title: Preterm infant saliva miRNA - G01 (BPD)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)

tag: age at sampling (days of life)

tag: rds

tag: surfactant administration

tag: mechanical ventilation from birth

tag: ivh


title: Preterm infant saliva miRNA - G02 (BPD)

status: Public on Jun 29 2026

type: RNA

city: Almaty

first: Iskander

last: Isgandarov

address: Timiryazev 45

country: Kazakhstan

institute: Institute of plant biology and biotechnology

hyb_protocol: Labeled samples hybridized to Affymetrix GeneChip miRNA 4.1 Array using GeneTitan Multi-Channel (MC) instrument, 96-well plate format, per Affymetrix miRNA Assay protocol.

scan_protocol: Arrays scanned using Affymetrix GeneTitan MC instrument.

data_processing: Raw CEL files imported in R using oligo package (v1.74.0). RMA normalization applied (background=FALSE). All 36,353 probe set intensity values (RMA log2 scale) provided in Matrix table. Probe set names correspond to Affymetrix miRNA-4_1-st-v1 annotation (20160922). For differential expression: human miRNA probes (n=2,578) filtered by mean log2 intensity >5; limma (v3.66.0) with empirical Bayes, Benjamini-Hochberg FDR correction.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Saliva

label_protocol: RNA (100 ng) labeled with Affymetrix FlashTag Biotin HSR RNA Labeling Kit per manufacturer protocol. Poly(A) tailing performed at 37°C for 15 min; ligation with 5X FlashTag Biotin HSR Ligation Mix and T4 DNA Ligase at 25°C for 30 min.

growth_protocol: N/A - clinical study; preterm newborns managed per standard NICU protocols.

extract_protocol: Saliva was collected from each preterm infant at days 10-14 of life, one hour prior to feeding, by sterile syringe aspiration. Samples were placed in RNAprotect Cell Reagent and transported to the laboratory within 2 hours on ice. After pre-clearing, 100 µl saliva served as input for RNA extraction. Total RNA including the miRNA fraction was isolated using the MagMAX mirVana Total RNA Isolation Kit (Thermo Fisher Scientific) on a KingFisher Flex automated platform, per manufacturer instructions.

treatment_protocol: N/A - no experimental treatment applied.

value: BPD

value: grade 3

value: yes

value: grade 2


title: M_D_5

type: SRA

city: Tel aviv

first: Nitay

last: Zuk-Bar

address: Chaim Levanon St 55

country: Israel

institute: Tel aviv university

description: Library name: M_D_5

library_source: transcriptomic

data_processing:
The E14 RNA-seq data were preprocessed using the Seq2Science pipeline (van der Sande et al. 2023) with the default settings. Briefly, we aligned the reads to the mm10 mouse reference genome using STAR (Dobin et al. 2013).
Gene counting was done using HTSeq (Anders et al. 2015), and transcripts per million (TPM) normalization was done using Salmon (Patro et al. 2017).
Assembly: mouse mm10
Supplementary files format and content: tab-separated text files include raw reads count for each samples
Library strategy: spatial transcriptomics

organism: Mus musculus

source_name: Dorsal

extract_protocol:
Geo-seq (Chen et al. 2017). E12 and E14 mouse embryonic heads were fresh frozen embedded in OCT and cryosectioned at a thickness of 12 μm.
Geo-seq (Chen et al. 2017). Total RNA pellets were dissolved in a lysis solution (4M GuSCN), followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen), and whole transcription amplification with KAPA HiFi HotStart ReadyMix (2×; KAPA Biosystems). cDNA library was constructed using the Nextera XT Library Prep Kit (Illumina).

tag: tissue

value: Dorsal

tag: genotype

value: Mutant

tag: batch

value: B


title: Preterm infant saliva miRNA - F12 (BPD)


title: clone16_17

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 366507
SMART-Seq v3

library_source: transcriptomic single cell

data_processing:
Alignment was performed using STAR (v.2.7.9a) on GRCm39 and Gencode vM27 with STAR parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --outFilterScoreMinOverLread 0.22, --outFilterMatchNminOverLread 0.22. Note that we only used the R2 reads from paired end sequencing for this analysis. Reads in exonic and intronic regions (Gencode vM27) were counted using the aligned bam files produced by STAR and summarizeOverlaps (GenomicAlignments v1.40.0, R v4.4.0) with singleEnd=TRUE, mode = "IntersectionNotEmpty", ignore.strand = T, inter.feature = T parameters.
Assembly: GRCm39
Supplementary files format and content: Matrix in csv format with columns corresponding to cells and rows to genes. One file for exonic and one file for intronic reads is given.

source_name: cerebral organoid

growth_protocol: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures.

extract_protocol:
Organoids with MADM clones induced at D13 were collected at D20 for MADM-CloneSeq. The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (PMID: 38968076). Organoids were kept in cell culture membrane (Millicell) in oxygenated (95% O2, 5% CO2) artificial cerebrospinal fluid (ACSF) containing (in mM): 118 NaCl, 2.5 KCl, 1.25 NaH2PO4, 1.5 MgSO4, 1 CaCl2, 10 Glucose, 3 Myo-inositol, 30 Sucrose, 30 NaHCO3 prepared   with ultra-distilled water; pH=7.4, at 35C, until sample collection. All work surface and equipment were cleaned using RNase away solution (Thermo Fisher Scientific) prior to experiments. Single organoids were transferred to a LNscope 240XY miscroscope (Luigs & Neumann) and superfused with ACSF at a rate of 0.5 ml/min at room temperature. Individual clones were visualized under a 20x objective and by using ImageJ software. To observe red or green fluorescence, light was emitted from a LED light source (CoolLED, Andover, UK). Glass pipettes (B150-86-10, Sutter Instrument, Novato, CA) previously autoclaved, were pulled using a P-1000 pipette puller (Sutter Instrument) to generate pipettes with an opening of around 3-5ym. Before use, each pipette was filled with 3.5yl of pipette solution which consisted of RNase inhibitor (Takara, 1.95%) in RNase-free PBS (Invitrogen) filtered through a 0.22mm filter. Red or green fluorescent neurons were approached with the pipette under positive pressure to avoid tissue contamination of the pipette tip. When contact with cell membrane was made, tight seal formation was achieved under IR/DIC visualization. The complete aspiration of the cell body was immediately performed by applying a gentle and steady suction while monitoring under fluorescence and typically takes 5-10 s. The negative pressure was removed immediately once the target cell was collected and the pipette was carefully withdrawn from the acute slice to avoid contamination. The content of each pipette was directly transferred into individual PCR tubes and kept at -80C until cDNA library preparation.
cDNA libraries for individual MADM-CloneSeq cells were were prepared using Smart-seq3 protocol (PMID 32518404) in 3 batches (96well plates).

treatment_protocol: Stock solutions of 4-hydroxytamoxifen (4-OHT, Sigma) were generated by dilution in 100% ethanol to a concentration 1000-fold greater (20-80 µM) than the working solution. A concentration of 60 nM 4-OHT was used for D13. If 4-OHT treatment occurred on a day without medium change, medium was removed from wells containing organoids to be treated and placed in a tube, 4-OHT was added, and medium was added back to wells. After 24 h, medium was completely replaced and organoids were washed 1x with PBS.

value: cerebral organoid

tag: plate

tag: cloneid

tag: color

value: G

tag: clone type

value: N

tag: clone size


title: CT_A_4

description: Library name: CT_A_4

source_name: Axons

value: Axons

value: Control


title: PPP1CA biol rep 1

city: Irvine

first: Yoseop

last: Yoon

state: CA

address: 1002 Health Sciences Rd

country: USA

institute: University of California Irvine

description: Library name: YY61

data_processing:
PAS-seq data analysis was conducted as described by (Wang et al., 2021).
Assembly: hg38
Supplementary files format and content: bigwig

molecule: polyA RNA

growth_protocol: All HEK293T cell lines were cultured in DMEM (Dulbecco's Modified Eagle Medium, high glucose, pyruvate) (Gibco, 11995065) supplemented with 10% FBS (fetal bovine serum) (Sigma, F0926-100ML).

extract_protocol:
TRIZOL
2µg of total RNA was used for PAS-seq library preparation, adhering to the protocol detailed in our methodological paper (Yoon et al., 2021).

treatment_protocol: Protein knockdown samples were generated using short targeting RNA (shRNA) plasmids from the MISSION lentiviral collection (Sigma-Aldrich). HEK293XT cells were seeded onto 12-well plates at a density of 0.1x106 cells per well in 1mL of DMEM (LifeTech, 11995065) + 10% FBS and grown overnight. The media was replaced the following day using fresh media containing 8ug/mL polybrene (Hexadimethrine bromide - Sigma Aldrich cat# H9268) and 100ul of lentivirus specific to RBP open reading frames. The lentiviral medium was removed after 24h and replaced with fresh media containing 4ug/mL Puromycin and incubated in a standard tissue culture incubator for 48h.

tag: cell line

tag: cell type

value: human embryonic kidney cell

tag: treatment

value: siRNA


title: clone16_16

description:
Library name: 366506
SMART-Seq v3


title: Preterm infant saliva miRNA - F11 (BPD)

tag: disease status

tag: gestational age (weeks)

tag: birth weight (g)

value: grade 1


title: HNRNPF biol rep 2

description: Library name: YY60


title: PTS_LGG_P60

city: Houston

first: Qi

last: Te

address: 1250 Moursund st

institute: Baylor College of Medicine

description:
Library name: sample 1
visium

data_processing:
Space Ranger (v2.0.0)
Assembly: mm10 mouse genome
Supplementary files format and content: matrix files and csv
Supplementary files format and content: images
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
For spatial transcriptomics, LGG-bearing mouse brains were processed and embedded in paraffin by the Pathology Core at BCM. The brains were sectioned into 6 µm thick coronal sections and attached within the capture area on the Visium slides. Tumor locations were identified using H&E staining.
For spatial transcriptomics, The libraries were prepared with the Visium Spatial Gene Expression Reagent Kits (10x Genomics, PN-1000187) and sequenced on an Illumina HiSeq1500 instrument and a paired-end flow cell (High output) according to manufacturer protocol.

value: brain

value: tumor and tumor microenviroment cells

tag: surgery

value: PTS


title: clone16_15

description:
Library name: 366505
SMART-Seq v3


title: HNRNPF biol rep 1

description: Library name: YY59


title: CT_D_4

description: Library name: CT_D_4


title: clone16_14

description:
Library name: 366504
SMART-Seq v3


title: MK rescued vehicle, rep4

city: Albany

first: Whitney

last: Longmate

state: New York

address: 43 New Scotland Avenue

department: Surgery-General Surgery

institute: Albany Medical College

description:
Library name: Sample16
Sample name in processed data file: T4-MK-Rescued-V

data_processing:
The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mis-match was allowed for index sequence identification. Reads were quantified using feature Counts with inbuilt Entrez annotations. Genes with CPM > 0.5 in ≥3 samples were retained, and gene symbols were assigned from NCBI. Counts were log2-CPM–transformed and normalized using TMM (edgeR). Differential expression was analyzed with limma-voom and empirical Bayes moderation. Genes with adjusted p < 0.05 were considered significant. PCA (base R, prcomp) was used for global variation.
Assembly: Reads were aligned to mm10 (mouse) with Rsubread (v2.10.5, align function, default parameters)
Supplementary files format and content: Comma-separated values (csv) file, raw counts

source_name: Immortalized Mouse keratinocytes

growth_protocol: Immortalized mouse keratinocytes (MK cells) that lack α3 integrin (MKα3-, null), and MK cells that express α3 integrin (MKα3+; MK-/- cells reconstituted with human α3 integrin, rescued) were cultured on collagen-coated culture dishes in supplemented low-calcium Minimum Essential Medium (MEM; Thermo Fisher Scientific) and incubated at 33°C with 8% CO2.

