title: ABERABLASTpoolTissuecDNA_biol rep 2

description: Targeted sequencing of cDNA from engineered differentiated skeletal muscle tissues from ABERA-edited myoblasts with DMD exon 44 deleted

data_processing:
RNA STAR Alignment
"--clip3pNbases" set to 100
GRCh38
Excel sheet containing splice junction data sorted by figure number


title: GFP-biol rep 1

status: Public on Jul 20 2023

type: SRA

city: Urbana

first: Michael

last: Gapinske

state: IL

address: 1406 W Green Street

department: BIOE

country: USA

institute: University of Illinois at Urbana-Champaign

description: Targeted sequencing of DMD exon 45 from transfected HEK293T cells

library_source: genomic

data_processing:
CRISPResso2
Reads with average phred scores below 30 were removed, and remaining reads were aligned to the expected amplicon sequences.
GRCh38
Excel sheet containing editing data sorted by figure number
txt file containing allele frequencies

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing and allele frequency

extract_protocol:
QIAgen DNeasy DNA extraction
Nextera XT Amplicon Library
OTHER: Amplicon Sequencing

tag: cell line

tag: genotype

value: WT

tag: treatment

value: plasmid transfection


title: 9G_M_336

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 9G_M_334


title: ABERABLASTpoolTissuecDNA_biol rep 3

library_source: transcriptomic

molecule: polyA RNA

source_name: muscle

growth_protocol: Rneasy RNA extraction; qScript cDNA synthesis; amplicon sequencing with Nextera XT library consruction; MiSeq; RNA Star alignment and splice junction quantification

extract_protocol:
QIAgen RNeasy RNA extraction
Nextera XT Amplicon Library
OTHER: Amplicon Sequencing

tag: tissue

value: muscle

tag: cell type

value: myoblast

value: ABERA Lentivirus

tag: Sex

value: male


title: 9G_M_333


title: ABERABLASTpoolTissuecDNA_biol rep 1


title: 9G_M_346


title: 9G_M_348


title: 9G_M_344


title: ABERABLASTcloneTissuecDNA_biol rep 3


title: 9G_M_332


title: ABERABLASTcloneTissuecDNA_biol rep 2


title: ABERABLASTcloneTissuecDNA_biol rep 1


title: 9G_M_331


title: BE3-biol rep 1


title: FNLS-biol rep 1


title: 9G_M_339


title: 9G_M_330


title: 9G_M_328


title: AB1190wtTissuecDNA_biol rep 3

description: Targeted sequencing of cDNA from engineered differentiated skeletal muscle tissues from myoblasts

data_processing:
RNA STAR Alignment
GRCh38
Excel sheet containing splice junction data sorted by figure number


title: 9G_M_327


title: AB1190wtTissuecDNA_biol rep 1


title: AB1190del44TissuecDNA_biol rep 2

description: Targeted sequencing of cDNA from engineered differentiated skeletal muscle tissues from myoblasts with DMD exon 44 deleted


title: 9G_M_326


title: 9G_M_325


title: AB1190del44TissuecDNA_biol rep 1


title: MouseTibialisAnterior_DMD45_bio_rep5

description: Targeted sequencing of mouse Dmd exon 45 from mouse abdominal muscle after systemic injection of SplitDMDABE8e AAV

data_processing:
CRISPResso2
Reads with average phred scores below 30 were removed, and remaining reads were aligned to the expected amplicon sequences.
mm10
Excel sheet containing editing data sorted by figure number

source_name: tibialis anterior

growth_protocol: Tibialis Anterior isolation, DNeasy DNA extraction, amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: tibialis anterior

value: SplitDMDABE8e AAV injection


title: peri-gastruloid, day 11, rep1

city: Dallas

first: Jun

last: Wu

state: Texas

address: 5323 harry Hines Blvd.

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center

library_source: transcriptomic single cell

data_processing:
All processing was done with the 10X cellranger "count" function using cellranger 7.1.0. Default parameters were used.
Assembly: GRCh38-3.0.0
Supplementary files format and content: The filtered scRNA count matrix is in the .h5 file format, and contains all confidently mapped reads for all cells.

molecule: total RNA

extract_protocol:
Day 11 peri-gastruloids were isolated via filter straining and centifugation before digestion in TrypLE. The resulting cell suspension was filtered and washed before loading into a 10X chromium chip.
10X Library preparation according to 10X Genomics’ protocol of Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index). Illumnia NovaSeq 2000 (138 max bps P2) with 10X Genomics Single cell 3' v3

value: embryonic stem cell

value: peri-gastruloid formation protocol


title: MouseTibialisAnterior_DMD45_bio_rep2


title: 9G_M_323


title: MouseTibialisAnterior_DMD45_bio_rep3


title: MouseTibialisAnterior_DMD45_bio_rep1


title: MouseTibialisAnterior_DMD45_bio_rep4


title: 9G_M_324


title: eggd-1 null mutant sequencing replicate 2

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Adapter trimming and quality assessment using TrimGalore and FASTQC.
Processed raw fastqs were aligned to genome with STAR and mapped to transposons with Salmon.
Reads were assigned to genomic features using FeatureCounts. Bam files were converted to BigWig files using DeepTools BamCoverage.
Downstream analysis was preformed using R/Python/IGV. Notably DESEQ2 was used for normalization and differential gene expression analysis.
Assembly: Wormbase WS279
Supplementary files format and content: Tab Delimmited Counts Matrix (Unnormalized)
Supplementary files format and content: BigWig Coverage File

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 celcius on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached adulthood.

extract_protocol:
Approximately 50,000 synchronized adult worms were collected with M9 using a glass Pasteur pipette. The worms were washed once with M9, rocked in fresh M9 for 5 min, washed once in ddH2O, and resuspended suspended in 1ml of TRI Reagent (Sigma). Worms were lysed using the Bead Mill 24 homogenizer (Thermo Fisher Scientific) and the lysate was transferred to a clean tube 1.5 ml centrifuge tube. 0.1 volumes of bromochloropropane were added to the mix and shaken by hand for 30 seconds. The mixture was then centrifuged at 15,000g and the aqueous phase was transferred to a fresh 1.5 ml microcentrifuge tube, followed by the addition of 1 volume of isopropanol. The tube was incubated at -20 °C for 1 hour to precipitate RNA and centrifuged for 15 mins at 14,000rpm at 4°C. The supernatant removed by pipetting and the pellet was washed twice by adding 1 mL 75% ethanol. The pellet of RNA was allowed to dry for 3 minutes to remove remaining ethanol, dissolved in ddH2O and stored at -80°C.
Ribosomal RNAs were depleted using the RNase H method (Adiconis et al. Nature Methods 2013). 3 μg total RNA were incubated with antisense DNA oligonucleotides targeting C. elegans and E. coli ribosomal RNAs, then treated with Hybridase Thermostable RNase H (Biosearch Technologies) at 45°C for 30 minutes. The rRNA-depleted samples were treated with Turbo DNase (Thermo Fisher Scientific) at 37°C for 30 minutes. RNAs longer than 200 nts were enriched using RNA Clean & Concentrator-5 (Zymo Research). mRNA sequencing libraries were constructed using Ultra II Directional RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s instructions. The library samples with unique barcodes were pooled and sequenced at the Illumina HiSeq 4000 platform (PE 150bp).

value: whole animal


title: MouseHeart_DMD45_bio_rep5

source_name: heart

growth_protocol: Heart isolation, DNeasy DNA extraction, amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: heart


title: MouseHeart_DMD45_bio_rep4


title: 9G_M_329


title: 9G_M_322


title: 9G_M_321


title: AB1190wtTissuecDNA_biol rep 2


title: control sequencing replicate 2


title: MouseHeart_DMD45_bio_rep1


title: AB1190del44TissuecDNA_biol rep 3


title: MouseHeart_DMD45_bio_rep3


title: control sequencing replicate 1


title: eggd-1 null mutant sequencing replicate 1


title: 9G_M_320


title: MouseHeart_DMD45_bio_rep2


title: MouseDiaphragm_DMD45_bio_rep4

source_name: diaphragm

growth_protocol: Diaphragm isolation, DNeasy DNA extraction, amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: diaphragm


title: MouseDiaphragm_DMD45_bio_rep3


title: 9G_M_319


title: MouseDiaphragm_DMD45_bio_rep1


title: 9G_M_190


title: MouseAbdominalMuscle_DMD45_bio_rep5

source_name: abdominal muscle

growth_protocol: Abdominal muscle isolation, DNeasy DNA extraction, amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: abdominal muscle


title: 9G_M_189


title: MouseAbdominalMuscle_DMD45_bio_rep4


title: 9G_M_188


title: MouseAbdominalMuscle_DMD45_bio_rep2


title: MouseAbdominalMuscle_DMD45_bio_rep1


title: genomic DNA from NC63

type: genomic

city: Jinan

first: Tiantian

last: Wang

state: 请选择

address: Beiyuan

country: China

institute: The Second Hospital of Shandong University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
The matrix_processed.txt contains Average Beta data

label: Cy5 and Cy3

source_name: normal PBMCs sample

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: cell  type

value: PBMCs

tag: disease state

value: normal


title: genomic DNA from NC65


title: genomic DNA from NC59


title: genomic DNA from NC58


title: genomic DNA from NC61


title: genomic DNA from NC62


title: genomic DNA from NC57


title: MouseTibialisAnterior_Rosa_bio_rep3

description: Targeted sequencing of mouse Dmd exon 45 from mouse abdominal muscle after systemic injection of control AAV

value: Control AAV injection


title: MouseTibialisAnterior_Rosa_bio_rep1


title: MouseTibialisAnterior_Rosa_bio_rep4


title: 9G_M_186


title: genomic DNA from NC56


title: MouseTibialisAnterior_Rosa_bio_rep2


title: 9G_M_185


title: MouseHeart_Rosa_bio_rep3


title: MouseHeart_Rosa_bio_rep4


title: MouseDiaphragm_DMD45_bio_rep2


title: genomic DNA from NC55


title: 9G_M_184


title: MouseHeart_Rosa_bio_rep1


title: MouseAbdominalMuscle_DMD45_bio_rep3


title: MouseDiaphragm_DMD45_bio_rep5


title: 9G_M_183


title: MouseDiaphragm_Rosa_bio_rep4


title: genomic DNA from NC54


title: MouseDiaphragm_Rosa_bio_rep3


title: 9G_M_187


title: 9G_M_182


title: MouseDiaphragm_Rosa_bio_rep2


title: 9G_M_181


title: MouseAbdominalMuscle_Rosa_bio_rep4


title: MouseDiaphragm_Rosa_bio_rep1


title: genomic DNA from NC50


title: genomic DNA from NC53


title: genomic DNA from NC49


title: MouseAbdominalMuscle_Rosa_bio_rep2


title: D45HamE-ABE8etrunc_biol rep 4

description: Targeted sequencing of mouse Dmd exon 45 from experimental AAV-injected male mouse biceps femoris

