title: Mixed Neuron Culture, CRISPRi region r14, replicate 4

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: r14 4
Column in counts file: r14_4

data_processing:
Trim reads with cutadapt for adaptor removal (AGATCGGAAGAGC) and quality (-m 30)
Align with STAR 2.7.5c to GENCODE v42 (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFileNamePrefix alignment/${sample}/ --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD)
Index with samtools 1.16.1
Filter duplicate reads with picard MarkDuplicates
Count with htseq-count 1.9, Gencode v42
Assembly: hg38
Supplementary files format and content: csv file including raw counts for each sample

growth_protocol: KOLF2.1J NPCs were differentiated into mixed neuron culture following Bardy et al. 2015 "Neuronal medium that supports basic synaptic functions and activity of human neurons in vitro." NPCs were transduced with CRISPRi and selected with puromyocin before differentiation into neurons

extract_protocol:
Norgen Total RNA Purification Kit (17270)
mRNA library prep (poly-A enrichment)

treatment_protocol: CRISPRi with puromycin selection

value: human mixed neuron culture

value: CRISPRi and puromycin selection


title: Rat lung tissues, IRI EVs, 2

status: Public on Mar 10 2026

type: SRA

city: guangzhou

first: Haoxiang

last: Yuan

address: 28 Qiaozhong Middle Road, Liwan District

department: Department of Thoracic Surgery and Oncology

country: China

institute: The First Affiliated Hospital of Guangzhou Medical University

description: Library name: Sample 5

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Star
count counting
Assembly: mRatBN7.2
Supplementary files format and content: TXT file contain counts for each sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Left lung

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction
The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

tag: tissue

value: Left lung

tag: genotype

value: WT

tag: treatment

value: IRI + Rg3@PACVs with NIR

tag: weight

tag: Sex

value: male

tag: disease

value: IRI

value: Rg3@PACVs + NIR


title: Rat lung tissues, IRI EVs, 1

description: Library name: Sample 4


title: mCDX2 OE in mESC RNA-seq rep2

status: Public on Mar 11 2026

city: Shenzhen

first: Guipeng

last: Li

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

description: MES_CDX2_rnaseq_featureCount_10samples_rep2.txt

data_processing:
STAR (v2.7.0d) was used to align the RNA-seq reads to mouse genome (mm10) with gene annotation. FeatuerCounts (v1.5.3) was used to count the read number of each gene (with parameters -T 12 -s 2 -p -g gene_name).
Fastp (v0.19.5) was first used to trimmed and removed low quality ATAC-seq reads and adapter sequences (-a CTGTCTCTTATA --detect_adapter_for_pe -w 12 --length_required 20 -q 30). Reads were aligned to mouse reference genome (hg38) using Bowtie2 v2.3.4.3 with parameters (-p 12 -X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom scripts. Sambamba (v0.7.0) was then used to sort the reads and remove duplicates. MACS2 was used to call peaks
paired-end ChIP-seq reads were first trimmed to remove adapter sequences using cutadapt v2.6 (-a AGATCGGAAGAG -A AGATCGGAAGAG -m 20 -q 30). Reads were aligned to mouse reference genome (mm10) using Bowtie2 v2.3.4.3 with parameters (-X 2000). Reads mapped to mitochondrial genome and low mapping quality reads (MAPQ < 20) were filtered out using custom script. Picard (v2.6.0, http://broadinstitute.github.io/picard/) was then used to sort the reads and remove duplicates.  MACS2 was used to call peaks (-g mm --keep-dup all -q 0.05 -B).
Genome_build: mm10
Supplementary_files_format_and_content: txt, read count

molecule: polyA RNA

organism: Mus musculus

source_name: mESC

extract_protocol:
(a) Total RNA were extracted from all the treated cells using TRIzol reagent according to the manufacturer’s protocol (Life Technologies).; (b) For ATAC-seq, samples were washed and then lysed in 50 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) for 3 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD501).; (c) The ChIP assay was performed according to the standard protocol provided by SimpleChIP Plus Sonication Chromatin IP Kit (CST, 56383)
(a) Truseq Stranded mRNA sequencing libraries were prepared with 2 μg total RNA according to the manufacturer’s protocol (Yeasen 12300ES24). (b) For ATAC-seq, PCR was then performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s followed by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 40s, and finally 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2 ×DNA clean beads (Vazyme Biotech, N411). (c) ChIP-seq libraries were prepared using standard protocol provided by VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme, ND607)

