title: 137-B_S18

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

description: Column ID at processed data: 137-B_S18

data_processing:
Sequence reads were trimmed and filtered with Trimmomatic [v0.39] with the following criteria: (1) palindrome mode allowing up to two mismatches; (2) filter reads with an average Phred quality score within a sliding window of 5 nucleotides of 20; (3) filter reads with a length below 36.
rRNA sequences were removed with the Bbduk function from BBTools [v37.62], using as reference the non-redundant ribosomal sequences from the SILVA database.
The pseudoaligner Kallisto [v0.48] was used for transcript level quantification, using gffread [v0.12.1] to extract the transcript sequences to build the needed index.
The estimated abundance files of Kallisto were imported to R studio and gene-level counts were achieved using the Tximport R package [v1.22.0].
Assembly: ARS-UI_Ramb_v2.0
Supplementary files format and content: Counts_Spleen.txt: Tab-delimited file including estimated counts at gene-level by Tximport for each sample.
Supplementary files format and content: Length_Spleen.txt: Tab-delimited file including effective gene lengths from Tximport for each sample. It must be used to calculate an offset matrix together with the count matrix for tools like DESeq2 and EdgeR. This approach corrects for potential changes in gene length across samples (e.g. from differential isoform usage).

organism: Ovis aries

source_name: Spleen

growth_protocol: The animals were kept under uniform housing conditions and nutritional regimens in Zaragoza (Spain). All experimental procedures were approved and licensed by the Ethical Committee of the University of Zaragoza (ref: PI15/14). Requirements of the Spanish Policy for Animal Protection (RED53/2013) and the European Union Directive 2010/63 on protection of experimental animals were always fulfilled.

extract_protocol:
Samples of 1 g of spleen from each sheep were taken at necropsy for RNA extraction and preserved in RNAlater solution (Ambion, Austin, TX, USA) at -80 ºC. Total RNA was isolated from spleen tissue using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and PureLink RNA Mini Kit (Invitrogen). 60 mg spleen tissue were homogenized in 1 mil of TRIzol Reagent using PrecellysR24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) combined with 1.4 and 2.8 mm ceramic beadsmix lying tubes (Bertin Technologies). RNA isolation was performed following manufacturer instructions and RNA was suspended in RNAse free water and stored at -80ºC. RNA quantity and purity were assesed with NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc, Bremen, Germany). RNA integrity wa assessed on an Agilent 2100 Bioanalyzer with Agilent RNA 6000 Nanochips (Agilent Technologies, Santa Clara, CA, USA), which estimates the 28S/18S (ribosomic RNAs) ration and the RNA integrity number (RIN value). The samples presented and average RIN value of 8.32 and a 260/280 ratio >1,7.
RNA libraries were prepared for sequencing using Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol

treatment_protocol: Rasa Aragonesa pure breed lambs were selected from a single pedigree ﬂock of certiﬁed good health at 3 months old and did not undergo any vaccination before the experiment. The ﬂock analyzed in this study was established at the experimental farm of the University of Zaragoza and was always maintained indoors, with ideal controlled conditions of housing, management and diet. The animals were kept 2 months to acclimatize to the new environment so they were 5 months old when the experiment started. The animals were treated with three different treatments: The first group was inoculated with nine different commercial vaccines, the second one was inoculated only with the adjuvant (aluminium hydroxide, AL(OH)3), giving an equivalent dose of aluminium and the third one with only with PBS (control group) Established legal periods between vaccinations were always fulfilled. The vaccination schedule was between February of 2015 and April of 2016, giving a total of 19 doses and 81.5 mg Al3+ per animal during that period.

value: Spleen

tag: breed

value: Rasa Aragonesa

tag: Sex

value: Male

tag: time

value: ~21 months

value: Control


title: 0.5 dpc, IA, Rep2

status: Public on Aug 23 2024

type: SRA

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

country: USA

institute: University of Missouri

description: 100bp read length

library_source: transcriptomic

data_processing:
For Bulk RNA-seq analysis: FASTQ files were pseudoaligned, and DEGs were determined using DESeq. DEGs were then plotted as Principal Component Analysis and heat maps through BioJupies.  For single cell RNA-seq analysis: CellRanger was used to align the sequencing data. Scanpy was used to as a secondary data analysis. The generated loom files were read in as anndata objects and concatenated into a master anndata object. Preprocessing and quality control were performed similarly to the methods described in Scanpys clustering tutorial.
Assembly: mm10
Supplementary files format and content: For bulk RNA-seq data: transcripts per million (TPM) values were exported into .csv files. For single cell RNA-seq data: .h5ad files were exported following standard codes in Scanpy tutorial.

molecule: polyA RNA

organism: Mus musculus

source_name: oviduct

growth_protocol: Oviductal tissues were collected from adult C57BL6/J mice and stored in pairs (one pair of oviducts per animal) at 0.5, 1.5, 2.5, and 3.5 dpc/dpp of natural fertilization and pseudopregnancy, respecitvely. For 0.5 dpc/dpp tissue, female mice were placed for mating at 21:00h. For 1.5, 2.5, and 3.5 dpc/dpp, female mice were placed for mating between 5-6 p.m.

extract_protocol:
Oviducts were dissected and kept in 1 mL Leibovitz-15 + 1% fetal bovine serum (FBS). Then, oviducts were sectioned into two regions (Infundibulum + Ampulla (IA), Isthmus + Uterotubal Junction (IU). Tissue samples were placed in a sterile Eppendorf tube and flash-frozen in liquid N2. Samples were stored at -80°C for later RNA extraction. The oviducts were collected at the same time points as their dpc counterparts for DPP samples. Total RNA were extracted utilizing the RNeasy Micro Kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions. DNA digestion was performed with all samples using a Qiagen RNase-free DNase Set (1500 K units). RNA was then shipped to the University of California San Diego (UCSD) for quality control, library preparation, and sequencing. RNA integrity (RIN) was verified using TapeStation for a minimum RIN value of 7. RNA from this study has an average RIN of 9.04. For singe cell-RNA seq analysis: Another set of mice was used for single-cell isolations and scRNA-seq analysis. Mating and tissue collection protocols were similar to bulk RNA isolation described above, with the exception that female mice were superovulated using the protocol described previously (73) to ensure sufficient numbers of female mice at each time point could be harvested for single cell isolation and library preparation within the same day (n= 3-4 mice/group). Superovulation was performed by intraperitoneal injection of 5 IU pregnant mare serum gonadotropin (PMSG, Prospect HOR-272, East Brunswick, NJ). Forty-eight hrs after PMSG injection, females were injected with 5 IU of human chorionic gonadotropin (hCG, Prospect HOR-250). Immediately after the hCG injection, females were placed in fertile male cages for mating. Oviducts were collected at 0.5, 1.5, and 2.5 dpc and dissected into IA and IU regions before single-cell isolation. For the control group, oviducts were collected 16 hrs post hCG injection. Trypsin-EDTA (0.25%, MilliporeSigma, T4049) was used for oviductal cell isolation.
For Bulk RNA-seq analysis: RNA libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina Inc., San Diego, CA). For single-cell RNA-seq analysis: The final cell concentration was targeted for 8,000 cells/run. Cell singlets were captured for the library preparation using 10X Chromium Controller and Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA). Libraries generated were then evaluated for quality using Fragment Analyzer (Agilent, Santa Clara, CA).
For Bulk RNA-seq analysis: Libraries were sequenced using the Illumina NovaSeqS4 platform with a read depth of 25M reads/sample (n=3/region/timepoint), paired-end, and 100bp read length. For single cell RNA-seq analysis:  Libraries were sequenced using Illumina HiSeq4000 at the University of Oregon, targeting 400 million reads/run, paired-end, and 100 bp read length.

tag: tissue

value: oviduct

tag: region

value: infundibulum and ampulla

tag: strain

tag: genotype

value: wild-type

tag: timepoint

value: 0.5 days post coitus (0.5 dpc)


title: 135-B_S16

description: Column ID at processed data: 135-B_S16

molecule: total RNA

tag: treatment


title: P32 Inguinal transp biol rep 1

city: St. Louis

first: Samantha

middle: A

last: Morris

address: 660 S Euclid Ave

institute: Washington University in St. Louis

library_source: transcriptomic single cell

data_processing:
Data was processed using Seurat 4.3.0. Using a standard Seurat analysis pipeline, we filtered out low-quality cells that had a high fraction of mitochondrial reads (greater than 0.05) and low total counts (less than 500). Cell cycle scoring and regression were performed. UMAP dimension reduction was performed with 10 principal components; UMAP and Louvain clustering algorithms were otherwise implemented with Seurat default parameters.
Assembly: mm10 with transgenes for GFP and CEBPA_DN
Supplementary files format and content: Hosted on Figshare

source_name: skin adipose

extract_protocol:
APCs and RNA were harvested as previously described by Rivera-Gonzalez et al. (doi 10.1016/j.stem.2016.09.002).
scRNA-seq libraries were generated using the Chromium Single Cell 3′, v3.1 Library & Gel Bead Kit (PN-1000268, 10X Genomics), Chromium Single Cell G Chip kit (PN-1000127, 10X Genomics), and Dual Index Kit TT Set A, PN-1000215

value: skin adipose


title: P32 Inguinal transp biol rep 2


title: 134-B_S15

description: Column ID at processed data: 134-B_S15


title: P32 No Cebpa_DN biol rep 1


title: HAp_short_1, Day 21

city: London

first: Jishizhan

last: Chen

address: 10 Pond St

department: Division of Surgery & Interventional Science

country: United Kingdom

institute: University College London

data_processing:
Quality checked by FastQC v.0.11.9
Trimmed the adapters, poorly expressed or nonexpressed genes via the Trimmomatic v.0.38.0 with following parameters: PE; ILLUMINACLIP: TruSeq3-PE.fa: 2:30:10; LEADING: 3; TRAILING: 3; SLIDINGWINDOW: 4:15; MINLEN: 50.
After that, the HISAT2 v.2.2.1 was utilised to map sequences to the UCSC Homo sapiens GRCh38 reference.
The table of read counts with Entrez gene IDs was generated using the featureCounts v.2.0.1.
Assembly: hg38
Supplementary files format and content: Tabular files of read counts for each Sample.

organism: Homo sapiens

source_name: bone marrow-derived mesenchymal stem cells

growth_protocol: hBMSCs were cultured in the Mesenchymal Stem Cell Osteogenic Differentiation Medium (MODM, ScienCell, Carlsbad, US) in humidified atmosphere with 5% CO2 at 37C for 21 days.

extract_protocol:
Total RNA extraction was performed using a Monarch Total RNA Miniprep Kit (New England Biolabs, Ipswich, US), according to the manufacturer’s protocol.
The RNA-Seq was carried out at the UCL Genomics facility. RNA concentration was measured on a Nanodrop spectrometer and 500 ng of RNA was used for cDNA synthesis and library preparation using the Kapa mRNA HyperPrep assay (Roche, Basel, Switzerland) and xGen UDI-UMI adapters (Integrated DNA Technology, Shanghai, China) , according to the manufacturer’s protocol. Sequencing of these libraries was performed on the NextSeq 2000 (Illumina, San Diego, US) P2 flow-cell with 56bp paired-end reads.

treatment_protocol: hBMSCs were culture on coated coverslips. Different groups were set up based on the coating substrates, which are hydroxyapatite nanorods (HAp NRs) with or without 4 mol% terbium (Tb) doping, in short- or long-range ordered patterns (fixed by PDMS). The coverslips coated with only PDMS were utilised as the control.

