title: Total thymic stroma (CD45-), E2FM11_1

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

description: 10X genomics

data_processing:
Demultiplexed with CellRanger v.7.
Downstream analyses were done with Seurat v.4 (Hao* & Hao* et al., 2021).
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Total thymic stroma (CD45-)

extract_protocol:
Excess blood vessels, connective tissues, and adipocytes were carefully removed in ice-chilled 4 sterile 1X PBS (w/o Ca2+, Mg2+). Thymi were finely cut into 1~2 mm3 fragments and transferred into digestion buffer (2% FBS/1640 RPMI (w/ 25mM HEPES), DNase I (20µg/µL), Collagenase/Dispase (1mg/mL)). Tubes containing the thymic fragments with digestion buffer were incubated in a 37 water bath for 20 minutes, 3 times. The solution was gently mixed up and down with transfer pipettes in between the incubations, 100 times each. To remove undigested thymic fragments, the solution was passed into a new tube, through a 70µm cell strainer. Single-cell suspension was then centrifuged for 10 minutes at 300rcf, 4, a condition for centrifugation throughout this protocol. After decanting the supernatant, erythrocytes were lysed with a 2-minute-long incubation in 2mL RBC Lysis Buffer (10X) (BioLegend 420301). After another centrifugation & decantation, cells were resuspended in MACS buffer (filtered and degassed 0.5% BSA/2mM EDTA/1X PBS (w/o Ca2+, Mg2+)). Post cell counting with a hemocytometer, cells underwent CD45 separation as per MACS separation guidelines with mouse CD45 microbeads (Miltenyi Biotec 130-052-301) to collect CD45- cells.
Library was constructed according to the manufacturer's instructions (single cell 3', 10X genomics).

value: Total thymic stroma (CD45-)


title: OE3

status: Public on Dec 31 2025

type: SRA

city: Nanchang

first: Jiaxuan

last: Qiu

state: Jiangxi

address: 17 Yongwai Zheng Street

country: China

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: sample 6
SNHG26 overexpression group, replicate biosample 3

library_source: transcriptomic

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 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: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

molecule: total RNA

organism: Homo sapiens

source_name: cell culture

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

tag: tissue

value: cell culture

tag: cell type

tag: genotype

value: SNHG26 overexpression


title: 4T1 DHO KO-1

city: Beijing

first: Yujia

last: Wang

address: Dongdan

institute: Peking Union Medical College

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCm39 using  HISTA2
Read count extraction and normalization were performed using HTSeq-count
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

extract_protocol:
RNA was harvested using TRIzol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

tag: cell line

value: Mouse breast cancer cell line

value: KO


title: rIL4-13-treated ASCs, rep4

city: Paris

first: Victoire

last: Baillet

address: 25-28 rue du Dr Roux

country: France

institute: Institut Pasteur

description: Library name: rIL4-13_Exp3_wt_S12

library_source: genomic

data_processing:
Reads were trimmed using Cutadapt v2.10 to remove sequencing adapters and low-quality bases (Q < 30), reads shorter than 25pb after trimming were discarded.
Reads were aligned to GRCm38 in paired-end mode using Bowtie2 with the following parameters: --very-sensitive -X 2000 --dovetail --no-mixed --no-discordant. Duplicates were removed using Picard MarkDuplicates v2.23.3, as well as reads mapping to blacklisted regions and to mitochondrial chromosome.
Peaks were called separately for each sample, converted as bed file, using MACS2 v2.2.6 with custom parameters (--nomodel --shift -100 --extsize 200 --keep-dup all --call-summits).
Peaks were then combined across replicates then across conditions to generate a consensus peaks list. Number of cutting events for each peak of the consensus peaks list were extracted using featureCounts.
TMM-normalized BigWig tracks for IGV visualization were produced using deepTools v3.4.1 using 1bp bins.
Assembly: mm10
Supplementary files format and content: TMM-normalized bigwigs

molecule: genomic DNA

source_name: Lung

growth_protocol: Adventitial stromal cells (ASCs) were isolated from the lungs of C57BL/6 mice following experimental treatments as described in the treatment protocol. After enzymatic digestion and mechanical dissociation, PDGFRα+Sca-1+ cells were sorted by fluorescence-activated cell sorting (FACS). Sorted cells were immediately processed for bulk ATAC-seq without further in vitro manipulation.

extract_protocol:
PDGFRα+Sca-1+ lung adventitial stromal cells were isolated following tissue digestion and cell sorting. Lungs were harvested from mice and digested for 45 minutes at room temperature in a solution containing dispase (25 mg/mL) and 1% low-melting agarose. The lungs were subsequently transferred to RPMI 1640 media with DNase I (2.4 U/mL), teased apart, and incubated on a shaker at 37°C for 10 minutes. Cells were then labeled with fluorescently conjugated antibodies specific for PDGFRα and Sca-1, and PDGFRα+Sca-1+ stromal cells were sorted using FACS. The sorted cells were then resuspended in appropriate media for downstream applications.
ATACseq librairies were performed on 90,000 FACS-purified ASCs using the ATACseq kit (Active Motif, 53150) according to the manufacturer’s instructions. Briefly, cells were lysed in ATAC lysis buffer to release nuclei. The nuclei were then resuspended in the transposase reaction mix, which contains the Tn5 transposase, and incubate for 30 minutes at 37°C to cut and tag the accessible regions of the chromatin with sequencing adapters. A limited-cycle PCR was performed to amplify the transposed DNA fragments and to add indexing adapters necessary for sequencing. The PCR products were then purified to remove primers, nucleotides, and other PCR components prior to Illumina sequencing.

treatment_protocol: Recombinant cytokines (rIL-4, rIL-13, rIFNγ; 2 µg/mouse), papain (20 µg/mouse), and CpG (8 µg/mouse) were administered intranasally. Anti-IL-4, anti-IL-13, and anti-IFNγ (200 µg/mouse) were delivered intraperitoneally.

value: Lung

value: Sorted mouse lung stromal cells (ASCs)

value: wild-type

tag: treatment

value: rIL-4 and rIL-13 (Intranasal) co-administration

tag: batch


title: Papain- and anti-IL4-13- treated ASCs, rep1

description: Library name: Pa_aIL4-13_Exp2_S3

value: Papain (Intranasal), aIL-4 and aIL-13 (Intraperitoneal) co-administration


title: ECRG4+ AD patients

city: Sapporo

first: Toru

last: Kondo

address: Kita-15, Nishi-7, Kita-ku

country: Japan

institute: Hokkaido University

description: Library name: ECRG4 positive

data_processing:
GeneGlobe Data Analysis Center (QIAGEN) Calibrate miRBase entries Trim adapter and low-quality bases Identify insert sequences and unique molecular index (UMI) sequences Align insert sequences Count reads and unique molecules assigned to miRNAs, piRNAs, tRNAs and otherRNAs
Supplementary files format and content: Excel® file includes read counts and clustered UMI counts for each sample

source_name: Plasma

extract_protocol:
Total RNA containing miRNA was extracted from the plasma of patients using the miRNeasy kit for plasma/serum (QIAGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were constructed using QIAseq miRNA Library Kit following the manufacturer's instructions.

value: Plasma

value: EDTA


title: Total thymic stroma (CD45-), E2FM11_2

country: USA

description: 10X genomics

library_source: transcriptomic single cell


title: OE2

description:
Library name: sample 5
SNHG26 overexpression group, replicate biosample 2


title: 4T1 DHO WT-2

value: WT


title: Papain- and anti-IL4-13- treated ASCs, rep2

description: Library name: Pa_aIL4-13_Exp2_S4


title: NC3

description:
Library name: sample 3
control group, replicate biosample 3


title: Atg5M2

city: Guangzhou

first: jiexing

last: tan

state: Guangdong

address: Experimental Animal Center, Nanfang Hospital, Southern Medical University No. 1838, North Guangzhou Avenue, Baiyun District, Guangzhou, Guangdong, China

data_processing:
Reads were further filtered by fastp  (version 0.18.0)
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default
The mapped reads of each sample were assembled by using StringTie v1.3.1.Genes with a false discovery rate < 0.05 and fold change > 2 were considered to be differentially expressed.
gene set enrichment analysis using software GSEAand MSigDB to identify whether a set of genes in specific GO terms\ pathways\ DO terms shows significant differences in two groups.
Assembly: Ensembl-release 104
Supplementary files format and content: xlsx, Gene expression level of each sample

source_name: RNA-Seq of mus musculus: adult male kidney macrophage

extract_protocol:
Total RNA was extracted from the kidney macrophages(10 mouse per group) .The obtained kidney single cell suspension was used to extract F4/80+ cells using the EasySepTM Mouse Biotin Positive Selection Kit II (STEMCELL, 17665), according to the manufacturer'’s instructions.
The constructed library was created using the Illumina TruSeq RNA Sample Preparation Kit v2(Illumina) with the standard protocol.

value: kidney

value: macrophage

tag: Sex

value: male

value: LysM-Cre-Atg5flox/flox (WT)

value: at 4 d after acute kidney injury


title: Atg5M3

institute: Nanfang Hospital, Southern Medical University

value: LysM-Cre+Atg5flox/flox (Macrophage Atg5 KO)


title: OE1

description:
Library name: sample 4
SNHG26 overexpression group, replicate biosample 1

value: cell culture

value: SNHG26 overexpression


title: Guide targeting Mcidas, mTECs at air/liquid interface for 5 days, replicate 1

city: San Francisco

first: Jeremy

last: Reiter

state: California

address: 555 Mission Bay Boulevard South

institute: UCSF

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: count matrix of integrated control, Gmnc, and Mcidas KO dataset
Supplementary files format and content: log-normalized count matrix of integrated control, Gmnc, and Mcidas KO dataset
Supplementary files format and content: csv of integrated control, Gmnc, and Mcidas KO dataset metadata

source_name: trachea

growth_protocol: Mouse tracheal epithelial cells (mTECs) were purified and cultured as previously described (You and Brody, 2013). mTECs were plated on collagen-coated 24 mm transwells (Corning, Cat #3450) at a density of 175,000 cells per well in mTEC Plus Expansion medium [mTEC Plus supplemented with 50 nM retinoic acid, 10 uM ROCK inhibitor, 1 uM A83-01 (Tocris, Cat #2939), 200 nM DMH-1 (Tocris Cat #4126) and 500 nM CHIR99021 (Tocris, Cat #4423)]. mTEC Plus Expansion medium formulation was modified from previously described medium (Mou et al., Cell Stem Cell, 2016). Cells were expanded with daily medium changes for 4 days and then removed from the transwell using 0.05% trypsin diluted in Cell Dissociation Buffer (Gibco, Cat #13151014). Cells were collected, counted, washed in PBS, then resuspended in P3 electroporation buffer (Lonza, Cat # V4SP-3096) at a concentration of 20,000 cells per 1 ul.

