_1_B4_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #9
single_trypanosomes_normalized_reads.csv


title: 0h_1_B4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #8
single_trypanosomes_normalized_reads.csv


title: 0h_1_B3

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #6
single_trypanosomes_normalized_reads.csv


title: control_RNAseq rep2


title: 0h_1_B3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #7
Excluded from analysis due to quality control criteria
single_trypanosomes_normalized_reads.csv


title: control_RNAseq rep1


title: 0h_1_A5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #5
single_trypanosomes_normalized_reads.csv


title: E15.5 Microglia Cx3cr1Cre:tdTomato+ve

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: # FACS sorted cells: 21,719 cells; Loaded: 977 cells on 10X: Recovered: 375 cells

data_processing:
All raw FASTQs reads were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes (1195 genes) was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering (run in Seurat at: res = 0.2) was used to select only fibroblasts for all subsequent analysis. Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

molecule: polyA RNA

source_name: E15.5 microglia

extract_protocol:
E15.5 brains were dissected from one dam (n = 5 brains pooled) and enzymatically dissociated with Accutase (StemCell Technologies) for 15 mins at 37oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 70 µm cell filters and centrifuged at 259 x g. Liberated single cells were re-suspended in 1% bovine serum album in HBSS before FACS purification. For FACS purification, a stringent initial forward and side scatter gates were used to exclude debris, and cell doublets. Cells from Cx3cr1CreERT2:tdTomato mice were purified.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 4061, 3776, 2604, and 3293 cells for Samples 1-4, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

treatment_protocol: Cre-recombination was initiated with two intraperitoneal injections of 4-hydroxy-tamoxifen (4-OHT; 1mg/20g in sterile corn oil, Sigma-Aldrich) on E10.5 and E11.5

value: microglia

tag: developmental stage

tag: background strain

tag: facs strategy

value: tdTomato+positive

tag: library preparation

value: 10X Genomics Single Cell RNAseq v2


title: P18__Normal__Colon__Tissue__stage__2

tag: tissue


title: 0h_1_A4_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #3
single_trypanosomes_normalized_reads.csv


title: P17__Normal__Colon__Tissue__stage__1


title: 0h_1_B5_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #11
single_trypanosomes_normalized_reads.csv


title: FP4_rep2

city: Wuhan

first: Ying

last: Wang

state: Hubei

address: No. 299 bayi road

department: College of Life Sciences

institute: Wuhan University

data_processing:
Raw reads of RNA-seq were aligned to the O.sativa Nipponbare release 7 of the MSU Rice Genome Annotation Project reference using HISAT2 with default parameters.
lncRNA analysis: The transcriptome was assembled using the StringTie (1.3.1) based on the reads mapped to the reference genome. The assembled transcripts were annotated using the gffcompare program.The unknowntranscripts were used to screen for putative lncRNAs. Three computational approaches include CPC/CNCI/Pfam/CPAT were combined to sort non-protein codingRNA candidates from putative protein-coding RNAs in the unknown transcripts.Putative protein-coding RNAs were filtered out using aminimum length and exon number threshold . Transcripts with lengths more than 200 nt and have more than two exons were selected as lncRNA candidates and further screened using CPC/CNCI/Pfam/CPAT that have the power to distinguish the protein-coding genes from the non-coding genes. As well as the different types of lncRNAs include lincRNA,introniclncRNA, anti-sense lncRNA ,sense lncRNA were selected using cuffcompare.
CircRNA analysis: The reads that could not be mapped to the genomes were obtained to screening the putative cicRNAs. For these unmapped reads, the 20-nt anchors were first extracted from both ends and aligned independently to the rice reference genomes to identify the unique anchor positions using the find_circ software. The reversed orientation of the aligned anchors suggested circRNA splicing. Then, the anchor alignments were extended to generate the GU/AG splice sites flanking the complete read alignments and breakpoints. Finally, a candidate circRNA was identified if it had at least two distinct back-spliced reads.
StringTie (1.3.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample . Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: MSU7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: Fertility male of WXS at microspore formation stage

growth_protocol: During summer in 2017, WXS rice was grown in the experimental field of Wuhan University (30°54′ N, 114°37′ E), Wuhan, Hubei province of China.

