title: pJ23106_timP, Mutazyme, KAPA, replicate 2

description: Library name: P_TimP_EP2_K


title: pJ23106_timP, Mutazyme, KAPA, replicate 3

status: Public on Mar 05 2026

type: SRA

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

country: France

institute: University of Bordeaux

description: Library name: P_TimP_EP3_K

library_source: genomic

data_processing:
Raw FASTQ files were generated by the sequencing platform.
(I) Quality control. Read quality was assessed using FastQC v0.11.9 and aggregated with MultiQC v1.22.1. Illumina adapter sequences were removed using Cutadapt v4.8  with the parameters “-e 0.10 -O 20 -m 30 --match-read-wildcards -n 2”. Low-quality bases at the 3′ end and low-quality reads were removed using Prinseq-lite v0.20.4 with “-trim_qual_right 28 -min_qual_mean 28”.
(II) Assembly of paired-end reads. Read pairs were recovered with cmpfastq and assembled into single sequences using PANDAseq v2.11 with parameters “-N -o 20 -O 0 -t 0.6 -A simple_bayesian -C empty”.
(III) Mapping to the reference. Assembled reads were aligned to the timP mRNA amplicon reference sequence (“promoter” or “no promoter” depending on the sample) using BWA-MEM (BWA v0.7.17) with parameters “-A 1 -B 4 -O 6 -E 1 -L 10,10”.
(IV) Extraction of mutated sequences. Reads containing a single nucleotide substitution and matching the expected length (330 or 308 nt for “promoter” and “no promoter”, respectively) were extracted using BamTools v2.5.2. Among those, sequences containing no substitutions in the promoter region (positions 1-35 or 1-13 for “promoter” and “no promoter”, respectively) and a single nucleotide substitution in the TimP mRNA sequence (295 nt) compared to the reference were retrieved using utilities from the GenomicAlignments 1.38.2, Rsamtools 2.18.0, and dplyr 1.1.4 packages in R 4.3.2.
(V) Statistical analysis. Differential expression analysis was performed to compare single substitution frequencies at each position between “no promoter” and “promoter” constructs using Trinity 2.15.1 and the R package DESeq2 1.42.1. Samples amplified with DreamTaq and Mutazyme II were analyzed independently, and in both cases, replicates amplified by KAPA and Phusion were pooled, and biological “no promoter” and “promoter” replicates paired. Substitutions were considered significantly over- or under-represented when the adjusted P-value (Padj, corresponding to the False Discovery Rate) was ≤ 0.05 and the absolute log2 fold change (|log2FC|) was ≥ 1.
Assembly: NC_016810.1 (positions 2672651-2672945)
Supplementary files format and content: format: Excel spreadsheet; content: normalized counts, log2 fold-changes, and p-values of combined replicates (statistical analysis of single substitutions by sequence)

molecule: genomic DNA

organism: Escherichia coli str. K-12 substr. MG1655

extract_protocol:
The genomic DNA of bacterial colonies was extracted using the EasyPure Bacteria Genomic DNA Kit (Transgen Biotech).
Two DNA sequences encoding timP mRNA of S. enterica under the control of the PJ23106 promoter (“promoter” library) or the native timP -10 box (“no promoter” library) and flanked with homology region for homologous recombination in E. coli chromosome were synthesized by Eurofins. These two DNA sequences were amplified by 30 cycles of PCR using the Dream Taq DNA polymerase (Thermo Fisher Scientific) and purified. One hundred ng of the purified DNA samples were further mutagenized using the GeneMorph II Random Mutagenesis kit (Mutazyme II DNA polymerase, Agilent) as per the manufacturer’s instructions with 30 PCR cycles. The PCR reactions were purified and 200 ng of the DreamTaq and the Mutazyme II PCR samples were introduced and recombined into the E. coli XTL632 chromosome. Recombinant bacteria were selected on Tet/SacB counter-selection plates at 42°C. Colonies were harvested from the plates and the DNA was extracted using the EasyPure Bacteria Genomic DNA Kit (Transgen Biotech). The experiment, including the PCR and mutagenesis steps, was repeated 3 times. The extracted DNA was amplified to add the Illumina adapters using the KAPA HiFi HotStart ReadyMix (Roche) as well as using the Phusion Hot Start polymerase (ThermoScientific). The amplicons were sequenced at the Bordeaux Transcriptome Genome Platform (PGBT, Cestas-Pierroton, France) using Illumina NextSeq 2000 P1 instrument in paired-end mode 2x300 nt (overlapping reads).

tag: strain

tag: genotype


title: female_hypothalamus_27 months_1377654

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

country: USA

institute: Regeneron Pharmaceuticals

description: Library name: 1377654

library_source: transcriptomic

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: Tab-separated raw counts

molecule: total RNA

organism: Mus musculus

source_name: hypothalamus

extract_protocol:
Mice were sacrificed by CO2 asphyxiation. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

tag: tissue

value: hypothalamus

tag: Sex

value: female

tag: age

value: 27 months


title: pJ23106_timP, DreamTaq, Phusion, replicate 3

description: Library name: P_TimP_DT3_P


city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: Library name: Ogataea-polymorpha_insitu-HiC-DpnII_rep1_reseq

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.7+ for all analyses. Briefly, raw fastq files were mapped to either NCBI RefSeq assembly GCF_001664045.1 reference genome for data from Ogataea polymorpha, or the newly constructed "Ohag_RefGenome_v1.fasta" reference genome detailed in this manuscript for data from Ogataea haglerorum using bowtie2 (version 2.5+), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings (with DpnII [GATC] restriction sites, as defined in the .bed files produced by the hicFindRestSites command in hicexplorer), and resulting images of the contact matrix images were made with hicPlotMatrix; (total) merged matrices were constructed by first merging all replicates using the cat command and processing them n an identical manner. Contact map images are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012), performed with the hicCorrectMatrix program, to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA. The command hicCorrelate was used to plot scatterplots and to calculate the Pearson correlation values of Hi-C replicates, while the commands hicFindTADs (with flags --correctForMultipleTesting fdr [false discovery rate], --thresholdComparisons 0.3, and --delta 0.15) and hicPlotTADs visualized TAD-like structures across Ogataea chromosomes.
Assembly: Assembly: NCBI RefSeq assembly GCF_001664045.1 for data from Ogataea polymorpha, or the newly constructed "Ohag_RefGenome_v1.fasta" detailed in this manuscript for data from Ogataea haglerorum.
Supplementary files format and content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins of a defined size (the resolution of the Hi-C contact matrix), and the interactions between the bins is reported - either raw contact counts or Knight-Ruiz corrected contact counts.

organism: Ogataea polymorpha

source_name: log phase cells

growth_protocol: Ogataea strains were grown from freezer stocks on YPD plates (1% w/v yeast extract, 2% w/v peptone, 2% w/v glucose, 2% w/v agar) at 30°C. Individual colonies were used to inoculate liquid cultures of YPD broth, which were grown for 16 hours (overnight) with shaking at 30oC. New Ogataea cultures were inoculated by backdiluting the overnight culture into fresh YPD medium and cultures were grown to log-phase (OD600 0.8 to 1.2) at 30oC with shaking.

extract_protocol:
First, the concentration of genomic DNA per cell pellet was determined by resuspending one cell pellet 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 ug proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 ug RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Using a fresh cell pellet, the approximate amount of that cell pellet containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x DpnII restriction enzyme buffer and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Cells were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used eight and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon on either an Illumina Hiseq 4000 as 100 nucleotide (nt) paired-end (PE100) reads or an Illumina Novaseq 6000 as 59 nt paired-end (PE59) reads.

treatment_protocol: Log-phase Ogataea cultures were then crosslinked 10 min in 1% formaldehyde (w/v) at room temperature, with shaking at 100 rpm, and then quenched with 0.3M glycine for 10 minutes at room temperature. Crosslinked cells were pelleted by centrifugation at 1,800xg, the supernatant was decanted, and cell pellets were stored at -80oC

value: SH4330 (NCYC495 MATa ura3)

tag: cell type

value: log phase cells

value: wild type


title: female_hypothalamus_18 months_1377655

description: Library name: 1377655

value: 18 months


title: Ogataea-polymorpha_H4K16ac_ChIPseq_rep2

description: Library name: Ogataea-polymorpha_H4K16ac_ChIPseq_rep2

data_processing:
Raw ChIP-seq data files, as fastq files, were mapped to the appropriate Ogataea species genome with bowtie2 (version 2.5.4), and output sam files were converted to sorted bam files using samtools (version 1.14), which were used by Deeptools (version 3.5.0) to produce bigwig files with 25 basepair bin resolution, normalized by Reads per Kilobase Per Million Reads (RPKM), for display on the Integrative Genomics Viewer (IGV)
Assembly: Assembly: NCBI RefSeq assembly GCF_001664045.1 for data from Ogataea polymorpha, or the newly constructed "Ohag_RefGenome_v1.fasta" detailed in this manuscript for data from Ogataea haglerorum.
Supplementary files format and content: the bigwig files are generated by Deeptools (Ramírez et al. 2016); briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin; the bigwig file format is a single column with the enrichment per bin displayed, and the seven headers indicate the chromosome and bin size.

extract_protocol:
Pellets were resuspended in ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + 1x Halt proteinase inhibitor cocktail [ThermoFisherScientific, cat #78441]) and cells were disrupted by sonication, which simultaneously sheared chromatin, using a Bioruptor Pico (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 2uL) and samples were nutated overnight at 4oC. The next day, equilibrated protein A/G magnetic agarose beads (Pierce/Thermo Scientific; cat # PI78609) was added to bind the antibody, incubated for 2 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were RNaseA treated for two hours at 50oC, then proteinase K treated for 2 hours at 50oC, the DNA was extracted with phenol:chloroform:IAA (25:24:1), and DNA was precipitated with ethanol, sodium acetate, and glycogen, and allowed to precipitate overnight at -80oC. The next day, samples were precipitated by centrifugation, washed, dried in a Speedvac and resuspended in 30uL TE. ChIP DNA was quantified with a Qubit 3.0 using the HS method.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the NEB Next Ultra II Library Preparation Kit (New England Biolabs, #E7645L) with the adapters from the NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1 [E7335L] or 2 [E7500L]) according to the manufacturer’s instructions, except that final libraries were only PCR-amplified using eight cycles for amplification.

