title: D3

city: Taiyuan

first: Ruhao

last: Zhou

email: zrhi1998@163.com, zhouruhao@sxmu.edu.cn

address: 382 Wuyi Road,

institute: Shanxi medical 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 normalizatlon were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Se1 Library Prep Kit following manufacturer's protocols.

value: cell line

value: osteosarcoma cells


title: Nebulized_FLAMOD_L1_6h_biol_rep1

status: Public on Mar 21 2025

type: SRA

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

country: France

institute: Institut Pasteur de Lille

description:
Library name: Library-362
RnaSeq Illumina NovaSeq (2x150)

library_source: transcriptomic

data_processing:
STAR-2.7.10a
Genome index was generated using the annotation file Macaca_fascicularis_6.0.110.gtf through STAR-2.7.10a (sjdbOverhang 149)
Sequence reads were mapped to generated genome using STAR-2.7.10a (-quantMode using bidirectional input (R1/R2))
_ReadsPerGene.out.tab file with four columns (gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA)  was generated by STAR for each sample
Assembly: Macaca_fascicularis_6.0.110
Supplementary files format and content: TAB files include read counts for each sample (only first two columns were used :Gene ID and read counts for unstranded RNA-seq)

molecule: polyA RNA

organism: Macaca fascicularis

source_name: Blood

growth_protocol: Experiments were conducted in female (n=11) cynomolgus macaques (Macaca Fascicularis, Vietnam), 3-3.5 kg, obtained from Bioprim® (Baziege, France).

extract_protocol:
Nasal, tracheal, bronchial, lung tissues and blood samples were collected for RNA extraction and sequencing. For Nasal, tracheal, bronchial and lung tissue RNA extraction, tissue was collected and preserved in NucleoProtect® RNA (Macherey-Nagel, Duren, Germany) at -80°C until ready for processing. Tissue was dried on paper towels and any visible cartilage was removed. The remaining tissue was added to 1 ml RA1 lysis buffer (Macherey-Nagel) supplemented with 2% TCEP (Sigma) and disintegrated with an UltraTurrax homogenizer (IKA-Werke, Staufen, Germany). For nasal, bronchial and tracheal samples, a pretreatment with proteinase K was performed to remove collagen. Briefly, 700 μl of undiluted lysate (nasal) or diluted lysate 1:1 (bronchial, tracheal) was added to 1190 μl water substituted with 20 μl proteinase K (20 mg/ml) and incubated at room temperature for 10 min, followed by a 10 min incubation at 55 °C and centrifugation at 10,000 rpm for 3 min. The supernatant was then mixed with equal parts volume of 100% ethanol and the mixture was loaded onto the NucleoSpin RNA Plus extraction kit columns, and RNA was extracted as per manufacturer’s instructions (Macherey-Nagel). Extracts were eluted in 20 μl (nasal) or 30 μl (bronchial, tracheal and lung) RNAse-free water. Blood samples (3 ml) were collected in TempusTM blood RNA tubes (Thermofisher Scientific) and stored at -20 °C. Tubes were thawed and the stabilized blood was diluted up to 12 ml with D-PBS (Gibco) and vortexed vigorously for 30 seconds followed by centrifugation at 4 °C, for 30 min at 3000 rcf. The pellet was dissolved in 1 ml RA1 buffer + 2% TCEP and 500 μl was loaded onto the NucleoSpin RNA Plus extraction kit columns and RNA was extracted as per manufacturer’s instructions (Macherey-Nagel). Extracts were eluted in 40 μl RNAse-free water. RNA quality was checked by spectrophotometry (Nanodrop), the molecular integrity was assessed with the TapeStation 4200 (Agilent Technologies), and the quantification was done using QuantiFluor RNA System (Promega).
RNA libraries for RNA-seq were prepared using QIAseq stranded mRNA library kit (Qiagen) as well as QIAseq FastSelect-Globin Kit for blood samples (Qiagen). 200 ng of total RNA.

treatment_protocol: For intravenous route (I.V.), macaques (n=3) were sedated (3 mg/kg ketamine, 125 µg/kg medetomidine), then anaesthetized with isoflurane 2%, intubated and maintained under mechanical ventilation as described for inhalation route. Then 100 µg of FLAMOD in 100 µL were rapidly injected in the saphenous vein. For the kinetic analyses, blood samples were collected at 0h, 1h15m, 3h, 6h and 24h. After a washout period, these same three macaques were nebulized with 1mg/ml of FLAMOD. One hour post-nebulization nasal, tracheal, bronchial and lung samples were collected. All samples were subjsected to RNA extraction and sequencing. For the high (n=3) and low dose  (n=5) FLAMOD nebulization experiments, macaques were administered xx mg/ml and xx mg/ml FLAMOD, respectively. For the kinetic analyses, blood samples were collected ay 0h, 1h15m or 1h30m, 3h, 6h and 24h post administration  and processed for RNA extraction and sequencing.

tag: tissue

value: Blood

tag: treatment

tag: batch


title: Nebulized_FLAMOD_L1_0h_biol_rep1

description:
Library name: Library-359
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L3_6h_biol_rep3

description:
Library name: Library-372
RnaSeq Illumina NovaSeq (2x150)


title: Br_4w_RNA_XistBxC_-+_XX_1

city: Munich

first: Sarah

last: Hoelzl

state: Bavaria

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: Technical University of Munich

data_processing:
Paired-end RNA-seq data were aligned using STAR. Reads characterized by intron sizes exceeding 100000, multimappers, and alignments containing non-canonical junctions were removed prior to subsequent analysis. Uniquely aligned reads were quantified using htseq-count and the –stranded reverse flag.
Allelic ratios were calculated using the Allelome.PRO pipeline
Assembly: mm10
Supplementary files format and content: Text file including the raw read counts for each sample

organism: Mus musculus

source_name: Brain

growth_protocol: BL6 Xist -/+ females were purchased from Riken BRC Japan (RBRC02655: B6;129-Xist<tm5Sado>) and crossed with wild-type CAST males (JAX: Strain #000928) to obtain experimental F1 hybrids. At the according age, organs were harvested, flash-frozen in liquid nitrogen and stored at -80 °C for further use.

extract_protocol:
Frozen organs of 4w-, 9w-, 1.5y-week old mice were homogenized in appropriate amounts of TRIzol reagent (1 ml TRIzol reagent per 50-100 mg tissue) using the GentleMACSTM Dissociator RNA_02_01 program. 1 ml of homogenized organs was used for RNA isolation. Frozen organs of E14.5 embryos were thawed in 500 µl TRIzol reagent. Embryonic organs were homogenized using a pellet pestle. Another 500 µl TRIzol reagent was added, and RNA isolation was performed for all time points according to manufacturer’s instructions (Invitrogen, TRIzol Reagent, Cat. #15596018). RNA concentration was measured by the NanoDrop Microvolume Spectrophotometer.
100 ng of RNA were used to generate poly-A captured RNA-seq libraries using lllumina’s Stranded mRNA Prep, Ligation kit according to manufacturer’s instructions. An eighth of reaction volume per sample was pipetted by the MANTIS liquid handler. Concentration and fragment distribution of completed RNA-seq libraries was measured on Agilent’s TapeStation System.

value: Brain

tag: breed (mother_x_father)

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ

tag: genotype

tag: Sex

value: female

tag: age


title: D2

country: China

molecule: total RNA

tag: cell line

tag: cell type


title: Nebulized_FLAMOD_H1_24h_biol_rep3

description:
Library name: Library-260
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H1_6h_biol_rep3

description:
Library name: Library-259
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H1_3h_biol_rep3

description:
Library name: Library-258
RnaSeq Illumina NovaSeq (2x150)


title: C3


title: C2


title: Nebulized_FLAMOD_H1_1h15_biol_rep3

description:
Library name: Library-257
RnaSeq Illumina NovaSeq (2x150)


title: C1


title: Nebulized_FLAMOD_H1_0h_biol_rep3

description:
Library name: Library-244
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H3_24h_biol_rep2

description:
Library name: Library-256
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H3_3h_biol_rep2

description:
Library name: Library-254
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_L1_3h_biol_rep1

description:
Library name: Library-361
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H3_1h15_biol_rep2

description:
Library name: Library-253
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H3_6h_biol_rep2

description:
Library name: Library-255
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H2_24h_biol_rep1

description:
Library name: Library-251
RnaSeq Illumina NovaSeq (2x150)


title: Microglia, sham

city: St. Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

country: USA

institute: Washington University in St. Louis

description: RNA was harvested from mice with a sham operation

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline 6.0.0. The output from the cellranger count pipeline has been uploaded as a folder containing count, barcode, and gene matrices.
See methods for more details
Assembly: mm10
Supplementary files format and content: Compressed folders containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Cortices

extract_protocol:
10X Genomics Chromium Single Cell preparation
NGS Illumina NextSeq (3' RNA-seq)

value: Cortices

value: Microglia

tag: strain

value: sham


title: SelpKO HSCs, PSGL-1 treated, rep3

city: New York

first: Daozheng

last: Yang

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
Initial quality control was performed with MultiQC (v1.10). Alignments were performed using STAR (2.7.5c) after indexing the reference genome. The genome sequence (mm10) and corresponding gene annotation file (refGene) used were downloaded from UCSC. Following the STAR alignment stage, raw read counts were generated by using FeatureCount, with the pair-read mode, counting exon regions and aggregated by gene ids. We took the reads count to call differentially expressed genes by using a R package DESeq2.
Assembly: mm10
Supplementary files format and content: table-delimited text file includes raw reads for each sample

source_name: bone marrow

growth_protocol: HSCs were maintained in StemSpan supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin, 10% FCS, 300 ng/mL SCF, 20 ng/mL IL-11 and 1 ng/mL Flt-3 ligand.

extract_protocol:
Total RNA was isolated from HSCs using RNeasy Plus Micro Kit (QIAGEN, 74034) according to the manufacturer’s instructions.
Library preparation was performed with SMART Ultra-Low Input kit v4 (Takara).

treatment_protocol: 125ng/mL PSGL-1 was added to HSCs culture for 24 hours.

value: bone marrow

value: hematopoietic stem cell

value: SelpKO

value: PSGL-1 treated


title: Nebulized_FLAMOD_H3_0h_biol_rep2

description:
Library name: Library-252
RnaSeq Illumina NovaSeq (2x150)


title: IMPACT_WID_21

first: Simon

last: Powell

state: NY

address: 1250 1st Ave

institute: Memorial Sloan Kettering Cancer Center

description: Library name: IMPACT_WID_21

data_processing:
RNA sequencing reads were first examined using FASTQC, then Illumina universal adapters were trimmed by cutadapt. The trimmed reads were aligned to the GRCh37 human genome using STAR RNA-Seq aligner, and then mapped single-end reads from transcripts were counted using the GenomicAlignments package in Bioconductor.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include gene read counts for each sample
Supplementary files format and content: tab-delimited text files include gene TPM values for each sample

organism: Homo sapiens

source_name: Skin

extract_protocol:
Following Institutional Review Board (IRB) approval, formalin-fixed paraffin-embedded (FFPE) tissues of 10 cases were retrieved from the pathology archives of Memorial Sloan Kettering Cancer Center (MSK). Two pathologists (F.P. and T.V.) reviewed cases and included tumors arising from different anatomic locations. Cases were microdissected from ten eight-micron-thick histologic sections under a stereomicroscope (Olympus SZ61) to ensure a tumor content ≥80%. RNA was extracted using the RNAeasy FFPE kit (Qiagen) and subjected to RNA-sequencing at MSK Integrated Genomics Operation (IGO).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.5-1 µg of total RNA with DV200 percentages varying from 17-38% underwent ribosomal depletion and library preparation using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE150 run, using the NovaSeq 6000 S4 Reagent Kit (300 Cycles) (Illumina).

