title: POND-FMR1-E204del_rep1


title: POND-FMR1-R138syn_rep1

status: Public on Jun 24 2026

type: SRA

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: HEK293T cell line

growth_protocol: HEK293T, Huh-7, and A549 cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml). V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor. H1 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2.

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

tag: cell line

value: HEK293T cell line

tag: genotype

tag: treatment


title: NEC_12d_hESC_rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic was employed to trim reads ends where average base calling qualities (in 5 bp windows) were below Q20. Only reads with minimum length of 30 bp were kept for further analyses.
We aligned all trimmed and filtered reads into human genome version hg38 (GRCh38) by using STAR version 2.7.1a.
Uniquely mapped reads were counted using featureCounts in Subread toolkit 1.6.473. By this approach, each read was only aligned and counted for the reference genome that had higher similarity to, and the reads with equal similarity to both genomes were excluded.
Counts normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2. Genes having absolute log2 fold-change higher than 1 and Benjamini-Hochberg adjusted P-value less than 0.05 were considered as significant differentially expressed genes (DEGs).
The shrinkage of log fold changes was performed using “ashr” shrinkage estimator. Visualization of the results was done by ggplot2, pheatmap and EnhancedVolcano packages. Overrepresentation analysis was performed in DAVID Bioinformatics Resources76. Gene set enrichment analysis was performed using Broad Institute GSEA software.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Txt file of raw counts

molecule: total RNA

source_name: RH6-derived NEC

extract_protocol:
miRNeasy micro kit (Qiagen)
Libraries for cell and tissue samples were generated by SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takar Bio).

value: RH6-derived NEC

tag: cell type

value: Neuroepithelial cells

value: WT

value: NEC differentiation

tag: time


title: CON_48H3

city: Hangzhou

first: Lingling

last: Ding

address: Shangtang street

institute: Zhejiang Provincial People’s Hospital

description: Library name: Sample 12

data_processing:
1. Raw sequencing data in FASTQ format were quality assessed using FastQC v0.11.9 (Babraham Bioinformatics).
2. Adapter sequences and low-quality bases were trimmed using Trimmomatic v0.39 with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
3. Clean reads were aligned to the human reference genome (GRCh38, GENCODE release 38) using STAR v2.7.9a with default parameters and --outSAMtype BAM SortedByCoordinate.
4. Gene expression quantification was performed using featureCounts v2.0.3 from the Subread package. Reads were counted against the GENCODE v38 gene annotation file with parameters: -t exon -g gene_id -s 2 -p --countReadPairs.
5. Raw counts were normalized to TPM (transcripts per million) using custom scripts in R v4.1.0.
6. Final expression matrix was generated with genes in rows and samples in columns.
Assembly: GRCh38
Supplementary files format and content: Gzip-compressed tab-delimited text file

molecule: polyA RNA

source_name: thyroid gland

extract_protocol:
Total RNA was isolated from 8505C cells using the RNeasy Mini Kit (Qiagen, Germany) following the manufacturer's protocol. Cells were washed with PBS, harvested by trypsinization, and pelleted by centrifugation at 300×g for 5 minutes. The cell pellet was lysed in Buffer RLT supplemented with 1% β-mercaptoethanol. The lysate was homogenized by passing through a QIAshredder column, mixed with 70% ethanol, and applied to the RNeasy spin column. On-column DNase I digestion was performed to remove genomic DNA contamination. After three wash steps, total RNA was eluted in 30 μL RNase-free water. RNA quantity and quality were determined using a Qubit fluorometer and Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme, China) following the manufacturer's protocol. Briefly, 1 μg of high-quality total RNA was used for mRNA capture with VAHTS RNA Clean Beads. The purified mRNA was fragmented at 94°C for 8 minutes and reverse transcribed using random primers. After second-strand synthesis, end repair and dA-tailing were performed, followed by adapter ligation. The ligated products were amplified by PCR for 13 cycles. Library purification was conducted with VAHTS DNA Clean Beads. Fragment size and concentration were evaluated using an Agilent 4200 TapeStation and Qubit dsDNA HS assay.

tag: tissue

value: thyroid gland

value: thyroid epithelial cell

value: 20 uM KU-57788  was used for erythroid differentiation of 8505C cells for 48 hour.


title: POND-FMR1-R138Q_rep2


title: preLSC, 540min, control, rep2

city: Edinburgh

first: Yuka

last: Kabayama

address: Max Born Crescent

country: United Kingdom

institute: University of Edinburgh

description: Library name: T9_ctl2

data_processing:
T to C conversion rates were obtained using the SlamDunk (v0.4.3).
Conversion rates across different time points were normalized to time 0 for each gene and were used to fit an exponential decay model to calculate half-lives.
Assembly: GRCm38
Supplementary files format and content: Output of slamdunk, tab-delimited text file.

organism: Mus musculus

source_name: preleukemic cells

growth_protocol: Meis1/Hoxa9 preleukemic cells were cultured at 200,000 cells/mL in IMDM supplemented with 10% FBS, Stem Cell Factor (40 ng/mL), IL-6 (20 ng/mL), IL-3 (20 ng/mL), Penicillin and Streptomycin, 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using QIAzol and alkylated in the dark room following manufactures protocol from Lexogen catabolic kit (cat. no. 062.24).
500 ng of total RNA was used for library preparation and 16 PCR cycles were performed using Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (cat. no. 015.24).

treatment_protocol: Medium with 2.9 μM of 4-thiouridine (4SU) was used for labelling preleukemic cells for 12 hours and was later replaced with 4SU-free medium (T0, 0min). Cells were collected into QIAzol reagent immediately after changing medium and at 1, 3, and 9 hours and frozen on dry ice.

value: preleukemic cells

value: control

tag: batch

value: 540 min


title: NEC_12d_hESC_rep2


title: Patient_9_pre

city: Southampton

first: Andres

middle: Felipe

last: Vallejo Pulido

address: University of Southampton

department: Medicine

institute: University of Southampton

description: FFPE

data_processing:
Fastq files were parsed on HTG Edge parser software and generated a gene expression count matrix.
Raw counts underwent processing using EdgeR R v4.3.2
Normalized using Trimmed Mean of M-values
Batch effect was corrected (batches 37 and 38)
Assembly: GRCh38
Supplementary files format and content: Raw counts

source_name: skin

extract_protocol:
Tissues were lysed using a lysis buffer from the HTG Molecular Diagnostics kit followed by the proteinase K digestion. Gene-specific nuclease protection probes with universal priming sites were then added. S1 nuclease was added to specifically digest non-hybridized molecules. The resulting DNA probes were quantitatively amplified using PCR, incorporating extended primers that included sequencing primer and sample barcode seqeunces for library preparation.
RNA sequencing of tissue with HTG EdgeSeq system's Precision Immuno-Oncology Panel was undertaked from all samples.

value: skin

value: pre


title: CON_48H2

description: Library name: Sample 11


title: preLSC, 540min, control, rep1

description: Library name: T9_ctl1


title: POND-FMR1-R138Q_rep1


title: NEC_12d_hESC_rep1


title: Placenta sample X31303.001

city: New York

first: Corina

last: Lesseur

state: NY

address: 1 Gustave L. Levy Pl

country: USA

institute: Icahn School of Medicine

description:
Library name: X31303.001
Column name in counts_nhbcs.csv.gz : X31303.001

data_processing:
Reads aligned with Splice Transcripts Alignment to a Reference (STAR) with GENCODE v47 (GRCh38) and quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv gzipped file with raw counts for each sample

source_name: Placenta villis fetal side

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany, cat. No. 74106), and the Norgen Tissue RNA Purification Kit (Norgen Biotek, Thorold, ON, Canada, Cat. No. 25700), following the manufacturer’s protocols.
Ribosomal RNA depletion was used to prepare RNA-sequencing (RNA-seq) libraries, transcriptome-wide RNA-sequencing was performed with paired-end 75 bp reads on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) .

value: Placenta villis fetal side

tag: baby race

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

value: AGA

tag: delivery method

value: C-section

tag: infant sex

value: Female

tag: maternal age

tag: rna integrity_number


title: CON_48H1

description: Library name: Sample 10


title: preLSC, 180min, control, rep3

description: Library name: T3_ctl3

value: 180 min


title: POND-FMR1-R201T_rep1

value: HEK293T cell line


title: Patient_8_post

description: FFPE

value: post


title: POND-FMR1-D136H_rep2


title: preLSC, 180min, control, rep2

description: Library name: T3_ctl2


title: CON_24H3

description: Library name: Sample 9

value: WT

value: 20 uM KU-57788  was used for erythroid differentiation of 8505C cells for 24 hour.


title: POND-FMR1-D136H_rep1


title: NEC_3d_hESC_rep3

value: RH6-derived NEC

value: Neuroepithelial cells

value: NEC differentiation


title: NEC_3d_hESC_rep2


title: CON_24H2

description: Library name: Sample 8

value: thyroid gland

value: thyroid epithelial cell


title: POND-FMR1-H127R_rep2


title: preLSC, 180min, control, rep1

description: Library name: T3_ctl1

value: preleukemic cells

value: control


title: NEC_3d_hESC_rep1


title: Placenta sample X31303.031

description:
Library name: X31303.031
Column name in counts_nhbcs.csv.gz : X31303.031

value: Placenta villis fetal side

tag: maternal smoking

value: No

value: LGA


title: preLSC, 60min, control, rep3

description: Library name: T1_ctl3

value: 60 min


title: CON_24H1

description: Library name: Sample 7


title: POND-FMR1-H127R_rep1


title: KU_48H3

description: Library name: Sample 6

value: 20 uM KU-57788  was used for erythroid differentiation of 8505C cells for 48 hour.


