title: WT_NACET_rep6

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

description: Library name: WT_NACET_rep6

data_processing:
Fastq files quality check was performed using FastQC
The fastq files were mapped to the mm9 genome using TopHat v2.1.0 with the following parameters –bowtie1 –no-coverage-search -a 5
The number of reads covered by each gene was calculated by HTSeq-Count 0.11.2 with -s no -a 0 -t exon -m intersection-nonempty parameters.
Assembly: mm9
Supplementary files format and content: HTSeq-Count txt files

source_name: retina

extract_protocol:
total RNA was purified using EuroGOLD TriFast™ (Euroclone, Milan, Italy). RNA quantity and quality were evaluated by Nanodrop 8000 (Thermo Fisher Scientific, Waltham, MA, USA) and Fragment Analyzer (Advanced Analytical Technologies, Heidelberg, Germany) using the DNF-471 Standard Sensitivity RNA Analysis Kit (15nt) (Agilent Technologies, Santa Clara, CA, USA).
RNA samples were  processed for mRNA-seq library preparation using the TruSeq RNA Sample preparation v2 kit according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: retina

value: N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg)


title: MAW-1_rep3

status: Public on Jan 21 2026

type: RNA

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

description: tumor

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851C) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the SureScan Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

molecule: total RNA

organism: Homo sapiens

source_name: Cranial neural crest cells from 414C2 hiPSC, tumor generated by injection subcutaneously  immune-deficient mice.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (Protocol version 6.9), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human iPSCs were maintained on feeder layers of mitomycin C-treated embryonic mouse fibroblasts in primate embryonic stem cell medium (REPROCELL, Tokyo, Japan) supplemented with 4 ng/mL recombinant human fibroblast growth factor 2 (FUJIFILM, Tokyo, Japan). Differentiation of iPSC into cranial NCC (cNCC) was induced using a previously described protocol (PMID: 25464501). Cranial NCCs were cultured in Iscove’s modified Dulbecco’s medium (Thermo Fisher Scientific)/Ham’s F-12 (Thermo Fisher Scientific) 1:1 supplemented with 1x chemically defined lipid concentrate (GIBCO), 15 mg/ml apo-transferrin (Sigma), 450 mM monothioglycerol (Sigma), 5 mg/ml purified BSA (Sigma), 7 mg/ml Insulin (FUJIFILM) and 50 μg/mL penicillin/streptomycin (Sigma). 20 ng/ml EGF (R&D) and 20 ng/ml FGF2 (FUJIFILM) were used to maintain cNCCs. Cultures were maintained at 37ºC under 5% CO2 in air.

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was guaranteed by an RNA Integrity Number (RIN) > 8.

treatment_protocol: In the preparation of the overexpression/lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the plasmids (pCDH-CMV-MYCN-EF1a-puro, pCDH-SFFV-ALK(WT)-EF1a-bsd or pCDH-SFFV-ALK(F1174L)-EF1a-bsd) and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 10^5 cNCCs were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene. The infected cNCCs were cultured in medium containing 1 μg/ml puromycin for 3 d or 4 µg/mL blasticidin for 4 d, and were mixed with 0.3% agar dissolved in growth medium (CDMi + SB431542 + EGF + FGF2) and plated on top of a bottom layer of 0.5% agar dissolved in growth medium in a 35 mm dish. The transformed clones were isolated and injected subcutaneously immune-deficient mice.

tag: cell type

value: human,  cell line

tag: genotype

value: female


title: 201209SHIN#20

type: SRA

city: Ulsan

first: YOU

last: SEONGJUN

country: South Korea

institute: Ulsan National Institute of Science and Technology

description: Library name: SAMPLE31

library_source: transcriptomic

data_processing:
For RNA sequencing data processing, adapter sequences were removed using Cutadapt(v2.9), reads were quality filtered using Trimmomatic (v0.39), which scanned reads from the 5’ end and discarded those shorter than 36 bases. The filtered reads in fastQ files were then aligned to the human reference genome (hg38) with Ensembl v103 annotations using STAR (v2.6.1). Gene quantification was performed using RSEM (v1.3.1) in conjunction with STAR, both operating with default parameters._Human
For RNA sequencing data processing, adapter sequences were removed using Cutadapt(v2.9), reads were quality filtered using Trimmomatic (v0.39), which scanned reads from the 5’ end and discarded those shorter than 36 bases. The filtered reads in fastQ files were then aligned to the mouse reference genome (M26) with Ensembl v103 annotations using STAR (v2.6.1). Gene quantification was performed using RSEM (v1.3.1) in conjunction with STAR, both operating with default parameters._Mouse
Assembly: human reference genome (hg38)
Assembly: mouse reference genome (M26)
Supplementary files format and content: length, effective length, expected count, TPM, FPKM

organism: Mus musculus

source_name: Intestinal adenomas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)_Human. For RNA extraction from mouse tissue, we followed the manufacturer's portocol using Trizol reagent(Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines. RNA quantity was measured using the Qubit HS RNA assay (Thermo Fisher Scientific)_Mouse
mRNA library preparation (poly A enrichment) , the kit we used was Fast RNA-seq Lib Prep Kit V2 (RK20306). 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. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection._Human.Library preparation was performed using the MGIEasy RNA Directional Library Prep Kit (MGI, Shenzhen, China), and paired-end sequencing (150 bp) was conducted on a DNBSEQ-T7 platform, following the manufacturer’s protocol._Mouse

tag: tissue

value: Intestinal adenomas

value: Nsmf-/-; Apc min/+


title: 201209SHIN#19

description: Library name: SAMPLE30


title: Cecum, with in situ polyadenylation

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Biomedical Engineering

country: USA

institute: Cornell University

description: Library name: C311

data_processing:
Raw sequencing reads were first trimmed using Cutadapt,  and aligned to the mouse genome using the STAR Solo pipeline (STAR version 2.7.10b), which generates a feature-by-spot barcode expression matrix. The GRCm39 reference genome with GENCODE M28 annotations was used, or alternatively, the same reference was appended with the Reovirus Type 1-Lang sequence and annotations. Unmapped reads were taxonomically classified using Kraken2(kraken2.09) to generate a taxon-by-spot barcode matrix.
Assembly: GRCm39
Supplementary files format and content: HDF5 files contain the raw gene expression count matrix (UMI counts) per spot barcode, along with complementary information, including spot barcode assignments to cells based on segmentation and the raw microbial NCBI taxid presence count matrix (UMI counts) per spot barcode
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Cecum

extract_protocol:
Cryosections were obtained from four cites of the intestine of  a 13 weeks old male mouse (proximal small intestine, ileum, cecum, distal colon) and from the proximal colon of a female 13 week old mouse. The tissue sections (10 µm thick) were processed with a modified Stereoseq (STOmics) protocol. The sections were mounted onto STOmics mini chip and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. Staining and imaging was performed according to the Stereoseq/STOmics protocol. In situ polyadenylation was performed using yeast Poly(A) Polymerase (yPAP; Thermo Scientific). Capture areas were equilibrated with 1X wash buffer, followed by the addition of yPAP enzyme mix and incubation at 37°C . After enzyme removal, a 12-minute enzymatic permeabilization step was conducted before continuing with the standard STOmics library preparation to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.

value: Cecum

tag: Sex

value: M

tag: age

value: 13 weeks

tag: tile id


title: MAW-2_rep1

description: tumor


title: WT_NACET_rep5

country: Germany

description: Library name: WT_NACET_rep5

tag: treatment


title: MAW-1_rep2

description: tumor


title: WT_NACET_rep4

description: Library name: WT_NACET_rep4


title: WT_NACET_rep2

description: Library name: WT_NACET_rep2


title: B. Females - Scan 3 | 009 | IBA1 _ TMEM119

city: Camden

first: Khalid

last: Hanafy

state: NJ

address: 401 Broadway,

department: Biomedical Sciences

institute: Cooper Medical School of Rowan Univ

description: Library name: DSP-1001660019265-C-A08_S25

library_source: other

data_processing:
FASTQ fileswere processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI. The number of raw reads was highly linearly correlated with the number of unique UMIs at all AOI sizes, suggesting largely uniform library amplification. However, to correct for any PCR amplification bias, all analyses in this study use UMI deduplicated counts. Data were exported to Excel for further analysis.
Supplementary files format and content: xlsx
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Brain

extract_protocol:
Frozen sections of 4%PFA perfused prefixed mouse brains were sent to the University of Minnesota Genomics Center for probe hybridization, immunofluorescence staining, and selection of ROIs for analysis. 1x Tris-EDTA (pH9.0) solution and steaming the solution to 95⁰C method were used for antigen retrieval followed by Proteinase K digestion at 37⁰C for 5 minutes (1 µg/mL) to expose RNA targets.
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual. The DSP aspirate was dried and resuspended in 10 μL DEPC-treated water, and 4 μL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled either in equal volumes or in proportion relative to AOI size, depending on the experiment, and purified with two rounds of AMPure XP beads (Beckman Coulter).Libraries were sequenced on an Illumina NextSeq 2000, according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.

tag: animal group

value: MG-cKO-females

value: Brain

value: Macrophage

value: MG-cKO


title: MAW-2_rep2

description: tumor


title: 414C2 cNCC MYC/ALK(WT) TF-2_rep3

description: cNCC

source_name: Cranial neural crest cells from 414C2 hiPSC, clone isolated from 414C2 cNCC MYC/ALK(WT) Bulk cells in soft agar.