value: Skin


title: Nebulized_FLAMOD_L1_1h30_biol_rep1

description:
Library name: Library-360
RnaSeq Illumina NovaSeq (2x150)


title: Microglia, ligated

description: RNA was harvested from ligated mice

value: dCLN-ligation


title: Nebulized_FLAMOD_H2_1h15_biol_rep1

description:
Library name: Library-249
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H2_0h_biol_rep1

description:
Library name: Library-248
RnaSeq Illumina NovaSeq (2x150)


title: Nebulized_FLAMOD_H2_3h_biol_rep1

description:
Library name: Library-250
RnaSeq Illumina NovaSeq (2x150)


title: SelpKO HSCs, PSGL-1 treated, rep2


title: Intravenous_FLAMOD_I_6h_biol_rep3

description:
Library name: Library-242
RnaSeq Illumina NovaSeq (2x150)


title: D1


title: SelpKO HSCs, PSGL-1 treated, rep1


title: Intravenous_FLAMOD_I_24h_biol_rep3

description:
Library name: Library-243
RnaSeq Illumina NovaSeq (2x150)


title: SelpKO HSCs, vehicle treated, rep3

value: vehicle treated


title: Intravenous_FLAMOD_I_0h_biol_rep3

description:
Library name: Library-239
RnaSeq Illumina NovaSeq (2x150)


title: Intravenous_FLAMOD_I_3h_biol_rep3

description:
Library name: Library-241
RnaSeq Illumina NovaSeq (2x150)


title: Intravenous_FLAMOD_I_1h15_biol_rep3

description:
Library name: Library-240
RnaSeq Illumina NovaSeq (2x150)


title: SelpKO HSCs, vehicle treated, rep2


title: SelpKO HSCs, vehicle treated, rep1


title: Intravenous_FLAMOD_A_6h_biol_rep2

description:
Library name: Library-237
RnaSeq Illumina NovaSeq (2x150)


title: Intravenous_FLAMOD_A_1h15_biol_rep2

description:
Library name: Library-235
RnaSeq Illumina NovaSeq (2x150)


title: Intravenous_FLAMOD_A_3h_biol_rep2

description:
Library name: Library-236
RnaSeq Illumina NovaSeq (2x150)


title: SelpWT HSCs, PSGL-1 treated, rep2

value: SelpWT


title: Intravenous_FLAMOD_A_0h_biol_rep2

description:
Library name: Library-234
RnaSeq Illumina NovaSeq (2x150)


title: Intravenous_FLAMOD_C_24h_biol_rep1

description:
Library name: Library-233
RnaSeq Illumina NovaSeq (2x150)


title: Intravenous_FLAMOD_C_6h_biol_rep1

description:
Library name: Library-232
RnaSeq Illumina NovaSeq (2x150)


title: SelpWT HSCs, PSGL-1 treated, rep1


title: Intravenous_FLAMOD_C_0h_biol_rep1

description:
Library name: Library-229
RnaSeq Illumina NovaSeq (2x150)


title: SelpWT HSCs, vehicle treated, rep3


title: Intravenous_FLAMOD_C_1h15_biol_rep1

description:
Library name: Library-230
RnaSeq Illumina NovaSeq (2x150)


title: 1918-XX-12_GGTATA-AATTGA_S4_R1_001.fastq.gz

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
Alignment with STAR
HTSeq for gene quantification
Assembly: hg19
Supplementary files format and content: read counts

source_name: skin

extract_protocol:
skin biopsy was extracted from normal skin of three patients
FFPE were used to fix the skin samples
RNA-seq library constructed and sequenced in the UM Advanced Genomic Core

value: skin

value: FFPE


title: 1918-XX-13_CGCCTG-TGGTTC_S5_R1_001.fastq.gz


title: HaloPROTAC3, HaloTag-IGF2BP3, 4-thiouridine, rep3

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

data_processing:
BCL files were converted to demultiplexed fastq files with bcl2fastq v2.20.0.422. The quality of fastq files was checked with fastqc 0.11.9. The fastq files were trimmed and aligned to human genome hg38 using the nf-core/slamseq analysis pipeline v1.0.0 {Neumann, 2019 #5562,Ewels, 2020 #5564} with default parameters with the following changes: multimappers were excluded, T2C reads were called if at least one T2C transition was detected, and a variant fraction cutoff was 0.2.
Assembly: hg38
Supplementary files format and content: csv, gene read counts, CPM, T to C read counts
Library strategy: SLAM-seq

growth_protocol: HCT116 conditionally expressing Tet-OsTIR1 were obtained from Masato Kanemaki Lab and cultured in McCoy's 5A (Modified) Medium (Sigma) with 10% Fetal Bovine Serum (Gibco), 2 mM Glutamine (Sigma), 1% Pen/Step (Sigma).

extract_protocol:
Cells were washed with PBS and collected in 1 mL of peqGOLD TriFast (Peqlab, VWR). 200 µL of chloroform:IAA (AppliChem) was added and samples were vortexed for 15 sec and centrifuged at 16,000 g for 15 min to separate the phases. DTT was added to the aqueous phase to 0.1 mM. RNA was precipitated by adding isopropanol (Sigma) in 1:1 ratio and 1 µL of 20 mg/mL glycogen (Thermo). RNA was incubated at the room temperature for 10 min, centrifuged at 20,000 g for 20 min at 4°C and washed with 75% ethanol supplemented with 0.1 mM DTT. The RNA pellets were resuspended in nuclease-free water supplemented with 1 mM DTT and RNaseIn (N2515, Promega) at 1:50 dilution and incubated for 10 in at 55°C. 10 µg of RNA was taken for alkylation reaction (10 µg of RNA, 5 µL of 100 mM iodoacetamide (Sigma) in ethanol, 50mM NaPO4 pH 8.0, 50% DMSO) and incubated at 50°C for 15 min. The reaction was quenched with 1 µL of 1 M DTT. The RNA was precipitated using ethanol method, washed with 75% ethanol and resuspended in nuclease-free water.
The sequencing libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit FWD with UDI (Lexogen)

treatment_protocol: Cells were treated with 500 nM HaloPROTAC3 for 7 hours, DMSO in 1:5000 dilution was used as a control. The newly synthesized RNAs were labeled with 250 µM 4-thiouridine (4SU) (Sigma) for last two hours of HaloPROTAC3 treatment.

value: human colorectal carcinoma

value: HaloTag-IGF2BP3, IGF2BP2 KO, Tet-OsTIR1-PURO

value: HaloPROTAC3 500 nM 7h, 4-thiouridine 250 uM last 2h


title: SelpWT HSCs, vehicle treated, rep1


title: 1918-XX-11_CACTAA-GCAGCG_S3_R1_001.fastq.gz


title: HaloPROTAC3, HaloTag-IGF2BP3, 4-thiouridine, rep2


title: SelpKO HSCs, freshly sorted, rep2

value: no treatment


title: HaloPROTAC3, HaloTag-IGF2BP3, 4-thiouridine, rep1


title: Intravenous_FLAMOD_A_24h_biol_rep2

description:
Library name: Library-238
RnaSeq Illumina NovaSeq (2x150)

value: Blood


title: Intravenous_FLAMOD_C_3h_biol_rep1

description:
Library name: Library-231
RnaSeq Illumina NovaSeq (2x150)


title: SelpKO HSCs, freshly sorted, rep1


title: SelpWT HSCs, freshly sorted, rep3


title: DMSO, HaloTag-IGF2BP3, 4-thiouridine, rep2

value: DMSO 1:5000 7h, 4-thiouridine 250 uM last 2h


title: BRAF K499E heterozygous, replicate 1

city: Seongbuk-gu, Seoul

first: Seoyeon

last: Kim

address: 145, Anam-ro

country: South Korea

institute: Korea University

description: KE 1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore.
Reads were aligned against reference using STAR and quantified with Salmon.
Assembly: Quantified estimates were converted into normalized gene-level counts using R package tximport, and differential gene expression analysis was performed with R package DESeq2.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include normalized count matrix table from DESeq

source_name: Cortical spheroid

extract_protocol:
Total RNA was extracted from cortical spheroids with TRIzol.
Library was constructed using TruSeq stranded mRNA kit.

value: Cortical spheroid

value: BRAF K499E heterozygous


title: SelpWT HSCs, freshly sorted, rep2

value: bone marrow

value: hematopoietic stem cell


title: DMSO, HaloTag-IGF2BP3, 4-thiouridine, rep1


title: Wildtype, replicate 3

description: WT 3

value: WT

value: Wildtype


title: SelpWT HSCs, vehicle treated, rep2


title: R24K-WT-2

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
A quality control check on the generated fastq ﬁles was performed using FastQC.
Peak analysis was conducted using HOMER software (v4.10; standard commands) after aligning fastq files to the mm10 mouse genome using bowtie2.
Assembly: mm10
Supplementary files format and content: bedgraph file of peaks (raw counts)

molecule: genomic DNA

source_name: muscle

extract_protocol:
Muscles were cryopowdered using a liquid nitrogen-cooled Retsch Cryomill. The cryopow-dered tissue was then fixed in 10 ml 1% PFA for 30 minutes at room temperature with gentle nutation. Fixation was quenched 1ml of 1.375M glycine (Cat # BP381-5, Fisher Scientific, Waltham, MA) with gentle nutation for 5 minutes at room temperature. After centrifugation at 3000g for 5 minutes at 4°C, the pellet was resuspended in cell lysis buffer as per reported conditions 69, supplementing the cell lysis buffer with 3mg/ml cytochalasin B and rotating for 10 minutes at 4°C.  Nuclei were pelleted at 300g for 10 min at 4°C, and subsequently processed fol-lowing the reported protocol with the adjustment of adding 3µg/ml cytochalasin B into all solutions for chromatin preparation and sonication, antibody incubation, and wash steps.  Chromatin was then sonicated for 15 cycles (30 sec, high power; 30 sec pause; 500µl volume) in a water bath sonicator set at 4°C (Bioruptor 300; Dia-genode, Denville, NJ).  After centrifuging at 10000g for 10 minutes at 4°C, sheared chromatin was checked on agarose gel for a shear band comprised between ~150 and ~600bp. Two µg of chromatin was kept for pooled input controls, whereas ~50µg chromatin were used for each pull-down reaction in a final volume of 2ml rotating at 4°C overnight. Primary antibody: rabbit polyclonal anti-GR (ABclonal #A2164). Chromatin complexes were precipitated with 100µl Dynabeads M-280 (sheep anti-rabbit #11203D; Thermo Scientific, Waltham, MA).  After washes and elution, samples were treated with proteinase K (cat #19131; Qiagen, Hilden, Germany) at 55°C and cross-linking was reversed through overnight incubation at 65°C. DNA was purified using the MinElute puri-fication kit (cat #28004; Qiagen, Hilden, Germany), quantitated using Qubit reader and reagents.
Library preparation and sequencing were conducted at the CCHMC DNA sequencing Core. Up to 30 ng of post-Immunoprecipitation dsDNA as measured by Invitrogen™ Qubit™ high- sensitivity spectroﬂuorometric measurement was made into Illumina-compatible NGS libraries using the ThruPLEX® DNA-Seq kit from Takara Bio Inc.
Each created library was dual-indexed with 8-base molecular barcodes for high level mul5plexing. Libraries were made with 13 cycles of PCR ampliﬁcation.

