title: Long reads polyA RNA from control ovaries for piRNA knockdown

description: Library name: ovaries_tjG4_arr2GD


title: siRif1_4C_5

status: Public on Mar 18 2025

type: SRA

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic

data_processing:
Sequencing reads were aligned to the mouse genome (GRCm38, primary assembly) using STAR aligner (version 2.7.6a) with the annotation (GRCm38.101) and ERCC92 (Thermofisher).
Reads were counted per gene with the same STAR run by setting quantMode GeneCounts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text with read counts per gene

molecule: polyA RNA

organism: Mus musculus

source_name: 4-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2 until they reached 4-cell and 8-cell stage.

extract_protocol:
Emrbyos were washed with PBS, placed in tubes with 1× Clontech lysis buffer (Z5013N) containing ERCC RNA Spike-In Mix (Invitrogen) and flash-frozen in liquid nitrogen.
Library preparation was carried out using the SMART-seq2 protocol.

treatment_protocol: 20 μM siControl (Dharmacon, D-001210-01) or 20 μM siRif1 (Dharmacon, D-040028-01) were injected into zygotes at 17-18 hours post-hCG injection and embryos were cultured until 63 and 70 hours post-hCG injection, respectively, at which point 4-cell and 8-cell embryos, respectively were collected.

tag: tissue

value: 4-cell embryo

tag: genotype

value: (C57BL/6J xCBA) x DBA/13J

tag: treatment

value: siRNA for Rif1 injected


title: HPSC,rep3,adult,hic-seq,3m

city: Guangzhou

first: Feifei

last: Li

state: Guangdong

address: Guangzhou Higher Education Mega Center, Panyu District

country: China

institute: South China University of Technology

library_source: genomic

data_processing:
HiC-Pro (v.3.1.0) was used for the processing of Hi-C data. Only uniquely mapped read pairs with mapping quality no less than 10 were saved for further analysis, and dangling end reads, self circled reads, religated reads were all trimmed out. Non-duplicated reads were used to generate Hi-C contact matrices at the binning resolution of 10kb, 50kb and 100 kb. To validate the reproducibility of data, we calculated the GenomeDisco score between two libraries. Contact heatmaps were generated with matrices at different resolutions by fanc (v.0.9.25). The p(s)-curves were calculated from genome distances of 20 kb to 50 Mb separated into 500 bins logarithmically.We applied the Von Neumann Entropy (VNE) approach to quantify the disorder of chromatin structure for 100-kb resolution intra-chromosomal matrices. Hi-C matrix (M) was converted to correlation matrix C using corr (log2[M]).
Compartments were called d by analyzing the first eigenvector of the KR normalized contact maps at 100 kb resolution. The compartments with higher gene density were assigned as type A, while the compartments with lower gene density were assigned as type B. Compartment strength was calculated using AB / AA + BB. Saddle plots were calculated as previously described. Hi-C matrix bins were sorted according to the PC1 values. Sorted frequencies were aggregated into 50 groups and averaged to obtain a compartmentalization saddle plot. Number of ATAC-seq peaks overlapped with compartments were analyzed by BEDtools with at least 1bp shared.
TADs and TAD boundaries were identified at 50 kb resolution as described. Shared TADs between different samples were defined as overlapping area larger than 75% for both samples. We calculated the standard deviations of the insulation score of each TAD boundary across three-cell stages and sorted boundaries by standard deviations. Then the top 1000 variable TAD boundaries were selected based on the ranking order. Clustering of boundaries was carried out using Pheatmap package in R.
Loops and interactions were detected with HiCCUPS in Juicer Tools at 10 kb resolution. Enhancer or promoter involved loops were those with at least one anchor overlapped with enhancer regions (distal H3K27ac ChIP-seq peaks) or promoter regions (TSS ± 3 kb). Enhancer–promoter (E–P), promoter–promoter (P–P), and enhancer–enhancer (E–E) interactions were also identifed. Shared loops were defined as loops with both anchors not shift more than one bin. Aggregate peak analysis was processed with ‘apa’ in Juicer Tools, which generated aggregate heatmaps and average contact signals.
Assembly: GRCz10
Supplementary files format and content: ValidPairs.txt

molecule: genomic DNA

organism: Danio rerio

source_name: hematopoietic stem cell

extract_protocol:
Cells sorted by FACS were fixed with freshly made 1% formaldehyde solution at room temperature for 10 min. 1.25M glycine solution was added to a final concentration of 0.2 M for quenching the reaction. Cells were lysed in ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, 1x protease inhibitor cocktail) for 15 min. Pelleted nuclei were washed once with 1x NEBuffer 2 and incubated in 0.5% sodium dodecyl sulfate (SDS) at 62°C for 5 min. After incubating, water and Triton X-100 were added to quench the SDS. MboI restriction enzyme (NEB, R0147M) was added and chromatin was digested at 37°C for 5 hr.
Cells were fixed with 1% formaldehyde and lysed in ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, 1x protease inhibitor cocktail) for 15 min. Pelleted nuclei were incubated in 0.5% sodium dodecyl sulfate at 62°C for 5 min. MboI restriction enzyme was added and chromatin was digested at 37°C for 5 hr. Biotin-14-dATP was used to mark the DNA ends followed by proximity ligation in intact nuclei. After crosslink reversal, DNA was sheared to a length of about 300 bp with Covaris M220. Biotin-labeled fragments were pulled down using Dynabeads MyOne Streptavidin C1 beads. The Hi-C libraries were amplified for 11-15 cycles with Q5 master mix following the operation manual. DNA was then purified and sequenced using NovaSeq platform.

value: hematopoietic stem cell

tag: cell line

tag: cell type

value: flow cytometry


title: T47D, Normoxia, ZHX2, replicate 2

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

data_processing:
raw fastq data were initially processed to remove adaptor sequences using Cutadapt with parameters [-u 10 -u -15 -U 10 -U -15 -m 30]. The cleaned reads were aligned to the human reference genome (GRCh38, Ensemble release 100) using bowtie2 with default settings. Peak identification was performed using MACS2 with input data as controls. Replicates of ChIP-seq data were pooled for downstream analysis.
Assembly: hg38
Supplementary files format and content: bigWig, Peak

organism: Homo sapiens

source_name: Breast

growth_protocol: The T47D cell line was maintained in RPMI medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin. Post-lentivirus infection, cells were selected using either hygromycin (200 μg/ml) or puromycin (2 μg/ml), based on the vector's resistance marker. All cells were maintained at 37°C in 5% CO2 incubator. Hypoxia treatments were conducted in a Baker Ruskinn's InvivO2 400 hypoxia workstation.

extract_protocol:
1×107 of T47D cells were fixed using 1% formaldehyde for 10 minutes and quenched with 125 mM glycine for 5 minutes (cells treated under hypoxia were fixed in hypoxia chamber). Post-fixation, cells were washed twice with cold PBS supplemented with protease inhibitors. Cells were lysed using LB1 buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) followed by LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) buffers. Nuclei were collected and sonicated using Bioruptor sonicator (15 cycles, 30 s on and 30 s off). After Triton X-100 treatment (1% final concentration), supernatants were collected post-centrifugation (20,000g, 10 min, 4 °C) and incubated with antibody-bounddynabeads for approximately 8 hours at 4 °C. Following washing, chromatin-protein complexes bound to beads were eluted, crosslinks reversed overnight at 65 °C, and treated with RNase (1 hour at 37 °C) and protease K (2 hours at 55 °C).
DNA was recovered using PCR purification kit and subjected to library preparation using the NEBNext Ultra II kit, following the manufacturer’s instructions.

value: Breast

value: Tumor cell

tag: chip antibody

value: Normoxia


title: MDA-MB-231 Cell Library 1KB3-P31

city: Austin

first: Daylin

last: Morgan

state: Texas

address: 107 W Dean Keeton St

department: BME

country: USA

institute: The Univeristy of Texas at Austin

description: Library name: 1KB3-P31

data_processing:
All data was processed using https://github.com/brocklab/pycashier. Paired-end reads were merged into contingous sequences using "pycashier merge". Then barcode sequences were extracted, corrected and filtered with "pycashier extract".
Supplementary files format and content: all processed data is tsvs with 5 columns: barcode, count, sample, percent, sample, n_samples

source_name: breast

extract_protocol:
DNA was extracted from frozen cell pellets containg 1e6 cells using the Invitrogen PureLink Genomic DNA kit (ThermoFisher, K182001) according to manufacturer’s instructions.
Amplification steps were performed following published ClonMapper barcode amplification procedures (up-to-date web protocol: https://docs.brocklab.com/clonmapper, published protocol:https://doi.org/10.1007/978-1-0716-1811-0_8).

treatment_protocol: Cells were seeded in a 24-well at 50,000 cells per well then treated with varying doses of doxorubicin for 48 hours. Samples were allowed to recover and expanded until they reached ~5e6 cells.

value: breast

value: TNBC


title: T47D, Normoxia.ZHX2, replicate 1


title: HPSC,rep2,adult,hic-seq,3m


title: siRif1_4C_4

value: (C57BL/6J xCBA) x DBA/12J


title: MDA-MB-231 Cell Library 1KB3-P29

description: Library name: 1KB3-P29


title: HPSC,rep1,adult,hic-seq,3m


title: T47D, Hypoxia, H3K27ac, replicate 1

value: Hypoxia


title: MDA-MB-231 Cell Library 1KB3-P27

description: Library name: 1KB3-P27


title: T47D, Normoxia, input, replicate 2


title: T47D, Hypoxia, H3K27ac, replicate 2


title: siRif1_4C_3

value: (C57BL/6J xCBA) x DBA/11J


title: Handling_1h30min_CRS1_v1

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

description: Library name: CRS1_v1

data_processing:
Transcript-level quantification was performed with Kallisto using the GENCODE M17 annotation.
Counts from protein-coding transcripts were aggregated for gene-level quantification.
Assembly: GRCm38
Supplementary files format and content: bulkRNA_GeneCounts.csv.zip : a matrix of counts per gene symbol.
Supplementary files format and content: bulkRNA.SE.rds.zip : A R SummarizedExperiment containing the gene counts, metadata, and DEA results.

source_name: Ventral hippocampus

extract_protocol:
One snap-frozen ventral hippocampus per animal was homogenized in 500 µl Trizol (Invitrogen 15596018) using metal beads (Qiagen 69989) in a tissue lyser bead mill (Qiagen, Germany) at 4°C for 2 min at 20 Hz. RNA was extracted according to the manufacturer’s recommendations.
The CRS1 experiment was prepared using the Illumina TruSeq stranded RNA kit, while the other libraries were prepared at Novogene using the NEBNext® Ultra RNA Library Prep Kit.

