title: THP1-DSF-MLL_S9,ChIP-seq

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

data_processing:
RNA-seq: Run data were demultiplexed and converted to fastq files using Illumina’s fastq Conversion Software v2.19.  Fastq files were pre-processed to remove adapter contamination and poor-quality sequences (trimmomatic v0.36) before being mapped to the human genome (GRCh38) using the STAR aligner (v2.5b). Mapped data were deduplicated using Picard Tools (v2.7.1) and the remaining reads per transcript were counted by FeatureCounts (v1.4.6p5). Normalisation, modelling and differential expression analysis were then carried out using SARTools (v1.3.2), an integrated QC and DESeq2 BioConductor wrapper. Significant genes, filtered by a desired Benjamini-Hochberg False Discovery Rate and fold change.
ChIP-seq: Sequenced reads were aligned against the UCSC human reference genome (GRCh38) with Burrows-Wheeler Aligner (BWA) program with default parameters. The BAM files were subjected to removal of potential PCR and optical duplicates using Picard MarkDuplicates option. Fragment length and quality measurement for each dataset were determined using PhantomPeakQualTools based on strand cross-correlation approach. Two metrics named normalized strand cross-correlation coefficient (NSC) and relative strand cross-correlation coefficient (RSC) were used for data quality assessment. BigWig files were generated using a custom bam to bigwig script.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: read counts per transcript. ChIP-seq: bigwig files.

growth_protocol: THP-1 cells were routinely cultured in Roswell Park Memorial Institute (RPMI) medium (Sigma-Aldrich), supplemented with 10% or 20% heat-inactivated FBS, penicillin-streptomycin (100µg/ml) and  L-glutamine (2mM) (all Sigma-Aldrich)

extract_protocol:
Total RNA was isolated using the RNAeasy Mini Kit (Qiagen).For MLL chromatin immunoprecipitation, 25 million cells were crosslinked with disuccinimidyl glutarate (DSG) 2mM, incubated for 30 minutes at room temperature on a rotating wheel and then washed three times with PBS. Subsequently, cell pellets were fixed in formaldehyde 1% for 15 minutes at room temperature on a rotating wheel and the crosslinking reaction was stopped by adding 0.125M glycine for 5 minutes at RT. For H3K4me3 and H3K27ac chromatin immunoprecipitation cells were crosslinked with formaldehyde 1% only. After single or dual crosslink cells were rinsed twice in cold PBS and cell pellets were suspended in buffer A (Triton X100 0.25%, EDTA 10mM, EGTA 0.5mM, HEPES 20mM pH 7.6). After incubation on rotating wheel at 4°C for 10 min cells were centrifuged and resuspended in buffer B (NaCl 150mM, EDTA 10mM, EGTA 0.5mM, HEPES 20mM pH 7.6). After 10 min on rotating wheel cells were centrifuged and cell pellet was resuspended in ChIP incubation buffer (SDS 0.15%, Triton X100 1%, NaCl 150mM, EDTA 10mM, EGTA 0.5mM, HEPES 20mM pH 7.6) supplemented with protease inhibitor cocktail (Roche) and incubated for 30min on ice. Chromatin was sonicated using a Bioruptor® Pico sonicator (Diagenode) for 13 cycles, 30sec ON and 30sec OFF. Sonicated chromatin was centrifuged at 13.200rpm for 10min and supernatant was collected for ChIP. For every ChIP 900µl of chromatin (corresponding to 15x106) were diluted 1:10 in incubation buffer supplemented with BSA 0.1%, protease inhibitor cocktail (Roche), 30µl of protein A beads (Millipore) and 3µg of antibody (MLL-N, Diagenode (cat no C15310265); H3K4me3 Active Motif (cat no 39915); H3K27ac Millipore (cat no Ab4729)) incubated overnight at 4°C on rotating wheel. Beads were washed twice with buffer 1 (SDS0.1%, sodium deoxycholate 0.1%, Triton X100 1%, NaCl 150mM, Tris 10mM pH8, EDTA 0.1mM, EGTA 0.5mM), one time with buffer 2 (SDS 0.1%, sodium deoxycholate 0.1%, Triton X100 1%, NaCl 500mM, Tris 10mM pH8.0, EDTA 0.1mM, EGTA 0.5mM), one time with buffer 3 (LiCl 0.25M, sodium deoxycholate 0.5%, NP40 0.5%,  Tris 10mM pH8.0, EDTA 0.1mM, EGTA 0.5mM), one time with buffer 4 (Tris 10mM pH8.0, EDTA 0.1mM, EGTA 0.5mM). Chromatin was eluted from the beads using 400µl of elution buffer (SDS 1%, NaHCO3 0.1M) at room temperature for 20 minutes. Protein-DNA crosslink were reversed in NaCl 200mM at 65°C overnight, after which DNA was subjected to RNase and proteinase K digestion for 2 hours at 55°C. The DNA was extracted by using the MinElute PCR purification kit (Qiagen)
Samples for RNA-seq were processed using the KAPA mRNA HyperPrep Kit (p/n KK8580) according to manufacturer’s instructions. Briefly, mRNA was isolated from total RNA using Oligo dT beads to pull down poly-adenylated transcripts. The purified RNA was fragmented using chemical hydrolysis (heat and divalent metal cation) and primed with random hexamers.  Strand-specific first strand cDNA was generated using Reverse Transcriptase in the presence of Actinomycin D. The second cDNA strand was synthesised using dUTP in place of dTTP, to mark the second strand. The resultant cDNA was then “A-tailed” at the 3’ end. Truncated adaptors, compatible with Illumina sequencing, were ligated to the A-Tailed cDNA. Ligated cDNA molecules were then enriched with limited cycle PCR (10-14 cycles – the actual number was dependent on the amount of input RNA). To make the library strand specific only the first strand was amplified for sequencing. Libraries were quantified (using Qubit and Bioanalyser), normalised and pooled before sequencing on a NextSeq 500 (Illumina, San Diego, US) generating 43bp read pairs per sample. ChIP-seq samples were processed using the NEB DNA Ultra II Library Kit (p/n E7645) according to manufacturer’s instructions. Briefly, 5ng of ChIP DNA was end-repaired then “A-tailed” at the 3’ end to prevent self-ligation and adapter dimerisation. Truncated 0.6µM adaptors, containing a T overhang were ligated to the A-Tailed cDNA before a “double-SPRI” bead size selection was used to remove both large (>300bp) and non-ligated adaptors (<150bp). Double ligated DNA molecules were then enriched with limited cycle PCR (12 cycles) utilising NEB’s Q5 high fidelity polymerase. The primers used in this PCR extend the adaptor to full length and contain sequences that allow each library to be uniquely identified by way of a sample-specific 6bp index sequence. Libraries to be multiplexed in the same run were pooled in equimolar quantities, calculated from Qubit and Bioanalyser fragment analysis. Samples were sequenced on the NextSeq 500 instrument (Illumina, San Diego, US) using a 43bp paired-end recipe.

treatment_protocol: THP-1 cells were treated for 4 hrs with DSF

value: DSF (4 hr) treated

tag: tag

value: ChIP-seq

value: MLL-N


title: Organoids, Cys247X.AS, D130, Rep1

status: Public on Aug 01 2022

type: SRA

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

country: France

institute: CNRS-Universite Paris Sud

library_source: transcriptomic

data_processing:
Image analysis and base calling is performed using the Illumina Real Time Analysis (3.4.4) software with default parameters.
Pass-filtered reads were mapped using STAR 2.7.3a
Count table of the gene features was obtained using FeatureCounts
Stattistics and Differential expression analysis done with EdgeR
Pathways analysis representation done with the package GOPlot
Assembly: Ensembl genome assembly GRCh38 (release 98)
Supplementary files format and content: Tab-delimited text files of the raw counts

molecule: total RNA

organism: Homo sapiens

source_name: patient derived Retinal organoids

extract_protocol:
Total RNAs were extracted using the NucleoSpin RNA XS kit according to the manufacturer’s protocol. RNA yields and quality were determined using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer.
For RPE cells, RNA-seq libraries were constructed from 1 µg of total RNAs using the TruSeq Stranded mRNA Sample Prep (Illumina) and paired-end sequencing of 75 bases length was performed on a HiSeq 4000 system (Illumina). For retinal organoids, RNA-seq libraries were constructed from 1 µg of total RNAs using the NEB Next Ultra II Directional RNA (New England Biolabs) and paired-end sequencing of 100 bases length was performed on a Novaseq system (Illumina).

tag: tissue

value: patient derived Retinal organoids

tag: cell line

value: iPSCs

tag: genotype

value: Asymptomatic

tag: time


title: elongating 0 day rep 2 (JA5)

city: Blacksburg

first: Song

last: Li

state: VA

country: USA

institute: Virginia Tech

data_processing:
raw reads were mapped using STAR, number of mapped reads were counted using featureCounts and differentially expressed genes were identified using DESeq2
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: ReadCounts_022017.xlsx

organism: Oryza sativa

source_name: elongating 0 day

growth_protocol: Rice plants were grown in pots in a greenhouse until the 4.2-leaf stage.

extract_protocol:
Total RNAs were extracted from frozen tissues using a miRNeasy Mini kit (Qiagen, Hilden, Germany). Genomic DNA was eliminated by on-column digestion.
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols
paired-end

treatment_protocol: Plants were completely submerged for 0, 1, 3, and 6 days. Immediately after de-submergence at each time point, the 5th (elongating) leaves and lower (non-elongating) leaves were separated, frozen in liquid nitrogen, and stored at -80C until use.

value: elongating leaves

tag: treatment

value: control

value: 0 day


title: C3wt

city: Columbus

first: Brenda

middle: J.

last: Lilly

state: OH

address: 700 CHILDREN'S DRIVE

institute: NATIONWIDE CHILDREN'S HOSPITAL

data_processing:
Analysis was performed employing a combination of programs including STAR, HTseq, Cufflink and wrapped scripts by Novagene.
Differential expression between the two groups were determined through edgeR (package 3.16.5).
Assembly: Mouse mm10
Supplementary files format and content: Gene normalized expression per sample csv file

organism: Mus musculus

source_name: Aorta

extract_protocol:
RNAeasy Mini spin columns (Qiagen)
Novagene

value: Aorta

value: Wild-type


title: Organoids, Control, D130, Rep5

value: Control


title: Organoids, Control, D130, Rep6


title: non-elongating 0 day rep 3 (JA3)

source_name: non-elongating 0 day

value: non-elongating leaves


title: elongating 0 day rep 1 (JA4)


title: THP1-DSF-H3K4_S7,ChIP-seq

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: C2wt


title: C1wt


title: THP1-DSF-H3K4_S5,ChIP-seq


title: THP1-DSF-H3K27_S3,ChIP-seq


title: non-elongating 0 day rep 2 (JA2)


title: Organoids, Control, D130, Rep4


title: non-elongating 0 day rep 1 (JA1)


title: non-elongating 0 day rep 1 (JA7)


title: THP1-DSF-H3K27_S1,ChIP-seq


title: Organoids, Control, D130, Rep2


title: Organoids, Control, D130, Rep3


title: THP1-CTRL-MLL_S10,ChIP-seq

value: untreated


title: Organoids, Control, D130, Rep1


title: THP1-CTRL-H3K4_S8,ChIP-seq


title: NoC ORX + T GC121203

city: Heverlee

first: Sarah

last: El Kharraz

address: Herestraat 49

country: Belgium

institute: KU Leuven

description: NoC ORX + T

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7
Adapters were filtered with ea-utils fastq-mcf v1.05 Erik Aronesty (2011), ea-utils: “Command-line tools for processing biological sequencing data”; https://github.com/ExpressionAnalysis/ea-utils)
Splice-aware alignment was performed with HiSAT2 against the mouse reference genome mm10. Reads mapping to multiple loci in the reference genome were discarded.
Resulting BAM files were handled with Samtools v1.5 (Li et al, Bioinformatics,2009). Quantification of reads per gene was performed with HT-seq Count v2.7.14.
Count-based differential expression analysis was done with R-based Bioconductor package DESeq2 (Love MI, Huber W, Anders S (2014), “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550).  Reported p-values were adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text files include DESeq2 normalized values for each
Supplementary files format and content: tab-delimited text files include size factor for normalization values for each