value: muscle

value: male

tag: background strain

tag: chip antibody

value: anti-GR


title: U2OS_Brunello_3_low

city: Adelaide

first: David

middle: C

last: Bersten

state: SA

address: Victoria Drive

department: Molecular and Biomedical Sciences

country: Australia

institute: The University of Adelaide

description: Library name: U2OS_Brunello_3_low

data_processing:
bcl2fastq for base calling, structure seletion with https://github.com/dcjones/fastq-tools. fastq-grep ".{28}ACCG(.{20})GT.{2,4}AGAGC" -b
barcode splitting with fastx_toolkit (version 0.0.14) fastx_barcode_splitter.pl function with the following parameters --mismatches 1 --bol --partial 1
sgRNAs were extracted from flanking sequences, mapped to a Brunello sgRNA ref using Bowtie 2 (v2.5.1) and count tables generated using a CRISPR_mapping perl script
Assembly: Brunello human sgRNA Ref
Supplementary files format and content: txt file for sgRNA counts
Library strategy: CRISPR Screen

extract_protocol:
genomic DNA extraction - Cell pellets were resuspended in a minimum of 500 ul (per 5 x10^7 cells) of Digestion Buffer ( 10 mM Tris-HCl pH8.0, 150 mM NaCl, 10 mM EDTA, 0.1% SDS) supplemented with 200 ug/ml of proteinase K (Thermo EO0491) and 30 ug/ml of RNAase A (DNAase and RNAase Free, Thermo EN0531) and incubated at 37oC for 3 hrs and then 55oC overnight. Lysates were then mixed 1:1 with Phenol/chloroform/isoamyl alcohol (PCI) solution (25:24:1) pH 7.8-8.2 (100mM Tris) (Sigma 25666) and centrifuged at >16,000g for 10 mins at room temperature. The supernatant was transferred to a new tube and 0.3 vol of 24:1 chloroform/isoamyl alcohol solution (Sigma C0549) added to the phenol extracts and reextracted by vortexing and centrifuging.  The supernatants were combined and 1 ul of 15 mg/ml GlycoBlue added with 0.5 vol of 7.5 M ammonium acetate (final concentration of 2.5 M).  0.7 Vol of Isopropanol was then added, mixed by inversion, incubated at room temperature for 5 mins and centrifuged at 16,000g for 30 mins at 4 oC. Genomic DNA pellets were washed with 70% ethanol, centrifuged at >16,000g for 5 mins at 4 oC, air dried at 42oC, resuspended in 10 mM Tris pH 8.0 overnight at 42oC and sheered by 5x -80oC freeze thawing prior to PCR.
For PCR amplification, gDNA was divided into 50 μL reactions such that each well had at most 5 μg of gDNA. 0.2  μl of AmpliTaq Gold (1U, 4311820, Thermo) was added per 50 ul reaction with 2 mM MgCl2 and 1 μl of 10 μM P5 F hU6 5’ TCTTGTGGAAAGGACGAAACACCG 3’ and P7 R sgRNA – 5’ TCTACTATTCTTTCCCCTGCACTGT 3’ primers in a PCR program of 95oC for 3 min, and 30 cycles of 94oC for 30 sec, 58oC for 30 sec, 72oC for 30 sec, followed by extension at 72oC for 10 mins. The PCR reactions from each condition were combined and purified by SPRI bead (Beckman Coulter B23317) purification, removing gDNA and primers. 10 ng of PCR product was then used in  the next set of 10 x PCRs using 15 cycles and staggered barcoding primers to add sequencing adaptors. The PCRs were then pooled and purified by SPRI bead purification, quantified and sequenced on an Illumina NextSeq500 1x75bp high output run at the South Australia Genome Centre (SAGC).

treatment_protocol: 0.5mM DMOG for 24hrs (HEK293T) or 48hrs (U2OS)

value: human osteosarcoma

value: 0.5mM DMOG


title: Background, parental, no 4-thiouridine

description: Background

value: human colorectal carcinoma

value: IGF2BP2 KO, Tet-OsTIR1-PURO


title: BRAF K499E heterozygous, replicate 3

description: KE 3


title: Wildtype, replicate 2

description: WT 2


title: SelpWT HSCs, freshly sorted, rep1

value: SelpWT


title: R24K-homo-2


title: Wildtype, replicate 1

description: WT 1


title: KrasLSL-G12DPtenFl/FlRictorFl/Fl_rep1

type: RNA

city: wuhan

first: xuejiao

last: zhao

state: hubei

address: jiefang avenue 1095#

institute: tongji hospital

description: Gene expression after AdCre-eGFP infected KrasLSL-G12DPtenFl/FlRictorFl/Fl OSE cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent GEx hybridization buffer was added to the fragmentation mixture and mix well by careful pipetting, then spin for 1min at RT at 13000rpm in a microcentrifuge. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Slowly dispense 100ul hybridization sample onto the gasket well. Slowly place an array 'active slide' down onto the SureHyb gasket slide, then place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces. Place assembled slide chamber in a hybridizeation oven, hybridize for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed following the manufacturer's recommendations.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Quick Amp Labeling  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNasey Mini kit (Qiagen p/n 74104) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: OSEs from different genotypes mice were isolated, then cultured in DMEM/F12 medium supplemented with several kinds of supplements.   The cultures were incubated for 3-5 days at 37 ºC in a humidified incubator with 5% CO2. then transfected with adenovirus.

value: OSE cells

tag: gender

value: female


title: BRAF K499E heterozygous, replicate 2

description: KE 2


title: KrasLSL-G12DPtenFl/FlRictorFl/Fl_rep2


title: KrasLSL-G12DPtenFl/Fl_rep3

description: Gene expression after AdCre-eGFP infected KrasLSL-G12DPtenFl/Fl OSE cells

source_name: OSE cells,KrasLSL-G12DPtenFl/Fl


title: D03

city: Bronx

first: Deepa

last: Rastogi

address: 3415 Bainbridge Ave

data_processing:
FastQC run to determine quality of samples
Trim Galore used to trim adaptor/low quality sequences
Trimmed reads were aligned to GRCh38/hg38 genome and read counts extracted using STAR alignment software
Read counts of the two different runs for each sample were added together (L001 and L002)
Normalization was performed using DESeq R package
Assembly: hg38
Supplementary files format and content: a single comma-separated value file containing normalized counts for all samples

source_name: Primary CD4+ T Cells

extract_protocol:
Zymo RNA Extraction Kit
Kapa stranded mRNA kit and Kap mRNA Hyper prep

tag: group

value: healthy weight children without asthma

value: Primary CD4+ T Cells


title: d6-H3k4me1_3

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description: Library name: iMT_d6-H3k4me1_3

data_processing:
Raw fastq files were processed using Cutadapt [v3.5] to remove adapter sequences (-a CTGTCTCTTATACACA and -A CTGTCTCTTATACACA), with the parameters set to a minimum read length of 20 (-m 20) and a minimum overlap of 12 bases for adapter matching (-O 12). Processed fastq files were aligned to mouse reference mm10 using bowtie2 [v2.3.4.3]. Duplicates were removed using Picard [v2.27.5] MarkDuplicates. Aligned reads were converted to BAM and sorted using Samtools [v1.14], with quality filter (“-q”) set to 2. Reads were then cleaned and sorted by BEDTools [v2.28.0]. In the end, only properly paired mapped reads were kept. Then, H3K4me3 peak calling was performed using MACS3 [v.3.0.0] with parameters [--scale-to large --keep-dup all --nomodel --shift 100 --extsize 200]. H3K4me1 peak calling was performed using MACS3 [v.3.0.0] with parameters [--scale-to large --keep-dup all --nomodel --shift 100 --extsize 200 --broad].
Assembly: GRCm38
Supplementary files format and content: bed
Library strategy: CUT&Tag

source_name: MEFs

growth_protocol: MEFs were isolated from E14.5 B6/C57 mouse embryos. Head, vertebral column, dorsal root ganglia and all internal organs were removed and discarded and the remaining embryonic tissue was manually cut into pieces and incubated in 0.25% trypsin for 5 min. Cells from embryos were plated onto a 15cm tissue culture dish in MEF medium containing DMEM (Life Technologies) and 10% fetal bovine serum (FBS, Gemini). MEFs were seeded at a density of 20 000 cells per 35 mm dish. The next day, MEF medium was replaced with the iMT media containing DMEM (Life Technologies) supplemented with 15% FBS (Gbico), 2 mM GlutaMax supplement (Life Technologies), 1% nonessential amino acids (Life Technologies), 0.1 mM β-mercaptoethanol (Sig- ma) and 40 ng/ml basic fibroblast growth factor (bFGF, Stemgent), as well as chemical components 6TCF (E616452,Tranylcypromine, CHIR99021, FSK) ). Media were changed every 4 days.

extract_protocol:
Cell dissociation
Concanavalin A (ConA) coated magnetic beads (Vazyme, N515-02) were activated just before use with Ca++ and Mn++ as described in the kit. The cells were collected and incubated in nuclei isolation buffer (5%BSA, 0.1%CA-630, 1mM DTT, 1 × Roche Complete Protease Inhibitor in DPBS) on ice for 3min. A total of 10,000 nuclei were washed once and resuspended in 50 μL of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine). The cell suspension was then mixed with 5 μL of activated ConA beads in PCR tubes and incubated at room temperature for 10 minutes. Then use a magnet to discard the supernatant. The beads were resuspended in 50 μL of antibody buffer (2 mM EDTA, 3% BSA, 0.05% digitonin, 1 × Roche Complete Protease Inhibitor in wash buffer) pre-mixed with antibody (1:100) with gentle vortexing, and incubated on a rotator at 4°C overnight. Following a quick spin, the bead suspension was discarded by using a magnet to remove the supernatant. Then the beads were resuspended in 50 μL of secondary antibody buffer [0.1% BSA, 1 × Roche Complete Protease Inhibitor in dig-wash buffer (0.05% digitonin in wash buffer)] pre-mixed with secondary antibody (1:100). The tubes were placed on a rotator for 1 hour at room temperature (10 rpm), the beads were washed three times with 200 μL of dig-wash buffer. Then the beads in each tube were suspended in 50 μL of dig300-wash buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin) pre-mixed with pG-Tn5 (1:100). The tubes were fixed on rotator (10 rpm) and incubated for 1 hour at room temperature. After a quick spin, the beads were washed three times with 200 μL of dig300-wash buffer. 200μL of tag buffer (10mM MgCl2, 1× Roche Complete Protease in Dig300-wash buffer) was added to each well, and the tubes were placed on a rotator at 37°C for 1 hour. After a quick spin, the beads were then washed once with 200 μL of 10 mM Tris-HCl and resuspended in 10 μL of 10 mM Tris-HCl pH 8.0. 2μL of lysis buffer (1.2%SDS, 0.1mg/ml Proteinase K in 10mM Tris-HCl pH 8.0) was added to each well, and the beads were incubated for 2 hours at 65°C. After a quick spin, 12 μL of 10% Tween-20 was added to each well and mixed thoroughly. Finally, 25 μL of TruePrep CUT&Tag Amplification Mix (Vazyme, TD612-01), 0.5 μL of 10 mM MGI-P5, and 0.5 μL of 10 mM MGI-P7 primer were added to each well. The PCR program was as follows: 72°C for 5 minutes; 95°C for 3 minutes; 12-15 cycles of 98°C for 10 seconds, 60°C for 5 seconds; 72°C for 1 minute; and 10°C hold. All the primers were listed in Supplementary Table 7. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library according to the manufacturer's instructions.