tag: chipseq antibody

value: ActiveMotif anti-H4K16ac antibody, cat# 39167, lot# 08719003


title: pJ23106_timP, DreamTaq, Phusion, replicate 2

description: Library name: P_TimP_DT2_P


title: male_right ventricle_24 months_1541691

description: Library name: 1541691

data_processing:
Sequencing reads were processed with ArrayStudio (11.7.4) RNA-seq pipeline to quantify gene expression levels
Assembly: Rn7
Supplementary files format and content: Tab-separated raw counts

organism: Rattus norvegicus

source_name: right ventricle

extract_protocol:
Rats were anesthetized with 3.5% isoflurane and sacrificed by exsanguination and thoracotomy. Organs were removed, tissues were dissected on ice, preserved in RNAlater® solution (Thermo Fisher Scientific) and stored at -80℃ until further processing. RNA was extracted using MagMax-96 total RNA isolation kit (Termo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies), and the integrity was assessed using Fragment Analyzer (Agilent).
Strand-specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen). RNA-seq libraries were sequenced at 100 million reads using Illumina Novo-Seq 6000 platforms in paired-end mode to a length of 2×76 bp base-pairs

value: Sprague Dawley

value: right ventricle

value: male

value: 24 months


title: female_hypothalamus_27 months_1377653

description: Library name: 1377653


title: female_hippocampus_18 months_1377652

description: Library name: 1377652

source_name: hippocampus

value: hippocampus


title: male_left atrium_24 months_1541688

description: Library name: 1541688

source_name: left atrium

value: left atrium


title: female_hippocampus_18 months_1377651

description: Library name: 1377651


title: pJ23106_timP, DreamTaq, KAPA, replicate 3

description: Library name: P_TimP_DT3_K


title: male_hypothalamus_18 months_1377650

description: Library name: 1377650


title: male_left atrium_24 months_1541687

description: Library name: 1541687


title: male_left atrium_24 months_1541690

description: Library name: 1541690


title: pJ23106_timP, DreamTaq, Phusion, replicate 1

description: Library name: P_TimP_DT1_P


title: male_right ventricle_24 months_1541693

description: Library name: 1541693


title: Ogataea-polymorpha_H4K16ac_ChIPseq_rep1

description: Library name: Ogataea-polymorpha_H4K16ac_ChIPseq_rep1


title: male_hypothalamus_12 months_1377649

description: Library name: 1377649

value: 12 months


title: Ogataea-polymorpha_H3K9ac_ChIPseq_rep2

description: Library name: Ogataea-polymorpha_H3K9ac_ChIPseq_rep2

value: ActiveMotif anti-H3K9ac antibody, cat# 39137, lot# 28720002


title: pJ23106_timP, DreamTaq, KAPA, replicate 1

description: Library name: P_TimP_DT1_K


title: Ogataea-polymorpha_H3K4me3_ChIPseq_rep2

description: Library name: Ogataea-polymorpha_H3K4me3_ChIPseq_rep2

value: ActiveMotif anti-H3K4me3 antibody, cat# 39159, lot# 31420006


title: male_left atrium_24 months_1541689

description: Library name: 1541689


title: pJ23106_timP, DreamTaq, KAPA, replicate 2

description: Library name: P_TimP_DT2_K


title: Ogataea-polymorpha_H3K9ac_ChIPseq_rep1

description: Library name: Ogataea-polymorpha_H3K9ac_ChIPseq_rep1


title: female_hypothalamus_6 months_1377648

description: Library name: 1377648

value: hypothalamus

value: 6 months


title: male_left atrium_24 months_1541685

description: Library name: 1541685


title: no_promoter_timP, Mutazyme, Phusion, replicate 2

description: Library name: NP_TimP_EP2_P


title: no_promoter_timP, Mutazyme, Phusion, replicate 3

description: Library name: NP_TimP_EP3_P


title: phage SH-Ab 15599 and its host lysates, 40min, replicate3

city: Shanghai

first: Haoyu

last: Ma

state: Shanghai

address: Zhongke Road, Pudong

department: iHuman institute

country: China

institute: ShanghaiTech University

description: Library name: HP_40min_3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.24.0 (parameters- -q 20 -u 40 -n 5 -l 15 -w 16 -c)
Trimmed sequence reads were mapped to genome of phage SH-Ab 15599(MH517022.1) and its Acinetobacter baumannii host(data to be deposited) using HISAT2 v2.2.1 (parameters- default)
Alignment files were processed with SAMtools v1.21 to calculate mapping coverage and sequencing depth.
Gene expression levels were quantified using featureCounts v2.0.6 (parameters- -p --countReadPairs -f -t CDS -g protein_id -O -B -M)
Differential gene expression analysis was performed using DESeq2 v1.46.0
Assembly: MH517022.1
Assembly: Ap15599HOST(In-house data that is to be deposited; the genome is placed in the attachment: Ap15599HOST.fasta)
Supplementary files format and content: tab-delimited text files include raw and zscore-normalized counts for each Sample, and differential gene expression analysis for 5,10,15,20,30,40 min compared with 0min.
Supplementary files format and content: fasta file include reference genome of Acinetobacter baumannii host that is not deposited to NCBI

organism: Acinetobacter phage SH-Ab 15599

source_name: prokaryotes and phages

growth_protocol: The host cells were grown to an OD600 of ~0.6 at 37 °C and infected with bacteriophage SH-Ab 15599 using a multiplicity of infection (MOI) of 20 in order to ensure the synchronicity of the infection.

extract_protocol:
The total RNA was extracted using Bacterial RNA Kit (Yeasen, 19301ES50) by following the manufacturer’s protocol.
Total RNA was first treated with a bacterial rRNA depletion kit to remove rRNA. Then, the rRNA-depleted RNA samples were used for RNA libraries preparation with VAHTS Stranded mRNA-seq V2 Library Prep Kit for Illumina.

treatment_protocol: Samples for RNA extraction were harvested from the uninfected host culture (negative control) and from the infected culture at multiple time points post-infection (0 min, 5 min, 10 min. 15 min, 20 min, 30 min, and 40 min), with three independent biological replicates collected for each condition.

value: prokaryotes and phages

tag: treatment

value: after phage infection of 40min


title: Ogataea-polymorpha_H3K4me3_ChIPseq_rep1

description: Library name: Ogataea-polymorpha_H3K4me3_ChIPseq_rep1

value: SH4330 (NCYC495 MATa ura3)

value: log phase cells


title: female_hypothalamus_6 months_1377647

description: Library name: 1377647

value: female


title: male_hypothalamus_6 months_1377646

description: Library name: 1377646


title: male_left atrium_24 months_1541684

description: Library name: 1541684


title: male_left atrium_24 months_1541686

description: Library name: 1541686


title: phage SH-Ab 15599 and its host lysates, 40min, replicate2

description: Library name: HP_40min_2


title: no_promoter_timP, Mutazyme, Phusion, replicate 1

description: Library name: NP_TimP_EP1_P


title: male_left atrium_24 months_1541683

description: Library name: 1541683


title: phage SH-Ab 15599 and its host lysates, 40min, replicate1

description: Library name: HP_40min_1


title: no_promoter_timP, Mutazyme, KAPA, replicate 3

description: Library name: NP_TimP_EP3_K


title: male_hypothalamus_21 months_1377645

description: Library name: 1377645

value: 21 months


title: male_left atrium_24 months_1541682

description: Library name: 1541682

value: Sprague Dawley


title: phage SH-Ab 15599 and its host lysates, 30min, replicate2

description: Library name: HP_30min_2

value: after phage infection of 30min


title: phage SH-Ab 15599 and its host lysates, 30min, replicate3

description: Library name: HP_30min_3


title: male_left atrium_24 months_1541681

description: Library name: 1541681

value: male


title: no_promoter_timP, Mutazyme, KAPA, replicate 1

description: Library name: NP_TimP_EP1_K


title: phage SH-Ab 15599 and its host lysates, 30min, replicate1

description: Library name: HP_30min_1


title: male_left atrium_24 months_1541680

description: Library name: 1541680

value: 24 months


title: male_cerebellum_6 months_1377642

description: Library name: 1377642

source_name: cerebellum

value: cerebellum


title: no_promoter_timP, DreamTaq, Phusion, replicate 3

description: Library name: NP_TimP_DT3_P


title: male_cerebellum_6 months_1377643

description: Library name: 1377643


title: no_promoter_timP, DreamTaq, Phusion, replicate 2

description: Library name: NP_TimP_DT2_P


title: male_left atrium_24 months_1541679

description: Library name: 1541679

value: left atrium


title: phage SH-Ab 15599 and its host lysates, 20min, replicate3

description: Library name: HP_20min_3

value: after phage infection of 20min


title: phage SH-Ab 15599 and its host lysates, 20min, replicate2

description: Library name: HP_20min_2


title: male_cerebellum_6 months_1377641

description: Library name: 1377641


title: male_left ventricle_24 months_1541678

description: Library name: 1541678

source_name: left ventricle

value: left ventricle


title: male_cerebellum_6 months_1377644

description: Library name: 1377644


title: female_cerebellum_6 months_1377640

description: Library name: 1377640


title: no_promoter_timP, DreamTaq, Phusion, replicate 1

description: Library name: NP_TimP_DT1_P


title: no_promoter_timP, DreamTaq, KAPA, replicate 3

description: Library name: NP_TimP_DT3_K


title: male_left ventricle_24 months_1541677

description: Library name: 1541677


title: male_left ventricle_24 months_1541676

description: Library name: 1541676


title: phage SH-Ab 15599 and its host lysates, 15min, replicate3

description: Library name: HP_15min_3

value: after phage infection of 15min


title: female_cerebellum_6 months_1377639

description: Library name: 1377639


title: no_promoter_timP, DreamTaq, KAPA, replicate 2

description: Library name: NP_TimP_DT2_K


title: phage SH-Ab 15599 and its host lysates, 20min, replicate1

description: Library name: HP_20min_1


title: no_promoter_timP, Mutazyme, KAPA, replicate 2

description: Library name: NP_TimP_EP2_K


title: male_left ventricle_24 months_1541675

description: Library name: 1541675


title: phage SH-Ab 15599 and its host lysates, 15min, replicate2

description: Library name: HP_15min_2


title: no_promoter_timP, DreamTaq, KAPA, replicate 1

description: Library name: NP_TimP_DT1_K


title: male_cerebellum_6 months_1377637

description: Library name: 1377637


title: Human glioma tissue, MR3 treatment, Patient P3

city: Palo Alto

first: Xinnan

last: Wang

state: CA

address: 1201 Welch Road, MSLS Building, Rm P151

department: Neurosurgery

institute: Stanford University

description:
Library name: P3_MR3
Column name in human_raw_count.csv: P3_MR3

data_processing:
Raw sequencing reads were processed using the Galaxy platform (usegalaxy.org).
Reads were aligned to the human reference genome hg19 using RNA STAR (Galaxy Version 2.7.11b+galaxy0).
Gene-level read counts were generated using featureCounts (Galaxy Version 2.1.1+galaxy0).
Gene identifiers were annotated to Ensembl gene IDs and gene symbols.
Raw count matrices were imported into R for differential expression analysis using DESeq2. A paired design (~ patient + treatment) was implemented. Genes with fewer than 5 counts in at least two samples were filtered out prior to normalization. Differential expression testing was performed using the Wald test. Genes with p-value < 0.05 and |log2 fold change| ≥ 1 were considered significantly differentially expressed.
Assembly: hg19 (GRCh37)
Supplementary files format and content: Processed data include a gene-level raw read count matrix in CSV format. In this file, rows represent genes (gene symbols as row names), and columns represent individual samples (sample IDs as column headers). Values correspond to raw read counts generated by featureCounts.
Supplementary files format and content: In addition, individual tab-delimited text files are provided for each sample. Each file contains gene-level raw read counts for a single sample.

organism: Homo sapiens

source_name: Glioma tumor

growth_protocol: Human glioma tumor core specimens were collected intra-operatively at Stanford Hospital following written informed consent under an Institutional Review Board–approved protocol (IRB-12625). Fresh tissues were immediately placed in Dulbecco’s Modified Eagle Medium (DMEM; Gibco) on ice prior to ex vivo culture or snap-freezing.