extract_protocol:
RNA was extracted using Trizol Extraction method.
The RNA sample were quantified using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA). The NEBNext Ultra II RNA Library Prep Kit for Illumina & NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA), including clustering and sequencing reagents, was utilized according to the manufacturer's recommendations. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3' ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by uantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: For LN332 treatments, plated MKα3- (null) and MKα3+ (rescued) cells were incubated in MK culture medium supplemented with 0.02 mg/mL LN332 (BioLamina) or equal volume of vehicle control (PBS/10% Glycine/0.02 NaN3) for 16-24 hours.  Cells were pelleted for RNA extraction, library preparation, and RNA-Seq.

value: Immortalized Mouse keratinocytes

value: Keratinocytes

value: alpha3 integrin-rescued (human ITGA3 expressed in MKalpha3- cells)

value: Vehicle control


title: SRP68 biol rep 2

description: Library name: YY58


title: CT_A_3

description: Library name: CT_A_3


title: MK rescued laminin, rep4

description:
Library name: Sample15
Sample name in processed data file: T4-MK-Rescued-Lam


title: clone16_13

description:
Library name: 366503
SMART-Seq v3


title: CT_V_3

description: Library name: CT_V_3

source_name: Ventral

value: Ventral


title: MK null vehicle, rep4

description:
Library name: Sample14
Sample name in processed data file: T4-MK-Null-V

value: alpha3 integrin-null (MKalpha3-)


title: clone16_12

description:
Library name: 366502
SMART-Seq v3

value: cerebral organoid


title: SCAF8 biol rep 2

description: Library name: YY56

value: B


title: CT_D_3

description: Library name: CT_D_3

value: Dorsal


title: MK null laminin, rep4

description:
Library name: Sample13
Sample name in processed data file: T4-MK-Null-Lam


title: clone16_11

description:
Library name: 366501
SMART-Seq v3

value: G

value: N


title: SCAF8 biol rep 1

description: Library name: YY55

value: human embryonic kidney cell


title: M_A_4

description: Library name: M_A_4

value: Axons

value: Mutant


title: clone16_10

description:
Library name: 366500
SMART-Seq v3


title: MK rescued vehicle, rep3

description:
Library name: Sample12
Sample name in processed data file: T3-MK-Rescued-V


title: RBM5 biol rep 2

description: Library name: YY54

value: siRNA


title: M_V_4

description: Library name: M_V_4


title: MK rescued laminin, rep3

description:
Library name: Sample11
Sample name in processed data file: T3-MK-Rescued-Lam


title: clone16_9

description:
Library name: 366499
SMART-Seq v3


title: A3_Patient_1_Region _1

city: St. Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 Euclid Ave

institute: Washington University School of Medicine

hyb_protocol: The Xenium Human Lung Gene Expression hLung_v1.1 was used with 289 genes.  Hybridization was performed by 10X Genomics Protocol CG000582_XeniumInSitu_GeneExpression_UserGuide_RevH

scan_protocol: Imaging, processing, decoding, QC, and multimodal cell segmentation was performed onboard the Xenium Analyzer . The instrument software version was 2.0.1.0 and the analysis version was xenium-2.0.0.10

data_processing: Onboard Analysis: xenium-2.0.0.10

label: Xenium probe set

source_name: lung

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE blocks were sectioned at 5 microns thickness onto Xenium Slides. Tissue was deparrafinized and decrosslinkd by 10x Genomics Protocl CG000580_Demonstrated_Protocol_Xenium_FFPE_Deparaffinization_Decrosslinking_RevB

value: lung

tag: tissue preservation method

value: FFPE

tag: rejection grade


title: RBM5 biol rep 1

description: Library name: YY53


title: M_D_4

description: Library name: M_D_4

tag: tissue


title: MK null vehicle, rep3

description:
Library name: Sample10
Sample name in processed data file: T3-MK-Null-V

value: Immortalized Mouse keratinocytes

tag: genotype


title: clone16_8

description:
Library name: 366498
SMART-Seq v3


title: RBM4 biol rep 2

description: Library name: YY52

tag: batch


title: clone16_7

description:
Library name: 366497
SMART-Seq v3

tag: plate


title: MK null laminin, rep3

description:
Library name: Sample9
Sample name in processed data file: T3-MK-Null-Lam

value: Keratinocytes


title: RBM4 biol rep 1

description: Library name: YY51


title: CT_V_2

description: Library name: CT_V_2

value: Control


title: MK rescued vehicle, rep2

description:
Library name: Sample8
Sample name in processed data file: T2-MK-Rescued-V

value: alpha3 integrin-rescued (human ITGA3 expressed in MKalpha3- cells)

value: Vehicle control


title: clone16_6

description:
Library name: 366496
SMART-Seq v3

tag: cloneid

value: R


title: CT_D_2

description: Library name: CT_D_2


title: RBM11 biol rep 2

description: Library name: YY50


title: MK rescued laminin, rep2

description:
Library name: Sample7
Sample name in processed data file: T2-MK-Rescued-Lam


title: RBM11 biol rep 1

description: Library name: YY49


title: clone16_5

description:
Library name: 366495
SMART-Seq v3

value: cerebral organoid

tag: color


title: MK null vehicle, rep2

description:
Library name: Sample6
Sample name in processed data file: T2-MK-Null-V

value: alpha3 integrin-null (MKalpha3-)


title: M_A_3

description: Library name: M_A_3

value: A


title: ROI 36, Patient 6, Primary tumor bed, MPR

city: Beijing

first: Rongzhen

last: Li

state: 北京Beijing

address: Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing 100730, China

country: China

institute: Peking Union Medical College

description: Library name: ROI 36

data_processing:
The raw FASTQ files were run through GeoMx NGS pipelines to acquire digital count conversions and initial data files for further analysis.
The initial data were further processed using quality control (QC) and normalization. RNA data were normalized using Total Count normalization with a scaling factor set at 10,210.
Assembly: mm10
Supplementary files format and content: csv file include normalized count data

source_name: Non-small cell lung cancer, Primary tumor bed

extract_protocol:
Formalin-fixed and paraffin-embedded (FFPE) tissues were used to construct tissue microarrays (TMAs). Cores (2.0 mm in diameter) were punched from each FFPE block and arrayed across two recipient TMA blocks. Five-μm-thick TMA sections were deparaffinized and rehydrated, and regions of interest (ROIs) were selected based on immunofluorescence morphology markers.
RNA extraction was performed using the NanoString GeoMx Digital Spatial Profiler according to the manufacturer’s protocol. Briefly, TMA sections were processed and regions of interest (ROIs) were selected based on immunofluorescence morphology markers. Each ROI was sequentially decoupled from the oligonucleotides using ultraviolet (UV) light. UV-cleavable oligos coupled with individual genes were cleaved and collected from all ROIs using a digital mirror device-guided UV illumination. The resultant oligos were amplified by polymerase chain reaction (PCR) amplified (Bio-Rad Laboratories, Hercules, CA, USA) using GeoMx Seq Code primers for downstream library construction.

treatment_protocol: Interventions included pembrolizumab at a fixed dose of 200 mg combined with carboplatin (area under the curve 5) or cisplatin 75mg/m2, pemetrexed at 500 mg/m2 for nonsquamous cell carcinoma, and paclitaxel at 175 mg/m2 or nab-paclitaxel at 260 mg/m2 for squamous cell carcinoma. Surgery was performed after at least two cycles of neoadjuvant therapy. All patients received adjuvant pembrolizumab for up to one year after surgery. To ensure that all patients received four cycles of perioperative chemotherapy, adjuvant chemotherapy was given to patients who had not received adequate neoadjuvant therapy. The surgical approaches were chosen by the surgeon.


title: M_V_3

description: Library name: M_V_3

value: Ventral


title: clone16_2

description:
Library name: 366492
SMART-Seq v3

value: G

tag: clone type

value: N


title: M_D_3

description: Library name: M_D_3

value: Dorsal


title: MK rescued vehicle, rep1

description:
Library name: Sample4
Sample name in processed data file: T1-MK-Rescued-V


title: MK null laminin, rep2

description:
Library name: Sample5
Sample name in processed data file: T2-MK-Null-Lam


title: PPIA biol rep 2

description: Library name: YY48

value: human embryonic kidney cell

value: B


title: clone16_3

description:
Library name: 366493
SMART-Seq v3

tag: clone size


title: clone16_4

description:
Library name: 366494
SMART-Seq v3


title: non-target 2 biol rep 6

description: Library name: YY46

tag: cell line

value: siRNA


title: M_A_2

description: Library name: M_A_2

value: Axons

value: Mutant


title: PPP1CA biol rep 2

description: Library name: YY62

tag: cell type


title: Circulating cells from day0,1,5 after VSV infection

city: Tokyo

first: Riho

last: Saito

address: 7-3-1 Hongo Bunkyo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

description:
Library name: Sample1
Macrogen Japan

data_processing:
Sequencing was carried out on an HiSeq X Ten platform (Macrogen Japan) with paired-end 150 bp reads. Raw sequencing data were processed and analyzed using the BD Rhapsody™ WTA Pipeline, executed on the Seven Bridges Platform (Seven Bridges Genomics, Inc., https://www.sevenbridges.com). The pipeline included read alignment, UMI-based de-duplication, and generation of gene expression matrices based on BD’s reference transcriptome. In total, 1,710 single cells were sequenced: 166 and 208 cells at 0 dpi, 313 and 189 cells at 1 dpi, 515 and 319 cells at 5 dpi, from the survival and lethal groups, respectively. Cells expressing < 200 features, > 2,500 features, or > 25% mitochondrial genes were excluded from the analysis.
Assembly: Mouse mm10 (GRCm38-PhiX-gencodevM19-20181206.tar.gz and gencodevM19-20181206.gtf files provided by BD)
Supplementary files format and content: txt files include barcode information and raw count matrix for each cell

source_name: Blood

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS before, 1 day and 5 days after the infection. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were fixed with CellCover (Anacyte, 800-125) at 4℃ for 15min to preserve RNA. Cells were then resuspended in CELLBANKER 1 (Nippon Zenyaku Kogyo Co., Ltd., 11910) and stored at -80℃.
Samples from the survival (n=2) and lethal (n=2) groups were processed for subsequent library preparation following mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol from BD Rhapsody™ Single-Cell Analysis System.