value: Ventral hippocampus

tag: Sex

value: female

tag: ars timepoint

value: Handling

tag: batch


title: HPSC,rep2,nascent,hic-seq,3d


title: T47D, Normoxia, input, replicate 1


title: T47D, Normoxia, CTCF, replicate 2


title: MDA-MB-231 Cell Library 1KB3-P23

description: Library name: 1KB3-P23


title: T47D, Normoxia, CTCF, replicate 1


title: HPSC,rep1,nascent,hic-seq,3d


title: HPSC,rep3,nascent,hic-seq,36h


title: T47D, Normoxia, H3K27ac, replicate 2


title: HPSC,rep2,nascent,hic-seq,36h


title: MDA-MB-231 Cell Library 1KB3-P25

description: Library name: 1KB3-P25


title: MDA-MB-231 Cell Library 1KB3-P21

description: Library name: 1KB3-P21


title: siCon_4C_7

value: (C57BL/6J xCBA) x DBA/8J

value: siRNA for control injected


title: T47D, Normoxia, H3K27ac, replicate 1


title: siRif1_4C_2

value: 4-cell embryo

value: (C57BL/6J xCBA) x DBA/10J


title: siRif1_4C_1

value: (C57BL/6J xCBA) x DBA/9J

value: siRNA for Rif1 injected


title: siCon_4C_6

value: (C57BL/6J xCBA) x DBA/7J


title: T47D, shZHX2, Hypoxia, replicate 3

data_processing:
The ATAC-seq data were first quality-checked by FastQC and then aligned to the hg38 reference genome using bowtie2 with default parameters. Subsequently, reads that aligned multiple times and PCR duplicates were removed using samtools. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: bigWig, Peak

extract_protocol:
Cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50,000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 °C. The transposed DNA fragments were purified immediately after with MinElute PCR Purification Kit (Qiagen).
After Samples were PCR-amplified using NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

value: Breast

value: Tumor cell


title: siCon_4C_5

value: (C57BL/6J xCBA) x DBA/6J


title: HPSC,ATAC,rep2,3m

data_processing:
ATAC-seq reads were mapped to GRCz10 zebrafish genome by Bowtie2 (v.2.5.0) with very-sensitive configuration.The uniquely aligned fragments with MAPQ ≥ 30 were extracted using SAMtools (v.1.9). Duplicates were removed by Picard tools MarkDuplicates (https://broadinstitute.github.io/picard/, v.2.27.4). ATAC-seq peaks were also called using MACS2 callpeak command (v.2.2.5) with parameters “--nomodel --shift -100 --extsize 200 -q 0.05”.
Peaks were first called in individual replicates. Then reads from different replicates were merged, and peak calling was performed with merged reads. Repeated peaks were then taken as those called from the merged reads that overlapped with those called in all replicates. Signal tracks were built using the bdgcmp sub-command of MACS2 with the fold enrichment over control (FE) mode.To obtain differentially accessible regions, we merged peaks from all samples to obtain a non redundant peak set. Read pair numbers for each non-redundant peak were calculated using HTseq (v0.8.0) and compared with DESeq2.
Assembly: GRCz10
Supplementary files format and content: narrowPeak

extract_protocol:
50000 fresh cells were resuspended in 50 μl of ATAC-seq resuspension buffer and incubated on ice for 3 min.  Nuclei were resuspended in 50μl of transposition mix (10μl 5XTTBL (Vazyme TD501), 5μl TTE Mix V50, and 35μl water) and pipetted up and down 20 times to mix. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer.
After the tagmentation, purify sample using the Ampure XP beads. The ATAC-seq library was amplified for 11 cycles of PCR with TAE mix (Vazyme TD501) following the manual. DNA was then sequenced using an Illumina sequencing platform.

value: hematopoietic stem cell

value: flow cytometry


title: HPSC,rep1,nascent,hic-seq,36h


title: MDA-MB-231 Cell Library 1KB3 Dox-550-4

description: Library name: C6

value: breast

value: TNBC

value: 550nM Dox


title: T47D, shZHX2, Hypoxia, replicate 2

value: Hypoxia


title: HPSC,ATAC,rep1,3m


title: siCon_4C_4

value: (C57BL/6J xCBA) x DBA/5J


title: siCon_4C_3

value: (C57BL/6J xCBA) x DBA/4J


title: MDA-MB-231 Cell Library 1KB3 Dox-550-3

description: Library name: C5


title: OVCAR5 ALDHplus Dot1Li RNA rep2

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

data_processing:
For quality control, raw fastq files were pre-processed using TrimGalore (v0.6.6) and cutadapt (v2.10) with single-end trimming mode, Phred score cutoff of 30, and minimum sequence length cutoff of 20 bp. After checking quality with the FastQC tool (v0.11.9), raw sequencing reads were aligned to human genome build hg38 using STAR v.2.5.2 (https://github.com/alexdobin/STAR) with standard settings.
Cell line identity was validated for all samples as OVCAR5 using NGSCheckmate.
Bigwig formatted track files were generated using deeptools v3.5.1 bamCoverage, from the STAR-aligned bam files described above, normalized to counts per million reads (CPM).
Assembly: hg38
Supplementary files format and content: Bigwig track files

source_name: Ovary

growth_protocol: OVCAR5 cells were cultured in the regular medium described in the manuscript. OVCAR5 derived ALDH plus and minus cells were culture in the low-attached plate and with Mammocult medium.

extract_protocol:
RNA was extracted using Qiagen RNeasy Micro kit according to the manufactuer instructions.
For each sample, 100 ng of total input RNA was extracted by Rneasy Micro Kit (Qiagen, Cat # 74004). mRNA was isolated by NEBNext Poly(A) mRNA Magnetic Isolation Module, and RNA-seq libraries were prepared using the NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs Inc., Ipswich, MA).  All the RNA-seq libraries were checked by using a BioAnalyzer (Agilent Technologies) and then sequenced on an Illumina HiSeq4000 system with single-end, 50-bp read length settings.

treatment_protocol: ALDHplus cancer stem cells and ALDHminus non-cancer stem cells were treated with DMSO, Dot1Li (500nM, 48 hours), cisplatin (1μM, 24 hours) and Dot1Li+cisplatin in combination

value: Ovary

value: ALDH plus


title: MDA-MB-231 Cell Library 1KB3-P19

description: Library name: 1KB3-P19


title: T47D, shCtrl, Hypoxia, replicate 3

value: shCtrl


title: OVCAR5 ALDHplus Dot1Li RNA rep1


title: T47D, shCtrl, Hypoxia, replicate 2


title: siCon_4C_1

value: 4-cell embryo

value: (C57BL/6J xCBA) x DBA/2J

value: siRNA for control injected


title: Activated_3

city: Dundee

first: Fiona

last: Haward

address: Life Sciences, Dow St

country: United Kingdom

institute: University of Dundee

description: rRNA depleted

data_processing:
Reads were aligned to mm10 with gencode vM24 annotation, and read counts for each gene calculated using STAR version 2.5.2b.
Differential gene expression analysis was performed to compare control and KCl-activated samples using EdgeR (Robinson et al., 2010).
Differential gene expression analysis was performed to compare control and KCl-activated samples using EdgeR (Robinson et al., 2010).
Assembly: mm10
Supplementary files format and content: Each processed data file contains a tab delimited table of reads per gene constructed by STAR during genome alignment. The first column indicates the ensembl gene id, the second column shows all alignments, the third shows forwards alignments, and the fourth shows reverse alignments (reverse aligned reads are the reads counts to use for this library strategy).

molecule: total RNA

source_name: KCl activated primary neurons

growth_protocol: Primary cortical neurons were isolated from brain cortices of E18 embryos. Cells were cultured in vitro on PDL-coated plates for 16 days prior to harvesting.

extract_protocol:
RNA isolation was performed using Trizol
Library preparation was perfomed by Genewiz for Illumina, strand-specific RNA-seq with rRNA depletion. Libraries underwent 2x150 bp sequencing on an Illumina NovaSeq

treatment_protocol: On day 2 after plating all cells were treated with AraC (2.5uM) for 24hrs. After 16 DIV, half the samples (the activated samples) were treated with KCl (50mM) for 5minutes before washing twice in fresh media. Cells were left to recover for 30minutes in conditioned media prior to harvesting. The other half of the samples remained untreated as a control.

value: Treated with 50uM KCl for 5mins

value: primary cortical neurons

tag: age

value: derived from E18 embyros and harvested after 16 DIV

value: brain cortex


title: MDA-MB-231 Cell Library 1KB3-P17

description: Library name: 1KB3-P17


title: OVCAR5 ALDHplus Dot1Li Cisplatin RNA rep1

value: Dot1Li, Cisplatin


title: T47D, shCtrl, Hypoxia, replicate 1

value: Breast

value: Tumor cell


title: T47D, shCtrl, Normoxia, replicate 3

value: Normoxia


title: OVCAR5 ALDHplus DMSO RNA rep2

value: DMSO


title: Activated_2

description: rRNA depleted


title: MDA-MB-231 Cell Library 1KB3 Dox-400-4

description: Library name: B5

value: breast

value: TNBC

value: 400nM Dox


title: Activated_1

description: rRNA depleted


title: T47D, shCtrl, Normoxia, replicate 2


title: siCon_4C_2

value: (C57BL/6J xCBA) x DBA/3J


title: OVCAR5 ALDHplus DMSO RNA rep1

value: Ovary

value: ALDH plus


title: MDA-MB-231 Cell Library 1KB3 Dox-400-3

description: Library name: B4


title: MDA-MB-231 Cell Library 1KB3 Dox-550-5

description: Library name: C4

value: 550nM Dox


title: Control_2

description: rRNA depleted

source_name: Non-treated primary neurons

value: Untreated


title: Control_3

description: rRNA depleted


title: MDA-MB-231 Cell Library 1KB3 Dox-400-2

description: Library name: B2


title: T47D, shCtrl, Normoxia, replicate 1

value: shCtrl


title: OVCAR5 ALDHplus Cisplatin RNA rep2

value: Cisplatin


title: LAB_RNA_6

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

country: Canada

institute: University of Toronto

data_processing:
Reads were trimmed using fastp (0.20.1) with default settings.
Reads were aligned to the hg38 genome using STAR version 2.7.4a at default settings
RNA-seq bedGraphs were generated using bamCompare (from Deeptools v3.3.2) with bam files at default settings
Read counts were done using featureCounts (v2.2.0) and differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: fastq
Supplementary files format and content: bedgraphs

source_name: Labouring Myometrium

extract_protocol:
After receiving written consent, myometrial biopsies from healthy women undergoing term-not-in-labor elective Caesarean sections (TNIL, n = 6) or spontaneous, non-induced term labor (LAB, n = 6) were collected. Tissues were crushed to a fine powder on dry ice and total RNA was extracted using Trizol and further treated with DNAseI for gDNA elimination. RNA was quality assessed and quantified using BioAnalyzer.
RNA samples were checked on the Agilent Bioanalyzer 2100 RNA Nano chip for RNA integrity (RIN > 7) and quantified using the Qubit RNA HS Assay. RNA library preparation was performed following the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus protocol to generate stranded data. In brief, 500 ng of total RNA was used as the input material for rRNA depletion. RNA was first hybridized with DNA probes complementary to rRNA targets which direct RNase H to digest the rRNA. Any remaining DNA probes were digested with DNase I, followed by bead purification to recover remaining intact RNA. Remaining RNA was fragmented to 200-300-bases range for 2 minutes at 94oC and converted to double stranded cDNA, which proceeded to library preparation and dual-index Illumina adapters were added through PCR. Final libraries were validated on the Fragment Analyzer using the High Sensitivity NGS Kit or on the Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size and absence of primer dimers, and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Validated libraries were pooled in equimolar quantities and sequenced on the IlluminaNovaseqplatform following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length.

