title: LCM_RNA_SVZ

city: Cambridge

first: Dario

last: Bressan

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description:
Laser-Capture microdissection performed on e16.5 fresh frozen mouse brain
LCM RNA-Seq

data_processing:
Raw paired-end sequencing files from each LCM-dissected area were first filtered using the cutadapt package (v4.1) to remove the Illumina sequencing adapters from both the 5’ and 3’ of each sequencing read.
The filtered read 1 was then mapped on the mm10 was mapped on the mm10 reference genome (source: Illumina igenomes) using the STAR package (v 2.7.9a) with the following options: --outReadsUnmapped Fastx –outSAMtype BAM Unsorted --quantmode GeneCounts.
The resulting BAM files were then sorted and indexed using the samtools package (v1.9) commands
To produce UMI counts for each gene (as opposed to the raw counts produced by STAR), each BAM file was ran through the featureCounts command from the Subread package (v2.0.3) with default options against the same mm10 genome annotation described above
The resulting annotated BAM file was sorted again using samtools sort.
Genome coverage was calculated using the bamCoverage command from the deeptools package (v3.5.1) with the following options --normalizeUsing RPKM --binSize 1.
Differential expression was performed by merging the count matrices produced by the procedure described above. Each count was normalized by dividing it by the total number of gene-assigned reads in the library and multiplying it by 1,000,000, then fold change and log10 change ratios between the SVZ and the cortical areas were calculated using excel.
Assembly: mm10
Supplementary files format and content: csv file including the raw number of counts as produced by the STAR package
Supplementary files format and content: Csv file including the read counts for each gene in each spatial area, as well as the normalized counts (normalized by total number of UMI), and the fold and log10 expression ratios between the two spatial areas.
Library strategy: LCM RNA-Seq

growth_protocol: All animal procedures were performed in accordance with the Animal (Scientific Procedures) Act 1986 under UK Home Office project license PAD85403A. Animals were housed under standard husbandry conditions per UK Home Office and Institute regulations. Individually ventilated cages housed four to five animals under a 12-h light, 12-h dark cycle at the CRUK Cambridge Institute animal facility. Relative humidity was kept between 45 and 65% with a temperature range of 20-24°C. Animals had free access to water and pelleted food. Embryos samples were taken at embryonic day 16.5 from ethically euthanised pregnant dams following timed mating.

extract_protocol:
For embryo collection, pregnant dams were euthanised by CO2 overdose with exposure to gas in rising concentration followed by cervical dislocation. Embryos were euthanised by cooling on ice followed by decapitation. Heads were frozen in OCT resin by immersion in a dry ice/isopentane bath followed by storage at -80C. Cryosections were cut using a XXXX cryostat under RNAse free conditions. The instrument was wiped with RNAse-ZAP prior to use and between different blocks. A different blade was used for each block. Sample blocks were equilibrated to the chamber temperature for 15 minutes prior to sectioning, and then mounted on the object holder. Sections were cut at a thickness of 10 uM and collected on RNAse-free SuperFrost Plus microscope slides (one section per slide). Slides were left at room temperature for 20-30 seconds to help tissue adhesion and then stored on dry ice (short term) or at -80C (long term).
Tissue sections from e16.5 mouse embryos (as described in the “Animal housing” section) were cut as described in the “Tissue collection” section. Sections were stained with Haematoxylin/Eosin using the following fast procedure: 1) 40 seconds in 75% ethanol, 2) 30 seconds in mQ water, 3) 30 seconds in Harris’ modified Haematoxylin solution (Sigma HHS16), 4) 3x 30 seconds in mQ water, 5) 30 seconds in a 1:1000 dilution o 28% Ammonium Hydroxide (Sigma 338818) in mQ water, 6) 10 seconds in 5% Eosin Y solution (Sigma 318906), 7) 30 seconds each in 70%, 95% and 100% ethanol, 7) 2x 20 seconds in Xylene. The stained sections were imaged and cut on a Leica LMD6000 LCM microscope. Areas corresponding to the sub-ventricular zone and to the cortex (matching the illumination areas for the BALI experiment) were used for cutting. Tissue fragments were collected in the caps of 0.5ml RNAse-free tubes in 50ul of lysis solution from the RNAqueous micro RNA extraction kit (Thermo Scientific). RNA extraction was performed according to the RNAqeous micro kit protocol for LCM extraction. In short: 1) 50ul of lysis buffer were added to the 50ul including the sample, and the tube was incubated at 42C for 30 minutes, 2) the collection column was pre-wetted with 30ul lysis solution, 3) 3ul LCM additive were added to each sample, 4) 129ul of 100ul Ethanol were added to each sample, 5) the samples were bound to the collection column, and the column was washed with 180ul wash solution 1 and twice with 180ul of wash solution 2/3, 6) RNA was eluted with a 5 minute incubation step with 10ul of pre-heated (95C) elution solution. Purified RNA was treated with DNAse1 using the optional DNAse treatment step in the RNAqueous kit: 1) 1ul of DNAse buffer and 1ul of DNAse I enzyme were added to each sample, 2) samples were incubated for 20 minutes at 37C, 3) 2ul of DNAse inactivation reagent were added to each sample, and the inactivated DNAse was removed by centrifugation. RNA abundance and quality were evaluated by Agilent Tapestation (DNA5000 High-Sensitivity screentape). RNA sequencing libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) according to the recommended protocol using 15ng RNA as input material. Library quality and abundance was measured by Tapestation (DNA5000 screentape) and qPCR (KAPA Illumina library quantification kit). Libraries were sequenced on a NextSeq500 instrument using paired end 75nt reads.

value: Brain

tag: age

tag: area 1

value: Subventricular zone

tag: barcode length


title: LCM_RNA_CTX

status: Public on Jun 03 2026

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Brain

tag: tissue

value: Cortex


title: CUT&RUN:_HLF_BAF155-KO_H3K27ac_1

city: Chapel Hill

first: Jesse

last: Raab

state: NC

address: Rm 5028 Genetic Medicine Building

country: USA

institute: UNC Chapel Hill - Raab Lab

description:
Library name: 381
H3K27ac

library_source: genomic

data_processing:
all fastq procesed with pipeline at github.com/raab-lab/cut-n-run
bowtie2 for alignment
picard MarkDuplicates
peak calls with macs2
bamCoverage using counts from csaw for normalized coverage bigwig for IGV
Assembly: hg38
Supplementary files format and content: normalized bigwig files
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

source_name: Liver Cancer

growth_protocol: 10% FBS DMEM + p/s

extract_protocol:
CUT&RUN protocol was adapted from Epicypher and Skene and Henikoff 2017]. Briefly, cells were detached from plates and counted for a total of ~500,000 cells per antibody per cell line. Cells were pelleted at RT for 3 minutes at 300 g. Cells were washed 2x with Wash Buffer (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, protease inhibitor (1 tablet/30mL Roche)). 11 μL of Concanavalin beads (Bangs Laboratories) per sample were 2x washed with cold Bead Activation Buffer (20mM HEPES ph7.9, 10mM KCl, 1mM CaCl2, and 1mM MnCl2). Cells were then added to beads and incubated with rotation for 5 minutes at RT. Samples were placed on a magnet to remove the supernatant and resuspended in 50 μL Wash Buffer with 0.05% Digitonin and 2mM EDTA. Corresponding antibodies were added to the samples and were incubated overnight at 4℃ with rotation. The following day, beads were washed on a magnet 3x with Digitonin-Wash Buffer (Wash Buffer, 0.05% Digitonin). Beads were resuspended in 50 μL Digitonin-Wash Buffer with guinea pig anti-rabbit secondary antibody (1:100, Novus, NBP1-72763) and incubated at 4℃ for 1 hour with rotation. Following secondary antibody binding, beads were washed 4x with cold Digitonin-Wash buffer on a magnet and then resuspended in 50 μL pAG Mnase solution (~700 ng/ul pAG-Mnase, Digitonin-Wash Buffer) (purified in-house [47]). Beads were incubated with pAG Mnase solution for 1 hour at 4℃ with rotation. Beads were washed 4x with cold Digitonin-Wash Buffer on a magnet and then resuspended in 50 μL cold Digitonin-Wash Buffer. 1 μL of 100 mM CaCl2 was added to the samples and incubated in a cold metal block in ice at 4℃ for 30 minutes. 50 μL of Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05µg/µL RNAseA (ThermoFisher, EN0531), 0.1% Triton X-100) was added to the samples and then incubated at 37℃ for 30 minutes in a thermocycler. DNA was purified from the samples using the Zymo ChIP Clean and Concentrator kit (Genesee Scientific,  11-379C) following the manufacturer’s protocol.
Libraries were prepared using the KAPA HyperPrep DNA kit with modifications. End-repair/A-tailing was performed in 25 μL volume reactions and performed on a thermocycler with the following protocol: 12℃ for 15 minutes, 37℃ for 15 minutes, 58℃ for 45 minutes, hold at 12℃. For adapter ligation, half volumes were used with 5 μL of 750 nM Kapa Unique Dual-Indexed Adapters (KAPA, 8861919702). Samples were incubated for 1 hour at RT and cleaned with a 1.1X KAPA Pure Bead clean up 2x. A library amplification was performed with KAPA HiFi HotStart ReadyMix with the following program: 98℃ for 45 seconds, 98℃ for 15 seconds, 60℃ for 10 seconds, Cycle to Step 2 13x, 71℃ for 60 seconds, hold at 4℃. A final KAPA Pure Bead 1X clean up was performed on the amplified libraries before being quantified and pooled on TapeStation 4200 and Qubit.

treatment_protocol: CRISPR/CAS9 Knockout with re-expression of BAF155 WT or R1064K Mutant by Lentivirus

value: Liver Cancer

tag: cell line

value: HLF

tag: genotype

tag: batch


title: CUT&RUN:_HLF_BAF155-KO_H3K27ac_3

description:
Library name: 617
H3K27ac


title: F5581_Mouse FoB/GCB/ABC/PB dataset_BCR

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA53563_v755_v793

data_processing:
Sequencing was performed on NovaSeq 6000 or NovaSeq X Plus platform in 28+90, 101+101 or 151+151 base paired-end mode.
Illumina Real Time Analysis RTA3 v3.4.4 or RTA4 v4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0 or 9.0.1, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and B cell receptor repertoire profiling.
Assembly: mm10, GRCh38 or GRCm39
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the BCR clonotype information
Library strategy: CITE-seq

source_name: Spleen

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides (HTO) or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 or v3 with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping User Guide.