extract_protocol:
On day five at air/liquid interface, mTECs were washed with PBS three times both apically and basally. Trypsin-EDTA at a concentration of 0.05% in Cell Dissociation Buffer (Gibco, Cat #13151014) was added both apically and basally and cells were incubated at 37°C for 10 min. Cells were lifted from the membrane with gentle pipetting and trypsin deactivated in mTEC Basic with 2% Nu-Serum (Corning, Cat #355100). Fresh 0.05% Trypsin-EDTA in Cell Dissociation Buffer was added to the apical surface and incubated at 37°C for 5 min. The pipetting, inactivation, and 5 min incubation steps were repeated twice. mTECs were filtered through a 100 uM cell strainer, washed and resuspended in 0.04% BSA in PBS at 1000 cells per uL to prepare for scRNA-seq.
Library was performed according to the manufacter’s instructions (Chromium Single Cell 3’ Next GEM Reagent kit protocol, 10x Genomics). Briefly, mTECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Guide RNAs targeting Gmnc, Mcidas or a control nontargeting guide were designed and synthesized (Synthego) (see Resource Table). RNPs were assembled by adding 90 pmol TrueCut Cas9 v2 protein (Thermo Fisher, Cat #A36499) to 180 pmol of sgRNA and incubating at room temperature for 15 min. 400,000 cells in 20 ul of P3 buffer were added to each RNP and electroporated using program 96-EA-104 on an Amaxa 4D-Nucleofector with a 96-well shuttle (Lonza # AAF-1003B/S). Immediately after electroporation, cells from each electroporation were collected in mTEC Plus Expansion medium and seeded onto five 6.5 mm collagen-coated transwells. Cells were expanded with daily media changes until they reached confluence (3-4 days post electroporation) at which point differentiation was initiated.

value: trachea

value: guide targeting Mcidas


title: NC2

description:
Library name: sample 2
control group, replicate biosample 2


title: 4T1 DHO WT-1

value: Mouse breast cancer cell line


title: NC1

description:
Library name: sample 1
control group, replicate biosample 1


title: Myelin Spheres Week 15

city: Leuven

first: Yoke Chin

last: Chai

state: Leuven

address: Herestraat 49, ON5

department: Development & Regeneration

country: Belgium

institute: KU Leuven

description:
Library name: KAH-004
10x genomics

data_processing:
The Cell Ranger pipeline (version 7.1.0, 10x Genomics) was employed for sample demultiplexing and the generation of FASTQ files for read 1, read 2, and the i7 sample index of the gene expression library. Read 2 sequences from the gene expression libraries were aligned to the reference genome (Human GRCh38 (GENCODE v32/Ensembl98)) using the STAR aligner through CellRanger. Subsequent processing steps, including barcode processing, filtering of unique molecular identifiers (UMIs), and gene counting, were conducted using the Cell Ranger suite version 7.1.0.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: iPSC derived brain spheroid model

growth_protocol: Sigma iPSC derived pre-differentiated NPCs were culture with or without OPCs to form MyS or NMS.

extract_protocol:
Week 8 or 15 old NMs and MyS (4-6 spheroids per sample) were transferred to 250 µL of ice-cold homogenization buffer (HB; 10 mM Tris pH 7.8, 0.1 mM EDTA, 320 mM sucrose, 5 mM CaCl2, 3 mM magnesium acetate, 0.1% NP40, 1X complete protease inhibitor (Roche), 1 mM β-mercaptoethanol, and RNase inhibitor (Promega)) for 3 min to preserve nuclear integrity. Samples were gently homogenized using pestle A (5 strokes) followed by pestle B (15 strokes) and the homogenates were passed through 70 µm EASYstrainer (Greiner). The homogenizer and the strainer were washed with additional 270 µL of HB, and 520 µL of gradient medium (10 mM Tris pH 7.8, 5 mM CaCl2, 50% Optiprep, 3 mM magnesium acetate, 1X complete protease inhibitor, 1 mM β-mercaptoethanol, and RNase inhibitor) was added to the samples. This solution was carefully layered onto a cushion solution (29% Optiprep, 150 mM KCl, 30 mM MgCl2, 60 mM Tris pH 7.8, and 250 mM sucrose) and centrifuged at 9000 rpm for 25 min at 4 °C. The supernatant was discarded carefully, and nuclei pellets were then resuspended in 25 µL of resuspension buffer (1X PBS, 2% bovine serum albumin (BSA)), filtered through Flowmi 40 µm cell strainers, and counted using a LUNA automated cell counter (Logos Biosystems) following the manufacturer’s instructions.
The diluted nuclei suspensions were subsequently loaded onto the 10X Chromium Single Cell Platform (10X Genomics) (Next GEM Single Cell 3′ library and Gel Bead Kit v3.1) in accordance with the manufacturer’s protocol (10X User Guide; CG000315, Revision E). Steps including generation of gel beads in emulsion (GEMs), barcoding, GEM-RT cleanup, complementary DNA amplification, and library construction were all performed according to protocol. Quality of individual samples was checked with a Fragment Analyzer (Agilent), and library quantification was done using a Qubit 4.0 (ThermoFisher Scientific) before pooling the libraries. The final pooled library was sequenced on a NovaSeq6000 (Illumina) instrument at the VIB Nucleomics Core, using the Illumina NovaSeq 6000 v1.5 sequencing kit S4 200 paired-end reads (28-10-10-90), 1% PhiX with 100-base-pair paired-end reads.

treatment_protocol: Doxycycline (3μg/ml) was added for one week after spheroid (MyS or NMS) formation.

value: iPSC derived brain spheroid model

value: NPCs+OPCs spheroid


title: Control nontargeting guide, mTECs at air/liquid interface for 5 days, replicate 1

description: 10X Genomics

value: control nontargeting guide


title: wild-type mTECs at air/liquid interface for 3 days, replicate 2

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: count matrix of integrated dataset
Supplementary files format and content: log-normalized count matrix of integrated dataset
Supplementary files format and content: csv of integrated dataset metadata

growth_protocol: Mouse tracheal epithelial cells (mTECs) were purified and cultured as previously described (You and Brody, 2013). mTECs were seeded on 6.5 mm transwells (Corning, Cat #3470) coated with 50 ug/ml rat tail collagen (Type I, Corning, Cat #CB354249) at a density of 33,000 cells per well. mTECs were allowed to proliferate for five days before initiating differentiation by removing media from the apical chamber and changing media in the basal chamber to mTEC Basic with 2% Nu-Serum (Corning, Cat #355100) and 50 nM retinoic acid. Placement at air/liquid interface was considered day zero of differentiation. Subsequent to placement at air/liquid interface, basal media was changed and the apical surface was rinsed twice with PBS every other day.

extract_protocol:
To generate single-cell suspensions for scRNA-seq from mTEC cultures, mTECs derived from wild-type mice and Foxj1-CreERT Rosa-tdTomato mice treated with 4-OHT on day two at air/liquid interface were cultured and differentiated. On day three at air/liquid interface, mTECs were washed with PBS three times both apically and basally. Trypsin-EDTA at a concentration of 0.05% in Cell Dissociation Buffer (Gibco, Cat #13151014) was added both apically and basally and cells were incubated at 37°C for 10 min. Cells were lifted from the membrane with gentle pipetting and trypsin deactivated in mTEC Basic with 2% Nu-Serum (Corning, Cat #355100). Fresh 0.05% Trypsin-EDTA in Cell Dissociation Buffer was added to the apical surface and incubated at 37°C for 5 min. The pipetting, inactivation, and 5 min incubation steps were repeated twice. Cells were washed in FACS buffer (2% FBS, 2% BSA, 5 mM EDTA, 25 mM HEPES in PBS) filtered through a 100 uM cell strainer and resuspended in FACS buffer with Fixable Viability dye (Invitrogen, Cat #65-0863-14) at a dilution of 1:1600. After a 15 min incubation on ice, cells were washed with FACS buffer and sorted on a fluorescence activated cell sorter (Sony SH800). tdTomato-expressing Foxj1-CreERT Rosa-tdTomato cells, representing cells within the multiciliated cell lineage, were sorted into mTEC Basic with 2% Nu-Serum. Wild-type cells and a fraction of Foxj1-CreERT Rosa-tdTomato cells were not sorted. Both tdTomato-expressing and unsorted cells were resuspended in 0.04% BSA in PBS at 1000 cells per uL to prepare for scRNA-seq.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagents kit, version 3, 10x Genomics). Briefly, mTECs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: mTECs derived from Foxj1-CreERT Rosa-tdTomato mice treated with 4-OHT on day two at air/liquid interface were cultured and differentiated.


title: Neuron Monoculture Spheroids Week 15

description:
Library name: KAH-003
10x genomics

value: NPCs spheroid


title: Testis_MDWD_male6

type: RNA

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: testicular gene expression data from MD-WD fed male mice

hyb_protocol: Following fragmentation and labeling, ss-cDNA were hybridized for 16 hr at 45°C oto Clariom S Human Arrays. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix, P/N 00-0079).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The raw CEL files were normalized using RMA background correction with quantile normalization, log2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes were considered significant if p-value with FDR ≤ 0.05 and fold-change of >2 or < -2.

label: biotin

source_name: Testis tissue, 8 weeks of MD-WD

label_protocol: Affymetrix GeneChipTM WT PLUS Reagent Kit

growth_protocol: Mice were housed in controlled 12/12 hours light/dark conditions with a constant temperature (21 ± 3 °C) and access to food and water ad libitum.

extract_protocol: Total RNA was extracted from frozen testicular tissues using the RNeasy Plus Mini Kit (Qiagen; UK) following the manufacturer’s instructions.

treatment_protocol: Males were randomly allocated to one of five diets, either a control diet (CD; 18 % casein, 21 % sugar, 10 % fat), an isocaloric low protein diet (LPD; 9 % casein, 24 % sugar, 10 % fat), a methyl donor/carrier-supplemented low protein diet (MD-LPD; LPD with the addition of 5 g/kg choline chloride, 15 g/kg betaine, 7.5 g/kg methionine, 15 mg/kg folic acid, and 1.5 mg/kg vitamin B12, a high-fat, high-sugar Western diet (WD; 19 % casein, 34 % sugar, 21 % fat), or a methyl donor/carrier-supplemented WD (MD-WD).

value: MD-WD

value: Male

tag: strain

tag: developmental stage

value: adult

value: testis


title: Testis_MDWD_male3


title: Testis_MDWD_male5


title: Neuron Monoculture Spheroids Week 8

description:
Library name: KAH-001
10x genomics


title: ST2 6h rWnt1_3

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom D Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0.1.36) using  default analysis settings (version 2) and Gene + Exon - SST-RMA as summarization and normalization method.