tag: cell type

value: PDMS + short-range ordered HAp


title: Estrus, IU, Rep3

description: 100bp read length

value: isthmus and uterotubal junction

value: Estrus


title: 0.5 dpc, IA, Rep1

description: 100bp read length


title: 133-B_S14

description: Column ID at processed data: 133-B_S14


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre2, Rep 4

city: Glasgow

first: Thomas

middle: G

last: Bird

address: Switchback Road, Bearsden

department: CRUK Scotland Institute

institute: Beatson Institute

data_processing:
Quality checks and trimming on the raw RNA-Seq data files were done using FastQC version 0.11.7, FastP [2] and FastQ Screen version 0.12.0. RNA-Seq paired-end reads were aligned to the GRCm38.92 version of the mouse genome and annotation using HiSat2 version 2.1.0. Expression levels were determined and statistically analysed by a combination of HTSeq version 0.9.1, the R environment version 3.4, utilizing packages from the Bioconductor data analysis suite [8] and differential gene expression analysis based on the negative binomial distribution using the DESeq2 package version 1.18.1
Assembly: GRCm38.92 version of the mouse genome and annotation
Supplementary files format and content: Count table normalized with version 1.18.1 of DESeq2

source_name: Kidney

extract_protocol:
Whole tissue RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74104)
RNA was tested on an Agilent 2200 TapeStation (D1000 screentape) using RNA screentape and only samples with a RIN>7 were further processed for library preparation. 20ng/ml of RNA were used to prepare libraries using the TruSeq Stranded mRNA Kit. Agilent 2200 Tapestation was used to assess library quality and Qubit (Thermo Fisher Scientific) was used to check concentration. The libraries were then run on the Illumina NextSeq 500 using the High Output 75 cycles kit (paired end, 2x36 bp cycle, dual index (I5 and I7 Illumina)).
TruSeq Stranded mRNA Kit

value: Kidney


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre2, Rep 3


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control2, Rep 4


title: Estrus, IU, Rep1

description: 100bp read length


title: Estrus, IU, Rep2

description: 100bp read length


title: 131-B_S13

description: Column ID at processed data: 131-B_S13


title: 126-B_S11

description: Column ID at processed data: 126-B_S11

value: Vaccine


title: Estrus, IA, Rep3

description: 100bp read length


title: 124-B_S10

description: Column ID at processed data: 124-B_S10


title: Control_2, Day 21

value: bone marrow-derived mesenchymal stem cells

value: PDMS


title: 136-B_S17

description: Column ID at processed data: 136-B_S17

value: Spleen


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control2, Rep 3


title: 0.5 dpc, IA, Rep3

description: 100bp read length


title: 122-B_S8

description: Column ID at processed data: 122-B_S8

value: Rasa Aragonesa


title: Mouse Kidney, Mdm2 Ex 5/6, Untreated Control, Rep 4


title: Mouse Kidney, Mdm2 Ex 5/6, Untreated Control, Rep 3


title: Estrus, IA, Rep2

description: 100bp read length


title: Estrus, IA, Rep1

description: 100bp read length


title: P32 No Cebpa_DN biol rep 2


title: 123-B_S9

description: Column ID at processed data: 123-B_S9

value: Male


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre4, Rep 4


title: d28_KO3_Tcm

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

country: Switzerland

institute: University of Lausanne

data_processing:
Smart-seq2 reads were trimmed and mapped with STAR to the mouse reference genome (mm10)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was extracted using the RNeasy® Mini Kit (Qiagen) following the instructions of the manufacturer
For the preparation of NGS libraries, we followed the Smart-seq2 protocol. The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina, San Diego, CA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

tag: cell line

value: T lymphocyte

value: central memory T cell (CD62l+ CD127+)

value: PPARbeta/delta KO


title: 127-B_S12

description: Column ID at processed data: 127-B_S12

value: ~21 months


title: 117-B_S6

description: Column ID at processed data: 117-B_S6

value: Adjuvant


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre4, Rep 3


title: d28_KO1_Tcm


title: 116-B_S5

description: Column ID at processed data: 116-B_S5


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control4, Rep 4


title: d28_WT3_Tcm

value: WT


title: 115-B_S4

description: Column ID at processed data: 115-B_S4


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control4, Rep 3


title: d28_WT1_Tcm


title: 114-B_S3

description: Column ID at processed data: 114-B_S3


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre2, Rep 1


title: 111-B_S1

description: Column ID at processed data: 111-B_S1


title: flu injured lung at 11 days post infection, without trachea, scRNA-seq

city: San Diego

first: Le

last: Xu

state: CA

address: 8018 Regents Road Atp. 301

department: Pediatrics

institute: University of California, San Diego

description: Flu_11D_20D_harmony_res13_Newlabel_08212023.rds

data_processing:
For bulk RNA-seq, FASTQ files were aligned to the mouse reference genome (mm10) by using Bowtie2 (Langmead and Salzberg, 2012) with default settings. Differential gene expression analysis was performed using Cufflinks (Trapnell et al., 2010). Heatmaps were generated by ggplot2 (version 3.3.2).
For scRNA-seq, Cell Ranger (version 3.0.2) was used to initially align the raw reads onto the mouse reference genome (mm10) and generate the feature-barcode matrix. Next, R package Seurat (version 4.0) (Hao et al., 2021) was used to perform data quality control, normalization, scaling, principal components analysis (PCA) and the canonical correlation analysis (CCA) based data integration. Briefly, to filter out low-quality cells or doublets, cells with fewer than 200 or more than 4,000 unique features, or more than 15% mitochondrial contents were removed from further analysis. Then "LogNormalize" was used to normalize the feature expression. A total of 2,000 top variable features were identified by function FindVariableFeatures and kept for PCA. Top 20 significant components were chosen to conduct dimensional reduction by uniform manifold approximation and projection (UMAP) with default parameters. The expression features of marker genes were profiled and visualize by R package ggplot2 (version 3.3.2).
Assembly: mouse mm10
Supplementary files format and content: For bulk RNA-seq, gene expression matrix.
Supplementary files format and content: For scRNA-seq, h5 files from cellranger.

source_name: whole lung cells

growth_protocol: Embryos used in this study were harvested from time-mated mice, counting noon the day when the vaginal plug was found as E0.5. All mice were in B6 background or have been back crossed to B6 background for at least 3 generations. Littermates were used as controls in all experiments. All mice were housed in facilities accredited by American Association for Accreditation of Laboratory Animal Care (AAALAC) at University of California San Diego. All animal husbandry and experiments were approved by Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Total RNA from embryonic or adult lungs were extracted by using Trizol (Invitrogen) and RNeasy Micro RNA extraction kit (Qiagen).
For bulk RNAseq, cDNA libraries were constructed by using Illumina TruSeq RNA Library Prep Kit V2 (Illumina). For scRNA, single cell libraries were generated from sorted epithelial cells by using Chromium Single Cell 3’ v3 kit (10X Genomics).

treatment_protocol: Tamoxifen dissolved in corn oil was administrated intraperitoneally at the dose of 50 mg/kg. Three times in every other day.

value: whole lung cells

tag: age

value: Adult, 11 days post flu infection

value: Wild type

value: intranasal influenza PR8


title: flu injured lung at 20 days post infection, without trachea, scRNA-seq

source_name: D31-;CD45- epithelial and mesenchymal cells

value: Adult, 20 days post flu infection


title: 113-B_S2

description: Column ID at processed data: 113-B_S2


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre4, Rep 2

value: Kidney


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre4, Rep 1


title: WILD TYPE STRAIN IN LIGHT REPLICA 2

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

institute: University of Seville

data_processing:
libraries were run on Genome Analyzer (Illumina NovaSeq 6000).
paired-end reads of 150 nucleotide each were mapped against the N. crassa OR74A genome by using Star 2.7
quality was checked using FastQC
automatic preprocessing of the reads was carried out with FASTP
Quantification was performed with featurecounts of the Subread package
Assembly: NO
Supplementary files format and content: raw_counts.txt, raw reads

organism: Neurospora crassa

source_name: Sexual development tissue

growth_protocol: Induction of formation of protoperithecia were carried out by spreading a total of 2x104 conidia into nitrogen-poor Synthetic Crossing Medium (SCM) agar´s plates and then incubated at 22°C with light or in darkness, depending on the experiment, for 7 days to allow the formation of protoperithecia. Conidia from a strain of opposing mating type were collected and suspended in 2.5% Tween 20. Formation of protoperithecia in each strain was examined using a stereomicroscope between days 5 to 7 prior to fertilization. Crosses were performed by applying 2 ml of a conidia suspension (5x105 conidia/ml with 2.5% Tween 20) to the surface of the protoperithecium plates. After fertilization, sexual development occurred under the same culture conditions as protoperithecium development, and all the process was monitored using stereomicroscope.

extract_protocol:
all tissues were immediately frozen in liquid nitrogen and stored at -80°C. Tissue samples from biological replicates were pooled for RNA extraction at each sample point. Mycelia was grinded using a precooled mortar and pestle, homogenized with TRI REAGENT (Invitrogen), and then phase separated by adding chloroform. The nucleic acid phase was precipitated with isopropanol, washed with 75% ethanol, and solubilized in RNase-free water. RNA clean-up and DNase treatment was performed using Nucleo-Spin RNA (MACHEREY-NAGEL) and RNase-free DNase Set (QIAGEN), following the manufacturer procedures. RNA quantity and quality were analyzed using Nano-drop ND-1000
Poly-A selection and cDNA libraries preparation for RNA were prepared according to the Illumina mRNA Sample Preparation Guide
Illumina RNA-seq strand specific first-strand

treatment_protocol: Samples were collected 1 day before fertilization

value: Sexual development tissue

value: WILD TYPE

value: LIGHT


title: control lung without flu injury, without trachea, scRNA-seq

value: D31-;CD45- epithelial and mesenchymal cells

value: Adult, 12-week old

value: intranasal PBS


title: Sox2creER;Lonp1, airway epithelium,adult, scRNA-seq

value: Adult, 39 days post inactivation

value: Tamoxifen injection at P39, 41, 43


title: WILD TYPE STRAIN IN LIGHT REPLICA 1


title: WILD TYPE STRAIN IN DARK REPLICA 3

value: DARK


title: d28_KO2_Tcm

value: Spleen

value: T lymphocyte

value: central memory T cell (CD62l+ CD127+)

value: PPARbeta/delta KO


title: Control_rep2

city: Chengdu

first: Zhihong

last: Xue

state: Sichuan

address: No. 20, 3rd section, South Renmin Road

country: China

institute: Sichuan University

description: WT mESCs

data_processing:
Untrimmed sequencing reads were first analyzed for quality control by fastqc software (v0.11.9).
The adaptor sequence and low-quality reads were then trimmed off using Cutadapt software (v4.1).
Clip-seq reads were aligned to the UCSC mm10 genome using STAR software (2.7.10a). Only uniquely mapping reads (quality score > 40) were retained.
To create Clip-seq coverage plots, the locations of the mapped Clip-seq reads were normalized using ChIPseqSpikeInFree software (v1.2.4), extended to 150 bp to represent sequenced fragments and reformatted in the bigWig file format using deeptools (v3.5.1).
Peaks were called using Clipper software (v2.1.2) with default settings.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CLIP-seq

growth_protocol: V6.5 ESC cells were maintained in the medium (DMEM, 10% fetal bovine serum (FBS), 2,000U/ml LIF, 1×non-essential amino acid solution, 1×GlutaMAX, 1mM sodium pyruvate, 0.1mM β-mercaptoethanol, 100U/ml penicillin, 100 mg/ml streptomycin) under the condition of 37oC and 5% CO2. Embryoid body cells were maintained in standard ESCs medium lacking LIF and ascorbic acid was added to a final concentration of 50 µg/ml from day 2 to day 9.

