title: siNC_H146_Day7_TAS1440_300nM_1

description: Library name: Sample64


title: siNC_H146_Day7_DMSO_2

status: Public on Jan 20 2026

type: SRA

city: chiba

first: YINGBO

last: GONG

department: Medicine

country: Japan

institute: CHIBA University

description: Library name: Sample62

library_source: transcriptomic

data_processing:
Deep sequencing was performed on an Illumina NovaSeq 6000 System (paired-end reads) according to the manufacturer’s protocols. Sequenced reads from the RNA-seq experiments were aligned using the Bowtie 2 and TopHat (version 1.3.2), and Cufflinks (version 2.0.2) was used for transcriptome assembly. Gene expression levels were expressed as fragments per kilobase of exons per million mapped sequence reads. DEGs were identified using the R software package (version 4.2.0). Heatmaps and dendrograms were generated using R, GraphPad Prism 9.0, or https://www.chiplot.online/. DEG-related and terms of the KEGG were analyzed by gene set enrichment analysis software (GSEA, version 4.2.3).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: NCI-1417 [H1417] (Cat. No. CRL-5869), NCI-H209 [H209] (HTB-172), SHP-77 (Cat. No. CRL-2195), NCI-H211 (Cat. No. CRL-5824), NCI-H196 (Cat. No. CRL-5823), NCI-H146 (Cat. No. HTB-173), NCI-H187 (Cat. No. CRL-5804), NCI-H69 (Cat. No. HTB-119), NCI-H446 [H446] (Cat. No. HTB-171), DMS 79 (Cat. No. CRL-2049), NCI-H510A [H510A, NCI-H510] (Cat. No. HTB-184), DMS 114 (Cat. No. CRL-2066), DMS 53 (Cat. No. CRL-2062), NCI-H2081 (Cat. No. CRL-5920), NCI-H524 [H524] (Cat. No. CRL-5831), NCI-H128 (Cat. No. HTB-120), NCI-H526 (Cat. No. CRL-5811), and NCI-H1694 (Cat. No. CRL-5888) cell lines were purchased from the American Type Culture Collection. Lu-135 (Cat. No. JCRB0170), COR-L51 (Cat. No. 92031916), CPC-N (Cat. No. ACC 306), and SBC-5 (Cat. No. JCRB0819) cell lines were obtained from the Japanese Collection of Research Bioresources, European Collection of Authenticated Cell Cultures, German Collection of Microorganisms and Cell Cultures GmbH, and Health Science Research Resources Bank, respectively. All of these are small-cell lung cancer cell lines and were cultured in RPMI1640 medium (Cat#: 189-02025, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% FBS (Cat#: 10270106, GIBCO Thermo Fisher Scientific, San Jose, CA) (NCI-1417, NCI-H209, SHP-77, NCI-H211, NCI-H196, Lu-135, and COR-L51), in conditioned, high-glucose RPMI1640 (Wako, Cat#: 187-02705) with 10% FBS (NCI-H146, NCI-H187, NCI-H69, NCI-H446, NCI-H526, NCI-H524, and DMS 79), in McCoy’s 5A (GIBCO, Cat#: 16600-082) with 10% FBS (CPC-N), in minimum essential medium (Cat#: 21442-25, Nacalai Tesque, Kyoto, Japan) with 10% FBS (SBC-5), in F-12K medium (GIBCO, Cat#: 11765-054) with 10% FBS (NCI-H510A), in Waymouth’s medium (GIBCO, Cat#: 11220-035) with 10% FBS (DMS 114 and DMS 53), in IMDM medium (GIBCO, Cat#: 12440-053) with 20% FBS (NCI-H128), or in HITES medium (GIBCO, 11330-032) with 10% FBS, Insulin (FUJIFILM, Cat#: 093-06351), Transferrin (Cat#: 10652202001, Roche Diagnostics, Rotkreuz, Switzerland), Hydrocortisone (Cat#: H6909-10ML, SIGMA-Aldrich, St. Louis, MO, USA), GlutaMAX (GIBCO, Cat#: 35050-061), Sodium Selenite (FUJIFILM, Cat#: 190-10844), and β-Estradiol (SIGMA-Aldrich, Cat#: E2758-250MG) (NCI-H2081 and NCI-H1694). INSM1 and LSD1 knockout NCI-H1417 and NCI-H146 cells were generated using CRISPR‒Cas9 genome editing as previously described (Ochiiwa et al., 2021). siRNA oligonucleotides against SMAD2 (Cat. No. AM16708) were purchased from Ambion Thermo Fisher Scientific. NCI-H1417 or NCI-H146  cells were transfected with siRNAs using Lipofectamine™ RNAiMAX (Thermo Fisher Scientific, Cat.No.13778150) following the manufacturer’s protocol. At 24 h after transfection, reagents were added, and subsequent experiments were performed.

extract_protocol:
SCLC cell lines were treated, for the indicated durations, with different LSD1 inhibitors. Total cellular RNA was extracted using a modified chloroform/phenol procedure (TRIzol™, Invitrogen Thermo Fisher Scientific). RNA integrity and concentration were measured using a 4200 TapeStation system for high-throughput automated electrophoresis (Agilent, Santa Clara, CA, USA)
RNA-Seq libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) following the manufacturers’ protocols.

treatment_protocol: The SCLC cell lines were seeded in plates. The following day, LSD1 inhibitors were serially diluted with DMSO and mixed with the culture medium. The mixtures were then added to each well on the plates. The final concentration of DMSO was set at 0.075 %. Cells were maintained with the inhibitors without any medium change.