source_name: Prostate

extract_protocol:
Ventral prostates were removed and snap-freezed in liquid nitrogen. RNA was extracted via Nucleospin Triprep column purification.
Libraries were generated with the Illumina TruSeq

value: Prostate

value: ARNoC/Y

value: Testosterone


title: NoC ORX + T GC121202

description: NoC ORX + T


title: NoC ORX + T GC121204

description: NoC ORX + T


title: NoC ORX + T GC121201

description: NoC ORX + T


title: THP1-CTRL-H3K4_S6,ChIP-seq


title: Control

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

description: singel cell RNA-seq of bone marrow cells

library_source: transcriptomic single cell

data_processing:
Initial data processing was performed using the Cell Ranger version 3.0 pipeline (10X Genomics)
Post-processing, including filtering by number of genes expressed per cell, was performed using the Seurat package.
Following clustering and visualization with UMAP Embedding.
Identification of cell clusters was performed on the final aligned object guided by marker genes.
Assembly: mm10
Supplementary files format and content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

molecule: polyA RNA

source_name: Bone marrow-derived cells

extract_protocol:
Single cell suspension of BM-derived cells in RT Master Mix (75 µl) was loaded on the Single Cell A Chip and partitioned with a pool of ~750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing: (i) an Illumina R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 10 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence. Upon dissolution of the Gel Beads in a GEM, the primers were released and mixed and incubated with cell lysate and RT Master Mix, producing barcoded, full-length cDNA from poly-adenylated mRNA.
Silane magnetic beads were used to isolate cDNA from leftover biochemical reagents and primers in the post GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient DNA for library construction. Enzymatic fragmentation and size selection were used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

tag: strain

value: Bone marrow

tag: disease

value: Atherosclerosis

tag: age

value: 6 months


title: Experimental


title: Gastric pit cells_multiplexed

city: Shanghai

first: Ying

last: Wei

address: No.800 Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

data_processing:
Raw data were preprocessed using FastQC software (Version 0.11.5). Low-quality RNA-seq reads were removed using Trimmomatic software (Version 0.35). Then, the reads were mapped onto the mouse genome
(mm10) using HISAT2 software (Version 2.1.0). Transcripts counting was accomplished using HTSeq-count software. The reads per million mapped reads (RPM) were used to measure transcript abundance.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: The file sample_metadata.txt contains the barcode for each individual sample.

source_name: Stomach

extract_protocol: The cDNA library was prepared using the protocol of SCRB-seq.The sequencing library was prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (#TD501, Vazyme, China) following manufacturer's protocols. All the samples are in one library.

tag: Sex

value: female

value: Stomach

tag: cell type

value: Gastric pit cells

value: WT

value: multiplexed sample:week 1,2,3,4,5 and 8


title: Organoids, Cys247X.Iso, D100, Rep3

value: patient derived Retinal organoids

value: iPSCs

value: Isogenic


title: Organoids, Cys247X.Iso, D100, Rep2


title: NoC ORX + T GC121200

description: NoC ORX + T


title: THP1-CTRL-H3K27_S4,ChIP-seq

value: ChIP-seq


title: Organoids, Cys247X.Iso, D100, Rep1


title: NoC ORX + V GC121199

description: NoC ORX + V

value: Vehicle


title: THP1-CTRL-H3K27_S2,ChIP-seq

value: untreated


title: NoC ORX + V GC121198

description: NoC ORX + V

value: Prostate


title: Organoids, Cys247X, D100, Rep5

value: Symptomatic


title: Suspension_1

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

country: Germany

institute: Max Planck Institute

description:
data from three samples of different organoid pools, grown in two different conditions each
Organoids_dome_vs_suspension_countmatrix.txt

data_processing:
Fastq files were processed with zUMIs (version 2.9.5) using its miniconda environment (Parekh et al. 2018) with STAR index 2.7 (Dobin et al. 2013), samtools (version 1.9) (Li et al. 2009) and “featureCounts” from Rsubread (version 1.32.4) (Liao et al. 2013). Reads were mapped to Mus musculus (mm10) with Ensembl annotation version GRCm38.93.
Libraries were  down-sampled  within  zUMIs,  depending  on  library  size  variability: Single organoid libraries were down sampled to 4-12 million reads and the suspension-dome data to 3-6 million reads. Passage 4 vs 11 orgsnoids bulk RNA-seq data was not downsampled.
Downstream computational analysis was conducted in R (version 3.6.3). The count matrix was normalized and filtered with edgeR (version 3.28.1) (Robinson et al. 2010) using “filterByExpr” with min.count = 3. For differential gene expression analysis, the limma-voom approached by limma (version 3.42.2) (Ritchie et al. 2015) was used with a pipeline including linear model fit (lmFit) and p-value adjustment for multiple testing (“topTableF” with adjust.method = ‘BH’, “decideTests” with method = ‘global’).
Assembly: mm10
Supplementary files format and content: countmatrix

source_name: organoids

growth_protocol: Organoids were maintained as 30 μl Matrigel domes in a 37 °C incubator at 5% CO2 and 20% O2. The medium was changed every 2 days and cultures passaged every 5-7 days with mechanical dissociation of the Matrigel. Organoids  cultured  in  a  dilute  suspension  culture were maintained in a 10% Matrigel mixture. The cultures were maintained on an orbital shaker at 80 r.p.m. in a 37 °C incubator, 5% CO2, 20%  O2.  Every  3-4  days,  the  organoids  were  passaged  by  mechanical  breakdown  of  the Matrigel.

extract_protocol:
The  mRNA  was  extracted  with  the  Dynabeads  mRNA  DIRECT  Kit  by  Fisher  Scientific (#61011)  with  a  few  modifications  and  self-made  buffers.  For  each  sample  (i.e., single organoid) 10 μl of resuspended beads were transferred to a 2 ml DNA low-binding tube and supernatant was discarded with the help of a magnet stand. Beads were resuspended in 50 μl room temperature Lysis/Binding Buffer. With a volume of 150 μl room temperature Lysis/Binding Buffer, each organoid was transferred to a 1.5 ml low-  binding tube already containing the equivalent amount of buffer. The content was pipetted up and  down  5  times  to  allow  lysis.  The  following  steps  were  performed  according  to  the manufacturer’s instructions.
Equal amounts of mRNA per sample were used for cDNA synthesis with Maxima H Minus reverse transcriptase  (Thermo  Fisher  Scientific).  During  reverse  transcription,  unique  barcodes including  unique  molecular  identifiers  (UMI)  were  attached  to  each  sample.  After  cDNA synthesis, all samples were pooled and processed in one single tube. After purification and ExoI treatment, cDNA was PCR-amplified for 12 cycles and subsequently purified. cDNA was tagmented in 10 technical replicates of 1 ng cDNA each   using the Nextera XT Kit (Illumina), according to the manufacturer's instructions.

value: liver organoid

value: 3-4 months old


title: Suspension_2


title: Suspension_3


title: THP1-DSF-4-16H_S11,RNA-seq

value: DSF (4 hr) treated

value: RNA-seq

value: no antibody


title: THP1-DSF-6-16H_S12,RNA-seq


title: NoC ORX + V GC121197

description: NoC ORX + V

value: ARNoC/Y


title: Dome_3


title: THP1-DSF-3-16H_S10,RNA-seq


title: NoC ORX + V GC121196

description: NoC ORX + V


title: Organoids, Cys247X, D100, Rep4


title: Organoids, Cys247X, D100, Rep3


title: NoC ORX + V GC121195

description: NoC ORX + V


title: Dome_1


title: THP1-CTRL-6-16H_S9,RNA-seq


title: Organoids, Cys247X, D100, Rep2


title: WT ORX + T GC121194

description: WT ORX + T

value: Wild type

value: Testosterone


title: Organoids, Cys247X.AS, D100, Rep3

value: Asymptomatic


title: Set4_9

description:
each sample is data from one organoid
singleOrganoids_countmatrix.txt


title: THP1-CTRL-3-16H_S7,RNA-seq


title: RNAseq, SW480 WT, replicate 2

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

data_processing:
Reads were quality filtered and adapter trimmed using Cutadapt.
Trimmed reads were mapped to the human genome (GRCh38) using STAR.
Mapping was converted to indexed bam files using SAMtools.
In R Studio, mapped reads were summarized to gene-level counts using SummarizeOverlaps from GenomicAlignments and differential expression analysis was done using DESEQ2
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx format, raw counts, DESeq2 processed data

source_name: SW480 WT

growth_protocol: SW480 WT or eIF5A2 KO were grown in DMEM supplemented with 10% FBS

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal carcinoma cells

value: WT


title: Organoids, Cys247X.AS, D100, Rep2

value: patient derived Retinal organoids

value: iPSCs


title: WT ORX + T GC121193

description: WT ORX + T


title: Set4_8


title: Organoids, Cys247X.AS, D100, Rep1


title: WT ORX + T GC121192

description: WT ORX + T


title: WT ORX + T GC121191

description: WT ORX + T


title: Set4_5


title: WT ORX + T GC121190

description: WT ORX + T


title: Set4_6


title: RNAseq, SW480 eIF5A2 KO, replicate 1

source_name: SW480 eIF5A2 KO

value: eIF5A2 KO


title: Organoids, Control, D100, Rep6

value: Control


title: RNAseq, SW480 eIF5A2 KO, replicate 2


title: Organoids, Control, D100, Rep5


title: THP1-CTRL-4-16H_S8,RNA-seq

value: untreated


title: Dome_2


title: Organoids, Cys247X, D100, Rep1

value: Symptomatic


title: Ribosome profiling, SW480 WT, replicate 2

data_processing:
Library strategy: Ribo-Seq
Reads were quality filtered and adapter trimmed using Cutadapt.
Trimmed reads were mapped to the human genome (GRCh38) using STAR.
Mapping was converted to indexed bam files using SAMtools.
In R Studio, mapped reads were summarized to gene-level counts using SummarizeOverlaps from GenomicAlignments and differential expression analysis was done using DESEQ2
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx format, raw counts, DESeq2 processed data


title: Set4_2

value: liver organoid


title: Set4_7

value: 3-4 months old


title: Organoids, Control, D100, Rep4


title: WT ORX + V GC121188

description: WT ORX + V

value: Prostate

value: Vehicle


title: WT ORX + V GC121187

description: WT ORX + V


title: Organoids, Control, D100, Rep3


title: Ribosome profiling, SW480 WT, replicate 1


title: RNAseq, SW480 WT, replicate 1


title: Ribosome profiling, SW480 eIF5A2 KO, replicate 1


title: Set4_1


title: Organoids, Control, D100, Rep1


title: WT ORX + V GC121185

description: WT ORX + V


title: Ribosome profiling, SW480 eIF5A2 KO, replicate 2


title: Set4_4


title: MBP29_3

city: La Jolla

first: Johannes

middle: Carolus Magnus

last: Schlachetzki

state: CA

address: 9500 Gilman Drive  #0651

department: Cellular and Molecular Medicine

institute: UCSD

data_processing:
FASTQ files demultiplexed by Illumina bcl2fastqs from HiSeq4000 sequencing experiments were mapped to the UCSC genome build mm10. STAR with default parameters was used to map RNA-seq experiments (Dobin et al., 2013). The “analyzeRepeats” function of HOMER was used to quantify the gene expression raw counts with the parameters “-raw -count exons -strand both -condenseGenes” and a table of transcripts per million mapped reads (TPM) values using “-tpm - -count exons -condenseGenes” (Heinz et al., 2010). Raw counts within each gene body were used as input for DESeq2 (Love et al., https://doi.org/10.1186/s13059-014-0550-8. Significance was assessed at a false discovery rate (FDR) of 0.05 using the Benjamini-Hochberg method and an effect size cutoff of 2-fold change in expression. For heatmaps, TPM of differentially expressed genes of sorted microglia of MBP29-ha-syn and WT mice or the cortex, the corpus callosum and the striatum on PLX5622- and control-treated MBP29-ha-syn and WT mice were determined. Average TPM values were calculated for each group. Heatmaps were based on Canberra distance matrices and Ward’s minimum variance method for hierarchical clustering of groups with the pheatmap package in R. Gene ontology (GO) enrichment analysis was done using Metascape (http://metascape.org) (Tripathi et al., 2015).
Regional log2 fold changes between MBP29-ha-syn and WT mice of the X genes commonly upregulated in microglia of MBP29-ha-syn mice were analyzed through Ingenuity Pathway Analysis (IPA®) from QIAGEN® (Krämer et al., 2014). Comparative analysis was performed and canonical pathways, upstream regulators, and diseases and functions were inferred after filtering for “mouse“ as species and “nervous system“ as the tissue of interest.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated TPM and raw counts

