title: sid2_360_NHP_rep2

city: Stanford

first: Mary Beth

last: Mudgett

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

data_processing:
Read data was initially assessed using FastQC. CLC Genomics Workbench version 11.0.2 (QIAGEN) was used for trimming adaptors and low-quality bases, reads trimmed below 20 bp were discarded, reads were then mapped to the Arabidopsis TAIR10 genome with the auto-detect paired distances option deselected. Raw count data was exported from CLC Genomics Workbench.
Assembly: TAIR10
Supplementary files format and content: comma-separated values file includes raw counts for each sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seeds were surface sterilized and stratified at 4°C in darkness for 3 days then placed into sterile six-well plates with half-strength Murashige and Skoog (MS) medium, 0.5% (w/v) sucrose, 0.05% (w/v) MES at pH 5.7. Plates were covered with a lid, sealed with micropore tape, and placed in a chamber on a 10 h light/14 h dark cycle. Liquid medium was agitated twice daily to facilitate gas exchange and after five days of growth, spent medium was replaced with fresh MS.

extract_protocol:
Total RNA was extracted from pooled seedlings using TRIsure™ reagent (Meridian Bioscience) according to the manufacturer’s instructions. 5 µg of total RNA was was used for cDNA library preparation.
The cDNA library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with NEBNext® Poly(A) mRNA Magnetic Isolation Module and then multiplexed via PCR amplification using NEBNext® Multiplex Oligos for Illumina® according to the manufacturer’s instructions (New England Biolabs). Library concentration was quantified with Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific) followed by measurement of quality and average cDNA length using the DNA 1000 Series II chip on a 2100 Bioanalyzer (Agilent Technologies). The multiplexed cDNA libraries were then pooled (two sets of 36 libraries) and sequenced using both lanes of the NovaSeq 6000 (Illumina) S1 flow cell with run type 100 bp paired-end reads at the Genome Sequencing Service Center by the Stanford Center for Genomics and Personalized Medicine.

treatment_protocol: At 10-days-post-germination, all liquid medium was removed from each well and fresh MS medium added. Seedlings were placed back into the growth chamber for an hour to acclimate. Whole seedlings were treated by the addition of a 2x solution of NHP (final concentration 0.5 mM) or mock (MS medium). Pooled seedlings from a single well were collected for each genotype, treatment, and time (15 min, 30 min, 3 h, and 6 h) combinations (n = 3), blotted dry, and flash frozen for mRNA isolation.

value: whole seedling

tag: ecotype

tag: timepoint

value: 360 min

value: NHP


title: CP-CTB_1347_5

status: Public on Aug 16 2024

type: SRA

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

description:
GeoMx spatial transcriptome sequencing
Normalized_Q3_Dataset2_060222_for_GEO.xlsx
Normalized_spatial_data.xlsx
rmorey_GNP_config.ini.txt
rmorey_LabWorksheet.csv
rmorey_SeqCodeIndices.csv

library_source: transcriptomic

data_processing:
Fastq files were converted into DCC files following the GeoMx NGS pipeline
DCC files were uploaded to the GeoMx DSP to generate the initial, spatially resolved, dataset
Gene counts were mapped to specific ROIs and normalized using Q3 normalization strategy in keeping with NanoString GeoMx recommendations. (https://nanostring.com/resources/introduction-to-geomx-normalization-cta-whitepaper/)
dcc-metadata = false; save-interim-files = false; quality-trim-score = 20; 2color-trimming = True; adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; adapter-trim-match-length = 10; adapter-trim-max-mismatch = 3; barcode-max-mismatch = 1; stitching-max-mismatch = 2; dedup-hd = 1; threads = 4
Assembly: GRCh38
Supplementary files format and content: Normalized_Q3_Dataset2_060222_for_GEO.xlsx - excel file with segment, target, and BioProbe properties along with the count matrix
Supplementary files format and content: Normalized_spatial_data.xlsx - excel file with normalized count matrix
Supplementary files format and content: rmorey_GNP_config.ini.txt - text file with process information, AOI list and target barcodes
Supplementary files format and content: rmorey_LabWorksheet.csv - csv file with sample ID and metadata
Supplementary files format and content: .dcc - digital count files
Supplementary files format and content: rmorey_SeqCodeIndices.csv - csv file with sample ID and i7 and i5 indexes
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: chorionic plate placenta

extract_protocol:
Sections were deparaffinized and incubated overnight with the Whole Transcriptomic Assay UV-cleavable biological probes according to manufacturer’s instructions. Samples were stained with CONFIRM® anti-EGFR (5B7) Rabbit Monoclonal Primary Antibody  (Ventana #790-4347, 1:20 dilution) and anti-HLA-G (4H48) mouse primary antibody (Abcam #ab52455, 1:1000 dilution) for 2 hours followed by secondary staining for 1h with Alexa Fluor anti-rabbit-647 (Life Technologies, 1:500 dilution), Alexa Fluor anti-mouse-594 (Life Technologies, 1:500 dilution), and SYTO13 (Nanostring, 1:10 dilution) for nuclei staining. Slides were scanned on a GeoMx digital spatial profiler machine r. Based on the morphology markers, areas of interest (AOIs) containing at least EGFR+/HLA-G- 100 nuclei were manually selected.
Spatial transcriptomic libraries were prepared with GeoMx reagents according to the manufacturer’s protocol - Direct PCR

treatment_protocol: Normal formalin-fixed paraffin-embedded placental blocks at 6-week gestational age with visible embryonic sac were selected so that the basal and chorionic areas were identifiable. 5μm sections were mounted on SuperFrostTM Plus slides and used within 2 weeks.

tag: tissue

value: chorionic plate placenta

tag: cell type

tag: placenta block

tag: roi number

tag: area

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: treatment

value: stained for EGFR and HLA-g


title: sid2_360_NHP_rep1

molecule: polyA RNA

tag: genotype

tag: ecotype


title: sid2_360_NHP_rep3

tag: tissue

tag: timepoint


title: CP-CTB_1347_3

tag: cell type

tag: placenta block


title: CP-CTB_1347_4

tag: roi number

tag: area


title: Kidney C_112

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Fastq Files were aligned to the hg38 genome using HISAT2
Counts table was produced using Rsubread
Normalisation was perfomed using DESeq2
Assembly: hg38

source_name: Kidney

growth_protocol: Samples were preserved by QUOD, Universty of Oxford

extract_protocol:
RNA was extracted from bladders using Ambion RNA mini kit
Libraries were produced using Illumina TruSeq total RNA

value: Kidney

tag: delayed graft function

value: NO

tag: person id


title: fmo1_360_NHP_rep3


title: Nasent RNA Eu 20min Mettl14 CKO mESCs rep1

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

description: nascent polyA RNA

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 (Bolger et al., 2014) and aligned to mouse genome (mm10, version M19, 2018-08-30) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific)  HISAT (version 2.1.0) with ‘--rna-strandness R -k 5’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq (Anders et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.

extract_protocol:
Total RNA was purified by Trizol and nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen). Before constructing libraries ERCC RNA spike-in control (Ambion) was added to each sample (0.01 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.
nascent RNA-seq

treatment_protocol: Eight 6-cm plates of mESCs were seeded and controlled to afford the same amount of cells. After 48 h, 5-ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, 20 min and 10 min before trypsinization collection.

value: mouse embryonic stem cells

tag: strain

tag: eu treatment time (min)


title: CP-CTB_1347_2

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: Kidney C_111


title: Nasent RNA Eu 20min Mettl14 CKO mESCs rep2

description: nascent polyA RNA


title: Nasent RNA Eu 10min Mettl14 CKO mESCs rep2

description: nascent polyA RNA


title: fmo1_360_NHP_rep2

tag: genotype

tag: ecotype

tag: treatment


title: Kidney C_106

tag: tissue


title: CP-CTB_1347_1

tag: cell type

tag: placenta block

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: fmo1_360_NHP_rep1

tag: timepoint


title: Nasent RNA Eu 30min Mettl14 CKO mESCs rep1

description: nascent polyA RNA

tag: strain

tag: eu treatment time (min)


title: col_360_NHP_rep3

value: wild type


title: Nasent RNA Eu 60min Mettl14 Control mESCs rep2

description: nascent polyA RNA


title: Kidney C_105

tag: delayed graft function

tag: person id


title: Nasent RNA Eu 10min Mettl14 CKO mESCs rep1

description: nascent polyA RNA


title: Kidney C_100


title: CP-CTB_1459_15

tag: roi number

tag: area

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: BP-CTB_1459_12

source_name: Basal Plate placenta

tag: tissue

value: Basal Plate placenta

tag: alignedreads

tag: deduplicatedreads

tag: treatment


title: col_360_NHP_rep1

tag: genotype

tag: ecotype


title: BP-CTB_1459_11

tag: cell type

tag: placenta block

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: col_360_NHP_rep2

tag: timepoint


title: Nasent RNA Eu 60min Mettl14 Control mESCs rep1

description: nascent polyA RNA

tag: strain

tag: eu treatment time (min)


title: Nasent RNA Eu 30min Mettl14 Control mESCs rep2

description: nascent polyA RNA


title: Kidney B_9

tag: delayed graft function

tag: person id


title: sid2_360_mock_rep3

value: mock


title: Nasent RNA Eu 30min Mettl14 Control mESCs rep1

description: nascent polyA RNA


title: Kidney B_84

value: Unknown


title: sid2_360_mock_rep2


title: Nasent RNA Eu 20min Mettl14 Control mESCs rep2

description: nascent polyA RNA


title: CP-CTB_1459_8

tag: roi number

tag: area

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: CP-CTB_1459_7

tag: tissue

tag: alignedreads

tag: deduplicatedreads

tag: treatment


title: sid2_360_mock_rep1

tag: genotype

tag: ecotype


title: Kidney B_82


title: Nasent RNA Eu 20min Mettl14 Control mESCs rep1

description: nascent polyA RNA

tag: cell type


title: fmo1_360_mock_rep3

tag: timepoint


title: fmo1_360_mock_rep2


title: Nasent RNA Eu 10min Mettl14 Control mESCs rep2

description: nascent polyA RNA

tag: strain

tag: eu treatment time (min)


title: CP-CTB_1459_6

tag: placenta block

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Nasent RNA Eu 10min Mettl14 Control mESCs rep1

description: nascent polyA RNA


title: Kidney B_81

tag: delayed graft function

tag: person id


title: CP-CTB_1459_5

tag: roi number

tag: area

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: BP-CTB_1459_10

tag: tissue

tag: alignedreads

tag: deduplicatedreads

tag: treatment


title: Kidney B_80


title: CP-CTB_1459_4

tag: cell type


title: fmo1_360_mock_rep1

tag: genotype

tag: ecotype

tag: timepoint


title: mRNA Mettl3 CKO mEBs 5uM GSK J4 rep3

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 (Bolger et al., 2014) and aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) using HISAT (version 2.1.0) with ‘--rna-strandness R -k 5’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq (Anders et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

source_name: Embronic bodies

extract_protocol:
Total RNA was purified by Trizol, before purified PolyA RNA with Dynabeads mRNA DIRECT Kit (Invitrogen).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.