extract_protocol:
The embryoid bodies (EBs) of 9 days were resuspended in the PBS buffer and treated with UV crosslinking (254nm, 400 mJ/cm2) using a Stratalinker. Crosslinked EBs were lysated in 1ml iCLIP lysis buffer (50mM Tris pH7.4, 100mM NaCl, 1% Igepal CA630, 0.1% SDS, 0.5% sodium deoxycholate, RNase inhibitor, and protease inhibitor cocktail).
We performed the CLIP-seq following the eCLIP-seq protocol (Van Nostrand et al., 2016) except several modifications as below. The V6.5 mESCs over-expressing V5-tagged Csrp1 and wildtype V6.5 mESCs were differentiated into embryoid bodies as described above separately. The embryoid bodies (EBs) of 9 days were resuspended in the PBS buffer and treated with UV crosslinking (254nm, 400 mJ/cm2) using a Stratalinker. Crosslinked EBs were resuspended in 1ml iCLIP lysis buffer (50mM Tris pH7.4, 100mM NaCl, 1% Igepal CA630, 0.1% SDS, 0.5% sodium deoxycholate, RNase inhibitor, and protease inhibitor cocktail) and then solubilized for 1 minute via sonication with a Covaris S220 instrument using following parameters: PIP 140W, Duty factor 5%, CPB 200. The lysates were limited digested with 0.4 µl RNase I for 5 minutes at 37oC and then centrifuged for 15 minutes with 15,000g. The 100 µl protein G magnetic beads were incubated with 10 µg anti-V5 tag antibody for 30 minutes at 4oC to prepare anti-V5 magnetic beads, and then added to the cell lysates and incubated for 2 hrs at 4oC. Next, the beads were washed as below: two times with 1ml high salt wash buffer (50mM Tris pH7.4, 1M NaCl, 1% Igepal CA630, 0.1% SDS, 0.5% sodium deoxycholate); two times with 1ml wash buffer (20mM Tris pH7.4, 10mM MgCl2, 0.2% Tween-20); two times with 1ml 1x DNase buffer (10mM Tris pH7.4, 2.5mM MgCl2, 0.5mM CaCl2). Beads were resuspended in 100ul 1x DNase buffer supplemented with 4U DNase I and incubated for 20mins at 37oC. Beads were then washed two times with 1ml PK buffer (20mM Tris pH7.4, 50mM NaCl, 1mM EDTA). Beads were resuspended in 260ul PK buffer and supplemented with 40 µl proteinase K (NEB). Beads were incubated for 2 hrs at 37oC and then mixed well with 200 µl phenol and 200µl 1-Bromo-3-chloropropane (BCP), which was then centrifuged at 13000rpm for 15 minutes at 4°C. The supernatant was transferred to a new tube, mixed with 200μl BCP, vortexed for 30 seconds and centrifuged at 13000rpm for 15 minutes at 4°C. The supernatant was transferred to a new tube and supplied with 30μl 3M sodium acetate (NaOAc) pH5.2, and 2μl glycogen (5mg/ml, ThermoFisher). The mixture was then precipitated by adding 2.5x volumes of 100% ethanol and centrifuged at 13000rpm for 15 minutes at 4°C. The pellets were washed with 80% ethanol twice, and then dissolved in 15µl H2O. The resultant RNAs were first ligated with 3′ barcoded (NNNNNNNNNNNNNNN) RNA adaptor and then 5′ RNA adaptor. cDNAs were synthesized with M-MLV reverse transcriptase (Vazyme) and amplified by VAHTS HiFi amplification mix (Vazyme). The PCR products were cleaned using DNA clean beads (Vazyme) and separated on agarose gel. The library was purified using MinElute Gel Extraction Kit (Qiagen) and evaluated using Qsep with S2 Cartridge. The libraries were finally sequenced on NovaSeq 6000 platform (Illumina) by Shenzhen Haplox Biotechnology.

value: WT

value: Embryoid body cell

tag: clip antibody

value: V5 tag (SinoBiological, #100378-T36)


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control2, Rep 2

value: Kidney


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control2, Rep 1


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Cre2, Rep 2


title: WILD TYPE STRAIN IN DARK REPLICA 1

value: Sexual development tissue


title: Control_rep1

description: WT mESCs


title: Mouse Kidney, Mdm2 Ex 5/6, Untreated Control, Rep 2


title: WILD TYPE STRAIN IN LIGHT REPLICA 3

value: WILD TYPE


title: WILD TYPE STRAIN IN DARK REPLICA 2


title: Csrp1_IP_rep1

description: Csrp1-V5 over-expressing mESCs

value: Csrp1-V5 over-expressing


title: Csrp1_IP_rep2

description: Csrp1-V5 over-expressing mESCs


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control4, Rep 2


title: Mouse Kidney, Mdm2 Ex 5/6, Untreated Control, Rep 1


title: Csrp1KO_EB9rep3

description: mRNAs

data_processing:
Untrimmed sequencing reads were first analyzed for quality control by fastqc software (v0.11.9). The adaptor sequence and low-quality reads were then trimmed off using trim_galore software (v0.6.7).
Ribosome RNAs were removed from trimmed reads using SortMeRNA software.
Reads without ribosome RNAs were mapped to mm10 reference genome using STAR software(v2.7.1a) as default parameters.
Raw readcounts were calculated using FeatureCounts software (v2.0.1). The raw readcounts were normalized by the FPKM method.
Assembly: mm10
Supplementary files format and content: *.csv: Comma-Separated Values CSV files include read count and FPKM values for each Sample.

extract_protocol:
Total RNAs were isolated using the Trizol Reagent.
Libraries were prepared from 1 µg total RNAs. We purified the mRNA using VAHTS mRNA capture beads (Vazyme). The libraries were generated using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme), and evaluated using Qsep with S2 Cartridge.


title: S20 Kras G12D d7 Female AAV-Cre on Kras HET genotype Kidney

data_processing:
Raw fastq.gz where quality trimmed with FastP and aligned to the GRCm38.92 genome with HiSat2. The reads where summarised using Feature Counts. FastQC, FastQ Screen and descriptive summary statistics (produced using R) where used for quality checks.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample produced using Feature Counts.

extract_protocol:
Whole tissue RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74104), including the optional DNase step, as described previously12. Briefly, 20-30mg of snap frozen tissue were homogenized in 600ml buffer RLT/1% β-mercaptoethanol using the Precellys Evolution homogenizer (Bertin Technologies) and the RNA was eluted in 30μl RNase-free water. RNA concentration was estimated with the Nanodrop 2000 and only samples with a 260/280 ratio≥2 were used for further analysis.
20ng/ml of RNA were used to prepare libraries using the TruSeq Stranded mRNA Kit. Agilent 2200 Tapestation was used to assess library quality and Qubit (Thermo Fisher Scientific) was used to check concentration.


title: S19 Kras G12D d7 Female AAV-Cre on Kras HET genotype Kidney


title: WHITE-COLLAR MUTANT IN LIGHT REPLICA 2

value: WHITE-COLLAR MUTANT

value: LIGHT


title: 121-B_S7

description: Column ID at processed data: 121-B_S7

value: Rasa Aragonesa

value: Male

value: ~21 months

value: Vaccine


title: WHITE-COLLAR MUTANT IN LIGHT REPLICA 3


title: Csrp1KO_EB9rep2

description: mRNAs


title: WHITE-COLLAR MUTANT IN LIGHT REPLICA 1


title: S18 Kras G12D d7 Male AAV-Cre on Kras HET genotype Kidney


title: control, airway epithelium,adult, scRNA-seq

value: Adult, 39 days post inactivation

value: Tamoxifen injection at P39, 41, 43


title: Csrp1KO_EB9rep1

description: mRNAs


title: WHITE-COLLAR MUTANT IN DARK REPLICA 2

value: DARK


title: S17 Kras G12D d7 Male AAV-Cre on Kras HET genotype Kidney


title: Csrp1KO_ESCrep3

description: mRNAs

value: Mouse embryonic stem cell


title: S16 Kras G12D d7 Male AAV-Cre on Kras HET genotype Kidney


title: WHITE-COLLAR MUTANT IN DARK REPLICA 1


title: Csrp1KO_ESCrep2

description: mRNAs


title: S15 Kras WT d7 Male AAV-Null on Kras HET genotype Kidney


title: VELVET MUTANT IN LIGHT REPLICA 3

value: VELVET MUTANT


title: VELVET MUTANT IN LIGHT REPLICA 2


title: Csrp1KO_ESCrep1

description: mRNAs


title: WT_EB9rep3

description: mRNAs

value: WT

value: Embryoid body cell


title: S14 Kras WT d7 Female AAV-Null on Kras HET genotype Kidney

value: Kidney


title: VELVET MUTANT IN LIGHT REPLICA 1

value: Sexual development tissue


title: WHITE-COLLAR MUTANT IN DARK REPLICA 3


title: S13 Kras WT d7 Male AAV-Null on Kras HET genotype Kidney


title: S11 Kras WT d7 Male AAV-Null on Kras HET genotype Kidney


title: S12 Kras WT d7 Male AAV-Null on Kras HET genotype Kidney


title: WT_EB9rep2

description: mRNAs


title: WT_EB9rep1

description: mRNAs


title: VELVET MUTANT IN DARK REPLICA 3


title: VELVET MUTANT IN DARK REPLICA 2


title: S09 Kras G12D d7 Female AAV-Cre on Kras HET genotype Liver

source_name: Liver

value: Liver


title: WT_ESCrep3

description: mRNAs


title: S10 Kras G12D d7 Female AAV-Cre on Kras HET genotype Liver


title: WT_ESCrep1

description: mRNAs


title: Immunocastrated pigs (pooled RNA) [skele_6]

city: Ljubljana

first: Klavdija

last: Poklukar Žnidaršič

state: Ljubljana

address: Hacquetova ulica 17

department: Animal Science department

country: Slovenia

institute: Agricultural Institute of Slovenia

data_processing:
Raw reads were filtered by (1) discarding the reads with adaptor contamination, (2) removing the reads with more than 10% of uncertain nucleotides, (3) discarding reads with low-quality nucleotides (base quality less than 20) constituting more than 50% of the read.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12 (default parameters allowing up to 2 bases mismatches).
HTSeq v0.6.1 was used to count the read numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The read counts were adjusted by edgeR program package through one scaling normalized factor.
Differential expression analysis  was performed using the DEGSeq R package (1.20.0) to compare the effect of sex-category on transcript expression in the LD and SSC muscles . The P-values were adjusted using the Benjamini & Hochberg method.
Genome_build: Sscrofa10.2 (Genbank assembly GCA_000003025.6)
Supplementary_files_format_and_content: tab-delimited csv file with FPKM values
Supplementary_files_format_and_content: tab-delimited csv file with read counts

organism: Sus scrofa

source_name: SSC muscle sample

extract_protocol:
At the end of the slaughterline (45 min post mortem), approx. 1 cm3 muscle samples were taken from the central part of LD at the level of the last rib and from the SSC i.e., from the central part of its m. biventer cervicis, at the level of the 4th cervical vertebra.  Muscles were sampled at the right side of the carcass, snap-frozen in liquid nitrogen and stored at –80°C until subsequent analysis. Total RNA was extracted using RNeasy plus Universal Mini Extraction Kit. Extracted RNA from 6 animal  samples (out of 12) were pooled in equal quantities for each male sex category group and muscle.
cDNA sequencing libraries were generated using NEBNext Ultra RNA Library preparation Kit for Illumina.

treatment_protocol: Immunocastrated pigs were vaccinated at the age of 12 and 21 weeks with a vaccine against GnRH (Improvac® vaccine, Zoetis) and surgically castrated pigs were castrated within the first week of life.

value: Landrace x Pietrain crosses

value: skeletal muscle tissue

value: immunocastration


title: S07 Kras G12D d7 Male AAV-Cre on Kras HET genotype Liver


title: DOUBLE MUTANT VE-WC IN LIGHT REPLICA 1

value: DOUBLE MUTANT

value: LIGHT


title: S08 Kras G12D d7 Male AAV-Cre on Kras HET genotype Liver


title: S06 Kras G12D d7 Male AAV-Cre on Kras HET genotype Liver


title: DOUBLE MUTANT VE-WC IN DARK REPLICA 3


title: DOUBLE MUTANT VE-WC IN DARK REPLICA 2


title: S05 Kras WT d7 Male AAV-Null on Kras HET genotype Liver


title: Surgically castrated pigs (pooled RNA) [skele_4]

value: surgical castration


title: DOUBLE MUTANT VE-WC IN DARK REPLICA 1


title: S04 Kras WT d7 Female AAV-Null on Kras HET genotype Liver


title: VELVET MUTANT IN DARK REPLICA 1


title: Surgically castrated pigs (pooled RNA) [skele_3]

source_name: LD muscle sample


title: Entire male pigs (pooled RNA) [skele_1]

value: no treatment


title: WT_ESCrep2

description: mRNAs


title: HJJ_3_5_2.raw_1/2.fastq

city: Lianyungang

first: wenhao

last: cheng

state: Jiangsu

address: 59 Cangwu Road, Haizhou District

department: College of Pharmacy

institute: Jiangsu Ocean University

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

source_name: Colon Cancer

growth_protocol: HCT116 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics, and the cells were treated with or without HJJ_3_5 for 24 hr, respectively, and incubated in 5% CO2 at 37oC.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Colon Cancer

value: Human Colon Cancer Cell


title: DOUBLE MUTANT VE-WC IN LIGHT REPLICA 3


title: HJJ_3_5_1.raw_1/2.fastq


title: DOUBLE MUTANT VE-WC IN LIGHT REPLICA 2


title: U-2 OS cells, Vpr_Q65R_36_10_UDI56_S10_R1_001

city: Los Angeles

first: Oliver

middle: I.