tag: cell line

tag: cell type

value: small-cell lung cancer

tag: genotype

value: siNC

tag: treatment

value: DMSO


title: siNC_H1417_Day7_DMSO_2

description: Library name: Sample56


title: siNC_H146_Day7_DMSO_1

description: Library name: Sample61


title: DMS79_INSM1OVER_Day7_TAS1440_300nM_3

description: Library name: Sample54

value: INSM1 overexpression


title: siNC_H1417_Day7_TAS1440_300nM_2

description: Library name: Sample59


title: siSMAD2_H1417_Day7_TAS1440_300nM_2

description: Library name: Sample71


title: siNC_H146_Day7_DMSO_3

description: Library name: Sample63


title: siNC_H1417_Day7_DMSO_1

description: Library name: Sample55


title: DMS79_INSM1OVER_Day7_TAS1440_300nM_2

description: Library name: Sample53


title: DMS79_INSM1OVER_Day7_DMSO_2

description: Library name: Sample50


title: DMS79_INSM1OVER_Day7_DMSO_1

description: Library name: Sample49


title: DMS79_INSM1OVER_Day7_DMSO_3

description: Library name: Sample51


title: H211_INSM1OVER_Day7_TAS1440_300nM_2

description: Library name: Sample47


title: H211_INSM1OVER_Day7_TAS1440_300nM_3

description: Library name: Sample48


title: siNC_H1417_Day7_TAS1440_300nM_1

description: Library name: Sample58


title: H211_INSM1OVER_Day7_DMSO_2

description: Library name: Sample44


title: H211_INSM1OVER_Day7_DMSO_3

description: Library name: Sample45


title: H196_INSM1OVER_Day7_TAS1440_300nM_3

description: Library name: Sample42


title: H211_INSM1OVER_Day7_DMSO_1

description: Library name: Sample43


title: DMS79_INSM1OVER_Day7_TAS1440_300nM_1

description: Library name: Sample52


title: DMS79_EMPTY_Day7_TAS1440_300nM_3

description: Library name: Sample36

value: Empty vector overexpression


title: H196_INSM1OVER_Day7_DMSO_1

description: Library name: Sample37


title: H196_INSM1OVER_Day7_TAS1440_300nM_2

description: Library name: Sample41


title: H196_INSM1OVER_Day7_DMSO_2

description: Library name: Sample38


title: DMS79_EMPTY_Day7_TAS1440_300nM_2

description: Library name: Sample35


title: H196_INSM1OVER_Day7_DMSO_3

description: Library name: Sample39


title: DMS79_EMPTY_Day7_DMSO_2

description: Library name: Sample32


title: H211_INSM1OVER_Day7_TAS1440_300nM_1

description: Library name: Sample46


title: DMS79_EMPTY_Day7_DMSO_3

description: Library name: Sample33


title: DMS79_EMPTY_Day7_DMSO_1

description: Library name: Sample31


title: NCI-H211_EMPTY_TAS1440_300nM_1

description: Library name: Sample28


title: H196_INSM1OVER_Day7_TAS1440_300nM_1

description: Library name: Sample40


title: NCI-H211_EMPTY_Day7_DMSO_2

description: Library name: Sample26


title: NCI-H211_EMPTY_Day7_DMSO_3

description: Library name: Sample27


title: NCI-H196_EMPTY_TAS1440_300nM_2

description: Library name: Sample23


title: NCI-H196_EMPTY_Day7_DMSO_3

description: Library name: Sample21


title: NCI-H211_EMPTY_TAS1440_300nM_3

description: Library name: Sample30


title: NCI-H196_EMPTY_TAS1440_300nM_3

description: Library name: Sample24


title: NCI-H196_EMPTY_Day7_DMSO_1

description: Library name: Sample19


title: NCI-H196_EMPTY_TAS1440_300nM_1

description: Library name: Sample22


title: NCI-H211_EMPTY_Day7_DMSO_1

description: Library name: Sample25


title: DMS79_EMPTY_Day7_TAS1440_300nM_1

description: Library name: Sample34


title: H1417_Day7_CC90011_300nM_3

description: Library name: Sample18

value: WT


title: H1417_Day7_SP2509_300nM_3

description: Library name: Sample12


title: H146_Day7_CC90011_300nM_2

description: Library name: Sample14


title: H1417_Day7_SP2509_300nM_2

description: Library name: Sample11


title: H146_Day7_CC90011_300nM_3

description: Library name: Sample15


title: H1417_Day7_CC90011_300nM_2

description: Library name: Sample17


title: H146_Day7_SP2509_300nM_1

description: Library name: Sample7


title: H146_Day7_CC90011_300nM_1

description: Library name: Sample13


title: H146_Day7_SP2509_300nM_2

description: Library name: Sample8


title: H146_Day7_SP2509_300nM_3

description: Library name: Sample9


title: H1417_Day7_DMSO_3

description: Library name: Sample6


title: H1417_Day7_SP2509_300nM_1

description: Library name: Sample10


title: H146_Day7_DMSO_2

description: Library name: Sample2


title: H146_Day7_DMSO_3

description: Library name: Sample3


title: H1417_Day7_CC90011_300nM_1

description: Library name: Sample16


title: H1417_Day7_DMSO_1

description: Library name: Sample4


title: H1417_Day7_DMSO_2

description: Library name: Sample5


title: NCI-H196_EMPTY_Day7_DMSO_2

description: Library name: Sample20


title: RF_scRNAseq

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

country: USA

institute: Yale University

description:
Library name: scRNA-seq sample2
10x Genomics

library_source: transcriptomic single cell

data_processing:
For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in). For scATAC‑seq, raw BCL files were demultiplexed, barcode‑processed, and aligned to the GRCh38 reference using Cell Ranger ATAC v2.2 (10x Genomics). The pipeline automatically performed single‑cell peak calling, fragment counting, quality‑control metric generation, and cross‑sample aggregation ( cellranger‑atac aggr ) according to the manufacturer’s standard workflow.
Assembly: GRCh38
Supplementary files format and content: For scRNA-seq, matrix, features and barcode files. For, scATAC-seq, matrix, barcode, peak files

source_name: Brain organoid

extract_protocol:
For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 20,000 cells were used for library contruction. For scATAC‑seq, organoids were gently homogenized, and nuclei were isolated using the 10x Genomics Nuclei Isolation Kit (PN‑1000494). Approximately 15,000 nuclei were loaded onto a Chromium Next GEM Chip H, and libraries were constructed.
For scRNA-seq, Library prep was performed following 3P v4 (GEM-X)  protocol (10X Genomics). For scATAC-seq, the Chromium Next GEM Single Cell ATAC v2 Library & Gel Bead Kit according to the manufacturer’s protocol.

value: Brain organoid

value: RF


title: RF+iBET_scATACseq

description:
Library name: scATAC-seq sample3
10x Genomics

library_source: genomic single cell

molecule: genomic DNA

value: RF, iBET


title: RF_scATACseq

description:
Library name: scATAC-seq sample2
10x Genomics


title: H146_Day7_DMSO_1

description: Library name: Sample1


title: RF+Aluminum foil_scRNAseq

description:
Library name: scRNA-seq sample3
10x Genomics

value: RF, Aluminum foil


title: Control_scATACseq

description:
Library name: scATAC-seq sample1
10x Genomics


title: RF+Shield_scRNAseq

description:
Library name: scRNA-seq sample4
10x Genomics

value: RF, shield


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM7

city: DUARTE

first: Dustin

last: Schones

state: CALIFORNIA

address: 1500 E Duarte Road

institute: City of Hope National Medical Centre

description: Library name: PMM7_lib1

data_processing:
For alignment of fastq files to the human reference genome (hg38; chromosomes 1–22, X, Y, and M), we used STAR in 2-pass mode with the following parameters: --twopassMode Basic --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterType BySJout --outFilterScoreMinOverLread 0.33 --outFilterMatchNminOverLread 0.33 --limitSjdbInsertNsj 1200000 --outSAMstrandField intronMotif --outFilterIntronMotifs None --alignSoftClipAtReferenceEnds Yes --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM Unsorted --outSAMunmapped Within --genomeLoad NoSharedMemory --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimOutType Junctions SeparateSAMold WithinBAM SoftClip --chimOutJunctionFormat 1 --chimMainSegmentMultNmax 1. Gene-level raw counts were generated by STAR using the --quantMode GeneCounts option.
Assembly: hg38
Supplementary files format and content: Columns 1 to 4 of the file represent the gene ID, total counts, counts from the Watson strand, and counts from the Crick strand, respectively.
Supplementary files format and content: Gene annotation used: GENCODE v46 (gencode_v46_chr_patch_hapl_scaff_annotation.gtf).

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patients were extracted for RNA with the Qiagen RNeasy FFPE Kit.
RNA libraries were prepared with assistance from the City of Hope Integrative Genomics Core, enriched for polyadenylated RNA, and sequenced using a dUTP-based, strand-specific (reverse-stranded) RNA-Seq protocol at a depth of approximately 200 million reads per sample.

tag: tissue

value: bone marrow


title: Con_scRNAseq

description:
Library name: scRNA-seq sample1
10x Genomics


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM6

description: Library name: PMM6_lib1


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM4

description: Library name: PMM4_lib1


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM16

description: Library name: PMM16_lib1


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM3

description: Library name: PMM3_lib1


title: siNC_H1417_Day7_DMSO_3

description: Library name: Sample57


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM15

description: Library name: PMM15_lib1


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM14

description: Library name: PMM14_lib1


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM11

description: Library name: PMM11_lib1


description: Library name: PMM7_lib2

library_source: genomic

data_processing:
The TrimGalore package was used to trim adapters from each fastq file using the following parameters: "--paired --clip_R1 8 --clip_R2 8 --three_prime_clip_R1 9 --three_prime_clip_R2 9". Trimmed fastq files were aligned to the hg38 genome using the Bismark package with parameters: "--bowtie1 --non_bs_mm --unmapped --phred33-quals". CpG methylation were extracted using the Bismark methylation extractor with the following parameters: "-p --no_overlap --comprehensive --merge_non_CpG --gzip --bedGraph --counts --buffer_size 20G --cytosine_report --zero_based". The output bedGraph files were then converted to bigWig format using the UCSC wigToBigWig tool.
Assembly: hg38
Supplementary files format and content: DNA methylation percentage data in BigWig format can be visualized in IGV or similar genome browsers.

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patients were extracted for RNA with the Qiagen QIAamp DNA FFPE Tissue Kit.
DNA libraries were prepared with assistance from the City of Hope Integrative Genomics Core, bisulfite-converted with >99% efficiency using the Zymo EZ DNA Methylation-Gold Kit, and sequenced to a depth of at least 200 million reads per sample.


title: NCI-H211_EMPTY_TAS1440_300nM_2

description: Library name: Sample29


description: Library name: PMM6_lib2


description: Library name: PMM3_lib2


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM18

description: Library name: PMM18_lib2


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM2

description: Library name: PMM2_lib2


description: Library name: PMM4_lib2


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM17

description: Library name: PMM17_lib2


description: Library name: PMM16_lib2


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM12

description: Library name: PMM12_lib2


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM13

description: Library name: PMM13_lib2


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM1

description: Library name: PMM1_lib2


description: Library name: PMM14_lib2


title: ffa1483057ce26f9;PLACEBO

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: ffa1483057ce26f9

data_processing:
Reads from all samples were processed using the MoTrPAC RNA-Seq pipeline
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts for each sample

source_name: Whole Blood

extract_protocol:
Human total RNA from blood (collected in PAXgene tubes, http://www.bdbiosciences.com/us/applications/blood-collection/cell-biomarker-preservation/paxgenereg-blood-rna-tube/p/762165) was extracted using the Agencourt RNAdvance blood kit (Beckman Coulter) on an automated Biomek Fxp workstation (Beckman Coulter).The purity of the RNA was assessed using a NanoDrop (Thermo Fisher Scientific) and quantified with the Quant-iT RiboGreen RNA Assay kit (Thermo Fisher Scientific). RNA integrity (RIN) was measured using the RNA Nano 6000 Assay kit on an Agilent Bioanalyzer 2100 system (Agilent Technologies) and the samples with RIN above 7.0 were processed to libraries.
The mRNA libraries were prepared using the Universal Plus mRNA-Seq Library preparation kit (NuGEN) on an automated Biomek i7 workstation (Beckman Coulter). In brief, mRNA was purified from 400 ng of total RNA using oligo-dT beads, and cDNA was synthesized according to NuGEN’s protocol. The AnyDeplete kit (NuGEN) was used to remove ribosomal RNA (rRNA) and globin transcripts before library amplification. The purified libraries were quantified with the Qubit dsDNA HS kit (Thermo Fisher Scientific), and their size and distribution were analyzed using a Bioanalyzer with the High Sensitivity DNA kit (Agilent). After library preparation, samples were pooled, and library integrity was verified by sequencing on an Illumina MiSeq. Deep sequencing was then conducted on a NovaSeq 6000 (Illumina, Inc., San Diego, CA), with an average depth of 30 million 100 bp paired-end reads per sample.