tag: cell type

value: mESC

tag: genotype/variation

value: mCDX2 OE


title: Mixed Neuron Culture, CRISPRi region r14, replicate 3

country: USA

description:
Library name: r14 3
Column in counts file: r14_3

organism: Homo sapiens

tag: cell line


title: Mixed Neuron Culture, CRISPRi region r14, replicate 1

description:
Library name: r14 1
Column in counts file: r14_1


title: Mixed Neuron Culture, CRISPRi region r14, replicate 2

description:
Library name: r14 2
Column in counts file: r14_2


title: Mixed Neuron Culture, CRISPRi region r12, replicate 5

description:
Library name: r12 5
Column in counts file: r12_5


title: Rat lung tissues, IRI, 1

description: Library name: Sample 1

value: control


title: Mixed Neuron Culture, CRISPRi region r13, replicate 5

description:
Library name: r13 5
Column in counts file: r13_5


title: Mixed Neuron Culture, CRISPRi region r13, replicate 2

description:
Library name: r13 2
Column in counts file: r13_2


title: Mixed Neuron Culture, CRISPRi region r13, replicate 3

description:
Library name: r13 3
Column in counts file: r13_3


title: Mixed Neuron Culture, CRISPRi region r12, replicate 4

description:
Library name: r12 4
Column in counts file: r12_4


title: Mixed Neuron Culture, CRISPRi region r13, replicate 4

description:
Library name: r13 4
Column in counts file: r13_4


title: Mixed Neuron Culture, CRISPRi region r12, replicate 2

description:
Library name: r12 2
Column in counts file: r12_2


title: Rat lung tissues, IRI, 2

description: Library name: Sample 2


title: Mixed Neuron Culture, CRISPRi region r14, replicate 5

description:
Library name: r14 5
Column in counts file: r14_5


title: Mixed Neuron Culture, CRISPRi region r12, replicate 3

description:
Library name: r12 3
Column in counts file: r12_3


title: Mixed Neuron Culture, CRISPRi region r11, replicate 5

description:
Library name: r11 5
Column in counts file: r11_5


title: Mixed Neuron Culture, CRISPRi region r12, replicate 1

description:
Library name: r12 1
Column in counts file: r12_1


title: Mixed Neuron Culture, CRISPRi region r13, replicate 1

description:
Library name: r13 1
Column in counts file: r13_1


title: Mixed Neuron Culture, CRISPRi region r11, replicate 4

description:
Library name: r11 4
Column in counts file: r11_4


title: Mixed Neuron Culture, CRISPRi region r11, replicate 3

description:
Library name: r11 3
Column in counts file: r11_3


title: Mixed Neuron Culture, CRISPRi region r11, replicate 2

description:
Library name: r11 2
Column in counts file: r11_2


title: Mixed Neuron Culture, CRISPRi region r10, replicate 2

description:
Library name: r10 2
Column in counts file: r10_2


title: Mixed Neuron Culture, CRISPRi region r10, replicate 4

description:
Library name: r10 4
Column in counts file: r10_4


title: Mixed Neuron Culture, CRISPRi region r10, replicate 1

description:
Library name: r10 1
Column in counts file: r10_1


title: Mixed Neuron Culture, CRISPRi region r10, replicate 5

description:
Library name: r10 5
Column in counts file: r10_5


title: Mixed Neuron Culture, CRISPRi region r11, replicate 1

description:
Library name: r11 1
Column in counts file: r11_1


title: Mixed Neuron Culture, CRISPRi region r10, replicate 3

description:
Library name: r10 3
Column in counts file: r10_3


title: Mixed Neuron Culture, CRISPRi region r9, replicate 4

description:
Library name: r9 4
Column in counts file: r9_4


title: Mixed Neuron Culture, CRISPRi region r9, replicate 5

description:
Library name: r9 5
Column in counts file: r9_5


title: Mixed Neuron Culture, CRISPRi region r9, replicate 3

description:
Library name: r9 3
Column in counts file: r9_3


title: Mixed Neuron Culture, CRISPRi region r8, replicate 3

description:
Library name: r8 3
Column in counts file: r8_3


title: Mixed Neuron Culture, CRISPRi region r8, replicate 5

description:
Library name: r8 5
Column in counts file: r8_5


title: Mixed Neuron Culture, CRISPRi region r9, replicate 1

description:
Library name: r9 1
Column in counts file: r9_1


title: Mixed Neuron Culture, CRISPRi region r7, replicate 5

description:
Library name: r7 5
Column in counts file: r7_5


title: Mixed Neuron Culture, CRISPRi region r7, replicate 1

description:
Library name: r7 1
Column in counts file: r7_1


title: Mixed Neuron Culture, CRISPRi region r8, replicate 2

description:
Library name: r8 2
Column in counts file: r8_2


title: Mixed Neuron Culture, CRISPRi region r7, replicate 3

description:
Library name: r7 3
Column in counts file: r7_3


title: Mixed Neuron Culture, CRISPRi region r7, replicate 4

description:
Library name: r7 4
Column in counts file: r7_4


title: Mixed Neuron Culture, CRISPRi region r8, replicate 4

description:
Library name: r8 4
Column in counts file: r8_4


title: Mixed Neuron Culture, CRISPRi region r7, replicate 2

description:
Library name: r7 2
Column in counts file: r7_2


title: Mixed Neuron Culture, CRISPRi region r6, replicate 1

description:
Library name: r6 1
Column in counts file: r6_1


title: Mixed Neuron Culture, CRISPRi region r9, replicate 2

description:
Library name: r9 2
Column in counts file: r9_2


title: Mixed Neuron Culture, CRISPRi region r8, replicate 1

description:
Library name: r8 1
Column in counts file: r8_1


title: Mixed Neuron Culture, CRISPRi region r5, replicate 5

description:
Library name: r5 5
Column in counts file: r5_5


title: Mixed Neuron Culture, CRISPRi region r5, replicate 3

description:
Library name: r5 3
Column in counts file: r5_3


title: Mixed Neuron Culture, CRISPRi region r5, replicate 4

description:
Library name: r5 4
Column in counts file: r5_4


title: Mixed Neuron Culture, CRISPRi region r5, replicate 2

description:
Library name: r5 2
Column in counts file: r5_2


title: Mixed Neuron Culture, CRISPRi region r6, replicate 5

description:
Library name: r6 5
Column in counts file: r6_5


title: Mixed Neuron Culture, CRISPRi region r5, replicate 1

description:
Library name: r5 1
Column in counts file: r5_1


title: Mixed Neuron Culture, CRISPRi region r4, replicate 3

description:
Library name: r4 3
Column in counts file: r4_3


title: Mixed Neuron Culture, CRISPRi region r6, replicate 4

description:
Library name: r6 4
Column in counts file: r6_4


title: Mixed Neuron Culture, CRISPRi region r6, replicate 3

description:
Library name: r6 3
Column in counts file: r6_3


title: Mixed Neuron Culture, CRISPRi region r4, replicate 2

description:
Library name: r4 2
Column in counts file: r4_2


title: Mixed Neuron Culture, CRISPRi region r4, replicate 4

description:
Library name: r4 4
Column in counts file: r4_4


title: Mixed Neuron Culture, CRISPRi region r4, replicate 5

description:
Library name: r4 5
Column in counts file: r4_5


title: Mixed Neuron Culture, CRISPRi region r4, replicate 1

description:
Library name: r4 1
Column in counts file: r4_1


title: Mixed Neuron Culture, CRISPRi region r3, replicate 5

description:
Library name: r3 5
Column in counts file: r3_5


title: Mixed Neuron Culture, CRISPRi region r6, replicate 2

description:
Library name: r6 2
Column in counts file: r6_2


title: Mixed Neuron Culture, CRISPRi region r3, replicate 1

description:
Library name: r3 1
Column in counts file: r3_1


title: Mixed Neuron Culture, CRISPRi region r2, replicate 1

description:
Library name: r2 1
Column in counts file: r2_1


title: Mixed Neuron Culture, CRISPRi region r1, replicate 5

description:
Library name: r1 5
Column in counts file: r1_5


title: Mixed Neuron Culture, CRISPRi region r3, replicate 3

description:
Library name: r3 3
Column in counts file: r3_3


title: Mixed Neuron Culture, CRISPRi region r1, replicate 4

description:
Library name: r1 4
Column in counts file: r1_4


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 9

description:
Library name: MAPT promoter 9
Column in counts file: prom_9


title: Mixed Neuron Culture, CRISPRi region r2, replicate 3

description:
Library name: r2 3
Column in counts file: r2_3


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 5

description:
Library name: MAPT promoter 5
Column in counts file: prom_5


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 8

description:
Library name: MAPT promoter 8
Column in counts file: prom_8


title: Mixed Neuron Culture, CRISPRi region r3, replicate 2

description:
Library name: r3 2
Column in counts file: r3_2


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 7

description:
Library name: MAPT promoter 7
Column in counts file: prom_7


title: Mixed Neuron Culture, CRISPRi region r2, replicate 4

description:
Library name: r2 4
Column in counts file: r2_4


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 3

description:
Library name: MAPT promoter 3
Column in counts file: prom_3


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 4

description:
Library name: MAPT promoter 4
Column in counts file: prom_4


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 2

description:
Library name: MAPT promoter 2
Column in counts file: prom_2


title: Mixed Neuron Culture, CRISPRi region r1, replicate 3

description:
Library name: r1 3
Column in counts file: r1_3


title: Mixed Neuron Culture, CRISPRi region r2, replicate 2

description:
Library name: r2 2
Column in counts file: r2_2


title: Mixed Neuron Culture, CRISPRi region r3, replicate 4

description:
Library name: r3 4
Column in counts file: r3_4


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 7

description:
Library name: Safe Harbor 7
Column in counts file: safeharbor_7


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 6

description:
Library name: MAPT promoter 6
Column in counts file: prom_6


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 9

description:
Library name: Safe Harbor 9
Column in counts file: safeharbor_9


title: Mixed Neuron Culture, CRISPRi region r1, replicate 2

description:
Library name: r1 2
Column in counts file: r1_2


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 8

description:
Library name: Safe Harbor 8
Column in counts file: safeharbor_8


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 6

description:
Library name: Safe Harbor 6
Column in counts file: safeharbor_6


title: Mixed Neuron Culture, CRISPRi MAPT promoter, replicate 1

description:
Library name: MAPT promoter 1
Column in counts file: prom_1


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 5

description:
Library name: Safe Harbor 5
Column in counts file: safeharbor_5


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 2

description:
Library name: Safe Harbor 2
Column in counts file: safeharbor_2


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 4

description:
Library name: Safe Harbor 4
Column in counts file: safeharbor_4


title: Mixed Neuron Culture, CRISPRi region r2, replicate 5

description:
Library name: r2 5
Column in counts file: r2_5


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 3

description:
Library name: Safe Harbor 3
Column in counts file: safeharbor_3


title: Mixed Neuron Culture, CRISPRi AAV Safe Harbor, replicate 1

description:
Library name: Safe Harbor 1
Column in counts file: safeharbor_1


title: Whole blood, donor D17B

city: Oxford

first: Matthew

last: Baxter

address: John Radcliffe Hospital

department: RDM

country: United Kingdom

institute: University of Oxford

description: Library name: D17B

data_processing:
Adapters were trimmed using cutadapt, reads were mapped using HISAT2, and duplicates were removed using samtools.
Read count tables were generated using FeatureCounts.
Assembly: Hg38
Supplementary files format and content: CSV files contain normalised read counts

source_name: Whole blood

extract_protocol:
RNA was extracted with TRIZOL
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Whole blood


title: Mixed Neuron Culture, CRISPRi region r1, replicate 1

description:
Library name: r1 1
Column in counts file: r1_1


title: Whole blood, donor D16B

description: Library name: D16B


title: Whole blood, donor D14A

description: Library name: D14A


title: Whole blood, donor D20A

description: Library name: D20A


title: Whole blood, donor D18B

description: Library name: D18B


title: Whole blood, donor D14B

description: Library name: D14B


title: Whole blood, donor D17A

description: Library name: D17A


title: Whole blood, donor D19A

description: Library name: D19A


title: Whole blood, donor D13A

description: Library name: D13A


title: Whole blood, donor D18A

description: Library name: D18A


title: Whole blood, donor D10B

description: Library name: D10B


title: Whole blood, donor D16A

description: Library name: D16A


title: Whole blood, donor D08B

description: Library name: D08B


title: Whole blood, donor D20B

description: Library name: D20B


title: Whole blood, donor D19B

description: Library name: D19B


title: Whole blood, donor D10A

description: Library name: D10A


title: Whole blood, donor D09B

description: Library name: D09B


title: Whole blood, donor D11A

description: Library name: D11A


title: Whole blood, donor D12B

description: Library name: D12B


title: Whole blood, donor D08A

description: Library name: D08A


title: Whole blood, donor D12A

description: Library name: D12A


title: Whole blood, donor D13B

description: Library name: D13B


title: Whole blood, donor D11B

description: Library name: D11B


title: Whole blood, donor D15B

description: Library name: D15B


title: Whole blood, donor D15A

description: Library name: D15A


title: Whole blood, donor D06A

description: Library name: D06A


title: Whole blood, donor D07B

description: Library name: D07B


title: Whole blood, donor D05A

description: Library name: D05A


title: Whole blood, donor D06B

description: Library name: D06B


title: Whole blood, donor D04A

description: Library name: D04A


title: Whole blood, donor D05B

description: Library name: D05B


title: MOLM13_SGI7079_03

city: Shenyang

first: Yan

address: No. 120 Dongling Road, Shenhe District

department: Plant Protection College

institute: Shenyang Agricultural University

description:
Library name: MOLM13_SGI7079_03
wt, replicate biosample 3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include ene count for each Sample

organism: Nicotiana tabacum

source_name: leaf

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: leaf

value: wt

value: Rhizoctonia solani AG3-TB


title: Whole blood, donor D07A

description: Library name: D07A


title: Whole blood, donor D03A

description: Library name: D03A


title: MOLM13_DMSO_02

description:
Library name: MOLM13_DMSO_02
NtWRKY70 over_expression group, replicate biosample 2

value: NtWRKY70 over_expression


title: Whole blood, donor D03B

description: Library name: D03B


title: MOLM13_SGI7079_01

description:
Library name: MOLM13_SGI7079_01
wt, replicate biosample 1


title: Whole blood, donor D02B

description: Library name: D02B


title: HNEC ALI RV1A+TPCA1 rep 2

city: New Haven

first: Bao

last: Wang

state: Connecticut

address: 333 Cedar Street

department: Deparment of Laboratory Medicine

institute: Yale University

description:
Library name: BW10
raw counts in BW10_HTSeq_counts.txt

data_processing:
Fasta files passed quality control by FastQC and were trimmed by Trim Galore.
Alignment was done using HISAT2 on GRCh38.09 genome. For viral reads, alignment was done using BowTie2 to HRV-1A genome (KC894166.1).
Transcript counting was performed using HTSeq-count.
Analysis on gene expression level was performed in R with DESeq2. Normalized count matrix is generated with DESeq2.
Assembly: GRCh38.09, KC894166.1
Supplementary files format and content: Comma delimited file includes normalized counts for all sample. Tab delimited file includes viral read counts for all sample.
Supplementary files format and content: "HTSeq_counts" txt files contains raw counts for each sample.

organism:
Homo sapiens
Human rhinovirus 1A

source_name: air-liquid interface organoid culture

growth_protocol: Primary nasal human airway epithelial cells from healthy adult donors were obtained from PromoCell. Cells were first expanded in ExPlus media (Stemcell Technologies) and then seeded in 0.4 µm pore 6.5 mm trans-well inserts (Costar, Corning). After air-lift, cells were maintained in PneumaCult ALI basal media (Stemcell Technologies) according to the manufacturer’s instructions, with 1:5 reduced hydrocortisone. Cells were cultured at air-liquid interface for 4 weeks for differentiation before they displayed beating cilia and mucus production.

extract_protocol:
Total RNA was extracted using the Aurum Total RNA Mini Kit (Bio- Rad) according to the manufacturer’s protocol.
poly-A selection

treatment_protocol: Cells were pretreated with media containing 6uM BX795 (Cayman Chemical), 25uM TPCA-1 or plain media 1 day before infection. To infect, cells were washed from the apical surface 3 times by pipitting 200uL warm PBS. Inoculum with MOI = 0.25 (assuming 1 million cells each culture well) was then applied apically in 200uL PBS with 0.1% Bovine Serum Albumin and infect for 40min to 1h. Cells were washed again with warm PBS after infection to remove residual virus. The infected cells were then incubated at 35°C. 200uL additional media was added to the basolateral chamber on day 3 post infection, with or without the corresponding drug treatment. Samples were collected 5 days post infection.

value: air-liquid interface organoid culture

value: primary human nasal epithelial cells

tag: age

value: 34 years old

value: female

value: TPCA1 25uM

tag: infection

value: RV1A MOI=0.25

tag: batch


title: Whole blood, donor D01B

description: Library name: D01B


title: MOLM13_DMSO_01

description:
Library name: MOLM13_DMSO_01
NtWRKY70 over_expression group, replicate biosample 1


title: No TRMT61B enzyme, DART, monosome, rep 4, Induro

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

description: Library name: NE_DART_80S_6

data_processing:
Raw fastq files were deconvoluted with Flexbar v3.5.0
Adapter trimming, removal of UMIs, and deduplication was carried out with BBDuk v39.49
Reads were aligned to m1Agenome_EndogenousPool.fasta with STAR v2.7.11a-GCC-12.2.0
Alignment counting and pileup was carried out with BBMap v39.52
Bamfiles were generated using SAMtools v1.21-GCC-12.2.0
Comparisons of transcript presence in input and 80S fractions for all enzyme treatments were carried out using DESeq2 v1.44.0
Assembly: synthetically designed 5'UTR/CDS human mRNA pool, as described in Lewis et al. 2025
Supplementary files format and content: csv files include normalized read counts for each comparison

source_name: synthetic pool of human and viral sequences

growth_protocol: RNA was in vitro transcribed using CleanCap AG (Trilink, N-7113) using the MEGAshortscript T7 transcription kit (Invitrogen, AM1354).

extract_protocol:
Following DART in vitro translation, 80S-bound RNA was isolated by fractionation on a sucrose gradient and purified with a hot phenol extraction as described in Lewis et al. 2025.
Pooled input RNA (post-methylation, treatments combined) and 80S-bound RNA were reverse transcribed using Induro RT (NEB, M0681) using oKA210 primer for 60C for 1 hour. cDNA was then purified on an 8% denaturing PAGE gel. 0.8 uL of 100 uM DART_5’Adapter was then ligated using High Concentration T4 RNA Ligase (NEB, M0437M) overnight, and then libraries were amplified using an Illumina i5 primer and oKA182 for an initial round of PCR, followed by purification with a Monarch Spin PCR & DNA Cleanup Kit (NEB, T1130S) and final PCR with i5 and i7 barcoded primers.