title: preLSC, 60min, control, rep2

description: Library name: T1_ctl2


title: POND-FMR1-T125I_rep2


title: hESC_rep3

value: Embryonic stem cell


title: KU_48H2

description: Library name: Sample 5


title: hESC_rep2


title: preLSC, 60min, control, rep1

description: Library name: T1_ctl1


title: POND-FMR1-A145S_rep1

value: HEK293T cell line


title: POND-FMR1-T125I_rep1


title: RNA-Seq data of lasermicrodissected PVN of hamster EH04_10 in torpor entry

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: Ulm University

data_processing:
FastQC 0.11.9
trim-galore 0.6.6
Trinity 2.8.5
Genome_build: GRCm39, Mus musculus
blastx 2.5.0+
extract_hits_from_fasta.rb (https://sourceforge.net/projects/prepare-transcript-to-gene-map/)
hits_to_genemap.rb (https://sourceforge.net/projects/prepare-transcript-to-gene-map/)
bowtie 1.3.0
rsem 1.3.1
Supplementary_files_format_and_content: .results, non-normalized gene expression
Supplementary_files_format_and_content: Trinity_SCN-PVN_Phodopus-ZT01.fasta (de novo assembly of transcriptomes)
Supplementary_files_format_and_content: Trinity_SCN-PVN_Phodopus-ZT01_aftermapping.fasta (assembly after mapping against Mus musculus (GRCm39))

organism: Cricetiscus sungorus

source_name: paraventricular nucleus (PVN)

growth_protocol: indoor breeding colony of Ulm University, Ulm, Germany

extract_protocol:
20 µm kryosections were prepared in a RNAse-poor environment on Poly-L-Lysine coated Carl Zeiss™ MembraneSlides 1.0 PEN (Fisher Scientific GmbH, Schwerte, Germany) using a cryostat “Microm HM 560” (Thermo Scientific, Walldorf, Germany). The sections were kresylviolett-stained to enable lasermicrodissection of the hypothalamic core areas SCN and PVN in Carl Zeiss™ adhesive-cap tube per sample (Fisher Scientific GmbH, Schwerte, Germany) on a PALM MicroBeam (Carl Zeiss Microscopy Deutschland GmbH, Oberkochen, Germany). Total RNA was purified using the RNeasy Plus Micro Kit with gDNA eliminator spin column (Qiagen GmbH, Hilden, Germany). Total RNA was checked for quality (Bioanalyzer, Agilent Technologies, Waldbronn, Germany) and quantity (RNA 6000 Pico Kit for very small RNA amounts of 50–5000pg/µL, Agilent Technologies, Waldbronn, Germany).
The mRNA were isolated, the library prepared (NEBNext® Single Cell / Low Input RNA library Prep Kit dual index), and the RNA-Seq performed on an Illumina NextSeq 500 (1 lane, 2x25 mio reads, 2 x 150 nt, 7.5 gb).

treatment_protocol: short photoperiod (8:16 L:D)

value: paraventricular nucleus (PVN)

tag: developmental stage

value: adult

tag: adapted to

value: short photoperiod (LD 8:16)

tag: Sex

value: male

value: torpor entry


title: KU_48H1

description: Library name: Sample 4

tag: cell line

tag: genotype

value: WT

tag: treatment


title: hESC_rep1

tag: cell type

tag: time


title: POND-FMR1-T125fs_rep2


title: Gonadotropin hashtag (TotalSeq-B) library

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

description:
Library name: Gonadotropin_CSP
10x Genomics TotalSeq-B hashtag oligonucleotide library used for sample multiplexing and demultiplexing.

library_source: other

data_processing:
Raw sequencing data were demultiplexed using Illumina bcl2fastq to generate FASTQ files.
Gene expression and hashtag libraries were processed using Cell Ranger (10x Genomics) to generate feature-barcode count matrices.
Hashtag oligonucleotide counts were used to assign cells to individual samples and identify multiplets.
Count matrices were imported into Seurat for quality control, normalization, dimensionality reduction, clustering, and downstream analysis.
Cells failing quality-control criteria or identified as multiplets were excluded from downstream analyses.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz contains the cell-by-gene count matrix. features.tsv.gz contains gene identifiers. barcodes.tsv.gz contains cell barcode identifiers. cell_metadata.csv contains cell-level annotations including sample assignment derived from hashtag oligonucleotides and downstream clustering results.
Supplementary files format and content: Processed data are provided in sparse matrix exchange (MEX) format with accompanying cell metadata to enable reproduction of downstream analyses.

molecule: other

source_name: Ovary

growth_protocol: Female C57BL/6J mice (10–12 weeks old) were maintained under standard housing conditions with ad libitum access to food and water.

extract_protocol:
Ovaries were dissociated into single-cell suspensions. Viable CD45+ immune cells were isolated by flow cytometric sorting. Individual samples were labeled with TotalSeq-B hashtag antibodies and pooled by treatment group prior to single-cell library preparation.
Single-cell gene expression and TotalSeq-B hashtag oligonucleotide libraries were generated using the 10x Genomics Chromium Single Cell 3' platform according to the manufacturer's protocol. Libraries were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Mice received gonadotropin treatment or saline control prior to tissue collection. Ovaries were harvested 48 hours after treatment.

tag: tissue

value: Ovary

value: CD45+ immune cells

value: Gonadotropin


title: preLSC, 0min, control, rep2

description: Library name: T0_ctl2

value: preleukemic cells

value: control

tag: batch

value: 0 min


title: KU_24H2

description: Library name: Sample 2

value: thyroid gland

value: thyroid epithelial cell

value: 20 uM KU-57788  was used for erythroid differentiation of 8505C cells for 24 hour.


title: KU_24H3

description: Library name: Sample 3


title: Gonadotropin pooled hashtagged scRNA-seq library

description:
Library name: Gonadotropin_RNA
10x Genomics scRNA-seq library generated from pooled gonadotropin-treated samples samples (n=5). Sample identities assigned downstream using hashtag/CSP libraries.

library_source: transcriptomic single cell


title: preLSC, 0min, control, rep1

description: Library name: T0_ctl1


title: Untreated hashtag (TotalSeq-B) library

description:
Library name: Untreated_CSP
10x Genomics TotalSeq-B hashtag oligonucleotide library used for sample multiplexing and demultiplexing.

value: Untreated


title: POND-FMR1-P120T_rep2

value: HEK293T cell line


title: KU_24H1

description: Library name: Sample 1


title: POND-FMR1-P120T_rep1


title: Untreated pooled hashtagged scRNA-seq library

description:
Library name: Untreated_RNA
10x Genomics scRNA-seq library generated from pooled untreated samples (n=5). Sample identities assigned downstream using hashtag/CSP libraries.


title: HCCC9810 cells, Isolinderalactone3, 24 hours

first: Wangyang

last: Chen

address: 261 Huansha Road, Hangzhou, Zhejiang, 310006, China

institute: Zhejiang University

description:
Library name: Sample_6
HCCC9810 cells treated with 20 μM ILL for 24 h

data_processing:
Raw reads were processed to remove adaptor sequences and low-quality reads. High-quality reads were mapped to the human reference genome. Gene abundance was quantified and normalized. Differentially expressed genes were identified using DESeq2 (q-value < 0.05, fold change > 2).
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) text file containing raw read counts for all samples. Rows represent gene symbols and columns represent samples.
Supplementary files format and content: Comma-separated values (CSV) text file containing normalized gene expression levels (FPKM) for all samples. Rows represent gene symbols and columns represent samples.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). RNA integrity was verified using an Agilent 2100 Bioanalyzer.
RNA libraries for RNA-seq were prepared using standard Illumina mRNA-seq library prep kits following manufacturer's protocols.

value: cholangiocarcinoma cells

value: wild type

value: 20 μM ILL for 24 h


title: MPTP, scRNAseq

city: Suzhou

first: QIEI

last: CONG

state: Jiangsu

address: No 199. Ren-ai Road

institute: Soochow University

description:
Library name: sample 2
10X Genomics

data_processing:
BCL files were converted to FASTQ using bcl2fastq. Reads were filtered with Cutadapt and aligned to the mouse reference genome (GRCm38) using Cell Ranger. Ambient RNA was removed with CellBender. Further quality control and analysis were performed in Seurat, including filtering low-quality cells and removing those with high mitochondrial gene expression.
Assembly: Mus musculus genome (GRCm38) reference
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
The hippocampal tissue was dissociated using Papain. Cell suspension was then assessed for concentration, viability, and cell size using a TC20 Automated Cell Counter.
Single cells were encapsulated with barcoded gel beads and partitioning oil to form GEMs (Gel Bead-in-Emulsions). After cell lysis, barcoded cDNA was synthesized, purified, and amplified. The cDNA was fragmented, end-repaired, and size-selected (~300 bp). Adaptors were ligated using T-A ligation, followed by PCR cleanup and validation before final library preparation.

treatment_protocol: Mice were treated with MPTP for 5 weeks. The hippocampus was subsequently isolated from 3-month-old mice for downstream single-cell RNA sequencing.

value: hippocampus

value: all neuronal and non-neuronal cells

value: MPTP


title: RNA-seq in WT (SP6KO littermate) bud ectoderm E10.5, rep3

city: Santander

first: Marian

last: Ros

address: 22nd Albert Einstein St.