treatment_protocol: The mESCs were incubated in EB medium ( DMEM supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid 0.1 mM 2-mercaptoethanol) for one week to differentiate into embryonic bodies (EBs) on Ultra-Low attachment 6-well plates without feeders, The Mettl3 CKO mESCs were treated with DMSO and 5μM GSK-J4,  Mettl14 CKO mESCs were treated with DMSO and 5μM GSK-343.

value: 7day mouse embryonic stem cells differentiation

tag: strain


title: col_360_mock_rep3


title: CP-CTB_1459_2

tag: placenta block

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Kidney B_7

tag: delayed graft function

tag: person id


title: Kidney B_85

value: Yes


title: Kidney B_79


title: TSC, patient 1278

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Data was mapped using the STARsolo function of STAR (v.2.7.10a) (Dobin, 2013). STARsolo performed error correction and demultiplexing of cell barcodes using user-input whitelist (3M-february-2018.txt for version 3 of the 10X Genomics Chromium System and 737K-august-2016.txt for version 2 data), mapped reads to the reference genome (GRCh38, version 32, Ensembl 98), deduplicated and error corrected UMIs, quantified per-cell gene expression, and spliced and unspliced reads similar to Velocyto. The following are the CellRanger mimicking commands used: --outFilterScoreMin 30 --readFilesCommand zcat --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter EmptyDrops_CR --soloUMIlen 12 --soloType CB_UMI_Simple --soloCBwhitelist 3M-february-2018.txt --clipAdapterType CellRanger4 --outFileNamePrefix name --outSAMattributes All --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --soloCBlen 16 --soloCBstart 1 --soloUMIstart 17 --soloFeatures Gene GeneFull SJ Velocyto.
Assembly: GRCh38, version 32, Ensembl 98
Supplementary files format and content: barcodes.tsv.gz:  tab-separated values for cell barcodes
Supplementary files format and content: features.tsv.gz:  tab-separated values list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expression count data in Matrix Market Exchange Format

growth_protocol: All tissue samples were processed within 2 hours of sample collection. Tissues were minced and subjected to sequential digestion with Trypsin and DNase, followed by Percoll gradient separation as previously described (PMID: 28167044). For trophoblast stem cell derivation, the CTBs were MACS-purified with with either a PE-conjugated anti-ITGA6 antibody (Biolegend #313612) or an APC-conjugated anti-EGFR antibody (Biolegend #352906).

extract_protocol:
Single cell suspensions were washed, filtered for cell debris, counted, and stained with a viability marker to ensure correct loading concentration and a high percentage of live cells. Cell suspensions were then loaded onto the 10x Genomics Controller for GEM generation.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: hTSCs were derived as explained in PMID: 34791028, PMID: 3454082.

tag: cell line

tag: gestational age_(weeksdays)


title: mRNA Mettl3 CKO mEBs 5uM GSK J4 rep2


title: col_360_mock_rep2

tag: tissue


title: Kidney B_83


title: Kidney B_78


title: Erbb2-deficient ApcMin, tumor, biol rep2

city: College. Station

first: David

last: Threadgill

state: Texas

address: 400 Bizzell St

department: Cell Biology and Genetics

institute: Texas A&M University

data_processing:
Sequence reads were trimmed of adapter sequences and low-quality bases using Trimmomatic following the authors recommendations
Filtered reads were aligned to mouse assembly mm39 using HISAT2 version 2.2.1
Raw transcript counts were generated using HTSeq version 2.0.2
Read counts were normalized, and gene expression analyses were performed using DESeq2
Assembly: mm39
Supplementary files format and content: tab-delimited text file contains raw counts

source_name: Colorectal tumor

growth_protocol: Mice were housed five per cage, fed Purina Mills Lab Diet 2919 and water ad libidum, and maintained at 22°C under a 12-hr light cycle

extract_protocol:
Total RNA from tumors and adjacent normal tissue was isolated using Maxwell LEV simplyRNA Tissue Kit (Promega AS1280) according to the manufacturer’s instructions.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Preparation Kit according to the manufacturer's instructions

value: Colorectal tumor

tag: age

value: 100 days


title: mRNA Mettl3 CKO mEBs rep3


title: TSC, patient 1000

description: 10x genomics


title: Kidney B_77


title: TSC, patient 906

description: 10x genomics


title: sid2_180_NHP_rep3

value: 180 min


title: mRNA Mettl3 CKO mEBs rep1


title: Chorionic Plate, patient 1290

description: 10x genomics


title: sid2_180_NHP_rep2

value: whole seedling


title: mRNA Mettl3 CKO mEBs rep2


title: Basal Plate, patient 1290

description: 10x genomics


title: Kidney B_75


title: sid2_180_NHP_rep1


title: mRNA Mettl3 Control mEBs rep2


title: Kidney B_74


title: Chorionic Plate, patient 1276

description: 10x genomics


title: Kidney B_73


title: fmo1_180_NHP_rep3


title: mRNA Mettl3 CKO mEBs 5uM GSK J4 rep1


title: col_360_mock_rep1

value: 360 min


title: Basal Plate, patient 1276

description: 10x genomics


title: Whole Placenta, patient 866, 10000, rep1

description: 10x genomics

source_name: whole placenta

value: whole placenta


title: mRNA Mettl14 CKO mEBs 5uM GSK343 rep3


title: Kidney B_76


title: Kidney B_70


title: mRNA Mettl3 Control mEBs rep1


title: Kidney B_6


title: mRNA Mettl3 Control mEBs rep3


title: mRNA Mettl14 CKO mEBs 5uM GSK343 rep1


title: Kidney B_71


title: col_180_NHP_rep1

value: NHP


title: fmo1_180_NHP_rep1


title: Whole Placenta, patient 861, 10000, rep1

description: 10x genomics


title: Whole Placenta, patient 860, 10000, rep2

description: 10x genomics


title: Kidney B_69


title: fmo1_180_NHP_rep2


title: sid2_180_mock_rep3


title: mRNA Mettl14 CKO mEBs rep3


title: Whole Placenta, patient 856, 10000, rep2

description: 10x genomics


title: col_180_NHP_rep3


title: mRNA Mettl14 CKO mEBs rep1


title: Kidney B_72


title: sid2_180_mock_rep1


title: mRNA Mettl14 CKO mEBs rep2


title: BP-CTB_1344_7

tag: roi number

tag: area

tag: nucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

value: stained for EGFR and HLA-g


title: Kidney B_68

value: Kidney


title: mRNA Mettl14 CKO mEBs 5uM GSK343 rep2

tag: cell type

tag: strain


title: sid2_180_mock_rep2

tag: genotype

tag: ecotype

tag: timepoint

tag: treatment


title: col_180_NHP_rep2


title: Kidney B_66

tag: delayed graft function

value: NO

tag: person id


title: REC-1, DMSO, Hi-C

city: Philadelphia

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

institute: University of Pennsylvania

library_source: genomic

data_processing:
Raw reads for each HiC sample were processed with HiC-Pro (version v2.8.1) (Servant et al., 2015) to obtain putative interactions with default parameters except LIGATION_SITE and GENOME_FRAGMENT provided by Arima.
Assembly: hg19
Supplementary files format and content: .hic formatted file for juicebox viewing of contact matrices

molecule: genomic DNA

growth_protocol: RPMI 1640  supplemented with 10% fetal bovine serum , 2 mM L-glutamine, 100 U/mL and 100 μg/mL penicillin/streptomycin, 100 mM nonessential amino acids, 1mM sodium pyruvate and 0.1mM of 2-mercaptoethanol

extract_protocol:
Arima HiC kit used per manufacture’s instructions
Accel-NGS 2S Plus DNA library kit

treatment_protocol: Parental and resistant cells were tretated with DMSO (parental) or ibrutinib (reistant) for 24 hours followed by BCR crosslinking with IgM for 5min. Cells used for Hi-C were subsequently fixed with 2% formaldehyde

tag: cell line

value: Mantle Cell Lymphoma

value: DMSO


title: mRNA Mettl14 Control mEBs rep3


title: Whole Placenta, patient 860, 5000, rep1

description: 10x genomics

tag: tissue

tag: gestational age_(weeksdays)


title: Kidney B_65


title: 293T, siC1QBP, biol rep 2

city: Daejeon

first: Sujin

last: Kim

address: 291, Daehak-ro

department: Chemical and Biomolecular Engineering

country: South Korea

institute: KAIST

data_processing:
Each raw paired-end RNA sequencing read produced in this paper was trimmed to 36 nucleotides using Trimmomatic v.0.39 (MINLEN:36).
Processed paired-end RNA sequencing reads were mapped to the reference human genome (build hg38) with Bismark v.0.22.3 using dafault parameters except with the option "-N 0 -X 500".
To extract the methylation level at each position, "bismark_methylation_extractor" command was used with "--comprehensive --bedGraph --CX" in Bismark v.0.22.3 after filtering not-converted cytosine with "filter_non_conversion --threshold 4".
The final COV files were analyzed in R v.3.6.1 using ggplot2 v.3.3.6, readxl v.1.3.1, dplyr v.1.0.9, pheatmap v.1.0.12, and ggrepel v.0.9.1.
Assembly: hg38
Supplementary files format and content: A cov file showing the methylation level at each position
Library strategy: RNA-seq Bisulfite-seq

extract_protocol:
RNAs were obtained using Trizol. Purified RNAs were digested with Dnase I.
After rRNA depletion using the RiboZero Plus rRNA depletion kit (Illumina), bisulfite converted RNAs with the EpiNext RNA-bisulfite conversion kit (Epigentek) were prepared using the TrueSeq Stranded Total RNA Library Prep kit (Illumina).

value: Human embryonic kidney cell


title: fmo1_180_mock_rep3

value: mock


title: mRNA Mettl14 Control mEBs rep1


title: Kidney B_64


title: fmo1_180_mock_rep2


title: Kidney B_63


title: Whole Placenta, patient 856, 5000, rep1

description: 10x genomics


title: REC-1, Ibrutinib Resistant, Hi-C

value: Ibrutinib


title: 293T, siC1QBP, biol rep 1


title: fmo1_180_mock_rep1


title: Kidney B_67

value: Unknown


title: col_180_mock_rep3

value: wild type


title: 293T, siLuc-C1QBP, biol rep 1

value: siLuc


title: 293T, siLuc-C1QBP, biol rep 2


title: Kidney B_62


title: caRNA m6A-MeRIP IP Mettl3 CKO mESCs rep1

description: chromatin-associated non-Rib RNA

data_processing:
Illumina Casava software used for basecalling
Raw reads were trimmed with Trimmomatic-0.38 and aligned to mouse genome (mm10, version M19, 2018-08-30) and spike-in genomes including unmodified control RNA (Cypridina Luciferase) and  m6A methylated control RNA (Gaussia Luciferase) (New England Biolabs) using HISAT (version 2.1.0) (Daehwan et al., 2015) with ‘-k 5 --rna-strandness RF’
Mapped reads were separated by strands with samtools (version 1.9) (Li et al., 2009) and m6A peaks on each strand were called using MACS (version 2) (Zhang et al., 2008) with parameter ‘-g 1.3e8 --tsize 150 --extsize 150  --nomodel --keep-dup 5’ separately.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peaks location: chromosome, start, end, name, int(-10*log10(q-value)), strand, fold_enrichment, -log10(p-value), -log10(q-value), summit position relative to peak start.