value: Whole Blood

value: PLACEBO


description: Library name: PMM11_lib2


title: ff0304c10964b1bd;MVA-NP+M1

description: Library name: ff0304c10964b1bd


title: fee986057d0783ae;MVA-NP+M1

description: Library name: fee986057d0783ae


title: ff2521e0f555d35b;MVA-NP+M1

description: Library name: ff2521e0f555d35b


title: fe5d20e5972c3010;PLACEBO

description: Library name: fe5d20e5972c3010


title: fe4a37e07e54929b;MVA-NP+M1

description: Library name: fe4a37e07e54929b


title: fe65e8208c6f31ff;MVA-NP+M1

description: Library name: fe65e8208c6f31ff


title: fe4c9cbc1ea5e62d;PLACEBO

description: Library name: fe4c9cbc1ea5e62d


title: fe68ede197dd6673;PLACEBO

description: Library name: fe68ede197dd6673


title: Formalin-fixed, paraffin-embedded (FFPE) tissue samples from plasmablastic multiple myeloma patient: PMM9

description: Library name: PMM9_lib2


title: fda158b5f803de9f;MVA-NP+M1

description: Library name: fda158b5f803de9f


title: fe6acfc4f55befae;MVA-NP+M1

description: Library name: fe6acfc4f55befae


title: fe3d7552c5239015;PLACEBO

description: Library name: fe3d7552c5239015


title: fc0fc85b753c4789;PLACEBO

description: Library name: fc0fc85b753c4789


title: fbf493da96185115;MVA-NP+M1

description: Library name: fbf493da96185115


title: fc545c923c22ab0f;PLACEBO

description: Library name: fc545c923c22ab0f


title: fb9f6858c0a75ce3;PLACEBO

description: Library name: fb9f6858c0a75ce3


title: f8a96602c740df4e;PLACEBO

description: Library name: f8a96602c740df4e


title: faaa07e3f72b26a4;MVA-NP+M1

description: Library name: faaa07e3f72b26a4


title: fb1bc595874332c1;MVA-NP+M1

description: Library name: fb1bc595874332c1


title: f7ea579955f61214;MVA-NP+M1

description: Library name: f7ea579955f61214


title: f8a8e12bb5ad8934;MVA-NP+M1

description: Library name: f8a8e12bb5ad8934


title: f7502fc48a9c1263;MVA-NP+M1

description: Library name: f7502fc48a9c1263


title: f7ba2cfbc64be755;MVA-NP+M1

description: Library name: f7ba2cfbc64be755


title: fc92d932529b5bec;MVA-NP+M1

description: Library name: fc92d932529b5bec


title: f7248624e5b7ed28;PLACEBO

description: Library name: f7248624e5b7ed28


title: f5d1887018539f6c;MVA-NP+M1

description: Library name: f5d1887018539f6c


title: f70fb4a7da61a2dd;PLACEBO

description: Library name: f70fb4a7da61a2dd


title: f4fd12ac6f20f6fd;MVA-NP+M1

description: Library name: f4fd12ac6f20f6fd


title: f73edf9062763db2;MVA-NP+M1

description: Library name: f73edf9062763db2


title: f6819ccae9e6903a;PLACEBO

description: Library name: f6819ccae9e6903a


title: f66277ad78883334;MVA-NP+M1

description: Library name: f66277ad78883334


title: f4b45a9724e4beae;PLACEBO

description: Library name: f4b45a9724e4beae


title: fbf249aef0ee7c8d;MVA-NP+M1

description: Library name: fbf249aef0ee7c8d


title: f3deff4d011fc320;PLACEBO

description: Library name: f3deff4d011fc320


title: f35234f6872241fb;PLACEBO

description: Library name: f35234f6872241fb


title: f2aa3de5ec4a9704;PLACEBO

description: Library name: f2aa3de5ec4a9704


title: f35d8b72598716b0;PLACEBO

description: Library name: f35d8b72598716b0


title: f10925877acc728c;MVA-NP+M1

description: Library name: f10925877acc728c


title: f3a1703115467616;PLACEBO

description: Library name: f3a1703115467616


title: f166cb1ef5db77a2;MVA-NP+M1

description: Library name: f166cb1ef5db77a2


title: f1345f01a2b95127;MVA-NP+M1

description: Library name: f1345f01a2b95127


title: f3815be9b6810214;MVA-NP+M1

description: Library name: f3815be9b6810214


title: f10699b20d4d335a;MVA-NP+M1

description: Library name: f10699b20d4d335a


description: Library name: PMM15_lib2


title: f0d2b0a3e49ed86e;PLACEBO

description: Library name: f0d2b0a3e49ed86e


title: f0d8b5946bac26e4;MVA-NP+M1

description: Library name: f0d8b5946bac26e4


title: f02ecf616d69e7ab;MVA-NP+M1

description: Library name: f02ecf616d69e7ab


title: f08379e00275cefb;MVA-NP+M1

description: Library name: f08379e00275cefb


title: f011b40524227c86;PLACEBO

description: Library name: f011b40524227c86


title: eff3cdd1794266b1;MVA-NP+M1

description: Library name: eff3cdd1794266b1


title: ef61738177d3ef4b;PLACEBO

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title: TRM1-009D4

city: Gainesville

first: Philip

middle: A

last: Efron

state: FL

address: 1600 SW ARCHER RD

department: MD-SURGERY-CRITICAL CARE

institute: University of Florida

description: Library name: TRM1-009D4

data_processing:
The overall quality check of the FASTQ files was conducted using FastQC (v0.12.1).
Each read was trimmed to a total length of 80 base pairs (bps) to filter bps with low quality score with a threshold of 15 using Cutadpat (v3.4).
The resulting FASTQ files were then mapped to the human GRCh38 genome assembly using the STAR aligner (v2.7.3a).
Afterwards, RNA-Seq by Expectation Maximization (RSEM) was utilized for transcript quantification, where reads were aligned to the reference transcriptome and gene- and transcript-level expression estimates were then generated as expected counts and TPM (Transcripts Per Million) values using rsem (v1.3.3).
Assembly: GRCh38
Supplementary files format and content: A txt file contians read counts with rows being genes and columns being samples.

source_name: blood

extract_protocol:
CD66b+ cells were isolated and total RNA isolated using RNeasy Mini kit (Qiagen 74104) following manufacturers’ recommendations.  RNA was quantified using Qubit RNA Broad Range Assay Kit (Ref# Q10210; Invitrogen, MA) and RNA integrity was assessed using RNA ScreenTape kit (Ref# 5067-5576) on TapeStation 4200 (Agilent).
Illumina Stranded mRNA Prep and Ligation kit (Ref# 20040534; Illumina, CA) were used to prepare sample libraries following the manufacturer’s recommendations. Very briefly, 300 ng/uL high quality RNA was captured and purified, followed by reverse transcription to convert the captured mRNA into first and second strands of cDNA. The resulting double stranded cDNA molecules were then enzymatically fragmented in preparation for unique dual indexing using IDT for Illumina RNA UD Set Ligation Indexes (Ref# 20091655; Illumina, CA). The ligated samples were subsequently enriched through PCR amplification on Bio-Rad Thermal cycler (T100; Bio-Rad, CA) and purified using AMPure XP magnetic beads (Ref# A63881; Beckman Coulter, CA). The average fragment length of the library insert was measured to be ~300–400 bp using the dsDNA 1000 kit (Ref# 5067-5582) on Agilent TapeStation. Optimized libraries were pooled to a final concentration of 150pM. The libraries were sequenced on NovaSeq X Plus Platform (Illumina, CA) at UF’s Interdisciplinary Center for Biotechnology Research (ICBR).