value: Spleen

tag: strain

value: Wild type

tag: treatment

value: Resiquimod

tag: library type

value: BCR


title: C2C12 cells, iMyoD1, no differentiation, dox treatment, biol rep 2

city: Berkeley

first: Oscar

last: Whitney

address: 1951 Oxford St

institute: UC Berkeley

description: Library name: 75k_GM_plusdox_rep2

data_processing:
nf-core/atacseq v 2.1.2 pipeline
Assembly: mm10
Supplementary files format and content: bigWig generated by deeptools
Supplementary files format and content: NarrowPeak files generated by MACS2 peak calling

source_name: skeletal muscle

growth_protocol: C2C12 skeletal muscle myoblasts were maintained in DMEM supplemented with 20% fetal bovine serum, penicillin streptomycin in a humidified atmosphere with 5% CO2 at 37C. Cells were seeded at 75,000 or 300,000 per well of a 12-well dish for no differentiation and 24 h serum starvation conditions

extract_protocol:
Fragment purification via Zymo DNA clean and concentrator-5.
Library preparation was performed using NEBNext Ultra II DNA library Prep kit for Illumina, following manufacturer protocols, employing custom Nextera primers

treatment_protocol: C2C12 were differentiated via 24 h of serum starvation (DM), and/or treated with doxycycline to induce exogenous MyoD1 expression

value: skeletal muscle

tag: cell type

value: skeletal muscle myoblast

value: endogenous MyoD1 + dox-inducible Halo-MyoD1

value: 24 h dox


title: CUT&RUN:_HLF_BAF155-KO_H3K27ac_2

description:
Library name: 405
H3K27ac


title: BALI_RNA_SVZ_vs_CTX_e165

description:
BALI RNA-Seq with single barcode, 2 areas, e16,5 fresh frozen mousebrain
BALI spatial profiling - RNA-Seq

data_processing:
the fastq files produced by high-throughput sequencing were processed through the following pipeline using custom bash shell scripts: 1) UMI extraction and annotation using the umitools package (v0.5.5) with the command umi_tools extract --bc-pattern=NNNNNN, 2) extraction of reads including each BALI barcode from both paired fastq files using the cutadapt package (v4.1) (options -g ^[barcode], -e 1, --pair-filter-both, --match-read-wildcards), 3) Extraction of the final adapter placed before the sequencing library itself (RT oligo) using the same command as above. This produced one fastq file for each spatial area.
The read 1 fastq file from each spatial region was mapped on the mm10 reference genome (source: Illumina igenomes) using the STAR package (v 2.7.9a) with the following options: --outReadsUnmapped Fastx –outSAMtype BAM Unsorted --quantmode GeneCounts
The resulting BAM files were then sorted and indexed using the samtools package (v1.9) commands
To produce UMI counts for each gene (as opposed to the raw counts produced by STAR), each BAM file was ran through the featureCounts command from the Subread package (v2.0.3) with default options against the same mm10 genome annotation described above
The resulting annotated BAM file was sorted again using samtools sort.
UMIs counts per gene were calculated using the umi_tools count command (from the umitools package v0.5.5) with options --per-gene --gene-tag=XT --assigned-status-tag=XS, and UMIs were deduplicated using the umi_tools group command (to produce an overall quantification of all UMIs in each region) and umi_tools dedup command (to produce a deduplicated BAM file)
The deduplicated BAM files were sorted and indexed a third time, and genome coverage was calculated using the bamCoverage command from the deeptools package (v3.5.1) with the following options --normalizeUsing RPKM --binSize 1.
Differential expression was performed by merging the UMI count matrices produced by the procedure described above. Each count was normalized by dividing it by the total number of gene-assigned UMIs in the library and multiplying it by 1,000,000, then fold change and log10 change ratios between the SVZ and the cortical areas were calculated using excel
Assembly: mm10
Supplementary files format and content: Excel file including the number of reads containing each spatial barcode
Supplementary files format and content: Csv file including the UMI counts for each gene in each spatial area, as well as the normalized counts (normalized by total number of UMI), and the fold and log10 expression ratios between the two spatial areas.
Library strategy: BALI RNA-Seq

molecule: polyA RNA

extract_protocol:
For embryo collection, pregnant dams were euthanised by CO2 overdose with exposure to gas in rising concentration followed by cervical dislocation. Embryos were euthanised by cooling on ice followed by decapitation. Heads were frozen in OCT resin by immersion in a dry ice/isopentane bath followed by storage at -80C. Cryosections were cut using a XXXX cryostat under RNAse free conditions. The instrument was wiped with RNAse-ZAP prior to use and between different blocks. A different blade was used for each block. Sample blocks were equilibrated to the chamber temperature for 15 minutes prior to sectioning, and then mounted on the object holder. Sections were cut at a thickness of 10 uM and collected on RNAse-free SuperFrost Plus microscope slides (one section per slide). Slides were left at room temperature for 20-30 seconds to help tissue adhesion and then stored on dry ice (short term) or at -80C (long term).
All steps were performed under RNAse-free conditions. Cryosections of embryonic E16.5 brain (coronal plane) were retrieved from cold storage and equilibrated for 5 minutes at room temperature and then heated for 5 minutes at 37C on a metal heat block. Pap-pen was used to draw a hydrophobic boundary around each section, and let dry for 5 minutes at room temperature. Sections were incubated with 500 uL PBS to dissolve and remove the OCT embedding matrix, and fixed with 500 uL of 0.5% PFA in PBS for exactly 5 minutes at room temperature. Fixation was quenched by removing the PFA and promptly adding 1.25M Glycine in PBS, one quick wash and one wash for 5 minutes at room temperature. After washing twice in PBS for 5 minutes each, the sections were permeabilised in Permeabilization buffer (0.5% TritonX100 in PBS) for 15 minutes at room temp, and then washed in PBS 3 times for 5 minutes. The sections were incubated with 0.1N HCl for 5 minutes and washed 3 times in PBS (two quick washes, one 5 minutes wash). The section were heated for 5 minutes in pre-warmed PBS at 65C in an hybridization oven, and then snap-cooled in ice-cold PBS on ice for 10 minutes. From this point onwards all steps performed in light protected conditions. For each slide, an first RT mix (14uL) was prepared containing 2.5 uL of dNTPs (stock 10 mM each), 1.5uL of caged RT primer (BL621, 100 uM stock) in water, denatured for 5 minutes in 65C and the snap cooled on ice for >2 minutes. A second RT mix (36 uL) was prepared with 10 uL of 5x SuperScript-IV buffer, 2.5uL SuperScript-IV enzyme, 1 uL of RNAsin, 3uL of 100 uM TSO oligo (BL617),  5 uL of 5M Betaine, 0.5 uL ET-SSB, 2.5 uL of 100 mM DTT in nuclease free water, and added to the first mix, up to a total RT reaction volume of 50uL. Any excess PBS was removed from the slides, and 50 uL of RT mix was added directly on top of the sections, which were then covered with a 22x22 mm coverslip and incubated overnight (~16hrs) at 42C in a sealed humid chamber. The index oligos for the ligations were annealed at 45uM final in 2xSCC in the following pairs: BL599/BL623 (cycle 1, SZV) and BL601/BL624 (cycle 1, cortex). The annealing thermocycler conditions were as follows: 1) 95C for 5 minutes, 2) ramp down to 65 at 0.1C/second, 3) hold at 65C for 5 minutes, 4) ramp down to 12C at 0.1C/second, 5) hold at 12C. The slides were retrieved from the RT reaction, washed one in PBS then twice in 2xSSC for 5 minutes each. Nuclei were stained by incubating the section with Draq 5 (1:1000 dilution in 2xSSC) for 10 minutes, and then washed 2 times for 5 minutes in 2xSSC. Since the RT primer was directly caged, we proceed with two consecutive rounds of uncaging/ligation to mark the SVZ and cortex areas (bilaterally). For the uncaging, the slides were mounted with 200 uL of 2xSSC and a thin glass coverslip (22x22mm). The uncaging was performed on a SP5 Leica confocal system fitted with a 30mW 405nm solid state laser, illuminating each ROI for 5 minutes with the 405nm laser at maximum power. The slides were washed in 2xSSC, once quickly and once for 5 minutes, and then incubated for 5 minutes in 1x Ligation buffer (50 mM TrisHCl pH7.4, 10 mM MgCl2, 10 mM DTT, 1mM ATP). For each sample, a ligation mix (50 uL) was prepared as follows: index oligos (3 uM, alternating BL599/BL623and BL624/BL601 as appropriate), T4 ligase (100U/uL, NEB) in 1x T4 ligation buffer. The ligation mix was added directly to the sections, covered with a 22x22mm glass coverslip, and the reactions were incubated for 30 minutes at 25C in a humid chamber. The slides were then washed in 2xSSC+Draq5 (1:1000) once for 10 minutes, 2xSSC+10%EC once for 5 minutes and 2xSSC once for 5 minutes. After the serial ligations, a hybridization chamber was mounted on the slides, and the sections were lysed in 200 uL of Lysis Buffer (0.8 U/mL in RIPA buffer) at 60C overnight (~16 hrs) in a sealed humid chamber. All the following steps were not light protected anymore. The lysate was collected and purified with MinElute Reaction Clean-up column, and eluted in 25 uL of EB buffer. A small aliquote of the lysate (2uL) was used as input for a qPCR to measure the optimal cycling conditions for the amplification of the libraries. The qPCR reaction was set up as follows: 2 uL of purified lysate, 25 uL of 2x Q5 master mix, 0.25 uL of 50 uM universal forward Truseq primer, 0.5 uL of 50 uM index A012 Truseq primer 2.5 uL of 20x EVA-Green. The cycling protocol was 98C for 3 minutes, 40 cycles of 98C for 15 seconds, 68C for 20 seconds, 72C for 20 seconds, plate reading step. The number of cycles required to reach 1/3 of the maximum signal was selected for the final amplification of the libraries. The final amplification reaction was set as follows: 10 uL of purified lysate, 25 uL of 2x Q5 master mix, 0.25 uL of 50 uM universal forward Truseq primer, 0.5 uL of 50 uM index A012 Truseq primer, 2.5 uL of 20x EVA-Green. The cycling conditions were the same as the qPCR. The PCR reactions were purified with AmpureXP beads (0.8x) and eluted in 20 uL of EB buffer. The libraries were analysed on a Tapestation (D5000 cartridge) and quantified with KAPA library quantification kit prior to pooling. Sequencing was performed on a Novaseq (Illumina) instrument.

tag: area 2


title: SW620 44C water bath 0h replicate 1

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description:
Library name: SW_44_4_0
SW620 colorectal cancer cells incubated in 44C water bath (positive HT control) and harvested immediately (0h); biological replicate 1

data_processing:
RNA-Seq reads were mapped to human reference genome GRCh38.p7 (GENCODE release 25 genome annotation) with STAR (version 2.7.3a) using the following parameters --outFileNamePrefix mapping/star/all_mates/U_AMRF_03_08_0/out/ --outSAMunmapped Within --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000). Reads were assigned to genes with FeatureCounts (v2.0.6) using the following parameters  -t exon -g gene_id   -s 2 -p (with GENCODE relase 25, GRCh38 annotation gft file)
Assembly: GRCh38.p7
Supplementary files format and content: Comma separated count matrix with Featurecounts output for all samples

source_name: colon

extract_protocol:
Total RNA was isolated using the RNA extraction kit from Roboklon (Berlin, Germany) according to the manufacturer's instructions. For 0 h samples, cells were pelleted immediately after treatment, washed with PBS, and stored at -80°C. For 24 h samples, cells were re-seeded in 10 cm petri dishes and incubated for 24 hours at 37°C with 5% CO2 before RNA extraction. RNA quality and quantity were assessed using a NanoDrop 2000/2000c spectrophotometer (Peqlab).
RNA-seq libraries were prepared from extracted total RNA using a stranded poly(A)-selected library preparation protocol. Briefly, poly(A)+ RNA was enriched, fragmented, reverse-transcribed into cDNA, adapter-ligated, PCR-amplified, and quality controlled prior to sequencing.

