title: SSc_0684


title: SSc_0685

status: Public on Jul 26 2023

type: SRA

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

country: USA

institute: Genentech

library_source: transcriptomic

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCh38.
Assembly: GRCh38
Supplementary files format and content: TSV count matrices

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA was extracted using PAXgene Blood RNA Kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

tag: tissue

value: blood

tag: disease state

value: systemic sclerosis


title: SSc_8794


title: SSc_0680


title: SSc_8787


title: SSc_8791


title: SSc_0675


title: SSc_0674


title: SSc_8792


title: SSc_0681


title: SSc_8800


title: SSc_0667


title: SSc_0670


title: SSc_0664


title: SSc_0665


title: SSc_0663


title: SSc_0679


title: SSc_0669


title: SSc_8799


title: SSc_0673


title: SSc_0677


title: SSc_0678


title: SSc_0662


title: SSc_0671


title: SSc_0666


title: SSc_8788


title: SSc_0660


title: SSc_0672


title: SSc_0653


title: SSc_0661


title: SSc_0659


title: Normal_8812

value: normal


title: Normal_8811


title: Normal_9000


title: SSc_0657


title: Normal_8810


title: SSc_0658


title: SSc_0656


title: Normal_8809


title: Normal_8808


title: Normal_8805


title: Normal_0691


title: Normal_0689


title: Normal_0692


title: Normal_8807


title: Normal_8806


title: Normal_0686


title: Normal_0687


title: Normal_8804


title: Normal_0688


title: Normal_0690


title: Normal_0693


title: SSc_0654


title: Donor 4

city: Muenster

first: Marcos

middle: J

last: Araúzo-Bravo

address: Rontgenstr. 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
replicate 1
data column header 3

data_processing:
We used the alevin pipeline integrated with the salmon software (version salmon-0.14.1) to process the 10X-Chromium v3 droplet-based single-cell RNA sequencing data (scRNA-Seq).
We performed cell barcode (CB) detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting.
Reads were aligned to the human GRCh38 reference genome, transcriptome and annotation downloaded from GENOME website, version 21, and annotated.
We used the --forceCells option of alevin set to 2000 for each of the 5 donors’ scRNA-Seq data to specify the number of Cell Barcodes (CB) to consider for white-listing.
Standard procedures for filtering, variable gene selection, dimension reduction and clustering were performed using the Scanpy toolkit version 1.6.0.
Cells with fewer than 200 detected genes were excluded.
A gene was counted as expressed if it was detected in at least 3 cells.
Genes with too many total counts (>100,000) were also removed.
For each cell we computed the fraction of counts in mitochondrial genes vs. all genes and filtered out the cells with this fraction greater than 0.15.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include counts values for each gene of cell

source_name: Donor 4

growth_protocol:
BM was obtained from donations of human femoral heads (patients aged 51-84 years) according to ethical rules (CHU Toulouse).
To isolate stromal cells from BM, fresh femoral heads were manually scraped.
The bone fragments were incubated and shaken in collagenase NB4 (Serva Electrophoresis GmbH) and dispase (Roche) in αMEM + glutamax (Gibco) for 2 h at 37°C.
The bones were washed extensively with PBS (Gibco) and dissociated cells were collected.
This stroma cell fraction was separated by density gradient centrifugation by using Products (Corp.) and counted.
BM cells were frozen at -80°C in DMSO and thawed before sorting.

extract_protocol:
For scRNA-seq libraries, we sorted the CD45- GYPA- BM cellular subsets from 5 patients (TF166-256-261-263-273) on a BD FACS Aria Fusion cell sorter into 384-well plates.
Total RNA was extracted from samples by using the RNeasy Plus Micro Kit (Life Technologies).
The libraries were generated by using the Chromium Controller Single-Cell Instrument and Chromium Single Cell 3′ Library and Gel Bead Kit v2 A Chip Kit and i7 Multiplex Kit (10x Genomics)
according to the manufacturer’s protocol (manual part no. CG00052 Rev A).
Libraries were run on an Illumina HiSeq 8000 as 150-bp reads, at one full lane per sample.
Sequencing results were demultiplexed and converted to a FASTQ format by using Illumina bcl2fastq software.
Alevin was used to align to the GRCh38 transcriptome and build the (cell, UMI) expression matrix for each sample.

treatment_protocol:
Cells were thawed and blocked in 0.1% human serum albumin (LFB Biomedicaments, Courtaboeuf, France),
then stained with CD45, GYPA, CD200, CD271, LEPR, CD49A (BD Biosciences, Franklin Lakes, NJ, USA),
staining was analyzed with an ADP Cyan flow cytometer (Beckman Coulter, Brea, CA, USA). Cells were sorted by using BD LSRFortessa.
Data were analyzed with Kaluza v1.2 (Beckman Coulter). Dead cells were excluded by DAPI staining (Sigma).

tag: donor

value: Donor 4

tag: cell type

value: bone marrow (BM) cells


title: GNLox t6HL, rep2

city: Freising

first: Peter

middle: Michael

last: Schröder

state: Bavaria

address: Emil-Ramann-Straße 8, Gebäude 4223

department: School of Life Sciences

institute: Technical University of Munich

description: 1x100bp, dual index

data_processing:
CLC Genomics Workbench v20.0.2
Sequence reads were trimmed using CLC Genomics Workbench - Quality limit: 0.05.
Trimmed sequence reads were mapped to the TAIR10 release of the Arabidopsis thaliana Col-0 genome using CLC Genomics Workbench - Mismatch cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.5, Similarity fraction: 0.8.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: TAIR10 release of Arabidopsis thaliana Col-0.
Supplementary files format and content: Tab-delimited text files, including TPM.

organism: Arabidopsis thaliana

source_name: 7 day old seedlings (1 replicate = 30 seedlings)

growth_protocol: Arabidopsis thaliana lines Col-0, hex (gnc gnl gata15 gata16 gata17 gata17l) and GNLox were grown on 1/2 MS medium in constant light at 60 µmol m-2 s-1 and 22°C for seven days.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit (Macherey-Nagel).
Illumina stranded mRNA Kit (Illumina, San Diego, USA) with IDT for Illumina RNA UD Indexes Set A and protocol 1000000124518v01 with 11 cycles of enrichment

treatment_protocol: The light treatments consisted of either six hours of high-light (HL) with 1200 µmol m-2 s-1 at 20-22°C (t6HL) or a six hour mock treatment under constant light with 60-70 µmol m-2 s-1 at 20-22°C (t6GL). One third of the plants were harvested and immediately frozen in liquid nitrogen each before the shift to high-light (t0), after six hours of high-light (t6HL) or six hours of mock (t6G¬L).

tag: age

value: 7 day old

value: seedlings

tag: genotype

value: GNLox

tag: treatment


title: Donor 5

description:
replicate 1
data column header 4

source_name: Donor 5

value: Donor 5


title: Donor 1

description:
replicate 1
data column header 0

source_name: Donor 1

value: Donor 1


title: Donor 3

description:
replicate 1
data column header 2

source_name: Donor 3

value: Donor 3


title: GNLox t6HL, rep3

description: 1x100bp, dual index


title: hex t6HL, rep2

description: 1x100bp, dual index

value: hex


title: Col-0 t6HL, rep3

description: 1x100bp, dual index

value: Col-0 (WT)


title: hex t6HL, rep1

description: 1x100bp, dual index


title: Col-0 t6HL, rep2

description: 1x100bp, dual index


title: GNLox t6HL, rep1

description: 1x100bp, dual index


title: Col-0 t6HL, rep1

description: 1x100bp, dual index


title: GNLox t6LL, rep3

description: 1x100bp, dual index


title: GNLox t6LL, rep1

description: 1x100bp, dual index


title: GNLox t6LL, rep2

description: 1x100bp, dual index


title: hex t6HL, rep3

description: 1x100bp, dual index


title: hex t6LL, rep3

description: 1x100bp, dual index


title: hex t6LL, rep2

description: 1x100bp, dual index


title: Col-0 t6LL, rep3

description: 1x100bp, dual index


title: Donor 2

description:
replicate 1
data column header 1

source_name: Donor 2

value: Donor 2


title: Col-0 t6LL, rep1

description: 1x100bp, dual index


title: Col-0 t6LL, rep2

description: 1x100bp, dual index


title: hex t0, rep3

description: 1x100bp, dual index


title: hex t0, rep2

description: 1x100bp, dual index


title: Col-0 t0, rep3

description: 1x100bp, dual index


title: GNLox t0, rep2

description: 1x100bp, dual index


title: hex t0, rep1

description: 1x100bp, dual index


title: GNLox t0, rep3

description: 1x100bp, dual index


title: Col-0 t0, rep1

description: 1x100bp, dual index


title: GNLox t0, rep1

description: 1x100bp, dual index


title: Col-0 t0, rep2

description: 1x100bp, dual index


title: Enteric glial culture, DIV4

city: London

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

description:
InVitroEnsData.h5ad
InVitroEnsDataCounts.csv
InVitroEnsDataCellMeta.csv
InVitroEnsDataGeneMeta.csv

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the Ensembl GRCm38 using 10x Genomics Cell Ranger 3.0.2.
Quality control, normalization and downstream analysis were performed using the software SCANPY.
Data was analysed in SCANPY. Cells with >1000 features and <10% mitochondrial counts were retained for downstream analysis. Predicted doublets were filtered using Scrublet. Contaminating neurons (n=35) were filtered using the expression of the marker Elavl4 (> 0 counts) and contaminating macrophages (n = 99) were filtered using expression of the marker Cd14 (> 0 counts) from DIV0 data.
Genes detected in fewer than 3 cells or with total counts < 10 were omitted from further analysis (23178 genes were retained). Counts were normalized to counts per million (CPM) and log transformed (after the addition of a pseudocount of 1).
Highly variable genes were detected in SCANPY and the top 4397 used as input to PCA. The first 20 PCs were selected for dimensionality reduction and clustering using the Louvain algorithm (resolution 0.6).
Assembly: GrCM38
Supplementary files format and content: Scanpy object containing normalized data and UMAP. Count matrix (CSV format). Gene and cell metadata (CSV format).

organism: Mus musculus

source_name: Enteric glial culture

growth_protocol: Mice used in this study were maintained according to standard practices and all procedures were approved by The Francis Crick Institute Animal Ethics Committee and conformed to UK Home Office requirements (ASPA 1986) and the ARRIVE guidelines.

extract_protocol:
nGFP+ cells were isolated from tunica muscularis preparations from 8 week old Sox10CreERT2(SER93);Rosa26-nuclearGFP mice that had been injected with tamoxifen (2 doses of tamoxifen at 100 μg/g of body weight 10 days prior isolation). Tunica muscularis tissue was incubated with 10 mg/ml collagenase IV (Worthington Biochemicals, CLS-4) in Hanks Balanced Salt Solution (HBSS, Thermo Fisher Scientific, 14170112) at 37 °C for 12 min, followed by wash in ice-cold HBSS and subsequent incubation with papain (1U, Worthington Biochemicals, PAP2) for 5 min at 37 °C. The digested samples were then washed and resuspended in L-15 medium without phenol red (Thermo Fisher, 21083027) containing penicillin–streptomycin (1%, Thermo Fisher Scientific, 15140122), BSA (1 mg/ml, Sigma-Aldrich, A9418), HEPES pH 7.4 (10 mM, Thermo Fisher Scientific, 15630106), Biowhittaker water (10%, Lonza, BE17-724F) and DNase I (400U, Grade II; Roche, 10104159001), filtered through a 70 μm and 40 μm strainer and subjected to FACS using DAPI (1 μg/ml) for live/dead cell discrimination.
Approximately 10,000 tdT+ cells post-FACS (from each EGC culture) and 10,000 nGFP+ cells post-FACS (freshly isolated EGCs) were loaded into a 10x Chromium Chip B (10x 3’v3) and partitioned into gel bead-in-emulsions (GEMs) using the 10x Chromium Controller.