country: Spain

institute: IBBTEC-CSIC-SODERCAN

description: Library name: RNASEQ_ect_sp6_WT_rep3

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and reads filtered and adaptor-trimmed with fastp (Chen et al 2018).
Reads were mapped to the mouse reference assembly (GRCm38), using HiSat2 (Kim et al 2019) with the option --dta-cufflinks, which enabled direct transcript assembly with StringTie (Pertea et al 2015)..
Read count means, fold-change (FC) and values were calculated with DEseq2 (Anders & Huber, 2010).
Assembly: mm10
Supplementary files format and content: Big Wig of RNAseq reads

source_name: limb bud ectoderm

extract_protocol:
Ectoderms were isolated with fine forceps from E10.5 forelimb buds of Sp8KO, SP6KO and WT embryos, after digestion with 0.25% trypsin for 20 min. on ice. The ectoderms of ~2 forelimb buds were used for each replicate.
SMART-Seq v4 Ultra Low Input RNA for Sequencing, Nextera XT DNA Library Preparation Kit

value: limb bud ectoderm

value: ectoderm

value: WT


title: MPTP_BONT_A, scRNAseq

description:
Library name: sample 3
10X Genomics


title: HCCC9810 cells, Isolinderalactone2, 24 hours

description:
Library name: Sample_5
HCCC9810 cells treated with 20 μM ILL for 24 h


title: Saline, scRNAseq

description:
Library name: sample 1
10X Genomics

value: Saline


title: POND-FMR1-K119N_rep1


title: RNA-seq in WT (SP6KO littermate) bud ectoderm E10.5, rep1

description: Library name: RNASEQ_ect_sp6_WT_rep1


title: RNA-seq in SP6KO bud ectoderm E10.5, rep3

description: Library name: RNASEQ_ect_sp6_KO_rep3


title: POND-FMR1-Y103syn_rep2


title: S. Paradoxus CBS 8841, 20C GPY,  rep2

city: Ploen

first: Fernanda

last: Giersdorf

address: August-Thienemann 2

department: Theoretical Biology

institute: Max Planck Institute for Evolutionary Biology

description: Library name: CBS8841_rep2

data_processing:
The genomic sequence and annotation were acquired from the Yeast PacBio Reference Panel (YPRP), where the CBS 8841 strain is named UFRJ50816. The GFF3 annotations were converted to the GTF format using gffread, excluding tRNAs. Custom genomic references were generated using the function mkref in Cell Ranger (9.0.0) . Single-cell gene expression matrices were made using the function count of Cell Ranger. Downstream processing was performed using Seurat. For each sample, a minimum threshold of 200 total RNA counts per cell was applied to remove low-quality barcodes. To remove potential doublets, an upper bound was set for each sample, defined as the median total RNA count plus three times the median absolute deviation of the sample.
Assembly: YPRP UFRJ50816
Supplementary files format and content: Comma separated tables where each row correspond to a gene (feature), each column corresponds to a cell(barcode), and the values are the number of unique molecular identifiers (UMIs) associated with the gene and cell

organism: Saccharomyces paradoxus

extract_protocol:
A zymolyase solution was prepared by dissolving 2,000 U of Zymolyase Ultra (Zymo Research, Art.-Nr. E1007-2) in 285.7 μL of 1× Quantiscript RT buffer (Qiagen QuantiTect Rev. Transcription Kit, Art. Nr. 205311). The solution was sterilized using a  0.22  μm centrifugal filter spun at 12,000 x g for 1 minute (Sigma Aldrich, Art.-Nr. UFC30GV0S). GEMs and libraries were constructed using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics, PN-1000268), following the user guide (CG000315) with the modification for fungal cell lysis from Vermeersch & Jariani et al. (2022). Cell suspensions were homogenized by pipetting up and down before loading the chips. The Gel Beads Kit v3.1 (PN-1000129) was thawed, and 1 μL of gel beads was removed from each tube and replaced with 1 μL of the zymolyase solution. The tubes were resealed with sequencing-plate tape, vortexed for 30 seconds, and centrifuged briefly (5 seconds). The beads were then loaded onto the Chromium Chip G following the standard v3.1 protocol.
Library construction was performed following standard Chromium Next GEM Single Cell 3’ Kit v3.1 protocol that can be found in the user guide CG000315 revision F.


title: S. Paradoxus CBS 8841, 20C GPY,  rep1

description: Library name: CBS8841_rep1


title: POND-FMR1-Y103syn_rep1


title: POND-FMR1-T102A_rep2


title: SA7hS2

city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

institute: DOE Joint Genome Institute

description: Library name: NTGPW

data_processing:
raw data are paired-end interleaved fastq files
BBTools v38.96 bbduk.sh was used to filter raw reads for 1) removal of artifact sequence, RNA spike-in reads, PhiX reads, and reads containing any N, 2) quality trimming with method set at Q6, and 3) removal of reads with <50 bases
Filtered reads from each library were aligned to the A. thaliana TAIR10 reference genome using HISAT2 v2.2.1127
featureCounts was used to generate raw gene counts using Araport 11 gene annotations. Only primary hits assigned to the reverse strand were included (-s 2 -p --primary options)
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: counts.txt: tab-separated matrix containing read counts for each gene (rows) in each library (columns)

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: seeds were sterilized, then planted on nylon mesh in agar plates containing 3mM Ca(NO3)2, 1.5mM MgSO4, 1.25mM NH4H2PO4, 1mM KCl, and 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seeds were sown on plates at a density of 3 rows per plate with ~30 plants per row and plates were placed vertically in a growth chamber under conditions of 16 h light at 22°C, 8 h dark at 19°C

extract_protocol:
mRNA was isolated from an input of 1000 ng of total RNA with oligo dT magnetic beads and fragmented to 300 bp - 400 bp with divalent cations at a high temperature.
Using TruSeq stranded mRNA kit (Illumina), the fragmented mRNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double stranded cDNA fragments were treated with A-tailing, ligation with NEXTFLEX UDI Barcodes (PerkinElmer) and enriched using 8.0 cycles of PCR. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell, using 2x150 bp paired-end sequencing.

treatment_protocol: On the 5th day, the nylon mesh and plants were transferred using forceps to agar plates containing either 2 μM ABA, 150 μM SA, or the standard growth medium without added hormones as a negative control. Samples were collected at time points of 0, 1, 2, 4, 7, 24, and 48 hours, separating root and shoot tissues with a single razor blade cut at the time of collection.

value: shoot

tag: strain

value: SA

tag: timepoint

tag: replicate


title: Input WT limb bud ectoderm E10.5, rep2

description: Library name: input_sp6_rep2

data_processing:
Fastq files were processed with nextflow pipeline "nf-core/chipseq" (https://github.com/nf-core/chipseq/tree/2.0.0) to obtain peaks and bigwigs
Assembly: mm10
Supplementary files format and content: Big Wig of ChIPmentation data for replicates 1 and 2

molecule: protein

extract_protocol:
Ectoderms were isolated with fine forceps from E10.5 forelimb buds of Sp8-FLAG homozygous embryos (for Sp8) and WT embryos (for Sp6) after digestion with 0.25% trypsin for 20 min. on ince. The ectoderms of 50 forelimb buds were used for each replicate.
ChIPmentation protocol was based on (Schmidl et al., 2015)


title: HCCC9810 cells, control1, 24 hours

description:
Library name: Sample_1
HCCC9810 control (vehicle) for 24 h

value: vehicle (DMSO) for 24 h


title: SA7hS1

description: Library name: NTGPU


title: Input WT limb bud ectoderm E10.5, rep1

description: Library name: input_sp6_rep1


title: POND-FMR1-T102A_rep1


title: Patient BM063215: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

city: Phoenix

first: Esteban

last: Braggio

state: AZ

address: 6161 E Mayo Blvd

department: Hematology

institute: Mayo Clinic

description: Library name: BM063215

data_processing:
An internally developed RNA-seq analysis workflow (MAPRSeq v2.0.0) was used to perform read alignment, quality control, and expression quantification. Paired-end reads were aligned by BWA against the hg19 (GRCh37/b37) genome with decoy contigs, quality control across genes was performed with RSeQC (v2.3.2; ref. 22), gene counts were generated with featureCounts from Subread package (http://subread.sourceforge.net/, v1.4.4). For each sample, gene counts were normalized using Conditional Quantile Normalization method (CQN) and generate gene and exon expression levels scaled against gene lengths and sample read depths (RPKM, reads per kilo base-pair per million mapped reads). Differentially expressed genes will be submitted to ingenuity pathway analysis (IPA, http://www.ingenuity.com/) for pathway enrichment analysis.
Assembly: hg19
Supplementary files format and content: RPKM RNA matrix (.csv), clinical metadata (.xlsx), bam index files (.bai)

source_name: Bone marrow

extract_protocol:
Bone marrow samples were collected after approval from the Institutional Review Board at Mayo Clinic, Rochester. CD138+ plasma cells were enriched from bone marrow aspirates and processed using AllPrep DNA/RNA/Protein extraction kit (Qiagen) using manufacturer’s protocol for DNA and RNA extraction. The flow-through from the RNA extraction step was precipitated with advanced protein precipitation buffer (Qiagen) to obtain the protein fraction and the protein pellets were stored at -80˚C until further processing.
RNA libraries were prepared using the TruSeq RNA sample prep kit v2 (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: Bone marrow

value: Plasma cells


title: SA7hS3

description: Library name: NTGPX


title: POND-FMR1-D100E_rep2


title: anti-Sp6 WT limb bud ectoderm E10.5, rep2

description: Library name: chipd_sp6_rep2


title: Patient BM063110: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM063110

value: Untreated


title: POND-FMR1-D100E_rep1

value: HEK293T cell line


title: anti-Sp6 WT limb bud ectoderm E10.5, rep1

description: Library name: chipd_sp6_rep1


title: SA7hR2

description: Library name: NTGSN

source_name: root

value: root


title: Patient BM063008: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM063008


title: Patient BM062008: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM062008


title: SA7hR3

description: Library name: NTGSO


title: Hi-C reads for Melampsora allii-populina 12AY07

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

description: Library name: map12ay07_1486711_S3HiC

library_source: genomic

data_processing:
Each Hi-C read-pairs was filtered and trimmed using Trimmomatic v0.39 with the following settings ILLUMINACLIP:${adapters}:2:30:10 LEADING:15 TRAILING:15 SLIDINGWINDOW:5:15 MINLEN:50.
Reads were mapped against the reference genome assembly of M. allii-populina and M. larici-populina, respectively using bwa-mem2.
The construction and analysis of Hi-C interaction matrices were performed using the HiCExplorer suite of tools.
Assembly: Melampsora larici-populina v3.0 and Melampsora allii-populina v2.0
Supplementary files format and content: .h5 Hi-C maps per haplotype

molecule: genomic DNA

organism: Melampsora allii-populina

source_name: urediniospores

extract_protocol:
Spores were fixed with formaldehyde according to PhaseGenomics instructions (Seattle, Washington, USA). Hi-C experiments were performed with the Phase Genomics Proximo Hi-C Kit (Fungal).
Libraries were prepared usung the Phase Genomics Proximo Hi-C Kit (Fungal) with the four restriction enzymes: DpnII (GATC), DdeI (CTNAG), HinfI (GANTC), and MseI (TTAA).