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). PolyA RNA was enriched from total RNA by using Dynabeads mRNA DIRECT Kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA/PolyA RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.
MeRIP-seq

value: mouse embryonic stem cells

tag: m6a antibody


title: Kidney B_61

value: Yes


title: caRNA m6A-MeRIP IP Mettl3 Control mESCs rep2

description: chromatin-associated non-Rib RNA

value: EpiMark N6-Methyladenosine Enrichment Kit


title: P12 w/ testosterone

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
The quality of raw reads was assessed using FastQC (v0.11.9). Adaptor sequence trimming and poor read removal were performed using the cutadapt (v3.5).
The qualified reads were aligned to the human reference genome GRCh38 using the STAR (v2.7.8a) with the two-pass mode. Gene count was quantified based on the annotation of Gencode (v35)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: ovarian follicle

growth_protocol: Follicular aspirates were collected during oocyte retrieval from both healthy control and PCOS patients undergoing in vitro fertilization for infertility treatment. Granulosa cells in follicular aspirates were isolated by using Ficoll density gradient centrifugation. The cells were cultured in RPMI 1640 medium supplemented with 15% fetal bovine serum, 1% MEM non-essential amino acids (NEAA), 1% GlutaMAX, and 1% antibiotic-antimycotic. Infection was preceded by 2 days of seeding 2-5×105 granulosa cells in a 35 mm dish. The virus infection procedures followed the manufacturer's instructions (Invitrogen) and the medium was replaced with fresh medium daily. One week after infection, the cells were collected using Accumax (eBioscience) and replated on mitomycin C-inactivated mouse embryo fibroblasts as feeder cells. On the next day, the medium was changed to DMEM/F12 medium supplemented with 20% knockout serum replacement (KOSR), 1% NEAA, 0.5% GlutaMAX, 1% penicillin-streptomycin, and 5 ng/ml basic fibroblast growth factor (bFGF, Peprotech). After one month of infection, the colonies were hand-picked and placed on feeder cells. The iPSCs were passed weekly through manual manipulation, with a daily medium replacement. When iPSCs were cultured without feeders,  iPSCs were maintained in Essential 8 medium on vitronectin-coated dishes. These cells were passed using 0.5% EDTA in Dulbecco's phosphate-buffered saline (DPBS) every 5 days, while the medium was changed daily. Cell culture media, serum, and buffers were procured from Life Technologies (Grand Island, NY). Unless otherwise stated, the chemicals were procured from Sigma-Aldrich (St. Louis, MO).

extract_protocol:
The extraction of total cell RNA was performed using either QIAzol Lysis Reagent (QIAGEN).
Libraries for RNA sequencing were prepared using the Illumina Stranded mRNA Prep kit (#20040534) following the manufacturer’s protocol

treatment_protocol: The STEMdiff mesenchymal progenitor kit (STEMCELL) was utilized to differentiate MPCs. 2 days before induction, iPSCs were cultured without feeder cells and exposed to 10 μM Y-27632 for 2 h. After 2 h, the iPSCs dissociated into single cells using TypLE, then replating at a concentration of 5×104 cells/cm2 in Essential 8 medium with 10 μM Y-27632. The fresh medium was replaced the following day. From the start of day 0 until day 3, the medium was switched to the mesenchymal induction medium. The medium was changed to MesenClut-ACF medium on day 4. On day 6, these cells were exposed to 10 μM Y-27632 for 2 h and dissociated using TypLE,  followed by plating at a concentration of 3-10x103 cells/cm2 in MesenClut-ACF medium MesenClut-ACF attachment substrate-coated plates. Once the cells reached 80% confluency, 10-7 M testosterone was added for three weeks, with the medium being changed weekly.

value: ovarian follicle

value: iPSC-derived MCP

tag: disease

value: PCOS


title: col_180_mock_rep2

value: whole seedling

value: 180 min


title: mRNA Mettl14 Control mEBs rep2

value: 7day mouse embryonic stem cells differentiation


title: caRNA m6A-MeRIP IP Mettl3 Control mESCs rep1

description: chromatin-associated non-Rib RNA


title: col_180_mock_rep1


title: sid2_30_NHP_rep3

value: NHP


title: P12

value: No


title: Kidney B_60

value: Kidney

value: NO


title: caRNA m6A-MeRIP Input Mettl3 CKO mESCs rep2

description: chromatin-associated non-Rib RNA


title: Kidney B_5


title: caRNA m6A-MeRIP IP Mettl3 CKO mESCs rep2

description: chromatin-associated non-Rib RNA


title: Kidney B_59


title: sid2_30_NHP_rep2

value: 30 min


title: P5 w/ testosterone


title: sid2_30_NHP_rep1


title: caRNA m6A-MeRIP Input Mettl3 CKO mESCs rep1

description: chromatin-associated non-Rib RNA


title: caRNA m6A-MeRIP Input Mettl3 Control mESCs rep2

description: chromatin-associated non-Rib RNA


title: caRNA m6A-MeRIP Input Mettl3 Control mESCs rep1

description: chromatin-associated non-Rib RNA


title: P5


title: Kidney B_58


title: Kidney B_57


title: fmo1_30_NHP_rep2


title: fmo1_30_NHP_rep3


title: caRNA m6A-MeRIP IP Mettl14 CKO mESCs rep2

description: chromatin-associated non-Rib RNA


title: fmo1_30_NHP_rep1


title: Kidney B_56


title: Kidney B_55


title: col_30_NHP_rep3


title: caRNA m6A-MeRIP IP Mettl14 CKO mESCs rep1

description: chromatin-associated non-Rib RNA


title: Kidney B_54


title: caRNA m6A-MeRIP IP Mettl14 Control mESCs rep2

description: chromatin-associated non-Rib RNA


title: C31 w/ testosterone

value: Control


title: col_30_NHP_rep2

value: wild type


title: caRNA m6A-MeRIP IP Mettl14 Control mESCs rep1

description: chromatin-associated non-Rib RNA


title: C31


title: P11


title: Kidney B_53


title: C32


title: col_30_NHP_rep1


title: caRNA m6A-MeRIP Input Mettl14 CKO mESCs rep2

description: chromatin-associated non-Rib RNA


title: C24 w/ testosterone


title: Kidney B_52


title: caRNA m6A-MeRIP Input Mettl14 CKO mESCs rep1

description: chromatin-associated non-Rib RNA


title: P2 w/ testosterone


title: Kidney B_51


title: P2


title: sid2_30_mock_rep2

value: mock


title: C25 w/ testosterone


title: sid2_30_mock_rep1


title: Kidney B_4


title: caRNA m6A-MeRIP Input Mettl14 Control mESCs rep1

description: chromatin-associated non-Rib RNA

value: mouse embryonic stem cells


title: Kidney B_50


title: fmo1_30_mock_rep3


title: C25


title: caRNA m6A-MeRIP Input Mettl14 Control mESCs rep2

description: chromatin-associated non-Rib RNA


title: mRNA m6A-MeRIP IP Mettl14 CKO mESCs rep2

description: polyA RNA


title: Ctrl2

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

description: Single-cell RNAseq data

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome and counted using Cell Ranger (version 5.0.1; 10x Genomics).
Assembly: GrCh38
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI counts for each sample

source_name: healthy trachea

extract_protocol:
Tissue samples dissociated using MACS Miltenyi Tumor  Dissociation Kit for mouse (Miltenyi)
libraries were prepared using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Nexxt GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA)

value: healthy trachea

tag: age

tag: Sex

value: Female


title: Kidney B_48


title: mRNA m6A-MeRIP IP Mettl14 CKO mESCs rep1

description: polyA RNA

value: EpiMark N6-Methyladenosine Enrichment Kit


title: Kidney B_49


title: fmo1_30_mock_rep2


title: fmo1_30_mock_rep1


title: Kidney B_47


title: Ctrl1

description: Single-cell RNAseq data


title: mRNA m6A-MeRIP IP Mettl14 Control mESCs rep2

description: polyA RNA


title: col_30_mock_rep3


title: Kidney B_46


title: mRNA m6A-MeRIP IP Mettl14 Control mESCs rep1

description: polyA RNA


title: C24

value: ovarian follicle

value: iPSC-derived MCP


title: ISGS3

description: Single-cell RNAseq data

source_name: idiopathic subglottic tracheal stenosis

value: idiopathic subglottic tracheal stenosis


title: mRNA m6A-MeRIP IP Mettl3 CKO mESCs rep2

description: polyA RNA


title: col_30_mock_rep2

value: whole seedling


title: ISGS1

description: Single-cell RNAseq data


title: col_30_mock_rep1


title: Kidney B_44


title: mRNA m6A-MeRIP IP Mettl3 CKO mESCs rep1

description: polyA RNA


title: ISGS2

description: Single-cell RNAseq data


title: CD19.CAR(41BBz)-Vδ2 T cells, HPL, donor 4

city: Houston

first: Norihiro

last: Watanabe

address: 1102 Bates Ave

institute: Baylor College of Medicine

data_processing:
RNA-seq reads were aligned to the human genome (GRCh37, primary assembly) and transcriptome (Gencode version 24 backmap 37 comprehensive gene annotation) using STAR v2.7.9a with the following non-standard parameters --outSAMstrandField intronMotif --outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 3 --alignEndsType EndToEnd. Only uniquely aligned reads were retained for downstream analysis
Read count extraction were performed using featureCounts version 1.5.0 with the following non-default parameters -s 0 -a and later lcpmtmm normalized
Differential gene expression analysis was conducted using DESeq2 performed on genes with at least 5 counts present in at least half of the samples
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include lcpmtmm normalized gene expression information for each sample and log2 fold changes of genes between conditions of comparison

source_name: peripheral blood monnuclear cells

growth_protocol: Cells were maintained in either 10%FBS- or 10%HPL-supplemented medium in a humidified atmosphere containing 5% carbon dioxide (CO2) at 37 °C

extract_protocol:
Total RNA was extracted from purified CAR(+)Vδ2(+) T cells using the RNeasy plus Mini kit (QIAGEN).
performed by Genewiz (Azenta Life Sciences)

treatment_protocol: Vγ9Vδ2 T cells were expanded from PBMCs treated with zoredronate (1 uM) and IL-2 (100 U/mL). CD19.CAR(41BBz) construct was transduced by retroviral transduction. CAR(+) and Vd2TCR (+) cells were purified before total RNA extraction.

