title: WT DB10-Y 3

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

institute: University of Western Ontario

description:
Library name: Sample 9
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.

data_processing:
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2022.1 (https://www.geneious.com)
Assembly: Staphylococcus aureus USA300_FPR3757
Supplementary files format and content: xlsx file format, contains TPM values and calculated differential expression, fold change and p-values for every transcript

organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

growth_protocol: An overnight culture of WT USA300 was inoculated 1:100 into TSB and grown to an OD600 of 1.5 at 37oC with shaking. 50uM of DB10-R, DB10-Y or an equivalent volume of DMSO was added to the treated cultures and all cultures were then grown for and additional hour.

extract_protocol:
To extract RNA from frozen S. aureus cell pellets were washed with TE buffer (pH 8.0) and re-suspended in a Tris-HCl mixture with 1 mg/mL lysostaphin (pH 7.5) to lyse for 1 hour at 37°C. RNA was extracted using 2 mL of TRI Reagent (Sigma) and 500 μL of BCP (Sigma). After mixing, the aqueous layer was added to an equal volume of ice-cold isopropanol, and the samples were then incubated overnight at -20C. Samples were pelleted at 4C for 20 minutes at 11 000 × g, resuspended in 500 μL of ice-cold 75% ethanol and pelleted again. Pellets were dried and resuspended in 86 μL of nuclease-free ddH2O before treatment with Invitrogen Turbo DNase for 1 h
RNA samples were processed by the Microbial Genome Sequencing Center in Pittsburgh, PA. Ribosomal RNA (rRNA) was depleted (Qiagen FastSelect5S/16S/23S) and cDNA libraries were generated (Qiagen Total Stranded RNA). cDNA libraries were sequenced using NextSeq 550 using a 75bp x 8bp x 8bp setup

treatment_protocol: Cells treated with the drug received 50μM DB10-R or DB10-Y or and equal volume of DMSO for the vehicle control.

value: 50μM DB10-Y


title: αTC1 cells, DMSO, 48 hrs, biol rep 5.

status: Public on Jun 18 2026

type: SRA

city: Shanghai

first: Guangxing

last: Lu

address: 上海市淞沪路2005号

country: China

institute: Fudan University

description: Library name: CON5

library_source: transcriptomic

data_processing:
The raw data were aligned using HISAT2 and quantified by Stringtie.
Differentially expressed genes were determined by DESeq2.
Assembly: mm10
Supplementary files format and content: comma-separated values file includes raw counts for each sample
Supplementary files format and content: comma-separated values file includes normalized counts (using DESeq2) for each sample

molecule: total RNA

organism: Mus musculus

source_name: Alpha TC1 cells

growth_protocol: The αTC1 cells were grown in low-glucose (1 g/L) DMEM medium with10% FBS, 50 U/mL penicilin, and 50 μg/mL streptomycin.

extract_protocol:
Total RNA was extracted from cells using RNAiso Plus reagent (Takara).
The RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN). Then, using the captured RNA as the starting sample, TIANSeq Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries.

treatment_protocol: The αTC1 cells were treated with 10 μM enzalutamide for 48 hrs.

tag: cell line

value: Alpha TC1 cells

tag: treatment

value: DMSO, 48 hrs


title: Amygdala CRS Input Replicate 4

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

country: USA

institute: University of California, Los Angeles

description:
Library name: AMY_CRS_COM_4
Amygdala CRS Input Replicate 4

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCm38
Supplementary files format and content: counts

source_name: Amygdala, Brain (BLA)

growth_protocol: Adult male and female Aldh1l1-Cre/ERT2 x Ribotag mice were housed under standard conditions (12-hour light/dark cycle, 22°C, 50% humidity) and provided standard chow and water ad libitum. Hemizygous transgenic-homozygous knock-in mice were injected with 75 mg/kg tamoxifen (Sigma-Aldrich, T5648) dissolved in corn oil once per day for 5 consecutive days at 6-8 weeks of age and used 2-3 weeks after tamoxifen injections for astrocyte RNAseq experiments. Mice were deeply anesthetized with isoflurane, then decapitated and the amygdala was quickly microdissected.

extract_protocol:
The tissue was homogenized in buffer as indicated in Bravo-Ferrer 2022 STAR Protocols. RNA was extracted from 10-20% of cleared lysate as input containing RNA from all cell types using RNA extraction kit (Qiagen, 74034). The remaining lysate was incubated with mouse anti-HA antibody (Biolegend, 901514) for 4 hr at 4 °C followed by addition of magnetic beads (Thermo Scientific, 88817) and overnight incubation at 4 °C. RNA was extracted from the immunoprecipitation (IP) samples containing astrocyte enriched RNA using RNA extraction kit (Qiagen, 74034).
TruSeq Stranded Total RNA with Ribozero Gold

treatment_protocol: Mice received control handling (US), chronic restraint stress (CRS) or water aversion stress (WAS) for two weeks.

tag: tissue

value: Amygdala, Brain (BLA)

value: Aldh1l1-Cre/ERT2 x Ribotag

tag: genotype

value: CRS


title: Amygdala CRS IP Replicate 1

description:
Library name: AMY_CRS_IP_1
Amygdala CRS IP Replicate 1


title: WT DB10-Y 2

country: Canada

description:
Library name: Sample 8
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.

tag: strain


title: αTC1 cells, DMSO, 48 hrs, biol rep 4.

description: Library name: CON4


title: RPE-1 TKO gene knockout of DDX5, replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

description: Library name: R030_TKO.DDX5.G220_r2

data_processing:
Base-calling Q-scores were obtained with RTA 3.4.4. Demultiplexing of raw sequencing data was performed using Illumina’s bclfastq.
Alternative splicing analysis was performed as follows: RNA-Seq data were processed using the vast-tools pipeline, version 2.5.1 https://github.com/vastgroup/vast-tools (Braunschweig et al., 2014; Irimia et al., 2014; Tapial et al., 2017). From primary output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW/VLOW for cassette exon [CE], microexon [MIC], and alternative 5' or 3' splice site [Alt5/3] events or coverage less than 10 reads for intron retention [IR] events; score 4 other than OK/B1/B2/Bl/Bn for CE and MIC events and score 5 of less than 0.05 for IR events). If more than one replicate was present, the point estimate from vast-tools diff was used and if the coverage/balance filtering step failed for an event in more than half of the replicates, its value was set to NA. Differential AS was assessed through the vast-tools diff module available with the main pipeline. Changes were considered significant if they were greater than 10 dPSI/dPIR and the expected minimum change was different from zero at p > 0.95 according to vast-tools’ diff module.
Gene expression changes were analyzed by pseudo-aligning pre-trimmed reads to GENCODE v43 transcripts using Salmon v1.10 (Patro et al., 2017) and aggregated per gene using the R package tximport (Soneson et al., 2015). Differential expression was then assessed using the classic mode (exactTest) edgeR (McCarthy et al., 2012), and genes with an FDR < 0.05 and a greater than 2-fold change were considered differential. For each comparison, only genes expressed at a minimum of 5 RPKM in one or both conditions were considered.
RNAseq.HAP1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Assembly: GENCODE v43
Supplementary files format and content: RNAseq.RPE1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Supplementary files format and content: RNAseq.RPE1_altSplicing.tab.gz is a tab-delimited file and contains mean percent-spliced-in values per treatment and significance calls for the difference vs intergenic hgRNA control.
Supplementary files format and content: Expression_RPE1.tab.gz is a tab-delimited file and contains RPKM, log2 fold-change and p-values per treatment vs intergenic hgRNA control.

organism: Homo sapiens

source_name: RPE-1 retinal pigment epithelium

growth_protocol: hTERT-RPE-1 cells were maintained under standard sterile cell culture conditions in Dulbecco's Modified Eagle Medium (DMEM; Sigma-Aldrich, #D5796) supplemented with 10% heat-inactivated FBS, penicillin/streptomycin, and sodium pyruvate (Gibco, #11360070) at 37°C in a humidified incubator containing 5% CO2 and at subconfluent densities (50-70%).

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Briefly, cells were washed in PBS twice and lysed directly in the vessel using RLT buffer supplemented with reducing agent β-Mercaptoethanol (Milipore #444203-250ML). All RNA samples were DNase-treated using RNase-Free DNase Set (Qiagen #79256) according to the manufacturer's protocol.
Biological duplicates were processed for RNA-Seq. Stranded/directional total RNA-Seq (ribo-depletion) libraries were prepared as follows. RNA concentration was measured using Qubit RNA BR (cat # Q10211, Thermo Fisher Scientific Inc., Waltham, USA) and RNA quality was assessed from 1 ng input on the Bioanalyzer RNA 6000 Pico kit (cat # 5067-1513, Agilent Technologies Inc., Santa Clara, USA). RIN score ranged from 8.4- 9.8 ; with a median RIN score of 9.6. For library preparation, 300 ng of DNase-treated RNA per sample was first subjected to rRNA depletion (H/M/R) and then processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat #E7760L; New England Biolabs; protocol 6.0_7/24), with 7.5 minutes of fragmentation at 94 °C and 12 cycles of amplification. To assess final library quality, 1 μl of the library was analyzed on the Agilent Bioanalyzer dsDNA High Sensitivity chip (cat # 5067-4626, Agilent Technologies Inc., Santa Clara, USA). The libraries were quantified using the Qubit 1X dsDNA HS (cat # Q33231, Thermo Fisher Scientific Inc., Waltham, USA) and were pooled at equimolar ratios after adjusting for fragment size. The final pool, with an average library size of ~395 bp was run on the Bioanalyzer and quantified using NEBNext Library Quant Kit for Illumina (cat # E7630L, New England Biolabs, Ipswich, USA).

treatment_protocol: Cells were transduced at an estimated MOI < 1 with lentivirus encoding the indicated hgRNAs from pLCHKO-EGFP-P2A-Puro vector. Cells were selected for the integration of the CHyMErA cassette by puromycin (Gibco A11138-03) at 20 µg/ml for 72 hours. At T0, puromycin was removed from the medium and cells were grown for 4 days prior to harvesting RNA at 50-70% confluency.

value: RPE-1 retinal pigment epithelium

value: Deletion of DDX5 with hybrid guide RNA comprising exonic TKOv3 Cas9 guide AAGTCTACTTGTATCTACGG and intergenic Cas12a guide ACCATTACCCCCTTCCCAGGACT.


title: Amygdala CRS Input Replicate 3

description:
Library name: AMY_CRS_COM_3
Amygdala CRS Input Replicate 3


title: RPE-1 TKO gene knockout of DDX5, replicate 1

description: Library name: R029_TKO.DDX5.G220_r1


title: WT DB10-Y 1

description:
Library name: Sample 7
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.


title: Amygdala CRS Input Replicate 2

description:
Library name: AMY_CRS_COM_2
Amygdala CRS Input Replicate 2


title: WT DB10-R 3

description:
Library name: Sample 6
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.

value: 50μM DB10-R


title: αTC1 cells, DMSO, 48 hrs, biol rep 3.