value: urediniospores

value: ND


title: POND-FMR1-F91S_rep1


title: Patient BM061529: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM061529


title: POND-FMR1-D63G_rep2


title: Patient BM061466: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM061466


title: SA4hS2

description: Library name: NTGOS


title: POND-FMR1-D63G_rep1


title: EO771_co2

city: Cold Spring Harbor

first: Yue

last: Wu

address: One Bungtown Rd, Demerec RM 120

department: Cancer and Neuroscience

institute: Cold Spring Harbor Laboratory

description: Library name: Sample8

data_processing:
JupyterHub platform
Quality control: FastQC, Trimming: cutadapt wrapper; Alignment: STAR; featureCounts;
Quantification: Differential expression: DESeq2 and visulization in JupyterHub with R kernel
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: EO771 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using Trizol. 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NextSeq2000 P1 PE150 mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: Breast cancer cell

value: coculture with DRG


title: NCC_rep3

data_processing:
Trimmomatic was employed to trim reads ends where average base calling qualities (in 5 bp windows) were below Q20. Only reads with minimum length of 30 bp were kept for further analyses.
To separate reads that originated from human and chicken cells, we concatenated Ensembl human genome version hg38 (GRCh38) and Ensembl chicken genome version galgal5 (5.0.90), created an index file for this “chimeric reference genome”, and aligned all trimmed and filtered reads into it by using STAR version 2.7.1a.
Uniquely mapped reads were counted using featureCounts in Subread toolkit 1.6.473. By this approach, each read was only aligned and counted for the reference genome that had higher similarity to, and the reads with equal similarity to both genomes were excluded.
Counts normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2. Genes having absolute log2 fold-change higher than 1 and Benjamini-Hochberg adjusted P-value less than 0.05 were considered as significant differentially expressed genes (DEGs).
The shrinkage of log fold changes was performed using “ashr” shrinkage estimator. Visualization of the results was done by ggplot2, pheatmap and EnhancedVolcano packages. Overrepresentation analysis was performed in DAVID Bioinformatics Resources76. Gene set enrichment analysis was performed using Broad Institute GSEA software.
Assembly: hg38 (GRCh38) / galgal5 (5.0.90)
Supplementary files format and content: Txt file of raw counts

organism: Gallus gallus

source_name: Cerebral cortex

value: Cerebral cortex


title: Patient BM060477: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM060477


title: SA4hS1

description: Library name: NTGOP


title: SA4hS3

description: Library name: NTGOT


title: POND-FMR1-N34S_rep2

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).


title: EO771_co1

description: Library name: Sample7


title: SA4hR3

description: Library name: NTGPG


title: Patient BM060196: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM060196


title: EO771_CM3

description: Library name: Sample6

value: DRG conditioned medium


title: POND-FMR1-I28L_rep2


title: EO771_CM2

description: Library name: Sample5


title: Patient BM060113: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM060113


title: SA48hS2

description: Library name: NTPTU


title: POND-FMR1-S27*_rep2


title: EO771_mono3

description: Library name: Sample3

value: monoculture


title: Patient BM054891: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM054891


title: SA4hR1

description: Library name: NTGPB


title: SA48hS1

description: Library name: NTPTT


title: SA4hR2

description: Library name: NTGPC


title: POND-FMR1-I28L_rep1


title: EO771_CM1

description: Library name: Sample4

value: WT


title: POND-FMR1-S27*_rep1


title: Patient BM059241: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM059241


title: EO771_mono2

description: Library name: Sample2


title: Patient BM054835: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM054835


title: SA48hS3

description: Library name: NTPTW


title: POND-FMR1-E25K_rep2


title: EO771_mono1

description: Library name: Sample1


title: Patient BM054653: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM054653


title: SA48hR1

description: Library name: NTPUG


title: preLSC, 0min, control, rep3

description: Library name: T0_ctl3

value: preleukemic cells

value: control

value: 0 min


title: POND-FMR1-E25K_rep1


title: Input DNA control sample 2

city: London

first: Marco

last: Di Antonio

address: 82 Wood Lane

department: Chemistry

institute: Imperial College London

description:
Library name: Input2
300 cycles; 46,695,581 reads

data_processing:
Read quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and adapter sequences were trimmed with fastp.
Trimmed reads were aligned to the 2018 genome assembly of the Lister 427 version 10 (Tb427v10) extracted from TriTrypDB, using Bowtie2 with default settings.
Reads were filtered and sorted using SAMtools with the following arguments -F 2308 and -q 10 to exclude unaligned, secondary, and supplementary reads, and reads with a mapping quality (MAPQ) < 10. Duplicate reads were removed using SAMtools. In the SAMtools workflow, properly paired reads were first filtered (samtools view -bh -f 0x2), followed by sorting (samtools sort), mate information correction (samtools fixmate), a second sorting step, and duplicate marking using samtools markdup.
Bowtie2 alignment files were analysed for peak calling (i.e., read enrichment) using MACS2 with a user-defined genome size of -g 2.67e7; 200 nt fragment size for shifting model (--nomodel --extsize 200); minimum false discovery rate: ≥0.01 (-q 0.01). Log2 ratio of ChIP signal to Input signal were generated using bamCompare from the deepTools suite (version 2.4.2) with a bin size of 50 bp.
Common and unique peaks between replicates were identified with bedtools intersect.
Assembly: T. brucei 2018 genome assembly of the Lister 427 strain version 10 (Tb427v10, https://tritrypdb.org)
Supplementary files format and content: Bigwig files are provided, containing Log2 ratio of ChIP signal to Input signal which were generated using bamCompare from the deepTools suite with a bin size of 50 bp.

organism: Trypanosoma brucei

source_name: Lister strain 427

growth_protocol: T. brucei Lister 427 bloodstream forms were grown in HMI-11 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Sigma-Aldrich) at 37°C and 5% CO2. The density of cell cultures was maintained below 1.5 × 10^6 cells/mL and sub-passaged every 24–48 hours.

extract_protocol:
For ChIP-Seq experiments, cells were cross-linked with 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode).
For ChIP-Seq experiments, libraries were prepared from input and immunoprecipitated DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, MA, USA).

treatment_protocol: Chromatin (59 ng/μL sample) was treated with the G4-targeting antobody BG4 BG4 (0.75 μL/sample; 136 ng/sample). Three technical replicates (ChIP samples) and one IP sample were performed in parallel.

value: Lister strain 427

value: bloodstream form

value: no treatment


title: Patient BM053621: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM053621

value: Bone marrow

value: Plasma cells

value: Untreated


title: SA48hR2

description: Library name: NTPUH

value: root

value: SA


title: POND-FMR1-H24R_rep2

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

value: HEK293T cell line


title: POND-FMR1-T125fs_rep1


title: G4 ChIP, sample 05

description:
Library name: G4ChIP_Rep5
300 cycles; 36,876,927 reads

value: BG4 antobody

value: Synthetic


title: SA48hR3

description: Library name: NTPUN


title: Patient BM053512: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM053512


title: POND-FMR1-H24R_rep1


title: POND-FMR1-K119N_rep2


title: G4 ChIP, sample 04

description:
Library name: G4ChIP_Rep4
300 cycles; 31,251,406 reads


title: Patient BM053063: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM053063


title: POND-FMR1-D22E_rep2


title: HCCC9810 cells, control3, 24 hours

description:
Library name: Sample_3
HCCC9810 control (vehicle) for 24 h

value: cholangiocarcinoma cells

value: wild type

value: vehicle (DMSO) for 24 h


title: SA2hS3

description: Library name: NTGNO

value: shoot


title: HCCC9810 cells, Isolinderalactone1, 24 hours

description:
Library name: Sample_4
HCCC9810 cells treated with 20 μM ILL for 24 h

value: 20 μM ILL for 24 h


title: PhenDC3 treatment, sample 4

description:
Library name: PhenDC3_rep4
S2 200 cycles; 15 million reads per sample.

data_processing:
The quality of sequence reads was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and sequence files were concatenated using the cat function (Unix version 8.30).
Sequencing adapter sequences were trimmed using fastp.
Trimmed reads were aligned to the 2018 genome assembly of the Lister 427 strain version 10 (Tb427v10, https://tritrypdb.org) using Bowtie2.
The alignments were converted from SAM to BAM format, sorted, indexed and filtered by alignment quality  ≥ 1 (-q 1) using SAMtools.
Reads were quantified using featureCounts from the subread package (v1.5.2).
Assembly: T. brucei 2018 genome assembly of the Lister 427 strain version 10 (Tb427v10, https://tritrypdb.org)
Supplementary files format and content: Feature counts file is provided as a csv file and it was generated using the featureCounts from the subread package.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Australia), following the manufacturer’s protocol.
Poly(A)-enriched RNA libraries were prepared using NEB mRNA polyA kit.

