title: WT Female 3 8 Week LNAME

first: Alireza

last: Khoddam

address: 303 E Superior St 8-400

department: Cardiology

institute: Northwestern University

description: Library name: V6200

data_processing:
for bulk RNA-seq: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2[2] as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. For scRNA-Seq: Sequencing data were aligned to mouse reference using the Cell Ranger 3.0.2 pipeline.
Assembly: Mouse mm10
Supplementary files format and content: csv contains raw counts for each sample (bullk RNA-seq). AnnData Object containing raw counts of scRNA seq data.

source_name: aorta

extract_protocol:
For bulk RNA-seq: mice were perfused with PBS, whole aortas were extraced and cleaned of peri-aortic fat. For scRNA-seq: A working enzyme solution was prepared on ice by combining Liberase TM (Roche #05401127001, Basel, Basel-Stadt, Switzerland) at 2 units/mL final concentration, Elastase (Worthington #LS002279, Columbus, OH, USA) at 2 units/mL final concentration, and DNase I at 60 units/mL (Roche #10104159001, Basel, Basel-Stadt, Switzerland) in HBSS with Ca2+ and Mg2+ (Gibco #14025092, Waltham, MA, USA).  After euthanization in a CO2 chamber for 2 minutes, mice were perfused with 10 mL HBSS (Gibco #14025092, Waltham, MA, USA) via left ventricular puncture, and the aorta was harvested. The aortas underwent extensive cleaning of periaortic fat and excess tissue while submerged in MACS Separation Buffer (Miltenyi Biotec #130-091-221, Bergisch Gladbach, Rhineland, Germany). The aorta was split open and minced using iris scissors, transferred to 1mL of the enzyme solution described above, and incubated at 37°C for 45 minutes while shaking at 300 RPM. The reaction digestion reaction was stopped by adding 5 mL of 2% FBS (Gibco #A38401-01, Waltham, MA, USA) in HBSS (Gibco #14025092, Waltham, MA, USA). The cell suspension was passed through a 70-μm strainer into a 50 mL conical tube, and residual liquid was collected by centrifugation 300 × g for 10 minutes. Isolated cells were transferred into a microcentrifuge tube and centrifuged at 300 × g for 5 minutes. All but 100 μL of supernatant was removed and cells were resuspended in the remaining 100 μL volume.
For bulk RNA-seq: RNA was isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, North Rhine-Westphalia, Germany) using the manufacturer protocol. For scRNA-seq: Single-cell mRNA libraries were built using the Chromium Next GEM Single Cell 3’ Library Construction V4 Kit.

value: aorta

value: 8-week LNAME treatment


title: WT Female 2 8 Week LNAME

status: Public on Sep 19 2025

type: SRA

city: Chicago

state: IL

country: USA

description: Library name: V6199

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

tag: treatment


title: WT Male 3 8 Week LNAME

description: Library name: V6198


title: WT Male 2 8 Week LNAME

description: Library name: V6196


title: MEF, mock, IgG, 1 [B256178]

city: Oxford

first: Aleksandr

last: Fedorov

address: John Radcliffe Hospital/Headley Way

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: B256178+2360303

library_source: other

data_processing:
All samples were aligned to a chimeric reference composed of the host (GRCm39) and viral reference sequences (HSV-1 and IAV) using a custom fork of the nf-core 'rnaseq' pipeline (https://github.com/alnfedorov/rnaseq, commit 41e95d6a4a24d1f4fe4f2c50bb4d9a4744158c9b). Briefly, reads were trimmed using fastp (v0.23.4), aligned using STAR (v2.7.10a), duplicates were marked with Picard (v3.1.1), and the abundance of individual RNAs was quantified using Salmon (v1.10.1).
Peak calling and dsRNA reconstruction of endogenous RNAs were performed using biobit (https://github.com/biomancy/biobit, v0.0.4). Inferred dsRNA clusters were tested for induction and enrichment using DESeq2 (v1.46.0) and apeglm (v1.28.0).
Aberrant transcription was analyzed with DEXSeq (v1.52.0) by treating each mRNA with a matched aberrant transcription region, or each intron with its matched 5′ constitutive exon, as regions belonging to the same group in DEXSeq.
Enrichment of viral RNAs was visualized using pyCirclize (v1.7.1). ViennaRNA (v2.7.0) and Z-Hunt[rs] (https://github.com/biomancy/zhuntrs, v0.0.4) were used to predict putative Z-prone RNA stems within the minimum free energy structures of individual vRNAs.
All code used to analyze sequencing data in this study is publicly available at https://github.com/alnfedorov/Z-DoTT.
Assembly: GRCm39, GCF_000865725.1, NC_001806.2
Supplementary files format and content: The counts.tsv.gz file includes five index columns followed by count columns, with column names corresponding to the library names provided in the submission. The index columns define the region being assessed: its unique ID, type, and localization (sequence ID, strand, and location). For split regions (e.g., exons), multiple coordinates are separated by semicolons. Each region represents either a normalization bin (used exclusively for library normalization) or a putative dsRNA cluster predicted from RIP data. This table can be used to identify dsRNA clusters that are strongly induced during infection and reproducibly enriched in RIP experiments from infected cells.

molecule: other

source_name: MEF

growth_protocol: MEFs were maintained in DMEM supplemented with 15% FBS, 1 mM sodium pyruvate, 1x GlutaMAX, and 1% penicillin/streptomycin. All cells were cultured at 37°C in 5% CO2, and routinely tested for mycoplasma.

extract_protocol:
RIP was conducted using the EZ-Magna RIP (Cross-Linked) RNA-Binding Protein Immunoprecipitation Kit (Millipore) following the manufacturer’s instructions. Briefly, cross-linked cell pellets were lysed in RIP lysis buffer, followed by incubation with RIP Buffer containing magnetic beads conjugated with anti-Z-NA antibody (clone Z22, Absolute Antibody), anti-FLAG antibody (F1804, Sigma-Aldrich) or their respective isotype control antibodies, at 4°C overnight. Samples were then incubated with proteinase K and immunoprecipitated RNAs were recovered by phenol:chloroform:isoamyl alcohol purification.  Ten percent of the cell lysate was used for total RNA extraction as the input, and the remaining ninety percent was used for immunoprecipitation.
Libraries were prepared from RIP or input RNA using the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Thermo Fisher Scientific) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired-end 150 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: FLAG-ZBP1 and FLAG-ZBP1 ΔZα MEFs were generated via stable retroviral transduction (pRetroX, Clontech) of immortalized Zbp1-/- MEFs with expression vectors encoding either FLAG-tagged full-length mouse ZBP1 or ZBP1 lacking both Zα domains (ΔZα). Cells were infected (MOI=2) with or without HSV-1 (F strain[VR-733]) or IAV (A/Puerto Rico/8/1934) for 8h.

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

value: Mock

tag: rip

value: IgG

tag: batch


title: WT Female 1 8 Week LNAME

description: Library name: V6190


title: MEF, IAV, FLAG, 1 [B256178]

description: Library name: B256178+2360308

value: IAV infection

value: FLAG


title: WT Male 1 8 Week LNAME

description: Library name: V6192


title: Het Female 3 8 Week LNAME

description: Library name: V6204


title: Het Female 2 8 Week LNAME

description: Library name: V6187


title: Het Female 1 8 Week LNAME

description: Library name: V6186


title: Multiplexed AKG12C treatment series

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

institute: CRUK Scotland Institute

description:
Library name: AKG12C
10x genomics GEMX-flex

library_source: transcriptomic single cell

data_processing:
Pooled sequencing data was demultiplexed, UMIs counted and count tables produced using CellRanger 9.0.0
Assembly: GRCm39
Supplementary files format and content: h5 matrix files

source_name: Colon

growth_protocol: Single 70uL injection of 100uM 4-OH tamoxifen into the colonic submucosa with weekly monitoring from two weeks post injection by colonoscope

extract_protocol:
Tumours were processed to single cells using a GEM-X Flex Sample preparation kit, before being incubated overnight at 4 degrees celcius in GEM-X flex Fixation Buffer B. Samples were washed in PBS then resuspended in GEM-X flex Quench Buffer, then dissiciated in RPMI and 5mg/ml Liberase TH. Homogenisation was then performed on a GentleMACS Octo Dissociator, cells were filtered with a 30 um strainer, pelleted and resuspended in GEM-X flex Quench buffer, then counted using equal parts of cell suspension and ReadyCount Green/Red Viability Stain on a CellDrop Automated Cell Counter.
Libraries were prepared using a 10X Genomics Gem-X Flex Gene Expression kit with the Mouse Transcriptome Probe panel, according to the manufacturer’s protocol

treatment_protocol: Mice were treated once  daily with AZD4625 (OG 100uL 100mg/kg) or vehicle (0.5% HPMC 0.1% Tween 80) for 4 days and sampled two hours post dose on the fourth day.

value: Colon


title: Het Male 3 8 Week LNAME

description: Library name: V6203


title: Het Male 1 8 Week LNAME

description: Library name: V6201


title: Het Male 2 8 Week LNAME

description: Library name: V6202


title: BPRNF SI Tum d1 Mulitplex

description:
Library name: BPRNF_d1
10x genomics GEMX-flex

source_name: Small Intestine

extract_protocol:
Tumours were processed to single cells using a GEM-X Flex Sample preparation kit, before being incubated overnight at 4 degrees celcius in GEM-X flex Fixation Buffer B. Samples were washed in PBS then resuspended in GEM-X flex Quench Buffer, then dissiciated in RPMI and 5mg/ml Liberase TH. Homogenisation was then performed on a GentleMACS Octo Dissociator, cells were filtered with a 30 um strainer, pelleted and resuspended in GEM-X flex Quench buffer, then counted using equal parts of cell suspension and ReadyCount Green/Red Viability Stain on a CellDrop Automated Cell Counter.
Libraries were constructed using a 10X Genomics Gem-X flex Gene Expression kit using the MouseTranscriptome Probe panel, as per the manufacturer’s instructions.

value: Small Intestine

tag: sample type

value: Primary Tumour

value: VilCreER BrafV600E/+ p53 fl/fl RNF43 fl/fl

tag: time point

value: Day 1


title: SCM 4

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: Library name: 2630550_MEH700

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to mouse genome assembly (mm10) (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on  GENCODE annotation (mouse release M22) .
Assembly: GRCm38(mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

source_name: Sternocleidomastoid muscle

extract_protocol:
For bulk tumor RNA sequencing, tumors were dissociated in Qizol on tissue lyser (Qiagen) for 5 min at 50 Hz. RNA was then extracted by miRNeasy minelute kit (Qiagen) per manufacturer instructions
For bulk tumor RNA sequencing libraries were prepeared from total RNA with TruSeq Stranded Total RNA Library Prep Kit (Illumina, #20020599) accoriding to manufacturer's instructions.