value: peripheral blood monnuclear cells

value: V[gamma]9V[delta]2 T cells

value: PBMCs were stimulated with zoledronate and IL-2 in HPL-supplemented medium

tag: time

value: Day14 post CD19.CAR transduction


title: mRNA m6A-MeRIP IP Mettl3 Control mESCs rep2

description: polyA RNA


title: CD19.CAR(41BBz)-Vδ2 T cells, HPL, donor 3


title: Kidney B_43

value: Kidney

value: Unknown


title: sid2_15_NHP_rep2

value: 15 min

value: NHP


title: mRNA m6A-MeRIP Input Mettl14 CKO mESCs rep2

description: polyA RNA


title: CD19.CAR(41BBz)-Vδ2 T cells, HPL, donor 2


title: mRNA m6A-MeRIP IP Mettl3 Control mESCs rep1

description: polyA RNA


title: Kidney B_42

value: NO


title: sid2_15_NHP_rep1


title: Kidney B_41


title: CD19.CAR(41BBz)-Vδ2 T cells, HPL, donor 1


title: fmo1_15_NHP_rep2


title: Kidney B_45


title: mRNA m6A-MeRIP Input Mettl14 CKO mESCs rep1

description: polyA RNA

value: mouse embryonic stem cells


title: fmo1_15_NHP_rep3


title: Kidney B_40


title: mRNA m6A-MeRIP Input Mettl14 Control mESCs rep1

description: polyA RNA


title: Kidney B_3


title: CD19.CAR(41BBz)-Vδ2 T cells, FBS, donor 4

value: PBMCs were stimulated with zoledronate and IL-2 in FBS-supplemented medium


title: mRNA m6A-MeRIP Input Mettl14 Control mESCs rep2

description: polyA RNA


title: Kidney B_39

value: Yes


title: fmo1_15_NHP_rep1


title: CD19.CAR(41BBz)-Vδ2 T cells, FBS, donor 2


title: col_15_NHP_rep3

value: wild type


title: sid2_15_NHP_rep3


title: mRNA m6A-MeRIP Input Mettl3 CKO mESCs rep2

description: polyA RNA


title: mRNA m6A-MeRIP Input Mettl3 CKO mESCs rep1

description: polyA RNA


title: CD19.CAR(41BBz)-Vδ2 T cells, FBS, donor 1


title: Kidney B_37


title: Kidney B_38


title: col_15_NHP_rep2


title: Kidney B_36


title: Sample from patient number 13 of the study.

city: Los Angeles

first: Daria

last: Kessler

state: California

address: 9139 Hargis St.

institute: Saint John's Health Center

data_processing:
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software
Initial analysis included alignment with TopHat2.
Gene expression counts were obtained using cufflinks.
FastQC was used for quality control.
Assembly: hg38 was used for alignment
Supplementary files format and content: tab-delimited .xlsx file includes raw counts for each Sample

source_name: FFPE tumor biopsy collected before treatment with NAC

extract_protocol:
Total RNA was isolated from selected tumor areas with the High Pure RNA Paraffin Kit (Roche Diagnostics). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase Kit (Roche) following manufacturer's protocols.

tag: treatment.

value: Methotrexate Vinblastine Sulfate Doxorubicin Hydrochloride Cisplatin

tag: response to_tratment

value: pCR


title: sid2_15_mock_rep3

value: mock


title: Kidney B_35


title: Sample from patient number 11 of the study.

value: FFPE tumor biopsy collected before treatment with NAC

value: Cisplatin + Gentamicin


title: sid2_15_mock_rep2

value: whole seedling


title: Kidney B_34


title: CD19.CAR(41BBz)-Vδ2 T cells, FBS, donor 3

value: peripheral blood monnuclear cells

tag: cell type

value: V[gamma]9V[delta]2 T cells


title: mRNA m6A-MeRIP Input Mettl3 Control mESCs rep1

description: polyA RNA

tag: strain


title: H3K27me3 Mettl14 CKO mESCs rep2

data_processing:
Basecalls performed using CASAVA.
Raw reads were trimmed with Trimmomatic-0.38 (Bolger et al., 2014) and mapped to mouse genome (mm10, version M19, 2018-08-30) using bowtie2 (version 2.4.1) (Langmead et al., 2012) in default mode: search for the multiple alignments, report the best one. Reads were deduplicated using samtools rmdup (Li et al., 2009).
Peaks were called using HOMER (Heinz et al., 2010)  in histone mode.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations in format of bed.

extract_protocol:
Chromatin immunoprecipitation was performed using Auto iDeal ChIP-seq kit for Histone (diagenode) with spike-in Chromatin (Active Motif) and spike-in Antibody (Active Motif) following the manufacturer’s protocols.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.

treatment_protocol: mESCs were resuspended in growth media with a concentration of 10e6 ml-1 and cross-linked by adding 1% formaldehyde directly to the media, slow shaked 10 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature with slowly shaking. The media was removed and the cells were washed twice with ice-cold PBS.

tag: chip antibody

value: rabbit anti-H3K27me3 (#9733, Cell Signaling Technology)


title: sid2_15_mock_rep1

tag: genotype

tag: ecotype

tag: timepoint


title: H3K27me3 Mettl14 CKO mESCs rep1


title: Kidney B_33

value: Kidney

tag: delayed graft function

tag: person id


title: fmo1_15_mock_rep3

tag: tissue

value: 15 min

tag: treatment


title: H3K27me3 Mettl14 Control mESCs rep2


title: Kidney B_32


title: Sample from patient number 10 of the study.


title: Sample from patient number 9 of the study.

value: non-pCR


title: H3K27me3 Mettl14 Control mESCs rep1


title: fmo1_15_mock_rep2


title: mRNA m6A-MeRIP Input Mettl3 Control mESCs rep2

description: polyA RNA

tag: m6a antibody


title: Kidney B_31


title: Sample from patient number 8 of the study.


title: Sample from patient number 7 of the study.


title: col_15_NHP_rep1

value: NHP


title: Sample from patient number 6 of the study.


title: Sample from patient number 12 of the study.

value: Cisplatin + Gentamicin + Pembrolizumab


title: Kidney B_2

value: NO


title: col_15_mock_rep2


title: col_15_mock_rep3


title: Kidney B_29

value: Unknown


title: H3K27ac Mettl14 Control mESCs rep2

value: mouse embryonic stem cells

value: rabbit anti-H3K4me3 (ab8580, Abcam)


title: Kidney B_30


title: col_15_mock_rep1

value: wild type


title: Sample from patient number 4 of the study.

value: pCR


title: Kidney B_28


title: Kidney B_27


title: Sample from patient number 3 of the study.

value: FFPE tumor biopsy collected before treatment with NAC

value: Methotrexate Vinblastine Sulfate Doxorubicin Hydrochloride Cisplatin


title: medulla_personE

first: Roy

last: Zhang

address: Cambridge Biomedical Campus, Francis Crick Ave

institute: MRC Laboratory of Molecular Biology

description:
Sample_10
rawcounts.txt

data_processing:
Libraries were sequenced on a Hiseq sequencer (Ilumina) by either Eurofins or Genewiz
Sequencing data was demultiplexed to give individual fastq files using Casava (Illumina)
FASTQC was used for quality control
Fastq files were aligned to the human genome (Hg38) using Hisat2
A table of gene counts was produced using the featureCounts function within Rsubread
normalisation performed using DESeq2 normalisation
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include unnormalised counts for each sample

source_name: medulla

extract_protocol:
RNA extracted using a pure-link RNA mini kit (Ambion)
0.3 - 0.75µg of RNA was used to produce sequencing libraries using TruSeq Stranded total RNA library prep kit (Illumina) with 14 PCR amplification cycles

value: medulla

tag: person

value: E

value: female

tag: donor type

value: DBD


title: H3K4me3 Mettl14 CKO mESCs rep2


title: cortex_personE

description:
Sample_9
rawcounts.txt

source_name: cortex

value: cortex

tag: Sex


title: Kidney B_26

value: Kidney


title: Sample from patient number 2 of the study.

value: Cisplatin + Gentamicin

value: non-pCR


title: fmo1_15_mock_rep1

value: whole seedling

value: 15 min

value: mock


title: Kidney B_25

value: Yes


title: H3K4me3 Mettl14 Control mESCs rep2

value: mouse embryonic stem cells

value: rabbit anti-H3K4me3 (ab8580, Abcam)


title: H3K27ac Mettl14 CKO mESCs rep2


title: H3K4me3 Mettl14 CKO mESCs rep1


title: Sample from patient number 1 of the study.


title: 293T, siPNPase, biol rep 3

data_processing:
*library strategy: RNA Bisulfite-seq
Each raw paired-end RNA sequencing read produced in this paper was trimmed to 36 nucleotides using Trimmomatic v.0.39 (MINLEN:36).
Processed paired-end RNA sequencing reads were mapped to the reference human genome (build hg38) with Bismark v.0.22.3 using dafault parameters except with the option "-N 0 -X 500".
To extract the methylation level at each position, "bismark_methylation_extractor" command was used with "--comprehensive --bedGraph --CX" in Bismark v.0.22.3 after filtering not-converted cytosine with "filter_non_conversion --threshold 4".
The final COV files were analyzed in R v.3.6.1 using ggplot2 v.3.3.6, readxl v.1.3.1, dplyr v.1.0.9, pheatmap v.1.0.12, and ggrepel v.0.9.1.
Assembly: hg38
Supplementary files format and content: A cov file showing the methylation level at each position

tag: cell line

value: Human embryonic kidney cell


title: H3K27ac Mettl14 CKO mESCs rep1


title: cortex_personD

description:
Sample_7
rawcounts.txt

value: D

value: male


title: medulla_personD

description:
Sample_8
rawcounts.txt

value: medulla


title: Sample from patient number 5 of the study.

value: FFPE tumor biopsy collected before treatment with NAC

tag: treatment.

value: pCR


title: Kidney B_24


title: H3K27ac Mettl14 Control mESCs rep1


title: H3K4me3 Mettl14 Control mESCs rep1


title: 293T, siPNPase, biol rep 2


title: medulla_personC

description:
Sample_6
rawcounts.txt

value: C

value: DCD


title: Input Mettl14 CKO mESCs rep2


title: 293T, siPNPase, biol rep 1


title: Input Mettl14 CKO mESCs rep1


title: Kidney B_22

value: Kidney


title: 293T, siLuc, biol rep 3

value: siLuc


title: medulla_personB

description:
Sample_4
rawcounts.txt

value: B


title: Input Mettl14 Control mESCs rep2


title: 293T, siLuc, biol rep 2


title: Kidney B_21


title: Input Mettl14 Control mESCs rep1


title: Kidney B_20

value: NO


title: Kidney B_23

value: Unknown


title: METTL3 CUT&RUN Mettl14 CKO mESCs rep2

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 (Bolger et al., 2014) and mapped to mouse genome (mm10, version M19, 2018-08-30) using bowtie2 (version 2.4.1) (Langmead et al., 2012) in default mode: search for the multiple alignments, report the best one. Reads were deduplicated using samtools rmdup (Li et al., 2009).
Peaks were called using HOMER (Heinz et al., 2010) in factor style with ‘-F 2 -L 2 -tagThreshold 10’ parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations in format of bed.