value: Labouring Myometrium


title: OVCAR5 ALDHplus Dot1Li Cisplatin RNA rep2


title: MDA-MB-231 Cell Library 1KB3 Dox-550-1

description: Library name: C2


title: MDA-MB-231 Cell Library 1KB3 Dox-550-2

description: Library name: C3


title: LAB_RNA_5


title: MDA-MB-231 Cell Library 1KB3 Dox-400-1

description: Library name: B1


title: Control_1

description: rRNA depleted

value: primary cortical neurons

value: derived from E18 embyros and harvested after 16 DIV

value: brain cortex


title: MDA-MB-231 Cell Library 1KB3 Dox-400-5

description: Library name: B6


title: UUO-5 [S10]

first: Andrew

last: Advani

address: 6-151 61 Queen Street East

department: Medicine

institute: St. Michael's Hospital

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
Transcript abundances for each sample were estimated with StringTie, and the FPKM  value for gene and transcript level were calculated with R package Ballgown
Assembly: GRCm38
Supplementary files format and content: FPKM

source_name: Whole mouse kidneys

extract_protocol:
Total RNA from kidney tissue was isolated using Trizol and quantified using NanoDrop ND-1000
Total RNA was used to prepare sequencing libraries with a KAPA Stranded RNA-Seq Library Prep Kit (Illumina)
Sequencing was carried out using an Illumina NovaSeq 6000

tag: strain

tag: surgery

value: Original UUO

value: Whole mouse kidneys


title: MDA-MB-231 Cell Library 1KB3 Dox-250-6

description: Library name: A6

value: 250nM Dox


title: OVCAR5 ALDHplus Cisplatin RNA rep1


title: OVCAR5 ALDHminus Dot1Li Cisplatin RNA rep1

value: ALDH minus

value: Dot1Li, Cisplatin


title: OVCAR5 ALDHminus Dot1Li RNA rep2


title: UUO-3 [S8]


title: LAB_RNA_3


title: OVCAR5 ALDHminus DMSO RNA rep2

value: DMSO


title: LAB_RNA_2


title: UUO-2 [S7]


title: MDA-MB-231 Cell Library 1KB3 Dox-250-3

description: Library name: A3

value: breast

value: TNBC


title: UUO-4 [S9]


title: UUO-1 [S6]


title: MDA-MB-231 Cell Library 1KB3 Dox-250-2

description: Library name: A2


title: OVCAR5 ALDHminus Cisplatin RNA rep2

value: Ovary


title: OVCAR5 ALDHminus DMSO RNA rep1


title: Sham-5 [S20]

value: Sham UUO


title: TNIL_RNA_6

source_name: Non-labouring Myometrium

value: Non-labouring Myometrium


title: MDA-MB-231 Cell Library 1KB3 Dox-250-1

description: Library name: A1


title: LAB_RNA_4


title: TNIL_RNA_5


title: Sham-4 [S19]


title: OVCAR5 ALDHminus Dot1Li Cisplatin RNA rep2


title: MDA-MB-231 Cell Library 1KB3 Pretreatment

description: Library name: 1KB3

value: pretreament


title: OVCAR5 ALDHminus Cisplatin RNA rep1

value: Cisplatin


title: TNIL_RNA_4


title: MDA-MB-231 Cell Library 1KB3 Dox-250-5

description: Library name: A5


title: Sham-3 [S18]


title: MDA-MB-231 Cell Library 1KB3 Dox-250-4

description: Library name: A4


title: TNIL_RNA_3


title: OVCAR5 ALDHplus CD133plus PBS RNA rep1

value: ALDH plus CD133 plus

value: PBS


title: MDA-MB-231 Cell Library 1KB3

description: Library name: libB3

value: initial


title: LAB_RNA_1

value: Labouring Myometrium


title: Sham-2 [S17]


title: MCF7 cells,  treated with CM obtained from PreNeu (cm-PreNeu), 72h, biological replicate 3

city: Bellinzona

first: Marco

last: Bolis

address: Via Francesco Chiesa

institute: IOR Institute of Oncology Research

description:
Library name: MCF7_cmPreNeu_biorep3_experiment_A
Column name in rawcounts_experiment_A.txt: MCF-7-CTRL3
rawcounts_experiment_A.txt

data_processing:
Quality of sequencing reads was evaluated using FastQC (v.0.11.9) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequences were mapped to the GRCh38 assembly of the human genome using STAR (v.2.6.1c). Alignments were conducted in 2-pass mode and soft-clipping of reads was allowed. Quantification of gene-counts using gencode-based annotations were performde by STAR v2.6.1c (experiment_1) or RSEM v1.3.3 (experiment_2).
Downstream analysis was performed in R using DESeq2 (v1.28.1).
Assembly: GRCh38
Supplementary files format and content: tab delimited txt files contain raw counts for each sample

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (250) (74106, Qiagen), following the manufacturer’s instructions.
10-100 ng total RNA was treated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Library construction was performed with the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®, according to the manufacturer’s protocol.

value: cancer cell-line

value: cm-PreNeu


title: TNIL_RNA_2


title: OVCAR5 ALDHplus CD133plus Cisplatin RNA rep2


title: Sham-1 [S16]

value: Whole mouse kidneys


title: MCF7 cells,  treated with CM obtained from PreNeu (cm-PreNeu), 72h, biological replicate 2

description:
Library name: MCF7_cmPreNeu_biorep2_experiment_A
Column name in rawcounts_experiment_A.txt: MCF-7-CTRL2
rawcounts_experiment_A.txt


title: OVCAR5 ALDHplus CD133plus Cisplatin RNA rep1


title: TNIL_RNA_1


title: OVCAR5 ALDHminus CD133minus PBS RNA rep2

value: ALDH minus CD133 minus


title: MCF7 cells,  treated with CM obtained from PreNeu (cm-PreNeu), 72h, biological replicate 1

description:
Library name: MCF7_cmPreNeu_biorep1_experiment_A
Column name in rawcounts_experiment_A.txt: MCF-7-CTRL1
rawcounts_experiment_A.txt


title: CUTTag_H3K27ac_GT38-GA-71

city: Shanghai

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

description: Library name: Sample4

data_processing:
Raw CUT&Tag reads were trimmed using Trim Galore v.0.6.6 (Babraham Institute) in paired-end mode.
Trimmed reads were aligned to mouse mm10 genome using Bowtie v.2.4.4 with the parameters “-N 1 -L 25 -X 700 --no-mixed --no-discordant”.
Duplicate reads were removed with Picard Tools v.2.25.5 and the reads were shifted to compensate for the offset in tagmentation site relative to the Tn5 binding site using the alignmentSieve function of deepTools v.3.5.1.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: Human HGC27 , and GT38 cells were grown in  RPMI 1640 (Gibco) supplemented with 10% FBS (Yeasen) and 1 × Penicillin-Streptomycin (Thermo) at 37 °C, 5% CO2.

extract_protocol:
Cell nuclei (1–2×10^6) were isolated using NE1 buffer (20 mM HEPES pH 7.5, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol) and coupled to ConA magpoly beads (Smart-lifesciences, SM04102).
The DNA was then purified using VAHTS DNA clean beads (VAHTS, N411) and amplified with the TruePrep DNA Library Prep Kit V2 for Illumina (VAHTS, TD501). The pooled library was sequenced on a NovaSeq (Illumina) platform, employing 150 bp paired-end reads. Rabbit monoclonal anti-H3 acetylation at lysine 27 (H3K27ac) antibody (Abclonal, A7253) and anti-GLI3 antibody (Bethyl, A303-417A-1) were used as the primary antibodies. Goat anti-rabbit IgG (Novoprotein, N269) was employed as the secondary antibody.

treatment_protocol: Cells were modified using the CRISPR/Cas9 system to change the genotype at the rs72856331 locus to GA.

value: gastric carcinoma cell line


title: GE_3_ANAK_96h

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters unstranded --minOverlap 10)
Differential expression analysis was computed with DESeq2
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

source_name: HSPCs experiencing the HS/AAV6+ANAK treatment (replicate 3)

extract_protocol:
miRNeasy micro kit (QIAGEN)
SMART-seq Ultra low input unstranded

value: Primary CB-derived HSPCs


title: OVCAR5 ALDHplus CD133plus PBS RNA rep2


title: GE_2_ANAK_96h

source_name: HSPCs experiencing the HS/AAV6+ANAK treatment (replicate 2)


title: OVCAR5 ALDHminus CD133minus PBS RNA rep1


title: CUTTag_H3K27ac_HGC27-GA6

description: Library name: Sample2


title: GE_1_ANAK_96h

source_name: HSPCs experiencing the HS/AAV6+ANAK treatment (replicate 1)


title: MCF7 cells, vehicle controls, 72h, biological replicate 2

description:
Library name: MCF7_control_biorep2_experiment_A
Column name in rawcounts_experiment_A.txt: MCF-7-CM2
rawcounts_experiment_A.txt

value: breast

value: vehicle


title: OVCAR5 ALDHminus CD133minus Cisplatin RNA rep2

value: Ovary


title: MCF7 cells, vehicle controls, 72h, biological replicate 3

description:
Library name: MCF7_control_biorep3_experiment_A
Column name in rawcounts_experiment_A.txt: MCF-7-CM3
rawcounts_experiment_A.txt


title: MCF7 cells, vehicle controls, 72h, biological replicate 1

description:
Library name: MCF7_control_biorep1_experiment_A
Column name in rawcounts_experiment_A.txt: MCF-7-CM1
rawcounts_experiment_A.txt


title: GE_3_96h

source_name: HSPCs experiencing the HS/AAV6 treatment (replicate 3)


title: CUTTag_IgG_HGC27-GA6

description: Library name: Sample1

value: IgG


title: OVCAR5 ALDHminus CD133minus Cisplatin RNA rep1


title: MCF7 cells, succinate 2mM, 24h, INPUT

description: Library name: MCF7_succinate (INPUT)

data_processing:
ChIP-seq data were analyzed using the nf-core/chipseq pipeline (version 2.1.0) implemented in Nextflow (version 24.10.4), with Singularity (1.3.6-1.el8) containers to ensure reproducibility. Raw FASTQ files were quality-checked using FastQC, followed by adapter trimming with Trim Galore!.Reads were aligned to the GRCh38 genome using BWA aligner, and PCR duplicates were marked with Picard. Multiple libraries per sample were merged, with duplicates re-marked, and low-quality or problematic reads (e.g., unmapped, multi-mapped, blacklisted, excessive mismatches) were removed using SAMtools, BEDTools, and BAMTools. Normalized coverage tracks were generated with BEDTools and bedGraphToBigWig, and IP enrichment relative to control was calculated using deepTools. Peaks were called with MACS3, annotated using HOMER, and merged into a consensus peak set for featureCounts-based quantification. Quality metrics, including library complexity (Preseq, Picard) and strand cross-correlation (phantompeakqualtools), were compiled via MultiQC, while PCA and clustering of consensus peak counts were performed with R-based tools such as DESeq2.
Assembly: GRCh38
Supplementary files format and content: bigWig, broadPeak (except for INPUT samples)

growth_protocol: Cells were plated in RPMI medium supplemented with 10% charcoal-stripped (CS) heat-inactivated FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin.

extract_protocol:
After 24 hours, cells were treated with 1% formaldehyde (Cat. F8775, Sigma-Aldrich) for 10 min at room temperature (RT). Ten, the reaction was quenched by adding glycine 0.125 M. After spinning and washing with PBS solution, the cross-linked tissue samples were stored at -80 °C. During ChIP experiments, lysis bufer 1 (50 mM Hepes–KOH, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, ddH2O), supplemented with protease inhibitors (Roche) was added to previously fixed-samples; they were homogenized using an ultra-turrax (VWR). After, samples were washed in lysis buffer 2 (10 mM Tris–HCl, 200 mM NaCl, mM EDTA, 0.5 mM EGTA, ddH2O) and lysis buffer 3 (10 mM Tris– HCl, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-Lauroylsarcosine, ddH2O), both supplemented with protease inhibitors (Roche). Obtained chromatin was sheared on Bioruptor sonicator (Diagenode) set at high potency for 30 pulses, each one comprised of 60 s ON and 30 s OFF. After checking the chromatin smear, 1% of the sample volume was collected and stored at -20 °C to be next used as input sample, while 2 µg of H3K9Me3 antibody (Cat 13969, Cell Signaling Technology), previously incubated all day at 4° C in a rotation wheel with Dynabeads (Thermo Fisher Scientific), was added to the remaining sample volume. After overnight incubation in a rotation wheel at 4° C, immunoprecipitated samples (IPs) were washed with RIPA wash buffer (50 mM Hepes–KOH, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate, ddH2O) for 6 times; after spinning, dynabeads were removed in a magnetic stand, samples were eluted in Elution Buffer (TE 1X and 2% SDS) and incubated overnight at 65° C to remove crosslinks.
The recovered material was purified using QIAquick PCR purification kit (Qiagen) and DNA was quantified using Qubit® dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific). As negative control of the ChIP protocol, an IP reaction against rabbit IgG (Cat. 2729S; Cell Signaling) was performed. ChIP-Seq libraries were created adapting the TruSeq ChIP protocol (Illumina): around 50 ng of IPs and input were used for library preparation. Libraries were run on a NextSeq 500 sequencer (Illumina) using a 1×75 bp high-output kit (Illumina) with 8 IPs (50 M reads per sample) or 4 input samples (100 M read per sample) for run.

