title: NSC201cb input

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10
Reads were then trimmed with cutadapt (1.9.1). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a human genome (hg19). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 /path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.4.1)
Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam
PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam)
Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species hg19 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were annotated by overlapping peak regions with Gencode hg19 annotations
Region-based fold enriched was calculated by mapped reads fold change between IP and Input. Each read was assigned to a single region with the following descending priority order: CDS, 5’UTR, 3’UTR, Intron. For each gene, reads were summed up across each region to calculate final region counts, and fold change.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include -log10pValues and Log2FoldChange values for each IDR peaks called after cutoff of 3,3 in each parameter

source_name: Normal cerebellar neural stem cells

growth_protocol: SU_MB002 and NSC201cb were expanded using BTIC enrichment media composed of NeuroCult complete media (StemCell Technologies, 10 ng/mL bFGF, 20 ng/mL EGF, 2 μg/mL heparin).

extract_protocol:
Biological replicates (according to ENCODE requirements) of cells were treated with 600mJ of UV using the Stratalinker 2400, harvested in ice cold PBS and pellets flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with Msi1 bound Dynabeads Subsequent protocol exactly as detailed in van Nostrant et al 2016. Sequencing was performed on Illumina 2000 Hi Seq paired end reads and data processed through Dr. Yeo's laboratory's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.

treatment_protocol: SU_MB002 and NSC201cb were UV cross-linked with 600mJ and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). Msi1 antibody employed for immunoprecipitation was ab52865 (Abcam)

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #

value: Brain

value: Cerebellar NSC


title: N14_SMT2_MII_WT_sc1

status: Public on Oct 28 2022

type: SRA

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description:
scRNA-sequencing data
N14_SMT2_MII_2C_counts.txt
N14_SMT2_MII_2C_counts_maternal.txt
N14_SMT2_MII_2C_counts_paternal.txt

library_source: transcriptomic

data_processing:
ACE-seq: Raw paired-end 150bp sequencing data of whole-genome ACE-seq were trimmed by using Trim Galore (v0.6.6) with default parameters. The low-quality reads and sequences of adapters were filtered and trimmed. Clean reads were further aligned to the mm9 mouse genome by using Bismark (v0.23.0) with the paired-end mode. For unmapped reads of Read1 and Read2, realignments were performed in single-end mode. Deduplications were then performed with sambamba markdup (v0.6.6). The deduplicated reads were used for downstream analysis. Cytosines in CpG, CHH, CHG sequence context were extracted and counted by using MethyDackel (v0.5.0). In this study, raw signals were defined as the percentage of C/(C+T) at each site.
RNA-seq: For Smart-seq2 data, raw sequencing data were processed as our previously reported (Gu et al., 2019). Briefly, the raw reads were trimmed by using Cutadapt (v1.15). The sequences for adapters, oligo-dT, TSO sequences were trimmed from raw reads. The trimmed reads were further aligned to the mm9 mouse transcriptome by using STAR (v2.6.0a). Raw counts for genes expression were quantified by using HTSeq (v0.10.0). For bulk RNA-seq, raw sequencing data was processed by Trim Galore (v0.6.6) and was further aligned to the mouse transcriptome by using STAR (v2.6.0a). The 33  featureCounts (v2.0.1) was used for raw counts of genes expression. In this study, for comparing among different datasets, gene expression levels were defined as log2(TPM+1).
scBS-seq: Adaptor sequences, random primers and low-quality bases were removed by Trim Galore (v0.6.6). Reads shorter than 50 bp after trimming were excluded. The retained reads were then mapped to the mouse reference genome mm9 by Bismark (v0.23.0) in paired-end mode, and unmapped reads were re-mapped to the reference genome in single-end mode. SAMtools (v0.1.18) were adopted to remove PCR duplicates. The methylation level of CpG and CH sites were quantified by MethylDackel (v0.5.0).
scCOOL-seq: The pipeline of data processing of single-cell COOL-seq data was basically the same as the pipeline of processing single-cell bisulfite sequencing data which has been described (Gu et al., 2019; Yan et al., 2021). After determination of CpG and CH methylation level by MethylDackel, the WCG (W=A or T) and GCH (H= A,T or C) sites were summed from each single cell.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files; Count matrix files in tab-separated format

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse MII oocyte

extract_protocol:
To collect preimplantation embryos, 6-8week old females (C57BL/6) were super-ovulated by injection of PMSG and hCG. MII oocytes were collected at 14-15 hours after hCG injection. As to preimplantation embryos, superovulated female mice were mated with either C57BL/6 or PWK males. Embryos were collected at 25-26 h (zygotes), 42-43 h (2-cell), 56-57 h (4-cell), 70-71 h (8-cell), and 94-96 h (blastocysts) after hCG injection. To isolate pronuclei, mouse zygotes at PN3- PN4 stages were collected and pronucleus were isolated as previously described (Guo et al., 2014). Zygotes which were maternally deficient in Tet3 were obtained through Zp3-Cre mediated conditional knockout in oocytes as previously described (Guo et al., 2014). To inhibit DNA replication, zygotes were treated with aphidicolin until the collection of pronuclei (Guo et al., 2014). The inhibition of DNA replication in mouse zygotes was validated by EdU incorporation assay.
ACE-seq: The construction of ACE-seq libraries followed the published protocol (Schutsky et al., 2018), with minor modifications. Fragmented gDNA was first modified using UDP- glucose and T4 Phage β-glucosyltransferase at 37 °C for 1 h. Then 0.1 N NaOH was added to the modified gDNA for denaturation at 55 °C for 10 min. APOBEC enzyme was used to deaminate gDNA at 37°C for 3 hrs. After deamination, gDNA was purified using Ampure XP beads before library construction according to the TAILS procedure (Gu et al., 2019; Yan et al., 2021). Finally, the ACE-seq libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. scBS-seq: The zona pellucida of MII oocytes and 2-cell embryos were firstly removed by Tyrode's Solution. Construction of the scBS-seq or scCOOL-seq libraries were performed as previously described (Guo et al., 2017a; Smallwood et al., 2014). DNA libraries were sequenced on a Novaseq sequencer for 150 bp paired-end sequencing. Single-cell RNA-seq: Single-cell RNA-seq of 2-cell embryos were conducted by using smart-seq2 protocol (Picelli et al., 2014). In brief, single cell was picked into lysis buffer and Poly(A)+ RNA was captured by Oligo(dT) primer. The first strand of cDNA was synthesized by reverse transcription, then amplified, purified and fragmented. Fragmented cDNA was processed to construct RNA-seq library by NEBNext UltraII DNA Library Prep Kit for Illumina.
ACE-seq, scBS-seq and scRNA-seq

tag: cell type

value: Mouse MII oocyte

tag: genotype

value: WT


title: NSC201cb rep1

country: USA

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line


title: S625807

first: Yanfei

last: Jia

address: South Fourth Ring West Road

department: Department of Neurosurgery

institute: Beijing Tiantan Hospital

description:
PCP
S625807

data_processing:
A total of 16 tissue samples (11 PCP tumor tissues and 5 normal tissues) were subjected  to whole transcriptome analysis using high-throughput sequencing. Ribosomal RNA  (rRNA) was removed from total RNA (1 μg) using the Ribo-Zero Gold rRNA kit  (Illumina, San Diego, CA, USA)
Strand-specific cDNA libraries were prepared using  the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the  manufacturer’s instructions without purification and enrichment of mRNAs.
RNA was ligated with T4 RNA Ligase 1 at the 3’ ends and T4 RNA Ligase 2 at the 5’  adapters, followed by reverse transcription into cDNA
After PCR amplification, the  products were purified using polyacrylamide gel electrophoresis.
The resulting libraries were validated using the Agilent Bioanalyzer 2100 system  (Agilent Technologies, CA, USA), followed by sequencing using the HiSeq™ 2000  platform (Illumina, San Diego, CA, USA). Subsequently, we applied Cutadapt adapters  (version 1.16) to trim the raw reads and used the FastQC software (v0.11.7) to obtain  quality control reports of the sequence reads.
Assembly: hg38
Supplementary files format and content: the sequencing data were aligned  to the human reference genome (hg38) using the STAR software (V2.3.0), and the count  data were normalized as the fragments per kilobase of transcript per million data after  filtering read count files with low expression.
Supplementary files format and content: The original sequence count data was  normalized by transcript per million (TPM) and then calculated by log(x+1)

source_name: Papillary Craniopharyngioma

extract_protocol:
Total RNA was extracted from PCP tissues using Trizol reagent (Thermo Fisher  Scientific, Waltham, MA, USA). The concentration and quality of total RNA were  evaluated using a NanoDrop ND 1000 spectrophotometer (NanoDrop Technologies,  Wilmington, DE, USA), and the integrity of total RNA was determined using the  Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
High-quality  RNA samples (RNA integrity number≥7) were used for further analysis.

value: Papillary Craniopharyngioma


title: frpe_d10_5fa_x1

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

data_processing:
All the sequenced raw reads were filtered and trimmed with Trim Galore (version 0.4.1)
the clean reads were mapped to the mouse genome (hg38) using Hisat2
the number of reads uniquely mapped to each gene was determined using featurecount
Genome_build: hg38
Supplementary_files_format_and_content: reads count per gene

source_name: frpe derived CiPCs

extract_protocol:
Total RNA was purified using RNeasy per manufacturer’s instructions (Qiagen)
PolyA-tailed RNA was purified from total RNA and libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit (NEB) following manufacturer’s recommendations.

tag: tag

tag: treatment

value: 5 Factors + ASO

tag: passage


title: HDF_ctrl_DR13

source_name: HDF

value: ctrl


title: N14_SMT2_MII_WT_sc4


title: HDF_d10_only_aso_x6

source_name: HDF with ASO treatment

value: ASO


title: MB002 input

source_name: Pediatric Group 3 medulloblastoma

value: Brain (medulloblastoma)

value: Group 3 MB


title: MB002 rep1


title: MB002 rep2


title: N14_COOL_2C_KO_C2_sc10

description: Bisulfite-sequencing data profiled by single-cell COOL-seq

library_source: genomic

data_processing:
Library strategy: COOL-seq
ACE-seq: Raw paired-end 150bp sequencing data of whole-genome ACE-seq were trimmed by using Trim Galore (v0.6.6) with default parameters. The low-quality reads and sequences of adapters were filtered and trimmed. Clean reads were further aligned to the mm9 mouse genome by using Bismark (v0.23.0) with the paired-end mode. For unmapped reads of Read1 and Read2, realignments were performed in single-end mode. Deduplications were then performed with sambamba markdup (v0.6.6). The deduplicated reads were used for downstream analysis. Cytosines in CpG, CHH, CHG sequence context were extracted and counted by using MethyDackel (v0.5.0). In this study, raw signals were defined as the percentage of C/(C+T) at each site.
RNA-seq: For Smart-seq2 data, raw sequencing data were processed as our previously reported (Gu et al., 2019). Briefly, the raw reads were trimmed by using Cutadapt (v1.15). The sequences for adapters, oligo-dT, TSO sequences were trimmed from raw reads. The trimmed reads were further aligned to the mm9 mouse transcriptome by using STAR (v2.6.0a). Raw counts for genes expression were quantified by using HTSeq (v0.10.0). For bulk RNA-seq, raw sequencing data was processed by Trim Galore (v0.6.6) and was further aligned to the mouse transcriptome by using STAR (v2.6.0a). The 33  featureCounts (v2.0.1) was used for raw counts of genes expression. In this study, for comparing among different datasets, gene expression levels were defined as log2(TPM+1).
scBS-seq: Adaptor sequences, random primers and low-quality bases were removed by Trim Galore (v0.6.6). Reads shorter than 50 bp after trimming were excluded. The retained reads were then mapped to the mouse reference genome mm9 by Bismark (v0.23.0) in paired-end mode, and unmapped reads were re-mapped to the reference genome in single-end mode. SAMtools (v0.1.18) were adopted to remove PCR duplicates. The methylation level of CpG and CH sites were quantified by MethylDackel (v0.5.0).
scCOOL-seq: The pipeline of data processing of single-cell COOL-seq data was basically the same as the pipeline of processing single-cell bisulfite sequencing data which has been described (Gu et al., 2019; Yan et al., 2021). After determination of CpG and CH methylation level by MethylDackel, the WCG (W=A or T) and GCH (H= A,T or C) sites were summed from each single cell.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files; Count matrix files in tab-separated format