treatment_protocol: T. brucei Lister 427 bloodstream forms (0.75 × 106/ml; 15 ml) were treated with 2 × EC50 concentrations of either PhenDC3, CX-5461, BMH-21, or without compound (control) for 4 hours. Four replicates were prepared for each experimental condition.


title: Patient BM052522: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM052522


title: POND-FMR1-D22E_rep1


title: SA2hS2

description: Library name: NTGNN


title: PhenDC3 treatment, sample 3

description:
Library name: PhenDC3_rep3
S2 200 cycles; 15 million reads per sample.


title: Patient BM051757: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM051757


title: SA2hS1

description: Library name: NTGNH


title: POND-FMR1-WT_rep-6


title: PhenDC3 treatment, sample 2

description:
Library name: PhenDC3_rep2
S2 200 cycles; 15 million reads per sample.


title: Patient BM051002: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM051002


title: SA2hR1

description: Library name: NTGNY


title: POND-FMR1-WT_rep-5


title: PhenDC3 treatment, sample 1

description:
Library name: PhenDC3_rep1
S2 200 cycles; 15 million reads per sample.


title: Patient BM050446: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM050446


title: SA2hR3

description: Library name: NTGOA


title: POND-FMR1-WT_rep-4


title: RNA-seq in SP6KO bud ectoderm E10.5, rep2

description: Library name: RNASEQ_ect_sp6_KO_rep2

value: limb bud ectoderm

value: ectoderm


title: SA7hR1

description: Library name: NTGSH


title: CX5461 treatment, sample 4

description:
Library name: CX5461_rep4
S2 200 cycles; 15 million reads per sample.

value: Lister strain 427

value: bloodstream form

value: Selleckchem.com (Catalog No.S2684)


title: Patient BM050038: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM050038

value: Bone marrow

value: Plasma cells


title: POND-FMR1-WT_rep-3


title: SA2hR2

description: Library name: NTGNZ

value: root


title: CX5461 treatment, sample 3

description:
Library name: CX5461_rep3
S2 200 cycles; 15 million reads per sample.


title: Patient BM049537: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM049537

value: Untreated


title: Hi-C reads for Melampsora larici-populina 98AG31

description: Library name: mlp98ag31_1486709_S3HiC

organism: Melampsora laricis-populina

value: urediniospores

value: ND


title: POND-FMR1-F91S_rep2

value: HEK293T cell line


title: SA24hS1

description: Library name: NTGWB

value: SA


title: POND-FMR1-WT_rep-2


title: CX5461 treatment, sample 2

description:
Library name: CX5461_rep2
S2 200 cycles; 15 million reads per sample.


title: SA24hS2

description: Library name: NTGWC


title: Patient BM045892: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM045892


title: POND-FMR1-WT_rep-1


title: SA24hS3

description: Library name: NTGWG


title: CX5461 treatment, sample 1

description:
Library name: CX5461_rep1
S2 200 cycles; 15 million reads per sample.


title: Patient BM044056: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM044056


title: Patient BM043138: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM043138


title: BMH21 treatment, sample 4

description:
Library name: BMH21_rep4
S2 200 cycles; 15 million reads per sample.

value: Cayman Chemicals (CAS 896705-16-1)


title: SA24hR3

description: Library name: NTPTC


title: Patient BM036560: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM036560


title: RNA-seq_293T-PABPC1-POND-TNFα-24h_celllysate-24h_rep-2

value: 100 ng TNFα plus 1 μM doxycycline


title: RNA-seq_293T-PABPC1-POND-TNFα-24h_celllysate-24h_rep-1


title: RNA-seq_293T-PABPC1-POND-untreated_celllysate-24h_rep-2

value: 1 μM doxycycline


title: SA24hR1

description: Library name: NTGWU


title: Patient BM030784: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM030784


title: BMH21 treatment, sample 3

description:
Library name: BMH21_rep3
S2 200 cycles; 15 million reads per sample.


title: BMH21 treatment, sample 1

description:
Library name: BMH21_rep1
S2 200 cycles; 15 million reads per sample.


title: RNA-seq_293T-PABPC1-POND-untreated_celllysate-24h_rep-1


title: Patient BM008518: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM008518


title: PABPC1-POND-293T-TNFα-24h_rep-2


title: SA1hS3

description: Library name: NSWSU

value: shoot


title: Patient BM008487: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM008487


title: PABPC1-POND-293T-TNFα-24h_rep-1


title: Patient BM008219: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM008219


title: SA1hS1

description: Library name: NSWNN


title: No treatment control, sample 3

description:
Library name: Control_rep3
S2 200 cycles; 15 million reads per sample.

value: no treatment


title: SA1hS2

description: Library name: NSWNO


title: No treatment control, sample 2

description:
Library name: Control_rep2
S2 200 cycles; 15 million reads per sample.


title: Patient BM008204: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM008204


title: SA1hR3

description: Library name: NSWTH


title: No treatment control, sample 1

description:
Library name: Control_rep1
S2 200 cycles; 15 million reads per sample.


title: Patient BM003658: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM003658


title: SA1hR2

description: Library name: NSWTG


title: Patient BM002019: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

description: Library name: BM002019


title: G4 ChIP, sample 03

description:
Library name: G4ChIP_Rep3
S2 200 cycles; 15 million reads per sample

data_processing:
Read quality was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and adapter sequences were trimmed with fastp.
Trimmed reads were aligned to the 2018 genome assembly of the Lister 427 version 10 (Tb427v10) extracted from TriTrypDB, using Bowtie2 with default settings.
Reads were filtered and sorted using SAMtools with the following arguments -F 2308 and -q 10 to exclude unaligned, secondary, and supplementary reads, and reads with a mapping quality (MAPQ) < 10. Duplicate reads were removed using Picard MarkDuplicates (https://broadinstitute.github.io/picard/) with the REMOVE_DUPLICATES=TRUE option.
Bowtie2 alignment files were analysed for peak calling (i.e., read enrichment) using MACS2 with a user-defined genome size of -g 2.67e7; 200 nt fragment size for shifting model (--nomodel --extsize 200); minimum false discovery rate: ≥0.01 (-q 0.01). Log2 ratio of ChIP signal to Input signal were generated using bamCompare from the deepTools suite (version 2.4.2) with a bin size of 50 bp.
Common and unique peaks between replicates were identified with bedtools intersect.
Assembly: T. brucei 2018 genome assembly of the Lister 427 strain version 10 (Tb427v10, https://tritrypdb.org)
Supplementary files format and content: Bigwig files are provided, containing Log2 ratio of ChIP signal to Input signal which were generated using bamCompare from the deepTools suite with a bin size of 50 bp.

treatment_protocol: Chromatin (76.2 ng/μL sample) was treated with the G4-targeting antobody BG4 BG4 (0.75 μL/sample; 136 ng/sample). Three technical replicates (ChIP samples) and one IP sample were performed in parallel.

value: BG4 antobody

value: Synthetic


title: PABPC1-POND-Mix_rep-1

source_name: Huh-7 & A549 cell line

value: Huh-7 & A549 cell line


title: SA1hR1

description: Library name: NSWTC


title: Erythroid cells, IgG, Day7

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

description: Library name: CUT_Tag_IgG

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest transcriptional start site (TSS) was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The day of CD34+ cell harvest was recorded as day 0. The cell culture procedure consisted of 3 phases. The basic culture medium consisted of Iscove's Modified Dulbecco's Medium (IMDM), 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL human holo-transferrin, 3 IU/mL heparin and 10 μg/mL insulin. From day 0 to day 7, CD34+ cells were cultured at a concentration of 105/mL in the presence of 10 ng/mL stem cell factor (SCF), 1 ng/mL interleukin-3 (IL-3) and 3 IU/mL erythropoietin (EPO).  The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-TAL1 and BRG1 antibodys, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. After transfection with lentivirus for 5 days, we performed a TAL1 CUT&Tag of control cells and a BRG1 CUT&Tag of shLuciferase and shTAL1 erythroblasts.

value: Cord blood

value: Erythroid cells

value: Control


title: PABPC1-POND-Mix_rep-2

city: Beijing


title: G4 ChIP, sample 02

description:
Library name: G4ChIP_Rep2
S2 200 cycles; 15 million reads per sample

value: Lister strain 427

value: bloodstream form


title: PABPC1-POND-293T-500ng_rep-2

source_name: HEK293T cell line


title: Erythroid cells, TAL1 rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_rep3


title: Cnt7hS2

description: Library name: NTGPN

value: control


title: PABPC1-POND-293T-500ng_rep-1


title: Erythroid cells, TAL1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_rep2


title: Cnt7hS1

description: Library name: NTGPH


title: PABPC1-POND-293T-100ng_rep-2


title: OVCAR-5-CisR siNUDT5 replicate 3

city: Los Angeles

first: Angelina

last: Flores

state: California

address: 610 Charles E Young Dr. East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description:
Library name: Sample 6
Column name for processed files: 12-siNUDT5-3

data_processing:
Alignment was performed using STAR with human reference genome GRCh38. The Ensembl Transcripts release GRCh38.108 GTF was used for gene feature annotation. For normalization of transcripts counts, counts per million (CPM) normalized counts were generated by adding 1.0E-4 followed by CPM normalization.
Assembly: GRCh38
Supplementary files format and content: 24-1078_Raw_Read_Counts_siNUDT5.csv includes raw counts for each sample
Supplementary files format and content: 24-1078_Add_00001_CPM_Normalized_counts_siNUDT5.csv includes counts per million per sample

growth_protocol: Human cisplatin-resistant ovarian cancer (OVCAR-5-CisR) cells were cultured in DMEM (+L-Glutamine, +Glucose, +Sodium Pyruvate, Gibco) supplemented with 10% fetal bovine serum (FBS, Gemini), 1% penicillin-streptomycin (VWR), and 10 µM cisplatin (Sigma-Aldrich).