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^8 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: Blood

value: Circulating cells

value: C57B6J WT

tag: treatment

value: VSV (New Jersey) intranasal infection


title: MK rescued laminin, rep1

description:
Library name: Sample3
Sample name in processed data file: T1-MK-Rescued-Lam

value: Immortalized Mouse keratinocytes

value: Keratinocytes

value: alpha3 integrin-rescued (human ITGA3 expressed in MKalpha3- cells)


title: clone16_1

description:
Library name: 366491
SMART-Seq v3

value: cerebral organoid


title: MK null vehicle, rep1

description:
Library name: Sample2
Sample name in processed data file: T1-MK-Null-V

value: alpha3 integrin-null (MKalpha3-)

value: Vehicle control


title: non-target 2 biol rep 5

description: Library name: YY45


title: M_V_2

description: Library name: M_V_2

value: Ventral

value: A


title: non-target 2 biol rep 4

description: Library name: YY44

value: human embryonic kidney cell


title: M_D_2

description: Library name: M_D_2

value: Dorsal


title: clone15_2

description:
Library name: 366489
SMART-Seq v3

value: G

value: SN


title: clone15_3

description:
Library name: 366490
SMART-Seq v3


title: PPIA biol rep 1

description: Library name: YY47

value: siRNA

value: B


title: CT_V_4

description: Library name: CT_V_4

value: Control


title: CT_A_1

description: Library name: CT_A_1

value: Axons


title: non-target 2 biol rep 3

description: Library name: YY43


title: PM cells VSV rep3

city: wuhan

first: Mi

last: Tian

state: Hubei

address: Bayi Street 229 in Wuchang district

department: College of life science

institute: Wuhan University

description: Library name: Sample 6

data_processing:
Raw reads filtered by fastp v0.18.0, rRNA removed via Bowtie2 v2.2.8.
Clean reads mapped to mouse genome using HISAT2 v2.1.0
FPKM/TPM calculated by StringTie v1.3.1 and RSEM
DEG calling via DESeq2, followed by GO/KEGG/GSEA and SNP/AS/PPI analysis
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: peritoneal cavity

growth_protocol: PM cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
After PM cells adhered for 24 hours, 2 μl of VSV with a viral titer of 1×10^8 was used to infect the PM cells. The cells were collected after 24 hours.
Total RNA was extracted from primary peritoneal macrophages using a standard TRIzol/chloroform method for total RNA isolation

treatment_protocol: Infect PM cells with VSV virus for 24 hours

value: peritoneal cavity

value: Primary cell

value: peritoneal macrophages

value: VSV infection


title: clone15_1

description:
Library name: 366488
SMART-Seq v3

value: cerebral organoid


title: SRP68 biol rep 1

description: Library name: YY57


title: CT_V_1

description: Library name: CT_V_1


title: PM cells VSV rep2

description: Library name: Sample 5


title: non-target 2 biol rep 2

description: Library name: YY42


title: clone14_3

description:
Library name: 366487
SMART-Seq v3


title: CT_D_1

description: Library name: CT_D_1


title: PM cells VSV rep1

description: Library name: Sample 4


title: clone14_2

description:
Library name: 366486
SMART-Seq v3


title: non-target 2 biol rep 1

description: Library name: YY41


title: M_A_1

description: Library name: M_A_1

value: Mutant


title: PCBP3 RNAi biol rep 1

description: Library name: YY39


title: PM cells MOCK rep3

description: Library name: Sample 3

value: Mock


title: MK null laminin, rep1

description:
Library name: Sample1
Sample name in processed data file: T1-MK-Null-Lam

value: Immortalized Mouse keratinocytes

value: Keratinocytes

value: alpha3 integrin-null (MKalpha3-)


title: M_V_1

description: Library name: M_V_1

value: Ventral

value: A


title: clone14_1

description:
Library name: 366485
SMART-Seq v3

value: R

value: SN


title: CT_A_2

description: Library name: CT_A_2

value: B


title: PCBP3 RNAi biol rep 2

description: Library name: YY40

value: human embryonic kidney cell

value: siRNA


title: PM cells MOCK rep2

description: Library name: Sample 2

value: peritoneal cavity


title: clone13_2

description:
Library name: 366484
SMART-Seq v3

value: G


title: M_D_1

description: Library name: M_D_1

value: Dorsal


title: ZC3HAV1 RNAi biol rep 2

description: Library name: YY38


title: PM cells MOCK rep1

description: Library name: Sample 1

value: Primary cell

value: peritoneal macrophages


title: clone13_1

description:
Library name: 366483
SMART-Seq v3

value: cerebral organoid


title: ZC3HAV1 RNAi biol rep 1

description: Library name: YY37


title: day1died_42

description: Library name: Sample78

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia. Their survival and body weight were monitored for 14 days. Mice lost more than 30% of body weight at the time of the infection or survived over 14 days after the infection was euthanized for humane endpoint.

value: Blood

value: CXCR2+ cells

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

tag: group

value: Lethal group


title: clone12_4

description:
Library name: 366482
SMART-Seq v3

value: N


title: TRNAU1AP RNAi biol rep 2

description: Library name: YY36

value: A


title: day1died_41

description: Library name: Sample77


title: Mouse5-Tunicamycin

city: Epalinges

first: Alexis

last: Jourdain

address: Boveresses 155, CP51

department: Immunobiology

country: Switzerland

institute: University of Lausanne

description:
Library name: 5-Tunica
Bone marrow-derived macrophages treated with IL-4/IL-13 and tunicamycin for 24 h.

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm39.110 genome using STAR (v. 2.7, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm39.110 gene annotation.
The estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Assembly: Mus musculus.GRCm39.110
Supplementary files format and content: htseq.genes.counts : tab-delimited raw counts per gene and per sample as summarized with htseq-count
Supplementary files format and content: rsem.genes.tpm: tab-delimited tags per milion per gene and per sample as estimated with rsem

source_name: Murine primary macrophages

growth_protocol: Bone marrow was isolated from femurs and tibia, passed through a 40 μm filter and used for the generation of BMDM in 50 μg/mL recombinant mM-CSF (Immunotools, 12343115) supplemented DMEM-GlutaMAX (Gibco, 31966021) with 10% heat-inactivated fetal bovine serum (FBS) (Gibco, A5256701), 100 U/mL penicillin/streptomycin (BioConcept, 4-01F00-H) and 10 mM HEPES buffer (BioConcept, 5-31F00-H). At day 3 of differentiation, fresh media supplemented with 50 μg/mL rmM-CSF was added. At day 6, BMDM were collected in cold 5 mM EDTA-supplemented PBS, counted, and plated accordingly to the experiments needs. Cells were cultured under 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using the RNeasy kit (QIAGEN, 74104) with the RNAse-Free DNAse on-column step (QIAGEN, 79254).
Watchmaker mRNA

treatment_protocol: BMDM were activated with either nothing (naive) or 20 ng/mL of interleukin-4 (IL-4) (Peprotech, 214-14) and 20 ng/mL of IL-13 (Peprotech, 210-13) for 24 hours. For the inhibitors, cells were pre-treated with the inhibitors for 1h and then the media was changed to media containing IL-4/IL-13 and the respective inhibitors. Oligomycin was used at 1 uM, ISRIB at 1 uM, Sal003 at 10 uM and tunicamycin at 5 ug/mL.

value: Murine primary macrophages

value: Murine bone marrow-derived primary  macrophages

value: WT

value: IL-4/IL-13 and tunicamycin

tag: replicate


title: day1died_40

description: Library name: Sample76


title: clone12_3

description:
Library name: 366481
SMART-Seq v3


title: Mouse5-Sal003

description:
Library name: 5-Sal003
Bone marrow-derived macrophages treated with IL-4/IL-13 and Sal003 for 24 h.

value: IL-4/IL-13 and Sal003


title: TRNAU1AP RNAi biol rep 1

description: Library name: YY35

value: human embryonic kidney cell

value: siRNA


title: day1died_39

description: Library name: Sample75


title: RBM14 RNAi biol rep 2

description: Library name: YY34


title: Mouse5-Oligomycin

description:
Library name: 5-Oli_ISR
Bone marrow-derived macrophages treated with IL-4/IL-13 and oligomycin for 24 h.

value: IL-4/IL-13 and oligomycin


title: Mouse5-Oligomycin_ISRIB

description:
Library name: 5-Oligo
Bone marrow-derived macrophages treated with IL-4/IL-13, oligomycin and ISRIB for 24 h.

value: IL-4/IL-13, oligomycin and ISRIB


title: RBM14 RNAi biol rep 1

description: Library name: YY33


title: clone12_1

description:
Library name: 366479
SMART-Seq v3

value: cerebral organoid

value: R


title: day1died_38

description: Library name: Sample74

value: Blood

value: CXCR2+ cells


title: clone12_2

description:
Library name: 366480
SMART-Seq v3


title: day1died_37

description: Library name: Sample73

value: C57B6J WT

value: VSV (New Jersey) intranasal infection


title: clone11_5

description:
Library name: 366478
SMART-Seq v3

value: G

value: SN


title: PARN RNAi biol rep 2

description: Library name: YY32

value: A


title: clone11_4

description:
Library name: 366477
SMART-Seq v3


title: day1died_36

description: Library name: Sample72

value: Lethal group


title: PARN RNAi biol rep 1

description: Library name: YY31


title: clone11_3

description:
Library name: 366476
SMART-Seq v3


title: LGALS3 RNAi biol rep 2

description: Library name: YY30


title: day1died_35

description: Library name: Sample71


title: Mouse4-Sal003

description:
Library name: 4-Sal003
Bone marrow-derived macrophages treated with IL-4/IL-13 and Sal003 for 24 h.

value: Murine primary macrophages

value: Murine bone marrow-derived primary  macrophages

value: WT


title: Mouse4-Tunicamycin

description:
Library name: 4-Tunica
Bone marrow-derived macrophages treated with IL-4/IL-13 and tunicamycin for 24 h.

value: IL-4/IL-13 and tunicamycin


title: LGALS3 RNAi biol rep 1

description: Library name: YY29

value: human embryonic kidney cell

value: siRNA


title: clone11_2

description:
Library name: 366475
SMART-Seq v3


title: Mouse5-M2

description:
Library name: 5-M2
Bone marrow-derived macrophages treated with IL-4/IL-13 for 24 h.


title: clone11_1

description:
Library name: 366474
SMART-Seq v3


title: day1died_34

description: Library name: Sample70


title: Mouse4-Oligomycin

description:
Library name: 4-Oli_ISR
Bone marrow-derived macrophages treated with IL-4/IL-13 and oligomycin for 24 h.

value: IL-4/IL-13 and oligomycin


title: day1died_33

description: Library name: Sample69


title: Mouse4-M2

description:
Library name: 4-M2
Bone marrow-derived macrophages treated with IL-4/IL-13 for 24 h.


title: day1died_32

description: Library name: Sample68


title: CNOT2 RNAi biol rep 2

description: Library name: YY26


title: clone10_1

description:
Library name: 366472
SMART-Seq v3

value: cerebral organoid


title: day1died_31

description: Library name: Sample67


title: Mouse4-M0

description:
Library name: 4-M0
Bone marrow-derived macrophages unstimulated for 24 h.


title: Mouse5-M0

description:
Library name: 5-M0
Bone marrow-derived macrophages unstimulated for 24 h.


title: CNOT2 RNAi biol rep 1

description: Library name: YY25


title: clone9_2

description:
Library name: 366471
SMART-Seq v3


title: day1died_30

description: Library name: Sample66


title: Mouse2-Tunicamycin

description:
Library name: 2-Tunica
Bone marrow-derived macrophages treated with IL-4/IL-13 and tunicamycin for 24 h.