title: 201209SHIN#14

description: Library name: SAMPLE26

source_name: Adjacent normal

value: Adjacent normal


title: MAW-1_rep1

description: tumor


title: B. Females - Scan 3 | 014 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-B01_S30

value: BMM-cKO-females

value: BMM-cKO


title: B. Females - Scan 3 | 004 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A03_S20

value: WT-females

value: WT


title: WT_NACET_rep1

description: Library name: WT_NACET_rep1

value: retina

value: N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg)


title: 201209SHIN#13

description: Library name: SAMPLE25


title: B. Females - Scan 3 | 003 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A02_S19

value: female


title: 201209SHIN#12

description: Library name: SAMPLE24

value: Intestinal adenomas

value: Nsmf+/+; Apc min/+


title: 414C2 cNCC MYC/ALK(WT) TF-2_rep2

description: cNCC

value: human,  cell line


title: B. Females - Scan 3 | 002 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A01_S18


title: B. Females - Scan 3 | 010 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A09_S26


title: WT_rep3

description: Library name: WT_rep3


title: 201209SHIN#16

description: Library name: SAMPLE28

value: Nsmf-/-; Apc min/+


title: 414C2 cNCC MYC/ALK(WT) TF-2_rep1

description: cNCC


title: WT_NACET_rep3

description: Library name: WT_NACET_rep3


title: 201209SHIN#11

description: Library name: SAMPLE23


title: B. Females - Scan 3 | 001 | IBA1 _ TMEM119

description: Library name: DSP-1001660009363-B-G05_S17


title: 414C2 cNCC MYC/ALK(WT) TF-1_rep3

description: cNCC


title: A. Males - Scan 2 | 011 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F11_S11

value: WT-males

value: male


title: WT_rep2

description: Library name: WT_rep2


title: AKITA_NACET_rep4

description: Library name: AKITA_NACET_rep4

value: Akita (C57BL/6-Ins2Akita/J):male


title: 414C2 cNCC MYC/ALK(WT) TF-1_rep2

description: cNCC


title: A. Males - Scan 2 | 012 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F12_S12

value: Brain

value: Macrophage


title: AKITA_NACET_rep5

description: Library name: AKITA_NACET_rep5


title: 201209SHIN#9

description: Library name: SAMPLE21

value: Adjacent normal


title: 201209SHIN#8

description: Library name: SAMPLE20


title: 201209SHIN#6

description: Library name: SAMPLE18

source_name: Normal

value: Normal

value: Nsmf-/-


title: AKITA_NACET_rep3

description: Library name: AKITA_NACET_rep3


title: 414C2 cNCC MYC/ALK(F1174L) Bulk_rep2

description: cNCC

source_name: Cranial neural crest cells from 414C2 hiPSC, infected with MYCN and ALK(F1174L) overexpression vector (pCDH-CMV-MYCN-EF1a-puro, pCDH-SFFV-ALK(F1174L)-EF1a-bsd),  Puromycin (1.0 μg/mL, 3 days) and Blasticidin (4.0 µg/ml, 4 days)-selected bulk cells.


title: 201209SHIN#10

description: Library name: SAMPLE22


title: A. Males - Scan 2 | 009 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F09_S9


title: 201209SHIN#5

description: Library name: SAMPLE17


title: 414C2 cNCC MYC/ALK(F1174L) Bulk_rep3

description: cNCC


title: A. Males - Scan 2 | 007 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F07_S7

value: MG-cKO-males

value: MG-cKO


title: WT_rep1

description: Library name: WT_rep1

value: retina


title: A. Males - Scan 2 | 008 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F08_S8


title: AKITA_NACET_rep2

description: Library name: AKITA_NACET_rep2

value: N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg)


title: 414C2 cNCC MYC/ALK(WT) Bulk_rep3

description: cNCC

source_name: Cranial neural crest cells from 414C2 hiPSC, infected with MYCN and ALK(WT) overexpression vector (pCDH-CMV-MYCN-EF1a-puro, pCDH-SFFV-ALK(WT)-EF1a-bsd),  Puromycin (1.0 μg/mL, 3 days) and Blasticidin (4.0 µg/ml, 4 days)-selected bulk cells.

value: female


title: 201209SHIN#4

description: Library name: SAMPLE16


title: 414C2 cNCC MYC/ALK(WT) TF-1_rep1

description: cNCC

source_name: Cranial neural crest cells from 414C2 hiPSC, isolated from 414C2 cNCC MYC/ALK(WT) Bulk cells in soft agar.


title: A. Males - Scan 2 | 010 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F10_S10

value: WT


title: A. Males - Scan 2 | 006 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F06_S6


title: AKITA_rep4

description: Library name: AKITA_rep4


title: 414C2 cNCC MYC/ALK(WT) Bulk_rep1

description: cNCC


title: 201209SHIN#3

description: Library name: SAMPLE15

value: Nsmf+/+


title: AKITA_rep3

description: Library name: AKITA_rep3


title: 201209SHIN#2

description: Library name: SAMPLE14


title: AKITA_rep2

description: Library name: AKITA_rep2


title: 414C2 cNCC MYC/ALK(WT) Bulk_rep2

description: cNCC

value: human,  cell line


title: 414C2 cNCC MYC/ALK(F1174L) Bulk_rep1

description: cNCC


title: 201209SHIN#1

description: Library name: SAMPLE13


title: A. Males - Scan 2 | 004 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F04_S4

value: BMM-cKO-males

value: BMM-cKO


title: AKITA_rep1

description: Library name: AKITA_rep1


title: A. Males - Scan 2 | 003 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F03_S3

value: male


title: A. Males - Scan 2 | 005 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F05_S5


title: 414C2 cNCC MYCN_rep3

description: cNCC

source_name: Cranial neural crest cells from 414C2 hiPSC, infected with MYCN overexpression vector (pCDH-CMV-MYCN-EF1a-puro),  Puromycin (1.0 μg/mL, 3 days)-selected bulk cells.


title: Ileum, without in situ Polyadenylation

description: Intestial tissue profiled with the STOmics  platform

data_processing:
Raw sequencing reads were trimmed using Cutadapt to remove polyA, polyG, and sequences related to the STOmics library preparation. The trimmed reads were then aligned to the mouse genome using the STAR Solo pipeline (STAR version 2.7.10b), which generates a feature-by-spot barcode expression matrix. The GRCm39 reference genome with GENCODE M28 annotations was used, or alternatively, the same reference was appended with the Reovirus Type 1-Lang sequence and annotations. Unmapped reads were taxonomically classified using Kraken2(kraken2.09) to generate a taxon-by-spot barcode matrix.
Assembly: GRCm39
Supplementary files format and content: HDF5 files contain the raw gene expression count matrix (UMI counts) per spot barcode, along with complementary information, including spot barcode assignments to cells based on segmentation and the raw microbial NCBI taxid presence count matrix (UMI counts) per spot barcode
Library strategy: Spatial transcriptomics

source_name: Ileum

extract_protocol:
Cryosection was obtained from the Ileum of a male, 13 weeks old mouse. The tissue section (10 µm thick) was processed with a modified Stereoseq (STOmics) protocol. The section was mounted onto STOmics mini chip chip ID C02927A211) and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. Staining and imaging was performed according to the Stereoseq/STOmics protocol.Next, a 12-minute enzymatic permeabilization step was conducted before continuing with the standard STOmics library preparation to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.

value: Ileum

value: ApcMin/+

tag: strain

value: 13 weeks


title: 19)  Old_NACET_rep5; age 574 days; sex:male

description: Library name: Old_NACET_rep5

growth_protocol: wild-type C57BL6/J mice were bred and maintained in a Specific Opportunist Pathogen Free (SOPF) animal facility in Fritz Lipmann Institute with12 h of light/dark cycle and fed with a standard mouse chow at Tem-perature 20 ± 2 °C, rlH 55% ± 15.

treatment_protocol: we treated young (8-20 weeks) and old (80-110 weeks) C57BL/6J mice with or N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg). After 5 days mice have been sacrificed by CO2 euthanasia, then we proceed with the dissection of the eyes to collect the retinas as described in Simmons and Fuerst, 2018 (Simmons AB, Fuerst PG. Analysis of Retinal Vascular Plexuses and Interplexus Connections. Methods Mol Biol. 2018;1753:317-330).

tag: batch

value: Old (574 days)


title: A. Males - Scan 2 | 002 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F02_S2

value: Brain

value: Macrophage


title: A. Males - Scan 2 | 001 | IBA1 _ TMEM119 +

description: Library name: DSP-1001660009363-B-F01_S1


title: AKITA_NACET_rep1

description: Library name: AKITA_NACET_rep1

value: Akita (C57BL/6-Ins2Akita/J):male


title: 414C2 cNCC mock_rep2

description: cNCC

source_name: Cranial neural crest cells from 414C2 hiPSC, infected with Mock vector (pCDH-CMV-EF1a-puro),  Puromycin (1.0 μg/mL, 3 days)-selected bulk cells.


title: 18)  Old_NACET_rep4; age 581 days; sex:male

description: Library name: Old_NACET_rep4

value: Old (581 days)


title: 414C2 cNCC MYCN_rep1

description: cNCC


title: 414C2 cNCC mock_rep3

description: cNCC


title: Ileum, with in situ Polyadenylation

description: Intestial tissue profiled with the STOmics  platform with in situ polyadenylation

extract_protocol:
Cryosection was obtained from the Ileum of a male, 13 weeks old mouse. The tissue section (10 µm thick) was processed with a modified Stereoseq (STOmics) protocol. The section was mounted onto STOmics mini chip chip ID C02927D611) and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. Staining and imaging was performed according to the Stereoseq/STOmics protocol. In situ polyadenylation was performed using yeast Poly(A) Polymerase (yPAP; Thermo Scientific). Capture areas were equilibrated with 1X wash buffer, followed by the addition of yPAP enzyme mix. The chambers were sealed and incubated at 37°C for 25 minutes. After enzyme removal, a 12-minute enzymatic permeabilization step was conducted before continuing with the standard STOmics library preparation to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.


title: fbln2-sjr7(-/-), 4 dpci heart ventricles

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

description:
Library name: sjr7-4dpci
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed individually in 10x Genomics Cloud Analysis using the Cell Ranger Count v6.1.2 pipeline and reads were aligned to GRCz11 v4.3.2 reference genome60. Filtered gene expression matrices were imported and further processed in Seurat v461. Samples were integrated to create a single aggregated Seurat object, and low-quality cells containing less than 200 unique features were removed. Batch effect correction was performed using the data integration and ScTransform functions in Seurat.
Assembly: GRCz11 v4.3.2 reference genome
Supplementary files format and content: Tab separated values files and matrix files

organism: Danio rerio

source_name: Heart ventricle

extract_protocol:
Pools of four uninjured ventricles and cryoinjured ventricles at 4 dpci were extracted from WT and fbln2PL-/- zebrafish. Anesthetized fish were dissected and ventricles extracted in calcium-, magnesium-free HBSS (Sigma, Cat. no. H9394) supplemented with 20 U/ml of heparin. Ventricles were washed in fresh HBSS and transferred into 1 ml of 1 mg/ml of collagenase (Gibco, Cat. no. 17101015) dissolved in HBSS for 30 min digestion on a thermal mixer at 32 ⁰C and 700 rpm. Ventricles were mechanically disrupted by pipetting every 10 min. Samples were centrifuged at 2000 rpm for 5 min at RT and supernatants discarded. Cells were digested with 1 ml of 1x TrypLE Express Enzyme (Gibco, Cat. no. 12605010) for 15 min on a thermal mixer at 32 ⁰C and 700 rpm and pipetted every 5 min. Enzymatic digestion was stopped by adding 1 ml of 20% fetal bovine serum in HBSS to extracts. Tissue extracts were strained through a 70 μm cell strainer and centrifuged at 2000 rpm for 5 min at RT. The supernatants were discarded, and pellets were washed with 1 ml of 20% fetal bovine serum in HBSS. After centrifuge at 2000 rpm for 5 min at RT, cells were resuspended in 80 μl of 20% fetal bovine serum in HBSS and strained through a 40 μm cell strainer. Cells were counted and viability (>85%) was assessed using 0.4% Trypan Blue. Cells were kept on ice and immediately processed for scRNA-seq.
For scRNA-seq experiment, 14000 cells were used for each sample and the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Cat. no. PN-1000269) was used following manufacturer’s protocol. Each sample was indexed individually using the Dual Index Kit TT Set A (10x Genomics, Cat. no. PN-1000215).