value: MEFs

tag: time

tag: antibody


title: KrasLSL-G12DPtenFl/FlRictorFl/Fl_rep3


title: KrasLSL-G12DPtenFl/Fl_rep2


title: R24K-WT-3


title: wild type_rep3

description: Gene expression after AdCre-eGFP infected wild type OSE cells

source_name: OSE cells,wild type

value: wild type


title: KrasLSL-G12DPtenFl/Fl_rep1


title: U2OS_Brunello_3

description: Library name: U2OS_Brunello_3


title: DMSO, HaloTag-IGF2BP3, 4-thiouridine, rep3

value: HaloTag-IGF2BP3, IGF2BP2 KO, Tet-OsTIR1-PURO

value: DMSO 1:5000 7h, 4-thiouridine 250 uM last 2h


title: wild type_rep1


title: U2OS_Brunello_3_high

description: Library name: U2OS_Brunello_3_high


title: R24K-WT-INPUT2

value: none (input)


title: U2OS_Brunello_2_low

description: Library name: U2OS_Brunello_2_low


title: d6NC-H3k4me1_3

description: Library name: iMT_d6NC-H3k4me1_3

value: no treatment


title: U2OS_Brunello_2_high

description: Library name: U2OS_Brunello_2_high


title: d6-H3k4me1_1

description: Library name: iMT_d6-H3k4me1_1


title: C07

value: obese children without asthma


title: C06


title: D01


title: d6NC-H3k4me1_2

description: Library name: iMT_d6NC-H3k4me1_2


title: U2OS_Brunello_2

description: Library name: U2OS_Brunello_2


title: D02


title: wild type_rep2


title: R24K-homo-INPUT2

value: muscle

value: male


title: U2OS_Brunello_1_low

description: Library name: U2OS_Brunello_1_low

value: human osteosarcoma

value: 0.5mM DMOG


title: R24K-WT-1

value: anti-GR


title: d6NC-H3k4me1_1

description: Library name: iMT_d6NC-H3k4me1_1


title: C05


title: U2OS_Brunello_1_high

description: Library name: U2OS_Brunello_1_high


title: R24K-homo-1


title: U2OS_Brunello_1

description: Library name: U2OS_Brunello_1


title: R24K-homo-3


title: C04


title: d0NC-H3k4me1_3

description: Library name: iMT_d0NC-H3k4me1_3


title: C03


title: RNA-seq_Homo1

data_processing:
A quality control check on the fastq files was performed using FastQC.
Upon passing basic quality metrics, the reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic 75 [Version 0.33].
The trimmed reads were then mapped to mm10 reference genome using default parameters with strandness (R for single-end and RF for paired-end) option in Hisat2 76 [Version 2.0.5].
In the next step, transcript/gene abundance was determined using kallisto 77 [Version 0.43.1].
We first created a transcriptome index in kallisto using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and counts per million (CPM).
Assembly: mm10
Supplementary files format and content: csv table containing isoform CPM

source_name: quadriceps muscle

extract_protocol:
RNA-seq was conducted on RNA extracted from muscle tissue. Total RNA was extracted from cryo-pulverized muscles with Trizol (#15596026; Thermo Fisher Scientific, Waltham, MA) and re-purified using the RNeasy Mini Kit (Cat #74104; Qiagen, Germantown, MD). RNA-seq was performed at the DNA Core (CCHMC) blinded to treatment groups.
150 to 300 ng of total RNA determined by Qubit (Cat#Q33238; Invitro-gen, Waltham, MA) high-sensitivity spectrofluorometric measurement was poly-A selected and reverse tran-scribed using Illumina’s TruSeq stranded mRNA library preparation kit (Cat# 20020595; Illumina, San Diego, CA).
Each sample was fitted with one of 96 adapters containing a different 8 base molecular barcode for high level multiplexing. After 15 cycles of PCR amplification, libraries were sequenced.

value: quadriceps muscle

value: 4 months-old

value: rs6190 allele +/+


title: RNA-seq_Homo3


title: HEK293T_Brunello_3_low

description: Library name: HEK293T_Brunello_3_low

value: Embryonic Kidney


title: d0NC-H3k4me1_1

description: Library name: iMT_d0NC-H3k4me1_1


title: B35

value: obese children with asthma

value: Primary CD4+ T Cells


title: RNA-seq_WT1

value: ref allele +/+


title: Br_E14.5_RNA_XistBxC_-+_XX_2

value: Brain

value: F1 hybrid of C57BL/6J∆Xist-/+ x CAST/EiJ

value: female


title: d8-H3K4me3_2

description: Library name: iMT_d8-H3K4me3_2

value: MEFs


title: d6-H3K4me3_2

description: Library name: iMT_d6-H3K4me3_2


title: RNA-seq_Homo2


title: HEK293T_Brunello_3_high

description: Library name: HEK293T_Brunello_3_high


title: RNA-seq_WT3


title: B34


title: HEK293T_Brunello_3

description: Library name: HEK293T_Brunello_3


title: HEK293T_Brunello_2_low

description: Library name: HEK293T_Brunello_2_low


title: B32


title: d4-H3K4me3_2

description: Library name: iMT_d4-H3K4me3_2


title: B33


title: B31


title: RNA-seq_WT2


title: HEK293T_Brunello_2_high

description: Library name: HEK293T_Brunello_2_high


title: d2-H3K4me3_2

description: Library name: iMT_d2-H3K4me3_2


title: d0NC-H3k4me1_2

description: Library name: iMT_d0NC-H3k4me1_2

value: no treatment


title: B30


title: d0NC-H3K4me3_3

description: Library name: iMT_d0NC-H3K4me3_3


title: Splenic macrophages, FABP4 WT cells, replicate 1, scRNA-Seq

city: Iowa City

first: Henry

last: Keen

state: IA

department: Pharmacology

institute: University of Iowa

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Single cell gene counting was performed by Cell Ranger (10X Genomics, version 7.1.0)
Assembly: mm10
Supplementary files format and content: matrix files in h5 format

source_name: spleen

extract_protocol:
Macrophages from mouse spleen were used for the 10 x Genomics 3’ expression single cell assay. Briefly, splenocytes were isolated from two pairs of age-matched WT and FABP4-/- female mice. Dead cells were excluded using Zombie-Violet and anti-CD16/32 antibody was used to block Fc receptors before additional staining with Alexa Fluor 488-conjugated anti-mouse F4/480 antibody and APC-conjugated anti-mouse CD11b antibody. The F4/80+/CD11b+/Zombie-Voilet- cells were sorted using a FACS Aira III instrument and resuspended at a concentration of 1000 cell/ul cold PBS with 0.04% non-acetylated BSA.
An equal number of 5000 targeted cells from each sample were prepared to create GEMs. The GEM generation/barcoding, post GEM-reverse transcription cDNA amplification, and library construction were performed according to the manufacturer’s guidelines

value: spleen

value: Macrophages

value: FABP4 +/+


title: HEK293T_Brunello_2

description: Library name: HEK293T_Brunello_2

value: 0.5mM DMOG


title: HEK293T_Brunello_1_low

description: Library name: HEK293T_Brunello_1_low


title: Splenic macrophages, FABP4 KO cells, replicate 2, scRNA-Seq

description: 10X Genomics

value: FABP4 -/-


title: B28


title: d35-H3K4me3_2

description: Library name: iMT_d35-H3K4me3_2


title: d6-H3k4me1_2

description: Library name: iMT_d6-H3k4me1_2


title: d28-H3K4me3_2

description: Library name: iMT_d28-H3K4me3_2


title: Splenic macrophages, FABP4 KO cells, replicate 1, scRNA-Seq

description: 10X Genomics


title: HEK293T_Brunello_1_high

description: Library name: HEK293T_Brunello_1_high


title: B27


title: HEK293T_Brunello_1

description: Library name: HEK293T_Brunello_1


title: IMPACT_WID_40

description: Library name: IMPACT_WID_40

source_name: Lung

value: Lung


title: d12-H3K4me3_2

description: Library name: iMT_d12-H3K4me3_2


title: Posterior dermis, Uninjured, rep 3

first: Elly

last: Tanaka

address: Campus-Vienna-Biocenter 1

institute: IMP (Research Institute of Molecular Pathology)

description: Column 82229 in matrix file MatrixCounts_allsamples.txt

data_processing:
Adaptors sequences were trimmed from the raw sequencing reads with Trimmomatic (version 0.39, Bolger et al. 2014), using parameters: ILLUMINACLIP:Adapters.fa:2:30:7 SLIDINGWINDOW:4:20 MINLEN:40 in single-end mode.
Poly(A) tails were trimmed with BBDuk (JGI), using parameters: ref=polyA.fa.gz k=13 ktrim=r useshortkmers=t mink=5 minlength=20. polyA.fa.gz contained 18 A nucleotides.
Trimmed sequenced reads were mapped to axolotl genome AmexG_v6.0-DD with HISAT2 (Kim et al. 2019), using parameters: --no-unal --summary-file Output.log -k 5 --very-sensitive -x DBGenome -U Reads.fq.gz > Alignment.sam
featureCounts (Liao et al. 2014) was used to generate a read counts table.
Assembly: AmexG_v6.0-DD
Supplementary files format and content: Tab-delimited text file includes raw rounts for each Sample

organism: Ambystoma mexicanum

source_name: Limb dermis

growth_protocol: We generated axolotls in which limb connective tissue cells are permanently labelled with mCherry. To achieve this, we treated axolotl embryos of genotype tgSceI(Mmu.Prrx1:TFPnls-T2A-ERT2-Cre-ERT2; Caggs:loxP-GFP-loxP-mCherry)Etnka with 4-hydroxytamoxifen (4-OHT) as described in Gerber et al. 2018 (PMID 30262634). Labelled axolotls were raised individually until they reached 12 cm in size.

extract_protocol:
RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific).
RNA libraries were prepared with QuantSeq 3' mRNA-Seq Library Prep Kit FWD V1 for Illumina (Lexogen), using 20.25 ng of input RNA. Input was 4.5 ul input RNA plus 0.5 ul of ERCC RNA Spike-In Mix (Thermo Fisher Scientific) pre-diluted 1:10,000 in water. Samples were multiplexed for sequencing, using i7 indices 7023 (CACACT, anterior rep 1), 7025 (TTTATG, anterior rep 2), 7022 (GGAGGT, posterior rep 1), 7024 (CCGCAA, posterior rep 2) and 7026 (AACGCC, posterior rep 3).

treatment_protocol: We harvested the skin from the lower forelimb (zeugopod) of connective tissue-labelled axolotls at steady state. Each replicate derived from 8 axolotls (16 lower arms). Each limb skin piece was dissected into an anterior and posterior piece, leaving a gap in between. Anterior and posterior samples were dissociated separately into single cell suspensions using Liberase TM enzyme. mCherry-positive dermal cells were purified by FACS and re-suspended in TRIzol Reagent for RNA extraction.

value: Limb dermis

value: CT cell labelled by mouse Prrx1 enhancer transgene

value: Uninjured


title: KO_2

city: Guangzhou

first: Yan

last: Li

state: Guangdong

address: Sun Yat-sen University, No. 74 Zhongshan Second Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080

institute: Sun Yat-sen University

description: 10X Genomics

library_source: genomic single cell

data_processing:
Cell Ranger 5.0.1 (10X Genomics) was applied to align the gene-expression libraries to the mm10 genome, and generate gene-cell count matrices using default parameters. The initial expression matrices were further filtered by Seurat 3.15 R package.
Cells that contained less than 500 molecular identifiers (UMIs) were filtered out; Cells with less than 200 or more than 6000 genes were removed.
Cells were excluded if contained higher than 15% mitochondrial counts or lower than 20% ribosomal counts.
Genes present in less than four cells were precluded.
DoubletFinder 2.03 in R was used to exclude 2.5% potential doublets.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: MC38 tumours

extract_protocol:
To obtain tumour-filtrating immune cells, tumours were sliced into small pieces of 1-2 mm in petri dishes and then digested in digestion buffer (10 mM HEPES, 1.25 mg/ml collagenase D, 0.85 mg/ml collagenase Ⅴ, 30 U/ml DNase I, 1 mg/ml dispase Ⅱ, and 10% FBS diluted in HBSS) for 45 min on a rotor at 37℃. The dissociated cells were passed through 70 µm and 40 µm cell-strainers (BD) sequentially and centrifuged at 600×g for 5 min at 4°C, then prepared as single-cell suspension.  Tumour-inflitrating immune cells were enriched from the tumour tissues by magnetic separation using mouse CD45 MicroBeads (Miltenyi Biotec, cat. no. 130-052-301).
Cellular suspensions were loaded onto a 10X Genomics GemCode Single-cell instrument to generate single-cell Gel Bead-In-EMulsion (GEMs).  Libraries were generated and sequencedfrom the cDNAs with Chromium Next GEM Single Cell 3’Reagent Kits v3.1.  Silane magnetic beads were used to remove leftover reagents and primers, and full-length, barcoded. cDNAs were amplified by PCR for library construction.  The libraries were constructed by adding specific primers during GEM incubation and library preparation steps, including End Repair, A-tailing, Adaptor Ligation, and PCR.