value: Sternocleidomastoid muscle


title: SCM 1

description: Library name: 2630547_MEH697


title: SCM 2

description: Library name: 2630548_MEH698


title: ASTOM 7

description: Library name: 2630545_MEH695

source_name: bulk tumor

value: bulk tumor

value: aP2-Cre; Patched flox/flox


title: ASTOM 6

description: Library name: 2630544_MEH694


title: SCM 3

description: Library name: 2630549_MEH699


title: ASTOM 5

description: Library name: 2630543_MEH693


title: ASTOM 8

description: Library name: 2630546_MEH696


title: APcKO 2

description: Library name: 2630540_MEH690


title: APcKO 4

description: Library name: 2630542_MEH692


title: APcKO 3

description: Library name: 2630541_MEH691


title: NBH_30_2, control condition 30 wpi replicate 2

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital of Zurich

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: NBH_30_2

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger default's setting
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissues_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Brain

extract_protocol:
Fresh frozen tissues were OCT embedded and 10 um section slides were cut with cryostat
Spatial Transcriptome sequencing library were prepared with 10xGenomics Spatial Visium Gene Expression Slides & Reagent kit according to manufactorer's construction

value: Brain

tag: timepoint

value: 30 week post inoculation

value: (NBH) Non-infectious Brain Homogenate


title: APcKO 1

description: Library name: 2630539_MEH689


title: RML6_30_2, prion condition 30 wpi replicate 2

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: RML6_30_2

value: (RML6) Prion-containing brain homogenate


title: RML6_30_1, prion condition 30 wpi replicate 1

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: RML6_30_1


title: NBH_TS_2, control condition terminal stage replicate 2

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: NBH_TS_2

value: Terminal stage


title: RML6_TS_1, prion condition terminal stage replicate 1

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: RML6_TS_1


title: NBH_30_1, control condition 30 wpi replicate 1

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: NBH_30_1


title: Cell_3504

city: Manchester

first: Georges

last: Lacaud

state: England

address: Wilmslow Raod

department: Stem Cell Biology

institute: Cancer Research UK Manchester Institute

description: SmartSeq2_Gene_log_normalized_counts.rds

data_processing:
Raw fastq files were obtained by bcltoFastq conversion (version 2.20.0.422)
Fastq files were aligned to the mm10 reference genome using STAR aligner (version 2.7.9a) with the argument ‘STARsolo’. This argument allowed simultaneous mapping of reads and quantification of gene expression. The reference genome and gene transfer format (GTF) file were downloaded from 10x genomic webpage at (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz).
The output of ‘STARsolo’ was loaded into R (version 4.1.0) using the Bioconducter package DropletUtils (version 1.12.1).
Downstream analyses were done in R using SingleCellExperiment (version 5271.14.1) and Seurat (version 4.0.6).
Cells with <2000 detected genes, >15% mitochondrial content and > 10% hemoglobin percentage were excluded.
For isoform analysis, fastq files of selected 432 cells (46 cells from HE-HSC (AGM), 198 from HE-LMP (YSm), and 188 cells from HE-EMP (YSb)) were aligned and quantifed using Salmon 1.4.0  in Mapping mode. GRCm39 M32 mouse reference genome, transcriptome, and GTF file were downloaded from GENCODE website. Resulting quant.sf files were fed into IsoformSwitchAnalyzer  2.01.07 where importIsoformExpression function was used to give TMM normalized abundance values.
Assembly: GRCm39 M32 Gencode reference for Isoform Analysis and mm10 10X genomics reference for gene level analysis
Supplementary files format and content: RDS file having log normalized counts for each sample-gene level analyses (1494 cells)
Supplementary files format and content: RDS file having TMM normalized abundance for each sample used for isoform analyses (432 cells)

molecule: polyA RNA

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol.
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)

tag: sequencing run


title: RML6_27, prion condition 27 wpi

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: RML6_27

value: 27 week post inoculation


title: Cell_3503


title: NBH_TS_1, control condition terminal stage 1

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: NBH_TS_1


title: Cell_3500


title: Cell_3499

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_3498


title: Cell_3497


title: Cell_3496


title: Cell_3495


title: Cell_3487


title: Cell_3491


title: Cell_3485


title: Cell_3484


title: Cell_3482


title: Cell_3483


title: Cell_3479


title: RML6_TS_2, prion condition terminal stage replicate 2

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: RML6_TS_2


title: Cell_3480


title: Cell_3477


title: Cell_3481


title: Cell_3473


title: Cell_3471


title: NBH_27, control condition 27 wpi

description:
Fresh Frozen Spatial transcriptome sequencing
sample IS: NBH_27


title: Cell_3468


title: Cell_3467


title: Cell_3462


title: Cell_3459


title: Cell_3457


title: Cell_3453


title: Cell_3463


title: Cell_3460


title: Cell_3451


title: Cell_3465


title: Cell_3449


title: Cell_3448


title: Cell_3444


title: Cell_3452


title: Cell_3446


title: Cell_3443


title: Cell_3447


title: Cell_3433


title: Cell_3436


title: Cell_3429


title: Cell_3427


title: Cell_3432


title: Cell_3423


title: Cell_3472


title: Cell_3466


title: Cell_3419


title: Cell_3420


title: Cell_3417


title: Cell_3418


title: Cell_3411


title: Cell_3415


title: Cell_3409


title: Cell_3410


title: Cell_3413


title: Cell_3434


title: Cell_3404


title: Cell_3407


title: Cell_3402


title: Cell_3438


title: Cell_3394


title: Cell_3405


title: Cell_3390


title: Cell_3424


title: Cell_3406


title: Cell_3408


title: Cell_3401


title: Cell_3399


title: Cell_3392


title: Cell_3389


title: Cell_3388


title: Cell_3386


title: Cell_3391


title: Cell_3385


title: Cell_3384


title: Cell_3383


title: Cell_3381


title: Cell_3382


title: Cell_3379


title: Cell_3377


title: Cell_3371


title: Cell_3372


title: Cell_3369


title: Cell_3364


title: Cell_3370


title: Cell_3363


title: Cell_3360


title: Cell_3355


title: Cell_3356


title: Cell_3358


title: Cell_3352


title: Cell_3346


title: Cell_3324


title: Cell_3328


title: Cell_3343


title: Cell_3320


title: Cell_3345


title: Cell_3319


title: Cell_3337


title: Cell_3329


title: Cell_3322


title: Cell_3318


title: Cell_3321


title: Cell_3317


title: Cell_3316


title: Cell_3313


title: Cell_3314


title: Cell_3312


title: Cell_3310


title: Cell_3309


title: Cell_3306


title: Cell_3349


title: Cell_3347


title: Cell_3330


title: Cell_3298


title: Cell_3300


title: Cell_3302


title: Cell_3297


title: Cell_3303


title: Cell_3286


title: Cell_3294


title: Cell_3281


title: Cell_3278


title: Cell_3296


title: Cell_3283


title: Cell_3279


title: Cell_3282


title: Cell_3315


title: Cell_3284


title: Cell_3266


title: Cell_3264


title: Cell_3259


title: Cell_3260


title: Cell_3277


title: Cell_3272


title: Cell_3258


title: Cell_3307


title: Cell_3255


title: Cell_3252


title: Cell_3251


title: Cell_3292


title: Cell_3276


title: MII oocytes, NTY, rep 2 [6B]

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description: in vivo

data_processing:
quality filtered and trimmed, and adaptor sequences were removed using  Quality filtering and adaptor removal using trim_galore (v0.4.1)
Mapping to mouse genome (mm10) using Tophat2
featureCounts software was used to quantify the number of reads mapped to each gene using gene annotation from Ensembl release 19
Assembly: mm10
Supplementary files format and content: tab-delimited text table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text table with TPM normalized counts for every gene and every sample

source_name: MII oocytes

growth_protocol: NRF study

extract_protocol:
Arcturus® Paradise® Plus RNA Extraction and Isolation Kit (#KIT0312I Arcturus Bioscience Inc., Mountain View, CA, USA) was used for isolation of total cellular RNA from the microdissected cells on the LCM caps, according to the manufacturer’s protocol. RNA from each cap was pooled for the same oocyte stage during extraction. Total cellular RNA from oocytes collected in vivo and in vitro was isolated using Picopure (#KIT0204 Arcturus Bioscience, Inc., Mountain View, CA, USA).
The Ovation® PICO SL WTA System V2 RNA amplification system (#3312 NuGen, Inc., San Carlos, CA, USA) was used for conversion of isolated RNA from the LCM-derived samples to cDNA and linear amplification. Library preparation for microdissected oocytes was performed using an Illumina TruSeq RNA Access kit at BGI, according to the manufacturer’s protocol. RNA sequencing was performed on an Illumina HiSeq platform with two lanes (5 gb per sample). Library preparation for collected oocytes in both groups was performed using the Smart-seq II method, and RNA sequencing was performed using the Illumina HiSeq platform with one lane (5 gb per sample).

tag: strain

value: C57Bl/6j x CBA/J

value: MII oocytes

value: NTY


title: Cell_3248


title: MII oocytes, NTY, rep 3 [6C]

description: in vivo


title: MII oocytes, sham, rep 3 [5C]

description: in vivo

value: sham


title: Cell_3243


title: MII oocytes, NTY, rep 1 [6A]

description: in vivo


title: Cell_3242


title: MII oocytes, sham, rep 1 [5A]

description: in vivo


title: Oocytes from primary follicles, NTY, rep 3 [2E2]

description: in vivo

source_name: Oocytes from primary follicles

value: Oocytes from primary follicles


title: MII oocytes, sham, rep 2 [5B]

description: in vivo


title: Oocytes from primary follicles, NTY, rep 2 [2E]

description: in vivo


title: Cell_3274


title: Cell_3241


title: Cell_3238


title: Oocytes from primordial follicles, NTY, rep 2 [2B]

description: in vivo

source_name: Oocytes from primordial follicles

value: Oocytes from primordial follicles


title: Oocytes from primordial follicles, NTY, rep 3 [2C]

description: in vivo


title: Oocytes from primordial follicles, NTY, rep 1 [2A]

description: in vivo


title: Cell_3235


title: Cell_3236


title: Cell_3240


title: Cell_3249


title: Cell_3245


title: Cell_3232


title: Cell_3244


title: Oocytes from primary follicles, sham, rep 3 [1F]

description: in vivo


title: Cell_3231


title: Cell_3230


title: Oocytes from primary follicles, sham, rep 2 [1E]

description: in vivo


title: Cell_3226


title: Cell_3225


title: Cell_3229


title: Oocytes from primary follicles, sham, rep 1 [1D]

description: in vivo


title: Oocytes from primordial follicles, sham, rep 3 [1C]

description: in vivo


title: CST 5

description: CST 618 - 2260513

source_name: FACS sorted tdTomato positive/PECAM1-negative tumor cells

extract_protocol:
For FACS sorted tumor samples, tumors were manually dissected from surrounding tissue, manually dissociated and then digested for 1 hour at 37C in 2U/mL Collagenase B (Roche, #11088831001), Dispase II (Roche, # 04942078001), 50 mM HEPES/KOH pH 7.4, 150 mM NaCl. Cells were then resuspended in 2x volume 10% FBS  in PBS to inactivate digestion enzymes. Samples were filtered through 70 uM filter, spun and supernatant spun again. Then filtered through a 40 uM filter to yield a single cell suspension. Samples were spun down and resuspending in 200 uL 1:50 dilution of CD31-APC antibody for 30 minutes. Samples were then resuspended in 5% FBS PBS and spun down again prior to sorting on a FACS Aria for CD31-/tdTomato+ cell populations with DAPI as a live/dead marker. Data were analyzed with FACSDiva and FlowJo software. Following FACS sorting RNA was isolated from CD31-/tdTomato+ cells with miRNeasy microelute kit (Qiagen) per manufacturer's instructions.
For FACS sorted samples low input RNA sequencing was used. One nanogram of total RNA was used to create SPIA-cDNA with a Tecan Ocation RNA seuqncing stem v2 protocol (Tecan, #7102-32) per manufacturer's instructions. 500 ng of purified cDNA was sheered ina Covaris LE220 focused ultra sonicator using a 96 microtube-50 AFA fiberr plate and target base pair size of 300 bp. Following sheering libraries were created using KAPA Hyper-Prep kit (Roche, #KK8504) per manufacturer's instructions based on initial cDNA input. UDI DNA indexes were used from Illumina (20022370).