value: colon

value: colorectal adenocarcinoma

value: wild type

value: 44C water bath 0h


title: CUT&RUN:_HLF_BAF155-KO_FLAG_4

description:
Library name: 973
FLAG


title: F5581_Mouse FoB/GCB/ABC/PB dataset_HTO

description: Library name: GA53564_v755

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-C0301 anti-mouse Hashtag 1 (FoB); TotalSeq-C0302 anti-mouse Hashtag 2 (GCB); TotalSeq-C0303 anti-mouse Hashtag 3 (ABC); TotalSeq-C0304 anti-mouse Hashtag 4 (PB)


title: mTreg_cKO

city: Wuhan

first: can

last: Lin

state: Hubei province

address: 237 Luoyu Road

department: School & Hospital of Stomatology

country: China

institute: Wuhan University

description: Library name: Sample 1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the wf-single-cell software v3.3.1.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
Regulatory T cells (Tregs) were isolated from Srsf3fl/+ Foxp3Cre-YFP female mice spleen by MACS using CD4+CD25+ Regulatory T Cell Isolation Kit according to the manufacturer's instructions.
Single-cell cDNA was generated using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index, 10× Genomics), amplified by PCR, and purified with SPRIselect magnetic beads (Beckman Coulter) according to the protocol. Full-length cDNA was enriched via biotin–streptavidin capture with Dynabeads M280 Streptavidin, then processed using the Oxford Nanopore Ligation Sequencing Kit V14 (SQK-NBD114.96) following manufacturer's guidelines. After barcoding with the Native Barcode Kit (NB01–NB96, SQK-NBD114.96)  and a 1× AMPure XP bead cleanup, 300 fmol of adapter ligated library was loaded onto a PromethION flow cell (vR10.4.4). The PromethION platform (Oxford Nanopore Technologies, ONT) generates an expression matrix with both gene-level (total gene expression) and transcript-level (individual isoform counts) data when used for single-cell third-generation sequencing, thanks to its full-length mRNA sequencing advantage.

treatment_protocol: No treatment.

value: spleen

value: Treg


title: brain, P53 KO (ONT)

city: Chengdu

first: chao

last: yang

state: Sichuan

address: No.20, Section 3, Renmin South Road

department: West China Second University Hospital

institute: Sichuan University

description: Library name: PKO-ONT

data_processing:
Nanopore raw data were basecalled and demutiplexed using Dorado (v.0.8.2) followed by read trimming with Porechop (0.2.4).
flair (v2.0.0) were used to align the mouse reference genome (mm10) and quantify
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: brain

extract_protocol:
Cells were harvested and  using Trizol to extract total RNA.
RNA libraries for Nanopore long-read RNA-seq were prepared using the cDNA-PCR Sequencing Kit (SQK-LSK110 + EXP-PCB096) following the manufacturers' protocols.

value: brain

value: primary cell

value: neural cells

value: Cre-LNP


title: brain, Tut1 and P53 KO

description: Library name: TPDKO

data_processing:
Sequence were trimmed for adaptor sequence/low-quality sequnce using Trimmomatic
Trimmed sequence reads were mapped to mm10 using hisat2
Stringtie were used to calculate TPM expression
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM expression for each sample

extract_protocol:
Cells were harvested and  using Trizol to extract total RNA.
RNA libraries for Illumina short-read RNA-seq were prepared using the Illumina Stranded mRNA Prep Ligation Kit following the manufacturers' protocols.


title: brain, Tut1 and P53 KO (ONT)

description: Library name: TPDKO-ONT


title: SW620 42C water bath plus RT 24h replicate 3

description:
Library name: SW_42RT_24_10_24
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested after 24h re-incubation; biological replicate 3

value: 42C water bath plus 8Gy gamma-radiation 24h


title: F5581_Mouse FoB/GCB/ABC/PB dataset_GEX

description: Library name: GA53562_v755

value: Spleen

value: Wild type

value: Resiquimod

value: mRNA


title: CUT&RUN:_HLF_BAF155-KO_BAF155me2_3

description:
Library name: 678
BAF155me2

value: Liver Cancer

value: HLF


title: SW620 42C water bath plus RT 0h replicate 3

description:
Library name: SW_42RT_24_10_0
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested immediately (0h); biological replicate 3

value: colon

value: colorectal adenocarcinoma

value: wild type

value: 42C water bath plus 8Gy gamma-radiation 0h


title: CUT&RUN:_HLF_BAF155-KO_FLAG_3

description:
Library name: 679
FLAG


title: SW620 42C water bath plus RT 24h replicate 2

description:
Library name: SW_42RT_10b_24
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested after 24h re-incubation; biological replicate 2


title: CUT&RUN:_HLF_BAF155-KO_BAF155me2_2

description:
Library name: 532
BAF155me2


title: brain, P53 KO

description: Library name: PKO


title: brain, Tut1 KO (ONT)

description: Library name: TKO-ONT


title: SW620 42C water bath plus RT 0h replicate 2

description:
Library name: SW_42RT_10b_0
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested immediately (0h); biological replicate 2


title: CUT&RUN:_HLF_BAF155-KO_FLAG_2

description:
Library name: 400
FLAG


title: brain, Tut1 KO

description: Library name: TKO


title: brain, wild type (ONT)

description: Library name: WT-ONT

value: empty LNP


title: CUT&RUN:_HLF_BAF155-KO_FLAG_1

description:
Library name: 376
FLAG


title: SW620 42C water bath plus RT 24h replicate 1

description:
Library name: SW_42RT_10_24
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested after 24h re-incubation; biological replicate 1


title: brain, wild type

description: Library name: WT


title: CUT&RUN:_HLF_BAF155-KO_BAF155me2_1

description:
Library name: 375
BAF155me2


title: Tut1_KO_repeat 2

description:
ko_2
nanopore sample 4
Nanopore RNA-seq

data_processing:
pychopper were used to identify, orient and rescue full-length cDNA reads.
Isoform counts were quantified by Flair v2.0.0.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Tab-delimited text file includes read counts for each Sample.

source_name: dorsal and medial palliums

extract_protocol:
RNA were harvested using RNeasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Ligation Sequencing Kit following manufacturer's protocols.

value: dorsal and medial palliums

tag: developmental stage

value: Tut1 knockout


title: SW620 42C water bath plus RT 0h replicate 1

description:
Library name: SW_42RT_10_0
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 42C water bath (HT+RT control) and harvested immediately (0h); biological replicate 1


title: Tut1_KO_repeat 1

description:
ko_1
nanopore sample 3
Nanopore RNA-seq


title: optic nerve, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 13

city: Mannheim

first: Lucas

last: Schirmer

address: Theodor-Kutzer-Ufer 1-3

institute: University of Heidelberg

description:
Library name: Sample 13
6 optic nerves pooled

data_processing:
The expression count matrices were generated by aligning the sequencing data to the GRCm39-2024-A reference transcriptome with Cell Ranger Count (v.7.0.0).
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated value files and matrix files

molecule: nuclear RNA

source_name: optic nerve

extract_protocol:
After nuclei isolation using Dounce homogenizers and ultracentrifugation at 107,163.6g for 2.5 h at 4°C, nuclei were loaded onto a microfluidic platform (Chromium X Series controller) aiming for 8,000 nuclei per reaction.
Libararies were generated according to the 10x Next GEM 3' Kit v.3.1 protocol.

value: optic nerve


title: SW620 42C water bath 24h replicate 3

description:
Library name: SW_42_09_11_24
SW620 colorectal cancer cells incubated in 42C water bath (HT control) and harvested after 24h re-incubation; biological replicate 3

value: 42C water bath 24h


title: CUT&RUN:_HLF_BAF155-WT_BAF155me2_3

description:
Library name: 528
BAF155me2


title: optic nerve, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 12

description:
Library name: Sample 12
6 optic nerves pooled


title: WT_repeat 2

description:
wt_2
nanopore sample 2
Nanopore RNA-seq

value: WT


title: SW620 42C water bath 0h replicate 3

description:
Library name: SW_42_09_11_0
SW620 colorectal cancer cells incubated in 42C water bath (HT control) and harvested immediately (0h); biological replicate 3

value: 42C water bath 0h


title: CUT&RUN:_HLF_BAF155-R1064K_BAF155me2_3

description:
Library name: 525
BAF155me2


title: SW620 42C water bath 24h replicate 2

description:
Library name: SW_42_25_10_24
SW620 colorectal cancer cells incubated in 42C water bath (HT control) and harvested after 24h re-incubation; biological replicate 2


title: WT_repeat 1

description:
wt_1
nanopore sample 1
Nanopore RNA-seq


title: optic nerve, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 11

description:
Library name: Sample 11
6 optic nerves pooled


title: CUT&RUN:_HLF_BAF155-WT_IgG_4

description:
Library name: 1002
IgG


title: Col_AA_polysome_rep3

city: Kaifeng

first: Xiaohong

last: Zhu

address: Jinming Street

institute: Henan University

data_processing:
Library strategy: Ribo-seq
illumina Novaseq6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Seedlings were grown vertically on 1/2 MS medium with 1% sucrose and 1.2% agar.

extract_protocol:
Total RNA of polysome or monosome fractions was precipitated and pooled for RNA-seq analysis. 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

treatment_protocol: Ten day old Col-0, 2OX and sextuple seedlings grown vertically on 1/2 MS agar plates were collected for monosomal and polysomal RNA isolation. Ten day old Col-0 seedlings were transferred from MS plates to 9-well plate containing 1mL 1/2 liquid MS medium per well and treated with 50uM antimycin for 5 hours (sample named as Col_AA), or treated with DMSO (sample named as Col_CK)

value: whole seedling

value: ten day old

value: wild type Col-0

tag: molecule subtype

value: polysomal RNA


title: SW620 42C water bath 0h replicate 2

description:
Library name: SW_42_25_10_0
SW620 colorectal cancer cells incubated in 42C water bath (HT control) and harvested immediately (0h); biological replicate 2


title: optic nerve, snRNA-seq, Olig2-cre;Piezo2f/f cKO, P120, Sample 10

description:
Library name: Sample 10
6 optic nerves pooled


title: CUT&RUN:_HLF_BAF155-R1064K_IgG_2

description:
Library name: 990
IgG

value: Liver Cancer


title: optic nerve, snRNA-seq, Piezo2f/f control, P120, Sample 4

description:
Library name: Sample 4
6 optic nerves pooled


title: Col_AA_polysome_rep2


title: SW620 42C water bath 24h replicate 1

description:
Library name: SW_42_24_10_24
SW620 colorectal cancer cells incubated in 42C water bath (HT control) and harvested after 24h re-incubation; biological replicate 1


title: CUT&RUN:_HLF_BAF155-R1064K_BAF155me2_2

description:
Library name: 987
BAF155me2

value: HLF


title: optic nerve, snRNA-seq, Piezo2f/f control, P120, Sample 3

description:
Library name: Sample 3
6 optic nerves pooled


title: SW620 42C water bath 0h replicate 1

description:
Library name: SW_42_24_10_0
SW620 colorectal cancer cells incubated in 42C water bath (HT control) and harvested immediately (0h); biological replicate 1

value: colon


title: Col_AA_polysome_rep1


title: CUT&RUN:_HLF_BAF155-WT_IgG_3

description:
Library name: 984
IgG


title: SW620 37C water bath plus RT 24h replicate 3

description:
Library name: SW_37RT_25_10_24
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 3