label: proprietary DNA Labeling Reagent, covalently linked to biotin

source_name: ST2,6h 100 ng rWnt1/Sfrp1

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: ST2 cells were plated at a density of 10000 cells/cm² in 12-well format cell culture dishes. Cells were cultured in alpha-MEM with 10% FCS at 37 °C, 5 % CO2, 95 % rH for 1 day.

extract_protocol: RNA was extraced 6 h after treatment using the Nucleospin RNA kit (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: ST2 cells were serum starved over night and treated with 100 ng recombinant murine Wnt1/Sfrp1 complex or the equivalent volume PBS for 6 h


title: wild-type mTEC at air/liquid interface for 3 days, replicate 1

description: 10X Genomics


title: ST2 6h PBS_1

source_name: ST2, 6h PBS

value: PBS


title: ST2 6h rWnt1_1


title: Testis_MDWD_male2


title: Foxj1-CreERT Rosa-tdTomato mTECs at air/liquid interface for 3 days, TdTomato sorted, replicate 1

description: 10X Genomics

value: Foxj1-CreERT Rosa-tdTomato

value: 4' OHT for 24 hours


title: Testis_MDWD_male7


title: Myelin Spheres Week 8

description:
Library name: KAH-002
10x genomics


title: AIF1_OE_2

city: shanghai

first: mingjuan

last: zhou

address: No.1665 Kongjiang Road, Yangpu District

department: Department of Obstetrics and Gynecology

institute: The affiliated Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University

description:
Library name: AIF1_OE_2
AIF1_OE_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: T-HESC

extract_protocol:
T-HESCs transfected with NC or AIF-1 plasmids for three days were collected using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AIF-1, and negative control (NC) plasmids (Genecopoeia) were transfected into cells using the X-tremeGENE HP DNA transfection reagent (06366236001; Roche), according to the manufacturer’s instructions.

value: T-HESC

value: endometrail stromal cell line

value: T-HESCs transfected with AIF-1 overexpression plasmid


title: Testis_WD_male6

description: testicular gene expression data from WD fed male mice

source_name: Testis tissue, 8 weeks of WD

value: WD


title: ST2 6h rWnt1_2


title: Testis_WD_male7


title: Testis_MDWD_male1


title: ST2 6h PBS_3


title: ST2 6h PBS_2


title: Foxj1-CreERT Rosa-tdTomato mTECs at air/liquid interface for 3 days, unsorted, replicate 1

description: 10X Genomics

value: trachea


title: Testis_WD_male3


title: Testis_MDL_Male5

description: testicular gene expression data from MD-LPD fed male mice

source_name: Testis tissue, 8 weeks of MD-LPD

value: MD-LPD


title: Testis_WD_male2


title: Testis_WD_male1


title: Testis_WD_male5


title: Guide targeting Gmnc, mTECs at air/liquid interface for 5 days, replicate 1

description: 10X Genomics

value: guide targeting Gmnc


title: Pancreatic islets of Sec16b-/- mice rep2

city: Shenzhen

first: li

last: anqi

address: No. 66, Gongchang Road, Guangming District

institute: School of Pharmaceutical Sciences (Shenzhen)

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gencode.vM12.annotation whole genome using hisat2 with parameters -p 6 -q -x genome -1.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: gencode.vM12.annotation
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: pancreatic islets

extract_protocol:
Pancreatic islets were isolated, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic islets

tag: age

value: 30 weeks

value: male


title: NC_2

description:
Library name: NC_2
NC_2

value: T-HESCs transfected with vector plasmid


title: Testis_MDL_Male2

value: Male


title: Pancreatic islets of Sec16b-/- mice rep1


title: AIF1_OE_1

description:
Library name: AIF1_OE_1
AIF1_OE_1


title: NC_1

description:
Library name: NC_1
NC_1


title: Pancreatic islets of Sec16b+/+ mice rep3


title: Pancreatic islets of Sec16b+/+ mice rep2


title: TMA SLHB15 08.10.2024 | 012 | Full ROI

city: Aachen

first: Janik

last: Riese

address: Pauwelsstraße 30

department: Institute of Pathology

institute: UK Aachen

description:
Library name: Sample63
GeoMx

data_processing:
GeoMx DSP pipeline was used for processing of DCC files
Probe QC: Exclude probes if ratio of probe geomean across all segments below 0.1 or failed Grubbs fail percent threshold or local segment outliers 2 standard deviations for LOQ
Normalization: Q3 normalization of NegProbe-WTX and sum
Assembly: mm10
Supplementary files format and content: Excel count file as outputted by GeoMx DSP software
Library strategy: Spatial Transcriptomics

source_name: Bladder cancer

extract_protocol:
Formalin-fixed paraffin-embedded tissue was cut in 10 µm sections.
Spatial transcriptome sequencing libraries were preprared with GeoMx Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instructions.

value: Bladder cancer

value: Stroma

value: Patient 7

value: Medium control (MSC)


title: TMA SLHB15 08.10.2024 | 011 | Full ROI

description:
Library name: Sample62
GeoMx


title: Pancreatic islets of Sec16b-/- mice rep3


title: Pancreatic islets of Sec16b+/+ mice rep1


title: H4

city: Zhuzhou

first: Guo

last: Yuan

state: Hunan

address: No. 116, Changjiang South Road, Tianyuan District

institute: Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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 N base 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.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package (3.8.1) and KEGG (http://www.genome.jp/kegg /) enrichment analysis of annotated different expressed gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count and FPKM for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000.

value: heart

value: HFD+L-NAME


title: Testis_MDL_Male6

value: adult

value: testis


title: SAD Patient_13 (Female)

city: Seongnam-si

first: Minsoo

last: Kwon

address: 335 Pangyo-ro

department: Pharmacology

country: South Korea

institute: CHA University

description: Library name: SAD_13

data_processing:
Trimming with Average Q20 using BBDuk
Mapping using STAR to reference genome
Calculation read count using HTSeq-count
TMM+CPM Normalization using EdgeR
Assembly: GRCh38 (NCBI)
Supplementary files format and content: Normalied counts.csv
Supplementary files format and content: Raw reads.csv

source_name: Peripheral blood

extract_protocol:
RNA quality was assessed with an Agilent 2100 bioanalyzer using an RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, Netherlands).
The library construction was performed using a QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria).

value: Peripheral blood

value: PBMC-derived microglia-like cell

tag: group

value: SAD

value: Female


title: H3


title: Testis_MDL_Male1

value: MD-LPD


title: SAD Patient_9 (Male)

description: Library name: SAD_9


title: H2


title: Testis_MDL_Male4


title: Testis_LPD_male4

description: testicular gene expression data from LPD fed male mice

source_name: Testis tissue, 8 weeks of LPD

value: LPD


title: Testis_LPD_male5


title: Testis_LPD_male2


title: Testis_MDL_Male3


title: Testis_NPD_male7

description: testicular gene expression data from CD fed male mice

source_name: Testis tissue, 8 weeks of CD

value: CD


title: Testis_LPD_male6


title: Testis_LPD_male1


title: Testis_NPD_male4


title: Testis_NPD_male6


title: H1

value: male


title: TMA SLHB15 08.10.2024 | 009 | Full ROI

description:
Library name: Sample60
GeoMx

value: Tumor


title: SAD Patient_11 (Female)

description: Library name: SAD_11


title: TMA SLHB15 08.10.2024 | 002 | Full ROI

description:
Library name: Sample57
GeoMx

value: Bladder cancer

value: Gemcitabine Cisplatine


title: E4

value: HFD+L-NAME+Exercise


title: TMA SLHB15 08.10.2024 | 001 | Full ROI

description:
Library name: Sample56
GeoMx

value: Patient 7


title: Testis_LPD_male3

value: Male


title: TMA SLHB15 08.10.2024 | 004 | Full ROI

description:
Library name: Sample59
GeoMx

value: Stroma


title: E3

value: heart


title: SAD Patient_8 (Male)

description: Library name: SAD_8


title: TMA SLHB15 08.10.2024 | 003 | Full ROI

description:
Library name: Sample58
GeoMx


title: SAD Patient_2 (Male)

description: Library name: SAD_2


title: TMA SLHB14 08.10.2024 | 012 | Full ROI

description:
Library name: Sample55
GeoMx

value: Patient 6

value: Medium control (MSC)


title: SAD Patient_7 (Male)

description: Library name: SAD_7

value: Peripheral blood

value: PBMC-derived microglia-like cell


title: E2


title: SAD Patient_1 (Male)

description: Library name: SAD_1

value: SAD


title: Testis_NPD_male2

value: adult

value: testis


title: OCD Patient_15 (Female)

description: Library name: OCD_15

value: OCD

value: Female


title: OCD Patient_12 (Female)

description: Library name: OCD_12


title: SAD Patient_6 (Male)

description: Library name: SAD_6


title: SAD Patient_4 (Male)

description: Library name: SAD_4


title: SAD Patient_3 (Male)

description: Library name: SAD_3


title: Testis_NPD_male5

value: CD


title: SAD Patient_5 (Male)

description: Library name: SAD_5


title: OCD Patient_9 (Female)

description: Library name: OCD_9


title: E1

value: male


title: OCD Patient_8 (Male)

description: Library name: OCD_8


title: TMA SLHB14 08.10.2024 | 010 | Full ROI

description:
Library name: Sample53
GeoMx

value: Bladder cancer

value: Tumor


title: OCD Patient_7 (Male)

description: Library name: OCD_7


title: OCD Patient_11 (Male)

description: Library name: OCD_11


title: Testis_NPD_male1


title: C2

value: Control


title: TMA SLHB14 08.10.2024 | 011 | Full ROI

description:
Library name: Sample54
GeoMx


title: OCD Patient_5 (Female)

description: Library name: OCD_5


title: TMA SLHB14 08.10.2024 | 009 | Full ROI

description:
Library name: Sample52
GeoMx


title: C4


title: TMA SLHB14 08.10.2024 | 002 | Full ROI

description:
Library name: Sample49
GeoMx

value: Gemcitabine Cisplatine


title: OCD Patient_3 (Male)

description: Library name: OCD_3

value: Male


title: OCD Patient_1 (Male)

description: Library name: OCD_1


title: C1

value: heart


title: C3


title: OCD Patient_6 (Male)

description: Library name: OCD_6


title: Healthy CON_19 (Female)

description: Library name: HC_19

value: Healthy


title: TMA SLHB14 08.10.2024 | 003 | Full ROI

description:
Library name: Sample50
GeoMx

value: Stroma

value: Patient 6


title: OCD Patient_4 (Male)

description: Library name: OCD_4

value: Peripheral blood

value: PBMC-derived microglia-like cell


title: TMA SLHB14 08.10.2024 | 004 | Full ROI

description:
Library name: Sample51
GeoMx


title: TMA SLHB13 08.10.2024 | 010 | Full ROI

description:
Library name: Sample46
GeoMx

value: Patient 5

value: Medium control (MSC)


title: Healthy CON_16 (Female)

description: Library name: HC_16


title: OCD Patient_2 (Female)