title: RBM10 RNAi biol rep 2

description: Library name: YY24


title: clone9_1

description:
Library name: 366470
SMART-Seq v3


title: day1died_29

description: Library name: Sample65


title: Mouse2-Sal003

description:
Library name: 2-Sal003
Bone marrow-derived macrophages treated with IL-4/IL-13 and Sal003 for 24 h.

value: IL-4/IL-13 and Sal003


title: RBM10 RNAi biol rep 1

description: Library name: YY23


title: clone8_4

description:
Library name: 366469
SMART-Seq v3


title: clone8_3

description:
Library name: 366468
SMART-Seq v3


title: day1died_28

description: Library name: Sample64

value: Blood


title: Mouse2-Oligomycin

description:
Library name: 2-Oli_ISR
Bone marrow-derived macrophages treated with IL-4/IL-13 and oligomycin for 24 h.


title: MBNL1 RNAi biol rep 2

description: Library name: YY22


title: day1died_27

description: Library name: Sample63

value: CXCR2+ cells


title: clone8_2

description:
Library name: 366467
SMART-Seq v3

value: R


title: Mouse2-Oligomycin_ISRIB

description:
Library name: 2-Oligo
Bone marrow-derived macrophages treated with IL-4/IL-13, oligomycin and ISRIB for 24 h.

value: IL-4/IL-13, oligomycin and ISRIB


title: day1died_26

description: Library name: Sample62

value: C57B6J WT

value: VSV (New Jersey) intranasal infection


title: MBNL1 RNAi biol rep 1

description: Library name: YY21

value: A


title: Mouse2-M2

description:
Library name: 2-M2
Bone marrow-derived macrophages treated with IL-4/IL-13 for 24 h.


title: EIF4B RNAi biol rep 2

description: Library name: YY20


title: day1died_25

description: Library name: Sample61

value: Lethal group


title: Mouse2-M0

description:
Library name: 2-M0
Bone marrow-derived macrophages unstimulated for 24 h.

value: Murine primary macrophages


title: clone7_2

description:
Library name: 366465
SMART-Seq v3

value: G

value: SN


title: day1died_24

description: Library name: Sample60


title: EIF4B RNAi biol rep 1

description: Library name: YY19


title: clone7_1

description:
Library name: 366464
SMART-Seq v3


title: day1died_23

description: Library name: Sample59


title: Mouse1-Sal003

description:
Library name: 1-Sal003
Bone marrow-derived macrophages treated with IL-4/IL-13 and Sal003 for 24 h.

value: Murine bone marrow-derived primary  macrophages

value: WT


title: MBNL2 RNAi biol rep 1

description: Library name: YY17

value: human embryonic kidney cell

value: siRNA


title: day1died_22

description: Library name: Sample58


title: clone6_3

description:
Library name: 366463
SMART-Seq v3

value: cerebral organoid


title: Mouse1-Oligomycin

description:
Library name: 1-Oli_ISR
Bone marrow-derived macrophages treated with IL-4/IL-13 and oligomycin for 24 h.

value: IL-4/IL-13 and oligomycin


title: clone6_2

description:
Library name: 366462
SMART-Seq v3


title: RBM22 RNAi biol rep 2

description: Library name: YY16


title: Mouse1-Oligomycin_ISRIB

description:
Library name: 1-Oligo
Bone marrow-derived macrophages treated with IL-4/IL-13, oligomycin and ISRIB for 24 h.


title: clone6_1

description:
Library name: 366461
SMART-Seq v3


title: RBM22 RNAi biol rep 1

description: Library name: YY15


title: day1died_20

description: Library name: Sample56

value: Blood


title: Mouse1-M2

description:
Library name: 1-M2
Bone marrow-derived macrophages treated with IL-4/IL-13 for 24 h.


title: clone5_5

description:
Library name: 366460
SMART-Seq v3


title: Mouse1-M0

description:
Library name: 1-M0
Bone marrow-derived macrophages unstimulated for 24 h.


title: clone5_4

description:
Library name: 366459
SMART-Seq v3


title: RNPS1 RNAi biol rep 1

description: Library name: YY13


title: day1died_18

description: Library name: Sample54

value: CXCR2+ cells


title: day1died_17

description: Library name: Sample53


title: GRB2 RNAi biol rep 2

description: Library name: YY12


title: CXCR3+ lung tumor Treg cells, rep 3

city: New York

first: Nicholas

last: Arpaia

address: 701 W 168TH ST HHSC 906

institute: Columbia University Irving Medical Center

description: Library name: NO316

data_processing:
Cells were run on Element Aviti
Base calling was performed utilizing RTA (Illumina). Bclfastq2 (version 2.19) was used to convert BCL to fastq format, coupled with adapter trimming.
Assembly: Ensembl v96, Mouse GRCm38.p6
Supplementary files format and content: tsv

source_name: lung tumor

extract_protocol:
RNA was extracted using a Aliglent RNA 6000 Pico Kit
We utilized the CLONTECH the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) to reverse transcribe and amplify small amounts of RNA. After creating cDNA, the library was prepared using Nextera XT (Illumina)

value: lung tumor

value: Treg (Foxp3+ CD4+) cells

value: C57B6J - Foxp3 GFP males


title: clone5_3

description:
Library name: 366458
SMART-Seq v3


title: GSTF1 RNAi biol rep 2

description: Library name: YY28


title: GRB2 RNAi biol rep 1

description: Library name: YY11


title: clone5_2

description:
Library name: 366457
SMART-Seq v3


title: clone10_2

description:
Library name: 366473
SMART-Seq v3


title: Mouse4-Oligomycin_ISRIB

description:
Library name: 4-Oligo
Bone marrow-derived macrophages treated with IL-4/IL-13, oligomycin and ISRIB for 24 h.

value: IL-4/IL-13, oligomycin and ISRIB


title: GSTF1 RNAi biol rep 1

description: Library name: YY27

value: A


title: CXCR3+ lung tumor Treg cells, rep 2

description: Library name: NO308


title: CPSF6 RNAi biol rep 2

description: Library name: YY10


title: clone5_1

description:
Library name: 366456
SMART-Seq v3


title: day1died_15

description: Library name: Sample51

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

value: Lethal group


title: CXCR3- lung tumor Treg cells, rep 2

description: Library name: NO307


title: clone4_6

description:
Library name: 366455
SMART-Seq v3

value: G

value: SN


title: CPSF6 RNAi biol rep 1

description: Library name: YY9


title: CXCR3+ lung tumor Treg cells, rep 1

description: Library name: NO304


title: day1died_14

description: Library name: Sample50


title: CPSF5 RNAi biol rep 2

description: Library name: YY8


title: clone4_5

description:
Library name: 366454
SMART-Seq v3


title: day1died_13

description: Library name: Sample49


title: CXCR3- lung tumor Treg cells, rep 1

description: Library name: NO303


title: clone4_4

description:
Library name: 366453
SMART-Seq v3

value: R


title: CPSF5 RNAi biol rep 1

description: Library name: YY7

value: human embryonic kidney cell


title: clone8_1

description:
Library name: 366466
SMART-Seq v3


title: day1died_12

description: Library name: Sample48


title: cdk8-1, Shoot, 0mM magnesium sulfate, 10 days, rep3

city: East Lansing

first: Gregg

last: Howe

state: Michigan

address: 612 Wilson Street

institute: Michigan State University

description:
Library name: cdk8_noS_rep3
Column name in TPMs_AllSamples.xlsx: cdk8_noS_Shoot3

data_processing:
RNA-seq was perfomed Novogene Co., Ltd., with a raw data filter step: Remove reads containing adapters; Remove reads containing N > 10%; Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Genome alignment was performed with STAR (v2.7.11b) and Araport11.
Number of reads was determined with featureCounts (v2.0.8) to get raw reads.
Raw reads were normalized through DESeq2 (v1.46) to get normalized counts for differential expression analysis. Raw reads were also normalized using TPM calculations.
Assembly: Araport11
Supplementary files format and content: .xlsx file includes TPM values for each sample

organism: Arabidopsis thaliana

source_name: plate-grown shoot

growth_protocol: A. thaliana seedlings were grown in the Percival chamber at 21˚C under 16-h-light/8-h-dark cycles. For experiments where seedlings were plated on the agar plates, seeds were surface sterilized using 70% ethanol (v/v) for 5 min, 30% bleach with 0.05% Tween 20 for 5 min, washed 3 times with sterile Ultrapure water, and then stratified at 4˚ C in the dark for 2 days. The agar plates were 1% agar containing half-strength Murashige and Skoog medium (Murashige & Skoog, 1962). The Difco agar (fisher scientific, catalog number 214010) was washed 5 times according to the following procedures: 16.5g agar was stirred in 1.5 L Ultrapure water for 1 hour, after which the agar was set in the flask for 20 min before pouring the washed water. After washing 5 times, the agar was collected by vacuum filtration. Washed agar was completely dried in 65˚C oven for 3 days before proceeded to make the half-strength MS medium. 30 mL medium was poured into a 6x6 petri dish (Fisherbrand, 100x100x15mm). S sufficient plates contained 1.5 mM MgSO4 and S deprived plates contained 1.5 mM MgCl2.

extract_protocol:
RNA was extracted using the NucleoSpin RNA Plant Kit (Macherey-Nagel).
RNA-seq library construction was performed by Novogene Co., Ltd., using NEBNext Ultra II Directional RNA Library Prep Kit following the manufacturer's protocols.

treatment_protocol: 10-day-old seedlings were harvested, using a razer blade to dissect the shoot, then flash froze in liquid nitrogen.

value: plate-grown shoot

value: Day 10


title: clone4_3

description:
Library name: 366452
SMART-Seq v3

value: cerebral organoid


title: non-target biol rep 6

description: Library name: YY6

value: siRNA


title: clone4_2

description:
Library name: 366451
SMART-Seq v3


title: cdk8-1, Shoot, 0mM magnesium sulfate, 10 days, rep2

description:
Library name: cdk8_noS_rep2
Column name in TPMs_AllSamples.xlsx: cdk8_noS_Shoot2


title: Mouse1-Tunicamycin

description:
Library name: 1-Tunica
Bone marrow-derived macrophages treated with IL-4/IL-13 and tunicamycin for 24 h.