treatment_protocol: In vitro transcribed RNA was methylated with purified TRMT61B protein with no, low, or high enzyme levels (NE/LE/HE). RNA was then purified with a 6% TBE-Urea gel and RNA from the three conditions combined in equimolar amounts. In vitro translation reactions with HeLa lysate were set up with 40 pmol of pooled RNA as described in Lewis et al. 2025 for Direct Analysis of Ribosome Targeting (DART)


title: Whole blood, donor D09A

description: Library name: D09A


title: HNEC ALI RV1A+BX795+TPCA1 rep 2

description:
Library name: BW08
raw counts in BW08_HTSeq_counts.txt

value: BX795 6uM + TPCA1 25uM


title: MOLM13_DMSO_03

description:
Library name: MOLM13_DMSO_03
NtWRKY70 over_expression group, replicate biosample 3


title: No TRMT61B enzyme, DART, monosome, rep 3, Induro

description: Library name: NE_DART_80S_5

value: synthetic pool of human and viral sequences


title: Whole blood, donor D02A

description: Library name: D02A


title: No TRMT61B enzyme, DART, monosome, rep 1, Induro

description: Library name: NE_DART_80S_3


title: Whole blood, donor D01A

description: Library name: D01A


title: MOLM13_SGI7079_02

description:
Library name: MOLM13_SGI7079_02
wt, replicate biosample 2


title: No TRMT61B enzyme, DART, monosome, rep 2, Induro

description: Library name: NE_DART_80S_4


title: HNEC ALI RV1A+BX795+TPCA1 rep 1

description:
Library name: BW07
raw counts in BW07_HTSeq_counts.txt


title: Whole blood, donor D04B

description: Library name: D04B


title: HNEC ALI RV1A+BX795 rep 2

description:
Library name: BW06
raw counts in BW06_HTSeq_counts.txt

value: BX795 6uM


title: HNEC ALI RV1A+TPCA1 rep 1

description:
Library name: BW09
raw counts in BW09_HTSeq_counts.txt


title: No TRMT61B enzyme, DART, input, rep 3, Induro

description: Library name: NE_DART_Input_3


title: No TRMT61B enzyme, DART, input, rep 2, Induro

description: Library name: NE_DART_Input_2


title: HNEC ALI RV1A rep 2

description:
Library name: BW04
raw counts in BW04_HTSeq_counts.txt

value: 2024 Feb 8th


title: No TRMT61B enzyme, DART, input, rep 1, Induro

description: Library name: NE_DART_Input_1


title: HNEC ALI RV1A rep 1

description:
Library name: BW03
raw counts in BW03_HTSeq_counts.txt


title: Low TRMT61B enzyme, DART, monosome, rep 2, Induro

description: Library name: LE_DART_80S_4


title: Low TRMT61B enzyme, DART, monosome, rep 3, Induro

description: Library name: LE_DART_80S_5


title: Low TRMT61B enzyme, DART, monosome, rep 4, Induro

description: Library name: LE_DART_80S_6


title: snRNA-seq_NICM, T1346

city: Saint Louis

first: Haewon

last: Shin

state: MO

address: 660 S Euclid

institute: Washington University School of Medicine in St. Louis

description: Library name: T1346

library_source: transcriptomic single cell

data_processing:
Find in Methods Shin and Nikhil et al, 2026
Assembly: GRCh38
Supplementary files format and content: Matrix.mtx.gz - Gene × cell UMI count matrix in Matrix Market format, filtered for high-quality cells. Rows are genes, columns are cells, values are UMI counts. Barcodes.tsv.gz - List of cell barcodes corresponding to the columns of the filtered UMI count matrix. One barcode per line. Features.tsv.gz - Gene annotation file corresponding to the rows of the filtered UMI count matrix. Columns are: gene ID, gene symbol, and optionally feature type.

molecule: nuclear RNA

source_name: human left ventricle

extract_protocol:
Frozen myocardial tissue from left ventricular assist device (LVAD) cores or the corresponding region from the apex of explanted donors were minced with a razor blade and dissociated with a plastic pestle in Chromium Nuclei Isolation Kit Lysis Buffer (10X Genomics, Pleasanton, CA). Samples were incubated on ice for 10 minutes, and the tissue suspension was pipetted onto the Nuclei Isolation Column and Collection Tube and centrifuged at 16,000 rcf for 20 seconds at 4°C. Flow-through in the Collection Tube was centrifuged again at 1,000 rcf for 3 minutes to pellet the nuclei and resuspended in 300 μl of Wash and Resuspension Buffer before staining with 1 μl  DRAQ5 (5 mM solution, ThermoFisher Scientific) and incubating on ice for 10 minutes. DRAQ5+ nuclei were sorted into Nuclei Wash Buffer on a BD FACS Melody (BD Biosciences) using a 100 μm nozzle. Recovered nuclei were centrifuged again under the above parameters and were gently resuspended in Nuclei Wash Buffer to a target concentration of 1,000 nuclei μl−1. Nuclei were counted on a hemocytometer and concentration was adjusted as necessary. Following flow cytometry, sorted DRAQ5+ nuclei were centrifuged at 2,000 rcf for 5 minutes at 4°C, and nuclei were resuspended in 100 µl 1X PBS, prior to loading into the 10X Chromium system.
After manually counting nuclei using Trypan Blue, based on the concentration, samples were loaded at a volume to target 20,000 nuclei. Libraries were prepared using the manufacturers’ instructions-10X 3’ v4 GEM-X (Chromium GEM-X Single Cell 3’ Reagent Kits v4 Document Number CG000731 Rev B August 2024) or 10X 5’ v3 GEM-X (Chromium GEM-X Single Cell 5’ Reagent Kits v3 Document Number CG000733 Rev A March 2024) kits (10X Genomics)- and sequenced on a NovaSeqX (Illumina, San Diego, CA) instrument following manufacturers’ guidelines: 28 X 10 X 10 X 90 [read1 X i7 index X i5 index X read2].

value: human left ventricle


title: snRNA-seq_NICM, T1227

description: Library name: T1227


title: Low TRMT61B enzyme, DART, monosome, rep 1, Induro

description: Library name: LE_DART_80S_3


title: KD062, KD071, MP099, MP103, MP105, MP108, MP118, MP126, NS056, NS068, NS071

city: London

first: James

middle: Royce

last: Barnacle

state: London

address: Francis Crick Institute, 1 Midland Road

department: Infectious Disease

institute: Imperial College London

description:
Library name: Multiplex 3
16-plex

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger v9.0.1 aligned to the human GRCh38 genome. Multiplex 1 used a 4-plex kit (BC001-004) and Multiplex 2 and 3 used a 16-plex kit (BC001-016). The barcode used for each sample can be found in the demultiplexing_barcodes.txt file.
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: CellRanger-generated HDF5 format with expression values and associated gene and cell annotations

molecule: other

source_name: Cerebrospinal fluid

extract_protocol:
CSF was obtained from an LP performed at day 7 following enrolment as part of the INTENSE-TBM trial (47). Up to 6 ml CSF was collected in a 15 ml falcon tube at the bedside after prioritising necessary clinical investigations. Samples were transferred to the biosafety level 3 laboratory at 4˚C and processed within two hours of collection. Fresh CSF was centrifuged at 400 RCF for 10 minutes at 4˚C and supernatant removed.
Cells were fixed in a 4% formaldehyde fixative solution, as described in the Demonstrated Protocols CG000478 and CG000553 and using Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics PN-1000414), then stored at -80˚C for up to 12 months. Fixed samples were processed following the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples Protocol (10x Genomics CG000527, Revision A) using the Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 4 BC  (10x Genomics PN-1000475) and 4 rxns x 16 BC (PN-1000476). Gene expression was measured using barcoded probe pairs designed to hybridise to mRNA specifically. Using a microfluidic chip, the fixed and probe-hybridised single cell suspensions were partitioned into nanolitre-scale Gel Beads-in-emulsion (GEMs). A pool of ~737,000 10x GEM Barcodes was sampled separately to index the contents of each partition. Inside the GEMs, probes were ligated and the 10x GEM Barcode was added, and all ligated probes within a GEM share a common 10x GEM Barcode. Barcoded and ligated probes were then pre-amplified in bulk, after which gene expression libraries were generated (User Guide: CG000527, Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples) and sequenced (NovaSeq 6000, NovaSeq X. Sequencing read configuration: 28-10-10-90). Samples were processed and sequenced in three batches. All samples in the same batch were multiplexed using sample-specific probe sets and sequenced together. Two samples in batch 3 were double barcoded to maximise use of the 16-plex kit. These samples therefore had twice the number of cells sequenced.

value: Cerebrospinal fluid


title: snRNA-seq_NICM, T1342

description: Library name: T1342


title: Low TRMT61B enzyme, DART, input, rep 3, Induro

description: Library name: LE_DART_Input_3


title: High TRMT61B enzyme, DART, monosome, rep 4, Induro

description: Library name: HE_DART_80S_6


title: KD050, KD051, KD057, KD064, MP081, MP082, MP092, MP109, NS043, NS060

description:
Library name: Multiplex 2
16-plex


title: Low TRMT61B enzyme, DART, input, rep 1, Induro

description: Library name: LE_DART_Input_1


title: High TRMT61B enzyme, DART, monosome, rep 3, Induro

description: Library name: HE_DART_80S_5


title: snRNA-seq_donor, D1118

description: Library name: D1118


title: snRNA-seq, NICM, T1346

description: Library name: T1346

data_processing:
Find in Methods Shin and Nikhil et al, 2026
Assembly: GRCh38
Supplementary files format and content: analyze_incl_introns_genematrix.csv: Processed gene × cell count matrix including intronic reads for single nuclei. Rows correspond to genes, columns to individual nuclei, and values represent UMI counts per gene per nucleus.  Gene_info_incl_introns.csv: Gene annotation file corresponding to the rows of the processed gene × cell count matrix. Includes gene IDs and gene symbols, and optionally feature type. Contains intronic features used in single-nucleus RNA-seq analysis.

extract_protocol:
Frozen myocardial tissue from left ventricular assist device (LVAD) cores or the corresponding region from the apex of explanted donors were minced with a razor blade and dissociated with a plastic pestle in Chromium Nuclei Isolation Kit Lysis Buffer (10X Genomics, Pleasanton, CA). Samples were incubated on ice for 10 minutes, and the tissue suspension was pipetted onto the Nuclei Isolation Column and Collection Tube and centrifuged at 16,000 rcf for 20 seconds at 4°C. Flow-through in the Collection Tube was centrifuged again at 1,000 rcf for 3 minutes to pellet the nuclei and resuspended in 300 μl of Wash and Resuspension Buffer before staining with 1 μl  DRAQ5 (5 mM solution, ThermoFisher Scientific) and incubating on ice for 10 minutes. DRAQ5+ nuclei were sorted into Nuclei Wash Buffer on a BD FACS Melody (BD Biosciences) using a 100 μm nozzle. Recovered nuclei were centrifuged again under the above parameters and were gently resuspended in Nuclei Wash Buffer to a target concentration of 1,000 nuclei μl−1. Nuclei were counted on a hemocytometer and concentration was adjusted as necessary. Following flow cytometry, sorted DRAQ5+ nuclei were centrifuged at 2,000 rcf for 5 minutes at 4°C, and nuclei were resuspended in 100 µl 1X PBS, prior to loading into the ICELL8 cx system.
Libraries were prepared using the manufacturers’ instructions- SMART-Seq Pro (ICELL8 cx Single-Cell System User Manual kit (Takara Bio, San Jose, CA)-and sequenced on a NovaSeqX (Illumina) instrument following manufacturers’ guidelines: 151 X 8 X 8 X 151 [read1 X i7 index X i5 index X read2].