extract_protocol:
The cells were then incubated with 2 mL nuclear isolation buffer (10 mM Tris-HCl, pH=7.5, 250 mM sucrose, 400 mM spermidine, 0.8% Triton X-100) and 6 mL H2O for 20 min on ice with frequent mixing. The pellets were collected by centrifugation at 2,500g for 15 min. Washed cell pellet with nuclear isolation buffer and antibody buffer (20 mM HEPES, pH=7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1 mg/mL BSA). The cell pellets were then incubated overnight with the antibody in Antibody buffer at 4°C. The following day, the supernatant was removed by centrifugation and the cell pellets were washed three times with wash buffer (20 mM HEPES, pH=7.5, 150 mM KCl, 0.5 mM spermidine). The cell pellets were then incubated with Protein A-MNase (1.5 µg in 300µL wash buffer) for 1 hr by rotation at 4°C. After three washes, the cell pellets were resuspended in 300µL wash buffer with 6µL 100 mM CaCl2, mixed rapidly by inversion and placed on ice for 30 min. The reactions were stopped by the addition of 300µL 2x stop buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05 mg/mL RNaseA, 0.05 mg/mL glycogen, 2 pg/mL spike-in DNA). The supernatant DNA was collected after centrifugation and further purified using phenol/chloroform/isoamyl alcohol (25 : 24 : 1) extractions and precipitated with 0.1 volume of 3 M sodium acetate, pH = 5.2, and 3 volumes of ethanol using glycogen as carrier.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.
CUT&RUN seq

value: Rabbit anti-METTL3 (ab195352, Abcam)


title: 293T, sgNSUN4, biol rep 2


title: Kidney B_1


title: METTL3 CUT&RUN Mettl14 CKOmESCs rep1


title: Kidney B_19

value: Yes


title: 293T, sgNSUN4, biol rep 1


title: cortex_personB

description:
Sample_3
rawcounts.txt

value: cortex


title: RV_2

first: Yingying

last: Xiao

address: No.355, Luding Road

institute: Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University

description: 10X Genomics

data_processing:
Use fastp to make basic statistics on the quality of data (raw reads) after disembarking.Then, raw read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
cellranger cellranger reanalyze takes feature-barcode matrices produced by cellranger count or cellranger aggr and reruns the dimensionality reduction, clustering, and gene expression algorithms using cellranger default parameter settings. Seurat The Seurat package was used to normalise data, dimensionality reduction, clustering,differential expression. we used Seurat alignment method canonical correlation analysis (CCA) [Nat. Biotechnol. 36, 411–420 (2018).] for integrated analysis of datasets. For clustering, highly variable genes were selected and the principal components based on those genes used to build a graph, which was segmented with a resolution of 0.6.
Based on filtered gene expression matrix by Seurat ,between samples differential expression analysis was carried out using the edgeR package to obtain zone-specific marker genes.
Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.  We usedclusterProfiler R package to test the statistical enrichment of markergenes in KEGG pathways. Reactome pathway-based analysis of marker genes was implemented by the ReactomePA R package.  Protein-Protein Interaction networks(PPI) analysis of marker genes was implemented by the STRINGdb R package.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: right ventricle

growth_protocol: Mice live with their mother under 19-22℃ with free access to food and water

extract_protocol:
Right ventricular tissue of mouse pups on postnatal day 21 were rapidly removed from executed mouse and flash frozen in -80℃ refrigerator. Samples were rinsed using PBS (calcium-magnesium-free), minced and transferred to collagenase-containing medium for 30 min of digestion. Resuspend the digested cells and enrich the CD45+ positive cells with CD45+ magnetic beads.
The cell suspension was loaded into Chromium microfluidic chips with 3' v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3' v3 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina Hiseq PE150 according to the manufacturer’s instructions (Illumina).

treatment_protocol: Neonatal mouse (within 24h after birth) were injected with AAV9 to knockout p300/CBP.

value: right ventricle

value: CBP flox/flox; p300 flox/flox; trap flox/flox

tag: age

value: treatment:postnatal day 1 harvest:postnatal day 21

value: p300/CBP knockout (inject AAV9 at postnatal day 1)


title: RV_1

description: 10X Genomics

value: CBP flox/flox; p300 flox/flox; Trap flox/flox


title: METTL3 CUT&RUN Mettl14 Control mESCs rep2

tag: cell type

value: mouse embryonic stem cells


title: Kidney B_18

data_processing:
Fastq Files were aligned to the hg38 genome using HISAT2
Counts table was produced using Rsubread
Normalisation was perfomed using DESeq2
Assembly: hg38


title: 293T, sgNC, biol rep 2

value: Human embryonic kidney cell

value: sgNC


title: METTL3 CUT&RUN Mettl14 Control mESCs rep1

tag: strain


title: Kidney B_17


title: SLTMV2

city: 长沙

first: 别帅骏

last: 别

state: 长沙

address: 芙蓉区远大二路892号

department: 实验大楼

institute: 湖南省农业科学院

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About xxxxx raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean reads. Then about xxxxxx clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2 2 . FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count4 . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of sample
Differential expression analysis was performed using the DESeq2 5 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. The radar map of top 30 genes was drew to show the expression of up-regulated or down-regulated DEGs using R packet gg
Based on the hypergeometric distribution, GO 6 , KEGG 7 pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagram and bubble diagram of the significant enrichment term
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software 8-9 . The anal used a predefined gene set, and the genes were ranked according to the degree of differentialexpression in the two types of samples.Then it is tested whether the predefined gene set wasenriched at the top or bottom of the rank
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM valued for each sample

organism: Nicotiana benthamiana

source_name: leaf

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protoco
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

value: leaf


title: Kidney B_16

extract_protocol:
RNA was extracted from bladders using Ambion RNA mini kit
Libraries were produced using Illumina TruSeq total RNA

value: Kidney


title: METTL14 CUT&RUN Mettl3 CKO mESCs rep2

tag: chip antibody

value: Rabbit anti-METTL14 (HPA038002, Sigma)


title: SLTMV1


title: 293T, siLuc, biol rep 1

value: siLuc


title: medulla_personA

description:
Sample_2
rawcounts.txt

value: medulla

value: A

value: male

value: DCD


title: METTL14 CUT&RUN Mettl3 CKO mESCs rep1


title: SL3


title: cortex_personC

description:
Sample_5
rawcounts.txt

value: cortex

value: C


title: GBOs_PFC_4MPT

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

description: Cells were dissociated by Trypsin-EDTA (Life Technology)  into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 9000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 degrees Celsius for 45 min, followed by 85 degrees Celsius for 5 min and final hold at 4 degrees Celsius. cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell with a paired-end 150 bp (PE150) reading strategy.

data_processing:
For the scRNA-seq, raw sequencing data was processed with Cell Ranger software version 3.1 (10X Genomics) for FASTQ generation and GRCh38 human reference genome was used for alignments. For filtering and unsupervised clustering, the gene expression matrixs from Cell Ranger results were used for downstream analysis, using R 4.1.1.
Assembly: hg38
Supplementary files format and content: outputs of cellranger software, which include barcodes, gene features and expression matrix for each sample

source_name: brain

extract_protocol:
For grafted organoids, cells were dissociated by Trypsin-EDTA (Life Technology)  into single cells; for organoid D42, Single cells were dissociated by trypLE (Life technology) into single cells.
For the scRNA-seq, S1000TM Touch Thermal Cycler (Bio Rad) was used for reverse transcription at 53°C  for 45 min, followed by 85°C for 5 min and final hold at 4°C. The quality of cDNA was accessed on Agilent 4200 (Agilent Technologies). Libraries of scRNA-seq were established by the Chromium Single Cell 3’ Library & Gel Bead Kit V3 (10X Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell.

value: brain

value: organoids

tag: genotype

value: WT


title: Kidney B_14

value: NO


title: GBOs_PFC_2MPT


title: METTL14 CUT&RUN Mettl3 Control mESCs rep2

value: mouse embryonic stem cells


title: SL2


title: Kidney B_13


title: METTL14 CUT&RUN Mettl3 Control mESCs rep1


title: SL1


title: CTMV3


title: Fish 28_2

city: Ås

first: Linn

middle: Haug

last: Eide

address: Oluf Thesens vei 6

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Raw reads cleaned by BBDuk (v34.56) to trim low quality reads, adapter sequences and PhiX (Illumina spike-in).
Fragments counted using featureCounts (c1.4.6-pl)
Differentially expressed genes estimated using SARTools R package (v1.7.3).
ShinyGO v0.76.3 used for enrichment analysis and funcitonal classification of differentially expressed genes
Term catergofies FDR < 0.05 displayed and sorted by fold enrichment (min GSSize = 2 %)
Assembly: Cleaned reads aligned to Salmo salar genome SSAL_v3.1 (GenBank assembly accession GCA_905237065.2

organism: Salmo salar

source_name: head kidney

extract_protocol:
RNA was isolated with 900 µL QIAzol lysis reagent (Qiagen, Hilden, Germany, cat. No. 79306) and a 5 mm  stainless steel bead (Qiagen, cat. No. 69989). The tissues were lysed with a Qiagen TissueLyser bead mill  (Retsch, Haan, Germany, cat. no. 85220)  at 20 Hz for 2 min (twice). 180 µL chloroform was added before  vortexing. Tubes were centrifuged at 12 000 rpm (4 °C) The upper phase containing RNA and water was  transferred to new tubes, and 450 µL isopropanol was added. Tubes were shaken by hand and incubated  for 10 min at room temperature, before centrifugation for 15 min. Excess liquid was removed and 200 µL  70 % ethanol was added before centrifugation at 10 min. The supernatant was removed, and the samples  were centrifugated for 3 min. With the lids open, the pellets dried for 5-10 min. The RNA was then  dissolved in 40 μL RNAse-free water, followed by a 10 min incubation at 55 °C. 20 ng/ul.
Poly A enrichment  and reverse transcription of cDNA.

value: head kidney


title: sid2_30_mock_rep3

data_processing:
Read data was initially assessed using FastQC. CLC Genomics Workbench version 11.0.2 (QIAGEN) was used for trimming adaptors and low-quality bases, reads trimmed below 20 bp were discarded, reads were then mapped to the Arabidopsis TAIR10 genome with the auto-detect paired distances option deselected. Raw count data was exported from CLC Genomics Workbench.
Assembly: TAIR10
Supplementary files format and content: comma-separated values file includes raw counts for each sample

source_name: whole seedling

extract_protocol:
Total RNA was extracted from pooled seedlings using TRIsure™ reagent (Meridian Bioscience) according to the manufacturer’s instructions. 5 µg of total RNA was was used for cDNA library preparation.
The cDNA library was prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with NEBNext® Poly(A) mRNA Magnetic Isolation Module and then multiplexed via PCR amplification using NEBNext® Multiplex Oligos for Illumina® according to the manufacturer’s instructions (New England Biolabs). Library concentration was quantified with Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific) followed by measurement of quality and average cDNA length using the DNA 1000 Series II chip on a 2100 Bioanalyzer (Agilent Technologies). The multiplexed cDNA libraries were then pooled (two sets of 36 libraries) and sequenced using both lanes of the NovaSeq 6000 (Illumina) S1 flow cell with run type 100 bp paired-end reads at the Genome Sequencing Service Center by the Stanford Center for Genomics and Personalized Medicine.