extract_protocol:
Frozen tumor tissues were pulverized in liquid nitrogen using DEPC-treated, autoclaved mortars and pestles. Approximately 0.5 mL STAT60 (AMSBIO) was added during homogenization, followed by an additional 0.5 mL to reach a final volume of 1 mL. Total RNA was isolated using chloroform-based phase separation according to the manufacturer’s instructions. RNA pellets were resuspended in 20–40 μL nuclease-free water. RNA concentration and purity were assessed using a NanoDrop spectrophotometer. Samples with concentrations >50 ng/μL and 260/280 ratios >1.7 were considered suitable for sequencing.
RNA-seq libraries were prepared by Novogene from high-quality total RNA samples following standard Illumina-compatible protocols. Poly(A) selection was used to enrich for mRNA, followed by fragmentation, reverse transcription, adaptor ligation, and PCR amplification. Libraries were quality-controlled and sequenced on an Illumina platform to generate high-throughput transcriptomic data.

treatment_protocol: Tumor specimens were transferred to six-well plates containing DMEM supplemented with either 10 μM MIRO1-binding compound (MR3) or vehicle control (DMSO). Samples were incubated at 37°C with 5% CO₂ for 24 hours. After incubation, tissues were dried to remove residual media or blood and sectioned under sterile conditions. Remaining tissues were snap-frozen in liquid nitrogen and stored at −80°C. One sample (P1_Plain) was snap-frozen immediately after resection without treatment.

value: Glioma tumor

value: MR3 (10µM), 24h ex vivo

tag: patient id

value: Female

tag: diagnosis

value: IDH-wildtype grade 4 glioblastoma; ATRX intact; P53 overexpressed


title: male_left ventricle_24 months_1541674

description: Library name: 1541674


title: phage SH-Ab 15599 and its host lysates, 15min, replicate1

description: Library name: HP_15min_1

value: prokaryotes and phages


title: male_cerebellum_27 months_1377638

description: Library name: 1377638

value: 27 months


title: male_left ventricle_24 months_1541673

description: Library name: 1541673


title: male_hypothalamus_6 months_1377635

description: Library name: 1377635

value: hypothalamus

value: 6 months


title: male_hypothalamus_6 months_1377636

description: Library name: 1377636


title: male_left ventricle_24 months_1541672

description: Library name: 1541672

value: Sprague Dawley


title: Human glioma tissue, DMSO treatment, Patient P3

description:
Library name: P3_DMSO
Column name in human_raw_count.csv: P3_DMSO

value: DMSO (vehicle), 24h ex vivo


title: Human glioma tissue, MR3 treatment, Patient P2

description:
Library name: P2_MR3
Column name in human_raw_count.csv: P2_MR3

value: IDH-mutant grade 2 astrocytoma; P53 overexpressed; ATRX lost; GFAP positive


title: female_hypothalamus_6 months_1377634

description: Library name: 1377634

value: female


title: phage SH-Ab 15599 and its host lysates, 10min, replicate1

description: Library name: HP_10min_1

value: after phage infection of 10min


title: phage SH-Ab 15599 and its host lysates, 10min, replicate2

description: Library name: HP_10min_2


title: phage SH-Ab 15599 and its host lysates, 5min, replicate3

description: Library name: HP_5min_3

value: after phage infection of 5min


title: male_left ventricle_24 months_1541670

description: Library name: 1541670

value: male

value: 24 months


title: female_hypothalamus_6 months_1377632

description: Library name: 1377632


title: female_hypothalamus_6 months_1377633

description: Library name: 1377633


title: male_left ventricle_24 months_1541671

description: Library name: 1541671

value: left ventricle


title: Human glioma tissue, MR3 treatment, Patient P1

description:
Library name: P1_MR3
Column name in human_raw_count.csv: P1_MR3

value: Glioma tumor

value: Male

value: IDH-mutant grade 2 oligodendroglioma;1p/19q-codeleted


title: phage SH-Ab 15599 and its host lysates, 5min, replicate2

description: Library name: HP_5min_2


title: Human glioma tissue, DMSO treatment, Patient P1

description:
Library name: P1_DMSO
Column name in human_raw_count.csv: P1_DMSO


title: male_left ventricle_24 months_1541669

description: Library name: 1541669


title: phage SH-Ab 15599 and its host lysates, 5min, replicate1

description: Library name: HP_5min_1


title: male_hypothalamus_12 months_1377630

description: Library name: 1377630

value: 12 months


title: female_hypothalamus_6 months_1377631

description: Library name: 1377631


title: male_left ventricle_24 months_1541667

description: Library name: 1541667


title: phage SH-Ab 15599 and its host lysates, 10min, replicate3

description: Library name: HP_10min_3

value: prokaryotes and phages


title: JB3

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

description: Library name: JB3_S45

data_processing:
CLC Genomics Workbench 24.0.5 (Qiagen)
Reads from FASTq files were filtered for quality and aligned to the miRbase-release_vs22 version
The data were normalised using the TMM method (trimmed Mean of M-values)
DE analysis was performed using Generalized Linear Model (GLM) and Trimmed mean of M-values (TMM) normalized counts (CPM) were used as input data
Assembly: GRCh38 human genome
Supplementary files format and content: FastQ files
Supplementary files format and content: CPM

molecule: cytoplasmic RNA

source_name: Blood

extract_protocol:
miRNA was extracted from PBMCs  using the micro RNA Purification Kit (Qiagen)
library preparation of miRNAs from PBMCs was obtained using QIAseq miRNA library kit

treatment_protocol: hypobaric hypoxia in a terraXcube chamber

value: Blood

value: peripheral blood mononuclear cells (PBMCs)

value: 72h Hyperbaric hypoxia


title: phage SH-Ab 15599 and its host lysates, 0min, replicate3

description: Library name: HP_0min_3

value: after phage infection of 0min


title: male_right atrium_9 months_1541666

description: Library name: 1541666

source_name: right atrium

value: Sprague Dawley

value: right atrium

value: 9 months


title: phage SH-Ab 15599 and its host lysates, 0min, replicate2

description: Library name: HP_0min_2


title: JB2

description: Library name: JB2_S44

value: 24h Hyperbaric hypoxia


title: male_hypothalamus_18 months_1377627

description: Library name: 1377627

value: hypothalamus

value: 18 months


title: Human glioma tissue, DMSO treatment, Patient P2

description:
Library name: P2_DMSO
Column name in human_raw_count.csv: P2_DMSO

value: DMSO (vehicle), 24h ex vivo

value: Female

value: IDH-mutant grade 2 astrocytoma; P53 overexpressed; ATRX lost; GFAP positive


title: male_right atrium_9 months_1541665

description: Library name: 1541665

value: male


title: Human glioma tissue,Plain, Patient P1

description:
Library name: P1_Plain
Column name in human_raw_count.csv: P1_Plain

value: Glioma tumor

value: Untreated baseline

value: Male

value: IDH-mutant grade 2 oligodendroglioma;1p/19q-codeleted


title: male_cerebellum_18 months_1377626

description: Library name: 1377626

value: cerebellum


title: JB1

description: Library name: JB1_S43

value: Blood

value: peripheral blood mononuclear cells (PBMCs)

value: 12h Hyperbaric hypoxia


title: male_left ventricle_24 months_1541668

description: Library name: 1541668

value: Sprague Dawley

value: left ventricle

value: 24 months


title: male_hypothalamus_12 months_1377629

description: Library name: 1377629

value: hypothalamus

value: 12 months


title: 7459,HEK293T cell,HEK4 +2 G•C to T•A/G•C to A•T, loop 2-modified epegRNA,rep3

city: Hangzhou

first: Lijia

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description: Library name: 7459_

data_processing:
Reads were align to the amplicon sequence by crispresso2 using --max_paired_end_reads_overlap 140 --min_paired_end_reads_overlap     10 --exclude_bp_from_left 0 --exclude_bp_from_right 0 --plot_window_size 20 --min_frequency_alleles_around_cut_to_plot 0.2
Assembly: FANCF,CAAGGCCCGGCGCACGGTGGCGGGGTCCCAGGTGCTGACGTAGGTAGTGCTTGAGACCGCCAGAAGCTCGGAAAAGCGAGCCAGGTGCTGCAGAAGGGATTCCATGAGGTGCGCGAAGGCCCTACTTCCGCTTTCACCTTGGAGACGGCGACTCTCTGCGTACTGATTGGAACATCCGCGAAATGATACGCCTCTCTGCAATGCTATTGGTCGAAATGCATG;RNF2,TACAGAAGTCAGGAATGCTTGAATATAAATTTATTATTACTCTATGTTCTATTTAAGTTTTCATGTTCTAAAAATGTATCCCAGTTTACACGTCTCATATGCCCCTTGGCAGTCATCTTAGTCATTACCTGAGGTGTTCGTTGTAACTCATATAAACTGAGTTCCCATGTTTTGCTTAATGGTTGAGTTCCGTTTGTCTGCACAGCCTGA;HEK4,AGGCCGGGCTGGGTGGAAGGAAGGGAGGAAGGGCGAGGCAGAGGGTCCAAAGCAGGATGACAGGCAGGGGCACCGCGGCGCCCCGGTGGCACTGCGGCTGGAGGTTGGGGTTAAAGCGGAGACTCTGGTGCTGTGTGACTACAGTGGGGGCCCTGCCCTCTCTGAGCCCCCGCCT;VEGFA,GGTGCCAAATTCTTCTCCCCTGGGAAGCATCCCTGGACACTTCCCAAAGGACCCCAGTCACTCCAGCCTGTTGGCTGCCGCTCACTTTGATGTCTGCAGGCCAGATGCGGGCTCCAGATGGCACATTGTCAGAGGGACACACTGTGGCCCCTGTGCCCAGCCCTGGGCTCTCTGTACATGAAGCAACTCCAGTCCC;EMX1,CTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTACAAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGTGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATGGGGAGGACATCGATGTCACCTCCAATGACTAGGGTGGGCAACCACAAACCC;DMNT1,CGGGCGTGTTCCCCAGAGTGACTTTTCCTTTTATTTCCCTTCAGCTAAAATAAAGGAGGAGGAAGCTGCTAAGGACTAGTTCTGCCCTCCCGTCACCCCTTTTTCTGGCACCAGGAATCCCCAACATGCACTGATGTTGTGTTTTTAACATGTCAATCTGTCCGTTCACATGTGTGGTACATGGTGTTTGTGGCCTTGGCTGACATGAAGC;RUNX1,GAGGCTGAAACAGTGACCTGTCTTGGTTTTCGCTCCGAAGGTAAAAGAAATCATTGAGTCCCCCGCCTTCAGAAGAGGGTGCATTTTCAGGAGGAAGAGATGGCTTCAGACAGCATATTTGAGTCATTTCCTTCGTACCCACAGTGCTTCATGAGAGGTGAGTACATGCTGGTCTT
Supplementary files format and content: Tally the CRISPResso2 results in an excel file that includes the sample name, UnModAll, UnModPerfect, ModAll, ModPerfect, indel and so on.

source_name: HEK293T cell

growth_protocol: The culture conditions for HEK293T cells typically involve maintaining the cells in a high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin antibiotic solution. The medium is further enriched with 2 mM L-glutamine for optimal cell growth and health. Cells should be cultured at 37°C in a humidified atmosphere with 5% CO2. Regular media replacement is essential, usually every 2-3 days, to prevent the accumulation of metabolic waste and to supply fresh nutrients. When the cell confluence reaches about 80-90%, subculturing is recommended to avoid overgrowth, commonly achieved by detaching the cells using trypsin and splitting them into fresh culture flasks at a suitable dilution ratio, typically around 1:10.