treatment_protocol: Cardiac cryoinjury

value: Heart ventricle

value: 3 months old

value: AB

value: cryoinjury


title: 414C2 cNCC MYCN_rep2

description: cNCC

value: female


title: 17)  Old_NACET_rep3; age 581 days; sex:male

description: Library name: Old_NACET_rep3

value: retina

value: N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg)


title: Liver derived from WT mice, WD for 16 weeks, Biol rep 3

city: New Haven

first: Abhishek

middle: K

last: Singh

state: CT

address: 10 Amistad Street

department: Pharmacology and VBT

institute: Yale University

data_processing:
Reads aligned to mm9 genome with STAR
Quantified to mm9 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: mm9
Supplementary files format and content: tab-delimited text file include cpm values for each Sample

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

value: Liver

value: WT

value: WD for 16 weeks


title: fbln2-sjr3(-/-), uninjured heart ventricles

description:
Library name: sjr3-uninj
10x Genomics


title: 16)  Old_NACET_rep2; age 668 days; sex:male

description: Library name: Old_NACET_rep2

value: Old (668 days)


title: Liver derived from Liver specific NgBR KO mice, WD for 16 weeks, Biol Rep 3

value: NgBR KO


title: 20)  Old_NACET_rep6; age 574 days; sex:male

description: Library name: Old_NACET_rep6

value: Old (574 days)


title: fbln2-sjr3(-/-), 4 dpci heart ventricles

description:
Library name: sjr3-4dpci
10x Genomics


title: WT, 4 dpci heart ventricles

description:
Library name: WT-4dpci
10x Genomics


title: 414C2 cNCC mock_rep1

description: cNCC

value: human,  cell line


title: WT, uninjured heart ventricles

description:
Library name: WT-uninj
10x Genomics


title: Ecoli_NCR169C_1

city: Szeged

first: Rui

middle: M.

last: Lima

address: Temesvari krt. 62

country: Hungary

institute: HUN-REN BRC

description:
Library name: 4_S10_R1_001
Column name in ExonReads and ExonTPM: 4_S10_R1_001

data_processing:
Primary data analysis (base-calling) was carried out with “bcl2fastq” software (v2.17.1.14, Illumina).
Assembly: Trinity
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Escherichia coli

source_name: ATCC 8739

growth_protocol: early logarithmic phase OD600=0.2

extract_protocol:
Total bacterial RNA was purified from samples using the RNeasy Mini Kit/QIAGEN (cat. no. 74104) following the instructions in the protocol, prior the purification with treatment of RNAprotect Bacterial Reagent/QIAGEN (cat. no. 76506). Residual DNA was eliminated using Ambion DNase I (RNase-free). The samples were precipitated with ethanol and resuspend in RNase free water. Quality and quantity was detected using 2200 TapeStation and Qubit RNA BR Assay.
Sequencing libraries were prepared for the transcriptome samples using Zymo-Seq RiboFree Total RNA Library Kit. Sequencing was carried out by Seqomics company. Single reads were generated on an Illumina NextSeq sequencer using NextSeq® 500/550 High Output Kit v2 (300 cycles).

treatment_protocol: 1.6 µM (sub-MBC dose) of the NCR169C(17-38) peptide or water (as control) for 20 minutes in culture medium (LSM).

tag: cell line

value: ATCC 8739

value: log phase

tag: time

value: 20 minutes


title: Ecoli_untreated_3

description:
Library name: 3_S9_R1_001
Column name in ExonReads and ExonTPM: 3_S9_R1_001

value: water


title: Ecoli_NCR169C_3

description:
Library name: 6_S12_R1_001
Column name in ExonReads and ExonTPM: 6_S12_R1_001


title: Liver derived from Liver specific NgBR KO mice, WD for 16 weeks, Biol Rep 2


title: Liver derived from WT mice, WD for 16 weeks, Biol rep 2


title: 14)  Old_Ctrl_rep4; age 668 days; sex:male

description: Library name: Old_Ctrl_rep4

source_name: retina


title: Ecoli_untreated_2

description:
Library name: 2_S8_R1_001
Column name in ExonReads and ExonTPM: 2_S8_R1_001


title: Liver derived from Liver specific NgBR KO mice, WD for 16 weeks, Biol Rep 1


title: Ecoli_NCR169C_2

description:
Library name: 5_S11_R1_001
Column name in ExonReads and ExonTPM: 5_S11_R1_001


title: Brainstem, mPES_2

city: Guangzhou

first: Yueqin

last: Tian

state: Guangdong

address: No. 600, Tianhe Road

country: China

institute: The Third Affiliated Hospital, SYSU

description:
Library name: Sample 4
10X Genomics

data_processing:
Sequencing data were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version 5.01). Sample demultiplexing, barcode processing, and single-cell 3' end gene counting were performed using the Cell Ranger workflow (version 3.1.0). Single-cell RNA sequencing data were aligned to the Ensembl genome GRCh38/GRCm38 reference genome. This study utilized the 10X Genomics Chromium single-cell 3' end sequencing solution. The output from Cell Ranger was imported into the Seurat platform (version 3.1.1) for dimensionality reduction analysis, clustering analysis, and subsequent analysis of single-cell RNA sequencing data.
Assembly: mRatBN7.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: Brainstem

extract_protocol:
1. Samples were cut into ~1 mm pieces and homogenized using a Dounce homogenizer (885302-0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer. 2. They were incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. 3. Grounded with a dounce(Sigma), resuspended by pipette，gentlely； 4. Incubated on ice for 6 min, then add 2 ml of ice-cold 4% BSA, resuspended by Pasteur pipette, then stop the reaction; 5. Centrifuged at 300g for 5 minutes at 4°C; 6. Add 2 ml of lysis buffer and 4% BSA, resuspended, Incubated on ice for 3 min; 7. De-fragment with Miltenyi (Debris Removal Solution); 8. The pellet was resuspended and washed with 4 ml of the buffer, and then, it was incubated on ice for 5 minutes. After another centrifugation; 9. The pellet was resuspended in Nuclei Suspension Buffer (1x PBS,0.07% BSA, and 0.1% RNase inhibitor); 10. Filtered through a 20-mm cell strainer(43-50020-50; pluriSelect), and counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-nuclei suspensions were loaded to 10x Chromium to capture 8000 single cell, according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .
The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) at a minimum depth of 20,000 reads per cell.

value: Brainstem

value: Sprague-Dawley


title: Tumor derived from Liver specific NgBR KO mice, WD for 16 weeks, Biol Rep 3

source_name: Tumor

value: Tumor


title: Liver derived from WT mice, WD for 16 weeks, Biol rep 1


title: 12)  Old_Ctrl_rep2; age 668 days; sex:male

description: Library name: Old_Ctrl_rep2


title: Brainstem, brainstem_ischemia_2

description:
Library name: Sample 2
10X Genomics


title: Tumor derived from Liver specific NgBR KO mice, WD for 16 weeks, Biol Rep 2


title: Brainstem, brainstem_ischemia_1

description:
Library name: Sample 1
10X Genomics


title: Brainstem, mPES_1

description:
Library name: Sample 3
10X Genomics


title: 15)  Old_NACET_rep1; age 668 days; sex:male

description: Library name: Old_NACET_rep1


title: bleomycin-injured P28, scRNA

city: Shanghai

first: Yan

last: Li

state: Shanghai

address: 555 Zuchongzhi Rd

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences,

description: 10X Genomics

data_processing:
Sequencing reads were aligned, annotated, and demultiplexed with CellRanger (v6.0.0) using the mm10-2020-A reference from 10X Genomics.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Lung

extract_protocol:
For lung cells, after euthanasia, the mice were perfused with 10 ml cold PBS through the right ventricle to flush out blood cells in the lung. Then the mice were inflated through the trachea with 2 ml digestion solution (Collagenase IV 0.2 mg/ml, FBS 5% and DNase I 60 U/ml in RPMI-1640 Media. FBS, Gibco, 10099141; RPMI-1640, Invitrogen, 22400089). The lungs were removed and minced into small pieces in 25 ml digestion solution for 30 mins at 37°C with shaking and frequent agitation. After digestion, the cells were filtered through a 70 μm strainer, centrifuged at 500 g for 5 mins at 4°C to discard supernatant. Next, cells were incubated in 1 ml Red Blood Cell lysis buffer (eBioscience, 00-4333-57) at room temperature for 5 mins. 9 ml cold PBS was added and centrifuged at the speed of 500 g for 5 mins at 4°C to discard supernatant. After red blood cell lysing, the cells were washed twice.
The isolated cell suspension was processed using the 10x Chromium system, with 13,000 cells loaded during the generation of GEMs. The library preparation followed the guidelines provided in the Single Cell 3’ Gene Expression Kit (v3.1) manual.

value: Lung

value: Immune cells

value: bleomycin-injured P28


title: Ecoli_untreated_1

description:
Library name: 1_S7_R1_001
Column name in ExonReads and ExonTPM: 1_S7_R1_001


title: bleomycin-injured P14, scRNA

description: 10X Genomics

value: bleomycin-injured P14


title: 10) Young_NACET_rep6; age 119 days; sex:female

description: Library name: Young_NACET_rep6

value: retina

value: N-acetilcysteine ethyl ester (NACET) added to drinking water (daily oral intake of 50 mg/Kg)

value: Young (129 days)


title: 11)  Old_Ctrl_rep1; age 668 days; sex:male

description: Library name: Old_Ctrl_rep1

value: Old (668 days)


title: liver of male 5-week-old EHBR_5

city: Kusatsu

first: Chieri

last: Fujino

state: Shiga

address: 1-1-1 Noji-higashi

institute: Ritsumeikan University

description: Library name: EHBRmale_5

data_processing:
RNA-seq and data analysis were conducted by Rhelixa, Inc. and used Trimmomatic (version 0.38), FastQC (version 0.11.7), HISAT2 (version 2.1.0), and featureCounts (version 1.6.3).
Assembly: rn6
Supplementary files format and content: Text files include FPKM, FPKM-UQ, TPM values for each sample

source_name: liver

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific).
Library preparation was carried out using NEBNext poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit.