description: Library name: CON3


title: RPE-1 HNPNPD intronic deletion hgRNA 1, replicate 2

description: Library name: R026_IDel.HNRNPD.G195_r2

value: Intronic deletion in HNRNPD generated with hybrid guide RNA comprising Cas9 guide ATAAGGGTAGGGTGTATGTG and Cas12a guide GAACAAATTGTCAACCACAATCA.


title: αTC1 cells, DMSO, 48 hrs, biol rep 2.

description: Library name: CON2


title: Amygdala CRS Input Replicate 1

description:
Library name: AMY_CRS_COM_1
Amygdala CRS Input Replicate 1


title: RPE-1 HNPNPD intronic deletion hgRNA 1, replicate 1

description: Library name: R025_IDel.HNRNPD.G195_r1


title: WT DB10-R 2

description:
Library name: Sample 5
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.


title: αTC1 cells, DMSO, 48 hrs, biol rep 1.

description: Library name: CON1


title: RPE-1 FNBP4 intronic deletion hgRNA 4, replicate 2

description: Library name: R024_IDel.FNBP4.enr.G192_r2

value: Deletion in FNBP4 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide CAACTACTCCTGATTAACCT and Cas12a guide TAAGTCTCATCTGTTGGAGTGAG.


title: WT DB10-R 1

description:
Library name: Sample 4
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.


title: αTC1 cells, EPZ011989, 7 days, biol rep 3.

description: Library name: EPZ3

library_source: other

data_processing:
Data from Illumina were quality controlled using Trim Galore and aligned to mm10 using Bowtie2 with default parameters.
Alignment results were transformed to bam using samtools.
For peak calling, macs2 callpeak were used with -f BAMPE \ -g mm \ --nomodel \ --shift -100 \ --extsize 200 and data from the same group were merged.
Differential peaks were detected using macs2 bdgdiff with the parameter --cutoff 2.
For motif enrichment, homer findMotifsGenome.pl were used.
Assembly: mm10
Supplementary files format and content: bigwig file includes interval axis information (e.g., chromatin accessibility, transcription factor binding regions) and associated scores

molecule: other

extract_protocol:
Nuclei were extracted using nuclei permeabilization buffer and 50,000 nuclei were mixed with tagmentation buffer for tagmentation. 1μL Tn5 transposase (from Yu Miao Lab) was added by pipetting 5 times and then incubated at 37 °C for 60 min in a thermomixer with 500 rpm. Directly following the incubation, sample were purified using the DNA Clean & Concentrator®-5 kit (Zymo research D4014).
Fragments were amplified with 2 × NEBNext® Ultra™ II Q5® Master Mix (Biolabs M0544S) and 1 μM primers. PCR conditions were as follows: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min for a total number of 14 cycles. Amplified libraries were purified using the DNA Clean & Concentrator®-5 kit. Size selection of libraries were followed using VAHTS DNA Clean Beads (1.5× sample volume; Vazyme N411). Final libraries were quantified using Equalbit dsDNA HS Assay Kit (Vazyme EQ111) and sent to TIANGEN for sequencing.

treatment_protocol: The αTC1 cells were treated with 4 μM EPZ011989 for 7 days.


title: Amygdala IP Replicate 4

description:
Library name: AMY_IP_4
Amygdala IP Replicate 4

treatment_protocol: The mice did not receive any treatment.

value: Control


title: Amygdala IP Replicate 3

description:
Library name: AMY_IP_3
Amygdala IP Replicate 3


title: RPE-1 FNBP4 intronic deletion hgRNA 4, replicate 1

description: Library name: R023_IDel.FNBP4.enr.G192_r1


title: αTC1 cells, EPZ011989, 7 days, biol rep 2.

description: Library name: EPZ2


title: Amygdala IP Replicate 2

description:
Library name: AMY_IP_2
Amygdala IP Replicate 2


title: WT vehicle 3

description:
Library name: Sample 3
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.

value: Vehicle control; DMSO


title: αTC1 cells, EPZ011989, 7 days, biol rep 1.

description: Library name: EPZ1


title: RPE-1 FNBP4 intronic deletion hgRNA 3, replicate 2

description: Library name: R022_IDel.FNBP4.enr.G189_r2

value: Deletion in FNBP4 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide TGTGAATTCCACGGTCCAAG and Cas12a guide TCCAATGTGTGGCTGGCCAAACT.


title: WT vehicle 2

description:
Library name: Sample 2
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.


title: WT vehicle 1

description:
Library name: Sample 1
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.


title: RPE-1 FNBP4 intronic deletion hgRNA 3, replicate 1

description: Library name: R021_IDel.FNBP4.enr.G189_r1


title: Amygdala IP Replicate 1

description:
Library name: AMY_IP_1
Amygdala IP Replicate 1


title: Amygdala Input Replicate 4

description:
Library name: AMY_COM_4
Amygdala Input Replicate 4


title: αTC1 cells, DMSO, 7 days, biol rep 3.

description: Library name: CON3

value: DMSO, 7 days


title: RPE-1 HDAC7 intronic deletion hgRNA 2, replicate 2

description: Library name: R020_IDel.HDAC7.G120_r2

value: Deletion in HDAC7 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide GTGGAAGACAGTGGTGCAGA and Cas12a guide GGGCTATGTCCCGGAGTGGGGAG.


title: H16, mesaconic acid, biol rep 2

city: Kaunas

first: Naglis

last: Malys

address: Radvilenu st. 19

country: Lithuania

institute: Kaunas University of Technology

description: Library name: WT_mes_2

data_processing:
Bioinformatic analysis was performed by Novogene (Cambridge, UK). Sequencing data filtering was performed by removing reads with adapter contamination, removing reads when uncertain nucleotides constitute more than 10% of either read (N > 10%), and removing reads when low quality nucleotides (Base Quality less than 5) constitute more than 50% of the read. Reads were mapped to the reference genome using Bowtie2.
Assembly: Cupriavidus necator H16 Chromosome 1 (NC_008313.1), Chromosome 2 (NC_008314.1) and megaplasmid pHG1 (NC_005241.1).
Supplementary files format and content: xls file includes raw counts for each sample

organism: Cupriavidus necator H16

source_name: Bacterial culture

growth_protocol: Individual colonies of Cupriavidus necator H16, grown on solid sodium gluconate minimal medium (SG-MM), were each used to inoculate 5 mL of SG-MM with gentamycin in 50-mL conical centrifuge tubes. Cultures were incubated overnight at 30℃ with orbital shaking at 200 rpm. The following day, main cultures were prepared by diluting the seed cultures 1:50 into 6 mL of fresh SG-MM containing gentamycin.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit, and residual DNA was removed using the TURBO DNA-free Kit (Thermo Fisher), following the respective manufacturer protocols. RNA integrity and concentration were determined using an Agilent 2100 Bioanalyzer.
Prokaryotic RNA library preparation and sequencing were performed by Novogene (Cambridge, UK). For rRNA removal, the Illumina Ribo-Zero Plus rRNA Depletion Kit was employed.

treatment_protocol: After six hours of incubation under the same conditions, cultures were supplemented with itaconate, methylsuccinate, or mesaconate to a final concentration of 5 mM. An untreated culture (gluconate only) served as a control. Following an additional six hours of incubation – by which time cultures had reached an OD600 of 0.4–0.6 – cells equivalent to one OD600 unit were harvested and immediately stabilised using RNAprotect Bacteria Reagent (Qiagen), according to the manufacturer’s instructions. The resulting cell pellets were flash-frozen in liquid nitrogen and stored at −80℃ until RNA extraction.

tag: cell type

value: Bacterial culture

value: WT

value: 5 mM mesaconic acid

tag: time

value: 6 hours


title: αTC1 cells, DMSO, 7 days, biol rep 2.

description: Library name: CON2

value: Alpha TC1 cells


title: Amygdala Input Replicate 3

description:
Library name: AMY_COM_3
Amygdala Input Replicate 3

value: Amygdala, Brain (BLA)

value: Aldh1l1-Cre/ERT2 x Ribotag


title: H16, mesaconic acid, biol rep 1

description: Library name: WT_mes_1


title: αTC1 cells, DMSO, 7 days, biol rep 1.

description: Library name: CON1


title: RPE-1 HDAC7 intronic deletion hgRNA 2, replicate 1

description: Library name: R019_IDel.HDAC7.G120_r1

value: RPE-1 retinal pigment epithelium


title: RPE-1 HDAC7 intronic deletion hgRNA 1, replicate 2

description: Library name: R018_IDel.HDAC7.G119_r2

value: Deletion in HDAC7 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide GTGGAAGACAGTGGTGCAGA and Cas12a guide AAGGGAGAGATGATCCTAAGCCC.


title: H16, methylsuccinic acid, biol rep 2

description: Library name: WT_msu_2

value: 5 mM methylsuccinic acid


title: Amygdala Input Replicate 2

description:
Library name: AMY_COM_2
Amygdala Input Replicate 2


title: αTC1 cells, EPZ011989, 7 days, biol rep 4

description: Library name: EPZ4


title: RPE-1 HDAC7 intronic deletion hgRNA 1, replicate 1

description: Library name: R017_IDel.HDAC7.G119_r1


title: H16, methylsuccinic acid, biol rep 1

description: Library name: WT_msu_1


title: αTC1 cells, EPZ011989, 7 days, biol rep 3

description: Library name: EPZ3


title: D0 R2

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: Library name: D0 R2

library_source: genomic

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated using a copy number aware UMI deduplicator. Pipeline available at https://github.com/laurabiggins/TrAEL-seq Samples were imported into Seqmonk v1.49.1, truncated to a single base, then quantified either as total read count or as strand bias (R-F)/(R+F) equivalent to RFD. Assembly: GRCm38
Assembly: GRCh38
Supplementary files format and content: Replication Fork Direction and was calculated in 20KB windows spaced 10kb

molecule: genomic DNA

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with GlutaMAX (Gibco, 61870-010), 10% fetal bovine serum (Gibco, A5256701), and 100 IU/mL penicillin–streptomycin (Sigma-Aldrich, P4333-100ML). Cells were maintained at 37°C in a humidified incubator with 5% CO₂ and passaged at 70–80% confluence using 0.25% trypsin–EDTA (Gibco, 25200056). Cells were thawed from authenticated master stocks and used within 10–12 passages. Mycoplasma contamination was excluded by routine PCR-based testing. All experiments were performed using cells in logarithmic growth phase unless otherwise stated

extract_protocol:
1-2x10^6 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl multiplexed TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: Cells were continuously exposed to 500 nM osimertinib dissolved in DMSO for up to 28 days. Media containing drug or vehicle was replaced every 3–4 days. Final DMSO concentration did not exceed 0.1% (v/v).

