title: HPAFII_GGMSC500_20h_3

city: Stockholm

first: Mehran

last: Ghaderi

state: Huddinge

address: Forskningsgatan 46

department: Clintech

institute: Karolinska Institutet

description: Library name: Sample 12

data_processing:
Transcriptome data were processed and analyzed using the Chipster virtual platform provided by the IT Center for Science (CSC), Finland. Adapter sequences were trimmed, and sequencing read quality was assessed with FastQC.
High-quality paired-end reads (15 to 20 million per sample) were aligned to the human reference genome (GRCh38.95) using the STAR aligner. Aligned reads (BAM files) were subsequently quantified at the gene level using HTSeq.
Differential gene expression analysis was performed with the DESeq2 package from Bioconductor. Normalized count matrices from treated and control groups were combined for the calculation of log₂ fold changes. Genes with an adjusted p-value (padj) ≤ 0.01 and absolute log₂ fold change ≥ 1 were considered significantly differentially expressed.
Assembly: GRCh38.95
Supplementary files format and content: Hierarchical clustering, heatmaps, and dendrograms were generated from raw gene counts normalized via DESeq2. Overrepresentation analysis of differentially expressed genes was performed using ConsensusPathDB, integrating pathways from over 30 publicly available databases.

source_name: HPAF-II

growth_protocol: HPAF-II cell lines maintained in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and incubated at 37 °C in a humidified atmosphere containing 5% CO₂. Antibiotics were not included in the culture medium.

extract_protocol:
Total RNA was extracted from HPAF-IIcell lines using the Maxwell® RSC simplyRNA Cells Kit. cDNA libraries were prepared according to the SMART™-seq2 protocol, which utilizes a template-switching oligonucleotide (TSO_II) for full-length cDNA synthesis.
RNA-seq libraries were prepared using 50 ng of purified cDNA with the Illumina DNA Prep Kit. The protocol included tagmentation, post-tagmentation cleanup, PCR amplification, and pooling of indexed libraries. Final libraries were then normalized to 4 nM. Library denaturation and dilution were performed following the Illumina NextSeq System Denature and Dilute Libraries Guide.

treatment_protocol: GGMSC (250 mM) stock solution was prepared by dissolving GGMSC in sterile distilled water. For RNA sequencing experiments, HPAF-II and HPAF-II cells were treated with 500 µM GGMSC for either 8 or 20 hours. Control cells were cultured under identical conditions without treatment. Each treatment group was performed in three independent biological replicates to ensure experimental consistency.

value: HPAF-II

value: PDAC

value: GGMSC_500 µM


title: HPAFII_GGMSC500_20h_2

status: Public on Oct 03 2025

type: SRA

country: Sweden

description: Library name: Sample 11

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT

tag: treatment

tag: batch


title: CD7p_MLPs_rep4

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.

extract_protocol:
no extraction_cell lysates
Cachiarelli et al. (Cell 162:412, 2015)


title: HPAFII_GGMSC500_20h_1

description: Library name: Sample 10


title: Pdgfbret/+, replicate 3, scRNAseq

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

institute: Lund University

library_source: transcriptomic single cell

data_processing:
The raw reads were processed, mapped, and quantified using Cell Ranger count (v6.1.2) with default settings, with an initial expected cell count of 10,000.
We used DoubletFinder (v2.0.3) to filter out "doublets" assuming a doublet formation rate of 7.5%. pN=0.25 and pK were adjusted for each sample using pN-pK parameter sweeps and meanvariance- normalized bimodality coefficient (BCmvn) using paramSweep_v3.
We used DecontX to filter out barcodes that had more than 25% of reads identified as ambient RNA contamination.
Further quality control was perfored using Seurat (v4.0.3). The seurat (rds) object provided contains only cells that had a total number of transcripts lower than 50,000, number of features larger than 250 and lower than 8000, and percentage of mitochondrial and ribosomal genes lower than 10% and 25%, respectively.  We filtered out mitochondrial and hemoglobin genes, as well as features with less than 20 counts across cells.
Assembly: mm10 modified mouse reference genome that contained the RCAS-PDGFB longest possible sequence following Cell Ranger instructions.
Supplementary files format and content: barcodes.tsv.gz:  Cell Ranger's filtered tab-separated barcodes file
Supplementary files format and content: features.tsv.gz:  Cell Ranger's filtered tab-separated gene IDs file
Supplementary files format and content: matrix.mtx.gz:  Cell Ranger's filtered counts matrix
Supplementary files format and content: Braun_2024_scRNAseq_seurat.rds: seurat object containing all samples including only cells and features that passed filtering criteria and were used in downstream analyses.

molecule: total RNA

organism: Mus musculus

source_name: brain tumor

extract_protocol:
Whole tumors were minced into smaller slices with a scalpel and incubated for 30 min with the supplier’s enzyme mixes, while being heated at 37°C and mechanically grinded in the gentle MACS Octo Dissociater with Heaters (Miltenyi). Samples were resuspended and applied to a 70 μm MACS SmartStrainer (Miltenyi), after which the single cell suspension underwent subsequent steps for debris removal and lysis of erythrocytes. For library preparation, 18,000 cells / 45 μl in 0.04% BSA.
Singlecell 3´ RNA-seq libraries were prepared using 10x Chromium system (v3.1). Samples were run using Read 1 28 cycles, i7 index 5 cycles, i5 index 0 cycles, Read 2 91 cycles on the Illumina NovaSeq 6000 to a depth of 50,000 reads/cell. This was performed in two different batches (time points). The first batch (batch1) included 3 samples, while the second batch (batch2) included 8 samples.

tag: tissue

value: brain tumor

value: Ntv-a, Pdgfbrret/+

value: batch 2


title: CD7p_MLPs_rep3


title: CD7p_MLPs_rep2


title: HPAFII_Control_20h_3

description: Library name: Sample 9

value: control


title: AGO2-L192P_input_rep2

city: Hamburg

first: Jan Broder

last: Engler

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description: Library name: MutN4

data_processing:
OASIS 2.0 miRNA pipline (Rahman et al., 2018)
Assembly: miRBase v21
Supplementary files format and content: miRNA_counts_raw.txt: Tab separated value file of raw miRNA counts
Supplementary files format and content: miRNA_counts_norm.txt: Tab separated value file of normalized miRNA counts

source_name: Primary mouse cortical neurons

extract_protocol:
miRNeasy Micro Kit (Qiagen)
TruSeq Small RNA Library Prep Kit (Illumina)

value: Primary mouse cortical neurons

value: AAV EGFP-AGO2-L192P

tag: sample type

value: input


title: AGO2-L192P_input_rep1

description: Library name: MutN3


title: HPAFII_Control_20h_1

description: Library name: Sample 7


title: Pdgfbret/ret, replicate 4

description:
1159_Retret
Fresh Frozen Spatial transcriptome sequencing

data_processing:
The raw reads were processed, mapped, and quantified using Space Ranger count (v2.0.1) with default settings.
Assembly: mm10 modified mouse reference genome that contained the RCAS-PDGFB longest possible sequence.
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatiall barcodes and the coordinates specifying spots
Supplementary files format and content: Braun_2024_ST_8samples_seurat.rds: the seurat object contains raw counts of all barcodes and processed information associated with the analyses shown in the original publication.
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh frozen tissue preparation was done according to the protocol "Tissue preparation guide" (CG000240; 10x GENOMICS). All steps were performed using the 10x Visium Spatial Gene Expression Slide & Reagent kit. Methanol fixation and immunofluorescence staining were done according to protocol CG000312. The optimal tissue optimization time (4 min) was determined in a time course experiment according to protocol CG000238RevE.
cDNA synthesis and library generation were done according to protocol CG000239RevD. cDNA synthesis was carried out according to the results obtained from qPCR testing with a KAPA FAST SYBR qPCR system (KAPA Biosystems). The amplified cDNA was processed according to protocol, using the SPRIselect Reagent kit (Beckman Coulter).

value: Ntv-a, Pdgfbrret/ret

value: no treatment applied


title: Pdgfbret/+, replicate 2, scRNAseq

value: batch 1


title: Pdgfbret/ret, replicate 1, scRNAseq


title: CD7p_MLPs_rep1


title: HPAFII_Control_20h_2

description: Library name: Sample 8


title: Pdgfbret/+, replicate 1, scRNAseq


title: CD7n_MLPs_rep9


title: med15, 35% fermentation, rep-2

city: Indianapolis

first: David

last: Cooper

state: IN

address: 350 PHSB, 4600 Sunset Ave.

country: USA

institute: Butler University

description: Library name: med15-B

data_processing:
Galaxy platform
Adapter sequences were trimmed from reads using TrimGalore! (Galaxy tool version 0.6.3). Trimmed reads shorter than 50 bp and orphaned reads discarded.
Paired-end reads were mapped to the S288C reference genome (sacCer3) using Bowtie2 (Galaxy tool version 2.3.4.2).
Counts were quantified using featureCounts (Galaxy tool version 1.6.3) to annotated “genes” in the S288C reference general feature format file (version R64-3-1)
Count normalization and differentially expression analysis was done using DESeq2 (Galaxy tool version 2.11.40.2)
Assembly: sacCer3
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

organism: Saccharomyces cerevisiae

source_name: whole yeast cell

growth_protocol: Individual fermentation reactions in 5 mL supplemented white grape juice. Weight loss was monitored, and yeast were pelleted and frozen at the 35% weight loss point (~37 hours for MED15 strains, and 48 hours for med15Δ strains).

extract_protocol:
RNA was extracted using a hot acid phenol protocol. Frozen cell pellets were resuspended in 400 µL TES solution. An equal volume of acid phenol was added to each tube and vortexed. Tubes were incubated in a 65°C water bath for 1 hour with vortexing every 10-12 minutes. Phases were separated by microcentrifugation in the cold for 5 minutes. The aqueous layer was extracted into a new tube. A second round of acid phenol extraction was conducted followed by a chloroform extraction. RNA was precipitated with 300 µL of 4 M LiCl in dry ice for 20 minutes followed by 5 minutes of high-speed centrifugation at 4°C. The pellet was washed with 500 µL ice cold 70% ethanol and dried for 10 minutes at 37°C. RNA pellets were resuspended in DEPC treated water and stored at -20°C. Contaminating genomic DNA was removed using the DNase Max Kit (Qiagen).
RNA sample quality was assessed using an Experion automated electrophoresis system with a HighSens chip (Bio-Rad). cDNA libraries were prepared using the Illumina Stranded mRNA Prep protocol (Illumina). A total of 150-200 ng of total RNA per sample and 13 cycles of amplification were used. The Illumina Dual Index Adapters set A (Integrated DNA Technologies) was ligated to the cDNA. cDNA libraries were quantified using fluorometry with PicoGreen. The integrity of the cDNA libraries was determined using an Agilent BioAnalyzer DNA chip. A KAPA qPCR was used to get precise quantification prior to loading samples for sequencing. The pooled libraries were run with the 2x150 bp protocol on one lane of an SP flow cell in an Illumina NovaSeq.