title: Oocytes from primordial follicles, sham, rep 2 [1B]

description: in vivo


title: Cell_3223


title: Cell_3224


title: CST 6

description: CST 769 - 2346400

value: FACS sorted tdTomato positive/PECAM1-negative tumor cells


title: Oocytes from primordial follicles, sham, rep 1 [1A]

description: in vivo


title: Cell_3222


title: ASTOM 8

description: ASTOM 187 - 1860292


title: Cell_3219


title: Oocytes from primary follicles, NTY, rep 1 [2D]

description: in vivo


title: Cell_3213


title: Cell_3217


title: ASTOM 6

description: ASTOM 169 - 1860290


title: ASTOM 7

description: ASTOM 167 - 1860291


title: MyoGM2 4

description: MyoG 10 - 1976324

value: Myog-Cre;R26 SmoM2


title: Cell_3216


title: MyoGM2 3

description: MyoG 5 - 1976323


title: Cell_3210


title: ASTOM 5

description: ASTOM 163 - 1860289


title: MyoGM2 2

description: MyoG 2 - 1976322


title: Cell_3211


title: Cell_3212


title: MyoGM2 1

description: MyoG 1 - 1976321


title: Cell_3209


title: Cell_3207


title: ASTOM 4

description: ASTOM 296 - 1976320


title: Cell_3205


title: ASTOM 3

description: ASTOM 295 - 1976319


title: ASTOM 2

description: ASTOM 292 - 1976318


title: CST 4

description: CST 286 - 1976316


title: Cell_3204


title: CST 3

description: CST 280L - 1976315


title: CST 2

description: CST 280R - 1976314


title: Cell_3199


title: Cell_3206


title: Cell_3201


title: Cell_3200


title: CST 1

description: CST 253 - 1976313


title: ASTOM 1

description: ASTOM 291 - 1976317


title: Cell_3198


title: Cell_3197


title: Cell_3196


title: Cell_3192


title: Cell_3191


title: Cell_3189


title: Cell_3194


title: Cell_3186


title: Cell_3184


title: Sample287

type: genomic

city: Changsha

first: Yu

last: Liu

address: 139# Road Renmin

country: China

institute: The Second Xiangya Hospital of Central South University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: CHAMP

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: genomic DNA from peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from blood samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: allopurinol-tolerant control

value: HLA-B*58:01 negative

value: blood


title: Cell_3183


title: Sample264


title: Cell_3182


title: Sample273


title: Sample289


title: Cell_3181


title: Cell_3180


title: Sample301


title: Cell_3174


title: Cell_3173


title: Sample310


title: Sample314


title: Cell_3171


title: Cell_3167


title: Sample332


title: Cell_3166


title: Sample344


title: MeT-5A-DKO-#2 with cerulenin treated

type: RNA

city: Nagakute

first: Karnan

last: Sivasundaram

state: Aichi

address: Yazakokarimata

department: Biochemisy

country: Japan

institute: Aichi Medical University

description: Gene expression in MeT-5A-DKO-#2with cerulenin treatedcell cells

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol:
MeT-5A were provided by the ATCC through the American Type Culture Collection , and were grown in RPMI containing 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 incubator.
HOMC-B1 cells were maintained in Iscove’s modified Dulbecco’s medium (IMDM; Gibco, Grand Island, NY), supplemented with 10% fetal bovine serum, penicillin (100U/ml) and streptomycin (100U/ml), at 37°C in 5% CO 2 and 95% air.

extract_protocol: RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: HOMC-B1and MeT-5A  and the established cell clones  were plated at 80% confluence and cultured for 24 hours

value: Human mesothelium

tag: gender

value: male

tag: age

value: unknown

value: cerulenin treated


title: MeT-5A-DKO-#2

description: Gene expression in MeT-5A-DKO-#2cells


title: MeT-5A-DKO-#1 with cerulenin treated

description: Gene expression in MeT-5A-DKO-#1with cerulenin treatedcell cells


title: HOMC-B1-DKO-#1 with cerulenin treated

description: Gene expression in HOMC-B1-DKO-#1 with cerulenin treatedcell cells


title: HOMC-B1-DKO-#2 with cerulenin treated

description: Gene expression in HOMC-B1-DKO-#2 with cerulenin treatedcell cells


title: MeT-5A-DKO-#1

description: Gene expression in MeT-5A-DKO-#1cells


title: HOMC-B1-DKO-#2

description: Gene expression in HOMC-B1-DKO-#2 cells


title: Sample366


title: HOMC-B1-DKO-#1

description: Gene expression in HOMC-B1-DKO-#1 cells


title: Cell_3163


title: Sample300


title: Sample368


title: Sample385


title: Cell_3159


title: Sample387


title: Cell_3156


title: Sample430


title: Cell_3158


title: Cell_3154


title: Sample450


title: Cell_3151


title: Sample498


title: Cell_3150


title: Cell_3164


title: Sample513


title: Cell_3142


title: Cell_3144


title: Sample539


title: Sample568


title: Cell_3140


title: Sample577


title: Cell_3138


title: Cell_3137


title: Sample599


title: Cell_3136


title: Sample446


title: adrd0041

value: allopurinol-induced SCAR patient

value: HLA-B*58:01 positive


title: Cell_3152


title: Cell_3135


title: Cell_3132


title: adrd0063


title: adrd0013


title: Sample506


title: Cell_3130


title: adrd0392


title: Cell_3134


title: adrd0572


title: Cell_3125


title: adrd1755


title: Sample558


title: adrd1626


title: Cell_3123


title: Cell_3141


title: Cell_3124


title: Cell_3120


title: adrd1805


title: Cell_3119


title: Cell_3115


title: adrd1936


title: adrd2042


title: adrd0059


title: adrd2095


title: Cell_3113


title: Cell_3114


title: Cell_3111


title: Cell_3131


title: Sample536


title: ADRC274


title: Sample365


title: adrd0554


title: Cell_3110


title: Cell_3109


title: Sample369


title: Sample551


title: Sample598


title: Cell_3122


title: Sample600


title: Cell_3106


title: Cell_3104


title: Cell_3105


title: Derm1963


title: Cell_3107


title: Sample292


title: Cell_3100


title: Sample547


title: Cell_3093


title: Sample459


title: Sample610


title: Sample534


title: Sample601


title: Sample532


title: Sample336


title: Cell_3091


title: Cell_3092


title: Cell_3089


title: Cell_3090


title: Cell_3088


title: Cell_3108


title: Sample531


title: Sample606


title: Cell_3096


title: adrd2684


title: adrd2697


title: Cell_3085


title: Cell_3084


title: adrd2165


title: Cell_3083


title: adrd0225


title: adrd2122


title: Cell_3081


title: Cell_3073


title: HT-29, IAV, FLAG-input, 3 [B831009]

description: Library name: B831009+3162361

data_processing:
All samples were aligned to a chimeric reference composed of the host (CHM13v2) and viral reference sequences (HSV-1 and IAV) using a custom fork of the nf-core 'rnaseq' pipeline (https://github.com/alnfedorov/rnaseq, commit 41e95d6a4a24d1f4fe4f2c50bb4d9a4744158c9b). Briefly, reads were trimmed using fastp (v0.23.4), aligned using STAR (v2.7.10a), duplicates were marked with Picard (v3.1.1), and the abundance of individual RNAs was quantified using Salmon (v1.10.1).
Peak calling and dsRNA reconstruction of endogenous RNAs were performed using biobit (https://github.com/biomancy/biobit, v0.0.4). Inferred dsRNA clusters were tested for induction and enrichment using DESeq2 (v1.46.0) and apeglm (v1.28.0).
Aberrant transcription was analyzed with DEXSeq (v1.52.0) by treating each mRNA with a matched aberrant transcription region, or each intron with its matched 5′ constitutive exon, as regions belonging to the same group in DEXSeq.
Enrichment of viral RNAs was visualized using pyCirclize (v1.7.1). ViennaRNA (v2.7.0) and Z-Hunt[rs] (https://github.com/biomancy/zhuntrs, v0.0.4) were used to predict putative Z-prone RNA stems within the minimum free energy structures of individual vRNAs.
All code used to analyze sequencing data in this study is publicly available at https://github.com/alnfedorov/Z-DoTT.
Assembly: CHM13v2, GCF_000865725.1, NC_001806.2
Supplementary files format and content: The counts.tsv.gz file includes five index columns followed by count columns, with column names corresponding to the library names provided in the submission. The index columns define the region being assessed: its unique ID, type, and localization (sequence ID, strand, and location). For split regions (e.g., exons), multiple coordinates are separated by semicolons. Each region represents either a normalization bin (used exclusively for library normalization) or a putative dsRNA cluster predicted from RIP data. This table can be used to identify dsRNA clusters that are strongly induced during infection and reproducibly enriched in RIP experiments from infected cells.

growth_protocol: HT-29 cells (American Type Culture Collection [ATCC], HTB-38) were maintained in DMEM supplemented with 10% fetal bovine serum, 1x GlutaMAX, and 1% penicillin/streptomycin. All cells were cultured at 37°C in 5% CO2, and routinely tested for mycoplasma.