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, 15596026) and the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s instructions. RNA quality and concentration were assessed by spectrophotometry (NanoDrop 8000, Thermo Fisher Scientific).
Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit with RiboErase Kit. Ribosomal RNA was depleted by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase and RNA fragmentation. First-strand cDNA synthesis was performed using random priming, followed by second-strand synthesis to convert cDNA:RNA hybrid to double-stranded cDNA and incorporates dUTP into the second cDNA strand. cDNA generation is followed by A-tailing, adaptor ligation, and PCR amplification.

treatment_protocol: OVCAR-5-CisR cells were plated in a 6-well dish at a density of 300,000 cells per well. The following day, RNA interference was performed using a Non-targeting Pool siRNA (Qiagen, 1027281) or NUDT5 siRNA (Qiagen, 1027418, GeneGlobe ID: SI04300128|S2). Forty-eight hours after transfection cells were harvested to isolate RNA and prepare the library.

value: Ovarian cancer cells

value: NUDT5 siRNA KD


title: Erythroid cells, TAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_TAL1_rep1


title: OVCAR-5-CisR siNUDT5 replicate 2

description:
Library name: Sample 5
Column name for processed files: 7-siNUDT5-2


title: Cnt7hR1

description: Library name: NTGPY

value: root


title: Erythroid cells, BRG1 shTAL1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_BRG1_shTAL1_rep2


title: Cnt7hR3

description: Library name: NTGSA


title: PABPC1-POND-293T-50ng_rep-2

value: HEK293T cell line


title: OVCAR-5-CisR siNUDT5 replicate 1

description:
Library name: Sample 4
Column name for processed files: 2-siNUDT5-1


title: Erythroid cells, BRG1 shTAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_BRG1_shTAL1_rep1


title: OVCAR-5-CisR siControl replicate 3

description:
Library name: Sample 3
Column name for processed files: 11-siControl-3

value: Scrambled siRNA


title: Cnt4hS2

description: Library name: NTGOC


title: RNA-seq_A549_celllysate_rep-2

description:
fig5_26
fig5_26

source_name: A549 cell line

value: A549 cell line

value: WT


title: Erythroid cells, BRG1 Control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_BRG1_control_rep1


title: Cnt4hS3

description: Library name: NTGOG

value: shoot


title: CREFLOX-14

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: Library name: CREFLOX-14

data_processing:
Raw fastq was trimmed using TrimGalore! And cutadapt to remove standard Illumina adapters. The trimmed reads were aligned to mouse reference genome GRCm38 with hisat2 v2.1.0 [1].  Gene wise counts were generated with featureCounts from the subread package v1.5.1 [2] for genes annotated by ensembl Mus_musculus.GRCm38.102.
Assembly: GRCm38
Supplementary files format and content: raw counts from featureCounts

source_name: lung

growth_protocol: Cx3cr1-CreERT2; Casp11^WT/WT (Cx3cr1-Cre control) and Cx3cr1-CreERT2; Casp11^flox/flox (Cx3cr1-MPS-Casp11⁻/⁻) mice were housed under standard specific-pathogen-free conditions at The Ohio State University. Both groups are homozygous for the Cx3cr1-CreERT2 knock-in allele. To induce Cre-mediated recombination, mice were administered tamoxifen at 75 mg/kg dissolved in corn oil via intraperitoneal injection for 7 consecutive days, followed by a 3-day washout period. Mice were 3–4 months of age at the time of infection. Food and water were provided ad libitum.

extract_protocol:
Total RNA was extracted from the left lung lobe using TRIzol reagent (Thermo Fisher Scientific, Cat. 15596026) according to the manufacturer's instructions. RNA cleaning and concentration were performed using the Zymo Research RNA Clean & Concentrator-5 kit (Cat. R1015). RNA integrity and quantity were assessed using an RNA Biochip and Qubit RNA Fluorescence Dye (Invitrogen).
The RNA sample received was quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification.

treatment_protocol: Mice were anesthetized by isoflurane induction at 2–3% concentration in an induction chamber for approximately 5 minutes. Mice were infected intranasally with 5×10⁵ TCID50 of mouse-adapted SARS-CoV-2 strain MA10 in 50 μL sterile PBS (25 μL per nare). Lungs were harvested at day 4 post-infection. The left lung lobe was snap frozen in liquid nitrogen and stored at −80°C prior to RNA extraction.

value: lung

value: Cx3cr1-CreERT2; Casp11^flox/flox


title: RNA-seq_A549_celllysate_rep-1

description:
fig5_25
fig5_25


title: OVCAR-5-CisR siControl replicate 1

description:
Library name: Sample 1
Column name for processed files: 1-siControl-1


title: Erythroid cells, WDR5 rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_WDR5_rep3
TPM_BZ1_WDR5.csv

data_processing:
The original data were filtered and compared with the reference genome, which can be downloaded from the Ensemble database (http://www.ensembl.org/index.html,human genome build GRCh38.87). Using HISAT2 version 2.2.1 (http://daehwankimlab.github.io/hisat2/) to read the counts for each gene in each sample and gene expression was assessed by StringTie (https://ccb.jhu.edu/software/stringtie/). TPM (Transcripts Per Kilobase of exon model per Million mapped reads) was calculated to evaluate the expression level. Differentially expressed genes (DEGs) were defined by p.adjust < 0.05 and fold change >1.2 using the DESeq2 version 1.38.3 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Gene ontology (GO) enrichment analysis and visualization of DEGs was performed using the Metascape (www.metascape.org/) online tool with q < 0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

extract_protocol:
Experiment procedure before sequencing: 2 million cells were collected and washed twice with PBS. RNA was extracted from cell culture using RNA extract kits (74104, Qiagen) according to the manufacturer’s instruction.
RNA was extracted and used as cDNA input, cDNA library was prepared by VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01,  Vazyme, China), and sequenced on Illumina NovaSeq 6000.

treatment_protocol: Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. Also BPTF inhibitor BZ1 and KMT2A inhibitor WDR5-0103 were dissolved in DMSO and administered to cell cultures at a final concentration of 1 and  0.1 μM at day 2. After transfection with lentivirus and treated with BZ1/WDR5-0103 for 5 days, we performed a RNA-seq.


title: Cnt4hS1

description: Library name: NTGOB


title: sh25

city: shanghai

first: Zuopeng

last: Su

address: 170 Xinsong Road, Xinzhuang Town, Minhang District,

department: Department of Neurosurgery,

institute: Minhang Hospital, Fudan University

description:
Library name: sample 53
Hypertension group (sh group),rep25

data_processing:
The raw reads were preprocessed and filtered using Trimmomatic  with the following steps:Removal of P7 and P5 adapter sequences (sequences provided above),trimming of bases with quality scores <20,discarding reads shorter than 50 bp and singleton reads.
Clean reads after quality control were aligned to the reference genome GRCh38.p13 using HISAT2 to acquire mapping positions.
Alignment outputs from HISAT2 were analyzed using htseq-count (v0.6.0)  to quantify read counts per transcript.
Alternative splice events that occurred in the samples were identified by Multivariate Analysis of Transcript Splicing (MATS, http://rnaseq-mats.sourceforge.net/).
Assembly: GRCh38
Supplementary files format and content: expression.xlsx

source_name: Peripheral Blood

extract_protocol:
RNA was harvested using TIANSeq mRNA Capture Kit (TIANGEN Biotech).
Libraries were constructed using the TIANSeq Fast RNA Library Prep Kit for Illumina (TIANGEN Biotech).

value: Peripheral Blood

value: Peripheral Blood Mononuclear Cells

tag: sample group

value: Hypertension group (sh group)


title: Erythroid cells, WDR5 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_WDR5_rep2
TPM_BZ1_WDR5.csv

value: Cord blood

value: Erythroid cells


title: PABPC1-POND-293T-50ng_rep-1


title: BxPC3, H3K4me3, no IFNγ, Replicate1, CUT&RUN

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

description:
Library name: BxPC3_H3K4me3_noIFNγ_Rep1
BxPC3_CUTRUN_H3K4me3_noIFNγ_3reps.bw
BxPC3_CUTRUN_H3K4me3_noIFNγ_3reps_peaks.narrowPeak

data_processing:
The fastq files were trimmed and quality-controlled with Trim Galore (version 0.6.10 with the default options in a pair-end mode. The resulting reads were aligned to hg38 using bowtie2 (version 2.4.4) with options --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700 (Langmead & Salzberg, 2012). The alignment files were sorted by coordinate, then unpaired reads were removed, and indexed with samtools (version 1.14) (Danecek et al., 2021).
For reads visualization on genome tracks, the processed bam files were merged with samtools and visualized via the Integrative Genomics Viewer (version 2.16.1) (Robinson et al., 2011).
For peak identification, peaks and summits were called with MACS2 (version 2.2.7.1) using all three individual bam files for all replicates targeting the protein of interest (-t) and all three targeting IgG as controls (-c) with options --format BAMPE --gsize 2.7e9 --keep-dup all (Zhang et al., 2008).sortRegions descend (Ramirez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&RUN