title: HNEC ALI RV1A+BX795 rep 1

description:
Library name: BW05
raw counts in BW05_HTSeq_counts.txt


title: snRNA-seq_donor, D1192

description: Library name: D1192


title: Low TRMT61B enzyme, DART, input, rep 2, Induro

description: Library name: LE_DART_Input_2


title: High TRMT61B enzyme, DART, monosome, rep 2, Induro

description: Library name: HE_DART_80S_4


title: snRNA-seq, NICM, T1227

description: Library name: T1227


title: High TRMT61B enzyme, DART, monosome, rep 1, Induro

description: Library name: HE_DART_80S_3


title: High TRMT61B enzyme, DART, input, rep 2, Induro

description: Library name: HE_DART_Input_2


title: snRNA-seq_donor, D1340

description: Library name: D1340


title: High TRMT61B enzyme, DART, input, rep 1, Induro

description: Library name: HE_DART_Input_1


title: snRNA-seq, NICM, T1342

description: Library name: T1342


title: High TRMT61B enzyme, DART, input, rep 3, Induro

description: Library name: HE_DART_Input_3


title: No TRMT61B enzyme, small reaction size, rep 1, round 1, uMRT

description: Library name: NE1_round1

data_processing:
Raw fastq files were deconvoluted with Flexbar v3.5.0
Adapter trimming, removal of UMIs, and deduplication was carried out with BBDuk v39.49
Reads were aligned to m1Agenome_EndogenousPool.fasta with STAR v2.7.11a-GCC-12.2.0
Alignment counting and pileup was carried out with BBMap v39.52
Bamfiles were generated using SAMtools v1.21-GCC-12.2.0
A mutational counts table were generated using fastq2EZbakR
An ad-hoc cutoff-based analysis pipeline was used to identify sites with significantly increased mutation rates in low/high enzyme treatment vs. no enzyme treatment samples.
Assembly: synthetically designed 5'UTR/CDS human mRNA pool, as described in Lewis et al. 2025
Supplementary files format and content: csv files include all single nucleotide sites for either high (HE) or low enzyme (LE) treatments that have at least 1% mutation rate in at least 2 of 3 replicates, with average mutation rates and p-values for statistical comparisons included

extract_protocol:
RNA was purified by gel extraction from a 6% TBE-Urea gel (Invitrogen). Gel slices were excised and incubated for 4 hours at RT in 200 uL gel elution buffer (20 mM Tris pH 7.5, 1 mM EDTA, 250 mM sodium acetate, 0.25% SDS), including 3X freeze-thaw on dry ice for 15 minutes each, followed by TRIzol extraction and purification
RNA was were reverse transcribed using ultraMarathonRT (RNAConnect) for 3 hours at 42C. cDNA was then purified on an 8% denaturing PAGE gel. 0.8 uL of 100 uM DART_5’Adapter was then ligated using High Concentration T4 RNA Ligase (NEB, M0437M) overnight, and then libraries were amplified using an Illumina i5 primer and oKA182 for an initial round of PCR, followed by purification with a Monarch Spin PCR & DNA Cleanup Kit (NEB, T1130S) and final PCR with i5 and i7 barcoded primers.

treatment_protocol: RNA was incubated with no enzyme, low, or high concentrations of purified TRMT61B in 1X methyltransferase buffer (10 mM HEPES pH 7.4, 100 mM KCl, 1.5 mM MgCl2, 1 mM DTT), with addition of 40 U Protector RNAse inhibitor (Roche), 1 mM d3SAM (CDN Isotopes), and up to 4% glycerol. One large (640-680 uL) reaction was carried out (with the majority for use in DART reactions) and two additional 40 uL reactions were carried out for additional TRMT61B methylation site identification replicates.


title: snRNA-seq, donor, D1118

description: Library name: D1118


title: No TRMT61B enzyme, small reaction size, rep 2, round 1, uMRT

description: Library name: NE2_round1


title: vim_high_le_ls_pt08

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: Library name: DSP-1001660008953-B-B06

data_processing:
The generated FASTQ files were converted to output DCC files using the GeoMx NGS Pipeline v2.5.1.
Assembly: Hs_R_NGS_WTA_v1.0.pkc (Nanostring provided probe conversion file)
Supplementary files format and content: probe count files (.dcc). Files include the read count for each of the probes, corresponding to a unique gene.
Library strategy: Spatial Transcriptomics

source_name: Skin

growth_protocol: Samples are biopsies

extract_protocol:
Prior to immunohistochemical staining, sections were deparaffinized and then rehydrated in a series of graded ethanols. Subsequently, antigen unmasking was accomplished using heated Tris-ethylene glycol tetraacetic acid buffer (pH 9) at pre-boiling temperature. The antibodies used were CD3, CD4, CD8, CD103, CD207, RORγt, FOXP3, Ki67, and MPO.
Library preparation was carried out according to the manufacturer's protocol (Nanostring Technologies).

treatment_protocol: Formalin-fixed, paraffin-embedded skin biopsies from 12 patients with psoriasis were analyzed using the GeoMx to capture spatially resolved high-plex RNA gene expression data.

value: Skin

tag: condition

value: Lesional


title: Low TRMT61B enzyme, small reaction size, rep 2, round 1, uMRT

description: Library name: LE2_round1


title: basal_layer_le_ls_pt08

description: Library name: DSP-1001660008953-B-B04


title: vim_low_le_ls_pt08

description: Library name: DSP-1001660008953-B-B07


title: High TRMT61B enzyme, large reaction size, rep 3, round 1, uMRT

description: Library name: HE3_round1


title: Low TRMT61B enzyme, small reaction size, rep 1, round 1, uMRT

description: Library name: LE1_round1


title: High TRMT61B enzyme, small reaction size, rep 2, round 1, uMRT

description: Library name: HE2_round1


title: derm_pap_le_ls_pt08

description: Library name: DSP-1001660008953-B-B05


title: vim_low_abdomen_nl_pt08

description: Library name: DSP-1001660008953-B-B02

value: Non-lesional


title: epidermis_le_ls_pt08

description: Library name: DSP-1001660008953-B-B03

value: epidermis


title: snRNA-seq, donor, D1340

description: Library name: D1340


title: basal_layer_abdomen_nl_pt08

description: Library name: DSP-1001660008953-B-A12


title: vim_high_abdomen_nl_pt08

description: Library name: DSP-1001660008953-B-B01


title: epidermis_abdomen_nl_pt08

description: Library name: DSP-1001660008953-B-A11


title: Low TRMT61B enzyme, large reaction size, rep 3, round 1, uMRT

description: Library name: LE3_round1


title: U2OS, Control overexpression, Input, rep 2

description: Library name: ControlOE_2_Input

data_processing:
Sequencing reads were trimmed using Trimmomatic v0.39
Trimmed sequence reads were mapped to GRCh38 using STAR v2.7.11a
Read counts were determined using Salmon v1.4.0
Normalized read counts were calculated using DESeq2 v1.44.0
A mutational counts table were generated using fastq2EZbakR and aligned bams
Differential mutational analysis was carried out using bakR
Assembly: hg38
Supplementary files format and content: csv files labeled "Counts" include normalized read counts for each comparison (61B IP vs Input or Control IP vs Input)
Supplementary files format and content: csv files labeled "bakR" include all single nucleotide sites called by bakR as have different mutation rates in TRMT61B overexpression IP vs Input samples

growth_protocol: U2OS cells were maintained in McCoy’s 5A Medium (Gibco, 16600082) with 10% fetal bovine serum and 1X penicillin-streptomycin at 37°C under a humidified atmosphere with 5% CO2. During transfection, cells were maintained in antibiotic-free media

extract_protocol:
Cells were lysed in Trizol and RNA was extracted following manufacturer instructions. Prior to m1A-IP, RNA was polyA-selected using the NEBNext® High Input Poly(A) mRNA Isolation Module (NEB, E3370S). An m1A-immunoprecipitation (IP) was carried out using polyA-selected RNA and an m1A antibody(Abcam, ab208196). In short, 1.5 ug of antibody was coupled to Dynabeads Protein G (Invitrogen, 10004D) for 1 hour, then 1.5 ug of RNA was immunoprecipiated with the antibody-bead complex. RNA was eluted from the beads using Trizol reagent and purified.
Libraries were prepared  using input and IP samples using the TruSeq Stranded mRNA Library Prep kit (Illumina, 20020594), following manufacturer instructions.

treatment_protocol: The day before transfection, 1.5 million cells were plated in 15 cm2 dishes. The next day, cells were transfected using Lipofectamine 3000 (Invitrogen) and 15 ug DNA (TRMT61B-FLAG or control overexpression plasmid), following manufacturer protocols. Cells were harvested after 48 hours.

value: osteosarcoma cultured cells

value: control plasmid overexpression for 48 hours


title: U2OS, Control overexpression, Input, rep 1

description: Library name: ControlOE-1_Input


title: High TRMT61B enzyme, small reaction size, rep 1, round 1, uMRT

description: Library name: HE1_round1


title: U2OS, Control overexpression, IP, rep 2

description: Library name: ControlOE-2_IP

value: control plasmid overexpression for 48 hours, m1A-IP


title: U2OS, Control overexpression, IP, rep 1

description: Library name: ControlOE-1_IP


title: basal_layer_scalp_ls_pt08

description: Library name: DSP-1001660008953-B-A08


title: vim_high_scalp_ls_pt08

description: Library name: DSP-1001660008953-B-A09


title: U2OS, TRMT61B overexpression, Input, rep 2

description: Library name: 61BOE-2_Input

value: TRMT61B overexpression for 48 hours


title: epidermis_scalp_ls_pt08

description: Library name: DSP-1001660008953-B-A07


title: No TRMT61B enzyme, large reaction size, rep 3, round 1, uMRT

description: Library name: NE3_round1


title: U2OS, TRMT61B overexpression, Input, rep 1

description: Library name: 61BOE-1_Input


title: U2OS, TRMT61B overexpression, IP, rep 2

description: Library name: 61BOE-2_IP

value: TRMT61B overexpression for 48 hours, m1A-IP


title: vim_low_scalp_ls_pt08

description: Library name: DSP-1001660008953-B-A10


title: U2OS, TRMT61B overexpression, IP, rep 1

description: Library name: 61BOE-1_IP


title: snRNA-seq, donor, D1192

description: Library name: D1192


title: derm_pap_ue_ls_pt08

description: Library name: DSP-1001660008953-B-A06


title: epidermis_ue_ls_pt08

description: Library name: DSP-1001660008953-B-A02


title: vim_high_ue_ls_pt08

description: Library name: DSP-1001660008953-B-A04


title: vim_low_ue_ls_pt08

description: Library name: DSP-1001660008953-B-A05


title: basal_layer_ue_ls_pt08

description: Library name: DSP-1001660008953-B-A03


title: basal_layer_scalp_ls_pt05

description: Library name: DSP-1001660008953-B-C11


title: BJAB_20_R3: BJAB cells, 20µM drug treatment, repeat 3

city: Columbus

first: Dawei

last: Zhou

state: OH

address: 400 W 12th Ave, Wiseman Hall 351C

department: Pathology

institute: The Ohio State University Wexner Medical Center

description: Library name: Sample 12

data_processing:
Raw reads were retrieved by fastp, trimmed with adapters, and aligned to human genome (GRCh38.p13) with HISAT2 aligner. Uniquely aligned reads were submitted to gencode.v39 annotation as inputs for mapping. Identification of differential gene expression (DEG) was performed using DESeq2 (Love et al., 2014). Adjusted p value < 0.05 was the criteria used for DEG filtering.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited files include reads counts for each sample

source_name: cell line

extract_protocol:
Total RNA samples were extracted by using the NucleoSpin RNA isolation kit (MACHEREY-NAGEL) following manufacturer’s instructions.
Total RNA sample were submitted to Novogene for QC, polyA selection, multiplexing and library preparation.