value: Murine primary macrophages

value: Murine bone marrow-derived primary  macrophages

value: WT

value: IL-4/IL-13 and tunicamycin


title: MBNL2 RNAi biol rep 2

description: Library name: YY18


title: non-target biol rep 5

description: Library name: YY5


title: day1survived_36

description: Library name: Sample36

value: Blood

value: CXCR2+ cells

value: Survival group


title: clone4_1

description:
Library name: 366450
SMART-Seq v3


title: non-target biol rep 4

description: Library name: YY4

value: A


title: day1survived_35

description: Library name: Sample35

value: C57B6J WT

value: VSV (New Jersey) intranasal infection


title: cdk8-1, Shoot, 1.5mM magnesium sulfate, 10 days, rep3

description:
Library name: cdk8_S_rep3
Column name in TPMs_AllSamples.xlsx: cdk8_S_Shoot3


title: non-target biol rep 3

description: Library name: YY3


title: day1survived_34

description: Library name: Sample34


title: clone3_4

description:
Library name: 366448
SMART-Seq v3

value: G

value: N


title: cdk8-1, Shoot, 1.5mM magnesium sulfate, 10 days, rep2

description:
Library name: cdk8_S_rep2
Column name in TPMs_AllSamples.xlsx: cdk8_S_Shoot2


title: non-target biol rep 2

description: Library name: YY2

value: human embryonic kidney cell


title: day1survived_33

description: Library name: Sample33


title: cdk8-1, Shoot, 1.5mM magnesium sulfate, 10 days, rep1

description:
Library name: cdk8_S_rep1
Column name in TPMs_AllSamples.xlsx: cdk8_S_Shoot1

value: plate-grown shoot


title: clone3_3

description:
Library name: 366447
SMART-Seq v3


title: non-target biol rep 1

description: Library name: YY1


title: day1survived_32

description: Library name: Sample32


title: day1survived_31

description: Library name: Sample31


title: Col-0, Shoot, 0mM magnesium sulfate, 10 days, rep2

description:
Library name: Col0_noS_rep2
Column name in TPMs_AllSamples.xlsx: Col0_noS_Shoot2

value: Day 10


title: shCrm_END-seq

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

library_source: genomic

data_processing:
Adapters were trimmed via cutadapt (v 4.1) with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25, then using bowtie with parameters s -n 3 -l 50 -k 1 aligned reads to dm6 and TE sequences.  Functions “view” and “sort” of samtools (v 1.9) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further deduplicated by picard (v2.18.7) and only the forward reads were retained. Then the R1.dedup.bam files were converted to bed files by the bedtools (v2.25.0) bamToBed command. BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig.
Assembly: dm6; Drosophila TE consensus sequence
Supplementary files format and content: bigwig
Library strategy: END-seq

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: pupa 4d hindgut

extract_protocol:
Hindguts were resuspended in cell suspension buffer and embedded in agarose plugs. Cells were lysed in agarose using proteinase K, follwed by RNase treatment. DNA was later precipitated after plug melting and shearing.
The DNA within the plugs was blunted, A-tailed and ligated with a biotin-labelled hairpin adaptor containing a 3' T overhang and Illumina's p5 sequence. Subsequently, DNA was extracted from the melted agarose and sheared by sonication. Biotinylated DNA was enriched by streptavidin coated beads and the DNA fragments were ligated to a second adaptor containing Illumina's p7 sequence followed by PCR amplification with Illumina sequencing primers for 22 cycles.

value: pupa 4d hindgut


title: day1survived_30

description: Library name: Sample30


title: clone3_1

description:
Library name: 366445
SMART-Seq v3

value: cerebral organoid


title: Col-0, Shoot, 0mM magnesium sulfate, 10 days, rep1

description:
Library name: Col0_noS_rep1
Column name in TPMs_AllSamples.xlsx: Col0_noS_Shoot1


title: clone2_4

description:
Library name: 366444
SMART-Seq v3

value: SN


title: Retinal Ganglion Cells, 2wks post ONC, anti-miR132-3p shRNA, rep 2

city: Farmington

first: Jacob

last: Brady

state: Connecticut

address: 263 Farmington Avenue

department: Neuroscience

institute: UConn School of Medicine

description: Library name: Sample 4

data_processing:
Trimmomatic v0.39; HISAT2 v2.2.1; SAMtools v1.10; Cufflinks suite (Cuffquant, Cuffnorm, Cuffdiff) v2.2.1
Raw paired-end sequence reads were trimmed for adaptor sequence and low-quality bases using Trimmomatic (parameters- ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:25 TRAILING:25 SLIDINGWINDOW:4:28 MINLEN:45)
Trimmed sequence reads were mapped to GRCm39/mm39 using HISAT2 with default parameters
Aligned reads were sorted by coordinate and indexed using SAMtools
Per-sample transcript abundances were quantified using Cuffquant against the GENCODE vM38 primary assembly annotation
Assembly: mm39 (vM38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: retina

extract_protocol:
Approximately, 5,000 RGCs (for each of the 2 replicates per condition) were collected by FACS and RNA was isolated immediately using the Quick-RNA Microprep Kit (ZR1050, Zymo Research)
cDNA libraries were prepared using polyA-selected RNA (TruSeq RNA Library Prep Kit, Illumina)

treatment_protocol: Optic nerve surgeries and intravitreal injections were carried out on mice of both sexes 8-12 weeks of age (average body weight 20-26 g) under general anesthesia, as described previously. The viruses included adeno-associated virus serotype 2 (AAV2) vectors expressing anti-miR132-3p (sequence: 5′-CGACCATGGCTGTAGACTGTTA-3′, against the targeted sequence: 5′-TAACAGTCTACAGCCATGGTCG-3′) and scrambled control (sequence: 5’-TCGAGGGCGACTTAACCTTAGG-3’) shRNAs (titers ~1 × 1013 GC/mL; VectorBuilder, Inc.). Both viral vectors co-expressed an mCherry reporter of transduction. Viruses (2 μl per eye) were injected intravitreally, avoiding injury to the lens, in 8-week-old mice, which were randomly assigned to experimental or control conditions, 2 weeks prior to ONC surgery

value: retina

value: Retinal Ganglion Cells

value: ONC, anti-miR132-3p shRNA AAV2


title: HNRNPF knockdown, rep1, group A

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Library name: HNRNPF-BG293LV06-55

data_processing:
Quality of reads were assessed using fastqc.
Reads were trimmed.
Reads were aligned to hg38 reference and quantified with salmon.
Assembly: hg38
Supplementary files format and content: quant.sf files contain transcript quantifications

growth_protocol: HEK293XT cells were seeded onto 12-well plates at a density of 0.1x106 cells per well in 1mL of DMEM + 10% FBS and grown overnight.

extract_protocol:
RNA extraction was completed using the Maxwell RSC simplyRNA tissue kit .
RNA-seq libraries were prepared using the TruSeq Stranded mRNA library preparation kit and the IDT for Illumina TruSeq RNA UD Index set for samples having greater than 50% knockdown of the RBP.

treatment_protocol: The media was replaced the following day using fresh media containing 8ug/mL polybrene (Hexadimethrine bromide) and 100ul of lentivirus specific to RBP open reading frames. The lentiviral medium was removed after 24h and replaced with fresh media containing 4ug/mL Puromycin and incubated in a standard tissue culture incubator for 48h.

value: human embryonic kidney

value: knockdown


title: Central hindlimb, wild-type-hZRS404G>A, H3K27me3, rep2

first: Evgeny

last: Kvon

address: 836 Health Sciences Road

institute: University of California, Irvine

description: Library name: Sample4

data_processing:
Paired-end reads were aligned to the mm10 reference genome using Bowtie2 with the following parameters: -end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 70.
Samtools, version 1.15.1 was used to generate, sort and index bam files, from which bigwig files were generated using deeptools, version 3.5.1.
Assembly: Wild-type samples = mm10 reference genome Wild-type + reporter samples = A custom mm10 genome (mm10 reference and an extra chromosome for the hZRS transgene reporter). Knock-in + reporter samples = A custom mm10 genome (mm10 with variant mouse ZRS allele replacing the wild type ZRS at chromosome 5 and an extra chrosome for the hZRS transgene reporter)
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: Central hindlimb

extract_protocol:
Hindlimb cells were dissected, dissociated, sorted, and then immobilized onto ConA-magnetic beads. Following the CUT&Tag-direct protocol (version 4), bead-bound cells were incubated with primary and secondary antibodies then Tn5 for transposition. DNA libraries were then barcoded and indexed before being sequenced.
cDNA library construction was performed by Novogene and pair-end sequenced to an average depth of 25M reads per sample.

value: Central hindlimb

tag: strain background

value: FVB

value: wild-type


title: Col-0, Shoot, 1.5mM magnesium sulfate, 10 days, rep3

description:
Library name: Col0_S_rep3
Column name in TPMs_AllSamples.xlsx: Col0_S_Shoot3


title: day1survived_29

description: Library name: Sample29

value: Blood

value: CXCR2+ cells

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

value: Survival group


title: HNRNH2 knockdown, rep1, group B

description: Library name: HNRNPH2-BG293LV06-71B


title: day1survived_28

description: Library name: Sample28


title: Col-0, Shoot, 1.5mM magnesium sulfate, 10 days, rep2

description:
Library name: Col0_S_rep2
Column name in TPMs_AllSamples.xlsx: Col0_S_Shoot2

value: plate-grown shoot

value: Day 10


title: day1survived_27

description: Library name: Sample27


title: Col-0, Shoot, 1.5mM magnesium sulfate, 10 days, rep1

description:
Library name: Col0_S_rep1
Column name in TPMs_AllSamples.xlsx: Col0_S_Shoot1


title: clone2_1

description:
Library name: 366441
SMART-Seq v3

value: cerebral organoid

value: R


title: Retinal Ganglion Cells, 2wks post ONC, scramble shRNA, rep 1

description: Library name: Sample 1

value: retina

value: WT

value: ONC, scramble shRNA AAV2


title: day1survived_26

description: Library name: Sample26


title: shcrm-Hindgut-Nanopore(merged)

description: Library name: sample5

data_processing:
Sequencing data were aligned to Drosophila melanogaster reference genome dm6/mm10 and corresponding transposon sequences via Minimap2 (v 2.17-r941). After mapping, two files, "dm6/mm10 PAF file" and "TE PAF file", were generated. The alignments with mapping quality less than 30 or target sequence length less than 200bp were filtered. Python script was written to process two filtered PAF files to find insertions.
Assembly: dm6 and Drosophila TE consensus sequence for fruitfly; mm10 and repBase sequence for mouse.
Supplementary files format and content: bed files contain TE insertion sites

source_name: Adult  hindgut

extract_protocol:
Genomic DNA from fly samples was extracted using Buffer A (100 mM Tris-HCl pH7.5, 100 mM EDTA, 100 mM NaCl, 0.5% SDS) and Buffer B (28.6% 5 M potassium acetate and 71.4% 6 M lithium chloride) reagents. Genomic DNA from fetal livers was extracted by using lysis buffer (100 mM Tris-HCl pH7.5, 50 mM NaCl, 5 mM EDTA, 0.2% SDS) with Protease K.
Genomic DNA extracted from Drosophila hindguts, ovaries and mouse fetal livers was sent toBenagen for quality control and Nanopore Sequencing.

value: Adult  hindgut


title: clone1_4

description:
Library name: 366440
SMART-Seq v3

data_processing:
Alignment was performed using STAR (v.2.7.9a) on GRCm39 and Gencode vM27 with STAR parameters: --outFilterMultimapNmax 1, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --outFilterScoreMinOverLread 0.22, --outFilterMatchNminOverLread 0.22. Note that we only used the R2 reads from paired end sequencing for this analysis. Reads in exonic and intronic regions (Gencode vM27) were counted using the aligned bam files produced by STAR and summarizeOverlaps (GenomicAlignments v1.40.0, R v4.4.0) with singleEnd=TRUE, mode = "IntersectionNotEmpty", ignore.strand = T, inter.feature = T parameters.
Assembly: GRCm39
Supplementary files format and content: Matrix in csv format with columns corresponding to cells and rows to genes. One file for exonic and one file for intronic reads is given.