molecule: genomic DNA

source_name: Mouse 2-Cell

value: Mouse 2-Cell

value: N14 maternal KO


title: NSC201cb rep2

data_processing:
Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1). Args: --length 10
Reads were then trimmed with cutadapt (1.9.1). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir mouse_repbase \  --readFilesIn path/to/read1 path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.4.0i) against a mouse genome (hg19). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 /path/to/read2 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.4.1)
Sorted reads were collapsed with barcodecollapsepe.py included in eclip 0.1.5+ pipelines. Args: -o preRmDup.bam -m metrics_file -b rmDup.bam
PCR de-duped reads from each inline barcode were then merged with samtools (1.4.1) merge (merged.bam)
Merged alignments were split to keep just read2 using samtools (1.4.1) view. Args: -h -b -f 128
Read2 BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species hg19 --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using read2 BAM files for IP against read2 BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Reproducible peaks were annotated by overlapping peak regions with Gencode hg19 annotations
Region-based fold enriched was calculated by mapped reads fold change between IP and Input. Each read was assigned to a single region with the following descending priority order: CDS, 5’UTR, 3’UTR, Intron. For each gene, reads were summed up across each region to calculate final region counts, and fold change.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include -log10pValues and Log2FoldChange values for each IDR peaks called after cutoff of 3,3 in each parameter


title: HDF_ctrl_S6


title: Teratoma_H9_6, scRNAseq, Microwell-seq

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

library_source: transcriptomic single cell

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The teratoma data were aligned to a merged hg19-mm10 reference genome, the ESCs data were aligned to GRCh38, and the mouse data were mapped to mm10. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. The TagReadWithGeneExon function was employed to recognize the reads that were mapped to the exonic regions of genes. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat. For teratoma data that mix human cells with mouse cells, the aligned BAM files should be divided into human.bam and mouse.bam before generating the digital expression matrices.
Assembly: Teratoma: A merged hg19-mm10 reference genome; ESCs: GRCh38; Mouse: mm10
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.

organism:
Homo sapiens
Mus musculus

extract_protocol:
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: strain

value: NOD/SCID

tag: age

value: 14-16 weeks

tag: Sex

value: female


title: N14_SMT2_MII_WT_sc5


title: frpe_D3_5fa_H3a

source_name: fRPE derived reprogramming intermediate

value: Day 3


title: N14_COOL_2C_KO_C2_sc8


title: Teratoma_H9_5, scRNAseq, Microwell-seq


title: N14_SMT2_MII_WT_sc3


title: frpe_D3_5f_H2b

value: 5 Factors


title: Teratoma_H9_4, scRNAseq, Microwell-seq


title: N14_COOL_2C_KO_C2_sc6


title: frpe_D3_5f_H2a


title: N14_COOL_2C_KO_C2_sc7


title: Teratoma_H9_3, scRNAseq, Microwell-seq


title: frpe_ctrl_H1b

source_name: fetal RPEs


title: N14_COOL_2C_KO_C2_sc9


title: frpe_ctrl_H1a


title: Teratoma_H9_2, scRNAseq, Microwell-seq


title: Teratoma_H9_1, scRNAseq, Microwell-seq


title: fRPE aso+5f d10_em9

data_processing:
The adaptor sequences and low quality bases were trimmed from the reads using the Trim Galore tool ver. 0.6.5.
Reads were aligned to the mouse genome using the Bismark alignment software.
The percentage of bisulfite converted cytosines (representing unmethylated cytosines) and non-converted cytosines (representing methylated cytosines) was calculated by bismark_methylation_extractor
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph

source_name: fRPE_derived CiPCs

extract_protocol:
Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen).
300ng of DNA was used for library construction using the NEBNext Enzymatic Methyl-Seq (NEB), respectively.

value: aso+5f d10


title: N14_COOL_2C_KO_C2_sc3


title: fRPE 5f d10_em8


title: N14_COOL_2C_KO_C2_sc4


title: UTC-WT_rep3

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, AS5-2057

department: RNA Therapeutics Institute

institute: UMASS Medical School

data_processing:
Transcript quantification (TPM especifically) was performed with kallisto(v0.4.0) using the hg38 reference genome together with annotations from ENSEMBL hg38 v95
Reads were mapped to ENSEMBL hg38 v95 using STAR (v2.7.0e)
Raw read counts were obtained using ht-seq (v0.10.0)
Assembly: hg38 v95 (ENSEMBL)
Supplementary files format and content: *kallisto.tsv abundance files from kallisto quant;"*.bam" alignment files from STAR, "htseq.tsv* counts files from ht-seq.

source_name: Primary dermal fibroblast (HDFa)

growth_protocol: Cells were cultured in Dulbeccoâ€™s Modified Eagleâ€™s Medium-high glucose (DMEM, D6429, MilliporeSigma) with 10% fetal bovine serum (FBS) and 1% non-essential amino acid (NEAA).

extract_protocol:
Total RNA was extracted using Trizol.
mRNA was enriched using the Poly(A) mRNA Magnetic Isolation Module (7490S, New England Biolabs).
Single-end 75cycles libraries were constructed using TruSeq Stranded Illumina Total RNA Preparation Kit

treatment_protocol: 3000 cells were seeded and cultured at 37 Â°C with 5% CO2. After 6-9hs, lipofectamine RNAiMAX (Invitrogen) was used to transfect a siRNA or ASO with a 1/4 of lipofectamine:oligonucleotide ratio of the manufacturerâ€™s recommended protocol. The cells were incubated with full media and transfection reagents for 72h.

value: Fibroblast

tag: mutations

value: 3000 cells were seeded and cultured at 37C with 5% CO2 and harvested after 72hs. Three independent replicates were done for this treatment.


title: HDF aso+5f d10_em6

source_name: HDF_derived CiPCs


title: N14_COOL_2C_KO_C2_sc2


title: UTC-FA_rep3

source_name: GM03816 cells

value: GAA repeat (330,380) on intron 1 of FXN


title: N14_COOL_2C_KO_C1_sc10


title: S10_L6_rep3

value: 3000 cells were seeded and cultured at 37C with 5% CO2. After 6-9hs, lipofectamine RNAiMAX (Invitrogen) was used to transfect ASO S10_L6 with a 1/4 of lipofectamine:oligonucleotide ratio of the manufacturer'srecommended protocol. The cells were incubated with full media and transfection reagents for 72h. Three independent replicates were done for this treatment.


title: N14_COOL_2C_KO_C2_sc1


title: HDF 5f d11_em5


title: N14_COOL_2C_KO_C1_sc9


title: S10+2_rep3

value: 3000 cells were seeded and cultured at 37C with 5% CO2. After 6-9hs, lipofectamine RNAiMAX (Invitrogen) was used to transfect ASO S10+2 with a 1/4 of lipofectamine:oligonucleotide ratio of the manufacturer'srecommended protocol. The cells were incubated with full media and transfection reagents for 72h. Three independent replicates were done for this treatment.


title: N14_COOL_2C_KO_C1_sc8


title: frpe_ctrl_M5

source_name: fRPE

value: control


title: ASO-NTC_rep3

value: 3000 cells were seeded and cultured at 37C with 5% CO2. After 6-9hs, lipofectamine RNAiMAX (Invitrogen) was used to transfect a non-targeting ASO with a 1/4 of lipofectamine:oligonucleotide ratio of the manufacturer'srecommended protocol. The cells were incubated with full media and transfection reagents for 72h. Three independent replicates were done for this treatment.


title: frpe_10d_5fa

data_processing:
Single-cell RNA-seq data was processed using mkfastq and count command from 10X Genomics CellRanger v3.0.1.
Genome_build: hg38

source_name: fRPE derived CiPCs

extract_protocol: Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol.

tag: Stage


title: N14_COOL_2C_KO_C1_sc7


title: frpe_3d_5fa


title: N14_COOL_2C_KO_C2_sc5


title: frpe_3d_5f


title: siNTC_rep3

value: 3000 cells were seeded and cultured at 37C with 5% CO2. After 6-9hs, lipofectamine RNAiMAX (Invitrogen) was used to transfect a non-targeting siRNA with a 1/4 of lipofectamine:oligonucleotide ratio of the manufacturer'srecommended protocol. The cells were incubated with full media and transfection reagents for 72h. Three independent replicates were done for this treatment.


title: N14_COOL_2C_KO_C1_sc6


title: UTC-WT_rep2

value: WT


title: frpe_ctrl

source_name: Fetal RPEs


title: Hippocampus 23:00 repl. 3

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

data_processing:
Data were demultiplexed with blc2fastq2
Total RNA-Seq reads were mapped to the mouse GRCm38 genome with BWA using -T 19
CircRNAs were identified using CIRI2 with default parameters
Assembly: GRCm38
Supplementary files format and content: Tab separated table with circRNA coordinates (which is considered as a unique identifier) and corresponding number of  read counts for each sample. Sample H7_3 was down-sampled (defined as H7_3d) to the first ~25% of the reads.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using the Lexogen SPLIT RNA Extraction kit (Cat. Nr. 008.48).
100 ng total RNA/sample were inputted for rRNA depletion with the NEBnext rRNA depletion kit V2 (Cat. Nr. E7400X) and total RNA library prep with the NEBnext Ultra II Library prep kit (Cat. Nr. E7770L).

value: Hippocampus

tag: timepoint


title: S30_rep3

value: 3000 cells were seeded and cultured at 37C with 5% CO2. After 6-9hs, lipofectamine RNAiMAX (Invitrogen) was used to transfect ASO S30 with a 1/4 of lipofectamine:oligonucleotide ratio of the manufacturer'srecommended protocol. The cells were incubated with full media and transfection reagents for 72h. Three independent replicates were done for this treatment.