value: cell line

value: BJAB

value: Burkitt lymphoma B cells


title: epidermis_scalp_ls_pt05

description: Library name: DSP-1001660008953-B-C09


title: BCBL1_C_R3: BCBL-1 cells, control treatment, repeat 3

description: Library name: Sample 9

value: Primary effusion lymphoma B cells


title: derm_pap_scalp_ls_pt05

description: Library name: DSP-1001660008953-B-C10


title: vim_low_abdomen_nl_pt05

description: Library name: DSP-1001660008953-B-C08


title: BCBL1_20_R2: BCBL-1 cells, 20µM drug treatment, repeat 2

description: Library name: Sample 6


title: basal_layer_abdomen_nl_pt05

description: Library name: DSP-1001660008953-B-C06


title: vim_high_abdomen_nl_pt05

description: Library name: DSP-1001660008953-B-C07


title: BCBL1_20_R3: BCBL-1 cells, 20µM drug treatment, repeat 3

description: Library name: Sample 10


title: BCBL1_20_R1: BCBL-1 cells, 20µM drug treatment, repeat 1

description: Library name: Sample 2


title: BCBL1_C_R2: BCBL-1 cells, control treatment, repeat 2

description: Library name: Sample 5


title: BJAB_20_R2: BJAB cells, 20µM drug treatment, repeat 2

description: Library name: Sample 8


title: BJAB_C_R1: BJAB cells, control treatment, repeat 1

description: Library name: Sample 3


title: Human mesangial cells, CitH3 4, 48hr

city: Bethesda

first: Kan

last: Jiang

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

description: Library name: CitH3_rep4_48hr

data_processing:
Raw sequencing data were processed with bcl2fastq (v2.20.0) to generate FASTQ files. Reads were aligned to the human reference genome (hg38) using STAR (v2.7.8a). Gene-level counts were quantified in Partek Flow using the Partek E/M annotation model and rounded to integers. Differential expression analysis was then performed with DESeq2
Assembly: hg38
Supplementary files format and content: Excel files include raw counts values for each samples

source_name: mesangial cells

growth_protocol: Primary human MCs were seeded at a density of 5 × 10⁴ cells per well in 12-well plates and cultured in RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 10% FBS for 24 hours at 37 °C. The medium was then replaced with RPMI-1640 medium containing 10% KnockOut Serum Replacement (Thermo Fisher Scientific) and the cells were cultured for an additional 24 hours.

extract_protocol:
Following stimulation, cells were washed with PBS and lysed in 500 µL of TRIzol Reagent (Thermo Fisher Scientific) for RNA extraction. Total RNA was isolated followed by column-based purification with RNA Clean & Concentrator-5 Kit (Zymo Research).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). cDNA concentrations were quantified using the PicoGreen dsDNA Assay (Thermo Fisher Scientific), normalized to 3 nM, pooled, and sequenced on the Illumina NovaSeq X Plus platform.

treatment_protocol: After washing with PBS, the cells were stimulated with either 50 µg spontaneously generated NETs for 72 hours or 5 µg recombinant citH3 for 48 hours at 37 °C.

value: mesangial cells

value: citH3 for 48hr


title: epidermis_ue_ls_pt05

description: Library name: DSP-1001660008953-B-C01


title: Human mesangial cells, CitH3 5, 48hr

description: Library name: CitH3_rep5_48hr


title: BCBL1_C_R1: BCBL-1 cells, control treatment, repeat 1

description: Library name: Sample 1


title: BJAB_C_R2: BJAB cells, control treatment, repeat 2

description: Library name: Sample 7


title: basal_layer_ue_ls_pt05

description: Library name: DSP-1001660008953-B-C03


title: Human mesangial cells, CitH3 3, 48hr

description: Library name: CitH3_rep3_48hr


title: derm_pap_ue_ls_pt05

description: Library name: DSP-1001660008953-B-C02


title: vim_high_ue_ls_pt05

description: Library name: DSP-1001660008953-B-C04


title: vim_low_hip_nl_pt10

description: Library name: DSP-1001660008952-A-H08


title: Human mesangial cells, CitH3 1, 48hr

description: Library name: CitH3_rep1_48hr


title: vim_high_hip_nl_pt10

description: Library name: DSP-1001660008952-A-H07


title: BJAB_20_R1: BJAB cells, 20µM drug treatment, repeat 1

description: Library name: Sample 4


title: BJAB_C_R3: BJAB cells, control treatment, repeat 3

description: Library name: Sample 11


title: epidermis_abdomen_nl_pt05

description: Library name: DSP-1001660008953-B-C05


title: Human mesangial cells, CitH3 2, 48hr

description: Library name: CitH3_rep2_48hr


title: basal_layer_hip_nl_pt10

description: Library name: DSP-1001660008952-A-H06


title: Human mesangial cells, control 5, 48hr

description: Library name: Media_rep5_48hr

value: control for 48h


title: epidermis_hip_nl_pt10

description: Library name: DSP-1001660008952-A-H05


title: vim_high_scalp_ls_pt10

description: Library name: DSP-1001660008952-A-H03


title: vim_low_scalp_ls_pt10

description: Library name: DSP-1001660008952-A-H04


title: basal_layer_scalp_ls_pt10

description: Library name: DSP-1001660008952-A-H02


title: Human mesangial cells, control 4, 48hr

description: Library name: Media_rep4_48hr


title: Human mesangial cells, control 3, 48hr

description: Library name: Media_rep3_48hr


title: Human mesangial cells, control 2, 48hr

description: Library name: Media_rep2_48hr


title: Human mesangial cells, control 2, 72hr

description: Library name: Media_rep2_72hr

value: control for 72h


title: Human mesangial cells, NETs 5, 72hr

description: Library name: NETs_rep5_72hr

value: NETs for 72hr


title: derm_pap_ue_ls_pt10

description: Library name: DSP-1001660008952-A-G08

value: Skin

value: Lesional


title: vim_high_ue_ls_pt10

description: Library name: DSP-1001660008952-A-G11


title: vim_high_le_ls_pt10

description: Library name: DSP-1001660008952-A-G04


title: Human mesangial cells, NETs 4, 72hr

description: Library name: NETs_rep4_72hr


title: derm_pap_le_ls_pt10

description: Library name: DSP-1001660008952-A-G03


title: Human mesangial cells, control 1, 72hr

description: Library name: Media_rep1_72hr


title: epidermis_ue_ls_pt10

description: Library name: DSP-1001660008952-A-G07

value: epidermis


title: epidermis_le_ls_pt10

description: Library name: DSP-1001660008952-A-G02


title: Human mesangial cells, control 1, 48hr

description: Library name: Media_rep1_48hr


title: basal_layer_le_ls_pt10

description: Library name: DSP-1001660008952-A-G06


title: basal_layer_ue_ls_pt10

description: Library name: DSP-1001660008952-A-G09


title: Human mesangial cells, control 3, 72hr

description: Library name: Media_rep3_72hr


title: basal_layer_le_ls_pt06

description: Library name: DSP-1001660008954-E-B01


title: Human mesangial cells, NETs 3, 72hr

description: Library name: NETs_rep3_72hr


title: vim_low_ue_ls_pt10

description: Library name: DSP-1001660008952-A-G10


title: Human mesangial cells, NETs 2, 72hr

description: Library name: NETs_rep2_72hr


title: Human mesangial cells, control 5, 72hr

description: Library name: Media_rep5_72hr


title: PC9-Cas9 cells, 10 µM erlotinib, replicate 2

city: Worcester

first: Michael

last: Lee

state: MA

address: 55 N Lake Ave

institute: Umass Chan Medical School

description:
Library name: S10-ERL-rep2_S10_L001_R1_001
Cells collected after being treated with 10 µM erlotinib for 72 hours.

library_source: genomic

data_processing:
The FASTX-Toolkit (0.0.13) was used to trim reads to get the CRISPR guide sequences (parameters: -f 23 -l 42)
Trimmed reads were mapped to the TKOv3 library with Bowtie (1.3.1) with the parameters -v 3 -m 1.
Assembly: TKOv3
Supplementary files format and content: CSV file of raw guide counts for each sample
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: PC9-Cas9 cells were grown in RPMI 1640 media supplemented with 10% fetal bovine serum and penicillin/streptomycin in an incubator with 5% CO2 at 37˚C

extract_protocol:
Genomic DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega).
Sequencing libraries were generated using 2 sequential PCR reactions. The first PCR amplified the sgRNAs from genomic DNA, and the second PCR added multiplexing barcodes.

treatment_protocol: Cas9-expressing PC9 cells were infected using a spin-fection protocol with the Toronto KnockOut Library v3 (TKOv3) sgRNA library at an MOI of 0.3, in duplicate, maintaining a coverage of >350x for each replicate. Cells were selected for 3 days using puromycin then seeded onto 15 cm plates and allowed to recover for 2 days. The following day, T0 samples were harvested. The remaining samples were treated with 0.1 µM osimertinib, 5 µM osimertinib, 10 µM erlotinib, or DMSO for 72 hours. At assay endpoint, cells were collected for the treatment conditions and the untreated sample, maintaining >350x coverage.

value: non-small cell lung cancer

value: 10 µM erlotinib

tag: time

value: 72 hours


title: epidermis_scalp_ls_pt10

description: Library name: DSP-1001660008952-A-G12


title: vim_low_le_ls_pt10

description: Library name: DSP-1001660008952-A-G05


title: Human mesangial cells, NETs 1, 72hr

description: Library name: NETs_rep1_72hr


title: PC9-Cas9 cells, 0.1 µM osimertinib, replicate 2

description:
Library name: S06-LOSI-rep2_S6_L001_R1_001
Cells collected after being treated with 0.1 µM osimertinib for 72 hours.

value: 0.1 µM osimertinib


title: derm_pap_scalp_ls_pt07

description: Library name: DSP-1001660008954-E-A12


title: PC9-Cas9 cells, 10 µM erlotinib, replicate 1

description:
Library name: S09-ERL-rep1_S9_L001_R1_001
Cells collected after being treated with 10 µM erlotinib for 72 hours.


title: Human mesangial cells, control 4, 72hr

description: Library name: Media_rep4_72hr


title: derm_pap_scalp_ls_pt10

description: Library name: DSP-1001660008952-A-H01


title: PC9-Cas9 cells, 0.1 µM osimertinib, replicate 1

description:
Library name: S05-LOSI-rep1_S5_L001_R1_001
Cells collected after being treated with 0.1 µM osimertinib for 72 hours.


title: vim_low_shoulder_nl_pt06

description: Library name: DSP-1001660008954-E-A06

value: Non-lesional


title: vim_high_shoulder_nl_pt06

description: Library name: DSP-1001660008954-E-A04


title: basal_layer_shoulder_nl_pt06

description: Library name: DSP-1001660008954-E-A05


title: PC9-Cas9 cells, T0, replicate 1

description:
Library name: S01-T0-rep1_S1_L001_R1_001
Cells collected at T0, the time of drugging for the treated samples.