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
We performed CUT&RUN in BxPC-3 cells using CUTANA ChIC/CUT&RUN Kit (EpiCypher) following the manufacturer’s protocol (Skene & Henikoff, 2017). In brief, 500,000 cells were trypsinized, washed, and bound to activated Concanavalin A-conjugated paramagnetic beads (EpiCypher). The cell-bead conjugates were then resuspended in recommended buffer with 0.5 μg antibody targeting the protein of interest: Anti-H3K27ac (Active Motif 39135), Anti-H3K4me3 (EpiCypher 13-0041k) as positive control, and Anti-IgG (EpiCypher 13-0042k) as negative control. The suspensions were incubated overnight at 4 °C with gentle shaking. Then, the cell-bead conjugates were washed twice with the kit’s permeabilization buffer, and incubated with pAG-MNase (Epicypher 15-1016) for 10 min at room temperature. Subsequently, the unbound pAG-MNase was washed away, and the MNase was activated by adding CaCl2 to a final concentration of 2 mM. The reaction was stopped after the pAG-MNase was allowed to digest and release the antibody-bound chromatin for 2 hours at 4 °C. Finally, the released DNA was purified with the spin columns provided by the kit (EpiCypher).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). The libraries were sequenced on a IlluminaNovaSeq 6000  SP using 2x50 bp reads.

value: PDAC

tag: cut&run antibody

value: H3K4me3 (EpiCypher 13-0041k)

value: no IFNγ


title: Cnt4hR3

description: Library name: NTGOX

value: control


title: Erythroid cells, BRG1 Control rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: CUT_Tag_BRG1_control_rep2

value: Control


title: RNA-seq_Huh-7_celllysate_rep-1

description:
fig5_23
fig5_23

source_name: Huh-7 cell line

value: Huh-7 cell line


title: sh24

description:
Library name: sample 52
Hypertension group (sh group),rep24


title: Erythroid cells, WDR5 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_WDR5_rep1
TPM_BZ1_WDR5.csv


title: OVCAR-5-CisR siControl replicate 2

description:
Library name: Sample 2
Column name for processed files: 6-siControl-2

value: Ovarian cancer cells

value: Scrambled siRNA


title: Cnt4hR2

description: Library name: NTGOW

value: root


title: sh23

description:
Library name: sample 51
Hypertension group (sh group),rep23


title: RNA-seq_293T_celllysate_rep-2

description:
fig4_18
fig4_18

value: HEK293T cell line

value: WT


title: Erythroid cells, BZ1 rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_BZ1_rep3
TPM_BZ1_WDR5.csv


title: Cnt4hR1

description: Library name: NTGOU


title: patient infected with Patient infected with GH-PitNET, a growth hormone-secreting pituitary neuroendocrine tumor

city: Wuhan

first: Haobin

last: Ren

state: Hubei

address: G9P7+CP8, Wuchang District

institute: Wuhan University

description: Library name: PAs101

data_processing:
FastQC for QC
Trim Galore for trimming
BWA-MEM for alignment
Circle-Map for ecDNA detection
Assembly: hg38
Supplementary files format and content: txt for identified ecDNA

source_name: Pituitary gland

extract_protocol:
ecDNA purification was performed on DNA extracted from meningioma, glioblastoma, pituitary adenoma and vestibular schwannoma. After confirming the successful enrichment of ecDNA from total DNA samples, Phi29-assisted ecDNA rolling circle amplification was performed before DNA library preparation.
Amplicon was sonicated into DNA fragments with average size as 350bp using Bioruptor. Library preparation was performed using Vazyme DNA library preparation kit (Vazyme) following the standard protocol starting with 300 ng of sonicated DNA per sample. Library quality and fragment size distribution were assessed using the Qsep400 system (BiOptic).

value: Pituitary gland

tag: infection


title: RNA-seq_293T_celllysate_rep-1

description:
fig4_17
fig4_17


title: sh22

description:
Library name: sample 50
Hypertension group (sh group),rep22

value: Peripheral Blood


title: Erythroid cells, BZ1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_BZ1_rep2
TPM_BZ1_WDR5.csv


title: Cnt48hS2

description: Library name: NTPTH

data_processing:
raw data are paired-end interleaved fastq files
BBTools v38.96 bbduk.sh was used to filter raw reads for 1) removal of artifact sequence, RNA spike-in reads, PhiX reads, and reads containing any N, 2) quality trimming with method set at Q6, and 3) removal of reads with <50 bases
Filtered reads from each library were aligned to the A. thaliana TAIR10 reference genome using HISAT2 v2.2.1127
featureCounts was used to generate raw gene counts using Araport 11 gene annotations. Only primary hits assigned to the reverse strand were included (-s 2 -p --primary options)
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: counts.txt: tab-separated matrix containing read counts for each gene (rows) in each library (columns)

value: shoot


title: PABPC1-POND-A549_DNASE_rep-2

value: A549 cell line


title: scRNA-seq of P3

city: Shanghai

first: Lei

last: Shi

state: 请选择

address: 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiaotong university

description: Library name: P3

data_processing:
The raw reads were mapped to the rat reference genome (refdata-gex-Rnor6-2022/Rnor_6) using DNBC4Tools (v 2.1.2) with default parameters, the digital expression matrix was extracted from the“filtered_feature_bc_matrix” folder outputted by the DNBC4Tools count pipeline.
Assembly: MM39
Supplementary files format and content: matrix

source_name: Knee joint synovial tissue

extract_protocol:
Samples were minced with a sterile scalpel into 1 mm3 fragments, suspended in 5ml of digestion buffer consisting of 2 mg/mL Collagenase type I (Sigma，C0130)，2 mg/mL Collagenase type II (Sigma, C6885) and 200U/ml DNase I (Worthington, LS006344) in RPMI medium (Coring,10-040-CV), and incubated in 37℃ water bath with shaking for 60 min. The suspension was passed through a 100 μm filter (Falcon,3523260) and centrifugated (400g, 10 min, 4℃). Pelleted cells were resuspended in red blood cell lysis buffer (Solarbio,R1010), incubated for 2 min, passed through a 40 μm filter (Falcon,3523240), collected by centrifugation (400g, 10 min, 4℃) and resuspended in PBS (BI, 02-024-1ACS)  containing 0.04% BSA (Sigma,B2064). Cells were manually counted by Trypan blue (Thermo, T10282) and AO-PI (LUNA, D23001) after each centrifugation (400g, 10 min, 4℃) and resuspended.
Single-cell libraries were constructed with the DNBelab C Series Single-Cell Library Prep Kit (MGI, Cat. # 940-001818-00). Briefly, single-cell suspensions were subjected to droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Library quantification and quality control were performed using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Q33216) and an Agilent 4200 TapeStation (Agilent, G2991AA), respectively. Finally, DNA nanoballs (DNBs) were loaded into patterned nanoarrays and sequenced on a DNBSEQ platform. The sequencing run was configured with the following read lengths: 30 bp for read 1, inclusive of 10 bp cell barcode 1, 10 bp cell barcode 2, and 10 bp unique molecular identifier (UMI), 100 bp of transcript sequence for read 2, and 10 bp for sample index.

value: Knee joint synovial tissue

tag: group

value: treat with PBS


title: sh21

description:
Library name: sample 49
Hypertension group (sh group),rep21

value: Peripheral Blood Mononuclear Cells

value: Hypertension group (sh group)


title: Erythroid cells, BZ1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_BZ1_rep1
TPM_BZ1_WDR5.csv

value: Cord blood

value: Erythroid cells


title: Cnt48hS3

description: Library name: NTPTN

value: control


title: PABPC1-POND-A549_DNASE_rep-1


title: Erythroid cells, control rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_control_rep3
TPM_BZ1_WDR5.csv

value: DMSO


title: sh20

description:
Library name: sample 48
Hypertension group (sh group),rep20


title: RNA-seq_Huh-7_celllysate_rep-2

description:
fig5_24
fig5_24

value: Huh-7 cell line


title: Cnt48hS1

description: Library name: NTPTG


title: PABPC1-POND-Huh7_DNASE_rep-2


title: BMH21 treatment, sample 2

description:
Library name: BMH21_rep2
S2 200 cycles; 15 million reads per sample.

value: Lister strain 427

value: bloodstream form

value: Cayman Chemicals (CAS 896705-16-1)


title: SA24hR2

description: Library name: NTPTB

value: root

value: SA


title: sh19

description:
Library name: sample 47
Hypertension group (sh group),rep19

value: Peripheral Blood


title: Erythroid cells, control rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_control_rep2
TPM_BZ1_WDR5.csv


title: Cnt48hR1

description: Library name: NTPTX


title: No treatment control, sample 4

description:
Library name: Control_rep4
S2 200 cycles; 15 million reads per sample.

value: no treatment


title: PABPC1-POND-Huh7_DNASE_rep-1


title: sh18

description:
Library name: sample 46
Hypertension group (sh group),rep18


title: Erythroid cells, control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_control_rep1
TPM_BZ1_WDR5.csv


title: Cnt48hR3

description: Library name: NTPTZ


title: Erythroid cells, shTAL3 rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_shTAL1_rep3
RNAseq_TPM_shTAL1.csv


title: PABPC1-POND-293T_DNASE_rep-2

value: HEK293T cell line


title: sh17

description:
Library name: sample 45
Hypertension group (sh group),rep17


title: PABPC1-POND-293T-24h_rep-2

value: 1 μM doxycycline


title: Cnt48hR2

description: Library name: NTPTY


title: PABPC1-POND-293T_DNASE_rep-1


title: sh16

description:
Library name: sample 44
Hypertension group (sh group),rep16


title: Erythroid cells, shTAL2 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_shTAL1_rep2
RNAseq_TPM_shTAL1.csv


title: Cnt2hS3

description: Library name: NSWTP

value: shoot


title: EPN-POND-293T_DNASE_rep-2


title: PABPC1-POND-293T-24h_rep-1


title: sh15

description:
Library name: sample 43
Hypertension group (sh group),rep15

value: Peripheral Blood Mononuclear Cells


title: Erythroid cells, shTAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_shTAL1_rep1
RNAseq_TPM_shTAL1.csv


title: Input DNA control sample

description:
Library name: Input
S2 200 cycles; 15 million reads per sample


title: EPN-POND-293T_DNASE_rep-1


title: Cnt2hS2

description: Library name: NSWTO


title: Cnt2hS1

description: Library name: NSWTN


title: Erythroid cells, shLuci rep3, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_shLuci_rep3
RNAseq_TPM_shTAL1.csv

value: shLuci


title: sh13

description:
Library name: sample 41
Hypertension group (sh group),rep13

value: Hypertension group (sh group)


title: ORF5-POND-293T_rep-2


title: Erythroid cells, shLuci rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_shLuci_rep2
RNAseq_TPM_shTAL1.csv

value: Cord blood

value: Erythroid cells


title: Cnt2hR3

description: Library name: NTGNT

value: control


title: ORF5-POND-293T_rep-1


title: sh14

description:
Library name: sample 42
Hypertension group (sh group),rep14


title: Cnt2hR2

description: Library name: NTGNS


title: Erythroid cells, shLuci rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description:
Library name: RNAseq_shLuci_rep1
RNAseq_TPM_shTAL1.csv


title: Cnt7hS3

description: Library name: NTGPO


title: POND-EPN_forTIA1_rep-2


title: sh11

description:
Library name: sample 39
Hypertension group (sh group),rep11


title: ATAC-Seq, Erythroid cells, shTAL1 rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_shTAL1_rep2