source_name: CD11B+CD45+ microglia

extract_protocol:
RNA isolation: 1) Microglia Isolation: MBP29-hα-syn and WT mice that were 16 weeks old were deeply anaesthetized with CO2 and subsequently perfused intracardially with ice-cold PBS. Afterwards, whole brains were removed and gently homogenized mechanically on ice in staining buffer (HBSS 1x (Life Technologies, 14175-095), 0.5% BSA, 1 mM EDTA) using a 2 ml polytetrafluoroethylene pestle (Wheaton, 358026), first in a 14 ml round-bottom tube (BD Falcon, 352059) and further in a 2 ml glass mortar (Wheaton 358004). Homogenates were filtered onto a 70 μm cell strainer (BD Falcon 352350) and centrifuged at 400 x g for 10 min. The Pellet was resuspended in 6 ml 37% isotonic Percoll (Sigma, P4937). After underlaying the pellet with 5 ml of 70% isotonic Percoll in a 15 ml centrifuge tube (Corning, 430790), the tubes were centrifuged at 600 x g for 40 min at 16-18°C, without acceleration or deceleration. Cells of interest at the 37%–70% Percoll interphase were recovered and washed once in 15 ml HBSS prior to FACS. Isolated microglia were first incubated in 200 µl staining buffer on ice with CD16/CD32 blocking antibody (eBioscience, 14-0161-82) for 15 min. About 5% of cells were taken for unstained control. The remaining cells were stained with anti-mouse CD11b-APC (eBioscience, 17-0112-82, clone M1/70, 1:100) and CD45-Alexa488 (BioLegend 103122, clone 30-F11, 1:100) antibodies for 30 min. DAPI (1:5000) was used to visualize dead cells. After washing with PBS, cells were centrifuged at 300 x g for 5 min. The pellet was then resuspended in 500–1000 µl staining buffer. Sorting of microglia from forebrains of 16 week old animals was performed on a BD Influx cell sorter. Microglia were defined as singlets, CD11b+CD45low events, which encompassed >95% of all CD11b+ events. For RNA isolation from three archived brain regions (corpus callosum, cortex, and striatum; n = 3 per brain region) after 12 weeks of treatment of MBP29-hα-syn and WT mice with PLX5622 or control, frozen samples were placed in 350 µl TRIzol (Life Technologies, 15596018). Samples were homogenized using Kontes cordless motor (VWR, KT749540-0000) with Kontes RNase-free pellet pestle grinders for 1.5-ml microtubes (VWR, KT-749521-1590). The lysate was then centrifuged for 5 min at 500 x g at 4–10°C, and the supernatant was transferred to new tubes. Total RNA from both microglia and bulk brain regions was extracted using the Direct-zol RNA MicroPrep Kit (Zymo Research, R2062) and stored at -80C until RNA-seq cDNA libraries preparation. Poly(A) selection of RNA was performed as previously described by Gosselin and colleagues (Gosselin et al., Science 2017).
Briefly, RNA samples were incubated with Oligo d(T) Magnetic Beads (NEB, Ipswich, MA, S1419S) and poly(A) enriched RNA was collected. To fragment poly(A) RNA, samples were incubated at 94°C for 9 min on beads in 2x Superscript III first-strand buffer with 10 mM DTT (Thermo Fisher Scientific). Next, RNA in 2x SuperScript III (Life Technologies, cat 18080-044) buffer was incubated for 1 min at 50°C on a PCR cycler with 2.5 µl of the following mix: 1.5 µg Random Primer (Life Technologies 48190-011), 10 µM Oligo d(T) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in dH2O. Samples were then immediately placed on ice for 5 min. First-strand synthesis was performed by incubation at 25°C for 10 min and 50°C for 50 min on a PCR cycler with 7.6 µl of the following mix: 0.2 µg actinomycin (Sigma A1410), 13.15 mM DTT (Life Technologies), 0.026% Tween-20, 100 units SuperScript III, in dH2O. After incubation, RNA/DNA complexes were isolated by adding 36 µl of Agencourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and 10 min on ice. Samples were placed on a magnet and beads were washed twice with 150 µl of 75% ethanol. Following washings, beads were air-dried for 10-12 min and eluted with 10 µl of water. Afterwards, second-strand synthesis was performed. RNA/DNA samples in 10 µl dH2O were incubated for 2.5 h at 16°C with 5 µl of the following mix: 3x Blue Buffer (Enzymatics), 1.0 µl PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 µl Sera-Mag SpeedBeads (Thermo Scientific, 651520505025), resuspended in 30 µl 20% PEG 8000/2.5 M NaCl, incubated at RT for 15 min and placed on a magnet for two rounds of bead washing with 80% ethanol. Beads were air dried for 10-12 min and DNA was eluted from the beads by adding 40 µl dH2O. Supernatant was collected on a magnet and placed on ice or stored at -20°C until DNA blunting, poly(A)-tailing, and adapter ligation. Sequencing libraries were prepared from generated cDNA by blunting, A-tailing, and adapter ligation as previously described7 using barcoded adapters (NextFlex, Bioo Scientific). Prior to final PCR amplification, RNA-seq libraries were digested by 30 min of incubation at 37°C with Uracil DNA Glycosylase (final concentration of 0.134 units per µl of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-350 bp) by gel extraction (10% TBE gels, Life Technologies EC62752BOX). RNA-seq libraries were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 (Illumina, San Diego, CA) according to manufacturer’s instruction. GO term analysis was performed on metascape.org website.

treatment_protocol: PLX5622 (1,200 mg/kg p.o.); Mice were treated with PLX5622 containing or standard AIN-76A chow beginning at 4 weeks of age for a period of 3 or 12 weeks

tag: group

value: MSA

value: CD11B+CD45+ microglia

tag: experimental

value: M


title: Set4_14


title: Hs_14w-ivc_MS309_228

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: cDNAs amiplified from 1 ng total RNA extracted from cells using SC3-seq technology

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_GRCh38.p12, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.

source_name: An oocyte from 14w-ivc rOvary

extract_protocol:
Fetal ovaries collected from human fetus were carefully dissected out in chilled PBS.  Fetal ovaries at 8-14 wpf were minced with scissors in 0.05% trypsin/EDTA/PBS solution (GIBCO, 15400-054), then incubated for 15 min at 37℃ with gentle pipetting every 5 min.  Dissociation medium [DMEM (GIBCO, 10313021) containing 10% FBS, 2mM L-glutamine (GIBCO, 25030081), 1X penicillin/streptomycin (GIBCO, 15070063), and 100μg/mL DNaseI (MERCK, DN25)] was added for further dissociation.  For SC3-seq analysis, cells were picked under the inverted microscope (OLYMPUS, IX71) to exclude multiplet cells.   For dissociating human rOvaries, tissues were incubated with TryPLE Express (1X) (GIBCO, 12604021) for 5 min.  After adding dissociation medium, cells were processed for single-cell analyses. Dissociated germ cells were manually picked using glass capillaries under the stereo microscope (Leica, S8 APO).  Following cDNA synthesis and amplification methods were previously described (Nakamura et al., 2015).
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).

tag: developmental stage

tag: in vitro culture period

value: 14 weeks

value: Germ cell


title: Hs_14w-ivc_MS321_225


title: Set4_13


title: D24_NACL_scRNAseq

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

description: 10X Genomics scRNAseq

data_processing:
Raw sequence reads were quality-checked using the FastQC software. The CellRanger version 4.0.0 was used to process, align and summarize unique molecular identifier (UMI) counts against the 10X Genomics pre-built human GRCh38 and mouse mm10 reference genome dataset (2020-A, July 7, 2020). Downstream analyses were performed on R using Seurat (v4.0.1) (Satija et al. 2015). Human cells were retained and mouse cells (MEFs) were filtered out by adjusting the number of counts per cell (nCount_RNA) and the number of mapped genes per cell (nFeature_RNA) to only keep cells that were mostly mapped to the human GRCh38 (hg38) genome. Cells with more than 25% of mitochondrial counts were filtered out. Count matrix was normalised with Seurat global-scaling normalization method “LogNormalize'' that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a 10000 scale factor, and log-transforms the result.
Assembly: Human GRCh38 (hg38) GENCODE v32/Ensembl 98 and mouse GRCm28 (mm10) GENCODE vM23/Ensembl 98 reference genome dataset (version 2020-A, July 7 2020).
Supplementary files format and content: count matrix includes counts per gene per cell (.csv) and annotations describes (.csv)

source_name: Human induced pluripotent stem cells

growth_protocol: Human naive (Sigma hiPSCs) to primitive endoderm and naive extraembryonic endoderm (nXEN)  conversions were done using the following previously described protocol (Linneberg-Agerholm et al. 2019). Naïve human PSCs were seeded at a high density (split ratio of 1:1 or 2:1) directly in RACL medium, which is Roswell Park Memorial Institute 1640 medium (RPMI; Gibco, 218750-34) supplemented with 1 X GlutaMAX, 1 X B27 minus insulin (Gibco, A18956- 01), 1 % (v/v) Pen/Strep, 100 ng/mL Activin A (PeproTech, 120-14E), 3 μM CHIR99021 and 10 ng/ml recombinant human LIF onto fresh MMC-MEF feeders in hypoxia. Cells were kept in RACL medium for at least 7-8 days and medium was refreshed every day. After primitive endoderm cells reached confluency, they were dissociated with TrypLE or Accutase and re-plated onto fresh MMC-MEF feeders at a ratio of 1:2 to 1:4 in NACL medium, which is composed of N2B27 supplemented with 100 ng/mL Activin A, 3 μM CHIR99021, 10ng/ml recombinant human LIF and 10μM Y-27632. These nXEN cells were subcultivated every 4-7 days with TrypLE or Accutase.

extract_protocol:
Cells were washed with 1X PBS before dissociation from the culture dish by TryplETM Express Enzyme (ThermoFisher, 12605-036) incubation for 8 minutes at 37°C. Single cell suspension was filtered through a Falcon 40 µm Cell Strainer and centrifuged at 200G for 5 min. After resuspension in 1X PBS with 0.04% BSA, the single cell suspension was counted with a Luna-FL automated Fluorescence Cell Counter (Logos Biosystems). TSCs were mixed with primed and naive hPSCs using the following ratio (H9 primed: Sigma primed: H9 naive: Sigma naive: Sigma TSCs = 1:1:1:1:2)
Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) targeting 2000 cells (Next GEM Single Cell 3’ library and Gel Bead Kit v3.1) according to the manufacturer’s protocol (10x User Guide; CG000204, Revision D). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification and library construction were all performed according to the manufacturer’s protocol. Individual sample quality was assessed using a Tapestation (Agilent). Qubit 2.0 (ThermoFisher Scientific) and KAPA Library Quantification Kit for Illumina Platform (KAPA Biosystems) were used for library quantification before pooling. The final library pool was sequenced on the NovaSeq6000 (Illumina) instrument using NovaSeq SP kit (Illumina) for 2 lanes of 100-base-pair paired-end reads.