description: Library name: OCD_2

value: OCD


title: C3H10_CMS,replicate 3

city: Shanghai

first: Lingyong

last: Jiang

state: Shanghai

address: No.639, zhi zao ju road

institute: Shanghai jiao tong University

description:
CMS3
CM.counts.txt

data_processing:
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5).
The clean reads were then mapped to the mouse reference genome (mm10) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015).
The raw counts files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R.
Assembly: mm10
Supplementary files format and content: counts

source_name: C3H10 T1/2 cells

extract_protocol:
C3H10 T1/2 cells were kindly provided by Stem Cell Bank, Chinese Academy of Sciences, and were cultured in MEM (Hyclone, SH30024.01) supplemented with 10% FBS and penicillin/streptomycin mix (50 mg⁄mL). Cells were plated at a density of 100000 cells/mL in 2 mL of medium on six-well flexible silicone rubber BioFlex culture plates coated with collagen type I (Flexcell International Corporation). The cells were cultured for 48 h, and then mechanical strain was applied. Cyclic mechanical strain (CMS) with a 0.5 Hz sinusoidal curve set at 10% elongation was applied for 8 h every day, with a FX-4000T™ Flexcell Tension Plus™ unit (Flexcell International Corporation, FX-4000T). The cultures were incubated in a humidified atmosphere at 37°C in 5% CO2 during stretching.
Total RNA was extracted by RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instructions. The cDNA was synthesized and amplified using the Single Cell Full Length mRNA-Amplification Kit (Vazyme, N712). The RNA-seq libraries were constructed from the amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, TD503). The PCR and size-selection of RNA-seq libraries were conducted as described in Hi-C library construction. The RNA-Seq libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode.

value: cyclic mechanical strain (CMS)


title: TMA SLHB14 08.10.2024 | 001 | Full ROI

description:
Library name: Sample48
GeoMx


title: Healthy CON_14 (Female)

description: Library name: HC_14

value: Female


title: C3H10_CMS,replicate 2

description:
CMS2
CM.counts.txt


title: Healthy CON_13 (Male)

description: Library name: HC_13


title: Healthy CON_18 (Female)

description: Library name: HC_18


title: TMA SLHB13 08.10.2024 | 009 | Full ROI

description:
Library name: Sample45
GeoMx


title: Healthy CON_12 (Male)

description: Library name: HC_12


title: TMA SLHB13 08.10.2024 | 011 | Full ROI

description:
Library name: Sample47
GeoMx


title: C3H10_CMS,replicate 1

description:
CMS1
CM.counts.txt


title: Healthy CON_17 (Female)

description: Library name: HC_17


title: Healthy CON_4 (Male)

description: Library name: HC_4


title: Healthy CON_5 (Male)

description: Library name: HC_5


title: TMA SLHB13 08.10.2024 | 008 | Full ROI

description:
Library name: Sample44
GeoMx


title: C3H10_Ctrl,replicate 1

description:
NC1
CM.counts.txt

value: control


title: OCD Patient_10 (Female)

description: Library name: OCD_10


title: TMA SLHB13 08.10.2024 | 003 | Full ROI

description:
Library name: Sample43
GeoMx

value: Bladder cancer


title: Healthy CON_2 (Male)

description: Library name: HC_2


title: Healthy CON_1 (Male)

description: Library name: HC_1


title: C3H10_Piezo1 knock out,replicate 2

data_processing:
Low-quality reads and adapters were trimmed by Trim Galore (Version 0.6.5).
The clean reads were mapped to the mm10 genome with bowtie2 (v2.4.2)(Langmead & Salzberg, 2012; Langmead, Wilks, Antonescu, & Charles, 2019) and duplicates were removed.
MACS2 call peak after ATAC shift
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeaks

source_name: Mouse embryo

growth_protocol: MEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells  were trypsinized with 0.25% trypsin-EDTA.
ATAC-seq libraries were performed according to the Omni-ATAC protocol. Briefly, nuclei were isolated from 50,000 cells for transposition reaction with Tn5 Transposase from a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech Co., TD501). DNA was purified and amplified according to the manufacturer.

value: Mouse embryo


title: TMA SLHB13 08.10.2024 | 002 | Full ROI

description:
Library name: Sample42
GeoMx


title: Healthy CON_3 (Male)

description: Library name: HC_3


title: C3H10_Ctrl,replicate 2

description:
NC2
CM.counts.txt


title: C3H10_Ctrl,replicate 3

description:
NC3
CM.counts.txt


title: TMA SLHB15 08.10.2024 | 010 | Full ROI

description:
Library name: Sample61
GeoMx

value: Tumor

value: Patient 7


title: SeV2, WM3835, D9, rep3

city: Kyoto

first: Koji

last: Eto

address: 53 Kawahara-cho, Shogoin Kawahara-cho, Sakyo-ku

department: CiRA

institute: Kyoto University

description: Library name: SeV2_WM3835_D9_3

data_processing:
Sequencing was performed on an Illumina NextSeq 550 platform with the single-end mode. Illumina RTA version v3.4.4 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.1. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.10a with the GENCODE (release 32, GRCh38.p13) gtf file.
Raw read counts for each gene were calculated using htseq-count v2.0.2 with the GENCODE gtf file.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: imMKCL

growth_protocol: imMKCLs were cultured in a humidified incubator at 37_x000E_C and 5% CO2 and passaged to maintain 105~106 cells/mL in basal medium supplemented with 15% fetal bovine serum and cocktail A. FBS was pre-treated with 35 kGy irradiation. Basal medium consisted of IMDM supplemented with L-glutamine , Insulin-transferrin-selenium, 50 mg/mL Ascorbic acid, and 450 mM 1-Thioglycerol. Cocktail A consisted of 50 ng/mL animal-derived-free recombinant human stem cell factor, 200 ng/mL TA-316, and 5 mg/mL Doxycycline.

extract_protocol:
Total RNA was extracted using the miRNeasy Micro Kit following the manufacturer’s protocol.
RNA-seq libraries were prepared from approximately 10 ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit.

treatment_protocol: imMKCLs culture in present of doxcycline with DMSO or 5 uM WM3835 for 9 days.

value: imMKCL

value: megakaryocyte

value: WT


title: C3H10_Piezo1 knock out,replicate 1


title: SeV2, WM3835, D9, rep2

description: Library name: SeV2_WM3835_D9_2


title: TMA SLHB12 08.10.2024 | 012 | Full ROI

description:
Library name: Sample40
GeoMx

value: Stroma

value: Patient 4


title: C3H10_GFP,replicate 1


title: Healthy CON_9 (Male)

description: Library name: HC_9

value: Peripheral blood

value: Healthy

value: Male


title: SeV2, DMSO, D9, rep3

description: Library name: SeV2_DMSO_D9_3

value: DMSO


title: SeV2, DMSO, D9, rep2

description: Library name: SeV2_DMSO_D9_2


title: TMA SLHB12 08.10.2024 | 011 | Full ROI

description:
Library name: Sample39
GeoMx

value: Medium control (MSC)


title: SeV2, DMSO, D9, rep1

description: Library name: SeV2_DMSO_D9_1


title: HCT116, Ab: SF3B1, DMSO: 2 hours, rep2, experiment3

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description: Library name: HCT116_SF3B1_DMSO_Rep2_ChIP-Seq_exp3

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA and resulting sam output was converted to bam using samtools.
Sequence reads with an alignment score <20 reads were discarded.
Duplicates were removed with samtools rmdup
Resulting bam files were converted into bedgraph format using the genomecov command of bedtools.
Assembly: GRCh38
Supplementary files format and content: bedGraph, read coverage per genome position

extract_protocol:
ChIP was performed using the following antibodies for each biological technical replicate: 40 30 ul of P CDK11 (Ab 2 or Ab 3), 5 μg of SF3B1 (MBL, MB-D221-3). in tTwo technical replicates that were pooled together to obtain one biological replicate. In brief, 20 µl of Dynabeads protein G (Thermo Fisher Scientific, 10009D) per immunoprecipitation were pre-blocked with 0.2 mg ml−1 BSA (Thermo Fisher Scientific, AM2616) for 4 hours, washed 3× with RIPA buffer, followed by incubation with the specific antibody at 4 °C for at least 4 hours. HCT116 cells (70 % confluency) were treated with 50 nM SY 351 for 2 h. Cells were cross-linked with 1 % formaldehyde for 10 min, and the reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed 2× with ice-cold PBS, scraped and split to several tubes so that there was about 20 µl packed cell pellet per tube. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20× 7 s (amplitude 0.85) using a 5/64 probe (QSonica Q55A). Supernatant (13000 g/4 °C/10 min) was pooled and pre-cleared by incubating with Dynabeads protein G (Thermo Fisher Scientific, 10009D) at 4 °C for 2‒4 hours. Pre-cleared extracts were split into two technical replicates (900 µl each) and incubated overnight with antibody (P CDK11, SF3B1)-bound Dynabeads protein G. Beads were sequentially washed once with low-salt buffer (20 mM Tris-Cl, (pH 8), 150 mM NaCl, 2 mM EDTA, 1% Triton X 100, 0.1% SDS), once with high-salt buffer (20 mM Tris-Cl, (pH 8), 500 mM NaCl, 2 mM EDTA, 1% Triton X 100, 0.1% SDS), once with LiCl buffer (20 mM Tris-Cl, (pH 8), 250 mM LiCl, 2 mM EDTA, 1% NP 40, 1% sodium deoxycholate) and 2× with TE buffer (10 mM Tris Cl, (pH 8), 1 mM EDTA). Immunoprecipitated complexes were eluted 2× 15 min with 250 µl of elution buffer (1% SDS, 0.1 M NaHCO3). NaCl was added to final concentration of 0.2 M and samples were incubated at 65 °C for at least 4 hours to reverse cross-linking. Tris, pH 7.8, proteinase K (Sigma-Aldrich, P5568) and GlycoBlue (Thermo Fisher Scientific, AM9516) were added to final concentration of 30 mM, 0.04 mg/ml and 0.06 mg/ml, respectively, and incubated at 42 °C for 2 hours. After phenol–chloroform extraction (Sigma-Aldrich, P3803), immunoprecipitated DNA was dissolved in 17 µl of water and technical replicates were pooled.
ChIP–seq libraries were generated using KAPA Biosystems Hyper Prep Kit (Roche, KK8502) and NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S, E7500S).

treatment_protocol: Indicated samples were treated with DMSO or 50nM SY-351 for 2 hours.