value: 0 hours


title: vim_high_scalp_ls_pt06

description: Library name: DSP-1001660008953-B-H12


title: vim_high_ue_ls_pt06

description: Library name: DSP-1001660008953-B-H08


title: epidermis_shoulder_nl_pt06

description: Library name: DSP-1001660008954-E-A03


title: vim_low_ue_ls_pt06

description: Library name: DSP-1001660008953-B-H07


title: derm_pap_scalp_ls_pt06

description: Library name: DSP-1001660008953-B-H10


title: PC9-Cas9 cells, T0, replicate 2

description:
Library name: S02-T0-rep2_S2_L001_R1_001
Cells collected at T0, the time of drugging for the treated samples.


title: PC9-Cas9 cells, Untreated, replicate 1

description:
Library name: S03-T72-rep1_S3_L001_R1_001
Untreated cells collected after 72 hours.

value: DMSO


title: epidermis_ue_ls_pt06

description: Library name: DSP-1001660008953-B-H04


title: epidermis_scalp_ls_pt06

description: Library name: DSP-1001660008953-B-H09


title: derm_pap_ue_ls_pt06

description: Library name: DSP-1001660008953-B-H06


title: Participant 046, Nasal mucosa, bulk RNAseq

city: Chicago

first: Manu

last: Jain

state: IL

address: 303 E Superio

institute: Northwestern University

description:
Library name: CFHV_bulk_subj_046
Raw sequence data not distributed per IRB approval

data_processing:
Single-cell data were processed using the Cell Ranger 7.0.0 pipeline with exon-only processing mode (10x Genomics) and aligned to GRCh38.98.
Bulk RNAseq data were demultiplexed with bclconvert (Illumina, v4.0.3) and processed using the nf-core/rnaseq pipeline (v3.10.1) with sequence alignment to GRCh38 using STAR (v2.7.9a) and transcript quantitation using Salmon (v1.9.0)
Assembly: scRNAseq: GRCh38.98
Assembly: bulk RNAseq: GRCh38.113
Supplementary files format and content: scRNAseq: tab-separated and matrix files
Supplementary files format and content: bulk RNAseq: tab-separated count file

source_name: Nasal mucosa

extract_protocol:
Samples for scRNAseq were placed immediately in 2mL HypoThermosol buffer (BioLife Solutions) and stored at 4°C until prompt processing. Samples for bulk RNAseq were placed immediately in RLT (Qiagen) buffer and cryopreserved at -80°C until processing.
A single-cell suspension was generated using the cold-active dispase protocol reported by Deprez et al. and Zaragosi and Barbry with slight modification. Specifically, EDTA was omitted and cells were dispersed by pipetting 20 every 5 min using a 1-ml tip instead of trituration using a 21G or 23G needle. Single-cell libraries were generated from the resulting single-cell suspension following the protocol for 5′ v1 (10x Genomics, protocol no. CG000086 Rev M) or v2 chemistry (10x Genomics, protocol no. CG000331 Rev A). Excess cells from two of the samples from healthy volunteers were pooled to generate one additional single-cell library. Libraries were prepared according to the manufacturer’s protocol.

value: Nasal mucosa

value: M

tag: disease state

value: HV


title: Participant 015, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_015
Raw sequence data not distributed per IRB approval

value: CF


title: Participant 011, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_011
Raw sequence data not distributed per IRB approval


title: basal_layer_ue_ls_pt06

description: Library name: DSP-1001660008953-B-H05


title: Participant 048, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_048
Raw sequence data not distributed per IRB approval

value: F


title: Participant 047, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_047
Raw sequence data not distributed per IRB approval


title: PC9-Cas9 cells, Untreated, replicate 2

description:
Library name: S04-T72-rep2_S4_L001_R1_001
Untreated cells collected after 72 hours.


title: Participant 045, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_045
Raw sequence data not distributed per IRB approval


title: Participant 003, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_003
Raw sequence data not distributed per IRB approval


title: Participant 049, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_049
Raw sequence data not distributed per IRB approval


title: Participant 004, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_004
Raw sequence data not distributed per IRB approval


title: vim_low_le_ls_pt06

description: Library name: DSP-1001660008953-B-H03


title: Participant 001, Nasal mucosa, bulk RNAseq

description:
Library name: CFHV_bulk_subj_001
Raw sequence data not distributed per IRB approval


title: vim_low_scalp_ls_pt06

description: Library name: DSP-1001660008954-E-A02


title: No TRMT61B enzyme, large reaction size, rep 3, round 2, round 3, uMRT

description: Library name: NE3_round2_round3

value: synthetic pool of human and viral sequences


title: vim_high_le_ls_pt06

description: Library name: DSP-1001660008953-B-H02


title: derm_pap_le_ls_pt06

description: Library name: DSP-1001660008953-B-H01


title: epidermis_le_ls_pt06

description: Library name: DSP-1001660008953-B-G12


title: No TRMT61B enzyme, small reaction size, rep 2, round 2, round 3, uMRT

description: Library name: NE2_round2_round3


title: vim_low_shoulder_nl_pt07

description: Library name: DSP-1001660008953-B-G07


title: No TRMT61B enzyme, small reaction size, rep 1, round 2, round 3, uMRT

description: Library name: NE1_round2_round3


title: Low TRMT61B enzyme, large reaction size, rep 3, round 2, round 3, uMRT

description: Library name: LE3_round2_round3


title: Low TRMT61B enzyme, small reaction size, rep 1, round 2, round 3, uMRT

description: Library name: LE1_round2_round3


title: vim_high_shoulder_nl_pt07

description: Library name: DSP-1001660008953-B-G06


title: Low TRMT61B enzyme, small reaction size, rep 2, round 2, round 3, uMRT

description: Library name: LE2_round2_round3


title: basal_layer_shoulder_nl_pt07

description: Library name: DSP-1001660008953-B-G05


title: High TRMT61B enzyme, small reaction size, rep 2, round 2, round 3, uMRT

description: Library name: HE2_round2_round3


title: High TRMT61B enzyme, small reaction size, rep 1, round 2, round 3, uMRT

description: Library name: HE1_round2_round3


title: vim_high_scalp_ls_pt07

description: Library name: DSP-1001660008953-B-G02


title: vim_low_scalp_ls_pt07

description: Library name: DSP-1001660008953-B-G03


title: epidermis_shoulder_nl_pt07

description: Library name: DSP-1001660008953-B-G04


title: basal_layer_scalp_ls_pt07

description: Library name: DSP-1001660008953-B-G01


title: retinal organoid, Day 285, wild type human iPSC

city: Linz

first: Jingjing

last: Qi

address: Altenberger Straße 69

department: Zentrum für Medizinische Forschung

country: Austria

institute: Johannes Kepler University Linz

description:
Library name: d285_wt
10x Genomics

data_processing:
The demultiplexing, barcoding, and read alignment was done by Dragen software (version 3.8.4)
Assembly: Human hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: induced retinal organoid

extract_protocol:
For each time point (D85 and D285), five retinal organoids pooled from three independent differentiations were washed in DPBS without Ca²⁺/Mg²⁺ (Thermo Fisher, 14190144), dissociated with Trypsin (PAN Biotech, P10-0235SP) for 7.5 min at 37 °C on a nutator, and gently triturated 4–5 times. The enzyme was quenched with 2× volume DMEM (Gibco, 12430054), the suspension was passed through a 40 µm strainer (Fisher Scientific, 15342931), and dissociation was completed within 20 min of Trypsin addition. Viability was assessed with 0.4% Trypan Blue (Invitrogen, T10282) on a Countess II FL instrument, and only samples with >90% viability were used. Cells were pelleted (700 g, 3 min) and resuspended in DMEM as a single-cell suspension for sci-Plex processing.
Single-cell 3′ gene-expression libraries were prepared with the Chromium Next GEM Single Cell 3' kit (10x Genomics, #1000268). About 5,000 live cells per sample were loaded on a Chromium Next GEM Chip G (10x Genomics, #1000127) and processed on a Chromium Controller (#120223/#120246) per the manufacturer’s instructions. Cells were partitioned into GEMs for poly(dT)-primed cDNA synthesis; Read 1 encodes cell barcode/UMI and Read 2 captures the cDNA insert. Libraries were amplified, fragmented, end-repaired, adapter-ligated, indexed, QC’d, and Illumina paired-end sequenced.

value: induced retinal organoid

value: WTSIi004-A (EBiSC)

value: iPSC

value: WT

value: Retinal organoid culture


title: retinal organoid, Day 85, PRPF31-mut human iPSC

description:
Library name: d85_mut
10x Genomics

value: UNEWi004-A (EBiSC)

value: PRPF31 MUT


title: retinal organoid, Day 285, PRPF31-mut human iPSC

description:
Library name: d285_mut
10x Genomics


title: vim_high_ue_ls_pt07

description: Library name: DSP-1001660008953-B-F10

value: Skin

value: Lesional


title: retinal organoid, Day 85, wild type human iPSC

description:
Library name: d85_wt
10x Genomics


title: epidermis_scalp_ls_pt07

description: Library name: DSP-1001660008953-B-F12

value: epidermis


title: epidermis_ue_ls_pt07

description: Library name: DSP-1001660008953-B-F08


title: basal_layer_ue_ls_pt07

description: Library name: DSP-1001660008953-B-F09


title: PMCs, DNP, 6 hours, biol rep3

city: Heidelberg

first: Qihua

last: Liang

state: Baden-Württemberg

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

country: Germany

institute: Universitat Heidelberg

description:
Library name: Sample 1.3.5
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_D_6_3

data_processing:
Raw RNA-Seq reads were processed using the nf-core/rnaseq pipeline (version 3.14.0). The pipeline was executed using Nextflow with the Singularity profile.
Adapter and quality trimming was performed using Trim Galore! with nf-core/rnaseq pipeline default settings.
Read alignment was performed against the Mus musculus GRCm39 reference genome (GRCm39.primary_assembly.genome.fa) using STAR (version 2.7.11a).
Gene-level quantification was carried out using RSEM (version 1.3.1) with annotations from GENCODE release M35 (gencode.vM35.primary_assembly.annotation.gtf).
Technical replicates were aggregated using the DESeq2 collapseReplicates function to produce a raw gene count matrix (raw_counts_All_Samples.txt). To account for technical variation, batch effects were corrected using ComBat-seq. Finally, library size normalization was applied via the DESeq2 median-of-ratios method, with the final output saved as normalized_counts_ComBatSeq_DESeq2_All_Samples.txt.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes batch adjusted and DESeq2 normalized counts for all samples

source_name: connective tissue

growth_protocol: The isolated cell suspension was cultured at 37∘C  and 5% CO2. Two days after the isolation, the culture medium was changed, and all non-adherent cells were removed by aspiration. On day nine, the cells were split and cultivated further at a concentration 1×10^6 of cells/mL. The PMCs were used for the experiments 12-16 days after isolation.

extract_protocol:
For RNA isolation, each sample (0.2 – 2 x 105 PMCs) was lysed in 400 µL RLT Buffer supplemented with 4 μL-Mercaptoethanol. RNA extraction was performed using the RNeasy Micro Kit (Qiagen, Cat. No. 74004). RNA was eluted in 14 µL of buffer, and 10 µL of the eluate was used for library preparation.
For samples 1.1–1.3, transcript libraries were constructed using the Ovation SoLo RNA-Seq Library Preparation Kit (NuGEN/Tecan), utilizing 25 ng of cDNA per sample as input. Sequencing was performed on an Illumina NextSeq 2000 platform (EMBL Heidelberg Genomics Core Facility). For samples 2.1–2.4, libraries were prepared using the MGIEasy Fast RNA Library Prep Set following ribosomal RNA removal with the MGIEasy rRNA Depletion Kit V1.3. Sequencing was conducted on the DNBSEQ-G400 platform (MGI Tech) using the DNBSEQ-G400RS High-throughput Sequencing Reagent Set (FCL PE100).

