title: ∆stemin, 10-14 h, ATAC

city: Okazaki

first: Ruan

middle: Morné

last: De Villiers

state: Aichi

address: 38 Nishigonaka, Myodaiji

department: Basic Biology

institute: National Institutes of Natural Sciences

description:
Library name: ste_T10_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

library_source: genomic single cell

data_processing:
Sequence alignment and pre-processing was performed using Cellranger-ARC (10xGENOMICS). The Version 6 of Physcomitrium patens genome (Bi et al., 2024: https://phytozome-next.jgi.doe.gov) was used for alignment. Cellranger-ARC output was analysed using Seurat and Signac packages (Hao et al., 2024; Stuart et al., 2021). For details on the packages used and the specific parameters selected for each function, the code is available at https://github.com/rdv-nibb/P.patens_reprogramming_snMultiome.
Cellranger-ARC analysis was run on all 8 samples. The 'Gene Expression' and 'Peaks' filtered feature barcode matrixes from the Cellranger-ARC output were imported to R studio and used to generate a SeuratObject for each sample with each modality as a separate assay ('RNA' and 'ATAC'). The following steps were performed in order using Seurat, Signac and Harmony package functions. Genomic regions were annotated using a GTF of the 6th version of the P. patens genome (Bi et al., 2024). The 8 individual sample SeuratObjects were merged into 1 object. Nucleosome signal streng and transcription start site (TSS) enrichment scores were calculated. Cells with fewer than 1000 or more than 20,000 RNA molecules, fewer than 5000 ATAC fragments or with TSS scores below 1 were discarded. ATAC peaks were called using MACS2 and called peaks were used to create a new "peaks" assay. Per sample normalisation and scaling of gene expression was performed using the SCTransform pipeline, and the PCA was performed on the resulting SCT assay. TF-IDF and SVD were run on the peaks assay to generate latent semantic indexing (lsi).  Harmony was run on the SCT and the peaks assays distinctly to remove batch effects. A multimodal nearest-neighbours graph was calculated using the 1st to 11th (1:11) PCs of the SCT assays, and the 2nd to 13th (2:13) LSIs of the peaks assays. The resultant weighted nearest-neighbours were used to calculate UMAP coordinates, with a minimum distribution of 0.01 and 20 nearest-neighbours per cell. Clusters were estimated using the Smart Local Moving algorith, at a resolution of 0.4. An R-script file for the preprocessing steps is available at https://github.com/rdv-nibb/P.patens_reprogramming_snMultiome
Assembly: Physcomitrium patens v6.1
Supplementary files format and content: SCT_data.mtx
Supplementary files format and content: peaks_data.mtx
Supplementary files format and content: Cellranger-ARC output gragments:*_atac_fragments.tsv.gz
Supplementary files format and content: Cellranger-ARC output fragment indexing: *atac_fragments.tsv.gz.tbi
Supplementary files format and content: links.gtf
Supplementary files format and content: umap_coordinates.tsv
Supplementary files format and content: metadata.tsv

organism: Physcomitrium patens

source_name: Disrupted gametophore

growth_protocol: To obtain a sufficient amount of tissue for sample preparations, gametophyte tissue was disrupted and spread on 15 cm plates of agar solidified BCDAT medium (Nishiyama et al., 2000) and allowed to regenerate at 25°C under continuous white light for 1 week, to propagate protonemata, or 22 days to generate gametophore enriched samples. For the 3-6h, 10-14 h and 24-36 samples. Gametophore enriched tissue was collected, disrupted, and then incubated in liquid BCDAT  medium in a 500 mL Erlenmeyer flask capped with a silicon sponge closure, on a 60 rpm shaker at 25°C under continuous white light for regeneration times as specified.

extract_protocol:
Nuclei were isolated by chopping collected tissue in 3 mL of chopping buffer (1% [w/v] BSA; 10 mM NaCl; 10 mM Tris-HCl, pH 7.5; 3 mM MgCl2; 1 mM DTT; 0.5 mM spermine; 0.5 mM spermidine; 1 U/µL Protector RNase Inhibitor, 1x cOmplete Mini, EDTA-free Protease Inhibitor Cocktail [Roche], 1% [w/v] PVP40; 0.3% [v/v] NP-40; 0.1 % [v/v] Tween 20 in RNase free water) for 3 minutes using a double-edged safety razor (FEATHER) in a 5 mL culture dish on ice. After a 2-minute incubation, the tissue was strained through a 20 µm CellTrics filter (Sysmex). The filter was rinsed with 1 mL of rinsing buffer (1% [w/v] BSA; 10 mM NaCl; 10 mM Tris-HCl, pH 7.5; 3 mM MgCl2; 1 mM DTT; 0.5 mM spermine; 0.5 mM spermidine; 1 U/µL Protector RNase Inhibitor, 1×cOmplete Mini, EDTA-free Protease Inhibitor Cocktail [Roche], 0.5 µg/mL 4',6-diamidino-2-phenylindole [DAPI]). The DAPI stained nuclei were isolated by fluorescence-activated nuclei sorting (FANS) using a using a BD FACSMelody fitted with a 100 µm sorting nozzle. Nuclei were sorted into a collection tube filled with 500 µL of rinsing buffer kept at 4˚C. To ensure equal representation across subsamples, nuclei were pooled during sorting, collecting 20,000 nuclei for each of three subsamples, resulting in a total of 60,000 nuclei per sample. For the two gametophore samples (T00), 60,000 nuclei for each line were used repectively. Collected nuclei were centrifuged at 500×g for 3 minutes with the centrifuge brake turned off in a swing-bucket centrifuge. Excess buffer was carefully removed, leaving a pellet of nuclei in approximately 10 µL of buffer. Nuclei were gently mixed in the remaining buffer by pipetting with a wide bore tip.
Library construction was done in accordance to the user guide (CG000338 Rev E) tailored for the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit.

treatment_protocol: For tissue disruption, gametophore tissue was collected from 22-day-old gametophyte plates and placed in a 50 mL conical tube, and the volume was Adjusted to 25 mL with liquid BCDAT medium. This tissue was disrupted with a POLYTRON 1200E at maximum speed for 1 min. The disrupted tissue was strained from cellular debris on a nylon filter cloth, rinced, and put into a 500 mL Erlenmeyer flask with 150 mL of liquid BCDAT medium. The tissue was allowed to regenerate from 3 to 36 h, as specified.

value: Disrupted gametophore

tag: tissue pooling

tag: library type

value: ATAC


title: RNA seq Mouse 7_Allo treated Hypoxia Ischemia whole brain

status: Public on Jul 16 2025

type: SRA

city: Hempstead

first: Anthony

last: Szema

state: New York

address: 500 Hofstra Blvd,

department: Department of Occupational Medicine, Epidemiology and Prevention,

country: USA

institute: Donald and Barbara Zucker School of Medicine

description: Library name: 50515_RB_7

library_source: transcriptomic

data_processing:
Partek Flow genomic suite is used for data processing steps genome assembly and differential gene expression are derived after alignment to mm10.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partekflow genomic suite (parameter- Quality limit: 0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes Normalized gene counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Neonatoal whole brain

extract_protocol:
RNA was harvested using the RNeasy Mini Plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads following manufacturer's protocols.

tag: tissue

value: Neonatoal whole brain

tag: genotype

value: WT

tag: treatment

value: Allopregananolone


title: Aep2 sel-mitoRP, rep3

city: Boston

first: Mary

middle: T

last: Couvillion

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Library name: Aep2_3

library_source: other

data_processing:
*library strategy: selective mitoRibo-seq
Reads were trimmed to remove ligated 3’ linker (CTGTAGGCACCATCAAT) with Cutadapt (Martin. EMBnet.journal, 2011. DOI:10.14806/ej.17.1.200). Reads without linker were discarded and the unique molecular identifier (UMI, consisting of 4 random nucleotides introduced at the 5’ end with the RT primer and 10 random nucleotides introduced at the 3’ end with the linker) was then extracted from remaining reads using a custom script. For all Aep1, Aep2, and the first two replicates of Cbs1 samples, synthetic COX2 RNA oligos of 40 and 33 nucleotides (UAACAACAUUCAUUAUGAAUGAUGUACCAACACCUUAUGC and UAACAACAUUCAUUAUGAAUGAUGUACCAACAC) were used as size markers in a separate gel lane during mitoribosome footprint size selection. The oligos contaminated some of the Aep1 and Aep2 samples that were run in adjacent lanes and were removed in silico using BBTools’ BBDuk (sourceforge.net/projects/bbmap/) with a k-mer length of 30.
Reads mapping to abundant non-coding RNAs (rRNA, tRNA) were filtered out after alignment using bowtie1 (Langmead et al. Genome Biology, 2009). Remaining reads were aligned to the S. cerevisiae genome assembly R64 (UCSC: sacCer3) using STAR 2.7.3 (Dobin et al. Bioinformatics, 2013). PCR duplicates were identified by their UMI and removed using a custom script.
Ribosome A site positions were determined using an offset from the 3’ end of each read, depending on its length: 37:[-15], 38:[-16], 39:[-17], 40:[-17], 41:[-17]. Shorter read lengths have ambiguous offsets and were omitted.
Unless otherwise noted, read counts at each A site position were summed across replicates (2 to 6 replicates for each sample) and normalized by total mitochondrial mRNA-mapping reads (rpm). Enrichment over total mitoribosomes was then calculated by summing rpm values in a sliding 9-nt window and dividing by the corresponding sum in the total (Mrps17) dataset.
A threshold was set so that if more than 3 positions had no coverage in either sample the enrichment value was set to 0. This was to avoid spurious signal due to low coverage.
Assembly: Saccharomyces cerevisiae  assembly R64 (UCSC: sacCer3)
Supplementary files format and content: Processed data files ending in *Mito_mRNA.noDups.Asite_37to41_P.rpm.bedGraph are rpm-normalized bedGraph files for each replicate. These have been A-site transformed and only use reads sized 37 to 41 nt.
Supplementary files format and content: Processed data files ending in *Mito_mRNA.noDups.Asite_37to41_PAll.rpm_Mrps17_normRollWin9_max3zeros_forIGV_nolog.bedGraph are made by summing the rpm values for each replicate of a sample then normalizing to the respective Mrps17 data, as described. Columns are 1) chromosome 2) Window-normalized A-site position - 1 3) Window-normalized A-site A-site position 4) Value (fold enrichement) 5) Log1p raw sample counts in window 6) Log1p raw norm sample counts in window
Supplementary files format and content: Only plus-strand data is included for all processed files

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown in YPGal (1% yeast extract, 2% peptone, 2% galactose), pH 5.0, until an OD600 of approximately 1.