value: XENs and EXMCs

value: ICSIG-1 Sigma hiPSC line


title: D6_RACL_scRNAseq

description: 10X Genomics scRNAseq

value: Primitive endoderm and EXMCs


title: Hs_14w-ivc_MS285_262


title: D70_sortedEXMC_scRNAseq

description: 10X Genomics scRNAseq

data_processing:
Raw sequence reads were quality-checked using the FastQC software. The CellRanger version 4.0.0 was used to process, align and summarize unique molecular identifier (UMI) counts against the 10X Genomics pre-built human GRCh38 and mouse mm10 reference genome dataset (2020-A, July 7, 2020). Downstream analyses were performed on R using Seurat (v4.0.1) (Satija et al. 2015). Human cells were retained and mouse cells (MEFs) were filtered out by adjusting the number of counts per cell (nCount_RNA) and the number of mapped genes per cell (nFeature_RNA) to only keep cells that were mostly mapped to the human GRCh38 (hg38) genome. Cells with more than 25% of mitochondrial counts were filtered out. Count matrix was normalised with Seurat global-scaling normalization method “LogNormalize'' that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a 10000 scale factor, and log-transforms the result.
Assembly: Human GRCh38 (hg38) GENCODE v32/Ensembl 98 and mouse GRCm28 (mm10) GENCODE vM23/Ensembl 98 reference genome dataset (version 2020-A, July 7 2020).
Supplementary files format and content: count matrix includes counts per gene per cell (.csv) and annotations describes (.csv).
Supplementary files format and content: loom files.

growth_protocol:
Naive hPSCs (H9 hESCs and Sigma hiPSCs) were cultured on mitotically inactivated MEF feeders in 5% O2 and 5% CO2 incubator under humidified conditions at 37°C. All naive hPSCs were cultured in PXGL medium (Bredenkamp/Guo Stem cell reports 2019 (PMID: 31708477) which consists of 1:1 DMEM/F12 and Neurobasal, 0.5% N2-supplement, 1% B27-Supplement, 2 mM L-Glutamine, 0.1 mM β-mercaptoethanol, 1x penicillin-streptomycin, 1 μM PD0325901 (Axon Medchem and Wellcome-MRC Cambridge Stem Cell Institute), 2 μM XAV939 (Sigma), 2 μM Gö6983 (Tocris), 20 ng/mL human LIF (PeproTech and Wellcome-MRC Cambridge Stem Cell Institute) and 10 μM Y-27632 (Tocris and Cell Guidance Systems). Naive hPSCs were passaged every 4-5 days in a ratio 1:2 or 1:3 by single-cell dissociation with Accutase followed by filtering through a 40 μm cell strainer.
Human naive to trophoblast and EXMC conversion was done using the following previously described protocol (Dong et al. 2020; Cinkornpumin et al. 2020). Naive hPSCs were seeded in such a way that expecting at least 90% confluency by Day 2 on mitomycin C treated MEFs after dissociating in single-cell using TryplE (for 15 min at 37°C) in their respective naive culture conditions supplemented with 10μM Y-27632. The very next day the media was switched from naive to trophoblast stem cell medium (Okae et al. 2018) consisting of DMEM/F12 (Gibco) supplemented with 0.3% BSA, 0.2% FBS, 1% Penicillin-streptomycin, 1% insulin-transferrin-selenium-ethanolamine-X 100 supplement, 1.5 μg/ml L-ascorbic acid, 0.5 μM A83-01, 1μM SB431542, 50ng/ml hEGF, 2uM CHIR99021, 0.8 mM Valproic acid, 0.1 mM β-mercapto-EtOH (Gibco) and 5 μM Y-27632. The medium was changed every two days supplemented with 5 μM Y-27632. From passage 1 onwards cultures were cultured and maintained on 5 μg/ml Collagen IV coated tissue culture treated plates in hypoxia conditions (5% O2 and 5% CO2) and passaged every 4 days in 1:3 or 1:6 splitting ratios.

value: EXMCs


title: WT ORX + V GC121189

description: WT ORX + V

value: Wild type


title: Set4_11


title: MBP29_2


title: Hs_14w-ivc_MS321_224


title: D18_ASECRiAV_scRNAseq

description: 10X Genomics scRNAseq

value: hTSCs and EXMCs


title: Hs_14w-ivc_MS285_260


title: MBP29_het_3

value: Control


title: Set4_10


title: Set4_12


title: MBP29_1


title: MBP29_het_2


title: D13_ASECRiAV_scRNAseq

description: 10X Genomics scRNAseq


title: Hs_14w-ivc_MS285_259


title: WT ORX + V GC121186

description: WT ORX + V


title: D8_ASECRiAV_scRNAseq

description: 10X Genomics scRNAseq


title: Set3_6


title: MBP29_het_1


title: Hs_14w-ivc_MS285_258


title: MSA_STR_PLX3

source_name: Bulk Striatum

value: Bulk Striatum

value: PLX


title: Set3_5

value: liver organoid

value: 3-4 months old


title: MSA_STR_PLX2


title: Set3_4


title: D2_ASECRiAV_scRNAseq

description: 10X Genomics scRNAseq


title: Hs_14w-ivc_MS285_257


title: D1_ASECRiAV_scRNAseq

description: 10X Genomics scRNAseq


title: MSA_STR_NoTx3

value: No treatment


title: D0_Naïve_PXGL_scRNAseq

description: 10X Genomics scRNAseq

value: naive pluripotent stem cells


title: Hs_14w-ivc_MS285_256


title: Hs_14w-ivc_MS277_070


title: MSA_STR_NoTx2

value: MSA


title: Set3_2


title: Set3_1


title: MSA_STR_NoTx1

value: M


title: CTRL_STR_PLX2

value: CTRL


title: Hs_14w-ivc_MS285_254

value: 14 weeks

value: Germ cell


title: D4_ASECRiAV_scRNAseq

description: 10X Genomics scRNAseq

value: ICSIG-1 Sigma hiPSC line


title: Set2_9


title: Hs_14w-ivc_MS285_253


title: Set2_8


title: CTRL_STR_NoTx2


title: CTRL_STR_PLX1


title: Hs_14w-ivc_MS277_073


title: Hs_14w-ivc_MS321_222


title: Set2_7


title: Set2_6


title: Hs_14w-ivc_MS321_221


title: CTRL_STR_NoTx1


title: Set2_5


title: Set4_3


title: MSA_CC_PLX3

source_name: Bulk Corpus Callosum

value: Bulk Corpus Callosum


title: Set3_3


title: Hs_14w-ivc_MS285_250


title: MSA_CC_PLX1


title: Hs_14w-ivc_MS285_249


title: Set2_4


title: Hs_14w-ivc_MS285_255


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 10 uM Retinoic acid [M10_c]

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
The processed reads were aligned with TopHat , allowing for 5 mismatches to the reference human genome  GRCh38, with annotations from Ensembl release 99.
Quantification was done with htseq-count. Counts of technical replicates were averaged and merged into a single sample (termed ab)
Normalization, quality control plots (PCA, MA-plots) and differential expression analysis were performed using the DESeq2 package
Pair-wise comparisons were tested with default parameters using the Wald test, without using the independent filtering algorithm. Significance threshold was taken as p-adj<0.1. In addition, significant genes were further filtered by the log2(fold change) value. This filtering was baseMean-dependent and required a baseMean above 5 and an absolute log2FoldChange higher than 5/sqrt(baseMean) + 0.6. For highly expressed genes this means a requirement for a fold change of at least 1.5, while genes with a very low expression would need a 7-fold change to pass the filtering
Assembly: GRCh38, with annotations from Ensembl release 99
Supplementary files format and content: DESeq2 normalized base mean conts per gene per samples after averaging of technical replicates raw counts

source_name: induced pluripoten stem (iPS)-derived brain microvascular endothelial-like cells (iBMECs)

growth_protocol: The experiments described in this manuscript were approved by the Soroka Medical Center, Beer sheva, under IRB-SCRO protocol 0005-14-SOR. iPSCs were cultured on Matrigel-coated 6-well plates in with daily replacements of Nutristem (Biological Industries, Ltd). Cells were cultured at 37°C and 5% CO2. Cells were passaged weekly using EZ-Lift (Millipore) according to the manufacturer’s instructions.

extract_protocol:
Total RNA Purification kit (Norgen Biotek Corp.)
NovaSeq6000 SP Reagent kit 100 cycles (Illumina, 20028401)

treatment_protocol: iPSCs were differentiated into iBMECs as previously described (Lippmann et al., 2014). Briefly, cells were cultured in Nutristem for 3 days after passaging. When cells reached a density of 2x105 cells per well, medium was replaced with 3 ml of unconditioned medium without bFGF (UMF, 1:1 DMEM:F12) supplemented with 20% Knock-out serum-free (KOSR, Gibco), 1% NEAA, 0.5% Glutamax (Gibco), 220 nM β-mercaptoethanol and 1% PSA. On day 6 the medium was replaced with human Endothelial Serum Free medium (ESFM, Gibco) supplemented with 20ng/ml bFGF and 0, 0.25, 1 or 10 µM of RA in DMSO. On day 8, transwells, plastic dishes or coverslips were pre-coated with 100 µg/ml fibronectin (BI) : 400 µg/ml collagen IV (Sigma) and incubated overnight. On the day of seeding the extracellular matrix solution was aspirated and left to dry for 30 mins. iBMECs were harvested in Accutase (Gibco) for 30 mins, then washed with ESFM, counted, and centrifuged. iBMECs were resuspended in ESFM at 1x106 cells/ml and plated on 12 mm with 0.4 µm pore polycarbonate membrane transwell inserts (Corning, cat# 3401); 1 ml of fresh ESFM was supplemented to the bottom chamber and 1 ml of ESFM with cells was applied per transwell. 100 μl were added to 96-wells and 500 μl were added to 24-well plates with coverslips.

value: POR-mutated line

tag: cell type_source

value: iPS-derived

value: POR-mutated (PORM)

value: 10 uM Retinoic acid


title: Hs_14w-ivc_MS285_248


title: MSA_CC_NoTx2


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 10 uM Retinoic acid [M10_b]

value: induced pluripoten stem (iPS)-derived brain microvascular endothelial-like cells (iBMECs)


title: Set2_2


title: MSA_CC_NoTx1


title: Hs_14w-ivc_MS285_247


title: CTRL_CC_PLX2

value: PLX


title: Set2_1

value: liver organoid


title: CTRL_CC_PLX1


title: CTRL_CC_NoTx3


title: Set2_10

value: 3-4 months old


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 1 uM Retinoic acid [M1_b]

value: 1 uM Retinoic acid


title: Hs_14w-ivc_MS277_058


title: Hs_14w-ivc_MS277_057


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 1 uM Retinoic acid [M1_a]


title: Hs_14w-ivc_MS285_245


title: CTRL_CC_NoTx2

value: No treatment


title: Set1_9


title: Set2_3


title: CTRL_CC_NoTx1


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [M025_c]

value: 0.25 uM Retinoic acid


title: Set1_8


title: MSA_CX_PLX3

source_name: Bulk cortex

value: Bulk cortex

value: MSA

value: M


title: Hs_14w-ivc_MS285_244

value: 14 weeks

value: Germ cell


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 10 uM Retinoic acid [M10_a]


title: Hs_14w-ivc_MS285_246


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [M025_b]


