title: KPC-EVRNA_Alkbh5KO_m6A-seq_Rep 3_IP


title: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 2

status: Public on Mar 26 2025

type: SRA

city: Irvine

first: Pavan

last: Nayak

address: 4462 Natural Sciences 2

country: USA

institute: UC Irvine

description: Library name: P45

library_source: transcriptomic

data_processing:
Reads were mapped to zebrafish GRCz10 and quantified using STAR v2.5.2A and RSEM 1.2.31. Differential expression analysis were performed using DESeq2 v.1.30.1
Assembly: GRCz10
Supplementary files format and content: DESeq2 normalized counts

molecule: total RNA

organism: Danio rerio

source_name: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos

extract_protocol:
For 48 hpf bulk RNA-seq alone transgenic Tg(scxa:mCherry) embryos, BTX-injected or un-injected siblings, were dissociated using Subtilisin A cold-active protease in a stock solution consisting of: 5 ul of 1M CaCl2, 100 ul of protease stock solution (100mg of Bacillus licheniformis protease (Sigma P5380) solubilized in 1 ml of Ca and Mg free PBS), 889ul of PBS, 1 ul of 0.5M EDTA (Sigma E5134) and 5ul of DNAse I  (Roche 10104159001) stock (25U/ul in PBS, stored at -80C) adapted from (O’Flanagan et al., 2019). Embryos were triturated once every 2 min for 15 seconds using a wide bore 1 ml pipette. Every 15 min, tissue solution as checked under dissecting scope to verify dissociation. Full dissociation took ~30 min per samples, and samples were subsequently run through a 40 mm filter to separate dissociated cells from clumps of aggregate undissociated tissue/ECM and washed with 10 ml of PBS/BSA (0.01% BSA in PBS, made fresh on the day of dissociation) and transferred to a 15 ml conical tube. Cells were centrifuged at 600g for 5 min at 4°C, supernatant is discarded, and cells are resuspended in 1 ml of ice-cold PBS/BSA before being placed on ice. High expressing mCherry+ cells were gated and sorted on a Bio-Rad FACS Aria II cell sorter.
Clontech SMARTer Stranded Total RNA-Seq v3 Kit

tag: tissue

tag: cell type

value: mCherry+ tenocytes

tag: genotype

value: WT Tg(scxa:mCherry) background

tag: treatment

value: 48 hpf embryos aBTX injected at single cell stage


title: CHIP2024_466_Wave5

city: Rochester

first: Neil

middle: Alistair

last: Robertson

state: MN

address: 200 1st Street

department: Quantitative Health Sciences

institute: MAYO CLINIC ROCHESTER

description: Library name: CHIP2024_466_Wave5

library_source: genomic

data_processing:
Reads were quality-filtered with a ‘phred’ score threshold of ≥30, and adapter sequences were removed using Trimmomatic (version 0.27) (Bolger et al. 2014). Afterward, guided alignment to the human genome assembly hg19 was performed using both bwa-mem (version 0.7.17) and bowtie2 (version 2.2.1) (Langmead & Salzberg 2012; Li & Durbin 2009). Unique molecular barcodes, introduced before PCR amplification, were utilized for deduplication to enable accurate multiplexed quantification and reliable mutation detection. Variant calling within targeted regions was conducted using three different tools: Lofreq (version 2.1.0) (Wilm et al. 2012), Freebayes (Garrison & Marth 2012), and Vision (ArcherDX version 6.2.7, unpublished). A consensus was generated by combining the results and selecting for agreement from all three variant callers (see Supplementary Table 3).
All filtered variants with a variant allele frequency (VAF) of 1% or 2% satisfied the following conditions: (1) the number of reads supporting the alternative allele exceeded the minimum coverage requirement without displaying directional bias (AO ≥ 5, UAO ≥ 3); (2) the variants were significantly underrepresented in the Genome Aggregation Database (gnomAD; P ≤ 0.05); (3) the variants were unlikely to be germline, as indicated by a stable VAF (50% or 100%) across all sequencing waves, which could have been underrepresented in gnomAD due to the limited geographic diversity of the LBC cohort; and (4) the variants included events, such as frameshift duplications and deletions, that were overrepresented in the dataset, likely reflecting misaligned artifacts from the capture method (see Supplementary Table 3) (Karczewski et al. 2020). Additionally, the list was manually curated, cross-referencing variants previously reported in COSMIC, Jaiswal et al., or other published studies (Tate et al. 2019). Finally, for any variant that met the above criteria with a VAF of ≥ 1% or 2% at any time point, all participant-matched data points were included, regardless of baseline VAF.
Assembly: hg19
Supplementary files format and content: tsv - custom variant file format - somatic and synonymous variant calls for 1% and 2% VAF

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Our expanded cohort longitudinally sampled from the LBC1936 was processed as per our previous work. Briefly, DNA was extracted from whole blood with Ethylenediaminetetraacetic acid (EDTA) using the Nucleon BACC3 kit (Sigma-Aldrich, GERPN8512), according to the manufacturer’s protocol.
Libraries were generated from 200 ng of each DNA sample using the Invitea/Archer VariantPlex® 75 Myeloid gene panel and the VariantPlex® Somatic Protocol for Illumina sequencing (Invitae, AB0108, and the VariantPlex®-HCG Myeloid Kit; see Supplementary Table 2), with adaptations for detecting low variant allele frequencies. Sequencing was performed on the NextSeq 550 platform (Illumina) using the NextSeq 500/550 High-Output version 2.5 kit (300 cycles). Two ‘Genome in a Bottle’ (GIAB) DNA samples (NA12878, Coriell Institute) were included in each sequencing batch to ensure reproducibility and support background error modeling and batch correction.

value: PBMCs

tag: batch


title: KPC-cell_Alkbh5KO_Snd1_PAR-CLIP_Rep2

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Sequenced reads were cleaned for adaptor and low-quality sequence, then m6A-seq and PAR CLIP-seq reads were mapped to mm10 using Bowtie 2, RNA-seq reads using STAR.
For RNS-seq, read counts were calculated using RSEM and the differentially expressed mRNAs were calculated by the R package DESeq2.
The m6A-enriched regions (peaks) in each sample were detected by exomePeak2. The m6A peaks were retained and merged using BEDTools and then annotated using HOMER. The read coverage of each peak in m6A-IP and input were calculated using Multicov from BEDTools.
For PAR CLIP-seq, peaks were calculated and selected with P < 0.0001 by using Piranha software (version 1.2.1) and then annotated by homer
Assembly: mm10
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: KPC cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
For RNA-seq, the clustering of the indexed samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). For RNA m6A-seq, sequencing libraries for m6A-IP and input samples were prepared and sequenced on an Illumina HiSeqX Ten PE150 platform. For PAR-CLIP, library construction was performed by employing the NEBNext small RNA library prep kit (E7330S) and then sequenced on an Illumina HiSeq 4000.
PARCLIP-seq, RNA-seq, RNA m6A-seq

tag: cell line

value: KPC cells

value: Murine pancreatic cancer cell line

value: Alkbh5 KO


title: CHIP2024_466_Wave3

description: Library name: CHIP2024_466_Wave3


title: Naïve Mouse 1

type: RNA

city: Bethesda

first: Jessica

middle: Caroline

last: Hargarten

state: MD

address: 10 Center Drive

department: LCIM

institute: NIAID/NIH

hyb_protocol: At time of hybridization, every sample was spiked in with the positive and negative controls provided with the panel. This technique utilizes capture and reporter probes specific for each gene labelled with a unique fluorescent barcode. Signals generated from these barcodes are automatically detected and quantified by the nCounter Pro Analysis System. The generated data were compiled as resource compiler (RCC) files.

data_processing:
RCC files were imported into nSolver 4.0 analysis software (NanoString), and quality control steps were performed following the manufacturer’s guidelines. Raw data were processed sequentially: first background subtraction was performed using the formula: read count of each gene − 2 × (mean + 2 × SD) of all negative controls. Next, the positive control normalization factor was calculated according to the manufacturer’s instructions using positive controls that were spiked into every sample. Then, the CodeSet content normalization factor (housekeeping normalization factor) was calculated using all reference genes to adjust for differences in analyte abundance and/or analyte quality across samples. The most stably expressed housekeeping genes (10 out of 14 for human data and 7 out of 14 for mouse data) were selected using the geNorm algorithm (PMID: 19531210). Normalization was performed per the default settings. The selection criteria for the positive control normalization factor were 0.3–3.0. Pathway scores were calculated as the first principal component of the pathway genes’ normalized expression. The software will orient the scores such that increased score corresponds with increased expression in a majority of the pathway genes. Scores of the cell type characteristic genes were analyzed using the default settings from the cell type profiling algorithm in the nSolver analysis software.
Normalized log2 count data

source_name: Mouse Brain

extract_protocol: RNA was extracted from whole brain homogenates using the Qiagen RNeasy Kit according to manufacturers' recommendations.

tag: Sex

value: Female


title: sorted mCherry+ tenocytes from aBTX injected 48 hpf Tg(scxa:mCherry) zebrafish embryos replicate 1

description: Library name: P44

value: FAC sorted mCherry+ tenocytes from whole Tg(scxa:mCherry) embryos


title: KPC-EVRNA_Alkbh5KO_m6A-seq_Rep 1_IP

library_source: other

molecule: other

tag: fraction

value: EV-packaged total RNA


title: KPC-EVRNA_SgCtrl_m6A-seq_Rep 2_IP

value: WT


title: EGFP SCs-3

first: Zhaowei

last: Zhu

address: NO. 58 Zhongshan 2nd Rd, Guangzhou

department: Department of Plastic Surgery

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
NGS (Next Generation Sequencing) technology applies high-throughput sequencers (such as Illumina NovaSeq6000) to sequence cDNA. The original image file obtained first is then subjected to base recognition and error filtering to obtain the original sequencing fragments that can be used for analysis. We call them Reads, and the results are stored in fastq format, which includes the base composition information of the sequence and its corresponding sequence quality information. Pair end sequencing is divided into two Reads files: 1 and 2.
Assembly: Apply the split mapping algorithm of Hisat2 (version: 2.0.4) to perform Genome mapping on preprocessed reads. This algorithm allows for the segmentation of reads that cannot be fully matched for mapping, making it more suitable for eukaryotic (with intron inter region) transcriptome sequencing data; Use default parameters. The alignment result generated by Mapping is a BAM file, using the genome version of Rnor_6.0
Supplementary files format and content: In transcriptome sequencing, we can estimate the level of gene expression by mapping the number of reads to the gene region, but the number of reads is not only proportional to the gene expression level, but also related to the length of the gene itself and the amount of sequencing data. In order to ensure comparability of gene expression levels between different genes and samples, reads were transformed into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for standardization of gene expression levels

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Schwann cells

extract_protocol:
The extracted total RNA was subjected to Agilent 4200 TapeStation (Agilent technologies Santa Clara, US) electrophoresis and quality inspection, and then RNA Lean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase Free DNase Set (Cat # 79254) were used, QIAGEN, GmBH, Germany)， Purify Total RNA.
Through amplification by SMART-Seq® HT kit HT Kit, cDNA was obtained and subjected to Qubit and Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US) electrophoresis for quality inspection before being used for backup. According to the experimental operation instructions, amplify fragment cDNA, perform end repair, add A at the 3 'end, connect connectors, and enrich to complete the construction of the sequencing sample library.
The concentration of constructed library was detected by Qubit® 2.0 Fluorometer, and its size was verified by Agilent 2100.

treatment_protocol: SCs from neonatal 3-5 day SD rats were isolated and purified. The purified P0 SCs were randomly divided into the Runx2-OE group and EGFP (empty vector) group. SCs were transfected with Runx2-OE or EGFP adenovirus at a concentration of MOI = 200. After 72 hours of incubation in the incubator, the changes in cell morphology were observed under laser confocal microscope. Smart-seq was performed as described previously.

value: Schwann cells

value: EGFP vector transfected (control)


title: KPC-EVRNA_Alkbh5KO_m6A-seq_Rep 2_IP


title: BLGSP-71-19-99999

type: genomic

city: Burnaby

first: Ryan

middle: D.