treatment_protocol: Neurogenic EGC cultures were established from Sox10Cre|tdT mice (24 hours after a single dose of tamoxifen injection at 100 μg/g of body weight) and Sox10CreERT2;Foxd3fl/fl;Rosa26-eYFP mice (48 hours after two doses of tamoxifen injection at 100μg/g of body weight). Longitudinal muscle-myenteric preparations were washed thoroughly in DMEM/F12 media containing fetal bovine serum (FBS, 2%, Sigma-Aldrich, F7524), penicillin-streptomycin (100U/ml, Thermo Fisher Scientific) and 12.5mM HEPES (12.5mM, Thermo Fisher Scientific). Post-rinsing, tissues were minced using fine scissors and incubated in a shaker at 37oC for 30 min with Type 1 collagenase (0.5 mg/ml, Sigma Aldrich, SCR103) and DNaseI (0.5 mg/ml, Sigma-Aldrich, DN25) in the buffer described above. Next, trituration of the sample using an unpolished glass pasteur pipette was carried out. Triturated samples were then washed twice with DMEM/F12 media containing 10% FBS with penicillin-streptomycin and plated onto two 60 mm (Corning) dishes coated with fibronectin (20 μg/ml; Sigma-Aldrich, F1141). Seeded cells were cultured overnight in DMEM/F12 media containing 10% FBS and penicillin-streptomycin. Next day, the culture medium was changed to serum-free media that contained DMEM/F12 supplemented with N2 (1%, Thermo Fisher Scientific, 17502048), G5 (1%, Thermo Fisher Scientific, 17503012) and NGF-7S (50 ng/ml, Thermo Fisher Scientific, 13290-010). To allow robust proliferation of glial cells, half of the medium was replaced with fresh medium on day three. On day four, cells were trypsinized using TrypLE express (Thermo Fisher Scientific, 12604013) and filtered using a 40 μm cell strainer to obtain a single cell suspension. Cells were counted (Countess II; Thermo Fisher Scientific) and then seeded at ~30,000 cells/cm2 onto fibronectin coated 60 mm dishes in proliferative medium. The passaged cells were collected using Accutase (Thermo Fisher Scientific, 00-4555-56) on day six and seeded onto Poly-D-Lysine/Laminin/Fibronectin coated 12 mm glass coverslips (Corning, #354087) at ~42,000 cells/cm2 in 24-well plates. Upon passaging, cells were maintained in media that constitutes both the proliferative and neuronal differentiating medium which comprises of DMEM/F12, N2 supplement (1%), GDNF (10 ng/ml, Peprotech, 450-44), BDNF (10 ng/ml, R&D systems, 248-BD), NT3 (10 ng/ml, R&D systems, 267-N3), NGF-7S (10 ng/ml), cAMP (0.5 mM, Sigma-Aldrich, D0260), Ascorbic Acid (0.2 mM, Sigma-Aldrich, A4034) and penicillin-streptomycin at a ratio of 1:2. On day eight, the culture medium was completely replaced with neuronal differentiating media. Subsequently, every two days, half of the medium was exchanged with fresh media. To label proliferating cells, cultures were exposed to EdU (10 μM) for an hour before fixation.  Cells were consistently maintained at 5% CO2.

tag: Stage

tag: strain


title: Enteric glial culture, DIV10


title: Enteric glial culture, DIV20_DMSO

value: DMSO


title: Enteric glial culture, DIV20_RA

value: Retinoic acid


title: Sox10::CreERT2;R26-tdTomato_DIV11_2

state: London

address: 1 Midland Road

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

extract_protocol:
Total RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies). Following quantification on a Qubit 3.0 fluorometer (Thermo Fisher Scientific), cDNA was fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies). A total of 7 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies). The libraries were then normalized to 2,5 nM, pooled and loaded onto a HiSeq4000 (Illumina) to generate 75bp single-end reads.

treatment_protocol:
Primary cells were cultured on wells coated with Poly-D-Lysine/Laminin/Fibronectin to support neuronal differentiation in neuronal differentiation media, which comprises of DMEM/F12 containing N2 (1%), NGF, BDNF, GDNF, NT3 (all at 10ng/mL), 0.5mM cAMP and 0.2mM Ascorbic Acid.
tdTomato+ cells were purified by FACS either directly from the adult tissues after dissociation (DIV0) or from cells harvested from tissue culture dishes using trypLE express (Thermo Fisher Scientific) on DIV4 or StemPro Accutase (Thermo Fisher Scientific) on DIV11 and DIV20.

tag: strain background

value: C57Bl/6JAX and CBA mixed

tag: genotype/variation

tag: tissue/cell type

value: Primary cells

value: Adult EGC-derived cells

tag: environmental condition

value: Incubator at 37°C with 5% CO2


title: Sox10::CreERT2;R26-tdTomato_DIV4_3

treatment_protocol:
Primary cells were cultured on fibronectin coated dishes in the presence of supplements from Thermo Fisher Scientific- N2 (1%) and G5 (1%) with NGF (50ng/mL) in DMEM/F12.
tdTomato+ cells were purified by FACS either directly from the adult tissues after dissociation (DIV0) or from cells harvested from tissue culture dishes using trypLE express (Thermo Fisher Scientific) on DIV4 or StemPro Accutase (Thermo Fisher Scientific) on DIV11 and DIV20.


title: Sox10::CreERT2;R26-tdTomato_DIV20_1


title: Sox10::CreERT2;R26-tdTomato_DIV11_3


title: Sox10::CreERT2;R26-tdTomato_DIV20_3


title: Sox10::CreERT2;R26-tdTomato_DIV4_2


title: Sox10::CreERT2;R26-tdTomato_DIV20_4


title: Sox10::CreERT2;R26-tdTomato_DIV20_2


title: hex t6LL, rep1

description: 1x100bp, dual index


title: Sox10::CreERT2;R26-tdTomato_DIV4_1


title: Sox10::CreERT2;R26-tdTomato_DIV11_1


title: Sox10::CreERT2;R26-tdTomato_DIV0_2

treatment_protocol:
LMMP peels were digested for 15 mins at 37°C with HBSS (Gibco, 14170112) containing 10 mg/mL collagenase IV (Worthington Biochemicals, CLS-4) followed by a wash step in ice-cold HBSS and subsequent incubation with 1U papain (Worthington Biochemicals, PAP2) for 5 mins at 37°C. Samples were then washed and resuspended in L15 medium without phenol red (Gibco, 21083027) containing 1% P/S (Gibco, 15140122), 1 mg/ml BSA (Sigma, A9418), 10 mM Hepes pH 7.4 (Gibco, 15630106), 10 % Biowhittaker water (Lonza, BE17-724F) and 400 U DNAse I (Grade II; Roche, 10104159001), filtered through a 70 μm and a 40 μm strainer and subjected to FACS on a FACS Aria (BD Biosciences) using DAPI (1 μg/ml) for live/ dead cell discrimination.
tdTomato+ cells were purified by FACS either directly from the adult tissues after dissociation (DIV0) or from cells harvested from tissue culture dishes using trypLE express (Thermo Fisher Scientific) on DIV4 or StemPro Accutase (Thermo Fisher Scientific) on DIV11 and DIV20.

value: Adult small intestines- duodenum

value: Enteric Glial Cells (EGCs)


title: Sox10::CreERT2;R26-tdTomato_DIV0_1


title: T42 (+4OHT-C2H2A)

city: Shenzhen

first: Jun

last: Zhang

state: Guangdong Province

address: Xueyuan Avenue

department: School of Medicine

country: China

institute: Shenzhen University

library_source: genomic

data_processing:
Sequence quality was evaluated by FastQC version 0.11.4
all reads were mapped to reference genome of illumina iGeomes UCSC  using Bowtie version 2.2.6
SAMtools version 0.1.1926 was used to convert files to bam format
Peaks were called using MACS version 2.2.1 under q value<0.05.
Assembly: hg19
Supplementary files format and content: peak text files

molecule: genomic DNA

source_name: AsiSI-ER-AID-U2OS cells

growth_protocol: Cells were routinely maintained in high glucose DMEM medium supplied with 10%FBS and 1% P/S in 37 degree incubator, and after 90% confluence, the cells were treated and harvested for ChIP assay.

extract_protocol:
Lysates were clarified from sonicated nuclei and pan-Kac-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD501-01). After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 500 nM 4-OHT treatment for 4 hours

value: cells

tag: chip actibody

value: pan-Lysine Acetylation (#9441L)

value: 4-OHT treatment


title: T1 (PDHE1α-4OHT)

value: untreated


title: T41 (PDHE1α+4OHT)


title: CK3 (WT+4OHT)


title: T43 (+4OHT-H2A)


title: T33 (+4OHT-WT)


title: Enteric glia, DIV0

source_name: Enteric glia


title: MDA-MB-231_shFOXC2-3_Rep1

city: Cambridge

first: Kirsty

last: Sawicka

address: Robinson Way

department: University of Cambridge

institute: CRUK Cambridge Insititute

data_processing:
Raw reads were aligned to hg19 using STAR and gene quantification was performed using featureCounts from the subreads package.
Normalization and differential expression analysis includin log2 fold change estimation, and FDR p-value calculation were done with DESeq2 (version 1.20.0) with analysis restricted to protein coding genes. Counts generated using featureCounts were used to determine expression differences of both FOXC2 hairpins relative to a control Renilla hairpin. betaPrior was set to TRUE resulting in log2 fold change shrinkage useful for ranking of genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with read counts for each sample
Supplementary files format and content: tab-delimited text file with output from DESeq2 DGE analysis

molecule: polyA RNA

source_name: Breast cancer

growth_protocol: MDA-MB-231 cells expressing control of FOXC2-targetting shRNAs were grown in RPMI supplemented with 10% fetal bovine serum (FBS) and L-glutamine.

extract_protocol:
Roche High Pure RNA extraction kit (Roche, 11828665001) according to the manufacturer's instructions.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) in accordance with the manufacturer’s instructions. Briefly, 500 ng of total RNA was used for polyA mRNA purification and fragmentation. Purified mRNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to illumina sequencing adapters, and amplified by PCR (using 8 cycles). Final libraries were evaluated using fluorescent-based assays and were sequenced on an Illumina HiSeq 2500 (v4 chemistry) using 2 x 50 bp cycles.

value: Breast cancer

tag: cell line

value: MDA-MB-231 cells

value: Cancer cells


title: MDA-MB-231_shREN_Rep2

value: shREN (Control)


title: MDA-MB-231_shFOXC2-1_Rep2


title: MDA-MB-231_shFOXC2-1_Rep1


title: CK2 (WT-4OHT)


title: T31 (+4OHT-C2A)


title: MDA-MB-231_shREN_Rep1


title: cells transfected with siRNAs targeting ROCK1, rep2

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

data_processing:
Fastq file were aligned using STAR (2.5.2b) on UCSC hg19 genome.
Bam file were counted using htseq-count (0.11.2.) with option -t exon -f bam -r pos -s reverse -m intersection-strict -nonunique none.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include raw counts.

source_name: HUVEC ROCK1 knockdown

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) were obtained from Lonza, Switerzland. HUVEC were maintained in EGM-2 (Lonza) supplemented with 1% Penicillin-Streptomycin (Gibco). Upon reception, HUVEC at P0 were expanded over 2 passages in collagen 1 (from rat tail, BD) coated flasks in complete EGM-2 medium supplemented with 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C in a 5% CO2 - 3% O2 humidified chamber.

extract_protocol:
Total RNA were extracted from HUVEC using the NucleoSpin RNA II kit (Macherey-Nagel) according to the manufacturer’s instructions.
cDNA libraries were prepared with the TruSeq Stranded mRNA Sample Preparation (Illumina) and sequenced on a HiSeq 2500 Illumina platform using single-end 50 basepair reads at the MGX facility (Montpellier).

treatment_protocol: HUVEC at passage 3 were transfected twice at 24 h-intervals with 30 nM siRNA and Lipofectamine RNAi max (Life Technologies, ref. 13778-150) according to the manufacturer’s instructions in 37°C in a regular 5% CO2 in a humidified chamber. For double transfections, 30 nM of each siRNA duplexes (Dharmacon smartpool ON-TARGET plus Thermo Scientific) was used. One million of siRNA transfected HUVEC were seeded at confluency the day after the second round of transfection in wells of 6-well plates coated with collagen 1 (from rat tail) and cultured for 48h in complete media at 37°C, 5% CO2.