extract_protocol:
RIP was conducted using the EZ-Magna RIP (Cross-Linked) RNA-Binding Protein Immunoprecipitation Kit (Millipore) following the manufacturer’s instructions. Briefly, cross-linked cell pellets were lysed in RIP lysis buffer, followed by incubation with RIP Buffer containing magnetic beads conjugated with anti-Z-NA antibody (clone Z22, Absolute Antibody) or anti-FLAG antibody (F1804, Sigma-Aldrich), at 4°C overnight. Samples were then incubated with proteinase K and immunoprecipitated RNAs were recovered by phenol:chloroform:isoamyl alcohol purification.  Ten percent of the cell lysate was used for total RNA extraction as the input, and the remaining ninety percent was used for immunoprecipitation.
Libraries were prepared from RIP or input RNA using the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Thermo Fisher Scientific) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired-end 150 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

treatment_protocol: HT-29 cells were stably reconstituted with FLAG-tagged human ZBP1 expression constructs using the Retro-X retroviral transduction system. Cells were infected (MOI=2) with or without HSV-1 (F strain[VR-733]) or IAV (A/Puerto Rico/8/1934) for 8h.

value: human colorectal adenocarcinoma

value: IAV infection

value: FLAG-input


title: HT-29, IAV, FLAG-input, 4 [B831009]

description: Library name: B831009+3162362


title: Cell_3072


title: HT-29, IAV, FLAG-input, 1 [B831009]

description: Library name: B831009+3162359


title: HT-29, IAV, FLAG-input, 2 [B831009]

description: Library name: B831009+3162360


title: Cell_3087


title: HT-29, IAV, Z22-input, 4 [B831009]

description: Library name: B831009+3162358


title: HT-29, IAV, Z22-input, 3 [B831009]

description: Library name: B831009+3162357


title: Cell_3070


title: Cell_3067


title: HT-29, IAV, Z22-input, 2 [B831009]

description: Library name: B831009+3162356


title: HT-29, IAV, Z22-input, 1 [B831009]

description: Library name: B831009+3162355


title: Cell_3068


title: HT-29, HSV-1, FLAG-input, 4 [B831009]

description: Library name: B831009+3162354

value: HSV-1 infection


title: Cell_3064


title: Cell_3080


title: HT-29, HSV-1, FLAG-input, 3 [B831009]

description: Library name: B831009+3162353


title: HT-29, HSV-1, FLAG-input, 2 [B831009]

description: Library name: B831009+3162352


title: adrd0915


title: Cell_3063


title: Cell_3062


title: Cell_3069


title: HT-29, HSV-1, FLAG-input, 1 [B831009]

description: Library name: B831009+3162351


title: Cell_3079


title: Cell_3055


title: HT-29, HSV-1, Z22-input, 4 [B831009]

description: Library name: B831009+3162350


title: Cell_3056


title: Cell_3071


title: Cell_3054


title: HT-29, HSV-1, Z22-input, 2 [B831009]

description: Library name: B831009+3162348


title: Cell_3066


title: Cell_3050


title: HT-29, mock, Z22-input, 4 [B831009]

description: Library name: B831009+3162346

value: Mock


title: HT-29, HSV-1, Z22-input, 1 [B831009]

description: Library name: B831009+3162347


title: Cell_3048


title: HT-29, HSV-1, Z22-input, 3 [B831009]

description: Library name: B831009+3162349


title: HT-29, mock, Z22-input, 3 [B831009]

description: Library name: B831009+3162345


title: Cell_3047


title: HT-29, mock, Z22-input, 2 [B831009]

description: Library name: B831009+3162344


title: Cell_3044


title: HT-29, mock, Z22-input, 1 [B831009]

description: Library name: B831009+3162343


title: Cell_3041


title: HT-29, IAV, FLAG, 4 [B831009]

description: Library name: B831009+3162342

value: FLAG


title: Cell_3046


title: Cell_3042


title: HT-29, IAV, FLAG, 1 [B831009]

description: Library name: B831009+3162339


title: HT-29, IAV, FLAG, 2 [B831009]

description: Library name: B831009+3162340


title: HT-29, IAV, FLAG, 3 [B831009]

description: Library name: B831009+3162341


title: Cell_3038


title: HT-29, IAV, Z22, 4 [B831009]

description: Library name: B831009+3162338


title: Cell_3032


title: HT-29, IAV, Z22, 3 [B831009]

description: Library name: B831009+3162337


title: Cell_3040


title: Cell_3036


title: HT-29, IAV, Z22, 2 [B831009]

description: Library name: B831009+3162336


title: Cell_3029


title: Cell_3028


title: HT-29, HSV-1, FLAG, 4 [B831009]

description: Library name: B831009+3162334


title: Cell_3021


title: Cell_3026


title: HT-29, HSV-1, FLAG, 3 [B831009]

description: Library name: B831009+3162333


title: HT-29, HSV-1, Z22, 3 [B831009]

description: Library name: B831009+3162329


title: HT-29, HSV-1, FLAG, 1 [B831009]

description: Library name: B831009+3162331


title: Cell_3027


title: Cell_3016


title: Cell_3020


title: Cell_3018


title: HT-29, IAV, Z22, 1 [B831009]

description: Library name: B831009+3162335


title: HT-29, HSV-1, Z22, 4 [B831009]

description: Library name: B831009+3162330


title: HT-29, HSV-1, FLAG, 2 [B831009]

description: Library name: B831009+3162332


title: Cell_3025


title: HT-29, HSV-1, Z22, 2 [B831009]

description: Library name: B831009+3162328


title: Cell_3014


title: HT-29, mock, Z22, 3 [B831009]

description: Library name: B831009+3162325


title: Cell_3012


title: HT-29, mock, Z22, 1 [B831009]

description: Library name: B831009+3162323


title: HT-29, mock, Z22, 4 [B831009]

description: Library name: B831009+3162326


title: Cell_3005


title: Cell_3011


title: Cell_3010


title: Cell_3013


title: Cell_3000


title: RRBS, SW1353, rep7

city: Shanghai

first: Yicen

last: Ding

address: 800 Dongchuan Road, Shanghai, China

institute: Shanghai Jiao Tong University

description: Library name: Sample 31

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor/low-quality sequence using trim-galore v0.6.10.
Trimmed sequence reads were mapped to hg38 using bismark v0.24.2.
Assembly: hg38
Supplementary files format and content: Text files include all samples for RRBS-seq.

growth_protocol: A549 and Jurkat cells were cultured with RPMI1640 medium, 10% fetal bovine serum (FBS), 1% penicillin and streptomycin. ARPE-19 cells were cultured using DMEM/F12 me-dium with 10% FBS and 1% penicillin and streptomycin. SW1353 cells were cultured with DMEM medium, 10% FBS, 1% penicillin and streptomycin.

extract_protocol:
Genomic DNA was extracted following the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) instructions from the cells.
DNA libraries for RRBS-seq were prepared using he NEB Next® Ultra™ II DNA Library Prep Kit (NEB, Ipswich, UK) following manufacturer's protocols.

value: chondrosarcoma cell


title: RRBS, SW1353, rep8

description: Library name: Sample 32


title: Cell_3007


title: RRBS, SW1353, rep6

description: Library name: Sample 30


title: Cell_2999


title: RRBS, SW1353, rep5

description: Library name: Sample 29


title: HT-29, HSV-1, Z22, 1 [B831009]

description: Library name: B831009+3162327


title: RRBS, SW1353, rep4

description: Library name: Sample 28


title: RRBS, SW1353, rep1

description: Library name: Sample 25


title: RRBS, SW1353, rep3

description: Library name: Sample 27


title: Cell_2992


title: Cell_2994


title: RRBS, Jurkat, rep8

description: Library name: Sample 24

source_name: Jurkat

value: Jurkat

value: T lymphoblast


title: Cell_2995


title: Cell_2993


title: RRBS, Jurkat, rep6

description: Library name: Sample 22


title: HT-29, mock, Z22, 2 [B831009]

description: Library name: B831009+3162324


title: Cell_2990


title: RRBS, Jurkat, rep7

description: Library name: Sample 23


title: RRBS, Jurkat, rep4

description: Library name: Sample 20


title: Cell_2986


title: RRBS, Jurkat, rep3

description: Library name: Sample 19


title: Cell_2985


title: RRBS, Jurkat, rep5

description: Library name: Sample 21


title: Cell_2982


title: Cell_2998


title: RRBS, SW1353, rep2

description: Library name: Sample 26


title: Cell_2997


title: RRBS, ARPE19, rep8

description: Library name: Sample 16

value: epithelial cell


title: Cell_2991


title: Cell_2981


title: Cell_2972


title: RRBS, ARPE19, rep7

description: Library name: Sample 15


title: RRBS, ARPE19, rep5

description: Library name: Sample 13


title: RRBS, ARPE19, rep6

description: Library name: Sample 14


title: Cell_2971


title: Cell_2970


title: Cell_2988


title: RRBS, ARPE19, rep2

description: Library name: Sample 10


title: RRBS, ARPE19, rep4

description: Library name: Sample 12


title: RRBS, ARPE19, rep1

description: Library name: Sample 9


title: RRBS, ARPE19, rep3

description: Library name: Sample 11


title: Cell_2964


title: Cell_2968


title: Cell_2969


title: RRBS, A549, rep8

description: Library name: Sample 8


title: Cell_2967


title: RRBS, Jurkat, rep1

description: Library name: Sample 17


title: Cell_2963


title: Cell_2984


title: RRBS, A549, rep7

description: Library name: Sample 7


title: RRBS, Jurkat, rep2

description: Library name: Sample 18


title: RRBS, A549, rep6

description: Library name: Sample 6


title: RRBS, A549, rep5

description: Library name: Sample 5


title: Cell_2962


title: RRBS, A549, rep4

description: Library name: Sample 4


title: Cell_2961


title: RRBS, A549, rep3

description: Library name: Sample 3


title: Cell_2956


title: RRBS, A549, rep2

description: Library name: Sample 2


title: RRBS, A549, rep1

description: Library name: Sample 1


title: Cell_2955


title: Cell_2954


title: RNA, SE1353, rep3

description: Library name: Sample 12

data_processing:
Sequence reads were trimmed for adaptor/low-quality sequence using trim-galore v0.6.10.
Trimmed sequence reads were mapped to hg38 using HISAT2 v2.2.1.
Read count extraction was performed using featureCounts v2.0.3 (GENCODE v35 annotation) for RNA-seq.
Assembly: hg38
Supplementary files format and content: Text files include raw counts for each RNA-seq Sample.

extract_protocol:
Total RNA was extracted using RNAiso Plus (Takara, Osaka, Japan) according to the protocol described by the manufacturer.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seq kit following manufacturer's protocols.