extract_protocol:
Frozen cells with lysis buffer were  mechanically lysed using liquid nitrogen-chilled 50 mL canisters for six cycles of 3 min at 15 Hz using a Retsch MM301 mixer mill
Lysates were treated with RNase I and pelleted through a 24% sucrose cushion to isolate ribosomes, crosslinks were reversed, and protected RNA fragments were isolated using acid phenol chloroform. Gel-purified RNA was treated with PNK and ligated to a pre-adenylated adapter (CTGTAGGCACCATCAATNNNNNNNNNN) using T4 RNA ligase 2, K227Q, truncated. Superscript III was used for reverse transcription and circ ligase for circularization. Illumina adapters were introduced by 10-14 cycles of PCR.

treatment_protocol: 150 mL of culture was snap chilled prior to formaldehyde crosslinking by pouring the culture into a prechilled 500 mL centrifuge bottle filled with 50 grams of frozen, crushed ice cubes made from MilliQ water. The culture was quickly swirled in the centrifuge bottle and placed on ice. 10 mL of 16% formaldehyde was added to the chilled culture and the crosslinking proceeded for 1 hr on ice with swirling every 15 minutes. 11 mL of 2.5 M glycine was added to the culture to quench the crosslinking reaction.

tag: cell line

tag: strain

value: mrps17::MRPS17-3XHA aep2::AEP2-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0

value: sucrose cushion


title: dCAS IFN-gamma alone control, biological rep2

type: RNA

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

data_processing: RMA extraction with background adjustment, quantile normalization and PLM summarization

label: Affymetrix Stain Cocktail

source_name: IFN alone control

label_protocol: Standard Affymetrix

extract_protocol: TRIzol

treatment_protocol: Intra-airway administration of dCas9-demethylases, followed by IFN-gamma.

tag: cell type

value: lung epithelial cells

tag: sample group

value: vehicle treated, IFN-stimulated mouse


title: dCAS negative control, biological rep3

source_name: negative control

value: vehicle treated, unstimulated mouse


title: MYCN_AKT_NT_50d_2

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: Library name: Sample26

data_processing:
Raw reads were aligned to the mouse reference genome UCSC mm10 (GRCm38) or the human reference genome (GRCh38/hg38) using salmon for quasi-mapping-based transcript quantification. Transcript abundance was reported as transcripts per million (TPM)
Assembly: mm10, hg38
Supplementary files format and content: CSV file includes TPM values from mouse liver tissues
Supplementary files format and content: CSV file includes TPM values from huaman HCC cells

source_name: liver

extract_protocol:
Total RNA was extracted using a FastGene RNA Basic Kit (NIPPON Genetics) and quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific)
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol

value: liver

tag: time point

value: MYCN and myristoylated AKT overexpression


title: ∆stemin, 3-6 h , ATAC

description:
Library name: ste_T03_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

molecule: genomic DNA


title: RNA seq Mouse 6_Allo treated Hypoxia Ischemia whole brain

description: Library name: 50515_RB_6


title: MYCN_AKT_early_50d_4

description: Library name: Sample31


title: dCAS IFN-gamma alone control, biological rep1


title: dCAS negative control, biological rep2


title: ∆stemin, gametophore, ATAC

description:
Library name: ste_T00_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

source_name: Gametophore enriched

value: Gametophore enriched

value: gametophore


title: dCAS negative control, biological rep5


title: dCAS negative control, biological rep4


title: RNA seq Mouse 5_Hypoxia Ischemia Whole brain

description: Library name: 50515_RB_5

value: No treatment


title: MYCN_AKT_T_50d_1

description: Library name: Sample25


title: Wild type, 10-14 h, ATAC

description:
Library name: Wt_T10_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

value: Wild type


title: Aep2 sel-mitoRP, rep1

description: Library name: Aep2_1

value: sucrose gradient


title: Aep1 sel-mitoRP, rep1

description: Library name: Aep1_1

value: mrps17::MRPS17-3XHA aep1::AEP1-3XF MATa GAL2 HAP1 MIP1[S] G1981A ura3{delta}0


title: dCAS negative control, biological rep1


title: RNA seq Mouse 4_Hypoxia Ischemia whole Brain

description: Library name: 50515_RB_4


title: RNA seq Mouse 3_Hypoxia Ischemia whole Brain

description: Library name: 5015_RB_3


title: MYCN_AKT_T_50d_2

description: Library name: Sample27


title: Aep2 sel-mitoRP, rep2

description: Library name: Aep2_2


title: dCAS negative control, biological rep6


title: Wild type, 3-6 h , ATAC

description:
Library name: Wt_T03_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

value: Disrupted gametophore

value: ATAC


title: RNA seq Mouse 2_Hypoxia Ischemia whole Brain

description: Library name: 5015_RB_2

value: Neonatoal whole brain

value: WT


title: AKT_50d_2

description: Library name: Sample22

value: myristoylated AKT overexpression


title: MYCN_AKT_NT_50d_1

description: Library name: Sample23


title: MYCN_AKT_early_50d_1

description: Library name: Sample24


title: RNA seq mouse 1_Hypoxia Ischemia Whole Brain

description: Library name: 5015_RB_1


title: ∆stemin, 10-14 h, GEx

description:
Library name: ste_T10_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv

library_source: transcriptomic single cell

molecule: nuclear RNA

value: mRNA


title: ERMS24_X

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Gene expression analysis of the RMS patient tumors and their corresponding PDX.

hyb_protocol: RNA hybridization was performed through the Human Genome U219 microarray, using the 24-array plate format following the 3’IVT Pico method anunder the manufacturer's recommendations (Thermo Fisher Scientific).

scan_protocol: The PrimeView Human Genome U219 Array Plate was scanned according to manufacturer's recommendations (Thermo Fisher Scientific).

data_processing: Data were quality controlled and normalized using the robust multichip average (RMA) algorithm using the R oligo package.

label: biotin

organism: Homo sapiens

source_name: Patient derived xenograft, subcutaneous

label_protocol: Biotinylated cRNA were prepared according to the standard GeneChip™ 3’ IVT Pico Kit protocol from  total RNA.

growth_protocol: Extracted Frozen human tissue.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tumor tissue from non-treated tumor biopsy or patient-derived xenografts (PDX).

value: Tumor

value: Embryonal

tag: patient

tag: response


title: AKT_50d_1

description: Library name: Sample21


title: ∆stemin, 3-6 h , GEx

description:
Library name: ste_T03_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv


title: Wild type, gametophore, ATAC

description:
Library name: Wt_T00_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf


title: T98G + Crotonate (ChIP)

city: 上海

first: 晋

last: 李

address: 上海市徐汇区东安路130号复旦大学上海医学院

country: China

institute: 复旦大学基础医学院药理学系

description: Library name: T98G + Crotonate

library_source: genomic

data_processing: Samples were sent to Lianchuan Bio for sequencing

extract_protocol:
Chromatin immunoprecipitation was performed using the ChIP Assay Kit (Beyotime, China)
VAHTSTM Universal DNA Library Prep Kit for Illumina V3 (Vazyme, China)

value: Crotonate


title: MYCN_50d_2

description: Library name: Sample20

value: liver

value: MYCN overexpression


title: T98G + Crotonate (Input)

address: 上海市徐汇区东安路130号复旦大学上海医学院

institute: 复旦大学基础医学院药理学系

description: Library name: T98G + Crotonate input


title: ∆stemin, gametophore, GEx

description:
Library name: ste_T00_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv

value: Gametophore enriched


title: ERMS11_X


title: Wild type, 10-14 h, GEx

description:
Library name: Wt_T10_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv


title: MYCN_50d_1

description: Library name: Sample19


title: Control_50d_2

description: Library name: Sample18


title: ERMS24_T

source_name: Patient biopsy, RMS tumor

value: PDX


title: Wild type, 3-6 h , GEx

description:
Library name: Wt_T03_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv


title: Control_50d_1

description: Library name: Sample17


title: ERMS11_T


title: MYCN_AKT_14d_2

description: Library name: Sample16

value: MYCN and myristoylated AKT overexpression


title: ARMS10_X

value: Alveolar


title: ∆stemin, 24-36 h +protonemata, ATAC

description:
Library name: ste_T24_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

source_name: Disrupted gametophore +protonemata

value: Disrupted gametophore +protonemata

value: 24-36 h +protonemata


title: BlaER1, STATKO, TAKdMRE, IFNB1

city: Paris

first: Yann

last: Loe-Mie

address: 25 rue du Dr Roux

department: Computational Biology

country: France

institute: Institut Pasteur

description: Library name: BlaER1_STATKO_TAKdMRE_IFNB1

data_processing:
Data were processed using c4ctus (https://github.com/NoordermeerLab/c4ctus) using the following primer file: >IFNB1|ttttcaaaccaaccagtcacagcccttttgatc|chr9:21078458-21078757|GATC|Exclude=chr9:21076458-21080757 ttttcaaaccaaccagtc >MRE|ctaagaaagataaaggcaaagagatc|chr9:20970181-20971214|GATC|Exclude=chr9:20968181-20973214 ctaagaaagataaaggca >ICE|TGAGAATAAAATCATACAACGCAGATAATAAGATC|chr9:21095837-21098117|GATC|Exclude=chr9:21093837-21100117 TGAGAATAAAATCATACA
Assembly: hg38
Supplementary files format and content: bedGraph
Library strategy: 4C-Seq

growth_protocol: PreB BlaER1 cells were transdifferentiated as described {Gaidt et.al DOI 10.1007/978-1-4939-7519-8_4}. Briefly, 0,5x106 cells per mL were seeded in 96 well plates in complete RPMI medium supplemented with 10ng/mL hrIL-3 (Peprotech), 10ng/mL hrM-CSF (Peprotech), and 100nM b-estradiol (Sigma).

extract_protocol:
10-15 million cells were collected, washed once with 1X PBS, and cross-linked using freshly prepared 2% formaldehyde solution by tumbling for 10 min at room temperature. The fixation was stopped by adding glycine and immediately transferring the tubes to ice. The cross-linked cells were collected at 300g for 5 min at 4℃ and washed once with 1X PBS. After removing the supernatant, the pellet was snap-freeze in liquid nitrogen and stored at -80°C. Chromatin fixation, cell lysis and 4C-seq procedure were done as described in Miranda et al, Methods in Molecular Biology 2022 using 10-15 million cells per cell experiment. MboI (New England Biolabs) was used as the primary restriction enzyme and NlaIII (New England Biolabs) as the secondary restriction enzyme.
4C-seq sequencing libraries were generated using a 2-step amplification approach with reduced amounts of input, as described in Haarhuis et al, Cell 2017 and Krijger et al, Methods 2020. In the first step, a total of 120ng of 4C material was amplified using the Expand Long Template PCR System (Roche Diagnostics) in 12 reactions in parallel for 12 cycles. All reactions were pooled, followed by clean-up of 1/6th of the material using Agencourt Ampure XP Beads (Beckman Coulter) to remove fragments smaller than 200 bp. In the second step, 20% of the purified PCR products were further amplified in 2 reactions using the Expand Long Template PCR System and universal index adapters for 20 cycles. Amplified 4C-seq libraries were again purified with Agencourt Ampure XP Beads to remove fragments smaller than 200 bp. Quality and size distribution of the PCR libraries was verified by Qubit ds DNA BR kit (Thermo Fisher Scientific) and Tapestation Genomic DNA reagents (Agilent).