value: colorectal adenocarcinoma

value: 37C water bath plus 8Gy gamma-radiation 24h


title: Col_CK_polysome_rep3


title: optic nerve, snRNA-seq, Piezo2f/f control, P120, Sample 2

description:
Library name: Sample 2
6 optic nerves pooled


title: optic nerve, snRNA-seq, Piezo2f/f control, P120, Sample 1

description:
Library name: Sample 1
6 optic nerves pooled


title: CUT&RUN:_HLF_BAF155-WT_IgG_2

description:
Library name: 694
IgG


title: Col_CK_polysome_rep2


title: SW620 37C water bath plus RT 0h replicate 3

description:
Library name: SW_37RT_25_10_0
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 37C water bath and harvested immediately (0h); biological replicate 3

value: wild type

value: 37C water bath plus 8Gy gamma-radiation 0h


title: Plasma EV RNA-Seq, B11 (PLWoH)

city: Atlanta

first: Erica

middle: L

last: Johnson

state: GA

address: 720 Westview Dr SW

department: Department of Microbiology, Biochemistry, and Immunology

institute: Morehouse School of Medicine

description:
Library name: B11
Maternal plasma-derived EV RNA; sex: F; RIN: 1.9; strand-specific; 2×150 bp; ~20M reads/sample

data_processing:
Quality control / trimming with COMPSRA Quality Control module: adapter removal and filtering of low-quality bases using Phred≥20 thresholds (COMPSRA defaults; e.g., -rh 20 -rt 20 -rr 20). Reads with kit-specific randomized bases at ligation junctions were trimmed; qualified small-RNA read lengths retained.
Alignment with COMPSRA Alignment module using STAR against the human reference GRCh38/hg38 (update here to hg19 if that is what you used). Unmapped reads were retained by COMPSRA but only human-mapped reads were taken forward for annotation/quantification.
Annotation with COMPSRA Annotation module against pre-built small-RNA databases: miRNA (miRBase), piRNA (piRNABank, piRBase, piRNAcluster), tRNA (gtRNAdb), snRNA/snoRNA (GENCODE r27), and circRNA (circBase). Where needed, coordinates were harmonized to the selected human assembly using UCSC LiftOver (built into COMPSRA).
Quantification: feature-level raw read counts were produced per sample and aggregated into a sample × feature matrix. The submitted processed file contains untransformed integer counts (no DE-based filtering). Downstream DE analyses for the manuscript were performed in R/DESeq2 and are supplied only as supplementary analysis files if included.
Assembly: Homo sapiens GRCh38 (hg38)
Supplementary files format and content: smRNA_expression_count.csv — comma-separated matrix of raw integer counts.

source_name: Plasma

extract_protocol:
Plasma was separated by centrifugation. Extracellular vesicles (EVs) were isolated per manufacturer’s instructions, and EV RNA was extracted using the Qiagen exoRNeasy midi kit. RNA quantity/quality were assessed; RIN values are reported but are not a reliable quality metric for EV RNA.
Plasma was separated by centrifugation. Extracellular vesicles (EVs) were isolated per manufacturer’s instructions, and EV RNA was extracted using the Qiagen exoRNeasy midi kit. RNA quantity/quality were assessed; RIN values are reported but are not a reliable quality metric for EV RNA.

treatment_protocol: No experimental treatment was administered. Maternal peripheral blood was collected during pregnancy from two groups: cART-suppressed people living with HIV (PLWH) and HIV-negative controls (PLWoH). Group (PLWH vs PLWoH) is recorded in sample attributes.

value: Plasma

value: HIV negative


title: hippo_HET2 snRNA-seq

city: Toronto

first: Paul

middle: M

last: McKeever

state: ON

address: 60 Leonard Ave., 4th floor - 4KD481

department: Tanz CRND

country: Canada

institute: University of Toronto

description:
Library name: GEX_hippo_HET2
hippo_metadata.tsv.gz
hippo_annotations.tsv.gz
hippo_umap.tsv.gz
hippo_filtered_feature_bc_matrix.h5
hippo_multiome_seurat.rds

data_processing:
Raw base call files were demultiplexed using Illumina software to generate FASTQ files.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
FASTQ files were processed using Cell Ranger ARC (10x Genomics) to perform alignment, barcode assignment, and generation of paired gene expression and chromatin accessibility count matrices.
Gene expression reads were aligned to the mouse reference genome mm10 using STAR within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Assembly: mm10
Supplementary files format and content: Processed data files include filtered gene expression count matrices, chromatin accessibility peak count matrices, fragment files, and associated cell metadata generated from Cell Ranger ARC and downstream Seurat/Signac analyses.
Supplementary files format and content: Processed files are provided in standard formats including HDF5 (.h5), Matrix Market (.mtx), tab-delimited text (.tsv), and compressed fragment files (.tsv.gz) containing single-nucleus transcriptomic and chromatin accessibility measurements.

source_name: hippocampus

growth_protocol: C9orf72 wild-type, heterozygous knockout, and homozygous knockout mice were maintained under standard laboratory housing conditions with ad libitum access to food and water on a 12 h light/dark cycle. Brain tissue was collected from approximately 3-month-old animals.

extract_protocol:
Nuclei were isolated from frozen hippocampus and frontal cortex tissue using region-specific nuclei isolation workflows optimized for each brain region. Hippocampal nuclei were isolated using an iodixanol density gradient purification protocol following mechanical homogenization and filtration to enrich for intact nuclei and reduce debris contamination. Frontal cortex nuclei were isolated using the 10x Genomics Nuclei Isolation Kit according to the manufacturer’s protocol. Purified nuclei were counted and assessed prior to loading onto the 10x Genomics Chromium platform. RNA and chromatin accessibility information were simultaneously captured from individual nuclei using the Chromium Single Cell Multiome ATAC + Gene Expression workflow.
Single-nucleus multiomic libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform according to the manufacturer’s instructions. Briefly, isolated nuclei were subjected to transposition using Tn5 transposase to generate ATAC fragments, followed by GEM generation for simultaneous barcoding of gene expression and chromatin accessibility molecules from individual nuclei. Gene expression and ATAC libraries were amplified separately and sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus instruments.

treatment_protocol: No experimental treatments were applied prior to tissue collection. Hippocampus and frontal cortex tissues were rapidly dissected from frozen brain samples for downstream single-nucleus isolation.

value: hippocampus

value: C9orf72 heterozygous knockout


title: Plasma EV RNA-Seq, B14 (PLWoH)

description:
Library name: B14
Maternal plasma-derived EV RNA; sex: F; RIN: 1.1; strand-specific; 2×150 bp; ~20M reads/sample


title: Col_CK_polysome_rep1


title: CUT&RUN:_HLF_BAF155-WT_BAF155me2_2

description:
Library name: 690
BAF155me2


title: retina, snRNA-seq, Piezo2f/f, P120, Sample 3

description:
Library name: Sample 3
6 retinae pooled, FACS sorted for RGCs

source_name: retina

extract_protocol:
After nuclei isolation using Dounce homogenizers and ultracentrifugation at 500g for 5 min,  pelleted nuclei were resuspended in staining buffer containing primary antibodies targeting NeuN and RBPMS to detect RGCs for 15 minutes at 4 °C. Nuclei were washed, centrifuged at 500 × g for 5 minutes, stained with secondary antibodies and sorted using a BD FACSDiva device. Sorted NeuN+/RBPMS+ nuclei were pelleted at 500 × g for 5 minutes at 4 °C, resuspended, counted in a Neubauer chamber and adjusted to a concentration of ~600 nuclei µl–1. Nuclei were then loaded onto a microfluidic platform (Chromium X Series controller) aiming for 8,000 nuclei per reaction.
Libararies were generated according to the 10x Next GEM 3' Kit v.3.1 protocol.

value: retina

tag: Sex

value: female


title: retina, snRNA-seq, Piezo2f/f, P120, Sample 4

description:
Library name: Sample 4
6 retinae pooled, FACS sorted for RGCs


title: sextuple_polysome_rep3

value: whole seedling

value: sextuple mutant


title: SW620 37C water bath plus RT 0h replicate 2

description:
Library name: SW_37RT_24_10_0
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 37C water bath and harvested immediately (0h); biological replicate 2


title: CUT&RUN:_HLF_BAF155-R1064K_IgG_1

description:
Library name: 688
IgG


title: retina, snRNA-seq, Piezo2f/f, P120, Sample 2

description:
Library name: Sample 2
6 retinae pooled, FACS sorted for RGCs


title: sextuple_polysome_rep2

value: ten day old


title: SW620 37C water bath plus RT 24h replicate 1

description:
Library name: SW_37RT_21_09_24
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 1


title: CUT&RUN:_HLF_BAF155-R1064K_FLAG_2

description:
Library name: 685
FLAG


title: retina, snRNA-seq, Piezo2f/f, P120, Sample 1

description:
Library name: Sample 1
6 retinae pooled, FACS sorted for RGCs


title: SW620 37C water bath plus RT 0h replicate 1

description:
Library name: SW_37RT_21_09_0
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 37C water bath and harvested immediately (0h); biological replicate 1


title: Mixed library for mouse Day6; biological replicates 1 and 2

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

description: Library name: sample2

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Mouse uterus

extract_protocol:
After cells were fixed by formaldehyde, the single-cell suspension was prepared by gentleMACS (Miletenyi Biotec).
Cells were treated for RNA sequencing library preparation with Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit, Chromium Fixed RNA Kit, Mouse Transcriptome, Chromium Mouse Transcriptome Probe Set v1.0.1, Chromium Next GEM Chip Q Single Cell Kit, Dual Index Kit TS Set A and Chromium X (10x genomics, USA) according to manufacturer's protocol.

value: Mouse uterus

value: wildtype


title: CUT&RUN:_HLF_BAF155-WT_FLAG_2

description:
Library name: 691
FLAG

value: Liver Cancer

value: HLF


title: sextuple_polysome_rep1

value: polysomal RNA


title: CUT&RUN:_HLF_BAF155-R1064K_BAF155me2_1

description:
Library name: 684
BAF155me2


title: 2OX_polysome_rep3


title: SW620 37C water bath plus RT 24h replicate 2

description:
Library name: SW_37RT_24_10_24
SW620 colorectal cancer cells irradiated with 8Gy and incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 2

value: colon

value: colorectal adenocarcinoma

value: 37C water bath plus 8Gy gamma-radiation 24h


title: CUT&RUN:_HLF_BAF155-WT_H3K27ac_3

description:
Library name: 611
H3K27ac


title: 2OX_polysome_rep2


title: SW620 37C water bath 24h replicate 3

description:
Library name: SW_37_24_10_24
SW620 colorectal cancer cells incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 3

value: wild type

value: 37C water bath 24h


title: CUT&RUN:_HLF_BAF155-WT_IgG_1

description:
Library name: 610
IgG


title: Mixed library for mouse Days 4, 5; biological replicates 1 and 2 for each pregnancy day

description: Library name: sample1


title: 2OX_polysome_rep1


title: SW620 37C water bath 0h replicate 3

description:
Library name: SW_37_24_10_0
SW620 colorectal cancer cells incubated in 37C water bath and harvested immediately (0h); biological replicate 3

value: 37C water bath 0h


title: native CharmeKO cardiac fibroblasts from 5-week-old mice Rep 3

city: Rome

first: Alessandro

last: Palma

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
Library name: Sample 6
B3-MB224_S106