value: liver


title: 8) Young_NACET_rep4; age 129 days; sex:male

description: Library name: Young_NACET_rep4


title: liver of male 5-week-old EHBR_4

description: Library name: EHBRmale_4


title: Liver derived from WT mice, HFD, 16 weeks, Biol Rep 4

value: Liver

value: WT

value: HFD for 16 weeks


title: 13)  Old_Ctrl_rep3; age 668 days; sex:male

description: Library name: Old_Ctrl_rep3


title: PBS-treated, scRNA

description: 10X Genomics

value: PBS-treated


title: Tumor derived from Liver specific NgBR KO mice, WD for 16 weeks, Biol Rep 1

value: NgBR KO

value: WD for 16 weeks


title: bleomycin-injured P7, scRNA

description: 10X Genomics

value: bleomycin-injured P7


title: 7) Young_NACET_rep3; age 129 days; sex:male

description: Library name: Young_NACET_rep3


title: bleomycin-injured P3, scRNA

description: 10X Genomics

value: bleomycin-injured P3


title: liver of male 5-week-old EHBR_2

description: Library name: EHBRmale_2


title: 9) Young_NACET_rep5; age 119 days; sex:female

description: Library name: Young_NACET_rep5

value: Young (119 days)


title: liver of male 5-week-old EHBR_3

description: Library name: EHBRmale_3


title: Liver derived from WT mice, HFD, 16 weeks, Biol Rep 3


title: Liver derived from liver specific NgBR (Nus1) KO mice, HFD, 16 weeks, Biol Rep 4


title: Liver derived from liver specific NgBR (Nus1) KO mice, HFD, 16 weeks, Biol Rep 3


title: 6) Young_NACET_rep2; age 129 days; sex:male

description: Library name: Young_NACET_rep2


title: OVU2AF2si3

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

description:
Library name: Sanple 6
N3_Count

data_processing:
Bridge amplification. Bridge PCR amplification was performed on the cBot instrument to generate clusters.
The Illumina sequencing platform uses a 2*150 sequencing mode for Sequencing by Synthesis. Four fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the flow cell for amplification. During the extension of the complementary strand in each sequencing cluster, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence. The sequencer captures the fluorescence signals, and computer software converts the light signals into sequencing peaks, thereby obtaining the sequence information of the target fragments.
The image data of sequencing fragments obtained by the high-throughput sequencer are converted into sequence data (reads) through CASAVA base calling, and the files are in fastq format, which mainly contains the sequence information of the sequencing fragments and their corresponding sequencing quality information. The raw data are in fastq format files, which include the base sequences of the reads and their sequencing quality values. Each read is represented by four lines of information: the first line is the unique identifier of the read in Illumina sequencing, the second line is the base sequence, the third line is a + sign followed by the omitted read identifier, and the fourth line is the base quality value.
Assembly: For each sample, the results of reads aligned to the reference genome were used by the StringTie software to assemble transcripts in the sample based on the known transcript location information file as a guide. Transcripts with expression levels equal to 0 were filtered out, and the StringTie-assembled transcripts from all samples were reassembled.
Supplementary files format and content: xls file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from cell samples, and a total of 1 μg of RNA was required for mRNA sequencing library construction.
1.mRNA Enrichment  For eukaryotic mRNA, enrichment was performed using Oligo (dT) magnetic beads to isolate poly(A)-tailed mRNA.  2.mRNA Fragmentation  The enriched mRNA was randomly fragmented into short fragments of approximately 200 bp using chemical or enzymatic methods.  3.Strand-Specific cDNA Synthesis  First-strand cDNA was synthesized using fragmented mRNA as a template and random primers for reverse transcription.  During second-strand cDNA synthesis, dTTP in the dNTP mix was replaced with dUTP to enable strand specificity.  4.Adapter Ligation  Double-stranded cDNA was purified using AMPure XP beads.  The cDNA ends were repaired and A-tailed using an End Repair Mix.  Sequencing adapters were ligated to the A-tailed cDNA.  5.Second-Strand cDNA Digestion  USER enzyme was used to digest the second-strand cDNA (containing dUTP), ensuring the final library contained only first-strand cDNA.  6.PCR Enrichment  The cDNA library was amplified by PCR for approximately 15 cycles using primers complementary to the sequencing adapters to enrich the final library.  7.Library Quality Control and Quantification  The quality of the library was assessed using an Agilent Bioanalyzer or similar instrument to confirm the expected fragment size distribution (~200-500 bp).  The library concentration was quantified using qPCR or a fluorometric method (e.g., Qubit) to ensure optimal concentration for sequencing.

value: Ovarian cancer

value: U2AF2 SI


title: liver of male 5-week-old EHBR_1

description: Library name: EHBRmale_1


title: OVU2AF2si2

description:
Library name: Sanple 5
N2_Count


title: liver of male 5-week-old SD rat_5

description: Library name: SDmale_5


title: 3) Young_Ctrl_rep3; age 119 days; sex:female

description: Library name: Young_Ctrl_rep3


title: liver of male 5-week-old SD rat_4

description: Library name: SDmale_4


title: 5) Young_NACET_rep1; age 129 days; sex:male

description: Library name: Young_NACET_rep1


title: Liver derived from liver specific NgBR (Nus1) KO mice, HFD, 16 weeks, Biol Rep 2


title: liver of male 5-week-old SD rat_2

description: Library name: SDmale_2


title: OVU2AF2si1

description:
Library name: Sanple 4
N1_Count


title: Liver derived from WT mice, HFD, 16 weeks, Biol Rep 1


title: OVU2AF2sinc2

description:
Library name: Sanple 2
S2_Count

value: U2AF2 SINC


title: Liver derived from WT mice, HFD, 16 weeks, Biol Rep 2


title: liver of male 5-week-old SD rat_3

description: Library name: SDmale_3


title: 4) Young_Ctrl_rep4; age 119 days; sex:female

description: Library name: Young_Ctrl_rep4

value: retina


title: 1) Young_Ctrl_rep1; age 119 days; sex:male

description: Library name: Young_Ctrl_rep1


title: OVU2AF2sinc3

description:
Library name: Sanple 3
S3_Count


title: CP BHI + 5% B. animalis AG02 CFS

status: Public on Jan 20 2026

city: Chapel Hill

first: Adam

last: Rosenthal

state: North Carolina

address: 1521 East Franklin Street, Apartment C213

department: Microbiology and Immunology

institute: UNC

description:
Library name: Sample 3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V7.1  and using custom scripts available from the Sahand Hormoz lab (https://gitlab.com/hormozlab/bacteria_scrnaseq)
Assembly: Probe-based genome builds for B subtilis, E coli and C perfringens are deposited alongside GTF files in the Hormoz lab github: https://gitlab.com/hormozlab/bacteria_scrnaseq
Supplementary files format and content: H5 files

molecule: cytoplasmic RNA

organism: Clostridium perfringens

source_name: Bacterial cells in suspension

growth_protocol: Freshly collected bacterial cells were fixed in 1% paraformaldehyde for 1 hour. Cells from 2 mL of cell culture were fixed using a 30-minute incubation in 1% paraformaldehyde (final concentration) at room temperature. Formaldehyde-fixed samples were washed with 0.02 % SSC (Saline Sodium Citrate - Invitrogen) by gentle centrifugation (6,000 x G) for 2.5 minutes. After the wash, cell pellets were resuspended in 1 mL MAAM (4:1 V:V dilution of methanol to glacial acetic acid). Samples were kept at -20oC for up to 2 days before further processing. For in-situ probe hybridization, 150 µL of fixed sample was centrifuged and washed once in PBS to remove methanol and acetic acid. After the wash step, cells were incubated in 200 µL PBS with 350 u/µL of lysozyme solution (Epicentre ready-lyse) for 30 minutes at room temperature. Lysozyme concentration was optimized and other enzyme combinations were tested to achieve a protocol with maximal probe signal and minimal cell lysis (see Supplementary Figure S12) After 30 minutes cells were pelleted and washed with 500 µL PBS-tween (PBS with 0.1 % Tween 20). Cells were then re-suspended with 100 µL of probe binding buffer consisting of 5x SSC, 30% formamide, 9mM citric acid (pH 6.0). 0.1% Tween 20, 50 ug/ml heparin, and 10% low MW dextran sulfate42. Cell suspensions were placed in a 50oC shaker-incubator and allowed to pre-equilibrate for 1 hour. After 1 hour 50 µL of probes, (600 ng/µL) were added to each cell suspension, and samples were left to incubate overnight. Following the overnight incubation samples were washed 5 times in pre-warmed (50oC) probe-wash solution (5 x SSC, 30% formamide, 9 mM citric acid pH 6.0, 0.1% Tween 20, and 50 ug/mL heparin).

extract_protocol:
Single cell
Library was performed according to specifications of McNulty et al bacterial scRNAseq protocols (single cell 3’ v2 protocol, 10x Genomics). Briefly, Single cell partitioning, barcoding, and cDNA library generation was achieved using the 10X Genomics Chromium Controller with the Chromium Single Cell 3’ Reagents Kit (v2 chemistry) as described by 10X Genomics (https://support.10Xgenomics.com/single cell-gene-expression/index/doc/user-guide-chromium-single cell-3-reagent-kits-user-guide-v2-chemistry). The protocol was modified to achieve bacterial scRNA-seq. For GEM generation (10X microfluidic encapsulation), a master mix containing the following reagents (per rxn, not accounting for excess volume) was prepared: 33 µL of 4X ddPCR Multiplex Supermix (BioRad), 4 µL of custom primer (10 µM), 2.4 µL additive A (10X Genomics), 26.8 µL dH2O. All other reagents specified by 10X Genomics were omitted. Prepared cell samples were washed 3X in PBS and diluted to 1000 cells/µL before loading on the microfluidic chip (“Chip A Single Cell”) with a targeted cell recovery of 10,000 cells.

value: Bacterial cells in suspension

value: Late log phase


title: Wild type VMM NH4Cl 2% Glucose Rep 3

first: Josh

last: Kerkaert

state: NY

address: 236 Tower Rd

description: Library name: yku70D_VMM_NH4_Glucose_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: VMM NH4 Glucose 8h


title: CP BHI + 3% L. acidophilus AG01 CFS

description:
Library name: Sample 4
10x Genomics


title: liver of male 5-week-old SD rat_1

description: Library name: SDmale_1

value: liver


title: OVU2AF2sinc1

description:
Library name: Sanple 1
S1_Count


title: C.cohnii, Glucose condition replicate 2

city: Bangkok

first: Vetaka

last: Tharasiriavat

address: Phaya Thai

department: Biochemistry

country: Thailand

institute: Chulalongkorn University

description:
Library name: Glu5-C.cohnii_rep2
Column name in counts_transcripts.txt: Glu5-C.cohnii_rep2

data_processing:
Raw sequencing reads were assessed for quality using FastQC software
Adapter sequences and low-quality reads were removed with Fastp to generate high-quality clean reads.
Read counts were quantified using RSEM, and differentially expressed genes (DEGs) were identified using DESeq2.
Assembly: Reference transcriptome was generated by de novo assembly of clean reads using Trinity. Redundant transcripts were removed using CD-HIT.
Supplementary files format and content: counts_transcripts.txt include transcript-level quantification of read counts for each sample

organism: Crypthecodinium cohnii

source_name: Unicellular dinoflagellate

growth_protocol: Cultivation in SYP medium supplemented with 5 g/L glucose for 5 days

extract_protocol:
Total RNA was extracted from C. cohnii using TRIzol® Reagent (Invitrogen, Life Technologies Corporation, Carlsbad, CA, USA) and purified with the RNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA concentration and purity were measured with DeNovix fluorometer and Nanodrop, and integrity was assessed using Agilent 2100 Bioanalyzer.
RNA-Seq libraries were prepared from 200 ng of total RNA using the QIAseq Stranded mRNA Library Kit (QIAGEN) and sequenced on an Illumina HiSeq platform (paired-end, 150 bp).