value: NSCLC

value: Untreated


title: Amygdala Input Replicate 1

description:
Library name: AMY_COM_1
Amygdala Input Replicate 1

value: Control


title: RPE-1 FNBP4 intronic deletion hgRNA 2, replicate 2

description: Library name: R016_IDel.FNBP4.G118_r2

value: Intronic deletion in FNBP4 generated with hybrid guide RNA comprising Cas9 guide TGTGAATTCCACGGTCCAAG and Cas12a guide CACTGCCAGCAACTCTGTGAATA.


title: H16, itaconic acid, biol rep 2

description: Library name: WT_ita_2

value: 5 mM itaconic acid


title: D28 R1

description: Library name: D28 R1

value: 28 days 500 nM osimertinib


title: αTC1 cells, EPZ011989, 7 days, biol rep 2

description: Library name: EPZ2


title: RPE-1 FNBP4 intronic deletion hgRNA 2, replicate 1

description: Library name: R015_IDel.FNBP4.G118_r1


title: αTC1 cells, EPZ011989, 7 days, biol rep 1

description: Library name: EPZ1


title: D14 R2

description: Library name: D14 R2

value: 14 days 500 nM osimertinib


title: H16, itaconic acid, biol rep 1

description: Library name: WT_ita_1

value: Bacterial culture


title: RPE-1 FNBP4 intronic deletion hgRNA 1, replicate 2

description: Library name: R014_IDel.FNBP4.G117_r2

value: Intronic deletion in FNBP4 generated with hybrid guide RNA comprising Cas9 guide CAATTGAGAATGGAGAACCA and Cas12a guide ATATCAAGAATATGAAATGTGAA.


title: H16, control, biol rep 1

description: Library name: WT_sg_1

value: WT

value: untreated


title: RPE-1 FNBP4 intronic deletion hgRNA 1, replicate 1

description: Library name: R013_IDel.FNBP4.G117_r1


title: αTC1 cells, DMSO, 7 days, biol rep 5

description: Library name: CON5

value: Alpha TC1 cells

value: DMSO, 7 days


title: D7 R2

description: Library name: D7 R2

value: 7 days 500 nM osimertinib


title: H16, control, biol rep 2

description: Library name: WT_sg_2

value: 6 hours


title: D28 R2

description: Library name: D28 R2


title: αTC1 cells, DMSO, 7 days, biol rep 4

description: Library name: CON4


title: RPE-1 DDX17 intronic deletion hgRNA 2, replicate 2

description: Library name: R012_IDel.DDX17.G110_r2

value: RPE-1 retinal pigment epithelium

value: Deletion in DDX17 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide TTAGGGGTCAGTAAAGACCG and Cas12a guide AGTAGGTAAAAATATACATTCAG.


title: orthotopic pancreatic tumors+anti-VSIG4-#3

city: Chengdu

first: Guoling

last: Huang

address: No. 4, Section 2, North Jianshe Road

institute: University of Electronic Science and Technoloogy of China

description:
Library name: T_44_3
MGI DNBSEQ-T7 platform

library_source: transcriptomic single cell

data_processing:
Reads were processed using the dnbc4 tools v2.1.2 pipeline with default and recommended parameters. FASTOs generated from lllumina sequencing output were aligned to the mice genome, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMls and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v4.11) R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were rum with default parameters, unless specified otherwise. We first filtered the matrices to exclude low-quality cells using a standard panel of three quality criteria: (1) number of detected transcripts (number of unique molecular identifiers); (2) detected genes; and (3) percent of reads mapping to mitochondrial genes The expression of mitochondria genes was calculated using Percentage Feature Set function of the seurat package. The normalized data (Normalize Data function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying 'anchors’ between datasets using Find Integration Anchors and Integrate Data in the seurat package. Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE).
Assembly: Mus musculus
Supplementary files format and content: .tsv and .mtx, respectively

source_name: tumor

extract_protocol:
All six C57BL/6J mice with orthotopic KPC tumors were randomly divided into two groups and treated with either IgG or #44-anti-mVSIG4 antibody. At 11 days post-inoculation, the tumor tissues were collected and sent to Shanghai Majorbio Co., Ltd., for scRNA-seq.
Library construction was performed via the DNBelab C TaiM4 V3.0 platform, and sequencing was conducted via the MGI DNBSEQ-T7 system. Bioinformatics analysis was carried out via the proprietary platform of Shanghai Majorbio Co., Ltd.

value: tumor

value: KPC

value: wild-type

value: anti-VSIG4 mAb


title: D14 R1

description: Library name: D14 R1

value: NSCLC


title: αTC1 cells, DMSO, 7 days, biol rep 3

description: Library name: CON3


title: RPE-1 DDX17 intronic deletion hgRNA 2, replicate 1

description: Library name: R011_IDel.DDX17.G110_r1


title: orthotopic pancreatic tumors+anti-VSIG4-#2

description:
Library name: T_44_2
MGI DNBSEQ-T7 platform


title: D7 R1

description: Library name: D7 R1


title: αTC1 cells, DMSO, 7 days, biol rep 2

description: Library name: CON2


title: RPE-1 DDX17 intronic deletion hgRNA 1, replicate 2

description: Library name: R010_IDel.DDX17.G109_r2

value: Deletion in DDX17 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide CTTTCCCGGAAAGCCCCCAG and Cas12a guide CTGGGGATTGGGATTGAGAGGGG.


title: orthotopic pancreatic tumors+anti-VSIG4-#1

description:
Library name: T_44_1
MGI DNBSEQ-T7 platform


title: RPE-1 DDX17 intronic deletion hgRNA 1, replicate 1

description: Library name: R009_IDel.DDX17.G109_r1


title: D0 R1

description: Library name: D0 R1

value: Untreated


title: orthotopic pancreatic tumors+IgG-#3

description:
Library name: C_IgG_3
MGI DNBSEQ-T7 platform

value: IgG


title: αTC1 cells, DMSO, 7 days, biol rep 1

description: Library name: CON1


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 3

description: Library name: Enza3

value: Enzalutamide, 10 μM, 48 hrs


title: Control_igG_C&R_R2

city: Odense M

first: Sanjeeb

middle: Kumar

last: Sahu

address: CAMPUSVEJ 55

department: Department of Molecular Medicine

country: Denmark

institute: University of Southern Denmark

data_processing:
Analysis was performed following the authors recommendations (Skene and Henikoff, 2017).
Assembly: hg19
Supplementary files format and content: File conaining list of enriched peaks.
Supplementary files format and content: Each CUT&RUN sample was normalized to both the control (IgG-CUT&RUN samples) separatly, hence 2 processed file for each sample.
Library strategy: CUT&RUN

source_name: Primary cell

growth_protocol: Human primary lung fibroblast IMR90 cells obtained from ATCC and were cultured in DMEM(Gibco), 10% FBS(Gibco), 1% penicillin/streptomycin (Invitrogen), along with 1x Glutamax (Invitrogen) and Non-Essential amino acids (Invitrogen).All cells were cultured at 37°C with 7% CO2 in a humid incubator. Cells were split at regular intervals when they reached around 70% confluency and the medium was changed every 2 days.

extract_protocol:
CUT&RUN
CUT&RUN, was performed according to PMID:31232687, with minor modifications. In brief, IMR90 cells were briefly trypsinized and washed twice with PBS. Cells were counted and 50000 cells/ assay were pull together depending upon total number of reaction. Cells were spun down at 600 × g for 3 min in swinging-bucket rotor and washed twice with 1.5 ml Wash buffer (20 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 0.5 mM Spermidine and 1X cOmplete™ EDTA-free protease inhibitor cocktail (04693159001, Roche)). During the cell washes, concanavalin A-coated magnetic beads (Bangs Laboratories, cat. No. BP531) (10 µl per condition) were washed twice in 1.5 mL binding buffer (20 mM HEPES-KOH (pH 7.5), 10 mM KCl, 1 mM CaCl, 1 mM MnCl2) and resuspended in 10 µl binding buffer per condition. Cells were then mixed with beads and rotated for 10 min at room temperature (RT) and samples were split into aliquots according to number of antibodies profiled per cell-type. We used 50,000 cells for each CUT&RUN reaction.  Cells were then collected on magnetic beads and resuspended in 50 µl antibody buffer (Wash buffer with 0.05% Digitonin and 2 mM EDTA) containing 1ug of the following antibodies Flag-M2 (Sigma), CHD4 (Abcam), RBBP4 (Abcam), GATAD2A (Abcam), MTA2 (Abcam), IgG (abcam) and ZNF512B.  Cells were incubated with antibodies for overnight at 4 °C and then washed once with 1 ml Digitonin buffer (Wash buffer with 0.05% Digitonin). Samples were incubated with 1:100 dilution in Digitonin buffer of secondary rabbit anti-mouse antibody (Invitrogen) for 10 min at RT and then washed once with 1 mL Digitonin buffer. Samples were then incubated with 700 ng/ml ProteinA-MNase fusion protein (CUTANA™ ChIC / CUT&RUN Assays, EpiCypher) for 10 min at room temperature followed by two washes with 1 ml Digitonin buffer. Cells were then resuspended in 100 µl Digitonin buffer and cooled down to 4 °C before addition of CaCl2 to a final concentration of 2 mM. Targeted digestion was performed for 30 min on ice until 100 µl of 2X STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% Digitonin, 250 mg RNase A, 250 µg Glycogen) were added. Cells were then incubated at 37 °C for 10 min to release cleaved chromatin fragments, spun down for 5 min at 16,000 × g at 4 °C and collected on magnet. Supernatant containing the cleaved chromatin fragments was then transferred and cleaned up using the Zymo Clean & Concentrator Kit. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7103) according to the manufacturer’s instructions. CUT&RUN libraries were sequenced on a NextSeq-500 using a paired-end run.

treatment_protocol: For all ZNF512B overexpression experiments, cells were seeded at the same starting density and transduced with Lentivirus harbouring ZNF512B and two days later antibiotics were added for selection. Upon completon of selection, cells were grown for 1 more pasage and along with control cells process for CUT&RUN assay.

value: Primary cell

value: Lung fibroblast

value: Control IMR90

value: no treatment


title: RPE-1 DDX5 intronic deletion hgRNA 2, replicate 2

description: Library name: R008_IDel.DDX5.G059_r2

value: Intronic deletion in DDX5 generated with hybrid guide RNA comprising Cas9 guide GACAATCGGAGGACTCGAGG and Cas12a guide CCACTTACTATGTGTGAGAAGTT.


title: orthotopic pancreatic tumors+IgG-#2

description:
Library name: C_IgG_2
MGI DNBSEQ-T7 platform


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 2

description: Library name: Enza2

value: Alpha TC1 cells


title: RPE-1 DDX5 intronic deletion hgRNA 2, replicate 1

description: Library name: R007_IDel.DDX5.G059_r1

value: RPE-1 retinal pigment epithelium


title: Control_igG_C&R_R1


title: orthotopic pancreatic tumors+IgG-#1

description:
Library name: C_IgG_1
MGI DNBSEQ-T7 platform


title: αTC1 cells, Enzalutamide, 48 hrs, biol rep 1

description: Library name: Enza1


title: RPE-1 DDX5 intronic deletion hgRNA 1, replicate 2

description: Library name: R006_IDel.DDX5.G058_r2

value: Intronic deletion in DDX5 generated with hybrid guide RNA comprising Cas9 guide GACGACTACTGTGTAGGTGA and Cas12a guide ACCTCTCTAATCGACTGGAAGCA.