title: UTC-FA_rep2


title: N14_COOL_2C_KO_C1_sc5

value: Mouse 2-Cell

value: N14 maternal KO


title: S30_rep2


title: N14_COOL_2C_KO_C1_sc3


title: N14_COOL_2C_KO_C1_sc4


title: S10_L6_rep2


title: S10+2_rep2


title: N14_COOL_2C_KO_C1_sc2


title: Hippocampus 19:00 repl. 3


title: Hippocampus 19:00 repl. 2


title: Hippocampus 19:00 repl. 1


title: N14_COOL_2C_WT_C2_sc10


title: N14_COOL_2C_KO_C1_sc1


title: siNTC_rep2


title: UTC-WT_rep1


title: N14_COOL_2C_WT_C2_sc9


title: Hippocampus 15:00 repl. 2


title: UTC-FA_rep1


title: S30_rep1


title: N14_COOL_2C_WT_C2_sc8


title: Hippocampus 23:00 repl. 2


title: N14_COOL_2C_WT_C2_sc7


title: Hippocampus 11:00 repl. 3


title: Hippocampus 23:00 repl. 1


title: Hippocampus 15:00 repl. 1


title: S10_L6_rep1


title: N14_COOL_2C_WT_C2_sc5


title: S10+2_rep1


title: Hippocampus 11:00 repl. 1


title: N14_COOL_2C_WT_C2_sc4


title: ASO-NTC_rep1


title: Hippocampus 11:00 repl. 2


title: N14_COOL_2C_WT_C2_sc6


title: N14_COOL_2C_WT_C2_sc11


title: Hippocampus 07:00 repl. 3


title: siNTC_rep1


title: N14_COOL_2C_WT_C2_sc3


title: ASO-NTC_rep2


title: Hippocampus 07:00 repl. 2


title: N14_COOL_2C_WT_C2_sc1


title: N14_COOL_2C_WT_C2_sc2


title: Hippocampus 15:00 repl. 3


title: Hippocampus 07:00 repl. 1


title: Hippocampus 03:00 repl. 3


title: WGS_CJW_Bb610_rep2

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads for ChIP-seq and WGS were mapped to the combined B. burgdorferi genome (NCBI GCA_000008685.2_ASM868v2) using CLC Genomics Workbench (CLC Bio, QIAGEN).
Assembly: Borrelia burgdorferi S9 NCBI GCA_000008685.2_ASM868v2
Supplementary files format and content: Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary files format and content: header/column information: genome position; reads
Supplementary files format and content: matrix value: number of reads at each genome position

organism: Borreliella burgdorferi

source_name: Borrelia burgdorferi

extract_protocol:
ChIP-seq experiments were performed using anti-GFP, anti-mCherry antibodies according to previous publications (Graham et al 2014, PMID: 24829297 and Ren et al 2022, PMID: 35101983).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.

treatment_protocol: Cells were growing in ABSK-II, fixed by 3% formaldehyde for 30min at room temperature

tag: developmental stage

value: BSK-II

value: ParA-GFP knock-in, parZ(N20), WGS rep2

value: Borrelia burgdorferi S9


title: N14_COOL_2C_WT_C1_sc10


title: Hippocampus 03:00 repl. 2


title: WGS_CJW_Bb101_rep2

value: ParZ-GFP on shuttle vector, WGS rep2


title: N14_COOL_2C_WT_C1_sc11


title: N14_COOL_2C_WT_C1_sc9


title: Hippocampus 03:00 repl. 1


title: antiGFP_CJW_Bb610_rep1

value: ParA-GFP knock-in, parZ(N20), anti-GFP ChIP rep1

tag: chip antibody

value: anti-GFP antibodies


title: Frontal cortex 23:00 repl. 3

source_name: Frontal cortex

value: Frontal cortex


title: Frontal cortex 23:00 repl. 2


title: WGS_S9_rep2

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads for ChIP-seq and WGS were mapped to the combined B. burgdorferi genome (NCBI GCA_000008685.2_ASM868v2) using CLC Genomics Workbench (CLC Bio, QIAGEN).
Assembly: Borrelia burgdorferi S9 NCBI GCA_000008685.2_ASM868v2
Supplementary files format and content: Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary files format and content: header information: genome position; reads
Supplementary files format and content: column information: genome position; reads
Supplementary files format and content: matrix value: number of reads at each genome position

treatment_protocol:
Cells were growing in ABSK-II, fixed by 3% formaldehyde for 30min at room temperature
None

value: WT S9, WGS rep2


title: antiGFP_CJW_Bb101_rep1

value: ParZ-GFP on shuttle vector, anti-GFP ChIP rep1


title: WGS_CJW_Bb610_rep1

value: ParA-GFP knock-in, parZ(N20), WGS rep1


title: Frontal cortex 19:00 repl. 3


title: N14_COOL_2C_WT_C1_sc7


title: N14_COOL_2C_WT_C1_sc5


title: N14_COOL_2C_WT_C1_sc6


title: Frontal cortex 19:00 repl. 2


title: WGS_CJW_Bb601_rep2

value: mCherry-SMC knock-in, WGS rep2


title: WGS_S9_rep1

value: WT S9, WGS rep1


title: WGS_CJW_Bb101_rep1

value: ParZ-GFP on shuttle vector, WGS rep1


title: WGS_CJW_Bb601_rep1

value: mCherry-SMC knock-in, WGS rep1


title: N14_COOL_2C_WT_C1_sc3

value: WT


title: Frontal cortex 15:00 repl. 2


title: N14_COOL_2C_WT_C1_sc4

value: Mouse 2-Cell


title: Frontal cortex 19:00 repl. 1


title: N14_COOL_2C_WT_C1_sc1


title: WGS_CJW_Bb525_rep2

value: mCherry-ParB knock-in delta-parAZ, WGS rep2


title: WGS_CJW_Bb525_rep1

value: BSK-II

value: mCherry-ParB knock-in delta-parAZ, WGS rep1


title: N14_PBAT_MII_KO_sc20

description: Bisulfite-sequencing data profiled by single-cell bisulfite sequencing

source_name: Mouse MII oocyte

value: Mouse MII oocyte

value: N14 maternal KO


title: Frontal cortex 23:00 repl. 1


title: Frontal cortex 15:00 repl. 3


title: Frontal cortex 15:00 repl. 1


title: N14_PBAT_MII_KO_sc19


title: WGS_CJW_Bb524_rep1

value: ParZ-GFP knock-in delta-parBS, WGS rep1


title: antiGFP_CJW_Bb610_rep2

value: ParA-GFP knock-in, parZ(N20), anti-GFP ChIP rep2

value: Borrelia burgdorferi S9

value: anti-GFP antibodies


title: Frontal cortex 11:00 repl. 3

value: Frontal cortex


title: N14_COOL_2C_WT_C1_sc8


title: N14_PBAT_MII_KO_sc18


title: Frontal cortex 11:00 repl. 2


title: antiGFP_CJW_Bb101_rep2

value: ParZ-GFP on shuttle vector, anti-GFP ChIP rep2


title: N14_PBAT_MII_KO_sc17


title: Frontal cortex 11:00 repl. 1


title: WGS_CJW_Bb519_rep2

value: ParA-GFP knock-in delta-parZ, WGS rep2


title: N14_PBAT_MII_KO_sc16


title: WGS_CJW_Bb520_rep2

value: ParA-GFP knock-in delta-parBS, WGS rep2


title: N14_COOL_2C_WT_C1_sc2


title: WGS_CJW_Bb519_rep1

value: ParA-GFP knock-in delta-parZ, WGS rep1


title: N14_PBAT_MII_KO_sc15


title: WGS_CJW_Bb488_rep2

value: ParA-GFP knock-in, WGS rep2


title: Frontal cortex 07:00 repl. 3


title: Frontal cortex 07:00 repl. 2


title: N14_PBAT_MII_KO_sc14


title: Frontal cortex 07:00 repl. 1


title: N14_PBAT_MII_KO_sc13


title: Frontal cortex 03:00 repl. 3


title: WGS_CJW_Bb488_rep1

value: ParA-GFP knock-in, WGS rep1


title: N14_PBAT_MII_KO_sc12


title: WGS_CJW_Bb473_rep2

value: GFP knock-in, WGS rep2


title: Frontal cortex 03:00 repl. 2


title: N14_PBAT_MII_KO_sc11


title: N14_PBAT_MII_KO_sc10


title: WGS_CJW_Bb520_rep1

value: ParA-GFP knock-in delta-parBS, WGS rep1


title: Frontal cortex 03:00 repl. 1


title: WGS_CJW_Bb403_rep2

value: BSK-II

value: ParZ-GFP knock-in mCherry-ParB shuttle vector, WGS rep2


title: WGS_CJW_Bb473_rep1

value: GFP knock-in, WGS rep1


title: WGS_CJW_Bb403_rep1

value: ParZ-GFP knock-in mCherry-ParB shuttle vector, WGS rep1


title: WGS_CJW_Bb379_rep2

value: mCherry-ParB knock-in, WGS rep2


title: WGS_CJW_Bb379_rep1

value: mCherry-ParB knock-in, WGS rep1


title: HEK293T_N3

first: Jiang

last: Penglei

department: School of basic medicine science

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced data were trimmed with trimmomatic and keep reads which length more than 17bp.
Clean data were mapped to rRNA reference (18S rRNA, 5.8S rRNA and 28S rRNA sequences were downloaded from https://www-snorna.biotoul.fr/index.php) using bowtie2 with parameter “--end-to-end -k 1”.
The sam files obtained from the alignment were converted to the bed files.
5’ and 3’ ends counting was done by bedtools (2.29.0) and combined to calculate RiboMeth score. The scores were normalized to average values for -6 and +6 nucleotides.
Assembly: hg18
Supplementary files format and content: BedGraph files with each sample RiboMeth score.

source_name: 293T cells

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

tag: genotype/variation

value: ectopic expression of SARS-COV-2 N protein


title: N14_PBAT_MII_KO_sc7

value: Mouse MII oocyte

value: N14 maternal KO


title: HEK293T_N2


title: HepG2_MIX(biolrepl2)_Control(biolrepl2)

type: RNA

city: Rome

first: Sabrina

last: Tait

state: Italy

address: Viale Regina Elena 299

department: Dpt. Infectious Diseases

country: Italy

institute: Istituto Superiore di Sanità

hyb_protocol: Cy3 and Cy5 labelled samples, to be hybridized on same slides, were mixed and added with Agilent Fragmentation Buffer following manufaturer's instructions. Following 30 min incubation at 60 °C, Agilent GEx Hybridization Buffer was added, volumes loaded on gasket slides into the Agilent SureHyb chamber, array slides placed over and chamber closed. Arrays were incubated for 17h at 65°C with a 10rpm rotation in an Agilent hybridization oven. Arrays were then washed with Agilent Gene Expression Buffers 1 and 2.

scan_protocol: Scanned on an Agilent G2505B Microarray Scanner System. Data extraction and array quality control were performed through the Agilent Feature Extraction Software v9.5.

data_processing: The limma package, part of Bioconductor within the R environment, was used for background subtraction, Global Loess normalization, Aquantile between-arrays normalization. Signals from the two channels were transformed in single channel data calculating the correlation between channels for the same spot. Differential gene expression analysis for each treated group vs control samples was performed applying a Bayesian model, setting significance at p < 0.01 and controlling for the False Discovery Rate (FRD) set < 5%.