last: Fregoso

address: 615 Charles E Young Dr S, Los Angeles CA 90095

department: Microbiology, Immunology and Molecular Genetics

institute: University of California Los Angeles

data_processing:
The raw reads are found in the following file OF_1Pool_RNA_S-21-0154_FA276/FastQC/fastqs.
Quality control of reads via TRIMMOMATIC and QUALIMAP_PATH.
Reads were aligned to the human genome GENOME_DIR_STAR
DESeq2 was used to analyze RNAseq data
Assembly: human genome GENOME_DIR_STAR
Supplementary files format and content: text file includes read counts for each sample
Supplementary files format and content: html file includes FastQC report for each sample

source_name: Bone- sarcoma of the tibia of a osteosarcoma female patient

growth_protocol: Human bone osteosarcoma epithelial (U2OS) were cultured as adherent cells directly on tissue culture plastic (Greiner) in Dulbecco’s modified Eagle’s medium (DMEM) growth medium (high glucose, L-glutamine, no sodium pyruvate; Gibco) with 10% fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (Gibco) at 37°C and 5% CO2.

extract_protocol:
At 36 hours post treatment, total RNA from U2OS cells was isolated using TRIzol® reagent (Invitrogen). RNA integrity was assessed using the Bioanalyzer TapeStation 4200 RNA High Sensitivity (Agilent).
Library Preparation was completed using the KAPA mRNA HyperPrep Kit (Illumina) enriching for Poly(A) RNA with magnetic oligo-dT beads and attaching unique dual indexed adapters. Quality control of the library was done with the Bioanalyzer TapeStation 4200 D1000 High Sensitivity (Agilent). RNA was sequenced using the Hiseq3000 1x50 at the UCLA Technology Center for Genomics & Bioinformatics core.

treatment_protocol: U2OS cells were infected with equal titers of rAAV expressing 3xFLAG-tagged Vpr WT, S79A, H71R, Q65R, or empty vector (EV) (negative control).

value: U-2 OS

value: 36 hours post treatment

value: Vpr Q65R rAAV


title: S01 Kras WT d7 Male AAV-Null on Kras HET genotype Liver


title: DMSO_2.raw_1/2.fastq

value: DMSO


title: S03 Kras WT d7 Male AAV-Null on Kras HET genotype Liver


title: U-2 OS cells, Vpr_Q65R_36_16_UDI62_S16_R1_001

value: Bone- sarcoma of the tibia of a osteosarcoma female patient

value: WT


title: Immunocastrated pigs (pooled RNA) [skele_5]


title: DMSO_1.raw_1/2.fastq


title: P21 Naive

description: 10X Genomics

data_processing:
Generation of fastq files viahttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome custom build with GFP and DN-CEBPA viahttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
CellRanger generated files matrix.mtx, features.tsv, barcodes.tsv, possorted_genome_bam.bam
Assembly: mm10
Supplementary files format and content: Rds Seurat object

growth_protocol: Donor cells were cultured in supplemented DMEM media

extract_protocol:
Cells were encapsulted and library prepared using the 10X Chromium instrument with the Single Cell 3' Reagent Kits (v2 chemistry)
10x Genomics Chromium single cell preparation

treatment_protocol: Transgenes were delivered through lentivirus treatment

value: skin adipose

value: mesenchymal

tag: developmental stage

value: pooled male and female


title: Entire male pigs (pooled RNA) [skele_2]

value: Landrace x Pietrain crosses

value: skeletal muscle tissue


title: P32 Sox9 OE preadip

description: 10X Genomics

value: Transgene overexpression or knockdown of Sox9 in CellTagged DPP4+ progenitors as sorted by FACS


title: U-2 OS cells, Vpr_Q65R_36_4_UDI44_S4_R1_001


title: primary OPCs, DPBS treated 3 hours, rep 3

city: guangzhou

first: Chen

address: tianhe

department: Department of Neurosurgery

institute: Lingnan hospital, branch of the Third Affiliated Hospital of Sun Yat-sen University

data_processing:
Raw data of fastq format were firstly processed through fastp v0.23.0.
Clean reads were aligned to the mouse genome using Hisat2 v2.2.1.
The gene expression level quantification was performed separately for each sample using the featureCounts v2.0.1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: brain

extract_protocol:
RNA extraction from cells was used TRIzol™ (Invitrogen™ 15596026) and Direct-zol™ RNA Miniprep(zymo R2050).
Sequencing libraries were generated using the Hieff NGS®Ultima Dual-mode mRNA Library Prep Kit(Cat#12309, China). A total amount of 0.2 µg RNA per sample was used as input material for the RNA sample preparations.

value: brain

value: primary OPCs

value: gliocyte

value: DPBS treated 3 hours


title: P32 Sox9 OE prog biol rep 2

description: 10X Genomics


title: P32 Sox9 OE prog biol rep 1

description: 10X Genomics


title: primary OPCs, DPBS treated 3 hours, rep 2


title: U-2 OS cells, Vpr_H71R_36_8_UDI54_S8_R1_001

value: Vpr H71R rAAV


title: U-2 OS cells, Vpr_H71R_36_14_UDI60_S14_R1_001

value: U-2 OS


title: primary OPCs, CLU treated 3 hours, rep 2

value: CLU treated 3 hours


title: U-2 OS cells, Vpr_S79A_36_15_UDI61_S15_R1_001

value: 36 hours post treatment

value: Vpr S79A rAAV


title: U-2 OS cells, Vpr_H71R_36_2_UDI42_S2_R1_001

value: Bone- sarcoma of the tibia of a osteosarcoma female patient


title: primary OPCs, DPBS treated 3 hours, rep 1

value: WT


title: P32 Naive biol rep 4

description: 10X Genomics

value: skin adipose

value: GFP and CellTag expression in donor cells


title: S02 Kras WT d7 Male AAV-Null on Kras HET genotype Liver

value: Liver


title: P32 Naive biol rep 3

description: 10X Genomics

value: mesenchymal

value: pooled male and female


title: primary OPCs, CLU treated 3 hours, rep 1


title: primary OPCs, CLU treated 3 hours, rep 3


title: U-2 OS cells, Vpr_S79A_36_9_UDI55_S9_R1_001


title: P32 Naive biol rep 2

description: 10X Genomics


title: U-2 OS cells, Vpr_Wt_36-1_UDI41_S1_R1_001

value: Vpr WT rAAV


title: P32 Naive biol rep 1

description: 10X Genomics


title: primary OPCs, DPBS treated 24 hours, rep 3

value: brain

value: DPBS treated 24 hours


title: U-2 OS cells, Vpr_S79A_36_3_UDI43_S3_R1_001


title: AVC, IWR1, scRNAseq

city: Yamagata

first: Ayano

last: Chiba

state: Yamagata

address: 2-2-2 Iida-Nishi

department: Department of Pharmacology

country: Japan

institute: Yamagata University

description: 10x Genomics

data_processing:
The 10x Genomics Cell Ranger pipeline (v6.1.1) was used to perform sample demultiplexing, alignment to the reference genome (Danio rerio GRCz11), barcode/UMI processing, and gene counting for each cell.
Assembly: GRCz11
Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

organism: Danio rerio

source_name: Heart

extract_protocol:
Hearts were resected from 1-month-old Tg(fli1:EGFP);Tg(myl7:GAL4db-TCFΔC);(5xUAS:NTR-mCherry) fish treated with DMSO or 10 μM MTZ for 48 h. The resected hearts were collected in 35-mm dishes containing HBSS without calcium and magnesium. The atrium and the ventricle were removed from AVCs. Only AVCs were transferred to a 12-well plate. The AVCs were digested with 3 mg/ml collagenase type IV (Worthington, LS004188)/HBSS for 30 min at 28.5 ºC. After pipetting, the cells were collected in low-binding tubes, pelleted (3000 rpm, 5 min at 4ºC), and washed in 0.5% FBS/DMEM (phenol red free). Cells were resuspended in 0.5% FBS/DMEM and counted using a cell counter (Thermofisher Scientific). The resulting cell suspension was loaded onto a 10X Chromium Controller (10X Genomics).
The scRNA-seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 (10X Genomics, 1000128), according to the manufacturer’s protocol. Following droplet generation and barcoding, cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 (Illumina). Raw sequencing data were processed using 10X Genomics Cell Ranger software (v6.1.1).

treatment_protocol: Fish were treated with DMSO or 10 μM MTZ dissolved in fish water for 48 h in the dark.

value: Heart


title: U-2 OS cells, Vpr_Wt_36_13_UDI59_S13_R1_001


title: AVC, DMSO, scRNAseq

description: 10x Genomics

value: DMSO


title: primary OPCs, DPBS treated 24 hours, rep 1

value: primary OPCs

value: gliocyte


title: primary OPCs, CLU treated 24 hours, rep 3

value: CLU treated 24 hours


title: U-2 OS cells, Vpr_Wt_36_7_UDI53_S7_R1_001

value: U-2 OS

value: 36 hours post treatment


title: EC, MTZ, scRNAseq

description:
Tg(fli1:EGFP);Tg(cryaa:EGFP, myl7:GAL4db-TCFΔC);(5xUAS:NTR-mCherry)
10x Genomics

extract_protocol:
Hearts were resected from Tg(fli1:EGFP);Tg(myl7:GAL4db-TCFΔC);(5xUAS:NTR-mCherry) fish treated DMSO or 5 mM MTZ for 4 weeks from 1 month old. The resected hearts were collected into a 35 mm dish containing HBSS without calcium and magnesium. Hearts were torn and were transferred into a 12-well plate. The hearts were digested with 3 mg/ml collagenase type IV (Worthington, LS004188)/HBSS for 30 min at 28.5 ºC. After pipetting, the cells were collected into low-binding tubes, pelleted (3000 rpm, 5 min at 4ºC), and washed in 0.5% FBS/DMEM (phenol red free). The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain (Thermofisher Scientific, S34857) and sorted by a FACSFusion cell sorter (BD Bioscience). Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter (Thermofisher scientific). The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller (10X Genomics).
The scRNA-seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 (10X Genomics, 1000128), according to the manufacturer’s protocol. Following droplet generation and barcoding, cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 (Illumina). Raw sequencing data were processed using 10X Genomics Cell Ranger software (v6.1.1).

treatment_protocol: Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. After exposure to chemicals, the water was changed to remove the chemicals, and the fish were kept in the tank without water circulation. Chemicals were treated every other day.