data_processing:
Q30-filtered raw reads were obtained from Illumina BaseSpace Reads and aligned to GRCh38 assembly using STAR aligner software (Dobin et al., 2013). Gene loci fragment quantification was performed on Ensemble (release 87) gene annotation gtf using STAR –quantMode GeneCounts parameter. The gtf file was edited adding CHARME gene genomic coordinates. Read counts of “reverse” configuration files were combined into a count matrix file.
Assembly: GRCm39
Supplementary files format and content: Processed data files are provided as a unique TXT file with DESeq2 normalized counts

source_name: native cardiac fibroblasts

growth_protocol: cells were grown in IMDM 20% FBS on fibronectin-coated plates

extract_protocol:
RNA was extracted using Qiagen MiRNeasy Micro kit
mRNAseq 30 milion reads   Nextflex Rapid Directional RNA-Seq kit 2.0 Kit with Poly(A) Beads 2.0

value: native cardiac fibroblasts

value: CharmeKO


title: SW620 37C water bath 24h replicate 2

description:
Library name: SW_37_9b_24
SW620 colorectal cancer cells incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 2


title: native CharmeKO cardiac fibroblasts from 5-week-old mice Rep 2

description:
Library name: Sample 5
B2-MB223_S104


title: Col_polysome_rep4

value: wild type Col-0


title: CUT&RUN:_HLF_BAF155-WT_FLAG_1

description:
Library name: 609
FLAG


title: SW620 37C water bath 0h replicate 2

description:
Library name: SW_37_9b_0
SW620 colorectal cancer cells incubated in 37C water bath and harvested immediately (0h); biological replicate 2


title: CUT&RUN:_HLF_BAF155-R1064K_H3K27ac_3

description:
Library name: 605
H3K27ac


title: native CharmeKO cardiac fibroblasts from 5-week-old mice Rep 1

description:
Library name: Sample 4
B1-MB222_S102


title: Col_polysome_rep3

value: whole seedling


title: 32-VP-026-01, healthy skin biopsy

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Library name: 32_VP_026_01_gezond_H4

data_processing:
Raw read QC was done using FastQC (v0.12.1)
Adapter and quality trimming was done using cutadapt (v5.0)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.11b)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.6)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.1)
Assembly: Homo sapiens  GRCh38 (Ensembl release 112)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

source_name: skin

extract_protocol:
The sampled tissue was lysed mechanically using a 1000 µL pipette tip, followed by shearing through a syringe (Terumo Corporation, Tokyo, Japan) fitted with a 20Gx1½ needle (Terumo Corporation). Total RNA was extracted using the conventional TriReagent/chloroform method and subsequently purified with the Direct-zol Microprep RNA Kit (Zymo Research), including on-column DNase I treatment, according to the manufacturer’s instructions. As residual genomic DNA was detected in some samples, an additional DNase treatment was performed using the TURBO DNA-free™ Kit (Invitrogen, Thermo Fisher Scientific) on all RNA extracts.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen)

value: skin


title: SW620 37C water bath 24h replicate 1

description:
Library name: SW_37_21_09_24
SW620 colorectal cancer cells incubated in 37C water bath and harvested after 24h re-incubation; biological replicate 1


title: 28-VP-022-01, perilesional skin biopsy

description: Library name: 28_VP_022_01_perilesioneel_D4


title: Plasma EV RNA-Seq, B1 (PLWH)

description:
Library name: B1
Maternal plasma-derived EV RNA; sex: F; RIN: 1.8; strand-specific; 2×150 bp; ~20M reads/sample

value: Plasma

value: cART-suppressed PLWH


title: mouse-muscle-cell-proliferating-3A-H3K27ac-ChIP

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

data_processing:
Sequencing reads were aligned to mm9 using BWA (Li and Durbin, 2009). Mapped reads were filtered for quality, and duplicates were removed for further analysis.
The bamCoverage script was used to generate and normalize bigwig files with the RPKM formula.
The peak calling was performed with the MACS2 (Zhang et al., 2008) against a reference input sample from the same cell line with standard settings and a q value of 0.05.
Assembly: mm9
Supplementary files format and content: bigwig file
Supplementary files format and content: peak file with H3K27ac peaks

source_name: C2C12 myoblasts

extract_protocol:
Chromatin for ChIP was prepared as previously described(Kouwenhoven et al., 2010). ChIP assays were performed following a standard protocol (Novakovic et al., 2016) with minor modifications. Antibodies against H3K27ac (1.2 μg) was used in each ChIP assay.
Resulted DNA fragments from four independent ChIP assays were purified and subjected to a ChIP-qPCR quality check. Afterward 5ng DNA fragments were pooled and proceeded on with library construction using KAPA Hyper Prep Kit according to the standard protocol. The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols.

value: C2C12 myoblasts

value: muscle cells

value: proliferation

tag: antibody

value: Anti-H3K27ac, Diagenode, Cat#C15410174


title: mouse-muscle-cell-differentiating-8A-ChIP-input

value: 72h differentiation

value: input


title: native wildtype cardiac fibroblasts from 5-week-old mice Rep 3

description:
Library name: Sample 3
A3-MB221_S105

value: wildtype


title: CUT&RUN:_HLF_BAF155-WT_H3K27ac_2

description:
Library name: 421
H3K27ac

data_processing:
all fastq procesed with pipeline at github.com/raab-lab/cut-n-run
bowtie2 for alignment
picard MarkDuplicates
peak calls with macs2
bamCoverage using counts from csaw for normalized coverage bigwig for IGV
Assembly: hg38
Supplementary files format and content: normalized bigwig files
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN protocol was adapted from Epicypher and Skene and Henikoff 2017]. Briefly, cells were detached from plates and counted for a total of ~500,000 cells per antibody per cell line. Cells were pelleted at RT for 3 minutes at 300 g. Cells were washed 2x with Wash Buffer (20mM HEPES pH 7.6, 150mM NaCl, 0.5mM Spermidine, protease inhibitor (1 tablet/30mL Roche)). 11 μL of Concanavalin beads (Bangs Laboratories) per sample were 2x washed with cold Bead Activation Buffer (20mM HEPES ph7.9, 10mM KCl, 1mM CaCl2, and 1mM MnCl2). Cells were then added to beads and incubated with rotation for 5 minutes at RT. Samples were placed on a magnet to remove the supernatant and resuspended in 50 μL Wash Buffer with 0.05% Digitonin and 2mM EDTA. Corresponding antibodies were added to the samples and were incubated overnight at 4℃ with rotation. The following day, beads were washed on a magnet 3x with Digitonin-Wash Buffer (Wash Buffer, 0.05% Digitonin). Beads were resuspended in 50 μL Digitonin-Wash Buffer with guinea pig anti-rabbit secondary antibody (1:100, Novus, NBP1-72763) and incubated at 4℃ for 1 hour with rotation. Following secondary antibody binding, beads were washed 4x with cold Digitonin-Wash buffer on a magnet and then resuspended in 50 μL pAG Mnase solution (~700 ng/ul pAG-Mnase, Digitonin-Wash Buffer) (purified in-house [47]). Beads were incubated with pAG Mnase solution for 1 hour at 4℃ with rotation. Beads were washed 4x with cold Digitonin-Wash Buffer on a magnet and then resuspended in 50 μL cold Digitonin-Wash Buffer. 1 μL of 100 mM CaCl2 was added to the samples and incubated in a cold metal block in ice at 4℃ for 30 minutes. 50 μL of Stop Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05µg/µL RNAseA (ThermoFisher, EN0531), 0.1% Triton X-100) was added to the samples and then incubated at 37℃ for 30 minutes in a thermocycler. DNA was purified from the samples using the Zymo ChIP Clean and Concentrator kit (Genesee Scientific,  11-379C) following the manufacturer’s protocol.
Libraries were prepared using the KAPA HyperPrep DNA kit with modifications. End-repair/A-tailing was performed in 25 μL volume reactions and performed on a thermocycler with the following protocol: 12℃ for 15 minutes, 37℃ for 15 minutes, 58℃ for 45 minutes, hold at 12℃. For adapter ligation, half volumes were used with 5 μL of 750 nM Kapa Unique Dual-Indexed Adapters (KAPA, 8861919702). Samples were incubated for 1 hour at RT and cleaned with a 1.1X KAPA Pure Bead clean up 2x. A library amplification was performed with KAPA HiFi HotStart ReadyMix with the following program: 98℃ for 45 seconds, 98℃ for 15 seconds, 60℃ for 10 seconds, Cycle to Step 2 13x, 71℃ for 60 seconds, hold at 4℃. A final KAPA Pure Bead 1X clean up was performed on the amplified libraries before being quantified and pooled on TapeStation 4200 and Qubit.

value: Liver Cancer

value: HLF


title: SW620 37C water bath 0h replicate 1

description:
Library name: SW_37_21_09_0
SW620 colorectal cancer cells incubated in 37C water bath and harvested immediately (0h); biological replicate 1

value: colon

value: colorectal adenocarcinoma

value: wild type

value: 37C water bath 0h


title: Col_polysome_rep2

value: whole seedling

tag: age

value: ten day old

value: wild type Col-0

value: polysomal RNA


title: native wildtype cardiac fibroblasts from 5-week-old mice Rep 2

description:
Library name: Sample 2
A2-MB220_S103

value: native cardiac fibroblasts


title: Col_polysome_rep1


title: Cnt_cloneF3_DMSO_Rep2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

description: Library name: Sample 16

data_processing:
Sequencing reads were aligned to hg19 build of the human genome using HISAT2
SAMtools was used to convert SAM files to BAM files
Read counts were normalized and analyzed for differential expression via the DESeq2 package in R
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads that mapped to known genes were assigned with featureCounts
Assembly: hg19
Supplementary files format and content: Gene counts (raw) in a text file

source_name: Ishikawa

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 3 days prior to 17beta-estradiol (E2) treatments, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Following treatment, cells were lysed with buffer RLT Plus (Qiagen) containing 1% beta-mercaptoethanol (Sigma-Aldrich). RNA was extracted and purified using a Quick RNA Mini Prep kit (Zymo Research).
NEBNext Ultra II Directional RNA Library Prep kit with poly(A) mRNA isolation was used to construct RNA-seq libraries according to the manufacturer’s instructions (NEB).