value: whole yeast cell

tag: strain

value: med15 deletion


title: HPAFII_GGMSC500_8h_3

description: Library name: Sample 6

value: 8 h


title: Pdgfbret/+, replicate 5, scRNAseq


title: Pdgfbret/+, replicate 4

description:
1070_Retpos
Fresh Frozen Spatial transcriptome sequencing


title: med15, 35% fermentation, rep-1

description: Library name: med15-A


title: CD7n_MLPs_rep8


title: CD7n_MLPs_rep7


title: Pdgfbret/ret, replicate 3

description:
1141_Retret
Fresh Frozen Spatial transcriptome sequencing


title: AGO2-L192P_IP_rep1

description: Library name: MutP1

value: EGFP-IP


title: AGO2-L192P_input_rep3

description: Library name: MutN5


title: CD7n_MLPs_rep6


title: HPAFII_GGMSC500_8h_1

description: Library name: Sample 4

value: HPAF-II

value: PDAC


title: Pdgfbret/ret, replicate 2

description:
1064_Retret
Fresh Frozen Spatial transcriptome sequencing


title: CD7n_MLPs_rep5


title: Pdgfbret/+, replicate 3

description:
1047_Retpos
Fresh Frozen Spatial transcriptome sequencing


title: CD7n_MLPs_rep4


title: Lab, 35% fermentation, rep-1

description: Library name: Lab-A

value: WT


title: WY23, 35% fermentation, rep-2

description: Library name: WY23-B

value: WY23 MED15


title: Pdgfbret/+, replicate 2

description:
1046_Retpos
Fresh Frozen Spatial transcriptome sequencing

value: brain tumor

value: Ntv-a, Pdgfbrret/+


title: HPAFII_Control_8h_3

description: Library name: Sample 3

value: control


title: HPAFII_Control_8h_1

description: Library name: Sample 1


title: WY23, 35% fermentation, rep-1

description: Library name: WY23-A


title: Pdgfbret/ret, replicate 1

description:
941_Retret
Fresh Frozen Spatial transcriptome sequencing


title: CD7n_MLPs_rep2


title: CAPAN2_GGMSC500_III_20h.tsv

description: Library name: Sample 12

data_processing:
Transcriptome data were processed and analyzed using the Chipster virtual platform provided by the IT Center for Science (CSC), Finland. Adapter sequences were trimmed, and sequencing read quality was assessed with FastQC.
High-quality paired-end reads (15 to 20 million per sample) were aligned to the human reference genome (GRCh38.95) using the STAR aligner. Aligned reads (BAM files) were subsequently quantified at the gene level using HTSeq.
Differential gene expression analysis was performed with the DESeq2 package from Bioconductor. Normalized count matrices from treated and control groups were combined for the calculation of log₂ fold changes. Genes with an adjusted p-value (padj) ≤ 0.01 and absolute log₂ fold change ≥ 1 were considered significantly differentially expressed.
fastx to trim reads
STAR alignment for paired-end reads
Assembly: GRCh38.95
Supplementary files format and content: Hierarchical clustering, heatmaps, and dendrograms were generated from raw gene counts normalized via DESeq2. Overrepresentation analysis of differentially expressed genes was performed using ConsensusPathDB, integrating pathways from over 30 publicly available databases.
Supplementary files format and content: TSV (txt)

growth_protocol: CAPAN-2 cell lines maintained in Eagle’s Minimum Essential Medium (EMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and incubated at 37 °C in a humidified atmosphere containing 5% CO₂. Antibiotics were not included in the culture medium.

extract_protocol:
Total RNA was extracted from CAPAN-2cell lines using the Maxwell® RSC simplyRNA Cells Kit. cDNA libraries were prepared according to the SMART™-seq2 protocol, which utilizes a template-switching oligonucleotide (TSO_II) for full-length cDNA synthesis.
RNA-seq libraries were prepared using 50 ng of purified cDNA with the Illumina DNA Prep Kit. The protocol included tagmentation, post-tagmentation cleanup, PCR amplification, and pooling of indexed libraries. Final libraries were then normalized to 4 nM. Library denaturation and dilution were performed following the Illumina NextSeq System Denature and Dilute Libraries Guide. SMARTseq_V2.

treatment_protocol: GGMSC (250 mM) stock solution was prepared by dissolving GGMSC in sterile distilled water. For RNA sequencing experiments, CAPAN-2 and HPAF-II cells were treated with 500 µM GGMSC for either 8 or 20 hours. Control cells were cultured under identical conditions without treatment. Each treatment group was performed in three independent biological replicates to ensure experimental consistency.

value: GGMSC_500 µM


title: HPAFII_Control_8h_2

description: Library name: Sample 2


title: CD7n_MLPs_rep3


title: Pdgfbret/+, replicate 1

description:
937_Retpos
Fresh Frozen Spatial transcriptome sequencing


title: WY15, 35% fermentation, rep-2

description: Library name: WY15-B

value: WY15 MED15


title: RNASeq-dd-rep2

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

country: China

institute: College of Life Science,Northeast Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Fragments per kilobase of exon per million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: mouse embryonic stem cells (mESCs)

extract_protocol:
We transferred the stem cells to the lysis solution for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryonic stem cells (mESCs)

value: treated with dd-linc1393


title: WY15, 35% fermentation, rep-1

description: Library name: WY15-A


title: Lab, 35% fermentation, rep-2

description: Library name: Lab-B


title: 117int_CD7p_MPPs_rep9


title: RNASeq-dd-rep1


title: CAPAN2_GGMSC500_I_20h.tsv

description: Library name: Sample 10


title: CAPAN2_GGMSC500_II_20h.tsv

description: Library name: Sample 11


title: HPAFII_GGMSC500_8h_2

description: Library name: Sample 5


title: 117int_CD7p_MPPs_rep8


title: CAPAN2_Control_III_20h.tsv

description: Library name: Sample 9


title: RNASeq-sd-rep2

value: treated with sd-linc1393


title: Cortex_G733R_rep5

description: Library name: G733R_5

data_processing:
Alignment with STAR (v2.7.9a)
Counting with featureCounts (v1.5.1)
Analysis with DESeq2 (v1.40.2)
Assembly: ensemble.mouse.GRCm39r104
Supplementary files format and content: RNA_counts_raw.txt: Tab separated value file of raw RNA counts
Supplementary files format and content: RNA_counts_norm.txt: Tab separated value file of normalized RNA counts

source_name: Cerebral cortex

extract_protocol:
RNeasy microkit (Qiagen)
Illumina Stranded mRNA Prep Kit

value: Cerebral cortex


title: RNASeq-sd-rep1


title: WY7, 35% fermentation, rep-1

description: Library name: WY7-A

value: whole yeast cell

value: WY7 MED15


title: CAPAN2_Control_II_20h.tsv

description: Library name: Sample 8


title: 117int_CD7p_MPPs_rep7


title: 117int_CD7p_MPPs_rep6


title: CAPAN2_Control_I_20h.tsv

description: Library name: Sample 7


title: Cortex_G733R_rep4

description: Library name: G733R_4


title: RNASeq-sh-rep1

value: treated with sh-linc1393


title: 117int_CD7p_MPPs_rep5


title: Cortex_G733R_rep3

description: Library name: G733R_3


title: RNASeq-sh-rep2


title: CD7n_MLPs_rep1


title: WY7, 35% fermentation, rep-2

description: Library name: WY7-B


title: 117int_CD7p_MPPs_rep4


title: CAPAN2_GGMSC500_III_8h.tsv

description: Library name: Sample 6

value: 8 h


title: CAPAN2_GGMSC500_II_8h.tsv

description: Library name: Sample 5


title: Cortex_G733R_rep2

description: Library name: G733R_2


title: RNASeq-control-rep2

value: untreated


title: Cortex_G733R_rep1

description: Library name: G733R_1


title: RNASeq-control-rep1


title: 117int_CD7p_MPPs_rep3


title: murine TCF3::HLF B-ALL cells_Rep3

city: Noda City

first: Aisa

last: Suzuki

state: Chiba

address: Yamasaki 2669

country: Japan

institute: Tokyo University of Science

description:
Library name: Sample 9
Column name in mB-ALL_FPKM_assembl.txt: HLF_Rep3

data_processing:
Sequence reads were processed and analyzed using the Galaxy platform (https://usegalaxy.org).
Quality control was performed using FastQC (Galaxy v0.72), and low-quality reads were filtered using Trimmomatic (Galaxy v0.36.5) with default parameters. Reads were aligned to the reference genome (NCBI build 37, mm9) using HISAT2 (Galaxy v2.1.0).
The alignments were assembled and quantified using StringTie (Galaxy v1.3.4), and differentially expressed genes (DEGs) were identified using DESeq2 (Galaxy v2.11.40.2) with a false discovery rate (FDR) < 0.05 as the threshold for significance. Identified DEGs were further analyzed and visualized using iDep (version 0.96).
Assembly: mm9 or GRCh38
Supplementary files format and content: txt files include FPKM values for each sample

source_name: Bone marrow

growth_protocol: YCUB2 cells were maintained in RPMI supplemented with 10% fatal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Poly(A)+ mRNA from total RNA of one million sorted pro-B cells of WT, TCF3::PBX1 positive-ALL and TCF3::HLF positive-ALL mice or IL1B-sufficient and deficient YCUB2 cells was isolated by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The library was then prepared by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

value: Bone marrow

value: Bone Marrow Pro-B cells


title: Cortex_WT_rep5

description: Library name: WT_5

value: WT


title: CAPAN2_GGMSC500_I_8h.tsv

description: Library name: Sample 4

value: PDAC


title: CAPAN2_Control_III_8h.tsv

description: Library name: Sample 3


title: 117int_CD7p_MPPs_rep2


title: murine TCF3::HLF B-ALL cells_Rep2

description:
Library name: Sample 8
Column name in mB-ALL_FPKM_assembl.txt: HLF_Rep2


title: 117int_CD7n_MPPs_rep9


title: 117int_CD7n_MPPs_rep8


title: Cortex_WT_rep2

description: Library name: WT_2


title: CAPAN2_Control_I_8h.tsv

description: Library name: Sample 1


title: Cortex_WT_rep3

description: Library name: WT_3


title: Cortex_WT_rep1

description: Library name: WT_1


title: murine TCF3::PBX1 B-ALL cells_Rep2

description:
Library name: Sample 5
Column name in mB-ALL_FPKM_assembl.txt: PBX1_Rep2


title: murine TCF3::PBX1 B-ALL cells_Rep3

description:
Library name: Sample 6
Column name in mB-ALL_FPKM_assembl.txt: PBX1_Rep3


title: 117int_CD7n_MPPs_rep7


title: CAPAN2_Control_II_8h.tsv

description: Library name: Sample 2


title: 117int_CD7n_MPPs_rep4


title: SCI_48h_Group_4

city: Frankfurt

first: Jason-Alexander

last: Hörauf

state: Hesse

address: Theodor-Stern-Kai 7

department: Trauma Surgery and Orthopedics

institute: University Hospital Frankfurt

description:
Library name: SAMPLE14
Plasma from SCI patient, timepoint 48h, replicate 4

data_processing:
Adapter and quality trimming were performed using Cutadapt. Unprocessed sequencing reads underwent adapter removal and low-quality trimming.
Unprocessed sequencing reads were trimmed to remove adapters and low-quality bases using Cutadapt. Deduplication was performed based on unique molecular identifiers using in-house scripts to ensure the accuracy of the data.
Quality checks were performed with FastQC.
Assembly: ENSEMBL - GRCh38
Supplementary files format and content: Processed data is provided in a TSV file, containing raw counts across all samples.

source_name: plasma

extract_protocol:
miRNA was extracted from 200 µL of plasma (Healthy_Control_Group, n=5; SCI_ER_Group, n=5; SCI_48h_Group, n=5) using miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany).
Small RNA libraries were prepared by GenXPro GmbH (Frankfurt, Germany). Sequencing was conducted on an Illumina NextSeq500 platform with 1x75 base pairs.

value: plasma


title: SCI_48h_Group_2

description:
Library name: SAMPLE12
Plasma from SCI patient, timepoint 48h, replicate 2


title: 117int_CD7p_MPPs_rep1


title: murine TCF3::HLF B-ALL cells_Rep1

description:
Library name: Sample 7
Column name in mB-ALL_FPKM_assembl.txt: HLF_Rep1


title: SCI_48h_Group_3

description:
Library name: SAMPLE13
Plasma from SCI patient, timepoint 48h, replicate 3


title: Wildtype S. pombe cells treated with 3 mM diamide for 60 minutes.