value: whole seedling

tag: ecotype

value: 30 min

value: mock


title: hiPS-CMs, D30, KO3

city: Zhengzhou

first: Ying

last: Peng

address: No.1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: ；The First Affiliated Hospital of Zhengzhou University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes row counts for each sample

source_name: heart

extract_protocol:
Total RNA was extracted through trizol reagent
polyA probes were used to retrieve mRNA from total RNA, then fragment and add adaptor to build a library

value: heart

value: Myh6 knock out


title: Fish 27_2


title: SLTMV3

value: leaf


title: Kidney B_12

source_name: Kidney

value: Kidney


title: GBOs_HIP_4MPT


title: Kidney B_10

value: Yes


title: CTMV1


title: hBOs_D0

description: Single cells were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 5000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 degrees Celsius for 45 min, followed by 85 degrees Celsius for 5 min and final hold at 4 degrees Celsius. cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell with a paired-end 150 bp (PE150) reading strategy.


title: hiPS-CMs, D30, KO2


title: Fish 23_2


title: CTMV2


title: GBOs_HIP_2MPT


title: CK3


title: Kidney B_11

value: Unknown


title: hiPS-CMs, D30, WT3


title: Fish 22_2


title: CK2


title: Kidney A_8


title: hiPS-CMs, D30, KO1


title: hiPS-CMs, D30, WT2


title: Fish 26_2


title: Kidney A_6


title: Fish 21_2


title: CK1


title: Kidney A_5


title: Fish 18_2


title: HiPSC-CMs, ABI_5

description:
ABI5
FPKM_allsamples.txt

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.1.0 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.1.0.
HTseq-count was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq25. Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package（v 3.2.0）, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3;WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite).
Assembly: GRCh38
Supplementary files format and content: FPKM

source_name: Human iPSC

extract_protocol:
RNA in iPSC-CMs was extracted using Trizol reagent(Invitrogen, CA, USA) according to the manufacturer’s recommendations.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V5 RNA-seq Library Prep Kit following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Human iPSC

value: Cardiomyocyte

tag: genetic modification

value: No

value: cultured for 7 days with ABI diluted in medium


title: Kidney A_4

tag: delayed graft function


title: hiPS-CMs, D30, WT1

value: WT


title: Fish 17_2


title: HiPSC-CMs, ABI_4

description:
ABI4
FPKM_allsamples.txt


title: Kidney A_9

value: NO

tag: person id


title: Fish 15_2

tag: tissue


title: Fish 16_2

tag: treatment


title: Kidney A_40


title: Fish 14_2


title: Kidney A_38


title: HiPSC-CMs, ABI_2

description:
ABI2
FPKM_allsamples.txt


title: Keratinocytes, mimics_ctrl_3

type: RNA

city: Chengdu

first: Qizhang

last: Wang

address: No. 14, Section 3rd, Renmin Nan Road. Chengdu, Sichuan 610041, China

institute: Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology,

hyb_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used

data_processing:
Expression data were analyzed by using Transcriptome Analysis Console 4.0. The follwoing criteria were used for data analysis:
Array Type: Clariom_S_Human
Analysis Type: Expression (Gene)
Analysis Version: version 2
Summarization Method: Gene Level - SST-RMA
Pos vs Neg AUC Threshold: 0,7
Genome Version: hg38 (Homo sapiens)
Annotation: Clariom_S_Human.r1.na36.hg38.a1.transcript.csv
Condition (Comparison): circRNA kd; ctr
Expression Analysis Settings:
• Gene-Level Fold Change < -2 or > 2
• Gene-Level P-Value < 0,05
• Anova Method: ebayes
• A Probeset (Gene/Exon) is considered expressed if ≥ 50% samples have DABG values below DABG Threshold.
• DABG < 0,05

label: biotin

source_name: Keratinocytes transfected with mimics control

label_protocol: One hundred fifty nanograms of total RNA was used to prepare cDNA following the GeneChip WT PLUS Reagent Kit labeling protocol

growth_protocol: Adult Human Epidermal Keratinocytes (HEKa) were cultured in EpiLife medium (Gibco™) supplemented with 10% Human Keratinocyte Growth Supplement (HKGS, Gibco™) and 1% penicillin/streptomycin (Gibco™) at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (ThermoFisher Scientific).

treatment_protocol: Third passage HEKa cells were seeded in 24-well plates. At 60-70% confluence, cells were transfected with 10nM miR-129-5p mimics or mimics control (GE Healthcare Dharmacon) using Lipofectamine 3000 (ThermoFisher Scientific). After 24 hours, cells were harvested for RNA extraction.

value: Skin

value: Keratinocytes

value: Control


title: Kidney A_37


title: HiPSC-CMs, ABI_1

description:
ABI1
FPKM_allsamples.txt


title: Fish 12_2

value: head kidney


title: 293T, sgNC, biol rep 1

extract_protocol:
RNAs were obtained using Trizol. Purified RNAs were digested with Dnase I.
After rRNA depletion using the RiboZero Plus rRNA depletion kit (Illumina), bisulfite converted RNAs with the EpiNext RNA-bisulfite conversion kit (Epigentek) were prepared using the TrueSeq Stranded Total RNA Library Prep kit (Illumina).

value: Human embryonic kidney cell

value: sgNC


title: HiPSC-CMs, Control_5

description:
Control6
FPKM_allsamples.txt

value: cultured for 7 days with ddH2O 1:1000 diluted in medium


title: Keratinocytes, mimics_ctrl_1

scan_protocol: Standardized array processing procedures recommended by Affymetrix, including hybridization, fluidics processing, and scanning, were used


title: Keratinocytes, mimics_ctrl_2


title: Keratinocytes, miR129_mimics _3

source_name: Keratinocytes transfected with miR-mimics

value: miR-129-5p overexpression


title: Fish 7_2


title: Kidney A_35

value: Kidney


title: HiPSC-CMs, Control_4

description:
Control5
FPKM_allsamples.txt


title: Fish 6_2


title: Kidney A_39


title: HiPSC-CMs, ABI_3

description:
ABI3
FPKM_allsamples.txt


title: Keratinocytes, miR129_mimics _1


title: HiPSC-CMs, Control_3

description:
Control4
FPKM_allsamples.txt


title: keratinocytes, Si-cASH1L-4

description: Keratinocytes transfected with si-cCHST15

source_name: Keratinocytes transfected with si-cASH1L

treatment_protocol: Third passage HEKa cells were seeded in 24-well plates. At 60-70% confluence, cells were transfected with 20nM siRNA against cASH1L or a non-targeting siRNA control (GE Healthcare Dharmacon) using Lipofectamine 3000 (ThermoFisher Scientific). After 24 hours, cells were harvested for RNA extraction.

value: si-cASH1L knockdown


title: Kidney A_31


title: Fish 3_2


title: HiPSC-CMs, Control_2

description:
Control3
FPKM_allsamples.txt


title: Fish 8_2


title: Kidney A_36

value: Yes


title: Kidney A_30


title: Fish 1_2


title: keratinocytes, Si-cASH1L-3


title: keratinocytes, Si-cASH1L-1


title: HiPSC-CMs, Control_1

description:
Control2
FPKM_allsamples.txt

value: Human iPSC


title: Fish 2_2


title: Keratinocytes, miR129_mimics _2


title: keratinocytes, Si-ctrl-3

description: Keratinocytes transfected with siRNA control


title: Kidney A_2


title: Kidney A_28


title: 786-0, MS023, rep2

city: Toronto

first: Laurie

last: Ailles

state: ON

address: 101 College St.

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Raw reads were processed using TrimGalore v0.6.6 to remove adaptor sequences (via cutadapt v3.0) and to assess read quality (via fastqc v0.11.5).
Reads then were mapped to the Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12) reference genome using STAR v2.7.9a.
Read counts per gene were subsequently obtained using the htseq-count command in the HTSeq v0.11.0 package alongside Gencode’s human genome annotation release 44.
Differential gene expression analysis based on the negative binomial distribution was performed on treated vs untreated cells using the DESeq2 R package v1.36.0. Genes were considered differentially expressed if they were found with a minimum |log2(fold-change)|≥ 0 and FDR adjusted p-value ≤ 0.01.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content:
DiffGeneList_243_7860_MS023.txt : Differential gene expression results from MS023 vs DMSO using DESeq2 R Package v1.36.0 (significant genes only)
DiffGeneList_243_7860_PRMT1KD : Differential gene expression results  from dox vs nodox using DESeq2 R Package v1.36.0 (significant genes only)
Other tab-delimited text files contain read counts per gene from HtSeq v0.110 using Gencode's human genome annotation release 44

source_name: ccRCC Tumor

growth_protocol: Cell lines in this study were routinely cultured in Iscove's Modified Dulbecco's Medium (IMDM, Wisent #319-105-CL) supplemented with 10% FBS (Thermo #12483020), and 1% penicillin/streptomycin (Wisent #450-201-EL) in a humidified incubator at 37oC with 5% CO2, 2%O2.

extract_protocol:
Cell pellets collected and washed in PBS. RNA isolation was performed using the Qiashredder kit (Qiagen, #79654) and the RNeasy mini kit (Qiagen, #74104). RNA quality was assessed on an RNA 6000 Pico chip (Agilent Technologies) using the Agilent Bioanalyzer to determine sample RNA integrity number (RIN) and quantified by the Qubit RNA HS assay kit (Life Technologies)
MS023: NEB stranded mRNA libraries were constructed and paired-end (100bp) next generation sequencing was performed on a Illumina NovaSeq 6000 S4 system. PRMT1 KnockDown: NEB stranded mRNA libraries were constructed and paired-end (150bp) next generation sequencing was performed on an Illumina NovaSeq X system.

treatment_protocol: 5uM MS023 (dissolved in DMSO) vs 0.1% DMSO alone was added to culture media for 3 days before cells harvested. For PRMT1 KnockDown condition, 1ug/mL dox (dissolved in sterile water) vs. no dox was added to culture media for 4 days before cells harvested.

value: ccRCC Tumor

value: 5uM MS023, 3 Days


title: Kidney A_29

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge


title: RNA_KO2

city: Wako city

first: Shintaro

last: Iwasaki

address: 2-1, Hirosawa

department: CPR

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: dm6
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
Testes were dissected from 2-3-day-adult-males in ice-cold PBS with 100 µg/ml cycloheximide. Dissected testes were immediately frozen with liquid nitrogen and stored at −80°C. We prepared 600 pairs of testes per sample. We prepared two replicates from WT (y1 w1118) and Mettl1-KO (Mettl1KO1) males, respectively.
Ribo-seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. RNA-seq: the libraries were prepared by a SEQuoia Express Standard RNA Library Prep Kit (Bio-Rad).