value: HUVEC

value: ROCK1 knockdown


title: cells transfected with siRNAs targeting ROCK2, rep2

source_name: HUVEC ROCK2 knockdown

value: ROCK2 knockdown


title: cells transfected with siRNAs targeting ROCK2, rep1


title: cells transfected with siRNAs targeting CCM2 and ROCK1, rep2

source_name: HUVEC CCM2+ROCK1 knockdown

value: CCM2+ROCK1 knockdown


title: cells transfected with siRNAs targeting ROCK1, rep3


title: cells transfected with siRNAs targeting CCM2 and ROCK2, rep2

source_name: HUVEC CCM2+ROCK2 knockdown

value: CCM2+ROCK2 knockdown


title: Sox10::CreERT2;R26-tdTomato_DIV0_3

treatment_protocol:
LMMP peels were digested for 15 mins at 37°C with HBSS (Gibco, 14170112) containing 10 mg/mL collagenase IV (Worthington Biochemicals, CLS-4) followed by a wash step in ice-cold HBSS and subsequent incubation with 1U papain (Worthington Biochemicals, PAP2) for 5 mins at 37°C. Samples were then washed and resuspended in L15 medium without phenol red (Gibco, 21083027) containing 1% P/S (Gibco, 15140122), 1 mg/ml BSA (Sigma, A9418), 10 mM Hepes pH 7.4 (Gibco, 15630106), 10 % Biowhittaker water (Lonza, BE17-724F) and 400 U DNAse I (Grade II; Roche, 10104159001), filtered through a 70 μm and a 40 μm strainer and subjected to FACS.
tdTomato+ cells were purified by FACS either directly from the adult tissues after dissociation (DIV0) or from cells harvested from tissue culture dishes using trypLE express (Thermo Fisher Scientific) on DIV4 or StemPro Accutase (Thermo Fisher Scientific) on DIV11 and DIV20.

value: C57Bl/6JAX and CBA mixed


title: cells transfected with siRNAs targeting CCM2 and ROCK1, rep3


title: cells transfected with siRNAs targeting CCM2 and ROCK2, rep1


title: cells transfected with siRNAs targeting ROCK1, rep1


title: MDA-MB-231_shFOXC2-3_Rep2


title: cells transfected with siRNAs targeting CCM2, rep3

source_name: HUVEC CCM2 knockdown

value: CCM2 knockdown


title: cells transfected with siRNAs targeting CCM2 and ROCK2, rep3


title: cells transfected with siRNAs targeting CCM2, rep2


title: control cells transfected with non targeting siRNA, rep1

source_name: HUVEC WT

value: WT


title: control cells transfected with non targeting siRNA, rep3


title: cells transfected with siRNAs targeting CCM2 and ROCK1, rep1


title: cells transfected with siRNAs targeting ROCK2, rep3


title: control cells transfected with non targeting siRNA, rep2


title: cells transfected with siRNAs targeting CCM2, rep1


title: MpB-GATA1ox t6HL, rep2

data_processing:
CLC Genomics Workbench v20.0.2
Sequence reads were trimmed using CLC Genomics Workbench - Quality limit: 0.05.
Trimmed sequence reads were mapped to the MpTak1v6.1 release of Marchantia polymorpha Tak genome using CLC Genomics Workbench - Mismatch cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.5, Similarity fraction: 0.8.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: MpTak1v6.1 release of Marchantia polymorpha Tak.
Supplementary files format and content: Tab-delimited text files, including TPM.

organism: Marchantia polymorpha

source_name: 3 weeks old thallus; entire plants

growth_protocol: Marchantia polymorpha lines BoGa, Mpb-gata1-1, Mpb-gata1-2, and MpB-GATA1ox3 were grown on 1/2 Gamborg's B5 medium in long day conditions (16L/8D) at 60 µmol m-2 s-1 and 22°C for two weeks. Plants were shifted to the high-light chambers for an additional growth- and acclimatization period of one week under constant light with 60-70 µmol m-2 s-1 (growth light; GL) at 20-22°C.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit (Macherey-Nagel).
TruSeq stranded mRNA Kit (Illumina, San Diego, USA) with TruSeq RNA Adapter Box Set A and B (Illumina, San Diego, USA) and protocol 1000000040498v00 (Elution-2-Frag-Prime step: 4 minutes at 94°C; 15 cycles enrichment)

value: 3 weeks old

value: thallus

value: MpB-GATA1ox mutant


title: MpB-GATA1ox t6HL, rep3


title: Mpb-gata1-2 t6HL, rep2

value: Mpb-gata1-2 mutant


title: MpB-GATA1ox t6HL, rep1


title: Mpb-gata1-2 t6HL, rep1


title: Mpb-gata1-2 t6HL, rep3


title: Mpb-gata1-1 t6HL, rep2

value: Mpb-gata1-1 mutant


title: Mpb-gata1-1 t6HL, rep1


title: BoGa t6HL, rep3

value: BoGa (WT)


title: Mpb-gata1-1 t6HL, rep3


title: BoGa t6HL, rep2


title: MpB-GATA1ox t6LL, rep2


title: MpB-GATA1ox t6LL, rep3


title: MpB-GATA1ox t6LL, rep1


title: HC041, DEX_SARS

city: Nijmegen

first: Nick

last: Keur

address: Geert Grooteplein Zuid 10

department: Internal medicine

country: Netherlands

institute: Radboudumc

description:
205-4+dex
Counts_PBMC_COVID.tsv

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using SOAPNUKE filters include the removal of the adapter sequence, contamination check, and removal of low-quality reads (Q ≥ 33)
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR aligner
Read count extraction and normalization were performed using Deseq2
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include Deseq2 normalized values for each sample

source_name: PBMC

extract_protocol:
Total RNA was extracted from whole blood collected in PAXgene® tubes (BD Biosciences) using PAXgene Blood RNA kit (QIAGEN). Total RNA was isolated from PBMCs, and on column DNase (QIAGEN) treated, using the RNeasy mini kit (QIAGEN) by following the manufacturer’s instructions
The RNA-Sequencing library was prepared by using the MGIEasy RNA Library Prep kit (MGI Tech). Strand specific RNA sequencing was performed on a DNBSEQ platform (paired-end, read length 100 bp

value: PBMC

value: Dexamethasone + Sars-Cov-2


title: HC049, DEX_SARS

description:
123-4+dex
Counts_PBMC_COVID.tsv


title: HC044, DEX_SARS

description:
41-4+dex
Counts_PBMC_COVID.tsv


title: NB4_H3K4me3_A10_S14

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

institute: Radboud University

data_processing:
Samples were sequenced on an Illumina NextSeq 500, using a 43bp, paired end configuration. Fastq was then demultiplexed and generated using Illumina bcl2fastq v2.19 before pre-processing (trimmomatic) to remove adapter read-through and poorquality sequences. Sequenced reads were aligned against the UCSC human reference genome (GRCh38) with Burrows-Wheeler Aligner (BWA) program with default parameters. The BAM files were subjected to removal of potential PCR and optical duplicates using Picard MarkDuplicates option. Fragment length and quality measurement for each dataset were determined using PhantomPeakQualTools based on strand cross-correlation approach. Two metrics named normalized strand cross-correlation coefficient (NSC) and relative strand cross-correlation coefficient (RSC) were used for data quality assessment. BigWig files were generated using a custom bam to bigwig script.
Assembly: GRCh38
Supplementary files format and content: ChIP-seq: bigwig files.

source_name: cell line

growth_protocol: The mononuclear cell (MNC) fraction of AML samples was obtained by density gradient centrifugation using lymphoprep (PAA, Cölbe, Germany) according to standard procedures.  MOLM13, NB4, and OCI-AML3 were cultured in RPMI-1640 (Gibco, The Netherlands) supplemented with 10% fetal calf serum (FCS) and 1% penicillin/streptomycin. Mono-Mac-6 cells were cultured in RPMI-1640 supplemented with 10% FCS, 1% penicillin/streptomycin (Gibco//Life Technologies Europe BV, Bleiswijk, Netherlands), nonessential amino acids (NEAA, Sigma-Aldrich), and 10 µg/mL human insulin (Sigma-Aldrich).

extract_protocol:
Primary AML cells and cell lines were crosslinked with 1% formaldehyde for 10 min at room temperature at a concentration of 30 × 106 cells/mL. The fixed cells were sonicated 10–15 cycles (30 sec on, 30 sec off) to a size of 200–600 bp. Sonicated chromatin was incubated overnight with either 5 µg TP53 antibody (Santa Cruz: DO-1, sc-126X) or 2 µg of antibody against H3K4me3, H3K27me3, or H3K27ac. The next day, antibody–protein complexes were bound to magnetic Protein G beads (Invitrogen, ThermoFisher, Netherlands) for ∼2 hours. Beads were washed with four different wash buffers, and chromatin was eluted from the beads. DNA proteins were de-crosslinked, and samples were purified using the Qiaquick MinElute PCR purification kit.
Sequencing samples were prepared according to the manufacturer's protocol (Illumina, Eindhoven, Netherlands). End repair was performed using the precipitated DNA using Klenow and T4 PNK, and subsequently a 3′ protruding A base was generated using Taq polymerase followed by adapter ligation. The DNA was amplified by PCR and ∼300 bp (ChIP fragment + adapters). Samples were sequenced on an Illumina NextSeq 500 system with 2×43 bp paired-end sequencing (PE43).

treatment_protocol: no treatment

value: AML

tag: antibody

value: Diagenode, C15410030

tag: icu admission

tag: chip target

value: ChIP-seq H3K4me3


title: Monomac6_H3K4me3_A27_S17


title: HC044, DEX

description:
154-3-dex
Counts_PBMC_COVID.tsv

value: Dexamethasone


title: HC041, DEX

description:
113-3-dex
Counts_PBMC_COVID.tsv


title: HC059, DEX

description:
195-3-dex
Counts_PBMC_COVID.tsv


title: Mpb-gata1-2 t6LL, rep3

tag: tissue


title: HC059, DMSO_SARS

description:
185-2+
Counts_PBMC_COVID.tsv

value: DMSO + Sars-Cov-2


title: HC059, DEX_SARS

description:
82-4+dex
Counts_PBMC_COVID.tsv


title: NB4_H3K27ac_A26_S16

value: Diagenode, C15410174

value: ChIP-seq H3K27ac


title: HC041, DMSO_SARS

description:
103-2+
Counts_PBMC_COVID.tsv


title: BoGa t6HL, rep1


title: Monomac6_H3K27me3_A28_S25

value: Diagenode, C15410195

value: ChIP-seq H3K27me3


title: Mpb-gata1-2 t6LL, rep2

value: 3 weeks old


title: HC069, DMSO_SARS

description:
21-2+
Counts_PBMC_COVID.tsv


title: HC049, DMSO_SARS

description:
62-2+
Counts_PBMC_COVID.tsv


title: Mpb-gata1-1 t6LL, rep3

value: thallus


title: Mpb-gata1-2 t6LL, rep1


title: MOLM13_H3K4me3_A04_S11


title: HC069, DEX_SARS

description:
164-4+dex
Counts_PBMC_COVID.tsv


title: NB4_H3K27me3_A25_S15


title: HC044_DMSO

description:
134-1-
Counts_PBMC_COVID.tsv

value: DMSO


title: HC049_DMSO

description:
52-1-
Counts_PBMC_COVID.tsv


title: HC069_DMSO

description:
11-1-
Counts_PBMC_COVID.tsv


title: MOLM13_H3K27ac_A08_S13


title: HC044, DMSO_SARS

description:
144-2+
Counts_PBMC_COVID.tsv


title: HC005, DEX_SARS

description:
10.4_HC005+SARS_COV2+DEX
Counts_PBMC_HEALTHY.tsv


title: HC003, DEX_SARS

description:
8.4_HC003+SARS_COV2+DEX
Counts_PBMC_HEALTHY.tsv


title: BoGa t6LL, rep2


title: Mpb-gata1-1 t6LL, rep2


title: HC059_DMSO

description:
175-1-
Counts_PBMC_COVID.tsv


title: HC001, DEX_SARS

description:
6.4_HC001+SARS_COV2+DEX
Counts_PBMC_HEALTHY.tsv


title: HC005, DEX

description:
10.3_HC005+DEX
Counts_PBMC_HEALTHY.tsv


title: Monomac6_H3K27ac_A29_S18


title: 15867_TP53_9_A35

source_name: primary patient

value: Santa Cruz:DO-1, sc-126X

value: ChIP-seq TP53


title: MpB-GATA1ox t0, rep3

value: MpB-GATA1ox mutant


title: BoGa t6LL, rep1

value: BoGa (WT)