treatment_protocol: When indicated, cells were treated with the SUMOi TAK-981 at a final concentration of 100nM, and with 100 ng/mL LPS.

value: STAT1-/- STAT2-/- MRE-/-


title: MYCN_AKT_14d_1

description: Library name: Sample15


title: PANC1_BA100_2

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

description: Gene expression of PANC1 cells treated with 100 uM of benzaldehyde for 24 hr

hyb_protocol: Labeled cRNA was hybridized to an oligo-nucleotide microarray (Whole Human Genome 4×44K, Agilent Technologies) at 65°C for 17 hours.

scan_protocol: After washing with the Gene Expression Wash Buffer kit (Agilent Technologies) and drying, the slides were scanned with a Agilent Microarray Scanner

data_processing: Data were extracted using Agilent Feature Extraction software, version 9.5.1 (Agilent Technologies).

source_name: PANC1, BA 100 uM

label_protocol: RNA samples were labeled using the Quick Amp Labeling kit (Agilent Technologies).

growth_protocol: All cells were cultured in DMEM or RPMI medium suplemented with 10% FBS, penicillin (100U/mL) and streptomycin (100U/mL) and  were  maintained  under  5%  CO2  at  37℃.

extract_protocol: Total RNA was then extracted from these cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: These cells were incubated for 24 hours with either DMSO or Benzaldehyde at concentrations of 100 μM and 500 μM.

value: Benzaldehyde 100 uM, 24 hr


title: ARMS7_X


title: PANC1_BA100_1


title: Wild type, 24-36 h +protonemata, ATAC

description:
Library name: Wt_T24_ATAC
ATAC (10x Multiome): read1 and read3 contain contain ATAC sequences, read2 contains barcode and spacer, index1 contains sample index
peaks_data.mtx
barcodes.tsv
peaks_features.tsv
umap_coordinates.tsv
metadata.tsv
annotation.gtf
links.gtf

value: Wild type

value: ATAC


title: PANC1_BA500_1

description: Gene expression of PANC1 cells treated with 500 uM of benzaldehyde for 24 hr

source_name: PANC1, BA 500 uM

value: Benzaldehyde 500 uM, 24 hr


title: ∆stemin, 24-36 h +protonemata, GEx

description:
Library name: ste_T24_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence, index1/index2 contain sample indexes  i7 and i5 respectively
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv

value: mRNA


title: ARMS7_T

value: Tumor


title: ARMS1_X


title: Wild type, 24-36 h +protonemata, GEx

description:
Library name: Wt_T24_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence, index1/index2 contain sample indexes  i7 and i5 respectively
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv


title: Wild type, gametophore, GEx

description:
Library name: Wt_T00_GEx
3' mRNA (10x Multiome): read1 contains cell barcode and UMI, read2 contains transcript sequence
SCT_data.mtx
barcodes.tsv
SCT_features.tsv
umap_coordinates.tsv
metadata.tsv

value: gametophore


title: PANC1_BA500_2


title: ARMS6_X


title: AKT_14d_1

description: Library name: Sample13

value: myristoylated AKT overexpression


title: PANC1_DMSO_2

description: Gene expression of PANC1 cells treated with DMSO for 24 hr

source_name: PANC1, DMSO

value: DMSO, 24 hr


title: Solanum nigrum genome methylation

city: Heslington, York

first: Sara

last: Franco Ortega

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: Centre for Novel Agricultural Products, University of York

description: Methylation calling of the genome with NCBI accession number JAZKKB000000000

data_processing:
Base calling with guppy for genome assembly
Flye for genome assembly
Racon 1.4.20 for genome assembly
Medaka 1.0.3 for genome assembly
f5c v1.2 to assess methylation using genome with NCBI accession number JAZKKB000000000 as reference
Assembly: NCBI accession number JAZKKB000000000
Supplementary files format and content: TSV file with methylation calling
Supplementary files format and content: TSV file with methylation frequency

organism: Solanum nigrum

source_name: Leaves

growth_protocol: Plant were grown in a growth room of the University of York (UK) with an average temperature of 20°C (±2°C) and 14h/10h light /dark for 3 months

extract_protocol:
gDNA extracted from high molecular weight gDNA extraction from plant leaves protocol, Oxford Nanopore Technologies [ONT], which utilised Carlson buffer and further purification using QIAGEN genomic-tip, see preprint Vaillancourt and Buell (2019) for details
the SQK-LSK109 ligation sequencing kit

value: Leaves


title: AKT_14d_2

description: Library name: Sample14

value: liver


title: Homozygous cdkl5sa21938 zebrafish, biol rep 5, 35 days post-fertilization

city: Faro

first: Tatiana

last: Varela

email: tatianacdv@gmail.com, a44770@ualg.pt

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

description: Library name: Homo_5_35dpf

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Raw reads were first trimmed to obtain clean reads using Novogene perl scripts through the elimination of low-quality reads, adapter-containing reads, and ploy-N-containing reads.
After filtering, clean reads were aligned to the zebrafish reference genome (Danio rerio GRCz11) using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the number of reads mapped to each gene. FPKM for each gene were then calculated, considering the gene length and the total number of mapped reads.
Assembly: GRCz11
Supplementary files format and content: one csv file include raw count values for 5dpf  samples (raw_counts_5dpf.csv)
Supplementary files format and content: one csv file include raw count values for 35dpf  samples (raw_counts_35dpf.csv)
Supplementary files format and content: one csv file include FPKM values for 5dpf  samples (FPKM_5dpf.csv)
Supplementary files format and content: one csv file include FPKM values for 35dpf  samples (FPKM_35dpf.csv)

organism: Danio rerio

source_name: whole zebrafish

extract_protocol:
Total RNA was isolated using the NZYOL reagent. DNase treatment was then performed using the RNase-Free DNase set from QIAGEN. RNA samples were subjected to the RNeasy kit (QIAGEN) clean-up protocol.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and subjected to fragmentation. Then, the first strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase, followed by the second strand cDNA synthesis using DNA polymerase I, RNase H and dUTP for directional library. The lasting overhangs were transformed into blunt ends through polymerase and exonuclease reactions. To prepare for hybridization, adaptors containing a hairpin loop structure were ligated to the previously 3’ ends adenylated DNA fragments. The AMPure XP system was used to purify the cDNA fragments with 370~420 bp in length that were then digested with USER enzyme. PCR was carried out using Phusion High-Fidelity DNA polymerase, universal PCR primers and Index (X) primer. The PCR products were purified, and the Agilent Bioanalyzer 2100 system was used to evaluate the library quality.

value: whole zebrafish

value: Homozygous cdkl5sa21938


title: Control_14d_2

description: Library name: Sample10

value: WT


title: MYCN_14d_1

description: Library name: Sample11

value: MYCN overexpression


title: Homozygous cdkl5sa21938 zebrafish, biol rep 4, 35 days post-fertilization

description: Library name: Homo_4_35dpf


title: Control_14d_1

description: Library name: Sample9


title: Homozygous cdkl5sa21938 zebrafish, biol rep 3, 35 days post-fertilization

description: Library name: Homo_3_35dpf


title: MYCN_14d_2

description: Library name: Sample12


title: MYCN_AKT_3d_2

description: Library name: Sample8

value: MYCN and myristoylated AKT overexpression


title: Homozygous cdkl5sa21938 zebrafish, biol rep 2, 35 days post-fertilization

description: Library name: Homo_2_35dpf


title: MYCN_AKT_3d_1

description: Library name: Sample7


title: AKT_3d_2

description: Library name: Sample6


title: ARMS1_T

value: Alveolar


title: WT zebrafish, biol rep 4, 35 days post-fertilization

description: Library name: WT_5_35dpf


title: AKT_3d_1

description: Library name: Sample5


title: ARMS6_T


title: MYCN_3d_2

description: Library name: Sample4


title: AsPC1_BA100_2

description: Gene expression of AsPC1 cells treated with 100 uM of benzaldehyde for 24 hr

source_name: AsPC1, BA 100 uM

value: Benzaldehyde 100 uM, 24 hr


title: Homozygous cdkl5sa21938 zebrafish, biol rep 1, 35 days post-fertilization

description: Library name: Homo_1_35dpf


title: PANC1_DMSO_1


title: AsPC1_BA500_2

description: Gene expression of AsPC1 cells treated with 500 uM of benzaldehyde for 24 hr

source_name: AsPC1, BA 500 uM


title: WT zebrafish, biol rep 3, 35 days post-fertilization

description: Library name: WT_3_35dpf


title: MYCN_3d_1

description: Library name: Sample3


title: WT zebrafish, biol rep 5, 35 days post-fertilization

description: Library name: WT_4_35dpf


title: WT zebrafish, biol rep 2, 35 days post-fertilization

description: Library name: WT_2_35dpf


title: AsPC1_DMSO_2

description: Gene expression of AsPC1 cells treated with DMSO for 24 hr

source_name: AsPC1, DMSO


title: Control_3d_2

description: Library name: Sample2


title: AsPC1_BA100_1


title: BxPC3_BA100_1

description: Gene expression of BxPC3 cells treated with 100 uM of benzaldehyde for 24 hr

source_name: BxPC3, BA 100 uM


title: AsPC1_BA500_1


title: AsPC1_DMSO_1


title: BxPC3_BA100_2


title: WT zebrafish, biol rep 1, 35 days post-fertilization

description: Library name: WT_1_35dpf


title: BxPC3_BA500_1

description: Gene expression of BxPC3 cells treated with 500 uM of benzaldehyde for 24 hr

source_name: BxPC3, BA 500 uM


title: THP-1_macrophage,Phagocytosis,Rep2

status: Public on Jul 15 2025

city: Nagoya

first: Hiromichi

last: Ebi

address: 1-1, Kanokoden, Chikusa-ku

department: Division of Molecular Therapeutics

institute: Aichi Cancer Center Research Institute

data_processing:
Fastp (v0.23.4) software for trimming adapter sequences from sequencing reads was applied to paired-end RNA-seq fastq files for each sample.
Kallisto (v0.46.2) software was used to estimate a transcript-level abundance from the trimmed reads with known transcript sequences and annotations in GENCODE Release 33.
Gene-level abundance values in transcripts per million (TPM) were estimated by summarizing the transcript-level estimates with the R package tximport (v1.22.0) in the R environment (v4.1.2) using a matching list between transcript ids and gene ids based on the annotations of GENCODE.
Assembly: GENCODE Release 33
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

molecule: polyA RNA

extract_protocol:
RNA was extracted using the NucleoSpin® RNA Plus (MACHEREY-NAGEL)
RNA-seq library was prepared using Universal Plus mRNA-Seq with NuQuant（TECAN, 0521-A1）


title: Control_3d_1

description: Library name: Sample1


title: THP-1_macrophage,Non-phagocytosis,Rep2


title: Dorsal-raphe_male_autism5 [A5_5000]

type: genomic

city: Setagaya

first: Kazuhiko

last: Nakabayashi

institute: NCCHD

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using iScan array scanner (illumina) using standard setting.