treatment_protocol: Cultivation in SYP medium supplemented with 15 g/L ethanol for 5 days

value: Unicellular dinoflagellate

value: Wild-type

value: Glucose

value: Day 5


title: C.cohnii, Glucose condition replicate 3

description:
Library name: Glu5-C.cohnii_rep3
Column name in counts_transcripts.txt: Glu5-C.cohnii_rep3


title: C.cohnii, Ethanol condition replicate 3

description:
Library name: EtOH15-C.cohnii_rep3
Column name in counts_transcripts.txt: EtOH15-C.cohnii_rep3

value: Ethanol


title: CP BHI Control

description:
Library name: Sample 1
10x Genomics


title: C.cohnii, Glucose condition replicate 1

description:
Library name: Glu5-C.cohnii_rep1
Column name in counts_transcripts.txt: Glu5-C.cohnii_rep1


title: 2) Young_Ctrl_rep2; age 119 days; sex:male

description: Library name: Young_Ctrl_rep2

extract_protocol:
total RNA was purified using EuroGOLD TriFast™ (Euroclone, Milan, Italy). RNA quantity and quality were evaluated by Nanodrop 8000 (Thermo Fisher Scientific, Waltham, MA, USA) and Fragment Analyzer (Advanced Analytical Technologies, Heidelberg, Germany) using the DNF-471 Standard Sensitivity RNA Analysis Kit (15nt) (Agilent Technologies, Santa Clara, CA, USA).
RNA samples were  processed for mRNA-seq library preparation using the TruSeq RNA Sample preparation v2 kit according to the manufacturer’s instructions (Illumina, San Diego, CA, USA).


title: Wild type VMM NH4Cl 2% Glucose Rep 1

description: Library name: yku70D_VMM_NH4_Glucose_Rep1


title: Liver derived from liver specific NgBR (Nus1) KO mice, HFD, 16 weeks, Biol Rep 1

value: Liver

value: NgBR KO

value: HFD for 16 weeks


title: enriched- cells stably expressing mitochondrial BS2-TRFLE and pAC-2 treated, biol rep 3

city: Chicago

first: Bryan

last: Dickinson

state: il

address: 929 E 57th St

institute: UChicago

description: Library name: SP-17

data_processing:
The RNA-seq library generated were mapped to the Homo sapiens GRCh38 reference genome using STAR, version 2.7.9a. ligned reads were quantified using Salmon, version 1.4.0
Annotation data from Gencode V34 was used to summarize data from transcript-level to gene-level. Filtering was carried out to remove particular gene biotypes or genes with low expression and selected the following gene biotypes of interest: protein coding, lncRNA, Mt_rRNA, Mt_tRNA, rRNA, snRNA, scRNA, snoRNA.
To identify differentially expressed genes, precision weights were applied to TMM-normalized gene counts based on within-group sample-level variance and gene-level mean-variance trends using VOOM. The count data was fitted to a gene-wise linear model with group status as a coefficient, and contrasts were specified for comparisons of interest.
The Limma empirical Bayes method was used to estimate the posterior odds of differential expression (|logFC| > 0) after adjusting for gene-level posterior residual standard deviations.
Assembly: GRCh38
Supplementary files format and content: Filtered and TMM normalized log2cpm reads for all samples.

source_name: Breast Tissue

growth_protocol: MDA-MB-231 cells were cultured in DMEM (GlutaMAX™, high glucose, sodium pyruvate, phenol red) supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin/streptomycin. Cells were maintained in a water-saturated, 5% CO2-containing, 37°C incubator. The stable cells expressing BS2-TRFLE in different compartments were cultured with additional 20 µg/mL of blasticidin in the culture media.

extract_protocol:
RNA was extracted with QIAGEN Rneasy Plus Mini Kit, followed by Click reaction with biotin and enrichment of biotinylated RNA. 60 µg RNA per sample was used as input.
The enriched RNAs for all the samples were subjected to polyA capture and subsequently the DNA library with dual-index adapters was generated and amplified using the mRNA Hyper Prep Kit (Kapa Biosystems, KK8581) following manufacturer’s protocol

treatment_protocol: Upon 90% confluency, cells were treated with 100µM pAC-2 for 5 min at 37°C, quenched with 1mM PMSF solution, washed twice with DPBS, and then RNA was harvested.

value: Breast Tissue

value: human triple negative breast cancer

value: stable expression of BS2-TRFLE in the mitochondria

value: pAC-2 treatment for 3 min


title: enriched- cells stably expressing mitochondrial BS2-TRFLE and pAC-2 treated, biol rep 2

description: Library name: SP-16


title: enriched- cells stably expressing mitochondrial BS2-TRFLE and pAC-2 treated, biol rep 1

description: Library name: SP-15


title: Wild type VMM NH4Cl 2% Glucose Rep 2

description: Library name: yku70D_VMM_NH4_Glucose_Rep2


title: enriched- cells stably expressing cytosolic BS2-TRFLE and pAC-2 treated, biol rep 2

description: Library name: SP-13

value: stable expression of BS2-TRFLE in the cytosol


title: enriched- cells stably expressing cytosolic BS2-TRFLE and pAC-2 treated, biol rep 1

description: Library name: SP-12


title: enriched- cells stably expressing nuclear BS2-TRFLE and pAC-2 treated, biol rep 2

description: Library name: SP-10

value: stable expression of BS2-TRFLE in the nucleus


title: enriched- cells stably expressing cytosolic BS2-TRFLE and pAC-2 treated, biol rep 3

description: Library name: SP-14


title: CP BHI + 2.5% B. animalis AG02 CFS

description:
Library name: Sample 2
10x Genomics

value: Bacterial cells in suspension

value: Late log phase


title: C.cohnii, Ethanol condition replicate 1

description:
Library name: EtOH15-C.cohnii_rep1
Column name in counts_transcripts.txt: EtOH15-C.cohnii_rep1


title: enriched wildtype cells and pAC-2 treated, biol rep 3

description: Library name: SP-08

value: WT


title: enriched wildtype cells and pAC-2 treated, biol rep 2

description: Library name: SP-07


title: enriched- cells stably expressing nuclear BS2-TRFLE and pAC-2 treated, biol rep 3

description: Library name: SP-11


title: input-cells stably expressing mitochondrial BS2-TRFLE;  pAC-2 treated

description: Library name: SP-04


title: enriched wildtype cells and pAC-2 treated, biol rep 1

description: Library name: SP-06


title: input-cells stably expressing nuclear BS2-TRFLE;  pAC-2 treated

description: Library name: SP-02


title: Hep3B cells, Hypoxia, oxamate sodium-2

city: GUANGZHOU

first: jiamin

last: chen

address: WAIHUAN EAST ROAD

institute: SOUTH CHINA UNIVERSITY OF TECHNOLOGY

description:
Library name: sample8
Hypoxia_oxamate-2

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Read counts were adjusted using the edgeR R package (3.22.5) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes FPKM value for each sample

growth_protocol: Hep3B cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃. Normal condition: 20% O2; Hypoxic condition: 1% O2.

extract_protocol:
RNA was harvested using TRIzol Reagent. A total amount of 3 µg of RNA per sample was used for the construction of sequencing libraries.
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.

treatment_protocol: Hypoxia exposure was achieved by placing cells into a modular chamber flushed with a gas mixture consisting of 1% O2, 5% CO2 and 94% N2 at 37 ℃.

value: liver

value: liver cancer cell

value: Hypoxic condition, oxamate sodium


title: Hep3B cells, Hypoxia, oxamate sodium-3

description:
Library name: sample9
Hypoxia_oxamate-3


title: Hep3B cells, Hypoxia-1

description:
Library name: sample4
Hypoxia-1

value: Hypoxic condition


title: input-wildtype cells and pAC-2 treated

description: Library name: SP-01


title: Hep3B cells, Hypoxia-2

description:
Library name: sample5
Hypoxia-2


title: Hep3B cells, Hypoxia, oxamate sodium-1

description:
Library name: sample7
Hypoxia_oxamate-1


title: enriched- cells stably expressing nuclear BS2-TRFLE and pAC-2 treated, biol rep 1

description: Library name: SP-09


title: Hep3B cells, Normoxia-3

description:
Library name: sample3
Normoxia-3

value: Normal condition


title: Hep3B cells, Hypoxia-3

description:
Library name: sample6
Hypoxia-3


title: Hep3B cells, Normoxia-1

description:
Library name: sample1
Normoxia-1


title: Hep3B cells, Normoxia-2

description:
Library name: sample2
Normoxia-2


title: input-cells stably expressing cytosolic BS2-TRFLE;  pAC-2 treated

description: Library name: SP-03


title: LTB8

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description:
Library name: V_8
LTB

data_processing:
Read mapping: STAR-2.7.10a
Quantification: FeatureCounts
Assembly: GRCh38.p13
Supplementary files format and content: tsv file includes raw counts for each sample

source_name: Colon

growth_protocol: RPMI with serum and antibiotics

extract_protocol:
Tryzol and Thermoscientific GeneJET RNA Cleanup and concentration micro kit.
Library was performed according to the manufacter's instructions (Truseq Stranded mRNA protocol, Illumina). The sequencing library is prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step which greatly increases the efficiency of the library preapration process. Adapter-ligated fragments are then PCR amplified with a PCR primer solution which anneals to the ends of each adapters. The library templated undergo quality control and quantification process.