value: blood

tag: time point

tag: age

tag: age group

tag: Sex

value: Female

tag: recovery

value: Unknown

tag: study arm

value: Trauma


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title: TRM1-0056m

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title: TRM1-0066m

description: Library name: TRM1-0066m

value: Under 46

value: Male


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value: SEPSIS


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title: RM1-103D4

description: Library name: RM1-103D4


title: b1f1d418b1b6eed4;MVA-NP+M1

description: Library name: b1f1d418b1b6eed4


title: RM1-098D4

description: Library name: RM1-098D4


title: RM1-099D4

description: Library name: RM1-099D4


title: b1f5f5f4d6b3ae5d;MVA-NP+M1

description: Library name: b1f5f5f4d6b3ae5d


title: RM1-096D4

description: Library name: RM1-096D4


title: RM1-0926m

description: Library name: RM1-0926m


title: RM1-096D14

description: Library name: RM1-096D14


title: b0e73c4af7a8b7d6;PLACEBO

description: Library name: b0e73c4af7a8b7d6


title: b1362cf5efd32dea;MVA-NP+M1

description: Library name: b1362cf5efd32dea


title: b0efe4646cda9f6a;PLACEBO

description: Library name: b0efe4646cda9f6a


title: RM1-095D4

description: Library name: RM1-095D4


title: b1949c898f2d2da3;PLACEBO

description: Library name: b1949c898f2d2da3


title: RM1-0916m

description: Library name: RM1-0916m


title: RM1-0816m

description: Library name: RM1-0816m


title: b0a1138811bda5ce;PLACEBO

description: Library name: b0a1138811bda5ce


title: afaba94d547d3d4d;PLACEBO

description: Library name: afaba94d547d3d4d


title: b06c776a83aad8c5;MVA-NP+M1

description: Library name: b06c776a83aad8c5


title: b05fcb04a5f16fb3;PLACEBO

description: Library name: b05fcb04a5f16fb3


title: afbd1263e01c9f22;MVA-NP+M1

description: Library name: afbd1263e01c9f22


title: b048d2001b207b97;MVA-NP+M1

description: Library name: b048d2001b207b97


title: RM1-0796m

description: Library name: RM1-0796m


title: af628ee7bbc88b85;PLACEBO

description: Library name: af628ee7bbc88b85


title: RM1-059con

description: Library name: RM1-059con


title: RM1-028con

description: Library name: RM1-028con


title: RM1-038con

description: Library name: RM1-038con


title: afb73608efa516ea;MVA-NP+M1

description: Library name: afb73608efa516ea


title: RM1-065con

description: Library name: RM1-065con


title: RM1-0886m

description: Library name: RM1-0886m


title: RM1-0866m

description: Library name: RM1-0866m


title: b8c142d679c68f92;PLACEBO

description: Library name: b8c142d679c68f92


title: aedc8d9cbdf6f611;PLACEBO

description: Library name: aedc8d9cbdf6f611


title: RM1-023con

description: Library name: RM1-023con


title: RM1-021con

description: Library name: RM1-021con


title: acb4052104f3b23a;MVA-NP+M1

description: Library name: acb4052104f3b23a


title: ac54d841c8bebc43;PLACEBO

description: Library name: ac54d841c8bebc43


title: ad5ba6f72aac9e44;PLACEBO

description: Library name: ad5ba6f72aac9e44


title: RM1-020con

description: Library name: RM1-020con


title: abe637e5946d7f2f;MVA-NP+M1

description: Library name: abe637e5946d7f2f


title: RM1-019con

description: Library name: RM1-019con


title: HeLa KO IPPK, Exp3

city: Marburg

first: Francisco

last: Venegas Solis

address: Hans-Meerwein-Straße

country: Germany

institute: Institute of Immunology, Philipps University of Marburg

description: Library name: Sample 11

data_processing:
Sequencing reads from all lanes were merged at the FASTQ level prior to analysis. Quality filtering and trimming were performed with fastp (v0.23.4) with the following non-default parameters: -q 25 -u 20 -e 30 --dont_eval_duplication -G -A. Reads shorter than 97 bp were discarded (--length_required 97), and reads longer than 100 bp were trimmed from the 3′ end to this length (--max_len1 100).
Transcript- and gene-level expression quantification was performed with Salmon (v1.10.2) using automatic library detection (-l A) and transcript-to-gene mapping (-g) based on a curated reference annotation. Reads were aligned to the human genome (hg38) with STAR (v2.7.3a) using parameters --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 600000 --outFilterMultimapNmax 1 to ensure unique alignments.
Differential expression analysis was performed on raw Salmon counts using DESeq2 (v1.48.1) in combination with tximport (v1.36.1) in R (v4.5.1). Genes with fewer than ten total counts across all samples were excluded. Log₂ fold changes were shrunk using the adaptive shrinkage (“ashr”) method to reduce noise from low-count genes. Significance was determined using false discovery rate (FDR)–adjusted p-values (Benjamini–Hochberg correction).
Global A-to-I RNA editing was quantified from STAR alignments using RNA Editing Indexer (v1.0) with the --genome hg38 flag to compute the Alu Editing Index (AEI). This index represents the mean editing level across all adenosines within Alu elements, weighted by their expression, and corresponds to the ratio of A-to-G mismatches to total aligned nucleotides in these regions — providing a robust global measure of A-to-I editing activity.
The Inverted Alu 3′UTR Editing Index was calculated similarly over inverted Alu clusters (-rb), defined as 3′UTR exons containing at least two Alu elements (each >200 bp) oriented on opposite strands. This metric captures editing activity within double-stranded RNA–forming 3′UTR structures, serving as a proxy for cytoplasmic A-to-I editing potential.
Site-specific RNA editing levels of the dataset of annotated editing sites described by Gabay et al. (https://doi.org/10.1038/s41467-022-28841-4) were quantified with REDItools 1.0 in known-site mode with the following non-default parameters: -v 1 -n 0.001 -r 1 -T5-5 -c 1.
Assembly: Reads were aligned to the human genome (hg38) with STAR (v2.7.3a) using parameters --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 600000 --outFilterMultimapNmax 1 to ensure unique alignments.
Supplementary files format and content: normalizedCounts.csv file contains normalized counts
Supplementary files format and content: DESeq2_results_allSamples.xlsx file includes DESeq2 results
Supplementary files format and content: RNA_Editing_Indexes.csv file contains Alu editing index and inverted alu 3′UTR editing index of all samples
Supplementary files format and content: Known_sites_editing_levels.csv file contain Site-specific RNA editing levels of the dataset of annotated editing sites

source_name: Uterus; Cervix

growth_protocol: HeLa cells were maintained at 37 °C and 5% CO2 in RPMI 1640 medium supplemented with 10% FCS, 2 mmol/L L-glutamine, 100 U/mL penicillin G and 0.1% 2-mercaptoethanol

extract_protocol:
total RNA was extracted using TRIzol reagent (Cat. #15596026, Invitrogen) according to the manufacturer’s instructions. Residual genomic DNA was removed with DNase I recombinant RNase-free (Cat. #04716728001, Roche), and RNA was subsequently purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
Library preparation was carried out using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) following the manufacturer’s protocol.

treatment_protocol: HeLa WT and HeLa KO IPPK cells were seeded in 12-well plate (500 000 cells/1mL) and treated with Pro-IP6 10 µM or DMSO as control for 24 h

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: KO IPPK

value: Control

tag: time


title: RM1-014con

description: Library name: RM1-014con

value: blood


title: abdd3dffe9e11849;MVA-NP+M1

description: Library name: abdd3dffe9e11849

value: Whole Blood


title: abb7e47633f122ac;PLACEBO

description: Library name: abb7e47633f122ac

value: PLACEBO


title: HeLa KO IPPK, Exp2

description: Library name: Sample 7


title: HeLa WT+Pro-IP6 10 µM, Exp2

description: Library name: Sample 6

value: WT

value: Pro-IP6 10 µM


title: HeLa KO IPPK+Pro-IP6 10 µM, Exp2

description: Library name: Sample 8


title: aad9462417b8280b;PLACEBO

description: Library name: aad9462417b8280b


title: ab5fccb58dc3ac1f;PLACEBO

description: Library name: ab5fccb58dc3ac1f


title: HeLa WT, Exp2

description: Library name: Sample 5


title: ab9ec08cf6cbfd6a;PLACEBO

description: Library name: ab9ec08cf6cbfd6a


title: HeLa WT+Pro-IP6 10 µM, Exp3

description: Library name: Sample 10


title: aaccb00e7788c2a8;MVA-NP+M1

description: Library name: aaccb00e7788c2a8


title: aaa2cb36808cac2e;MVA-NP+M1

description: Library name: aaa2cb36808cac2e


title: ab35346a78855314;PLACEBO

description: Library name: ab35346a78855314


title: HeLa WT, Exp3

description: Library name: Sample 9


title: HeLa KO IPPK+Pro-IP6 10 µM, Exp1

description: Library name: Sample 4


title: ab899fa0a7f63d02;MVA-NP+M1

description: Library name: ab899fa0a7f63d02


title: aa2abfa3b6672e0a;MVA-NP+M1

description: Library name: aa2abfa3b6672e0a


title: aa0411b2696b42ee;MVA-NP+M1

description: Library name: aa0411b2696b42ee


title: HeLa KO IPPK+Pro-IP6 10 µM, Exp3

description: Library name: Sample 12


title: HeLa WT, Exp1

description: Library name: Sample 1


title: a955dfb29d62c93f;MVA-NP+M1

description: Library name: a955dfb29d62c93f


title: a926cd46ea4edc34;MVA-NP+M1

description: Library name: a926cd46ea4edc34


title: a8e9973657e7690b;MVA-NP+M1

description: Library name: a8e9973657e7690b


title: full-length SAA at 120 minutes

city: Baltimore

first: George

middle: Henry

last: Sack

state: Maryland

address: 725 N. Wolfe Street

department: Department of Physiology, Pharmacology and Therapeutics

institute: Johns Hopkins University School of Medicine

description: Library name: GSac-7_lib6

data_processing:
Reads were initially quality checked using Fastqc (0.11.9).
Reads were aligned to the hg38 human reference genome using STAR aligner (2.7.10a).
Counts were extracted using htseq (2.0.5).
Differential RNA expression analysis was performed on R (4.4.0) using Deseq2 (1.44.0).
The adjusted p-value was calculated with Benjamini Hochberg False Discover Rate Correction (FDR).
Assembly: hg-38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Small Intestine

growth_protocol: Human enteroids (107C P19 111021) were grown in transwells using NDM media (gift of Drs. Mark Donowitz and Jennifer Foulk-Abel).

extract_protocol:
For harvest, medium was removed, and cells were washed with 0.5 ml of PBS at 4°C. RNA was isolated from both apical and basolateral compartments using the PureLink® RNA MiniKit. Cells were lysed in 300 µl “Lysis Buffer,” triturated, and transferred to a fresh tube. 300 µl of 70% ethanol was added, and tubes were placed at -20°C overnight. RNA isolation continued per kit instructions, yielding a final volume of 50 µl. Samples were frozen at -20°C prior to transcriptional analysis.
Libraries were prepared using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit with 100 ng total RNA input. RNA quantitation was performed with Nanodrop, and RNA quality was assessed on an Agilent Fragment Analyzer (High Sensitivity Total RNA assay). Library concentrations were measured using Qubit, and quality was checked on an Agilent Fragment Analyzer (High Sensitivity Large Fragment method). Libraries were normalized to 5 nM for pooling, and pool concentration was verified by both Fragment Analyzer assay and qPCR. Libraries were diluted to 4 nM in 50 µl for sequencing on NovaSeq X Plus.

treatment_protocol: For N-terminal oligomer studies, decapeptides corresponding to the N-terminus of bovine mSAA (sequence #1 M-W-G-T-F-L-K-E-A-G) and a scrambled sequence (#2 G-K-F-A-W-E-G-M-T-L) were prepared at 100 µg/ml in PBS (gift of Dr. Thomas McDonald, purity verified by mass spectrometry). For experiments, the solution containing decapeptide #1 was added to both the apical (10 µl [8.8 pmole]/100 µl) and basolateral (60 µl [53 pmole]/600 µl) compartments of the transwells. Control wells received equivalent PBS volumes. Incubation continued for up to 4 hrs at 37°C.