extract_protocol:
Total RNA was extracted using TRIzol reagent. A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Under natural conditions, with daily average temperatures that were higher than 24 ℃ and average day lengths that were longer than 12 h, WXS could produce male-sterility rice (WXS (S)) that did not form pollen. When the panicle length was approximately 1 cm, some of the rice plants were transferred into a fully intelligent artificial climate plant incubator for a short period of sunshine treatment under short lighting (12 h light/12 h dark) at low day average temperatures (approximately 21 °C) for 3-4 weeks. These WXS plants treated with short sunshine and low temperatures would become male-fertile rice (WXS (F)), with a normal anther morphology. The young panicles of WXS (S) and WXS (F) were harvested upon formation of the pollen mother cell (PMC) (P2), meiosis of the PMC (P3) and formation of the microspore (P4) stages, and correspondingly designated as SP2, SP3, SP4, FP2, FP3 and FP4, respectively. Immediately upon harvesting, the panicles were frozen in liquid nitrogen and stored at -80 °C.

value: panicle

tag: Stage

value: microspore formation


title: FP4_rep3


title: 0h_1_A5

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #4
single_trypanosomes_normalized_reads.csv


title: 0h_1_A3_1

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #1
single_trypanosomes_normalized_reads.csv


title: P16__Cancer__Tissue__stage__4


title: P15__Cancer__Tissue__stage__4


title: P2__Exo__Exosome__stage__1


title: FP4_rep1


title: TRPS1KD_RNAseq rep1


title: SP4_rep2

source_name: Sterility male of WXS at microspore formation stage


title: P14__Cancer__Tissue__stage__3


title: Single cell seq S2 cells plate2

city: Utrecht

first: Wessel

middle: van

last: Leeuwen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
tRNA genes and pseudogenes were identified using tRNAscan-SE (version 2.0.7)
Adapter and homopolymer sequences were first trimmed from read 2 using cutadapt (version 3.2)
Trimmed reads were depleted of rRNA sequences by aligning to a ribosomal reference using bwa aln (version 0.7.17-r1188) and bwa mem, and discarding any read that aligned using either method
Depleted reads were then two-pass aligned to the reference genome using STARSolo (version 2.7.7a)
Aligned reads were deduplicated with UMI-tools (version 1.1.1)
Variant identification followed the GATK RNA-seq short variant discovery best-practices workflow using GATK (version 4.1.9.0)
Allele frequency and statistics were determined using an in-house written script
Genome_build: BDGP6

organism: Drosophila melanogaster

source_name: S2 cell

extract_protocol:
Direct-zol RNA microprep kit (Zymo)
See Muraro et al. 2016

treatment_protocol: S2 cells were treated with CuSO4 to induce protein expression, neuron expression was induced by RU486. Cells were stressed with 0.5mM sodium arsenite

value: S2 cells

value: Well 1-6 contains cells treated:4h induced + 4h Schneider's, well 7-12 contains cells treated:4h induced + 4h Krebs Ringer Bicarbonate buffer, well 13-18 contains cells treated:4h induced + 4h 0.5mM sodium arsenite in Schneider's, well 19-23 contains cells treated 2h induced + 2h Schneider's, well 24 is empty


title: P19__Normal__Colon__Tissue__stage__3


title: Single cell seq S2 cells plate1


title: SP4_rep3


title: SP4_rep1


title: P13__Cancer__Tissue__stage__3


title: 0h_1_A4

description:
Metacyclic form harvested from salivary gland-positive tsetse flies, #2
single_trypanosomes_normalized_reads.csv