value: DMSO:2 hours


title: HCT116, Ab: none, DMSO: 2 hours, rep2, experiment3

description: Library name: HCT116_noAb_DMSO_Rep2_ChIP-Seq_exp3


title: HCT116, Ab: SF3B1, DMSO: 2 hours, rep1, experiment3

description: Library name: HCT116_SF3B1_DMSO_Rep1_ChIP-Seq_exp3


title: HCT116, Ab: P-T-loop CDK11, 50nM SY-351: 2 hours, rep2, experiment1

description: Library name: HCT116_P-CDK11_SY351_rep2_ChIP-Seq_exp1

value: 50nM SY-351:2 hours


title: TMA SLHB13 08.10.2024 | 001 | Full ROI

description:
Library name: Sample41
GeoMx

value: Patient 5

value: Gemcitabine Cisplatine


title: HCT116, Ab: none, DMSO: 2 hours, rep1, experiment3

description: Library name: HCT116_noAb_DMSO_Rep1_ChIP-Seq_exp3


title: HCT116, Ab: none, DMSO: 2 hours, rep1, experiment1

description: Library name: HCT116_noAb_DMSO_rep1_ChIP-Seq_exp1


title: HCT116, Ab: none, DMSO: 2 hours, rep2, experiment1

description: Library name: HCT116_noAb_DMSO_rep2_ChIP-Seq_exp1


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-48]

city: Chicago

first: Brian

last: Popko

state: IL

address: 303 E. Chicago Avenue

department: Neurology

institute: Northwestern University

data_processing:
Beta galactosidase gene quantification: map reads to gene reference, counts reads per sample and cross reference to metadata
QC of raw data
Map reads to reference genome (STAR)
Quantify gene expression (featureCounts) on Ensembl gene annotations
Quantify isoform expression against isoform transcriptome annotation (Kallisto)
Normalize gene expression to counts per million units (CPM) (EdgeR)
Average gene expression across sample groups
Principle component analysis and plot of log-scaled CPMs to assess sample clustering and outliers
Differental expression - Three way ANOVA: FDR correction to adjust for multiple testing, output is p-values and q-values (FDRs)
Pairwise comparisons: FDR correction for each comparison, output is log2 fold-change, log2 CPM, p-value, and q-value
Genome_build: mm
Supplementary_files_format_and_content: txt

growth_protocol: Cells were acquired through isolation and immunopanning purification of oligodendrocyte progenitor cells (OPCs) from 6 day old mouse pup brain cortices. OPCs were initially grown in proliferation media, taken through 2 passage cycles at 37 C, and allowed to differentiate for 12-14 hours. Plates were then randomly designated for treatment.

extract_protocol:
Total OPC RNA was extracted using the Rneasy mini columns kit (Qiagen, Crawley, UK) and treated with Dnase I (Qiagen). RNA concentration and purity were determined by Nanodrop spectrophotometry and QC. RNA quality was determined using Agilent Bioanalyzer RNA Analysis (Agilent Technologies, Santa Clara, CA, USA) and QC.
Expression wa analyzed by sequencing using Illumina HiSeQ technology (Illumina Next Generation Sequencing Services, University of Chicago). Raw data was processed by the University of Illinois in Chicago Bioinformatics Core.

treatment_protocol: Both experimental groups were treated with either IFN-gamma (200 U/ml) or thapsigargin (Sigma, 200 uM) and RNA was extracted at designated timepoints throughout the treatment process.

tag: strain background

tag: treatment timepoint

value: 48 hours

value: Whole brain

value: Developing oligodendrocyte


title: TMA SLHB12 08.10.2024 | 003 | Full ROI

description:
Library name: Sample35
GeoMx

value: Bladder cancer


title: HCT116, Ab: P-T-loop CDK11, 50nM SY-351: 2 hours, rep1, experiment1

description: Library name: HCT116_P-CDK11_SY351_rep1_ChIP-Seq_exp1


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-47]

value: Interferon-gamma (200 U/ml)


title: SeV2, WM3835, D9, rep1

description: Library name: SeV2_WM3835_D9_1

value: imMKCL

value: megakaryocyte

value: WT


title: TMA SLHB12 08.10.2024 | 002 | Full ROI

description:
Library name: Sample34
GeoMx

value: Tumor

value: Patient 4


title: C3H10_GFP,replicate 2

value: Mouse embryo


title: TMA SLHB12 08.10.2024 | 009 | Full ROI

description:
Library name: Sample37
GeoMx


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-45]


title: HCT116, Ab: P-T-loop CDK11, DMSO: 2 hours, rep1, experiment1

description: Library name: HCT116_P-CDK11_DMSO_rep1_ChIP-Seq_exp1


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-46]


title: NC6

first: Baiguang

last: Yu

address: 639 Zhizaoju Road

department: Department of Ophthalmology

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw FASTQ files were processed with fastp with default parameters. Quality control and data filtering are performed using Cutadapt and Trimmomatic. Bowtie2 was used to map the sequencing reads to a population of human reference genomes. Abundance quantification of miRNAs is performed with miRDeep2.
Assembly: miRbase
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample and tab-delimited text files for each Sample

source_name: orbital connective tissues

extract_protocol:
Total RNA was extracted from orbital connective tissues by using TRIzol. Then RNA was quantified with a NanoDrop 2000. RNA sequencing libraries were constructed with 1μg high-quality RNA of each sample according to the instructions of TruSeq Small RNA Library Preparation Kit (Illumina) for sequencing.
The libraries were sequenced on an Illumina NextSeq 550 sequencer.

value: orbital connective tissues

tag: disease state

value: healthy


title: HCT116, Ab: P-T-loop CDK11, DMSO: 2 hours, rep2, experiment1

description: Library name: HCT116_P-CDK11_DMSO_rep2_ChIP-Seq_exp1

value: DMSO:2 hours


title: TMA SLHB12 08.10.2024 | 010 | Full ROI

description:
Library name: Sample38
GeoMx

value: Medium control (MSC)


title: NC4


title: TMA SLHB12 08.10.2024 | 001 | Full ROI

description:
Library name: Sample33
GeoMx


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-50]


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-49]


title: Untreated WT Developing Oligodendrocytes [HS-44]

value: wild type


title: TMA SLHB08 08.10.24 neu | 012 | Full ROI

description:
Library name: Sample32
GeoMx

value: Stroma

value: Patient 3


title: NC3


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-43]

value: 48 hours

value: Whole brain


title: TMA SLHB12 08.10.2024 | 004 | Full ROI

description:
Library name: Sample36
GeoMx

value: Bladder cancer

value: Gemcitabine Cisplatine


title: NC2


title: TMA SLHB08 08.10.24 neu | 010 | Full ROI

description:
Library name: Sample30
GeoMx


title: TED6

value: thyroid eye disease


title: NC1


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-42]

value: Interferon-gamma (200 U/ml)

value: Developing oligodendrocyte


title: TMA SLHB08 08.10.24 neu | 011 | Full ROI

description:
Library name: Sample31
GeoMx


title: TED7


title: Untreated WT Developing Oligodendrocytes [HS-41]


title: TMA SLHB08 08.10.24 neu | 009 | Full ROI

description:
Library name: Sample29
GeoMx

value: Tumor


title: NC5


title: TMA SLHB08 08.10.24 neu | 004 | Full ROI

description:
Library name: Sample28
GeoMx


title: TED5


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-40]

value: 24 hours


title: TED3


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-39]


title: TED2


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-38]


title: R PDA 4T biol rep 3

city: Louisville

first: Michael

middle: H

last: Perlin

state: KY

address: 214 W. Barbee Street Walk

department: Biology

institute: University of Louisville

data_processing:
Sequencing was perfromed by CD Genomics
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the M. v. pavonius reference genome assembly (Microbotryum violaceum pavonius  ) using Star version 2.6
Read counts for gene regions were obtained with HTSeq v.0.10.0 using M. v. pavonius
Assembly: MvDp-1065-A1.contigs-A2sexchrom

organism: Microbotryum violaceum

source_name: M. violaceum pavonius

growth_protocol: All the M. v. pavonius strains were streaked onto PDA medium for haploid strains;  or, for mating M. v. pavonius strains of opposite mating type  (a1 and a2 cultures) were first grown separately in yeast extract peptone dextrose broth overnight. Cell density was measured with a spectrophotometer. The concentration of each culture was adjusted to O.D.600 1.0. Equal volumes of the two haploid cultures were mixed and plated on water agar. These plates were incubated for 4 days at 14 °C, after which wet mounts were prepared from each mated plate to verify the presence of conjugation tubes, indicating active mating behavior.

extract_protocol:
RNA was extracted for haploid samples and also for mated samples on water agar using Zymo Research Directzol Microprep kit following the manufacturer's protocols. 1 μg of total RNA was subjected for sequencing libraries.
RNA libraries for RNA-seq were prepared using CD Genomics mRNA-seq Library Prep Kit for Illumina.

treatment_protocol: Haploid growth on Potato Dextrose Agar (PDA) at 22 C or Mating on Water agar at 14 C.

value: Growth on PDA plates at 28 C for 24 h


title: TMA SLHB08 08.10.24 neu | 003 | Full ROI

description:
Library name: Sample27
GeoMx


title: TMA SLHB08 08.10.24 neu | 002 | Full ROI

description:
Library name: Sample26
GeoMx


title: Q PDA 6P biol rep 3


title: TMA SLHB08 08.10.24 neu | 001 | Full ROI

description:
Library name: Sample25
GeoMx


title: TED1

value: orbital connective tissues


title: TED4


title: Untreated WT Developing Oligodendrocytes [HS-37]


title: P PDA 6D biol rep 3


title: Untreated WT Developing Oligodendrocytes [HS-36]


title: TMA SLHB07 22.10.24 | 012 | Full ROI

description:
Library name: Sample24
GeoMx

value: Patient 2


title: R PDA 4T biol rep 2


title: P PDA 6D biol rep 2


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-35]


title: N PDA 4T biol rep 1


title: TMA SLHB07 22.10.24 | 011 | Full ROI

description:
Library name: Sample23
GeoMx


title: O PDA 6P biol rep 1


title: M51-3LM

city: Ariake

first: Ryoji

last: Yao

state: Tokyo

institute: Cancer Institute, JFCR

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Raw data produced from the 10x Genomic platform were processed by Cell Ranger (v6.1.2).
Assembly: GRCH38
Supplementary files format and content: A cell x gene data matrix in AnnData format

source_name: colorectal cancer

extract_protocol:
Organoids were colected and signle cells were prepared in TrypLE.
10x Genomics Chromium was used for single cell capture and cDNA preparations according to the Single Cell 3' v3 Protocol recommended by the manufacturer.