source_name: biceps femoris

growth_protocol: Biceps femoris isolation; nucleus extraction; GFP+ Nuclei enrichment; DNeasy DNA extraction; amplicon sequencing with Nextera XT library consruction; MiSeq; CRISPResso2 alignment and quantification of base editing

value: biceps femoris


title: MouseAbdominalMuscle_Rosa_bio_rep3


title: MouseAbdominalMuscle_Rosa_bio_rep1


title: 9G_M_180


title: D45HamE-ABE8etrunc_biol rep 2


title: 9G_M_179


title: D45HamE-ABE8etrunc_biol rep 3


title: genomic DNA from NC47


title: MouseHeart_Rosa_bio_rep2


title: 9G_M_178


title: 9G_M_177


title: D45HamE-Rosa_biol rep 4

description: Targeted sequencing of mouse Dmd exon 45 from control AAV-injected male mouse biceps femoris


title: D45HamE-Rosa_biol rep 3


title: genomic DNA from NC46


title: D45HamE-Rosa_biol rep 2


title: genomic DNA from NC45


title: 9G_M_176


title: 9G_M_175


title: genomic DNA from NC52


title: genomic DNA from NC44


title: Bulk ATAC-seq LOAD Caudate

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

institute: Stanford University

description: Bulk ATAC-seq LOAD Caudate

data_processing:
The count normalized peak matrix was derived using featureCount.
Assembly: HG38

source_name: brain

extract_protocol:
Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP.
Transposed fragments were purified and amplified as described previously (Buenrostro et al., Nature Methods 2015) with slight modification. Briefly, transposed fragments were pre-amplified for 3 cycles. Concentration of pre-amplified fragments was determined by qPCR and this concentration was used to estimate the total number of cycles required to obtain 160 femtomoles of fragments. A second PCR was performed to amplify the pre-amplified fragments for the desired number of cycles. Final libraries were again purified. Prior to sequencing, libraries were pooled and run on a 6% PAGE gel and excess primers and primer dimers below 125 bp were removed.

value: brain


title: Bulk ATAC-seq LOAD Hippocampus

description: Bulk ATAC-seq LOAD Hippocampus


title: genomic DNA from NC43


title: genomic DNA from NC42


title: 9G_M_173


title: 9G_M_174


title: Bulk ATAC-seq Control Middle Temporal Gyri


title: 9G_M_172


title: D45HamE-ABE8etrunc_biol rep 1


title: genomic DNA from NC41


title: 9G_M_171


title: Bulk ATAC-seq Control Hippocampus

description: Bulk ATAC-seq Control Hippocampus


title: Bulk ATAC-seq Control Caudate

description: Bulk ATAC-seq Control Caudate


title: genomic DNA from NC34


title: Patinet 9 PDAC

city: Tübingen

first: MENGJIE

last: QIU

address: Otfried-Müller-Str. 37

country: Germany

institute: M3 Forschungszentrum für Malignom, Metabolom und Mikrobiom

data_processing:
Sequencing was performed on an Illumina HiSeq 4000.
De-multiplexing and barcode processing were performed using the Cell Ranger Software Suite (Version 4.0.0). Specifically, the reads were aligned to the human hg19 using CellRanger v4.0.0. Finally, a gene-barcode matrix containing the cell barcodes and gene expression counts for each individual sample was generated by counting the single-cell 3’ UMIs.
The gene barcode matrix was then imported to Seurat v3 in R (v4.0.2). Data were filtered to include cells with at least 100 genes and no more than 25% mitochondrial genes. Then, the data was normalized, scaled and integrated within Seurat v3 to remove batch effects across samples.
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample; A gene expression matrix, a document of barcodes and a document of all features are included for each sample.

source_name: Human Pancreatic Biopsy

growth_protocol: Pancreatic tumor tissues were immediately processed, Single cells were isolated, quantified and stored in FBS+20%DMSO till further processing.

extract_protocol:
The tissue was minced and processed as per instructions from the m manufacturers of Miltenyi tumor dissociation kit ( 130-095-929).  Tissue was digested for around 30 minutes, after which the digestion was stopped with RPMI supplemented with 20%FBS. The cell suspension was passed through 70um cell strainer to remove any debris and centrifuged at 500g for 10min to collect cell pellet. The cells were extensively washed with RPM1, counted, resuspended in FBS+20% DMSO and stored in multiple aliquots till further processing.
Library generation was performed according to manufactor´s protocol (Chromium Next EM Single Cell 3`GEM, 10000128)

treatment_protocol: Human Pancreatic tissue samples were collected from treatmnet naïve patinets.

tag: pathology

value: PDAC

value: Pancreatic

value: CD45+ Single cells from Pancreas


title: 9G_M_170


title: genomic DNA from NC32


title: Liver_normal_rep3

type: RNA

city: Tokyo

first: Kotaro

last: Soeda

address: 1-21-1 toyama, shinjuku-ku

department: Department of Molecular Diabetic Medicine

country: Japan

institute: National Center for Global Health and Medicine

hyb_protocol: Cyanine-3 (Cy3) labeled cRNA was hybridized by Gene Expression Hybridization Kit (Agilent) according to the manufacturer’s instructions. After hybridization, microarrays were washed with Gene Expression Wash Buffers Pack following the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on SureScan Microarray Scanner (G2600D, Agilent).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent).

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.

extract_protocol: Tissue Total RNA Mini Kit (FAVORGEN)

tag: model

value: Liver

value: male


title: genomic DNA from NC31


title: 9G_M_169


title: Bulk ATAC-seq LOAD Middle Temporal Gyri

description: Bulk ATAC-seq LOAD Middle Temporal Gyri


title: 9G_M_168


title: Patinet 9 Adjacent Normal Tissue

value: Adjacent Normal Tissue


title: Patinet 8 PDAC


title: D45HamE-Rosa_biol rep 1


title: 9G_M_167


title: genomic DNA from NC27


title: genomic DNA from NC30


title: Liver_normal_rep1


title: Patinet 8 Adjacent Normal Tissue


title: 9G_M_166


title: Patinet 7 PDAC


title: Liver_insulin_treatment_STAM_rep3

value: STAM

value: insulin


title: Liver_insulin_treatment_STAM_rep2


title: 9G_M_165


title: Patinet 7 Adjacent Normal Tissue


title: genomic DNA from NC24


title: HCA2 cells, senescent-3

city: Minato ku

first: Satotaka

last: Omori

state: tokyo

address: shirokanedai, 4-6-1

institute: the university of Tokyo

data_processing:
The libraries were sequenced on a Ion Proton System platform
The sequencing reads were aligned to the hg19/GRCh37 reference human genome using Bowtie2 (v2.0.0) and STAR (v2.3.0).
Data normalization and differential expression analysis were performed using a edgeR package  in the R language (v3.2.2).
Genome_build: hg19
Supplementary_files_format_and_content: Transcriptome among young and senescent fibroblasts.xlsx

source_name: HCA2 (MJ90)

growth_protocol: Cells were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Rneasy mini kit (Qiagen)  according to the manufacturer’s instructions.
Ion Total RNA-Seq kit v2 (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: RO3306 (9 uM) + Nulin3a (5 uM)

value: HCA2 (MJ90)

value: skin fibroblast

tag: cell condition

value: RO3306+Nutlin3a treatment

tag: phenotype

value: senescent


title: genomic DNA from NC26

value: Female

value: PBMCs


title: Liver_normal_rep2

value: normal


title: Liver_non_treatment_STAM_rep2


title: Liver_insulin_treatment_STAM_rep1


title: genomic DNA from NC23


title: 9G_M_164


title: Patinet 6 PDAC


title: Liver_non_treatment_STAM_rep1


title: genomic DNA from NC14


title: 9G_M_163


title: genomic DNA from BC97

source_name: BC PBMCs sample

value: BC


title: Patinet 6 Adjacent Normal Tissue


title: 9G_M_162


title: HCA2 cells, senescent-1


title: Patinet 5 PDAC


title: HCA2 cells, young (uninduced)-3

value: low passage

value: young (uninduced)


title: HCA2 cells, young (uninduced)-2


title: genomic DNA from BC92


title: genomic DNA from BC87


title: 9G_M_160


title: 9G_M_161


title: HCA2 cells, young (uninduced)-1


title: Patinet 4 PDAC

value: PDAC

value: Pancreatic


title: Patinet 5 Adjacent Normal Tissue

value: CD45+ Single cells from Pancreas


title: genomic DNA from BC83


title: Liver_non_treatment_STAM_rep3

value: Liver

value: male


title: genomic DNA from BC82


title: HCA2 cells, senescent-2


title: Patinet 4 Adjacent Normal Tissue

value: Adjacent Normal Tissue


title: Patinet 3 PDAC


title: 9G_M_158


title: HEK293T, ERCC spike-in mix, pooling of 10 indexed cells,CEL-seq2

city: Bethesda

last: Lyu

state: Maryland

address: 37 Convent Drive

department: Laboratory of Biochemistry and Molecular Biology

institute: National cancer institute

description: AGACTC,AGCTTC,CATGAG,CAGATC,TCACAG,GTCTAG,GTTGCA,GTGACA,ACTCGA,TGCAGA; the first 5 encode ERCC

data_processing:
sequencing data were converted to fastq file by bcl2fastq v2.20
Data were mapped and quantified by zUMIs v.2.9.7
Assembly: GRCh38
Supplementary files format and content: matrix files in csv format

extract_protocol:
Single cells were flow-sorted into 96-well plates with 2 µl lysis buffer in each well, containing 0.1% Triton X-100, 2 nM LAST-seq primer, 0.1 U/µl Rnase Inhibitor, 0.5 mM dNTP, 60 pg RNA carriers, and the RNA spike-in. The plate was then sealed with aluminum films (MilliporeSigma), briefly spun down, and lysed at 65°C for 5 min before keeping on ice.
Single cells were sorted into 96-well plates containing lysis buffer, followed by 65°C heating and 30min vacuum evaporation.  RNase H and DNA pol mixture were added to each well, followed by quick shaking, centrifuge, and 30min incubation at 37°C. The reaction buffer in each well was pooled and purified by RNA cleanup beads. The beads were rehydrated by IVT reaction buffer and incubated at 37°C up to 16 hrs. The resultant product was purified by RNA cleanup beads and was converted to cDNA by reverse transcription. Then, the cDNA was amplified by primers containing P5/P7 adaptors and purified by DNA cleanup beads. The resultant product was enriched by PCR and subjected to illumina sequencing.
LAST-seq, Cel-seq2 and SMART-seq V4 kit


title: 9G_M_159


title: 9G_M_157


title: Patinet 3 Adjacent Normal Tissue


title: hSCG_diseased3

city: Munich

first: Karin

middle: A.