title: Cell_2953


title: RNA, SE1353, rep1

description: Library name: Sample 10


title: RNA, SE1353, rep2

description: Library name: Sample 11


title: Cell_2966


title: RNA, Jurkat, rep3

description: Library name: Sample 9


title: Cell_2949


title: RNA, Jurkat, rep1

description: Library name: Sample 7


title: Cell_2952


title: Cell_2944


title: Cell_2943


title: RNA, Jurkat, rep2

description: Library name: Sample 8


title: Cell_2948


title: Cell_2946


title: Cell_2950


title: RNA, ARPE19, rep3

description: Library name: Sample 6


title: RNA, ARPE19, rep2

description: Library name: Sample 5


title: Cell_2960


title: RNA, ARPE19, rep1

description: Library name: Sample 4


title: Cell_2941


title: RNA, A549, rep3

description: Library name: Sample 3


title: Cell_2940


title: RNA, A549, rep2

description: Library name: Sample 2


title: Cell_2938


title: RNA, A549, rep1

description: Library name: Sample 1


title: Cell_2937


title: Cell_2932


title: Cell_2931


title: XLAS moderate model, ASO treated, iPSC-derived, Day 38, Replicate 3

city: Paris

first: Hassan

last: Saei

address: 24 boulevard de Montparnasse

department: Imagine Institute of Genetic Diseases

country: France

institute: Universite Paris Cite

description: Library name: SAMPLE 15

data_processing:
Imagine Institutes in-house data processing protocol at bioinformatic platform - illumina Dragen IT for read aligmant and FeatureCounts for generating count matrix
Sequence reads were quality checked, trimed and aligned to the human genome GRCh38 using illumina Dragen IT pipeline
Read counts extraction was performed by FeatureCounts and normalization was perfomed by DESeq2 package in R
Assembly: GRCh38 (hg38)
Supplementary files format and content: Supplementary files format and content: Tab-delimited text file includes raw and normalized counts for each sample

source_name: iPSC-derived kidney Organoid

growth_protocol: Induced pluripotent stem cells were differentiated into kidney organoids using a modified version of the Morizane et al. protocol and cultured in Advanced RPMI 1640 medium in a humidified atmosphere with 5% CO₂ at 37°C

extract_protocol:
Total RNA was extracted using Rnasey mini plus Kit (Qiagen, 74136) from a pool of nine organoids, and 200ng of total RNA was used for library preparation.
RNA libraries for RNA-seq was prepared using TECAN Universal Plus mRNA-seq library preparation kit, Tecan

treatment_protocol: XLAS organoid models were treated with either a scrambled or functional ASO starting on day 14 of culture and continuing until day 38

value: iPSC-derived kidney Organoid

value: Male - Line 004.17

value: Induced pluripotent stem cells

value: ASO treated


title: Brain metastasis sample JMS2

city: Madison

first: Yixuan

last: Xie

state: Wisconsin

address: 320 East Wilson Street, 602

department: Department of Biostatistics and Medical Informatics

institute: University of Wisconsin - Madison

description:
Library name: JMS2_S157
Brain metastasis tissue from NSCLC patient; resected and sequenced using 10x Genomics Chromium

data_processing:
Raw FASTQ files were processed using the Cell Ranger pipeline (v7.1.0) with default parameters to generate gene-barcode matrices.
Assembly: GRCh38
Supplementary files format and content: RDS file containing the full Seurat object (`data_merge.RDS`), including raw and normalized counts, metadata

source_name: Brain metastasis

growth_protocol: Not applicable (patient-derived brain metastasis tissue).

extract_protocol:
Brain metastasis tissues were resected and dissociated using enzymatic and mechanical digestion to obtain single-cell suspensions following 10x Genomics guidelines.
Single-cell libraries were constructed using the 10x Genomics Chromium Single Cell 3â€² Reagent Kit v3 according to manufacturerâ€™s instructions.

treatment_protocol: Patients were enrolled in clinical trial NCT03398694. Resection performed for symptomatic brain metastases under institutional review board approval.

value: Brain metastasis

value: Tumor


title: Cell_2927


title: Cell_2930


title: Brain metastasis sample JMS1-R

description:
Library name: JMS1-R_S156
Brain metastasis tissue from NSCLC patient; resected and sequenced using 10x Genomics Chromium


title: XLAS moderate model, ASO treated, iPSC-derived, Day 38, Replicate 1

description: Library name: SAMPLE 13


title: XLAS moderate model, ASO treated, iPSC-derived, Day 38, Replicate 2

description: Library name: SAMPLE 14


title: Cell_2929


title: XLAS severe model, ASO treated, iPSC-derived, Day 38, Replicate 3

description: Library name: SAMPLE 12


title: Cell_2925


title: XLAS moderate model, iPSC-derived, Day 38, Replicate 3

description: Library name: SAMPLE 9

value: Scramble ASO treated


title: Cell_2922


title: Cell_2920


title: XLAS moderate model, iPSC-derived, Day 38, Replicate 2

description: Library name: SAMPLE 8


title: XLAS severe model, ASO treated, iPSC-derived, Day 38, Replicate 1

description: Library name: SAMPLE 10


title: XLAS severe model, ASO treated, iPSC-derived, Day 38, Replicate 2

description: Library name: SAMPLE 11


title: XLAS severe model, iPSC-derived, Day 38, Replicate 2

description: Library name: SAMPLE 5


title: XLAS severfe model, iPSC-derived, Day 38, Replicate 3

description: Library name: SAMPLE 6


title: Cell_2924


title: XLAS severe model, iPSC-derived, Day 38, Replicate 1

description: Library name: SAMPLE 4


title: XLAS moderate model, iPSC-derived, Day 38, Replicate 1

description: Library name: SAMPLE 7


title: Cell_2915


title: Cell_2912


title: Cell_2910


title: Cell_2911


title: Cell_2914


title: Isogenic control, iPSC-derived, Day 38, Replicate 3

description: Library name: SAMPLE 3

value: Healthy

value: Untreated


title: Cell_2905


title: Isogenic control, iPSC-derived, Day 38, Replicate 2

description: Library name: SAMPLE 2


title: Cell_2904


title: Isogenic control, iPSC-derived, Day 38, Replicate 1

description: Library name: SAMPLE 1


title: Cell_2903


title: control rep1

city: Baoding

first: Haisong

last: Zhang

address: 212 Yuhua East Road, Lianchi District

institute: Hebei University

description:
Library name: con1
con1

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Firstly, fastp software (v0.20.0) was used to trim adaptor and filter low-quality reads to get high-quality clean reads. Then, clean reads were aligned to the human miRNA databases miRbase v22.1 using Novoalign software (v3.09.04) with at most one mismatch. The mapped miRNA read counts were defined as the raw expression levels of that miRNA.
Assembly: miRBase v22.1
Supplementary files format and content: mature miRNA raw counts

source_name: exosome

extract_protocol:
Total RNA was extracted from samples with the Universal RNA Extraction CZ Kit (RNC643, ONREW)according to the manufacturer’s instructions.  RNA quantity was analysed using Qubit 4.0 (Invitrogen) and  quality  examined by electrophoresis on a denaturing agarose gel
After the RNA quality inspection, VAHTS® Small RNALibrary Prep Kit for Illumina (Vazyme)was used to prepare the miRNA library from samples. Libraries were sequenced in Illumina Novaseq 6000 platform.

value: exosome


title: control rep2

description:
Library name: con2
con2


title: case rep3

description:
Library name: case3
case3


title: Cell_2902


title: Cell_2897


title: Cell_2895


title: case rep2

description:
Library name: case2
case2


title: Cell_2892


title: Cell_2891


title: Cell_2888


title: case rep1

description:
Library name: case1
case1


title: Cell_2887


title: Cell_2890


title: Cell_2889


title: human myotubes, siControl, Hours72, static

first: Catherine

last: Coirault

address: 47 bd de l'Hôpital

institute: Inserm

description:
Library name: ctrl1
run1

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on hg38 reference genome and quantification with gencode v37 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: Format TSV: gene and transcript counts in each sample

source_name: myotubes

growth_protocol: Human immortalized muscle cell precursors, clone 8220, were cultured with 5% CO2 at 37°C in growth medium consisting of 1 vol 199 Medium/4 vol DMEM (Life Technologies, Carlsbad, CA, USA) supplemented with 20% fetal calf serum (Life technologies, Carlsbad, CA, USA), 5 ng/mL hEGF (Life Technologies, Carlsbad, CA, USA), 0.5 ng/mL βFGF, 0.1 mg/mL dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 50 μg/mL fetuin (Life Technologies, Carlsbad,CA, USA), 5 μg/mL insulin (Life Technologies, Carlsbad, CA, USA), and 50 mg/mL Gentamycin (Gibco™, Life Technologies, Carlsbad, CA, USA).

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 for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Differentiation into myotubes was induced by switching confluent myoblasts to differentiation medium containing DMEM (Gibco) and 50 mg/mL gentamycin. Gentamycin was removed when siRNA treatment is applied. The siRNA transfections were done with Lipofectamine RNAiMAX (Life Technologies, Carlsbad, CA, 13778-150) according to manufacturer’s instructions 24h and 48h after switching confluent myoblasts to differentiation medium using 50 nM of siRNA. Gene or protein of interest was analyzed 72 h after the first transfection

tag: clone

value: myotubes

value: WT

value: myogenic differentiation

tag: time

value: Day 3


title: Cell_2886

tag: tissue


title: iPSC-derived HBVO;HS bio-hybrid matrix rep3

city: Chongqing

first: Yue

last: Sun

address: gaotanyan street

department: Department of Anatomy

institute: Third Military Medical  University

description:
Library name: Sample6
10xGenomics

data_processing:
Quality control
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.7.5a
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Assembly: GRCh38 (hg38)
Supplementary files format and content: expression matrix file using RNA raw count

source_name: HiPSC

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

treatment_protocol: the specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times and minced into 1–2 mm pieces. The tissue pieces were digested in 2ml GEXSCOPETM Tissue Dissociation

value: HiPSC

value: pluripotent stem cells

value: HS


title: Cell_2882


title: iPSC-derived HBVO;HS bio-hybrid matrix rep2

description:
Library name: Sample5
10xGenomics


title: 10x 3' cell surface protein library (blood, bone marrrow, and spleen from MaGIC mice)

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street

institute: Yale University

description: Library name: neutrophils_CSPL

data_processing:
Raw sequencing data were processed using Cell Ranger (v7.1.0) and aligned to the GRCh38-2020-A reference genome. The filtered feature-barcode matrix output from Cell Ranger was used for downstream analysis in R (v4.2.3) with the Seurat package (v5.0.1). The analysis pipeline included normalization, data scaling using ScaleData, and principal component analysis
Cells were demultiplexed based on the hashing antibody barcodes. Cells with TotalSeqB0251 and TotalSeqB0252 barcodes were assigned as blood and spleen cells respectively and unassigned cells were labeled as bone marrow cells.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files: barcodes, matrices, and features, assignment_confidence_table.csv
Supplementary files format and content: only_neutrophils.rds (subset of neutrophils from this used in the paper)

molecule: protein

source_name: blood, bone marrow, spleen

extract_protocol:
Sorted cells based on expression of human CD45 and human CD66b from blood and spleen of MaGIC humanized mice were incubated with barcoded hashing antibodies (TotalSeqB0251, TotalSeqB0252; BioLegend) and pooled with cells from bone marrow to a final concentration of 1,500 cells/µL and loaded onto the 10x Chromium Controller using the Chromium Next GEM technology.
Library preparation was performed in-house using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics), including cell surface feature barcoding. Sequencing was conducted on the NovaSeq 6000 system (Illumina).