value: colorectal cancer

value: organoid


title: TMA SLHB07 22.10.24 | 010 | Full ROI

description:
Library name: Sample22
GeoMx

value: Medium control (MSC)


title: human stellate cells - SMRT-seq

city: Boston

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing:
Polished sequence consensus of PacBio generated BAM files was generated using the CCS program from the IsoSeq v3 pipeline (https://github.com/PacificBiosciences/IsoSeq). We merged SMRT cells from two independent runs into one movie. The Lima package was used to remove cDNA primers from the end of the reads. The consensus sequences were then refined to identify and trim polyA and concatemer sequences. The movie was then clustered using the cluster function of the isoSeq 3.1 pipeline (https://github.com/PacificBiosciences/pbbioconda). To generate higher-quality reads we then used the polish function of isoSeq workflow which in turn mapped to the human genome (hg38) using minimap2 (Li 2018). The mapped reads were processed by the TAMA suite of scripts to collapse into unique isoforms and remove potentially 5’-end degraded isoforms (Kuo et al. 2020). SQANTI3 was used on the final transcripts dataset to classify isoform structure and protein-coding potential (Tardaguila et al. 2018).
Reads were quality asssed using the FASTQC (v 0.11.9).
Genome_build: GRCh38

molecule: polyA RNA

source_name: primary human stellate cells

growth_protocol: Adult HSCs were grown in DMEM (Gibco) containing 10 percent FBS.

extract_protocol:
HSCs were rinsed with PBS and lysed using Trizol reagent (Thermo Fisher). The mixture was vortexed and incubated at room temperature to ensure complete lysis of cells and separation of protein-RNA complexes. RNA was then extracted using chloroform (Sigma) and precipitated using ethanol and centrifuged at 13,000 RPM for 20 min to form an RNA pellet. The RNA pellet was rinsed with 75% ethanol. The RNA was resuspended in nuclease free water and incubated with DNase I (Thermo Fisher) to remove potentially contaminating genomic DNA fragments. The RNA was then extracted using acidic phenol chloroform, precipitated in ethanol, and resuspended in nuclease free water. RNA samples with RIN score of >9 were sequenced.
Clontech SMARTer Polymerase Chain Reaction kit (Takara) was used to produce compatible polyA-transcript cDNA. The cDNA was purified using AMPure XP magnetic beads (Beckman Coulter). The SMRTbell adapters were then ligated to the cDNA product using SMRTbell Template Prep Kit (Pacific Biosciences). The library was then sequenced using PacBio Sequel II.

value: Untreated

tag: molecule

value: polyA RNA


title: M PDA 6D biol rep 1


title: K Buds Special bio rep 2

source_name: D. pavonius infected with M. violaceum pavonius

value: Microbotryum Infected Dianthus pavonius grown in a growth chamber


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-32]

value: Whole brain


title: J Buds Other biol rep 4


title: Buds Other biol rep 3


title: K Buds Special bio rep 3


title: TMA SLHB07 22.10.24 | 009 | Full ROI

description:
Library name: Sample21
GeoMx

value: Bladder cancer


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-31]


title: TMA SLHB07 22.10.24 | 004 | Full ROI

description:
Library name: Sample20
GeoMx

value: Stroma

value: Gemcitabine Cisplatine


title: Buds Other biol rep 1


title: Buds Other biol rep 2


title: I Buds Special biol rep 1


title: D Buds 18-20 biol rep 2


title: TMA SLHB07 22.10.24 | 002 | Full ROI

description:
Library name: Sample18
GeoMx


title: Q PDA 6P biol rep 2


title: D Buds 18-20 biol rep 1


title: Thapsigargin-treated Nrf2-mutant Developing Oligodendrocytes [HS-29]

value: Thapsigargin (200 uM)

value: 8 hours


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-30]

value: Interferon-gamma (200 U/ml)

value: Developing oligodendrocyte


title: TMA SLHB07 22.10.24 | 001 | Full ROI

description:
Library name: Sample17
GeoMx

value: Tumor


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-34]

value: 24 hours


title: A Mated biol rep 3

value: Mated 6P and 6P cells were plated on water agar petri dishes before incubation at 13° Celsius for 48 hours.


title: A Mated biol rep 2


title: Thapsigargin-treated WT Developing Oligodendrocytes [HS-27]

value: wild type


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-33]


title: TMA SLHB06 22.10.24 | 012 | Full ROI

description:
Library name: Sample16
GeoMx

value: Patient 1


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-28]


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-25]


title: Thapsigargin-treated Nrf2-mutant Developing Oligodendrocytes [HS-24]


title: TMA SLHB06 22.10.24 | 009 | Full ROI

description:
Library name: Sample13
GeoMx

value: Medium control (MSC)


title: TMA SLHB06 22.10.24 | 011 | Full ROI

description:
Library name: Sample15
GeoMx


title: Untreated WT Developing Oligodendrocytes [HS-26]


title: Artery EC Control Rep3

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

description: Library name: AC3

data_processing:
The paired-end reads were mapped to the hg38 reference genome using STAR (v2.7.9a).
Gene counts were generated with featureCounts in the Subread package.
DESeq2 (v1.34.0) was used to identify differentially expressed genes  (Padj < 0.05).
Ensemble IDs were converted to gene symbols using the org.Hs.eg.db package.
Assembly: hg38
Supplementary files format and content: counts.csv includes raw count files for each dataset
Supplementary files format and content: NormalizedCounts.csv includeds counts normalized with DESeq2
Supplementary files format and content: LEC_DFOvsCon.csv includes differential expression results of LECs treated with DFO compared to controls
Supplementary files format and content: AEC_DFOvsCon.csv includes differential expression results of artery ECs treated with DFO compared to controls

source_name: Human coronary artery endothelial cells

extract_protocol:
Quick-RNA MiniPrep (Zymo Research)
PE150 reads were generated with the Illumina NovoSeq X plus platform

value: Human coronary artery endothelial cells

value: Vehicle (media)

tag: time


title: Artery EC Control Rep1

description: Library name: AC1


title: Artery EC DFO Rep2

description: Library name: AD2

value: Deferoxamine (100 uM)


title: LEC DFO Rep3

description: Library name: LD3

source_name: Human dermal lymphatic endothelial cells


title: LEC Control Rep2

description: Library name: LC2

value: Human dermal lymphatic endothelial cells


title: Artery EC DFO Rep3

description: Library name: AD3


title: TMA SLHB06 22.10.24 | 002 | Full ROI

description:
Library name: Sample10
GeoMx

value: Bladder cancer


title: LEC Control Rep1

description: Library name: LC1


title: A Mated biol rep 1


title: Artery EC DFO Rep1

description: Library name: AD1


title: Artery EC Control Rep2

description: Library name: AC2


title: TMA SLHB06 22.10.24 | 010 | Full ROI

description:
Library name: Sample14
GeoMx


title: HEK_PRE_ADARcdMUT-1000ng_rep2 (RBPscan)

city: Québec

first: Dmitry

last: Kretov

state: Québec

department: Oncology Division

country: Canada

institute: CRCHU de Québec - Université Laval

description: Library name: HEK_PRE_ADARcdMUT-1000ng_rep2

library_source: other

data_processing:
paired-end reads were merged using the BBMap suite.
Counting of A-to-G conversions in Recorder mRNA associated with specific PREs was conducted using a custom Python script.
Assembly: N/A.
Supplementary files format and content: A CSV file containing sequences of PREs and associated metrics was generated, including occurrence, number of edited reads, total number of A-to-G edits, total number of reads in the library for all motifs, and the percentage of A-to-G editing.

molecule: other

extract_protocol:
Total RNA from zebrafish embryos was extracted using TRIzol (ThermoFisher #15596026).
Sequencing was performed on PCR amplicons of the 3' UTR of Recorder mRNA containing 1,000 PRE sequences. The PCR reaction was carried out to amplify the 3' UTR region of the Recorder mRNA, which includes PRE motifs and the Recorder hairpin. Partial Illumina adapters present in the Recorder mRNA are complementary to sections of the i5 and i7 TruSeq Illumina primers, which also contain unique barcodes and sequencing adapters.

value: human embryonic kidney

value: WT


title: TMA SLHB06 22.10.24 | 004 | Full ROI

description:
Library name: Sample12
GeoMx

value: Stroma

value: Gemcitabine Cisplatine


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-23]

value: Interferon-gamma (200 U/ml)

value: 8 hours

value: Whole brain


title: TMA SLHB06 22.10.24 | 003 | Full ROI

description:
Library name: Sample11
GeoMx


title: TMA SLHB05 08.10.24 neu | 012 | Full ROI

description:
Library name: Sample8
GeoMx


title: HEK_PRE_hsPUM2-ADARcdMUT-250ng_rep3 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-250ng_rep3


title: Untreated WT Developing Oligodendrocytes [HS-19]

value: Developing oligodendrocyte


title: LEC DFO Rep1

description: Library name: LD1

value: 24 hours


title: LEC Control Rep3

description: Library name: LC3


title: TMA SLHB05 08.10.24 neu | 011 | Full ROI

description:
Library name: Sample7
GeoMx


title: HEK_PRE_hsPUM2-ADARcdMUT-25ng_rep3 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-25ng_rep3


title: HEK_PRE_hsPUM2-ADARcdMUT-250ng_rep1 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-250ng_rep1


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-22]

value: wild type


title: TMA SLHB07 22.10.24 | 003 | Full ROI

description:
Library name: Sample19
GeoMx

value: Patient 2


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-21]


title: HEK_PRE_ADARcdMUT-1000ng_rep3 (RBPscan)

description: Library name: HEK_PRE_ADARcdMUT-1000ng_rep3


title: HEK_PRE_hsPUM2-ADARcdMUT-25ng_rep2 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-25ng_rep2


title: TMA SLHB06 22.10.24 | 001 | Full ROI

description:
Library name: Sample9
GeoMx

value: Tumor

value: Patient 1


title: HEK_PRE_hsPUM2-ADARcdMUT-25ng_rep1 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-25ng_rep1


title: Thapsigargin-treated WT Developing Oligodendrocytes [HS-20]

value: Thapsigargin (200 uM)


title: HEK_PRE_hsPUM2-ADARcdMUT-non-induced_rep3 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-non-induced_rep3


title: HEK_PRE_hsPUM2-ADARcdMUT--non-induced_rep2 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-non-induced_rep2


title: HEK_PRE_ADARcdMUT-1000ng_rep1 (RBPscan)

description: Library name: HEK_PRE_ADARcdMUT-1000ng_rep1


title: LEC DFO Rep2

description: Library name: LD2

value: Deferoxamine (100 uM)


title: HEK_PRE_hsPUM2-ADARcdMUT-non-induced_rep1 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-non-induced_rep1


title: TMA SLHB05 08.10.24 neu | 010 | Full ROI

description:
Library name: Sample6
GeoMx

value: Medium control (MSC)


title: HEK_PRE_hsPUM2-ADARcdMUT-250ng_rep2 (RBPscan)

description: Library name: HEK_PRE_hsPUM2-ADARcdMUT-250ng_rep2


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-18]


title: Thapsigargin-treated Nrf2-mutant Developing Oligodendrocytes [HS-17]