treatment_protocol: The day after the plating media was replaced with fresh complete RPMI with CS-FBS and Succinate 2mM (Cat. S9512, Sigma-Aldrich) or control.

value: cancer-cell line

value: succinate 2mM


title: GE_2_96h

source_name: HSPCs experiencing the HS/AAV6 treatment (replicate 2)


title: OVCAR5 ALDHplus RNA rep2

value: ALDH plus


title: MCF7 cells, succinate 2mM, 24h, H3K9me3 IP, biological replicate 3

description: Library name: MCF7_succinate_biorep3, H3K9me3 (ChIP)

value: H3K9Me3 antibody (Cat 13969, Cell Signaling Technology)


title: H3_159_GE_ANAK_24h

data_processing:
Reads wuality control checked with FASTQC
trimming with Trim Galore, (parameters --quality 20 --length 25)
Alignment with STAR 2.7.6a (parameters --outSAMstrandField intronMotif --outSAMmultNmax 1 --outFilterMismatchNmax 10)
count with featureCounts (parameters -s 2 --minOverlap 10)
Differential expression analysis was computed with DESeq2
Assembly: GENCODE version hg38 primary assembly v35
Supplementary files format and content: tab-delimited text files include read counts values for each Sample

extract_protocol:
miRNeasy Micro Kit (QIAGEN)
TruSeq Stranded mRNA (Illumina)

value: HSPCs experiencing the HS/AAV6+ANAK treatment


title: MCF7 cells, succinate 2mM, 24h, H3K9me3 IP, biological replicate 2

description: Library name: MCF7_succinate_biorep2, H3K9me3 (ChIP)


title: OVCAR5 ALDHminus RNA rep2

value: ALDH minus


title: CUTTag_IgG_GT38-GA-71

description: Library name: Sample3


title: H2_159_GE_ANAK_24h


title: MCF7 cells, succinate 2mM, 24h, H3K9me3 IP, biological replicate 1

description: Library name: MCF7_succinate_biorep1, H3K9me3 (ChIP)


title: OVCAR5 ALDHminus RNA rep1


title: MCF7 cells, control, 24h, INPUT

description: Library name: MCF7_control (INPUT)

value: control


title: D3_159_GE_ANAK_24h


title: MCF7 cells, control, 24h, H3K9me3 IP, biological replicate 3

description: Library name: MCF7_control_biorep3, H3K9me3 (ChIP)


title: G3_159_GE_24h

value: HSPCs experiencing the HS/AAV6 treatment


title: MCF7 cells, control, 24h, H3K9me3 IP, biological replicate 2

description: Library name: MCF7_control_biorep2, H3K9me3 (ChIP)


title: G2_159_GE_24h


title: C3_159_GE_24h

source_name: HSPCs experiencing the HS/AAV6 treatment (replicate 1)


title: 5xFAD, MS1262, m6A-IP, biol rep 3

city: Chapel Hill

first: John

last: Wrobel

state: NC

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

data_processing:
Raw sequencing data were de-multiplexed using bcl2fastq2 v2.17.1.14 (Illumina) and adapters were removed using Trimmomatic-0.32 software. Then, single-end reads from input and m6A IP samples were mapped to the GRCm38/mm10 mouse reference genome using STAR version 2.7.6a [Bioinformatics 29, 15-21 (2013)]. Expression at the gene level was quantified with Salmon 1.4.0 [Nature Methods 14, 417–419 (2017)]. The resulting bam files from the STAR alignment were sorted and indexed using SAMtools version 1.10 [Bioinformatics 25, 2078-2079 (2009)] and MACS2 version 2.1.2 [Genome Biology 9, 1-9 (2008)] was used to call m6A peaks using the bam files for each m6A-IP/input pair.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values text files for gene expression matrix (salmon) and m6A peaks (macs2)
Library strategy: MeRIP-Seq

source_name: hippocampus

extract_protocol:
The m6A/MeRIP-Seq was performed as described with some modifications [Neuron 97, 313-325.e6 (2018)]. Total RNA was extracted from hippocampus of 5x-FAD (AD, n = 4), MS1262 treated 5x-FAD (AD-tr, n = 4), and age matched wildtype (WT, n = 4) controls using TRIzol (Life Technologies) followed by purification using illustra RNA spin Mini kit (GE Healthcare, UK). Then, mRNA was isolated from 10 μg total RNA using Dynabeads Oligo (dT)25 (Thermo Fisher; 61006) according to manufacturer’s instructions. 10% of a total of 150 ng mRNA was used as input, while the rest was incubated with 3 ug anti-m6A polyclonal antibody (Synaptic Systems; 202003) that was pre-conjugated to Dynabeads Protein A (Thermo Fisher; 10001D) in 500 uL IP buffer (50 mM Tris, pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630) for 2 hours at 4°C. After washing the beads twice with IP-buffer and twice with high-salt wash buffer (50 mM Tris pH 7.4, 500 mM NaCl, 0.1% Igepal CA-630) for 5 min each, the m6A-tagged mRNA was eluted using 100 uL IP-buffer containing 6.7 mM N6-Methyladenosine (Sigma-Aldrich; M2780) and 40 U RNase Inhibitor (NEB, M0314S) followed by recovery using RNA Clean and Concentrator-5 spin columns (Zymo; R1015).
The input and m6A-IPed mRNA were subjected to library generation using SMART-seq protocol as described [Nature Protocols 9, 171-181 (2014)]. For first strand cDNA synthesis, the mRNA was mixed with 0.25 µL RNase inhibitor and 1 µL CDS primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) and heated to 70 °C for 2 min. Then the mixture containing 0.5 µL of 100 mM DTT, 0.3 µL of 200 mM MgCl2, 1 µL of 10 mM dNTPs, 0.25 µL RNase inhibitor, 1 µL of 10 µM TSO primer (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’), 2 µL of 5X SMARTScribe RT buffer and 0.5 µL SMARTScribe reverse transcriptase (Takara, 639536) was added to perform reverse transcription. The cDNA was then amplified by Advantage Polymerase Mix (TAKARA, 639201) with IS primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’). After purification with 0.8X AMPure XP beads (Fisher Scientific, A63880), the fragmentation of 100 pg cDNA was performed with EZ Tn5 Transposase (Lucigen, TNP92110). Fragments of cDNA were amplified by KAPA HiFi hotstart readymix (EMSCO/FISHER, KK2601) with the Nextera i7 primer and Nextera i5 primer. The DNA was purified with 0.8X AMPure XP beads and quantified by qPCR with KAPA Library Quantification Kit (Fisher, NC0078468). The DNA from different samples was pooled at equal molar amounts, and the final sequencing library was loaded at concentrations of 2.7 pM and sequenced on a NextSeq 550 (Illumina) for single-end sequencing.

value: hippocampus

tag: disease state

value: AD

tag: fraction

value: m6A IP

tag: rip antibody

tag: replicate


title: 5xFAD, MS1262, m6A-IP, biol rep 1

value: anti-m6A polyclonal antibody (Synaptic Systems; 202003)


title: 5xFAD, vehicle, m6A-IP, biol rep 4


title: hLAB_JUND_Rep2_ChIP

data_processing:
Reads were trimmed using fastp at default settings.
Reads were aligned to the mm10 genome using STAR version 2.7a at default settings
ChIP-seq bedGraphs were generated using bamCompare (from Deeptools) with bam files at default settings and normalized to input
Peaks were called using MACS2 with a cutoff of p < 0.01 and normalized to input
Assembly: hg38
Supplementary files format and content: narrowPeak
Supplementary files format and content: bedGraph

source_name: Myometrium

extract_protocol:
Frozen, crushed human myometrium tissue was fixed with DSG for 1 hour at room temperature, prior to crosslinking with formaldehyde for 10 minutes. After quenching the reaction with glycine for 15 minutes, tissue was lysed with three lysis buffers at 4 degrees and sonicated using a probe sonicator. Lysates were incubated overnight with 5ug of JUND antibody (ab181615), proceeded with an overnight incubation with Dynabeads (protein A). Lysates were reverse crosslinked overnight at 65 degrees and then extracted via phenol-chloroform.
ChIP seq  libraries were prepared for sequencing using standard Illumina HiSeq 2500 protocols
DNA samples were quantified using Qubit High Sensitivity Assay. 3 ng of DNA was used as input for library preparation using the NEB Ultra II DNA Library Prep Kit following the manufacturer’s recommended protocol. In brief, DNA was end-repaired, A-tailed and ligated with Illumina-compatible adapters. Bead size-selection was performed to keep all fragments <700bp, and fragments were enriched with PCR using dual-indexed primers. Final libraries were validated on the Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size and absence of primer dimers, and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Validated libraries were pooled in equimolar quantities and paired-end sequenced on the Illumina Novaseq platform following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length.

value: Myometrium

tag: antibody

value: JUND

tag: phenotype

value: LAB


title: MCF7 cells, control, 24h, H3K9me3 IP, biological replicate 1

description: Library name: MCF7_control_biorep1, H3K9me3 (ChIP)

tag: tissue

value: breast


title: Sorafenib-3_Fraction 2

city: Sevilla

first: Alfonso

last: Rodriguez Gil

email: alfrodgil@gmail.com, arg@us.es

state: Sevilla

address: Avda. Manuel Siurot s/n

department: Oncohematology

country: Spain

institute: Instituto de Biomedicina de Sevilla (IBiS)

description:
Library name: Sample 12
Lib12_S1_trim_nat

library_source: other

data_processing:
RNA-Seq data were first filtered using the FASTQ Toolkit v1.0.0 program and then analyzed using the BaseSpace Onsite v3.22.91.158 from Illumina.
Assembly: GRCh38.p12
Supplementary files format and content: Tab delimited. Raw counts
Library strategy: Ribo-Seq

molecule: other

source_name: Hepatocellular carcinoma

growth_protocol: The HepG2 cell lines was obtained from the American Type Culture Collection (LGC Standards, Spain). The Huh7 cell line was purchased from Apath, LLC (Brooklyn, NY). Both cell lines tested negative for mycoplasma contamination. Cells were cultured in minimal essential medium (MEM) with Earle's balanced salts with L-glutamine (ref. E15-825, PAA Laboratories Inc., Canada) supplemented with 10% fetal bovine serum (FBS, ref. F7524, Sigma Aldrich, USA), 1% sodium pyruvate (ref. S11-003, PAA Laboratories Inc.), 1% non-essential amino acids (ref. M11-003, PAA Laboratories Inc.) and penicillin-streptomycin solution (100 U/ml-100 μg/ml; ref. P11-010, PAA Laboratories Inc.).