extract_protocol:
Genomic DNA was extracted by the addition of 20 µl of freshly prepared lysis buffer (10 mM Tris-HCl, pH 7.5; 0.05% SDS (ThermoFisher Scientific); 25 µg/ml proteinase K (Tiangen)) directly into each tube which 30,000 cells were sorted from each sample. The genomic DNA mixture was incubated at 37 °C for 1.5 h, followed by an 80 °C enzyme inactivation step for 30 min.
Use site-specific primers with second-generation sequencing adapters to amplify target sites via PCR for library construction. Amplicon-seq.

treatment_protocol: HEK293T cells were seeded on 12-well poly-d-lysine coated plates (Corning). Between 16 and 24 h after seeding, cells were transfected at approximately 70% confluency with lipofectamine 3000 (ThermoFisher Scientific) according to the manufacturer’s protocols and 3249 ng All in one(PE2) plasmid, and 1083 ng sgRNA plasmid (for PE2 and PE3). Unless otherwise stated, cells were cultured for 2 days following transfection, after which the medium was removed, the cells were washed with 1 ml 1×PBS (ThermoFisher Scientific), then digested with 0.25% Trypsin-EDTA (1X) (Gibco) for 1 min, 1 ml DMEM complete medium was added to terminate the reaction. Centrifugation at 300 g for 5 min, discard supernatant and resuspended with 150 ul 1×PBS (ThermoFisher Scientific). After resuspended, all positive cells (single or double fluorescence positive) were sorted and collected into a 1.5 ml low adsorption centrifuge tube (ThermoFisher Scientific) by MULTI-APPLICATION CELL SORTER MA900 (Sony). Centrifugation at 11,200 g for 1 min, discard supernatant and store at -20°C for a long time.

tag: cell line

value: HEK293T cell

tag: sample group


title: JB0

description: Library name: JB0_S42

value: Normoxia


title: female_cerebellum_18 months_1377625

description: Library name: 1377625

value: female

value: 18 months


title: H-B3

description: Library name: H-B3_S41

value: 72h Hyperbaric hypoxia


title: male_right atrium_9 months_1541664

description: Library name: 1541664

value: right atrium

value: male

value: 9 months


title: 7458,HEK293T cell,HEK4 +2 G•C to T•A/G•C to A•T, loop 2-modified epegRNA,rep2

description: Library name: 7458_


title: male_right atrium_9 months_1541663

description: Library name: 1541663


title: male_right atrium_9 months_1541662

description: Library name: 1541662


title: 7454,HEK293T cell,RNF2 +4 A•T to C•G/A•T to G•C, loop 2-modified epegRNA,rep2

description: Library name: 7454_


title: male_right atrium_9 months_1541659

description: Library name: 1541659


title: 7452,HEK293T cell,RNF2 +4 A•T to C•G/A•T to G•C, loop 2-modified epegRNA,rep1

description: Library name: 7452_


title: male_cerebellum_18 months_1377620

description: Library name: 1377620

value: cerebellum


title: male_right atrium_9 months_1541658

description: Library name: 1541658


title: GB3

description: Library name: GB3_S45

value: Blood


title: GB2

description: Library name: GB2_S44

value: peripheral blood mononuclear cells (PBMCs)

value: 24h Hyperbaric hypoxia


title: male_cerebellum_18 months_1377619

description: Library name: 1377619


title: 7451,HEK293T cell,FANCF +7 A•T to C•G/A•T to G•C, loop 2-modified epegRNA,rep3

description: Library name: 7451_


title: male_right atrium_9 months_1541657

description: Library name: 1541657

value: Sprague Dawley


title: GB1

description: Library name: GB1_S43

value: 12h Hyperbaric hypoxia


title: 7449,HEK293T cell,FANCF +7 A•T to C•G/A•T to G•C, loop 2-modified epegRNA,rep2

description: Library name: 7449_


title: 7448,HEK293T cell,FANCF +7 A•T to C•G/A•T to G•C, loop 2-modified epegRNA,rep1

description: Library name: 7448_


title: male_right atrium_9 months_1541656

description: Library name: 1541656


title: GB0

description: Library name: GB0_S42


title: female_cerebellum_12 months_1377617

description: Library name: 1377617


title: 7457,HEK293T cell,HEK4 +2 G•C to T•A/G•C to A•T, loop 2-modified epegRNA,rep1

description: Library name: 7457_


title: female_cerebellum_18 months_1377624

description: Library name: 1377624


title: H-B2

description: Library name: H-B2_S40


title: male_right atrium_9 months_1541661

description: Library name: 1541661


title: phage SH-Ab 15599 and its host lysates, 0min, replicate1

description: Library name: HP_0min_1

value: prokaryotes and phages

value: after phage infection of 0min


title: male_right atrium_9 months_1541655

description: Library name: 1541655


title: 5618,HEK293T cell,VEGFA +3 A•T to C•G, tetraloop-modified sgRNA,rep1

description: Library name: 5618_


title: female_cerebellum_12 months_1377623

description: Library name: 1377623

value: 12 months


title: 5617,HEK293T cell,VEGFA +3 A•T to C•G, tetraloop-modified sgRNA,rep1

description: Library name: 5617_

value: HEK293T cell


title: EB2

description: Library name: EB2_S37


title: H-B0

description: Library name: H-B0_S38

value: Normoxia


title: female_cerebellum_12 months_1377615

description: Library name: 1377615

value: female


title: female_cerebellum_12 months_1377616

description: Library name: 1377616


title: male_right atrium_9 months_1541660

description: Library name: 1541660


title: H-B1

description: Library name: H-B1_S39


title: EB3

description: Library name: EB3_S41


title: EB1

description: Library name: EB1_S36


title: male_cerebellum_12 months_1377614

description: Library name: 1377614


title: male_right ventricle_9 months_1541653

description: Library name: 1541653

value: right ventricle


title: 5616,HEK293T cell,VEGFA +3 A•T to C•G, tetraloop-modified sgRNA,rep1

description: Library name: 5616_


title: male_right ventricle_9 months_1541654

description: Library name: 1541654


title: male_cerebellum_18 months_1377621

description: Library name: 1377621

value: 18 months


title: male_cerebellum_18 months_1377622

description: Library name: 1377622


title: 7443,HEK293T cell,RUNX1 +2 ATG deletion, loop 2-modified epegRNA,rep3

description: Library name: 7443_


title: male_cerebellum_12 months_1377613

description: Library name: 1377613


title: EB0

description: Library name: EB0_S35


title: male_right ventricle_9 months_1541651

description: Library name: 1541651


title: male_right ventricle_9 months_1541652

description: Library name: 1541652


title: female_cerebellum_12 months_1377618

description: Library name: 1377618


title: male_cerebellum_18 months_1377612

description: Library name: 1377612


title: 7444,HEK293T cell,RUNX1 +2 ATG deletion, epegRNA,rep1

description: Library name: 7444_

value: RUNX1 +2 ATG deletion, epegRNA


title: male_cerebellum_12 months_1377611

description: Library name: 1377611

value: male


title: D-B3

description: Library name: D-B3_S16

value: 72h Hyperbaric hypoxia


title: D-B2

description: Library name: D-B2_S15


title: 7445,HEK293T cell,RUNX1 +2 ATG deletion, epegRNA,rep2

description: Library name: 7445_


title: D-B0

description: Library name: D-B0_S13


title: 7440,HEK293T cell,RUNX1 +2 ATG deletion, loop 2-modified epegRNA,rep1

description: Library name: 7440_


title: female_cerebellum_12 months_1377609

description: Library name: 1377609

value: cerebellum


title: D-B1

description: Library name: D-B1_S14

value: Blood


title: 7455,HEK293T cell,RNF2 +4 A•T to C•G/A•T to G•C, loop 2-modified epegRNA,rep3

description: Library name: 7455_


title: 7447,HEK293T cell,RUNX1 +2 ATG deletion, epegRNA,rep3

description: Library name: 7447_


title: male_right ventricle_9 months_1541648

description: Library name: 1541648

value: 9 months


title: male_right ventricle_9 months_1541649

description: Library name: 1541649


title: 7441,HEK293T cell,RUNX1 +2 ATG deletion, loop 2-modified epegRNA,rep2

description: Library name: 7441_


title: C-B3

description: Library name: C-B3_S12

value: peripheral blood mononuclear cells (PBMCs)


title: male_right ventricle_9 months_1541650

description: Library name: 1541650

value: Sprague Dawley


title: C-B2

description: Library name: C-B2_S11

value: 24h Hyperbaric hypoxia


title: male_cerebellum_12 months_1377610

description: Library name: 1377610


title: 7434,HEK293T cell,RUNX1 +1 ATG insertion, loop 2-modified epegRNA,rep3

description: Library name: 7434_


title: female_cerebellum_6 months_1377607

description: Library name: 1377607

value: 6 months


title: female_cerebellum_6 months_1377608

description: Library name: 1377608


title: male_right ventricle_9 months_1541645

description: Library name: 1541645


title: male_cerebellum_12 months_1377606

description: Library name: 1377606


title: male_right ventricle_9 months_1541644

description: Library name: 1541644


title: male_right ventricle_9 months_1541647

description: Library name: 1541647


title: male_left atrium_9 months_1541642

description: Library name: 1541642

value: left atrium


title: 7433,HEK293T cell,RUNX1 +1 ATG insertion, loop 2-modified epegRNA,rep2

description: Library name: 7433_


title: female_cerebellum_6 months_1377604

description: Library name: 1377604


title: C-B0

description: Library name: C-B0_S9


title: 7438,HEK293T cell,RUNX1 +1 ATG insertion, epegRNA,rep2

description: Library name: 7438_

value: RUNX1 +1 ATG insertion, epegRNA


title: B-B1

description: Library name: B-B1_S6

value: 12h Hyperbaric hypoxia


title: male_left ventricle_9 months_1541640

description: Library name: 1541640

value: left ventricle


title: C-B1

description: Library name: C-B1_S10


title: 7432,HEK293T cell,RUNX1 +1 ATG insertion, loop 2-modified epegRNA,rep1

description: Library name: 7432_

value: HEK293T cell


title: 7431,HEK293T cell,DNMT1 +2 AGG deletion, loop 2-modified epegRNA,rep3

description: Library name: 7431_


title: male_right ventricle_9 months_1541643

description: Library name: 1541643

value: right ventricle


title: B-B3

description: Library name: B-B3_S8


title: male_cerebellum_12 months_1377603

description: Library name: 1377603

value: 12 months


title: B-B2

description: Library name: B-B2_S7


title: male_left atrium_9 months_1541641

description: Library name: 1541641


title: male_left ventricle_9 months_1541639

description: Library name: 1541639


title: 7436,HEK293T cell,RUNX1 +1 ATG insertion, epegRNA,rep1

description: Library name: 7436_


title: A-B3

description: Library name: A-B3_S4


title: female_cerebellum_6 months_1377605

description: Library name: 1377605

value: female


title: male_left ventricle_9 months_1541637

description: Library name: 1541637

value: male


title: 7428,HEK293T cell,DNMT1 +2 AGG deletion, loop 2-modified epegRNA,rep2

description: Library name: 7428_


title: B-B0

description: Library name: B-B0_S5

value: Normoxia


title: female_cerebellum_12 months_1377601

description: Library name: 1377601

value: cerebellum


title: female_cerebellum_12 months_1377602

description: Library name: 1377602


title: female_cerebellum_6 months_1377600

description: Library name: 1377600


title: male_cerebellum_21 months_1377599

description: Library name: 1377599

value: 21 months


title: 7439,HEK293T cell,RUNX1 +1 ATG insertion, epegRNA,rep3

description: Library name: 7439_


title: male_left ventricle_9 months_1541638

description: Library name: 1541638

value: 9 months


title: A-B2

description: Library name: A-B2_S3

value: Blood

value: peripheral blood mononuclear cells (PBMCs)