title: HC004, DEX

description:
9.3_HC004+DEX
Counts_PBMC_HEALTHY.tsv

value: PBMC


title: 15864_TP53_19_A45_Monomac6

value: AML


title: HC004, DEX_SARS

description:
9.4_HC004+SARS_COV2+DEX
Counts_PBMC_HEALTHY.tsv

value: Dexamethasone + Sars-Cov-2


title: HC041_DMSO

description:
93-1-
Counts_PBMC_COVID.tsv


title: Mpb-gata1-1 t6LL, rep1

value: Mpb-gata1-1 mutant


title: HC003, DEX

description:
8.3_HC003+DEX
Counts_PBMC_HEALTHY.tsv

value: Dexamethasone


title: MOLM13_H3K27me3_A07_S12


title: MpB-GATA1ox t0, rep2


title: HC002, DEX_SARS

description:
7.4_HC002+SARS_COV2+DEX
Counts_PBMC_HEALTHY.tsv


title: HC002, DEX

description:
7.3_HC002+DEX
Counts_PBMC_HEALTHY.tsv


title: 15862_TP53_15_A41_MOLM13


title: HC001, DEX

description:
6.3_HC001+DEX
Counts_PBMC_HEALTHY.tsv


title: BoGa t6LL, rep3


title: 15861_TP53_5_A31


title: HC004, DMSO_SARS

description:
9.2_HC004+SARS_COV2
Counts_PBMC_HEALTHY.tsv

value: DMSO + Sars-Cov-2


title: Mpb-gata1-2 t0, rep3

value: Mpb-gata1-2 mutant


title: HC005, DMSO_SARS

description:
10.2_HC005+SARS_COV2
Counts_PBMC_HEALTHY.tsv


title: 15863_TP53_17_A43_N4


title: HC002, DMSO_SARS

description:
7.2_HC002+SARS_COV2
Counts_PBMC_HEALTHY.tsv


title: 16194_3P_CB3_shTP53_Z23

data_processing:
Seq2science RNA-seq analysis.
Sequence reads were trimmed using default fastp.
Trimmed sequence reads were mapped to GRCh38 using STAR.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited value .tsv file include raw counts for each Sample

growth_protocol: Umbilical cord blood (CB) was derived from healthy full-term pregnancies from the obstetrics departments of the Martini Hospital and University Medical Center in Groningen, The Netherlands, after patients provided informed consent. CD34+ cells were isolated by MACS separation (Miltenyi, Leiden, Netherlands). CD34+ cells were maintained in Stemline II (Sigma-Aldrich, Amsterdam, Netherlands), supplemented with 100 ng/mL stem cell factor (SCF, c-kit ligand), 100 ng/mL thyropoietin (TPO), and 100 ng/mL Fms-like tyrosine kinase receptor 3 (FLT3) ligand until further use (24–48 hours).

extract_protocol:
RNA was isolated by separation of the aqueous phase with TRIzol Reagent (ThermoFisher, Bleiswijk, Netherlands) according to the manufacturer's protocol. The aqueous phase was mixed with 70% ethanol (1:1), and isolation was continued using the RNeasy microkit (Qiagen, Hilden, Germany) including on-column DNase I treatment.
RNA libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer's protocol (KR1351–v1.16, Roche Sequencing Solutions). In brief, 25 ng to 1 µg of input RNA was depleted from ribosomal RNA by oligohybridization, RNaseH treatment, and DNase digestion. rRNA-depleted RNA was fragmented to ∼200-bp fragments, and first-strand synthesis was performed using random primers. The second strand was synthesized using dUTP for strand specificity. After adapter ligation, library amplification was performed, and the number of cycles was dependent on the amount of starting material. A bioanalyzer using a high-sensitivity DNA Chip (Agilent) was used to check fragment size. Samples were sequenced on an Illumina NextSeq 500 system with 2×43-bp paired-end sequencing (PE43)

treatment_protocol: TP53 constructs were created by polymerase chain reaction (PCR) from cDNA from TP53 mutant and wild-type cell lines and subcloned into a pRRL–SFFV–iGFP vector, and the correct insert was validated by sequencing. Lentiviral particle production was performed using Fugene (Promega Benelux, Leiden, Netherlands), and transduction of CB cells was performed using 2 µg/mL polybrene (Sigma-Aldrich). After 48–72 hours, cells were sorted on GFP+ and/or CD34+CD38– cell fractions.

value: Umbilical cord blood (CB)

value: shRNA TP53 transduced CB cells


title: Mpb-gata1-2 t0, rep2


title: HC003, DMSO_SARS

description:
8.2_HC003+SARS_COV2
Counts_PBMC_HEALTHY.tsv


title: HC001, DMSO_SARS

description:
6.2_HC001+SARS_COV2
Counts_PBMC_HEALTHY.tsv


title: HC005, DMSO

description:
10.1_HC005+DMSO
Counts_PBMC_HEALTHY.tsv


title: Mpb-gata1-2 t0, rep1


title: 16193_3S_CB3_shSCR_Z19

value: shRNA control transduced CD34+ cells


title: HC004, DMSO

description:
9.1_HC004+DMSO
Counts_PBMC_HEALTHY.tsv


title: HC001, DMSO

description:
6.1_HC001+DMSO
Counts_PBMC_HEALTHY.tsv


title: Mpb-gata1-1 t0, rep3

value: 3 weeks old


title: 16192_3T_CB3_TP53R273H_Z07

value: TP53R273H transduced CD34+ cells


title: HC002, DMSO

description:
7.1_HC002+DMSO
Counts_PBMC_HEALTHY.tsv

value: DMSO


title: CDX1012pre, Post-treatment, Day 4

description:
CDX2012post
Counts_WB_COVID.tsv

source_name: Whole blood

value: Whole blood

tag: time

value: Day 4


title: CDX1011pre, Post-treatment, Day 4

description:
CDX2011post
Counts_WB_COVID.tsv

tag: cell type


title: 15866_TP53_7_A33

value: Santa Cruz:DO-1, sc-126X

value: ChIP-seq TP53


title: MpB-GATA1ox t0, rep1

tag: age

value: thallus

value: MpB-GATA1ox mutant


title: 16191_3E_CB3_EV_Z06

value: empty vector transduced CD34+ cells


title: Mpb-gata1-1 t0, rep2

tag: genotype

value: Mpb-gata1-1 mutant


title: CDX1010pre, Post-treatment, Day 4

description:
CDX2010post
Counts_WB_COVID.tsv

tag: treatment

value: Dexamethasone


title: 16190_1P_CB1_shTP53_Z05


title: 15860_TP53_3_A29

value: AML


title: CDX1009pre, Post-treatment, Day 4

description:
CDX2009post
Counts_WB_COVID.tsv


title: CDX1008pre, Post-treatment, Day 4

description:
CDX2008post
Counts_WB_COVID.tsv


title: HC003, DMSO

description:
8.1_HC003+DMSO
Counts_PBMC_HEALTHY.tsv

value: PBMC


title: CDX1007pre, Post-treatment, Day 4

description:
CDX2007post
Counts_WB_COVID.tsv


title: Mpb-gata1-1 t0, rep1


title: CDX1006pre, Post-treatment, Day 4

description:
CDX2006post
Counts_WB_COVID.tsv


title: CDX1005pre, Post-treatment, Day 4

description:
CDX2005post
Counts_WB_COVID.tsv


title: BoGa t0, rep2

value: BoGa (WT)


title: CDX1002pre, Post-treatment, Day 4

description:
CDX2002post
Counts_WB_COVID.tsv


title: 16188_1T_CB1_TP53R273H_Z03

value: Umbilical cord blood (CB)


title: CDX1001pre, Post-treatment, Day 4

description:
CDX2001post
Counts_WB_COVID.tsv


title: 16187_1E_CB1_EV_Z02


title: CDX1012pre, Pre-treatment, Day 0

description:
CDX1012pre
Counts_WB_COVID.tsv

value: Untreated

value: Day 0


title: 16 DAP END, Input, Replicate 3

city: Olomouc

first: Ales

last: Pecinka

address: Šlechtitelů 31

country: Czech Republic

institute: Institute of Experimental Botany of the AS CR

description: 16 DAP endosperm Input replicate 3

data_processing:
Illumina RTA3 was used for basecalling and .cbcl files were converted to .fastq using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence and low-quality sequence and then mapped to Morex v3 whole genome using hisat2 v2.1.0 with default parameters.
Duplicates were removed using MakrDuplicates in GATK and the peak calling was performed using MACS2.
ChIP-seq coverage plot were generated using deepTools bamCoverage with parameters binSize 10, smoothLength 50, normalizeUsing BPM.
Assembly: Mascher, Martin, et al. "Long-read sequence assembly: a technical evaluation in barley."The Plant Cell33.6 (2021): 1888-1906.
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for input samples)

organism: Hordeum vulgare

source_name: endosperm

growth_protocol: Seeds of six-rowed spring barley Hordeum vulgare subsp. vulgare cv. Morex were germinated for 3 days at 25 ° and then moved into the peat pots containing mixture of soil and sand. Plants were grown in climatic chamber under long-day regime (16 h day 20 °C, 8 h night 16 °C; humidity 60 %). After 10 days plants were transfered into 15 x 15 cm pots containing the same soil and cultivated in the same conditions until flowering.

extract_protocol:
Approximately 2 g of 16 DAP endosperm tissue were isolated and cross-linked under vacuum in 1% formaldehyde for 15 min at room temperature. The cross-linking was quenched by adding glycine to a final concentration of 0.1 M, and the vacuum was applied for 5 min. Endosperm tissue was rinsed with water and frozen in liquid nitrogen. Isolated nuclei were resuspended in Nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5% SDS, cOmplete™, EDTA-free Protease Inhibitor Cocktail (Roche)) and incubated at 4°C under gentle agitation for 20 min. The chromatin solution was sonicated using a Biorupter Plus (Diagenode) with 10 cycles of 30 sec pulse/90 sec cooling at high power at 4°C. The resulting sheared chromatin was pooled and diluted 1:4 with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.25 mM EDTA, 1.25% Triton X-100, 1 cOmplete™, EDTA-free Protease Inhibitor Cocktail). 600 µl aliquots of diluted chromatin were incubated with 7 µl of the Anti-trimethyl-Histone H3 (Lys27) Antibody (Millipore, cat. no. 07-449) in a rotator at 4°C overnight. Samples without antibody were used as negative controls. The next day, 40 µl of the Dynabeads Protein A (Invitrogen) were added to each tube, and the samples were further incubated for 2 hours. Afterward, beads were washed with a sequence of buffers, and immune complexes were eluted as described. Control chromatin aliquots (‘input DNA‘) were taken prior to immunoprecipitation. Reverse crosslinking was performed for all samples, and  DNA was extracted and purified using the ChIP DNA Clean & Concentrator™ kit (Zymo Research).
Sequencing libraries were prepared and 150-bp pair-end reads were sequenced using Illumina NovaSeq 6000 platform (Illumina) by Novogene Ltd.

value: endosperm

tag: developmental stage

value: 16 days after pollination

value: Morex


title: CDX1011pre, Pre-treatment, Day 0

description:
CDX1011pre
Counts_WB_COVID.tsv

value: Whole blood


title: 16 DAP END, Input, Replicate 2

description: 16 DAP endosperm Input replicate 2


title: CDX1009pre, Pre-treatment, Day 0

description:
CDX1009pre
Counts_WB_COVID.tsv


title: CDX1010pre, Pre-treatment, Day 0

description:
CDX1010pre
Counts_WB_COVID.tsv


title: 16 DAP END, Input, Replicate 1

description: 16 DAP endosperm Input replicate 1


title: CDX1008pre, Pre-treatment, Day 0

description:
CDX1008pre
Counts_WB_COVID.tsv


title: 16 DAP END, H3K27me3, ChIP, Replicate 3

description: 16 DAP endosperm H3K27me3 replicate 3


title: CordBlood, PND0, SGA15

city: Halifax

first: Alejandro

last: Lomniczi

state: NS

address: 5850 College Street

department: Physiology and Biophysics

country: Canada

institute: Dalhousie University

data_processing:
The quality of the bisulfite-converted sequencing reads was assessed with FastQC.
Reads were trimmed and aligned to the human reference genome (GRCh38/hg38), and then the bisulfite conversion rates were evaluated, ensuring all libraries were >98% converted, and CpG methylation was evaluated using Bismark
The methylation rates were calculated as the ratio of methylated reads over the total number of reads. Methylation rates for CpGs with fewer than 5 reads were excluded from further analysis
The RnBeads filtering module was set for SNP filtering, removal of sex chromosome, and removal of high coverage outliers
Filtering for missing quantile values was set to 0.05, and a filtering deviation threshold of 0.005, with no imputation method employed.
Assembly: GRCh38/hg38

source_name: Cord Blood

extract_protocol:
Genomic DNA was immediately extracted from whole umbilical cord blood using an automated DNA extractor (BioRobot EZ1, QIAGEN, Hilden, Germany).
Genome-wide bisulphite sequencingapproach was performed to specifically study DNA methylation using theIllumina TruSeq Methyl Capture EPIC kit (Illumina, Cambridge, UK), which targets over 3.3 million CpGs. Libraries were prepared following the manufacturer’s protocol.