last: Ziegler

address: Biedersteiner Str. 29

institute: Technical University of Munich

description: Illumina TruSeq Stranded mRNA

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
RNA STAR (in Galaxy) with default parameters for alignment
StringTie (in Galaxy) was used for transcript assembly and quantification
Assembly: DESeq2 (in Galaxy) for differential expression analysis and normalizing the counts
Supplementary files format and content: GRCh38, Gencode annotation v34
Supplementary files format and content: Excel files include gene abundance values for each sample

source_name: sympathetic ganglion

extract_protocol:
Total RNA was isolated using RNeasy midi-prep kit (Qiagen). The integrity and quantity of RNA was determined using Agilent TapeStation 4200.
Libraries were prepared from 1 µg RNA using Illumina TruSeq Stranded mRNA kit.

value: sympathetic ganglion

value: heart disease


title: genomic DNA from BC78


title: genomic DNA from BC79


title: Patinet 2 PDAC


title: 9G_M_156


title: genomic DNA from BC77


title: hSCG_diseased2

description: Illumina TruSeq Stranded mRNA


title: 9G_M_155


title: hSCG_healthy3

description: Illumina TruSeq Stranded mRNA

value: heart healthy


title: hSCG_diseased1

description: Illumina TruSeq Stranded mRNA


title: genomic DNA from BC73


title: Patinet 2 Adjacent Normal Tissue


title: Patinet 1 PDAC


title: Patinet 1 Adjacent Normal Tissue


title: 9G_M_154


title: hSCG_healthy1

description: Illumina TruSeq Stranded mRNA


title: 9G_M_151


title: genomic DNA from BC64


title: genomic DNA from BC65


title: eHAP1, SCC4KO, pooling of 80 indexed cells for two batches, LAST-seq

description:
eHAP1_SCC4KO
barcode sequences were deposited at https://github.com/lyuj2022/LAST-seq


title: 9G_M_153


title: Soman_14d_1/2LD50_rep2

city: Beijing

first: Zhenpeng

last: Zhang

address: 38 Life Science Park Road

institute: Beijing Proteome Research Center

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The mice were housed in a room with maintained temperature of 21-25°C with 12 h light-dark cycles.

extract_protocol:
RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: Mice were administered soman subcutaneously at 1/10, 1/5 or 1/2 of the 50% lethal dose and were sampled at 1, 3, 7 and 14 days.

value: brain

value: treated with 1/2LD50 soman for 14 day


title: Soman_14d_1/2LD50_rep3


title: 9G_M_149


title: 9G_M_150


title: genomic DNA from BC63

value: Female


title: 9G_M_148


title: eHAP1, pooling of 80 indexed  cells for two batches, LAST-seq

description:
eHAP1_WT
barcode sequences were deposited at https://github.com/lyuj2022/LAST-seq


title: genomic DNA from BC59

value: PBMCs


title: 9G_M_147


title: HEK293T, single cell lysate, ERCC spike-in mix SMART-seq V4

description:
SMARTseqonlysateERCC
library prepared using NEBNext Ultra II DNA Kits


title: genomic DNA from BC60


title: HEK293T, single cell, SMART-seq V4

description:
SMARTseqonHEK293
library prepared using NEBNext Ultra II DNA Kits


title: Soman_14d_1/5LD50_rep1

value: treated with 1/5LD50 soman for 14 day


title: genomic DNA from BC57

value: BC


title: HEK293T, single cell lysate, A60 spike-in mix SMART-seq V4

description:
SMARTseqonlysateA60
library prepared using NEBNext Ultra II DNA Kits


title: genomic DNA from BC55


title: Soman_14d_1/10LD50_rep3

value: treated with 1/10LD50 soman for 14 day


title: Soman_14d_1/5LD50_rep2


title: hSCG_healthy2

description: Illumina TruSeq Stranded mRNA


title: HEK293T, ERCC and A60 spike-in mix, pooling of 10 indexed cells,CEL-seq2

description:
CELseq2onHEK293ERCCandA60
AGACTC,AGCTTC,CATGAG,CAGATC,TCACAG,GTCTAG,GTTGCA,GTGACA,ACTCGA,TGCAGA


title: 9G_M_144


title: Soman_14d_1/5LD50_rep3


title: HEK293T, pooling of 10 indexed cell lysate, CEL-seq2

description:
CELseq2onlysate
AGACTC,AGCTTC,CATGAG,CAGATC,TCACAG,GTCTAG,GTTGCA,GTGACA,ACTCGA,TGCAGA; the first 5 encode ERCC and the last 5 encode A60


title: 9G_M_145


title: HEK293T lysate, A60 spike-in mix, pooling of 10 indexed  cell lysates, LAST-seq

description:
LASTseqonlysateA60
GTATCC,CATTGG,GGAGAA,CGAAGA,TCCAGA,ATCCAG,TTGCTG,ACTGTC,TCGACT,CAGTCT


title: Soman_14d_1/2LD50_rep1


title: genomic DNA from BC61


title: genomic DNA from BC53


title: 15 pg total RNA, pooling of 10 indexed samples, LAST-seq

description:
LASTseqonRNA
GTATCC,CATTGG,GGAGAA,CGAAGA,TCCAGA,ATCCAG,TTGCTG,ACTGTC,TCGACT,CAGTCT


title: 9G_M_146


title: 9G_M_142


title: genomic DNA from BC54


title: HEK293T, A60 spike-in mix, pooling of 10 indexed cells, LAST-seq

description:
LASTseqonHEK293A60
GTATCC,CATTGG,GGAGAA,CGAAGA,TCCAGA,ATCCAG,TTGCTG,ACTGTC,TCGACT,CAGTCT


title: genomic DNA from BC46


title: A549, shUBR52, DEX_48h, rep2

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

institute: Dana Farber Cancer Institute

description:
A549_ECs.csv
A549_Meta.csv
A549_SizeFactors.csv

data_processing:
Alignment/gene quantification: Sequenced reads were aligned within cell-type to the hg38 reference genome using RSEM (v1.3.3) which internally called STAR (v2.7.5b). As part of the RSEM call, aligned reads are quantified as the expected number of sequenced transcripts or "expected counts" (ECs).
Normalization: Sample-specific size-factors are computed within cell-type by the method of median-ratio as described in DESeq.
Assembly: hg38
Supplementary files format and content: Processed *ECs.csv files contain the "expected count" transcript quantification output of RSEM.
Supplementary files format and content: Processed *Meta.csv files contain metadata relating to the columns of the count matrices.
Supplementary files format and content: Processed *SizeFactors.csv files contain sample-specific normalization size-factors. Normalized ECs can be derived by dividing the columns in the appropriate *ECs.csv file by the corresponding size-factor.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were sent to Novogene (NB4s) or prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols (A549s)

value: Lung Epithelium

value: UBR5 knockdown 2

value: Dexamethasone

tag: time


title: 9G_M_143


title: Soman_14d_1/10LD50_rep2


title: Soman_14d_1/10LD50_rep1


title: genomic DNA from BC42


title: Soman_7d_1/2LD50_rep3

value: treated with 1/2LD50 soman for 7 day


title: Soman_7d_1/5LD50_rep1

value: treated with 1/5LD50 soman for 7 day


title: genomic DNA from BC50


title: Soman_7d_1/5LD50_rep3


title: 9G_M_136


title: A549, shUBR52, DEX_48h, rep1

tag: cell line


title: genomic DNA from BC51


title: Soman_7d_1/10LD50_rep2

value: treated with 1/10LD50 soman for 7 day


title: HEK293T, ERCC spike-in mix, pooling of 10 indexed cells, LAST-seq

description:
LASTseqonHEK293ERCC
GTATCC,CATTGG,GGAGAA,CGAAGA,TCCAGA,ATCCAG,TTGCTG,ACTGTC,TCGACT,CAGTCT


title: 9G_M_141


title: 9G_M_135


title: genomic DNA from BC34


title: Soman_7d_1/10LD50_rep1


title: Soman_7d_1/2LD50_rep2


title: Soman_3d_1/2LD50_rep3

value: treated with 1/2LD50 soman for 3 day


title: genomic DNA from BC49


title: Soman_7d_1/2LD50_rep1


title: 9G_M_132


title: A549, shUBR52, DMSO, rep1

tag: genotype

value: DMSO


title: genomic DNA from BC35


title: Soman_3d_1/2LD50_rep2

tag: treatment


title: 9G_M_131

tag: brain region


title: 9G_M_138

tag: age


title: genomic DNA from BC45


title: Soman_7d_1/5LD50_rep2


title: A549, shUBR52, DEX_24h, rep2


title: 9G_M_133

tag: strain


title: 9G_M_139


title: 9G_M_140


title: 9G_M_137


title: A549, shUBR52, DEX_24h, rep1


title: genomic DNA from BC39


title: genomic DNA from BC31


title: A549, shUBR52, DMSO, rep2


title: Soman_7d_1/10LD50_rep3

tag: tissue


title: 9G_M_134


title: A549, shUBR51, DEX_48h, rep2

tag: cell type

value: UBR5 knockdown 1


title: genomic DNA from BC33


title: A549, shUBR51, DMSO, rep2


title: A549, shUBR51, DEX_48h, rep1


title: genomic DNA from BC32


title: 9G_M_129


title: A549, shUBR51, DEX_24h, rep2


title: Soman_3d_1/5LD50_rep2

value: treated with 1/5LD50 soman for 3 day


title: Soman_3d_1/2LD50_rep1

value: brain


title: Soman_3d_1/5LD50_rep1


title: 9G_M_130


title: Soman_3d_1/5LD50_rep3


title: A549, shUBR51, DEX_24h, rep1


title: genomic DNA from BC24


title: genomic DNA from BC22


title: Soman_3d_1/10LD50_rep2

value: treated with 1/10LD50 soman for 3 day


title: A549, shControl2, DEX_24h, rep2

value: Luciferase knockdown 2


title: TAC_42d_4

description: Illumina Stranded mRNA prep

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
RNA STAR (in Galaxy) with default parameters for alignment
StringTie (in Galaxy) was used for transcript assembly and quantification
Assembly: DESeq2 (in Galaxy) for differential expression analysis and normalizing the counts
Supplementary files format and content: GRCm38 vM21
Supplementary files format and content: Excel files include gene abundance values for each sample

source_name: Pineal gland

extract_protocol:
Total RNA from SCGs was isolated using RNeasy mini-prep kit (Qiagen). Total RNA from pineal glands was isolated using TRIzol according to manufacturer’s instructions (Thermo Fisher Scientific). The integrity and quantity of RNA was determined using Agilent TapeStation 4200.
Libraries were prepared from ≥ 20 ng RNA using Illumina TruSeq Stranded mRNA kit for SCG libraries and Illumina Stranded mRNA prep for pineal gland libraries.