city: Sevilla

first: Antonio

middle: J

last: Perez-Pulido

state: Sevilla

address: Ctra/ Utrera, km.1

department: Genetics

country: Spain

institute: University Pablo de Olavide

description: Library name: D60

data_processing:
Read assembly was performed using STAR 2.7.10a
The final count matrix was performed with htseq-count from package HTSeq 2.0.1.
Assembly: Mapping was performed on the S. pombe genome version ASM294v2.48 using SAMtools 1.3
Supplementary files format and content: xlsx file has all the comparison vs controls, with log2FC and p-values
Supplementary files format and content: txt files have counts for each sample

organism: Schizosaccharomyces pombe

source_name: Whole cell

growth_protocol: 200 mL cultures grown in agitation at 30ºC, then incubated under the desired conditions.

extract_protocol:
Cells were pelleted and ruptured using a precooled mortar with liquid nitrogen. After cell lysis, debris was recovered and snap-frozen in liquid nitrogen. RNAase-free water was then added to the pellets and RNA was extracted using the RNAeasy kit (74104; Qiagen). Final RNA concentration was adjusted to 5 ng and sent to BGI for sequencing.
Library construction was performed by BGI using the library type DNBSEQ Eukaryotic Strand-specific mRNA library

treatment_protocol: Untreated cultures [C-]; cultures treated with 75 mM HU for 60 minutes [HU60] and for 150 minutes [HU150]; and cultures treated with 3 mM DIA for 30 minutes [DIA30] and for 60 minutes [DIA60].

value: Whole cell

value: ascomycete fungi

value: wildtype

value: 3 mM DIA for 60 min


title: murine TCF3::PBX1 B-ALL cells_Rep1

description:
Library name: Sample 4
Column name in mB-ALL_FPKM_assembl.txt: PBX1_Rep1


title: SCI_48h_Group_1

description:
Library name: SAMPLE11
Plasma from SCI patient, timepoint 48h, replicate 1


title: SCI_48h_Group_5

description:
Library name: SAMPLE15
Plasma from SCI patient, timepoint 48h, replicate 5


title: SCI_ER_Group_5

description:
Library name: SAMPLE10
Plasma from SCI patient, timepoint ER, replicate 5


title: 117int_CD7n_MPPs_rep5


title: Wildtype S. pombe cells treated with 3 mM diamide for 30 minutes.

description: Library name: D30

value: 3 mM DIA for 30 min


title: WT mouse Pro-B cells_Rep1

description:
Library name: Sample 1
Column name in mB-ALL_FPKM_assembl.txt: WT_Rep1


title: WT mouse Pro-B cells_Rep2

description:
Library name: Sample 2
Column name in mB-ALL_FPKM_assembl.txt: WT_Rep2


title: Cortex_WT_rep4

description: Library name: WT_4


title: Wildtype S. pombe cells treated with 75 mM hydroxyurea for 150 minutes.

description: Library name: HU150

value: 75 mM HU for 150 min


title: 117int_CD7n_MPPs_rep6


title: WT mouse Pro-B cells_Rep3

description:
Library name: Sample 3
Column name in mB-ALL_FPKM_assembl.txt: WT_Rep3


title: Wildtype S. pombe cells treated with 75 mM hydroxyurea for 60 minutes.

description: Library name: HU60

value: 75 mM HU for 60 min


title: 117int_CD7n_MPPs_rep3


title: Magnetized water treated tomato sample from full ripening of berries phase (biol rep 3)

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

data_processing:
The quality control (QC) was done for analyse the raw FASTQ files with FastQC v0.12.1 (https://github.com/s-andrews/FastQC). After the QC, paired-end FASTQ files were trimmed with TrimGalore v0.6.10 (https://github.com/FelixKrueger/TrimGalore). From the 5′ end of the reads, 10 bp were removed because to avoid sequence biases caused by oligo(dT) and random hexamer primers (Hansen et al. 2010). The STAR v2.7.10b (https://github.com/alexdobin/STAR) RNA-seq aligner was used to align trimmed reads to the S. lycopersicum (SL3.0: https://plants.ensembl.org/Solanum_lycopersicum/Info/Index) reference genome (Sato et al. 2012). STAR script identified known splice sites from the GFF annotation file. The aligned reads in BAM files were analysed with SeqMonk v1.48.1 (https://github.com/s-andrews/SeqMonk). The statistically differentially expressed genes (DEGs) were identified with edgeR (Empirical Analysis of Digital Gene Expression Data in R; Robinson et al. 2010; McCarthy et al. 2012; p < 0.05 with multiple testing correction) and DESeq2 (differential gene expression analysis based on the negative binominal distribution; Love et al. 2014; p < 0.05 with multiple testing correction) in R v4.2.3, and Intensity Difference Filter (p < 0.05 ) in SeqMonk with Benjamini and Hochberg multiple testing correction based on the raw counts of reads. The intersection between three (edgeR, DESeq2 and Intensity Difference Filter) lists giving high confidence for the DEGs, which we used for the analysis.
Assembly: NCBI SL3.1 Solanum lycopersicum genome (GCA_000188115.4)
Supplementary files format and content: Raw read counts from SeqMonk in txt file

organism: Solanum lycopersicum

source_name: leaf and stem

growth_protocol: 200 tomato seeds were sown individually in Jiffy peat discs, one half of which was pre-soaked with normal tap water and the other half with magnetized tap water. Four-four Jiffy discs were placed into one Veg-box, and all closed Vegboxes were placed into climate chamber (24 °C, photoperiod of 16/8 h day/night) and were cultivated there for four weeks. After four weeks each seedlings were plotted into pots of 10 cm in diameter. The soil in pots consisted of a 1:1: 1 mixture of perlite: sand: forest soil.

extract_protocol:
Total RNA was isolated from each wheat sample (control and ultrasound) in three biological replicates using the Direct-zol™ kit (Zymo Research) and TRIzol reagent according to the manufacturer's methodology.
After purifying total RNA, three quality control (QC) methods were used: (1) preliminary quantification with an Implen N50 spectrophotometer (Implen); (2) agarose gel electrophoresis to assess RNA degradation and potential contamination; and (3) Agilent Bioanalyzer 2100 system (Agilent). Novogene, a genome sequencing company, performed mRNA capturing, cDNA library preparation, and sequencing after the three-step QC. mRNA is produced using the company's methodology (rRNA-depleted RNA-seq). The oligo(dT) beads were used to enrich mRNA from the two wheat samples. Plant Ribo-Zero rRNA removal kit (Illumina) was used to remove rRNA according to the manufacturer's procedure. For mRNA-seq library preparation from wheat samples, the Illumina TruSeq Stranded mRNA kit (Illumina) was used. To quantify and optimize library concentration, Qubit 2.0 fluorometric quantitation (Thermo Fischer Scientific), Agilent Bioanalyzer 2100 (Agilent), and AriaMX qPCR (Agilent) were used.

treatment_protocol: Magnetized water was produced from normal tap water using the internationally patented ND Water magnetic device (Patent No: PCT/HU2019/050020). The maximum water flow in the static magnetic device was 4,800 l h-1, and the intensity of MF was 260 mT. Pots were placed into a cultivation room and were watered twice a week, as before, with either normal water or magnetized water, until harvesting of ripe fruits.

tag: cultivar

value: MicroTom

value: leaf and stem

value: Magnetized water treatment

tag: sample collection_time

value: full ripening of berries


title: Control untreated wildtype S. pombe cells

description: Library name: C


title: 117int_CD7n_MPPs_rep2


title: SCI_ER_Group_4

description:
Library name: SAMPLE9
Plasma from SCI patient, timepoint ER, replicate 4


title: 117int_CD7n_MPPs_rep1


title: Magnetized water treated tomato sample from full ripening of berries phase (biol rep 1)


title: Magnetized water treated tomato sample from full ripening of berries phase (biol rep 2)


title: 2023_Xenium_Breast_nTMA

type: RNA

city: Cambridge

first: Samouil

middle: L

last: Farhi

state: MA

address: 75 Ames St

department: Spatial Technology Platform

institute: Broad Institute of MIT and Harvard

description: A normal TMA of 45 cores 1.2 mm in diameter representing a broad range of normal tissues. Samples were sourced from the same patient in either duplicate or triplicate. This TMA was chosen for the breadth of tissue lineages included and the relatively large core size.

hyb_protocol: 10x Xenium samples were processed in three batches according to manufacturer protocols “Probe Hybridization, Ligation & Amplification, User Guide CG0000582” and “Decoding & Imaging, User Guide CG000584”. Samples were stained utilizing 10x’s predesigned Human Breast (10x, PN 1000463), Human Multi-Tissue and Cancer (10x, PN 1000626), and Human Lung panels (10x, PN 1000601), as they became available from the manufacturer. Slides were stained with a Xenium imaging kit according to manufacturer instructions (10x, PN 1000460). Briefly, padlock probes were incubated overnight before rolling circle amplification and native protein autofluorescence was reduced with a chemical autofluorescence quencher. Slides were processed on a 10 Xenium Analyzer, with ROIs selected to cover the entire TMA region. Data was processed on premises through the standard 10x workflow to generate cell by gene and transcript by location matrices. The 10x multimodal segmentation kit and protocol was used for 2024 but not for 2023 data acquisition.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Data was processed through the standard 10x workflow to generate cell by gene and transcript by location matrices. After data acquisition, the resulting outputs were uploaded to a Google bucket associated with a terra.bio Workspace for distribution and follow on analysis.To facilitate standardized data formatting and subsequent analytical processes, we built a data ingestion pipeline with the following objectives: a) to grab cell-level and transcript-level data from diverse platforms and normalize the data structure; b) to tag each cell and transcript with essential metadata including tissue type, tumor status, PD-L1 status, among others to transform the data into various formats tailored to the requirements of particularized analyses. Specifically, to tag the data, core centers in the TMA were manually identified using DAPI images (Xenium) or cell metadata that contains global coordinates (MERSCOPE and CosMx) using QGIS(version:3.16.10-Hannover). Cells or transcripts within a specified radius were then labeled with core metadata via spatial joining (implemented by GeoPandas, version:0.13.0). In instances where cores are in close proximity or when a uniform radius cannot be applied effectively, we manually generated the core boundary masks.
*_analysis_summary.html: Standard Xenium output analysis sumamry.
*_cell_boundaries.parquet: Standard Xenium output cell boundaries.
*_gene_panel.json: Standard Xenium output gene panel.
*_morphology.ome.tif: Standard Xenium output morphology.ome.tif.
*_transcripts.parquet: Standard Xenium output transcirpts.parquet

source_name: A normal tissue TMA (nTMA) contained forty-five 1.2 mm diameter cores spanning sixteen normal tissue types isolated with each tissue type coming from one patient and represented in 2-3 cores.

growth_protocol: Three TMAs were constructed using FFPE clinical discards at Brigham and Women’s Hospital Pathology Core and were acquired with a waiver of consent for non-sequencing based readouts under IRB 2014P001026

treatment_protocol: Sequential sections were prepared according to manufacturer instructions (“Tissue Preparation Guide Demonstrated Protocol CG000578” for Xenium) at the Brigham and Women’s Hospital Pathology Core. Prior to collecting samples, ~50 µm of each TMA were faced off to reach deeper into the sample where RNA integrity was likely higher. 5 µm sequential sections were then collected, floated in a 37˚C water bath, and adhered to Xenium slides (10x, PN 1000460). TMAs were sliced as close to the center of the active area as possible for each platform.  Samples were baked at 42˚C for 3 hours for Xenium. Sections were stored in a desiccator at room temperature.