treatment_protocol: Cells were treated with either 10 nm 17beta-estradiol (E2) or 0.1% DMSO for 8 hours

value: Ishikawa

value: endometrioid adenocarcinoma

value: WT

value: DMSO


title: CUT&RUN:_HLF_BAF155-R1064K_H3K27ac_2

description:
Library name: 413
H3K27ac

source_name: Liver Cancer


title: Col_AA_monosome_rep3

value: monosomal RNA


title: native wildtype cardiac fibroblasts from 5-week-old mice Rep 1

description:
Library name: Sample 1
A1-MB219_S101

value: wildtype


title: CUT&RUN:_HLF_BAF155-WT_H3K27ac_1

description:
Library name: 397
H3K27ac

value: Liver Cancer


title: Cnt_cloneF3_DMSO_Rep1

description: Library name: Sample 15


title: Col_AA_monosome_rep2


title: cultured CharmeKO cardiac fibroblasts from 5-week-old mice Rep 3

description:
Library name: Sample 6
PCC-Pagano-B3_S116

source_name: cultured cardiac fibroblasts

value: cultured cardiac fibroblasts

value: CharmeKO


title: Cnt_cloneF3_E2_Rep2

description: Library name: Sample 14

value: 10 nm 17beta-estradiol


title: CUT&RUN:_HLF_BAF155-WT_BAF155me2_1

description:
Library name: 391
BAF155me2

value: HLF


title: cultured CharmeKO cardiac fibroblasts from 5-week-old mice Rep 2

description:
Library name: Sample 5
PCC-Pagano-B2_S114


title: Col_AA_monosome_rep1


title: cultured CharmeKO cardiac fibroblasts from 5-week-old mice Rep 1

description:
Library name: Sample 4
PCC-Pagano-B1_S112


title: Cnt_cloneE5_DMSO_Rep2

description: Library name: Sample 12


title: Col_CK_monosome_rep3


title: Cnt_cloneF3_E2_Rep1

description: Library name: Sample 13


title: CUT&RUN:_HLF_BAF155-R1064K_H3K27ac_1

description:
Library name: 389
H3K27ac


title: Col_CK_monosome_rep2


title: cultured wildtype cardiac fibroblasts from 5-week-old mice Rep 3

description:
Library name: Sample 3
PCC-Pagano-A3_S115


title: C42B Enz 20 + Tala 10 C

city: Sacramento

first: Alan

last: Lombard

state: CA

address: 4500 2nd Avenue, Rm 4674

institute: University of California, Davis

description: Library name: LLG057

data_processing:
Raw sequencing data were processed using the nf-core/rnaseq pipeline (version 3.14.0, DOI 10.5281/zenodo.10471647), which includes quality control, alignment, and quantification steps
Reads were trimmed using Trim Galore
reads were mapped to the Homo sapiens reference genome (GRCh38) using STAR (Dobin et al., 2013). Gene-level quantification was performed using Salmon (Patro et al., 2017) against the GENCODE v45 gene annotation
Raw counts were extracted from the Salmon file outputs
Assembly: GRCh38 and GENCODE v45 gene annotation
Supplementary files format and content: tab-delimited text file contains raw counts for each sample and associated Ensembl gene id from the GENCODE v45 gene annotation.

growth_protocol: Cells are maintained in RPMI 1640 supplemented with 10% FBS and 1% pen/strep in humidified incubator at 5% CO2.

extract_protocol:
RNA was isolated from cultured cells using Trizol reagent (Thermofisher) following manufacturer’s instructions and further purified using the RNeasy kit (Qiagen) with the optional on-column DNase step according to the manufacturer’s protocols. Total RNA was eluted from the columns in nuclease-free water and stored at -80°C
Indexed, stranded mRNA-seq libraries were prepared from total RNA (1000 ng) using the KAPA Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s standard protocol for mRNA capture, fragmentation, random-primed first strand synthesis, second strand synthesis with dUTP marking, A-tailing, adaptor ligation, and library amplification. Libraries were pooled and multiplex sequenced on an Illumina NovaSeqX Plus System

treatment_protocol: Cells were plated in 60mm and treated as indicated the following day. For LLG001-LLG018, treatment duration is indicated. For LLG037-LLG057, treatment was for 5-days.

value: Enzalutamide 20μM + Talazoparib 10nM


title: Cnt_cloneE5_DMSO_Rep1

description: Library name: Sample 11


title: C42B Enz 20 + Tala 10 B

description: Library name: LLG056


title: cultured wildtype cardiac fibroblasts from 5-week-old mice Rep 2

description:
Library name: Sample 2
PCC-Pagano-A2_S113


title: Col_CK_monosome_rep1

value: whole seedling


title: Cnt_cloneE5_E2_Rep2

description: Library name: Sample 10


title: cultured wildtype cardiac fibroblasts from 5-week-old mice Rep 1

description:
Library name: Sample 1
PCC-Pagano-A1_S111


title: C42B Abi 5 + Ola 1 C

description: Library name: LLG054

value: Abiraterone Acetate 5μM + Olaparib 1μM


title: Cnt_cloneE5_E2_Rep1

description: Library name: Sample 9


title: M4- CD20+ T cells

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. of Immunology

institute: University Medical Center Mainz

description: Library name: Sample 12

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v24.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files including raw counts, TPM and RPKM. Expression values in manuscript=TPM

source_name: spleen and inguinal lymph node

growth_protocol: Mice were held in IVC cages and killed via CO2 and cervical dislokation.

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen).
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 70 ng total RNA (RIN>8) using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA assay. Sequencing (PE150) was done at Novogene (Cambridge, UK) on a NovaSeq 6000 (Illumina).

treatment_protocol: Spleens were isolated and passed through a 70 µm strainer to generate single cells. The splenocytes were stained for fluorescence activated cell sorting and sorted for CD3 (T cells), CD20, and CD19 (B cells) positivity.

value: spleen and inguinal lymph node

value: T cells

value: untreated


title: SOX17KO_cloneE3_DMSO_Rep2

description: Library name: Sample 8

value: Ishikawa

value: SOX17 KO


title: C42B Abi 5 + Ola 1 B

description: Library name: LLG053


title: SOX17KO_cloneE3_DMSO_Rep1

description: Library name: Sample 7

value: endometrioid adenocarcinoma


title: M4- CD20- T cells

description: Library name: Sample 11


title: C42B Abi 5 + Ola 1 A

description: Library name: LLG052


title: M4- B cells

description: Library name: Sample 10

value: B cells


title: C42B Tala 10 C

description: Library name: LLG051

value: Talazoparib 10nM


title: M3- CD20+ T cells

description: Library name: Sample 9


title: M3- CD20- T cells

description: Library name: Sample 8


title: 2OX_monosome_rep1

value: ten day old

value: monosomal RNA


title: SOX17KO_cloneA3_DMSO_Rep2

description: Library name: Sample 4

value: DMSO


title: M3- B cells

description: Library name: Sample 7


title: C42B Tala 10 A

description: Library name: LLG049


title: SOX17KO_cloneA3_DMSO_Rep1

description: Library name: Sample 3


title: C42B Ola 1 C

description: Library name: LLG048

value: Olaparib 1μM


title: M2- CD20+ T cells

description: Library name: Sample 6


title: Col_monosome_rep3

value: wild type Col-0


title: SOX17KO_cloneA3_E2_Rep2

description: Library name: Sample 2

value: 10 nm 17beta-estradiol


title: C42B Ola 1 B

description: Library name: LLG047


title: M2- CD20- T cells

description: Library name: Sample 5


title: SOX17KO_cloneA3_E2_Rep1

description: Library name: Sample 1


title: C42B Ola 1 A

description: Library name: LLG046


title: M2- B cells

description: Library name: Sample 4


title: Ishikawa_Cnt_cloneF3_E2_ER

description: Library name: Sample 7

data_processing:
Reads were aligned to the hg19 build of the human genome using Bowtie: -m1 -t -best -q -S -l 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
MACS2 was used to call peaks with a P-value cutoff of 1x10-10 and mfold parameter between 15 and 100
Assembly: hg19
Supplementary files format and content: BigWig files
Supplementary files format and content: narrowPeak files from MACS2

growth_protocol: Cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. 5 days prior to treatment, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific) with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed using 1% formaldehyde (Sigma Aldrich, 252549) for 10 minutes at room temperature to cross-link DNA and proteins. Cross-linking was stopped by addition of glycine (Fisher Scientific, BP381) to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via scraping in Farnham lysis buffer supplemented with protease and phosphatase inhibitors (Thermo Scientific, A32959).
ChIP and library construction was performed as described in Reddy et al, Genome Research, 2009.

treatment_protocol: Cells were treated with 0.1% DMSO for one hour (SOX17 ChIP), or 10 nM 17beta-estradiol for one hour (ER ChIP), or 0.1% DMSO for 8 hours (H3K4me1)

value: endometrial adenocarcinoma

value: WT

value: 10 nM 17beta-estradiol


title: C42B Enz 20 C

description: Library name: LLG045

value: Enzalutamide 20μM


title: M1- CD20+ T cells

description: Library name: Sample 3

value: spleen and inguinal lymph node

value: T cells


title: small RNA, Arabidopsis 14 dpi gall (replicate 3)

city: Toledo

first: Carolina

last: Escobar Lucas

state: Toledo

address: Avda Carlos III, s/n, Campus Fábrica de armas, Edificio Sabatini, laboratorio 08

department: Plant physiology

country: Spain

institute: University of Castilla-la Mancha

description:
Library name: 14dpi_gall_R3
Three biological replicates consisting of independent pools of galls (14 dpi). Libraries represent size-selected small RNAs (18–25 nt).

data_processing:
Base-calling / raw read generation: Raw signal intensities from the Illumina HiSeq X platform were converted into base calls and stored as FASTQ files.
Quality filtering: Low-quality reads, reads containing primer contaminants, reads lacking adapter sequences, poly-A reads, and reads shorter than 18 nt were removed.
Adapter trimming: 3′ adapter sequences were removed using Cutadapt (v3.1), retaining reads corresponding to bona fide small RNAs.
Read selection by size: Reads between 19 and 25 nt were retained for downstream analyses.
Read alignment: Processed reads were mapped to the Arabidopsis thaliana TAIR10 reference genome using Bowtie v1.2 allowing zero mismatches (-v 0). Two mapping strategies were applied, retaining either multi-mapping reads (-m 50) or uniquely mapping reads (-m 1).
Small RNA quantification: Reads were quantified using two approaches: (1) sequence-based counting of individual small RNA species, and (2) genomic bin-based counting using 200 bp genomic windows to capture loci producing heterogeneous siRNA populations.
Differential accumulation analysis: Statistical analysis was performed using edgeR with TMM normalization. Differentially expressed small RNA loci were identified using generalized linear models with Benjamini–Hochberg multiple-testing correction (FDR < 0.05).
Assembly: Arabidopsis thaliana reference genome TAIR10 was used for small RNA mapping and analysis.
Supplementary files format and content: sRNA_bins200_14dpi_normalized_counts.txt.gz, Tab-delimited file containing normalized counts per 200 bp genomic bin (rows) across biological replicates (columns).
Supplementary files format and content: sRNA_species_14dpi_normalized_counts.txt.gz, Tab-delimited file containing normalized counts of individual small RNA sequences across biological replicates.

source_name: Root gall

growth_protocol: Arabidopsis thaliana (Col-0) seeds were surface sterilized and germinated on Gamborg B5 medium supplemented with sucrose. Plants were grown in vitro under controlled environmental conditions (16 h light / 8 h dark photoperiod, 23 °C) prior to nematode inoculation.

extract_protocol:
Total RNA was extracted from hand-dissected galls and equivalent uninfected root segments using the AllPrep® DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions, as described in Silva et al. (2019). RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer.
Small RNA libraries were constructed from total RNA following size selection of 18-25 nt RNA fragments, adapter ligation, reverse transcription, and PCR amplification according to Illumina small RNA library preparation workflows. Libraries were indexed and sequenced as single-end reads on an Illumina HiSeq X platform at Macrogen Inc. (Seoul, South Korea).

treatment_protocol: Seedlings were inoculated with Meloidogyne javanica to induce gall formation on the roots. Control plants were maintained under identical conditions without nematode infection. Root tissues containing galls and corresponding non infected root controls were collected at 14 days post-inoculation (dpi).