data_processing:
GenomeStudio V2011.1 was used to determine the methylation level at each CpG site as beta value. Normalization to internal controls and background subtraction were applied to determine normalized average beta values.
Matrix signal int_KI0415.txt: unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Dorsal raphe regions of the post-mortem brain of a male with autism

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from brain tissues using AllPrep DNeasy Blood & Tissue Kit (Qiagen).

value: Dorsal raphe nucleus from post-mortem brain

tag: gender

value: Male

tag: diagnosis

value: Autism


title: THP-1_macrophage,Phagocytosis,Rep1


title: THP-1_macrophage,Non-phagocytosis,Rep1


title: BxPC3_BA500_2

value: Benzaldehyde 500 uM, 24 hr


title: BxPC3_DMSO_2

description: Gene expression of BxPC3 cells treated with DMSO for 24 hr

source_name: BxPC3, DMSO


title: Dorsal-raphe_male_autism4 [A4_4899]


title: BxPC3_DMSO_1


title: OB1/EC

city: Nantes

first: Julie

last: Gavard

address: 8 quai Moncousu

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to Affymetrix Human Gene 1.0 ST Array [HuGene-1_0-st] at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. RMA normalization is performed using TAC4.0 (Affymetrix) with default parameters

source_name: glioblastoma

label_protocol: 100 ng of RNA was labeled using [Affymetrix GeneChip WT PLUS kit / 3' IVT kit], according to the manufacturer’s protocol.

growth_protocol: Patient-derived mesenchymal GSCs (TG1, TG10, TG16, OB1) were maintained as non-adherent tumorspheres in NS34 serum-free media (DMEM/F12 with N2, G5, and B27 supplements, plus Glutamax and antibiotics, Life Technologies).

extract_protocol: Total RNA was extracted using RNAesay kit Qiagen, RNA integrity was assessed using Bioanalyser

treatment_protocol: They were cocultured with the conditioned media harvested from human brain endothelial cells.

value: tumor

value: cocultured


title: MDA231_ELK3-KD_rep1

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

description: Gene expression of MDA-MB-231 cells transduced with ELK3-shRNA plasmid pLV[shRNA]-EGFP:T2A:Puro-U6>hELK3[shRNA#1] (#VB900040-9805gbm, VectorBuider)

hyb_protocol: The probes were hybridized for 17 h at 65oC on Agilent SurePrint G3 Human GE 8x60k arrays

scan_protocol: The slides were scanned with Agilent G2505C Microarray Scanner at 3 µm resolution

data_processing: Microarray images were processed with Agilent Feature Extraction software v. 11.5.1.1.

source_name: triple-negative breast cancer cell line, inhibited expression

label_protocol: Microarray probes labeled with Cy3 were synthesized from 50 ng of total RNA with Low Input Quick Amp Labeling Kit and checked for quality and quantity with NanoDrop ND-1000 (Thermo Fischer Scientific)

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin and 1% glutamine.

extract_protocol: Total RNA was extracted using the phenol-chloroform method following cell lysis with TriReagent solution

tag: elk3 expression

value: inhibited expression


title: MDA231_ELK3-KD_rep4


title: Dorsal-raphe_male_autism1 [A1_797]


title: MDA231_CTR-KD_rep3

description: Gene expression of MDA-MB-231 cells transduced with sh-control plasmid pLV[shRNA]-EGFP:T2A:Puro-U6>Scramble_shRNA (#VB010000-0009mxc, VectorBuider)

source_name: triple-negative breast cancer cell line, basal expression

value: basal expression


title: MDA231_CTR-KD_rep2


title: MDA231_CTR-KD_rep1


title: Dorsal-raphe_male_control7 [C7_4722]

source_name: Dorsal raphe regions of the post-mortem brain of a male control

value: Normal control


title: MDA231_CTR-KD_rep4


title: Dorsal-raphe_male_control2 [C2_1297]


title: Dorsal-raphe_male_control4 [C4_1793]


title: Dorsal-raphe_male_control6 [C6_4543]


title: Dorsal-raphe_male_autism2 [A2_4231]


title: MDA231_ELK3-KD_rep2


title: Keima-DNAJC5 delJ, neutral, n1

city: Bethesda

first: Yihong

last: Ye

state: MD

address: 5 Center Drive

institute: NIH

description:
Library name: JL4981_4_S4_L005_R1_001
DJ_final_rep1

data_processing:
MAGeCK, version 0.5.9, was used to quantify and to identify differentially expressed sgRNAs. MAGeCK count command was run on the GECKO library A to quantify. Differentially expressed sgRNAs with statistical significance were determined by running the MAGeCK test command in unpaired mode. Genes were ranked based on the number of unique sgRNA enriched in the mKeima neutral population versus the mKeima acidic population. Data was derived from two biological repeats for each screen. Up- and down-regulated genes and sgRNAs by comparing final (neutral) vs. initial (acidic) with statistical significance by False Discovery Rate (FDR) cutoff of 0.05.  Here, up means more reads for final in reference to initial. P-values (unpaired student’s t-test, two-tailed) and FDR values were calculated by considering duplicates.
Assembly: hg38
Supplementary files format and content: The excel file "Counts_non_paired_2020_03_05.xlsx" contains raw counts and normalized counts per sample.  Normalization is based on median with all the replicate samples present.
Supplementary files format and content: Up- and down-regulated genes and sgRNAs by comparing final (Keima neutral) vs. initial (Keima acidic) with statistical significance by False Discovery Rate (FDR) cutoff of 0.05.  Here, up means more reads for final in reference to initial.  MAGeCK authors use ‘pos’ for this ‘up’.  ‘Down’ and ‘neg’ are in the same context.  P-values and FDR values were calculated by considering duplicates.
Library strategy: CRISPR Screen

source_name: human embryonic kidneys

growth_protocol: 60 million of 293T stably expressing mKeima-tagged human DNAJC5 WT or ΔJ mutant supplemented with 8 μg/mL polybrene (Sigma-Aldrich, catalog No. TR-0003) were seeded in two 12-well plates at a density of 3 million cells per well.

extract_protocol:
Genomic DNA was extracted from each cell population using a QIAGEN Blood Maxi kit (for mKeima acidic cells; Qiagen, catalog No. 51192) or QIAGEN Blood Midi kit (for mKeima neutral cells; Qiagen, catalog No. 51183) according to the manufacturer’s protocols.
sgRNAs sequences were amplified from genomic DNA samples using the Herculase II Fusion DNA Polymerase (Agilent, catalog No. 600675) in two PCR steps as follows. In the first PCR, the genomic region containing sgRNAs were amplified from ~250 μg and ~20 μg of total DNA from acidic and neutral samples respectively, using the following primers: Forward: 5′-AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG-3′; Reverse: 5′- TTCAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTTGATAAC-3′. In total, 32 and three PCR reactions for acidic and neutral samples respectively were performed in parallel, with 8 μg genomic DNA in each reaction using Herculase II Fusion DNA Polymerase (Agilent) for 18 cycles and the resulting PCR products were combined. In the second step PCR, 5 μL of first PCR product was used in a 100 μL reaction volume and 12 PCR cycles were used. The primers used for the second PCR include stagger sequences of variable lengths and a 6 bp barcode for multiplexing of different biological samples. The following PCR primers were used in the second step: Forward: 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-(1-7bp variable length sequences)-(6bp barcode)-TTGTGGAAAGGACGAAACACCG -3’; Reverse: 5′-CAAGCAGAAGACGGCATACGAGAT-(6bp barcode)-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCAAGTTGATAACGGACTAGCC-3′. The final PCR products were gel extracted, quantified, and sequenced using a NovaSeq sequencer (Illumina) by the NHLBI DNA Sequencing and Genomics Core. sgRNA sequences were obtained per sample by extracting 20 bps followed by the index sequence of “TTGTGGAAAGGACGAAACACCG” on the de-multiplexed FASTQ files from Illumina’s NGS sequencer using the Cutadapt software, version 2.8 (https://doi.org/10.14806/ej.17.1.200). FASTQC, version 0.11.9 was used to assess the sequencing quality (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

treatment_protocol: Concentrated GeCKO v2 lentivirus (library A) was added to each well at a multiplicity of infection (MOI) at 0.3. Cells were then spun at 1,000 x g at room temperature for 2 h followed by incubation at 37 °C in a humidified incubator for 1 h. After the medium was removed, fresh growth medium was added, and cells were incubated for 48 h before the start of the selection for lentiviral integration using puromycin (0.3 μg/mL). The transduced cells were subcultured in medium supplemented with puromycin every 2 days for a total of 8 days and 80 million cells were maintained for each passage. After puromycin treatment, cells were recovered in a medium lacking puromycin for 24 h before cell sorting. In total, 100 million cells were sorted into mKeima neutral (3% of total cells) or mKeima acidic (97% of total cells) cell populations by a FACSAria™ Fusion Flow Cytometer (BD Bioscience)

value: human embryonic kidneys

value: HEK293T cell

value: Cells stably expressing Keima-DNAJC5 delJ reporter were infected with GeckoV2 libraries (A)


title: Keima-DNAJC5 delJ, neutral, n2

description:
Library name: JL4981_4_S4_L006_R1_001
DJ_final_rep2

value: WT


title: Keima-DNAJC5 delJ, acidic, n2

description:
Library name: JL4981_3_S3_L006_R1_001
DJ_initial_rep2


title: TG10/EC


title: Dorsal-raphe_male_control5 [C5_1860]


title: TG1

value: not cocultured


title: EC

value: EC


title: MDA231_ELK3-KD_rep3


title: TG16


title: Keima-DNAJC5 WT, neutral, n2

description:
Library name: JL4981_2_S2_L006_R1_001
WT_final_rep2

value: Cells stably expressing Keima-DNAJC5 WT reporter were infected with GeckoV2 libraries (A)


title: TG10


title: EC TG1


title: Keima-DNAJC5 WT, acidic, n2

description:
Library name: JL4981_1_S1_L006_R1_001
WT_initial_rep2


title: EC TG10


title: EC OB1


title: Keima-DNAJC5 WT, acidic, n1

description:
Library name: JL4981_1_S1_L005_R1_001
WT_initial_rep1


title: TG16/EC


title: EC TG16


title: OB1


title: Dorsal-raphe_male_control3 [C3_1790]


title: PatientA

city: Farmington

first: Ching

middle: C

last: Lau

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description:
Library name: SC2200680_CL_Vi_002
10x Genomics

data_processing:
Illumina base call files for all libraries were converted to FASTQs using bcl2fastq v2.20.0.422 (Illumina). Whole Visium slide images were uploaded to a local OMERO server.  For each capture area of the Visium slide, a rectangular region of interest (ROI) containing just the capture area was drawn on the whole slide image via OMERO.web, and OMETIFF images of each ROI were programmatically generated using the OMERO Python API.  FASTQ files and associated OMETIFF corresponding to each capture area were aligned to the GRCh38-specific filtered probe set (10x Genomics Human Probeset v1.0.0) using the version 2.1.0 Space Ranger count pipeline (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: List of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of gene IDs
Supplementary files format and content: matrix.tsv.gz: Gene expression count data in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Osteosarcoma