value: Cord Blood

tag: group

value: SGA


title: BoGa t0, rep3

value: 3 weeks old

value: thallus


title: CordBlood, PND0, SGA13


title: 16189_1S_CB1_shSCR_Z04

value: shRNA control transduced CD34+ cells


title: Rrm4-Ada-Gfp_rep2, replicate 2

city: Düsseldorf

first: Prof. Dr. Michael

last: Feldbrügge

state: North Rheine-Westphalia

address: Universitätsstraße 1

department: Department of Biology

institute: Heinrich Heine University of Düsseldorf

data_processing:
Briefly, RNA-seq reads were trimmed based on sequencing quality (Phred score) using Trimmomatic (version 0.39; Bolger et al., 2014). Specifically, reads with the Phred score of less than 25 were trimmed and removed when the read length fell below 19 nt.
The trimmed reads were then mapped to the U. maydis genome sequence and gene annotation using STAR (version 2.5.2b; Dobin et al., 2013), allowing reads that were mapped to exactly one location, had a minimum of 16 matched bases and contained no more than 7% mismatches per mapped length.
The A-to-G editing events on transcripts were identified using the wtRNA-RNA approach from the previously established hyperTRIBE pipeline. Uniquely mapped alignments in SAM format were loaded into a MySQL table with genomic coordinates.
The nucleotides at each position in the test mRNA libraries (Rrm4-Ada-Gfp, Khd4-Ada-Gfp, control-Ada) were compared with those of the control mRNA library (WtRNA; Khd4-Gfp or Rrm4-Gfp) to identify A-to-G editing sites.
Only editing events with a minimum of 20 read coverage and 5% editing were considered for further analysis.
Assembly: The bioinformatics analyses were based on the U. maydis 521 genome sequence (Ustilago_maydis.Umaydis521_2.0.dna_rm.chromosome.1) and the associated gene annotation (Ustilago_maydis.Umaydis521_2.0.41.gff3; both downloaded from http://ftp.ensemblgenomes.org/pub/fungi/release-53/fasta/ustilago_maydis/dna/; Kämper et al., 2006). We manually extended all genes by 300 nt on each side to include potential 5´ UTR and 3´ UTR regions which are not currently annotated in the U. maydis genome. The extended GTF file was converted to refFlat format using the UCSC gtfToGenePred tool.
Supplementary files format and content: bedgraph files containing the information about all detected editing  sites (A-to-G mutation) for each protein (Rrm4-Ada-Gfp, Khd4-Ada-Gfp and control-Ada) and replicate.

organism: Mycosarcoma maydis

source_name: AB33 Pcrg1: rrm4-ada-gfp / rrm4delta

growth_protocol: The conditions used for cultivation of U. maydis are described in Brachmann et al., Mol Genet Genomics, 2004 (DOI: 10.1007/s00438-004-1047-z). Starting cultures were grown in CM medium supplemented with glucose.

extract_protocol:
RNA was harvested using RNeasy Plant Mini Kit (74904; Qiagen, Hilden, Germany) following the manufacturer’s instructions.  500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-01/02; Vazyme) following manufacturer's protocols.

treatment_protocol: For the induction of hyphal growth of lab strain AB33 and derivates, 50ml cultures were grown to an OD600 of 0.5 in CM-glucose medium and shifted to nitrate minimal medium supplemented with 1% glucose. HyperTRIBE analyses was performed 6 hours post induction.

tag: strain

value: AB33 Pcrg1:rrm4-ada-gfp / rrm4delta


title: CordBlood, PND0, SGA12


title: BoGa t0, rep1


title: CDX1007pre, Pre-treatment, Day 0

description:
CDX1007pre
Counts_WB_COVID.tsv


title: Rrm4-Ada-Gfp_rep1, replicate 1


title: CDX1006pre, Pre-treatment, Day 0

description:
CDX1006pre
Counts_WB_COVID.tsv


title: CordBlood, PND0, SGA10


title: khd4D filament RNAseq replicate 2

data_processing:
Briefly, RNA-seq reads were trimmed based on sequencing quality (Phred score) using Trimmomatic (version 0.39; Bolger et al., 2014). Specifically, reads with the Phred score of less than 25 were trimmed and removed when the read length fell below 19 nt.
RNAseq data analysis was carried out in Galaxy, an open-source platform (Afgan et al., 2018).
The raw sequencing reads were quality filtered based on their quality score and length with Trimmomatic (Version 0.36; Bolger et al., 2014). Specifically, the reads were trimmed 20 nt from the start, trimmed from the end when the Phred score dropped below 30, and discarded if the read length is less than 20 nt.
STAR (version 2.7.2b) was used to align the trimmed reads to the U. maydis genome (see HyperTRIBE experiment and data processing; Dobin et al., 2013), allowing up to 4% mismatches in the mapped read length while limiting the mapping to one locus.
Uniquely mapped reads on each gene were counted using htseq-count (version 0.9.1; Anders et al., 2014).
The resulting raw counts of mRNA libraries were used as input for the subsequent differential gene expression analysis. All differential gene expression analysis was performed using the R/Bioconductor package DESeq2 (Love et al., 2014). Genes with an absolute fold change > 1.5 (after fold change shrinkage) and an adjusted p-value < 0.05 (Benjamini-Hochberg correction) were considered differentially expressed.
Assembly: The bioinformatics analyses were based on the U. maydis 521 genome sequence (Ustilago_maydis.Umaydis521_2.0.dna_rm.chromosome.1) and the associated gene annotation (Ustilago_maydis.Umaydis521_2.0.41.gff3; both downloaded from http://ftp.ensemblgenomes.org/pub/fungi/release-53/fasta/ustilago_maydis/dna/; Kämper et al., 2006). We manually extended all genes by 300 nt on each side to include potential 5´ UTR and 3´ UTR regions which are not currently annotated in the U. maydis genome. The extended GTF file was converted to refFlat format using the UCSC gtfToGenePred tool.
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: hyphae

value: AB33 khd4D

value: hyphae

value: khd4 deletion

value: switch from yeast to hyphal growth

value: 9 hours post induction


title: CordBlood, PND0, SGA7


title: wildtype filament RNAseq replicate 1

value: wildtype


title: CDX1005pre, Pre-treatment, Day 0

description:
CDX1005pre
Counts_WB_COVID.tsv

value: Untreated

value: Day 0


title: CDX1001pre, Pre-treatment, Day 0

description:
CDX1001pre
Counts_WB_COVID.tsv


title: TO_58N_8

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Raw data files were aligned to the reference genome and the mirbase database using Torrent Suite default parameters.
Assembly: hg19

source_name: Plasma

extract_protocol:
Plasma was isolated from EDTA or Lithium Heparin blood samples within 1 hour from collection, with a standard procedure to prevent haemolysis.
Total RNA was extracted with miRNeasy serum/plasma kit (Qiagen) using Exiqon protocol, with the batteriophage MS2RNA carrier (Roche Diagnostics) to promote RNA precipitation and purification on membranes.
For library preparation, smallRNA enriched samples were converted in barcoded cDNA libraries following the Ion Total RNA-Seq kit v2 protocol (Thermo Fisher) with the recommendations for low input RNA quantity. First, RNA samples were enriched for smallRNA fraction using a magnetic bead-based technology. After hybridization and ligation steps, through which 3' and 5' adaptors are directionally and simultaneously attached, reverse transcription was performed to obtain cDNA. cDNA was subsequently purified and size selected and then amplified using barcoded primers (obtained from Ion Xpress™ RNA-Seq Barcode 01-16 Kit, Thermo Fisher or synthesized by Eurofins Genomics as custom oligonucleotides (barcodes 17-24)). Finally, libraries were purified with beads. All the purification steps were performed by means of the Magnetic Bead Cleanup Module included in the kit. Libraries were checked for yield and size distribution by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) and 24 differentially barcoded smallRNA libraries were pooled. Pools were checked by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) to determine the library dilution required for template preparation. Ion Chef™ System (Thermo Fisher) was used for automated templated Ion Sphere Particles preparation and chip loading. Ion 540 chips (Thermo Fisher) were sequenced using Ion GeneStudio S5 System (Thermo Fisher).

value: Plasma

tag: disease state

value: control


title: R22_f3HIMφ

city: Solna

first: Daniel

last: Ramsköld

address: Solnavägen 9

department: Dept of Cell and Melecular Biology

country: Sweden

institute: Karolinska Institutet

description: Hippocampal infiltrating macrophages age P12, 3 days after hypoxia

data_processing:
Reads were aligned using STAR 2.4.2a with default settings against Mus musculus reference genome (assembly mm10, without unplaced contigs).
Non-uniquely aligned reads were discarded from the alignment.
Reads per kilobase of gene per million mapped reads (RPKM) and read counts were generated using the python script rpkmforgenes (available at https://github.com/danielramskold/S3_species-specific_sequencing/) with settings -readcount -fulltranscript -mRNAnorm -rmnameoverlap -bothendceil and RefSeq gene annotation.
Assembly: mm10
Supplementary files format and content: tab-separated values, RPKM and read count

source_name: Hippocampus

extract_protocol:
RNeasy Micro Kit, Qiagen
Smart-seq2, Picelli et al. Nature 2014

value: Hippocampus

value: Macrophages

tag: pup id

tag: Sex

value: female

value: 3 days

value: Hypoxia


title: wildtype filament RNAseq replicate 2


title: khd4D yeast RNAseq replicate 2

source_name: yeast

value: yeast


title: CordBlood, PND0, LGA13

value: Cord Blood

value: LGA


title: R21_f3HIMφ


title: TO_04N_8


title: 16 DAP END, H3K27me3, ChIP, Replicate 2

description: 16 DAP endosperm H3K27me3 replicate 2

value: endosperm

value: 16 days after pollination

value: Morex


title: R6_m1HIMφ

description: Hippocampal infiltrating macrophages age P10, 1 day after hypoxia

value: male

value: 1 day


title: CordBlood, PND0, LGA12


title: TO_06N_8


title: CordBlood, PND0, SGA11

value: SGA


title: 16 DAP END, H3K27me3, ChIP, Replicate 1

description: 16 DAP endosperm H3K27me3 replicate 1


title: khd4D filament RNAseq replicate 3

value: AB33 khd4D

value: hyphae

value: khd4 deletion

value: switch from yeast to hyphal growth

value: 9 hours post induction


title: TO_64N_8

value: Plasma

value: control


title: CordBlood, PND0, SGA9


title: TO_56T_8

value: case


title: khd4D filament RNAseq replicate 1


title: CordBlood, PND0, SGA8


title: R16_m3HIMφ

value: Hippocampus

value: Macrophages

value: 3 days

value: Hypoxia


title: TO_55T_8


title: wildtype filament RNAseq replicate 3

value: wildtype


title: R18_m3HIMφ


title: TO_52T_8


title: CordBlood, PND0, SGA5

value: Cord Blood


title: R28_f3HIMφ

value: female


title: TO_54T_8


title: CordBlood, PND0, SGA3


title: R26_f3HIMφ


title: khd4D yeast RNAseq replicate 3

value: yeast


title: CordBlood, PND0, SGA2

value: SGA


title: BI_11N_8


title: TO_49N_8


title: khd4D yeast RNAseq replicate 1

value: AB33 khd4D


title: wildtype yeast RNAseq replicate 3


title: R27_f3HIMφ


title: wildtype yeast RNAseq replicate 2


title: CordBlood, PND0, LGA10

value: LGA


title: Rrm4-Gfp, Wildtype RNA control

source_name: AB33 Pcrg1: rrm4-gfp / rrm4delta

value: AB33 Pcrg1:rrm4-gfp / rrm4delta


title: CordBlood, PND0, SGA1


title: CordBlood, PND0, SGA14


title: R5_m1HIMφ

value: male

value: 1 day


title: TO_05N_8

value: Plasma


title: wildtype yeast RNAseq replicate 1


title: CordBlood, PND0, LGA9


title: TO_74N_8

value: control


title: R4_m1HIMφ


title: CordBlood, PND0, LGA8


title: R12_f1HIMφ


title: control-Ada, replicate 2

data_processing:
Briefly, RNA-seq reads were trimmed based on sequencing quality (Phred score) using Trimmomatic (version 0.39; Bolger et al., 2014). Specifically, reads with the Phred score of less than 25 were trimmed and removed when the read length fell below 19 nt.
The trimmed reads were then mapped to the U. maydis genome sequence and gene annotation using STAR (version 2.5.2b; Dobin et al., 2013), allowing reads that were mapped to exactly one location, had a minimum of 16 matched bases and contained no more than 7% mismatches per mapped length.
The A-to-G editing events on transcripts were identified using the wtRNA-RNA approach from the previously established hyperTRIBE pipeline. Uniquely mapped alignments in SAM format were loaded into a MySQL table with genomic coordinates.
The nucleotides at each position in the test mRNA libraries (Khd4-Ada-Gfp, control-Ada) were compared with those of the control mRNA library (WtRNA; Khd4-Gfp) to identify A-to-G editing sites.
Only editing events with a minimum of 20 read coverage and 5% editing were considered for further analysis.
Assembly: The bioinformatics analyses were based on the U. maydis 521 genome sequence (Ustilago_maydis.Umaydis521_2.0.dna_rm.chromosome.1) and the associated gene annotation (Ustilago_maydis.Umaydis521_2.0.41.gff3; both downloaded from http://ftp.ensemblgenomes.org/pub/fungi/release-53/fasta/ustilago_maydis/dna/; Kämper et al., 2006). We manually extended all genes by 300 nt on each side to include potential 5´ UTR and 3´ UTR regions which are not currently annotated in the U. maydis genome. The extended GTF file was converted to refFlat format using the UCSC gtfToGenePred tool.
Supplementary files format and content: bedgraph files containing the information about all detected editing  sites (A-to-G mutation) for each protein (Khd4-Ada-Gfp and control-Ada) and replicate.