value: blood, bone marrow, spleen

value: neutrophils/immune cells

value: control

tag: library type

value: ADT


title: control rep3

description:
Library name: con3
con3


title: 10x 3' GEX (blood, bone marrrow, and spleen from MaGIC mice)

description: Library name: neutrophils_mRNA

tag: treatment

value: mRNA


title: iPSC-derived HBVO;matrigel rep2

description:
Library name: Sample2
10xGenomics

tag: cell line

value: matrigel


title: iPSC-derived HBVO;matrigel rep3

description:
Library name: Sample3
10xGenomics

tag: cell type


title: Cell_2877


title: iPSC-derived HBVO;matrigel rep1

description:
Library name: Sample1
10xGenomics


title: iPSC-derived HBVO;HS bio-hybrid matrix  rep1

description:
Library name: Sample4
10xGenomics


title: Cell_2893


title: Cell_2876


title: TC32_3days_DMSO_rep3

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

institute: Seattle Children's Research Institute

description: Library name: Sample30

data_processing:
Raw sequencing reads were checked for quality using FastQC.
Adapter sequences were trimmed from the raw sequencing reads using Trim Galore
The raw sequencing reads were aligned to the GRCh38 assembly using gencode v39 and STAR.
RSeQC was used to check for the quality of the alignments.
Differential expression analysis for RNAseq data was performed using R.Bioconductor package DESeq2.
Assembly: hg38
Supplementary files format and content: tab delimited file including raw counts for each sample

source_name: cell line

growth_protocol: A673 and TC32 cell lines were grown in RPMI1640 +10% FBS +2mM L-glutamine. CHLA10 cell lines were gorwn in IMDM + 20% FBS _ 2mM L-glutamine + 1X ITS-X

extract_protocol:
RNA extraction using RNeasy Mini Kit (Qiagen)
mRNA library (polyA enrichment) was performed by Novogene per standard protocols and sequenced on an Illumina NovaSeq 6000 (paired end 150bp reads)

treatment_protocol: 2 million cells were plated on day 1 and exposed to DMSO or 5nM BMS-986158. After 72hrs cells were collected for total RNA extraction. Persister cells (exposure for 20 days) were generated as per methods section, and exposed to 5nM BMS-986158 continuously for 20 days. Cells were split when they reached confluency. Media + 5nM BMS-986158 was changed every 72hrs when cells were static.

value: cell line

value: Ewing sarcoma

tag: genotype

value: Vehicle


title: Cell_2874


title: TC32_3days_DMSO_rep1

description: Library name: Sample28

tag: batch


title: Cell_2871


title: TC32_3days_DMSO_rep2

description: Library name: Sample29


title: Cell_2868


title: TC32_3days_BETi_rep3

description: Library name: Sample27


title: TC32_3days_BETi_rep2

description: Library name: Sample26


title: Cell_2857


title: Cell_2854


title: Cell_2859


title: Cell_2856


title: A673_20days_DMSO_rep3

description: Library name: Sample24


title: Cell_2879


title: TC32_3days_BETi_rep1

description: Library name: Sample25


title: A673_20days_DMSO_rep1

description: Library name: Sample22


title: A673_20days_BETi_rep3

description: Library name: Sample21


title: Cell_2853


title: Cell_2851


title: Cell_2852


title: A673_20days_BETi_rep2

description: Library name: Sample20


title: Cell_2850


title: Cell_2845


title: Cell_2849


title: Cell_2843


title: A673_3days_DMSO_rep1

description: Library name: Sample16


title: Cell_2867


title: A673_3days_BETi_rep2

description: Library name: Sample14


title: A673_3days_BETi_rep3

description: Library name: Sample15


title: Cell_2841


title: A673_3days_BETi_rep1

description: Library name: Sample13


title: A673_20days_DMSO_rep2

description: Library name: Sample23


title: Cell_2840


title: Cell_2836


title: Cell_2838


title: CHLA10_20days_DMSO_rep1

description: Library name: Sample10


title: CHLA10_20days_BETi_rep3

description: Library name: Sample9


title: CHLA10_20days_DMSO_rep2

description: Library name: Sample11


title: CHLA10_20days_BETi_rep2

description: Library name: Sample8


title: Cell_2831


title: Cell_2837


title: A673_20days_BETi_rep1

description: Library name: Sample19


title: A673_3days_DMSO_rep3

description: Library name: Sample18


title: A673_3days_DMSO_rep2

description: Library name: Sample17


title: CHLA10_20days_BETi_rep1

description: Library name: Sample7


title: Cell_2830


title: CHLA10_3days_DMSO_rep2

description: Library name: Sample5


title: CHLA10_3days_DMSO_rep3

description: Library name: Sample6


title: Cell_2828


title: Cell_2827


title: Cell_2839


title: CHLA10_3days_BETi_rep1

description: Library name: Sample1


title: CHLA10_3days_BETi_rep2

description: Library name: Sample2


title: CHLA10_20days_DMSO_rep3

description: Library name: Sample12


title: Cell_2824


title: CHLA10_3days_BETi_rep3

description: Library name: Sample3


title: CHLA10_3days_DMSO_rep1

description: Library name: Sample4


title: Cell_2822


title: OS-RC-2, PT, Rep2

city: Boston

first: Qinqin

last: Jiang

state: Ma

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: OS-RC-2_PT_biol_rep_2

data_processing:
Fastq files were generated using Illumina Bcl2fastq v2.18, reads were then aligned to the UCSC hg38 reference genome assembly and gene counts were quantified using STAR (v2.7.3a) and Salmon. Differential gene expression testing was performed by DESeq2 (v1.22.1). RNAseq analysis was performed using the VIPER snakemake pipeline.
Assembly: hg38
Supplementary files format and content: An excel file, which contains the differential fold change and significance for all genes under all conditions
Library strategy: Polysome-seq

growth_protocol: OS-RC-2 cells were obtained from RIKEN Bioresource Research Center Cell Bank and were cultured in RPMI-1640 (Gibco 11875119) supplemented with 10% FBS (GeminiBio 100-106) and 1% penicillin-streptomycin (Gibco 15140122)

extract_protocol:
1×107-2×107 adherent cells were washed once with ice-cold PBS and subsequently lysed/scraped directly from the plates on ice using a polysome extraction buffer [(25 mM HEPES pH 7.5, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 1% Triton X-100, 0.1 mg/ml cycloheximide, 0.05 U/l RNase inhibitor (Invitrogen AM2696), and 1× Roche-complete EDTA-free protease inhibitor cocktail (Roche 4693132001)]. The lysates were homogenized with 5-6 strokes in a glass Dounce homogenizer on ice, then cleared at 10,000xg for 5 min at 4°C. Cleared lysates were loaded on top of 10-50% linear sucrose gradients (mixed using a BioComp gradient mixer gradients containing 25 mM HEPES pH 7.5, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 0.1 mg/ml cycloheximide, and 1× Roche-complete EDTA-free protease inhibitor cocktail) and centrifuged in a Beckman Coulter ultracentrifuge at 40,000 rpm for 3 h at 4°C in a SW41Ti rotor. After centrifugation, gradients were fractionated and analyzed using a BioComp fractionator monitoring absorbance at 260 nm. Polysome profiles were manually inspected to determine fractions containing polysomes, and these fractions were pooled for RNA purification (polysome-containing fractions were identified as all fractions heavier than the monosome peak which was excluded). RNA was purified from pooled polysome sucrose gradient fractions using Trizol LS (Invitrogen 10296028) followed by sequential isopropanol and ethanol precipitations. RNA quality was analyzed using an Agilent RNA TapeStation (RIN values all > 9).
Libraries were prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara 634873). The sequencing libraries were quantified using Qubit HS DNA assays and an Agilent High Sensitivity TapeStation. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: OS-RC-2 cells were treated with either 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours and were harvested at the end of 72 hours.

value: ccRCC

value: Treated with PT2399 (2 mM) for 72 hours


title: Cell_2823


title: OS-RC-2, PT, Rep1

description: Library name: OS-RC-2_PT_biol_rep_1


title: Cell_2825


title: Cell_2821


title: Cell_2818


title: Cell_2820


title: Cell_2812


title: OS-RC-2, Veh, Rep2

description: Library name: OS-RC-2_Veh_biol_rep_2

value: Treated with vehicle (Veh) for 72 hours


title: OS-RC-2, Veh, Rep3

description: Library name: OS-RC-2_Veh_biol_rep_3


title: Cell_2829


title: OS-RC-2, PT, Rep3

description: Library name: OS-RC-2_PT_biol_rep_3


title: OS-RC-2, Veh, Rep1

description: Library name: OS-RC-2_Veh_biol_rep_1


title: Cell_2810


title: OS-RC-2, sgHIF2a, Rep2

description:
Library name: OS-RC-2_sgHIF2a_biol_rep_2
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx

data_processing:
Fastq files were generated using Illumina Bcl2fastq v2.18, reads were then aligned to the UCSC hg38 reference genome assembly and gene counts were quantified using STAR (v2.7.3a) and Salmon. Differential gene expression testing was performed by DESeq2 (v1.22.1). RNAseq analysis was performed using the VIPER snakemake pipeline.
Assembly: hg38
Supplementary files format and content: An excel file, which contains the differential fold change and significance for all genes under all conditions

extract_protocol:
OS-RC-2 cells were homogenized with QIAshredder columns (Qiagen 79654), and total RNA was extracted from homogenized cell lysates using the RNeasy Mini Kit (Qiagen 74106) according to manufacturer’s protocol. The RNA was quantified on a NanoDrop spectrophotometer (Thermo Scientific ND-8000-GL).
Ribosomal RNA (rRNA)-depleted libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche) from 100 ng of total RNA according to manufacturer’s protocol. Briefly, mRNA or non-coding RNA were enriched and then purified using KAPA pure beads and fragmented at 94°C for 8 min. 1st strand and 2nd strand were subsequently synthesized. cDNA fragments were end-repaired and adenylated at the 3′ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment with 14 cycles of PCR post-adapter ligation on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: OS-RC-2 cells were treated with either 2 uM PT2399 (PT) or vehicle (Veh) for 72 hours and were harvested at the end of 72 hours. OS-RC-2 cells that were edited with a HIF2a sgRNA or a contrl sgRNA (sgCtrl) were also collected.