extract_protocol:
Organoids with MADM clones induced at D13 were collected at D20 for MADM-CloneSeq. The sample collection steps for MADM-CloneSeq were adapted from previously published protocols (PMID: 38968076). Organoids were kept in cell culture membrane (Millicell) in oxygenated (95% O2, 5% CO2) artificial cerebrospinal fluid (ACSF) containing (in mM): 118 NaCl, 2.5 KCl, 1.25 NaH2PO4, 1.5 MgSO4, 1 CaCl2, 10 Glucose, 3 Myo-inositol, 30 Sucrose, 30 NaHCO3 prepared   with ultra-distilled water; pH=7.4, at 35C, until sample collection. All work surface and equipment were cleaned using RNase away solution (Thermo Fisher Scientific) prior to experiments. Single organoids were transferred to a LNscope 240XY miscroscope (Luigs & Neumann) and superfused with ACSF at a rate of 0.5 ml/min at room temperature. Individual clones were visualized under a 20x objective and by using ImageJ software. To observe red or green fluorescence, light was emitted from a LED light source (CoolLED, Andover, UK). Glass pipettes (B150-86-10, Sutter Instrument, Novato, CA) previously autoclaved, were pulled using a P-1000 pipette puller (Sutter Instrument) to generate pipettes with an opening of around 3-5ym. Before use, each pipette was filled with 3.5yl of pipette solution which consisted of RNase inhibitor (Takara, 1.95%) in RNase-free PBS (Invitrogen) filtered through a 0.22mm filter. Red or green fluorescent neurons were approached with the pipette under positive pressure to avoid tissue contamination of the pipette tip. When contact with cell membrane was made, tight seal formation was achieved under IR/DIC visualization. The complete aspiration of the cell body was immediately performed by applying a gentle and steady suction while monitoring under fluorescence and typically takes 5-10 s. The negative pressure was removed immediately once the target cell was collected and the pipette was carefully withdrawn from the acute slice to avoid contamination. The content of each pipette was directly transferred into individual PCR tubes and kept at -80C until cDNA library preparation.
cDNA libraries for individual MADM-CloneSeq cells were were prepared using Smart-seq3 protocol (PMID 32518404) in 3 batches (96well plates).

value: G

value: SN


title: DNA from ATRT tumor patient INI332

type: genomic

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

hyb_protocol: please refer to GEO:GSE175892

scan_protocol: please refer to GEO:GSE175892

data_processing: RnBeads Bioconductor R package version 2.12.2 was used to process the data from IDAT files. All samples and all probes were kept after quality control. Probe intensities were normalized using the rnb.execute.normalization() function with the “swan” method. Probes outside CpG context, targeting single nucleotide polymorphisms or targeting X and Y chromosomes were all filtered out before subsequent analysis.

label: Cy3 and Cy5

source_name: DNA from ATRT tumor patient

label_protocol: please refer to GEO:GSE175892

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. In order to induce SMARCB1 expression, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline.

extract_protocol: please refer to GEO:GSE175892

treatment_protocol: I2A cells were treated with DMSO as a control for 21 days.

value: tumor

value: Rhabdoid tumor


title: day1survived_25

description: Library name: Sample25

value: Blood


title: DNA from ATRT tumor patient INI323


title: clone1_3

description:
Library name: 366439
SMART-Seq v3

source_name: cerebral organoid


title: shwhite-Ovary-Nanopore

description: Library name: sample4

source_name: Adult ovary

value: Adult ovary

value: sh-white


title: shwhite-Hindgut-Nanopore

description: Library name: sample3


title: Stingfl/fl Cdh5-Cre- mouse liver, biological replicate 2

city: Xi'an

first: Lin

last: Wang

state: Shaanxi

address: West Changle Road 169

institute: Xijing Hospital, Air Force Medical University

description:
Library name: NC-97
Bulk RNA-seq of mouse liver tissue.

data_processing:
Raw reads were quality-controlled using fastp (v0.23.2) and aligned to the mm10 reference genome using HISAT2 (v2.2.1).
Gene expression was quantified as read counts and normalized TPM values using RSEM (v1.3.3).
Differential expression analysis was performed using DESeq2 (v1.38.3).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-delimited text files containing gene expression values (read counts and TPM) for all samples.

source_name: liver

growth_protocol: Mice were maintained under specific pathogen-free conditions. Stingfl/fl Cdh5-Cre+ and Stingfl/fl Cdh5-Cre- mice were generated and maintained on a normal chow diet until 8 weeks of age.

extract_protocol:
Total RNA was extracted from liver tissues using standard RNA extraction protocols.
Strand-specific RNA-seq libraries were constructed using the standard protocol for Illumina sequencing. mRNA was enriched using Oligo(dT) magnetic beads to capture polyA-tailed transcripts, fragmented, and reverse-transcribed into cDNA. After end repair, A-tailing, and adapter ligation, ~200 bp cDNA fragments were selected using AMPure XP beads, PCR-amplified, and sequenced.

treatment_protocol: Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) for 10 weeks to induce MASH.

value: liver

value: liver sinusoidal endothelial cells

value: Stingfl/fl Cdh5-Cre- (littermate control)

value: CDAHFD for 10 weeks


title: clone35_5

first: Florian

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

description:
Library name: 366586
SMART-Seq v3

value: cerebral organoid

value: N


title: CPSF6 knockdown, rep2, group A

description: Library name: CPSF6-BG293LV06-6

value: human embryonic kidney

value: knockdown


title: DZIP3 knockdown, rep1, group A

description: Library name: DZIP3-BG293LV06-59


title: clone1_2

description:
Library name: 366438
SMART-Seq v3

value: R


title: day1survived_23

description: Library name: Sample23

value: CXCR2+ cells

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

value: Survival group


title: shcrm-Ovary-Nanopore

description: Library name: sample2


title: clone1_1

description:
Library name: 366437
SMART-Seq v3

value: SN


title: DNA from meningioangiomatosis tumor patient INI256_MAM

value: tumor

value: Meningioangiomatosis tumor


title: day1survived_22

description: Library name: Sample22

value: Blood


title: shcrm-Hindgut-Nanopore

description: Library name: sample1

value: Adult  hindgut


title: DNA from ATRT tumor patient INI253

value: Rhabdoid tumor


title: day1survived_21

description: Library name: Sample21


title: DNA from ATRT tumor patient INI249


title: D25 organoid from line A1/A2/B1/B2

description:
Library name: 285846
10X Geomics FLEX

data_processing:
Fastq files were analysed using the Cell Ranger pipeline (10xGenomics, version 8.0.0) with Gfp and tdTom sequence added to Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv to generate count matrices
Assembly: mm10
Supplementary files format and content: feature-barcode matrices HDF5

growth_protocol: Organoids: mESCs were plated at high density so that colonies covered approximately half of the well area after 2 days of incubation. Medium was changed 1-2 hours prior to dissociation with StemPro Accutase (Thermo Fisher Scientific) or CTS TrypLE (Thermo Fisher Scientific) for 5 min at 37°C. Cells were counted with an automated cell counter, and were only used if >90% of cells were alive based on Trypan blue staining (Thermo Fisher Scientific). mESCs were centrifuged for 5 min at 200 x g, resuspended in Solution 1, and plated at a density of 3500 cells/microwell in a 24w-Aggrewell plate (Stem Cell Technologies). Solution 1 contained G-MEM (Thermo Fisher Scientific), 10% knockout serum replacement (Thermo Fisher Scientific), 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin and WNT inhibitor (3 µM, IWR1, Sigma). No SMAD inhibitors were used as they were not required to direct cortical differentiation in mouse. Embryoid bodies were generated by day (D) 1, which were then transferred to 10 cm dishes with fresh Solution 1 and 2% growth factor-reduced Matrigel (Corning). On D5, organoids were gently pipetted to remove Matrigel and Solution 2 was added, containing DMEM/F12 (Thermo Fisher Scientific), 1% N2 supplement (Thermo Fisher Scientific), 0.1 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml Penicillin/Streptomycin, 1% chemically defined lipid concentrate (Thermo Fisher Scientific), and heparin (1 mg/ml; Sigma). On D7, organoids were transferred to 6-well plates and placed on an orbital shaker at low speed (50 r.p.m.) to prevent organoid fusion. From D9, organoids were grown in medium containing a 50:50 mix of DMEM/F12 and Neurobasal (Thermo Fisher Scientific), 0.5% N2, 1% B27 (Thermo Fisher Scientific), 0.5 mM non-essential amino acids, 2 mM GlutaMAX, 50 U/ml pen/strep, 1% chemically defined lipid concentrate, and 50 mM 2-mercaptoethanol. Throughout the protocol medium was replaced as necessary every 2-3 days, and orbital shaker speed was increased after D9 (80 r.p.m.). Fused organoids and/or organoids that failed to grow were discarded throughout the procedure. Standard cell culture conditions (37°C with 5% CO2) were applied throughout all procedures. Mice: All animal procedures were approved by the Austrian Federal Ministry of Women, Science and Research in accordance with the Austrian and European Union animal law. Experimental mice were bred and maintained according to regulations approved by institutional animal care and use committee, institutional ethics committee and the guidelines of the preclinical facility (PCF) at ISTA. Mice were bred and maintained in experimental rodent facilities (room temperature 21 ± 1°C [mean ± SEM]; relative humidity 40%–55%; photoperiod 12L:12D). Food (V1126, Ssniff Spezialitaten GmbH, Soest, Germany) and tap water were available ad libitum. Emx1-Cre (PMID: 12151506) and mTmG reporter (PMID: 17868096) mouse lines have been reported previously. All mouse lines were kept in a mixed C57/Bl6 and CD1 genetic background. Mice were used at an age range from 2 – 8 months for general breeding. All efforts were made to minimize the number of animals by following the 3R principles.

extract_protocol:
In order to collect 1-2 million fixed cells per replicate, appropriate numbers of organoids/embryos were pooled for dissociation per replicate. Embryos: A total 40, 30, 10, and 4 brains were pooled from 8, 4, 2, and 2 litters for E10, E13, E16 and P1 timepoints, respectively. Organoids D8: organoids generated from 4-5 Aggrewells, ~800 organoids; D13: ~300 organoids; D20: 80 organoids; D25: 60 organoids). Organoids/Embryos were dissociated following a previously published protocol with some modifications (PMID: 33377108). Organoids/Embryos were first incubated in Earle’s Balanced Salt Solution (EBSS, Thermo Fischer Scientific) containing Papain (Worthington) and DNaseI (Worthington) for a total of 20 (D8, D13) or 25 min at 37°C with gentle shaking at 150 rpm. Organoids/Embryos were gently pipetted 3x with a P1000 tip. After adding Ovomucoid I-Albumin (Worthington), tissue suspension was briefly dissociated mechanically with a pipette. After centrifugation at 1000 rpm for 10 mins at room temperature, the cell pellet was re-suspended and further mechanically dissociated until a homogeneous cell suspension was obtained (up to 20X with a P1000 tip). The cell suspension was passed through a 70 µm filter, and centrifuged again at 1500 rpm for 10 mins at room temperature. Samples were next processed to remove debris prior to fixation. Cell pellets were re-suspended and mixed with cold Debris Removal Solution (Miltenyi Biotec). The mixture was carefully overlaid with cold PBS before centrifugation at 3000 x g for 10 mins at 4°C. The top two layers containing PBS and debris were then aspirated and removed. The remaining cleaned cell suspension was collected by a last centrifugation step at 1000 x g for 10 mins at 4°C. Following manual cell counting with Trypan blue, 1-2 million cells were collected and pelleted. Cells were then fixed with the kit and protocol for Chromium Fixed RNA Profiling (10X Genomics, protocol CG000478, RevD). Pellets were re-suspended in a solution containing 4% formaldehyde and 1X Fix and Perm Buffer, and were stored at 4°C for 22h. Cells were then pelleted and re-suspended in a solution containing 1X Quenching Buffer. Cells were counted again, followed by addition of Enhancer solution and glycerol, after which samples were stored at -80°C until processed.
Library construction performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF-NGS), member of the Vienna BioCenter (VBC), Austria. Single cell libraries were prepared based on the 10X Genomics Flex workflow according to manufacturer’s instructions (CG000527). Four samples were barcoded (BC001 – BC004) and processed together. In order to detect Gfp and tdTom mRNA expression, custom probes were designed according to 10X Genomics Technical Note CG000621 and ordered from Integrated DNA Technologies (IDT) as 4 different oPools, one for each FLEX barcode sequence (BC001 - BC004, custom probe sequence are provided as supplementary file in tab separated text format). Custom probes were added to the mouse probes (PN-100496, 10X Genomics) following manufacturer instructions (CG000621).