source_name: AB33 Pcrg1: khd4-ada-gfp / khd4{delta}

value: AB33 Pcrg1:khd4-ada-gfp / khd4{delta}


title: Khd4-Gfp, Wildtype RNA control

source_name: AB33 Pcrg1: khd4-gfp / khd4{delta}

value: AB33 Pcrg1:khd4-gfp / khd4{delta}


title: R11_f1HIMφ

value: Hippocampus

value: Macrophages


title: control-Ada, replicate 1


title: CordBlood, PND0, LGA6


title: R10_f1HIMφ

value: Hypoxia


title: TO_42T_8

value: case


title: CordBlood, PND0, LGA7

value: Cord Blood


title: CordBlood, PND0, LGA5


title: G12_m3HIµg

description: Hippocampal microglia age P12, 3 days after hypoxia

value: Microglia

value: 3 days


title: TO_57T_8


title: TO_49T_8


title: Khd4-Ada-Gfp, replicate 1

source_name: AB33 Pcrg1:kat-ada-gfp

value: AB33 Pcrg1:kat-ada-gfp


title: TO_66N_8


title: CordBlood, PND0, LGA3


title: TO_25T_8


title: Khd4-Ada-Gfp, replicate 2


title: CordBlood, PND0, AGA20

value: AGA


title: CordBlood, PND0, AGA19


title: 16 DAP seed maternal tissues replicate 3 [97742_SMT_16_REP3]

description:
raw_counts.txt
TPM_counts.txt

data_processing:
Illumina RTA3 was used for basecalling and .cbcl files were converted to .fastq using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence and low-quality sequence and then mapped to Morex v3 whole genome using hisat2 v2.1.0 with default parameters. Hisat2 output was converted and sorted by samtools view and samtools sort, respectively.
The number of reads falling in the exons of transcripts were counted using subread v1.5.2 with parameters -p -t exon -g Parent.
Transcripts Per Million (TPM) were calculated in R using standard formula.
Assembly: Mascher, Martin, et al. "Long-read sequence assembly: a technical evaluation in barley."The Plant Cell33.6 (2021): 1888-1906.
Supplementary files format and content: Tab-delimited text file including RAW counts for each Sample
Supplementary files format and content: Excel table including RAW counts for each Sample, calculated mean, standard deviation and transcript per million values

source_name: seed maternal tissues

growth_protocol: Seeds of six-rowed spring barley Hordeum vulgare cv. Morex were germinated for 3 days at 25 ° and then moved into the peat pots containing mixture of soil and sand. Plants were grown in climatic chamber under long-day regime (16 h day 20 °C, 8 h night 16 °C; humidity 60 %). After 10 days plants were transfered into 15 x 15 cm pots containing the same soil and cultivated in the same conditions until flowering.

extract_protocol:
Total RNA was isolated using Rneasy(R) Plant Mini Kit (QIAGEN) and Spectrum ™ Plant Total RNA Kit (Sigma-Aldrich) according to the manufacturer's instructions including on-column DNase I (Sigma-Aldrich) treatment and stored at -80 °C until use.
The RNA quality was checked using Bioanalyzer 2100 with RNA 6000 Pico Chips (all Agilent) and samples with RNA integrity number > 6.8 were processed into RNA-Seq mRNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® with poly-A selection.
The polyA RNA-enriched libraries were sequenced as single end 100-bp RNA seq reads on the HiSeq2500 instrument (Illumina) at Vienna BioCenter.

value: seed maternal tissues

value: 16 days after pollination

value: Morex


title: 16 DAP seed maternal tissues replicate 2 [97741_SMT_16_REP2]

description:
raw_counts.txt
TPM_counts.txt


title: CordBlood, PND0, AGA16


title: G22_f3HIµg

value: female


title: G14_m3HIµg

value: male


title: CordBlood, PND0, LGA4

value: LGA


title: 24 DAP seed maternal tissues replicate 3 [97745_SMT_24_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: 24 days after pollination


title: TO_35T_7

value: Plasma


title: 16 DAP seed maternal tissues replicate 1 [97740_SMT_16_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: CordBlood, PND0, AGA15


title: TO_33T_7


title: TO_57N_7

value: control


title: G16_m3HIµg

value: Hippocampus


title: TO_63N_7


title: 24 DAP seed maternal tissues replicate 2 [97744_SMT_24_REP2]

description:
raw_counts.txt
TPM_counts.txt


title: CordBlood, PND0, LGA2


title: G28_f3HIµg

value: Hypoxia


title: TO_38N_7


title: 24 DAP seed maternal tissues replicate 1 [97743_SMT_24_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: G26_f3HIµg


title: TO_37T_7

value: case


title: CordBlood, PND0, AGA7

value: Cord Blood


title: 4 DAP seed maternal tissues replicate 3 [89201_SMT_04_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: 4 days after pollination


title: TO_53T_7


title: G20_f3HIµg

value: Microglia

value: 3 days


title: G1_m3Nµg

description: Hippocampal microglia age P12


title: 4 DAP seed maternal tissues replicate 1 [89199_SMT_04_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: TO_51N_7


title: CordBlood, PND0, AGA3

value: AGA


title: G7_f3Nµg

description: Hippocampal microglia age P12


title: CordBlood, PND0, AGA2


title: 32 DAP embryo replicate 2 [104714_EMB_32_REP2]

description:
raw_counts.txt
TPM_counts.txt

source_name: embryo

value: embryo

value: 32 days after pollination


title: TO_43T_7


title: G6_m1HIµg

description: Hippocampal microglia age P10, 1 day after hypoxia

value: 1 day


title: 24 DAP embryo replicate 3 [97733_EMB_24_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: Morex


title: Colorectal Carcinoma patient 60 years old, Tumor tissue

city: Kolkata

first: Sudarshana

last: Basu

state: West Bengal

address: 3081, Nayabad, New Garia

department: Molecular Biology

country: India

institute: Netaji Subhash Chandra Bose Cancer Research Institute

data_processing:
pipeline FastQC-Fastp-SortMeRNA-miRDeep2-edgeR
Total twenty fastq files were subjected to Fastqc (v.0.11.9) for the sequence quality check
Fastp (v.0.23.2) was used to trim adapter sequences.
Reads of every samples were subjected to SortMeRNA (v.4.3.2) for removal of ribosomal RNA sequences. Four data bases, silva-euk-28s-id98, silva-euk-18s-id95, rfam-5.8s-database-id98 and rfam-5s-database-id98 were utilized in the rRNAs removal analysis (https://github.com/biocore/sortmerna/archive/2.1.tar.gz).
Read mappings of small RNA-seq data were performed by miRDeep2 (v.2.0.1.2) using a genome reference sequence Homo_sapiens.GRCh38.dna.primary_assembly.fa along with mature and hairpin miRNAs sequences specific to human (hsa as a species) retreived from the miRBase (v22.1) database (https://www.mirbase.org/ftp.shtml).
Processed reads were used to generate collapsed reads using mapper.pl module of the  miRDeep2 package with minimum length 18 parameter. For predicting miRNAs, known and novel, the collapsed reads were passed to miRDeep2.pl module of the package.
Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes count for each sample normalized by the Count Per Million (CPM) method

source_name: Tumor tissue

growth_protocol: Colon tumour and normal colonic mucosa tissues were collected in RNALater and stored at -80°C till RNA extraction.

extract_protocol:
Total RNA isolation was performed using the Qiagen AllPrep® DNA/RNA/miRNA Universal kit as per manufacturers’ protocol. Elution was done in Nuclease free water.
1 µg total RNA  was proceeded for library preparation using the NEBNext® Small RNA Library Prep Set for Illumina®. Adapters in this kit are directly, and specifically, ligated to miRNAs. This was followed by reverse transcription to double stranded cDNA, PCR amplification, and pooled gel purification to generate a library product.

treatment_protocol: RNA isolation was performed from fresh frozen colorectal (tumour and normal) tissues stored in RNALater at -80°C.

value: Tumor tissue

value: female

tag: tumor stage

tag: tumor grade

tag: histopathological type

value: adenocarcinoma

tag: location

value: Rectum


title: G5_m1HIµg

value: male


title: TO_48T_7

value: Plasma


title: G18_f3HIµg

value: Hippocampus

value: Hypoxia


title: 8 DAP seed maternal tissues replicate 3 [88541_SMT_08_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: seed maternal tissues

value: 8 days after pollination


title: Colorectal Carcinoma patient 66 years old, Normal colonic mucosa

source_name: Normal colonic mucosa

value: Normal colonic mucosa

value: normal colonic mucosa


title: CordBlood, PND0, AGA14

value: Cord Blood

value: AGA


title: TO_58T_7

value: case


title: G4_m3Nµg

description: Hippocampal microglia age P12

value: Microglia

value: 3 days


title: 8 DAP seed maternal tissues replicate 2 [89203_SMT_08_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: Morex


title: Colorectal Carcinoma patient 47 years old, Tumor tissue

value: Tumor tissue

value: Ascending colon and cecum


title: CordBlood, PND0, AGA9


title: G23_f1HIµg

value: female

value: 1 day


title: TO_45T_7

value: Plasma


title: G3_m3Nµg

description: Hippocampal microglia age P12

value: Hippocampus

value: male


title: BI_05N_7

value: control


title: 8 DAP seed maternal tissues replicate 1 [89202_SMT_08_REP1]

description:
raw_counts.txt
TPM_counts.txt

value: seed maternal tissues

value: 8 days after pollination


title: 16 DAP embryo replicate 2 [83691_EMB_16_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: embryo

value: 16 days after pollination


title: TO_53N_7


title: CordBlood, PND0, AGA6

value: Cord Blood

value: AGA


title: G2_m3Nµg

description: Hippocampal microglia age P12

value: Microglia


title: TO_40N_6


title: G10_f1HIµg

value: Hypoxia


title: 16 DAP embryo replicate 1 [83690_EMB_16_REP1]

description:
raw_counts.txt
TPM_counts.txt

value: Morex


title: 8 DAP embryo replicate 3 [88539_EMB_08_REP3]

description:
raw_counts.txt
TPM_counts.txt


title: G30_m1Nµg

description: Hippocampal microglia age P10


title: 4 DAP seed maternal tissues replicate 2 [89200_SMT_04_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: 4 days after pollination


title: TO_01N_7


title: Colorectal Carcinoma patient 44 years old, Normal colonic mucosa

value: Normal colonic mucosa

value: normal colonic mucosa

value: Rectosigmoid colon


title: CordBlood, PND0, AGA4


title: Colorectal Carcinoma patient 39 years old, Tumor tissue

value: Tumor tissue

value: female

value: adenocarcinoma

value: Junction of ascending and transverse colon


title: G8_f3Nµg

description: Hippocampal microglia age P12

value: Hippocampus

value: 3 days


title: TO_30N_6

value: Plasma

value: control


title: BI_23N_6


title: TO_50T_7

value: case


title: 32 DAP embryo replicate 3 [104715_EMB_32_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: embryo

value: 32 days after pollination


title: G6_f3Nµg

description: Hippocampal microglia age P12

value: Microglia


title: TO_44T_7


title: CordBlood, PND0, AGA1

value: Cord Blood

value: AGA


title: 32 DAP endosperm replicate 2 [104711_END_32_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: endosperm

value: Morex


title: G5_f3Nµg

description: Hippocampal microglia age P12


title: 32 DAP embryo replicate 1 [104713_EMB_32_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: 32 DAP endosperm replicate 1 [104710_END_32_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: TO_73N_7


title: HUVEC-CVA10-0h

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

data_processing:
clean reads were screened from the raw reads
sequences 18~35 nt long from the clean reads of each sample were matched to the reference genome via Bowtie V1.1.2
Mapped reads were further mapped to Rfam database (http://rfam.xfam.org, version 11.0) and RepeatMasker, and the protein-coding genes, repeat sequences, ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs) were discovered
remaining small RNA reads were further aligned to the miRNA precursors of the reference species in the miRBase 21.0 database (http://www.mirbase.org/) to identify known miRNA, and also aligned to miReap program (http://sourceforge.net/projects/mireap/) to predict potential novel miRNAs
Supplementary files format and content: microsoft excel files include raw counts for each sample
Supplementary files format and content: microsoft excel files include TPM values for each sample

source_name: umbilical cord

growth_protocol: HUVECs were acquired from American Type Culture Collection (ATCC) and grown in Roswell Park Memorial Institute-1640 (RPMI-1640; Corning, USA) supplemented with heat-inactivated 10% fetal bovine serum (FBS; Gibco®, USA) plus 100 μg/ml penicillin and streptomycin at 37°C in a humid incubator with 5% carbon dioxide (CO2).