value: MC38 tumours

value: tumour-infiltrating CD45+ cells

value: CD45+ cells


title: B26

value: obese children with asthma

value: Primary CD4+ T Cells


title: KO_1

description: 10X Genomics


title: Posterior dermis, Uninjured, rep 2

description: Column 82227 in matrix file MatrixCounts_allsamples.txt


title: B25


title: Splenic macrophages, FABP4 WT cells, replicate 2, scRNA-Seq

description: 10X Genomics


title: B29


title: d8-H3K4me3_1

description: Library name: iMT_d8-H3K4me3_1


title: Anterior dermis, Uninjured, rep 2

description: Column 82228 in matrix file MatrixCounts_allsamples.txt


title: Posterior dermis, Uninjured, rep 1

description: Column 82221 in matrix file MatrixCounts_allsamples.txt


title: WT_2

description: 10X Genomics


title: B24


title: WT_1

description: 10X Genomics


title: d21-H3K4me3_2

description: Library name: iMT_d21-H3K4me3_2


title: Braf+/+, replicate 5

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore.
Reads were aligned against reference using STAR and quantified with Salmon.
Assembly: Quantified estimates were converted into normalized gene-level counts using R package tximport, and differential gene expression analysis was performed with R package DESeq2.
Supplementary files format and content: GRCm39
Supplementary files format and content: tab-delimited text files include normalized count matrix table from DESeq

source_name: Hippocampus

extract_protocol:
Adult mice were given a short anesthesia to extract mice brain. Total RNA was extracted from dissected hippocampal tissues.
Library was constructed using TruSeq stranded mRNA kit.

value: Hippocampus

value: WT

value: Braf+/+


title: B23


title: d6-H3K4me3_1

description: Library name: iMT_d6-H3K4me3_1

value: MEFs


title: B22


title: Braf+/+, replicate 4


title: d4-H3K4me3_1

description: Library name: iMT_d4-H3K4me3_1


title: B21


title: Anterior dermis, Uninjured, rep 1

description: Column 82226 in matrix file MatrixCounts_allsamples.txt


title: Braf+/+, replicate 3


title: TREATED_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw data were checked for quality, adapter content and duplication rates using FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Embryonic lung

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 2µg of total RNA was used as input for VaZyme_VAHTS Universal Stranded mRNA-seq - V6 (Vazyme). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: Embryonic lung

value: Alveolar cells

value: Recombinant SPARCL1


title: d35-H3K4me3_1

description: Library name: iMT_d35-H3K4me3_1


title: TREATED_2


title: d16-H3K4me3_2

description: Library name: iMT_d16-H3K4me3_2


title: A16

value: healthy weight children


title: Braf+/+, replicate 1


title: CONTROL_3

value: Control


title: Nestin;BrafKE/+, replicate 4

value: Nestin;BrafKE/+


title: d2-H3K4me3_1

description: Library name: iMT_d2-H3K4me3_1


title: A12


title: d16-H3K4me3_1

description: Library name: iMT_d16-H3K4me3_1


title: A11


title: Braf+/+, replicate 2


title: TREATED_1


title: d12-H3K4me3_1

description: Library name: iMT_d12-H3K4me3_1


title: Splenocyte_18mo_WT_2

city: Nashville

first: Seung Woo

last: Kang

state: TN

address: MRBIV 10475, 2215 Garland Avenue

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

description: 10X genomics

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

source_name: Total splenocytes

growth_protocol: N/A. Primary cells directly submitted for the single-cell RNA sequencing.

extract_protocol:
The thymus from three 1-month-old ZZ homozygotes and wild-type littermates were collected and pooled per single-cell dataset. Connective tissues, excess blood vessels, and adipocytes were carefully removed in 4'C sterile 1X DPBS. Clean thymuses were then transferred to digestion buffer (2% FBS/1640 RPMI (w/ 25mM HEPES), DNase I (20µg/µL), Collagenase/Dispase (1mg/mL)) to be thinly sliced into 1~2mm fragments. The digestion solution containing the thymic fragments was then incubated at 37'C for 1 hour. In between the incubation period, the solution was gently mixed up and down with transfer pipettes every 20 minutes, 100 times each. Post-digestion, the solution was passed through a 70µm cell strainer to remove undigested fragments. Cells were centrifuged at 300 x g, 4'C for 10 minutes. Red blood cells were then removed with a 2-minute incubation in RBC Lysis Buffer (10X) (BioLegend 420301). The solution was centrifuged again at 300 x g, 4'C for 10 minutes. Cells were then resuspended in 3mL MACS buffer (filtered 0.5% BSA/2mM EDTA/1X DPBS). As per MACS separation guidelines, cells underwent CD45 separation with CD45 microbeads, mouse (Miltenyi Biotec 130-052-301). Spleens were freshly collected and gently meshed through 70µm cell strainer. After RBC removal, single-cell suspension was made before sample submission.
Library was constructed according to the manufacturer's instructions (single cell 3', 10X genomics).

value: Total splenocytes

value: Female

value: 18 months

value: Wild-type


title: A14


title: d28-H3K4me3_1

description: Library name: iMT_d28-H3K4me3_1


title: d21-H3K4me3_1

description: Library name: iMT_d21-H3K4me3_1


title: CONTROL_2


title: A13


title: CONTROL_1


title: Nestin;BrafKE/+, replicate 3


title: d0NC-H3K4me3_2

description: Library name: iMT_d0NC-H3K4me3_2

value: no treatment


title: Nestin;BrafKE/+, replicate 1


title: Nestin;BrafKE/+, replicate 2


title: D24

value: healthy weight children without asthma


title: Splenocyte_1mo_ZZ_2

description: 10X genomics

value: 1 month

value: lacZ/lacZ


title: d35_ATAC-2

description: Library name: iMT_d35_ATAC-2

data_processing:
Raw fastq files were processed using Cutadapt [v3.5] to remove adapter sequences (-a CTGTCTCTTATACACA and -A CTGTCTCTTATACACA), with the parameters set to a minimum read length of 20 (-m 20) and a minimum overlap of 12 bases for adapter matching (-O 12). Processed fastq files were aligned to mouse reference mm10 using bowtie2 [v2.3.4.3]. Duplicates were removed using Picard [v2.27.5] MarkDuplicates. Aligned reads were converted to BAM and sorted using Samtools [v1.14], with quality filter (“-q”) set to 2. Reads were then cleaned and sorted by BEDTools [v2.28.0]. In the end, only properly paired mapped reads were kept. Then, atac peak calling was performed using MACS3 [v.3.0.0] with parameters [--scale-to large --keep-dup all --nomodel --shift 100 --extsize 200].
Assembly: GRCm38
Supplementary files format and content: bed

extract_protocol:
Cell dissociation
Permeabilized nuclei were counted and diluted in PBST (0.5% Tween-20 in DPBS) to a concentration of 25,000/mL. 2 µL of nuclei suspension was added to 13 µL of tagmentation mix [7.5 µL of 2 × TD buffer (20mM Tris-HCl pH7.6, 10mM MgCl2, 20% Dimethylformamide in ddH2O), 4.2 µL of PBS, 0.15 µL of 1% digitoxin, 0.15 µL of 10% Tween-20, 1 µL of TTE (Not diluted with storage buffer)]. Then the tagmentation was carried out at 55°C for 30 minutes. Add 200 µL of PBS and centrifuged at 2,000 × g for 5 minutes at 4°C, and the pellet was directly resuspended in 10 µL RSB buffer. Add 2μL of lysis buffer (1.2% SDS, 0.1mg/ml Proteinase K in 10mM Tris-HCl pH 8.0) in each well, and the nuclei were incubated at 55°C for 30 minutes. After a quick spin, 12 μL of 10% Tween-20 was added to each well and mixed thoroughly. 25 μL of 2 × TruePrep CUT&Tag Amplification Mix, 0.5 μL of 10 mM MGI-P5, and 0.5 μL of 10 mM MGI-P7 primer were added to each well. The PCR program was as follows: 72°C for 5 minutes; 95°C for 3 minutes; 11-12 cycles of 98°C for 10 seconds, 60°C for 5 seconds; 72°C for 1 minute; and 10°C hold. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library according to the manufacturer's instructions


title: B45

value: obese children with asthma

value: Primary CD4+ T Cells


title: A04


title: Splenocyte_18mo_WT_1

description: 10X genomics


title: d0NC-H3K4me3_1

description: Library name: iMT_d0NC-H3K4me3_1

value: MEFs


title: A31


title: Ova_LN_2

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

data_processing:
CellRanger v3.1.0 was used to aligne reads to the mm10 genome.
Seurat V4 was used for subsequent data processing. Cells with mitochondrial counts > 10% were filtered.
Filtered cells were scaled and normalized and clustered using the sctransform normalization workflow.
Assembly: mm10
Supplementary files format and content: barcode.tsv, features.tsv and matrix.mtx output from CellRanger.

source_name: EAE LN

extract_protocol:
Lymph nodes were harvested two days following treatment and cells were sorted into 4 populations : TCR-b+, CD19+, CD11c+ and CD11b+ CD11c-. Cells were recombined at a 1:1:1:1 ratio. When there were not enough CD11c+ Cells, additional CD11b+ cells were added to get to 10,000 total cells.
For the CNS samples, mice were perfused with 10 mL ice cold PBS then the spinal cord was harvested. The spinal cord was then disociated with a gentlemacs dissociator and suspended in 0.33mg/mL Collagenase A for 25 minutes. Samples were then placed in 30% percoll and underlayed with 70% percoll and spun at 650G for 25 minutes no brake. Samples were then sorted for CD45+ cells for sequencing.
Enriched cells were prepared for single cell libraries using the 10X Genomics Chromium Single Cell 3' Reagent Kits according to the manufacturer's instructions.
scRNA-seq

treatment_protocol: C57/BL6 Mice were induced with EAE using MOG/CFA Emulsion followed by Pertussis toxin injection. Mice were treated with specific dMP formulations in advanced disease (score of 3).

value: inguinal lymph nodes

value: Ova DMP


title: Ova_LN_1


title: Splenocyte_1mo_ZZ_1

description: 10X genomics


title: d35_ATAC-1

description: Library name: iMT_d35_ATAC-1


title: C25

value: obese children without asthma


title: Splenocyte_1mo_WT_2

description: 10X genomics


title: d28_ATAC-2

description: Library name: iMT_d28_ATAC-2


title: d28_ATAC-1

description: Library name: iMT_d28_ATAC-1


title: Splenocyte_1mo_WT_1

description: 10X genomics


title: C24


title: Mog_LN_2

value: Mog DMP


title: Ova_CNS_1

source_name: EAE CNS

value: spinal cord


title: Mog_CNS_1


title: Mog_LN_1


title: Stroma_1mo_ZZ_2

description: 10X genomics

source_name: CD45- total thymic stroma

value: CD45- total thymic stroma


title: Stroma_1mo_ZZ_3

description: 10X genomics


title: d21_ATAC-2

description: Library name: iMT_d21_ATAC-2


title: d16_ATAC-2

description: Library name: iMT_d16_ATAC-2


title: D23


title: D22


title: d12_ATAC-2

description: Library name: iMT_d12_ATAC-2


title: Stroma_1mo_ZZ_1

description: 10X genomics


title: D19


title: Stroma_1mo_WT_2

description: 10X genomics


title: d8_ATAC-2

description: Library name: iMT_d8_ATAC-2


title: C23


title: d6_ATAC-2

description: Library name: iMT_d6_ATAC-2


title: RPCC_60_min

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: DNA labeling. 30 min sample. IP + WCE , three replicates each one

hyb_protocol: GRO: All in vivo labeled RNA was utilized for hybridization (0.35-3.5 x 10^7 dpm).