last: Morin

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human Infinium Methylation EPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: HiScan with standard recommended settings

data_processing: minfi package (v.1.40.0) in R environment (v.4.1.3)

label: Cy3 and Cy5

source_name: Normal centroblasts

label_protocol: Standard Illumina Protocol

extract_protocol: Standard Protocol

value: Normal centroblasts


title: EGFP SCs-2


title: BLGSP-71-19-99998


title: KPC-cell_Vehicle-treatment_m6A-seq_Rep 3_IP

value: Vehicle treatment


title: KPC-cell_Vehicle-treatment_m6A-seq_Rep 2_IP


title: CHIP2024_419_Wave5

description: Library name: CHIP2024_419_Wave5


title: BLGSP-71-19-99997


title: Runx2-OE SCs-3

value: Runx2 over-expressed vector transfected


title: CHIP2024_419_Wave3

description: Library name: CHIP2024_419_Wave3


title: KPC-cell_Vehicle-treatment_m6A-seq_Rep 1_IP


title: Naïve Mouse 2


title: Runx2-OE SCs-2


title: BLGSP-71-19-99996


title: EGFP SCs H3K4me3 cut tag

data_processing:
CUT&TAG raw reads were filtered and trimmed by using Trimmomatic (version 0.39) to remove the sequencing adaptor and low-quality reads. Quality control was processed by using multiQC (version 1.22.1). After quality control, clean reads were mapped to the reference genome UCSC Rn6 by using Bowtie2 (version 2.5.1). R package ATACseqQC (version 1.28.0) was chosen to perform post-alignment quality assessment. Only the uniquely mapped reads were kept to process the next step of analysis. The bam file generated by the unique mapped reads was sorted by using samtools (version 1.20) and the sorted bam file was chosen to process peak calling by using MACS2 (version 2.2.9.1) with default parameters. R package Diffbind (version 3.14. 0) was chosen to perform the differential peak analysis. Peaks were called differently if the p-value <0.05. Differential peaks were annotated by using annotatePeaks.pl tool from HOMER software (version 4.11). Motif enrichment analysis of differential peaks was processed by using the findMotifsGenome.pl tool from HOMER software (version 4.11). Function enrichment was performed on the genes associated with differential peaks by using the R package clusterProfiler (version 4.6.0). The sorted bam file was converted into bigwig format by using the bamCoverage tools of deeptools (version 2.0). The metagene plot was calculated by using computeMatrix tools and plotted by plotProfile tools, both of which were from deeptools (version 2.0). IGV was chosen to visualize the peaks and signals of CUT&TAG targets.
Assembly: rn6
Supplementary files format and content: bed, peaks

extract_protocol:
1×10^6 cells were washed twice gently with cell wash buffer. A total of 10μL Concanavalin A coated magnetic beads were added per sample and incubated at room temperature for 10 minutes. Unbound supernatant was removed.
Bead-bound cells were resuspended with Dig wash buffer and incubated with a 1:50 dilution of primary antibody (H3K27ac, H3K27me3, H3K4me3) on a rotating platform overnight at 4℃. The primary antibody was removed using a magnet stand. The secondary antibody was diluted 1:100 in Dig wash buffer and cells were incubated at room temperature for 60 min. Cells were washed using the magnet stand 2-3 times in the Dig wash buffer. A 1:100 dilution of the pA-Tn5 adapter complex was prepared in Dig-med buffer and incubated with cells at room temperature for 1h. Cells were washed 2-3 times for 5 min in 1 mL Dig-med buffer. Then cells were resuspended in Tagmentation buffer and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. DNA fragments ranging from 250 to 350 bp were kept to execute library preparation. The library products were sequenced by using the Illumina Novaseq 6000 system.


title: CHIP2024_419_Wave1

description: Library name: CHIP2024_419_Wave1


title: CHIP2024_476_Wave5

description: Library name: CHIP2024_476_Wave5


title: KPC-cell_NA-treatment_m6A-seq_Rep 3_IP

value: NA treatment


title: KPC-cell_NA-treatment_m6A-seq_Rep 2_IP


title: BLGSP-71-19-99988


title: Runx2-OE SCs H3K4me3 cut tag


title: CHIP2024_466_Wave1

description: Library name: CHIP2024_466_Wave1


title: BLGSP-71-30-00682

source_name: Tumour

value: Burkitt lymphoma biopsy


title: KPC-cell_SgCtrl_m6A-seq_Rep 3_IP


title: CHIP2024_476_Wave1

description: Library name: CHIP2024_476_Wave1


title: EGFP SCs H3K27ac cut tag


title: BLGSP-71-30-00680


title: BLGSP-71-30-00681


title: CHIP2024_476_Wave3

description: Library name: CHIP2024_476_Wave3


title: CHIP2024_416_Wave4

description: Library name: CHIP2024_416_Wave4


title: CHIP2024_416_Wave3

description: Library name: CHIP2024_416_Wave3


title: KPC-cell_SgCtrl_m6A-seq_Rep 2_IP


title: EGFP SCs H3K27me4 cut tag


title: BLGSP-71-30-00678


title: BLGSP-71-19-99989


title: CHIP2024_416_Wave1

description: Library name: CHIP2024_416_Wave1


title: KPC-cell_Alkbh5KO_m6A-seq_Rep 3_IP


title: EGFP SCs IgG-2 cut tag

extract_protocol:
1×10^6 cells were washed twice gently with cell wash buffer. A total of 10μL Concanavalin A coated magnetic beads were added per sample and incubated at room temperature for 10 minutes. Unbound supernatant was removed.
Bead-bound cells were resuspended with Dig wash buffer and incubated with a 1:50 dilution of primary antibody (Runx2、CTCF、cJun、C/EBP-β) on a rotating platform overnight at 4℃. The primary antibody was removed using a magnet stand. The secondary antibody was diluted 1:100 in Dig wash buffer and cells were incubated at room temperature for 60 min. Cells were washed using the magnet stand 2-3 times in the Dig wash buffer. A 1:100 dilution of the pA-Tn5 adapter complex was prepared in Dig-med buffer and incubated with cells at room temperature for 1h. Cells were washed 2-3 times for 5 min in 1 mL Dig-med buffer. Then cells were resuspended in Tagmentation buffer and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. DNA fragments ranging from 250 to 350 bp were kept to execute library preparation. The library products were sequenced by using the Illumina Novaseq 6000 system.


title: KPC-cell_Alkbh5KO_m6A-seq_Rep 2_IP


title: EGFP SCs IgG-1 cut tag


title: CHIP2024_475_Wave4

description: Library name: CHIP2024_475_Wave4


title: KPC-cell_Alkbh5KO_m6A-seq_Rep 1_IP


title: KPC-cell_NA-treatment_m6A-seq_Rep 1_IP


title: BLGSP-71-30-00676


title: Runx2-OE SCs IgG-2 cut tag


title: CHIP2024_475_Wave3

description: Library name: CHIP2024_475_Wave3


title: Runx2-OE SCs H3K27ac cut tag


title: BLGSP-71-30-00675


title: CHIP2024_475_Wave1

description: Library name: CHIP2024_475_Wave1


title: BLGSP-71-30-00677


title: Runx2-OE SCs IgG-1 cut tag


title: BLGSP-71-30-00673


title: CHIP2024_465_Wave4

description: Library name: CHIP2024_465_Wave4


title: KPC-cell_SgCtrl_m6A-seq_Rep 1_IP


title: KPC-EVRNA_SgCtrl_m6A-seq_Rep 2_INPUT


title: CHIP2024_481_Wave3

description: Library name: CHIP2024_481_Wave3


title: BLGSP-71-30-00672


title: CHIP2024_465_Wave3

description: Library name: CHIP2024_465_Wave3


title: EGFP SCs CTCF cut tag


title: KPC-EVRNA_SgCtrl_m6A-seq_Rep 1_INPUT


title: BLGSP-71-30-00671


title: Runx2-OE SCs CTCF cut tag


title: CHIP2024_465_Wave1

description: Library name: CHIP2024_465_Wave1


title: KPC-EVRNA_Alkbh5KO_m6A-seq_Rep 3_INPUT


title: EGFP SCs C/EBP-β-2 cut tag


title: KPC-EVRNA_Alkbh5KO_m6A-seq_Rep 2_INPUT


title: BLGSP-71-30-00669


title: BLGSP-71-30-00670


title: KPC-EVRNA_SgCtrl_m6A-seq_Rep 3_INPUT


title: BLGSP-71-30-00667


title: CHIP2024_474_Wave5

description: Library name: CHIP2024_474_Wave5


title: CHIP2024_474_Wave3

description: Library name: CHIP2024_474_Wave3


title: CHIP2024_474_Wave1

description: Library name: CHIP2024_474_Wave1


title: EGFP SCs C/EBP-β-1 cut tag


title: KPC-cell_Vehicle-treatment_m6A-seq_Rep 3_INPUT


title: BLGSP-71-30-00665


title: CHIP2024_415_Wave4

description: Library name: CHIP2024_415_Wave4


title: BLGSP-71-30-00664


title: KPC-cell_Vehicle-treatment_m6A-seq_Rep 1_INPUT


title: CHIP2024_415_Wave1

description: Library name: CHIP2024_415_Wave1


title: Runx2-OE SCs cJun-2 cut tag


title: KPC-cell_NA-treatment_m6A-seq_Rep 3_INPUT


title: EGFP SCs cJun-1 cut tag


title: BLGSP-71-30-00662


title: Runx2-OE SCs cJun-1 cut tag


title: CHIP2024_464_Wave4

description: Library name: CHIP2024_464_Wave4


title: KPC-cell_NA-treatment_m6A-seq_Rep 2_INPUT


title: BLGSP-71-30-00660


title: CHIP2024_464_Wave3

description: Library name: CHIP2024_464_Wave3


title: Runx2-OE SCs C/EBP-β-1 cut tag


title: KPC-cell_NA-treatment_m6A-seq_Rep 1_INPUT


title: EGFP SCs cJun-2 cut tag


title: BLGSP-71-30-00659


title: BLGSP-71-30-00666


title: EGFP SCs Runx2-1 cut tag


title: CHIP2024_464_Wave1

description: Library name: CHIP2024_464_Wave1


title: KPC-cell_Vehicle-treatment_m6A-seq_Rep 2_INPUT


title: CHIP2024_415_Wave3

description: Library name: CHIP2024_415_Wave3


title: Runx2-OE SCs Runx2-2 cut tag


title: KPC-cell_SgCtrl_m6A-seq_Rep 3_INPUT


title: CHIP2024_473_Wave5

description: Library name: CHIP2024_473_Wave5


title: KPC-cell_SgCtrl_m6A-seq_Rep 2_INPUT


title: Runx2-OE SCs Runx2-1 cut tag


title: KPC-cell_SgCtrl_m6A-seq_Rep 1_INPUT


title: CHIP2024_473_Wave3

description: Library name: CHIP2024_473_Wave3


title: BLGSP-71-30-00657


title: CHIP2024_473_Wave1

description: Library name: CHIP2024_473_Wave1


title: EGFP SCs Runx2-2 cut tag


title: BLGSP-71-30-00653


title: HeLa cells, charge-scrambled Treacle-2S (ChIP)

city: Moscow

first: Artem

last: Luzhin

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

description: Library name: HeLa, Treacle-2S CS, ChIP

data_processing:
Chip-seq reads were mapped to the reference human genome hg38 assembly using Bowtie v2.2.3 with the ‘–very-sensitive’ mode.
Non-uniquely mapped reads, possible PCR and optical duplicates were filtered out using SAMtools v1.5.
The bigWig files with the ratio of RPKM normalized ChIP-seq signal to the input were generated using deepTools v3.4.2 bamCompare function.
Assembly: hg38
Supplementary files format and content: bigWig (exept for Input file)

source_name: HeLa

growth_protocol: Human HeLa (ATCC® CCL-2™) cells were cultured in DMEM (PanEco) supplemented with 10% fetal bovine serum (FBS; HyClone/GE Healthcare) and penicillin/streptomycin. The cells were cultured at 37C in a conventional humidified CO2 incubator.

extract_protocol:
Living cells were fixed for 15 min with 1% formaldehyde at room temperature, and crosslinking was quenched by adding 125 mM glycine for 5 min. Cell sorting was performed if needed. Cells were harvested in PBS, and nuclei were prepared by incubation in FL buffer (5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% NP40) supplemented with Protease Inhibitor Cocktail (Bimake) and Phosphatase Inhibitor Cocktail (Bimake) for 30 min on ice. Next, chromatin was sonicated in RIPA buffer (10 mM Tris–HCl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) with a VirSonic 100 to an average length of 200-500 bp. Per ChIP reaction, 10–20 µg chromatin was incubated with 2–4 µg antibodies anti-Katushka2S overnight at 4C. The next day, Protein A/G Magnetic Beads (Thermo Scientific) were added to each sample and incubated for 4 h at 4C. Immobilized complexes were washed two times for 10 min at 4C in low salt buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) and high salt buffer (20 mM Tris–HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100). Samples were incubated with RNase A (Thermo Scientific) for 30 min at room temperature. The DNA was eluted from the beads and de-crosslinked by proteinase K digestion for 4 h at 55C and subsequent incubation at 65C for 12 h. Next, DNA was purified using phenol/chloroform extraction.
The sequencing libraries were then prepared with NEBNext Ultra II kit according manufacturer’s protocol. Final libraries were PCR amplificated and adapter dimers were cleaned with 1:1 MagPure magnetic beads (Magen Biotechnology). Resulted DNA was resuspended in 30 mkl 10 mM Tris-HCl buffer ph 8.0 and were sequenced on Illumina machine.