value: Endothelial cells

value: MTZ


title: primary OPCs, CLU treated 24 hours, rep 2

value: WT


title: U-2 OS cells, Empty_vector_36_17_UDI63_S17_R1_001

value: Bone- sarcoma of the tibia of a osteosarcoma female patient

value: Empty Vector rAAV


title: primary OPCs, CLU treated 24 hours, rep 1


title: EC, DMSO, scRNAseq


title: CM, GFP+, replicate 2, RNAseq

description:
RNAseq_Posi-2_CM_GFP+
Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry)

data_processing:
RNA-seq data were analyzed on the CLC genomics workbench v.20.0.4 (Qiagen) according to the manufacturer’s instructions. Trimmed and filtered reads were aligned to the zebrafish genome (GRCz 11.99).
Assembly: GRCz 11.99
Supplementary files format and content: Tab-delimited text files include total counts for each Sample

extract_protocol:
The AVC region was resected from hearts of Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry) fish at 4-8-month-old. The resected tissues were washed in HBSS without calcium and magnesium and were transferred into a 12-well plate. The hearts were digested with 3 mg/ml collagenase type IV (Worthington, LS004188)/HBSS for 30 min at 28.5 ºC. After pipetting, the cells were collected into low-binding tubes, pelleted (3000 rpm, 5 min at 4ºC), and washed in 0.5% FBS/DMEM (phenol red free). The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain (Thermofisher Scientific, S34857) and sorted by a FACSAria III cell sorter (BD Bioscience). Total RNAs were prepared from mCherry+ EGFP+ cells (β-cat ON CMs) and mCherry- EGFP+ cells (β-cat OFF CMs) using a NucleoSpin XS kit (Macherey-Nagel, 740902.50) according to the manufacturer’s instruction. Reverse transcription (RT) and cDNA library preparation were performed with a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, 634888).
Libraries were prepared using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760)

tag: sorted fraction

value: mCherry+ EGFP+ cells (β-cat ON CMs)

value: Cardiomyocytes


title: Old donor - male - 71yo

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

data_processing:
Sequencing of the libraries obtained from young HSC donors was done on the NovaSeq 6000 Illumina Sequencing system in paired end mode, 125bp PE reads, 100.000-200.000 reads expected per cell. Sequencing of the libraries obtained from old HSC donors was done on the NovaSeq 6000 Illumina Sequencing system in paired end mode, 150bp PE reads. Base call files were converted to fastq ones as well as the sample demultiplexing was done using longranger mkfastq version 2.1.6 for the young donor HSC data and using cellranger mkfastq version 5.0.1 for the old donor HSC data.
Read alignment, assembly of the raw cell x gene UMI count matrix and elimination of datapoints from empty droplets was done using the count functionality of the cellranger pipeline (version 3.1.0)
Genome_build: 10X Cell Ranger reference GRCh38 v3.1.0 -  GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: .tsv & .mtx files - gzip compressed

source_name: Bone marrow

extract_protocol:
Lin–CD34+CD38–CD90+CD45RA– single cells were purified from young and old human BM samples (N=3 for each, male donors) into Eppendorf tubes containing bovine serum albumin solution (0.04% end concentration).
Libraries were prepared using the Chromium Single Cell 3’ Reagent Kits v2 (10X Genomics, USA) following the manufacturer’s protocol (CG00052, Rev F). cDNA concentrations were assessed using a Qubit dsDNA HS kit (Invitrogen) and a Qubit fluorometer (Invitrogen). Fragment sizes were checked using an Agilent high-sensitivity chip (Agilent Technologies) on an Agilent 2100 Bioanalyzer (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: Samples from donors 1 to 3 were obtained from healthy young donors (21-24 yo) and samples from donors 4 to 6 from healthy old donors (68-75 yo)

tag: donor age

value: male

value: old


title: U-2 OS cells, Untreated_36_12_UDI58_S12_R1_001

value: Untreated


title: CM, GFP+, replicate 3, RNAseq

description:
RNAseq_Posi-3_CM_GFP+
Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry)

value: Heart


title: primary OPCs, DPBS treated 24 hours, rep 2

value: brain

value: DPBS treated 24 hours


title: U-2 OS cells, Untreated_36_18_UDI64_S18_R1_001


title: Old donor - male - 68yo


title: CM, GFP-, replicate 3, RNAseq

description:
RNAseq_Cont-3_CM_GFP-
Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry)

value: mCherry- EGFP+ cells (β-cat OFF CMs)


title: Old donor - male - 75yo


title: primary Astrocytes, DPBS treated 24 hours, rep 2

value: primary Astrocytes

value: gliocyte


title: CM, GFP+, replicate 1, RNAseq

description:
RNAseq_Posi-1_CM_GFP+
Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry)


title: U-2 OS cells, Untreated_36_6_UDI46_S6_R1_001

value: U-2 OS

value: 36 hours post treatment


title: primary Astrocytes, DPBS treated 24 hours, rep 1


title: Young donor - male - 22yo

value: young


title: primary Astrocytes, CLU treated 24 hours, rep 3

value: WT

value: CLU treated 24 hours


title: Young donor - male - 24yo


title: U-2 OS cells, Empty_vector_36_11_UDI57_S11_R1_001

value: Bone- sarcoma of the tibia of a osteosarcoma female patient

value: Empty Vector rAAV


title: CM, GFP-, replicate 2, RNAseq

description:
RNAseq_Cont-2_CM_GFP-
Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry)

value: Cardiomyocytes


title: Huh7, shMETTL3

city: Guangzhou

first: Yongrui

last: Lv

state: Guangdong

address: 651 Dongfengdong Road

institute: Sun Yat-sen University Cancer Center

description:
Huh7-sh33
Expression_Transcript.xlsx

data_processing:
Raw sequencing data were checked with Quality control and reimmed for adaptor sequence or low-quality sequence.
Trimmed sequnces were mapped to hg19 genome.
Read count extraction and normalization were performed.
Assembly: hg19
Supplementary files format and content: Excel file includes FPKM values for each Sample

extract_protocol:
RNA was extracted with Trizol (life). 1 ug total RNA was used for construction of sequencing libraries
mRNA was purified with NEBNext poly(A) Magnetic Isolation Module and subjected for library construction with KAPA Standard RNA-Seq Library Prep Kit (Illumina).

value: hepatocellular carcinoma


title: primary Astrocytes, CLU treated 24 hours, rep 2


title: Young donor - male - 21yo

value: male


title: U-2 OS cells, Empty_vector_36_5_UDI45_S5_R1_001


title: Huh7, shNC

description:
Huh7-shNC
Expression_Transcript.xlsx

value: shNC


title: primary Astrocytes, DPBS treated 24 hours, rep 3


title: CBell_B7333

status: Public on Aug 22 2024

city: Bangkok

first: Tewarit

last: Sarachana

address: 154 Rama 1 Rd. Wangmai Pathumwan

country: Thailand

institute: Chulalongkorn University

data_processing:
Sequencing data filtering were performed using the filtering software SOAPnuke developed by BGI independently for filtering.
Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) is software used for mapping RNA-seq reads.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw read and fpkm for each sample

source_name: postmortem cerebellum tissue

growth_protocol: Frozen postmortem brain tissues were homogenized using 0.5 mm glass beads in the tube containing the lysis solution. Homogenization was performed by using Disruptor Genie (Scientific Industries, USA)

extract_protocol:
Total RNA was extracted from post-mortem brain tissue using mirVana miRNA Isolation Kit (Ambion, USA) according to the manufacturer’s protocol.
Total RNA was prepared using DNBSEQ Eukaryotic Stranded Transcriptome library preparation- Stranded mRNA Library

value: postmortem cerebellum tissue

tag: subject status

value: unaffected


title: primary Astrocytes, CLU treated 24 hours, rep 1

value: brain


title: CBell_B6994

value: ADD


title: CBell_B5718


title: CBell_B6337

value: ASD


title: CBell_B5251


title: CBell_B5000


title: CBell_B5173


title: CBell_B6677


title: CBell_B5873


title: clsy1234, rep2

city: Strasbourg

first: Todd

middle: L

last: Blevins

address: 12 Rue du Général-Zimmer

country: France

institute: CNRS

description:
clsy1234_02
Small RNA-SeqGel-free

data_processing:
cutadapt -a AACTGTAGGCACCATCAAT -m 15 (v1.18) (Martin, 2011)
ShortStack --mismatches 1 -mmap f (v3.8.5) (Axtell, 2013)
JSON_findPerfectMatches_and_TerminalMisMatches_v3 (Zhou et al., 2018) (with bamtools v2.5.1)
makeTagDirectory -format sam -mis 1 -keepAll (HOMER v4.10) (Heinz et al., 2010)
splitTagDirectoryByLength.dev2.pl (Zhou et al., 2018)
annotatePeaks.pl -noadj -fpkm (HOMER v4,10) (Heinz et al., 2010)
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file including RPKM values for each Sample on each smallRNA cluster

organism: Arabidopsis thaliana

source_name: flowers

extract_protocol:
Total RNA from flower tissue was extracted with TRIzol reagent, treated with DNaseI, and then purified again via phenol-chloroform extraction and ethanol precipitation.
Fasteris NGS services (ngs@fasteris.com) of Genesupport SA constructed the small RNA-seq libraries using QIAseq-miRNA low input reagents. In brief, low molecular weight RNA was enriched using size-selective beads, 3’ and 5’-adapters were successively ligated to the single-stranded RNA inserts, and cDNA synthesis was performed using reverse transcriptase. Each library was PCR amplified with adapters including sample-specific barcodes and a unique molecular identifier (UMI) region that can be used downstream for the bioinformatic elimination of PCR amplification bias. This service at Fasteris is known as the "Small RNA-Seq gel free protocol".

value: flowers

value: clsy1-7 clsy2-1 clsy3-1 clsy4-1


title: CBell_B4925


title: CBell_B7369


title: clsy1234, rep1

description:
clsy1234_01
Small RNA-SeqGel-free


title: CBell_B5144


title: Plasmid rep 2 [plasmid_3]

city: Stanford

first: Paul

last: Khavari

address: 269 Campus Drive, CCSR, Room 2150

department: Dermatology

institute: Stanford University

library_source: genomic

data_processing:
library strategy: Massively parallel reporter assay (MPRA)
Read 1 was unzipped and trimmed to the first 20bp containing the barcode using fastx_trimmer (fastx_trimmer -f 1 -l 20 -Q33)
Reverse complement of barcode was taken (fastx_reverse_complement -Q33)
UMI was extracted from index 2 (umi_tools extract --bc-pattern=NNNNNNNNNNNN)
Reads were aligned to the barcode library using bowtie2 (bowtie2 -p 8 -k 1 --norc -x)
Sam file was converted to a bam file (samtools view -S -b)
Bam file was sorted and indexed (samtools sort, samtools index)
Reads were deduplicated (umi_tools dedup -I --out-sam --no-sort-output)
File was converted to a tsv  (awk '$1 !~ /^@/ {print $1"\t"$3}')
Counts per barcode were tabulated (umi_tools count_tab)
Genome_build: NA
Supplementary_files_format_and_content: Tab-delimited files with barcode counts for each oligo in each condition

molecule: genomic DNA

organism: synthetic construct

source_name: plasmid

extract_protocol:
Reactions containing 50ng plasmid DNA were amplified with a forward primer containing a sample index and UMI (GGW610-505) and DR539 for 3 cycles, then treated with Exonuclease I and concentrated using MN Nucleospin Gel and PCR Cleanup kit. Product was then amplified for until a linear rise was seen with indexed primer GGW133-701 and GGW612 then gel purified.
Total RNA and DNA representing roughly 12 million cells were isolated using Qiagen’s AllPrep DNA/RNA Mini Kit. mRNA was then isolated from the total RNA using Dynabeads mRNA DIRECT purification kit (Thermo Fisher)
Reactions containing 500ng mRNA and 100nM of a gene-specific primer containing a sample index and UMI (GGW610-501 – GGW610-508, Table S5) were reverse transcribed using Superscript IV (Thermo Fisher), along with a no reverse transcriptase control. Reactions were incubated with 1ul thermolabile exonuclease I (NEB) for 10 min at 37C, followed by heat inactivation for 5min at 85C. The cDNA was cleaned with Ampure XP beads (Beckman Coulter) at a ratio of 1:1.1 sample to beads and eluted in the initial volume. The cDNA was amplified in 50ul reactions containing 5ul cDNA, LK612 at 80nM, one of LK134-701-LK134-712 at 80nM (Table S5), SYBR green (Thermo Fisher), and PrimeStar Max DNA Polymerase (Takara Bio). The reactions were amplified until they were just beginning to rise, then they were pooled and concentrated. The libraries were then gel purified and quantified using the KAPA library quantification kit (Roche). The 42 samples were put into 3 pools which were sequenced using an Illumina NextSeq Sequencer.