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 1 uM Retinoic acid [M1_c]


title: Set2_11


title: Hs_14w-ivc_MS285_243


title: Set1_6


title: MSA_CX_PLX1


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 0 uM Retinoic acid [M0_c]

value: 0 uM Retinoic acid


title: MSA_CX_PLX2


title: Set1_5


title: Hs_14w-ivc_MS285_242


title: Set1_4


title: MSA_CX_NoTx3


title: Set1_3


title: MSA_CX_NoTx2


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 0 uM Retinoic acid [M0_a]

value: POR-mutated line


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 10 uM Retinoic acid [P10_c]

value: POR-deficient patient

value: iPS-derived

value: POR-deficient (PORD)


title: Hs_14w-ivc_MS277_051


title: Hs_14w-ivc_MS277_055


title: Set1_7


title: Set1_2


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [M025_a]

value: induced pluripoten stem (iPS)-derived brain microvascular endothelial-like cells (iBMECs)

value: POR-mutated (PORM)


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 10 uM Retinoic acid [P10_b]

value: 10 uM Retinoic acid


title: Set1_1

value: liver organoid

value: 3-4 months old


title: CTRL_CX_PLX3

value: CTRL

value: PLX


title: CTRL_CX_PLX2

value: Bulk cortex


title: Hs_14w-ivc_MS277_049


title: Set1_10


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 10 uM Retinoic acid [P10_a]


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 1 uM Retinoic acid [P1_b]

value: 1 uM Retinoic acid


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 1 uM Retinoic acid [P1_c]


title: POR-mutated line (PORM) iPS-derived BMECs differentuated with 0 uM Retinoic acid [M0_b]


title: Hs_14w-ivc_MS277_048


title: Hs_14w-ivc_MS285_241


title: CTRL_CX_NoTx3

value: No treatment

value: M


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 1 uM Retinoic acid [P1_a]


title: Hs_14w-ivc_MS277_047

value: 14 weeks

value: Germ cell


title: MSA_CX_NoTx1

value: MSA


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [P025_c]

value: POR-deficient patient

value: 0.25 uM Retinoic acid


title: Hs_14w-ivc_MS277_046


title: CTRL_CX_NoTx2


title: CTRL_CX_NoTx1


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [P025_b]

value: iPS-derived

value: POR-deficient (PORD)


title: Hs_14w-ivc_MS277_050


title: Hs_14w-ivc_MS285_240


title: Set4_15


title: Hs_14w-ivc_MS285_238


title: Hs_14w-ivc_MS321_219


title: LN_rep3

first: Ye Ji

last: Shin

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Low quality and adapter sequence were trimmed from the sequenced read.
Reads were aligned to mm10 using Bowtie2 or STAR
Artifacts derived from clonal amplification were circumvented by considering a maximum of three tags from each unique genomic position
Fragments per kilobase of exon per million fragments mapped(FPKM) value and Transcript Per Million(TPM) were caculated using StringTie v2.1.3b or RSEM.
Differentially expressed genes were identified by statistical analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene count, FPKM and TPM values for each sample

source_name: lung

extract_protocol:
Neutrophils were sorted by FACS Aria III, and RNA was isolated with Trizoal reagent. 1 μg of total RNA was prepared for the library by Illumina TruSeq Standard mRNA Sample Prep Kit.
RNA libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit

value: Lung

value: neutrophil

value: wild type


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [P025_a]

value: induced pluripoten stem (iPS)-derived brain microvascular endothelial-like cells (iBMECs)


title: LN_rep2


title: mE_22_25_1_scRNA-seq

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome or mm9 mouse transcriptome  (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Mouse Embryonic Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

value: Mouse Embryonic Cells

tag: Stage


title: Hs_14w-ivc_MS285_237


title: mE_26_scRNA-seq

tag: tissue


title: LN_rep1


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 0 uM Retinoic acid [P0_c]

value: 0 uM Retinoic acid


title: CTRL_CX_PLX1

value: Bulk cortex

value: CTRL

value: PLX


title: mE_22_25_scRNA-seq


title: mE_20_21_scRNA-seq


title: Hs_14w-ivc_MS285_236


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 0 uM Retinoic acid [P0_b]


title: BN_rep3

source_name: blood

value: Peripheral blood


title: Hs_14w-ivc_MS285_235

value: 14 weeks


title: BN_rep2


title: Hs_14w-ivc_MS285_234

value: Germ cell


title: mE_15_19_scRNA-seq


title: BN_rep1


title: Control iPS-derived BMECs differentuated with 10 uM Retinoic acid [C10_c]

value: Control

value: Healthy control

value: 10 uM Retinoic acid


title: POR-deficient patient (PORD) iPS-derived BMECs differentuated with 0 uM Retinoic acid [P0_a]

value: POR-deficient patient

value: iPS-derived


title: mE_14_scRNA-seq


title: Control iPS-derived BMECs differentuated with 10 uM Retinoic acid [C10_b]


title: Hs_14w-ivc_MS285_233


title: mE_13_14_scRNA-seq


title: BMN_rep2

source_name: bone marrow

value: Bone marrow


title: BMN_rep1

value: neutrophil


title: mE_11_12_scRNA-seq


title: Hs_14w-ivc_MS285_232


title: Control iPS-derived BMECs differentuated with 10 uM Retinoic acid [C10_a]


title: Hs_8w-ivc_MS321_238

source_name: An oocyte from 8w-ivc rOvary

value: 8 weeks


title: mE_6_10_27_scRNA-seq


title: Hs_8w-ivc_MS321_237


title: Control iPS-derived BMECs differentuated with 1 uM Retinoic acid [C1_c]

value: induced pluripoten stem (iPS)-derived brain microvascular endothelial-like cells (iBMECs)

value: 1 uM Retinoic acid


title: Control iPS-derived BMECs differentuated with 1 uM Retinoic acid [C1_b]


title: mE_4_scRNA-seq

value: Mouse Embryonic Cells


title: Control iPS-derived BMECs differentuated with 1 uM Retinoic acid [C1_a]


title: RNA-seq_Veh_rep3

extract_protocol:
Neutrophils were isolated with Percoll gradient and 10 μM of PGE2 or vehicle were treated for 24 hours. After that, RNA was isolated with Trizoal reagent. 1 μg of total RNA was prepared for the library by Illumina TruSeq Standard mRNA Sample Prep Kit.
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit

value: neutrophils

value: wild type

value: vehicle


title: Hs_8w-ivc_MS285_298


title: RNA-seq_Veh_rep2


title: mE_5_scRNA-seq


title: mE_1_3_scRNA-seq


title: Hs_8w-ivc_MS321_236


title: Hs_8w-ivc_MS285_296


title: BMN_rep3


title: Control iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [C025_c]

value: 0.25 uM Retinoic acid


title: RNA-seq_PGE2_rep3

value: 10 uM PGE2


title: Control iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [C025_b]


title: RNA-seq_PGE2_rep2


title: RNA-seq_PGE2_rep1


title: Hs_8w-ivc_MS285_295

value: Germ cell


title: Control iPS-derived BMECs differentuated with 0.25 uM Retinoic acid [C025_a]

value: Control


title: Hs_8w-ivc_MS321_235


title: Ythdf2 cKO

city: duarte

first: Shoubao

last: Ma

state: California

address: 1500 East Duarte Road

institute: City of Hope

data_processing:
Cell Ranger (version 5.0.1) was used to process the raw data, demultiplex cellular barcodes, map reads to the transcriptome, and down-sample reads (as required to generate normalized aggregate data across samples). Genes with less detected cell numbers (less than 3) and cells with less detected genes (less than 200) were removed. Low-quality cells were removed if the number of expressed genes was smaller than 200 or larger than 5000. Cells were also removed if their proportions of mitochondrial gene expression were larger than 7.5%. Finally, 19,530 single cells remained, and they were applied in downstream analyses. To cluster single cells by their expression, the unsupervised graph-based clustering algorithm implemented in Seurat R package (version 4.0.4) was used for each data set. Top 2,500 variable genes identified by vst method were used to perform principal component analysis. 1-30 PCs were used in FindNeighbors function. The FindClusters function was used to determine the clusters (res = 0.7), and then they were visualized with 2D tSNE plots.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include clusters and marker genes

source_name: mouse immune cells

growth_protocol: Tumors from WT or cKO mice were extracted and digested with collagenase type IV (1 mg/ml) and DNase type I (30 U/ml) for 30 min at 37 °C. The cells were filtered through the 70 μm cell strainers, washed with phosphate-buffered saline (PBS), lysed in red blood cell buffer, and resuspended in PBS. Tumor-infiltrating immune cells (CD45+ cells) were sorted by FACSAria Fusion Flow Cytometer (BD Biosciences).

extract_protocol:
The cell suspension (300-600 living cells per microliter) was loaded onto the Chromium single cell controller (10 x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
Libraries were subsequently prepared sing Single Cell 5’Library and Gel Bead Kit and sequenced on an Illumina NovaSeq 6000 instrument with pair-end 100 bp (PE100) reading strategy.

treatment_protocol: Tumor-infiltrating immune cells (CD45+ cells) were purified  from WT or Ythdf2 cKO mice.

value: tumor

tag: genotype/variation

value: Ythdf2 cKO


title: Control iPS-derived BMECs differentuated with 0 uM Retinoic acid [C0_c]

tag: genotype

value: Healthy control

value: 0 uM Retinoic acid


title: Hs_8w-ivc_MS321_234


title: Hs_8w-ivc_MS285_292


title: Control iPS-derived BMECs differentuated with 0 uM Retinoic acid [C0_a]

value: iPS-derived


title: Hs_8w-ivc_MS321_233


title: RNA-seq_Veh_rep1

value: Bone marrow


title: RAS5

type: RNA

city: NEW YORK

first: Mukundan

last: Attur

state: NY

address: 301E, 17TH STREET

institute: NYU GROSSMAN SCHOOL OF MEDICINE

hyb_protocol: Biotinylated fragmented cRNA probes were hybridized in the microarray U133A (Affymetrix, Santa Clara, CA). Hybridization was performed at 45°C for 16 h in a hybridization oven (Affymetrix). The microarrays were washed and stained with streptavidin–phycoerythrin conjugate in an Affymetrix GeneChip Fluidics Station.

scan_protocol: Fluorescence intensities were scanned with a GeneArray Scanner (Affymetrix), and image analysis was performed with GCOS (Affymetrix). GeneChip Scanner 3000 (Affymetrix) was used for scanning, and image analysis was performed with GCOS (Affymetrix).

data_processing: Dchip used and normalized expression values of all probe sets included in an excel file (synovium all expression)

label: BIOTIN

source_name: KNEE Synovium

label_protocol: Five micrograms of total RNA was used for double-stranded (ds) cDNA synthesis by the Gibco BRL SuperScript Choice System (Life Technologies). Purified ds cDNA was used to synthesize biotin-labeled cRNA with the ENZO BioArray High-yield RNA transcript labeling kit (Affymetrix). The biotinylated cRNA was purified with the RNeasy kit (Qiagen) and fragmented at 95°C for 35 min for target preparation.

extract_protocol: The freshly obtained synovium specimens were washed in sterile PBS, and the samples were immediately snap-frozen in liquid nitrogen and subsequently stored at –140 °C until RNA extraction. Total RNA was extracted from synovium using TRIzol as described previously (Bournazou E et al., Int J Mol Sci. 2019;20(11):2642) and purified using Qiagen RNeasy mini kit according to the manufacturer’s RNA clean-up protocol (Qiagen, Valencia, CA, and the USA). The quality and quantity of RNA were confirmed using a Beckman Spectrophotometer.