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004. GRO data were normalized by genomic hybridization data on the same filter (F1-F7). RPCC data were obtained by dividing the Immunopreciptation of RNA pol II (IP) data by the whole cell extract (WCE) data.

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: GRO: Labelled RNA, obtained after centrifugation and washing, was spectrophotometrically quantified.

growth_protocol: Cells were synchronized in G1 with 1 µg/ml of alpha factor. The percentage of unbudded cells at this stage in all three experiments was higher than 90%. Cultures were then washed in fresh media to eliminate the pheromone and released in new media. Samples for total RNA pol II (ChIP), active RNA pol II (GRO), FACS and microscopy were taken at 0, 30 and 60 minutes. To define which cell cycle stage was enriched at each time point we initially performed flow cytometry and budding index analysis. The combination of both analyses determined that at time 0 most of the cells remained in G1 (unbudded cells with or without shmoo, and a 1C DNA content) and very few had finished mitosis at 60 minutes (two differentiated nuclear masses). These two analyses are useful to discriminate the G1 (no bud or shmoo) and mid-late M (nucleus has started to split up) population but are not so efficient differentiating S, G2 and early M-phase. Median levels of total and active RNA pol II at each time point of well-established cell cycle genes (Santos et al. , 2014) were used to better infer which cell cycle stages were enriched in each time point analysed

extract_protocol:
Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.
GRO protocol: ≈ 5 x 108 exponentially growing yeast cells were permeabilized washing twice with 0.5% N-lauryl sarcosine sodium sulfate (sarkosyl) and recovered through low-speed centrifugation. In vivo transcription was then performed in a solution containing 120 µL of 2.5X transcription buffer (50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2), 16 µL of AGC mix (10 mM each of CTP, ATP, and GTP) 6 µL of DTT (0.1 M), 16 µL of [α33P] UTP (3000 Ci/mmol, 10 µCi/µL) and distilled water up to 300 µL. The mixture was incubated for 5 minutes at 30ºC to facilitate transcription elongation and halted by adding 1 mL of cold distilled water. Non-incorporated radioactive nucleotides were removed by two centrifugation wash cycles. Total RNA extraction was carried out using the Fast-Prep (Bio101 Inc.) device. Cells were resuspended in 500 µL of LETS buffer (0.1 M LiCl, 10 mM EDTA, 0.2% SDS, 10 mM Tris-HCl pH 7.4), along with 200 µL of glass beads and 500 µL of water-saturated acid phenol. Contaminants were eliminated by chloroform extraction, and labelled RNA was precipitated using 0.1 volume of 5 M LiCl and 2.5 volumes of cold ethanol for a minimum of 2 hours at -20ºC. Labelled RNA, obtained after centrifugation and washing, was spectrophotometrically quantified. All in vivo labeled RNA was utilized for hybridization (0.35-3.5 x 10^7 dpm).
RPCC: ≈ 5 x 108 cells were crosslinked with formaldehyde (FC 1%) for 15 minutes at room temperature. Cross-link was quenched with glycine (FC 125 mM) and washed 4 times with 30 mL ice-cold TBS buffer (20mM Tris-HCl, 140 mM NaCl, pH 7.5) and frozen. Cells were thawed on ice and resuspended in 300 µL lysis buffer [50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 mM benzamidine and 1 pill of protease inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) dissolved in every 50 ml of buffer)]. The equivalent of 0.3 ml of frozen glass beads (425-600 mm; Sigma-Aldrich, St Louis, MO, USA) Cell lysis was carried out in a Fast-Prep (Bio101 Inc.) device by 2 cycles of 30 seconds. Samples were cooled down 5 minutes in ice between cycles. Samples were then sonicated in ice-cold water using a Bioruptor (Diagenode SA, Liège, Belgium) with 15´ pulses at High output (200W) during 2 cycles of 15 minutes. DNA fragments obtained ranged from 200 and 500 bp. Cell debris was removed by centrifugation at 12,000 rpm at 4°C for 5 minutes. An aliquot of 10 µL of this whole cell extract (WCE) was kept as positive control. 50 µL of Dynabeads Protein G (Dynal Invitrogen Corp., Carlsbad, CA, USA) were washed with 5 mg/ml bovine serum albumin (BSA) in PBS buffer (140 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4, pH 7,4) and incubated with anti-Rpb3 antibodies (ab81859; Abcam). Beads were washed with PBS/BSA to remove unbound antibody and incubated for 1.5-2 hours in agitation to enrich the samples in the DNA fragments specifically cross-linked to the RNA pol II.  Beads were washed twice with lysis buffer, twice with 360 mM NaCl lysis buffer, twice with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxycholate, 1 mM EDTA pH 8.0, 1 mM PMSF, 1 mM benzamidine and 1 pill of protease inhibitor cocktail/25 mL (Roche), and once with TE (10 mM Tris-HCl, pH 8.0, 1 mM EDTA). Two successive washes were performed with 30 µL of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubating for 10 minutes at 65°C each time. The final volume of all the samples (IP, NA and WCE) was raised to 300 µL with TE and treated overnight at 65°C to reverse the cross-linking.  Proteins were degraded by adding 150 µg of proteinase K for 1h 30 min at 37°C. DNA was purified using QIAquick PCR purification columns (Qiagen Inc., Valencia, CA, USA). Ligation Mediated PCR [3] was used for DNA amplification. Briefly, DNA was blunted by T4 phage DNA polymerase in a reaction volume of 124 µL (T4 DNA Pol buffer, 40 µg/µL BSA, 80 µM dNTPs, 0.6 U T4 DNA Polymerase (Roche, Basel, Switzerland). The reaction was allowed to proceed for 20 minutes at 12°C. After phenol/chloroform/isoamylic alcohol extraction, DNA was ethanol-precipitated in the presence of 12 µg of glycogen and was ligated in a final volume of 50 µL with the annealed linkers oJW102 and oJW103 (1.5 µM of each primer). The reaction was carried out overnight at 16°C and ligated DNA was precipitated and resuspended in 25 µL milliQ water. The ligated DNA was dissolved in a final volume of 40 µL (1x DNA pol buffer: 2 mM MgCl2, 0.25 mM dNTPs, 1.25 µM oligonucleotide oJW102). The reaction was started by incubating for 2 minutes at 55°C, then pausing to add 10 µL of the reaction mix (1x DNA pol buffer, 2 mM MgCl2 and 5 U DNA polymerase from Biotools, Madrid, Spain). The program was resumed for 5 minutes at 72°C, 2 minutes at 95°C and 33 cycles of 30 s at 95°C, 30 s at 55°C and 2 minutes at 72°C. DNA was precipitated overnight and resuspended in 50 µL of milliQ water. A 5 µL DNA aliquot of the LM-PCR was analyzed on a 1.2% agarose gel to check the size (average size of 300-400 bp) and PCR efficiency. The PCR product was used as a template for the radioactive labelling reaction. The reaction mixture contained 5-15 µL of amplified DNA in 50 µL (1x DNA pol buffer, 2 mM MgCl2, 0.2 mM dATP, dTTP and dGTP, 25 µM dCTP, 1 µM oJW102, 0.8 µCi/µL α-33P-dCTP and 5 U DNA polymerase). The mix was denatured for 5 minutes at 95°C, annealed 5 minutes at 50°C, and amplified for 30 minutes at 72°C. The reaction product was purified through a ProbeQuant G-50 column (Amersham Biosciences, Piscataway, NJ, USA) to remove unincorporated 33P-dCTP and oligonucleotides.


title: RPCC_30_min

description: DNA labeling. 60 min sample. IP + WCE , three replicates each one


title: RPCC_start

description: DNA labeling. Start sample. IP + WCE , three replicates each one


title: K562 SF3B1-MUT STAG2-MUT replicate 2

city: Pavia

first: Martina

last: Sarchi

address: Via Ferrata 9

department: Dept. of Molecular Medicine

country: Italy

institute: University of Pavia

description:
Library name: Sample 15
K700SC8
SS_splicing.csv

data_processing:
For gene expression analysis, reads were pseudoaligned using kallisto.
Differential gene expression was determined using the DESeq2 package.
For splicing analysis, RSEM v1.2.4 was used to map all RNA-seq reads to this transcriptome annotation.
Remaining unaligned reads were then mapped a database of all possible junctions between annotated 5' and 3' splice sites of the transcriptome annotation, as well as to the genome sequence, with TopHat v2.0.8b, and the resulting aligned reads were merged with the RSEM output
The expression levels of isoforms annotated in MISO v2.0’s annotation were estimated with MISO v2.0.
To identify events that were differentially spliced, we defined the metric deltaPSI (ΔPSI) as the isoform ratio (absolute percentage of mRNA) in SF3B1-mutant samples - isoform ratio in SF3B1-WT cells, and computed a significance statistic using Wagenmakers’s Bayesian framework for single-sample comparisons or the Mann-Whitney U test for group comparisons. An event was classified as differentially spliced if it exhibited an absolute change of ΔPSI ≥ 10% and Bayes factor ≥ 5 or p < 0.05.
Assembly: For gene expession analysis, hg38 reference genome was used.
Assembly: For splicing analysis, transcriptome annotation for the hg19/GRCh37 human genome assembly was created by merging gene annotations from Ensembl v71.1, the UCSC knownGene track, and MISO v2.0 isoform annotations.
Supplementary files format and content: comma-separated values file including normalised counts for 5F-HPCs with wild-type or mutant SF3B1 and AAVS1, RUNX1 or STAG2 editing.
Supplementary files format and content: comma-separated values file including pairwise comparisons for SF3B1-mutant RUNX1-edited versus SF3B1-mutant AAVS1-edited 5F-HPCs.
Supplementary files format and content: comma-separated values file including pairwise comparisons for SF3B1-mutant STAG2-edited versus SF3B1-mutant AAVS1-edited 5F-HPCs.
Supplementary files format and content: comma-separated values file including pairwise comparisons for SF3B1-WT RUNX1-edited versus SF3B1-WT AAVS1-edited 5F-HPCs.
Supplementary files format and content: comma-separated values file including pairwise comparisons for SF3B1-WT STAG2-edited versus SF3B1-WT AAVS1-edited 5F-HPCs.
Supplementary files format and content: comma-separated values files including splicing analysis for K562 cells: SF3B1/RUNX1-mutant vs wild-type (SR_splicing.csv), SF3B1/STAG2-mutant vs wild-type (SS_splicing.csv),  including dPSI and PSI values.

source_name: Hematopoietic

growth_protocol:
5F-HPCs were generated as previously described (PMID: 34861039, 31010849). 5F-HPCs were cultured in StemSpan SFEM II (StemCell Technologies) with 50 ng/ml SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL-6, 10 ng/ml IL-3 (all Peprotech) and 100 U/mL penicillin/streptomycin (Fisher). Doxycycline was added at 2 μg/ml (Sigma). Cultures were maintained at <1.5 x 10^6 cells/ml, and media was exchanged every 3-4 days. 5F-HPCs were maintained in culture between 60-100 days prior to CRISPR/Cas9 editing.
SF3B1-mutant (K700E) and wild-type control K562 clones were grown in Iscove’s modified Dulbecco’s media (IMDM) with 10% FBS and 100 U/mL penicillin/streptomycin (Fisher), and cultures were maintained at <1.5 x 10^6 cells/ml.