tag: molecule subtype

value: Plasmid DNA


title: Plasmid rep 1 [plasmid_2]


title: Mut10_D1_CYC-AAAA, rep2

description:
Mut10_02
Small RNA-SeqGel-free

value: NRPD1-3xFLAG (Mut10_CYC-AAAA) nrpd1-3


title: CM, GFP-, replicate 1, RNAseq

description:
RNAseq_Cont-1_CM_GFP-
Tg(myl7:GAL4db-TCFΔC-2A-mCherry);Tg(UAS:EGFP);Tg(myl7:NLS-mCherry)

value: Heart

value: mCherry- EGFP+ cells (β-cat OFF CMs)


title: Mut10_D1_CYC-AAAA, rep1

description:
Mut10_01
Small RNA-SeqGel-free


title: Mut9_D1_AAA-YPMF, rep1

description:
Mut9_01
Small RNA-SeqGel-free

value: NRPD1-3xFLAG (Mut9_AAA-YPMF) nrpd1-3


title: WT_D1_CYC-YPMF, rep1

description:
WT_01
Small RNA-SeqGel-free

value: NRPD1-3xFLAG (WT_CYC-YPMF) nrpd1-3


title: CBell_B6401


title: WT_D1_CYC-YPMF, rep2

description:
WT_02
Small RNA-SeqGel-free


title: Col-0, rep2

description:
Col-0_02
Small RNA-SeqGel-free


title: nrpd1-3, rep1

description:
nrpd1-3_01
Small RNA-SeqGel-free


title: Mut9_D1_AAA-YPMF, rep2

description:
Mut9_02
Small RNA-SeqGel-free


title: HD2

city: Munich

first: Maryam

last: Kazerani

address: Feodor-Lynen-Strasse 25

country: Germany

institute: LMU Gene Center

data_processing:
Sequencing reads were aligned to release101 of Ensembl GRCh38 prior to counting reads per gene with Star (version 2.7.6a) using default parameters
Values for expression (in transcripts per million, TPM) were calculated with RSEM (1.3.3) using default parameters.
Assembly: GRCh38

source_name: bone marrow drived CD3+ T cells

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit (cat no. KIT0204) according to the manufacturer instructions, but eluted in 11  μl prewarmed H2O (37◦C)
protocol Smarter ultra low input-v4 (Clontech 634888) and Microplex-v2 (Diagenode C05010012) - 10ng input RNA

treatment_protocol: Human bone marrow mononuclear cells were thawed and stained for CD3 marker. Then, 5000 CD3+ cells  were FACS sorted in 100 μl of Extraction Buffer from PicoPure RNA Isolation Kit (cat no. KIT0204).

value: bone marrow drived CD3+ T cells

value: CD3+ T cells

tag: disease state

value: healthy donor

tag: disease state_abbreviation

value: HD


title: HD1

tag: tissue


title: T5_RL

value: relapse

value: RL


title: T7_RL


title: Col-0, rep1

description:
Col-0_01
Small RNA-SeqGel-free


title: T6_RL


title: T4_RL


title: T2_RL


title: T1_RL


title: T7_ID

value: initial diagnosis

value: ID


title: T3_RL


title: T6_ID


title: T3_ID


title: T2_ID


title: T4_ID


title: T1_ID


title: T6_RL

data_processing:
The PEPATAC pipeline (version 0.10.3) was applied for primary analysis and quality controls with default settings.
In brief, after adapter trimming by Skewer, reads were pre-aligned with bowtie212 to human_chrM2x mitochondrial genome to remove mitochondrial reads and subsequently mapped to the hg38 human genome.
Assembly: GRCh38
Supplementary files format and content: bigWig files were generated from Homer tag directories using makeBigWig.pl

extract_protocol:
ATAC-seq was done as previously described (Buenrostro et al., 2013). Briefly, 50000 FACS sorted CD3+ T cells were washed in 1xPBS, re-suspended in 50 ul of lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40,) and spun at 500g for 10 min at 4 °C to collect nuclei. Nuclei were subsequently re-suspended in 50 µl Transposase reaction containing 25µL 2x tagmentation buffer, 22.5 µl water, 2.5 µl Tn5 Transposase (Illumina Nextera DNA Library Preparation Kit, cat. FC-121-1030). Reactions were incubated for 30 min at 37° C in a thermomixer shaking at 300 rpm and DNA purified using Qiagen PCR clean-up MinElute kit (Qiagen).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as described (Buenrostro et al., 2013). After 4 cycles libraries were then monitored with qPCR: 5 µl PCR sample in a 15 µl reaction with the same primers. qPCR output was monitored for the ΔRN; 0.25 ΔRN cycle number was used to estimate the number of additional cycles of the PCR reaction needed for the remaining PCR samples. Amplified libraries were purified with the Qiagen PCR clean-up MinElute kit (Qiagen) and size selected for fragments less than 600 bp using the Agencourt AMPure XP beads (Beckman Coulter). Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis.


title: T6_ID


title: T3_RL


title: T5_ID


title: T2_RL


title: T4_ID


title: T5_ID


title: T4_RL


title: T2_ID


title: SW948 2D rep 2 (sample_54)

data_processing:
Library strategy: CRISPR KO
The UMI was extracted using umi_tools extract (umi_tools extract --bc-pattern=NNNNNNNNN)
The read was trimmed down to the guide barcode (f 22 -l 41 -Q33)
Reads were aligned to the barcode library using bowtie2 (bowtie2 -p 8 -k 1 --norc -x)
Sam file was converted to a bam file (samtools view -S -b)
Bam file was sorted and indexed (samtools sort, samtools index)
Reads were deduplicated (umi_tools dedup -I --out-sam --no-sort-output)
File was converted to a tsv  (awk '$1 !~ /^@/ {print $1"\t"$3}')
Counts per barcode were tabulated (umi_tools count_tab)
Genome_build: NA
Supplementary_files_format_and_content: Tab delimited files for each cell type showing counts for tumorigenesis and cell culture screens

growth_protocol: Cells were cultured with DMEM with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Cells were cultured for a further 3 weeks, then harvested.

extract_protocol:
DNA was extracted using the DNEasy blood and tissue kit.
DNA was amplified using PrimeSTAR Max DNA polymerase (Takara Bio) in 14 reactions of 500ng gDNA each, with primers GGW130 (which contains a 9 base pair UMI) and GGW209 (Supp. table 5) with an annealing temperature of 56C for 10 cycles. Reactions were purified and concentrated using DNA Clean and Concentrator-100 (Zymo Research). Ampure XP beads were used at a ratio of 1:1.1. Then libraries were amplified again, using different indices of GGW132 and GGW133 (Supp. table 5). The qPCR reaction was stopped when libraries reached the end of the exponential phase, then concentrated using NucleoSpin Gel and PCR clean up kit (Macherey-Nagel) and gel purified.


title: T5_RL


title: SW948 2D rep 1 (sample_53)


title: SW948 Day 0 rep 2 (sample_52)

growth_protocol: Cells were cultured with DMEM with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin, then harvested after selection.


title: SW948 tumor rep 9 (sample_49)

growth_protocol: Cells were cultured with DMEM with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Nod scid gamma mice were injected with 3 million cells mixed 1:1 with Matrigel in each flank. Tumors were allowed to grow until most were 2cm in diameter (around 4 weeks). Tumors were harvested and stored at -80°C.

extract_protocol:
Thawed tumors were separated into 2-4 pieces, added to tubes containing lysing matrix A (MP Biomedicals) with 1ml buffer ALT from the DNEasy blood and tissue kit (Qiagen) then homogenized at 6m/s for 40sec. Tubes were then spun down in a 4C centrifuge for 5min at 14,000g. 1ml from each tumor was treated with proteinase K overnight at 56C, then 20ul of RNase A was added for 2min at room temperature. DNA was extracted using the DNEasy blood and tissue kit.
DNA was amplified using PrimeSTAR Max DNA polymerase (Takara Bio) in 14 reactions of 500ng gDNA each, with primers GGW130 (which contains a 9 base pair UMI) and GGW209 (Supp. table 5) with an annealing temperature of 56C for 10 cycles. Reactions were purified and concentrated using DNA Clean and Concentrator-100 (Zymo Research). Ampure XP beads were used at a ratio of 1:1.1. Then libraries were amplified again, using different indices of GGW132 and GGW133 (Supp. table 5). The qPCR reaction was stopped when libraries reached the end of the exponential phase, then concentrated using NucleoSpin Gel and PCR clean up kit (Macherey-Nagel) and gel purified.


title: SW948 Day 0 rep 1 (sample_51)


title: SW948 tumor rep 8 (sample_48)


title: SW948 tumor rep 7 (sample_47)


title: SW948 tumor rep 6 (sample_46)


title: SW948 tumor rep 4 (sample_44)


title: SW948 tumor rep 2 (sample_42)


title: HCT116 Day 0 rep 2 (sample_32)

growth_protocol: Cells were cultured with McCoy's 5A with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin, then harvested after selection.


title: HCT116 2D rep 2 (sample_34)

growth_protocol: Cells were cultured with McCoy's 5A with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Cells were cultured for a further 3 weeks, then harvested.


title: SW948 tumor rep 5 (sample_45)


title: SW948 tumor rep 3 (sample_43)


title: HCT116 2D rep 1 (sample_33)


title: HCT116 Day 0 rep 1 (sample_31)


title: HCT116 tumor rep 9 (sample_29)

growth_protocol: Cells were cultured with McCoy's 5A with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Nod scid gamma mice were injected with 3 million cells mixed 1:1 with Matrigel in each flank. Tumors were allowed to grow until most were 2cm in diameter (around 4 weeks). Tumors were harvested and stored at -80°C.


title: HCT116 tumor rep 10 (sample_30)


title: T3_ID


title: HCT116 tumor rep 8 (sample_28)


title: HCT116 tumor rep 7 (sample_27)


title: HCT116 tumor rep 6 (sample_26)


title: HCT116 tumor rep 5 (sample_25)


title: SW948 tumor rep 10 (sample_50)


title: HCT116 tumor rep 3 (sample_23)


title: HCT116 tumor rep 2 (sample_22)


title: HCT116 tumor rep 1 (sample_21)

growth_protocol: Cells were cultured with McCoy's 5A with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Nod scid gamma mice were injected with 3 million cells mixed 1:1 with Matrigel in each flank. Tumors were allowed to grow until most were 2cm in diameter (around 4 weeks). Tumors were harvested and stored at -80C. Thawed tumors were separated into 2-4 pieces, added to tubes containing lysing matrix A (MP Biomedicals) with 1ml buffer ALT from the DNEasy blood and tissue kit (Qiagen) then homogenized at 6m/s for 40sec. Tubes were then spun down in a 4C centrifuge for 5min at 14,000g. 1ml from each tumor was treated with proteinase K overnight at 56C, then 20ul of RNase A was added for 2min at room temperature. DNA was extracted using the DNEasy blood and tissue kit.


title: DLD1 2D rep 1 (sample_13)

growth_protocol: Cells were cultured with RPMI 1640 with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Cells were cultured for a further 3 weeks, then harvested.


title: HCT116 tumor rep 4 (sample_24)


title: DLD1 2D rep 2 (sample_14)


title: SW948 tumor rep 1 (sample_41)

growth_protocol: Cells were cultured with DMEM with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Nod scid gamma mice were injected with 3 million cells mixed 1:1 with Matrigel in each flank. Tumors were allowed to grow until most were 2cm in diameter (around 4 weeks). Tumors were harvested and stored at -80C. Thawed tumors were separated into 2-4 pieces, added to tubes containing lysing matrix A (MP Biomedicals) with 1ml buffer ALT from the DNEasy blood and tissue kit (Qiagen) then homogenized at 6m/s for 40sec. Tubes were then spun down in a 4C centrifuge for 5min at 14,000g. 1ml from each tumor was treated with proteinase K overnight at 56C, then 20ul of RNase A was added for 2min at room temperature. DNA was extracted using the DNEasy blood and tissue kit.


title: DLD1 Day 0 (sample_11)

growth_protocol: Cells were cultured with RPMI 1640 with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin, then harvested after selection.