title: A-B1

description: Library name: A-B1_S2


title: 7424,HEK293T cell,DNMT1 +2 AGG deletion, loop 2-modified epegRNA,rep1

description: Library name: 7424_


title: 7427,HEK293T cell,DNMT1 +2 AGG deletion, epegRNA,rep3

description: Library name: 7427_

value: DNMT1 +2 AGG deletion, epegRNA


title: male_left ventricle_9 months_1541635

description: Library name: 1541635

value: Sprague Dawley


title: male_left ventricle_9 months_1541636

description: Library name: 1541636


title: 7426,HEK293T cell,DNMT1 +2 AGG deletion, epegRNA,rep2

description: Library name: 7426_


title: male_cerebellum_21 months_1377598

description: Library name: 1377598


title: 7425,HEK293T cell,DNMT1 +2 AGG deletion, epegRNA,rep1

description: Library name: 7425_


title: male_cerebellum_21 months_1377596

description: Library name: 1377596


title: female_cerebellum_21 months_1377597

description: Library name: 1377597


title: male_left ventricle_9 months_1541634

description: Library name: 1541634


title: A-B0

description: Library name: A-B0_S1


title: male_left ventricle_9 months_1541633

description: Library name: 1541633


title: male_left ventricle_9 months_1541631

description: Library name: 1541631


title: J-T3

description: Library name: J-T3_S16

data_processing:
CLC Genomics Workbench 24.0.5 (Qiagen)
Reads from FASTq files were filtered for quality and aligned to the GRCh38  version of the reference human genome
The data were normalised using the TMM method (trimmed Mean of M-values)
DE analysis was performed using Generalized Linear Model (GLM) and Trimmed mean of M-values (TMM)
Assembly: GRCh38 human genome
Supplementary files format and content: CPM - Expression values

extract_protocol:
RNA was extracted from PBMCs  using the  RNA Purification Kit (Qiagen)
library preparation of mRNAs from PBMCs was obtained using TruSeq Stranded mRNA (Illumina).

value: 72h Hyperbaric hypoxia


title: male_cerebellum_21 months_1377595

description: Library name: 1377595


title: male_left ventricle_9 months_1541632

description: Library name: 1541632


title: 7531,HEK293T cell,DNMT1 +0 ATC insertion, loop 2-modified epegRNA,rep3

description: Library name: 7531_


title: 7529,HEK293T cell,DNMT1 +0 ATC insertion, loop 2-modified epegRNA,rep2

description: Library name: 7529_


title: J-T2

description: Library name: J-T2_S15

value: 24h Hyperbaric hypoxia


title: male_cerebellum_21 months_1377594

description: Library name: 1377594


title: 7423,HEK293T cell,DNMT1 +0 ATC insertion, epegRNA,rep2

description: Library name: 7423_

value: DNMT1 +0 ATC insertion, epegRNA


title: male_left ventricle_9 months_1541629

description: Library name: 1541629

value: left ventricle


title: female_cerebellum_18 months_1377593

description: Library name: 1377593

value: 18 months


title: male_left ventricle_9 months_1541630

description: Library name: 1541630


title: J-T0

description: Library name: J-T0_S13


title: 7418,HEK293T cell,DNMT1 +0 ATC insertion, loop 2-modified epegRNA,rep1

description: Library name: 7418_

value: HEK293T cell


title: male_cerebellum_6 months_1377592

description: Library name: 1377592

value: 6 months


title: H-T3

description: Library name: H-T3_S4


title: J-T1

description: Library name: J-T1_S14

value: 12h Hyperbaric hypoxia


title: 7420,HEK293T cell,DNMT1 +0 ATC insertion, epegRNA,rep1

description: Library name: 7420_


title: 7532,HEK293T cell,DNMT1 +0 ATC insertion, epegRNA,rep3

description: Library name: 7532_


title: female_cerebellum_24 months_1377590

description: Library name: 1377590

value: female

value: 24 months


title: male_left atrium_9 months_1541628

description: Library name: 1541628

value: left atrium

value: male


title: 7411,HEK293T cell,RNF2 +3 AGG deletion, loop 2-modified epegRNA,rep3

description: Library name: 7411_


title: male_cerebellum_21 months_1377591

description: Library name: 1377591

value: cerebellum

value: 21 months


title: H-T1

description: Library name: H-T1_S2

value: Blood

value: peripheral blood mononuclear cells (PBMCs)


title: 7409,HEK293T cell,RNF2 +3 AGG deletion, loop 2-modified epegRNA,rep1

description: Library name: 7409_


title: male_left atrium_9 months_1541627

description: Library name: 1541627

value: Sprague Dawley

value: 9 months


title: 7410,HEK293T cell,RNF2 +3 AGG deletion, loop 2-modified epegRNA,rep2

description: Library name: 7410_


title: H-T2

description: Library name: H-T2_S3

value: 24h Hyperbaric hypoxia


title: G-T2

description: Library name: G-T2_S11


title: male_cerebellum_24 months_1377587

description: Library name: 1377587


title: male_left atrium_9 months_1541626

description: Library name: 1541626


title: H-T0

description: Library name: H-T0_S1

value: Normoxia


title: 7413,HEK293T cell,RNF2 +3 AGG deletion, epegRNA,rep2

description: Library name: 7413_

value: RNF2 +3 AGG deletion, epegRNA


title: male_left atrium_9 months_1541624

description: Library name: 1541624


title: female_cerebellum_24 months_1377589

description: Library name: 1377589


title: male_cortex_27 months_1377711

description: Library name: 1377711

source_name: cortex

value: cortex

value: 27 months


title: G-T1

description: Library name: G-T1_S10


title: male_cerebellum_24 months_1377586

description: Library name: 1377586


title: G-T0

description: Library name: G-T0_S9


title: G-T3

description: Library name: G-T3_S12

value: 72h Hyperbaric hypoxia


title: female_cerebellum_18 months_1377588

description: Library name: 1377588

value: 18 months


title: male_cerebellum_24 months_1377585

description: Library name: 1377585


title: male_left atrium_9 months_1541622

description: Library name: 1541622


title: male_left atrium_9 months_1541625

description: Library name: 1541625


title: 7415,HEK293T cell,RNF2 +3 AGG deletion, epegRNA,rep3

description: Library name: 7415_

value: HEK293T cell


title: E-T3

description: Library name: E-T3_S8


title: female_cerebellum_24 months_1377583

description: Library name: 1377583

value: female

value: 24 months


title: male_left atrium_9 months_1541623

description: Library name: 1541623

value: left atrium

value: male


title: E-T2

description: Library name: E-T2_S7


title: 7412,HEK293T cell,RNF2 +3 AGG deletion, epegRNA,rep1

description: Library name: 7412_


title: male_cerebellum_24 months_1377582

description: Library name: 1377582

value: cerebellum


title: female_cerebellum_24 months_1377584

description: Library name: 1377584


title: male_left atrium_9 months_1541621

description: Library name: 1541621


title: D-T3

description: Library name: D-T3_S11

value: Blood


title: 7404,HEK293T cell,RNF2 +0 GTA insertion, loop 2-modified epegRNA,rep1

description: Library name: 7404_


title: E-T0

description: Library name: E-T0_S5

value: peripheral blood mononuclear cells (PBMCs)


title: 7407,HEK293T cell,RNF2 +0 GTA insertion, loop 2-modified epegRNA,rep3

description: Library name: 7407_


title: male_left atrium_9 months_1541620

description: Library name: 1541620

value: Sprague Dawley


title: 7406,HEK293T cell,RNF2 +0 GTA insertion, loop 2-modified epegRNA,rep2

description: Library name: 7406_


title: female_cerebellum_24 months_1377579

description: Library name: 1377579


title: 69962,HEK293T cell,EMX1 +5 G•C to T•A, loop 2-modified sgRNA,rep1

description: Library name: 69962_


title: E-T1

description: Library name: E-T1_S6

value: 12h Hyperbaric hypoxia


title: female_cerebellum_18 months_1377580

description: Library name: 1377580


title: 7400,HEK293T cell,RNF2 +0 GTA insertion, epegRNA,rep1

description: Library name: 7400_

value: RNF2 +0 GTA insertion, epegRNA


title: male_cerebellum_6 months_1377577

description: Library name: 1377577

value: 6 months


title: 7523,HEK293T cell,RNF2 +0 GTA insertion, epegRNA,rep3

description: Library name: 7523_


title: male_right atrium_27 months_1541617

description: Library name: 1541617

value: right atrium


title: D-T2

description: Library name: D-T2_S10

value: 24h Hyperbaric hypoxia


title: male_right atrium_27 months_1541616

description: Library name: 1541616

value: 27 months


title: female_cerebellum_6 months_1377578

description: Library name: 1377578


title: male_left atrium_9 months_1541619

description: Library name: 1541619

value: 9 months


title: D-T1

description: Library name: D-T1_S9


title: male_right atrium_27 months_1541615

description: Library name: 1541615


title: D-T0

description: Library name: D-T0_S8

value: Normoxia


title: male_right atrium_27 months_1541618

description: Library name: 1541618


title: male_right atrium_27 months_1541614

description: Library name: 1541614


title: 7522,HEK293T cell,RNF2 +0 GTA insertion, epegRNA,rep2

description: Library name: 7522_

value: HEK293T cell


title: female_cerebellum_18 months_1377581

description: Library name: 1377581

value: female

value: 18 months


title: 60461,HEK293T cell,EMX1 +5 G•C to T•A, loop 2-modified sgRNA,rep2

description: Library name: 60461_


title: C-T3

description: Library name: C-T3_S16

value: 72h Hyperbaric hypoxia


title: male_cerebellum_6 months_1377576

description: Library name: 1377576

value: male


title: male_right atrium_27 months_1541612

description: Library name: 1541612


title: C-T2

description: Library name: C-T2_S7


title: male_right atrium_27 months_1541613

description: Library name: 1541613


title: male_cerebellum_27 months_1377574

description: Library name: 1377574

value: cerebellum


title: male_cerebellum_27 months_1377575

description: Library name: 1377575


title: 6118,HEK293T cell,EMX1 +5 G•C to T•A, loop 2-modified sgRNA,rep1

description: Library name: 6118_


title: female_cerebellum_27 months_1377572

description: Library name: 1377572


title: 60561,HEK293T cell,EMX1 +5 G•C to T•A, loop 2-modified sgRNA,rep3

description: Library name: 60561_


title: male_right atrium_27 months_1541611

description: Library name: 1541611


title: 5904,HEK293T cell,EMX1 +5 G•C to T•A, loop 2-modified sgRNA,rep1

description: Library name: 5904_


title: C-T1

description: Library name: C-T1_S6

value: Blood


title: male_left atrium_27 months_1541610

description: Library name: 1541610

value: left atrium


title: male_cerebellum_27 months_1377573

description: Library name: 1377573


title: male_left atrium_27 months_1541609

description: Library name: 1541609

value: Sprague Dawley


title: 6103,HEK293T cell,EMX1 +5 G•C to T•A, loop 2-modified sgRNA,rep3

description: Library name: 6103_


title: B-T3

description: Library name: B-T3_S15

value: peripheral blood mononuclear cells (PBMCs)