extract_protocol:
Cells were resuspended in Trizol (ThermoFisher, cat. #15596026), and RNA extracted per manufacturer protocol.
RNA sequencing was performed at Omega Bioservices with TruSeq Stranded mRNA kit with polyA selection.

treatment_protocol: 5F-HPCs were CRISPR-edited by lentiviral mediated delivery of Cas9 and sgRNAs targeting AAVS1, RUNX1 or STAG2 genes. 5F-HPCs were transduced in a 48-well plate in standard media with polybrene. 600,000 cells were transduced at an MOI of 5 and spun at 2300 rpm, 30 minutes prior to incubation at 37°C. Cells were washed 16-24 hours later and resuspended in fresh 5F-HPCs media for additional 48 hours prior to FACS-sorting.

value: Hematopoietic

value: SF3B1-K700E STAG2-MUT


title: K562 SF3B1-MUT STAG2-MUT replicate 1

description:
Library name: Sample 14
K700SC6
SS_splicing.csv


title: d2_ATAC-2

description: Library name: iMT_d2_ATAC-2


title: D18

institute: Albert Einstein College of Medicine


title: K562 SF3B1-MUT RUNX1-MUT

description:
Library name: Sample 13
K700RA1
SR_splicing.csv

value: SF3B1-K700E RUNX1-MUT


title: d0NC_ATAC-2

description: Library name: iMT_d0NC_ATAC-2


title: C21


title: D20


title: C19


title: GRO_60_min

description: GRO labelling for 60 min sample. Replicates 1-3


title: d21_ATAC-1

description: Library name: iMT_d21_ATAC-1


title: D17


title: SF3B1-MUT RUNX1-edited replicate 2

description:
Library name: Sample 10
E6RC4
5F_NormCounts.csv

value: iPSC-derived 5F-HPCs

value: SF3B1-G742D RUNX1-MUT


title: SF3B1-MUT STAG2-edited replicate 1

description:
Library name: Sample 11
12A4
5F_NormCounts.csv

value: SF3B1-G742D STAG2-MUT


title: D16

value: healthy weight children without asthma


title: d12_ATAC-1

description: Library name: iMT_d12_ATAC-1


title: C22


title: Stroma_1mo_WT_1

description: 10X genomics

value: Female

value: 1 month

value: Wild-type


title: d4_ATAC-2

description: Library name: iMT_d4_ATAC-2

value: MEFs


title: d8_ATAC-1

description: Library name: iMT_d8_ATAC-1


title: SF3B1-MUT STAG2-edited replicate 2

description:
Library name: Sample 12
E6SB4
5F_NormCounts.csv


title: D15

value: Primary CD4+ T Cells


title: SF3B1-MUT RUNX1-edited replicate 1

description:
Library name: Sample 9
E6RC3
5F_NormCounts.csv


title: C18


title: CBN 20 μM, biological rep3

city: Laurel

first: Xiugong

last: Gao

state: MD

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 20 μM

hyb_protocol: Hybridization, wash, and staining were carried out using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit on an Affymetrix Fluidics Station 450 following the manufacturer’s protocols.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G and the image (.DAT) files were preprocessed using the Affymetrix GeneChip Command Console (AGCC) software v.4.0 to generate cell intensity (.CEL) files.

data_processing: Data were processed using the Affymetrix Transcriptome Analysis Console (TAC) software (v.4.0).

label: biotin

source_name: iPSC-derived hepatocytes exposed to CBNa at 20 μM

label_protocol: The total RNA samples (100 ng each) were labeled using the GeneChip 3’ IVT PLUS Reagent Kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: Commercial iPSC-derived hepatocytes (iCell Hepatocytes 2.0) from FUJIFILM Cellular Dynamics (Madison, WI) were cultured following the manufacturer’s protocols.

extract_protocol: Cells were lysed in RLT buffer (Qiagen) supplemented with β-mercaptoethanol, homogenized by QIAshredder (Qiagen), and kept in a -80 °C freezer until further processing. Total RNA was isolated on the EZ1 Advanced XL (Qiagen) automated RNA purification instrument using the EZ1 RNA Cell Mini Kit (Qiagen) following the manufacturer’s protocol, including an on-column DNase digestion.

treatment_protocol: Cells cultured at day 6 after seeding were exposed to CBN at varying concentrations (0.1-20 µM) in triplicate for 24 h.

value: hepatocyte


title: CBN 20 μM, biological rep2


title: d6_ATAC-1

description: Library name: iMT_d6_ATAC-1


title: d4_ATAC-1

description: Library name: iMT_d4_ATAC-1


title: SF3B1-MUT AAVS1-edited replicate 1

description:
Library name: Sample 7
E6A3
5F_NormCounts.csv

value: SF3B1-G742D AAVS1-MUT


title: SF3B1-MUT AAVS1-edited replicate 2

description:
Library name: Sample 8
E6A4
5F_NormCounts.csv


title: SF3B1-WT STAG2-edited replicate 2

description:
Library name: Sample 6
12SB4
5F_NormCounts.csv

value: SF3B1-WT STAG2-MUT


title: GRO_30_min

description: GRO labelling for 30 min sample. Replicates 1-2


title: CBN 20 μM, biological rep1


title: CBN 10 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 10 μM

source_name: iPSC-derived hepatocytes exposed to CBNs at 10 μM


title: GRO_start

description: GRO labelling for start sample. Replicates 1-3


title: A29

source_name: Primary CD4+ T Cells

value: healthy weight children


title: C17

value: obese children without asthma


title: CBN 10 μM, biological rep2


title: d0NC_ATAC-1

description: Library name: iMT_d0NC_ATAC-1

source_name: MEFs

value: no treatment


title: d2_ATAC-1

description: Library name: iMT_d2_ATAC-1


title: B44

value: obese children with asthma


title: CBN 10 μM, biological rep1


title: SF3B1-WT STAG2-edited replicate 1

description:
Library name: Sample 5
12SB3
5F_NormCounts.csv

value: Hematopoietic


title: SF3B1-WT RUNX1-edited replicate 2

description:
Library name: Sample 4
12RC4
5F_NormCounts.csv

value: iPSC-derived 5F-HPCs

value: SF3B1-WT RUNX1-MUT


title: B43


title: CBN 5.0 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 5.0 μM

source_name: iPSC-derived hepatocytes exposed to CBNa at 5.0 μM


title: d8NC_RNA-1

description: Library name: iMT_d8NC_RNA-1

data_processing:
Raw fastq files were processed using Cutadapt [v3.5] to remove adapter sequences (-a CTGTCTCTTATACACA and -A CTGTCTCTTATACACA), with the parameters set to a minimum read length of 20 (-m 20) and a minimum overlap of 12 bases for adapter matching (-O 12). Processed fastq files were aligned to mouse reference mm10 using STAR [v 2.7.10a]. Processed fastq files were aligned to the mouse reference mm10 using STAR [v2.7.10a] and converted to BAM files. The aligned BAM files were used with FeatureCounts [v1.6.0] to generate count files, with parameters [-T 10 -t exon -g gene_id -p].
Assembly: GRCm38
Supplementary files format and content: counts files recording results of FeatureCounts captured by RNA-seq

extract_protocol:
Cell dissociation
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01) according to the manufacturer's instructions. Subsequently, add 2 µL of RNA with a total amount of approximately 100-400 ng to a PCR tube containing 1 µL of dNTP and 1 µL of TSO-oligodT. Incubate the PCR tube at 65°C for 5 minutes and then place it immediately on ice for 2 minutes. 0.4 μL of ddH2O, 2 μL of 5× PrimeScript II Buffer (Takara), 2 μL of Betaine (Sigma), 0.5 μL of 100 mM DTT, 0.15 μL of 0.4 M MgCl2, 0.2 μL of 50 mM TSO LNA primer, 0.25 μL of RNase inhibitor (Vazyme), and 0.5 μL of PrimeScript II RTase (Takara) were added. The reaction was gently mixed and carried out in a PCR thermocycler programmed as follows: 42°C 120 minutes, 70°C, 10 minutes; 10°C hold. Following the reaction, a PCR amplification mix was prepared with 12.5 μL of 2×HiFi HotStart ReadyMix, 1 μL of TSO-PCR primer (10 μM), and 1.5 μL of ddH2O. The PCR program was as follows: 95°C for 3 minutes; 7-16 cycles (adjust cycles based on RNA input) of 98°C for 30 seconds, 65°C for 15 seconds, and 72°C for 6 minutes; 72°C for 5 minutes; and 10°C hold. Purification was then performed using 0.9 × of VAHTS DNA Clean Beads according to the manufacturer's instructions. Sequencing library construction was using TruePrep DNA Library Prep Kit for MGI (Vazyme, TDM503-01) according to the manufacturer's instructions.


title: CBN 5.0 μM, biological rep2


title: SF3B1-WT AAVS1-edited replicate 2

description:
Library name: Sample 2
E6SB3
5F_NormCounts.csv

value: SF3B1-WT AAVS1-MUT


title: C16


title: CBN 5.0 μM, biological rep1


title: d8_RNA-3

description: Library name: iMT_d8_RNA-3


title: D14

value: healthy weight children without asthma


title: CBN 1.0 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 1.0 μM

source_name: iPSC-derived hepatocytes exposed to CBNa at 1.0 μM


title: SF3B1-WT AAVS1-edited replicate 1

description:
Library name: Sample 1
12A3
5F_NormCounts.csv


title: d8_RNA-2

description: Library name: iMT_d8_RNA-2


title: A28


title: A27


title: d8_RNA-1

description: Library name: iMT_d8_RNA-1


title: Pten_P53 KO in vitro tumoroid, biol rep 2

first: Gerda

last: Egger

address: Waehringer Guertel 18-20

department: Pathology

institute: Medical University of Vienna

description: Library name: 1091_23

data_processing:
Data was analyzed using 100 nt single end read length, with 5 million reads on average per sample. Results were mapped to mouse genome GRCm38.101 using STAR aligner and quality control was performed with the RSEQC Quality control package (Python). Changes in gene expression were analysed using DESeq2 normalization method of variance stabilizing transformation (VST), to be used primarily for visualisation. Genes with an adjusted p-value < 0.05 and an absolute Log2fold > 0 between groups were considered significant.
Assembly: GRCm38
Supplementary files format and content: Processed data file is in txt format and contains VST normalised gene counts

source_name: derived from healthy prostate (lox sites)

extract_protocol:
Organoid and tumoroid lines were grown in ECM domes for 7 days. Lysis buffer (Qiagen KIT) was added directly to wells to collect the cells. Cells/buffer were vortexed for 10sec and incubated on ice for 5min before transferring to -80°C. RNA was extracted from all samples on the same day using Qiagen RNeasy Kit # 74104. 80ng/µl RNA was used for the construction of sequencing libraries.
Libraries were constructed using Lexogen’s QuantSeq 3' mRNA-Seq Library Prep Kit FWD V2. cDNA libraries were sequenced with an Illumina NextSeq 2000 platform

value: tumoroid

value: cancer cell


title: SF3B1-WT RUNX1-edited replicate 1

description:
Library name: Sample 3
12RC3
5F_NormCounts.csv


title: A26


title: CBN 1.0 μM, biological rep1


title: Pten_P53 KO in vitro tumoroid, biol rep 3

description: Library name: 1091_24

value: derived from healthy prostate (lox sites)