treatment_protocol: Non-OA (N=7) synovium (subjects aged 50–74 years, 29% female) was procured from the National Disease Research Interchange (NDRI, Philadelphia, PA, USA). Human OA (n=7) and RA (N=2) synovium were obtained under the guidelines of the Institutional Review Board of New York University (NYU) Grossman School of Medicine (IRB #i9018) for the use of surgically discarded human tissues from the knees of patients with a diagnosis of advanced OA (patients aged 50–62 years, 57% female) or RA (N=2) who underwent knee replacement surgery. OA and RA knee synovium samples were obtained from the operating room within 2–4 h of surgery and normal synovium within 2–16 h of death. Non-OA synovium was procured from donors with no history of joint diseases.

value: Late stage RA - synovium procured during knee replacement surgery


title: WT

value: Tumor-infiltrating immune cells (CD45+ cells)

value: WT


title: RAS7


title: YTHDF2_IP_WT_rep2

description:
YTHDF2 IP.txt
Project_COHP_44435_1_KBMRS

data_processing:
Sequencing reads were mapped to the mouse genome using HISAT2 (Version: v101)
Mapped reads of IP and input libraries were provided for R package exomePeak
The m6A binding motif was analyzed by HOMER.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker
Peak calling results with IP and input libraries were generated by R package RIPSeeker
Called peaks were annotated by intersection with gene and transcript architecture using ChIPpeakAnno
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, peak text files

growth_protocol: Bone marrow was extracted from the femurs and tibias of WT or Ythdf2 cKO mice. The whole bone marrow cells were flushed out and filtered using a 70 µm Cell Strainer. After centrifugation, red blood cells were lysed. The resultant bone marrow cells were resuspended in RPMI-1640 (Gibco) supplemented with 10% FBS (Gibco), 1% penicillin/streptomycin (Gibco), 50 μM 2-Mercaptoethanol (Sigma) in the presence of 20 ng/mL M-CSF (PeproTech) for 7 days. BMDMs were stimulated with 100 ng/ml LPS (Sigma) plus 20 ng/ml IFN-γ (PeproTech)  for 24 h to obtain M1 type macrophages.

extract_protocol:
For m6A-seq, total RNA was isolated by TRIzol reagent. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen). Fragmented mRNA (5 μg mRNA) was used for m6A immunoprecipitation (m6A-IP) using an m6A antibody (Synaptic, 202003) following the standard protocol of the Magna MeRIP m6A Kit (Merck Millipore). For Ythdf2 RIP-seq, fifty million BMDMs were harvested and washed twice with cold PBS, and the cell pellet was lysed with two volumes of lysis buffer [10 mM HEPES pH 7.6, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 Protease Inhibitor cocktail (Thermo Fisher Scientific), and 400 U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific)]. The lysate was incubated on ice for 5 min and centrifuged for 15 min to clear the lysate. One-tenth volume of cell lysate was saved as input. The rest of the cell lysate was incubated with 5 μg anti-YTHDF2 (MBL, Cat No. RN123PW) that was pre-coupled with Protein A magnetic beads (Invitrogen, Cat: 10001D) at 4℃ for 2h with gentle rotation. Afterward, the beads were washed five times with 1 ml ice-cold washing buffer (50 mM HEPES pH 7.6, 200 mM NaCl, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, and 200 U/mL RNase inhibitor). Immunoprecipitated samples were subjected to Proteinase K digestion in wash buffer supplemented with 1% SDS and 2 mg/mL Proteinase K (Thermo Fisher Scientific) incubated with shaking at 1200 rpm at 55℃ for 1 h. Total RNA was extracted from both input and immunoprecipitated RNA by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo Research).
For m6A-seq,RNA was enriched through RNA Clean & Concentration- 5 (Zymo Research) for library generation with a KAPA RNA HyperPrep Kit (Roche). Sequencing was performed at the City of Hope Genomics Facility on an Illumina NovaSeq 6000  machine with 100-bp paired-end reads (PE100). For Ythdf2 RIP-seq, cDNA library generation was produced with a KAPA RNA HyperPrep Kit (Roche) and sequenced on Illumina NovaSeq 6000 platform.

treatment_protocol: M1-type BMDMs were purified  from WT or Ythdf2 cKO mice.

value: M1-type macrophages

tag: antibody

value: YTHDF2 (MBL, RN123PW)


title: 4-hydroxytamoxifen resistant T47D cells - treated with erdafitinib + 4-OHT - rep_3

city: Oslo

first: Torbjørn

middle: Amundsen

last: Lien

state: OSLO

address: Ullernchausseen 64

department: Department of Cancer Genetics

country: Norway

institute: Institute for Cancer Research

data_processing:
Adaptor sequences and low-quality reads were trimmed and removed using the R-package BBMap (v.34.56)
Clean RNA-seq reads were mapped to the human genome (GRCh38 p13) using HISAT2 (v.2.1.0)
Mapped read counts were quantified using featureCounts (v.1.4.6-p1)
Assembly: GRCh38
Supplementary files format and content: featureCounts output matrix table with raw gene counts for every gene

source_name: Breast cancer cell line

growth_protocol:
PAR01 cells were grown in RPMI 1640 supplemented with 5 % FBS, 8 μg/mL insulin and glutamax
TR01 cells were grown in RPMI 1640 supplemented with 2 % charcoal-stripped FBS, 8 μg/mL insulin, glutamax and 1 μM 4-OHT

extract_protocol:
Total RNA was isolated from cell lines with an RNeasy isolation kit (Qiagen) according to the manufacturer’s protocol (Life Technologies). A NanoDrop™ 2000 spectrophotometer (Thermo Fisher Scientific), an Agilent TapeStation system (Agilent, Santa Clara, CA) and a Qubit fluorometer (Thermo Fisher Scientific) were used to assess the quality and quantity of extracted RNA.
Sequencing and library preparation were performed by the Norwegian Sequencing Centre (University of Oslo, Norway). Libraries were prepared using 100 ng total RNA as input material for the TruSeq Stranded RNA Library Prep Kit (Illumina) and standard Illumina adaptors for multiplexing. Libraries for each individual sample were sequenced using the NovaSeq SP Illumina platform, creating paired-end 150 bp reads with an average library size of 650 million reads.

treatment_protocol: Cells were seeded in their respective growth medium for 24 hours in 6-well plates until proper cell attachment. Cells were then washed with PBS, and serum-starved for 48 hours in phenol red-free RPMI 1640 supplemented with 2 % charcoal-stripped FBS, 8 μg/mL insulin, and glutamax. After 48 hours serum-starvation, cells were treated with one of the following treatment conditions: vehicle (0.05% DMSO), 4-OHT (1 μM), erdafitinib (5 μM), or erdafitinib (5 μM) + 4-OHT (1 μM) for 120 hours.

tag: 4-oht response phenotype

value: Resistant

tag: treatment

value: 120 hour treatmed with 5 uM erdafitinib + 1 uM 4-OHT


title: YTHDF2_Input_WT_rep2

description:
YTHDF2 IP.txt
Project_COHP_44437_1_KBMRS

tag: strain


title: 4-hydroxytamoxifen resistant T47D cells - treated with erdafitinib + 4-OHT - rep_2


title: YTHDF2_Input_WT_rep1

description:
YTHDF2 IP.txt
Project_COHP_44436_1_KBMRS


title: YTHDF2_IP_WT_rep1

description:
YTHDF2 IP.txt
Project_COHP_44434_1_KBMRS


title: 4-hydroxytamoxifen resistant T47D cells - treated with erdafitinib - rep_3

value: 120 hour treatmed with 5 uM erdafitinib


title: Hs_8w-ivc_MS321_231

value: 8 weeks


title: Hs_8w-ivc_MS285_288

value: Germ cell


title: 4-hydroxytamoxifen resistant T47D cells - treated with erdafitinib + 4-OHT - rep_1


title: OAS10

value: Late stage OA - synovium procured during knee replacement surgery


title: 4-hydroxytamoxifen resistant T47D cells - treated with erdafitinib - rep_2


title: OAS8


title: OAS9


title: OAS6


title: Control iPS-derived BMECs differentuated with 0 uM Retinoic acid [C0_b]

value: induced pluripoten stem (iPS)-derived brain microvascular endothelial-like cells (iBMECs)

value: Control


title: Hs_8w-ivc_MS285_287


title: Hs_8w-ivc_MS321_232


title: m6A_Input_cKO_rep2

description:
m6A_Input_genes_expression.tsv
Project_COHP_44415_1_KBMRS

data_processing:
Library strategy: m6a-seq
Sequencing reads were mapped to the mouse genome using HISAT2 (Version: v101)
Mapped reads of IP and input libraries were provided for R package exomePeak
The m6A binding motif was analyzed by HOMER.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker
Peak calling results with IP and input libraries were generated by R package RIPSeeker
Called peaks were annotated by intersection with gene and transcript architecture using ChIPpeakAnno
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, peak text files

value: Ythdf2 cKO

value: m6A (Synaptic, 202003)


title: OAS7


title: Hs_8w-ivc_MS321_230


title: m6A_Input_cKO_rep1

description:
m6A_Input_genes_expression.tsv
Project_COHP_44414_1_KBMRS


title: OAS2


title: OAS1


title: 4-hydroxytamoxifen resistant T47D cells - treated with erdafitinib - rep_1


title: m6A_IP_cKO_rep2

description:
WT m6A exomepeak2.txt
Project_COHP_44411_1_KBMRS


title: NS10

value: Normal synovium procured at autopsy


title: m6A_IP_cKO_rep1

description:
WT m6A exomepeak2.txt
Project_COHP_44410_1_KBMRS


title: Hs_8w-ivc_MS285_286


title: 4-hydroxytamoxifen resistant T47D cells - treated with 4-OHT - rep_3

value: 120 hour treatmed with 1 uM 4-OHT


title: 4-hydroxytamoxifen resistant T47D cells - treated with 4-OHT - rep_2


title: Hs_8w-ivc_MS285_284


title: Hs_8w-ivc_MS285_283


title: NS8


title: m6A_Input_WT_rep2

description:
m6A_Input_genes_expression.tsv
Project_COHP_44413_1_KBMRS


title: m6A_Input_WT_rep1

description:
m6A_Input_genes_expression.tsv.txt
Project_COHP_44412_1_KBMRS


title: 4-hydroxytamoxifen resistant T47D cells - treated with 4-OHT - rep_1


title: Hs_8w-ivc_MS285_282


title: NS5


title: 4-hydroxytamoxifen resistant T47D cells - treated with vehicle - rep_2

value: 120 hour treatmed with vehicle (DMSO)


title: m6A_IP_WT_rep2

description:
WT m6A exomepeak2.txt
Project_COHP_44409_1_KBMRS


title: Hs_8w-ivc_MS285_280


title: 4-hydroxytamoxifen resistant T47D cells - treated with vehicle - rep_3


title: m6A_IP_WT_rep1

description:
WT m6A exomepeak2.xls.txt
Project_COHP_44408_1_KBMRS


title: NS4


title: 4-hydroxytamoxifen resistant T47D cells - treated with vehicle - rep_1


title: Hs_8w-ivc_MS285_281


title: K3Y, replicate 3

city: Paris

first: Frédérique

last: Peronnet

address: 9, quai saint-Bernard

department: UMR7622-Developmental biology

institute: CNRS-SU

description:
raw.counts.txt
normalized.counts.txt

data_processing:
Quality checking with fastqc (Galaxy Version 0.72)
Alignement using STAR (Galaxy Version 2.6.0b-2)
Read count using Featurecount (Galaxy Version 1.6.0.6)
Normalization and differential analysis using DESeq 2 (Version 1.32.0)
Genome_build: dm6, r6.30
Supplementary_files_format_and_content: Raw and DESeq2 normalized count data for gene features are provided as a matrices for each genotype (pools of the 4 lines)

organism: Drosophila melanogaster

source_name: Third instar female larva wing imaginal discs

growth_protocol: Flies were raised on standard yeast-cornmeal medium at 25°C

extract_protocol:
Wing imaginal discs from third instar female larvae were dissected, and total RNAs were extracted using the RNA easy mini kit (Qiagen).  Samples wc_1, wc_2, corto[L1]/corto[420]_1, corto[L1]/corto[420]_2 were treated and sequenced  as described (Coléno-Costes et al., 2012).  For the other samples, the protocole was the same except that 150 discs were homogenized by pipetting and used for each extraction.
For samples wc_1, wc_2, corto[L1]/corto[420]_1, corto[L1]/corto[420]_2, libraries were prepared as described (Coléno-Costes et al., 2012).  For the other samples, libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina) (1 µg de mRNA per sample).
For samples wc_1, wc_2, corto[L1]/corto[420]_1, corto[L1]/corto[420]_2, see Coléno-Costes et al., 2012.  The other samples were multiplexed by 15. Each genotyped was deposited on 4 flowcell lanes.