value: Pineal gland

tag: Sex

value: male

value: heart disease


title: genomic DNA from BC20

tag: gender

value: Female

value: PBMCs

value: BC


title: genomic DNA from BC28

tag: cell  type


title: A549, shUBR51, DMSO, rep1

value: Lung Epithelium


title: genomic DNA from BC27

tag: disease state


title: A549, shControl2, DEX_48h, rep2

value: Dexamethasone


title: 9G_M_128


title: A549, shControl2, DEX_48h, rep1


title: A549, shControl2, DEX_24h, rep1


title: Soman_3d_1/10LD50_rep1


title: genomic DNA from BC26


title: Soman_3d_1/10LD50_rep3


title: TAC_42d_3

description: Illumina Stranded mRNA prep


title: genomic DNA from BC17


title: Soman_1d_1/2LD50_rep1

value: treated with 1/2LD50 soman for 1 day


title: Soman_1d_1/2LD50_rep3


title: genomic DNA from BC18


title: A549, shControl2, DMSO, rep2


title: A549, shControl1, DEX_48h, rep1

value: Luciferase knockdown 1


title: Sham_2

description: Illumina Stranded mRNA prep

value: heart healthy


title: genomic DNA from BC13


title: A549, shControl1, DEX_48h, rep2


title: A549, shControl2, DMSO, rep1

value: DMSO


title: Soman_1d_1/5LD50_rep3

value: treated with 1/5LD50 soman for 1 day


title: TAC_42d_1

description: Illumina Stranded mRNA prep


title: A549, shControl1, DEX_24h, rep2


title: genomic DNA from BC16


title: Soman_1d_1/2LD50_rep2


title: Sham_3

description: Illumina Stranded mRNA prep


title: genomic DNA from BC8


title: genomic DNA from BC14


title: alphaTC1 cell line treated with DMSO rep3

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
NovaSeq Control Software (NCS) 1.8.0 was used for sequencing instrument control and raw data acquisition.
The basecalling was peromrd on instrument with Real-Time Analysis Software (RTA) 3.4.5.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.14 package DESeq2 1.34.0, running under R 4.1.3.
Assembly: UCSC mm10 based on GRCm38
Supplementary files format and content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: alphaTC1 mouse glucagonoma cell line

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

value: alphaTC1 mouse glucagonoma cell line

value: glucagonoma


title: alphaTC1 cell line treated with DMSO rep2


title: genomic DNA from BC12


title: genomic DNA from BC6


title: A549, Input, UBR5-matched, DEX24, rep1

description:
A549_ChIP_UBR5_dex_peaks.bed
A549_MergedPeakList.bed
A549_NormPeakFragments.csv
A549_PeakMetaData.csv

data_processing:
Alignment/filtering: Sequenced reads were aligned to the hg38 reference genome with the STAR (v2.7.5b) algorithm. Aligned reads were filtered with samtools (v1.10) to reomve those entirely contained within the Encode GRCh38 exclusion regions (ENCFF356LFX), duplicate aligned reads, and aligned reads with fragment length (TLEN) greater than 1000 BP.
Replicate merging: To facilitate concition-specific peak calling, aligned reads across multiple replicates (where applicable) were merged with the larger sample down-sampled to the fragment count of the smaller.
Peak calling: Peaks were called from merged reads using MACS2 (v2.2.7.1). Peaks were merged across conditions to facilitate cross-condition testing first by taking a fragment-length region centered on the summit of any discovered peak and second by merging any such "trimmed" peaks which overlap.
Normalization/peak quantification: Sample-specific scale vectors are calculated by binning aligned fragments, filtering to remove low-binding regions, and running a version of the median-ratio method described in DESeq. Normalized peak count matrices were constructed by counting fragments with centers contained in merged peak regions and scaled by sample-specific scale-factors.
Assembly: hg38
Supplementary files format and content: Processed *.bw files contain genome-wide signal tracks of aligned and filtered fragments, normalized by scaling with the sample-specific scale-factor.
Supplementary files format and content: Processed *.narrowPeak/*peaks.bed files contain sample-specific peaks as called by MACS2.
Supplementary files format and content: Processed *MergedPeakList.bed files contain trimmed peak regions merged across those discovered in sample-specific testing.
Supplementary files format and content: Processed *NormPeakFragments.csv files contain normalized fragment counts corresponding to each cell-type-specific merged peak.
Supplementary files format and content: Processed *PeakMetaData.csv files contain metadata on the columns of the normalized fragment counts for each cell-type.

extract_protocol:
Cells were fixed with DSG for 30 minutes and 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the ThruPLEX DNA-Seq Kit (Takara) with DNA Single Index Kit for barcodes (Takara).Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: chip antibody


title: A549, shControl1, DMSO, rep1


title: Soman_1d_1/5LD50_rep1

value: brain


title: A549, shControl1, DEX_24h, rep1


title: Soman_1d_1/5LD50_rep2


title: genomic DNA from BC5


title: Soman_1d_1/10LD50_rep1

value: treated with 1/10LD50 soman for 1 day


title: Soman_0_rep2

value: treated with saline


title: alphaTC1 cell line treated with G786-1089 rep2


title: Soman_1d_1/10LD50_rep2


title: genomic DNA from BC4


title: alphaTC1 cell line treated with G786-1089 rep3


title: A549, shControl1, DMSO, rep2


title: Soman_0_rep3


title: A549, Input, UBR5-matched, DEX15, rep1

description:
A549_ChIP_UBR5_DEX15_peaks.bed
A549_MergedPeakList.bed
A549_NormPeakFragments.csv
A549_PeakMetaData.csv


title: genomic DNA from BC3


title: Soman_1d_1/10LD50_rep3


title: A549, Input, UBR5-matched, DMSO, rep1

description:
A549_ChIP_UBR5_DMSO_peaks.bed
A549_MergedPeakList.bed
A549_NormPeakFragments.csv
A549_PeakMetaData.csv


title: alphaTC1 cell line treated with DMSO rep1


title: BM_LK_Expt2_STM2457_2

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG36834

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v6.0.1 .
Assembly: mm10

source_name: Bone marrow

growth_protocol: Mice were kept in standard germ-free conditions  and according to UK Home Office regulations.

extract_protocol:
Murine bone marrow cells were collected from the femora, tibiae and ilia. Red cells were lysed with ammonium chloride STEMCELL Technologies, Vancouver, Canada) and haematopoietic progenitors enriched using the EasySepTM Mouse Hematopoietic Progenitor Cell Enrichment Kit (STEMCELL Technologies).  Cells were stained with fluorophore conjugated antibodies c-Kit APC-Cy7 (Biolegend, clone 2B8, 1/200), CD150 PE-Cy7 (Biolegend, clone TC15-12F12.2 1/200), CD48 APC (eBioscience, clone HM48-1, 1/200), EPCR PE (STEMCELL Technologies, clone RMEPCR1560, 1/400), Sca1 BV421 (Biolegend, clone D7, 1/100). The EasySepTM Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies) and BV510 streptavidin (Biolegend) was used to stain lineage-positive cells. Dead cells were excluded using 7-aminoactinomycin D (Thermo Fisher Scientific). An aliquot of non-lineage- depleted cells was retained for unstained and single-stain controls. Cells were analysed and sorted on an Influx sorter (BD Biosciences); 20,000 Lineage-negative, c-kit +cells per mouse were sorted into PBS + 2% FCS for scRNA-seq analysis
Cells were processed according to manufacturer’s protocol using Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 reagents.

treatment_protocol: 50mg STM2457 or Vehicle was administered intraperitoneally once daily for 14 days.

value: 6-10 weeks

value: F

value: Bone marrow

value: Lineage negative kit positive

value: WT

value: STM2457 50mg/kg IP OD 14 days


title: Soman_0_rep1


title: A549, Input, GR-matched, DEX24, rep1

description:
A549_ChIP_NR3C1_dex_peaks.bed
A549_MergedPeakList.bed
A549_NormPeakFragments.csv
A549_PeakMetaData.csv

value: Lung Epithelium


title: genomic DNA from BC7

value: Female

value: PBMCs

value: BC


title: BM_LK_Expt2_Vehicle_2

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG36832

value: DMSO 50mg/kg IP OD 14 days


title: genomic DNA from BC2


title: A549, Input, GR-matched, DEX15, rep1

description:
A549_ChIP_NR3C1_DEX15_peaks.bed
A549_MergedPeakList.bed
A549_NormPeakFragments.csv
A549_PeakMetaData.csv


title: alphaTC1 cell line treated with G786-1089 rep1


title: BM_LK_Expt1_Vehicle_2

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG35070


title: BM_LK_Expt2_Vehicle_1

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG36831


title: Tregs,Vehicle,rep3

city: Atlanta

first: Qian

last: Xu

state: GA

address: 101 Woodruff Circle

institute: Emory University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 100-400ng of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Spleen

value: Tregs

value: vehicle


title: Tregs,Vehicle,rep2


title: A549, Input, GR-matched, DMSO, rep1

description:
A549_ChIP_NR3C1_DMSO_peaks.bed
A549_MergedPeakList.bed
A549_NormPeakFragments.csv
A549_PeakMetaData.csv

value: DMSO


title: JCML2_scRNA

city: Guangzhou

first: Meiling

last: Yang

address: No. 106, Zhongshan Road,Yuexiu District

institute: Guangdong Provincial People’s Hospital（Guangdong Academy of Medical Sciences）

description: 10x Genomics

data_processing:
Raw data were processed using Cell Ranger (v3.0.2) to align reads, generate feature-barcode matrices, and perform gene expression analysis. We used the mkfastq pipelines to make fastq files and used the cell count pipelines for alignment (with reference genome Hg19), filtering, barcode counting, and UMI counting.
Assembly: hg19
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every single cell in the specific patients (barcodes.tsv, features.tsv, matrix.mtx).

source_name: advanced colon cancer

extract_protocol:
Fresh tumor biopsy tissues from an advanced colon cancer patient were transferred to the tube with digestive enzyme from Tumor Dissociation Kit (Cat# 130-095-929, Miltenyi Biotec) and incubated at 37 ℃ for 30 min on a shaker. After digestion, 2% FBS was added to neutralize enzyme lysate, and the tissues were filtered through a 70 μm filter. Subsequently, the samples were centrifuged at 350 × g for 5 min and the supernatants were discarded. To remove red blood cells, the cell pellets were suspended in red blood cell lysis buffer (Beyotime) for 30 s. The solution was then centrifuged at 350 × g for 5 min and resuspended in Dulbecco’s phosphate-buffered saline (DPBS; Thermo Fisher). The samples were stained with trypan blue (Solarbio) and the cellular viability was evaluated. Finally, single cells were encapsulated into emulsion droplets using the Chromium Controller (10× Genomics).
The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit (10x Genomics).