extract_protocol:
Polysome profile analysis was carried out in Sfb-treated and control HepG2 cells as previously described 10. Briefly, cells were grown to ca. 70% confluency in 100 mm dishes as above described. Normally, two dishes were used per condition assayed. Before harvesting, 200 μg/ml cycloheximide (ref. C7698, Sigma Aldrich) was added to dishes and incubated for 5 min at 37 ºC. Each dish was then placed on ice, the media aspirated and the cultures washed twice with PBS without Ca2+ and Mg2+ containing 200 μg/ml cycloheximide. Then, 600 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 150 mM NaCl, 10 mM MgCl2, 200 μg/ml cycloheximide, 2 mM DTT, 0.5% NP40) was added to one dish, cells were scraped, and transferred to the second dish. After scraping the cells corresponding to the second dish, the whole juice was transferred to a 1.5 ml-Eppendorf tube. Tubes were incubated at 4 ºC with gentle end-over-end rotation for 10 min and then centrifuged at 16,000 x g for 8 min at 4 ºC in a refrigerated microfuge. The corresponding supernatants were recovered and the A260 measured using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, USA). About 11 A260 units were layered on top of 10-50% (w/v) sucrose gradients prepared in a buffer containing 50 mM Tris-acetate, pH 7.5, 50 mM NH4Cl, 12 mM MgCl2, and 1 mM DTT. The gradients were centrifuged at 260,110 x g (39,000 rpm) in a Beckman SW41Ti rotor at 4 ºC for 2 h 45 min. Fractionation was performed with an ISCO UA-6 system (ISCO, Inc. Lincoln, USA) equipped to continuously monitor the A254.  When required, fractions of 1 ml were collected from the gradients. Fractions corresponding to the low-molecular complex peak and the peaks corresponding to free 40S and 60S ribosomal subunits and 80S ribosomes were pooled and named "low-translated fraction" or V1. Fractions corresponding to the polysome peaks were pooled and named "high-translated fraction" or V2.
Libraries were prepared using the RNA collected from the V1 and V2 fractions described above. Samples were treated with a proteinase K solution (per 1 ml: 37.5 μl 10 % SDS, 7.5 μl 0.5 M EDTA, and 4 μl 20 mg/ml proteinase K, ref. A7932, Sigma Aldrich) for 1 h at 50 ºC. An equal volume of phenol acidic:choroform:isoamyl alcohol (25:24:1, v/v) was added to the sucrose fractions; samples were mixed during 30 s using a vortex and centrifuge 10 min at maximum speed at 4 C. Approximately 80% of the aqueous phase was placed in a new tube and an equal volume of chloroform was added. After mixing for 30 s using a vortex, samples were centrifuged 10 min at maximum speed at 4 ºC. Again, 80% of the aqueous phase was placed in a new tube and the RNA was precipitated using 1:10 of 3 M sodium acetate, pH 5.2 and 1.5 volumes of absolute ethanol. The mixture was incubated overnight at -20 ºC. Samples were then centrifuged at maximum speed for 30 min at 4 ºC, the pellet was washed with 70% ethanol and finally resuspended in RNase-free water.  The concentration and quality of RNAs were assessed with Qubit (QubitTM DNA HS assay, Thermo Fisher Scientific) and a 2100 Bioanalyzed Nano Chip (Agilent Technologies Genomics, USA), respectively. The RNA Integrity Number (RIN) values were > 9 in all the RNA samples. Polyadenylated RNA was isolated from total RNA samples using NEBNext Oligo d(T)25 beads (New England Biolabs, USA) according to the manufacturer's instructions. The same RNA concentration for each sample was used to create the libraries for Illumina Sequencing. Three independent experiments were carried out for the sequencing analysis.

treatment_protocol: Cells were grown in culture flasks at 37 ºC in a humidified incubator with 5% CO2 until reaching a density of 100,000 cells/cm2. Sorafenib (Sfb, Sorafenib tosylate, ref. FS10808; Carbosynth Ltd., Compton, UK) was dissolved in dimethyl sulfoxide (DMSO) as a stock solution (100 mM), aliquoted, and stored at -80 ºC. For drug treatment, cells were plated for 24 h, Sfb was added at a concentration of 10 μM, and lysates were obtained after a 12 h treatment. Control cells were treated with the vehicle DMSO.

value: Hepatocellular carcinoma

value: epithelial like

tag: genotype

value: WT

tag: treatment

value: Sorafenib


title: GE_1_96h

tag: cell type

value: Primary CB-derived HSPCs


title: Sorafenib-3_Fraction 1

description:
Library name: Sample 11
Lib11_S11_trim_nat

tag: cell line


title: Sorafenib-2_Fraction 2

description:
Library name: Sample 10
Lib10_S10_trim_nat


title: 5xFAD, vehicle, m6A-IP, biol rep 3

value: vehicle


title: hLAB_Input


title: hLAB_JUND_Rep1_ChIP


title: OVCAR5 ALDHplus RNA rep1

value: Ovary

value: ALDH plus


title: 5xFAD, vehicle, m6A-IP, biol rep 2


title: Sorafenib-2_Fraction 1

description:
Library name: Sample 9
Lib9_S9_trim_nat


title: 5xFAD, MS1262, m6A-IP, biol rep 4


title: hTNIL_JUND_Rep3_ChIP

value: TNIL


title: Sorafenib-1_Fraction 2

description:
Library name: Sample 8
Lib8_S8_trim_nat


title: wild-type, no treatment, m6A-IP, biol rep 4

value: hippocampus

value: wild-type


title: Sorafenib-1_Fraction 1

description:
Library name: Sample 7
Lib7_S7_trim_nat


title: 5xFAD, MS1262, m6A-IP, biol rep 2

value: AD

value: m6A IP


title: hTNIL_JUND_Rep2_ChIP

value: Myometrium


title: 5xFAD, vehicle, m6A-IP, biol rep 1

value: anti-m6A polyclonal antibody (Synaptic Systems; 202003)


title: hTNIL_JUND_Rep1_ChIP

value: JUND


title: Control-3_Fraction 2

description:
Library name: Sample 6
Lib6_S6_trim_nat

value: Control


title: hTNIL_Input


title: hCO_XG_d65_aggr

city: STANFORD

first: Yuki

last: Miura

state: California

address: 318 Campus Drive, W200

department: Department of Psychiatry and Behavioral Sciences

institute: Stanford University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Quality control, UMI counting of Ensembl genes, and aggregation of samples were performed by the ‘count’ and ‘aggr’ functions using Cell Ranger software (version, Cellranger-6.0.1) on the 10x cloud platform
Assembly: Human: GRCh38
Supplementary files format and content: Count matrices, features, and barcodes (barcode-1 represents organoids cultured in control medium, barcode-2 represents organoids cultured in XG-supplemented medium)

source_name: hiPS cell-derived cortical organoids

extract_protocol:
Cells were loaded onto a Chromium Single cell 3’ chip (Chromium Chip B Single Cell Kit, 10x Genomics, PN-1000154) with Chromium Single Cell 3’ Library & Gel Bead kit v3 (10x Genomics, PN-1000075) and proceeded according to manufacturer’s instructions.
cDNA library was generated with the Chromium Single Cell 3’ GEM, Library & Gel Bead kit v3 (10x Genomics, PN-1000078) according to manufacturer’s instructions.

value: hiPS cell-derived cortical organoids

value: Day 65

value: mixed samples (control and XG-supplemented medium)


title: wild-type, no treatment, m6A-IP, biol rep 3

value: WT


title: Control-2_Fraction 1

description:
Library name: Sample 3
Lib3_S3_trim_nat

value: Hepatocellular carcinoma

value: epithelial like


title: wild-type, no treatment, m6A-IP, biol rep 1


title: Y21SS00323

first: Tianyuan

last: Zhang

address: The First Affiliated Hospital of Jinan University

institute: Jinan university

description: 10x Genomics

data_processing:
Single cell RNA-seq raw data were processed by Cell Ranger version 3.1.0 (10X Genomics) and aligned to the GRCm38 (mm10) mouse reference genome and GRCh38 (h19) human genome reference sequence
Seurat V4.05 was used for the downstream analysis, including tSNE, heatmap, and violin plots  We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Assembly: h19 (and mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Humanized mouse with humanized T cells, MCAO, Day3

extract_protocol:
Human peripheral blood mononuclear cells (PBMCs) were transferred into immunodeficient mice to generate a mouse model with humanized T cells. Ischemic hemispheres of humanized mice were perfused with ice-cold saline and freshly harvested at 0 or 3 days after tMCAO. Single cell suspensions were prepared for flow cytometry. Single cells were incubated with FITC anti-human CD45 and APC/Cyanine7 anti-mouse CD45 for 30 minutes on ice at 4 ℃ in the dark before stained with 7-AAD for 5 minutes. The live CD45high cells (human and mouse) were sorted by FACS Aria SORP (BD Bioscience). At last, we mix human and mouse CD45high cells with equal proportion
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Humanized T cells

value: Ischemic hemispheres

value: B-NDG mice

value: 8-12 weeks old


title: Y21SS00296

description: 10x Genomics

source_name: Humanized mouse with humanized T cells, Control

value: hemispheres


title: 5xFAD, MS1262, Input, biol rep 4

value: hippocampus

value: AD

value: input


title: Control-2_Fraction 2

description:
Library name: Sample 4
Lib4_S4_trim_nat


title: Control-1_Fraction 2

description:
Library name: Sample 2
Lib2_S2_trim_nat


title: 5xFAD, MS1262, Input, biol rep 2


title: H6_HF16

first: Fabio

last: Martelli

address: Via Olgettina 58

institute: IRCCS Policlinico San Donato

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39).
RNA-seq: The remaining reads were mapped to the reference human genome GRCh38, using STAR aligner (version 2.5.3a)
RNA-seq: Uniquely mapped reads were assigned to the corresponding genes using the featureCounts (version1.6.4). Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode release 28).
circRNA: circRNA quantification was performed  with CIRIquant v1.2 (CIRIquant command) using same genome build and annotation as for the RNAseq pipeline.
circRNA: The matrix of back spliced junction (bsj) expression level was produced from the generated GTF files with "prep_CIRIquant" of CIRIquant toolkit.
Assembly: GRCh38
Supplementary files format and content: RNA-seq: Matrix tables with raw gene counts for every gene and every sample
Supplementary files format and content: circRNAcomma separated matrix tables with raw bsj counts for every detected bsj and every sample

source_name: Heart

extract_protocol: NGS libraries were generated with the TruSeq Stranded Total RNA- rRNA protocol. Libraries were barcoded, pooled and sequenced on Illumina Nova-Seq 6000 or Illumina NextSeq 500 sequencing system in paired-end reads mode, with reads 100-150nt long.

value: Heart left ventricle

tag: condition

value: Heart Failure


title: Control-1_Fraction 1

description:
Library name: Sample 1
Lib1_S1_trim_nat

value: Control


title: 5xFAD, MS1262, Input, biol rep 3


title: H5_HF8


title: 5xFAD, MS1262, Input, biol rep 1


title: oeRNH1_RNAseq_rep2

first: Ying

middle: liang

last: Sheng

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

data_processing:
the reads generated by RNA-seq were aligned to human (hg38) reference genome using STAR.
Assembly: hg38
Supplementary files format and content: TPM

extract_protocol:
Total RNAs were extracted with TRIzol.
RNA sequencing libraries were constructed using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme).

value: Human embryonic kidney


title: siRif1_8C_rep3

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

institute: Helmholtz Zentrum München

data_processing:
library strategy: Low-input LaminB1 DamID
Samples were sequenced using HiSeq2500 platform in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic. Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools. Duplicates were removed using picard to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values (average signal of all three biological replicates).
Assembly: GRCm38
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD coordinates are provided in bed files.