value: normal tissue

tag: gene panel

value: Breast panel

tag: year


title: SCI_ER_Group_2

description:
Library name: SAMPLE7
Plasma from SCI patient, timepoint ER, replicate 2


title: Magnetized water treated tomato sapmle from beginning of berry formation phase (biol rep 3)

value: begenning of berry formation


title: SCI_ER_Group_3

description:
Library name: SAMPLE8
Plasma from SCI patient, timepoint ER, replicate 3


title: 117hi_CD7p_MPPs_rep3


title: 117hi_CD7p_MPPs_rep4


title: Healthy_Control_Group_5

description:
Library name: SAMPLE5
Plasma from healthy control, replicate 5


title: Magnetized water treated tomato sapmle from beginning of berry formation phase (biol rep 2)


title: SCI_ER_Group_1

description:
Library name: SAMPLE6
Plasma from SCI patient, timepoint ER, replicate 1


title: Magnetized water treated tomato sapmle from beginning of berry formation phase (biol rep 1)


title: Healthy_Control_Group_4

description:
Library name: SAMPLE4
Plasma from healthy control, replicate 4


title: 2023_Xenium_Lung_tTMA1

description: A tumor TMA of 170 cores, 0.6 mm in diameter, including a variety of cancer samples and healthy lymphoid tissue as a positive staining control. The TMA samples were selected from samples previously characterized by ImmunoProfile and were selected to encompass both high and low levels of the biomarkers in the ImmunoProfile panel [CD8, PD-1, PD-L1, Foxp3, tumor marker (Cytokeratin, Sox10, or PAX8)]. Annotations were performed by KF and SR based on H&E and immunofluorescence staining. Cores included both tumor and healthy control annotation, though for the purpose of this study, all were combined under their tumor label. Tumors were also chosen to be a mixture of PD-L1 high and PD-L1 low. This TMA had previously been studied by both H&E, and several highly multiplexed immunostaining approaches, and was known to be of high morphological integrity.

source_name: Tumor TMA 1 (tTMA1) consisted of one hundred and seventy 0.6 mm diameter cores (i.e. sampled regions) from seven different cancer types, with 3-6 patients per cancer type, and 3-6 cores per patient.

value: tumor

value: Lung panel


title: 2023_Xenium_Multitissue_tTMA1

value: Multitissue panel


title: 2023_Xenium_Breast_tTMA1


title: Magnetized water treated tomato sample from blooming phase (biol rep 3)

source_name: leaf, stem and flower

value: leaf, stem and flower

value: blooming


title: Healthy_Control_Group_3

description:
Library name: SAMPLE3
Plasma from healthy control, replicate 3

value: plasma


title: 2024_Xenium_Breast_tTMA2

description: A tumor TMA of 48 cores, 1.2 mm in diameter, including a variety of cancer. This TMA was chosen for the breadth of tissue lineages included and the relatively large core size.

source_name: Tumor TMA 2 (tTMA2) consisted of forty-eight 1.2 mm diameter cores from nineteen different cancer types, with each tissue type coming from one or two patients and represented in 2-3 cores.


title: 117hi_CD7n_MPPs_rep8


title: Healthy_Control_Group_2

description:
Library name: SAMPLE2
Plasma from healthy control, replicate 2


title: 2023_Xenium_Lung_nTMA


title: 2024_Xenium_Breast_tTMA1


title: Magnetized water treated tomato sample from blooming phase (biol rep 1)


title: 117hi_CD7n_MPPs_rep9


title: 117hi_CD7p_MPPs_rep2


title: 117hi_CD7n_MPPs_rep7


title: 117hi_CD7n_MPPs_rep6


title: SU016WT-24h-S4

city: Berkeley

first: Shivani

last: Upadhyaya

address: Koshland Hall

institute: University of California Berkeley

description: Library name: HWCNH

data_processing:
The raw read fastq files were realigned to the updated genome annotation file published in (Cz.v.5.3.annotations.gff3, (7)). For further analysis, a decoy aware transcriptome index was generated with the reference genome v5.3 using the salmon-index generator tool. Reads were quantified from fastq files using the salmon pseudoalignment tool (v1.10.2) and the GC bias of the genome was incorporated by passing the -gcBias flag in salmon. The transcripts per million counts obtained from salmon were then used for differential expression analysis using the DESeq2 package (v1.46.0) in R.
Assembly: Phytozome
Supplementary files format and content: txt file with tpm counts

organism: Chromochloris zofingiensis

source_name: cell pellet

extract_protocol:
For RNA extraction, cells were collected at different time points by centrifugation (3200 g, 5 min at 4oC) and frozen in liquid nitrogen. RNA extraction and purification was performed as previously described with certain modifications (6). Briefly, 50 mL culture was pelleted via centrifugation (3,200 g, 5 min, 4°C) and the pellet was flash frozen in liquid nitrogen followed by fragmentation with a spatula on dry ice. Cells are then suspended in cold ethanol, transferred to Lysing Matrix D tubes, homogenized using the MP Biomedicals FastPrep-24TM 5G homogenizer (60 s, 6.5 m/s, 3 cycles), and lysed in fresh buffer containing SDS/proteinase K. The lysate is clarified by centrifugation, mixed with TRIzol (Thermo Scientific) and centrifuged to separate phases; the aqueous phase is combined with ethanol and loaded onto miRNeasy columns (Qiagen) under vacuum. After on-column DNase digestion (15 min, 30°C) RNA was eluted in water, precipitated with sodium acetate and ice-cold ethanol, incubated (−20°C, 30 min), and pelleted by centrifugation. The RNA pellet is washed with 70% ethanol, air-dried, and resuspended in RNase-free water. Finally, RNA quality is assessed via NanoDropTM (Thermo Scientific) spectrophotometry and a 2100 Bioanalyzer (Agilent) (RIN > 8, distinct 18S/28S peaks).
Around 3 µg RNA was submitted to Joint Genome Institute in NovoSeq S4 plates. Further steps involved creation of polyA selection-based cDNA library for 2X151 paired end read sequencing using Illumina NovoSeq. Following quality trimming of reads using the in-house JGI program BBDUK, samples had an average rRNA contamination of 0.3% and a genome mapping rate of 99.57%.

value: cell pellet

value: unicellular eukaryotic

value: WT


title: 2023_Xenium_Multitissue_nTMA


title: SU016WT-24h-S3

description: Library name: HWCNG


title: Healthy_Control_Group_1

description:
Library name: SAMPLE1
Plasma from healthy control, replicate 1


title: 117hi_CD7p_MPPs_rep1


title: LSK_H17_S5

city: New Haven

first: Shangqin

last: Guo

state: CT

address: 10 Amistad Street

department: Department of Cell Biology

institute: Yale University

description: Library name: H17_S5

library_source: genomic

data_processing:
Adapter sequences were removed with Trim Galore (http://bioinformatics.babraham.ac.uk./projects/trim_galore)
Sequencing reads were aligned to mouse genome (mm10) with Bowtie2
Reads were filtered, sorted and mitochondrial reads were removed with Samtools
Duplicates were removed with Picard (http://broadinstitute.github.io/picard)
Sorted .bam files were converted to .bed files with Bedtools
Coverage tracks (bigWig format) were generated with bamCoverage from deepTools (version 2.5.7)
Assembly: mm10
Supplementary files format and content: bigwig (.bw) files showing gene accessibility

molecule: genomic DNA

extract_protocol:
LSK cells were sorted from XwtXwt mice and XiH1.0-GFPXiH1.0-GFP mice treated with Dox water for 3 weeks
ATAC-seq was performed on 50,000 cells per sample using a commercially available kit (Active Motif, 53150)

value: Bone marrow

value: Lin- Sca1 cKit+ (LSK)

value: dox water


title: Magnetized water treated tomato sample from blooming phase (biol rep 2)

value: MicroTom

value: Magnetized water treatment


title: Magnetized water treated tomato sample from 6-week-old intensive vegetative growth phase (biol rep 2)

value: leaf and stem

value: intensive vegetative growth (6-week-old)


title: LSK_H16_S4

description: Library name: H16_S4


title: 117hi_CD7n_MPPs_rep4


title: 117hi_CD7n_MPPs_rep5


title: Magnetized water treated tomato sample from 6-week-old intensive vegetative growth phase (biol rep 1)


title: LSK_H15_S3

description: Library name: H15_S3


title: SU016WT-24h-S2

description: Library name: HWCNC


title: Magnetized water treated tomato sample from 3-week-old seedling (biol rep 3)

source_name: seedling

value: seedling

value: seedling (3-week-old)


title: LSK_WT2_S2

description: Library name: WT2_S2


title: 117hi_CD7n_MPPs_rep3


title: SU016WT-24h-GA4

description: Library name: HWCNA


title: Magnetized water treated tomato sample from 3-week-old seedling (biol rep 2)


title: 117hi_CD7n_MPPs_rep2


title: LSK_WT1_S1

description: Library name: WT1_S1


title: Magnetized water treated tomato sample from 3-week-old seedling (biol rep 1)


title: SU016WT-24h-GA3

description: Library name: HWCHZ


title: Magnetized water treated tomato sample from 6-week-old intensive vegetative growth phase (biol rep 3)


title: KO3, Lm-stimulated

city: Magdeburg

first: Tobias

last: Franz

address: Leipziger Str. 44

department: Molecular and Clinical Immunology

institute: Otto-von-Guericke University Magdeburg

description:
Library name: Sample 4, Biol rep 3
KO3_Lm-Read_List_filtered_on_read_quality_metrics

data_processing:
The sequencing of the library pool was performed on two lanes of a HiSeq 2500 RapidRun flow cell (190122_SN552_0334_AH5YJWBCX2) in the single-read (SR) mode: 62 cycles for read 1, 9 cycles for the sample index read.
Bcl-to-Fastq conversion and de-multiplexing of read1 cycle 9-62 were performed with the Illumina CASAVA 1.8.2 software using standard settings; additionally, the unique molecular identifiers (UMI) were extracted from cycles 1 to 8 of read1.
Trimming and alignment: In step 1 of the analysis, the read1 Fastq files of each sample were subjected to adapter and polyA trimming using the Trimmomatic-0.30 software tool with appropriate adapter sequences and settings
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and rpkm values for each sample

source_name: bone marrow

growth_protocol: Bone marrow-derived macrophages (BMDMs) were generated by culturing bone marrow cells for 9 days in DMEM (1000 mg/L glucose) supplemented with 10% heat-inactivated fetal calf serum, 100 U/mL penicillin/streptomycin, and 10 ng/mL M-CSF (Peprotec, Thermo Fisher Scientific). On days 4, 6, and 7, an additional 30% of the initial culture volume was added as fresh medium containing 10 ng/mL M-CSF. After 8 days, adherent cells were detached using trypsin/EDTA solution (20 min, 37 °C).

extract_protocol:
Total RNA was isolated from BMDMs using the Maxwell® 16 LEV simplyRNA Purification Kits and the Maxwell® 16 Instrument (Promega, Mannheim, Germany)
A single library pool containing all samples was generated for sequencing and quantified using the NEB Library Quant kit, a SYBRgreen-based qPCR method

treatment_protocol: For stimulation experiments, BMDMs were seeded in 60-mm dishes at a density of 5 × 10⁵ cells per dish and incubated overnight. Prior to infection, the medium was changed to culture medium lacking M-CSF, FCS, and antibiotics. For RNA-sequencing analysis BMDMs were infected with 1 × 10⁶ CFU L. monocytogenes for 6 h.