value: Small Intestine

value: human intestinal enteroid

value: Full SAA


title: full-length SAA at 0 minutes

description: Library name: GSac-5_lib4


title: full-length SAA at 60 minutes

description: Library name: GSac-6_lib5


title: a8a4cb9bdfd4104c;PLACEBO

description: Library name: a8a4cb9bdfd4104c


title: a89af3cdae739582;MVA-NP+M1

description: Library name: a89af3cdae739582


title: HeLa KO IPPK, Exp1

description: Library name: Sample 3


title: a7663571b1d0680b;MVA-NP+M1

description: Library name: a7663571b1d0680b


title: a8a2dac44ec5c340;MVA-NP+M1

description: Library name: a8a2dac44ec5c340


title: 10-mer at 60 minutes

description: Library name: GSac-2_lib2

value: SAA


title: HeLa WT+Pro-IP6 10 µM, Exp1

description: Library name: Sample 2


title: 10-mer at 0 minutes

description: Library name: GSac-1_lib1


title: a6eecce4e1fbc871;MVA-NP+M1

description: Library name: a6eecce4e1fbc871


title: Skin CD45+ cells-5

city: San Francisco

first: Henry

last: Rodriguez

address: 1322 3rd avenue

institute: University of California San Francisco

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L005
10X Genomics

data_processing:
Human raw sequencing data were aligned and quantified against the human reference genome GRCh38 using CellRanger (10X Genomics). Cells with more than 15% mitochondrial and 60% ribosomal content were excluded. Donor samples were then demultiplexed based on sequenced SNPs using the Demuxlet software. Intrasample doublets were removed using DoubletFinder. Cell cycle scores were computed, then data was normalized and scaled while regressing out mitochondrial and ribosomal content, number of genes, UMIs, and cell cycle scores. PCA, UMAP, and differentially expressed genes (DEGs) were then calculated. Cell clusters were manually annotated and grouped into major immune cell types, including B-cells, T-cells, NK-cells and myeloid cells, and quantified for each donor. Myeloid cell clusters were subset, normalized, scaled, and PCAs, neighbor identification, clustering, and UMAP were analyzed. DEGs and cluster annotations were performed as described above.
Assembly: human reference genome GRCh38
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: myeloid_cells.rds
Supplementary files format and content: skin_cells.rds
Supplementary files format and content: XDEV-POOL-DB11-SCG1.clust1.samples.reduced.tsv
Supplementary files format and content: XDEV-POOL-DB11-SCG1_processed.rds

source_name: Skin

extract_protocol:
Samples were processed using a dermatome to isolate the top layer of the epidermis at a thickness of 0.6 µM and subsequently cut into pieces no larger than 4mm by 4mm. Skin pieces were cryopreserved with FCS with 10% DMSO at -80°C until thawing and processing. Tissue pieces were thawed with complete media (RPMI 1640, 10% FCS, 1% PSG, 1% HEPES) and rinsed with fresh complete media to thoroughly remove residual DMSO from the freezing media. Skin tissue was digested in resting media (89% RPMI 1640, 10% FCS and 1% Pen-Strep-Glut) containing 750 ug/ml Collagenase IV and 20 ug/ml DNase I for 2 hours at 37°C. Cells were filtered through a 100 µm strainer, centrifuged at 500g for 5 minutes at 4°C, counted, and resuspended for flow cytometry staining. Cells were transferred to a 96-well v-bottom plate and stained with LIVE/DEAD Fixable Aqua (1:500 in 1X PBS, 20 million cells per 1mL). Cells were washed with 150uL of sort buffer (2mM EDTA, 2% FBS in 1X PBS), centrifuged at 500g for 5 minutes at 4°C, and incubated with the antibody surface cocktail for 30 minutes at 4°C. Cells were washed with 150uL of sort buffer and centrifuged at 500g for 5 minutes at 4°C. Live CD45+ cells were sorted with FACSAria Fusion Flow Cytometer.
Cells from four donors were evenly pooled (approximately 14K cells per donor) and encapsulated using the Chromium Next GEM Single Cell 5’ Reagent Kits V2 (Dual Index) according to the manufacturer’s instructions. Libraries were amplified with 13 cycles of cDNA amplification. Sequencing was performed on the NovaSeq X Plus instrument at the UCSF Center for Advanced Technology.

value: Skin

tag: subject status

value: healthy human donor


title: a5f2fac8fbc19737;PLACEBO

description: Library name: a5f2fac8fbc19737


title: Skin CD45+ cells-6

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L006
10X Genomics


title: Skin CD45+ cells-7

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L007
10X Genomics


title: Skin CD45+ cells-4

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L004
10X Genomics


title: a6f5bb3346dbf5c5;PLACEBO

description: Library name: a6f5bb3346dbf5c5


title: a40da0029f02fded;PLACEBO

description: Library name: a40da0029f02fded


title: b6c217cb424ece00;PLACEBO

description: Library name: b6c217cb424ece00


title: Skin CD45+ cells-3

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L003
10X Genomics


title: a412fff8592a9568;MVA-NP+M1

description: Library name: a412fff8592a9568


title: Skin CD45+ cells-2

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L002
10X Genomics


title: Skin CD45+ cells-1

description:
Library name: XDEV-POOL-DB11-SCG1_S31_L001
10X Genomics


title: Well 4, baseline control, no additions.

description: Library name: GSac-4_lib3


title: a31d95fd858aa53f;MVA-NP+M1

description: Library name: a31d95fd858aa53f


title: a353cb350be5a993;PLACEBO

description: Library name: a353cb350be5a993


title: BRMi_3, RNA-seq

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

data_processing:
Raw fastq files were aligned using STAR v2.6.0. Raw counts were calculated by STAR, FPKM values were calculated by in-house perl script
Assembly: hg38
Supplementary files format and content: txt files of raw counts and FPKM values

source_name: Breast

growth_protocol: MDA-MB-468 breast cancer cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), penicillin sodium (100 U/mL), and streptomycin sulfate (100 µg/mL).

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA) following the manufacturer’s instructions.
RNA-seq libraries were prepared from 0.5 μg of high-quality DNA-free RNA using NEBNext Ultra RNA Library Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: MDA-MB-468 cells were treated with either DMSO, IPZ (10µM) for 24 hours, or BRMi (1µM) for 72 hours and then collected for RNA analysis.

value: Breast

value: Breast cancer cell

value: BRMi #3


title: a17bf811d523b8eb;PLACEBO

description: Library name: a17bf811d523b8eb


title: a1dcf2af44e79d95;PLACEBO

description: Library name: a1dcf2af44e79d95


title: BRMi_1, RNA-seq

value: BRMi #1


title: a1ab2f71c4d8c526;PLACEBO

description: Library name: a1ab2f71c4d8c526


title: IPZ_3, RNA-seq

value: IPZ #3


title: a196e6f2970c6b87;MVA-NP+M1

description: Library name: a196e6f2970c6b87


title: BRMi_2, RNA-seq

value: BRMi #2


title: IPZ_2, RNA-seq

value: IPZ #2


title: IPZ_1, RNA-seq

value: IPZ #1


title: 9f78539cf7ac9274;MVA-NP+M1

description: Library name: 9f78539cf7ac9274

value: Whole Blood


title: a063a8a8d59e505f;MVA-NP+M1

description: Library name: a063a8a8d59e505f


title: Control_3, RNA-seq

value: WT

value: Control #3


title: 9f42cabe0e6cd993;PLACEBO

description: Library name: 9f42cabe0e6cd993

value: PLACEBO


title: Control_2, RNA-seq

value: Control #2


title: 9f62e974571a9184;MVA-NP+M1

description: Library name: 9f62e974571a9184


title: 9f0f95182e874998;MVA-NP+M1

description: Library name: 9f0f95182e874998


title: BRMi_2, ATAC-seq

data_processing:
FastQC was used to check data quality. ATAC-seq reads were aligned to the Human Reference Genome hg38 using Bowtie2. PCR duplicate reads were removed with picard. Adaptors were trimmed with Trimmomatic. ATAC-seq peak identification, overlapping, subtraction, and feature annotation of enriched regions were performed using the HOMER (Hypergeometric Optimization of Motif EnRichment) suite.
Assembly: hg38
Supplementary files format and content: bigwig files generated by deepTools using CPM values

extract_protocol:
50,000 cells were washed once with 1 × PBS and resuspended in 100 μl lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP 40, 0.1% Tween-20, 0.01% Digitonin) for 3min on ice, followed by adding 1ml of wash buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) to remove cytoplasm and mitochondria fraction.
The nuclei were resuspended in 25 μl transposition mix (12.5 ul 2x TD buffer, 2.5 μl Tn5 Transposome, 8.25 μl 1xPBS, 0.25 μl 1% digitonin, 0.25 μl 10% Tween-20, 1.25 μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 300 r.p.m. mixing. The tagmented DNA was purified using the DNA Clean & Concentrator-5 kit (ZYMO Research). Libraries were amplified and adapter dimers and primer dimers were cleaned up. Paired-end reads (50 bp) were sequenced using an Illumina HiSeq 4000.

treatment_protocol: MDA-MB-468 cells were treated with either DMSO, IPZ (10µM), or BRMi (1µM) for 24 hours and then collected for ATAC-seq analysis.


title: BRMi_1, ATAC-seq


title: 9ec098b0ef7faf96;MVA-NP+M1

description: Library name: 9ec098b0ef7faf96


title: Control_2, ATAC-seq


title: 9e4fdda092dfc3a4;PLACEBO

description: Library name: 9e4fdda092dfc3a4


title: 9ddc5241494583af;MVA-NP+M1

description: Library name: 9ddc5241494583af


title: 9ccecae7ca43128d;PLACEBO

description: Library name: 9ccecae7ca43128d


title: IPZ_2, ATAC-seq


title: Control_1, RNA-seq

value: Control #1


title: 9ca57d43c808f711;MVA-NP+M1

description: Library name: 9ca57d43c808f711


title: Control_1, ATAC-seq


title: IPZ_1, ATAC-seq


title: 9d3ae244b60d56c6;PLACEBO

description: Library name: 9d3ae244b60d56c6


title: a031d74c6d1962b1;PLACEBO

description: Library name: a031d74c6d1962b1


title: Wild type Succinate Rep 3

city: Ithaca

first: Josh

last: Kerkaert

address: 236 Tower Rd

institute: Cornell University

description: Library name: yku70D_Succinate_Rep3

data_processing:
The fastq files were generated using the Illumina software pipeline v. 2.18.
Sequenced reads were trimmed using fastp v. 0.23.4 with the --trim_poly_x setting and aligned to the R. toruloides IFO0880 genome (v4) using STAR v. 2.7.11b with --alignIntronMin set to 5. BAM files were indexed using Samtools v. 1.20. All the wild type BAM files output by STAR were combined and used as input for the tool peaks2utr v. 1.4.1 in order to annotate any missing or trucated 3’UTRs. Reads were counted using HTSeq v. 2.0.9 with --nonunique set to random, -t set to mRNA, and -i set to ProteinId using the peaks2utr output GFF3 file.
Assembly: Rhodosporidium toruloides IFO0880 (NBRC0880) v.4 (https://mycocosm.jgi.doe.gov/Rhoto_IFO0880_4/Rhoto_IFO0880_4.home.html)
Supplementary files format and content: Tab-delimited text file with counts per million (CPM) values the succinate samples that is compatible with the previously submitted processed data. The succinate samples were only used for better 3'UTR annotation, but were sequenced on the same sequencing run as the previously uploaded samples and the files were processed in the same manner.
Supplementary files format and content: Tab-delimited text file with counts per million (CPM) values for the Vogel's minimal media samples. These samples are from a separate sequencing run from the rest of the uploaded samples. We needed a better annotation of the 3'UTRs for this genome and these samples were used as part of that process.