treatment_protocol: Each PMC preparation was stimulated with four experimental conditions: adenosine (ADO, 10 µM) for 2 hours, compound 48/80 (C48/80, 50µg/mL) for 6 hours, antigen (dinitrophenyl (DNP)-human serum albumin 100 ng/mL) for 2 hours, and antigen (dinitrophenyl (DNP)-human serum albumin 100 ng/mL) for 6 hours.

value: connective tissue

tag: strain

value: primary peritoneal mast cells

value: DNP

value: 6 hours


title: PMCs, DNP, 2 hours, biol rep3

description:
Library name: Sample 1.3.4
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_D_2_3

value: 2 hours


title: vim_low_le_ls_pt07

description: Library name: DSP-1001660008953-B-F07


title: High TRMT61B enzyme, large reaction size, rep 3, round 2, round 3, uMRT

description: Library name: HE3_round2_round3


title: PMCs, C48/80, 6 hours, biol rep3

description:
Library name: Sample 1.3.3
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_C_6_3


title: PMCs, ADO, 2 hours, biol rep3

description:
Library name: Sample 1.3.2
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_A_2_3

value: ADO


title: vim_low_ue_ls_pt07

description: Library name: DSP-1001660008953-B-F11


title: derm_pap_le_ls_pt07

description: Library name: DSP-1001660008953-B-F05


title: PMCs, CONTROL, 0 hour, biol rep3

description:
Library name: Sample 1.3.1
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_A_0_3

value: CONTROL

value: 0 hour


title: basal_layer_scalp_ls_pt06

description: Library name: DSP-1001660008953-B-H11


title: epidermis_le_ls_pt07

description: Library name: DSP-1001660008953-B-F03


title: PMCs, DNP, 6 hours, biol rep2

description:
Library name: Sample 1.2.5
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_D_6_2


title: basal_layer_le_ls_pt07

description: Library name: DSP-1001660008953-B-F04


title: vim_low_ue_ls_pt05

description: Library name: DSP-1001660008953-B-F02


title: PMCs, DNP, 2 hours, biol rep2

description:
Library name: Sample 1.2.4
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_D_2_2


title: PMCs, C48/80, 6 hours, biol rep2

description:
Library name: Sample 1.2.3
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_C_6_2


title: basal_layer_hip_nl_pt12

description: Library name: DSP-1001660008953-B-E07

value: Non-lesional


title: vim_high_hip_nl_pt12

description: Library name: DSP-1001660008953-B-E06


title: vim_low_hip_nl_pt12

description: Library name: DSP-1001660008953-B-E08


title: PMCs, CONTROL, 0 hour, biol rep2

description:
Library name: Sample 1.2.1
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_A_0_2


title: PMCs, ADO, 2 hours, biol rep2

description:
Library name: Sample 1.2.2
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_A_2_2


title: epidermis_hip_nl_pt12

description: Library name: DSP-1001660008953-B-E05


title: derm_pap_scalp_ls_pt12

description: Library name: DSP-1001660008953-B-E04


title: PMCs, DNP, 6 hours, biol rep1

description:
Library name: Sample 1.1.5
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_D_6_1


title: vim_high_le_ls_pt07

description: Library name: DSP-1001660008953-B-F06


title: vim_low_scalp_ls_pt12

description: Library name: DSP-1001660008953-B-E02


title: PMCs, DNP, 2 hours, biol rep1

description:
Library name: Sample 1.1.4
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_D_2_1


title: PMCs, ADO, 2 hours, biol rep1

description:
Library name: Sample 1.1.2
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_A_2_1


title: PP_M9gluc_wo_TE_rep1

city: La Jolla

first: Heera

last: Bajpe

state: CA

address: 9500 Gilman Dr.

institute: UC San Diego

description: Library name: PP_M9gluc_wo_TE_1

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts were generated using featureCounts
Assembly: AE015451.2
Supplementary files format and content: Supplementary files format and content: Comma-delimited text file containing logTPM values for each sample.

organism: Pseudomonas putida KT2440

source_name: bacterial cell

growth_protocol: Cells were grown overnight at 30 °C with shaking in 4 mL of the base medium (M9 or CAMHB). The following day, fresh cultures were inoculated in duplicate to an initial OD600 of 0.05. For iron starvation (2,2' dipyridyl treatment) and nitrogen starvation (nitrogen-free M9 media with addition of eighteen amino acids, with the exception of cysteine and methionine) conditions, cultures were grown in medium supplemented as specified. Cultures were harvested at mid-log phase (OD₆₀₀ ≈ 0.5) and 3 mL of culture was immediately mixed with 6 mL of RNAprotect reagent for the following conditions: growth in M9 glucose media (with and without trace element solution), CAMHB media, mixed carbon source (succinate, fructose, and toluene treatment), iron starvation, and nitrogen starvation. Cells were pelleted and stored at −80 °C until RNA extraction and RNA-seq library preparation.

extract_protocol:
Total RNA was isolated and prepared from cell pellets using reagents from Zymo Research and silica-coated magnetic beads (Luna Nanotech) accroding to the vendor's manual. Concentrations and quality of the RNA were assessed using an Agilent TapeStation and Nanodrop, respectively. For each sample, 1 ug was used as input for the standard RiboRid procedure.
RNA-seq libraries were prepared from 5 uL of the rRNA-subtracted RNA using KAPA RNA HyperPrep Kit (Roche) according to the manufacturer’s protocol with volumes reduced by half. The final PCR amplification step was modified by incorporating SYBR and using a qPCR instrument. Samples were removed from the thermal cycler just before entering the plateau phase of amplification to avoid biases being potentially introduced by reagent depletion. The quality and concentrations of the libraries were checked with an Agilent TapeStation and Qubit instrument, respectively. Pooled libraries were then run on an AVITI instrument (Element Biosciences).

treatment_protocol: For ceftazidime treatment conditions, ceftazidime (¼ of minimum inhibitory concentration) was added at OD₆₀₀ ≈ 0.2, and cultures were incubated for 1 h prior to collection. For osmotic stress (NaCl treatment), oxidative stress (H2O2 treatment), and metal ion stress (CuSO4 and ZnSO4 treatment) conditions, cultures were grown to OD₆₀₀ ≈ 0.5 before addition of the corresponding supplement to the final concentration indicated. This was followed by incubation for an additional 30 min (osmotic and oxidative stress conditions) or 1 h (metal ion stress conditions) before mixing 3 mL of culture with 6 mL of RNAprotect reagent.

value: bacterial cell

value: wild-type

value: glucose (2 g/L)

tag: medium

value: M9 media


title: PMCs, C48/80, 6 hours, biol rep1

description:
Library name: Sample 1.1.3
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_C_6_1

tag: tissue

value: WT


title: vim_high_scalp_ls_pt12

description: Library name: DSP-1001660008953-B-E01

value: Skin


title: epidermis_scalp_ls_pt12

description: Library name: DSP-1001660008953-B-D12

value: Lesional


title: PP_NFM9gluc_rep1

description: Library name: PP_NFM9gluc_1

tag: genotype

value: glucose (2 g/L) and amino acids (0.05g/L) (all except methionine and cysteine)

value: M9 media without NH4Cl


title: PP_NFM9gluc_rep2

description: Library name: PP_NFM9gluc_2

tag: treatment


title: vim_low_ue_ls_pt12

description: Library name: DSP-1001660008953-B-D11


title: basal_layer_scalp_ls_pt12

description: Library name: DSP-1001660008953-B-E03


title: PP_M9gluc_wo_TE_rep2

description: Library name: PP_M9gluc_wo_TE_2


title: derm_pap_ue_ls_pt12

description: Library name: DSP-1001660008953-B-D09


title: PP_M9gluc_DPD_rep2

description: Library name: PP_M9gluc_DPD_2

value: glucose (2 g/L), trace element solution (Without FeCl3), and 2,2' dipyridyl (0.2 mM)


title: C2C12_CnR_D1_A485_2h_IgG

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 83

data_processing:
Basecalls performed using Bcl2fastq.
CUT&RUN and ChIP-Seq reads were aligned to the mm10 genome assembly using bowtie2.
CUT&RUN and ChIP-Seq peaks were called using SICER (v2) with following configuration: For Arid1a, GR, and KMT2D, a window size of 50 bp, gap size of 50 bp , and a false discovery rate of 1E-10 were used. For MyoD and p300, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all CUT&RUN or ChIP-Seq data.
Assembly: mm10
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM
Library strategy: CUT&Run

growth_protocol: Preadipocytes were maintained in growth media (DMEM plus 10% Foundation FBS).

extract_protocol:
CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN Kit (#14-1048, Epicypher), following the manufacturer’s instructions with the following modifications. 0.5 million cells were used for each CUT&RUN reaction. Cells were gently fixed with 0.1% formaldehyde for 1 min. Cells were resuspended in cold Nuclei Extract Buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 1 mM MgCl2 supplemented with protease inhibitor and 0.5 mM Spermidine), lysed on ice for 10 mins, and centrifuged at 600 g for 3 min 4°C. Nuclei were resuspended in 100 uL cold Nuclei Extract Buffer and incubated with activated 10 uL/reaction Concanavalin A beads for 10 min at RT. The following steps are performed according to the manufacturer’s instructions.
Libraries were prepared following the instruction of CUTANA™ CUT&RUN Library Prep Kit for Illumina sequencing. CUT&RUN enriched DNA were used to construct libraries, using NEBNext® Ultra™ II DNA Library Prep kit (#E7645L, NEB) with AMPure XP magnetic beads (Beckman Coulter).
Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: MyoD-ER-T7 preadipocytes were grown in growth media (DMEM plus 10% Foundation FBS) for 2 days. On the day of experiments, growth medium was replaced with differentiation medium (DMEM plus 2% horse serum), and cells were rested for 3h. Cells were then pretreated with 1 µM BRM014 or 3 µM A-485 for 1h; 1 µM 5Ph-IAA for 2h; or 250 nM dCBP-1 for 3h, before 400 nM 4-OHT was added for 1h to induced MyoD nuclear translocation.