treatment_protocol: Endogenous Treacle was depleted by siRNA-mediated knockdown (Treacle kd). Next, Treacle-depleted cells were transfected with siRNA-resistant full-length Treacle-2S (Treacle-2S full), charge-scrambled Treacle-2S (Treacle-2S CS) or Treacle-2S Δ83-1121 deletion mutant (Treacle-2S Δ83-1121).

value: HeLa

value: cervical cancer

value: Treacle KD, transfection with siRNA-resistant charge-scrambled Treacle-2S


title: HeLa cells, full-length Treacle-2S (ChIP)

description: Library name: HeLa, Treacle-2S full, ChIP

value: Treacle KD, transfection with siRNA-resistant full-length Treacle-2S


title: BLGSP-71-30-00658


title: CHIP2024_410_Wave3

description: Library name: CHIP2024_410_Wave3

value: PBMCs


title: BLGSP-71-30-00652


title: BLGSP-71-30-00650


title: KPC-cell_Alkbh5 KO_m6A-seq_Rep 1_INPUT

value: KPC cells

value: Murine pancreatic cancer cell line

value: Alkbh5 KO


title: CHIP2024_410_Wave1

description: Library name: CHIP2024_410_Wave1


title: BLGSP-71-30-00648


title: B16F10_rep3

city: Hoersholm

first: Christian

last: Garde

address: Dr Neergaards Vej 5F

country: Denmark

institute: Evaxion Biotech

description:
B16F10 Tumor, Replicate 3
HFKMYDSXY_104100-001-003_GAACGCTT-CTGCACTT_L003

data_processing:
Raw fastq files were preprocessed using cutadapt v1.18 and trimmomatic v0.38.
A combined GTF annotation was created by concatenating Ensembl:GRCm38.v102 and gEVE v1.1. The reference GRCm38 genome fasta files and the combined annotation were used to create STAR and RSEM indexes.
Preprocessed RNA reads were mapped to the combined reference using STAR v2.7.9a and transcript expression was quantified using RSEM v1.3.1.
Assembly: GRCm38.102 (Ensembl)
Supplementary files format and content: *.isoforms.results: Tab-delimited text files with read counts, normalized read counts (transcripts per million), and FPKM values.

source_name: B16F10 Tumor

growth_protocol: The BALB/c syngeneic colon cancer cell line CT26 (#CRL2638) was purchased from ATCC and cultured in R10 medium prepared from RPMI (Gibco #72400-021) supplemented with 10% heat inactivated fetal calf serum (FCS, Gibco # 10500-064) at 37 °C and 5% CO2 as per supplier’s instructions. The murine melanoma cell line B16F10 derived from a C57BL/6 mouse (ATCC, cat# CRL-6475) was purchased from ATCC and grown in DMEM (Sigma, cat# D6546) supplemented with 10% Fetal Bovine Serum (Gibco, cat# 10500-064) and 1% Glutamax (Gibco, cat# 35050-061). Cells were grown to 60-70% confluency, trypsinized and washed 2x in serum free RPMI in preparation for inoculation in mice. Female BALB/cJRj and C57BL/6JRj SPF mice were acquired from Janvier Labs (France). The mice were acclimated for one week before initiation of experiments. Female BALB/cJRj and C57BL/6JRj mice were subcutaneously (s.c.) inoculated with 2 x 10^5 CT26 or B16F10 tumor cells, respectively, on the left flank in a volume of 100 μl serum free RPMI. B16F10 tumors were harvested on day 15 and CT26 tumors were harvested on day 19-21. Tumors were immersed in RNAlater for RNA-seq.

extract_protocol:
The RNeasy Plus Mini Kit (Qiagen cat. no. 74134) was used for RNA extraction according to manufacturer's protocols.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L).

value: B16F10 Tumor

tag: condition

value: Inoculated with B16F10 melanoma cells


title: CHIP2024_402_Wave5

description: Library name: CHIP2024_402_Wave5


title: BLGSP-71-30-00647


title: HeLa cells, Treacle-2S Δ83-1121 deletion mutant (ChIP)

description: Library name: HeLa, Treacle-2S delta 83-1121, ChIP

value: Treacle KD, transfection with siRNA-resistant Treacle-2S Δ83-1121 deletion mutant


title: KPC-cell_Alkbh5 KO_m6A-seq_Rep 3_INPUT


title: BLGSP-71-30-00655


title: CHIP2024_402_Wave3

description: Library name: CHIP2024_402_Wave3


title: B16F10_rep2

description:
B16F10 Tumor, Replicate 2
HFKMYDSXY_104100-001-002_TGCCATTC-CGTGATCA_L003


title: DH_100 d82 C11M1 (F)

city: Borstel

first: David

last: Hertz

address: Parkallee 22

country: Germany

institute: Research Center Borstel

hyb_protocol: Standard Nanostring™ hybridization protocol was used, available at: https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

scan_protocol: Standard Nanostring™ scan protocol was used, available at: https://jp.nanostring.com/wp-content/uploads/MAN-10147-03-nCounter-Pro-Analysis-System-User-Manual.pdf

data_processing: Raw gene expression data were analyzed using NanoString’s software nSolver v4.0 with the Advanced Analysis Module v2.0.134. The raw counts from Nanostring™ of each desired comparison were placed together and normalized. The p-values, adjusted p-values, log2Fold-change, and baseMean were then calculated.

label: single molecule fluorescent barcodes through nucleotide hybridization

source_name: tuberculosis

label_protocol: Standard Nanostring™ label protocol was used, available at: https://jp.nanostring.com/wp-content/uploads/MAN-10147-03-nCounter-Pro-Analysis-System-User-Manual.pdf

growth_protocol: B cell IL-10 KO mice and their littermates were infected mit Mtb HN878 via aerosol chamber and lung removed aseptically on day 82 post infection.

extract_protocol: RNA was extracted with RNeasy FFPE Kit (Qiagen, Germantown, USA) from tissue sections, dissolved in nuclease-free water and RNA integrity analyzed using a 2100 Bioanalyzer (RNA 6000 Nano Kit, Agilent Technologies, Waldbronn, Germany). Samples with DV200 values >30% were included for gene expression analysis.

treatment_protocol: Superior lung lobes from infected mice were fixed with 4% w/v paraformaldehyde for 24 h and embedded in paraffin.

value: lung

tag: day post infection

value: female

tag: genetic background

value: B cell IL-10 KO


title: DH_100 d82 C11M2 (F)

value: littermate


title: DH_100 d82 C11M3 (F)


title: B16F10_rep1

description:
B16F10 Tumor, Replicate 1
HFKMYDSXY_104100-001-001_GACTATGC-CGTTGAGT_L003


title: DH_100 d82 C12M3 (F)


title: BLGSP-71-30-00643


title: CHIP2024_410_Wave5

description: Library name: CHIP2024_410_Wave5


title: CT26_rep3

description:
CT26 Tumor, Replicate 3
HK3Y2DSXX_103655-001-S04_ATAACGCC-CAGGTTCA_L001

source_name: CT26 Tumor

value: CT26 Tumor

value: Inoculated with CT26 colon cancer cells


title: DH_100 d82 C12M4 (F)


title: CHIP2024_472_Wave4

description: Library name: CHIP2024_472_Wave4


title: CT26_rep2

description:
CT26 Tumor, Replicate 2
HK3Y2DSXX_103655-001-S03_GTCGATTG-AAGACCGT_L001


title: BLGSP-71-30-00641

value: Burkitt lymphoma biopsy


title: DH_100 d82 C14M1 (F)


title: CHIP2024_472_Wave3

description: Library name: CHIP2024_472_Wave3


title: BLGSP-71-30-00637


title: CT26_rep1

description:
CT26 Tumor, Replicate 1
HK3Y2DSXX_103655-001-S02_TCCATTGC-TACGGTCT_L001


title: BLGSP-71-30-00645


title: DH_100 d82 C15M1 (M)

value: male


title: CHIP2024_472_Wave1

description: Library name: CHIP2024_472_Wave1


title: BLGSP-71-29-00546

source_name: Cell line

value: Mutu

value: Cell line


title: BLGSP-71-29-00543

value: Raji


title: CHIP2024_400_Wave3

description: Library name: CHIP2024_400_Wave3

value: PBMCs


title: CHIP2024_400_Wave5

description: Library name: CHIP2024_400_Wave5


title: CHIP2024_402_Wave1

description: Library name: CHIP2024_402_Wave1


title: BLGSP-71-29-00545

value: Daudi


title: DH_100 d82 C15M4 (M)


title: CHIP2024_400_Wave1

description: Library name: CHIP2024_400_Wave1


title: BLGSP-71-29-00541

value: JIYOYE


title: DH_100 d82 C16M1 (M)


title: CHIP2024_471_Wave5

description: Library name: CHIP2024_471_Wave5


title: BLGSP-71-29-00537

value: Namalwa


title: CHIP2024_471_Wave3

description: Library name: CHIP2024_471_Wave3


title: DH_100 d82 C17M1 (M)


title: DH_100 d82 C15M3 (M)


title: BLGSP-71-29-00533

value: Defauw


title: DH_100 d82 C19M2 (M)


title: ΔmutT4::mutT4 +RppH replicate 3

city: Worcester

first: Junpei

last: Xiao

state: MA

address: 100 Institute Rd

institute: Worcester Polytechnic Institute

description: Library name: mutT4_comp_with_rpph_3

data_processing:
Reads were aligned to the NC_000962 reference genome using the Burrows-Wheeler Aligner
Read 1 corresponds to the sequence of an endogenous RNA, with its first nucleotide representing the 5'-most nucleotide of that RNA molecule, and Read 2 corresponds to the reverse complement of part of an RNA. Samtools was used to remove Read 2 and separate Read 1 into plus and minus strand files.
Bedtool2 was used to obtain the read depth for each coordinate at the 5’ end of a Read 1, representing the 5’ end of an RNA used to construct the library.
A pseudocount of 1 was added to each coordinate to eliminate zero counts.
The total number of reads mapped to spike-in controls in each library was used to normalize the coordinate-based coverage of 5' ends.
Assembly: NC_000962
Supplementary files format and content: txt files contain normalized coverage for 5' ends mapping to each coordinate (5' end counts per coordinate for each replicate sample).

organism: Mycobacterium tuberculosis

source_name: mc26030 (H37Rv delta RD1 delta panCD) derivative

growth_protocol: M. tuberculosis mc26030 H37Rv ΔRD1 ΔpanCD (37) and derivative strains were cultured in Middlebrook 7H9 supplemented with OADC (0.05 g/L oleic acid, 5 g/L bovine serum albumin fraction V, 2 g/L glucose, 0.85 g/L NaCl, and 4 mg/L catalase), 0.2% glycerol, 0.05% Tween 80, and 24 μg/mL pantothenate at 37 °C and 200 rpm shaking

extract_protocol:
were centrifuged at 3,900 rpm for 7 min at 4 °C. The bacterial pellets were resuspended in 1 mL of TRI Reagent (Molecular Research Center, TR118) and transferred to bead-beating tubes (OPS Diagnostics 100 µm zirconium beads, PFMB 100-100-12). Cells were lysed with 3 cycles at 7 m/s, 30 seconds per cycle in a FastPrep-24 bead-beater (MP Biomedicals) and then 300 µL of chloroform was added. Samples were centrifuged 15,000 rpm for 15 min at 4 °C and RNA from the aqueous phase was purified using Direct-Zol RNA miniprep kit (Zymo Research, R2052) following the manufacturer's instructions. DNase treatment was performed on-column and the purified RNA was stored at -80 °C.
rRNA was depleted as described in (Culviner, P.H., Guegler, C.K. and Laub, M.T. (2020) A simple, cost-effective, and robust method for rRNA depletion in RNA-sequencing studies. MBio, 11, 10.1128/mbio. 00010-00020.). Samples were then treated with E. coli RppH or mock-treated, and 5'-end directed RNAseq libraries were constructed as described (Martini, M.C., Sun, H. and Shell, S.S. (2021) RNA Sequencing for Transcript 5'-End Mapping in Mycobacteria. Methods Mol Biol, 2314, 513-531). A set of in-vitro transcribed, RppH-treated transcripts was added at the adapter ligation step to faciliate normalization of the data.