value: advanced colon cancer

value: FOLFOX-bevacizumab


title: Tregs,Vehicle,rep1


title: JCML1_scRNA

description: 10x Genomics

value: naive


title: BM_LK_Expt2_STM2457_1

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG36833

value: 6-10 weeks

value: F


title: A549, UBR5, DEX24, rep1

value: UBR5 (CST, D6O8Z)


title: BM_LK_Expt1_STM2457_1

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG35069

value: Bone marrow

value: Lineage negative kit positive

value: WT


title: EndoC-BH5 + cytokine replicate 2

city: Paris

first: Philippe

last: Ravassard

address: ICM 47 bd de l'hopital

country: France

institute: Paris Brain Institute

data_processing:
Raw read FASTQ files were processed using the opensource BIOWDL RNAseq pipeline v5.0.0 (https://zenodo.org/record/5109461#.Ya2yLFPMJhE) developed at the LUMC
Adapter clipping was performed using Cutadapt (v2.10) with default settings
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome
The read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=yes”.
The gene annotation used for quantification was Ensembl version 104. Additional data quality controls were performed using fastqc (v0.11.9), Picard (v2.23.2) and MultiQC (v1.9).
Assembly: hg38
Supplementary files format and content: Differential expression table results with cpm gene counts

source_name: endocrine pancreas

extract_protocol:
For cytokine treatment RNA was extracted using Nucleospin miRNA Kit (Bioke).
For cytokine treatment libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: endocrine pancreas

value: Pancreatic beta cell

value: Interfero gamma + IL1b


title: EndoC-BH5 + cytokine replicate 3


title: Tregs,DT-061,rep2


title: BM_LK_Expt1_Vehicle_1

description:
10X Chromium 3' v 3
GEO_submission_adata.h5ad
RBG35068

value: DMSO 50mg/kg IP OD 14 days


title: Tregs,DT-061,rep1

value: Spleen


title: YKTH (YAP1 KO TAZ Heterozygote) [LM250]

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

institute: University of Pittsburgh School of Medicine

description: LM250_1 (GE) - TPM

data_processing:
Samples were sequenced by llumina Novaseq 6000 with paired-end 150bp reads, with 20 million reads per end per sample, by Novogene Inc. Base-calling was performed by Novogene Inc. with the latest Illumina software. They also trimmed adapters, removed reads containing N > 10%, and removed reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
CLC Genomics Workbench 20.0.3 was used to align reads to the transcriptome (GRCm38), perform log2-transform and TMM normalization, and analyze differential expression using edgeR to calculate TPM values.
Assembly: GRCm38
Supplementary files format and content: For comparison of YAP KO TAZ Heterozygote to WT (C57BL6-FVB mixed background): Tab-delimited text file containing TPM values for each gene by sample, and log-fold change and FDR p-value after comparing gene expression
Supplementary files format and content: For comparison of YAP KO to WT (C57BL6 background): Tab-delimited text file containing TPM values for each gene by sample, and log-fold change and FDR p-value after comparing gene expression

source_name: liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen and stored at -80C. RNA was harvested using Trizol reagent and purified with Qiagen RNeasy Mini Prep kit (Cat.No. 74104). DNA was digested using Qiagen RNase-free DNase Set (Cat.No 79254).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

value: liver

value: female

value: YAP1 KO TAZ Heterozygote

value: mixed C57BL/6-FVB


title: A549, GR, DEX15, rep1

value: Lung Epithelium

value: GR (Diagenode, C15200010; Santa Cruz Biotechnology, sc-393232X)


title: EndoC-BH5 + cytokine replicate 1


title: YKTH (YAP1 KO TAZ Heterozygote) [LM251]

description: LM251_1 (GE) - TPM


title: EndoC-BH5 + vehicle replicate 2

value: vehicle


title: Tregs,DT-061,rep3

value: Tregs


title: A549, UBR5, DMSO, rep1

value: UBR5 (CST, D6O8Z)

value: DMSO


title: A549, GR, DMSO, rep1


title: EndoC-BH5 + vehicle replicate 3


title: A549, UBR5, DEX15, rep1


title: A549, GR, DEX24, rep1


title: WT (mixed C57BL/6-FVB background) [LM227]

description: LM227_1 (GE) - TPM

value: Wild type


title: TAC_18d_3

description: Illumina TruSeq Stranded mRNA

source_name: Sympathetic ganglion

value: Sympathetic ganglion

value: male

value: heart disease


title: WT (mixed C57BL/6-FVB background) [LM230]

description: LM230_1 (GE) - TPM


title: TAC_18d_2

description: Illumina TruSeq Stranded mRNA


title: WT (mixed C57BL/6-FVB background) [LM226]

description: LM226_1 (GE) - TPM


title: NB4, Input, ATRA, rep2

description:
NB4_ChIP_RARA_ATRA_10uM_24h_peaks.narrowPeak
NB4_MergedPeakList.bed
NB4_NormPeakFragments.csv
NB4_PeakMetaData.csv

value: Acute Promyelyctic Leukemia

value: ATRA


title: EndoC-BH5 + vehicle replicate 1

value: endocrine pancreas

value: Pancreatic beta cell

value: WT


title: EndoC-BH5 Batch 5

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on hg38 reference genome and quantification with gencode v39 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: Matrix table with cpm and tpm gene counts for every gene and sample EndoC-BH1 and BH5

extract_protocol:
For comaparison of EndoC-BH1 and BH5, total RNA was extracted using  the RNeasy Micro Kit 50 (Qiagen).
For comaparison of EndoC-BH1 and BH5, sequencing libraries were prepared using KAPA mRNA hyperprep from (ROCHE).


title: NB4, Input, ATRA, rep1


title: EndoC-BH5 Batch 4


title: YKTH (YAP1 KO TAZ Heterozygote) [LM225]

description: LM225_1 (GE) - TPM

value: liver

value: female

value: YAP1 KO TAZ Heterozygote


title: NB4, Input, DMSO, rep2

description:
NB4_ChIP_RARA_DMSO_0h_peaks.narrowPeak
NB4_MergedPeakList.bed
NB4_NormPeakFragments.csv
NB4_PeakMetaData.csv


title: TAC_18d_1

description: Illumina TruSeq Stranded mRNA


title: Control_4

description: Illumina TruSeq Stranded mRNA

value: heart healthy


title: EndoC-BH5 Batch 3


title: NB4, Input, DMSO, rep1


title: WT (C57BL/6 background) [LM192]

description: LM192_1 (GE) - TPM


title: WT (C57BL/6 background) [LM193]

description: LM193_1 (GE) - TPM


title: NB4, UBR5, ATRA, rep2

description:
NB4_ChIP_UBR5_ATRA_10uM_24h_peaks.narrowPeak
NB4_MergedPeakList.bed
NB4_NormPeakFragments.csv
NB4_PeakMetaData.csv


title: EndoC-BH5 Batch 2


title: YAP1 KO [LM191]

description: LM191_1 (GE) - TPM

value: YAP1 KO


title: Control_3

description: Illumina TruSeq Stranded mRNA


title: EndoC-BH5 Batch 1


title: Control_2

description: Illumina TruSeq Stranded mRNA


title: NB4, UBR5, ATRA, rep1


title: Control_1

description: Illumina TruSeq Stranded mRNA


title: EndoC-BH1 Batch 5


title: EndoC-BH1 Batch 4


title: NB4, UBR5, DMSO, rep2

description:
NB4_ChIP_UBR5_DMSO_0h_peaks.narrowPeak
NB4_MergedPeakList.bed
NB4_NormPeakFragments.csv
NB4_PeakMetaData.csv


title: YAP1 KO [LM189]

description: LM189_1 (GE) - TPM


title: bTSC_2_WGBSseq

city: Gainesville

first: Zongliang

last: Jiang

state: Florida

address: 2033 Mowry Rd, Cancer & Genetics Research Bldg, Room 303

department: Dept. of Animal Sciences

institute: University of Florida

data_processing:
WGBS raw data were removed first 12-bp at the 5’ end of both pairs, and reads with adapters and low-quality bases by using TrimGalore-0.4.3. The trimmed sequences were mapped to the bovine genome (ARS-UCD1.2) using Bismark. Uniquely mapped reads were then removed PCR duplicated reads and non-converted reads using deduplicate_bismark and filter_non_conversion. For avoiding the sequencing bias, only reads with 10x coverage was used in the downstream analysis. Methylation of each CpG site was calculated and methylation DNA methylation of each sample was calculated by averaging the consecutive genomic window of 300-bp tiles’ methylation. Differentially methylated regions (DMRs) were defined as common 300-bp tiles between two compared groups, which methylation levels ≥ 75% in one group, while ≤25% in another, and were significantly different by Fisher’s exact test (P-value ≤ 0.05, FDR ≤ 0.05). Hyper- and hypo-methylated tiles were those with DNA methylation levels ≥ 75% and ≤25%, respectively. …. The gene ontology and pathway analysis were performed by means of the David tool
Assembly: ARS-UCD1.2
Supplementary files format and content: CpG

organism: Bos taurus

source_name: Embryonic cells

extract_protocol: Not provided

value: trophoblast stem cells (TSCs)


title: bTSC_1_WGBSseq


title: NB4, UBR5, DMSO, rep1

value: UBR5 (CST, D6O8Z)


title: EndoC-BH1 Batch 3


title: WT (C57BL/6 background) [LM75]

description: LM75_1 (GE) - TPM


title: NB4, RARA, ATRA, rep2

value: RARA (Diagenode, C15310155)


title: D7_TE_3_WGBSseq

value: trophectoderm (TE)

tag: timepoint


title: EndoC-BH1 Batch 2


title: NB4, RARA, ATRA, rep1


title: KL-31, WT, Female, RoomAir

city: Philadelphia

first: Abiud

last: Cantu

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Neonatology

institute: Children's Hospital of Philadelphia

data_processing:
Quantification was performed using Salmon 1.9.0
Assembly: mm10
Supplementary files format and content: quant.tar includes Salmon output files.

source_name: Lung

extract_protocol:
Total RNA from frozen lung samples was isolated using the Zymo micro kit  (Zymo Research, Irvine, CA). Sample concentration was assayed using Nanodrop-8000 (Thermo Scientific, Wilmington, DE), and quality checks were done using the NanoDrop spectrophotometer and the Agilent Bioanalyzer.
RNA QC was done using AATI or Agilent 2100. Libraries were created using the NEBNext Ultra™ II RNA Library Prep Kit. Briefly, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Lung

value: PND 21

value: Mixed

value: Room Air

value: Female


title: KL-47, WT, Female, RoomAir


title: EndoC-BH1 Batch 1

value: endocrine pancreas


title: D7_TE_1_WGBSseq


title: C4-2 CSS 3

city: Hachioji

first: Shoko

last: Nishihara

state: Tokyo

address: 1-236 Tangi-machi

department: Graduate School of Engineering

institute: Soka University

data_processing:
Illumina bcl2fastq2-v2.20 software was used to demultiplex data and convert BCL files from Novaseq6000 systems running RTA versions v3.4.4 to standard FASTQ file formats for downstream analysis.
To remove the reads derived from ribosomal RNA (rRNA), the reads were aligned to rRNA sequence obtained from Ensembl by bowtie (v2.2.4).
The remaining reads were aligned to the reference human genome with the guide of RefSeq transcript model by STAR (v2.6.0a).
Read count was performed using featureCounts (v1.6.2). TPM values of each gene was calculated as a gene expression value.
Assembly: hg38
Supplementary files format and content: xlsx includes TPM values for each sample

growth_protocol: For hormone-dependent growth, cells were maintained in RPMI medium (Gibco) containing 10% FBS (Gibco) and 1% penicillin/streptomycin (Invitrogen). For hormone-independent growth, 10% CSS (Invitrogen) was use instead of FBS.