value: Myoblast

value: A-485 (2h) + myogenic differentiation

tag: chip antibody

value: Anti-IgG (13-0042K, Epicypher)


title: vim_high_ue_ls_pt12

description: Library name: DSP-1001660008953-B-D08


title: basal_layer_ue_ls_pt12

description: Library name: DSP-1001660008953-B-D10


title: epidermis_ue_ls_pt12

description: Library name: DSP-1001660008953-B-D07

value: epidermis


title: vim_low_le_ls_pt12

description: Library name: DSP-1001660008953-B-D06


title: vim_high_scalp_ls_pt05

description: Library name: DSP-1001660008953-B-C12


title: C2C12_CnR_D1_A485_2h_MyoD_5_8A

description: Library name: Sample 82

value: Anti-MyoD (5.8A) (Santa Cruz sc-32758)


title: vim_low_scalp_ls_pt05

description: Library name: DSP-1001660008953-B-D01


title: snRNA-Seq NCH631b

first: Christel

last: Herold-Mende

department: Department of Neurosurgery

institute: University Hospital Heidelberg

description: Library name: exp_snRNA_NCH631b

data_processing:
FASTQ files for each sequencing batch were processed with Cell Ranger (v 7.1.0) using the human reference (GRCh38) with intronic reads enabled (--include-introns) to accommodate nuclear-localized transcripts. For the sequencing batch with multiplexed samples, cell barcodes were demultiplexed using an in-house developed genotype-based pipeline, scSNPdemux. In brief, scSNPdemux took aligned reads (BAM file) and gene expression count matrix of the batch from Cell Ranger, population SNP information from 1000 genomes phase 3 dataset and SNPs genotyped using Infinium OncoArray-500K (Illumina) from the multiplexed samples in VCF format, which are mapped to the human genome reference GRCh38, as inputs, incorporated Cellsnp-lite for single cell SNP calling and selection, followed by SNP-based demultiplexing step based on Vireo. The output per-nuclei sample identity and its likelihood, as well as cross-sample doublets were added as metadata to the Seurat object.
Assembly: GRCh38
Supplementary files format and content: Seurat object in a RDS file

source_name: BCBM

extract_protocol:
Nuclei were isolated from cryo-preserved 100 µm BCBM tissue slices, which had been prepared under tissue quality control as described above, immediately before further downstream analysis by single nuclei RNA sequencing using an optimized protocol in part adapted from published sources. All reagents and materials were pre-cooled to 4°C. Tissue slices were stored at -80°C and transported on dry ice. For a combined chemical and mechanical lysis, five tissue slices were chopped with scissors for 5 min in 3 ml TST buffer (Tween with salts and tris buffer, 146 mM NaCl, 10 mM Tris, 1 mM CaCl2, 21 mM MgCl2, 0.03 % Tween-20, 0.01 % BSA), followed by addition of 2 ml TST buffer, transfer to a douncer, and application of 12 hits with the pestle of size A, then 15 hits with the pestle of size B. Finally, cell debris and free RNA were removed by filtering through a 40 µm strainer and washing by addition of 40 ml ST buffer (salts and tris buffer, 146 mM NaCl, 10 mM Tris, 1 mM CaCl2, 21 mM MgCl2) and centrifugation for 5 min at 1000xg at 4 °C. The pellet was resuspended in ST buffer, nuclei were counted and further processed immediately.
Single nuclei RNA-sequencing was performed using the Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index, 10x Genomics) according to the manufacturer´s instructions, and 5´gene expression dual index libraries were constructed from the generated full-length cDNA. 10,000 - 30,000 nuclei were loaded per sample, and 28 samples were pooled using 1-3 samples per run, resulting in 12 runs in total. Samples were sequenced in batches using a NovaSeq 6000 SP, NovaSeq 6000 S1, or NovaSeq 6000 S4 (all Illumina). To allow for in silico demultiplexing of pooled samples and patient assignment using single-nucleotide polymorphisms (SNPs), genotyping arrays via Infinium OncoArray-500K BeadChip (Illumina) were performed with patient-individual DNA from blood or, if not available, tumor tissue as a reference.

tag: ghga accession

value: BCBM

tag: gender

value: FEMALE

tag: patient

value: Exp. 1

tag: bcbm location

value: Cerebrum

tag: nuclei loaded

tag: snp array

value: no

tag: snp array_dna_source


title: PP_M9gluc_Zn_rep2

description: Library name: PP_M9gluc_Zn_2

tag: cell type

value: bacterial cell

value: wild-type

value: glucose (2 g/L), trace element solution, and ZnSO4 ( 0.7 mM)

value: M9 media


title: snRNA-Seq NCH724Y

description: Library name: exp_snRNA_NCH724Y

tag: age

tag: batch

value: Exp. 2


title: C2C12_CnR_D1_DMSO_2h_MyoD_5_8A

description: Library name: Sample 80

tag: cell line

value: myogenic differentiation

tag: time


title: C2C12_CnR_D1_DMSO_2h_IgG

description: Library name: Sample 81


title: PP_M9gluc_Zn_rep1

description: Library name: PP_M9gluc_Zn_1

tag: strain

tag: medium


title: snRNA-Seq NCH5616

description: Library name: exp_snRNA_NCH5616

tag: tissue

value: Exp. 7, pool B

value: yes

value: blood


title: snRNA-Seq NCH6077

description: Library name: exp_snRNA_NCH6077


title: PP_M9gluc_Cu_rep1

description: Library name: PP_M9gluc_Cu_1

tag: genotype

tag: treatment

value: glucose (2 g/L), trace element solution, and CuSO4 (0.2 mM)


title: PMCs, CONTROL, 0 hour, biol rep1

description:
Library name: Sample 1.1.1
Column name in raw_counts_All_Samples.txt and normalized_counts_ComBatSeq_DESeq2_All_Samples.txt: WT_A_0_1

value: connective tissue

value: primary peritoneal mast cells

value: WT

value: CONTROL

value: 0 hour


title: C2C12_CnR_A485_2h_IgG

description: Library name: Sample 79

value: Myoblast

value: A-485 (2h) + myogenic differentiation

tag: chip antibody

value: Anti-IgG (13-0042K, Epicypher)


title: snRNA-Seq NCH5557

description: Library name: exp_snRNA_NCH5557

tag: ghga accession

value: BCBM

tag: gender

value: FEMALE

value: Cerebrum


title: snRNA-Seq NCH6115

description: Library name: exp_snRNA_NCH6115

tag: patient

value: Exp. 7, pool A

tag: bcbm location


title: PP_M9gluc_H2O2_rep2

description: Library name: PP_M9gluc_H2O2_2

value: bacterial cell

value: wild-type

value: glucose (2 g/L) and H2O2 (5 mM)

value: M9 media


title: C2C12_CnR_A485_2h_MyoD_5_8A

description: Library name: Sample 78

value: Anti-MyoD (5.8A) (Santa Cruz sc-32758)


title: snRNA-Seq NCH747q

description: Library name: exp_snRNA_NCH747q

tag: nuclei loaded

tag: snp array

value: yes

value: tumor


title: snRNA-Seq NCH1638

description: Library name: exp_snRNA_NCH1638

tag: snp array_dna_source

value: blood


title: snRNA-Seq NCH998

description: Library name: exp_snRNA_NCH998

tag: age

value: Exp. 6, pool B


title: C2C12_CnR_DMSO_2h_IgG

description: Library name: Sample 77

tag: cell type

value: myogenic differentiation


title: snRNA-Seq NCH7592

description: Library name: exp_snRNA_NCH7592

tag: batch


title: C2C12_CnR_DMSO_2h_MyoD_5_8A

description: Library name: Sample 76

tag: cell line

value: Myoblast

tag: time


title: snRNA-Seq NCH4033

description: Library name: exp_snRNA_NCH4033

value: Exp. 6, pool A


title: snRNA-Seq NCH767

description: Library name: exp_snRNA_NCH767


title: C2C12_CnR_unt_IgG

description: Library name: Sample 75

value: Anti-IgG (13-0042K, Epicypher)


title: snRNA-Seq NCH576b

description: Library name: exp_snRNA_NCH576b

value: BCBM


title: snRNA-Seq NCH5474

description: Library name: exp_snRNA_NCH5474

value: FEMALE

value: Exp. 5, pool B


title: PP_M9gluc_DPD_rep1

description: Library name: PP_M9gluc_DPD_1

tag: strain

value: glucose (2 g/L), trace element solution (Without FeCl3), and 2,2' dipyridyl (0.2 mM)

tag: medium


title: PP_M9gluc_NaCl_rep1

description: Library name: PP_M9gluc_NaCl_1

value: bacterial cell

tag: genotype

value: glucose (2 g/L) and NaCl (0.35 M)


title: C2C12_CnR_unt_MyoD_5_8A

description: Library name: Sample 74


title: snRNA-Seq NCH5597

description: Library name: exp_snRNA_NCH5597

tag: tissue

value: Exp. 5, pool A

value: Cerebrum


title: snRNA-Seq NCH6248

description: Library name: exp_snRNA_NCH6248

value: no


title: snRNA-Seq NCH5475

description: Library name: exp_snRNA_NCH5475


title: PP_CAMHB_ceftazidime_rep2

description: Library name: PP_CAMHB_ceftazidime_2

value: wild-type

tag: treatment

value: ceftazidime (1 ug/mL)

value: CAMHB media


title: BMDM Snx5 knockout, infected with MTB Erdman,  24H, biol rep 3

city: Dallas

last: Shiloh

state: TX

address: 5323 Harry Hines Blvd. Y9.308

department: Internal Medicine

institute: University of Texas Southwestern Medical Center - UTSW

description:
Library name: KO_3_Infected_24h
614_KO_plus_MTB_24

data_processing:
Single-end 100 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads from fastq files for each library was mapped to human reference genome using STAR (v2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes corresponding to  igenomes gtf file
Normalized read counts were  generated using edgeR
Assembly: mm10
Supplementary files format and content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow cells from Snx5-/- or wild-type mice femurs and tibia were flushed and used to generate bone marrow-derived macrophages (BMDMs) and bone marrow dendritic cells (BMDCs). To obtain BMDMs, bone marrow cells were cultivated in DMEM (Gibco, 11965-092) containing 20% heat-inactivated endotoxin-free FBS (Gibco, 1600-044), 30% L929 cell-conditioned media, Glutamax (Gibco, 35050-061), 1 mM sodium pyruvate (Gibco, 11360-070), 1 mM HEPES (Cytiva, SH30237.01), and 50 mM b-mercaptoethanol (Gibco, 21985-023). Media was replaced after 3 days of culture. After 7 days, adherent BMDMs were detached from Petri dishes (100x15mm) with 1 mM EDTA in PBS and cultured in DMEM supplemented with 10% FBS and 5% L929 cell-conditioned media.

extract_protocol:
After 4 or 24 h of infection, samples were lysed using TRIzol (Invitrogen, 15596018) for 5 min, incubated with chloroform, and centrifuged at 12,000 x g for 5 min at 4 °C. Then, the aqueous phase was subject to RNA extraction using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol.
Samples were analyzed on an Agilent Tapestation 4200 to determine level of degradation to ensure that only high quality RNA was used (RIN Score 8 or higher). We used a Qubit® 4.0 Fluorimeter (ThermoFisher) to determine RNA concentration prior to starting library prep. One microgram of total DNAse treated RNA was then prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Poly-A RNA was purified and fragmented before strand-specific cDNA synthesis. cDNA was then A-tailed and indexed adapters ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200. Before being normalized and pooled, samples were quantified by Qubit then sequenced on the Illumina NextSeq 2000 using a P2-100 flowcell.

treatment_protocol: WT and Snx5-/- BMDMs from 3 different animals were plated in 6-well plates (106) and infected or not with Mtb (MOI of 5).

value: Bone marrow derived macrophages

value: Primary

value: KO

value: Infected with Mtb Erdman 24h


title: snRNA-Seq NCH1367

description: Library name: exp_snRNA_NCH1367

tag: ghga accession

value: Exp. 4, pool B

value: Cerebellum

value: yes

value: blood


title: PP_M9gluc_Cu_rep2

description: Library name: PP_M9gluc_Cu_2

value: glucose (2 g/L), trace element solution, and CuSO4 (0.2 mM)

value: M9 media


title: PP_M9gluc_NaCl_rep2

description: Library name: PP_M9gluc_NaCl_2

value: bacterial cell

value: glucose (2 g/L) and NaCl (0.35 M)


title: snRNA-Seq NCH7611

description: Library name: exp_snRNA_NCH7611

value: BCBM

tag: gender

value: FEMALE

value: Exp. 6, pool B

value: Cerebrum