value: Colon

value: Primary human colonic fibroblasts

value: LTB


title: CTRL9

description:
Library name: V_9
CTRL of LTB10, TNF12, TGFB11

value: CTRL


title: LTB6

description:
Library name: V_6
LTB


title: TGFB30

description:
Library name: V_30
TGFB

value: TGFB


title: LTB4

description:
Library name: V_4
LTB


title: TNF31

description:
Library name: V_31
TNF

value: TNF


title: LTB2

description:
Library name: V_2
LTB2


title: CTRL3

description:
Library name: V_3
CTRL of LTB4


title: CTRL5

description:
Library name: V_5
CTRL of LTB6


title: CTRL7

description:
Library name: V_7
CTRL of LTB8


title: TNF28

description:
Library name: V_28
TNF


title: CTRL1

description:
Library name: V_1
CTRL of LTB2


title: TNF21

description:
Library name: V_21
TNF


title: CTRL26

description:
Library name: V_26
CTRL of TNF28, TGFB27


title: CTRL29

description:
Library name: V_29
CTRL of TNF31,TGFB30


title: TGFB22

description:
Library name: V_22
TGFB


title: CTRL20

description:
Library name: V_20
CTRL of TNF21,TGFB22


title: TGFB27

description:
Library name: V_27
TGFB


title: CTRL17

description:
Library name: V_17
CTRL of TNF18,TGFB19


title: TNF18

description:
Library name: V_18
TNF


title: TNF16

description:
Library name: V_16
TNF


title: TGFB19

description:
Library name: V_19
TGFB


title: CTRL13

description:
Library name: V_13
CTRL of LTB14,TNF16,TGFB15


title: LTB14

description:
Library name: V_14
LTB


title: TGFB11

description:
Library name: V_11
TGFB


title: LTB10

description:
Library name: V_10
LTB


title: TNF12

description:
Library name: V_12
TNF


title: MCF10A TGFB rep2

city: Oslo

first: Fabiana

last: Patalano

address: Blindernveien 31

country: Norway

institute: University of Oslo

description: Library name: Sample 6

library_source: genomic

data_processing:
Samples were processed using nf-core/hic v2.1.0 and nf-core/rnaseq version 3.14.0
Assembly: hg38
Supplementary files format and content: .mcool files are HiC contact matrix bigWig with read coverage (reverse) bigWig with read coverage (forward)

molecule: genomic DNA

source_name: mammary gland

growth_protocol: MCF10A cell lines were maintained in Dulbecco's modified Eagle's medium/Nutrient F12 (DMEM/F12) (Sigma-Aldrich) supplemented with 5% horse serum (MCF10A), 14 mM NaHCO3, 10 μg/mL insulin, 2 mM L-glutamine, 20 ng/mL human epidermal growth factor, 500 ng/mL Hydrocortisone and 100 ng/mL cholera Toxin.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Plus kit following manufacturer’s instructions. HiC Libraries were prepared in duplicates for each cell type using the Arima-HiC+ kit (Arima Genomics, USA) according to manufacturer instructions. For each cell line, 1 million cells were used per HiC reaction. Cells were fixed with 1.2% formaldehyde for 12 min. All subsequent steps were carried out according to the Arima protocol. Resulting libraries were amplified with 5 PCR cycles and sequenced on an Illumina NovaSeq 6000 instrument in paired-end run with 2×101 bp.
Total RNA was isolated using the Qiagen RNeasy Plus kit following manufacturer’s instructions. HiC Libraries were prepared in duplicates for each cell type using the Arima-HiC+ kit (Arima Genomics, USA) according to manufacturer instructions. For each cell line, 1 million cells were used per HiC reaction. Cells were fixed with 1.2% formaldehyde for 12 min. All subsequent steps were carried out according to the Arima protocol. Resulting libraries were amplified with 5 PCR cycles and sequenced on an Illumina NovaSeq 6000 instrument in paired-end run with 2×101 bp.

treatment_protocol: To generate lentiviral particles, HEK293T cells were co-transfected using the calcium phosphate method with 20 µg of the pGFP-C-shLenti shHP1α plasmid (OriGene Technologies), 15 µg of psPAX2 (a gift from Didier Trono (Addgene plasmid # 12260; http://n2t.net/addgene:12260; RRID:Addgene_12260)), and 6 µg of pMD2.G (a gift from Didier Trono (Addgene plasmid # 12259; http://n2t.net/addgene:12259; RRID:Addgene_12259)). Viral supernatant was collected 48 hours after transfection and filtered through a 0.45 µm membrane. MCF10A cells were then transduced with the viral mixture supplemented with 4 µg/mL polybrene and 10 mM HEPES (pH 7.5). Following a 24-hour incubation, the viral medium was replaced with fresh growth media. The cells were cultured for an additional 24 hours to allow GFP expression, after which fluorescence-activated cell sorting (FACS) was performed to isolate a fully transduced cell population for downstream assays. For EMT induction, MCF10A cells were treated with 5 ng/mL TGF-β1 (R&D Systems) for 8 days.

value: mammary gland

value: epithelial cell

value: TGFB treatment


title: MCF10A TGFB rep1

description: Library name: Sample 5


title: PBMCs, AD patient, lecanemab, ARIA-H, 65-69M, E4/E4, Gene Expression

city: Lexington

first: Joshua

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

description:
Library name: Patient4_GEX
PBMCs from male AD patient (age 65-69y) with APOE E4/E4, lecanemab treatment, ARIA-H positive, infusion #23, gene expression library

data_processing:
Illumina NovaSeq 6000. GEX: 28bp R1, 90bp R2. ADT: 28bp R1, 90bp R2. VDJ: 150bp R1, 150bp R2.
Cell Ranger multi v9.0.1, GRCh38 reference. QC: <10% mitochondrial genes, doublet removal (scDblFinder v1.20.2), ambient RNA correction (decontX v1.4.1). Integration: Seurat v5.3.0 with SCTransform. Cell types: multimodal RNA+protein with weighted nearest neighbor analysis. VDJ: scRepertoire v2.3.4.
Assembly: GRCh38
Supplementary files format and content: H5 matrices with gene expression and ADT counts. VDJ: clonotypes, filtered contigs. Cell annotations include cell types and UMAP coordinates. TotalSeq-C antibody panel provided.

source_name: peripheral blood

growth_protocol: PBMCs were isolated from whole blood using density gradient centrifugation with SepMate tubes. Cells were washed, counted, and cryopreserved in 90% FBS/10% DMSO in liquid nitrogen.

extract_protocol:
Cryopreserved PBMCs were thawed at 37C and resuspended in RPMI-1640 + 10% FBS for immediate processing.
10x Genomics Chromium Single Cell 5 prime v2 with TotalSeq-C CITE-seq (137 antibodies). Gene expression and ADT libraries from same cDNA. V(D)J libraries enriched using 10x Human T Cell V(D)J kit.

treatment_protocol: Patients received bi-weekly intravenous infusions of lecanemab (10 mg/kg). Blood was collected immediately prior to infusion.

value: peripheral blood

value: peripheral blood mononuclear cells

tag: library type

value: mRNA

value: lecanemab 10 mg/kg bi-weekly

tag: aria status

value: ARIA-H

tag: infusion#

value: M

tag: mmse


title: PBMCs, AD patient, lecanemab, control, 75-79F, E4/E4, Gene Expression

description:
Library name: Patient5_GEX
PBMCs from female AD patient (age 75-79y) with APOE E4/E4, lecanemab treatment, ARIA status negative (control), infusion #13, gene expression library

value: Control

value: F


title: PBMCs, AD patient, lecanemab, ARIA-H, 65-69M, E4/E4, CITE-seq ADT

description:
Library name: Patient4_ADT
PBMCs from male AD patient (age 65-69y) with APOE E4/E4, lecanemab treatment, ARIA-H positive, infusion #23, antibody-derived tag library with 137 TotalSeq-C antibodies

data_processing:
Illumina NovaSeq 6000. GEX: 28bp R1, 90bp R2. ADT: 28bp R1, 90bp R2. VDJ: 150bp R1, 150bp R2.
Cell Ranger multi v9.0.1, GRCh38 reference. QC: <10% mitochondrial genes, doublet removal (scDblFinder v1.20.2), ambient RNA correction (decontX v1.4.1). Integration: Seurat v5.3.0 with SCTransform. Cell types: multimodal RNA+protein with weighted nearest neighbor analysis. VDJ: scRepertoire v2.3.4.
Assembly: GRCh38
Supplementary files format and content: H5 matrices with gene expression and ADT counts. VDJ: clonotypes, filtered contigs. Cell annotations include cell types and UMAP coordinates. TotalSeq-C antibody panel provided.
Library strategy: CITE-seq

molecule: protein

value: ADT

tag: adt

value: 137 TotalSeq-C antibodies (see TotalSeq-C_antibody_panel.csv)


title: PBMCs, AD patient, lecanemab, control, 70-74M, E4/E4, CITE-seq ADT

description:
Library name: Patient3_ADT
PBMCs from male AD patient (age 70-74y) with APOE E4/E4, lecanemab treatment, ARIA status negative (control), infusion #24, antibody-derived tag library with 137 TotalSeq-C antibodies

tag: cell type


title: PBMCs, AD patient, lecanemab, ARIA-E+H, 70-74F, E4/E4, TCR VDJ

description:
Library name: Patient6_VDJ
PBMCs from female AD patient (age 70-74y) with APOE E4/E4, lecanemab treatment, ARIA-E and ARIA-H positive, infusion #13, T cell receptor V(D)J sequencing library

data_processing:
Illumina NovaSeq 6000. GEX: 28bp R1, 90bp R2. ADT: 28bp R1, 90bp R2. VDJ: 150bp R1, 150bp R2.
Cell Ranger multi v9.0.1, GRCh38 reference. QC: <10% mitochondrial genes, doublet removal (scDblFinder v1.20.2), ambient RNA correction (decontX v1.4.1). Integration: Seurat v5.3.0 with SCTransform. Cell types: multimodal RNA+protein with weighted nearest neighbor analysis. VDJ: scRepertoire v2.3.4.
Assembly: GRCh38
Supplementary files format and content: H5 matrices with gene expression and ADT counts. VDJ: clonotypes, filtered contigs. Cell annotations include cell types and UMAP coordinates. TotalSeq-C antibody panel provided.
Library strategy: VDJ-seq

value: VDJ

tag: genotype

value: ARIA-EH


title: PBMCs, AD patient, lecanemab, control, 70-74M, E4/E4, Gene Expression

description:
Library name: Patient3_GEX
PBMCs from male AD patient (age 70-74y) with APOE E4/E4, lecanemab treatment, ARIA status negative (control), infusion #24, gene expression library

tag: tissue


title: PBMCs, AD patient, lecanemab, control, 75-79F, E4/E4, CITE-seq ADT

description:
Library name: Patient5_ADT
PBMCs from female AD patient (age 75-79y) with APOE E4/E4, lecanemab treatment, ARIA status negative (control), infusion #13, antibody-derived tag library with 137 TotalSeq-C antibodies

tag: Sex


title: PBMCs, AD patient, lecanemab, control, 70-74M, E4/E4, TCR VDJ

description:
Library name: Patient3_VDJ
PBMCs from male AD patient (age 70-74y) with APOE E4/E4, lecanemab treatment, ARIA status negative (control), infusion #24, T cell receptor V(D)J sequencing library

tag: age


title: PBMCs, AD patient, lecanemab, ARIA-H, 65-69M, E4/E4, TCR VDJ

description:
Library name: Patient4_VDJ
PBMCs from male AD patient (age 65-69y) with APOE E4/E4, lecanemab treatment, ARIA-H positive, infusion #23, T cell receptor V(D)J sequencing library