treatment_protocol: Cultures were grown to mid-log phase (OD600nm = 0.8 – 1.6) .

value: delta mutT4::mutT4

value: exponential phase


title: Runx2-OE SCs H3K27me3 cut tag

value: Schwann cells

value: Runx2 over-expressed vector transfected


title: KPC-EVRNA_Alkbh5KO_m6A-seq_Rep 1_INPUT

value: KPC cells

value: Murine pancreatic cancer cell line

value: Alkbh5 KO

value: EV-packaged total RNA


title: ΔmutT4::mutT4 +RppH replicate 2

description: Library name: mutT4_comp_with_rpph_2

value: mc26030 (H37Rv delta RD1 delta panCD) derivative


title: CHIP2024_471_Wave1

description: Library name: CHIP2024_471_Wave1


title: BLGSP-71-29-00532


title: BLGSP-71-29-00530


title: CHIP2024_470_Wave5

description: Library name: CHIP2024_470_Wave5


title: ΔmutT4::mutT4 +RppH replicate 1

description: Library name: mutT4_comp_with_rpph_1


title: ΔmutT4::mutT4 -RppH replicate 3

description: Library name: mutT4_comp_no_rpph_3


title: BLGSP-71-29-00529

value: Gumbus


title: CAL51 DDP

city: Shanghai

first: Xiang

last: Zhou

address: DongAn Road 270

institute: Fudan University

description: Gene expression after p53 activation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CAL51 + DDP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: CAL51 cells were cultured in DMEM containing 10% fetal bovine serum, penicillin (100 U/ml), and streptomycin (0.1 mg/ml).

extract_protocol: Total RNA was extracted from cells and tissues using RNAiso Plus (Takara, Japan) according to the manufacturer’s protocol.

treatment_protocol: CAL51 cells were treated with DMSO, 5-FU, DDP, or Nutlin-3 for 48 hours.

value: DDP


title: CHIP2024_470_Wave1

description: Library name: CHIP2024_470_Wave1


title: CAL51 Nutlin

description: Gene expression after p53 activation

source_name: CAL51 + Nutlin

value: Nutlin


title: CHIP2024_470_Wave3

description: Library name: CHIP2024_470_Wave3

value: PBMCs


title: Fesource_bulk_rep3

city: Verona

first: Anita

last: Zamboni

address: Strada Le Grazie, 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom Array 4x44K (GPL22578) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent G2565CA Mycroarray Scanner System (Agilent) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (GE1_105_Dec08 and Grid: 085544_D_20180510) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Cucumis sativus

source_name: Roots of plants grown for 24 h in a NS without FeNaEDTA and supplied with non-nano FePO4 (bulk) as source of Fe.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
Cucumis sativus Viridis F1 hybrid (Franchi Sementi S.p.A.)  were germinated on paper soaked with 1 mM CaSO4 in dark at 25°C. Six seedlings have been transferred in one pot filled with 1.8 L of nutrient solution (NS) maintained continuously aerated. For each treatments was set-up one pot. The  growth and treatment experiment was repeated three indipendent times (biological replicates).
Plants were grown into a 16/8 day/light photoperiod at 25°C and at 200 μmol m-2 sec-1 PPFD (Photosynthetic Photon Flux Density). The roots of three seedlings of each pot (treatment) were sampled after 24 h and pooled (one biological replicate).

extract_protocol: Total RNA was isolated using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol:
C (control): plant grown in NS with the following composition: 0.7 mM K2SO4, 2 mM Ca(NO3)2, 0.5 mM MgSO4, 0.1 mM KH2PO4, 0.1 mM KCl, 100 μM FeNaEDTA, 10 μM H3BO3, 0.5 μM MnSO4, 0.5 μM ZnSO4, 0.2 μM CuSO4 and 0.01 μM (NH4)6Mo7O24; -P: plants grown in NS without KH2PO4; PNP: plants grown in the NS without KH2PO4 and supplied with FePO4 NPs as P source;
PB: plants grown in the NS without KH2PO4 and supplied with non-nano FePO4 (bulk) as source of P; -Fe: plants grown in the NS without FeNaEDTA; FeNP: plants grown in the NS without FeNaEDTA and supplied with FePO4 NPs as Fe source; FeB: plants grown in the NS without FeNaEDTA and supplied with non-nano FePO4 (bulk) as source of Fe.

value: root


title: CAL51 NC2

description: Gene expression after p53 activation

source_name: CAL51 + DMSO2

value: DMSO


title: Fesource_bulk_rep2


title: ΔmutT4::mutT4 -RppH replicate 2

description: Library name: mutT4_comp_no_rpph_2


title: Fesource_bulk_rep1


title: BLGSP-71-29-00528

value: Cell line


title: CAL51 NC1

description: Gene expression after p53 activation

source_name: CAL51 + DMSO1


title: Islets, vehicle control, biol rep3

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

institute: Carleton University

data_processing:
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10b
Gene counts were performed with QuasR R package (1.38.0)
Differential gene expression analysis was performed with DESeq2 v1.44.0
Assembly: Biospyder TempO-Seq MouseWT v1.1 probe set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the STAR alignments

source_name: Pancreatic islets

extract_protocol:
Following exposure, RNA lysate was isolated using the TempO-Seq enhanced Lysis buffer according to manufacturer’s instructions (BioSpyder). Lysates were stored at -80°C.
RNA libraries were prepared directly from the RNA lysates using the 96-sample TempO-Seq Mouse whole transcriptome panel v1.1 assay (1x96 Index E Low) (BioSpyder) following manufacturer's instructions.
TempO-Seq MouseWT v1.1 probe set

treatment_protocol: Pancreatic islets were incubated with complete RPMI media (10% FBS and 1% PenStrep) containing vehicle (0.9% saline) or 10 uM cisplatin for 48 hours. Islets were maintained in a 5% CO2 incubator at 37C.

value: Pancreatic islets

value: WT

tag: strain

value: Saline Vehicle Control

tag: biosample id

value: male

tag: plate layout_position


title: CAL51 NC3

description: Gene expression after p53 activation

source_name: CAL51 + DMSO3


title: CAL51 5-FU

description: Gene expression after p53 activation

source_name: CAL51 + 5-FU


title: ΔmutT4::mutT4 -RppH replicate 1

description: Library name: mutT4_comp_no_rpph_1

value: delta mutT4::mutT4

value: exponential phase


title: Islets, vehicle control, biol rep1


title: Islets, vehicle control, biol rep2


title: ΔmutT4 +RppH replicate 2

description: Library name: mutT4_with_rpph_2

value: delta mutT4


title: ΔmutT4 +RppH replicate 3

description: Library name: mutT4_with_rpph_3


title: BLGSP-71-27-00513

value: Burkitt lymphoma biopsy


title: BLGSP-71-29-00527


title: ΔmutT4 +RppH replicate 1

description: Library name: mutT4_with_rpph_1


title: Islets, 10 uM cisplatin, biol rep2

value: 10 uM cisplatin


title: BLGSP-71-29-00526


title: Fesource_NP_rep2

source_name: Roots of plants grown for 24 h in a NS without FeNaEDTA and supplied with FePO4 NPs as Fe source.


title: Fe-deficient_rep3

source_name: Roots of plants grown for 24 h in a NS without FeNaEDTA.


title: Fesource_NP_rep3


title: BLGSP-71-27-00512

source_name: Tumour


title: ΔmutT4 -RppH replicate 3

description: Library name: mutT4_no_rpph_3

value: mc26030 (H37Rv delta RD1 delta panCD) derivative


title: Fe-deficient_rep2


title: Fesource_NP_rep1


title: BLGSP-71-29-00524

value: Ramos


title: Islets, 10 uM cisplatin, biol rep1


title: BLGSP-71-27-00509


title: ΔmutT4 -RppH replicate 2

description: Library name: mutT4_no_rpph_2


title: ΔmutT4 -RppH replicate 1

description: Library name: mutT4_no_rpph_1


title: Fe-deficient_rep1


title: BLGSP-71-27-00429


title: WT +RppH replicate 3

description: Library name: WT_log_with_rpph_3

source_name: mc26030 (H37Rv delta RD1 delta panCD)

value: mc26030 (H37Rv delta RD1 delta panCD)


title: Mouse DRG, P9, Stress, Male1

city: Cincinnati

first: Mark

middle: L

last: Baccei

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

data_processing:
Illumina BaseSpace Sequence Hub RNA-Seq Alignment v2.0.2
Reads were aligned to mm10 mouse reference genome using STAR, then quantified using Salmon. Normalization and Differential Gene Expression analysis was performed with DESeq2.
mm10
STAR
Salmon
Assembly: DESeq2
Supplementary files format and content: DESeq2 differential gene analysis merged with normalized expression data for all samples.

source_name: Dorsal root ganglia

extract_protocol:
Total RNA was extracted using Norgen Total RNA Purification Plus micro kit (NORGEN) including genomic DNA removal.
cDNA libraries were constructed using NEBNext Ultra II Directional Library Prep kit (New England Biosciences)

treatment_protocol: Dam and pups underwent neonatal limited bedding (NLB, which induces chronic early life stress) or control bedding protocol from postnatal day (P)2-P9.

value: Dorsal root ganglia

value: neonatal limited bedding protocol (stress)


title: BLGSP-71-27-00430


title: Mouse DRG, P9, Stress, Male3


title: BLGSP-71-27-00427


title: WT +RppH replicate 2

description: Library name: WT_log_with_rpph_2


title: WT +RppH replicate 1

description: Library name: WT_log_with_rpph_1


title: Mouse DRG, P9, Stress, Female3

value: female


title: Islets, 10 uM cisplatin, biol rep3


title: Mouse DRG, P9, Stress, Male2


title: BLGSP-71-27-00428


title: Psource_bulk_rep3

source_name: Roots of plants grown for 24 h in a NS without KH2PO4 and supplied with non-nano FePO4 (bulk) as source of P.

value: root


title: WT -RppH replicate 3

description: Library name: WT_log_no_rpph_3


title: Mouse DRG, P9, Stress, Female1


title: Mouse DRG, P9, Stress, Female2


title: WT -RppH replicate 2

description: Library name: WT_log_no_rpph_2


title: Psource_bulk_rep2


title: BLGSP-71-27-00421


title: Mouse DRG, P9, Control, Male3

value: control bedding protocol (control)


title: Psource_bulk_rep1


title: WT -RppH replicate 1

description: Library name: WT_log_no_rpph_1


title: BLGSP-71-27-00414


title: Psource_NP_rep3

source_name: Roots of plants grown for 24 h in a NS without KH2PO4 and supplied with FePO4 NPs as P source.


title: Psource_NP_rep2


title: BLGSP-71-27-00422


title: P-deficient_rep3

source_name: Roots of plants grown for 24 h in a NS without KH2PO4.


title: Psource_NP_rep1


title: Mouse DRG, P9, Control, Male2


title: Mouse DRG, P9, Control, Male1


title: Mouse DRG, P9, Control, Female3


title: AV13_03_Young_biological replicate 1

city: Manchester

first: Amaya

last: Viros

address: Wilmslow Road

department: Skin Cancer Ageing

country: United Kingdom

institute: Cancer Research UK

description: Library name: Sample 3

data_processing:
Fastq files were aligned to hg38 (ensembl release 85)  BAM alignments were quantified in R (version 3.6.1) using featureCounts from the Rsubread library (version 2.0.1).
Assembly: GRCm38_ensembl_102
Supplementary files format and content: text with raw data

source_name: mammary fat pad

growth_protocol: Mammary fat pads of young and aged c57b/6j animals, 8 weeks and 14 months

extract_protocol:
RNA was extracted using Qiagen RNA extraction kit (Qiagen, Cat no. 74104) as per manual instructions. As for mammary fat pads, tissues were chopped into small pieces and digested in buffer using tungsten carbide beads (Cat no. 69997, Qiagen) and tissue lyser for 30s. Lysed tissues were immediately processed as per manual’s instructions (Cat no. 74014, Qiagen). 1mg of purified RNA was sent for RNA sequencing analysis.
Total RNASeq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, E7760) and the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs, E7400). An input of 1000ng of total RNA was used with 9 cycles of amplification.