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) samples of two primary OS pre-treatment biopsy tissue samples (Patients A and B) were obtained from CCMC and stored at 4 °C in the dark. Prior to Visium transcriptomics, RNA quality of FFPE samples was determined by DV200 score using Agilent (Santa Clara, California) TapeStation 4200 High Sensitivity DNA ScreenTape. Tissue blocks with DV200 scores above 50% were used for downstream processing.  Briefly, FFPE sections were placed on a 10x Visium FFPE Gene Expression slide, deparaffinized, H&E stained, then imaged in brightfield using a NanoZoomer SQ (Hamamatsu Photonics, Shizuoka, Japan) slide scanner,  followed by incubation with human-specific probe sets provided by the manufacturer for subsequent mRNA labeling.
Incubation with human-specific probe sets provided by the manufacturer for mRNA labeling and library generation was performed according to the manufacturer's protocol using the 10x Genomics Visium FFPE Gene Expression Slide. Libraries were pooled for sequencing on an Illumina NovaSeq 6000 200-cycle S4 flow cell using a 28-10-10-90 read configuration, targeting 100,000 read pairs per spot covered by tissue.

value: Osteosarcoma

tag: patient sex

tag: sample source

value: Connecticut Children's Medical Center


title: PatientB

description:
Library name: SC2200681_CL_Vi_003
10x Genomics

value: Female


title: OS.C.21.BX.OCT

description:
Library name: NC_OS.C.21.BC.OCT
10x Genomics

data_processing:
10X Genomics Cell Ranger (3.0.2) was used for read alignment (version 3.0.0, GRCh38) and count matrix generation (https://www.10xgenomics.com/support/software/cell-ranger/latest). Reads from each sample were initially filtered using multiple criteria: during FASTQ generation, reads with more than one mismatch in the 8bp i7 index are excluded. Only reads aligned to annotated transcripts with MAPQ scores greater than 255 are retained. Reads containing bases with Q30 scores below 3 are also excluded. Following alignment, cell barcodes were filtered against a whitelist of barcodes provided by 10X Genomics (<2 mismatches). Barcodes associated with cells are distinguished from those associated with ambient mRNA using an adaptively computed UMI threshold via Cell Ranger, and a digital counts matrix is generated for each sample. Single-cell RNA expression data from an additional 6 samples described in Liu et al. (Front Oncol, 2021) was downloaded from the Gene Expression Omnibus (GSE162454). For all samples, additional preprocessing was performed using Seurat (version 4.0.5) in R (version 4.1.1). For each cell, the percentage of reads mapping to mitochondrial and ribosomal genes was calculated, and cells were filtered out according to the following criterion: >20% mtRNA, >50% rRNA, or <500 features expressed. Doublet detection and removal was performed using the R-package DoubletFinder (default parameters).
Assembly: GRCh38
Supplementary files format and content: Tab-separated barcodes, features, and matrix files for each sample provided

extract_protocol:
Tumor tissue specimens of six OS patients were collected at Connecticut Children’s Medical Center (CCMC) or Children’s Hospital Colorado (CHCO). All specimen collection and experiments were reviewed and approved by the Institutional Review Board of CCMC or CHCO, respectively. Written informed consent was obtained prior to acquisition of tissue from patients. Diagnosis was confirmed by pathologist assessment. CCMC-sourced specimens were stored in MACS tissue storage solution (Miltenyi Biotec, Bergisch Gladbach, Germany), then transferred to The Jackson Laboratory for Genomic Medicine for the tissue dissociation process. For CCMC samples, the tissue specimens were minced and enzymatically dissociated in DMEM medium supplemented with Collagenase II (250U/ml, Gibco #17101-015, Waltham, Massachusetts, USA) and DNase (1μg/ml, Stemcell #07900, Cambridge, Massachusetts, USA) for up to 3 cycles of 37 °C 15 minutes dissociation with agitation. After each cycle, undigested tissue pieces were settled down by gravity and supernatant was transferred to cold Buffer I solution (10% FBS/DMEM medium supplemented by EDTA (2mM) and 2% BSA (Lampire #7500854, Pipersville, Pennsylvania, USA). Fresh dissociation solution was applied to the undigested tissue for next digestion cycle. Cells collected from each cycle were merged, spun down and resuspended with ACK lysis buffer (Gibco #A1049201) to remove red blood cells. After 3 minutes on ice, lysis reaction was quenched by adding Buffer I solution. After centrifugation, cells were resuspended in Buffer I solution and strained through a 70-μm cell strainer. Cells were stained with propidium iodide (PI) and Calcein Violet (Thermo Fisehr Scientific). PI-negative and Calcien Violet-positive viable cells were sorted out using FACSAria Fusion system (BD Biosciences, Franklin Lakes, New Jersey, USA). For CHCO samples, tissue specimens were viably cryopreserved in 90% FBS 10% DMSO immediately after collection. Tissue specimens were thawed at 37 °C, then enzymatically dissociated in a 0.1% DNase and Liberase 400g/mL (Roche/Sigma-Aldrich, St. Louis, Missouri, USA) cocktail. Cells were then selected for viability using the FACSAria I cell sorter (BD Biosciences) in the Allergy and Clinical Immunology Flow Cytometry Facility at the Division of Allergy and Clinical Immunology, University of Colorado School of Medicine.
Cells were washed and resuspended in PBS containing 0.04% BSA. Cells were counted on Countess II automated cell counter (Thermo Fisher, Waltham, Massachusetts, USA), and up to 12,000 cells were loaded per lane on 10x Chromium microfluidic chips (10x Genomics, Pleasanton, California, USA). Single-cell capture, barcoding, and library preparation were performed using the 10x Chromium X version 3 chemistry, and according to the manufacturer’s protocol. cDNA and libraries were checked for quality on Agilent 4200 Tapestation and quantified by KAPA qPCR before sequencing using a Novaseq 6000 (Illumina, San Diego, California, USA) v1.5 cycle flow cell lane at 100,000 reads per cell, with a 28-10-10-90 asymmetric read configuration.

value: Male

value: Children's Hospital Colorado


title: 010_BX_COM

description:
Library name: INT_CL21001
10x Genomics


title: Keima-DNAJC5 delJ, acidic, n1

description:
Library name: JL4981_3_S3_L005_R1_001
DJ_initial_rep1


title: Dorsal-raphe_male_control1 [C1_1065]

value: Dorsal raphe nucleus from post-mortem brain


title: OS.C.33.BX

description:
Library name: NC_OS.C.33.BX
10x Genomics


title: 003_BX_COM

description:
Library name: INT_CL19005
10x Genomics


title: HCT116 LD Replicate 1

city: Houston

first: Stephen

middle: Qi Rong

last: Wong

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist

description: Library name: HCT116 LD 1

data_processing:
Peak calling was performed using MACS2 (v2.1.2). Bigwig files were generated and used to plot ATAC-seq peaks in target genes using IGV and deeptools/pyGenomeTracks.
Assembly: GrCh38
Supplementary files format and content: bigwig files for each sample

source_name: Colon

growth_protocol: HCT116 cells are cultured in McCoy supplemented with 10% FBS, 1% Pen-Stre and 1% Sodium Pyruvate.

extract_protocol:
Cells were washed twice with ice-cold PBS before being scrapped and transferred to eppendorf tube. Samples were then prepared according to protocol from ATAC-seq Kit (53150, ACTIVE MOTIF)
According to ATAC-seq kit used (53150, ACTIVE MOTIF).

treatment_protocol: HCT116 cells were treated with 0.5 uM (low dose; LD), 5 uM (mid dose; MD) or 80 uM (high dose; HD) for 72 hours before changing to drug free media. Cells were then subcultured and treated again with the same dose for 72 hours. Cells were treated for 10 cycles. Cells were subsequently cultured in drug free media and used for downstream experiments.

value: Colon

value: Epithelial


title: HCT116 LD Replicate 2

description: Library name: HCT116 LD 2


title: 001_BX_COM

description:
Library name: INT_CL19004
10x Genomics


title: OS.C.32.BX

description:
Library name: NC_OS.C.32.BX
10x Genomics


title: HCT116 HD Replicate 2

description: Library name: HCT116 HD 2


title: Dorsal-raphe_male_autism3 [A3_4721]

value: Autism


title: HCT116 HD Replicate 1

description: Library name: HCT116 HD 1


title: CTG2440-61

city: San Diego

first: Celia

last: Fontanillo

state: CA

address: 10300 Campus Point Dr

institute: Bristol Myers Squibb

description:
Library name: SRS22-28-061
Column name in counts_matrix.tsv: SRS22.28.061.Human

data_processing:
Paired-end reads were analyzed using the Seven Bridges platform (Seven Bridges Genomics). FASTQ reads were aligned to reference genome GRCh38 using STAR with default parameters
Transcriptome gene-level abundance estimated through RSEM v1.3.0 with Ensembl GRCh38 v91 gene annotation
Assembly: GRCh38ERCC-ensembl91
Supplementary files format and content: TSV file includes counts matrix for the samples.

source_name: tumor tissue

extract_protocol:
Trizol Extraction followed by Qiagen RNeasy Mini Kit
Standard GENEWIZ/Azenta Illumina compatible library prep kit. Library preparation, Illumina, strand-specific RNA-seq with Poly-A Enrichment (w/ ERCC spike-in).