source_name: HepG2, MIX treatment 1nM, biolrepl2

label_protocol: cDNA and cRNA synthesis, amplification and labelling was performed using the Quick Amp Labelling Kit, Two Colors (Agilent), with spike-in internal controls (Agilent) following manufacturer’s instructions, with 1 µg of total RNA as input

growth_protocol: HepG2 cell line was grown in DMEM/F12 medium without phenol red, supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were maintained in a humidified Steri-Cult 200 Incubator at 37 °C and 5% CO2.

extract_protocol: HepG2 cell pellets were extracted for their total RNA content by the Norgen kit (Norgen Biotek Corp., Thorold, Canada) according to manufacturer's protocol.

treatment_protocol: Cells were plated and incubated overnight at 37 °C, then medium was replaced with fresh medium containing BDE-47, BDE-99 or BDE-209 congeners at 1 nM concentration, the equimolar mixture of the three congeners at 1 nM concentration (MIX), or medium alone as control, incubating cells for 72h at 37 °C.

value: Liver

tag: cancer type

value: hepatocellular carcinoma

value: MIX treatment 1nM

source_name: HepG2, Control medium treatment, biolrepl2

value: Control medium treatment


title: WGS_CJW_Bb378_rep2

value: ParZ-GFP knock-in, WGS rep2


title: N14_PBAT_MII_KO_sc6

tag: cell type


title: WGS_CJW_Bb378_rep1

tag: genotype

value: ParZ-GFP knock-in, WGS rep1


title: antimCherry_CJW_Bb601_rep2

description: ChIP using anti-mCherry antibodies

value: mCherry-SMC knock-in, anti-mCherry ChIP rep2


title: HepG2_BDE-209(biolrepl3)_BDE-99(biolrepl3)

source_name: HepG2, BDE-209 treatment 1nM, biolrepl3

tag: tissue

value: BDE-209 treatment 1nM

source_name: HepG2, BDE-99 treatment 1nM, biolrepl3

value: BDE-99 treatment 1nM


title: HepG2_BDE-99(biolrepl3)_Control(biolrepl3)

tag: cell line

source_name: HepG2, Control medium treatment, biolrepl3


title: HepG2_BDE-47(biolrepl3)_BDE-209(biolrepl3)

source_name: HepG2, BDE-47 treatment 1nM, biolrepl3

value: BDE-47 treatment 1nM


title: N14_PBAT_MII_KO_sc9


title: HEK293T_C2

value: control


title: HEK293T_C3


title: N14_PBAT_MII_KO_sc5


title: antimCherry_CJW_Bb601_rep1

description: ChIP using anti-mCherry antibodies

value: BSK-II

value: mCherry-SMC knock-in, anti-mCherry ChIP rep1


title: N14_PBAT_MII_KO_sc4


title: N14_PBAT_MII_KO_sc8


title: HepG2_MIX(biolrepl1)_Control(biolrepl1)

source_name: HepG2, MIX treatment 1nM, biolrepl1

source_name: HepG2, Control medium treatment, biolrepl1


title: HEK293T_C1


title: N14_PBAT_MII_KO_sc3


title: antimCherry_CJW_Bb525_rep2

description: ChIP using anti-mCherry antibodies

value: mCherry-ParB knock-in delta-parAZ, anti-mCherry ChIP rep2


title: HEK293T_N1

value: ectopic expression of SARS-COV-2 N protein


title: N14_PBAT_MII_KO_sc2

value: Mouse MII oocyte


title: m6A-CP3_S6

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

data_processing:
Data were analysed by Eclipse Bioinnovations according to their standard m6A-eCLIP analysis pipeline
Demultiplexing by umi_tools
Quality check with FastQC
Adaptor trimming by Cutadapt
Reference genome aligment by STAR
Identification of cluster of reads by CLIPper
Crosslink sites at a single nucleotide resolution by PureCLIP
Genome_build: UCSC version GRCh38/hg38

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in RPMI medium supplemented with 10% FBS

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA samples were subjected m6A e-CLIP protocol

treatment_protocol: Hela cells were treated with 0,1% DMSO and 80uM CP for 16h.

value: cervix epithelial

tag: passages

value: CP


title: N14_PBAT_MII_KO_sc1

value: N14 maternal KO


title: HepG2_Control(biolrepl3)_BDE-47(biolrepl3)

value: Liver

value: hepatocellular carcinoma

tag: treatment


title: N14_PBAT_MII_WT_sc18

value: WT


title: m6A-CP1_S4


title: antimCherry_CJW_Bb403_rep2

description: ChIP using anti-mCherry antibodies

value: ParZ-GFP knock-in mCherry-ParB shuttle vector, anti-mCherry ChIP rep2


title: antimCherry_CJW_Bb379_rep2

description: ChIP using anti-mCherry antibodies

value: mCherry-ParB knock-in, anti-mCherry ChIP rep2


title: HepG2_BDE-209(biolrepl2)_MIX(biolrepl2)

source_name: HepG2, BDE-209 treatment 1nM, biolrepl2

value: BDE-209 treatment 1nM

value: MIX treatment 1nM


title: HepG2_BDE-47(biolrepl2)_BDE-99(biolrepl2)

source_name: HepG2, BDE-47 treatment 1nM, biolrepl2

value: BDE-47 treatment 1nM

source_name: HepG2, BDE-99 treatment 1nM, biolrepl2

value: BDE-99 treatment 1nM


title: m6A-DMSO3_S3

value: DMSO


title: antimCherry_CJW_Bb379_rep1

description: ChIP using anti-mCherry antibodies

value: BSK-II

value: mCherry-ParB knock-in, anti-mCherry ChIP rep1


title: m6A-DMSO2_S2


title: antiGFP_CJW_Bb524_rep1

description: ChIP using anti-GFP antibodies

value: ParZ-GFP knock-in delta-parBS, anti-GFP ChIP rep1


title: N14_PBAT_MII_WT_sc15

value: Mouse MII oocyte


title: N14_PBAT_MII_WT_sc16


title: N14_PBAT_MII_WT_sc17


title: HepG2_Control(biolrepl2)_BDE-47(biolrepl2)

value: Control medium treatment


title: antimCherry_CJW_Bb525_rep1

description: ChIP using anti-mCherry antibodies

value: mCherry-ParB knock-in delta-parAZ, anti-mCherry ChIP rep1


title: m6A-CP2_S5

value: cervix epithelial

value: CP


title: N14_PBAT_MII_WT_sc14


title: antiGFP_CJW_Bb520_rep2

description: ChIP using anti-GFP antibodies

value: ParA-GFP knock-in delta-parBS, anti-GFP ChIP rep2


title: m6A-DMSO1_S1


title: KeaA-HA_IP_biol_rep_3

city: Warsaw

first: Agnieszka

last: Dzikowska

address: Pawinskiego 5A

country: Poland

institute: University of Warsaw

description: 2x100 bp paired-end sequencing

data_processing:
Raw reads were trimmed with Trimmomatic software (Bolger et al., 2014). All reads with quality less than 20 were trimmed. Reads shorter than 50 nucleotides were discarded.
Trimmed reads were mapped to the reference genome with the use of BWA (Li et al.., 2010).
Duplicated reads were removed with the use of Picard tool (http://broadinstitute.github.io/picard/).
Peak calling was performed in R software (Team and Core, 2013), with the use of packages – systemPipeR, CHIPpeakAnno, GenomicFeatures, ChIPseeker and Biostrings. All biological replicates (fastq files) were merged into one file for input and IP. Peak calling with input/IP sample was performed with the use of MACS2 (Zhang, Yong et al., 2008) callpeak algorithm.
Differential binding analysis between control and treatment was performed with the use of edgeR (Robinson et al., 2010) package.
Motifs discovery was performed with the use of MEME-ChIP (Machanick et al., 2011) algorithm. Analysis was performed against YEASTRACT_20130918 database (Teixeira, Miguel et al., 2006).
Assembly: Aspergillus_nidulans.ASM1142v1 reference (https://fungi.ensembl.org/index.html)
Supplementary files format and content: Excel output of peak calling input/IP from MACS2: JG_T_FR.bam_macs2_peaks.xls
Supplementary files format and content: BED output of peak calling input/IP from MACS2: JG_T_FR.bam_macs2_summits.bed
Supplementary files format and content: Fasta sequences for each peak from MAC2: JG_T_FR.bam_macs2_peaks.fasta
Supplementary files format and content: Excel otput of peaks annotation on reference genome from MACS2: JG_T_FR.bam_macs2_peaks_annotated.xlsx
Supplementary files format and content: Excel output of reads counting for each peak from MACS2: JG_T_FR.bam_macs2_peaks.countDF.xls
Supplementary files format and content: Excel output of differential binding analysis between input and IP from edgeR: JG_T_FR.bam_macs2_peaks.edgeR.xls
Supplementary files format and content: TSV output from Interproscan for annotation with GO, Pfam and KEGG databases: JG_T_FR.bam_macs2_peaks_GO_PFAM_KEGG_annotated.tsv

organism: Aspergillus nidulans

source_name: anti-HA immunoprecipitated biological replicate 3

growth_protocol: Mycellium was grown in liquid minimal medium.

extract_protocol:
ChIP was conducted according to Boedi et al., 2012 (Meth. in Mol. Biol., vol.  944, p.221-236; Springer Protocols). 1% formaldehade for 15 min was used as crosslinking agent, mycelia were grinded in mortar, extracts were sonicated using Bioruptor 200 (Diagenode) with 2 min "on"/1 min "off"/power "high" settings for 25 min and anti-HA 12CA5 antibody was used for chromatine immunoprecipitation (Roche, #11583816001).
ChIP-seq libraries were prepared using KAPA HyperPrep Kit and KAPA Dual-Indexed adapters (Kapa Biosciences) with 10 cycles of amplification. The size distribution was assessed using the Agilent 2100 Bioanalyzer and High Sensitvity DNA kit. The concentration of the libraries was determined by qPCR using the Kapa Library Quantification kit (Kapa Biosciences) and Roche LC480II cycler. Sequencing was performed on the Illumina NovaSeq 6000 instrument using the NovaSeq 6000 S2 Reagent Kit (100 cycles) (Illumina), with 2 × 100 cycles pair-end reading mode.

value: mycellium

value: KaeA-HA

value: (kaeA::HA, A.f. pyrG), pyrG89; argB2; pabaB22, nkuA{delta}::argB; riboB7


title: HepG2_BDE-99(biolrepl1)_BDE-209(biolrepl1)

source_name: HepG2, BDE-99 treatment 1nM, biolrepl1

value: Liver

value: hepatocellular carcinoma

source_name: HepG2, BDE-209 treatment 1nM, biolrepl1

value: BDE-209 treatment 1nM


title: 7_TFH_Blood

city: RENNES

first: Laure

last: Michel

address: 2 rue Henri Le Guilloux

department: Neurology

country: France

institute: CHU Pontchaillou

data_processing:
FastQC control quality
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR with parameters :                     --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts
The read counts were called using Subread
Differential gene expression analysis was performed for all populations (dn, FDC, FRC, FL_DN, FL_FDC, BM and FL_FRC) cells using DESeq2 in R Bioconductor.
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample ...