treatment_protocol: No treatment

value: wing imaginal discs

value: Third instar larvae


title: NS2


title: NS3


title: Parental T47D cells - treated with vehicle - rep_3

value: Sensitive


title: female KO rep6 [ExpI_L_24]

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
bcl2fastq v2.19 software used for demultiplexing + basecalling
fastp v0.20 used for trimming adapter sequences and low quality reads
STAR v2.7a used for read mapping
Rsubread v2.2.4 used for quantifying gene expression
EdgeR v3.28.1 used for differential gene expression analysis
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited raw counts

source_name: female KO_liver

extract_protocol:
At twelve weeks of age mice were sacrificed by cardiac puncture and liver samples were taken and snap frozen. Total RNA was extracted using the All Prep DNA/RNA Extraction Kit (QIAGEN).
TruSeq Stranded mRNA library prep kit (Illumina)

tag: strain background

value: female

value: KO

value: liver


title: Parental T47D cells - treated with vehicle - rep_2


title: Hs_8w-ivc_MS285_279


title: Hs_8w-ivc_MS285_277


title: Organoids, Control, D100, Rep2

city: Saclay

first: Jerome

last: Roger

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

institute: CNRS-Universite Paris Sud

data_processing:
Image analysis and base calling is performed using the Illumina Real Time Analysis (3.4.4) software with default parameters.
Pass-filtered reads were mapped using STAR 2.7.3a
Count table of the gene features was obtained using FeatureCounts
Stattistics and Differential expression analysis done with EdgeR
Pathways analysis representation done with the package GOPlot
Assembly: Ensembl genome assembly GRCh38 (release 98)
Supplementary files format and content: Tab-delimited text files of the raw counts

source_name: patient derived Retinal organoids

extract_protocol:
Total RNAs were extracted using the NucleoSpin RNA XS kit according to the manufacturer’s protocol. RNA yields and quality were determined using a NanoDrop ND-1000 Spectrophotometer and an Agilent 2100 Bioanalyzer.
For RPE cells, RNA-seq libraries were constructed from 1 µg of total RNAs using the TruSeq Stranded mRNA Sample Prep (Illumina) and paired-end sequencing of 75 bases length was performed on a HiSeq 4000 system (Illumina). For retinal organoids, RNA-seq libraries were constructed from 1 µg of total RNAs using the NEB Next Ultra II Directional RNA (New England Biolabs) and paired-end sequencing of 100 bases length was performed on a Novaseq system (Illumina).

value: patient derived Retinal organoids

tag: cell line

value: iPSCs

tag: time


title: Hs_8w-ivc_MS285_278

value: 8 weeks

tag: cell type

value: Germ cell


title: K3Y, replicate 1

description:
raw.counts.txt
normalized.counts.txt

tag: age


title: male WT rep5 [ExpI_L_21]

source_name: male WT_liver

tag: Sex

value: male

value: WT


title: female KO rep5 [ExpI_L_23]


title: K3Y, replicate 2

description:
raw.counts.txt
normalized.counts.txt


title: K3A, replicate 3

description:
raw.counts.txt
normalized.counts.txt


title: male WT rep6 [ExpI_L_22]


title: Parental T47D cells - treated with vehicle - rep_1


title: NS1


title: Hs_8w-ivc_MS321_229

tag: developmental stage


title: K3A, replicate 2

description:
raw.counts.txt
normalized.counts.txt


title: male WT rep4 [ExpI_L_19]


title: K3A, replicate 1

description:
raw.counts.txt
normalized.counts.txt


title: female KO rep4 [ExpI_L_20]


title: Hs_8w-ivc_MS285_275

tag: in vitro culture period


title: Control, N, 7

first: Jiahao

last: Shi

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District,

department: Department of Ophthalmology

institute: Shanghai 9th Peoples Hospital Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Illumina bcl2fastq software used for basecalling and original sequenced reads conversion, called Raw Data. And fastQC software were used for base quality control.
Sequenced reads were trimmed off primer/adaptor contaminated reads,and masked for  Low quality reads and N overtop reads,called clean reads
The clean reads were mapped onto the reference gene set by using Bowtie1 software
Use Stringtie software to calculate the reads count and convert it to the FPKM of the transcript.And then the low-abundance transcripts,  were removed
The differential expressed genes were identified by using limma R package after normalization. A |log2FC|>=1 and p-Value<=0.05 were set as the threshold for DEGs
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: aesthetic orbital plastic surgery specimen

extract_protocol:
Total RNA were isolated from tissues by using the Trizol Reagent according to the manufacture’s protocol
The poly-A containing mRNA molecules were purified from the 3 μg of total RNA by using poly-T oligo-attached magnetic beads. The cleaved RNA fragments were reversely transcribed into first strand cDNA using random hexamers, following by second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments were purified, end blunted, 'A' tailed, and adaptor ligated. PCR was used to selectively enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. The number of PCR cycles was minimized to avoid skewing the representation of the library. The library were qualified by Agilent 2100 bioanalyzer and quantified by Qubit and qPCR.

value: orbit

tag: subgroup

value: normal

tag: condition


title: Control, N, 6

tag: tissue

value: aesthetic orbital plastic surgery specimen


title: Control, N, 12


title: Hs_8w-ivc_MS285_274


title: female WT rep6 [ExpI_L_18]

source_name: female WT_liver


title: Control, N, 5


title: Hs_8w-ivc_MS285_273


title: Hs_8w-ivc_MS285_272


title: female WT rep5 [ExpI_L_17]


title: Control, IOI, 13

source_name: idiopathic orbital inflammation

value: inflammation

value: idiopathic orbital inflammation


title: Hs_8w-ivc_MS285_271


title: w, replicate 1

description:
raw.counts.txt
normalized.counts.txt

value: wing imaginal discs

value: w


title: female WT rep4 [ExpI_L_16]


title: male WT rep3 [ExpI_L_15]


title: corto[L1]/corto[420]

description:
includes 2 biological replicates
raw.counts.txt
normalized.counts.txt

value: Third instar larvae


title: female KO rep3 [ExpI_L_13]

value: female


title: Control, LP, 3

source_name: orbital reactive lymphoid hyperplasia

value: orbital reactive lymphoid hyperplasia


title: w, replicate 3

description:
raw.counts.txt
normalized.counts.txt


title: H-WT3

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

data_processing:
Raw reads (fastq files) were aligned to mouse reference (mm10) using STAR aligner (version 2.6) with default settings, read count files were generated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text for gene read count, sample information, and gene annotation

extract_protocol:
Frozen liver samples harvested at ZT8 were used to prepare total RNA using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were injected intraperitoneally with tamoxifen (10 mg/mL) in corn oil for 5 consecutive days at 8 weeks of age. In the BH-HF group, mice were fed a high-fat diet at ten weeks of age for 35 weeks.

value: B6.129X1(FVB)-Hnf4atm1.1Gonz/J(129X1/SvJ)- Albtm1(cre/ERT2)Mtz(129S2/SvPas * C57BL/6)

value: 10 weeks

value: Tamoxifen

value: liver


title: Control, N, 1


title: Control, LP, 2


title: female KO rep2 [ExpI_L_12]

value: KO


title: Hs_8w-ivc_MS277_086

value: 8 weeks

value: Germ cell


title: Hs_8w-ivc_MS321_228


title: Hs_8w-ivc_MS277_087


title: male KO rep5 [ExpI_L_11]

source_name: male KO_liver

value: male


title: w, replicate 2

description:
raw.counts.txt
normalized.counts.txt


title: Control, IOI, 9

value: orbit


title: H-WT1


title: H-WT2


title: H-KO2


title: Hs_8w-ivc_MS285_270


title: Control, N, 3

value: normal

value: aesthetic orbital plastic surgery specimen


title: male KO rep6 [ExpI_L_14]


title: male WT rep2 [ExpI_L_9]

value: WT


title: Hs_8w-ivc_MS285_267


title: maleKO rep4 [ExpI_L_10]


title: Hs_8w-ivc_MS285_269


title: Hs_8w-ivc_MS285_266


title: H-KO3


title: Control, IOI, 8

value: inflammation

value: idiopathic orbital inflammation


title: female WT rep3 [ExpI_L_8]


title: wc

value: wing imaginal discs

value: w

value: Third instar larvae


title: H-KO1

value: B6.129X1(FVB)-Hnf4atm1.1Gonz/J(129X1/SvJ)- Albtm1(cre/ERT2)Mtz(129S2/SvPas * C57BL/6)


title: Hs_8w-ivc_MS277_082


title: Control, LP, 1

value: orbital reactive lymphoid hyperplasia


title: Control, IOI, 7


title: Hs_8w-ivc_MS285_265


title: BH-WT3

value: 10 weeks

value: Tamoxifen


title: BH-WT2

value: liver


title: female KO rep1 [ExpI_L_7]

value: female

value: KO


title: BH-WT1


title: Control, IOI, 4


title: Hs_Adult_MS252_225

source_name: An oocyte from adult ovary

value: Adult

value: Germ cell


title: Control, IOI, 2

value: orbit


title: female WT rep1 [ExpI_L_5]


title: female WT rep2 [ExpI_L_6]


title: Control, IOI, 3


title: Hs_Adult_MS252_223


title: male KO rep3 [ExpI_L_4]

value: male


title: Control, IOI, 11


title: Oxy210 rep7 [Y7]

city: Bethesda

first: Ying

middle: E

last: Zhang

state: Maryland

address: 37 Convent Dr., Bldg.37, Rm.2056

department: LCMB/CCR

institute: National Cancer Institute, NIH

data_processing:
We removed adaptor sequences, dropped leading/trailing low quality bases and short reads (< 25nt), and performed sliding window trimming using Trimmomatic/0.39 with the arguments "LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:25".  The adaptor sequences ligated to the framents are 1) 5' Adapter: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' ; 2) 3' Adapter(The underlined 6bp bases is Index): 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG-3' .
A combined reference genome of human (Gencode Release 37 - GRCh38.p13) and mouse (Gencode Release M26 - GRCm39) was created.
Trimmed reads were aligned to the combined reference genome using STAR/2.7.6a, and only alignments mapped to the human reference genome were extracted.
Gene expression was quantified by summarizing the number of human reads that were uniquely mapped to each human gene using featureCounts from subread/2.0.1.
Assembly: GRCh38
Supplementary files format and content: raw_gene_counts_xenograft.txt : tab-delimited text file containing raw counts for each human gene and each sample
Supplementary files format and content: normalized_data_logcpm_V1-V7_X1-X4.txt:  a tab-delimited text file with TMM-normalized log-cpm gene expression data for samples V1-V7 and X1-X4. Genes of very low counts were excluded.

source_name: Xenograft

growth_protocol: Resuspended A549-Luc2 cells (ATCC) were mixed with Matrigel at a 1:1 ratio and 100 ul suspension containing 1x10^7 cells was injected subcutaneously in the hind flank of 6-8 weeks old female athymic nu/nu mice (Charles River Laboratories). When the tumor size reached an average of 80-100 mm3, the mice were then randomized into three groups with 10 mice in each group.