organism: Rhodotorula toruloides

growth_protocol: R. toruloides cells were inoculated into yeast extract peptone dextrose (YPD) medium and grown overnight at 28C with constant shaking at 250RPM in constant light until cells were in exponenetial growth phase.

extract_protocol:
Cells were harvested by centrifugation and flash frozen using liquid nitrogen. RNA was isolated using the Zymo Quick-RNA Fungal/Bacterial Ki according to manufacturer's protocols. RNA was treated with DNaseI (NEB) at 37C for 10 minutes followed by RNA cleanup using the Monarch Spin RNA Cleanup (NEB). RNA integrity was checked via agarose gel and spot-checked via BioAnalyzer.
RNA libraries were prepared for sequencing using the Lexogen QuantSeq FWD V2 kit.

treatment_protocol: For succinate samples, cells were washed 3 times in yeast nitrogen base with NH4SO4 w/out amino acids + 12mM K2HPO4 + 38mM KH2PO4 + 100nM Fe(II)SO4 pH 6.2 (YNB) medium without a carbon source. Cells were then transferred to 100mL of YNB with 1% succinate at an OD600 of 0.1 and incubated at 28C with constant shaking at 200RPM in constant light for 24 hours. For glucose samples, cells were washed 3 times in Vogel's minimal media with 50mM NH4Cl instead of 25mM NH4NO3 (VMM_NH4Cl) + 2% glucose. Cells were then transferred to 100mL of VMM_NH4Cl + 2% glucose at an OD600 of 0.1 and incubated at 28C with constant shaking at 200RPM in constant light for 8 hours.

value: Yeast cells

value: Succinate 24h


title: Wild type Succinate Rep 1

description: Library name: yku70D_Succinate_Rep1


title: 9b2d1e02dc42c75a;PLACEBO

description: Library name: 9b2d1e02dc42c75a


title: 9c1dc8a4ff72f805;PLACEBO

description: Library name: 9c1dc8a4ff72f805


title: Wild type Succinate Rep 2

description: Library name: yku70D_Succinate_Rep2


title: tct1∆ Citrate Rep 2

description: Library name: tct1D_Citrate_Rep2

data_processing:
The fastq files were generated using the Illumina software pipeline v. 2.18.
Sequenced reads were trimmed using fastp v. 0.23.4 with the --trim_poly_x setting and aligned to the R. toruloides IFO0880 genome (v4) using STAR v. 2.7.11b with --alignIntronMin set to 5. BAM files were indexed using Samtools v. 1.20. All the BAM files output by STAR were combined and used as input for the tool peaks2utr v. 1.4.1 in order to annotate any missing or trucated 3’UTRs. Reads were counted using HTSeq v. 2.0.9 with --nonunique set to random, -t set to mRNA, and -i set to ProteinId using the peaks2utr output GFF3 file.
Assembly: Rhodosporidium toruloides IFO0880 (NBRC0880) v.4 (https://mycocosm.jgi.doe.gov/Rhoto_IFO0880_4/Rhoto_IFO0880_4.home.html)
Supplementary files format and content: Tab-delimited text file with counts per million (CPM) values for each sample.
Supplementary files format and content: GFF3 file generated by peaks2utr. This GFF3 file was used for determining counts of each gene with HTSeq in the data processing.

extract_protocol:
Cells were harvested by centrifugation and flash frozen using liquid nitrogen. RNA was isolated using the Zymo Quick-RNA Fungal/Bacterial Ki according to manufacturer's protocols. RNA was treated with DNaseI (NEB) at 37C for 10 minutes followed by RNA cleanup using the Monarch Spin RNA Cleanup (NEB). RNA integrity was checked via agarose gel and spot-checked via BioAnalyzer.
RNA were prepared for sequencing using poly-A enrichment and standard Illumina protocols.

treatment_protocol: Cells were washed 3 times in yeast nitrogen base with NH4SO4 w/out amino acids + 12mM K2HPO4 + 38mM KH2PO4 + 100nM Fe(II)SO4 pH 6.2 (YNB) medium without a carbon source. Cells were then transferred to 100mL of YNB with either 1% fucose, 1% cellobiose, or 1% citrate as indicated at an OD600 of 0.1 and incubated at 28C with constant shaking at 200RPM in constant light. Fucose cultures were incubated for 8 hours, cellobiose cultures were incubated for 4 hours, and citrate cultures were incubated for 24 hours prior to harvesting for RNA extraction.

value: yku70::HygR tct1::G418R

value: Citrate 24h


title: tct1∆ Citrate Rep 1

description: Library name: tct1D_Citrate_Rep1


title: 9d6c052e7d53e804;PLACEBO

description: Library name: 9d6c052e7d53e804


title: cbr1∆ Citrate Rep 3

description: Library name: cbr1D_Citrate_Rep3

value: yku70::HygR cbr1::NatR


title: tct1∆ Citrate Rep 3

description: Library name: tct1D_Citrate_Rep3


title: 9aa8eb7452f3ffdd;PLACEBO

description: Library name: 9aa8eb7452f3ffdd


title: cbr1∆ Citrate Rep 2

description: Library name: cbr1D_Citrate_Rep2


title: 9b1e029f940ae81e;PLACEBO

description: Library name: 9b1e029f940ae81e


title: 9a02a0a9e79aa03a;MVA-NP+M1

description: Library name: 9a02a0a9e79aa03a


title: 9a015e9fc8a03e84;MVA-NP+M1

description: Library name: 9a015e9fc8a03e84


title: 9a9422e409b19713;MVA-NP+M1

description: Library name: 9a9422e409b19713


title: cbr1∆ Citrate Rep 1

description: Library name: cbr1D_Citrate_Rep1


title: 9a66174faa78082e;MVA-NP+M1

description: Library name: 9a66174faa78082e


title: 99960ff11f609250;PLACEBO

description: Library name: 99960ff11f609250


title: b6e060ae159731f6;MVA-NP+M1

description: Library name: b6e060ae159731f6


title: Wild type Citrate Rep 3

description: Library name: yku70D_Citrate_Rep3


title: Wild type Citrate Rep 1

description: Library name: yku70D_Citrate_Rep1


title: 999bcf0ae20152f7;MVA-NP+M1

description: Library name: 999bcf0ae20152f7


title: bgl1∆bgl2∆ Cellobiose Rep 3

description: Library name: bgl1Dbgl2D_Cellobiose_Rep3

value: yku70::HygR bgl1bgl2::NatR

value: Cellobiose 4h


title: Wild type Citrate Rep 2

description: Library name: yku70D_Citrate_Rep2


title: bgl1∆bgl2∆ Cellobiose Rep 1

description: Library name: bgl1Dbgl2D_Cellobiose_Rep1


title: bgl1∆bgl2∆ Cellobiose Rep 2

description: Library name: bgl1Dbgl2D_Cellobiose_Rep2


title: 997316ccbe110de9;PLACEBO

description: Library name: 997316ccbe110de9


title: 991734ec4fa8c148;MVA-NP+M1

description: Library name: 991734ec4fa8c148


title: cbr1∆ Cellobiose Rep 3

description: Library name: cbr1D_Cellobiose_Rep3


title: cd6ed21cb8f76bc1;MVA-NP+M1

description: Library name: cd6ed21cb8f76bc1


title: 9b92b5a7991f0b22;MVA-NP+M1

description: Library name: 9b92b5a7991f0b22


title: TRM1-009D14

description: Library name: TRM1-009D14

value: blood

value: Female

value: Unknown

value: Trauma


title: 9aef4181b204207f;MVA-NP+M1

description: Library name: 9aef4181b204207f

value: Whole Blood


title: 97d3e82027f649ba;MVA-NP+M1

description: Library name: 97d3e82027f649ba


title: 96c4fca2257bd571;PLACEBO

description: Library name: 96c4fca2257bd571


title: cbr1∆ Cellobiose Rep 2

description: Library name: cbr1D_Cellobiose_Rep2


title: cbr1∆ Cellobiose Rep 1

description: Library name: cbr1D_Cellobiose_Rep1


title: 96fb50a888d771c6;MVA-NP+M1

description: Library name: 96fb50a888d771c6


title: Wild type Cellobiose Rep 3

description: Library name: yku70D_Cellobiose_Rep3


title: 96a3af735c4a116e;PLACEBO

description: Library name: 96a3af735c4a116e


title: Wild type Cellobiose Rep 2

description: Library name: yku70D_Cellobiose_Rep2


title: 967d11708d4faa23;MVA-NP+M1

description: Library name: 967d11708d4faa23


title: 95c1e5bd63c0b362;PLACEBO

description: Library name: 95c1e5bd63c0b362


title: 95e032e173920dc4;PLACEBO

description: Library name: 95e032e173920dc4


title: Wild type Cellobiose Rep 1

description: Library name: yku70D_Cellobiose_Rep1


title: cbr1∆ Fucose Rep 1

description: Library name: cbr1D_Fucose_Rep1

value: Fucose 8h


title: 940ba7eeffe186ee;PLACEBO

description: Library name: 940ba7eeffe186ee


title: 947e125a230c9ed0;PLACEBO

description: Library name: 947e125a230c9ed0


title: cbr1∆ Fucose Rep 3

description: Library name: cbr1D_Fucose_Rep3


title: Wild type Fucose Rep 3

description: Library name: yku70D_Fucose_Rep3


title: Wild type Fucose Rep 1

description: Library name: yku70D_Fucose_Rep1


title: 93e6d0928a44284b;MVA-NP+M1

description: Library name: 93e6d0928a44284b


title: 9413dab9ec1f5cb4;PLACEBO

description: Library name: 9413dab9ec1f5cb4


title: cbr1∆ Fucose Rep 2

description: Library name: cbr1D_Fucose_Rep2


title: 93e30cf75ee46a33;MVA-NP+M1

description: Library name: 93e30cf75ee46a33


title: Wild type Fucose Rep 2

description: Library name: yku70D_Fucose_Rep2


title: 92f07ce462c14b18;PLACEBO

description: Library name: 92f07ce462c14b18


title: 930f8a22126508d0;PLACEBO

description: Library name: 930f8a22126508d0


title: 935df861d8ca5dc1;PLACEBO

description: Library name: 935df861d8ca5dc1


title: HN95 leaves under saline-alkaline stress with nano-SiO2+MT  treatment，the treatment，biol rep 1