value: tumor tissue

value: mCRPC tumor


title: CTG2440-60

description:
Library name: SRS22-28-060
Column name in counts_matrix.tsv: SRS22.28.060.Human


title: HCT116 MD Replicate 2

description: Library name: HCT116 MD 2


title: Keima-DNAJC5 WT, neutral, n1

description:
Library name: JL4981_2_S2_L005_R1_001
WT_final_rep1

value: human embryonic kidneys

value: HEK293T cell


title: CTG2440-55

description:
Library name: SRS22-28-055
Column name in counts_matrix.tsv: SRS22.28.055.Human

value: Vehicle


title: CTG2440-52

description:
Library name: SRS22-28-052
Column name in counts_matrix.tsv: SRS22.28.052.Human

value: Enzalutamide


title: HCT116 Control Replicate 2

description: Library name: HCT116 Control 2


title: HCT116 Control Replicate 1

description: Library name: HCT116 Control 1


title: CTG2440-51

description:
Library name: SRS22-28-051
Column name in counts_matrix.tsv: SRS22.28.051.Human


title: CTG2440-63

description:
Library name: SRS22-28-063
Column name in counts_matrix.tsv: SRS22.28.063.Human


title: CTG2440-50

description:
Library name: SRS22-28-050
Column name in counts_matrix.tsv: SRS22.28.050.Human


title: CTG2440-62

description:
Library name: SRS22-28-062
Column name in counts_matrix.tsv: SRS22.28.062.Human


title: CTG2440-65

description:
Library name: SRS22-28-065
Column name in counts_matrix.tsv: SRS22.28.065.Human


title: CTG2440-58

description:
Library name: SRS22-28-058
Column name in counts_matrix.tsv: SRS22.28.058.Human


title: CTG2440-59

description:
Library name: SRS22-28-059
Column name in counts_matrix.tsv: SRS22.28.059.Human


title: CTG2440-57

description:
Library name: SRS22-28-057
Column name in counts_matrix.tsv: SRS22.28.057.Human


title: CTG2440-64

description:
Library name: SRS22-28-064
Column name in counts_matrix.tsv: SRS22.28.064.Human


title: CTG2440-49

description:
Library name: SRS22-28-049
Column name in counts_matrix.tsv: SRS22.28.049.Human


title: CTG2440-42

description:
Library name: SRS22-28-042
Column name in counts_matrix.tsv: SRS22.28.042.Human


title: CTG2440-54

description:
Library name: SRS22-28-054
Column name in counts_matrix.tsv: SRS22.28.054.Human


title: CTG2440-47

description:
Library name: SRS22-28-047
Column name in counts_matrix.tsv: SRS22.28.047.Human


title: CTG2440-56

description:
Library name: SRS22-28-056
Column name in counts_matrix.tsv: SRS22.28.056.Human


title: H2452 cells sgNF2-1_3

city: Nanjing

first: Tong

last: Hu

address: No. 300 Guangzhou Road

institute: Nanjing Medical University

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to eachgene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files includes FPKM values for each sample

source_name: tumor

growth_protocol: Cells were cultured in RPMI-1640 medium, supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin solution.

extract_protocol:
Total RNA was extracted from sgCtrl or NF2-KO PM cells via the QIAwave RNA Mini Kit.An input of 1 μg of RNA per sample was employed for the RNA sample preparations.
In alignment with the manufacturer's guidelines, sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), with index codes incorporated to facilitate the assignment of sequences to each sample.

value: tumor

value: pleural mesothelioma


title: CTG2440-53

description:
Library name: SRS22-28-053
Column name in counts_matrix.tsv: SRS22.28.053.Human


title: CTG2440-46

description:
Library name: SRS22-28-046
Column name in counts_matrix.tsv: SRS22.28.046.Human


title: CTG2440-43

description:
Library name: SRS22-28-043
Column name in counts_matrix.tsv: SRS22.28.043.Human


title: H2452 cells sgNF2-1_2

description: Library name: Sample 5


title: H2452 cells sgCtrl_1

description: Library name: Sample 1

value: WT


title: CTG2440-44

description:
Library name: SRS22-28-044
Column name in counts_matrix.tsv: SRS22.28.044.Human


title: H2452 cells sgCtrl_3

description: Library name: Sample 3


title: H2452 cells sgCtrl_2

description: Library name: Sample 2


title: CTG2440-48

description:
Library name: SRS22-28-048
Column name in counts_matrix.tsv: SRS22.28.048.Human


title: SBI_rep3

city: Chicago

first: Elizabeth

middle: Thomas

last: Bartom

state: IL

address: 303 E Superior Ave, SQBRC 7-406

department: Biochemistry and Molecular Genetics

institute: NORTHWESTERN UNIVERSITY AT CHICAGO

description:
Library name: SBI_rep3
Column name in Table S1: SBI.rep3

data_processing:
Raw reads in FASTQ format were run through a variety of quality control steps. These include FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to check for overall score distribution and repetitiveness, FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) to check for RNAs of non-human origin (including mycoplasmal reads), and NGSCheckMate, to check that the only significant genetic match of the RNA reads in the Cancer Cell Line Encyclopedia was to the HEL cell line and its derivative HEL9217.
Reads were trimmed with Trimmomatic (TRAILING:30 MINLEN:20), and then aligned to the hg38 genome with STAR to generate BAM files.
Genic reads were quantified using HTSeq-count and the Ensembl 78 version of the hg38 gene annotation.  RNA tracks in Bigwig format were generated from BAM files using the GenomicRanges library in R, normalized for library size (CPM).
The R package edgeR was used to identify differentially expressed genes in both ULK101 and SBI treated cells relative to Control DMSO treated cells. The resulting statistics are included in the processed data file Table S1.
Assembly: hg38
Supplementary files format and content: The R package edgeR was used to identify differentially expressed genes in both ULK101 and SBI treated cells relative to Control DMSO treated cells. The resulting statistics are included in the processed data file Table S1 as an Excel file.

source_name: HEL

growth_protocol: HEL cells (#TIB-180; ATCC) were grown in RPMI 1640 medium (Gibco) supplemented with 10% FBS and antibiotics at 37°C and 5% CO2 .

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions
Library construction and stranded mRNA sequencing were conducted at Novogene. Briefly, quality control for RNA samples was performed using Nanodrop and agarose gel electrophoresis. Next, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. The enriched mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. After a series of end terminal repair, A tailing, sequencing adapter ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. Quality control for the library was performed using Qubit fluorometer and quantitative real time-PCR for quantification and Agilent Bioanalyzer 2100 for size distribution detection.
Quantified libraries were pooled and sequenced on the Illumina NovaSeq 6000 (S4 flowcell), using a paired-end 150bp (PE150) sequencing strategy. The clustering of the index coded samples was performed according to the manufacturer’s instructions.

treatment_protocol: HEL cells were plated as four biological replicates and were treated for 6 hours with either vehicle (DMSO), SBI-0206965 (5mM) or ULK101 (5mM).

value: HEL

value: erythroblast cell line

value: SBI


title: SBI_rep4

description:
Library name: SBI_rep4
Column name in Table S1: SBI.rep4


title: ULK101_rep2

description:
Library name: ULK101_rep2
Column name in Table S1: ULK101.rep2


title: ULK101_rep1

description:
Library name: ULK101_rep1
Column name in Table S1: ULK101.rep1


title: Ctrl_rep4

description:
Library name: Ctrl_rep4
Column name in Table S1: Ctrl.rep4

value: DMSO


title: SBI_rep2

description:
Library name: SBI_rep2
Column name in Table S1: SBI.rep2


title: SBI_rep1

description:
Library name: SBI_rep1
Column name in Table S1: SBI.rep1


title: Ctrl_rep3

description:
Library name: Ctrl_rep3
Column name in Table S1: Ctrl.rep3


title: Ctrl_rep2

description:
Library name: Ctrl_rep2
Column name in Table S1: Ctrl.rep2


title: Ctrl_rep1

description:
Library name: Ctrl_rep1
Column name in Table S1: Ctrl.rep1


title: HEL_ATAC_SBI_rep3

description:
Library name: HEL_ATAC_SBI_rep3
Log2ratio SBI-treated to DMSO-treated ATACseq coverage track (CPM) for short fragments (<140 bp)

data_processing:
The library was sequenced as 150 bp paired-end reads on the Illumina NovaSeq 6000 platform.
ATAC-seq analysis was carried out using the NF-core ATACseq pipeline v2.0.  Briefly, read quality was checked with FastQC v0.11.9, trimmed reads aligned to human reference genome GRCh38 with bwa v0.7.17, CPM-normalized bigwig tracks generated with BEDTools v2.30.0 and bedGraphToBigWig 377 and narrow peaks called with MACS2 v2.2.7.1.  The UCSC genome browser was used for detailed inspection of ATAC-seq tracks in the context of the gene loci differentially expressed in response to either ULK101 or SBI-0206965.  Consensus regions of chromatin accessibility were also checked for read counts across all samples systematically, to identify any differentially accessible regions with DESeq2 v1.28.0.
Assembly: GRCh38
Supplementary files format and content: Bigwig track files are supplied for visualizing the data in the UCSC genome browser.  First, nucleosome free regions were identified by pulling ATAC-seq fragments < 140 bp in length from the aligned BAM files for each sample using samtools v1.6.  Deeptools v3.5.5 was then used to generate CPM normalized tracks (such as HEL.DMSO_REP1.max140.NFR.bw) with bamCoverage, and log2ratio tracks were generated from these using deeptools bigwigCompare.

extract_protocol:
50,000 HEL cells from each treatment condition were washed with PBS and subjected to nuclei extraction using a cold lysis buffer (Resuspension Buffer: 1M Tris-HCl, pH 7.5; 5M NaCl; 1M MgCl2; 10% NP-40; 10% Tween-20; and 1% Digitonin). The lysis conditions, optimized for HEL cells, involved incubation on ice for 3–7 minutes, followed by the addition of 1 mL of Wash Buffer (Resuspension Buffer and 10% Tween-20) to stop the lysis. Optimal cell lysis was monitored under a microscope. Next, the transposition reaction mix (2X Tagment DNA Buffer, 1X PBS, 10% Tween-20, 1% Digitonin), and Tn5 Transposase (Illumina #15027865) was added, followed by incubation at 37°C for 30 minutes. DNA was then purified using the QIAGEN PCR Purification Kit (Qiagen #28006).
PCR amplification was performed with 20 µL of transposed DNA, Nextera PCR Primers, and KAPA HiFi HotStart Ready Mix (#KR0370) for 8 cycles. Size selection was carried out using KAPA Pure beads (Roche #KK8002). Library verification was done by running 1 µL on a 4200 TapeStation (Agilent #G2991BA) to check for nucleosome patterns, confirming the success of the assay.