title: DLD1 tumor rep 9 (sample_9)

growth_protocol: Cells were cultured with RPMI 1640 with 10% FBS and 1% Pen/Strep. Cells were infected with Cas9 and selected with 8ug/ml blasticidin. Cells were then infected with the guide library and selected with 1% puromycin. Nod scid gamma mice were injected with 3 million cells mixed 1:1 with Matrigel in each flank. Tumors were allowed to grow until most were 2cm in diameter (around 4 weeks). Tumors were harvested and stored at -80°C.


title: DLD1 tumor rep 10 (sample_10)


title: DLD1 Day 0 (sample_12)


title: nrpd1-3, rep2

description:
nrpd1-3_02
Small RNA-SeqGel-free


title: DLD1 tumor rep 8 (sample_8)


title: DLD1 tumor rep 6 (sample_6)


title: DLD1 tumor rep 2 (sample_2)


title: DLD1 tumor rep 1 (sample_1)


title: DLD1 tumor rep 4 (sample_4)


title: DLD1 tumor rep 7 (sample_7)


title: DLD1 tumor rep 3 (sample_3)


title: DLD1 tumor rep 5 (sample_5)


title: High Fat Diet vs High Fat Diet plus pirfenidone

type: RNA

city: Guadalajara

first: Ana

middle: Soledad

last: Sandoval-Rodriguez

state: Jalisco

address: Sierra Mojada 950

department: Molecular Biology and Genomics

country: Mexico

institute: University of Guadalajara

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in humid hybridization chambers. After hybridization, slides were washed sequential and centrifuged to dry.

scan_protocol: Scanned on a ScanArray 4000 Packard BioChips.

data_processing: Images were quantified using Array-Pro Analyzer Software (version 6.3).

source_name: Liver, mice

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM PolyT deoxioligonucleotide DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP and 25 µM Alexa-555-label or Alexa-647-label

growth_protocol: Male C57BL/6J mice were fed with normo-diet, or high fat/carbohydrate diet (HF) for 16 weeks.  A HF-subgroup was treated with PFD 300 mg/kg/d from week 8th to the end of protocol. Insulin tolerance test and liver and fat histological and biochemical analyses were carried out. Hepatic transcriptome was examined.  Liver proteins were studied by western blot (WB) and Chromatin immunoprecipitation. In vitro, lipotoxicity was induced in HepG2 cells and proteins were evaluated using WB. Molecular docking was used to explore binding of PFD to JMJD2B.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: 60% fat in diet +high-carbohydrate beverage, treated with aprx 300 mg/kg/day pirfenidone for 8 weeks

tag: mouse strain

value: 22 weeks at sacrifice

value: Liver


title: High Fat Diet vs Control Diet (Normodiet)

tag: strain


title: Astrocytes, siAPOE NTC, day 2

city: Ann Arbor

first: Vivian

last: Cheung

state: MI

address: 210 Washtenaw Ave.

institute: University of Michigan

data_processing:
Sequencing reads were aligned to the GRCh38 (hg38) human reference sequence using GSNAP (v. 2021-12-17) (Wu and Nacu, 2010) with one mismatch allowed, and soft-clipping on.
Expression was quantified using Cufflinks v.2.2.1 (Trapnell et al 2012).
Assembly: hg38
Supplementary files format and content: bigWig (stranded)

source_name: astrocytes

growth_protocol: Primary human astrocytes (ScienCell) were seeded on poly-L-lysine-coated (2ug/cm2) T-75 culture flasks with complete astrocyte medium (Sciencell).  The medium was changed every three days, until cells were approximately 70% confluent and then changed daily until the cell confluence reached 90% confluence.  Astrocytes were passaged when cells reach 90-95% confluency.

extract_protocol:
From astrocytes treated with siRNA against AANCR, APOE or non-target siRNA, sequencing libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit (Illumina).
From astrocytes treated with siRNA against AANCR, APOE or non-target siRNA, sequencing libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit (Illumina).

treatment_protocol:
Cells were seeded in 6-well plates or T-25 flasks until they reached 50-60% confluence and were transfected with siRNA using Lipofectamine RNAiMax to a final concentration of 5 nM for astrocytes.  24 to 48 hours post-transfection cells were washed in PBS and collected by cell scraping for downstream gene expression analysis or for protein analysis. The siRNA targeting AANCR and APOE are listed in the Resource table.
Cells were grown to a confluence of 50% in T-25 flasks or 6-well plates. The AANCR GapmeR (Qiagen GeneGlobe ID:LG00801555-EDA ) was transfected at 10 nM using Lipofectamine 3000 in astrocytes.  Four days post-transfection cells were washed in PBS and collected by cell scraping harvested for downstream analysis.

value: astrocytes


title: Astrocytes, siAPOE pool, day 2


title: Astrocytes, siAPOE 4, day 2


title: Astrocytes, siAPOE 2, day 2


title: Astrocytes, siAANCR NTC, day 2


title: Astrocytes, siAPOE 3, day 2


title: Astrocytes, siAANCR pool, day 2


title: Astrocytes, siAANCR 3, day 2


title: Astrocytes, siAANCR+siAP1, day 2


title: Astrocytes, siAANCR 2, day 2


title: Control Diet (Normodiet) vs High Fat Diet plus pirfenidone


title: Astrocytes, AANCR-ASO, day 4


title: IMR32_Rep2

city: Badalona

first: David

last: Corujo

address: Ctra de Can Ruti, Camí de les Escoles

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Sequencing data was analyzed using MaGeCK software (PMID: 25476604)  and by UMI lineage dropout analysis (PMID:28993443)
A list of mitochondrial and ribosomal genes (n=638) was obtained using the R package biomaRt (MT, rRNA, rRNA_pseudogene, and ribozyme biotypes) and excluded to reduce total gene search space
For each comparison, gene essentiality scores were determined for individual gRNA using MAGeCK
Depleted genes were selected based on the distribution of essentiality scores using a predefined cut-off, i.e. mean-2 standard deviation (SD) for donor 1 (-0.22) and donor 2 (-0.24), respectively
Assembly: N/A
Supplementary files format and content: .csv, gRNA counts

source_name: Brain

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 using IMDM (Thermo Scientific) supplemented with 10% heat-inactivated FBS and 1% Penicillin-Streptomycin (Thermo Scientific).

extract_protocol:
Genomic DNA isolation was performed using QIAmp DNA Blood Maxi kit (Qiagen).
Guide cassettes were amplified by PCR using modified primers as described in Schmierer et al., 2017 (PMID:28993443)
CRISPR screen

treatment_protocol: Library-transduced Cas9+ IMR32 cells were cultured overnight in T175 flasks with IMDM complete media prior to setting up of co-culture systems. The following day, CD14-depleted fresh human lymphocytes were added to library-transduced Cas9+ IMR32 cells, with or without nivolumab at 10 µg/ml. HLA typing was not possible in order to maintain the anonymity of the blood donors. Cas9-expressing IMR-32 cells cultured alone were used as controls. On day 5, floating cells were gently washed off and adherent cancer cells were harvested.

value: Brain

value: Neuroblastoma

tag: genotype

value: control


title: IMR32_lymphocytes_Rep2

value: lymphocyte co-culture


title: IMR32_lymphocytes_Rep1


title: IMR32_lymphocytes_nivo_Rep1

value: lymphocyte co-culture, nivolumab


title: Astrocytes, siAPOE 5, day 2


title: IMR32_Rep1


title: RKO-dox-Cas9, sgAAVS1, nucleus, CHX treated, biol rep 2

city: Vienna

first: Gijs

middle: A.

last: Versteeg

address: Dr. -Bohrgasse 9

department: Department of Microbiology

country: Austria

institute: Max Perutz Labs, University of Vienna

data_processing:
RNA-seq analysis was performed using the nf-core/rnaseq pipeline (v3.13.2)
The following relevant parameters were used (.json format): {     "trimmer": "fastp",     "min_trimmed_reads": 2000,     "remove_ribo_rna": true,     "pseudo_aligner": "salmon", }
The following software versions were used (.yml format): BEDTOOLS_GENOMECOV:   bedtools: 2.30.0 CUSTOM_DUMPSOFTWAREVERSIONS:   python: 3.12.0   yaml: 6.0.1 CUSTOM_GETCHROMSIZES:   getchromsizes: 1.16.1 DESEQ2_QC_PSEUDO:   bioconductor-deseq2: 1.28.0   r-base: 4.0.3 DESEQ2_QC_STAR_SALMON:   bioconductor-deseq2: 1.28.0   r-base: 4.0.3 DUPRADAR:   bioconductor-dupradar: 1.28.0   r-base: 4.2.1 FASTP:   fastp: 0.23.4 FASTQC_RAW:   fastqc: 0.12.1 FASTQC_TRIM:   fastqc: 0.12.1 FQ_SUBSAMPLE:   fq: 0.9.1 (2022-02-22) GTF2BED:   perl: 5.26.2 GTF_FILTER:   python: 3.9.5 GUNZIP_FASTA:   gunzip: '1.10' GUNZIP_GTF:   gunzip: '1.10' MAKE_TRANSCRIPTS_FASTA:   rsem: 1.3.1   star: 2.7.10a MULTIQC_CUSTOM_BIOTYPE:   python: 3.9.5 PICARD_MARKDUPLICATES:   picard: 3.0.0 QUALIMAP_RNASEQ:   qualimap: 2.2.2-dev RSEQC_BAMSTAT:   rseqc: 3.0.1 RSEQC_INFEREXPERIMENT:   rseqc: 3.0.1 RSEQC_INNERDISTANCE:   rseqc: 3.0.1 RSEQC_JUNCTIONANNOTATION:   rseqc: 3.0.1 RSEQC_JUNCTIONSATURATION:   rseqc: 3.0.1 RSEQC_READDISTRIBUTION:   rseqc: 3.0.1 RSEQC_READDUPLICATION:   rseqc: 3.0.1 SALMON_INDEX:   salmon: 1.10.1 SALMON_QUANT:   salmon: 1.10.1 SAMTOOLS_FLAGSTAT:   samtools: '1.17' SAMTOOLS_IDXSTATS:   samtools: '1.17' SAMTOOLS_INDEX:   samtools: '1.17' SAMTOOLS_SORT:   samtools: '1.17' SAMTOOLS_STATS:   samtools: '1.17' SE_GENE:   bioconductor-summarizedexperiment: 1.24.0   r-base: 4.1.1 SORTMERNA:   sortmerna: 4.3.4 STAR_ALIGN:   gawk: 5.1.0   samtools: 1.16.1   star: 2.7.9a STAR_GENOMEGENERATE:   gawk: 5.1.0   samtools: 1.16.1   star: 2.7.9a STRINGTIE_STRINGTIE:   stringtie: 2.2.1 SUBREAD_FEATURECOUNTS:   subread: 2.0.1 TX2GENE:   python: 3.9.5 TXIMPORT:   bioconductor-tximeta: 1.12.0   r-base: 4.1.1 UCSC_BEDCLIP:   ucsc: '377' UCSC_BEDGRAPHTOBIGWIG:   ucsc: '445' Workflow:   Nextflow: 23.04.2   nf-core/rnaseq: 3.13.2
Generation of "forward.bigWig" files were done from the ".markdup.sorted.bam" files (rnaseq NF-core pipeline) by using deeptools (version 3.5.4-foss-2022a) "bamCoverage" command with the following options: -of bigwig --filterRNAstrand forward --normalizeUsing CPM -bs 1 -p max
Generation of "reverse.bigWig" files were done from the ".markdup.sorted.bam" files (rnaseq NF-core pipeline) by using deeptools (version 3.5.4-foss-2022a) "bamCoverage" command with the following options: -of bigwig --filterRNAstrand reverse --normalizeUsing CPM -bs 1 -p max
Intron retention was analyzed with IRFinder (v. 2.0.0), and reference genome was made based on NF-core pipeline output using the following software versions: perl (5.36.0-gcccore-10.2.0), star (2.7.9a-gcc-10.2.0), samtools (1.14-gcc-10.2.0), bedtools (2.30.0-gcc-10.2.0), and minimap2 (2.18-gcccore-10.2.0)
Assembly: GRCh38 v110 (hg38)
Supplementary files format and content: tab-delimited .tsv file includes transcript count values for each sample
Supplementary files format and content: tab-delimited .tsv file includes transcript tpm values for each sample
Supplementary files format and content: tab-delimited .tsv file includes transcript length values for each sample
Supplementary files format and content: bigWig files with CPM normalized reads information for "+" strand genome track
Supplementary files format and content: bigWig files with CPM normalized reads information for "-" strand genome track
Supplementary files format and content: tab-delimited .txt files for IRFinder output information including intron IRratio values

molecule: nuclear RNA

source_name: Colon carcinoma

growth_protocol: RKO cells were maintained in RPMI 1640 (Thermo Fisher Scientific, 21875) supplemented with  10% FBS (Sigma-Aldrich, F7524),L-glutamine (4 mM, Sigma-Aldrich, G7513), sodium pyruvate (1 mM, Sigma-Aldrich, S8636),  and 1% penicillin/streptomycin (Sigma-Aldrich, P4333) in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
For subcellular fractionation, ~2x10^6 cells were gently lysed in REAP buffer (0.1% NP-40 in 1x PBS) at 4°C. Nuclei and cytoplasmic fractions were separated through centrifugation at 3k g for 60 sec at 4°C twice. RNA isolation was done with High Performance RNA Isolation kit (Vienna, VBC Molecular Tools Shop, RNAisomag) and a KingFisher Flex robot (Thermo Fisher Scientific).
Poly-A enriched RNA-seq libraries using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) were generated according to manufacturer's recommendations.