value: testis


title: Kidney A_34

first: John


title: RNA_KO1


title: Fish 28

source_name: distal intestine

value: distal intestine


title: 786-0, MS023, rep1


title: Kidney A_26

value: NO


title: 786-0, DMSO, rep2

value: 0.1% DMSO, 3 Days


title: keratinocytes, Si-ctrl-2

source_name: Keratinocytes transfected with siRNA control

value: Skin

value: Keratinocytes


title: keratinocytes, Si-ctrl-1

value: Control


title: RNA_WT2

value: CT


title: 786-0, DMSO, rep1


title: Fish 24


title: RNA_WT1


title: Fish 27


title: Fish 23


title: RCC243, MS023, rep2


title: Kidney A_24


title: RCC243, MS023, rep1


title: Fish 22


title: Ribo_KO2

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: dm6
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling


title: RCC243, DMSO, rep2


title: Fish 26


title: Fish 21


title: Kidney A_22


title: RCC243, DMSO, rep1


title: Ribo_KO1


title: Kidney A_21


title: Ribo_WT1


title: RCC243, -dox, rep3

value: no dox, 4 days


title: Fish 17


title: RCC243, -dox, rep2


title: Kidney A_20


title: Kidney A_23


title: Kidney A_25


title: Fish 18


title: Kidney A_1


title: RCC243, -dox, rep1


title: Fish 15


title: Sample B1

city: Dallas

first: Sneha

last: Korlakunta

state: TX

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

data_processing:
*library strategy: Spatial Transcriptomics
Raw sequencing data were processed with the 10X Genomics Space Ranger pipeline to generate FASTQ files. Sequences were aligned to the mm10 genome to gene expression count using Space Ranger's default settings.
Assembly: mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes, gene IDs
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv.gz: enrichment of features in the tissue
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions.csv.gz: list of spatial barcodes and the coordinates specifying spots

source_name: Tendon

growth_protocol: 10 week old C57BL/6 mice

extract_protocol:
V1 Visium FFPE
Spatial transcriptomics sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

treatment_protocol: 7 days post burn/tenotomy procedure

value: Tendon

value: 10 weeks

value: wild-type

value: burn/tenotomy procedure

tag: time point

value: 7 days post-injury


title: Sample A1


title: Kidney A_19

city: Cambridge

value: Kidney


title: Fish 16


title: Ribo_WT2


title: RCC243, +dox, rep3

value: ccRCC Tumor

value: 1ug/mL dox, 4 days


title: RCC243, +dox, rep2


title: TMV, biol rep 4

city: Cerdanyola del Vallès

first: Ignacio

last: Rubio-Somoza

state: Barcelona

address: Carrer de la Vall Moronta s/n, Campus UAB - Edifici CRAG

country: Spain

institute: CRAG

data_processing:
“FastQC” and “TrimGalore!” software was used for raw Illumina reads quality control analysis and  trimming  of  reads  containing  adaptor-   or  vector-derived  sequences, respectively
rRNA was detected and removed using “SortMeRNA 2.1b” software
Cleaned reads together with the transcriptome of Marchantia polymorpha as of  January 19th, 2021, were used to quantify gene expression at transcript level using the software “Salmon v1.4.0”
Raw counts aggregated by gene were obtained using tximport and the result was used as input to DESeq2 (software versions as of 19 January 2021). Then, genes adding up to less than 10 counts across all 8 samples were removed
Assembly: Marchantia polymorpha MpTak1v5.1_r1.mrna.fasta file from https://marchantia.info/download/tak1v5.1/, as of January 19th 2021
Supplementary files format and content: Tab-delimited matrix table with unnormalized gene counts for every gene and all 8 samples, after removing genes with less than 10 counts across all samples

organism: Marchantia polymorpha

source_name: thallus

growth_protocol: Marchantia gemmas were grown for 2 weeks in B5 media in sterile conditions upon continous light and 23ºC. After sap incubation, plants were transplanted to soil during 2 more weeks under the same light and temperature conditions

extract_protocol:
Acid phenol method followed by RNA clean up using columns from the Qiagen RNAeasy kit
Illumina Truseq poly A RNA kit was used following the instructions from manufacturer

treatment_protocol: Marchantia plants were incubated in sap from tobacco WT or TMV infected plants

value: thallus

value: all

value: Tak 1

value: TMV


title: Kidney A_18

value: Yes


title: Fish 14

value: distal intestine


title: Fish 12


title: TMV, biol rep 3


title: Kidney A_17


title: Fish 8


title: TMV, biol rep 2


title: RCC243, +dox, rep1


title: Fish 7


title: 786-0, -dox, rep3


title: Kidney A_15


title: TMV, biol rep 1


title: 786-0, -dox, rep2


title: Fish 6


title: mock , biol rep 4

value: mock


title: Kidney A_13

value: NO


title: mock , biol rep 3


title: 786-0, -dox, rep1

value: no dox, 4 days


title: Fish 3


title: Kidney A_12


title: Fish 2


title: 786-0, +dox, rep3


title: 786-0, +dox, rep2


title: Kidney A_16


title: mock , biol rep1


title: Fish 1


title: 786-0, +dox, rep1


title: KO MPP4_2

status: Public on Aug 15 2024

first: Srikanth

last: Kodali

address: 1 Baylor Plaza

data_processing:
Raw sequencing files (FASTQ format) were aligned to the mouse reference genome mm39
Duplicates were removed using SAMtools v.1.12
Differential expression analysis was performed using R package DESeq2
Assembly: mm39
Supplementary files format and content: csv file includes read counts for each sample

source_name: Blood

growth_protocol: Hematopoietic stem cells and multipotent progenitor populations were sorted from  bone marrow of mice

extract_protocol:
Total RNAs were extracted using the miRNeasy Micro Kit (QIAGEN).
RNA libraries were constructed according to NEBNext® Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tamoxifen

value: Blood

value: Hematopoietic

tag: cell subset

value: MPP

value: KO


title: KO MPP2_2


title: KO MPP4_3


title: KO MPP1_3


title: KO MPP2_1


title: KO MPP4_1


title: KO MPP1_2


title: KO MPP1_1


title: KO HSC_3

value: HSC


title: Kidney A_10

value: Kidney


title: Kidney B_15


title: KO HSC_1


title: KO HSC_2


title: WT MPP1_3

value: WT


title: WT MPP4_2


title: mock , biol rep 2


title: WT MPP4_1


title: Kidney A_11


title: WT MPP1_1


title: WT MPP1_2


title: WT MPP2_2


title: WT MPP2_3


title: WT HSC_2


title: WT HSC_1


title: WT MPP4_3


title: WT MPP2_1


title: KO MPP2_3


title: WT HSC_3


title: Wildtype-DMBA3

city: London, United Kingdom

first: Norzawani

middle: Binti

last: Buang

state: London

address: 9N15 Commonwealth Buidling, Ducane Road

institute: Imperial College London

data_processing:
Illumina CASAVA-1.8.4 software used for basecalling.
The reads quality was checked using FastQC (v0.12.1) and summarized with MultiQC (v1.11).
Reads were aligned to the FVB/NJ mice transcriptome (Mus_musculus_Fvb_Nj.FVB__NJ_v1.cdna.all.fa) using Salmon package (v.1.5.2).
Mapping quality, read distribution, gene body coverage, GC content, and rRNA contamination, were checked using picard-collecRNAseqmetrics (v.3.0.0) software.
Transcript level read counts were computed using Salmon package (v.1.5.2). Gene-level counts were generated from Salmon output using tximport (v1.26.1).
Assembly: FVB: Mus_musculus_Fvb_Nj.FVB__NJ_v1.cdna.all.fa
Supplementary files format and content: .sf count file from Salmon

source_name: Skin

extract_protocol:
Total RNA was extracted using Qiagen Rneasy mini kit with an additional purification step by on-column DNAse treatment using Rnase-free Dnase Kit (Qiagen)
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2 by Imperial BRC Genomic Facility

value: Skin

value: WT FVB

value: Naïve


title: TCRbko-DMBA3

value: TCRbko FVB

value: DMBA


title: TCRbko-DMBA2


title: Wildtype-DMBA2


title: Wildtype-Naive3


title: TCRbko---Tregs-DMBA3

value: DMBA+Tregs


title: TCRbko-DMBA1


title: TCRbko---Tregs-DMBA1


title: Wildtype-Naive1


title: Wildtype-Naive2


title: SBM1-1

city: Qinzhou City

first: Xin

last: Lu

address: 12 Binhai Avenue, Qinnan District, Qinzhou City, Guangxi, China

institute: Beibu Gulf University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Danio rerio
Supplementary files format and content: tab-delimited text fles include FPKM values for each Sample

organism: Danio rerio

source_name: intestine

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA Ilbraries for RNA-seq were prepared using SMAR TER mRNA-Seq library Prep Kit following manufacturer's protocols.

value: intestine


title: SBM1-2


title: SBM1-3


title: FM1-3


title: FM1-1


title: FM1-2


title: D3-4-3


title: D3-4-1


title: D3-4-2


title: Yusa plasmid

city: Portland

first: Peter

last: Ryabinin

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description:
LIB191203BD_S10_Yusa_plasmid_S10_L003
LIB191203BD_yusa_counts.txt

data_processing:
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Assembly: Custom reference created from CRISPR library
Supplementary files format and content: Read counts per sgRNA for each sample
Library strategy: CRISPR/Cas9 Genome Wide Screen

organism: synthetic construct

growth_protocol: MOLM13 cells constitutively expressing Cas9 were expanded in RPM1 supplemented with 10%FBS, 2% glutamine, and 1% Penicillin-Streptomycin to reach 300 million. Cells were then transduced with virus encoding Yusa CRISPR library and selected with puromycin and maintained in the same medium.

extract_protocol:
30 million cells were collected from Idasanutlin-treated flasks on day 14. DNA was extracted using Qiagen DNA extraction kit.
100 micrograms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)

treatment_protocol: Samples were treated with Idasanutlin (200nM or 50nM) or DMSO for 14 days.

tag: sample type

value: plasmid


title: TCRbko---Tregs-DMBA2


title: 10 DIV iMG rep 2

first: Emile

last: Wogram

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

data_processing:
Reads were aligned to the human (GRCh38) genomes using STAR v2.7.1a (indexed using Ensembl 96 transcript models).
Gene levels were determined with the methods used by Gosselin et al.  Briefly, SAM files were converted to HOMER tags, which were used (with Ensembl 96 transcript models) to generate raw counts with HOMER’s analyzeRepeats.pl.
Genes profiled were compared to those from Gosselin at el.  Raw counts and genes present in both experiments were used for further analysis.
Raw counts from both datasets were normalized with DESeq2 v1.22.2 using fitType="mean", log2-transformed, and then batch-corrected with ComBat (with data source as covariate) using the svn package in R.
Assembly: GRCh38 / hg38
Supplementary files format and content: Gene symbol and raw counts from HOMER
Supplementary files format and content: Gene symbol and DESeq2-normalized counts for all samples

source_name: Human foreskin fibroblasts from Coriell Institute (AG07095) were reprogrammed to pluripotent stem cells and differentiated to microglia

growth_protocol: Cells were cultured in microglia differentiation media containing Neurobasal media (Life Technologies, #21103049) supplemented with Gem21 without Vitamin A (Gemini Bio-Products, #400161), 2 mM GlutaMax (Life Technologies), 100 U/mL penicillin, 100 μg/mL streptomycin with full media changes every 5-7 days.