extract_protocol:
Total RNA from xenograft tissues were extracted with the Direct-zol RNA Kit (Zymo research).
Libraries were prepared with NEBNext UltraTM II RNA Librart Prep Kit from RNAs with RIN>8.0

treatment_protocol: Oxy186 or Oxy210, formulated in 3% DMSO + 7% Ethanol + 5% PEG400 + 85% corn oil, was administered to the mice daily by oral gavage as a dose of 50 mg/kg. The control group was given the formulation solution.

value: A549-Luc2 (ATCC)

value: Xenograft


title: BH-KO2


title: Hs_Adult_MS257_219

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_GRCh38.p12, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.


title: male KO rep2 [ExpI_L_3]


title: Hs_Adult_MS252_146


title: Oxy210 rep6 [Y6]


title: BH-HF-WT3

value: 45 weeks

value: Tamoxifen-HF


title: male KO rep1  [ExpI_L_1]


title: BH-KO1


title: Hs_11w4d_MS321_217

source_name: An oocyte from 11w4d fetal ovary


title: Oxy210 rep5 [Y5]


title: Hs_11w4d_MS321_216


title: male WT rep1 [ExpI_L_2]

value: WT


title: BH-HF-WT1


title: Oxy210 rep4 [Y4]


title: BH-HF-WT2


title: Hs_11w4d_MS309_215


title: Oxy210 rep3 [Y3]


title: S9Rosa26GAP-P15

first: Andrew

last: K Groves

state: Texas

address: One Baylor Plaza, Baylor College of Medicine

institute: Baylor College of Medicine

data_processing:
The libraries were sequenced on the NovaSeq 6000 System using a S1 flowcell. Library quantification by qPCR and Bioanalyzer - A qPCR assay was performed on the libraries to determine the concentration of adapter ligated fragments using the Applied Biosystems ViiA 7 Quantitative PCR instrument and a KAPA Library Quant Kit (p/n KK4824). All samples were pooled at equimolar amounts and re-quantitated by qPCR, and re-assessed on the Bioanalyzer. Using the concentration from the ViiA7 TM qPCR machine above, 300pM of pooled library was loaded onto a NovaSeq S1 flowcell (Illumina p/n 20012865), using the Standard Workflow loading conditions designated by the manufacturer and amplified by exclusion amplification (ExAMP) for patterned flowcells using the Illumina NovaSeq 6000 sequencing instrument. PhiX Control v3 adapter-ligated library (Illumina p/n FC110-3001) was spiked-in at 1% by weight to ensure balanced diversity and to monitor clustering and sequencing performance. A paired end run, using 28 cycles for Read 1, 8 cycles for Index 1 Read and 91 cycles for Read 2 was set to sequence the flowcell on a NovaSeq 6000 Sequencing System to achieve a minimum of approximately 300M reads per sample. FastQ file generation and QC assessment was achieved using the 10X Cell Ranger software for 10X Chromium Platforms.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Inner ear

growth_protocol: Sox9CreER; Rosa26-tdtomato; Rosa26 A/GA/GAP/+ mice were bred

extract_protocol:
Papain dissociation of cells, FACS on red channel
In brief, a single cell suspension was loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) in which full length cDNA was synthesized and barcoded. Subsequently the GEMS are broken and cDNAs from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads (Thermo Fisher, 370020), cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Finally, PCR amplification was carried out to produce the library.
Single cell 3’ RNA seq libraries were prepared using the Chromium single cell 3’ reagent kit v3 (10x Genomics).

treatment_protocol: Tamoxifen administered at P1 samples analyzed at P8, Tamoxifen administered at P8 samples analyzed at P15,

value: Reporter expressing GFI1 ATOH1 POU4F3 induced P15 cochlear cells


title: S9Rosa26GA-P15

value: Reporter expressing GFI1 ATOH1 induced P15 cochlear cells


title: BH-HF-KO3


title: Hs_11w4d_MS321_214

extract_protocol:
Fetal ovaries collected from human fetus were carefully dissected out in chilled PBS.  Fetal ovaries at 8-14 wpf were minced with scissors in 0.05% trypsin/EDTA/PBS solution (GIBCO, 15400-054), then incubated for 15 min at 37℃ with gentle pipetting every 5 min.  Dissociation medium [DMEM (GIBCO, 10313021) containing 10% FBS, 2mM L-glutamine (GIBCO, 25030081), 1X penicillin/streptomycin (GIBCO, 15070063), and 100μg/mL DNaseI (MERCK, DN25)] was added for further dissociation.  For SC3-seq analysis, cells were picked under the inverted microscope (OLYMPUS, IX71) to exclude multiplet cells.   For dissociating human rOvaries, tissues were incubated with TryPLE Express (1X) (GIBCO, 12604021) for 5 min.  After adding dissociation medium, cells were processed for single-cell analyses. Dissociated germ cells were manually picked using glass capillaries under the stereo microscope (Leica, S8 APO).  Following cDNA synthesis and amplification methods were previously described (Nakamura et al., 2015).
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).


title: BH-KO3


title: S9Rosa26A-P15

value: Reporter expressing ATOH1 induced P15 cochlear cells


title: BH-HF-KO2


title: Oxy210 rep1 [Y1]


title: S9WT-P15

value: Reporter expressing uninduced P15 cochlear cells


title: Hs_11w4d_MS321_218


title: Oxy186 rep7 [X7]


title: Hs_11w4d_MS321_213


title: S9Rosa26GAP-P8

value: Reporter expressing GFI1 ATOH1 POU4F3 induced P8 cochlear cells


title: BH-HF-KO1

value: liver


title: Hs_11w4d_MS321_212


title: Oxy186 rep5 [X5]


title: Hs_11w4d_MS321_211


title: TKO5

first: Yangpo

last: Cao

address: 320 Longwood Ave

institute: Boston Children's hospital

description:
SMART-Seq2
S23

data_processing:
alignment by STAR to mm10
generate reads count matrix with FeatureCount
Differential expression analysis by DESeq2

source_name: heart

extract_protocol:
PureLink RNA Micro Scale Kit
SMART Seq v4 kit, Nextera XT library construction kit
Dual indexed library, enzymatic

treatment_protocol: AAV treatment of mice, Langendorff isolation of cardiomyocytes, FACS purification of cardiomyocytes

value: heart

value: cardiomyocyte

value: AAV-Myocd-sgRNA

value: Mrfta-/-; Mrtfb-F/F; Rosa-Cas9/Cas9

value: 4 week old


title: S9Rosa26A-P8

value: Reporter expressing ATOH1 induced P8 cochlear cells


title: Oxy210 rep2 [Y2]

value: A549-Luc2 (ATCC)


title: S9Rosa26GA-P8

value: Reporter expressing GFI1 ATOH1 induced P8 cochlear cells


title: TKO6

description:
SMART-Seq2
S24


title: Oxy186 rep4 [X4]

value: Xenograft


title: S9WT-P8

value: Reporter expressing uninduced P8 cochlear cells


title: Oxy186 rep3 [X3]


title: Hs_11w4d_MS285_222

value: Germ cell


title: TKO2

description:
SMART-Seq2
S20


title: TKO3

description:
SMART-Seq2
S21


title: aged PF4 treated ADT

city: San Francisco

first: Karishma

middle: Joanne Bhatia

last: Pratt

address: 513 Parnassus Ave, Med. Sci. Bldg S1364

department: Anatomy

institute: UCSF

description: Antibody Feature Barcode

data_processing:
Library strategy: CITE-seq
NovaSeq 6000 S4
10X Cell Ranger
Cell Ranger aggr
Seurat single cell anlalysis pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Splenocytes

extract_protocol:
Splenocytes isolated from five mice per group and labeled with Total-seqB antibodies
10x Genomics Chromium Single Cell Expression Solution 3' kit with Feature Barcode Technology (v3.1)

treatment_protocol: Saline or recombinant mouse PF4 (5 μg/mL; Prospec) was systemically administered to mice (100 μL/injection) via intravenous tail vein injection 8 times over 24 days.

value: 20 months

value: Splenocytes


title: TKO4

description:
SMART-Seq2
S22


title: aged PF4 treated RNA

description: total RNA


title: Oxy186 rep1 [X1]


title: Oxy186 rep2 [X2]


title: Hs_11w4d_MS321_208

first: Yukihiro

last: Yabuta

address: Yoshida-Konoe-cho, Sakyo-ku


title: aged saline control ADT

description: Antibody Feature Barcode

value: saline


title: DKO6

description:
SMART-Seq2
S18

value: AAV-Cre


title: Oxy186 rep6 [X6]


title: aged saline control RNA

description: total RNA


title: Hs_11w4d_MS321_209


title: Hs_11w4d_MS321_210


title: Control rep6 [V6]

value: Control


title: Hs_11w4d_MS285_219


title: DKO5

description:
SMART-Seq2
S17


title: Control rep7 [V7]


title: young saline control ADT

description: Antibody Feature Barcode

value: 3 months


title: young saline control RNA

description: total RNA


title: Hs_11w4d_MS285_217


title: Hs_11w4d_MS285_216


title: DKO4

description:
SMART-Seq2
S16

value: heart


title: Control rep4 [V4]


title: Beta1 integrin KO normal

city: Nashville

first: Scott

middle: Mattox

last: Haake

state: TN

address: 2220 Pierce Ave, PRB 606

department: Medicine, Division of Hematology/Oncology

institute: Vanderbilt University Medical Center

description: single cell

data_processing:
RTA (version 2.4.11; Illumina) was used for base calling and analysis was completed using 10X Genomics Cell Ranger software v2.1.1.
After alignment and demultiplexing, samples were jointly analyzed using a standard Seurat (2)/Scanpy (3) pipeline as previously described (4).
Briefly, cells containing fewer than 500 genes, <0.5% or >10% mitochondrial reads were filtered and excluded from downstream analysis.
Libraries were merged and jointly normalized and scaled using SCTransform (4) in Seurat v3.2 including “percent.mt” as a regression variable, followed by principal components analysis using variable genes and graph-based clustering.
Immune (Ptprc+), epithelial (Epcam+) and stromal (Pecam1+ or Col1a1+) cells were independently extracted, followed by recursive clustering, doublet exclusion (clusters containing nonphysiologic marker combinations), and cell-type annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Contains detected cellular barcodes.

source_name: Lung

extract_protocol:
Tumors and normal adjacent tissue of two WT and two integrin b1-KO mice were macrodissected and disassociated using the Miltenyi Biotec gentleMacs dissociator and the mouse tumor dissociation kit (Miltenyi Biotec #130-096-730). 10,000 viable cells were captured for each tissue.
scRNA-seq libraries were prepared using the 10X Chromium Single Cell Platform (10X Genomics #1000006, 1000080, and 1000020) following the manufacturer's protocol.
Other:single cell RNA-seq

tag: tissue type

value: Normal adjacent lung

value: Type 2 alveolar epithelial cell integrin beta1 KO


title: DKO3

description:
SMART-Seq2
S15

value: cardiomyocyte

tag: genotype

value: Mrfta-/-; Mrtfb-F/F; Rosa-Cas9/Cas9


title: Control rep3 [V3]


title: DKO2

description:
SMART-Seq2
S14

value: 4 week old


title: TKO1

description:
SMART-Seq2
S19

value: AAV-Myocd-sgRNA


title: Beta1 integrin KO tumor

description: single cell

value: Tumor

value: Wild type


title: DKO1

description:
SMART-Seq2
S13


title: Hs_11w4d_MS285_218

institute: Kyoto University, Graduate school of medicine


title: Control rep2 [V2]

value: A549-Luc2 (ATCC)

value: Xenograft


title: Control rep1 [V1]


title: Wild type tumor

description: single cell


title: Control rep5 [V5]


title: Hs_11w4d_MS321_206

value: Germ cell