city: Daqing

first: Qiang

middle: zihan zhao

last: Zhao

state: Heilongjiang

address: 5 Xinfeng Road

country: China

institute: Heilongjiang Bayi Agricultural University

description:
Library name: Sample 10
FPKM.SMT_1

data_processing:
Qualified libraries with an average insert size of ~300 bp and concentration > 2 nM were pooled and sequenced on an Illumina NovaSeq 6000 platform (Illumina) using a 150 bp paired-end (PE150) sequencing strategy, generating approximately 6 Gb of clean data per sample. The sequencing data was analyzed using the LC-Cloud platform (https://www.omicstudio.cn/home). Differential expression analysis between treatment groups was conducted using DESeq2 (v1.34.0) in R software (v4.1.2).
Assembly: GCA_000004515.6
Supplementary files format and content: Supplemantary_liles_fomat_and_cnnient processed dala

organism: Glycine max

source_name: leaves

growth_protocol: Soybean plants was growth in the propylene pots filled with 20 kg of mixed soil consisting of peat soil and vermiculite (v:v = 3:1). The 3 L of mixed saline-alkali solution (containing 40 mM NaCl, 40 mM Na2CO3, 320 mM NaHCO3, and 320 mM Na2SO4)

extract_protocol:
The total RNA was extracted from 0.1g fresh samples preserved at -80℃ using the TransZol Plant (TRANS) following the manufacturer's instructions.
mRNA was enriched from 1 μg of high-quality total RNA using oligo(dT) magnetic beads (Illumina). Purified mRNA was fragmented into ~200 bp fragments using divalent cations under elevated temperature. The first-strand and second-strand cDNA were synthesized sequentially, and amplified by PCR to generate final cDNA libraries.

treatment_protocol: 200 mg/L nano-SiO2,300 μM melatonin, and 200 mg/L nano-SiO2+300 μM melatonin was foliar spray sprayed on the soybean leaves,respectively

value: leaves

value: WT

value: 200 mg/L nano-SiO2+300 μM melatonin

tag: batch


title: 9293e10d098251fd;PLACEBO

description: Library name: 9293e10d098251fd

value: PLACEBO


title: HN95 leaves under saline-alkaline stress with nano-SiO2+MT treatment，the treatment，biol rep 3

description:
Library name: Sample 12
FPKM.SMT_3


title: HN95 leaves under saline-alkaline stress with MT treatment，the treatment，biol rep 3

description:
Library name: Sample 9
FPKM.MT_3

value: 300 μM melatonin


title: HN95 leaves under saline-alkaline stress with MT treatment，the treatment，biol rep 2

description:
Library name: Sample 8
FPKM.MT_2


title: HN95 leaves under saline-alkaline stress with nano-SiO2+MT treatment，the treatment，biol rep 2

description:
Library name: Sample 11
FPKM.SMT_2


title: 91c23af49035193a;MVA-NP+M1

description: Library name: 91c23af49035193a


title: HN95 leaves under saline-alkaline stress with nano-SiO2  treatment，the treatment，biol rep 3

description:
Library name: Sample 6
FPKM.SIO2_3

value: 200 mg/L nano-SiO₂


title: HN95 leaves under saline-alkaline stress with nano-SiO2  treatment，the treatment，biol rep 2

description:
Library name: Sample 5
FPKM.SIO2_2


title: 90624685250bfd51;MVA-NP+M1

description: Library name: 90624685250bfd51


title: 902d810811256855;MVA-NP+M1

description: Library name: 902d810811256855


title: HN95 leaves under saline-alkaline stress with MT treatment，the treatment，biol rep 1

description:
Library name: Sample 7
FPKM.MT_1


title: HN95 leaves under saline-alkaline stress with nano-SiO2  treatment，the treatment，biol rep 1

description:
Library name: Sample 4
FPKM.SIO2_1

value: 200 mg/L nano-SiO2


title: 9012857851166988;MVA-NP+M1

description: Library name: 9012857851166988


title: 8f263d0495763688;MVA-NP+M1

description: Library name: 8f263d0495763688


title: 8f21499255746d8d;PLACEBO

description: Library name: 8f21499255746d8d


title: 8e968bae741c7d73;PLACEBO

description: Library name: 8e968bae741c7d73


title: HN95 leaves under saline-alkaline stress，the control，biol rep 3

description:
Library name: Sample 3
FPKM.CK_3


title: HN95 leaves under saline-alkaline stress with MSNs treatment，the treatment，biol rep 3

description:
Library name: Sample 6
FPKM.b_3

treatment_protocol: 20mg/L MSNs was foliar spray sprayed on the soybean leaves

value: 22mg/L MSNs


title: HN95 leaves under saline-alkaline stress，the control，biol rep 1

description:
Library name: Sample 1
FPKM.CK_1


description:
Library name: Sample 3
FPKM.a_3


title: 8e281cd4c642d0ce;MVA-NP+M1

description: Library name: 8e281cd4c642d0ce


title: HN95 leaves under saline-alkaline stress with MSNs treatment，the treatment，biol rep 2

description:
Library name: Sample 5
FPKM.b_2

value: 21mg/L MSNs


title: 8dab09917de8563d;MVA-NP+M1

description: Library name: 8dab09917de8563d


title: HN95 leaves under saline-alkaline stress with MSNs treatment，the treatment，biol rep 1

description:
Library name: Sample 4
FPKM.b_1

value: 20mg/L MSNs


title: 90db9447386d9803;MVA-NP+M1

description: Library name: 90db9447386d9803


description:
Library name: Sample 1
FPKM.a_1


title: 8d697b530c0376cc;MVA-NP+M1

description: Library name: 8d697b530c0376cc


title: 8c830fa782784d43;PLACEBO

description: Library name: 8c830fa782784d43


title: ASO_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: lung

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 600ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: lung

value: IPF Precision-cut lung slices

value: live sections

value: ION363 (FUS-ASO)


title: HN95 leaves under saline-alkaline stress，the control，biol rep 2

description:
Library name: Sample 2
FPKM.CK_2


title: 8d6d96810e12dac1;PLACEBO

description: Library name: 8d6d96810e12dac1


title: ASO_1

description: Library name: Sample 4


title: 8e4ecb5dbfbb7610;MVA-NP+M1

description: Library name: 8e4ecb5dbfbb7610


title: 8a323b142c7902cc;MVA-NP+M1

description: Library name: 8a323b142c7902cc


title: 898c67e8f1fcbca0;MVA-NP+M1

description: Library name: 898c67e8f1fcbca0


title: 89b41c55f7094d3c;MVA-NP+M1

description: Library name: 89b41c55f7094d3c


title: ASO_2

description: Library name: Sample 5


title: Scr_1

description: Library name: Sample 1

value: Scr-ASO


title: Scr_2

description: Library name: Sample 2


title: 894f7ae7f10d6b1b;MVA-NP+M1

description: Library name: 894f7ae7f10d6b1b

value: Whole Blood


title: Scr_3

description: Library name: Sample 3


title: 894aa6b403d57a9f;MVA-NP+M1

description: Library name: 894aa6b403d57a9f


title: 8918b51d12813e44;MVA-NP+M1

description: Library name: 8918b51d12813e44


description:
Library name: Sample 2
FPKM.a_2


title: siFUS_3

description: Library name: Sample 15

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 1¬µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit HI Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: Primary human IPF lung fibroblasts

value: primary cells, fibroblasts

value: siRNA for FUS


title: siFUS_4

description: Library name: Sample 16


title: 88fdb36b991aa4b8;MVA-NP+M1

description: Library name: 88fdb36b991aa4b8


title: 88d63d3093b9f571;MVA-NP+M1

description: Library name: 88d63d3093b9f571


title: 8d66dea92c51f0b6;MVA-NP+M1

description: Library name: 8d66dea92c51f0b6


title: scr-siFUS_4

description: Library name: Sample 12

value: non-targeting siRNA (Scr)


title: 88ba47ab6d28749e;MVA-NP+M1

description: Library name: 88ba47ab6d28749e


title: siFUS_2

description: Library name: Sample 14


title: siFUS_1

description: Library name: Sample 13


title: scr-siFUS_3

description: Library name: Sample 11


title: 881bca805d19e8f0;MVA-NP+M1

description: Library name: 881bca805d19e8f0


title: ION-363_2

description: Library name: Sample 6


title: 88b3baaf829afc0e;MVA-NP+M1

description: Library name: 88b3baaf829afc0e


title: 870ccedb2d20ca1c;MVA-NP+M1

description: Library name: 870ccedb2d20ca1c


title: scr-siFUS_1

description: Library name: Sample 9


title: 876ff2a608f4de88;PLACEBO

description: Library name: 876ff2a608f4de88

value: PLACEBO


title: ION-363_4

description: Library name: Sample 8


title: 86b20b925b17fbe9;MVA-NP+M1

description: Library name: 86b20b925b17fbe9


title: ION-363_1

description: Library name: Sample 5


title: ION-363_3

description: Library name: Sample 7


title: scr-siFUS_2

description: Library name: Sample 10


title: 86249db66f54e95f;MVA-NP+M1

description: Library name: 86249db66f54e95f


title: 85a18194161f21f7;PLACEBO

description: Library name: 85a18194161f21f7


title: scr-ION-363_3

description: Library name: Sample 3


title: scr-ION-363_1

description: Library name: Sample 1


title: scr-ION-363_2

description: Library name: Sample 2


title: 86477266171e5650;MVA-NP+M1

description: Library name: 86477266171e5650


title: scr-ION-363_4

description: Library name: Sample 4


title: IPF530-IP_1

description: Library name: Sample 16

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Primary human IPF lung fibroblasts

growth_protocol: Primary fibroblasts from explanted donor and IPF fibroblasts were cultured in DMEM F12 medium supplemented with 10% FBS and antibiotics and cultivated in humidified incubator at 37°C.