title: 6413,HEK293T cell,EMX1 +5 G•C to T•A, tetraloop-modified sgRNA,rep1

description: Library name: 6413_


title: B-T2

description: Library name: B-T2_S14


title: male_left atrium_27 months_1541607

description: Library name: 1541607


title: male_left atrium_27 months_1541608

description: Library name: 1541608


title: C-T0

description: Library name: C-T0_S5


title: male_cerebellum_27 months_1377571

description: Library name: 1377571


title: 6415,HEK293T cell,EMX1 +5 G•C to T•A, tetraloop-modified sgRNA,rep3

description: Library name: 6415_


title: 5198,HEK293T cell,EMX1 +5 G•C to T•A, pegRNA,rep3

description: Library name: 5198_

value: EMX1 +5 G•C to T•A, pegRNA


title: 5183,HEK293T cell,VEGFA +3 A•T to C•G, pegRNA,rep3

description: Library name: 5183_

value: VEGFA +3 A•T to C•G, pegRNA


title: female_cerebellum_21 months_1377567

description: Library name: 1377567

value: 21 months


title: A-T2

description: Library name: A-T2_S3

value: 24h Hyperbaric hypoxia


title: B-T1

description: Library name: B-T1_S13

value: 12h Hyperbaric hypoxia


title: A-T1

description: Library name: A-T1_S2


title: B-T0

description: Library name: B-T0_S12


title: female_cerebellum_27 months_1377570

description: Library name: 1377570

value: 27 months


title: 5182,HEK293T cell,VEGFA +3 A•T to C•G, pegRNA,rep2

description: Library name: 5182_


title: male_left atrium_27 months_1541606

description: Library name: 1541606


title: 5181,HEK293T cell,VEGFA +3 A•T to C•G, pegRNA,rep1

description: Library name: 5181_


title: MALAT1 reporter pDual-GFP-(558-695) IRES-RFP, Unmodified, Replicate 2

city: New Haven

first: Tanja

last: Hann

state: CT

address: 260 Whitney Avenue, YSB 308

department: Molecular Biophysics & Biochemistry

institute: Yale University

description:
Library name: MALAT1-rep-558-695_Unmod_Rep2
Each set of modified/unmodified samples share processed data files

data_processing:
All sequencing data were analyzed using ShapeMapper 2.2 with DMS mode (--dms), aligning reads to endogenous mouse Malat1 or Malat1 bi-cistronic reporter constructs.
Assembly: Endogenous mouse Malat1 (GenBank: 72289) or Malat1 bi-cistronic reporter constructs (pDual-GFP-(1-739) IRES-RFP and pDual-GFP-(558-695) IRES-RFP), reporter sequences available in Xiao et al., Mol Cell 2025
Supplementary files format and content: Each set of modified/unmodified samples share processed data files, including a profile.txt file containing per-nucleotide mutation rates and normalized fbDMS reactivities, and a .map file containing fbDMS ractivity data and accompanying information used for subsequent RNA secondary structure modeling.

growth_protocol: N2a cells were cultured in DMEM with 10% fetal bovine serum (FBS) and 10 U/ml Penicillin-Streptomycin. BV2 cells were cultured in DMEM with 5% FBS, 1% non-essential amino acid solution and 10 U/mL Penicillin-Streptomycin. All cells were cultured with 5% CO2 at 37°C.

extract_protocol:
For RNA extraction, 900 µL TRIzol was added into each tube. Next, 180 uL of chloroform:isoamyl alcohol (24:1) was added and incubated for 5 min and subsequently centrifuged at 3,000 g for 15 min at 4°C. The aqueous phase was then transferred to a new tube and precipitated by EtOH (at a final concentration of 70%) overnight at -20°C. The following day, RNA was pelleted at 15,000 g for 30 min at 4°C and resuspended in 1x ME buffer (10mM MOPS, 0,1mM EDTA, pH 6.5) with 1:100 RNase inhibitor. RNA was then purified with the QIAGEN RNeasy Kit (Cat. No. 74104) and eluted with 1x ME with 1:100 RNase inhibitor.
RT reactions were prepared by mixing 1 μg of total cellular RNA with 1uL of 1uM RT primer for each amplicon, annealed at 68°C for 5 min and cooled to room temperature. Next, 8uL of 2.5 x MarathonRT buffer (125mM 1M Tris-HCl pH 8.3, 500mM KCl, 12.5mM DTT, 1.25mM dNTPs, 2.5mM Mn2+), 4µL 100% glycerol and 0.5µL MarathonRT were added and incubated at 42°C for 3 h. The enzyme was then inactivated at 70°C for 15 min, followed by cDNA purification using AmpureXP at a 1.8x bead-to-sample ratio. Purified cDNA was eluted in 10uL nuclease-free water. Malat1 amplicons were generated using 5 μL of cDNA and gene-specific forward and reverse primers with NEB Q5 High-Fidelity 2x Master Mix under touchdown cycling PCR conditions (68 to 58 °C annealing temperature gradient). PCR products were purified with AmpureXP at a 1.8x bead-to-sample ratio and analyzed on a 1% agarose gel to verify the amplicon sizes. For library preparation, amplicon concentrations were measured with the Qubit dsDNA HS Assay Kit and amplicons diluted to 0.2 ng/μL. Libraries were generated using the Illumina NexteraXT DNA Library Preparation Kit according to the manufacturer’s protocols, but at 1/5th the recommended volume. Library concentration and average fragment size were quantified with a Qubit dsDNA HS Assay Kitand a BioAnalyzer High Sensitivity DNA Analysis kit, respectively. Final libraries were diluted according to the manufacturer’s protocols and sequenced on an Illumina NextSeq 2000 platform using a 300 cycle output kit.

treatment_protocol: For endogenous mouse Malat1 DMS probing, BV2 cells from two confluent 150mm tissue culture dishes were briefly washed with 1x PBS and then dislodged with cell scrapers in 10mL 1x PBS. After centrifugation at 1,000g for 5 min at 4°C, cell pellets were resuspended in 500 µL 1 M bicine buffer (pH 8.3) and then divided into 2 tubes with 250 µL each. The cell suspensions were either modified with 25 µL 1.7 M DMS or treated with 25 µL EtOH as a control and mixed well by pipetting. The samples were then incubated for 6 min at 37°C protected from light. For re-probing Malat1 IRES in the the bi-cistronic reporters, pDual-GFP-(1-739) IRES-RFP or pDual-GFP-(558-695) IRES-RFP constructs were transfected into N2a cells in a 6-well plate for 48h. Cells were washed with 1x PBS, dislodged with cell scrapers and DMS probing was performed as described above.

value: Murine neuroblastoma cell line

value: Unmodified (Ethanol)


title: female_cerebellum_24 months_1377566

description: Library name: 1377566

value: female

value: 24 months


title: male_left ventricle_27 months_1541602

description: Library name: 1541602

value: left ventricle


title: PBMC/23059SubLib09

city: Tubingen

first: Yogesh

last: Singh

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: Tubingen University

description: Library name: 23059SubLib09

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed and aligned to the human reference genome GRCh38 (hg38) using the Parse Biosciences splitpipe v1.1.2 pipeline to generate cell-by-gene count matrices for each sample. The matrices were imported into Seurat v5.1.0 for downstream analysis. Cells were filtered out if they contained <800 or >10,000 unique molecular identifiers (UMIs), <200 or >5,000 detected genes, or ≥10% mitochondrial gene content. Potential doublets were identified and removed using DoubletFinder v1.18.0. Gene counts were log-normalized, and the top 2,000 highly variable genes were selected for principal component analysis (PCA). To correct for batch effects, datasets from the three groups— HC, CONV, and LTCS—were integrated using canonical correlation analysis (CCA). Dimensionality reduction was performed with uniform manifold approximation and projection (UMAP) based on the first 20 principal components. Unsupervised clustering was conducted using a graph-based algorithm with a resolution of 1.0, and cell types were annotated according to canonical marker genes. Doublet detection was performed using the scDoubletFinder algorithm to identify and remove potential cell doublets from the single-cell RNA-sequencing data. The method estimates the expected doublet rate based on cell loading density and sequencing depth, generates artificial doublets, and assigns each cell a doublet score by comparing its transcriptional profile to simulated doublets and real singlets. Cells classified as highconfidence doublets a ccording to the recommended scDoubletFinder thresholds were excluded from downstream analyses to ensure data quality and accurate cell-type identification.
Assembly: GRCh38 (hg38)
Supplementary files format and content: The processed single-cell RNA-seq data are provided as an integrated Seurat object in .rds format (LTCS_pbmc.Rds), containing normalized expression values, cell metadata, and clustering annotations for all samples.

molecule: polyA RNA

source_name: blood/PBMC

extract_protocol:
Cryopreserved PBMCs were thawed in a 37°C water bath until only a small amount offrozen material remained, as described in the surface and intracellular staining section. PBMCs (0.5 × 106–2 × 106 cells) were processed using the Evercode Fixation Kit v2.02 (Parse Biosciences, Seattle, WA, USA; SKU: ECF2001) according to the manufacturer’s protocol. Briefly, PBMCs were counted using a TC20™ Automated Cell Counter (Bio-Rad), and 0.5 × 106–2 × 106 live cells per sample were transferred into a 15-mL tube and kept on ice. The cells were centrifuged at 400×g for 5 min, the supernatant was discarded, and the pellet was resuspended in 750 μL of cold Cell Prefixation Buffer. The suspension was passed through a 40-μm cell strainer into a new 15 mL Falcon tube and kept on ice. Next, 250 μL of Cell Fixation Solution was added to the cell suspension, mixed gently by pipetting up and down three times, and incubated on ice for 10 min. Following fixation, 80 μL of Cell Permeabilization Solution was added, mixed by pipetting three times, and incubated on ice for an additional 3 min. After incubation, 1 mL of Cell Neutralization Buffer was added, the tube was gently inverted once to mix, and cells were centrifuged at 400×g for 5 min. The supernatant was discarded, and the pellet was resuspended in 100 μL of cold cell buffer. Subsequently, 5 μL of DMSO was added, the mixture was pipetted gently three times to avoid bubble formation, and the cells were incubated on ice for 1 min. Cells were then counted and divided equally into two cryovials, which were placed in a freezing container under standard freezing conditions for fixed cells and stored at −80°C until library preparation. In total, approximately 700,000 cells from 48 donors were processed, yielding an average of 2,000–2,500 cells per donor.
Prior to cell barcoding and library preparation, fixed PBMC samples were removed from −80°C, thawed in a 37°C water bath, placed on ice, and recounted for viability and cell number. Libraries were constructed using the Single Cell Whole Transcriptome Kit v2 (Parse Biosciences, Seattle, WA, USA) according to the manufacturer’s instructions. The resulting scRNA-seq libraries were sequenced on an Illumina NovaSeq 6000 platform, generating 200 bp paired-end reads with an average depth of >20,000 reads per cel