value: Infected with a HIF2a giude RNA (sgHIF2a)


title: Cell_2808

extract_protocol:
Single cells were FACS sorted into 384-well plates containing lysis buffer and snap frozen. Libraries were prepared using a modified version of the Smart-Seq2 protocol.
cDNA was prepared using a Mantis platform (Formulatrix) and quantified with quantIT picogreen reagent (Thermo Fisher). Dual indexed sequencing libraries were prepared from 0.1ng cDNA using an Echo525 automation system (Labcyte) in miniaturized reaction volumes. The library pool was quantified by qPCR using a Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems)


title: OS-RC-2, sgHIF2a, Rep3

description:
Library name: OS-RC-2_sgHIF2a_biol_rep_3
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: Cell_2809


title: Cell_2807


title: Cell_2806


title: Cell_2826


title: OS-RC-2, sgCtrl, Rep2

description:
Library name: OS-RC-2_sgCtrl_biol_rep_2
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx

value: Infected with a ctrl giude RNA (sgCtrl)


title: OS-RC-2, sgCtrl, Rep1

description:
Library name: OS-RC-2_sgCtrl_biol_rep_1
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: OS-RC-2, sgHIF2a, Rep1

description:
Library name: OS-RC-2_sgHIF2a_biol_rep_1
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: Cell_2802

description: SmartSeq2_Gene_log_normalized_counts.rds


title: OS-RC-2, sgCtrl, Rep3

description:
Library name: OS-RC-2_sgCtrl_biol_rep_3
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: OS-RC-2, PT2399 72 h, Rep3

description:
Library name: OS-RC-2_PT_biol_rep_3
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: Cell_2799

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_2795


title: OS-RC-2, PT2399 72 h, Rep1

description:
Library name: OS-RC-2_PT_biol_rep_1
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: Cell_2793


title: OS-RC-2, Veh 72 h, Rep2

description:
Library name: OS-RC-2_Veh_biol_rep_2
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: OS-RC-2, Veh 72 h, Rep3

description:
Library name: OS-RC-2_Veh_biol_rep_3
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: Cell_2792


title: OS-RC-2, Veh 72 h, Rep1

description:
Library name: OS-RC-2_Veh_biol_rep_1
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: Cell_2791


title: myotubes, siControl, Hours72, stretch,rep 4

description:
Library name: Sctrl6
run1

extract_protocol:
The siRNA transfections were done with Lipofectamine RNAiMAX (Life Technologies, Carlsbad, CA, 13778-150) according to manufacturer’s instructions 24h and 48h after switching confluent myoblasts to differentiation medium using 50 nM of siRNA. Gene or protein of interest was analyzed 72 h after the first transfection
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 for RNA-seq were prepared using mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Differentiation into myotubes was induced by switching confluent myoblasts to differentiation medium containing DMEM (Gibco) and 50 mg/mL gentamycin. Gentamycin was removed when siRNA treatment is applied.

value: myotubes

value: WT

value: myogenic differentiation

value: Day 3


title: myotubes, siControl, Hours72, stretch,rep 3

description:
Library name: Sctrl5
run1


title: Cell_2805


title: Cell_2788


title: myotubes, siControl, Hours72, stretch,rep2

description:
Library name: Sctrl4
run1


title: Cell_2785


title: Cell_2790


title: myotubes, siLaminsA/C, Hours72, static, rep3

description:
Library name: si-3
run1

value: lamin A/C knockdown


title: myotubes, siControl, Hours72, stretch, rep1

description:
Library name: Sctrl3
run1


title: myotubes, siLaminsA/C, Hours72, static, rep2

description:
Library name: si-2
run1


title: OS-RC-2, PT2399 72 h, Rep2

description:
Library name: OS-RC-2_PT_biol_rep_2
HIF-responsive genes based on OS-RC-2 RNA-Seq (QJ10650).xlsx


title: myotubes, siControl, Hours72, static, rep2

description:
Library name: ctrl3
run1


title: Cell_2779


title: Cell_2796


title: Cell_2773


title: Cell_2771


title: Cell_2778


title: Cell_2770


title: Cell_2777


title: Cell_2787


title: human myotubes, siLaminsA/C, Hours72, stretch, rep1

description: Library name: Stretch-siLMNA-3

data_processing:
Quality of raw data was evaluated with FastQC. Poor quality sequences (minimum length: 50bp) and adapters were trimmed or removed with trimmomatic.
Paired-end reads were mapped to the human reference genome (build hg38) with Bowtie2. Reaps mapping to mitochondrial DNA were excluded from the analysis. Duplicates and reads in Encode blacklist regions were discarded with the Picard tools.
Peaks were called using the MACS2, with the significance cut-off q-value <=0.05. Peaks annotations were obtained from the HOMER hg38 database.
Concensus peakset was generated according peaks reproductibility within replicates by conditions.
Peak count matrix was generated using FeatureCounts and the consensus peakset gtf
Assembly: hg38
Supplementary files format and content: narrowPeak
Supplementary files format and content: Format CSV: gene and transcript counts in each sample (Peak count matrix)

extract_protocol:
The siRNA transfections were done with Lipofectamine RNAiMAX (Life Technologies, Carlsbad, CA, 13778-150) according to manufacturer’s instructions 24h and 48h after switching confluent myoblasts to differentiation medium using 50 nM of siRNA. Gene or protein of interest was analyzed 72 h after the first transfection
The ATACseq experience was made using the ATACseq kit of Active Motif (Waterloo, Belgium) according to manufacturer instructions.

tag: group

value: stretch


title: myotubes, siLaminsA/C, Hours72, static, rep1

description:
Library name: si-1
run1


title: Cell_2767

data_processing:
Raw fastq files were obtained by bcltoFastq conversion (version 2.20.0.422)
Fastq files were aligned to the mm10 reference genome using STAR aligner (version 2.7.9a) with the argument ‘STARsolo’. This argument allowed simultaneous mapping of reads and quantification of gene expression. The reference genome and gene transfer format (GTF) file were downloaded from 10x genomic webpage at (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz).
The output of ‘STARsolo’ was loaded into R (version 4.1.0) using the Bioconducter package DropletUtils (version 1.12.1).
Downstream analyses were done in R using SingleCellExperiment (version 5271.14.1) and Seurat (version 4.0.6).
Cells with <2000 detected genes, >15% mitochondrial content and > 10% hemoglobin percentage were excluded.
For isoform analysis, fastq files of selected 432 cells (46 cells from HE-HSC (AGM), 198 from HE-LMP (YSm), and 188 cells from HE-EMP (YSb)) were aligned and quantifed using Salmon 1.4.0  in Mapping mode. GRCm39 M32 mouse reference genome, transcriptome, and GTF file were downloaded from GENCODE website. Resulting quant.sf files were fed into IsoformSwitchAnalyzer  2.01.07 where importIsoformExpression function was used to give TMM normalized abundance values.
Assembly: GRCm39 M32 Gencode reference for Isoform Analysis and mm10 10X genomics reference for gene level analysis
Supplementary files format and content: RDS file having log normalized counts for each sample-gene level analyses (1494 cells)
Supplementary files format and content: RDS file having TMM normalized abundance for each sample used for isoform analyses (432 cells)


title: myotubes, siControl, Hours72, static, rep1

description:
Library name: ctrl2
run1


title: Cell_2774


title: human myotubes, siLaminsA/C, Hours72, static, rep3

description: Library name: siLMNA5

value: static


title: human myotubes, siLaminsA/C, Hours72, stretch, rep3

description: Library name: Stretch-siLMNA-5


title: human myotubes, siLaminsA/C, Hours72, stretch, rep2

description: Library name: Stretch-siLMNA-4


title: Cell_2772


title: human myotubes, siControl, Hours72, stretch, rep3

description: Library name: Stretch-Control-4


title: human myotubes, siControl, Hours72, static, rep3

description: Library name: Control-4


title: Cell_2769


title: human myotubes, siControl, Hours72, stretch, rep4

description: Library name: Stretch-Control-5


title: Cell_2775


title: human myotubes, siLaminsA/C, Hours72, static, rep4

description: Library name: siLMNA6


title: human myotubes, siControl, Hours72, stretch, rep2

description: Library name: Stretch-Control-2


title: Cell_2755


title: human myotubes, siControl, Hours72, static, rep2

description: Library name: Control-3


title: human myotubes, siControl, Hours72, stretch, rep1

description: Library name: Stretch-Control-1


title: Cell_2761


title: Cell_2753


title: Cell_2760


title: inactive UC, colonoids, iUC16

city: Palo Alto

first: Michael

middle: J.

last: Rosen

state: CA

address: 1701 Page Mill Rd, #262

institute: Stanford University

data_processing:
nf-core/rnaseq (v3.5)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: Colon

growth_protocol: Organoids grown in growth factor-reduced Matrigel and cultured in Intesticult Organoid Growth Medium (STEMCELL Technologies) at 37C, 5% CO2

extract_protocol:
Matrigel was removed and Total RNA was extracted using the RNeasy Micro Kit (Qiagen)
poly A enrichment

treatment_protocol: Organoids were washed in PBS and differentiated in Intesticult Organoid Differentiation Medium (STEMCELL Technologies) for 3 days at 37C, 5% CO2