extract_protocol:
RNA was purified using a RNeasy Mini Kit with an RNase-free DNase Set (QIAGEN), according to the supplier’s manual.
The libraries were prepared using TruSeq Stranded mRNA Prep Kit (Illumina), according to the supplier's manual.

value: Prostate cancer

value: CSS


title: C4-2 CSS 2


title: NB4, RARA, DMSO, rep1

value: Acute Promyelyctic Leukemia

value: DMSO


title: KL-42, WT, Male, RoomAir

value: WT

value: Male


title: KL-30, WT, Female, RoomAir


title: Human Pancreatic Biopsy 8

data_processing:
Reference genomes (GRCh37) were constructed and gene expression values were extracted by using the 10x Genomics Space Ranger 1.3.0 software. For the removal of ambient RNA, SpotClean(31) was utilized. The R package Seurat v.4.0.1 was used for normalization by negative binomial regression, dimensionality reduction by Uniform Manifold Approximation and Projection (UMAP), and clustering of the data by a shared nearest neighbor modularity optimization based on the Louvain algorithm(54). Cell type annotations were performed manually and by using the databases Human Primary and Blueprint Encode in SingleR(55).
Assembly: GRCh37
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample; A gene expression matrix, a document of barcodes and a document of all features are included for each sample.

source_name: Pancrease

growth_protocol: Tissue slices approximately 10um in size were cut from fresh frozen OCT embedded tissue sections and placed on the Visium slide.

extract_protocol:
RNA  was isolated as per the instructions described in the 10X Genomics Spatial protocols with permeabilization time of around 24 minutes
Dual indexed library was prepared as per manufacturesrs instructions

treatment_protocol: Fresh tissue sections without any treatment were used for the generation of sptaial library

tag: pathology

value: PDAC

value: Pancreatic


title: D14_TE_2_WGBSseq


title: D14_TE_3_WGBSseq


title: YAP1 KO [LM74]

description: LM74_1 (GE) - TPM

value: liver

value: female

value: YAP1 KO


title: KL-41, WT, Male, RoomAir

value: Lung


title: D14_TE_1_WGBSseq

value: trophectoderm (TE)


title: Human Pancreatic Biopsy 7


title: KL-29, WT, Male, RoomAir

value: PND 21

value: Mixed


title: Human Pancreatic Biopsy 6


title: C4-2 FBS 2

value: FBS


title: NB4, RARA, DMSO, rep2

value: RARA (Diagenode, C15310155)


title: KL-28, WT, Male, RoomAir

value: Room Air


title: D7_TE_2_WGBSseq


title: C4-2 FBS 1

value: Prostate cancer


title: Human Pancreatic Biopsy 5


title: Human Pancreatic Biopsy 4


title: TE-2-RNA-seq

data_processing:
The Salmon tool was applied to quantify the gene expression profile from the raw sequencing data, by using the Ensembl bovine genome annotation (ARS-UCD1.2). Transcript per million reads (TPM) was used as the unit of gene expression. The edgeR tool was applied to identify differentially expressed genes. The TMM algorithm implemented in the edgeR package was used to perform normalization of the read counts and estimation of the effective library sizes. Differential expression analysis was performed by the likelihood ratio test implemented in the edgeR package. Principal component analysis (PCA) on the gene expression profile was performed by using the “dudi.pca” function within the package “ade4”. All the heatmaps were plotted by the “heatmap.2” function within the package “gplots”. The gene ontology and pathway analysis were performed by means of the David tool.
Assembly: ARS-UCD1.2
Supplementary files format and content: gene count

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared using Smart-seq2 v4 Kit following manufacturer's protocols.


title: KL-52, WT, Female, Oxygen

value: Hyperoxia

value: Female


title: NB4, shUBR52, ATRA_48h, rep2

description:
NB4_ECs.csv
NB4_Meta.csv
NB4_SizeFactors.csv

value: Acute Promyelocytic Leukemia

value: UBR5 knockdown 2

value: ATRA


title: Human Pancreatic Biopsy 3

value: PDAC

value: Pancreatic


title: bTSC-2-RNA-seq

value: trophoblast stem cells (TSCs)


title: C4-2 CSS 1

value: CSS


title: NB4, shUBR52, ATRA_48h, rep1


title: KL-38, WT, Female, Oxygen

value: Lung

value: WT


title: bTSC-1-RNA-seq


title: TE-3-RNA-seq

value: trophectoderm (TE)


title: C4-2 FBS 3


title: Human Pancreatic Biopsy 1


title: NB4, shUBR52, ATRA_24h, rep2


title: KL-48, WT, Female, RoomAir

value: PND 21

value: Mixed


title: BNCD6-2-RNA-seq

value: differentiated trophoblast stem cells (TSCs)


title: BNCD6-1-RNA-seq


title: KL-36, WT, Female, Oxygen


title: KL-51, WT, Male, Oxygen

value: Male


title: NB4, shUBR52, ATRA_24h, rep1


title: NB4, shUBR52, ATRA_8h, rep2


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70T]

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Genome_build: GenBank database under accession number JRVD00000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Penicillium oxalicum

source_name: Mycelium

growth_protocol: Fresh spores of the MuKu70 or MuPOX00158 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with % (w/v) Avicel, and incubated in a shaker at 180 rpm and 28°C for 24 h.

extract_protocol:
Total RNA were extracted using TRIzol RNA Kit
A cDNA library with 100 bp of length was constructed using the extracted total RNA, and assessed with the ABI StepOnePlus Real-Time PCR System and the Agilent 2100 Bioanalyzer. The eligible cDNA library was sequenced via the Illumina HiSeq 4000 system


title: NB4, shUBR52, ATRA_8h, rep1


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70F]


title: TE-1-RNA-seq


title: BNCD5-2-RNA-seq


title: BNCD5-1-RNA-seq


title: NB4, shUBR52, DMSO, rep2

value: DMSO


title: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours [POXKu70S]


title: KL-34, WT, Male, Oxygen

value: Hyperoxia


title: Mycelium of 1 gram Mutant POX0158 were cultured in 1% Avicel liquid medium for 24 hours [MuPOX00158T]


title: KL-35, WT, Male, Oxygen


title: KL-39, WT, Male, Oxygen


title: Mycelium of 1 gram Mutant POX0158 were cultured in 1% Avicel liquid medium for 24 hours [MuPOX00158S]


title: Human Pancreatic Biopsy 2

city: Tübingen

last: QIU

address: Otfried-Müller-Str. 37

institute: M3 Forschungszentrum für Malignom, Metabolom und Mikrobiom


title: NB4, shUBR51, ATRA_48h, rep2

value: UBR5 knockdown 1


title: BNCD4-1-RNA-seq


title: BNCD4-2-RNA-seq


title: Mycelium of 1 gram Mutant POX0158 were cultured in 1% Avicel liquid medium for 24 hours [MuPOX00158F]


title: BNCD3-2-RNA-seq


title: NB4, shUBR51, ATRA_48h, rep1

value: Acute Promyelocytic Leukemia


title: KL-19, KO, Female, RoomAir

value: Gdf15 knockdown

value: Room Air

value: Female


title: BNCD3-1-RNA-seq


title: NB4, shUBR51, ATRA_24h, rep2

value: ATRA


title: KL-18, KO, Female, RoomAir


title: NB4, shUBR52, DMSO, rep1

value: UBR5 knockdown 2


title: BNCD2-2-RNA-seq


title: PAwt_sat2_S

city: shanghai

first: yujuw

last: wang

state: shanghai

address: 199 huanke road

institute: shanghaitech university

data_processing:
majorbio prokaryotic transcriptome sequencing platform
sequence reads were removed for adaptors sequence and low-quality reads by SeqPrep and Sickle.
The sequencing reads were mapped to the reference sequence by Burrows-Wheeler (NC_002516)
Total mapped unique reads were extracted and sorted using samtools.
DESeq2 was used to identify differential expression
Assembly: NC_002516
Supplementary files format and content: last 6 columns for sample-specific data is TPM

organism: Pseudomonas aeruginosa

extract_protocol:
P. aeruginosa PAO1 wild-type and rccR-deletion mutant strains were cultured in LB medium at 37℃ and harvested at the exponential phase and stationary phase, respectively. The total RNAs were extracted using the MiniBEST Universal RNA Extraction Kit (Takara).
The library was constructed using the TruSeqTM Stranded Total RNA Library Prep Kit for Illumina according to the manufacturer’s instruction.

tag: growth phase

value: stationary phase cell

value: bacterial cell


title: PAwt_log2_S

value: exponential phase cell

value: WT


title: KL-62, KO, Female, RoomAir

value: Lung

value: PND 21


title: BNCD2-1-RNA-seq

value: differentiated trophoblast stem cells (TSCs)


title: NB4, shUBR51, ATRA_8h, rep2

data_processing:
Alignment/gene quantification: Sequenced reads were aligned within cell-type to the hg38 reference genome using RSEM (v1.3.3) which internally called STAR (v2.7.5b). As part of the RSEM call, aligned reads are quantified as the expected number of sequenced transcripts or "expected counts" (ECs).
Normalization: Sample-specific size-factors are computed within cell-type by the method of median-ratio as described in DESeq.
Assembly: hg38
Supplementary files format and content: Processed *ECs.csv files contain the "expected count" transcript quantification output of RSEM.
Supplementary files format and content: Processed *Meta.csv files contain metadata relating to the columns of the count matrices.
Supplementary files format and content: Processed *SizeFactors.csv files contain sample-specific normalization size-factors. Normalized ECs can be derived by dividing the columns in the appropriate *ECs.csv file by the corresponding size-factor.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were sent to Novogene (NB4s) or prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols (A549s)

tag: time


title: KL-58, KO, Male, RoomAir

value: Mixed

value: Male


title: KL-57, KO, Male, RoomAir


title: KL-17, KO, Male, RoomAir


title: NB4, shUBR51, ATRA_24h, rep1

tag: cell line


title: PAwt_sat1_S

tag: genotype


title: KL-61, KO, Female, RoomAir

tag: treatment


title: BL-6-RNA-Seq

value: blastocyst (BL)


title: NB4, shUBR51, DMSO, rep1

value: UBR5 knockdown 1

value: DMSO


title: BL-1-RNA-Seq


title: BL-5-RNA-Seq


title: NB4, shUBR51, ATRA_8h, rep1

value: Acute Promyelocytic Leukemia


title: PAko_log2_S

value: RccR knockdown


title: NB4, shUBR51, DMSO, rep2


title: PAko_sat2_S


title: PAko_sat1_S


title: KL-54, KO, Female, Oxygen

value: Gdf15 knockdown

value: Hyperoxia

value: Female


title: NB4, shControl2, ATRA_48h, rep2

value: Luciferase knockdown 2

value: ATRA


title: PAko_log1_S

value: exponential phase cell

value: bacterial cell


title: sgNT_bulk

city: Dallas

first: Tao

last: Wang

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: WES

data_processing:
Exome-seq reads were aligned to the human reference genome (GRCh38) using BWA-MEM
Picard was used to add read group information and sambamba was used to mark PCR duplicates. The calculation of read coverage was performed after duplicate removal.
The GATK toolkit was used to perform base quality score recalibration and local realignment around Indels.
Various algorithms were used to call SNPs and Indels, including MuTect ,VarScan, Shimmer, SpeedSeq, Manta, and Strelka2  and mutation called by more than 3 of these algorithms was retained.
Annovar was used to annotate SNPs and Indels
Assembly: GRCh38
Library strategy: WES

source_name: Prostate

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 4 days.