title: Semaglutide (100 μg/kg twice weekly via subcutaneous injection), LIDPAD, 4 weeks, replicate 3

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

country: Singapore

institute: Nanyang Technological University

description:
Library name: Sema_3
Column name in Fcount.txt: FABP2.19_aligned.sam

data_processing:
Reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2.
Gene counting was performed using FeatureCounts.
Assembly: Mus musculus reference genome (GRCm39)
Supplementary files format and content: .txt file; raw count data

source_name: Intestinal epithelium

extract_protocol:
Intestinal mucosa of mice treated with different FAHFAs were harvested by scraping the luminal surface of the small intestine. Total RNA was extracted using the Pure-NA Fastspin Total RNA Extraction Kit (Everlife, Singapore).
RNA sequencing libraries were prepared and sequenced on a DNBSEQ-T7 (BGI, China) with 150 bp paired-end reads.

treatment_protocol: Male C57BL/6J mice (8–10 weeks old) were maintained under thermoneutral conditions (30 ± 2°C) on a 12-hour dark/light cycle with free access to LIDPAD for four weeks to induce obesity and metabolic syndrome. Control mice received a matched control diet. Treatment groups received either semaglutide subcutaneously (100 μg/kg; twice weekly) or FAHFAs (12-SAHSA, 12-TAHSA, 12-SAASA, 12-TAASA, or 12-HDTZSA; 100 mg/kg; daily via oral gavage) concurrent with the LIDPAD diet. After four weeks of treatment, animals were euthanized using an overdose of xylazine/ketamine prior to tissue collection. Collected tissues were fixed with 4% PFA or snap frozen with liquid nitrogen for subsequent analyses.

value: Intestinal epithelium

value: Semaglutide


title: αTC1 cells, DMSO, 48 hrs, biol rep 3

description: Library name: CON3

value: DMSO, 48 hrs


title: RPE-1 DDX5 intronic deletion hgRNA 1, replicate 1

description: Library name: R005_IDel.DDX5.G058_r1


title: ZNF512B-OE_MTA2_C&R_R2

description: Each CUT&RUN sample was normalized to both the control (IgG CUT&RUN samples) separatly, hence 2 processed file for each sample.

value: ZNF512B over expression


title: ZNF512B-OE_MTA2_C&R_R1


title: αTC1 cells, DMSO, 48 hrs, biol rep 2

description: Library name: CON2


title: Semaglutide (100 μg/kg twice weekly via subcutaneous injection), LIDPAD, 4 weeks, replicate 2

description:
Library name: Sema_2
Column name in Fcount.txt: FA.8_aligned.sam


title: RPE-1 intergenic control hgRNA 2, replicate 2

description: Library name: R004_IDel.ctrl.gui2_r2

value: Intergenic-intergenic control hybrid guide RNA comprising Cas9 guide TCCGTTAGCTTCATCCTATC and Cas12a guide GCCTGAGACCTAAAGGGCTATTG.


title: Control_MTA2_C&R_R2


title: Semaglutide (100 μg/kg twice weekly via subcutaneous injection), LIDPAD, 4 weeks, replicate 1

description:
Library name: Sema_1
Column name in Fcount.txt: FA.7_aligned.sam


title: αTC1 cells, DMSO, 48 hrs, biol rep 1

description: Library name: CON1


title: Control_MTA2_C&R_R1


title: RPE-1 intergenic control hgRNA 2, replicate 1

description: Library name: R003_IDel.ctrl.gui2_r1


title: GAK_WT biol rep 4

city: New Haven

first: Patricia

last: Bunda

state: CT

address: 300 Cedar St S370

institute: Yale School of Medicine

description:
Library name: GAK_WT_4
ribosomal RNA (rRNA) reduction prep

data_processing:
fastp
HISAT2
Stringtie
Assembly: GRCm39
Supplementary files format and content: csv

molecule: polyA RNA

source_name: kidney

growth_protocol: 3-4 weeks old male and female mice

extract_protocol:
podocyte-specific TRAP-seq
ribosomal RNA (rRNA) reduction prep

value: kidney

value: podocyte

value: wildtype

tag: batch


title: Vehicle (corn oil; daily via oral gavage), LIDPAD, 4 weeks, replicate 3

description:
Library name: LIDPAD_3
Column name in Fcount.txt: FABP2.15_aligned.sam

value: LIDPAD


title: ZNF512B-OE_GATAD2A_C&R_R2

value: Primary cell


title: RPE-1 intergenic control hgRNA 1, replicate 2

description: Library name: R002_IDel.ctrl.gui1_r2

value: Intergenic-intergenic control hybrid guide RNA comprising Cas9 guide CTATCCAGAGTAGATCATTA and Cas12a guide AAACCCAGTCCCCAATGTGATGA.


title: GAK_WT biol rep 3

description:
Library name: GAK_WT_3
ribosomal RNA (rRNA) reduction prep


title: Vehicle (corn oil; daily via oral gavage), LIDPAD, 4 weeks, replicate 2

description:
Library name: LIDPAD_2
Column name in Fcount.txt: FABP2.14_aligned.sam


title: RPE-1 intergenic control hgRNA 1, replicate 1

description: Library name: R001_IDel.ctrl.gui1_r1


title: ZNF512B-OE_GATAD2A_C&R_R1

value: Lung fibroblast


title: Vehicle (corn oil; daily via oral gavage), LIDPAD, 4 weeks, replicate 1

description:
Library name: LIDPAD_1
Column name in Fcount.txt: FA.6_aligned.sam


title: Control_GATAD2A_C&R_R2

value: Control IMR90

value: no treatment


title: GAK_WT biol rep 2

description:
Library name: GAK_WT_2
ribosomal RNA (rRNA) reduction prep


title: HAP1 siRNA knockdown of SFPQ, replicate 2

description: Library name: H046_siKD.SFPQ.r2

data_processing:
Base-calling Q-scores were obtained with RTA 3.4.4. Demultiplexing of raw sequencing data was performed using Illumina’s bclfastq.
Alternative splicing analysis was performed as follows: RNA-Seq data were processed using the vast-tools pipeline, version 2.5.1 https://github.com/vastgroup/vast-tools (Braunschweig et al., 2014; Irimia et al., 2014; Tapial et al., 2017). From primary output, events with poor coverage or junction balance were filtered out (vast-tools quality column score 3 other than SOK/OK/LOW/VLOW for cassette exon [CE], microexon [MIC], and alternative 5' or 3' splice site [Alt5/3] events or coverage less than 10 reads for intron retention [IR] events; score 4 other than OK/B1/B2/Bl/Bn for CE and MIC events and score 5 of less than 0.05 for IR events). If more than one replicate was present, the point estimate from vast-tools diff was used and if the coverage/balance filtering step failed for an event in more than half of the replicates, its value was set to NA. Differential AS was assessed through the vast-tools diff module available with the main pipeline. Changes were considered significant if they were greater than 10 dPSI/dPIR and the expected minimum change was different from zero at p > 0.95 according to vast-tools’ diff module.
Gene expression changes were analyzed by pseudo-aligning pre-trimmed reads to GENCODE v43 transcripts using Salmon v1.10 (Patro et al., 2017) and aggregated per gene using the R package tximport (Soneson et al., 2015). Differential expression was then assessed using the classic mode (exactTest) edgeR (McCarthy et al., 2012), and genes with an FDR < 0.05 and a greater than 2-fold change were considered differential. For each comparison, only genes expressed at a minimum of 5 RPKM in one or both conditions were considered.
RNAseq.HAP1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Assembly: GENCODE v43
Supplementary files format and content: RNAseq.HAP1_vastTools.tab.gz is a tab-delimited file and contains vast-tools output, i.e. event information and raw percent-spliced-in values and quality scores per sample. See https://github.com/vastgroup/vast-tools#combine-output-format.
Supplementary files format and content: RNAseq.HAP1_altSplicing.tab.gzz is a tab-delimited file and contains mean percent-spliced-in values per treatment and significance calls for the difference vs intergenic hgRNA control.
Supplementary files format and content: Expression_HAP1.tab.gz is a tab-delimited file and contains RPKM, log2 fold-change and p-values per treatment vs intergenic hgRNA control.

source_name: HAP1 chronic myelogenous leukemia

growth_protocol: HAP1 cells (clone C631; male, with Y chromosome loss; Horizon Genomics, RRID: CVCL_Y019) were maintained under standard sterile cell culture conditions at 37°C in a humidified incubator containing 5% CO2 at subconfluent densities (50-70%). HAP1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco, #12440053) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Gibco, #26140079) and penicillin/streptomycin (Gibco, #15140-122).

treatment_protocol: For CHyMErA deletions, cells were transduced at an estimated MOI < 1 with lentivirus encoding the indicated hgRNAs in pLCHKO-EGFP-P2A-Puro vector. Cells were subsequently selected for the integration of the CHyMErA cassette by puromycin (Gibco A11138-03) at 1 µg/ml for 48 hours. At T0, puromycin was removed from the medium and cells were grown for three days prior to harvesting RNA at 60-80% confluency. For siRNA-mediated knockdowns, reverse transfection was performed for 350K HAP1 cells using 80 pmoles of siRNA and 6 µL of Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, #13778100). RNA was harvested 48 hours post-transfection.

value: HAP1 chronic myelogenous leukemia

value: siRNA-mediated knockdown of SFPQ with Dharmacon smartpool Catalog ID:M-006455-02-0005


title: Vehicle (corn oil; daily via oral gavage), control diet, 4 weeks, replicate 3

description:
Library name: Control_3
Column name in Fcount.txt: FABP2.16_aligned.sam

value: Control


title: HAP1 siRNA knockdown of SRRM2, replicate 2

description: Library name: H044_siKD.SRRM2.r2

value: siRNA-mediated knockdown of SRRM2 with Dharmacon smartpool Catalog ID:M-015368-02-0005


title: ZNF512B-OE_RBBP4_C&R_R2


title: GAK_WT biol rep 1

description:
Library name: GAK_WT_1
ribosomal RNA (rRNA) reduction prep


title: Vehicle (corn oil; daily via oral gavage), control diet, 4 weeks, replicate 2

description:
Library name: Control_2
Column name in Fcount.txt: FA.3_aligned.sam

value: Intestinal epithelium


title: Control_GATAD2A_C&R_R1


title: Vehicle (corn oil; daily via oral gavage), control diet, 4 weeks, replicate 1

description:
Library name: Control_1
Column name in Fcount.txt: FA.2_aligned.sam


title: GAK_KO biol rep 4

description:
Library name: GAK_KO_4
ribosomal RNA (rRNA) reduction prep

value: Gak-KO


title: HAP1 siRNA knockdown of SFPQ, replicate 1

description: Library name: H045_siKD.SFPQ.r1


title: GAK_KO biol rep 3

description:
Library name: GAK_KO_3
ribosomal RNA (rRNA) reduction prep


title: ZNF512B-OE_RBBP4_C&R_R1

value: ZNF512B over expression


title: HAP1 siRNA knockdown of SRRM2, replicate 1

description: Library name: H043_siKD.SRRM2.r1


title: GAK_KO biol rep 2

description:
Library name: GAK_KO_2
ribosomal RNA (rRNA) reduction prep


title: 12-TAHSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 3

description:
Library name: 12TAHSA_3
Column name in Fcount.txt: FA.15_aligned.sam


title: Control_RBBP4_C&R_R2

description: Each CUT&RUN sample was normalized to both the control (IgG CUT&RUN samples) separatly, hence 2 processed file for each sample.