value: bone marrow

value: macrophages

value: Bone marrow-derived macrophages (BMDMs)

value: global Tgr5-deficiency

value: 1 × 10⁶ CFU L. monocytogenes for 6h


title: 117hi_CD7n_MPPs_rep1


title: SU016WT-24h-GA1

description: Library name: HWCHX

value: cell pellet


title: Control tomato sample from full ripening of berries phase (biol rep 3)

value: Control, no treatment

value: full ripening of berries


title: SU016WT-24h-S1

description: Library name: HWCNB

value: unicellular eukaryotic

value: WT


title: KO3, Untreated control

description:
Library name: Sample 3, Biol rep 3
KO3_control-Read_List_filtered_on_read_quality_metrics

value: untreated control


title: HPCs_rep1

source_name: HPCs

value: HPCs


title: KO2, Lm-stimulated

description:
Library name: Sample 4, Biol rep 2
KO2_Lm-Read_List_filtered_on_read_quality_metrics


title: SU016WT-24h-AZD4

description: Library name: HWCHW


title: HPCs_rep2


title: KO2, Untreated control

description:
Library name: Sample 3, Biol rep 2
KO2_control-Read_List_filtered_on_read_quality_metrics


title: Control tomato sample from full ripening of berries phase (biol rep 1)

value: MicroTom


title: Control tomato sample from full ripening of berries phase (biol rep 2)

value: leaf and stem


title: SU016WT-24h-AZD2

description: Library name: HWCHT


title: HSCs_rep15

source_name: HSCs

value: HSCs


title: Control tomato sapmle from beginning of berry formation phase (biol rep 3)

value: begenning of berry formation


title: SU016WT-24h-AZD1

description: Library name: HWCHS


title: SU016WT-24h-AZD3

description: Library name: HWCHU


title: KO1, Untreated control

description:
Library name: Sample 3, Biol rep 1
KO1_control-Read_List_filtered_on_read_quality_metrics


title: Control tomato sapmle from beginning of berry formation phase (biol rep 2)


title: HSCs_rep14


title: Control tomato sapmle from beginning of berry formation phase (biol rep 1)


title: SU016WT-24h-Glu4

description: Library name: HWCHP


title: Control tomato sample from blooming phase (biol rep 3)

value: leaf, stem and flower

value: blooming


title: HPCs_rep3


title: WT3, Untreated control

description:
Library name: Sample 1, Biol rep 3
WT3_control-Read_List_filtered_on_read_quality_metrics

value: bone marrow

value: macrophages

value: wildtype


title: SU016WT-24h-Glu2

description: Library name: HWCHN


title: SU016WT-24h-Glu1

description: Library name: HWCHH


title: KO1,  Lm-stimulated

description:
Library name: Sample 4, Biol rep 1
KO1_Lm-Read_List_filtered_on_read_quality_metrics

value: Bone marrow-derived macrophages (BMDMs)

value: global Tgr5-deficiency

value: 1 × 10⁶ CFU L. monocytogenes for 6h


title: WT2, Lm-stimulated

description:
Library name: Sample 2, Biol rep 2
WT2_Lm-Read_List_filtered_on_read_quality_metrics


title: SU016WT-24h-None4

description: Library name: HWCHG

value: cell pellet


title: Control tomato sample from 6-week-old intensive vegetative growth phase (biol rep 3)

value: Control, no treatment

value: intensive vegetative growth (6-week-old)


title: Control tomato sample from blooming phase (biol rep 2)


title: Control tomato sample from 6-week-old intensive vegetative growth phase (biol rep 2)


title: HSCs_rep11


title: HSCs_rep9


title: SU016WT-24h-None3

description: Library name: HWCHC

value: unicellular eukaryotic

value: WT


title: WT1, Untreated control

description:
Library name: Sample 1, Biol rep 1
WT1_control-Read_List_filtered_on_read_quality_metrics

value: untreated control


title: SU016WT-24h-None2

description: Library name: HWCHB


title: HSCs_rep10


title: WT2, Untreated control

description:
Library name: Sample 1, Biol rep 2
WT2_control-Read_List_filtered_on_read_quality_metrics


title: Control tomato sample from blooming phase (biol rep 1)

value: MicroTom


title: HSCs_rep7

value: HSCs


title: Control tomato sample from 6-week-old intensive vegetative growth phase (biol rep 1)

value: leaf and stem


title: WT3, Lm-stimulated

description:
Library name: Sample 2, Biol rep 3
WT3_Lm-Read_List_filtered_on_read_quality_metrics


title: HSCs_rep13


title: SU016WT-24h-None1

description: Library name: HWCHA


title: Control tomato sample from 3-week-old seedling (biol rep 3)

value: seedling

value: seedling (3-week-old)


title: SU016WT-24h-Glu3

description: Library name: HWCHO


title: HSCs_rep12


title: HSCs_rep6


title: SU017WT-1h-GA4

description: Library name: HWCGZ


title: HSCs_rep8


title: OLD_UNINFECTED [HEART974]

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
HEART974
raw.txt

data_processing:
Basecalls were generated using CASAVA v1.8.
Data quality was assessed using FastQC v0.11.8.
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a.
Reads were annotated to genes using Homer v4.10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw.txt: Tab-delimited text file includes the raw counts for each sample.

source_name: Heart

extract_protocol:
RNA were extracted following the protocol from Allprep DNA/RNA Mini Kit (Qiagen) and RNA integrity number were measured through Agilent 2200 TapeStation system.
Libraries generated using Illumina TruSeq Stranded mRNA Sample Prep Kit, pooled and sequenced using an Illumina HiSeq 2500 with 75-bp single-read chemistry.

value: Heart

value: wild type

tag: age

value: Old

value: uninfected

tag: disease state

value: healthy


title: WT1,  Lm-stimulated

description:
Library name: Sample 2, Biol rep 1
WT1_Lm-Read_List_filtered_on_read_quality_metrics

value: bone marrow

value: macrophages

value: Bone marrow-derived macrophages (BMDMs)

value: wildtype

value: 1 × 10⁶ CFU L. monocytogenes for 6h


title: Control tomato sample from 3-week-old seedling (biol rep 2)

value: Control, no treatment


title: HSCs_rep5

data_processing:
16 bases are initially read, and all must have a quality score > 10. The unique sample-specific barcode corresponds to first 6 bp, and the unique molecular identifier (UMI) corresponds to the following 10 bp.
Human reference transcriptome from the UCSC website (release hg38) using BWA version 0.7.4.4  was used to align the second reads
Assembly: hg38
Supplementary files format and content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 28,307 genes detected.


title: Control tomato sample from 3-week-old seedling (biol rep 1)


title: HSCs_rep4


title: OLD_UNINFECTED [HEART973]

description:
HEART973
raw.txt


title: HSCs_rep3


title: OLD_UNINFECTED [HEART975]

description:
HEART975
raw.txt


title: SU017WT-1h-GA2

description: Library name: HWCGX

value: cell pellet

value: unicellular eukaryotic

value: WT


title: Pituitary_HighRFI_H4

city: Mueang Nakhon Ratchasima

first: Panpradup

last: Sinpru

state: Nakhon Ratchasima

address: 111 University Ave.

country: Thailand

institute: Suranaree University of Technology

data_processing:
High-quality clean reads from the samples were mapped to the chicken reference genome using the HISAT2 version 2.0.5 software.
Differential gene expression analysis between high- and low-FCR samples was performed using DESeq2 version 1.20.0 package in R.
Assembly: GRCg6a
Supplementary files format and content: Column 1, gene_id: gene number; Column 2-19, Sample count: raw read count values of each sample; Column 22, gene_name: gene name; Column 23-29, gene_chr, gene_start, gene_end, gene_strand, gene length, gene_biotype, gene_description
Supplementary files format and content: Column 1, gene_id: gene number; Column 2-19, Sample FPKM: FPKM of each gene for each sample; Column 22, gene_name: gene name; Column 23-29, gene_chr, gene_start, gene_end, gene_strand, gene length, gene_biotype, gene_description

organism: Gallus gallus

source_name: Pituitary gland

growth_protocol: A total of 200 male KRC chicks were wing-banded and individually weighed at wk 0. The chicks were raised in individual cages and fed ad libitum with commercial feed (CPF Co., Ltd., Nakhon Ratchasima, Thailand). Body weight (BW) and FI of the KRC were recorded individually from wk 1 to wk 10. At 10 wk of age, the calculation of RFI is performed according to the method descripted by Poompramun et al. (2021b). Based on RFI values at 10 wk, 10 chickens with extremely low RFI and 10 chickens with extremely high RFI were identified, forming the low RFI and high RFI groups

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent.One μg of total RNA with RIN value ≥ 7.7  was used for the following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s instruction (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Chickens seletected with High and Low RFI value

value: Pituitary gland


title: SU017WT-1h-GA3

description: Library name: HWCGY


title: HSCs_rep2

extract_protocol:
no extraction_cell lysates
Cachiarelli et al. (Cell 162:412, 2015)

value: HSCs


title: YOUNG_UNINFECTED [HEART969]

description:
HEART969
raw.txt

value: Young


title: YOUNG_UNINFECTED [HEART967]

description:
HEART967
raw.txt

value: Heart


title: SU017WT-1h-S4

description: Library name: HWCGU


title: Pituitary_HighRFI_H3


title: Pituitary_HighRFI_H5


title: OLD_HEALTHY_INFECTED [HEART75]

description:
HEART75
raw.txt

value: wild type

value: infected


title: SU017WT-1h-S3

description: Library name: HWCGT


title: HSCs_rep1


title: OLD_HEALTHY_INFECTED [HEART73]

description:
HEART73
raw.txt

value: Old


title: Pituitary_HighRFI_H2


title: 2023_CosMx_Multitissue_nTMA

description:
A normal TMA of 45 cores 1.2 mm in diameter representing a broad range of normal tissues. Samples were sourced from the same patient in either duplicate or triplicate. This TMA was chosen for the breadth of tissue lineages included and the relatively large core size.
2023_tTMA1_nTMA.RDS (sample col = s1)

hyb_protocol: NanoString CosMx samples were prepared with one 1000 plex panel. Samples were hybridized with probes and stained with cell markers. Samples were loaded onto the CosMx SMI at the same time for imaging, during which branched fluorescent probes were hybridized onto the samples to amplify the signal above the background.   NanoString CosMx samples were prepared with Human Universal Cell Characterization 1000 Plex Panel (part number 122000157) according to manufacturer protocol “MAN-10159-01 CosMx SMI Manual Slide Preparation Manual”. Firstly, slides were baked at 60℃ overnight for better tissue adherence. After baking, slides were treated sequentially with deparaffinization, target retrieval (15 min at 100℃), permeabilization (3µg/mL proteinase K, 15 min at 40℃), fiducials application, post-fixation, NHS-acetate application and then hybridized with denatured probes from universal panel and default add-on panel. After in situ hybridization (18 hours at 37℃), slides were washed and incubated with DAPI (15 min at RT) and marker stain mix (with PanCK, CD45, CD68 and cell segmentation marker CD298/B2M). Slides were washed and loaded onto the CosMx SMI for UV bleaching, imaging, cycling and scanning. Raw images were decoded by default pipeline on Atomx SIP (cloud-based service). Machine: CosMx_0020. Serial Number: INS2301H0020

data_processing:
Raw images were decoded by default pipeline on Atomx SIP (cloud-based service). Machine: CosMx_0020. Serial Number: INS2301H0020. After data acquisition, the resulting outputs were uploaded to a Google bucket associated with a terra.bio Workspace for distribution and follow on analysis.To facilitate standardized data formatting and subsequent analytical processes, we built a data ingestion pipeline with the following objectives: a) to grab cell-level and transcript-level data from diverse platforms and normalize the data structure; b) to tag each cell and transcript with essential metadata including tissue type, tumor status, PD-L1 status, among others to transform the data into various formats tailored to the requirements of particularized analyses. Specifically, to tag the data, core centers in the TMA were manually identified using DAPI images (Xenium) or cell metadata that contains global coordinates (MERSCOPE and CosMx) using QGIS(version:3.16.10-Hannover). Cells or transcripts within a specified radius were then labeled with core metadata via spatial joining (implemented by GeoPandas, version:0.13.0). In instances where cores are in close proximity or when a uniform radius cannot be applied effectively, we manually generated the core boundary masks.
*RDS: Raw output from CosMx, including tTMA1 and nTMA (identifiable by sample column)
*metadata.csv: Cell metadata including locations and cell level transcript counts.
*transcripts.csv: Locaton of each transcirpt and gene name.