title: Ribo_Cell_3

city: Madison

first: Finn

last: Kuusisto

state: WI

address: 1205 University Ave

institute: University of Wisconsin-Madison

description: Library name: Ribo_Cell_3

data_processing:
Skop Lab - We use fastp (ver 0.23.4) quality filtering, adapter trimming, and quality profiling with default settings for paired-end. We use kallisto (ver 0.46.1) for quantification with an index k-mer size of 31, and otherwise default settings. We build the index against the Ensembl human cDNA FASTA for all genes, release 109.
Iwasaki Lab - Sequencing reads were processed as previously described (Kashiwagi et al. 2021; Mito et al. 2023). fastp (ver. 0.21.0) for the read quality filtering and adapter trimming. cutadapt (ver. 3.7) for demultiplexing by linker barcodes. UMI-tools (ver. 1.1.2) for deduplication based on unique molecule identifier. Alignment to genome with STAR v2.7.0a.
Assembly: hg38
Supplementary files format and content: Skop Lab - text files contain output of kallisto quant, five columns: 1. Ensembl transcript ID; 2. transcript length; 3. adjusted transcript length; 4. read counts; 5. TPM
Supplementary files format and content: Iwasaki Lab - text files contain three columns: 1. transcript name; 2. CDS region used for read counting; 3. read counts
Library strategy: Ribo-Seq

source_name: HeLa

extract_protocol:
Skop Lab - Cells were harvested when 80% confluent with Trypsin or Versene, counted, washed with 2 mL PBS and cell pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water. MBRs were isolated by ultracentrifugation of cleared culture media. Cells were cultured until 80% confluent. Culture media was collected and centrifuged at 1,000×g for 10 min to clear cell debris. Cleared culture media was transferred to ultracentrifuge tubes and centrifuged at 10,000×g for 30 min at 4°C. MBR pellets were washed with 2mL sterile PBS, centrifuged at 10,000×g for 30 min at 4°C and MBR pellets used for RNA extraction using the Qiagen RNeasy mini kit. RNA was eluted in RNase free water.
Iwasaki Lab - Cells were directly lysed in lysis buffer on culture dishes. Purification of desthiobiotinylated ribosomes and RNAs were performed. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription and PCR amplification.
Skop Lab - For RNA-seq, libraries were prepared by Azenta Life Sciences using standard protocols to assess integrity, remove contaminants, and deplete ribosomal RNA. For RNA sequencing library preparation, the NEBNext Ultra II RNA Library Preparation Kit for Illumina was used according to the manufacturer’s instructions. Detailed steps and reagents are available from Azenta documentation upon request.
Iwasaki Lab - For Ribo-Seq, lysates were used for Thor‑Ribo‑Seq library preparation (Mito et al. 2023).

value: HeLa

tag: lab

value: Iwasaki


title: TMA SLHB05 08.10.24 neu | 009 | Full ROI

description:
Library name: Sample5
GeoMx

tag: tissue

value: Bladder cancer


title: Ribo_Cell_1

description: Library name: Ribo_Cell_1

tag: cell type


title: Ribo_Cell_2

description: Library name: Ribo_Cell_2


title: TMA SLHB05 08.10.24 neu | 003 | Full ROI

description:
Library name: Sample3
GeoMx

value: Stroma

tag: genotype


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-16]


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-15]

value: 1 hour


title: Thapsigargin-treated Nrf2-mutant Developing Oligodendrocytes [HS-14]


title: Ribo_mBR_2

description: Library name: Ribo_mBR_2


title: TMA SLHB05 08.10.24 neu | 001 | Full ROI

description:
Library name: Sample1
GeoMx

value: Gemcitabine Cisplatine


title: TMA SLHB05 08.10.24 neu | 002 | Full ROI

description:
Library name: Sample2
GeoMx


title: Ribo_mBR_1

description: Library name: Ribo_mBR_1


title: Ribo_mBR_3

description: Library name: Ribo_mBR_3


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-13]


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-12]

value: Interferon-gamma (200 U/ml)


title: MDA-MB-468 cells, Paclitaxel-resistant cells

city: Hachioji-shi

first: Takahio

last: Ohashi

address: 7-1, Minamiosawa 4-chome

institute: Zenyaku Kogyo Co., Ltd.

description: Library name: Sample C

data_processing:
Raw sequencing reads were first processed using Trimmomatic (v0.39) to remove adapter sequences and low-quality bases. The trimmed FASTQ files were then subjected to quality assessment using an in-house QC script.
For read alignment, we used HISAT2 (v2.2.1) to map the trimmed reads to the Homo sapiens reference genome (GRCh38), utilizing known splice junctions from GENCODE v39 annotation.
The resulting aligned BAM files were analyzed with StringTie (v2.2.1) for transcript assembly and gene expression quantification. StringTie produced both gene- and transcript-level expression profiles in terms of read counts, FPKM, and TPM values. Novel transcript identification and alternative splicing events were also detected using StringTie.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw read counts, FPKM values, and TPM values for each gene across all samples.

source_name: Breast

growth_protocol: MDA-MB-468 cells were cultured in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 100 μg/mL kanamycin sulfate (Thermo Fisher Scientific) at 37 °C in a 5% CO2 incubator.

extract_protocol:
RNA was harvested using the MagMAX mirVana Total RNA Isolation Kit (Thermo Fisher Scientific). 1.0 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer's protocols.

treatment_protocol: MDA-MB-468 cells were exposed to adriamycin (HY-15142, Nacalai Tesque) or paclitaxel (Merck) at concentrations of 10 to 140 nM and 2 to 320 nM, respectively, to establish drug-resistant cell lines. Surviving cells were designated as adriamycin-resistant and paclitaxel-resistant MM468 cells.

value: Breast

tag: cell line

value: epithelial cell

value: WT

value: Paclitaxel


title: Sen

city: Nanchang

first: Jiaxuan

last: Qiu

address: 17 Yongwai Zheng Street

institute: The First Affiliated Hospital of Nanchang University

description:
Library name: sample2
Cisplatin sensitivity, 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tongue muscles

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Tongue muscles

tag: condition

value: Cisplatin sensitivity


title: Thapsigargin-treated Nrf2-mutant Developing Oligodendrocytes [HS-11]

tag: treatment

value: Whole brain

value: Developing oligodendrocyte


title: MDA-MB-468 cells, Adriamycin-resistant cells

description: Library name: Sample B

value: Adriamycin


title: Res

description:
Library name: sample1
Cisplatin resistance, 10x Genomics

value: Cisplatin resistance


title: BT549 cell, Nab-Paclitaxe

city: Beijing

first: Yuqi

last: Xing

state: Beijing

address: Peking University

institute: Peking University

description: Library name: BT549-NP

data_processing:
Adapter sequences were trimmed for both forward and reverse reads using cutadapt. Read quality was assessed using fastQC (v 0.11.9). Trimmed sequences were aligned to the mouse reference genome mm10, the human reference genome hg38. The resulting SAM files were converted to a binary format (BAM), sorted by queryname, and indexed using samtools.
Assembly: hg38 and mm10
Supplementary files format and content: bigWig

source_name: BT549 cell

extract_protocol:
ATAC-seq was performed using a modified method based on Corces et al. Cell were lysed and transposed simultaneously in 25 µL of transposition mix in Tagment DNA Buffer. The transposition was incubated at 37 °C for 30 min in a thermomixer with shaking at 1000 rpm. After tagmentation, the reactions were stopped with addition of stop buffer. The transposed DNA fragments were purfied by DNA Purification Kits and amplified using PCR.
The final libraries were purified using pure beads and quantified using a Qubit 2.0 Fluorometer. Puried DNA libraries were sequenced on a Illimina Novaseq platform.

value: BT549 cell

value: Human breast cancer cell

value: Nab-Paclitaxe


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-10]


title: BT549 cell, PBS

description: Library name: BT549-PB

value: PBS


title: KB39_28_BC1242

city: Mancehster

first: Kiran

last: Batta

address: Paterson Building, Wilmslow Rd

department: Division of Cancer Research

institute: University of Manchester

description: Library name: KB39_28_lib

data_processing:
Sample libraries were prepared by 3’ Quantseq (Lexogen) protocol and were sequenced using the Novaseq (Illumina) platform. Basecalls were converted to fastq files using bcl2fastq (Illumina). Fastq files were aligned to GRCh38 using Star aligner (version 2.5.1b; Ensembl85). BAM alignments were quantified in R (version 3.6.1) using featureCounts from the Rsubread library (version 2.0.1) and the Ensemble GTF annotation (Homo_sapiens.GRCh38.85.gtf). Differential expression (DE) was evaluated comparing the gene level integer read count data for between patient/sample groups using the DESeq2.v 1.26.0 Bioconductor package.   DESeq2 DEG estimation involves multiple steps. In brief, it uses normalization factor to model read counts to account for sequencing depth. Then it estimates gene-wise dispersions and perform shrinkage analysis to generate more accurate estimates of dispersion to model the counts. Finally, it fits the negative binomial model and performs hypothesis testing using the Wald test.
Assembly: GRCh38.85
Supplementary files format and content: DESeq2's output: Gene-by-gene log2fold change, adjusted p-value for the rejection of non-differential expression, and ormalised (TPM) transcript counts in tab-delimited format. Genes with an adjusted p-value > 0.5 have been removed, and all the results are sorted by increasing adjusted p-value.

source_name: Fresh peripheral blood

extract_protocol:
RNA was extracted from 5 x 105 granulocytes isolated from fresh healthy volunteer and CMML patient peripheral blood using RNeasy Micro Plus kit (QIAGEN, 74034), according to manufacturer’s recommendations.
3' Quantseq (Lexogen)

value: Fresh peripheral blood

value: CMML


title: IFN gamma-treated Nrf2-mutant Developing Oligodendrocytes [HS-9]

value: Interferon-gamma (200 U/ml)

value: 1 hour


title: BT549 cell, DMSO

description: Library name: BT549-D

value: DMSO


title: KB39_27_YHB7

description: Library name: KB39_27_lib

value: Healthy Young


title: BT549 cell, Paclitaxe

description: Library name: BT549-P

value: Paclitaxe


title: TMA SLHB05 08.10.24 neu | 004 | Full ROI

city: Aachen

first: Janik

last: Riese

institute: UK Aachen

description:
Library name: Sample4
GeoMx

data_processing:
GeoMx DSP pipeline was used for processing of DCC files
Probe QC: Exclude probes if ratio of probe geomean across all segments below 0.1 or failed Grubbs fail percent threshold or local segment outliers 2 standard deviations for LOQ
Normalization: Q3 normalization of NegProbe-WTX and sum
Assembly: mm10
Supplementary files format and content: Excel count file as outputted by GeoMx DSP software
Library strategy: Spatial Transcriptomics

source_name: Bladder cancer

extract_protocol:
Formalin-fixed paraffin-embedded tissue was cut in 10 µm sections.
Spatial transcriptome sequencing libraries were preprared with GeoMx Spatial Gene Expression Slides & Reagent kit according to the manufacturer's instructions.