extract_protocol:
Three replicates of CV-A10-infected cells at different time were mixed together and used for RNA extraction. In brief, total RNA isolation was conducted using a TRIzol™ reagent (Invitrogen, USA) according to manufacturer’s guidelines. The concentration of total RNA was determined using a NanoDrop 2000 spectrophotometer. The RNA purity and the RNA integrity number (RIN) were assessed using an Agilent 2100 bioanalyzer. When the extracted RNA reached “An RIN score≥7.0 and rRNA 28S/18S≥1.6”, it was required in the following study.
Total RNA was purified by polyacrylamide gel electrophoresis (PAGE) to enrich 15~35 nt molecules, then proprietary adapters were ligated to the 5’ and 3’ terminal of the RNA and the samples were used as templates for cDNA synthesis. The cDNA was amplified using the appropriate number of PCR cycles to produce sequencing libraries, which were subsequently subjected to the proprietary Solexa sequencing-by-synthesis method using the Illumina Genome Analyzer (SanDiego, USA). Sequencing was carried out at the ANOROAD Genome Inc. (Beijing, China).

treatment_protocol: For virus infection, single-cell suspension at a density of 5 × 105 cells/ml was added into 6-well plates. When the cells were reached 80% confluences, the cells were incubated with CV-A10 (sub-genotype C, GenBank: MN557275), which isolated from an epidemic in Xiangyang, China, in 2017, at a multiplicity of infection (MOI) of 1 at 37°C for 2 h absorption. Subsequently, the infected-cells were continued to culture in RPMI-1640 containing 2% FBS and antibiotics at 37 °C in an atmosphere of 5% CO2, and collected with a cell scraper at 0, 24 and 72 h. Cells infected with CV-A10 at 0 hpi were regarded as control.

value: umbilical cord

tag: cell line

value: HUVEC

value: umbilical vein endothelial cells

value: WT


title: HUVEC-CVA10-24h

tag: tissue

value: CV-A10 infection 24h


title: Expt3_bud7_lowP_rep3

city: Auckland

first: Zhiwei

last: Luo

state: Auckland

address: 120 Mt Albert Road

country: New Zealand

institute: PLANT AND FOOD RESEARCH

data_processing:
nf-core (https://nf-co.re/rnaseq, version 1.4.2 for experiment 1 and version 3.0 for experiment 3)
Trim Galore (https://github.com/FelixKrueger/TrimGalore)
FastQC
STAR aligner (https://github.com/alexdobin/STAR)
Salmon
Assembly: Petunia axillarisdraft genome sequence v1.6.2

organism: Petunia x hybrida

source_name: axillary buds

growth_protocol: hydroponic

extract_protocol:
sigma spectrum plant RNA kit
mRNA library

value: axillary buds

value: 5 uM phosphate


title: 24 DAP endosperm replicate 3 [88543_END_24_REP3]

description:
raw_counts.txt
TPM_counts.txt

source_name: endosperm

value: 24 days after pollination


title: TO_24N_6

value: Plasma

value: control


title: Expt3_bud7_lowP_rep2


title: Colorectal Carcinoma patient 60 years old, Normal colonic mucosa

value: Normal colonic mucosa

value: female

value: normal colonic mucosa

value: Rectum


title: TO_40T_7

value: case


title: TO_36N_6


title: NIP-Input

city: Wuhan

first: Qingxiao

last: Jia

state: Hubei

address: No.1,Shizishan Street

institute: HZAU

data_processing:
RNA-Seq
The RNA-seq clean data were mapped against the MSU version 7.0 rice genome with the corresponding annotation by hisat2 using default parameters
FeatureCounts (v2.0.0)and DESeq2 (v1.26.0)were used to calculate DEGs.
ChIP-Seq
the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15.
The ChIP clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
The DESeq2 method implemented in DiffBind was used to test the differential peak
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: tab-delimited text file include counts for each Sample
Supplementary files format and content: bigWig, broadPeak,narrowPeak (except for Input sample)

organism: Oryza sativa Japonica Group

source_name: seedling

extract_protocol:
Genomic DNA was extracted using DNeasy plant mini kit (QIAGEN, Germany) according to the manufacturer’s instructions.
ChIP DNA libraries were prepared using a TruSeq DNA Sample Preparation Kit v2 (Illumina, San Diego, CA, USA)

value: seedling

tag: chip antibody


title: 24 DAP embryo replicate 2 [83683_EMB_24_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: embryo

value: Morex


title: Colorectal Carcinoma patient 66 years old, Tumor tissue

value: Tumor tissue

value: male

value: adenocarcinoma


title: G4_m1HIµg

value: Hippocampus

tag: cell type

value: Microglia

value: 1 day

value: Hypoxia


title: 16 DAP endosperm replicate 3 [89204_END_16_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: endosperm

value: 16 days after pollination


title: TO_35N_6

value: Plasma

value: control


title: alkbh1-Anti-ALKBH1-1

value: ALKBH1 knockout


title: 24 DAP embryo replicate 1 [83682_EMB_24_REP1]

description:
raw_counts.txt
TPM_counts.txt

value: 24 days after pollination


title: 16 DAP endosperm replicate 2 [83681_END_16_REP2]

description:
raw_counts.txt
TPM_counts.txt


title: TO_30T_6

value: case


title: G24_f1HIµg

value: female


title: 16 DAP embryo replicate 3 [88542_EMB_16_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: embryo


title: Colorectal Carcinoma patient 47 years old, Normal colonic mucosa

value: Normal colonic mucosa

value: normal colonic mucosa

value: Ascending colon and cecum


title: Colorectal Carcinoma patient 44 years old, Tumor tissue

value: Tumor tissue

value: adenocarcinoma

value: Rectosigmoid colon


title: G60_m1Nµg

description: Hippocampal microglia age P10

value: Hippocampus

value: Microglia

value: male

value: 1 day


title: TO_16T_6

value: Plasma


title: TO_15T_6


title: 8 DAP embryo replicate 2 [83687_EMB_08_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: 8 days after pollination

value: Morex


title: 8 DAP embryo replicate 1 [83686_EMB_08_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: Colorectal Carcinoma patient 39 years old, Normal colonic mucosa

value: Junction of ascending and transverse colon


title: G10_m1Nµg

description: Hippocampal microglia age P10


title: G70_f1Nµg

description: Hippocampal microglia age P10


title: 8 DAP endosperm replicate 3 [88540_END_08_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: endosperm


title: HUVEC-CVA10-72h

value: umbilical cord

value: HUVEC

value: umbilical vein endothelial cells

value: WT

value: CV-A10 infection 72h


title: Expt3_bud3_lowP_rep2

value: axillary buds

value: 5 uM phosphate


title: BI_06N_6

value: control


title: G50_f1Nµg

description: Hippocampal microglia age P10

value: Hippocampus

value: female


title: TO_33N_6


title: NIP-Anti-ALKBH1-1

value: seedling


title: 32 DAP endosperm replicate 3 [104712_END_32_REP3]

description:
raw_counts.txt
TPM_counts.txt

value: 32 days after pollination


title: alkbh1-6mA-Input

data_processing:
RNA-Seq
The RNA-seq clean data were mapped against the MSU version 7.0 rice genome with the corresponding annotation by hisat2 using default parameters
FeatureCounts (v2.0.0)and DESeq2 (v1.26.0)were used to calculate DEGs.
ChIP-Seq
the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15.
The ChIP clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
The DESeq2 method implemented in DiffBind was used to test the differential peak
Assembly: MSU version 7.0 rice genome
Supplementary files format and content: tab-delimited text file include counts for each Sample
Supplementary files format and content: bigWig, broadPeak,narrowPeak (except for Input sample)
Library strategy: 6mA-seq

value: ALKBH1 knockout


title: TO_48N_6

value: Plasma


title: G40_f1Nµg

description: Hippocampal microglia age P10

value: Microglia

value: 1 day


title: alkbh1-Input


title: 24 DAP endosperm replicate 2 [83685_END_24_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: endosperm

value: 24 days after pollination

value: Morex


title: Expt3_bud7_lowP_rep1


title: 24 DAP endosperm replicate 1 [83684_END_24_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: TO_47T_6

value: case


title: Expt3_bud6_lowP_rep3


title: alkbh1-Anti-ALKBH1-2


title: Expt3_bud6_lowP_rep2


title: 4 DAP endosperm replicate 2 [102866_END_04_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: 4 days after pollination


title: Expt3_bud2_lowP_rep1


title: TO_31T_6


title: Expt3_bud6_lowP_rep1


title: NIP-IgG-2

value: WT


title: alkbh1-6mA-1


title: TO_42N_6


title: 16 DAP endosperm replicate 1 [83680_END_16_REP1]

description:
raw_counts.txt
TPM_counts.txt

value: 16 days after pollination


title: Expt3_bud7_highP_rep3

value: axillary buds

value: 250 uM phosphate


title: TO_36T_5


title: Expt3_bud7_highP_rep1


title: Expt3_bud6_highP_rep3


title: Expt3_bud3_lowP_rep3

value: 5 uM phosphate


title: TO_29T_6


title: NIP-IgG-1


title: BI_15T_5


title: dox off-ffmA, +dox, biol rep1, tech rep1,2

city: Iowa City

first: Scott

last: Moye-Rowley

state: Iowa

address: 6-530 Bowen Science Bldg./Dept. of Mol Physio

department: Molecular Physiology & Biophysics

institute: University of Iowa

data_processing:
Paired end reads were mapped to the Af293 A. fumigatus genome using HISAT2.  Transcript assembly, quantification of expression levels and analysis of differential expression were done using Stringtie and the DESeq2 R package. Bigwig files were generated using the GenomicAlignments and rtracklayer R packages
Assembly: FungiDB-47_AfumigatusAf293_Genome.fasta (from FungiDB-2020)
Supplementary files format and content: BigWig files corresponding to read depth for RNA-seq

organism: Aspergillus fumigatus

growth_protocol: Cell lysates were prepared from mycelial biofilm cultures formed upon inoculating 1X10^6 spores in a petri dish containing 20 ml of Sabouraud dextrose broth and grown for 24 hours at 37°C under non-shaking conditions.

extract_protocol:
Mycelia that formed as a biofilm on the top were collected (∼100 mg) and ground into a fine powder in liquid nitrogen using a mortar and pestle. Total RNA was then isolated from the ground mycelium using the Trizol reagent (Ambion) according to the manufacturer's instructions. Total RNA was isolated and purified using an RNeasy minikit (Qiagen). Traces of contaminating genomic DNA were eliminated by treating the RNA with turbo DNase followed by a DNase inactivation reagent (both reagents from Ambion).
Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina, Inc., San Diego, CA) and following Illumina's sample preparation guide, started with 500ng of input total RNA.

value: dox off-ffmA

value: "+dox"


title: NIP-Anti-ALKBH1-2

value: seedling


title: 8 DAP endosperm replicate 2 [83689_END_08_REP2]

description:
raw_counts.txt
TPM_counts.txt

value: 8 days after pollination


title: TO_69N_6

value: Plasma

value: control


title: Expt3_bud3_lowP_rep1


title: TO_67N_6


title: 8 DAP endosperm replicate 1 [83688_END_08_REP1]

description:
raw_counts.txt
TPM_counts.txt


title: NIP-H3K27me3-2


title: Expt3_bud6_highP_rep2


title: Expt3_bud2_lowP_rep3


title: 4 DAP endosperm replicate 3 [102867_END_04_REP3]

description:
raw_counts.txt
TPM_counts.txt


title: NIP-H3K27me3-1


title: alkbh1-6mA-2

value: ALKBH1 knockout


title: Expt3_bud3_highP_rep3


title: TO_46N_6


title: OEALKBH1-RNA-seq-2

extract_protocol:
Total RNA was extracted from the indicated tissues using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s protocol.
RNA-seq library construction using the TruSeq RNA Library Preparation Kit (Illumina, USA), according to the manufacturer’s recommendations.