value: mammary fat pad


title: BLGSP-71-26-00400


title: P-deficient_rep1


title: AV13_02_Young_biological replicate 2

description: Library name: Sample 2


title: BLGSP-71-26-00399


title: BLGSP-71-26-00398


title: AV13_01_Old_biological replicate 1

description: Library name: Sample 1


title: Mouse DRG, P9, Control, Female1

value: WT


title: Control_rep2

source_name: Roots of plants grown fro 24 h in a complete NS.


title: Control_rep3


title: Ex vivo cultured HBC 48-2, scRNAseq

city: Baltimore

first: Guanghui

last: Yang

address: 3400 North Charles Street

department: Biology

institute: Howard Hughes Medical Institute/The Johns Hopkins University

description: Library name: HBC_pair_48-2

library_source: transcriptomic single cell

data_processing:
Base calling was finished with RTA2.
Sequenced reads were trimmed using Trimmomatic ver. 0.39 by indicating “NexteraPE-PE.fa” as the adapter sequence file. Trimmed paired reads were then mapped to the reference genome using STAR ver. 2.7.11a. The reference genome contains sequences of GRCm38 and ERCC spike-in.
StringTie ver. 2.2.1 was used to generate counts of genes in the GTF reference downloaded from ENSEMBL(release 100) as well as all ERCC spike-in genes.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM, TPM values for each sample.

source_name: Olfactory epithelium

growth_protocol: Mouse olfactory epithelium (OE) tissues were dissected from adult mice (6-8 weeks old) 2 days after the methimazole injection. The collected OE tissue was finely minced in complete HBC culture medium and subjected to multiple enzymatic digestions to collect horizontal basal cells (HBCs). HBCs were cultured in dishes pre-coated with suitable extracellular matrix based on experimental needs and complete HBC medium was used in all experiments.

extract_protocol:
Single daughter cells after division of ex vivo cultured primary HBC cells were collected individually using mouth pipette with pairing information noted. Each cell was lysed and 1 ml of pre-diluted (1:10^6) ERCC spike-in was added to the single cell lysate.
RNAs inside single cell lysate were captured by oligo-dT beads and then processed following the G&T-seq protocol to construct the single cell RNA-Seq library.

value: Olfactory epithelium

value: Horizontal basal cell

value: Wild type


title: BLGSP-71-26-00397


title: WKO_3_5

city: Trieste

first: Roberto

last: Amadio

address: Padriciano 99

institute: ICGEB Trieste

description: Library name: Sample 10

data_processing:
Library sequencing was performed by Macrogen Europe nad raw FTP files containinf FastQ were provided.
FastQ files were md5sum checked
FastQC, Trimming by Trimgalore and alignment to GRCm38/mm10 by STAR were performed in R software
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file contain normalized reads as count matrix

source_name: Primary BMDM

growth_protocol: BMDM were flushed from femours of WT or WASp KO mice and differentiated in culture for 7 days in RPMI, supplemented with 20 ng/mL of recombinant mouse MCSF.

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen) and 5 ng of total RNA were used for mRNA library preparation
RNA-seq libraries were prepared using mRNA Library Prep Kit (WATCHMAKER) following manufacture instruction.

treatment_protocol: Vertical confinement based on PDMS micropillars was used to confined cells at 3µm of height for 1 h.

value: Primary BMDM

value: WKO

value: Confined


title: P-deficient_rep2


title: WKO_3_2

description: Library name: Sample 9


title: GD2438_NPC_HSPG2_OE

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to human genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: hg38
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

source_name: NPSCs

growth_protocol: Cells were cultured in complete medium [αMEM supplemented with 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin, and 0.25 μg/mL fungizone (Invitrogen, Carlsbad, CA, USA)] in a humidified incubator at 37°C, 5% CO2, and 21% O2 with medium change every other day.

extract_protocol:
Total RNAs were isolated by using Trizol (Invitrogen) and purified by using an RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instructions.
RNA-Seq library were prepared by using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) following manufacturer’s instructions.

treatment_protocol: Passage 5 cells were transduced with lentiviral vectors of GFP (pRSC-SFFV-Puro-GFP-wpre), HSPG2-KO (pRSC-U6-sgHSPG2-SFFV-Cas9-puro-wpre), and HSPG2-OE (pRSC-SFFV-HSPG2-E2A-Puro-wpre) in the presence of 4 μg/mL protamine sulfate (MilliporeSigma) followed by puromycin selection.

value: NPSCs

value: HSPG2 OE


title: BLGSP-71-26-00396

value: Burkitt lymphoma biopsy


title: Ex vivo cultured HBC 48-1, scRNAseq

description: Library name: HBC_pair_48-1


title: GD2437_NPC_Ctrl

value: Ctrl


title: BLGSP-71-27-00411


title: Ex vivo cultured HBC 47-2, scRNAseq

description: Library name: HBC_pair_47-2


title: WKO_3_1

description: Library name: Sample 8


title: BLGSP-71-23-00440


title: Control_rep1


title: Mouse DRG, P9, Control, Female2

value: Dorsal root ganglia


title: GD2436_NPC_HSPG2_KO2

value: HSPG2 KO2


title: BLGSP-71-23-00436


title: WT_3_6

description: Library name: Sample 7


title: GD2435_NPC_HSPG2_KO1

value: HSPG2 KO1


title: Ex vivo cultured HBC 46-2, scRNAseq

description: Library name: HBC_pair_46-2


title: WT_3_3

description: Library name: Sample 6


title: BLGSP-71-23-00408


title: GD2434_NPC_GFP

value: GFP


title: Ex vivo cultured HBC 46-1, scRNAseq

description: Library name: HBC_pair_46-1


title: WT_3_2

description: Library name: Sample 5


title: BLGSP-71-23-00405


title: Ex vivo cultured HBC 45-2, scRNAseq

description: Library name: HBC_pair_45-2


title: GD2433_IPFSC_HSPG2_OE

source_name: IPFSCs

value: IPFSCs


title: GD2432_IPFSC_Ctrl


title: WKO_NC1

description: Library name: Sample 3

value: Control


title: GD2431_IPFSC_HSPG2_KO2


title: WKO_NC3

description: Library name: Sample 4


title: Ex vivo cultured HBC 45-1, scRNAseq

description: Library name: HBC_pair_45-1


title: BLGSP-71-23-00361


title: BLGSP-71-22-00347


title: WT_NC3

description: Library name: Sample 2

value: WT


title: Ex vivo cultured HBC 47-1, scRNAseq

description: Library name: HBC_pair_47-1

value: Olfactory epithelium


title: Ex vivo cultured HBC 44-1, scRNAseq

description: Library name: HBC_pair_44-1

value: Horizontal basal cell


title: BLGSP-71-22-00339


title: WT_NC1

description: Library name: Sample 1


title: GD2429_IPFSC_GFP


title: Ex vivo cultured HBC 43-2, scRNAseq

description: Library name: HBC_pair_43-2

value: Wild type


title: BLGSP-71-22-00338


title: Sorghum-Root-7 d-ZnLim-3

city: Cold Spring Harbor

first: Sunita

last: Kumari

state: New York

address: One Bungtown Road

institute: Cold Spring Harbor Lab

description:
Library name: S33R_4
RNA-seq of Sorghum: Root-7 d-ZnLim-3

data_processing:
For mapping reads we used Sorghum bicolor v3.1BTx623 (Cooper et al., 2019). reference genome (https://phytozome-next.jgi.doe.gov/info/Sbicolor_v3_1_1). RNAseq data was analyzed with the DRAGEN Bio-IT Platform (v3.8) using default parameters (Cooper et al., 2019).
Assembly: reference genome (https://phytozome-next.jgi.doe.gov/info/Sbicolor_v3_1_1)
Supplementary files format and content: FullTPMMatrix_SampleMean_Annotations.csv

organism: Sorghum bicolor

source_name: Root

growth_protocol: Seeds of Sorghum bicolor cv. BTx623 were germinated on filter paper in 6 cm petri dishes, then transplanted to a hydroponic growth system with a temperature setting of 21-27ºC in a greenhouse. S. bicolor cv. BTx623 seedlings were transplanted into modified Hoagland’s solution (1.25 mM KNO3, 1.25 mM Ca(NO3)2, 250 µM NH4NO3, 500 µM MgSO4, 250 µM KH2PO4, 50 µM H3BO3, 10 µM MnSO4, 0.2 µM CuSO4, 0.5 µM Na2MoO4, 1 µM ZnSO4, 50 µM NaFe(III)EDTA, pH 5.6) 7 days after germination.

extract_protocol:
Total RNA was extracted from root and leaf samples using the Spectrum Plant Total RNA kit (Sigma-Aldrich). Approximately 100 mg of ground tissues were lysed in 850 µl of preheated CTAB buffer. Proteins were removed by mixing with 600 µl of chloroform-isoamyl alcohol (24:1 v:v). After centrifugation, the supernatant was passed through the filter column provided in the Spectrum Plant Total RNA kit (Sigma-Aldrich) and total RNAs were extracted following the manufacturer's manual.
A total of 181 RNAseq libraries from sorghum samples were generated and sequenced by Texas A&M University Genomics and Bioinformatics Service (https://www.txgen.tamu.edu) using Perkin Elmer Nextflex Rapid Directional RNA-seq kit 2.0 including Nextflex Poly-A-Selection 2.0 beads for polyA enrichment. All 181 samples were sequenced using a 2X150 v1.5 bp paired end (PE) approach and four lanes on an Illumina Novaseq 6000 S4 instrument targeting 20-30 million reads per sample.

treatment_protocol: After three-week acclimation in the hydroponic system, seedlings were randomized and transplanted into modified Hoagland’s solutions with different ZnSO4 and NaFe(III)EDTA concentrations: control solution (1 µM ZnSO4, 50 µM NaFe(III)EDTA), Zn deficiency (ZnLim) solution (0 µM ZnSO4, 50 µM NaFe(III)EDTA), excess Zn (ZnEx) solution (100 µM ZnSO4, 50 µM NaFe(III)EDTA), Fe deficiency (FeLim) solution (1 µM ZnSO4, 0 µM NaFe(III)EDTA), and excess Fe (FeEx) solution (1 µM ZnSO4, 1 mM NaFe(III)EDTA). Samples for RNA extraction were collected between 10:00 AM and 12:00 PM from three individual plants to represent three biological replicates. Leaf and root samples were collected at the same time points in parallel for RNA extraction and ICP-MS measurements.

value: Root


title: PC3 ATPS Rep2

city: Toronto

first: Gobi

last: Thillainadesan

state: Ontario

address: 2075 Bayview Ave., S1-18

institute: Sunnybrook Research Institute

description:
Sample_6366
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv

data_processing:
Quality control of sequencing reads was performed by discarding those with a quality score below Q20 on a 4bp sliding window.
Size selection was subsequently applied, retaining reads ranging from 18 to 35 base pairs in length.
Alignment done using STAR aligner to the hg38 human genome and annotation of the small RNAs were conducted using the Comprehensive Platform for Small RNA-Seq data Analysis (COMPSRA).
Normalization of the reads was executed by converting the raw counts to Transcripts Per Million (TPM) to facilitate comparative analysis across different sample groups.
Small RNAs were annotated into categories such as microRNA, circRNA, and snoRNA.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains TPM normalized values for microRNA counts
Supplementary files format and content: tab-delimited text file contains TPM normalized values for snoRNA counts
Supplementary files format and content: tab-delimited text file contains TPM normalized values for circRNA counts

source_name: Prostate

growth_protocol: PC3 and MDA-231 cells were obtained from ATCC (CRL-1435) and maintained in Dulbecco's Modified Eagle Medium (DMEM) (Wisent Bio Products) supplemented with 5% FBS.

extract_protocol:
EV RNA isolation in this study was conducted using TRIzol-choloroform method followed by isopropanol precipitation and purification using Qiagen exoRNeasy Midi Kit, following the manufacture's protocol. For ATPS isolated EVs after dextranase treatment, ratio between the volume of EV samples, TRIzol (Thermo Fisher Scientific) and choloroform (Fisher Scientific) was 1:5:1. Top aqueouse layer after TRIzol-choloroform separation was mixed with isopropanol (Sigma-Aldrich), 1:1 in volume. RNA was precipitated overnight at -20 °C. For UC isolated EVs, EV pellets were directly mixed with TRIzol. RNA isolation from human cells were conducted using the same TRIzol method.
Single-end Small RNA sequencing libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (NEB#E7560S), following manufacture’s instruction.