title: d6NC_RNA-3

description: Library name: iMT_d6NC_RNA-3

value: MEFs


title: Pten_P53 KO in vitro tumoroid, biol rep 1

description: Library name: 1091_22


title: CBN 1.0 μM, biological rep2


title: d8NC_RNA-3

description: Library name: iMT_d8NC_RNA-3


title: d6NC_RNA-1

description: Library name: iMT_d6NC_RNA-1


title: C15

value: Primary CD4+ T Cells


title: d6_RNA-3

description: Library name: iMT_d6_RNA-3


title: CBN 0.5 μM, biological rep1

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 0.5 μM

source_name: iPSC-derived hepatocytes exposed to CBNa at 0.5 μM

value: hepatocyte


title: Pten_Stat3 KO in vitro tumoroid, biol rep 2

description: Library name: 1091_20


title: C14


title: CBN 0.5 μM, biological rep2


title: d6_RNA-2

description: Library name: iMT_d6_RNA-2


title: CBN 0.1 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 0.1 μM

source_name: iPSC-derived hepatocytes exposed to CBNa at 0.1 μM


title: Pten_Stat3 KO in vitro tumoroid, biol rep 1

description: Library name: 1091_19


title: A25


title: Pten KO in vitro tumoroid, biol rep 3

description: Library name: 1091_18

value: Ptenlox/loxCre


title: CBN 0.5 μM, biological rep3


title: CBN 0.1 μM, biological rep2


title: d6_RNA-1

description: Library name: iMT_d6_RNA-1


title: B42


title: A24


title: d4NC_RNA-3

description: Library name: iMT_d4NC_RNA-3


title: CBN 0.1 μM, biological rep1


title: D13


title: Pten KO in vitro tumoroid, biol rep 2

description: Library name: 1091_17


title: d4NC_RNA-1

description: Library name: iMT_d4NC_RNA-1


title: d4_RNA-3

description: Library name: iMT_d4_RNA-3


title: Pten_Stat3 KO in vitro tumoroid, biol rep 3

description: Library name: 1091_21


title: d4_RNA-2

description: Library name: iMT_d4_RNA-2


title: D11


title: CBN 0.0 μM (control), biological rep2

description: Gene expression data from iPSC-derived hepatocytes exposed to CBN at 0.0 μM (control)

source_name: iPSC-derived hepatocytes exposed to CBNa at 0.0 μM (control)


title: WT in vitro organoid, biol rep 2

description: Library name: 1091_14

value: organoid

value: epithelial cell

value: Ptenlox/loxStat3lox/loxCreCut (WT)


title: D10


title: CBN 0.0 μM (control), biological rep1


title: CBN 0.0 μM (control), biological rep3


title: d4_RNA-1

description: Library name: iMT_d4_RNA-1


title: WT in vitro organoid, biol rep 1

description: Library name: 1091_13

value: Ptenlox/loxCreCut (WT)


title: d35NC_RNA-3

description: Library name: iMT_d35NC_RNA-3

value: no treatment


title: Pten KO in vitro tumoroid, biol rep 1

description: Library name: 1091_16


title: CBC 40 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 40 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 40 μM

treatment_protocol: Cells cultured at day 6 after seeding were exposed to CBC at varying concentrations (0.1-40 µM) in triplicate for 24 h.


title: d35NC_RNA-1

description: Library name: iMT_d35NC_RNA-1


title: C13

value: obese children without asthma


title: Pten_P53 KO in vivo tumoroid, biol rep 3

description: Library name: 1091_12

source_name: derived from PCa tumour

value: derived from PCa tumour


title: C10


title: d35_RNA-4

description: Library name: iMT_d35_RNA-4


title: WT in vitro organoid, biol rep 3

description: Library name: 1091_15

value: Ptenlox/loxP53lox/loxCreCut (WT)


title: B39

value: obese children with asthma


title: D08

value: healthy weight children without asthma


title: CBC 40 μM, biological rep1


title: Pten_P53 KO in vivo tumoroid, biol rep 2

description: Library name: 1091_11

value: tumoroid


title: Pten_P53 KO in vivo tumoroid, biol rep 1

description: Library name: 1091_10

value: cancer cell


title: CBC 20 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 20 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 20 μM


title: d35_RNA-3

description: Library name: iMT_d35_RNA-3


title: B38


title: Pten_Stat3 KO in vivo tumoroid, biol rep 3

description: Library name: 1091_09


title: CBC 40 μM, biological rep2


title: B41


title: D07


title: d35_RNA-1

description: Library name: iMT_d35_RNA-1


title: d35_RNA-2

description: Library name: iMT_d35_RNA-2


title: CBC 10 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 10 μM

source_name: iPSC-derived hepatocytes exposed to CBCs at 10 μM


title: d2NC_RNA-3

description: Library name: iMT_d2NC_RNA-3


title: B37


title: Pten_Stat3 KO in vivo tumoroid, biol rep 1

description: Library name: 1091_07


title: d2NC_RNA-1

description: Library name: iMT_d2NC_RNA-1


title: Pten KO in vivo tumoroid, biol rep 3

description: Library name: 1091_06

value: Ptenlox/loxPbCre


title: Pten KO in vivo tumoroid, biol rep 1

description: Library name: 1091_04


title: D06


title: Pten KO in vivo tumoroid, biol rep 2

description: Library name: 1091_05


title: D05


title: B36


title: d28NC_RNA-3

description: Library name: iMT_d28NC_RNA-3

value: MEFs


title: d28NC_RNA-1

description: Library name: iMT_d28NC_RNA-1


title: Pten_Stat3 KO in vivo tumoroid, biol rep 2

description: Library name: 1091_08


title: d28_RNA-4

description: Library name: iMT_d28_RNA-4


title: CBC 5.0 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 5.0 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 5.0 μM


title: WT in vivo organoid, biol rep 2

description: Library name: 1091_02

value: derived from healthy prostate (lox sites)

value: Ptenlox/lox (WT)


title: CBC 20 μM, biological rep1

value: hepatocyte


title: CBC 5.0 μM, biological rep1


title: CBC 10 μM, biological rep1


title: d28_RNA-3

description: Library name: iMT_d28_RNA-3


title: CBC 20 μM, biological rep2


title: B20

value: Primary CD4+ T Cells


title: CBC 10 μM, biological rep2


title: CBC 1.0 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 1.0 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 1.0 μM


title: WT in vivo organoid, biol rep 3

description: Library name: 1091_03

value: organoid

value: epithelial cell

value: Ptenlox/loxStat3loxlox (WT)


title: WT in vivo organoid, biol rep 1

description: Library name: 1091_01


title: d28_RNA-2

description: Library name: iMT_d28_RNA-2


title: CBC 1.0 μM, biological rep2


title: B19


title: d28_RNA-1

description: Library name: iMT_d28_RNA-1


title: B18


title: F75_RNA_SEQ_genes

city: Springfield

first: Shannon

last: Kinney

state: MA

address: 1215 Wilbraham Road Center for Sciences and Pharmacy

department: Pharmaceutical and Administrative Sciences

institute: Western New England University

data_processing:
Resulting indexed libraries were sequenced by the UNMC Sequencing Core Facility using an Illumina NextSeq 500 Genome Analyzer.
Adaptor sequences and low quality (Phred score < 20) ends were trimmed from sequences using Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Resulting fastq files were aligned to the mouse genome (GRCm38-MM10) using the software TopHat (v2.0.8).
The software Cufflinks (v2.1.1) was used to estimate the expression values, and Cuffdiff (v2.1.1) was used to determine differential gene expression.
Assembly: GRCm38-MM10
Supplementary files format and content: Gene based FPKM values with the following column format: tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status, Gene_Exp_Level

source_name: F75 TRAMP Mouse Prostate Tumor

extract_protocol:
All prostate and tumor tissues were microdissected at necropsy, flash frozen in liquid nitrogen, and stored at -80°C
Total RNA was purified from TRAMP tumor samples that were also evaluated through hMeDIP-seq as there was sufficient tissue for both DNA and RNA extraction from the tumors.
To obtain sufficient total RNA for normal mouse prostate RNA-seq analysis, only RNA or DNA could be extracted from a single normal mouse prostate due to their small size.
All total RNAs were extracted using TRI Reagent according to the manufacturer's instructions.
Purity and concentration were assessed by measurement of the A260/280 ratios using a Nanodrop intrument and potential degradation was assessed by analysis with Advanced Analytical Technical Instruments Fragment Analyzer.
Libraries were developed using TruSeq V2 RNA sequencing library kit from Illumina following recommended procedures.
Libraries were sequenced with the Illumina NextSeq 500 Sequencer.

treatment_protocol:
Normal prostate samples were obtained from adult f1 males generated by crosses of C57BL/6 and FVB strain mice.
TRAMP prostate tissues were obtained from 24-28 week old f1 Probasin-SV40 transgene heterozygous males generated by crosses of C57BL/6 TRAMP males (homozygous for the transgene) with wildtype FVB females.

value: TRAMP Tumor

value: C57BL/6:FVB TRAMP SV40 L Tag

tag: Stage

value: Late Stage 24 Weeks

value: TRAMP SV40 Tag, Rat probasin Promoter

value: Tumor


title: CBC 1.0 μM, biological rep1


title: F15_RNA_SEQ_genes

source_name: F15 TRAMP Mouse Prostate Tumor

tag: tissue


title: C09

data_processing:
FastQC run to determine quality of samples
Trim Galore used to trim adaptor/low quality sequences
Trimmed reads were aligned to GRCh38/hg38 genome and read counts extracted using STAR alignment software
Read counts of the two different runs for each sample were added together (L001 and L002)
Normalization was performed using DESeq R package
Assembly: hg38
Supplementary files format and content: a single comma-separated value file containing normalized counts for all samples

extract_protocol:
Zymo RNA Extraction Kit
Kapa stranded mRNA kit and Kap mRNA Hyper prep

value: obese children without asthma


title: A10

value: healthy weight children


title: SM513_RNA_SEQ_genes

source_name: SM513 Normal Mouse Prostate

value: Normal Mouse Prostate

value: Adult Male 22 Weeks

value: WT

tag: treatment

value: Normal


title: A09

source_name: Primary CD4+ T Cells


title: CBC 5.0 μM, biological rep2


title: CBC 0.5 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 0.5 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 0.5 μM


title: d21NC_RNA-1

description: Library name: iMT_d21NC_RNA-1

source_name: MEFs

value: MEFs

value: no treatment


title: CBC 0.5 μM, biological rep2

value: hepatocyte


title: SM512_RNA_SEQ_genes

source_name: SM512 Normal Mouse Prostate


title: CBC 0.5 μM, biological rep1


title: B17

value: obese children with asthma

value: Primary CD4+ T Cells


title: d21_RNA-2

description: Library name: iMT_d21_RNA-2


title: d16_ATAC-1

description: Library name: iMT_d16_ATAC-1


title: d21NC_RNA-3

description: Library name: iMT_d21NC_RNA-3


title: d21_RNA-3

description: Library name: iMT_d21_RNA-3


title: abl_AR2

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to human reference genome GRCh38 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes  ENSEMBL id  and FPKM values for each gene, in each sample

source_name: LNCap-abl cell

extract_protocol:
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate; derived from LNCaP cells grown in the absence of androgens

tag: sirna

value: siAR

tag: growth condition

value: 10% CSS RPMI


title: B14


title: B16


title: abl_AR3


title: d21_RNA-1

description: Library name: iMT_d21_RNA-1


title: B13


title: d2_RNA-2

description: Library name: iMT_d2_RNA-2


title: A07


title: abl_63

value: siGUGUUUGC (seed)


title: B12


title: abl_AR1


title: d2_RNA-1

description: Library name: iMT_d2_RNA-1


title: CBC 0.1 μM, biological rep3

description: Gene expression data from iPSC-derived hepatocytes exposed to CBC at 0.1 μM

source_name: iPSC-derived hepatocytes exposed to CBCa at 0.1 μM


title: CBC 0.1 μM, biological rep1