value: ALKBH1 overexpression


title: 4 DAP endosperm replicate 1 [102865_END_04_REP1]

description:
raw_counts.txt
TPM_counts.txt

value: endosperm


title: NIP-6mA-Input


title: dox off-ffmA, +dox, biol rep3, tech rep1,2


title: Expt3_bud7_highP_rep2


title: Wild-type, biol rep2, tech rep1,2

value: wild-type


title: NIP-6mA-2


title: BI_19N_5


title: dox off-ffmA, +dox, biol rep2, tech rep1,2


title: Wild-type, biol rep1, tech rep1,2


title: alkbh1-RNA-seq-2


title: NIP-6mA-1


title: TO_34T_5

value: case


title: Expt3_bud2_highP_rep3


title: alkbh1-H3K27me3-2


title: dox off-ffmA, no dox, biol rep3, tech rep1,2

value: "-dox"


title: alkbh1-H3K27me3-1


title: TO_19N_5


title: alkbh1-RNA-seq-1


title: dox off-ffmA, no dox, biol rep2, tech rep1,2


title: dox off-ffmA, no dox, biol rep1, tech rep1,2


title: Expt3_bud6_highP_rep1


title: BI_17T_5


title: Expt1_bud7_lowP_rep3


title: SPF185, No primary antibody, rep1

data_processing:
Reads were mapped using HISAT2 software and peaks assigned using MACS2.  Peak annotation was done using ChIPpeakAnno R package. Bigwig files were generated using the GenomicAlignments and rtracklayer R packages and visualized using IGV software.
Assembly: FungiDB-47_AfumigatusAf293_Genome.fasta (from FungiDB-2020)
Supplementary files format and content: BigWig files showing sequencing depth across the genome.

growth_protocol: 1×106spores/mL ofA.fumigatusstrains AfS35 or SPF185 (dox off-FLAG-ffmA) were grown in 50 mL of Sabouroud dextrose medium in 250 mL shaking flask cultures for 16 h.

extract_protocol:
Cross linked mycelia were harvested and then ground after freezing in liquid nitrogen. Samples were hydrated in ChIP lysis buffer (CLB: 50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Deoxycholate (Sigma D6750), 0.1% SDS, 1 mM PMSF, 1× fungal proteinase inhibitor cocktail (Sigma)), then sheared using Covaris sonication. Sheared chromatin was precipitated withanti-FfmA or anti-FLAG (Sigma)antibodies and recovered using magnetic beads. Cross links were reversed and DNA recovered for library preparation.
Libraries were generated using the Rubicon ThruPlex DNAseq kit as described by the supplier.

value: Dox off-FLAG-ffmA


title: TO_34N_5


title: TO_28N_5


title: Wild-type, biol rep3, tech rep1,2


title: Wild-type, anti-FfmA, rep2


title: TO_32N_5


title: NIP-RNA-seq-1

value: WT


title: Expt3_bud3_highP_rep2

value: axillary buds


title: Expt3_bud2_lowP_rep2


title: OEALKBH1-RNA-seq-1


title: Expt1_bud3_lowP_rep3


title: Expt3_bud3_highP_rep1

value: 250 uM phosphate


title: TO_07T_5


title: Wild-type, anti-FfmA, rep1


title: Expt3_bud2_highP_rep2


title: SPF185, anti-FLAG antibody, rep2


title: TO_03T_5


title: SPF185, anti-FLAG antibody, rep1


title: SPF185, No primary antibody, rep2


title: NIP-RNA-seq-2


title: Expt1_bud7_lowP_rep2

value: 5 uM phosphate


title: TO_24T_5


title: TO_23T_5


title: Expt3_bud2_highP_rep1


title: Expt1_bud6_lowP_rep3


title: Wild-type, No primary antibody, rep1


title: Mp, Mpb-gata1-2, rep3

first: Peter

last: Schröder

address: Emil-Ramann-Straße 8, Gebäude 4223

institute: Technical University of Munich

data_processing:
CLC Genomics Workbench v20.0.2
Sequence reads were trimmed using CLC Genomics Workbench - Quality limit: 0.05.
Trimmed sequence reads were mapped to the MpTak1v5.1 release of Marchantia polymorpha Tak1 genome using CLC Genomics Workbench - Mismath cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.5, Similarity fraction: 0.8.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: MpTak1v5.1 release of Marchantia polymorpha Tak1.
Supplementary files format and content: Tab-delimited text files, including TPM.

source_name: 3 weeks old thallus; entire plants (1 replicate = 3 plants)

growth_protocol: BoGa, Mpb-gata1-1 and Mpb-gata1-2 were grown on 1/2 Gamborg's B5 medium in long day conditions (16L/8D) at 40 µmol m-2 s-1 and 22°C for three weeks.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit (Macherey-Nagel).
TruSeq stranded mRNA Kit (Illumina, San Diego, USA) with TruSeq RNA Adapter Box Set B (Illumina, San Diego, USA) and protocol 1000000040498v00 (Elution-2-Frag-Prime step: 4 minutes at 94°C; 15 cycles enrichment).

treatment_protocol: No treatment was performed.

tag: age

value: 3 weeks old

value: thallus

value: Mpb-gata1-2 mutant


title: Expt1_bud3_lowP_rep2


title: TO_9N_4


title: TO_28T_5


title: Expt1_bud2_lowP_rep3


title: TO_27T_5


title: TO_38T_5


title: Tet2KO ctl rep 1 batch 1 [SJ4-2]

city: Boston

first: Philipp

last: Rauch

state: MA

address: 450 Brookline Ave

institute: DFCI

data_processing:
Reads were mapped to the Mus musculus mm10 reference genome with the CLC Genomics Server program v. 9.0.1. Normalized read counts were obtained from the resulting BAM files using the BiocLite (https://bioconductor.org/biocLite.R) package in R.
Assembly: mm10
Supplementary files format and content: .csv, normalized read counts

source_name: BMDM

growth_protocol: Single cell suspensions from murine whole bone marrow from 10-14 week old mice were differentiated for 6 days in the presence of 10 ng/ml of mM-CSF.

extract_protocol:
Trizol followed by RNeasy Mini columns (Qiagen) followed by DNase (Life Technologies) treatment and Ribo-Zero Kit (Illumina).
Library preparation using poly-A selection, multiplexing, and sequencing were done by Genewiz (South Plainfield, NJ).

treatment_protocol: Day 6 BMDM were allowed to rest for 24h after replating, followed by stimulation with 200 mg/dL of LDL or vehicle control.

value: BMDM

tag: genotype

value: ctl


title: Tet2KO ctl rep 2 batch 1 [SJ5-2]

tag: treatment


title: Tet2KO ctl rep 3 batch 1 [SJ6-2]


title: Tet2KO LDL rep 2 batch 1 [SJ15-2]

value: LDL


title: Tet2KO LDL rep 1 batch 1 [SJ14-2]


title: TO_12T_4

source_name: Plasma

value: Plasma


title: BI_25N_4

value: control


title: WT ctl rep 3 batch 1 [SJ3-2]


title: Wild-type, No primary antibody, rep2


title: TO_22N_5


title: Expt1_bud6_lowP_rep2


title: Mp, Mpb-gata1-1, rep2

city: Freising

value: Mpb-gata1-1 mutant


title: TO_07N_5


title: Mp, Mpb-gata1-2, rep2


title: Expt1_bud2_lowP_rep2


title: Expt1_bud6_lowP_rep1


title: WT LDL rep 2 batch 1 [SJ11-2]


title: Mp, Mpb-gata1-1, rep3


title: Expt1_bud7_lowP_rep1


title: BI_19T_4


title: WT ctl rep 2 batch 1 [SJ2-2]


title: Mp, Mpb-gata1-2, rep1


title: WT LDL rep 1 batch 1 [SJ10-2]


title: Jak2VF LDL rep 3


title: WT ctl rep 1 batch 1 [SJ1-2]


title: Mp, Mpb-gata1-1, rep1


title: TO_29N_4


title: Expt1_bud3_lowP_rep1


title: Expt1_bud6_highP_rep3


title: Jak2VF ctl rep 3


title: Expt1_bud2_lowP_rep1


title: TO_11T_4


title: Mp, BoGa, rep3

value: BoGa (WT)


title: Jak2VF LDL rep 2


title: Expt1_bud7_highP_rep3


title: TO_22T_4

value: case


title: TO_9T_4


title: Mp, BoGa, rep2


title: Jak2VF ctl rep 2


title: Jak2VF ctl rep 1


title: Spared lumbar area of injured spinal cord, LOCS, 6 months

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting  were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: snRNA-seq

molecule: nuclear RNA

organism: Macaca mulatta

source_name: spinal cord

extract_protocol:
For cell preparation, tissues were digested using a papain dissociation system according to the manufacturer’s protocol (LS003126, Worthington). Spinal cords were roughly cut into small pieces and then incubated in papain solution containing DNase I at 37℃ for 1-1.5 h with occasional pipetting. Albumin-ovomucoid inhibitor solution was used to terminate the enzymatic reaction. Subsequently, the cell suspension was further pipetted to generate a single-cell suspension, which was centrifuged at 400 g for 5 min to obtain a cell pellet. Then the cell pellet was resuspended with 20% Percoll (P1644, Sigma) and centrifuged at 400 g for 10 min to remove myelin debris. The cells were resuspended in PBS with 0.04% BSA.  For nuclei extract, the spinal cord was dissociated and homogenized using a glass dounce tissue grinder (D8938, Sigma) in cold Nuclei EZ lysis buffer (NUC101-1KT, Sigma) on ice. The lysate was then diluted with cold sucrose buffer and centrifuged for cell debris removal. Nuclei deposited on the tube wall were suspended in Nuclei Suspension Buffer consisting of 1xPBS and 0.01% BSA and 0.1% RNase inhibitor (2313A, TaKaRa).
Cells and nuclei were processed using Chromium Single Cell V3 Chemistry Library Kits (10xGenomics) according to the manufacturer's instructions. In brief, nuclei were partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller, followed by full-length cDNA generated, barcoded, and sequenced on an Illumina NovaSeq 6000.

value: tissue

value: spinal cord

value: female

value: 4-7 years old

tag: developmental stage

value: adult

value: complete spinal cord injury+LOCS


title: Spared but activated area of injured spinal cord, 30 days, rep2

description: 10x Genomics

value: complete spinal cord injury


title: Tet2KO LDL rep 3


title: TO_18T_4


title: Spared but activated area of injured spinal cord, 14 days, rep1

description: 10x Genomics


title: Expt1_bud3_highP_rep3

value: axillary buds

value: 250 uM phosphate


title: Jak2VF LDL rep 1

value: BMDM


title: Expt1_bud3_highP_rep2


title: TO_6T_4


title: Spared but activated area of injured spinal cord, 14 days, rep2

description: 10x Genomics


title: Spared but activated area of injured spinal cord, 7 days, rep2

description: 10x Genomics


title: Tet2KO ctl rep 3

value: ctl


title: Expt1_bud7_highP_rep1


title: Mp, BoGa, rep1

value: 3 weeks old

value: thallus


title: BI_4N_3

value: Plasma

value: control


title: Expt1_bud6_highP_rep1


title: Spared but activated area of injured spinal cord, 7 days, rep1

description: 10x Genomics


title: Tet2KO ctl rep 1


title: Expt1_bud2_highP_rep2


title: Degenerative area of injured spinal cord, 6 months

description: 10x Genomics


title: Expt1_bud2_highP_rep3


title: TO_19T_4


title: TO_20T_4


title: Dnmt3aKO LDL rep 3

value: LDL


title: Expt1_bud6_highP_rep2


title: Dnmt3aKO LDL rep 2


title: TO_17N_3


title: TO_8N_3


title: Dnmt3aKO LDL rep 1


title: Degenerative area of injured spinal cord, 14 days, rep2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting  were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: Tet2KO LDL rep 2


title: TO_5T_3

value: case


title: TO_4T_3


title: BI_12N_3


title: Degenerative area of injured spinal cord, 30 days, rep1

description: 10x Genomics

value: tissue