treatment_protocol: HEL cells were plated as three biological replicates and HEL were treated with either vehicle (DMSO), 5µM of ULK101 or 5µM of SBI-0206965 for 4 hours and assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed


title: HCT116 MD Replicate 1

description: Library name: HCT116 MD 1


title: HEL_ATAC_ULK101_rep1

description:
Library name: HEL_ATAC_ULK101_rep1
Log2ratio ULK101-treated to DMSO-treated ATACseq coverage track (CPM) for short fragments (<140 bp)


title: CTG2440-45

description:
Library name: SRS22-28-045
Column name in counts_matrix.tsv: SRS22.28.045.Human


title: HEL_ATAC_ULK101_rep3

description:
Library name: HEL_ATAC_ULK101_rep3
Log2ratio ULK101-treated to DMSO-treated ATACseq coverage track (CPM) for short fragments (<140 bp)


title: HEL_ATAC_SBI_rep1

description:
Library name: HEL_ATAC_SBI_rep1
Log2ratio SBI-treated to DMSO-treated ATACseq coverage track (CPM) for short fragments (<140 bp)


title: HEL_ATAC_ULK101_rep2

description:
Library name: HEL_ATAC_ULK101_rep2
Log2ratio ULK101-treated to DMSO-treated ATACseq coverage track (CPM) for short fragments (<140 bp)


title: ULK101_rep4

description:
Library name: ULK101_rep4
Column name in Table S1: ULK101.rep4


title: HEL_ATAC_DMSO_rep3

description:
Library name: HEL_ATAC_DMSO_rep3
DMSO ATACseq Nucleosome free region coverage track (CPM)


title: HEL_ATAC_DMSO_rep1

description:
Library name: HEL_ATAC_DMSO_rep1
DMSO ATACseq Nucleosome free region coverage track (CPM)


title: ULK101_rep3

description:
Library name: ULK101_rep3
Column name in Table S1: ULK101.rep3


title: pi-2

city: Shenzhen

first: Ma

last: Jianshuai

address: No. 3025, Shennan Middle Road, Futian District

department: the Eighth Affiliated Hospital

institute: Sun Yat-sen University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: all.fpkm_anno.xls

source_name: Vascular

extract_protocol:
RNA Reagent kit
VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina

value: Vascular

value: Smooth muscle cell

value: Pi


title: HEL_ATAC_DMSO_rep2

description:
Library name: HEL_ATAC_DMSO_rep2
DMSO ATACseq Nucleosome free region coverage track (CPM)


title: NRTIs-3

value: LINE1 intervention-2

value: Pi+NRTIs


title: pi-1


title: si-line1-3

value: LINE1 intervention-1


title: TG1/EC

value: cocultured


title: si-line1-2


title: NRTIs-1


title: pi-3


title: si-nc-3

value: Pi+si-NC


title: si-line1-1


title: si-nc-1


title: TF knockdown, BMP4 patterned NGN2 iNeurons, 409B2 genotype

city: Basel

first: Jasper

last: Janssens

address: Mattenstrasse 26

department: DBSSE

country: Switzerland

institute: ETH Zurich

description: 10x Genomics RNA 5' v2

data_processing:
ParseBio snRNAreads were aligned against the human genome (hg38, sourced from Parse Biosciences) by split-pipe (v1.0.4, Parse Biosciences)
10x Multiome reads were aligned against the human genome (hg38, sourced from 10x Genomics) by Cell Ranger ARC (v2.0.0, 10x Genomics)
scRNA-seq samples were loaded into scanpy. Next, cells were filtered on quality using the following thresholds: minimum number of genes = 750 and minimum number of UMI counts = 1000. Furthermore, cells that were more than 5 standard deviations in log1p(total_counts), log1p(number of genes) and percentage of counts in top 20 genes were also removed. Next, we removed cells that showed too high percentage of mitochondrial reads (5% for NGN2-iNs, 6% for ASCL1/DLX2 post-patterned iNs, 8% for ASCL1/DLX2 pre-patterned iNs). Finally, we used Scrublet to remove predicted doublets.
10x 5' scRNA reads from TF knockdown (TF-KD) were mapped to the human genome (hg38, sourced from 10x Genomics), and gRNAs were quantified using cellranger multi.
10x 3' v3.1 scRNA reads from TF overexpression (TF-OE) were aligned against the human genome (hg38, sourced from 10x Genomics) by Cell Ranger (cellranger-7.0.1). TF and FB libraries were mapped against artificial reference genomes generated using cellranger -mkref on TF CDS sequences. Information for the custom genomes is added as .csv files.
bulk RNA-seq samples were preprocessed using fastp, and mapped using STAR against hg38. Data was then analyzed using DESEQ2.
Assembly: hg38
Supplementary files format and content: scRNA-seq data is represented by adata objects (Scanpy), containing raw expression values for both the ParseBio snRNA and 10x multiome samples. Treatment information and analysis results are given as .tsv files.
Supplementary files format and content: 10x multiome ATAC processed data is given by fragment files
Supplementary files format and content: bulk RNA-seq samples are represented by count matrices and meta data files given as .tsv files
Supplementary files format and content: 10x scRNA data from perturbation experiments is represented by adata objects (Scanpy), containing raw expression values and TF/FB/gRNA quantification. Additional information is given as meta .tsv files.

source_name: NGN2-inducible iPSCs, 409B2 background

growth_protocol: All cells were cultured under standard conditions of 37°C and 5% CO2

extract_protocol:
For ParseBio, to obtain single cell suspension, induced neurons cultured in 12-well plates were washed with PBS and incubated with 300 μL accutase at 37°C for 5 min. Dissociation reaction were stopped with 700 μL PBS containing 0.04% BSA, and cells were gently trituated into single cell suspension. Cells were washed twice with 500 μL PBS containing 0.04% BSA before nuclei isolation. To isolate the nuclei from single cell suspension, cells were trituated ten times in 100 μL lysis buffer (10 mM Tris-Cl pH7.4, 3 mM NaCl, 10 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 0.2U/μL RNase inhibitor (Takara), 0.1% NP-40, 0.01% Digitonin (Invitrogen)) and incubate 2 min on ice. The isolated nuclei underwent two subsequent washes in 500 μL wash buffer (10 mM Tris-Cl pH7.4, 3 mM NaCl, 10 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT, 0.2U/μL RNase inhibitor). Isolated nuclei were fixed and cryopreserved for snRNA-seq according to the instructions provided by the manufacturer (Parse Biosciences).
For 10x Multiome, single-cell suspensions obtained from each NGN2-iN pre-patterning condition were divided into two distinct pools (Supplementary Table 1). Subsequently, each pool, along with the control NGN2-inducible iPSCs, underwent nuclei isolation individually following provider’s instruction (10x Genomics user guide CG000365).
For bulk RNA-seq, to extract RNA, cells were individually collected and lysed in Trizol (Invitrogen). Subsequently, RNA extraction was performed in the multi-well format using the MagMAX™-96 for microarrays total RNA isolation kit (Invitrogen). Quality assessment of the isolated RNAs from each condition was conducted using the RNA 6000 Pico Kit and the 2100 Bioanalyzer Systems (Agilent), while quantification was carried out using the Qubit system (Invitrogen). cDNA reverse transcription and amplification were carried out according to the smart-seq2 protocol (64). The preparation of the sequencing library was based on the Nextera XT DNA Library Prep protocol (Illumina), and subsequently sequenced using the Illumina NextSeq High Output paired-end 2x75 parameter (NGN2 pre-patterned progenitors) or NovaSeq SP paired-end 2x51 (reproducibility, stability and ASCL1-DLX2 pre-patterned progenitors). Sequencing reads from the fastq file were aligned against the hg38 reference genome (obtained from 10x Genomics) using the STAR RNA-seq aligner with default parameters.
FACS sorted NGN2-iNs + TF-OE were pooled for GEM generation and cDNA preparation according to the 10x-Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) protocol. The resulting cDNA was split for separate transcriptome and feature barcode library preparation and pooled for sequencing on the Illumina NovaSeq 6000 platform using 28/10/10/90 as cycle parameters.
FACS sorted TF-KO NGN2-iNs from the same morphogen condition (RA or BMP4) and their respective non-targeting control were pooled for scRNA-seq + CRISPR gRNA detection following the Chromium Next GEM Single Cell 5’ v2 (Dual Index) kit protocol. The transcriptome libraries and gRNA libraries were pooled and sequenced on the NovaSeq 6000 platform using 26/10/10/90 as cycle parameters. For sample demultiplexing and generation of count matrices, cellranger -multi (10x Genomics) was utilized. To facilitate efficient gRNA detection, the pattern and sequence entries in the feature reference files were adjusted to 12bp. For gRNA label assignment, the 10x gRNA calling outputs (protospacer_calls_per_cell.csv) were further filtered to retain only cells with gRNAs targeting a single gene. Cells lacking gRNAs or those with gRNAs targeting multiple genes were excluded from further analysis. Cells with effective perturbations were identified using Mixscape (PMID: 33649593) as implemented in Seurat (PMID: 34062119). To visualize the enrichment or depletion of KO cells relative to controls, the densities of both control and KO cells on the UMAP embedding were estimated using Nebulosa (PMID: 33459785) with weight=1. KO cell densities were matched to the nearest control cells based on UMAP coordinates. The difference in density between the KO and corresponding control cells was then calculated and visualized on the UMAP embedding.
Libraries were constructed according to the manufacter's instructions. For 10x Genomics user guide CG000338 was used.

treatment_protocol: Cells were treated with varying concentrations of BMP4, SHH, RA, XAV, CHIR, FGF8 and CycA on different media types and different timings

value: NGN2-inducible iPSCs, 409B2 background


title: HEL_ATAC_SBI_rep2

description:
Library name: HEL_ATAC_SBI_rep2
Log2ratio SBI-treated to DMSO-treated ATACseq coverage track (CPM) for short fragments (<140 bp)


title: TF knockdown, retinoic acid patterned NGN2 iNeurons, 409B2 genotype

description: 10x Genomics RNA 5' v2


title: patterned NGN2 iNeurons, 12 conditions x 6 timepoints, 409B2 genotype

description: bulk RNA-seq


title: TF overexpression NGN2 iNeurons, batch 1, 409B2 genotype

description: 10x Genomics RNA 3' v3.1


title: patterned NGN2 iNeurons, 12 conditions x 3 replicates, SC102A1 genotype

description: bulk RNA-seq

source_name: NGN2-inducible iPSCs, SC102A1 background


title: patterned NGN2 iNeurons, 12 conditions x 3 replicates, WTC genotype

description: bulk RNA-seq

source_name: NGN2-inducible iPSCs, WTC background

value: NGN2-inducible iPSCs, WTC background


title: patterned NGN2 iNeurons, 12 conditions x 3 replicates, 409B2 genotype

description: bulk RNA-seq


title: NRTIs-2


title: BICR10_shYEATS2_2

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

data_processing:
FastQC was used for quality assessment of raw Fastq reads.
Fastq files were mapped to human GRCh38 genome using STAR aligner.
For RNA-seq HTSeq was used to count the reads numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files with raw counts for each sample.

growth_protocol: BICR10 cells were cultured in media recommended by European Collection of Authenticated Cell Cultures in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol:
For RNA-seq, total RNA was extracted from shControl and shYEATS2 cells using TRIzol (Invitrogen, 15596026).
Library was prepared using the QIAseq Stranded mRNA Lib Kit (Qiagen, Cat. No. 180441 ) (mRNA enrichment method was used for RNA-seq).
150 bp paired-end sequencing was done using Illumina NovaSeq 6000.

treatment_protocol: BICR10 cells were silenced for YEATS2 using lentiviral transduction of either control or shYEATS2 plasmid

value: Head and neck cancer


title: BICR10_shControl_2

value: shControl


title: BICR10_shYEATS2_Input

data_processing:
FastQC was used for quality assessment of raw Fastq reads.
Fastq files were mapped to human GRCh38 genome.
For ChIP-seq data, macs2 was used for peak calling. Each BAM file was converted into bigWig file using DeepTools BamCoverage.
Assembly: GRCh38
Supplementary files format and content: BigWig

extract_protocol:
For YEATS2 ChIP-seq, chromatin extracted from BICR10 cells was used. For H3K27Cr ChIP-seq, chromatin extracted from either shControl or shYEATS2 BICR10 cells was used. ChIP was performed as described previously (Shukla et al., 2011; Khoury et al., 2020)
Library was prepared using TruSeq ChIP Library Preparation Kit (IP-202-1012) for YEATS2 ChIP-seq and NEBNext Ultra II DNA lib preparation for Illumina Kit (NEBNext #E7645S) for H3K27Cr ChIP-seq.
100 bp (for YEATS2 ChIP-seq) or 150 bp (H3K27Cr ChIP-seq) paired-end sequencing was done using Illumina NovaSeq 6000.