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential atac peaks of were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The ATAC peak/region <1000bp from the nearest transcriptional start site (TSS) was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig,narrowPeak

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature.20,000 cells were lysed with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.03% Tween-20), and centrifuged at 500 g for 8 min at 4 °C. The supernatant was carefully removed, and the nuclei was resuspended with Tn5 transposase reaction mix (25 μl 2 × TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free water) (Illumina) at 37 °C for 30 min. Immediately after the transposition reaction, DNA was purified using a Qiagen MinElute kit. Libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, China) under manufacturer’s instructions and were then sequenced on an Illumina HiSeq X Ten sequencer to an average read depth of 52 million pair-end reads per sample. The ATAC-seq experiment and library sequencing were performed by Frasergen Bioinformatics Co., Ltd, Wuhan, China.
ATAC libraries were constructed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, China) under manufacturer’s instructions and were then sequenced on an Illumina HiSeq X Ten sequencer to an average read depth of 52 million pair-end reads per sample.

treatment_protocol: Cells were transfected with lentivirus containing shTAL1 at day 2, compared with the scramble control. After transfection with lentivirus for 5 days, we performed ATAC assay of  shLuciferase and shTAL1 erythroblasts.


title: POND-EPN_forTIA1_rep-1


title: sh10

description:
Library name: sample 38
Hypertension group (sh group),rep10


title: Cnt2hR1

description: Library name: NTGNP

extract_protocol:
mRNA was isolated from an input of 1000 ng of total RNA with oligo dT magnetic beads and fragmented to 300 bp - 400 bp with divalent cations at a high temperature.
Using TruSeq stranded mRNA kit (Illumina), the fragmented mRNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double stranded cDNA fragments were treated with A-tailing, ligation with NEXTFLEX UDI Barcodes (PerkinElmer) and enriched using 8.0 cycles of PCR. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell, using 2x150 bp paired-end sequencing.


title: Cnt24hS1

description: Library name: NTGUU


title: sh9

description:
Library name: sample 37
Hypertension group (sh group),rep9


title: POND-TIA1_rep-2


title: ATAC-Seq, Erythroid cells, shTAL1 rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_shTAL1_rep1


title: G4 ChIP, sample 01

description:
Library name: G4ChIP_Rep1
S2 200 cycles; 15 million reads per sample

value: BG4 antobody

value: Synthetic


title: ATAC-Seq, Erythroid cells, Control rep2, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_control_rep2

value: Control


title: Cnt24hS2

description: Library name: NTGUW


title: scRNA-seq of P1

description: Library name: P1

value: Knee joint synovial tissue

value: treat with PBS


title: POND-TIA1_rep-1


title: sh12

description:
Library name: sample 40
Hypertension group (sh group),rep12


title: sh8

description:
Library name: sample 36
Hypertension group (sh group),rep8


title: ATAC-Seq, Erythroid cells, Control rep1, Day7

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

description: Library name: ATAC_control_rep1


title: Cnt24hS3

description: Library name: NTGUX


title: POND-EPN_forFMR1_rep-2


title: sh7

description:
Library name: sample 35
Hypertension group (sh group),rep7


title: Cnt24hR3

description: Library name: NTGWO

value: root


title: POND-EPN_forFMR1_rep-1


title: PABPC1-POND-293T-100ng_rep-1


title: POND-YTHDF2-R527A_rep-1


title: Cnt24hR1

description: Library name: NTGWH


title: sh6

description:
Library name: sample 34
Hypertension group (sh group),rep6

value: Peripheral Blood


title: POND-YTHDF2-K416A_rep-2


title: sh5

description:
Library name: sample 33
Hypertension group (sh group),rep5


title: Cnt24hR2

description: Library name: NTGWN


title: POND-FMR1_rep-2


title: sh4

description:
Library name: sample 32
Hypertension group (sh group),rep4


title: POND-YTHDF2-K416A_rep-1


title: POND-FMR1_rep-1


title: Cnt1hS1

description: Library name: NSWHZ


title: POND-EPN24_exp2_rep2


title: sh3

description:
Library name: sample 31
Hypertension group (sh group),rep3


title: Cnt1hS3

description: Library name: NSWNB


title: sh2

description:
Library name: sample 30
Hypertension group (sh group),rep2


title: POND-EPN24_exp2_rep1


title: POND-YTHDF2-WT_rep-1


title: Cnt1hS2

description: Library name: NSWNA


title: Cnt7hR2

description: Library name: NTGPZ


title: POND-IGF2BP1_exp2_rep2


title: ICH28

description:
Library name: sample 28
Hypertension with cerebral hemorrhage group (ICH group),rep28


title: sh1

description:
Library name: sample 29
Hypertension group (sh group),rep1


title: POND-IGF2BP1-DelKH3-4_rep-2


title: POND-IGF2BP1_exp2_rep1


title: Cnt1hR2

description: Library name: NSWSX


title: POND-IGF2BP1-DelKH3-4_rep-1


title: POND-IGF2BP1_100ng_rep2


title: ICH27

description:
Library name: sample 27
Hypertension with cerebral hemorrhage group (ICH group),rep27


title: Cnt1hR3

description: Library name: NSWSY


title: POND-YTHDF2-WT_rep-2


title: POND-YTHDF2-R527A_rep-2


title: Cnt1hR1

description: Library name: NSWSW


title: POND-IGF2BP1-DelKH1-2_rep-2


title: Placenta sample X31303.063

city: New York

first: Corina

last: Lesseur

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine

description:
Library name: X31303.063
Column name in counts_nhbcs.csv.gz : X31303.063

data_processing:
Reads aligned with Splice Transcripts Alignment to a Reference (STAR) with GENCODE v47 (GRCh38) and quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv gzipped file with raw counts for each sample

source_name: Placenta villis fetal side

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany, cat. No. 74106), and the Norgen Tissue RNA Purification Kit (Norgen Biotek, Thorold, ON, Canada, Cat. No. 25700), following the manufacturer’s protocols.
Ribosomal RNA depletion was used to prepare RNA-sequencing (RNA-seq) libraries, transcriptome-wide RNA-sequencing was performed with paired-end 75 bp reads on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) .

value: Placenta villis fetal side

tag: maternal smoking

value: No

tag: baby race

value: White

tag: gestational age

tag: birthweight percentile

tag: birthweight fenton_group

value: AGA

tag: delivery method

value: C-section

tag: infant sex

value: Male

tag: maternal age

tag: rna integrity_number


title: POND-FMR1-Y265syn_rep2

tag: cell line

value: HEK293T cell line

tag: genotype

tag: treatment


title: POND-IGF2BP1_100ng_rep1


title: THP1_lenti-ctrl_LPS

city: Marburg

first: Leon

middle: Nicolas

last: Schulte

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps-Universität Marburg

description: Library name: Sample15

data_processing:
Fastq data were loaded into the CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed using the CLC workbench with quality score limit set to 0.05 and 25 nt minimal read length
Trimmed sequences were mapped to the GRCh38 human reference genome using the CLC workbench with the following parameters: Mismatch cost: 2. Insertion cost: 3. Deletion cost: 3. Length fraction: 0.8. Similarity fraction: 0.8. Max. hits for a read: 10. Strand specific: both.
Normalized expression values (e.g. RPKM) were calculated based on unique read counts
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file, including gene identifiers and coordinates, read counts and RPKM values for each sample.

source_name: blood

growth_protocol: Primary macrophages were cultured in X-Vivo-15 medium (Lonza), supplemented with 5 % FCS.  THP1 cells were cultivated in RPMI Glutamax medium, supplemented with 5 % FCS. All cells were cultured at 37 °C with humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted with Trizol reagent and DNaseI-treated, using established protocols. PolyA RNA was selected using magnetic beads.
Libraries were generated using the TruSeq Stranded mRNA Kit (Illumina)

treatment_protocol:
Blood-derived monocytes (CD14 MACS purification) were differentiated into macrophages using 15 ng / ml recombinant GM-CSF or M-CSF for 7 days. THP1 cells were differentiated with PMA (20 nM) for two days.
Upon differentiation / attachment, cells were treated with different immune-stimuli at the following concentrations: LPS: 100 ng / ml. Salmonella Typhimurium: multiplicity of infection (MOI) = 10

tag: tissue

value: blood

tag: cell type

value: monocytic

value: Control lenti-vector

value: lipopolysaccharide

tag: batch


title: ICH26

description:
Library name: sample 26
Hypertension with cerebral hemorrhage group (ICH group),rep26

value: Peripheral Blood Mononuclear Cells

tag: sample group


title: POND-IGF2BP1-DelKH1-2_rep-1