title: HAP1 siRNA knockdown of SRSF3, replicate 2

description: Library name: H042_siKD.SRSF3.r2

value: siRNA-mediated knockdown of SRSF3 with Dharmacon smartpool Catalog ID:M-030081-00-0005


title: GAK_KO biol rep 1

description:
Library name: GAK_KO_1
ribosomal RNA (rRNA) reduction prep

value: kidney


title: Control_RBBP4_C&R_R1


title: 12-TAHSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 2

description:
Library name: 12TAHSA_2
Column name in Fcount.txt: FA.14_aligned.sam


title: HAP1 siRNA knockdown of SRSF3, replicate 1

description: Library name: H041_siKD.SRSF3.r1


title: 12-TAHSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 1

description:
Library name: 12TAHSA_1
Column name in Fcount.txt: FA.13_aligned.sam


title: GAK_C62 biol rep 4

description:
Library name: GAK_C62_4
ribosomal RNA (rRNA) reduction prep

value: podocyte

value: C62 Gak-KO


title: HAP1 control non-targeting siRNA knockdown, replicate 2

description: Library name: H040_siKD.siCtrl.r2

value: Control non-targeting siRNA-mediated knockdown with Dharmacon ON-TARGETplus Non-targeting pool (D-001810-10)


title: ZNF512B-OE_CHD4_C&R_R2

value: Primary cell


title: 12-TAASA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 3

description:
Library name: 12TAASA_3
Column name in Fcount.txt: FABP2.7_aligned.sam


title: ZNF512B-OE_CHD4_C&R_R1


title: GAK_C62 biol rep 3

description:
Library name: GAK_C62_3
ribosomal RNA (rRNA) reduction prep


title: HUVEC premature senescence replicate 3

city: Kyoto

first: Tomoya

last: Kitani

address: 465 Kajii-cho Kawaramachi-Hirokoji Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

description:
Library name: HUVEC_PreSen_3
premature senescence

data_processing:
Reads were trimmed using Trim Galore, aligned to the GRCh38 genome using STAR, and quantified using featureCounts.
Assembly: GRCh38 (GENCODE release 44)
Supplementary files format and content: Gene-level count matrix with one column per sample and one row per gene.

source_name: HUVEC

growth_protocol: HUVECs were cultured in EGM-2 medium at 37°C and 5 percent CO2.

extract_protocol:
Total RNA was extracted with the Zymo Quick-RNA Miniprep Kit according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Exome kit.

treatment_protocol: Premature senescence was induced by retroviral overexpression of TRF2ΔBΔM. Replicative senescence was generated by repeated passaging until growth arrest.

value: HUVEC

value: endothelial cell

value: TRF2 mutant overexpression


title: VCaP_DMSO_POL2

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

description: Library name: SI_41145

data_processing:
ChIP-seq reads were trimmed using Trimmomatic (v0.39, settings TruSeq3-PE-2.fa:2:30:10, minlen 50). Alignment was then performed separately to both the human genome (hg38) and the drosophila genome (dm6) using BWA (v0.7.17 “bwa mem”, options -5S -T0, version 0.7.17-r1198-dirty). Low-quality and duplicate reads were filtered with SAMtools and Picard, respectively. Normalization ratios were calculated based on the lowest amount of uniquely aligned reads per ChIP target to each genome as reccomended in ActiveMotifs protocols. Reads were then downsampled per the normalization ratios. P300 Samples did not have this normalization step. Then peak calling was performed with MACS2 using narrow or broad settings depending on the target, and blacklisted genomic regions were removed using BEDTools with the ENCODE exclusion list. MACS was run with a bam vcap IgG control. Processed data were converted to BigWig format using UCSC wigToBigWig for visualization. Read density heatmaps and average enrichment profiles were generated using deepTools. For histone marks, signals were plotted within ±2.5 kb of the reference point, and for other transcriptome factors within ±1 kb. The parameters --skipZeros, --averageType mean, and --plotType se were applied. ENCODE blacklist regions (ENCFF356LFX) were excluded from analysis.
Assembly: hg38
Supplementary files format and content: .bed: peak locations from macs bed calling with blacklist removed; .bw: signal files

source_name: VCaP

growth_protocol: VCaP cells were maintained in DMEM GlutaMAX supplemented with 10% FBS (Thermo Fisher Scientific).

extract_protocol:
In brief, cells were crosslinked in 1% formaldehyde, quenched with glycine, and lysed for chromatin extraction. Chromatin was sheared to 200–600 bp fragments using a Bioruptor (Diagenode) and subjected to immunoprecipitation with antibodies against transcription factors (AR, FOXA1, p300, ERG and BRD4) or histone marks (H3K27ac, H2BK20ac, and RNA Pol II) using the iDeal ChIP-seq Kit (Diagenode). Drosophila spike-in chromatin (Active Motif, 53083) and spike-in antibody (Active Motif, 61686) were added during the overnight incubation. After reverse crosslinking and DNA purification, sequencing libraries were prepared and sequenced on an Illumina HiSeq 2500 platform.
ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 1 and 3 hours

value: VCaP

value: prostate cancer

value: DMSO


title: VCaP_100nM_DALTAC_1_1h_AR

description: Library name: SI_41140

value: 100 nM DALTAC-1 1h


title: VCaP_100nM_DALTAC_1_1h_P300

description: Library name: SI_40568


title: HUVEC replicative senescence replicate 1

description:
Library name: HUVEC_RepSen_1
replicative senescence

value: replicative senescence


title: 12-TAASA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 2

description:
Library name: 12TAASA_2
Column name in Fcount.txt: FABP2.6_aligned.sam

value: Intestinal epithelium


title: HAP1 control non-targeting siRNA knockdown, replicate 1

description: Library name: H039_siKD.siCtrl.r1

value: HAP1 chronic myelogenous leukemia


title: GAK_C62 biol rep 2

description:
Library name: GAK_C62_2
ribosomal RNA (rRNA) reduction prep


title: Control_CHD4_C&R_R2

value: Lung fibroblast

value: Control IMR90

value: no treatment


title: 12-TAASA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 1

description:
Library name: 12TAASA_1
Column name in Fcount.txt: FABP2.5_aligned.sam


title: GAK_C62 biol rep 1

description:
Library name: GAK_C62_1
ribosomal RNA (rRNA) reduction prep

value: kidney

value: podocyte


title: HAP1 TKO gene knockout of SRRT, replicate 2

description: Library name: H038_TKO.SRRT.G229_r2

value: Deletion of SRRT with hybrid guide RNA comprising exonic TKOv3 Cas9 guide AGAGAGATGAAAGACGTCGA and intergenic Cas12a guide ACAGACCTGAGTTTGAGCCCCAG.


title: RNA Pol II_input_LB100_2

city: Göttingen

first: Nignjun

last: Duan

address: Robert-Koch-Straße 40

country: Germany

institute: Universitätsmedizin Göttingen

description: Library name: RNA Pol II_input_LB100_2

data_processing:
ChIP-seq reads were aligned to GRCm39 build of the mouse genome using bwa-mem (v0.7.18).
Aligned reads were filtered and sorted by Samtools (v1.21).
Read enrichment at specific chromatin regions was quantified using featureCounts (v2.1.1)
Coverage tracks were generated with bamCoverage (deepTools v3.5.6)
Assembly: GRCm39
Supplementary files format and content: bigwig

extract_protocol:
ChIP-seq was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads, Cell Signaling Technology, #9003) according to the manufacturer’s protocol.
Sequencing library was preparied with DNA Library Prep Kit for Illumina Systems (ChIP-seq, CUT&RUN) #56795 and Multiplex Oligos for Illumina Systems (Dual Index Primers) (ChIP-seq, CUT&RUN) #47538 according to the manufacturer’s protocol.

value: mesenchymal


title: Control_CHD4_C&R_R1

value: Primary cell


title: HAP1 TKO gene knockout of SRRT, replicate 1

description: Library name: H037_TKO.SRRT.G229_r1


title: 12-SAHSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 3

description:
Library name: 12SAHSA_3
Column name in Fcount.txt: FA.12_aligned.sam


title: ZNF512B-OE_Flag_C&R_R2

value: ZNF512B over expression


title: 12-SAHSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 2

description:
Library name: 12SAHSA_2
Column name in Fcount.txt: FA.11_aligned.sam


title: RNA Pol II_input_LB100_1

description: Library name: RNA Pol II_input_LB100_1


title: HAP1 TKO gene knockout of SRRM2, replicate

description: Library name: H036_TKO.SRRM2.G227_r2

value: Deletion of SRRM2 with hybrid guide RNA comprising exonic TKOv3 Cas9 guide GTTGCGCTGGACGTAGCCGT and intergenic Cas12a guide AGAGTCTACTATAATGTGTACTG.


title: 12-SAHSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 1

description:
Library name: 12SAHSA_1
Column name in Fcount.txt: FA.10_aligned.sam


title: ZNF512B-OE_Flag_C&R_R1


title: HAP1 TKO gene knockout of SRRM2, replicate 1

description: Library name: H035_TKO.SRRM2.G227_r1


title: RNA Pol II_LB100_2

description: Library name: RNA Pol II_LB100_2


title: HAP1 TKO gene knockout of SON, replicate 2

description: Library name: H034_TKO.SON.G226_r2

value: Deletion of SON with hybrid guide RNA comprising exonic TKOv3 Cas9 guide GATGCTAGCATCCAACACCA and intergenic Cas12a guide ATAAAATAGCCACAACATATTTA.


title: 12-SAASA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 3

description:
Library name: 12SAASA_3
Column name in Fcount.txt: FABP2.3_aligned.sam


title: RNA Pol II_LB100_1

description: Library name: RNA Pol II_LB100_1


title: Control_ZNF512B_C&R_R1

description: Each CUT&RUN sample was normalized to both the control (IgG CUT&RUN samples) separatly, hence 2 processed file for each sample.


title: Control_ZNF512B_C&R_R2


title: 12-SAASA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 2

description:
Library name: 12SAASA_2
Column name in Fcount.txt: FABP2.2_aligned.sam


title: HAP1 TKO gene knockout of SON, replicate 1

description: Library name: H033_TKO.SON.G226_r1


title: HAP1 TKO gene knockout of PFN1, replicate 2

description: Library name: H032_TKO.PFN1.G209_r2

value: Deletion of PFN1 with hybrid guide RNA comprising exonic TKOv3 Cas9 guide GTAGCAGCGCCATGGCCGGG and intergenic Cas12a guide TAGAGACAAAATGTTAATGATAA.