extract_protocol: For RNAseq and WES samples: When treated with 10 µM enzalutamide, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum. For scRNAseq samples: When treated with 10 µM enzalutamide or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum for 5 days or 14 days.

value: Prostate

value: LNCaP/AR

value: prostate cancer cells

value: Vehicle DMSO


title: NB4, shControl2, ATRA_24h, rep2


title: KL-53, KO, Female, Oxygen

value: Lung

value: PND 21

value: Mixed


title: PAwt_log1_S

value: WT


title: NTSC2

description: WES


title: KL-16, KO, Male, RoomAir

value: Room Air

value: Male


title: NTSC3

description: WES


title: NTSC1

description: WES


title: KL-2, KO, Female, Oxygen

value: Gdf15 knockdown


title: KL-4, KO, Female, Oxygen

value: Hyperoxia


title: KL-56, KO, Male, Oxygen


title: NB4, shControl2, ATRA_24h, rep1

value: Acute Promyelocytic Leukemia


title: SKSC18

description: WES


title: NB4, shControl2, ATRA_8h, rep2

value: Luciferase knockdown 2


title: NB4, shControl2, DMSO, rep2

value: DMSO


title: KL-3, KO, Male, Oxygen


title: NB4, shControl2, ATRA_8h, rep1

value: ATRA


title: NB4, shControl2, DMSO, rep1


title: Embryonic hindbrain, rep 2

city: Takatsuki

first: Hisato

last: Kondoh

state: Osaka

address: 1-1 Murasaki-cho

institute: Biohistory Research Hall

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Data were processed using SUBIO software.

source_name: Embryonic tissue

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Exon Analysis protocol_Low Input Quick Amp WT labeling (Agilent Technology, V 6.5, 2010). Briefly, 140ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

growth_protocol: The basic culture medium: 50% DMEM/50% Neurobasal Medium, 0.004% BSA, 2 mM L-glutamine, and 0.5´ N-2 and 0.5´ B-27 supplements. Additions for different culture conditions: E, 20 ng/ml Activin A, 10 ng/ml FGF2, and 2 µM XAV939; X, 10 ng/ml EGF, 10 ng/ml FGF2, and 10 µM XAV939; K, 10 ng/ml EGF and 10 ng/ml FGF2; C, 10 ng/ml EGF, 10 ng/ml FGF2, and 2 µM CHIR99021.

extract_protocol: RNA extraction using TRIzol plus

treatment_protocol: Details of culture handling are reported in Nakamura et al. (to be submitted).

tag: developmental stage

value: E10.5, 5 embryos


title: NB4, shControl1, ATRA_48h, rep2

value: Luciferase knockdown 1


title: KL-55, KO, Male, Oxygen

tag: age


title: SKSC16

description: WES

value: Prostate

value: LNCaP/AR


title: SKSC17

description: WES

value: prostate cancer cells

value: Vehicle DMSO


title: ksp5

city: Tokyo

first: Kotaro

last: Soeda

address: 1-21-1 toyama, shinjuku-ku

institute: National Center for Global Health and Medicine

description: biol rep 5

data_processing:
CLC Genomics Workbench v20.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality score: NCBI/Sanger or Illumina Pipeline 1.8 or later)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include expression values for each Sample

source_name: intestinal epithelial insulin receptor knock-out STAM mice treated with insulin

extract_protocol:
Tissue Total RNA Mini Kit (FAVORGEN)
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Ileum

value: Vilin-Cre(+); InsR-flox

value: insulin treatment (+)


title: Embryonid cervical spinalcord, rep 2

tag: strain


title: NB4, shControl2, ATRA_48h, rep1


title: NB4, shControl1, ATRA_24h, rep2


title: Embryonic forebrain, rep 2


title: Embryonic midbrain, rep 2


title: NB4, shControl1, ATRA_48h, rep1


title: Embryonic midbrain, rep 1

value: E10.5, 6 embryos


title: KL-1, KO, Male, Oxygen

tag: tissue

value: Lung

value: PND 21

value: Mixed

value: Male


title: ksp6

description: biol rep 6


title: Embryonic hindbrain, rep 1


title: Embryonic forebrain, rep 1


title: NB4, shControl1, ATRA_8h, rep2

tag: cell type

value: Acute Promyelocytic Leukemia


title: ksp2

description: biol rep 2


title: SKSC10

description: WES


title: SKSC15

description: WES


title: Embryonid cervical spinalcord, rep 1


title: SKSC14

description: WES


title: ksp4

description: biol rep 4


title: csp6

description: biol rep 6

source_name: control genotype STAM mice (non-Cre; IR-floxd) treated with insulin

value: Vilin-Cre(-); InsR-flox


title: ksp3

description: biol rep 3


title: Neural stem cell line CN1, rep 1

source_name: Cell culture, condition C


title: NB4, shControl1, DMSO, rep1

value: DMSO


title: SKSC7

description: WES


title: SKSC11

description: WES


title: csp5

description: biol rep 5


title: NB4, shControl1, ATRA_24h, rep1

value: ATRA


title: SKSC12

description: WES


title: ksp1

description: biol rep 1


title: Neural stem cell line CN4, rep 2


title: NB4, shControl1, ATRA_8h, rep1

value: Luciferase knockdown 1


title: Neural stem cell line CN4, rep 1


title: SKSC9

description: WES

value: Prostate


title: SKSC6

description: WES

value: LNCaP/AR


title: SKSC8

description: WES

value: prostate cancer cells


title: SKSC5

description: WES

value: Vehicle DMSO


title: NB4, shControl1, DMSO, rep2


title: SKSC4

description: WES


title: Neural stem cell line KN1, rep 1

source_name: Cell culture, condition K


title: Neural stem cell line KN1, rep 2


title: shNT_Prolonged_Enz GEX_XL5

description:
shNT_Prolonged_Enz
scRNAseq

data_processing:
Bulk RNAseq:
Briefly, Agilent 2100 Bioanalyzer was used to determine the sample degradation level and only high-quality RNA is used (RIN Score 8 or higher). Sample concentration was determined by Qubit fluorometer before starting library preparation. TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina was used to prepare 4 mg DNase treated RNA. Before strand specific cDNA synthesis, poly-A RNA is purified and fragmented. cDNA is then a-tailed and ligated with indexed adapters. Samples are amplified by PCR and purified with Ampure XP beads after adapter ligation, following validation on the Agilent 2100 Bioanalyzer. Qubit is used to quantify samples before they were normalized and pooled. Then all samples were run as paired end read 150 nucleotides in length on the Illumina HiSeq 2500 using SBS v3 reagents. Alignment, quantification, and differential analysis were performed using the QBRC_BulkRnaSeqDE pipeline (https://github.com/QBRC/QBRC_BulkRnaSeqDE). Briefly, Alignment of reads to human reference genome (GRCh38) was done using (v2.7.2b) (Dobin et al., 2013)(Ref: 23104886). FeatureCounts (v1.6.4) (Liao, 2014 #607)[REF: 24227677] was then used gene count quantification.
WES:
Exome-seq reads were aligned to the human reference genome (GRCh38) using BWA-MEM
Picard was used to add read group information and sambamba was used to mark PCR duplicates. The calculation of read coverage was performed after duplicate removal.
The GATK toolkit was used to perform base quality score recalibration and local realignment around Indels.
Various algorithms were used to call SNPs and Indels, including MuTect ,VarScan, Shimmer, SpeedSeq, Manta, and Strelka2  and mutation called by more than 3 of these algorithms was retained.
Annovar was used to annotate SNPs and Indels
scRNAseq:
Single-cell gene expression libraries were generated according to the manufacturer’s instructions and single-cell expression sequencing was run on a NovaSeq 6000 (Novogene Co., Ltd). All the subsequent steps were performed following the standard manufacturer’s protocols. 10x scRNA-seq data was processed using the Cell Ranger software (5.0.0). We used the “mkfastq”, “count” and ‘aggr’ commands to process the 10x scRNA-seq output into one cell by gene expression count matrix, using default parameters.
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: HDF5 Feature Barcode Matrix Format

source_name: prostate cancer cells

extract_protocol:
For RNAseq samples: LNCaP/AR cells transduced with different shRNA constructs were treated with enzalutamide or vehicle for 6 days before the total RNA was extracted using Trizol. For scRNAseq samples: Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and cells were counted by Countess II FL automatic cell counter (Invitrogen) and cell viability was above 90%. The concentration of single cell suspensions was adjusted to 900-1100 cells/l. Cells were loaded between 10,000 and 17,000 cells/chip position using the Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V1 barcoding chemistry).
For RNAseq samples: RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA. For scRNAseq samples: Single-cell gene expression libraries were generated according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols.
For RNAseq samples: RNA-Seq. For scRNAseq samples: Single-cell RNA-seq were performed by the 10x Genomic single cell 5’library platform.

treatment_protocol: For RNAseq and WES samples: When treated with 10 µM enzalutamide, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum. For scRNAseq samples: When treated with 10 µM enzalutamide or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum for 5 days or 14 days.