value: Root gall

tag: ecotype

value: Meloidogyne javanica infection (14 dpi)


title: Ishikawa_SOX17KO_cloneE3_E2_ER

description: Library name: Sample 6

value: Ishikawa

value: SOX17 KO


title: C42B Enz 20 B

description: Library name: LLG044


title: M1- CD20- T cells

description: Library name: Sample 2

value: untreated


title: CUT&RUN:_HLF_BAF155-R1064K_FLAG_1

city: Chapel Hill

first: Jesse

last: Raab

address: Rm 5028 Genetic Medicine Building

institute: UNC Chapel Hill - Raab Lab

description:
Library name: 603
FLAG

value: Liver Cancer

value: HLF


title: Ishikawa_SOX17KO_cloneA3_E2_ER

description: Library name: Sample 5


title: small RNA, Arabidopsis 14 dpi gall (replicate 1)

description:
Library name: 14dpi_gall_R1
Three biological replicates consisting of independent pools of galls (14 dpi). Libraries represent size-selected small RNAs (18–25 nt).


title: M1- B cells

description: Library name: Sample 1

value: B cells


title: HCIEC23_DMSO_H3K4me1_Rep2

description: Library name: Sample 3

value: DMSO


title: C42B Abi 5 C

description: Library name: LLG042

value: Abiraterone Acetate 5μM


title: small RNA, Arabidopsis root control (replicate 3)

description:
Library name: RC_R3
Three biological replicates consisting of independent pools of equivalent uninfected root segments. Libraries represent size-selected small RNAs (18–25 nt).

source_name: Root

value: Root

value: Uninfected


title: C42B Abi 5 B

description: Library name: LLG041


title: M2

description: Library name: Sample 2

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v24 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files including raw counts, TPM and RPKM. Expression values in manuscript=TPM

source_name: spleen

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen).
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Total RNA (RIN>8) was sent to Novogene (Cambridge, UK) for library preparation and sequencing (PE150) on a NovaSeq 6000 (Illumina).

treatment_protocol: Spleens were isolated and passed through a 70 µm strainer to generate single cells. The splenocytes were stained for fluorescence activated cell sorting and sorted for CD11b positivity.

value: spleen

value: CD11b+ monocytes


title: small RNA, Arabidopsis root control (replicate 2)

description:
Library name: RC_R2
Three biological replicates consisting of independent pools of equivalent uninfected root segments. Libraries represent size-selected small RNAs (18–25 nt).


title: HCIEC23_DMSO_input

description: Library name: Sample 1

value: endometrial adenocarcinoma

value: WT

value: pooled input


title: M1

description: Library name: Sample 1


title: small RNA, Arabidopsis root control (replicate 1)

description:
Library name: RC_R1
Three biological replicates consisting of independent pools of equivalent uninfected root segments. Libraries represent size-selected small RNAs (18–25 nt).


title: sextuple_monosome_rep2

value: whole seedling

value: ten day old

value: sextuple mutant

value: monosomal RNA


title: Arabidopsis 14 dpi gall (replicate 3)

description:
Library name: 14dpi_gall_R3
Three biological replicates consisting of independent pools of galls (14 dpi)

data_processing:
Base-calling / raw read generation: Raw signal intensities from the Illumina HiSeq X platform were converted into base calls and stored as FASTQ files.
Quality control: Raw reads were evaluated for quality using FastQC v0.11.9, and summary reports were generated with MultiQC.
Trimming / filtering: Adapter sequences were removed using Cutadapt v3.4. Reads shorter than 20 bp after trimming were discarded.
Read alignment: Clean paired-end reads were aligned to a composite reference genome including Arabidopsis thaliana (TAIR10/Araport11 annotation) and Meloidogyne javanica using STAR aligner v2.7.10b.
Count table generation: Gene level read counts were obtained using HTSeq-count v0.13.5 in strand-specific mode against the Araport11 gene annotation.
Differential expression analysis: Statistical analysis was performed using edgeR with TMM normalization. Differential expression between galls and control roots was assessed using generalized linear models and likelihood ratio tests, with multiple testing correction by the Benjamini-Hochberg method (FDR < 0.05).
Assembly: Composite reference genome including Arabidopsis thaliana TAIR10 (Araport11 annotation) and Meloidogyne javanica genome.
Supplementary files format and content: Arabidopsis_14dpi_RNAseq_normalized_counts.txt.gz file containing normalized gene expression values. Each row corresponds to an Arabidopsis gene identifier (TAIR10 locus), and columns represent biological replicates from 14 dpi galls and uninfected root controls (three replicates per condition).
Supplementary files format and content: 14dpi_gall_vs_RC_deg.txt.gz file containing differential expression results. Each row corresponds to one gene and includes expression statistics metrics, log2 fold change between galls and control roots, statistical test values, raw p-values, and Benjamini-Hochberg adjusted p-values (FDR).

extract_protocol:
Total RNA was extracted from hand-dissected galls and equivalent uninfected root segments using the AllPrep® DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions, as described in Silva et al. (2019). RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer.
Strand-specific mRNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) with poly(A) enrichment. Libraries were dual-indexed, pooled in equimolar amounts, and sequenced as 150 bp paired-end reads on an Illumina HiSeq X platform at Macrogen Inc. (Seoul, South Korea).

value: Root gall

value: Meloidogyne javanica infection (14 dpi)


title: Usb1_KO

description: scRNAseq sample 2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: whole embryo

extract_protocol:
Embryos were dissociated into single-cell suspension, loaded into Chromium microfluidic chips with 3’ reagent kit (v3.1 chemistry), and barcoded with a 10X Chromium Controller (10X Genomics).
Libraries were performed according to the manufacturer’s instructions (single cell 3’ V3.1, 10X Genomics).

value: whole embryo

value: Usb1 knockout


title: sextuple_monosome_rep1

extract_protocol:
Total RNA of polysome or monosome fractions was precipitated and pooled for RNA-seq analysis. 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


title: 2OX_monosome_rep3


title: IWP2_BR_DIV65 n2

city: Paris

first: Michela

last: Deleidi

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, INSERM UMR1163

description:
Library name: D8
10xGenomics

data_processing:
The sequencing data was analyzed with the Cell Ranger software (version 6.0.1) provided by 10x Genomics. Demultiplexing of the sequencing reads was performed with cellranger mkfastq.
For each sample, FASTQ files generated with cellranger mkfastq were subsequently processed with cellranger count. Cellranger count performs alignment, filtering, barcode counting and UMI counting. Using the filtered barcodes, it also generates feature-barcode matrices
Assembly: GRCh38-3.0.0
Supplementary files format and content: cellranger output files for 'filtered_feature_bc_matrix' (barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz)

source_name: iPSC-derived midbrain organoids

growth_protocol: Human induced pluripotent stem cells were used to generate human midbrain organoids (hMOs). iPSCs were dissociated into single cells and seeded at a density of 9,000 cells per well in U-bottom 96-well plates to form embryoid bodies (EBs). The initial neuroinduction medium consisted of a DMEM/F12 and Neurobasal base supplemented with N2, B27, NEAA, and was guided by dual SMAD inhibition (SB431542 and LDN) and Wnt activation (CHIR99021). From day 4, midbrain patterning was promoted by the addition of SHH and FGF8. On day 7, EBs were embedded in Matrigel and transferred to six-well plates. From day 8 onwards, organoids were cultured in a maturation medium containing neurotrophic factors, including BDNF and GDNF, as well as ascorbic acid and db-cAMP. On day 20, the organoids were mechanically freed from the Matrigel and transferred to either an orbital shaker or a spinning bioreactor for long-term dynamic culture.

extract_protocol:
Midbrain organoids were dissociated into single-cell suspension following the Worthington Papain Dissociation System kit instructions (Worthington Biochemical) with intermittent trituration steps. The final solution was centrifuge 300g per 7 min, cell pellet were resuspended in PBS-0,04% BSA and filtered twice (40um, 30um) to obtain single-cell suspensions.
Cells loaded to Chromium Chip (target cell recovery): 10,000 cells. Library Preparation Kit: Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics). Sequencing parameters: NovaSeq X, SP Flow Cell, 100 cycles. Read 1: 28 bp, i7-index: 10 bp, i5-index 10 bp, Read 2: 90 bp.

treatment_protocol: The Wnt-TriP protocol was developed as a modification of the standard growth protocol to investigate the role of temporal Wnt gradients on dopaminergic neuron development. Following the initial neuroinduction and midbrain patterning stages, a key treatment window was introduced between DIV 11 and DIV 18. During this period, the Wnt activator CHIR99021 was removed from the culture medium. Concurrently, the medium was supplemented with the Wnt-signalling inhibitor IWP-2 at a final concentration of 2.2 µM. Organoids in the "Standard" protocol, serving as the control, did not receive IWP-2 and were instead cultured with decreasing concentrations of CHIR99021 during this same timeframe. After DIV 18, the Wnt-TriP organoids were subsequently maintained in the final maturation medium, identical to that used for the standard condition.

value: iPSC-derived midbrain organoids

value: Wnt-TriP

tag: incubation

value: Bioreactor

tag: days in_vitro

value: DIV 65


title: 2OX_monosome_rep2

data_processing:
Library strategy: Ribo-seq
illumina Novaseq6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: seedling

tag: tissue


title: SOX17KO_cloneE3_E2_Rep1

description: Library name: Sample 5

tag: cell line

value: Ishikawa

value: endometrioid adenocarcinoma

tag: genotype

value: SOX17 KO

value: 10 nm 17beta-estradiol


title: C42B Tala 10 B

description: Library name: LLG050

value: Talazoparib 10nM


title: Arabidopsis 14 dpi gall (replicate 2)

description:
Library name: 14dpi_gall_R2
Three biological replicates consisting of independent pools of galls (14 dpi)


title: IWP2_BR_DIV65 n1

description:
Library name: A8
10xGenomics


title: BMDM_IFNg_24H_3

city: Lansing

first: Kayla

middle: N

last: Conner

state: Michigan

address: 4125 Beaumont Rd

institute: Michigan State University

data_processing:
RNASeq read quality assessment, mapping, and counting were performed using a custom pipeline built in Snakemake version 7.32.4 (https://github.com/kaylaconner/olivelab-rnaseq/tree/main)1. Read quality was assessed using FastQC version 0.12.12. Read mapping was performed against the GRCm39 mouse reference genome using Bowtie2 version 2.5.13. Aligned reads counts were assessed using the featurecounts function from the Subread package version 2.0.64. Differential gene expression analysis was conducted using the DESeq2 package version 1.42.0 in R version 4.3.25. Pre-filtering was performed to keep only genes that had >10 counts in 3 or more samples.
Assembly: Mouse GRCm39
Supplementary files format and content: RawCounts.csv - Contains raw read counts produced by Feature Counts for all samples combined into a single data matrix
Supplementary files format and content: normalizedcounts.csv - Contains normalized read counts produced by DESeq2 for all samples combined into a single data matrix

source_name: Primary Cells

extract_protocol:
A Direct-zol RNA Extraction Kit (Zymo Research, Cat no. R2072) was used to extract RNA according to the manufacturer’s protocol.
Illumina Sequencing was carried out by SeqCenter (Pittsburgh, PA).

value: Primary Cells

value: Primary BMDM

value: IFNg + Mab Infected - 24H


title: C42B DMSO A

description: Library name: LLG037

value: DMSO


title: Arabidopsis 14 dpi gall (replicate 1)

description:
Library name: 14dpi_gall_R1
Three biological replicates consisting of independent pools of galls (14 dpi)

value: Root gall


title: Col_monosome_rep2

value: whole seedling

value: ten day old

value: wild type Col-0

value: monosomal RNA


title: C4-2B Ola 5-3 5-day

description: Library name: LLG018

value: Ola 5μM


title: BMDM_IFNg_24H_2


title: CTRL_BR_DIV65 n3

description:
Library name: F7
10xGenomics

value: iPSC-derived midbrain organoids

value: Standart

value: Bioreactor


title: Col_monosome_rep1


title: Arabidopsis root control (replicate 3)

description:
Library name: RC_R3
Three biological replicates consisting of independent pools of gall (14 dpi) equivalent uninfected root segments.