title: KO6

city: Nanjing

first: Bai

last: xueya

address: No. 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu, China

institute: Nanjing Medical University

description:
Library name: sample12
KO6_fpkm

data_processing:
Raw sequencing reads, containing adapters or low-quality bases, were filtered using Fastp (v0.18.0) to obtain high-quality clean reads. The filtering steps included: (1) removing adapter-containing reads; (2) removing reads with more than 10% unknown nucleotides (N); and (3) removing low-quality reads with over 50% bases having a Q-value ≤ 20. Subsequently, Bowtie2 (v2.2.8) was used to align reads to the ribosomal RNA (rRNA) database, and rRNA-mapped reads were removed. The remaining clean reads were used for assembly and gene abundance calculations.
Assembly: An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2 2.1.0 and other parameters set as a default.
Supplementary files format and content: The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.

source_name: aorta

extract_protocol:
Aortic endothelial cells were isolated from Ang II-infused wildtype and Glra2-/- mice treated with glycine or saline. Total RNA was extracted using Trizol (TaKaRa).
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the  Illumina Novaseq

value: aorta

value: endothelial cells

value: Glra2 global knockout

value: Ang II infusion and glycine 800mg/kg/day(i.p)


title: 12-SAASA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 1

description:
Library name: 12SAASA_1
Column name in Fcount.txt: FABP2.1_aligned.sam

value: Intestinal epithelium


title: RNA Pol II_input_control_2

description: Library name: RNA Pol II_input_control_2


title: RNA Pol II_input_control_1

description: Library name: RNA Pol II_input_control_1


title: HAP1 TKO gene knockout of PFN1, replicate 1

description: Library name: H031_TKO.PFN1.G209_r1

value: HAP1 chronic myelogenous leukemia


title: KO5

description:
Library name: sample11
KO5_fpkm

value: Ang II infusion and glycine 80 mg/kg/day(i.p)


title: RNA Pol II_control_2

description: Library name: RNA Pol II_control_2


title: KO4

description:
Library name: sample10
KO4_fpkm


title: 12-HDTZSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 3

description:
Library name: 12HDTZSA_3
Column name in Fcount.txt: FABP2.12_aligned.sam


title: HAP1 SRSF3 intronic deletion hgRNA 2, replicate 2

description: Library name: H028_IDel.SRSF3.G181_r2

value: Intronic deletion in SON generated with hybrid guide RNA comprising Cas9 guide CTGATTGGCCAGGAATGTGT and Cas12a guide GGTAGTGAAGTTAGTTTGACATG.


title: 12-HDTZSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 2

description:
Library name: 12HDTZSA_2
Column name in Fcount.txt: FABP2.11_aligned.sam


title: RNA Pol II_control_1

description: Library name: RNA Pol II_control_1


title: KO3

description:
Library name: sample9
KO3_fpkm

value: Ang II infusion and saline(i.p)


title: HAP1 SRSF3 intronic deletion hgRNA 2, replicate 1

description: Library name: H027_IDel.SRSF3.G181_r1


title: VCaP_100nM_ARi_p300i_12hr_Rep1

description: Library name: SI_40724

data_processing:
Alignment was  performed using kalliso (v0.46.1) quant to human (hg38/GRCh38) reference (Homo_sapiens.GRCh38.96.gtf gene reference). Read counts were adjusted for normalization then filtered in R via package EdgeR. Package Limma-Voom (vlimma_3.53.10) was involved for differential expression analysis. GSEA analysis and corresponding heatmaps and figures were created using R package fgsea (vfgsea_1.24.0), ComplexHeatmap and ggplot2.
Assembly: hg38
Supplementary files format and content: Counts Matrix

extract_protocol:
Total RNA was extracted from cells using QIAzol Lysis Reagent (QIAGEN). Initially, 1x10^6 cells were lysed with 700 µL of QIAzol. The lysates were incubated at room temperature for 5 minutes to dissociate nucleoproteins, then mixed with 140 µL chloroform and centrifuged at 12,000 g for 15 minutes at 4°C to achieve phase separation. The aqueous phase was then mixed with 1.5x volume of ethanol and applied to a RNeasy Mini spin column (QIAGEN) for RNA purification, following the miRNeasy Mini Kit protocol. The RNA was then eluted in RNase-free water, and its concentration and purity assessed using a NanoDrop spectrophotometer.
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. PolyA+ RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2 × 100 nucleotide read length) with sequence coverage to 15–20M paired reads.

treatment_protocol: The cells were treated with 100 nM DALTAC-1 or p300i+ARi for 4, 12 and 24 hours

value: VCaP

value: prostate cancer


title: differentiated FGCs,Dif-FGCs. D2.IP

first: Ji

last: Wu

address: No.800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: D2.IP

data_processing:
Cutadapt used for triming reads. It can bin reads based on mapping to multiple references at once
Mapping sequencing RNA reads to align genome assembly using sofeware Hisat2
Peak calling was performed independently for each sample using MACS2
Differential acetylation genes were identified using diffReps. Peaks located on mRNA exons were screened using in-house programs and annotated accordingly
Assembly: MM10
Supplementary files format and content: Tab-delimited text files include the number of reads, relative RPKM values, and P-values for control and experimental group Sample.

source_name: Ovary

extract_protocol:
total RNA was isolated from FGSCs and Dif-FGCs.NEBNext rRNA Depletion Kit v2 was used to remove rRNA and the GenSeq® ac4C-IP Kit was used to immuneprecipitate RNA.
For library preparation, RNA Fragmentation Reagents were used to fragment the RNA to ~200 nt. Then The RNA fragments incubated with the protein A beads/ ac4C antibody complexes for 4 h at 4 °C. Eluted the ac4C-enriched RNA fragments off the beads by proteinase K digestion, and purify the RNA fragments by phenol-chloroform. Subsequently, the RNA fragments used for the RNA library construction.

value: Ovary

value: FGSCs

value: germ stem cells

value: differentiated group


title: VCaP_100nM_p300i_ARi_4hr_Rep1

description: Library name: SI_40720


title: 12-HDTZSA (100 mg/kg; daily via oral gavage), LIDPAD, 4 weeks, replicate 1

description:
Library name: 12HDTZSA_1
Column name in Fcount.txt: FABP2.10_aligned.sam


title: KO2

description:
Library name: sample8
KO2_fpkm


title: sorted Tscm cells, RA5

city: Seoul

first: Eun Bong

last: Lee

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

description: Library name: RA5

data_processing:
The fastq files were aligned to the human reference genome (GRCh38-2020-A) by using the CellRanger count command (version 7.1.0).
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated using density gradient centrifugation. Cells were washed with PBS, stained with Tscm marker dye (CD3, CCR7, CD45RA, CD27, CD95), washed and resuspended in FACS buffer (1% v/v FBS in PBS). Tscm cells were sorted (CD3+CCR7+CD45RA+CD27+CD95high) by fluorescence-activated cell sorting (FACS) using a FACSAria III instrument (BD Biosciences). The sorted Tscm cells were washed in FACS buffer and subsequently used for single-cell RNA sequencing.
Cells were loaded into a Chromium Single Cell Controller (10x Genomics) using either the Chromium Single Cell 5′ Reagent Kit v1.1 or v2.0, targeting for a cell recovery of 10,000 cells per sample. Gel bead-in-emulsion (GEM) generation, barcoding, reverse transcription, and cDNA amplification were performed according to the manufacturer’s protocol to construct 5′ gene expression libraries. Libraries were sequenced on an Illumina NovaSeq 6000 platform. Raw base call files were converted to FASTQ format using bcl2fastq2.

value: Blood

value: sorted Tscm cells

tag: individual

tag: Sex

value: female

tag: disease state

value: Rheumatoid Arthritis

value: JAK inhibitor


title: HAP1 SRSF3 intronic deletion hgRNA 1, replicate 2

description: Library name: H026_IDel.SRSF3.G180_r2

value: Intronic deletion in SON generated with hybrid guide RNA comprising Cas9 guide CATGCTCGGGAACCAAAGGG and Cas12a guide GTGTGGTGTTTGGGTAGTGAAGT.


title: differentiated FGCs, Dif-FGCs. D1.IP

description: Library name: D1.IP


title: KO1

description:
Library name: sample7
KO1_fpkm

value: aorta

value: endothelial cells

value: Glra2 global knockout


title: eq_OA_Ctrl_GJA09

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: Library name: sample49

data_processing:
All paired end RNA-seq reads were assessed for quality using Partek® Flow® software (Illumina, San Diego, CA). Low quality reads (Q ≤ 20) were filtered and adapter sequences were trimmed with CUTadapt (version 1.12)
Filtered reads were mapped to the Equcab 3.0 reference genome (GCA_002863925.1; https://www.ensembl.org/Equus_caballus/Info/Index) using STAR (version 2.7.3a)
HTSeq (version 0.11.0)[54] was used to count the number of reads aligning to annotated genes. Genes with read counts greater than 10 and expressed in ≥ 10 horses (~50% of OA group) were retained for downstream analysi
Reads were normalized using Remove Unwanted Variation from RNA-Seq Data (RUVSeq) accounting for residuals (RUVr)
Differential expression analysis was performed with limma-voom (version 3.64.1) in RStudio (version 2024.04.2) [59,60] with correction for multiple testing (Padj ≤ 0.05, 1.5 ≤ Log2Fold Change ≤ -1.5)
Assembly: Equcab 3.0
Supplementary files format and content: csv file includes raw counts from each sample

organism: Equus caballus

source_name: PBMC

growth_protocol: peripheral blood mononuclear cells (PBMC) isolated using ficol gradient.

extract_protocol:
Ficol gradiant seperation from whole blood
Library construction was performed with a polyA capture protocol with the ABclonal mRNA-seq Lib Prep Kit for Illumina (ABclonal Technology, Woburn MA).

treatment_protocol: healthy horse PBMC compared to horses with naturally occuring OA

value: PBMC

value: Ctrl


title: HAP1 SRSF3 intronic deletion hgRNA 1, replicate 1

description: Library name: H025_IDel.SRSF3.G180_r1

value: HAP1 chronic myelogenous leukemia


title: WT6

description:
Library name: sample6
WT6_fpkm

value: WT

value: Ang II infusion and glycine 800mg/kg/day(i.p)


title: differentiated FGCs,Dif-FGCs. D2.Input

description: Library name: D2.Input

value: Ovary

value: FGSCs


title: eq_OA_OA_GJA65

description: Library name: sample47

value: OA


title: HAP1 SRRT intronic deletion hgRNA 2, replicate 2

description: Library name: H024_IDel.SRRT.G179_r2

value: Deletion in SRRT spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide GCCAGATAGCAAAAGCCCAG and Cas12a guide GGAGGACGCCACAGCCACACAGG.