value: Prostate

value: epithelial


title: Ex vivo cultured HBC 43-1, scRNAseq

description: Library name: HBC_pair_43-1


title: PC3 ATPS Rep1

description:
Sample_6365
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Ex vivo cultured HBC 42-2, scRNAseq

description: Library name: HBC_pair_42-2


title: Sorghum-Root-7 d-ZnLim-1

description:
Library name: S40R_4
RNA-seq of Sorghum: Root-7 d-ZnLim-1


title: Ex vivo cultured HBC 44-2, scRNAseq

description: Library name: HBC_pair_44-2


title: BLGSP-71-23-00401

extract_protocol: Standard Protocol


title: BLGSP-71-22-00337


title: BLGSP-71-22-00334


title: MDA cell Rep1

description:
Sample_6363
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv

source_name: Breast

value: Breast


title: MDA cel Rep2

description:
Sample_6364
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Sorghum-Root-7 d-ZnLim-2

description:
Library name: S18R_4
RNA-seq of Sorghum: Root-7 d-ZnLim-2


title: BLGSP-71-22-00332


title: PC3 cell Rep2

description:
Sample_6362
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: GD2430_IPFSC_HSPG2_KO1


title: Ex vivo cultured HBC 42-1, scRNAseq

description: Library name: HBC_pair_42-1


title: Sorghum-Root-7 d-ZnEx-4

description:
Library name: S46R_4
RNA-seq of Sorghum: Root-7 d-ZnEx-4


title: BLGSP-71-22-00335


title: Sorghum-Root-7 d-ZnEx-3

description:
Library name: S58R_4
RNA-seq of Sorghum: Root-7 d-ZnEx-3


title: BLGSP-71-21-00243


title: Sorghum-Root-7 d-ZnEx-5

description:
Library name: S50R_4
RNA-seq of Sorghum: Root-7 d-ZnEx-5


title: PC3 cell Rep1

description:
Sample_6361
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Ex vivo cultured HBC 41-2, scRNAseq

description: Library name: HBC_pair_41-2


title: Ex vivo cultured HBC 40-2, scRNAseq

description: Library name: HBC_pair_40-2


title: BLGSP-71-22-00330


title: Sorghum-Root-7 d-ZnEx-2

description:
Library name: S67R_4
RNA-seq of Sorghum: Root-7 d-ZnEx-2


title: Ex vivo cultured HBC 41-1, scRNAseq

description: Library name: HBC_pair_41-1


title: MDA Qiagen Rep2

description:
Sample_6376
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Ex vivo cultured HBC 40-1, scRNAseq

description: Library name: HBC_pair_40-1


title: Sorghum-Root-7 d-ZnEx-1

description:
Library name: S19R_4
RNA-seq of Sorghum: Root-7 d-ZnEx-1


title: MDA Qiagen Rep1

description:
Sample_6375
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Ex vivo cultured HBC 39-2, scRNAseq

description: Library name: HBC_pair_39-2


title: Sorghum-Root-7 d-FeLim-3

description:
Library name: S59R_4
RNA-seq of Sorghum: Root-7 d-FeLim-3


title: PC3 Qiagen Rep2

description:
Sample_6374
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: BLGSP-71-21-00186


title: Ex vivo cultured HBC 39-1, scRNAseq

description: Library name: HBC_pair_39-1


title: PC3 Qiagen Rep1

description:
Sample_6373
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Sorghum-Root-7 d-FeLim-1

description:
Library name: S15R_4
RNA-seq of Sorghum: Root-7 d-FeLim-1


title: BLGSP-71-19-00523


title: MDA VC Rep2

description:
Sample_6372
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Sorghum-Root-7 d-FeEX-2

description:
Library name: S16R_4
RNA-seq of Sorghum: Root-7 d-FeEX-2


title: PC3 VC Rep2

description:
Sample_6370
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Sorghum-Root-7 d-Control-3

description:
Library name: S10R_4
RNA-seq of Sorghum: Root-7 d-Control-3


title: MDA VC Rep1

description:
Sample_6371
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: BLGSP-71-19-00520


title: Ex vivo cultured HBC 37-1, scRNAseq

description: Library name: HBC_pair_37-1


title: BLGSP-71-19-00521


title: Ex vivo cultured HBC 37-2, scRNAseq

description: Library name: HBC_pair_37-2


title: PC3 VC Rep1

description:
Sample_6369
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: Sorghum-Root-7 d-FeEX-1

description:
Library name: S4R_4
RNA-seq of Sorghum: Root-7 d-FeEX-1


title: BLGSP-71-21-00187


title: BLGSP-71-19-00519


title: Sorghum-Root-7 d-Control-2

description:
Library name: S29R_4
RNA-seq of Sorghum: Root-7 d-Control-2


title: Ex vivo cultured HBC 36-2, scRNAseq

description: Library name: HBC_pair_36-2


title: KPC-cell_Alkbh5 KO_m6A-seq_Rep 2_INPUT

city: Guangzhou

first: Zhou

last: yifan

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Sequenced reads were cleaned for adaptor and low-quality sequence, then m6A-seq and PAR CLIP-seq reads were mapped to mm10 using Bowtie 2, RNA-seq reads using STAR.
For RNS-seq, read counts were calculated using RSEM and the differentially expressed mRNAs were calculated by the R package DESeq2.
The m6A-enriched regions (peaks) in each sample were detected by exomePeak2. The m6A peaks were retained and merged using BEDTools and then annotated using HOMER. The read coverage of each peak in m6A-IP and input were calculated using Multicov from BEDTools.
For PAR CLIP-seq, peaks were calculated and selected with P < 0.0001 by using Piranha software (version 1.2.1) and then annotated by homer
Assembly: mm10
Supplementary files format and content: bigwig

source_name: KPC cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
For RNA-seq, the clustering of the indexed samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). For RNA m6A-seq, sequencing libraries for m6A-IP and input samples were prepared and sequenced on an Illumina HiSeqX Ten PE150 platform. For PAR-CLIP, library construction was performed by employing the NEBNext small RNA library prep kit (E7330S) and then sequenced on an Illumina HiSeq 4000.
PARCLIP-seq, RNA-seq, RNA m6A-seq

value: KPC cells

value: Murine pancreatic cancer cell line

value: Alkbh5 KO


title: BLGSP-71-21-00185

data_processing: minfi package (v.1.40.0) in R environment (v.4.1.3)

value: Burkitt lymphoma biopsy


title: Ex vivo cultured HBC 36-1, scRNAseq

description: Library name: HBC_pair_36-1


title: Sorghum-Root-7 d-Control-1

description:
Library name: S25R_4
RNA-seq of Sorghum: Root-7 d-Control-1


title: Sorghum-Root-7 d-FeLim-2

description:
Library name: S34R_4
RNA-seq of Sorghum: Root-7 d-FeLim-2


title: MDA ATPS Rep2

description:
Sample_6368
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: BLGSP-71-19-00133


title: BLGSP-71-19-00522


title: Ex vivo cultured HBC 38-2, scRNAseq

description: Library name: HBC_pair_38-2


title: Ex vivo cultured HBC 38-1, scRNAseq

description: Library name: HBC_pair_38-1


title: Sorghum-Root-4 d-ZnLim-3

description:
Library name: S17R_3
RNA-seq of Sorghum: Root-4 d-ZnLim-3


title: Ex vivo cultured HBC 35-2, scRNAseq

description: Library name: HBC_pair_35-2


title: MDA ATPS Rep1

description:
Sample_6367
240403_miRNA_TPM_innate.csv
240415_circRNA_TPM_innate.csv
240415_snoRNA_TPM_innate.csv


title: BLGSP-71-19-00130


title: iNeu-3

first: Xing

institute: GIBH

description: Library name: Sample 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Assembly: GRCh38/hg38
Supplementary files format and content: count

source_name: iPSCs derived

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSCs derived

value: iPSCs derived granulocytes

value: granulocytes differentiation


title: Ex vivo cultured HBC 35-1, scRNAseq

description: Library name: HBC_pair_35-1


title: BLGSP-71-19-00129

first: Ryan

institute: Simon Fraser University

source_name: Tumour


title: Ex vivo cultured HBC 34-2, scRNAseq

description: Library name: HBC_pair_34-2


title: iNeu-2

description: Library name: Sample 5


title: Sorghum-Root-4 d-ZnLim-1

description:
Library name: S76R_3
RNA-seq of Sorghum: Root-4 d-ZnLim-1


title: iNeu-1

description: Library name: Sample 4


title: BLGSP-71-19-00127


title: Sorghum-Root-4 d-ZnEx-2

description:
Library name: S69R_3
RNA-seq of Sorghum: Root-4 d-ZnEx-2


title: PB-Neu-3

description: Library name: Sample 3

source_name: Peripheral blood

value: Peripheral blood

value: Peripheral blood mobilized CD15+ cells

value: no treatment


title: Ex vivo cultured HBC 33-2, scRNAseq

description: Library name: HBC_pair_33-2

value: Olfactory epithelium


title: BLGSP-71-19-00125


title: Ex vivo cultured HBC 33-1, scRNAseq

description: Library name: HBC_pair_33-1

value: Horizontal basal cell


title: PB-Neu-2

description: Library name: Sample 2

value: WT


title: PB-Neu-1

description: Library name: Sample 1

value: Peripheral blood  CD15+ cells


title: BLGSP-71-19-00123


title: BLGSP-71-19-00126


title: Ex vivo cultured HBC 32-2, scRNAseq

description: Library name: HBC_pair_32-2

value: Wild type


title: P14, non-diseased

city: Bratislava

first: Natália

last: Matyašovská

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

data_processing:
Raw miRNA sequencing data were analyzed using the Qiagen GeneGlobe online tool (https://geneglobe.qiagen.com/us/analyze)
Data was processed for normalization to VST values and differential expression analysis was conducted using DESeq2 v1.36.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw read counts data for each sample

source_name: FFPE

extract_protocol:
Total RNA was isolated from FFPE tissue, using NucleoSpin totalRNA FFPE XS extraction kit.
Small RNA cDNA libraries were generated using QIAseq miRNA library kit, implementing 16 amplification cycles for 100 ng input, and 19 PCR cycles for 10 ng input.

value: FFPE

tag: tissue type

value: non-diseased pancreatic tissue delineated from pancreatic adenocarcinoma tissues