value: enzalutamide 10uM for 14 days


title: KL-37, WT, Female, Oxygen

value: WT

value: Hyperoxia

tag: Sex

value: Female


title: Neural stem cell line KN3, rep 1


title: csp4

description: biol rep 4

value: Ileum

value: insulin treatment (+)


title: Neural stem cell line CN1, rep 2


title: shSYNCRIP_Prolonged_Enz GEX_XL6

description:
shSYNCRIP_Prolonged_Enz
scRNAseq


title: shSYNCRIP_Acute_Enz GEX_XL4

description:
shSYNCRIP_Acute_Enz
scRNAseq

value: enzalutamide 10uM for 5 days


title: csp1

description: biol rep 1


title: csp2

description: biol rep 2


title: SKSC2

description: WES


title: Neural stem cell line XN1, rep 2

source_name: Cell culture, condition X


title: shNT_Veh GEX_XL1

description:
shNT_Veh
scRNAseq


title: shSYNCRIP_Veh GEX_XL2

description:
shSYNCRIP_Veh
scRNAseq


title: shNT_Acute_Enz GEX_XL3

description:
shNT_Acute_Enz
scRNAseq


title: SKSC3

description: WES


title: Neural stem cell line KN3, rep 2


title: csp3

description: biol rep 3


title: shNT_Veh WES_NTFS3

description:
shNT_Veh
WES


title: csn4

description: biol rep 4

source_name: control genotype STAM mice (non-Cre; IR-floxd) without insulin treatment

value: insulin treatment (-)


title: Neural stem cell line XN1, rep 1


title: SREX14

description: WES

value: enzalutamide 10mg for 16 weeks


title: csn3

description: biol rep 3

value: Vilin-Cre(-); InsR-flox


title: SKSC1

description: WES


title: csn2

description: biol rep 2


title: SREX12

description: WES


title: Chap cells, differentiated 156 days-4

city: Cleveland

first: Ya

last: Chen

state: OH

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: Drop-seq

data_processing:
McCarroll laboratory Drop-seq protocol
Assembly: GRCh38

source_name: Skin

growth_protocol: iPSC cells were cultured on a feeder layer of iMEF cells in hES medium containing DMEM/F12 (Gibco:11330-032), 20% knockout serum replacement (Gibco:10828-028), 1% GlutaMAX (Gibco: 35050-061), 1% Non-essential AA (Gibco:11140-050). Prior to the experiment, ReleSR media (StemCell Technologies:5872) was used to remove iMEF cells, and the iPSC cells were then plated onto vitronectin-coated culture dish (Life Technology; A31804) and culture in E8 medium (Life Technology:A1517001) until they reached about 60% confluence

extract_protocol:
We followed the McCarroll laboratory Drop-seq protocol. We used barcoded beads (ChemGenes Corporation, Macosko-2011-10(V+)) suspended at 120000 beads/ml in drop-seq lysis buffer containing 200mM Tris pH 7.5, 6% Ficoll PM-400, 0.2% Sarkosyl, 20mM EDTA, 50mM DTT. We dissociated 4 libraries from Chap D55 organoids, 3 libraries from D80 organoids and 4 libraries from D156 organoids (3 organoids/library, repeated one batch), or one time point, D80 (2 libraries) from the other control line, into single-cell suspension using Papain kit (Worthington Biochemical Co. LK003153) (27), then suspended the cells in PBS with 0.01% BSA at 0.2x106 cells/ml. To generate droplets, we injected the cells, beads, and oil (Bio-Rad, 186-4006) at flow rates of 2ml/h, 2ml/h and 7.5ml/h, respectively, using syringe pumps.
After droplet generation, we broke the droplet, washed, and collected the beads. We subjected the beads to reverse transcription using TSO_RNA hybris primer, followed by exonuclease I digestion. The libraries were multiplexed and sequenced on HiSeqX PE150 (Medgenome) to generate ~200M total pair reads per library in gzip-compressed FASTQ files.

treatment_protocol: iPSC cells were plated at a density of 6x103 -1x104 cells per well of V-shape 96-well plate in CDM medium, which contained DMEM/F12 (Gibco:11330-032), 5mg/ml BSA (Sigma: A2153), 15µg/ml apo-transferrin (Sigma:T1147), 39nl/ml 1-thioglycerol (Sigma:M6145), and 7µg/ml insulin (Sigma: I2643). On the first day, half of the CDM medium was replaced with fresh medium containing 50ng/ml Fgf2 (GoldBio:1140-02-1000) and 10µM SB431542 (ED millopore:61646).  On day 7 of the differentiation protocol, fresh CDM medium containing 25ng/ml Fgf2 and 5µM SB431542 was added to the cells. On day 14, the organoids were transferred from the V-shape 96-well plate to a U-shape 96-well plate containing new CDM medium supplemented with 100ng/ml Fgf19 (R&D system:969-FG-025). On day 21, the culture medium was switched to CMM1 medium, which contained neurobasal medium (Thermo Fisher:21103049), N2 supplement (Thermo Fisher: 17502048), and 1% Penicillin- streptomycin. On day 28, fresh CMM1 medium containing 300ng/ml recombinant human SDF-1a (CXCL12) (Pepro TECH:300-28A) was added. From day 35 onwards, all organoids were maintained in CMM1 medium

value: Skin

value: Chap

value: induced pluripotent stem cells

value: cerebellar differentiation 156 days


title: shNT_Enz WES_NTCE3

description:
shNT_Enz
WES

value: enzalutamide 10uM


title: Chap cells, differentiated 156 days-2

description: Drop-seq


title: shNT_Enz WES_NTCE2

description:
shNT_Enz
WES

value: prostate cancer cells


title: SREX11

description: WES

value: Prostate

value: LNCaP/AR


title: csn1

description: biol rep 1


title: shNT_Enz WES_NTCE1

description:
shNT_Enz
WES


title: Epiblast stem cells, rep 2

source_name: Cell culture, condition E


title: shNT_Veh WES_NTFS2

description:
shNT_Veh
WES

value: Vehicle DMSO


title: Neural stem cell line XN4, rep 1


title: Neural stem cell line XN4, rep 2


title: SREX13

description: WES


title: Chap cells, differentiated 80 days-2

description: Drop-seq

value: WT

value: cerebellar differentiation 80 days


title: C. elegans-fasted-no heat shock-Rep4

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

institute: UCL

description:
FAST_NOHS_D
FAST_NOHSvsFED_NOHS_deg_all

data_processing:
Sequenced reads were trimmed for adaptor sequences and polyN and low quality reads were removed before mapping reads to the WBcel235 reference genome using  Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene and FPKM for each gene was then calculated
DESeq2 was then used for differential expression analysis
Assembly: WBcel235
Supplementary files format and content: Table with raw gene counts and normalised abundance for every gene and every sample

source_name: Whole animals

growth_protocol: Worms were grown on standard NGM plates with OP50 at 20degC

extract_protocol:
Worms were lysed in Trizol by vortexing at 4degC for 20 minutes. RNA was then purified using a Qiagen Rneasy Minelute kit as per manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were fasted at the mid-L4 stage by moving worms to plates without food for 24 hours. Following this, worms were allowed to recover for 24 hours and were then exposed to heat shock at 35C for 30 minutes by submerging plates in a water bath.

value: Whole animals

value: N2 - Wild-type

value: Fasted no heat shock


title: C. elegans-fasted-no heat shock-Rep3

description:
FAST_NOHS_C
FAST_NOHSvsFED_NOHS_deg_all


title: Epiblast stem cells, rep 1


title: shSYNCRIP_Veh WES_KDFS2

description:
shSYNCRIP_Veh
WES


title: C. elegans-fasted-heat shock-Rep4

description:
FAST_HS_D
FAST_HSvsFED_HS_deg_all

value: Fasted heat shock


title: SREX7

description: WES

value: enzalutamide 10mg for 16 weeks


title: shNT_Veh WES_NTFS1

description:
shNT_Veh
WES


title: Chap cells, differentiated 156 days-3

description: Drop-seq


title: C. elegans-fasted-heat shock-Rep3

description:
FAST_HS_C
FAST_HSvsFED_HS_deg_all


title: shSYNCRIP_Veh WES_KDFS1

description:
shSYNCRIP_Veh
WES


title: C. elegans-fed-heat shock-Rep4

description:
FED_HS_D
FAST_HSvsFED_HS_deg_all

value: Fed heat shock


title: SREX15

description: WES


title: Chap cells, differentiated 55 days-3

description: Drop-seq

value: Skin

value: cerebellar differentiation 55 days


title: C. elegans-fasted-heat shock-Rep1

description:
FAST_HS_A
FAST_HSvsFED_HS_deg_all


title: Chap cells, differentiated 156 days-1

description: Drop-seq

value: Chap

value: induced pluripotent stem cells


title: SREX10

description: WES


title: Chap cells, differentiated 80 days-3

description: Drop-seq


title: SREX4

description: WES


title: shSYNCRIP_Enz WES_KDCE1

description:
shSYNCRIP_Enz
WES

value: enzalutamide 10uM


title: SREX3

description: WES

value: prostate cancer cells


title: Chap cells, differentiated 55 days-1

description: Drop-seq


title: SREX9

description: WES

value: Prostate


title: Sftpc:KrasG12D Lung 3

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics,https://cloud.10xgenomics.com/cloud-analysis).
BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline.
The spaceranger count pipeline was then used for read alignment to human reference genome mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.
Assembly: mm10
Supplementary files format and content: UMI count matrices
Library strategy: Spatial transcriptomics

growth_protocol: The Sftpc-CreERT2 mouse line has been used previously to track AT2 cell fate. Gramd2-CreERT2 mice were generated by homologous recombination insertion of a cassette including CreERT2- downstream of the endogenous Gramd2 gene stop codon within exon 12. These were separately crossed to heterozygous KrasLSL-G12D mice (Jackson laboratory, Stock: #008179). Gramd2-CreERT2 and Sftpc-CreERT2 mice were in a B6/129 mixed strain background (129 N1), while KrasLSL-G12D mice are in a B6/129S4 mixed strain background (C57BL/6 N10).

extract_protocol:
Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, two biological replicates (one block for each) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes.
Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing.

treatment_protocol: Tamoxifen (Sigma, CAS: 10540-29-1) powder was first dissolved in 100% ethanol (SHBJ8384, Sigma-Aldrich) and then diluted to a final concentration of 40 mg/mL with corn oil (Sigma, CAS: 8001-30-7). To ensure that tamoxifen was fully dissolved, the mixture was gently shaken in a shaking incubator (SHEL LAB, model: SSI5R; cat: #33-804R) at 55℃ for 2 hours. Six-week-old mice were injected with tamoxifen via intraperitoneal injection. For Gramd2-CreERT2; Sftpc-CreERT2, KrasLSL-G12D and WT mice, 40 mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 200 mg/Kg according to the body weight of each mouse. Tamoxifen was given three times over a period of one week. For Sftpc::KrasLSL-G12D mice, 40mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 100 mg/Kg according to the body weight of each mouse. Tamoxifen was given twice over a period of one week.

value: Lung

value: Sftpc-CreERT2; Kras-LSL-G12D

value: Tamoxifen


title: SREX8

description: WES

value: LNCaP/AR


title: shNT_Veh NTFS2

description:
shNT_Veh
RNAseq

value: Vehicle DMSO


title: C. elegans-fasted-no heat shock-Rep2

description:
FAST_NOHS_B
FAST_NOHSvsFED_NOHS_deg_all

value: Whole animals

value: N2 - Wild-type


title: Chap cells, differentiated 80 days-1

description: Drop-seq

value: WT

value: cerebellar differentiation 80 days


title: C. elegans-fasted-heat shock-Rep2

description:
FAST_HS_B
FAST_HSvsFED_HS_deg_all

value: Fasted heat shock


title: shSYNCRIP_Veh WES_KDFS3

description:
shSYNCRIP_Veh
WES


title: SREX6

description: WES

value: enzalutamide 10mg for 16 weeks