title: eq_OA_Ctrl_GJA08

description: Library name: sample48


title: WT5

description:
Library name: sample5
WT5_fpkm


title: differentiated FGCs, Dif-FGCs. D1.Input

description: Library name: D1.Input

value: germ stem cells

value: differentiated group


title: HAP1 SRRT intronic deletion hgRNA 2, replicate 1

description: Library name: H023_IDel.SRRT.G179_r1


title: eq_OA_OA_GJA60

description: Library name: sample46


title: WT4

description:
Library name: sample4
WT4_fpkm


title: HAP1 SRRT intronic deletion hgRNA 1, replicate 1

description: Library name: H021_IDel.SRRT.G178_r1

value: Deletion in SRRT spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide GAGGACGCCACAGCCACACA and Cas12a guide CTACGTTAGTGTTTCCCAGAGAT.


title: eq_OA_Ctrl_GJA05

description: Library name: sample45


title: WT3

description:
Library name: sample3
WT3_fpkm

value: Ang II infusion and saline(i.p)


title: HAP1 SRRT intronic deletion hgRNA 1, replicate 2

description: Library name: H022_IDel.SRRT.G178_r2


title: female germline stem cells, FGSCs. C2.Input

description: Library name: C2.Input

value: control group


title: eq_OA_OA_GJA57

description: Library name: sample44


title: female germline stem cells, FGSCs. C1.IP

description: Library name: C1.IP


title: WT2

description:
Library name: sample2
WT2_fpkm

value: aorta


title: female germline stem cells, FGSCs. C1.Input

description: Library name: C1.Input


title: WT1

description:
Library name: sample1
WT1_fpkm

value: endothelial cells


title: HAP1 SRRM2 intronic deletion hgRNA 2, replicate 2

description: Library name: H020_IDel.SRRM2.G177_r2

value: Deletion in SRRM2 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide TTTGGGGGAGGTGAGTAAAG and Cas12a guide TTTCGTTCTGATGTATATGGACT.


title: eq_OA_OA_GJA55

description: Library name: sample42

value: PBMC


title: E18 cortex scRNA-seq

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

description: Library name: E18 cortex

data_processing:
Raw data was processed through Cell Ranger v4. For the E18 cortex sample, reads were aligned to the wild-type mouse genome (mm10). For the P2 Emx1 lineage-traced dataset, reads were aligned to a custom reference gnome containing the Eyfp open reading frame concatenated to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files.

source_name: Brain (dorsal ventricular-subventricular zone and cortex)

extract_protocol:
For single-cell isolation of the E18 cortex, thick coronal sections rostral to the hippocampus were generated and tissue dorsal to the lateral ventricles, including the ventricular-subventricular zone (V-SVZ), was dissected out. For single-cell isolation of the P2 V-SVZ, the cortex was removed to expose the lateral ventricles, and the dorsolateral V-SVZ was microdissected out and collected. During dissections, collected tissue was placed in either DMEM (Gibco) or Hibernate A without calcium (BrainBits) supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane) and left on ice until subsequent processing steps. Tissue collection was immediately followed by an enzymatic digestion step. Samples were incubated in 20 units/mL Papain with 1 mM L-cysteine, 0.5 mM EDTA, and 0.005% DNase I (Worthington) dissolved in Hibernate A medium without calcium (BrainBits) and DRAQ5 (Abcam) diluted 1:3000 for 30 minutes at 37°C to simultaneously enzymatically digest the tissue and label nuclei. Following enzyme treatment, cells were spun down at 300 g for 5 minutes and resuspended in media, either DMEM (Gibco) or Hibernate A medium without calcium, supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane). Following enzymatic digestion or immediately following collection, tissue was triturated using blunt needles with sequentially decreasing diameters (McMaster-Carr). Cells were then spun down at 300 g for 5 minutes and resuspended in 0.25% BSA (Jackson) in HBSS, after which the cell suspension was filtered through a 40 µm cell strainer and incubated in 1:1000 propidium iodide (PI) (Abcam) to label dead/damaged cells. Samples were then FACS sorted using a MoFlo Cell Sorter (Beckman Coulter) or Aria Fusion A (Becton Dickinson) to enrich for viable (PI-negative, DRAQ5-positive) cells, which were collected in media, either DMEM or Hibernate A without calcium, supplemented with 2% B27 and 500 µM L-glutamine.
Libraries were constructed according to the manufacturer's instructions (Single Cell 3' v2, 10x Genomics).

tag: age

value: Embryonic day 18

value: Late embryonic cortical cell types


title: HAP1 SRRM2 intronic deletion hgRNA 2, replicate 1

description: Library name: H019_IDel.SRRM2.G177_r1

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Briefly, cells were washed in PBS twice and lysed directly in the vessel using RLT buffer supplemented with reducing agent β-Mercaptoethanol (Milipore #444203-250ML). All RNA samples were DNase-treated using RNase-Free DNase Set (Qiagen #79256) according to the manufacturer's protocol.
Biological duplicates were processed for RNA-Seq. Stranded/directional total RNA-Seq (ribo-depletion) libraries were prepared as follows. RNA concentration was measured using Qubit RNA BR (cat # Q10211, Thermo Fisher Scientific Inc., Waltham, USA) and RNA quality was assessed from 1 ng input on the Bioanalyzer RNA 6000 Pico kit (cat # 5067-1513, Agilent Technologies Inc., Santa Clara, USA). RIN score ranged from 8.4- 9.8 ; with a median RIN score of 9.6. For library preparation, 300 ng of DNase-treated RNA per sample was first subjected to rRNA depletion (H/M/R) and then processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (cat #E7760L; New England Biolabs; protocol 6.0_7/24), with 7.5 minutes of fragmentation at 94 °C and 12 cycles of amplification. To assess final library quality, 1 μl of the library was analyzed on the Agilent Bioanalyzer dsDNA High Sensitivity chip (cat # 5067-4626, Agilent Technologies Inc., Santa Clara, USA). The libraries were quantified using the Qubit 1X dsDNA HS (cat # Q33231, Thermo Fisher Scientific Inc., Waltham, USA) and were pooled at equimolar ratios after adjusting for fragment size. The final pool, with an average library size of ~395 bp was run on the Bioanalyzer and quantified using NEBNext Library Quant Kit for Illumina (cat # E7630L, New England Biolabs, Ipswich, USA).

value: HAP1 chronic myelogenous leukemia


title: HAP1 SRRM2 intronic deletion hgRNA 1, replicate 2

description: Library name: H018_IDel.SRRM2.G176_r2

value: Deletion in SRRM2 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide TATGGACTGCCAGAATAGGG and Cas12a guide GTCGCACAACTCAAATCATTCAC.


title: eq_OA_OA_GJA56

description: Library name: sample43


title: Replicate 2 of FMRP-KO RNA

city: Montreal

first: Senthilkumar

last: Kailasam

state: Quebec

address: 740 Dr. Penfield Avenue, #4200

department: Human Genetics

institute: McGill University

description:
Library name: FMRP_RNA_rep2
Second replicate of RNA from FMRP knockout mice.

data_processing:
The raw reads were trimmed with Cutadapt 2.10, removing adapters and bases below quality thresholds, and then demultiplexed using UMI barcodes (ID1=ATCGT, ID2=AGCTA, ID3=CGTAA) with specific options for base trimming and sequence length.
Reads mapping to non-coding and ribosomal RNAs were filtered using Bowtie2 (version 2.3.5) against the Mus musculus reference (GRCm38, Ensembl release 102), set for high sensitivity. Remaining reads were aligned to the Mus musculus genome with STAR aligner 2.7.8a, outputting sorted BAM files. PCR duplicates were marked and removed using Picard MarkDuplicates (version 2.26.6) and samtools (version 1.19.2).
Raw counts were obtained using featurecounts (version 2.2.0).
Assembly: Mus musculus GRCm38, Ensembl release 102.
Supplementary files format and content: bed files
Supplementary files format and content: Comma-separated values (.csv) file includes information for all the samples.

source_name: brain

extract_protocol:
The RNA of RC and RG was extracted through the trizole chloroform method followed by isopropanol precipitation to concentrate the samples. The samples were loaded onto Urea gel (catalog # EC68852Box, #EC68752Box, #EC62152Box, ThermoFisher) to select for RPF size. Segments between 25b and just above 40b were excised and retrieved to account for the possible longer fragments of the RPFs. The excised gels were frozen for 30 minutes on ice and then thawed overnight at room temperature. The RNA was extracted again with trizole chloroform extraction.
The steps were adopted from Glincy & Ingolia, 2017. The concentration from the RNA footprint was calculated from Bioanalyzer small RNA kid (catalog # 5067-1548, Agilent). An equal amount of RNA was calculated and transferred to a new tube for each sample to ensure each sample has a relatively equal amount after pooling. 3 different linkers (NI-810, NI-811, BI-812) were attached to each of the replicates. The samples were first dephosphorylated with T4PNK linker (catalog # M0351L, NEB), and then pre-adenylated linkers are attached through T4 Rnl2 (catalog # M0351L, NEB). The linked RNA was purified through excision of urea gel between 50bp and 70bp. Samples in the same variables were then pooled together with their gel fragment combined. The RNA was extracted from the gel with the steps stated previously containing all three replicates, followed by Reverse transcription. MyOne Streptavidin C1 DynaBeads (catalog#65001, ThermoFisher) was used for rRNA depletion. Lastly, PCR was performed. The samples were sequenced through the McGill University Genome Center on NovaSeq S1/2 flow cells.