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 10ng of total RNA was used as input for SMARTer¬Æ Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

treatment_protocol: No treatments, cells were harvested for CLIP-Seq upon reaching confluency.

value: No treatments


title: 85b7f0abcf6784d8;MVA-NP+M1

description: Library name: 85b7f0abcf6784d8


title: 8581bfab69c795db;PLACEBO

description: Library name: 8581bfab69c795db


title: 882b7d9901ae0a6d;PLACEBO

description: Library name: 882b7d9901ae0a6d


title: IPF389-IP_1

description: Library name: Sample 15


title: IPF384-IP_1

description: Library name: Sample 14


title: 870b5e5ce6513a2c;PLACEBO

description: Library name: 870b5e5ce6513a2c


title: 85674d4bdf59720a;PLACEBO

description: Library name: 85674d4bdf59720a


title: 838bc93f10e8ac7e;PLACEBO

description: Library name: 838bc93f10e8ac7e


title: 83625d236f69e878;MVA-NP+M1

description: Library name: 83625d236f69e878


title: 83480543c40b7d27;PLACEBO

description: Library name: 83480543c40b7d27


title: 84a81dfd788ba48f;PLACEBO

description: Library name: 84a81dfd788ba48f


title: 8640a21ea1980996;MVA-NP+M1

description: Library name: 8640a21ea1980996


title: DO540-IP_1

description: Library name: Sample 10

source_name: Primary human Donor lung fibroblasts

value: Primary human Donor lung fibroblasts


title: 82e808bbd0e2c9b9;MVA-NP+M1

description: Library name: 82e808bbd0e2c9b9


title: 82b918cd16ecafa8;MVA-NP+M1

description: Library name: 82b918cd16ecafa8


title: DO545-IP_1

description: Library name: Sample 11


title: IPF381-Input_1

description: Library name: Sample 5


title: 856c0a7cd46757dc;MVA-NP+M1

description: Library name: 856c0a7cd46757dc


title: DO546-Input_1

description: Library name: Sample 4


title: DO538-IP_1

description: Library name: Sample 9


title: 8089618b013cfc64;PLACEBO

description: Library name: 8089618b013cfc64


title: IPF389-Input_1

description: Library name: Sample 7


title: 80a999256b5a914e;PLACEBO

description: Library name: 80a999256b5a914e


title: DO545-Input_1

description: Library name: Sample 3


title: 81e612e4406af4b3;MVA-NP+M1

description: Library name: 81e612e4406af4b3


title: DO540-Input_1

description: Library name: Sample 2


title: DO546-IP_1

description: Library name: Sample 12


title: 82db2459312ab238;MVA-NP+M1

description: Library name: 82db2459312ab238


title: 808d3b1749c3d39a;PLACEBO

description: Library name: 808d3b1749c3d39a


title: IPF384-Input_1

description: Library name: Sample 6


title: IPF530-Input_1

description: Library name: Sample 8


title: IPF381-IP_1

description: Library name: Sample 13


title: 7fda253714ff0050;MVA-NP+M1

description: Library name: 7fda253714ff0050


title: H661-K4K119-R2

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: H661-K4K119-R2

data_processing:
Single-end reads in fastqs were trimmed and filtered for quality (phred33 score > 20) and length (>20bp) using TrimGalore (https://github.com/FelixKrueger/TrimGalore) v0.6.6 in single-end mode.
Trimmed and quality filtered reads were then aligned to the hg38 human genome GRCh38.p13 using bwa-mem (bwa v0.7.13) with default parameters. Alignments were then converted to the bam format and indexed using samtools v1.9. Duplicate alignments were marked with using MarkDuplicates (picard v2.6.0, https://broadinstitute.github.io/picard/) and re-indexed with samtools. bigWig files containing CPM/bp normalised coverage values for each sample were derived from duplicate marked bam files using bamCoverage (DeepTools v3.5.0) where reads were extended to 147bp.
The resultant BAM files were then input to EPIC2 (v0.0.52) (--bin-size 100 –gaps-allowed 1 –fragment-size 147 -- false-discovery-rate-cutoff 0.05) using matched NCI-H661 genomic inputs as the control.
Assembly: GRCh38.p13
Supplementary files format and content: Peak files output by EPIC2.
Supplementary files format and content: Bigwig files output by deepTools summarising read density across the genome with values as CPM/bp.

source_name: lung cancer

growth_protocol: Non-small cell lung cancer cell line NCI-H661 was cultured in RPMI-1640 (Gibco) growth medium and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). This cell line was also STR profiled to ensure authenticity. NCI-H661 was purchased from ATCC.

extract_protocol:
For each reChIP 1x10^6 single-crosslinked NCI-H661 cells were used. Pellets of single-crosslinked NCI-H661 cells were washed twice with 1mL NP buffer (10mM Tris-HCl, 1M sorbitol, 50mM NaCl, 5mM MgCl2, 1mM CaCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20 in H2O freshly supplemented 1x protease inhibitor tablet) on ice. Nuclei were pooled and resuspended in 800µL ChIP buffer (as for ChIP), then left to incubate on ice for at least 5 minutes. Chromatin was transfered to a milliTUBE AFA Snap Fibre sonication vial (Covaris, #520135) and sheared on a Covaris ME220 instrument for 20mins (4C, 75% power, 15% duty factor, 1000 cycles) and debris were pelleted at 12,000xg for 15 mins at 4°C. The supernatant containing chromatin was pre-cleared by adding 20µL washed Protein-A dynabeads resuspended in ChIP dilution buffer: 67mM Tris-HCl, 100mM NaCl, 5mM EDTA, 0.33% SDS, 1.67% Triton-X) and incubated at 4°C with rotation for at least 3 hours. 10µL of the pre-cleared chromatin was set aside as 5% input. For each reChIP, 200µL of pre-cleared chromatin (1x106 cells) was made up to 500µL in a dilution buffer to get a final concentration of 67mM Tris-HCl, 100mM NaCl, 5mM EDTA, 0.33% SDS, 1.67% Triton-X, 0.1μM PMSF, 1x protease inhibitors (reChIP buffer). 20µL Protein-A dynabeads were pre-incubated (as for ChIP) with either 0.5µg H3K4me3 (CST, #9751) or H2AK119ub (CST, #8240) antibodies or Rabbit IgG (Invitrogen, #02-6102), then resuspended in the 500µL diluted chromatin. The first immunoprecipitation was performed overnight at 4°C with rotation, antibody-chromatin complexes were then washed three times in 500µL low-salt buffer (as for ChIP), three times in 500µL high-salt buffer (as for ChIP), twice in 200µL LiCl buffer (as for ChIP) and twice in 500µL 10mM TrisCl pH7.5 on ice. Complexes were eluted in 100µL ChIP elution buffer (as for ChIP) supplemented with 0.1μM PMSF and 1x protease inhibitors for 37°C for 30 mins on a thermomixer at 300RPM, of which 10µL were put aside as a 10% single ChIP control. To dilute the SDS, the eluate volume was increased to 300µL with reChIP buffer and purified using Amicon Ultra-0.5ml 3kDa filter columns (Millipore, #UFC5003) according to the manufacturer’s instructions, with chromatin being additionally washed twice with 400µL ChIP dilution buffer. Purified chromatin was made up to 500µL in reChIP buffer for the second immunoprecipitation, which was performed using the alternate antibody or IgG control bead conjugates overnight at 4°C with rotation. Complexes were washed (as for ChIP) and resuspended in 100µL ChIP elution buffer. Samples were treated with 2µL RNase A and 2µL Proteinase K, then reversed crosslinked (as for ChIP). DNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB) and eluted in 25µL H2O for qPCR and library preparation for sequencing.
reChIP libraries were prepared using the NEBNext UltraII DNA Library Preparation Kit (NEB) according to the manufacturer’s instruction. During library preparation the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) were used to enable library multiplexing. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and HSD1000 High Sensitivity DNA kit (Agilent) on the TapeStation 4150 (Agilent). Libraries were pooled and sequenced on the NextSeq2000 platform in a single-end configurations with 100bp read lengths.

treatment_protocol: No treatments were made.

value: lung cancer

value: lung large cell carcinoma

value: Parental

tag: replicate

tag: antibody 1

tag: antibody 2

tag: target 1

tag: target 2


title: 7efb531324e216e5;PLACEBO

description: Library name: 7efb531324e216e5


title: DO538-Input_1

description: Library name: Sample 1

tag: cell line


title: 7ed0c65fa703efe8;MVA-NP+M1

description: Library name: 7ed0c65fa703efe8

tag: treatment


title: H661-K4K119-R1

description: Library name: H661-K4K119-R1

tag: tissue

tag: cell type

tag: genotype


title: H661-K119K4-R2

description: Library name: H661-K119K4-R2


title: 7e7b749cc577ad01;MVA-NP+M1

description: Library name: 7e7b749cc577ad01


title: 7dc29e50cf6cbe33;MVA-NP+M1

description: Library name: 7dc29e50cf6cbe33


title: H661-K119K4-R1

description: Library name: H661-K119K4-R1


title: 7d8019c89d4f1a69;PLACEBO

description: Library name: 7d8019c89d4f1a69


title: 7b78a753f0b60086;MVA-NP+M1

description: Library name: 7b78a753f0b60086


title: 7ccf50cb32b9b5e6;MVA-NP+M1

description: Library name: 7ccf50cb32b9b5e6