value: Bladder cancer

value: Stroma

value: Patient 1

value: Gemcitabine Cisplatine

tag: batch


title: DNA barcode Tag

city: Kumamoto

first: Ken

last: Takashima

state: Kumamoto

address: 1-1-1, Honjo, Chuo-ku

department: Department of Immunology

institute: Kumamoto University

description:
Library name: Tag
Tag information. The correspondence between samples and tags is as follows: Control (Saline): A0955, ARNAX-120: A0962, poly(I:C): A0963, Alum: A0964, and miR-192-LNP: A0965.

data_processing:
Adapter trimming, homopolymer trimming, and quality filtering were performed using Cutadapt. Cell barcode assignment and read mapping to the GRCh38 release-107 reference genome were carried out using STARsolo (v2.7.10b), resulting in the generation of gene count tables.
Assembly: GRCh38
Supplementary files format and content: WTA1_barcodes.tsv.gz
Supplementary files format and content: WTA1_features.tsv.gz
Supplementary files format and content: WTA1_matrix.mtx.gz
Supplementary files format and content: Tag1_barcodes.tsv.gz
Supplementary files format and content: Tag1_features.tsv.gz
Supplementary files format and content: Tag1_matrix.mtx.gz
Supplementary files format and content: matrix_inflection_demulti_WTA1.txt.gz(count read table)
Supplementary files format and content: WTA1_Tag1_barcode.csv(the correspondence between samples and barcodes)

source_name: PBMC

growth_protocol: Cryopreserved human peripheral blood mononuclear cells (PBMCs) were purchased from Charles River Inc. Cells were thawed and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/mL), and streptomycin (100 µg/mL) under 5% CO₂ at 37 °C. A total of 4 × 10⁶ PBMCs were seeded per well in a 24-well plate and incubated for 2 hours. Following incubation, cells were stimulated with the indicated reagents.

extract_protocol:
For multiplex analysis, cells were barcoded using BioLegend Hashtag DNA. Single-cell capture and reverse transcription were performed using the BD Rhapsody system
cDNA amplification was carried out using the Terminator-assisted solid-phase cDNA amplification sequencing (TAS-Seq) method (Shichino et al., Commun. Biol., 2022), in collaboration with ImmunoGeneTeqs Inc.

treatment_protocol: Human PBMC were treated for 24 hours with saline (as Control), ARNAX-120 (10 µg/mL), poly(I:C) (10 µg/mL), Alum (500 µg/mL), or miR-192-LNP (200 pmol/mL).

value: PBMC


title: KB39_26_HB1

description: Library name: KB39_26_lib

value: Healthy Old


title: Untreated Nrf2-mutant Developing Oligodendrocytes [HS-7]

value: Whole brain

value: Developing oligodendrocyte


title: PDGF-BB-1

city: Xi'an

first: XIAN

last: GUO

address: Xinyi Road

institute: Air Force Medical University

description: Library name: PDGF-BB-1

data_processing:
The reads were aligned to the human genome hg19 for all the samples. lncRNA-seq: differential gene expression analysis was performed using DESeq2 package in R .
Assembly: hg19
Supplementary files format and content: differential gene expression analysis result

source_name: human aortic smooth muscle cell

extract_protocol:
Refer to the instruction manual of Trizol (Invitrogen, CA, USA) to extract total RNA.RNA contamination was assessed by 1.5% agarose gel.
After the RNA sample passed the test, rRNA was removed from it. The remaining RNA was then fragmented using a fragmentation buffer. The fragmented RNA was used as a template for reverse transcription with 6nt random hexamers to synthesize the first - strand cDNA. The second - strand cDNA was synthesized by adding buffer, dNTPs (with dTTP replaced by dUTP), DNA polymerase I, and RNase H. After purification, end - repair, A - tailing, and sequencing adapter ligation, the double - stranded cDNA was degraded with USER enzyme and enriched by PCR. Finally, the PCR products were purified using AMPure XP Beads to obtain the final strand - specific libraries.

value: human aortic smooth muscle cell


title: PDGF-BB-2

description: Library name: PDGF-BB-2


title: Whole Transcriptome amplification (cDNA)

description:
Library name: WTA
Multiplex scRNA-seq data containing five groups including Control (Saline): A0955, ARNAX-120: A0962, poly(I:C): A0963, Alum: A0964, and miR-192-LNP: A0965.

value: mixed sample [Control (Saline):A0955, ARNAX-120:A0962, poly(I:C):A0963, Alum:A0964, and miR-192-LNP:A0965]


title: Thapsigargin-treated Nrf2-mutant Developing Oligodendrocytes [HS-8]

value: Thapsigargin (200 uM)


title: KB39_24_BC1238

description: Library name: KB39_24_lib

value: Fresh peripheral blood

value: CMML


title: Vehicle-2

description: Library name: Vehicle-2


title: KB39_25_HB9

description: Library name: KB39_25_lib


title: IFN gamma-treated WT Developing Oligodendrocytes [HS-6]

value: wild type

value: Interferon-gamma (200 U/ml)

value: 1 hour


title: Thapsigargin-treated WT Developing Oligodendrocytes [HS-5]


title: MDA-MB-468 cells, wild type

description: Library name: Sample A

value: Breast

value: epithelial cell

value: WT

value: Non-treatment


title: KB39_23_HB12

description: Library name: KB39_23_lib


title: H3K27ac_PDGF-BB

description: Library name: H3K27ac_PDGF-BB

data_processing:
Trimmomatic was used with parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:8:true and MINLEN:8.
FastQC was used to assess the quality of paired - end raw data.
Trimmed reads were mapped to the human (hg19) genome using Bowtie2 v2.3.3 with standard settings for paired reads.
Peaks were called using macs3 with default settings. Detected peaks were visualized using deeptools. Downstream analyses were performed using DiffBind 3.2.4.
Assembly: hg19
Supplementary files format and content: bed format of each samples
Library strategy: CUT&Tag

extract_protocol:
100,000 cells were harvested and centrifuged for 3 min at 600×g at room temperature. Cells were washed twice in 300 μL Wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. 10 μL of activated concanavalin A - coated magnetic beads were added per sample and incubated at RT for 10 min. The unbound supernatant was removed, and bead - bound cells were resuspended in 50 μL Dig - wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2mM EDTA and a 1:50 dilution of the appropriate primary antibody. Primary antibody incubation was performed on a rotating platform for 2 h at RT. Then the liquid was removed on the magnet stand. An appropriate secondary antibody (Goat anti - Rabbit IgG or Rabbit Anti - Mouse IgG) was diluted 1:50 in 50μL of Dig - Wash buffer, and cells were incubated at RT for 1 h. For constructing the negative control library (IgG), only the secondary antibody was added without the primary antibody. Cells were washed twice using the magnet stand for 1 min in 500 μL Dig - Wash buffer to remove unbound antibodies. A 1:200 dilution of pG - Tn5 adapter complex (~0.04 μM) was prepared in Dig - 300 Buffer (0.01% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail). After removing the liquid, 100 μL was added to the cells with gentle vortexing and incubated with pG - Tn5 at RT for 1 h. Cells were washed twice for 1 min in 500 μL Dig - 300 Buffer to remove unbound pG - Tn5 protein. Next, cells were resuspended in 300 μL Tagmentation buffer (10mM MgCl2 in Dig - 300 Buffer) and incubated at 37 °C for 1 h. To stop tagmentation, 10 μL of 0.5M EDTA, 3 μL of 10% SDS, and 2.5 μL of 20 mg/mL Proteinase K were added to 300 μL of sample, which was incubated at 55 °C for 1h, purified using phenol - chloroform - isoamyl alcohol and ethanol, washed with 100% ethanol, and suspended in water. The DNA was amplified by PCR as follows: 3 min at 72 °C, 30 s at 98 °C, followed by 16 cycles of 15 s at 98 °C, 30 s at 60 °C, and 30 s at 72 °C, with a final extension at 72 °C for 3 min. Finally, the amplified DNA was purified using Ampure XP beads. Libraries were sequenced on the Illumina Nova - seq platform.
Libraries were sequenced on the Illumina Nova - seq platform


title: H3K4me1_PDGF-BB

description: Library name: H3K4me1_PDGF-BB


title: H3K4me1_Vehicle

description: Library name: H3K4me1_Vehicle


title: Untreated WT Developing Oligodendrocytes [HS-4]


title: KB39_22_YHB6

description: Library name: KB39_22_lib

value: Healthy Young


title: Thapsigargin-treated WT Developing Oligodendrocytes [HS-3]


title: icSHAPE, U-2 OS, Whole Cell, NaAsO2Shield, DMSO, biological replicate 1

city: Singapore

first: Jovi

last: Lim

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description: Library name: U2OS_NaAsO2Shield_DMSO_rep1

data_processing:
Briefly, icSHAPE libraries were de-duplicated and adapter-trimmed. Remaining reads were mapped to genome. RT stops and base coverage were called out for each nucleotide. Genomic coordinates were converted to transcript coordinate for downstream analysis.
Assembly: ENSEMBL GRCh38 release 98
Supplementary files format and content: Processed data consists of icSHAPE reactivity for all detected transcripts in each sample i.e. files ending with "shape.txn.txt". Each row in the files represent one transcript. Each entry (tab delimited) in each row represent the reactivity of each nucleotide. SPLASH txt files contain the information of all detected chimeras in each sample. eCLIP txt.gz files contain the enriched windows for each sample (refer to software Skipper for details https://doi.org/10.1016/j.xgen.2023.100317). Translation Efficiency data are recorded in "tpm_te.csv"  files. Transcript per million (TPM) was quantified for each gene. Translation efficiency was quantified by dividing TPM of Ribo-seq samples with that of RNA-seq.

source_name: Bone

extract_protocol:
RNA was harvested using TRIzol/TRIzol LS reagent following manufacturer's instructions. The amount of 500ng and 1,500ng RNA were used for generating icSHAPE and SPLASH libraries, repectively. For SRSF1 eCLIP libraries, cells were fixed with UV (254nm, 400mJ/cm^2) in prior to proceeding to immunoprecipitation and library preparation.
icSHAPE library preparation was carried out according to the protocol described before (Flynn, et al, 2016); SPLASH library preparation was performed according to the protocol described before (Aw, et al, 2016); eCLIP library preparation was performed according to the protocol described before (Blue, et al, 2022).

value: Bone

value: U-2 OS

value: Osteosarcoma

value: DMSO


title: icSHAPE, U-2 OS, Whole Cell, NaAsO2Shield, NAIN3, biological replicate 1

description: Library name: U2OS_NaAsO2Shield_NAIN3_rep1


title: KB39_21_BC1214

description: Library name: KB39_21_lib


title: icSHAPE, U-2 OS, Whole Cell, NaAsO2, NAIN3, biological replicate 1

description: Library name: U2OS_NaAsO2_NAIN3_rep1