title: Drosophila L3 brain arsenite rep3

source_name: Drosophila L3 brain cells

value: Drosophila L3 brain cells

value: 4h 0.5mM sodium arsenite in Schneider's


title: Drosophila L3 brain arsenite rep2


title: Drosophila L3 brain arsenite rep1


title: P11__Cancer__Tissue__stage__2

value: colorectal cancer


title: P12__Cancer__Tissue__stage__2


title: P10__Cancer__Tissue__stage__1

value: Stage 1


title: FP3_rep2

source_name: Fertility male of WXS at meiosis stage

value: meiosis


title: FP3_rep1


title: P1__Exo__Exosome__stage__1

value: exosome


title: Drosophila L3 brain Schneider's rep1

value: 4h Schneider's


title: s200930N9

city: Changsha

first: Yong

last: Zhong

state: Hunan province

address: 87 Xiangya Road

department: Nephrology

institute: Xiangya Hospital, Central South University

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Star 2.5.3a software was used for comparative analysis between sequencing data of single cell RNA and reference genome of Ensembl database
Quantify gene expression using read2 by featureCounts1.6.2 software
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: kidney, healthy control

extract_protocol:
A moderate amount of renal tissue was taken from the selected patients during renal puncture, and GEXSCOPE ® Single Cell RNA Library Kit Tissue was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Normal tissue

tag: age

tag: proteinuria

value: normal urine

value: kidney


title: Drosophila L3 brain Schneider's rep2

tag: treatment


title: SP3_rep3

source_name: Sterility male of WXS at meiosis stage


title: SP3_rep2


title: FP3_rep3


title: s200929N8


title: SP3_rep1


title: Bulk S2 cells arsenite rep3

value: 4h 1mM coppersulfate in Schneider's followed by 4h 0.5mM sodium arsenite in Schneider's


title: Drosophila L3 brain Schneider's rep3


title: s200910M8

source_name: kidney, IMN

value: idiopathic membranous nephropathy

value: proteinuria conform to nephrotic syndrome


title: FP2_rep3

source_name: Fertility male of WXS at PMC formation stage

value: panicle

value: PMC formation


title: Bulk S2 cells arsenite rep2

value: S2 cells


title: s200821M6

value: proteinuria not conform to nephrotic syndrome


title: FP2_rep2


title: Hela_plusDrug_mitoRP

description:
Hela_plusDrug_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
Hela_Plus_drugs

source_name: HeLa S3

tag: cell line/type

value: HeLa S3

value: WT

value: 15 minutes with 100 ug/mL of chloramphenicol (Sigma, CAT C3175) and 5 minutes with 100 ug/mL cycloheximide (Sigma, CAT C769)

tag: mouse spike-in%

tag: umi

tag: molecule subtype

value: mitoribosome protected fragments


title: Hela_noDrug_mitoRP

description:
Hela_noDrug_mitoRP
processed data file: OXPHOS_RelativeExpression.xlsx
HeLa_No_drugs

tag: genotype

value: untreated


title: Drosophila L3 brain not-induced

value: Drosophila L3 brain cells


title: s200813M5


title: FP2_rep1


title: Bulk S2 cells arsenite rep1


title: Hela-5_RNAseq

description:
Hela_NT_1_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
HeLa_TotalRNA-1_S3_L001

value: rRNA-depleted total RNA


title: Bulk S2 cells Schneider's rep3

value: 4h 1mM coppersulfate in Schneider's followed by 4h Schneider's


title: s200724M1


title: s200813M3


title: s200806M2


title: Hela-6_RNAseq

description:
Hela_NT_2_RNAseq
processed data file: OXPHOS_RelativeExpression.xlsx
HeLa_TotalRNA-2_S4_L001