value: Colon

tag: diagnosis

value: Inactive UC

value: Male

tag: endoscopy mayo_score

tag: medication

value: Oral 5-ASA

value: patient-derived epithelial organoids

value: colonoids

tag: organoid state

value: differentiated, Day 3


title: human myotubes, siLaminsA/C, Hours72, static, rep2

description: Library name: siLMNA4


title: Cell_2759

tag: sequencing run


title: human myotubes, siLaminsA/C, Hours72, static, rep1

description: Library name: siLMNA2


title: Cell_2758


title: Cell_2754


title: Cell_2752


title: human myotubes, siControl, Hours72, static, rep1

description: Library name: Control-2


title: inactive UC, colonoids, iUC15

tag: gender


title: inactive UC, colonoids, iUC6

tag: age


title: Cell_2751


title: inactive UC, colonoids, iUC14


title: Cell_2750


title: Cell_2745


title: inactive UC, colonoids, iUC13


title: inactive UC, colonoids, iUC8

value: Female

value: Anti-TNF biologic


title: active UC, colonoids, aUC9

value: Active UC

value: Oral 5-ASA, Infliximab


title: Cell_2744


title: Cell_2735


title: inactive UC, colonoids, iUC7

value: Oral 5-ASA, Anti-TNF biologic


title: Cell_2743


title: active UC, colonoids, aUC4


title: Cell_2742


title: Cell_2762


title: Cell_2740


title: active UC, colonoids, aUC3


title: active UC, colonoids, aUC12

value: Oral 5-ASA, Oral Steroids


title: Cell_2741


title: Cell_2732


title: Cell_2739


title: active UC, colonoids, aUC10

value: Rectal Steroids, Vedolizumab


title: active UC, colonoids, aUC11


title: non-IBD control, colonoids, C11

value: non-IBD control


title: Cell_2737


title: Cell_2734


title: Cell_2726


title: non-IBD control, colonoids, C10


title: active UC, colonoids, aUC2

value: Oral 5-ASA, Oral Steroids, Rectal Steroids


title: Cell_2723


title: non-IBD control, colonoids, C9


title: Cell_2725


title: Cell_2721


title: inactive UC, colonoids, iUC5


title: Cell_2716


title: non-IBD control, colonoids, C4


title: Cell_2718


title: non-IBD control, colonoids, C2


title: inactive UC, spheroids, iUC15

value: spheroids

value: undifferentiated


title: inactive UC, spheroids, iUC13

value: Colon

value: Inactive UC


title: Cell_2709


title: Cell_2715


title: Cell_2707


title: non-IBD control, colonoids, C1


title: Cell_2705


title: Cell_2708


title: inactive UC, spheroids, iUC14

value: Male

value: Oral 5-ASA


title: inactive UC, spheroids, iUC8

value: patient-derived epithelial organoids


title: active UC, colonoids, aUC1

value: colonoids

value: differentiated, Day 3


title: non-IBD control, colonoids, C12

value: Female

value: Oral Steroids


title: Cell_2722


title: Cell_2703


title: active UC, spheroids, aUC12

value: Active UC


title: Cell_2704


title: Cell_2699


title: Cell_2712


title: inactive UC, spheroids, iUC6


title: inactive UC, spheroids, iUC16


title: Cell_2701


title: non-IBD control, colonoids, C3


title: Cell_2719


title: active UC, spheroids, aUC9

value: Oral 5-ASA, Infliximab


title: active UC, spheroids, aUC10


title: Cell_2700


title: active UC, spheroids, aUC11


title: Cell_2697


title: active UC, spheroids, aUC3


title: Cell_2690


title: active UC, spheroids, aUC4


title: active UC, spheroids, aUC2


title: inactive UC, spheroids, iUC7

value: Oral 5-ASA, Anti-TNF biologic


title: non-IBD control, spheroids, C12


title: active UC, spheroids, aUC1

value: Oral 5-ASA, Oral Steroids


title: Cell_2688


title: non-IBD control, spheroids, C11

value: non-IBD control


title: Cell_2691


title: Cell_2686


title: Cell_2687


title: inactive UC, spheroids, iUC5


title: Cell_2684


title: Cell_2683


title: Cell_2698


title: Cell_2685


title: Cell_2692


title: Cell_2680


title: non-IBD control, spheroids, C3


title: Cell_2670


title: Cell_2681


title: non-IBD control, spheroids, C4


title: non-IBD control, spheroids, C9


title: Treg HD - 6

city: Daejeon

first: So-Young

last: Kim

state: Daejeon

address: GSMSE, 291, Daehak-ro, Yuseong-gu, Daejeon, Rep, E18-1

country: South Korea

institute: KAIST

description:
Healthy donor
HD_6

data_processing:
Reads were aligned and mapped to the human genomic DNA reference (GRch38/hg38) using STAR
RSEM was used to quantify the aligned reads (47). The DESeq2 R package was used for downstream analysis
Assembly: hg38
Supplementary files format and content: Count matrix

source_name: Peripheral blood

extract_protocol:
Cells were lysed after centrifugation (13200 rpm, 15min RT)
Libraries were prepared from the sorted TREG cells using the SMART-seq v4 Ultra Low Input RNA Kit (Takara/Clontech Bui, Shiga, Japan), following the manufacturer’s instructions.

treatment_protocol: Thawed PBMCs were isolated from the gate of viable CD4+CD25+CD127− T cells using a FACS Aria II cell sorter (BD Biosciences).

value: Peripheral blood


title: non-IBD control, spheroids, C2

value: spheroids


title: Cell_2679


title: Treg HD - 5

description:
Healthy donor
HD_5


title: non-IBD control, spheroids, C1

value: undifferentiated


title: Treg HD - 4

description:
Healthy donor
HD_4


title: Cell_2666


title: non-IBD control, spheroids, C10

value: Colon


title: Cell_2665


title: Cell_2668


title: Cell_2667


title: Cell_2657


title: Treg HD - 1

description:
Healthy donor
HD_1


title: Cell_2663


title: Cell_2662


title: Treg HCV LTFU - 6

description:
HCV patients long term follow up after SVR12
HCV_P6_FU


title: Treg HCV LTFU - 5

description:
HCV patients long term follow up after SVR12
HCV_P5_FU


title: Cell_2655


title: Treg HD - 3

description:
Healthy donor
HD_3


title: Treg HCV Pre - 4

description:
HCV patients before at SVR12
HCV_P4_Pre


title: Treg HD - 2

description:
Healthy donor
HD_2


title: Treg HCV LTFU - 4

description:
HCV patients long term follow up after SVR12
HCV_P4_FU


title: Cell_2654


title: Cell_2652


title: Cell_2651


title: Treg HCV SVR12 - 4

description:
HCV patients long term follow up after SVR12
HCV_P4_SVR12


title: Cell_2649


title: Treg HCV Pre - 3

description:
HCV patients before at SVR12
HCV_P3_Pre


title: Cell_2673


title: Treg HCV LTFU - 2

description:
HCV patients before at SVR12
HCV_P2_FU


title: Treg HCV SVR12 - 3

description:
HCV patients before at SVR12
HCV_P3_SVR12


title: Treg HCV LTFU - 3

description:
HCV patients before at SVR12
HCV_P3_FU


title: Cell_2647


title: Cell_2645


title: Treg HCV SVR12 - 2

description:
HCV patients before DAA treatment
HCV_P2_SVR12


title: Cell_2644


title: Cell_2637


title: Treg HCV Pre - 2

description:
HCV patients before DAA treatment
HCV_P2_Pre


title: Treg HCV Pre - 1

description:
HCV patients before DAA treatment
HCV_P1_Pre


title: Cell_2638

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Treg HCV SVR12 - 1

description:
HCV patients before DAA treatment
HCV_P1_SVR12


title: MEP diploid ALD6 deletion, 48h, rep 3

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: ALD6-3-48H

data_processing:
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.48.1
Assembly: R64-1-1
Supplementary files format and content: Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: All cells were grown in YPD media (2% peptone, 1% yeast extract, 2% glucose) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPD and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPD then inoculated in 125 ml YPD at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 hours. An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.

extract_protocol:
Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit. 150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

value: whole organism

value: ALD6 KO


title: MEP diploid ALD6 deletion, 48h, rep 2

description: Library name: ALD6-2-48H


title: MEP diploid wild type, 48h, rep 6

description: Library name: WT-6-48H

value: wild type


title: Cell_2629


title: Cell_2636


title: Cell_2633


title: Cell_2628


title: Treg HCV LTFU - 1

description:
HCV patients before DAA treatment
HCV_P1_FU


title: Cell_2631


title: MEP diploid ALD6 deletion, 48h, rep 1

description: Library name: ALD6-1-48H


title: Cell_2635


title: Cell_2627


title: Cell_2620


title: MEP diploid ALD6 deletion, log, rep 1

description: Library name: ALD6-1-LOG

value: log


title: MEP diploid wild type, 48h, rep 4

description: Library name: WT-4-48H


title: Cell_2622


title: Cell_2619


title: MEP diploid ALD6 deletion, log, rep 3

description: Library name: ALD6-3-LOG


title: MEP diploid wild type, log, rep 6

description: Library name: WT-6-LOG


title: Cell_2618


title: Cell_2617


title: MEP diploid ALD6 deletion, log, rep 2

description: Library name: ALD6-2-LOG


title: MEP diploid wild type, log, rep 5

description: Library name: WT-5-LOG


title: Microbiota from stool CER_39 T1

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

description:
Library name: BC72
87s rRNA v3-v4 sequencing of human stool

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
qiime demux summarize  --i-data trim-seqs.qza --o-visualization quality.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trim-seqs.qza --p-trunc-len-f 253 --p-trunc-len-r 219 --o-table Featuredada.qza --o-representative-sequences data-trunc.qza --o-denoising-stats denoising-stats.qza
bowtie2 -x INDEXED_GRCh38_analysis_set_BOWTIE2/GRCh38_noalt_as  -U dna-sequences.fasta --un filtered.fasta
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software for further analysis
Supplementary files format and content: filtered.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: otu_table.csv: CSV text file containing the abundance table
Supplementary files format and content: taxonomy.csv: TSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16S rRNA-seq

source_name: Stool

extract_protocol:
Total DNA was extracted from stools, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene were sequenced in paired-end mode (2 × 300 cycles) on the AVITI™ System.
For detailed library preparation please contact IGA Technology Services (Udine, Italy)

value: Stool


title: Cell_2614

first: Georges

last: Lacaud

address: Wilmslow Raod

institute: Cancer Research UK Manchester Institute


title: Cell_2613


title: Cell_2616


title: MEP diploid wild type, log, rep 4

description: Library name: WT-4-LOG


title: MEP diploid wild type, 48h, rep 5

description: Library name: WT-5-48H


title: Microbiota from stool CER_36 T1

description:
Library name: BC69
84s rRNA v3-v4 sequencing of human stool


title: Cell_2610


title: Cell_2615


title: Microbiota from stool CER_33 T1

description:
Library name: BC66
81s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_37 T1

description:
Library name: BC70
85s rRNA v3-v4 sequencing of human stool


title: Cell_2609


title: Cell_2603


title: Microbiota from stool CER_35 T1

description:
Library name: BC68
83s rRNA v3-v4 sequencing of human stool


title: Cell_2602

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds


title: Cell_2612


title: Microbiota from stool CER_32 T1

description:
Library name: BC65
80s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_30 T1

description:
Library name: BC63
78s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_31 T1

description:
Library name: BC64
79s rRNA v3-v4 sequencing of human stool


title: Cell_2599


title: Cell_2596


title: Microbiota from stool CER_38 T1

description:
Library name: BC71
86s rRNA v3-v4 sequencing of human stool


title: Cell_2597


title: Microbiota from stool CER_28 T1

description:
Library name: BC62
77s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_26 T1

description:
Library name: BC60
75s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_27 T1

description:
Library name: BC61
76s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_25 T1

description:
Library name: BC59
74s rRNA v3-v4 sequencing of human stool


title: Cell_2595

description: SmartSeq2_Gene_log_normalized_counts.rds


title: Microbiota from stool CER_34 T1

description:
Library name: BC67
82s rRNA v3-v4 sequencing of human stool


title: Cell_2593


title: Cell_2585


title: Microbiota from stool CER_24 T1

description:
Library name: BC58
73s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_23 T1

description:
Library name: BC57
72s rRNA v3-v4 sequencing of human stool


title: Cell_2584


title: Microbiota from stool CER_22 T1

description:
Library name: BC56
71s rRNA v3-v4 sequencing of human stool


title: Cell_2582


title: Cell_2578


title: Microbiota from stool CER_20 T1

description:
Library name: BC54
69s rRNA v3-v4 sequencing of human stool


title: Cell_2575


title: Microbiota from stool CER_21 T1

description:
Library name: BC55
70s rRNA v3-v4 sequencing of human stool


title: Cell_2576


title: Cell_2577


title: Microbiota from stool CER_18 T1

description:
Library name: BC52
67s rRNA v3-v4 sequencing of human stool


title: Microbiota from stool CER_17 T1

description:
Library name: BC51
66s rRNA v3-v4 sequencing of human stool


title: Cell_2569

description:
SmartSeq2_Gene_log_normalized_counts.rds
SmartSeq2_Isoform_TMM_Normalized_Abundance.rds