source_name: 8-cell embryo

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
For DamID sample collection, the zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C for 5 minutes. Polar bodies were separated from the embryos by gentle pipetting after trypsin treatment and discarded. For each replicate, a pool of 16-24 blastomeres (four to six 4-cell embryos or two to three 8-cell embryos) was collected in 2 μL DamID buffer (10 mM TRIS acetate pH 7.5, 10 mM magnesium acetate, 50 mM potassium acetate) and stored at -80 °C until downstream processing.
Approximately 300 ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation, DNA was PCR amplified with Illumina primers for 8 cycles.

treatment_protocol: Early zygotes were collected and injected with 20 µM siRNA at 17-18 hours post-hCG injection, followed by culture in KSOM until the late 2-cell stage. At 46-48 hphCG, both blastomeres of the 2-cell embryos were injected with 250 ng/μL Tir1, 100 ng/μL membrane-eGFP, and 20 ng/μL AID-Dam-LaminB1, and subsequently cultured in medium containing auxin (500 μM). For mapping LADs in the 4-cell stage, auxin was removed at 54 hours post-hCG injection, and late 4-cell embryos were collected at 60–62 hours post-hCG injection. For DamID in the late 8-cell stage, auxin was washed out from 66 to 72-74 hours post-hCG injection, and embryos were cultured in KSOM.

value: 8-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: H2_C16


title: oeRNH1_RNAseq_rep1


title: siRif1_8C_rep2


title: 5xFAD, vehicle, Input, biol rep 4

value: vehicle


title: H1_C8


title: wild-type, no treatment, m6A-IP, biol rep 2

value: wild-type

value: WT

value: m6A IP

value: anti-m6A polyclonal antibody (Synaptic Systems; 202003)


title: Control-3_Fraction 1

description:
Library name: Sample 5
Lib5_S5_trim_nat

value: Hepatocellular carcinoma

value: epithelial like


title: oeFlag_RNAseq_rep2


title: T47D, shZHX2, Hypoxia, replicate 1

first: gao

last: chuan

address: bayi road

institute: Wuhan university

data_processing:
The ATAC-seq data were first quality-checked by FastQC and then aligned to the hg38 reference genome using bowtie2 with default parameters. Subsequently, reads that aligned multiple times and PCR duplicates were removed using samtools. Peaks were called using MACS2.
Assembly: hg38
Supplementary files format and content: bigWig, Peak

source_name: Breast

extract_protocol:
Cells were harvested from cell culture and lysed in lysis buffer. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 50,000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 °C. The transposed DNA fragments were purified immediately after with MinElute PCR Purification Kit (Qiagen).
After Samples were PCR-amplified using NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

value: Breast

value: Tumor cell

value: Hypoxia


title: 5xFAD, vehicle, Input, biol rep 3

value: hippocampus

value: AD

value: input


title: G6_HF15

value: Heart left ventricle

value: Heart Failure


title: oeFlag_RNAseq_rep1

value: Human embryonic kidney


title: siRif1_4C_rep3

source_name: 4-cell embryo

value: 4-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: 5xFAD, vehicle, Input, biol rep 2

value: vehicle


title: siRif1_8C_rep1

value: 8-cell embryo


title: G5_HF7


title: 5xFAD, vehicle, Input, biol rep 1


title: HEK293T cells, oeRNH1_RIANseq_rep2

data_processing:
the reads generated by RIAN-seq were aligned to human (hg38) reference genome using Bowtie2
Reads of low mapping quality were filtered out utilizing SAMtools with the parameters ‘-F 1804 -f 2 -q 20’. potential PCR duplicates were eliminated using Sambamba.
The Bigwig files were generated by DeepTools with the parameter ‘-normalizeUsing RPKM -binSize 1 --extendReads 200’.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
The genomic DNA was purified from HEK293T or mES cells via phenol/chloroform extraction and ethanol precipitation, or genomic DNA extraction kit.
1 µg DNA was incubated with NEB restriction enzyme mix (Alu I, Mbo I, Mse I, Dde I), Nuclease P1, T5 exonuclease, Lambda exonuclease at 4 °C for 2 hr. As controls, RNase H (NEB, M0297S) was added during the incubation stage. 0.2 µL of Proteinase (Thermo Scientific, EO0491) was added before incubation at 55 °C for 30 min and 70 °C for 30 min. 0.3 µL 1M Tris-HCl (pH 8.0), 0.15 µL 1M MgCl2, 1.5 µL PEG200, 4.8 µL 50% PEG8000 and 1 µL transposase (Vazyme, TD501) were added and incubated at 55 °C for 10 min. The transposition was stopped by the addition of 5 µL 0.25% SDS and incubation for 5 min at room temperature. Transposed DNA was gap-filled by addition of 2 µL Bst3.0 DNA polymerase (NEB, M0374S) and 25 µL NEBNext Q5 HotStart HiFi PCR Master Mix (NEB, M0543S). The mixture was incubated at 72 °C for 15 min and 80 °C for 10 min. For library amplification, the mixture was mixed with a barcoded i5 primer and a barcoded i7 primer PCR was performed to amplify the libraries using the following PCR conditions: 98 °C for 45 s; thermocycling for 10 cycles at 98 °C for 15 s, 65 °C for 75 s; followed by 65 °C for 5 min. The final libraries were purified with the 1× AMPure beads (Beckman, A63882) size selection and were subjected to next-generation sequencing.


title: siRif1_4C_rep2


title: wild-type, no treatment, Input, biol rep 4

value: wild-type

value: WT


title: G2_C15

value: Control


title: HEK293T cells, oeRNH1_RIANseq_rep1


title: siRif1_4C_rep1


title: wild-type, no treatment, Input, biol rep 3


title: F6_HF14


title: HEK293T cells, oeFlag_RIANseq_rep2


title: siControl_8C_rep3

value: siControl


title: wild-type, no treatment, Input, biol rep 2


title: siControl_8C_rep2


title: HEK293T cells, oeFlag_RIANseq_rep1


title: wild-type, no treatment, Input, biol rep 1


title: F2_C14


title: siControl_8C_rep1


title: siControl_4C_rep3


title: HEK293T cells, Triptolide_RIANseq_rep1


title: HEK293T cells, Triptolide_RIANseq_rep2


title: F2_C14_lib2


title: RNA_dTAG_GPATCH1-dTAG_E14_Rep2

description: Library name: Sample 8

data_processing:
The paired raw reads were quality-checked using FastQC (v0.11.9) (Babraham Institute).
Adapter sequences and low-quality reads were trimmed using Trim Galore (v0.6.6) (Babraham Institute) with the parameter -q 25.
The trimmed reads were then aligned to the mouse mm10 and human hg19 assemblies using STAR (v2.7.5c), following the preprocessing instructions specified for JUM.
Differential expression analysis was then performed using DESeq2 R package (v1.26.0). Differentially spliced introns were identified using JUM (v3.0.0), with splicing events deemed significant at a p-value < 0.05. Additionally, a minimum threshold of 5 supporting reads was applied to ensure event reliability.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: Mouse serum ES cells (R1) (used in CUT&RUN validation) were cultured on 0.1% gelatin-precoated dishes in Knockout DMEM (10829-018; Gibco) containing 15% FBS (A5669701; Gibco), Sodium Pyruvate (11360-070; Gibco), MEM-NEAA (11140050; Gibco), Pen Strep glutamine (10378-016; Gibco), 2-mercaptoethanol (21985023; Gibco), PD0325901(Selleck; S1036), CHIR99021(Selleck; S1263), Mouse LIF Protein (ESG1107; Millipore) at 37 °C, 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol
Human DLD-1 total RNA was included as a spike-in control and mixed with the extracted RNA samples for normalization during downstream sequencing analysis. Ribosomal RNA (rRNA) was removed. The remaining RNA was used for subsequent sequencing libraries preparation with Stranded mRNA-seq Lib Prep Module for Illumina (Abclonal).

treatment_protocol: Cells were treated with either DMSO (control) or dTAG-13 (Tocris) at a final concentration of 200 nM for 4 hours to induce protein degradation.

value: Embryo stem cell

value: 200nM dTAG-13


title: RNA_dTAG_GPATCH1-dTAG_E14_Rep1

description: Library name: Sample 7


title: HEK293T cells, DRB_RIANseq_rep2


title: F1_C6


title: HEK293T cells, DRB_RIANseq_rep1


title: RNA_DMSO_GPATCH1-dTAG_E14_Rep2

description: Library name: Sample 6

value: DMSO


title: G1_C7


title: siControl_4C_rep1


title: HEK293T cells, DMSO_RIANseq_rep2


title: G13D,rep3

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

data_processing:
Raw reads were aligned to mm10 genome using STAR
The number of raw counts in each known gene were enumerated using htseq-count from the HTSeq package. Differential expression between samples and across different conditions will be assessed for statistical significance using the R/ Bioconductor package DESeq2
Assembly: mm10
Supplementary files format and content: raw count in xlsx format

source_name: Colon

growth_protocol: Mouse colon epithelial cells were maintained in RPMI + GlutaMAX supplemented  with 10% fetal bovine serum, and 1% antibiotic in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA extracted using TRIzol (sigma) per manufacturer's intructions
RNA libraries for RNA-seq were constructed following the Illumina Stranded mRNA Prep Ligation guide protocol (Illumina Document #1000000124518 v03)

value: Colon

value: colon epithelial

value: Apc-/- KRAS G13D


title: E6_HF13

value: Heart left ventricle


title: RNA_dTAG_DHX35-dTAG_E14_Rep2

description: Library name: Sample 4


title: RNA_DMSO_GPATCH1-dTAG_E14_Rep1

description: Library name: Sample 5


title: G13D,rep2


title: E5_HF5

value: Heart Failure


title: F5_HF6


title: RNA_dTAG_DHX35-dTAG_E14_Rep1

description: Library name: Sample 3


title: HEK293T_Spike-in_RNASEH

data_processing:
the reads generated by RIAN-seq were aligned to human (hg38) reference genome using Bowtie2
Reads of low mapping quality were filtered out utilizing SAMtools with the parameters ‘-F 1804 -f 2 -q 20’. potential PCR duplicates were eliminated using Sambamba.
The Bigwig files were generated by DeepTools with the parameter ‘-normalizeUsing RPKM -binSize 1 --extendReads 200’.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: RIAN-seq

extract_protocol:
The genomic DNA was purified from HEK293T or mES cells via phenol/chloroform extraction and ethanol precipitation, or genomic DNA extraction kit.
1 µg DNA was incubated with NEB restriction enzyme mix (Alu I, Mbo I, Mse I, Dde I), Nuclease P1, T5 exonuclease, Lambda exonuclease at 4 °C for 2 hr. As controls, RNase H (NEB, M0297S) was added during the incubation stage. 0.2 µL of Proteinase (Thermo Scientific, EO0491) was added before incubation at 55 °C for 30 min and 70 °C for 30 min. 0.3 µL 1M Tris-HCl (pH 8.0), 0.15 µL 1M MgCl2, 1.5 µL PEG200, 4.8 µL 50% PEG8000 and 1 µL transposase (Vazyme, TD501) were added and incubated at 55 °C for 10 min. The transposition was stopped by the addition of 5 µL 0.25% SDS and incubation for 5 min at room temperature. Transposed DNA was gap-filled by addition of 2 µL Bst3.0 DNA polymerase (NEB, M0374S) and 25 µL NEBNext Q5 HotStart HiFi PCR Master Mix (NEB, M0543S). The mixture was incubated at 72 °C for 15 min and 80 °C for 10 min. For library amplification, the mixture was mixed with a barcoded i5 primer and a barcoded i7 primer PCR was performed to amplify the libraries  using the following PCR conditions: 98 °C for 45 s; thermocycling for 10 cycles at 98 °C for 15 s, 65 °C for 75 s; followed by 65 °C for 5 min. The final libraries were purified with the 1× AMPure beads (Beckman, A63882) size selection and were subjected to next-generation sequencing.