treatment_protocol: BICR10 cells were silenced for YEATS2 using lentiviral transduction of either control or shYEATS2 plasmid.

tag: chip antibody


title: BICR10_shYEATS2_H3K27Cr_1

value: H3K27Cr (PTM Bio, #PTM-545RM)


title: BICR10_shControl_Input


title: BICR10_shControl_H3K27Cr_2


title: si-nc-2


title: BICR10_Input_2


title: BICR10_Input_1


title: BICR10_shControl_H3K27Cr_1


title: AB_84, small RNA, Pancreas

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Avenue

department: Laboratory Medicine and Pathology

country: Canada

institute: University of Alberta

data_processing:
The libraries were normalized, pooled, and denatured. Pooled libraries were loaded on Illumina NovaSeq SP lane using Xp protocol per manufacturer's recommendations.
Base-calling was performed with RTA v.3.4.4. Program bcl2fastq2 was used to demultiplex and generate fastq reads. Raw fastq files were subjected to cutadapt for  adapter trimming. Trimmed Reads were aligned to human genome 38 using Bowtie.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw count data for each sample

source_name: Rectus abdominis muscle

growth_protocol: Not Applicable

extract_protocol:
RNA extraction was performed using the Trizol method and Qiagen RNAeasy midi kit (Mississauga, ON). The optical density (OD) 260/280 ratio was measured using Nanodrop, and RNA integrity number (RIN) was assessed using Agilent Bio-analyzer 2100 for all the samples.
Libraries were genrated using NEBNext Multiplex Small RNA library Prep kit for Illumina as per the manufacturer's recommendations.

treatment_protocol: Not Applicable

value: Rectus abdominis muscle

value: Skeletal muscle tissue


title: BICR10_YEATS2_2

value: YEATS2 (ProteinTech, #24717-1-AP)


title: AB_83, small RNA, Colorectal


title: BICR10_YEATS2_1


title: AB_81, small RNA, Colorectal


title: AB_80, small RNA, Colorectal


title: AB_79, small RNA, Pancreas


title: TF overexpression NGN2 iNeurons, batch 2, 409B2 genotype

description: 10x Genomics RNA 3' v3.1


title: BICR10_shYEATS2_1


title: AB_75, small RNA, Pancreas


title: AB_77, small RNA, Colorectal


title: AB_73, small RNA, Colorectal


title: AB_72, small RNA, Colorectal


title: AB_74, small RNA, Colorectal


title: BICR10_shControl_1


title: H2452 cells sgNF2-1_1

description: Library name: Sample 4

value: tumor

value: pleural mesothelioma


title: AB_78, small RNA, Pancreas


title: AB_76, small RNA, Colorectal


title: AB_82, small RNA, Pancreas


title: THP-1-derived macrophages, si-SLC40A1-2, biol rep 3

city: Guangzhou

first: Xinyu

last: Pan

address: No. 135 West Xingang Road, Haizhu District

institute: Sun Yat-Sen University Department of Biochemistry

description:
Library name: sample9
column name in counts.txt: s23

data_processing:
Paired-end RNA-seq reads were quality- and adapter-trimmed using Cutadapt (v1.18).
Cleaned reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.2.1) with default parameters.
Aligned reads were filtered using SAMtools (v1.6) to retain uniquely mapped reads with mapping quality of at least 20, then sorted and indexed.
Gene-level read counts were quantified using featureCounts (v2.0.6)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37 °C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using a standard poly(A) mRNA enrichment protocol and sequenced using paired-end reads.

treatment_protocol:
THP-1 cells were treated with 50 ng/mL phorbol 12-myristate 13-acetate (PMA) for 48 hours to induce differentiation into macrophage-like cells.
Differentiated cells were then transfected with either SLC40A1-targeting siRNA (two independent sequences) or negative control siRNA using Lipofectamine RNAiMAX reagent according to the manufacturer's instructions.

value: macrophage

value: SLC40A1 knockdown

value: PMA-induced differentiation + si-SLC40A1-2 transfection


title: BICR10_shYEATS2_H3K27Cr_2


title: AB_71, small RNA, Colorectal


title: AB_70, small RNA, Colorectal


title: THP-1-derived macrophages, si-SLC40A1-2, biol rep 1

description:
Library name: sample7
column name in counts.txt: s21


title: NGN2 progenitors, 96 conditions

description: bulk RNA-seq


title: QS_IP.

city: Chongqing

first: Jianmin

last: Li

address: shapingba xinqiaozhengjie 183

institute: Army Medical University

data_processing:
Raw data quality control were performed using FastQC (version v0.11.5).
Remove joint contamination. That is, remove the connector sequence at the end of the reads and filter out the reads whose length is shorter than 15bp.
ChIP-seq reads were aligned to the Rattus_norvegicus.Rnor_6.0 genome to obtain comprehensive transcript information.
In the ChIP-seq analysis of transcription factors with Input and IP, we take Input as the background, use Macs2 to call peak IP, and use narrow peak mode for peak calling.
The MACS2 software (Version 2.1.1) was used for peak calling.
using STAR software (version 2.5.3a) with default parameters.
Assembly: Rnor_6.0
Supplementary files format and content: Tab-delimited text files include peak abundances.

organism: Rattus norvegicus

source_name: Nucleus pulposus cells

growth_protocol: Nucleus pulposus cells were cultured in a DMEM-F12 medium containing 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Gibco) at 37°C humidified with 5% CO2.

extract_protocol:
The DNA of input and IP was extracted by phenol-chloroform method.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer with PE150 model.

treatment_protocol: Nucleus pulposus cells were cultured in a medium with 0.1% FBS (serum-starvation).

value: Nucleus pulposus cells

tag: condition

value: Serum starved


title: QS_Input.


title: NC_IP.

value: Serum


title: MCF7 DMSO 18hrs (3 replicates)

city: Haifa

first: Elazar

last: Besser

address: Kiryat Hatechnion

country: Israel

institute: Technion

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses cutadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: HTseq-count version 0.11.2
Normalization and differential expression analysis: DESeq2 R package version 1.24.0
Assembly: Genome: Human_GRCh38; Annotation: Homo_sapiens.GRCh38.89

growth_protocol: MCF7 cells were grown in Dulbecco's Modified Eagle's Medium supplemented with 10% Fetal Bovine Serum, 100 units/mL penicillin G and 100 μg/mL streptomycin and maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells (5×10^5/sample) and isolated using TRI reagents (Sigma, UK), according to the manufacturer’s protocol.
The RNA was prepared for sequencing with Illumina TruSeq RNA Library Preparation Kit v2.

treatment_protocol: MCF7 cells were seeded in 6-well plates, at 5×10^5 cells per well. Following 18-24 hours, the media was replaced to phenol red-free DMEM and treated with either DMSO control or Cannabis extract CANN14 for 18 hrs.

value: ER+ breast cancer

value: WT

value: DMSO


title: MCF7 CANN14 18 hrs (3 replicates)

value: Cannabis extract CANN14


title: NC_Input.


title: AB_68, small RNA, Colorectal

tag: tissue


title: Sox10Cre/Yap/Taz cKO, replicate 2, scRNA-seq

city: Albany

first: Paolo

middle: Emanuele

last: Forni

state: NY

address: 1400 Washington Avenue

department: Biology

institute: University at Albany

description:
Library name: Sample 4 - Sox10Cre_YapTaz_Mut6
10x genomics

data_processing:
Our lab used cellranger count (version4) to perform alignment, filtering, barcode counting, and UMI counting on the fastq files of 6 separate libraries.
We used filtered processed files as input and Seurat 4.3.0 package in R studio to do quality control and downstream cell clustering analysis. Cells with mitochondrial read rate >5% and expressed < 200 genes were  filtered out from our data set.
Assembly: mm10
Supplementary files format and content: tsv and mtx files containing cell barcodes and gene count matrix

source_name: Whole Embryonic Nose

extract_protocol:
"2 embryonic noses at embryonic day 14.5 C57Bl/6J mice and 2 embryonic noses at embryonic day 14.5 Sox10cre/Yap/Taz mice were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate.
Single cell library preparation and sequencing were conducted by the Center of Functional Genomics (CFG) (https://www.albany.edu/genomics/ngs.html, Albany, NY) and Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cell suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 5 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

value: Whole Embryonic Nose

tag: genotype

value: Embryonic day 14.5


title: ASCL1-DLX2 progenitors, 96 conditions

description: bulk RNA-seq

source_name: ASCL1-DLX2-inducible iPSCs,  iLB-C-133bm-s4 background


title: AB_67, small RNA, Colorectal

value: Rectus abdominis muscle


title: THP-1-derived macrophages, si-SLC40A1-1, biol rep 2

description:
Library name: sample5
column name in counts.txt: s12

tag: treatment

value: PMA-induced differentiation + si-SLC40A1-1 transfection


title: Sox10Cre/Yap/Taz cKO, replicate 1, scRNA-seq

description:
Library name: Sample 3 - Sox10Cre_YapTaz_Mut3
10x genomics


title: AB_66, small RNA, Pancreas

tag: cell line

value: Skeletal muscle tissue


title: THP-1-derived macrophages, si-SLC40A1-1, biol rep 1

description:
Library name: sample4
column name in counts.txt: s11


title: WT, replicate 2, scRNA-seq

description:
Library name: Sample 2 - Sox10Cre_YapTaz_Cntrl11
10x genomics


title: THP-1-derived macrophages, si-NC, biol rep 3

description:
Library name: sample3
column name in counts.txt: NC3

value: PMA-induced differentiation + si-NC transfection


title: WT, replicate 1, scRNA-seq

description:
Library name: Sample 1 - Sox10Cre_YapTaz_Cntrl1
10x genomics


title: PCKS_adenine_FGF23_4

city: Bern

first: Matthias

middle: B.

last: Moor

address: Freiburgstrasse

institute: University Hospital Bern

data_processing:
Basecalling and demultiplexing were performed using Illumina bcl2fastq (v2.20.0).
Sequence data quality was assessed using FastQC (v0.11.8).
Counts for each gene were estimated using featureCounts (v1.5.1).
Assembly: Reads were aligned to the Ensembl GRCm38 reference genome using STAR (v2.7.9a).
Supplementary files format and content: tab-delimited text file contains raw counts for each sample.

source_name: kidney

extract_protocol:
RNA was extracted using Qiagen midi RNA extraction kit and purified.
Illumina stranded mRNA prep ligation sample preparation protocol was used with starting concentration between 25-1000 ng total RNA.

tag: strain

tag: Sex

value: male

value: kidney

tag: biol rep

tag: disease


title: THP-1-derived macrophages, si-NC, biol rep 2

description:
Library name: sample2
column name in counts.txt: NC2

tag: cell type

value: macrophage