title: SP2_rep2

source_name: Sterility male of WXS at PMC formation stage


title: Bulk S2 cells Schneider's rep2


title: SP2_rep3


title: Bulk S2 cells Schneider's rep1


title: WT replicate 3

status: Public on May 29 2021

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: rRNA-depleted total RNA

data_processing:
Basecalling was done on the Illumina NextSeq sequencer with the Illumina Real Time Analysis software version 2.11.3
Reads were aligned to a combined human (GRCh38.99) and SARS2 (NC_045512.2) reference genomes in a splice-site aware fashion using STAR aligner (2.7.3a) (Dobin et al. 2013).
Uniquely mapping reads were assigned to exonic regions of genes using htseq-count (0.11.3) (Anders et al. 2015) in a strand-specific fashion, counting only uniquely assigning reads.
Genome_build: GRCh38.99 (human) and NC_045512.2 (SARS2)
Supplementary_files_format_and_content: Tab-delimited tables with counts for each gene

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

growth_protocol: Cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
24hpi cells were detached and lysed in Trizol LS, total RNA extraction was performed following manufacturers recommendation
RNA sequencing libraries were prepared using the Illumina Total RNA Prep with Ribo-Zero Plus library kit (Cat# 20040525) according to manufacturers guidelines. Briefly, 100ng of total RNA was first depleted of the abundant ribosomal RNA present in the samples by rRNA targeted DNA probe capture followed by enzymatic digestion. Samples were then purified by Beckman Coulter RNAClean XP beads (Cat #A63987). Obtained rRNA-depleted RNA was fragmented, reverse transcribed, converted to dsDNA, end repaired and A-tailed. The A-tailed DNA fragments were ligated to anchors allowing for PCR amplification with Illumina dual indexing primers (Cat#20040553). Libraries were pooled in equimolar concentrations and sequenced on an Illumina NextSeq 500 sequencer using a high-output cartridge (Cat# 20024907), generating single 150bp long reads.

treatment_protocol: Knockdown was induced by treatment with 1ug/ml Doxycyclin; Cells were seeded into 2.5x10^5/well into 24well plates and infected at MOI=0.1 for 24hpi

value: A549-ACE2 shDDX1 uninduced

value: SARS2 virus infection at 0.1 MOI 24hpi (strain hCoV-19/England/02/2020 (Public Health England propagated viral isolate Feb 2020, EPI_ISL_407073) )


title: hdSEs (G2_2)

data_processing:
CellRanger v3.1.0 (10x Genomics) was used to process scRNAseq data. To generate a digital gene expression (DGE) matrix, reads were mapped to the human reference genome GRCh38 and the number of UMIs for each gene in each cell was recorded.
Genome_build: GRCh38
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis

source_name: two skin models

extract_protocol:
The dermis of two individual hdSEs at day 23 was separated from the epidermis with forceps and subsequently cut into small pieces and incubated in 1 ml of TDB containing 250 μg Liberase TL for 45 min at 37 °C. To isolate NHEK the epidermis was incubated in 3 ml of PBS- with gentle agitation. PBS- was aspirated, the epidermis cut into small pieces and 1 ml of 0.05 % Trypsin/EDTA were added for 15 min at 37 °C. 100 μl of FCS were added and NHEK were released by thorough resuspension. Cells were collected by centrifugation at 300 g for 5 min, resuspended in 500 μl INF medium containing 0.5 μg DAPI and filtered through a 35 μm cell strainer. Viable NHDF and NHEK were sorted based on their negative DAPI signal with a FACSAria III cytometer (BD Biosciences) and collected in a single tube.
Cell density was evaluated by microscopy using a hemocytometer and adjusted to 1000 cells/μl. Subsequently, the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) were used for reverse transcription, cDNA amplification, and library construction according to the manufacturers’ instructions. 16.5 μl of cell suspension were used to recover 10,000 cells and libraries were quantified with a Qubit 3 Fluorometer (Thermo Fisher Scientific). Quality was checked using a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). Sequencing was performed in paired-end mode with a SP flow cell (2 x 50 cycles) using NovaSeq 6000 sequencer (Illumina).

tag: sample type

value: high-density skin equivalents

tag: index id

tag: index sequences

value: TGATTCTA,ACTAGGAG,CAGCCACT,GTCGATGC