source_name: Blood

extract_protocol:
Tfh cells were obtained from CSF and blood by fluorescence-activated cell-sorting and RNA were extracted using Nucleospin RNA XS Plus kit (Macherey-Nagel)
cDNA were obtained using SmartSEQ v4 UltraLowInput RNA kit (Takara Bio) ; library protocol : KAPA Hyper Plus Library

tag: disease state

value: multiple sclerosis

value: follicular helper T cells (Tfh)

tag: compartment

value: Blood


title: KeaA-HA_IP_biol_rep_2

description: 2x100 bp paired-end sequencing

source_name: anti-HA immunoprecipitated biological replicate 2

value: (kaeA::HA, A.f. pyrG), pyrG89; argB2; pabaB22, nkuA{delta}::argB; riboB6


title: HepG2_BDE-209(biolrepl1)_MIX(biolrepl1)

value: MIX treatment 1nM


title: N14_PBAT_MII_WT_sc13

data_processing:
ACE-seq: Raw paired-end 150bp sequencing data of whole-genome ACE-seq were trimmed by using Trim Galore (v0.6.6) with default parameters. The low-quality reads and sequences of adapters were filtered and trimmed. Clean reads were further aligned to the mm9 mouse genome by using Bismark (v0.23.0) with the paired-end mode. For unmapped reads of Read1 and Read2, realignments were performed in single-end mode. Deduplications were then performed with sambamba markdup (v0.6.6). The deduplicated reads were used for downstream analysis. Cytosines in CpG, CHH, CHG sequence context were extracted and counted by using MethyDackel (v0.5.0). In this study, raw signals were defined as the percentage of C/(C+T) at each site.
RNA-seq: For Smart-seq2 data, raw sequencing data were processed as our previously reported (Gu et al., 2019). Briefly, the raw reads were trimmed by using Cutadapt (v1.15). The sequences for adapters, oligo-dT, TSO sequences were trimmed from raw reads. The trimmed reads were further aligned to the mm9 mouse transcriptome by using STAR (v2.6.0a). Raw counts for genes expression were quantified by using HTSeq (v0.10.0). For bulk RNA-seq, raw sequencing data was processed by Trim Galore (v0.6.6) and was further aligned to the mouse transcriptome by using STAR (v2.6.0a). The 33  featureCounts (v2.0.1) was used for raw counts of genes expression. In this study, for comparing among different datasets, gene expression levels were defined as log2(TPM+1).
scBS-seq: Adaptor sequences, random primers and low-quality bases were removed by Trim Galore (v0.6.6). Reads shorter than 50 bp after trimming were excluded. The retained reads were then mapped to the mouse reference genome mm9 by Bismark (v0.23.0) in paired-end mode, and unmapped reads were re-mapped to the reference genome in single-end mode. SAMtools (v0.1.18) were adopted to remove PCR duplicates. The methylation level of CpG and CH sites were quantified by MethylDackel (v0.5.0).
scCOOL-seq: The pipeline of data processing of single-cell COOL-seq data was basically the same as the pipeline of processing single-cell bisulfite sequencing data which has been described (Gu et al., 2019; Yan et al., 2021). After determination of CpG and CH methylation level by MethylDackel, the WCG (W=A or T) and GCH (H= A,T or C) sites were summed from each single cell.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files; Count matrix files in tab-separated format

source_name: Mouse MII oocyte

value: Mouse MII oocyte

value: WT


title: antiGFP_CJW_Bb520_rep1

description: ChIP using anti-GFP antibodies

source_name: Borrelia burgdorferi

value: BSK-II

value: ParA-GFP knock-in delta-parBS, anti-GFP ChIP rep1


title: HepG2_Control(biolrepl1)_BDE-47(biolrepl1)

value: Control medium treatment

source_name: HepG2, BDE-47 treatment 1nM, biolrepl1

value: BDE-47 treatment 1nM


title: HepG2_BDE-47(biolrepl1)_BDE-99(biolrepl1)

value: BDE-99 treatment 1nM


title: N14_PBAT_MII_WT_sc12


title: 8_TFH_Blood


title: antiGFP_CJW_Bb519_rep2

description: ChIP using anti-GFP antibodies

value: ParA-GFP knock-in delta-parZ, anti-GFP ChIP rep2


title: KeaA-HA_IP_biol_rep_1

description: 2x100 bp paired-end sequencing

source_name: anti-HA immunoprecipitated biological replicate 1

value: mycellium

value: KaeA-HA

value: (kaeA::HA, A.f. pyrG), pyrG89; argB2; pabaB22, nkuA{delta}::argB; riboB5


title: 5_TFH_Blood


title: 6_TFH_Blood


title: 4_TFH_Blood


title: N14_PBAT_MII_WT_sc11


title: 3_TFH_Blood


title: antiGFP_CJW_Bb488_rep1

description: ChIP using anti-GFP antibodies

value: ParA-GFP knock-in, anti-GFP ChIP rep1


title: KeaA-HA_input_biol_rep_1

description: 2x100 bp paired-end sequencing

source_name: input biological replicate 1

value: (kaeA::HA, A.f. pyrG), pyrG89; argB2; pabaB22, nkuA{delta}::argB; riboB2


title: antiGFP_CJW_Bb488_rep2

description: ChIP using anti-GFP antibodies

value: ParA-GFP knock-in, anti-GFP ChIP rep2


title: antiGFP_CJW_Bb519_rep1

description: ChIP using anti-GFP antibodies

value: ParA-GFP knock-in delta-parZ, anti-GFP ChIP rep1


title: antiGFP_CJW_Bb473_rep2

description: ChIP using anti-GFP antibodies

value: GFP knock-in, anti-GFP ChIP rep2


title: N14_PBAT_MII_WT_sc10


title: N14_PBAT_MII_WT_sc9


title: antiGFP_CJW_Bb473_rep1

description: ChIP using anti-GFP antibodies

value: GFP knock-in, anti-GFP ChIP rep1


title: 1_TFH_Blood

value: multiple sclerosis

value: follicular helper T cells (Tfh)

value: Blood


title: N14_PBAT_MII_WT_sc7

value: Mouse MII oocyte

value: WT


title: antiGFP_CJW_Bb403_rep1

description: ChIP using anti-GFP antibodies

value: BSK-II

value: ParZ-GFP knock-in mCherry-ParB shuttle vector, anti-GFP ChIP rep1


title: N14_PBAT_MII_WT_sc6


title: KeaA-HA_input_biol_rep_2

description: 2x100 bp paired-end sequencing

source_name: input biological replicate 2

value: (kaeA::HA, A.f. pyrG), pyrG89; argB2; pabaB22, nkuA{delta}::argB; riboB3


title: N14_PBAT_MII_WT_sc8


title: HepG2_BDE-99(biolrepl2)_BDE-209(biolrepl2)

value: Liver

value: hepatocellular carcinoma

value: BDE-99 treatment 1nM

value: BDE-209 treatment 1nM


title: KeaA-HA_input_biol_rep_3

description: 2x100 bp paired-end sequencing

source_name: input biological replicate 3

value: mycellium

value: KaeA-HA

value: (kaeA::HA, A.f. pyrG), pyrG89; argB2; pabaB22, nkuA{delta}::argB; riboB4


title: 8_TFH_CSF

source_name: CSF

value: CSF


title: antiGFP_CJW_Bb378_rep2

description: ChIP using anti-GFP antibodies

value: ParZ-GFP knock-in, anti-GFP ChIP rep2

tag: strain


title: N14_PBAT_MII_WT_sc5


title: N14_PBAT_MII_WT_sc4


title: wt5_biol_rep_1

description:
2x75 bp paired-end sequencing
kaeA25_vs_wt5.xlsx

data_processing:
Raw single reads were subjected to sequence quality control using FastQC.
Alignment was done using Tophat v.2 (Trapnell et al., 2009) and Bowtie2 (Langmead et al., 2012). Mapped reads were filtered to retain only those where both reads of the pair aligned in the correct relative orientation.
Fragment counting was done using ShortRead (Morgan et al., 2009).
The mapped readings were analysed using Python, with Pandas and Seaborn modules (Seabold et al., 2010).
Fragment counts were used to assess differential gene expression, after normalization for library size, using the R package edgeR (Robinson et al., 2010, Robinson & Oshlack, 2010).
Assembly: A_nidulans_FGSC_A4 version s09-m04-r07 (Aspergillus Genome Database - AspGD; http://www.aspergillusgenome.org/).
Supplementary files format and content: Relative expression (mutant vs wild-type), xlsx output from the R package edgeR.

source_name: mycellium

extract_protocol:
Total RNAs were isolated according to (Schmitt et al., 1990) and then treated with RQ1 DNase I (Promega). Ribosomal RNA was depleted with Epicenter Ribo-Zero™ Magnetic Gold Kit* (Yeast). Sample quality was assessed using an Agilent 2100 Bioanalyzer and RNA 6000 Nano kit (total RNA) or pico kit (rRNA-depleted RNA).
17.5 ng of rRNA-depleted RNA as input and Epicentre ScriptSeq v2 RNA-Seq Library Preparation Kit was used. 10 cycles of cDNA amplification were applied. Libraries were purified using AMPure XP beads and quantified using a Qubit 2.0 fluorimeter. The size distribution was assessed using the Agilent 2100 Bioanalyzer and High Sensitvity DNA kit. The quantity of each library was assessed by qPCR using the Illumina Library Quantification Kit from Kapa and a Roche Light Cycler LC480II. The libraries were sequenced on the Illumina NextSeq 500 instrument using NextSeq High Output 150 cycles chemistry v1 (2x75 bp paired-end).

value: wild-type  kaeA+ for kaeA25

value: proA6, adF9, yA2; phenA2

value: biological replicate 1


title: antiGFP_CJW_Bb378_rep1

description: ChIP using anti-GFP antibodies

value: ParZ-GFP knock-in, anti-GFP ChIP rep1


title: wt5_biol_rep_2

value: wild-type kaeA+ for kaeA25

value: biological replicate 2


title: keaA25_biol_repl_2

value: keaA25 mutant

value: proA6, kaeA25, adF9, yA2; phenA2


title: 2_TFH_Blood

value: multiple sclerosis

value: follicular helper T cells (Tfh)

value: Blood


title: 6_TFH_CSF


title: N14_PBAT_MII_WT_sc3

value: Mouse MII oocyte

value: WT


title: wt4_biol_rep_3

description:
2x75 bp paired-end sequencing
kaeA19_vs_wt4.xlsx

value: mycellium

value: wild-type kaeA+ for kaeA19

value: proA6, pabaA9, biA1

value: biological replicate 3


title: keaA25_biol_repl_1


title: HeLa shPPIB_2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, FDR <= 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
The RNA was treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were assessed by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of each RNA sample was further verified by 1.5% agarose gel electrophoresis.electrophoresis.
A total 1μg RNA for each sample was used for RNA-seq library preparation. PolyA mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The frag¬mented RNA wereend repaired and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.

treatment_protocol: To knockdown PPIB, shRNA against human PPIB transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for analysis.