title: Sorghum-Root-4 d-FeLim-2

description:
Library name: S54R_3
RNA-seq of Sorghum: Root-4 d-FeLim-2

value: Root


title: Sorghum-Root-4 d-FeLim-3

description:
Library name: S27R_3
RNA-seq of Sorghum: Root-4 d-FeLim-3


title: BLGSP-71-19-00121

city: Burnaby

last: Morin

address: 8888 University Drive


title: P13, non-diseased


title: Sorghum-Root-4 d-ZnLim-2

description:
Library name: S38R_3
RNA-seq of Sorghum: Root-4 d-ZnLim-2


title: Ex vivo cultured HBC 32-1, scRNAseq

description: Library name: HBC_pair_32-1


title: BLGSP-71-19-00128


title: AV13_04_Old_biological replicate 2

description: Library name: Sample 4

value: mammary fat pad


title: Sorghum-Root-4 d-FeLim-1

description:
Library name: S23R_3
RNA-seq of Sorghum: Root-4 d-FeLim-1


title: BLGSP-71-19-00118


title: Ex vivo cultured HBC 31-1, scRNAseq

description: Library name: HBC_pair_31-1


title: P12, non-diseased


title: Ex vivo cultured HBC 34-1, scRNAseq

description: Library name: HBC_pair_34-1


title: Sorghum-Root-4 d-FeEX-3

description:
Library name: S55R_3
RNA-seq of Sorghum: Root-4 d-FeEX-3


title: Sorghum-Root-4 d-ZnEx-3

description:
Library name: S11R_3
RNA-seq of Sorghum: Root-4 d-ZnEx-3


title: P11, non-diseased


title: BLGSP-71-19-00115


title: Sorghum-Root-4 d-FeEX-2

description:
Library name: S5R_3
RNA-seq of Sorghum: Root-4 d-FeEX-2


title: Ex vivo cultured HBC 30-2, scRNAseq

description: Library name: HBC_pair_30-2


title: P10, non-diseased


title: BLGSP-71-19-00114


title: Sorghum-Root-4 d-FeEX-1

description:
Library name: S24R_3
RNA-seq of Sorghum: Root-4 d-FeEX-1


title: Ex vivo cultured HBC 30-1, scRNAseq

description: Library name: HBC_pair_30-1


title: Sorghum-Root-4 d-Control-3

description:
Library name: S72R_3
RNA-seq of Sorghum: Root-4 d-Control-3


title: Ex vivo cultured HBC 31-2, scRNAseq

description: Library name: HBC_pair_31-2


title: P8, non-diseased


title: Ex vivo cultured HBC 29-2, scRNAseq

description: Library name: HBC_pair_29-2


title: Ex vivo cultured HBC 29-1, scRNAseq

description: Library name: HBC_pair_29-1


title: P7, non-diseased


title: BLGSP-71-19-00113


title: BLGSP-71-19-00111


title: P6, tumor

value: pancreatic neuroendocrine cancer sample


title: BLGSP-71-19-00110

value: Burkitt lymphoma biopsy


title: Sorghum-Root-4 d-Control-1

description:
Library name: S14R_3
RNA-seq of Sorghum: Root-4 d-Control-1


title: BLGSP-71-19-00116


title: BLGSP-71-19-00107


title: Ex vivo cultured HBC 28-2, scRNAseq

description: Library name: HBC_pair_28-2


title: Sorghum-Root-21 d-ZnLim-3

description:
Library name: S32R_6
RNA-seq of Sorghum: Root-21 d-ZnLim-3


title: P4, tumor


title: Sorghum-Root-21 d-ZnLim-2

description:
Library name: S37R_6
RNA-seq of Sorghum: Root-21 d-ZnLim-2


title: Ex vivo cultured HBC 27-2, scRNAseq

description: Library name: HBC_pair_27-2


title: BLGSP-71-19-00106


title: Ex vivo cultured HBC 27-1, scRNAseq

description: Library name: HBC_pair_27-1


title: BLGSP-71-19-00105


title: Ex vivo cultured HBC 26-2, scRNAseq

description: Library name: HBC_pair_26-2


title: Sorghum-Root-21 d-ZnEx-3

description:
Library name: S70R_6
RNA-seq of Sorghum: Root-21 d-ZnEx-3


title: Sorghum-Root-4 d-Control-2

description:
Library name: S68R_3
RNA-seq of Sorghum: Root-4 d-Control-2


title: BLGSP-71-19-00104


title: P1, tumor


title: BLGSP-71-19-00102


title: Ex vivo cultured HBC 26-1, scRNAseq

description: Library name: HBC_pair_26-1


title: Sorghum-Root-21 d-ZnEx-2

description:
Library name: S51R_6
RNA-seq of Sorghum: Root-21 d-ZnEx-2


title: P5, tumor


title: Ex vivo cultured HBC 25-2, scRNAseq

description: Library name: HBC_pair_25-2


title: Sorghum-Root-21 d-ZnEx-1

description:
Library name: S36R_6
RNA-seq of Sorghum: Root-21 d-ZnEx-1


title: HeLa-NAT10_RNA-seq_Mock treated_#2

city: Austin

first: Blerta

last: Xhemalce

state: Texas

address: 2500 Speedway

institute: University of Texas at Austin

data_processing:
Analysis of TGIRT-seq small RNA libraries: For all samples, reads were adapter trimmed using Cutadapt v3.2 from both the 3' end [adapter AGATCGGAAGAG] and 5' end [adapter GATCGTCGGACT], and requiring a minimum read size of 18 bp. Read pairs were merged using Flash v1.2.11 requiring a minimum of 5 bp of overlap, and only merged fragments were used for alignment. We assembled a custom human small RNA reference from several published databases, including nuclear tRNAs from tRNAdb, mitochondrial tRNAs from mitotRNAdb, piwiRNAs from piRNAdb, microRNAs from miRBase, and ribosomal RNA from annotations in the UCSC Genome Table Browser. We padded both ends of each sequence with 10 N’s (to capture non-templated end modifications), concatenated the resulting FASTA files, and built a reference genome using STAR v2.5.2b with default parameters, except for the following: --genomeSAindexNbases 7 --genomeChrBinNbits 10 (to accommodate the high count and short length of human sRNA sequences). We mapped all processed libraries against this reference using STAR v2.5.2b with default parameters, except for the following: --outSAMprimaryFlag AllBestScore --seedSearchStartLmax 15 --outFilterScoreMinOverLread 0.25 --seedSearchLmax 15. Counts per sRNA were obtained using samtools idxstats. Allelic counts were obtained using the pysamstats utility (https://github.com/alimanfoo/pysamstats) and detected variants were filtered to require a depth of at least 50 reads in each sample. The allelic proportions were used to compute Bhattacharya coefficients, in-group and out-group distances, and finally Bhattacharya distance differences. Analysis of RNA-seq libraries: For all samples, reads were adapter trimmed using Cutadapt v3.2 from both the 3' end [adapter AGATCGGAAGAGCACACGTC] and 5' end [adapter AGATCGGAAGAGCGTCGTG], and requiring a minimum read size of 18 bp. Trimmed reads were aligned against the hg38 reference genome using STAR v2.5.2b with default parameters, sorted, and indexed using samtools. Gene counts were generated against the Gencode v21 annotation set using featureCounts only counting fragments identified as Primary by STAR. Allele counts were generated using bcftools mpileup, and required a read to be uniquely aligned and have base quality > 20. Allelic counts were filtered to remove indels and exported to tab-delimited text files using bcftools filter, bcftools norm, and bcftools query.
Assembly: hg38
Supplementary files format and content: Small RNA counts for TGIRT-seq samples contains two columns, where the first is the small RNA name and the second is the read count. Gene counts for RNA-seq samples is structured as the standard output format from featureCounts.

source_name: HeLa

growth_protocol: Cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ).

extract_protocol:
Total RNA was extracted using the Norgen RNA and Protein purification kit.
Libraries from the gel-purified tRNAs were constructed using the TGIRT-seq protocol. Libraries from rRNA depleted total RNA were constructed using an RNA-seq (strand specific) protocol.

treatment_protocol: Control and NAT10-KO cells were used. 3 µg of total RNA was treated with Mock or Sodium Cyanobohydride (NaCNBH3). 1 µg of RNA was used for gel purification of full length tRNA and TGIRT-seq, and 1 µg was used for rRNA depletion and RNA-seq.

value: HeLa

value: Mock


title: BLGSP-71-17-00359


title: Sorghum-Root-21 d-FeLim-3

description:
Library name: S44R_6
RNA-seq of Sorghum: Root-21 d-FeLim-3


title: Ex vivo cultured HBC 25-1, scRNAseq

description: Library name: HBC_pair_25-1


title: BLGSP-71-17-00357


title: HeLa-NAT10_RNA-seq_Mock treated_#1


title: HeLa-WT_RNA-seq_Mock treated_#2


title: BLGSP-71-17-00356


title: Sorghum-Root-21 d-FeLim-2

description:
Library name: S43R_6
RNA-seq of Sorghum: Root-21 d-FeLim-2


title: P3, tumor


title: Ex vivo cultured HBC 24-1, scRNAseq

description: Library name: HBC_pair_24-1


title: P2, tumor


title: Sorghum-Root-21 d-ZnLim-1

description:
Library name: S1R_6
RNA-seq of Sorghum: Root-21 d-ZnLim-1


title: BLGSP-71-17-00238


title: Sorghum-Root-4 d-ZnEx-1

description:
Library name: S57R_3
RNA-seq of Sorghum: Root-4 d-ZnEx-1


title: Sorghum-Root-21 d-FeLim-1

description:
Library name: S12R_6
RNA-seq of Sorghum: Root-21 d-FeLim-1


title: HeLa-WT_RNA-seq_Mock treated_#1


title: Ex vivo cultured HBC 23-2, scRNAseq

description: Library name: HBC_pair_23-2


title: HeLa-NAT10-KO_RNA-seq_NaCNBH3 treated_#2


title: BLGSP-71-17-00234


title: Sorghum-Root-21 d-FeEX-3

description:
Library name: S28R_6
RNA-seq of Sorghum: Root-21 d-FeEX-3


title: BLGSP-71-17-00232


title: Sorghum-Root-21 d-FeEX-2

description:
Library name: S6R_6
RNA-seq of Sorghum: Root-21 d-FeEX-2


title: Ex vivo cultured HBC 23-1, scRNAseq

description: Library name: HBC_pair_23-1


title: HeLa-NAT10-KO_RNA-seq_NaCNBH3 treated_#1


title: HeLa-WT_RNA Seq_NaCNBH3 treated_#2


title: BLGSP-71-17-00231


title: Ex vivo cultured HBC 22-2, scRNAseq

description: Library name: HBC_pair_22-2


title: Sorghum-Root-21 d-FeEX-1

description:
Library name: S35R_6
RNA-seq of Sorghum: Root-21 d-FeEX-1


title: Ex vivo cultured HBC 28-1, scRNAseq

description: Library name: HBC_pair_28-1


title: Sorghum-Root-21 d-Control-3

description:
Library name: S22R_6
RNA-seq of Sorghum: Root-21 d-Control-3


title: HeLa-NAT10-KO_tRNA_TGIRT-seq_Mock treated_#2

data_processing:
Analysis of TGIRT-seq small RNA libraries: For all samples, reads were adapter trimmed using Cutadapt v3.2 from both the 3' end [adapter AGATCGGAAGAG] and 5' end [adapter GATCGTCGGACT], and requiring a minimum read size of 18 bp. Read pairs were merged using Flash v1.2.11 requiring a minimum of 5 bp of overlap, and only merged fragments were used for alignment. We assembled a custom human small RNA reference from several published databases, including nuclear tRNAs from tRNAdb, mitochondrial tRNAs from mitotRNAdb, piwiRNAs from piRNAdb, microRNAs from miRBase, and ribosomal RNA from annotations in the UCSC Genome Table Browser. We padded both ends of each sequence with 10 N’s (to capture non-templated end modifications), concatenated the resulting FASTA files, and built a reference genome using STAR v2.5.2b with default parameters, except for the following: --genomeSAindexNbases 7 --genomeChrBinNbits 10 (to accommodate the high count and short length of human sRNA sequences). We mapped all processed libraries against this reference using STAR v2.5.2b with default parameters, except for the following: --outSAMprimaryFlag AllBestScore --seedSearchStartLmax 15 --outFilterScoreMinOverLread 0.25 --seedSearchLmax 15. Counts per sRNA were obtained using samtools idxstats. Allelic counts were obtained using the pysamstats utility (https://github.com/alimanfoo/pysamstats) and detected variants were filtered to require a depth of at least 50 reads in each sample. The allelic proportions were used to compute Bhattacharya coefficients, in-group and out-group distances, and finally Bhattacharya distance differences. Analysis of RNA-seq libraries: For all samples, reads were adapter trimmed using Cutadapt v3.2 from both the 3' end [adapter AGATCGGAAGAGCACACGTC] and 5' end [adapter AGATCGGAAGAGCGTCGTG], and requiring a minimum read size of 18 bp. Trimmed reads were aligned against the hg38 reference genome using STAR v2.5.2b with default parameters, sorted, and indexed using samtools. Gene counts were generated against the Gencode v21 annotation set using featureCounts only counting fragments identified as Primary by STAR. Allele counts were generated using bcftools mpileup, and required a read to be uniquely aligned and have base quality > 20. Allelic counts were filtered to remove indels and exported to tab-delimited text files using bcftools filter, bcftools norm, and bcftools query.
Assembly: hg38
Supplementary files format and content: Small RNA counts for TGIRT-seq samples contains two columns, where the first is the small RNA name and the second is the read count. Gene counts for RNA-seq samples is structured as the standard output format from featureCounts.
Library strategy: TGIRT-seq