treatment_protocol: Sequential sections were prepared according to manufacturer instructions (“MAN-10159-01CosMx SMI Manual Slide Preparation Manual” ) at the Brigham and Women’s Hospital Pathology Core. Prior to collecting samples, ~50 µm of each TMA were faced off to reach deeper into the sample where RNA integrity was likely higher. 5 µm sequential sections were then collected, floated in a 37˚C water bath, and adhered to Superfrost+ slides (Leica BOND PLUS slides, Leica Biosystems S21.2113.A). TMAs were sliced as close to the center of the active area as possible for each platform.  Samples were baked at 60˚C for 16 hours. Sections were stored at 4˚C.

value: mixed

value: Multitissue panel


title: SU017WT-1h-S2

description: Library name: HWCGS


title: Pituitary_HighRFI_H1


title: OLD_MORBID_INFECTED [HEART72]

description:
HEART72
raw.txt

value: morbid


title: 2023_CosMx_Multitissue_tTMA1

description:
A tumor TMA of 170 cores, 0.6 mm in diameter, including a variety of cancer samples and healthy lymphoid tissue as a positive staining control. The TMA samples were selected from samples previously characterized by ImmunoProfile and were selected to encompass both high and low levels of the biomarkers in the ImmunoProfile panel [CD8, PD-1, PD-L1, Foxp3, tumor marker (Cytokeratin, Sox10, or PAX8)]. Annotations were performed by KF and SR based on H&E and immunofluorescence staining. Cores included both tumor and healthy control annotation, though for the purpose of this study, all were combined under their tumor label. Tumors were also chosen to be a mixture of PD-L1 high and PD-L1 low. This TMA had previously been studied by both H&E, and several highly multiplexed immunostaining approaches, and was known to be of high morphological integrity.
2023_tTMA1_nTMA.RDS (sample col = s0)

scan_protocol: After in situ hybridization (18 hours at 37℃), slides were washed and incubated with DAPI (15 min at RT) and marker stain mix (with PanCK, CD45, CD68 and cell segmentation marker CD298/B2M). Slides were washed and loaded onto the CosMx SMI for UV bleaching, imaging, cycling and scanning. Raw images were decoded by default pipeline on Atomx SIP (cloud-based service). Machine: CosMx_0020. Serial Number: INS2301H0020


title: SU017WT-1h-S1

description: Library name: HWCGP


title: 2024_CosMx_Multitissue_tTMA2

description:
A tumor TMA of 48 cores, 1.2 mm in diameter, including a variety of cancer. This TMA was chosen for the breadth of tissue lineages included and the relatively large core size.
2024_tTMA1_tTMA2.RDS (sample col = s2)


title: YOUNG_UNINFECTED [HEART968]

description:
HEART968
raw.txt

value: uninfected

value: healthy


title: SU017WT-1h-GA1

description: Library name: HWCGW


title: Pituitary_LowRFI_L5


title: OLD_MORBID_INFECTED [HEART70]

description:
HEART70
raw.txt


title: YOUNG_MORBID_INFECTED [HEART230]

description:
HEART230
raw.txt


title: SU017WT-1h-AZD3

description: Library name: HWCGO


title: YOUNG_MORBID_INFECTED [HEART223]

description:
HEART223
raw.txt


title: 2024_CosMx_Multitissue_tTMA1

description:
A tumor TMA of 170 cores, 0.6 mm in diameter, including a variety of cancer samples and healthy lymphoid tissue as a positive staining control. The TMA samples were selected from samples previously characterized by ImmunoProfile and were selected to encompass both high and low levels of the biomarkers in the ImmunoProfile panel [CD8, PD-1, PD-L1, Foxp3, tumor marker (Cytokeratin, Sox10, or PAX8)]. Annotations were performed by KF and SR based on H&E and immunofluorescence staining. Cores included both tumor and healthy control annotation, though for the purpose of this study, all were combined under their tumor label. Tumors were also chosen to be a mixture of PD-L1 high and PD-L1 low. This TMA had previously been studied by both H&E, and several highly multiplexed immunostaining approaches, and was known to be of high morphological integrity.
2024_tTMA1_tTMA2.RDS (sample col = s1)


title: Mock control crispant (3)

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

description: Library name: SJMOCK3

data_processing:
HISAT2 was used to align processed reads to the GRCz10/danRer10 genome
Differentially expressed genes were called using DESeq2
Assembly: ensembl_80_danio_rerio_grcz10_toplevel
Supplementary files format and content: Excel file containing Gene ID, The readcount of genes of sample, The FPKM of genes of sample, The mean value of normalised readcounts in treat group, The mean value of normalised readcounts in control group, log2FoldChange value of a comparison group, pvalue value of a comparison group, padj value of a comparison group

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
Zebrafish embryos were homogenised using TRIzol and total RNA was isolated using the Quick-RNA Microprep Kit (Zymo Research). Residual genomic DNA was then removed using DNA-free™ DNA Removal Kit (ThermoFisher Scientific)
polyA RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for strand specific library.

value: Whole embryo


title: SU017WT-1h-AZD2

description: Library name: HWCGH


title: SU017WT-1h-AZD1

description: Library name: HWCGG


title: Pituitary_LowRFI_L2


title: SU017WT-1h-Glu4

description: Library name: HWCGC


title: Pituitary_LowRFI_L4


title: YOUNG_HEALTHY_INFECTED [HEART222]

description:
HEART222
raw.txt


title: Mock control crispant (2)

description: Library name: SJMOCK2


title: Pituitary_LowRFI_L1


title: Hypothalamus_HighRFI_H5

source_name: Hypothalamus

value: Hypothalamus


title: SU017WT-1h-Glu3

description: Library name: HWCGB

value: cell pellet


title: YOUNG_HEALTHY_INFECTED [HEART219]

description:
HEART219
raw.txt


title: F0 dancr crispant (3)

description: Library name: SJDANCR3


title: Mock control crispant (1)

description: Library name: SJMOCK1


title: Hypothalamus_HighRFI_H4


title: SU017WT-1h-Glu2

description: Library name: HWCGA

value: unicellular eukaryotic


title: YOUNG_HEALTHY_INFECTED [HEART216]

description:
HEART216
raw.txt


title: F0 dancr crispant (2)

description: Library name: SJDANCR2


title: F0 dancr crispant (1)

description: Library name: SJDANCR1


title: YOUNG_HEALTHY_INFECTED [HEART215]

description:
HEART215
raw.txt


title: SU017WT-1h-None4

description: Library name: HWCCY

value: WT


title: Hypothalamus_HighRFI_H2


title: Hypothalamus_HighRFI_H3


title: SU017WT-1h-Glu1

description: Library name: HWCCZ


title: Pituitary_LowRFI_L3

value: Pituitary gland


title: YOUNG_MORBID_INFECTED [HEART214]

description:
HEART214
raw.txt


title: YOUNG_MORBID_INFECTED [HEART229]

description:
HEART229
raw.txt


title: SU017WT-1h-None3

description: Library name: HWCCX


title: SU017WT-1h-None1

description: Library name: HWCCU


title: Hypothalamus_LowRFI_L4


title: Hypothalamus_LowRFI_L5


title: YOUNG_MORBID_INFECTED [HEART211]

description:
HEART211
raw.txt


title: OLD_MORBID_INFECTED [HEART210]

description:
HEART210
raw.txt


title: Hypothalamus_HighRFI_H1


title: OLD_MORBID_INFECTED [HEART209]

description:
HEART209
raw.txt


title: SU017WT-1h-None2

description: Library name: HWCCW


title: pSUC2:NFT-Rep2

city: Seattle

first: Josh

last: Cuperus

state: WA

address: 3720 15th Ave NE, Foege Building Room s310

institute: University of Washington

description: single Cell RNA sequencing library prepared from whole cells using a 10x 3' v3.1 Dual Index Gene Expression kit.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: TAIR10
Supplementary files format and content: Count Matrix (RDS file)

organism: Arabidopsis thaliana

source_name: FANS sorted FT expressing cells

growth_protocol: Plants were grown un LD+FR light conditions

extract_protocol: Sorted cells were subjected to the standard 10x workflow for Single Cell 3' v3.1 Dual Index Gene Expression kit.

treatment_protocol: Isolated nuclei were sorted based on expression

value: FANS sorted FT expressing cells


title: Hypothalamus_LowRFI_L3


title: YOUNG_HEALTHY_INFECTED [HEART213]

description:
HEART213
raw.txt

value: Young


title: pSUC2:NFT-Rep1


title: Hypothalamus_LowRFI_L2


title: OLD_HEALTHY_INFECTED [HEART206]

description:
HEART206
raw.txt

value: Heart


title: Hypothalamus_LowRFI_L1


title: OLD_HEALTHY_INFECTED [HEART201]

description:
HEART201
raw.txt

value: wild type


title: cell_line WWTR1 DOX + TDI rep1

status: Public on Oct 02 2025

city: Vienna

first: CCRI

last: BiCU

address: Zimmermannpl. 10

department: Bioinformatics Core Unit

country: Austria

institute: St. Anna Children's Cancer Research Institute

description: Library name: OE_WWTR1_dox_TDI_RNA_S165178_R1

data_processing:
Illumina HiSeq Control Software (HCS) HD was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis
BCL to BAM file conversion and demultiplexing
Conversion of Bam files to FASTQ with samtools (v1.17)
Processing of the data with Nextflow/rna-seq pipeline (v3.14)
Assembly: GRCh38/hg38
Supplementary files format and content: RDS/Rdata, tsv files with raw gene counts

source_name: SK-N-SH

extract_protocol:
Cells were detached and dissociated using accutase and washed 1x with DPBS before RNA isolation using the RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions, including homogenization with QIAshredder columns (Qiagen) and on-column DNAse digest with RNase-free DNase set (Qiagen). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer instrument (Agilent).
RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs) according to manufacturer’s instructions. NGS library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent).

value: SK-N-SH

value: Neuroblastoma

value: TDI-011356 1uM + Doxycycline 1ug/ml


title: cell_line WWTR1 DMSO rep1

description: Library name: OE_WWTR1_DMSO_RNA_S165191_R1

value: DMSO


title: cell_line WWTR1 DOX rep1

description: Library name: OE_WWTR1_dox_RNA_S165189_R1

value: Doxycycline 1ug/ml


title: pFT:NFT


title: SK-N-SH k-975 control treatment rep2

description: Library name: SH_control_2


title: SK-N-SH k-975 control treatment rep1

description: Library name: SH_control_1


title: cell_line WWTR1 TDI rep1

description: Library name: OE_WWTR1_TDI_RNA_S165188_R1


title: Cultured Rat fibroblasts - K2

city: Saitama

first: MANABU

last: SHIRAISHI

address: Omiya-ku

institute: Jichi Medical Unversity

hyb_protocol: 1. Total RNA QC check was performed using an Agilent 2100 Bioanalyzer. 2. 100 ng of Total RNA was aliquoted. 3. the GeneChipTM WT PLUS Reagent Kit was used and the kit protocol (GeneChipTM WT PLUS Reagent Kit User Manual) was followed. WT PLUS Reagent Kit User Manual), prepare Fragmented and Labeled cDNA samples, and then prepare 100 μL of the following hybridization solution. 4. the array was incubated in a GeneChipTM Hybridization Oven 645 at 45°C, temperature of 1.5 °C, and humidity of 1.5 °C, according to the protocol supplied with the kit.Incubate the array at 45°C for 16 hours (60 rpm) using GeneChipTM Hybridization Oven 645 according to the protocol supplied with the kit. 5. Wash the array with GeneChipTM Fluidics Station 450 according to the kit protocol. Wash the arrays with GeneChipTM Fluidics Station 450 according to the protocol supplied with the kit.