value: transfected with PPIB shRNA


title: N14_PBAT_MII_WT_sc2


title: 5_TFH_CSF

value: CSF


title: 4_TFH_CSF


title: N14_PBAT_MII_WT_sc1


title: 3_TFH_CSF


title: ACE_Sperm_rep2

description: Bisulfite-sequencing data profiled by ACE-seq

data_processing:
Raw sequencing data were trimmed and filtered with Trim Galore (v0.6.6).
Clean reads were aligned to the mm9 mouse genome by using Bismark (v0.23.0).
Reads were deduplicated and were discarded if reads were with  more than 3 consecutive non-converted cytosines in non-CpG context.
Cytosines in CpG sequence context were extracted and counted by MethyDackel (v0.5.0). Raw signals were defined as the percentage of C/(C+T) at each site.
Genome_build: mm9
Supplementary_files_format_and_content: *bw: bigwig files

source_name: Mouse sperm

extract_protocol:
MII oocytes were collected 14-15 hours after hCG injection.
For mammalian gDNA samples of n sperm, 50-100 ng of purified gDNA was combined with 100 pg of each phage spike-ins to a total volume of 130 μl. For mouse MII oocytes, 10 pg of each phage spike-ins were added to the digested gDNA to a total volume of 130 μl. Then, each sample was sheared to ~200 bp by using Covaris M220 sonicator and purified once using 1× Ampure XP beads (Beckman coulter, Cat# A63882). Next, gDNA was modified using UDP-glucose and T4 Phage β-glucosyltransferase (New England Biolabs, Cat# M0357) in a total volume of 20 µl at 37 °C for 1 h. After incubation, add 5 µl of freshly prepared 0.1 N NaOH (Sigma-Aldrich, Cat# 795429) to the 20 µl of modified gDNA to denaturation at 55 °C for 10 min. Then, quickly add 1 µl of APOBEC (New England Biolabs, Cat# E7125), 1 µl of BSA and 10 µl of APOBEC Reaction Buffer to the denatured gDNA in a total volume of 100 μl. Incubate at 37 °C for 3hrs to deamination. After deamination, purify the sample once using 1× Ampure XP beads before library construction according to the TAILS procedure.

value: sperm


title: keaA25_biol_repl_3


title: wt5_biol_rep_3

value: proA6, adF9, yA2; phenA2


title: wt4_biol_rep_1

value: biological replicate 1


title: wt4_biol_rep_2

value: biological replicate 2


title: HeLa shPPIB_1st


title: HeLa shCtrl empty vector_1st

value: transfected with empty vector


title: WT RNA-seq Rep 2

city: Boston

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 100 nt.
Untreated RNA-seq samples were mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
siNT and siINTS11 were first mapped to an ERCC spike genome, and reads not mappping to spike were subsequently mapped to mm10 using STAR (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
bigWigs output from STAR were used for downstream analysis and visualization.
Assembly: mm10
Supplementary files format and content: bigWigs representing coverage (no normalization for untreated; DEseq-normalized for siNT and siINTS11)

source_name: Embryonic stem cell

growth_protocol: INTS11Halo cells were maintained in SFES+2i/LIF.

extract_protocol:
RNA was extracted in Trizol and purified.
Libraries were generated with the llumina TruSeq Stranded Total RNA kit using standard protocols.

treatment_protocol: Cells were either not treated or treated with siRNA (siNT or siINTS11) for 48 hours.

value: Embryonic stem cell


title: ACE_Sperm_rep1


title: 2_TFH_CSF

value: multiple sclerosis


title: 7_TFH_CSF

value: follicular helper T cells (Tfh)


title: keaA19_biol_repl_3

value: keaA19 mutant

value: proA6, kaeA19,pabaA9, biA4


title: 1_TFH_CSF


title: ACE_MII_rep2

value: Mouse MII oocyte


title: WT INTS11 ChIP-seq Rep 2

data_processing:
Sequencing reads were filtered (requiring a mean quality score over 20) and trimmed to 50 bp.
Data from WT cells were mapped to a genome representing mm10 rRNA genes. Reads not mapping here were mapped to mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Data from INTS11Halo cells were first mapped to the Drosophila dm3 genome (spike) and reads not mapping here were subsequently mapped mm10 using Bowtie 1.2.2 (-v2 -k1 --best)
Mapped reads were converted to bedGraphs representing deduplicated fragment midpoints using extract_fragments.pl (DOI 10.5281/zenodo.5519914), which were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: INTS11Halo bigWigs represent deduplicated, background-subtracted, normalized fragment centers. WT bigWigs represent deduplicated fragment centers.

extract_protocol:
Cells were crosslinked with formaldehyde for 10 minutes and quenched with glycine. After washing, cell pellets were resuspended in sonication buffer and sonicated using the Qsonica Q800R3 system. Chromatin was pre-cleared with Protein A agarose and incubated with the indicated antibody overnight. Protein A agarose beads were added and allowed to bind antibody-epitope complexes. IPs were washed extensively and eluted twice. DNA was purified using phenol/chloroform.
INTS11Halo eluates were spiked with Drosophila DNA. All libraries were constructed with the NEB NEBNext Ultra II DNA Library kit .

treatment_protocol: WT cells were not treated. INTS11Halo cells were treated with DMSO or 500 nM PROTAC for 4 hours.

value: WT

value: INTS11 (Sigma, HPA029025)


title: keaA19_biol_repl_2

value: mycellium

value: proA6, kaeA19,pabaA9, biA3


title: WT RNA-seq Rep 1


title: WGS_CJW_Bb523_rep1

treatment_protocol: Cells were growing in 40 mL BSK-II medium to a density of ~3-6 x 107 cells/mL. The culture was pelleted at 4,000 x g for 10 min in the swinging bucket rotor, resuspended in 1 mL cold HN buffer, and re-pelleted.

value: BSK-II

value: clonal isolate of strain B31 MI wild-type, WGS rep1

value: Strain B31 MI wild-type


title: keaA19_biol_repl_1

value: proA6, kaeA19,pabaA9, biA2


title: WGS_CJW_Bb523_rep2

value: clonal isolate of strain B31 MI wild-type, WGS rep2


title: HeLa shCtrl empty vector_2nd


title: ACE_MII_rep1


title: Control male

status: Public on Oct 27 2022

city: Kyoto

first: Yoshihiko

last: Kobayashi

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Institute for Life and Medical Sciences

country: Japan

institute: Kyoto University

data_processing:
Libraries were sequenced using HiSeq X ten
FASTQ files were processed using Cell Ranger v6.0.1 to get UMI expression matrix files.
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: Dissociated total kidney cells

extract_protocol:
Kidneys were dissociated with liberase TM, hyaluronidase, DNaseI at 37C for 20 min, followed by incubation with 0.25% trypsin EDTA at 37C for 10 min. Trypsin was inactivated using 10% fetal bovine serum in PBS. Cells were then resuspended in PBS supplemented with 0.01% bovine serum albumin then filtered through 40 µm strainer and utelized for GEM generation
Followed standard procedure of Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: Genetic Gpx4 deletion was induced by doxycycline feeding for 7 days. Kidneys were harvested on day 10 after initiating doxycyline feeding..

tag: age

value: 9 weeks

value: Kidney

value: Gpx4 f/f


title: Control female


title: Gpx4 cKO female

value: Pax8rtTA; tetO-Cre; Gpx4 f/f


title: Gpx4 cKO male


title: WT INTS11 ChIP-seq Rep 1

value: Embryonic stem cell


title: WT2

first: Qiong

last: Xiao

address: street of luojia mountain

institute: College of Life Sciences, Wuhan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of Fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: mice mammary tumor

extract_protocol:
For cell RNA extraction, cells were scraped down and collected with centrifugation. Total RNA was extracted with RNA extraction kit (Aidlab). For tissue RNA extraction, 20 mg tissues were homogenized and collected with centrifugation. Total RNA was extracted with RNA extraction kit (CWBIO) according to the manufacturer’s manual.
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111)

value: Trim11+/- C57BL/6N and FVB/N-Tg (MMTV-PyVT) 635Mul/J hybrid

value: breast cancer tumor

value: 3-month old

value: wild type

value: Wild  type  MMTV-PyVT mice


title: WT1

value: Trim11+/- C57BL/6N and FVB/N-Tg (MMTV-PyVT) 634Mul/J hybrid


title: Fraction_17

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

institute: National institute of infectious diseases

data_processing:
Adapter clipping: cutadapt
Read mapping: READemption align and segemehl
Coverage calculator: READemption coverage
Assembly: NC_00913.3
Supplementary files format and content: wiggle

organism: Escherichia coli

growth_protocol: Overnight cultures of E. coli MG1655 were 100-fold diluted in 100 ml of fresh LB medium, grown to an OD600 of 2.0, cooled down in an ice-water bath, and then harvested by centrifugation.

extract_protocol:
RNA from each fraction was extratced by P/C/I while the lysate RNA was extracted by TRIzol method. The aqueous phases were precipitated with GlycoBlue and ethanol/3M sodium acetate, pH 6.5 (30:1) overnight at −20°C. The RNA was pelleted by centrifugation, washed with 70% ethanol. Thereafter, RNA was dissolved in DEPC-treated H2O and DNase-digested . The DNase-treated RNA was purified by  P/C/I. The purified, DNase-treated RNA was dissolved in DEPC-treated H2O.
RNA samples were fragmented, ligated with 3’ adapter, and reverse-transcribed with MMLV reverse transcriptase. Purified first-strand cDNA was then ligated with the 5’ Illumina TruSeq sequencing adapter, followed by PCR amplification. The cDNA samples were purified with the Agencourt AMPure XP kit and pooled with ratios according to the input samples' RNA concentrations. Finally, cDNA with a size range of 200-550 bp was gel-eluted.

treatment_protocol: The cells were resuspended in ice-cold lysis buffer and lysed by vortexing with 0.1 mm glass beads. The lysate was cleared by centrifugation. The cleared lysate was then injected into the equilibrated column connected to ÄKTA pure purification system. Each fraction was automatically collected using fraction collector F9-R at 4°C.