extract_protocol:
RNA was isolated using the Qiagen MicroRNeasy+ kit according to the manufacturer’s protocol.
3 ng of RNA was prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines.

treatment_protocol: For microglia neural co-cultures, 1 million neurons were dissociated and cultured for another 4 weeks, during which they multiplied. Then, 1 million microglia precursor cells were added and microglia differentiation media was used in media changes every 4-7 days.

value: pluripotent stem cell derived microglia

value: normal karyotype, male

value: cultured in monocultures


title: 10 DIV iMG rep 4

value: Human foreskin fibroblasts from Coriell Institute (AG07095) were reprogrammed to pluripotent stem cells and differentiated to microglia


title: 10 DIV iMG rep 5


title: 10 DIV iMG co-culture rep 6

source_name: Human foreskin fibroblasts from Coriell Institute (AG07095) were reprogrammed to pluripotent stem cells and differentiated to microglia and neural cells

value: pluripotent stem cell derived microglia and neural cells

value: cultured together with isogenic, human pluripotent stem cell-rerived neural cells


title: 10 DIV iMG rep 1


title: 10 DIV iMG co-culture rep 5

value: Human foreskin fibroblasts from Coriell Institute (AG07095) were reprogrammed to pluripotent stem cells and differentiated to microglia and neural cells


title: 10 DIV iMG co-culture rep 3


title: Wildtype-DMBA1


title: MOLM13 Idasanutlin 50nM D14 Replicate 1

description:
LIB191203BD_D14_Ida_50nM_L006
LIB191203BD_yusa_counts.txt

value: Idasanutlin (50nM)


title: 10 DIV iMG co-culture rep 1


title: 10 DIV iMG co-culture rep 2


title: MOLM13 Idasanutlin 200nM D14 Replicate 2

description:
LIB191203BD_D14_Ida_200nM_2_L006
LIB191203BD_yusa_counts.txt

value: Idasanutlin (200nM)


title: 10 DIV iMG co-culture rep 4


title: MOLM13 DMSO D14 Replicate 1

description:
LIB191203BD_D14_DMSO_1_L006
LIB191203BD_yusa_counts.txt

value: DMSO


title: MOLM13 Idasanutlin 200nM D14 Replicate 1

description:
LIB191203BD_D14_Ida_200nM_1_L006
LIB191203BD_yusa_counts.txt


title: Myc-CLK2+GFP-CPSF6

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing data were analyzed with our in-house pipeline (Fu et al. 2011, 2015)
Sequencing reads were mapped to the human hg19 reference genomes, and internal priming was filtered.
poly(A) sites were defined for each sample by clustering the unique mapped reads, and then, the poly(A) sites were merged together across samples.
Assembly: hg19
Supplementary files format and content: Wiggle Track format files containing a graphical trace on a genome

growth_protocol: HEK293T were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested and total RNA was extracted with TRIzol
1 ug total RNA was used to prepare the IVT-SAPAS library according to the previous report (Fu et al., 2015). The quality of the library was evaluated with a Qsep400 Advance.

treatment_protocol: HEK293T cells were transiently transfected with plasmids carrying Myc tagged CLK2(Myc-CLK2) or carrying PEGFP tagged CPSF6/CPSF6_6SA

value: Human embryonic kidney cells

value: Myc-CLK2+GFP-CPSF6 overexpression


title: Myc+GFP-CPSF6_6SA

value: GFP-CPSF6_6SA overexpression


title: Myc+GFP

value: WT


title: Myc+GFP-CPSF6

value: GFP-CPSF6 overexpression


title: Myc-CLK2+GFP

value: Myc-CLK2 overexpression


title: 10 DIV iMG rep 6


title: Myc-CLK2+GFP-CPSF6_6SA

value: Myc-CLK2+GFP-CPSF6_6SA overexpression


title: 10 DIV iMG rep 3

value: pluripotent stem cell derived microglia


title: Patient_082_During [PAT_082_D_IgA]

type: protein

city: Manchester

first: Fidel

last: Ramirez Bencomo

state: England

address: Michael Smith Building

department: FBMH/SBS/EIGen

institute: The University of Manchester

description:
PT_IgA_Slide_1.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection

hyb_protocol: Slides were blocked with 200 µL of SuperG Blocking Buffer (Grace Biolabs, US) per well and incubated for one hour at room temperature (RT). Washes were done three times with 300μL TBS‐T (0.05% Tween‐20) and once in TBS for 10 min, slides were incubated in the dark for 1hr at 20°C with 100μL of Goat Anti-Human IgG Fc (DyLight 650) pre-adsorbed secondary antibody (ab98622, Abcam, UK), using a working dilution of 1:5000 in blocking agent. The arrays were incubated for IgA detection with 100 μL of Goat Anti-Human IgA alpha chain (DyLight 650) pre-adsorbed secondary antibody (ab96998, Abcam, UK), using a working dilution of 1:5000 in blocking agent. Slides were rinsed in de-ionised water and dried by centrifugation at 200 x g for 2 min.

scan_protocol: Slides were scanned in an InnoScan 710 (Innopsys, France) with the photomultiplier tube set to 40% for 635 nm. Image analysis and data quantification was carried out using Mapix v9.1.0 - Microarray image acquisition and analysis software (Innopsys, France).

data_processing: Microarray spot intensities were quantified using Mapix v9.1.0 Microarray Image Analysis software (Innopsys, France), which utilises automatic background subtraction for each spot. The spot intensities for each protein were recorded in quintuplicate; arithmetic means were determined, and spot intensities for buffer-only controls were subtracted

molecule: protein

source_name: Gonococcal infection

label_protocol: Secondary antibodies were purchased from Abcam: Goat Anti-Human IgG Fc (DyLight® 650) pre-adsorbed secondary antibody (ab98622, Abcam, UK) and Goat Anti-Human IgA alpha chain (DyLight® 650) pre-adsorbed secondary antibody (ab96998, Abcam, UK)

extract_protocol: Human sera collected from the KEMRI clinics in Mtwapa and Malindi and from clinical trial NCT 04297436

tag: Sex

value: Male

tag: subject group

value: Individual with confirmed infection

value: Blood

tag: tissue subtype

value: Serum


title: Patient_080_After [PAT_080_A_IgA]

description:
PT_IgA_Slide_5.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection

label: Goat Anti-Human IgA alpha chain (DyLight® 650) pre-adsorbed secondary antibody


title: Patient_080_During [PAT_080_D_IgA]


title: Patient_082_Before [PAT_082_B_IgA]


title: Patient_079_During [PAT_079_D_IgA]


title: MOLM13 DMSO D14 Replicate 2

description:
LIB191203BD_D14_DMSO_2_L006
LIB191203BD_yusa_counts.txt

tag: cell line


title: Patient_077_During [PAT_077_D_IgA]

description:
PT_IgA_Slide_4.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_078_After [PAT_078_A_IgA]


title: Patient_079_Before [PAT_079_B_IgA]


title: Patient_076_During [PAT_076_D_IgA]


title: Patient_078_During [PAT_078_D_IgA]


title: Patient_077_After [PAT_077_A_IgA]


title: Patient_075_Before [PAT_075_B_IgA]


title: Patient_076_Before [PAT_076_B_IgA]


title: Patient_075_During [PAT_075_D_IgA]


title: Patient_075_After [PAT_075_A_IgA]


title: Patient_074_During [PAT_074_D_IgA]


title: Patient_081_During [PAT_081_D_IgA]


title: Patient_074_Before [PAT_074_B_IgA]


title: Patient_070_Before [PAT_070_B_IgA]

description:
PT_IgA_Slide_3.gpr
A historical cohort of individuals with laboratory-confirmed gonococcal infection


title: Patient_068_After [PAT_068_A_IgA]


title: Patient_070_During [PAT_070_D_IgA]


title: Patient_071_Before [PAT_071_B_IgA]


title: Patient_072_During [PAT_072_D_IgA]


title: Patient_073_Before [PAT_073_B_IgA]


title: Patient_072_Before [PAT_072_B_IgA]


title: Patient_067_During [PAT_067_D_IgA]


title: Patient_068_During [PAT_068_D_IgA]


title: Patient_066_During [PAT_066_D_IgA]


title: Patient_066_Before [PAT_066_B_IgA]


title: Patient_074_After [PAT_074_A_IgA]


title: P2_PNEU_Day8_K2

city: Bielefeld

first: Ingo

last: Todt

address: Morgenbreede 1

department: Ear, nose and throat medicine

country: Germany

institute: University of Bielefeld

data_processing:
The ATAC-seq reads of each sample were mapped to the human reference genome GRCh38 using Bowtie2 v2.5.0 with default settings. Samtools v1.16.1 was used for formatting, quality filtering, and removing duplicates to guarantee unique mapping; the MAPQ (mapping quality, 0=non-unique, >10 probably unique) was set to a sophisticated value of 30.
After examining each replicate separately, replicates of respected groups were combined to maximize the peak calling strength using the samtools merge function. MACS3 v3.0.0b1 was used for peak calling with the parameters “–nomodel –nolambda –keep-dup auto –call summits” the peaks were filtered by a q-value cutoff of 0.05. The sequences of peaks from 250 bp upstream and 250 bp downstream of the peaks were extracted with R v4.2.2 and Bedtools v2.30.0 (R-Citation). In R v4.2.2 GenomicRanges v1.42.0 linked the ATAC-Seq peaks with the nearest genes. The promoter was defined as the region within 2 kb of the reference transcript start site. Enriched motifs in the peak sequences were analyzed with MEME-ChIP v5.5.1 and default settings. Gene ontology analysis of the identified motifs was done with GOMo v5.5.1. The differential peak analysis of the ATAC-seq was performed using HOMER2 v4.11 with a replicate FDR cutoff of 0.05 for peak identification calculated by DESeq2 v1.24.0. The genomic annotation of the peaks was determined using ChIPSeeker v1.34.1. The genomic distribution of peaks was visualized using Adobe Illustrator 2023 (Adobe Inc., San Jose, USA).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file

source_name: Tongue base

extract_protocol:
ATAC-seq analysis was performed with technical replicates (n=3). ATAC-seq was performed according to Buenrostro et al. with harvested P1 and P2 cells, including isolation of intact nuclei and tagging with Tn5 transposase.
After cell preparation, transposition reaction, library preparation, and purification, the quality of libraries was assessed using an Agilent Bioanalyzer High Sensitivity DNA Analysis kit. Sequencing was performed first on an Illumina MiSeq system in paired-end mode 2 x 50 bp and finally on the Illumina NextSeq 2000 system in paired-end mode 2 x 50 bp with P3 chemistry

value: Tongue base

tag: cell type

value: epithelial cancer cells

value: undifferentiated


title: P2_CFM_Day8_C1

value: differentiated


title: P2_PNEU_Day8_K3