scan_protocol: The GeneChipTM Scanner 3000 7G was used to scan the arrays according to the accompanying manual <GeneChipTM Command Console (AGCC) 4.0 User Manual>.  Command Console (AGCC) 4.0 User Manual. at Filgen, Inc.

data_processing: Expression Console (sst-rma-gene-full)

label: biotin

organism: Rattus norvegicus

source_name: Healthy heart

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).

growth_protocol: Cardiac fibroblasts were isolated from the hearts of Sprague-Dawley rats.

extract_protocol: RNA was isolated from cultured fibroblasts with the Gene Jet PCR purification Kit (Thermo Scientific), according to the manufacturer’s instructions.

treatment_protocol: Cardiac fibroblasts were plated on a 0.1% gelatin-coated CytoSoft 6-well dish  and cultured.

value: heart

value: cardiac fibroblasts

value: Fibroblasts were cultured in medium with an elastic modulus of 64 KPa plus TGF-beta recombinant protein.


title: SK-N-SH k-975 treatment 24h rep3

description: Library name: SH_24h_3


title: Cultured Rat fibroblasts - L2

value: Fibroblasts were cultured in 64 KPa modulus medium with TGF-beta recombinant protein and then transferred to 16 KPa medium.


title: Cultured Rat fibroblasts - I1

value: Fibroblasts were cultured in a medium with an elastic modulus of 16 Kpa.


title: Cultured Rat fibroblasts - L1


title: SK-N-SH k-975 treatment 48h rep3

description: Library name: SH_48h_3


title: SK-N-SH k-975 treatment 24h rep1

description: Library name: SH_24h_1


title: CLB-Ma k-975 control treatment rep2

description: Library name: CM_control_2

source_name: CLB-Ma

value: CLB-Ma


title: Cultured Rat fibroblasts - I2


title: CLB-Ma k-975 control treatment rep3

description: Library name: CM_control_3


title: Cultured Rat fibroblasts - K1


title: CLB-Ma k-975 control treatment rep1

description: Library name: CM_control_1


title: CLB-Ma k-975 treatment 48h rep2

description: Library name: CM_48h_2


title: SK-N-SH k-975 treatment 24h rep2

description: Library name: SH_24h_2


title: CLB-Ma k-975 treatment 48h rep3

description: Library name: CM_48h_3


title: CLB-Ma k-975 treatment 48h rep1

description: Library name: CM_48h_1


title: CLB-Ma k-975 treatment 24h rep3

description: Library name: CM_24h_3


title: CLB-Ma k-975 treatment 24h rep2

description: Library name: CM_24h_2


title: CLB-Ma k-975 treatment 24h rep1

description: Library name: CM_24h_1


title: SK-N-SH cells expressing dox-inducible WWTR1, treatment with doxycycline and TDI-011356

description: Library name: OE_WWTR1_dox_TDI_ATAC_S165175

data_processing:
Illumina HiSeq Control Software (HCS) HD was used for the data acquisition on the sequencing instrument
On-instrument base-calling performed by the Illumina Real-Time Analysis
BCL to BAM file conversion and demultiplexing
Conversion of Bam files to FASTQ with samtools (v1.17)
Processing with a pipeline that includes mapping reads with STAR (v2.7.10a), identification of duplicates with Picard (v2.27.4),  peak calling with MACS2 (v2.2.7.1), annotation of peaks with HOMER (v4.11), identification of consensus peaks with BEDTools (v2.30.0) and counting reads in peaks with featureCOunts (v2.0.1)
Assembly: GRCh38/hg38
Supplementary files format and content: csv tables with read counts and annotations for consensus peaks performed by HOMER
Supplementary files format and content: bigWig files containting track information for genome browser

extract_protocol:
50 000 cells were detached and dissociated using accutase and washed 1x with DPBS. Cell pellets were lysed in 25 µl Tagment DNA Enzyme and Buffer (Illumina), supplemented with 0.01 % digitonin (Promega) and 2x cOmplete, EDTA-free protease inhibitor cocktail (Roche). Samples were incubated at 37 °C for 30 min before placing on ice and subsequent purification using MinElute PCR purification kit (Qiagen) according to manufacturer’s instructions, with elution in 12 µl.
1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. The remaining 10 μl of each library were amplified for the number of cycles corresponding to the Cq value (that is, the cycle number at which fluorescence has increased above background levels) from the qPCR. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.


title: SK-N-SH cells expressing dox-inducible WWTR1, DMSO control

description: Library name: OE_WWTR1_DMSO_ATAC_S165172


title: SK-N-SH cells expressing dox-inducible WWTR1, treatment with doxycycline

description: Library name: OE_WWTR1_dox_ATAC_S165177


title: SK-N-SH cells expressing dox-inducible WWTR1, treatment with TDI-011356

description: Library name: OE_WWTR1_TDI_ATAC_S165176


title: CLB-Ma_MES cells, treated with 100 nM K-975 for 48h

description: Library name: CM_48h_ATAC_S165167


title: SK-N-SH k-975 treatment 48h rep1

description: Library name: SH_48h_1


title: SK-N-SH k-975 treatment 48h rep2

description: Library name: SH_48h_2


title: CLB-Ma_MES cells, treated with 100 nM K-975 for 24h

description: Library name: CM_24h_ATAC_S165170


title: CLB-Ma_MES cells, DMSO control

description: Library name: CM_control_ATAC_S165169


title: SK-N-SH_MES cells, treated with 100 nM K-975 for 48h

description: Library name: SH_48h_ATAC_S165165


title: SK-N-SH_MES cells, treated with 100 nM K-975 for 24h

description: Library name: SH_24h_ATAC_S165164


title: HEK293T cells, ZAK-KO, untreated, biol rep 1

city: Baltimore

first: James

last: Saba

state: MD

address: 725 N Wolfe St, 714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins

description: Library name: IP-17_ZAK-KO_UT

data_processing:
Programs used: umi_tools extract (extract UMIs); trim_galore (trim adapters); STAR (align to genome), samtools (sort and index); umi_tools dedup (deduplicate reads); RScript (posted to github) for downstream processing and peak calling.  All code and scripts for data processing can be found in github at the following URL: https://github.com/jakesaba/2025_ZAK.
Assembly: GRCh38
Supplementary files format and content: CSV file that contains called peaks from protein-coding genes using our peak-calling criteria of: a) window size > 20 b) > 2-fold enrichment relative to ZAK-KO c) average signal > 10 RPM  The file contains the following columns: 1) Sample: sample name for the called peak 2) Gene: gene name 3) Transcript: canonical transcript name 4) Chromosome: chromosome name for the called peak 5) Start: beginning chromosomal coordinates for the called peak 6) End: end chromosomal coordinates for the called peak 7) Width: nucleotide window size of the called peak 8) Signal: average coverage signal over the peak window 9) Control: average coverage signal for the control (ZAK-KO) over the peak window 10) P_value: p-value of the called peak (one-sided Poisson test of signal compared to control over the peak width) 11) FDR: false discovery rate of called peak (using Benjamini-Hochberg procedure) 12) FoldChange: fold change of the called peak (Signal/Control)  ZAK (MAP3K20) was excluded from this analysis because the overexpression of ZAK caused spurious peaks to emerge across the entire ZAK locus compared to the ZAK-KO sample
Library strategy: iCLIP

source_name: Kidney

growth_protocol: DMEM + 10% FBS

extract_protocol:
Cells at ~70% confluency in a 10cm dish were crosslinked at 254 nM UV, lysed, clarified, and RNAseI digested (Invitrogen AM2295). IP was performed overnight at 4C using 13 uL of anti-FLAG M2 affinity resin (Millipore A2220).
Following IP, samples were washed, dephosphorylated with FastAP enzyme (Thermo EF0654) and T4 PNK (NEB M0201L). The 3' RNA adapter was ligated (NEB M0437M). A small amount of sample was run on a Criterion XT 4-12% Bis-Tris gel and transferred to PVDF to perform a diagnostic WB probing for ZAK expression and size. The remaining sample was run on a Criterion XT 4-12% Bis-Tris gel (Bio-Rad 3450124) and transferred to a nitrocellulose membrane and a region was cut corresponding to the ZAK protein size to plus ~75 kDa. Membrane pieces were digested with Proteinase K (NEB P8107S). RNA was purified on a clean and concentrator column and reverse transcribed with SuperScript III (Thermo 18080044). The RNA and free primer was digested and the RT-DNA purified with MyOne Silane beads (Thermo 37002D), and the 5' DNA adapter was ligated (NEB M0437M). Following cleanup, a pilot qPCR was performed. Samples were amplified for the determined number of PCR cycles, gel-extracted for products corresponding to 175-350 bp, and submitted for next generation paired-end sequencing with 2 x 150 bp read length.

treatment_protocol: 0.38 micromolar anisomycin, 15 minutes

value: Kidney

value: Human embryonic kidney

value: untreated


title: HEK293T cells, ZAK-ko, untreated, biol rep 2

description: Library name: IP-18_ZAK-KO_UT


title: HEK293T cells, ZAK-OX-ActLoopD, anisomycin 15min, biol rep 1

description: Library name: IP-15_OX-ActLoopD_ANS

value: anisomycin 15min


title: HEK293T cells, ZAK-OX-ActLoopD, anisomycin 15min, biol rep 2

description: Library name: IP-16_OX-ActLoopD_ANS


title: HEK293T cells, ZAK-1-649, anisomycin 15min, biol rep 2

description: Library name: IP-12_RBRdel_ANS


title: HEK293T cells, ZAK-1-649, untreated, biol rep 2

description: Library name: IP-10_RRBdel_UT


title: HEK293T cells, ZAK-ActLoopD, anisomycin 15min, biol rep 1

description: Library name: IP-7_ActLoopD_ANS


title: HEK293T cells, ZAK-1-649, untreated, biol rep 1

description: Library name: IP-9_RBRdel_UT


title: HEK293T cells, ZAK-OX-ActLoopD, untreated, biol rep 1

description: Library name: IP-13_OX-ActLoopD_UT


title: HEK293T cells, ZAK-ActLoopD, untreated, biol rep 2

description: Library name: IP-6_ActLoopD_UT


title: HEK293T cells, ZAK-1-649, anisomycin 15min, biol rep 1

description: Library name: IP-11_RBRdel_ANS


title: HEK293T cells, ZAK-ActLoopD, untreated, biol rep 1

description: Library name: IP-5_ActLoopD_UT


title: SK-N-SH_MES cells, DMSO control

description: Library name: SH_control_ATAC_S165166


title: HEK293T cells, ZAK-WT, anisomycin 15min, biol rep 2

description: Library name: IP-4_WT_ANS


title: HEK293T cells, ZAK-WT, anisomycin 15min, biol rep 1

description: Library name: IP-3_WT_ANS


title: HEK293T cells, ZAK-WT, untreated, biol rep 2

description: Library name: IP-2_WT_UT


title: HEK293T cells, ZAK-WT, untreated, biol rep 1

description: Library name: IP-1_WT_UT


title: F552

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

institute: CIC bioGUNE

description: Library name: S_12

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (Mus musculus.GRCm38.mm10) and read counts obtained for each gene
Assembly: hg38
Supplementary files format and content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: Prostate

growth_protocol: In vivo orthotopic primary tumor growth

extract_protocol:
Total RNA was extracted using Maxwell RSC simplyRNA Cells Kit (Promega; AS1390)
Total-RNAseq sequencing libraries were prepared using “TruSeq Stranded Total RNA with Ribo-Zero Globin” kit (Illumina Inc., Cat.# 20020612) and “TruSeq RNA CD Index Plate” (Illumina Inc., Cat.# 20019792) following “TruSeq Stranded Total RNA Sample Prep-guide (Part # 15031048 Rev. E)”.