value: blood/PBMC


title: PBMC/23059SubLib08

description: Library name: 23059SubLib08


title: female_cerebellum_21 months_1377569

description: Library name: 1377569

value: cerebellum


title: MALAT1 reporter pDual-GFP-(558-695) IRES-RFP, Unmodified, Replicate 1

description:
Library name: MALAT1-rep-558-695_Unmod_Rep1
Each set of modified/unmodified samples share processed data files


title: PBMC/23059SubLib07

description: Library name: 23059SubLib07


title: MALAT1 reporter pDual-GFP-(558-695) IRES-RFP, Modified, Replicate 1

description:
Library name: MALAT1-rep-558-695_Mod_Rep1
Each set of modified/unmodified samples share processed data files

value: Modified (DMS)


title: male_left ventricle_27 months_1541598

description: Library name: 1541598

value: male


title: 5197,HEK293T cell,EMX1 +5 G•C to T•A, pegRNA,rep2

description: Library name: 5197_

value: HEK293T cell


title: PBMC/23059SubLib06

description: Library name: 23059SubLib06


title: male_left ventricle_27 months_1541599

description: Library name: 1541599

value: Sprague Dawley


title: male_left ventricle_27 months_1541600

description: Library name: 1541600


title: female_cerebellum_18 months_1377561

description: Library name: 1377561

value: 18 months


title: male_cerebellum_12 months_1377560

description: Library name: 1377560

value: 12 months


title: PBMC/23059SubLib05

description: Library name: 23059SubLib05


title: male_left atrium_27 months_1541605

description: Library name: 1541605

value: left atrium


title: A-T3

description: Library name: A-T3_S4

value: Blood

value: peripheral blood mononuclear cells (PBMCs)

value: 72h Hyperbaric hypoxia


title: female_cerebellum_21 months_1377568

description: Library name: 1377568

value: 21 months


title: 5196,HEK293T cell,EMX1 +5 G•C to T•A, pegRNA,rep1

description: Library name: 5196_

value: EMX1 +5 G•C to T•A, pegRNA


title: male_left ventricle_27 months_1541604

description: Library name: 1541604

value: 27 months


title: male_left ventricle_27 months_1541596

description: Library name: 1541596


title: MALAT1 reporter pDual-GFP-(1-739) IRES-RFP, Unmodified, Replicate 2

description:
Library name: MALAT1-rep-739_Unmod_Rep2
Each set of modified/unmodified samples share processed data files

value: Murine neuroblastoma cell line

value: pDual-GFP-(1-739) IRES-RFP transfected

value: Unmodified (Ethanol)


title: A-T0

description: Library name: A-T0_S1

value: Normoxia


title: male_left ventricle_27 months_1541603

description: Library name: 1541603

value: left ventricle


title: male_cerebellum_27 months_1377564

description: Library name: 1377564

value: cerebellum

value: male


title: PBMC/23059SubLib04

description: Library name: 23059SubLib04

value: blood/PBMC


title: male_left ventricle_27 months_1541601

description: Library name: 1541601

value: Sprague Dawley


title: MALAT1 reporter pDual-GFP-(558-695) IRES-RFP, Modified, Replicate 2

description:
Library name: MALAT1-rep-558-695_Mod_Rep2
Each set of modified/unmodified samples share processed data files

value: Modified (DMS)


title: female_cerebellum_24 months_1377565

description: Library name: 1377565

value: female

value: 24 months


title: female_cerebellum_21 months_1377563

description: Library name: 1377563


title: male_cerebellum_12 months_1377555

description: Library name: 1377555

value: 12 months


title: male_cerebellum_18 months_1377562

description: Library name: 1377562

value: 18 months


title: MALAT1 reporter pDual-GFP-(1-739) IRES-RFP, Unmodified, Replicate 1

description:
Library name: MALAT1-rep-739_Unmod_Rep1
Each set of modified/unmodified samples share processed data files


title: PBMC/23059SubLib02

description: Library name: 23059SubLib02


title: MALAT1 reporter pDual-GFP-(1-739) IRES-RFP, Modified, Replicate 2

description:
Library name: MALAT1-rep-739_Mod_Rep2
Each set of modified/unmodified samples share processed data files


title: male_left ventricle_27 months_1541593

description: Library name: 1541593


title: male_left ventricle_27 months_1541594

description: Library name: 1541594


title: male_left ventricle_27 months_1541597

description: Library name: 1541597


title: Endogenous mMALAT1, Unmodified, Replicate 2

description:
Library name: mMALAT1_Unmod_Rep2
Each set of modified/unmodified samples share processed data files

value: Murine microglial cell line

value: WT


title: male_right ventricle_27 months_1541591

description: Library name: 1541591

value: right ventricle

value: 27 months


title: male_cerebellum_24 months_1377558

description: Library name: 1377558


title: female_cerebellum_18 months_1377556

description: Library name: 1377556


title: male_right ventricle_27 months_1541592

description: Library name: 1541592


title: female_cerebellum_21 months_1377554

description: Library name: 1377554

value: 21 months


title: Endogenous mMALAT1, Modified, Replicate 1

description:
Library name: mMALAT1_Mod_Rep1
Each set of modified/unmodified samples share processed data files


title: male_right ventricle_27 months_1541590

description: Library name: 1541590


title: LBM-RIH-3, Human Brain Metastasis Tissue, Visium

city: Los Angeles

first: Bodour

last: Salhia

address: 1450 Biggy Street

department: Department of Cancer Biology

institute: University of Southern California

description:
Library name: LBM_RIH_3_HPT
Fresh frozen spatial transcriptomics

data_processing:
Visium spatial transcriptomics data were processed using functions from the Seurat R package. Quality control of the raw count data was performed by filtering out low quality spots where the number of genes detected per spot was < 200 and the mitochondrial percentage per spot > 15%. Counts were then normalized using the Seurat function LogNormalize. To annotate spots, we utilized our scRNA-seq dataset described above as a reference and performed an integration analysis between the scRNA-seq reference and Visium datasets. For the reference scRNA-seq dataset, counts per cell were normalized by LogNormalize and anchors between the reference and Visium data were identified using the Seurat function FindTransferAnchors. The prediction scores for each cell type were transferred to the Visium data set using the Seurat function TransferData. We performed this analysis separately for the breast-to-brain BM samples and lung-to-brain BM samples. Scores for the four CAF subpopulations and the CAF subpopulation subcluster annotations were visualized using the SpatialFeaturePlot function in Seurat.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz = list of spatial barcodes
Supplementary files format and content: features.tsv.gz = list of gene IDs
Supplementary files format and content: matrix.mtx.gz = gene expression count data
Supplementary files format and content: filtered_feature_bc_matrix.h5 = compressed binary HDF5-formatted sparse matrix of gene expression counts per barcode
Supplementary files format and content: aligned_fiducials.jpg = aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg = image of the aligned tissue
Supplementary files format and content: detected_tissue_image.jpg = image of the detected tissue with spots
Supplementary files format and content: scalefactors_json.json = scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv = spatial distribution of features / Gene IDs
Supplementary files format and content: tissue_hires_image.png = hi resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png = low resolution image of tissue
Supplementary files format and content: tissue_positions.csv = list of spatial barcodes and coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Brain metastasis

extract_protocol:
Fresh brain metastasis tissue samples were collected, transferred to a tube containing MACS© tissue storage solution (Miltenyi) and placed on ice before being processed for tissue snap freezing, OCT cryopreservation or cell dissociation within 24h. The proportion of each tissue sample designated for spatial transcriptomics analysis was embedded in OCT, immediately flash frozen in isopentane chilled by liquid nitrogen and stored at -80°C until further processing. BBM-USC-5-1, LBM-USC-2-1, LBM-RIH-2 and LBM-RIH-3 BM patient-derived tissue samples were used for spatial transcriptomics analysis using 10x Genomics Visium. OCT-embedded tissues were transferred to the Tissue Procurement Core (TPC) of the USC Norris Comprehensive Cancer Center (NCCC) for further processing. Tissues were cut by TPC into 10mm sections for the Visium protocol, as well as scrolls for RNA QC. Tissue sections and scrolls were then submitted to Molecular Genomics Core (MGC) at the USC NCCC where the rest of the Visium procedures were performed. Suitability of tissue samples for Visium was carefully assessed by MGC. RNA QC was performed by measuring the RNA Integrity Number or DV200 of RNA to confirm tissues met minimum requirements to proceed into spatial profiling. A tissue section per sample was stained with hematoxylin & eosin (H&E) to determine the region of interest (ROI) for spatial profiling.
10mm tissue sections were then mounted onto 10x Genomics Visium slides (6.5 x 6.5mm spot) and further processed for fixation, H&E staining, whole transcriptome probe-mediated mRNA detection, reverse transcription, and library preparation, according to the ‘Visium CytAssist Spatial Gene Expression User Guide’. Sequencing was performed on a NextSeq 2000 (Illumina).

value: Brain metastasis


title: MALAT1 reporter pDual-GFP-(1-739) IRES-RFP, Modified, Replicate 1

description:
Library name: MALAT1-rep-739_Mod_Rep1
Each set of modified/unmodified samples share processed data files

value: Murine neuroblastoma cell line

value: pDual-GFP-(1-739) IRES-RFP transfected


title: PBMC/23059SubLib03

description: Library name: 23059SubLib03


title: PBMC/23059SubLib01

description: Library name: 23059SubLib01


title: Endogenous mMALAT1, Modified, Replicate 2

description:
Library name: mMALAT1_Mod_Rep2
Each set of modified/unmodified samples share processed data files


title: female_cerebellum_21 months_1377552

description: Library name: 1377552

value: cerebellum


title: male_left ventricle_27 months_1541595

description: Library name: 1541595

value: left ventricle

value: male


title: female_cerebellum_21 months_1377553

description: Library name: 1377553


title: LBM-USC-2-1, Human Brain Metastasis Tissue, Visium

description:
Library name: LBM_USC_2_1_HPT
Fresh frozen spatial transcriptomics


title: Endogenous mMALAT1, Unmodified, Replicate 1

description:
Library name: mMALAT1_Unmod_Rep1
Each set of modified/unmodified samples share processed data files

value: Unmodified (Ethanol)


title: male_cerebellum_24 months_1377559

description: Library name: 1377559


title: male_right ventricle_27 months_1541587

description: Library name: 1541587

value: Sprague Dawley


title: female_cerebellum_27 months_1377549

description: Library name: 1377549

value: female


title: control_BM_LK_1

city: Edinburgh

first: Alasdair

last: Duguid

address: 5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

description:
Library name: control_BM_LK_1
15-1-LK; normalised_count_data_control.csv

data_processing:
The Cogent NGS Analysis Pipeline v2.0 (TaKaRa) in the command line was used for data preprocessing. SummarizedExperiment objects containing count matrices were created using the GenomicAlignments package and the aligned BAM files. SummarizedExperiment objects were transformed into DESeqDataSet objects, prefiltered, normalised and a results table created using the DESeq2 package.
Assembly: GRCm39
Supplementary files format and content: FASTQ format files containing raw sequencing reads for each sample.
Supplementary files format and content: normalized gene expression values

source_name: BM

extract_protocol:
RNA was extracted from freshly sorted leukaemia propagating cells and haematopoietic stem and progenitor cells harvesed from the bone marrow and central nervous system of mice that developed terminal leukaemia and controls using the Quick-RNA Microprep Kit (Zymo, R1050).
cDNA library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian (TaKaRa, 634487).