tag: growth phase

value: Early stationary (OD 2.0)

value: fractionation by superose 6 increase column


title: WT3

value: Trim11+/- C57BL/6N and FVB/N-Tg (MMTV-PyVT) 636Mul/J hybrid


title: Fraction_20


title: Fraction_13


title: Fraction_14


title: Fraction_15


title: Fraction_19


title: Fraction_18


title: Fraction_16


title: Trim11-KD3

value: Trim11+/- C57BL/6N and FVB/N-Tg (MMTV-PyVT) 639Mul/J hybrid

value: exon 2-6 region of Trim11 was deleted based on CRISPR/Cas9 system to generate Trim11 knockout MMTV-PyVT mice


title: Trim11-KD1

value: Trim11+/- C57BL/6N and FVB/N-Tg (MMTV-PyVT) 637Mul/J hybrid


title: Fraction_11


title: Fraction_09


title: Fraction_10


title: Fraction_08


title: Trim11-KD2

value: Trim11+/- C57BL/6N and FVB/N-Tg (MMTV-PyVT) 638Mul/J hybrid


title: Fraction_05


title: Fraction_07


title: Fraction_03


title: Fraction_06


title: Fraction_01


title: Fraction_02


title: Fraction_00L

value: cleared lysate


title: RNA, PPARg WT, rep2

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description:
Counts_RNA_FPLD3_mm10.txt
SM3045

data_processing:
Alignment to mm10 genome using STAR
ChIP-seq and ATAC-seq data was deduplicated using Picard Tools (Broard Institutte http://broadinstitute.github.io/picard/)
Nucleosome-free accessible regions were extracted as fragments <120 bp using SamTools (ATAC-seq)
Tag-directories were generated using HOMER makeTagDirectories (RNA-, ChIP, and ATAC-seq)
HOMER findPeaks was used to call peaks (ChIP- and ATAC-seq)
HOMER annotatePeaks.pl was used to count tags within called peaks (ChIP- and ATAC-seq)
HOMER analyzeRepeats.pl was used to count reads within exons (RNA-seq)
DESeq2 was used to identify differential binding of HA-PPARg and Med1, acetylation of H3K27 (ChIP-seq), accessibility of chromatin (ATAC-seq), and gene expression (RNA-seq).
Assembly: mm10
Supplementary files format and content: bigwig-file: contain file for visualization of sequenced reads in the UCSC genome browser.
Supplementary files format and content: bed-file: contains positions for called peaks
Supplementary files format and content: Counts_RNA_FPLD3_mm10.txt: count matrix for exon-counts within all RNA samples

source_name: PPARg-/-MEF-CAR cells

growth_protocol: PPARγ-/- MEF-CAR cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) 4.5 g/L D-glucose supplemented with 10% fetal bovine serum (Gibco), and 100 μg penicillin/ml and 100 μg streptomycin/ml (Invitrogen)

extract_protocol:
Cells were harvested in Trizol (Thermo Fisher) and RNA purified according to the manufacturer’s instructions . Sample was prepared for sequencing using polydT-enriched cDNA synthesis.
Purified RNA was subjected to polydT-enriched cDNA synthesis before sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of HA-, Med1, and H3K27ac-enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279). ATAC-seq libraries were prepared for sequencing according to manufacturer's instructions (Illumina).

treatment_protocol: PPARγ-/- MEF-CAR cells were transduced with adenoviral vectors expressing HA-tagged mPPARγ2-WT, mPPARγ2-E379K or mPPARγ2-R212Q. Control cells were not subjected to adenovirus. After two hours of virus exposure, the medium was removed, and cells were treated with medium containing either vehicle dimethyl sulfoxide (DMSO) or 1 µM rosiglitazone (Alexis) for another 6 hours before harvest.

value: PPARg-/-MEF-CAR cells

tag: transduction

tag: ligand

value: 1 µM Rosiglitazone


title: RNA, PPARg E379K, rep2

description:
Counts_RNA_FPLD3_mm10.txt
SM3046


title: RNA, PPARg R212Q, rep2

description:
Counts_RNA_FPLD3_mm10.txt
SM3047


title: RNA, untransduced control, rep2

description:
Counts_RNA_FPLD3_mm10.txt
SM3048

value: Untransduced

value: DMSO


title: RNA, PPARg E379K, rep1

description:
Counts_RNA_FPLD3_mm10.txt
SM3042


title: Fraction_04


title: C57BL/6, Spleen, 58A2 , d34, 19

city: Brussels

first: Christophe

last: Vanderaa

address: Avenue Hippocrate 74

country: Belgium

institute: UCLouvain

description:
JDX180419-rawcounts.txt
JDX180419-19

data_processing:
Sequences were aligned using the STAR software
Read counts were determined with the HTSeqCount software
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with raw RNA counts

source_name: MPLW508A mice

growth_protocol: Mouse spleen were collected and stored at -80°C until processing.

extract_protocol:
Spleens were disrupted using Ultra Turrax (Ika). Total RNA was extracted using NucleoSpin RNA kit (Macherey Nagel, 740955.50)
Illumina TruSeq Stranded Total RNA

treatment_protocol: Mice received weekly intraperitoneal (i.p.) injections of isotype control (motavizumab, mIgG2a) or anti-GARP:TGF-β1 (clone 58A2, mIgG2a WT or mIgG2a FcDead) mAbs (400 μg/mouse), starting from the day before the transplantation.

value: Spleen

tag: time post transplantation

tag: response

tag: ID


title: C57BL/6, Spleen, ISO, d34, 8

description:
JDX180419-rawcounts.txt
JDX180419-8

value: ISO


title: C57BL/6, Spleen, 58A2 , d34, 31

description:
JDX180419-rawcounts.txt
JDX180419-31


title: C57BL/6, Spleen, 58A2 , d34, 4

description:
JDX180419-rawcounts.txt
JDX180419-4


title: C57BL/6, Spleen, 58A2 , d34, 29

description:
JDX180419-rawcounts.txt
JDX180419-29


title: C57BL/6, Spleen, ISO, d34, 26

description:
JDX180419-rawcounts.txt
JDX180419-26


title: C57BL/6, Spleen, 58A2 , d34, 25

description:
JDX180419-rawcounts.txt
JDX180419-25


title: C57BL/6, Spleen, ISO, d34, 20

description:
JDX180419-rawcounts.txt
JDX180419-20


title: C57BL/6, Spleen, 58A2 , d34, 16

description:
JDX180419-rawcounts.txt
JDX180419-16


title: C57BL/6, Spleen, 58A2 , d34, 27

description:
JDX180419-rawcounts.txt
JDX180419-27


title: C57BL/6, Spleen, ISO, d34, 28

description:
JDX180419-rawcounts.txt
JDX180419-28


title: C57BL/6, Spleen, ISO, d34, 2

description:
JDX180419-rawcounts.txt
JDX180419-2


title: RNA, PPARg R212Q, rep1

description:
Counts_RNA_FPLD3_mm10.txt
SM3043


title: C57BL/6, Spleen, ISO, d34, 11

description:
JDX180419-rawcounts.txt
JDX180419-11


title: reporter library on plasmid

city: New Haven

first: Carson

middle: C

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

description: plasmid

data_processing:
Basecalls performed using CASAVA 1.8.
In one step, read by read, sequenced reads were trimmed for adaptor sequences and counted using a custom script. For all RNA molecules the 3’ adapter sequence GCCGCAGCCGCCGCCATCGTCGACGC was removed, whereas for the DNA molecules (from plasmid) the same 3’ adapter as well as the 5’ adapter sequence AGAGCTGGTTTAGTGAACCGTC were removed. For the RNA-derived libraries, a read was only counted if the trimmed sequence was 1) 7-mers not starting with a G or N, or 2) 8-mers starting with a G. This first G would be removed before counting. For the plasmid-derived library all trimmed sequences that were 7-mers were counted. In this same first step all reads corresponding to the spike-in RNA (containing sequence CTCTTCCCATGGCCGCAGCCGCCGCCATCGTCGACGCGCGCT) were counted.
Using DESeq2, read counts were normalized using spike-in counts first. Then RNA stability and RNA translation rate and the fold change in each (Torin1/DMSO) were calculated per 5’ end 7-mer sequence. RNA stability was estimated by calculating the ratio of actinomycinD-treated over untreated normalized read counts, per condition (Torin1 or control-treated). RNA translation rates were estimated as the ratio of polysomal over subpolysomal normalized read counts per condition.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: counts

organism: synthetic construct

source_name: plasmid

growth_protocol: HeLa cells were grown in high-glucose DMEM supplemented with 10% (vol/vol) heat-inactivated FBS and penicillin/streptomycin. Cells were seeded on 15 cm plates at indicated numbers per plate the day before experiment.

extract_protocol:
Either total RNA was extracted directly with Trizol containing a capped RNA spike-in molecule, or cells were lysed on plate in 20 mM Tris pH 7.4; 150 mM NaCl; 5 mM MgCl2; 1% Triton X-100; 1 mM DTT; 100 ug/ml cycloheximide. Clarified lysates were then separated into a subpolysomal and polysomal fraction on a 5-50% sucrose gradient, and an equal amount of the capped spike-in RNA described above was added to each fraction. Total RNA was retrieved from both fractions by proteinase K treatment followed by acid phenol extraction.
The Renilla luciferase RNA was reverse transcribed with a gene-specific primer, followed by alkaline RNA hydrolysis. The 3’ end of the cDNA was then ligated to a double stranded DNA linker with a 3’ NNNNNN or GNNNNN (mixed in 1:4 ratio). A 3’ adapter sequence was added by PCR, followed by a second PCR that incorporates Illumina  sequences with dual index. Sequencing libraries from plasmid were prepared by adding adapter sequences in a first PCR step, followed by incorporation of Illumina  sequences in a second PCR reaction.

treatment_protocol: Cells were treated with 250 nM Torin1 or an equal volume of DMSO (0.025% final concentration) for 2 hours. Then cells were either lysed or 2 ug/ml actinomycinD was added followed by another 2 hour incubation.

value: reporter library

tag: rna fraction


title: RNA, untransduced control, rep1

description:
Counts_RNA_FPLD3_mm10.txt
SM3044


title: C57BL/6, Spleen, ISO, d34, 23

description:
JDX180419-rawcounts.txt
JDX180419-23


title: C57BL/6, Spleen, ISO, d34, 17

description:
JDX180419-rawcounts.txt
JDX180419-17


title: C57BL/6, Spleen, 58A2 , d34, 13

description:
JDX180419-rawcounts.txt
JDX180419-13


title: RNA, PPARg WT, rep1

description:
Counts_RNA_FPLD3_mm10.txt
SM3041


title: LV heart tissue, Rbm20 knockout, male (ko_m_128-2)

city: Heidelberg

first: Maarten

last: van den Hoogenhof

state: (select)

address: In Neuenheimer Feld 669

institute: Institute of Experimental Cardiology

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_128-2)
Column name in processed data files: 546

data_processing:
BGI processed all sequenced reads using standard methods
Trimmed reads were then aligned with STAR (2.7.10a) to Gencode mm39 reference genome with parameters:STAR --genomeDir $GENOME_DIR --readFilesCommand zcat --readFilesIn $INPUT_DIR/fastq/${VAR}.txt.gz --sjdbGTFfile $GENOME_DIR/gencode.v28.annotation.gtf --sjdbOverhang 99 --quantMode GeneCounts --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${RESULTS_DIR}/Alignment/${VAR}_
DESeq2 (2.7.10a) within R (4.1.2) was then run to get to final differential expression results comparing RBM20 vs. WT mice for male and female mice.
Assembly: GRCm39.primary
Supplementary files format and content: 4 excel files with output from differential expression analysis (DESeq and DEXSeq), including STAR-generated normalized counts
Supplementary files format and content: sample numbers in the excel files can be found under 'description' in the SAMPLES section

source_name: Heart (LV)

extract_protocol:
RNA was isolated using TRI Reagent from LV tissue
RNA libraries were prepared for sequencing using standard BGI protocols for the BGISEQ-500 Transcriptome

value: Heart (LV)

tag: Sex

value: male

value: Rbm20 knockout


title: C51_Forskolin

first: Ryuji

last: Morizane

state: Massachusetts

address: 149 13th Street

department: Nephrology Division

institute: Massachusetts General Hospital

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc.) was used for scanning. Images were quantified using Extraction (Toray Industries Inc.).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: C51 kidney organoids treated with Forskolin

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: H9-derived PKHD1 mutants were maintained on hESC-qualified Geltrex coated plates using StemFit ® Basic02 supplemented with 10 ng/ml of FGF2. The hPSC lines were passaged weekly, using Accutase for dissociation and Y27632 to facilitate adhesion on passaging. Kidney organoids were then differentiated and maintained following protocol reported in Morizane R et al Nat. Protoc. 2017; 12(1): 195-207.