title: MCF10A shHPA rep1

description: Library name: Sample 3

value: HP1a knockdown


title: PBMCs, AD patient, lecanemab, ARIA-E, 70-74F, E3/E4, CITE-seq ADT

description:
Library name: Patient2_ADT
PBMCs from female AD patient (age 70-74y) with APOE E3/E4, lecanemab treatment, ARIA-E positive, infusion #16, antibody-derived tag library with 137 TotalSeq-C antibodies

value: ARIA-E


title: PBMCs, AD patient, lecanemab, ARIA-E+H, 70-74F, E4/E4, Gene Expression

description:
Library name: Patient6_GEX
PBMCs from female AD patient (age 70-74y) with APOE E4/E4, lecanemab treatment, ARIA-E and ARIA-H positive, infusion #13, gene expression library


title: MCF10A shHPA rep2

description: Library name: Sample 4

value: mammary gland


title: PBMCs, AD patient, lecanemab, control, 75-79F, E3/E4, TCR VDJ

description:
Library name: Patient1_VDJ
PBMCs from female AD patient (age 75-79y) with APOE E3/E4, lecanemab treatment, ARIA status negative (control), infusion #17, T cell receptor V(D)J sequencing library


title: MCF10A, rep2

description: Library name: Sample 2

value: epithelial cell

value: WT


title: PBMCs, AD patient, lecanemab, control, 75-79F, E4/E4, TCR VDJ

description:
Library name: Patient5_VDJ
PBMCs from female AD patient (age 75-79y) with APOE E4/E4, lecanemab treatment, ARIA status negative (control), infusion #13, T cell receptor V(D)J sequencing library

value: peripheral blood


title: PBMCs, AD patient, lecanemab, control, 75-79F, E3/E4, Gene Expression

description:
Library name: Patient1_GEX
PBMCs from female AD patient (age 75-79y) with APOE E3/E4, lecanemab treatment, ARIA status negative (control), infusion #17, gene expression library

value: peripheral blood mononuclear cells


title: TGFB15

description:
Library name: V_15
TGFB

value: Colon

value: Primary human colonic fibroblasts

value: TGFB


title: SKOV3 IDO1 KD cells treated with IFN-γ control for 24 hours, replicate 4

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

description: Library name: IDO1 KD IFN-γ rep 4

data_processing:
Reads were mapped to the human genome GRCh38 using STAR version 2.7.10b
reads were quantified using HTseq tool69 in Python
sample normalization and differential expression analysis was done using DESeq2 package70 (R 4.3.3, DESeq version 1.42.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited file containing DESeq2-normalized counts for each sample per column

growth_protocol: SKOV3 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) at 37°C in 5% CO2

extract_protocol:
Cells were lysed using Trizol at -80 °C, followed by chloroform precipitation. The RNA fraction was precipitated with isopropanol and washed with 70% ethanol. Finally, the pellet was left to dry and resuspended in RNAse-free water.
libraries were prepared with 500ng of total RNA of each sample using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760, NEB) with NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEB), according to standard manufacturer’s protocol. Total RNA and the final library quality controls were performed using Qubit™ Flex Fluorometer (Q33327, Thermo Fisher Scientific) and 4200 TapeStation System (G2991BA, Agilent) before and after library preparation.

treatment_protocol: 400.000 cells were seeded in 10cm dishes for each condition. The next day cells were stimulated with 10ng/ml of IFN-γ for 24 hours before cells were collected for RNA extraction.

value: IDO1 knock-down

value: 10ng/ml IFN-γ

value: 24 hours


title: Patient 17 CSF sample gene expression

first: Paula

last: Nieto

state: Spain

address: Barcelona Science Park, Carrer de Baldiri Reixac, 4, tower I, 08028 Barcelona

department: CNAG

institute: CNAG

description: Library name: P17_cDNA

data_processing:
Sequencing reads were processed with 10X Genomics' software CellRanger version 7.0.0
All CSF cell count matrices (all patients and samples) were combined to construct the joint count matrix.
Assembly: GRCh38
Supplementary files format and content: CSF_all_cells_counts.txt contains all CSF raw counts merged.
Supplementary files format and content: CSF_all_cells_metadata.txt contains cell and patient level metadata of all merged CSF cells.

source_name: CSF

extract_protocol:
CSF samples were collected during routine clinical care, primarily through lumbar puncture, except for four samples collected by ventricular CSF sampling. Cells were cryopreserved prior to sequencing.
Libraries were prepared following 10x Genomics’ 5-prime protocol.

value: CSF


title: PBMCs, AD patient, lecanemab, control, 75-79F, E3/E4, CITE-seq ADT

description:
Library name: Patient1_ADT
PBMCs from female AD patient (age 75-79y) with APOE E3/E4, lecanemab treatment, ARIA status negative (control), infusion #17, antibody-derived tag library with 137 TotalSeq-C antibodies

value: ADT

value: 137 TotalSeq-C antibodies (see TotalSeq-C_antibody_panel.csv)

value: lecanemab 10 mg/kg bi-weekly

value: Control

value: F


title: PBMCs, AD patient, lecanemab, ARIA-E, 70-74F, E3/E4, Gene Expression

description:
Library name: Patient2_GEX
PBMCs from female AD patient (age 70-74y) with APOE E3/E4, lecanemab treatment, ARIA-E positive, infusion #16, gene expression library

value: mRNA

value: ARIA-E


title: PBMCs, AD patient, lecanemab, ARIA-E+H, 70-74F, E4/E4, CITE-seq ADT

description:
Library name: Patient6_ADT
PBMCs from female AD patient (age 70-74y) with APOE E4/E4, lecanemab treatment, ARIA-E and ARIA-H positive, infusion #13, antibody-derived tag library with 137 TotalSeq-C antibodies

value: ARIA-EH


title: PBMCs, AD patient, lecanemab, ARIA-E, 70-74F, E3/E4, TCR VDJ

description:
Library name: Patient2_VDJ
PBMCs from female AD patient (age 70-74y) with APOE E3/E4, lecanemab treatment, ARIA-E positive, infusion #16, T cell receptor V(D)J sequencing library

value: peripheral blood

value: VDJ


title: MCF10A, rep1

description: Library name: Sample 1

value: mammary gland

value: epithelial cell

value: WT


title: SKOV3 IDO1 KD cells treated with IFN-γ control for 24 hours, replicate 3

description: Library name: IDO1 KD IFN-γ rep 3

value: IDO1 knock-down


title: Patient 17 CSF sample TCR

description: Library name: P17_VDJ-T

data_processing:
Sequencing reads were processed with 10X Genomics' software CellRanger version 7.0.0
All CSF cell count matrices (all patients and samples) were combined to construct the joint count matrix.
Assembly: GRCh38
Supplementary files format and content: CSF_all_cells_counts.txt contains all CSF raw counts merged.
Supplementary files format and content: CSF_all_cells_metadata.txt contains cell and patient level metadata of all merged CSF cells.
Library strategy: TCR-Seq


title: SKOV3 IDO1 KD cells treated with IFN-γ control for 24 hours, replicate 2

description: Library name: IDO1 KD IFN-γ rep 2

value: 10ng/ml IFN-γ


title: SKOV3 IDO1 KD cells treated with DMSO control for 24 hours, replicate 3

description: Library name: IDO1 KD DMSO rep 3

value: DMSO

value: 24 hours


title: SKOV3 IDO1 KD cells treated with DMSO control for 24 hours, replicate 4

description: Library name: IDO1 KD DMSO rep 4


title: SKOV3 IDO1 KD cells treated with DMSO control for 24 hours, replicate 1

description: Library name: IDO1 KD DMSO rep 1


title: SKOV3 cells treated with IFN-γ control for 24 hours, replicate 3

description: Library name: IFN-γ rep 3


title: SKOV3 cells treated with IFN-γ control for 24 hours, replicate 1

description: Library name: IFN-γ rep 1


title: SKOV3 cells treated with DMSO control for 24 hours, replicate 3

description: Library name: DMSO rep 3


title: SKOV3 cells treated with DMSO control for 24 hours, replicate 4

description: Library name: DMSO rep 4


title: SKOV3 cells treated with IFN-γ control for 24 hours, replicate 4

description: Library name: IFN-γ rep 4


title: SKOV3 cells treated with IFN-γ control for 24 hours, replicate 2

description: Library name: IFN-γ rep 2


title: SKOV3 cells treated with DMSO control for 24 hours, replicate 2

description: Library name: DMSO rep 2


title: H146_Anti-H3K27ace_ORY1001_rep3

city: chiba

first: YINGBO

last: GONG

department: Medicine

institute: CHIBA University

description: Library name: Sample88

data_processing:
The reads were mapped to the human genome assembly (GRCh37.p13 (hg19)) using the Bowtie 2 mapping tool with default settings. Peaks were called using MACS2 software with the broad option, and those identified in three replicates were used for further analyses. Data quantification was conducted using the “Annotate Peaks” command in Partek Flow software (https://www.partek.com/). DARs were detected using the “Gene-Specific Analysis” command in Partek Flow software. IGV was used for visualization.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: NCI-1417 [H1417] (Cat. No. CRL-5869) and NCI-H146 [H146] (Cat. No. HTB-173) cell line were purchased from the American Type Culture Collection 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)

extract_protocol:
NCI-H1417, NCI-H1417-INSM1KD or NCI-H146 cells were cross-linked at 37°C for 10 min with 1% formaldehyde. After quenching the cross-linking reaction with 1.25 M glycine, cells were lysed in swelling buffer (25 mM HEPES pH 7.9, 1.5 mM MgCl2, 10 mM KCl, and 0.1% (v/v) NP-40) containing a protease inhibitor cocktail (Nacalai Tesque). The mixture was subsequently centrifuged at 5000×g for 5 min at 4°C. Pelleted nuclei were re-suspended in sonication buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) SDS and 0.1 (w/v) Na-deoxycholate containing a protease inhibitor cocktail, ~5x106 cell/mL), sonicated on a Q700 (QSONICA, Newtown, CT) for 20–25 cycles of 15 s of sonication, followed by 45 s rest, at an amplitude of 60 (total 6000 J).
ChIP-seq libraries were constructed using an NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) according to the manufacturer’s protocols.