value: BM

tag: disease state

value: control

value: LK/CLP

value: miR-scramble overexpressing Kmt2a-AFF1+

tag: mouse id


title: control_BM_LK_2

description:
Library name: control_BM_LK_2
15-4-LK; normalised_count_data_control.csv


title: control_BM_LMPP_4

description:
Library name: control_BM_LMPP_4
15-14-LMP; normalised_count_data_control.csv

value: LMPP


title: female_cerebellum_27 months_1377557

description: Library name: 1377557


title: female_cerebellum_27 months_1377548

description: Library name: 1377548


title: LBM-RIH-2, Human Brain Metastasis Tissue, Visium

description:
Library name: LBM_RIH_2_HPT
Fresh frozen spatial transcriptomics


title: male_cerebellum_24 months_1377546

description: Library name: 1377546

value: 24 months


title: control_BM_LK_4

description:
Library name: control_BM_LK_4
15-14-LK; normalised_count_data_control.csv


title: male_right ventricle_27 months_1541585

description: Library name: 1541585

value: right ventricle

value: 27 months


title: control_BM_LMPP_1

description:
Library name: control_BM_LMPP_1
15-1-LMP; normalised_count_data_control.csv


title: male_right ventricle_27 months_1541582

description: Library name: 1541582


title: male_right ventricle_27 months_1541589

description: Library name: 1541589


title: Spatial transcriptomics library from donor YA.3

first: Marcello

last: DiStasio

address: 300 George St. Rm. 353D Rm. 353D

department: Pathology

institute: Yale School of Medicine

description: Library name: YA_6_spatial

data_processing:
Raw sequencing reads were processed using Curio Bioscience Seeker data processing pipelines. Reads were demultiplexed, aligned to the human reference genome (GRCh38), and spatially resolved gene expression matrices were generated for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Processed h5ad data files consist of anndata objects containing spatial gene expression matrices generated by the Curio Bioscience Seeker platform. Files include spatially resolved UMI count matrices with associated spatial coordinates for each capture area.
Library strategy: Spatial Transcriptomics

source_name: Choroid Plexus

extract_protocol:
Frozen human choroid plexus tissue sections were prepared for spatial transcriptomic profiling according to the Curio Bioscience Seeker platform workflow (Seeker v1.1, 3×3 mm). Tissue handling and processing were performed under RNase-free conditions following manufacturer guidelines.
Spatial transcriptomic libraries were generated using the Curio Bioscience Seeker platform (Seeker v1.1, 3×3 mm). Tissue sections were mounted onto Seeker capture areas, where spatially resolved barcoded probes captured transcripts in situ. Reverse transcription, amplification, and library construction were performed according to the manufacturer’s protocol to generate spatially barcoded cDNA libraries.

value: Choroid Plexus


title: Spatial transcriptomics library from donor YA.2

description: Library name: YA_5_spatial


title: control_BM_HSC_4

description:
Library name: control_BM_HSC_4
15-14-HSC; normalised_count_data_control.csv

value: HSC/MPP


title: control_BM_LK_3

description:
Library name: control_BM_LK_3
15-10-LK; normalised_count_data_control.csv


title: male_right ventricle_27 months_1541588

description: Library name: 1541588


title: male_right ventricle_27 months_1541581

description: Library name: 1541581


title: male_cerebellum_21 months_1377551

description: Library name: 1377551

value: 21 months


title: male_cerebellum_21 months_1377550

description: Library name: 1377550

value: cerebellum


title: BBM-USC-5-1, Human Brain Metastasis Tissue, Visium

description:
Library name: BBM_USC_5_1_HPT
Fresh frozen spatial transcriptomics

value: Brain metastasis


title: control_BM_HSC_3

description:
Library name: control_BM_HSC_3
15-10-HSC; normalised_count_data_control.csv


title: female_cerebellum_24 months_1377543

description: Library name: 1377543


title: male_right atrium_27 months_1541580

description: Library name: 1541580

value: right atrium

value: male


title: male_right ventricle_27 months_1541586

description: Library name: 1541586

value: Sprague Dawley


title: control_BM_LMPP_3

description:
Library name: control_BM_LMPP_3
15-10-LMP; normalised_count_data_control.csv


title: male_right atrium_27 months_1541579

description: Library name: 1541579


title: male_cerebellum_18 months_1377547

description: Library name: 1377547

value: 18 months


title: male_left atrium_27 months_1541578

description: Library name: 1541578

value: left atrium


title: male_right ventricle_27 months_1541584

description: Library name: 1541584


title: female_cerebellum_27 months_1377541

description: Library name: 1377541

value: female


title: male_right ventricle_27 months_1541583

description: Library name: 1541583


title: female_cerebellum_27 months_1377540

description: Library name: 1377540


title: control_BM_LMPP_2

description:
Library name: control_BM_LMPP_2
15-4-LMP; normalised_count_data_control.csv

value: BM

value: control


title: mixed_leukaemia_CNS_LK_4

description:
Library name: mixed_leukaemia_CNS_LK_4
10-1-1-C; normalised_count_data_130b.csv

source_name: CNS

value: CNS

value: leukaemia

value: LK/CLP

value: miR-130b overexpressing Kmt2a-AFF1+


title: male_cerebellum_24 months_1377545

description: Library name: 1377545

value: 24 months


title: mixed_leukaemia_BM_LK_4

description:
Library name: mixed_leukaemia_BM_LK_4
10-1-1-B; normalised_count_data_130b.csv


title: snRNA-seq library from donor YA.2

description:
Library name: YA_2_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.

data_processing:
Raw sequencing data were converted to FASTQ files and processed using the 10x Genomics Cell Ranger pipeline. Reads were aligned to the human reference genome (GRCh38), and gene–barcode count matrices were generated according to standard 10x Genomics workflows for single-nucleus RNA sequencing.
Assembly: hg38 (GRCh38)
Supplementary files format and content: Processed data files consist of filtered gene–barcode expression matrices generated by the 10x Genomics Cell Ranger pipeline. For each sample, the processed data include a sparse count matrix in Matrix Market format (matrix.mtx.gz) along with corresponding feature annotation (features.tsv.gz) and barcode identifiers (barcodes.tsv.gz). Matrices contain UMI counts for genes detected in high-quality nuclei after Cell Ranger filtering.

source_name: choroid plexus

extract_protocol:
Nuclei were isolated from frozen retinal tissue on ice using the Nuclei EZ Prep Kit (NUC-101, Sigma-Aldrich) with minor modifications. All steps were performed on ice or at 4 °C. Tissue was dounce-homogenized (25 strokes with loose pestle A followed by 25 strokes with tight pestle B) in 2 mL EZ Lysis Buffer using a KIMBLE Dounce Tissue Grinder. The homogenate was transferred to a 15 mL tube, supplemented with an additional 2 mL EZ Lysis Buffer, incubated on ice for 5 min, and centrifuged at 500 × g for 5 min at 4 °C. The supernatant was discarded, and the nuclei pellet was resuspended in 4 mL EZ Lysis Buffer, incubated on ice for 5 min, and centrifuged again at 500 × g for 5 min at 4 °C. Nuclei were washed in 4 mL ice-cold Nuclei Suspension Buffer (1× PBS containing 0.01% BSA and 0.1% RNase inhibitor), resuspended in 1 mL Nuclei EZ Storage Buffer, and filtered through a 40 µm nylon cell strainer. Nuclei were counted using trypan blue exclusion with a hemocytometer prior to library preparation.
RNA libraries of barcoded single nuclei were generated using the 10x Genomics Chromium Next GEM Single Cell 3′ Library & Gel Bead Kit according to the manufacturer’s instructions. Briefly, isolated nuclei were loaded onto the Chromium Controller, where individual nuclei were partitioned into Gel Beads-in-Emulsion (GEMs) for barcoding. Within each GEM, reverse transcription was performed to generate barcoded cDNA molecules containing unique cell barcodes and unique molecular identifiers (UMIs). Following GEM cleanup and cDNA amplification, sequencing libraries were constructed through fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR. Final libraries were quantified and assessed for quality prior to sequencing.

value: choroid plexus


title: male_cerebellum_24 months_1377539

description: Library name: 1377539


title: male_cerebellum_24 months_1377544

description: Library name: 1377544


title: female_cerebellum_27 months_1377538

description: Library name: 1377538

value: 27 months


title: snRNA-seq library from donor A.6

description:
Library name: A_6_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.


title: male_left atrium_27 months_1541575

description: Library name: 1541575


title: male_left atrium_27 months_1541574

description: Library name: 1541574


title: female_cerebellum_27 months_1377536

description: Library name: 1377536

value: cerebellum


title: snRNA-seq library from donor A.4

description:
Library name: A_4_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.


title: male_right atrium_27 months_1541572

description: Library name: 1541572


title: Spatial transcriptomics library from donor YA.1

description: Library name: YA_4_spatial

value: Choroid Plexus


title: control_BM_HSC_2

description:
Library name: control_BM_HSC_2
15-4-HSC; normalised_count_data_control.csv

value: HSC/MPP

value: miR-scramble overexpressing Kmt2a-AFF1+


title: snRNA-seq library from donor A.3

description:
Library name: A_3_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.

value: male


title: mixed_leukaemia_BM_LK_3

description:
Library name: mixed_leukaemia_BM_LK_3
8-2-4-B; normalised_count_data_130b.csv


title: female_cerebellum_24 months_1377542

description: Library name: 1377542


title: snRNA-seq library from donor YA.3

description:
Library name: YA_3_snRNAseq
Single-nucleus RNA sequencing library from human choroid plexus; Paired-end sequencing (Read 1: 28 bp, Read 2: 91 bp) on an Illumina NovaSeq 6000.


title: control_BM_HSC_1

description:
Library name: control_BM_HSC_1
15-1-HSC; normalised_count_data_control.csv


title: male_cerebellum_27 months_1377534

description: Library name: 1377534


title: Spatial transcriptomics library from donor A.5

description: Library name: A_5_spatial


title: male_right atrium_18 months_1541570

description: Library name: 1541570

value: Sprague Dawley

value: right atrium

value: 18 months


title: male_left atrium_27 months_1541577

description: Library name: 1541577

value: left atrium


title: 7C6-hIgG1, replicate 2

city: New York

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description: Library name: 2B

data_processing:
Sequencing reads, raw and TPM counts
Assembly: NCBI
Supplementary files format and content: tab-deliminated TPM and count text files

source_name: NK cell

extract_protocol:
Total mRNA was isolated using the RNeasy Plus Mini Kit (Qiagen), which included on-column genomic DNA removal, according to the manufacturer’s instructions
Prepared by Genewiz (Azenta Life Sciences)

value: NK cell


title: 7C6-hIgG1, replicate 1

description: Library name: 2A


title: 7C6-GAALIE, replicate 1

description: Library name: 3A


title: hIgG1 isotype, replicate 1

description: Library name: 1A


title: 7C6-GAALIE, replicate 2

description: Library name: 3B


title: hIgG1 isotype, replicate 2

description: Library name: 1B