value: Prostate

value: Prostate cancer cell line

value: shRNA


title: F521

description: Library name: S_07


title: F550

description: Library name: S_11


title: F582

description: Library name: S_06

value: shScramble


title: F522

description: Library name: S_08


title: F585

description: Library name: S_05


title: F525

description: Library name: S_09


title: HEK293T cells, ZAK-OX-ActLoopD, untreated, biol rep 2

description: Library name: IP-14_OX-ActLoopD_UT


title: F548

description: Library name: S_10


title: F544

description: Library name: S_03


title: HEK293T cells, ZAK-ActLoopD, anisomycin 15min, biol rep 2

description: Library name: IP-8_ActLoopD_ANS


title: F543

description: Library name: S_02


title: CU24_94pre

city: Chiba-shi

first: Hiroaki

last: Kanzaki

address: 1-8-1 Inohana, Chuo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, Chiba University

description: Library name: CU24_94pre

data_processing:
The resultant paired raw sequencing reads were first subject to a basic quality check using FastQC, trimmed by Trim Galore to ensure that reads had a minimum length of 30 bp, a minimum sequencing quality of 20, with unpaired reads removed from the fastq files. The fastq pair files were then mapped to the hg38 reference genome using the Subread aligner via the R wrapper package Rsubread, and transcript abundance data were generated by the companion tool featureCounts with the built-in hg38 annotation and the option of allowing multiple overlaps.
Assembly: hg38
Supplementary files format and content: The .gct file format (tab-delimited text) contains transcript abundance data in HCC tumor tissues from 73 patients.

source_name: Liver

extract_protocol:
Total RNA samples were extracted from fresh frozen tissue using AllPrep DNA/RNA Mini Kit (Qiagen) or from three to ﬁve 10-μm-thick FFPE tissue sections by RNeasy FFPE Kit (Qiagen).
SMART-Seq Stranded Kit (Takara Bio Inc.) following manufacturer’s protocol.

value: Liver

tag: timing

value: tumor sample before atezolizumab plus bevacizumab therapy

tag: Sex

value: male

tag: pathological diagnosis_of_hcc

value: yes


title: F583

description: Library name: S_04

tag: cell line


title: F540

description: Library name: S_01

tag: cell type


title: CU24_91pre

description: Library name: CU24_91pre

value: female


title: CU24_92pre

description: Library name: CU24_92pre


title: CU24_86pre

description: Library name: CU24_86pre


title: CU24_85post

description: Library name: CU24_85post

value: tumor sample after atezolizumab plus bevacizumab therapy


title: CU24_87pre

description: Library name: CU24_87pre


title: CU24_84post

description: Library name: CU24_84post


title: CU24_83pre

description: Library name: CU24_83pre


title: CU24_82pre

description: Library name: CU24_82pre


title: SK-N-SH k-975 control treatment rep3

description: Library name: SH_control_3

value: SK-N-SH

value: Neuroblastoma

value: DMSO


title: CU24_81post

description: Library name: CU24_81post


title: CU24_84pre

description: Library name: CU24_84pre


title: CU24_81pre

description: Library name: CU24_81pre


title: CU24_79pre

description: Library name: CU24_79pre


title: CU24_78pre

description: Library name: CU24_78pre


title: CU24_75pre

description: Library name: CU24_75pre


title: CU24_76pre

description: Library name: CU24_76pre

value: no


title: CU24_74post

description: Library name: CU24_74post


title: CU24_74pre

description: Library name: CU24_74pre


title: CU24_71pre

description: Library name: CU24_71pre


title: CU24_70pre

description: Library name: CU24_70pre


title: CU24_69pre

description: Library name: CU24_69pre


title: CU24_67pre

description: Library name: CU24_67pre


title: CU24_68pre

description: Library name: CU24_68pre


title: CU24_85pre

description: Library name: CU24_85pre


title: CU24_65pre

description: Library name: CU24_65pre


title: CU24_66pre

description: Library name: CU24_66pre


title: CU24_64pre

description: Library name: CU24_64pre


title: CU24_59pre

description: Library name: CU24_59pre


title: CU24_62pre

description: Library name: CU24_62pre


title: CU24_65post

description: Library name: CU24_65post


title: CU24_57post

description: Library name: CU24_57post


title: CU24_60pre

description: Library name: CU24_60pre


title: CU24_57pre

description: Library name: CU24_57pre


title: CU24_56pre

description: Library name: CU24_56pre


title: CU24_54pre

description: Library name: CU24_54pre


title: CU24_51pre

description: Library name: CU24_51pre


title: CU24_50pre

description: Library name: CU24_50pre


title: CU24_49pre

description: Library name: CU24_49pre


title: CU24_48pre

description: Library name: CU24_48pre


title: CU24_47pre

description: Library name: CU24_47pre


title: CU24_45pre

description: Library name: CU24_45pre


title: CU24_43pre

description: Library name: CU24_43pre


title: CU24_39pre

description: Library name: CU24_39pre


title: CU24_41pre

description: Library name: CU24_41pre


title: CU24_34pre

description: Library name: CU24_34pre


title: CU24_32pre

description: Library name: CU24_32pre


title: CU24_31pre

description: Library name: CU24_31pre


title: CU24_33pre

description: Library name: CU24_33pre


title: CU24_64post

description: Library name: CU24_64post


title: CU24_28pre

description: Library name: CU24_28pre


title: CU24_30pre

description: Library name: CU24_30pre


title: CU24_26ontreatment

description: Library name: CU24_26ontreatment

value: tumor sample undergoing treatment with atezolizumab plus bevacizumab therapy


title: CU24_55pre

description: Library name: CU24_55pre


title: CU24_53pre

description: Library name: CU24_53pre


title: CU24_26pre

description: Library name: CU24_26pre


title: CU24_24pre

description: Library name: CU24_24pre


title: CU24_23pre

description: Library name: CU24_23pre


title: CU24_25pre

description: Library name: CU24_25pre


title: CU24_18pre

description: Library name: CU24_18pre


title: CU24_21post

description: Library name: CU24_21post


title: CU24_21pre

description: Library name: CU24_21pre


title: CU24_29pre

description: Library name: CU24_29pre


title: CU24_19post

description: Library name: CU24_19post


title: CU24_17pre

description: Library name: CU24_17pre


title: CU24_19pre

description: Library name: CU24_19pre


title: CU24_52pre

description: Library name: CU24_52pre


title: CU24_42pre

description: Library name: CU24_42pre


title: CU24_16pre

description: Library name: CU24_16pre


title: CU24_15pre

description: Library name: CU24_15pre


title: CU24_14pre

description: Library name: CU24_14pre


title: CU24_13pre

description: Library name: CU24_13pre


title: CU24_12pre

description: Library name: CU24_12pre


title: CU24_11pre

description: Library name: CU24_11pre


title: CU24_09pre

description: Library name: CU24_09pre


title: CU24_08pre

description: Library name: CU24_08pre


title: CU24_07pre

description: Library name: CU24_07pre


title: CU24_20pre

description: Library name: CU24_20pre


title: CU24_05pre

description: Library name: CU24_05pre


title: CU24_04pre

description: Library name: CU24_04pre


title: CU24_01post

description: Library name: CU24_01post


title: CU24_01pre

description: Library name: CU24_01pre


title: CU24_06pre

description: Library name: CU24_06pre


title: 38_KMS12PE_VDAC2STOP_7

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
Samples demultiplexing is performed with a python script. It will transform the raw paired-end fastq files into a single-end fastq file for each sample
Alignment on refseq reference transcriptome is performed using bwa
Aligned reads are parsed and UMI are counted for each gene in each sample to create an expression matrix
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) and sequenced on 3’ends
The libraries are prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcriptase. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA. A library of 350–800 bp length is run on an Illumina NovaSeq 6000 using NovaSeq 6000 SP Reagent Kit 100 cycles (ref #20027464)
RNA-Seq (3'SRP)

value: myeloma cell

tag: group

tag: replicate


title: 37_KMS12PE_edit_ctr9


title: 39_KMS12PE_VDAC2STOP_8


title: 35_KMS12PE_edit_ctr6


title: 32_KMS12PE_VDAC2STOP_8


title: 40_KMS12PE_VDAC2STOP_12


title: 36_KMS12PE_edit_ctr7


title: 31_KMS12PE_VDAC2STOP_7


title: 28_KMS12PE_edit_ctr6


title: 29_KMS12PE_edit_ctr7


title: 33_KMS12PE_VDAC2STOP_12


title: 25_KMS12PE_VDAC2STOP_8


title: 26_KMS12PE_VDAC2STOP_12


title: 23_KMS12PE_edit_ctr9


title: 24_KMS12PE_VDAC2STOP_7


title: 19_KMM1_VDAC2STOP_11


title: 22_KMS12PE_edit_ctr7


title: 21_KMS12PE_edit_ctr6


title: CU24_10pre

description: Library name: CU24_10pre


title: 17_KMM1_VDAC2STOP_1


title: 18_KMM1_VDAC2STOP_6


title: CU24_02pre

description: Library name: CU24_02pre


title: 16_KMM1_edit_ctr4


title: 15_KMM1_edit_ctr3


title: 13_KMM1_VDAC2STOP_11


title: 12_KMM1_VDAC2STOP_6


title: 11_KMM1_VDAC2STOP_1


title: 10_KMM1_edit_ctr4


title: 30_KMS12PE_edit_ctr9


title: 7_KMM1_VDAC2STOP_11


title: 4_KMM1_edit_ctr4


title: 6_KMM1_VDAC2STOP_6


title: 5_KMM1_VDAC2STOP_1


title: 3_KMM1_edit_ctr3


title: LacZ replicate 2

city: Rome

first: Alessandro

last: Palma

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

data_processing:
Adaptors were removed with fastp tool and roaw reads in FASTQ format aligned to the reference genome using STAR tool. Gene loci fragment quantification was performed using a customized genome annotation file (GRCh38_primary.86_LNCMB3.gtf). Read counts with "reverse" configuration were used as quantifcation of genes.
Assembly: GRCh38.p13, Gencode Release 38, GRCh38.primary_assembly.genome.fa
Supplementary files format and content: tab-delimited text files include rounded row counts values for each Sample

source_name: D283 Med cells

growth_protocol: Rea J, Carissimo A, Trisciuoglio D, Illi B, Picard D, Remke M, Laneve P, Caffarelli E. Identification and Functional Characterization of Novel MYC-Regulated Long Noncoding RNAs in Group 3 Medulloblastoma. Cancers (Basel). 2021 Jul 30;13(15):3853. doi: 10.3390/cancers13153853. PMID: 34359754; PMCID: PMC8345409.

extract_protocol:
miRNeasy Micro Kit (Qiagen)
TruSeq Stranded mRNA Library

treatment_protocol: Tollis P, Vitiello E, Migliaccio F, D'Ambra E, Rocchegiani A, Garone MG, Bozzoni I, Rosa A, Carissimo A, Laneve P, Caffarelli E. The long noncoding RNA nHOTAIRM1 is necessary for differentiation and activity of iPSC-derived spinal motor neurons. Cell Death Dis. 2023 Nov 14;14(11):741. doi: 10.1038/s41419-023-06196-y. PMID: 37963881; PMCID: PMC10646148.

value: D283 Med cells

value: G3 Medulloblastoma

tag: genotype

value: WT

tag: treatment

value: Native RNA Pulldown


title: ODD replicate 2


title: INPUT replicate 2


title: LacZ replicate 1


title: EVEN replicate 1


title: INPUT replicate 1


title: EVEN replicate 2