treatment_protocol: NCI-H1417 or NCI-H146 were seeded in plates. For NCI-H1417-INSM1KD cells, siRNA oligonucleotides against INSM1 (Cat. No. AM16708) were purchased from Ambion Thermo Fisher Scientific. NCI-H1417 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. 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. Cells were treated with DMSO or 300 nM LSD1 inhibitor (TAS1440, ORY-1001, GSK2879552) for 5 days

value: small-cell lung cancer

tag: chip antibody


title: SKOV3 cells treated with DMSO control for 24 hours, replicate 1

description: Library name: DMSO rep 1

tag: treatment


title: H146_Anti-H3K27ace_TAS1440_rep3

description: Library name: Sample87


title: H146_Anti-H3K27ace_GSK2879552_rep3

description: Library name: Sample89


title: H146_Anti-H3K27ace_GSK2879552_rep2

description: Library name: Sample85


title: H146_Anti-H3K27ace_DMSO_rep2

description: Library name: Sample82


title: H146_Anti-H3K27ace_DMSO_rep1

description: Library name: Sample78


title: SKOV3 IDO1 KD cells treated with IFN-γ control for 24 hours, replicate 1

description: Library name: IDO1 KD IFN-γ rep 1


title: H146_Anti-H3K27ace_GSK2879552_rep1

description: Library name: Sample81


title: H146_Anti-H3K27ace_TAS1440_rep2

description: Library name: Sample83


title: H146_Anti-H3K27ace_ORY1001_rep1

description: Library name: Sample80


title: H146_Anti-H3K4me3_GSK2879552_rep3

description: Library name: Sample77


title: H146_Anti-H3K4me3_ORY1001_rep3

description: Library name: Sample76


title: H146_Anti-H3K4me3_TAS1440_rep3

description: Library name: Sample75


title: H146_Anti-H3K27ace_ORY1001_rep2

description: Library name: Sample84


title: SKOV3 IDO1 KD cells treated with DMSO control for 24 hours, replicate 2

description: Library name: IDO1 KD DMSO rep 2


title: H146_Anti-H3K4me3_ORY1001_rep2

description: Library name: Sample72


title: H146_Anti-H3K4me3_DMSO_rep3

description: Library name: Sample74


title: H146_Anti-H3K4me3_DMSO_rep2

description: Library name: Sample70


title: H146_Anti-H3K4me3_TAS1440_rep2

description: Library name: Sample71


title: H146_Anti-H3K4me3_GSK2879552_rep1

description: Library name: Sample69


title: H146_Anti-H3K27ace_DMSO_rep3

description: Library name: Sample86


title: H146_Anti-H3K4me3_GSK2879552_rep2

description: Library name: Sample73


title: H146_Anti-H3K4me3_TAS1440_rep1

description: Library name: Sample67


title: H146_Anti-H3K4me3_ORY1001_rep1

description: Library name: Sample68


title: H146_Anti-H3K27ace_TAS1440_rep1

description: Library name: Sample79


title: H146_Anti-H3K4me2_GSK2879552_rep3

description: Library name: Sample65


title: H146_Anti-H3K4me2_ORY1001_rep3

description: Library name: Sample64


title: H146_Anti-H3K4me2_TAS1440_rep3

description: Library name: Sample63


title: H146_Anti-H3K4me2_DMSO_rep3

description: Library name: Sample62


title: H146_Anti-H3K4me2_GSK2879552_rep1

description: Library name: Sample57


title: H146_Anti-H3K4me2_ORY1001_rep2

description: Library name: Sample60


title: H146_Anti-H3K4me2_DMSO_rep2

description: Library name: Sample58


title: H146_Anti-H3K4me2_GSK2879552_rep2

description: Library name: Sample61


title: H146_Anti-H3K4me2_TAS1440_rep2

description: Library name: Sample59


title: H146_Anti-H3K4me2_ORY1001_rep1

description: Library name: Sample56


title: H146_Anti-H3K4me2_TAS1440_rep1

description: Library name: Sample55


title: H146_Anti-H3K4me1_ORY1001_rep3

description: Library name: Sample52


title: H146_Anti-H3K4me1_ORY1001_rep2

description: Library name: Sample48


title: H146_Anti-H3K4me1_GSK2879552_rep2

description: Library name: Sample49


title: H146_Anti-H3K4me2_DMSO_rep1

description: Library name: Sample54


title: H146_Anti-H3K4me1_DMSO_rep3

description: Library name: Sample50


title: H146_Anti-H3K4me1_TAS1440_rep3

description: Library name: Sample51


title: H146_Anti-H3K4me1_GSK2879552_rep3

description: Library name: Sample53


title: H146_Anti-H3K4me1_ORY1001_rep1

description: Library name: Sample44


title: H146_Anti-H3K4me1_TAS1440_rep2

description: Library name: Sample47


title: H146_Anti-H3K4me1_DMSO_rep2

description: Library name: Sample46


title: H146_Anti-H3K4me1_DMSO_rep1

description: Library name: Sample42


title: H146_Anti-H3K4me3_DMSO_rep1

description: Library name: Sample66


title: H146_Anti-H3K4me1_TAS1440_rep1

description: Library name: Sample43


title: H146_INPUT_ORY1001_rep3

description: Library name: Sample40


title: H146_INPUT_TAS1440_rep3

description: Library name: Sample39


title: H146_INPUT_DMSO_rep3

description: Library name: Sample38


title: H146_INPUT_GSK2879552_rep3

description: Library name: Sample41


title: H146_INPUT_GSK2879552_rep2

description: Library name: Sample37


title: H146_INPUT_TAS1440_rep2

description: Library name: Sample35


title: H146_INPUT_ORY1001_rep1

description: Library name: Sample32


title: H146_INPUT_ORY1001_rep2

description: Library name: Sample36


title: Anti-H3K27ace_INSM1KD_TAS1440_rep2

description: Library name: Sample27


title: H146_INPUT_DMSO_rep2

description: Library name: Sample34


title: Anti-H3K27ace_INSM1KD_TAS1440_rep3

description: Library name: Sample29


title: H146_INPUT_DMSO_rep1

description: Library name: Sample30


title: H146_INPUT_GSK2879552_rep1

description: Library name: Sample33


title: Anti-H3K27ace_INSM1KD_DMSO_rep3

description: Library name: Sample28


title: Anti-H3K27ace_INSM1KD_TAS1440_rep1

description: Library name: Sample25


title: H146_INPUT_TAS1440_rep1

description: Library name: Sample31


title: Anti-H3K4me3_INSM1KD_DMSO_rep3

description: Library name: Sample22


title: H146_Anti-H3K4me1_GSK2879552_rep1

description: Library name: Sample45


title: Anti-H3K27ace_INSM1KD_DMSO_rep1

description: Library name: Sample24


title: Anti-H3K4me3_INSM1KD_DMSO_rep1

description: Library name: Sample19


title: Anti-H3K4me3_INSM1KD_DMSO_rep2

description: Library name: Sample21


title: Anti-H3K27ace_INSM1KD_DMSO_rep2

description: Library name: Sample26


title: Anti-H3K4me3_INSM1KD_TAS1440_rep3

description: Library name: Sample23


title: Anti-H3K4me2_INSM1KD_DMSO_rep2

description: Library name: Sample15


title: Anti-H3K4me3_INSM1KD_TAS1440_rep1

description: Library name: Sample20


title: Anti-H3K4me2_INSM1KD_TAS1440_rep1

description: Library name: Sample14


title: Anti-H3K4me2_INSM1KD_DMSO_rep3

description: Library name: Sample17


title: Anti-H3K4me1_INSM1KD_TAS1440_rep3

description: Library name: Sample12


title: Anti-H3K4me2_INSM1KD_TAS1440_rep2

description: Library name: Sample16


title: Anti-H3K4me2_INSM1KD_DMSO_rep1

description: Library name: Sample13


title: Anti-H3K4me1_INSM1KD_DMSO_rep3

description: Library name: Sample11


title: Anti-H3K4me1_INSM1KD_TAS1440_rep2

description: Library name: Sample10


title: Anti-H3K4me1_INSM1KD_DMSO_rep2

description: Library name: Sample9


title: Anti-H3K4me1_INSM1KD_DMSO_rep1

description: Library name: Sample7


title: INPUT_INSM1KD_TAS1440_rep2

description: Library name: Sample4


title: Anti-H3K4me1_INSM1KD_TAS1440_rep1

description: Library name: Sample8


title: INPUT_INSM1KD_TAS1440_rep3

description: Library name: Sample6


title: INPUT_INSM1KD_DMSO_rep2

description: Library name: Sample3


title: INPUT_INSM1KD_DMSO_rep3

description: Library name: Sample5


title: Anti-H3K4me2_INSM1KD_TAS1440_rep3

description: Library name: Sample18


title: H1417_K661A_TAS1440_300nM_3

description: Library name: Sample96

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

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.

value: LSD1KO and LSD1K661A vector overexpression


title: H1417_K661A_TAS1440_300nM_1

description: Library name: Sample94


title: H1417_LSD1_TAS1440_300nM_3

description: Library name: Sample90

value: LSD1KO and LSD1 vector overexpression


title: H1417_K661A_DMSO_1

description: Library name: Sample91


title: H1417_K661A_DMSO_2

description: Library name: Sample92


title: H1417_LSD1_DMSO_3

description: Library name: Sample87


title: H1417_LSD1_TAS1440_300nM_2

description: Library name: Sample89


title: H1417_LSD1_DMSO_2

description: Library name: Sample86


title: INPUT_INSM1KD_TAS1440_rep1

description: Library name: Sample2


title: H1417_LSD1_DMSO_1

description: Library name: Sample85


title: H1417_EMPTY_TAS1440_300nM_3

description: Library name: Sample84

value: LSD1KO and Empty vector overexpression


title: H1417_LSD1_TAS1440_300nM_1

description: Library name: Sample88


title: siSMAD2_H146_Day7_TAS1440_300nM_3

description: Library name: Sample78


title: H1417_EMPTY_TAS1440_300nM_1

description: Library name: Sample82


title: H1417_EMPTY_DMSO_3

description: Library name: Sample81


title: H1417_EMPTY_DMSO_1

description: Library name: Sample79


title: siSMAD2_H146_Day7_TAS1440_300nM_2

description: Library name: Sample77


title: H1417_EMPTY_TAS1440_300nM_2

description: Library name: Sample83


title: INPUT_INSM1KD_DMSO_rep1

description: Library name: Sample1


title: H1417_K661A_TAS1440_300nM_2

description: Library name: Sample95


title: siSMAD2_H146_Day7_DMSO_3

description: Library name: Sample75


title: H1417_K661A_DMSO_3

description: Library name: Sample93


title: siSMAD2_H1417_Day7_TAS1440_300nM_3

description: Library name: Sample72


title: siSMAD2_H146_Day7_TAS1440_300nM_1

description: Library name: Sample76


title: siSMAD2_H146_Day7_DMSO_2

description: Library name: Sample74


title: siSMAD2_H1417_Day7_TAS1440_300nM_1

description: Library name: Sample70


title: siSMAD2_H146_Day7_DMSO_1

description: Library name: Sample73


title: H1417_EMPTY_DMSO_2

description: Library name: Sample80


title: siSMAD2_H1417_Day7_DMSO_1

description: Library name: Sample67


title: siSMAD2_H1417_Day7_DMSO_2

description: Library name: Sample68


title: siNC_H146_Day7_TAS1440_300nM_2

description: Library name: Sample65

value: siNC


title: siNC_H146_Day7_TAS1440_300nM_3

description: Library name: Sample66


title: siNC_H1417_Day7_TAS1440_300nM_3

description: Library name: Sample60


title: siSMAD2_H1417_Day7_DMSO_3

description: Library name: Sample69