tag: barcode

tag: age


title: Transcriptiome of 30 hour Marchantia spores, 2nd biological replicate, lane 5

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

institute: Weizmann Institute of Science

description:
Library name: spores_30h_rep2_lane5
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates

data_processing:
Raw reads were returned as fastq.gz files.Reads passing quality control (Phred +33 quality score >30 assessed with FastQC) were trimmed by removing the first and last 10 bases, and adapters were removed using Trimmomatic (v0.32). Paired-end reads were interleaved. Residual bacterial rRNA sequences were filtered with SortMeRNA (v2.1b). Reads were error-corrected using BayesHammer within SPAdes (v3.10.1) and aligned to the Marchantia polymorpha reference genome JGI (v3.1) and its association gene annotations, using Salmon. Differential gene expression analysis was performed with DESeq2.Gene annotations were obtained from the Marchantia polymorpha reference genome (v3.1) (functional annotation downloaded from https://marchantia.info/download/v31/). Pairwise comparisons were conducted, with an adjusted p-value (padj) <0.05 considered significant. Genes with log2FoldChange <0 were classified as downregulated, >0 as upregulated, and NA indicated no significant change.
Assembly: Marchantia polymorpha Takaragaike-1 (MpTak1_v3.1)
Supplementary files format and content: Dataset1_DESeq2_output_annotated_2021.xlsx; Excel sheet; Shows pairwise differential expression analysis, genome-wide, based on Marchantia polymorpha JGI 3.1 reference genome and its associated gene predictions (v3.1), including Log2FoldChanges and statsitical significance values for per-gene comparisons between samples and conditions.
Supplementary files format and content: Normalized_Read_Counts_2_transcriptome_shared_final.xlsx; Excel sheet; Contains genome-wide read counts across all samples and biological replicates, normalized by sampling depth.

organism: Marchantia polymorpha

source_name: spores

growth_protocol: Wild type Marchantia polymorpha sporangia, derived from a cross of Tak-1 and Tak-2, were collected and surface-sterilized with 1% NaDCC, followed by washing three times with sterile water. The spore suspension was plated and maintained under continuous white light (PFD 50-60 µmol m⁻² s⁻¹) for the indicated durations.

extract_protocol:
For collection of samples, the cellophane with adhered spores was peeled from the medium, flash-frozen in liquid nitrogen, and ground to a fine powder using a mixer mill (RETSCH MM 400) at 30 Hz for 4 minutes. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions, followed by Turbo DNase treatment to remove residual genomic DNA.
mRNA library preparation, RNA sequencing was performed at the Wellcome Trust Centre for Human Genetics, University of Oxford, using an Illumina HiSeq 4000 platform generating 75 bp paired-end reads. Each sample was sequenced in five technical replicates, with replicates distributed across five independent sequencing lanes.

treatment_protocol: Spores were grown under standard white light for 0, 15, or 30 hours after plating.

value: spores

value: spore

value: Takaragaike-1 (Tak-1, male) x Takaragaike-2 (Tak-2, female)

value: 30 hours


title: day1survived_20

description: Library name: Sample20


title: D20 organoid from line A1/A2/B1/B2

city: Klosterneuburg

description:
Library name: 285840
10X Geomics FLEX

value: cerebral organoid


title: DNA from ATRT tumor patient INI247


title: clone35_1

description:
Library name: 366582
SMART-Seq v3

value: G

value: N


title: Transcriptiome of 30 hour Marchantia spores, 2nd biological replicate, lane 3

description:
Library name: spores_30h_rep2_lane3
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates


title: day1survived_19

description: Library name: Sample19

value: CXCR2+ cells


title: DNA from ATRT tumor patient INI245


title: Transcriptiome of 30 hour Marchantia spores, 2nd biological replicate, lane 2

description:
Library name: spores_30h_rep2_lane2
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates


title: D8 organoid from line A1/A2/B1/B2

description:
Library name: 285828
10X Geomics FLEX


title: DNA from ATRT tumor patient INI244


title: Transcriptiome of 30 hour Marchantia spores, 2nd biological replicate, lane 1

description:
Library name: spores_30h_rep2_lane1
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates


title: Pull-down at 72 hours with miR-497-5p-RE miRNA, Rep 3

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

institute: Arizona State University

description: Library name: Pull-down_72h_miR-497-5p-RE_3

data_processing:
The libraries were paired-end sequenced (2 x 150bp) using an Illumina HiSeq.
Reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
The number of mapped reads per transcript were calculated using featureCounts from the Subread package v.1.5.2, and only unique reads that fell within the exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: Processed files are provided as counts files.

growth_protocol: Grown as monolayers in 5% CO2 in RPMI 1640 supplemented with 10% FBS and 1 % PenStrep at 37 degrees C.

extract_protocol:
All steps involved in the biotin-miRNA streptavidin pulldown affinity purification were performed per established protocol 24. At both timepoints, purified miRNA-bound products were obtained from the experimental and control cells. In parallel, at both timepoints, transcripts altered (up- and down-regulated) by miRNA mimics were isolated (i.e. input). Cytoplasmic extract and Streptavidin-Dynabeads (M-280, Invitrogen) were prepared, then incubated for 4 hours. Biotin-miR-mRNA complexes were collected in a magnetic stand. (PMID = 25240884)
For high-throughput RNA-sequencing (RNA-seq), libraries were constructed with Poly(A) selection by GeneWiz© for both the 12h (pulldown and input) and 72h (pulldown and input) products. In the manuscript pulldown is referred to as bound targets, and input is treated as RNA-seq to find differentially expressed genes. (PMID = 25240884)

treatment_protocol: Lipofectamine RNAiMAX was used to Lipofectamine RNAiMAX was used to transfect a custom-made 3’-biotinylated miR-497-5p mimic (experimental) or 3’-biotinylated scrambled, non-targeting miRNA mimic (control) for 12 hours and 72 hours (20 nM, Dharmacon).

tag: cellosaurus accession

tag: time (hours)

tag: method

value: Pull-down

tag: captures

value: mRNA targets of miR-497-5p

tag: method long

value: Biotinylated miRNA target pull-down


title: DNA from ATRT tumor patient INI242

tag: tissue

tag: genotype


title: day1survived_16

description: Library name: Sample16

value: C57B6J WT

value: VSV (New Jersey) intranasal infection

tag: batch

value: Survival group


title: Transcriptiome of 30 hour Marchantia spores, 1st biological replicate, lane 5

description:
Library name: spores_30h_rep1_lane5
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates


title: RNA-seq at 72 hours with miR-497-5p-RE miRNA, Rep 3

description: Library name: RNA-seq_72h_miR-497-5p-RE_3

value: RNA-seq

value: mRNA expression


title: DNA from ATRT tumor patient INI241

value: tumor

value: Rhabdoid tumor


title: day1survived_15

description: Library name: Sample15

value: Blood


title: Transcriptiome of 30 hour Marchantia spores, 1st biological replicate, lane 4

description:
Library name: spores_30h_rep1_lane4
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates

value: spores

value: spore

value: Takaragaike-1 (Tak-1, male) x Takaragaike-2 (Tak-2, female)


title: Pull-down at 72 hours with miR-497-5p-RE miRNA, Rep 2

description: Library name: Pull-down_72h_miR-497-5p-RE_2


title: DNA from ATRT tumor patient INI238


title: Transcriptiome of 30 hour Marchantia spores, 1st biological replicate, lane 3

description:
Library name: spores_30h_rep1_lane3
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates

value: 30 hours


title: RNA-seq at 72 hours with miR-497-5p-RE miRNA, Rep 2

description: Library name: RNA-seq_72h_miR-497-5p-RE_2


title: DNA from ATRT tumor patient INI236


title: day1survived_13

description: Library name: Sample13


title: Transcriptiome of 30 hour Marchantia spores, 1st biological replicate, lane 2

description:
Library name: spores_30h_rep1_lane2
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates


title: Pull-down at 72 hours with miR-497-5p-RE miRNA, Rep 1

description: Library name: Pull-down_72h_miR-497-5p-RE_1


title: DNA from ATRT tumor patient INI231


title: day1survived_12

description: Library name: Sample12


title: Transcriptiome of 30 hour Marchantia spores, 1st biological replicate, lane 1

description:
Library name: spores_30h_rep1_lane1
RNAseq derived from spores of six sporangia 30 hours after their culture on agar plates


title: RNA-seq at 72 hours with miR-497-5p-RE miRNA, Rep 1

description: Library name: RNA-seq_72h_miR-497-5p-RE_1


title: DNA from ATRT tumor patient INI230


title: day1survived_11

description: Library name: Sample11


title: Transcriptiome of 15 hour Marchantia spores, 2nd biological replicate, lane 5

description:
Library name: spores_15h_rep2_lane5
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates

value: 15 hours


title: Pull-down at 72 hours with Control miRNA, Rep 3

description: Library name: Pull-down_72h_Control_3

value: Control


title: DNA from ATRT tumor patient INI171


title: RNA-seq at 72 hours with Control miRNA, Rep 3

description: Library name: RNA-seq_72h_Control_3


title: DNA from ATRT tumor patient INI070


title: day1ICAM1negative_3

description:
Library name: Sample6
Survival group

data_processing:
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads. Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS at 1 day after the infection. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were fixed with DSP solution (1mg/ml in DMSO, filtered through a 20 µm mesh filter (pluriSelect)) at room temperature for 30min to inactivate virus, and the fixation step was stopped by adding 1M tris (pH7.5) for the final concentration of 20mM. Cells were incubated at 4°C for 10 min firstly with purified anti-mouse CD16/32 (1:50, clone 93, Biolegend, 101301), washed, and subsequently with the set of staining antibodies; PerCP/Cyanine5.5 anti-mouse CD45.2 (1:100, clone 104, Biolegend, 109828), APC/Cyanine7 anti-mouse CD11b (1:100, clone M1/70, Biolegend, 101226), PE anti-mouse CD182 (CXCR2) (1:100, clone SA044G4, Biolegend, 149303), APC anti-mouse CD54 (ICAM1) (1:300, clone YN1/1.7.4, Biolegend, 116120). Subsequently, cells were subjected to collected with Fluorescence-activated cell sorting (FACS) using FACS Aria III or IIIu (BD Biosciences). Total RNA was isolated from isolated cells or tissues of mice with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.