title: BLGSP-71-08-00217


title: HeLa-WT_RNA Seq_NaCNBH3 treated_#1


title: BLGSP-71-08-00508


title: Ex vivo cultured HBC 21-2, scRNAseq

description: Library name: HBC_pair_21-2


title: Ex vivo cultured HBC 22-1, scRNAseq

description: Library name: HBC_pair_22-1


title: Sorghum-Root-21 d-Control-2

description:
Library name: S2R_6
RNA-seq of Sorghum: Root-21 d-Control-2


title: Ex vivo cultured HBC 21-1, scRNAseq

description: Library name: HBC_pair_21-1


title: HeLa-NAT10-KO_tRNA_TGIRT-seq_Mock treated_#1


title: Sorghum-Root-21 d-Control-1

description:
Library name: S20R_6
RNA-seq of Sorghum: Root-21 d-Control-1


title: BLGSP-71-08-00213


title: BLGSP-71-08-00212


title: HeLa-WT_tRNA_TGIRT-seq_Mock treated_#2


title: BLGSP-71-08-00210


title: HeLa-WT_tRNA_TGIRT-seq_Mock treated_#1


title: Sorghum-Root-2 d-ZnLim-2

description:
Library name: S9R_2
RNA-seq of Sorghum: Root-2 d-ZnLim-2


title: Sorghum-Root-2 d-ZnLim-1

description:
Library name: S8R_2
RNA-seq of Sorghum: Root-2 d-ZnLim-1


title: Ex vivo cultured HBC 20-1, scRNAseq

description: Library name: HBC_pair_20-1


title: HeLa-NAT10-KO_tRNA_TGIRT-seq_NaCNBH3 treated_#1


title: HeLa-NAT10-KO_tRNA_TGIRT-seq_NaCNBH3 treated_#2


title: BLGSP-71-08-00207


title: Sorghum-Root-2 d-ZnEx-3

description:
Library name: s50R_2
RNA-seq of Sorghum: Root-2 d-ZnEx-3


title: Ex vivo cultured HBC 19-2, scRNAseq

description: Library name: HBC_pair_19-2


title: BLGSP-71-08-00206


title: Ex vivo cultured HBC 18-1, scRNAseq

description: Library name: HBC_pair_18-1


title: HeLa-WT_tRNA_TGIRT-seq_NaCNBH3 treated_#2


title: Sorghum-Root-2 d-FeLim-3

description:
Library name: S7R_2
RNA-seq of Sorghum: Root-2 d-FeLim-3


title: HeLa-WT_tRNA_TGIRT-seq_NaCNBH3 treated_#1


title: Ex vivo cultured HBC 18-2, scRNAseq

description: Library name: HBC_pair_18-2


title: Sorghum-Root-2 d-ZnEx-1

description:
Library name: S58R_2
RNA-seq of Sorghum: Root-2 d-ZnEx-1


title: BLGSP-71-08-00205


title: Sorghum-Root-2 d-ZnLim-3

description:
Library name: S49R_2
RNA-seq of Sorghum: Root-2 d-ZnLim-3


title: BLGSP-71-08-00204


title: pSpc4_CLI

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description:
The Click-iT® RNA Alexa Fluor® 488 Imaging Kit from Invitrogen was used to label and detect newly synthesized RNA
FPKM_CLI_genes.csv
FPKM_CLI_genes.5Scorrected.csv

data_processing:
Spike-in mapping and quantification were performed as follows. Raw reads from the EU-RNA-seq and RNA-seq datasets were mapped onto the mouse genome (mm10) by using STAR (v2.5.2a). The StringTie tool was used for transcript assembly while Ballgown was used for quantification to get a FPKM expression matrix. After quantification, the resulting FPKM expression matrix from the EU-RNA-seq dataset was corrected using the expression of 5S ribosomal genes which are considered to be transcriptionally stable during spermatogenesis. The expression matrix was divided by the scaled sum of all 5S ribosomal genes.
Assembly: mm10
Supplementary files format and content: FPKM_TOT_genes.csv: FPKM expression matrix of total RNA (comma-separated format)
Supplementary files format and content: FPKM_CLI_genes.csv: FPKM expression matrix of RNA extracted from the ERCC RNA Spike-in Mix (comma-separated format)
Supplementary files format and content: FPKM_CLI_genes.5Scorrected.csv: FPKM expression matrix of RNA extracted from the ERCC RNA Spike-in Mix (comma-separated format). Data were normalized according to the level of 5S RNA

source_name: testis

growth_protocol: NMRI mice were housed in controlled photoperiod conditions (lights on from 08:00 to 20:00) and supplied with commercial food and tap water ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN) and ERCC RNA Spike-in Mix (Life technologies 4456740) were added.
RNA-seq libraries were generated using Next Ultra II Directional RNA Library Prep kit (NEB) and ribosomal RNA depletion according to the manufacturer’s protocols. EU-RNA-seq libraries were made like the RNA-seq but without any depletion.

treatment_protocol: Synchronisation of spermatogenesis in NMRI mice was performed using WIN18,446 and retinoic acid as described by Hogarth et al. (Biol Reprod, 2013; 88, 40). Two mg of 5-ethynyl uridine (EU, Click-iT™ Nascent RNA Capture Kit, Invitrogen) per mouse were injected at 24 days post-partum (dpp) to label nascent RNA. Three hours later mice were sacrificed and cells were FACS-sorted based on their ploidy to isolate spermatogonia, leptotene and pachytene spermatocytes.

value: testis

value: pachytene spermatocytes

value: wild-type

tag: individual


title: Sorghum-Root-2 d-FeLim-2

description:
Library name: S13R_2
RNA-seq of Sorghum: Root-2 d-FeLim-2


title: Ex vivo cultured HBC 17-2, scRNAseq

description: Library name: HBC_pair_17-2


title: BLGSP-71-08-00200


title: Sorghum-Root-2 d-FeLim-1

description:
Library name: S3R_2
RNA-seq of Sorghum: Root-2 d-FeLim-1


title: pSpc3_CLI


title: Ex vivo cultured HBC 17-1, scRNAseq

description: Library name: HBC_pair_17-1


title: BLGSP-71-08-00199


title: pSpc2_CLI


title: Ex vivo cultured HBC 24-2, scRNAseq

description: Library name: HBC_pair_24-2


title: Ex vivo cultured HBC 19-1, scRNAseq

description: Library name: HBC_pair_19-1


title: lSpc4_CLI

value: leptotene spermatocytes


title: BLGSP-71-08-00197


title: Ex vivo cultured HBC 16-1, scRNAseq

description: Library name: HBC_pair_16-1

value: Olfactory epithelium


title: BLGSP-71-08-00194


title: pSpc1_CLI


title: Ex vivo cultured HBC 16-2, scRNAseq

description: Library name: HBC_pair_16-2

value: Horizontal basal cell


title: Sorghum-Root-2 d-FeEX-3

description:
Library name: S65R_2
RNA-seq of Sorghum: Root-2 d-FeEX-3


title: Sorghum-Root-2 d-FeEX-2

description:
Library name: S42R_2
RNA-seq of Sorghum: Root-2 d-FeEX-2


title: Ex vivo cultured HBC 15-2, scRNAseq

description: Library name: HBC_pair_15-2


title: BLGSP-71-08-00191


title: BLGSP-71-08-00059


title: lSpc3_CLI


title: Sorghum-Root-2 d-FeEX-1

description:
Library name: S31R_2
RNA-seq of Sorghum: Root-2 d-FeEX-1


title: Sorghum-Root-2 d-Control-3

description:
Library name: S45R_2
RNA-seq of Sorghum: Root-2 d-Control-3


title: lSpc2_CLI


title: Ex vivo cultured HBC 15-1, scRNAseq

description: Library name: HBC_pair_15-1


title: Sorghum-Root-2 d-Control-2

description:
Library name: S48R_2
RNA-seq of Sorghum: Root-2 d-Control-2


title: BLGSP-71-08-00057


title: lSpc1_CLI


title: Ex vivo cultured HBC 14-1, scRNAseq

description: Library name: HBC_pair_14-1


title: Sorghum-Root-2 d-Control-1

description:
Library name: S30R_2
RNA-seq of Sorghum: Root-2 d-Control-1


title: BLGSP-71-08-00056


title: Ex vivo cultured HBC 14-2, scRNAseq

description: Library name: HBC_pair_14-2


title: BLGSP-71-08-00053


title: Sorghum-Root-14 d-ZnLim-2

description:
Library name: s39R_5
RNA-seq of Sorghum: Root-14 d-ZnLim-2


title: Ex vivo cultured HBC 13-2, scRNAseq

description: Library name: HBC_pair_13-2


title: plSpc_CLI

value: preleptotene spermatocytes


title: Ex vivo cultured HBC 13-1, scRNAseq

description: Library name: HBC_pair_13-1


title: Sorghum-Root-14 d-ZnLim-1

description:
Library name: S61R_5
RNA-seq of Sorghum: Root-14 d-ZnLim-1


title: BLGSP-71-08-00050


title: Ex vivo cultured HBC 12-2, scRNAseq

description: Library name: HBC_pair_12-2


title: BLGSP-71-08-00048


title: Spg1_CLI

value: spermatogonia


title: Sorghum-Root-14 d-ZnEx-2

description:
Library name: S52R_5
RNA-seq of Sorghum: Root-14 d-ZnEx-2


title: Sorghum-Root-14 d-ZnEx-1

description:
Library name: S47R_5
RNA-seq of Sorghum: Root-14 d-ZnEx-1


title: Ex vivo cultured HBC 12-1, scRNAseq

description: Library name: HBC_pair_12-1

value: Wild type


title: pSpc4_TOT


title: Sorghum-Root-14 d-FeLim-3

description:
Library name: S26R_5
RNA-seq of Sorghum: Root-14 d-FeLim-3


title: BLGSP-71-08-00041


title: Spg2_CLI


title: BLGSP-71-08-00043


title: pSpc3_TOT


title: Ex vivo cultured HBC 11-1, scRNAseq

description: Library name: HBC_pair_11-1


title: Spg3_CLI


title: BLGSP-71-08-00040


title: BLGSP-71-08-00039


title: Ex vivo cultured HBC 20-2, scRNAseq

description: Library name: HBC_pair_20-2


title: Sorghum-Root-14 d-FeLim-2

description:
Library name: s53R_5
RNA-seq of Sorghum: Root-14 d-FeLim-2


title: Sorghum-Root-14 d-FeLim-1

description:
Library name: s66R5
RNA-seq of Sorghum: Root-14 d-FeLim-1


title: pSpc1_TOT


title: pSpc2_TOT


title: Ex vivo cultured HBC 10-1, scRNAseq

description: Library name: HBC_pair_10-1


title: Ex vivo cultured HBC 10-2, scRNAseq

description: Library name: HBC_pair_10-2


title: lSpc4_TOT


title: Sorghum-Root-14 d-FeEX-3

description:
Library name: s60R_5
RNA-seq of Sorghum: Root-14 d-FeEX-3


title: Ex vivo cultured HBC 11-2, scRNAseq

description: Library name: HBC_pair_11-2


title: Ex vivo cultured HBC 9-2, scRNAseq

description: Library name: HBC_pair_9-2


title: BLGSP-71-08-00036


title: Sorghum-Root-14 d-FeEX-2

description:
Library name: S75R_5
RNA-seq of Sorghum: Root-14 d-FeEX-2


title: lSpc3_TOT


title: Ex vivo cultured HBC 9-1, scRNAseq

description: Library name: HBC_pair_9-1


title: lSpc2_TOT


title: BLGSP-71-08-00035


title: lSpc1_TOT


title: Sorghum-Root-14 d-FeEX-1

description:
Library name: S56R_5
RNA-seq of Sorghum: Root-14 d-FeEX-1


title: BLGSP-71-08-00033


title: Ex vivo cultured HBC 8-2, scRNAseq

description: Library name: HBC_pair_8-2


title: Ex vivo cultured HBC 8-1, scRNAseq

description: Library name: HBC_pair_8-1


title: Sorghum-Root-14 d-Control-2

description:
Library name: S41R_5
RNA-seq of Sorghum: Root-14 d-Control-2


title: plSpc_TOT


title: BLGSP-71-08-00030


title: Ex vivo cultured HBC 7-2, scRNAseq

description: Library name: HBC_pair_7-2


title: BLGSP-71-08-00038


title: Spg3_TOT


title: Sorghum-Root-14 d-Control-1

description:
Library name: S71R_5
RNA-seq of Sorghum: Root-14 d-Control-1


title: Ex vivo cultured HBC 7-1, scRNAseq

description: Library name: HBC_pair_7-1


title: Sorghum-Root-14 d-Control-3

description:
Library name: S62R_5
RNA-seq of Sorghum: Root-14 d-Control-3


title: Sorghum-Root-1 h-ZnLim-2

description:
Library name: S37R_1
RNA-seq of Sorghum: Root-1 h-ZnLim-2


title: Spg2_TOT


title: BLGSP-71-08-00028


title: BLGSP-71-08-00029


title: BLGSP-71-08-00034


title: Sorghum-Root-1 h-ZnLim-3

description:
Library name: S32R_1
RNA-seq of Sorghum: Root-1 h-ZnLim-3


title: Spg1_TOT


title: Ex vivo cultured HBC 6-1, scRNAseq

description: Library name: HBC_pair_6-1


title: BLGSP-71-08-00027


title: Sorghum-Root-1 h-ZnLim-1

description:
Library name: S1R_1
RNA-seq of Sorghum: Root-1 h-ZnLim-1