value: Root

value: Unifected


title: CTRL_BR_DIV65 n2

description:
Library name: C7
10xGenomics

value: DIV 65


title: C4-2B Ola 5-2 5-day

description: Library name: LLG017


title: Arabidopsis root control (replicate 2)

description:
Library name: RC_R2
Three biological replicates consisting of independent pools of gall (14 dpi) equivalent uninfected root segments.


title: BMDM_IFNg_24H_1


title: CTRL_BR_DIV65 n1

description:
Library name: H7
10xGenomics


title: C4-2B Ola 5-1 5-day

description: Library name: LLG016


title: BMDM_IFNg_6H_3

value: IFNg + Mab Infected - 6H


title: C42B Enz 20 A

description: Library name: LLG043

value: Enzalutamide 20μM


title: small RNA, Arabidopsis 14 dpi gall (replicate 2)

description:
Library name: 14dpi_gall_R2
Three biological replicates consisting of independent pools of galls (14 dpi). Libraries represent size-selected small RNAs (18–25 nt).

value: Meloidogyne javanica infection (14 dpi)


title: IWP2_DIV65 n3

description:
Library name: D7
10xGenomics

value: Wnt-TriP


title: BMDM_IFNg_6H_2

value: Primary Cells

value: Primary BMDM


title: C4-2B Ola 1-3 5-day

description: Library name: LLG015

value: Ola 1μM


title: Cannabis sativa L. Leav, Cold stress with Putrescine 0.9mM treatment, miRNA-seq, R3

city: Chuncheon-si

first: Byeong-Ryeol

last: Ryu

state: Gangwon-state

address: 1, Kangwondaehak-gil

department: Department of Bio-Health Convergence

country: South Korea

institute: Kangwon National Univsersity

description: Library name: Sample12

data_processing:
Pre-processing was carried out using cutadapt (v4.6; --max-n 0, -m 18, -M 30, -q 20) to trim adapter sequences and discard low-quality reads.
miRNA libraries from related Rosaceae species (Fragaria vesca, Malus domestica, Prunus persica) were downloaded from miRbase (https://www.mirbase.org, accessed Jan 6, 2025). The Cannabis sativa reference genome was indexed for compatibility with miRDeep2 (v0.1.3) using Bowtie (v1.3.1)
To predict C. sativa miRNAs, trimmed small RNA reads were merged and collapsed into a unique FASTA file using mapper.pl (-c, -j, -m) against the genome index. Collapsed reads and Rosaceae miRNA libraries were then supplied to miRDeep2.pl to predict known and novel hairpin sequences. As these miRNAs lack in vitro validation, they were assigned temporary identifiers (e.g., Cannabis_001) rather than standard miR nomenclature.
For expression quantification, collapsed reads were remapped to the predicted miRNA reference using mapper.pl and quantifier.pl, and counts were used as input for DESeq2.
miRNA target prediction was performed with psRNATarget (Schema V2)
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes quantifier.pl (package of miRDeep2) result for each sample (header = T).
Supplementary files format and content: tab-delimited text file includes DESeq normalized counts for each sample (header = T).

organism: Cannabis sativa

source_name: Leaf

growth_protocol: C. sativa cv. Pink Pepper seeds were used in this experiment. Seeds were soaked in 1 % hydrogen peroxide solution (DAEJUNG Chemicals & Metals Co., Siheung, Korea) for 10 h, then sown in 105‐well seedling trays (42 mL per well) filled with potting soil (Anong Sangto, Asiaseed Co., Seoul, Korea). Seedlings were grown for 15 days under controlled conditions (25 ± 2°C; 43 ± 7% RH) and watered with 30 mL tap water per plant every 3 days. After germination, seedlings were transplanted into 600 mL pots and cultivated for 3 weeks at 23 ± 2°C and 43 ± 7% RH, with 300 mL tap water per plant every 3 days. Lighting was provided by red and blue LEDs (BISSOLLED, Seoul, Korea) at a photosynthetic photon flux density (PPFD) of 312.9 ± 0.5 µmol m-2 s-1 under an 18 h photoperiod.

extract_protocol:
Leaves collected for transcriptome analysis were immediately frozen in liquid nitrogen. Total RNA was extracted using the Rneasy Micro Kit (Qiagen, Hilden, Germany), and RNA concentration was measured with the Quant-iT™ RiboGreen RNA Assay Kit (ThermoFisher Scientific Inc., Waltham, MA, USA). RNA integrity was asseessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples with an RNA integrity number (RIN) of 7.0 were used.
Libraries were prepared with the TruSeq Small RNA Library Prep Kit (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Plants were exposed to cold stress in a growth chamber (HanKuk Scientific Co., Ltd., Hwaseong, Korea) at 5 ± 1°C for 168 h. Control plants were maintained under the same conditions at 23 ± 1°C. Putrescine (Duchefa Biochemie, Haarlem, Netherlands) was dissolved in ultrapure water and foliar-sprayed at 5 mL per plant onto the shoots. To prevent cross-contamination, putrescine treated plants were allowed to air-dry for 5 min after spraying and then grown in an independent chanber. Relative humidity was maintained at 40 ± 3% RH for all treatments, and the PPFD was set to 150 µmol m-2 s-1.

value: Leaf

value: Cannabis sativa L. cv. Pink Pepper

value: Cold stress with Putrescine 0.9mM


title: BMDM_IFNg_6H_1


title: Cannabis sativa L. Leav, Cold stress with Putrescine 0.9mM treatment, miRNA-seq, R2

description: Library name: Sample11


title: HCIEC23_DMSO_H3K4me1_Rep1

description: Library name: Sample 2

value: endometrial adenocarcinoma

value: WT

value: DMSO


title: IWP2_DIV65 n1

description:
Library name: C8
10xGenomics

value: iPSC-derived midbrain organoids

value: Standart


title: Cannabis sativa L. Leav, Cold stress with Putrescine 0.9mM treatment, miRNA-seq, R1

description: Library name: Sample10


title: BMDM_IFNg_Uninf_3

value: IFNg


title: C4-2B Ola 1-1 5-day

description: Library name: LLG013


title: CTRL_DIV65 n3

description:
Library name: G7
10xGenomics

value: DIV 65


title: C4-2B Ola 0-3 5-day

description: Library name: LLG012


title: BMDM_IFNg_Uninf_1


title: C4-2B Ola 0-2 5-day

description: Library name: LLG011


title: Cannabis sativa L. Leaf, Putrescine 0.9mM treatment, miRNA-seq, R2

description: Library name: Sample8

value: Putrescine 0.9mM


title: CTRL_DIV65 n1

description:
Library name: B8
10xGenomics


title: BMDM_24H_3

value: Mab Infected - 24H


title: Cannabis sativa L. Leaf, Putrescine 0.9mM treatment, miRNA-seq, R1

description: Library name: Sample7


title: IWP2_BR_DIV40 n3

description:
Library name: H8
10xGenomics

value: Bioreactor

value: DIV 40


title: C4-2B Ola 5-3 1-day

description: Library name: LLG009

value: Ola 5μM


title: BMDM_24H_2

value: Primary Cells

value: Primary BMDM


title: BMDM_IFNg_Uninf_2


title: Cannabis sativa L. Leaf, Cold stress, miRNA-seq, R3

description: Library name: Sample6

value: Leaf

value: Cold stress


title: C4-2B Ola 5-2 1-day

description: Library name: LLG008


title: IWP2_BR_DIV40 n2

description:
Library name: H9
10xGenomics

value: Wnt-TriP


title: Cannabis sativa L. Leaf, Cold stress, miRNA-seq, R2

description: Library name: Sample5

value: Cannabis sativa L. cv. Pink Pepper


title: BMDM_6H_3

value: Mab Infected -- 6H


title: IWP2_BR_DIV40 n1

description:
Library name: D9
10xGenomics


title: Cannabis sativa L. Leaf, Cold stress, miRNA-seq, R1

description: Library name: Sample4


title: CTRL_BR_DIV40 n3

description:
Library name: G8
10xGenomics


title: BMDM_6H_2


title: C4-2B Ola 1-3 1-day

description: Library name: LLG006

value: Ola 1μM


title: Cannabis sativa L. Leaf, Control, miRNA-seq, R3

description: Library name: Sample3

value: Control


title: C4-2B Ola 1-2 1-day

description: Library name: LLG005


title: CTRL_BR_DIV40 n2

description:
Library name: G9
10xGenomics

value: iPSC-derived midbrain organoids

value: Standart


title: Cannabis sativa L. Leaf, Control, miRNA-seq, R2

description: Library name: Sample2


title: CTRL_BR_DIV40 n1

description:
Library name: C9
10xGenomics


title: BMDM_Uninf_3

value: Uninfected


title: C4-2B Ola 1-1 1-day

description: Library name: LLG004


title: Cannabis sativa L. Leaf, Control, miRNA-seq, R1

description: Library name: Sample1


title: IWP2_DIV40 n3

description:
Library name: F8
10xGenomics


title: C4-2B Ola 0-3 1-day

description: Library name: LLG003

value: DMSO


title: BMDM_Uninf_2


title: Cannabis sativa L. Leav, Cold stress with Putrescine 0.9mM treatment, RNA-seq, R3

description: Library name: Sample12

data_processing:
Sequencing-generated mRNA reads were quality-controlled using fastp (v0.24.0) to remove adapter sequences and low-quality reads.
Filtered reads were aligned to index the C. sativa reference genome (RefSeq: GCF_029168945.1) with STAR (v2.7.11b; --runmode genomeGenerate, --sjdbOverhang 150).
Gene-level read counts were obtained using featureCounts (v2.0.8).
The resulting count matrix was analyzed in DESeq2 (v1.44.0) to quantify gene expression.
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes featureCounts for each sample (header = T).
Supplementary files format and content: tab-delimited text file includes DESeq normalized counts for each sample (header = F).

extract_protocol:
Leaves collected for transcriptome analysis were immediately frozen in liquid nitrogen. Total RNA was extracted using the Rneasy Micro Kit (Qiagen, Hilden, Germany), and RNA concentration was measured with the Quant-iT™ RiboGreen RNA Assay Kit (ThermoFisher Scientific Inc., Waltham, MA, USA). RNA integrity was asseessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and samples with an RNA integrity number (RIN) of 7.0 were used.
mRNA libraries were prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina Inc., San Diego, CA, USA).

value: Cold stress with Putrescine 0.9mM


title: IWP2_DIV40 n2

description:
Library name: F9
10xGenomics


title: C4-2B Ola 0-2 1-day

description: Library name: LLG002


title: BMDM_Uninf_1


title: Cannabis sativa L. Leav, Cold stress with Putrescine 0.9mM treatment, RNA-seq, R2

description: Library name: Sample11


title: C4-2B Ola 0-1 1-day

description: Library name: LLG001


title: Cannabis sativa L. Leav, Cold stress with Putrescine 0.9mM treatment, RNA-seq, R1

description: Library name: Sample10