treatment_protocol: 8 weeks old C57B6J WT male mice received intranasal vesicular stomatitis virus infection with 1.0 x 10^7 PFU in 50μl PBS under 5% isoflurane anesthesia.

tag: strain

value: CXCR2+ cells

value: WT


title: Pull-down at 72 hours with Control miRNA, Rep 2

description: Library name: Pull-down_72h_Control_2

tag: cell line

value: Pull-down

value: mRNA targets of miR-497-5p

value: Biotinylated miRNA target pull-down


title: I2A cells, DNMT3A-knockout cells, clone 1C10

source_name: I2A cells, DNMT3A-knockout cells

tag: cell type

value: Rhabdoid tumor cells

value: SMARCB1-negative DNMT3A knockout


title: day1ICAM1negative_2

description:
Library name: Sample5
Survival group

tag: treatment

value: VSV (New Jersey) intranasal infection


title: Transcriptiome of 15 hour Marchantia spores, 2nd biological replicate, lane 2

description:
Library name: spores_15h_rep2_lane2
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates


title: RNA-seq at 72 hours with Control miRNA, Rep 2

description: Library name: RNA-seq_72h_Control_2

value: RNA-seq

value: mRNA expression


title: Transcriptiome of 15 hour Marchantia spores, 2nd biological replicate, lane 3

description:
Library name: spores_15h_rep2_lane3
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates


title: I2A cells, DNMT3A-knockout cells, clone 1C1


title: GRB2, HEK293T, IP, replicate 2 eCLIP

description: Library name: GRB2-HEK293T-2 IP

data_processing:
eCLIP data was analyzed using Skipper (Boyle et al., 2023) with default parameters and sample-matched adapter sequences.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing reproducible enriched RBP binding regions identified using Skipper.

growth_protocol: HEK293T cells were cultured in 10cm cell culture dishes for each RBP

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I and complexes were immunoprecipitated with RBP specific or V5-antibody.
eCLIP library construction was performed in accordance with Yeo laboratory standard operating procedures (Blue et al., 2022)

value: human embryonic kidney


title: day1ICAM1negative_1

description:
Library name: Sample4
Survival group

value: Blood


title: day1survived_18

description: Library name: Sample18

data_processing:
Sequences were mapped to the mouse reference genome (mm10) with the use of STAR (v 2.7.10a). Raw read counts of each gene was calculated using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample

extract_protocol:
Approximately 150 µl of blood was collected from the tail artery into a tube containing 100 µl of 50 mM EDTA-2K in PBS. The red blood cells were lysed with ACK lysing buffer (Thermo, A1049201). Cells were incubated at 4°C for 15 min firstly with anti-CXCR2 antibody (1:50, clone SA044G4, BioLegend, 149304) and subsequently with anti-PE microbeads (1:100, Miltenyi Biotec, 130-048-801). Subsequently, cells were subjected to Magnetic Activated Cell Sorting (MACS) (Miltenyi Biotec) and magnetically retained cells were eluted from the MS column and collected by centrifugation for 5 min at 400 x g/4°C. Total RNA was isolated from isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.
Sequencing was carried out on an Illumina NextSeq 2000 platform with paired-end 36 bp reads or on a DNBSEQ-G400RS platform with 100 bp single-end reads. For DNBSEQ-G400RS sequencing, adaptor sequences were converted into the DNBSEQ format using the MGIEasy Universal Library Conversion Kit (App-A) (MGI).

value: C57B6J WT

tag: group

value: Survival group


title: Transcriptiome of 15 hour Marchantia spores, 2nd biological replicate, lane 1

description:
Library name: spores_15h_rep2_lane1
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates

value: spores

value: spore

value: Takaragaike-1 (Tak-1, male) x Takaragaike-2 (Tak-2, female)


title: Pull-down at 72 hours with Control miRNA, Rep 1

description: Library name: Pull-down_72h_Control_1

value: Control

tag: replicate


title: I2A cells, DNMT3A-knockout cells, clone 1B12


title: day1survived_17

description: Library name: Sample17

value: CXCR2+ cells


title: day1ICAM1positive_3

description:
Library name: Sample3
Survival group

value: WT


title: Transcriptiome of 15 hour Marchantia spores, 1st biological replicate, lane 5

description:
Library name: spores_15h_rep1_lane5
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates

value: 15 hours


title: RNA-seq at 72 hours with Control miRNA, Rep 1

description: Library name: RNA-seq_72h_Control_1


title: I2A cells, DNMT3B-knockout cells, clone D11

source_name: I2A cells, DNMT3B-knockout cells

value: SMARCB1-negative DNMT3B knockout


title: day1ICAM1positive_2

description:
Library name: Sample2
Survival group


title: Transcriptiome of 15 hour Marchantia spores, 1st biological replicate, lane 4

description:
Library name: spores_15h_rep1_lane4
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates


title: Pull-down at 12 hours with miR-497-5p-RE miRNA, Rep 3

description: Library name: Pull-down_12h_miR-497-5p-RE_3

value: Pull-down

value: mRNA targets of miR-497-5p

value: Biotinylated miRNA target pull-down


title: I2A cells, DNMT3B-knockout cells, clone E9

value: Rhabdoid tumor cells


title: day1ICAM1positive_1

description:
Library name: Sample1
Survival group

value: VSV (New Jersey) intranasal infection


title: Transcriptiome of 15 hour Marchantia spores, 1st biological replicate, lane 3

description:
Library name: spores_15h_rep1_lane3
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates


title: day1survived_14

description: Library name: Sample14


title: I2A cells, DNMT3B-knockout cells, clone F2


title: RNA-seq at 12 hours with miR-497-5p-RE miRNA, Rep 3

description: Library name: RNA-seq_12h_miR-497-5p-RE_3

value: RNA-seq

value: mRNA expression


title: day1BMdied_6

description:
Library name: Sample12
Survival group

extract_protocol:
Mice anesthetized with 200 µl of combination anesthetic and cells were aspirated with a syringe 27G needle inserted directly from knee into the femur at 1 day after the infection. Total RNA was isolated with the use of RNAiso Plus reagent (Takara).
RNA libraries were prepared using SMART-Seq Stranded Kit (Takara) following manufacturer’s protocols.

value: Blood


title: Transcriptiome of 15 hour Marchantia spores, 1st biological replicate, lane 2

description:
Library name: spores_15h_rep1_lane2
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates


title: Pull-down at 12 hours with miR-497-5p-RE miRNA, Rep 2

description: Library name: Pull-down_12h_miR-497-5p-RE_2


title: I2A cells, SMARCB1-reexpression, day 14, rep5

source_name: I2A cells, SMARCB1-positive, day 14 of reexpression


title: day1BMdied_5

description:
Library name: Sample11
Survival group

source_name: Blood


title: Transcriptiome of 15 hour Marchantia spores, 1st biological replicate, lane 1

description:
Library name: spores_15h_rep1_lane1
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates


title: RNA-seq at 12 hours with miR-497-5p-RE miRNA, Rep 2

description: Library name: RNA-seq_12h_miR-497-5p-RE_2


title: I2A cells, SMARCB1-reexpression, day 14, rep4


title: day1BMdied_4

description:
Library name: Sample10
Survival group


title: Transcriptiome of 0 hour Marchantia spores, 2nd biological replicate, lane 5

description:
Library name: spores_0h_rep2_lane5
RNAseq derived from spores of six sporangia at their collection (time zero)

value: 0 hours


title: Pull-down at 12 hours with miR-497-5p-RE miRNA, Rep 1

description: Library name: Pull-down_12h_miR-497-5p-RE_1


title: I2A cells, SMARCB1-reexpression, day 14, rep3


title: Transcriptiome of 0 hour Marchantia spores, 2nd biological replicate, lane 4

description:
Library name: spores_0h_rep2_lane4
RNAseq derived from spores of six sporangia at their collection (time zero)

value: spores


title: day1BMdied_3

description:
Library name: Sample9
Survival group


title: RNA-seq at 12 hours with miR-497-5p-RE miRNA, Rep 1

description: Library name: RNA-seq_12h_miR-497-5p-RE_1


title: I2A cells, SMARCB1-reexpression, day 14, rep2


title: day1BMdied_2

description:
Library name: Sample8
Survival group


title: Transcriptiome of 0 hour Marchantia spores, 2nd biological replicate, lane 3

description:
Library name: spores_0h_rep2_lane3
RNAseq derived from spores of six sporangia at their collection (time zero)

value: spore


title: I2A cells, SMARCB1-reexpression, day 14, rep1


title: Pull-down at 12 hours with Control miRNA, Rep 3

description: Library name: Pull-down_12h_Control_3


title: day1survived_10

description: Library name: Sample10

value: C57B6J WT

value: Survival group


title: day1BMdied_1

description:
Library name: Sample7
Survival group

value: CXCR2+ cells


title: Transcriptiome of 0 hour Marchantia spores, 2nd biological replicate, lane 2

description:
Library name: spores_0h_rep2_lane2
RNAseq derived from spores of six sporangia at their collection (time zero)

value: Takaragaike-1 (Tak-1, male) x Takaragaike-2 (Tak-2, female)


title: RNA-seq at 12 hours with Control miRNA, Rep 3

description: Library name: RNA-seq_12h_Control_3

value: Control


title: I2A cells, SMARCB1-reexpression, day 10, rep3

source_name: I2A cells, SMARCB1-positive, day 10 of reexpression


title: Transcriptiome of 15 hour Marchantia spores, 2nd biological replicate, lane 4

description:
Library name: spores_15h_rep2_lane4
RNAseq derived from spores of six sporangia 15 hours after their culture on agar plates

value: 15 hours


title: day1BMsurvived_6

description:
Library name: Sample6
Survival group

value: WT


title: Pull-down at 12 hours with Control miRNA, Rep 2

description: Library name: Pull-down_12h_Control_2

value: Pull-down

value: mRNA targets of miR-497-5p


title: I2A cells, SMARCB1-reexpression, day 10, rep2

value: Rhabdoid tumor cells


title: Transcriptiome of 0 hour Marchantia spores, 2nd biological replicate, lane 1

description:
Library name: spores_0h_rep2_lane1
RNAseq derived from spores of six sporangia at their collection (time zero)


title: day1BMsurvived_5

description:
Library name: Sample5
Survival group

value: VSV (New Jersey) intranasal infection


title: day1died_19

description: Library name: Sample55

value: Lethal group


title: RNA-seq at 12 hours with Control miRNA, Rep 2

description: Library name: RNA-seq_12h_Control_2

value: RNA-seq

value: mRNA expression


title: Transcriptiome of 0 hour Marchantia spores, 1st biological replicate, lane 5

description:
Library name: spores_0h_rep1_lane5
RNAseq derived from spores of six sporangia at their collection (time zero)

value: 0 hours