treatment_protocol:
Cas9 induced knockouts were generated by 5 days of doxycycline (Sigma-Aldrich,D9891) treatment (100 ng/mL).
Inhibition of translationally coupled processes was done by treating the cells with cycloheximide (Sigma-Aldrich, C1988) at 25 μg/mL or DMSO (negative control) for 4 hours.

value: Colon carcinoma

value: RKO

value: CHX

tag: time

value: 5 days dox


title: RKO-dox-Cas9, sgERH, nucleus, CHX treated, biol rep 2

value: sgERH

tag: treatment


title: RKO-dox-Cas9, sgERH, nucleus, CHX treated, biol rep 1


title: RKO-dox-Cas9, sgAAVS1, nucleus, CHX treated, biol rep 3


title: RKO-dox-Cas9, sgAAVS1, nucleus, CHX treated, biol rep 1


title: RKO-dox-Cas9, sgERH, nucleus, DMSO treated, biol rep 3

value: DMSO


title: RKO-dox-Cas9, sgERH, nucleus, DMSO treated, biol rep 1


title: RKO-dox-Cas9, sgAAVS1, nucleus, DMSO treated, biol rep 3


title: RKO-dox-Cas9, sgAAVS1, nucleus, DMSO treated, biol rep 2


title: RKO-dox-Cas9, sgERH, cytoplasm, CHX treated, biol rep 3

molecule: cytoplasmic RNA


title: RKO-dox-Cas9, sgERH, cytoplasm, CHX treated, biol rep 2


title: RKO-dox-Cas9, sgERH, cytoplasm, CHX treated, biol rep 1


title: IMR32_lymphocytes_nivo_Rep2

tag: cell type


title: AG-CAR-Vδ1T

city: Suzhou

first: Licui

last: Jiang

state: None Selected

address: Dushuhu Campus, Soochow University, No. 199, Ren'ai Road/Street

institute: Soochow University

description: γδT

data_processing:
Quality control
scRNA-seq reads were aligned to the Homo_sapiens_ensembl_92 genome assembly using STAR version 2.7.5a
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Assembly: Homo_sapiens_ensembl_92
Supplementary files format and content: expression matrix file using RNA raw count,and all cells annotated and T cells individually extracted annotated RDS

source_name: PBMC

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

treatment_protocol: the specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times and minced into 1–2 mm pieces. The tissue pieces were digested in 2ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) at 37°C for 15min in a 15ml centrifuge tube with continuous agitation

value: PBMC

value: Human T cells


title: AQ-CAR-Vδ1T

description: γδT


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, CHX treated, biol rep 2

tag: cell line


title: RKO-dox-Cas9, sgERH, nucleus, CHX treated, biol rep 3


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, CHX treated, biol rep 3


title: RKO-dox-Cas9, sgERH, cytoplasm, DMSO treated, biol rep 3


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, CHX treated, biol rep 1


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, DMSO treated, biol rep 3


title: RKO-dox-Cas9, sgERH, nucleus, DMSO treated, biol rep 2


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, DMSO treated, biol rep 2


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, DMSO treated, biol rep 1


title: RKO-dox-Cas9, sgERH, cytoplasm, DMSO treated, biol rep 2


title: RKO-dox-Cas9, sgERH, cytoplasm, DMSO treated, biol rep 1


title: Mouse Kidney, Mdm2 Ex 5/6, AAV8-Control4, Rep 1

city: Glasgow

first: Thomas

last: Bird

address: Switchback Road, Bearsden

institute: Beatson Institute

data_processing:
Quality checks and trimming on the raw RNA-Seq data files were done using FastQC version 0.11.7, FastP [2] and FastQ Screen version 0.12.0. RNA-Seq paired-end reads were aligned to the GRCm38.92 version of the mouse genome and annotation using HiSat2 version 2.1.0. Expression levels were determined and statistically analysed by a combination of HTSeq version 0.9.1, the R environment version 3.4, utilizing packages from the Bioconductor data analysis suite [8] and differential gene expression analysis based on the negative binomial distribution using the DESeq2 package version 1.18.1
Assembly: GRCm38.92 version of the mouse genome and annotation
Supplementary files format and content: Count table normalized with version 1.18.1 of DESeq2

source_name: Kidney

extract_protocol:
Whole tissue RNA was extracted using the Qiagen RNeasy kit (Qiagen, 74104)
RNA was tested on an Agilent 2200 TapeStation (D1000 screentape) using RNA screentape and only samples with a RIN>7 were further processed for library preparation. 20ng/ml of RNA were used to prepare libraries using the TruSeq Stranded mRNA Kit. Agilent 2200 Tapestation was used to assess library quality and Qubit (Thermo Fisher Scientific) was used to check concentration. The libraries were then run on the Illumina NextSeq 500 using the High Output 75 cycles kit (paired end, 2x36 bp cycle, dual index (I5 and I7 Illumina)).
TruSeq Stranded mRNA Kit

value: Kidney


title: d28_WT2_Tcm

city: Epalinges

first: Ping-Chih

last: Ho

address: Ch. des Boveresses 155

institute: University of Lausanne

data_processing:
Smart-seq2 reads were trimmed and mapped with STAR to the mouse reference genome (mm10)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Spleen

extract_protocol:
RNA was extracted using the RNeasy® Mini Kit (Qiagen) following the instructions of the manufacturer
For the preparation of NGS libraries, we followed the Smart-seq2 protocol. The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina, San Diego, CA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

value: Spleen

value: T lymphocyte

value: central memory T cell (CD62l+ CD127+)

value: WT


title: RKO-dox-Cas9, sgPOLDIP3-1, cytoplasm, biol rep 3

description: RNA input for library preparation: 500 ng

data_processing:
For RNA-seq analysis, reads were pre-processed with fastp (v0.20.1) which was configured to extract 6nt UMIs and trim 4nt from the read 5’-ends along standard quality and adapter trimming settings. Quality controls was done with fastqc (v0.11.8). Reads were mapped to 3’-ends with the nf-core/slamseq pipeline v0.1. For the 3’-end annotations we used the previously published set from Muhar et al, 2018 but extended it with GENCODE annotations for missing genes. Read and UMI counts were collapsed per gene and counted with a custom Python script.
The following software versions were used for the NF-core pipeline: nf-core/slamseq v0.1 Nextflow v21.10.6 FastQC v0.11.9 TrimGalore v0.6.4_dev Slamdunk v0.4.3 R v3.5.1 DESeq2 v1.22.1 MultiQC v1.8
Assembly: hg38 (to download the 3'end genome build: "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE100708&format=file&file=GSE100708%5Fhg38%5Frefseq%5F062016%5Fensemblv84%5F3UTR%2Ebed%2Egz")
Supplementary files format and content: tab-delimited .tsv files including count and UMI values with Entrez gene ids
Supplementary files format and content: tab-delimited .tsv files including UMI statistics

extract_protocol:
For subcellular fractionation, ~2x10^6 cells were gently lysed in REAP buffer (0.1% NP-40 in 1x PBS) at 4°C. Nuclei and cytoplasmic fractions were separated through centrifugation at 3k g for 60 sec at 4°C twice. RNA isolation was done with High Performance RNA Isolation kit (Vienna, VBC Molecular Tools Shop, RNAisomag) and a KingFisher Flex robot (Thermo Fisher Scientific).
Generation of 3’ mRNA sequencing libraries was done according to manufacturer’s recommendations (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, UMI Second Strand Synthesis Module for QuantSeq FWD, and PCR Add-on Kit for Illumina, Lexogen).

treatment_protocol: Cas9 induced knockouts were generated by 5 days of doxycycline (Sigma-Aldrich,D9891) treatment (100 ng/mL).

value: non-treated


title: RKO-dox-Cas9, sgPOLDIP3-1, cytoplasm, biol rep 1


title: RKO-dox-Cas9, sgPOLDIP3-1, cytoplasm, biol rep 2


title: RKO-dox-Cas9, sgALYREF-1, nucleus, biol rep 3

value: sgALYREF


title: RKO-dox-Cas9, sgPOLDIP3-1, nucleus, biol rep 1


title: RKO-dox-Cas9, sgALYREF-1, nucleus, biol rep 2


title: RKO-dox-Cas9, sgMAGOH-1, nucleus, biol rep 1

description: RNA input for library preparation: 280 ng

value: sgMAGOH


title: RKO-dox-Cas9, sgMAGOH-1, nucleus, biol rep 2


title: RKO-dox-Cas9, sgPOLDIP3-1, nucleus, biol rep 2


title: RKO-dox-Cas9, sgMAGOH-1, cytoplasm, biol rep 3


title: RKO-dox-Cas9, sgALYREF-1, nucleus, biol rep 1


title: RKO-dox-Cas9, sgALYREF-1, cytoplasm, biol rep 1


title: RKO-dox-Cas9, sgALYREF-1, cytoplasm, biol rep 3


title: RKO-dox-Cas9, sgALYREF-1, cytoplasm, biol rep 2


title: RKO-dox-Cas9, sgSRSF1-1, nucleus, biol rep 3


title: RKO-dox-Cas9, sgSRSF1-1, cytoplasm, biol rep 3


title: RKO-dox-Cas9, sgSRSF1-1, nucleus, biol rep 1


title: RKO-dox-Cas9, sgSRSF1-1, cytoplasm, biol rep 2


title: RKO-dox-Cas9, sgPOLDIP3-1, nucleus, biol rep 3


title: RKO-dox-Cas9, sgMAGOH-1, nucleus, biol rep 3


title: RKO-dox-Cas9, sgMAGOH-1, cytoplasm, biol rep 2


title: RKO-dox-Cas9, sgERH, nucleus, biol rep 3


title: RKO-dox-Cas9, sgSRSF1-1, cytoplasm, biol rep 1


title: RKO-dox-Cas9, sgAAVS1, nucleus, DMSO treated, biol rep 1


title: RKO-dox-Cas9, sgERH, nucleus, biol rep 1


title: RKO-dox-Cas9, sgERH, cytoplasm, biol rep 3


title: RKO-dox-Cas9, sgSRSF1-1, nucleus, biol rep 2


title: RKO-dox-Cas9, sgMAGOH-1, cytoplasm, biol rep 1


title: RKO-dox-Cas9, sgERH, cytoplasm, biol rep 2


title: RKO-dox-Cas9, sgAAVS1, nucleus, biol rep 3


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, biol rep 2


title: RKO-dox-Cas9, sgAAVS1, nucleus, biol rep 2


title: RKO-dox-Cas9, sgERH, cytoplasm, biol rep 1


title: RKO-dox-Cas9, sgAAVS1, cytoplasm, biol rep 1


title: RKO-dox-Cas9, sgAAVS1, nucleus, biol rep 1