treatment_protocol: All preparations used brains that were flashed frozen using either liquid nitrogen or ethanol dry ice bath after dissection. 10 mouse brains from postnatal day 5 C57BL/6 mouse and FMR1-KO mouse from Charles Rivers Laboratory were used. Samples were homogenized in either the previous (Anadolu et al, 2023) RNA Granule Buffer (20 mM Tris-HCl pH 7.4 (catalog #BP152-1, Thermo Fisher Scientific), 150 mM NaCl (catalog # BP358-212, Thermo Fisher Scientific), 2.5 mM MgCl2 (catalog# M33-500, Thermo Fisher Scientific)) or high Mg2+ RNA Granule Buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 10 mM MgCl2. These buffers were supplemented with 1mM DTT (catalog #D9163, Sigma-Aldrich), and 1mM EGTA (catalog # E8145 Sigma-Aldrich) for homogenization. The homogenate was centrifuged 15min in a Thermo Fisher Scientific T865 fixed-angle rotor at 6117 x g at 4oC to separate debris, such as lipid and extracellular matrix, from the ribosomes. The supernatant was collected with some set aside as starter fraction. The rest of the supernatant was then clarified with 1% iGEPAL CA-630 (catalog #04693132001, Roche) for 5 min at 4 C. Sucrose solution was produced by suspending sucrose (catalog #8550, Calbiochem) with RNA Granule buffer. The samples were loaded onto a 60% sucrose pad in a Sorvall 36 ml tube (Kendro, catalog #3141, Thermo Fisher Scientific) and centrifuged at 56,660 x g for two hours in AH-629 swing-bucket rotor to retrieve the polyribosomes. The polyribosome was resuspended in RNA Granule buffer then reloaded onto 15%-60% sucrose gradient and centrifuged at 56,660 xg for 45 min to separate the ribosomes into monosomes, ribosomal clusters (RC) and RNA Granule (RG). Each fraction was 3.5 ml and collected from the top. We retrieved RCs from fraction 5 and 6, RNA Granules from the pellet. The RC samples were loaded onto a 60% sucrose pad and centrifuged to concentrate the samples, while the RG samples were resuspended with 2ml of normal Granule buffer or high Mg2+ buffer. For normal nuclease treatment groups, 1µl of RNase I (100U/µ l; catalog #AM2294, Thermo Fisher Scientific) was administered to the RC and RG and rotated at 4ºC for 30min. Then, 4ul of SuperaseIN (20U/µl; catalog # AM2969, Invitrogen) was added to the solution to halt the reaction. The samples are then loaded onto 15% to 60% sucrose gradient and centrifuged at 56,660 x g for 45 minutes to retrieve the monosomes from fraction 2 and 3. For high nuclease treatment group, RNase I (10 U/ul, catalog #N6901K, Epicentre) was adjusted to the concentration of RC and RG via the A260 read from the Nanodrop. The OD obtained from the A260 read equals 6 unit. In other words, the amount of nuclease (µl) added equals A260 * 6 (U)/ 10 (µl/U). In addition, the samples are incubated at room temperature for 30min instead of 4 ºC. Then, 6ul of SuperaseIN were added to halt the reaction. The samples were then spin at 68,000 xg for 3hrs on a Beckman tabletop ultracentrifuge to concentrate the monosomes, which pellets.

value: brain

value: control


title: eq_OA_OA_GJA52

description: Library name: sample41

value: OA


title: eq_OA_Ctrl_GJA04

description: Library name: sample40

value: Ctrl


title: HAP1 SON intronic deletion hgRNA 2, replicate 2

description: Library name: H016_IDel.SON.G175_r2

value: Intronic deletion in SON generated with hybrid guide RNA comprising Cas9 guide ATACTTGCTTTATAGTAGAA and Cas12a guide TACATACTGTAGTGTGTATGTTC.


title: AGPS KO, TGFB treated, rep1

first: Whitney

last: Henry

state: MA

address: 500 Main St

department: Biology

institute: MIT

description: Library name: AGPS.KO.SCC10.TGFB_1

data_processing:
Mapping was performed with STAR (2.7.1a) using the canonical chromosomes from GRCm38/mm10, with an index built with genes from Ensembl 96 and '--sjdbOverhang 49'.
Gene counts were obtained using featureCounts (v1.6.2) and Ensembl 96 gene annotations and '-s 2'.
Gene counts were normalized and differential expression assayed with DESeq2 (v1.26.0), using 'independentFiltering=FALSE'.
Assembly: GRCm38/mm10
Supplementary files format and content: Ensembl gene ID, raw counts
Supplementary files format and content: Ensembl gene ID, matrix of DESeq2-normalized counts

source_name: Breast

growth_protocol: Cells were cultured in DMEM high glucose supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 1% glutamine.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared for RNA-Seq using Roche Diagnostics KAPA mRNA HyperPrep Kit, according to manufacturer’s directions.

treatment_protocol: Cells were treated with 2 ng/ml TGF- β treatment for 10 days

value: Breast

value: PyMT-1099 AGPS KO

value: TGF-B treated


title: Replicate 1 of FMRP-KO RNA

description:
Library name: FMRP_RNA_rep1
First replicate of RNA from FMRP knockout mice.


title: HAP1 SON intronic deletion hgRNA 2, replicate 1

first: Ulrich

last: Braunschweig

address: 160 College Street

institute: University of Toronto

description: Library name: H015_IDel.SON.G175_r1


title: AGPS KO, untreated, rep2

description: Library name: AGPS.KO.SCC10_2

value: Untreated


title: eq_OA_Ctrl_GJA01

description: Library name: sample38


title: AGPS KO, untreated, rep1

description: Library name: AGPS.KO.SCC10_1


title: HAP1 SON intronic deletion hgRNA 1, replicate 2

description: Library name: H014_IDel.SON.G174_r2

value: Intronic deletion in SON generated with hybrid guide RNA comprising Cas9 guide ACTTGCTTTATAGTAGAATG and Cas12a guide TACATACTGTAGTGTGTATGTTC.


title: SiHa PR-3, parental conteraparts

city: Guangzhou

first: Li

last: Yuan

address: 58, Zhongshan 2nd road

institute: sun yat-sen university

description: Library name: Sample 9

data_processing:
The libraries were quality controlled with Agilent 2200 and sequenced by  Illumina NovaSeq 6000 on a 150 bp paired-end run.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to genome using the Hisat2.
HTseq was used to get gene expression.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: SiHa cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qjagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

value: SiHa cells

value: cervical cancer cells

value: parental conteraparts


title: Replicate 1 of Wild Type RNA

description:
Library name: WT_RNA_rep1
First replicate of RNA from wild type mice.

value: WT


title: Replicate 2 of Wild Type RNA

description:
Library name: WT_RNA_rep2
Second replicate of RNA from wild type mice.


title: WT parental, TGFB treated, rep1

description: Library name: 1099.TGFB_1

value: PyMT-1099 parental


title: Replicate 2 of FMRP-KO RNA using M protocol

description:
Library name: FMRP_RNA_M_rep2
Second replicate of RNA from FMRP knockout mice, using M protocol.

value: M-protocol


title: eq_OA_Ctrl_GJA14

description: Library name: sample35

value: PBMC


title: Cortical organoids. MECP2[R306C] mutation, rep2

first: Tatsuya

last: Osaki

address: 43 Vassar street, 46-6227

department: Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

description:
Library name: CO_Rett_patient-derived_R306C_2
Feature_count_matirx

data_processing:
Fastq files were combined and aligned with STAR 2.0.4b Gene counts derived with Subread:featureCount 1.45. RPKM and CPM calculated from gene counts with custom R scripting.
Assembly: GRCh37/hg19
Supplementary files format and content: Feature counts matrix
Supplementary files format and content: Differential_gene_expression_data

growth_protocol: All hiPS cells were maintained on Matrigel-coated 6-well plates in mTeSR Plus medium (STEMCELL Technologies) with 10 μM Y-23632 (Rock inhibiter, STEMCELL Technologies) for the first day after each passage and subcultured every 5–7 days using ReLeSR reagent (STEMCELL Technologies). To generate cerebral organoids, two mutant hiPS cell lines and isogenic control iPS cells on 6-well plates were dissociated into single cells with TrypLE express and then plated at 30,000 cells per well on U-bottom ultra-low attachment 96-well plates (Corning) with mTeSR Plus supplemented with 20 μM of Y-23632. After 24 h, the culture medium was replaced with neural induction medium (knockout DMEM-F12, 15% (v/v) knockout serum replacement, 1% (v/v) MEM-NEAA, 1% (v/v) GlutaMAX, 100 nM LDN-193189, 10 μM SB431542, and 10 μM XAV939) and changed every other day. After 10 days of culture, the culture medium was replaced with 1:1 mixture of knockout DMEM/F12 and neurobasal medium supplemented with 0.5% (v/v) N2 supplement, 1% (v/v) B27 plus supplement with vitamin A, 1% (v/v) GlutaMAX, 1% (v/v) MEM-NEAA, and 2.5 ng/ml (v/v) human insulin solution. This medium was changed every 2 days until 18 days of culture had elapsed. After 18 days, the organoids were transferred to flat-bottom ultra-low attachment 24-well plates (Corning) on a rocking shaker (120 rpm) and switched to a maintenance medium (Neurobasal medium supplemented with 1% (v/v) N2 supplement, 2% (v/v) B27 supplement with vitamin A, 1% (v/v) GlutaMAX, 1% (v/v) MEM-NEAA, 0.25 mg/ml (v/v) human insulin solution, 20 ng/ml BDNF, 200 μM ascorbic acid, 100 μM dibutyryl-cAMP (Sigma-Aldrich), and 1% (v/v) Penicillin/Streptomycin). After 30 days from differentiation, the culture medium was changed twice per week with BrainPhys medium supplemented with 2% (v/v) B27 supplement with vitamin A, 1% (v/v) GlutaMAX, 20 ng/ml BDNF, 20 ng/ml GDNF, and 1%(v/v) Penicillin/Streptomycin until the time of imaging.

extract_protocol:
Total RNA was isolated from the cells from 2D culture using RNAeasy Mini Kit (Qiagen) following manufacture protocol.
NA libraries for RNA sequencing were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Globin library prep kit according to the manufacturer’s instructions.

value: Female

value: Cortical organoids

tag: replicate

value: biol rep2


title: Replicate 2 of Wild Type RNA using M protocol

description:
Library name: WT_RNA_M_rep2
Second replicate of RNA from wild type mice, using M protocol.

value: brain


title: GSK3B wild-type RKO RNA-Seq 3

status: Public on Jun 19 2026

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

institute: Soochow University

description: Library name: GSK3B wild-type RKO RNA-Seq 3

data_processing:
Sequencing reads were mapped to the human reference genome (hg38) with TopHat software. Then, read counts were calculated using GFOLD software. Differentially expressed genes were identified with the limma-edgeR workflow.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: RKO

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's guidelines. The purity and concentration of the RNA were measured with a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Subsequently, libraries were prepared with the VAHTS Universal V6 RNA-seq Library Prep Kit in accordance with the manufacturer's instructions. The sequencing of the RNA-Seq libraries was carried out on an illumina X10 platform, generating 150 bp paired-end reads.

value: RKO


title: HAP1 SRRM2 intronic deletion hgRNA 1, replicate 1

city: Toronto

description: Library name: H017_IDel.SRRM2.G176_r1

value: HAP1 chronic myelogenous leukemia

value: Deletion in SRRM2 spanning a PTC exon generated with hybrid guide RNA comprising Cas9 guide TATGGACTGCCAGAATAGGG and Cas12a guide GTCGCACAACTCAAATCATTCAC.


title: AGPS KO, TGFB treated, rep2

description: Library name: AGPS.KO.SCC10.TGFB_2

value: Breast

value: PyMT-1099 AGPS KO

value: TGF-B treated


title: Replicate 3 of Wild Type RNA

description:
Library name: WT_RNA_rep3
Third replicate of RNA from wild type mice.

value: control


title: HAP1 SON intronic deletion hgRNA 1, replicate 1

description: Library name: H013_IDel.SON.G174_r1

value: Intronic deletion in SON generated with hybrid guide RNA comprising Cas9 guide ACTTGCTTTATAGTAGAATG and Cas12a guide TACATACTGTAGTGTGTATGTTC.


title: WT parental, TGFB treated, rep2

description: Library name: 1099.TGFB_2