value: Human embryonic kidney

value: Treatment with 25 U RNase H and addition of spike-in for normalization


title: E1_C5


title: G13D,rep1


title: E2_C13


title: HEK293T_Spike-in_Ctrl_rep2

value: Addition of spike-in for normalization


title: G12V,rep3

value: Apc-/- KRAS G12R


title: D7_HF20


title: HEK293T_Spike-in_Ctrl_rep1


title: siControl_4C_rep2

value: 4-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: G12V,rep2


title: mESC_Spike-in_RNASEH

data_processing:
the reads generated by RIAN-seq were aligned to mm10 reference genome using Bowtie2
Reads of low mapping quality were filtered out utilizing SAMtools with the parameters ‘-F 1804 -f 2 -q 20’. potential PCR duplicates were eliminated using Sambamba.
The Bigwig files were generated by DeepTools with the parameter ‘-normalizeUsing RPKM -binSize 1 --extendReads 200’.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: RIAN-seq

value: embryonic stem cells


title: RNA_DMSO_DHX35-dTAG_E14_Rep1

description: Library name: Sample 1


title: HEK293T-100U-RNASEH

value: Treatment with 100 U RNase H


title: D6_HF12


title: G12V,rep1


title: RNA_DMSO_DHX35-dTAG_E14_Rep2

description: Library name: Sample 2


title: D5_HF4


title: D1_C4

value: Control


title: HEK293T-50U-RNASEH

value: Treatment with 50 U RNase H


title: D2_C12


title: HEK293T_WT_rep2


title: C7_HF19


title: mESC_Spike-in_Ctrl_rep2


title: HEK293T cells, DMSO_RIANseq_rep1


title: mESC_WT_rep2


title: G12D,rep3

value: Apc-/- KRAS G12D


title: mESC_Spike-in_Ctrl_rep1


title: HEK293T_WT_rep1


title: Hi-C, T47D, shZHX2, Hypoxia, replicate 1

data_processing:
In situ Hi-C datasets were processed using the HiC-Pro pipeline with default parameters as previously described. MboI served as the restriction enzyme, and reads were aligned to the hg38 human reference genome. Invalid pairs and PCR duplications were filtered out using HiC-Pro.
Assembly: hg38
Supplementary files format and content: cool, ICE normalized 50kb resolution hic matix

extract_protocol:
T47D cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature and quenched with 0.125M final concentration of glycine for 5 minutes (cells treated under hypoxia were fixed in hypoxia chamber). Post-fixation, the cells were pelleted at 300g for 5 minutes at 4°C, washed with cold PBS, and lysed in a solution containing 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, and protease inhibitors (Sigma) for 15 minutes on ice. Endogenous nucleases were inactivated with 0.3% SDS and incubated for 7 minutes at 62°C. This was followed by quenching with Triton X-100 and water at 37°C for 15 minutes. Chromatin was digested overnight with 100U MboI (NEB) at 37°C with rotation. Post digestion, the reactions were incubated at 62°C for 20 minutes to inactivate MboI and then cooled to room temperature. Biotin-14-dCTP (Invitrogen) was used to mark the digested chromatin, and fragments were ligated using 50U T4 DNA ligase (NEB). The ligated DNA was purified using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer's instructions.
The purified DNA was sheared into 300- to 500-bp fragments using an LE220 Covaris Focused-ultrasonicator and size-selected using AMPure XP beads. The DNA fragments were then blunt-end repaired, A-tailed, and ligated with sequencing adaptors. This was followed by biotin-streptavidin–mediated pull-down and PCR amplification. The final Hi-C libraries were quantified and sequenced on the MGI-seq platform, ensuring deep coverage for comprehensive 3D genome architecture analysis.

value: Breast

value: Tumor cell

value: Hypoxia


title: D3_C20


title: C5_HF3


title: Hi-C, T47D, shCtrl, Hypoxia, replicate 2

value: shCtrl


title: PKI_1

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

description:
Library name: Sample 7
10X Genomics Chromium Next GEM Single Cell 3’v3.1

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.0.1 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.0.1 (STAR 2.7.2a).
Assembly: Mouse mm10
Supplementary files format and content: Cell ranger filtered matrix H5 files

source_name: Tail Epidermis

extract_protocol:
Keratinocytes were isolated from BCC mice and controls 28 days post-tumor induction. Tail skin was removed from mice, cleaned using 10% iodine in PBS and washed with sterile PBS several times. Each tail was cut into pieces and then incubated overnight at 4°C in 2.5 parts of 0.25% trypsin (Gibco 15050-057) and 1 part of 5U/mL dispase (Stem Cell Technologies 07913). The next day, the epidermis was scraped from the dermis and minced in 0.25% trypsin with EDTA (Gibco 25200056). Trypsin was neutralized in DMEM with 10% FBS and cells were strained in a 100μm cell strainer followed by a 40μm cell strainer. After centrifugation at 500G for 8 minutes, cells were collected in EpiLife media and processed for single-cell RNAseq.
The cellular samples were loaded in the lanes according to the 10X Genomics Chromium Next GEM Single Cell 3’v3.1 (Dual Index) User Guide with a single capture lane per sample. All subsequent steps of library preparation and quality control were performed as described in the user guide on the Chromium Connect. Two NovaSeq runs for GEX were performed (indicated as Seq1 and Seq2).

value: Tail Epidermis


title: C3_C19

value: Heart left ventricle


title: PKI_2

description:
Library name: Sample 8
10X Genomics Chromium Next GEM Single Cell 3’v3.1


title: Gnas-eKO_2

description:
Library name: Sample 6
10X Genomics Chromium Next GEM Single Cell 3’v3.1


title: HEK293T-25U-RNASEH

value: Human embryonic kidney

value: Treatment with 25 U RNase H


title: Cre-R3-1week

city: Ottawa

first: Yalun

last: Zhu

address: 501 Smyth Road

institute: University of Ottawa

description: Library name: Sample6

data_processing:
Transcript quantification for each sample was performed using Kallisto (v0.46.2) with the GRCm38 transcriptome reference and the -b 50 bootstrap option.
Assembly: The R package Sleuth (v0.30.1) was then used to construct general linear models for the log-transformed expression of each gene across experimental conditions.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Ovarian surface epitheliam

extract_protocol:
Total RNA was extracted with the RNeasy Mini kit (Qiagen)
mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs).

value: Ovarian surface epitheliam

value: Lats1/2 knockout


title: G12R,rep3

value: Colon

value: colon epithelial

value: Apc-/- KRAS G12V


title: G12R,rep2


title: Hi-C, T47D, shZHX2, Hypoxia, replicate 2


title: G12D,rep1


title: G12R,rep1


title: C6_HF11

value: Heart Failure


title: mESC_WT_rep1

value: embryonic stem cells


title: G12D,rep2


title: Hi-C, T47D, shCtrl, Hypoxia, replicate 1


title: Hi-C, T47D, shCtrl, Normoxia, replicate 2

value: Normoxia


title: Gnas-eKO_1

description:
Library name: Sample 5
10X Genomics Chromium Next GEM Single Cell 3’v3.1


title: SmoM2_2

description:
Library name: Sample 4
10X Genomics Chromium Next GEM Single Cell 3’v3.1


title: Cre-R1-1week

description: Library name: Sample4


title: Cre-R2-1week

description: Library name: Sample5


title: C2_C11

value: Control


title: Hi-C, T47D, shCtrl, Normoxia, replicate 1

value: Breast


title: C1_C3


title: GFP-R3-1week

description: Library name: Sample3

value: WT


title: Con_2

description:
Library name: Sample 2
10X Genomics Chromium Next GEM Single Cell 3’v3.1


title: B7_HF18


title: Con_1

description:
Library name: Sample 1
10X Genomics Chromium Next GEM Single Cell 3’v3.1


title: B6_HF10


title: GFP-R2-1week

description: Library name: Sample2


title: GFP-R1-1week

description: Library name: Sample1


title: B5_HF2


title: scRNA, Handling_3h_S6

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

institute: ETH Zürich

description: Library name: S6

data_processing:
Pre-processing was performed using cellranger-arc 2.0.2 using the optimized mm10 transcriptome as described previously (Pool et al., 2023).
A RNA quantification using alevin-fry (He et al., 2022) was also performed to estimate splicing proportions. Decontamination was performed using cellbender 0.3.0 (Fleming et al., 2023) with custom initialization, and doublet identification with scDblFinder 1.19.0 (Germain et al., 2022). For the RNA modality, scDblFinder was run using standard parameters twice (i.e. with two seeds) and the scores averaged, the AMULET method was used on the ATAC modality. Cells were excluded as doublets if they were called as such using both scDblFinder runs, or if their mean doublet score was above 0.2 and their amulet q-value below 0.01. Only cells with at least 500 fragments (after decontamination), less than 60% contamination, less than 1% mitochondrial reads, more than 20% unspliced fragments (before decontamination) and less than 50% of the fragments assigned to the top 10% features were used for further analysis.
Cell annotation was performed based on the RNA modality (see publication for details).
Assembly: mm10
Supplementary files format and content: Cellranger barcodes, counts and feature files, along with a csv of cell annotations.

source_name: ventral hippocampus

extract_protocol:
Nuclei isolation was performed similarly as for the bulk ATAC-Seq, with the addition of RNase inhibitors as previously described (Grandi et al., 2022). All steps were performed on ice. Briefly, one vHC was homogenized in lysis buffer (26 mM Sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH (pH 7.8), 1 mM DTT, 0.5 mM Spermidine, 0.15 mM Spermine, 0.3% NP-40, Complete protease inhibitor, 0.2 U/μl RNAse inhibitor in nuclease-free water) by 10 strokes with pestle A and 20 strokes with pestle B. The sample was filtered through a 70 μm Flowmi strainer and centrifuged for 5 min at 400 g at 4°C. Supernatant was removed and additional lysis buffer was added to resuspend the pellet. The sample was then mixed with 50% Iodixanol solution (30 mM KCl, 26 mM Sucrose, 10 mM MgCl2, 20mM Tricine-KOH (pH 7.8), 50% Iodixanol solution in nuclease-free water) and underlaid by 30% Iodixanol solution (50% Iodixanol solution in lysis buffer) and 40% Iodixanol (50% Iodixanol solution in lysis buffer) layers. The sample was centrifuged for 20 min at 3000 g at 4°C with brakes off. The nuclei band was collected and mixed with ATAC buffer (10 mM NaCl, 10 mMTris-HCl (pH7.5), 3 mM MgCl2, 0.1% Tween20, 0.2 U/μl RNase inhibitor in nuclease-free water) before the nuclei count was assessed. The sample was centrifuged for 5 min at 500g at 4°C and supernatant was removed. Diluted nuclei buffer (0.1 M DTT, 1 U/μl RNase inhibitor, 1X Nuclei buffer (10X) in nuclease-free water) was added to achieve the desired nuclei concentration.
10X Multiome libraries were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (CG000338, Rev. F, 10X Genomics) with a targeted nuclei recovery of 10’000 nuclei (1 sample failed due to clogging). 7 cycles were performed for sample index PCR during ATAC library preparation. 6 cycles were used for cDNA amplification and a total of 13 cycles was performed for sample index PCR for gene expression library preparation. RNA integrity was assessed on an Agilent Tapestation, according to the manufacturer’s protocol. Samples of each library type were pooled. Both libraries (gene expressions and ATAC) were then sequenced on one Illumina X Plus 25B flow cell on individual lanes with an adjusted read configuration (150-10-24-150 bp).