extract_protocol: Total RNA samples were isolated from kidney organoids with TRIzol (Thermo Fisher Scientific) according to the manufacturer’s protocol.

treatment_protocol:
Flow: PKHD1 mutant organoids on day 14 of differentiation were placed on engineered ECM layer. The ECM comprised a gelbrin network, which contains gelatin, fibrinogen, CaCl2, transglutaminase, and thrombin. Fluid shear stress was applied to whole organoids at a flow rate of 4.27 ml/min from day 15 to day 35. Medium was changed every other day.
ECM: PKHD1 mutant organoids were placed onto engineered ECM layer and cultured without fluidic flow. Medium was changed every other day.
Forskolin: PKHD1 mutant organoids were treated with 20 μM of forskolin from Day 14 to Day 35. Medium was changed every other day.

value: H9 ESCs

tag: cell type

value: kidney organoids derived from human embryonic stem cells (H9 ESCs)

tag: days cultured

tag: genotype


title: C9_Forskolin

source_name: C9 kidney organoids treated with Forskolin

tag: cell line


title: LV heart tissue, Rbm20 knockout, male (ko_m_106-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_106-2)
Column name in processed data files: 570

tag: tissue


title: C51_ECM

source_name: C51 kidney organoids on ECM


title: C57BL/6, Spleen, 58A2 , d34, 10

description:
JDX180419-rawcounts.txt
JDX180419-10

tag: treatment


title: LV heart tissue, Rbm20 knockout, male (ko_m_130-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_130-2)
Column name in processed data files: 550


title: C57BL/6, Spleen, ISO, d13, 2

description:
SLE200402-rawcounts.txt
200402_2


title: C9_ECM

source_name: C9 kidney organoids on ECM


title: C57BL/6, Spleen, 58A2 , d34, 1

description:
JDX180419-rawcounts.txt
JDX180419-1


title: C57BL/6, Spleen, ISO, d20, 51

description:
SLE200402-rawcounts.txt
200402_51


title: LV heart tissue, Rbm20 knockout, male (ko_m_97-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_97-2)
Column name in processed data files: 542


title: LV heart tissue, Rbm20 knockout, female (ko_f_95-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_95-2)
Column name in processed data files: 568

value: female


title: C9_Flow

source_name: C9 kidney organoids under fluid flow


title: LV heart tissue, Rbm20 knockout, male (ko_m_127-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_127-2)
Column name in processed data files: 544


title: LV heart tissue, Rbm20 knockout, female (ko_f_150-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_150-2)
Column name in processed data files: 523


title: LV heart tissue, Rbm20 knockout, female (ko_f_155-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_155-2)
Column name in processed data files: 531


title: C57BL/6, Spleen, ISO, d13, 4

description:
SLE200402-rawcounts.txt
200402_4


title: LV heart tissue, Rbm20 knockout, female (ko_f_154-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_154-2)
Column name in processed data files: 529


title: LV heart tissue, Rbm20 knockout, female (ko_f_151-2)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_151-2)
Column name in processed data files: 526


title: C51_Flow

source_name: C51 kidney organoids under fluid flow


title: C57BL/6, Spleen, ISO, d13, 3

description:
SLE200402-rawcounts.txt
200402_3


title: C57BL/6, Spleen, ISO, d20, 19

description:
SLE200402-rawcounts.txt
200402_19


title: C57BL/6, Spleen, ISO, d13, 5

description:
SLE200402-rawcounts.txt
200402_5


title: C57BL/6, Spleen, ISO, d13, 1

description:
SLE200402-rawcounts.txt
200402_1


title: C57BL/6, Spleen, ISO, d20, 21

description:
SLE200402-rawcounts.txt
200402_21


title: C57BL/6, Spleen, ISO, d20, 16

description:
SLE200402-rawcounts.txt
200402_16


title: LV heart tissue, wildtype, male (wt_m_139-2)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_139-2)
Column name in processed data files: 521

value: wildtype


title: LV heart tissue, wildtype, male (wt_m_113-2)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_113-2)
Column name in processed data files: 515


title: LV heart tissue, wildtype, male (wt_m_125-2)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_125-2)
Column name in processed data files: 519


title: LV heart tissue, wildtype, male (wt_m_124-2)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_124-2)
Column name in processed data files: 517


title: LV heart tissue, wildtype, male (wt_m_112-2)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_112-2)
Column name in processed data files: 512


title: LV heart tissue, wildtype, female (wt_f_144-2)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_144-2)
Column name in processed data files: 510


title: LV heart tissue, wildtype, female (wt_f_142-2)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_142-2)
Column name in processed data files: 506


title: C57BL/6, Spleen, ISO, d20, 22

description:
SLE200402-rawcounts.txt
200402_22


title: Mouse spleen, healty, replicate 2, sphere BC

city: Zürich

first: Kristina

last: Handler

address: Winterthurerstrasse

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zürich

description: Hashing BC

data_processing:
deMULTIplex (v1.0.2)
genome building/assembly: -
UMI count matrix for MULTI-seq barcodes per cell; column "Barcode" contains the allocated MULTI-seq BC (.txt format)

source_name: Spleen

extract_protocol:
in-vitro digestion
MULTI-seq cell hashing

value: Splenocytes

value: no treatment

tag: disease state

value: healty

tag: termination

value: 6-8 weeks old


title: Mouse spleen, healty, replicate 1, sphere BC

description: Hashing BC

tag: strain

tag: age


title: LV heart tissue, wildtype, female (wt_f_141-2)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_141-2)
Column name in processed data files: 504


title: Mouse spleen, healty, replicate 2, WTA

description: 5' RNA

data_processing:
Cell Ranger (v5.0.0)
genome building/assembly: GRCm38 v2020genome building/assembly: -A genecode
Cell barcodes corresponding to column indices of matrix.mtx.gz (.tsv.gz format)
Feature ID and name in the first and second column, features correspond to row indices of matrix.mtx.gz (.tsv.gz format)
Sparse feature barcode count matrix (mtx.gz format)

extract_protocol:
in-vitro digestion
10X Genomics: 5' WTA kit


title: Mouse liver, metastatic, replicate 9, sphere BC

description: Hashing BC

source_name: Liver

value: Liver cells

value: Liver

value: intrasplenic injection with mouse colon cancer organoids

value: metastatic liver

value: 2 weeks after injection

value: 8-10 weeks old


title: Mouse liver, metastatic, replicate 1, Visium

description: polyA RNA

data_processing:
Space Ranger (v1.2.09)
genome building/assembly: GRCm38 v2020genome building/assembly: -A genecode
Cell barcodes corresponding to column indices of matrix.mtx.gz (.tsv.gz format)
Feature ID and name in the first and second column, features correspond to row indices of matrix.mtx.gz (.tsv.gz format)
Sparse feature barcode count matrix (mtx.gz format)
Scalefactors of pixel posiitons (.json format)
Full-resolution image (.png format)
Table with rows corresponding to spots (.csv format)

extract_protocol:
in-vitro digestion
Visium


title: LV heart tissue, wildtype, female (wt_f_140-2)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_140-2)
Column name in processed data files: 502

value: Heart (LV)


title: Mouse liver, metastatic, replicate 2, Visium

description: polyA RNA


title: Mouse spleen, healty, replicate 1, WTA

description: 5' RNA

value: Spleen


title: Mouse liver, healty, sphere BC

description: Hashing BC


title: LV heart tissue, Rbm20 knockout, male (ko_m_130-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_130-1)
Column name in processed data files: 548

value: male

value: Rbm20 knockout


title: LV heart tissue, Rbm20 knockout, male (ko_m_128-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_128-1)
Column name in processed data files: 545


title: LV heart tissue, Rbm20 knockout, male (ko_m_127-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_127-1)
Column name in processed data files: 543


title: Mouse liver, healty, WTA

description: polyA RNA

data_processing:
zUMIs (v. 2.9.4)
genome building/assembly: GRCm38 vM25 genecode
3 UMI and 3 read count tables; gene-wise counts for exon, intron and exon+intron (.rds format)
Cell barcodes in first column and total UMI counts in second column (.txt format)

extract_protocol:
in-vitro digestion
BD Rhapsody: WTA kit


title: Mouse liver, metastatic, replicate 9, WTA

description: polyA RNA


title: LV heart tissue, Rbm20 knockout, male (ko_m_97-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_97-1)
Column name in processed data files: 541


title: Mouse liver, metastatic, replicate 8, sphere BC

description: Hashing BC


title: Mouse liver, metastatic, replicate 7, sphere BC

description: Hashing BC


title: LV heart tissue, wildtype, female (wt_f_143-2)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_143-2)
Column name in processed data files: 508


title: Mouse liver, metastatic, replicate 8, WTA

description: polyA RNA


title: Mouse liver, metastatic, replicate 6, sphere BC

description: Hashing BC


title: Mouse liver, metastatic, replicate 7, WTA

description: polyA RNA


title: LV heart tissue, Rbm20 knockout, female (ko_f_95-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_95-1)
Column name in processed data files: 567


title: LV heart tissue, Rbm20 knockout, female (ko_f_155-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_155-1)
Column name in processed data files: 530


title: LV heart tissue, Rbm20 knockout, female (ko_f_154-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_154-1)
Column name in processed data files: 527


title: LV heart tissue, Rbm20 knockout, male (ko_m_106-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, male (ko_m_106-1)
Column name in processed data files: 569


title: Mouse liver, metastatic, replicate 6, WTA

description: polyA RNA


title: Mouse liver, metastatic, replicate 5, sphere BC

description: Hashing BC


title: Mouse liver, metastatic, replicate 4, WTA

description: polyA RNA


title: Mouse liver, metastatic, replicate 5, WTA

description: polyA RNA


title: Mouse liver, metastatic, replicate 4, sphere BC

description: Hashing BC


title: LV heart tissue, Rbm20 knockout, female (ko_f_150-1)

description:
Mouse left ventricular heart tissue, Rbm20 knockout, female (ko_f_150-1)
Column name in processed data files: 522


title: Mouse liver, metastatic, replicate 3, WTA

description: polyA RNA


title: LV heart tissue, wildtype, male (wt_m_124-1)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_124-1)
Column name in processed data files: 516


title: Mouse liver, metastatic, replicate 3, sphere BC

description: Hashing BC


title: LV heart tissue, wildtype, male (wt_m_125-1)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_125-1)
Column name in processed data files: 518


title: LV heart tissue, wildtype, male (wt_m_113-1)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_113-1)
Column name in processed data files: 513


title: LV heart tissue, wildtype, male (wt_m_112-1)

description:
Mouse left ventricular heart tissue, wildtype, male (wt_m_112-1)
Column name in processed data files: 511


title: Mouse liver, metastatic, replicate 2, WTA

description: polyA RNA


title: LV heart tissue, wildtype, female (wt_f_144-1)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_144-1)
Column name in processed data files: 509


title: Mouse liver, metastatic, replicate 2, sphere BC

description: Hashing BC


title: Mouse liver, metastatic, replicate 1, sphere BC

description: Hashing BC


title: LV heart tissue, wildtype, female (wt_f_143-1)

description:
Mouse left ventricular heart tissue, wildtype, female (wt_f_143-1)
Column name in processed data files: 507