value: ventral hippocampus

tag: Sex

value: Female

tag: ars timepoint

value: Handling


title: scRNA, Handling_Control_S7

description: Library name: S7

tag: batch


title: Mouse brain inoculated with SB28 tumor cells, A1

city: San Francisco

first: Hideho

last: Okada

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

description:
Library name: A1
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger (v1.3.1) pipeline to generate FASTQ files.
FASTQ sequencing files and the H&E staining image files were integrated using the 10x Genomics Space Ranger (v1.3.1) pipeline.
Initial count matrices for each unique molecular identifier (UMI) at every location was constructed using the mouse reference (refdata-gex-mm10-2020-A), and output files were generated for subsequent analyses.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scale_factors_json.json.gz: scale factors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: brain

growth_protocol: SB28 tumor cells (10,000 cells/uL/mouse) were inoculated intracerebrally targeting right striatum of 5-7 week-old female C57BL/6J mice.

extract_protocol:
FFPE tissue blocks were made from tumor-harboring mouse brain tissues immediately post-euthanasia and cardiac perfusion with PBS, and 5 µm-thick sections were mounted onto each spatially barcoded capture area of the Visium Spatial Gene Expression slide.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent Kit according to manufacturer’s protocol.

value: brain

value: mouse syngeneic glioma cell

tag: age

value: 8-10 weeks old

tag: strain


title: Mouse brain inoculated with SB28 tumor cells, B1

description:
Library name: B1
FFPE Spatial transcriptome sequencing


title: scRNA, Restraint_3h_S8

description: Library name: S8


title: scRNA, Handling_15min_S9

description: Library name: S9


title: B3_C18

value: Heart left ventricle


title: Ac4ManNAz-treated, rep 3

city: Nijmegen

first: Daan

last: Smits

address: Geert Grooteplein 26

department: MBS

country: Netherlands

institute: RadboudUMC

description:
Library name: DS006
rRNA depletion, strand-specific library

data_processing:
The fluorescence image files obtained from the Illumina platform were processed into short reads (raw data) in FASTQ format through base calling, containing both sequence and quality information73. Quality control was performed using Fastp74 (v0.23.1) to remove reads with adapter contamination, over 10% uncertain bases (N), or more than 50% low-quality bases (Phred quality <5). Clean reads were then aligned to the reference genome using Hisat275, which efficiently processes large datasets and ensures high-precision mapping and junction read detection. Stringtie76 (v1.3.3) was used to assemble and quantify transcripts based on mapping results, with library-specific parameters enhancing accuracy. Transcripts from concatenated samples were merged, removing those with uncertain strand orientation or lengths under 200 nt, and compared against known databases using Gffcompare (v0.10.6) to filter known transcripts and predict coding potential. Finally, transcript expression levels were quantified using fragments per kilobase of transcripts per million mapped reads (FPMK).
Assembly: mm18
Supplementary files format and content: csv files containing FPKM values for each sample

source_name: melanoma

growth_protocol: B16F10-OVA melanoma cells were maintained in glutamate-containing RPMI supplemented with 1% sodium pyruvate, 10% FCS and 1% Pen/Strep

extract_protocol:
RNA was isolated according to manufacturer instruction of the Aurum™ Total RNA Mini Kit (Bio-Rad, Cat# 7326820). Afterwards, RNA concentration was measured using a Nanodrop™ 2000 spectrophotometer (Thermo Scientific™), where samples with ratio of absorbance at 260/280 nm >1.8 and concentration >100 ng/µl (in 30 µl) were further used for bulk RNA sequencing
Total RNA is used as input material for the RNA sample preparations. rRNA is removed from total RNA by using specific probes. Fragmentation is carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA is synthesized using random hexamer primer and reverse transcriptase. Then the second strand of cDNA is synthesized by adding buffer and dNTPs (dTTP in dNTP is replaced by dUTP). The synthesized double-stranded cDNA is treated by terminal repair, adding A, connecting adaptors, and PCR enrichment is performed after fragment selection. In order to select cDNA fragments with a length of 370-420bp, PCR products are purified with AMPure XP beads to obtain strandspecific library. After the library construction is completed, preliminary quantification is carried out using Qubit. Subsequently, the inserted fragments of the library are detected. Once the inserted fragments meet expectations, the effective concentration of the library is accurately quantified using qRT-PCR to ensure the quality of the library. The qualified libraries are pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol: Treatment with 50 µM Ac4ManNAz was initated at day 0 and RNA was isolated at day 5. In between, cells were passaged at day 3.

value: melanoma

value: cancer cell

value: Ovalbumin-expressing

value: Ac4ManNAz 5-day metabolic labelling


title: Untreated, rep 3

description:
Library name: DS005
rRNA depletion, strand-specific library

value: Untreated


title: scRNA, Restraint_45min_S5

description: Library name: S5


title: Ac4ManNAz-treated, rep 2

description:
Library name: DS004
rRNA depletion, strand-specific library


title: SmoM2_1

description:
Library name: Sample 3
10X Genomics Chromium Next GEM Single Cell 3’v3.1

value: Tail Epidermis


title: B1_C2


title: Untreated, rep 2

description:
Library name: DS003
rRNA depletion, strand-specific library


title: scRNA, Handling_15min_S4

description: Library name: S4


title: neurons - Sheep IgG size matched input

first: Fiona

last: Haward

address: Life Sciences, Dow St

institute: University of Dundee

description: Sheep IgG IP seCLIP library

data_processing:
Libraries were sequenced using the Illumina NextSeq Mid Output (150 cycle flow cell) platform to yield 2x75bp reads. Only read 1 was processed further for analysis as read 2 does not contain additional information (consistent with single-end (se) CLIP protocol).
Barcodes were extracted using umi_tools in extract mode, then adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) trimmed from the extracted reads using cutadapt.
Reads were aligned to the mouse genome (mm10) with gencode vM24 annotation using STAR version 2.5.2b, then demultiplexed using umi_tools in dedup mode to remove PCR duplicates.
Bedgraph files were generated using deeptools, options -bs 10 --Offset 1 1  -of bedgraph
Assembly: mm10
Supplementary files format and content: Bedgraph files have the counts of reads starting within the 10bp windows, read start sites should be 1 nt downstream of crosslinked nucleotides.

source_name: Primary cortical neurons

growth_protocol: Primary cortical neurons were isolated from brain cortices of E18 embryos. Cells were cultured in vitro on PDL-coated plates for 16 days prior to harvesting. 5x10cm dishes were used per sample

extract_protocol:
Lysis steps for seCLIP were performed as described previously (Van Nostrand et al, 2017).
Lysates were precleared with protein G dynabeads (Thermo Fisher Scientific) at 4°C for 1hour, prior to immunoprecipitation with 50µl of protein G dynabeads preincubated with 5 µg of either RNMT, or isotype control antibody overnight at 4°C. 10% of each sample was subsequently removed to serve as the size-matched input control. IP samples were were washed three times for 5 minutes with high salt wash buffer supplemented with 2M urea. Downstream library preparation was performed as described previously (Van Nostrand et al, 2017). Libraries underwent sequencing using the Illumina MiSeq v3 150 flow cell (2x75bp reads).

treatment_protocol: On day 2 after plating all cells were treated with AraC (2.5uM) for 24hrs. After 16 DIV, cells were washed once with cold PBS and either crosslinked using 254nm UV light (400mJ/cm2) or non-crosslinked prior to snap freezing on dry ice.

value: Primary cortical neurons

value: Sheep IgG (Fisher, 31243)

value: derived from E18 embyros and harvested after 16 DIV

tag: uv treatment

value: Non-crosslinked


title: scRNA, Restraint_Control_S3

description: Library name: S3

value: ventral hippocampus

value: Control


title: A7_HF17

value: Heart Failure


title: Ac4ManNAz-treated, rep 1

description:
Library name: DS002
rRNA depletion, strand-specific library


title: A6_HF9


title: scRNA, Handling_45min_S24

description: Library name: S24

value: Female

value: Handling


title: Untreated, rep 1

description:
Library name: DS001
rRNA depletion, strand-specific library


title: neurons - RNMT 3 IP

description: RNMT 3 IP seCLIP library

value: RNMT (anti-sheep, in house)

value: 254nm UV crosslinked (400mJ/cm2)


title: B2_C10

value: Heart left ventricle


title: scRNA, Handling_15min_S23

description: Library name: S23


title: neurons - RNMT 3 size matched input

description: RNMT 3 size matched input seCLIP library


title: A5_HF1


title: neurons - RNMT 2 IP

description: RNMT 2 IP seCLIP library


title: A3_C17


title: A2_C9


title: scRNA, Restraint_Control_S22

description: Library name: S22


title: RE_LPM_BAC-2

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

department: School of Medicine

institute: Guangxi University

description: Library name: Sample15

data_processing:
Use fastqc and multiqc to check the data quality · Use fastp software to perform quality control on the fastq data, filter low-quality reads ·
Assembly: mm10
Supplementary files format and content: .gz

source_name: Peritoneal macrophages

extract_protocol:
Trizol reagent protocol
SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing Protocol

value: Peritoneal macrophages

value: LPM


title: RE_SPM_BAC-2

description: Library name: Sample16

value: SPM


title: neurons - RNMT 1 IP

description: RNMT 1 IP seCLIP library


title: RE_SPM_BAC+2

description: Library name: Sample14


title: wt, leaves, rep3

city: Athens

first: Gerasimos

last: Daras

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
RNA-seq data were analyzed using SOAPnuke (version 1.5.2) with parameters “-l 15 -q 0.2 -n 0.05"
We used Bowtie2 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample. DESeq2 was used to identify differentially expressed genes.
Bowtie2 version：v2.2.5 | Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM version：v1.2.8 | Parameters：-p 8 --forward-prob 0.5 --paired-end
Assembly: Arabidopsis_thaliana_NCBI_GCF_000001735.4_TAIR10.1
Supplementary files format and content: Excel file with gene expression values and log2FoldChange between samples as generated by DEseq2

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized and sown in 120×120 mm2 Petri dishes containing 0.5×Murashige and Skoog (MS) medium (Duchefa, Haarlem, the Netherlands), pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma, Gillingham, UK). After 48h of stratification at 4oC, seedlings were positioned to grow at 22oC in a Fitotron (Weiss Gallenkamp, Loughborough, UK) growth chamber under a long-day photoperiod with 16h of light and 8h of darkness per day and 75 μmol m−2s−1 light intensity. After two weeks plants were transferred to soil and grown under the same conditions.

extract_protocol:
Total RNA was extracted  from three distinct rosette leaf  stages namely green, pale green and chlorotic variation using the Direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis.
RNA-seq libraries were generated using the polyA Strand-Specific Transcriptome Library method of BGI  for DNBSEQ platform.
Sequencing was performed on DNBSEQ-G400 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

value: leaves

value: wild-type rosette leaves


title: scRNA, Restraint_45min_S20

city: Zürich

description: Library name: S20


title: scRNA, Restraint_15min_S21

description: Library name: S21


title: neurons - RNMT 2 size matched input

description: RNMT 2 size matched input seCLIP library

value: Primary cortical neurons


title: RE_LPM_BAC+2

description: Library name: Sample13


title: neurons - Sheep IgG IP

description: Sheep IgG size matched input seCLIP library


title: neurons - RNMT 1 size matched input

description: RNMT 1 size matched input seCLIP library


title: scRNA, Handling_Control_S19

description: Library name: S19


title: RE_SPM_BAC-1

description: Library name: Sample12